Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 8 of 26
Found at i:1070181 original size:19 final size:19
Alignment explanation
Indices: 1070144--1070180 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1070134 AGTATACGTA
1070144 CTTTAATTGACTTTTTTTT
1 CTTTAATTGACTTTTTTTT
*
1070163 CTTTAATTTA-TTTTTTTT
1 CTTTAATTGACTTTTTTTT
1070181 TTGTTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (19 bp):
CTTTAATTGACTTTTTTTT
Found at i:1070671 original size:20 final size:20
Alignment explanation
Indices: 1070646--1070684 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1070636 TTTCTTTTGA
*
1070646 ACTAATTAAAATAATCATAT
1 ACTAATTAAAATAACCATAT
1070666 ACTAATTAAAATAACCATA
1 ACTAATTAAAATAACCATA
1070685 AATGTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (20 bp):
ACTAATTAAAATAACCATAT
Found at i:1072813 original size:5 final size:5
Alignment explanation
Indices: 1072803--1072832 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
1072793 ATTATTATAA
1072803 TTATT TTATT TTAATT TTATT TTATT TTAT
1 TTATT TTATT TT-ATT TTATT TTATT TTAT
1072833 AAAATAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:1072819 original size:11 final size:10
Alignment explanation
Indices: 1072803--1072832 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
1072793 ATTATTATAA
1072803 TTATTTTATT
1 TTATTTTATT
1072813 TTAATTTTATT
1 TT-ATTTTATT
1072824 TTATTTTAT
1 TTATTTTAT
1072833 AAAATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTATTTTATT
Found at i:1073529 original size:15 final size:15
Alignment explanation
Indices: 1073505--1073545 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1073495 TATGATCGAA
1073505 TTAAATTTAAAATAAT
1 TTAAA-TTAAAATAAT
*
1073521 TTAAATTAAAATTAT
1 TTAAATTAAAATAAT
*
1073536 TTTAATTAAA
1 TTAAATTAAA
1073546 TTTTTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTAAATTAAAATAAT
Found at i:1079277 original size:19 final size:19
Alignment explanation
Indices: 1079253--1079294 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1079243 TCTGCTTTCA
1079253 CTGTGGCCTGCCTTGAAGT
1 CTGTGGCCTGCCTTGAAGT
1079272 CTGTGGCCTGCCTTGAAGT
1 CTGTGGCCTGCCTTGAAGT
1079291 CTGT
1 CTGT
1079295 AATCAAAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.10, C:0.26, G:0.31, T:0.33
Consensus pattern (19 bp):
CTGTGGCCTGCCTTGAAGT
Found at i:1082390 original size:29 final size:29
Alignment explanation
Indices: 1082324--1082384 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
1082314 TAGCTAAACC
* *
1082324 TTAAGAGGATAAGTGAATATTTTTTAAATA
1 TTAAAAGGATAAGTG-ATATTTTTTAAAAA
1082354 TTAAAAGGATAAGTG-TATTTTTTATAAAA
1 TTAAAAGGATAAGTGATATTTTTTA-AAAA
1082383 TT
1 TT
1082385 TTAAGGGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.32
29 5 0.18
30 14 0.50
ACGTcount: A:0.43, C:0.00, G:0.15, T:0.43
Consensus pattern (29 bp):
TTAAAAGGATAAGTGATATTTTTTAAAAA
Found at i:1082738 original size:22 final size:22
Alignment explanation
Indices: 1082680--1082740 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
1082670 AAAAACTCTC
* *
1082680 TCATCATATTTTT-AAATTTTA
1 TCATTATATTTTTAAAATTATA
*
1082701 T-TTTAT-TTATTATAAAATTATA
1 TCATTATATT-TT-TAAAATTATA
1082723 TCATTATATTTTTAAAAT
1 TCATTATATTTTTAAAAT
1082741 GAAAAATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
19 2 0.06
20 5 0.16
21 2 0.06
22 14 0.45
23 6 0.19
24 2 0.06
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (22 bp):
TCATTATATTTTTAAAATTATA
Found at i:1088510 original size:23 final size:24
Alignment explanation
Indices: 1088479--1088523 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1088469 AATAATTAAA
* *
1088479 TAATAAATATTTTTTATAATAATT
1 TAATAAATAATTTTTACAATAATT
1088503 TAAT-AATAATTTTTACAATAA
1 TAATAAATAATTTTTACAATAA
1088524 ATAATTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATAAATAATTTTTACAATAATT
Found at i:1088532 original size:23 final size:23
Alignment explanation
Indices: 1088475--1088532 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
1088465 TTAAAATAAT
* * *
1088475 TAAATAATAAATATTTTTTATAA
1 TAAATAATTAATAATTTTTACAA
*
1088498 TAATTTAA-TAATAATTTTTACAA
1 TAA-ATAATTAATAATTTTTACAA
1088521 TAAATAATTAAT
1 TAAATAATTAAT
1088533 TTATTTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 3 0.11
23 22 0.79
24 3 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAATAATTAATAATTTTTACAA
Found at i:1088684 original size:22 final size:20
Alignment explanation
Indices: 1088658--1088710 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
1088648 ATAAAAAATT
1088658 TTAAAAATTTAAGCTTTTATAA
1 TTAAAAATTTAA-CTTTTA-AA
* *
1088680 TTAAAAAATTAATTTTTAAA
1 TTAAAAATTTAACTTTTAAA
1088700 TTAAATAATTT
1 TTAAA-AATTT
1088711 TATTTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.26
21 9 0.33
22 11 0.41
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TTAAAAATTTAACTTTTAAA
Found at i:1088701 original size:20 final size:22
Alignment explanation
Indices: 1088658--1088709 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 22
1088648 ATAAAAAATT
*
1088658 TTAAAAATTTAAGCTTTTATAA
1 TTAAAAAATTAAGCTTTTATAA
*
1088680 TTAAAAAATTAA-TTTTTA-AA
1 TTAAAAAATTAAGCTTTTATAA
*
1088700 TTAAATAATT
1 TTAAAAAATT
1088710 TTATTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 11 0.41
21 5 0.19
22 11 0.41
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
TTAAAAAATTAAGCTTTTATAA
Found at i:1088756 original size:39 final size:39
Alignment explanation
Indices: 1088711--1088791 Score: 112
Period size: 38 Copynumber: 2.1 Consensus size: 39
1088701 TAAATAATTT
* *
1088711 TATTTTTTTATATCTGT-AAATTTTT-ATTATTTTAAATA
1 TATTTTTTTATAT-TATCAAATTTTTAATTATTTTAAAAA
*
1088749 TATTTTTTTATATTATCAAATTTTTAATTTTTTTAAAAA
1 TATTTTTTTATATTATCAAATTTTTAATTATTTTAAAAA
1088788 TATT
1 TATT
1088792 ACTTTTTTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 2 0.05
38 21 0.55
39 15 0.39
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (39 bp):
TATTTTTTTATATTATCAAATTTTTAATTATTTTAAAAA
Found at i:1089536 original size:20 final size:20
Alignment explanation
Indices: 1089513--1089626 Score: 91
Period size: 20 Copynumber: 5.8 Consensus size: 20
1089503 ATAATTTATT
1089513 ATATTATA-ATTATATTTAAA
1 ATATTATATATTA-ATTTAAA
1089533 ATATTATATATTAATTTAAA
1 ATATTATATATTAATTTAAA
*
1089553 AT-TTAATATATTAA--TAATTT
1 ATATT-ATATATTAATTTAA--A
1089573 ATATTATATA--AATTTTAAA
1 ATATTATATATTAA-TTTAAA
*
1089592 ATAATTATATATTTATTT--A
1 AT-ATTATATATTAATTTAAA
*
1089611 ATATTATATTTTAATT
1 ATATTATATATTAATT
1089627 ATTTTTTTTA
Statistics
Matches: 78, Mismatches: 5, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
18 17 0.22
19 7 0.09
20 41 0.53
21 12 0.15
22 1 0.01
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATTATATATTAATTTAAA
Found at i:1089576 original size:15 final size:15
Alignment explanation
Indices: 1089503--1089576 Score: 57
Period size: 15 Copynumber: 4.7 Consensus size: 15
1089493 TCTTATTCAT
1089503 ATAATTTATTATATT-
1 ATAATTTA-TATATTA
1089518 ATAA-TTATAT-TTA
1 ATAATTTATATATTA
1089531 A-AATATTATATATTA
1 ATAAT-TTATATATTA
1089546 ATTTAAAATTTAATATATTA
1 A--T--AATTT-ATATATTA
1089566 ATAATTTATAT
1 ATAATTTATAT
1089577 TATATAAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 20
0.71 0.00 0.29
Matches are distributed among these distances:
12 4 0.08
13 4 0.08
14 9 0.18
15 12 0.24
16 5 0.10
18 1 0.02
19 2 0.04
20 12 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATAATTTATATATTA
Found at i:1089577 original size:33 final size:33
Alignment explanation
Indices: 1089533--1089629 Score: 94
Period size: 33 Copynumber: 2.9 Consensus size: 33
1089523 TATATTTAAA
*
1089533 ATATTATATATTAATTTAAAATTTAATATATTA-
1 ATATT-TATATTAATTTAAATTTTAATATATTAT
* *
1089566 ATAATTTATATT-ATATAAATTTTAAAATAATTAT
1 AT-ATTTATATTAATTTAAATTTTAATAT-ATTAT
*
1089600 ATATTTAT-TTAATATTATATTTTAAT-TATT
1 ATATTTATATTAAT-TTAAATTTTAATATATT
1089630 TTTTTTATGT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
32 18 0.34
33 21 0.40
34 14 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
ATATTTATATTAATTTAAATTTTAATATATTAT
Found at i:1089601 original size:38 final size:36
Alignment explanation
Indices: 1089518--1089619 Score: 88
Period size: 38 Copynumber: 2.8 Consensus size: 36
1089508 TTATTATATT
1089518 ATAATTATATTTAA-AATATTATA-TAT-TAATTTAAA
1 ATAATTATA-TTAATAAT-TTATATTATATAATTTAAA
1089553 ATTTAA-TATATTAATAATTTATATTATATAAATTTTAAA
1 A--TAATTATATTAATAATTTATATTATAT-AA-TTTAAA
* *
1089592 ATAATTATA-TATTTATTTAATATTATAT
1 ATAATTATATTAATAATTT-ATATTATAT
1089620 TTTAATTATT
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
35 10 0.18
36 10 0.18
37 14 0.25
38 15 0.27
39 7 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
ATAATTATATTAATAATTTATATTATATAATTTAAA
Found at i:1089956 original size:19 final size:19
Alignment explanation
Indices: 1089934--1089979 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
1089924 TATATAAATA
*
1089934 TTAATATAATATAATTTTT
1 TTAATATAATATAATATTT
*
1089953 TTAATAT--TTTAATATTT
1 TTAATATAATATAATATTT
1089970 TTAA-ATAATA
1 TTAATATAATA
1089980 ATTTCCAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
16 2 0.09
17 12 0.55
18 1 0.05
19 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTAATATAATATAATATTT
Found at i:1090510 original size:2 final size:2
Alignment explanation
Indices: 1090503--1090541 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1090493 AATAAATTTC
1090503 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1090542 CACGTCTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1091065 original size:2 final size:2
Alignment explanation
Indices: 1091058--1091107 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
1091048 AAAAGCCTTA
* *
1091058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1091100 AT AT AT AT
1 AT AT AT AT
1091108 TGTTGATATG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1091153 original size:72 final size:72
Alignment explanation
Indices: 1091076--1091230 Score: 283
Period size: 72 Copynumber: 2.2 Consensus size: 72
1091066 ATATATATAT
*
1091076 ATATATATATATACATATATATAAATATATATTGTTGATATGTCTCAAAATGGATAAATAGGAAG
1 ATATATATATATACATACATATAAATATATATTGTTGATATGTCTCAAAATGGATAAATAGGAAG
1091141 TTCATAC
66 TTCATAC
*
1091148 ATATATATATATACATACATATAAATATATATTGTTGATATGTCTCAAAATGGATCAATAGGAAG
1 ATATATATATATACATACATATAAATATATATTGTTGATATGTCTCAAAATGGATAAATAGGAAG
*
1091213 TTCATAT
66 TTCATAC
1091220 ATATATATATA
1 ATATATATATA
1091231 ACAACCTTTT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 80 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (72 bp):
ATATATATATATACATACATATAAATATATATTGTTGATATGTCTCAAAATGGATAAATAGGAAG
TTCATAC
Found at i:1091166 original size:18 final size:18
Alignment explanation
Indices: 1091143--1091178 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1091133 ATAGGAAGTT
*
1091143 CATACATATATATATATA
1 CATACATATAAATATATA
1091161 CATACATATAAATATATA
1 CATACATATAAATATATA
1091179 TTGTTGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (18 bp):
CATACATATAAATATATA
Found at i:1099399 original size:20 final size:21
Alignment explanation
Indices: 1099371--1099409 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1099361 TGCCTGCATC
1099371 TATCAATACAT-TGAATAATG
1 TATCAATACATCTGAATAATG
*
1099391 TATCGATACATCTGAATAA
1 TATCAATACATCTGAATAA
1099410 AAAATCAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (21 bp):
TATCAATACATCTGAATAATG
Found at i:1100831 original size:381 final size:380
Alignment explanation
Indices: 1100075--1100785 Score: 935
Period size: 381 Copynumber: 1.9 Consensus size: 380
1100065 TTTCCTATTG
* * ** * *
1100075 TTATACCATATATGAAGCTTGCCATAAGTGGTAATGGTAATCCTTTTCGTAAAAATCTAGATTTA
1 TTATACAATATAAGAAGCTTGCCATAAGTGACAATGGTAACCCTTTTCATAAAAATCTAGATTTA
* * *
1100140 CTATATATGAAGCGAATAATTACTTGTGGAATAAGGTTGACCACTAAGACTAAAACTTAATCTTA
66 CCATATATAAAGCGAATAATTACTTATGGAATAAGGTTGACCACTAAGACTAAAACTTAATCTTA
* * ****
1100205 AAGTATAAAACCCTAAATCCTTGCAAGAAAATTTATATAAGGTGAGGTAAAGGTATCCTCAAACC
131 AAGTATAAAACCCTAAATCCTTACAAGAAAATCTATATAAAACAAGGTAAAGGTATCCTCAAACC
* ** * * ** *
1100270 CAAGCTTAGCTAGGTAGCATTCATAGCATCTTTGTTTCTTTTCTTTAGCTAATTTAAGCATCGGA
196 CAAGCTCAGCTAAATAGCATACATAGCATCTTTGTTTCTTTTCCTTAGCTAACATAAGCATCAGA
* * * * * * * *
1100335 GTGTATACCGAAATACAAACTCTGATGTCTTTTAATTCTTTTTTTGTCTTGCAAAATCTTGATTG
261 GTGCACACCGAAATACAAACTCTGATGCCATCTAATTCCTTCTTTGTCTTGCAAAATCTTGATTA
*
1100400 AAGACCTAAAGAACCACCTTCTGATCCAATCATTCTCACAATTACATCAACGATTA
326 AAGACCTAAAGAA-CACCTTCTAATCCAATCATTCTCACAATTACATCAACGATTA
* *
1100456 TTATACAATATAAGAAGCTTTCCATAAGTGACAATGGTAACCCTTTTCATAAAAATCTAGATTTT
1 TTATACAATATAAGAAGCTTGCCATAAGTGACAATGGTAACCCTTTTCATAAAAATCTAGATTTA
* * * * *
1100521 CCATATGTAAAGTGAATAGTTATTTATGGAATAAGGTTAGTCGC-C-AAGACTAAAA-TTCAA-C
66 CCATATATAAAGCGAATAATTACTTATGGAATAAGGTT-GAC-CACTAAGACTAAAACTT-AATC
* * *
1100582 TTTAAAGTATGAAACTCTAAATCCTTACAAGAAAATCTATATAAAACAAGGTAAATGTATCCTCA
128 -TTAAAGTATAAAACCCTAAATCCTTACAAGAAAATCTATATAAAACAAGGTAAAGGTATCCTCA
*
1100647 AACCCAAGCTCAGCTAAATAGCATAGATAGCATCTTTGTTTCTTTTCCTTAGCTAACATAAGCAT
192 AACCCAAGCTCAGCTAAATAGCATACATAGCATCTTTGTTTCTTTTCCTTAGCTAACATAAGCAT
* * *
1100712 TAGAGTGCACATCGGAATACAAACTCTGATGCCATCTAATTCCTTCTTTGTCTTGCAAAATCTTG
257 CAGAGTGCACACCGAAATACAAACTCTGATGCCATCTAATTCCTTCTTTGTCTTGCAAAATCTTG
1100777 ATTAAAGAC
322 ATTAAAGAC
1100786 TTGAGAAATC
Statistics
Matches: 281, Mismatches: 45, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
380 3 0.01
381 274 0.98
382 3 0.01
383 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.33
Consensus pattern (380 bp):
TTATACAATATAAGAAGCTTGCCATAAGTGACAATGGTAACCCTTTTCATAAAAATCTAGATTTA
CCATATATAAAGCGAATAATTACTTATGGAATAAGGTTGACCACTAAGACTAAAACTTAATCTTA
AAGTATAAAACCCTAAATCCTTACAAGAAAATCTATATAAAACAAGGTAAAGGTATCCTCAAACC
CAAGCTCAGCTAAATAGCATACATAGCATCTTTGTTTCTTTTCCTTAGCTAACATAAGCATCAGA
GTGCACACCGAAATACAAACTCTGATGCCATCTAATTCCTTCTTTGTCTTGCAAAATCTTGATTA
AAGACCTAAAGAACACCTTCTAATCCAATCATTCTCACAATTACATCAACGATTA
Found at i:1109446 original size:2 final size:2
Alignment explanation
Indices: 1109439--1109465 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1109429 CTTAAATTAT
1109439 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1109466 CAAAATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1110283 original size:20 final size:20
Alignment explanation
Indices: 1110245--1110283 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1110235 ATTTTTATTT
*
1110245 TATTATAATTATATTTAAAA
1 TATTATAATTATATATAAAA
1110265 TATTATATATT-TATATAAA
1 TATTATA-ATTATATATAAA
1110284 TTTTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTATAATTATATATAAAA
Found at i:1110351 original size:17 final size:16
Alignment explanation
Indices: 1110302--1110367 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 16
1110292 ATGTTATTAA
1110302 TTTATATTATATAAATT
1 TTTATATTATAT-AATT
1110319 TTTAAAATATTTATATAATT
1 TTT---ATA-TTATATAATT
* *
1110339 TTTTTATTCATATTATT
1 TTTATATT-ATATAATT
1110356 TTTATATTATAT
1 TTTATATTATAT
1110368 TTCAAATCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
16 6 0.15
17 19 0.46
20 10 0.24
21 6 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATATTATATAATT
Found at i:1110533 original size:19 final size:20
Alignment explanation
Indices: 1110509--1110611 Score: 86
Period size: 19 Copynumber: 5.0 Consensus size: 20
1110499 ATATTTAATC
1110509 ATTTATATATTTATATTA-A
1 ATTTATATATTTATATTATA
*
1110528 ATTTATATTTTTTTATATTATA
1 ATTTATA--TATTTATATTATA
*
1110550 ATATAT-TATTTAAAATATTATA
1 ATTTATATATTT---ATATTATA
* *
1110572 TATTTATATATTTTTAATAT-
1 -ATTTATATATTTATATTATA
*
1110592 ATTTATATAATTATATTATA
1 ATTTATATATTTATATTATA
1110612 TACATATTAT
Statistics
Matches: 66, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
19 27 0.41
21 15 0.23
22 14 0.21
23 5 0.08
24 5 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTATATATTTATATTATA
Found at i:1110570 original size:27 final size:26
Alignment explanation
Indices: 1110540--1110623 Score: 84
Period size: 26 Copynumber: 3.2 Consensus size: 26
1110530 TTATATTTTT
1110540 TTATATTATAATATATTATTTAAAATA
1 TTATA-TATAATATATTATTTAAAATA
* *
1110567 TTATATATTTATATATT-TTTAATATA
1 TTATATA-TAATATATTATTTAAAATA
* *
1110593 TT-TATATAATTATATTATAT-ACATA
1 TTATATATAA-TATATTATTTAAAATA
1110618 TTATAT
1 TTATAT
1110624 TTATTTTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
24 2 0.04
25 16 0.33
26 17 0.35
27 13 0.27
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (26 bp):
TTATATATAATATATTATTTAAAATA
Found at i:1110690 original size:62 final size:60
Alignment explanation
Indices: 1110560--1110691 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 60
1110550 ATATATTATT
*
1110560 TAAAA-TATTATATATTTATATATTTTTAATATATTTATATAATTATATTATATACATAT
1 TAAAATTATTATATATTTATATATTTTTAATATATTTATATAATTATATTATATACATAC
* * * *
1110619 TATATTTATTTTATA-TTATATCACTTTTTAAT-TATTTATATATATTATTATTATAT-TATACC
1 TAAAATTATTATATATTTATAT-A-TTTTTAATATATTTATATA-ATTA-TATTATATACATA-C
1110681 TAAAATTATTA
1 TAAAATTATTA
1110692 AATCTTAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
59 9 0.15
60 19 0.32
61 15 0.25
62 16 0.27
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (60 bp):
TAAAATTATTATATATTTATATATTTTTAATATATTTATATAATTATATTATATACATAC
Found at i:1111679 original size:3 final size:3
Alignment explanation
Indices: 1111673--1111707 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1111663 TACTTACTAA
1111673 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1111708 CATAACCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1111797 original size:2 final size:2
Alignment explanation
Indices: 1111790--1111827 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1111780 AACATGTGAT
*
1111790 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1111828 AGTGGAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1112164 original size:22 final size:22
Alignment explanation
Indices: 1112150--1112196 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1112140 ATTAATACAT
*
1112150 ATAATATGTTATATTATATGGC
1 ATAATATGTTATATTATATGAC
*
1112172 ATAATATGTTATATTATATGGC
1 ATAATATGTTATATTATATGAC
1112194 ATA
1 ATA
1112197 GTCATCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (22 bp):
ATAATATGTTATATTATATGAC
Found at i:1112552 original size:17 final size:16
Alignment explanation
Indices: 1112530--1112564 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1112520 TATTAAATTA
*
1112530 AATAATATAAATTATAT
1 AATAATA-AAAATATAT
1112547 AATAATAAAAATATAT
1 AATAATAAAAATATAT
1112563 AA
1 AA
1112565 ACATCTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAATAAAAATATAT
Found at i:1113437 original size:43 final size:44
Alignment explanation
Indices: 1113342--1113437 Score: 117
Period size: 42 Copynumber: 2.2 Consensus size: 44
1113332 ATTAATGTTT
** *
1113342 ATATAAAAATAATTATTTTTATTTAAATTTAATTATAAATATTA
1 ATATAAAAATAATTATTAATATTTAAATTTAATTATAAATAATA
* *
1113386 ATAT-AAAATAATT-TTAATATTTTAATATT-ATTTTAAATAATA
1 ATATAAAAATAATTATTAATATTTAAAT-TTAATTATAAATAATA
1113428 ATATAAAAAT
1 ATATAAAAAT
1113438 TTAAGCTGCT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
42 25 0.56
43 16 0.36
44 4 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (44 bp):
ATATAAAAATAATTATTAATATTTAAATTTAATTATAAATAATA
Found at i:1114289 original size:22 final size:21
Alignment explanation
Indices: 1114234--1114290 Score: 53
Period size: 23 Copynumber: 2.7 Consensus size: 21
1114224 AAAATATTTA
* *
1114234 AAAAATTA-TTTTATATATTT
1 AAAAATAATTTTTATATATAT
* *
1114254 AAATATATTATTTTATTATATAT
1 AAAAATAAT-TTTTA-TATATAT
1114277 AAAAATAATTTTTA
1 AAAAATAATTTTTA
1114291 CATTAATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 5 0.18
22 10 0.36
23 13 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAAATAATTTTTATATATAT
Found at i:1115226 original size:5 final size:5
Alignment explanation
Indices: 1115216--1115257 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
1115206 AAAGTGCATT
* *
1115216 TTATA TTATA TTATT TTTTA TTATA TTATA TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT
1115258 TTTAGGGTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (5 bp):
TTATA
Found at i:1115779 original size:20 final size:19
Alignment explanation
Indices: 1115756--1115804 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1115746 AATTAAAATG
*
1115756 TATATAATATTAATTATTAA
1 TATATAATATTAA-TATAAA
* *
1115776 TATATTAAAATTTATATAAA
1 TATA-TAATATTAATATAAA
1115796 TATATAATA
1 TATATAATA
1115805 CATTATAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.17
20 13 0.54
21 7 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATAATATTAATATAAA
Found at i:1118819 original size:13 final size:13
Alignment explanation
Indices: 1118801--1118833 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1118791 ATTAAGTAAT
*
1118801 GATAACATGATAA
1 GATAACATAATAA
1118814 GATAACATAATAA
1 GATAACATAATAA
1118827 GATAACA
1 GATAACA
1118834 ACAAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
GATAACATAATAA
Found at i:1119571 original size:28 final size:29
Alignment explanation
Indices: 1119540--1119599 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
1119530 CATTTGTTGG
1119540 TATCATATTCAT-ATTA-TTTTTCATATCA
1 TATCATATT-ATAATTATTTTTTCATATCA
* *
1119568 TATCATATTTTAATTATTTTTTCATATTA
1 TATCATATTATAATTATTTTTTCATATCA
1119597 TAT
1 TAT
1119600 GATCGTATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 1 0.04
28 13 0.46
29 14 0.50
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (29 bp):
TATCATATTATAATTATTTTTTCATATCA
Found at i:1122050 original size:45 final size:44
Alignment explanation
Indices: 1121956--1122099 Score: 155
Period size: 45 Copynumber: 3.2 Consensus size: 44
1121946 GTGCTCAAGC
* * * * *
1121956 ACCAAGGCCCCAACAGTGCCGATGGTACTCAAGGCAGGTGC-CAGC
1 ACCAAGG-CCAAACAGTGCCGATGGTACTCAGGGCTGGTACAC-GA
*
1122001 ACCAAGGTCCAAACAGTGCCAATGGTACTCAGGGCTGGTACACGA
1 ACCAAGG-CCAAACAGTGCCGATGGTACTCAGGGCTGGTACACGA
* * * *
1122046 ACCAAGGCCTAGCTGGTGCCGATGGTGCTCAGGGCTGGTACACGA
1 ACCAAGGCCAAAC-AGTGCCGATGGTACTCAGGGCTGGTACACGA
1122091 ACCAAGGCC
1 ACCAAGGCC
1122100 TAGGTGGTGC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
44 4 0.05
45 80 0.94
46 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.14
Consensus pattern (44 bp):
ACCAAGGCCAAACAGTGCCGATGGTACTCAGGGCTGGTACACGA
Found at i:1122100 original size:45 final size:45
Alignment explanation
Indices: 1122016--1122116 Score: 175
Period size: 45 Copynumber: 2.2 Consensus size: 45
1122006 GGTCCAAACA
1122016 GTGCCAATGGTACTCAGGGCTGGTACACGAACCAAGGCCTAGCTG
1 GTGCCAATGGTACTCAGGGCTGGTACACGAACCAAGGCCTAGCTG
* * *
1122061 GTGCCGATGGTGCTCAGGGCTGGTACACGAACCAAGGCCTAGGTG
1 GTGCCAATGGTACTCAGGGCTGGTACACGAACCAAGGCCTAGCTG
1122106 GTGCCAATGGT
1 GTGCCAATGGT
1122117 TGCCCAAGGC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.22, C:0.25, G:0.35, T:0.19
Consensus pattern (45 bp):
GTGCCAATGGTACTCAGGGCTGGTACACGAACCAAGGCCTAGCTG
Found at i:1126814 original size:52 final size:51
Alignment explanation
Indices: 1126729--1126852 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
1126719 ATATGAAAAG
* *
1126729 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
1126780 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
1126832 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1126853 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:1126865 original size:51 final size:51
Alignment explanation
Indices: 1126729--1126872 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
1126719 ATATGAAAAG
*
1126729 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
1126781 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
1126832 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1126873 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1126879 original size:13 final size:13
Alignment explanation
Indices: 1126861--1126885 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1126851 CAAAGATCAG
1126861 TGTATCGATACAA
1 TGTATCGATACAA
1126874 TGTATCGATACA
1 TGTATCGATACA
1126886 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1126953 original size:20 final size:20
Alignment explanation
Indices: 1126924--1126981 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1126914 GCAGTAGCTT
1126924 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
1126943 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
1126963 TTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
1126982 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:1127762 original size:32 final size:33
Alignment explanation
Indices: 1127700--1127767 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
1127690 ATGTTTAAAG
*
1127700 TATTTTATATTTATATAAATTTTGATACATTAA
1 TATTTTATATTTATATAAATTTTGAGACATTAA
* * * *
1127733 TATTTTGTA-TTATATATATTTTTAGACATTCA
1 TATTTTATATTTATATAAATTTTGAGACATTAA
1127765 TAT
1 TAT
1127768 ATTCATGTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 22 0.73
33 8 0.27
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (33 bp):
TATTTTATATTTATATAAATTTTGAGACATTAA
Found at i:1130353 original size:5 final size:5
Alignment explanation
Indices: 1130345--1130374 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1130335 AAAAAATACT
1130345 ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA
1130375 TAGTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:1131189 original size:20 final size:19
Alignment explanation
Indices: 1131153--1131191 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1131143 ATTTATAAAT
1131153 TATAAATTATAAAAATTTA
1 TATAAATTATAAAAATTTA
*
1131172 TATAAATATATAATAATTTA
1 TATAAAT-TATAAAAATTTA
1131192 AACATGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TATAAATTATAAAAATTTA
Found at i:1135194 original size:2 final size:2
Alignment explanation
Indices: 1135187--1135212 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1135177 AGCAGCCCAA
1135187 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1135213 GAAACAGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1135975 original size:19 final size:19
Alignment explanation
Indices: 1135932--1135995 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
1135922 TTCATAAATT
*
1135932 TTAAA-AATTATATTTATA
1 TTAAATAATTATAATTATA
1135950 -TATAATAATTATAATTATA
1 TTA-AATAATTATAATTATA
* *
1135969 TTAAATAATAATAAATA-A
1 TTAAATAATTATAATTATA
*
1135987 TAAAATAAT
1 TTAAATAAT
1135996 AGTACGTGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.05
18 11 0.28
19 24 0.62
20 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAATAATTATAATTATA
Found at i:1136287 original size:2 final size:2
Alignment explanation
Indices: 1136280--1136311 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1136270 AACTATTTGT
1136280 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
1136312 AAAAGCCAAG
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):
TC
Found at i:1138428 original size:15 final size:15
Alignment explanation
Indices: 1138408--1138449 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
1138398 TTTTTTTAAA
1138408 AAAATTATAAATTTT
1 AAAATTATAAATTTT
*
1138423 AAAATT-TAAAATTT
1 AAAATTATAAATTTT
*
1138437 AAATTTATTAAAT
1 AAAATTA-TAAAT
1138450 ATTATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 12 0.55
15 6 0.27
16 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATTATAAATTTT
Found at i:1138477 original size:13 final size:14
Alignment explanation
Indices: 1138461--1138493 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1138451 TTATATTTTA
*
1138461 AAATTAATTATA-T
1 AAATTAATTAAATT
1138474 AAATTAATTAAATT
1 AAATTAATTAAATT
1138488 AAATTA
1 AAATTA
1138494 TAAATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATTAATTAAATT
Found at i:1139446 original size:27 final size:27
Alignment explanation
Indices: 1139388--1139467 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
1139378 TAATCATGTA
* * *
1139388 ATAAAAA-TAATATAAATATGATACAAT
1 ATAAAAATTAA-ATAAATATAAAAAAAT
1139415 ATAAAAATTAAATAAATATAAAAAAAT
1 ATAAAAATTAAATAAATATAAAAAAAT
*
1139442 -TTAAAATTAAAATAAA-ATTAAAAAAA
1 ATAAAAATT-AAATAAATA-TAAAAAAA
1139468 AATGAAATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 8 0.17
27 35 0.76
28 3 0.07
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (27 bp):
ATAAAAATTAAATAAATATAAAAAAAT
Found at i:1139448 original size:17 final size:17
Alignment explanation
Indices: 1139428--1139477 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
1139418 AAAATTAAAT
*
1139428 AAATATAAAA-AAATTTA
1 AAAT-TAAAATAAAATTA
1139445 AAATTAAAATAAAATTA
1 AAATTAAAATAAAATTA
* *
1139462 AAA-AAAAATGAAATTA
1 AAATTAAAATAAAATTA
1139478 TCACGTGGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
AAATTAAAATAAAATTA
Found at i:1139475 original size:27 final size:27
Alignment explanation
Indices: 1139418--1139477 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
1139408 ATACAATATA
**
1139418 AAAATT-AAATAAATATAAAAAAATTT
1 AAAATTAAAATAAATATAAAAAAAAAT
1139444 AAAATTAAAATAAA-ATTAAAAAAAAAT
1 AAAATTAAAATAAATA-TAAAAAAAAAT
*
1139471 GAAATTA
1 AAAATTA
1139478 TCACGTGGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.27
Consensus pattern (27 bp):
AAAATTAAAATAAATATAAAAAAAAAT
Found at i:1141008 original size:32 final size:31
Alignment explanation
Indices: 1140945--1141018 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 31
1140935 ATATTAATTG
*
1140945 TAAATTTGAT-AAATTAAACATAATTATTAA
1 TAAATTTGATAAAATTAAACATAATTACTAA
* *
1140975 TAAATTTGATAAATATTATATATAATTACTAA
1 TAAATTTGATAAA-ATTAAACATAATTACTAA
*
1141007 TAAATTGGATAA
1 TAAATTTGATAA
1141019 CCATTAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 10 0.26
31 2 0.05
32 26 0.68
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (31 bp):
TAAATTTGATAAAATTAAACATAATTACTAA
Found at i:1141822 original size:21 final size:21
Alignment explanation
Indices: 1141798--1141848 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1141788 CTATTGATAC
*
1141798 AAAAGTTATCA-AATTATATAA
1 AAAAGTTATCATAAGTATAT-A
*
1141819 AAAAGTTATCATAAGTATATT
1 AAAAGTTATCATAAGTATATA
1141840 AAAAGTTAT
1 AAAAGTTAT
1141849 TAAAATTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (21 bp):
AAAAGTTATCATAAGTATATA
Found at i:1141945 original size:20 final size:20
Alignment explanation
Indices: 1141901--1141974 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
1141891 AAAGGTTCCT
* * *
1141901 AAATTATATCACAAGTTATTT
1 AAATTATATTA-AATTTATTA
*
1141922 AAATTCTA-TAAATATTATTA
1 AAATTATATTAAAT-TTATTA
1141942 AAATTATATTAAATTTATTA
1 AAATTATATTAAATTTATTA
*
1141962 AAATCATATTAAA
1 AAATTATATTAAA
1141975 AACTATTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.04
20 31 0.69
21 12 0.27
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.43
Consensus pattern (20 bp):
AAATTATATTAAATTTATTA
Found at i:1141951 original size:11 final size:11
Alignment explanation
Indices: 1141937--1141975 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1141927 CTATAAATAT
1141937 TATTAAAATTA
1 TATTAAAATTA
1141948 TATT-AAATT-
1 TATTAAAATTA
*
1141957 TATTAAAATCA
1 TATTAAAATTA
1141968 TATTAAAA
1 TATTAAAA
1141976 ACTATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 4 0.16
10 9 0.36
11 12 0.48
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAAATTA
Found at i:1141996 original size:20 final size:21
Alignment explanation
Indices: 1141957--1142005 Score: 82
Period size: 20 Copynumber: 2.4 Consensus size: 21
1141947 ATATTAAATT
*
1141957 TATTAAAATCATATTAAAAAC
1 TATTAAAATCACATTAAAAAC
1141978 TATTAAAATCACA-TAAAAAC
1 TATTAAAATCACATTAAAAAC
1141998 TATTAAAA
1 TATTAAAA
1142006 GCATATCAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (21 bp):
TATTAAAATCACATTAAAAAC
Found at i:1142361 original size:20 final size:20
Alignment explanation
Indices: 1142336--1142377 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1142326 GTTACTTATT
1142336 ATTATACTAATGTTATCAAA
1 ATTATACTAATGTTATCAAA
* * *
1142356 ATTATATTAATTTTATTAAA
1 ATTATACTAATGTTATCAAA
1142376 AT
1 AT
1142378 CATATTAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTATACTAATGTTATCAAA
Found at i:1142394 original size:21 final size:21
Alignment explanation
Indices: 1142368--1142424 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
1142358 TATATTAATT
* *
1142368 TTATTAAAATCATATTAAAGA
1 TTATTAAAATCATATAAAAAA
1142389 TTATTAAAATCATATAAAAAA
1 TTATTAAAATCATATAAAAAA
*
1142410 TTATTAAAAGCATAT
1 TTATTAAAATCATAT
1142425 CAATTGTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (21 bp):
TTATTAAAATCATATAAAAAA
Found at i:1145923 original size:17 final size:17
Alignment explanation
Indices: 1145901--1145938 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1145891 GATATCCATC
*
1145901 AAATATTCAAATTTCTT
1 AAATATTCAAATTTATT
*
1145918 AAATATTTAAATTTATT
1 AAATATTCAAATTTATT
1145935 AAAT
1 AAAT
1145939 CAAATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATATTCAAATTTATT
Found at i:1146545 original size:9 final size:9
Alignment explanation
Indices: 1146533--1146581 Score: 53
Period size: 9 Copynumber: 5.0 Consensus size: 9
1146523 TTTTTATATG
1146533 ATTTTAATA
1 ATTTTAATA
1146542 ATTTTTTATATA
1 A--TTTTA-ATA
*
1146554 ATTTTGATA
1 ATTTTAATA
1146563 ATTTTAATA
1 ATTTTAATA
1146572 ATATTTAATA
1 AT-TTTAATA
1146582 CAATTTTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
9 14 0.41
10 11 0.32
11 5 0.15
12 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (9 bp):
ATTTTAATA
Found at i:1146546 original size:20 final size:20
Alignment explanation
Indices: 1146503--1146567 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
1146493 TTTAATAGTT
* **
1146503 TTTTTATAAGATTTTGATGG
1 TTTTTATATGATTTTGATAA
*
1146523 TTTTTATATGATTTTAATAA
1 TTTTTATATGATTTTGATAA
*
1146543 TTTTTTATATAATTTTGATAA
1 -TTTTTATATGATTTTGATAA
1146564 TTTT
1 TTTT
1146568 AATAATATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 20 0.53
21 18 0.47
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (20 bp):
TTTTTATATGATTTTGATAA
Found at i:1146547 original size:21 final size:21
Alignment explanation
Indices: 1146523--1146567 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1146513 ATTTTGATGG
*
1146523 TTTTTATATGATTTTAATAAT
1 TTTTTATATAATTTTAATAAT
*
1146544 TTTTTATATAATTTTGATAAT
1 TTTTTATATAATTTTAATAAT
1146565 TTT
1 TTT
1146568 AATAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTTATATAATTTTAATAAT
Found at i:1146619 original size:21 final size:21
Alignment explanation
Indices: 1146560--1146694 Score: 76
Period size: 21 Copynumber: 6.4 Consensus size: 21
1146550 TATAATTTTG
* * *
1146560 ATAATTTTAATAATATTTAAT
1 ATAATTTTGATAATTTTTGAT
*
1146581 ACAATTTT-AGT-ATCTTTTGAT
1 ATAATTTTGA-TAAT-TTTTGAT
* *
1146602 ATTATTTTGATAATTTTTTAT
1 ATAATTTTGATAATTTTTGAT
** *
1146623 ATAATTTTGATAAGATTTGGT
1 ATAATTTTGATAATTTTTGAT
** *
1146644 ATAATTTTTGATAACCTTTAAT
1 ATAA-TTTTGATAATTTTTGAT
* ** *
1146666 ATGATTTTCTTAACTTTTGAT
1 ATAATTTTGATAATTTTTGAT
*
1146687 AAAATTTT
1 ATAATTTT
1146695 CGATTTTGAT
Statistics
Matches: 87, Mismatches: 22, Indels: 10
0.73 0.18 0.08
Matches are distributed among these distances:
20 3 0.03
21 65 0.75
22 19 0.22
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.54
Consensus pattern (21 bp):
ATAATTTTGATAATTTTTGAT
Found at i:1146784 original size:21 final size:21
Alignment explanation
Indices: 1146758--1146813 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
1146748 GAAATGTGAT
*
1146758 AACTTTTGATATAATTAAAAA
1 AACTTTTAATATAATTAAAAA
* *
1146779 AACTTTTTATATAATTATAAA
1 AACTTTTAATATAATTAAAAA
*
1146800 AACTTATAATATAA
1 AACTTTTAATATAA
1146814 GGCATCAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (21 bp):
AACTTTTAATATAATTAAAAA
Found at i:1147006 original size:21 final size:22
Alignment explanation
Indices: 1146975--1147022 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
1146965 TTTCTAATCT
1146975 ATTTTCGATAAATTTTGAT-ATA
1 ATTTTCGAT-AATTTTGATAATA
*
1146997 ATTTT-GATAATTTTTATAATA
1 ATTTTCGATAATTTTGATAATA
1147018 ATTTT
1 ATTTT
1147023 TGTAACTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 11 0.46
22 5 0.21
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (22 bp):
ATTTTCGATAATTTTGATAATA
Found at i:1147053 original size:21 final size:21
Alignment explanation
Indices: 1147029--1147075 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1147019 TTTTTGTAAC
*
1147029 TTTTGTTAA-CTTTAGAAATAA
1 TTTTATTAACCTTTA-AAATAA
*
1147050 TTTTATTAACCTTTAAAATGA
1 TTTTATTAACCTTTAAAATAA
1147071 TTTTA
1 TTTTA
1147076 ATATGCTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.51
Consensus pattern (21 bp):
TTTTATTAACCTTTAAAATAA
Found at i:1157612 original size:3 final size:3
Alignment explanation
Indices: 1157606--1157637 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1157596 AGATGATGAA
*
1157606 AAG AAG AAG AAG AAG AAG AAG AAG AGG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1157638 AATAGCATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1158310 original size:21 final size:21
Alignment explanation
Indices: 1158286--1158328 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1158276 ATTTTTAATT
*
1158286 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAAAATA
1158307 TAAATATTAATATAAAAAATA
1 TAAATATTAATATAAAAAATA
1158328 T
1 T
1158329 TTTTTAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAAAATA
Found at i:1164921 original size:21 final size:21
Alignment explanation
Indices: 1164883--1164930 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
1164873 ATTTTAATAT
1164883 AATTTTTAAAATCTTA-TTCA
1 AATTTTTAAAATCTTATTTCA
*
1164903 AATTTTTAAAGAT-TATATTTTA
1 AATTTTTAAA-ATCT-TATTTCA
1164925 AATTTT
1 AATTTT
1164931 GAATTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 11 0.46
21 4 0.17
22 9 0.38
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (21 bp):
AATTTTTAAAATCTTATTTCA
Found at i:1166255 original size:50 final size:50
Alignment explanation
Indices: 1165898--1166251 Score: 386
Period size: 50 Copynumber: 7.1 Consensus size: 50
1165888 GTATATTTTA
* * * * *
1165898 TGTTGACTATTCTTTACCAATCTTT-AGCAATAGAGAGAGGTAATCGTAAT
1 TGTTGACTATTCTTCACCAACCTTTGA-TAATAGAGAGAGGTGACCGTAAT
* * * *
1165948 TGTTGACTATTTTTCACTAACTTTTGATAATAAAGAGAGGTGACCGTAAT
1 TGTTGACTATTCTTCACCAACCTTTGATAATAGAGAGAGGTGACCGTAAT
* * * * *
1165998 TGTTGACTATTTTTTACCAACCTTTGATAATCGAGAGAGGTGGCTGTAAT
1 TGTTGACTATTCTTCACCAACCTTTGATAATAGAGAGAGGTGACCGTAAT
* * * * *
1166048 TATTGACTATTTTTCACCAACCTTTGATAATCGAGAGAGGTGGCCATAAT
1 TGTTGACTATTCTTCACCAACCTTTGATAATAGAGAGAGGTGACCGTAAT
*
1166098 TGTTGACCATTCTTCACCAACCTTTGATAATAGAGAGAGGTGACCGTAAT
1 TGTTGACTATTCTTCACCAACCTTTGATAATAGAGAGAGGTGACCGTAAT
* * * * * * *
1166148 TATTAACTATTCTTCACAAACTTTTGACAATAAAGAGAGATGACCGTAAT
1 TGTTGACTATTCTTCACCAACCTTTGATAATAGAGAGAGGTGACCGTAAT
* * * * * * *
1166198 TATTAACTATTCTTCACCAGCCATTGACAATAGAGAGAGGTGATCATAAT
1 TGTTGACTATTCTTCACCAACCTTTGATAATAGAGAGAGGTGACCGTAAT
1166248 TGTT
1 TGTT
1166252 AACTTTAAGC
Statistics
Matches: 260, Mismatches: 43, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
50 259 1.00
51 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (50 bp):
TGTTGACTATTCTTCACCAACCTTTGATAATAGAGAGAGGTGACCGTAAT
Found at i:1170656 original size:50 final size:50
Alignment explanation
Indices: 1170599--1170809 Score: 280
Period size: 50 Copynumber: 4.2 Consensus size: 50
1170589 CAAGTAGGAG
1170599 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCGT
* * * * *
1170649 AATTGTTGACTATTCTTCATCAACCTTTGATAATCGAGAGAGGTAGTCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCGT
* ***
1170699 AATTGTTGACTATTCTTCACCAACATTTGTA-AATAGAGAGAGGTGATAGT
1 AATTGTTGACTATTCTTCACCAACCTTTG-ACAATAGAGAGAGGTGGCCGT
* * *
1170749 AATTGTTGACTATTCTTCATCAACCATTGGCAATAGAGAGAGGTGGCCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCGT
* *
1170799 AGTTATTGACT
1 AATTGTTGACT
1170810 TTAAGCAACT
Statistics
Matches: 139, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
50 138 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (50 bp):
AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCGT
Found at i:1172801 original size:22 final size:22
Alignment explanation
Indices: 1172776--1172819 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1172766 ATAATTGCAT
1172776 AATATATTATTATATCTATTTA
1 AATATATTATTATATCTATTTA
1172798 AATATATTATTATATCTATTTA
1 AATATATTATTATATCTATTTA
1172820 CAAAGAAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATATTATTATATCTATTTA
Found at i:1172854 original size:10 final size:10
Alignment explanation
Indices: 1172840--1172876 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1172830 AAGACAAGTT
1172840 TTTAAAAGCT-
1 TTTAAAA-CTC
1172850 TTT-AAACTC
1 TTTAAAACTC
1172859 TTTAAAACTC
1 TTTAAAACTC
1172869 TTTAAAAC
1 TTTAAAAC
1172877 CAATGTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 2 0.08
9 6 0.24
10 17 0.68
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.41
Consensus pattern (10 bp):
TTTAAAACTC
Found at i:1176520 original size:12 final size:12
Alignment explanation
Indices: 1176505--1176530 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1176495 TATTATCAGA
1176505 TTAATTATTTAT
1 TTAATTATTTAT
1176517 TTAATTATTTAT
1 TTAATTATTTAT
1176529 TT
1 TT
1176531 TTATTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTAATTATTTAT
Found at i:1178113 original size:13 final size:13
Alignment explanation
Indices: 1178095--1178121 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1178085 TTATTTCACA
1178095 AAAAATATTTTTT
1 AAAAATATTTTTT
1178108 AAAAATATTTTTT
1 AAAAATATTTTTT
1178121 A
1 A
1178122 TATTTCCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAAATATTTTTT
Found at i:1178491 original size:16 final size:17
Alignment explanation
Indices: 1178470--1178502 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1178460 CATTTAATAT
1178470 TTTAATA-AAAATATTA
1 TTTAATACAAAATATTA
1178486 TTTAATACAAAATATTA
1 TTTAATACAAAATATTA
1178503 ATATATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAATACAAAATATTA
Found at i:1178624 original size:49 final size:48
Alignment explanation
Indices: 1178571--1178677 Score: 114
Period size: 51 Copynumber: 2.2 Consensus size: 48
1178561 AAAATGTTTT
*
1178571 TATTAATA-TTTTAATAATAAATATAT-AATTATACTTTATAAATATT-TAA-
1 TATTAATATTTTTAAT-ATAAAAATATCAA-TATA-TTT-T-AATATTGTAAG
1178620 TATTAAATATTTTTTAATATAAAAATATCAATATATTTTAATATTGTAAG
1 TATT-AATA-TTTTTAATATAAAAATATCAATATATTTTAATATTGTAAG
1178670 TATTAATA
1 TATTAATA
1178678 GAAATAATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
48 6 0.12
49 12 0.24
50 11 0.22
51 13 0.25
52 9 0.18
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (48 bp):
TATTAATATTTTTAATATAAAAATATCAATATATTTTAATATTGTAAG
Found at i:1178677 original size:25 final size:23
Alignment explanation
Indices: 1178576--1178677 Score: 69
Period size: 24 Copynumber: 4.0 Consensus size: 23
1178566 GTTTTTATTA
* *
1178576 ATATTTTAATAATAAATATATAATT
1 ATATTTTAATATTTAATAT-TAA-T
1178601 ATACTTTATAAATATTTAATATTAAAT
1 ATA-TTT-T-AATATTTAATATT-AAT
* ** *
1178628 ATTTTTTAATATAAAAATATCAAT
1 ATATTTTAATAT-TTAATATTAAT
1178652 ATATTTTAATATTGTAAGTATTAAT
1 ATATTTTAATATT-TAA-TATTAAT
1178677 A
1 A
1178678 GAAATAATAT
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
24 21 0.35
25 16 0.27
26 6 0.10
27 5 0.08
28 12 0.20
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATTTTAATATTTAATATTAAT
Found at i:1178718 original size:10 final size:10
Alignment explanation
Indices: 1178703--1178729 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1178693 TAATTATTGC
1178703 AATATTTTTA
1 AATATTTTTA
1178713 AATATTTTTA
1 AATATTTTTA
1178723 AATATTT
1 AATATTT
1178730 ATAATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
AATATTTTTA
Found at i:1178875 original size:15 final size:15
Alignment explanation
Indices: 1178857--1178909 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 15
1178847 AAAATTTTTA
1178857 ATAATAAATATTATT
1 ATAATAAATATTATT
*
1178872 ATAATAGTTTAAATATTAAT
1 AT-A-A---TAAATATTATT
1178892 ATAATAAATATTATT
1 ATAATAAATATTATT
1178907 ATA
1 ATA
1178910 CTATTTAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
15 15 0.48
16 1 0.03
17 1 0.03
18 1 0.03
19 1 0.03
20 12 0.39
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
ATAATAAATATTATT
Found at i:1178958 original size:14 final size:13
Alignment explanation
Indices: 1178876--1178963 Score: 56
Period size: 15 Copynumber: 6.5 Consensus size: 13
1178866 ATTATTATAA
1178876 TAGT-TTAAATAT
1 TAGTATTAAATAT
*
1178888 TAATATAATAAATAT
1 TAGTAT--TAAATAT
* *
1178903 TATTA-T-ACTATT
1 TAGTATTAAATA-T
1178915 TAGTATTAAATAT
1 TAGTATTAAATAT
*
1178928 TACTATTTGAAATAT
1 TAGTA-TT-AAATAT
1178943 TAGTATTAATATAT
1 TAGTATTAA-ATAT
*
1178957 TAATATT
1 TAGTATT
1178964 TAAAAAAATA
Statistics
Matches: 59, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
11 3 0.05
12 9 0.15
13 9 0.15
14 17 0.29
15 21 0.36
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (13 bp):
TAGTATTAAATAT
Found at i:1179045 original size:12 final size:12
Alignment explanation
Indices: 1179025--1179057 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1179015 TTATTATTTG
1179025 AAAAA-TAAAAA
1 AAAAATTAAAAA
1179036 AAAAATTAAAAA
1 AAAAATTAAAAA
*
1179048 AATAATTAAA
1 AAAAATTAAA
1179058 CAGTAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAATTAAAAA
Found at i:1179139 original size:14 final size:15
Alignment explanation
Indices: 1179115--1179147 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1179105 ATTTTTAAAT
1179115 TTTTTTAAAAATTAA
1 TTTTTTAAAAATTAA
1179130 TTTTTTAAAAATTAA
1 TTTTTTAAAAATTAA
1179145 TTT
1 TTT
1179148 CAGTGGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTTTAAAAATTAA
Found at i:1179612 original size:17 final size:19
Alignment explanation
Indices: 1179582--1179619 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1179572 AATATAATAA
*
1179582 AAAAATTATCATTTTT-TT
1 AAAAATTATAATTTTTATT
1179600 AAAAATTA-AATTTTTATT
1 AAAAATTATAATTTTTATT
1179618 AA
1 AA
1179620 TTAAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAAATTATAATTTTTATT
Found at i:1179650 original size:25 final size:23
Alignment explanation
Indices: 1179609--1179663 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
1179599 TAAAAATTAA
*
1179609 ATTTT-TAT-TAATTAAATATTT
1 ATTTTATATATAATAAAATATTT
1179630 ATATTTGATATATAATAAAATATTT
1 AT-TTT-ATATATAATAAAATATTT
1179655 ATTTTATAT
1 ATTTTATAT
1179664 TTTTTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 2 0.07
22 3 0.10
23 4 0.14
24 6 0.21
25 14 0.48
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTTATATATAATAAAATATTT
Found at i:1179673 original size:23 final size:25
Alignment explanation
Indices: 1179617--1179663 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1179607 AAATTTTTAT
*
1179617 TAATTAAATATTTATATTTGATATA
1 TAATAAAATATTTATATTTGATATA
1179642 TAATAAAATATTTAT-TTT-ATAT
1 TAATAAAATATTTATATTTGATAT
1179664 TTTTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 3 0.14
25 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TAATAAAATATTTATATTTGATATA
Found at i:1179693 original size:21 final size:21
Alignment explanation
Indices: 1179599--1179708 Score: 53
Period size: 22 Copynumber: 4.9 Consensus size: 21
1179589 ATCATTTTTT
1179599 TAAAAATTAAATTTTTATTAATTA
1 TAAAAATT--ATTTTTA-TAATTA
* * * *
1179623 -AATATTTATATTTGATATATAA
1 TAAAAATTAT-TTTTATA-ATTA
* *
1179645 TAAAATATT-TATTTTATATTTT
1 TAAAA-ATTAT-TTTTATAATTA
*
1179667 TTAAAATTATTTTTATAATTA
1 TAAAAATTATTTTTATAATTA
1179688 TAAAAAATATGATTTTTATAA
1 T-AAAAAT-T-ATTTTTATAA
1179709 AAAATATAAA
Statistics
Matches: 64, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
21 17 0.27
22 18 0.28
23 17 0.27
24 12 0.19
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TAAAAATTATTTTTATAATTA
Found at i:1179999 original size:23 final size:21
Alignment explanation
Indices: 1179964--1180007 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
1179954 TTGTATTATT
*
1179964 TTATTTAAAATAAATTAATTA
1 TTATTTAAAATAAACTAATTA
1179985 TTATTTAAAAGATAAACTAATTA
1 TTATTT-AAA-ATAAACTAATTA
1180008 AATAAAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 3 0.15
23 11 0.55
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
TTATTTAAAATAAACTAATTA
Found at i:1180045 original size:16 final size:18
Alignment explanation
Indices: 1180007--1180045 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
1179997 TAAACTAATT
1180007 AAATAAAGTATTTATTAA
1 AAATAAAGTATTTATTAA
*
1180025 TAATAAA-TATTT-TTAA
1 AAATAAAGTATTTATTAA
1180041 AAATA
1 AAATA
1180046 TTAAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 8 0.42
17 5 0.26
18 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
AAATAAAGTATTTATTAA
Found at i:1185761 original size:42 final size:42
Alignment explanation
Indices: 1185664--1185761 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
1185654 TTGTGTCGTG
* * * * *
1185664 TAAGATGATTAAAAATTGGAGATTTGTATAAGTTGTATTGTA
1 TAAGATGATTAAAAAGTGAAAATTCGTATAAGTTATATTGTA
* *
1185706 TAAGATGACTAAAAAGTGAAAATTCGTATAAGTTATGTTGTA
1 TAAGATGATTAAAAAGTGAAAATTCGTATAAGTTATATTGTA
*
1185748 TAAGATAATTAAAA
1 TAAGATGATTAAAA
1185762 GGTGGAGATT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.36
Consensus pattern (42 bp):
TAAGATGATTAAAAAGTGAAAATTCGTATAAGTTATATTGTA
Found at i:1186106 original size:14 final size:15
Alignment explanation
Indices: 1186082--1186110 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1186072 ATTTTCATGT
1186082 AAATTTATTTATTTA
1 AAATTTATTTATTTA
1186097 AAATTT-TTTATTTA
1 AAATTTATTTATTTA
1186111 GACTCATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AAATTTATTTATTTA
Found at i:1187205 original size:14 final size:12
Alignment explanation
Indices: 1187178--1187217 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 12
1187168 TAAAGAGCTT
1187178 AAATTTAATTTA
1 AAATTTAATTTA
1187190 AAATTTAATTTTTA
1 AAATTTAA--TTTA
1187204 AAATTTAAATTTA
1 AAATTT-AATTTA
1187217 A
1 A
1187218 TTTAAGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 8 0.32
13 5 0.20
14 10 0.40
15 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AAATTTAATTTA
Found at i:1188075 original size:25 final size:25
Alignment explanation
Indices: 1188044--1188100 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
1188034 TTTATTTTAT
1188044 ATATAAAAATTACATA-A-TATATAA
1 ATATAAAAATTA-ATATATTATATAA
1188068 A-ATATAAAATTAATATATTATATAA
1 ATATA-AAAATTAATATATTATATAA
*
1188093 TTATAAAA
1 ATATAAAA
1188101 TGGACATACC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 6 0.21
24 9 0.32
25 10 0.36
26 3 0.11
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
ATATAAAAATTAATATATTATATAA
Found at i:1188097 original size:24 final size:24
Alignment explanation
Indices: 1188044--1188101 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
1188034 TTTATTTTAT
1188044 ATATAAAAATTACATAATATATAAA
1 ATAT-AAAATTACATAATATATAAA
1188069 ATATAAAATTA-AT-ATATTATATAA
1 ATATAAAATTACATAATA-TATA-AA
*
1188093 TTATAAAAT
1 ATATAAAAT
1188102 GGACATACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 3 0.10
23 6 0.20
24 17 0.57
25 4 0.13
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATAAAATTACATAATATATAAA
Found at i:1191086 original size:2 final size:2
Alignment explanation
Indices: 1191079--1191127 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
1191069 AATAATGGCA
* * *
1191079 AT AT AT AT GAT AT AT AT A- AT AT AC AT TT AT AT TT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1191121 AT AT AT A
1 AT AT AT A
1191128 ATGTAGGAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1192015 original size:12 final size:14
Alignment explanation
Indices: 1191998--1192030 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1191988 AGACATATAC
1191998 ATATTT-TAAAT-T
1 ATATTTATAAATAT
1192010 ATATTTATAAATAT
1 ATATTTATAAATAT
1192024 ATATTTA
1 ATATTTA
1192031 ATTTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 5 0.26
14 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATTTATAAATAT
Found at i:1192484 original size:17 final size:17
Alignment explanation
Indices: 1192455--1192490 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
1192445 ACTTGAATTT
1192455 AAAAATTTTAATT-ATG
1 AAAAATTTTAATTCATG
1192471 AAAAATTTTAAATTCATG
1 AAAAATTTT-AATTCATG
1192489 AA
1 AA
1192491 TTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 4 0.22
18 5 0.28
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (17 bp):
AAAAATTTTAATTCATG
Found at i:1192512 original size:7 final size:7
Alignment explanation
Indices: 1192473--1192564 Score: 112
Period size: 7 Copynumber: 13.0 Consensus size: 7
1192463 TAATTATGAA
1192473 AAATTTT
1 AAATTTT
*
1192480 AAATTCAT
1 AAATT-TT
* *
1192488 GAATTTA
1 AAATTTT
* *
1192495 AAAATTA
1 AAATTTT
1192502 AAATTTT
1 AAATTTT
1192509 AAATTTT
1 AAATTTT
1192516 AAATTTT
1 AAATTTT
*
1192523 AAAGTTT
1 AAATTTT
1192530 AAATTTT
1 AAATTTT
1192537 AAATTTT
1 AAATTTT
*
1192544 AAAGTTT
1 AAATTTT
1192551 AAATTTT
1 AAATTTT
1192558 AAATTTT
1 AAATTTT
1192565 CAAACATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
7 67 0.93
8 5 0.07
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (7 bp):
AAATTTT
Found at i:1198602 original size:7 final size:7
Alignment explanation
Indices: 1198590--1198623 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1198580 ACGATAAATA
1198590 TTATTTT
1 TTATTTT
1198597 TTATTTT
1 TTATTTT
1198604 TTATTTT
1 TTATTTT
*
1198611 AT-TTTT
1 TTATTTT
1198617 TTATTTT
1 TTATTTT
1198624 AAAAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTATTTT
Found at i:1198612 original size:12 final size:13
Alignment explanation
Indices: 1198595--1198624 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1198585 AAATATTATT
1198595 TTTTA-TTTTTTA
1 TTTTATTTTTTTA
1198607 TTTTATTTTTTTA
1 TTTTATTTTTTTA
1198620 TTTTA
1 TTTTA
1198625 AAAATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:1201786 original size:20 final size:20
Alignment explanation
Indices: 1201757--1201806 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1201747 AACTTTAAAT
*
1201757 AAAATATAAAATTATTTTA-A
1 AAAATTTAAAATT-TTTTATA
1201777 AAAATTT-AAATTTTTTATTA
1 AAAATTTAAAATTTTTTA-TA
1201797 AAAATTTAAA
1 AAAATTTAAA
1201807 TCTCGTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
20 14 0.54
21 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATTTAAAATTTTTTATA
Found at i:1201787 original size:19 final size:19
Alignment explanation
Indices: 1201765--1201807 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
1201755 ATAAAATATA
1201765 AAATTATTTTA-AAAAATTT
1 AAATT-TTTTATAAAAATTT
1201784 AAATTTTTTATTAAAAATTT
1 AAATTTTTTA-TAAAAATTT
1201804 AAAT
1 AAAT
1201808 CTCGTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.23
19 5 0.23
20 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTTTTTATAAAAATTT
Found at i:1201815 original size:20 final size:20
Alignment explanation
Indices: 1201776--1201816 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1201766 AATTATTTTA
* **
1201776 AAAAATTTAAATTTTTTATT
1 AAAAATTTAAATCTCGTATT
1201796 AAAAATTTAAATCTCGTATT
1 AAAAATTTAAATCTCGTATT
1201816 A
1 A
1201817 TTCTATTCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (20 bp):
AAAAATTTAAATCTCGTATT
Found at i:1205079 original size:1 final size:1
Alignment explanation
Indices: 1205073--1205102 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
1205063 AACTGAAATG
1205073 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1205103 CCAAAATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1207982 original size:13 final size:13
Alignment explanation
Indices: 1207964--1207992 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1207954 AAATATTTAC
1207964 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
1207977 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
1207990 AAA
1 AAA
1207993 CCTTGATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:1208273 original size:18 final size:18
Alignment explanation
Indices: 1208250--1208285 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1208240 AATAATATTA
1208250 CATATTTA-ATTTATAAAT
1 CATATTTATATTTA-AAAT
1208268 CATATTTATATTTAAAAT
1 CATATTTATATTTAAAAT
1208286 TTATATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
CATATTTATATTTAAAAT
Found at i:1208305 original size:17 final size:16
Alignment explanation
Indices: 1208277--1208308 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1208267 TCATATTTAT
1208277 ATTTAAAATTTATATA
1 ATTTAAAATTTATATA
1208293 ATTTAATAATTTATAT
1 ATTTAA-AATTTATAT
1208309 TATATTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTAAAATTTATATA
Found at i:1208872 original size:26 final size:25
Alignment explanation
Indices: 1208830--1208901 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 25
1208820 ATTAAAAATT
*
1208830 TTAAAAAATAATTTTATATTAATTAA
1 TTAAAAAATTATTTTATATTAA-TAA
* *
1208856 TTAAAAAATTATATTATAATTTATAA
1 TTAAAAAATTATTTTAT-ATTAATAA
1208882 -TATAAAAATTATTTTATATT
1 TTA-AAAAATTATTTTATATT
1208902 GATATATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 5 0.12
26 31 0.77
27 4 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAAAAAATTATTTTATATTAATAA
Found at i:1215360 original size:2 final size:2
Alignment explanation
Indices: 1215355--1215381 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1215345 GGGGGGGGGG
1215355 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 G
1215382 GAAAAAGCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1221836 original size:11 final size:11
Alignment explanation
Indices: 1221807--1221837 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1221797 CCAAAGCAAT
1221807 AAAAAAGAAAA
1 AAAAAAGAAAA
*
1221818 AAAGAAGAAAA
1 AAAAAAGAAAA
1221829 AAAAAAGAA
1 AAAAAAGAA
1221838 CAAGAACAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:1222443 original size:21 final size:18
Alignment explanation
Indices: 1222400--1222463 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
1222390 TATAACATGT
*
1222400 TTAATAAATATAAATAAA
1 TTAATAAAAATAAATAAA
1222418 TTAATAAAAAATAAATATAA
1 TTAAT-AAAAATAAATA-AA
** *
1222438 TATAATGTATATAAATAAGA
1 T-TAATAAAAATAAATAA-A
1222458 TTAATA
1 TTAATA
1222464 TGATACATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 5 0.14
19 15 0.41
20 13 0.35
21 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
TTAATAAAAATAAATAAA
Found at i:1222525 original size:19 final size:19
Alignment explanation
Indices: 1222501--1222542 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1222491 GTTTTGTATT
1222501 TTATA-TTTAATAATTTATA
1 TTATATTTTAAT-ATTTATA
*
1222520 TTATATTTTAATATTTATG
1 TTATATTTTAATATTTATA
1222539 TTAT
1 TTAT
1222543 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTATATTTTAATATTTATA
Found at i:1222564 original size:16 final size:17
Alignment explanation
Indices: 1222543--1222580 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1222533 TTTATGTTAT
1222543 TAAAATA-AAAAATATA
1 TAAAATATAAAAATATA
*
1222559 TAAAATATTATAAATATA
1 TAAAATA-TAAAAATATA
1222577 TAAA
1 TAAA
1222581 TCGTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
18 12 0.63
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATATAAAAATATA
Found at i:1223437 original size:18 final size:20
Alignment explanation
Indices: 1223409--1223450 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1223399 ACTTAAACAT
*
1223409 AAAATCATATTT-TTTTAAA
1 AAAATCATATTTCTTTCAAA
1223428 AAAATC-TATTTCTTTCAAA
1 AAAATCATATTTCTTTCAAA
1223447 AAAA
1 AAAA
1223451 ATTATTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATCATATTTCTTTCAAA
Done.