Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 79 of 185
Found at i:24305624 original size:115 final size:112
Alignment explanation
Indices: 24305482--24305868 Score: 365
Period size: 115 Copynumber: 3.4 Consensus size: 112
24305472 GCAGCATCGT
* * *
24305482 TTTTATCCTT-TTCTTTAGCGGTGTTTCCTCAAAAACGCCGCAACAGGTTGTTCTTTACCGGCGT
1 TTTTAT-CTTGTT-TTTAGTGGCGTTTCCTCAAAAACGCCGCAAAAGGTTGTTCTTTACCGGCGT
*
24305546 TTTCAACAAAAATGCCGCAAATATGCATTAAGAGTGCAAAACGTCGTCA
64 TTTCAACAAAAACGCCGCAAATATGCATTAAGAGTGCAAAACGTCGTCA
* * * * *
24305595 TTTTCCATGCTTGTTTTTAGTGGCGTTTCCTTAGAAACGTCGCAAAATGTTGTTCTTTATCGGCG
1 TTTT--AT-CTTGTTTTTAGTGGCGTTTCCTCAAAAACGCCGCAAAAGGTTGTTCTTTACCGGCG
** * * * * * *
24305660 TTCACAACAAAAACGCCACAAAAATGCATTAAGAGTACAAAATGTTGTCGTT
63 TTTTCAACAAAAACGCCGCAAATATGCATTAAGAGTGCAAAACGTCGTC--A
* * * *
24305712 TTTTATCATTG-TTTTAGTGGC-TTTCCACAAAAAATGCCGCAAAAGGTTGTGCATTACCGGCGT
1 TTTTATC-TTGTTTTTAGTGGCGTTTCCTC-AAAAACGCCGCAAAAGGTTGTTCTTTACCGGCGT
* *
24305775 TTTCAA-AAAAACGCCGCTAAGT-TGTATTAAGAGTGCAAAACGTTCG-CA
64 TTTCAACAAAAACGCCGC-AAATATGCATTAAGAGTGCAAAACG-TCGTCA
* *
24305823 TTTGTATCCTTGTTTTTAGTGGCATTT-TTGACAAAAACGCCGCAAA
1 TTT-TAT-CTTGTTTTTAGTGGCGTTTCCT--CAAAAACGCCGCAAA
24305869 TATGTATTGT
Statistics
Matches: 219, Mismatches: 40, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
111 3 0.01
112 6 0.03
113 48 0.22
114 62 0.28
115 94 0.43
116 2 0.01
117 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (112 bp):
TTTTATCTTGTTTTTAGTGGCGTTTCCTCAAAAACGCCGCAAAAGGTTGTTCTTTACCGGCGTTT
TCAACAAAAACGCCGCAAATATGCATTAAGAGTGCAAAACGTCGTCA
Found at i:24305864 original size:74 final size:74
Alignment explanation
Indices: 24305781--24306025 Score: 269
Period size: 74 Copynumber: 3.3 Consensus size: 74
24305771 GCGTTTTCAA
* * * * *
24305781 AAAAACGCCGCTAAGT-TGTATTAAGAGTGCAAAACGTTCG-CATTTGTATCCTTGTTTTTAGTG
1 AAAAACGCCGC-AAATATGTATTAAGAGAGCAAAACG-TCGTCGTTTTTATCATTGTTTTTAGTG
*
24305844 GCATTTTTGAC
64 GCATTTTCGAC
** * * *
24305855 AAAAACGCCGCAAATATGTATTGTGAGAGAAAAATGACGTCGTTTTTATCATTGTTTTTAGTGGC
1 AAAAACGCCGCAAATATGTATTAAGAGAGCAAAACGTCGTCGTTTTTATCATTGTTTTTAGTGGC
*
24305920 ATTTTCGGC
66 ATTTTCGAC
* * * **
24305929 ATAAACGCTGCAAATATGTATTAAGAGAGCAAAGCGTCGTCGTTTTTATCATTGTTTTTACCGGC
1 AAAAACGCCGCAAATATGTATTAAGAGAGCAAAACGTCGTCGTTTTTATCATTGTTTTTAGTGGC
* *
24305994 GTTTTCAAC
66 ATTTTCGAC
* *
24306003 AAAAACGCCGCAGATGTGTATTA
1 AAAAACGCCGCAAATATGTATTA
24306026 GTTGTTTATG
Statistics
Matches: 140, Mismatches: 29, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
73 5 0.04
74 135 0.96
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (74 bp):
AAAAACGCCGCAAATATGTATTAAGAGAGCAAAACGTCGTCGTTTTTATCATTGTTTTTAGTGGC
ATTTTCGAC
Found at i:24308292 original size:19 final size:19
Alignment explanation
Indices: 24308270--24308331 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
24308260 ATTTTTAAAA
*
24308270 TTATATAATTTGGATTAAT
1 TTATATAATTTGAATTAAT
*
24308289 TTATTTAAATATT-AATTAAT
1 TTATAT-AAT-TTGAATTAAT
* *
24308309 TAATATAATTTGCATTAAT
1 TTATATAATTTGAATTAAT
24308328 TTAT
1 TTAT
24308332 TTAAATATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.06
19 17 0.50
20 13 0.38
21 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (19 bp):
TTATATAATTTGAATTAAT
Found at i:24308306 original size:20 final size:20
Alignment explanation
Indices: 24308283--24308348 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
24308273 TATAATTTGG
24308283 ATTAATTTATTTAAATATTA
1 ATTAATTTATTTAAATATTA
* * *
24308303 ATTAATTAATAT-AAT-TTGC
1 ATTAATTTATTTAAATATT-A
24308322 ATTAATTTATTTAAATATTA
1 ATTAATTTATTTAAATATTA
*
24308342 TTTAATT
1 ATTAATT
24308349 AGAATAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 2 0.06
19 13 0.36
20 19 0.53
21 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
ATTAATTTATTTAAATATTA
Found at i:24308320 original size:39 final size:39
Alignment explanation
Indices: 24308268--24308358 Score: 141
Period size: 39 Copynumber: 2.4 Consensus size: 39
24308258 CAATTTTTAA
*
24308268 AATT-ATATAATTTGGATTAATTTATTTAAATATTAATT
1 AATTAATATAATTTGCATTAATTTATTTAAATATTAATT
*
24308306 AATTAATATAATTTGCATTAATTTATTTAAATATTATTT
1 AATTAATATAATTTGCATTAATTTATTTAAATATTAATT
24308345 AATTAGA-ATAATTT
1 AATTA-ATATAATTT
24308359 TTATAAATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
38 4 0.08
39 44 0.90
40 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (39 bp):
AATTAATATAATTTGCATTAATTTATTTAAATATTAATT
Found at i:24308344 original size:15 final size:15
Alignment explanation
Indices: 24308326--24308374 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
24308316 ATTTGCATTA
24308326 ATTTATTTAAATATT
1 ATTTATTTAAATATT
*
24308341 ATTTAATTAGAATA--
1 ATTTATTTA-AATATT
24308355 ATTT-TTATAAATATT
1 ATTTATT-TAAATATT
24308370 ATTTA
1 ATTTA
24308375 ACTAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
13 5 0.19
14 6 0.22
15 12 0.44
16 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
ATTTATTTAAATATT
Found at i:24308357 original size:29 final size:29
Alignment explanation
Indices: 24308324--24308390 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
24308314 TAATTTGCAT
* *
24308324 TAATTTATT-TAAATATTATTTAATTAGAA
1 TAATTT-TTATAAATATTATTTAACTAAAA
24308353 TAATTTTTATAAATATTATTTAACTAAAA
1 TAATTTTTATAAATATTATTTAACTAAAA
24308382 TAAATTTTT
1 T-AATTTTT
24308391 TCCAGGTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 2 0.06
29 25 0.74
30 7 0.21
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (29 bp):
TAATTTTTATAAATATTATTTAACTAAAA
Found at i:24308579 original size:9 final size:9
Alignment explanation
Indices: 24308565--24308790 Score: 105
Period size: 9 Copynumber: 25.8 Consensus size: 9
24308555 TACATGATAT
24308565 CATAACTTA
1 CATAACTTA
24308574 CATAACTTA
1 CATAACTTA
24308583 CATAA--TA
1 CATAACTTA
*
24308590 CATAA-ATA
1 CATAACTTA
* * *
24308598 TATATCATA
1 CATAACTTA
*
24308607 TGATAACTTA
1 -CATAACTTA
**
24308617 TGTAACTTA
1 CATAACTTA
24308626 CATAACTTA
1 CATAACTTA
24308635 CATAA--TA
1 CATAACTTA
*
24308642 CATAA-ATA
1 CATAACTTA
* *
24308650 TATATCATATA
1 CATAAC-T-TA
24308661 -ATAACTTA
1 CATAACTTA
24308669 CATAACTTA
1 CATAACTTA
24308678 CATAACTTA
1 CATAACTTA
*
24308687 CGTAA--TA
1 CATAACTTA
*
24308694 CATAA-ATA
1 CATAACTTA
* ** *
24308702 TATTTCATA
1 CATAACTTA
*
24308711 TCATAATTTA
1 -CATAACTTA
24308721 CATAACTTA
1 CATAACTTA
*
24308730 CATACCTTA
1 CATAACTTA
*
24308739 CATAAATT-
1 CATAACTTA
* * *
24308747 TATATCATA
1 CATAACTTA
*
24308756 TCATAGCTTA
1 -CATAACTTA
24308766 CATAACTTA
1 CATAACTTA
*
24308775 CAAAACTTA
1 CATAACTTA
*
24308784 CTTAACT
1 CATAACT
24308791 CACGTAATAC
Statistics
Matches: 166, Mismatches: 38, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
7 20 0.12
8 20 0.12
9 104 0.63
10 20 0.12
11 2 0.01
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (9 bp):
CATAACTTA
Found at i:24308624 original size:52 final size:52
Alignment explanation
Indices: 24308565--24308809 Score: 298
Period size: 52 Copynumber: 4.7 Consensus size: 52
24308555 TACATGATAT
*
24308565 CATAACTTACATAACTTACATAATACATAAATATATATCATATGATAACTTA
1 CATAACTTACATAACTTACATAATACATAAATATATATCATATAATAACTTA
**
24308617 TGTAACTTACATAACTTACATAATACATAAATATATATCATATAATAACTTA
1 CATAACTTACATAACTTACATAATACATAAATATATATCATATAATAACTTA
* * * *
24308669 CATAACTTACATAACTTACGTAATACATAAATATATTTCATATCATAATTTA
1 CATAACTTACATAACTTACATAATACATAAATATATATCATATAATAACTTA
* **
24308721 CATAACTTACATACCTTACAT-A-A-ATTTATATCATATCATAGCTTACATAACTTA
1 CATAACTTACATAACTTACATAATACATAAATAT-ATATCATA---TA-ATAACTTA
* * * *
24308775 CAAAACTTACTTAACTCACGTAATACATAAATATA
1 CATAACTTACATAACTTACATAATACATAAATATA
24308810 CACTTGAAAA
Statistics
Matches: 162, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
49 6 0.04
50 8 0.05
51 1 0.01
52 114 0.70
53 1 0.01
54 23 0.14
55 1 0.01
56 2 0.01
57 6 0.04
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.36
Consensus pattern (52 bp):
CATAACTTACATAACTTACATAATACATAAATATATATCATATAATAACTTA
Found at i:24308756 original size:45 final size:43
Alignment explanation
Indices: 24308627--24308776 Score: 147
Period size: 45 Copynumber: 3.2 Consensus size: 43
24308617 TGTAACTTAC
24308627 ATAACTTACATAATACATAAATATATATCATATAATAACTTACATAACTTAC
1 ATAACTTACATAATACATAAATATATATC-----AT-A--T-CATAACTTAC
* * *
24308679 ATAACTTACGTAATACATAAATATATTTCATATCATAATTTAC
1 ATAACTTACATAATACATAAATATATATCATATCATAACTTAC
* * *
24308722 ATAACTTACATACCTTACATAAATTTATATCATATCATAGCTTAC
1 ATAACTTACATA--ATACATAAATATATATCATATCATAACTTAC
24308767 ATAACTTACA
1 ATAACTTACA
24308777 AAACTTACTT
Statistics
Matches: 87, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
43 20 0.23
44 1 0.01
45 36 0.41
46 1 0.01
47 2 0.02
52 27 0.31
ACGTcount: A:0.45, C:0.17, G:0.01, T:0.37
Consensus pattern (43 bp):
ATAACTTACATAATACATAAATATATATCATATCATAACTTAC
Found at i:24308784 original size:45 final size:45
Alignment explanation
Indices: 24308669--24308784 Score: 155
Period size: 45 Copynumber: 2.6 Consensus size: 45
24308659 TAATAACTTA
* *
24308669 CATAACTTACATAACTTACGTAA--TACATAAATATATTTCATAT
1 CATAACTTACATAACTTACATAACTTACATAAATATATATCATAT
* * *
24308712 CATAATTTACATAACTTACATACCTTACATAAATTTATATCATAT
1 CATAACTTACATAACTTACATAACTTACATAAATATATATCATAT
* *
24308757 CATAGCTTACATAACTTACAAAACTTAC
1 CATAACTTACATAACTTACATAACTTAC
24308785 TTAACTCACG
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 20 0.32
45 42 0.68
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (45 bp):
CATAACTTACATAACTTACATAACTTACATAAATATATATCATAT
Found at i:24314159 original size:13 final size:14
Alignment explanation
Indices: 24314143--24314171 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
24314133 TTATAAATAT
24314143 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
24314156 TTATAATGGTTTAA
1 TTATAATGGTTTAA
24314170 TT
1 TT
24314172 CATCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:24333545 original size:29 final size:29
Alignment explanation
Indices: 24333500--24333615 Score: 121
Period size: 29 Copynumber: 4.0 Consensus size: 29
24333490 TACCTGTATC
* *
24333500 TGGCCCATTATGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
24333528 TGGCCCCTTTAGGCCCAAATCACCTGT-ATA
1 TGG-CCCATTAGGCCCAAATCACAT-TCATA
*
24333558 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* * *
24333587 TGGCCCGTTAGGCTC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
24333615 T
1 T
24333616 TCATGCTCAC
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
28 16 0.22
29 45 0.61
30 12 0.16
31 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:24333696 original size:17 final size:18
Alignment explanation
Indices: 24333674--24333707 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24333664 TGCCTATTAT
24333674 GGGCCCA-ATAGCCCATC
1 GGGCCCATATAGCCCATC
*
24333691 GGGCCCATTTAGCCCAT
1 GGGCCCATATAGCCCAT
24333708 TCTGGCCCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.38, G:0.24, T:0.18
Consensus pattern (18 bp):
GGGCCCATATAGCCCATC
Found at i:24333847 original size:16 final size:16
Alignment explanation
Indices: 24333826--24333868 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
24333816 GTAGCCAAAC
24333826 TTTCAGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
24333842 TTTCAGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
*
24333858 TTTCAACTTTT
1 TTTCAGCTTTT
24333869 ACCGATTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.49
Consensus pattern (16 bp):
TTTCAGCTTTTCGGCA
Found at i:24339363 original size:26 final size:26
Alignment explanation
Indices: 24339331--24339401 Score: 99
Period size: 26 Copynumber: 2.7 Consensus size: 26
24339321 CGGTCACCTA
24339331 TTCTCTCCCTTGCTGAATTCTTTTAC
1 TTCTCTCCCTTGCTGAATTCTTTTAC
* *
24339357 TTTTCTCCCTTG-TCGAATTCTTTTTC
1 TTCTCTCCCTTGCT-GAATTCTTTTAC
*
24339383 TTCTCTCCCTTGCCGAATT
1 TTCTCTCCCTTGCTGAATT
24339402 TATTTGCTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 1 0.03
26 38 0.97
ACGTcount: A:0.10, C:0.31, G:0.08, T:0.51
Consensus pattern (26 bp):
TTCTCTCCCTTGCTGAATTCTTTTAC
Found at i:24344033 original size:23 final size:23
Alignment explanation
Indices: 24343981--24344033 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
24343971 AACATGGACA
* **
24343981 ACATTAAGACAATGTTTAAATGC
1 ACATTAAGACAAGGTTTAAACAC
24344004 ACATTAAGACAAGGTTTAAACAC
1 ACATTAAGACAAGGTTTAAACAC
*
24344027 ACTTTAA
1 ACATTAA
24344034 TTTGTAGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.28
Consensus pattern (23 bp):
ACATTAAGACAAGGTTTAAACAC
Found at i:24344191 original size:38 final size:39
Alignment explanation
Indices: 24344094--24344206 Score: 174
Period size: 38 Copynumber: 2.9 Consensus size: 39
24344084 TGTAAACAAG
* *
24344094 TATTAAAGATGTTCAAACTATGACATAATTAAAGACCCA
1 TATTAATGATGTTCAAATTATGACATAATTAAAGACCCA
* *
24344133 TATTAATGATGTTCAGATTATGACATAATTAAA-ACTCA
1 TATTAATGATGTTCAAATTATGACATAATTAAAGACCCA
*
24344171 TATTAATGATATTCAAATTATGACATAATTAAAGAC
1 TATTAATGATGTTCAAATTATGACATAATTAAAGAC
24344207 TTAATGTAAC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
38 35 0.52
39 32 0.48
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.34
Consensus pattern (39 bp):
TATTAATGATGTTCAAATTATGACATAATTAAAGACCCA
Found at i:24345589 original size:27 final size:27
Alignment explanation
Indices: 24345559--24345736 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
24345549 ATATTGAGTC
* * * *
24345559 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
24345586 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
24345613 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
24345641 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
24345668 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
24345695 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
24345722 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
24345737 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:24345698 original size:82 final size:81
Alignment explanation
Indices: 24345580--24345735 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
24345570 TGCTATATAA
* *
24345580 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
24345645 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
24345662 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
24345726 CACTTAGTGC
65 CACTTAGTGC
24345736 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:24347713 original size:15 final size:14
Alignment explanation
Indices: 24347641--24347723 Score: 53
Period size: 15 Copynumber: 5.6 Consensus size: 14
24347631 CATCAAAACT
*
24347641 TAAATAAATAATAA
1 TAAATAAAAAATAA
* * *
24347655 TACTATACATAATAA
1 TA-AATAAAAAATAA
*
24347670 T-AATAGGAAAACTAA
1 TAAATA--AAAAATAA
24347685 T-AATAATAATAATAA
1 TAAATAA-AA-AATAA
24347700 TAAACTAAAAAATAA
1 TAAA-TAAAAAATAA
24347715 TAAATAAAA
1 TAAATAAAA
24347724 TGTAAAAGTG
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
13 4 0.07
14 9 0.16
15 35 0.64
16 4 0.07
17 3 0.05
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (14 bp):
TAAATAAAAAATAA
Found at i:24347713 original size:24 final size:23
Alignment explanation
Indices: 24347663--24347717 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
24347653 AATACTATAC
*
24347663 ATAATAATAATAGGAAAACTAATA
1 ATAATAATAATA-GAAAACTAAAA
24347687 ATAATAATAATA-ATAAACTAAAAA
1 ATAATAATAATAGA-AAACT-AAAA
24347711 ATAATAA
1 ATAATAA
24347718 ATAAAATGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 1 0.04
23 5 0.18
24 22 0.79
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (23 bp):
ATAATAATAATAGAAAACTAAAA
Found at i:24347717 original size:3 final size:3
Alignment explanation
Indices: 24347647--24347702 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
24347637 AACTTAAATA
* **
24347647 AAT AAT AAT ACT -AT ACAT AAT AAT AAT AGG AA- AACT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
24347692 AAT AAT AAT AA
1 AAT AAT AAT AA
24347703 ACTAAAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
2 3 0.07
3 36 0.82
4 5 0.11
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:24349220 original size:46 final size:47
Alignment explanation
Indices: 24349168--24349262 Score: 138
Period size: 47 Copynumber: 2.0 Consensus size: 47
24349158 GTTGAATTTA
* **
24349168 AAGCTTGCTAAA-TTGCTCTTAATATTTCTGGATAAGTTACTTAGTT
1 AAGCTTGCTAAATTTGCCCTTAATATTTCCAGATAAGTTACTTAGTT
* *
24349214 AAGCTTGTTAAATTTGCCCTTATTATTTCCAGATAAGTTACTTAGTT
1 AAGCTTGCTAAATTTGCCCTTAATATTTCCAGATAAGTTACTTAGTT
24349261 AA
1 AA
24349263 AGAAAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
46 11 0.26
47 32 0.74
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (47 bp):
AAGCTTGCTAAATTTGCCCTTAATATTTCCAGATAAGTTACTTAGTT
Found at i:24350133 original size:45 final size:45
Alignment explanation
Indices: 24350069--24350288 Score: 350
Period size: 45 Copynumber: 4.9 Consensus size: 45
24350059 CGCACAGTAT
* *
24350069 TATTCGAGCCTTCGAGCCTAGCAGGCTATAATACCGGTGAGATAC
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* *
24350114 TATTCGGGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* * *
24350159 TATTTGGGCCTTCGACCCTAGCAGGCTATAATGCCGATGAGATAC
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* *
24350204 TATTCGGGCCTTCGAACTTAGCAGGCTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
*
24350249 TATTCGGGCTTTCGAGCCTAGCAGGCTATAATGCCGGTGA
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
24350289 ATGAATTCAG
Statistics
Matches: 159, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 159 1.00
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (45 bp):
TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
Found at i:24356677 original size:31 final size:31
Alignment explanation
Indices: 24356642--24356717 Score: 143
Period size: 31 Copynumber: 2.5 Consensus size: 31
24356632 CTTCCTGATT
24356642 AAATCCAACCAAAAATAGCAAATATAGCATG
1 AAATCCAACCAAAAATAGCAAATATAGCATG
*
24356673 AAATCCAACCAAAAATATCAAATATAGCATG
1 AAATCCAACCAAAAATAGCAAATATAGCATG
24356704 AAATCCAACCAAAA
1 AAATCCAACCAAAA
24356718 CCATTAAATC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.57, C:0.21, G:0.07, T:0.16
Consensus pattern (31 bp):
AAATCCAACCAAAAATAGCAAATATAGCATG
Found at i:24356977 original size:21 final size:21
Alignment explanation
Indices: 24356953--24356993 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
24356943 TCTACTGCCA
*
24356953 TCGTTGCTACCTCTGCCTCCT
1 TCGTTGCTACCACTGCCTCCT
*
24356974 TCGTTGTTACCACTGCCTCC
1 TCGTTGCTACCACTGCCTCC
24356994 CTCTCTACTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.41, G:0.15, T:0.37
Consensus pattern (21 bp):
TCGTTGCTACCACTGCCTCCT
Found at i:24357443 original size:13 final size:14
Alignment explanation
Indices: 24357417--24357445 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
24357407 ACTAATGACG
24357417 AATTAAAGCATTAT
1 AATTAAAGCATTAT
24357431 AATTAAA-CATTAT
1 AATTAAAGCATTAT
24357444 AA
1 AA
24357446 ATATTTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.34
Consensus pattern (14 bp):
AATTAAAGCATTAT
Found at i:24362524 original size:9 final size:9
Alignment explanation
Indices: 24362510--24362666 Score: 85
Period size: 9 Copynumber: 18.0 Consensus size: 9
24362500 TTACGTAAGT
*
24362510 TAAGTTTTG
1 TAAGTTATG
24362519 TAAGTTATG
1 TAAGTTATG
24362528 TAAGTTATG
1 TAAGTTATG
* *
24362537 ATATGCTAT-
1 -TAAGTTATG
* *
24362546 AAATTTATG
1 TAAGTTATG
*
24362555 TAAGGTATG
1 TAAGTTATG
24362564 TAAGTTATG
1 TAAGTTATG
*
24362573 TAAATTATG
1 TAAGTTATG
* ** *
24362582 ATATGAAATA
1 -TAAGTTATG
*
24362592 T-ATTTATG
1 TAAGTTATG
**
24362600 T-A-TTACA
1 TAAGTTATG
*
24362607 TAATTTATG
1 TAAGTTATG
*
24362616 TAAGTTATA
1 TAAGTTATG
*
24362625 T-ATTTATG
1 TAAGTTATG
24362633 T-A-TTATG
1 TAAGTTATG
*
24362640 TAAGTTTTG
1 TAAGTTATG
24362649 TAAGTTATG
1 TAAGTTATG
24362658 TAAGTTATG
1 TAAGTTATG
24362667 ATATGATATA
Statistics
Matches: 109, Mismatches: 32, Indels: 14
0.70 0.21 0.09
Matches are distributed among these distances:
7 10 0.09
8 17 0.16
9 72 0.66
10 10 0.09
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:24362627 original size:33 final size:33
Alignment explanation
Indices: 24362589--24362656 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
24362579 ATGATATGAA
24362589 ATATATTTATGTATTACATAA-TTTATGTAAGTT
1 ATATATTTATGTATTACATAAGTTT-TGTAAGTT
**
24362622 ATATATTTATGTATTATGTAAGTTTTGTAAGTT
1 ATATATTTATGTATTACATAAGTTTTGTAAGTT
24362655 AT
1 AT
24362657 GTAAGTTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (33 bp):
ATATATTTATGTATTACATAAGTTTTGTAAGTT
Found at i:24362631 original size:17 final size:16
Alignment explanation
Indices: 24362589--24362638 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
24362579 ATGATATGAA
24362589 ATATATTTATGT-ATT
1 ATATATTTATGTAATT
*
24362604 ACATAATTTATGTAAGTT
1 ATAT-ATTTATGTAA-TT
24362622 ATATATTTATGT-ATT
1 ATATATTTATGTAATT
24362637 AT
1 AT
24362639 GTAAGTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 7 0.23
16 9 0.30
17 9 0.30
18 5 0.17
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (16 bp):
ATATATTTATGTAATT
Found at i:24362651 original size:85 final size:88
Alignment explanation
Indices: 24362523--24362682 Score: 236
Period size: 85 Copynumber: 1.9 Consensus size: 88
24362513 GTTTTGTAAG
24362523 TTATGTAAGTTATGATATGCTATAAATTTATGTAAGGTATGTAAGTTATGTAAATTATGATATGA
1 TTATGTAAGTTATGATATGCTATAAATTTATGTAAGGTATGTAAGTTATGTAAATTATGATATGA
24362588 AATATATTTATGTATTACATAAT
66 AATATATTTATGTATTACATAAT
* ** * * *
24362611 TTATGTAAGTTAT-ATAT-TTATGTA-TTATGTAAGTTTTGTAAGTTATGTAAGTTATGATATGA
1 TTATGTAAGTTATGATATGCTATAAATTTATGTAAGGTATGTAAGTTATGTAAATTATGATATGA
*
24362673 TATATATTTA
66 AATATATTTA
24362683 ACATTAAGAT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
85 44 0.68
86 4 0.06
87 4 0.06
88 13 0.20
ACGTcount: A:0.36, C:0.01, G:0.15, T:0.47
Consensus pattern (88 bp):
TTATGTAAGTTATGATATGCTATAAATTTATGTAAGGTATGTAAGTTATGTAAATTATGATATGA
AATATATTTATGTATTACATAAT
Found at i:24363953 original size:20 final size:20
Alignment explanation
Indices: 24363928--24363968 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
24363918 GATGGTAGAG
24363928 TCGATTCCAGCAAATTAAAT
1 TCGATTCCAGCAAATTAAAT
24363948 TCGATTCCAGCAAATTAAAT
1 TCGATTCCAGCAAATTAAAT
24363968 T
1 T
24363969 ACACCTGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (20 bp):
TCGATTCCAGCAAATTAAAT
Found at i:24366885 original size:41 final size:41
Alignment explanation
Indices: 24366840--24366918 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
24366830 GCGTTTGGAT
*
24366840 AAAAAATGTCGCTATATATCAACTTTTT-GCGGCGTTTGTTA
1 AAAAAATGCCGCTATATATC-ACTTTTTAGCGGCGTTTGTTA
* * *
24366881 AAAAAATGCCGCTATTTCTCAGTTTTTAGCGGCGTTTG
1 AAAAAATGCCGCTATATATCACTTTTTAGCGGCGTTTG
24366919 GACTATAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 6 0.18
41 27 0.82
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (41 bp):
AAAAAATGCCGCTATATATCACTTTTTAGCGGCGTTTGTTA
Found at i:24366933 original size:41 final size:41
Alignment explanation
Indices: 24366882--24367071 Score: 245
Period size: 41 Copynumber: 4.6 Consensus size: 41
24366872 CGTTTGTTAA
*
24366882 AAAAATGCCGCTATTTCTCAGTTTTTAGCGGCGTTTGGACT
1 AAAAACGCCGCTATTTCTCAGTTTTTAGCGGCGTTTGGACT
* * * * *
24366923 ATAAACGCCGCTATTTCTGAGTTTTTAGCGGCATTTGAACC
1 AAAAACGCCGCTATTTCTCAGTTTTTAGCGGCGTTTGGACT
* * * *
24366964 AAAAACACCGCTATTTCTGAGCTTTTAGCAGCGTTTGGACT
1 AAAAACGCCGCTATTTCTCAGTTTTTAGCGGCGTTTGGACT
* * *
24367005 AAAAACGCCACTATTGCTCAGTTTTTAGCGGCGTTTGGATT
1 AAAAACGCCGCTATTTCTCAGTTTTTAGCGGCGTTTGGACT
* *
24367046 AAAAACGCCGATATTGCTCAGTTTTT
1 AAAAACGCCGCTATTTCTCAGTTTTT
24367072 TGCAACATTT
Statistics
Matches: 127, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 127 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (41 bp):
AAAAACGCCGCTATTTCTCAGTTTTTAGCGGCGTTTGGACT
Found at i:24366935 original size:82 final size:81
Alignment explanation
Indices: 24366830--24367041 Score: 198
Period size: 82 Copynumber: 2.6 Consensus size: 81
24366820 ATTTTTTATG
* * * **
24366830 GCGTTTGGA-TAAAAAATGTCGCTATATATC-AACTTTTT-GCGGCGTTTGTTAA-AAAAATGCC
1 GCGTTTGGACT-AAAAACGCCGCTAT-T-TCTAACTTTTTAGCGGCATTTG--AACAAAAACACC
* *
24366891 GCTATTTCTCAGTTTTTAGCG
61 GCTATTTCTCAGCTTTTAGCA
* * *
24366912 GCGTTTGGACTATAAACGCCGCTATTTCTGAGTTTTTAGCGGCATTTGAACCAAAAACACCGCTA
1 GCGTTTGGACTAAAAACGCCGCTATTTCTAACTTTTTAGCGGCATTTGAA-CAAAAACACCGCTA
*
24366977 TTTCTGAGCTTTTAGCA
65 TTTCTCAGCTTTTAGCA
* * * * *
24366994 GCGTTTGGACTAAAAACGCCACTATTGCTCAGTTTTTAGCGGCGTTTG
1 GCGTTTGGACTAAAAACGCCGCTATTTCTAACTTTTTAGCGGCATTTG
24367042 GATTAAAAAC
Statistics
Matches: 109, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
80 4 0.04
81 7 0.06
82 97 0.89
83 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (81 bp):
GCGTTTGGACTAAAAACGCCGCTATTTCTAACTTTTTAGCGGCATTTGAACAAAAACACCGCTAT
TTCTCAGCTTTTAGCA
Found at i:24367945 original size:36 final size:36
Alignment explanation
Indices: 24367871--24367946 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
24367861 ATTAACATCG
* *
24367871 AATAGGATAATAGTTTATGTTGCATTTTATCTTCAT
1 AATAGGATAATAGTTTATATTGCATTTTATATTCAT
* * *
24367907 AATAGGATAATTGTTTATATTGCATTTTTTATTTAT
1 AATAGGATAATAGTTTATATTGCATTTTATATTCAT
24367943 AATA
1 AATA
24367947 TATATTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (36 bp):
AATAGGATAATAGTTTATATTGCATTTTATATTCAT
Found at i:24368290 original size:16 final size:17
Alignment explanation
Indices: 24368271--24368308 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
24368261 AAAAAAATTT
24368271 TAAATTT-TTAAAAAAA
1 TAAATTTATTAAAAAAA
**
24368287 TAAATTTATTTTAAAAA
1 TAAATTTATTAAAAAAA
24368304 TAAAT
1 TAAAT
24368309 CCAGATGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTATTAAAAAAA
Found at i:24370896 original size:22 final size:23
Alignment explanation
Indices: 24370870--24370920 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
24370860 TATTATTTTA
*
24370870 ATTTTAGAATAT-A-TATATTGTT
1 ATTTTAAAATATGATTATA-TGTT
*
24370892 TTTTTAAAATATGATTATATGTT
1 ATTTTAAAATATGATTATATGTT
24370915 ATTTTA
1 ATTTTA
24370921 CTAATCTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 10 0.42
23 10 0.42
24 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (23 bp):
ATTTTAAAATATGATTATATGTT
Found at i:24370988 original size:66 final size:66
Alignment explanation
Indices: 24370918--24371056 Score: 269
Period size: 66 Copynumber: 2.1 Consensus size: 66
24370908 ATATGTTATT
24370918 TTACTAATCTTGTTTACATAATTTGAAATTTTTATTGATGAGAGATAATTTCTTATATATTTTGA
1 TTACTAATCTTGTTTACATAATTTGAAATTTTTATTGATGAGAGATAATTTCTTATATATTTTGA
24370983 C
66 C
24370984 TTACTAATCTTGTTTACATAATTTGAAATTTTTATTGATGAGAGATAATTTCTTATATATTTTGA
1 TTACTAATCTTGTTTACATAATTTGAAATTTTTATTGATGAGAGATAATTTCTTATATATTTTGA
24371049 C
66 C
*
24371050 CTACTAA
1 TTACTAA
24371057 ATGATTAACT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 72 1.00
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.49
Consensus pattern (66 bp):
TTACTAATCTTGTTTACATAATTTGAAATTTTTATTGATGAGAGATAATTTCTTATATATTTTGA
C
Found at i:24371308 original size:29 final size:28
Alignment explanation
Indices: 24371276--24371342 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 28
24371266 ATCTTAATAT
24371276 TAACAATATTTTTTAATACTTTTTTGAAC
1 TAAC-ATATTTTTTAATACTTTTTTGAAC
*
24371305 TAACCGTATTTTTTAATACTTTTTTGAAC
1 TAA-CATATTTTTTAATACTTTTTTGAAC
24371334 TAACATATT
1 TAACATATT
24371343 ATATACAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 5 0.14
29 29 0.83
30 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (28 bp):
TAACATATTTTTTAATACTTTTTTGAAC
Found at i:24372121 original size:17 final size:17
Alignment explanation
Indices: 24372096--24372152 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
24372086 ATGAGAAGCA
24372096 AAATCCAATCTAATAAC
1 AAATCCAATCTAATAAC
* *
24372113 AAATGCAA--TAA-AAA
1 AAATCCAATCTAATAAC
24372127 AAATCCAATCTAATAAC
1 AAATCCAATCTAATAAC
*
24372144 AAATGCAAT
1 AAATCCAAT
24372153 AAAAAAATAC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 9 0.28
15 3 0.09
16 3 0.09
17 17 0.53
ACGTcount: A:0.58, C:0.18, G:0.04, T:0.21
Consensus pattern (17 bp):
AAATCCAATCTAATAAC
Found at i:24372130 original size:31 final size:31
Alignment explanation
Indices: 24372095--24372159 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
24372085 TATGAGAAGC
24372095 AAAATCCAATCTAATAACAAATGCAATAAAA
1 AAAATCCAATCTAATAACAAATGCAATAAAA
24372126 AAAATCCAATCTAATAACAAATGCAATAAAA
1 AAAATCCAATCTAATAACAAATGCAATAAAA
24372157 AAA
1 AAA
24372160 TACTAAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.63, C:0.15, G:0.03, T:0.18
Consensus pattern (31 bp):
AAAATCCAATCTAATAACAAATGCAATAAAA
Found at i:24374504 original size:24 final size:24
Alignment explanation
Indices: 24374477--24374524 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
24374467 TTATTTCCTT
24374477 GTACAGATTTCTCATCTATGTATA
1 GTACAGATTTCTCATCTATGTATA
24374501 GTACAGATTTCTCATCTATGTATA
1 GTACAGATTTCTCATCTATGTATA
24374525 AATACTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (24 bp):
GTACAGATTTCTCATCTATGTATA
Found at i:24379243 original size:122 final size:127
Alignment explanation
Indices: 24379061--24379310 Score: 316
Period size: 126 Copynumber: 2.0 Consensus size: 127
24379051 AAAAAAGAAA
* * *
24379061 AAGCAACTGAGGGTTGGAAAGAGAGAAATAAACAGCCAACAATTCTCCAAAACTGTT-AAAAG-A
1 AAGCAACTGAGGGTTGGAAAGAGAGAAATAAACAGCAAACAACTCTCCAAAACTCTTAAAAAGAA
* * * ** ** *
24379124 -C-TGTTTTAGACATG-TGTTATGTTTCTTTATGTCTGTGTTTACATACCTGAGAATATCTTT
66 CCGTGTTTCAGACATGCT-TCAGGCATCTCAATGTCTGTGTTTACATACCTGAGAATATATTT
*
24379184 AAGCAATTGA-GGTTGG-AAGAGAGAAATAAACAGCAAACAACTCTTCCAAAACTCTTAAAAAGA
1 AAGCAACTGAGGGTTGGAAAGAGAGAAATAAACAGCAAACAACTC-TCCAAAACTCTTAAAAAGA
*
24379247 ACCGTGTTTCAGACATGCTTCAGGCATCTCAATGTCTGTGTTTACCTACCTGAGAATATATTT
65 ACCGTGTTTCAGACATGCTTCAGGCATCTCAATGTCTGTGTTTACATACCTGAGAATATATTT
24379310 A
1 A
24379311 GATTTTTTTT
Statistics
Matches: 108, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
121 25 0.23
122 17 0.16
123 14 0.13
124 1 0.01
125 1 0.01
126 49 0.45
127 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Consensus pattern (127 bp):
AAGCAACTGAGGGTTGGAAAGAGAGAAATAAACAGCAAACAACTCTCCAAAACTCTTAAAAAGAA
CCGTGTTTCAGACATGCTTCAGGCATCTCAATGTCTGTGTTTACATACCTGAGAATATATTT
Found at i:24382220 original size:14 final size:13
Alignment explanation
Indices: 24382198--24382246 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
24382188 TCAGAGGAAT
24382198 CAATTAATCTATA
1 CAATTAATCTATA
*
24382211 CAAGTTAATCTGTA
1 CAA-TTAATCTATA
*
24382225 CCAATTACTCTATA
1 -CAATTAATCTATA
24382239 CAAATTAA
1 C-AATTAA
24382247 AATAATTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 4 0.14
14 22 0.76
15 3 0.10
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.35
Consensus pattern (13 bp):
CAATTAATCTATA
Found at i:24383634 original size:13 final size:13
Alignment explanation
Indices: 24383618--24383683 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
24383608 TTTAAACTAA
*
24383618 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
* *
24383631 ACTTCTCAAAAGT
1 ACTTTTCAAAAGC
* *
24383644 ACTTCTCAAAAAC
1 ACTTTTCAAAAGC
*
24383657 ACTTTTTC-ACAGC
1 AC-TTTTCAAAAGC
24383670 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
24383683 A
1 A
24383684 TTGCCAAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
12 5 0.11
13 35 0.80
14 4 0.09
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:24384920 original size:66 final size:67
Alignment explanation
Indices: 24384813--24384954 Score: 191
Period size: 66 Copynumber: 2.1 Consensus size: 67
24384803 AGCCTCTAAA
* * * *
24384813 GGTACCCC-TTTCTTATATGCATGATAACTTACTAACGATGTTTTTGGATCTAACACGGTCTAGC
1 GGTACCCCTTTTCTTACATGCATGATAACTTACTAACAATGTTTTTGGATCTAACACAGTCCAGC
*
24384877 TT
66 AT
*
24384879 GGTACCCCTTTTC-TACATGTATGGA-AACTTACTAACAATGTTTTTGGATCTAACACAGTCCAG
1 GGTACCCCTTTTCTTACATGCAT-GATAACTTACTAACAATGTTTTTGGATCTAACACAGTCCAG
24384942 CAT
65 CAT
*
24384945 GGTCCCCCTT
1 GGTACCCCTT
24384955 CGAGCTCTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
66 61 0.91
67 6 0.09
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (67 bp):
GGTACCCCTTTTCTTACATGCATGATAACTTACTAACAATGTTTTTGGATCTAACACAGTCCAGC
AT
Found at i:24391454 original size:25 final size:26
Alignment explanation
Indices: 24391415--24391463 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
24391405 TTACAGATAA
24391415 AAAATTCTCTAAAGAGATTATTCTAG
1 AAAATTCTCTAAAGAGATTATTCTAG
* *
24391441 AAAATT-TCTAAAGATATTTTTCT
1 AAAATTCTCTAAAGAGATTATTCT
24391464 GATTTACAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (26 bp):
AAAATTCTCTAAAGAGATTATTCTAG
Found at i:24392257 original size:15 final size:15
Alignment explanation
Indices: 24392237--24392356 Score: 54
Period size: 15 Copynumber: 7.6 Consensus size: 15
24392227 AATTGTTTAC
24392237 AATGTTATATTATGT
1 AATGTTATATTATGT
24392252 AATGTTATA-TA--T
1 AATGTTATATTATGT
* *
24392264 ACATGTTTTATAATTGTTT
1 A-ATG--TTAT-ATTATGT
24392283 ACAATGTTATATTATGT
1 --AATGTTATATTATGT
24392300 AATGTTATA-TA--T
1 AATGTTATATTATGT
* *
24392312 ACATGTTTTATAATTGTTT
1 A-ATG--TTAT-ATTATGT
24392331 ACAATGTTATATTATGT
1 --AATGTTATATTATGT
24392348 AATGTTATA
1 AATGTTATA
24392357 ATTGTGATAT
Statistics
Matches: 81, Mismatches: 6, Indels: 36
0.66 0.05 0.29
Matches are distributed among these distances:
12 4 0.05
13 6 0.07
14 4 0.05
15 35 0.43
16 2 0.02
17 12 0.15
18 8 0.10
19 2 0.02
20 6 0.07
21 2 0.02
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (15 bp):
AATGTTATATTATGT
Found at i:24392279 original size:48 final size:48
Alignment explanation
Indices: 24392208--24392356 Score: 289
Period size: 48 Copynumber: 3.1 Consensus size: 48
24392198 ACCTATCCCC
*
24392208 TTATATATACATGTTTCATAATTGTTTACAATGTTATATTATGTAATG
1 TTATATATACATGTTTTATAATTGTTTACAATGTTATATTATGTAATG
24392256 TTATATATACATGTTTTATAATTGTTTACAATGTTATATTATGTAATG
1 TTATATATACATGTTTTATAATTGTTTACAATGTTATATTATGTAATG
24392304 TTATATATACATGTTTTATAATTGTTTACAATGTTATATTATGTAATG
1 TTATATATACATGTTTTATAATTGTTTACAATGTTATATTATGTAATG
24392352 TTATA
1 TTATA
24392357 ATTGTGATAT
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 100 1.00
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.52
Consensus pattern (48 bp):
TTATATATACATGTTTTATAATTGTTTACAATGTTATATTATGTAATG
Found at i:24410357 original size:30 final size:31
Alignment explanation
Indices: 24410323--24410382 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
24410313 AGCTCCAACC
24410323 AGCTCACTTGAGCTTGCTT-CAGCTCGTTTT
1 AGCTCACTTGAGCTTGCTTCCAGCTCGTTTT
** * *
24410353 AGCTCGTTTTAGCTTTCTTCCAGCTCGTTT
1 AGCTCACTTGAGCTTGCTTCCAGCTCGTTT
24410383 CTTATTCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.12, C:0.27, G:0.18, T:0.43
Consensus pattern (31 bp):
AGCTCACTTGAGCTTGCTTCCAGCTCGTTTT
Found at i:24421667 original size:75 final size:75
Alignment explanation
Indices: 24421578--24421730 Score: 306
Period size: 75 Copynumber: 2.0 Consensus size: 75
24421568 GTTTACTTTG
24421578 CTTTCTTTTAAGTCTTTTCATAATCTTGTGATCATGTTACTATGGTAATACTCTGCAAGAAGATA
1 CTTTCTTTTAAGTCTTTTCATAATCTTGTGATCATGTTACTATGGTAATACTCTGCAAGAAGATA
24421643 ATGCTAACAT
66 ATGCTAACAT
24421653 CTTTCTTTTAAGTCTTTTCATAATCTTGTGATCATGTTACTATGGTAATACTCTGCAAGAAGATA
1 CTTTCTTTTAAGTCTTTTCATAATCTTGTGATCATGTTACTATGGTAATACTCTGCAAGAAGATA
24421718 ATGCTAACAT
66 ATGCTAACAT
24421728 CTT
1 CTT
24421731 CTGCCATTTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (75 bp):
CTTTCTTTTAAGTCTTTTCATAATCTTGTGATCATGTTACTATGGTAATACTCTGCAAGAAGATA
ATGCTAACAT
Found at i:24425276 original size:2 final size:2
Alignment explanation
Indices: 24425269--24425302 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
24425259 TTAGACCAAA
*
24425269 CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
24425303 TTGTCCTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:24430008 original size:20 final size:20
Alignment explanation
Indices: 24429983--24430061 Score: 61
Period size: 20 Copynumber: 4.0 Consensus size: 20
24429973 AAGGAGGAAG
24429983 TACTGGTAGTTTATCTACAT
1 TACTGGTAGTTTATCTACAT
* * *
24430003 TACTGGTGGCTTGA-CCACAT
1 TACTGGTAG-TTTATCTACAT
* * * **
24430023 TACTAGTAGCTTATTTGTAT
1 TACTGGTAGTTTATCTACAT
*
24430043 TACTGGCAGTTTATCTACA
1 TACTGGTAGTTTATCTACA
24430062 ATATTGGCAG
Statistics
Matches: 40, Mismatches: 17, Indels: 4
0.66 0.28 0.07
Matches are distributed among these distances:
19 2 0.05
20 35 0.88
21 3 0.08
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (20 bp):
TACTGGTAGTTTATCTACAT
Found at i:24430087 original size:60 final size:60
Alignment explanation
Indices: 24429983--24430108 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 60
24429973 AAGGAGGAAG
* * ** * ** *
24429983 TACTGGTAGTTTATCTACATTACTGGTGGCTTGACCACATTACTAGTAGCTTATTTGTAT
1 TACTGGCAGTTTATCTACAATACTGGCAGCTTGACCACACTACTACCAGCTTATTTGCAT
* *
24430043 TACTGGCAGTTTATCTACAATATTGGCAGCTTG-CCTACACTACTACCAGTTTATTTGCAT
1 TACTGGCAGTTTATCTACAATACTGGCAGCTTGACC-ACACTACTACCAGCTTATTTGCAT
24430103 TACTGG
1 TACTGG
24430109 TGGCTTAACC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 2 0.04
60 53 0.96
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (60 bp):
TACTGGCAGTTTATCTACAATACTGGCAGCTTGACCACACTACTACCAGCTTATTTGCAT
Found at i:24430154 original size:20 final size:20
Alignment explanation
Indices: 24430098--24430156 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
24430088 CCAGTTTATT
**
24430098 TGCATTACTGGTGGCTTAAC
1 TGCATTACTGGTGGCTTGTC
** * **
24430118 CACATTACTAGAAGCTTGTC
1 TGCATTACTGGTGGCTTGTC
24430138 TGCATTACTGGTGGCTTGT
1 TGCATTACTGGTGGCTTGT
24430157 ACACAAATTA
Statistics
Matches: 27, Mismatches: 12, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
TGCATTACTGGTGGCTTGTC
Found at i:24432151 original size:28 final size:27
Alignment explanation
Indices: 24432083--24432156 Score: 94
Period size: 28 Copynumber: 2.7 Consensus size: 27
24432073 AACATGACGG
** **
24432083 TAAATGTGATTCAGCCTAATGGCCGTA
1 TAAATGTGATTGGGCCTAATGGCCACA
24432110 TAAATGTGATTTGGGCCTAATGGGCCACA
1 TAAATGTGA-TTGGGCCTAAT-GGCCACA
24432139 TAAATGTGATTGGGCCTA
1 TAAATGTGATTGGGCCTA
24432157 GTTGGCCATA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
27 9 0.22
28 18 0.44
29 14 0.34
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (27 bp):
TAAATGTGATTGGGCCTAATGGCCACA
Found at i:24436133 original size:28 final size:27
Alignment explanation
Indices: 24436101--24436191 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 27
24436091 AGGAAGCGTC
24436101 CTGGTGGCTATGCCACAAATTATCTGTT
1 CTGGTGGC-ATGCCACAAATTATCTGTT
* *
24436129 TTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGG-CATGCCACAAATTATCTGTT
* *
24436157 CTGGTGACAGTGCCACAAAATATCTGTAT
1 CTGGTGGCA-TGCCACAAATTATCTGT-T
24436186 CTGGTG
1 CTGGTG
24436192 ACTCTGTCAC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 1 0.02
28 45 0.83
29 8 0.15
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (27 bp):
CTGGTGGCATGCCACAAATTATCTGTT
Found at i:24436189 original size:29 final size:28
Alignment explanation
Indices: 24436111--24436202 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 28
24436101 CTGGTGGCTA
* * *
24436111 TGCCACAAATTATCTGTTTTGGTGGCCC
1 TGCCACAAATTATCTGTTCTGGTGACAC
*
24436139 TGCCACAAATTATCTGTTCTGGTGACAG
1 TGCCACAAATTATCTGTTCTGGTGACAC
* *
24436167 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAATTATCTGT-TCTGGTGACAC
*
24436196 TGTCACA
1 TGCCACA
24436203 TTTTCTGTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 40 0.73
29 15 0.27
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (28 bp):
TGCCACAAATTATCTGTTCTGGTGACAC
Found at i:24436216 original size:56 final size:55
Alignment explanation
Indices: 24436111--24436216 Score: 124
Period size: 56 Copynumber: 1.9 Consensus size: 55
24436101 CTGGTGGCTA
* * *
24436111 TGCCACAAATTATCTGTTTTGGTGGCCCTGCCACAAATTATCTGTTCTGGTGACAG
1 TGCCACAAAATATCTGTTCTGGTGACCCTGCCAC-AATTATCTGTTCTGGTGACAG
* * *
24436167 TGCCACAAAATATCTGTATCTGGTGACTCTGTCAC-ATTTTCTGTATCTGG
1 TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACAATTATCTGT-TCTGG
24436217 CAGCCATGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
55 8 0.19
56 21 0.50
57 13 0.31
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.36
Consensus pattern (55 bp):
TGCCACAAAATATCTGTTCTGGTGACCCTGCCACAATTATCTGTTCTGGTGACAG
Found at i:24442855 original size:40 final size:40
Alignment explanation
Indices: 24442711--24442855 Score: 182
Period size: 40 Copynumber: 3.6 Consensus size: 40
24442701 TACTTGAATG
* *
24442711 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCT-AGCGACT
* * * *
24442752 ACATCCGGACTAAGATCCGAAGGTATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
* * * *
24442792 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
*
24442832 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
24442856 CTTGTGCGAG
Statistics
Matches: 88, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 61 0.69
41 27 0.31
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
Found at i:24444130 original size:79 final size:81
Alignment explanation
Indices: 24443994--24444176 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
24443984 TCGAATGATG
* *
24443994 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
24444058 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
24444073 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
24444135 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
24444153 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
24444177 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:24444192 original size:40 final size:40
Alignment explanation
Indices: 24443995--24444178 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
24443985 CGAATGATGT
* * * *
24443995 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
24444035 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
24444075 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
24444113 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
24444154 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
24444179 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:24444200 original size:79 final size:79
Alignment explanation
Indices: 24444047--24444211 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
24444037 GGACTAAGAT
* **
24444047 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
24444112 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
24444126 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
24444189 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
24444205 CCGAAGG
1 CCGAAGG
24444212 TACGTGATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:24449454 original size:28 final size:28
Alignment explanation
Indices: 24449414--24449481 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
24449404 TAGATATACT
*
24449414 ATTATACCCCTATGTATGCAAAATTACC
1 ATTATACCCCTATGTATGCAAAATGACC
24449442 ATTATACCCCTATGTATGCAAAATGACC
1 ATTATACCCCTATGTATGCAAAATGACC
*
24449470 TTTATACCCCTA
1 ATTATACCCCTA
24449482 GGGTTAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.32
Consensus pattern (28 bp):
ATTATACCCCTATGTATGCAAAATGACC
Found at i:24449688 original size:29 final size:28
Alignment explanation
Indices: 24449587--24449677 Score: 121
Period size: 28 Copynumber: 3.2 Consensus size: 28
24449577 AGGAAGCGTC
24449587 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAATTATCTGTT
* *
24449615 CTGGTGGCCCTGCCACAAATTATCTATT
1 CTGGTGGCACTGCCACAAATTATCTGTT
* *
24449643 CTGGTGGCACTACCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAATTATCTGT-T
24449672 CTGGTG
1 CTGGTG
24449678 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 48 0.87
29 7 0.13
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAATTATCTGTT
Found at i:24458265 original size:50 final size:50
Alignment explanation
Indices: 24458171--24458267 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
24458161 CCGTGTCATC
* * * **
24458171 GGCCGTGTGCTAGACCGTGTAAAACCTGCACTAAAATTTCCAAGACATAT
1 GGCCATGTGATAGACCGTGTAAAACCTGCACTAAAAATGACAAGACATAT
*
24458221 GGCCATGTGATAGACCGTGTGAAACCTGCACTAAAAATGACAAGACA
1 GGCCATGTGATAGACCGTGTAAAACCTGCACTAAAAATGACAAGACA
24458268 CACGGCTGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.21
Consensus pattern (50 bp):
GGCCATGTGATAGACCGTGTAAAACCTGCACTAAAAATGACAAGACATAT
Found at i:24462472 original size:47 final size:47
Alignment explanation
Indices: 24462358--24462629 Score: 265
Period size: 46 Copynumber: 5.8 Consensus size: 47
24462348 TAACTTATGT
* *
24462358 GAGCCAGTGTAAGAAC-TGTCTGGGACATGCATCGGCCACTT--TATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGG-CA-TTGAGATGA
* * *
24462404 GAGCCAGTATAAGACCGTGTCTGGGACATGGCATCGGCATTGAGACGA
1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCATTGAGATGA
* * * *
24462452 GAGCTAGTGTAAGA-CATGTCTGGGACATGCATCAGCCTCGAGATGTA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCATTGAGATG-A
*
24462499 -AGCCAGTGTAAGA-CATGTCTGGGACATGCATCGGC-TACGAGATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCAT-TGAGATGA
* * * *
24462544 TAGTCAGTGTAAGACCGTGTCTGGGACATGGCATCGAC-TTGAGAT-A
1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCATTGAGATGA
* *
24462590 TGAGCCAGTGTAAGACCGTGTCTAGGACATGGCATCGGCA
1 -GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCA
24462630 CCTTACCCAC
Statistics
Matches: 194, Mismatches: 21, Indels: 20
0.83 0.09 0.09
Matches are distributed among these distances:
45 2 0.01
46 82 0.42
47 80 0.41
48 30 0.15
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCATTGAGATGA
Found at i:24462612 original size:140 final size:141
Alignment explanation
Indices: 24462354--24462625 Score: 372
Period size: 140 Copynumber: 1.9 Consensus size: 141
24462344 TGGGTAACTT
* ***
24462354 ATGTGAGCCAGTGTAAGAACTGTCTGGGACATGCATCGGCCACTTTATGAGAGCCAGTATAAGAC
1 ATGTAAGCCAGTGTAAGAACTGTCTGGGACATGCATCGGCCACGAGATGAGAGCCAGTATAAGAC
* * *
24462419 CGTGTCTGGGACATGGCATCGGCATTGAGACGAGAGCTAGTGTAAGACATGTCTGGGACAT-GCA
66 CGTGTCTGGGACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGACATGTCTAGGACATGGCA
24462483 TCAGCCTCGAG
131 TCAGCCTCGAG
* * * *
24462494 ATGTAAGCCAGTGTAAG-ACATGTCTGGGACATGCATCGGCTACGAGATGATAGTCAGTGTAAGA
1 ATGTAAGCCAGTGTAAGAAC-TGTCTGGGACATGCATCGGCCACGAGATGAGAGCCAGTATAAGA
* *
24462558 CCGTGTCTGGGACATGGCATCGAC-TTGAGA-TATGAGCCAGTGTAAGACCGTGTCTAGGACATG
65 CCGTGTCTGGGACATGGCATCGACATTGAGACGA-GAGCCAGTGTAAGA-CATGTCTAGGACATG
24462621 GCATC
128 GCATC
24462626 GGCACCTTAC
Statistics
Matches: 115, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
138 1 0.01
139 21 0.18
140 88 0.77
141 5 0.04
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.23
Consensus pattern (141 bp):
ATGTAAGCCAGTGTAAGAACTGTCTGGGACATGCATCGGCCACGAGATGAGAGCCAGTATAAGAC
CGTGTCTGGGACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGACATGTCTAGGACATGGCA
TCAGCCTCGAG
Found at i:24466227 original size:40 final size:40
Alignment explanation
Indices: 24466143--24466327 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
24466133 TCGAATGATG
* *
24466143 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
24466182 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
24466223 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTCACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
24466262 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
24466301 AACCGGGCTATGTCCCGAAGGAATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
24466328 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:24466279 original size:79 final size:80
Alignment explanation
Indices: 24466143--24466321 Score: 231
Period size: 79 Copynumber: 2.2 Consensus size: 80
24466133 TCGAATGATG
* * *
24466143 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTGGTGCTAAGTCACTAAATCCGGACTAAGATCCGAAGGCATTT
24466208 GTGCGAGTTACTA-A
66 GTGCGAGTTACTATA
* **
24466222 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTCACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGC-TTGGTGCTAAGTCACTAAATCCGGACTAAGAT-CCGAAGGCA
24466284 TTTGTGCGAGTTACTATA
63 TTTGTGCGAGTTACTATA
* *
24466302 ACCGGGCTATGTCCCGAAGG
1 TCCGGGCTAAGTCCCGAAGG
24466322 AATTTGAACG
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
78 1 0.01
79 60 0.69
80 26 0.30
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTGGTGCTAAGTCACTAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTATA
Found at i:24474361 original size:39 final size:39
Alignment explanation
Indices: 24474255--24474396 Score: 166
Period size: 39 Copynumber: 3.6 Consensus size: 39
24474245 TCGAATGATG
* *
24474255 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATA
24474295 TCC-GGCTAAG-CCGAAGGCATTTGTGCGAGTTACTA-A
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTATA
* *
24474331 TTCCGGGCTAAGCCCGAAGGCATTTATGCGAGTTATTATA
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTATA
* *
24474371 ACCGGGCTATATCCCGAAGGCATTTG
1 TCCGGGCTA-AGCCCGAAGGCATTTG
24474397 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 7, Indels: 12
0.82 0.06 0.11
Matches are distributed among these distances:
36 1 0.01
37 18 0.20
38 14 0.16
39 38 0.43
40 18 0.20
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTATA
Found at i:24477741 original size:24 final size:24
Alignment explanation
Indices: 24477714--24477762 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
24477704 AAAGTAATAA
24477714 TTAAATAATTCTAATACGATTTAG
1 TTAAATAATTCTAATACGATTTAG
*
24477738 TTAAATAATTCTAATATGATTTAG
1 TTAAATAATTCTAATACGATTTAG
24477762 T
1 T
24477763 ACATTCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (24 bp):
TTAAATAATTCTAATACGATTTAG
Found at i:24478469 original size:19 final size:19
Alignment explanation
Indices: 24478447--24478484 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
24478437 TAATAAATTA
*
24478447 TAAAATACAAGAATTAAAT
1 TAAAATACAAAAATTAAAT
*
24478466 TAAAATATAAAAATTAAAT
1 TAAAATACAAAAATTAAAT
24478485 CAAGACCAAA
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:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (19 bp):
TAAAATACAAAAATTAAAT
Found at i:24481448 original size:20 final size:21
Alignment explanation
Indices: 24481423--24481478 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
24481413 GTTTTAAGAA
*
24481423 TTGTTTT-GTATTATTTTTAT
1 TTGTTTTAATATTATTTTTAT
24481443 TTGTTTTAATATT-TTTTT-T
1 TTGTTTTAATATTATTTTTAT
*
24481462 ATGTTTTAA-ATATATTT
1 TTGTTTTAATAT-TATTT
24481479 GATTATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 2 0.06
19 10 0.32
20 15 0.48
21 4 0.13
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (21 bp):
TTGTTTTAATATTATTTTTAT
Found at i:24481460 original size:21 final size:20
Alignment explanation
Indices: 24481422--24481470 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
24481412 TGTTTTAAGA
*
24481422 ATTGTTTT-GTATTATTTTT
1 ATTGTTTTAATATTATTTTT
*
24481441 ATTTGTTTTAATATTTTTTTT
1 A-TTGTTTTAATATTATTTTT
24481462 A-TGTTTTAA
1 ATTGTTTTAA
24481471 ATATATTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 9 0.35
20 7 0.27
21 10 0.38
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.71
Consensus pattern (20 bp):
ATTGTTTTAATATTATTTTT
Found at i:24481466 original size:19 final size:18
Alignment explanation
Indices: 24481434--24481470 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
24481424 TGTTTTGTAT
24481434 TATTTTTATTTGTTTTAA
1 TATTTTTATTTGTTTTAA
*
24481452 TATTTTTTTTATGTTTTAA
1 TATTTTTATT-TGTTTTAA
24481471 ATATATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (18 bp):
TATTTTTATTTGTTTTAA
Found at i:24494306 original size:79 final size:82
Alignment explanation
Indices: 24494195--24494379 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 82
24494185 GCTACTCGTT
* * *
24494195 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* * *
24494258 GGATTTAGTAAC-TCGCG
65 GGATATAGTAACTTAGCA
* **
24494275 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
24494338 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
24494355 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
24494380 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.60
80 33 0.37
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:24494379 original size:40 final size:40
Alignment explanation
Indices: 24494176--24494379 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
24494166 CGGAATTTAA
** *
24494176 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
24494216 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
24494256 CCGGATTTAGTAACTCGCGCAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
24494295 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
24494335 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
24494375 CCGGA
1 CCGGA
24494380 CATCATTCAA
Statistics
Matches: 137, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 91 0.66
41 12 0.09
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:24500790 original size:51 final size:51
Alignment explanation
Indices: 24500714--24500856 Score: 182
Period size: 51 Copynumber: 2.8 Consensus size: 51
24500704 ATGCTATCTA
* * *
24500714 GTACACATAGTAG-TCTACACTTAGTACTACATATGTGACCAATA-CCATCCG
1 GTACACATAGTAGCT-TGCACTTAGTACTACAAATGTGACCAA-AGCCACCCG
* * *
24500765 GTACACATAGTAGCTTGCACATAGTACTACAAACGTGACCAAAGCTACCCG
1 GTACACATAGTAGCTTGCACTTAGTACTACAAATGTGACCAAAGCCACCCG
* *
24500816 GTACACATAGTAGCGTGCACTTAGTACTACACATGTGACCA
1 GTACACATAGTAGCTTGCACTTAGTACTACAAATGTGACCA
24500857 TAACTATCTT
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
50 1 0.01
51 78 0.98
52 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.24
Consensus pattern (51 bp):
GTACACATAGTAGCTTGCACTTAGTACTACAAATGTGACCAAAGCCACCCG
Found at i:24506396 original size:32 final size:31
Alignment explanation
Indices: 24506351--24506446 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
24506341 CTTAGATAAT
24506351 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
24506382 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
24506414 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
24506445 TT
1 TT
24506447 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:24506797 original size:4 final size:4
Alignment explanation
Indices: 24506748--24506781 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
24506738 ATCTATCCTT
24506748 TTTA TTTA TTTA TTTA TTTA TTTA -TTA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
24506782 ACTAATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:24507042 original size:44 final size:44
Alignment explanation
Indices: 24506971--24507064 Score: 172
Period size: 44 Copynumber: 2.1 Consensus size: 44
24506961 AATAGTTAAT
24506971 AAAAAAAAGTTGAGAAAAATCTAAAAAAAAAGCAAACAGCGCAA
1 AAAAAAAAGTTGAGAAAAATCTAAAAAAAAAGCAAACAGCGCAA
24507015 AAAAAAAGAGTTGAGAAAAATCT-AAAAAAAAGCAAACAGCGCAA
1 AAAAAAA-AGTTGAGAAAAATCTAAAAAAAAAGCAAACAGCGCAA
24507059 AAAAAA
1 AAAAAA
24507065 GTTGCCTACC
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 34 0.69
45 15 0.31
ACGTcount: A:0.67, C:0.11, G:0.14, T:0.09
Consensus pattern (44 bp):
AAAAAAAAGTTGAGAAAAATCTAAAAAAAAAGCAAACAGCGCAA
Found at i:24512627 original size:32 final size:31
Alignment explanation
Indices: 24512582--24512677 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
24512572 CTTAGATAAT
24512582 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
24512613 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
24512645 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
24512676 TT
1 TT
24512678 GTAATTTTCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:24517657 original size:17 final size:18
Alignment explanation
Indices: 24517621--24517658 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
24517611 ATTTTCTTGT
24517621 TAACATAAAACTACTAAA
1 TAACATAAAACTACTAAA
* *
24517639 TAACTTAAAA-TACTTAA
1 TAACATAAAACTACTAAA
24517656 TAA
1 TAA
24517659 TTACCAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (18 bp):
TAACATAAAACTACTAAA
Found at i:24526852 original size:25 final size:26
Alignment explanation
Indices: 24526822--24526877 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
24526812 AGCCAGATCG
* *
24526822 GGAAGCTC-CAGAGAGCCATTT-ATTA
1 GGAAGCTCACAAAGAGCC-TTTAATCA
24526847 GGAAGCTCACAAAGAGCCTTTAATCA
1 GGAAGCTCACAAAGAGCCTTTAATCA
24526873 GGAAG
1 GGAAG
24526878 TTCTGAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.20
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCTTTAATCA
Found at i:24527546 original size:20 final size:20
Alignment explanation
Indices: 24527508--24527545 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
24527498 CCATATATTT
*
24527508 CATAAAATTTAGAATTTTTC
1 CATAAAATTTACAATTTTTC
*
24527528 CATAAATTTTAC-ATTTTT
1 CATAAAATTTACAATTTTT
24527546 TGAATTTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.50
Consensus pattern (20 bp):
CATAAAATTTACAATTTTTC
Found at i:24530061 original size:25 final size:26
Alignment explanation
Indices: 24530033--24530088 Score: 96
Period size: 25 Copynumber: 2.2 Consensus size: 26
24530023 AATTTTTCAA
24530033 ATACATATGCCAAAAGCATA-TATTT
1 ATACATATGCCAAAAGCATACTATTT
24530058 ATACATATGCCAAAAGCATATCTATTT
1 ATACATATGCCAAAAGCATA-CTATTT
24530085 ATAC
1 ATAC
24530089 TTATCAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 20 0.69
27 9 0.31
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (26 bp):
ATACATATGCCAAAAGCATACTATTT
Found at i:24530377 original size:41 final size:41
Alignment explanation
Indices: 24530319--24530593 Score: 397
Period size: 41 Copynumber: 6.7 Consensus size: 41
24530309 TTAACTTAAA
*
24530319 CAGATTCACTGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
*
24530361 CAGATCACCAGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* * * * *
24530402 CAGTTCACCTGCACTTAGCATGCTAGGCTTATAGCCCGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* **
24530443 CAAATCACCAACACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
24530484 CAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
24530525 TAAATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
24530566 CAGTTCACTGGCACTTAGCCTGCTAGGC
1 CAGATCACCGGCACTTAGCCTGCTAGGC
24530594 ACTAAGCCTG
Statistics
Matches: 206, Mismatches: 27, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
41 202 0.98
42 4 0.02
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:24530604 original size:82 final size:82
Alignment explanation
Indices: 24530323--24530593 Score: 454
Period size: 82 Copynumber: 3.3 Consensus size: 82
24530313 CTTAAACAGA
* *
24530323 TTCACTGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCAGCACTTAGCCTGCTAGG
1 TTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAATCACCAGCACTTAGCCTGCTAGG
24530388 CTTATAACCTGATTCAG
66 CTTATAACCTGATTCAG
* * *
24530405 TTCACCT-GCACTTAGCATGCTAGGCTTATAGCCCGATTCAAATCACCAACACTTAGCCTGCTAG
1 TTCA-CTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAATCACCAGCACTTAGCCTGCTAG
24530469 GCTTATAACCTGATTCAG
65 GCTTATAACCTGATTCAG
* * *
24530487 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTTAAATCACCGGCACTTAGCCTGCTAGG
1 TTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAATCACCAGCACTTAGCCTGCTAGG
24530552 CTTATAACCTGATTCAG
66 CTTATAACCTGATTCAG
24530569 TTCACTGGCACTTAGCCTGCTAGGC
1 TTCACTGGCACTTAGCCTGCTAGGC
24530594 ACTAAGCCTG
Statistics
Matches: 175, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
81 1 0.01
82 172 0.98
83 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (82 bp):
TTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAATCACCAGCACTTAGCCTGCTAGG
CTTATAACCTGATTCAG
Found at i:24537556 original size:47 final size:47
Alignment explanation
Indices: 24537504--24538197 Score: 1091
Period size: 47 Copynumber: 14.6 Consensus size: 47
24537494 GATAATTGTG
* * *
24537504 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGGTGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
24537551 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
24537598 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
24537647 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
24537694 ATGTGAAAGTGTATATATATGTGACAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
24537743 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
24537792 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGTTGTGGTGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
24537839 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
24537886 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
24537935 ATGTGAAAGTGTAGATATATGTGATAAGGCCTAATGGCCTATGTGATGA
1 ATGTGAAAGTGT--ATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
24537984 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
24538031 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
24538078 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * * *
24538125 ATGTGAAAATGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
24538172 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
24538198 TCCCGAAGGG
Statistics
Matches: 604, Mismatches: 35, Indels: 16
0.92 0.05 0.02
Matches are distributed among these distances:
47 374 0.62
49 230 0.38
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:24537629 original size:96 final size:96
Alignment explanation
Indices: 24537504--24538197 Score: 1111
Period size: 96 Copynumber: 7.3 Consensus size: 96
24537494 GATAATTGTG
*
24537504 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATGGCCGGTGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
24537567 ATGTGATAAGGCCGAATGGCCGATGTGATGA
66 ATGTGATAAGGCCGAATGGCCGATGTGATGA
24537598 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
24537663 ATGTGATAAGGCCGAATGGCCGATGTGATGA
66 ATGTGATAAGGCCGAATGGCCGATGTGATGA
*
24537694 ATGTGAAAGTGTATATATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
*
24537759 ATATGTGATAAGGCCTAATGGCCGATGTGATGA
64 ATATGTGATAAGGCCGAATGGCCGATGTGATGA
* *
24537792 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGTTGTGGTGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
*
24537855 ATGTGATAAGGCCGAATGGCCAATGTGATGA
66 ATGTGATAAGGCCGAATGGCCGATGTGATGA
24537886 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAGAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT--AT
* *
24537951 ATATGTGATAAGGCCTAATGGCCTATGTGATGA
64 ATATGTGATAAGGCCGAATGGCCGATGTGATGA
*
24537984 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* *
24538047 ATGTGATGAGGCCTAATGGCCGATGTGATGA
66 ATGTGATAAGGCCGAATGGCCGATGTGATGA
* *
24538078 ATGTGAAAGTG--TATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* * * * * *
24538141 ATGTGACAGGGCCGAGTGGCCAACGTGATGG
66 ATGTGATAAGGCCGAATGGCCGATGTGATGA
24538172 ATGTGAAAGTGTATA-A-ATGTGATAAG
1 ATGTGAAAGTGTATATATATGTGATAAG
24538198 TCCCGAAGGG
Statistics
Matches: 563, Mismatches: 27, Indels: 20
0.92 0.04 0.03
Matches are distributed among these distances:
94 186 0.33
95 3 0.01
96 284 0.50
98 90 0.16
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (96 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCCGAATGGCCGATGTGATGA
Found at i:24539807 original size:41 final size:41
Alignment explanation
Indices: 24539751--24540037 Score: 430
Period size: 41 Copynumber: 7.0 Consensus size: 41
24539741 GGGTGTTACA
* * *
24539751 CTTATAACCTGATTCAGTTCACTGGCACTTAGCTTGCTAGA
1 CTTATAACCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
* ** *
24539792 CTTATAGCCTGATTCAAATCACCGACACTTAGCCTGCTAGG
1 CTTATAACCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
**
24539833 CTTATAACCTGATTCAGTTCACCTACACTTAGCCTGCTAGG
1 CTTATAACCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
* * *
24539874 CTTATAGCCTGATTTAGATCACCGGCACTTAGCCTGCTAGG
1 CTTATAACCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
24539915 CTTATAACCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
1 CTTATAACCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
* *
24539956 CTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 CTTATAACCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
* *
24539997 CTTATAACCTGATTCGGTTCACCAGCACTTAGCCTGCTAGG
1 CTTATAACCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
24540038 TGGTAAGCGT
Statistics
Matches: 221, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 221 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (41 bp):
CTTATAACCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
Found at i:24554653 original size:59 final size:61
Alignment explanation
Indices: 24554578--24554694 Score: 148
Period size: 62 Copynumber: 1.9 Consensus size: 61
24554568 ATCTCTTTAA
* * * *
24554578 TATTAAATTAATATAATATTTA-T-CAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAAAATAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATCT
* * *
24554637 TATTAAAATAAAATAATGTTTATCTACAATATAAACATTAAATTTAATTTAATATTAA
1 TATTAAAATAAAATAATATTTA-CTACAAGATAAACATTAAATTAAATTTAATATTAA
24554695 GATAATCACT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 19 0.40
61 1 0.02
62 28 0.58
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (61 bp):
TATTAAAATAAAATAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:24554733 original size:25 final size:25
Alignment explanation
Indices: 24554679--24554733 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
24554669 AAACATTAAA
*
24554679 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
24554704 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
24554728 TATTAA
1 T-TTAA
24554734 GATGAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:24556181 original size:16 final size:16
Alignment explanation
Indices: 24556160--24556190 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24556150 CTATGCATGC
*
24556160 AAAATATAAAAGACAG
1 AAAATAGAAAAGACAG
24556176 AAAATAGAAAAGACA
1 AAAATAGAAAAGACA
24556191 TAATAGTGAA
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:0.71, C:0.06, G:0.13, T:0.10
Consensus pattern (16 bp):
AAAATAGAAAAGACAG
Found at i:24571519 original size:66 final size:66
Alignment explanation
Indices: 24571411--24571548 Score: 222
Period size: 66 Copynumber: 2.1 Consensus size: 66
24571401 AAAGAGCTCG
* * * *
24571411 AGGGGGGACCAAGCTAGACCGTGTTAGATCCGAAAACGTCGTTAGTAAGTTTTCATGCATATAGG
1 AGGGGGGACCAAGCTAGACCGTGTTAGATCCAAAAACATCGTTAGTAAGTTGTCATGCATATAAG
24571476 A
66 A
* *
24571477 AGGGGGTACCAAGCTAGACCGTGTTAGATCCAAAAATATCGTTAGTAAGTTGTCATGCATATAAG
1 AGGGGGGACCAAGCTAGACCGTGTTAGATCCAAAAACATCGTTAGTAAGTTGTCATGCATATAAG
24571542 A
66 A
24571543 AGGGGG
1 AGGGGG
24571549 AACCTTTAGA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (66 bp):
AGGGGGGACCAAGCTAGACCGTGTTAGATCCAAAAACATCGTTAGTAAGTTGTCATGCATATAAG
A
Found at i:24578235 original size:118 final size:118
Alignment explanation
Indices: 24578027--24578270 Score: 443
Period size: 118 Copynumber: 2.1 Consensus size: 118
24578017 TCAAGCCAAA
* * * *
24578027 CATTGTTTCAGTCTAGCCATTTCTTCCTTATTGTCTCCTGTCATCACTACGTCATCAGTATATAC
1 CATTGTTTCAGTCGAGCCATTTCTTCCTTATCGTCTCCTATCATCACTACGTCATCAATATATAC
24578092 AATAAGAAGAGTGATTTTACCCTTGTGATGTTTCATGAAAATGGTATGATCAG
66 AATAAGAAGAGTGATTTTACCCTTGTGATGTTTCATGAAAATGGTATGATCAG
*
24578145 CATTGTTTCAGTCGAGCCATTTCTTCCTTATCGTCTCTTATCATCACTACGTCATCAATATATAC
1 CATTGTTTCAGTCGAGCCATTTCTTCCTTATCGTCTCCTATCATCACTACGTCATCAATATATAC
24578210 AATAAGAAGAGTGATTTTACCCTTGTGATGTTTCATGAAAATGGTATGATCAG
66 AATAAGAAGAGTGATTTTACCCTTGTGATGTTTCATGAAAATGGTATGATCAG
24578263 CATTGTTT
1 CATTGTTT
24578271 TGTTGATAAT
Statistics
Matches: 121, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 121 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (118 bp):
CATTGTTTCAGTCGAGCCATTTCTTCCTTATCGTCTCCTATCATCACTACGTCATCAATATATAC
AATAAGAAGAGTGATTTTACCCTTGTGATGTTTCATGAAAATGGTATGATCAG
Found at i:24579089 original size:18 final size:18
Alignment explanation
Indices: 24579068--24579110 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
24579058 CAATCTCCTT
*
24579068 TTGAACAGT-AGTCTCCCC
1 TTGAACAGTAACT-TCCCC
*
24579086 TTGAGCAGTAACTTCCCC
1 TTGAACAGTAACTTCCCC
24579104 TTGAACA
1 TTGAACA
24579111 ATGGTGCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (18 bp):
TTGAACAGTAACTTCCCC
Found at i:24587040 original size:29 final size:29
Alignment explanation
Indices: 24587008--24587063 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
24586998 AATTTCTTTT
24587008 TAAAAAAT-ATTTAGAAA-TTATAAAAAACA
1 TAAAAAATCA-TTA-AAAGTTATAAAAAACA
24587037 TAAAAAATCATTAAAAGTTATAAAAAA
1 TAAAAAATCATTAAAAGTTATAAAAAA
24587064 ATTATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 3 0.12
29 21 0.84
30 1 0.04
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.27
Consensus pattern (29 bp):
TAAAAAATCATTAAAAGTTATAAAAAACA
Found at i:24587822 original size:31 final size:31
Alignment explanation
Indices: 24587779--24587842 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
24587769 GAAAATTTAA
24587779 ATTCCTTCATATTTGTTTCATATACATAGAG
1 ATTCCTTCATATTTGTTTCATATACATAGAG
* *
24587810 ATTCTTTCATATTTGTTTCATATTCATAGAG
1 ATTCCTTCATATTTGTTTCATATACATAGAG
24587841 AT
1 AT
24587843 AGGGGACATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.48
Consensus pattern (31 bp):
ATTCCTTCATATTTGTTTCATATACATAGAG
Found at i:24588602 original size:15 final size:14
Alignment explanation
Indices: 24588573--24588620 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
24588563 AAATTAAGCC
24588573 TAAAAATTTATATT
1 TAAAAATTTATATT
*
24588587 TAAAAATTTCTAATT
1 TAAAAATTTAT-ATT
* *
24588602 TTAAAATATATATT
1 TAAAAATTTATATT
24588616 ATAAA
1 -TAAA
24588621 TAAATAATGC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (14 bp):
TAAAAATTTATATT
Found at i:24626273 original size:16 final size:16
Alignment explanation
Indices: 24626252--24626302 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
24626242 TTTCTAGTAT
*
24626252 TTTATTTACTAGCGTG
1 TTTATTTACTAGCGTA
*
24626268 TTTATTTCCTAGCGTA
1 TTTATTTACTAGCGTA
*
24626284 TTTATTTACTACCGTA
1 TTTATTTACTAGCGTA
24626300 TTT
1 TTT
24626303 GCTCTTTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.20, C:0.16, G:0.12, T:0.53
Consensus pattern (16 bp):
TTTATTTACTAGCGTA
Found at i:24631478 original size:21 final size:21
Alignment explanation
Indices: 24631444--24631484 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24631434 AAAATACAAG
*
24631444 TGAAAAAGAAGAAAATGAAAA
1 TGAAAAAGAAGAAAAGGAAAA
**
24631465 TGAAAAAGGCGAAAAGGAAA
1 TGAAAAAGAAGAAAAGGAAA
24631485 GCGAGAGAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.02, G:0.24, T:0.07
Consensus pattern (21 bp):
TGAAAAAGAAGAAAAGGAAAA
Found at i:24639366 original size:14 final size:14
Alignment explanation
Indices: 24639347--24639373 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24639337 TTCGAGAGAT
24639347 TTGTGAGGTTTTTG
1 TTGTGAGGTTTTTG
24639361 TTGTGAGGTTTTT
1 TTGTGAGGTTTTT
24639374 ATTTTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.00, G:0.33, T:0.59
Consensus pattern (14 bp):
TTGTGAGGTTTTTG
Found at i:24641126 original size:24 final size:23
Alignment explanation
Indices: 24641094--24641144 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
24641084 AAATGAGAGA
*
24641094 AAAAGAAAA-GAGTGAAAACAAAG
1 AAAAGAAAATGAG-AAAAACAAAG
*
24641117 AAAAGAAAAATGAGAAAAAGAAAG
1 AAAAG-AAAATGAGAAAAACAAAG
24641141 AAAA
1 AAAA
24641145 TCTGAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.21
24 16 0.67
25 3 0.12
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.04
Consensus pattern (23 bp):
AAAAGAAAATGAGAAAAACAAAG
Found at i:24641154 original size:20 final size:20
Alignment explanation
Indices: 24641094--24641154 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 20
24641084 AAATGAGAGA
24641094 AAAAGAAAAGAGTGAAAACAAAG
1 AAAAGAAAA-A-TGAAAA-AAAG
*
24641117 AAAAGAAAAATGAGAAAAAG
1 AAAAGAAAAATGAAAAAAAG
*
24641137 -AAAGAAAATCTGAAAAAA
1 AAAAGAAAA-ATGAAAAAA
24641155 GAGAGTGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 8 0.24
20 11 0.32
21 5 0.15
22 1 0.03
23 9 0.26
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAATGAAAAAAAG
Found at i:24645426 original size:6 final size:6
Alignment explanation
Indices: 24645415--24645441 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
24645405 TCCATTCCTT
24645415 ACCTAA ACCTAA ACCTAA ACCTAA ACC
1 ACCTAA ACCTAA ACCTAA ACCTAA ACC
24645442 GAATTTGACC
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:0.48, C:0.37, G:0.00, T:0.15
Consensus pattern (6 bp):
ACCTAA
Found at i:24649134 original size:24 final size:24
Alignment explanation
Indices: 24649102--24649164 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
24649092 CCTTTTTGAG
24649102 CCATTTCGTACCAAAAATCCC-ATA
1 CCATTTCGTACCAAAAA-CCCAATA
* *
24649126 CCATTTCGTACC-AATACCCAATT
1 CCATTTCGTACCAAAAACCCAATA
*
24649149 CCAATTCGTACCAAAA
1 CCATTTCGTACCAAAA
24649165 CCAAAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 3 0.09
23 16 0.48
24 14 0.42
ACGTcount: A:0.37, C:0.33, G:0.05, T:0.25
Consensus pattern (24 bp):
CCATTTCGTACCAAAAACCCAATA
Found at i:24655736 original size:13 final size:12
Alignment explanation
Indices: 24655704--24655735 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
24655694 ACGAGATTGT
24655704 AAAAAAAATTCG
1 AAAAAAAATTCG
*
24655716 AAAAAAAATTTG
1 AAAAAAAATTCG
24655728 AAAAAAAA
1 AAAAAAAA
24655736 AATTATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:24657814 original size:14 final size:14
Alignment explanation
Indices: 24657795--24657822 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
24657785 TCTATTGAGC
24657795 GAGAAAAACAAAAA
1 GAGAAAAACAAAAA
24657809 GAGAAAAACAAAAA
1 GAGAAAAACAAAAA
24657823 CAGTGAAAAG
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:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (14 bp):
GAGAAAAACAAAAA
Found at i:24667889 original size:21 final size:20
Alignment explanation
Indices: 24667829--24667890 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 20
24667819 AAGAAATAAA
*
24667829 AGAAAAAGAACAAGAAA-T-
1 AGAAAAAGAAAAAGAAATTG
* * * *
24667847 CGAAAAAGAAAATGAGAGTG
1 AGAAAAAGAAAAAGAAATTG
24667867 AGAAAAAGAAAAAAGAAATTG
1 AGAAAAAG-AAAAAGAAATTG
24667888 AGA
1 AGA
24667891 TTGAAAAAGG
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
18 13 0.39
19 1 0.03
20 7 0.21
21 12 0.36
ACGTcount: A:0.66, C:0.03, G:0.23, T:0.08
Consensus pattern (20 bp):
AGAAAAAGAAAAAGAAATTG
Found at i:24669876 original size:20 final size:21
Alignment explanation
Indices: 24669853--24669898 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
24669843 TAAATAAAAC
24669853 AAGACAC-AATTAATTAAGTT
1 AAGACACTAATTAATTAAGTT
**
24669873 AAGAC-CTAATTAATTCGGTT
1 AAGACACTAATTAATTAAGTT
24669893 AAGACA
1 AAGACA
24669899 AGACACATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (21 bp):
AAGACACTAATTAATTAAGTT
Found at i:24672370 original size:20 final size:20
Alignment explanation
Indices: 24672347--24672400 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
24672337 AGTTTTTCCC
*
24672347 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
24672367 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
24672387 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
24672401 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:24672382 original size:30 final size:30
Alignment explanation
Indices: 24672347--24672420 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
24672337 AGTTTTTCCC
24672347 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
24672377 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
24672407 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
24672421 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:24672410 original size:20 final size:20
Alignment explanation
Indices: 24672347--24672411 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
24672337 AGTTTTTCCC
* * * *
24672347 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
24672367 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
24672386 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
24672407 AGCTC
1 AGCTC
24672412 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:24674995 original size:20 final size:21
Alignment explanation
Indices: 24674972--24675025 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
24674962 AGCTCGTTTC
* *
24674972 AGCTCCAA-TCAGCTTATTTG
1 AGCTCCAATTCAGCTCATTCG
24674992 AGCT-CAATTCAGCTCATTCG
1 AGCTCCAATTCAGCTCATTCG
*
24675012 AGCT-CAATTTAGCT
1 AGCTCCAATTCAGCT
24675026 TTCTATCAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (21 bp):
AGCTCCAATTCAGCTCATTCG
Found at i:24676952 original size:20 final size:21
Alignment explanation
Indices: 24676919--24676977 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
24676909 CAGCTCCTTT
* *
24676919 AGCTCGTTTCAGCTCCAA-TC
1 AGCTCATTTGAGCTCCAATTC
24676939 AGCTCATTTGAGCT-CAATTC
1 AGCTCATTTGAGCTCCAATTC
*
24676959 AGCTCATTCGAGCT-CAATT
1 AGCTCATTTGAGCTCCAATT
24676978 TAACTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 3 0.09
20 32 0.91
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (21 bp):
AGCTCATTTGAGCTCCAATTC
Found at i:24678277 original size:18 final size:19
Alignment explanation
Indices: 24678254--24678289 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24678244 ATACATTCAA
24678254 TTTTTCA-CTTGCTTTTTC
1 TTTTTCATCTTGCTTTTTC
*
24678272 TTTTTCATCTTTCTTTTT
1 TTTTTCATCTTGCTTTTT
24678290 TCTCGCTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTTTCATCTTGCTTTTTC
Done.