Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold86
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1697160
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 169504 characters in sequence are not A, C, G, or T
File 6 of 6
Found at i:1281298 original size:23 final size:23
Alignment explanation
Indices: 1281268--1281316 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
1281258 AAAACAATTT
*
1281268 CAAATTAGAAGCCGATATCAGAA
1 CAAATTAGAAGCCGATATCAAAA
1281291 CAAATTAGAAGCCGATATCAAAA
1 CAAATTAGAAGCCGATATCAAAA
1281314 CAA
1 CAA
1281317 TGGGTAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.16
Consensus pattern (23 bp):
CAAATTAGAAGCCGATATCAAAA
Found at i:1284848 original size:166 final size:166
Alignment explanation
Indices: 1284562--1284897 Score: 478
Period size: 166 Copynumber: 2.0 Consensus size: 166
1284552 AAAAGTCATG
* * * **
1284562 TAAACATTTTTTCTATGTATTTGTATGTTAAACTTTGAACCCAACCTGGGGCCCCAATTTTGGTC
1 TAAACATTTTTCCTATGTATTTCTATGTTAAACTTTGAACCCAACCTGAGGCCCCAATTTTAATC
* * * * *
1284627 CGGGGGTCACGATTTTTACAATTTAGAATCTTCACCATATATACAAGCTTTTGTGTTAATAT-TG
66 CGAGGGTCACGATTTTTACAATTTAGAATCTTAACCATATATACAAGCTTTTGTGTAAAAATAAG
*
1284691 ACATTTCTGGTGCAGTGGTTCTTGAGAAGAAGATTTT
131 -CATTTCTGGTGCAATGGTTCTTGAGAAGAAGATTTT
** *
1284728 ATAAACA-TTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCCTGAGGCCCCACTTTTAAT
1 -TAAACATTTTTCCTATGTATTTCTATGTTAAACTTTGAACCCAACCTGAGGCCCCAATTTTAAT
* *
1284792 CCGAGGGTCACGATTTTTACAATTTATAATCTTAACTATATATACAAGCTTTTGTGTAAAAATAA
65 CCGAGGGTCACGATTTTTACAATTTAGAATCTTAACCATATATACAAGCTTTTGTGTAAAAATAA
* *
1284857 GCATTTCTGGTGGAATGGTTCTTGAGGAGAAGATTTT
130 GCATTTCTGGTGCAATGGTTCTTGAGAAGAAGATTTT
1284894 TAAA
1 TAAA
1284898 GACACACAAC
Statistics
Matches: 150, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
165 4 0.03
166 139 0.93
167 7 0.05
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38
Consensus pattern (166 bp):
TAAACATTTTTCCTATGTATTTCTATGTTAAACTTTGAACCCAACCTGAGGCCCCAATTTTAATC
CGAGGGTCACGATTTTTACAATTTAGAATCTTAACCATATATACAAGCTTTTGTGTAAAAATAAG
CATTTCTGGTGCAATGGTTCTTGAGAAGAAGATTTT
Found at i:1285081 original size:12 final size:12
Alignment explanation
Indices: 1285064--1285117 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
1285054 TGAAAAGTTT
*
1285064 ACAGACGGACGG
1 ACAGACAGACGG
*
1285076 ACAGACAGACAG
1 ACAGACAGACGG
1285088 ACAGACAGACGG
1 ACAGACAGACGG
*
1285100 ACGGAC-GACGG
1 ACAGACAGACGG
1285111 ACA-ACAG
1 ACAGACAG
1285118 GTGATCAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
10 2 0.06
11 8 0.22
12 26 0.72
ACGTcount: A:0.41, C:0.26, G:0.33, T:0.00
Consensus pattern (12 bp):
ACAGACAGACGG
Found at i:1285106 original size:4 final size:4
Alignment explanation
Indices: 1285064--1285097 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
1285054 TGAAAAGTTT
* *
1285064 ACAG ACGG ACGG ACAG ACAG ACAG ACAG ACAG AC
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG AC
1285098 GGACGGACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.44, C:0.26, G:0.29, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:1293920 original size:2 final size:2
Alignment explanation
Indices: 1293913--1293991 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
1293903 ACATTACCAC
1293913 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1293955 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1293992 NNNNNNNNNN
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1300142 original size:2 final size:2
Alignment explanation
Indices: 1300135--1300193 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1300125 AGGATACAAT
1300135 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1300177 GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA G
1300194 CGAGCGAGCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1304525 original size:4 final size:4
Alignment explanation
Indices: 1304516--1304584 Score: 102
Period size: 4 Copynumber: 17.2 Consensus size: 4
1304506 TTTGAAGAAT
1304516 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
* * * *
1304564 AAAG GGAG AAAG AAAG AGAG A
1 AGAG AGAG AGAG AGAG AGAG A
1304585 AAGATGGTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (4 bp):
AGAG
Found at i:1312548 original size:2 final size:2
Alignment explanation
Indices: 1312543--1312568 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1312533 TGGAACACAC
1312543 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1312569 CATGAGCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1326219 original size:19 final size:20
Alignment explanation
Indices: 1326179--1326215 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1326169 ACCTTGAAAT
1326179 AAAATTTTTAGGTCAAGGTC
1 AAAATTTTTAGGTCAAGGTC
1326199 AAAATTTTT-GGT-AAGGT
1 AAAATTTTTAGGTCAAGGT
1326216 TCAACTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (20 bp):
AAAATTTTTAGGTCAAGGTC
Found at i:1329987 original size:30 final size:29
Alignment explanation
Indices: 1329953--1330014 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
1329943 ATTTTGAACT
* *
1329953 GCCGGTCAATAGACTGTGATTTATTAGACC
1 GCCGGTCAATAGACT-CGATCTATTAGACC
*
1329983 GCCGGTCAATAGACTCGATCTATTGGACC
1 GCCGGTCAATAGACTCGATCTATTAGACC
1330012 GCC
1 GCC
1330015 TGTATGTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (29 bp):
GCCGGTCAATAGACTCGATCTATTAGACC
Found at i:1343087 original size:21 final size:17
Alignment explanation
Indices: 1343044--1343078 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1343034 AAATAAATTG
1343044 ATGTAAATAGATTTCAA
1 ATGTAAATAGATTTCAA
1343061 ATGTAAATAGATTTCAA
1 ATGTAAATAGATTTCAA
1343078 A
1 A
1343079 CTTATGTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (17 bp):
ATGTAAATAGATTTCAA
Found at i:1348613 original size:13 final size:13
Alignment explanation
Indices: 1348595--1348619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1348585 CACTGGATGC
1348595 GCAATGAAATCCG
1 GCAATGAAATCCG
1348608 GCAATGAAATCC
1 GCAATGAAATCC
1348620 TGGTGACTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (13 bp):
GCAATGAAATCCG
Found at i:1370310 original size:21 final size:21
Alignment explanation
Indices: 1370271--1370311 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1370261 CTATAGGAAA
*
1370271 TTCACTATATACATGTTTTCT
1 TTCACCATATACATGTTTTCT
*
1370292 TTCACCATACTACATTTTTT
1 TTCACCATA-TACATGTTTT
1370312 GCTACAGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.24, C:0.22, G:0.02, T:0.51
Consensus pattern (21 bp):
TTCACCATATACATGTTTTCT
Found at i:1370465 original size:32 final size:33
Alignment explanation
Indices: 1370428--1370490 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
1370418 TTGATCTTTT
*
1370428 TAAATGTAATTAATTAC-TCTCAATTACTTTGA
1 TAAATGTAATTAATTACATCTCAAATACTTTGA
*
1370460 TAAATGTAATTAATTACATTTCAAATACTTT
1 TAAATGTAATTAATTACATCTCAAATACTTT
1370491 ATTTTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (33 bp):
TAAATGTAATTAATTACATCTCAAATACTTTGA
Found at i:1371036 original size:11 final size:11
Alignment explanation
Indices: 1371016--1371052 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1371006 AACTTGGAAA
1371016 AAAAGTAATTG
1 AAAAGTAATTG
* *
1371027 AGATGTAATTG
1 AAAAGTAATTG
1371038 AAAAGTAATTG
1 AAAAGTAATTG
1371049 AAAA
1 AAAA
1371053 TACACAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (11 bp):
AAAAGTAATTG
Found at i:1374934 original size:15 final size:15
Alignment explanation
Indices: 1374916--1374945 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1374906 GAGAATACAG
1374916 AATTTATAATTGTAA
1 AATTTATAATTGTAA
1374931 AATTTATAATTGTAA
1 AATTTATAATTGTAA
1374946 TGCATACGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
AATTTATAATTGTAA
Found at i:1376738 original size:17 final size:17
Alignment explanation
Indices: 1376716--1376748 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1376706 TATACGCCAA
1376716 TAAACTACTACCACTAC
1 TAAACTACTACCACTAC
*
1376733 TAAACTACTACTACTA
1 TAAACTACTACCACTA
1376749 TATTATCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAACTACTACCACTAC
Found at i:1380595 original size:10 final size:11
Alignment explanation
Indices: 1380557--1380604 Score: 71
Period size: 11 Copynumber: 4.5 Consensus size: 11
1380547 CACCCCTCTG
1380557 TACCCCAAGGA
1 TACCCCAAGGA
*
1380568 TACCCCATGGA
1 TACCCCAAGGA
1380579 TACCCCAAGGA
1 TACCCCAAGGA
*
1380590 -ACCCCAAAGA
1 TACCCCAAGGA
1380600 TACCC
1 TACCC
1380605 TAATGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.35, C:0.40, G:0.15, T:0.10
Consensus pattern (11 bp):
TACCCCAAGGA
Found at i:1381457 original size:21 final size:20
Alignment explanation
Indices: 1381432--1381485 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 20
1381422 CCATCATTGA
1381432 GGTATCTATGGGGTTCTCA-G
1 GGTATCT-TGGGGTTCTCATG
1381452 GTGTATCCTTGGGGTTCTCATG
1 G-GTAT-CTTGGGGTTCTCATG
1381474 GGTATCCTTGGG
1 GGTAT-CTTGGG
1381486 ATTTATTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.03
21 26 0.84
22 4 0.13
ACGTcount: A:0.11, C:0.17, G:0.35, T:0.37
Consensus pattern (20 bp):
GGTATCTTGGGGTTCTCATG
Found at i:1381805 original size:10 final size:10
Alignment explanation
Indices: 1381792--1381849 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
1381782 TTTCTATTAG
1381792 TGGGGTTCCT
1 TGGGGTTCCT
1381802 TGGGGTT-CT
1 TGGGGTTCCT
* *
1381811 TATGAGTATCCT
1 T-GGGGT-TCCT
*
1381823 TGGGGTTCAT
1 TGGGGTTCCT
1381833 TGGGGTATCCT
1 TGGGGT-TCCT
1381844 TGGGGT
1 TGGGGT
1381850 ACTAAAAGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
9 3 0.08
10 19 0.50
11 13 0.34
12 3 0.08
ACGTcount: A:0.09, C:0.14, G:0.38, T:0.40
Consensus pattern (10 bp):
TGGGGTTCCT
Found at i:1381822 original size:21 final size:21
Alignment explanation
Indices: 1381798--1381849 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1381788 TTAGTGGGGT
*
1381798 TCCTTGGGGTTC-TTATGAGTA
1 TCCTTGGGGTTCATT-GGAGTA
*
1381819 TCCTTGGGGTTCATTGGGGTA
1 TCCTTGGGGTTCATTGGAGTA
1381840 TCCTTGGGGT
1 TCCTTGGGGT
1381850 ACTAAAAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.10, C:0.15, G:0.35, T:0.40
Consensus pattern (21 bp):
TCCTTGGGGTTCATTGGAGTA
Found at i:1381848 original size:11 final size:11
Alignment explanation
Indices: 1381816--1381850 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1381806 GTTCTTATGA
1381816 GTATCCTTGGG
1 GTATCCTTGGG
*
1381827 GT-TCATTGGG
1 GTATCCTTGGG
1381837 GTATCCTTGGG
1 GTATCCTTGGG
1381848 GTA
1 GTA
1381851 CTAAAAGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.11, C:0.14, G:0.37, T:0.37
Consensus pattern (11 bp):
GTATCCTTGGG
Found at i:1381948 original size:11 final size:10
Alignment explanation
Indices: 1381919--1381958 Score: 71
Period size: 10 Copynumber: 3.9 Consensus size: 10
1381909 CTATCATTGA
1381919 GGTTCCTTGG
1 GGTTCCTTGG
1381929 GGTTCCTTGG
1 GGTTCCTTGG
1381939 GGTATCCTTGG
1 GGT-TCCTTGG
1381950 GGTTCCTTG
1 GGTTCCTTG
1381959 CGGTAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 19 0.66
11 10 0.34
ACGTcount: A:0.03, C:0.20, G:0.38, T:0.40
Consensus pattern (10 bp):
GGTTCCTTGG
Found at i:1381948 original size:21 final size:21
Alignment explanation
Indices: 1381922--1381963 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1381912 TCATTGAGGT
*
1381922 TCCTTGGGGTTCCTTGGGGTA
1 TCCTTGGGGTTCCTTGCGGTA
1381943 TCCTTGGGGTTCCTTGCGGTA
1 TCCTTGGGGTTCCTTGCGGTA
1381964 AAAAGATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.21, G:0.36, T:0.38
Consensus pattern (21 bp):
TCCTTGGGGTTCCTTGCGGTA
Found at i:1385245 original size:41 final size:42
Alignment explanation
Indices: 1385156--1385252 Score: 108
Period size: 41 Copynumber: 2.3 Consensus size: 42
1385146 TATTAAGAAA
* ** **
1385156 AAAAAAAAAGGAAAATTACATTTTAACAATGTATATTATTAAG
1 AAAAAAAAA-GAAAATTACATTCTAACAATGTATAACAAAAAG
*
1385199 -TAAAAAAAGAAAATTACATTCTAACAATGTA-AACAAAAAG
1 AAAAAAAAAGAAAATTACATTCTAACAATGTATAACAAAAAG
*
1385239 AAAAAAAAACAAAA
1 AAAAAAAAAGAAAA
1385253 ACCATAATGA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
40 5 0.11
41 33 0.73
42 7 0.16
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.22
Consensus pattern (42 bp):
AAAAAAAAAGAAAATTACATTCTAACAATGTATAACAAAAAG
Found at i:1386111 original size:26 final size:26
Alignment explanation
Indices: 1386077--1386127 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1386067 TGTACATAAA
1386077 ATGGCGTGATATGCTTTGTCAACCAT
1 ATGGCGTGATATGCTTTGTCAACCAT
* * *
1386103 ATGGTGTGATATGGTTTTTCAACCA
1 ATGGCGTGATATGCTTTGTCAACCA
1386128 ATCAACAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (26 bp):
ATGGCGTGATATGCTTTGTCAACCAT
Found at i:1386526 original size:26 final size:26
Alignment explanation
Indices: 1386492--1386542 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1386482 TGTACATAAA
1386492 ATGGCGTGATATGCTTTGTCAACCAT
1 ATGGCGTGATATGCTTTGTCAACCAT
* * *
1386518 ATGGTGTGATATGGTTTTTCAACCA
1 ATGGCGTGATATGCTTTGTCAACCA
1386543 ATCAACAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (26 bp):
ATGGCGTGATATGCTTTGTCAACCAT
Found at i:1392267 original size:15 final size:15
Alignment explanation
Indices: 1392244--1392290 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
1392234 ACAGTAAAAC
1392244 ATGCTTATAGTGAAG
1 ATGCTTATAGTGAAG
*
1392259 ACT-CTTATAATGAATTG
1 A-TGCTTATAGTGAA--G
1392276 ATGCTTATAGTGAAG
1 ATGCTTATAGTGAAG
1392291 TGATTTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
15 12 0.46
16 2 0.08
17 12 0.46
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (15 bp):
ATGCTTATAGTGAAG
Found at i:1397832 original size:11 final size:12
Alignment explanation
Indices: 1397805--1397834 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1397795 CATTTTCCGT
*
1397805 TTTTTTCATGTA
1 TTTTTTCATGCA
1397817 TTTTTTCATGCA
1 TTTTTTCATGCA
1397829 TTTTTT
1 TTTTTT
1397835 TTTCAATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTTTTCATGCA
Found at i:1401042 original size:10 final size:10
Alignment explanation
Indices: 1401027--1401056 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1401017 ACTACTAAAC
1401027 AGAGAACTCT
1 AGAGAACTCT
*
1401037 AGAGAACTTT
1 AGAGAACTCT
1401047 AGAGAACTCT
1 AGAGAACTCT
1401057 GGGGATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (10 bp):
AGAGAACTCT
Found at i:1402069 original size:10 final size:10
Alignment explanation
Indices: 1402042--1402081 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1402032 AAAAAATCCC
1402042 AGAGTTCTCT
1 AGAGTTCTCT
1402052 AG-GATTCTCT
1 AGAG-TTCTCT
*
1402062 AGAGTTCTTT
1 AGAGTTCTCT
1402072 AGAGTTCTCT
1 AGAGTTCTCT
1402082 GTTTAGTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 1 0.04
10 24 0.92
11 1 0.04
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.42
Consensus pattern (10 bp):
AGAGTTCTCT
Found at i:1407530 original size:332 final size:332
Alignment explanation
Indices: 1406924--1407585 Score: 1315
Period size: 332 Copynumber: 2.0 Consensus size: 332
1406914 ATTGAAACTG
*
1406924 GGATTATAAATCGGTAATAAATGCATATATAGAGGGGCAATTACTACTTGTTTTAATATAATGTG
1 GGATTATAAATCGGTAATAAATGCATATATAGAGGGGCAATTACTACTTGTTTCAATATAATGTG
1406989 CCTTCTTTGACACCTCCGCCATTATCGAATGTTGGGGATTTTCCAAGATCTAAAAATAGCACAAT
66 CCTTCTTTGACACCTCCGCCATTATCGAATGTTGGGGATTTTCCAAGATCTAAAAATAGCACAAT
1407054 GTTCCCTCGATGGAGTTACCTTGGTTGTGCTATGATTGAACTGTTTATTTGTCGTAAAAATATTG
131 GTTCCCTCGATGGAGTTACCTTGGTTGTGCTATGATTGAACTGTTTATTTGTCGTAAAAATATTG
1407119 GAAACTTGAGACCAAATGTACTCAAATAAGAAAACAATATACAGTTAAGCTTGATTGCAAGTCAT
196 GAAACTTGAGACCAAATGTACTCAAATAAGAAAACAATATACAGTTAAGCTTGATTGCAAGTCAT
1407184 ATACGGAAGCGATGTCATATTACTATAACATAGAGACACCGTATAGTATGCCTCTGAAAATGACT
261 ATACGGAAGCGATGTCATATTACTATAACATAGAGACACCGTATAGTATGCCTCTGAAAATGACT
1407249 GTGTATA
326 GTGTATA
1407256 GGATTATAAATCGGTAATAAATGCATATATAGAGGGGCAATTACTACTTGTTTCAATATAATGTG
1 GGATTATAAATCGGTAATAAATGCATATATAGAGGGGCAATTACTACTTGTTTCAATATAATGTG
1407321 CCTTCTTTGACACCTCCGCCATTATCGAATGTTGGGGATTTTCCAAGATCTAAAAATAGCACAAT
66 CCTTCTTTGACACCTCCGCCATTATCGAATGTTGGGGATTTTCCAAGATCTAAAAATAGCACAAT
1407386 GTTCCCTCGATGGAGTTACCTTGGTTGTGCTATGATTGAACTGTTTATTTGTCGTAAAAATATTG
131 GTTCCCTCGATGGAGTTACCTTGGTTGTGCTATGATTGAACTGTTTATTTGTCGTAAAAATATTG
1407451 GAAACTTGAGACCAAATGTACTCAAATAAGAAAACAATATACAGTTAAGCTTGATTGCAAGTCAT
196 GAAACTTGAGACCAAATGTACTCAAATAAGAAAACAATATACAGTTAAGCTTGATTGCAAGTCAT
1407516 ATACGGAAGCGATGTCATATTACTATAACATAGAGACACCGTATAGTATGCCTCTGAAAATGACT
261 ATACGGAAGCGATGTCATATTACTATAACATAGAGACACCGTATAGTATGCCTCTGAAAATGACT
1407581 GTGTA
326 GTGTA
1407586 CACATGTAAT
Statistics
Matches: 329, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
332 329 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (332 bp):
GGATTATAAATCGGTAATAAATGCATATATAGAGGGGCAATTACTACTTGTTTCAATATAATGTG
CCTTCTTTGACACCTCCGCCATTATCGAATGTTGGGGATTTTCCAAGATCTAAAAATAGCACAAT
GTTCCCTCGATGGAGTTACCTTGGTTGTGCTATGATTGAACTGTTTATTTGTCGTAAAAATATTG
GAAACTTGAGACCAAATGTACTCAAATAAGAAAACAATATACAGTTAAGCTTGATTGCAAGTCAT
ATACGGAAGCGATGTCATATTACTATAACATAGAGACACCGTATAGTATGCCTCTGAAAATGACT
GTGTATA
Found at i:1421000 original size:12 final size:12
Alignment explanation
Indices: 1420976--1421017 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
1420966 ATCACATTTT
1420976 GTCTGTC-GTCC
1 GTCTGTCTGTCC
1420987 GTCTGTCTGTCC
1 GTCTGTCTGTCC
*
1420999 GTCCGTCTGTCC
1 GTCTGTCTGTCC
1421011 GTCTGTC
1 GTCTGTC
1421018 CGTAAACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
11 7 0.25
12 21 0.75
ACGTcount: A:0.00, C:0.36, G:0.26, T:0.38
Consensus pattern (12 bp):
GTCTGTCTGTCC
Found at i:1421012 original size:8 final size:8
Alignment explanation
Indices: 1420983--1421020 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
1420973 TTTGTCTGTC
1420983 GTCCGTCT
1 GTCCGTCT
* *
1420991 GTCTGTCC
1 GTCCGTCT
1420999 GTCCGTCT
1 GTCCGTCT
1421007 GTCCGTCT
1 GTCCGTCT
1421015 GTCCGT
1 GTCCGT
1421021 AAACTTTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.00, C:0.37, G:0.26, T:0.37
Consensus pattern (8 bp):
GTCCGTCT
Found at i:1421489 original size:10 final size:10
Alignment explanation
Indices: 1421471--1421525 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
1421461 TATTCTGATA
1421471 CACGAACGAT
1 CACGAACGAT
*
1421481 CACGCACGAT
1 CACGAACGAT
1421491 ACACGAACGAT
1 -CACGAACGAT
*
1421502 CACGCACGAT
1 CACGAACGAT
*
1421512 ACACGGACGAT
1 -CACGAACGAT
1421523 CAC
1 CAC
1421526 TAACTTACTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 21 0.54
11 18 0.46
ACGTcount: A:0.36, C:0.35, G:0.20, T:0.09
Consensus pattern (10 bp):
CACGAACGAT
Found at i:1421491 original size:21 final size:21
Alignment explanation
Indices: 1421467--1421525 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
1421457 GCACTATTCT
1421467 GATACACGAACGATCACGCAC
1 GATACACGAACGATCACGCAC
1421488 GATACACGAACGATCACGCAC
1 GATACACGAACGATCACGCAC
*
1421509 GATACACGGACGATCAC
1 GATACACGAACGATCAC
1421526 TAACTTACTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.37, C:0.32, G:0.20, T:0.10
Consensus pattern (21 bp):
GATACACGAACGATCACGCAC
Found at i:1421500 original size:11 final size:11
Alignment explanation
Indices: 1421467--1421522 Score: 71
Period size: 11 Copynumber: 5.3 Consensus size: 11
1421457 GCACTATTCT
1421467 GATACACGAAC
1 GATACACGAAC
*
1421478 GAT-CACGCAC
1 GATACACGAAC
1421488 GATACACGAAC
1 GATACACGAAC
*
1421499 GAT-CACGCAC
1 GATACACGAAC
*
1421509 GATACACGGAC
1 GATACACGAAC
1421520 GAT
1 GAT
1421523 CACTAACTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 18 0.46
11 21 0.54
ACGTcount: A:0.38, C:0.30, G:0.21, T:0.11
Consensus pattern (11 bp):
GATACACGAAC
Found at i:1422387 original size:21 final size:21
Alignment explanation
Indices: 1422362--1422415 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1422352 ATTTTCCTGA
*
1422362 TACACGCACGATC-CCGCACGT
1 TACACGAACGATCACC-CACGT
*
1422383 TACACGAACTATCACCCACGT
1 TACACGAACGATCACCCACGT
1422404 TACACGAACGAT
1 TACACGAACGAT
1422416 TTAACACGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.31, C:0.37, G:0.15, T:0.17
Consensus pattern (21 bp):
TACACGAACGATCACCCACGT
Found at i:1424545 original size:12 final size:13
Alignment explanation
Indices: 1424516--1424554 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
1424506 ATTTGTTCTA
1424516 AAATATAGAGACT
1 AAATATAGAGACT
1424529 AAATATAGAGA-T
1 AAATATAGAGACT
1424541 AAATATAGAGACT
1 AAATATAGAGACT
1424554 A
1 A
1424555 CAGTACAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.23
Consensus pattern (13 bp):
AAATATAGAGACT
Found at i:1438325 original size:15 final size:15
Alignment explanation
Indices: 1438305--1438335 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1438295 TTATGTCATT
*
1438305 AAATGAATTTGAGAA
1 AAATGAAATTGAGAA
1438320 AAATGAAATTGAGAA
1 AAATGAAATTGAGAA
1438335 A
1 A
1438336 TGATAAATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (15 bp):
AAATGAAATTGAGAA
Found at i:1440054 original size:17 final size:17
Alignment explanation
Indices: 1440032--1440065 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1440022 CAAATGTTGA
*
1440032 GTCACGTTATGTCCGCC
1 GTCACGATATGTCCGCC
1440049 GTCACGATATGTCCGCC
1 GTCACGATATGTCCGCC
1440066 ACTTTTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.35, G:0.24, T:0.26
Consensus pattern (17 bp):
GTCACGATATGTCCGCC
Found at i:1440154 original size:51 final size:51
Alignment explanation
Indices: 1440032--1440202 Score: 245
Period size: 51 Copynumber: 3.3 Consensus size: 51
1440022 CAAATGTTGA
* *
1440032 GTCACGTTATGTCCGCCGTCACGATATGTCCGCCACTTTTTTGAAAAAAAATC
1 GTCACGTTATGTCCGCCATCACGAAATGTCCGCCACTTTTTTG--AAAAAATC
* *
1440085 GTCACGTTATGTCTGCCATCACGAAATGTCCACCACTTTTTTGAAAAAATC
1 GTCACGTTATGTCCGCCATCACGAAATGTCCGCCACTTTTTTGAAAAAATC
** *
1440136 GTCACGTTATGTCCGCCATCACGAAATGTCCGCCACTTTTTT-TTAACATC
1 GTCACGTTATGTCCGCCATCACGAAATGTCCGCCACTTTTTTGAAAAAATC
*
1440186 GTCACATTATGTCCGCC
1 GTCACGTTATGTCCGCC
1440203 TCCTTGTAAA
Statistics
Matches: 108, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
50 21 0.19
51 48 0.44
53 39 0.36
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (51 bp):
GTCACGTTATGTCCGCCATCACGAAATGTCCGCCACTTTTTTGAAAAAATC
Found at i:1441995 original size:78 final size:78
Alignment explanation
Indices: 1441846--1441997 Score: 207
Period size: 78 Copynumber: 1.9 Consensus size: 78
1441836 CCTTATATAC
* * *
1441846 AGCACAGACAGTTGACACAGCACATGATGTTCCTTCCTTTTCACAGGGTCCAACACCGGACACCC
1 AGCACAGACAGTTAACACAACACATGATGTTCCTTCCTTTTCACAGGGTCCAACACCGGAAACCC
1441911 ACGAAAACTGCCA
66 ACGAAAACTGCCA
* * * * *
1441924 AGCACAGACAGTTAACACAACACCTGATGTTTCTT-CTTTATCACAGGGTCTAACACCTGAAATC
1 AGCACAGACAGTTAACACAACACATGATGTTCCTTCCTTT-TCACAGGGTCCAACACCGGAAACC
*
1441988 CATGAAAACT
65 CACGAAAACT
1441998 ACAGCAAATC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
77 4 0.06
78 60 0.94
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.22
Consensus pattern (78 bp):
AGCACAGACAGTTAACACAACACATGATGTTCCTTCCTTTTCACAGGGTCCAACACCGGAAACCC
ACGAAAACTGCCA
Found at i:1443579 original size:11 final size:11
Alignment explanation
Indices: 1443563--1443609 Score: 76
Period size: 11 Copynumber: 4.2 Consensus size: 11
1443553 CTGATTTCAG
1443563 ATTATCTATAC
1 ATTATCTATAC
1443574 ATTATCTATAC
1 ATTATCTATAC
*
1443585 ATATATCTTTAC
1 AT-TATCTATAC
1443597 ATTATCTATAC
1 ATTATCTATAC
1443608 AT
1 AT
1443610 CAGGTGAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
11 23 0.70
12 10 0.30
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTATCTATAC
Found at i:1443597 original size:23 final size:23
Alignment explanation
Indices: 1443565--1443609 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1443555 GATTTCAGAT
1443565 TATCTATACATTATCTATACATA
1 TATCTATACATTATCTATACATA
*
1443588 TATCTTTACATTATCTATACAT
1 TATCTATACATTATCTATACAT
1443610 CAGGTGAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.47
Consensus pattern (23 bp):
TATCTATACATTATCTATACATA
Found at i:1450894 original size:46 final size:46
Alignment explanation
Indices: 1450792--1450886 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
1450782 AATCTTCCAC
*
1450792 GCTTGCGTCAATATTGTTTTCTTGTAATATACTTGTTACGGAATGA
1 GCTTGCGTCAAGATTGTTTTCTTGTAATATACTTGTTACGGAATGA
*
1450838 GCTTGCGTCAAGATTTTTTTCTTGTAATATACTTGTTACGGAATGA
1 GCTTGCGTCAAGATTGTTTTCTTGTAATATACTTGTTACGGAATGA
1450884 GCT
1 GCT
1450887 CTTGTCAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (46 bp):
GCTTGCGTCAAGATTGTTTTCTTGTAATATACTTGTTACGGAATGA
Found at i:1465872 original size:12 final size:12
Alignment explanation
Indices: 1465855--1465881 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1465845 ACCCTTGTGT
1465855 GTCTGTCTGTCC
1 GTCTGTCTGTCC
1465867 GTCTGTCTGTCC
1 GTCTGTCTGTCC
1465879 GTC
1 GTC
1465882 CGTAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.33, G:0.26, T:0.41
Consensus pattern (12 bp):
GTCTGTCTGTCC
Found at i:1466672 original size:165 final size:166
Alignment explanation
Indices: 1465908--1467032 Score: 1582
Period size: 166 Copynumber: 6.8 Consensus size: 166
1465898 GTCGCATTTA
* *
1465908 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTTAGGCATGCCATAT
* *
1465973 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGATAAATGACGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TTT
*
1466038 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
1466075 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTTAGGCATGCCATAT
** *
1466140 CGTGGGATATATTTTTGTACCAATCAAACGTCAACTTCCTGTTTAATGACGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
* *
1466205 TAG-CAAAACTTTTCAAACAAATTTCCGTCAAAGAAT
131 TAGCCAAAA-TTTTCAAACAAATTTTCGTCAAAGATT
* * * *
1466241 TCTCAGCAACTGTTTACCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCTATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTTAGGCATGCCATAT
* * *
1466306 CGTGGGATATATTTTTGAACCAATCGGACGTCAACGTCCTGTGT-AATGACAACTTTGTTTATTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGT-TAAATGACGACTTTGTTTATTT
** *
1466370 TTAG-CAAAACTTTAAAAACAAA-TTTCTGTCAAAGAAT
130 TTAGCCAAAA-TTTTCAAACAAATTTTC-GTCAAAGATT
* * *
1466407 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCTATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTTAGGCATGCCATAT
* *
1466472 CATGGGATGTATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
* *
1466537 AAGCCAAAATTTTCAAACAAATTTTCATCAAAGATT
131 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * * *
1466573 TCTCAGCAGCTATTT-TTGGAGATGCTTGAAATTTGTACACAGTGTTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTTAGGCATGCCATAT
* * * * * * *
1466637 TGTGGGATATATTTTTGTATCAATCAGATGTCAACTTCCTGTTAAATAATGACTTTGTTAATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
*
1466702 TAGCCAAAATATTCAAACAAATTTTCGTCAAAGATT
131 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * * *
1466738 TCTCAGCAGCTTTTTATCGGAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTTAGGCATGCCATAT
* *
1466803 TGTGGGATATATCTTTT-TACCAATCGGACGTCATCTTCCTGTTAAATGA-GTACTTTGTTTA-T
66 CGTGGGATATAT-TTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGTTTATT
*
1466865 TTTAGCCAAAATTTTCAAACAAATTTTCCTCAAAGATT
129 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * *
1466903 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTTAGGCATGCCATAT
* * * * * * *
1466968 TGTGGGATATATTTCTGTACCAATCGGATGCCAACTTTCTGTTAAATGTCGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
1467033 GCATATTCAC
Statistics
Matches: 869, Mismatches: 77, Indels: 25
0.89 0.08 0.03
Matches are distributed among these distances:
164 3 0.00
165 301 0.35
166 434 0.50
167 131 0.15
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (166 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTTAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
Found at i:1466826 original size:331 final size:330
Alignment explanation
Indices: 1465908--1467032 Score: 1595
Period size: 331 Copynumber: 3.4 Consensus size: 330
1465898 GTCGCATTTA
*
1465908 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTAAGGCATGCCATAT
* *
1465973 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGATAAATGACGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTG-TTAATTT
*
1466038 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTGTTTATCGCAGATGCTT
130 TTAGCCAAAA-TTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTGTTTATCGCAGATGCTT
**
1466103 GAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAAA
194 GAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGGA
* * *
1466168 CGTCAACTTCCTGTTTAATGACGACTTTGTTTATTTTTAG-CAAAACTTTTCAAACAAATTTCCG
259 CGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TTTTAGCCAAAA-TTTTCAAACAAATTTTCA
*
1466232 TCAAAGAAT
322 TCAAAGATT
* * *
1466241 TCTCAGCAACTGTTTACCGCAGATGCTTGAAATTTTTACACAGTATTTG-TATAGGCATGCTATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTA-AGGCATGCCATA
* * * *
1466305 TCGTGGGATATATTTTTGAACCAATCGGACGTCAACGTCCTGTGT-AATGACAACTTTGTTTATT
65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGT-TAAATGACGACTTTGTTAATT
* *
1466369 TTTAG-CAAAACTTTAAAAACAAA-TTTCTGTCAAAGAATTCTCAGCAACTGTTTATCGCAGATG
129 TTTAGCCAAAA-TTT-CAAACAAATTTTC-GTCAAAGATTTCTCAGCAACTGTTTATCGCAGATG
* * *
1466432 CTTGAAATTTTTACACAGTATTTGTATAGGCATGCTATATCATGGGATGTATTTTTGTACCAATC
191 CTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATC
1466497 GGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTAAGCCAAAATTTTCAAACAAATTTT
256 GGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT-AGCCAAAATTTTCAAACAAATTTT
1466562 CATCAAAGATT
320 CATCAAAGATT
* * * * * *
1466573 TCTCAGCAGCTATTT-TTGGAGATGCTTGAAATTTGTACACAGTGTTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTAAGGCATGCCATAT
* * * * * *
1466637 TGTGGGATATATTTTTGTATCAATCAGATGTCAACTTCCTGTTAAATAATGACTTTGTTAATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTAATTTT
* * *
1466702 TAGCCAAAATATTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTTTTTATCGGAGATGCTTG
131 TAGCCAAAAT-TTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTGTTTATCGCAGATGCTTG
* *
1466767 AAATTTTTACACAGTGTTTGT-TAAGGCATGCCATATTGTGGGATATATCTTTT-TACCAATCGG
195 AAATTTTTACACAGTATTTGTAT-AGGCATGCCATATCGTGGGATATAT-TTTTGTACCAATCGG
* *
1466830 ACGTCATCTTCCTGTTAAATGA-GTACTTTGTTTATTTTAGCCAAAATTTTCAAACAAATTTTCC
258 ACGTCAACTTCCTGTTAAATGACG-ACTTTGTTTATTTTAGCCAAAATTTTCAAACAAATTTTCA
1466894 TCAAAGATT
322 TCAAAGATT
* * *
1466903 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTAAGGCATGCCATAT
* * * * * *
1466968 TGTGGGATATATTTCTGTACCAATCGGATGCCAACTTTCTGTTAAATGTCGACTTTGCTT-ATTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTG-TTAATTT
1467032 T
130 T
1467033 GCATATTCAC
Statistics
Matches: 707, Mismatches: 69, Indels: 34
0.87 0.09 0.04
Matches are distributed among these distances:
330 52 0.07
331 337 0.48
332 203 0.29
333 114 0.16
334 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (330 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTAAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTAATTTT
TAGCCAAAATTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTGTTTATCGCAGATGCTTGA
AATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGGACG
TCAACTTCCTGTTAAATGACGACTTTGTTTATTTTAGCCAAAATTTTCAAACAAATTTTCATCAA
AGATT
Found at i:1481029 original size:281 final size:276
Alignment explanation
Indices: 1480510--1481066 Score: 1024
Period size: 281 Copynumber: 2.0 Consensus size: 276
1480500 TTTACTCTCT
*
1480510 CACTTCTCACATACTCACATTTCATCCCATATTGTATTATAAAATAAAGAGTAGGGTAGTTGCTT
1 CACTTCTCACATACTCACATTTCATCCCATATTGTAATATAAAATAAAGAGTAGGGTAGTTGCTT
*
1480575 GTGATAGTTATGCCTATGCAGTAAAACTGCAATCCATGTGAAAAAAACCAGACAAACAAACCAAA
66 GTGATAGTTATGCCTATGCAGTAAAACTGCAATCCATGTGAAAAAAAACAGACAAACAAACCAAA
* *
1480640 GAAAGAAAAAAAACAGAATACCAAAAAACAAAAAACTTAAAAATATTAAATTGATGCATTATTGT
131 GAAAGAAAAAAAACAGAAAACCAAAAAACAAAAAACATAAAAATATTAAATTGATGCATTATTGT
1480705 ACACATGTTAATTCTAAACTGCCAGATGATTAATAAAATCAATCCAAGGAGACCATGCTTTTTCA
196 ACACATGTTAATTCTAAACTGCCAGATGATTAATAAAATCAATCCAAGGAGACCATGCTTTTTCA
1480770 AATTCATCAATTTCTG
261 AATTCATCAATTTCTG
1480786 NCACTTCTCACATACTCACATTTTCATCCCATATTGTAATATAAAATAAAGAGTAGGGTAGTTGC
1 -CACTTCTCACATACTCACA-TTTCATCCCATATTGTAATATAAAATAAAGAGTAGGGTAGTTGC
*
1480851 TTGTGATAGTTATGCCTATGCAGTAAAACTGCAATCCATGTGAAAAAAAAACAGACAAACAGACC
64 TTGTGATAGTTATGCCTATGCAGTAAAACTGCAATCCATGTG-AAAAAAAACAGACAAACAAACC
1480916 AAAGAAAGAAAAAAAAAACAGAAAACCAAAAAACAAAAAACATAAAAATATTAAATTGATGCATT
128 AAAGAAAG--AAAAAAAACAGAAAACCAAAAAACAAAAAACATAAAAATATTAAATTGATGCATT
1480981 ATTGTACACATGTTAATTCTAAACTGCCAGATGATTAATAAAATCAATCCAAGGAGACCATGCTT
191 ATTGTACACATGTTAATTCTAAACTGCCAGATGATTAATAAAATCAATCCAAGGAGACCATGCTT
1481046 TTTCAAATTCATCAATTTCTG
256 TTTCAAATTCATCAATTTCTG
1481067 ATTTCTGAAT
Statistics
Matches: 271, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
277 19 0.07
278 85 0.31
279 28 0.10
281 139 0.51
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (276 bp):
CACTTCTCACATACTCACATTTCATCCCATATTGTAATATAAAATAAAGAGTAGGGTAGTTGCTT
GTGATAGTTATGCCTATGCAGTAAAACTGCAATCCATGTGAAAAAAAACAGACAAACAAACCAAA
GAAAGAAAAAAAACAGAAAACCAAAAAACAAAAAACATAAAAATATTAAATTGATGCATTATTGT
ACACATGTTAATTCTAAACTGCCAGATGATTAATAAAATCAATCCAAGGAGACCATGCTTTTTCA
AATTCATCAATTTCTG
Found at i:1485210 original size:2 final size:2
Alignment explanation
Indices: 1485203--1485236 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1485193 TAATAAGTTT
*
1485203 GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1485237 ACAAAAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1488062 original size:2 final size:2
Alignment explanation
Indices: 1488055--1488114 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1488045 TTGATTGACT
1488055 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1488097 GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA
1488115 AACAATGTAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1489730 original size:2 final size:2
Alignment explanation
Indices: 1489723--1489786 Score: 83
Period size: 2 Copynumber: 32.0 Consensus size: 2
1489713 TTGATTGACT
* * * * *
1489723 GA GA GA GA GA GA AA GA GC GA GC GA GA GT GA GA GA GA GA GA AA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1489765 GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
1489787 ATGTACTACT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.03, G:0.47, T:0.02
Consensus pattern (2 bp):
GA
Found at i:1507102 original size:13 final size:13
Alignment explanation
Indices: 1507084--1507112 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1507074 ACACGAAAAA
1507084 TCGCAAAATAATG
1 TCGCAAAATAATG
1507097 TCGCAAAATAATG
1 TCGCAAAATAATG
1507110 TCG
1 TCG
1507113 TTGCAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (13 bp):
TCGCAAAATAATG
Found at i:1511411 original size:2 final size:2
Alignment explanation
Indices: 1511406--1511444 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1511396 ATATATATAT
1511406 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1511445 AGACGAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1513445 original size:62 final size:62
Alignment explanation
Indices: 1513305--1513655 Score: 451
Period size: 62 Copynumber: 5.6 Consensus size: 62
1513295 ATATTCGATC
* * * * *
1513305 TTTTCCATTTGTATTATTTACATATTC-ATTTGTATTGTATGATTTTCCATTTGTATAGTATAA
1 TTTTCCATTTGTATTGTATA-ATTTTCAATTTGTATTGTATAATTTT-CATTTGTATTGTATAA
** *
1513368 TTTTCCATTTGTATTGTATAATTTTTTATTTGTATTGTATGAATATT-ATTTGTATTGTATAA
1 TTTTCCATTTGTATTGTATAATTTTCAATTTGTATTGTAT-AATTTTCATTTGTATTGTATAA
* * **
1513430 TTTTCTATTTGTATTGTATAATTTTCAATTTGCATTGTATAAAATTCATTTGTA-TGTA-AGA
1 TTTTCCATTTGTATTGTATAATTTTCAATTTGTATTGTATAATTTTCATTTGTATTGTATA-A
**
1513491 TTTTCCATTTGTATTGTATAATTTTCCGTTTGTATTGTATAATTTTTCATTTGTATTGTATAA
1 TTTTCCATTTGTATTGTATAATTTTCAATTTGTATTGTATAA-TTTTCATTTGTATTGTATAA
*
1513554 -GTTCCATTTGTATTGTATAATTTTCAATTTGTATTGTATAATTTTTCATTTGTATTGTATAA
1 TTTTCCATTTGTATTGTATAATTTTCAATTTGTATTGTATAA-TTTTCATTTGTATTGTATAA
* * *
1513616 TTTTCAATTTGTATTTTATCATTTTCAATTTGTATTGTAT
1 TTTTCCATTTGTATTGTATAATTTTCAATTTGTATTGTAT
1513656 CCGAGGGATT
Statistics
Matches: 255, Mismatches: 25, Indels: 16
0.86 0.08 0.05
Matches are distributed among these distances:
60 1 0.00
61 48 0.19
62 130 0.51
63 71 0.28
64 5 0.02
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57
Consensus pattern (62 bp):
TTTTCCATTTGTATTGTATAATTTTCAATTTGTATTGTATAATTTTCATTTGTATTGTATAA
Found at i:1513605 original size:144 final size:145
Alignment explanation
Indices: 1513328--1513655 Score: 484
Period size: 144 Copynumber: 2.3 Consensus size: 145
1513318 TTATTTACAT
*
1513328 ATTCATTTGTATTGTATGATTTTCCATTTGTATAGTATAATTTTCCATTTGTATTGTATAATTTT
1 ATTCATTTGTATTGTATGATTTTCCATTTGTATTGTATAATTTTCCATTTGTATTGTATAATTTT
* * *
1513393 TTATTTGTATTGTATGAATATTATTTGTATTGTATAATTTTCTATTTGTATTGTATAATTTTCAA
66 TCATTTGTATTGTATGAATATCATTTGTATTGTATAATTTTCAATTTGTATTGTATAATTTTCAA
1513458 TTTGCATTGTATAAA
131 TTTGCATTGTATAAA
* *
1513473 ATTCATTTGTA-TGTAAGATTTTCCATTTGTATTGTATAATTTTCCGTTTGTATTGTATAATTTT
1 ATTCATTTGTATTGTATGATTTTCCATTTGTATTGTATAATTTTCCATTTGTATTGTATAATTTT
1513537 TCATTTGTATTGTAT-AAGT-TCCATTTGTATTGTATAATTTTCAATTTGTATTGTATAATTTTT
66 TCATTTGTATTGTATGAA-TAT-CATTTGTATTGTATAATTTTCAATTTGTATTGTATAA-TTTT
* *
1513600 C-ATTTGTATTGTATAAT
128 CAATTTGCATTGTATAAA
* * * *
1513617 TTTCAATTTGTATTTTATCATTTTCAATTTGTATTGTAT
1 ATTC-ATTTGTATTGTATGATTTTCCATTTGTATTGTAT
1513656 CCGAGGGATT
Statistics
Matches: 165, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
143 3 0.02
144 117 0.71
145 23 0.14
146 22 0.13
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (145 bp):
ATTCATTTGTATTGTATGATTTTCCATTTGTATTGTATAATTTTCCATTTGTATTGTATAATTTT
TCATTTGTATTGTATGAATATCATTTGTATTGTATAATTTTCAATTTGTATTGTATAATTTTCAA
TTTGCATTGTATAAA
Found at i:1513656 original size:21 final size:21
Alignment explanation
Indices: 1513305--1513655 Score: 428
Period size: 21 Copynumber: 16.9 Consensus size: 21
1513295 ATATTCGATC
* *
1513305 TTTTCCATTTGTATTATTTACA
1 TTTTCCATTTGTATTGTATA-A
* *
1513327 TATT-CATTTGTATTGTATGA
1 TTTTCCATTTGTATTGTATAA
*
1513347 TTTTCCATTTGTATAGTATAA
1 TTTTCCATTTGTATTGTATAA
1513368 TTTTCCATTTGTATTGTATAA
1 TTTTCCATTTGTATTGTATAA
**
1513389 TTTTTTATTTGTATTGTATGAA
1 TTTTCCATTTGTATTGTAT-AA
*
1513411 TATT--ATTTGTATTGTATAA
1 TTTTCCATTTGTATTGTATAA
*
1513430 TTTTCTATTTGTATTGTATAA
1 TTTTCCATTTGTATTGTATAA
* *
1513451 TTTTCAATTTGCATTGTATAA
1 TTTTCCATTTGTATTGTATAA
**
1513472 AATT-CATTTGTA-TGTA-AGA
1 TTTTCCATTTGTATTGTATA-A
1513491 TTTTCCATTTGTATTGTATAA
1 TTTTCCATTTGTATTGTATAA
*
1513512 TTTTCCGTTTGTATTGTATAA
1 TTTTCCATTTGTATTGTATAA
*
1513533 TTTTTCATTTGTATTGTATAA
1 TTTTCCATTTGTATTGTATAA
*
1513554 -GTTCCATTTGTATTGTATAA
1 TTTTCCATTTGTATTGTATAA
*
1513574 TTTTCAATTTGTATTGTATAA
1 TTTTCCATTTGTATTGTATAA
*
1513595 TTTTTCATTTGTATTGTATAA
1 TTTTCCATTTGTATTGTATAA
* * *
1513616 TTTTCAATTTGTATTTTATCA
1 TTTTCCATTTGTATTGTATAA
*
1513637 TTTTCAATTTGTATTGTAT
1 TTTTCCATTTGTATTGTAT
1513656 CCGAGGGATT
Statistics
Matches: 286, Mismatches: 34, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
18 1 0.00
19 12 0.04
20 49 0.17
21 215 0.75
22 9 0.03
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57
Consensus pattern (21 bp):
TTTTCCATTTGTATTGTATAA
Found at i:1515259 original size:17 final size:17
Alignment explanation
Indices: 1515237--1515271 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1515227 GGGTTGTTGC
*
1515237 AACCACTATTTAAATAA
1 AACCACTATTGAAATAA
1515254 AACCACTATTGAAATAA
1 AACCACTATTGAAATAA
1515271 A
1 A
1515272 TTATTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.17, G:0.03, T:0.26
Consensus pattern (17 bp):
AACCACTATTGAAATAA
Found at i:1516102 original size:57 final size:57
Alignment explanation
Indices: 1516039--1516222 Score: 172
Period size: 53 Copynumber: 3.4 Consensus size: 57
1516029 GGGGATGTAC
* * *
1516039 TTCATTA-AGACCAATATTGAATGAAATAAATTATTTCAATAGTGGTTGGGTGTGCGT
1 TTCATTACA-ACCACTATTGAATGAAATAAATTATTTCAATAGTGGTTAGGTGTGCAT
* * *
1516096 TTCATTATAACCACTA-T---TGAAATATATTATTTCAATAGTGGTTAGGTTTGCAT
1 TTCATTACAACCACTATTGAATGAAATAAATTATTTCAATAGTGGTTAGGTGTGCAT
* * * **
1516149 TTCATTACAACCACTATTGAAT----TAATTTATTTCAATTGTGGTTAAGG-ATGCGG
1 TTCATTACAACCACTATTGAATGAAATAAATTATTTCAATAGTGGTT-AGGTGTGCAT
*
1516202 TTCATTACAACCATTATTGAA
1 TTCATTACAACCACTATTGAA
1516223 ATAAAATATT
Statistics
Matches: 108, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
53 88 0.81
54 4 0.04
56 1 0.01
57 14 0.13
58 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (57 bp):
TTCATTACAACCACTATTGAATGAAATAAATTATTTCAATAGTGGTTAGGTGTGCAT
Found at i:1516135 original size:53 final size:53
Alignment explanation
Indices: 1516060--1516243 Score: 235
Period size: 53 Copynumber: 3.5 Consensus size: 53
1516050 CAATATTGAA
* * *
1516060 TGAAATAAATTATTTCAATAGTGGTTGGGTGTGCGTTTCATTATAACCACTAT
1 TGAAATAAATTATTTCAATAGTGGTTAGGTATGCGTTTCATTACAACCACTAT
* * *
1516113 TGAAATATATTATTTCAATAGTGGTTAGGTTTGCATTTCATTACAACCACTAT
1 TGAAATAAATTATTTCAATAGTGGTTAGGTATGCGTTTCATTACAACCACTAT
* * * * *
1516166 TGAATTAATTTATTTCAATTGTGGTTAAGG-ATGCGGTTCATTACAACCATTAT
1 TGAAATAAATTATTTCAATAGTGGTT-AGGTATGCGTTTCATTACAACCACTAT
* *
1516219 TGAAATAAAATATTTTAATAGTGGT
1 TGAAATAAATTATTTCAATAGTGGT
1516244 AGGATGTTAT
Statistics
Matches: 112, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
53 109 0.97
54 3 0.03
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (53 bp):
TGAAATAAATTATTTCAATAGTGGTTAGGTATGCGTTTCATTACAACCACTAT
Found at i:1516527 original size:53 final size:52
Alignment explanation
Indices: 1516470--1516660 Score: 224
Period size: 53 Copynumber: 3.6 Consensus size: 52
1516460 AATGCATCAT
*
1516470 CAACCACTATTGAAATACTTTATTTCAATAGTGGTTGAAATGAAAGGTATCCC
1 CAACCACTATTGAAATAATTTATTTCAATAGTGGTTGAAATGAAA-GTATCCC
* * * *
1516523 CAACCACTATTGAAATAAATTATTTCAATAGTGGTTGAAATGAATCGCATCCT
1 CAACCACTATTGAAATAATTTATTTCAATAGTGGTTGAAATGAA-AGTATCCC
* * * * * *
1516576 TAACCACTATTGAAATAATATATTTCAAAAGTGGTCGTAATG-AAGTAACCCC
1 CAACCACTATTGAAATAATTTATTTCAATAGTGGTTGAAATGAAAGT-ATCCC
*
1516628 CAACCCCTATTGAAATAATTTATATT-AATAGTG
1 CAACCACTATTGAAATAATTTAT-TTCAATAGTG
1516661 ATATTTATAA
Statistics
Matches: 116, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
51 1 0.01
52 30 0.26
53 85 0.73
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (52 bp):
CAACCACTATTGAAATAATTTATTTCAATAGTGGTTGAAATGAAAGTATCCC
Found at i:1517043 original size:33 final size:32
Alignment explanation
Indices: 1516952--1517030 Score: 140
Period size: 32 Copynumber: 2.4 Consensus size: 32
1516942 CCTAGCCATC
1516952 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
*
1516984 CTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1517016 TTTCCCCCACGGAAA
1 TTTCCCCC-CGGAAA
1517031 GCTGACTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 38 0.86
33 6 0.14
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (32 bp):
TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
Found at i:1519534 original size:17 final size:17
Alignment explanation
Indices: 1519501--1519534 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1519491 AGGTTTTCCG
*
1519501 GGGGGAAAAGCTACTAT
1 GGGGGAAAAACTACTAT
*
1519518 GGGGGAAAAACTGCTAT
1 GGGGGAAAAACTACTAT
1519535 ACAACACCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.18
Consensus pattern (17 bp):
GGGGGAAAAACTACTAT
Found at i:1519667 original size:17 final size:17
Alignment explanation
Indices: 1519645--1519679 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1519635 ATTGAAATAA
1519645 TTTATTTCAATAGTGGT
1 TTTATTTCAATAGTGGT
1519662 TTTATTTCAATAGTGGT
1 TTTATTTCAATAGTGGT
1519679 T
1 T
1519680 GCAAAGTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (17 bp):
TTTATTTCAATAGTGGT
Found at i:1519709 original size:84 final size:84
Alignment explanation
Indices: 1519572--1519767 Score: 322
Period size: 84 Copynumber: 2.3 Consensus size: 84
1519562 TTGTTTTAGA
* * * *
1519572 AGTGGTTGTATTTCAATAGTGGTTGTAAAGTGATTCTTCAGATGAAATACATTCCCAACCAGTAT
1 AGTGGTTTTATTTCAATAGTGGTTGCAAAGTGATTCTTCAGATAAAATACATTCCCAACCACTAT
1519637 TGAAATAATTTATTTCAAT
66 TGAAATAATTTATTTCAAT
* *
1519656 AGTGGTTTTATTTCAATAGTGGTTGCAAAGTGATTTTTCTA-ATAAAATGCATTCCCAACCACTA
1 AGTGGTTTTATTTCAATAGTGGTTGCAAAGTGATTCTTC-AGATAAAATACATTCCCAACCACTA
1519720 TTGAAATAATTTATTTCAAT
65 TTGAAATAATTTATTTCAAT
1519740 AGTGGTTTTATTTCAATAGTGGTTGCAA
1 AGTGGTTTTATTTCAATAGTGGTTGCAA
1519768 CATATGTTTA
Statistics
Matches: 105, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
84 104 0.99
85 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (84 bp):
AGTGGTTTTATTTCAATAGTGGTTGCAAAGTGATTCTTCAGATAAAATACATTCCCAACCACTAT
TGAAATAATTTATTTCAAT
Found at i:1519751 original size:17 final size:17
Alignment explanation
Indices: 1519729--1519763 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1519719 ATTGAAATAA
1519729 TTTATTTCAATAGTGGT
1 TTTATTTCAATAGTGGT
1519746 TTTATTTCAATAGTGGT
1 TTTATTTCAATAGTGGT
1519763 T
1 T
1519764 GCAACATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (17 bp):
TTTATTTCAATAGTGGT
Found at i:1540410 original size:177 final size:174
Alignment explanation
Indices: 1540102--1540500 Score: 471
Period size: 177 Copynumber: 2.3 Consensus size: 174
1540092 NNNNNNNNNN
* *
1540102 ATCCATGGAAGTCTGGTGAAGTTAGGACAAGTAATAACTAAGATATAATCATCAGAGGGCACCTG
1 ATCCATGGAAGTCTGGTGAAGTTAGGACAAGTAATAACTAAGATAT-ATCATCAAAGGGAACCTG
*** *
1540167 TTTCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTCCAGCATCCGAACCCTATGGCTCAG
65 CAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTCCAGCATCCGAA-CATATGGCTCAG
* ** * *
1540232 ATTCAGCATTCAAGCCTGTCTGGTGCATCAGTA-TCATAAGATGCACC
129 ATTCAGCATCCAAGCCTGTCAAGTCCATAAGTAGTC--AAGATGCACC
*
1540279 ATCCATGGAAGTCTGGTGAAGTTAGGACAAGTAGTAACTAAGATAT-TGCTATCAAAGGGAACCT
1 ATCCATGGAAGTCTGGTGAAGTTAGGACAAGTAATAACTAAGATATAT-C-ATCAAAGGGAACCT
* * * *
1540343 GCAACAAAAACTTTAACCTGGTCTAAAAACCTTAACCTCCTTCAGCATCTGAA-ATATAGGACTC
64 GCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTCCAGCATCCGAACATAT-GG-CTC
* * * *
1540407 AGATTCAGCATCCAAGTCTTTCAAGTCCATAAGTAGGTCCAGATGCATC
127 AGATTCAGCATCCAAGCCTGTCAAGTCCATAAGTA-GTCAAGATGCACC
* * * * *
1540456 ATCCATGCAAGTTTGGTGAAGATAGGACAAGTAATAGCTTAGATA
1 ATCCATGGAAGTCTGGTGAAGTTAGGACAAGTAATAACTAAGATA
1540501 CATGACCTGC
Statistics
Matches: 190, Mismatches: 26, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
175 4 0.02
176 3 0.02
177 181 0.95
179 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (174 bp):
ATCCATGGAAGTCTGGTGAAGTTAGGACAAGTAATAACTAAGATATATCATCAAAGGGAACCTGC
AACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTCCAGCATCCGAACATATGGCTCAGAT
TCAGCATCCAAGCCTGTCAAGTCCATAAGTAGTCAAGATGCACC
Found at i:1541418 original size:7 final size:7
Alignment explanation
Indices: 1541403--1541469 Score: 71
Period size: 7 Copynumber: 9.6 Consensus size: 7
1541393 ATTAGATATT
1541403 GAATCTC
1 GAATCTC
*
1541410 GAATTTC
1 GAATCTC
*
1541417 GAATCTT
1 GAATCTC
1541424 GAATCTC
1 GAATCTC
* *
1541431 GTATTTC
1 GAATCTC
1541438 GAATCTC
1 GAATCTC
* * *
1541445 GTATTTT
1 GAATCTC
1541452 GAATCTC
1 GAATCTC
1541459 GAATCTC
1 GAATCTC
1541466 GAAT
1 GAAT
1541470 GATCCTTCTC
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (7 bp):
GAATCTC
Found at i:1543364 original size:18 final size:18
Alignment explanation
Indices: 1543341--1543380 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1543331 GTCCGAATTA
1543341 AATTATGATAAAAACTAC
1 AATTATGATAAAAACTAC
1543359 AATTATGATAAAAACTAC
1 AATTATGATAAAAACTAC
1543377 AATT
1 AATT
1543381 TTTTCACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (18 bp):
AATTATGATAAAAACTAC
Found at i:1545517 original size:15 final size:15
Alignment explanation
Indices: 1545497--1545525 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1545487 CATAAATATA
1545497 TCCTTGGTGTAACAG
1 TCCTTGGTGTAACAG
1545512 TCCTTGGTGTAACA
1 TCCTTGGTGTAACA
1545526 AGAAAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (15 bp):
TCCTTGGTGTAACAG
Found at i:1552151 original size:12 final size:12
Alignment explanation
Indices: 1552134--1552159 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1552124 GTCGTATAAG
1552134 ATATTTACCAAC
1 ATATTTACCAAC
1552146 ATATTTACCAAC
1 ATATTTACCAAC
1552158 AT
1 AT
1552160 GATATTACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (12 bp):
ATATTTACCAAC
Found at i:1553890 original size:14 final size:11
Alignment explanation
Indices: 1553838--1553925 Score: 68
Period size: 11 Copynumber: 7.6 Consensus size: 11
1553828 TATGTTCCTT
1553838 TCATATGTGGA
1 TCATATGTGGA
***
1553849 TCATATGACAA
1 TCATATGTGGA
1553860 TCATATGTGGA
1 TCATATGTGGA
1553871 TCATATGTAGGA
1 TCATATGT-GGA
* *
1553883 GGTCATATGAGAA
1 --TCATATGTGGA
***
1553896 TCATATGAACA
1 TCATATGTGGA
1553907 CTCATATGTGGA
1 -TCATATGTGGA
1553919 TCATATG
1 TCATATG
1553926 AAGCAATATG
Statistics
Matches: 60, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
11 40 0.67
12 11 0.18
13 2 0.03
14 7 0.12
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (11 bp):
TCATATGTGGA
Found at i:1554118 original size:11 final size:11
Alignment explanation
Indices: 1554104--1554134 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1554094 ATATGATCCA
1554104 CATATGTGGAT
1 CATATGTGGAT
1554115 CATATGTGGAT
1 CATATGTGGAT
1554126 CATATGTGG
1 CATATGTGG
1554135 CGAAGTTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.35
Consensus pattern (11 bp):
CATATGTGGAT
Found at i:1557697 original size:2 final size:2
Alignment explanation
Indices: 1557690--1557726 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1557680 ACCTAATCTA
1557690 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1557727 CAGACAGACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1557731 original size:4 final size:4
Alignment explanation
Indices: 1557724--1557772 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
1557714 AGAGAGAGAG
1557724 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC
1557772 A
1 A
1557773 AAGATGAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.51, C:0.24, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:1560575 original size:96 final size:96
Alignment explanation
Indices: 1560411--1560593 Score: 366
Period size: 96 Copynumber: 1.9 Consensus size: 96
1560401 TTTTCAAACT
1560411 TTGATGTCCTTGTGACAGGTTACAGTGGTTACTGGTAACATTGGTTACAAAATAGAGTTAGGTTT
1 TTGATGTCCTTGTGACAGGTTACAGTGGTTACTGGTAACATTGGTTACAAAATAGAGTTAGGTTT
1560476 GGGTTAGGGTTAGGGGTTAGGGTCCTTGATG
66 GGGTTAGGGTTAGGGGTTAGGGTCCTTGATG
1560507 TTGATGTCCTTGTGACAGGTTACAGTGGTTACTGGTAACATTGGTTACAAAATAGAGTTAGGTTT
1 TTGATGTCCTTGTGACAGGTTACAGTGGTTACTGGTAACATTGGTTACAAAATAGAGTTAGGTTT
1560572 GGGTTAGGGTTAGGGGTTAGGG
66 GGGTTAGGGTTAGGGGTTAGGG
1560594 GTTAGGGTTA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 87 1.00
ACGTcount: A:0.22, C:0.09, G:0.34, T:0.35
Consensus pattern (96 bp):
TTGATGTCCTTGTGACAGGTTACAGTGGTTACTGGTAACATTGGTTACAAAATAGAGTTAGGTTT
GGGTTAGGGTTAGGGGTTAGGGTCCTTGATG
Found at i:1560581 original size:6 final size:6
Alignment explanation
Indices: 1560563--1560618 Score: 62
Period size: 6 Copynumber: 9.3 Consensus size: 6
1560553 ACAAAATAGA
* *
1560563 GTTA-G GTTTGG GTTAGG GTTAGGG GTTAGGG GTTAGG GTTA-G TTTAGG
1 GTTAGG GTTAGG GTTAGG GTTA-GG GTTA-GG GTTAGG GTTAGG GTTAGG
1560611 GTTAGG GT
1 GTTAGG GT
1560619 AACCATTGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
5 7 0.16
6 24 0.55
7 13 0.30
ACGTcount: A:0.14, C:0.00, G:0.48, T:0.38
Consensus pattern (6 bp):
GTTAGG
Found at i:1560590 original size:7 final size:7
Alignment explanation
Indices: 1560572--1560604 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1560562 AGTTAGGTTT
1560572 GGGTTA-
1 GGGTTAG
1560578 GGGTTAG
1 GGGTTAG
1560585 GGGTTAG
1 GGGTTAG
1560592 GGGTTA-
1 GGGTTAG
1560598 GGGTTAG
1 GGGTTAG
1560605 TTTAGGGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.15, C:0.00, G:0.55, T:0.30
Consensus pattern (7 bp):
GGGTTAG
Found at i:1560590 original size:13 final size:12
Alignment explanation
Indices: 1560563--1560618 Score: 62
Period size: 11 Copynumber: 4.7 Consensus size: 12
1560553 ACAAAATAGA
*
1560563 GTTA-GGTTTGG
1 GTTAGGGTTAGG
1560574 GTTAGGGTTAGGG
1 GTTAGGGTTA-GG
1560587 GTTAGGGGTTAGG
1 GTTA-GGGTTAGG
*
1560600 GTTA-GTTTAGG
1 GTTAGGGTTAGG
1560611 GTTAGGGT
1 GTTAGGGT
1560619 AACCATTGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
11 14 0.37
12 6 0.16
13 12 0.32
14 6 0.16
ACGTcount: A:0.14, C:0.00, G:0.48, T:0.38
Consensus pattern (12 bp):
GTTAGGGTTAGG
Found at i:1560882 original size:101 final size:102
Alignment explanation
Indices: 1560703--1560926 Score: 245
Period size: 101 Copynumber: 2.2 Consensus size: 102
1560693 CCAAGAGAAT
* * **
1560703 ATATAGCTGTAACCATTGTAACCATTCATTGTAACCGAAAAAATAAGACCCTCTTTTAAACAGAA
1 ATATAGCTGTAACCATTGTAACC--TCATTGTAACCAAAAAAATAAGACCCCCTGCTAAACAGAA
*
1560768 AAAAACCCATCACCTCTGTTACCTTTTGACACAAATGGA
64 AAAAACCCATCACCTCTGTTACCTTTTGACACAAATAGA
* * *
1560807 TTATAGCTGTTACCATTGTAA-C-CATTGTAACTAAATAAAATAAGACCCCCTGCTAAACAGAAA
1 ATATAGCTGTAACCATTGTAACCTCATTGTAACCAAA-AAAATAAGACCCCCTGCTAAACAGAAA
**** * * * * *
1560870 AAGGTTCGTCACCTTTGTTACTTTTTGTCACCAATAGA
65 AAAACCCATCACCTCTGTTACCTTTTGACACAAATAGA
*
1560908 ATATAGTTGTAACCATTGT
1 ATATAGCTGTAACCATTGT
1560927 TACTGGATGA
Statistics
Matches: 99, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
100 11 0.11
101 68 0.69
103 1 0.01
104 19 0.19
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (102 bp):
ATATAGCTGTAACCATTGTAACCTCATTGTAACCAAAAAAATAAGACCCCCTGCTAAACAGAAAA
AAACCCATCACCTCTGTTACCTTTTGACACAAATAGA
Found at i:1568569 original size:31 final size:31
Alignment explanation
Indices: 1568531--1568592 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1568521 TCAAACCTTC
1568531 ATGTGTGGTTGGATGTCACACTGCAAAAAGG
1 ATGTGTGGTTGGATGTCACACTGCAAAAAGG
1568562 ATGTGTGGTTGGATGTCACACTGCAAAAAGG
1 ATGTGTGGTTGGATGTCACACTGCAAAAAGG
1568593 GAGGAAGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (31 bp):
ATGTGTGGTTGGATGTCACACTGCAAAAAGG
Found at i:1570225 original size:16 final size:13
Alignment explanation
Indices: 1570192--1570216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1570182 CAGGGATGGG
1570192 GTAATGGTAATTT
1 GTAATGGTAATTT
1570205 GTAATGGTAATT
1 GTAATGGTAATT
1570217 GAGTGTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (13 bp):
GTAATGGTAATTT
Found at i:1570702 original size:21 final size:23
Alignment explanation
Indices: 1570678--1570732 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
1570668 TAACTGTTTT
1570678 ATTA-ACAAACA-AGTTATCTAA
1 ATTATACAAACAGAGTTATCTAA
* *
1570699 ATTATATAAACAGTGTTATCTAA
1 ATTATACAAACAGAGTTATCTAA
*
1570722 ATTATATAAAC
1 ATTATACAAAC
1570733 TATCAAGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 4 0.13
22 6 0.20
23 20 0.67
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (23 bp):
ATTATACAAACAGAGTTATCTAA
Found at i:1571428 original size:11 final size:11
Alignment explanation
Indices: 1571412--1571437 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1571402 AAAAATCGTG
1571412 TAATGGTAATT
1 TAATGGTAATT
1571423 TAATGGTAATT
1 TAATGGTAATT
1571434 TAAT
1 TAAT
1571438 TGAATGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (11 bp):
TAATGGTAATT
Found at i:1578027 original size:9 final size:9
Alignment explanation
Indices: 1578015--1578062 Score: 62
Period size: 9 Copynumber: 5.2 Consensus size: 9
1578005 ATACTATTTA
1578015 AAATAAATG
1 AAATAAATG
*
1578024 AAATAAATA
1 AAATAAATG
1578033 AAATAAAAT-
1 AAAT-AAATG
1578042 AAATGAAATG
1 AAAT-AAATG
1578052 AAATAAATG
1 AAATAAATG
1578061 AA
1 AA
1578063 TTTTAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 27 0.77
10 8 0.23
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (9 bp):
AAATAAATG
Found at i:1578060 original size:14 final size:14
Alignment explanation
Indices: 1578015--1578062 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
1578005 ATACTATTTA
1578015 AAAT-AAATGAAAT
1 AAATGAAATGAAAT
* *
1578028 AAATAAAATAAAAT
1 AAATGAAATGAAAT
1578042 AAATGAAATGAAAT
1 AAATGAAATGAAAT
1578056 AAATGAA
1 AAATGAA
1578063 TTTTAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
13 4 0.13
14 27 0.87
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (14 bp):
AAATGAAATGAAAT
Found at i:1580167 original size:2 final size:2
Alignment explanation
Indices: 1580160--1580185 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1580150 AGGTAAAGGG
1580160 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1580186 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1585100 original size:32 final size:32
Alignment explanation
Indices: 1585054--1586833 Score: 1170
Period size: 32 Copynumber: 57.2 Consensus size: 32
1585044 ATTCATGCCG
*
1585054 TTACATACTA-GCCATTGG-GTCAATATACATCA
1 TTACATAC-AGGCCA-TGGTGTCAATATCCATCA
*
1585086 TTACATACAGGCCATGGTGTCATTATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* *
1585118 TTGCAAACAGGCCATGGTGTCAATATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * * *
1585150 TTTCATACAAGCCATGGTGGCAATATCCATTA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * **
1585182 TTACACACGGGCCATGGTGTCAATATTTATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * * *
1585214 TTTCATACTGACCATGGTGTCAATAGTCAATATCCATAA
1 TTACATACAGGCCAT-G-G----T-GTCAATATCCATCA
1585253 TTACATACAGGCCATGGTG------T-CA--A
1 TTACATACAGGCCATGGTGTCAATATCCATCA
*
1585276 -TACATACAGGCCTTGGTGTCAA---------
1 TTACATACAGGCCATGGTGTCAATATCCATCA
*
1585298 -TACATACAGGCCTTGGTGTCAA---------
1 TTACATACAGGCCATGGTGTCAATATCCATCA
*
1585320 -TACATACAGGCCTTGGTGTCAA---------
1 TTACATACAGGCCATGGTGTCAATATCCATCA
*
1585342 -TACATACAGGCCTTGGTGTCAA--T--A-C-
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* *
1585367 ----ATACAGGCCTTGGTGTCAAT-TCAATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * * **
1585394 TTATATACAGTCCATTGTGTCAATATCCATGG
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * * * *
1585426 TAAAATACAGTCAACGGTGTCAATATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
*
1585458 TTACATACAGGCCATGGT-TC-ATACCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * * *
1585488 TAACATACATGTGGC--GGCGTCAATAACCATCA
1 TTACATACA-G-GCCATGGTGTCAATATCCATCA
** * * * * *
1585520 AAACATTCATGCCACGATGTCAATATTCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
*
1585552 TTACATACAGGCCGTGGTGTCAATATCCATC-
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * *
1585583 TAAACATACATGCC-TCGGTGTCAATATTCATCA
1 T-TACATACAGGCCAT-GGTGTCAATATCCATCA
*
1585616 TTACTTACAGGCCATGGTGTCAA-ATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * *
1585647 TTACATACAAGCCATGGTGTCATTATTCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* *
1585679 GTACATACAGGCCATGGTGTCAATATTCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * * * * *
1585711 TAATATACTGGCCATCGTGTCAGTATCCGTCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* *
1585743 TAACATACTGGCCATGGTGTCAA-ATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
*
1585774 TTACATACAGACCATGGTGTCAATATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* *
1585806 TTACAAACAGGCCATTGTGTCAATATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
*
1585838 TTACATACAGACCATGGTGTCAATATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * ** *
1585870 TTACATACTGGCCATCGTGTCAGCATCCGTCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * *
1585902 TTACATACAGGCCATGTTATCAATATCCATTA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* ** * *
1585934 TTACACACAACCCGTCGTGTCAATATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* **
1585966 TTACAAACAGGCCATTTTGTCAATATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
*
1585998 TTACATACAGGCCATTGTGTCAATATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* *
1586030 TTACAAACATGCCATGGTGTCAATATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * * ** *
1586062 TTACATACTGGTCATCGTGTCAGCATCCGTCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
1586094 TTACATACAGGCCATGGTGTCAATATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
1586126 TTACATACAGGCCATGGTGTCAATATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* **
1586158 TTACAAACAGGCCATTTTGTCAATATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
*** * * *
1586190 TTACATACAAATCGTGGTGTC-GTAACCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
*** * * * *
1586221 TTACATACAAATCGTGGTGTC-GTAACCATTA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * *
1586252 TTACATACAGGTCGTGGTGTCAATATCCATTA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * *
1586284 TTACATACAGGTCGTGGTGTCAATATCCATTA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * *
1586316 TTACATACAGGTCGTGGTGTCAATATCCATAA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * *
1586348 TTACATACAGGCCATGGTGTTATTATTCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* *
1586380 GTACATACAGGCCATGGTGTCAATATTCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * * *
1586412 TTACATACTGGCCATCGTGTCAGTATCCGTCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * *
1586444 TTACAAACAGGCCGTGGTGTCAGTAT-C-T-A
1 TTACATACAGGCCATGGTGTCAATATCCATCA
**** * * ** *
1586473 TTATCAT-CA-G-CATTAAATGAATTTTTAGCTAA
1 TTA-CATACAGGCCATGGTGTCAATATCCA--TCA
** * ** ** * * *** **
1586505 GTTGATGTA-A-ACTTTTATTTTAATAGAGAAAA
1 -TT-ACATACAGGCCATGGTGTCAATATCCATCA
**** * * * ** **
1586537 TATA-AT-GTTTCAATCGGTTCTTCATATGTGTATTT
1 T-TACATACAGGCCAT-GG-T-GTCA-ATATCCATCA
* * * *
1586572 TTA-ATGCTGACCACGGTGTCAATATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
*
1586603 TTACATACAGGCCGTGGTGTCAATATCCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * * *
1586635 TTACATACAGGCCGTGGTATCTATATCCATTA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * *
1586667 TTACATACAGGTCGTGGTGTCAATATCCATTA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * *
1586699 TTACATACAGGTCGTGGTGTCAATATCCATAA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * *
1586731 TTACATACAGGCCATGGTGTTATTATTCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* *
1586763 GTACATACAGGCCATGGTGTCAATATTCATCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
* * *
1586795 TTACATACAGGCCGTGGTGTCAGTATCCGTCA
1 TTACATACAGGCCATGGTGTCAATATCCATCA
1586827 TTACATA
1 TTACATA
1586834 TATAGGATTT
Statistics
Matches: 1428, Mismatches: 262, Indels: 116
0.79 0.15 0.06
Matches are distributed among these distances:
22 102 0.07
23 2 0.00
25 3 0.00
26 2 0.00
27 6 0.00
28 1 0.00
29 6 0.00
30 25 0.02
31 153 0.11
32 1066 0.75
33 10 0.01
34 19 0.01
35 7 0.00
37 1 0.00
38 2 0.00
39 23 0.02
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (32 bp):
TTACATACAGGCCATGGTGTCAATATCCATCA
Found at i:1585282 original size:22 final size:22
Alignment explanation
Indices: 1585254--1585386 Score: 257
Period size: 22 Copynumber: 6.0 Consensus size: 22
1585244 TATCCATAAT
*
1585254 TACATACAGGCCATGGTGTCAA
1 TACATACAGGCCTTGGTGTCAA
1585276 TACATACAGGCCTTGGTGTCAA
1 TACATACAGGCCTTGGTGTCAA
1585298 TACATACAGGCCTTGGTGTCAA
1 TACATACAGGCCTTGGTGTCAA
1585320 TACATACAGGCCTTGGTGTCAA
1 TACATACAGGCCTTGGTGTCAA
1585342 TACATACAGGCCTTGGTGTCAA
1 TACATACAGGCCTTGGTGTCAA
1585364 TACATACAGGCCTTGGTGTCAA
1 TACATACAGGCCTTGGTGTCAA
1585386 T
1 T
1585387 TCAATCATTA
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 110 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (22 bp):
TACATACAGGCCTTGGTGTCAA
Found at i:1587997 original size:82 final size:84
Alignment explanation
Indices: 1587841--1587999 Score: 223
Period size: 82 Copynumber: 1.9 Consensus size: 84
1587831 TTCAGATGTT
* * * *
1587841 AAATCTCTTGCTTAATTTTTAGCAAAACTTTTATCATAACATTTGTAAGTTTGTGTAATAAACAA
1 AAATCTCTTGCTTAATGTTTAGCAAAAC-TTTATCATAACAGTTGCAAGTTTGTATAATAAACAA
1587906 ACACATGGTAAAGAGATATC
65 ACACATGGTAAAGAGATATC
* * *
1587926 AAATCTCTTGCTTAATGTTTAGTAAAAC-TT-TCATAACAGTTGCAAGTTTGTATGATAAACAAT
1 AAATCTCTTGCTTAATGTTTAGCAAAACTTTATCATAACAGTTGCAAGTTTGTATAATAAACAAA
*
1587989 CACGTGGTAAA
66 CACATGGTAAA
1588000 TATTTTTTTG
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
82 38 0.58
83 2 0.03
85 26 0.39
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (84 bp):
AAATCTCTTGCTTAATGTTTAGCAAAACTTTATCATAACAGTTGCAAGTTTGTATAATAAACAAA
CACATGGTAAAGAGATATC
Found at i:1590095 original size:24 final size:24
Alignment explanation
Indices: 1590067--1590113 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1590057 CTAATATTTC
*
1590067 CTAAACACAATAGATTTAATAATT
1 CTAAACAAAATAGATTTAATAATT
* *
1590091 CTAAATAAAATAGATTTCATAAT
1 CTAAACAAAATAGATTTAATAAT
1590114 CAGTATCCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.34
Consensus pattern (24 bp):
CTAAACAAAATAGATTTAATAATT
Found at i:1591452 original size:28 final size:28
Alignment explanation
Indices: 1591412--1591497 Score: 145
Period size: 28 Copynumber: 3.1 Consensus size: 28
1591402 TGCTTGCCAG
1591412 GTAGGAAAATGTTAAACCATTTTACTGT
1 GTAGGAAAATGTTAAACCATTTTACTGT
* *
1591440 GTAGGAAAATGTTAAACCTTTTTACGGT
1 GTAGGAAAATGTTAAACCATTTTACTGT
*
1591468 GTAGGGAAATGTTAAACCATTTTACTGT
1 GTAGGAAAATGTTAAACCATTTTACTGT
1591496 GT
1 GT
1591498 TATTCTATTC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (28 bp):
GTAGGAAAATGTTAAACCATTTTACTGT
Found at i:1591942 original size:31 final size:31
Alignment explanation
Indices: 1591782--1592101 Score: 140
Period size: 31 Copynumber: 10.7 Consensus size: 31
1591772 TCCCTGGTGT
* * * *
1591782 TTTTTGACAGTTACAAAAATCTTC-CGGATAT
1 TTTTCGACAGTTACATAAATC-CCACGGATAA
* *
1591813 TTTTCGACAGCT-CATTAAATTCCC-CGGATAT
1 TTTTCGACAGTTACA-TAAA-TCCCACGGATAA
* * * * *
1591844 TTTTCGACAGTTTCATTAGTCCCCCGGAT-T
1 TTTTCGACAGTTACATAAATCCCACGGATAA
* * * * *
1591874 TTTTGGTCTGTTACATAATTTCCA-GGAT-A
1 TTTTCGACAGTTACATAAATCCCACGGATAA
1591903 -TTT---CAGTTACATAAATCCCACGGATAA
1 TTTTCGACAGTTACATAAATCCCACGGATAA
*
1591930 TTTTCGATAGTTACAT-AATCCCTA-GGAT-A
1 TTTTCGACAGTTACATAAATCCC-ACGGATAA
* * * * * *
1591959 TTTTTGACAGTTATATTATTTCCA--GAAAA
1 TTTTCGACAGTTACATAAATCCCACGGATAA
* ** * *
1591988 TTTTTGACAGCAACAT-AATCCCTA-AGATAT
1 TTTTCGACAGTTACATAAATCCC-ACGGATAA
* *
1592018 TTTTCTACAGTTACATAAATCCCCCGGAT-A
1 TTTTCGACAGTTACATAAATCCCACGGATAA
*
1592048 TTTATCGACAGTTACATAAATCCCTCGG--AA
1 TTT-TCGACAGTTACATAAATCCCACGGATAA
* *
1592078 TATATCGACAATTACATAAATCCC
1 T-TTTCGACAGTTACATAAATCCC
1592102 CAGAATATTT
Statistics
Matches: 225, Mismatches: 44, Indels: 41
0.73 0.14 0.13
Matches are distributed among these distances:
25 14 0.06
26 4 0.02
27 1 0.00
28 12 0.05
29 34 0.15
30 76 0.34
31 80 0.36
32 4 0.02
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (31 bp):
TTTTCGACAGTTACATAAATCCCACGGATAA
Found at i:1592086 original size:30 final size:29
Alignment explanation
Indices: 1592024--1592109 Score: 118
Period size: 30 Copynumber: 2.9 Consensus size: 29
1592014 ATATTTTTCT
*
1592024 ACAGTTACATAAATCCCCCGGATATTTATCG
1 ACAGTTACATAAAT-CCCCGGA-ATATATCG
1592055 ACAGTTACATAAATCCCTCGGAATATATCG
1 ACAGTTACATAAATCCC-CGGAATATATCG
* *
1592085 ACAATTACATAAATCCCCAGAATAT
1 ACAGTTACATAAATCCCCGGAATAT
1592110 TTTTCGGTAG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 7 0.14
30 26 0.51
31 18 0.35
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.27
Consensus pattern (29 bp):
ACAGTTACATAAATCCCCGGAATATATCG
Found at i:1593916 original size:17 final size:18
Alignment explanation
Indices: 1593894--1593932 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
1593884 TTCGGTCAAA
1593894 TTTTATCTT-TTTA-TTAT
1 TTTTAT-TTATTTATTTAT
1593911 TTTTATTTATTTATTTAT
1 TTTTATTTATTTATTTAT
1593929 TTTT
1 TTTT
1593933 TTTGGTCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 2 0.10
17 10 0.50
18 8 0.40
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTATTTATTTATTTAT
Found at i:1606012 original size:27 final size:26
Alignment explanation
Indices: 1605981--1606032 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
1605971 TTAAAGTTTT
1605981 CAATAAATTTAA-TTAGCAGAGATGTCC
1 CAATAAA-TTAACTT-GCAGAGATGTCC
1606008 CAATAAATTAAGCTTGCAGAGATGT
1 CAATAAATTAA-CTTGCAGAGATGT
1606033 TGTCAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 4 0.17
27 17 0.74
28 2 0.09
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (26 bp):
CAATAAATTAACTTGCAGAGATGTCC
Found at i:1606220 original size:24 final size:24
Alignment explanation
Indices: 1606188--1606234 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1606178 AATATTCAGC
1606188 GATAAATATCCAAGGATTTTGTCT
1 GATAAATATCCAAGGATTTTGTCT
* * * *
1606212 GATATATATTCAATGTTTTTGTC
1 GATAAATATCCAAGGATTTTGTC
1606235 CGAGAATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45
Consensus pattern (24 bp):
GATAAATATCCAAGGATTTTGTCT
Found at i:1611442 original size:13 final size:13
Alignment explanation
Indices: 1611424--1611448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1611414 AAGAGGAAAT
1611424 ATTATGTTAAAAC
1 ATTATGTTAAAAC
1611437 ATTATGTTAAAA
1 ATTATGTTAAAA
1611449 TCTTTATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (13 bp):
ATTATGTTAAAAC
Found at i:1616937 original size:2 final size:2
Alignment explanation
Indices: 1616930--1616980 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1616920 NNNNNNNNNN
1616930 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1616972 CT CT CT CT C
1 CT CT CT CT C
1616981 GGGAGAGGGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1617362 original size:12 final size:12
Alignment explanation
Indices: 1617345--1617369 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1617335 TGATACTTTG
1617345 TCTTCTTTTTTT
1 TCTTCTTTTTTT
1617357 TCTTCTTTTTTT
1 TCTTCTTTTTTT
1617369 T
1 T
1617370 TATTTGCCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TCTTCTTTTTTT
Found at i:1618056 original size:2 final size:2
Alignment explanation
Indices: 1618049--1618075 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1618039 AAACATCATT
1618049 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1618076 AAGAAGACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1632598 original size:22 final size:22
Alignment explanation
Indices: 1632573--1632617 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1632563 GTAAAAAGGC
1632573 GACTCAACTAGTGTATTATGGT
1 GACTCAACTAGTGTATTATGGT
**
1632595 GACTCATTTAGTGTATTATGGT
1 GACTCAACTAGTGTATTATGGT
1632617 G
1 G
1632618 CATGGCTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.40
Consensus pattern (22 bp):
GACTCAACTAGTGTATTATGGT
Found at i:1635149 original size:12 final size:11
Alignment explanation
Indices: 1635129--1635158 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1635119 TCATGTGTTG
1635129 TTGTTTTTTTT
1 TTGTTTTTTTT
1635140 TTGTTTTTTTT
1 TTGTTTTTTTT
1635151 TTGTTTTT
1 TTGTTTTT
1635159 GGGGGGGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (11 bp):
TTGTTTTTTTT
Found at i:1635628 original size:2 final size:2
Alignment explanation
Indices: 1635621--1635680 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1635611 TAATTCTTTT
1635621 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1635663 GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA
1635681 TGTGCGCGTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1635743 original size:2 final size:2
Alignment explanation
Indices: 1635738--1635768 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1635728 NGAGAGAAAA
1635738 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1635769 TGTACGTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1642085 original size:76 final size:76
Alignment explanation
Indices: 1641993--1642148 Score: 303
Period size: 76 Copynumber: 2.1 Consensus size: 76
1641983 TCAGTCTGCC
1641993 TGTTACTATTATGTATTGAATAGTCTACGATTTGGTGTATTACCGTATGATAACAGACGAATAAT
1 TGTTACTATTATGTATTGAATAGTCTACGATTTGGTGTATTACCGTATGATAACAGACGAATAAT
1642058 TTTATGAGTTT
66 TTTATGAGTTT
*
1642069 TGTTACTATTATGTATTGAATAGTCTACGATTTTGTGTATTACCGTATGATAACAGACGAATAAT
1 TGTTACTATTATGTATTGAATAGTCTACGATTTGGTGTATTACCGTATGATAACAGACGAATAAT
1642134 TTTATGAGTTT
66 TTTATGAGTTT
1642145 TGTT
1 TGTT
1642149 TACGTCCGAT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 79 1.00
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (76 bp):
TGTTACTATTATGTATTGAATAGTCTACGATTTGGTGTATTACCGTATGATAACAGACGAATAAT
TTTATGAGTTT
Found at i:1646555 original size:16 final size:16
Alignment explanation
Indices: 1646534--1646567 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1646524 ACAATTCAGG
*
1646534 AAACATTTTTACAATT
1 AAACATATTTACAATT
1646550 AAACATATTTACAATT
1 AAACATATTTACAATT
1646566 AA
1 AA
1646568 TCTGATTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
AAACATATTTACAATT
Found at i:1649789 original size:19 final size:18
Alignment explanation
Indices: 1649578--1649791 Score: 83
Period size: 19 Copynumber: 11.5 Consensus size: 18
1649568 GCTGTACAAT
* *
1649578 TGAGGATTTGCTAACTAAC
1 TGAGG-TTTGCTATCTTAC
* *
1649597 TGAGATTTGCTATATTAC
1 TGAGGTTTGCTATCTTAC
* ** *
1649615 TGAGGAATCCCTATCTTAT
1 TGAGG-TTTGCTATCTTAC
** **
1649634 TGGAATTTTGCTATGGTAC
1 T-GAGGTTTGCTATCTTAC
* *
1649653 CGAGGCTTGCTATCTCT-C
1 TGAGGTTTGCTATCT-TAC
* * **
1649671 TTAGGTGTTGTTATCTTGT
1 TGAGGT-TTGCTATCTTAC
* *
1649690 TGGGGCTTTGCTGA-CTCAC
1 TGAGG-TTTGCT-ATCTTAC
*
1649709 TGAGGTTTGCTATCTCAC
1 TGAGGTTTGCTATCTTAC
* *
1649727 TAAGGTTTG-TAATCTTAA
1 TGAGGTTTGCT-ATCTTAC
* *
1649745 TGAGGGTTTGCTATCTAAA
1 TGA-GGTTTGCTATCTTAC
*
1649764 TGGGGTTTTGCTATCTTAC
1 TGAGG-TTTGCTATCTTAC
1649783 TGAGGTTTG
1 TGAGGTTTG
1649792 GCGGCGTCCT
Statistics
Matches: 138, Mismatches: 45, Indels: 25
0.66 0.22 0.12
Matches are distributed among these distances:
17 2 0.01
18 60 0.43
19 71 0.51
20 5 0.04
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (18 bp):
TGAGGTTTGCTATCTTAC
Found at i:1649790 original size:37 final size:36
Alignment explanation
Indices: 1649707--1649791 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 36
1649697 TTGCTGACTC
* *
1649707 ACTGAGGTTTGCTATCTCACTAAGGTTTGTAATCTT
1 ACTGAGGTTTGCTATCTAAATAAGGTTTGTAATCTT
* **
1649743 AATGAGGGTTTGCTATCTAAATGGGGTTTTGCT-ATCTT
1 ACTGA-GGTTTGCTATCTAAATAAGG-TTTG-TAATCTT
1649781 ACTGAGGTTTG
1 ACTGAGGTTTG
1649792 GCGGCGTCCT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
36 4 0.10
37 22 0.55
38 13 0.32
39 1 0.03
ACGTcount: A:0.21, C:0.13, G:0.25, T:0.41
Consensus pattern (36 bp):
ACTGAGGTTTGCTATCTAAATAAGGTTTGTAATCTT
Found at i:1660662 original size:28 final size:28
Alignment explanation
Indices: 1660622--1660677 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1660612 CAATACACCA
1660622 TTACAAGTTAATTACAGCAGCTTGAGGT
1 TTACAAGTTAATTACAGCAGCTTGAGGT
1660650 TTACAAGTTAATTACAGCAGCTTGAGGT
1 TTACAAGTTAATTACAGCAGCTTGAGGT
1660678 GACATAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (28 bp):
TTACAAGTTAATTACAGCAGCTTGAGGT
Found at i:1660686 original size:28 final size:28
Alignment explanation
Indices: 1660624--1660686 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 28
1660614 ATACACCATT
*
1660624 ACAAGTTAATTACAGCAGCTTGAGGTTT
1 ACAAGTTAATTACAGCAGCTTGAGGTTG
1660652 ACAAGTTAATTACAGCAGCTTGAGG-TG
1 ACAAGTTAATTACAGCAGCTTGAGGTTG
1660679 ACATAGTT
1 ACA-AGTT
1660687 TATATACTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
27 4 0.12
28 29 0.88
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30
Consensus pattern (28 bp):
ACAAGTTAATTACAGCAGCTTGAGGTTG
Found at i:1665445 original size:166 final size:166
Alignment explanation
Indices: 1665171--1666256 Score: 1481
Period size: 166 Copynumber: 6.5 Consensus size: 166
1665161 AGATCACCTG
* * *
1665171 AGGGTGGGGCCACAATGGGGGGTCGAAGTTTAACAAATGAATATATAGAGTAAATCTTTAAAAAT
1 AGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAAT
* * *
1665236 CTTCTCCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCATCAGGTAATGT
66 CTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGT
* * *
1665301 AGATACAAATTTGTGAAAATCATGATCCCCGGAGGT
131 AGATTCAAATTTGTGAAAATCATGAACCCCGGGGGT
** * *
1665337 AGGGTGGGGCCACAATGAAGGATCGAAGTTTTACATAGGAATATATAGAATAAATCTTTAAAAAT
1 AGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAAT
* * * *
1665402 CTTCTTCTCAGAAACTAATCGGCCAGGAAAGCTGACACTTGTGTGGAAGGATCCTCAGGTAGTGT
66 CTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGT
* * *
1665467 AGATTCAAAGTTGTAAAAAAAAATCATG-ACCCCCGGGGT
131 AGATTCAAATTTGT----GAAAATCATGAACCCCGGGGGT
* * *
1665506 ACGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATAAACAGAGTAAATCTTTAAAAAT
1 AGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAAT
*
1665571 CTTCTTCTCAGAAACTAATCAGCCAAGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGT
66 CTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGT
* *
1665636 AGATTCATAGTTGTGAAAATCATG-ACCACCGGGGGT
131 AGATTCAAATTTGTGAAAATCATGAACC-CCGGGGGT
*
1665672 AGGGTGGGGCCACAATGGGGGATCGAAGTTTAAAATAGGAATATATAGAGTAAATCTTTAAAAAT
1 AGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAAT
* * * * * *
1665737 CTTCTTCTCAGAAACTAATCAGCTAGCAATGCTGAAACTTCT-TCGGAAGCATTCTCAGGTAGTG
66 CTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGT-GAAAGCATCCTCAGGTAGTG
* * * *
1665801 TTGATTCAAAATTGTGAAAATAAT-AACACCTGGGGGT
130 TAGATTCAAATTTGTGAAAATCATGAAC-CCCGGGGGT
** * * *
1665838 AGAATGGGGCCACAATGGGGGTTCGAAGTTTAACATATGATTATATAGAGTAAATCTTTAAAAAT
1 AGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAAT
* * *
1665903 CTTCTTCTCAGAAACTAATTAGCCAGGAAAGCTGAAACCTGTGTGGAAGCATCCTCAGGTAGTGT
66 CTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGT
*
1665968 AGATTCAAATTTGTGAAAATCAT-AACCCTGGGGGT
131 AGATTCAAATTTGTGAAAATCATGAACCCCGGGGGT
* * * * * *
1666003 AGGTTTGGGCCACAATGGGAGG-TCGATGTTTTACATAGGAATAAACAGAGTAAATCTTTAAAAA
1 AGGGTGGGGCCACAATGGG-GGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAA
*
1666067 TCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAATCTTGTGTGAAAGCATCCTCAGGTAGTG
65 TCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTG
* * *
1666132 TAGATTCATAGTTT-TGAAAATCATGATCCCCAGGGGT
130 TAGATTCA-AATTTGTGAAAATCATGAACCCCGGGGGT
* * * *
1666169 AGGGTGGGGCCACAATGGGGGGTCAAAGTTTAACAAAGGAATATATAGGGTAAATCTTTAAAAA-
1 AGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAAT
1666233 --TCTTCTCAGAAACTAATCAGCCAG
66 CTTCTTCTCAGAAACTAATCAGCCAG
1666257 ATGTTCTTTA
Statistics
Matches: 814, Mismatches: 93, Indels: 29
0.87 0.10 0.03
Matches are distributed among these distances:
163 24 0.03
165 155 0.19
166 485 0.60
167 2 0.00
169 139 0.17
170 9 0.01
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (166 bp):
AGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAAT
CTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGT
AGATTCAAATTTGTGAAAATCATGAACCCCGGGGGT
Found at i:1665595 original size:335 final size:330
Alignment explanation
Indices: 1665173--1666256 Score: 1495
Period size: 335 Copynumber: 3.3 Consensus size: 330
1665163 ATCACCTGAG
*
1665173 GGTGGGGCCACAATGGGGGGTCGAAGTTTAACAAATGAATATATAGAGTAAATCTTTAAAAATCT
1 GGTGGGGCCACAATGGGGGGTCGAAGTTTAACAAAGGAATATATAGAGTAAATCTTTAAAAATCT
* * *
1665238 TCTCCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCATCAGGTAATGTAG
66 TCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAG
* * *
1665303 ATACAAATTTGTGAAAATCATGATCCCCGGAGGTAGGGTGGGGCCACAATGAAGGATCGAAGTTT
131 ATTCAAATTTGTGAAAATCATGA-CCCCGGGGGTAGGGTGGGGCCACAATGGAGGATCGAAGTTT
* *
1665368 TACATAGGAATATATAGAATAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCGGCCAGGAAAG
195 TACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAG
*
1665433 CTGACACTTGTGTGGAAGGATCCTCAGGTAGTGTAGATTCAAAGTTGTAAAAAAAAATCATGACC
260 CTGA-ACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGT--AAAAAAATCATGACC
*
1665498 CCCGGGGTA
322 CCAGGGGTA
* * * *
1665507 CGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATAAACAGAGTAAATCTTTAAAAATC
1 -GGTGGGGCCACAATGGGGGGTCGAAGTTTAACAAAGGAATATATAGAGTAAATCTTTAAAAATC
*
1665572 TTCTTCTCAGAAACTAATCAGCCAAGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTA
65 TTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTA
* * *
1665637 GATTCATAGTTGTGAAAATCATGACCACCGGGGGTAGGGTGGGGCCACAATGGGGGATCGAAGTT
130 GATTCAAATTTGTGAAAATCATGACC-CCGGGGGTAGGGTGGGGCCACAATGGAGGATCGAAGTT
* * * * *
1665702 TAAAATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCTAGCAAT
194 TTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAA
* * * * *
1665767 GCTGAAACTTCT-TCGGAAGCATTCTCAGGTAGTGTTGATTCAAAATTGTGAAAATAAT-A--AC
259 GCTG-AACTTGTGT-GGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGT-AAAAAAATCATGAC
**
1665828 ACCTGGGGGTA
321 -CCCAGGGGTA
* * * * *
1665839 GAATGGGGCCACAATGGGGGTTCGAAGTTTAACATATGATTATATAGAGTAAATCTTTAAAAATC
1 G-GTGGGGCCACAATGGGGGGTCGAAGTTTAACAAAGGAATATATAGAGTAAATCTTTAAAAATC
* * *
1665904 TTCTTCTCAGAAACTAATTAGCCAGGAAAGCTGAAACCTGTGTGGAAGCATCCTCAGGTAGTGTA
65 TTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTA
* * * * *
1665969 GATTCAAATTTGTGAAAATCATAACCCTGGGGGTAGGTTTGGGCCACAATGGGAGG-TCGATGTT
130 GATTCAAATTTGTGAAAATCATGACCCCGGGGGTAGGGTGGGGCCACAAT-GGAGGATCGAAGTT
* *
1666033 TTACATAGGAATAAACAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAA
194 TTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAA
* * **
1666098 GCTGAATCTTGTGTGAAAGCATCCTCAGGTAGTGTAGATTCATAGTT-T-TGAAAATCATGATCC
259 GCTGAA-CTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTAAAAAAATCATGA-CC
1666161 CCAGGGGTA
322 CCAGGGGTA
* *
1666170 GGGTGGGGCCACAATGGGGGGTCAAAGTTTAACAAAGGAATATATAGGGTAAATCTTTAAAAA--
1 -GGTGGGGCCACAATGGGGGGTCGAAGTTTAACAAAGGAATATATAGAGTAAATCTTTAAAAATC
1666233 -TCTTCTCAGAAACTAATCAGCCAG
65 TTCTTCTCAGAAACTAATCAGCCAG
1666257 ATGTTCTTTA
Statistics
Matches: 661, Mismatches: 75, Indels: 33
0.86 0.10 0.04
Matches are distributed among these distances:
328 27 0.04
329 1 0.00
330 3 0.00
331 188 0.28
332 156 0.24
333 1 0.00
334 10 0.02
335 274 0.41
336 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (330 bp):
GGTGGGGCCACAATGGGGGGTCGAAGTTTAACAAAGGAATATATAGAGTAAATCTTTAAAAATCT
TCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAG
ATTCAAATTTGTGAAAATCATGACCCCGGGGGTAGGGTGGGGCCACAATGGAGGATCGAAGTTTT
ACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGC
TGAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTAAAAAAATCATGACCCCAG
GGGTA
Found at i:1670117 original size:36 final size:37
Alignment explanation
Indices: 1670066--1670142 Score: 147
Period size: 36 Copynumber: 2.1 Consensus size: 37
1670056 CAGGTTGATG
1670066 CAGTAAACCTCAGACAAAGGTCAGATTTGTCAACATT
1 CAGTAAACCTCAGACAAAGGTCAGATTTGTCAACATT
1670103 CAGTAAA-CTCAGACAAAGGTCAGATTTGTCAACATT
1 CAGTAAACCTCAGACAAAGGTCAGATTTGTCAACATT
1670139 CAGT
1 CAGT
1670143 GATTCTCTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 33 0.82
37 7 0.17
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (37 bp):
CAGTAAACCTCAGACAAAGGTCAGATTTGTCAACATT
Found at i:1683296 original size:2 final size:2
Alignment explanation
Indices: 1683291--1683325 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1683281 TTTTAAAGTT
1683291 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1683326 TGCATGATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1686415 original size:86 final size:86
Alignment explanation
Indices: 1686270--1686440 Score: 342
Period size: 86 Copynumber: 2.0 Consensus size: 86
1686260 TTGATAACAT
1686270 CAAATTGATGAAAATCCATTGTCGGTCTTGCATAAGCTTACTGACTTCTACATGTATTGAGCTTT
1 CAAATTGATGAAAATCCATTGTCGGTCTTGCATAAGCTTACTGACTTCTACATGTATTGAGCTTT
1686335 TTAGCTCACCTGAGCTGAAAA
66 TTAGCTCACCTGAGCTGAAAA
1686356 CAAATTGATGAAAATCCATTGTCGGTCTTGCATAAGCTTACTGACTTCTACATGTATTGAGCTTT
1 CAAATTGATGAAAATCCATTGTCGGTCTTGCATAAGCTTACTGACTTCTACATGTATTGAGCTTT
1686421 TTAGCTCACCTGAGCTGAAA
66 TTAGCTCACCTGAGCTGAAA
1686441 GCTCAAGTGA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (86 bp):
CAAATTGATGAAAATCCATTGTCGGTCTTGCATAAGCTTACTGACTTCTACATGTATTGAGCTTT
TTAGCTCACCTGAGCTGAAAA
Found at i:1687007 original size:166 final size:166
Alignment explanation
Indices: 1686648--1687513 Score: 1418
Period size: 166 Copynumber: 5.2 Consensus size: 166
1686638 AGAATTTTTC
* *
1686648 AAAAATCTTCTTCTCA-AGAACCAGA-AAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
1 AAAAATCTTCTTCTCAGA-AACTA-ATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* * * *
1686711 GGCAGTGTAGATTCAAAGTTGTGAAATTCATGATCCCTGGGGGTAGGGTGGGG-CACAATGGGGG
64 GGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
1686775 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
129 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
1686813 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1686878 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
1686943 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
131 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
1686979 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1687044 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
1687109 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
131 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
1687145 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * *
1687210 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCTCGGGGTTAGGGT-GGTCCACAATGGGGGGT
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
*
1687274 CGAAGTTTTACATAGAAATATATAGAGTAAATCTTT
131 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
1687310 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTAGAAGTATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* ** * *
1687375 TAGTGTAGATTCAAAGTTGTGAAAA-CATGATCCCTTGGGGTAGGGTGAGGCCACATTGGGGGGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAT-------
** *
1687439 GGGGGGTTAAAGTTTTACAAAGGAATATATAGAGTAAATCTTT
124 GGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
1687482 TAAAATCTTCTTCTCAGAAACTAATTAGCCAG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAG
1687514 ATGATTCTTT
Statistics
Matches: 664, Mismatches: 26, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
164 17 0.03
165 252 0.38
166 326 0.49
172 69 0.10
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
Found at i:1687274 original size:331 final size:332
Alignment explanation
Indices: 1686648--1687513 Score: 1436
Period size: 331 Copynumber: 2.6 Consensus size: 332
1686638 AGAATTTTTC
* *
1686648 AAAAATCTTCTTCTCA-AGAACCAGA-AAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
1 AAAAATCTTCTTCTCAGA-AACTA-ATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* *
1686711 GGCAGTGTAGATTCAAAGTTGTGAAATTCATGATCCCTGGGGGTAGGGTGGGG-CACAATGGGGG
64 GGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATGGGGG
1686775 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCA
129 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCA
1686840 GCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATC
194 GCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATC
*
1686905 ATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAGAG
259 ATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGAAATATATAGAG
1686970 TAAATCTTT
324 TAAATCTTT
1686979 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* *
1687044 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGT
1687109 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGC
131 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGC
1687174 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCAT
196 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCAT
* * *
1687239 GACCCTCGGGGTTAGGGT-GGTCCACAATGGGGGGTCGAAGTTTTACATAGAAATATATAGAGTA
261 GACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGAAATATATAGAGTA
1687303 AATCTTT
326 AATCTTT
* *
1687310 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTAGAAGTATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * *
1687375 TAGTGTAGATTCAAAGTTGTGAAAA-CATGATCCCTTGGGGTAGGGTGAGGCCACATTGGGGGGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAAT-------
** * *
1687439 GGGGGGTTAAAGTTTTACAAAGGAATATATAGAGTAAATCTTTTAAAATCTTCTTCTCAGAAACT
124 GGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACT
*
1687504 AATTAGCCAG
189 AATCAGCCAG
1687514 ATGATTCTTT
Statistics
Matches: 503, Mismatches: 22, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
330 28 0.06
331 245 0.49
332 160 0.32
337 70 0.14
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (332 bp):
AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGT
CGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGC
CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCAT
GACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGAAATATATAGAGTA
AATCTTT
Found at i:1692129 original size:12 final size:12
Alignment explanation
Indices: 1692109--1692138 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1692099 TGCAGCCCTC
1692109 AAATATTAGCTA
1 AAATATTAGCTA
*
1692121 AAATGTTAGCTA
1 AAATATTAGCTA
1692133 AAATAT
1 AAATAT
1692139 CTGCATAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (12 bp):
AAATATTAGCTA
Done.