Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold433
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: 1285081
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 132229 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1087768 original size:340 final size:338
Alignment explanation
Indices: 1087118--1087801 Score: 946
Period size: 340 Copynumber: 2.0 Consensus size: 338
1087108 AACTAAGATA
* * *
1087118 TAATCATCAGAGGGCACCTGCTCCAAAAGCTTTAACAAGCTCTTAAAACCTTAACCTCATCCAGC
1 TAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACAAGCTCTAAAAACCTTAACCTCATCCAGC
* * *
1087183 ATCTGAAACCTATGGCTCAGATTCAGCATTCATGCCTGTCAGGTACATCAGTATCATAAGACGCA
66 ATCTGAAACCTATGGCTCAGATTCAGCATTAAAGCATGTCAGGTACATCAGTATCATAAGACGCA
* * *
1087248 CCATCTATGCAAGTTCGTTGAAGTTAGGACCAGTAATAACTAAGTTATAATCATCAAAGTGCACC
131 CCATCCATGCAAGTTCGGTGAAGTTAGGACCAGTAATAACTAAG-TATAATCATCAAAGGGCACC
* *
1087313 TGCTCCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCATCCAGCATCAGAAACCTATGGCTC
195 TGCACCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCATCCAGCATCAGAAACCTATGGCCC
** * *
1087378 AGATTCAGCATTCCTGCCTGCCAGGTACATCAGTATCATAAGACGCACCATCTATGCAAGTTCGG
260 AGATTCAGCATTCAAGCCTGCCAAGTACATCAGTATCA-AAGACGCACCATCCATGCAAGTTCGG
* *
1087443 TGAAGTTAGGACCAG
324 TGAAGATAGGACAAG
*
1087458 TAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCATCCAGC
1 TAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACAAGCTCTAAAAACCTTAACCTCATCCAGC
* * *
1087523 ATCTGAAACCTATGGCTCAGATTCAGCATTAAAGCATGTCTGGTGCATCAGTATCATAAGATGCA
66 ATCTGAAACCTATGGCTCAGATTCAGCATTAAAGCATGTCAGGTACATCAGTATCATAAGACGCA
* *
1087588 CCATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACCT-AG-A-AATTGCTATCAAAGGGC
131 CCATCCATGCAAGTTCGGTGAAGTTAGGACCAGTAATAA-CTAAGTATAA-T-C-ATCAAAGGGC
* * *
1087650 ACCTGCACCAAAAACTTTAACCTGCTCTAAAAACCTTAACCTCCTCCAGCATCTGAAA-CTCATG
192 ACCTGCACCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCATCCAGCATCAGAAACCT-ATG
* * ** * * *
1087714 GCCCTGATTCAGCATTCAAGTCTTTCAAGTCCATGAGTAGGTC-AAGATGCACCATCCATGCAAG
256 GCCCAGATTCAGCATTCAAGCCTGCCAAGTACATCAGTA--TCAAAGACGCACCATCCATGCAAG
*
1087778 TTTGGTGAAGATAGGACAAG
319 TTCGGTGAAGATAGGACAAG
1087798 TAAT
1 TAAT
1087802 AACTTAGATA
Statistics
Matches: 303, Mismatches: 34, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
337 2 0.01
338 2 0.01
339 3 0.01
340 292 0.96
341 2 0.01
342 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.25
Consensus pattern (338 bp):
TAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACAAGCTCTAAAAACCTTAACCTCATCCAGC
ATCTGAAACCTATGGCTCAGATTCAGCATTAAAGCATGTCAGGTACATCAGTATCATAAGACGCA
CCATCCATGCAAGTTCGGTGAAGTTAGGACCAGTAATAACTAAGTATAATCATCAAAGGGCACCT
GCACCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCATCCAGCATCAGAAACCTATGGCCCA
GATTCAGCATTCAAGCCTGCCAAGTACATCAGTATCAAAGACGCACCATCCATGCAAGTTCGGTG
AAGATAGGACAAG
Found at i:1099968 original size:11 final size:11
Alignment explanation
Indices: 1099935--1099960 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1099925 AAAAATGTTG
1099935 AGCTCTATAAA
1 AGCTCTATAAA
1099946 AGCTCTATAAA
1 AGCTCTATAAA
1099957 AGCT
1 AGCT
1099961 TGATAAAACT
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:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (11 bp):
AGCTCTATAAA
Found at i:1114913 original size:34 final size:34
Alignment explanation
Indices: 1114637--1114900 Score: 415
Period size: 34 Copynumber: 7.8 Consensus size: 34
1114627 ATAGTTGATG
1114637 TGGATTGTAGATGATATCCTAGCATTAGCAAATT
1 TGGATTGTAGATGATATCCTAGCATTAGCAAATT
*
1114671 TGGATTGTAGATGATATTCTAGCATTAGCAAATT
1 TGGATTGTAGATGATATCCTAGCATTAGCAAATT
* ** *
1114705 TGGATTGTAGATGATATTCTAGCATTAGCTCATA
1 TGGATTGTAGATGATATCCTAGCATTAGCAAATT
* * *
1114739 TGGACTGTAGATGATATCCTAGCTTTAGCACATT
1 TGGATTGTAGATGATATCCTAGCATTAGCAAATT
* * *
1114773 TGGATTGTAGATGATATCATAGCTTTTGCAAATT
1 TGGATTGTAGATGATATCCTAGCATTAGCAAATT
1114807 TGGATTGTAGATGATA-CCTAGCATTAGCAAATT
1 TGGATTGTAGATGATATCCTAGCATTAGCAAATT
1114840 TGGATTGTAGATGATA-CCTAGCATTAGCAAATT
1 TGGATTGTAGATGATATCCTAGCATTAGCAAATT
1114873 TGGATTGTAGATGATATCCTAGCATTAG
1 TGGATTGTAGATGATATCCTAGCATTAG
1114901 TTGATATGGA
Statistics
Matches: 213, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
33 63 0.30
34 150 0.70
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (34 bp):
TGGATTGTAGATGATATCCTAGCATTAGCAAATT
Found at i:1115230 original size:34 final size:34
Alignment explanation
Indices: 1115187--1115664 Score: 545
Period size: 34 Copynumber: 14.1 Consensus size: 34
1115177 AATGTATAAA
** * **
1115187 ATATCCTAGCGCTAGCTGATGTGGATTAAAGATG
1 ATATCCTAGCATTAGCTAATGTGGATTGTAGATG
* *
1115221 ATATCCTAGCATTAGCAAATGTGGATTATAGATG
1 ATATCCTAGCATTAGCTAATGTGGATTGTAGATG
* ** *
1115255 ATATCTTAGCATTAGCTGTTGTGGATTGTAGAAG
1 ATATCCTAGCATTAGCTAATGTGGATTGTAGATG
* *
1115289 AAATCCTAGCATTAGCAAATGTGGATTGTAGATG
1 ATATCCTAGCATTAGCTAATGTGGATTGTAGATG
* *
1115323 ATATCCTAGCATTAGCAAATTTGGATTGTAGATG
1 ATATCCTAGCATTAGCTAATGTGGATTGTAGATG
* *
1115357 ATA-CCTAGCATTAGCAAATTTGGATTGTAGATG
1 ATATCCTAGCATTAGCTAATGTGGATTGTAGATG
* *
1115390 ATATCCTAGCATTAGCAAATGTGGATTG-AAATG
1 ATATCCTAGCATTAGCTAATGTGGATTGTAGATG
*
1115423 ATATTCCTAGCATTAGCAAATGTGGATTGTAGATG
1 ATA-TCCTAGCATTAGCTAATGTGGATTGTAGATG
* * * *
1115458 ATAACCTATG-ACTAGCTGATGAGGATTGTAGATG
1 ATATCCTA-GCATTAGCTAATGTGGATTGTAGATG
1115492 ATATCCTAGCATTAG-TAAATGT-GATTGTAGATG
1 ATATCCTAGCATTAGCT-AATGTGGATTGTAGATG
* * * *
1115525 ATATCCTAGCATTAGCTGATCTGGATTATCGATG
1 ATATCCTAGCATTAGCTAATGTGGATTGTAGATG
* * *
1115559 ATATCCTAGCATTAGCTGATGTGAATTGTATATG
1 ATATCCTAGCATTAGCTAATGTGGATTGTAGATG
* **
1115593 ATGTCCTAG-AGTTAGCTGGTGTGGATTGTAGATG
1 ATATCCTAGCA-TTAGCTAATGTGGATTGTAGATG
* * *
1115627 ATATCTTAGCACTAGCTGATGTGGATTGTAGATG
1 ATATCCTAGCATTAGCTAATGTGGATTGTAGATG
1115661 ATAT
1 ATAT
1115665 TCTATACTGA
Statistics
Matches: 386, Mismatches: 48, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
33 72 0.19
34 305 0.79
35 9 0.02
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.34
Consensus pattern (34 bp):
ATATCCTAGCATTAGCTAATGTGGATTGTAGATG
Found at i:1115413 original size:135 final size:135
Alignment explanation
Indices: 1115199--1115664 Score: 580
Period size: 135 Copynumber: 3.4 Consensus size: 135
1115189 ATCCTAGCGC
** * *
1115199 TAGCTGATGTGGATTAAAGATGATATCCTAGCATTAGCAAATGTGGATTATAGATGATATCTTAG
1 TAGCTGATGTGGATTGTAGATGATATCCTAGCATTAGCAAATGTGGATTGTAGATGATATCCTAG
*
1115264 CATTAGCTGTTGTGGATTGTAGAAGAAATCCTAGCATTAGCAAATGTGGATTGTAGATGATATCC
66 CATTAGCTGATGTGGATTGTAGAAGAAATCCTAGCATTAGCAAATGTGGATTGTAGATGATATCC
1115329 TAGCAT
131 TAG-AT
** * *
1115335 TAGCAAATTTGGATTGTAGATGATA-CCTAGCATTAGCAAATTTGGATTGTAGATGATATCCTAG
1 TAGCTGATGTGGATTGTAGATGATATCCTAGCATTAGCAAATGTGGATTGTAGATGATATCCTAG
** * *
1115399 CATTAGCAAATGTGGATTG-A-AATGATATTCCTAGCATTAGCAAATGTGGATTGTAGATGATAA
66 CATTAGCTGATGTGGATTGTAGAA-GA-AATCCTAGCATTAGCAAATGTGGATTGTAGATGATAT
*
1115462 CCTATGAC
129 CCTA-GAT
* *
1115470 TAGCTGATGAGGATTGTAGATGATATCCTAGCATTAGTAAATGT-GATTGTAGATGATATCCTAG
1 TAGCTGATGTGGATTGTAGATGATATCCTAGCATTAGCAAATGTGGATTGTAGATGATATCCTAG
* * * * * ** * * *
1115534 CATTAGCTGATCTGGATTATCGATGATATCCTAGCATTAGCTGATGTGAATTGTATATGATGTCC
66 CATTAGCTGATGTGGATTGTAGAAGAAATCCTAGCATTAGCAAATGTGGATTGTAGATGATATCC
1115599 TAGAGT
131 TAGA-T
* * * **
1115605 TAGCTGGTGTGGATTGTAGATGATATCTTAGCACTAGCTGATGTGGATTGTAGATGATAT
1 TAGCTGATGTGGATTGTAGATGATATCCTAGCATTAGCAAATGTGGATTGTAGATGATAT
1115665 TCTATACTGA
Statistics
Matches: 280, Mismatches: 42, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
133 2 0.01
134 5 0.02
135 218 0.78
136 54 0.19
137 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.34
Consensus pattern (135 bp):
TAGCTGATGTGGATTGTAGATGATATCCTAGCATTAGCAAATGTGGATTGTAGATGATATCCTAG
CATTAGCTGATGTGGATTGTAGAAGAAATCCTAGCATTAGCAAATGTGGATTGTAGATGATATCC
TAGAT
Found at i:1115495 original size:169 final size:168
Alignment explanation
Indices: 1115208--1115664 Score: 582
Period size: 169 Copynumber: 2.7 Consensus size: 168
1115198 CTAGCTGATG
* *
1115208 TGGATTAAAGATGATATCCTAGCATTAGCAAATGTGGATT-ATAGATGATATCTTAGCATTAGCT
1 TGGATTATAGATGATATCCTAGCATTAGCAAATGTGGATTGA-A-ATGATATCCTAGCATTAGCT
* * * **
1115272 GTTGTGGATTGTAGAAGA-AATCCTAGCATTAGCAAATGTGGATTGTAGATGATATCCTAGCATT
64 GATGTGGATTGTAGATGATAA-CCTAGCACTAGCTGATGTGGATTGTAGATGATATCCTAGCATT
* *
1115336 AGCAAATTTGGATTGTAGATGATA-CCTAGCATTAGCAAATT
128 AGCAAATGT-GATTGTAGATGATATCCTAGCATTAGCAAATC
* **
1115377 TGGATTGTAGATGATATCCTAGCATTAGCAAATGTGGATTGAAATGATATTCCTAGCATTAGCAA
1 TGGATTATAGATGATATCCTAGCATTAGCAAATGTGGATTGAAATGATA-TCCTAGCATTAGCTG
*
1115442 ATGTGGATTGTAGATGATAACCTATG-ACTAGCTGATGAGGATTGTAGATGATATCCTAGCATTA
65 ATGTGGATTGTAGATGATAACCTA-GCACTAGCTGATGTGGATTGTAGATGATATCCTAGCATTA
* **
1115506 GTAAATGTGATTGTAGATGATATCCTAGCATTAGCTGATC
129 GCAAATGTGATTGTAGATGATATCCTAGCATTAGCAAATC
* ** * * *
1115546 TGGATTATCGATGATATCCTAGCATTAGCTGATGTGAATTGTATATGATGTCCTAG-AGTTAGCT
1 TGGATTATAGATGATATCCTAGCATTAGCAAATGTGGATTG-AAATGATATCCTAGCA-TTAGCT
* * *
1115610 GGTGTGGATTGTAGATGATATCTTAGCACTAGCTGATGTGGATTGTAGATGATAT
64 GATGTGGATTGTAGATGATAACCTAGCACTAGCTGATGTGGATTGTAGATGATAT
1115665 TCTATACTGA
Statistics
Matches: 251, Mismatches: 29, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
168 22 0.09
169 219 0.87
170 10 0.04
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.34
Consensus pattern (168 bp):
TGGATTATAGATGATATCCTAGCATTAGCAAATGTGGATTGAAATGATATCCTAGCATTAGCTGA
TGTGGATTGTAGATGATAACCTAGCACTAGCTGATGTGGATTGTAGATGATATCCTAGCATTAGC
AAATGTGATTGTAGATGATATCCTAGCATTAGCAAATC
Found at i:1120106 original size:2 final size:2
Alignment explanation
Indices: 1120101--1120134 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1120091 CCTCTGACTC
1120101 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
1120135 GGAGCAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1121714 original size:3 final size:3
Alignment explanation
Indices: 1121706--1121755 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
1121696 ACTGAAAGTT
* *
1121706 AAC AAC AAC AAC AAC AAC AAC AAA AAC -AC AGC AAC AA- AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1121752 AAC A
1 AAC A
1121756 CTTAAGAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.68, C:0.30, G:0.02, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1126284 original size:2 final size:2
Alignment explanation
Indices: 1126279--1126338 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
1126269 TTCTCTTTTT
* * *
1126279 TC TC TC TC TC TC TC TC TC CC TG TC TG 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
1126321 TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC
1126339 CACGCTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.48, G:0.03, T:0.48
Consensus pattern (2 bp):
TC
Found at i:1133044 original size:2 final size:2
Alignment explanation
Indices: 1133037--1133075 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1133027 CATTTTATCA
1133037 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1133076 TTTTTTTTTT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1137750 original size:165 final size:166
Alignment explanation
Indices: 1137383--1138009 Score: 889
Period size: 166 Copynumber: 3.8 Consensus size: 166
1137373 NNNNNNNNNN
* *
1137383 TACACTACCTGAGGATGCTTTCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAA
1 TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTAATTAGTTTCTGAGAAGAA
* * * * * ** * *
1137448 GATTTTTAAATATTTACTCTATTTATTCCTATGTAAAACATCGACCTCCCATTGTGGCCAAAACT
66 GATTTTTAAAGATTTACTCTATATATTCATATGTAAAACTTCGACCCCCCATTGTGGCCCCACCC
*
1137513 TACCCCCAGGGGTCATGATTTTCACAACTTTGAATC
131 TACCCCCGGGGGTCATGATTTTCACAACTTTGAATC
* *
1137549 TACACTATCTGAGGATGCTTCCACAC-ATTTTCAGCTTTCCTGGCTAATTAGTTTCTGAGAAGAA
1 TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTAATTAGTTTCTGAGAAGAA
* * * * *
1137613 GATTTCTAAAGATTTGCTTTATATATTCATATGTTAAACTTCGA-CCCCCATTGGGGCCCCACCC
66 GATTTTTAAAGATTTACTCTATATATTCATATGTAAAACTTCGACCCCCCATTGTGGCCCCACCC
1137677 TACCCCCGGGGGTCATGATTTTCACAACTTTGAATC
131 TACCCCCGGGGGTCATGATTTTCACAACTTTGAATC
* **
1137713 TACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCCGATTAGTTTCTGAGAAGAA
1 TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTAATTAGTTTCTGAGAAGAA
* * * * * *
1137778 CATTTTTAAAGATTTACTCTATATACTCCTATGTAAAACTTCAATCTCCCATTGTGGCCCCACCC
66 GATTTTTAAAGATTTACTCTATATATTCATATGTAAAACTTCGACCCCCCATTGTGGCCCCACCC
* * *
1137843 TACCCCCGGGGTTCATGATTTTCACAAATTTGAATG
131 TACCCCCGGGGGTCATGATTTTCACAACTTTGAATC
* * * * *
1137879 AACATTACCTGATGATGCTTTCACAAAAGTTTCAGCTTTCCTGGCTAATTAGTTTCTGAGAAGAA
1 TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTAATTAGTTTCTGAGAAGAA
* * *
1137944 GATTTTTAAAGATTTACTCTATATATTCATTTGTTAAACTGCGACCCCCCATTGTGGCCCCACCC
66 GATTTTTAAAGATTTACTCTATATATTCATATGTAAAACTTCGACCCCCCATTGTGGCCCCACCC
1138009 T
131 T
1138010 CAGGTGAGCT
Statistics
Matches: 405, Mismatches: 54, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
164 74 0.18
165 142 0.35
166 189 0.47
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (166 bp):
TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTAATTAGTTTCTGAGAAGAA
GATTTTTAAAGATTTACTCTATATATTCATATGTAAAACTTCGACCCCCCATTGTGGCCCCACCC
TACCCCCGGGGGTCATGATTTTCACAACTTTGAATC
Found at i:1138081 original size:80 final size:79
Alignment explanation
Indices: 1137948--1138105 Score: 280
Period size: 80 Copynumber: 2.0 Consensus size: 79
1137938 GAAGAAGATT
*
1137948 TTTAAAGATTTACTCTATATATTCATTTGTTAAACTGCGACCCCCCATTGTGGCCCCACCCTCAG
1 TTTAAAGATTTACTCTATATATTCATTTGTTAAACTGCGACCCCCAATTGTGGCCCCACCCTCAG
1138013 GTGAGCTAAAAAGA
66 GTGAGCTAAAAAGA
* *
1138027 NTTTAAAGATTTACTCTTTATATTCATTTGTTAAACTTCGACCCCCAATTGTGGCCCCACCCTCA
1 -TTTAAAGATTTACTCTATATATTCATTTGTTAAACTGCGACCCCCAATTGTGGCCCCACCCTCA
1138092 GGTGAGCTAAAAAG
65 GGTGAGCTAAAAAG
1138106 GTTAAGTTTA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (79 bp):
TTTAAAGATTTACTCTATATATTCATTTGTTAAACTGCGACCCCCAATTGTGGCCCCACCCTCAG
GTGAGCTAAAAAGA
Found at i:1139347 original size:16 final size:15
Alignment explanation
Indices: 1139326--1139360 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
1139316 AAAGTTTACA
1139326 GACAGACAGACGGACG
1 GACAGACAGAC-GACG
1139342 GACAGACAGACGACG
1 GACAGACAGACGACG
1139357 GACA
1 GACA
1139361 AAATGTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.40, C:0.26, G:0.34, T:0.00
Consensus pattern (15 bp):
GACAGACAGACGACG
Found at i:1140841 original size:13 final size:13
Alignment explanation
Indices: 1140823--1140847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1140813 AAGTTCACAT
1140823 ATTTCACACATAC
1 ATTTCACACATAC
1140836 ATTTCACACATA
1 ATTTCACACATA
1140848 TATTAAATAT
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:0.28, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTTCACACATAC
Found at i:1143313 original size:17 final size:18
Alignment explanation
Indices: 1143282--1143315 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1143272 CTAAAAAAAG
*
1143282 TTTTACTTAGTAATCATT
1 TTTTACTTAGAAATCATT
1143300 TTTTACTTA-AAATCAT
1 TTTTACTTAGAAATCAT
1143316 ATTGATAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.12, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTTACTTAGAAATCATT
Found at i:1143577 original size:63 final size:63
Alignment explanation
Indices: 1143478--1143605 Score: 220
Period size: 63 Copynumber: 2.0 Consensus size: 63
1143468 CTAAAAACAA
* * *
1143478 AACATGATTTACTAAGTAATTCCTTTATTGATATTTGTTATGATAAGGAACTATCATATACTT
1 AACATGATTTACTAAGTAAATCCTTTACTGATATTTGTTATGATAAAGAACTATCATATACTT
*
1143541 AACATGATTTACTTAGTAAATCCTTTACTGATATTTGTTATGATAAAGAACTATCATATACTT
1 AACATGATTTACTAAGTAAATCCTTTACTGATATTTGTTATGATAAAGAACTATCATATACTT
1143604 AA
1 AA
1143606 AGCAAAAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (63 bp):
AACATGATTTACTAAGTAAATCCTTTACTGATATTTGTTATGATAAAGAACTATCATATACTT
Found at i:1143644 original size:2 final size:2
Alignment explanation
Indices: 1143639--1143704 Score: 116
Period size: 2 Copynumber: 33.5 Consensus size: 2
1143629 AGTATATTAT
*
1143639 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GC GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1143681 GA GA GA GA GA G- GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
1143705 TTTGCACACA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.47, C:0.02, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1149238 original size:2 final size:2
Alignment explanation
Indices: 1149233--1149263 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1149223 CTTTATTTTG
1149233 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 G
1149264 TCATACACTT
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1151694 original size:14 final size:14
Alignment explanation
Indices: 1151677--1151711 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1151667 CAGTCGATTT
1151677 TAACAGTTCCAATC
1 TAACAGTTCCAATC
*
1151691 TAACAGTTCCAGTC
1 TAACAGTTCCAATC
*
1151705 CAACAGT
1 TAACAGT
1151712 CAAAATGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.26
Consensus pattern (14 bp):
TAACAGTTCCAATC
Found at i:1153774 original size:4 final size:4
Alignment explanation
Indices: 1153767--1153801 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1153757 GCTGCTGTCT
* *
1153767 GTCG GTCG GTCA GTCG GTCG GTCT GTCG GTCG GTC
1 GTCG GTCG GTCG GTCG GTCG GTCG GTCG GTCG GTC
1153802 CACCAACAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.03, C:0.26, G:0.43, T:0.29
Consensus pattern (4 bp):
GTCG
Found at i:1153784 original size:12 final size:12
Alignment explanation
Indices: 1153767--1153801 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1153757 GCTGCTGTCT
1153767 GTCGGTCGGTCA
1 GTCGGTCGGTCA
*
1153779 GTCGGTCGGTCT
1 GTCGGTCGGTCA
1153791 GTCGGTCGGTC
1 GTCGGTCGGTC
1153802 CACCAACAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.03, C:0.26, G:0.43, T:0.29
Consensus pattern (12 bp):
GTCGGTCGGTCA
Found at i:1159912 original size:2 final size:2
Alignment explanation
Indices: 1159905--1159970 Score: 73
Period size: 2 Copynumber: 33.5 Consensus size: 2
1159895 TTAAATCCGC
*
1159905 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG CA- AG AA
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG
* * *
1159947 AG AG A- AA AA AG AG AG AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1159971 TGCAACAATG
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
1 2 0.04
2 53 0.95
3 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.41, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1161465 original size:16 final size:16
Alignment explanation
Indices: 1161444--1161474 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1161434 AGTAGCGTCT
*
1161444 ACAGACAGATGGACAA
1 ACAGACAGACGGACAA
1161460 ACAGACAGACGGACA
1 ACAGACAGACGGACA
1161475 GGGTGAAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.23, G:0.26, T:0.03
Consensus pattern (16 bp):
ACAGACAGACGGACAA
Found at i:1167498 original size:2 final size:2
Alignment explanation
Indices: 1167491--1167528 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1167481 TTTGACTTAC
1167491 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
1167529 TGTAAACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1175454 original size:20 final size:20
Alignment explanation
Indices: 1175429--1175470 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1175419 TGTACATAAC
*
1175429 TATATAAAATATAGTTATTA
1 TATATAAAATATAATTATTA
*
1175449 TATATAATATATAATTATTA
1 TATATAAAATATAATTATTA
1175469 TA
1 TA
1175471 AGAATCTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TATATAAAATATAATTATTA
Found at i:1176225 original size:36 final size:36
Alignment explanation
Indices: 1176175--1176246 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1176165 ATTTATATGG
*
1176175 AAAAAAAATTGATACTGTAATAACAAAAAAATCGGA
1 AAAAAAAATGGATACTGTAATAACAAAAAAATCGGA
1176211 AAAAAAAATGGATACTGTAATAACAAAAAAATCGGA
1 AAAAAAAATGGATACTGTAATAACAAAAAAATCGGA
1176247 CCAAGCAGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.61, C:0.08, G:0.12, T:0.18
Consensus pattern (36 bp):
AAAAAAAATGGATACTGTAATAACAAAAAAATCGGA
Found at i:1181739 original size:10 final size:10
Alignment explanation
Indices: 1181721--1181775 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
1181711 GATTCTGATA
1181721 CACGAACGAT
1 CACGAACGAT
*
1181731 CACGCACGAT
1 CACGAACGAT
1181741 ACACGAACGAT
1 -CACGAACGAT
*
1181752 CACGCACGAT
1 CACGAACGAT
*
1181762 ACACGGACGAT
1 -CACGAACGAT
1181773 CAC
1 CAC
1181776 TAACTAACTG
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:1181741 original size:21 final size:21
Alignment explanation
Indices: 1181717--1181775 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
1181707 GCACGATTCT
1181717 GATACACGAACGATCACGCAC
1 GATACACGAACGATCACGCAC
1181738 GATACACGAACGATCACGCAC
1 GATACACGAACGATCACGCAC
*
1181759 GATACACGGACGATCAC
1 GATACACGAACGATCAC
1181776 TAACTAACTG
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:1181750 original size:11 final size:11
Alignment explanation
Indices: 1181717--1181772 Score: 71
Period size: 11 Copynumber: 5.3 Consensus size: 11
1181707 GCACGATTCT
1181717 GATACACGAAC
1 GATACACGAAC
*
1181728 GAT-CACGCAC
1 GATACACGAAC
1181738 GATACACGAAC
1 GATACACGAAC
*
1181749 GAT-CACGCAC
1 GATACACGAAC
*
1181759 GATACACGGAC
1 GATACACGAAC
1181770 GAT
1 GAT
1181773 CACTAACTAA
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:1185524 original size:23 final size:23
Alignment explanation
Indices: 1185483--1185526 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1185473 TAAAGTTGCA
**
1185483 TTGTTGAAAAGTTTCAGTTGATT
1 TTGTTGAAAAGTTAAAGTTGATT
*
1185506 TTGTTGACAAGTTAAAGTTGA
1 TTGTTGAAAAGTTAAAGTTGA
1185527 CTTTAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.43
Consensus pattern (23 bp):
TTGTTGAAAAGTTAAAGTTGATT
Found at i:1186345 original size:4 final size:4
Alignment explanation
Indices: 1186288--1186338 Score: 84
Period size: 4 Copynumber: 12.8 Consensus size: 4
1186278 GAATCACCTT
* *
1186288 GTCC GTCC GTCC GTCT GTCC GTCC GTCC GTCC GTCC GTCC GTCT GTCC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
1186336 GTC
1 GTC
1186339 TGTCTGTTCG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.00, C:0.45, G:0.25, T:0.29
Consensus pattern (4 bp):
GTCC
Found at i:1186613 original size:146 final size:147
Alignment explanation
Indices: 1186349--1187044 Score: 938
Period size: 147 Copynumber: 4.8 Consensus size: 147
1186339 TGTCTGTTCG
*
1186349 ATTCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTAGAAGTTCTTACTTCACACAAAGATT
1 ATTCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATT
* * **
1186414 GCTTATGACCTAAGGGTGTGTCATGACCTTGAACCAAGGTCATTCGGGCAAGGTCAAGGTCACCA
66 GCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTG
1186479 ACAG-AAAAAGTGCAAA
131 ACAGAAAAAAGTGCAAA
1186495 ATTCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTT-TTAACTTCACACAAAGAT
1 ATTCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTT-ACTTCACACAAAGAT
* * *
1186559 TGCTAATGACCCAAGGGTGTGTCATGACCTTAACCCAAGGTCATTTGGGCAAGGTCAAGGTCACT
65 TGCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACT
*
1186624 GACAGAAAAAATTGCAAA
130 GACAGAAAAAAGTGCAAA
** * *
1186642 ATTCGTGTCCGGTTTATATCTTT-TTAATGGAGAAACATTGGAAGTTCTTTCTTCACCCAAAGAT
1 ATTCGTGTCCGGTCCATATCTTTCTT-ATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGAT
* *
1186706 TGCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGACAAGGTCAAGGTCAAT
65 TGCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACT
*
1186771 GGCAGAAAAAAGTGCAAA
130 GACAGAAAAAAGTGCAAA
* * * *
1186789 ATTCTTGTCCGGTCCATATCTTTCTTCTGGAGAAACATTGGAAGTTCTCAGTTCACACAAAGATT
1 ATTCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATT
* * * * * *
1186854 GCTTATAAGCTATGGGTTTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGCCAAGGACACTT
66 GCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCAC-T
**
1186919 G-CAG--AAAAGTATAAA
130 GACAGAAAAAAGTGCAAA
* * * * * * * *
1186934 ACTCGTGTCCAGTCCATATCTTTCTAATGGACAAATATTGGAAGTTCTTAATTCACATC-TAGAA
1 ATTCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACA-CAAAGAT
* * * * *
1186998 TGCTTATAACCTGAGAGTATGTCATGACCTTGACCAAAGGTCATTTG
65 TGCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTG
1187045 AGGAAGTTTA
Statistics
Matches: 488, Mismatches: 55, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
145 103 0.21
146 126 0.26
147 253 0.52
148 6 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (147 bp):
ATTCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATT
GCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTG
ACAGAAAAAAGTGCAAA
Found at i:1196480 original size:16 final size:16
Alignment explanation
Indices: 1196456--1196489 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1196446 TGTGAAGCCT
1196456 GAAGAATTGCCACCAA
1 GAAGAATTGCCACCAA
* *
1196472 GAAGTATTGTCACCAA
1 GAAGAATTGCCACCAA
1196488 GA
1 GA
1196490 CACTCTGGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (16 bp):
GAAGAATTGCCACCAA
Found at i:1197052 original size:34 final size:33
Alignment explanation
Indices: 1197000--1197068 Score: 111
Period size: 34 Copynumber: 2.1 Consensus size: 33
1196990 CATGAATAAA
* *
1197000 ATTCATAATGATATTCATGAACAGTTCATTAAG
1 ATTCATAAAGATATTCATGAACAGTTCATGAAG
1197033 ATTCATTAAAGATATTCATGAACAGTTCATGAAG
1 ATTCA-TAAAGATATTCATGAACAGTTCATGAAG
1197067 AT
1 AT
1197069 CCGATGAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 5 0.15
34 28 0.85
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35
Consensus pattern (33 bp):
ATTCATAAAGATATTCATGAACAGTTCATGAAG
Found at i:1199515 original size:25 final size:25
Alignment explanation
Indices: 1199468--1199515 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1199458 CAGAAAGCCG
* *
1199468 ATTCAAAACTGTCCTAAATATTACA
1 ATTCAAAACTCTCCTAAAGATTACA
*
1199493 ATTCAAAACTCTCCTGAAGATTA
1 ATTCAAAACTCTCCTAAAGATTA
1199516 AAATGAAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (25 bp):
ATTCAAAACTCTCCTAAAGATTACA
Found at i:1203390 original size:25 final size:25
Alignment explanation
Indices: 1203356--1203408 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1203346 GATATCCAGA
1203356 TGTTTGTCCCAAAACTTTGCCTGAT
1 TGTTTGTCCCAAAACTTTGCCTGAT
1203381 TGTTTGTCCCAAAACTTTGCCTGAT
1 TGTTTGTCCCAAAACTTTGCCTGAT
1203406 TGT
1 TGT
1203409 CTAAGTAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.42
Consensus pattern (25 bp):
TGTTTGTCCCAAAACTTTGCCTGAT
Found at i:1209808 original size:12 final size:12
Alignment explanation
Indices: 1209791--1209824 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1209781 TGAAAAGTTT
1209791 ACAGACGGACAG
1 ACAGACGGACAG
* *
1209803 ACAGACGGTCGG
1 ACAGACGGACAG
1209815 ACAGACGGAC
1 ACAGACGGAC
1209825 GACGGACAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.26, G:0.35, T:0.03
Consensus pattern (12 bp):
ACAGACGGACAG
Found at i:1209830 original size:7 final size:8
Alignment explanation
Indices: 1209791--1209832 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
1209781 TGAAAAGTTT
1209791 ACAGACGG
1 ACAGACGG
*
1209799 ACAGACAG
1 ACAGACGG
* *
1209807 ACGGTCGG
1 ACAGACGG
1209815 ACAGACGG
1 ACAGACGG
1209823 AC-GACGG
1 ACAGACGG
1209830 ACA
1 ACA
1209833 AAATGTGATC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.36, C:0.26, G:0.36, T:0.02
Consensus pattern (8 bp):
ACAGACGG
Found at i:1216658 original size:54 final size:54
Alignment explanation
Indices: 1216594--1216703 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
1216584 GTTGAGGTAG
1216594 CCTAAAGCCCATGTATGAAACGATATAACTTGAGGTACAAGAACATGATGCCGA
1 CCTAAAGCCCATGTATGAAACGATATAACTTGAGGTACAAGAACATGATGCCGA
*
1216648 CCTAAAGCCCATGTATGCAACGATATAACTTGAGGTACAAGAACATGATGCCGA
1 CCTAAAGCCCATGTATGAAACGATATAACTTGAGGTACAAGAACATGATGCCGA
1216702 CC
1 CC
1216704 CCAGCTGATG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (54 bp):
CCTAAAGCCCATGTATGAAACGATATAACTTGAGGTACAAGAACATGATGCCGA
Found at i:1218696 original size:18 final size:18
Alignment explanation
Indices: 1218673--1218769 Score: 104
Period size: 18 Copynumber: 5.2 Consensus size: 18
1218663 CGATTTGCAC
*
1218673 CATCATATAAAAAAGCAT
1 CATCACATAAAAAAGCAT
* *
1218691 CATCATATAATAAAGCACCAT
1 CATCACATAA-AAA--AGCAT
* *
1218712 CTTCACATAAAAAAGCAC
1 CATCACATAAAAAAGCAT
*
1218730 CTTCACATAAAAAAGCAT
1 CATCACATAAAAAAGCAT
*
1218748 CATCACATAAAAAAGCAC
1 CATCACATAAAAAAGCAT
1218766 CATC
1 CATC
1218770 TTCATATAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
18 50 0.74
19 3 0.04
20 3 0.04
21 12 0.18
ACGTcount: A:0.51, C:0.25, G:0.05, T:0.20
Consensus pattern (18 bp):
CATCACATAAAAAAGCAT
Found at i:1218712 original size:21 final size:21
Alignment explanation
Indices: 1218688--1218853 Score: 209
Period size: 21 Copynumber: 8.2 Consensus size: 21
1218678 TATAAAAAAG
*
1218688 CATCATCATATAATAAAGCAC
1 CATCTTCATATAATAAAGCAC
* *
1218709 CATCTTCACATAAAAAAGCA-
1 CATCTTCATATAATAAAGCAC
* * *
1218729 C--CTTCACATAAAAAAGCAT
1 CATCTTCATATAATAAAGCAC
*
1218748 CATC-ACATA-AA-AAAGCAC
1 CATCTTCATATAATAAAGCAC
1218766 CATCTTCATATAATAAAGCAC
1 CATCTTCATATAATAAAGCAC
*
1218787 CATCTTCATATAATAAGGCAC
1 CATCTTCATATAATAAAGCAC
*
1218808 CACCTTCATATAATAAAGCAC
1 CATCTTCATATAATAAAGCAC
1218829 CATCTTCATATAATAAAGCAC
1 CATCTTCATATAATAAAGCAC
1218850 CATC
1 CATC
1218854 NNNNNNNNNN
Statistics
Matches: 128, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
18 27 0.21
19 7 0.05
20 6 0.05
21 88 0.69
ACGTcount: A:0.45, C:0.26, G:0.05, T:0.23
Consensus pattern (21 bp):
CATCTTCATATAATAAAGCAC
Found at i:1218829 original size:18 final size:18
Alignment explanation
Indices: 1218669--1218850 Score: 112
Period size: 21 Copynumber: 9.3 Consensus size: 18
1218659 TCAGCGATTT
* *
1218669 GCACCATCATATAAAAAA
1 GCACCTTCATATAATAAA
* *
1218687 GCATCATCATATAATAAA
1 GCACCTTCATATAATAAA
* *
1218705 GCACCATCTTCACATAAAAAA
1 GCA-C--CTTCATATAATAAA
* *
1218726 GCACCTTCACATAAAAAA
1 GCACCTTCATATAATAAA
* * * *
1218744 GCATCATCACATAAAAAA
1 GCACCTTCATATAATAAA
1218762 GCACCATCTTCATATAATAAA
1 GCA-C--CTTCATATAATAAA
1218783 GCACCATCTTCATATAATAAGGCA
1 GCA-C--CTTCATATAATAA---A
*
1218807 CCACCTTCATATAATAAA
1 GCACCTTCATATAATAAA
1218825 GCACCATCTTCATATAATAAA
1 GCA-C--CTTCATATAATAAA
1218846 GCACC
1 GCACC
1218851 ATCNNNNNNN
Statistics
Matches: 138, Mismatches: 14, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
18 56 0.41
19 1 0.01
20 2 0.01
21 75 0.54
23 1 0.01
24 3 0.02
ACGTcount: A:0.46, C:0.25, G:0.06, T:0.23
Consensus pattern (18 bp):
GCACCTTCATATAATAAA
Found at i:1226607 original size:2 final size:2
Alignment explanation
Indices: 1226600--1226627 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1226590 NNNNNNNNNN
1226600 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
1226628 AGATGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1226876 original size:21 final size:21
Alignment explanation
Indices: 1226837--1226913 Score: 58
Period size: 21 Copynumber: 3.9 Consensus size: 21
1226827 AGAGACAGAC
* *
1226837 AGACAGA-ACCGACAAAGAA-
1 AGACAGAGACAGACAGAGAAT
*
1226856 AGGCAGAAGACAGACAGAGAAT
1 AGACAG-AGACAGACAGAGAAT
* *
1226878 AGACAGAGAGAGACAGA-CAT
1 AGACAGAGACAGACAGAGAAT
1226898 --ACAGAGACAGA-AGAGA
1 AGACAGAGACAGACAGAGA
1226914 GAGAAGAGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
17 3 0.07
18 10 0.22
19 5 0.11
20 3 0.07
21 20 0.43
22 5 0.11
ACGTcount: A:0.53, C:0.16, G:0.29, T:0.03
Consensus pattern (21 bp):
AGACAGAGACAGACAGAGAAT
Found at i:1226903 original size:14 final size:14
Alignment explanation
Indices: 1226827--1226917 Score: 62
Period size: 14 Copynumber: 6.4 Consensus size: 14
1226817 GAGAGAGGAG
1226827 AGAGACAGACAGAC
1 AGAGACAGACAGAC
* *
1226841 AGA-ACCGACAAAGAA
1 AGAGACAGAC--AGAC
1226856 AGGCAGA-AGACAGAC
1 A-G-AGACAGACAGAC
* *
1226871 AGAGAATAGACAGAG
1 AGAG-ACAGACAGAC
*
1226886 AGAGACAGACATAC
1 AGAGACAGACAGAC
*
1226900 AGAGACAGA-AGAG
1 AGAGACAGACAGAC
1226913 AGAGA
1 AGAGA
1226918 AGAGAAGAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 15
0.71 0.12 0.18
Matches are distributed among these distances:
13 14 0.23
14 21 0.35
15 19 0.32
16 1 0.02
17 4 0.07
18 1 0.02
ACGTcount: A:0.53, C:0.15, G:0.30, T:0.02
Consensus pattern (14 bp):
AGAGACAGACAGAC
Found at i:1228046 original size:15 final size:14
Alignment explanation
Indices: 1228026--1228071 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
1228016 AAGAGGCGAA
1228026 AGACAGACAGAGAAC
1 AGACAGACAGAG-AC
*
1228041 AGACAGAAAGAGAC
1 AGACAGACAGAGAC
* *
1228055 AGACATACAGACAC
1 AGACAGACAGAGAC
1228069 AGA
1 AGA
1228072 GACAAAGGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.54, C:0.20, G:0.24, T:0.02
Consensus pattern (14 bp):
AGACAGACAGAGAC
Found at i:1238357 original size:161 final size:161
Alignment explanation
Indices: 1238075--1238534 Score: 568
Period size: 161 Copynumber: 2.8 Consensus size: 161
1238065 CCACCAACAG
* * *
1238075 TTTCCGTTCATTTTCTTCGCAGAGGATGAACATATTGGAATGAAATTTGGTATAC-AGCTTTATC
1 TTTCCGCTCATTTTCTTCACAGAGGATGAACATATTGGAATGAAATTTGGTATACAAGTTTTATC
* * **
1238139 ATGATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTATCAACAGAGTTATGGCC
66 ATGATAATATCTAGGTCAAGTTTGATATTGGGTATGATCGAGCAATT-TTGACAGAGTTATGGCC
* *
1238204 CTTGGACGTAGAAAAATTCCAGTTATTTGCAA
130 CTTGGACATAGAAAAATTCCAGTAATTTGCAA
* * * * *
1238236 TTTCTGCTCATTTTCTTCCCAGAGGATAAAAATATTGGAATGAAATTTAGTATACAAG-TTTATC
1 TTTCCGCTCATTTTCTTCACAGAGGATGAACATATTGGAATGAAATTTGGTATACAAGTTTTATC
* * *
1238300 ATGATAATATCTAGGTTAAGTTTGATATTGGGTATGATCTAGCATATTTTGACAGAGTTATGGCT
66 ATGATAATATCTAGGTCAAGTTTGATATTGGGTATGATCGAGCA-ATTTTGACAGAGTTATGGCC
* *
1238365 CTTGGACATTGAAAAATTCCAGTAATTTGCAG
130 CTTGGACATAGAAAAATTCCAGTAATTTGCAA
* * * * *
1238397 TTTCCGCTCATTTTCTTTACAGAGGGTGCACATATT-GATATGAAATCTGGTATACATGTTTTTA
1 TTTCCGCTCATTTTCTTCACAGAGGATGAACATATTGGA-ATGAAATTTGGTATACAAG-TTTTA
* * * * *
1238461 TC-TAAATAATATCTAGGTCAAGTTTGATTTTGGGCATGATAGAGCAATTTTCGACAGAGTTATA
64 TCAT-GATAATATCTAGGTCAAGTTTGATATTGGGTATGATCGAGCAATTTT-GACAGAGTTATG
*
1238525 CCCCTTGGAC
127 GCCCTTGGAC
1238535 TTCCAATTAT
Statistics
Matches: 256, Mismatches: 36, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
160 2 0.01
161 182 0.71
162 11 0.04
163 61 0.24
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Consensus pattern (161 bp):
TTTCCGCTCATTTTCTTCACAGAGGATGAACATATTGGAATGAAATTTGGTATACAAGTTTTATC
ATGATAATATCTAGGTCAAGTTTGATATTGGGTATGATCGAGCAATTTTGACAGAGTTATGGCCC
TTGGACATAGAAAAATTCCAGTAATTTGCAA
Found at i:1238698 original size:18 final size:18
Alignment explanation
Indices: 1238675--1238709 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1238665 GTCTGGGCGG
1238675 ACTCCGAAAAAGGAGTAA
1 ACTCCGAAAAAGGAGTAA
*
1238693 ACTCCGAAAACGGAGTA
1 ACTCCGAAAAAGGAGTA
1238710 TTTGGCACCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (18 bp):
ACTCCGAAAAAGGAGTAA
Found at i:1239563 original size:4 final size:4
Alignment explanation
Indices: 1239554--1239605 Score: 50
Period size: 4 Copynumber: 13.0 Consensus size: 4
1239544 TTTACCCTTG
* ** * * *
1239554 TGTC TGTC TGTC TGTC CGTC CATC TGTC TGTC GGTC CGTC CGTC TGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
1239602 TGTC
1 TGTC
1239606 CGTCCGTAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.02, C:0.33, G:0.25, T:0.40
Consensus pattern (4 bp):
TGTC
Found at i:1239581 original size:20 final size:20
Alignment explanation
Indices: 1239556--1239612 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
1239546 TACCCTTGTG
*
1239556 TCTGTCTGTCTGTCCGTCCA
1 TCTGTCTGTCCGTCCGTCCA
* *
1239576 TCTGTCTGTCGGTCCGTCCG
1 TCTGTCTGTCCGTCCGTCCA
1239596 TCTGTCTGTCCGTCCGT
1 TCTGTCTGTCCGTCCGT
1239613 AACAAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.02, C:0.35, G:0.25, T:0.39
Consensus pattern (20 bp):
TCTGTCTGTCCGTCCGTCCA
Found at i:1239612 original size:16 final size:16
Alignment explanation
Indices: 1239559--1239609 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
1239549 CCTTGTGTCT
1239559 GTCTGTCTGTCCGTCC
1 GTCTGTCTGTCCGTCC
* *
1239575 ATCTGTCTGTCGGTCC
1 GTCTGTCTGTCCGTCC
* *
1239591 GTCCGTCTGTCTGTCC
1 GTCTGTCTGTCCGTCC
1239607 GTC
1 GTC
1239610 CGTAACAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.02, C:0.35, G:0.25, T:0.37
Consensus pattern (16 bp):
GTCTGTCTGTCCGTCC
Found at i:1242382 original size:50 final size:49
Alignment explanation
Indices: 1242302--1242401 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 49
1242292 AGCCTTAATG
*
1242302 TTTGAATTGAAAAGTCTAGTTTAAGACCTAAAATGAATGTGTTAGGAAA
1 TTTGAATTGAAAAGTCCAGTTTAAGACCTAAAATGAATGTGTTAGGAAA
* *
1242351 TTTGAATTGAAAATTTCCAGTTTTAGACCTAAAATGAATGTGTTAGGAAA
1 TTTGAATTGAAAA-GTCCAGTTTAAGACCTAAAATGAATGTGTTAGGAAA
1242401 T
1 T
1242402 GTTTTTTATA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 13 0.28
50 34 0.72
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.35
Consensus pattern (49 bp):
TTTGAATTGAAAAGTCCAGTTTAAGACCTAAAATGAATGTGTTAGGAAA
Found at i:1247836 original size:20 final size:20
Alignment explanation
Indices: 1247811--1247850 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1247801 AGCTAATTAG
* *
1247811 ATTTTTAATTGGTTGATTTT
1 ATTTTTAATCGATTGATTTT
1247831 ATTTTTAATCGATTGATTTT
1 ATTTTTAATCGATTGATTTT
1247851 TAATTCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.03, G:0.12, T:0.62
Consensus pattern (20 bp):
ATTTTTAATCGATTGATTTT
Found at i:1249947 original size:14 final size:15
Alignment explanation
Indices: 1249928--1249956 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1249918 ATTGGGTCTC
1249928 GTATGTT-ACTTCGA
1 GTATGTTAACTTCGA
1249942 GTATGTTAACTTCGA
1 GTATGTTAACTTCGA
1249957 TTTTTTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (15 bp):
GTATGTTAACTTCGA
Found at i:1250341 original size:10 final size:10
Alignment explanation
Indices: 1250326--1250367 Score: 75
Period size: 10 Copynumber: 4.2 Consensus size: 10
1250316 ACTACTAAAC
1250326 AGAGAACTCT
1 AGAGAACTCT
*
1250336 AGAGAACTTT
1 AGAGAACTCT
1250346 AGAGAACTCT
1 AGAGAACTCT
1250356 AGAGAACTCT
1 AGAGAACTCT
1250366 AG
1 AG
1250368 TGTTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (10 bp):
AGAGAACTCT
Found at i:1250706 original size:8 final size:8
Alignment explanation
Indices: 1250693--1250745 Score: 67
Period size: 8 Copynumber: 6.9 Consensus size: 8
1250683 GGGTCCATAT
1250693 TTTTTTTA
1 TTTTTTTA
1250701 TTTTTTT-
1 TTTTTTTA
1250708 TTATTTTTA
1 TT-TTTTTA
1250717 TTTTTTTA
1 TTTTTTTA
*
1250725 --TTTTGA
1 TTTTTTTA
1250731 TTTTTTTA
1 TTTTTTTA
1250739 TTTTTTT
1 TTTTTTT
1250746 TTGTATTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 5 0.13
7 2 0.05
8 30 0.77
9 2 0.05
ACGTcount: A:0.11, C:0.00, G:0.02, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1250743 original size:38 final size:36
Alignment explanation
Indices: 1250693--1250781 Score: 108
Period size: 38 Copynumber: 2.4 Consensus size: 36
1250683 GGGTCCATAT
* *
1250693 TTTTTTTATTTTTTTTTAT-TTTTATTTTTTTATTTTG
1 TTTTTTTATTTTTTTTTATATTTGA--TTTTAATTTTG
*
1250730 ATTTTTTTATTTTTTTTTGTATTTGATTTTAATTTTG
1 -TTTTTTTATTTTTTTTTATATTTGATTTTAATTTTG
*
1250767 TTTTTTGATTTTTTT
1 TTTTTTTATTTTTTT
1250782 GTTTACTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
36 14 0.30
37 10 0.22
38 18 0.39
39 4 0.09
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (36 bp):
TTTTTTTATTTTTTTTTATATTTGATTTTAATTTTG
Found at i:1250771 original size:50 final size:47
Alignment explanation
Indices: 1250692--1250794 Score: 116
Period size: 50 Copynumber: 2.1 Consensus size: 47
1250682 AGGGTCCATA
** * * * *
1250692 TTTTTTTTATTTTTTTTTATTTTTATTTTTTTATTTTGATTTTTTTATT
1 TTTTTTTTATTTGATTTTAATTTTATTTTTTGATTTT--TTTGTTTACT
*
1250741 TTTTTTTGTATTTGATTTTAATTTTGTTTTTTGATTTTTTTGTTTACT
1 TTTTTTT-TATTTGATTTTAATTTTATTTTTTGATTTTTTTGTTTACT
1250789 TTTTTT
1 TTTTTT
1250795 GGAGGGAGGG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
48 14 0.30
49 7 0.15
50 25 0.54
ACGTcount: A:0.12, C:0.01, G:0.06, T:0.82
Consensus pattern (47 bp):
TTTTTTTTATTTGATTTTAATTTTATTTTTTGATTTTTTTGTTTACT
Found at i:1252189 original size:10 final size:10
Alignment explanation
Indices: 1252174--1252214 Score: 73
Period size: 10 Copynumber: 4.1 Consensus size: 10
1252164 TATATAATCT
1252174 TAGAGTTCTC
1 TAGAGTTCTC
1252184 TAGAGTTCTC
1 TAGAGTTCTC
*
1252194 TAGAGTTCTT
1 TAGAGTTCTC
1252204 TAGAGTTCTC
1 TAGAGTTCTC
1252214 T
1 T
1252215 GTTTAGTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.44
Consensus pattern (10 bp):
TAGAGTTCTC
Found at i:1252744 original size:8 final size:8
Alignment explanation
Indices: 1252733--1252776 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
1252723 GCGTCCGCCA
1252733 GTCCGTCT
1 GTCCGTCT
*
1252741 GTCCGTCC
1 GTCCGTCT
*
1252749 GTCCGTCC
1 GTCCGTCT
1252757 GTCCGTCT
1 GTCCGTCT
*
1252765 GTCTGTCT
1 GTCCGTCT
1252773 GTCC
1 GTCC
1252777 CACTTCAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.00, C:0.41, G:0.25, T:0.34
Consensus pattern (8 bp):
GTCCGTCT
Found at i:1252748 original size:12 final size:12
Alignment explanation
Indices: 1252733--1252767 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1252723 GCGTCCGCCA
1252733 GTCCGTCTGTCC
1 GTCCGTCTGTCC
*
1252745 GTCCGTCCGTCC
1 GTCCGTCTGTCC
1252757 GTCCGTCTGTC
1 GTCCGTCTGTC
1252768 TGTCTGTCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.43, G:0.26, T:0.31
Consensus pattern (12 bp):
GTCCGTCTGTCC
Found at i:1252775 original size:4 final size:4
Alignment explanation
Indices: 1252724--1252763 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
1252714 CTTTCCTCTG
*
1252724 CGTC CG-C CAGTC CGTC TGTC CGTC CGTC CGTC CGTC CGTC
1 CGTC CGTC C-GTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC
1252764 TGTCTGTCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 2 0.06
4 28 0.88
5 2 0.06
ACGTcount: A:0.03, C:0.47, G:0.25, T:0.25
Consensus pattern (4 bp):
CGTC
Found at i:1269584 original size:156 final size:156
Alignment explanation
Indices: 1269300--1269603 Score: 520
Period size: 156 Copynumber: 1.9 Consensus size: 156
1269290 CTTACAAGGT
*
1269300 CACAAAGTCCCATTACTCCAACAAAAAGTATCGACCAATGCTAATTTTCGAACTTGACCAAGATA
1 CACAAAGTCCCATAACTCCAACAAAAAGTATCGACCAATGCTAATTTTCGAACTTGACCAAGATA
* * *
1269365 ATAGTGGTATAAACATTTGGTATAAATTTAATGAAAATCCGTCAAAGGTTGTAGGCATGAGAGCG
66 ATAGTGCTATAAACATTTGGAATAAATTTAATGAAAATCCGTCAAAAGTTGTAGGCATGAGAGCG
1269430 CTTACAAAAAAGTGTGATAAATGCGC
131 CTTACAAAAAAGTGTGATAAATGCGC
*
1269456 CACAAAGTCCCATAACTCCAACAAAAAGTATCGACCAATGCTGATTTTCGAACTTGACCAA-AGT
1 CACAAAGTCCCATAACTCCAACAAAAAGTATCGACCAATGCTAATTTTCGAACTTGACCAAGA-T
* * *
1269520 ATTAGTGCTATAAACATTTGGAATAAATTTAATGAAAATCGGTCAAAATTTGTAGGCATGAGAGC
65 AATAGTGCTATAAACATTTGGAATAAATTTAATGAAAATCCGTCAAAAGTTGTAGGCATGAGAGC
1269585 GCTTACAAAAAAGTGTGAT
130 GCTTACAAAAAAGTGTGAT
1269604 GGACGGACGC
Statistics
Matches: 139, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
155 1 0.01
156 138 0.99
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (156 bp):
CACAAAGTCCCATAACTCCAACAAAAAGTATCGACCAATGCTAATTTTCGAACTTGACCAAGATA
ATAGTGCTATAAACATTTGGAATAAATTTAATGAAAATCCGTCAAAAGTTGTAGGCATGAGAGCG
CTTACAAAAAAGTGTGATAAATGCGC
Found at i:1271873 original size:13 final size:13
Alignment explanation
Indices: 1271855--1271882 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1271845 ACGAAGATCA
1271855 TTTTTGGTAGTAC
1 TTTTTGGTAGTAC
1271868 TTTTTGGTAGTAC
1 TTTTTGGTAGTAC
1271881 TT
1 TT
1271883 CTGAGTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.21, T:0.57
Consensus pattern (13 bp):
TTTTTGGTAGTAC
Found at i:1278516 original size:166 final size:164
Alignment explanation
Indices: 1278000--1278844 Score: 1011
Period size: 166 Copynumber: 5.2 Consensus size: 164
1277990 GGTATTTTTC
* * * * * *
1278000 AAAAATCTTCCTCTCAAAAACTATTCGGCCTGAAAAGCTTAAACTTATGTGGAGGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTAAGTGGAAGCATCCTCAGG
* *
1278065 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTTAGGGTAGGGAGGGGCCACAA-AGGGGGA
65 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCC-TGGGGTAGGGTGGGGCCACAATAGGGGGA
1278129 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
129 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* *
1278165 AAAAATCTTCTTCTCAAAAACTATCAGGCCAGAAAAGCTCAAATTAAATGGAAGCATCCTCAGGT
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAGTGGAAGCATCCTCAGGT
* *
1278230 AGTGTAGATTCAA-TTTCATTCAAATCATGGTCCCTGTGGGTAGGGTGGGG-CACAATACGGGGA
66 AGTGTAGATTCAAGTTT-GTTCAAATCATGGTCCCTG-GGGTAGGGTGGGGCCACAATAGGGGGA
*
1278293 TCAAGTTTTACATAGGAATATACAGAGAAAATCTTT
129 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
*
1278329 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATT-AAGTGGAAGCATCCTCAGG
* * * *
1278394 TAGTGGAGATTCTAGTTTGTTCAAATCATAGTCCCTTGGGGTAGGGTGGGGCCACAATGGGGGGA
65 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCC-TGGGGTAGGGTGGGGCCACAATAGGGGGA
* *
1278459 TCAAGATTAACATAGGAATATATAGAGAAAATCTTT
129 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * * * *
1278495 AAAAATCCTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTAAGTAGAAGCATTCTCAGA
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTAAGTGGAAGCATCCTCAGG
* * * * *
1278560 TAGTGTAGATTCAAGTTCGTTCAAATCATGGTTCCCGGGGGTAGGATGGGGCAACAATTGGGGGA
65 TAGTGTAGATTCAAGTTTGTTCAAATCATGG-TCCCTGGGGTAGGGTGGGGCCACAATAGGGGGA
* * * * *
1278625 TAAATTTTTATACAGGAATATATAGAGAAAATCTAT
129 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
** * * * ** *
1278661 AAAAAAATTCTT-TTAAAAACTATTTGGCCA-AGAAAGCTCCAATTGGCGTGTAA-CTATCCTCA
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGA-AAAGCTCAAATT-AAGTGGAAGC-ATCCTCA
* * *
1278723 GATAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGAGGTAGGGCGGGGCCACAAT-GGGG
63 GGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGG-GGTAGGGTGGGGCCACAATAGGGG
*
1278787 GAT-AAATTTT---T----ATATATAGAGAAAATCTTT
127 GATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
*
1278817 AAAAAAAATATTCTTCTC-AAAACTATTA
1 ---AAAAATCTTCTTCTCAAAAACTATTA
1278845 AGTGGGACCA
Statistics
Matches: 595, Mismatches: 68, Indels: 40
0.85 0.10 0.06
Matches are distributed among these distances:
156 18 0.03
159 20 0.03
160 1 0.00
163 15 0.03
164 161 0.27
165 179 0.30
166 195 0.33
167 6 0.01
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (164 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAGTGGAAGCATCCTCAGGT
AGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGTAGGGTGGGGCCACAATAGGGGGATC
AAGTTTTACATAGGAATATATAGAGAAAATCTTT
Found at i:1279240 original size:21 final size:21
Alignment explanation
Indices: 1279211--1279273 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
1279201 ATTTTTCTGT
1279211 TAATTATGTCGACATGCAAGA
1 TAATTATGTCGACATGCAAGA
* * *
1279232 TATTTATGTCAACATGCAACA
1 TAATTATGTCGACATGCAAGA
* *
1279253 TAACTATGTTGACATGCAAGA
1 TAATTATGTCGACATGCAAGA
1279274 AAACTGCAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (21 bp):
TAATTATGTCGACATGCAAGA
Found at i:1279381 original size:21 final size:21
Alignment explanation
Indices: 1279355--1279415 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1279345 CGCTACCTTA
*
1279355 TTTATGTTAACAGGCAACTTC
1 TTTATGTCAACAGGCAACTTC
* * *
1279376 TTTATGTCGACATGCAACTTG
1 TTTATGTCAACAGGCAACTTC
* *
1279397 TTTATGTCGACATGCAACT
1 TTTATGTCAACAGGCAACT
1279416 AAGTTATGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (21 bp):
TTTATGTCAACAGGCAACTTC
Found at i:1279402 original size:42 final size:42
Alignment explanation
Indices: 1279355--1279436 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
1279345 CGCTACCTTA
* ***
1279355 TTTATGTTAACAGGCAACTTCTTTATGTCGACATGCAACTTG
1 TTTATGTCAACAGGCAACTAAGTTATGTCGACATGCAACTTG
* *
1279397 TTTATGTCGACATGCAACTAAGTTATGTCGACATGCAACT
1 TTTATGTCAACAGGCAACTAAGTTATGTCGACATGCAACT
1279437 AAGTTATGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (42 bp):
TTTATGTCAACAGGCAACTAAGTTATGTCGACATGCAACTTG
Found at i:1279422 original size:21 final size:21
Alignment explanation
Indices: 1279377--1279520 Score: 116
Period size: 21 Copynumber: 6.9 Consensus size: 21
1279367 GGCAACTTCT
*
1279377 TTATGTCGACATGCAACT-TG
1 TTATGTCGACATGCAACTAAG
1279397 TTTATGTCGACATGCAACTAAG
1 -TTATGTCGACATGCAACTAAG
1279419 TTATGTCGACATGCAACTAAG
1 TTATGTCGACATGCAACTAAG
* * *
1279440 TTATGAT-AACATTCAAGATAA-
1 TTATG-TCGACATGCAA-CTAAG
* * *
1279461 ATATGTTGACATGCAAC-ATAT
1 TTATGTCGACATGCAACTA-AG
* *
1279482 TTATGTTGACATGCAACTTAG
1 TTATGTCGACATGCAACTAAG
* * *
1279503 TAATGTTGACATACAACT
1 TTATGTCGACATGCAACT
1279521 TATAAGTTGC
Statistics
Matches: 103, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
19 1 0.01
20 2 0.02
21 95 0.92
22 5 0.05
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (21 bp):
TTATGTCGACATGCAACTAAG
Found at i:1279521 original size:21 final size:20
Alignment explanation
Indices: 1279463--1279538 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 20
1279453 CAAGATAAAT
* *
1279463 ATGTTGACATGCAACATATTT
1 ATGTTGACATGCAACTTA-TA
1279484 ATGTTGACATGCAACTTAGTA
1 ATGTTGACATGCAACTTA-TA
*
1279505 ATGTTGACATACAACTTATA
1 ATGTTGACATGCAACTTATA
1279525 A-GTTG-CATGTCAAC
1 ATGTTGACATG-CAAC
1279539 ATATTTATCT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 3 0.06
19 8 0.16
20 3 0.06
21 35 0.71
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
ATGTTGACATGCAACTTATA
Found at i:1279551 original size:21 final size:21
Alignment explanation
Indices: 1279527--1279603 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
1279517 AACTTATAAG
1279527 TTGCATGTCAACATATTTATC
1 TTGCATGTCAACATATTTATC
* * **
1279548 TTGCATGTAAACATGA-CTAAG
1 TTGCATGTCAACAT-ATTTATC
*
1279569 TTGCATGTCAACATATTCATC
1 TTGCATGTCAACATATTTATC
*
1279590 TCGCATGTCAACAT
1 TTGCATGTCAACAT
1279604 TAGTAAGTTG
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 1 0.02
21 42 0.95
22 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (21 bp):
TTGCATGTCAACATATTTATC
Found at i:1279625 original size:42 final size:42
Alignment explanation
Indices: 1279523--1279615 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
1279513 ATACAACTTA
* *
1279523 TAAGTTGCATGTCAACATATTTATCTTGCATGTAAACATGAC
1 TAAGTTGCATGTCAACATATTCATCTCGCATGTAAACATGAC
* * *
1279565 TAAGTTGCATGTCAACATATTCATCTCGCATGTCAACATTAG
1 TAAGTTGCATGTCAACATATTCATCTCGCATGTAAACATGAC
1279607 TAAGTTGCA
1 TAAGTTGCA
1279616 AGTTGACATA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (42 bp):
TAAGTTGCATGTCAACATATTCATCTCGCATGTAAACATGAC
Found at i:1279651 original size:21 final size:21
Alignment explanation
Indices: 1279592--1279667 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
1279582 TATTCATCTC
* * *
1279592 GCATGTCAACATTAGTAAGTT
1 GCATGTCGACATAAATAAGTT
* *
1279613 GCAAGTTGACAT-AA-AAGTT
1 GCATGTCGACATAAATAAGTT
1279632 GCATGTCGACATAAATAAGTT
1 GCATGTCGACATAAATAAGTT
1279653 GCATGTCGACATAAA
1 GCATGTCGACATAAA
1279668 AAGGTAGCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 15 0.32
20 3 0.06
21 29 0.62
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (21 bp):
GCATGTCGACATAAATAAGTT
Found at i:1279651 original size:40 final size:40
Alignment explanation
Indices: 1279592--1279668 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
1279582 TATTCATCTC
* * *
1279592 GCATGTCAACATTAGTAAGTTGCAAGTTGACATAAAAGTT
1 GCATGTCAACATAAATAAGTTGCAAGTCGACATAAAAGTT
* *
1279632 GCATGTCGACATAAATAAGTTGCATGTCGACATAAAA
1 GCATGTCAACATAAATAAGTTGCAAGTCGACATAAAA
1279669 AGGTAGCATC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (40 bp):
GCATGTCAACATAAATAAGTTGCAAGTCGACATAAAAGTT
Found at i:1279807 original size:20 final size:20
Alignment explanation
Indices: 1279746--1279824 Score: 95
Period size: 21 Copynumber: 3.9 Consensus size: 20
1279736 TGCAATTTTA
** *
1279746 TTGCATGTTAACATAATTATG
1 TTGCATGTCGACAT-ATTATC
*
1279767 TTGCATGTTGACATAATTATC
1 TTGCATGTCGACAT-ATTATC
*
1279788 TTGCATGTCGATATATTATC
1 TTGCATGTCGACATATTATC
1279808 TTGCATGTCGACATATT
1 TTGCATGTCGACATATT
1279825 TTATAAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 22 0.42
21 31 0.58
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (20 bp):
TTGCATGTCGACATATTATC
Found at i:1280697 original size:18 final size:18
Alignment explanation
Indices: 1280670--1280704 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1280660 GGGAGAGGGT
1280670 ATGGACACCACCCAGGAG
1 ATGGACACCACCCAGGAG
*
1280688 ATGGATACCACCCAGGA
1 ATGGACACCACCCAGGA
1280705 AGAGGAGCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.31, G:0.26, T:0.09
Consensus pattern (18 bp):
ATGGACACCACCCAGGAG
Found at i:1282872 original size:41 final size:42
Alignment explanation
Indices: 1282809--1282890 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 42
1282799 CAATTTTTTA
1282809 ATTATTAAGAAAAGAAAAGAAAAATACATTTTAACAATGTAT
1 ATTATTAAGAAAAGAAAAGAAAAATACATTTTAACAATGTAT
* * * *
1282851 ATTATTAAGTATA-AAAAGAAAATTACATTTTAACTATGTA
1 ATTATTAAGAAAAGAAAAGAAAAATACATTTTAACAATGTA
1282891 AACAAAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 25 0.69
42 11 0.31
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.33
Consensus pattern (42 bp):
ATTATTAAGAAAAGAAAAGAAAAATACATTTTAACAATGTAT
Done.