Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 167 of 198
Found at i:52513601 original size:24 final size:24
Alignment explanation
Indices: 52513573--52513624 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
52513563 TTTCTAGAAG
* **
52513573 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
52513597 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
52513621 ATTT
1 ATTT
52513625 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:52517488 original size:28 final size:27
Alignment explanation
Indices: 52517456--52517526 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 27
52517446 AAAATATAAC
52517456 AAATATATATATGTATATATAAATTATA
1 AAATATATATA-GTATATATAAATTATA
* **
52517484 AAATATATGTA-TATATATGTATTATA
1 AAATATATATAGTATATATAAATTATA
*
52517510 AAATGTATATAAGTATA
1 AAATATATAT-AGTATA
52517527 CGTATATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 21 0.58
27 1 0.03
28 14 0.39
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (27 bp):
AAATATATATAGTATATATAAATTATA
Found at i:52518588 original size:16 final size:16
Alignment explanation
Indices: 52518547--52518590 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 16
52518537 TATATGCTAA
* *
52518547 AAAATGAAAAAGAAAG
1 AAAATGAAAAAGAGAC
52518563 AAAA--AAAAAGAGAC
1 AAAATGAAAAAGAGAC
52518577 AAAATGAAAAAGAG
1 AAAATGAAAAAGAG
52518591 GAAAGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 12 0.50
16 12 0.50
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (16 bp):
AAAATGAAAAAGAGAC
Found at i:52518917 original size:23 final size:24
Alignment explanation
Indices: 52518891--52518937 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
52518881 CCTGATTGTG
52518891 TTGA-ATTTTTGGGCTTA-TTGGGC
1 TTGATATTTTTGGGC-TAGTTGGGC
*
52518914 TTGATTTTTTTGGGCTAGTTGGGC
1 TTGATATTTTTGGGCTAGTTGGGC
52518938 CATTTGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.11, C:0.09, G:0.32, T:0.49
Consensus pattern (24 bp):
TTGATATTTTTGGGCTAGTTGGGC
Found at i:52519407 original size:9 final size:9
Alignment explanation
Indices: 52519393--52519441 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
52519383 TTTGGTTAAA
52519393 AATTAACCG
1 AATTAACCG
52519402 AATTAACCG
1 AATTAACCG
* *
52519411 AATTATCCT
1 AATTAACCG
52519420 AATTAACCG
1 AATTAACCG
*
52519429 AATTAATCG
1 AATTAACCG
52519438 AATT
1 AATT
52519442 GAATCACTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (9 bp):
AATTAACCG
Found at i:52521597 original size:13 final size:13
Alignment explanation
Indices: 52521579--52521606 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52521569 AATCGTTTAA
52521579 AAATTATAAAAAT
1 AAATTATAAAAAT
52521592 AAATTATAAAAAT
1 AAATTATAAAAAT
52521605 AA
1 AA
52521607 TAAAATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATTATAAAAAT
Found at i:52524743 original size:28 final size:29
Alignment explanation
Indices: 52524711--52525009 Score: 151
Period size: 29 Copynumber: 10.3 Consensus size: 29
52524701 ACAAAGTTTG
* *
52524711 CCAC-AAGGCATTCCTTTAATAGAGATGG
1 CCACAAAGGCATTCCTTTAACAGAGATGA
* *
52524739 GCACAAAGACA-TCCTTTTAACAGAGATGA
1 CCACAAAGGCATTCC-TTTAACAGAGATGA
* *
52524768 CCACAAAGGCATTCATTTAACAAAGAT-A
1 CCACAAAGGCATTCCTTTAACAGAGATGA
* * *
52524796 GCGACAAAGACATTCATTTAACTA-AGAT-A
1 -CCACAAAGGCATTCCTTTAAC-AGAGATGA
* * *
52524825 GCGACAAAGACATTCATTTAACTA-AGAT-A
1 -CCACAAAGGCATTCCTTTAAC-AGAGATGA
** * *
52524854 GCCACAAACACA-TCCTTTTAACAGAAATCA
1 -CCACAAAGGCATTCC-TTTAACAGAGATGA
* ** * *
52524884 CCACAAAGGCTTTCCCATAACAGGGACCG-
1 CCACAAAGGCATTCCTTTAACAGAGA-TGA
*
52524913 CCACAAAGGC-TTCCTTAAACTAGAGATCG-
1 CCACAAAGGCATTCCTTTAAC-AGAGAT-GA
*
52524942 CCACAAAGGC-TTCCATTTAACAGAGATCA
1 CCACAAAGGCATTCC-TTTAACAGAGATGA
*
52524971 CTACAAA-G-ATTTCCATTTAACAGAGATCG-
1 CCACAAAGGCA-TTCC-TTTAACAGAGAT-GA
52525000 CCACAAAGGC
1 CCACAAAGGC
52525010 TCACTTATAT
Statistics
Matches: 219, Mismatches: 33, Indels: 35
0.76 0.11 0.12
Matches are distributed among these distances:
28 18 0.08
29 188 0.86
30 13 0.06
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.21
Consensus pattern (29 bp):
CCACAAAGGCATTCCTTTAACAGAGATGA
Found at i:52524803 original size:58 final size:57
Alignment explanation
Indices: 52524711--52524893 Score: 192
Period size: 58 Copynumber: 3.2 Consensus size: 57
52524701 ACAAAGTTTG
* * * *
52524711 CCAC-AAGGCATTCCTTTAATAGAGAT-GGGCACAAAGACATCCTTTTAACAGAGATGA
1 CCACAAAGGCATTCATTTAACAAAGATAGCG-ACAAAGACATCCTTTTAACAGAGAT-A
* *
52524768 CCACAAAGGCATTCATTTAACAAAGATAGCGACAAAGACATTCATTTAACTA-AGATA
1 CCACAAAGGCATTCATTTAACAAAGATAGCGACAAAGACATCCTTTTAAC-AGAGATA
* * * * * *
52524825 GCGACAAAGACATTCATTTAACTAAGATAGCCACAAACACATCCTTTTAACAGAAATCA
1 -CCACAAAGGCATTCATTTAACAAAGATAGCGACAAAGACATCCTTTTAACAGAGAT-A
52524884 CCACAAAGGC
1 CCACAAAGGC
52524894 TTTCCCATAA
Statistics
Matches: 104, Mismatches: 16, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
57 6 0.06
58 94 0.90
59 4 0.04
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.21
Consensus pattern (57 bp):
CCACAAAGGCATTCATTTAACAAAGATAGCGACAAAGACATCCTTTTAACAGAGATA
Found at i:52524992 original size:87 final size:86
Alignment explanation
Indices: 52524844--52525010 Score: 203
Period size: 87 Copynumber: 1.9 Consensus size: 86
52524834 ACATTCATTT
* * *
52524844 AACTAAGATAGCCACAAACACATCCTTTTAACAGAAATCACCACAAAGGCTTTCCCATAACAGGG
1 AACTAAGATAGCCACAAACACATCCATTTAACAGAAATCACCACAAAGGATTTCCCATAACAGAG
52524909 ACCGCCACAAAGGCTTCCTTA
66 ACCGCCACAAAGGCTTCCTTA
* ** * * *
52524930 AACTAGAGATCGCCACAAAGGCTTCCATTTAACAGAGATCACTACAAA-GATTT-CCATTTAACA
1 AACTA-AGATAGCCACAAACACATCCATTTAACAGAAATCACCACAAAGGATTTCCCA--TAACA
*
52524993 GAGATCGCCACAAAGGCT
63 GAGACCGCCACAAAGGCT
52525011 CACTTATATA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
85 3 0.04
86 9 0.13
87 56 0.82
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (86 bp):
AACTAAGATAGCCACAAACACATCCATTTAACAGAAATCACCACAAAGGATTTCCCATAACAGAG
ACCGCCACAAAGGCTTCCTTA
Found at i:52525507 original size:39 final size:39
Alignment explanation
Indices: 52525451--52525600 Score: 228
Period size: 39 Copynumber: 3.8 Consensus size: 39
52525441 CGTAGAAATG
* *
52525451 CGGTGATTATTCAGGCTATGTGCCTAGCAGGCTATGTGC
1 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGC
*
52525490 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGT
1 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGC
*
52525529 CGGTGATTCTTCGGGCTATGTGCCTAGCAGGCTGTGTGC
1 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGC
* * * *
52525568 CGATGTTTATTCGGGCTCTGTGCCCAGCAGGCT
1 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCT
52525601 TTGTATTGGT
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 101 1.00
ACGTcount: A:0.13, C:0.22, G:0.33, T:0.31
Consensus pattern (39 bp):
CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGC
Found at i:52528918 original size:7 final size:7
Alignment explanation
Indices: 52528906--52528939 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
52528896 AAAGGTTCTA
52528906 AATTATG
1 AATTATG
52528913 AATTATG
1 AATTATG
52528920 AATTATG
1 AATTATG
52528927 AATTATGG
1 AATTAT-G
52528935 AATTA
1 AATTA
52528940 GTGTAGCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (7 bp):
AATTATG
Found at i:52530516 original size:40 final size:40
Alignment explanation
Indices: 52530441--52530544 Score: 97
Period size: 40 Copynumber: 2.6 Consensus size: 40
52530431 ATATGCATAA
* *
52530441 CAGGGGAACCAAAGTGCAATCAGGAGCACGAATGTGTGA-T
1 CAGGGGAACCAAAGTGCAATCAGGAGCAAGAATGTG-CATT
* *
52530481 CAGGGGCACCAAAGTGCAAAT-AGGGGCATAG-ATGTGCATT
1 CAGGGGAACCAAAGTGC-AATCAGGAGCA-AGAATGTGCATT
* * *
52530521 CAGGGGTACCAAAGTACAAGCAGG
1 CAGGGGAACCAAAGTGCAATCAGG
52530545 GGCACTGATG
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
39 3 0.06
40 46 0.87
41 4 0.08
ACGTcount: A:0.35, C:0.18, G:0.33, T:0.14
Consensus pattern (40 bp):
CAGGGGAACCAAAGTGCAATCAGGAGCAAGAATGTGCATT
Found at i:52530532 original size:80 final size:81
Alignment explanation
Indices: 52530441--52530685 Score: 234
Period size: 80 Copynumber: 3.1 Consensus size: 81
52530431 ATATGCATAA
* * * ** * *
52530441 CAGGGGAACCAAAGTGCAATCAGGAGCAC-GAATGTGTGATCAGGGGCACCAAAGTGCAAATAGG
1 CAGGGGTACCAAAGTACAAGCAGGAGCACTG-ATGTGCAAACAGGGGCACCAAAGTACAAATAGG
*
52530505 GGCATAGATGTGC-ATT
65 GGCATAGATGTGCAAAT
* * * * *
52530521 CAGGGGTACCAAAGTACAAGCAGGGGCACTGATGTGCAAACATGTGTACCAAAGTACAATTAGGG
1 CAGGGGTACCAAAGTACAAGCAGGAGCACTGATGTGCAAACAGGGGCACCAAAGTACAAATAGGG
*
52530586 GCATTGATGTGCAAAT
66 GCATAGATGTGCAAAT
* ** * *
52530602 -AGGGGTACCAAAGTAGAAATAGG-GTACTGATGTGCAAACAGGGGTACCAAAGTAC-AATCAGG
1 CAGGGGTACCAAAGTACAAGCAGGAGCACTGATGTGCAAACAGGGGCACCAAAGTACAAAT-AGG
*
52530664 GGCACT-GATGTGTAAA-
65 GGCA-TAGATGTGCAAAT
52530680 CAGGGG
1 CAGGGG
52530686 GATTTTTTCA
Statistics
Matches: 138, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
78 2 0.01
79 50 0.36
80 83 0.60
81 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (81 bp):
CAGGGGTACCAAAGTACAAGCAGGAGCACTGATGTGCAAACAGGGGCACCAAAGTACAAATAGGG
GCATAGATGTGCAAAT
Found at i:52530546 original size:40 final size:40
Alignment explanation
Indices: 52530479--52530685 Score: 224
Period size: 40 Copynumber: 5.2 Consensus size: 40
52530469 CGAATGTGTG
* *
52530479 ATCAGGGGCACCAAAGTGCAAATAGGGGCA-TAGATGTGCA
1 ATCAGGGGTACCAAAGTACAAATAGGGGCACT-GATGTGCA
* **
52530519 TTCAGGGGTACCAAAGTACAAGCAGGGGCACTGATGTGCA
1 ATCAGGGGTACCAAAGTACAAATAGGGGCACTGATGTGCA
* * * * *
52530559 AACATGTGTACCAAAGTACAATTAGGGGCATTGATGTGCAA
1 ATCAGGGGTACCAAAGTACAAATAGGGGCACTGATGTGC-A
* *
52530600 AT-AGGGGTACCAAAGTAGAAATA-GGGTACTGATGTGCA
1 ATCAGGGGTACCAAAGTACAAATAGGGGCACTGATGTGCA
* *
52530638 AACAGGGGTACCAAAGTAC-AATCAGGGGCACTGATGTGTA
1 ATCAGGGGTACCAAAGTACAAAT-AGGGGCACTGATGTGCA
*
52530678 AACAGGGG
1 ATCAGGGG
52530686 GATTTTTTCA
Statistics
Matches: 139, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
38 5 0.04
39 28 0.20
40 103 0.74
41 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (40 bp):
ATCAGGGGTACCAAAGTACAAATAGGGGCACTGATGTGCA
Found at i:52530621 original size:20 final size:21
Alignment explanation
Indices: 52530596--52530655 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
52530586 GCATTGATGT
52530596 GCAAATAGGGGTACCAAAGTA
1 GCAAATAGGGGTACCAAAGTA
** *
52530617 G-AAATA-GGGTACTGATGT-
1 GCAAATAGGGGTACCAAAGTA
*
52530635 GCAAACAGGGGTACCAAAGTA
1 GCAAATAGGGGTACCAAAGTA
52530656 CAATCAGGGG
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
18 1 0.03
19 13 0.45
20 14 0.48
21 1 0.03
ACGTcount: A:0.40, C:0.13, G:0.30, T:0.17
Consensus pattern (21 bp):
GCAAATAGGGGTACCAAAGTA
Found at i:52530663 original size:20 final size:20
Alignment explanation
Indices: 52530520--52530665 Score: 55
Period size: 20 Copynumber: 7.3 Consensus size: 20
52530510 AGATGTGCAT
52530520 TCAGGGGTACCAAAGTACAA
1 TCAGGGGTACCAAAGTACAA
* * ** * *
52530540 GCAGGGGCACTGATGTGCAA
1 TCAGGGGTACCAAAGTACAA
* * *
52530560 ACATGTGTACCAAAGTACAA
1 TCAGGGGTACCAAAGTACAA
* * *** * *
52530580 TTAGGGGCATTGATGTGCAAA
1 TCAGGGGTACCAAAGTAC-AA
*
52530601 T-AGGGGTACCAAAGTAGAAA
1 TCAGGGGTACCAAAGTA-CAA
** * *
52530621 T-A-GGGTACTGATGTGCAA
1 TCAGGGGTACCAAAGTACAA
*
52530639 ACAGGGGTACCAAAGTACAA
1 TCAGGGGTACCAAAGTACAA
52530659 TCAGGGG
1 TCAGGGG
52530666 CACTGATGTG
Statistics
Matches: 80, Mismatches: 42, Indels: 8
0.62 0.32 0.06
Matches are distributed among these distances:
18 2 0.03
19 10 0.12
20 65 0.81
21 3 0.04
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.18
Consensus pattern (20 bp):
TCAGGGGTACCAAAGTACAA
Found at i:52530665 original size:79 final size:79
Alignment explanation
Indices: 52530481--52530685 Score: 243
Period size: 79 Copynumber: 2.6 Consensus size: 79
52530471 AATGTGTGAT
* * * * *
52530481 CAGGGGCACCAAAGTGCAAATAGGGGCATAGATGTGC-ATTCAGGGGTACCAAAGTACAAGCAGG
1 CAGGGGTACCAAAGTAC-AATAGGGGCATTGATGTGCAAAT-AGGGGTACCAAAGTACAAACAGG
52530545 GGCACTGATGTGCAAA
64 GGCACTGATGTGCAAA
* * * *
52530561 CATGTGTACCAAAGTACAATTAGGGGCATTGATGTGCAAATAGGGGTACCAAAGTAGAAATA-GG
1 CAGGGGTACCAAAGTACAA-TAGGGGCATTGATGTGCAAATAGGGGTACCAAAGTACAAACAGGG
*
52530625 GTACTGATGTGCAAA
65 GCACTGATGTGCAAA
* * *
52530640 CAGGGGTACCAAAGTACAATCAGGGGCACTGATGTGTAAACAGGGG
1 CAGGGGTACCAAAGTACAAT-AGGGGCATTGATGTGCAAATAGGGG
52530686 GATTTTTTCA
Statistics
Matches: 107, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
79 57 0.53
80 47 0.44
81 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (79 bp):
CAGGGGTACCAAAGTACAATAGGGGCATTGATGTGCAAATAGGGGTACCAAAGTACAAACAGGGG
CACTGATGTGCAAA
Found at i:52538603 original size:2 final size:2
Alignment explanation
Indices: 52538596--52538631 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
52538586 TATAATTGTG
*
52538596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52538632 GAGATGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:52541991 original size:17 final size:16
Alignment explanation
Indices: 52541964--52541995 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
52541954 TGATAGATCT
52541964 CTGATGAGCTTCCAAA
1 CTGATGAGCTTCCAAA
52541980 CTGATCGAGCTTCCAA
1 CTGAT-GAGCTTCCAA
52541996 TAATATATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (16 bp):
CTGATGAGCTTCCAAA
Found at i:52546388 original size:19 final size:19
Alignment explanation
Indices: 52546352--52546389 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
52546342 AGCATGAGTC
* *
52546352 ATCATTAATTTGAGTACCA
1 ATCATTAATTTCAATACCA
52546371 ATCATTAATTTCAATACCA
1 ATCATTAATTTCAATACCA
52546390 TTCAATACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (19 bp):
ATCATTAATTTCAATACCA
Found at i:52556623 original size:52 final size:52
Alignment explanation
Indices: 52556561--52556705 Score: 281
Period size: 52 Copynumber: 2.8 Consensus size: 52
52556551 ATATAGGTTT
52556561 ATATTATGCTTATGGTTATATGAGCTTACTAAGCATTCATTATGGAAATGTA
1 ATATTATGCTTATGGTTATATGAGCTTACTAAGCATTCATTATGGAAATGTA
52556613 ATATTATGCTTATGGTTATATGAGCTTACTAAGCATTCATTATGGAAATGTA
1 ATATTATGCTTATGGTTATATGAGCTTACTAAGCATTCATTATGGAAATGTA
*
52556665 ATATTATGCTTATGGTTATACGAGCTTACTAAGCATTCATT
1 ATATTATGCTTATGGTTATATGAGCTTACTAAGCATTCATT
52556706 GCTTATGTGG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 92 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.41
Consensus pattern (52 bp):
ATATTATGCTTATGGTTATATGAGCTTACTAAGCATTCATTATGGAAATGTA
Found at i:52558819 original size:29 final size:29
Alignment explanation
Indices: 52558767--52558864 Score: 153
Period size: 29 Copynumber: 3.3 Consensus size: 29
52558757 CCGAAGCAAC
52558767 CCCTTTTCACGTT-TTGATGGTCGTCACCAA
1 CCCTTTTCA--TTGTTGATGGTCGTCACCAA
*
52558797 CCCTTTTCATTGTTGATGATCGTCACCAA
1 CCCTTTTCATTGTTGATGGTCGTCACCAA
*
52558826 CCCTTTTCATTGTTGATGGTCGTCACCAT
1 CCCTTTTCATTGTTGATGGTCGTCACCAA
52558855 CCCTTTTCAT
1 CCCTTTTCAT
52558865 AATTTTATAG
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
28 2 0.03
29 53 0.83
30 9 0.14
ACGTcount: A:0.16, C:0.30, G:0.14, T:0.40
Consensus pattern (29 bp):
CCCTTTTCATTGTTGATGGTCGTCACCAA
Found at i:52558922 original size:30 final size:29
Alignment explanation
Indices: 52558853--52559041 Score: 161
Period size: 29 Copynumber: 6.4 Consensus size: 29
52558843 GGTCGTCACC
**
52558853 ATCCCTTTTCATAATTTTATAGCCAGAGCT
1 ATCCCTTTTCAT-ATTCGATAGCCAGAGCT
** * *
52558883 ATCTGTTTTCATGATTTGATAGCC-GAAGCC
1 ATCCCTTTTCAT-ATTCGATAGCCAG-AGCT
* * * *
52558913 ATCCCTTTTCATAGTTCGATGGTCATCA-CC
1 ATCCCTTTTCATA-TTCGATAGCCA-GAGCT
* * *
52558943 ATCCCTTTTCATAATCGATAGTC-GAAACT
1 ATCCCTTTTCATATTCGATAGCCAG-AGCT
*
52558972 ATCCCTTTTCATAATCGATAGCCAGAGCT
1 ATCCCTTTTCATATTCGATAGCCAGAGCT
52559001 ATCCCTTTTCATATTCGATAGCC-GAAGCT
1 ATCCCTTTTCATATTCGATAGCCAG-AGCT
52559030 ATCCCTTTTCAT
1 ATCCCTTTTCAT
52559042 TTGTCAATGA
Statistics
Matches: 133, Mismatches: 18, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
28 2 0.02
29 74 0.56
30 56 0.42
31 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.37
Consensus pattern (29 bp):
ATCCCTTTTCATATTCGATAGCCAGAGCT
Found at i:52559013 original size:58 final size:58
Alignment explanation
Indices: 52558853--52559041 Score: 209
Period size: 58 Copynumber: 3.2 Consensus size: 58
52558843 GGTCGTCACC
** ** * *
52558853 ATCCCTTTTCATAATTTTATAGCCAGAGCTATCTGTTTTCATGATTTGATAGCCGAAGCC
1 ATCCCTTTTCATAA-TCGATAGCCAGAGCTATCCCTTTTCAT-ATTCGATAGCCGAAGCT
* * * * * * * *
52558913 ATCCCTTTTCATAGTTCGATGGTCATCA-CCATCCCTTTTCATAATCGATAGTCGAAACT
1 ATCCCTTTTCATA-ATCGATAGCCA-GAGCTATCCCTTTTCATATTCGATAGCCGAAGCT
52558972 ATCCCTTTTCATAATCGATAGCCAGAGCTATCCCTTTTCATATTCGATAGCCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCAGAGCTATCCCTTTTCATATTCGATAGCCGAAGCT
52559030 ATCCCTTTTCAT
1 ATCCCTTTTCAT
52559042 TTGTCAATGA
Statistics
Matches: 104, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
57 1 0.01
58 47 0.45
59 25 0.24
60 30 0.29
61 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.37
Consensus pattern (58 bp):
ATCCCTTTTCATAATCGATAGCCAGAGCTATCCCTTTTCATATTCGATAGCCGAAGCT
Found at i:52578729 original size:42 final size:42
Alignment explanation
Indices: 52578670--52578756 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
52578660 CTATTCCTTG
* * * * *
52578670 ACACACATTATAGCAAATTTGTAAGAGAATTTATTCCCTGAC
1 ACACACATAATAGCAAATTTGAAACAAAATTTATTCCCTAAC
52578712 ACACACACTAATA-CAAATTTGAAACAAAATTTATTCCCTAAC
1 ACACACA-TAATAGCAAATTTGAAACAAAATTTATTCCCTAAC
52578754 ACA
1 ACA
52578757 AATGACATTG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 35 0.90
43 4 0.10
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.28
Consensus pattern (42 bp):
ACACACATAATAGCAAATTTGAAACAAAATTTATTCCCTAAC
Found at i:52579844 original size:44 final size:44
Alignment explanation
Indices: 52579796--52579884 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
52579786 AAATATTCTT
52579796 TTGTCTTCTAATGGGGATAATAATCTAGAAGTTCTCCTTCTTCG
1 TTGTCTTCTAATGGGGATAATAATCTAGAAGTTCTCCTTCTTCG
52579840 TTGTCTTCTAATGGGGATAATAATCTAGAAGTTCTCCTTCTTCG
1 TTGTCTTCTAATGGGGATAATAATCTAGAAGTTCTCCTTCTTCG
52579884 T
1 T
52579885 AAAAATCTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (44 bp):
TTGTCTTCTAATGGGGATAATAATCTAGAAGTTCTCCTTCTTCG
Found at i:52588663 original size:27 final size:28
Alignment explanation
Indices: 52588622--52588818 Score: 137
Period size: 27 Copynumber: 7.3 Consensus size: 28
52588612 AAAGGCTGTT
* *
52588622 AAATGACCGATATACCCTTGA-AAGGTA
1 AAATGACCGAAATACCCTTCATAAGGTA
* *
52588649 AAATTATCGAAATACCC-TCATAAGGTA
1 AAATGACCGAAATACCCTTCATAAGGTA
* *
52588676 GAATGACCGAAATACCC-TCATAGGGTA
1 AAATGACCGAAATACCCTTCATAAGGTA
* * *
52588703 GAATGAGCAAAATACCC--CATAAGGTA
1 AAATGACCGAAATACCCTTCATAAGGTA
* *
52588729 AAATGACCGAAATACTC-TCAT-AGGAAA
1 AAATGACCGAAATACCCTTCATAAGG-TA
* * * *
52588756 AAATGA-CTATAATACCC-CCATAGGGTT
1 AAATGACCGA-AATACCCTTCATAAGGTA
**
52588783 AAATGAAAGAAATA-CC-TCTATAAGGTA
1 AAATGACCGAAATACCCTTC-ATAAGGTA
52588810 AAATGACCG
1 AAATGACCG
52588819 TAATGCCCCT
Statistics
Matches: 134, Mismatches: 29, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
26 31 0.23
27 100 0.75
28 3 0.02
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.21
Consensus pattern (28 bp):
AAATGACCGAAATACCCTTCATAAGGTA
Found at i:52588761 original size:53 final size:53
Alignment explanation
Indices: 52588658--52588798 Score: 158
Period size: 53 Copynumber: 2.6 Consensus size: 53
52588648 AAAATTATCG
* ** *
52588658 AAATACCCTCATAAGGTAGAATGACCGAAATACCCTCATAGGGTAGAATGAGC-A
1 AAATACCC-CATAAGGTAAAATGACCGAAATACCCTCATAGGAAAAAATGA-CTA
*
52588712 AAATACCCCATAAGGTAAAATGACCGAAATACTCTCATAGGAAAAAATGACTA
1 AAATACCCCATAAGGTAAAATGACCGAAATACCCTCATAGGAAAAAATGACTA
* * * **
52588765 TAATACCCCCATAGGGTTAAATGAAAGAAATACC
1 AAATA-CCCCATAAGGTAAAATGACCGAAATACC
52588799 TCTATAAGGT
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
52 1 0.01
53 42 0.57
54 31 0.42
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.19
Consensus pattern (53 bp):
AAATACCCCATAAGGTAAAATGACCGAAATACCCTCATAGGAAAAAATGACTA
Found at i:52588761 original size:80 final size:81
Alignment explanation
Indices: 52588643--52588818 Score: 200
Period size: 80 Copynumber: 2.2 Consensus size: 81
52588633 ATACCCTTGA
* * * * *
52588643 AAGGTAAAATTATCGAAATACCCTCATAAGGTAGAATGACCGA-AATACCCTCATAGGG-TAGAA
1 AAGGTAAAATGACCGAAATACCCTCATAAGGAAAAATGA-CGATAATACCCCCATAGGGTTA-AA
*
52588706 TGAGCA-AAATACC-CCAT
64 TGA-AAGAAATACCTCCAT
* *
52588723 AAGGTAAAATGACCGAAATACTCTCAT-AGGAAAAAATGACTATAATACCCCCATAGGGTTAAAT
1 AAGGTAAAATGACCGAAATACCCTCATAAGG-AAAAATGACGATAATACCCCCATAGGGTTAAAT
*
52588787 GAAAGAAATACCTCTAT
65 GAAAGAAATACCTCCAT
52588804 AAGGTAAAATGACCG
1 AAGGTAAAATGACCG
52588819 TAATGCCCCT
Statistics
Matches: 82, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
79 6 0.07
80 56 0.68
81 20 0.24
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.20
Consensus pattern (81 bp):
AAGGTAAAATGACCGAAATACCCTCATAAGGAAAAATGACGATAATACCCCCATAGGGTTAAATG
AAAGAAATACCTCCAT
Found at i:52588905 original size:23 final size:24
Alignment explanation
Indices: 52588859--52588954 Score: 108
Period size: 24 Copynumber: 4.0 Consensus size: 24
52588849 GCCCATCGAG
* *
52588859 TGTAAATGATTGATTTGTCCGTGA
1 TGTAAATGACTGATTTGTCTGTGA
*
52588883 TGTAAATGACTCA-TTGTCTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
*
52588906 TTTAAATGACTGATTTGTCTGTGAA
1 TGTAAATGACTGATTTGTCTGTG-A
*
52588931 TGGT--ATGACGGATTTGTCTGTGA
1 T-GTAAATGACTGATTTGTCTGTGA
52588954 T
1 T
52588955 TTGTATGACT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
23 22 0.35
24 37 0.60
25 2 0.03
26 1 0.02
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (24 bp):
TGTAAATGACTGATTTGTCTGTGA
Found at i:52588939 original size:47 final size:47
Alignment explanation
Indices: 52588861--52588965 Score: 115
Period size: 47 Copynumber: 2.2 Consensus size: 47
52588851 CCATCGAGTG
* *
52588861 TAAATGATTGATTTGTCCGTGATGTAAATGACTCA-TTGTCTGTGATT
1 TAAATGACTGATTTGTCCGTGATGT-AATGACGCATTTGTCTGTGATT
* *
52588908 TAAATGACTGATTTGTCTGTGAATGGT-ATGACGGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCCGTG-AT-GTAATGACGCATTTGTCTGTGATT
**
52588956 TGTATGACTG
1 TAAATGACTG
52588966 GTTCTAAGCA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
47 25 0.51
48 22 0.45
49 2 0.04
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.42
Consensus pattern (47 bp):
TAAATGACTGATTTGTCCGTGATGTAATGACGCATTTGTCTGTGATT
Found at i:52588960 original size:24 final size:24
Alignment explanation
Indices: 52588896--52588963 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
52588886 AAATGACTCA
** *
52588896 TTGTCTGTGATTTAAATGACTGAT
1 TTGTCTGTGATTTGTATGACGGAT
* *
52588920 TTGTCTGTGAATGGTATGACGGAT
1 TTGTCTGTGATTTGTATGACGGAT
52588944 TTGTCTGTGATTTGTATGAC
1 TTGTCTGTGATTTGTATGAC
52588964 TGGTTCTAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (24 bp):
TTGTCTGTGATTTGTATGACGGAT
Found at i:52589080 original size:27 final size:27
Alignment explanation
Indices: 52589040--52589096 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
52589030 AGTATTGTAT
*
52589040 TGGTGGCTCTGCCACA-ATCACTGTTAC
1 TGGTGGCTCTGCCACATAT-ACTATTAC
52589067 TGGTGGCT-TGGCCACATATACTATTAC
1 TGGTGGCTCT-GCCACATATACTATTAC
52589094 TGG
1 TGG
52589097 CAACTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 1 0.04
27 24 0.89
28 2 0.07
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (27 bp):
TGGTGGCTCTGCCACATATACTATTAC
Found at i:52591827 original size:43 final size:43
Alignment explanation
Indices: 52591758--52591882 Score: 119
Period size: 43 Copynumber: 2.9 Consensus size: 43
52591748 GGCTCGTACA
** * * * *
52591758 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACAGA-TCG
1 ATGCCAATATCCCAGACGTGGACTTACACGAAAACACA-ATTCG
* *
52591801 ATGCCACTATCCCAGACAG-GGACTTACACGAAAACATAATTCG
1 ATGCCAATATCCCAGAC-GTGGACTTACACGAAAACACAATTCG
* * *
52591844 ATGCCAATATCCCAGATGTAGTCTTACACGAAAACACAA
1 ATGCCAATATCCCAGACGTGGACTTACACGAAAACACAA
52591883 ATCGGAGATC
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
42 2 0.03
43 63 0.95
44 1 0.02
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (43 bp):
ATGCCAATATCCCAGACGTGGACTTACACGAAAACACAATTCG
Found at i:52598437 original size:30 final size:30
Alignment explanation
Indices: 52598401--52598564 Score: 107
Period size: 30 Copynumber: 5.5 Consensus size: 30
52598391 ATGGTTGTCA
* * *
52598401 CCATCCCTTTTCATAATTTGATAGCCGGAT
1 CCATCCCTTTTCATAATTCGATAGCCGAAG
* *
52598431 CTATCCC-TTTCTATGATTCGATAGCCGAAG
1 CCATCCCTTTTC-ATAATTCGATAGCCGAAG
* * * *
52598461 CCATCTCTTTTCATAATTCAACAGCTGAAG
1 CCATCCCTTTTCATAATTCGATAGCCGAAG
** ** * *
52598491 CCATCTGTTTTCATTGTTTGACAGCCGAAG
1 CCATCCCTTTTCATAATTCGATAGCCGAAG
* * * * * *
52598521 CTATCCGTTTTCATAGTTCGATGGTCGTCA-
1 CCATCCCTTTTCATAATTCGATAGCCG-AAG
52598551 CCATCCCTTTTCAT
1 CCATCCCTTTTCAT
52598565 TGTTAATGTT
Statistics
Matches: 104, Mismatches: 27, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
29 4 0.04
30 95 0.91
31 5 0.05
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.37
Consensus pattern (30 bp):
CCATCCCTTTTCATAATTCGATAGCCGAAG
Found at i:52600954 original size:22 final size:23
Alignment explanation
Indices: 52600926--52600983 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 23
52600916 TTTCTTTGGG
52600926 TCACACGGGAGTGTGCTGCCT-T
1 TCACACGGGAGTGTGCTGCCTAT
*
52600948 TCACAC-GGA-TGTG-TTCCTAT
1 TCACACGGGAGTGTGCTGCCTAT
*
52600968 TCACACGGGCGTGTGC
1 TCACACGGGAGTGTGC
52600984 CACCTTCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 4 0.13
20 11 0.37
21 5 0.17
22 10 0.33
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.28
Consensus pattern (23 bp):
TCACACGGGAGTGTGCTGCCTAT
Found at i:52604065 original size:21 final size:21
Alignment explanation
Indices: 52604033--52604086 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
52604023 GACGATTTCT
52604033 ACACGGGT-GTGTATTCTAGAC
1 ACAC-GGTCGTGTATTCTAGAC
* * * *
52604054 ACACGGTCGTGTCTTGTGGGC
1 ACACGGTCGTGTATTCTAGAC
52604075 ACACGGTCGTGT
1 ACACGGTCGTGT
52604087 CTACCCTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (21 bp):
ACACGGTCGTGTATTCTAGAC
Found at i:52606706 original size:27 final size:27
Alignment explanation
Indices: 52606676--52606731 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
52606666 TGAAGAAGAG
* **
52606676 CCATTGGAGAAAGCCTTAGAACTTGAC
1 CCATTGGAAAAAAACTTAGAACTTGAC
*
52606703 CCATTGGAAAAAAACTTAGTACTTGAC
1 CCATTGGAAAAAAACTTAGAACTTGAC
52606730 CC
1 CC
52606732 TTTAGAGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (27 bp):
CCATTGGAAAAAAACTTAGAACTTGAC
Found at i:52619605 original size:42 final size:42
Alignment explanation
Indices: 52619551--52619636 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
52619541 TTATGTTTCA
52619551 TATTGGTTGAATAAATGTTCGTTGAATGTTGTTAACTTCCGG
1 TATTGGTTGAATAAATGTTCGTTGAATGTTGTTAACTTCCGG
52619593 TATTGGTTGAATAAATGTTCGTTGAATGTTGTTAACTTCCGG
1 TATTGGTTGAATAAATGTTCGTTGAATGTTGTTAACTTCCGG
52619635 TA
1 TA
52619637 ATGCTCCATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.43
Consensus pattern (42 bp):
TATTGGTTGAATAAATGTTCGTTGAATGTTGTTAACTTCCGG
Found at i:52626834 original size:15 final size:15
Alignment explanation
Indices: 52626797--52626834 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
52626787 ATAATCATTA
*
52626797 ATAATT-ATCTTAAT
1 ATAATTAATCCTAAT
52626811 ATTAATTAATCCTAAT
1 A-TAATTAATCCTAAT
52626827 ATAATTAA
1 ATAATTAA
52626835 AATAGAGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 12 0.57
16 8 0.38
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAATCCTAAT
Found at i:52635489 original size:21 final size:21
Alignment explanation
Indices: 52635463--52635514 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
52635453 CACGGCCTGT
*
52635463 TCACACGGCCATG-TCCTTAGG
1 TCACACGGCCATGCGCCTTA-G
*
52635484 TCACACAGG-CGTGCGCCTTAG
1 TCACAC-GGCCATGCGCCTTAG
52635505 TCACACGGCC
1 TCACACGGCC
52635515 CGTGTACGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 2 0.08
21 17 0.65
22 7 0.27
ACGTcount: A:0.19, C:0.37, G:0.25, T:0.19
Consensus pattern (21 bp):
TCACACGGCCATGCGCCTTAG
Found at i:52635580 original size:21 final size:20
Alignment explanation
Indices: 52635527--52635582 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
52635517 TGTACGTTCT
*
52635527 CTCACACGGGCATGTGCTTA
1 CTCACACGGGCATGTGCCTA
* *
52635547 CTCACACGAGCATGTGCCTC
1 CTCACACGGGCATGTGCCTA
*
52635567 CTCCACATGGGCATGT
1 CT-CACACGGGCATGT
52635583 TTACCCCACA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.20, C:0.34, G:0.23, T:0.23
Consensus pattern (20 bp):
CTCACACGGGCATGTGCCTA
Found at i:52638613 original size:27 final size:27
Alignment explanation
Indices: 52638574--52638820 Score: 243
Period size: 27 Copynumber: 9.1 Consensus size: 27
52638564 ATTCGTGGGC
52638574 AAATTACTGAAATACCCTCAAAGGGTA
1 AAATTACTGAAATACCCTCAAAGGGTA
* *
52638601 AAATTACTAAAATACCCTCGAAGGGTA
1 AAATTACTGAAATACCCTCAAAGGGTA
* *
52638628 CAATTATTGAAATACCCTCAAAGGGTA
1 AAATTACTGAAATACCCTCAAAGGGTA
* * *
52638655 AAATTACCGAAATACCTTCGAAGGGTA
1 AAATTACTGAAATACCCTCAAAGGGTA
*
52638682 AAATTA-TCGAAATACCCTCAAAGAGTA
1 AAATTACT-GAAATACCCTCAAAGGGTA
52638709 AAATTA-TCGAAATATCCC-CGAAA-GGTA
1 AAATTACT-GAAATA-CCCTC-AAAGGGTA
* * *
52638736 AAATTATTAAAATACCCTCGAAGGGTA
1 AAATTACTGAAATACCCTCAAAGGGTA
* * * *
52638763 AAATGACCGAATTACCCTCGAAGGGTA
1 AAATTACTGAAATACCCTCAAAGGGTA
* * * *
52638790 AAATGACCGAGATACCCCTC-TAGGGTA
1 AAATTACTGAAATA-CCCTCAAAGGGTA
52638817 AAAT
1 AAAT
52638821 GACCAAAATA
Statistics
Matches: 187, Mismatches: 26, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
26 5 0.03
27 170 0.91
28 12 0.06
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCAAAGGGTA
Found at i:52638640 original size:54 final size:54
Alignment explanation
Indices: 52638574--52638833 Score: 308
Period size: 54 Copynumber: 4.8 Consensus size: 54
52638564 ATTCGTGGGC
* **
52638574 AAATTACTGAAATACCCTCAAAGGGTAAAATTACTAAAATACCCTCGAAGGGTA
1 AAATTATTGAAATACCCTCAAAGGGTAAAATTACCGAAATACCCTCGAAGGGTA
* *
52638628 CAATTATTGAAATACCCTCAAAGGGTAAAATTACCGAAATACCTTCGAAGGGTA
1 AAATTATTGAAATACCCTCAAAGGGTAAAATTACCGAAATACCCTCGAAGGGTA
* * * *
52638682 AAATTATCGAAATACCCTCAAAGAGTAAAATTATCGAAATATCCC-CGAAAGGTA
1 AAATTATTGAAATACCCTCAAAGGGTAAAATTACCGAAATA-CCCTCGAAGGGTA
* * * *
52638736 AAATTATTAAAATACCCTCGAAGGGTAAAATGACCGAATTACCCTCGAAGGGTA
1 AAATTATTGAAATACCCTCAAAGGGTAAAATTACCGAAATACCCTCGAAGGGTA
* ** * * * *
52638790 AAATGACCGAGATACCCCTC-TAGGGTAAAATGACCAAAATACCC
1 AAATTATTGAAATA-CCCTCAAAGGGTAAAATTACCGAAATACCC
52638834 CTATAAGGTA
Statistics
Matches: 176, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
53 3 0.02
54 166 0.94
55 7 0.04
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (54 bp):
AAATTATTGAAATACCCTCAAAGGGTAAAATTACCGAAATACCCTCGAAGGGTA
Found at i:52638817 original size:81 final size:81
Alignment explanation
Indices: 52638574--52638820 Score: 282
Period size: 81 Copynumber: 3.0 Consensus size: 81
52638564 ATTCGTGGGC
* ** * *
52638574 AAATTACTGAAATACCCTCAAAGGGTAAAATTACTAAAATACCCTCGAAGGGTACAATTATTGAA
1 AAATTACTGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTATCGAA
52638639 ATA-CCCTCAAAGGGTA
66 ATACCCCTC-AAGGGTA
* * * * *
52638655 AAATTACCGAAATACCTTCGAAGGGTAAAATTATCGAAATACCCTCAAAGAGTAAAATTATCGAA
1 AAATTACTGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTATCGAA
* *
52638720 ATATCCCC-GAAAGGTA
66 ATA-CCCCTCAAGGGTA
* * * * * * *
52638736 AAATTATTAAAATACCCTCGAAGGGTAAAATGACCGAATTACCCTCGAAGGGTAAAATGACCGAG
1 AAATTACTGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTATCGAA
*
52638801 ATACCCCTCTAGGGTA
66 ATACCCCTCAAGGGTA
52638817 AAAT
1 AAAT
52638821 GACCAAAATA
Statistics
Matches: 136, Mismatches: 27, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
80 4 0.03
81 129 0.95
83 3 0.02
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (81 bp):
AAATTACTGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTATCGAA
ATACCCCTCAAGGGTA
Found at i:52638821 original size:27 final size:26
Alignment explanation
Indices: 52638757--52638850 Score: 109
Period size: 27 Copynumber: 3.5 Consensus size: 26
52638747 ATACCCTCGA
*
52638757 AGGGTAAAATGACCGAATTA-CCCTCGA
1 AGGGTAAAATGACCGAA-TACCCCTC-T
52638784 AGGGTAAAATGACCGAGATACCCCTCT
1 AGGGTAAAATGACCGA-ATACCCCTCT
* *
52638811 AGGGTAAAATGACCAAAATACCCCTAT
1 AGGGTAAAATGACC-GAATACCCCTCT
*
52638838 AAGGTAAAATGAC
1 AGGGTAAAATGAC
52638851 AATAATGCCC
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
27 53 0.88
28 7 0.12
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.18
Consensus pattern (26 bp):
AGGGTAAAATGACCGAATACCCCTCT
Found at i:52638829 original size:81 final size:81
Alignment explanation
Indices: 52638574--52638850 Score: 272
Period size: 81 Copynumber: 3.4 Consensus size: 81
52638564 ATTCGTGGGC
** * * ** * *
52638574 AAATTACTGAAATACCCTCAAAGGGTAAAATTACTAAAATACCCTCGAAGGGTACAATTATTGAA
1 AAATTACCAAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATTATCGAA
52638639 ATA-CCCTCAAAGGGTA
66 ATACCCCTC-AAGGGTA
* * * * * *
52638655 AAATTACCGAAATACCTTCGAAGGGTAAAATTATCGAAATACCCTCAAAGAGTAAAATTATCGAA
1 AAATTACCAAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATTATCGAA
* *
52638720 ATATCCCC-GAAAGGTA
66 ATA-CCCCTCAAGGGTA
** * * * *
52638736 AAATTATTAAAATACCCTCGAAGGGTAAAATGACCGAATTACCCTCGAAGGGTAAAATGACCGAG
1 AAATTACCAAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATTATCGAA
*
52638801 ATACCCCTCTAGGGTA
66 ATACCCCTCAAGGGTA
* * *
52638817 AAATGACCAAAATACCC-CTATAAGGTAAAATGAC
1 AAATTACCAAAATACCCTCGA-AGGGTAAAATGAC
52638851 AATAATGCCC
Statistics
Matches: 160, Mismatches: 32, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
80 6 0.04
81 151 0.94
83 3 0.02
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (81 bp):
AAATTACCAAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATTATCGAA
ATACCCCTCAAGGGTA
Found at i:52638870 original size:27 final size:26
Alignment explanation
Indices: 52638744--52638876 Score: 76
Period size: 27 Copynumber: 5.0 Consensus size: 26
52638734 TAAAATTATT
*
52638744 AAAATACCCTC-GAAGGGTAAAATGACC
1 AAAATACCCCCAG-AGGGTAAAATGA-C
* * *
52638771 GAATTACCCTC-GAAGGGTAAAATGACC
1 AAAATACCCCCAG-AGGGTAAAATGA-C
* * *
52638798 GAGATACCCCTC-TAGGGTAAAATGACC
1 AAAATACCCC-CAGAGGGTAAAATGA-C
* * *
52638825 AAAATACCCCTATAAGGTAAAATGAC
1 AAAATACCCCCAGAGGGTAAAATGAC
*
52638851 AATAATGCCCCCAGAGGGT-AAATGAC
1 AA-AATACCCCCAGAGGGTAAAATGAC
52638877 TATTTTGCCC
Statistics
Matches: 89, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
26 10 0.11
27 78 0.88
28 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.17
Consensus pattern (26 bp):
AAAATACCCCCAGAGGGTAAAATGAC
Found at i:52639193 original size:32 final size:32
Alignment explanation
Indices: 52639152--52639367 Score: 170
Period size: 32 Copynumber: 6.8 Consensus size: 32
52639142 GATGTTGCTA
52639152 ATGGCTTTGTGTAGATCATATTACCGTTACTG
1 ATGGCTTTGTGTAGATCATATTACCGTTACTG
** * ** * *
52639184 ATGGCTTTGTACAGGTCATACCACTGCTACTG
1 ATGGCTTTGTGTAGATCATATTACCGTTACTG
* * *
52639216 ATGGCTTTGTGTTGGTCATATTACTGTTACTG
1 ATGGCTTTGTGTAGATCATATTACCGTTACTG
** * *
52639248 ATGG-TTGTGTGCCGATCATATCA-CTTCTACTG
1 ATGGCTT-TGTGTAGATCATATTACCGT-TACTG
*
52639280 ATGGCTTTAG-GTCGATCATATTACCGTTACTG
1 ATGGCTTT-GTGTAGATCATATTACCGTTACTG
* * * * * *
52639312 ATGGCTGTGTGTCGATCACATCACTGCTACTG
1 ATGGCTTTGTGTAGATCATATTACCGTTACTG
*
52639344 ATGGCTTTGTGCCA-ATCATATTAC
1 ATGGCTTTGTG-TAGATCATATTAC
52639368 TGTATTTATG
Statistics
Matches: 145, Mismatches: 32, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
31 4 0.03
32 136 0.94
33 5 0.03
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (32 bp):
ATGGCTTTGTGTAGATCATATTACCGTTACTG
Found at i:52639226 original size:64 final size:63
Alignment explanation
Indices: 52639152--52639367 Score: 260
Period size: 64 Copynumber: 3.4 Consensus size: 63
52639142 GATGTTGCTA
* *
52639152 ATGGCTTTGTGTAGATCATATTACCGTTACTGATGGCTT-TGTACAGGTCATACCACTGCTACTG
1 ATGGCTTTGTGTAGATCATATTACCGTTACTGATGGCTTGTGT-C-GATCATATCACTGCTACTG
* * * *
52639216 ATGGCTTTGTGTTGGTCATATTACTGTTACTGATGG-TTGTGTGCCGATCATATCACTTCTACTG
1 ATGGCTTTGTGTAGATCATATTACCGTTACTGATGGCTTGTGT--CGATCATATCACTGCTACTG
* *
52639280 ATGGCTTTAG-GTCGATCATATTACCGTTACTGATGGCTGTGTGTCGATCACATCACTGCTACTG
1 ATGGCTTT-GTGTAGATCATATTACCGTTACTGATGGCT-TGTGTCGATCATATCACTGCTACTG
*
52639344 ATGGCTTTGTGCCA-ATCATATTAC
1 ATGGCTTTGTG-TAGATCATATTAC
52639368 TGTATTTATG
Statistics
Matches: 131, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
63 3 0.02
64 120 0.92
65 3 0.02
66 5 0.04
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (63 bp):
ATGGCTTTGTGTAGATCATATTACCGTTACTGATGGCTTGTGTCGATCATATCACTGCTACTG
Found at i:52641993 original size:233 final size:233
Alignment explanation
Indices: 52641586--52642042 Score: 842
Period size: 233 Copynumber: 2.0 Consensus size: 233
52641576 ACACGGGCGC
52641586 GTGTCTCAGCCGTGTGTGACACACAGCCTAGCACATAGATGTGTGGTTTGGCCGTGTGTCCCCTG
1 GTGTCTCAGCCGTGTGTGACACACAGCCTAGCACATAGATGTGTGGTTTGGCCGTGTGTCCCCTG
*
52641651 CATCTTTAAAATTCAAAACAGAATGCTCAGAATTTCTCACACAGCCTAGCATACGGGCATGTGGC
66 CATCTTTAAAATTCAAAACAGAATGCTCAGAATTTCTCACACAGCCTAGCACACGGGCATGTGGC
52641716 TTGGCCGTGTGACCTAAGTAAGAATGCTCCCAAATTTGGACACAGGCTGGGACACGGCCGTGTGC
131 TTGGCCGTGTGACCTAAGTAAGAATGCTCCCAAATTTGGACACAGGCTGGGACACGGCCGTGTGC
*
52641781 TCTACTTCGAATGCCTACACGGCCTAAGATACGAGCAT
196 TCTACTTCGAATGCCCACACGGCCTAAGATACGAGCAT
* *
52641819 GTGTCTCAGCTGTGTGTGACACACAGCCTAGCACATAGGTGTGTGGTTTGGCCGTGTGTCCCCTG
1 GTGTCTCAGCCGTGTGTGACACACAGCCTAGCACATAGATGTGTGGTTTGGCCGTGTGTCCCCTG
* *
52641884 CATCTTTAAAATTCAAAACAGAATGCTCAGAATTTCTCACATAGCCTAGCACACGGGCGTGTGGC
66 CATCTTTAAAATTCAAAACAGAATGCTCAGAATTTCTCACACAGCCTAGCACACGGGCATGTGGC
52641949 TTGGCCGTGTGACCTAAGTAAGAATGCTCCCAAATTTGGACACAGGCTGGGACACGGCCGTGTGC
131 TTGGCCGTGTGACCTAAGTAAGAATGCTCCCAAATTTGGACACAGGCTGGGACACGGCCGTGTGC
**
52642014 TCTACTTCGAATGCCCACGTGGCCTAAGA
196 TCTACTTCGAATGCCCACACGGCCTAAGA
52642043 CACGGGTATG
Statistics
Matches: 216, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
233 216 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.25
Consensus pattern (233 bp):
GTGTCTCAGCCGTGTGTGACACACAGCCTAGCACATAGATGTGTGGTTTGGCCGTGTGTCCCCTG
CATCTTTAAAATTCAAAACAGAATGCTCAGAATTTCTCACACAGCCTAGCACACGGGCATGTGGC
TTGGCCGTGTGACCTAAGTAAGAATGCTCCCAAATTTGGACACAGGCTGGGACACGGCCGTGTGC
TCTACTTCGAATGCCCACACGGCCTAAGATACGAGCAT
Found at i:52645341 original size:81 final size:81
Alignment explanation
Indices: 52645200--52645455 Score: 307
Period size: 81 Copynumber: 3.2 Consensus size: 81
52645190 GTGCGATTCG
* * * * * * *
52645200 TGGGTATAATTATCGAAATACCCTCGATGGATAAAATTATCGAAATACCCCCAATGGGTAAAATT
1 TGGGTAAAATTACCAAAATACCCTCGATGGGTAAAATTACCGAAATACCCCTAATAGGTAAAATT
52645265 ACCGAAATACCCTCGA
66 ACCGAAATACCCTCGA
* * * *
52645281 TGGGTAATATTACCAAAATACCCCCAATGGGTAAAATTACCAAAATACCCCTAATAGGTAAAATT
1 TGGGTAAAATTACCAAAATACCCTCGATGGGTAAAATTACCGAAATACCCCTAATAGGTAAAATT
* *
52645346 ATCGAAATA-CCTCTAA
66 ACCGAAATACCCTC-GA
* * * * *
52645362 TGGGTAAAATTACCGAAATAACCTTGATGGGTAAAATTACTGAAATACCTCTAATAGGTAAAATT
1 TGGGTAAAATTACCAAAATACCCTCGATGGGTAAAATTACCGAAATACCCCTAATAGGTAAAATT
* *
52645427 ACCAAAATACCCCCGA
66 ACCGAAATACCCTCGA
*
52645443 TAGGTAAAATTAC
1 TGGGTAAAATTAC
52645456 TGTAATACCC
Statistics
Matches: 146, Mismatches: 27, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
80 4 0.03
81 139 0.95
82 3 0.02
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (81 bp):
TGGGTAAAATTACCAAAATACCCTCGATGGGTAAAATTACCGAAATACCCCTAATAGGTAAAATT
ACCGAAATACCCTCGA
Found at i:52645468 original size:27 final size:27
Alignment explanation
Indices: 52645200--52645467 Score: 275
Period size: 27 Copynumber: 9.9 Consensus size: 27
52645190 GTGCGATTCG
* * * *
52645200 TGGGTATAATTATCGAAATACCCTCGA
1 TGGGTAAAATTACCGAAATACCCCCAA
* *
52645227 TGGATAAAATTATCGAAATACCCCCAA
1 TGGGTAAAATTACCGAAATACCCCCAA
* *
52645254 TGGGTAAAATTACCGAAATACCCTCGA
1 TGGGTAAAATTACCGAAATACCCCCAA
* *
52645281 TGGGTAATATTACCAAAATACCCCCAA
1 TGGGTAAAATTACCGAAATACCCCCAA
* *
52645308 TGGGTAAAATTACCAAAATACCCCTAA
1 TGGGTAAAATTACCGAAATACCCCCAA
* * * *
52645335 TAGGTAAAATTATCGAAATACCTCTAA
1 TGGGTAAAATTACCGAAATACCCCCAA
* ***
52645362 TGGGTAAAATTACCGAAATAACCTTGA
1 TGGGTAAAATTACCGAAATACCCCCAA
* * *
52645389 TGGGTAAAATTACTGAAATACCTCTAA
1 TGGGTAAAATTACCGAAATACCCCCAA
* * *
52645416 TAGGTAAAATTACCAAAATACCCCCGA
1 TGGGTAAAATTACCGAAATACCCCCAA
* * *
52645443 TAGGTAAAATTACTGTAATACCCCC
1 TGGGTAAAATTACCGAAATACCCCC
52645468 GTTAGGGTAA
Statistics
Matches: 203, Mismatches: 38, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 203 1.00
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.25
Consensus pattern (27 bp):
TGGGTAAAATTACCGAAATACCCCCAA
Found at i:52648835 original size:11 final size:11
Alignment explanation
Indices: 52648821--52648870 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
52648811 ATTAATCATT
52648821 TAATAATAAAA
1 TAATAATAAAA
*
52648832 TAATACTAAAAA
1 TAATAAT-AAAA
*
52648844 TATTAATAAAA
1 TAATAATAAAA
* *
52648855 TATTAATTAAA
1 TAATAATAAAA
52648866 TAATA
1 TAATA
52648871 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
11 24 0.73
12 9 0.27
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:52653863 original size:37 final size:36
Alignment explanation
Indices: 52653821--52653940 Score: 102
Period size: 35 Copynumber: 3.4 Consensus size: 36
52653811 TTTTGATTTA
*
52653821 CATGTTAAACATGTTAATA-TTCTGATGTTCTGATTCG
1 CATGTTAAACATGTTAATATTTCTGA--TTATGATTCG
* ** *
52653858 TATGTTAAGTATG-TCATATTTCTGATTATGATTCG
1 CATGTTAAACATGTTAATATTTCTGATTATGATTCG
* * * * *
52653893 CATGTTAAACATG-TCATATTTTTTATTCTAATTCG
1 CATGTTAAACATGTTAATATTTCTGATTATGATTCG
*
52653928 CATGTTAAGCATG
1 CATGTTAAACATG
52653941 CCTACTGTAA
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
35 49 0.71
36 4 0.06
37 16 0.23
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (36 bp):
CATGTTAAACATGTTAATATTTCTGATTATGATTCG
Found at i:52653898 original size:35 final size:35
Alignment explanation
Indices: 52653851--52653940 Score: 117
Period size: 35 Copynumber: 2.6 Consensus size: 35
52653841 TCTGATGTTC
* *
52653851 TGATTCGTATGTTAAGTATGTCATATTTCTGATTA
1 TGATTCGCATGTTAAGCATGTCATATTTCTGATTA
* * * *
52653886 TGATTCGCATGTTAAACATGTCATATTTTTTATTC
1 TGATTCGCATGTTAAGCATGTCATATTTCTGATTA
*
52653921 TAATTCGCATGTTAAGCATG
1 TGATTCGCATGTTAAGCATG
52653941 CCTACTGTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.46
Consensus pattern (35 bp):
TGATTCGCATGTTAAGCATGTCATATTTCTGATTA
Found at i:52655405 original size:96 final size:96
Alignment explanation
Indices: 52655241--52655431 Score: 373
Period size: 96 Copynumber: 2.0 Consensus size: 96
52655231 GGAATAAGAA
52655241 AGTTTACACTCAGAACTTAGAGTAGGGGTTTAGGCTACTCCTAAGCTCCCATTTAACACTATGAA
1 AGTTTACACTCAGAACTTAGAGTAGGGGTTTAGGCTACTCCTAAGCTCCCATTTAACACTATGAA
52655306 TCGTGACTACAAGCAGTGATTCTAAACACTC
66 TCGTGACTACAAGCAGTGATTCTAAACACTC
*
52655337 AGTTTACACTCAGAACTTAGAGTAGGGGTTTAGGCTACTCCTAAGCTTCCATTTAACACTATGAA
1 AGTTTACACTCAGAACTTAGAGTAGGGGTTTAGGCTACTCCTAAGCTCCCATTTAACACTATGAA
52655402 TCGTGACTACAAGCAGTGATTCTAAACACT
66 TCGTGACTACAAGCAGTGATTCTAAACACT
52655432 TACCGTTCAC
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (96 bp):
AGTTTACACTCAGAACTTAGAGTAGGGGTTTAGGCTACTCCTAAGCTCCCATTTAACACTATGAA
TCGTGACTACAAGCAGTGATTCTAAACACTC
Found at i:52658012 original size:58 final size:58
Alignment explanation
Indices: 52657921--52658039 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 58
52657911 TTACCCTTGT
52657921 TTTTGAGCATGGAAGTAGTAATGTTTTATTTTTTTACTTAAGCGTAATATAGGCCTTC
1 TTTTGAGCATGGAAGTAGTAATGTTTTATTTTTTTACTTAAGCGTAATATAGGCCTTC
*
52657979 TTTTGAGCATGGAAGTAGTAATGTTTTTATTTTTTTTACTTAAGGGTAATATAGGCCTTC
1 TTTTGAGCATGGAAGTAGTAATG-TTTTA-TTTTTTTACTTAAGCGTAATATAGGCCTTC
52658039 T
1 T
52658040 AATATAAGGC
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
58 23 0.40
59 5 0.09
60 30 0.52
ACGTcount: A:0.25, C:0.09, G:0.19, T:0.46
Consensus pattern (58 bp):
TTTTGAGCATGGAAGTAGTAATGTTTTATTTTTTTACTTAAGCGTAATATAGGCCTTC
Found at i:52671474 original size:25 final size:24
Alignment explanation
Indices: 52671433--52671493 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
52671423 AGCTCATGCT
52671433 AGCTAAATATC-AGTAAGCACAT-ACG
1 AGCTAAA-ATCGA-TAAGCAC-TCACG
*
52671458 AGCTAAGAATCGATAAGCTCTCACG
1 AGCTAA-AATCGATAAGCACTCACG
52671483 AGCTAAAATCG
1 AGCTAAAATCG
52671494 GTAACCCTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 6 0.19
25 24 0.75
26 2 0.06
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (24 bp):
AGCTAAAATCGATAAGCACTCACG
Found at i:52679887 original size:57 final size:57
Alignment explanation
Indices: 52679772--52679887 Score: 162
Period size: 57 Copynumber: 2.0 Consensus size: 57
52679762 TTTACGTCCT
* * * * *
52679772 GTATCACGTGGCCCGGCTCAAGGAGTTTCGGAGAAAACGAGCGGGATTTGGGCCGGC
1 GTATCACGTGGCCCGACTCAAGGAGTATCAGAGAAAACGAACGGGATTAGGGCCGGC
*
52679829 GTATCACGTGGCCCGACTCAAGGAGTATCAGAGAAAACGAACAGGG-TTAGGGCTGGC
1 GTATCACGTGGCCCGACTCAAGGAGTATCAGAGAAAACGAAC-GGGATTAGGGCCGGC
52679886 GT
1 GT
52679888 CCCCTGGAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 49 0.94
58 3 0.06
ACGTcount: A:0.25, C:0.22, G:0.36, T:0.17
Consensus pattern (57 bp):
GTATCACGTGGCCCGACTCAAGGAGTATCAGAGAAAACGAACGGGATTAGGGCCGGC
Found at i:52685821 original size:30 final size:30
Alignment explanation
Indices: 52685782--52685842 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
52685772 TTTATTAGGA
* *
52685782 GTTGGTTAGAACCATTTGTGAAGGTTATTG
1 GTTGATTAGAACCATTTGTAAAGGTTATTG
*
52685812 GTTGATTAGAACCATTTGTAAAGGTTGTTG
1 GTTGATTAGAACCATTTGTAAAGGTTATTG
52685842 G
1 G
52685843 AGATTCTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.07, G:0.30, T:0.39
Consensus pattern (30 bp):
GTTGATTAGAACCATTTGTAAAGGTTATTG
Found at i:52688005 original size:16 final size:15
Alignment explanation
Indices: 52687982--52688024 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
52687972 TTTGATAAAT
52687982 TGAAAAATTAAGTGC
1 TGAAAAATTAAGTGC
* * *
52687997 TGAAAAAATAAATGT
1 TGAAAAATTAAGTGC
52688012 TGAAAAATTAAGT
1 TGAAAAATTAAGT
52688025 ATTGAATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.16, T:0.28
Consensus pattern (15 bp):
TGAAAAATTAAGTGC
Found at i:52688029 original size:15 final size:15
Alignment explanation
Indices: 52687980--52688030 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
52687970 TGTTTGATAA
52687980 ATTGAAAAATTAAGT
1 ATTGAAAAATTAAGT
** * *
52687995 GCTGAAAAAATAAAT
1 ATTGAAAAATTAAGT
*
52688010 GTTGAAAAATTAAGT
1 ATTGAAAAATTAAGT
52688025 ATTGAA
1 ATTGAA
52688031 TTTAAATTAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.53, C:0.02, G:0.16, T:0.29
Consensus pattern (15 bp):
ATTGAAAAATTAAGT
Found at i:52688232 original size:5 final size:5
Alignment explanation
Indices: 52688222--52688261 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
52688212 ATAATATAAT
*
52688222 ATTAA AATAA A-TAA ATTAA ATTAA ATTAA ATTAA ATTAA A
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA A
52688262 AATATTCTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
ATTAA
Found at i:52688251 original size:15 final size:14
Alignment explanation
Indices: 52688217--52688261 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
52688207 ATAGGATAAT
*
52688217 ATAATATTAAAATAA
1 ATAA-ATTAAATTAA
52688232 ATAAATTAAATTAA
1 ATAAATTAAATTAA
52688246 ATTAAATTAAATTAA
1 A-TAAATTAAATTAA
52688261 A
1 A
52688262 AATATTCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAAATTAAATTAA
Found at i:52689038 original size:38 final size:38
Alignment explanation
Indices: 52688996--52689102 Score: 171
Period size: 38 Copynumber: 2.8 Consensus size: 38
52688986 CACTATTTTG
52688996 TATGAGTCATAAAAGTAAGTTTGTTTGTTATGT-AAATC
1 TATGAGTCATAAAAGTAAGTTTGTTTGTTATGTGAAA-C
*
52689034 TATGAGTCATAAAAGTAAGTTTGTTTGTTATGTGAAAG
1 TATGAGTCATAAAAGTAAGTTTGTTTGTTATGTGAAAC
* *
52689072 TATGAGTTAAAAAAGTAAGTTTGTTTGTTAT
1 TATGAGTCATAAAAGTAAGTTTGTTTGTTAT
52689103 ATGAGTCATA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
38 62 0.95
39 3 0.05
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.42
Consensus pattern (38 bp):
TATGAGTCATAAAAGTAAGTTTGTTTGTTATGTGAAAC
Found at i:52689108 original size:30 final size:30
Alignment explanation
Indices: 52689072--52689132 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
52689062 TATGTGAAAG
* *
52689072 TATGAGTTAAAAAAGTAAGTTTGTTTGTTA
1 TATGAGTCAAAAAAGTAAGTTTGTTTATTA
* *
52689102 TATGAGTCATAAAAGTAAGTTTTTTTATTA
1 TATGAGTCAAAAAAGTAAGTTTGTTTATTA
52689132 T
1 T
52689133 GTAAATGAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.46
Consensus pattern (30 bp):
TATGAGTCAAAAAAGTAAGTTTGTTTATTA
Found at i:52689906 original size:25 final size:27
Alignment explanation
Indices: 52689872--52689922 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
52689862 ATATTATTAA
52689872 TATAATATA-TAA-ATGTTATAATAAG
1 TATAATATATTAATATGTTATAATAAG
52689897 TATAATATATTAATATGTTATAATAA
1 TATAATATATTAATATGTTATAATAA
52689923 ACATTAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 9 0.38
26 3 0.12
27 12 0.50
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (27 bp):
TATAATATATTAATATGTTATAATAAG
Found at i:52698018 original size:25 final size:27
Alignment explanation
Indices: 52697984--52698034 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
52697974 ATATTATTAA
52697984 TATAATATA-TAA-ATGTTATAATAAG
1 TATAATATATTAATATGTTATAATAAG
52698009 TATAATATATTAATATGTTATAATAA
1 TATAATATATTAATATGTTATAATAA
52698035 ACATTAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 9 0.38
26 3 0.12
27 12 0.50
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (27 bp):
TATAATATATTAATATGTTATAATAAG
Found at i:52699002 original size:42 final size:42
Alignment explanation
Indices: 52698925--52699004 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
52698915 CTGATATGTG
** *
52698925 TTTTCGTGTAAGACCAAGTCTGGGACATTGGCATCAATTTGT
1 TTTTCGTGTAAGACCAAGTCTGGGACAGCGACATCAATTTGT
**
52698967 TTTTCGTGTAAGACCCTGTCTGGGACAGCGACATCAAT
1 TTTTCGTGTAAGACCAAGTCTGGGACAGCGACATCAAT
52699005 CTGAGATTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (42 bp):
TTTTCGTGTAAGACCAAGTCTGGGACAGCGACATCAATTTGT
Found at i:52700741 original size:2 final size:2
Alignment explanation
Indices: 52700734--52700758 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52700724 TCATAAATAC
52700734 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
52700759 AGCATAGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52701274 original size:15 final size:15
Alignment explanation
Indices: 52701256--52701293 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
52701246 AAAATATTTT
52701256 TTATAAAATTCTAAA
1 TTATAAAATTCTAAA
*
52701271 TTATATAATTCTAAA
1 TTATAAAATTCTAAA
*
52701286 TTTTAAAA
1 TTATAAAA
52701294 ATTCAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (15 bp):
TTATAAAATTCTAAA
Found at i:52701428 original size:26 final size:27
Alignment explanation
Indices: 52701390--52701442 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
52701380 TTTAAATACC
52701390 TTTTTAGAATTTTATAAA-AAATTTTA
1 TTTTTAGAATTTTATAAATAAATTTTA
* *
52701416 TTTTTA-AACTTTTCTAAATAACTTTTA
1 TTTTTAGAA-TTTTATAAATAAATTTTA
52701443 CATTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 2 0.09
26 14 0.61
27 7 0.30
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (27 bp):
TTTTTAGAATTTTATAAATAAATTTTA
Found at i:52701544 original size:17 final size:18
Alignment explanation
Indices: 52701524--52701571 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
52701514 AAATTTTATT
52701524 TTTATAATTTTTTATA-A
1 TTTATAATTTTTTATAGA
*
52701541 TTTAT-ATTTTTTCTAGA
1 TTTATAATTTTTTATAGA
52701558 TTATATATATTTTT
1 TT-TATA-ATTTTT
52701572 CCAAATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 9 0.35
17 8 0.31
18 3 0.12
20 6 0.23
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATAATTTTTTATAGA
Found at i:52701988 original size:23 final size:23
Alignment explanation
Indices: 52701962--52702006 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
52701952 GTACCTGAAC
52701962 TCTTTATAAATTTT-AGAATTCAG
1 TCTTT-TAAATTTTCAGAATTCAG
* *
52701985 TCTTTTAATTTTTCAGATTTCA
1 TCTTTTAAATTTTCAGAATTCA
52702007 ATTAACATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.53
Consensus pattern (23 bp):
TCTTTTAAATTTTCAGAATTCAG
Found at i:52702198 original size:28 final size:29
Alignment explanation
Indices: 52702166--52702220 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
52702156 TTTATCAAGT
52702166 TAAAAG-AAAAATA-AAGAGATTAAATTTC
1 TAAAAGTAAAAATATAAG-GATTAAATTTC
*
52702194 TAAAAGTAAAGATATAAGGATTAAATT
1 TAAAAGTAAAAATATAAGGATTAAATT
52702221 GTAAATTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 6 0.25
29 15 0.62
30 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.13, T:0.27
Consensus pattern (29 bp):
TAAAAGTAAAAATATAAGGATTAAATTTC
Found at i:52704357 original size:45 final size:45
Alignment explanation
Indices: 52704306--52704391 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
52704296 TTCATCATCT
*
52704306 GAAATTGTGAACACGTCAATGGGATTCGGATTTGGGGTACCTTCA
1 GAAATTGTGAACACGTCAATGGGATTCGGATTTAGGGTACCTTCA
* *
52704351 GAAATTGTGACCGCGTCAATGGGATTCGGATTTAGGGTACC
1 GAAATTGTGAACACGTCAATGGGATTCGGATTTAGGGTACC
52704392 CAAAGCTTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (45 bp):
GAAATTGTGAACACGTCAATGGGATTCGGATTTAGGGTACCTTCA
Found at i:52707939 original size:2 final size:2
Alignment explanation
Indices: 52707932--52707963 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52707922 TGCAGAATAC
52707932 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52707964 TTGGGTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52716132 original size:32 final size:30
Alignment explanation
Indices: 52716053--52716138 Score: 84
Period size: 32 Copynumber: 2.8 Consensus size: 30
52716043 ATTTATTTTA
* *
52716053 TTTGTTTTCTTTTTAGTTTTCTTTTCTTTTCT
1 TTTGTTTTATTTTTA--TTTCTCTTCTTTTCT
* * *
52716085 TTTCTTTTATGTTTATTTCTCTTCTTAGTTGT
1 TTTGTTTTATTTTTATTTCTCTTCTT--TTCT
52716117 TTTGTTTTATTTTTATTT-TCTT
1 TTTGTTTTATTTTTATTTCTCTT
52716139 GTACTTCTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
30 10 0.22
31 4 0.09
32 31 0.69
ACGTcount: A:0.07, C:0.10, G:0.07, T:0.76
Consensus pattern (30 bp):
TTTGTTTTATTTTTATTTCTCTTCTTTTCT
Found at i:52726425 original size:7 final size:7
Alignment explanation
Indices: 52726413--52726452 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
52726403 TTTGGTGGTG
52726413 CTCATCA
1 CTCATCA
52726420 CTCATCA
1 CTCATCA
52726427 CTCATCA
1 CTCATCA
52726434 CTCATCA
1 CTCATCA
52726441 CTCATCA
1 CTCATCA
52726448 CTCAT
1 CTCAT
52726453 TCTTTTACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.28, C:0.42, G:0.00, T:0.30
Consensus pattern (7 bp):
CTCATCA
Found at i:52730166 original size:95 final size:95
Alignment explanation
Indices: 52730066--52730379 Score: 467
Period size: 95 Copynumber: 3.3 Consensus size: 95
52730056 GTTTTTAGAT
* * * *
52730066 TTTAGGG-TTTTAAGGAAAAAATTAAATAAATAAGGGTTTAGGGTTTCTTAATTAAATTAATTAT
1 TTTAGGGTTTTTAAGG-AAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
*
52730130 AAATTTTAAAAAATTAGATTAGGGTTTAGTG
65 AAATTTTAAAAAATTAGATTGGGGTTTAGTG
52730161 TTTAGGGTTTTTAAGGAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATA
1 TTTAGGGTTTTTAAGGAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATA
52730226 AATTTTTTAAAAGAATTAGATTGGGGTTTAGTG
66 AA--TTTTAAAA-AATTAGATTGGGGTTTAGTG
* *
52730259 TTTAGGG-TTTTAAGGAAAAAATAAA-AAATTAGGGTTTAGGGTTACTTGAGTAAATTATTTATA
1 TTTAGGGTTTTTAAGGAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATA
* *
52730322 AA-TTAAAAAAATTAGATTGGGGTTTAGTA
66 AATTTTAAAAAATTAGATTGGGGTTTAGTG
*
52730351 TTTAGGGTTTTTAA-GAAAAATCAAATAAA
1 TTTAGGGTTTTTAAGGAAAAATTAAATAAA
52730380 ACCAGTTGTT
Statistics
Matches: 202, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
92 35 0.17
93 15 0.07
95 54 0.27
96 47 0.23
97 25 0.12
98 26 0.13
ACGTcount: A:0.40, C:0.01, G:0.19, T:0.39
Consensus pattern (95 bp):
TTTAGGGTTTTTAAGGAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATA
AATTTTAAAAAATTAGATTGGGGTTTAGTG
Found at i:52730321 original size:96 final size:95
Alignment explanation
Indices: 52730066--52730379 Score: 460
Period size: 96 Copynumber: 3.3 Consensus size: 95
52730056 GTTTTTAGAT
* * * *
52730066 TTTAGGG-TTTTAAGGAAAAAATTAAATAAATAAGGGTTTAGGGTTTCTTAATTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAA-TAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
*
52730130 AAATTTTAAAAAATTAGATTAGGGTTTAGTG
65 AAATTTTAAAAAATTAGATTGGGGTTTAGTG
*
52730161 TTTAGGGTTTTTAAGGAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATA
1 TTTAGGGTTTTTAAGGAAAAAATAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATA
52730226 AATTTTTTAAAAGAATTAGATTGGGGTTTAGTG
66 AA--TTTTAAAA-AATTAGATTGGGGTTTAGTG
*
52730259 TTTAGGG-TTTTAAGGAAAAAATAAA-AAATTAGGGTTTAGGGTTACTTGAGTAAATTATTTATA
1 TTTAGGGTTTTTAAGGAAAAAATAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATA
* *
52730322 AA-TTAAAAAAATTAGATTGGGGTTTAGTA
66 AATTTTAAAAAATTAGATTGGGGTTTAGTG
52730351 TTTAGGGTTTTTAA-G-AAAAATCAAATAAA
1 TTTAGGGTTTTTAAGGAAAAAAT-AAATAAA
52730380 ACCAGTTGTT
Statistics
Matches: 202, Mismatches: 10, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
91 6 0.03
92 30 0.15
93 15 0.07
95 48 0.24
96 52 0.26
97 25 0.12
98 26 0.13
ACGTcount: A:0.40, C:0.01, G:0.19, T:0.39
Consensus pattern (95 bp):
TTTAGGGTTTTTAAGGAAAAAATAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATA
AATTTTAAAAAATTAGATTGGGGTTTAGTG
Found at i:52735692 original size:21 final size:21
Alignment explanation
Indices: 52735668--52735707 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
52735658 CAAAATAACG
52735668 TAGTTTTG-CATTTTAACTTAA
1 TAGTTTTGAC-TTTTAACTTAA
52735689 TAGTTTTGACTTTTAACTT
1 TAGTTTTGACTTTTAACTT
52735708 TAGAAAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (21 bp):
TAGTTTTGACTTTTAACTTAA
Found at i:52735825 original size:31 final size:31
Alignment explanation
Indices: 52735790--52735848 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
52735780 GTGTAATTCA
*
52735790 TATTCGAGGTAAACCAAAAAACTTAATTTTT
1 TATTCAAGGTAAACCAAAAAACTTAATTTTT
* * * *
52735821 TATTCAAGTTGATCCAAATAACTTAATT
1 TATTCAAGGTAAACCAAAAAACTTAATT
52735849 AACTCAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (31 bp):
TATTCAAGGTAAACCAAAAAACTTAATTTTT
Found at i:52738644 original size:23 final size:24
Alignment explanation
Indices: 52738618--52738664 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
52738608 CATATAATCA
52738618 CATATATACAC-TAAATTAAATTC
1 CATATATACACATAAATTAAATTC
52738641 CATATATACACATAAATTAAATTC
1 CATATATACACATAAATTAAATTC
52738665 AATCTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (24 bp):
CATATATACACATAAATTAAATTC
Found at i:52738672 original size:24 final size:23
Alignment explanation
Indices: 52738619--52738672 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
52738609 ATATAATCAC
*
52738619 ATATATACACTAAATTAAATTCC
1 ATATATACACTAAATTAAATTCA
52738642 ATATATACACATAAATTAAATTCA
1 ATATATACAC-TAAATTAAATTCA
*
52738666 ATCTATA
1 ATATATA
52738673 ATAATTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (23 bp):
ATATATACACTAAATTAAATTCA
Found at i:52745378 original size:41 final size:42
Alignment explanation
Indices: 52745316--52745419 Score: 113
Period size: 41 Copynumber: 2.5 Consensus size: 42
52745306 TTAACGATGC
* * * *
52745316 TTTACCTACAAACGCCGCTAAAGATCATGACCTTTAG-GGCG-
1 TTTACATA-AAACGCCGCTAAAGACCATAACCTTTAGCGCCGT
* *
52745357 TTTAGATAAAAGCGCCGCTAAAGGCCATAACCTTTAGCGCCGT
1 TTTACATAAAA-CGCCGCTAAAGACCATAACCTTTAGCGCCGT
*
52745400 TTTACATAAAACGCCACTAA
1 TTTACATAAAACGCCGCTAA
52745420 CTTTTAAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
40 3 0.06
41 28 0.54
42 11 0.21
43 10 0.19
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (42 bp):
TTTACATAAAACGCCGCTAAAGACCATAACCTTTAGCGCCGT
Found at i:52750587 original size:20 final size:20
Alignment explanation
Indices: 52750562--52750600 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
52750552 TGTATGAATA
*
52750562 TATATATATTATAAAAAATC
1 TATATATATTAGAAAAAATC
52750582 TATATATATTAGAAAAAAT
1 TATATATATTAGAAAAAAT
52750601 ATGCGTGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
TATATATATTAGAAAAAATC
Found at i:52750624 original size:3 final size:3
Alignment explanation
Indices: 52750616--52750663 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
52750606 TGTCTATAGA
*
52750616 AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
52750664 GATGATGATG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:52750668 original size:3 final size:3
Alignment explanation
Indices: 52750662--52750688 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
52750652 AATAATAATA
52750662 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
52750689 CAATATCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:52756186 original size:2 final size:2
Alignment explanation
Indices: 52756179--52756206 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52756169 CAATAATGAA
52756179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52756207 GGAAGACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52757716 original size:22 final size:22
Alignment explanation
Indices: 52757688--52757729 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
52757678 ATTCTAATCG
*
52757688 TTCCATATATGCGTGTCATTCT
1 TTCCATATATGCATGTCATTCT
52757710 TTCCATATATGCATGTCATT
1 TTCCATATATGCATGTCATT
52757730 TTACATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.45
Consensus pattern (22 bp):
TTCCATATATGCATGTCATTCT
Found at i:52759407 original size:9 final size:9
Alignment explanation
Indices: 52759393--52759423 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
52759383 GTAGTGATTC
52759393 AATTCGGTT
1 AATTCGGTT
*
52759402 AATTCGGAT
1 AATTCGGTT
52759411 AATTCGGTT
1 AATTCGGTT
52759420 AATT
1 AATT
52759424 TTTAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:52761981 original size:20 final size:19
Alignment explanation
Indices: 52761935--52762036 Score: 68
Period size: 20 Copynumber: 5.3 Consensus size: 19
52761925 AAATTAATAT
52761935 TTATTTTTAAATATTTTTA
1 TTATTTTTAAATATTTTTA
52761954 TTAATTTTTAAATA-TTTTA
1 TT-ATTTTTAAATATTTTTA
* **
52761973 TAATTTTTTATAA-ATTTCAA
1 TTA-TTTTTA-AATATTTTTA
*
52761993 TCA-TTTTAAATAATTTTCTA
1 TTATTTTTAAAT-ATTTT-TA
* *
52762013 -TATTTTAAAATAATTCTTA
1 TTATTTTTAAAT-ATTTTTA
52762032 TTATT
1 TTATT
52762037 ATTTGAAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
17 2 0.03
18 6 0.09
19 22 0.34
20 35 0.54
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATTTTTAAATATTTTTA
Found at i:52761982 original size:19 final size:20
Alignment explanation
Indices: 52761932--52761980 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
52761922 TTTAAATTAA
*
52761932 TATTTATTTTTAAATATTTT
1 TATTAATTTTTAAATATTTT
52761952 TATTAATTTTTAAATA-TTT
1 TATTAATTTTTAAATATTTT
52761971 TA-TAATTTTT
1 TATTAATTTTT
52761981 TATAAATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 8 0.29
19 5 0.18
20 15 0.54
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTAATTTTTAAATATTTT
Found at i:52762213 original size:29 final size:29
Alignment explanation
Indices: 52762171--52762235 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
52762161 CGTAGCAAAA
* **
52762171 ATGCCATGTTAATGTGAGGTACACATGGC
1 ATGCCACGTTAATGTGAAATACACATGGC
52762200 ATGCCACGTTAATGTGAAATACACATGGC
1 ATGCCACGTTAATGTGAAATACACATGGC
52762229 ATGCCAC
1 ATGCCAC
52762236 ATGTTGCTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (29 bp):
ATGCCACGTTAATGTGAAATACACATGGC
Found at i:52762916 original size:17 final size:17
Alignment explanation
Indices: 52762890--52762933 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
52762880 AAGATGGAAG
*
52762890 TATTAAGAGTACGCCAA
1 TATTATGAGTACGCCAA
52762907 TATTATGAGTACGCCAA
1 TATTATGAGTACGCCAA
52762924 TATTATGAGT
1 TATTATGAGT
52762934 CTTCTTTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (17 bp):
TATTATGAGTACGCCAA
Found at i:52770696 original size:28 final size:29
Alignment explanation
Indices: 52770651--52770732 Score: 91
Period size: 28 Copynumber: 2.9 Consensus size: 29
52770641 GTATTAGTTT
* *
52770651 ATTAATTTAATCTCATTAAGTTATTTTA-G
1 ATTAA-TTAATTTAATTAAGTTATTTTAGG
*
52770680 ATTAATTAATTTAATTAGGTTATTTTAGG
1 ATTAATTAATTTAATTAAGTTATTTTAGG
*
52770709 A-TAATTAGTTTAATT-AG-TATTTTA
1 ATTAATTAATTTAATTAAGTTATTTTA
52770733 ATTTTTTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.15
27 1 0.02
28 32 0.68
29 7 0.15
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.52
Consensus pattern (29 bp):
ATTAATTAATTTAATTAAGTTATTTTAGG
Found at i:52777010 original size:75 final size:75
Alignment explanation
Indices: 52776887--52777027 Score: 237
Period size: 75 Copynumber: 1.9 Consensus size: 75
52776877 TGTGTTATTT
* * * *
52776887 TAGACCAGATATTGCTTTCACTGCGAGCAGTTTAAGTAGATTCACAAGCAATCTAGGGGAAAACC
1 TAGACCAGATATTACTTTCACCGCGAGCAATTTAAGTAGATTCACAAGCAATCCAGGGGAAAACC
52776952 ACTGCTGTAC
66 ACTGCTGTAC
*
52776962 TAGACCAGATATTACTTTCACCGTGAGCAATTTAAGTAGATTCACAAGCAATCCAGGGGAAAACC
1 TAGACCAGATATTACTTTCACCGCGAGCAATTTAAGTAGATTCACAAGCAATCCAGGGGAAAACC
52777027 A
66 A
52777028 TTGGAAAGCA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (75 bp):
TAGACCAGATATTACTTTCACCGCGAGCAATTTAAGTAGATTCACAAGCAATCCAGGGGAAAACC
ACTGCTGTAC
Found at i:52780017 original size:23 final size:26
Alignment explanation
Indices: 52779958--52780018 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
52779948 ACTTGTGCGT
*
52779958 TTATA-ATTAAAAATAAATAATTAAAA
1 TTATATATT-AAATTAAATAATTAAAA
*
52779984 TTATATTTTAAATTAAATAA-T-AAA
1 TTATATATTAAATTAAATAATTAAAA
52780008 -TATATATTAAA
1 TTATATATTAAA
52780019 AATTGTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 10 0.32
24 3 0.10
25 1 0.03
26 15 0.48
27 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TTATATATTAAATTAAATAATTAAAA
Found at i:52780021 original size:25 final size:26
Alignment explanation
Indices: 52779959--52780022 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
52779949 CTTGTGCGTT
52779959 TATA-ATTAAAAA-TAAATAATTAAA
1 TATATATTAAAAATTAAATAATTAAA
**
52779983 -ATTATATTTTAAATTAAATAA-TAAA
1 TA-TATATTAAAAATTAAATAATTAAA
52780008 TATATATTAAAAATT
1 TATATATTAAAAATT
52780023 GTGTTTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
23 1 0.03
24 2 0.06
25 21 0.66
26 8 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TATATATTAAAAATTAAATAATTAAA
Found at i:52780047 original size:18 final size:18
Alignment explanation
Indices: 52779988--52780048 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
52779978 TTAAAATTAT
*
52779988 ATTTTAAATTAAATAATA
1 ATTTTATATTAAATAATA
* * *
52780006 AATATATATTAAA-AATT
1 ATTTTATATTAAATAATA
*
52780023 GTGTTTATATTAAATAATA
1 AT-TTTATATTAAATAATA
52780042 ATTTTAT
1 ATTTTAT
52780049 GGGTAAACTA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
17 3 0.09
18 25 0.78
19 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (18 bp):
ATTTTATATTAAATAATA
Found at i:52781045 original size:16 final size:16
Alignment explanation
Indices: 52781020--52781050 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52781010 TGACAAATTA
*
52781020 TAAAATTTTATTTTAC
1 TAAAAATTTATTTTAC
52781036 TAAAAATTTATTTTA
1 TAAAAATTTATTTTA
52781051 AATAAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TAAAAATTTATTTTAC
Found at i:52784498 original size:56 final size:52
Alignment explanation
Indices: 52784280--52784584 Score: 381
Period size: 56 Copynumber: 5.8 Consensus size: 52
52784270 GATAATAACA
* ** *
52784280 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATA--TCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCTCGG
**
52784331 TGTCC-ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTC--ATCTCGG
1 TG-CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCTCGG
* *
52784381 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATA--TCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCTCGG
*
52784431 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-ATCTC--GG
52784486 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-ATCTC--GG
*
52784542 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
52784585 TTACCCAAAT
Statistics
Matches: 228, Mismatches: 14, Indels: 19
0.87 0.05 0.07
Matches are distributed among these distances:
48 1 0.00
49 2 0.01
50 90 0.39
51 32 0.14
52 3 0.01
53 2 0.01
55 2 0.01
56 96 0.42
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCTCGG
Found at i:52784577 original size:112 final size:102
Alignment explanation
Indices: 52784279--52784584 Score: 395
Period size: 100 Copynumber: 2.9 Consensus size: 102
52784269 TGATAATAAC
**
52784279 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCA-GTGTCC-ATGCCA
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCAGGTG-CCAATGCCA
**
52784342 TGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
64 TGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
52784381 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATATC-GGTGCCAAAGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGGTGCCAATGCCATG
52784444 TCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
66 TCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
*
52784486 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGATGCCAATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC-AGG-TGCCAATG
*
52784551 CCATGTCCCAGACATGGTCTTACATGGGATCTCT
61 CCATGTCCCAGACATGGTCTTACATGGGACCTCT
52784585 TTACCCAAAT
Statistics
Matches: 179, Mismatches: 11, Indels: 18
0.86 0.05 0.09
Matches are distributed among these distances:
99 2 0.01
100 46 0.26
101 36 0.20
103 5 0.03
105 2 0.01
106 43 0.24
107 1 0.01
109 2 0.01
111 2 0.01
112 40 0.22
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (102 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGGTGCCAATGCCATG
TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:52791495 original size:50 final size:50
Alignment explanation
Indices: 52791378--52791733 Score: 390
Period size: 50 Copynumber: 6.9 Consensus size: 50
52791368 TGATAATAAC
* ** *
52791378 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCG
* * * *
52791429 TTGCCCATGCCATGTCCTAGACATGGTCTTACCA-GGGACCTCTCATCTCG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTA-CATGGGACCTCTCATCTCG
* *
52791479 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATATCG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * *
52791529 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTTTCATGATCTCAAGG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACC--TC-TCATCTC---G
* *
52791585 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATCTCG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * *
52791635 GTGCCAACGCCATGTCCCAGAAATGGTCTTACATGAGACCTCTCATGATCTCAAGG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---G
* * *
52791691 ATGCCAATGCCATGTCCCATACATGGTCTTACATGGGATCTCT
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
52791734 TTACCCAAAT
Statistics
Matches: 257, Mismatches: 34, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
49 2 0.01
50 128 0.50
51 31 0.12
52 3 0.01
53 16 0.06
54 1 0.00
56 76 0.30
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:52791620 original size:106 final size:105
Alignment explanation
Indices: 52791378--52791728 Score: 507
Period size: 106 Copynumber: 3.4 Consensus size: 105
52791368 TGATAATAAC
* ** * * *
52791378 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGTTGCCCATGCCATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTT-TCATATCGGTGCCAACGCCATG
* * *
52791443 TCCTAGACATGGTCTTACCA-GGGACC-TC-TCATCTC---G
65 TCCCAGACATGGTCTTA-CATGAGACCTTCATGATCTCAAGG
*
52791479 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATATCGGTGCCAACGCCATGT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATATCGGTGCCAACGCCATGT
52791544 CCCAGACATGGTCTTACATGAGACCTTTCATGATCTCAAGG
66 CCCAGACATGGTCTTACATGAGACC-TTCATGATCTCAAGG
*
52791585 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATCTCGGTGCCAACGCCATGT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATATCGGTGCCAACGCCATGT
*
52791650 CCCAGAAATGGTCTTACATGAGACCTCTCATGATCTCAAGG
66 CCCAGACATGGTCTTACATGAGACCT-TCATGATCTCAAGG
*
52791691 ATGCCAATGCCATGTCCCATACATGGTCTTACATGGGA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
52791729 TCTCTTTACC
Statistics
Matches: 229, Mismatches: 13, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
99 2 0.01
100 40 0.17
101 39 0.17
102 2 0.01
103 6 0.03
105 1 0.00
106 139 0.61
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (105 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATATCGGTGCCAACGCCATGT
CCCAGACATGGTCTTACATGAGACCTTCATGATCTCAAGG
Found at i:52791661 original size:156 final size:155
Alignment explanation
Indices: 52791378--52791725 Score: 447
Period size: 156 Copynumber: 2.2 Consensus size: 155
52791368 TGATAATAAC
* * *
52791378 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGTTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTCTCATATCGATGCCAATGCCATG
* *
52791443 TCCTAGACATGGTCTTACCAGGGACCTCTCATCTCGATGCCAACGCCATGTCCCAGACATGGTCT
66 TCCCAGACATGGTCTTACCAGGGACCTCTCATCTCGATGCCAACGCCATGTCCCAGAAATGGTCT
* *
52791508 TACATGGGACCTTTCAT-A-TC-GG
131 TACATGAGACCTCTCATGACTCAGG
* * *
52791530 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCT-TTCATGATCTCAAGGATGCCAAT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGA--TGTTC-TCATATC---GATGCCAAT
* *
52791593 GCCATGTCCCAGACATGGTCTTA-CATGGGACCTTTCATCTCGGTGCCAACGCCATGTCCCAGAA
60 GCCATGTCCCAGACATGGTCTTACCA-GGGACCTCTCATCTCGATGCCAACGCCATGTCCCAGAA
52791657 ATGGTCTTACATGAGACCTCTCATGATCTCAAGG
124 ATGGTCTTACATGAGACCTCTCATGA-CTC-AGG
* *
52791691 ATGCCAATGCCATGTCCCATACATGGTCTTACATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATG
52791726 GGATCTCTTT
Statistics
Matches: 169, Mismatches: 14, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
151 35 0.21
152 3 0.02
153 6 0.04
155 2 0.01
156 86 0.51
157 1 0.01
159 2 0.01
161 2 0.01
162 32 0.19
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.26
Consensus pattern (155 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTCTCATATCGATGCCAATGCCATG
TCCCAGACATGGTCTTACCAGGGACCTCTCATCTCGATGCCAACGCCATGTCCCAGAAATGGTCT
TACATGAGACCTCTCATGACTCAGG
Found at i:52804868 original size:22 final size:23
Alignment explanation
Indices: 52804841--52804886 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
52804831 AAAATTTATG
52804841 AAAAG-ACTTGATG-AAAAGCTTA
1 AAAAGAACTTGATGCAAAA-CTTA
52804863 AAAAGAACTTGATGCAAAACTTA
1 AAAAGAACTTGATGCAAAACTTA
52804886 A
1 A
52804887 TAAAAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.22
Consensus pattern (23 bp):
AAAAGAACTTGATGCAAAACTTA
Found at i:52804940 original size:14 final size:13
Alignment explanation
Indices: 52804802--52804947 Score: 63
Period size: 12 Copynumber: 11.2 Consensus size: 13
52804792 AGCTTAATTG
*
52804802 AAAAACTTAATGA
1 AAAAACTTGATGA
* *
52804815 TTAAAAACTTAATGG
1 --AAAAACTTGATGA
*
52804830 AAAAA-TTTATGA
1 AAAAACTTGATGA
*
52804842 AAAGACTTGATG-
1 AAAAACTTGATGA
*
52804854 AAAAGCTT-A--A
1 AAAAACTTGATGA
52804864 AAAGAACTTGATG-
1 AAA-AACTTGATGA
* * *
52804877 CAAAACTTAATAAA
1 AAAAACTTGAT-GA
* *
52804891 AAAAACTTGGTAA
1 AAAAACTTGATGA
52804904 TTAAAAACTTGAT-A
1 --AAAAACTTGATGA
52804918 AAAGAACTTGATGA
1 AAA-AACTTGATGA
*
52804932 AAAACACTTGAAGA
1 AAAA-ACTTGATGA
52804946 AA
1 AA
52804948 GAAAACACTT
Statistics
Matches: 102, Mismatches: 16, Indels: 27
0.70 0.11 0.19
Matches are distributed among these distances:
10 3 0.03
11 5 0.05
12 26 0.25
13 23 0.23
14 23 0.23
15 22 0.22
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.25
Consensus pattern (13 bp):
AAAAACTTGATGA
Found at i:52805660 original size:68 final size:67
Alignment explanation
Indices: 52805581--52805790 Score: 336
Period size: 68 Copynumber: 3.1 Consensus size: 67
52805571 TCAAGTTTGT
*
52805581 TTTACTAATCAAATGTTAGATTTTGTTACATAAATTTATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTGTTACA-AAATTAATACAATTAATACAATTAATAATTTGAT
52805646 AAA
65 AAA
52805649 TTTACTAATCAAATGTTAGATTTTAG-TACAACAATTAATACAATTAATACAATTAATAATTTGA
1 TTTACTAATCAAATGTTAGATTTT-GTTACAA-AATTAATACAATTAATACAATTAATAATTTGA
52805713 TAAA
64 TAAA
*
52805717 TTTACTAATCAAATGTTAGATTTTATTACAAAAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTGTTAC-AAAATTAATACAATTAATACAATTAATAATTTGAT
*
52805780 AAT
65 AAA
52805783 TTTACTAA
1 TTTACTAA
52805791 CAATTAATTT
Statistics
Matches: 135, Mismatches: 3, Indels: 10
0.91 0.02 0.07
Matches are distributed among these distances:
66 27 0.20
67 2 0.01
68 103 0.76
69 3 0.02
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (67 bp):
TTTACTAATCAAATGTTAGATTTTGTTACAAAATTAATACAATTAATACAATTAATAATTTGATA
AA
Found at i:52805693 original size:9 final size:9
Alignment explanation
Indices: 52805679--52805706 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
52805669 TTTTAGTACA
52805679 ACAATTAAT
1 ACAATTAAT
52805688 ACAATTAAT
1 ACAATTAAT
52805697 ACAATTAAT
1 ACAATTAAT
52805706 A
1 A
52805707 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:52805800 original size:16 final size:16
Alignment explanation
Indices: 52805779--52805820 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
52805769 AATAATTTGA
*
52805779 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
52805795 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
52805811 TAGTTTTAAT
1 TAATTTTAAT
52805821 TTTATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:52805804 original size:22 final size:23
Alignment explanation
Indices: 52805794--52805855 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
52805784 TTACTAACAA
* * *
52805794 TTAATTTTA-ATAACAATTAGTT
1 TTAATTTTATATAAAAAATAATT
*
52805816 TTAATTTTATTTAAAAAATAATT
1 TTAATTTTATATAAAAAATAATT
*
52805839 TTAATTTTA-ATTAAAAA
1 TTAATTTTATATAAAAAA
52805856 CGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTAATTTTATATAAAAAATAATT
Found at i:52811237 original size:11 final size:10
Alignment explanation
Indices: 52811210--52811262 Score: 54
Period size: 11 Copynumber: 5.0 Consensus size: 10
52811200 AAATAAATCC
52811210 TTTCTCT-AA
1 TTTCTCTCAA
52811219 TTTCCTCTCAA
1 TTT-CTCTCAA
52811230 TTTGCTCTCAA
1 TTT-CTCTCAA
*
52811241 TTTTCTTTCAAA
1 -TTTCTCTC-AA
52811253 TTTCTCTCAA
1 TTTCTCTCAA
52811263 ATCCCTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
9 3 0.08
10 6 0.16
11 23 0.62
12 5 0.14
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.51
Consensus pattern (10 bp):
TTTCTCTCAA
Found at i:52811242 original size:22 final size:22
Alignment explanation
Indices: 52811210--52811262 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
52811200 AAATAAATCC
52811210 TTTCTCT-AATTTCCTCTC-AA
1 TTTCTCTCAATTTCCTCTCAAA
* *
52811230 TTTGCTCTCAATTTTCTTTCAAA
1 TTT-CTCTCAATTTCCTCTCAAA
52811253 TTTCTCTCAA
1 TTTCTCTCAA
52811263 ATCCCTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 3 0.11
21 4 0.14
22 16 0.57
23 5 0.18
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTCTCTCAATTTCCTCTCAAA
Found at i:52814656 original size:126 final size:126
Alignment explanation
Indices: 52814424--52814714 Score: 456
Period size: 126 Copynumber: 2.3 Consensus size: 126
52814414 CAGGCCATGC
* * *
52814424 GCCACTATAGCAAAAGCGCGTCCACATGGGAGCTTCTTTCAGTATTTCTGCTGACAAAGCATCCT
1 GCCACTGTAGCAAAAGCGCGTCCACATGGAAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
* * *
52814489 GCTTAAAGCGTTTTTGACACTGTTTACTCATAAACGTCTACTCAAAATTATTTTTTCAAGA
66 GCTTAAAGCGTTTTTGACACTATTTACTCAGAAACGTCTACTCAAAATTATTTTCTCAAGA
* *
52814550 GCTACTGTAGCAAAAGCGCGTCCACATGGAAGCTTTTTTCAGTACTTCTGCTGACAAAGCATCCT
1 GCCACTGTAGCAAAAGCGCGTCCACATGGAAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
* * *
52814615 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTCTCAGGA
66 GCTTAAAGCGTTTTTGACACTATTTACTCAGAAACGTCTACTCAAAATTATTTTCTCAAGA
** *
52814676 GCCACTGTAGCAAAAGCGCGTCCATGTGGGAGCTTCTTT
1 GCCACTGTAGCAAAAGCGCGTCCACATGGAAGCTTCTTT
52814715 AAATTAACAA
Statistics
Matches: 149, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 149 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (126 bp):
GCCACTGTAGCAAAAGCGCGTCCACATGGAAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
GCTTAAAGCGTTTTTGACACTATTTACTCAGAAACGTCTACTCAAAATTATTTTCTCAAGA
Found at i:52815187 original size:6 final size:6
Alignment explanation
Indices: 52815170--52815210 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
52815160 ATACCAAAAA
*
52815170 CCTAAC CTTAAC CCTAAC CCTAAC CCTAAC CCTAAC CCTAA
1 CCTAAC CCTAAC CCTAAC CCTAAC CCTAAC CCTAAC CCTAA
52815211 ACCAATAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.34, C:0.46, G:0.00, T:0.20
Consensus pattern (6 bp):
CCTAAC
Found at i:52816225 original size:16 final size:16
Alignment explanation
Indices: 52816197--52816229 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52816187 TGCATCTAAC
52816197 ATTTATATTTTTTTTA
1 ATTTATATTTTTTTTA
52816213 ATTTA-ATTCTTTTTTA
1 ATTTATATT-TTTTTTA
52816229 A
1 A
52816230 GCTTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTATATTTTTTTTA
Found at i:52822821 original size:13 final size:13
Alignment explanation
Indices: 52822803--52822828 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52822793 AAAAAGTACA
52822803 TTATTTTATTTTT
1 TTATTTTATTTTT
52822816 TTATTTTATTTTT
1 TTATTTTATTTTT
52822829 GTTCATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTATTTTATTTTT
Done.