Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold131
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1240061
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 48773 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:1143934 original size:29 final size:30
Alignment explanation
Indices: 1143888--1143967 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
1143878 GAATTGGATC
1143888 AAATC-AAGATTTCATGTATAAAATTGCACA-
1 AAATCAAAG-TTT-ATGTATAAAATTGCACAT
* *
1143918 AAATCAAAGTTTATGTATACAATTGTACATT
1 AAATCAAAGTTTATGTATAAAATTGCACA-T
* *
1143949 AAATCATAGTTCATGTATA
1 AAATCAAAGTTTATGTATA
1143968 GTTTTAGTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
29 15 0.35
30 8 0.19
31 20 0.47
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (30 bp):
AAATCAAAGTTTATGTATAAAATTGCACAT
Found at i:1143965 original size:31 final size:29
Alignment explanation
Indices: 1143888--1143967 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
1143878 GAATTGGATC
*
1143888 AAATCAAGATTTCATGTATAAAATTGCACA
1 AAATCAA-AGTTCATGTATAAAATTGCACA
* * *
1143918 AAATCAAAGTTTATGTATACAATTGTACA
1 AAATCAAAGTTCATGTATAAAATTGCACA
*
1143947 TTAAATCATAGTTCATGTATA
1 --AAATCAAAGTTCATGTATA
1143968 GTTTTAGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 18 0.43
30 7 0.17
31 17 0.40
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (29 bp):
AAATCAAAGTTCATGTATAAAATTGCACA
Found at i:1149686 original size:13 final size:13
Alignment explanation
Indices: 1149668--1149693 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1149658 ATTGAAAACA
1149668 ATTTTTATGAAAT
1 ATTTTTATGAAAT
1149681 ATTTTTATGAAAT
1 ATTTTTATGAAAT
1149694 CTGCCAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATTTTTATGAAAT
Found at i:1177391 original size:50 final size:50
Alignment explanation
Indices: 1177337--1177494 Score: 121
Period size: 50 Copynumber: 3.2 Consensus size: 50
1177327 TCTTAGTAAG
1177337 AATATAAAAAATAATTTATTATAATTTGTTGTTAATATTTTAATATATGA
1 AATATAAAAAATAATTTATTATAATTTGTTGTTAATATTTTAATATATGA
* * ** * * * *
1177387 AATAT---AAAT--TTTA-AAAAATAAGTTAGTTAATCTTATGATATCTTAGTAA
1 AATATAAAAAATAATTTATTATAATTTGTT-GTTAATATT-TTA-AT-ATA-TGA
* * *
1177436 GAATATAAAACACAATTTATTATAATTTTTTGTTAATATTTTAATATATGA
1 -AATATAAAAAATAATTTATTATAATTTGTTGTTAATATTTTAATATATGA
1177487 AATATAAA
1 AATATAAA
1177495 TTTTAAATAT
Statistics
Matches: 77, Mismatches: 19, Indels: 24
0.64 0.16 0.20
Matches are distributed among these distances:
44 7 0.09
45 12 0.16
46 2 0.03
47 6 0.08
48 2 0.03
49 2 0.03
50 18 0.23
51 2 0.03
52 2 0.03
53 4 0.05
54 2 0.03
55 12 0.16
56 6 0.08
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (50 bp):
AATATAAAAAATAATTTATTATAATTTGTTGTTAATATTTTAATATATGA
Found at i:1177407 original size:57 final size:56
Alignment explanation
Indices: 1177341--1177501 Score: 134
Period size: 57 Copynumber: 3.1 Consensus size: 56
1177331 AGTAAGAATA
1177341 TAAAAAATAATTTATTATAATTTGTTGTTAATATTTTAATATATGAAATATAAATTT
1 TAAAAAATAATTTATTATAATTT-TTGTTAATATTTTAATATATGAAATATAAATTT
* * * * *
1177398 TAAAAAATAAGTTAGT-TAATCTTATG---ATATCTTAGTA-A-G-AATAT--A---
1 TAAAAAATAATTTATTATAAT-TTTTGTTAATATTTTAATATATGAAATATAAATTT
* *
1177443 -AA-ACACAATTTATTATAATTTTTTGTTAATATTTTAATATATGAAATATAAATTT
1 TAAAAAATAATTTATTATAA-TTTTTGTTAATATTTTAATATATGAAATATAAATTT
1177498 TAAA
1 TAAA
1177502 TATTTTTAAG
Statistics
Matches: 76, Mismatches: 12, Indels: 32
0.63 0.10 0.27
Matches are distributed among these distances:
43 8 0.11
44 9 0.12
45 1 0.01
47 9 0.12
48 2 0.03
49 1 0.01
50 10 0.13
51 1 0.01
52 2 0.03
53 9 0.12
56 8 0.11
57 16 0.21
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.45
Consensus pattern (56 bp):
TAAAAAATAATTTATTATAATTTTTGTTAATATTTTAATATATGAAATATAAATTT
Found at i:1177424 original size:100 final size:100
Alignment explanation
Indices: 1177309--1177501 Score: 350
Period size: 100 Copynumber: 1.9 Consensus size: 100
1177299 AATATTCAAA
*
1177309 TTAGTTAATATTATGATATCTTAGTAAGAATATAAAAAATAATTTATTATAATTTGTTGTTAATA
1 TTAGTTAATATTATGATATCTTAGTAAGAATATAAAAAACAATTTATTATAATTTGTTGTTAATA
1177374 TTTTAATATATGAAATATAAATTTTAAAAAATAAG
66 TTTTAATATATGAAATATAAATTTTAAAAAATAAG
* * *
1177409 TTAGTTAATCTTATGATATCTTAGTAAGAATATAAAACACAATTTATTATAATTTTTTGTTAATA
1 TTAGTTAATATTATGATATCTTAGTAAGAATATAAAAAACAATTTATTATAATTTGTTGTTAATA
1177474 TTTTAATATATGAAATATAAATTTTAAA
66 TTTTAATATATGAAATATAAATTTTAAA
1177502 TATTTTTAAG
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 89 1.00
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (100 bp):
TTAGTTAATATTATGATATCTTAGTAAGAATATAAAAAACAATTTATTATAATTTGTTGTTAATA
TTTTAATATATGAAATATAAATTTTAAAAAATAAG
Found at i:1178464 original size:71 final size:72
Alignment explanation
Indices: 1178328--1178467 Score: 264
Period size: 72 Copynumber: 2.0 Consensus size: 72
1178318 AAATTGTAAG
*
1178328 TAAAACGAAATTTAAACACAAAAAAATACATCAAATTAGAAATAAAAAAATGAGTACAATTCTTT
1 TAAAACGAAATTTAAACACAAAAAAATACATCAAATTAAAAATAAAAAAATGAGTACAATTCTTT
1178393 ATCAAAT
66 ATCAAAT
1178400 TAAAACGAAATTTAAACACAAAAAAATACATCAAATTAAAAAT-AAAAAATGAGTACAATTCTTT
1 TAAAACGAAATTTAAACACAAAAAAATACATCAAATTAAAAATAAAAAAATGAGTACAATTCTTT
1178464 ATCA
66 ATCA
1178468 TGGTGTTGGT
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
71 25 0.37
72 42 0.63
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (72 bp):
TAAAACGAAATTTAAACACAAAAAAATACATCAAATTAAAAATAAAAAAATGAGTACAATTCTTT
ATCAAAT
Found at i:1183251 original size:6 final size:6
Alignment explanation
Indices: 1183228--1183297 Score: 63
Period size: 6 Copynumber: 11.0 Consensus size: 6
1183218 AAAGAAAAAA
1183228 ATTTTT AATTTTCCT ATTTTT ATTATTT ATTTTT ACTATTTT A-TTTT
1 ATTTTT -ATTTT--T ATTTTT ATT-TTT ATTTTT A-T-TTTT ATTTTT
*
1183275 A-TTTT ATTTTC ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT
1183298 GCAAGAAAAC
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
5 10 0.18
6 22 0.40
7 12 0.22
8 10 0.18
9 1 0.02
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (6 bp):
ATTTTT
Found at i:1183260 original size:13 final size:12
Alignment explanation
Indices: 1183228--1183297 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 12
1183218 AAAGAAAAAA
1183228 ATTTTTAATTTTCCT
1 ATTTTT-ATTTT--T
1183243 ATTTTTATTATTT
1 ATTTTTATT-TTT
1183256 ATTTTTACTATTTT
1 ATTTTTA-T-TTTT
1183270 A-TTTTA-TTTT
1 ATTTTTATTTTT
*
1183280 ATTTTCATTTTT
1 ATTTTTATTTTT
1183292 ATTTTT
1 ATTTTT
1183298 GCAAGAAAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
10 5 0.10
11 4 0.08
12 9 0.19
13 13 0.27
14 8 0.17
15 9 0.19
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:1183260 original size:21 final size:21
Alignment explanation
Indices: 1183230--1183294 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
1183220 AGAAAAAAAT
1183230 TTTTAATTTTCCTATTTTTATTA
1 TTTT-ATTTT-CTATTTTTATTA
*
1183253 -TTTATTTTTACTATTTTATTTTA
1 TTTTA-TTTT-CTATTTT-TATTA
1183276 TTTTATTTTC-ATTTTTATT
1 TTTTATTTTCTATTTTTATT
1183295 TTTGCAAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
20 3 0.08
21 6 0.17
22 15 0.42
23 8 0.22
24 4 0.11
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTATTTTCTATTTTTATTA
Found at i:1183261 original size:22 final size:24
Alignment explanation
Indices: 1183230--1183284 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 24
1183220 AGAAAAAAAT
* *
1183230 TTTTAATTTTCCTATTTT-TATTA
1 TTTTATTTTTACTATTTTATATTA
*
1183253 -TTTATTTTTACTATTTTATTTTA
1 TTTTATTTTTACTATTTTATATTA
1183276 TTTTATTTT
1 TTTTATTTT
1183285 CATTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.56
23 4 0.15
24 8 0.30
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTATTTTTACTATTTTATATTA
Found at i:1187527 original size:2 final size:2
Alignment explanation
Indices: 1187520--1187550 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1187510 TAATATGCTG
1187520 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1187551 CTTCATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1189658 original size:18 final size:16
Alignment explanation
Indices: 1189616--1189658 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
1189606 TGTCGTTTGT
1189616 TTTCAAAATATTATTCA
1 TTTC-AAATATTATTCA
1189633 TTTACAAATCATTATTCAA
1 TTT-CAAAT-ATTATTC-A
1189652 TTTCAAA
1 TTTCAAA
1189659 ACGTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTCAAATATTATTCA
Found at i:1190609 original size:17 final size:18
Alignment explanation
Indices: 1190577--1190611 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1190567 CCATGATGTT
1190577 CGCCCGAGTGGGCCCACA
1 CGCCCGAGTGGGCCCACA
*
1190595 CGCCCGTGT-GGCCCACA
1 CGCCCGAGTGGGCCCACA
1190612 TGACCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.46, G:0.31, T:0.09
Consensus pattern (18 bp):
CGCCCGAGTGGGCCCACA
Found at i:1196227 original size:36 final size:36
Alignment explanation
Indices: 1196185--1196283 Score: 162
Period size: 36 Copynumber: 2.8 Consensus size: 36
1196175 TTTGAGTACT
* *
1196185 TCTGATCAAGAGACAAAGTGATAAGTGTTATAATTA
1 TCTGATCAAGTGACAAAGTGATAAGTGCTATAATTA
* *
1196221 TCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGCTATAATTA
1196257 TCTGATCAAGTGACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
1196284 GTAGCTTAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.29
Consensus pattern (36 bp):
TCTGATCAAGTGACAAAGTGATAAGTGCTATAATTA
Found at i:1198022 original size:38 final size:36
Alignment explanation
Indices: 1197962--1198035 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 36
1197952 AATCACTCTA
*
1197962 ATTAAATTAATATAATACTTATTAAGATAAGTATTAT
1 ATTAAATTAATATAATACTTATTAAAATAA-TATTAT
*
1197999 ATTAAATTTAATATTAA-ATTTATTAAAATAATATTAT
1 ATTAAA-TTAATA-TAATACTTATTAAAATAATATTAT
1198036 TTTTGGAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 12 0.36
38 18 0.55
39 3 0.09
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (36 bp):
ATTAAATTAATATAATACTTATTAAAATAATATTAT
Found at i:1198493 original size:21 final size:21
Alignment explanation
Indices: 1198469--1198531 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
1198459 ATTTTGCTTG
1198469 ATCAAAATTCATTTTCTCAAA
1 ATCAAAATTCATTTTCTCAAA
1198490 ATCAAAATTCATTTTCTCAAA
1 ATCAAAATTCATTTTCTCAAA
* *
1198511 ATCAAAATTAAATTTCTCAAA
1 ATCAAAATTCATTTTCTCAAA
1198532 CATAATTGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (21 bp):
ATCAAAATTCATTTTCTCAAA
Found at i:1199407 original size:20 final size:20
Alignment explanation
Indices: 1199368--1199407 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1199358 ACACACAACG
** *
1199368 AACGCAACAAACGCACAAAA
1 AACGCAACAAAAACAAAAAA
1199388 AACGCAACAAAAACAAAAAA
1 AACGCAACAAAAACAAAAAA
1199408 CAACAGCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.25, G:0.07, T:0.00
Consensus pattern (20 bp):
AACGCAACAAAAACAAAAAA
Found at i:1200884 original size:27 final size:26
Alignment explanation
Indices: 1200853--1200910 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
1200843 AATTCATACA
* *
1200853 TTTTTCATGCACATTAATTTATTTAG
1 TTTTTCATGAACATTAAATTATTTAG
* * *
1200879 TGTTTTGATGAACTTTAAATTCTTTAG
1 T-TTTTCATGAACATTAAATTATTTAG
1200906 TTTTT
1 TTTTT
1200911 AAGTGTTAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.24, C:0.09, G:0.10, T:0.57
Consensus pattern (26 bp):
TTTTTCATGAACATTAAATTATTTAG
Found at i:1205003 original size:22 final size:23
Alignment explanation
Indices: 1204978--1205020 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1204968 TATAATGATA
1204978 AAATTATA-ATACTATA-ATATCT
1 AAATTATATATA-TATATATATCT
1205000 AAATTATATATATATATATAT
1 AAATTATATATATATATATAT
1205021 ATATATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATTATATATATATATATATCT
Found at i:1206570 original size:72 final size:72
Alignment explanation
Indices: 1206453--1206593 Score: 219
Period size: 72 Copynumber: 2.0 Consensus size: 72
1206443 TGCCCTTATA
* * *
1206453 CAGATAAAACAAATTAGAACATACTAGTTGCACATATAGTTTAACAGATAAAAAACATGCTACTG
1 CAGATAAAACAAATCAGAACATACTAATTGCACATATAGTTTAACAAATAAAAAACATGCTACTG
1206518 GCATATT
66 GCATATT
** * *
1206525 CAGATAAAACGGATCAGAACATACTAATTGCACATATAGTTTAACAAATCAAAAACATGCTATTG
1 CAGATAAAACAAATCAGAACATACTAATTGCACATATAGTTTAACAAATAAAAAACATGCTACTG
1206590 GCAT
66 GCAT
1206594 GTTCGACCAT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (72 bp):
CAGATAAAACAAATCAGAACATACTAATTGCACATATAGTTTAACAAATAAAAAACATGCTACTG
GCATATT
Found at i:1206582 original size:36 final size:36
Alignment explanation
Indices: 1206470--1206582 Score: 95
Period size: 36 Copynumber: 3.1 Consensus size: 36
1206460 AACAAATTAG
* *
1206470 AACATACTAGTTGCACATATAGTTTAACAGATAAAA
1 AACATACTAATTGCACATATAGTTTAACAGATCAAA
* * * * ** * *
1206506 AACATGCTACTGGCATAT-TCAGATAAAACGGATC-AG
1 AACATACTAATTGCACATAT-AG-TTTAACAGATCAAA
*
1206542 AACATACTAATTGCACATATAGTTTAACAAATCAAA
1 AACATACTAATTGCACATATAGTTTAACAGATCAAA
1206578 AACAT
1 AACAT
1206583 GCTATTGGCA
Statistics
Matches: 55, Mismatches: 18, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
35 8 0.15
36 39 0.71
37 8 0.15
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.26
Consensus pattern (36 bp):
AACATACTAATTGCACATATAGTTTAACAGATCAAA
Found at i:1211748 original size:30 final size:30
Alignment explanation
Indices: 1211712--1211778 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
1211702 CCACAAGCCT
* * *
1211712 AGGCACACGGGCGTGTGTCTAAGCCGTGTG
1 AGGCACACGAGCGTGGGTCCAAGCCGTGTG
*
1211742 AGGCACACGAGTGTGGGTCCAAGCCGTGTG
1 AGGCACACGAGCGTGGGTCCAAGCCGTGTG
*
1211772 AGCCACA
1 AGGCACA
1211779 TGGCCATGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.21, C:0.25, G:0.37, T:0.16
Consensus pattern (30 bp):
AGGCACACGAGCGTGGGTCCAAGCCGTGTG
Found at i:1225120 original size:6 final size:6
Alignment explanation
Indices: 1225109--1225141 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1225099 GTTGTTAGCC
1225109 TATCTA TATCTA TATCTA TATCTA TATCTA TAT
1 TATCTA TATCTA TATCTA TATCTA TATCTA TAT
1225142 TTATTATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (6 bp):
TATCTA
Found at i:1230964 original size:26 final size:23
Alignment explanation
Indices: 1230930--1230983 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 23
1230920 AAAACATATG
1230930 AAATAATATATATATGGAAATTAAAA
1 AAATAATATATA-AT--AAATTAAAA
*
1230956 TAATAATATATAATAAATTAAAA
1 AAATAATATATAATAAATTAAAA
1230979 AAATA
1 AAATA
1230984 TTAATACATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 13 0.50
25 2 0.08
26 11 0.42
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATAATATATAATAAATTAAAA
Found at i:1230997 original size:19 final size:20
Alignment explanation
Indices: 1230960--1230997 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1230950 TTAAAATAAT
*
1230960 AATATATAATAAATTAAAAA
1 AATATATAATAAATGAAAAA
*
1230980 AATAT-TAATACATGAAAA
1 AATATATAATAAATGAAAA
1230998 GCTTAGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
AATATATAATAAATGAAAAA
Found at i:1232179 original size:14 final size:15
Alignment explanation
Indices: 1232154--1232183 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1232144 CATTTGGGCC
1232154 TGTAATTGGGTTTGA
1 TGTAATTGGGTTTGA
1232169 TGTAA-TGGGTTTGA
1 TGTAATTGGGTTTGA
1232183 T
1 T
1232184 TTTTGGGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (15 bp):
TGTAATTGGGTTTGA
Found at i:1232778 original size:22 final size:22
Alignment explanation
Indices: 1232753--1232795 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1232743 TCTCCCTATT
1232753 TTGCTACCATTTTGTTATTATG
1 TTGCTACCATTTTGTTATTATG
* *
1232775 TTGCTACTATTTTGTTGTTAT
1 TTGCTACCATTTTGTTATTAT
1232796 TGTTTGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58
Consensus pattern (22 bp):
TTGCTACCATTTTGTTATTATG
Found at i:1232861 original size:30 final size:30
Alignment explanation
Indices: 1232827--1232885 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1232817 TTATTTTATT
1232827 GTTAATTTTGTTATTAATTTAAAGGCATTC
1 GTTAATTTTGTTATTAATTTAAAGGCATTC
*
1232857 GTTAATTTTGTTATTATTTTAAAGGCATT
1 GTTAATTTTGTTATTAATTTAAAGGCATT
1232886 TGCTTGTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.53
Consensus pattern (30 bp):
GTTAATTTTGTTATTAATTTAAAGGCATTC
Found at i:1233843 original size:11 final size:11
Alignment explanation
Indices: 1233821--1233859 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
1233811 AACAAATCTT
1233821 CTCTCAAATTTC
1 CTCTC-AATTTC
1233833 CTCTCAATTTC
1 CTCTCAATTTC
1233844 CTCTCAATTT-
1 CTCTCAATTTC
1233854 CTCTCA
1 CTCTCA
1233860 TATTCATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 6 0.22
11 16 0.59
12 5 0.19
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:1236401 original size:22 final size:22
Alignment explanation
Indices: 1236375--1236446 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
1236365 TTTTAACTTT
* *
1236375 AAAACCCCACACCCTTAGCCTA
1 AAAACCCCAAACCCTTAACCTA
* *
1236397 AAAACCCTAAAACCTTAACCTA
1 AAAACCCCAAACCCTTAACCTA
*
1236419 AACACCCCAAACCC-TAACCTTA
1 AAAACCCCAAACCCTTAACC-TA
1236441 AAAACC
1 AAAACC
1236447 ATATTTCGCA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 5 0.12
22 36 0.88
ACGTcount: A:0.44, C:0.40, G:0.01, T:0.14
Consensus pattern (22 bp):
AAAACCCCAAACCCTTAACCTA
Found at i:1239388 original size:22 final size:22
Alignment explanation
Indices: 1239361--1239405 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1239351 CTGACTTTGA
*
1239361 AAAATCACCAAAAATTGTAGAG
1 AAAATCACAAAAAATTGTAGAG
1239383 AAAATCACAAAAAATTGTAGAG
1 AAAATCACAAAAAATTGTAGAG
1239405 A
1 A
1239406 TTGAATTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (22 bp):
AAAATCACAAAAAATTGTAGAG
Done.