Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 95 of 313
Found at i:31655529 original size:22 final size:22
Alignment explanation
Indices: 31655504--31655546 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
31655494 TATCCAAACA
31655504 ATAATAACAAAATAGTAGCAAT
1 ATAATAACAAAATAGTAGCAAT
* *
31655526 ATAATAATAAAATGGTAGCAA
1 ATAATAACAAAATAGTAGCAA
31655547 AATAGGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.23
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAT
Found at i:31659361 original size:33 final size:33
Alignment explanation
Indices: 31659312--31659556 Score: 131
Period size: 33 Copynumber: 7.5 Consensus size: 33
31659302 ATGGACTTTT
* * *
31659312 CCTTTTCTAGTTGTACACTCGAGGTGTACATTC
1 CCTTTTCAAGTTGTACACTCGAAGTGTACATAC
* *
31659345 CCTTTTCAAGTGGTACACACGAAGTGTACATAC
1 CCTTTTCAAGTTGTACACTCGAAGTGTACATAC
* * * * *
31659378 CCTTTTCAATTTGTACACTCAAAGTGCATATAA
1 CCTTTTCAAGTTGTACACTCGAAGTGTACATAC
* * **
31659411 CATTTTCAAG-TGTACACAT--ATAGTGTACCTTT
1 CCTTTTCAAGTTGTACAC-TCGA-AGTGTACATAC
* * * * * * **
31659443 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
1 CCTTTTCAAGTTGTACACTCGAAGTGTACATAC
* * * * * * **
31659476 CCTTTTCATA-TGGTATACACAAAGTATACCTTT
1 CCTTTTCA-AGTTGTACACTCGAAGTGTACATAC
* * *
31659509 CCTTTTCAAG-TGTACACACAAAGTGTACATAA
1 CCTTTTCAAGTTGTACACTCGAAGTGTACATAC
31659541 CCTTTTCAAGTTGTAC
1 CCTTTTCAAGTTGTAC
31659557 CATTTGGGTA
Statistics
Matches: 174, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
31 1 0.01
32 49 0.28
33 122 0.70
34 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (33 bp):
CCTTTTCAAGTTGTACACTCGAAGTGTACATAC
Found at i:31659449 original size:32 final size:32
Alignment explanation
Indices: 31659413--31659556 Score: 164
Period size: 33 Copynumber: 4.4 Consensus size: 32
31659403 GCATATAACA
* * *
31659413 TTTTCAAGTGTACACATATAGTGTACCTTTCC
1 TTTTCAAGTGTACACACAAAGTATACCTTTCC
*
31659445 TTTTCAAGTGGTATACACAAAGTATACCTTTCC
1 TTTTCAAGT-GTACACACAAAGTATACCTTTCC
*
31659478 TTTTCATA-TGGTATACACAAAGTATACCTTTCC
1 TTTTCA-AGT-GTACACACAAAGTATACCTTTCC
* * **
31659511 TTTTCAAGTGTACACACAAAGTGTACATAACC
1 TTTTCAAGTGTACACACAAAGTATACCTTTCC
31659543 TTTTCAAGTTGTAC
1 TTTTCAAG-TGTAC
31659557 CATTTGGGTA
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
32 36 0.36
33 62 0.63
34 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (32 bp):
TTTTCAAGTGTACACACAAAGTATACCTTTCC
Found at i:31659466 original size:65 final size:61
Alignment explanation
Indices: 31659345--31659556 Score: 174
Period size: 65 Copynumber: 3.2 Consensus size: 61
31659335 GTGTACATTC
* ** * *
31659345 CCTTTTCAAGTGGTACACACGAAGTGTACATACCCTTTTCAATTTGTACACTCAAAGTGCATATA
1 CCTTTTCAAGT-GTACACA--AAGTGTACCTTTCCTTTTCAA-GTGTACACACAAAGTG-ATATA
31659410 A
61 A
* * *
31659411 CATTTTCAAGTGTACACATATAGTGTACCTTTCCTTTTCAAGTGGTATACACAAAGT-ATACCTT
1 CCTTTTCAAGTGTACACA-A-AGTGTACCTTTCCTTTTCAAGT-GTACACACAAAGTGATA--TA
*
31659475 T
61 A
* * *
31659476 CCTTTTCATATGGTATACACAAAGTATACCTTTCCTTTTCAAGTGTACACACAAAGTGTACATAA
1 CCTTTTCA-A--GTGTACACAAAGTGTACCTTTCCTTTTCAAGTGTACACACAAAGTG-ATATAA
31659541 CCTTTTCAAGTTGTAC
1 CCTTTTCAAG-TGTAC
31659557 CATTTGGGTA
Statistics
Matches: 118, Mismatches: 18, Indels: 23
0.74 0.11 0.14
Matches are distributed among these distances:
62 1 0.01
63 7 0.06
64 3 0.03
65 64 0.54
66 32 0.27
67 3 0.03
68 8 0.07
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (61 bp):
CCTTTTCAAGTGTACACAAAGTGTACCTTTCCTTTTCAAGTGTACACACAAAGTGATATAA
Found at i:31660286 original size:21 final size:22
Alignment explanation
Indices: 31660240--31660287 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
31660230 TGTAAAAGTG
* *
31660240 ATTTATCTATCAACAATCTTTT
1 ATTTATCTATCAACAAACTTTA
31660262 ATTT-TCTATCAA-AAACTTTCA
1 ATTTATCTATCAACAAACTTT-A
31660283 ATTTA
1 ATTTA
31660288 CAGCATATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.27
21 12 0.55
22 4 0.18
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTATCTATCAACAAACTTTA
Found at i:31667048 original size:33 final size:33
Alignment explanation
Indices: 31666965--31667075 Score: 123
Period size: 33 Copynumber: 3.3 Consensus size: 33
31666955 ATGGACTTTT
* * *
31666965 CCTTTTCTAGTTGTACACTCGAGGTGCACATTC
1 CCTTTTCAAGTTGTACACTCGAAGTGCACATAC
* * *
31666998 CCTTTTTCAAGTGGTACACACGAAGTGTACATAC
1 CC-TTTTCAAGTTGTACACTCGAAGTGCACATAC
* * * *
31667032 CCTTTTCAATTTGTACACTCAAAGTGCATATAA
1 CCTTTTCAAGTTGTACACTCGAAGTGCACATAC
31667065 CCTTTTCAAGT
1 CCTTTTCAAGT
31667076 ATAGTGTACC
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
33 36 0.57
34 27 0.43
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.35
Consensus pattern (33 bp):
CCTTTTCAAGTTGTACACTCGAAGTGCACATAC
Found at i:31667119 original size:33 final size:33
Alignment explanation
Indices: 31667082--31667197 Score: 155
Period size: 33 Copynumber: 3.5 Consensus size: 33
31667072 AAGTATAGTG
31667082 TACCTTTCCTTTTCAAGTGGTATACACAAAGTA
1 TACCTTTCCTTTTCAAGTGGTATACACAAAGTA
*
31667115 TACCTTTCATTTTCATA-TGGTATACACAAAGTA
1 TACCTTTCCTTTTCA-AGTGGTATACACAAAGTA
* *
31667148 TACCTTTCCTTTTCAAGT-GTACACACAAAGTG
1 TACCTTTCCTTTTCAAGTGGTATACACAAAGTA
* **
31667180 TACATAACCTTTTCAAGT
1 TACCTTTCCTTTTCAAGT
31667198 TGTACCATTT
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
32 28 0.38
33 45 0.61
34 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (33 bp):
TACCTTTCCTTTTCAAGTGGTATACACAAAGTA
Found at i:31667928 original size:20 final size:22
Alignment explanation
Indices: 31667886--31667933 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
31667876 TGTAAAAGTG
*
31667886 ATTTATCTATCAATAATCTTTC
1 ATTTATCTATCAATAAACTTTC
31667908 ATTT-TCTATCAA-AAACTTTC
1 ATTTATCTATCAATAAACTTTC
31667928 AATTTA
1 -ATTTA
31667934 CAGCATATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 7 0.30
21 12 0.52
22 4 0.17
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTATCTATCAATAAACTTTC
Found at i:31671745 original size:18 final size:17
Alignment explanation
Indices: 31671712--31671750 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
31671702 TTTATGTGCA
* *
31671712 TTTATTTTTGTTTTTAT
1 TTTATTTTTATGTTTAT
31671729 GTTTATTTTTATGTTTAT
1 -TTTATTTTTATGTTTAT
31671747 TTTA
1 TTTA
31671751 ATTTCTATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (17 bp):
TTTATTTTTATGTTTAT
Found at i:31671750 original size:11 final size:12
Alignment explanation
Indices: 31671712--31671749 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
31671702 TTTATGTGCA
* *
31671712 TTTATTTTTGTT
1 TTTATGTTTATT
31671724 TTTATGTTTATT
1 TTTATGTTTATT
31671736 TTTATGTTTATT
1 TTTATGTTTATT
31671748 TT
1 TT
31671750 AATTTCTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (12 bp):
TTTATGTTTATT
Found at i:31674711 original size:55 final size:54
Alignment explanation
Indices: 31674521--31674775 Score: 283
Period size: 55 Copynumber: 4.8 Consensus size: 54
31674511 ACACGGGTAC
* * * * *
31674521 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCCTT---TT-GA-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAA
* *
31674570 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAA
* * *
31674623 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTATAG-AA
* * *
31674678 CTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGA-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAA
* *
31674731 CCTTACCAATTGCCATGCCTTGGCATGGCCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
31674776 AAACCCTAAT
Statistics
Matches: 176, Mismatches: 19, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
49 40 0.23
52 4 0.02
53 46 0.26
54 8 0.05
55 76 0.43
56 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.35
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAA
Found at i:31674712 original size:108 final size:110
Alignment explanation
Indices: 31674568--31674768 Score: 336
Period size: 108 Copynumber: 1.8 Consensus size: 110
31674558 ATCCTTTTGA
*
31674568 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTA-GAAACCTCACCAA
*
31674631 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGCCTTACATGGGACCTTTGCCTTATAGT
* *
31674676 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAACCTCACCAAT
31674741 TGCCATGCCTTGGCATGGCCTTACATGG
66 TGCCATGCCTTGGCATGGCCTTACATGG
31674769 TATCCTTAAA
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
107 1 0.01
108 51 0.59
109 7 0.08
110 27 0.31
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.33
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGCCTTACATGGGACCTTTGCCTTATAGT
Found at i:31681549 original size:58 final size:58
Alignment explanation
Indices: 31681463--31681615 Score: 191
Period size: 58 Copynumber: 2.7 Consensus size: 58
31681453 CACAAATTAC
* * * *
31681463 ATCCCT-CTAAACACACTAGAGAGCACTAAAATGCTAAACTTGAAAATAATAGATCAA
1 ATCCCTCCAAAACACACCAAAGAGCACTAAAATGCTAAACTTGAAAACAATAGATCAA
* * * * *
31681520 ATCCCTCCAAAATACACCGAAGAGCACTAAAGTGCTAAACTTGAAGACAATAGATCAC
1 ATCCCTCCAAAACACACCAAAGAGCACTAAAATGCTAAACTTGAAAACAATAGATCAA
* * *
31681578 ATCCCTCTAAAACACACCAAAAAGCACTAAGATGCTAA
1 ATCCCTCCAAAACACACCAAAGAGCACTAAAATGCTAA
31681616 GCCCAAAGAC
Statistics
Matches: 80, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
57 6 0.08
58 74 0.93
ACGTcount: A:0.46, C:0.25, G:0.11, T:0.18
Consensus pattern (58 bp):
ATCCCTCCAAAACACACCAAAGAGCACTAAAATGCTAAACTTGAAAACAATAGATCAA
Found at i:31681625 original size:58 final size:57
Alignment explanation
Indices: 31681461--31681638 Score: 171
Period size: 58 Copynumber: 3.1 Consensus size: 57
31681451 GCCACAAATT
* * * *
31681461 ACATCCCTCT-AAACACACTAGAGAGCACTAAAATGCTAAACTTGAAA-ATAATAGATC
1 ACATCCCTCTAAAACACACCAAAGAGCACT-AAATGCTAAAC-TCAAAGACAATAGATC
* * * * **
31681518 AAATCCCTCCAAAATACACCGAAGAGCACTAAAGTGCTAAACTTGAAGACAATAGATC
1 ACATCCCTCTAAAACACACCAAAGAGCACTAAA-TGCTAAACTCAAAGACAATAGATC
* * * * *
31681576 ACATCCCTCTAAAACACACCAAAAAGCACTAAGATGCTAAGCCCAAAGACAACAAATC
1 ACATCCCTCTAAAACACACCAAAGAGCACTAA-ATGCTAAACTCAAAGACAATAGATC
31681634 ACATC
1 ACATC
31681639 TCACATCATT
Statistics
Matches: 97, Mismatches: 20, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
57 14 0.14
58 82 0.85
59 1 0.01
ACGTcount: A:0.46, C:0.26, G:0.11, T:0.17
Consensus pattern (57 bp):
ACATCCCTCTAAAACACACCAAAGAGCACTAAATGCTAAACTCAAAGACAATAGATC
Found at i:31682488 original size:40 final size:40
Alignment explanation
Indices: 31682444--31682521 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
31682434 AACAACCATG
* * *
31682444 TGGGGATAAAATCGACCCATCCATCCCTGCACACCATATA
1 TGGGGATAAAATCAACCCATCCAACCCTACACACCATATA
31682484 TGGGGATAAAATCAACCCATCCAACCCTACACACCATA
1 TGGGGATAAAATCAACCCATCCAACCCTACACACCATA
31682522 AAGTACCGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.36, C:0.33, G:0.13, T:0.18
Consensus pattern (40 bp):
TGGGGATAAAATCAACCCATCCAACCCTACACACCATATA
Found at i:31692948 original size:80 final size:81
Alignment explanation
Indices: 31692859--31693054 Score: 238
Period size: 80 Copynumber: 2.4 Consensus size: 81
31692849 TGTGCGTATT
31692859 GAGATAGCTTCGGCTATATAAAGCACTTAGTGTGCAAATCGGAATAGCTTCGACTATATAAAGCA
1 GAGATAGCTTCGGCTATATAAAGCACTTAGTGTGCAAATCGGAATAGCTTCGACTATATAAAGCA
*
31692924 CTTACTGTGTGA-ATCA
66 CTTACTGTGCGAGA-CA
* * * * * **
31692940 GA-ATAGCTTCAGTTATATATAA-AACTTAGTGTGCGAATCGGAATAGCTTCGGCTATATATGGC
1 GAGATAGCTTCGGCTATATA-AAGCACTTAGTGTGCAAATCGGAATAGCTTCGACTATATAAAGC
* *
31693003 ACTTAGTGTGCGAGACT
65 ACTTACTGTGCGAGACA
*
31693020 GAGATAGCTTCGGCTATGA-AAGGCACTTAGTGTGC
1 GAGATAGCTTCGGCTAT-ATAAAGCACTTAGTGTGC
31693055 GAGATTATAA
Statistics
Matches: 96, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
80 66 0.69
81 29 0.30
82 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (81 bp):
GAGATAGCTTCGGCTATATAAAGCACTTAGTGTGCAAATCGGAATAGCTTCGACTATATAAAGCA
CTTACTGTGCGAGACA
Found at i:31693045 original size:41 final size:41
Alignment explanation
Indices: 31692862--31693059 Score: 210
Period size: 40 Copynumber: 4.9 Consensus size: 41
31692852 GCGTATTGAG
* *
31692862 ATAGCTTCGGCTATATAAAGCACTTAGTGTGC-AAATCGGA
1 ATAGCTTCGGCTATATAAGGCACTTAGTGTGCGAGATCGGA
* * * * *
31692902 ATAGCTTCGACTATATAAAGCACTTACTGTGTGA-ATCAGA
1 ATAGCTTCGGCTATATAAGGCACTTAGTGTGCGAGATCGGA
* * **
31692942 ATAGCTTCAGTTATATATA-AAACTTAGTGTGCGA-ATCGGA
1 ATAGCTTCGGCTATATA-AGGCACTTAGTGTGCGAGATCGGA
* *
31692982 ATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGA-CTGA
1 ATAGCTTCGGCTATATAAGGCACTTAGTGTGCGAGATCGGA
31693022 GATAGCTTCGGCTATGA-AAGGCACTTAGTGTGCGAGAT
1 -ATAGCTTCGGCTAT-ATAAGGCACTTAGTGTGCGAGAT
31693060 TATAATAGCT
Statistics
Matches: 132, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
40 95 0.72
41 36 0.27
42 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (41 bp):
ATAGCTTCGGCTATATAAGGCACTTAGTGTGCGAGATCGGA
Found at i:31693078 original size:41 final size:41
Alignment explanation
Indices: 31693000--31693101 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 41
31692990 GGCTATATAT
* **
31693000 GGCACTTAGTGTGCGAGACTGAGATAGCTTCGGCTATG-AAA
1 GGCACTTAGTGTGCGAGA-TGAAATAGCTTCAACTATGCAAA
* **
31693041 GGCACTTAGTGTGCGAGATTATAATAGCTTCAACTATGCTTTA
1 GGCACTTAGTGTGCGAGATGA-AATAGCTTCAACTATGC-AAA
31693084 -GCACTTAGTGTGCGAGAT
1 GGCACTTAGTGTGCGAGAT
31693102 ATCGAGTATT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
40 2 0.04
41 31 0.60
42 18 0.35
43 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.29
Consensus pattern (41 bp):
GGCACTTAGTGTGCGAGATGAAATAGCTTCAACTATGCAAA
Found at i:31693633 original size:26 final size:25
Alignment explanation
Indices: 31693611--31693663 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
31693601 TATAATGCTT
31693611 TATGTGTTGGCTTCTTTGGAATGATTA
1 TATG-GTT-GCTTCTTTGGAATGATTA
* *
31693638 TATGGTTGCTTTTTTGG-ATAATTA
1 TATGGTTGCTTCTTTGGAATGATTA
31693662 TA
1 TA
31693664 AGTTATGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 9 0.38
26 3 0.12
27 4 0.17
ACGTcount: A:0.21, C:0.06, G:0.23, T:0.51
Consensus pattern (25 bp):
TATGGTTGCTTCTTTGGAATGATTA
Found at i:31696420 original size:39 final size:39
Alignment explanation
Indices: 31696198--31696402 Score: 374
Period size: 39 Copynumber: 5.3 Consensus size: 39
31696188 ATTCAGTGAT
31696198 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
1 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
31696237 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
1 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
31696276 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
1 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
31696315 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
1 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
* *
31696354 TTATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAA
1 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
* *
31696393 ATATGTCCGG
1 TTATATCCGG
31696403 GCTAAAGTCC
Statistics
Matches: 162, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 162 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (39 bp):
TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
Found at i:31696429 original size:117 final size:117
Alignment explanation
Indices: 31696198--31696440 Score: 366
Period size: 117 Copynumber: 2.1 Consensus size: 117
31696188 ATTCAGTGAT
*
31696198 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGGTCCGCAGG
1 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGTCCGCAGG
* * ** *
31696263 CTATGTGCTGGAATTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
66 CTACGTGCTGGAAATATATCCGGACTTAAAGTCCGCAGGCTATGAGCTGGAA
31696315 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGTCCGCAGG
1 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGTCCGCAGG
* * *
31696380 CTACGTGCTGGAAATATGTCCGGGC-TAAAGTCCCGCAGGCT-TCGAGCTGGTA
66 CTACGTGCTGGAAATATATCCGGACTTAAAGT-CCGCAGGCTAT-GAGCTGGAA
31696432 TTATA-CCGG
1 TTATATCCGG
31696441 GTTTAAATTC
Statistics
Matches: 115, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
116 9 0.08
117 106 0.92
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (117 bp):
TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGTCCGCAGG
CTACGTGCTGGAAATATATCCGGACTTAAAGTCCGCAGGCTATGAGCTGGAA
Found at i:31696455 original size:78 final size:78
Alignment explanation
Indices: 31696198--31696467 Score: 305
Period size: 78 Copynumber: 3.5 Consensus size: 78
31696188 ATTCAGTGAT
** * **
31696198 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGGTCCGCAGG
1 TTATATCCGGACTTAAAGTCCGCAGGCTATGTGCTGGAAATATATCCGGACTTAAAGTCCGCAGG
*
31696263 CTATGTGCTGGAA
66 CTATGAGCTGGAA
** * **
31696276 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGGTCCGCAGG
1 TTATATCCGGACTTAAAGTCCGCAGGCTATGTGCTGGAAATATATCCGGACTTAAAGTCCGCAGG
*
31696341 CTATGTGCTGGAA
66 CTATGAGCTGGAA
* * * *
31696354 TTATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATGTCCGGGC-TAAAGTCCCGCAG
1 TTATATCCGGACTTAAAGTCCGCAGGCTATGTGCTGGAAATATATCCGGACTTAAAGT-CCGCAG
*
31696418 GCT-TCGAGCTGGTA
65 GCTAT-GAGCTGGAA
** *
31696432 TTATA-CCGGGTTTAAATTCCCGCAGGCT-TGTGCTGG
1 TTATATCCGGACTTAAAGT-CCGCAGGCTATGTGCTGG
31696468 TAATTGGTTT
Statistics
Matches: 175, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
77 21 0.12
78 154 0.88
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (78 bp):
TTATATCCGGACTTAAAGTCCGCAGGCTATGTGCTGGAAATATATCCGGACTTAAAGTCCGCAGG
CTATGAGCTGGAA
Found at i:31696455 original size:117 final size:117
Alignment explanation
Indices: 31696198--31696472 Score: 342
Period size: 117 Copynumber: 2.4 Consensus size: 117
31696188 ATTCAGTGAT
** *
31696198 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGGTCCGCAGG
1 TTATATCCGGACTTAAAGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGTCCGCAGG
* * ** *
31696263 CTATGTGCTGGAATTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAA
66 CTACGTGCTGGAAATATATCCGGACTTAAAGTCCGCAGGCTATGAGCTGGAA
**
31696315 TTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGTCCGCAGG
1 TTATATCCGGACTTAAAGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGTCCGCAGG
* * *
31696380 CTACGTGCTGGAAATATGTCCGGGC-TAAAGTCCCGCAGGCT-TCGAGCTGGTA
66 CTACGTGCTGGAAATATATCCGGACTTAAAGT-CCGCAGGCTAT-GAGCTGGAA
** *
31696432 TTATA-CCGGGTTTAAATTCCCGCAGGCT-TGTGCTGGTAATT
1 TTATATCCGGACTTAAAGT-CCGCAGGCTATGTGCTGG-AATT
31696473 GGTTTCAAGT
Statistics
Matches: 140, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
116 21 0.15
117 119 0.85
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (117 bp):
TTATATCCGGACTTAAAGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGTCCGCAGG
CTACGTGCTGGAAATATATCCGGACTTAAAGTCCGCAGGCTATGAGCTGGAA
Found at i:31696467 original size:38 final size:38
Alignment explanation
Indices: 31696217--31696472 Score: 200
Period size: 39 Copynumber: 6.6 Consensus size: 38
31696207 GACTTAGGGT
* **
31696217 CCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGGT-
1 CCGCAGGCTATGTGCTGGAATTATA-CCGG-GTTAAAGTC
* **
31696256 CCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGGT-
1 CCGCAGGCTATGTGCTGGAATTATA-CCGG-GTTAAAGTC
* **
31696295 CCGCAGGCTATGTGCTGGAATTATATCCGGACTTAGGGT-
1 CCGCAGGCTATGTGCTGGAATTATA-CCGG-GTTAAAGTC
* *
31696334 CCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGT-
1 CCGCAGGCTATGTGCTGGAATTATA-CCGG-GTTAAAGTC
* * * *
31696373 CCGCAGGCTACGTGCTGGAAATATGTCCGGGCTAAAGTC
1 CCGCAGGCTATGTGCTGGAATTAT-ACCGGGTTAAAGTC
* * *
31696412 CCGCAGGCT-TCGAGCTGGTATTATACCGGGTTTAAATTC
1 CCGCAGGCTAT-GTGCTGGAATTATACCGGG-TTAAAGTC
31696451 CCGCAGGCT-TGTGCTGGTAATT
1 CCGCAGGCTATGTGCTGG-AATT
31696473 GGTTTCAAGT
Statistics
Matches: 196, Mismatches: 16, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
38 16 0.08
39 180 0.92
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (38 bp):
CCGCAGGCTATGTGCTGGAATTATACCGGGTTAAAGTC
Found at i:31700622 original size:23 final size:24
Alignment explanation
Indices: 31700578--31700624 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
31700568 AGACTGTACC
* * *
31700578 TAGATCGATTTTTTGTTGTATTCA
1 TAGATCGATATTTTGATATATTCA
31700602 TAGAT-GATATTTTGATATATTCA
1 TAGATCGATATTTTGATATATTCA
31700625 CGAGATGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (24 bp):
TAGATCGATATTTTGATATATTCA
Found at i:31706377 original size:40 final size:40
Alignment explanation
Indices: 31706333--31706463 Score: 169
Period size: 40 Copynumber: 3.2 Consensus size: 40
31706323 ATCGATATAA
**
31706333 CTTCGGCTATATAAAGCACTTAGTGTCTGAATCGGAATAG
1 CTTCGGCTATATATGGCACTTAGTGTCTGAATCGGAATAG
*
31706373 CTTCGGCTATATATGGAACTTAGTG-CGTGAATCGGAATAG
1 CTTCGGCTATATATGGCACTTAGTGTC-TGAATCGGAATAG
*
31706413 CTTCGGCTATATATGGCACTTAGTGTGC-GAGA-CTGAGATAG
1 CTTCGGCTATATATGGCACTTAGTGT-CTGA-ATCGGA-ATAG
31706454 CTTCGGCTAT
1 CTTCGGCTAT
31706464 GAAAGGCATT
Statistics
Matches: 81, Mismatches: 5, Indels: 9
0.85 0.05 0.09
Matches are distributed among these distances:
39 1 0.01
40 64 0.79
41 15 0.19
42 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (40 bp):
CTTCGGCTATATATGGCACTTAGTGTCTGAATCGGAATAG
Found at i:31706495 original size:41 final size:42
Alignment explanation
Indices: 31706333--31706521 Score: 137
Period size: 40 Copynumber: 4.6 Consensus size: 42
31706323 ATCGATATAA
* *
31706333 CTTCGGCTAT-ATAAAGCACTTAGTGT-CTGA-A-TCGGAATAG
1 CTTCGGCTATGATAAGGCACTTAGTGTGC-GAGACT-GAAATAG
* * * * *
31706373 CTTCGGCTAT-ATATGGAACTTA--GTGCGTGAATCGGAATAG
1 CTTCGGCTATGATAAGGCACTTAGTGTGCGAGACT-GAAATAG
* *
31706413 CTTCGGCTAT-ATATGGCACTTAGTGTGCGAGACTGAGATAG
1 CTTCGGCTATGATAAGGCACTTAGTGTGCGAGACTGAAATAG
* *
31706454 CTTCGGCTATGA-AAGGCATTTAGTGTGCGAGA-TTATAATAG
1 CTTCGGCTATGATAAGGCACTTAGTGTGCGAGACTGA-AATAG
* * **
31706495 CTTCAGCTATGCTTTGGCACTTAGTGT
1 CTTCGGCTATGATAAGGCACTTAGTGT
31706522 ATGAGATATC
Statistics
Matches: 123, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
38 3 0.02
39 2 0.02
40 51 0.41
41 47 0.38
42 20 0.16
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (42 bp):
CTTCGGCTATGATAAGGCACTTAGTGTGCGAGACTGAAATAG
Found at i:31717545 original size:16 final size:16
Alignment explanation
Indices: 31717524--31717555 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31717514 TAAAGGAGGA
31717524 GAATAAATTTTTTCTT
1 GAATAAATTTTTTCTT
31717540 GAATAAATTTTTTCTT
1 GAATAAATTTTTTCTT
31717556 TATTTTTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (16 bp):
GAATAAATTTTTTCTT
Found at i:31719188 original size:6 final size:6
Alignment explanation
Indices: 31719177--31719210 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
31719167 GACCAAGGCG
* *
31719177 GCTGTT GCTGTT GCTGTT GTTGTT GCGGTT GCTG
1 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTG
31719211 AGCAGCAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.15, G:0.38, T:0.47
Consensus pattern (6 bp):
GCTGTT
Found at i:31733121 original size:18 final size:17
Alignment explanation
Indices: 31733100--31733156 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
31733090 ACTCCCCTTA
31733100 TTTATTTTCCCTCAAACT
1 TTTATTTTCCC-CAAACT
* * *
31733118 TTTACTCT-CCAAAACTT
1 TTTATTTTCCCCAAAC-T
31733135 TTTATTTTCCCCTAAACT
1 TTTATTTTCCCC-AAACT
31733153 TTTA
1 TTTA
31733157 CTTCTCACTT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 4 0.13
17 9 0.30
18 13 0.43
19 4 0.13
ACGTcount: A:0.25, C:0.26, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTATTTTCCCCAAACT
Found at i:31739551 original size:105 final size:101
Alignment explanation
Indices: 31739360--31739552 Score: 244
Period size: 105 Copynumber: 1.9 Consensus size: 101
31739350 AATTGACGGA
* * *
31739360 TAAGACCATGGTTGGAGCATGACAAAATTTAAATGTAAGACCATAGCTGGGCTATGGCATTTCAG
1 TAAGACCATGGTTGGACCATGACAAAATTTAAATGTAAGACCATAGCTAGGCTATGGCATCTCAG
**
31739425 TGACAAGACCATAACTGGGTTATGGCACTGTGAACG
66 TGACAAGACCATAACAAGGTTATGGCACTGTGAACG
* * *
31739461 TAAGACCATGGTTGGACCATGTCAGTATATGTATAAGTGTAAGACCATAGCTAGGCTATGGCATC
1 TAAGACCATGGTTGGACCATGACA--AAAT-T-TAAATGTAAGACCATAGCTAGGCTATGGCATC
* *
31739526 -CTGATGATAAGACCATAACAAGGTTAT
62 TCAG-TGACAAGACCATAACAAGGTTAT
31739553 TATATTACGA
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
101 22 0.29
103 3 0.04
104 3 0.04
105 49 0.64
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGACAAAATTTAAATGTAAGACCATAGCTAGGCTATGGCATCTCAG
TGACAAGACCATAACAAGGTTATGGCACTGTGAACG
Found at i:31740683 original size:22 final size:23
Alignment explanation
Indices: 31740666--31740725 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
31740656 AGCTCAACAC
*
31740666 CGTAGACAGGACT-ACTCAATGT
1 CGTAGACAGGACTGACTCAACGT
31740688 CGTAGACAGGA-TGACTCAACGT
1 CGTAGACAGGACTGACTCAACGT
*
31740710 CGTAGATAGGAC-GACT
1 CGTAGACAGGACTGACT
31740726 AAAGGCCGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGACAGGACTGACTCAACGT
Found at i:31740735 original size:22 final size:22
Alignment explanation
Indices: 31740658--31740735 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
31740648 AACAGAACAG
* *
31740658 CTCAACACCGTAGACAGGACTA
1 CTCAACGCCGTAGACAGGACGA
* * *
31740680 CTCAATGTCGTAGACAGGATGA
1 CTCAACGCCGTAGACAGGACGA
* *
31740702 CTCAACGTCGTAGATAGGACGA
1 CTCAACGCCGTAGACAGGACGA
* *
31740724 CTAAAGGCCGTA
1 CTCAACGCCGTA
31740736 ATTATCGCAG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.18
Consensus pattern (22 bp):
CTCAACGCCGTAGACAGGACGA
Found at i:31740999 original size:27 final size:27
Alignment explanation
Indices: 31740969--31741034 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
31740959 GGGCATAATC
31740969 GTCATTCTACCA-TACAAGGGTATTACG
1 GTCATT-TACCACTACAAGGGTATTACG
** *
31740996 GTCATTTTGCACTACAAGGGTATTTCG
1 GTCATTTACCACTACAAGGGTATTACG
*
31741023 GTGATTTTACCA
1 GTCA-TTTACCA
31741035 ATATTAGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 3 0.10
27 23 0.74
28 5 0.16
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (27 bp):
GTCATTTACCACTACAAGGGTATTACG
Found at i:31747088 original size:17 final size:18
Alignment explanation
Indices: 31747055--31747088 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31747045 TTTAAAGAAG
31747055 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
31747073 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
31747089 TTTCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:31747890 original size:22 final size:22
Alignment explanation
Indices: 31747865--31747929 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
31747855 CACCAAGTCA
31747865 ACAGGACGACTCAACGCCGTAG
1 ACAGGACGACTCAACGCCGTAG
**
31747887 ACAGGACGACTCAACATCGTAG
1 ACAGGACGACTCAACGCCGTAG
* * * *
31747909 AAAAGACGACTAAAGGCCGTA
1 ACAGGACGACTCAACGCCGTA
31747930 AATATCACAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.38, C:0.26, G:0.25, T:0.11
Consensus pattern (22 bp):
ACAGGACGACTCAACGCCGTAG
Found at i:31759888 original size:17 final size:17
Alignment explanation
Indices: 31759866--31759958 Score: 68
Period size: 17 Copynumber: 5.3 Consensus size: 17
31759856 ACTAAACAGA
31759866 CCACTAACTCCATCACC
1 CCACTAACTCCATCACC
31759883 CCACTAACTCCATCATCCTAC
1 CCACTAACTCCATCA--C--C
*
31759904 TTGCCACTAATTCCATCACC
1 ---CCACTAACTCCATCACC
31759924 CCACTAA----ATCACC
1 CCACTAACTCCATCACC
* *
31759937 CCACTAACCCCATTACC
1 CCACTAACTCCATCACC
31759954 CCACT
1 CCACT
31759959 TGCCTAGGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 22
0.72 0.02 0.25
Matches are distributed among these distances:
13 13 0.21
17 32 0.51
19 1 0.02
20 1 0.02
21 1 0.02
22 1 0.02
24 14 0.22
ACGTcount: A:0.29, C:0.48, G:0.01, T:0.22
Consensus pattern (17 bp):
CCACTAACTCCATCACC
Found at i:31759936 original size:13 final size:13
Alignment explanation
Indices: 31759918--31759943 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31759908 CACTAATTCC
31759918 ATCACCCCACTAA
1 ATCACCCCACTAA
31759931 ATCACCCCACTAA
1 ATCACCCCACTAA
31759944 CCCCATTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (13 bp):
ATCACCCCACTAA
Found at i:31763842 original size:92 final size:93
Alignment explanation
Indices: 31763734--31763918 Score: 318
Period size: 92 Copynumber: 2.0 Consensus size: 93
31763724 GAGTTGCCAG
* *
31763734 GAAATAATAGAAAAAAGATGAATAAACAATTAAACCCAAAACAAAATCTCTAATCAGAGTTCAAT
1 GAAATAATAGAAAAAAGAGGAATAAACAATTAAACCCAAAACAAAATCTCTAATCAGAGCTCAAT
*
31763799 CCTAA-TAAAGTAAATAAAGGCGAAGAA
66 CCTAACAAAAGTAAATAAAGGCGAAGAA
*
31763826 GAAATAATAGAAAAAAGAGGAATCAACAATTAAACCCAAAACAAAATCTCTAATCAGAGCTCAAT
1 GAAATAATAGAAAAAAGAGGAATAAACAATTAAACCCAAAACAAAATCTCTAATCAGAGCTCAAT
*
31763891 CCTAACAAAAGTAAATAAAGGCTAAGAA
66 CCTAACAAAAGTAAATAAAGGCGAAGAA
31763919 AAGGATTGCT
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 67 0.77
93 20 0.23
ACGTcount: A:0.56, C:0.15, G:0.12, T:0.17
Consensus pattern (93 bp):
GAAATAATAGAAAAAAGAGGAATAAACAATTAAACCCAAAACAAAATCTCTAATCAGAGCTCAAT
CCTAACAAAAGTAAATAAAGGCGAAGAA
Found at i:31766478 original size:14 final size:14
Alignment explanation
Indices: 31766459--31766525 Score: 89
Period size: 14 Copynumber: 4.7 Consensus size: 14
31766449 GTTTGCAGGT
*
31766459 AAAATGTTTTCTGA
1 AAAATGATTTCTGA
31766473 AAAATGATTTCTGA
1 AAAATGATTTCTGA
* *
31766487 AAAATAATTTTTTGA
1 AAAATGA-TTTCTGA
*
31766502 AAAATGATTTCTGG
1 AAAATGATTTCTGA
31766516 AAAATGATTT
1 AAAATGATTT
31766526 ACTTTTCTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 34 0.74
15 12 0.26
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.40
Consensus pattern (14 bp):
AAAATGATTTCTGA
Found at i:31766502 original size:29 final size:29
Alignment explanation
Indices: 31766465--31766525 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
31766455 AGGTAAAATG
31766465 TTTTCTGAAAAATGATTTCTGAAAAATAA
1 TTTTCTGAAAAATGATTTCTGAAAAATAA
* * *
31766494 TTTTTTGAAAAATGATTTCTGGAAAATGA
1 TTTTCTGAAAAATGATTTCTGAAAAATAA
31766523 TTT
1 TTT
31766526 ACTTTTCTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.43
Consensus pattern (29 bp):
TTTTCTGAAAAATGATTTCTGAAAAATAA
Found at i:31767009 original size:22 final size:22
Alignment explanation
Indices: 31766983--31767031 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
31766973 ATCCAAGTGC
*
31766983 ATAACTAATAGTACACCATATG
1 ATAACTAATAGTACACCACATG
*
31767005 ATAACTAATATTACACCACATG
1 ATAACTAATAGTACACCACATG
31767027 ATAAC
1 ATAAC
31767032 AACAATATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.27
Consensus pattern (22 bp):
ATAACTAATAGTACACCACATG
Found at i:31767605 original size:15 final size:15
Alignment explanation
Indices: 31767585--31767613 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31767575 TTCTCAAGTA
31767585 ATGACTAAAGTTACC
1 ATGACTAAAGTTACC
31767600 ATGACTAAAGTTAC
1 ATGACTAAAGTTAC
31767614 ACTTATACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (15 bp):
ATGACTAAAGTTACC
Found at i:31771893 original size:11 final size:11
Alignment explanation
Indices: 31771877--31771913 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
31771867 AATTTTAGTC
31771877 AAAAATTAATA
1 AAAAATTAATA
*
31771888 AAAAA-T-ACA
1 AAAAATTAATA
31771897 AAAAATTAATA
1 AAAAATTAATA
31771908 AAAAAT
1 AAAAAT
31771914 ACCATGTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 7 0.32
10 2 0.09
11 13 0.59
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAAATTAATA
Found at i:31771902 original size:20 final size:20
Alignment explanation
Indices: 31771877--31771915 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
31771867 AATTTTAGTC
31771877 AAAAATTAATAAAAAATACA
1 AAAAATTAATAAAAAATACA
31771897 AAAAATTAATAAAAAATAC
1 AAAAATTAATAAAAAATAC
31771916 CATGTATCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAATTAATAAAAAATACA
Found at i:31777516 original size:17 final size:17
Alignment explanation
Indices: 31777494--31777526 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31777484 CTGTAGAATA
31777494 GGTATTTATGTTCTATG
1 GGTATTTATGTTCTATG
31777511 GGTATTTATGTTCTAT
1 GGTATTTATGTTCTAT
31777527 CTTTGCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.06, G:0.21, T:0.55
Consensus pattern (17 bp):
GGTATTTATGTTCTATG
Found at i:31780525 original size:25 final size:24
Alignment explanation
Indices: 31780497--31780556 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 24
31780487 CTGTAAGGTT
*
31780497 AAAAATAGTGTTAAGACATTCATACA
1 AAAAATA-T-TTAAGACATTCAGACA
*
31780523 AAATAATATTTAAGCCATTCAGACA
1 AAA-AATATTTAAGACATTCAGACA
31780548 AAAATATAT
1 AAAA-ATAT
31780557 CAATAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 1 0.03
25 21 0.70
26 4 0.13
27 4 0.13
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.28
Consensus pattern (24 bp):
AAAAATATTTAAGACATTCAGACA
Found at i:31786281 original size:33 final size:33
Alignment explanation
Indices: 31786226--31786290 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
31786216 TATGCTTGGG
31786226 CCTCAGTTTACTAGGGCTAGCGCTTTTTTTGCA
1 CCTCAGTTTACTAGGGCTAGCGCTTTTTTTGCA
* *
31786259 CCTCGGTTTACTCGGG-TGAGCGCTTTTTTTGC
1 CCTCAGTTTACTAGGGCT-AGCGCTTTTTTTGC
31786291 GTCTTGCGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 28 0.97
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.40
Consensus pattern (33 bp):
CCTCAGTTTACTAGGGCTAGCGCTTTTTTTGCA
Found at i:31787427 original size:1 final size:1
Alignment explanation
Indices: 31787421--31787488 Score: 127
Period size: 1 Copynumber: 68.0 Consensus size: 1
31787411 TTGCAGCAGC
*
31787421 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31787486 AAA
1 AAA
31787489 GGAATTGATT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.99, C:0.00, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:31787552 original size:43 final size:43
Alignment explanation
Indices: 31787491--31787578 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
31787481 AAAGAAAAGG
*
31787491 AATTGATTACTAAATGCTTAGTCTGCTGCACAAATGTTAAACT
1 AATTGATTACTAAATGCTTAGTCTGCTGCACAAATATTAAACT
*
31787534 AATTGATTACTAAATGCTTAGTCTGCTGCACAACTATTAAACT
1 AATTGATTACTAAATGCTTAGTCTGCTGCACAAATATTAAACT
31787577 AA
1 AA
31787579 CCTATGCTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (43 bp):
AATTGATTACTAAATGCTTAGTCTGCTGCACAAATATTAAACT
Found at i:31789907 original size:348 final size:348
Alignment explanation
Indices: 31789265--31789953 Score: 1144
Period size: 348 Copynumber: 2.0 Consensus size: 348
31789255 TATAATTAGG
*
31789265 AGAGATCCTGAAGGATAGGCCTCAGTTGGGATTCTAAAAGCTTCCAAGTGGAAAAGGCTGTCTGT
1 AGAGATCCTGAAGGATAGGCCTCAGTTGGGATTCTAAAAGCTTCCAAGTGCAAAAGGCTGTCTGT
31789330 TGTCACCATAGAAGTTAGGCATTTGCCAATAGCCTTATTGTTTTTTGGTAGAGTGCTGAACTCTT
66 TGTCACCATAGAAGTTAGGCATTTGCCAATAGCCTTATTGTTTTTTGGTAGAGTGCTGAACTCTT
** *
31789395 AGTTCTAGCGAGTACTGACCATGGATCAAAGCTTTGGAAACCTCCAATGTAAAAGGAATAAGTAG
131 AGTTCTAGCGAGTACTGACCATGGATCAAAGCTTCAGAAACCTCCAATATAAAAGGAATAAGTAG
* *
31789460 GAAACAGACCATGAGGTTTTAAGCTTCACTCATGTCCACCGCAGAATAACTTATCTGCCCTTCAA
196 GAAACAGACCATGAGGTTTTAAGCTTCACTCATGTCCACCACAGAATAACTTATCCGCCCTTCAA
* * * * * *
31789525 TTAAAAGTTGGATTTGTAACTGTCTCCCTTTTGCTACATTCTTAAGGCAAATCCTATGTCTGTGA
261 CTAAAAATTGGATTTGTAACTGTCTCCCTTTTGCTAAATTCTTAAGGCAAACCCTATGTATATGA
31789590 ATCATTTAAAAATGAGAACTAGC
326 ATCATTTAAAAATGAGAACTAGC
* *
31789613 AGAGATCCTGAAGGATAGGCCTTAGTTGGGATTCTAAAAGCTTCCAAGTGCAAAATGCTGTCTGT
1 AGAGATCCTGAAGGATAGGCCTCAGTTGGGATTCTAAAAGCTTCCAAGTGCAAAAGGCTGTCTGT
* * *
31789678 TGTCACCATAGAAGTTAGGCATTTTCCAATGGCCTTGTTGTTTTTTGGTAGAGTGCTGAACTCTT
66 TGTCACCATAGAAGTTAGGCATTTGCCAATAGCCTTATTGTTTTTTGGTAGAGTGCTGAACTCTT
* * *
31789743 AGTTCTAGTGAGTAGTGACCATGGGTCAAAGCTTCAGAAACCTCCAATATAAAAGGAATAAGTAG
131 AGTTCTAGCGAGTACTGACCATGGATCAAAGCTTCAGAAACCTCCAATATAAAAGGAATAAGTAG
* * * *
31789808 GAATCAGACCATTAGGTTTTAAGCTTCACTCATGTCCAGCACAGAATAACTTATCCGCCCTTTAA
196 GAAACAGACCATGAGGTTTTAAGCTTCACTCATGTCCACCACAGAATAACTTATCCGCCCTTCAA
* *
31789873 CTAAAAATTGGATTTGTAACTGTCTCCTTTTTGCTAAATTCTTTAGGCAAACCCTATGTATATGA
261 CTAAAAATTGGATTTGTAACTGTCTCCCTTTTGCTAAATTCTTAAGGCAAACCCTATGTATATGA
31789938 ATCATTTAAAAATGAG
326 ATCATTTAAAAATGAG
31789954 TGTTTCATCC
Statistics
Matches: 315, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
348 315 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (348 bp):
AGAGATCCTGAAGGATAGGCCTCAGTTGGGATTCTAAAAGCTTCCAAGTGCAAAAGGCTGTCTGT
TGTCACCATAGAAGTTAGGCATTTGCCAATAGCCTTATTGTTTTTTGGTAGAGTGCTGAACTCTT
AGTTCTAGCGAGTACTGACCATGGATCAAAGCTTCAGAAACCTCCAATATAAAAGGAATAAGTAG
GAAACAGACCATGAGGTTTTAAGCTTCACTCATGTCCACCACAGAATAACTTATCCGCCCTTCAA
CTAAAAATTGGATTTGTAACTGTCTCCCTTTTGCTAAATTCTTAAGGCAAACCCTATGTATATGA
ATCATTTAAAAATGAGAACTAGC
Found at i:31801860 original size:57 final size:57
Alignment explanation
Indices: 31801772--31801886 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
31801762 CATAGACTTG
31801772 ATAGGTCATTTTGCAATGATGATTGGTAGAGGTTTGCCCTGAATACAACAATCAAAC
1 ATAGGTCATTTTGCAATGATGATTGGTAGAGGTTTGCCCTGAATACAACAATCAAAC
*
31801829 ATAGGTCATTTTGCAATGATGATTGGTAGAGGTTTGCCTTGAATACAACAATCAAAC
1 ATAGGTCATTTTGCAATGATGATTGGTAGAGGTTTGCCCTGAATACAACAATCAAAC
31801886 A
1 A
31801887 CCTTTATAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (57 bp):
ATAGGTCATTTTGCAATGATGATTGGTAGAGGTTTGCCCTGAATACAACAATCAAAC
Found at i:31809083 original size:40 final size:37
Alignment explanation
Indices: 31809039--31809132 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 37
31809029 ACCAGAATGG
*
31809039 CGACCAACGCCTCATCGGAT-AGTTCGAAGCAAATAAGTGA
1 CGACCAACGCCTCATCGGATAAG-CCGAAGC--A-AAGTGA
* *
31809079 CGACCAACGTCTCATCGGCTAAGCCGAAGCAAAGTGA
1 CGACCAACGCCTCATCGGATAAGCCGAAGCAAAGTGA
*
31809116 TGACCAACGCCTCATCG
1 CGACCAACGCCTCATCG
31809133 AATCTATCCG
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
37 21 0.44
38 1 0.02
40 24 0.50
41 2 0.04
ACGTcount: A:0.32, C:0.30, G:0.22, T:0.16
Consensus pattern (37 bp):
CGACCAACGCCTCATCGGATAAGCCGAAGCAAAGTGA
Found at i:31810237 original size:3 final size:3
Alignment explanation
Indices: 31810223--31810253 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
31810213 CTGTCTCAAT
31810223 TAA TAGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
31810254 GTATCTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:31810395 original size:60 final size:59
Alignment explanation
Indices: 31810329--31810454 Score: 173
Period size: 60 Copynumber: 2.1 Consensus size: 59
31810319 CATGTATTCA
* *
31810329 TTCTCTATCTTACACATGT-CACTAATTTGGTTTAATTACTAATTTAGTCCCTTATCATTT
1 TTCTCTATCTTA-AAAT-TACACTAAGTTGGTTTAATTACTAATTTAGTCCCTTATCATTT
* * *
31810389 TTCTCTATTTTAAAATTAACACTAAGTTGGTTTAATTACTAATTTAGTCCTTTGTCATTT
1 TTCTCTATCTTAAAATT-ACACTAAGTTGGTTTAATTACTAATTTAGTCCCTTATCATTT
31810449 TTCTCT
1 TTCTCT
31810455 TTTTTATAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
58 1 0.02
59 3 0.05
60 55 0.93
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.50
Consensus pattern (59 bp):
TTCTCTATCTTAAAATTACACTAAGTTGGTTTAATTACTAATTTAGTCCCTTATCATTT
Found at i:31810460 original size:60 final size:60
Alignment explanation
Indices: 31810348--31810466 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
31810338 TTACACATGT
*
31810348 CACTAATTTGGTTTAATTACTAATTTAGTCCCTTATCATTTTTCTCTATTTTAAAATTAA
1 CACTAAGTTGGTTTAATTACTAATTTAGTCCCTTATCATTTTTCTCTATTTTAAAATTAA
* * * *
31810408 CACTAAGTTGGTTTAATTACTAATTTAGTCCTTTGTCATTTTTCTCTTTTTTATAATTA
1 CACTAAGTTGGTTTAATTACTAATTTAGTCCCTTATCATTTTTCTCTATTTTAAAATTA
31810467 TTCTTTTACA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (60 bp):
CACTAAGTTGGTTTAATTACTAATTTAGTCCCTTATCATTTTTCTCTATTTTAAAATTAA
Found at i:31811781 original size:39 final size:39
Alignment explanation
Indices: 31811720--31811970 Score: 360
Period size: 39 Copynumber: 6.4 Consensus size: 39
31811710 TATTGGAAAA
* * *
31811720 ATATTCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTT
1 ATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
31811759 ATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
1 ATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
* **
31811798 ATATCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGCT
1 ATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
*
31811837 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
1 ATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
** * **
31811876 ATATCAAGGCTAAGTCCTGAAGGCATTTGTGCTGGTGCT
1 ATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
* *
31811915 CTATCCGGGCTAAGTCCCT-AAGGCATTCGTGCTGGCATT
1 ATATCCGGGCTAAGT-CCTGAAGGCATTCGTGCTGGTATT
31811954 ATATCCGGGCTAAGTCC
1 ATATCCGGGCTAAGTCC
31811971 CGAAAATCTC
Statistics
Matches: 187, Mismatches: 24, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
38 2 0.01
39 182 0.97
40 3 0.02
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.29
Consensus pattern (39 bp):
ATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
Found at i:31816246 original size:21 final size:21
Alignment explanation
Indices: 31816222--31816261 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31816212 CCATTCTACT
* *
31816222 AATTTTCATATCCCTTAAAGC
1 AATTTACATAACCCTTAAAGC
*
31816243 AATTTACTTAACCCTTAAA
1 AATTTACATAACCCTTAAA
31816262 AAAATCCCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.38
Consensus pattern (21 bp):
AATTTACATAACCCTTAAAGC
Found at i:31817644 original size:25 final size:25
Alignment explanation
Indices: 31817610--31817658 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
31817600 ACTGGAAATA
31817610 TGAAAAAATTAGAGATGACTCAATT
1 TGAAAAAATTAGAGATGACTCAATT
31817635 TGAAAAAATTAGAGATGACTCAAT
1 TGAAAAAATTAGAGATGACTCAAT
31817659 CCGAAGTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (25 bp):
TGAAAAAATTAGAGATGACTCAATT
Found at i:31821384 original size:30 final size:30
Alignment explanation
Indices: 31821349--31821405 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
31821339 ACACCAGGGG
* *
31821349 ACACACGACCGTGAAACATGCCCGTGTGTC
1 ACACACGACCGAGAAACACGCCCGTGTGTC
* *
31821379 ACACACGACTGAGACACACGCCCGTGT
1 ACACACGACCGAGAAACACGCCCGTGT
31821406 CTCTGCCCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.28, C:0.35, G:0.23, T:0.14
Consensus pattern (30 bp):
ACACACGACCGAGAAACACGCCCGTGTGTC
Found at i:31824044 original size:27 final size:27
Alignment explanation
Indices: 31824014--31824078 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
31824004 GAATGAATCA
31824014 CCTTTGTGGCGTACCCTCTATAGATAG
1 CCTTTGTGGCGTACCCTCTATAGATAG
* ** * * *
31824041 CCTTTGTGGCATACTTTGTATGGATCG
1 CCTTTGTGGCGTACCCTCTATAGATAG
31824068 CCTTTGTGGCG
1 CCTTTGTGGCG
31824079 CACTTTGATT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.14, C:0.23, G:0.26, T:0.37
Consensus pattern (27 bp):
CCTTTGTGGCGTACCCTCTATAGATAG
Found at i:31828340 original size:20 final size:20
Alignment explanation
Indices: 31828312--31828353 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
31828302 GAAAACGAAA
*
31828312 ATAGTCCAAATAGAATGTTT
1 ATAGCCCAAATAGAATGTTT
31828332 ATAGCCCAAATAGAATGTTT
1 ATAGCCCAAATAGAATGTTT
31828352 AT
1 AT
31828354 CACTTACCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (20 bp):
ATAGCCCAAATAGAATGTTT
Found at i:31833240 original size:48 final size:48
Alignment explanation
Indices: 31833134--31833410 Score: 262
Period size: 48 Copynumber: 5.8 Consensus size: 48
31833124 AAGGGTATGT
* *
31833134 GAGCCAGTGT-AGATCATGTTTGGAACATGGCATCGACATT--TATAC
1 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACCTTGATATAC
* * *
31833179 GAGAGCTAATGTAAGACCATGTTTGGGACATGGCATCGACCTTGATATAC
1 --GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACCTTGATATAC
*
31833229 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATT--TATAC
1 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACCTTGATATAC
* * * * **
31833275 GAGAACTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGATATGT
1 GAG--CCAGTGTAAGACCATGTTTGGAACATGGCATCGACCTTGATATAC
* * * *
31833325 GAGCTAGTGTAAGACCATGTTTGGAACATGGAATC-AGCAC-AGATATAT
1 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGA-C-CTTGATATAC
* * *
31833373 GAGTGCCAGTGTAAGACCATGTCTGGGATATGGCATCG
1 GA--GCCAGTGTAAGACCATGTTTGGAACATGGCATCG
31833411 GCATCTTGCC
Statistics
Matches: 192, Mismatches: 26, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
46 8 0.04
47 8 0.04
48 136 0.71
49 1 0.01
50 39 0.20
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (48 bp):
GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACCTTGATATAC
Found at i:31833312 original size:96 final size:96
Alignment explanation
Indices: 31833134--31833410 Score: 385
Period size: 96 Copynumber: 2.9 Consensus size: 96
31833124 AAGGGTATGT
* *
31833134 GAGCCAGTGT-AGATCATGTTTGGAACATGGCATCGACATTTATACGAGAGCTAATGTAAGACCA
1 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTATACGAGAGCTAGTGTAAGACCA
*
31833198 TGTTTGGGACATGGCATCGACCTTGATATAC
66 TGTTTGGGACATGGCATCGACCTCGATATAC
*
31833229 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTATACGAGAACTAGTGTAAGACCA
1 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTATACGAGAGCTAGTGTAAGACCA
* **
31833294 TGTTTGGGACATGGCATCGGCCTCGATATGT
66 TGTTTGGGACATGGCATCGACCTCGATATAC
* * ** * * *
31833325 GAGCTAGTGTAAGACCATGTTTGGAACATGGAATCAGCACAGATATATGAGTGCCAGTGTAAGAC
1 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATC-G-ACATTTATACGAGAGCTAGTGTAAGAC
* *
31833390 CATGTCTGGGATATGGCATCG
64 CATGTTTGGGACATGGCATCG
31833411 GCATCTTGCC
Statistics
Matches: 162, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
95 10 0.06
96 111 0.69
97 1 0.01
98 40 0.25
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (96 bp):
GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTATACGAGAGCTAGTGTAAGACCA
TGTTTGGGACATGGCATCGACCTCGATATAC
Found at i:31833726 original size:33 final size:33
Alignment explanation
Indices: 31833689--31833756 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
31833679 TAATTATTTA
* *
31833689 CTTGTAACTTACTAAGCTTTATGCTTACTTCTT
1 CTTGTAACTTAATAAGCTTTATGCTAACTTCTT
31833722 CTTGTAACTTAATAAGCTTTATGCTAACTTCTT
1 CTTGTAACTTAATAAGCTTTATGCTAACTTCTT
31833755 CT
1 CT
31833757 CTTTTCCATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.47
Consensus pattern (33 bp):
CTTGTAACTTAATAAGCTTTATGCTAACTTCTT
Found at i:31840130 original size:30 final size:30
Alignment explanation
Indices: 31840063--31840133 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
31840053 CATGTGCCAG
* **
31840063 CCCGTGTGTCTCACACGCCCAGTAGACACG
1 CCCGTGTGTCTCACACGACCAGTAGACAAA
* *
31840093 CCTGTGTGTCTCACATGACCAGTAGACAAA
1 CCCGTGTGTCTCACACGACCAGTAGACAAA
31840123 CCCGTGTGTCT
1 CCCGTGTGTCT
31840134 AGGCCGTGTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.21, C:0.34, G:0.23, T:0.23
Consensus pattern (30 bp):
CCCGTGTGTCTCACACGACCAGTAGACAAA
Found at i:31843223 original size:13 final size:13
Alignment explanation
Indices: 31843201--31843233 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
31843191 AATGATTTGT
31843201 TTAT-TAAACTAA
1 TTATCTAAACTAA
31843213 TTATCTAAACTAA
1 TTATCTAAACTAA
*
31843226 TTAACTAA
1 TTATCTAA
31843234 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:31845807 original size:6 final size:5
Alignment explanation
Indices: 31845778--31845865 Score: 58
Period size: 6 Copynumber: 16.8 Consensus size: 5
31845768 TATGTCTTTC
* *
31845778 AAAAT AAAAT --AAT AAAATT GAAAT GAAAAT AAAAAT AAAAAGA AAAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT -AAAAT -AAAA-T AAAAT
31845826 AAAA- ATAAAT AAAAT AAAAT AAAAAT AAGAAT -AAAT AAAA
1 AAAAT A-AAAT AAAAT AAAAT -AAAAT AA-AAT AAAAT AAAA
31845866 AAATAGGAGG
Statistics
Matches: 68, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
3 3 0.04
4 4 0.06
5 30 0.44
6 31 0.46
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:31845813 original size:12 final size:11
Alignment explanation
Indices: 31845778--31845870 Score: 73
Period size: 12 Copynumber: 8.0 Consensus size: 11
31845768 TATGTCTTTC
31845778 AAAATAAAATAA
1 AAAATAAAAT-A
* *
31845790 TAAAATTGAAATG
1 -AAAA-TAAAATA
31845803 AAAATAAAAATA
1 AAAAT-AAAATA
*
31845815 AAAAGAAAAATA
1 AAAA-TAAAATA
31845827 AAAAT-AAAT-
1 AAAATAAAATA
31845836 AAAATAAAATA
1 AAAATAAAATA
31845847 AAAATAAGAATA
1 AAAATAA-AATA
*
31845859 AATAAAAAAATA
1 AA-AATAAAATA
31845871 GGAGGATTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
9 5 0.08
10 8 0.12
11 8 0.12
12 32 0.48
13 8 0.12
14 5 0.08
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.18
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:31845850 original size:26 final size:25
Alignment explanation
Indices: 31845778--31845870 Score: 91
Period size: 24 Copynumber: 3.8 Consensus size: 25
31845768 TATGTCTTTC
* ** *
31845778 AAAATAAAATAATAAAATTGAAATG
1 AAAATAAAAAAATAAAATAAAAATA
* *
31845803 AAAATAAAAATA-AAAAGAAAAATA
1 AAAATAAAAAAATAAAATAAAAATA
31845827 AAAATAAATAAAATAAAATAAAAATA
1 AAAATAAA-AAAATAAAATAAAAATA
* *
31845853 AGAATAAATAAA-AAAATA
1 AAAATAAAAAAATAAAATA
31845871 GGAGGATTCA
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
24 22 0.39
25 16 0.29
26 18 0.32
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.18
Consensus pattern (25 bp):
AAAATAAAAAAATAAAATAAAAATA
Found at i:31845851 original size:44 final size:44
Alignment explanation
Indices: 31845778--31845870 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 44
31845768 TATGTCTTTC
* *
31845778 AAAAT-AAAATAATAAAATTGAAATGAAAATAAAAATAAA-AAGA
1 AAAATAAAAATAATAAAATTAAAATAAAAATAAAAATAAATAA-A
*
31845821 AAAATAAAAATAAATAAAA-TAAAATAAAAATAAGAATAAATAAA
1 AAAATAAAAAT-AATAAAATTAAAATAAAAATAAAAATAAATAAA
31845865 AAAATA
1 AAAATA
31845871 GGAGGATTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
43 5 0.11
44 30 0.68
45 9 0.20
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.18
Consensus pattern (44 bp):
AAAATAAAAATAATAAAATTAAAATAAAAATAAAAATAAATAAA
Found at i:31845863 original size:10 final size:10
Alignment explanation
Indices: 31845804--31845853 Score: 61
Period size: 9 Copynumber: 5.2 Consensus size: 10
31845794 ATTGAAATGA
31845804 AAATAAAAAT
1 AAATAAAAAT
*
31845814 AAA-AAGAA-
1 AAATAAAAAT
31845822 AAATAAAAAT
1 AAATAAAAAT
31845832 AAAT-AAAAT
1 AAATAAAAAT
31845841 AAAATAAAAAT
1 -AAATAAAAAT
31845852 AA
1 AA
31845854 GAATAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
8 3 0.09
9 13 0.38
10 13 0.38
11 5 0.15
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:31845868 original size:38 final size:40
Alignment explanation
Indices: 31845779--31845870 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 40
31845769 ATGTCTTTCA
* *
31845779 AAATAAAATAATAAAATTGAAATGAAAATAAAAATAAAAAG
1 AAATAAAAAAAT-AAATTAAAATGAAAATAAAAATAAAAAG
* *
31845820 AAA-AATAAAAATAAA-TAAAAT-AAAATAAAAATAAGAAT
1 AAATAA-AAAAATAAATTAAAATGAAAATAAAAATAAAAAG
31845858 AAATAAAAAAATA
1 AAATAAAAAAATA
31845871 GGAGGATTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
38 25 0.56
39 7 0.16
40 5 0.11
41 8 0.18
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.18
Consensus pattern (40 bp):
AAATAAAAAAATAAATTAAAATGAAAATAAAAATAAAAAG
Found at i:31851213 original size:13 final size:13
Alignment explanation
Indices: 31851191--31851223 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
31851181 AAGGATTTGT
31851191 TTAT-TAAACTAA
1 TTATCTAAACTAA
31851203 TTATCTAAACTAA
1 TTATCTAAACTAA
*
31851216 TTAACTAA
1 TTATCTAA
31851224 GTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:31854262 original size:43 final size:43
Alignment explanation
Indices: 31854184--31854297 Score: 115
Period size: 43 Copynumber: 2.7 Consensus size: 43
31854174 TCGTATGTCG
* ** * *
31854184 ATGCCAACGTCCCAGATGTGGTCTTACACGAAATCA-TATAATG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAGGATAA-A
**
31854227 ATGCCAATGTCTTAGACATGGTCTTACAC-ATAATCAGGATAAA
1 ATGCCAATGTCCCAGACATGGTCTTACACGA-AATCAGGATAAA
**
31854270 ATTTCAATGTCCCAGACATGGTCTTACA
1 ATGCCAATGTCCCAGACATGGTCTTACA
31854298 TGTAATTTCA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
42 1 0.02
43 53 0.91
44 4 0.07
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAGGATAAA
Found at i:31859346 original size:13 final size:13
Alignment explanation
Indices: 31859324--31859357 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
31859314 ATCTACACCC
*
31859324 CCATTTACCATTA
1 CCATTAACCATTA
31859337 CCATTAACCATTA
1 CCATTAACCATTA
31859350 CCATTAAC
1 CCATTAAC
31859358 TTCCTTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (13 bp):
CCATTAACCATTA
Found at i:31860303 original size:22 final size:21
Alignment explanation
Indices: 31860274--31860318 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
31860264 CTGCTGTTAA
31860274 AAGTA-TTTTGTTAGTGTATTT
1 AAGTATTTTTGTTAGT-TATTT
31860295 AAGTCATTTTTGTTAGTTATTT
1 AAGT-ATTTTTGTTAGTTATTT
31860317 AA
1 AA
31860319 AAAAATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.18
22 8 0.36
23 10 0.45
ACGTcount: A:0.27, C:0.02, G:0.16, T:0.56
Consensus pattern (21 bp):
AAGTATTTTTGTTAGTTATTT
Found at i:31865122 original size:41 final size:41
Alignment explanation
Indices: 31865065--31865144 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
31865055 ATTTGAGGAA
*
31865065 GTGATAAGAATGTCCCGAAAAACCGGGGGGGGGGGGGGACC
1 GTGATAAGAATGTCCCGAAAAACCGGGGGGCGGGGGGGACC
31865106 GTGATAAGAATGTCCCGAAAAACCGGGGGGCGGGGGGGA
1 GTGATAAGAATGTCCCGAAAAACCGGGGGGCGGGGGGGA
31865145 GCACAAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.28, C:0.16, G:0.46, T:0.10
Consensus pattern (41 bp):
GTGATAAGAATGTCCCGAAAAACCGGGGGGCGGGGGGGACC
Found at i:31868389 original size:20 final size:20
Alignment explanation
Indices: 31868327--31868399 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
31868317 GTTTAGGGTA
31868327 TTAGGGTTAATTGATTAAA-
1 TTAGGGTTAATTGATTAAAT
* **
31868346 TTATGG---ATTGATTTAGGGT
1 TTAGGGTTAATTGA-TTA-AAT
31868365 TTAGGGTTAATTGATTAAAT
1 TTAGGGTTAATTGATTAAAT
31868385 TTAGGGTTAATTGAT
1 TTAGGGTTAATTGAT
31868400 ACATACAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
16 5 0.12
17 3 0.07
19 10 0.24
20 16 0.38
21 3 0.07
22 5 0.12
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (20 bp):
TTAGGGTTAATTGATTAAAT
Found at i:31868935 original size:126 final size:126
Alignment explanation
Indices: 31868706--31869210 Score: 750
Period size: 126 Copynumber: 4.0 Consensus size: 126
31868696 TTTTTGCAAG
* * * * *
31868706 AATAATTCTAAGCAGACATTTCTGGAA-AAATAGTGTCAGAAAACGCTTCAAGCAGGATGCACTG
1 AATAATTCTGAGTAGACGTTTCT-AAACAAATAGTG-CCGAAAACGCTTCAAGCAGGATGCACTG
* * *
31868770 TCAGCAAAATTT-TCGAAAAAAGCTCCTACGTGGACGCTCTTTTGCTACAGTAGTTCTTAGAAA
64 TCAGCAAAATTTCT-GGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
*
31868833 AATAATTTTGAGTAGACGTTTCTAAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
1 AATAATTCTGAGTAGACGTTTCTAAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
* * *
31868898 AGCAAAATTTCTAGAAAAAGCTCCCACGTGGATGCTCTTTTGCTACAGTAGTTCGTTGAAA
66 AGCAAAATTTCTGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
* * * *
31868959 AATAATTCTGAGTAGACGTTTCTCAACAAATAGCGCCGAAAATGCTTCAAGCAAGATGCACTGTC
1 AATAATTCTGAGTAGACGTTTCTAAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
*
31869024 AGCAAAATTTCTGGAAAAAGCTCTCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
66 AGCAAAATTTCTGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
* * *
31869085 AATAATTCTGAGTAGACATTTCTGAACAAATAGTGCCG--AA-GTTTCAAGCAGGATGCACTGTC
1 AATAATTCTGAGTAGACGTTTCTAAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
* *
31869147 AGCAAAATTTCTGGAAAAAGCTCCGACGTGGACGCTATTTTGCTACAGTAGTTCGTAGAAA
66 AGCAAAATTTCTGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
31869208 AAT
1 AAT
31869211 GAGGCTATAA
Statistics
Matches: 347, Mismatches: 29, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
123 81 0.23
124 2 0.01
126 236 0.68
127 28 0.08
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (126 bp):
AATAATTCTGAGTAGACGTTTCTAAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
AGCAAAATTTCTGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
Found at i:31872723 original size:18 final size:18
Alignment explanation
Indices: 31872697--31872739 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
31872687 GACTAGGAAA
* *
31872697 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
31872715 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
31872733 AGGATAC
1 AGGATAC
31872740 GCACCTGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:31873127 original size:25 final size:25
Alignment explanation
Indices: 31873099--31873151 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
31873089 TGTGCTCATC
* *
31873099 ATCAAACACATCGGGTGCCATGAGA
1 ATCAAACACATCGAGTGCCACGAGA
31873124 ATCAAACACATCGAGTGCCACGAGA
1 ATCAAACACATCGAGTGCCACGAGA
31873149 ATC
1 ATC
31873152 GGTTGTCGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (25 bp):
ATCAAACACATCGAGTGCCACGAGA
Found at i:31874435 original size:48 final size:48
Alignment explanation
Indices: 31874371--31874477 Score: 130
Period size: 48 Copynumber: 2.2 Consensus size: 48
31874361 AAAAAAAGCT
*
31874371 GTATTGAAATTGTAATTATAA-TTGCATAAATGAATAA-AATATTAAATA
1 GTATTGAAATTGTAATTA-AATTTGCATAAATGAA-AATAATATCAAATA
* *
31874419 GTATTGCAAATT-TAATTAAATTTGCATAAATTAAAATAATATCGAATA
1 GTATTG-AAATTGTAATTAAATTTGCATAAATGAAAATAATATCAAATA
*
31874467 GTATTTAAATT
1 GTATTGAAATT
31874478 TTAAAATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
47 9 0.17
48 38 0.73
49 5 0.10
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (48 bp):
GTATTGAAATTGTAATTAAATTTGCATAAATGAAAATAATATCAAATA
Found at i:31874634 original size:11 final size:11
Alignment explanation
Indices: 31874615--31874678 Score: 67
Period size: 11 Copynumber: 5.9 Consensus size: 11
31874605 TTTTAAACAA
31874615 AGAATTTTGAT
1 AGAATTTTGAT
*
31874626 AGAAATTTGAT
1 AGAATTTTGAT
*
31874637 AGAATTTTGAG
1 AGAATTTTGAT
* **
31874648 AAAATTTCAAT
1 AGAATTTTGAT
31874659 -GAATTTTGAT
1 AGAATTTTGAT
*
31874669 AGATTTTTGA
1 AGAATTTTGA
31874679 AGGGAATATT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
10 7 0.17
11 34 0.83
ACGTcount: A:0.39, C:0.02, G:0.17, T:0.42
Consensus pattern (11 bp):
AGAATTTTGAT
Found at i:31874654 original size:21 final size:21
Alignment explanation
Indices: 31874614--31874667 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
31874604 ATTTTAAACA
* *
31874614 AAGAATTTTGATAGAAATTTG
1 AAGAATTTTGAGAGAAATTTC
31874635 ATAGAATTTTGAGA-AAATTTC
1 A-AGAATTTTGAGAGAAATTTC
31874656 AATGAATTTTGA
1 AA-GAATTTTGA
31874668 TAGATTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 1 0.03
21 17 0.59
22 11 0.38
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.39
Consensus pattern (21 bp):
AAGAATTTTGAGAGAAATTTC
Found at i:31875613 original size:21 final size:21
Alignment explanation
Indices: 31875589--31875629 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31875579 TGGGTTTGGA
*
31875589 ATTTAAGGTTCATGGTTCAAG
1 ATTTAAGGTTCAGGGTTCAAG
*
31875610 ATTTAATGTTCAGGGTTCAA
1 ATTTAAGGTTCAGGGTTCAA
31875630 ATTCGAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (21 bp):
ATTTAAGGTTCAGGGTTCAAG
Found at i:31876416 original size:20 final size:19
Alignment explanation
Indices: 31876379--31876422 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
31876369 ATAAAAAAAG
* * *
31876379 AAGAAGAAAGAAACGTTGTA
1 AAGAACAAAAAAAAGTTG-A
31876399 AAGAACAAAAAAAAGTTGA
1 AAGAACAAAAAAAAGTTGA
31876418 AAGAA
1 AAGAA
31876423 AATGTTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.64, C:0.05, G:0.20, T:0.11
Consensus pattern (19 bp):
AAGAACAAAAAAAAGTTGA
Found at i:31877675 original size:171 final size:171
Alignment explanation
Indices: 31877390--31877732 Score: 650
Period size: 171 Copynumber: 2.0 Consensus size: 171
31877380 ATAATATTTG
*
31877390 TTGTTTAGTAAAAAAATGAAATTTCAGTAATTTCATAACTAAGTTGAAACTCAATTAAGAGATAA
1 TTGTTTAGTAAAAAAATAAAATTTCAGTAATTTCATAACTAAGTTGAAACTCAATTAAGAGATAA
* *
31877455 CATTAACTCAATCTTAATAATAATATGAATATAATTATGAGAAGCAGAAAATGTCACATTAGTGT
66 CATTAACTCAATATTAATAATAATATGAATATAAATATGAGAAGCAGAAAATGTCACATTAGTGT
31877520 TCAAAGGGATAAATAAAATTAAGCAAGATAACAAATACTTA
131 TCAAAGGGATAAATAAAATTAAGCAAGATAACAAATACTTA
*
31877561 TTGTTTAGTAAAAAAATAAAATTTCAGTAATTTCATAACTAAGTTGAAACTCAATTGAGAGATAA
1 TTGTTTAGTAAAAAAATAAAATTTCAGTAATTTCATAACTAAGTTGAAACTCAATTAAGAGATAA
31877626 CATTAACTCAATATTAATAATAATATGAATATAAATATGAGAAGCAGAAAATGTCACATTAGTGT
66 CATTAACTCAATATTAATAATAATATGAATATAAATATGAGAAGCAGAAAATGTCACATTAGTGT
31877691 TCAAAGGGATAAATAAAATTAAGCAAGATAACAAATACTTA
131 TCAAAGGGATAAATAAAATTAAGCAAGATAACAAATACTTA
31877732 T
1 T
31877733 AGTTATATTA
Statistics
Matches: 168, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
171 168 1.00
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.30
Consensus pattern (171 bp):
TTGTTTAGTAAAAAAATAAAATTTCAGTAATTTCATAACTAAGTTGAAACTCAATTAAGAGATAA
CATTAACTCAATATTAATAATAATATGAATATAAATATGAGAAGCAGAAAATGTCACATTAGTGT
TCAAAGGGATAAATAAAATTAAGCAAGATAACAAATACTTA
Found at i:31877835 original size:22 final size:23
Alignment explanation
Indices: 31877795--31877852 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
31877785 TATTGTAATA
*
31877795 AATATTTTATATTAAAATATT-AG
1 AATATTTT-TAATAAAATATTAAG
*
31877818 TATATTTTTAATAAAATATTAAG
1 AATATTTTTAATAAAATATTAAG
31877841 AATATTATTTAA
1 AATATT-TTTAA
31877853 AATTATTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.37
23 14 0.47
24 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (23 bp):
AATATTTTTAATAAAATATTAAG
Found at i:31882498 original size:25 final size:25
Alignment explanation
Indices: 31882470--31882560 Score: 155
Period size: 25 Copynumber: 3.6 Consensus size: 25
31882460 CATATATATT
*
31882470 CGCACACATAGTGCCATAAAATTTC
1 CGCACACTTAGTGCCATAAAATTTC
*
31882495 CGCACACTTAGTGCCATACAATTTC
1 CGCACACTTAGTGCCATAAAATTTC
*
31882520 CGCACACTTAGTGCCATATAATTTC
1 CGCACACTTAGTGCCATAAAATTTC
31882545 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
31882561 AGTCATTTCG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 63 1.00
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.26
Consensus pattern (25 bp):
CGCACACTTAGTGCCATAAAATTTC
Found at i:31895853 original size:30 final size:30
Alignment explanation
Indices: 31895813--31895869 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
31895803 ACAGCCATGA
* *
31895813 CACACAGGCGTGTGGCCTACCCGTGTGTCT
1 CACACAGGCGTGTAGACTACCCGTGTGTCT
* *
31895843 CACACGGGCGTGTAGATTACCCGTGTG
1 CACACAGGCGTGTAGACTACCCGTGTG
31895870 GAAGTGTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.16, C:0.30, G:0.32, T:0.23
Consensus pattern (30 bp):
CACACAGGCGTGTAGACTACCCGTGTGTCT
Found at i:31897419 original size:45 final size:45
Alignment explanation
Indices: 31897350--31897472 Score: 129
Period size: 45 Copynumber: 2.7 Consensus size: 45
31897340 TAGCAACCTG
* * * * * * *
31897350 ATGAGTAGTTTATGCATAATGTACTAGCAGCTTTTATTTGCATCA
1 ATGAGTGGTTTATCCACAACGTACTAGCAGCTTTTATCTACACCA
* *
31897395 ATGAGTGGTTTATTCACAACGTACTAGCAACTTTTATCTACACCA
1 ATGAGTGGTTTATCCACAACGTACTAGCAGCTTTTATCTACACCA
* * * *
31897440 ATAAATGGTTTATCCACACCGTACTACCAGCTT
1 ATGAGTGGTTTATCCACAACGTACTAGCAGCTT
31897473 GTCTGCAAAC
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (45 bp):
ATGAGTGGTTTATCCACAACGTACTAGCAGCTTTTATCTACACCA
Found at i:31900265 original size:18 final size:18
Alignment explanation
Indices: 31900244--31900278 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
31900234 TCCTCATGAA
31900244 ACTATAATACTTAGGAGG
1 ACTATAATACTTAGGAGG
31900262 ACTATAATACTTAGGAG
1 ACTATAATACTTAGGAG
31900279 AATTTCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (18 bp):
ACTATAATACTTAGGAGG
Found at i:31904778 original size:17 final size:15
Alignment explanation
Indices: 31904753--31904799 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
31904743 TATTATAAAA
31904753 ATATAAAAATCAAATT
1 ATATAAAAAT-AAATT
*
31904769 ATATTAAAAATTAA-T
1 ATA-TAAAAATAAATT
31904784 ATATAAAAATTAAATT
1 ATATAAAAA-TAAATT
31904800 TTAAAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 6 0.23
15 7 0.27
16 6 0.23
17 7 0.27
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
ATATAAAAATAAATT
Found at i:31904790 original size:14 final size:15
Alignment explanation
Indices: 31904753--31904796 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
31904743 TATTATAAAA
*
31904753 ATATAAAAATCAAATT
1 ATATAAAAAT-TAATT
31904769 ATATTAAAAATTAA-T
1 ATA-TAAAAATTAATT
31904784 ATATAAAAATTAA
1 ATATAAAAATTAA
31904797 ATTTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 10 0.38
15 4 0.15
16 5 0.19
17 7 0.27
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (15 bp):
ATATAAAAATTAATT
Found at i:31904803 original size:7 final size:7
Alignment explanation
Indices: 31904793--31904839 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
31904783 TATATAAAAA
31904793 TTAAATT
1 TTAAATT
*
31904800 TTAAAAT
1 TTAAATT
*
31904807 TTGAATT
1 TTAAATT
*
31904814 TTGAATT
1 TTAAATT
*
31904821 TTGAATT
1 TTAAATT
31904828 TTAAA-T
1 TTAAATT
31904834 TTAAAT
1 TTAAAT
31904840 ATAATAGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 6 0.17
7 29 0.83
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (7 bp):
TTAAATT
Found at i:31904823 original size:14 final size:14
Alignment explanation
Indices: 31904796--31904835 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
31904786 ATAAAAATTA
*
31904796 AATTTTAAAATTTG
1 AATTTTAAATTTTG
*
31904810 AATTTTGAATTTTG
1 AATTTTAAATTTTG
31904824 AATTTTAAATTT
1 AATTTTAAATTT
31904836 AAATATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
AATTTTAAATTTTG
Found at i:31910420 original size:17 final size:17
Alignment explanation
Indices: 31910397--31910436 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
31910387 AATTTTATAA
31910397 ATTATATACTATAAATT
1 ATTATATACTATAAATT
* * *
31910414 TTTATATATTTTAAATT
1 ATTATATACTATAAATT
31910431 ATTATA
1 ATTATA
31910437 GGCTTTTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATATACTATAAATT
Found at i:31911097 original size:11 final size:12
Alignment explanation
Indices: 31911077--31911119 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
31911067 CAAAATTATT
31911077 AAAAGATAAAGA
1 AAAAGATAAAGA
31911089 AAAAG-TAAA-A
1 AAAAGATAAAGA
*
31911099 AAAAGACAAAGA
1 AAAAGATAAAGA
*
31911111 AAAATATAA
1 AAAAGATAA
31911120 TTATCATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 6 0.23
11 7 0.27
12 13 0.50
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (12 bp):
AAAAGATAAAGA
Found at i:31912626 original size:15 final size:15
Alignment explanation
Indices: 31912606--31912701 Score: 97
Period size: 15 Copynumber: 6.4 Consensus size: 15
31912596 GTTATAGGTT
31912606 CACATAAAGGGTTCG
1 CACATAAAGGGTTCG
*
31912621 CACATATAGGGTTCG
1 CACATAAAGGGTTCG
* *
31912636 CGCATATAGGGTTCG
1 CACATAAAGGGTTCG
*
31912651 CACATACAA-GGATCG
1 CACATA-AAGGGTTCG
* *
31912666 TACATATAA-GGTTCA
1 CACATA-AAGGGTTCG
*
31912681 CACATATAGGGTTCG
1 CACATAAAGGGTTCG
31912696 CACATA
1 CACATA
31912702 CAGGAACGCT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
14 1 0.01
15 65 0.97
16 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (15 bp):
CACATAAAGGGTTCG
Found at i:31912648 original size:30 final size:30
Alignment explanation
Indices: 31912606--31912701 Score: 120
Period size: 30 Copynumber: 3.2 Consensus size: 30
31912596 GTTATAGGTT
*
31912606 CACATAAAGGGTTCGCACATATAGGGTTCG
1 CACATATAGGGTTCGCACATATAGGGTTCG
* * * *
31912636 CGCATATAGGGTTCGCACATACAAGGATCG
1 CACATATAGGGTTCGCACATATAGGGTTCG
* * *
31912666 TACATATAAGGTTCACACATATAGGGTTCG
1 CACATATAGGGTTCGCACATATAGGGTTCG
31912696 CACATA
1 CACATA
31912702 CAGGAACGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (30 bp):
CACATATAGGGTTCGCACATATAGGGTTCG
Found at i:31912809 original size:15 final size:15
Alignment explanation
Indices: 31912770--31912818 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
31912760 TAGGATTTAT
* **
31912770 ACATGTAGGGTTTAC
1 ACATATAGGGTTCGC
*
31912785 ACATACAGGGTTCGC
1 ACATATAGGGTTCGC
31912800 ACATATAGGGTTCGC
1 ACATATAGGGTTCGC
31912815 ACAT
1 ACAT
31912819 TTAATTCACA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (15 bp):
ACATATAGGGTTCGC
Found at i:31912809 original size:30 final size:29
Alignment explanation
Indices: 31912598--31912818 Score: 92
Period size: 30 Copynumber: 7.6 Consensus size: 29
31912588 ACACATACGT
*
31912598 TATA-GGTTCACATA-AAGGGTTCGCACA
1 TATAGGGTTCACACATAAGGGTTCGCACA
* *
31912625 TATAGGGTTCGCGCATATAGGGTTCGCACA
1 TATAGGGTTCACACATA-AGGGTTCGCACA
* * * * *
31912655 TACAAGGATCGTACATATAA-GGTTCACACA
1 TATAGGGTTC--ACACATAAGGGTTCGCACA
* ** **
31912685 TATAGGGTTCGCACATACA-GGAACGCTTA
1 TATAGGGTTCACACATA-AGGGTTCGCACA
** * * * * *
31912714 TATACTGTTTAGACGTAAGGTTTCTCACA
1 TATAGGGTTCACACATAAGGGTTCGCACA
* * ***
31912743 T-TCAAGGTTCACACATATAGGATTTATACA
1 TAT-AGGGTTCACACATA-AGGGTTCGCACA
* *
31912773 TGTAGGGTTTACACATACAGGGTTCGCACA
1 TATAGGGTTCACACATA-AGGGTTCGCACA
*
31912803 TATAGGGTTCGCACAT
1 TATAGGGTTCACACAT
31912819 TTAATTCACA
Statistics
Matches: 133, Mismatches: 51, Indels: 17
0.66 0.25 0.08
Matches are distributed among these distances:
27 4 0.03
28 14 0.11
29 32 0.24
30 77 0.58
31 2 0.02
32 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (29 bp):
TATAGGGTTCACACATAAGGGTTCGCACA
Found at i:31912880 original size:34 final size:34
Alignment explanation
Indices: 31912835--31912949 Score: 205
Period size: 34 Copynumber: 3.4 Consensus size: 34
31912825 CACAAAGTAC
*
31912835 ATAACAT-GGGGTTCACATACTACGTCATACTAT
1 ATAACATGGGGGTTCACATACTACTTCATACTAT
31912868 ATAACATGGGGGTTCACATACTACTTCATACTAT
1 ATAACATGGGGGTTCACATACTACTTCATACTAT
31912902 ATAACATGGGGGTTCACATACTACTTCATACTAT
1 ATAACATGGGGGTTCACATACTACTTCATACTAT
*
31912936 ATAACATTGGGGTT
1 ATAACATGGGGGTT
31912950 TGCATGCTAA
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
33 7 0.09
34 72 0.91
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (34 bp):
ATAACATGGGGGTTCACATACTACTTCATACTAT
Found at i:31913047 original size:15 final size:15
Alignment explanation
Indices: 31913027--31913077 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
31913017 TTCGTCTATA
31913027 GGGTTCATATACAGG
1 GGGTTCATATACAGG
** *
31913042 GGGTTCGCATACA-T
1 GGGTTCATATACAGG
* *
31913056 GGGCTCATGTACAGG
1 GGGTTCATATACAGG
31913071 GGGTTCA
1 GGGTTCA
31913078 CCTATACAGA
Statistics
Matches: 26, Mismatches: 9, Indels: 2
0.70 0.24 0.05
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.25
Consensus pattern (15 bp):
GGGTTCATATACAGG
Found at i:31917445 original size:22 final size:24
Alignment explanation
Indices: 31917411--31917461 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
31917401 ATATTTCAAC
* *
31917411 TATTTTTTCTTCTTTGTTTATT-T
1 TATTTTATCTTCTTTCTTTATTAT
*
31917434 TATTTTAT-TTCTTTCTTTCTTAT
1 TATTTTATCTTCTTTCTTTATTAT
31917457 TATTT
1 TATTT
31917462 ATAGTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (24 bp):
TATTTTATCTTCTTTCTTTATTAT
Found at i:31917910 original size:56 final size:56
Alignment explanation
Indices: 31917824--31917935 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
31917814 ACTTCATAAG
31917824 GAAAGATTGTTTGCAAATCTTTCATGACAAATTGAATTTTGCTTCAGATGTAAATA
1 GAAAGATTGTTTGCAAATCTTTCATGACAAATTGAATTTTGCTTCAGATGTAAATA
31917880 GAAAGATTGTTTGCAAATCTTTCATGACAAATTGAATTTTGCTTCAGATGTAAATA
1 GAAAGATTGTTTGCAAATCTTTCATGACAAATTGAATTTTGCTTCAGATGTAAATA
31917936 AACACACATT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (56 bp):
GAAAGATTGTTTGCAAATCTTTCATGACAAATTGAATTTTGCTTCAGATGTAAATA
Found at i:31919082 original size:16 final size:17
Alignment explanation
Indices: 31919063--31919106 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
31919053 TCTTATAATA
31919063 ATTTTAAAATAAAT-GT
1 ATTTTAAAATAAATAGT
*
31919079 ATTTT-AAATAAATATT
1 ATTTTAAAATAAATAGT
*
31919095 ATTTAAAAATAA
1 ATTTTAAAATAA
31919107 CTAGATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.33
16 10 0.42
17 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTTTAAAATAAATAGT
Found at i:31926849 original size:73 final size:73
Alignment explanation
Indices: 31926730--31926877 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 73
31926720 GAAAGTAATA
*
31926730 TTGTTAGTGCTCGGGTTGCCTCCCGAGAAACGCTTATTTAAAGTCTAAGCTAGACTTTACTGTGT
1 TTGTTAGTGCTCGGGTTGCCTCCCGAGAAACGCTTATTTAAAGTCTAAGCTAGACTTTACCGTGT
31926795 GAGTATAC
66 GAGTATAC
31926803 TTGTTAGTGCTCGGGTTGCCTCCCGAGAAACGCTTATTTAAAGTCTAAGCTAGACTTTACCGTGT
1 TTGTTAGTGCTCGGGTTGCCTCCCGAGAAACGCTTATTTAAAGTCTAAGCTAGACTTTACCGTGT
31926868 GAGTATAC
66 GAGTATAC
31926876 TT
1 TT
31926878 AAGGAGATTT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (73 bp):
TTGTTAGTGCTCGGGTTGCCTCCCGAGAAACGCTTATTTAAAGTCTAAGCTAGACTTTACCGTGT
GAGTATAC
Found at i:31940218 original size:13 final size:13
Alignment explanation
Indices: 31940199--31940234 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
31940189 AGCACACGAG
31940199 CGTGTGACTTGGC
1 CGTGTGACTTGGC
*
31940212 TGTGTGACTTGGC
1 CGTGTGACTTGGC
31940225 CGTGTGACTT
1 CGTGTGACTT
31940235 CAATTTCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.08, C:0.19, G:0.36, T:0.36
Consensus pattern (13 bp):
CGTGTGACTTGGC
Found at i:31963639 original size:18 final size:17
Alignment explanation
Indices: 31963607--31963640 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31963597 CAACCGCGAT
*
31963607 AAACGCAATGCGACCGA
1 AAACGCAACGCGACCGA
31963624 AAACGCAACCGCGACCG
1 AAACGCAA-CGCGACCG
31963641 CAATTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.35, G:0.24, T:0.03
Consensus pattern (17 bp):
AAACGCAACGCGACCGA
Found at i:31964846 original size:27 final size:27
Alignment explanation
Indices: 31964816--31964867 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
31964806 TTATAATAAA
*
31964816 TAATAACTTAAGT-TTAATTTGATGAAT
1 TAATAAC-TAAATATTAATTTGATGAAT
*
31964843 TAATAACTAAATATTAATTTTATGA
1 TAATAACTAAATATTAATTTGATGA
31964868 TCTCACCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (27 bp):
TAATAACTAAATATTAATTTGATGAAT
Found at i:31965055 original size:30 final size:31
Alignment explanation
Indices: 31965021--31965081 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
31965011 TAATAGGATA
31965021 AATATCAAAGTTA-TATATGAATTTTGATTT
1 AATATCAAAGTTAGTATATGAATTTTGATTT
** * *
31965051 AATATTTAATTTAGTCTATGAATTTTGATTT
1 AATATCAAAGTTAGTATATGAATTTTGATTT
31965082 TGTGCAACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (31 bp):
AATATCAAAGTTAGTATATGAATTTTGATTT
Found at i:31970594 original size:10 final size:10
Alignment explanation
Indices: 31970562--31970610 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
31970552 TTAAATTCTA
31970562 AAAGATAAAT
1 AAAGATAAAT
*
31970572 ACAA-TTAAAT
1 A-AAGATAAAT
*
31970582 AAAGATAATT
1 AAAGATAAAT
31970592 AAAGATAAAT
1 AAAGATAAAT
31970602 AAAGATAAA
1 AAAGATAAA
31970611 AGCTAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 2 0.06
10 29 0.88
11 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:31971252 original size:8 final size:8
Alignment explanation
Indices: 31971241--31971297 Score: 78
Period size: 8 Copynumber: 6.8 Consensus size: 8
31971231 TAATACATTA
31971241 CTTTTTTT
1 CTTTTTTT
31971249 CTTTTTTTT
1 C-TTTTTTT
31971258 CTTTTTTCTT
1 C-TTTTT-TT
31971268 CTTTTTTT
1 CTTTTTTT
31971276 CTTTTTTT
1 CTTTTTTT
*
31971284 CTTATTTT
1 CTTTTTTT
31971292 CTTTTT
1 CTTTTT
31971298 ATCATTATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
8 23 0.51
9 19 0.42
10 3 0.07
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (8 bp):
CTTTTTTT
Found at i:31971269 original size:19 final size:20
Alignment explanation
Indices: 31971242--31971296 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 20
31971232 AATACATTAC
31971242 TTTTT-TTCTTTTTTTTC-T
1 TTTTTCTTCTTTTTTTTCTT
31971260 TTTTTCTTC-TTTTTTTCTT
1 TTTTTCTTCTTTTTTTTCTT
*
31971279 TTTTTCTTATTTTCTTTT
1 TTTTTCTTCTTTT-TTTT
31971297 TATCATTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 13 0.41
19 12 0.38
20 3 0.09
21 4 0.12
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTCTTCTTTTTTTTCTT
Found at i:31971271 original size:27 final size:27
Alignment explanation
Indices: 31971241--31971294 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
31971231 TAATACATTA
31971241 CTTTTTTTCTTTTTTTTCTT-TTTTCTT
1 CTTTTTTTC-TTTTTTTCTTATTTTCTT
31971268 CTTTTTTTCTTTTTTTCTTATTTTCTT
1 CTTTTTTTCTTTTTTTCTTATTTTCTT
31971295 TTTATCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (27 bp):
CTTTTTTTCTTTTTTTCTTATTTTCTT
Found at i:31971305 original size:17 final size:16
Alignment explanation
Indices: 31971267--31971305 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31971257 TCTTTTTTCT
* *
31971267 TCTTTTTTTCTTTTTT
1 TCTTATTTTCTTTTTA
31971283 TCTTATTTTCTTTTTA
1 TCTTATTTTCTTTTTA
31971299 TCATTAT
1 TC-TTAT
31971306 AATTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTTATTTTCTTTTTA
Found at i:31973983 original size:7 final size:7
Alignment explanation
Indices: 31973964--31974023 Score: 61
Period size: 7 Copynumber: 8.6 Consensus size: 7
31973954 AATATCCAAA
31973964 AATAAAGT
1 AATAAA-T
31973972 AATAAAT
1 AATAAAT
31973979 AATAAAAT
1 AAT-AAAT
*
31973987 TATAAAT
1 AATAAAT
*
31973994 TATAAAT
1 AATAAAT
*
31974001 TAT-AA-
1 AATAAAT
31974006 AATAAAT
1 AATAAAT
31974013 AATAAAT
1 AATAAAT
31974020 AATA
1 AATA
31974024 TAAATAATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
5 2 0.04
6 4 0.09
7 29 0.62
8 12 0.26
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (7 bp):
AATAAAT
Found at i:31973984 original size:15 final size:14
Alignment explanation
Indices: 31973964--31974023 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 14
31973954 AATATCCAAA
31973964 AATAAAGTAATAAAT
1 AATAAA-TAATAAAT
*
31973979 AATAAAATTATAAAT
1 AAT-AAATAATAAAT
* *
31973994 TATAAATTAT-AA-
1 AATAAATAATAAAT
31974006 AATAAATAATAAAT
1 AATAAATAATAAAT
31974020 AATA
1 AATA
31974024 TAAATAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 8 0.21
13 4 0.11
14 11 0.29
15 12 0.32
16 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (14 bp):
AATAAATAATAAAT
Done.