Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold601
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: 1259944
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 136746 characters in sequence are not A, C, G, or T
File 6 of 5
Found at i:1212572 original size:108 final size:108
Alignment explanation
Indices: 1212130--1212549 Score: 517
Period size: 108 Copynumber: 3.9 Consensus size: 108
1212120 TTCTTCAGTA
* * * * * * * *
1212130 GTAGTCTGTTCTTCGGTTGTTGTTTG-TTCAGTGGTTGTTGTTTGCTCCTCAGTTGTAGTTGGTT
1 GTAGTCTGTTCTTCAGTTGTTG-TTGATTCAATAGTTGTTGTCTGTTCTTCAGTTGTTGTTGATT
* * *
1212194 CAATGGTTGTTGTCTGTTCTTCAGTTGTTGTTGGTTCAATAATT
65 CAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCAATAGTT
* *
1212238 GTAGTCTGTTCTTCAGTTGTTGTTAATTCAATACTTGTTGTCTGTTCTTC-GATTGTTGTTGATT
1 GTAGTCTGTTCTTCAGTTGTTGTTGATTCAATAGTTGTTGTCTGTTCTTCAG-TTGTTGTTGATT
*
1212302 CAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCCGA-AGTT
65 CAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTT-CAATAGTT
* * * * *
1212346 GTTGTCTGTTCTTCGGTTGTTGTCGATTCAATAGTTGTAGTCTGTTCTTCAGTTGTTGTTAATTC
1 GTAGTCTGTTCTTCAGTTGTTGTTGATTCAATAGTTGTTGTCTGTTCTTCAGTTGTTGTTGATTC
*
1212411 AATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGATTCAATAGTT
66 AATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCAATAGTT
* * * *
1212454 GTAGTCTGTTCTTCAGTTGTTGTTGGTTCCGA-AGTTGTTGTCTGTTCTTCGGTTGTTGTTGGTT
1 GTAGTCTGTTCTTCAGTTGTTGTTGATT-CAATAGTTGTTGTCTGTTCTTCAGTTGTTGTTGATT
* * *
1212518 CCGA-AGTTGTTGTCTGTTCTTCGGTTGTTGTT
65 -CAATAGTTGTAGTCTGTTCTTCAGTTGTTGTT
1212550 TTTTCGGTGG
Statistics
Matches: 270, Mismatches: 35, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
107 5 0.02
108 258 0.96
109 7 0.03
ACGTcount: A:0.12, C:0.13, G:0.25, T:0.50
Consensus pattern (108 bp):
GTAGTCTGTTCTTCAGTTGTTGTTGATTCAATAGTTGTTGTCTGTTCTTCAGTTGTTGTTGATTC
AATAGTTGTAGTCTGTTCTTCAGTTGTTGTTGGTTCAATAGTT
Found at i:1212733 original size:18 final size:18
Alignment explanation
Indices: 1212670--1212752 Score: 67
Period size: 18 Copynumber: 4.4 Consensus size: 18
1212660 TCCTTCGGTT
*
1212670 GTTGTTGTTGTTGGATTAACT
1 GTTGTTGTTGTTGG--T-ACA
*
1212691 GTTGTTGTTGTTGGTACG
1 GTTGTTGTTGTTGGTACA
* * *
1212709 GTGGTTGTTGTTTGTTCA
1 GTTGTTGTTGTTGGTACA
* *
1212727 GTTGTTGTTGTCGGTGCA
1 GTTGTTGTTGTTGGTACA
*
1212745 CTTGTTGT
1 GTTGTTGT
1212753 CGTAATTCGC
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
18 37 0.71
19 1 0.02
21 14 0.27
ACGTcount: A:0.07, C:0.07, G:0.34, T:0.52
Consensus pattern (18 bp):
GTTGTTGTTGTTGGTACA
Found at i:1214700 original size:14 final size:14
Alignment explanation
Indices: 1214681--1214714 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1214671 GGTCGATTTA
1214681 AACAGTTCCAATCC
1 AACAGTTCCAATCC
*
1214695 AACAGTTCCAGTCC
1 AACAGTTCCAATCC
1214709 AACAGT
1 AACAGT
1214715 CAAAATGCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.12, T:0.21
Consensus pattern (14 bp):
AACAGTTCCAATCC
Found at i:1218382 original size:19 final size:19
Alignment explanation
Indices: 1218358--1218608 Score: 461
Period size: 19 Copynumber: 13.3 Consensus size: 19
1218348 TGGAGTCTGA
1218358 AAAAATAACATATAGCTGG
1 AAAAATAACATATAGCTGG
1218377 AAAAATAACATATAGCTGG
1 AAAAATAACATATAGCTGG
1218396 -AAAATAACATATAGCTGG
1 AAAAATAACATATAGCTGG
1218414 AAAAATAACATATAGCTGG
1 AAAAATAACATATAGCTGG
1218433 -AAAATAACATATAGCTGGG
1 AAAAATAACATATAGCT-GG
1218452 AAAAATAACATATAGCTGG
1 AAAAATAACATATAGCTGG
1218471 AAAAATAACATATAGCTGG
1 AAAAATAACATATAGCTGG
1218490 AAAAATAACATATAGCTGG
1 AAAAATAACATATAGCTGG
*
1218509 AAAAATAAGATATAGCTGG
1 AAAAATAACATATAGCTGG
1218528 AAAAATAACATATAGCTGG
1 AAAAATAACATATAGCTGG
*
1218547 AAAAATAGCATATAGCTGG
1 AAAAATAACATATAGCTGG
1218566 AAAAATAACATATAGCTGG
1 AAAAATAACATATAGCTGG
1218585 AAAAATAACATATAGCTGG
1 AAAAATAACATATAGCTGG
1218604 AAAAA
1 AAAAA
1218609 AAAATTAGCA
Statistics
Matches: 225, Mismatches: 4, Indels: 6
0.96 0.02 0.03
Matches are distributed among these distances:
18 34 0.15
19 175 0.78
20 16 0.07
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.21
Consensus pattern (19 bp):
AAAAATAACATATAGCTGG
Found at i:1221163 original size:22 final size:22
Alignment explanation
Indices: 1221135--1221201 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
1221125 GACAATAGTG
*
1221135 TTAGTACCTTATGGATTAACGA
1 TTAGTACCTTATGGATTAACAA
1221157 TTAGTACCTTATGGATTAACAA
1 TTAGTACCTTATGGATTAACAA
1221179 TTAGTACCTTATGGATTAACAA
1 TTAGTACCTTATGGATTAACAA
1221201 T
1 T
1221202 CGTGGGATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (22 bp):
TTAGTACCTTATGGATTAACAA
Found at i:1221948 original size:25 final size:25
Alignment explanation
Indices: 1221906--1221967 Score: 106
Period size: 25 Copynumber: 2.4 Consensus size: 25
1221896 ATTCAAGGAT
*
1221906 ATCAACAAGTTGGTATTTTTCTTGAA
1 ATCAACAA-CTGGTATTTTTCTTGAA
1221932 ATCAACAACTGGTATTTTTCTTGAA
1 ATCAACAACTGGTATTTTTCTTGAA
1221957 ATCAACAACTG
1 ATCAACAACTG
1221968 CGGATTTCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 27 0.77
26 8 0.23
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (25 bp):
ATCAACAACTGGTATTTTTCTTGAA
Found at i:1222118 original size:42 final size:42
Alignment explanation
Indices: 1222014--1222271 Score: 462
Period size: 42 Copynumber: 6.1 Consensus size: 42
1222004 AGAAAGTCAG
*
1222014 CAGATATTTTAGGATGTCAACACGCATTGATTAGATGGATTCC
1 CAGATATTGTAGGATGTCAACACGCATTGATTAGATGGATT-C
1222057 AGCAGATATTGTAGGATGTCAACACGCATTGATTAGATGGATTC
1 --CAGATATTGTAGGATGTCAACACGCATTGATTAGATGGATTC
1222101 CAGATATTGTAGGATGTCAACACGCATTGATTAGATGGATTC
1 CAGATATTGTAGGATGTCAACACGCATTGATTAGATGGATTC
1222143 CAGATATTGTAGGATGTCAACACGCATTGATTAGATGGATTC
1 CAGATATTGTAGGATGTCAACACGCATTGATTAGATGGATTC
*
1222185 CAGATATTGTAGGATGTCAACACGCATTGATTAGATGTATTC
1 CAGATATTGTAGGATGTCAACACGCATTGATTAGATGGATTC
*
1222227 CAGATATTGTAGGATGTCAACACGCATTGATTAGATGGAGTC
1 CAGATATTGTAGGATGTCAACACGCATTGATTAGATGGATTC
1222269 CAG
1 CAG
1222272 CATTGATTAG
Statistics
Matches: 209, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
42 168 0.80
44 1 0.00
45 40 0.19
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (42 bp):
CAGATATTGTAGGATGTCAACACGCATTGATTAGATGGATTC
Found at i:1222221 original size:21 final size:21
Alignment explanation
Indices: 1222197--1222263 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
1222187 GATATTGTAG
1222197 GATGTCAACACGCATTGATTA
1 GATGTCAACACGCATTGATTA
* *
1222218 GATGT-ATTC-CAGATATTG--TA
1 GATGTCA-ACAC-G-CATTGATTA
1222238 GGATGTCAACACGCATTGATTA
1 -GATGTCAACACGCATTGATTA
1222260 GATG
1 GATG
1222264 GAGTCCAGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
20 8 0.24
21 18 0.53
22 8 0.24
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (21 bp):
GATGTCAACACGCATTGATTA
Found at i:1222274 original size:21 final size:21
Alignment explanation
Indices: 1222250--1222338 Score: 178
Period size: 21 Copynumber: 4.2 Consensus size: 21
1222240 ATGTCAACAC
1222250 GCATTGATTAGATGGAGTCCA
1 GCATTGATTAGATGGAGTCCA
1222271 GCATTGATTAGATGGAGTCCA
1 GCATTGATTAGATGGAGTCCA
1222292 GCATTGATTAGATGGAGTCCA
1 GCATTGATTAGATGGAGTCCA
1222313 GCATTGATTAGATGGAGTCCA
1 GCATTGATTAGATGGAGTCCA
1222334 GCATT
1 GCATT
1222339 TATTGACCTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 68 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (21 bp):
GCATTGATTAGATGGAGTCCA
Found at i:1222296 original size:84 final size:83
Alignment explanation
Indices: 1222014--1222313 Score: 437
Period size: 84 Copynumber: 3.5 Consensus size: 83
1222004 AGAAAGTCAG
*
1222014 CAGATATTTTAGGATGTCAACACGCATTGATTAGATGGATTCCAGCAGATATTGTAGGATGTCAA
1 CAGATATTGTAGGATGTC-ACACGCATTGATTAGATGGATT-C--CAGATATTGTAGGATGTCAA
1222079 CACGCATTGATTAGATGGATTC
62 CACGCATTGATTAGATGGATTC
1222101 CAGATATTGTAGGATGTCAACACGCATTGATTAGATGGATTCCAGATATTGTAGGATGTCAACAC
1 CAGATATTGTAGGATGTC-ACACGCATTGATTAGATGGATTCCAGATATTGTAGGATGTCAACAC
1222166 GCATTGATTAGATGGATTC
65 GCATTGATTAGATGGATTC
*
1222185 CAGATATTGTAGGATGTCAACACGCATTGATTAGATGTATTCCAGATATTGTAGGATGTCAACAC
1 CAGATATTGTAGGATGTC-ACACGCATTGATTAGATGGATTCCAGATATTGTAGGATGTCAACAC
*
1222250 GCATTGATTAGATGGAGTC
65 GCATTGATTAGATGGATTC
*
1222269 CAGCATTGATTAG-ATGGA-GTC-CA-GCATTGATTAGATGGAGTCCAG
1 CAG-A-T-ATT-GTA-GGATGTCACACGCATTGATTAGATGGATTCCAG
1222314 CATTGATTAG
Statistics
Matches: 203, Mismatches: 5, Indels: 13
0.92 0.02 0.06
Matches are distributed among these distances:
84 147 0.72
85 3 0.01
86 2 0.01
87 47 0.23
88 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (83 bp):
CAGATATTGTAGGATGTCACACGCATTGATTAGATGGATTCCAGATATTGTAGGATGTCAACACG
CATTGATTAGATGGATTC
Found at i:1222296 original size:126 final size:125
Alignment explanation
Indices: 1222014--1222313 Score: 446
Period size: 126 Copynumber: 2.4 Consensus size: 125
1222004 AGAAAGTCAG
*
1222014 CAGATATTTTAGGATGTCAACACGCATTGATTAGATGGATTCCAGCAGATATTGTAGGATGTCAA
1 CAGATATTGTAGGATGTC-ACACGCATTGATTAGATGGATT-C--CAGATATTGTAGGATGTCAA
*
1222079 CACGCATTGATTAGATGGATTCCAGATATTGTAGGATGTCAACACGCATTGATTAGATGGATTC
62 CACGCATTGATTAGATGGATTCCAGATATTGTAGGATGTCAACACGCATTGATTAGATGGAGTC
1222143 CAGATATTGTAGGATGTCAACACGCATTGATTAGATGGATTCCAGATATTGTAGGATGTCAACAC
1 CAGATATTGTAGGATGTC-ACACGCATTGATTAGATGGATTCCAGATATTGTAGGATGTCAACAC
*
1222208 GCATTGATTAGATGTATTCCAGATATTGTAGGATGTCAACACGCATTGATTAGATGGAGTC
65 GCATTGATTAGATGGATTCCAGATATTGTAGGATGTCAACACGCATTGATTAGATGGAGTC
*
1222269 CAGCATTGATTAG-ATGGA-GTC-CA-GCATTGATTAGATGGAGTCCAG
1 CAG-A-T-ATT-GTA-GGATGTCACACGCATTGATTAGATGGATTCCAG
1222314 CATTGATTAG
Statistics
Matches: 162, Mismatches: 4, Indels: 13
0.91 0.02 0.07
Matches are distributed among these distances:
126 106 0.65
127 3 0.02
128 2 0.01
129 47 0.29
130 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (125 bp):
CAGATATTGTAGGATGTCACACGCATTGATTAGATGGATTCCAGATATTGTAGGATGTCAACACG
CATTGATTAGATGGATTCCAGATATTGTAGGATGTCAACACGCATTGATTAGATGGAGTC
Found at i:1222993 original size:20 final size:20
Alignment explanation
Indices: 1222968--1223407 Score: 745
Period size: 20 Copynumber: 22.0 Consensus size: 20
1222958 TCATTCTCTT
*
1222968 TATGATACTCTCTGACACAC
1 TATGATACTCTCTGACGCAC
1222988 TATGATACTCTCTGACGCAC
1 TATGATACTCTCTGACGCAC
*
1223008 TATGATACTCTCTGACACAC
1 TATGATACTCTCTGACGCAC
*
1223028 TATGATACTCTCTGATGCAC
1 TATGATACTCTCTGACGCAC
1223048 TATGATACTCTCTGACGCAC
1 TATGATACTCTCTGACGCAC
1223068 TATGATACTCTCTGACGCAC
1 TATGATACTCTCTGACGCAC
1223088 TATGATACTCTCTGACGCAC
1 TATGATACTCTCTGACGCAC
*
1223108 TATGATACTCTCTGACGTAC
1 TATGATACTCTCTGACGCAC
1223128 TATGATACTCTCTGACGCAC
1 TATGATACTCTCTGACGCAC
* *
1223148 TATGATACTCTCTGTCGTAC
1 TATGATACTCTCTGACGCAC
1223168 TATGATACTCTCTGACGCAC
1 TATGATACTCTCTGACGCAC
*
1223188 TATGATACTCTCTGACGTAC
1 TATGATACTCTCTGACGCAC
*
1223208 TATGATACTCTCTGACGTAC
1 TATGATACTCTCTGACGCAC
1223228 TATGATACTCTCTGACGCAC
1 TATGATACTCTCTGACGCAC
1223248 TATGATACTCTCTGACGCAC
1 TATGATACTCTCTGACGCAC
* *
1223268 TATGGTACCCTCTGACGCAC
1 TATGATACTCTCTGACGCAC
1223288 TATGATACTCTCTGACGCAC
1 TATGATACTCTCTGACGCAC
*
1223308 TATGGTACTCTCTGACGCAC
1 TATGATACTCTCTGACGCAC
1223328 TATGATACTCTCTGACGCAC
1 TATGATACTCTCTGACGCAC
* *
1223348 TATGATACTCTCTGTCGTAC
1 TATGATACTCTCTGACGCAC
*
1223368 TATGATACTCTCTGACACAC
1 TATGATACTCTCTGACGCAC
*
1223388 TATGATACTCTCTGTCGCAC
1 TATGATACTCTCTGACGCAC
1223408 ATTGACCTGA
Statistics
Matches: 394, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 394 1.00
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.32
Consensus pattern (20 bp):
TATGATACTCTCTGACGCAC
Found at i:1224416 original size:44 final size:43
Alignment explanation
Indices: 1224346--1224471 Score: 130
Period size: 44 Copynumber: 2.9 Consensus size: 43
1224336 GACAGAATTT
1224346 ATAACGAAGAACTTACA-TTACTTCTGTACTAT-GAAACAGACTCC
1 ATAACGAAGAAC-TACATTTA-TTCTGTACTATAG-AACAGACTCC
* * * *
1224390 ATAATGAAGAACATACATTTAGTCTGTACTGTAGGACAGACTCC
1 ATAACGAAGAAC-TACATTTATTCTGTACTATAGAACAGACTCC
* * *
1224434 AGAACAAAGAACTCACATTTATTCTGTACTGTAGAACA
1 ATAACGAAGAACT-ACATTTATTCTGTACTATAGAACA
1224472 ACCTCTAGAT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
43 1 0.01
44 64 0.93
45 4 0.06
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (43 bp):
ATAACGAAGAACTACATTTATTCTGTACTATAGAACAGACTCC
Found at i:1224535 original size:31 final size:31
Alignment explanation
Indices: 1224500--1225173 Score: 444
Period size: 31 Copynumber: 20.5 Consensus size: 31
1224490 TCACATTAGC
1224500 CCTGTACTGTAGAACAAGAACTCACGTCTAG
1 CCTGTACTGTAGAACAAGAACTCACGTCTAG
* * * * *
1224531 CCTGTACTGTTGACCCTCTAGATAGAAGGACTCACATTTGG
1 CCTGTAC---TG------TAGA-ACAAGAACTCACGTCTAG
* * *
1224572 CCTGTACTGTAGAACCAGAACTAAC-TTTAGG
1 CCTGTACTGTAGAACAAGAACTCACGTCTA-G
* *
1224603 CCTGTACTGTGGAAGAAGAACTCACGTCTAG
1 CCTGTACTGTAGAACAAGAACTCACGTCTAG
* * * * *
1224634 CCTGTACTGTTGACCCTCTAGATAGAAGGACTCACATTTGG
1 CCTGTAC---TG------TAGA-ACAAGAACTCACGTCTAG
* * *
1224675 CCTGTACTGTAGAACCAGAACTAAC-TTTAGG
1 CCTGTACTGTAGAACAAGAACTCACGTCTA-G
* * *
1224706 CCTGTACTGTGGAAGAAGAACTCACGTCTGG
1 CCTGTACTGTAGAACAAGAACTCACGTCTAG
* **
1224737 CCTGTATTGTAGAACCTCTAGATAGAAGGACTCAC-AATAGG
1 CCTGTACTGTAGAA---C---A-AG-A--ACTCACGTCTA-G
* *
1224778 CCTGTACTGTAGAACCAA-AACTTAC-TTTAGG
1 CCTGTACTGTAGAA-CAAGAACTCACGTCTA-G
*
1224809 CCTGTGCTGTAGAACAAGAACTCACGTCTAG
1 CCTGTACTGTAGAACAAGAACTCACGTCTAG
*
1224840 CCTGTACTGTAGAACAAGAACTCGCGTCTAG
1 CCTGTACTGTAGAACAAGAACTCACGTCTAG
*
1224871 CCTGTACTGTAGAACAAGAACTCGCGTCTAG
1 CCTGTACTGTAGAACAAGAACTCACGTCTAG
** * * *
1224902 CCTGTGTTGGAGAACCAGAACTCGCGTCTAG
1 CCTGTACTGTAGAACAAGAACTCACGTCTAG
* *
1224933 CCTGTACTGTAGAACAAGAACTAAC-TTTAGG
1 CCTGTACTGTAGAACAAGAACTCACGTCTA-G
1224964 CCTGTACTGTAGAACAAGAACTCACGTCTAG
1 CCTGTACTGTAGAACAAGAACTCACGTCTAG
* * *
1224995 CCTGTACTGTAGAATAAAAACTCGCGTCTAG
1 CCTGTACTGTAGAACAAGAACTCACGTCTAG
*
1225026 CCTGTACTGTAGAACAAGAACTCGCGTCTAG
1 CCTGTACTGTAGAACAAGAACTCACGTCTAG
* * * *
1225057 CCTGTATTGGAGAACCAGAACTCACGTCTGG
1 CCTGTACTGTAGAACAAGAACTCACGTCTAG
* *
1225088 CCTGTATTGTAGAACCTCTAATAGAGGGACTCACAT-TAGG
1 CCTGTACTGTAGAA---C--A-AGA---ACTCACGTCTA-G
* *
1225128 CCTTTACTGTAGAACCAGAACTCACGTCTAG
1 CCTGTACTGTAGAACAAGAACTCACGTCTAG
*
1225159 CCTGTATTGTAGAAC
1 CCTGTACTGTAGAAC
1225174 TCACATTTAG
Statistics
Matches: 513, Mismatches: 80, Indels: 100
0.74 0.12 0.14
Matches are distributed among these distances:
30 12 0.02
31 366 0.71
32 21 0.04
33 1 0.00
34 8 0.02
35 1 0.00
36 1 0.00
37 5 0.01
38 6 0.01
39 3 0.01
40 28 0.05
41 61 0.12
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (31 bp):
CCTGTACTGTAGAACAAGAACTCACGTCTAG
Found at i:1224576 original size:72 final size:72
Alignment explanation
Indices: 1224473--1224612 Score: 192
Period size: 72 Copynumber: 1.9 Consensus size: 72
1224463 TGTAGAACAA
* * * *
1224473 CCTCTAGATATAGGGGCTCACATTAGCCCTGTACTGTAGAACAAGAACTCACGTCTA-GCCTGTA
1 CCTCTAGATAGAAGGACTCACATTAGCCCTGTACTGTAGAACAAGAACTAAC-TCTAGGCCTGTA
1224537 CTGTTGAC
65 CTGTTGAC
* * * *
1224545 CCTCTAGATAGAAGGACTCACATTTGGCCTGTACTGTAGAACCAGAACTAACTTTAGGCCTGTAC
1 CCTCTAGATAGAAGGACTCACATTAGCCCTGTACTGTAGAACAAGAACTAACTCTAGGCCTGTAC
1224610 TGT
66 TGT
1224613 GGAAGAAGAA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
71 3 0.05
72 56 0.95
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (72 bp):
CCTCTAGATAGAAGGACTCACATTAGCCCTGTACTGTAGAACAAGAACTAACTCTAGGCCTGTAC
TGTTGAC
Found at i:1224679 original size:103 final size:103
Alignment explanation
Indices: 1224495--1224849 Score: 584
Period size: 103 Copynumber: 3.4 Consensus size: 103
1224485 GGGGCTCACA
*
1224495 TTAGCCCTGTACTGTAGAACAAGAACTCACGTCTAGCCTGTACTGTTGACCCTCTAGATAGAAGG
1 TTAGGCCTGTACTGTAGAACAAGAACTCACGTCTAGCCTGTACTGTTGACCCTCTAGATAGAAGG
1224560 ACTCACATTTGGCCTGTACTGTAGAACCAGAACTAACT
66 ACTCACATTTGGCCTGTACTGTAGAACCAGAACTAACT
* *
1224598 TTAGGCCTGTACTGTGGAAGAAGAACTCACGTCTAGCCTGTACTGTTGACCCTCTAGATAGAAGG
1 TTAGGCCTGTACTGTAGAACAAGAACTCACGTCTAGCCTGTACTGTTGACCCTCTAGATAGAAGG
1224663 ACTCACATTTGGCCTGTACTGTAGAACCAGAACTAACT
66 ACTCACATTTGGCCTGTACTGTAGAACCAGAACTAACT
* * * * * *
1224701 TTAGGCCTGTACTGTGGAAGAAGAACTCACGTCTGGCCTGTATTGTAGAACCTCTAGATAGAAGG
1 TTAGGCCTGTACTGTAGAACAAGAACTCACGTCTAGCCTGTACTGTTGACCCTCTAGATAGAAGG
* * * *
1224766 ACTCACAATAGGCCTGTACTGTAGAACCAAAACTTACT
66 ACTCACATTTGGCCTGTACTGTAGAACCAGAACTAACT
*
1224804 TTAGGCCTGTGCTGTAGAACAAGAACTCACGTCTAGCCTGTACTGT
1 TTAGGCCTGTACTGTAGAACAAGAACTCACGTCTAGCCTGTACTGT
1224850 AGAACAAGAA
Statistics
Matches: 236, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 236 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (103 bp):
TTAGGCCTGTACTGTAGAACAAGAACTCACGTCTAGCCTGTACTGTTGACCCTCTAGATAGAAGG
ACTCACATTTGGCCTGTACTGTAGAACCAGAACTAACT
Found at i:1224851 original size:103 final size:103
Alignment explanation
Indices: 1224495--1225040 Score: 580
Period size: 103 Copynumber: 5.5 Consensus size: 103
1224485 GGGGCTCACA
* * *
1224495 TTAGCCCTGTACTGTAGAACAAGAACTCACGTCTAGCCTGTACTGTTGACCCTCTAGATAGAAGG
1 TTAGGCCTGTACTGTAGAACAAGAACTCACGTCTAGCCTGTACTGTAGAACCTCTAGATAGAAGG
1224560 ACTCACATTTGGCCTGTACTGTAGAACCAGAACTAACT
66 ACTCACATTTGGCCTGTACTGTAGAACCAGAACTAACT
* * * *
1224598 TTAGGCCTGTACTGTGGAAGAAGAACTCACGTCTAGCCTGTACTGTTGACCCTCTAGATAGAAGG
1 TTAGGCCTGTACTGTAGAACAAGAACTCACGTCTAGCCTGTACTGTAGAACCTCTAGATAGAAGG
1224663 ACTCACATTTGGCCTGTACTGTAGAACCAGAACTAACT
66 ACTCACATTTGGCCTGTACTGTAGAACCAGAACTAACT
* * * *
1224701 TTAGGCCTGTACTGTGGAAGAAGAACTCACGTCTGGCCTGTATTGTAGAACCTCTAGATAGAAGG
1 TTAGGCCTGTACTGTAGAACAAGAACTCACGTCTAGCCTGTACTGTAGAACCTCTAGATAGAAGG
* * * *
1224766 ACTCACAATAGGCCTGTACTGTAGAACCAAAACTTACT
66 ACTCACATTTGGCCTGTACTGTAGAACCAGAACTAACT
*
1224804 TTAGGCCTGTGCTGTAGAACAAGAACTCACGTCTAGCCTGTACTGTAGAA---C---A-AG-A--
1 TTAGGCCTGTACTGTAGAACAAGAACTCACGTCTAGCCTGTACTGTAGAACCTCTAGATAGAAGG
* * * * * **
1224859 ACTCGCGTCTAGCCTGTACTGTAGAACAAGAACTCGCGT
66 ACTCACATTTGGCCTGTACTGTAGAACCAGAACTAAC-T
* ** * * *
1224898 CTA-GCCTGTGTTGGAGAACCAGAACTCGCGTCTAGCCTGTACTGTAGAA---C---A-AG-A--
1 TTAGGCCTGTACTGTAGAACAAGAACTCACGTCTAGCCTGTACTGTAGAACCTCTAGATAGAAGG
* * *
1224952 ACTAAC-TTTAGGCCTGTACTGTAGAACAAGAACTCACGT
66 ACTCACATTT-GGCCTGTACTGTAGAACCAGAACTAAC-T
* * * *
1224991 CTA-GCCTGTACTGTAGAATAAAAACTCGCGTCTAGCCTGTACTGTAGAAC
1 TTAGGCCTGTACTGTAGAACAAGAACTCACGTCTAGCCTGTACTGTAGAAC
1225041 AAGAACTCGC
Statistics
Matches: 398, Mismatches: 42, Indels: 15
0.87 0.09 0.03
Matches are distributed among these distances:
92 2 0.01
93 148 0.37
94 3 0.01
95 1 0.00
96 2 0.01
97 1 0.00
100 1 0.00
103 240 0.60
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (103 bp):
TTAGGCCTGTACTGTAGAACAAGAACTCACGTCTAGCCTGTACTGTAGAACCTCTAGATAGAAGG
ACTCACATTTGGCCTGTACTGTAGAACCAGAACTAACT
Found at i:1225173 original size:25 final size:25
Alignment explanation
Indices: 1225144--1225198 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1225134 CTGTAGAACC
* *
1225144 AGAACTCACGTCTAGCCTGTATTGT
1 AGAACTCACATCTAGCCTGTACTGT
* *
1225169 AGAACTCACATTTAGTCTGTACTGT
1 AGAACTCACATCTAGCCTGTACTGT
1225194 AGAAC
1 AGAAC
1225199 AGACTCCAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (25 bp):
AGAACTCACATCTAGCCTGTACTGT
Found at i:1226277 original size:15 final size:14
Alignment explanation
Indices: 1226254--1226306 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
1226244 TTGCATTAAC
1226254 CATATTGATATTAT
1 CATATTGATATTAT
1226268 CATATATGATATTAT
1 CATAT-TGATATTAT
** *
1226283 CATTATCAATATTAA
1 CA-TATTGATATTAT
1226298 CATATTGAT
1 CATATTGAT
1226307 TTGGCAGAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 10 0.31
15 19 0.59
16 3 0.09
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (14 bp):
CATATTGATATTAT
Found at i:1226345 original size:40 final size:40
Alignment explanation
Indices: 1226297--1226531 Score: 344
Period size: 40 Copynumber: 5.9 Consensus size: 40
1226287 ATCAATATTA
* * * *
1226297 ACATATTGATTTGGCAGAGACGATCGTATATATATCGTAT
1 ACATATTGAGTCGGCAGAGATGATCGTATACATATCGTAT
* *
1226337 ACATATTGAGTCGTCAGAGAAGATCGTATACATATCGTAT
1 ACATATTGAGTCGGCAGAGATGATCGTATACATATCGTAT
*
1226377 ACATATTGATTCGGCAGAGATGATCGTATACATATCGTAT
1 ACATATTGAGTCGGCAGAGATGATCGTATACATATCGTAT
* * *
1226417 ACATATTGAGTCGTCAGAGAGGATCATATACATATCGTAT
1 ACATATTGAGTCGGCAGAGATGATCGTATACATATCGTAT
* * *
1226457 ACGTATTGATTCGGCAGAGATGATCGTATAAATATCGTAT
1 ACATATTGAGTCGGCAGAGATGATCGTATACATATCGTAT
*
1226497 ACATATTGAGTCGTCAGAGATGATCGTATACATAT
1 ACATATTGAGTCGGCAGAGATGATCGTATACATAT
1226532 AATGACCGTG
Statistics
Matches: 173, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 173 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (40 bp):
ACATATTGAGTCGGCAGAGATGATCGTATACATATCGTAT
Found at i:1226393 original size:80 final size:80
Alignment explanation
Indices: 1226297--1226531 Score: 398
Period size: 80 Copynumber: 2.9 Consensus size: 80
1226287 ATCAATATTA
* * *
1226297 ACATATTGATTTGGCAGAGACGATCGTATATATATCGTATACATATTGAGTCGTCAGAGAAGATC
1 ACATATTGATTCGGCAGAGATGATCGTATAAATATCGTATACATATTGAGTCGTCAGAGAAGATC
1226362 GTATACATATCGTAT
66 GTATACATATCGTAT
* *
1226377 ACATATTGATTCGGCAGAGATGATCGTATACATATCGTATACATATTGAGTCGTCAGAGAGGATC
1 ACATATTGATTCGGCAGAGATGATCGTATAAATATCGTATACATATTGAGTCGTCAGAGAAGATC
*
1226442 ATATACATATCGTAT
66 GTATACATATCGTAT
* *
1226457 ACGTATTGATTCGGCAGAGATGATCGTATAAATATCGTATACATATTGAGTCGTCAGAGATGATC
1 ACATATTGATTCGGCAGAGATGATCGTATAAATATCGTATACATATTGAGTCGTCAGAGAAGATC
1226522 GTATACATAT
66 GTATACATAT
1226532 AATGACCGTG
Statistics
Matches: 146, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 146 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (80 bp):
ACATATTGATTCGGCAGAGATGATCGTATAAATATCGTATACATATTGAGTCGTCAGAGAAGATC
GTATACATATCGTAT
Found at i:1226893 original size:2 final size:2
Alignment explanation
Indices: 1226886--1226957 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
1226876 AAATTCAGTA
1226886 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1226928 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1226958 GTTCGTTATA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1227103 original size:21 final size:21
Alignment explanation
Indices: 1227077--1227306 Score: 338
Period size: 21 Copynumber: 11.0 Consensus size: 21
1227067 CTCATTGGCC
1227077 TATAACATCAGATACTTCTCA
1 TATAACATCAGATACTTCTCA
*
1227098 TATAACATCAGATATTTCTCA
1 TATAACATCAGATACTTCTCA
*
1227119 TATAACATCAGGTACTTCTCA
1 TATAACATCAGATACTTCTCA
*
1227140 TATAATATCAGATACTTCTCA
1 TATAACATCAGATACTTCTCA
* *
1227161 TATAACATCAGGTA-TTTTCA
1 TATAACATCAGATACTTCTCA
* * *
1227181 TATAATATCAGCTACATCTCA
1 TATAACATCAGATACTTCTCA
*
1227202 TATAACATCAGATACTTTTCA
1 TATAACATCAGATACTTCTCA
*
1227223 TATAATATCAGATACTTCTCA
1 TATAACATCAGATACTTCTCA
*
1227244 TATAACATCAGATACTTTTCA
1 TATAACATCAGATACTTCTCA
*
1227265 TATAATATCAGATACTTCTCA
1 TATAACATCAGATACTTCTCA
1227286 TATAACATCAGAT-CTTCTCA
1 TATAACATCAGATACTTCTCA
1227306 T
1 T
1227307 CAGCGATCTG
Statistics
Matches: 185, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
20 25 0.14
21 160 0.86
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (21 bp):
TATAACATCAGATACTTCTCA
Found at i:1227136 original size:42 final size:42
Alignment explanation
Indices: 1227077--1227439 Score: 372
Period size: 42 Copynumber: 8.3 Consensus size: 42
1227067 CTCATTGGCC
* * *
1227077 TATAACATCAGATACTTCTCATATAACATCAGATATTTCTCA
1 TATAACATCAGATACTTTTCATATAATATCAGATACTTCTCA
* *
1227119 TATAACATCAGGTACTTCTCATATAATATCAGATACTTCTCA
1 TATAACATCAGATACTTTTCATATAATATCAGATACTTCTCA
* * *
1227161 TATAACATCAGGTA-TTTTCATATAATATCAGCTACATCTCA
1 TATAACATCAGATACTTTTCATATAATATCAGATACTTCTCA
1227202 TATAACATCAGATACTTTTCATATAATATCAGATACTTCTCA
1 TATAACATCAGATACTTTTCATATAATATCAGATACTTCTCA
1227244 TATAACATCAGATACTTTTCATATAATATCAGATACTTCTCA
1 TATAACATCAGATACTTTTCATATAATATCAGATACTTCTCA
* ** * *
1227286 TATAACATCAGAT-CTTCTCATCAGCGATCTGACAGA-ACGATCTCAGACCATTGGCC
1 TATAACATCAGATACTTTTCAT-A-TAATAT--CAGATAC--T-T-----C--T--CA
* * *
1227342 TATAACATCAGATACTTCTCATATAACATCAGATACTTTTCA
1 TATAACATCAGATACTTTTCATATAATATCAGATACTTCTCA
* * * *
1227384 TATAATATCAGATACTTCTCATATAACATCAGATACTTTTCA
1 TATAACATCAGATACTTTTCATATAATATCAGATACTTCTCA
*
1227426 TATAATATCAGATA
1 TATAACATCAGATA
1227440 ACATCAGATC
Statistics
Matches: 281, Mismatches: 21, Indels: 38
0.83 0.06 0.11
Matches are distributed among these distances:
41 44 0.16
42 190 0.68
43 3 0.01
44 3 0.01
45 4 0.01
46 1 0.00
47 1 0.00
51 1 0.00
52 2 0.01
53 4 0.01
54 3 0.01
55 2 0.01
56 15 0.05
57 8 0.03
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (42 bp):
TATAACATCAGATACTTTTCATATAATATCAGATACTTCTCA
Found at i:1227177 original size:63 final size:63
Alignment explanation
Indices: 1227077--1227439 Score: 390
Period size: 63 Copynumber: 5.9 Consensus size: 63
1227067 CTCATTGGCC
* *
1227077 TATAACATCAGATACTTCTCATATAACATCAGATATTTCTCATATAACATCAGGTACTTCTCA
1 TATAATATCAGATACTTCTCATATAACATCAGATATTTCTCATATAACATCAGATACTTCTCA
* * * *
1227140 TATAATATCAGATACTTCTCATATAACATCAGGTATTT-TCATATAATATCAGCTACATCTCA
1 TATAATATCAGATACTTCTCATATAACATCAGATATTTCTCATATAACATCAGATACTTCTCA
* * * * *
1227202 TATAACATCAGATACTTTTCATATAATATCAGATACTTCTCATATAACATCAGATACTTTTCA
1 TATAATATCAGATACTTCTCATATAACATCAGATATTTCTCATATAACATCAGATACTTCTCA
* * **
1227265 TATAATATCAGATACTTCTCATATAACATCAGAT-CTTCTC--AT--CAGC-GAT-C-TGACA
1 TATAATATCAGATACTTCTCATATAACATCAGATATTTCTCATATAACATCAGATACTTCTCA
* * * ** * * *
1227320 GA-ACGATCTCAGA-CCATTGGCCTATAACATCAGATACTTCTCATATAACATCAGATACTTTTC
1 TATA--ATATCAGATAC-TTCTCATATAACATCAGATATTTCTCATATAACATCAGATACTTCTC
1227383 A
63 A
*
1227384 TATAATATCAGATACTTCTCATATAACATCAGATACTTT-TCATATAATATCAGATA
1 TATAATATCAGATACTTCTCATATAACATCAGATA-TTTCTCATATAACATCAGATA
1227440 ACATCAGATC
Statistics
Matches: 248, Mismatches: 37, Indels: 30
0.79 0.12 0.10
Matches are distributed among these distances:
54 1 0.00
55 5 0.02
56 24 0.10
57 9 0.04
58 3 0.01
59 2 0.01
60 2 0.01
61 3 0.01
62 63 0.25
63 128 0.52
64 7 0.03
65 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (63 bp):
TATAATATCAGATACTTCTCATATAACATCAGATATTTCTCATATAACATCAGATACTTCTCA
Found at i:1227366 original size:21 final size:21
Alignment explanation
Indices: 1227342--1227439 Score: 160
Period size: 21 Copynumber: 4.7 Consensus size: 21
1227332 ACCATTGGCC
1227342 TATAACATCAGATACTTCTCA
1 TATAACATCAGATACTTCTCA
*
1227363 TATAACATCAGATACTTTTCA
1 TATAACATCAGATACTTCTCA
*
1227384 TATAATATCAGATACTTCTCA
1 TATAACATCAGATACTTCTCA
*
1227405 TATAACATCAGATACTTTTCA
1 TATAACATCAGATACTTCTCA
*
1227426 TATAATATCAGATA
1 TATAACATCAGATA
1227440 ACATCAGATC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (21 bp):
TATAACATCAGATACTTCTCA
Found at i:1227598 original size:4 final size:4
Alignment explanation
Indices: 1227589--1227664 Score: 152
Period size: 4 Copynumber: 19.0 Consensus size: 4
1227579 ATTTAGAGAT
1227589 TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA
1 TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA
1227637 TGAA TGAA TGAA TGAA TGAA TGAA TGAA
1 TGAA TGAA TGAA TGAA TGAA TGAA TGAA
1227665 AACAGGAATA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
TGAA
Found at i:1234734 original size:2 final size:2
Alignment explanation
Indices: 1234727--1234781 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
1234717 GTGGGGCTTC
*
1234727 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA 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
1234769 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
1234782 ATCATTTACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1237363 original size:84 final size:87
Alignment explanation
Indices: 1237275--1237436 Score: 213
Period size: 88 Copynumber: 1.9 Consensus size: 87
1237265 ATTGTGTTGG
* * *
1237275 GTTTGATAAATTCAA-TGGTTCACAAAAAAACTTATAT-GA-AAAGGATGACAAGCATTTTTTGC
1 GTTTGATAAAATCAACTGGTCCACAAAAAAACTTATATAGACAAAGGATCACAAGCATTTTTTGC
1237337 AAATGCAAATCCCTAAAGATGC
66 AAATGCAAATCCCTAAAGATGC
* ** ** *
1237359 GTTTGATAAAATCAACTTGGTCCATAGGAAATTTTATATATACAAAGGATCACAAGCATTTTTTG
1 GTTTGATAAAATCAAC-TGGTCCACAAAAAAACTTATATAGACAAAGGATCACAAGCATTTTTTG
1237424 CAAATGCAAATCC
65 CAAATGCAAATCC
1237437 ATAGTTGTGT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
84 14 0.22
86 16 0.25
87 1 0.02
88 34 0.52
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (87 bp):
GTTTGATAAAATCAACTGGTCCACAAAAAAACTTATATAGACAAAGGATCACAAGCATTTTTTGC
AAATGCAAATCCCTAAAGATGC
Found at i:1243600 original size:2 final size:2
Alignment explanation
Indices: 1243593--1243634 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1243583 TAAATTAGGA
1243593 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
1243635 GTGGTTCTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1243700 original size:2 final size:2
Alignment explanation
Indices: 1243693--1243724 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1243683 CTCGATTTTN
1243693 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
1243725 GTGGTTCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1243729 original size:90 final size:89
Alignment explanation
Indices: 1243602--1243782 Score: 353
Period size: 90 Copynumber: 2.0 Consensus size: 89
1243592 ACTCTCTCTC
1243602 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGGTTCTATGCTGAAATAGTTATATCAATAA
1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGGTTCTATGCTGAAATAGTTATATCAATAA
1243667 GAAAATCTAACACAGTCTCGATTT
66 GAAAATCTAACACAGTCTCGATTT
1243691 TNCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGGTTCTATGCTGAAATAGTTATATCAATA
1 T-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGGTTCTATGCTGAAATAGTTATATCAATA
1243756 AGAAAATCTAACACAGTCTCGATTT
65 AGAAAATCTAACACAGTCTCGATTT
1243781 TC
1 TC
1243783 AATTGTTTTT
Statistics
Matches: 91, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
89 2 0.02
90 89 0.98
ACGTcount: A:0.22, C:0.27, G:0.10, T:0.40
Consensus pattern (89 bp):
TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGGTTCTATGCTGAAATAGTTATATCAATAA
GAAAATCTAACACAGTCTCGATTT
Found at i:1246092 original size:89 final size:89
Alignment explanation
Indices: 1245941--1246107 Score: 300
Period size: 89 Copynumber: 1.9 Consensus size: 89
1245931 TGTACTCCTA
*
1245941 AATGCCCCAGTCACACATTCACGGATCAACTCCACGGTTCTATTACGGAATATTTTCCACGGTTG
1 AATGCCCCAGTCACACATTCACGGATCAACTCCACGGTTCTACTACGGAATATTTTCCACGGTTG
1246006 ACACCGGAAAATCAAATAATCGTT
66 ACACCGGAAAATCAAATAATCGTT
*
1246030 AATGCCCCAGTCACACATTCACGGATCAACTCCTA-GGTTCTACTACGGATTATTTTCCACGGTT
1 AATGCCCCAGTCACACATTCACGGATCAACTCC-ACGGTTCTACTACGGAATATTTTCCACGGTT
1246094 GACACCGGAAAATC
65 GACACCGGAAAATC
1246108 CAATGATATG
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
89 74 0.99
90 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (89 bp):
AATGCCCCAGTCACACATTCACGGATCAACTCCACGGTTCTACTACGGAATATTTTCCACGGTTG
ACACCGGAAAATCAAATAATCGTT
Found at i:1246173 original size:10 final size:10
Alignment explanation
Indices: 1246160--1246184 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1246150 AAATTGATAC
1246160 ATACGAATTT
1 ATACGAATTT
1246170 ATACGAATTT
1 ATACGAATTT
1246180 ATACG
1 ATACG
1246185 TACGAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (10 bp):
ATACGAATTT
Found at i:1249661 original size:42 final size:42
Alignment explanation
Indices: 1249597--1249676 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
1249587 TTGTTACATC
* *
1249597 AGTTACCTGTATGAGGGTCAGCGGTTTACTGGTGACCTTAGT
1 AGTTACCTGTATCAGGGCCAGCGGTTTACTGGTGACCTTAGT
1249639 AGTTACCTGTATCAGGGCCAGCGGTTTACTGGTGACCT
1 AGTTACCTGTATCAGGGCCAGCGGTTTACTGGTGACCT
1249677 GGGCCAGACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (42 bp):
AGTTACCTGTATCAGGGCCAGCGGTTTACTGGTGACCTTAGT
Found at i:1252924 original size:13 final size:13
Alignment explanation
Indices: 1252905--1253003 Score: 80
Period size: 13 Copynumber: 7.4 Consensus size: 13
1252895 GTATTAACTT
1252905 TACTGTAAACTGG
1 TACTGTAAACTGG
* *
1252918 AACTGTATTAACT-T
1 TACTGTA--AACTGG
1252932 TACTGTAAACTGG
1 TACTGTAAACTGG
*
1252945 TACTGTATTAACT-T
1 TACTGTA--AACTGG
1252959 TACTGTAAACTGG
1 TACTGTAAACTGG
1252972 TACTGTATTAACT--
1 TACTGTA--AACTGG
1252985 TCACTGTAAACTGG
1 T-ACTGTAAACTGG
1252999 TACTG
1 TACTG
1253004 ACTTTTGTAT
Statistics
Matches: 69, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
12 12 0.17
13 25 0.36
14 20 0.29
15 12 0.17
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TACTGTAAACTGG
Found at i:1252930 original size:27 final size:27
Alignment explanation
Indices: 1252891--1253003 Score: 208
Period size: 27 Copynumber: 4.2 Consensus size: 27
1252881 AAGCATGTTT
1252891 TACTGTATTAACTTTACTGTAAACTGG
1 TACTGTATTAACTTTACTGTAAACTGG
*
1252918 AACTGTATTAACTTTACTGTAAACTGG
1 TACTGTATTAACTTTACTGTAAACTGG
1252945 TACTGTATTAACTTTACTGTAAACTGG
1 TACTGTATTAACTTTACTGTAAACTGG
*
1252972 TACTGTATTAACTTCACTGTAAACTGG
1 TACTGTATTAACTTTACTGTAAACTGG
1252999 TACTG
1 TACTG
1253004 ACTTTTGTAT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 83 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (27 bp):
TACTGTATTAACTTTACTGTAAACTGG
Found at i:1254437 original size:103 final size:103
Alignment explanation
Indices: 1254301--1255206 Score: 1740
Period size: 103 Copynumber: 8.8 Consensus size: 103
1254291 AGCCGCCTAG
* *
1254301 CTTCCCTCTGTGATGGCGGGGAGGTTTATCAGCACGTACTGCTGACAGAGCGCCTGTAACTGCTG
1 CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
1254366 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
66 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
* *
1254404 CTTCCCTCTGTGATGGCGGGGAGGTTTATCAGCACGTACTGCTGACAGAGCGCCTGTAACTGCTG
1 CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
1254469 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
66 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
1254507 CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
1 CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
1254572 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
66 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
1254610 CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
1 CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
1254675 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
66 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
* * * *
1254713 CTTCCCTCTGTGGTGGCGGGGGGGGTGATCAGCACGTACTGCTGACAGAGCGCCTGTAACTGCTG
1 CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
1254778 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
66 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
1254816 CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
1 CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
1254881 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
66 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
1254919 CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
1 CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
1254984 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
66 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
1255022 CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
1 CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
1255087 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
66 GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
1255125 CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
1 CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
1255190 GGCGTTGTACAGAGTGG
66 GGCGTTGTACAGAGTGG
1255207 ACAATTCCAA
Statistics
Matches: 793, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 793 1.00
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (103 bp):
CTTCCCTCTGTGATGGCGGGGAGGTTGATCAGCACGTACTGCTGACAGAGAGCCTGTAACTGCTG
GGCGTTGTACAGAGTGGTTAACTATAACACATACATAC
Found at i:1257655 original size:38 final size:37
Alignment explanation
Indices: 1257496--1257712 Score: 251
Period size: 37 Copynumber: 5.7 Consensus size: 37
1257486 TTGACTGTGT
*
1257496 TTGTCTGAATATATTTTGACCTTTTTATACA-TTAAA
1 TTGTCTGATTATATTTTGACCTTTTTATACATTTAAA
* *
1257532 TTGTCCGATTATATTTTGACCTTTTTGATA-TTTTAAA
1 TTGTCTGATTATATTTTGACCTTTTT-ATACATTTAAA
*
1257569 TTGTCTGATTATATTTTGACCTTCTTTATACATGTACATTAAG
1 TTGTCTGATTATATTTTGACCTT-TTTATACA--T---TTAAA
*
1257612 TTGTCTGATTATATCTTGACCTTTTTAATACATTTAAA
1 TTGTCTGATTATATTTTGACCTTTTT-ATACATTTAAA
* * *
1257650 TTGTCTGATTACATTTTGACCTTTTTCATA-AATTAAT
1 TTGTCTGATTATATTTTGACCTTTTT-ATACATTTAAA
*
1257687 TTGTCTCATTATATTTTGACCTTTTT
1 TTGTCTGATTATATTTTGACCTTTTT
1257713 TGTATATCAA
Statistics
Matches: 156, Mismatches: 15, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
36 24 0.15
37 62 0.40
38 34 0.22
40 1 0.01
41 1 0.01
42 3 0.02
43 31 0.20
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (37 bp):
TTGTCTGATTATATTTTGACCTTTTTATACATTTAAA
Found at i:1257702 original size:118 final size:116
Alignment explanation
Indices: 1257496--1257709 Score: 329
Period size: 118 Copynumber: 1.8 Consensus size: 116
1257486 TTGACTGTGT
* * *
1257496 TTGTCTGAATATATTTTGACCTTTTTATACATTAAATTGTCCGATTATATTTTGACCTTTTTGAT
1 TTGTCTGAATATATCTTGACCTTTTTATACATTAAATTGTCCGATTACATTTTGACCTTTTTCAT
** *
1257561 ATTTTAAATTGTCTGATTATATTTTGACCTTCTTTATACATGTACATTAAG
66 AAATTAAATTGTCTCATTATATTTTGACCTTCTTTATACATGTACATTAAG
* *
1257612 TTGTCTGATTATATCTTGACCTTTTTAATACATTTAAATTGTCTGATTACATTTTGACCTTTTTC
1 TTGTCTGAATATATCTTGACCTTTTT-ATACA-TTAAATTGTCCGATTACATTTTGACCTTTTTC
*
1257677 ATAAATTAATTTGTCTCATTATATTTTGACCTT
64 ATAAATTAAATTGTCTCATTATATTTTGACCTT
1257710 TTTTGTATAT
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
116 24 0.28
117 5 0.06
118 58 0.67
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.51
Consensus pattern (116 bp):
TTGTCTGAATATATCTTGACCTTTTTATACATTAAATTGTCCGATTACATTTTGACCTTTTTCAT
AAATTAAATTGTCTCATTATATTTTGACCTTCTTTATACATGTACATTAAG
Found at i:1259925 original size:19 final size:18
Alignment explanation
Indices: 1259889--1259925 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1259879 ACGCCTGCCG
*
1259889 ACGCCTGCCGGGGAAAAC
1 ACGCCTGCCGGAGAAAAC
1259907 ACGCCTGCCGAGAGAAAAC
1 ACGCCTGCCG-GAGAAAAC
1259926 CGCACGCCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.32, C:0.32, G:0.30, T:0.05
Consensus pattern (18 bp):
ACGCCTGCCGGAGAAAAC
Done.