Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006746.1 Hibiscus syriacus cultivar Beakdansim tig00016946_pilon, whole genome shotgun sequence
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: 60442
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3106 original size:26 final size:25
Alignment explanation
Indices: 3059--3110 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
3049 TTTCATGTCA
3059 AGTCCAATCAATTCCAAAGTCCAAT
1 AGTCCAATCAATTCCAAAGTCCAAT
*
3084 AGTCCAAATCCAATTCC-AGGTCCAAT
1 AGTCC-AAT-CAATTCCAAAGTCCAAT
3110 A
1 A
3111 ATGATCCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 5 0.21
26 12 0.50
27 7 0.29
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.23
Consensus pattern (25 bp):
AGTCCAATCAATTCCAAAGTCCAAT
Found at i:6049 original size:14 final size:16
Alignment explanation
Indices: 6013--6049 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
6003 TATTAATGTA
6013 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
6030 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
6045 T-AATA
1 TGAATA
6050 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:6716 original size:130 final size:130
Alignment explanation
Indices: 6512--6759 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
6502 AATTTTCTTC
*
6512 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
* ** *
6577 TCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
6642 TAATTAGGTGGTGACATGTGTCACTAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
6707 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
6760 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:7213 original size:35 final size:35
Alignment explanation
Indices: 7152--7227 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
7142 AATTGAATTT
* * *
7152 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGAAAATTAGGGTTTAGAATGA
*
7187 AATTGAATTACTTTGAAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGAAAATTAGGGTTTAGAATGA
7222 AATTGA
1 AATTGA
7228 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGAAAATTAGGGTTTAGAATGA
Found at i:7886 original size:52 final size:52
Alignment explanation
Indices: 7829--7978 Score: 250
Period size: 52 Copynumber: 2.9 Consensus size: 52
7819 ATTCTACGGA
* *
7829 TGTGAGTGTTCAATGTCAAATAGTTGAGAGTTATTTTTGAATAGATACTA-T
1 TGTGAGTGTTCAATGTCAAATGGTTGAGAGTTATCTTTGAATAGATACTACT
*
7880 GTGTGAGTGTTCAATGTCAAATGGTTGAGAGTTATCTTTGAACAGATACTACT
1 -TGTGAGTGTTCAATGTCAAATGGTTGAGAGTTATCTTTGAATAGATACTACT
7933 TGTGAGTGTTCAATGTCAAATGGTTGAG-GTTATCTTTGAATAGATA
1 TGTGAGTGTTCAATGTCAAATGGTTGAGAGTTATCTTTGAATAGATA
7979 ATACCTTATA
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
51 17 0.18
52 75 0.81
53 1 0.01
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (52 bp):
TGTGAGTGTTCAATGTCAAATGGTTGAGAGTTATCTTTGAATAGATACTACT
Found at i:8048 original size:45 final size:45
Alignment explanation
Indices: 7961--8048 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
7951 AATGGTTGAG
* *
7961 GTTATCTTTGAATAGATAATACCTTATACTGATCCCAAATTAAGA
1 GTTATCTTTGAACAGATAATACCTTATACTGATCACAAATTAAGA
* * *
8006 GTTATCTTTGAACATG-TACTACCTTATACTTATCACAGATTAA
1 GTTATCTTTGAACA-GATAATACCTTATACTGATCACAAATTAA
8049 TAATAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
45 36 0.97
46 1 0.03
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (45 bp):
GTTATCTTTGAACAGATAATACCTTATACTGATCACAAATTAAGA
Found at i:12453 original size:29 final size:29
Alignment explanation
Indices: 12411--12467 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
12401 AGTGTTGGCC
12411 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
12440 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
12468 ACCCTTGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.35, G:0.32, T:0.19
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:12559 original size:29 final size:29
Alignment explanation
Indices: 12526--12610 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
12516 TCCCAAAACA
*
12526 TAGGTCGCCATGCCCTCCAGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
12555 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
* *
12584 TAGGTCACCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
12611 ACCATCGCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.14, C:0.38, G:0.28, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:12645 original size:23 final size:24
Alignment explanation
Indices: 12615--12670 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
12605 CGACCTACCA
12615 TCGCTCGGATT-CCCTAGCATAGC
1 TCGCTCGGATTGCCCTAGCATAGC
*
12638 TCGCTCGG-TTGCCCTTGCATAGC
1 TCGCTCGGATTGCCCTAGCATAGC
*
12661 TCGTTCGGAT
1 TCGCTCGGAT
12671 GGCCTCGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 2 0.07
23 26 0.90
24 1 0.03
ACGTcount: A:0.12, C:0.32, G:0.25, T:0.30
Consensus pattern (24 bp):
TCGCTCGGATTGCCCTAGCATAGC
Found at i:12680 original size:10 final size:10
Alignment explanation
Indices: 12665--12698 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
12655 CATAGCTCGT
12665 TCGGATGGCC
1 TCGGATGGCC
12675 TCGGAT-GCTC
1 TCGGATGGC-C
12685 TCGGATGGCC
1 TCGGATGGCC
12695 TCGG
1 TCGG
12699 TCGAATGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:12708 original size:14 final size:14
Alignment explanation
Indices: 12689--12726 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
12679 ATGCTCTCGG
12689 ATGGCCTCGGTCGA
1 ATGGCCTCGGTCGA
*
12703 ATGGCCTCGGTCGG
1 ATGGCCTCGGTCGA
12717 ATGGCCTCGG
1 ATGGCCTCGG
12727 ATGCCCAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.11, C:0.29, G:0.39, T:0.21
Consensus pattern (14 bp):
ATGGCCTCGGTCGA
Found at i:12806 original size:29 final size:29
Alignment explanation
Indices: 12769--12826 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
12759 GCAATCTCTT
*
12769 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* * *
12798 GTAGGTCGCCCGGAAGGCATGGCGTCCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
12827 CGGTCAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.28, G:0.36, T:0.16
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:14951 original size:58 final size:57
Alignment explanation
Indices: 14888--15008 Score: 215
Period size: 58 Copynumber: 2.1 Consensus size: 57
14878 CTTTAGTTTT
* *
14888 AAGTTTCACTTTAGTACACCAGTTCAAAATTTAACATTAAGTTTTGAAAAAAATTTGA
1 AAGTTTCACTTTAGGACACCAATTCAAAATTTAACATTAAGTTTTGAAAAAAA-TTGA
14946 AAGTTTCACTTTAGGACACCAATTCAAAATTTAACATTAAGTTTTGAAAAAAATTGA
1 AAGTTTCACTTTAGGACACCAATTCAAAATTTAACATTAAGTTTTGAAAAAAATTGA
15003 AAGTTT
1 AAGTTT
15009 AGGTATTAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 10 0.16
58 51 0.84
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.36
Consensus pattern (57 bp):
AAGTTTCACTTTAGGACACCAATTCAAAATTTAACATTAAGTTTTGAAAAAAATTGA
Found at i:16994 original size:12 final size:12
Alignment explanation
Indices: 16977--17001 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16967 GTGGACTGCT
16977 GTTTAACTGAAA
1 GTTTAACTGAAA
16989 GTTTAACTGAAA
1 GTTTAACTGAAA
17001 G
1 G
17002 AGCTCAGGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (12 bp):
GTTTAACTGAAA
Found at i:17547 original size:21 final size:21
Alignment explanation
Indices: 17521--17568 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
17511 CAGCGATACC
*
17521 CGCAATAGTGCTCT-TTATATT
1 CGCAATAGCGCT-TGTTATATT
17542 CGCAATAGCGCTTGTTATATT
1 CGCAATAGCGCTTGTTATATT
17563 CGCAAT
1 CGCAAT
17569 TGCGGCAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (21 bp):
CGCAATAGCGCTTGTTATATT
Found at i:20727 original size:2 final size:2
Alignment explanation
Indices: 20720--20749 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20710 AGCATCGATA
20720 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
20750 TTGTTGAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22373 original size:16 final size:16
Alignment explanation
Indices: 22349--22387 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
22339 TTGACTTCCG
22349 AATCAAGTAGGAACCA
1 AATCAAGTAGGAACCA
*
22365 AATCTAGTAGGAACCA
1 AATCAAGTAGGAACCA
22381 AATCAAG
1 AATCAAG
22388 CAGGGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.15
Consensus pattern (16 bp):
AATCAAGTAGGAACCA
Found at i:23359 original size:23 final size:23
Alignment explanation
Indices: 23333--23378 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
23323 TAAGAGATGA
23333 CCAACAGAAACCAAGAAAAAAAG
1 CCAACAGAAACCAAGAAAAAAAG
*
23356 CCAATAGAAACCAAGAAAAAAAG
1 CCAACAGAAACCAAGAAAAAAAG
23379 AGAGATGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.65, C:0.20, G:0.13, T:0.02
Consensus pattern (23 bp):
CCAACAGAAACCAAGAAAAAAAG
Found at i:24424 original size:26 final size:26
Alignment explanation
Indices: 24388--24441 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
24378 TGATGTGGCC
*
24388 AGCAATTTGGATGTGGCCAGCTTTGT
1 AGCAATTTGGATGTGGCCAGATTTGT
*
24414 AGCAATTTGGATGTGTCCAGATTTGT
1 AGCAATTTGGATGTGGCCAGATTTGT
24440 AG
1 AG
24442 GCAGCATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (26 bp):
AGCAATTTGGATGTGGCCAGATTTGT
Found at i:26034 original size:33 final size:33
Alignment explanation
Indices: 25995--26065 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
25985 TTCACTTAGA
25995 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
26028 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
26061 TTTCA
1 TTTCA
26066 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:26223 original size:19 final size:20
Alignment explanation
Indices: 26145--26237 Score: 116
Period size: 21 Copynumber: 4.5 Consensus size: 20
26135 TGCAGAAGAG
26145 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
26166 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
26186 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
*
26208 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
26227 TCGCAACGAGA
1 TCGCAACGAGA
26238 GAATCGCAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
19 18 0.30
20 9 0.15
21 24 0.39
22 10 0.16
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:26240 original size:42 final size:41
Alignment explanation
Indices: 26145--26237 Score: 134
Period size: 42 Copynumber: 2.3 Consensus size: 41
26135 TGCAGAAGAG
* * **
26145 TCGCAACGAGATAAATGAAAATCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAAATGAAAATCGCAACGCGAAAATGAAAA
26186 TCTGCAACGAGAAAAATGAAAATCGCAACGCG-AAATGAAAA
1 TC-GCAACGAGAAAAATGAAAATCGCAACGCGAAAATGAAAA
26227 TCGCAACGAGA
1 TCGCAACGAGA
26238 GAATCGCAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
40 9 0.19
41 11 0.23
42 27 0.57
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (41 bp):
TCGCAACGAGAAAAATGAAAATCGCAACGCGAAAATGAAAA
Found at i:26313 original size:24 final size:24
Alignment explanation
Indices: 26279--26325 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
26269 GATTCACATC
26279 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
26303 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
26326 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:27046 original size:20 final size:20
Alignment explanation
Indices: 27018--27246 Score: 244
Period size: 20 Copynumber: 11.4 Consensus size: 20
27008 AAATTTCAGT
* * *
27018 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
27038 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
27058 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
27078 GTTGCGATTTACTGATTATC
1 GTTGCGATTTACGGATTCGC
*
27098 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
27118 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
27138 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
27158 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
27178 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
27198 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
27218 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
27238 GTTGCGATT
1 GTTGCGATT
27247 CTGTAAAATC
Statistics
Matches: 184, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 183 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:27264 original size:21 final size:20
Alignment explanation
Indices: 27240--27310 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 20
27230 ATATTCGCGT
27240 TGCGATTCTGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
27261 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
**
27282 TGCGA-TTGTCAAGAATCGCGT
1 TGCGATTTGT-AA-AATCGCAA
27303 TGCGATTT
1 TGCGATTT
27311 TGGAAACTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
19 4 0.10
20 2 0.05
21 29 0.73
22 5 0.12
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:32144 original size:64 final size:64
Alignment explanation
Indices: 32071--32233 Score: 292
Period size: 64 Copynumber: 2.5 Consensus size: 64
32061 ATGCAATCAG
*
32071 TGCATCGATGCATAAGGAGTGCATCGATGCACCTGCTTAAAATACAAACATCGAATAGGATTTA
1 TGCACCGATGCATAAGGAGTGCATCGATGCACCTGCTTAAAATACAAACATCGAATAGGATTTA
32135 TGCACCGATGCATAAGGAGTGCATCGATGCACCTGCTTAAAATACAAACATCGAATAGGATTTA
1 TGCACCGATGCATAAGGAGTGCATCGATGCACCTGCTTAAAATACAAACATCGAATAGGATTTA
*
32199 TGCACCGATGCATGAA-TAGTGCATCGATGCACCTG
1 TGCACCGATGCAT-AAGGAGTGCATCGATGCACCTG
32234 TCAAGGGATG
Statistics
Matches: 96, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
64 94 0.98
65 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (64 bp):
TGCACCGATGCATAAGGAGTGCATCGATGCACCTGCTTAAAATACAAACATCGAATAGGATTTA
Found at i:32919 original size:23 final size:24
Alignment explanation
Indices: 32867--32919 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 24
32857 TAAGGAGTGG
*
32867 TCCTTCGGGACAAATACAATCATAGG
1 TCCTTCGGGACAAAT--AATCATAGC
*
32893 TCCTTCGGGACAAAT-TTCATAGC
1 TCCTTCGGGACAAATAATCATAGC
32916 TCCT
1 TCCT
32920 AGTGGGACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 10 0.40
26 15 0.60
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (24 bp):
TCCTTCGGGACAAATAATCATAGC
Found at i:35545 original size:34 final size:34
Alignment explanation
Indices: 35498--35578 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
35488 TTTTCACCCT
*
35498 AAACC-CGACCCCGACCCGAATATCACACGTAAAA
1 AAACCTCGA-CCCGACCCGAATATCAAACGTAAAA
* *
35532 AAACCTCGACCCGACCCGAATATCAAACTTTAAA
1 AAACCTCGACCCGACCCGAATATCAAACGTAAAA
35566 AAA-CTCGACCCGA
1 AAACCTCGACCCGA
35579 AGCCGATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 10 0.23
34 30 0.70
35 3 0.07
ACGTcount: A:0.41, C:0.36, G:0.11, T:0.12
Consensus pattern (34 bp):
AAACCTCGACCCGACCCGAATATCAAACGTAAAA
Found at i:35632 original size:33 final size:34
Alignment explanation
Indices: 35571--35640 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
35561 TTAAAAAACT
* *
35571 CGACCCGAAGCCGATTTTTTTTAAAAATCCGACC
1 CGACCCGAACCCGATTTTTTTTAAAAATCCAACC
*
35605 CGACCCGAACCCGATTTTTTTT-TAAATCCAACC
1 CGACCCGAACCCGATTTTTTTTAAAAATCCAACC
35638 CGA
1 CGA
35641 ATACCAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 12 0.36
34 21 0.64
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (34 bp):
CGACCCGAACCCGATTTTTTTTAAAAATCCAACC
Found at i:37562 original size:25 final size:24
Alignment explanation
Indices: 37534--37596 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 24
37524 AAATTGTAAA
37534 TAACATTTATAAAATTGATA-TATTT
1 TAACATTTATAAAA-T-ATACTATTT
*
37559 TAAC-TTATATATAAATATACTCTTT
1 TAACATT-TATA-AAATATACTATTT
37584 TAACATTTTATAA
1 TAACA-TTTATAA
37597 TTTATATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
24 5 0.16
25 18 0.56
26 7 0.22
27 2 0.06
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.48
Consensus pattern (24 bp):
TAACATTTATAAAATATACTATTT
Found at i:39580 original size:23 final size:24
Alignment explanation
Indices: 39539--39589 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
39529 ATTTACACGT
39539 ATTTATTTATATATATTTTTAAAA
1 ATTTATTTATATATATTTTTAAAA
* * *
39563 ATTTA-TTATTTATTTTTTTAATA
1 ATTTATTTATATATATTTTTAAAA
39586 ATTT
1 ATTT
39590 TTAAATACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTTATTTATATATATTTTTAAAA
Found at i:39892 original size:48 final size:48
Alignment explanation
Indices: 39801--39892 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
39791 TCATTAAAAA
* * *
39801 CTTAACGCATTTAATACCTAAATCATCGATTTTAATGTGTTTTATTAC
1 CTTAACGCATTTAATACATAAATCATCGATTTTAATATATTTTATTAC
* *
39849 CTTAACGCATTTAGTACATAAATTATCGATTTTAATATATTTTA
1 CTTAACGCATTTAATACATAAATCATCGATTTTAATATATTTTA
39893 ATAATTAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.45
Consensus pattern (48 bp):
CTTAACGCATTTAATACATAAATCATCGATTTTAATATATTTTATTAC
Found at i:42146 original size:8 final size:8
Alignment explanation
Indices: 42133--42571 Score: 256
Period size: 8 Copynumber: 58.8 Consensus size: 8
42123 AAGATTTAAC
42133 TTTAATGA
1 TTTAATGA
42141 TTTAATGA
1 TTTAATGA
42149 TTTAATGA
1 TTTAATGA
42157 TTTAAT-A
1 TTTAATGA
* *
42164 -ATAATTA
1 TTTAATGA
42171 CTTTAATGA
1 -TTTAATGA
*
42180 TTTAA--C
1 TTTAATGA
42186 TTTAATGA
1 TTTAATGA
*
42194 TTTAA--C
1 TTTAATGA
42200 TTTAATGA
1 TTTAATGA
42208 TTTAAT-A
1 TTTAATGA
* *
42215 -ATAATTA
1 TTTAATGA
42222 CTTTAATGA
1 -TTTAATGA
42231 TTTAAT--
1 TTTAATGA
42237 TTTAATGA
1 TTTAATGA
42245 TTTAAT-A
1 TTTAATGA
* *
42252 -ATAATTA
1 TTTAATGA
42259 CTTTAATGA
1 -TTTAATGA
42268 TTTAAT--
1 TTTAATGA
42274 TTTAATGA
1 TTTAATGA
42282 TTTAATGA
1 TTTAATGA
*
42290 TTTAA--C
1 TTTAATGA
42296 TTTAATGA
1 TTTAATGA
42304 TTTAAT-A
1 TTTAATGA
* *
42311 -ATAATTA
1 TTTAATGA
42318 CTTTAATGA
1 -TTTAATGA
42327 TTTAAT-A
1 TTTAATGA
* *
42334 -ATAATTA
1 TTTAATGA
42341 CTTTAATGA
1 -TTTAATGA
*
42350 TTTAA--C
1 TTTAATGA
*
42356 TTTAATGC
1 TTTAATGA
42364 TTTAAT-A
1 TTTAATGA
* *
42371 -ATAATTA
1 TTTAATGA
42378 CTTTAATGA
1 -TTTAATGA
42387 TTTAATGA
1 TTTAATGA
42395 TTTAATGA
1 TTTAATGA
42403 TTTAAT-A
1 TTTAATGA
* *
42410 -ATAATTA
1 TTTAATGA
42417 CTTTAATGA
1 -TTTAATGA
*
42426 TTTAA--C
1 TTTAATGA
*
42432 TTTAATGC
1 TTTAATGA
42440 TTTAAT-A
1 TTTAATGA
* *
42447 -ATAATTA
1 TTTAATGA
42454 CTTTAATGA
1 -TTTAATGA
42463 TTTAATGA
1 TTTAATGA
42471 TTTAATGA
1 TTTAATGA
42479 TTTAATGA
1 TTTAATGA
42487 TTTAAT-A
1 TTTAATGA
* *
42494 -ATAATTA
1 TTTAATGA
42501 CTTTAATGA
1 -TTTAATGA
42510 TTTAAT--
1 TTTAATGA
*
42516 TTTAATAA
1 TTTAATGA
42524 TTTAAT-A
1 TTTAATGA
* *
42531 -ATAATTA
1 TTTAATGA
*
42538 CTTAAT--
1 TTTAATGA
42544 TTTAATGA
1 TTTAATGA
42552 TTTAAT--
1 TTTAATGA
42558 TTTAATGA
1 TTTAATGA
42566 TTTAAT
1 TTTAAT
42572 AATAATTACT
Statistics
Matches: 342, Mismatches: 40, Indels: 98
0.71 0.08 0.20
Matches are distributed among these distances:
6 94 0.27
7 18 0.05
8 185 0.54
9 45 0.13
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (8 bp):
TTTAATGA
Found at i:42177 original size:23 final size:23
Alignment explanation
Indices: 42149--42515 Score: 231
Period size: 23 Copynumber: 15.6 Consensus size: 23
42139 GATTTAATGA
42149 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATAATAATTAC
*
42172 TTTAATGATTTAACTTTAATGATTTAAC
1 TTTAATGATTTAA---TAAT-AATT-AC
42200 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATAATAATTAC
** *
42223 TTTAATGATTTAATTTTAATGA-
1 TTTAATGATTTAATAATAATTAC
* * * *
42245 TTTAATAATAATTACT-TTAATGA-
1 TTTAATGAT--TTAATAATAATTAC
*
42268 TTTAAT--TTTAATGATTTAATGATTTAAC
1 TTTAATGATTT-A--A--TAAT-AATT-AC
42296 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATAATAATTAC
42319 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATAATAATTAC
* *
42342 TTTAATGATTTAACT-TTAA-TGC
1 TTTAATGATTTAA-TAATAATTAC
* * * *
42364 TTTAATAATAATTACT-TTAATGA-
1 TTTAATGAT--TTAATAATAATTAC
* *
42387 TTTAATGATTTAATGAT--TTAA
1 TTTAATGATTTAATAATAATTAC
* * *
42408 TAATAATTACTTTAATGAT--TTAAC
1 T-TTAATGA-TTTAATAATAATT-AC
*
42432 TTTAATGCTTTAATAATAATTAC
1 TTTAATGATTTAATAATAATTAC
* *
42455 TTTAATGATTTAATGATTTAATGA-
1 TTTAATGATTTAAT-A-ATAATTAC
42479 TTTAATGATTTAATAATAATTAC
1 TTTAATGATTTAATAATAATTAC
42502 TTTAATGATTTAAT
1 TTTAATGATTTAAT
42516 TTTAATAATT
Statistics
Matches: 278, Mismatches: 34, Indels: 64
0.74 0.09 0.17
Matches are distributed among these distances:
19 2 0.01
20 3 0.01
21 6 0.02
22 37 0.13
23 146 0.53
24 34 0.12
25 14 0.05
26 6 0.02
27 5 0.02
28 21 0.08
29 1 0.00
30 3 0.01
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (23 bp):
TTTAATGATTTAATAATAATTAC
Found at i:42225 original size:37 final size:37
Alignment explanation
Indices: 42184--42484 Score: 399
Period size: 37 Copynumber: 7.8 Consensus size: 37
42174 TAATGATTTA
42184 ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
*
42221 ACTTTAATGATTTAATTTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
* *
42258 ACTTTAATGATTTAATTTTAATGATTTAATGAT--TT
1 ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
42293 AACTTTAATGATTTAATAATAATTACTTTAATGATTTAATAATAATT
1 -ACTTTAATGA--T--T--T-A--ACTTTAATGATTTAATAATAATT
*
42340 ACTTTAATGATTTAACTTTAATGCTTTAATAATAATT
1 ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
*
42377 ACTTTAATGATTTAATGATTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAA--CTTTAATGATTTAATAATAATT
*
42416 ACTTTAATGATTTAACTTTAATGCTTTAATAATAATT
1 ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
*
42453 ACTTTAATGATTTAATGATTTAATGATTTAAT
1 ACTTTAATGATTTAA--CTTTAATGATTTAAT
42485 GATTTAATAA
Statistics
Matches: 237, Mismatches: 11, Indels: 30
0.85 0.04 0.11
Matches are distributed among these distances:
35 2 0.01
36 10 0.04
37 140 0.59
38 1 0.00
39 49 0.21
40 2 0.01
42 2 0.01
43 1 0.00
44 1 0.00
45 17 0.07
46 10 0.04
47 2 0.01
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.50
Consensus pattern (37 bp):
ACTTTAATGATTTAACTTTAATGATTTAATAATAATT
Found at i:42416 original size:76 final size:77
Alignment explanation
Indices: 42319--42582 Score: 381
Period size: 84 Copynumber: 3.3 Consensus size: 77
42309 TAATAATTAC
42319 TTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGCTTTAATAATAATTAC-TTTA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGCTTTAATAATAATTACTTTTA
42383 ATGATTTAATGA
66 ATGATTTAATGA
42395 TTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGCTTTAATAATAATTACTTTAA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGCTTTAATAATAATTAC-----
42460 TGATTTAATGATTTAATGA
61 T--TTTAATGATTTAATGA
* **
42479 TTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATAATTTAATAATAATTACTTAAT
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGCTTTAATAATAATTAC----T
42544 TTTAATGATTTAAT--
62 TTTAATGATTTAATGA
42558 TTTAATGATTTAATAATAATTACTT
1 TTTAATGATTTAATAATAATTACTT
42583 GACTTTAATG
Statistics
Matches: 177, Mismatches: 3, Indels: 13
0.92 0.02 0.07
Matches are distributed among these distances:
76 60 0.34
79 25 0.14
81 14 0.08
83 5 0.03
84 73 0.41
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (77 bp):
TTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGCTTTAATAATAATTACTTTTA
ATGATTTAATGA
Found at i:42521 original size:23 final size:23
Alignment explanation
Indices: 42141--42571 Score: 206
Period size: 23 Copynumber: 18.7 Consensus size: 23
42131 ACTTTAATGA
*
42141 TTTAATGA-TTTAATGATTTAAT
1 TTTAATTACTTTAATGATTTAAT
**
42163 AATAATTACTTTAATGATTTAACT
1 TTTAATTACTTTAATGATTTAA-T
*
42187 TTAATGATTTAACTTTAATGATTTAAT
1 TT--T-AATT-ACTTTAATGATTTAAT
**
42214 AATAATTACTTTAATGATTTAAT
1 TTTAATTACTTTAATGATTTAAT
* * *
42237 TTTAATGA-TTTAATAATAATT-AC
1 TTTAATTACTTTAATGAT--TTAAT
*
42260 TTTAATGA-TTTAAT--TTTAAT
1 TTTAATTACTTTAATGATTTAAT
42280 GATTTAATGATTTAACTTTAATGATTTAAT
1 --TTT-A--A-TT-ACTTTAATGATTTAAT
**
42310 AATAATTACTTTAATGATTTAAT
1 TTTAATTACTTTAATGATTTAAT
** *
42333 AATAATTACTTTAATGATTTAAC
1 TTTAATTACTTTAATGATTTAAT
* * *
42356 TTTAA-TGCTTTAATAATAATT-AC
1 TTTAATTACTTTAATGAT--TTAAT
*
42379 TTTAATGA-TTTAATGATTTAAT
1 TTTAATTACTTTAATGATTTAAT
* *
42401 GATTTAA-TA--ATAATTACTTTAAT
1 --TTTAATTACTTTAATGA-TTTAAT
*
42424 GATTT-A--ACTTTAATGCTTTAAT
1 --TTTAATTACTTTAATGATTTAAT
**
42446 AATAATTACTTTAATGATTTAAT
1 TTTAATTACTTTAATGATTTAAT
*
42469 GATTTAATGA-TTTAATGATTTAAT
1 --TTTAATTACTTTAATGATTTAAT
**
42493 AATAATTACTTTAATGATTTAAT
1 TTTAATTACTTTAATGATTTAAT
* *
42516 TTTAA-TAATTTAAT-A-ATAAT
1 TTTAATTACTTTAATGATTTAAT
42536 TACTTAA-T--TTTAATGATTTAAT
1 T--TTAATTACTTTAATGATTTAAT
*
42558 TTTAATGA-TTTAAT
1 TTTAATTACTTTAAT
42572 AATAATTACT
Statistics
Matches: 321, Mismatches: 48, Indels: 80
0.71 0.11 0.18
Matches are distributed among these distances:
19 2 0.01
20 17 0.05
21 7 0.02
22 68 0.21
23 154 0.48
24 29 0.09
25 8 0.02
26 2 0.01
27 6 0.02
28 22 0.07
30 6 0.02
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (23 bp):
TTTAATTACTTTAATGATTTAAT
Found at i:42603 original size:14 final size:13
Alignment explanation
Indices: 42125--42613 Score: 244
Period size: 14 Copynumber: 37.6 Consensus size: 13
42115 AGGAAAAAAA
42125 GATTTAACTTTAAT
1 GATTTAA-TTTAAT
42139 GATTTAATGATTTAAT
1 GATTT-A--ATTTAAT
42155 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
42166 -AATTACTTTAAT
1 GATTTAATTTAAT
42178 GATTTAACTTTAAT
1 GATTTAA-TTTAAT
42192 GATTTAACTTTAAT
1 GATTTAA-TTTAAT
42206 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
42217 -AATTACTTTAAT
1 GATTTAATTTAAT
42229 GATTTAATTTTAAT
1 GATTTAA-TTTAAT
42243 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
42254 -AATTACTTTAAT
1 GATTTAATTTAAT
42266 GATTTAATTTTAAT
1 GATTTAA-TTTAAT
42280 G-----ATTTAAT
1 GATTTAATTTAAT
42288 GATTTAACTTTAAT
1 GATTTAA-TTTAAT
42302 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
42313 -AATTACTTTAAT
1 GATTTAATTTAAT
42325 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
42336 -AATTACTTTAAT
1 GATTTAATTTAAT
42348 GATTTAACTTTAAT
1 GATTTAA-TTTAAT
*
42362 GCTTTAA--TAAT
1 GATTTAATTTAAT
* *
42373 -AATTACTTTAAT
1 GATTTAATTTAAT
42385 GATTTAATGATTTAAT
1 GATTT-A--ATTTAAT
42401 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
42412 -AATTACTTTAAT
1 GATTTAATTTAAT
42424 GATTTAACTTTAAT
1 GATTTAA-TTTAAT
* *
42438 GCTTTAATAATAAT
1 GATTTAAT-TTAAT
*
42452 TACTTTAATGATTTAAT
1 GA-TTT-A--ATTTAAT
42469 GATTTAATGATTTAAT
1 GATTT-A--ATTTAAT
42485 GATTTAA--TAAT
1 GATTTAATTTAAT
* *
42496 -AATTACTTTAAT
1 GATTTAATTTAAT
42508 GATTTAATTTTAAT
1 GATTTAA-TTTAAT
* *
42522 AATTTAATAATAAT
1 GATTTAAT-TTAAT
* *
42536 TACTTAATTTTAAT
1 GATTTAA-TTTAAT
42550 GATTTAATTTTAAT
1 GATTTAA-TTTAAT
*
42564 GATTTAATAATAAT
1 GATTTAAT-TTAAT
* * *
42578 TACTTGACTTTAAT
1 GA-TTTAATTTAAT
*
42592 GATTTATATTTACT
1 GATTTA-ATTTAAT
*
42606 GATATAAT
1 GATTTAAT
42614 AATAGTAAAT
Statistics
Matches: 366, Mismatches: 57, Indels: 105
0.69 0.11 0.20
Matches are distributed among these distances:
8 7 0.02
9 1 0.00
10 31 0.08
11 32 0.09
12 32 0.09
13 43 0.12
14 158 0.43
15 12 0.03
16 42 0.11
17 6 0.02
18 2 0.01
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (13 bp):
GATTTAATTTAAT
Found at i:43086 original size:6 final size:6
Alignment explanation
Indices: 43071--43101 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
43061 GGTGAGAAGA
*
43071 ACTCCT ACTCCC ACTCCC ACTCCC ACTCCC A
1 ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC A
43102 GTCCTTCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.61, G:0.00, T:0.19
Consensus pattern (6 bp):
ACTCCC
Found at i:45132 original size:172 final size:173
Alignment explanation
Indices: 44837--45195 Score: 578
Period size: 172 Copynumber: 2.1 Consensus size: 173
44827 AACATCAAAT
* *
44837 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTTGCAATTTAATCACTAAATT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
*
44902 TATAAATTCTTTCAAATTTAACCAATTAAGCATATTAATACTAAATTCAAGCATAGTATACCAAC
66 TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
* *
44967 TTTTTATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTGC
131 TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
* *
45010 AAAACGATCCCTAATTACTATTTGGTTCTCAACATTTTCAAAGTTAGCAATTTAATC-CATAAAT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCAC-TAAAT
* * *
45074 TT-TAAATTCTTTCTAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATAGCAA
65 TTATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAA
* *
45138 CTTTTAATAATTTACTCTTATTCCTTAAATTCCTTAAATTTTAC
130 CTTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
*
45182 AAAACGGTCCCTAA
1 AAAACGATCCCTAA
45196 AACTTTACAA
Statistics
Matches: 172, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
172 112 0.65
173 60 0.35
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (173 bp):
AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
Found at i:45498 original size:41 final size:41
Alignment explanation
Indices: 45438--45515 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
45428 CCCTCTCAGG
*
45438 CTCTCACTGCTTCTGTAATTGTGAATTGCCTCAGCCCCAAA
1 CTCTCACTGCTTCTATAATTGTGAATTGCCTCAGCCCCAAA
45479 CTCTCACTGCTTCTATAATTGTGAATTGCCTCAGCCC
1 CTCTCACTGCTTCTATAATTGTGAATTGCCTCAGCCC
45516 GAGCAGTCTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.21, C:0.32, G:0.14, T:0.33
Consensus pattern (41 bp):
CTCTCACTGCTTCTATAATTGTGAATTGCCTCAGCCCCAAA
Found at i:45696 original size:23 final size:23
Alignment explanation
Indices: 45670--45713 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
45660 AGTTGCATGC
45670 CCCCCACATGCAGACGTGCAGGA
1 CCCCCACATGCAGACGTGCAGGA
45693 CCCCCACATGCAGACGTGCAG
1 CCCCCACATGCAGACGTGCAG
45714 CCCTGCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.41, G:0.25, T:0.09
Consensus pattern (23 bp):
CCCCCACATGCAGACGTGCAGGA
Found at i:45832 original size:34 final size:34
Alignment explanation
Indices: 45789--45873 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
45779 CATGCACAGC
*
45789 ACTGAAGACGCCGAGATTTCCTACGAAGAATCCA
1 ACTGAAGACGCCGAGAGTTCCTACGAAGAATCCA
*
45823 ACTGAAGACGCCGAGAGTTCCTATGAAGAATCCA
1 ACTGAAGACGCCGAGAGTTCCTACGAAGAATCCA
45857 ACTGAAGACGCCGAGAG
1 ACTGAAGACGCCGAGAG
45874 ATCAATCATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (34 bp):
ACTGAAGACGCCGAGAGTTCCTACGAAGAATCCA
Found at i:52472 original size:3 final size:3
Alignment explanation
Indices: 52464--52490 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
52454 ACCTTTCATT
52464 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
52491 CTACTATGTC
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:57852 original size:31 final size:31
Alignment explanation
Indices: 57817--57902 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
57807 ATGATTTTAA
*
57817 AAAATTGAAAGTTTAGGTACTAAAAAGGACC
1 AAAATTGATAGTTTAGGTACTAAAAAGGACC
*
57848 AAAATTGATAGTTTAGGTACTAAAAAGGATC
1 AAAATTGATAGTTTAGGTACTAAAAAGGACC
*
57879 AAAACTGATAGTTTAGGTACTAAA
1 AAAATTGATAGTTTAGGTACTAAA
57903 CATGTAATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.27
Consensus pattern (31 bp):
AAAATTGATAGTTTAGGTACTAAAAAGGACC
Done.