Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 9 of 259
Found at i:2565538 original size:9 final size:9
Alignment explanation
Indices: 2565524--2565557 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2565514 GTTTTCGAAT
*
2565524 TCGAATAAC
1 TCGAATAAA
*
2565533 TCGAATAAT
1 TCGAATAAA
2565542 TCGAATAAA
1 TCGAATAAA
2565551 TCGAATA
1 TCGAATA
2565558 TCAAACTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (9 bp):
TCGAATAAA
Found at i:2565542 original size:18 final size:18
Alignment explanation
Indices: 2565521--2565557 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2565511 TGAGTTTTCG
*
2565521 AATTCGAATAACTCGAAT
1 AATTCGAATAAATCGAAT
2565539 AATTCGAATAAATCGAAT
1 AATTCGAATAAATCGAAT
2565557 A
1 A
2565558 TCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (18 bp):
AATTCGAATAAATCGAAT
Found at i:2567031 original size:51 final size:51
Alignment explanation
Indices: 2566976--2567141 Score: 208
Period size: 57 Copynumber: 3.1 Consensus size: 51
2566966 GTCTTTTTCT
* * *
2566976 TTTTCTTTTTGGAGAAAACCACATTCATTTCCAAATGATTCCATTTCTCCA
1 TTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTCCATTTCTCCA
* *
2567027 TTTTCATTTTGGAGAAAACTATAATCATTTCCAAATGATTTCATTTCTCCATTTCCA
1 TTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTCCA-TT-T-C---TCCA
2567084 TTTTCATTTTGGAGAAAACCATAATCATTTCCAAAT-ATTTCCCATTTCTCCA
1 TTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGA-TT-CCATTTCTCCA
2567136 TTTTCA
1 TTTTCA
2567142 CCATTTCTAT
Statistics
Matches: 100, Mismatches: 7, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
51 38 0.38
52 12 0.12
53 1 0.01
54 1 0.01
55 1 0.01
56 2 0.02
57 43 0.43
58 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.43
Consensus pattern (51 bp):
TTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTCCATTTCTCCA
Found at i:2573163 original size:17 final size:15
Alignment explanation
Indices: 2573139--2573175 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
2573129 AATAAAGAAT
2573139 TAATTTTTTTAAAAA
1 TAATTTTTTTAAAAA
2573154 GTAATATTTTTTAAAAA
1 -TAAT-TTTTTTAAAAA
2573171 TAATT
1 TAATT
2573176 ATAATTTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 8 0.40
17 11 0.55
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
TAATTTTTTTAAAAA
Found at i:2578652 original size:73 final size:72
Alignment explanation
Indices: 2578575--2578757 Score: 186
Period size: 73 Copynumber: 2.5 Consensus size: 72
2578565 GGCTGTATAG
* * * * *
2578575 CGGGAAGCTCATAAGAGCCATAATCAGGAAGCTCATGCGAGCCAATAACAAGTAGCTCCAAAGAG
1 CGGGAAGCTCAAAAGAGCCATAATCAGGAAGCTCAAGCGAGCC-ATAACAAGAAGCCCCAAAGAA
2578640 CCATTAAT
65 CCATTAAT
*** * * * * * *
2578648 CGGGAAGCTCCGGATAGCCATATATCAGGAAGTTCAAGTGAGCCATATCGAGAAGCCCCGAAGAA
1 CGGGAAGCTCAAAAGAGCCATA-ATCAGGAAGCTCAAGCGAGCCATAACAAGAAGCCCCAAAGAA
2578713 CCATTAAT
65 CCATTAAT
* *
2578721 CAGGAAGCTCACAAAGAGCCATTAATCGGGAAGCTCA
1 CGGGAAGCTCA-AAAGAGCCA-TAATCAGGAAGCTCA
2578758 CGAAGAGCCA
Statistics
Matches: 87, Mismatches: 20, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
73 50 0.57
74 35 0.40
75 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.16
Consensus pattern (72 bp):
CGGGAAGCTCAAAAGAGCCATAATCAGGAAGCTCAAGCGAGCCATAACAAGAAGCCCCAAAGAAC
CATTAAT
Found at i:2578658 original size:25 final size:25
Alignment explanation
Indices: 2578628--2578777 Score: 112
Period size: 26 Copynumber: 6.0 Consensus size: 25
2578618 AATAACAAGT
2578628 AGCTCCAAAGAGCCATTAATCGGGA
1 AGCTCCAAAGAGCCATTAATCGGGA
** * *
2578653 AGCTCCGGATAGCCA-TATATCAGGA
1 AGCTCCAAAGAGCCATTA-ATCGGGA
* * *
2578678 AG-TTCAAGTGAGCCA-T-ATCGAGA
1 AGCTCCAA-AGAGCCATTAATCGGGA
* * * *
2578701 AGCCCCGAAGAACCATTAATCAGGA
1 AGCTCCAAAGAGCCATTAATCGGGA
2578726 AGCTCACAAAGAGCCATTAATCGGGA
1 AGCTC-CAAAGAGCCATTAATCGGGA
*
2578752 AGCTCACGAAGAGCCATATAA-CGGGA
1 AGCTC-CAAAGAGCCAT-TAATCGGGA
2578778 CACTCATAAG
Statistics
Matches: 95, Mismatches: 23, Indels: 13
0.73 0.18 0.10
Matches are distributed among these distances:
23 12 0.13
24 7 0.07
25 35 0.37
26 38 0.40
27 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (25 bp):
AGCTCCAAAGAGCCATTAATCGGGA
Found at i:2583214 original size:5 final size:5
Alignment explanation
Indices: 2583206--2583237 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
2583196 AATCTTTTAA
2583206 TTATT TTATT TTATT TTATT TTATTT TTATT T
1 TTATT TTATT TTATT TTATT TTA-TT TTATT T
2583238 CAAAAATCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:2584668 original size:22 final size:23
Alignment explanation
Indices: 2584641--2584694 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
2584631 AGCTTACCGA
* *
2584641 TTTCAGCTCGTATGAACTTACTG
1 TTTCAGCTCGAAAGAACTTACTG
* *
2584664 -TTCAGATCGAAAGAGCTTACTG
1 TTTCAGCTCGAAAGAACTTACTG
2584686 TTTCAGCTC
1 TTTCAGCTC
2584695 AATAGAGTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (23 bp):
TTTCAGCTCGAAAGAACTTACTG
Found at i:2584701 original size:23 final size:23
Alignment explanation
Indices: 2584629--2584733 Score: 92
Period size: 23 Copynumber: 4.6 Consensus size: 23
2584619 TCATCTCATA
* *
2584629 AGAGCTTACCGATTTCAGCTC-GT
1 AGAGCTTACTG-TTTCAGCTCAAT
* *
2584652 ATGAACTTACTG-TTCAGATCGAA-
1 A-GAGCTTACTGTTTCAGCTC-AAT
2584675 AGAGCTTACTGTTTCAGCTCAAT
1 AGAGCTTACTGTTTCAGCTCAAT
* *
2584698 AGAG-TGTACAGTTTCAGCTCATT
1 AGAGCT-TACTGTTTCAGCTCAAT
2584721 AGAGCTTACTGTT
1 AGAGCTTACTGTT
2584734 CATCAGCTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
22 19 0.29
23 38 0.58
24 9 0.14
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (23 bp):
AGAGCTTACTGTTTCAGCTCAAT
Found at i:2586107 original size:11 final size:11
Alignment explanation
Indices: 2586091--2586115 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2586081 ATTTTTTTCC
2586091 AAAAATAAAAT
1 AAAAATAAAAT
2586102 AAAAATAAAAT
1 AAAAATAAAAT
2586113 AAA
1 AAA
2586116 GTAAGTATTA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:2587823 original size:41 final size:41
Alignment explanation
Indices: 2587775--2587855 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
2587765 ATAGGACAAG
2587775 TCTAAATTTTGCTTGTCTAGAAATAAGGTCTTTAGGATCCA
1 TCTAAATTTTGCTTGTCTAGAAATAAGGTCTTTAGGATCCA
2587816 TCTAAATTTTGCTTGTCTAGAAATAAGGTCTTTAGGATCC
1 TCTAAATTTTGCTTGTCTAGAAATAAGGTCTTTAGGATCC
2587856 TTATAGTGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (41 bp):
TCTAAATTTTGCTTGTCTAGAAATAAGGTCTTTAGGATCCA
Found at i:2592876 original size:12 final size:12
Alignment explanation
Indices: 2592859--2592897 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2592849 CGGCCCGCCC
2592859 ATATTAATTTTT
1 ATATTAATTTTT
*
2592871 ATATTATTTTTT
1 ATATTAATTTTT
*
2592883 ATATT-ATTTTA
1 ATATTAATTTTT
2592894 ATAT
1 ATAT
2592898 ATATATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:2593059 original size:29 final size:30
Alignment explanation
Indices: 2593017--2593078 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
2593007 ACTTAACAAG
* * *
2593017 CAAATGTTTCTAAAA-AATAACAAAATTAA
1 CAAATGTCTATAAAATAATAAAAAAATTAA
2593046 CAAATGTCTATAAAATAATAAAAAAATTAA
1 CAAATGTCTATAAAATAATAAAAAAATTAA
2593076 CAA
1 CAA
2593079 TAAAATAAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.61, C:0.10, G:0.03, T:0.26
Consensus pattern (30 bp):
CAAATGTCTATAAAATAATAAAAAAATTAA
Found at i:2593133 original size:22 final size:22
Alignment explanation
Indices: 2593108--2593150 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2593098 TATCTAAACA
2593108 ATAAAAACAAAATAGTAGCAAC
1 ATAAAAACAAAATAGTAGCAAC
* **
2593130 ATAATAGTAAAATAGTAGCAA
1 ATAAAAACAAAATAGTAGCAA
2593151 AATAGAGAGA
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:0.09, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAAAAACAAAATAGTAGCAAC
Found at i:2593154 original size:11 final size:11
Alignment explanation
Indices: 2593115--2593155 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
2593105 ACAATAAAAA
2593115 CAAAATAGTAG
1 CAAAATAGTAG
* *
2593126 CAACATAATAG
1 CAAAATAGTAG
*
2593137 TAAAATAGTAG
1 CAAAATAGTAG
2593148 CAAAATAG
1 CAAAATAG
2593156 AGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:2593163 original size:22 final size:22
Alignment explanation
Indices: 2593116--2593165 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2593106 CAATAAAAAC
* *
2593116 AAAATAGTAGCAACATAATAGT
1 AAAATAGTAGCAAAATAAGAGT
2593138 AAAATAGTAGCAAAATAGAGAG-
1 AAAATAGTAGCAAAATA-AGAGT
2593160 AAAATA
1 AAAATA
2593166 ATAAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.60, C:0.06, G:0.16, T:0.18
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGT
Found at i:2604376 original size:88 final size:88
Alignment explanation
Indices: 2604222--2604401 Score: 324
Period size: 88 Copynumber: 2.0 Consensus size: 88
2604212 CTTCTTTACC
* *
2604222 CTTGGCAAGTAACTCAAACATTGACAATCTTCTATTTCCTTTGTGCCACTTCTTAGGAGTCCCAT
1 CTTGGCAAGTAACTCAAACATTGACAATCTTCTATTTCCTTTGTGCCACTTCCTAGGAGTCACAT
2604287 ATGTAAAGATTTCAATAAAGAGA
66 ATGTAAAGATTTCAATAAAGAGA
*
2604310 CTTGGCAAGTAACTCAAACTTTGACAATCTTCTATTTCCTTTGTGCCACTTCCTAGGAGTCACAT
1 CTTGGCAAGTAACTCAAACATTGACAATCTTCTATTTCCTTTGTGCCACTTCCTAGGAGTCACAT
*
2604375 ATGTAAAGATTTTAATAAAGAGA
66 ATGTAAAGATTTCAATAAAGAGA
2604398 CTTG
1 CTTG
2604402 AAGAAGTTGA
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (88 bp):
CTTGGCAAGTAACTCAAACATTGACAATCTTCTATTTCCTTTGTGCCACTTCCTAGGAGTCACAT
ATGTAAAGATTTCAATAAAGAGA
Found at i:2611109 original size:25 final size:25
Alignment explanation
Indices: 2611075--2611128 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
2611065 CTAGAATACT
2611075 AATGGATGCCATGAAAATGGTTCTC
1 AATGGATGCCATGAAAATGGTTCTC
2611100 AATGGATGCCATGAAAATGGTTCTC
1 AATGGATGCCATGAAAATGGTTCTC
2611125 AATG
1 AATG
2611129 AATGAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (25 bp):
AATGGATGCCATGAAAATGGTTCTC
Found at i:2620536 original size:28 final size:29
Alignment explanation
Indices: 2620496--2620550 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
2620486 GCAATTACTT
* *
2620496 GTTAACATTTAAC-AA-ATTAAAAGAATA
1 GTTAACATATAACTAAGATAAAAAGAATA
2620523 GTTAGACATATAACTAAGATAAAAAGAA
1 GTTA-ACATATAACTAAGATAAAAAGAA
2620551 ATTTTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 8 0.35
29 2 0.09
30 9 0.39
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.25
Consensus pattern (29 bp):
GTTAACATATAACTAAGATAAAAAGAATA
Found at i:2620676 original size:22 final size:24
Alignment explanation
Indices: 2620651--2620699 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2620641 GTATAATGAG
*
2620651 AATAATAA-TATAATATAATT-TA
1 AATAATAATTAAAATATAATTATA
2620673 AATAATAATTTAAAATATAATTATA
1 AATAATAA-TTAAAATATAATTATA
2620698 AA
1 AA
2620700 CATATAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
24 11 0.48
25 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATAATAATTAAAATATAATTATA
Found at i:2620682 original size:12 final size:12
Alignment explanation
Indices: 2620651--2620699 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
2620641 GTATAATGAG
*
2620651 AATAATAATAT-
1 AATAATAATTTA
2620662 AAT-ATAATTTA
1 AATAATAATTTA
2620673 AATAATAATTTA
1 AATAATAATTTA
2620685 AA-ATATAATTATA
1 AATA-ATAATT-TA
2620698 AA
1 AA
2620700 CATATAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 6 0.18
11 7 0.21
12 16 0.48
13 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATAATAATTTA
Found at i:2624144 original size:24 final size:24
Alignment explanation
Indices: 2624102--2624151 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2624092 TTCCAGAAGG
* *
2624102 TAAAAGTGGGGCCTATGTATTTTT
1 TAAAAGTGGGCCCTATGTACTTTT
2624126 TAAAAGTGGGCCC-ATTGTACTTTT
1 TAAAAGTGGGCCCTA-TGTACTTTT
2624150 TA
1 TA
2624152 GGGATTACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (24 bp):
TAAAAGTGGGCCCTATGTACTTTT
Found at i:2628880 original size:40 final size:39
Alignment explanation
Indices: 2628820--2628954 Score: 162
Period size: 40 Copynumber: 3.4 Consensus size: 39
2628810 TAAATAACAG
* * * * *
2628820 GCTTTGTGCTAGTATATTTATCGGGCTTTGTGCTTAGCA
1 GCTTTGTGCTGGTGTGTTTATTGGGCTTTGTGCCTAGCA
* *
2628859 GACTTTGTGCTGGTGTGTTTATTGGGCTTTATGCCTAGTA
1 G-CTTTGTGCTGGTGTGTTTATTGGGCTTTGTGCCTAGCA
*
2628899 GGCTTTATGCTGGTGTGTTTATTGGGCTTTGTGCCTAGCA
1 -GCTTTGTGCTGGTGTGTTTATTGGGCTTTGTGCCTAGCA
*
2628939 TGCCTTGTGCTGGTGT
1 -GCTTTGTGCTGGTGT
2628955 TGTCTATCAG
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 79 0.98
41 1 0.01
ACGTcount: A:0.11, C:0.15, G:0.30, T:0.44
Consensus pattern (39 bp):
GCTTTGTGCTGGTGTGTTTATTGGGCTTTGTGCCTAGCA
Found at i:2630779 original size:33 final size:33
Alignment explanation
Indices: 2630719--2630782 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
2630709 GAACTATCTT
* ** * *
2630719 TGTGTTTATTGTCCTAGTAGACTTTCTCTATTC
1 TGTGTTTATTGTCCCAACAAACATTCTCTATTC
2630752 TGTGTTTATTGTCCCAACAAACATTCTCTAT
1 TGTGTTTATTGTCCCAACAAACATTCTCTAT
2630783 GGGTTTCATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.47
Consensus pattern (33 bp):
TGTGTTTATTGTCCCAACAAACATTCTCTATTC
Found at i:2631483 original size:20 final size:20
Alignment explanation
Indices: 2631458--2631497 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2631448 CATGACGGAA
2631458 GCAGC-AACAGAAACAGAAAC
1 GCAGCAAACAGAAACA-AAAC
*
2631478 GCAGCAAACAGTAACAAAAC
1 GCAGCAAACAGAAACAAAAC
2631498 AACAATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.25, G:0.17, T:0.03
Consensus pattern (20 bp):
GCAGCAAACAGAAACAAAAC
Found at i:2632629 original size:18 final size:18
Alignment explanation
Indices: 2632597--2632661 Score: 85
Period size: 18 Copynumber: 3.4 Consensus size: 18
2632587 TTATAACTAT
*
2632597 TTATATATATCTTTATATC
1 TTAT-TATATATTTATATC
2632616 TTATTATATATTTATATC
1 TTATTATATATTTATATC
2632634 TTATTATATATCTATATATC
1 TTATTATATAT-T-TATATC
*
2632654 TTTTTATA
1 TTATTATA
2632662 AACATATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
18 24 0.57
19 5 0.12
20 13 0.31
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATATATTTATATC
Found at i:2632840 original size:30 final size:30
Alignment explanation
Indices: 2632768--2632840 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
2632758 TACGTCTATT
* *
2632768 TTCTTTTATATATACATATACATACTTACA
1 TTCTTTTATTTTTACATATACATACTTACA
* *
2632798 TTGTTTTA-TTTTACGATATACATACTTATA
1 TTCTTTTATTTTTAC-ATATACATACTTACA
2632828 -TCTTTTATTTTTA
1 TTCTTTTATTTTTA
2632841 TGTAATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 10 0.28
30 26 0.72
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (30 bp):
TTCTTTTATTTTTACATATACATACTTACA
Found at i:2634799 original size:19 final size:20
Alignment explanation
Indices: 2634759--2634802 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
2634749 GTCTCTTTAG
* *
2634759 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
2634778 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
2634797 GCATTA
1 GCATTA
2634803 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:2638314 original size:15 final size:15
Alignment explanation
Indices: 2638294--2638326 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2638284 GAAGAATAAG
2638294 ATGAAAAAA-TGAAAA
1 ATGAAAAAAGT-AAAA
2638309 ATGAAAAAAGTAAAA
1 ATGAAAAAAGTAAAA
2638324 ATG
1 ATG
2638327 GAGAGGCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (15 bp):
ATGAAAAAAGTAAAA
Found at i:2639708 original size:83 final size:82
Alignment explanation
Indices: 2639602--2639878 Score: 267
Period size: 83 Copynumber: 3.3 Consensus size: 82
2639592 TAAAGAAGCA
2639602 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAGGATAGTAATCCTATCTCCTTGAGATTA
1 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAA-GATAGTAATCCTATCTCCTTGAGATTA
2639667 CAATGGAGCGGATTAAAG
65 CAATGGAGCGGATTAAAG
* ** * * * * *
2639685 GATCTTATCTCTCTGA-AGTTACAGTAGAGAAGATC-ACATCAG--GTCTTATCTCCCTGAGATT
1 GATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCAAGAT-AGTAATCCTATCTCCTTGAGATT
* * * * **
2639746 ATAGTGGAACAGACCAAAG
64 ACAATGGAGCGGATTAAAG
*
2639765 AATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGGTCAAAGATAGTAATCCTATCTCCTT
1 -------GATCTTATCTCCCTGAGATTACAGCGGAGCAGATC-AAGATAGTAATCCTATCTCCTT
2639830 GAGATTACAATGGAGCGGATTAAAG
58 GAGATTACAATGGAGCGGATTAAAG
*
2639855 GATCTTATCTCTCTGA-AGTTACAG
1 GATCTTATCTCCCTGAGA-TTACAG
2639879 TAGAGAAGAT
Statistics
Matches: 149, Mismatches: 30, Indels: 30
0.71 0.14 0.14
Matches are distributed among these distances:
80 29 0.19
81 2 0.01
82 5 0.03
83 50 0.34
87 28 0.19
88 3 0.02
89 3 0.02
90 29 0.19
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (82 bp):
GATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAGATAGTAATCCTATCTCCTTGAGATTAC
AATGGAGCGGATTAAAG
Found at i:2639810 original size:46 final size:43
Alignment explanation
Indices: 2639576--2640096 Score: 292
Period size: 44 Copynumber: 12.1 Consensus size: 43
2639566 CCTTCATTGG
* * * *
2639576 TTACAGTGGAGCTGGTTAAAGAAGCAGATCTTATCTCCCTGAGA
1 TTACAGTGGAGCAGATCAAAG-ATCAGATCTTATCTCCCTGAGA
* * * *
2639620 TTACAGCGGAGCAGATCAAGGAT-AGTAATCCTATCTCCTTGAGA
1 TTACAGTGGAGCAGATCAAAGATCAG--ATCTTATCTCCCTGAGA
* * * *
2639664 TTACAATGGAGCGGATTAAAG----GATCTTATCTCTCTGA-A
1 TTACAGTGGAGCAGATCAAAGATCAGATCTTATCTCCCTGAGA
* * * *
2639702 GTTACAGTAGAGAAGATC--ACATCAGGTCTTATCTCCCTGAGA
1 -TTACAGTGGAGCAGATCAAAGATCAGATCTTATCTCCCTGAGA
* * *
2639744 TTATAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGA
1 TTACAGTGGAGCAGATCAAAG-A--TCAGATCTTATCTCCCTGAGA
* * * *
2639790 TTACAGCGGAGCAGGTCAAAGAT-AGTAATCCTATCTCCTTGAGA
1 TTACAGTGGAGCAGATCAAAGATCAG--ATCTTATCTCCCTGAGA
* * * *
2639834 TTACAATGGAGCGGATTAAAG----GATCTTATCTCTCTGA-A
1 TTACAGTGGAGCAGATCAAAGATCAGATCTTATCTCCCTGAGA
* * * *
2639872 GTTACAGTAGAGAAGATC--ACATCAGGTCTTATCTCCCTGAGA
1 -TTACAGTGGAGCAGATCAAAGATCAGATCTTATCTCCCTGAGA
** * * *
2639914 TTACAGTGGAATAGACCAAAGAATTTCGGATCTTATCTCCCTGAGG
1 TTACAGTGGAGCAGATCAAAG-A--TCAGATCTTATCTCCCTGAGA
** *
2639960 TTACAGTGGAGCAGATTGAAGCCA-GAGATCTTATCTCCCTGAGA
1 TTACAGTGGAGCAGATCAAAG--ATCAGATCTTATCTCCCTGAGA
* * *
2640004 TTACAGCGGAGCAGATCGAAA-A-CACTATCCTATCTCCCTGA-A
1 TTACAGTGGAGCAGATC-AAAGATCA-GATCTTATCTCCCTGAGA
* * * * *
2640046 GTTACAGTGGAGCGGATTAAA-ATAAAGGATCTTATCTCTCTGAGG
1 -TTACAGTGGAGCAGATCAAAGAT-CA-GATCTTATCTCCCTGAGA
2640091 TTACAG
1 TTACAG
2640097 CAGAGTAGAT
Statistics
Matches: 358, Mismatches: 86, Indels: 66
0.70 0.17 0.13
Matches are distributed among these distances:
37 2 0.01
38 2 0.01
39 48 0.13
41 55 0.15
42 13 0.04
43 32 0.09
44 132 0.37
45 3 0.01
46 70 0.20
47 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (43 bp):
TTACAGTGGAGCAGATCAAAGATCAGATCTTATCTCCCTGAGA
Found at i:2639882 original size:170 final size:170
Alignment explanation
Indices: 2639600--2639975 Score: 689
Period size: 170 Copynumber: 2.2 Consensus size: 170
2639590 GTTAAAGAAG
*
2639600 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAGGATAGTAATCCTATCTCCTTGAGAT
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGAT
2639665 TACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTC
66 TACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTC
*
2639730 TTATCTCCCTGAGATTATAGTGGAACAGACCAAAGAATTT
131 TTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTT
*
2639770 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGGTCAAAGATAGTAATCCTATCTCCTTGAGAT
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGAT
2639835 TACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTC
66 TACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTC
*
2639900 TTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTT
131 TTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTT
* * *
2639940 CGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGAT
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGAT
2639976 TGAAGCCAGA
Statistics
Matches: 198, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
170 198 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (170 bp):
CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGAT
TACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTC
TTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTT
Found at i:2640038 original size:87 final size:87
Alignment explanation
Indices: 2639947--2640108 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 87
2639937 TTTCGGATCT
* * * *
2639947 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGC-CAGAGATCTTATCTCCCTGAGATTACAGC
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAG-GATCTTATCTCCCTGAGATTACAGC
*
2640011 GGAGCAGATCGAAAACACTATCC
65 AGAGCAGATCGAAAACACTATCC
* * * *
2640034 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCA
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
*
2640099 GAGTAGATCG
66 GAGCAGATCG
2640109 CATCAGGTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
87 62 0.97
88 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (87 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
GAGCAGATCGAAAACACTATCC
Found at i:2640212 original size:218 final size:213
Alignment explanation
Indices: 2639771--2640212 Score: 464
Period size: 218 Copynumber: 2.0 Consensus size: 213
2639761 AAAGAATTTC
* * * *
2639771 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGGTCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
*
2639836 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
66 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAGGTCT
* * ** * * *
2639901 TATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTCGGATCTTATCTCCCTGAGGTTACAG
131 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAAATAAGGA-CGTATCTCCCTAAAGTTACAG
* ** *
2639966 TGGAGCAGATTGAAGCCAG
195 CGGAGCAGACAGAAGACAG
2639985 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAA-ACACT-ATCCTATCTCCCTGA-AG
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATC-AAAGACACTAATCCTATCTCCCTGAGA-
* * * *
2640047 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCAT
64 TTACAATGGAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACAT
* * * * *
2640112 CAGGTCTTATTTCCCTGAAGA-TGCAGTGGAACAGACTGAAA-ACAATAAGG-CGTGTCTCCTTA
124 CAGGTCTTATCTCCCTG-AGATTACAGTGGAACAGAC-CAAAGA-AATAAGGACGTATCTCCCTA
** * *
2640174 AAGTTGTAGCGGAGCGGACAGAAGATAG
186 AAGTTACAGCGGAGCAGACAGAAGACAG
*
2640202 TGATTCTTATC
1 AGA-TCTTATC
2640213 ATGTCTAATC
Statistics
Matches: 187, Mismatches: 30, Indels: 18
0.80 0.13 0.08
Matches are distributed among these distances:
212 1 0.01
213 28 0.15
214 39 0.21
215 3 0.02
217 29 0.16
218 77 0.41
219 10 0.05
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (213 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAGGTCT
TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAAATAAGGACGTATCTCCCTAAAGTTACAGC
GGAGCAGACAGAAGACAG
Found at i:2640484 original size:86 final size:86
Alignment explanation
Indices: 2640293--2640565 Score: 361
Period size: 86 Copynumber: 3.2 Consensus size: 86
2640283 GGTTGTGATA
* ** * * *
2640293 GAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAA
1 GAGCTGGTTAAAGA-AGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-A-ACAAA
*
2640358 -CCTTGCCTCTC-TCGGTTGTAGTG
63 GCCTTGCCTC-CATCGGTTGCAGTG
*
2640381 GAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAAACAAAGCC
1 GAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCC
* *
2640446 TTGCATCCATCGATTGCAGTG
66 TTGCCTCCATCGGTTGCAGTG
* * * *
2640467 GAGCTAGTTAAAGAAGCAGATCTTGCCTTCCTGCATTAACAGCAAAGTAGATCAAAAACAAAGCC
1 GAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCC
*
2640532 TTGCCTCCATCGGTTGCATTG
66 TTGCCTCCATCGGTTGCAGTG
2640553 GAGCTGGTTAAAG
1 GAGCTGGTTAAAG
2640566 GTTACAGATT
Statistics
Matches: 164, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
85 6 0.04
86 109 0.66
87 36 0.22
88 13 0.08
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.24
Consensus pattern (86 bp):
GAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCC
TTGCCTCCATCGGTTGCAGTG
Found at i:2640748 original size:44 final size:43
Alignment explanation
Indices: 2640699--2640816 Score: 114
Period size: 44 Copynumber: 2.7 Consensus size: 43
2640689 TGGAAATTAC
* * *
2640699 AGATCTTGTCCCCCTGAAGTTACAGTGGAGTAGATTGAAGCCA
1 AGATCTTATCCCCCTGAAGTTACAGTGGAGTAGATCGAAGACA
* *
2640742 GAGATCTTATCTCCCC-G-AGATTACAGCGGAGCAGATCGAAGACA
1 -AGATCTTATC-CCCCTGAAG-TTACAGTGGAGTAGATCGAAGACA
** * *
2640786 CTATCCTATCTCCCTGAAGTTACAGTGGAGT
1 AGATCTTATCCCCCTGAAGTTACAGTGGAGT
2640817 GGGTTAAAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
42 3 0.05
43 20 0.34
44 32 0.54
45 4 0.07
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (43 bp):
AGATCTTATCCCCCTGAAGTTACAGTGGAGTAGATCGAAGACA
Found at i:2640809 original size:43 final size:44
Alignment explanation
Indices: 2640710--2640815 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 44
2640700 GATCTTGTCC
* * * *
2640710 CCCTGAAGTTACAGTGGAGTAGATTGAAGCCAGAGATCTTATCT
1 CCCTGAAGTTACAGTGGAGCAGATCGAAGACAGAGATCCTATCT
* * **
2640754 CCCCG-AGATTACAGCGGAGCAGATCGAAGACA-CTATCCTATCT
1 CCCTGAAG-TTACAGTGGAGCAGATCGAAGACAGAGATCCTATCT
2640797 CCCTGAAGTTACAGTGGAG
1 CCCTGAAGTTACAGTGGAG
2640816 TGGGTTAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
43 24 0.48
44 26 0.52
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.23
Consensus pattern (44 bp):
CCCTGAAGTTACAGTGGAGCAGATCGAAGACAGAGATCCTATCT
Found at i:2641375 original size:20 final size:20
Alignment explanation
Indices: 2641350--2641389 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2641340 CATGACGGAA
2641350 GCAGC-AACAGAAACAGAAAC
1 GCAGCAAACAGAAACA-AAAC
*
2641370 GCAGCAAACAGTAACAAAAC
1 GCAGCAAACAGAAACAAAAC
2641390 AACAATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.25, G:0.17, T:0.03
Consensus pattern (20 bp):
GCAGCAAACAGAAACAAAAC
Found at i:2642525 original size:18 final size:18
Alignment explanation
Indices: 2642493--2642557 Score: 85
Period size: 18 Copynumber: 3.4 Consensus size: 18
2642483 TTATAACTAT
*
2642493 TTATATATATCTTTATATC
1 TTAT-TATATATTTATATC
2642512 TTATTATATATTTATATC
1 TTATTATATATTTATATC
2642530 TTATTATATATCTATATATC
1 TTATTATATAT-T-TATATC
*
2642550 TTTTTATA
1 TTATTATA
2642558 AACATATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
18 24 0.57
19 5 0.12
20 13 0.31
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATATATTTATATC
Found at i:2642736 original size:30 final size:30
Alignment explanation
Indices: 2642664--2642736 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
2642654 TACGTCTATT
* *
2642664 TTCTTTTATATATACATATACATACTTACA
1 TTCTTTTATTTTTACATATACATACTTACA
* *
2642694 TTGTTTTA-TTTTACGATATACATACTTATA
1 TTCTTTTATTTTTAC-ATATACATACTTACA
2642724 -TCTTTTATTTTTA
1 TTCTTTTATTTTTA
2642737 TGTAATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 10 0.28
30 26 0.72
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (30 bp):
TTCTTTTATTTTTACATATACATACTTACA
Found at i:2647523 original size:32 final size:32
Alignment explanation
Indices: 2647476--2647539 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
2647466 TTAAAGGGAG
** *
2647476 ATAGTTTGTTGTGGATAATATAGTAAGAGCTC
1 ATAGTTTGTCATGGATAATAGAGTAAGAGCTC
*
2647508 ATAGTTTGTCATGGATATTAGAGTAAGAGCTC
1 ATAGTTTGTCATGGATAATAGAGTAAGAGCTC
2647540 CTTTTAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (32 bp):
ATAGTTTGTCATGGATAATAGAGTAAGAGCTC
Found at i:2648145 original size:43 final size:43
Alignment explanation
Indices: 2648097--2648183 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
2648087 TCCCGTCTTA
2648097 AAGGCATTATATAATCGATCTAAATGAAACTTGTTTAGTGGTT
1 AAGGCATTATATAATCGATCTAAATGAAACTTGTTTAGTGGTT
2648140 AAGGCATTATATAATCGATCTAAATGAAACTTGTTTAGTGGTT
1 AAGGCATTATATAATCGATCTAAATGAAACTTGTTTAGTGGTT
2648183 A
1 A
2648184 TGTCATAGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (43 bp):
AAGGCATTATATAATCGATCTAAATGAAACTTGTTTAGTGGTT
Found at i:2652823 original size:22 final size:22
Alignment explanation
Indices: 2652795--2652836 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
2652785 ATTATATTAA
2652795 GAGTTAGATTGCATTTTGCTAG
1 GAGTTAGATTGCATTTTGCTAG
2652817 GAGTTAGATTGCATTTTGCT
1 GAGTTAGATTGCATTTTGCT
2652837 CTCTTTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.26, T:0.43
Consensus pattern (22 bp):
GAGTTAGATTGCATTTTGCTAG
Found at i:2655371 original size:30 final size:29
Alignment explanation
Indices: 2655299--2655382 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
2655289 AAAATTATTA
2655299 TAAT-ATTATTATAATTTTTTATAACATTT
1 TAATAATT-TTATAATTTTTTATAACATTT
* * * * *
2655328 AAAAAAATCTATAATTTTTCTATTACATTT
1 TAATAATTTTATAATTTTT-TATAACATTT
2655358 TAATAATTTTATAATTTATTTATAA
1 TAATAATTTTATAATTT-TTTATAA
2655383 TTTTCTAACA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
29 12 0.29
30 28 0.67
31 2 0.05
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.54
Consensus pattern (29 bp):
TAATAATTTTATAATTTTTTATAACATTT
Found at i:2655419 original size:24 final size:23
Alignment explanation
Indices: 2655392--2655455 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
2655382 ATTTTCTAAC
2655392 AAAATTTTAATAATTTATATTTTT
1 AAAATTTTAATAATTT-TATTTTT
2655416 AAAA--TT-AT-A-TTTATTTTT
1 AAAATTTTAATAATTTTATTTTT
2655434 -AAATTTTAATAACTTTTTATTT
1 AAAATTTTAATAA--TTTTATTT
2655456 AAATAATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
17 3 0.09
18 7 0.21
19 4 0.12
20 3 0.09
21 3 0.09
22 2 0.06
24 11 0.33
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
AAAATTTTAATAATTTTATTTTT
Found at i:2655425 original size:14 final size:16
Alignment explanation
Indices: 2655396--2655427 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
2655386 TCTAACAAAA
2655396 TTTTAATAATTTATAT
1 TTTTAATAATTTATAT
2655412 TTTTAA-AA-TTATAT
1 TTTTAATAATTTATAT
2655426 TT
1 TT
2655428 ATTTTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAATAATTTATAT
Found at i:2656448 original size:43 final size:43
Alignment explanation
Indices: 2656383--2656486 Score: 173
Period size: 43 Copynumber: 2.5 Consensus size: 43
2656373 TCAAAGTAAG
2656383 AATAAAATAATTAAA--AA--T-AATTTTATTTCAAAATAAAA
1 AATAAAATAATTAAATTAAGGTGAATTTTATTTCAAAATAAAA
2656421 AATAAAATAATTAAATTAAGGTGAATTTTATTTCAAAATAAAA
1 AATAAAATAATTAAATTAAGGTGAATTTTATTTCAAAATAAAA
2656464 AATAAAATAATTAAATTAAGGTG
1 AATAAAATAATTAAATTAAGGTG
2656487 TTGTTTTTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
38 15 0.25
40 2 0.03
42 1 0.02
43 43 0.70
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.34
Consensus pattern (43 bp):
AATAAAATAATTAAATTAAGGTGAATTTTATTTCAAAATAAAA
Found at i:2664078 original size:21 final size:21
Alignment explanation
Indices: 2664038--2664091 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
2664028 TTATTTAAAA
*
2664038 AATATTTTTTAGATAATTTT-
1 AATATTTTTTAAATAATTTTG
*
2664058 AATAATTTTTAAATAACTTTTG
1 AATATTTTTTAAATAA-TTTTG
2664080 AAT-TTTTTTAAA
1 AATATTTTTTAAA
2664092 ATTTTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.48
21 12 0.41
22 3 0.10
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (21 bp):
AATATTTTTTAAATAATTTTG
Found at i:2670537 original size:43 final size:43
Alignment explanation
Indices: 2670472--2670553 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
2670462 AACGAAGGAA
* * *
2670472 GTATTAGCAGCTTGCTTGCACCGGTTAGTTGTTTATCCACACT
1 GTATTAGCAGCTTGCTTACACCGATTAGTGGTTTATCCACACT
*
2670515 GTATTAGTAGCTTG-TCTACACCGATTAGTGGTTTATCCA
1 GTATTAGCAGCTTGCT-TACACCGATTAGTGGTTTATCCA
2670554 TACCTATTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.03
43 33 0.97
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (43 bp):
GTATTAGCAGCTTGCTTACACCGATTAGTGGTTTATCCACACT
Found at i:2672125 original size:18 final size:20
Alignment explanation
Indices: 2672093--2672139 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
2672083 AGTGAGGGAT
* *
2672093 AAAAGCATAGCAATGA-TTA
1 AAAAGCATTGCAATGAGTGA
2672112 AAAAGCATTG-AATGAGTGA
1 AAAAGCATTGCAATGAGTGA
2672131 AAAA-CATTG
1 AAAAGCATTG
2672140 TGGGTGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.51, C:0.09, G:0.19, T:0.21
Consensus pattern (20 bp):
AAAAGCATTGCAATGAGTGA
Found at i:2675677 original size:21 final size:21
Alignment explanation
Indices: 2675653--2675697 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2675643 AAAATTTATA
* *
2675653 TTTCTTTAC-ATTTTGTATAAT
1 TTTC-TTACGATTTTATAAAAT
2675674 TTTCTTACGATTTTATAAAAT
1 TTTCTTACGATTTTATAAAAT
2675695 TTT
1 TTT
2675698 ATAAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTCTTACGATTTTATAAAAT
Found at i:2675698 original size:10 final size:10
Alignment explanation
Indices: 2675683--2675710 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2675673 TTTTCTTACG
2675683 ATTTTATAAA
1 ATTTTATAAA
2675693 ATTTTATAAA
1 ATTTTATAAA
2675703 ATTTTATA
1 ATTTTATA
2675711 TTTCTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATTTTATAAA
Found at i:2675734 original size:10 final size:9
Alignment explanation
Indices: 2675684--2675853 Score: 80
Period size: 9 Copynumber: 18.6 Consensus size: 9
2675674 TTTCTTACGA
*
2675684 TTTTATAAAA
1 TTTTAT-AAT
*
2675694 TTTTATAAAA
1 TTTTAT-AAT
2675704 TTTTAT-AT
1 TTTTATAAT
*
2675712 TTCTAT-AT
1 TTTTATAAT
2675720 ATTTTATAACT
1 -TTTTATAA-T
*
2675731 TTTTATGAT
1 TTTTATAAT
*
2675740 TTTTATAAAA
1 TTTTAT-AAT
*
2675750 TTTTACAAT
1 TTTTATAAT
*
2675759 TTTTCTAAT
1 TTTTATAAT
*
2675768 TTTTATAAA
1 TTTTATAAT
2675777 TTTTA-AAT
1 TTTTATAAT
*
2675785 ATTTA-AAT
1 TTTTATAAT
*
2675793 TTTTATTAAAA
1 TTTTA-T-AAT
*
2675804 TTTAATAAT
1 TTTTATAAT
* **
2675813 ATTTATAGC
1 TTTTATAAT
*
2675822 TTTTATTGAT
1 TTTTA-TAAT
* *
2675832 TTTAAT-TT
1 TTTTATAAT
2675840 TTTTATAAT
1 TTTTATAAT
2675849 TTTTA
1 TTTTA
2675854 ATAAAAGCAA
Statistics
Matches: 121, Mismatches: 30, Indels: 19
0.71 0.18 0.11
Matches are distributed among these distances:
8 27 0.22
9 51 0.42
10 36 0.30
11 7 0.06
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (9 bp):
TTTTATAAT
Found at i:2675750 original size:56 final size:59
Alignment explanation
Indices: 2675624--2675754 Score: 155
Period size: 58 Copynumber: 2.3 Consensus size: 59
2675614 TGATGCGATA
** * * *
2675624 ATTTTTATAACTTTTTTTCAAAATTTATATTTCTTTACATTTTGTATAATTTTCTTACG
1 ATTTTTATAAAATTTTATCAAAATTTATATTTCTATACATTTTGTATAACTTTCTTACG
* *
2675683 A-TTTTATAAAATTTTAT-AAAATTTTATATTTCTATATA-TTT-TATAACTTT-TTATG
1 ATTTTTATAAAATTTTATCAAAA-TTTATATTTCTATACATTTTGTATAACTTTCTTACG
2675738 ATTTTTATAAAATTTTA
1 ATTTTTATAAAATTTTA
2675755 CAATTTTTCT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
55 5 0.08
56 23 0.37
57 7 0.11
58 27 0.43
59 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (59 bp):
ATTTTTATAAAATTTTATCAAAATTTATATTTCTATACATTTTGTATAACTTTCTTACG
Found at i:2675780 original size:56 final size:53
Alignment explanation
Indices: 2675684--2675806 Score: 131
Period size: 56 Copynumber: 2.2 Consensus size: 53
2675674 TTTCTTACGA
* * * *
2675684 TTTTATAAAATTTTATAAAATTTTATATTTCTATATATTTTATAACTTTTTATGAT
1 TTTTATAAAATTTTACAAAATTTTATATTTCTATAAATTTTA-AA-TATTTA-AAT
* * *
2675740 TTTTATAAAATTTTAC-AATTTTTCTAATTTTTATAAATTTTAAATATTTAAAT
1 TTTTATAAAATTTTACAAAATTTTAT-ATTTCTATAAATTTTAAATATTTAAAT
2675793 TTTTATTAAAATTT
1 TTTTA-TAAAATTT
2675807 AATAATATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
53 7 0.12
54 13 0.22
55 9 0.16
56 29 0.50
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (53 bp):
TTTTATAAAATTTTACAAAATTTTATATTTCTATAAATTTTAAATATTTAAAT
Found at i:2675814 original size:28 final size:26
Alignment explanation
Indices: 2675684--2675817 Score: 92
Period size: 28 Copynumber: 4.9 Consensus size: 26
2675674 TTTCTTACGA
* *
2675684 TTTTATAAAATTTTATAAAATTTTATAT
1 TTTTATAAAATTTTA-AATA-TTTAAAT
* * * *
2675712 TTCTAT-ATATTTTATAACTTTTTATGAT
1 TTTTATAAAATTTTA-AA-TATTTA-AAT
* *
2675740 TTTTATAAAATTTTACAATTTTTCTAAT
1 TTTTATAAAATTTTA-AATATTT-AAAT
2675768 TTTTAT-AAATTTTAAATATTTAAAT
1 TTTTATAAAATTTTAAATATTTAAAT
*
2675793 TTTTATTAAAATTTAATAATATTTA
1 TTTTA-TAAAATTTTA-AATATTTA
2675818 TAGCTTTTAT
Statistics
Matches: 86, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
25 8 0.09
26 7 0.08
27 29 0.34
28 33 0.38
29 9 0.10
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (26 bp):
TTTTATAAAATTTTAAATATTTAAAT
Found at i:2676828 original size:14 final size:14
Alignment explanation
Indices: 2676809--2676836 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2676799 TTTAGGATTT
2676809 TACCTAAAGTTGTC
1 TACCTAAAGTTGTC
2676823 TACCTAAAGTTGTC
1 TACCTAAAGTTGTC
2676837 AATCTTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (14 bp):
TACCTAAAGTTGTC
Found at i:2680982 original size:16 final size:18
Alignment explanation
Indices: 2680943--2680984 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
2680933 GGAAATCAAG
*
2680943 GAAGGAAGAGATGAGAAA
1 GAAGAAAGAGATGAGAAA
2680961 -AAGAAAGAGA-GA-AAA
1 GAAGAAAGAGATGAGAAA
2680976 GAAGAAAGA
1 GAAGAAAGA
2680985 ATTCGGCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 10 0.45
17 9 0.41
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.02
Consensus pattern (18 bp):
GAAGAAAGAGATGAGAAA
Found at i:2686813 original size:34 final size:34
Alignment explanation
Indices: 2686766--2686836 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
2686756 TCTCTACCTT
* *
2686766 TTTTATTTGCATAATTAACATTGACTTTATAATA
1 TTTTATTTCCATAATTAACATTGACCTTATAATA
2686800 TTTTATTTCCATAATTAACATTGACCTTATAATA
1 TTTTATTTCCATAATTAACATTGACCTTATAATA
2686834 TTT
1 TTT
2686837 AGGTTCACAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (34 bp):
TTTTATTTCCATAATTAACATTGACCTTATAATA
Found at i:2687251 original size:25 final size:23
Alignment explanation
Indices: 2687187--2687251 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 23
2687177 ATTATCACAC
*
2687187 TTTTATAAC-ATATAAATTATTT
1 TTTTATAACTTTATAAATTATTT
*
2687209 TTTATAATAA-TTTCTAAATATATTT
1 TTT-T-ATAACTTTATAAAT-TATTT
2687234 TTGTTATAACTTTATAAA
1 TT-TTATAACTTTATAAA
2687252 ATGCATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
22 3 0.09
23 1 0.03
24 14 0.41
25 15 0.44
26 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTATAACTTTATAAATTATTT
Found at i:2688400 original size:24 final size:23
Alignment explanation
Indices: 2688354--2688412 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
2688344 ATATTTATAG
2688354 AAATAAAATTAATTAAGTTAAATT
1 AAATAAAA-TAATTAAGTTAAATT
**
2688378 ATTTAAAATAATATAA-TTAAAATT
1 AAATAAAATAAT-TAAGTT-AAATT
2688402 AAATAAAATAA
1 AAATAAAATAA
2688413 AATTTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAATAAAATAATTAAGTTAAATT
Found at i:2691338 original size:115 final size:115
Alignment explanation
Indices: 2691157--2691367 Score: 341
Period size: 115 Copynumber: 1.8 Consensus size: 115
2691147 CAAAGTACAT
* * *
2691157 TAATGTTATCCATGAATAATTTTATTAACCAATCTGTTTGAAAAAATTATAAGTGTACAAATGAA
1 TAATGTAATCCATGAATAATTTTACTAACCAATCTGTTCGAAAAAATTATAAGTGTACAAATGAA
*
2691222 TATACTACACTTAGGGTACCAGATCTAACAAGGACAACATACAAAAGGTA
66 TATACTACACTTAGGGCACCAGATCTAACAAGGACAACATACAAAAGGTA
* * *
2691272 TAATGTAATTCATGAATAATTTTACTAACTAGTCTGTTCGAAAAAATTATAAGTGTACAAATGAA
1 TAATGTAATCCATGAATAATTTTACTAACCAATCTGTTCGAAAAAATTATAAGTGTACAAATGAA
* *
2691337 TATACTACATTTAGGGCACTAGATCTAACAA
66 TATACTACACTTAGGGCACCAGATCTAACAA
2691368 TCTTCAACTT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
115 87 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (115 bp):
TAATGTAATCCATGAATAATTTTACTAACCAATCTGTTCGAAAAAATTATAAGTGTACAAATGAA
TATACTACACTTAGGGCACCAGATCTAACAAGGACAACATACAAAAGGTA
Found at i:2697825 original size:54 final size:54
Alignment explanation
Indices: 2697766--2697878 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
2697756 CATGGCTCCT
* *
2697766 AGAACAGATA-ATGAGACAGAGTCACCAAATACAGATAATCGTGGCAGAGCCACC
1 AGAACAGATATATGAGACAGAGCCACCAAAT-CAGATAATCATGGCAGAGCCACC
* * * * * *
2697820 AGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTATGGCATAGCCACC
1 AGAACAGATATATGAGACAGAGCCACCAAATCAGATAATCATGGCAGAGCCACC
2697874 AGAAC
1 AGAAC
2697879 GCTTCCTCCA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
54 34 0.68
55 16 0.32
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (54 bp):
AGAACAGATATATGAGACAGAGCCACCAAATCAGATAATCATGGCAGAGCCACC
Found at i:2697826 original size:27 final size:26
Alignment explanation
Indices: 2697766--2697878 Score: 118
Period size: 27 Copynumber: 4.2 Consensus size: 26
2697756 CATGGCTCCT
* * *
2697766 AGAACAGATAATGAGACAGAGTCACC
1 AGAACAGATAATGTGGCAGAGCCACC
*
2697792 AAATACAGATAATCGTGGCAGAGCCACC
1 AGA-ACAGATAAT-GTGGCAGAGCCACC
2697820 AGAACAGATATATGTGGCAGAGCCACC
1 AGAACAGATA-ATGTGGCAGAGCCACC
* * * *
2697847 AGATCAGATATTTATGGCATAGCCACC
1 AGAACAGATA-ATGTGGCAGAGCCACC
2697874 AGAAC
1 AGAAC
2697879 GCTTCCTCCA
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
26 2 0.03
27 57 0.77
28 15 0.20
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (26 bp):
AGAACAGATAATGTGGCAGAGCCACC
Found at i:2699525 original size:26 final size:26
Alignment explanation
Indices: 2699489--2699623 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
2699479 CATGAAATTC
* *
2699489 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
* *
2699515 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
*
2699541 TTATCATGGAACATTTACCTAATCTA
1 TTATCATGGAACATTTACCTAACCTA
2699567 TTATCATGGAACATTTA-CTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
2699592 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
2699618 TTATCA
1 TTATCA
2699624 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
25 24 0.23
26 80 0.77
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.35
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:2702645 original size:17 final size:15
Alignment explanation
Indices: 2702614--2702643 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2702604 CGCAACAAAA
2702614 AAAATTTTGTTTTTG
1 AAAATTTTGTTTTTG
2702629 AAAATCTTTGTTTTT
1 AAAAT-TTTGTTTTT
2702644 TGTAAACCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.60
Consensus pattern (15 bp):
AAAATTTTGTTTTTG
Found at i:2703667 original size:54 final size:54
Alignment explanation
Indices: 2703608--2703722 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 54
2703598 AGCATGGCTG
* *
2703608 CCAGAACAGATA-ATGAGACAGAGTCACCAAATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGAGACAGAGCCACCAAAT-CAGATAATCATGGCAGAGCCA
* * * * * *
2703662 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTATGGCATAGCCA
1 CCAGAACAGATATATGAGACAGAGCCACCAAATCAGATAATCATGGCAGAGCCA
2703716 CCAGAAC
1 CCAGAAC
2703723 GCTTCCTCCA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 36 0.69
55 16 0.31
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.16
Consensus pattern (54 bp):
CCAGAACAGATATATGAGACAGAGCCACCAAATCAGATAATCATGGCAGAGCCA
Found at i:2703670 original size:27 final size:26
Alignment explanation
Indices: 2703608--2703722 Score: 122
Period size: 27 Copynumber: 4.3 Consensus size: 26
2703598 AGCATGGCTG
* * *
2703608 CCAGAACAGATAATGAGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
2703634 CCAAATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
2703662 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * * *
2703689 CCAGATCAGATATTTATGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
2703716 CCAGAAC
1 CCAGAAC
2703723 GCTTCCTCCA
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.05
27 57 0.75
28 15 0.20
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:2705362 original size:26 final size:26
Alignment explanation
Indices: 2705324--2705432 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
2705314 CATGAAATTC
* *
2705324 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
*
2705350 TTATAATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
2705376 TTATCATGGAACATTTA-CTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
2705401 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
2705427 TTATCA
1 TTATCA
2705433 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
25 25 0.32
26 53 0.68
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:2705411 original size:51 final size:52
Alignment explanation
Indices: 2705324--2705432 Score: 184
Period size: 51 Copynumber: 2.1 Consensus size: 52
2705314 CATGAAATTC
2705324 TTATCATGAAACATTTACCTAACCCATTATAATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCATTATAATGGAACATTTACCTAACCTA
* * *
2705376 TTATCATGGAACATTTA-CTAACCTATTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCATTATAATGGAACATTTACCTAACCTA
2705427 TTATCA
1 TTATCA
2705433 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 38 0.70
52 16 0.30
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (52 bp):
TTATCATGAAACATTTACCTAACCCATTATAATGGAACATTTACCTAACCTA
Found at i:2713412 original size:28 final size:28
Alignment explanation
Indices: 2713372--2713429 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
2713362 AACGGTCTGT
*
2713372 ATCACCGGTACATAGTACCTGCTAAATG
1 ATCACCGGCACATAGTACCTGCTAAATG
* *
2713400 ATCACCTGCACATAGTACCTTCTAAATG
1 ATCACCGGCACATAGTACCTGCTAAATG
2713428 AT
1 AT
2713430 TACCAGCTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.28
Consensus pattern (28 bp):
ATCACCGGCACATAGTACCTGCTAAATG
Found at i:2714823 original size:15 final size:16
Alignment explanation
Indices: 2714803--2714840 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
2714793 ACTAACCACT
*
2714803 AATTCAATTAATT-AA
1 AATTCAATCAATTCAA
2714818 AATTC-ATCAATTCAA
1 AATTCAATCAATTCAA
2714833 AATTCAAT
1 AATTCAAT
2714841 ATAAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 6 0.30
15 12 0.60
16 2 0.10
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTCAATCAATTCAA
Found at i:2724847 original size:21 final size:20
Alignment explanation
Indices: 2724823--2724864 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
2724813 AATTTTCAAA
2724823 AATTT-TCAAAGTTTTAATAAG
1 AATTTCTCAAA-TTTT-ATAAG
*
2724844 AATTTCTTAAATTTTATAAG
1 AATTTCTCAAATTTTATAAG
2724864 A
1 A
2724865 GGTTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (20 bp):
AATTTCTCAAATTTTATAAG
Found at i:2725001 original size:3 final size:3
Alignment explanation
Indices: 2724993--2725018 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2724983 GTTTGAAATG
2724993 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2725019 ATTTAAGGGT
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:2725312 original size:20 final size:20
Alignment explanation
Indices: 2725270--2725323 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
2725260 AAAAATTTAT
2725270 AAAATATTAAATTTT-AGAA
1 AAAATATTAAATTTTAAGAA
*
2725289 AAAATATTAAATTTTAATAA
1 AAAATATTAAATTTTAAGAA
*
2725309 AAAAT-TTAAAATTTA
1 AAAATATTAAATTTTA
2725324 TTGAAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 24 0.75
20 8 0.25
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAATATTAAATTTTAAGAA
Found at i:2725330 original size:20 final size:21
Alignment explanation
Indices: 2725270--2725330 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 21
2725260 AAAAATTTAT
*
2725270 AAAATATT-AAATTTTA-GAA
1 AAAATATTAAAATTTAATGAA
*
2725289 AAAATATTAAATTTTAAT-AA
1 AAAATATTAAAATTTAATGAA
*
2725309 AAAAT-TTAAAATTTATTGAA
1 AAAATATTAAAATTTAATGAA
2725329 AA
1 AA
2725331 TTAGATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
AAAATATTAAAATTTAATGAA
Found at i:2725574 original size:10 final size:10
Alignment explanation
Indices: 2725561--2725599 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
2725551 TTTTATGAAA
2725561 TTTATATTTC
1 TTTATATTTC
* *
2725571 TTTACATTTT
1 TTTATATTTC
2725581 TTTATATTTC
1 TTTATATTTC
*
2725591 TATATATTT
1 TTTATATTT
2725600 TATAATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATATTTC
Found at i:2725599 original size:20 final size:20
Alignment explanation
Indices: 2725561--2725620 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2725551 TTTTATGAAA
* *
2725561 TTTATATTTCTTTACATTTT
1 TTTATATTTCTATATATTTT
2725581 TTTATATTTCTATATATTTT
1 TTTATATTTCTATATATTTT
* *
2725601 ATAATATTT-TATAATATTTT
1 TTTATATTTCTAT-ATATTTT
2725621 ATAATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.09
20 32 0.91
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATATTTCTATATATTTT
Found at i:2725607 original size:10 final size:10
Alignment explanation
Indices: 2725584--2725630 Score: 78
Period size: 10 Copynumber: 4.7 Consensus size: 10
2725574 ACATTTTTTT
2725584 ATATTTCTAT-
1 ATATTT-TATA
2725594 ATATTTTATA
1 ATATTTTATA
2725604 ATATTTTATA
1 ATATTTTATA
2725614 ATATTTTATA
1 ATATTTTATA
2725624 ATATTTT
1 ATATTTT
2725631 GAAAGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
9 3 0.08
10 33 0.92
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (10 bp):
ATATTTTATA
Found at i:2725784 original size:90 final size:88
Alignment explanation
Indices: 2725626--2725792 Score: 203
Period size: 90 Copynumber: 1.9 Consensus size: 88
2725616 ATTTTATAAT
* * * * ** *
2725626 ATTTTGAAAGTTTAAGTACCTAATTGAGTGCAAAAAAAATGTAGGGGCTTAATTGCTTTTTTTGA
1 ATTTTAAAAATTTAAGTACCCAAATGAGTGCAAAAAAAAAATAAGGGCTTAATT-CTTTTTTTG-
2725691 AAAAATTTGAGAGCCTTTTTGATGC
64 AAAAATTTGAGAGCCTTTTTGATGC
2725716 ATTTTAAAAATTTAAGTACCCAAATGAGTGTCAAAAAAAAAATAAGGG-TTCAATT-TTTATTTT
1 ATTTTAAAAATTTAAGTACCCAAATGAGTG-CAAAAAAAAAATAAGGGCTT-AATTCTTT-TTTT
*
2725779 TAAAAATTTGAGAG
63 GAAAAATTTGAGAG
2725793 ATTTTTACAC
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
89 16 0.24
90 32 0.48
91 18 0.27
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.37
Consensus pattern (88 bp):
ATTTTAAAAATTTAAGTACCCAAATGAGTGCAAAAAAAAAATAAGGGCTTAATTCTTTTTTTGAA
AAATTTGAGAGCCTTTTTGATGC
Found at i:2732838 original size:28 final size:28
Alignment explanation
Indices: 2732793--2732848 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2732783 AAAAAAGATA
*
2732793 AAAATATATAGTATAAATTAAAAATTTT
1 AAAATATATAGTAAAAATTAAAAATTTT
* *
2732821 AAAATATTATA-TAAAAATTGAAATTTTT
1 AAAATA-TATAGTAAAAATTAAAAATTTT
2732849 TTATAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (28 bp):
AAAATATATAGTAAAAATTAAAAATTTT
Found at i:2733120 original size:20 final size:21
Alignment explanation
Indices: 2733095--2733184 Score: 62
Period size: 20 Copynumber: 4.4 Consensus size: 21
2733085 AAATTTTGAA
2733095 TTTTATATAAT-TTTTAAATT
1 TTTTATATAATATTTTAAATT
* *
2733115 TTTTATACAATATTTT-TATT
1 TTTTATATAATATTTTAAATT
* *
2733135 TTTTAAATTTATATTTTAGAATT
1 TTTTATA-TAATATTTTA-AATT
* * *
2733158 TGTTAAAT-A-ATTTTGAATT
1 TTTTATATAATATTTTAAATT
*
2733177 ATTTATAT
1 TTTTATAT
2733185 TTTATATATG
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
19 9 0.16
20 24 0.44
21 12 0.22
22 1 0.02
23 9 0.16
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (21 bp):
TTTTATATAATATTTTAAATT
Found at i:2735334 original size:252 final size:251
Alignment explanation
Indices: 2734690--2735822 Score: 1085
Period size: 252 Copynumber: 4.5 Consensus size: 251
2734680 CCTATCATCC
* *
2734690 ATTTATGTCATGGTGTCACTGAAAGTTAGGCTTTGTATAAGCTGCATTTGTTAATCCGAGTTCGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTG-TAATCCGAGTTCGG
* * * *
2734755 GTTCAGCTCTCATATAATAGA-TT-TGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGC
65 GTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTATGAGCTGC
* * * * * * ** *
2734818 ATTTGTAATCCGAGTTCAAGTTCAGCTCTCATATAATAGATTTACGATATGGTGTCGTTCAAAGT
130 ATTTGTAACCCAATTTCAGGTTCAGCTCTCATATAATAGATTTATGTTAT-GTGTCACTGAAAGT
* * * * * * *
2734883 TAAGACTTTGTTTAAGCTGTATTTGTGATCCGAGTTCTGGTTTAGCCCTCATTTGATAG
194 T-AGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGGTTCAGCCCTCATGTAATAG
* * * * * *
2734942 ATTTATGTTATTGAGTCGCTGAAAGTTAGACATTGTAGAAGCTGCATTTGTAATCTGAGTTCGGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
* * * * *
2735007 TTTGGCTCTCATATGATATATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGTA
66 TTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTATGAGCTGCA
*
2735072 TTTGTAACCCAATTTCGGGTTCAGCTCTCATATAATAGATTTATGTTATGATGTCACTGAAAGTT
131 TTTGTAACCCAATTTCAGGTTCAGCTCTCATATAATAGATTTATGTTATG-TGTCACTGAAAGTT
* * * * * *
2735137 AGACTTTGGACAAGCTGCATTTGTAATCCAAGTTCGGGTTCAGCTCTCATATAATAT
195 AGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGGTTCAGCCCTCATGTAATAG
* * * *
2735194 ATTTATGTTGTGGTGTCACTGAAAGTTAGACTTTGTATAAGTTGCATTTGTAATCCAAGTTCAGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
* * * * *
2735259 TTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCGCTGAAAGTTAGACTTTGCATGAGCTGCA
66 TTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTATGAGCTGCA
* * * * * * *
2735324 TTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAAAGTT
131 TTTGTAACCCAATTTCAGGTTCAGCTCTCATATAATAGATTTATGTTA-TGTGTCACTGAAAGTT
* * * *
2735389 A-ACCTTTGCATGAGCTGCATTTATAA-CCTGAGTTCGGGCTT-AGCTCT-ATTGTAATAG
195 AGA-CTTTGTATAAGCTGCATTTGTAATCC-GAGTTCGGG-TTCAGCCCTCA-TGTAATAG
* * ** * * * * * * *
2735446 ATTTAT-ATATGGTTTTGCTGAATGTTAGACTTTTTATGAGTTGTATTTGTAATCCGATTTCAGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
* * * * *
2735510 TTTAGCTCTTGA-ATTATAGATTTTATGTTACGGTGTTGCTGAAAGTTAGACTTTGTGTGAGCTG
66 TTTAGCTC-TCATATGATAGA-TTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTATGAGCTG
* * ** ** *
2735574 CATTTGCAATCTGATTTTGGGATT-AGCTCTCGA-ATCATAGATTTATGTTATG-G----TG-AA
129 CATTTGTAACCCAATTTCAGG-TTCAGCTCTC-ATATAATAGATTTATGTTATGTGTCACTGAAA
* * * **
2735631 GTTAGACTTTGTATGAGCTGCATTTGTAATCTGAGTTTGGGTTCAGCCCTCATGCCATAG
192 GTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGGTTCAGCCCTCATGTAATAG
* * * ** * * * * *
2735691 ATTTGTCTTATGGTATCACTGCCACTTGGACTTTGTATGAGCTGCATTTCTAA-CCTCAGTTCGG
1 ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCC-GAGTTCGG
* * * * * *
2735755 GTTTAGCTCTCAAATCATAGATTTATATTATGTTGTTGCTGAAAGTTAGACTTTGTATGTGCTGC
65 GTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTATGAGCTGC
2735820 ATT
130 ATT
2735823 CGTACTAAGA
Statistics
Matches: 728, Mismatches: 134, Indels: 45
0.80 0.15 0.05
Matches are distributed among these distances:
244 2 0.00
245 97 0.13
246 59 0.08
250 1 0.00
251 96 0.13
252 374 0.51
253 99 0.14
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (251 bp):
ATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGG
TTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTATGAGCTGCA
TTTGTAACCCAATTTCAGGTTCAGCTCTCATATAATAGATTTATGTTATGTGTCACTGAAAGTTA
GACTTTGTATAAGCTGCATTTGTAATCCGAGTTCGGGTTCAGCCCTCATGTAATAG
Found at i:2735690 original size:77 final size:76
Alignment explanation
Indices: 2735552--2735704 Score: 202
Period size: 77 Copynumber: 2.0 Consensus size: 76
2735542 GTGTTGCTGA
* * *
2735552 AAGTTAGACTTTGTGTGAGCTGCATTTGCAATCTGATTTTGGGATTAGCTCTCGAATCATAGATT
1 AAGTTAGACTTTGTATGAGCTGCATTTGCAATCTGAGTTTGGGATTAGCCCTC-AATCATAGATT
*
2735617 TATGTTATGGTG
65 TATCTTATGGTG
*
2735629 AAGTTAGACTTTGTATGAGCTGCATTTGTAATCTGAGTTTGGG-TTCAGCCCTC-ATGCCATAGA
1 AAGTTAGACTTTGTATGAGCTGCATTTGCAATCTGAGTTTGGGATT-AGCCCTCAAT--CATAGA
*
2735692 TTTGTCTTATGGT
63 TTTATCTTATGGT
2735705 ATCACTGCCA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
75 2 0.03
76 2 0.03
77 63 0.94
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (76 bp):
AAGTTAGACTTTGTATGAGCTGCATTTGCAATCTGAGTTTGGGATTAGCCCTCAATCATAGATTT
ATCTTATGGTG
Found at i:2735812 original size:84 final size:83
Alignment explanation
Indices: 2734662--2735822 Score: 966
Period size: 84 Copynumber: 13.9 Consensus size: 83
2734652 AAGGTAATCA
* * * * ** * * *
2734662 GAGTCCGGTTTTAGCTCTCCTATCATCCATTTATGTCATGGTGTCACTGAAAGTTAGGCTTTGTA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
*
2734727 TAAGCTGCATTTGTTAATCC
66 TGAGCTGCATTTG-TAA-CC
* *
2734747 GAGTTCGGGTTCAGCTCTCATATAATAGA-TT-TGTTATGGTGTCACTGAAAGTTAGACTTTGTA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
*
2734810 TAAGCTGCATTTGTAATCC
66 TGAGCTGCATTTGTAA-CC
** * * * * *
2734829 GAGTTCAAGTTCAGCTCTCATATAATAGATTTACGATATGGTGTCGTTCAAAGTTAAGACTTTGT
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTT-AGACTTTGT
* * * *
2734894 TTAAGCTGTATTTGTGATCC
65 ATGAGCTGCATTTGT-AACC
* * * * * * *
2734914 GAGTTCTGGTTTAGCCCTCATTTGATAGATTTATGTTATTGAGTCGCTGAAAGTTAGACATTGTA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
*
2734979 -GAAGCTGCATTTGTAATCT
66 TG-AGCTGCATTTGTAA-CC
* * * *
2734998 GAGTTCGGGTTTGGCTCTCATATGATATATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
* *
2735063 TAAGCTGTATTTGTAACCC
66 TGAGCTGCATTTGTAA-CC
* * * * * *
2735082 AATTTCGGGTTCAGCTCTCATATAATAGATTTATGTTATGATGTCACTGAAAGTTAGACTTTGGA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
**
2735147 CAAGCTGCATTTGTAATCC
66 TGAGCTGCATTTGTAA-CC
* * * * *
2735166 AAGTTCGGGTTCAGCTCTCATATAATATATTTATGTTGTGGTGTCACTGAAAGTTAGACTTTGTA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
* *
2735231 TAAGTTGCATTTGTAATCC
66 TGAGCTGCATTTGTAA-CC
* * * * * * * *
2735250 AAGTTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCGCTGAAAGTTAGACTTTGCA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
*
2735315 TGAGCTGCATTTATAACCC
66 TGAGCTGCATTTGTAA-CC
* * * * * * * * * *
2735334 AAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAAAGTTA-ACCTTTGC
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGA-CTTTGT
*
2735398 ATGAGCTGCATTTATAACC
65 ATGAGCTGCATTTGTAACC
* * * * * * *
2735417 TGAGTTCGGGCTTAGCTCT-ATTGTAATAGATTTAT-ATATGGTTTTGCTGAATGTTAGACTTTT
1 -GAGTTCGGGTTTAGCTCTCA-TATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTG
* *
2735480 TATGAGTTGTATTTGTAATCC
64 TATGAGCTGCATTTGTAA-CC
* * * * * *
2735501 GATTTCAGGTTTAGCTCTTGA-ATTATAGATTTTATGTTACGGTGTTGCTGAAAGTTAGACTTTG
1 GAGTTCGGGTTTAGCTC-TCATATAATAGA-TTTATGTTATGGTGTCGCTGAAAGTTAGACTTTG
* * *
2735565 TGTGAGCTGCATTTGCAATCT
64 TATGAGCTGCATTTGTAA-CC
* * * *
2735586 GATTTTGGGATTAGCTCTCGA-ATCATAGATTTATGTTA---TG--G-TG-AAGTTAGACTTTGT
1 GAGTTCGGGTTTAGCTCTC-ATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGT
*
2735643 ATGAGCTGCATTTGTAATCT
65 ATGAGCTGCATTTGTAA-CC
* * * *** * * * * ** * *
2735663 GAGTTTGGGTTCAGCCCTCATGCCATAGATTTGTCTTATGGTATCACTGCCACTTGGACTTTGTA
1 GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
*
2735728 TGAGCTGCATTTCTAACC
66 TGAGCTGCATTTGTAACC
* * * * * *
2735746 TCAGTTCGGGTTTAGCTCTCAAATCATAGATTTATATTATGTTGTTGCTGAAAGTTAGACTTTGT
1 -GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGT
*
2735811 ATGTGCTGCATT
65 ATGAGCTGCATT
2735823 CGTACTAAGA
Statistics
Matches: 891, Mismatches: 159, Indels: 53
0.81 0.14 0.05
Matches are distributed among these distances:
76 1 0.00
77 60 0.07
78 2 0.00
79 1 0.00
80 1 0.00
81 2 0.00
82 33 0.04
83 105 0.12
84 534 0.60
85 151 0.17
86 1 0.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (83 bp):
GAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGGTGTCGCTGAAAGTTAGACTTTGTA
TGAGCTGCATTTGTAACC
Found at i:2741707 original size:23 final size:22
Alignment explanation
Indices: 2741681--2741731 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
2741671 AATATGAATT
*
2741681 AAATTAATATTT-TTAATAAATAA
1 AAATTAA-ATTTCTAAAT-AATAA
2741704 AAATTTAAATTTCTAAATAATAA
1 AAA-TTAAATTTCTAAATAATAA
2741727 AAATT
1 AAATT
2741732 TTGAAGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 15 0.60
24 8 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATTAAATTTCTAAATAATAA
Found at i:2742138 original size:17 final size:18
Alignment explanation
Indices: 2742110--2742143 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2742100 TTAAAAATAA
2742110 TTTAACAATAATAAATTT
1 TTTAACAATAATAAATTT
*
2742128 TTTAA-AATAATTAATT
1 TTTAACAATAATAAATT
2742144 CGATTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAACAATAATAAATTT
Found at i:2746296 original size:28 final size:26
Alignment explanation
Indices: 2746265--2746327 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
2746255 TATTTTTTCA
*
2746265 ATTTTTAAATAATACTTTTAATTTATAT
1 ATTTTTAAATAATAATTTT--TTTATAT
* * **
2746293 ATTTCTAATTTCTAATTTTTTTATAT
1 ATTTTTAAATAATAATTTTTTTATAT
2746319 ATTTTTAAA
1 ATTTTTAAA
2746328 AGTTTTGTGC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
26 14 0.50
28 14 0.50
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTTTAAATAATAATTTTTTTATAT
Found at i:2746360 original size:19 final size:19
Alignment explanation
Indices: 2746338--2746374 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2746328 AGTTTTGTGC
2746338 ATTTT-TTATTTCTATATAG
1 ATTTTATTATTT-TATATAG
2746357 ATTTTATTATTTTATATA
1 ATTTTATTATTTTATATA
2746375 TTTTTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTTATTATTTTATATAG
Found at i:2760602 original size:27 final size:27
Alignment explanation
Indices: 2760569--2760775 Score: 315
Period size: 27 Copynumber: 7.6 Consensus size: 27
2760559 TAAATTGTGC
*
2760569 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
2760596 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
2760624 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
2760651 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
2760679 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2760706 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * *
2760734 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2760761 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2760776 GACTTAATAT
Statistics
Matches: 168, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
27 91 0.54
28 77 0.46
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:2760633 original size:55 final size:55
Alignment explanation
Indices: 2760569--2760775 Score: 360
Period size: 55 Copynumber: 3.8 Consensus size: 55
2760559 TAAATTGTGC
2760569 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
2760624 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* *
2760679 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * * *
2760734 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCG
2760776 GACTTAATAT
Statistics
Matches: 147, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 147 1.00
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:2768689 original size:27 final size:27
Alignment explanation
Indices: 2768656--2768862 Score: 315
Period size: 27 Copynumber: 7.6 Consensus size: 27
2768646 TAAATTGTGC
*
2768656 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
2768683 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
2768711 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
2768738 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
2768766 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2768793 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * *
2768821 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2768848 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2768863 GACTTAATAT
Statistics
Matches: 168, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
27 91 0.54
28 77 0.46
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:2768720 original size:55 final size:55
Alignment explanation
Indices: 2768656--2768862 Score: 360
Period size: 55 Copynumber: 3.8 Consensus size: 55
2768646 TAAATTGTGC
2768656 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
2768711 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* *
2768766 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * * *
2768821 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCG
2768863 GACTTAATAT
Statistics
Matches: 147, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 147 1.00
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:2773852 original size:48 final size:50
Alignment explanation
Indices: 2773778--2773913 Score: 168
Period size: 48 Copynumber: 2.8 Consensus size: 50
2773768 TCATTACGGG
* * *
2773778 ATACATTGATTTGACTTCGGGCCATGATATTGGCACTTCCGGTGCGAGCT
1 ATACATTGATTTGGCTTCGGGCCATGATATTGGCACTTCCGGTGCAAGAT
* *
2773828 -T-CATTGATTTGGCTTCGGGCCATGATATTAGCACTTCGGGTGCAAGAT
1 ATACATTGATTTGGCTTCGGGCCATGATATTGGCACTTCCGGTGCAAGAT
* * * * *
2773876 ATATATTAAGTTGGCTTCGAGCCATAATATTGGCACTT
1 ATACATTGATTTGGCTTCGGGCCATGATATTGGCACTT
2773914 AGTGTGTGAG
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
48 42 0.58
49 2 0.03
50 29 0.40
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (50 bp):
ATACATTGATTTGGCTTCGGGCCATGATATTGGCACTTCCGGTGCAAGAT
Found at i:2803463 original size:105 final size:105
Alignment explanation
Indices: 2803276--2803491 Score: 423
Period size: 105 Copynumber: 2.1 Consensus size: 105
2803266 GAAGAACTAG
*
2803276 AGTGACATAGATCAGTAAGCATTCAAATGATGTTCTAAGAAGTTTGAAGCTAAAAACCAAAGGCA
1 AGTGGCATAGATCAGTAAGCATTCAAATGATGTTCTAAGAAGTTTGAAGCTAAAAACCAAAGGCA
2803341 AAAAAATTCGGTGAATGTATCTGAGAGGTCTCTCTATTAT
66 AAAAAATTCGGTGAATGTATCTGAGAGGTCTCTCTATTAT
2803381 AGTGGCATAGATCAGTAAGCATTCAAATGATGTTCTAAGAAGTTTGAAGCTAAAAACCAAAGGCA
1 AGTGGCATAGATCAGTAAGCATTCAAATGATGTTCTAAGAAGTTTGAAGCTAAAAACCAAAGGCA
2803446 AAAAAATTCGGTGAATGTATCTGAGAGGTCTCTCTATTAT
66 AAAAAATTCGGTGAATGTATCTGAGAGGTCTCTCTATTAT
2803486 AGTGGC
1 AGTGGC
2803492 CTCAACAATT
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 110 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.27
Consensus pattern (105 bp):
AGTGGCATAGATCAGTAAGCATTCAAATGATGTTCTAAGAAGTTTGAAGCTAAAAACCAAAGGCA
AAAAAATTCGGTGAATGTATCTGAGAGGTCTCTCTATTAT
Found at i:2807155 original size:19 final size:19
Alignment explanation
Indices: 2807112--2807148 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2807102 ATTTTCAATT
2807112 TTTTATATTTTTTAATTATA
1 TTTT-TATTTTTTAATTATA
2807132 TTTTTATTTTTT-ATTAT
1 TTTTTATTTTTTAATTAT
2807149 TGTTTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTATTTTTTAATTATA
Found at i:2810872 original size:12 final size:12
Alignment explanation
Indices: 2810857--2810900 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
2810847 TTAAGGTTGG
2810857 AATTAAAAATAA
1 AATTAAAAATAA
2810869 AATTAAAAATTAA
1 AATTAAAAA-TAA
* *
2810882 AAATAAAATTTAA
1 AATTAAAA-ATAA
2810895 AATTAA
1 AATTAA
2810901 GGGATCTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AATTAAAAATAA
Found at i:2810879 original size:7 final size:7
Alignment explanation
Indices: 2810857--2810900 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
2810847 TTAAGGTTGG
2810857 AATTAAA
1 AATTAAA
2810864 AA-T-AA
1 AATTAAA
2810869 AATTAAA
1 AATTAAA
2810876 AATTAAA
1 AATTAAA
2810883 AA-T-AA
1 AATTAAA
*
2810888 AATTTAA
1 AATTAAA
2810895 AATTAA
1 AATTAA
2810901 GGGATCTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
5 8 0.25
6 4 0.12
7 20 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AATTAAA
Found at i:2810881 original size:19 final size:19
Alignment explanation
Indices: 2810857--2810900 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
2810847 TTAAGGTTGG
2810857 AATTAAAAATAAAATTAAA
1 AATTAAAAATAAAATTAAA
*
2810876 AATTAAAAATAAAATTTAA
1 AATTAAAAATAAAATTAAA
2810895 AATTAA
1 AATTAA
2810901 GGGATCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTAAAAATAAAATTAAA
Found at i:2818883 original size:12 final size:12
Alignment explanation
Indices: 2818866--2818943 Score: 86
Period size: 12 Copynumber: 6.2 Consensus size: 12
2818856 GCTTAAGTTT
2818866 TTCTTCTTCCTC
1 TTCTTCTTCCTC
2818878 TTCTTCTT-CTGC
1 TTCTTCTTCCT-C
*
2818890 TTCTGCTTCTGCTTC
1 TTCTTCTTC--C-TC
2818905 TTCTTCTTCCTC
1 TTCTTCTTCCTC
*
2818917 TTCCTCTTCCTC
1 TTCTTCTTCCTC
*
2818929 TTCCTCTTCCTC
1 TTCTTCTTCCTC
2818941 TTC
1 TTC
2818944 GGATTCTCCA
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
11 2 0.03
12 44 0.76
13 1 0.02
15 10 0.17
16 1 0.02
ACGTcount: A:0.00, C:0.41, G:0.04, T:0.55
Consensus pattern (12 bp):
TTCTTCTTCCTC
Found at i:2818885 original size:6 final size:6
Alignment explanation
Indices: 2818866--2818943 Score: 75
Period size: 6 Copynumber: 13.0 Consensus size: 6
2818856 GCTTAAGTTT
* * * *
2818866 TTCTTC TTCCTC TTCTTC TTCTGC TTCTGC TTCTGC TTCTTC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * * * *
2818914 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
2818944 GGATTCTCCA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.00, C:0.41, G:0.04, T:0.55
Consensus pattern (6 bp):
TTCTTC
Found at i:2818892 original size:18 final size:18
Alignment explanation
Indices: 2818866--2818943 Score: 86
Period size: 18 Copynumber: 4.2 Consensus size: 18
2818856 GCTTAAGTTT
*
2818866 TTCTTCTTCCTCTTCTTC
1 TTCTTCTTCCTCTTCCTC
*
2818884 TTCTGCTT-CTGCTTCTGCTTC
1 TTCTTCTTCCT-CTTC--C-TC
2818905 TTCTTCTTCCTCTTCCTC
1 TTCTTCTTCCTCTTCCTC
*
2818923 TTCCTCTTCCTCTTCCTC
1 TTCTTCTTCCTCTTCCTC
2818941 TTC
1 TTC
2818944 GGATTCTCCA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
17 2 0.04
18 33 0.65
19 1 0.02
21 13 0.25
22 2 0.04
ACGTcount: A:0.00, C:0.41, G:0.04, T:0.55
Consensus pattern (18 bp):
TTCTTCTTCCTCTTCCTC
Found at i:2829591 original size:5 final size:6
Alignment explanation
Indices: 2829575--2829601 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2829565 AAAGCTCACC
2829575 ATTTTT ATTTTT ATTTTT ATTTTT ATT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATT
2829602 CTCTGCTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:2830530 original size:3 final size:3
Alignment explanation
Indices: 2830524--2830553 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2830514 GGCGGAGGTA
*
2830524 TGG TGG TGC TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
2830554 CAGGCCATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.03, G:0.63, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:2831663 original size:19 final size:20
Alignment explanation
Indices: 2831639--2831688 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
2831629 AAATATAAAT
*
2831639 TTTGGAATTTTTAT-AATTA
1 TTTGGAATTTTTATAAATCA
*
2831658 TTTGG-ATTTTAATAAATCA
1 TTTGGAATTTTTATAAATCA
*
2831677 TTTTGAATTTTT
1 TTTGGAATTTTT
2831689 TTTAAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 7 0.28
19 13 0.52
20 5 0.20
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.58
Consensus pattern (20 bp):
TTTGGAATTTTTATAAATCA
Found at i:2831686 original size:20 final size:19
Alignment explanation
Indices: 2831637--2831687 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
2831627 TTAAATATAA
* *
2831637 ATTTTGGAATTTTTATAATT
1 ATTTT-GAATTTTAATAATC
*
2831657 A-TTTGGATTTTAATAAATC
1 ATTTTGAATTTTAAT-AATC
2831676 ATTTTGAATTTT
1 ATTTTGAATTTT
2831688 TTTTAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 8 0.32
19 7 0.28
20 10 0.40
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
ATTTTGAATTTTAATAATC
Found at i:2833135 original size:12 final size:12
Alignment explanation
Indices: 2833118--2833149 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
2833108 TCATCTATAC
2833118 TTGAAATTGCTT
1 TTGAAATTGCTT
2833130 TTGAAATTGCTT
1 TTGAAATTGCTT
2833142 TTGAAATT
1 TTGAAATT
2833150 TAAGATGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (12 bp):
TTGAAATTGCTT
Found at i:2834008 original size:18 final size:18
Alignment explanation
Indices: 2833973--2834008 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2833963 GTTTGTGATG
* *
2833973 TTTTATATTATGTTATTT
1 TTTTATATTATATAATTT
2833991 TTTTATATTATATAATTT
1 TTTTATATTATATAATTT
2834009 ATAACACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTATATTATATAATTT
Found at i:2834114 original size:30 final size:26
Alignment explanation
Indices: 2834061--2834127 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 26
2834051 TAATATGGCT
*
2834061 ATATATAAAATTTTAATAAATTAAAAA
1 ATATATAAATTTTTAATAAATT-AAAA
2834088 ATATATAAATTTATTAAATCAAATTAAAA
1 ATATATAAATTT-TT-AAT-AAATTAAAA
2834117 ATAATATAAAT
1 AT-ATATAAAT
2834128 ATAATTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
27 11 0.31
28 2 0.06
29 9 0.26
30 13 0.37
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (26 bp):
ATATATAAATTTTTAATAAATTAAAA
Found at i:2834722 original size:28 final size:28
Alignment explanation
Indices: 2834690--2834746 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
2834680 TACAAATGTG
*
2834690 TTAAAATTATTAATTAAAAATAAAAAAA
1 TTAAAATCATTAATTAAAAATAAAAAAA
2834718 TTAAAATCATTAATTAAAAATAAAAAAA
1 TTAAAATCATTAATTAAAAATAAAAAAA
2834746 T
1 T
2834747 ATTTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (28 bp):
TTAAAATCATTAATTAAAAATAAAAAAA
Found at i:2835082 original size:13 final size:13
Alignment explanation
Indices: 2835066--2835103 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2835056 TTTAAACTAA
2835066 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
2835079 ACTTTCTCATAA-C
1 ACTTT-TCAAAAGC
2835092 ACTTTTCAAAAG
1 ACTTTTCAAAAG
2835104 TATTGCCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 5 0.24
13 11 0.52
14 5 0.24
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:2835806 original size:25 final size:26
Alignment explanation
Indices: 2835743--2835819 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 26
2835733 AAAATAATTA
*
2835743 TAAAAATAAAATAAATAAATAAAAAATCT
1 TAAAAATAAAATAAAT--A-AAAAAATCG
2835772 TAAAAATAAAATAAATAAAAAAAT-G
1 TAAAAATAAAATAAATAAAAAAATCG
* * *
2835797 TATAATTAAATATTAATAAAAAA
1 TAAAAATAAA-ATAAATAAAAAA
2835820 GAAAAATCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
25 8 0.19
26 18 0.42
27 1 0.02
29 16 0.37
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (26 bp):
TAAAAATAAAATAAATAAAAAAATCG
Found at i:2848025 original size:16 final size:17
Alignment explanation
Indices: 2848004--2848039 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2847994 TTATGCTTAA
*
2848004 TTAATAATTT-TTATTT
1 TTAATAATTTATTAATT
2848020 TTAATAATTTATTAATT
1 TTAATAATTTATTAATT
2848037 TTA
1 TTA
2848040 TTTTAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTAATAATTTATTAATT
Found at i:2850897 original size:13 final size:14
Alignment explanation
Indices: 2850883--2850937 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
2850873 GTACCCTTCT
*
2850883 ACGA-TACCTTCCT
1 ACGAGTACCTTCCC
*
2850896 ACGAGTACCCTCCC
1 ACGAGTACCTTCCC
*
2850910 ATGAGTACCTTCCC
1 ACGAGTACCTTCCC
*
2850924 ACGACTACC-TCCC
1 ACGAGTACCTTCCC
2850937 A
1 A
2850938 AAGTACCCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 9 0.26
14 26 0.74
ACGTcount: A:0.24, C:0.44, G:0.11, T:0.22
Consensus pattern (14 bp):
ACGAGTACCTTCCC
Found at i:2850947 original size:27 final size:28
Alignment explanation
Indices: 2850887--2850949 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
2850877 CCTTCTACGA
* * *
2850887 TACCTTCCTACGAGTACCCTCCCATGAG
1 TACCTTCCCACGACTACCCTCCCATAAG
2850915 TACCTTCCCACGACTA-CCTCCCA-AAG
1 TACCTTCCCACGACTACCCTCCCATAAG
2850941 TACCCTTCC
1 TA-CCTTCC
2850950 ACGGAACCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 4 0.13
27 13 0.42
28 14 0.45
ACGTcount: A:0.22, C:0.44, G:0.10, T:0.24
Consensus pattern (28 bp):
TACCTTCCCACGACTACCCTCCCATAAG
Found at i:2854849 original size:26 final size:26
Alignment explanation
Indices: 2854813--2854864 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2854803 TAAACTAGAC
2854813 TGCCTGTATATCTGTTTCAAATATAT
1 TGCCTGTATATCTGTTTCAAATATAT
2854839 TGCCTGTATATCTGTTTCAAATATAT
1 TGCCTGTATATCTGTTTCAAATATAT
2854865 CTTTGAGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (26 bp):
TGCCTGTATATCTGTTTCAAATATAT
Found at i:2859540 original size:28 final size:28
Alignment explanation
Indices: 2859508--2859571 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
2859498 TATATGATTA
2859508 AATAAATA-ATAATTAT-ATAATATTAAAT
1 AATAAATATATAATT-TCATAAT-TTAAAT
*
2859536 AATAAA-ATATAATTTCATAATTTTAAT
1 AATAAATATATAATTTCATAATTTAAAT
2859563 AATAAATAT
1 AATAAATAT
2859572 TTTATCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 13 0.41
28 19 0.59
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
AATAAATATATAATTTCATAATTTAAAT
Found at i:2863007 original size:16 final size:16
Alignment explanation
Indices: 2862986--2863018 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2862976 ACATGGATAT
2862986 GTTCAAAATTTTAAGA
1 GTTCAAAATTTTAAGA
2863002 GTTCAAAATTTTAAGA
1 GTTCAAAATTTTAAGA
2863018 G
1 G
2863019 ACGTCTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (16 bp):
GTTCAAAATTTTAAGA
Found at i:2865752 original size:77 final size:76
Alignment explanation
Indices: 2865649--2865798 Score: 203
Period size: 77 Copynumber: 2.0 Consensus size: 76
2865639 GCTAGTCTTC
* * * * *
2865649 AAGAAACTCGATAATGATTCTGATACTCAAGCAACTGGCAGTCAAGAAGCTTTATCTCAGACTGT
1 AAGAAACTCGACAATGATTCTGATACTCAAGCAACCGGCAGTCAAGAAGCTTCATCACAAACTGT
2865714 CTGAAAGTTGG
66 CTGAAAGTTGG
** *
2865725 AAGAAACTCAGACAATGATT-TGGATACTTGAGCAACCGGCAGTCGAGAAGCTTCATCACAAACT
1 AAGAAACTC-GACAATGATTCT-GATACTCAAGCAACCGGCAGTCAAGAAGCTTCATCACAAACT
2865789 GTCTGAAAGT
64 GTCTGAAAGT
2865799 GAATAACTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
76 10 0.16
77 54 0.84
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.24
Consensus pattern (76 bp):
AAGAAACTCGACAATGATTCTGATACTCAAGCAACCGGCAGTCAAGAAGCTTCATCACAAACTGT
CTGAAAGTTGG
Found at i:2866595 original size:31 final size:31
Alignment explanation
Indices: 2866557--2866615 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2866547 TGGACAAAAA
2866557 AATTCAAACCCTAATATGA-AAATAATTACCT
1 AATTCAAACCCTAATATGAGAAA-AATTACCT
* *
2866588 AATTCAAACCTTAATGTGAGAAAAATTA
1 AATTCAAACCCTAATATGAGAAAAATTA
2866616 TTAAATTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (31 bp):
AATTCAAACCCTAATATGAGAAAAATTACCT
Done.