Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 175 of 198
Found at i:54831443 original size:22 final size:22
Alignment explanation
Indices: 54831418--54831459 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54831408 ATTTGGAGAT
*
54831418 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
54831440 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
54831460 TTTGAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:54831486 original size:22 final size:22
Alignment explanation
Indices: 54831461--54831530 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 22
54831451 ATTTGAGAGT
* *
54831461 TTGAAAGAATTTTGGAAGAAAA
1 TTGAGAGAATTTTGGAAGGAAA
* *
54831483 TTGAGAGAATTTTTGAAGGGAA
1 TTGAGAGAATTTTGGAAGGAAA
54831505 TTGAGAGAA-TTTGTGAAGGAAA
1 TTGAGAGAATTTTG-GAAGGAAA
54831527 TTGA
1 TTGA
54831531 TATTGAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 3 0.07
22 38 0.93
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.30
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:54831767 original size:22 final size:22
Alignment explanation
Indices: 54831739--54831891 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
54831729 TTTATTGTTC
*
54831739 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
54831761 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
54831783 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
54831805 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
54831827 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
54831849 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
54831871 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
54831892 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:54834932 original size:128 final size:130
Alignment explanation
Indices: 54834701--54834943 Score: 391
Period size: 128 Copynumber: 1.9 Consensus size: 130
54834691 TTTATTTTCA
* * *
54834701 TTTTAACCCAACCAAAAACCAAAAGGGAAAAAAATGGTAAGAACAAAAATCATTCAACATATCTC
1 TTTTAACCAAACCAAAAACCAAAA-GGAAAAAAATGGTAAGAACAAAAATCATTCAACACATCCC
*
54834766 CAAGAGGGAAACTTGCAGCAAATTAAAGAGAAACTTTGATTGAGTTAATTTACGATAGATGGATG
65 CAAGAGGGAAACTTGCAACAAATTAAAGAGAAACTTTGATTGAGTTAATTTACGATAGATGGATG
54834831 T
130 T
**
54834832 TTTTAACCAAACCAAAAAGGAAAA-G-AAAAAATGGTAAGAACAAAAATCATTCAACACATCCCC
1 TTTTAACCAAACCAAAAACCAAAAGGAAAAAAATGGTAAGAACAAAAATCATTCAACACATCCCC
* *
54834895 AAGGGGGAAACTTGCAACAAATTGAAGAGAAACTTTGATTGAGTTAATT
66 AAGAGGGAAACTTGCAACAAATTAAAGAGAAACTTTGATTGAGTTAATT
54834944 CACAGTCATT
Statistics
Matches: 104, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
128 82 0.79
129 1 0.01
131 21 0.20
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.22
Consensus pattern (130 bp):
TTTTAACCAAACCAAAAACCAAAAGGAAAAAAATGGTAAGAACAAAAATCATTCAACACATCCCC
AAGAGGGAAACTTGCAACAAATTAAAGAGAAACTTTGATTGAGTTAATTTACGATAGATGGATGT
Found at i:54835477 original size:19 final size:20
Alignment explanation
Indices: 54835443--54835494 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
54835433 ATAAAAGAAA
54835443 AAATAACTTA-TATATTAATT
1 AAATAA-TTACTATATTAATT
*
54835463 AAA-AATTACTATATTTATT
1 AAATAATTACTATATTAATT
*
54835482 AAATATTTACTAT
1 AAATAATTACTAT
54835495 TTTATTGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 14 0.50
20 11 0.39
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATAATTACTATATTAATT
Found at i:54835481 original size:23 final size:22
Alignment explanation
Indices: 54835441--54835483 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
54835431 AAATAAAAGA
54835441 AAAAATAACTTATATATTAATT
1 AAAAATAACTTATATATTAATT
* *
54835463 AAAAATTACTATATTTATTAA
1 AAAAATAACT-TATATATTAA
54835484 ATATTTACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAAATAACTTATATATTAATT
Found at i:54838750 original size:31 final size:30
Alignment explanation
Indices: 54838706--54838764 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
54838696 TTTAGAGATA
* *
54838706 AATATCAAAGCTATACTTGAATTTTGATCC
1 AATATCAAAGCTATACATGAACTTTGATCC
* *
54838736 AATATGCAATGCTATCCATGAACTTTGAT
1 AATAT-CAAAGCTATACATGAACTTTGAT
54838765 TTTGTATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (30 bp):
AATATCAAAGCTATACATGAACTTTGATCC
Found at i:54841799 original size:3 final size:3
Alignment explanation
Indices: 54841791--54841877 Score: 158
Period size: 3 Copynumber: 29.3 Consensus size: 3
54841781 AATTTCAAAG
*
54841791 TAT TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54841839 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
54841878 GTGGATAAGA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 79 0.98
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:54842609 original size:18 final size:19
Alignment explanation
Indices: 54842572--54842610 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54842562 ACATATAATT
* *
54842572 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACACTA
54842591 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACACTA
54842609 TT
1 TT
54842611 AAGTAATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAATTTAATAACACTA
Found at i:54842961 original size:37 final size:37
Alignment explanation
Indices: 54842914--54842984 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
54842904 AGTATTACTT
*
54842914 AATAATTTATTAAATTAAAATAGATTTATTAAATGAG
1 AATAATTTATTAAATTAAAATAGAGTTATTAAATGAG
*
54842951 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAATTTATTAAATTAAAATAGAGTTATTAAAT
54842985 AAAAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (37 bp):
AATAATTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:54842989 original size:19 final size:19
Alignment explanation
Indices: 54842914--54842988 Score: 102
Period size: 18 Copynumber: 4.1 Consensus size: 19
54842904 AGTATTACTT
54842914 AATA-ATTTATTAAATTAA
1 AATAGATTTATTAAATTAA
* *
54842932 AATAGATTTATTAAATGAG
1 AATAGATTTATTAAATTAA
54842951 AATAG-TTTATTAAATTAA
1 AATAGATTTATTAAATTAA
*
54842969 AATAGAGTTATTAAA-TAA
1 AATAGATTTATTAAATTAA
54842987 AA
1 AA
54842989 AAATAAGTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
18 25 0.50
19 25 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (19 bp):
AATAGATTTATTAAATTAA
Found at i:54843111 original size:27 final size:26
Alignment explanation
Indices: 54843062--54843139 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 26
54843052 ATTTTTTTCC
54843062 CTTTGGCACCATGGTGCCGCCAATGA
1 CTTTGGCACCATGGTGCCGCCAATGA
* *
54843088 CTTTGGCACCAATGGTGCCACCAATTTA
1 CTTTGGCACC-ATGGTGCCGCCAA-TGA
*
54843116 -TTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACC-ATGGTGCCGCCAAT
54843140 ACCATTGGGG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
26 11 0.24
27 32 0.71
28 2 0.04
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.28
Consensus pattern (26 bp):
CTTTGGCACCATGGTGCCGCCAATGA
Found at i:54843242 original size:28 final size:28
Alignment explanation
Indices: 54843205--54843302 Score: 153
Period size: 28 Copynumber: 3.5 Consensus size: 28
54843195 TTTTTTTGAT
*
54843205 ATATTTTGGTAAATAAAAAAAAATT-TA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
54843232 TATATTTTGGTAAATAAAAAAAAGTTGTA
1 -ATATTTTGGTAAATAAAAAAAAGTTGTA
*
54843261 ATATTTTCGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
*
54843289 CTATTTTGGTAAAT
1 ATATTTTGGTAAAT
54843303 TTTTATTTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
28 63 0.97
29 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:54852630 original size:12 final size:12
Alignment explanation
Indices: 54852613--54852639 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
54852603 TAGTATTATT
54852613 ATAAAATATATA
1 ATAAAATATATA
54852625 ATAAAATATATA
1 ATAAAATATATA
54852637 ATA
1 ATA
54852640 TTATAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAAAATATATA
Found at i:54852637 original size:21 final size:20
Alignment explanation
Indices: 54852610--54852673 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 20
54852600 TAATAGTATT
54852610 ATTATAAAATATATAATAAA
1 ATTATAAAATATATAATAAA
* *
54852630 ATATATAATATTATAAAATAAA
1 AT-TATAA-AATATATAATAAA
* *
54852652 GTTATTAAAT-TAT-ATAAA
1 ATTATAAAATATATAATAAA
54852670 ATTA
1 ATTA
54852674 AAATAAAAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 8 0.23
19 2 0.06
20 4 0.11
21 9 0.26
22 12 0.34
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
ATTATAAAATATATAATAAA
Found at i:54852665 original size:29 final size:29
Alignment explanation
Indices: 54852609--54852690 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
54852599 TTAATAGTAT
*
54852609 TATTATAAAATATATAATAAAATATATAA
1 TATTATAAAATAAATAATAAAATATATAA
* *
54852638 TATTATAAAATAAAGTTATTAAATTATATAA
1 TATTATAAAATAAA--TAATAAAATATATAA
* *
54852669 -AAT-TAAAATAAAAAGATAAAAT
1 TATTATAAAATAAATA-ATAAAAT
54852691 CACCACAAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
27 1 0.02
28 5 0.12
29 22 0.51
30 2 0.05
31 13 0.30
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (29 bp):
TATTATAAAATAAATAATAAAATATATAA
Found at i:54854681 original size:19 final size:17
Alignment explanation
Indices: 54854654--54854703 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
54854644 ATGTTTTTAA
54854654 TTTTTATTTTATGTTATT
1 TTTTTATTTTATGTT-TT
54854672 TTTATTATTTTAAT-TTTT
1 TTT-TTATTTT-ATGTTTT
54854690 TTTTGTATTTTATG
1 TTTT-TATTTTATG
54854704 CAGGTAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 3 0.11
18 14 0.50
19 9 0.32
20 2 0.07
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTTATTTTATGTTTT
Found at i:54855663 original size:14 final size:14
Alignment explanation
Indices: 54855644--54855678 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
54855634 TAACATTTTT
*
54855644 TTCTAATGATACTA
1 TTCTAACGATACTA
*
54855658 TTCTAACGGTACTA
1 TTCTAACGATACTA
54855672 TTCTAAC
1 TTCTAAC
54855679 AAGTAATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:54856325 original size:12 final size:12
Alignment explanation
Indices: 54856304--54856339 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
54856294 TGCCGGATAT
*
54856304 AGAGGCTGAGCC
1 AGAGCCTGAGCC
*
54856316 AGAGCTTGAGCC
1 AGAGCCTGAGCC
54856328 AGAGCCTGAGCC
1 AGAGCCTGAGCC
54856340 CAAACGGTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.25, C:0.28, G:0.36, T:0.11
Consensus pattern (12 bp):
AGAGCCTGAGCC
Found at i:54860201 original size:27 final size:27
Alignment explanation
Indices: 54860163--54860237 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
54860153 CTAGGTGTGT
54860163 CGCCTATCAGATAGGCACCACCAGTGC
1 CGCCTATCAGATAGGCACCACCAGTGC
** **
54860190 CGCCTATCAGATAAGG-GTCACTGGTGC
1 CGCCTATCAGAT-AGGCACCACCAGTGC
54860217 CGCCTATCAGATAGGCACCAC
1 CGCCTATCAGATAGGCACCAC
54860238 ACGCCTTTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 3 0.08
27 34 0.85
28 3 0.08
ACGTcount: A:0.25, C:0.33, G:0.24, T:0.17
Consensus pattern (27 bp):
CGCCTATCAGATAGGCACCACCAGTGC
Found at i:54860329 original size:9 final size:9
Alignment explanation
Indices: 54860315--54860342 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
54860305 CCACTACTAA
54860315 AATATTATT
1 AATATTATT
54860324 AATATTATT
1 AATATTATT
54860333 AATATTATT
1 AATATTATT
54860342 A
1 A
54860343 TTAACTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
AATATTATT
Found at i:54860839 original size:20 final size:20
Alignment explanation
Indices: 54860792--54860841 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
54860782 CCCAAAACTT
*
54860792 CAAATCTT-AAACTCAAACT
1 CAAATCTTGAAACTCAAACC
* * *
54860811 CAAACCTTGAACCTCGAACC
1 CAAATCTTGAAACTCAAACC
54860831 CAAATCTTGAA
1 CAAATCTTGAA
54860842 TCCAAGTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.42, C:0.30, G:0.06, T:0.22
Consensus pattern (20 bp):
CAAATCTTGAAACTCAAACC
Found at i:54862405 original size:23 final size:23
Alignment explanation
Indices: 54862379--54862425 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
54862369 TTCATTTAAG
* *
54862379 TTAAACGAACAAGTTCATGAATA
1 TTAAACAAACAAGTCCATGAATA
*
54862402 TTAAACAAACATGTCCATGAATA
1 TTAAACAAACAAGTCCATGAATA
54862425 T
1 T
54862426 GTTCATGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.28
Consensus pattern (23 bp):
TTAAACAAACAAGTCCATGAATA
Found at i:54863071 original size:24 final size:25
Alignment explanation
Indices: 54863038--54863087 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
54863028 GGGAAGCCTT
* *
54863038 TGGGACGTGGTCGGGGTCGTGGCCG
1 TGGGACGTGGACGGGGTCGAGGCCG
*
54863063 TGGG-CGTGGACGTGGTCGAGGCCG
1 TGGGACGTGGACGGGGTCGAGGCCG
54863087 T
1 T
54863088 TAAATATGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.06, C:0.20, G:0.54, T:0.20
Consensus pattern (25 bp):
TGGGACGTGGACGGGGTCGAGGCCG
Found at i:54867088 original size:24 final size:25
Alignment explanation
Indices: 54867035--54867094 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 25
54867025 TTGGCTGTCA
* *
54867035 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTATATAGCTCTTG
54867060 CGAGCTTCCCGTTA-ATAGCTCTT-
1 CGAGCTTCCCGTTATATAGCTCTTG
54867083 CGGAGCTTCCCG
1 C-GAGCTTCCCG
54867095 ATTGGTTGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 1 0.03
24 17 0.53
25 14 0.44
ACGTcount: A:0.13, C:0.30, G:0.23, T:0.33
Consensus pattern (25 bp):
CGAGCTTCCCGTTATATAGCTCTTG
Found at i:54867169 original size:25 final size:25
Alignment explanation
Indices: 54867149--54867283 Score: 102
Period size: 25 Copynumber: 5.5 Consensus size: 25
54867139 ATGAGCGTCT
*
54867149 CGATATATGGCTCCCTGGAGCTTCC
1 CGATATATGGCTCCCTAGAGCTTCC
*
54867174 CGAT-TAATGGCTCTCTAGAGCTTCC
1 CGATAT-ATGGCTCCCTAGAGCTTCC
*
54867199 CGATAT-TGGCT-CGTATGAGCTTCC
1 CGATATATGGCTCCCTA-GAGCTTCC
* *
54867223 CGTTA-ATGGCTCTCC-GGAGCTTCC
1 CGATATATGGCTC-CCTAGAGCTTCC
* * *
54867247 CGTTACATGGCTCAC-ATGAGCTTCC
1 CGATATATGGCTCCCTA-GAGCTTCC
* *
54867272 TGTTATATGGCT
1 CGATATATGGCT
54867284 TGGAAGAGTT
Statistics
Matches: 91, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
23 2 0.02
24 37 0.41
25 50 0.55
26 2 0.02
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (25 bp):
CGATATATGGCTCCCTAGAGCTTCC
Found at i:54867218 original size:24 final size:24
Alignment explanation
Indices: 54867166--54867259 Score: 91
Period size: 24 Copynumber: 3.8 Consensus size: 24
54867156 TGGCTCCCTG
*
54867166 GAGCTTCCCGATTAATGGCTCTCTA
1 GAGCTTCCCGA-TAATGGCTCTATA
*
54867191 GAGCTTCCCGATATTGGCTCGTAT-
1 GAGCTTCCCGATAATGGCTC-TATA
* ***
54867215 GAGCTTCCCGTTAATGGCTCTCCG
1 GAGCTTCCCGATAATGGCTCTATA
*
54867239 GAGCTTCCCGTTACATGGCTC
1 GAGCTTCCCGATA-ATGGCTC
54867260 ACATGAGCTT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.02
24 39 0.65
25 20 0.33
ACGTcount: A:0.16, C:0.30, G:0.23, T:0.31
Consensus pattern (24 bp):
GAGCTTCCCGATAATGGCTCTATA
Found at i:54867219 original size:49 final size:49
Alignment explanation
Indices: 54867149--54867283 Score: 148
Period size: 49 Copynumber: 2.7 Consensus size: 49
54867139 ATGAGCGTCT
* * *
54867149 CGATATATGGCTC-CCTGGAGCTTCCCGATTAATGGCTCTCTAGAGCTTCC
1 CGATACATGGCTCACAT-GAGCTTCCCG-TTAATGGCTCTCCAGAGCTTCC
* ** *
54867199 CGATA-TTGGCTCGTATGAGCTTCCCGTTAATGGCTCTCCGGAGCTTCC
1 CGATACATGGCTCACATGAGCTTCCCGTTAATGGCTCTCCAGAGCTTCC
* *
54867247 CGTTACATGGCTCACATGAGCTTCCTGTTATATGGCT
1 CGATACATGGCTCACATGAGCTTCCCGTTA-ATGGCT
54867284 TGGAAGAGTT
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
48 24 0.33
49 36 0.50
50 12 0.17
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (49 bp):
CGATACATGGCTCACATGAGCTTCCCGTTAATGGCTCTCCAGAGCTTCC
Found at i:54868786 original size:20 final size:20
Alignment explanation
Indices: 54868749--54868790 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
54868739 AAATAAAAAC
* *
54868749 AAATAGAAATACATGTATTAA
1 AAATAGAAATAAAAGTA-TAA
54868770 AAATAG-AATAAAAGTATAA
1 AAATAGAAATAAAAGTATAA
54868789 AA
1 AA
54868791 GTATGCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 8 0.42
21 6 0.32
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.24
Consensus pattern (20 bp):
AAATAGAAATAAAAGTATAA
Found at i:54869104 original size:3 final size:3
Alignment explanation
Indices: 54869096--54869127 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
54869086 GTATGTAGGC
54869096 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
54869128 GTACAACATT
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:54878710 original size:31 final size:30
Alignment explanation
Indices: 54878663--54878727 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
54878653 ATTAGGATTG
*
54878663 AAAATTTAAAATTTAAAACGTATAAATACT
1 AAAATTTAAAATTTAAAACGTATAAAGACT
* *
54878693 AAAATTTACCAATTTAAAATGTATAAAGACT
1 AAAATTTA-AAATTTAAAACGTATAAAGACT
54878724 AAAA
1 AAAA
54878728 CTGGCCAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.31
Consensus pattern (30 bp):
AAAATTTAAAATTTAAAACGTATAAAGACT
Found at i:54879204 original size:12 final size:12
Alignment explanation
Indices: 54879187--54879211 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54879177 GTATATAAAT
54879187 TTATTAAAAAAA
1 TTATTAAAAAAA
54879199 TTATTAAAAAAA
1 TTATTAAAAAAA
54879211 T
1 T
54879212 AAATGAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTATTAAAAAAA
Found at i:54887151 original size:12 final size:11
Alignment explanation
Indices: 54887134--54887222 Score: 52
Period size: 12 Copynumber: 7.4 Consensus size: 11
54887124 CTCTTCTCTT
54887134 TTTTTTTTCAAA
1 TTTTTTTTC-AA
54887146 TTTTTTTTCAA
1 TTTTTTTTCAA
**
54887157 TTTTTTTCTCTCTCT
1 -TTTTTT-T-TC-AA
*
54887172 TTTTTTTGCTCGA
1 TTTTTTT--TCAA
*
54887185 TTTTTTTTCACT
1 TTTTTTTTCA-A
*
54887197 TTTTTTTTGAA
1 TTTTTTTTCAA
*
54887208 TTTTTTTTCGA
1 TTTTTTTTCAA
54887219 TTTT
1 TTTT
54887223 CTTTGTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
11 17 0.28
12 24 0.39
13 9 0.15
14 11 0.18
ACGTcount: A:0.11, C:0.12, G:0.04, T:0.72
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:54887188 original size:39 final size:39
Alignment explanation
Indices: 54887128--54887202 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
54887118 GAAATCCTCT
*
54887128 TCTCTTTTTTTTTTCAAATTTTTTTTCAATTTTTTTCTC
1 TCTCTTTTTTTTCTCAAATTTTTTTTCAATTTTTTTCTC
* *
54887167 TCTCTTTTTTTTGCTC-GATTTTTTTTCACTTTTTTT
1 TCTCTTTTTTTT-CTCAAATTTTTTTTCAATTTTTTT
54887203 TTGAATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 30 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.16, G:0.03, T:0.72
Consensus pattern (39 bp):
TCTCTTTTTTTTCTCAAATTTTTTTTCAATTTTTTTCTC
Found at i:54887548 original size:14 final size:14
Alignment explanation
Indices: 54887529--54887555 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54887519 AAAGGTTGGC
54887529 TAAAGATAAAATAA
1 TAAAGATAAAATAA
54887543 TAAAGATAAAATA
1 TAAAGATAAAATA
54887556 TAAGATATTC
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:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (14 bp):
TAAAGATAAAATAA
Found at i:54889835 original size:20 final size:21
Alignment explanation
Indices: 54889798--54889840 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
54889788 CCGTGGGTTC
*
54889798 TTCTTTCTTTCTC-TTTTTCT
1 TTCTTTCTTTCTCATTTTGCT
54889818 TTCTTTCTGTT-TCATTTTGCT
1 TTCTTTCT-TTCTCATTTTGCT
54889839 TT
1 TT
54889841 TGTCTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.02, C:0.21, G:0.05, T:0.72
Consensus pattern (21 bp):
TTCTTTCTTTCTCATTTTGCT
Found at i:54892618 original size:46 final size:46
Alignment explanation
Indices: 54892560--54892868 Score: 283
Period size: 46 Copynumber: 6.8 Consensus size: 46
54892550 AACCTAATGT
* * *
54892560 CATATTGTCTTTCAACTATGATCTTATTCATTTTTCGTCATATTGC
1 CATAGTGTCTTTCAACTATGGTCTTATTCATTTTTCGTCATGTTGC
* *
54892606 CATAATGTCTTTCAACTATGGTCTTATTCATTTTCCGTCATGTTGC
1 CATAGTGTCTTTCAACTATGGTCTTATTCATTTTTCGTCATGTTGC
* *
54892652 CATAGTGTCTTTCAACTATGGTCATATTCA-TTTTCTGTCATGTTGT
1 CATAGTGTCTTTCAACTATGGTCTTATTCATTTTTC-GTCATGTTGC
54892698 CATAGTGTCTTTCAACTATGGTCTTATTCATTTTT-GAT-ATAG-TGC
1 CATAGTGTCTTTCAACTATGGTCTTATTCATTTTTCG-TCAT-GTTGC
* * * * * * *
54892743 TATAGCGTCTTTCAGCTATGGTGTTACTCGTTTGATTCGTGATG-T--
1 CATAGTGTCTTTCAACTATGGTCTTATTCATTT--TTCGTCATGTTGC
* * * * * * *
54892788 CATAGCGTCTTTCAACTATGGTCCTACTCGTTTTT-TTCGTGATGC
1 CATAGTGTCTTTCAACTATGGTCTTATTCATTTTTCGTCATGTTGC
* * * * *
54892833 CATAGCGTCTTTTAGCTATGGTCTTACTCGTTTTTC
1 CATAGTGTCTTTCAACTATGGTCTTATTCATTTTTC
54892869 AACCAACAAA
Statistics
Matches: 225, Mismatches: 26, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
42 3 0.01
43 3 0.01
45 97 0.43
46 110 0.49
47 9 0.04
48 3 0.01
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.46
Consensus pattern (46 bp):
CATAGTGTCTTTCAACTATGGTCTTATTCATTTTTCGTCATGTTGC
Found at i:54892822 original size:90 final size:90
Alignment explanation
Indices: 54892612--54892865 Score: 251
Period size: 90 Copynumber: 2.8 Consensus size: 90
54892602 TTGCCATAAT
* * ** * * * *
54892612 GTCTTTCAACTATGGTCTTATTCATTTTCCGTCATGTTGCCATAGTGTCTTTCAACTATGGTCAT
1 GTCTTTCAACTATGGTCCTACTCATTTT-TATCATGATGCCATAGCGTCTTTCAGCTATGGTCTT
* * ** * * *
54892677 ATTCATTTTCTGTCATGTTGTCATAGT
65 ACTCGTTTGAT-TCGTGATGTCATAGC
* * * *
54892704 GTCTTTCAACTATGGTCTTATTCATTTTTGAT-AT-AGTGCTATAGCGTCTTTCAGCTATGGTGT
1 GTCTTTCAACTATGGTCCTACTCATTTTT-ATCATGA-TGCCATAGCGTCTTTCAGCTATGGTCT
54892767 TACTCGTTTGATTCGTGATGTCATAGC
64 TACTCGTTTGATTCGTGATGTCATAGC
* * * *
54892794 GTCTTTCAACTATGGTCCTACTCGTTTTTTTCGTGATGCCATAGCGTCTTTTAGCTATGGTCTTA
1 GTCTTTCAACTATGGTCCTACTCATTTTTATCATGATGCCATAGCGTCTTTCAGCTATGGTCTTA
54892859 CTCGTTT
66 CTCGTTT
54892866 TTCAACCAAC
Statistics
Matches: 135, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
89 1 0.01
90 72 0.53
91 33 0.24
92 29 0.21
ACGTcount: A:0.17, C:0.19, G:0.18, T:0.46
Consensus pattern (90 bp):
GTCTTTCAACTATGGTCCTACTCATTTTTATCATGATGCCATAGCGTCTTTCAGCTATGGTCTTA
CTCGTTTGATTCGTGATGTCATAGC
Found at i:54892866 original size:45 final size:45
Alignment explanation
Indices: 54892603--54892867 Score: 192
Period size: 45 Copynumber: 5.8 Consensus size: 45
54892593 TTCGTCATAT
** * * * ** * *
54892603 TGCCATAATGTCTTTCAACTATGGTCTTATTCATTTTCCGTCATGT
1 TGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTTTT-TTTCGTGA
* * * * * * * *
54892649 TGCCATAGTGTCTTTCAACTATGGTCATATTCATTTTCTGTCATGT
1 TGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTTTT-TTTCGTGA
* * * * * * *
54892695 TGTCATAGTGTCTTTCAACTATGGTCTTATTCATTTTTGAT-AT-A
1 TGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTTTTT-TTCGTGA
* * **
54892739 GTGCTATAGCGTCTTTCAGCTATGGTGTTACTCGTTTGATTCGTGA
1 -TGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTTTTTTTCGTGA
* * *
54892785 TGTCATAGCGTCTTTCAACTATGGTCCTACTCGTTTTTTTCGTGA
1 TGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTTTTTTTCGTGA
*
54892830 TGCCATAGCGTCTTTTAGCTATGGTCTTACTCGTTTTT
1 TGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTTTTT
54892868 CAACCAACAA
Statistics
Matches: 186, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.01
45 105 0.56
46 80 0.43
ACGTcount: A:0.18, C:0.19, G:0.17, T:0.46
Consensus pattern (45 bp):
TGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTTTTTTTCGTGA
Found at i:54903408 original size:15 final size:16
Alignment explanation
Indices: 54903388--54903418 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54903378 GGATGAGTTG
54903388 ATTCGG-TTTAAATTA
1 ATTCGGATTTAAATTA
54903403 ATTCGGATTTAAATTA
1 ATTCGGATTTAAATTA
54903419 TCTGAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (16 bp):
ATTCGGATTTAAATTA
Found at i:54903459 original size:14 final size:16
Alignment explanation
Indices: 54903435--54903466 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
54903425 TTTAAGGTTA
54903435 TTTATA-TTTTTTGGG
1 TTTATATTTTTTTGGG
54903450 TTTA-ATTTTTTTGGG
1 TTTATATTTTTTTGGG
54903465 TT
1 TT
54903467 GGTTGGAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 1 0.06
15 15 0.94
ACGTcount: A:0.12, C:0.00, G:0.19, T:0.69
Consensus pattern (16 bp):
TTTATATTTTTTTGGG
Found at i:54906871 original size:19 final size:19
Alignment explanation
Indices: 54906847--54906885 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
54906837 CGCCGCCCCC
54906847 ACTTGCGCCGTCACCTGCA
1 ACTTGCGCCGTCACCTGCA
54906866 ACTTGCGCCGTCACCTGCA
1 ACTTGCGCCGTCACCTGCA
54906885 A
1 A
54906886 GACACGCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.18, C:0.41, G:0.21, T:0.21
Consensus pattern (19 bp):
ACTTGCGCCGTCACCTGCA
Found at i:54908244 original size:73 final size:74
Alignment explanation
Indices: 54908125--54908268 Score: 247
Period size: 73 Copynumber: 2.0 Consensus size: 74
54908115 TCTTTTCAAA
* *
54908125 CTCAAGTTTTAAATGATCTCGGGAATTAAGAAGAAATCGTGTCCTAACTTACTGGGCATGATC-C
1 CTCAAGTTTTAAACGATCTCAGGAATTAAGAAGAAATCGTGTCCTAACTTACTGGGCATGATCTC
54908189 TTTTTTTTT
66 TTTTTTTTT
54908198 CTCAAGTTTTAAACGATCTCAGGAATTAAGAA-AAGATCGTGTCCTAACTTACTGGGCATGATCT
1 CTCAAGTTTTAAACGATCTCAGGAATTAAGAAGAA-ATCGTGTCCTAACTTACTGGGCATGATCT
54908262 CTTTTTT
65 CTTTTTT
54908269 AAATTCGAGA
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
72 2 0.03
73 58 0.87
74 7 0.10
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (74 bp):
CTCAAGTTTTAAACGATCTCAGGAATTAAGAAGAAATCGTGTCCTAACTTACTGGGCATGATCTC
TTTTTTTTT
Found at i:54909804 original size:19 final size:19
Alignment explanation
Indices: 54909780--54909826 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
54909770 ACGTCCTTTT
*
54909780 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
54909799 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
54909818 TATGCATTA
1 TTTGCATTA
54909827 AAGTCTACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:54912774 original size:40 final size:39
Alignment explanation
Indices: 54912718--54912795 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
54912708 AGAGAACCAA
*
54912718 GGTGAAAACCCACAAAGGGCGCTATGAGTTCTAAAAAAAG
1 GGTGAAAACCCACAAAGGGCGCTATGAG-TCCAAAAAAAG
* * *
54912758 GGTGAAAACCCGCAAAGGGCGTTTTGAGTCCAAAAAAA
1 GGTGAAAACCCACAAAGGGCGCTATGAGTCCAAAAAAA
54912796 TAAAAAATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 9 0.26
40 25 0.74
ACGTcount: A:0.41, C:0.18, G:0.26, T:0.15
Consensus pattern (39 bp):
GGTGAAAACCCACAAAGGGCGCTATGAGTCCAAAAAAAG
Found at i:54914113 original size:88 final size:88
Alignment explanation
Indices: 54913955--54914141 Score: 250
Period size: 88 Copynumber: 2.1 Consensus size: 88
54913945 AGAAAACAGC
* * * * * * *
54913955 AGATATTGTCTTCCTGTACTGGCAGTGAAGTAGATCAAAAACATCAGCCTTATCTCCCTGAGTAT
1 AGATCTTGTCTTCCTGTACTGACAGTGAAGCAAATCAAAAACACCAGCCTTATCTCCCTGAGCAG
* **
54914020 TAGTGGAGTAGGTTTAAGATTGT
66 CAGTGGAGTAGGTCGAAGATTGT
*
54914043 AGATCTTGTCTTCCTGTACTGACAGTGAAGCAAATCAAAAACACCAATCC-TATCTCCCTGAGCA
1 AGATCTTGTCTTCCTGTACTGACAGTGAAGCAAATCAAAAACACC-AGCCTTATCTCCCTGAGCA
54914107 GCAGTGGAGTAGGTCGAAGATTGT
65 GCAGTGGAGTAGGTCGAAGATTGT
*
54914131 AAATCTTGTCT
1 AGATCTTGTCT
54914142 CCCTAAGCAG
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
88 83 0.97
89 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (88 bp):
AGATCTTGTCTTCCTGTACTGACAGTGAAGCAAATCAAAAACACCAGCCTTATCTCCCTGAGCAG
CAGTGGAGTAGGTCGAAGATTGT
Found at i:54914341 original size:132 final size:132
Alignment explanation
Indices: 54914085--54914347 Score: 314
Period size: 132 Copynumber: 2.0 Consensus size: 132
54914075 AATCAAAAAC
* * * * *
54914085 ACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAAATCTTGTCTCCCTAAGC
1 ACCAATCCTATCTCCCTAAGCAGAAGTGGAGTAGGTCGAAGATTGCAAATCCTGCCTCCCTAAGC
* * ** * * * *
54914150 AGTAGTGGAGCATATCAAAGACGGTGAATCTTATCTTACCAGGGTAGTAGGGAAGCAAATTTAAG
66 AGTAGTGGAGCAGATCAAAGACAGCAAATCTTATCTTACCAGCGTAGCAGAGAAGCAAATTAAAG
54914215 CA
131 CA
* * *
54914217 ACCAGTCCTATCTCCCTAAGCAGAAGTGGAGTAGGTTGAAGATTGCAGATCCTGCCTCCCTAAGC
1 ACCAATCCTATCTCCCTAAGCAGAAGTGGAGTAGGTCGAAGATTGCAAATCCTGCCTCCCTAAGC
* * * *
54914282 AGTAGTGGAGCAGATCGAAGACAGCAAATCTTAT-TTCCCTAGCTTTGCAGTAGAA-CAAATTAA
66 AGTAGTGGAGCAGATCAAAGACAGCAAATCTTATCTTACC-AGCGTAGCAG-AGAAGCAAATTAA
54914345 AGC
129 AGC
54914348 TAAAGGTAGC
Statistics
Matches: 109, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
131 4 0.04
132 102 0.94
133 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (132 bp):
ACCAATCCTATCTCCCTAAGCAGAAGTGGAGTAGGTCGAAGATTGCAAATCCTGCCTCCCTAAGC
AGTAGTGGAGCAGATCAAAGACAGCAAATCTTATCTTACCAGCGTAGCAGAGAAGCAAATTAAAG
CA
Found at i:54914370 original size:51 final size:52
Alignment explanation
Indices: 54914308--54914413 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 52
54914298 GAAGACAGCA
* *
54914308 AATCTTATTTCCCTAGCTTTGCAGTAGAACAAATTAAAGCTAAAG-GTAGCG
1 AATCTTATTTCCCTAGCATTGCAGTAGAACAAATTAAAGCTAAAGTGAAGCG
* * * * * * *
54914359 AATCTTGTTTCCCTGGCATTGTAGTGGAATAGATTAAAGCTGAAGTGAAGCG
1 AATCTTATTTCCCTAGCATTGCAGTAGAACAAATTAAAGCTAAAGTGAAGCG
54914411 AAT
1 AAT
54914414 TAAAGCTGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
51 37 0.82
52 8 0.18
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (52 bp):
AATCTTATTTCCCTAGCATTGCAGTAGAACAAATTAAAGCTAAAGTGAAGCG
Found at i:54914667 original size:45 final size:43
Alignment explanation
Indices: 54914616--54915172 Score: 187
Period size: 44 Copynumber: 12.8 Consensus size: 43
54914606 ATGGCAAATA
* * *
54914616 TTATCTCCTTAAAGTTGCAGTTGAGCAGATTAAAGCCAACAAGTC
1 TTATCTCCCTAAAGTTACAGTAGAGCAGATTAAAGCC-ACAA-TC
* * * * * *
54914661 TTATCTCCCTGAAGTTGCACTAGAGCAGATTGAAGTCACTAATA
1 TTATCTCCCTAAAGTTACAGTAGAGCAGATTAAAGCCAC-AATC
* * *
54914705 TTATCTCCCTAAAGTTACAGTGGATCAGATTAAAGCCACAAACC
1 TTATCTCCCTAAAGTTACAGTAGAGCAGATTAAAGCCAC-AATC
** * * * ** *
54914749 TTATCTCTATAAAGTTACAGTAGAGTAGGTTGAAGTAACAAACC
1 TTATCTCCCTAAAGTTACAGTAGAGCAGATTAAAGCCAC-AATC
* * * * * * **
54914793 TTATCCCCCTAAAGTTATAGTGGGGCAGGTTGAAGATACAAGTC
1 TTATCTCCCTAAAGTTACAGTAGAGCAGATTAAAGCCACAA-TC
* * * * * * ** * *
54914837 TTATCTCTCTCAACTTGCAGTGGAGCTGAAGATAG-C-GAATC
1 TTATCTCCCTAAAGTTACAGTAGAGCAGATTAAAGCCACAATC
* * ** * * * * *
54914878 TTATTTCCCTGAAGTTGTAATGGAACAGATTGAAGCTATAAATTACAGATC
1 TTATCTCCCTAAAGTTACAGTAGAGCAGATTAAAGC-------CACA-ATC
* * * * * * * *
54914929 TTATCTCTCTGAAGTTGCAGTAGAGCAAATCATA-TCA-AACC
1 TTATCTCCCTAAAGTTACAGTAGAGCAGATTAAAGCCACAATC
* * * *
54914970 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAA--C-CAATC
1 TTATCTCCCTAAAGTTACAGTAGAGCAGATTAAAGCCACAATC
** * * * *
54915010 TTATCTCATTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAATC
1 TTATCTCCCTAAAGTTACAGTAGAGCAGATTAAAGCCAC-AATC
* * *
54915054 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAA-AC-CAATC
1 TTATCTCCCTAAAGTTACAGTAGAGCAGATTAAAGCCACAATC
* * ** * *
54915095 TTATCTCCTTAAAGTTGCAGCGGAGCAGATTGAAGCTACTAATC
1 TTATCTCCCTAAAGTTACAGTAGAGCAGATTAAAGCCAC-AATC
* * * * * *
54915139 CTATCTCCCTGAAGTTGCAATTGAGCGGATTAAA
1 TTATCTCCCTAAAGTTACAGTAGAGCAGATTAAA
54915173 ACGATGAATC
Statistics
Matches: 385, Mismatches: 107, Indels: 41
0.72 0.20 0.08
Matches are distributed among these distances:
40 34 0.09
41 90 0.23
42 5 0.01
43 6 0.02
44 189 0.49
45 33 0.09
50 1 0.00
51 27 0.07
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (43 bp):
TTATCTCCCTAAAGTTACAGTAGAGCAGATTAAAGCCACAATC
Found at i:54914803 original size:88 final size:89
Alignment explanation
Indices: 54914610--54914820 Score: 226
Period size: 88 Copynumber: 2.4 Consensus size: 89
54914600 CTGAAGATGG
* * * * ** * *
54914610 CAAATATTATCTCCTTAAAGTTGCAGTTGAGCAGATTAAAGCCAACAAGTCTTATCTCCCTGAAG
1 CAAACATTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCCAACAAACCTTATCTCCATAAAG
* *
54914675 TTGCACTAGAGCAGATTGAAGTCA
66 TTACACTAGAGCAGATTGAAGTAA
* * * *
54914699 CTAATATTATCTCCCTAAAGTTACAGTGGATCAGATTAAAGCC-ACAAACCTTATCTCTATAAAG
1 CAAACATTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCCAACAAACCTTATCTCCATAAAG
* * *
54914763 TTACAGTAGAGTAGGTTGAAGTAA
66 TTACACTAGAGCAGATTGAAGTAA
* * * *
54914787 CAAACCTTATCCCCCTAAAGTTATAGTGGGGCAG
1 CAAACATTATCTCCCTAAAGTTACAGTGGAGCAG
54914821 GTTGAAGATA
Statistics
Matches: 100, Mismatches: 22, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
88 62 0.62
89 38 0.38
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (89 bp):
CAAACATTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCCAACAAACCTTATCTCCATAAAG
TTACACTAGAGCAGATTGAAGTAA
Found at i:54915339 original size:44 final size:44
Alignment explanation
Indices: 54914926--54915748 Score: 411
Period size: 44 Copynumber: 18.7 Consensus size: 44
54914916 TAAATTACAG
* * * * * *
54914926 ATCTTATCTCTCTGAAGTTGCAGTAGAGCA-AAT-CATAT-CAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACCA
* *
54914967 ACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTT--A-A-ACCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACCA
** * ** *
54915007 ATCTTATCTCATTGAAGTTGCAGTGGAGCAGATTGAAGCCACTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACCA
*
54915051 ATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATT-AA-A-ACCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACCA
* * * * * *
54915092 ATCTTATCTCCTTAAAGTTGCAGCGGAGCAGATTGAAGCTACTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACCA
* * * * *
54915136 ATCCTATCTCCCTGAAGTTGCAATTGAGCGGATTAAAACGAT--GA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAA-GATACCA
* * * * *
54915180 ATCCTATGC-CTCTGAAGTTGCAGTAGG-TC-GAATTAATTCTACCATAACA
1 ATCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAG-ATTAA----A-GATACCA
* * *
54915229 AGTCTAATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACCA
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAT-ACCA
* *
54915275 ACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGATACCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACCA
* * * * **
54915319 ATCTTATCTCCCTGATGTTGCAGTGGAGAAGATTGAAGCTATTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACCA
* * * *
54915363 ATCCTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAA-ACCACGA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGA-TACCA
** * * * * *
54915407 ATCTCCTCCCCCTGAAGTCGCAGTGGAGGAGGTTGAAA-A-AACA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGATACCA
* * * * * *
54915450 GGTCGTATCTCTTTCTAAAGTTGCAGTGGAGTAGA-TAAAGATAGCA
1 -ATCTTATCTC--CCTGAAGTTGCAGTGGAGCAGATTAAAGATACCA
* * * * * *
54915496 GACCTTATCTCCCTGGAGTTGCAGGGGAACAGGTTGAAA-ATATCA
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGATACCA
* * * * ** *
54915541 ATATTATCTCCCTGAAGTTACAATGGAGCAGATTGAAGCCACTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACCA
* * *
54915585 ATCTTATC-CCTCTGAACTTGCAGCGGAGCAGATTAAAG--CCGCA
1 ATCTTATCTCC-CTGAAGTTGCAGTGGAGCAGATTAAAGATAC-CA
* ** * * * * * *
54915628 AACATTATCTCTATGAAGTCGCAGTAGAGTAGGTTGAAG-TAACAA
1 ATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAT-ACCA
* * * * * *
54915673 ACCTTATCCCCCTAAAGTTGCAGT-GAGGCAGGTTGAAGATA-TA
1 ATCTTATCTCCCTGAAGTTGCAGTGGA-GCAGATTAAAGATACCA
* *
54915716 AGTCTTATCTCCCTAAAGTTGTAGTGGAGCAGA
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
54915749 CTGTAGATAG
Statistics
Matches: 593, Mismatches: 144, Indels: 87
0.72 0.17 0.11
Matches are distributed among these distances:
40 33 0.06
41 63 0.11
42 5 0.01
43 18 0.03
44 344 0.58
45 59 0.10
46 39 0.07
47 4 0.01
49 5 0.01
50 22 0.04
51 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACCA
Found at i:54915368 original size:183 final size:179
Alignment explanation
Indices: 54915056--54915386 Score: 421
Period size: 183 Copynumber: 1.8 Consensus size: 179
54915046 CACTAATCTT
* * *
54915056 ATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCAATCTTATCTCCTTAAAGTTGCAGCGGAGC
1 ATCTCCCTAAAGTTGCAGTGGAGCAGATAAAAACCAACCTTATCTCCCTAAAGTTGCAGCGGAGC
* * * * **
54915121 AGATTGAAGCTACTAATCCTATCTCCCTGAAGTTGCAATTGAGCGGATTAAAACGATGAATCCTA
66 AGATTAAAGATACCAATCCTATCTCCCTGAAGTTGCAATGGAGAAGATTAAAACGATGAATCCTA
54915186 T-GCCTCTGAAGTTGCAGTAGGTCGAATTAATTCTACCATAACAAGTCTA
131 TCGCCT-TGAAGTTGCAGTAGGTCGAATTAATTCTACCATAACAAGTCTA
* * *
54915235 ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACCAACCTTATCTCCCTGAAGTTGCAGTG
1 ATCTCCCTAAAGTTGCAGTGGAGCAGA-T-AA-A-AACCAACCTTATCTCCCTAAAGTTGCAGCG
* * * * * * * *
54915300 GAGCAGGTTAAAGATACCAATCTTATCTCCCTGATGTTGCAGTGGAGAAGATTGAAGCTATTAAT
62 GAGCAGATTAAAGATACCAATCCTATCTCCCTGAAGTTGCAATGGAGAAGATTAAAACGATGAAT
*
54915365 CCTATCTCCTTGAAGTTGCAGT
127 CCTATCGCCTTGAAGTTGCAGT
54915387 GGAGCAGATT
Statistics
Matches: 126, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
179 26 0.21
180 1 0.01
181 1 0.01
182 1 0.01
183 94 0.75
184 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (179 bp):
ATCTCCCTAAAGTTGCAGTGGAGCAGATAAAAACCAACCTTATCTCCCTAAAGTTGCAGCGGAGC
AGATTAAAGATACCAATCCTATCTCCCTGAAGTTGCAATGGAGAAGATTAAAACGATGAATCCTA
TCGCCTTGAAGTTGCAGTAGGTCGAATTAATTCTACCATAACAAGTCTA
Found at i:54915664 original size:222 final size:223
Alignment explanation
Indices: 54915244--54915665 Score: 530
Period size: 222 Copynumber: 1.9 Consensus size: 223
54915234 AATCTCCCTG
* * *
54915244 AAGTTGCAGTGGAGCAGACTGAAGATAACCAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTT
1 AAGTTGCAGTGGAGCAGACTAAAGATAACCAACCTTATCTCCCTGAAGTTGCAGGGGAACAGGTT
* * * * * *
54915309 AAAGATACCAATCTTATCTCCCTGATGTTGCAGTGGAGAAGATTGAAGCTATTAATCCTATCTCC
66 AAAGATACCAATATTATCTCCCTGAAGTTACAATGGAGAAGATTGAAGCCACTAATCCTATCTCC
* * * * * *
54915374 TTGAAGTTGCAGTGGAGCAGATTAAAACCACGAATCTCCTCCCCCTGAAGTCGCAGTGGAGGAGG
131 TTGAACTTGCAGCGGAGCAGATTAAAACCACGAAACTCATCCCCATGAAGTCGCAGTAGAGGAGG
54915439 TTGAAAAAACAGGTCGTATCTCTTTCTA
196 TTGAAAAAACAGGTCGTATCTCTTTCTA
* * *
54915467 AAGTTGCAGTGGAGTAGA-TAAAGAT-AGCAGACCTTATCTCCCTGGAGTTGCAGGGGAACAGGT
1 AAGTTGCAGTGGAGCAGACTAAAGATAACCA-ACCTTATCTCCCTGAAGTTGCAGGGGAACAGGT
* * *
54915530 TGAAA-ATATCAATATTATCTCCCTGAAGTTACAATGGAGCAGATTGAAGCCACTAATCTTATC-
65 T-AAAGATACCAATATTATCTCCCTGAAGTTACAATGGAGAAGATTGAAGCCACTAATCCTATCT
* * * * *
54915593 CCTCTGAACTTGCAGCGGAGCAGATTAAAGCCGC-AAACATTATCTCTATGAAGTCGCAGTAGAG
129 CCT-TGAACTTGCAGCGGAGCAGATTAAAACCACGAAAC-TCATCCCCATGAAGTCGCAGTAGAG
*
54915657 TAGGTTGAA
192 GAGGTTGAA
54915666 GTAACAAACC
Statistics
Matches: 168, Mismatches: 27, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
221 9 0.05
222 139 0.83
223 20 0.12
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (223 bp):
AAGTTGCAGTGGAGCAGACTAAAGATAACCAACCTTATCTCCCTGAAGTTGCAGGGGAACAGGTT
AAAGATACCAATATTATCTCCCTGAAGTTACAATGGAGAAGATTGAAGCCACTAATCCTATCTCC
TTGAACTTGCAGCGGAGCAGATTAAAACCACGAAACTCATCCCCATGAAGTCGCAGTAGAGGAGG
TTGAAAAAACAGGTCGTATCTCTTTCTA
Found at i:54920551 original size:74 final size:73
Alignment explanation
Indices: 54920438--54920582 Score: 256
Period size: 74 Copynumber: 2.0 Consensus size: 73
54920428 TCTTTTCAAA
*
54920438 CTCAAGTTTTAAATGATCTCGGGAATTAAGAAGAAATCGTGTCCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAATGATCTCGGGAATTAAGAAGAAATCGTGTCCTAACTTACTGGGCAGGAT-CC
54920503 CTTTTTTTT
65 CTTTTTTTT
54920512 CTCAAGTTTTAAATGATCTCGGGAATTAAGAA-AAGATCGTGTCCTAACTTACTGGGCAGGATCC
1 CTCAAGTTTTAAATGATCTCGGGAATTAAGAAGAA-ATCGTGTCCTAACTTACTGGGCAGGATCC
54920576 CTTTTTT
65 CTTTTTT
54920583 AAATCCGAGA
Statistics
Matches: 69, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
73 11 0.16
74 58 0.84
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (73 bp):
CTCAAGTTTTAAATGATCTCGGGAATTAAGAAGAAATCGTGTCCTAACTTACTGGGCAGGATCCC
TTTTTTTT
Found at i:54925648 original size:22 final size:23
Alignment explanation
Indices: 54925597--54925649 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
54925587 TAATTAAAAT
* * *
54925597 TAAAATTAAAATTATTTTTTTAA
1 TAAAATTAAAACTATATTGTTAA
*
54925620 TAAAATTAAAACTA-ATTGTTAG
1 TAAAATTAAAACTATATTGTTAA
54925642 TAAAATTA
1 TAAAATTA
54925650 TCAAATTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (23 bp):
TAAAATTAAAACTATATTGTTAA
Found at i:54925799 original size:9 final size:9
Alignment explanation
Indices: 54925787--54925814 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
54925777 TTTATCAAAT
54925787 TATTAATTG
1 TATTAATTG
54925796 TATTAATTG
1 TATTAATTG
54925805 TATTAATTG
1 TATTAATTG
54925814 T
1 T
54925815 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:54925839 original size:68 final size:65
Alignment explanation
Indices: 54925638--54925844 Score: 360
Period size: 65 Copynumber: 3.1 Consensus size: 65
54925628 AAACTAATTG
* *
54925638 TTAGTAAAATTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAATCTAACATTTGA
1 TTAGTAAATTTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAAAAAATCTAACATTTGA
54925703 TTAGTAAATTTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTG
1 TTAGTAAATTTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAA-AAAATCTAACATTTG
54925768 A
65 A
54925769 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAA-AAAATCTAACATT
54925834 TGA
63 TGA
54925837 TTAGTAAA
1 TTAGTAAA
54925845 ACAAACTTGA
Statistics
Matches: 136, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
65 48 0.35
66 42 0.31
68 46 0.34
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (65 bp):
TTAGTAAATTTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAAAAAATCTAACATTTGA
Found at i:54925935 original size:21 final size:23
Alignment explanation
Indices: 54925909--54925952 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
54925899 GTAAATAAAC
*
54925909 TTTAAAAA-AAAACTAT-TATAT
1 TTTAAAAATAAAAATATATATAT
54925930 TTTAAAAATAAAAATATATATAT
1 TTTAAAAATAAAAATATATATAT
54925953 AATATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 7 0.35
23 5 0.25
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TTTAAAAATAAAAATATATATAT
Found at i:54927765 original size:56 final size:58
Alignment explanation
Indices: 54927667--54927779 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 58
54927657 AAAAAATTCA
54927667 AAATAAATAATAAAAATTTAAAATTTAAAATACATTTTAAAATT-ATCTTTTTGGTAC
1 AAATAAATAATAAAAATTTAAAATTTAAAATACATTTTAAAATTAATCTTTTTGGTAC
* * * *
54927724 AAATAAATAATAATAATTT-AAATTTGAAATATATTTTAAAATTAATTTTTTTGGTA
1 AAATAAATAATAAAAATTTAAAATTTAAAATACATTTTAAAATTAATCTTTTTGGTA
54927780 TCGATCTATA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 22 0.43
57 29 0.57
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (58 bp):
AAATAAATAATAAAAATTTAAAATTTAAAATACATTTTAAAATTAATCTTTTTGGTAC
Found at i:54928933 original size:14 final size:16
Alignment explanation
Indices: 54928896--54928933 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
54928886 TCAAATATTT
*
54928896 TATAAAACATAAATAA
1 TATAAAATATAAATAA
54928912 TATAAAATATAAA-AA
1 TATAAAATATAAATAA
54928927 T-TAAAAT
1 TATAAAAT
54928934 TACATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 3 0.14
16 12 0.57
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
TATAAAATATAAATAA
Found at i:54931588 original size:15 final size:15
Alignment explanation
Indices: 54931568--54931605 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
54931558 CTACATCTTT
54931568 TATAATAAT-TTATA
1 TATAATAATATTATA
54931582 GTATAATAATACTTATA
1 -TATAATAATA-TTATA
54931599 TATAATA
1 TATAATA
54931606 GTAATACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 7 0.33
17 5 0.24
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (15 bp):
TATAATAATATTATA
Found at i:54931632 original size:14 final size:15
Alignment explanation
Indices: 54931613--54931641 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54931603 ATAGTAATAC
54931613 ATTATATATT-TATT
1 ATTATATATTATATT
54931627 ATTATATATTATATT
1 ATTATATATTATATT
54931642 GCTTGAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTATATATTATATT
Found at i:54931837 original size:30 final size:30
Alignment explanation
Indices: 54931803--54931879 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 30
54931793 TATATTATAA
54931803 TAATAGTTATATATGTATTAATA-ATTTTA-G
1 TAATAGTTATATAT-TA-TAATATATTTTATG
54931833 TAATAGTTATATATTATAATATTATTTTATG
1 TAATAGTTATATATTATAATA-TATTTTATG
* *
54931864 TATTAGTAATATATTA
1 TAATAGTTATATATTA
54931880 ATTTAGTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 5 0.12
29 2 0.05
30 20 0.48
31 15 0.36
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (30 bp):
TAATAGTTATATATTATAATATATTTTATG
Found at i:54947102 original size:2 final size:2
Alignment explanation
Indices: 54947095--54947154 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
54947085 TAGTCGGGGG
54947095 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54947137 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
54947155 GAGAGAGAGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54947283 original size:2 final size:2
Alignment explanation
Indices: 54947278--54947317 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
54947268 TCTCTCTCTC
54947278 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54947318 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54952140 original size:9 final size:9
Alignment explanation
Indices: 54952126--54952153 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
54952116 TTTTGTTACA
54952126 ACAATTAAT
1 ACAATTAAT
54952135 ACAATTAAT
1 ACAATTAAT
54952144 ACAATTAAT
1 ACAATTAAT
54952153 A
1 A
54952154 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:54952175 original size:68 final size:66
Alignment explanation
Indices: 54952096--54952233 Score: 240
Period size: 68 Copynumber: 2.1 Consensus size: 66
54952086 TCAAGTTTGT
*
54952096 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
54952161 AAA
64 AAA
54952164 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
54952229 T
66 A
54952230 TTTA
1 TTTA
54952234 TTAACAATTA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 23 0.34
67 1 0.01
68 44 0.65
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:54952247 original size:16 final size:16
Alignment explanation
Indices: 54952226--54952267 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
54952216 AATAATTTGA
*
54952226 TAATTTTATTAACAAT
1 TAATTTTAATAACAAT
54952242 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
54952258 TAGTTTTAAT
1 TAATTTTAAT
54952268 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:54952251 original size:22 final size:22
Alignment explanation
Indices: 54952241--54952301 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
54952231 TTATTAACAA
* * * *
54952241 TTAATTTTAATAACAATTAGTT
1 TTAATTTTATTAAAAAATAATT
54952263 TTAATTTTATTAAAAAATAATT
1 TTAATTTTATTAAAAAATAATT
54952285 TTAATTTTAATTAAAAA
1 TTAATTTT-ATTAAAAA
54952302 CGGGTCGGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 26 0.76
23 8 0.24
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATTTTATTAAAAAATAATT
Found at i:54954398 original size:15 final size:15
Alignment explanation
Indices: 54954380--54954408 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54954370 AATTCTTAAA
54954380 AGATAAATGTTTTAG
1 AGATAAATGTTTTAG
54954395 AGATAAATGTTTTA
1 AGATAAATGTTTTA
54954409 TTCGGCATTC
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:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (15 bp):
AGATAAATGTTTTAG
Found at i:54957995 original size:3 final size:3
Alignment explanation
Indices: 54957989--54958038 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
54957979 GTTGTTGGGT
54957989 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54958037 AT
1 AT
54958039 TTCGATTGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:54961914 original size:397 final size:393
Alignment explanation
Indices: 54960998--54962158 Score: 1738
Period size: 397 Copynumber: 2.9 Consensus size: 393
54960988 TCTTGTGGTT
* * *
54960998 TTCAATCTACTCCACTGCTGCCCAGGGAAGTAGAATTTCTGGCTTCAATGTACTCTACTGTAACC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
*
54961063 ACGAGGAGGTAAAATTCACCATCTTGGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAA
66 AC-AGGAGGTAAAATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAA
*
54961128 TCTTCAATCTATTCCACTGCTACCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAA
130 TCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAA
* * * *
54961193 CCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCACTACTGCTTAGGAGATAAGATCTGTA
195 CCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTGGGAGACAAGATCTGAA
* ** *
54961258 ATCTTCAGTCTATTCCACTATTGCCCAGGG-AGATAGAATTACTGGCTTCAATATACTACACTGC
260 ATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATATACTCCACTGC
* *
54961322 AACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGAGATAAGATCTG
324 AACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGAGACAAGATCTA
*
54961387 TAATC
389 AAATC
* * * *
54961392 TTCAGTCTATTCCACTGTTGCCCAGGG-AGATAGAATTACTGGCTTCAATATACTCCACTGCAAC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAAC
** * * *
54961456 CTTAGGGAGGTAAAA-TCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
65 CACA-GGAGGTAAAATTC-ACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGA
*
54961520 AATCTTCAATCTATTCCACTGTTGCCCAGGG-AGATAGAATTACTGGCTTCAATGTACTCCACTG
128 AATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTG
*
54961584 CAACCTCAGGGAGGTAAAATCTACCATCTTTGATCTGCTCCACTACTGCTTGGGGAGACAAGATC
192 CAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTT-GGGAGACAAGATC
* * * **
54961649 TGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTTGAATTACTAGCTTTCGATGCACTCCA
256 TGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGC-TTCAATATACTCCA
* * *
54961714 CTGCAACCTCAGGGAGGTAAAATATGTCATCTTTGATCTGCTCCACTACTGCTTGGGGAGACAAG
320 CTGCAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTT-AGGAGACAAG
54961779 ATCTAAAATC
384 ATCTAAAATC
54961789 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
54961854 ACAGGAAGGTAAAATTCACCATCTTTGATCTGC-CTCACTACTGCTTAGGGAGACAAGATCTGAA
66 ACAGG-AGGTAAAATTCACCATCTTTGATCTGCTC-CACTACTGCTTAGGGAGACAAGATCTGAA
* *
54961918 ATCTTCAATCTATTCCACTGCTGCCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTA
129 ATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCA
* * *
54961983 ACCACAGGAAGGTAAAACCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTG
194 ACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTT-GGGAGACAAGATCTG
* * *
54962048 AAATATTCAATCTATTTCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATATACTCCACTG
258 AAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATATACTCCACTG
* * * * * *
54962113 TAACCACAGGGAAGTAAAATCCGCCATATTTGATCTGTTCCACTAC
323 CAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTAC
54962159 AACCGAGGGA
Statistics
Matches: 686, Mismatches: 68, Indels: 24
0.88 0.09 0.03
Matches are distributed among these distances:
393 7 0.01
394 215 0.31
395 52 0.08
396 119 0.17
397 287 0.42
398 6 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (393 bp):
TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
ACAGGAGGTAAAATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAAT
CTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAAC
CTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTGGGAGACAAGATCTGAAA
TCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATATACTCCACTGCAA
CCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGAGACAAGATCTAAA
ATC
Found at i:54962169 original size:132 final size:132
Alignment explanation
Indices: 54960998--54962158 Score: 1701
Period size: 132 Copynumber: 8.8 Consensus size: 132
54960988 TCTTGTGGTT
* * * *
54960998 TTCAATCTACTCCACTGCTGCCCAGGGAAGTAGAATTTCTGGCTTCAATGTACTCTACTGTAACC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACC
* * *
54961063 AC-GAGGAGGTAAAAT-TCACCATCTTGGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGA
66 TCAG-GGAGGTAAAATCT-GCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGA
54961126 AATC
129 AATC
*
54961130 TTCAATCTATTCCACTGCTACCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACC
* * *
54961195 TCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCACTACTGCTTA-GGAGATAAGATCTGTAA
66 TCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAA
54961259 TC
131 TC
* ** * *
54961261 TTCAGTCTATTCCACTATTGCCCAGGG-AGATAGAATTACTGGCTTCAATATACTACACTGCAAC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGCAAC
* *
54961325 CTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTA-GGAGATAAGATCTGTA
65 CTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAA
54961389 ATC
130 ATC
* * *
54961392 TTCAGTCTATTCCACTGTTGCCCAGGG-AGATAGAATTACTGGCTTCAATATACTCCACTGCAAC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGCAAC
* * *
54961456 CTTAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
65 CTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAA
54961521 ATC
130 ATC
*
54961524 TTCAATCTATTCCACTGTTGCCCAGGG-AGATAGAATTACTGGCTTCAATGTACTCCACTGCAAC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGCAAC
* *
54961588 CTCAGGGAGGTAAAATCTACCATCTTTGATCTGCTCCACTACTGCTTGGGGAGACAAGATCTGAA
65 CTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAA
54961653 ATC
130 ATC
* * * *
54961656 TTCAATCTATTCCACTGCTGCCCAGGGAAGTTGAATTACTAGCTTTCGATGCACTCCACTGCAAC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGC-TTCAATGTACTCCACTGCAAC
* * * *
54961721 CTCAGGGAGGTAAAATATGTCATCTTTGATCTGCTCCACTACTGCTTGGGGAGACAAGATCTAAA
65 CTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAA
54961786 ATC
130 ATC
*
54961789 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACC
* * *
54961854 ACAGGAAGGTAAAAT-TCACCATCTTTGATCTGC-CTCACTACTGCTTAGGGAGACAAGATCTGA
66 TCAGGGAGGTAAAATCT-GCCATCTTTGATCTGCTC-CACTACTGCTTAGGGAGACAAGATCTGA
54961917 AATC
129 AATC
* *
54961921 TTCAATCTATTCCACTGCTGCCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACC
* * *
54961986 ACAGGAAGGTAAAACCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAA
66 TCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAA
*
54962051 TA
131 TC
* * * *
54962053 TTCAATCTATTTCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATATACTCCACTGTAACC
1 TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACC
* * * * *
54962118 ACAGGGAAGTAAAATCCGCCATATTTGATCTGTTCCACTAC
66 TCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTAC
54962159 AACCGAGGGA
Statistics
Matches: 957, Mismatches: 62, Indels: 20
0.92 0.06 0.02
Matches are distributed among these distances:
130 2 0.00
131 249 0.26
132 576 0.60
133 130 0.14
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (132 bp):
TTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACC
TCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAA
TC
Found at i:54963765 original size:7 final size:7
Alignment explanation
Indices: 54963749--54963789 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
54963739 AGCCTCTCCA
*
54963749 TTTTCTT
1 TTTTCAT
54963756 TTTTCAT
1 TTTTCAT
54963763 TTTTCA-
1 TTTTCAT
54963769 TTTTCAT
1 TTTTCAT
54963776 CTTTTCAT
1 -TTTTCAT
54963784 TTTTCA
1 TTTTCA
54963790 CATCACTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 6 0.19
7 18 0.58
8 7 0.23
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTCAT
Found at i:54963782 original size:21 final size:20
Alignment explanation
Indices: 54963747--54963789 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
54963737 TTAGCCTCTC
*
54963747 CATTTTCTTTTTTCATTTTT
1 CATTTTCTCTTTTCATTTTT
54963767 CATTTTCATCTTTTCATTTTT
1 CATTTTC-TCTTTTCATTTTT
54963788 CA
1 CA
54963790 CATCACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (20 bp):
CATTTTCTCTTTTCATTTTT
Found at i:54963801 original size:21 final size:22
Alignment explanation
Indices: 54963753--54963801 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
54963743 TCTCCATTTT
**
54963753 CTTTTTTCATTTTTCATTTTCA
1 CTTTTTTCATTTTTCATCATCA
*
54963775 -TCTTTTCATTTTTCA-CATCA
1 CTTTTTTCATTTTTCATCATCA
54963795 CTTTTTT
1 CTTTTTT
54963802 TTTGGACTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.65
Consensus pattern (22 bp):
CTTTTTTCATTTTTCATCATCA
Found at i:54964757 original size:19 final size:19
Alignment explanation
Indices: 54964733--54964771 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
54964723 GGTTTGGCAG
54964733 AAAAATCCAAAAGAATGAA
1 AAAAATCCAAAAGAATGAA
**
54964752 AAAAATCGTAAAGAATGAA
1 AAAAATCCAAAAGAATGAA
54964771 A
1 A
54964772 GAATATTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (19 bp):
AAAAATCCAAAAGAATGAA
Found at i:54965960 original size:17 final size:17
Alignment explanation
Indices: 54965927--54965960 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54965917 TTGTGTTTTG
*
54965927 TGCAAAAAGGGCTAAAT
1 TGCAAAAAGGGCAAAAT
*
54965944 TGCAAAAAGTGCAAAAT
1 TGCAAAAAGGGCAAAAT
54965961 GTGAGGGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
TGCAAAAAGGGCAAAAT
Found at i:54966204 original size:21 final size:21
Alignment explanation
Indices: 54966178--54966219 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
54966168 AGAATATATA
*
54966178 TATGTTCTATAAGCTGAATTT
1 TATGTTCTATAAGCTAAATTT
54966199 TATGTTCTATAAGCTAAATTT
1 TATGTTCTATAAGCTAAATTT
54966220 GATTTTATGA
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:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (21 bp):
TATGTTCTATAAGCTAAATTT
Found at i:54966551 original size:2 final size:2
Alignment explanation
Indices: 54966539--54966584 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
54966529 GAATGAAATG
54966539 AT AT GAT 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
54966582 AT A
1 AT A
54966585 AGAGGTTAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54966903 original size:41 final size:41
Alignment explanation
Indices: 54966858--54966960 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 41
54966848 GGCTATGTGC
* * *
54966858 CTAGCAGGCTTGATGCCGGTGAAATAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* * * *
54966899 CTAGCAGGCTTAATGCCGGTGATACATTTCGGACTATAGGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* *
54966940 CTAGCAGGCTAAAAGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
54966961 TACTGAATCA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
Found at i:54973388 original size:17 final size:17
Alignment explanation
Indices: 54973355--54973388 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54973345 TTGTGTTTTG
*
54973355 TGCAAAAAGGGCTAAAT
1 TGCAAAAAGGGCAAAAT
*
54973372 TGCAAAAAGTGCAAAAT
1 TGCAAAAAGGGCAAAAT
54973389 GTGAGGGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
TGCAAAAAGGGCAAAAT
Found at i:54973635 original size:21 final size:21
Alignment explanation
Indices: 54973606--54973647 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
54973596 AGAATATATA
*
54973606 TATGCTCTATAAGCTGAATTT
1 TATGCTCTATAAGCTAAATTT
*
54973627 TATGTTCTATAAGCTAAATTT
1 TATGCTCTATAAGCTAAATTT
54973648 GATTTTATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (21 bp):
TATGCTCTATAAGCTAAATTT
Found at i:54974316 original size:41 final size:41
Alignment explanation
Indices: 54974259--54974361 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 41
54974249 GGCTATGTGC
* * *
54974259 CTAGCAGGCTTGATGCCGGTGAAATAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* * * *
54974300 CTAGCAGGCTTAATGCCGGTGATACATTTCGGACTATAGGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* *
54974341 CTAGCAGGCTAAAAGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
54974362 TACTGAATCA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
Found at i:54978783 original size:14 final size:14
Alignment explanation
Indices: 54978742--54978784 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
54978732 TATATAAAGT
*
54978742 ATAAAGCATATAAA
1 ATAAAGAATATAAA
*
54978756 AAAAAGAA-AGTAAA
1 ATAAAGAATA-TAAA
54978770 ATAAAGAATATAAA
1 ATAAAGAATATAAA
54978784 A
1 A
54978785 AGTATGTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 1 0.04
14 22 0.92
15 1 0.04
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (14 bp):
ATAAAGAATATAAA
Found at i:54981103 original size:15 final size:15
Alignment explanation
Indices: 54981080--54981121 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
54981070 ATTTCTAAAA
*
54981080 TTATGATAAAAATAT
1 TTATTATAAAAATAT
*
54981095 TTATTAT-AATATAT
1 TTATTATAAAAATAT
54981109 TTAATTATAAAAA
1 TT-ATTATAAAAA
54981122 GTTAAAAGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 8 0.36
15 11 0.50
16 3 0.14
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
TTATTATAAAAATAT
Found at i:54989086 original size:3 final size:3
Alignment explanation
Indices: 54989078--54989105 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54989068 TAAAAAATGA
54989078 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
54989106 TCATCTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54989964 original size:18 final size:17
Alignment explanation
Indices: 54989929--54989975 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
54989919 CCTAAAATGA
*
54989929 AATTTTAATATTATTAT
1 AATTTTAATATTAATAT
54989946 AATTTTAATTATTAATAT
1 AATTTTAA-TATTAATAT
* *
54989964 AAATATAATATT
1 AATTTTAATATT
54989976 TAAATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTTAATATTAATAT
Found at i:54989970 original size:24 final size:24
Alignment explanation
Indices: 54989929--54989983 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
54989919 CCTAAAATGA
* *
54989929 AATTTTAATATTATTATAAT-TTT
1 AATTTTAATATAAATATAATATTT
54989952 AATTATTAATATAAATATAATATTT
1 AATT-TTAATATAAATATAATATTT
*
54989977 AAATTTA
1 AATTTTA
54989984 TTATTATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 17 0.63
25 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AATTTTAATATAAATATAATATTT
Found at i:54995187 original size:22 final size:22
Alignment explanation
Indices: 54995162--54995233 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
54995152 GAACTAAACC
54995162 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
54995184 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
54995206 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
54995228 CTCATG
1 CTCATG
54995234 TTCACAACCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:55001616 original size:23 final size:23
Alignment explanation
Indices: 55001590--55001634 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
55001580 TTTCTTACTG
55001590 TAGTAATTTTTAGGG-TATTACAA
1 TAGTAATTTTT-GGGATATTACAA
55001613 TAGTAATTTTTGGGATATTACA
1 TAGTAATTTTTGGGATATTACA
55001635 CACTTTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.44
Consensus pattern (23 bp):
TAGTAATTTTTGGGATATTACAA
Found at i:55001967 original size:13 final size:13
Alignment explanation
Indices: 55001949--55001973 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55001939 TTCATGGCGG
55001949 AACCCAAAAATTA
1 AACCCAAAAATTA
55001962 AACCCAAAAATT
1 AACCCAAAAATT
55001974 TTCCCCAAAA
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:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (13 bp):
AACCCAAAAATTA
Found at i:55006202 original size:26 final size:26
Alignment explanation
Indices: 55006173--55006254 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 26
55006163 TAAATTTTAT
*
55006173 TTAAATTTAATTACAAAATATTAATA
1 TTAAATTTAATTAAAAAATATTAATA
* * * *
55006199 TT-AATATAAATATAAAATTATTTAT-
1 TTAAATTTAATTA-AAAAATATTAATA
55006224 TTAAATTTAATTATAAAAATATTAATA
1 TTAAATTTAATTA-AAAAATATTAATA
55006251 TTAA
1 TTAA
55006255 TATAATTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
25 10 0.23
26 30 0.68
27 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAAATTTAATTAAAAAATATTAATA
Found at i:55006260 original size:26 final size:26
Alignment explanation
Indices: 55006187--55006261 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
55006177 ATTTAATTAC
*
55006187 AAAATATTAATATTAATATAAATATA
1 AAAATATTAATATTAATATAATTATA
* * *
55006213 AAATTATTTAT-TTAAATTTAATTATA
1 AAAATATTAATATT-AATATAATTATA
55006239 AAAATATTAATATTAATATAATT
1 AAAATATTAATATTAATATAATT
55006262 TTATATTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 2 0.05
26 36 0.90
27 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AAAATATTAATATTAATATAATTATA
Found at i:55020808 original size:28 final size:28
Alignment explanation
Indices: 55020740--55020799 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
55020730 TAAAACAAAG
*
55020740 GAATAAATAAGAGAATGGAAGGGACAAT
1 GAATAAATAAGAGAACGGAAGGGACAAT
55020768 GAATAAATAAGAGAACGGAAGGGACAAT
1 GAATAAATAAGAGAACGGAAGGGACAAT
55020796 GAAT
1 GAAT
55020800 TAGAAAGAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.53, C:0.05, G:0.28, T:0.13
Consensus pattern (28 bp):
GAATAAATAAGAGAACGGAAGGGACAAT
Found at i:55024543 original size:19 final size:19
Alignment explanation
Indices: 55024495--55024533 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
55024485 AATAAATATT
55024495 ATATATATTATTATCTTTA
1 ATATATATTATTATCTTTA
55024514 ATATATATTATTATCTTTA
1 ATATATATTATTATCTTTA
55024533 A
1 A
55024534 GCTTAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATATATTATTATCTTTA
Found at i:55025601 original size:33 final size:33
Alignment explanation
Indices: 55025538--55025602 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 33
55025528 AACCTTACAT
55025538 ACCAAACAATAAATTAAATTGTTTACTTATTTAC
1 ACCAAACAATAAATTAAATTGTTTA-TTATTTAC
*
55025572 ACCAAA-AATGAATTAACATTGCTTT-TTATTT
1 ACCAAACAATAAATTAA-ATTG-TTTATTATTT
55025603 CATATTATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 15 0.54
34 10 0.36
35 3 0.11
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (33 bp):
ACCAAACAATAAATTAAATTGTTTATTATTTAC
Found at i:55028649 original size:17 final size:18
Alignment explanation
Indices: 55028619--55028652 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55028609 ATGTTTTTAG
55028619 TATTTTTGATAAATTATT
1 TATTTTTGATAAATTATT
*
55028637 TATTTTTTA-AAATTAT
1 TATTTTTGATAAATTAT
55028653 ATAAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TATTTTTGATAAATTATT
Found at i:55028668 original size:12 final size:12
Alignment explanation
Indices: 55028645--55028678 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
55028635 TTTATTTTTT
55028645 AAAATT-ATATA
1 AAAATTAATATA
55028656 AAAATTAATATA
1 AAAATTAATATA
55028668 AAAATTAATAT
1 AAAATTAATAT
55028679 GGGCCAACCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:55035068 original size:14 final size:14
Alignment explanation
Indices: 55035051--55035080 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55035041 ATATATAATT
*
55035051 ATTTTAATATTTTA
1 ATTTTAAAATTTTA
55035065 ATTTTAAAATTTTA
1 ATTTTAAAATTTTA
55035079 AT
1 AT
55035081 CAAAGTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTTAAAATTTTA
Found at i:55040104 original size:2 final size:2
Alignment explanation
Indices: 55040097--55040123 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55040087 ACAGAGACAT
55040097 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
55040124 AGGATTTATT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55043383 original size:2 final size:2
Alignment explanation
Indices: 55043376--55043428 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
55043366 AAATATTGTT
55043376 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55043418 TA TA TA TA TA T
1 TA TA TA TA TA T
55043429 TACAAGGTCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55048176 original size:27 final size:27
Alignment explanation
Indices: 55048137--55048201 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
55048127 TATATATTAA
*
55048137 ATATATATTTTTTATTTTCAATCAAAT
1 ATATATATATTTTATTTTCAATCAAAT
* *
55048164 TTATATATATTTTATTTTTAATCAAAT
1 ATATATATATTTTATTTTCAATCAAAT
55048191 ATATATTATAT
1 ATATA-TATAT
55048202 ATTAAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 28 0.85
28 5 0.15
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (27 bp):
ATATATATATTTTATTTTCAATCAAAT
Found at i:55050715 original size:30 final size:31
Alignment explanation
Indices: 55050680--55050758 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 31
55050670 GGACTCCAAA
* *
55050680 AAGTTTAAATACCAACTTA-AAAAAAATGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAATGTC
* * *
55050710 AAGTTTAGGTACTAAATTAGAAAAAACTGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAATGTC
*
55050741 AAGTTTGAGTACCAAATT
1 AAGTTTAAGTACCAAATT
55050759 GGGCCAGGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 15 0.38
31 25 0.62
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGAAAAAAATGTC
Found at i:55054160 original size:18 final size:17
Alignment explanation
Indices: 55054118--55054160 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
55054108 TTTAAAAGTT
*
55054118 TGTAATATTTTATATTA
1 TGTAATTTTTTATATTA
55054135 TGCT-ATTTTTATATATTA
1 TG-TAATTTTT-TATATTA
55054153 TGTAATTT
1 TGTAATTT
55054161 ATAAACAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (17 bp):
TGTAATTTTTTATATTA
Found at i:55055526 original size:26 final size:26
Alignment explanation
Indices: 55055495--55055546 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
55055485 CTTTATTTAT
55055495 TTTTACAT-AATACTTTTATAAATATA
1 TTTTACATAAAT-CTTTTATAAATATA
*
55055521 TTTTACATAAATTTTTTATAAATATA
1 TTTTACATAAATCTTTTATAAATATA
55055547 AAATATATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTTACATAAATCTTTTATAAATATA
Found at i:55056974 original size:29 final size:30
Alignment explanation
Indices: 55056932--55056990 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
55056922 CAACGATTCT
* *
55056932 ATTTTTTAAAAAA-TGATGGTCAAATTTAA
1 ATTTTTTAAAAAATTAAGGGTCAAATTTAA
55056961 ATTTTTTAAAAAATTAAGGGTCAAATTTAA
1 ATTTTTTAAAAAATTAAGGGTCAAATTTAA
55056991 CTAAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (30 bp):
ATTTTTTAAAAAATTAAGGGTCAAATTTAA
Found at i:55060446 original size:3 final size:3
Alignment explanation
Indices: 55060438--55060497 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
55060428 ATATATGGCT
55060438 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55060486 ATA ATA ATA ATA
1 ATA ATA ATA ATA
55060498 GTGTAAAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55083317 original size:23 final size:23
Alignment explanation
Indices: 55083290--55083335 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
55083280 ATTTTCACGA
*
55083290 AACATTAACCATGTAAATTTTTT
1 AACATTAACAATGTAAATTTTTT
*
55083313 AACATTAACAATGTAGATTTTTT
1 AACATTAACAATGTAAATTTTTT
55083336 GAGTTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (23 bp):
AACATTAACAATGTAAATTTTTT
Found at i:55083520 original size:39 final size:40
Alignment explanation
Indices: 55083402--55083525 Score: 126
Period size: 40 Copynumber: 3.1 Consensus size: 40
55083392 GCGTTTGGAT
* * * *
55083402 AAAAAGCGCCACTAAAAATCAAGCATTAGCGGCGCTCTTCT-
1 AAAAA-CGCCGCTAAAAATCAAGCATTAGTGGCG-TTTTTTG
* ** * *
55083443 AAAAACGCCGCTAAAGATGGAGCATTAGTGACGCTTTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGTGGCGTTTTTTG
*
55083483 AAAAACGTCGCTAAAAAT-AAGCATTAGTGGCGTTTTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGTGGCGTTTTTTG
55083522 AAAA
1 AAAA
55083526 GCGCTGCAAA
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
39 25 0.37
40 38 0.56
41 5 0.07
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGTGGCGTTTTTTG
Found at i:55083538 original size:39 final size:39
Alignment explanation
Indices: 55083463--55083538 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
55083453 CTAAAGATGG
*
55083463 AGCATTAGTGACGCTTTTTGAAAAACGTCGCTAAAAATA
1 AGCATTAGTGACGCTTTTTGAAAAACGTCGCAAAAAATA
* * *
55083502 AGCATTAGTGGCGTTTTTTGAAAAGCG-CTGCAAAAAA
1 AGCATTAGTGACGCTTTTTGAAAAACGTC-GCAAAAAA
55083539 CCTAAGACTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (39 bp):
AGCATTAGTGACGCTTTTTGAAAAACGTCGCAAAAAATA
Found at i:55083634 original size:41 final size:41
Alignment explanation
Indices: 55083572--55083649 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
55083562 CTGAGTTTTG
*
55083572 GGGCTTTTAGCGGCGTTTTTGA-AATAGCACCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAGAA-AGCACCGCTAATGCTC
*
55083613 GGGCCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAAT
1 GGGCCTTTAGCGGCGTTTTTGAGAAAGCACCGCTAAT
55083650 AATAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
41 32 0.94
42 2 0.06
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.29
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAGAAAGCACCGCTAATGCTC
Found at i:55084181 original size:21 final size:20
Alignment explanation
Indices: 55084155--55084264 Score: 85
Period size: 17 Copynumber: 5.8 Consensus size: 20
55084145 AGATTTAAGG
55084155 TTTAAGGGTTAGGGGTTATGA
1 TTTAAGGGTTAGGGG-TATGA
55084176 TTTAAGGGTTAGAGGG---GA
1 TTTAAGGGTTAG-GGGTATGA
* *
55084194 TTTAAGAGTTAGGGGCTATGC
1 TTTAAGGGTTAGGGG-TATGA
*
55084215 TTTAGGGGTTAGGGG-A--A
1 TTTAAGGGTTAGGGGTATGA
*
55084232 TTTAGGGGTTAGGGG---GA
1 TTTAAGGGTTAGGGGTATGA
*
55084249 TTTAGGGGTTAGGGGT
1 TTTAAGGGTTAGGGGT
55084265 TTAGGGTTTC
Statistics
Matches: 77, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
17 34 0.44
18 13 0.17
19 1 0.01
21 26 0.34
22 3 0.04
ACGTcount: A:0.22, C:0.02, G:0.44, T:0.33
Consensus pattern (20 bp):
TTTAAGGGTTAGGGGTATGA
Found at i:55084197 original size:18 final size:17
Alignment explanation
Indices: 55084174--55084263 Score: 90
Period size: 17 Copynumber: 5.0 Consensus size: 17
55084164 TAGGGGTTAT
*
55084174 GATTTAAGGGTTAGAGGG
1 GATTTAGGGGTTAG-GGG
* *
55084192 GATTTAAGAGTTAGGGG
1 GATTTAGGGGTTAGGGG
*
55084209 CTATGCTTTAGGGGTTAGGGG
1 ----GATTTAGGGGTTAGGGG
*
55084230 AATTTAGGGGTTAGGGG
1 GATTTAGGGGTTAGGGG
55084247 GATTTAGGGGTTAGGGG
1 GATTTAGGGGTTAGGGG
55084264 TTTAGGGTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
17 34 0.56
18 13 0.21
21 14 0.23
ACGTcount: A:0.22, C:0.02, G:0.46, T:0.30
Consensus pattern (17 bp):
GATTTAGGGGTTAGGGG
Found at i:55084199 original size:39 final size:38
Alignment explanation
Indices: 55084155--55084246 Score: 121
Period size: 39 Copynumber: 2.4 Consensus size: 38
55084145 AGATTTAAGG
* *
55084155 TTTAAGGGTTAGGGGTTATGATTTAAGGGTTAGAGGGGA
1 TTTAAGGGTTAGGGGCTATGATTTAAGGGTTAG-GGGAA
* * *
55084194 TTTAAGAGTTAGGGGCTATGCTTTAGGGGTTAGGGGAA
1 TTTAAGGGTTAGGGGCTATGATTTAAGGGTTAGGGGAA
*
55084232 TTTAGGGGTTAGGGG
1 TTTAAGGGTTAGGGG
55084247 GATTTAGGGG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
38 17 0.37
39 29 0.63
ACGTcount: A:0.23, C:0.02, G:0.42, T:0.33
Consensus pattern (38 bp):
TTTAAGGGTTAGGGGCTATGATTTAAGGGTTAGGGGAA
Found at i:55084950 original size:7 final size:7
Alignment explanation
Indices: 55084940--55085050 Score: 60
Period size: 7 Copynumber: 14.9 Consensus size: 7
55084930 GATTTAAGGT
55084940 TTAGGGG
1 TTAGGGG
55084947 TTAGGGG
1 TTAGGGG
* **
55084954 TTATGCT
1 TTAGGGG
55084961 TTAGGGG
1 TTAGGGG
55084968 TTAGGGGG
1 TTA-GGGG
*
55084976 ATTTAGGAG
1 --TTAGGGG
55084985 TTAGGGG
1 TTAGGGG
* **
55084992 TTATGCT
1 TTAGGGG
*
55084999 TTAAGGG
1 TTAGGGG
55085006 TTAGGTGG
1 TTAGG-GG
*
55085014 ATTTAAGGG
1 --TTAGGGG
55085023 TTAGGGG
1 TTAGGGG
*
55085030 TTAGGGA
1 TTAGGGG
*
55085037 TTTGGGG
1 TTAGGGG
55085044 TTTAGGG
1 -TTAGGG
55085051 TTTTAACGGT
Statistics
Matches: 76, Mismatches: 21, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
7 53 0.70
8 11 0.14
9 5 0.07
10 7 0.09
ACGTcount: A:0.18, C:0.02, G:0.45, T:0.35
Consensus pattern (7 bp):
TTAGGGG
Found at i:55084963 original size:21 final size:21
Alignment explanation
Indices: 55084939--55085010 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
55084929 GGATTTAAGG
55084939 TTTAGGGGTTAGGGGTTATGC
1 TTTAGGGGTTAGGGGTTATGC
*
55084960 TTTAGGGGTTAGGGG----GA
1 TTTAGGGGTTAGGGGTTATGC
*
55084977 TTTAGGAGTTAGGGGTTATGC
1 TTTAGGGGTTAGGGGTTATGC
*
55084998 TTTAAGGGTTAGG
1 TTTAGGGGTTAGG
55085011 TGGATTTAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
17 15 0.36
21 27 0.64
ACGTcount: A:0.18, C:0.03, G:0.43, T:0.36
Consensus pattern (21 bp):
TTTAGGGGTTAGGGGTTATGC
Found at i:55084982 original size:17 final size:17
Alignment explanation
Indices: 55084960--55085029 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
55084950 GGGGTTATGC
*
55084960 TTTAGGGGTTAGGGGGA
1 TTTAAGGGTTAGGGGGA
*
55084977 TTT-AGGAGTTAGGGGTTATGC
1 TTTAAGG-GTTAGGGG----GA
*
55084998 TTTAAGGGTTAGGTGGA
1 TTTAAGGGTTAGGGGGA
55085015 TTTAAGGGTTAGGGG
1 TTTAAGGGTTAGGGG
55085030 TTAGGGATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
16 2 0.05
17 26 0.62
21 11 0.26
22 3 0.07
ACGTcount: A:0.20, C:0.01, G:0.44, T:0.34
Consensus pattern (17 bp):
TTTAAGGGTTAGGGGGA
Found at i:55085045 original size:38 final size:38
Alignment explanation
Indices: 55084939--55085032 Score: 145
Period size: 38 Copynumber: 2.5 Consensus size: 38
55084929 GGATTTAAGG
*
55084939 TTTAGGGGTTAGGGGTTATGCTTTAGGGGTTAGGGGGA
1 TTTAAGGGTTAGGGGTTATGCTTTAGGGGTTAGGGGGA
* *
55084977 TTT-AGGAGTTAGGGGTTATGCTTTAAGGGTTAGGTGGA
1 TTTAAGG-GTTAGGGGTTATGCTTTAGGGGTTAGGGGGA
55085015 TTTAAGGGTTAGGGGTTA
1 TTTAAGGGTTAGGGGTTA
55085033 GGGATTTGGG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
37 2 0.04
38 46 0.90
39 3 0.06
ACGTcount: A:0.19, C:0.02, G:0.43, T:0.36
Consensus pattern (38 bp):
TTTAAGGGTTAGGGGTTATGCTTTAGGGGTTAGGGGGA
Found at i:55085443 original size:18 final size:18
Alignment explanation
Indices: 55085403--55085443 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
55085393 AATATAAGAA
55085403 AAAATAAAATAAAAAAAT
1 AAAATAAAATAAAAAAAT
* * *
55085421 TAAATGAAATAAAAAACT
1 AAAATAAAATAAAAAAAT
55085439 AAAAT
1 AAAAT
55085444 TTATACATGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (18 bp):
AAAATAAAATAAAAAAAT
Done.