Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 302 of 335
Found at i:89800513 original size:136 final size:137
Alignment explanation
Indices: 89800269--89800554 Score: 502
Period size: 136 Copynumber: 2.1 Consensus size: 137
89800259 CATTGGGCCT
** * * *
89800269 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGAGCCTT
89800334 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
89800398 CATATGC
131 CATATGC
*
89800405 AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGAGCTTT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGAGCCTT
*
89800470 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
89800535 CATATGC
131 CATATGC
89800542 AAGCCCATTTGGG
1 AAGCCCATTTGGG
89800555 GAGACTACTC
Statistics
Matches: 142, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
136 120 0.85
137 22 0.15
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGAGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
CATATGC
Found at i:89802381 original size:26 final size:26
Alignment explanation
Indices: 89802329--89802409 Score: 123
Period size: 26 Copynumber: 3.2 Consensus size: 26
89802319 CATGAAATTC
89802329 TTATCATGAAACATTT---TAACCCA
1 TTATCATGAAACATTTACCTAACCCA
89802352 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
89802378 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
89802404 TTATCA
1 TTATCA
89802410 ATTTGTATCA
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
23 16 0.30
26 37 0.70
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:89806410 original size:134 final size:137
Alignment explanation
Indices: 89806164--89806447 Score: 493
Period size: 134 Copynumber: 2.1 Consensus size: 137
89806154 CATTGGGCCT
** * *
89806164 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
89806229 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
89806293 CATATGC
131 CATATGC
*
89806300 AAGCCCATTTGGGTAATAGTGATACTGGGCCAAAGCCCTTTTCAGATTACAATAAACT-GG-CTT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
89806363 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
89806428 CATATGC
131 CATATGC
89806435 AAGCCCATTTGGG
1 AAGCCCATTTGGG
89806448 GAGACTACTC
Statistics
Matches: 141, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
134 64 0.45
135 24 0.17
136 53 0.38
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
CATATGC
Found at i:89808263 original size:26 final size:26
Alignment explanation
Indices: 89808227--89808310 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
89808217 CATGAAACTC
*
89808227 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
89808253 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
89808279 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
89808305 TTATCA
1 TTATCA
89808311 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:89810041 original size:18 final size:18
Alignment explanation
Indices: 89810018--89810099 Score: 76
Period size: 18 Copynumber: 4.5 Consensus size: 18
89810008 TCAAACACTA
*
89810018 TTATTATTGCTATTTCTG
1 TTATTATTACTATTTCTG
* *
89810036 TTATTATTTCTATTCCTG
1 TTATTATTACTATTTCTG
* * *
89810054 TCATTATTACTATTTTTT
1 TTATTATTACTATTTCTG
*
89810072 TGTATTATTA-TCATTACTG
1 T-TATTATTACT-ATTTCTG
89810091 TTATTATTA
1 TTATTATTA
89810100 TCTTAGTATT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
18 39 0.76
19 12 0.24
ACGTcount: A:0.22, C:0.11, G:0.06, T:0.61
Consensus pattern (18 bp):
TTATTATTACTATTTCTG
Found at i:89810318 original size:3 final size:3
Alignment explanation
Indices: 89810312--89810581 Score: 162
Period size: 3 Copynumber: 90.0 Consensus size: 3
89810302 TTGTGTCATC
89810312 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * * * *
89810360 ATT -TT CA-T ATAT ATT AGC ATT -TAC ATT ATC GTT ATT ATT ACT ATT
1 ATT ATT -ATT AT-T ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
* * * * * * * *
89810405 ATT AAT ACT CTT ATT ATT ACT ACT ATT TTT ATT CCTT -CT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT A-TT
*
89810451 ATT ATCG ATAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT AT-T AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
89810498 -TT TTT TTT TTT TTT ATT -TA ACAT ATT ATT ATT ATT ACTA ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT A-TT ATT ATT
* * * *
89810542 ATT ATC ATT ATT ACT ATT -GT ATT ATT ATT ACT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
89810582 TTCATCTATA
Statistics
Matches: 208, Mismatches: 42, Indels: 34
0.73 0.15 0.12
Matches are distributed among these distances:
2 13 0.06
3 179 0.86
4 16 0.08
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:89810690 original size:17 final size:19
Alignment explanation
Indices: 89810659--89810713 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 19
89810649 ATATCTATAT
*
89810659 TATTATTTCACTATTGTTA
1 TATTATTTCACTATTATTA
89810678 TATT-TTTCA-TATTATTA
1 TATTATTTCACTATTATTA
*
89810695 TCATCA--TCACTATTATTA
1 T-ATTATTTCACTATTATTA
89810713 T
1 T
89810714 CTTTTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 11 0.35
18 16 0.52
19 4 0.13
ACGTcount: A:0.29, C:0.13, G:0.02, T:0.56
Consensus pattern (19 bp):
TATTATTTCACTATTATTA
Found at i:89815704 original size:24 final size:26
Alignment explanation
Indices: 89815651--89815710 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
89815641 CCAAATCGAA
**
89815651 CCTTTGTGGTGAATTATCTATAAAGC
1 CCTTTGTGGCAAATTATCTATAAAGC
*
89815677 CC-TTGTGGCAAATTATCTA-AAAGG
1 CCTTTGTGGCAAATTATCTATAAAGC
89815701 CCTTTGTGGC
1 CCTTTGTGGC
89815711 TTATTATTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.20
25 22 0.73
26 2 0.07
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (26 bp):
CCTTTGTGGCAAATTATCTATAAAGC
Found at i:89818736 original size:24 final size:24
Alignment explanation
Indices: 89818701--89818748 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
89818691 GGTAAATTAC
*
89818701 AAGAATAGCCACTCAATTATTTCA
1 AAGAATAACCACTCAATTATTTCA
89818725 AAGAATAACCACTCAATTATTTCA
1 AAGAATAACCACTCAATTATTTCA
89818749 TTCATTCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (24 bp):
AAGAATAACCACTCAATTATTTCA
Found at i:89822013 original size:44 final size:45
Alignment explanation
Indices: 89821923--89822051 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
89821913 GACAGAACGA
*
89821923 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
89821969 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
89822013 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
89822052 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:89829393 original size:44 final size:45
Alignment explanation
Indices: 89829303--89829431 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
89829293 GACAGAACGA
*
89829303 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
89829349 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
89829393 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
89829432 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:89834318 original size:21 final size:21
Alignment explanation
Indices: 89834292--89834339 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
89834282 TCAACTTAGA
89834292 GCGGAGGCAGCAGCGAGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
*
89834313 GCGGAGGCAGCAGTGAGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
89834334 GCGGAG
1 GCGGAG
89834340 CAGAACAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.17, G:0.58, T:0.02
Consensus pattern (21 bp):
GCGGAGGCAGCAGCGAGGGAG
Found at i:89834682 original size:43 final size:43
Alignment explanation
Indices: 89834635--89834796 Score: 216
Period size: 44 Copynumber: 3.7 Consensus size: 43
89834625 CTGGGCAAAT
* * *
89834635 TAGCGGCGTTTTTTAAAAAAGTGCCGCTAAAAATACAGGTCTA
1 TAGCGGCGTTTTTTACAAAAGCGCCGCTAAAAGTACAGGTCTA
* *
89834678 TAGCGGCGTTTTTTTACAAAATCGCTGCTAAAAGTACAGGTCTA
1 TAGCGGCG-TTTTTTACAAAAGCGCCGCTAAAAGTACAGGTCTA
* *
89834722 TAGCGGCTTTTTTTTACAAAAGCGCCGCTAAAAGTACAGGTCTC
1 TAGCGGC-GTTTTTTACAAAAGCGCCGCTAAAAGTACAGGTCTA
* * *
89834766 TAGCGGCGATTTTTATAAAAGCGTCGCTAAA
1 TAGCGGCGTTTTTTACAAAAGCGCCGCTAAA
89834797 GTTCTTGGTC
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
43 28 0.27
44 76 0.73
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (43 bp):
TAGCGGCGTTTTTTACAAAAGCGCCGCTAAAAGTACAGGTCTA
Found at i:89838109 original size:64 final size:64
Alignment explanation
Indices: 89838036--89838246 Score: 142
Period size: 64 Copynumber: 3.2 Consensus size: 64
89838026 CTGGGCCAGA
*
89838036 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
89838100 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
89838162 ACTGGGCCAGA-
54 A-TGGCCCATAG
* *
89838173 GCCCTTTTCAGATTATAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
89838237 GCCCATTTCA
1 GCCCATTTCA
89838247 AAATACATGC
Statistics
Matches: 102, Mismatches: 28, Indels: 34
0.62 0.17 0.21
Matches are distributed among these distances:
63 9 0.09
64 25 0.25
65 5 0.05
66 1 0.01
67 11 0.11
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 15 0.15
74 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:89838248 original size:137 final size:137
Alignment explanation
Indices: 89838002--89838288 Score: 538
Period size: 137 Copynumber: 2.1 Consensus size: 137
89837992 TATTGGGCCT
**
89838002 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
89838067 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
89838132 CATATGC
131 CATATGC
*
89838139 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTATAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
89838204 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
89838269 CATATGC
131 CATATGC
89838276 AAGCCCATTTGGG
1 AAGCCCATTTGGG
89838289 GAGACTACTC
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 146 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
CATATGC
Found at i:89840109 original size:26 final size:26
Alignment explanation
Indices: 89840073--89840208 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
89840063 CATGATATTC
*
89840073 TTATCATGAAACATTTACCTAACTCA
1 TTATCATGAAACATTTACCTAACCCA
89840099 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
89840125 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
89840151 TTATCATGAAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
89840177 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
89840203 TTATCA
1 TTATCA
89840209 ATTTGTATCA
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 100 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:89844848 original size:4 final size:4
Alignment explanation
Indices: 89844839--89844939 Score: 130
Period size: 4 Copynumber: 25.2 Consensus size: 4
89844829 ATGATAAATT
*
89844839 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG GGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
* * * * * * *
89844887 AGAG AGAG AGAG AGGG AGAG GGAG GGAG GGAG GGAG GGGG AGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
89844935 AGAG A
1 AGAG A
89844940 TGCATGGGTG
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 89 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (4 bp):
AGAG
Found at i:89844850 original size:6 final size:6
Alignment explanation
Indices: 89844839--89844939 Score: 130
Period size: 6 Copynumber: 16.8 Consensus size: 6
89844829 ATGATAAATT
*
89844839 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGGG AGAGAG
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG
* * * * * * *
89844887 AGAGAG AGAGAG AGGGAG AGGGAG GGAGGG AGGGAG GGGGAG AGAGAG
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG
89844935 AGAGA
1 AGAGA
89844940 TGCATGGGTG
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 83 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (6 bp):
AGAGAG
Found at i:89846805 original size:53 final size:53
Alignment explanation
Indices: 89846725--89846829 Score: 201
Period size: 53 Copynumber: 2.0 Consensus size: 53
89846715 TTCTGTTTAC
89846725 CACTTTAAATTGAGTATTCGTTTCCCTCCCTTTTCTGCTAGGATTGGAAATCT
1 CACTTTAAATTGAGTATTCGTTTCCCTCCCTTTTCTGCTAGGATTGGAAATCT
*
89846778 CACTTTAAATTGAGTATTCGTTTCCCTCCCTTTTCTGCTAGGATTGGGAATC
1 CACTTTAAATTGAGTATTCGTTTCCCTCCCTTTTCTGCTAGGATTGGAAATC
89846830 CTATATTTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (53 bp):
CACTTTAAATTGAGTATTCGTTTCCCTCCCTTTTCTGCTAGGATTGGAAATCT
Found at i:89851959 original size:20 final size:22
Alignment explanation
Indices: 89851931--89851971 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
89851921 GTTGTATATT
*
89851931 TAAT-TTTTATTTTTT-AATTG
1 TAATCTTTAATTTTTTGAATTG
89851951 TAATCTTTAATTTTTTGAATT
1 TAATCTTTAATTTTTTGAATT
89851972 TTAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (22 bp):
TAATCTTTAATTTTTTGAATTG
Found at i:89856933 original size:15 final size:15
Alignment explanation
Indices: 89856913--89856941 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
89856903 ACTCCAATAA
89856913 ATTGAGACGAGTCAT
1 ATTGAGACGAGTCAT
89856928 ATTGAGACGAGTCA
1 ATTGAGACGAGTCA
89856942 ACATCAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (15 bp):
ATTGAGACGAGTCAT
Found at i:89860748 original size:14 final size:14
Alignment explanation
Indices: 89860731--89860764 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
89860721 AGAAGAAACG
89860731 AAAAAGAAAGAAAA
1 AAAAAGAAAGAAAA
89860745 AAAAAGAAAGAAAA
1 AAAAAGAAAGAAAA
*
89860759 AGAAAG
1 AAAAAG
89860765 GAAAATAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAGAAAA
Found at i:89860762 original size:24 final size:25
Alignment explanation
Indices: 89860723--89860769 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
89860713 AGAACAGGAG
89860723 AAGAAACGAAAAAGAAAGAAAAAAA
1 AAGAAACGAAAAAGAAAGAAAAAAA
*
89860748 AAGAAA-GAAAAAGAAAGGAAAA
1 AAGAAACGAAAAAGAAAGAAAAA
89860770 TAGGGTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (25 bp):
AAGAAACGAAAAAGAAAGAAAAAAA
Found at i:89871784 original size:21 final size:21
Alignment explanation
Indices: 89871758--89871800 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
89871748 CTTAAAATTG
89871758 AGTCTTGTGATATTTATAGTA
1 AGTCTTGTGATATTTATAGTA
89871779 AGTCTTGTGATATTTATAGTA
1 AGTCTTGTGATATTTATAGTA
89871800 A
1 A
89871801 TAGGCATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.47
Consensus pattern (21 bp):
AGTCTTGTGATATTTATAGTA
Found at i:89872285 original size:20 final size:19
Alignment explanation
Indices: 89872262--89872300 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
89872252 TTTTCTGATT
*
89872262 TTTTTAATATTTTTTTATGA
1 TTTTTAAT-TATTTTTATGA
89872282 TTTTTAATTATTTTTATGA
1 TTTTTAATTATTTTTATGA
89872301 GAAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTTAATTATTTTTATGA
Found at i:89872865 original size:2 final size:2
Alignment explanation
Indices: 89872858--89872899 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
89872848 TTCTGAGATC
89872858 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
89872900 CGACCTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89879407 original size:3 final size:3
Alignment explanation
Indices: 89879401--89879660 Score: 115
Period size: 3 Copynumber: 87.0 Consensus size: 3
89879391 ATAGTACTAG
* * * *
89879401 TAA TAA T-A CAA TAA TAA TAA -AG TAGA AAA TAA TAA TAA TAA GAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* * * * * * * *
89879445 TAA GAA TAA GAA TAA GAA TAA CAC CAA TAT TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
89879493 -AA -AA TAA CAA TAA TAA TAA TAA TAAA TAA GGAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA -TAA TAA TAA TAA TAA
** * * * * *
89879538 TAA CCA TAA T-A TAAA TAA GAA CAA TAA TAGA -AA TAG TAA CAA CAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
* * * *
89879583 TAA TAA TAA -AA T-A TAA GTAA TAG TGA GAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * *
89879627 TAAA TGG TAA TAA TAGA -AT TAA TAA TAA AAA TAA
1 T-AA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
89879661 AGTCGATTAA
Statistics
Matches: 186, Mismatches: 55, Indels: 32
0.68 0.20 0.12
Matches are distributed among these distances:
2 13 0.07
3 157 0.84
4 16 0.09
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.25
Consensus pattern (3 bp):
TAA
Found at i:89881690 original size:12 final size:12
Alignment explanation
Indices: 89881673--89881717 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
89881663 CAGCCTGCCC
89881673 ATATTAATTTTT
1 ATATTAATTTTT
89881685 ATATTAATTTTT
1 ATATTAATTTTT
89881697 ATATTAA-TTTT
1 ATATTAATTTTT
89881708 ATA-TAATTTT
1 ATATTAATTTT
89881718 AAAAAGATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 3 0.09
11 10 0.31
12 19 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:89881705 original size:24 final size:22
Alignment explanation
Indices: 89881673--89881717 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
89881663 CAGCCTGCCC
89881673 ATATTAATTTTTATATTAATTTTT
1 ATATTAA-TTTTATA-TAATTTTT
89881697 ATATTAATTTTATATAATTTT
1 ATATTAATTTTATATAATTTT
89881718 AAAAAGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.33
23 7 0.33
24 7 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATATTAATTTTATATAATTTTT
Found at i:89881877 original size:30 final size:30
Alignment explanation
Indices: 89881841--89881899 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
89881831 CTTAACAAGC
89881841 AAATGTCTCTAAAATAATAACAAAATTAAT
1 AAATGTCTCTAAAATAATAACAAAATTAAT
*
89881871 AAATGTCTTTAAAATAATAACAAAATTAA
1 AAATGTCTCTAAAATAATAACAAAATTAA
89881900 CAATAAAATA
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:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (30 bp):
AAATGTCTCTAAAATAATAACAAAATTAAT
Found at i:89885592 original size:9 final size:9
Alignment explanation
Indices: 89885576--89885612 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
89885566 ATATTTTTTC
89885576 TTATTTTAT
1 TTATTTTAT
89885585 TT-TATTTAT
1 TTAT-TTTAT
89885594 TTATTTTAT
1 TTATTTTAT
89885603 TTA-TTTAT
1 TTATTTTAT
89885611 TT
1 TT
89885613 TTTGTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.31
9 17 0.65
10 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTATTTTAT
Found at i:89885596 original size:13 final size:13
Alignment explanation
Indices: 89885580--89885613 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
89885570 TTTTTCTTAT
89885580 TTTATTTTATTTA
1 TTTATTTTATTTA
89885593 TTTATTTTATTTA
1 TTTATTTTATTTA
89885606 TTTATTTT
1 TTTATTTT
89885614 TTGTTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:89885688 original size:23 final size:23
Alignment explanation
Indices: 89885629--89885696 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
89885619 ATTAAATTTA
89885629 AAAATTTTGAAATATATA--TTTG
1 AAAATTTT-AAATATATATTTTTG
* *
89885651 AAATGTTTTATAATATATATTTTTT
1 AAA-ATTTTA-AATATATATTTTTG
89885676 AAAATTTTAAATAT-TATTTTT
1 AAAATTTTAAATATATATTTTT
89885697 AAATTATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 11 0.28
23 17 0.44
24 5 0.13
25 6 0.15
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
AAAATTTTAAATATATATTTTTG
Found at i:89885715 original size:21 final size:23
Alignment explanation
Indices: 89885691--89885736 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 23
89885681 TTTAAATATT
89885691 ATTTTTAAAT-TAT-TTTTTAAA
1 ATTTTTAAATATATATTTTTAAA
*
89885712 A-TTTTAAATATATATTTTTGAA
1 ATTTTTAAATATATATTTTTAAA
89885734 ATT
1 ATT
89885737 ATGTCTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 8 0.38
21 4 0.19
22 8 0.38
23 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
ATTTTTAAATATATATTTTTAAA
Found at i:89885735 original size:22 final size:20
Alignment explanation
Indices: 89885693--89885736 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
89885683 TAAATATTAT
89885693 TTTTAAATTATTTTTTAAAA
1 TTTTAAATTATTTTTTAAAA
*
89885713 TTTTAAATATATATTTTTGAAA
1 TTTTAAAT-TAT-TTTTTAAAA
89885735 TT
1 TT
89885737 ATGTCTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 3 0.14
22 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTAAATTATTTTTTAAAA
Found at i:89885761 original size:36 final size:34
Alignment explanation
Indices: 89885668--89885946 Score: 200
Period size: 36 Copynumber: 7.9 Consensus size: 34
89885658 TTATAATATA
89885668 TATTTTTTA-AAATTTT-AAATATTATTTTTAAAT
1 TATTTTTTATAAATTTTAAAATA-TATTTTTAAAT
89885701 TATTTTTTA-AAATTTTAAATATATATTTTTGAAAT
1 TATTTTTTATAAATTTTAAA-ATATATTTTT-AAAT
* * *
89885736 TATGTCTTATAAATTTTAACAATATATATTTGAAAT
1 TATTTTTTATAAATTTTAA-AATATAT-TTTTAAAT
*
89885772 TAATTTTTCTAAATTTTAAATTTT-AAATATATTTTT-AAG
1 T-ATTTTT-T--A---TAAATTTTAAAATATATTTTTAAAT
* * * ***
89885811 AATATATTTTTAAACAAAATAAAATA-A-TTTTAAAT
1 TAT-TTTTTATAAA--TTTTAAAATATATTTTTAAAT
*
89885846 ATATATTTT-TAAATTTTAAATATATATTTTTGAAAT
1 -TATTTTTTATAAATTTTAAA-ATATATTTTT-AAAT
*
89885882 TATTTCTTATAAATTTTAAAAATATATTTTTAAAT
1 TATTTTTTATAAATTTT-AAAATATATTTTTAAAT
89885917 TATTTTTTA-AAATTTT-AAATATTATTTTTA
1 TATTTTTTATAAATTTTAAAATA-TATTTTTA
89885947 TAAAAATTCT
Statistics
Matches: 197, Mismatches: 23, Indels: 52
0.72 0.08 0.19
Matches are distributed among these distances:
32 9 0.05
33 31 0.16
34 25 0.13
35 43 0.22
36 49 0.25
37 11 0.06
38 4 0.02
39 5 0.03
40 4 0.02
41 7 0.04
42 1 0.01
43 8 0.04
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (34 bp):
TATTTTTTATAAATTTTAAAATATATTTTTAAAT
Found at i:89885814 original size:14 final size:14
Alignment explanation
Indices: 89885797--89885823 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
89885787 TTAAATTTTA
89885797 AATATATTTTTAAG
1 AATATATTTTTAAG
89885811 AATATATTTTTAA
1 AATATATTTTTAA
89885824 ACAAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (14 bp):
AATATATTTTTAAG
Found at i:89885860 original size:21 final size:22
Alignment explanation
Indices: 89885836--89885882 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
89885826 AAAATAAAAT
89885836 AATTTTAAATATATATTTTT-A
1 AATTTTAAATATATATTTTTGA
89885857 AATTTTAAATATATATTTTTGA
1 AATTTTAAATATATATTTTTGA
89885879 AATT
1 AATT
89885883 ATTTCTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
AATTTTAAATATATATTTTTGA
Found at i:89885932 original size:57 final size:56
Alignment explanation
Indices: 89885836--89885950 Score: 135
Period size: 57 Copynumber: 2.0 Consensus size: 56
89885826 AAAATAAAAT
* * *
89885836 AATTTTAAATATATATTTTTAAATTTTAAATATATATTTTTGAA-ATTATTTCTTATA
1 AATTTTAAAAATATATTTTTAAATTTTAAATATA-AATTTTAAATATTATTT-TTATA
***
89885893 AATTTTAAAAATATATTTTTAAATTATTTTTTA-AAATTTTAAATATTATTTTTATA
1 AATTTTAAAAATATATTTTTAAATT-TTAAATATAAATTTTAAATATTATTTTTATA
89885949 AA
1 AA
89885951 AATTCTTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
56 14 0.28
57 32 0.64
58 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.56
Consensus pattern (56 bp):
AATTTTAAAAATATATTTTTAAATTTTAAATATAAATTTTAAATATTATTTTTATA
Found at i:89885934 original size:20 final size:23
Alignment explanation
Indices: 89885907--89885951 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
89885897 TTAAAAATAT
*
89885907 ATTTTTAA-ATTATTTTT-TAAA
1 ATTTTAAATATTATTTTTATAAA
89885928 ATTTTAAATATTATTTTTATAAA
1 ATTTTAAATATTATTTTTATAAA
89885951 A
1 A
89885952 ATTCTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 9 0.43
23 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTTAAATATTATTTTTATAAA
Found at i:89885971 original size:57 final size:57
Alignment explanation
Indices: 89885922--89886037 Score: 191
Period size: 57 Copynumber: 2.1 Consensus size: 57
89885912 TAAATTATTT
*
89885922 TTTAAA-ATTTTAAATATTATTTTTATAAAAATTCTTTTAAAAAGGTTTAAATAAACA
1 TTTAAATATTTTAAATAAT-TTTTTATAAAAATTCTTTTAAAAAGGTTTAAATAAACA
*
89885979 TTTAAATTTTTTAAATAATTTTTTATAAAAATTCTTTTAAAAAGGTTTAAATAAA-A
1 TTTAAATATTTTAAATAATTTTTTATAAAAATTCTTTTAAAAAGGTTTAAATAAACA
89886035 TTT
1 TTT
89886038 TTATACAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
56 4 0.07
57 42 0.75
58 10 0.18
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (57 bp):
TTTAAATATTTTAAATAATTTTTTATAAAAATTCTTTTAAAAAGGTTTAAATAAACA
Found at i:89886011 original size:13 final size:12
Alignment explanation
Indices: 89885982--89886021 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
89885972 ATAAACATTT
89885982 AAATTTTTTAAA
1 AAATTTTTTAAA
*
89885994 TAATTTTTTATAA
1 AAATTTTTTA-AA
89886007 AAATTCTTTTAAA
1 AAATT-TTTTAAA
89886020 AA
1 AA
89886022 GGTTTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 9 0.38
13 10 0.42
14 5 0.21
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (12 bp):
AAATTTTTTAAA
Found at i:89886361 original size:14 final size:15
Alignment explanation
Indices: 89886342--89886377 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
89886332 AATATATATT
89886342 TAATATTT-AAAAAG
1 TAATATTTAAAAAAG
89886356 TAATATTTAAAAAAG
1 TAATATTTAAAAAAG
89886371 TAATATT
1 TAATATT
89886378 CAAATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
TAATATTTAAAAAAG
Found at i:89886415 original size:22 final size:23
Alignment explanation
Indices: 89886390--89886450 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
89886380 AATTTTAAAA
89886390 AAAATAATTTAAAATA-ATATT-T
1 AAAAT-ATTTAAAATATATATTAT
*
89886412 AAAAT-GTTAAAATATATATTAT
1 AAAATATTTAAAATATATATTAT
* *
89886434 AAAACATTTTAAATATA
1 AAAATATTTAAAATATA
89886451 CATTTCAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 8 0.25
21 5 0.16
22 10 0.31
23 9 0.28
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
AAAATATTTAAAATATATATTAT
Found at i:89886446 original size:24 final size:21
Alignment explanation
Indices: 89886397--89886463 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 21
89886387 AAAAAAATAA
89886397 TTTAAAATA-ATATTTAAAAT
1 TTTAAAATATATATTTAAAAT
*
89886417 GTTAAAATATATATTATAAAACAT
1 TTTAAAATATATATT-T-AAA-AT
* *
89886441 TTT-AAATATACATTTCAAAT
1 TTTAAAATATATATTTAAAAT
89886461 TTT
1 TTT
89886464 TTAAAATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 13 0.33
21 7 0.18
22 2 0.05
23 13 0.33
24 4 0.10
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (21 bp):
TTTAAAATATATATTTAAAAT
Found at i:89886520 original size:24 final size:23
Alignment explanation
Indices: 89886472--89886529 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
89886462 TTTTAAAATT
*
89886472 AATAACAAAAAATAAATAAAATAA
1 AATAAGAAAAAAT-AATAAAATAA
89886496 AATAAGAAAAAAT-ATAAAACTTAA
1 AATAAGAAAAAATAATAAAA--TAA
89886520 AA-AAGAAAAA
1 AATAAGAAAAA
89886530 GAATTAATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 6 0.19
23 8 0.26
24 17 0.55
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (23 bp):
AATAAGAAAAAATAATAAAATAA
Found at i:89886594 original size:27 final size:26
Alignment explanation
Indices: 89886565--89886615 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
89886555 AAAAAAGTAA
89886565 AAAAAAAATCAAAAGCATGTCAGGTT
1 AAAAAAAATCAAAAGCATGTCAGGTT
*
89886591 AAAAAAAATCAGAAGCATGTCAGGT
1 AAAAAAAATCAAAAGCATGTCAGGT
89886616 CTGGTGGCGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (26 bp):
AAAAAAAATCAAAAGCATGTCAGGTT
Found at i:89886948 original size:33 final size:33
Alignment explanation
Indices: 89886911--89886980 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
89886901 TGGTAGTTCC
89886911 TTTTAAAAGTAACTAAAAAATTTTAAATTTATT
1 TTTTAAAAGTAACTAAAAAATTTTAAATTTATT
*
89886944 TTTTAAAAGTAACTAAAATATTTTAAATTTATT
1 TTTTAAAAGTAACTAAAAAATTTTAAATTTATT
89886977 TTTT
1 TTTT
89886981 TATTTTCTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (33 bp):
TTTTAAAAGTAACTAAAAAATTTTAAATTTATT
Found at i:89888304 original size:14 final size:14
Alignment explanation
Indices: 89888269--89888308 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
89888259 CAATGTTGAG
*
89888269 TTTTGAATTTTTTA
1 TTTTTAATTTTTTA
89888283 TATATTTAATTTTTTA
1 T-T-TTTAATTTTTTA
89888299 TTTTTAATTT
1 TTTTTAATTT
89888309 CAAATAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 9 0.39
15 2 0.09
16 12 0.52
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTTTAATTTTTTA
Found at i:89888339 original size:15 final size:14
Alignment explanation
Indices: 89888316--89888355 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
89888306 TTTCAAATAG
*
89888316 TTTTTTATTTTGTAA
1 TTTTATATTTT-TAA
89888331 TTTTATATTTTTAA
1 TTTTATATTTTTAA
*
89888345 ATTTATATTTT
1 TTTTATATTTT
89888356 AAAAAAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTTATATTTTTAA
Found at i:89888349 original size:14 final size:15
Alignment explanation
Indices: 89888321--89888355 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
89888311 AATAGTTTTT
*
89888321 TATTTTGTAATTTTA
1 TATTTTGTAAATTTA
89888336 TATTTT-TAAATTTA
1 TATTTTGTAAATTTA
89888350 TATTTT
1 TATTTT
89888356 AAAAAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TATTTTGTAAATTTA
Found at i:89888409 original size:25 final size:25
Alignment explanation
Indices: 89888355--89888409 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
89888345 ATTTATATTT
*
89888355 TAAAAAAAAGTAAGGACCAAAATGG
1 TAAAAAAAAGTAAGGACCAAAATAG
**
89888380 T-AAAAAATTTAAGGACCAAAATAG
1 TAAAAAAAAGTAAGGACCAAAATAG
89888404 TAAAAA
1 TAAAAA
89888410 TTGTAAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.62, C:0.07, G:0.15, T:0.16
Consensus pattern (25 bp):
TAAAAAAAAGTAAGGACCAAAATAG
Found at i:89889955 original size:16 final size:16
Alignment explanation
Indices: 89889934--89889988 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
89889924 GTTTGGTTCA
*
89889934 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
* *
89889950 CTGTAATTGAATATAG
1 CTGTAATGGAATAGAG
*
89889966 TTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
89889982 CTATAAT
1 CTGTAAT
89889989 CAGTAATTCA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.33
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:89890168 original size:25 final size:26
Alignment explanation
Indices: 89890135--89890185 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
89890125 GTTCGTAGAT
*
89890135 GATTATTGTT-ATTAAATTTTAATAA
1 GATTATTGTTAAATAAATTTTAATAA
*
89890160 GATTATTGTTAAATATATTTTAATAA
1 GATTATTGTTAAATAAATTTTAATAA
89890186 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (26 bp):
GATTATTGTTAAATAAATTTTAATAA
Found at i:89890264 original size:12 final size:11
Alignment explanation
Indices: 89890237--89890311 Score: 52
Period size: 12 Copynumber: 6.8 Consensus size: 11
89890227 TATTAACTAC
89890237 AATTTAATAA-
1 AATTTAATAAT
89890247 AA--TAATATAT
1 AATTTAATA-AT
89890257 AATTTAATAAT
1 AATTTAATAAT
*
89890268 ATTATTAAT-AT
1 AAT-TTAATAAT
*
89890279 AGTTATTAATAAT
1 A-AT-TTAATAAT
89890292 -ATTTAATAAT
1 AATTTAATAAT
89890302 AATTTTAATA
1 AA-TTTAATA
89890312 TAAAATTATT
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
8 5 0.09
9 1 0.02
10 12 0.22
11 9 0.17
12 25 0.46
13 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (11 bp):
AATTTAATAAT
Found at i:89895099 original size:20 final size:20
Alignment explanation
Indices: 89895047--89895103 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
89895037 TGAAAATAGT
* * *
89895047 TATTTTTAA-ATAAAAACAG
1 TATTTTTAATATTAAAATAA
89895066 TATTTATT-AT-TTAAAATAA
1 TATTT-TTAATATTAAAATAA
89895085 TATTTTTAATATTAAAATA
1 TATTTTTAATATTAAAATA
89895104 TTTATTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.06
19 19 0.61
20 10 0.32
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TATTTTTAATATTAAAATAA
Found at i:89895113 original size:19 final size:21
Alignment explanation
Indices: 89895066--89895117 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
89895056 ATAAAAACAG
*
89895066 TATTTATTATTTAAAATAATAT
1 TATTTAATA-TTAAAATAATAT
89895088 T-TTTAATATTAAAAT-AT-T
1 TATTTAATATTAAAATAATAT
89895106 TATTTAAT-TTAA
1 TATTTAATATTAA
89895118 GAAAAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 6 0.21
19 8 0.29
20 7 0.25
21 6 0.21
22 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTAATATTAAAATAATAT
Found at i:89898846 original size:5 final size:5
Alignment explanation
Indices: 89898836--89898878 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
89898826 TTACTAATGA
*
89898836 TAAAT TAAAT TAAAT TAAAT TAAAT T-AAT TAAAAT CAAAT TAA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT T-AAAT TAAAT TAA
89898879 GAAAAATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 4 0.12
5 27 0.79
6 3 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (5 bp):
TAAAT
Found at i:89900117 original size:30 final size:30
Alignment explanation
Indices: 89900083--89900141 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
89900073 ATTATTTTAT
89900083 TGTTAATTTTGTTATTATTTTAAAGACATC
1 TGTTAATTTTGTTATTATTTTAAAGACATC
*
89900113 TGTTAATTTTGTTATTATTTTAGAGACAT
1 TGTTAATTTTGTTATTATTTTAAAGACAT
89900142 TTGCTTGTTA
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:0.12, T:0.54
Consensus pattern (30 bp):
TGTTAATTTTGTTATTATTTTAAAGACATC
Found at i:89914238 original size:21 final size:21
Alignment explanation
Indices: 89914212--89914253 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
89914202 AAGGTAGCTT
*
89914212 GCCAAGCAATACCGAAACTAA
1 GCCAAGCAACACCGAAACTAA
89914233 GCCAAGCAACACCGAAACTAA
1 GCCAAGCAACACCGAAACTAA
89914254 CTCAAAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.31, G:0.14, T:0.07
Consensus pattern (21 bp):
GCCAAGCAACACCGAAACTAA
Found at i:89916639 original size:4 final size:4
Alignment explanation
Indices: 89916630--89916756 Score: 56
Period size: 4 Copynumber: 32.5 Consensus size: 4
89916620 CCCCATTTCT
89916630 TTTA TTTA -TTA -TTA -TTA TTTA TTTA TTCTA TTTTA TTTA TTTA TTTCA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA -TTTA TTTA TTTA TTT-A
** * * * * *
89916678 -TTA TTCTA -TTA TTTTA TTCC TTTA CTTA TTTA GTTC TTTG TTT- CTTA
1 TTTA TT-TA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
89916725 TTTA -TTA -TTG TTTA ATTA TTTTA TTT- TTTA TT
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TT
89916757 GCTTATTTTT
Statistics
Matches: 95, Mismatches: 16, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
3 22 0.23
4 58 0.61
5 13 0.14
6 2 0.02
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:89916649 original size:22 final size:22
Alignment explanation
Indices: 89916631--89916675 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
89916621 CCCATTTCTT
89916631 TTATT-TATTATTA-TTATTTAT
1 TTATTCTATT-TTATTTATTTAT
89916652 TTATTCTATTTTATTTATTTAT
1 TTATTCTATTTTATTTATTTAT
89916674 TT
1 TT
89916676 CATTATTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (22 bp):
TTATTCTATTTTATTTATTTAT
Found at i:89916661 original size:26 final size:25
Alignment explanation
Indices: 89916635--89916695 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 25
89916625 TTTCTTTTAT
89916635 TTATTATTATTATTT-ATTTATTCTA
1 TTATTATTATTATTTCA-TTATTCTA
89916660 TT-TTATTTATTTATTTCATTATTCTA
1 TTATTA-TTA-TTATTTCATTATTCTA
89916686 TTATT-TTATT
1 TTATTATTATT
89916696 CCTTTACTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
24 5 0.16
25 8 0.25
26 16 0.50
27 3 0.09
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (25 bp):
TTATTATTATTATTTCATTATTCTA
Found at i:89916667 original size:18 final size:18
Alignment explanation
Indices: 89916630--89916682 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
89916620 CCCCATTTCT
89916630 TTTATTTA-TTATTATTA
1 TTTATTTATTTATTATTA
89916647 TTTATTTATTCTATT-TTA
1 TTTATTTATT-TATTATTA
89916665 TTTATTTATTTCATTATT
1 TTTATTTATTT-ATTATT
89916683 CTATTATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.28
18 17 0.53
19 6 0.19
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTATTTATTATTA
Found at i:89916694 original size:13 final size:13
Alignment explanation
Indices: 89916632--89916696 Score: 57
Period size: 13 Copynumber: 5.0 Consensus size: 13
89916622 CCATTTCTTT
*
89916632 TATTTA-TTATTAT
1 TATTTATTTATT-C
89916645 TATTTATTTATTC
1 TATTTATTTATTC
89916658 TATTTTATTTATT-
1 TA-TTTATTTATTC
89916671 TATTTCA-TTATTC
1 TATTT-ATTTATTC
89916684 TA-TTATTTTATTC
1 TATTTA-TTTATTC
89916697 CTTTACTTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
11 1 0.02
12 10 0.22
13 19 0.42
14 15 0.33
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTTATTTATTC
Found at i:89916748 original size:23 final size:20
Alignment explanation
Indices: 89916722--89916781 Score: 57
Period size: 23 Copynumber: 2.8 Consensus size: 20
89916712 TCTTTGTTTC
89916722 TTATTTATTATTGTTTAATTATT
1 TTATTTATTATTGTTT-A-T-TT
* *
89916745 TTATTTTTTATTGCTTATTT
1 TTATTTATTATTGTTTATTT
89916765 TTATTCATATTATTGTT
1 TTATT--TATTATTGTT
89916782 AGTCATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 7 0.23
21 1 0.03
22 9 0.29
23 14 0.45
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.70
Consensus pattern (20 bp):
TTATTTATTATTGTTTATTT
Found at i:89918464 original size:6 final size:6
Alignment explanation
Indices: 89918453--89918519 Score: 57
Period size: 6 Copynumber: 11.3 Consensus size: 6
89918443 TTTTGGTCCA
* * *
89918453 TTTATT TTTA-T TTT-CT TCTATT TTTATT ATTAGTT TTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-TT TTTATT TTTATT
* * *
89918500 TTTCTG TTTATT TGTATT TT
1 TTTATT TTTATT TTTATT TT
89918520 CCTAAACTTT
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
5 7 0.15
6 35 0.74
7 5 0.11
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:89923846 original size:26 final size:27
Alignment explanation
Indices: 89923811--89923861 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
89923801 CCATTTCCAA
89923811 TCTCAATTTCAATTC-ACAATTCAATTT
1 TCTCAATTTC-ATTCAACAATTCAATTT
*
89923838 TCTC-ATTTCATTCAATAATTCAAT
1 TCTCAATTTCATTCAACAATTCAAT
89923862 CAATCAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 14 0.64
27 4 0.18
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.45
Consensus pattern (27 bp):
TCTCAATTTCATTCAACAATTCAATTT
Found at i:89924980 original size:12 final size:12
Alignment explanation
Indices: 89924956--89924987 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
89924946 AAACCCTAAA
89924956 TTTCTTCTTTTCT
1 TTTCTT-TTTTCT
89924969 TTTCTTTTTTCT
1 TTTCTTTTTTCT
89924981 TTTCTTT
1 TTTCTTT
89924988 CTGTTTCGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTCTTTTTTCT
Found at i:89925045 original size:2 final size:2
Alignment explanation
Indices: 89925038--89925071 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
89925028 TTCTTTAGTT
89925038 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
89925072 ATTAAAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:89926596 original size:62 final size:59
Alignment explanation
Indices: 89926482--89926600 Score: 141
Period size: 62 Copynumber: 2.0 Consensus size: 59
89926472 GTACAAACTG
* ****
89926482 TTTTTATATTATTTCATTTAATAAAATAAAAGTTGTTTTGAATATTTTAATAGTAAATTA
1 TTTTTATATTATTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGGCAATAG-AAATTA
*
89926542 TTTTTATATT-TTGTCCTATTTAATAAAATAGAAGTTCTTTTGAATAAGGCAATAGAAAT
1 TTTTTATATTATT-T-C-ATTTAATAAAATAAAAGTTCTTTTGAATAAGGCAATAGAAAT
89926601 AATGCAACAT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
59 2 0.04
60 11 0.22
61 5 0.10
62 32 0.64
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (59 bp):
TTTTTATATTATTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGGCAATAGAAATTA
Found at i:89928740 original size:37 final size:37
Alignment explanation
Indices: 89928690--89928764 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
89928680 GCATGTAGGC
*
89928690 TGGAGGCGAGTATGCCCTAAATCACAGATTTTCTTCT
1 TGGAGGCAAGTATGCCCTAAATCACAGATTTTCTTCT
* * *
89928727 TGGAGGCAAGTATGCTCTAAATTACGGATTTTCTTCT
1 TGGAGGCAAGTATGCCCTAAATCACAGATTTTCTTCT
89928764 T
1 T
89928765 CTTCTAAACC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (37 bp):
TGGAGGCAAGTATGCCCTAAATCACAGATTTTCTTCT
Found at i:89929948 original size:126 final size:126
Alignment explanation
Indices: 89929590--89930236 Score: 796
Period size: 127 Copynumber: 5.1 Consensus size: 126
89929580 GGCCAAACAC
* * *
89929590 GAACTACTGTAGAAAAAGATCGTCCACCTAGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAACGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* *
89929655 CTACTTGAAGCATTTTTGACACTATTTTTTTTAGAACCATCTTCTCAAAATTATTTTTCCAA
66 CTACTTGAAGCATTTTTGACACTA-TTTTTTTAGAACCGTCTTCTCAAAATTATTTTTCTAA
* * * * * * *
89929717 GAACTACTGTGGAAAAAAAACGTCCACGTGAGAACTTTTTTTTTAGTAATTTTACTGACAATGCA
1 GAACTACTGTAGAAAAAGAACGTCCACGTGGGAGC--TTTTTTCAGTAATTTTGCTGACAGTGCA
* * *
89929782 TCCTGCTTGAAGCATTTTTGACACTATATTTTTAGAACCGTCTTCTCAAAATTATTTTTCCAA
64 TCCTACTTGAAGCATTTTTGACACTATTTTTTTAGAACCGTCTTCTCAAAATTATTTTTCTAA
* *
89929845 GAACTACTGTAGAAAAAGAACGTCCACGTGTGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAACGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* * * * *
89929910 CTACTTGAAGCATTTTTGAAAGTATTTTTTGAGAACCGTCTTCTCAAAATCATTTTT-TAG
66 CTACTTGAAGCATTTTTGACACTATTTTTTTAGAACCGTCTTCTCAAAATTATTTTTCTAA
* * *
89929970 GAACTATTGTAGAAAAAGAGCGTTCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAACGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* * * * * *
89930035 CTGCTTGAAGCGTTTTTTAAAGTATTTTTTTAGAACCGTCTTCTCAAAATTATTTTT-TTA
66 CTACTTGAAGCATTTTTGACACTATTTTTTTAGAACCGTCTTCTCAAAATTATTTTTCTAA
* * * * * * * **
89930095 GAAACTACTGTAGAAAAAAAAGCATCTAAGTGGGAGCTTCTTTCAGTAATTCTGCTAACAACGCA
1 G-AACTACTGTAGAAAAAGAA-CGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
* * ** * * *
89930160 TCCTACTTGAAGCGTTTTTGACATTACCTTTTCAGAACCATCTTATCAAAATTAATTTTTCTAA
64 TCCTACTTGAAGCATTTTTGACACTATTTTTTTAGAACCGTCTTCTCAAAATT-ATTTTTCTAA
89930224 -AACTACTGTAGAA
1 GAACTACTGTAGAA
89930237 GAAAAATAAA
Statistics
Matches: 453, Mismatches: 61, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
125 115 0.25
126 95 0.21
127 119 0.26
128 72 0.16
129 52 0.11
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAACGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
CTACTTGAAGCATTTTTGACACTATTTTTTTAGAACCGTCTTCTCAAAATTATTTTTCTAA
Found at i:89930351 original size:34 final size:34
Alignment explanation
Indices: 89930313--89930421 Score: 123
Period size: 34 Copynumber: 3.2 Consensus size: 34
89930303 AAAAAAAAAA
*
89930313 CTAAACCCTAATTTAATTAACTTT-TTAAAAAATT
1 CTAAACCCTAATTTAATTAA-TTTATTAAAAAATC
* * *
89930347 CTAAACCCTAATTTAATGAATTTATTTAAAACTC
1 CTAAACCCTAATTTAATTAATTTATTAAAAAATC
* * *
89930381 CTAAAACCTAATTTAATTAATTTA-AAAAAAAAC
1 CTAAACCCTAATTTAATTAATTTATTAAAAAATC
89930414 TCTAAACC
1 -CTAAACC
89930422 TTGGTTTATT
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
33 8 0.13
34 54 0.87
ACGTcount: A:0.47, C:0.17, G:0.01, T:0.36
Consensus pattern (34 bp):
CTAAACCCTAATTTAATTAATTTATTAAAAAATC
Found at i:89934070 original size:55 final size:56
Alignment explanation
Indices: 89933994--89934118 Score: 155
Period size: 55 Copynumber: 2.2 Consensus size: 56
89933984 CATGTTTCTT
*
89933994 CATAAATTATTACAACTTTTGTAATA-TTTAGTATAATTATATAAAAA-TTACTCAATTA
1 CATAAATTA-T-CAA-TTTTGTAATATTTTA-TATAATTATAAAAAAACTTACTCAATTA
* * *
89934052 CATAATTTATCAATTTTGTAATATTTTATGTAATTATAAAAAAACGTTACTTAATTA
1 CATAAATTATCAATTTTGTAATATTTTATATAATTATAAAAAAAC-TTACTCAATTA
89934109 CATAAATTAT
1 CATAAATTAT
89934119 TACAACATTC
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
55 24 0.41
56 7 0.12
57 20 0.34
58 8 0.14
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (56 bp):
CATAAATTATCAATTTTGTAATATTTTATATAATTATAAAAAAACTTACTCAATTA
Found at i:89942444 original size:13 final size:13
Alignment explanation
Indices: 89942426--89942451 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
89942416 AACTTTGAGC
89942426 TCTCATGCCTCCA
1 TCTCATGCCTCCA
89942439 TCTCATGCCTCCA
1 TCTCATGCCTCCA
89942452 AATGGTATCC
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:0.15, C:0.46, G:0.08, T:0.31
Consensus pattern (13 bp):
TCTCATGCCTCCA
Found at i:89948030 original size:21 final size:23
Alignment explanation
Indices: 89948004--89948049 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
89947994 CATGAGAAAC
* *
89948004 AAAGAACTCATAAT-AAA-CTTT
1 AAAGAAATCAAAATGAAATCTTT
89948025 AAAGAAATCAAAATGAAATCTTT
1 AAAGAAATCAAAATGAAATCTTT
89948048 AA
1 AA
89948050 TCTTGATGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
22 3 0.14
23 6 0.29
ACGTcount: A:0.57, C:0.11, G:0.07, T:0.26
Consensus pattern (23 bp):
AAAGAAATCAAAATGAAATCTTT
Found at i:89959976 original size:20 final size:20
Alignment explanation
Indices: 89959931--89959978 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
89959921 TACTGATTAG
*
89959931 TATTTTAAAACATAAAAATA
1 TATTTTAAAACATAAAAAAA
* * *
89959951 TTTTTTTAAATATAAAAAAA
1 TATTTTAAAACATAAAAAAA
89959971 TATTTTAA
1 TATTTTAA
89959979 CAAGGGAACT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTTTAAAACATAAAAAAA
Found at i:89962943 original size:2 final size:2
Alignment explanation
Indices: 89962936--89962974 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
89962926 TGCTTTTGTA
89962936 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
89962975 AAACAAATAT
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:89966172 original size:21 final size:21
Alignment explanation
Indices: 89966146--89966185 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
89966136 CAAAACATTC
* *
89966146 AACAGAAAATTAAAGAAGAAA
1 AACAGAAAATAAAAAAAGAAA
89966167 AACAGAAAATAAAAAAAGA
1 AACAGAAAATAAAAAAAGA
89966186 GTTCAGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.75, C:0.05, G:0.12, T:0.07
Consensus pattern (21 bp):
AACAGAAAATAAAAAAAGAAA
Found at i:89971591 original size:32 final size:33
Alignment explanation
Indices: 89971555--89971628 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 33
89971545 TCATAAATTT
89971555 ATAAATTGATT-ATTTGAATTT-AGTAACTCA-TG
1 ATAAATTGATTAATTT-AATTTGA-TAACTCATTG
*
89971587 ATAAATTAATTAATTTAATTTGATAACTCATTG
1 ATAAATTGATTAATTTAATTTGATAACTCATTG
*
89971620 ATTAATTGA
1 ATAAATTGA
89971629 ACTTGTTAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 22 0.61
33 14 0.39
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (33 bp):
ATAAATTGATTAATTTAATTTGATAACTCATTG
Found at i:89974906 original size:48 final size:49
Alignment explanation
Indices: 89974851--89974945 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 49
89974841 TAGAGAGATG
* *
89974851 AAATTCCT-AAAAATAAAAGTATGGAGATTAAATTCCAAATATACGACT
1 AAATTCCTAAAAAATAAAAGTACGAAGATTAAATTCCAAATATACGACT
* *
89974899 AAATTCCTAAAAAATAAAAGTACGAAGATTAAATTCTACATATACGA
1 AAATTCCTAAAAAATAAAAGTACGAAGATTAAATTCCAAATATACGA
89974946 AGAGTACAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 8 0.19
49 34 0.81
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (49 bp):
AAATTCCTAAAAAATAAAAGTACGAAGATTAAATTCCAAATATACGACT
Found at i:89976147 original size:26 final size:27
Alignment explanation
Indices: 89976101--89976157 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
89976091 GTACTTCATG
* *
89976101 TTTATTTTTTTATATA-TTTTTTGAAT
1 TTTATTTTTTTATATAGTTTTATAAAT
89976127 TTTAGTTTTTTTA-ATAGTTTTATAAAT
1 TTTA-TTTTTTTATATAGTTTTATAAAT
89976154 TTTA
1 TTTA
89976158 AAATATTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (27 bp):
TTTATTTTTTTATATAGTTTTATAAAT
Found at i:89977559 original size:11 final size:11
Alignment explanation
Indices: 89977538--89977588 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
89977528 TGTTTCTGGA
89977538 TTTGTGTTCAAT
1 TTTGTG-TCAAT
89977550 TTTGTGTCAAT
1 TTTGTGTCAAT
* * **
89977561 TTTATTTGGA-
1 TTTGTGTCAAT
89977571 TTTGTGTCAAT
1 TTTGTGTCAAT
89977582 TTTGTGT
1 TTTGTGT
89977589 TCAAATCATT
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
10 6 0.20
11 18 0.60
12 6 0.20
ACGTcount: A:0.16, C:0.06, G:0.20, T:0.59
Consensus pattern (11 bp):
TTTGTGTCAAT
Found at i:89981906 original size:16 final size:16
Alignment explanation
Indices: 89981887--89981944 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 16
89981877 CTTTCCTATA
89981887 TTCTTTCTTCTCACTT
1 TTCTTTCTTCTCACTT
*
89981903 TTCTTTCATCTTTC-CTAT
1 TTCTTTC-T-TCTCACT-T
89981921 ATTCTTTCTTCTCACTT
1 -TTCTTTCTTCTCACTT
89981938 TTCTTTC
1 TTCTTTC
89981945 CTACCAAGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
16 14 0.40
17 7 0.20
18 7 0.20
19 7 0.20
ACGTcount: A:0.09, C:0.29, G:0.00, T:0.62
Consensus pattern (16 bp):
TTCTTTCTTCTCACTT
Found at i:89981919 original size:35 final size:35
Alignment explanation
Indices: 89981873--89981944 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
89981863 TGAAAAATGA
89981873 TCATCTTTCCTATATTCTTTCTTCTCACTTTTCTT
1 TCATCTTTCCTATATTCTTTCTTCTCACTTTTCTT
89981908 TCATCTTTCCTATATTCTTTCTTCTCACTTTTCTT
1 TCATCTTTCCTATATTCTTTCTTCTCACTTTTCTT
89981943 TC
1 TC
89981945 CTACCAAGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (35 bp):
TCATCTTTCCTATATTCTTTCTTCTCACTTTTCTT
Found at i:89981925 original size:19 final size:19
Alignment explanation
Indices: 89981873--89981928 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
89981863 TGAAAAATGA
89981873 TCATCTTTCCTATATTCTT
1 TCATCTTTCCTATATTCTT
*
89981892 TC-T-TCTCACT-T-TTCTT
1 TCATCTTTC-CTATATTCTT
89981908 TCATCTTTCCTATATTCTT
1 TCATCTTTCCTATATTCTT
89981927 TC
1 TC
89981929 TTCTCACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
16 7 0.23
17 7 0.23
18 7 0.23
19 9 0.30
ACGTcount: A:0.12, C:0.29, G:0.00, T:0.59
Consensus pattern (19 bp):
TCATCTTTCCTATATTCTT
Found at i:89982066 original size:17 final size:17
Alignment explanation
Indices: 89982040--89982074 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
89982030 TCAAGCACAC
89982040 CCTTAATGCTAGAATGG
1 CCTTAATGCTAGAATGG
*
89982057 CCTTAGTGCTAGAATGG
1 CCTTAATGCTAGAATGG
89982074 C
1 C
89982075 ATCTTGGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (17 bp):
CCTTAATGCTAGAATGG
Found at i:89989896 original size:18 final size:18
Alignment explanation
Indices: 89989821--89989896 Score: 98
Period size: 18 Copynumber: 4.2 Consensus size: 18
89989811 TCCCAACTAT
*
89989821 TGTATACGTGAACAGTAC
1 TGTATACGTGAATAGTAC
* *
89989839 CGTATACGTGAATAGTGC
1 TGTATACGTGAATAGTAC
* * *
89989857 CGTATATGTGAATAGTAA
1 TGTATACGTGAATAGTAC
89989875 TGTATACGTGAATAGTAC
1 TGTATACGTGAATAGTAC
89989893 TGTA
1 TGTA
89989897 AACGATCGTA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.32
Consensus pattern (18 bp):
TGTATACGTGAATAGTAC
Found at i:89991338 original size:2 final size:2
Alignment explanation
Indices: 89991331--89991361 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
89991321 TAATATTTAT
89991331 TA TA 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 TA TA T
89991362 GAGTTTGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:89991512 original size:9 final size:9
Alignment explanation
Indices: 89991483--89991512 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
89991473 TGAATGTTAC
89991483 AATTCAAAT
1 AATTCAAAT
*
89991492 AACTCAAAT
1 AATTCAAAT
89991501 AATTCAAAT
1 AATTCAAAT
89991510 AAT
1 AAT
89991513 AGATTGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (9 bp):
AATTCAAAT
Found at i:89991624 original size:28 final size:28
Alignment explanation
Indices: 89991588--89991641 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
89991578 CAAAACTTAC
89991588 AAAAAATTTAAAATAAATT-TAAAATTCG
1 AAAAAATTTAAAA-AAATTCTAAAATTCG
* *
89991616 AAAATATTTATAAAAATTCTAAAATT
1 AAAAAATTTAAAAAAATTCTAAAATT
89991642 TATATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (28 bp):
AAAAAATTTAAAAAAATTCTAAAATTCG
Found at i:89992307 original size:2 final size:2
Alignment explanation
Indices: 89992300--89992326 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
89992290 AATAGATAAC
89992300 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 A
89992327 AATGTGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:90004235 original size:29 final size:28
Alignment explanation
Indices: 90004176--90004245 Score: 70
Period size: 31 Copynumber: 2.4 Consensus size: 28
90004166 AATAAGATTT
90004176 AAATAATATAAATTTTATTATAACTTTATA
1 AAATAATATAAATTTTATTATAAC--TATA
*
90004206 AAATACATATAAATTATTTTTATAAC-ATA
1 AAATA-ATATAAATT-TTATTATAACTATA
* *
90004235 AATTATTATAA
1 AAATAATATAA
90004246 TGATTATGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 5 0.14
29 7 0.20
30 5 0.14
31 9 0.26
32 9 0.26
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (28 bp):
AAATAATATAAATTTTATTATAACTATA
Found at i:90005206 original size:11 final size:11
Alignment explanation
Indices: 90005169--90005213 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
90005159 ACAAATTCTG
90005169 CTATTTTCTTA
1 CTATTTTCTTA
*
90005180 CTGTTTTGC-TA
1 CTATTTT-CTTA
90005191 CTATTTTCTTA
1 CTATTTTCTTA
*
90005202 TTATTTTCTTA
1 CTATTTTCTTA
90005213 C
1 C
90005214 CGTTTTACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 1 0.04
11 26 0.93
12 1 0.04
ACGTcount: A:0.16, C:0.18, G:0.04, T:0.62
Consensus pattern (11 bp):
CTATTTTCTTA
Found at i:90011975 original size:13 final size:13
Alignment explanation
Indices: 90011957--90011987 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
90011947 TTTTCTCATG
*
90011957 TATTTATTTTATT
1 TATTTATCTTATT
90011970 TATTTATCTTATT
1 TATTTATCTTATT
90011983 TATTT
1 TATTT
90011988 TAATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTTATCTTATT
Found at i:90015976 original size:9 final size:9
Alignment explanation
Indices: 90015962--90015988 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
90015952 AGTTGAAATT
90015962 TGCAAGTTG
1 TGCAAGTTG
90015971 TGCAAGTTG
1 TGCAAGTTG
90015980 TGCAAGTTG
1 TGCAAGTTG
90015989 CAATGAAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.33, T:0.33
Consensus pattern (9 bp):
TGCAAGTTG
Found at i:90020106 original size:46 final size:46
Alignment explanation
Indices: 90020046--90020357 Score: 385
Period size: 46 Copynumber: 7.0 Consensus size: 46
90020036 TTTGACATGA
* * * * * *
90020046 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAGGT
*** *
90020092 TGCCATGGTATCTTTCAACCATGGTCTTGTTCA-TTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC-TATCAGGT
* *
90020138 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TCTCATATTAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC-TATCAGGT
* *
90020184 TGCCATGGTATCTTTCAGCCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAGGT
*
90020230 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAGGT
90020276 TGCCATGGTATCTTTCAACCATGGTCTT--ACA----C--TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAGGT
90020314 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC-TATCAG
90020358 AGAGCACACT
Statistics
Matches: 237, Mismatches: 19, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
38 34 0.14
40 3 0.01
43 1 0.00
44 3 0.01
45 4 0.02
46 190 0.80
47 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAGGT
Found at i:90020294 original size:138 final size:130
Alignment explanation
Indices: 90020046--90020357 Score: 426
Period size: 138 Copynumber: 2.3 Consensus size: 130
90020036 TTTGACATGA
* * * * * * *
90020046 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAAC
***
90020111 CATGGTCTTGTTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATCTCA
66 CATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTT--ACA-CTC-
90020176 TATTAGGT
127 ----AGGT
*
90020184 TGCCATGGTATCTTTCAGCCATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAAC
* *
90020249 CATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACTCAGGT
66 CATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACTCAGGT
*
90020314 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAG
90020358 AGAGCACACT
Statistics
Matches: 159, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
130 46 0.29
135 3 0.02
136 3 0.02
138 107 0.67
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (130 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACTCAGGT
Found at i:90020321 original size:38 final size:38
Alignment explanation
Indices: 90020270--90020345 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
90020260 ACATTTTATA
90020270 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
90020308 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
90020346 ATTTCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:90022456 original size:11 final size:11
Alignment explanation
Indices: 90022440--90022491 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
90022430 TATACTAAAT
90022440 AAATAATAATA
1 AAATAATAATA
*
90022451 AAATAAT-ATT
1 AAATAATAATA
* *
90022461 AAATATCTCATA
1 AAATA-ATAATA
*
90022473 AAATATTAATA
1 AAATAATAATA
90022484 AAATAATA
1 AAATAATA
90022492 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:90024445 original size:3 final size:3
Alignment explanation
Indices: 90024437--90024468 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
90024427 TGAGATTGAC
90024437 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
90024469 TACCACTCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:90036560 original size:21 final size:21
Alignment explanation
Indices: 90036518--90036560 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
90036508 GGGGAAAAAG
*
90036518 ATGATCGCTTCGATAATGTTA
1 ATGATCGCTTCGATAATCTTA
*
90036539 ATGAT-GCTTTGATAAATCTTA
1 ATGATCGCTTCGAT-AATCTTA
90036560 A
1 A
90036561 GTAAGAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (21 bp):
ATGATCGCTTCGATAATCTTA
Found at i:90039657 original size:21 final size:21
Alignment explanation
Indices: 90039633--90039676 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
90039623 GAGAGTGCTC
90039633 AAGAAACTGAGTTTTAGTTAT
1 AAGAAACTGAGTTTTAGTTAT
90039654 AAGAAACTGAGTTTTAGTTAT
1 AAGAAACTGAGTTTTAGTTAT
90039675 AA
1 AA
90039677 TGTTTAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (21 bp):
AAGAAACTGAGTTTTAGTTAT
Found at i:90042379 original size:2 final size:2
Alignment explanation
Indices: 90042372--90042469 Score: 70
Period size: 2 Copynumber: 49.0 Consensus size: 2
90042362 CATCAAAATC
* * * * * *
90042372 AT AT AT AT AC AT AT AT AT AT AC AC AT AT AC AC AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
90042414 AT AT AT AT AC AT AT AC AC AC AT AT AC AC AT AT AT AC 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
*
90042456 AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT
90042470 GTGTGTATAT
Statistics
Matches: 78, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.49, C:0.13, G:0.01, T:0.37
Consensus pattern (2 bp):
AT
Found at i:90042386 original size:10 final size:10
Alignment explanation
Indices: 90042371--90042468 Score: 92
Period size: 10 Copynumber: 10.0 Consensus size: 10
90042361 TCATCAAAAT
90042371 CATATATATA
1 CATATATATA
90042381 CATATATATA
1 CATATATATA
* * *
90042391 TACACATATA
1 CATATATATA
*
90042401 CACATATATA
1 CATATATATA
90042411 CATATATAT-
1 CATATATATA
*
90042420 -ATACATATA
1 CATATATATA
* *
90042429 CACACATATA
1 CATATATATA
*
90042439 CACATATATA
1 CATATATATA
90042449 CATATATATA
1 CATATATATA
* *
90042459 TATATGTATA
1 CATATATATA
90042469 TGTGTGTATA
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
8 7 0.09
10 67 0.91
ACGTcount: A:0.49, C:0.14, G:0.01, T:0.36
Consensus pattern (10 bp):
CATATATATA
Found at i:90042387 original size:8 final size:8
Alignment explanation
Indices: 90042374--90042463 Score: 80
Period size: 8 Copynumber: 11.8 Consensus size: 8
90042364 TCAAAATCAT
90042374 ATATATAC
1 ATATATAC
90042382 ATATAT--
1 ATATATAC
*
90042388 ATATACAC
1 ATATATAC
*
90042396 ATATACAC
1 ATATATAC
90042404 ATATATAC
1 ATATATAC
90042412 ATATAT--
1 ATATATAC
* *
90042418 ATATACAT
1 ATATATAC
* *
90042426 ATACACAC
1 ATATATAC
*
90042434 ATATACAC
1 ATATATAC
90042442 ATATATAC
1 ATATATAC
*
90042450 ATATATAT
1 ATATATAC
90042458 ATATAT
1 ATATAT
90042464 GTATATGTGT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
6 10 0.14
8 60 0.86
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATATAC
Found at i:90042408 original size:30 final size:30
Alignment explanation
Indices: 90042374--90042448 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
90042364 TCAAAATCAT
*
90042374 ATATATACATATATATATACACATATACAC
1 ATATATACATATATATATACACATACACAC
*
90042404 ATATATACATATATATATACATATACACAC
1 ATATATACATATATATATACACATACACAC
*
90042434 ATATACACATATATA
1 ATATATACATATATA
90042449 CATATATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (30 bp):
ATATATACATATATATATACACATACACAC
Found at i:90042498 original size:18 final size:18
Alignment explanation
Indices: 90042457--90042503 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
90042447 TACATATATA
* *
90042457 TATATATGTATATGTGTG
1 TATATGTGTGTATGTGTG
90042475 TATATGTGTGTATGTGTG
1 TATATGTGTGTATGTGTG
*
90042493 TGTATGTGTGT
1 TATATGTGTGT
90042504 GTATATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (18 bp):
TATATGTGTGTATGTGTG
Found at i:90042502 original size:20 final size:20
Alignment explanation
Indices: 90042463--90042509 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
90042453 TATATATATA
90042463 TGTATATGTGTGTATATGTG
1 TGTATATGTGTGTATATGTG
* *
90042483 TGTATGTGTGTGTATGTGTG
1 TGTATATGTGTGTATATGTG
90042503 TGTATAT
1 TGTATAT
90042510 ATATATACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.32, T:0.51
Consensus pattern (20 bp):
TGTATATGTGTGTATATGTG
Found at i:90042571 original size:44 final size:44
Alignment explanation
Indices: 90042485--90042575 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
90042475 TATATGTGTG
90042485 TATGTGTGTGTATGTGTGTGTATATATATATACATATATATATA
1 TATGTGTGTGTATGTGTGTGTATATATATATACATATATATATA
* * *
90042529 TATGTGTGTGTATGTGTGTGTATATATATATCCATGTGTATATA
1 TATGTGTGTGTATGTGTGTGTATATATATATACATATATATATA
90042573 TAT
1 TAT
90042576 ACACACACAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.29, C:0.03, G:0.20, T:0.48
Consensus pattern (44 bp):
TATGTGTGTGTATGTGTGTGTATATATATATACATATATATATA
Found at i:90042589 original size:10 final size:10
Alignment explanation
Indices: 90042572--90042608 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
90042562 ATGTGTATAT
90042572 ATATACACAC
1 ATATACACAC
*
90042582 ACATACACAC
1 ATATACACAC
90042592 ATATACACAC
1 ATATACACAC
90042602 ATATACA
1 ATATACA
90042609 TATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (10 bp):
ATATACACAC
Found at i:90042613 original size:2 final size:2
Alignment explanation
Indices: 90042602--90042649 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
90042592 ATATACACAC
* * *
90042602 AT AT AC AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90042644 AT AT AT
1 AT AT AT
90042650 GTGTATATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:90042615 original size:10 final size:10
Alignment explanation
Indices: 90042568--90042646 Score: 50
Period size: 10 Copynumber: 7.9 Consensus size: 10
90042558 ATCCATGTGT
90042568 ATATATATAC
1 ATATATATAC
* * *
90042578 ACACACATAC
1 ATATATATAC
* *
90042588 ACACATATAC
1 ATATATATAC
* *
90042598 ACACATATAC
1 ATATATATAC
*
90042608 ATATATATAT
1 ATATATATAC
*
90042618 ATATATATAT
1 ATATATATAC
* *
90042628 ATGTATATAT
1 ATATATATAC
*
90042638 ATATGTATA
1 ATATATATA
90042647 TATGTGTATA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 59 1.00
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.35
Consensus pattern (10 bp):
ATATATATAC
Found at i:90042615 original size:20 final size:20
Alignment explanation
Indices: 90042568--90042616 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
90042558 ATCCATGTGT
90042568 ATATATATACACACACATAC
1 ATATATATACACACACATAC
* * *
90042588 ACACATATACACACATATAC
1 ATATATATACACACACATAC
90042608 ATATATATA
1 ATATATATA
90042617 TATATATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (20 bp):
ATATATATACACACACATAC
Found at i:90042654 original size:10 final size:10
Alignment explanation
Indices: 90042613--90042664 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
90042603 TATACATATA
* *
90042613 TATATATATA
1 TATATATGTG
*
90042623 TATATATGTA
1 TATATATGTG
*
90042633 TATATATATG
1 TATATATGTG
90042643 TATATATGTG
1 TATATATGTG
*
90042653 TATATGTGTG
1 TATATATGTG
90042663 TA
1 TA
90042665 AAATAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (10 bp):
TATATATGTG
Found at i:90050013 original size:15 final size:14
Alignment explanation
Indices: 90049984--90050010 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
90049974 GCAATTTTAT
90049984 AATTTTTAAAGTTG
1 AATTTTTAAAGTTG
90049998 AATTTTTAAAGTT
1 AATTTTTAAAGTT
90050011 TGAGGGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (14 bp):
AATTTTTAAAGTTG
Found at i:90050729 original size:40 final size:40
Alignment explanation
Indices: 90050622--90050763 Score: 203
Period size: 41 Copynumber: 3.5 Consensus size: 40
90050612 AAACGCCATT
* * *
90050622 AAAAGCTGAGCAATAGTGGCGTTTTCATTCAAAACGCCGCT
1 AAAAACTGAGAAATAGTGGCGTTTT-ATTCAAAACGCCGCA
* *
90050663 AAAAACTGAGTAATAGTGGCGTTTTTATTCAAAACGCAGCA
1 AAAAACTGAGAAATAGTGGCG-TTTTATTCAAAACGCCGCA
90050704 AAAAACTGAGAAATAGTGGCGTTTTATTCAAAACGCCGCA
1 AAAAACTGAGAAATAGTGGCGTTTTATTCAAAACGCCGCA
* *
90050744 AAAAGCTGAGATATAGTGGC
1 AAAAACTGAGAAATAGTGGC
90050764 ACTTTAGGTC
Statistics
Matches: 92, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
40 36 0.39
41 52 0.57
42 4 0.04
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (40 bp):
AAAAACTGAGAAATAGTGGCGTTTTATTCAAAACGCCGCA
Found at i:90050801 original size:81 final size:82
Alignment explanation
Indices: 90050622--90050809 Score: 208
Period size: 81 Copynumber: 2.3 Consensus size: 82
90050612 AAACGCCATT
* **
90050622 AAAAGCTGAGCAATAGTGGCGTTTTCATTCAAAACGCCGCTAAAAACTGAGTAATAGTGGCGTTT
1 AAAAACTGAGCAATAGTGGCGTTTTCATTCAAAACGCCGCTAAAAACTGAGTAATAGTGGCGACT
*
90050687 TTATTCAAAACGCAGCA
66 TTATCCAAAACGCAGCA
*
90050704 AAAAACTGAGAAATAGTGGCGTTTT-ATTCAAAACGCCGC-AAAAAGCTGAG-ATATAGTGGC-A
1 AAAAACTGAGCAATAGTGGCGTTTTCATTCAAAACGCCGCTAAAAA-CTGAGTA-ATAGTGGCGA
90050765 CTTTAGGTCCAAACAC-CA-CA
64 CTTTA--TCCAAA-ACGCAGCA
*** *
90050785 AAAGGTTGAGCTATAGTGGCGTTTT
1 AAAAACTGAGCAATAGTGGCGTTTT
90050810 TGTAAAAACG
Statistics
Matches: 91, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
80 10 0.11
81 49 0.54
82 30 0.33
83 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (82 bp):
AAAAACTGAGCAATAGTGGCGTTTTCATTCAAAACGCCGCTAAAAACTGAGTAATAGTGGCGACT
TTATCCAAAACGCAGCA
Found at i:90051406 original size:29 final size:29
Alignment explanation
Indices: 90051351--90051406 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
90051341 AAAATATGAA
*
90051351 GCCTAACCCCTAAATCATAATCGATGACC
1 GCCTAACCCCTAAATCATAACCGATGACC
* *
90051380 GCCTAATCCCTAAATCATAACCTATGA
1 GCCTAACCCCTAAATCATAACCGATGA
90051407 TCTAAACTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.32, G:0.09, T:0.23
Consensus pattern (29 bp):
GCCTAACCCCTAAATCATAACCGATGACC
Done.