Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 180 of 214
Found at i:52917434 original size:24 final size:24
Alignment explanation
Indices: 52917402--52917453 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
52917392 TAATTTATAT
*
52917402 TTTATATATCATTGT-ATTAAATTA
1 TTTAAATATCATT-TAATTAAATTA
52917426 TTTAAATATCATTTAAATTAAATTA
1 TTTAAATATCATTT-AATTAAATTA
52917451 TTT
1 TTT
52917454 TTATTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 1 0.04
24 12 0.48
25 12 0.48
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTAAATATCATTTAATTAAATTA
Found at i:52918346 original size:17 final size:18
Alignment explanation
Indices: 52918310--52918349 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
52918300 AAAATATATA
*
52918310 TTTATTTGTAAATGTTTT
1 TTTATTTGTAAATGTATT
*
52918328 TTTATTT-TATATGTATT
1 TTTATTTGTAAATGTATT
52918345 TTTAT
1 TTTAT
52918350 AAAAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (18 bp):
TTTATTTGTAAATGTATT
Found at i:52920589 original size:22 final size:22
Alignment explanation
Indices: 52920564--52920655 Score: 105
Period size: 22 Copynumber: 4.2 Consensus size: 22
52920554 AAATTCAATA
* *
52920564 TCAATTTCTTTCAAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
52920586 TCAATTCCTTTCAAAATTTCTC
1 TCAATTCCCTTCAAAAATTCTC
*
52920608 TCAATTCCCTTCAAAATTTC-C
1 TCAATTCCCTTCAAAAATTCTC
* *
52920629 ATCAATTTCCTTCCAAAATTCTC
1 -TCAATTCCCTTCAAAAATTCTC
52920652 TCAA
1 TCAA
52920656 ACTCTCAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
21 1 0.02
22 60 0.97
23 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.41
Consensus pattern (22 bp):
TCAATTCCCTTCAAAAATTCTC
Found at i:52920621 original size:44 final size:44
Alignment explanation
Indices: 52920564--52920655 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
52920554 AAATTCAATA
* * *
52920564 TCAATTTCTTTCAAAAATTCTC-TCAA-TTCCTTTCAAAATTTCTC
1 TCAATTCCCTTCAAAAATTC-CATCAATTTCCTTCCAAAA-TTCTC
*
52920608 TCAATTCCCTTCAAAATTTCCATCAATTTCCTTCCAAAATTCTC
1 TCAATTCCCTTCAAAAATTCCATCAATTTCCTTCCAAAATTCTC
52920652 TCAA
1 TCAA
52920656 ACTCTCAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 30 0.71
45 11 0.26
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.41
Consensus pattern (44 bp):
TCAATTCCCTTCAAAAATTCCATCAATTTCCTTCCAAAATTCTC
Found at i:52920671 original size:52 final size:51
Alignment explanation
Indices: 52920605--52920707 Score: 122
Period size: 52 Copynumber: 2.0 Consensus size: 51
52920595 TTCAAAATTT
* *
52920605 CTCTCAATTCCCTTC-AAAATTTCC-ATCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCGAAAA--TCCTATCAATTTCCTTCAAAAAATCTC-CAAA
*
52920657 CTCTCAAATT-CCTTCGAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCGAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
52920708 TCCATATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
51 7 0.16
52 30 0.67
53 8 0.18
ACGTcount: A:0.33, C:0.32, G:0.01, T:0.34
Consensus pattern (51 bp):
CTCTCAATTCCCTTCGAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
Found at i:52920682 original size:22 final size:22
Alignment explanation
Indices: 52920657--52920698 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
52920647 TTCTCTCAAA
*
52920657 CTCTCAAATTCCTTCGAAAATC
1 CTCTCAAATTCCTTCAAAAATC
*
52920679 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCAAAAA
52920699 ATCTCCAAAT
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:0.31, G:0.02, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCAAAAATC
Found at i:52920792 original size:27 final size:27
Alignment explanation
Indices: 52920740--52920794 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
52920730 ATTAAATTTC
** *
52920740 ATTTTTTAAGAAAATTTTTTATTTTTT
1 ATTTTTTAAGAAAATTTTAAAATTTTT
52920767 ATTTTTTAA-AATAATTTTAAAATTTTT
1 ATTTTTTAAGAA-AATTTTAAAATTTTT
52920794 A
1 A
52920795 ATATTTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
ATTTTTTAAGAAAATTTTAAAATTTTT
Found at i:52920946 original size:24 final size:23
Alignment explanation
Indices: 52920891--52920946 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
52920881 TAAATTTTAA
*
52920891 ATTTTTTTAAGATATTTTTATTT
1 ATTTTTTTAAGATATTTTTATAT
52920914 ATGTATTTTT-AGATATTTATTAATAT
1 AT-T-TTTTTAAGATATTT-TT-ATAT
52920940 ATTTTTT
1 ATTTTTT
52920947 GTTATAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 2 0.07
24 13 0.46
25 8 0.29
26 5 0.18
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (23 bp):
ATTTTTTTAAGATATTTTTATAT
Found at i:52923097 original size:17 final size:18
Alignment explanation
Indices: 52923075--52923109 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52923065 TAAAATCCCT
52923075 AACCCT-ACTTAATTAAA
1 AACCCTAACTTAATTAAA
*
52923092 AACCCTAATTTAATTAAA
1 AACCCTAACTTAATTAAA
52923110 TTAAAAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (18 bp):
AACCCTAACTTAATTAAA
Found at i:52923159 original size:24 final size:23
Alignment explanation
Indices: 52923063--52923151 Score: 117
Period size: 23 Copynumber: 3.8 Consensus size: 23
52923053 ACATTATTTG
*
52923063 ATTAAAATCCCTAACCCTACTTA
1 ATTAAAAACCCTAACCCTACTTA
** *
52923086 ATTAAAAACCCTAA-TTTAATTAA
1 ATTAAAAACCCTAACCCTACTT-A
52923109 ATTAAAAACCCTAAACCCTACTTA
1 ATTAAAAACCCT-AACCCTACTTA
52923133 ATTAAAAACCCTAACCCTA
1 ATTAAAAACCCTAACCCTA
52923152 ACCTAATTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
22 4 0.07
23 33 0.59
24 15 0.27
25 4 0.07
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (23 bp):
ATTAAAAACCCTAACCCTACTTA
Found at i:52923177 original size:28 final size:28
Alignment explanation
Indices: 52923095--52923409 Score: 254
Period size: 28 Copynumber: 11.5 Consensus size: 28
52923085 AATTAAAAAC
*
52923095 CCTAATTTAATTAAATTAAAAACCCTAAA
1 CCTAACTTAATTAAATTAAAAACCCT-AA
*
52923124 CCCT-ACTTAATTAAA--AACCCTAACCCTAA
1 -CCTAACTTAATTAAATTAA---AAACCCTAA
*
52923153 CCTAATTTAATTAAATTAAAAACCCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA
*
52923181 CCTAACCTAATTTAATTAAATCAAAAACCCTAA
1 CCTAA-C----TTAATTAAATTAAAAACCCTAA
* * * *
52923214 CCCAACCTAATTTAATTAAAAACCTTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA
* *
52923242 CCTAACCTAATTTAATTAAAAA--C---
1 CCTAACTTAATTAAATTAAAAACCCTAA
*
52923265 CCTAACTTAATTTAATTAAAAACCCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA
* *
52923293 CCTAACCTAATTTAATTAAAAACCCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA
52923321 CCTAA--T--TT-AATTAAAAACCCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA
52923344 CCT-AC----TTAAATTAAAAACCCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA
* * *
52923367 CCTAACCTAATTTAATTAAAAACCTTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA
52923395 CCT-ACTTAAATTAAA
1 CCTAACTT-AATTAAA
52923410 ACCCTAATTA
Statistics
Matches: 242, Mismatches: 19, Indels: 50
0.78 0.06 0.16
Matches are distributed among these distances:
22 3 0.01
23 57 0.24
24 4 0.02
25 1 0.00
26 1 0.00
27 5 0.02
28 112 0.46
29 22 0.09
30 9 0.04
31 2 0.01
32 1 0.00
33 25 0.10
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (28 bp):
CCTAACTTAATTAAATTAAAAACCCTAA
Found at i:52923190 original size:33 final size:33
Alignment explanation
Indices: 52923132--52923261 Score: 189
Period size: 33 Copynumber: 4.1 Consensus size: 33
52923122 AACCCTACTT
52923132 AATTAAAAACCCTAACCCTAACCTAATTTAATTA
1 AATTAAAAACCCTAA-CCTAACCTAATTTAATTA
52923166 AATTAAAAACCCTAACCTAACCTAATTTAATTA
1 AATTAAAAACCCTAACCTAACCTAATTTAATTA
* *
52923199 AATCAAAAACCCTAACCCAACCTAA--T--TT-
1 AATTAAAAACCCTAACCTAACCTAATTTAATTA
*
52923227 AATTAAAAACCTTAACCTAACCTAATTTAATTA
1 AATTAAAAACCCTAACCTAACCTAATTTAATTA
52923260 AA
1 AA
52923262 AACCCTAACT
Statistics
Matches: 86, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
28 22 0.26
29 2 0.02
30 1 0.01
31 1 0.01
32 2 0.02
33 43 0.50
34 15 0.17
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.28
Consensus pattern (33 bp):
AATTAAAAACCCTAACCTAACCTAATTTAATTA
Found at i:52923243 original size:23 final size:23
Alignment explanation
Indices: 52923217--52923410 Score: 181
Period size: 23 Copynumber: 7.8 Consensus size: 23
52923207 ACCCTAACCC
52923217 AACCTAATTTAATTAAAAACCTTAACCT
1 AACCTAATTTAATTAAAAACC-T----T
*
52923245 AACCTAATTTAATTAAAAACCCT
1 AACCTAATTTAATTAAAAACCTT
*
52923268 AACTTAATTTAATTAAAAACCCTAACCT
1 AACCTAATTTAATTAAAAA-CCT----T
*
52923296 AACCTAATTTAATTAAAAACCCT
1 AACCTAATTTAATTAAAAACCTT
*
52923319 AACCTAATTTAATTAAAAACCCT
1 AACCTAATTTAATTAAAAACCTT
* *
52923342 AACCTACTTAAATTAAAAACCCTAACCT
1 AACCTAATTTAATTAAAAA-CCT----T
52923370 AACCTAATTTAATTAAAAACCTT
1 AACCTAATTTAATTAAAAACCTT
* *
52923393 AACCTACTTAAATTAAAA
1 AACCTAATTTAATTAAAA
52923411 CCCTAATTAA
Statistics
Matches: 144, Mismatches: 12, Indels: 25
0.80 0.07 0.14
Matches are distributed among these distances:
23 77 0.53
24 4 0.03
27 5 0.03
28 58 0.40
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (23 bp):
AACCTAATTTAATTAAAAACCTT
Found at i:52923297 original size:51 final size:51
Alignment explanation
Indices: 52923212--52923398 Score: 258
Period size: 51 Copynumber: 3.7 Consensus size: 51
52923202 CAAAAACCCT
*
52923212 AACCC-AACCTAATTTAATTAAAAACCTTAACCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAA
*
52923262 AACCCTAACTTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAA
* *
52923313 AACCCTAACCTAATTTAATTAAAAACCCTAACCT-ACTTAAATTAA--AAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAA
*
52923361 CCCTAA-CCTAACCTAATTTAATTAAAAACCTTAACCTA
1 ----AACCCTAACCTAATTTAATTAAAAACCCTAACCTA
52923399 CTTAAATTAA
Statistics
Matches: 125, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
48 3 0.02
50 14 0.11
51 106 0.85
52 2 0.02
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (51 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAA
Found at i:52923399 original size:51 final size:52
Alignment explanation
Indices: 52923196--52923416 Score: 232
Period size: 51 Copynumber: 4.3 Consensus size: 52
52923186 CCTAATTTAA
* * *
52923196 TTAAATCAAAAACCCTAACCCAACCTAATTTAATTAAAAACCTTAACCTAACC
1 TTAAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAA-C
*
52923249 TAATTTAATTAAAAACCCTAA-CT----TAATTTAATTAAAAACCCTAACCTAAC
1 ---TTAAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAAC
* *
52923299 CTAATTTAATTAAA----AACCCTAACCTAATTTAATTAAAAACCCTAACCT-AC
1 TTAAATTAA--AAACCCTAA-CCTAACCTAATTTAATTAAAAACCCTAACCTAAC
*
52923349 TTAAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCTTAACCT-AC
1 TTAAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAAC
52923400 TTAAATT-AAAACCCTAA
1 TTAAATTAAAAACCCTAA
52923417 TTAAATTGTA
Statistics
Matches: 143, Mismatches: 10, Indels: 30
0.78 0.05 0.16
Matches are distributed among these distances:
45 2 0.01
47 8 0.06
48 3 0.02
49 3 0.02
50 20 0.14
51 88 0.62
52 2 0.01
55 1 0.01
56 16 0.11
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.29
Consensus pattern (52 bp):
TTAAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTAAC
Found at i:52926751 original size:85 final size:87
Alignment explanation
Indices: 52926556--52926762 Score: 382
Period size: 85 Copynumber: 2.4 Consensus size: 87
52926546 CAAACTTGCT
*
52926556 ACTGTAGCGAAATCGCATCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAACAAAA
1 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAACAAAA
52926621 AAAAATATTTCCTACATGACCA
66 AAAAATATTTCCTACATGACCA
52926643 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTC-A-AAAA
1 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAACAAAA
*
52926706 AAAATTATTTCCTACATGACCA
66 AAAAATATTTCCTACATGACCA
52926728 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTT
1 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTT
52926763 CACAATTTCT
Statistics
Matches: 118, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
85 60 0.51
86 1 0.01
87 57 0.48
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (87 bp):
ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAACAAAA
AAAAATATTTCCTACATGACCA
Found at i:52926893 original size:123 final size:125
Alignment explanation
Indices: 52926672--52926950 Score: 354
Period size: 123 Copynumber: 2.2 Consensus size: 125
52926662 CACGAGGGCG
*
52926672 CGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
1 CGATTTGACACTATTTCCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
* * * *
52926737 AAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAA
66 AAATCACGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTATCAA
* *
52926797 CGATTTTATACTATTTCCTCAGAAAACGTC-AAAAAAAATTATTT-CTCACAT-ACC-ACTGTAG
1 CGATTTGACACTATTTCCTCAG-AAACGTCAAAAAAAAATTATTTCCT-ACATGACCAACTGTAG
* * * *
52926858 CGAAATCACGTCCACGAGGCCACTATTTCACAATTTCTTCTTAAATAGCATCCTAGTA-GAA
64 CGAAATCACGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTATCAA
** *
52926919 GCGATTTCCCACTATTTAAC-CAGAAACGTCAA
1 -CGATTTGACACTATTT-CCTCAGAAACGTCAA
52926951 CTCGAAAAAA
Statistics
Matches: 134, Mismatches: 15, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
122 9 0.07
123 75 0.56
124 6 0.04
125 37 0.28
126 7 0.05
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (125 bp):
CGATTTGACACTATTTCCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
AAATCACGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTATCAA
Found at i:52927271 original size:3 final size:3
Alignment explanation
Indices: 52927263--52927301 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
52927253 TCCTGTATTA
52927263 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
52927302 TCATTGAGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:52928566 original size:20 final size:20
Alignment explanation
Indices: 52928541--52928591 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 20
52928531 AAAATATTAA
52928541 AATAATATTTTTACAT-TTTT
1 AATAATATTTTTA-ATATTTT
52928561 AAT-A-ATTTTTAATATTTT
1 AATAATATTTTTAATATTTT
*
52928579 AAAAATAGTTTTT
1 AATAATA-TTTTT
52928592 TTTAAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 2 0.08
18 13 0.50
19 2 0.08
20 4 0.15
21 5 0.19
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
AATAATATTTTTAATATTTT
Found at i:52933347 original size:22 final size:22
Alignment explanation
Indices: 52933319--52933361 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
52933309 ATATAAAAAT
52933319 AAAAATACCTTGAAAATAATAG
1 AAAAATACCTTGAAAATAATAG
** *
52933341 AAAAATATTTTTAAAATAATA
1 AAAAATACCTTGAAAATAATA
52933362 TTTGTTACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (22 bp):
AAAAATACCTTGAAAATAATAG
Found at i:52940680 original size:14 final size:14
Alignment explanation
Indices: 52940644--52940677 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
52940634 TCATCATTTG
52940644 CCTATAACCAAAAC
1 CCTATAACCAAAAC
52940658 CCTATAACCAAAAC
1 CCTATAACCAAAAC
52940672 CC-ATAA
1 CCTATAA
52940678 ACCCATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:52942966 original size:60 final size:60
Alignment explanation
Indices: 52942899--52943019 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
52942889 TAATGCATAC
52942899 TATCTATTATTTAATATATAATAAAACCTTCTAAAGAGTATGTTGGTAAGAAAAATAATT
1 TATCTATTATTTAATATATAATAAAACCTTCTAAAGAGTATGTTGGTAAGAAAAATAATT
52942959 TATCTATTATTTAATATATAATAAAACCTTCTAAAGAGTATGTTGGTAAGAAAAATAATT
1 TATCTATTATTTAATATATAATAAAACCTTCTAAAGAGTATGTTGGTAAGAAAAATAATT
52943019 T
1 T
52943020 TGAGCTATTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.39
Consensus pattern (60 bp):
TATCTATTATTTAATATATAATAAAACCTTCTAAAGAGTATGTTGGTAAGAAAAATAATT
Found at i:52944021 original size:26 final size:26
Alignment explanation
Indices: 52943985--52944037 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
52943975 CCCATAGACA
52943985 ACACCTATTATTATAACAATTAAGTT
1 ACACCTATTATTATAACAATTAAGTT
52944011 ACACCTATTATTATAACAATTAAGTT
1 ACACCTATTATTATAACAATTAAGTT
52944037 A
1 A
52944038 TACAAAGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.38
Consensus pattern (26 bp):
ACACCTATTATTATAACAATTAAGTT
Found at i:52947480 original size:9 final size:9
Alignment explanation
Indices: 52947431--52947486 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
52947421 TAAAAACTTT
*
52947431 AAATTTATA
1 AAATTTAAA
52947440 AAATATT-AA
1 AAAT-TTAAA
52947449 AAATTTAAA
1 AAATTTAAA
*
52947458 AATACATTAAA
1 AA-A-TTTAAA
52947469 AAATTTAAA
1 AAATTTAAA
*
52947478 AAATATAAA
1 AAATTTAAA
52947487 GAAAAACCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 2 0.05
9 26 0.67
10 4 0.10
11 7 0.18
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (9 bp):
AAATTTAAA
Found at i:52948377 original size:11 final size:11
Alignment explanation
Indices: 52948361--52948385 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52948351 TAATTATTTA
52948361 TAATTAATAAT
1 TAATTAATAAT
52948372 TAATTAATAAT
1 TAATTAATAAT
52948383 TAA
1 TAA
52948386 ATTTGTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TAATTAATAAT
Found at i:52948837 original size:21 final size:21
Alignment explanation
Indices: 52948805--52948845 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
52948795 AGCTCGAACC
52948805 CTAAACATTAAA-CTTTAAACT
1 CTAAACATTAAATC-TTAAACT
52948826 CTAAAC-TCTAAATCTTAAAC
1 CTAAACAT-TAAATCTTAAAC
52948846 ACCAAACCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 1 0.06
21 16 0.89
22 1 0.06
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (21 bp):
CTAAACATTAAATCTTAAACT
Found at i:52951566 original size:30 final size:29
Alignment explanation
Indices: 52951532--52951693 Score: 218
Period size: 30 Copynumber: 5.4 Consensus size: 29
52951522 TATATATTTC
52951532 CGAATTGATTTGTATATAGATATACATTG
1 CGAATTGATTTGTATATAGATATACATTG
*
52951561 TCGAATTGATTTGTATATGGATATACATTG
1 -CGAATTGATTTGTATATAGATATACATTG
*
52951591 TCGAATTGATTTGTATATGGATATACATTG
1 -CGAATTGATTTGTATATAGATATACATTG
*
52951621 CTGAATTGATTTGTATATAGATACACATTG
1 C-GAATTGATTTGTATATAGATATACATTG
*
52951651 CCGAATTGATTTGTATAT-GTATATATATTG
1 -CGAATTGATTTGTATATAG-ATATACATTG
*
52951681 CTAAATTGATTTG
1 C-GAATTGATTTG
52951694 AGCATTGGAT
Statistics
Matches: 122, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
29 3 0.02
30 118 0.97
31 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.43
Consensus pattern (29 bp):
CGAATTGATTTGTATATAGATATACATTG
Found at i:52957791 original size:24 final size:19
Alignment explanation
Indices: 52957738--52957776 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
52957728 ATTCATGATG
52957738 ATTGATTAATTTAATTTTT
1 ATTGATTAATTTAATTTTT
52957757 ATTGATTAATTTAATTTTT
1 ATTGATTAATTTAATTTTT
52957776 A
1 A
52957777 GTTTGAACTT
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:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
ATTGATTAATTTAATTTTT
Found at i:52960567 original size:25 final size:25
Alignment explanation
Indices: 52960537--52960627 Score: 119
Period size: 25 Copynumber: 3.6 Consensus size: 25
52960527 TGTCAACAGT
* *
52960537 AAGCTCTTCCGAGCTAAATAACGGG
1 AAGCTCATGCGAGCTAAATAACGGG
*
52960562 AAGCTCATGCGAGCTAAATAACTGG
1 AAGCTCATGCGAGCTAAATAACGGG
* * **
52960587 AAGCTCTTGCGAACTGTATAACGGG
1 AAGCTCATGCGAGCTAAATAACGGG
52960612 AAGCTCATGCGAGCTA
1 AAGCTCATGCGAGCTA
52960628 TGGTGTGTCT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 55 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (25 bp):
AAGCTCATGCGAGCTAAATAACGGG
Found at i:52975610 original size:39 final size:39
Alignment explanation
Indices: 52975556--52975634 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
52975546 AAGTAGATTC
*
52975556 CATAACTATCCACCTATTACTCTACCATGTTCTGAAACA
1 CATAACTATCCACCTATTACTCTACCATGTTCAGAAACA
*
52975595 CATAACTATCCACCTATTACTCTTCCATGTTCAGAAACA
1 CATAACTATCCACCTATTACTCTACCATGTTCAGAAACA
52975634 C
1 C
52975635 TTAGCACTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (39 bp):
CATAACTATCCACCTATTACTCTACCATGTTCAGAAACA
Found at i:52976421 original size:21 final size:21
Alignment explanation
Indices: 52976397--52976442 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
52976387 GCGTCGGGGG
* *
52976397 TTTGGGTA-GAAGGAGTGTCGT
1 TTTGGGGAGGAAGG-GTATCGT
52976418 TTTGGGGAGGAAGGGTATCGT
1 TTTGGGGAGGAAGGGTATCGT
52976439 TTTG
1 TTTG
52976443 AGGTGGGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.17, C:0.04, G:0.43, T:0.35
Consensus pattern (21 bp):
TTTGGGGAGGAAGGGTATCGT
Found at i:52988932 original size:103 final size:104
Alignment explanation
Indices: 52988753--52989016 Score: 406
Period size: 103 Copynumber: 2.5 Consensus size: 104
52988743 ACCGTTATTA
* * * *
52988753 GTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAA
1 GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
** * *
52988818 TCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATATG
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
52988856 GTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGGA
52988920 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
65 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
* **
52988960 GTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
52989017 TTATGTACAA
Statistics
Matches: 147, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
102 1 0.01
103 81 0.55
104 64 0.44
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (104 bp):
GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
Found at i:52991290 original size:10 final size:10
Alignment explanation
Indices: 52991277--52991301 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
52991267 TTGAAAAAAA
52991277 TAAAATTATT
1 TAAAATTATT
52991287 TAAAATTATT
1 TAAAATTATT
52991297 TAAAA
1 TAAAA
52991302 ATAGGGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TAAAATTATT
Found at i:52991355 original size:51 final size:51
Alignment explanation
Indices: 52991300--52991397 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
52991290 AATTATTTAA
52991300 AAATAGGGATTTAAGAGAAATTTAAGAA-GAACTTGAGAGCAAATTGAAATT
1 AAATAGGGATTTAAGAGAAATTT-AGAAGGAACTTGAGAGCAAATTGAAATT
* * * * * *
52991351 AAATATGGATTTGATATAAATTTTGAAGGAATTTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGA
52991398 GAGGAAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
50 3 0.08
51 37 0.93
ACGTcount: A:0.46, C:0.03, G:0.21, T:0.30
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAAATT
Found at i:52991397 original size:11 final size:12
Alignment explanation
Indices: 52991380--52991412 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
52991370 ATTTTGAAGG
52991380 AATTTGAGAGCA
1 AATTTGAGAGCA
*
52991392 AA-TTGAGAGGA
1 AATTTGAGAGCA
52991403 AATTTGAGAG
1 AATTTGAGAG
52991413 AGGATTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.42, C:0.03, G:0.30, T:0.24
Consensus pattern (12 bp):
AATTTGAGAGCA
Found at i:52994815 original size:13 final size:13
Alignment explanation
Indices: 52994797--52994821 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52994787 AACGAATATC
52994797 AAATAAAATAAAT
1 AAATAAAATAAAT
52994810 AAATAAAATAAA
1 AAATAAAATAAA
52994822 ATTAGTAACC
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:52995731 original size:3 final size:3
Alignment explanation
Indices: 52995723--52995748 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52995713 AATATTTTAA
52995723 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
52995749 CAAAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:53014362 original size:13 final size:13
Alignment explanation
Indices: 53014344--53014368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53014334 AACGAATATC
53014344 AAATAAAATAAAT
1 AAATAAAATAAAT
53014357 AAATAAAATAAA
1 AAATAAAATAAA
53014369 ATTAGTAACC
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:53033913 original size:13 final size:13
Alignment explanation
Indices: 53033895--53033919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53033885 AACGAATATC
53033895 AAATAAAATAAAT
1 AAATAAAATAAAT
53033908 AAATAAAATAAA
1 AAATAAAATAAA
53033920 ATTAGTAACC
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:53052125 original size:5 final size:5
Alignment explanation
Indices: 53052115--53052172 Score: 93
Period size: 5 Copynumber: 11.8 Consensus size: 5
53052105 AATTATGTTT
53052115 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
53052164 TTATA TTAT
1 TTATA TTAT
53052173 TATATATATA
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 41 0.82
6 5 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:53052249 original size:40 final size:40
Alignment explanation
Indices: 53052192--53052287 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
53052182 ATGACAAAGA
53052192 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
53052233 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
*
53052273 AAGGAAGGAAAGAAA
1 AA-GAAAGAAAGAAA
53052288 AAAAGAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (40 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:53053049 original size:29 final size:30
Alignment explanation
Indices: 53052990--53053047 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
53052980 TCCGAGCCTT
*
53052990 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
53053020 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
53053048 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:53053277 original size:13 final size:13
Alignment explanation
Indices: 53053259--53053290 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
53053249 TTTCCAGCAA
53053259 TTATGAATTTATT
1 TTATGAATTTATT
53053272 TTATGAATTTATT
1 TTATGAATTTATT
*
53053285 TGATGA
1 TTATGA
53053291 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:53053477 original size:50 final size:50
Alignment explanation
Indices: 53053385--53053626 Score: 252
Period size: 50 Copynumber: 4.7 Consensus size: 50
53053375 ATTTGGGTAA
* * * *
53053385 AGAGATCCCATGTAAGACCATGTCTGGGACATGTCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATCGGCA-CC----GA-GATG
* * *
53053441 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGATG
* *
53053491 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGATG
* * * * **
53053541 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATCGGCACCGA-GATG
**
53053591 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
53053627 TTTGGCATGT
Statistics
Matches: 163, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.56
51 31 0.19
55 2 0.01
56 38 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGATG
Found at i:53053572 original size:100 final size:103
Alignment explanation
Indices: 53053384--53053634 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 103
53053374 CATTTGGGTA
*
53053384 AAGAGATCCCATGTAAGACCATGTCTGGGACATGTCATTGGCATCCTTAAGATCATGAGAGGTCC
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCC
* *
53053449 CCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GAC
63 CCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCAC
* * * *
53053490 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCT
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCT
53053552 ATAAGACCATGTCTGGGACATGGCATGGGCACCATCAC
66 ATAAGACCATGTCTGGGACATGGCATGGGCACCATCAC
* *
53053590 AAGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AAG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
53053635 GTTATTATCA
Statistics
Matches: 131, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 39 0.30
105 2 0.02
106 39 0.30
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (103 bp):
AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCT
ATAAGACCATGTCTGGGACATGGCATGGGCACCATCAC
Found at i:53055125 original size:41 final size:41
Alignment explanation
Indices: 53055079--53055178 Score: 119
Period size: 41 Copynumber: 2.4 Consensus size: 41
53055069 GCCTTTAGCT
* * * *
53055079 TGCTAGACTTATAGTCTGAAATGCGTCACCGGCATTAAGCC
1 TGCTAGACGTAAAGTCTGAAATACGTCACCGGCATCAAGCC
* * ** *
53055120 TGCTAGACGTAAAGTCTGTATTATTTCACCGGTATCAAGCC
1 TGCTAGACGTAAAGTCTGAAATACGTCACCGGCATCAAGCC
53055161 TGCTAGACGTAAAGTCTG
1 TGCTAGACGTAAAGTCTG
53055179 TATTACATTC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (41 bp):
TGCTAGACGTAAAGTCTGAAATACGTCACCGGCATCAAGCC
Found at i:53055179 original size:41 final size:41
Alignment explanation
Indices: 53055104--53055183 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
53055094 CTGAAATGCG
*
53055104 TCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGTATTATT
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTATT
*
53055145 TCACCGGTATCAAGCCTGCTAGACGTAAAGTCTGTATTA
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTA
53055184 CATTCGATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (41 bp):
TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTATT
Found at i:53058440 original size:23 final size:23
Alignment explanation
Indices: 53058414--53058472 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
53058404 CAGCTCGTAT
* *
53058414 GAGCTTACCGTTTCAGCTCTACG
1 GAGCTTACCGTTTCAGCTCAACA
*
53058437 GAGCTTACCGTTTCAGCTCAATA
1 GAGCTTACCGTTTCAGCTCAACA
53058460 GAGCTTACCGTTT
1 GAGCTTACCGTTT
53058473 ATCAGCTCGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.32
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGCTCAACA
Found at i:53066872 original size:29 final size:29
Alignment explanation
Indices: 53066819--53066874 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
53066809 TCATGATCAT
*
53066819 TATTAATATAATAAAATTTTATATTTACA
1 TATTAATATAATAAAAATTTATATTTACA
53066848 TATTAA-ATACATAAATAATTT-TATTTA
1 TATTAATATA-ATAAA-AATTTATATTTA
53066875 TCAAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.12
29 17 0.71
30 4 0.17
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (29 bp):
TATTAATATAATAAAAATTTATATTTACA
Found at i:53067120 original size:53 final size:53
Alignment explanation
Indices: 53067009--53067120 Score: 199
Period size: 52 Copynumber: 2.1 Consensus size: 53
53066999 AAAACTGATG
*
53067009 TAATTTATATTATCTTTTTTCATGACAGTCGAAGGGCCCATCACAACCTAACT
1 TAATTTATATTATCTTTTTTCATGACAGTCGAAGAGCCCATCACAACCTAACT
53067062 TAATTTATATTATCTTTTTTCAT-ACAGTCGAAGAGCCCATCACAACCTAACT
1 TAATTTATATTATCTTTTTTCATGACAGTCGAAGAGCCCATCACAACCTAACT
53067114 TCAATTT
1 T-AATTT
53067121 GAACCACTTG
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 29 0.51
53 28 0.49
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (53 bp):
TAATTTATATTATCTTTTTTCATGACAGTCGAAGAGCCCATCACAACCTAACT
Found at i:53068974 original size:25 final size:25
Alignment explanation
Indices: 53068920--53068974 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
53068910 TCTACAAGCA
* * *
53068920 TGTA-AACCGGAAGCTCTTCCGAGC
1 TGTATAACCGGAAGCTCATACGAAC
**
53068944 CATATAACCGGAAGCTCATACGAAC
1 TGTATAACCGGAAGCTCATACGAAC
53068969 TGTATA
1 TGTATA
53068975 TTGGGAAGCT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (25 bp):
TGTATAACCGGAAGCTCATACGAAC
Found at i:53069000 original size:25 final size:25
Alignment explanation
Indices: 53068972--53069036 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
53068962 TACGAACTGT
*
53068972 ATATTGGGAAGCTC-TTGCGAGCCAA
1 ATATTGGGAAGCTCATT-AGAGCCAA
* *
53068997 ATATCGAGAAGCTCATTAGAGCCAA
1 ATATTGGGAAGCTCATTAGAGCCAA
* *
53069022 GTATTGGGAAACTCA
1 ATATTGGGAAGCTCA
53069037 AGAGAGCTGT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
25 30 0.94
26 2 0.06
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (25 bp):
ATATTGGGAAGCTCATTAGAGCCAA
Found at i:53069391 original size:16 final size:15
Alignment explanation
Indices: 53069351--53069393 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
53069341 TATATGAATG
* *
53069351 AATTTAACTCAATTT
1 AATTTAATTCAATTC
*
53069366 AATATAATTCATATTC
1 AATTTAATTCA-ATTC
53069382 AATTTAATTCAA
1 AATTTAATTCAA
53069394 CATGCATCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTTAATTCAATTC
Found at i:53076473 original size:3 final size:3
Alignment explanation
Indices: 53076465--53076490 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
53076455 GTGACAAAAG
53076465 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
53076491 ATATCAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:53082014 original size:40 final size:41
Alignment explanation
Indices: 53081937--53082053 Score: 132
Period size: 40 Copynumber: 2.9 Consensus size: 41
53081927 TTGACCTTTT
* *
53081937 GGGGCTTTAGCGGCATTTTTGAAAAAGCGCCTCTAATGCTC
1 GGGGCTTTAACAGCATTTTTGAAAAAGCGCCTCTAATGCTC
*
53081978 GGGGCTTTAACAGCGTTTTTG-AAAAGCGCCGT-TAATGCTC
1 GGGGCTTTAACAGCATTTTTGAAAAAGCGCC-TCTAATGCTC
* ** *
53082018 GGGGATTT-AGTGACATTTTTGAAAAAGCGCCGCTAA
1 GGGGCTTTAACAG-CATTTTTGAAAAAGCGCCTCTAA
53082054 AAACATTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
39 2 0.03
40 31 0.48
41 31 0.48
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (41 bp):
GGGGCTTTAACAGCATTTTTGAAAAAGCGCCTCTAATGCTC
Found at i:53082663 original size:7 final size:7
Alignment explanation
Indices: 53082647--53082838 Score: 59
Period size: 7 Copynumber: 26.9 Consensus size: 7
53082637 TATAATTATA
*
53082647 GTTTAAG
1 GTTTAGG
53082654 GTTTAGG
1 GTTTAGG
53082661 GTTTAGG
1 GTTTAGG
* *
53082668 GTATATG
1 GTTTAGG
* *
53082675 GTGTAAG
1 GTTTAGG
*
53082682 GTTTAAG
1 GTTTAGG
*
53082689 GTTTAAGA
1 GTTT-AGG
53082697 GTTACTA--
1 GTT--TAGG
* *
53082704 TTTTAAG
1 GTTTAGG
*
53082711 GTTTATG
1 GTTTAGG
*
53082718 GATTATGG
1 GTTTA-GG
53082726 GTTTAGG
1 GTTTAGG
* *
53082733 GATTACG
1 GTTTAGG
*
53082740 GTTTATG
1 GTTTAGG
**
53082747 GTTTATT
1 GTTTAGG
53082754 GTTTAAGG
1 GTTT-AGG
*
53082762 G-TCAGG
1 GTTTAGG
* *
53082768 ATTTAAG
1 GTTTAGG
*
53082775 GTTCAGG
1 GTTTAGG
53082782 GATTTAGG
1 G-TTTAGG
53082790 GTTTAGG
1 GTTTAGG
*
53082797 AG-TTATG
1 -GTTTAGG
* *
53082804 TTTTATG
1 GTTTAGG
**
53082811 GTTTATA
1 GTTTAGG
53082818 GTTTAGGG
1 GTTTA-GG
53082826 GTTTAGG
1 GTTTAGG
53082833 GTTTAG
1 GTTTAG
53082839 ATTAATTAGT
Statistics
Matches: 138, Mismatches: 35, Indels: 24
0.70 0.18 0.12
Matches are distributed among these distances:
5 2 0.01
6 3 0.02
7 108 0.78
8 23 0.17
9 1 0.01
10 1 0.01
ACGTcount: A:0.22, C:0.02, G:0.32, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:53082728 original size:15 final size:15
Alignment explanation
Indices: 53082710--53082752 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
53082700 ACTATTTTAA
*
53082710 GGTTTATGGATTATG
1 GGTTTATGGATTATC
*
53082725 GGTTTAGGGATTA-C
1 GGTTTATGGATTATC
*
53082739 GGTTTATGGTTTAT
1 GGTTTATGGATTAT
53082753 TGTTTAAGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.47
Consensus pattern (15 bp):
GGTTTATGGATTATC
Found at i:53082796 original size:64 final size:64
Alignment explanation
Indices: 53082705--53082827 Score: 160
Period size: 64 Copynumber: 1.9 Consensus size: 64
53082695 GAGTTACTAT
* * *
53082705 TTTAAGGTTTATGGATTATGGGTTTAGG-GATTACGGTTTATGGTTTATTGTTTAAGGGTCAGGA
1 TTTAAGGTTCAGGGATTATGGGTTTAGGAG-TTACGGTTTATGGTTTATAGTTTAAGGGTCAGGA
* * *
53082769 TTTAAGGTTCAGGGATT-TAGGGTTTAGGAGTTATGTTTTATGGTTTATAGTTTAGGGGT
1 TTTAAGGTTCAGGGATTAT-GGGTTTAGGAGTTACGGTTTATGGTTTATAGTTTAAGGGT
53082828 TTAGGGTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
63 1 0.02
64 49 0.96
65 1 0.02
ACGTcount: A:0.21, C:0.02, G:0.32, T:0.45
Consensus pattern (64 bp):
TTTAAGGTTCAGGGATTATGGGTTTAGGAGTTACGGTTTATGGTTTATAGTTTAAGGGTCAGGA
Found at i:53089852 original size:48 final size:48
Alignment explanation
Indices: 53089773--53089914 Score: 232
Period size: 48 Copynumber: 3.0 Consensus size: 48
53089763 AGGGAATTCT
* * **
53089773 GTTGAATCCTTTATTGTTGCGAGTT-GAGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCTTTATAGGTGAAAGTTAG-GCTGACTTAGGCGTTTTTACG
53089821 GTTGAATCCTTTATAGGTGAAAGTTAGGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCTTTATAGGTGAAAGTTAGGCTGACTTAGGCGTTTTTACG
53089869 GTTGAATCCTTTATAGGTGAAAGTTAGGCTGACTTAGGCGTTTTTA
1 GTTGAATCCTTTATAGGTGAAAGTTAGGCTGACTTAGGCGTTTTTA
53089915 AGCCAAGAAA
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
48 88 0.99
49 1 0.01
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.39
Consensus pattern (48 bp):
GTTGAATCCTTTATAGGTGAAAGTTAGGCTGACTTAGGCGTTTTTACG
Found at i:53092477 original size:48 final size:48
Alignment explanation
Indices: 53092398--53092506 Score: 166
Period size: 48 Copynumber: 2.3 Consensus size: 48
53092388 AGGGAATTCT
* * **
53092398 GTTGAATCCTTTATTGTTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCTTTATAGGTGAAAGTTGAGCTGACTTAGGCGTTTTTACG
53092446 GTTGAATCCTTTATAGGTGAAAGTT-AGGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCTTTATAGGTGAAAGTTGA-GCTGACTTAGGCGTTTTTACG
53092494 GTTGAATCCTTTA
1 GTTGAATCCTTTA
53092507 CGTTTGATTC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
47 1 0.02
48 55 0.98
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.40
Consensus pattern (48 bp):
GTTGAATCCTTTATAGGTGAAAGTTGAGCTGACTTAGGCGTTTTTACG
Found at i:53094332 original size:12 final size:12
Alignment explanation
Indices: 53094305--53094351 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
53094295 AATTTAAAGC
53094305 ATATATACATAA-
1 ATATATACA-AAT
*
53094317 ATATTTACAAAT
1 ATATATACAAAT
*
53094329 ATATATACAAGT
1 ATATATACAAAT
53094341 ATAGTATACAA
1 ATA-TATACAA
53094352 GTAAACTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 2 0.07
12 21 0.70
13 7 0.23
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (12 bp):
ATATATACAAAT
Found at i:53094992 original size:12 final size:12
Alignment explanation
Indices: 53094977--53095015 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
53094967 GATAGAGATG
*
53094977 ATGATAGTAATA
1 ATGATAATAATA
53094989 ATGATAATATATA
1 ATGATAATA-ATA
53095002 AT-ATAATAATA
1 ATGATAATAATA
53095013 ATG
1 ATG
53095016 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 5 0.21
12 14 0.58
13 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (12 bp):
ATGATAATAATA
Found at i:53095982 original size:48 final size:48
Alignment explanation
Indices: 53095903--53095996 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
53095893 AGGGAATTCT
* * **
53095903 GTTGAATCCTTTATTGTTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCTTTATAGGTGAAAGTTGAGCTGACTTAGGCGTTTTTACG
53095951 GTTGAATCCTTTATAGGTGAAAGTT-AGGCTGACTTAGGCGTTTTTA
1 GTTGAATCCTTTATAGGTGAAAGTTGA-GCTGACTTAGGCGTTTTTA
53095997 AGCCAAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 1 0.02
48 40 0.98
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (48 bp):
GTTGAATCCTTTATAGGTGAAAGTTGAGCTGACTTAGGCGTTTTTACG
Found at i:53097124 original size:16 final size:16
Alignment explanation
Indices: 53097093--53097129 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
53097083 ATATGAAGAA
53097093 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
53097109 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
53097125 TATTA
1 TATTA
53097130 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:53097168 original size:16 final size:16
Alignment explanation
Indices: 53097149--53097183 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
53097139 TGAAATATTA
*
53097149 AATAATTTATTAAAAT
1 AATAAATTATTAAAAT
*
53097165 AATAAATTATTAATAT
1 AATAAATTATTAAAAT
53097181 AAT
1 AAT
53097184 TTATTATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATAAATTATTAAAAT
Found at i:53097189 original size:16 final size:15
Alignment explanation
Indices: 53097144--53097190 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 15
53097134 AAAATTGAAA
53097144 TATTAAATAATTTAT
1 TATTAAATAATTTAT
**
53097159 TA--AAATAATAAAT
1 TATTAAATAATTTAT
53097172 TATTAATATAATTTAT
1 TATTAA-ATAATTTAT
53097188 TAT
1 TAT
53097191 ATGATTAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
13 11 0.44
15 4 0.16
16 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTAAATAATTTAT
Found at i:53100206 original size:12 final size:12
Alignment explanation
Indices: 53100179--53100225 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
53100169 AATTTAAAGC
53100179 ATATATACATAA-
1 ATATATACA-AAT
*
53100191 ATATTTACAAAT
1 ATATATACAAAT
*
53100203 ATATATACAAGT
1 ATATATACAAAT
53100215 ATAGTATACAA
1 ATA-TATACAA
53100226 GTAAACTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 2 0.07
12 21 0.70
13 7 0.23
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (12 bp):
ATATATACAAAT
Found at i:53100865 original size:12 final size:12
Alignment explanation
Indices: 53100850--53100888 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
53100840 GATAGAGATG
*
53100850 ATGATAGTAATA
1 ATGATAATAATA
53100862 ATGATAATATATA
1 ATGATAATA-ATA
53100875 AT-ATAATAATA
1 ATGATAATAATA
53100886 ATG
1 ATG
53100889 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 5 0.21
12 14 0.58
13 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (12 bp):
ATGATAATAATA
Found at i:53102461 original size:45 final size:44
Alignment explanation
Indices: 53102406--53102495 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
53102396 AAGACTTGTA
* * **
53102406 TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCA-CACCAATACAGGAAGACAAGATCTGCTT
* *
53102451 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTT
53102495 T
1 T
53102496 TTCAATCGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 24 0.62
45 15 0.38
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (44 bp):
TCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTT
Found at i:53102764 original size:44 final size:44
Alignment explanation
Indices: 53102708--53103174 Score: 322
Period size: 45 Copynumber: 10.5 Consensus size: 44
53102698 AGACCTACTA
* *
53102708 TCTTTGATCTACTTCACGCCAGTACATGAAGACACGATCTGTTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
* * * * *** *
53102752 TCTTCGACCTACTCCACCACCAGTATGGGGAGACAAGATCTG-TT
1 TCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGCTT
53102796 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
* * *** *
53102840 TCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTG-TT
1 TCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGCTT
* *
53102884 GACTTTAATCTACTTCACGCC-GATACATGAAGACAAGATCTGCTT
1 -TCTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTGCTT
* * *** *
53102929 TCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTG-TT
1 TCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGCTT
* * * *
53102973 GACTTTGATCTACTTCACG-CTGATACATGAAGACAATATCTACTT
1 -TCTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTGCTT
* * * * * * *
53103018 TCTTTCGATCTGCTTCGCCACCAGTATGA-GAAGGCGAGATCTG-TA
1 TCTTT-GATCTACTTC-ACGCCAGTA-CATGAAGACAAGATCTGCTT
* *
53103063 TATTTGATCTACTTCACGCTAGTACATGAAGACAAGATCTG-TAT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT-T
* * * * *** ***
53103107 TCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGTGAGATCTG-TT
1 T-CTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTT
53103152 ATCTTTGATCTACTTCACGCCAG
1 -TCTTTGATCTACTTCACGCCAG
53103175 AAGACAAGAT
Statistics
Matches: 318, Mismatches: 85, Indels: 40
0.72 0.19 0.09
Matches are distributed among these distances:
42 1 0.00
43 42 0.13
44 113 0.36
45 126 0.40
46 33 0.10
47 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (44 bp):
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
Found at i:53102931 original size:89 final size:88
Alignment explanation
Indices: 53102709--53103174 Score: 598
Period size: 89 Copynumber: 5.2 Consensus size: 88
53102699 GACCTACTAT
* * * *
53102709 CTTTGATCTACTTCACGCCAGTACATGAAGACACGATCTGTTTTCTTCGACCTACTCCACCACCA
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACCA
*
53102774 GTATGGGGAGACAAGATCTGTTT
66 GTATGGGGAGACAAGATCTGTTA
53102797 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACCA
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACCA
53102862 GTATGGGGAGACAAGATCTGTTGA
66 GTATGGGGAGACAAGATCTGTT-A
*
53102886 CTTTAATCTACTTCACGCC-GATACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACC
1 CTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACC
53102950 AGTATGGGGAGACAAGATCTGTTGA
65 AGTATGGGGAGACAAGATCTGTT-A
* * * * * *
53102975 CTTTGATCTACTTCACG-CTGATACATGAAGACAATATCTACTTTCTTTCGATCTGCTTCGCCAC
1 CTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTGCTTTCTTT-GATCTACTCCACCAC
* * * *
53103039 CAGTATGAGAAGGCGAGATCTGTATA
64 CAGTATGGGGAGACAAGATCTGT-TA
* * * * *
53103065 -TTTGATCTACTTCACGCTAGTACATGAAGACAAGATCTG-TATTCCTTCGATCTGCTTCGCCAC
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT-TT-CTTTGATCTACTCCACCAC
* ***
53103128 CAGTATGGGAAGGTGAGATCTGTTA
64 CAGTATGGGGAGACAAGATCTGTTA
53103153 TCTTTGATCTACTTCACGCCAG
1 -CTTTGATCTACTTCACGCCAG
53103175 AAGACAAGAT
Statistics
Matches: 344, Mismatches: 24, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
88 88 0.26
89 200 0.58
90 55 0.16
91 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (88 bp):
CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACCA
GTATGGGGAGACAAGATCTGTTA
Found at i:53103028 original size:45 final size:43
Alignment explanation
Indices: 53102708--53103102 Score: 203
Period size: 44 Copynumber: 8.9 Consensus size: 43
53102698 AGACCTACTA
* *
53102708 TCTTTGATCTACTTCACGCC-AGTACATGAAGACACGATCTGTTT
1 TCTTTGATCTACTTCACGCCGA-TACATGAAGACAAGATCT-CTT
* * * * *** * *
53102752 TCTTCGACCTACTCCAC-CACCAGTATGGGGAGACAAGATCTGTT
1 TCTTTGATCTACTTCACGC-CGA-TACATGAAGACAAGATCTCTT
53102796 TCTTTGATCTACTTCACGCC-AGTACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACGCCGA-TACATGAAGACAAGATCT-CTT
* * *** * *
53102840 TCTTTGATCTACTCCAC-CACCAGTATGGGGAGACAAGATCTGTT
1 TCTTTGATCTACTTCACGC-CGA-TACATGAAGACAAGATCTCTT
* *
53102884 GACTTTAATCTACTTCACGCCGATACATGAAGACAAGATCTGCTT
1 -TCTTTGATCTACTTCACGCCGATACATGAAGACAAGATCT-CTT
* * *** * *
53102929 TCTTTGATCTACTCCAC-CACCAGTATGGGGAGACAAGATCTGTT
1 TCTTTGATCTACTTCACGC-CGA-TACATGAAGACAAGATCTCTT
* * *
53102973 GACTTTGATCTACTTCACGCTGATACATGAAGACAATATCTACTT
1 -TCTTTGATCTACTTCACGCCGATACATGAAGACAAGATCT-CTT
* * * * * * * *
53103018 TCTTTCGATCTGCTTCGC-CACCAGTATGA-GAAGGCGAGATCTGTA
1 TCTTT-GATCTACTTCACGC-CGA-TA-CATGAAGACAAGATCTCTT
* *
53103063 TATTTGATCTACTTCACG-CTAGTACATGAAGACAAGATCT
1 TCTTTGATCTACTTCACGCCGA-TACATGAAGACAAGATCT
53103103 GTATTCCTTC
Statistics
Matches: 262, Mismatches: 69, Indels: 41
0.70 0.19 0.11
Matches are distributed among these distances:
42 1 0.00
43 35 0.13
44 113 0.43
45 98 0.37
46 14 0.05
47 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (43 bp):
TCTTTGATCTACTTCACGCCGATACATGAAGACAAGATCTCTT
Found at i:53103223 original size:86 final size:87
Alignment explanation
Indices: 53102706--53103236 Score: 451
Period size: 89 Copynumber: 6.0 Consensus size: 87
53102696 TAAGACCTAC
* * * * * *
53102706 TATCTTTGATCTACTTCACGCCAGTACATGAAGACACGATCT-GTTTT-CTTCGACCTACTCCAC
1 TATCTTTGATCTACTTCACG-C---ACATGAAGACAAGATCTACTTTTCCTTCGATCTGCTTCGC
* * *
53102769 CACCAGTATGGGGAGACAAGATCTGT
62 CACCAGTATGGGAAGGCGAGATCTGT
* * * * *
53102795 T-TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC-TTT-CTTTGATCTACTCCAC
1 TATCTTTGATCTACTTCACG-C---ACATGAAGACAAGATCTACTTTTCCTTCGATCTGCTTCGC
* * *
53102857 CACCAGTATGGGGAGACAAGATCTGT
62 CACCAGTATGGGAAGGCGAGATCTGT
* * * * * *
53102883 TGA-CTTTAATCTACTTCACGCCGATACATGAAGACAAGATCTGC-TTT-CTTTGATCTACTCCA
1 T-ATCTTTGATCTACTTCACG-C---ACATGAAGACAAGATCTACTTTTCCTTCGATCTGCTTCG
* * *
53102945 CCACCAGTATGGGGAGACAAGATCTGT
61 CCACCAGTATGGGAAGGCGAGATCTGT
* *
53102972 TGA-CTTTGATCTACTTCACGCTGATACATGAAGACAATATCTAC-TTTCTTTCGATCTGCTTCG
1 T-ATCTTTGATCTACTTCACGC----ACATGAAGACAAGATCTACTTTTCCTTCGATCTGCTTCG
*
53103035 CCACCAGTATGAGAAGGCGAGATCTG-
61 CCACCAGTATGGGAAGGCGAGATCTGT
* * *
53103061 TATATTTGATCTACTTCACGCTAGTACATGAAGACAAGATCT-GTATTCCTTCGATCTGCTTCGC
1 TATCTTTGATCTACTTCACGC----ACATGAAGACAAGATCTACTTTTCCTTCGATCTGCTTCGC
*
53103125 CACCAGTATGGGAAGGTGAGATCTGT
62 CACCAGTATGGGAAGGCGAGATCTGT
*
53103151 TATCTTTGATCTACTTCACGC-CA-GAAGACAAGATCTACTTTTTCCTTCGATCTGTTTCGCCAC
1 TATCTTTGATCTACTTCACGCACATGAAGACAAGATCTAC-TTTTCCTTCGATCTGCTTCGCCAC
53103214 CAGTATGGGAAGGCGAGATCTGT
65 CAGTATGGGAAGGCGAGATCTGT
53103237 ATATTCGATC
Statistics
Matches: 399, Mismatches: 33, Indels: 23
0.88 0.07 0.05
Matches are distributed among these distances:
84 13 0.03
85 2 0.01
86 44 0.11
88 85 0.21
89 203 0.51
90 52 0.13
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (87 bp):
TATCTTTGATCTACTTCACGCACATGAAGACAAGATCTACTTTTCCTTCGATCTGCTTCGCCACC
AGTATGGGAAGGCGAGATCTGT
Found at i:53104677 original size:52 final size:50
Alignment explanation
Indices: 53104572--53104679 Score: 119
Period size: 52 Copynumber: 2.1 Consensus size: 50
53104562 AGCCTCTCCA
* * * * * *
53104572 TTTTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACTTGGTCTTTCTCTT
1 TTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACTTAGTC-TCCACTT
*
53104623 TTTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCTTAGTC-CCACGT
1 TTTTTTTTT-ACTCAAAGCGCCCTTTGTAGGCTTTCA-CTTAGTCTCCACTT
53104674 TTTTTT
1 TTTTTT
53104680 AAGCAGAGTA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
51 18 0.38
52 24 0.50
53 6 0.12
ACGTcount: A:0.12, C:0.23, G:0.15, T:0.50
Consensus pattern (50 bp):
TTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACTTAGTCTCCACTT
Found at i:53107394 original size:20 final size:20
Alignment explanation
Indices: 53107365--53107404 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53107355 TAAAGGTCTT
* *
53107365 TAATGCATATGATGTGATGC
1 TAATGAATATGATGCGATGC
53107385 TAATGAATATGATGCGATGC
1 TAATGAATATGATGCGATGC
53107405 ATGAGGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.33
Consensus pattern (20 bp):
TAATGAATATGATGCGATGC
Found at i:53111160 original size:129 final size:129
Alignment explanation
Indices: 53110840--53111169 Score: 514
Period size: 129 Copynumber: 2.6 Consensus size: 129
53110830 TACAGTTTCA
* *
53110840 AGGAA-ATAGGAA-TACTGGCTTCAACGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCAT
1 AGGAAGATA-GAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGT-AAATCCACCAT
53110903 C-TTGATCTGCTCCACTACTGCTTAGGGAGATAAATCTGTAATCTTTAATCTATTCCACGTTGCC
64 CTTTGATCTGCTCCACTACTGCTTAGGGAGATAAATCTGTAATCTTTAATCTATTCCACGTTGCC
53110967 C
129 C
*
53110968 AGG-AGATAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCA-GGAGGTAAATCCACTATCT
1 AGGAAGATAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAATCCACCATCT
53111031 TTGATCTGCTCCACTACTGCTTA-GGAGATAAGATCTGTAATCTTTAATCTATTCCACTGTTGCC
66 TTGATCTGCTCCACTACTGCTTAGGGAGATAA-ATCTGTAATCTTTAATCTATTCCAC-GTTGCC
53111095 C
129 C
53111096 AGGAAGATAGAATTACTGGCTTCAATGTACTCCACTGCAACC-CAGGGAGGTAAAT-CAGCCATC
1 AGGAAGATAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAATCCA-CCATC
**
53111159 TTCAATCTGCT
65 TTTGATCTGCT
53111170 TCGCTGTTTA
Statistics
Matches: 188, Mismatches: 6, Indels: 15
0.90 0.03 0.07
Matches are distributed among these distances:
126 19 0.10
127 58 0.31
128 50 0.27
129 61 0.32
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (129 bp):
AGGAAGATAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAATCCACCATCT
TTGATCTGCTCCACTACTGCTTAGGGAGATAAATCTGTAATCTTTAATCTATTCCACGTTGCCC
Found at i:53111754 original size:44 final size:43
Alignment explanation
Indices: 53111549--53111761 Score: 160
Period size: 44 Copynumber: 5.0 Consensus size: 43
53111539 GACCTACTCC
*
53111549 CACCACCAGTATGGGAGACAAGATCTGTT-TC-TTGATCTACTT
1 CACCACCAGTATGGGAGACAAGATCTGTTGACTTTGATCTAC-T
* * * * *
53111591 CACGCA-TA-CAT-GAAGACAAGATCTCTT-TCTTTGATCTACT
1 CAC-CACCAGTATGGGAGACAAGATCTGTTGACTTTGATCTACT
* *
53111631 CACCACTAGTATGGGAGACAAGGTCTGTTGACTTTGATCTACTT
1 CACCACCAGTATGGGAGACAAGATCTGTTGACTTTGATCTAC-T
* * * *
53111675 CA-CGCC-GATACAT-GAAGGCAAGATCTGCTT-TCTTTGATCTACT
1 CACCACCAG-T--ATGGGAGACAAGATCTG-TTGACTTTGATCTACT
53111718 CCACCACCAGTATGGGGAGACAAGAT-TGTTGACTTTGATCTACT
1 -CACCACCAGTAT-GGGAGACAAGATCTGTTGACTTTGATCTACT
53111762 TCACGCTGAT
Statistics
Matches: 135, Mismatches: 19, Indels: 32
0.73 0.10 0.17
Matches are distributed among these distances:
39 2 0.01
40 22 0.16
41 13 0.10
42 18 0.13
43 21 0.16
44 41 0.30
45 17 0.13
46 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (43 bp):
CACCACCAGTATGGGAGACAAGATCTGTTGACTTTGATCTACT
Found at i:53111866 original size:177 final size:172
Alignment explanation
Indices: 53111492--53112029 Score: 630
Period size: 177 Copynumber: 3.1 Consensus size: 172
53111482 ACAGACCTAC
* * *
53111492 TATTTGATCTACTTCACGCCA-TACATGAAGAC-CGATCTGTTTTCTTCGACCTACTCCCACCAC
1 TATTCGATCTACTTCACG-CAGTACATGAAGACAAGATCTG-TTTCTTCGATCTACT-CCACCAC
*
53111555 CAGTAT-GGGAGACAAGATCTGTTTC-TTGATCTACTTCACGC-ATACATGAAGACAAGATCTCT
63 CAGTATGGGGAGACAAGATCTGTTACTTTGATCTACTTCACGCGATACATGAAGACAAGATCTCT
* * * * * *
53111617 TTCTTT-GATCTAC-TCACCACTAGTATGGGAGACAAGGTCTGT-
128 TTCTTTCGATCTGCTTCGCCACCAGTATGGGAGGCGAGATCTGTA
* * * *
53111659 TGACTTTGATCTACTTCACGCCGATACATGAAGGCAAGATCTGCTTTCTTTGATCTACTCCACCA
1 T-A-TTCGATCTACTTCACGCAG-TACATGAAGACAAGATCTG-TTTCTTCGATCTACTCCACCA
*
53111724 CCAGTATGGGGAGACAAGAT-TGTTGACTTTGATCTACTTCACGCTGATACATGAAGACAATATC
62 CCAGTATGGGGAGACAAGATCTGTT-ACTTTGATCTACTTCACGC-GATACATGAAGACAAGATC
53111788 TACTTTCTTTCGATCTGCTTCGCCACCAGTATGGGAAGGCGAGATCTGTA
125 T-CTTTCTTTCGATCTGCTTCGCCACCAGTATGGG-AGGCGAGATCTGTA
* * *
53111838 TATTCGATCTACTTCACGCTAGTACATGAAGACAAGATCTGTATTCCTTCGATCTGCTTCGCCAC
1 TATTCGATCTACTTCACGC-AGTACATGAAGACAAGATCTGT-TT-CTTCGATCTACTCCACCAC
* * *
53111903 CAGTATGGGAAGGCGAGATCTGTTA-TCTTGATCTACTTCACGC-AGTACATGAAGACAAGATCT
63 CAGTATGGGGAGACAAGATCTGTTACT-TTGATCTACTTCACGCGA-TACATGAAGACAAGATCT
*
53111966 GCTTTTCCTTCGATCTGCTTCGCCACCAGTATGGGAGGCGAGATCTGTA
126 -C-TTTCTTTCGATCTGCTTCGCCACCAGTATGGGAGGCGAGATCTGTA
*
53112015 TATTCGATCCACTTC
1 TATTCGATCTACTTC
53112030 GCTACCAATA
Statistics
Matches: 321, Mismatches: 28, Indels: 34
0.84 0.07 0.09
Matches are distributed among these distances:
167 1 0.00
168 2 0.01
169 16 0.05
170 27 0.08
171 32 0.10
172 16 0.05
174 18 0.06
175 8 0.02
176 8 0.02
177 97 0.30
178 91 0.28
179 5 0.02
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (172 bp):
TATTCGATCTACTTCACGCAGTACATGAAGACAAGATCTGTTTCTTCGATCTACTCCACCACCAG
TATGGGGAGACAAGATCTGTTACTTTGATCTACTTCACGCGATACATGAAGACAAGATCTCTTTC
TTTCGATCTGCTTCGCCACCAGTATGGGAGGCGAGATCTGTA
Found at i:53112029 original size:88 final size:85
Alignment explanation
Indices: 53111492--53112029 Score: 570
Period size: 89 Copynumber: 6.2 Consensus size: 85
53111482 ACAGACCTAC
* * * *
53111492 TATTTGATCTACTTCACGCCA-TACATGAAGAC-CGATCTGTTTTCTTCGACCTACTCCCACCAC
1 TATTTGATCTACTTCACG-CAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACT-TCACCAC
53111555 CAGTATGGGAGACAAGATCTGT
64 CAGTATGGGAGACAAGATCTGT
* *
53111577 T-TCTTGATCTACTTCACGCA-TACATGAAGACAAGATCT-CTTTCTTTGATCTAC-TCACCACT
1 TAT-TTGATCTACTTCACGCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACC
*
53111638 AGTATGGGAGACAAGGTCTGT
65 AGTATGGGAGACAAGATCTGT
* * * *
53111659 TGACTTTGATCTACTTCACGCCGATACATGAAGGCAAGATCTGCTTTCTTTGATCTACTCCACCA
1 T-A-TTTGATCTACTTCACGCAG-TACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCA
53111724 CCAGTATGGGGAGACAAGAT-TGT
63 CCAGTAT-GGGAGACAAGATCTGT
* * * * *
53111747 TGACTTTGATCTACTTCACGCTGATACATGAAGACAATATCTACTTTCTTTCGATCTGCTTCGCC
1 T-A-TTTGATCTACTTCACGCAG-TACATGAAGACAAGATCTGCTTTC-TTCGATCTACTTCACC
* *
53111812 ACCAGTATGGGAAGGCGAGATCTGT
62 ACCAGTATGGG-AGACAAGATCTGT
* * *
53111837 ATATTCGATCTACTTCACGCTAGTACATGAAGACAAGATCTG-TATTCCTTCGATCTGCTTCGCC
1 -TATTTGATCTACTTCACGC-AGTACATGAAGACAAGATCTGCT-TT-CTTCGATCTACTTCACC
* *
53111901 ACCAGTATGGGAAGGCGAGATCTGT
62 ACCAGTATGGG-AGACAAGATCTGT
* *
53111926 TATCTTGATCTACTTCACGCAGTACATGAAGACAAGATCTGCTTTTCCTTCGATCTGCTTCGCCA
1 TAT-TTGATCTACTTCACGCAGTACATGAAGACAAGATCTGC-TTT-CTTCGATCTACTTCACCA
* *
53111991 CCAGTATGGGAGGCGAGATCTGT
63 CCAGTATGGGAGACAAGATCTGT
* *
53112014 ATATTCGATCCACTTC
1 -TATTTGATCTACTTC
53112030 GCTACCAATA
Statistics
Matches: 403, Mismatches: 29, Indels: 39
0.86 0.06 0.08
Matches are distributed among these distances:
82 27 0.07
84 42 0.10
85 22 0.05
86 17 0.04
87 15 0.04
88 109 0.27
89 163 0.40
90 7 0.02
91 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (85 bp):
TATTTGATCTACTTCACGCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCA
GTATGGGAGACAAGATCTGT
Found at i:53112030 original size:43 final size:43
Alignment explanation
Indices: 53111796--53112036 Score: 154
Period size: 43 Copynumber: 5.5 Consensus size: 43
53111786 TCTACTTTCT
*
53111796 TTCGATCTGCTTCGCCACCAGTATGGGAAGGCGAGATCTGTATA
1 TTCGATCTACTTCGCCACCAGTATGGG-AGGCGAGATCTGTATA
* * * * * * *
53111840 TTCGATCTACTTC-ACGCTAGTACAT-GAAGACAAGATCTGTATTCC
1 TTCGATCTACTTCGCCACCAGT--ATGGGAGGCGAGATCTGTA-T-A
*
53111885 TTCGATCTGCTTCGCCACCAGTATGGGAAGGCGAGATCTGT-TA
1 TTCGATCTACTTCGCCACCAGTATGGG-AGGCGAGATCTGTATA
* * * * * *
53111928 TCTTGATCTACTT---CACGCAGTACAT-GAAGACAAGATCTGCTTTTCC
1 T-TCGATCTACTTCGCCAC-CAGT--ATGGGAGGCGAGATCTG--TAT-A
*
53111974 TTCGATCTGCTTCGCCACCAGTATGGGAGGCGAGATCTGTATA
1 TTCGATCTACTTCGCCACCAGTATGGGAGGCGAGATCTGTATA
* *
53112017 TTCGATCCACTTCGCTACCA
1 TTCGATCTACTTCGCCACCA
53112037 ATATAGGAAG
Statistics
Matches: 146, Mismatches: 32, Indels: 39
0.67 0.15 0.18
Matches are distributed among these distances:
41 3 0.02
42 14 0.10
43 36 0.25
44 31 0.21
45 27 0.18
46 28 0.19
47 4 0.03
48 3 0.02
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (43 bp):
TTCGATCTACTTCGCCACCAGTATGGGAGGCGAGATCTGTATA
Found at i:53113370 original size:46 final size:46
Alignment explanation
Indices: 53113318--53113407 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
53113308 AGCCTCTCCA
* * * *
53113318 TTTTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCCTGGTCTC
1 TTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCTC
*
53113364 TTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTC
1 TTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTC
53113408 CCACCTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.12, C:0.26, G:0.18, T:0.44
Consensus pattern (46 bp):
TTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCTC
Found at i:53113417 original size:46 final size:46
Alignment explanation
Indices: 53113321--53113417 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 46
53113311 CTCTCCATTT
* * * * * ***
53113321 TTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCCTGGTCTCTTT
1 TTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCCCACC
*
53113367 TTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTCCCACC
1 TTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCCCACC
53113413 TTTTT
1 TTTTT
53113418 AAGCAGAGTA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.12, C:0.28, G:0.16, T:0.43
Consensus pattern (46 bp):
TTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCCCACC
Found at i:53120036 original size:132 final size:132
Alignment explanation
Indices: 53119876--53120213 Score: 590
Period size: 132 Copynumber: 2.6 Consensus size: 132
53119866 ACAGTTTCAA
* *
53119876 GGAGATAGGAA-TACTGGCTTCAACGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCT
1 GGAGATA-GAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCCACCATCT
53119940 TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGTTGCC
65 TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGTTGCC
53120005 CAG
130 CAG
*
53120008 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCCACTATCTT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCCACCATCTT
53120073 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGTTGCCC
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGTTGCCC
53120138 AG
131 AG
*
53120140 GAAGATAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAAT-CAGCCATCT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCCA-CCATCT
**
53120204 TCAATCTGCT
65 TTGATCTGCT
53120214 TCGCTGTTTA
Statistics
Matches: 197, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
131 5 0.03
132 192 0.97
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
GGAGATAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCCACCATCTT
TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGTTGCCC
AG
Found at i:53120146 original size:44 final size:44
Alignment explanation
Indices: 53119936--53120146 Score: 133
Period size: 44 Copynumber: 4.8 Consensus size: 44
53119926 AAAATCCACC
* * * **
53119936 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTA
* * *
53119980 ATCTTTAATCTATTCCACTGTTGCCCAGGGAGAT-AGA-AT-TA
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTA
* * * ** * * **
53120021 CTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCCACT-
1 AT--CTTTAATCTACTCCACTGCTGCC-CAGGGAGATAAGAT-CTGTA
* * * **
53120068 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTA
* * *
53120112 ATCTTTAATCTATTCCACTGTTGCCCAGGAAGATA
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATA
53120147 GAATTACTGG
Statistics
Matches: 118, Mismatches: 41, Indels: 16
0.67 0.23 0.09
Matches are distributed among these distances:
41 3 0.03
42 1 0.01
43 22 0.19
44 73 0.62
45 17 0.14
47 1 0.01
48 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (44 bp):
ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTA
Found at i:53120297 original size:44 final size:44
Alignment explanation
Indices: 53120229--53120332 Score: 163
Period size: 44 Copynumber: 2.4 Consensus size: 44
53120219 GTTTATGTAG
* * *
53120229 GAAGGCAAGATCTTCTATATTTGATCTACTTGACGCCAGTACAT
1 GAAGACAAGATCTGCTATATTTGATCTACTTCACGCCAGTACAT
* *
53120273 GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGCTATATTTGATCTACTTCACGCCAGTACAT
53120317 GAAGACAAGATCTGCT
1 GAAGACAAGATCTGCT
53120333 TTTTCAATCG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATATTTGATCTACTTCACGCCAGTACAT
Found at i:53120778 original size:89 final size:88
Alignment explanation
Indices: 53120548--53121080 Score: 608
Period size: 89 Copynumber: 6.0 Consensus size: 88
53120538 GACCTACTAT
* * * *
53120548 CTTTGATCTACTTCACGCCAGTACATGAAGACACGATCTGTTTTCTTCGACCTACTCCACCACCA
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACCA
*
53120613 GTATGGGGAGACAAGATCTGTTT
66 GTATGGGGAGACAAGATCTGTTA
* *
53120636 CTTTGATCTACTTCACG-CAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACTA
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACCA
*
53120700 GTATGGGGAGACAAGGTCTGTTGA
66 GTATGGGGAGACAAGATCTGTT-A
*
53120724 CTTTGATCTACTTCACGCC-GATACATGAAGGCAAGATCTGCTTTCTTTGATCTACTCCACCACC
1 CTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACC
*
53120788 AGTATGGGGAGACAAGATTTGTTGA
65 AGTATGGGGAGACAAGATCTGTT-A
* * * * * *
53120813 CTTTGATCTACTTCACG-CTGATACATGAAGACAATATCTACTTTCTTTCGATCTGCTTCGCCAC
1 CTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTGCTTTCTTT-GATCTACTCCACCAC
* * *
53120877 CAGTATGGGAAGGCGAGATCTGTATA
64 CAGTATGGGGAGACAAGATCTGT-TA
* * * * * *
53120903 -TTCGATCTACTTCACGCTAGTACATGAAGACAAGATCTG-TATTCCTTCGATCTGCTTCGCCAC
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT-TT-CTTTGATCTACTCCACCAC
* * *
53120966 CAGTATGGGAAGGCGAGATCTGTTA
64 CAGTATGGGGAGACAAGATCTGTTA
* * * *
53120991 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTCCTTCGATCTGCTTCGCC
1 -CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC--TTT-CTTTGATCTACTCCACC
* * *
53121056 ACCAGTATGGGAAGGCGAGATCTGT
62 ACCAGTATGGGGAGACAAGATCTGT
53121081 ATATTCGATC
Statistics
Matches: 400, Mismatches: 31, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
87 62 0.16
88 38 0.09
89 180 0.45
90 73 0.18
91 1 0.00
92 45 0.11
93 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (88 bp):
CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACCA
GTATGGGGAGACAAGATCTGTTA
Found at i:53120818 original size:45 final size:44
Alignment explanation
Indices: 53120576--53120824 Score: 220
Period size: 45 Copynumber: 5.6 Consensus size: 44
53120566 CAGTACATGA
* * *
53120576 AGACACGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
1 AGACAAGATCTG-TTTCTTTGATCTACTCCACCACCAGTATGGGG
* *** *
53120621 AGACAAGATCTGTTTCTTTGATCTACTTCACGCA--A-TACATGA
1 AGACAAGATCTGTTTCTTTGATCTACTCCAC-CACCAGTATGGGG
*
53120663 AGACAAGATCTGCTTTCTTTGATCTACTCCACCACTAGTATGGGG
1 AGACAAGATCTG-TTTCTTTGATCTACTCCACCACCAGTATGGGG
* * * * *** *
53120708 AGACAAGGTCTGTTGACTTTGATCTACTTCA-CGCC-GATACATGA
1 AGACAAGATCTGTT-TCTTTGATCTACTCCACCACCAG-TATGGGG
*
53120752 AGGCAAGATCTGCTTTCTTTGATCTACTCCACCACCAGTATGGGG
1 AGACAAGATCTG-TTTCTTTGATCTACTCCACCACCAGTATGGGG
* *
53120797 AGACAAGATTTGTTGACTTTGATCTACT
1 AGACAAGATCTGTT-TCTTTGATCTACT
53120825 TCACGCTGAT
Statistics
Matches: 159, Mismatches: 34, Indels: 22
0.74 0.16 0.10
Matches are distributed among these distances:
42 17 0.11
43 20 0.13
44 50 0.31
45 71 0.45
46 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (44 bp):
AGACAAGATCTGTTTCTTTGATCTACTCCACCACCAGTATGGGG
Found at i:53121023 original size:179 final size:175
Alignment explanation
Indices: 53120552--53121096 Score: 693
Period size: 179 Copynumber: 3.1 Consensus size: 175
53120542 TACTATCTTT
* *
53120552 GATCTACTTCACGCCAGTACATGAAGACACGATCTGTTTTCTTCGACCTACTCCACCACCAGTAT
1 GATCTACTTCACG-CAGTACATGAAGACAAGATCTG-TTTCTTCGATCTACTCCACCACCAGTAT
*
53120617 GGGGAGACAAGATCTGTT-TCTTTGATCTACTTCACGCAATACATGAAGACAAGATCTGCTTTCT
64 GGGGAGACAAGATCTGTTATCTTTGATCTACTTCACGCAGTACATGAAGACAAGATCTGCTTTCT
* * * * * * * * *
53120681 TT-GATCTACTCCACCACTAGTATGGGGAGACAAGGTCTGT-TGACTTT
129 TTCGATCTGCTTCGCCACCAGTATGGGAAGGCGAGATCTGTAT-A-TTC
* * *
53120728 GATCTACTTCACGCCGATACATGAAGGCAAGATCTGCTTTCTTTGATCTACTCCACCACCAGTAT
1 GATCTACTTCACGCAG-TACATGAAGACAAGATCTG-TTTCTTCGATCTACTCCACCACCAGTAT
* * * *
53120793 GGGGAGACAAGATTTGTTGA-CTTTGATCTACTTCACGCTGATACATGAAGACAATATCTACTTT
64 GGGGAGACAAGATCTGTT-ATCTTTGATCTACTTCACGCAG-TACATGAAGACAAGATCTGCTTT
53120857 CTTTCGATCTGCTTCGCCACCAGTATGGGAAGGCGAGATCTGTATATTC
127 CTTTCGATCTGCTTCGCCACCAGTATGGGAAGGCGAGATCTGTATATTC
* * *
53120906 GATCTACTTCACGCTAGTACATGAAGACAAGATCTGTATTCCTTCGATCTGCTTCGCCACCAGTA
1 GATCTACTTCACGC-AGTACATGAAGACAAGATCTGT-TT-CTTCGATCTACTCCACCACCAGTA
* * *
53120971 TGGGAAGGCGAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTT
63 TGGGGAGACAAGATCTGTTATCTTTGATCTACTTCACG-CAGTACATGAAGACAAGATCTGC--T
*
53121036 TTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCGAGATCTGTATATTC
125 TTCTTTCGATCTGCTTCGCCACCAGTATGGGAAGGCGAGATCTGTATATTC
*
53121087 GATCCACTTC
1 GATCTACTTC
53121097 GCTACCAATA
Statistics
Matches: 321, Mismatches: 35, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
175 2 0.01
176 73 0.23
177 19 0.06
178 62 0.19
179 102 0.32
180 3 0.01
181 60 0.19
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (175 bp):
GATCTACTTCACGCAGTACATGAAGACAAGATCTGTTTCTTCGATCTACTCCACCACCAGTATGG
GGAGACAAGATCTGTTATCTTTGATCTACTTCACGCAGTACATGAAGACAAGATCTGCTTTCTTT
CGATCTGCTTCGCCACCAGTATGGGAAGGCGAGATCTGTATATTC
Found at i:53122466 original size:46 final size:46
Alignment explanation
Indices: 53122414--53122503 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
53122404 AGCCTCTCCA
* * * *
53122414 TTTTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCCTGGTCTC
1 TTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCTC
*
53122460 TTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTC
1 TTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTC
53122504 CCACCTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.12, C:0.26, G:0.18, T:0.44
Consensus pattern (46 bp):
TTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCTC
Found at i:53122513 original size:46 final size:46
Alignment explanation
Indices: 53122417--53122513 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 46
53122407 CTCTCCATTT
* * * * * ***
53122417 TTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCCTGGTCTCTTT
1 TTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCCCACC
*
53122463 TTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTCCCACC
1 TTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCCCACC
53122509 TTTTT
1 TTTTT
53122514 TAAGCAGAGT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.12, C:0.28, G:0.16, T:0.43
Consensus pattern (46 bp):
TTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCCTGGTCCCACC
Found at i:53133068 original size:10 final size:10
Alignment explanation
Indices: 53133048--53133078 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
53133038 ATACTGTGGC
53133048 ATATGCCAACT
1 ATAT-CCAACT
53133059 ATATCCAACT
1 ATATCCAACT
53133069 ATATCCAACT
1 ATATCCAACT
53133079 TTACCCGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.39, C:0.29, G:0.03, T:0.29
Consensus pattern (10 bp):
ATATCCAACT
Found at i:53137212 original size:50 final size:50
Alignment explanation
Indices: 53137151--53137483 Score: 203
Period size: 47 Copynumber: 6.9 Consensus size: 50
53137141 TATAATGTCG
*
53137151 GGGAAGCAAGATTCGCCATTGTAGCTTTAATCTGTTCCACTGCACCGCCA
1 GGGAAGCAAGATTCGCCATTGTAGCTTTAATCTGTTCCACTGCACTGCCA
* * * * ** * * *
53137201 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCG
1 GGGAAGCAAGATTCGCCATTGTAGCTTTAATCTGTTCCACTGCACTGCCA
* * * * *
53137251 GGGAAGCAAGATTCACCAATGTGGC-TTAATCTGTTCCAC-GC-CCGCCT
1 GGGAAGCAAGATTCGCCATTGTAGCTTTAATCTGTTCCACTGCACTGCCA
* ** * ** * *
53137298 GGGAAGTAAGATTCGCTGTTGTAGC-TTAATCTTTTTAACTGCAATGTCA
1 GGGAAGCAAGATTCGCCATTGTAGCTTTAATCTGTTCCACTGCACTGCCA
* * *
53137347 -GGAA-CAAGATTCACCGA-TGTGGCTTTAATC-GTTCCACTGCACTGCCT
1 GGGAAGCAAGATTCGCC-ATTGTAGCTTTAATCTGTTCCACTGCACTGCCA
* * * * ** * *
53137394 GAGAAGTAAGATTC-AC-TGTGTAGCTTTAATCTTTTTAAC-GCAATGTC-
1 GGGAAGCAAGATTCGCCAT-TGTAGCTTTAATCTGTTCCACTGCACTGCCA
* * *
53137441 GGGAAGCAATATTCACCGTTG--GCTTTAATCTGTT--ACTGCACTG
1 GGGAAGCAAGATTCGCCATTGTAGCTTTAATCTGTTCCACTGCACTG
53137484 GCTGAGAGAG
Statistics
Matches: 211, Mismatches: 60, Indels: 29
0.70 0.20 0.10
Matches are distributed among these distances:
44 2 0.01
45 5 0.02
46 12 0.06
47 67 0.32
48 39 0.18
49 25 0.12
50 61 0.29
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (50 bp):
GGGAAGCAAGATTCGCCATTGTAGCTTTAATCTGTTCCACTGCACTGCCA
Found at i:53137356 original size:47 final size:48
Alignment explanation
Indices: 53137152--53137569 Score: 162
Period size: 47 Copynumber: 8.6 Consensus size: 48
53137142 ATAATGTCGG
* * ** ** *
53137152 GGAAGCAAGATTCGCCAT-TGTAGCTTTAATCTGTTCCACTGCACCGCCA
1 GGAAGCAAGATTC-AC-TGTGTAGCTTTAATCTTTTTAACTGCAATGTCA
* * * * *
53137201 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
1 -GGAAGCAAGATTCACTG-TGTAGCTTTAATCTTTTTAACTGCAATGTC-A
** * * ** ** * *
53137252 GGAAGCAAGATTCACCAATGTGGC-TTAATCTGTTCCAC-GC-CCGCCTG
1 GGAAGCAAGATTCA-CTGTGTAGCTTTAATCTTTTTAACTGCAATGTC-A
* *
53137299 GGAAGTAAGATTCGCTGTTGTAGC-TTAATCTTTTTAACTGCAATGTCA
1 GGAAGCAAGATTCACTG-TGTAGCTTTAATCTTTTTAACTGCAATGTCA
* * * ** * * *
53137347 GGAA-CAAGATTCACCGATGTGGCTTTAATC-GTTCCACTGCACTGCCT
1 GGAAGCAAGATTCACTG-TGTAGCTTTAATCTTTTTAACTGCAATGTCA
* *
53137394 GAGAAGTAAGATTCACTGTGTAGCTTTAATCTTTTTAAC-GCAATGTCG
1 G-GAAGCAAGATTCACTGTGTAGCTTTAATCTTTTTAACTGCAATGTCA
* * * * * * *
53137442 GGAAGCAATATTCACCGT-TGGCTTTAATC-TGTT-ACTGCACTGGCT
1 GGAAGCAAGATTCACTGTGTAGCTTTAATCTTTTTAACTGCAATGTCA
** * *
53137487 GAGAGAGTGAGATTC-GTCGTTGT-GACTTTAATCCTTTTAACTGCAATGTC-
1 G-GA-AGCAAGATTCACT-G-TGTAG-CTTTAATCTTTTTAACTGCAATGTCA
* *
53137537 GGAAAGCAAGATTCACCGTTGTGGCTTTAATCT
1 GG-AAGCAAGATTCACTG-TGTAGCTTTAATCT
53137570 GCTTCACTGA
Statistics
Matches: 270, Mismatches: 75, Indels: 47
0.69 0.19 0.12
Matches are distributed among these distances:
44 2 0.01
45 10 0.04
46 13 0.05
47 79 0.29
48 38 0.14
49 59 0.22
50 59 0.22
51 10 0.04
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (48 bp):
GGAAGCAAGATTCACTGTGTAGCTTTAATCTTTTTAACTGCAATGTCA
Found at i:53137394 original size:96 final size:99
Alignment explanation
Indices: 53137126--53137578 Score: 533
Period size: 96 Copynumber: 4.7 Consensus size: 99
53137116 TAACTCGTAA
** ** * *
53137126 TTTAATCTACTTAACTATAATGTCGGGGAAGCAAGATTCGCC-ATTGTAGCTTTAATCTGTTCCA
1 TTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACCGA-TGTGGCTTTAATCTGTTCCA
* * * *
53137190 CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGGC
64 CTGCACCGCCTGAGAAGTAAGATTCGCTGTTGTAGC
*
53137226 TTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCAATGTGGC-TTAATCTGTTCCAC
1 TTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCAC
*
53137290 -GC-CCGCCTGGGAAGTAAGATTCGCTGTTGTAGC
65 TGCACCGCCTGAGAAGTAAGATTCGCTGTTGTAGC
*
53137323 -TTAATCTTTTTAACTGCAATGTCAGGAA-CAAGATTCACCGATGTGGCTTTAATC-GTTCCACT
1 TTTAATCTTTTTAACTGCAATGTCGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACT
* *
53137385 GCACTGCCTGAGAAGTAAGATTCACTG-TGTAGC
66 GCACCGCCTGAGAAGTAAGATTCGCTGTTGTAGC
*
53137418 TTTAATCTTTTTAAC-GCAATGTCGGGAAGCAATATTCACCG-T-TGGCTTTAATCTGTT--ACT
1 TTTAATCTTTTTAACTGCAATGTCGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACT
* * *
53137478 GCACTGGCTGAGAGAGTGAGATTCG-TCGTTGT-GAC
66 GCACCGCCTGAGA-AGTAAGATTCGCT-GTTGTAG-C
* * *
53137513 TTTAATCCTTTTAACTGCAATGTCGGAAAGCAAGATTCACCGTTGTGGCTTTAATCTGCTT-CAC
1 TTTAATCTTTTTAACTGCAATGTCGGGAAGCAAGATTCACCGATGTGGCTTTAATCTG-TTCCAC
53137577 TG
65 TG
53137579 ATTGCCAGGG
Statistics
Matches: 315, Mismatches: 22, Indels: 32
0.85 0.06 0.09
Matches are distributed among these distances:
93 16 0.05
94 47 0.15
95 52 0.17
96 93 0.30
97 29 0.09
98 15 0.05
99 16 0.05
100 46 0.15
101 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (99 bp):
TTTAATCTTTTTAACTGCAATGTCGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACT
GCACCGCCTGAGAAGTAAGATTCGCTGTTGTAGC
Found at i:53137733 original size:35 final size:35
Alignment explanation
Indices: 53137694--53137777 Score: 93
Period size: 34 Copynumber: 2.4 Consensus size: 35
53137684 AATCTAAATC
53137694 TTGTTATTCACTGTAATCCGGGAGTAATT-AAATTT
1 TTGTTATTCACTGTAAT-CGGGAGTAATTGAAATTT
* **
53137729 TTGTTATTCCCT-TAATTTGGAGTAATTGAAATTT
1 TTGTTATTCACTGTAATCGGGAGTAATTGAAATTT
*
53137763 TTCTT-TTCCACTGTA
1 TTGTTATT-CACTGTA
53137778 TCTCAGGAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
33 11 0.27
34 17 0.41
35 13 0.32
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.48
Consensus pattern (35 bp):
TTGTTATTCACTGTAATCGGGAGTAATTGAAATTT
Found at i:53149281 original size:14 final size:15
Alignment explanation
Indices: 53149234--53149271 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
53149224 AGAAAACAAA
53149234 TTTTGAAAAAATTGT
1 TTTTGAAAAAATTGT
53149249 TTTTGAAAAAATTGT
1 TTTTGAAAAAATTGT
53149264 TTTTGAAA
1 TTTTGAAA
53149272 TATTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
TTTTGAAAAAATTGT
Found at i:53150119 original size:31 final size:31
Alignment explanation
Indices: 53150083--53150141 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
53150073 ATTAAGAACA
*
53150083 AAATCTTTTCGAAAGTGCTCAAATAAGGACT
1 AAATCTTTTCAAAAGTGCTCAAATAAGGACT
*
53150114 AAATCTTTTTAAAAGTGCTCAAATAAGG
1 AAATCTTTTCAAAAGTGCTCAAATAAGG
53150142 GCTTCTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (31 bp):
AAATCTTTTCAAAAGTGCTCAAATAAGGACT
Found at i:53153550 original size:22 final size:22
Alignment explanation
Indices: 53153525--53153571 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
53153515 TTAAAATAAT
*
53153525 TAATATATAAAATAACTTAAAA
1 TAATATACAAAATAACTTAAAA
*
53153547 TAATATACAAAATAACTTAACA
1 TAATATACAAAATAACTTAAAA
53153569 TAA
1 TAA
53153572 ATAATTTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATATACAAAATAACTTAAAA
Found at i:53153573 original size:26 final size:25
Alignment explanation
Indices: 53153518--53153583 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 25
53153508 AATAATTTTA
* *
53153518 AAATAATTAATATATAAAATAACTT
1 AAATAAATAATATACAAAATAACTT
53153543 --A-AAATAATATACAAAATAACTT
1 AAATAAATAATATACAAAATAACTT
*
53153565 AACATAAATAATTTACAAA
1 AA-ATAAATAATATACAAA
53153584 GCAAGTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 19 0.56
23 1 0.03
25 1 0.03
26 13 0.38
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (25 bp):
AAATAAATAATATACAAAATAACTT
Found at i:53159318 original size:17 final size:18
Alignment explanation
Indices: 53159286--53159319 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53159276 AATTAAAAAA
53159286 ATTTAAAATAAAATAATG
1 ATTTAAAATAAAATAATG
*
53159304 ATTTAAACT-AAATAAT
1 ATTTAAAATAAAATAAT
53159320 ATGTATACAC
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:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
ATTTAAAATAAAATAATG
Found at i:53177167 original size:18 final size:17
Alignment explanation
Indices: 53177130--53177181 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
53177120 CTAAAGGACG
* *
53177130 ACAAATAATCGATAAAT
1 ACAAATAAGCAATAAAT
53177147 ACAAATAAGCAATACAAT
1 ACAAATAAGCAATA-AAT
*
53177165 ACACATGAGAGCAATAA
1 ACAAAT-A-AGCAATAA
53177182 TCTTACATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 12 0.41
18 8 0.28
19 2 0.07
20 7 0.24
ACGTcount: A:0.58, C:0.15, G:0.10, T:0.17
Consensus pattern (17 bp):
ACAAATAAGCAATAAAT
Found at i:53180390 original size:103 final size:103
Alignment explanation
Indices: 53180133--53180489 Score: 581
Period size: 103 Copynumber: 3.4 Consensus size: 103
53180123 GGGTAGCTGT
* * * *
53180133 GTGCTGATTCCCCAATTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCTTTGAAATGTGAA
1 GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCGTATCTTTGAAATG-AAA
53180197 AGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
64 AGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
53180237 GTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAA
1 GTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAA
*
53180302 GGGGGTTGCTATGTGCTGATTCCCCCCAGGGGTTGCTAA
65 GGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
* * *
53180341 GTGCAGATTTCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAAG
1 GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAAG
53180406 GGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
66 GGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
* * *
53180444 GTGCTGATTCCCCGATTCAGTGCTGGTGCTAAGTGCGAGATCCACC
1 GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
53180490 AATAACGGTT
Statistics
Matches: 236, Mismatches: 15, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
103 127 0.54
104 67 0.28
105 41 0.17
106 1 0.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (103 bp):
GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAAG
GGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
Found at i:53183129 original size:20 final size:22
Alignment explanation
Indices: 53183082--53183122 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53183072 TAACGGTACA
*
53183082 ATAATATTAAATATATTAAAAT
1 ATAATAATAAATATATTAAAAT
*
53183104 AAAATAATAAATAT-TTAAA
1 ATAATAATAAATATATTAAA
53183123 TGTAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAATAATAAATATATTAAAAT
Found at i:53183746 original size:13 final size:13
Alignment explanation
Indices: 53183730--53183754 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53183720 TTCTCCTTCC
53183730 CTTTCCCCTACCT
1 CTTTCCCCTACCT
53183743 CTTTCCCCTACC
1 CTTTCCCCTACC
53183755 CCTTCCCCGT
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:0.08, C:0.56, G:0.00, T:0.36
Consensus pattern (13 bp):
CTTTCCCCTACCT
Found at i:53187118 original size:41 final size:41
Alignment explanation
Indices: 53187073--53187234 Score: 227
Period size: 41 Copynumber: 4.0 Consensus size: 41
53187063 AAATTATTCA
*
53187073 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCG
* * * * *
53187114 GACTATATGTCTAGCAGGATAAATGTCGGTGAATTGAATCG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCG
53187155 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCAG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATC-G
* * *
53187197 G-CTACAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAAT
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAAT
53187235 TAAACTATAA
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
41 106 0.98
42 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.23
Consensus pattern (41 bp):
GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCG
Found at i:53187247 original size:41 final size:41
Alignment explanation
Indices: 53187070--53187269 Score: 222
Period size: 41 Copynumber: 4.9 Consensus size: 41
53187060 GTGAAATTAT
* *
53187070 TCAGACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAA
1 TCAGACTATAAGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * * * * *
53187111 TCGGACTATATGTCTAGCAGGATAAATGTCGGTGAATTGAA
1 TCAGACTATAAGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
* *
53187152 TCGGACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
1 TCAGACTATAAGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * *
53187193 TCAGGCTACAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
1 TCAGACTATAAGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * * * *
53187234 TTAAACTATAAGCCTATCAGG-TGAAGTGCCAGTGAA
1 TCAGACTATAAGTCTAGCAGGCT-AAGTGCCGGTGAA
53187270 TCTGTTTAAA
Statistics
Matches: 137, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
40 1 0.01
41 136 0.99
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.23
Consensus pattern (41 bp):
TCAGACTATAAGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
Found at i:53189111 original size:32 final size:33
Alignment explanation
Indices: 53189075--53189161 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 33
53189065 AACTTTTCTG
* * *
53189075 GAAAATATTTT-CAGGAAATCTACCAAACAGCA
1 GAAAATATTTTACAGCAAATCAACCAAACACCA
*
53189107 GAAAATATTTTACA-CAAACTCAATCAAACACCA
1 GAAAATATTTTACAGCAAA-TCAACCAAACACCA
* *
53189140 GAAAATATTTTCCAGTAAATCA
1 GAAAATATTTTACAGCAAATCA
53189162 TTTTACAGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
32 14 0.30
33 29 0.63
34 3 0.07
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCAACCAAACACCA
Found at i:53189195 original size:34 final size:35
Alignment explanation
Indices: 53189141--53189207 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
53189131 CAAACACCAG
*
53189141 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
53189176 AAAACATTTTCTAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
53189208 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:53190693 original size:28 final size:25
Alignment explanation
Indices: 53190661--53190724 Score: 85
Period size: 24 Copynumber: 2.5 Consensus size: 25
53190651 GTAAAAAATA
53190661 ACCAAAATGATATAACTTTTTTTTATTT
1 ACCAAAAT-ATATAA--TTTTTTTATTT
*
53190689 ACCAAAATAT-TTATTTTTTTATTT
1 ACCAAAATATATAATTTTTTTATTT
53190713 ACCAAAATATAT
1 ACCAAAATATAT
53190725 CAAAAAAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
24 21 0.62
25 1 0.03
26 2 0.06
27 2 0.06
28 8 0.24
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (25 bp):
ACCAAAATATATAATTTTTTTATTT
Found at i:53190886 original size:19 final size:19
Alignment explanation
Indices: 53190864--53190969 Score: 90
Period size: 20 Copynumber: 5.4 Consensus size: 19
53190854 AAAGAAGGAA
53190864 AGAAAAAGGAAAGGAGAAG
1 AGAAAAAGGAAAGGAGAAG
* *
53190883 AGAAAAAAAGAAAGAAAGAAG
1 AG-AAAAAGGAAAG-GAGAAG
*
53190904 A-AGAAAAGGAAATGAGAAG
1 AGA-AAAAGGAAAGGAGAAG
* *
53190923 A-AAAAAAGAAAGAAAGAAGG
1 AGAAAAAGGAAAG-GAGAA-G
*
53190943 AAAGAAAAGGAAAGGAGAAG
1 AGA-AAAAGGAAAGGAGAAG
53190963 AGAAAAA
1 AGAAAAA
53190970 AAAAGAAGAA
Statistics
Matches: 69, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
18 8 0.12
19 18 0.26
20 23 0.33
21 11 0.16
22 9 0.13
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (19 bp):
AGAAAAAGGAAAGGAGAAG
Found at i:53190911 original size:40 final size:42
Alignment explanation
Indices: 53190844--53190971 Score: 192
Period size: 40 Copynumber: 3.1 Consensus size: 42
53190834 AAGGAGAGGG
53190844 AAAGAAAGAAAAAGAAGGAAAGAAAAAGGAAAGGAGAAGAGAAAA
1 AAAGAAAG--AAAGAAGGAAAG-AAAAGGAAAGGAGAAGAGAAAA
*
53190889 AAAGAAAGAAAGAA-G-AAGAAAAGGAAATGAG-A-AGAAAA
1 AAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAA
53190927 AAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAA
1 AAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAA
53190969 AAA
1 AAA
53190972 AAGAAGAAGA
Statistics
Matches: 77, Mismatches: 2, Indels: 11
0.86 0.02 0.12
Matches are distributed among these distances:
38 20 0.26
39 2 0.03
40 27 0.35
41 4 0.05
42 10 0.13
43 6 0.08
45 8 0.10
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (42 bp):
AAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAA
Found at i:53190975 original size:40 final size:40
Alignment explanation
Indices: 53190844--53191008 Score: 187
Period size: 40 Copynumber: 4.1 Consensus size: 40
53190834 AAGGAGAGGG
53190844 AAAGAAAGAAAAAGAAGGAAAGAAAAAGGAAAGGAGAAGAGAAAA
1 AAAGAAAG--AAAGAA-GAAAG-AAAAGGAAAGGAGAAGAG-AAA
*
53190889 AAAGAAAGAAAGAAG-AAGAAAAGGAAATGAGAAGA-AAA
1 AAAGAAAGAAAGAAGAAAGAAAAGGAAAGGAGAAGAGAAA
53190927 AAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
1 AAAGAAAGAAAGAA-GAAAGAAAAGGAAAGGAGAAGAGAAA
** * *
53190968 AAA-AAAG-AAGAAGAAGAGGGAAGG-AAGGAAAAAAGAAA
1 AAAGAAAGAAAGAAGAA-AGAAAAGGAAAGGAGAAGAGAAA
53191006 AAA
1 AAA
53191009 AAGTAATTTT
Statistics
Matches: 110, Mismatches: 6, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
38 35 0.32
39 12 0.11
40 39 0.35
41 9 0.08
42 1 0.01
43 6 0.05
45 8 0.07
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (40 bp):
AAAGAAAGAAAGAAGAAAGAAAAGGAAAGGAGAAGAGAAA
Found at i:53190990 original size:28 final size:28
Alignment explanation
Indices: 53190862--53191006 Score: 78
Period size: 28 Copynumber: 5.3 Consensus size: 28
53190852 AAAAAGAAGG
53190862 AAAGAAAAAGGAAAGGAGAA-G-AGAAAA
1 AAAG-AAAAGGAAAGGAGAAGGAAGAAAA
* *
53190889 AAAG-AAA-GAAAGAAGAAGAAAAGGAAATGA
1 AAAGAAAAGGAAAGGAGAAG-GAA-GAAA--A
* * **
53190919 GAAGAAAA--AAA-GA-AAGAAAGAAGG
1 AAAGAAAAGGAAAGGAGAAGGAAGAAAA
53190943 AAAGAAAAGGAAAGGAGAAGAGAA-AAAA
1 AAAGAAAAGGAAAGGAGAAG-GAAGAAAA
*
53190971 AAAGAAGAA-GAAGAGG-GAAGGAAGGAAA
1 AAAGAA-AAGGAA-AGGAGAAGGAAGAAAA
53190999 AAAGAAAA
1 AAAGAAAA
53191007 AAAAGTAATT
Statistics
Matches: 92, Mismatches: 11, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
24 16 0.17
25 3 0.03
26 6 0.07
27 15 0.16
28 34 0.37
29 8 0.09
30 7 0.08
31 3 0.03
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.01
Consensus pattern (28 bp):
AAAGAAAAGGAAAGGAGAAGGAAGAAAA
Found at i:53191004 original size:80 final size:81
Alignment explanation
Indices: 53190844--53191009 Score: 225
Period size: 80 Copynumber: 2.0 Consensus size: 81
53190834 AAGGAGAGGG
*
53190844 AAAGAAAGAAAAAGAAGGAAAGAAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAA
1 AAAGAAAG-AAAAGAAGGAAAGAAAAAGGAAAGGAGAAGAGAAAAAAAAAAAGAAAGAAGAAGAA
53190909 AAGGAAATGAGAAGAAAA
65 AAGGAAA-GAGAAGAAAA
*
53190927 AAAGAAAG-AAAGAAGGAAAG-AAAAGGAAAGGAGAAGAGAAAAAAAAAGAAG-AAGAAGAGGGA
1 AAAGAAAGAAAAGAAGGAAAGAAAAAGGAAAGGAGAAGAGAAAAAAAAA-AAGAAAGAAGA-AGA
53190989 AGGAAGGAAA-A-AAGAAAA
64 A--AAGGAAAGAGAAGAAAA
53191007 AAA
1 AAA
53191010 AGTAATTTTT
Statistics
Matches: 77, Mismatches: 2, Indels: 11
0.86 0.02 0.12
Matches are distributed among these distances:
80 43 0.56
81 19 0.25
83 15 0.19
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (81 bp):
AAAGAAAGAAAAGAAGGAAAGAAAAAGGAAAGGAGAAGAGAAAAAAAAAAAGAAAGAAGAAGAAA
AGGAAAGAGAAGAAAA
Found at i:53191007 original size:34 final size:36
Alignment explanation
Indices: 53190852--53191005 Score: 140
Period size: 35 Copynumber: 4.2 Consensus size: 36
53190842 GGAAAGAAAG
* * * *
53190852 AAAAAGAAGGAAAGAAAAAGGAAAGGAGAA-G-AGAA
1 AAAAAGAAAGAAAGAAGAAGAAAAGGA-AAGGAAGGA
*
53190887 AAAAAGAAAGAAAGAAGAAGAAAAGGAAATGAGAAGAA
1 AAAAAGAAAGAAAGAAGAAGAAAAGGAAA-G-GAAGGA
53190925 AAAAAGAAAGAAAGAAGGAAAGAAAAGGAAAGG-A-GA
1 AAAAAGAAAGAAAGAA-G-AAGAAAAGGAAAGGAAGGA
* *
53190961 AGAGAAA-AAA-AAAGAAGAAGAAGAGGGAAGGAAGGA
1 A-A-AAAGAAAGAAAGAAGAAGAAAAGGAAAGGAAGGA
53190997 AAAAAGAAA
1 AAAAAGAAA
53191006 AAAAAGTAAT
Statistics
Matches: 102, Mismatches: 6, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
34 17 0.17
35 30 0.29
36 11 0.11
37 6 0.06
38 24 0.24
39 2 0.02
40 12 0.12
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (36 bp):
AAAAAGAAAGAAAGAAGAAGAAAAGGAAAGGAAGGA
Found at i:53194112 original size:18 final size:17
Alignment explanation
Indices: 53194089--53194131 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
53194079 ATCCCAATGA
53194089 TCGCCACTACATTCTTCT
1 TCGCCAC-ACATTCTTCT
*
53194107 TCGCCAGCACCTTCTTCT
1 TCGCCA-CACATTCTTCT
*
53194125 TCACCAC
1 TCGCCAC
53194132 CAACCATGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.16, C:0.44, G:0.07, T:0.33
Consensus pattern (17 bp):
TCGCCACACATTCTTCT
Found at i:53194988 original size:3 final size:3
Alignment explanation
Indices: 53194980--53195017 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
53194970 TCTTAGTACT
53194980 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
53195018 TAATAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:53195101 original size:19 final size:21
Alignment explanation
Indices: 53195077--53195115 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
53195067 ACTAAAACAA
*
53195077 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
53195096 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
53195116 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:53195286 original size:27 final size:27
Alignment explanation
Indices: 53195256--53195313 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
53195246 CCAATCAGTA
* *
53195256 TGGCACCATTGGTGCCGCCAATGGTTT
1 TGGCACCATTGGTGCCACCAATAGTTT
*
53195283 TGGCACCTTTGGTGCCACCAATAGTTT
1 TGGCACCATTGGTGCCACCAATAGTTT
53195310 TGGC
1 TGGC
53195314 GTGACCAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.31
Consensus pattern (27 bp):
TGGCACCATTGGTGCCACCAATAGTTT
Found at i:53195402 original size:21 final size:20
Alignment explanation
Indices: 53195362--53195403 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
53195352 GTTTTTTTAT
53195362 ATATTTTGGTAAATAAAAAA
1 ATATTTTGGTAAATAAAAAA
53195382 ATATTTTGGTAAATAAAAAA
1 ATATTTTGGTAAATAAAAAA
53195402 AT
1 AT
53195404 TATAACATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.36
Consensus pattern (20 bp):
ATATTTTGGTAAATAAAAAA
Done.