Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004799.1 Hibiscus syriacus cultivar Beakdansim tig00010812_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: 81397
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1714 original size:37 final size:37
Alignment explanation
Indices: 1623--1720 Score: 166
Period size: 36 Copynumber: 2.7 Consensus size: 37
1613 AAAGGTTAGT
1623 AAAATTAAAAAATAATTT-TA-ATTTTCACTTTATTTC
1 AAAA-TAAAAAATAATTTATATATTTTCACTTTATTTC
1659 AAAAT-AAAAATAATTTATATATTTTCACTTTATTTC
1 AAAATAAAAAATAATTTATATATTTTCACTTTATTTC
1695 AAAATAAAAAATAATTTATATATTTT
1 AAAATAAAAAATAATTTATATATTTT
1721 TATACAAATT
Statistics
Matches: 59, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
34 11 0.19
35 3 0.05
36 25 0.42
37 20 0.34
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (37 bp):
AAAATAAAAAATAATTTATATATTTTCACTTTATTTC
Found at i:1965 original size:19 final size:18
Alignment explanation
Indices: 1905--1975 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 18
1895 ATTCTGTACA
* *
1905 ATATTATTTAAAATTAAAT
1 ATATTATTTCAAA-TAATT
* * *
1924 AGATAATTTTAAA-AATT
1 ATATTATTTCAAATAATT
*
1941 ATATTATTTGAAATAATT
1 ATATTATTTCAAATAATT
1959 AATATTATTTCAAATAA
1 -ATATTATTTCAAATAA
1976 ATAAATAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
17 13 0.31
18 4 0.10
19 25 0.60
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (18 bp):
ATATTATTTCAAATAATT
Found at i:2077 original size:21 final size:20
Alignment explanation
Indices: 2015--2078 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
2005 AATATTAAAA
*
2015 ATAATTTCATAATATTATAAT
1 ATAATTTTATAATA-TATAAT
* * *
2036 ATACTTTTAGAATAATTTAAT
1 ATAATTTTATAAT-ATATAAT
2057 ATAATTTTATAAGTATATAAT
1 ATAATTTTATAA-TATATAAT
2078 A
1 A
2079 ATTATTAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
ATAATTTTATAATATATAAT
Found at i:10055 original size:21 final size:21
Alignment explanation
Indices: 10031--10075 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
10021 GGATTTATAA
*
10031 TTTAGAGG-TTATGATTTAGGG
1 TTTAG-GGTTTATAATTTAGGG
10052 TTTAGGGTTTATAATTTAGGG
1 TTTAGGGTTTATAATTTAGGG
10073 TTT
1 TTT
10076 TAAGTTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (21 bp):
TTTAGGGTTTATAATTTAGGG
Found at i:15630 original size:2 final size:2
Alignment explanation
Indices: 15623--15664 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
15613 TATTTACTTC
15623 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
15665 TATATATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:15669 original size:2 final size:2
Alignment explanation
Indices: 15664--15690 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15654 ACACACACAC
15664 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
15691 ATGCCATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18028 original size:15 final size:16
Alignment explanation
Indices: 18008--18042 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
17998 AAGGAATGTT
18008 TTTACTTTG-GTTTAA
1 TTTACTTTGTGTTTAA
*
18023 TTTACTTTGTGTTTAT
1 TTTACTTTGTGTTTAA
18039 TTTA
1 TTTA
18043 TTTTCATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.66
Consensus pattern (16 bp):
TTTACTTTGTGTTTAA
Found at i:32853 original size:61 final size:59
Alignment explanation
Indices: 32749--32879 Score: 156
Period size: 61 Copynumber: 2.2 Consensus size: 59
32739 GACATCTATT
*** **
32749 AAAAAAATACTTTAGGTACCTACATGAAAAAGGTGGTACACCTTAGG-TACATTGTTTGACC
1 AAAAAAATA-TTTAGGTACCTACATGAAAAAGGCAATACACCTTAGGTTAC-TACTTTGA-C
* *
32810 AAAAAAATATTATAGGTACCTAGATGAAAAAGGCAATATACCTTAGGTTACTACTTTGAC
1 AAAAAAATATT-TAGGTACCTACATGAAAAAGGCAATACACCTTAGGTTACTACTTTGAC
32870 AAAAAAATAT
1 AAAAAAATAT
32880 AGGTACTTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
60 13 0.21
61 45 0.74
62 3 0.05
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (59 bp):
AAAAAAATATTTAGGTACCTACATGAAAAAGGCAATACACCTTAGGTTACTACTTTGAC
Found at i:40461 original size:7 final size:7
Alignment explanation
Indices: 40449--40485 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
40439 GTCAAAGAAA
40449 GTCAACG
1 GTCAACG
40456 GTCAACG
1 GTCAACG
40463 GTC-ACG
1 GTCAACG
40469 GTCAACG
1 GTCAACG
40476 GTCAACG
1 GTCAACG
40483 GTC
1 GTC
40486 GGGTCGTGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:40471 original size:13 final size:14
Alignment explanation
Indices: 40449--40485 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
40439 GTCAAAGAAA
40449 GTCAACGGTCAACG
1 GTCAACGGTCAACG
40463 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
40476 GTCAACGGTC
1 GTCAACGGTC
40486 GGGTCGTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:40498 original size:17 final size:17
Alignment explanation
Indices: 40475--40532 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
40465 CACGGTCAAC
40475 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
40492 TGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
**
40509 GGTCAACAATCGGGTCG
1 GGTCAACGGTCGGGTCG
40526 GGTCAAC
1 GGTCAAC
40533 CCGGTTCAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.17, C:0.24, G:0.40, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:40550 original size:19 final size:19
Alignment explanation
Indices: 40526--40597 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
40516 AATCGGGTCG
*
40526 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
40545 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
40564 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
40583 GGTCAAACCGGTTCA
1 GGTCAAACCGGTTCA
40598 AAACTGGTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
18 1 0.02
19 49 0.98
ACGTcount: A:0.25, C:0.32, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:40556 original size:9 final size:9
Alignment explanation
Indices: 40526--40614 Score: 79
Period size: 9 Copynumber: 9.3 Consensus size: 9
40516 AATCGGGTCG
*
40526 GGTCAACCC
1 GGTCAAACC
*
40535 GGTTCAGACC
1 GG-TCAAACC
40545 GGTCAAACC
1 GGTCAAACC
*
40554 GGTTCAGACC
1 GG-TCAAACC
40564 GGTCAAACC
1 GGTCAAACC
*
40573 GGTTCGAACC
1 GG-TCAAACC
40583 GGTCAAACC
1 GGTCAAACC
*
40592 GGTTCAAAACT
1 GG-TC-AAACC
*
40603 GGTTAAACC
1 GGTCAAACC
40612 GGT
1 GGT
40615 TTTCCAGCAG
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
9 33 0.51
10 26 0.40
11 6 0.09
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:46542 original size:41 final size:41
Alignment explanation
Indices: 46485--46564 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
46475 AAAAATAAAT
* *
46485 AAAACAGTGCTAGAAACAAGATACAATGTTCTGAAGATAAC
1 AAAACAGTGCTAGAAACAAGATAAAACGTTCTGAAGATAAC
46526 AAAACAGTGCTAGAAACAAGATAAAACGTTCTGAAGATA
1 AAAACAGTGCTAGAAACAAGATAAAACGTTCTGAAGATA
46565 TCAATAGCAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (41 bp):
AAAACAGTGCTAGAAACAAGATAAAACGTTCTGAAGATAAC
Found at i:47502 original size:36 final size:36
Alignment explanation
Indices: 47453--47525 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
47443 TAAACCGTCT
*
47453 TTGCGGCCCTTGTTTGCATTATCTGAAGGGAAAACC
1 TTGCAGCCCTTGTTTGCATTATCTGAAGGGAAAACC
*
47489 TTGCAGCCTTTGTTTGCATTATCTGAAGGGAAAACC
1 TTGCAGCCCTTGTTTGCATTATCTGAAGGGAAAACC
47525 T
1 T
47526 CAACCTGATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (36 bp):
TTGCAGCCCTTGTTTGCATTATCTGAAGGGAAAACC
Found at i:48381 original size:516 final size:517
Alignment explanation
Indices: 47689--48630 Score: 1345
Period size: 516 Copynumber: 1.8 Consensus size: 517
47679 CACCGATATT
* * * *
47689 TCGCAATTCTCTGCTTTCTATCCCATTGCCTGCTGAATTCTCTTTACTAGCACCATTTTCATCCG
1 TCGCAATTCTCTGCATTCTATCCCATTGCCTGCAGAATTCCCTTTACTAGCACCATTTTCATCAG
* * * *
47754 CAACGGAACCATTCACCTTCTCCATCTTTCGTTTCTTCTTCTTCTCCCCCTTGACGTATCCCTCT
66 CAACAGAACCATTCACCTTCTCCAGCTTTCGTTTCTTCTTCTTCTCCCCCTTCACATATCCCTCT
47819 TCTCCTCCGTACACAATCTTAATAGAGTCTTCAGGGCTGCAGATTTTCTGTTCCTCAGAATCATT
131 TCTCCTCCGTACACAATCTTAATAGAGTCTTCAGGGCTGCAGATTTTCTGTTCCTCAGAATCATT
*
47884 TATCACTGACTTTGATTTATTCTTCTTCTTGCATCCAATACCATCTTCGATATCACCACCGGC-A
196 TATCACTGACTTTGATTTATTCTTCTTCTTGCATCCAATACCATCTTCGATATCACCACC-ACTA
* *
47948 TCTAGCAATTTTCTGCTTTCTATCTCATTGCCTGCTGAATTCACTTTACTAGTTCCATTTTCAT-
260 TCTAGCAATTTTCTGCATTCTATCTCATTGCCTGCTGAATTCACTTTACTAGTACCATTTTCATA
* ** * **
48012 CAGCACTATGCACCTTCTCCGGCTCTTGTTTCTTCTTCTTTTTTGGCTTCTGGTATGCCTCTTCC
325 CAGCACCATGCACCTTCTCAAGCTCTTGTTTCTTCTTCTTCTTCCGCTTCTGGTATGCCTCTTCC
* * * *
48077 TCTCCCTGCGCAATCTTATTAGTGTCTTCAAGGGTGCAGATTTTCTGTTCCTCAGTATCATTGAT
390 TCTCCATCCACAATCTTATTAGCGTCTTCAAGGGTGCAGATTTTCTGTTCCTCAGTATCATTGAT
48142 CACTGATTTTGATTTCTTCTTCTTGTTGTGTCCGTTACCAACTTCAAAATCACTAGCAGTATC
455 CACTGATTTTGATTTCTTCTTCTTGTTGTGTCCGTTACCAACTTCAAAATCACTAGCAGTATC
* * * *
48205 TCGCAATTTTCTGCATTCTA-CCTCATTGCCTGCAGAATTCCCTTTACTGGTACCTTTTTCATCA
1 TCGCAATTCTCTGCATTCTATCC-CATTGCCTGCAGAATTCCCTTTACTAGCACCATTTTCATCA
* * * * **
48269 GCAACAGCACCATTCACCTTCTCCAGCTCTT-GTTTCTTCTTCTTCTTCCGCTTCTCATATGTCT
65 GCAACAGAACCATTCACCTTCTCCAGCT-TTCGTTTCTTCTTCTTCTCCCCCTTCACATATCCCT
* * * *
48333 CTTC-CTCTCCGTGCACAATCTTATTAGCGTCTTCATGGCTGCAGATTTTCTGTTCCTCAGAATC
129 CTTCTC-CTCCGTACACAATCTTAATAGAGTCTTCAGGGCTGCAGATTTTCTGTTCCTCAGAATC
* * * * *
48397 ATTTATCACTGATTTTGATTTCTTCTTCTTCTTGCGTCCATTACCATCTTCGATATCACCAGCAC
193 ATTTATCACTGACTTTGATTTATTCTTCTTCTTGCATCCAATACCATCTTCGATATCACCACCAC
* * *
48462 TATCTCGCAATTTTCTGCATTCTATCTCATTGCCTGTTGAATTCTCTTTACTAGTACCATTTTCA
258 TATCTAGCAATTTTCTGCATTCTATCTCATTGCCTGCTGAATTCACTTTACTAGTACCATTTTCA
* * *
48527 TCAGCAACAGCACCATTCACCTTCTCAAGCTCTTGTTTCTTCTTCTTCTTCCGCTTCTTGTCTGC
323 T-----ACAGCACCATGCACCTTCTCAAGCTCTTGTTTCTTCTTCTTCTTCCGCTTCTGGTATGC
*
48592 CTCTTCTTCTCCATCCACAATCTTATTAGCGTCTTCAAG
383 CTCTTCCTCTCCATCCACAATCTTATTAGCGTCTTCAAG
48631 CCCATCCCTG
Statistics
Matches: 369, Mismatches: 47, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
515 4 0.01
516 280 0.76
517 2 0.01
522 83 0.22
ACGTcount: A:0.18, C:0.30, G:0.12, T:0.41
Consensus pattern (517 bp):
TCGCAATTCTCTGCATTCTATCCCATTGCCTGCAGAATTCCCTTTACTAGCACCATTTTCATCAG
CAACAGAACCATTCACCTTCTCCAGCTTTCGTTTCTTCTTCTTCTCCCCCTTCACATATCCCTCT
TCTCCTCCGTACACAATCTTAATAGAGTCTTCAGGGCTGCAGATTTTCTGTTCCTCAGAATCATT
TATCACTGACTTTGATTTATTCTTCTTCTTGCATCCAATACCATCTTCGATATCACCACCACTAT
CTAGCAATTTTCTGCATTCTATCTCATTGCCTGCTGAATTCACTTTACTAGTACCATTTTCATAC
AGCACCATGCACCTTCTCAAGCTCTTGTTTCTTCTTCTTCTTCCGCTTCTGGTATGCCTCTTCCT
CTCCATCCACAATCTTATTAGCGTCTTCAAGGGTGCAGATTTTCTGTTCCTCAGTATCATTGATC
ACTGATTTTGATTTCTTCTTCTTGTTGTGTCCGTTACCAACTTCAAAATCACTAGCAGTATC
Found at i:48386 original size:261 final size:261
Alignment explanation
Indices: 47614--48630 Score: 1271
Period size: 261 Copynumber: 3.9 Consensus size: 261
47604 CACCCTCCGC
** * *
47614 ATCATTTATCACTGATTTTGATTTCTTCTTCTTCTTCTTGCGTCCATCGCCGTCTTCTATATCAC
1 ATCATTTATCACTGATTTTGA--T-TTCTTCTTCTTCTTGCGTCCATTACCATCTTCGATATCAC
* * * * *
47679 CA-CCGATATTTCGCAATTCTCTGCTTTCTATCC-CATTGCCTGCTGAATTCTCTTTACTAGCAC
63 CAGCAG-TATCTCGCAATTTTCTGCATTCTA-CCTCATTGCCTGCTGAATTCTCTTTACTAGTAC
* * * * * *
47742 CATTTTCATCCGCAACGGAACCATTCACCTTCTCCATCT-TTCGTTTCTTCTTCTTCTCCCCCTT
126 CATTTTCATCAGCAACAGCACCATTCACCTTCTCCAGCTCTT-GTTTCTTCTTCTTCTTCCGCTT
** * * * * *
47806 GACGTATCCCTCTT-CTCCTCCGTACACAATCTTAATAGAGTCTTCAGGGCTGCAGATTTTCTGT
190 CTCGTATGCCTCTTCCT-CTCCGTGCACAATCTTATTAGCGTCTTCAAGGCTGCAGATTTTCTGT
47870 TCCTCAGA
254 TCCTCAGA
* * * * *
47878 ATCATTTATCACTGACTTTGATTTATTCTTCTTCTTGCATCCAATACCATCTTCGATATCACCAC
1 ATCATTTATCACTGATTTTGATTTCTTCTTCTTCTTGCGTCCATTACCATCTTCGATATCACCAG
* * * * * * *
47943 CGGCATCTAGCAATTTTCTGCTTTCTATCTCATTGCCTGCTGAATTCACTTTACTAGTTCCATTT
66 CAGTATCTCGCAATTTTCTGCATTCTACCTCATTGCCTGCTGAATTCTCTTTACTAGTACCATTT
* * * * ** *
48008 TCAT------CAGCACTATGCACCTTCTCCGGCTCTTGTTTCTTCTTCTTTTTTGGCTTCTGGTA
131 TCATCAGCAACAGCACCATTCACCTTCTCCAGCTCTTGTTTCTTCTTCTTCTTCCGCTTCTCGTA
* * * *
48067 TGCCTCTTCCTCTCCCTGCGCAATCTTATTAGTGTCTTCAAGGGTGCAGATTTTCTGTTCCTCAG
196 TGCCTCTTCCTCTCCGTGCACAATCTTATTAGCGTCTTCAAGGCTGCAGATTTTCTGTTCCTCAG
*
48132 T
261 A
* * * * * * * *
48133 ATCATTGATCACTGATTTTGATTTCTTCTTCTTGTTGTGTCCGTTACCAACTTCAAAATCACTAG
1 ATCATTTATCACTGATTTTGATTTCTTCTTCTTCTTGCGTCCATTACCATCTTCGATATCACCAG
* * * *
48198 CAGTATCTCGCAATTTTCTGCATTCTACCTCATTGCCTGCAGAATTCCCTTTACTGGTACCTTTT
66 CAGTATCTCGCAATTTTCTGCATTCTACCTCATTGCCTGCTGAATTCTCTTTACTAGTACCATTT
*
48263 TCATCAGCAACAGCACCATTCACCTTCTCCAGCTCTTGTTTCTTCTTCTTCTTCCGCTTCTCATA
131 TCATCAGCAACAGCACCATTCACCTTCTCCAGCTCTTGTTTCTTCTTCTTCTTCCGCTTCTCGTA
* *
48328 TGTCTCTTCCTCTCCGTGCACAATCTTATTAGCGTCTTCATGGCTGCAGATTTTCTGTTCCTCAG
196 TGCCTCTTCCTCTCCGTGCACAATCTTATTAGCGTCTTCAAGGCTGCAGATTTTCTGTTCCTCAG
48393 A
261 A
48394 ATCATTTATCACTGATTTTGATTTCTTCTTCTTCTTGCGTCCATTACCATCTTCGATATCACCAG
1 ATCATTTATCACTGATTTTGATTTCTTCTTCTTCTTGCGTCCATTACCATCTTCGATATCACCAG
* * *
48459 CACTATCTCGCAATTTTCTGCATTCTATCTCATTGCCTGTTGAATTCTCTTTACTAGTACCATTT
66 CAGTATCTCGCAATTTTCTGCATTCTACCTCATTGCCTGCTGAATTCTCTTTACTAGTACCATTT
* * *
48524 TCATCAGCAACAGCACCATTCACCTTCTCAAGCTCTTGTTTCTTCTTCTTCTTCCGCTTCTTGTC
131 TCATCAGCAACAGCACCATTCACCTTCTCCAGCTCTTGTTTCTTCTTCTTCTTCCGCTTCTCGTA
* * *
48589 TGCCTCTTCTTCTCCATCCACAATCTTATTAGCGTCTTCAAG
196 TGCCTCTTCCTCTCCGTGCACAATCTTATTAGCGTCTTCAAG
48631 CCCATCCCTG
Statistics
Matches: 641, Mismatches: 102, Indels: 23
0.84 0.13 0.03
Matches are distributed among these distances:
255 203 0.32
256 4 0.01
260 1 0.00
261 410 0.64
262 3 0.00
264 20 0.03
ACGTcount: A:0.18, C:0.30, G:0.11, T:0.41
Consensus pattern (261 bp):
ATCATTTATCACTGATTTTGATTTCTTCTTCTTCTTGCGTCCATTACCATCTTCGATATCACCAG
CAGTATCTCGCAATTTTCTGCATTCTACCTCATTGCCTGCTGAATTCTCTTTACTAGTACCATTT
TCATCAGCAACAGCACCATTCACCTTCTCCAGCTCTTGTTTCTTCTTCTTCTTCCGCTTCTCGTA
TGCCTCTTCCTCTCCGTGCACAATCTTATTAGCGTCTTCAAGGCTGCAGATTTTCTGTTCCTCAG
A
Found at i:49398 original size:14 final size:14
Alignment explanation
Indices: 49373--49413 Score: 64
Period size: 14 Copynumber: 2.8 Consensus size: 14
49363 TCTTATTGTG
49373 ATTATCTATATTTTA
1 ATTAT-TATATTTTA
49388 ATTATTATATTTTA
1 ATTATTATATTTTA
49402 ATTATTTATATT
1 ATTA-TTATATT
49414 ATTTATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATTATATTTTA
Found at i:50908 original size:20 final size:21
Alignment explanation
Indices: 50883--50934 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
50873 TTTTCCCAAT
*
50883 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
50903 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
50924 TCGCAATGCGA
1 TCGCAATGCGA
50935 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:50948 original size:20 final size:20
Alignment explanation
Indices: 50923--51016 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
50913 AATTGGGAAA
50923 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
50943 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
50964 ATCGCAATGAGATACTGAAT
1 ATCGCAATGCGATACTGACT
* * *
50984 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
51004 TTCGCAACGCGAT
1 ATCGCAATGCGAT
51017 TTACATAGCG
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.03
20 43 0.72
21 14 0.23
22 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:51620 original size:19 final size:19
Alignment explanation
Indices: 51573--51614 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
51563 ACGAGAGAAT
*
51573 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
51592 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
51611 CGCA
1 CGCA
51615 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:51637 original size:19 final size:19
Alignment explanation
Indices: 51610--51794 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
51600 GAAACAAAAA
*
51610 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
51629 TTGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
51648 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
51667 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
51686 TCGCGGTTGCGATTGTC---
1 TCGC-GTTGCGATTTTCATT
* **
51703 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
51720 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
51734 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
51753 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
51773 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
51793 TC
1 TC
51795 AACCAAAATA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 20 0.15
16 3 0.02
17 4 0.03
18 1 0.01
19 66 0.49
20 41 0.30
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:51721 original size:34 final size:34
Alignment explanation
Indices: 51683--51769 Score: 124
Period size: 33 Copynumber: 2.6 Consensus size: 34
51673 TGCGATTTTT
* *
51683 ATTTCGCGGTTGCGATTGTCTGGTCGCGATAGTC
1 ATTTCGCGGTTGCGATTCTCTCGTCGCGATAGTC
*
51717 ATTTCGC-GTTGCGATTCTCTCGTTGCGATAGTC
1 ATTTCGCGGTTGCGATTCTCTCGTCGCGATAGTC
51750 ATTTC-CGCGTTGCGATTCTC
1 ATTTCGCG-GTTGCGATTCTC
51770 ATTATCTCGT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
32 1 0.02
33 28 0.58
34 19 0.40
ACGTcount: A:0.11, C:0.24, G:0.26, T:0.38
Consensus pattern (34 bp):
ATTTCGCGGTTGCGATTCTCTCGTCGCGATAGTC
Found at i:51771 original size:20 final size:20
Alignment explanation
Indices: 51737--51794 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
51727 GCGATTCTCT
**
51737 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
51757 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
51777 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
51795 AACCAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:53878 original size:21 final size:21
Alignment explanation
Indices: 53854--53920 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
53844 TCATTCCTCG
53854 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
53875 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
53896 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
53917 AGAG
1 AGAG
53921 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:53878 original size:42 final size:42
Alignment explanation
Indices: 53802--53920 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
53792 GACTCGCCTG
* * * * * * *
53802 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
53844 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
53886 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
53921 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:55299 original size:14 final size:14
Alignment explanation
Indices: 55280--55315 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
55270 ATTGTTTAAT
55280 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
55294 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
55308 TGATTTGT
1 TGATTTGT
55316 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:55484 original size:19 final size:19
Alignment explanation
Indices: 55422--55475 Score: 90
Period size: 20 Copynumber: 2.8 Consensus size: 19
55412 AAAAAGTACT
*
55422 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
55441 ATCGCAACGCGAAAATGAAA
1 ATCGCAACGCG-AAATGAAA
55461 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
55476 TAAATTCGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:55526 original size:33 final size:32
Alignment explanation
Indices: 55484--55610 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
55474 ATTAAATTCG
*
55484 CGTTGCGATTTTCATTTTGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
55517 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
55550 CGTTGCGATTTTCATTTTGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
55583 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
55611 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:55541 original size:19 final size:19
Alignment explanation
Indices: 55480--55610 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
55470 CGAAATTAAA
*
55480 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
55499 TTTGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
55515 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
55532 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
55546 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
55565 TTTGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
55581 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
55598 TTCGCATTGCGAT
1 TTCGCATTGCGAT
55611 AGTAATTTCC
Statistics
Matches: 81, Mismatches: 16, Indels: 30
0.64 0.13 0.24
Matches are distributed among these distances:
14 23 0.28
16 11 0.14
17 13 0.16
19 34 0.42
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:55573 original size:66 final size:66
Alignment explanation
Indices: 55477--55609 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
55467 ACGCGAAATT
*
55477 AAATTCGCGTTGCGATTTTCATTTTGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTTGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
55542 G
66 G
*
55543 AAATTAGCGTTGCGATTTTCATTTTGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTTGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
55608 G
66 G
55609 A
1 A
55610 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.43
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTTGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:57919 original size:12 final size:12
Alignment explanation
Indices: 57902--57926 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57892 TCTTCGGGGA
57902 CTTTTTCTTCTT
1 CTTTTTCTTCTT
57914 CTTTTTCTTCTT
1 CTTTTTCTTCTT
57926 C
1 C
57927 AGAATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:58135 original size:24 final size:24
Alignment explanation
Indices: 58101--58154 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
58091 CTGAAACATC
* *
58101 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
58125 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
58149 ATCAAA
1 ATCAAA
58155 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:59216 original size:20 final size:20
Alignment explanation
Indices: 59191--59228 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
59181 ATTCATTTGA
*
59191 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
59211 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
59229 CGCAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:59287 original size:19 final size:19
Alignment explanation
Indices: 59265--59367 Score: 108
Period size: 19 Copynumber: 5.6 Consensus size: 19
59255 CGATTTTTCG
59265 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
59284 TTGCGATTTTC---TCG--
1 TTGCGATTTTCATTTCGCA
*** *
59298 TTGCGATAGCCATTTTCGCG
1 TTGCGATTTTCA-TTTCGCA
*
59318 TTGCGATTTTCATTTTCACA
1 TTGCGATTTTCA-TTTCGCA
59338 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
59357 TTGCGATTTTC
1 TTGCGATTTTC
59368 TCGTTGCGAT
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
14 8 0.12
16 3 0.04
18 3 0.04
19 28 0.41
20 27 0.39
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:59385 original size:53 final size:53
Alignment explanation
Indices: 59247--59377 Score: 162
Period size: 53 Copynumber: 2.5 Consensus size: 53
59237 GAAATGAAAA
* *
59247 TCGCATTACGATTTT-TCGTTGCGATTTTCA-TTTCGCATTGCGATTTTCTCGT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTTCACATTGCGATTTTCTC-T
* * *
59299 T-GCGATAGCCATTTTCGCGTTGCGATTTTCATTTTCACATTGCGATTTTCAT-T
1 TCGC-ATTGCGATTTTCTCGTTGCGATTTTCATTTTCACATTGCGATTTTC-TCT
59352 TCGCATTGCGATTTTCTCGTTGCGAT
1 TCGCATTGCGATTTTCTCGTTGCGAT
59378 AGCCATTTCG
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
51 2 0.03
52 9 0.14
53 35 0.53
54 19 0.29
55 1 0.02
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (53 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTTCACATTGCGATTTTCTCT
Found at i:59503 original size:14 final size:15
Alignment explanation
Indices: 59484--59521 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
59474 CATCAATTAA
59484 ACAAATCAAT-ATTT
1 ACAAATCAATCATTT
*
59498 ACAAATC-ATCTTTT
1 ACAAATCAATCATTT
59512 ACAAATCAAT
1 ACAAATCAAT
59522 TAAACAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (15 bp):
ACAAATCAATCATTT
Found at i:61411 original size:20 final size:19
Alignment explanation
Indices: 61388--61455 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
61378 GAAACTTAAA
61388 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
61408 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
61428 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
61447 ATCGCAACG
1 ATCGCAACG
61456 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:61463 original size:14 final size:14
Alignment explanation
Indices: 61444--61501 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
61434 ATGCGAAATG
61444 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
61458 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
61474 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
61490 AAAATCGCAACG
1 AAAATCGCAACG
61502 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:61486 original size:32 final size:33
Alignment explanation
Indices: 61428--61506 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
61418 GGAAATGGCT
*
61428 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
61461 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
61493 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
61507 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:61535 original size:19 final size:17
Alignment explanation
Indices: 61513--61608 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
61503 GAAACACAAA
61513 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
61532 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
61548 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
61564 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
61580 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
61597 TCGCATTGCGAT
1 TCGC-TTGCGAT
61609 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:61554 original size:14 final size:14
Alignment explanation
Indices: 61535--61592 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
61525 TTTCATTTCG
61535 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
61549 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
61565 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
61581 CGTTGCGATTTT
1 CGTTGCGATTTT
61593 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:61599 original size:33 final size:33
Alignment explanation
Indices: 61518--61608 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
61508 ACAAATCGCA
61518 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
61551 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
61583 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
61609 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:61627 original size:20 final size:19
Alignment explanation
Indices: 61593--61647 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
61583 TTGCGATTTT
*
61593 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
61612 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
61632 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
61648 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:62155 original size:18 final size:18
Alignment explanation
Indices: 62129--62173 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
62119 GTCGATCAGA
*
62129 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
62147 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
62165 TGATGGCTC
1 TGATGGCTC
62174 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:63517 original size:20 final size:20
Alignment explanation
Indices: 63492--63529 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
63482 AATAGTTTCT
63492 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
63512 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
63530 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:63821 original size:22 final size:22
Alignment explanation
Indices: 63794--63837 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
63784 GATGGAGATA
63794 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
63816 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
63838 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:64128 original size:41 final size:41
Alignment explanation
Indices: 64011--64140 Score: 147
Period size: 41 Copynumber: 3.2 Consensus size: 41
64001 GAAAATAGCA
*
64011 TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCG
1 TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCGCG
* * * * *
64052 TTGCGA--AAGTCAGTATCGTGTTGCGAAAGTAAGTATCTCG
1 TTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGTATCGCG
* * * *
64092 TTGCGATTTTGTATTATCGCATTGCGATAGTCAGTATCGCA
1 TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCGCG
64133 TTGCGATT
1 TTGCGATT
64141 TTCCCAATTC
Statistics
Matches: 71, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
39 3 0.04
40 30 0.42
41 36 0.51
42 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (41 bp):
TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCGCG
Found at i:64139 original size:20 final size:20
Alignment explanation
Indices: 64025--64138 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
64015 GATTATGTAT
64025 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
64045 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
64065 TATCGTGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
64085 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
64106 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
64126 TATCGCATTGCGA
1 TATCGCGTTGCGA
64139 TTTTCCCAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 61 0.78
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:64157 original size:21 final size:21
Alignment explanation
Indices: 64128--64220 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
64118 ATAGTCAGTA
64128 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
64149 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
64169 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
64190 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
64210 TCGCATTGCGA
1 TCGCATTGCGA
64221 ATTAGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:64158 original size:41 final size:41
Alignment explanation
Indices: 64128--64220 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
64118 ATAGTCAGTA
* *
64128 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* *
64169 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
64210 TCGCATTGCGA
1 TCGCATTGCGA
64221 ATTAGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:69742 original size:72 final size:72
Alignment explanation
Indices: 69615--69763 Score: 244
Period size: 72 Copynumber: 2.1 Consensus size: 72
69605 GATACTTGTT
* *
69615 CAAAACTCCATTGTTAAAGCATAGGAAGCTATGCTATAAGCTTAGATTAACCTTGTTTTCTCTGC
1 CAAAACTCCATTGTTAAAGCATAGGAAGCTATGCTATAAGCTTAGATTAACCTTGTTATCTCAGC
69680 TTTAATC
66 TTTAATC
* * * *
69687 CAAAACTCCATTGTTTAAGCATAGGAAGCTATGCTATAAGCTTATATTTAGCTTGTTATCTCAGC
1 CAAAACTCCATTGTTAAAGCATAGGAAGCTATGCTATAAGCTTAGATTAACCTTGTTATCTCAGC
69752 TTTAATC
66 TTTAATC
69759 CAAAA
1 CAAAA
69764 ATAAACAGAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (72 bp):
CAAAACTCCATTGTTAAAGCATAGGAAGCTATGCTATAAGCTTAGATTAACCTTGTTATCTCAGC
TTTAATC
Found at i:72334 original size:31 final size:32
Alignment explanation
Indices: 72279--72338 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
72269 ATTTAAATTA
72279 TTATAAAATCATCATTAAAATTTATCGAAATG
1 TTATAAAATCATCATTAAAATTTATCGAAATG
* *
72311 TTATAAAATGAT-ATTTAAATTTATCGAA
1 TTATAAAATCATCATTAAAATTTATCGAA
72339 CTCTGACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (32 bp):
TTATAAAATCATCATTAAAATTTATCGAAATG
Found at i:72488 original size:2 final size:2
Alignment explanation
Indices: 72481--72508 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
72471 GTACTTTGCC
72481 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
72509 TGTATCAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:78868 original size:2 final size:2
Alignment explanation
Indices: 78863--78894 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
78853 GCACTCTCCA
*
78863 TC TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
78895 GTTGGCTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Done.