Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014834.1 Kokia drynarioides strain JFW-HI SEQ_129876, 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: 475149
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 280 characters in sequence are not A, C, G, or T
Found at i:1146 original size:27 final size:27
Alignment explanation
Indices: 1112--1166 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1102 ACTTAGATTT
* *
1112 AAATTATTACAAACTAATTATTATAAA
1 AAATTATTACAAAATAATTATTACAAA
*
1139 AAATTATTATAAAATAATTATTACAAA
1 AAATTATTACAAAATAATTATTACAAA
1166 A
1 A
1167 TAAGTGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (27 bp):
AAATTATTACAAAATAATTATTACAAA
Found at i:1166 original size:14 final size:14
Alignment explanation
Indices: 1113--1169 Score: 80
Period size: 14 Copynumber: 4.1 Consensus size: 14
1103 CTTAGATTTA
*
1113 AATTATTACAAACT
1 AATTATTACAAAAT
*
1127 AATTATTATAAAA-
1 AATTATTACAAAAT
*
1140 AATTATTATAAAAT
1 AATTATTACAAAAT
1154 AATTATTACAAAAT
1 AATTATTACAAAAT
1168 AA
1 AA
1170 GTGTTTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
13 13 0.33
14 26 0.67
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTATTACAAAAT
Found at i:1453 original size:81 final size:82
Alignment explanation
Indices: 1364--1533 Score: 245
Period size: 81 Copynumber: 2.1 Consensus size: 82
1354 TAACCTTCCT
* * * *
1364 TAAAAATGATAA-ATTTTTTATTTAATCTTTTAAAAATTACATTTTTATTATCATAAAAATTACA
1 TAAAAATGATAACA-TTTTGATTTAATCCTCTAAAAATTACATTTTTACTATCATAAAAATTACA
*
1428 ATTTAACTTTGGCCC-CC
65 ATTTAACTTTGACCCTCC
* *
1445 TAAAAATGATAACATTTTGATTTAATCCTCTAAAAATTACATTTTTACTATCATAAAATTTATAA
1 TAAAAATGATAACATTTTGATTTAATCCTCTAAAAATTACATTTTTACTATCATAAAAATTACAA
1510 TTTAACTTTGACCCTTCC
66 TTTAACTTTGACCC-TCC
1528 TAAAAA
1 TAAAAA
1534 AATTTTCTAT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
81 70 0.89
82 1 0.01
83 8 0.10
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.42
Consensus pattern (82 bp):
TAAAAATGATAACATTTTGATTTAATCCTCTAAAAATTACATTTTTACTATCATAAAAATTACAA
TTTAACTTTGACCCTCC
Found at i:1565 original size:2 final size:2
Alignment explanation
Indices: 1558--1583 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1548 GCCCCTATCC
1558 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
1584 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6419 original size:4 final size:4
Alignment explanation
Indices: 6410--6448 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
6400 AGGAATCATG
* * *
6410 TACA TACA TACA TGCA TACC TACA TGCA TACA TACA TAC
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC
6449 TCTGTTCTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.41, C:0.28, G:0.05, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:6433 original size:12 final size:12
Alignment explanation
Indices: 6412--6446 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
6402 GAATCATGTA
6412 CATACATACATG
1 CATACATACATG
*
6424 CATACCTACATG
1 CATACATACATG
6436 CATACATACAT
1 CATACATACAT
6447 ACTCTGTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.40, C:0.29, G:0.06, T:0.26
Consensus pattern (12 bp):
CATACATACATG
Found at i:11622 original size:27 final size:28
Alignment explanation
Indices: 11592--11646 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
11582 AAAATTACAT
11592 TTTGATTT-TCCTTAAAAATGATAAAAG
1 TTTGATTTATCCTTAAAAATGATAAAAG
* *
11619 TTTGATTTGATCTTTAAAAATTATAAAA
1 TTTGATTT-ATCCTTAAAAATGATAAAA
11647 ATAAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.33
29 16 0.67
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (28 bp):
TTTGATTTATCCTTAAAAATGATAAAAG
Found at i:11666 original size:17 final size:17
Alignment explanation
Indices: 11634--11673 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
11624 TTTGATCTTT
11634 AAAA-ATTATAAAAATA
1 AAAATATTATAAAAATA
11650 AAAATATTA-AAATAATA
1 AAAATATTATAAA-AATA
11667 AAAATAT
1 AAAATAT
11674 ACAATTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATATTATAAAAATA
Found at i:13539 original size:21 final size:21
Alignment explanation
Indices: 13513--13559 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
13503 CTATAGATTC
13513 CATGTTTCAATGTTCATGTAA
1 CATGTTTCAATGTTCATGTAA
*
13534 CATGTTTCAATTTTCATGTAA
1 CATGTTTCAATGTTCATGTAA
13555 CATGT
1 CATGT
13560 AACATGTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.45
Consensus pattern (21 bp):
CATGTTTCAATGTTCATGTAA
Found at i:13558 original size:7 final size:7
Alignment explanation
Indices: 13548--13579 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
13538 TTTCAATTTT
13548 CATGTAA
1 CATGTAA
13555 CATGTAA
1 CATGTAA
13562 CATGTAA
1 CATGTAA
13569 CATGTAA
1 CATGTAA
13576 CATG
1 CATG
13580 CTTAGCTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (7 bp):
CATGTAA
Found at i:14211 original size:15 final size:15
Alignment explanation
Indices: 14175--14213 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
14165 CTGCAAGTTT
*
14175 CAAGAATATAATCAA
1 CAAGAATATCATCAA
*
14190 C-AGAATATCATGAA
1 CAAGAATATCATCAA
14204 CAAGAATATC
1 CAAGAATATC
14214 CTTCAAAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.21
Consensus pattern (15 bp):
CAAGAATATCATCAA
Found at i:16047 original size:7 final size:7
Alignment explanation
Indices: 16032--16064 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
16022 TGATTAAATA
*
16032 AGCAATC
1 AGCAGTC
16039 AGCAGTC
1 AGCAGTC
16046 AGCAGTC
1 AGCAGTC
16053 AGCAGTC
1 AGCAGTC
16060 AGCAG
1 AGCAG
16065 CACCTTGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.33, C:0.27, G:0.27, T:0.12
Consensus pattern (7 bp):
AGCAGTC
Found at i:16332 original size:23 final size:23
Alignment explanation
Indices: 16306--16362 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
16296 AAAATTAAAT
16306 TATAATTTTTATGATAATAAA-AA
1 TATAATTTTTATGAT-ATAAATAA
* *
16329 TATAA-TTTTATTATTTAAATAA
1 TATAATTTTTATGATATAAATAA
16351 TATATATTTTTA
1 TATA-ATTTTTA
16363 CAATTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 4 0.14
22 14 0.48
23 6 0.21
24 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATAATTTTTATGATATAAATAA
Found at i:16460 original size:17 final size:17
Alignment explanation
Indices: 16425--16463 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
16415 TTATTTTACT
* *
16425 AATTTAAAACTTTAAAA
1 AATTTAAAACATGAAAA
*
16442 AATTTAAAACATGATAA
1 AATTTAAAACATGAAAA
16459 AATTT
1 AATTT
16464 TCAGACGCGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (17 bp):
AATTTAAAACATGAAAA
Found at i:17681 original size:31 final size:30
Alignment explanation
Indices: 17645--17731 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 30
17635 TTGAGAAACC
17645 TTTATTTGAACACTTTCGAAAATGTTTGATCA
1 TTTATTTGAACACTTT-GAAAATGTTTGA-CA
* * *
17677 -TTATTTGACCA-TTTTAAAAAGTTTTGACA
1 TTTATTTGAACACTTTGAAAATG-TTTGACA
* *
17706 TTTATTTGAGCACTTTTGTAAATGTT
1 TTTATTTGAACAC-TTTGAAAATGTT
17732 AGACTCATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
29 7 0.16
30 18 0.41
31 12 0.27
32 7 0.16
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (30 bp):
TTTATTTGAACACTTTGAAAATGTTTGACA
Found at i:18067 original size:252 final size:252
Alignment explanation
Indices: 17741--18224 Score: 625
Period size: 252 Copynumber: 1.9 Consensus size: 252
17731 TAGACTCATA
* * *
17741 TATGACTATTTTGAAAGGTATTATCTAAACATGATTATGAGTAAGGTTGGGTCAATGCAAAATCT
1 TATGACTATTTTAAAAGGTATTATCTAAACATGATCATGAGTAAGGTTGGGTCAATGCAAAATAT
* * ** *
17806 TAAGCTTGTTTTCTAACCTCGAGCCTGACTTGAAAAGGGGCCTAAAGTTCTACCCAAGC-CTGAC
66 TAAGCTTGTTTTCTAACCTCAAGCCCGACCCGAAAAAGGGCCTAAAGTTCTACCCAAGCTC-GAC
* * *
17870 CCGAATTAAAAATACTACACTCGAGCCTAACCCTACCGGCCCATATTAATTTTTTTAGATTATTT
130 CCAAATTAAAAATACTACACTCAAGCCTAA-CCTACCGGCCCATATTAAATTTTTTAGATTATTT
* *
17935 TTCATATAAAAATAAATT-TAAAATATAATACATCAAATTTGTAAAAGTTAAACCTGTG
194 TTCATATAAAAACAAATTAAAAAATATAATACATCAAATTTGTAAAAGTTAAACCTGTG
** *
17993 TATGACTATTTTAAAAGGTATTATCTAAATTTTATCATG-G-ATAGGATTGGGTCAATGCAAAAT
1 TATGACTATTTTAAAAGGTATTATCTAAACATGATCATGAGTA-AGG-TTGGGTCAATGCAAAAT
* * * * *
18056 ATTAGGCTTGTTTTTTAAGCTCAAGCCCGACCCGAAAAATGGCCTAAAGTTCTACCTAAGCTCGA
64 ATTAAGCTTGTTTTCTAACCTCAAGCCCGACCCGAAAAAGGGCCTAAAGTTCTACCCAAGCTCGA
* * ** * * * **
18121 CCCAAATTAAAAATGCTACACTCAAGCTTAATTTTCCTGTCTGTATTAAATTTTTTAGATTATTT
129 CCCAAATTAAAAATACTACACTCAAGCCTAACCTACCGGCCCATATTAAATTTTTTAGATTATTT
*
18186 TTTATATAAAAACAAATTAAAAAATATAATACATCAAAT
194 TTCATATAAAAACAAATTAAAAAATATAATACATCAAAT
18225 ACACTAAAAA
Statistics
Matches: 197, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
250 1 0.01
251 46 0.23
252 149 0.76
253 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (252 bp):
TATGACTATTTTAAAAGGTATTATCTAAACATGATCATGAGTAAGGTTGGGTCAATGCAAAATAT
TAAGCTTGTTTTCTAACCTCAAGCCCGACCCGAAAAAGGGCCTAAAGTTCTACCCAAGCTCGACC
CAAATTAAAAATACTACACTCAAGCCTAACCTACCGGCCCATATTAAATTTTTTAGATTATTTTT
CATATAAAAACAAATTAAAAAATATAATACATCAAATTTGTAAAAGTTAAACCTGTG
Found at i:20849 original size:16 final size:16
Alignment explanation
Indices: 20830--20860 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20820 GTAAAAAATA
20830 ATATAAAATTTATAAT
1 ATATAAAATTTATAAT
*
20846 ATATAACATTTATAA
1 ATATAAAATTTATAA
20861 AAATATTTTA
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:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAAAATTTATAAT
Found at i:23652 original size:41 final size:41
Alignment explanation
Indices: 23593--23805 Score: 160
Period size: 41 Copynumber: 5.1 Consensus size: 41
23583 TAGGGCGTTT
* * * *
23593 CTAAAGGTCAGAGCATTAGCTGCGTTTATGAGGAAACGCAG
1 CTAAAAGTCAGAGCATTAGCGGCGTTTATGAGAAAACACAG
23634 CTAAAAGTCAGA-CTATTAGCGGCGTTTATGAGAAAACACAG
1 CTAAAAGTCAGAGC-ATTAGCGGCGTTTATGAGAAAACACAG
* ** * * ** *
23675 CT-AAAGATCAGAGCATTAACGATGTTTACGAAAAAATGCCG
1 CTAAAAG-TCAGAGCATTAGCGGCGTTTATGAGAAAACACAG
* * * * *
23716 CTAAAATTTAGAGCATTAGCAGCGTTGTTTATGAGAAAACGCTG
1 CTAAAAGTCAGAGCATTAGC-G-G-CGTTTATGAGAAAACACAG
* * * * * *
23760 CTAGAAGGCAGAACATTAGTGGCGTTTATGAGAAAACGCCG
1 CTAAAAGTCAGAGCATTAGCGGCGTTTATGAGAAAACACAG
23801 CTAAA
1 CTAAA
23806 GAAAAAAACA
Statistics
Matches: 136, Mismatches: 29, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
40 5 0.04
41 95 0.70
42 6 0.04
43 1 0.01
44 29 0.21
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (41 bp):
CTAAAAGTCAGAGCATTAGCGGCGTTTATGAGAAAACACAG
Found at i:23818 original size:126 final size:127
Alignment explanation
Indices: 23616--23848 Score: 308
Period size: 126 Copynumber: 1.8 Consensus size: 127
23606 CATTAGCTGC
* *
23616 GTTTATGAGGAAACGCAGCTAAAAGTCAGACTATTAGCGGCGTTTATGAGAAAACACAGCTAAAG
1 GTTTATGAGAAAACGCAGCTAAAAGGCAGACTATTAGCGGCGTTTATGAGAAAACACAGCTAAAG
** * * * * *
23681 ATCAGAGCATTAACGATGTTTACG-AAAAAATGCCGCTAAAATTTAGAGCATTAGCAGCGTT
66 AAAAAAACATTAACGACGTTTACGTAAAAAAGGCCACTAAAATTTAGAGCATTAGCAGCGTT
* * * * *
23742 GTTTATGAGAAAACGCTGCTAGAAGGCAGAAC-ATTAGTGGCGTTTATGAGAAAACGCCGCTAAA
1 GTTTATGAGAAAACGCAGCTAAAAGGCAG-ACTATTAGCGGCGTTTATGAGAAAACACAGCTAAA
*
23806 GAAAAAAACATTAACGACGTTTACGTGAAAAAGGCCACTAAAA
65 GAAAAAAACATTAACGACGTTTACGTAAAAAAGGCCACTAAAA
23849 ATTAAGTAGT
Statistics
Matches: 90, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
126 74 0.82
127 16 0.18
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (127 bp):
GTTTATGAGAAAACGCAGCTAAAAGGCAGACTATTAGCGGCGTTTATGAGAAAACACAGCTAAAG
AAAAAAACATTAACGACGTTTACGTAAAAAAGGCCACTAAAATTTAGAGCATTAGCAGCGTT
Found at i:23827 original size:41 final size:41
Alignment explanation
Indices: 23742--23828 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
23732 TAGCAGCGTT
* ** * ** *
23742 GTTTATGAGAAAACGCTGCTAGAAGGCAGAACATTAGTGGC
1 GTTTATGAGAAAACGCCGCTAGAAGAAAAAACATTAACGAC
23783 GTTTATGAGAAAACGCCGCTA-AAGAAAAAAACATTAACGAC
1 GTTTATGAGAAAACGCCGCTAGAAG-AAAAAACATTAACGAC
23824 GTTTA
1 GTTTA
23829 CGTGAAAAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.08
41 35 0.92
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (41 bp):
GTTTATGAGAAAACGCCGCTAGAAGAAAAAACATTAACGAC
Found at i:24021 original size:36 final size:38
Alignment explanation
Indices: 23940--24010 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 38
23930 TAATATTAAT
*
23940 AATTATTTTACAACTTATATAAACTAAAAAAAATTCTA
1 AATTATTTTAAAACTTATATAAACTAAAAAAAATTCTA
* *
23978 AA--ATTTTAAAATTTATATAAACTAAAAATAATT
1 AATTATTTTAAAACTTATATAAACTAAAAAAAATT
24011 AAATTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 28 0.93
38 2 0.07
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (38 bp):
AATTATTTTAAAACTTATATAAACTAAAAAAAATTCTA
Found at i:27530 original size:46 final size:46
Alignment explanation
Indices: 27438--27585 Score: 171
Period size: 46 Copynumber: 3.2 Consensus size: 46
27428 CACTAGTGCG
* *
27438 CTCTCTGTTTAGCACGTCTTGTGCT-CTCTGTT-ATTAGCACTGTGTGTA
1 CTCTCTGTTTAGCAC-T-TTGTG-TGCTCT-TTGATTAGTACTTTGTGTA
* *
27486 CTCTCTGATTAGCACTTTGTGTGCTCTTTGATTAGTACTTTGTGTG
1 CTCTCTGTTTAGCACTTTGTGTGCTCTTTGATTAGTACTTTGTGTA
*
27532 CTCTCTGTTTAGCA-TTGTGTGTGCTCTCTG-TTAGTACTTTG-GTA
1 CTCTCTGTTTAGCACTT-TGTGTGCTCTTTGATTAGTACTTTGTGTA
27576 CTCTCTGTTT
1 CTCTCTGTTT
27586 GTTTCGTATA
Statistics
Matches: 90, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
44 12 0.13
45 16 0.18
46 47 0.52
47 1 0.01
48 14 0.16
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.47
Consensus pattern (46 bp):
CTCTCTGTTTAGCACTTTGTGTGCTCTTTGATTAGTACTTTGTGTA
Found at i:27584 original size:21 final size:23
Alignment explanation
Indices: 27437--27582 Score: 147
Period size: 23 Copynumber: 6.3 Consensus size: 23
27427 ACACTAGTGC
* *
27437 GCTCTCTGTTTAGCACGTCT-TGT
1 GCTCTCTGATTAGCAC-TTTGTGT
*
27460 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTTTGTGT
*
27485 ACTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* *
27508 GCTCTTTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
*
27531 GCTCTCTGTTTAGCA-TTGTGTGT
1 GCTCTCTGATTAGCACTT-TGTGT
*
27554 GCTCTCTG-TTAGTACTTTG-GT
1 GCTCTCTGATTAGCACTTTGTGT
*
27575 ACTCTCTG
1 GCTCTCTG
27583 TTTGTTTCGT
Statistics
Matches: 106, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.08
22 9 0.08
23 69 0.65
24 2 0.02
25 17 0.16
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.46
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTTGTGT
Found at i:34952 original size:21 final size:21
Alignment explanation
Indices: 34928--34974 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
34918 TGTCTACTGA
34928 TTTTTTTTATTTGA-AAATCTC
1 TTTTTTTTATTTGATAAA-CTC
* *
34949 TTTTTTTTTTTTTATAAACTC
1 TTTTTTTTATTTGATAAACTC
34970 TTTTT
1 TTTTT
34975 CTAATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTTTTTATTTGATAAACTC
Found at i:42001 original size:19 final size:21
Alignment explanation
Indices: 41977--42018 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
41967 AAAAGTTCTG
*
41977 AATTTAAT-ATTT-ATATTTT
1 AATTTAATCATTTCAAATTTT
41996 AATTTAATCATTTCAAATTTT
1 AATTTAATCATTTCAAATTTT
42017 AA
1 AA
42019 AAAATATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 4 0.20
21 8 0.40
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTTAATCATTTCAAATTTT
Found at i:47413 original size:18 final size:20
Alignment explanation
Indices: 47390--47427 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
47380 ACGTGGCAGT
47390 CCAAC-TAAATTTT-AAATG
1 CCAACTTAAATTTTCAAATG
*
47408 CCAACTTGAATTTTCAAATG
1 CCAACTTAAATTTTCAAATG
47428 AGATGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 7 0.41
20 5 0.29
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (20 bp):
CCAACTTAAATTTTCAAATG
Found at i:47455 original size:16 final size:17
Alignment explanation
Indices: 47434--47470 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
47424 AATGAGATGA
47434 AAATAAATTT-TTAATT
1 AAATAAATTTATTAATT
47450 AAATAAATTTAATTAATT
1 AAATAAATTT-ATTAATT
47468 AAA
1 AAA
47471 AATTTTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAAATTTATTAATT
Found at i:95904 original size:16 final size:17
Alignment explanation
Indices: 95864--95905 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
95854 TTTTTAAGAC
95864 AAAACTGTTAAAGCATG
1 AAAACTGTTAAAGCATG
95881 AGAAACTGTTATAA-CA-G
1 A-AAACTGTTA-AAGCATG
95898 AAAACTGT
1 AAAACTGT
95906 AAAATAGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 7 0.30
17 3 0.13
18 11 0.48
19 2 0.09
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.24
Consensus pattern (17 bp):
AAAACTGTTAAAGCATG
Found at i:98301 original size:14 final size:14
Alignment explanation
Indices: 98261--98302 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
98251 TGATGTTTTA
98261 AAAAAAAT-TAATTC
1 AAAAAAATATAA-TC
98275 AAAAAAATA-AATC
1 AAAAAAATATAATC
*
98288 AATAAAATATAATC
1 AAAAAAATATAATC
98302 A
1 A
98303 TTAACAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAAAAATATAATC
Found at i:100384 original size:29 final size:30
Alignment explanation
Indices: 100352--100409 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
100342 TATGGTTTAA
*
100352 TGTGCAATTATATATAT-AAACTTTGATTG
1 TGTGCAATTATATACATGAAACTTTGATTG
* *
100381 TGTGCAATTTTATACATGAAATTTTGATT
1 TGTGCAATTATATACATGAAACTTTGATT
100410 TGATCCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.47
Consensus pattern (30 bp):
TGTGCAATTATATACATGAAACTTTGATTG
Found at i:103394 original size:35 final size:37
Alignment explanation
Indices: 103355--103434 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 37
103345 TTTAAAATGT
103355 AAAATTAAATCA-T-TTTAAATAGAAATGTAGTGACA
1 AAAATTAAATCATTGTTTAAATAGAAATGTAGTGACA
*
103390 AAAATTAAATCATTTGTTTAAATAGAAGTGTAGTGACA
1 AAAATTAAATCA-TTGTTTAAATAGAAATGTAGTGACA
103428 AAAATTA
1 AAAATTA
103435 TTCTCTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 12 0.29
37 1 0.02
38 28 0.68
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (37 bp):
AAAATTAAATCATTGTTTAAATAGAAATGTAGTGACA
Found at i:103609 original size:21 final size:20
Alignment explanation
Indices: 103595--103637 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 20
103585 TTAATTTATA
103595 ATTCAATCAATTTAATCATTT
1 ATTCAATCAATTTAAT-ATTT
103616 ATTCAATCAATTTAAATATTT
1 ATTCAATCAATTT-AATATTT
103637 A
1 A
103638 ATTAATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTCAATCAATTTAATATTT
Found at i:105030 original size:23 final size:23
Alignment explanation
Indices: 104997--105120 Score: 115
Period size: 23 Copynumber: 5.3 Consensus size: 23
104987 GCTGGGTAAT
*
104997 AGAGAGCACACACGGTGCTAAAC
1 AGAGAGCACACACAGTGCTAAAC
* * * * *
105020 AGAGAGTACACAAAATACTAATC
1 AGAGAGCACACACAGTGCTAAAC
* *
105043 AGAGAGCACACAAAGTGCTAATC
1 AGAGAGCACACACAGTGCTAAAC
* *
105066 AGAGAACACACACAATGCTAATAAC
1 AGAGAGCACACACAGTGCT-A-AAC
*
105091 AGAGAGCACGAGAC-GTGCTAAAC
1 AGAGAGCAC-ACACAGTGCTAAAC
105114 AGAGAGC
1 AGAGAGC
105121 GCGCTAGTGT
Statistics
Matches: 82, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
23 63 0.77
24 2 0.02
25 14 0.17
26 3 0.04
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (23 bp):
AGAGAGCACACACAGTGCTAAAC
Found at i:105047 original size:46 final size:45
Alignment explanation
Indices: 104993--105120 Score: 141
Period size: 46 Copynumber: 2.8 Consensus size: 45
104983 AGGTGCTGGG
*
104993 TAAT-AGAGAGCACACACGGTGCTAAACAGAGAGTACACAAAATAC
1 TAATCAGAGAGCACACAC-GTGCTAAACAGAGAGCACACAAAATAC
* * * * *
105038 TAATCAGAGAGCACACAAAGTGCTAATCAGAGAACACACACAATGC
1 TAATCAGAGAGCACAC-ACGTGCTAAACAGAGAGCACACAAAATAC
*
105084 TAATAACAGAGAGCACGAGACGTGCTAAACAGAGAGC
1 TAAT--CAGAGAGCAC-ACACGTGCTAAACAGAGAGC
105121 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
45 4 0.06
46 37 0.54
47 1 0.01
48 25 0.37
49 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (45 bp):
TAATCAGAGAGCACACACGTGCTAAACAGAGAGCACACAAAATAC
Found at i:119931 original size:29 final size:28
Alignment explanation
Indices: 119860--119940 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 28
119850 TTTTTTAGAA
*
119860 GAATATGTTGGTTTTAAAAAATAATTAGG
1 GAATAAGTTGGTTTT-AAAAATAATTAGG
* *
119889 GATTTACA-TCGGTTTTAAAAATAATTAAGG
1 GA-ATA-AGTTGGTTTTAAAAATAATT-AGG
119919 GAATAAGTTGGTTTTAAAAATA
1 GAATAAGTTGGTTTTAAAAATA
119941 TTCGTGATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
28 1 0.02
29 28 0.65
30 14 0.33
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.37
Consensus pattern (28 bp):
GAATAAGTTGGTTTTAAAAATAATTAGG
Found at i:137047 original size:29 final size:27
Alignment explanation
Indices: 136986--137047 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
136976 ATTTTTTTAA
*
136986 AATTAAAAAATAAAAAAATTTAAAATT
1 AATTAAAAAATAAAAAAATTTAAAAAT
* * *
137013 ATTTAAGAAATATAAAAATTATGAAAAAT
1 AATTAAAAAATAAAAAAATT-T-AAAAAT
137042 AATTAA
1 AATTAA
137048 TTAATACGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 17 0.61
28 1 0.04
29 10 0.36
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (27 bp):
AATTAAAAAATAAAAAAATTTAAAAAT
Found at i:137398 original size:20 final size:20
Alignment explanation
Indices: 137354--137398 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
137344 ATCCTGAAAA
137354 ATTAAAATCTAAATAAAATT
1 ATTAAAATCTAAATAAAATT
* * *
137374 TTTAAAATTTAAATAACATT
1 ATTAAAATCTAAATAAAATT
137394 ATTAA
1 ATTAA
137399 CGTAATATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTAAAATCTAAATAAAATT
Found at i:147007 original size:2 final size:2
Alignment explanation
Indices: 147000--147037 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
146990 TTTATGTTGG
147000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
147038 TTGAAAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:150068 original size:269 final size:270
Alignment explanation
Indices: 149589--150133 Score: 957
Period size: 269 Copynumber: 2.0 Consensus size: 270
149579 CTGACTTGAG
149589 TTCTTTGTGATTCTCTTGTAACAGACAAATGGTGAAAAGCAGTGCAAGTTTCTTGTGGAATACAT
1 TTCTTTGTGATTCTCTTGTAACAGACAAATGGTGAAAAGCAGTGCAAGTTTCTTGTGGAATACAT
*
149654 TGAGAATGAGAAGCCAGGCAGCTTTCGCGATCTGAACATAGTATCTGATTTTGCTGGTATCCAAC
66 TGAGAATGAGAAGCCAGGCAGCTTTCGCGATATGAACATAGTATCTGATTTTGCTGGTATCCAAC
*
149719 GATTTGTGATGGGATTCCGTCAATGAATGGAATGATCAGTAAATACCTCGGTTTACATTGGTCAC
131 GATTTGTGATGGGATTCCGTCAATGAATGGAATGACCAGTAAATACCTCGGTTTACATTGGTCAC
* *
149784 TAAGAACAAAAAGCAAGGAAATGGTCACTGTTCCCAGCAGTTTAGTAGATTACTTTTGATAAAAT
196 GAAGAACAAAAAGCAAGGAAAAGGTCACTGTTCCCAGCAGTTTAGTAGATTACTTTTGATAAAAT
149849 GATTTATGA-
261 GATTTATGAT
149858 TTCTTTGTGATTCTCTTGTAACAGACAAATGGTGAAAAGCAGTGCAAGTTTCTTGTGGAATACAT
1 TTCTTTGTGATTCTCTTGTAACAGACAAATGGTGAAAAGCAGTGCAAGTTTCTTGTGGAATACAT
* *
149923 TGAGAATGAGAAGCCAGGCAGCTTTCGCGATATGAACTTAGTATCTGATTTTGCTTGTATCCAAC
66 TGAGAATGAGAAGCCAGGCAGCTTTCGCGATATGAACATAGTATCTGATTTTGCTGGTATCCAAC
* * * * * *
149988 GTTTTGTGATGGGATTTCGTCGATGAATGGAGTGACCGGTAGATACCTCGGTTTACATTGGTCAC
131 GATTTGTGATGGGATTCCGTCAATGAATGGAATGACCAGTAAATACCTCGGTTTACATTGGTCAC
*
150053 GAAGAACAAAAAGCAAGGAAAAGGTCACTGTTCCCAGCAGTTTAGTAGATTACTTTTGATAAATT
196 GAAGAACAAAAAGCAAGGAAAAGGTCACTGTTCCCAGCAGTTTAGTAGATTACTTTTGATAAAAT
*
150118 GTTTTATGAT
261 GATTTATGAT
150128 TTCTTT
1 TTCTTT
150134 TCCATTGATG
Statistics
Matches: 261, Mismatches: 14, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
269 255 0.98
270 6 0.02
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (270 bp):
TTCTTTGTGATTCTCTTGTAACAGACAAATGGTGAAAAGCAGTGCAAGTTTCTTGTGGAATACAT
TGAGAATGAGAAGCCAGGCAGCTTTCGCGATATGAACATAGTATCTGATTTTGCTGGTATCCAAC
GATTTGTGATGGGATTCCGTCAATGAATGGAATGACCAGTAAATACCTCGGTTTACATTGGTCAC
GAAGAACAAAAAGCAAGGAAAAGGTCACTGTTCCCAGCAGTTTAGTAGATTACTTTTGATAAAAT
GATTTATGAT
Found at i:169030 original size:7 final size:7
Alignment explanation
Indices: 169020--169053 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
169010 TTATGTATTA
169020 TTTAAAT
1 TTTAAAT
169027 TTTAAAT
1 TTTAAAT
169034 TTTAAAT
1 TTTAAAT
169041 TTT-AA-
1 TTTAAAT
169046 TTTAAAT
1 TTTAAAT
169053 T
1 T
169054 ATAATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 3 0.12
6 4 0.16
7 18 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTAAAT
Found at i:169039 original size:14 final size:12
Alignment explanation
Indices: 169019--169059 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
169009 TTTATGTATT
169019 ATTTAAATTTTAA
1 ATTTAAATTTT-A
169032 ATTTTAAATTTTA
1 A-TTTAAATTTTA
*
169045 ATTTAAATTATA
1 ATTTAAATTTTA
169057 ATT
1 ATT
169060 ATAATATTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 13 0.50
13 3 0.12
14 10 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTAAATTTTA
Found at i:171574 original size:13 final size:13
Alignment explanation
Indices: 171556--171581 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
171546 TTCATCTTAT
171556 ATAGAATAATGTA
1 ATAGAATAATGTA
171569 ATAGAATAATGTA
1 ATAGAATAATGTA
171582 TTCTTGATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
ATAGAATAATGTA
Found at i:173575 original size:6 final size:6
Alignment explanation
Indices: 173566--173594 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
173556 TTAACATGTG
173566 CATATA CATATA CATATA CATATA CATAT
1 CATATA CATATA CATATA CATATA CATAT
173595 TTAATGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.34
Consensus pattern (6 bp):
CATATA
Found at i:188112 original size:18 final size:17
Alignment explanation
Indices: 188088--188132 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
188078 CATTGTTTTT
188088 TAAAAGTATTTTTGAGA
1 TAAAAGTATTTTTGAGA
**
188105 TAAAAAGTGCTTTTGAGA
1 T-AAAAGTATTTTTGAGA
188123 TAAAAGTATT
1 TAAAAGTATT
188133 ATTAAATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (17 bp):
TAAAAGTATTTTTGAGA
Found at i:189716 original size:2 final size:2
Alignment explanation
Indices: 189709--189742 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
189699 CGTAATCTTT
189709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
189743 AGTAATAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:194382 original size:23 final size:23
Alignment explanation
Indices: 194356--194404 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
194346 CACTAGCGCT
194356 CTCTCTGATTAGCACTGTGTGTG
1 CTCTCTGATTAGCACTGTGTGTG
* *
194379 CTCTCTGTTTAGCACTTTGTGTG
1 CTCTCTGATTAGCACTGTGTGTG
194402 CTC
1 CTC
194405 AGTATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (23 bp):
CTCTCTGATTAGCACTGTGTGTG
Found at i:203351 original size:121 final size:120
Alignment explanation
Indices: 203210--203438 Score: 377
Period size: 121 Copynumber: 1.9 Consensus size: 120
203200 ATTTTAGCAT
* * * * * *
203210 AATACATATTAATCATCCTTGTATGTATAGCCAATTTTAGCATCATATTGAAAATTTTTATCTTT
1 AATACACATTAATCAACCTTGTATGCATAACCAACTTTAGCATCATATTGAAAATTTTCATCTTT
203275 TTCCGAAAAAACTATCTTCCATTTCATCATTTTGGACAAAATTTTAACACAAACTA
66 TTCCG-AAAAACTATCTTCCATTTCATCATTTTGGACAAAATTTTAACACAAACTA
203331 AATACACATTAATCAACCTTGTATGCATAACCAACTTTAGCATCATATTGAAAATTTTCATCTTT
1 AATACACATTAATCAACCTTGTATGCATAACCAACTTTAGCATCATATTGAAAATTTTCATCTTT
* *
203396 TTTCGAAAAATTATCTTCCATTTCATCATTTTGGACAAAATTT
66 TTCCGAAAAACTATCTTCCATTTCATCATTTTGGACAAAATTT
203439 GTCTCAACAT
Statistics
Matches: 100, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
120 37 0.37
121 63 0.63
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.40
Consensus pattern (120 bp):
AATACACATTAATCAACCTTGTATGCATAACCAACTTTAGCATCATATTGAAAATTTTCATCTTT
TTCCGAAAAACTATCTTCCATTTCATCATTTTGGACAAAATTTTAACACAAACTA
Found at i:219492 original size:19 final size:19
Alignment explanation
Indices: 219455--219493 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
219445 ACATAACTTT
219455 TAAAAGTAAAAATTAAAAA
1 TAAAAGTAAAAATTAAAAA
219474 TAAAA-TAAAATATTGAAAAA
1 TAAAAGTAAAA-ATT-AAAAA
219494 AATAATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
TAAAAGTAAAAATTAAAAA
Found at i:224959 original size:117 final size:117
Alignment explanation
Indices: 224753--224987 Score: 434
Period size: 117 Copynumber: 2.0 Consensus size: 117
224743 GGAGGCTGTA
* *
224753 TCCTGGGGATAGAGAATGGGTTGTTAGTGCTGGAATTAAGCTCAGGCATGCAAGATGCCACGTTG
1 TCCTGGGGATAGAGAATGGGTTGTTAGTGCTGGAATTAACCTCAGGCATGCAAGATGCCACGTCG
224818 TAAAGGTGGTTGTATGAACCAACTGGTCTAAACCCTGATTTTACATACACCC
66 TAAAGGTGGTTGTATGAACCAACTGGTCTAAACCCTGATTTTACATACACCC
* *
224870 TCCTGGGGATAGAGAATGTGTTGTTAGTGCTGGAATTAACCTCAGGCATGCAAGATGCCATGTCG
1 TCCTGGGGATAGAGAATGGGTTGTTAGTGCTGGAATTAACCTCAGGCATGCAAGATGCCACGTCG
224935 TAAAGGTGGTTGTATGAACCAACTGGTCTAAACCCTGATTTTACATACACCC
66 TAAAGGTGGTTGTATGAACCAACTGGTCTAAACCCTGATTTTACATACACCC
224987 T
1 T
224988 TACTTATGCC
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 114 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (117 bp):
TCCTGGGGATAGAGAATGGGTTGTTAGTGCTGGAATTAACCTCAGGCATGCAAGATGCCACGTCG
TAAAGGTGGTTGTATGAACCAACTGGTCTAAACCCTGATTTTACATACACCC
Found at i:228102 original size:37 final size:37
Alignment explanation
Indices: 228052--228125 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
228042 CGGCCTCCTC
228052 TTTAATTTCTTTCATGTTATGAACTGTTCGTTTTTTT
1 TTTAATTTCTTTCATGTTATGAACTGTTCGTTTTTTT
228089 TTTAATTTCTTTCATGTTATGAACTGTTCGTTTTTTT
1 TTTAATTTCTTTCATGTTATGAACTGTTCGTTTTTTT
228126 CTGGTGATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.62
Consensus pattern (37 bp):
TTTAATTTCTTTCATGTTATGAACTGTTCGTTTTTTT
Found at i:238269 original size:12 final size:11
Alignment explanation
Indices: 238251--238280 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
238241 ATGTATACTC
238251 ATTTTTTTAAA
1 ATTTTTTTAAA
238262 ATTTTTTTAAA
1 ATTTTTTTAAA
238273 ATTTTTTT
1 ATTTTTTT
238281 GAAGTATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTTTTTTAAA
Found at i:247970 original size:16 final size:17
Alignment explanation
Indices: 247951--247990 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
247941 TTTATTAATT
247951 TAAAATTTTAAA-AAAA
1 TAAAATTTTAAATAAAA
247967 TAAAGA-TTTAAATAAAA
1 TAAA-ATTTTAAATAAAA
247984 -AAAATTT
1 TAAAATTT
247991 CCATTTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 1 0.05
16 15 0.71
17 5 0.24
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAATTTTAAATAAAA
Found at i:260157 original size:2 final size:2
Alignment explanation
Indices: 260150--260176 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
260140 AATTTTAAAG
260150 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
260177 AAAAAGAAAA
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:262759 original size:18 final size:18
Alignment explanation
Indices: 262736--262773 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
262726 ATTTTGGATC
262736 TTCCTGTCTGTGTAGCAT
1 TTCCTGTCTGTGTAGCAT
262754 TTCCTGTCTGTGTAGCAT
1 TTCCTGTCTGTGTAGCAT
262772 TT
1 TT
262774 AATTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (18 bp):
TTCCTGTCTGTGTAGCAT
Found at i:267024 original size:8 final size:7
Alignment explanation
Indices: 267007--267038 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
266997 AAAACAACTC
267007 AAAATGAA
1 AAAAT-AA
267015 AAAATAA
1 AAAATAA
267022 AAAATAA
1 AAAATAA
267029 AAAATAA
1 AAAATAA
267036 AAA
1 AAA
267039 GAGAGTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:268573 original size:20 final size:20
Alignment explanation
Indices: 268550--268588 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
268540 CATATTTATT
268550 TTTTAAATATTAAA-ATAAAC
1 TTTTAAATA-TAAAGATAAAC
*
268570 TTTTATATATAAAGATAAA
1 TTTTAAATATAAAGATAAA
268589 GTGATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
TTTTAAATATAAAGATAAAC
Found at i:278683 original size:21 final size:21
Alignment explanation
Indices: 278657--278699 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
278647 TCCTCGCTAG
278657 AGTCGCATGATCATTAACTAA
1 AGTCGCATGATCATTAACTAA
278678 AGTCGCATGATCATTAACTAA
1 AGTCGCATGATCATTAACTAA
278699 A
1 A
278700 AAGTGGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (21 bp):
AGTCGCATGATCATTAACTAA
Found at i:284269 original size:4 final size:4
Alignment explanation
Indices: 284260--284289 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
284250 ATTGAATTGT
284260 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
284290 CCTCTTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:293697 original size:2 final size:2
Alignment explanation
Indices: 293684--293715 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
293674 CAAAATAGTA
*
293684 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
293716 TGCTTACATT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:296769 original size:30 final size:30
Alignment explanation
Indices: 296729--296786 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
296719 GATCCCAATG
296729 ACAAAACAGTCACT-TAACTTTCAAAAAATA
1 ACAAAACAGTC-CTATAACTTTCAAAAAATA
*
296759 ACAAATCAGTCCTACTAACTTTCAAAAA
1 ACAAAACAGTCCTA-TAACTTTCAAAAA
296787 GTCATACACC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 2 0.08
30 10 0.40
31 13 0.52
ACGTcount: A:0.50, C:0.22, G:0.03, T:0.24
Consensus pattern (30 bp):
ACAAAACAGTCCTATAACTTTCAAAAAATA
Found at i:298586 original size:16 final size:17
Alignment explanation
Indices: 298550--298587 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
298540 ATAAATTTAA
298550 ATTTTTTAATTGAACAT
1 ATTTTTTAATTGAACAT
*
298567 -TTTTTTATTTGAA-AT
1 ATTTTTTAATTGAACAT
298582 ATTTTT
1 ATTTTT
298588 CAAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (17 bp):
ATTTTTTAATTGAACAT
Found at i:300471 original size:14 final size:14
Alignment explanation
Indices: 300448--300481 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
300438 TGATAAATTA
*
300448 AAATTT-AATTGTT
1 AAATTTAAATTATT
300461 AAATTTAAATTATT
1 AAATTTAAATTATT
300475 AAATTTA
1 AAATTTA
300482 TTTGATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
AAATTTAAATTATT
Found at i:303176 original size:19 final size:20
Alignment explanation
Indices: 303148--303198 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
303138 TGATTACGTT
303148 TATT-TTTTTTAAATTAAGA
1 TATTATTTTTTAAATTAAGA
* *
303167 T-TTATTTTTTAATTTAATA
1 TATTATTTTTTAAATTAAGA
303186 TATTATTTATTTA
1 TATTATTT-TTTA
303199 TTTTATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 2 0.07
19 15 0.56
20 6 0.22
21 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TATTATTTTTTAAATTAAGA
Found at i:303205 original size:16 final size:16
Alignment explanation
Indices: 303167--303215 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
303157 TAAATTAAGA
* *
303167 TTTATTTTTTAATTTAA
1 TTTATTATTT-ATTTAT
*
303184 TATATTATTTATTTAT
1 TTTATTATTTATTTAT
*
303200 TTTATTATTTTTTTAT
1 TTTATTATTTATTTAT
303216 ATGTAATTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 19 0.70
17 8 0.30
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATTATTTATTTAT
Found at i:313623 original size:18 final size:18
Alignment explanation
Indices: 313600--313636 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
313590 TTACCAGGGT
313600 ACAATGGGTGCCAGTTTA
1 ACAATGGGTGCCAGTTTA
313618 ACAATGGGTGCCAGTTTA
1 ACAATGGGTGCCAGTTTA
313636 A
1 A
313637 AAGTTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (18 bp):
ACAATGGGTGCCAGTTTA
Found at i:318002 original size:12 final size:11
Alignment explanation
Indices: 317981--318013 Score: 57
Period size: 12 Copynumber: 2.9 Consensus size: 11
317971 ATTGTATAAA
317981 TATTATTTTAT
1 TATTATTTTAT
317992 TATTAATTTTAT
1 TATT-ATTTTAT
318004 TATTATTTTA
1 TATTATTTTA
318014 AATGTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:318993 original size:51 final size:53
Alignment explanation
Indices: 318844--319182 Score: 174
Period size: 56 Copynumber: 6.2 Consensus size: 53
318834 GATTTTGTAA
* * * *
318844 AAAAAAAGTTGGTGTTGGCCAATGCA-TGATCGACACCACCTTTTTTGTCA-GAC
1 AAAAAAATTTGGTGTTGGTC-ATGCATTGACCGACACCACCTTTTTTAT-ATGAC
* * * * *
318897 AAAAAAATTTTGTGTTAGTCATGCATT-AGCCGAGACCA-GTATTTTT-TATCA-
1 AAAAAAATTTGGTGTTGGTCATGCATTGA-CCGACACCACCT-TTTTTATATGAC
* * *
318948 AAAAAAATTTGGTGTTGGTCATGCATTGACCAACACCATCTTTTTTATATGAT
1 AAAAAAATTTGGTGTTGGTCATGCATTGACCGACACCACCTTTTTTATATGAC
** * *
319001 AAAAAATATTTTTTTTTGTTGGTCATGTATTGACCGACACCACC-TTTTTATCA-GAT
1 AAAAAA-A---TTTGGTGTTGGTCATGCATTGACCGACACCACCTTTTTTAT-ATGAC
* * * * * *
319057 AAAAATATATTTTTGGTGTAGGCCAT-TACTTGGCCGACACCACCTTTATTATCTGAC
1 AAAAA-A-A--TTTGGTGTTGGTCATGCA-TTGACCGACACCACCTTTTTTATATGAC
** * * *
319114 AAAAAATTCAAATTTTTTGGTGTTGGTCATGCATTGGTCGACACCACATTCTTTATCTGAC
1 --AAAA---AAA---TTTGGTGTTGGTCATGCATTGACCGACACCACCTTTTTTATATGAC
319175 AAAAAAAT
1 AAAAAAAT
319183 CAATTTTTTT
Statistics
Matches: 228, Mismatches: 34, Indels: 48
0.74 0.11 0.15
Matches are distributed among these distances:
51 38 0.17
52 15 0.07
53 36 0.16
54 1 0.00
55 2 0.01
56 45 0.20
57 40 0.18
59 8 0.04
60 1 0.00
61 40 0.18
62 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (53 bp):
AAAAAAATTTGGTGTTGGTCATGCATTGACCGACACCACCTTTTTTATATGAC
Found at i:319033 original size:57 final size:57
Alignment explanation
Indices: 318960--319070 Score: 163
Period size: 57 Copynumber: 1.9 Consensus size: 57
318950 AAAAATTTGG
*
318960 TGTTGGTCATGCATTGACCAACACCATCTTTTTTAT-ATGATAAAAA-ATATTTTTTTT
1 TGTTGGTCATGCATTGACCAACACCA-CCTTTTTATCA-GATAAAAATATATTTTTTTT
* *
319017 TGTTGGTCATGTATTGACCGACACCACCTTTTTATCAGATAAAAATATATTTTT
1 TGTTGGTCATGCATTGACCAACACCACCTTTTTATCAGATAAAAATATATTTTT
319071 GGTGTAGGCC
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
56 16 0.33
57 33 0.67
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (57 bp):
TGTTGGTCATGCATTGACCAACACCACCTTTTTATCAGATAAAAATATATTTTTTTT
Found at i:319473 original size:118 final size:118
Alignment explanation
Indices: 319266--319611 Score: 516
Period size: 118 Copynumber: 2.9 Consensus size: 118
319256 TATGTTGACT
* * * * *
319266 ATTTTTTAGCCAACATCACCTTTTTTGTCTGATAAAAAATT-TAAATTTTTTAGTGTTGACCATG
1 ATTTTTTGGCCGACATCACCTTTTTTATCTGATAAAAAATTCAAAATTTTTTGGTGTTGACCATG
** * *
319330 CATTGATTGACACCAATATTTTTTTATCAGATAAAAAAAATTTGGTGTCGGTC
66 CATTGGCTGACACCAATATTTTTTTATCAAATAAAAAAAAATTGGTGTCGGTC
319383 ATTTTTTGGCCGACATCACCTTTTTTATCTGATAAAAAATTCAAAATTTTTTGGTGTTGACCATG
1 ATTTTTTGGCCGACATCACCTTTTTTATCTGATAAAAAATTCAAAATTTTTTGGTGTTGACCATG
* *
319448 CATTGGCCGACACCAACATTTTTTTATCAAATAAAAAAAAATTGGTGTCGGTC
66 CATTGGCTGACACCAATATTTTTTTATCAAATAAAAAAAAATTGGTGTCGGTC
** * * *
319501 A-TTGCTGGACCGACACCACCTTTTTTATCTGATAAAAAATTCAAATTTTTTTGGTGTTGGCCAT
1 ATTTTTTGG-CCGACATCACCTTTTTTATCTGATAAAAAATTCAAAATTTTTTGGTGTTGACCAT
319565 GCATTGGCTGACACCAATATTTTTTTATCAAATAAAAAAAAAATTGG
65 GCATTGGCTGACACCAATATTTTTTTATCAAAT-AAAAAAAAATTGG
319612 ATAAAAAAAT
Statistics
Matches: 208, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
117 43 0.21
118 152 0.73
119 13 0.06
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (118 bp):
ATTTTTTGGCCGACATCACCTTTTTTATCTGATAAAAAATTCAAAATTTTTTGGTGTTGACCATG
CATTGGCTGACACCAATATTTTTTTATCAAATAAAAAAAAATTGGTGTCGGTC
Found at i:319578 original size:62 final size:62
Alignment explanation
Indices: 319066--319808 Score: 332
Period size: 62 Copynumber: 12.1 Consensus size: 62
319056 TAAAAATATA
* * * *
319066 TTTTTGGTGTAGGCCAT-TACTTGGCCGACACCACCTTTATTATCTGACAAAAAATTCAAA-T
1 TTTTTGGTGTTGGCCATGCA-TTGGCCGACACCACCTTTTTTATCTGATAAAAAATTCAAATT
* * * * * * *
319127 TTTTTGGTGTTGGTCATGCATTGGTCGACACCACATTCTTTATCTGACAAAAAAATCAATTT
1 TTTTTGGTGTTGGCCATGCATTGGCCGACACCACCTTTTTTATCTGATAAAAAATTCAAATT
* * * * *
319189 TTTTTTGTGTTAGCCAT-TATTTGGCCGACACCACCTTTATTATCT-A-ACAAAAATATCAATTT
1 TTTTTGGTGTTGGCCATGCA-TTGGCCGACACCACCTTTTTTATCTGATA-AAAAAT-TCAAATT
** * * *** * * * * *
319251 TTTTTTATGTTGACTATTTTTTAGCCAACATCACCTTTTTTGTCTGATAAAAAATTTAAA-T
1 TTTTTGGTGTTGGCCATGCATTGGCCGACACCACCTTTTTTATCTGATAAAAAATTCAAATT
* * *** ** *
319312 TTTTTAGTGTTGACCATGCATTGATTGACACCAATATTTTTTTATCAGAT-AAAAA---AAA--
1 TTTTTGGTGTTGGCCATGCATTGGCCGACACC-A-CCTTTTTTATCTGATAAAAAATTCAAATT
* * *** * *
319370 --TTTGGTGTCGGTCATTTTTTGGCCGACATCACCTTTTTTATCTGATAAAAAATTCAAAAT
1 TTTTTGGTGTTGGCCATGCATTGGCCGACACCACCTTTTTTATCTGATAAAAAATTCAAATT
* * **
319430 TTTTTGGTGTTGACCATGCATTGGCCGACACCAACATTTTTTTATCAAATAAAAAA---AAA--
1 TTTTTGGTGTTGGCCATGCATTGGCCGACACC-AC-CTTTTTTATCTGATAAAAAATTCAAATT
* *
319489 ---TTGGTGTCGGTCATTGC--TGGACCGACACCACCTTTTTTATCTGATAAAAAATTCAAATT
1 TTTTTGGTGTTGGCCA-TGCATTGG-CCGACACCACCTTTTTTATCTGATAAAAAATTCAAATT
* ** * *
319548 TTTTTGGTGTTGGCCATGCATTGGCTGACACCAATATTTTTTTATCAAATAAAAAAAAAATTGGA
1 TTTTTGGTGTTGGCCATGCATTGGCCGACACC-A-CCTTTTTTATC---T-GATAAAAAA-T---
* **
319613 TAAAAAA
56 TCAAATT
* * * * * * *
319620 ATATTGGTGTTGGTCATTGC-TTGACCGACACCACTTTTTTTATTTGATAAAAAATTTAAATT
1 TTTTTGGTGTTGGCCA-TGCATTGGCCGACACCACCTTTTTTATCTGATAAAAAATTCAAATT
* * * * * **
319682 TTTTT-ATGTTGGCCATGCATTGGCTAGTACTAGCA-TTTTTTTATCAGAT-----ATT--TTTT
1 TTTTTGGTGTTGGCCATGCATTGGC-CG-AC-ACCACCTTTTTTATCTGATAAAAAATTCAAATT
* * * *
319738 TTTTTTGTGTTGGCTATTGC-TTGGTCGACACCACCTTTTTTATTTGATAAAAAATTCAAAATT
1 TTTTTGGTGTTGGCCA-TGCATTGGCCGACACCACCTTTTTTATCTGATAAAAAATTC-AAATT
319801 TTTTTGGT
1 TTTTTGGT
319809 ACCTTTTTAT
Statistics
Matches: 504, Mismatches: 120, Indels: 114
0.68 0.16 0.15
Matches are distributed among these distances:
54 32 0.06
55 24 0.05
56 45 0.09
57 18 0.04
58 9 0.02
59 3 0.01
60 7 0.01
61 95 0.19
62 135 0.27
63 48 0.10
64 30 0.06
65 1 0.00
66 7 0.01
67 2 0.00
68 7 0.01
69 1 0.00
70 9 0.02
71 1 0.00
72 27 0.05
73 3 0.01
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.41
Consensus pattern (62 bp):
TTTTTGGTGTTGGCCATGCATTGGCCGACACCACCTTTTTTATCTGATAAAAAATTCAAATT
Found at i:322825 original size:22 final size:23
Alignment explanation
Indices: 322771--322826 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
322761 ATAGCATTGA
322771 ACCATCCAAATTCCAGCTCACCT
1 ACCATCCAAATTCCAGCTCACCT
* *
322794 A-AATCAAAATTCCAGCTCACC-
1 ACCATCCAAATTCCAGCTCACCT
*
322815 ACCACCCAAATT
1 ACCATCCAAATT
322827 TCGTCGTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.38, C:0.39, G:0.04, T:0.20
Consensus pattern (23 bp):
ACCATCCAAATTCCAGCTCACCT
Found at i:323956 original size:52 final size:50
Alignment explanation
Indices: 323841--323984 Score: 130
Period size: 50 Copynumber: 2.8 Consensus size: 50
323831 TGTAAGATAT
* * * * * *
323841 ATTTTCAAATTTTTATAATTTTTTTTTTCTA-TTTCTGAAATATTTTTTAA
1 ATTTTCGAATTTTTAAAAATTATTTTTTATATTTTC-GAAATATTTATTAA
*
323891 ATTTTCGAATTTTTAAAAATAATATTTTTTATATTTTCGAAATATTTATTAG
1 ATTTTCGAATTTTTAAAAAT--TATTTTTTATATTTTCGAAATATTTATTAA
* ** * *
323943 CTTTTC-AATTTTTTTTAAATTATTTTTTATATCTTCAAAATA
1 ATTTTCGAA-TTTTTAAAAATTATTTTTTATATTTTCGAAATA
323985 AAAATTTTTA
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
50 37 0.47
51 2 0.03
52 35 0.45
53 4 0.05
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (50 bp):
ATTTTCGAATTTTTAAAAATTATTTTTTATATTTTCGAAATATTTATTAA
Found at i:325038 original size:30 final size:31
Alignment explanation
Indices: 325004--325125 Score: 189
Period size: 30 Copynumber: 4.1 Consensus size: 31
324994 ATTTTGATTT
*
325004 TTTCGTTTAT-TTTTAAATTTTAATTTGTAA
1 TTTCGTTTATATTTTAAATTTTAATTTCTAA
325034 TTTCGTTTATATTTTAAA-TTTAATTTCTAA
1 TTTCGTTTATATTTTAAATTTTAATTTCTAA
*
325064 TTTCGTGTATATTTT-AATTTTAATTTCTAA
1 TTTCGTTTATATTTTAAATTTTAATTTCTAA
*
325094 TTTCGTTTATATTTTAAA-TTTCATTTCTAA
1 TTTCGTTTATATTTTAAATTTTAATTTCTAA
325124 TT
1 TT
325126 ATTATTTTTT
Statistics
Matches: 85, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
29 2 0.02
30 74 0.87
31 9 0.11
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.61
Consensus pattern (31 bp):
TTTCGTTTATATTTTAAATTTTAATTTCTAA
Found at i:326236 original size:62 final size:60
Alignment explanation
Indices: 325970--326590 Score: 442
Period size: 62 Copynumber: 10.4 Consensus size: 60
325960 GAAAGTTAGC
* * * * *
325970 GTCGGTCAATGCATGACCAACACCAAAAATATTTATTTTTTTATCTGATAAAAAA-GTGGT
1 GTCGGCCAATGCATGGCCAACACCAAAAA-AATTAATTTTTTATCAGATAAAAAAGGTGGT
** *
326030 GTCGGCCAATGCATGTTCAATACCAAAAAAATTAAATTTTTTATCAGATAAAAAAGGTGGT
1 GTCGGCCAATGCATGGCCAACACCAAAAAAATT-AATTTTTTATCAGATAAAAAAGGTGGT
* * * * ** * *
326091 GTTGGCCAA-GTAATGACCAACA-C----TAATTTTTTTTTTATCTGATAAAAAAGTATTGGT
1 GTCGGCCAATG-CATGGCCAACACCAAAAAAATTAATTTTTTATCAGATAAAAAAG--GTGGT
* * *
326148 GTCAGCTAATGCATGGCCAACGCCAAAAAAATTTGAATTTTTTATCAGATAAAAAAGGTGGT
1 GTCGGCCAATGCATGGCCAACACCAAAAAAA-TT-AATTTTTTATCAGATAAAAAAGGTGGT
* * *
326210 GTCGGCCGA-GCAATGGCCTACACC----AAA-T--TTTTTTATCTA-ATAAAAAATGTTGGT
1 GTCGGCCAATGC-ATGGCCAACACCAAAAAAATTAATTTTTTATC-AGATAAAAAA-GGTGGT
* * * *
326264 GTCGGCCAATGCATGGTCAACACAAAAAAAATTTGAATTTTTTATCAGACAAAAAAGGTGAT
1 GTCGGCCAATGCATGGCCAACACCAAAAAAA-TT-AATTTTTTATCAGATAAAAAAGGTGGT
* * * ** * * * * *
326326 ATCAGCCAA-ACAATGGTGAACACAAAAAAAATTTGAACTTTTTGTCAGATAATAAAGATGGT
1 GTCGGCCAATGC-ATGGCCAACACCAAAAAAA-TT-AATTTTTTATCAGATAAAAAAGGTGGT
* * ** * * *
326388 GTCGACTAATGCATGGCCAACATAAAAAAAAATAAATTTTTTGTCAGATAATAAAGGTGGT
1 GTCGGCCAATGCATGGCCAACA-CCAAAAAAATTAATTTTTTATCAGATAAAAAAGGTGGT
* * * **
326449 GTCGGTCAA-GAAATGACCAACACCAAAAAAA-T-ATTTTTTATTTGATAAAAAA-GTGGT
1 GTCGGCCAATG-CATGGCCAACACCAAAAAAATTAATTTTTTATCAGATAAAAAAGGTGGT
* * *
326506 GTCGGCCAATGCATGGCCAACA-CAAAAAAAAT-ATTTTTTATGAGATAAAAAAGATGGT
1 GTCGGCCAATGCATGGCCAACACCAAAAAAATTAATTTTTTATCAGATAAAAAAGGTGGT
* **
326564 GTCGACCAATGCATAACCAACACCAAA
1 GTCGGCCAATGCATGGCCAACACCAAA
326591 TTTTTTTTGA
Statistics
Matches: 443, Mismatches: 83, Indels: 71
0.74 0.14 0.12
Matches are distributed among these distances:
53 17 0.04
54 23 0.05
55 21 0.05
56 13 0.03
57 59 0.13
58 48 0.11
59 7 0.02
60 55 0.12
61 63 0.14
62 91 0.21
63 27 0.06
64 19 0.04
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (60 bp):
GTCGGCCAATGCATGGCCAACACCAAAAAAATTAATTTTTTATCAGATAAAAAAGGTGGT
Found at i:326676 original size:109 final size:107
Alignment explanation
Indices: 326483--326707 Score: 251
Period size: 109 Copynumber: 2.1 Consensus size: 107
326473 AAAAAAATAT
** *
326483 TTTTTATTTGATAAAAAAGTGGTGTCGGCCAATGCATGGCCAACACAAAAAAAATATTTTTTATG
1 TTTTT-TTTGATAAAAAAGTGGTGTCAACCAATGCATGGCCAACACAAAAAAAAAATTTTTTATG
* *
326548 AGATAAAAAAGATGGTGTCGACCAATGCA-TAACCAACACCAAA
65 ACATAAAAAAGATGATGTCGACC-ATGCATTAACCAACACCAAA
* *
326591 TTTTTTTTGATAAAAAATATTGGTGTCAACCACTGCATGGCCAACACTTAAAAAAAAAATTTTGT
1 TTTTTTTTGAT-AAAAA-AGTGGTGTCAACCAATGCATGGCCAACAC--AAAAAAAAAATTTT-T
** ** *
326656 T-TGACA-AAAAAAG-TGATGTCGGTCATGCATTGGCCAACACCAAT
61 TATGACATAAAAAAGATGATGTCGACCATGCATTAACCAACACCAAA
326700 TTTTTTTT
1 TTTTTTTT
326708 TCTCAAAATA
Statistics
Matches: 99, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
107 6 0.06
108 15 0.15
109 52 0.53
110 7 0.07
111 17 0.17
112 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (107 bp):
TTTTTTTTGATAAAAAAGTGGTGTCAACCAATGCATGGCCAACACAAAAAAAAAATTTTTTATGA
CATAAAAAAGATGATGTCGACCATGCATTAACCAACACCAAA
Found at i:329025 original size:21 final size:21
Alignment explanation
Indices: 329001--329042 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
328991 TTAGTAATGC
* *
329001 TTTTATCT-CAAAAATATTTT
1 TTTTTTCTCCAAAAATACTTT
*
329021 TTTTTTGTCCAAAAATACTTT
1 TTTTTTCTCCAAAAATACTTT
329042 T
1 T
329043 GAGAAACAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.31, C:0.12, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTTTTCTCCAAAAATACTTT
Found at i:338054 original size:13 final size:13
Alignment explanation
Indices: 338036--338061 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
338026 AAGACATGGA
338036 GATAGAAAAACAT
1 GATAGAAAAACAT
338049 GATAGAAAAACAT
1 GATAGAAAAACAT
338062 AACAAGTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (13 bp):
GATAGAAAAACAT
Found at i:339107 original size:134 final size:134
Alignment explanation
Indices: 338867--339138 Score: 526
Period size: 134 Copynumber: 2.0 Consensus size: 134
338857 GAAGGCATAC
*
338867 CTCTGTTCTTTGTTTCCTTTCATGATTAACAAAAGCAAGGGTTGTATCAAAATCTTGCTGAAGAA
1 CTCTGTTCTTTGTTTCCTTTCATGATTAACAAAAGCAAGGGTTGTACCAAAATCTTGCTGAAGAA
338932 ATCTCCTACAAAAATATACACATTTTAAGCACAAGGAAAAGAACTCGTACTAAAATTATTGAGTT
66 ATCTCCTACAAAAATATACACATTTTAAGCACAAGGAAAAGAACTCGTACTAAAATTATTGAGTT
338997 TCAA
131 TCAA
339001 CTCTGTTCTTTGTTTCCTTTCATGATTAACAAAAGCAAGGGTTGTACCAAAATCTTGCTGAAGAA
1 CTCTGTTCTTTGTTTCCTTTCATGATTAACAAAAGCAAGGGTTGTACCAAAATCTTGCTGAAGAA
*
339066 ATCTCCTACAGAAATATACACATTTTAAGCACAAGGAAAAGAACTCGTACTAAAATTATTGAGTT
66 ATCTCCTACAAAAATATACACATTTTAAGCACAAGGAAAAGAACTCGTACTAAAATTATTGAGTT
339131 TCAA
131 TCAA
339135 CTCT
1 CTCT
339139 TCAGCAGACA
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 136 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (134 bp):
CTCTGTTCTTTGTTTCCTTTCATGATTAACAAAAGCAAGGGTTGTACCAAAATCTTGCTGAAGAA
ATCTCCTACAAAAATATACACATTTTAAGCACAAGGAAAAGAACTCGTACTAAAATTATTGAGTT
TCAA
Found at i:343347 original size:117 final size:117
Alignment explanation
Indices: 343141--343371 Score: 408
Period size: 117 Copynumber: 2.0 Consensus size: 117
343131 AGATATTTCT
*
343141 TTTTCAATTTATCCTCTTTGAAATTATCATCAAATGATAGAGCCATCTAAAAACTACACAATCCA
1 TTTTCAATTTATCCTCTTTGAAATTATCATCAAATGATAAAGCCATCTAAAAACTACACAATCCA
* * *
343206 GCTGAAATCATTCAAATTCTATGAATAGTAAGCCCTTCCATATCGTCATGGA
66 GATGAAATCACTCAAATTCTATGAATAGTAAGCCCTTCCACATCGTCATGGA
*
343258 TTTTCAATTTATCCTCTTTGAAATTATCATCAAATGATAAAGCCATCTAAAAACTACACACTCCA
1 TTTTCAATTTATCCTCTTTGAAATTATCATCAAATGATAAAGCCATCTAAAAACTACACAATCCA
*
343323 GATGAAATCACTCAAATTCTATGAATAGTAAGCCCTTCCACATCTTCAT
66 GATGAAATCACTCAAATTCTATGAATAGTAAGCCCTTCCACATCGTCAT
343372 AGATAATCAC
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
117 108 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (117 bp):
TTTTCAATTTATCCTCTTTGAAATTATCATCAAATGATAAAGCCATCTAAAAACTACACAATCCA
GATGAAATCACTCAAATTCTATGAATAGTAAGCCCTTCCACATCGTCATGGA
Found at i:345736 original size:41 final size:41
Alignment explanation
Indices: 345679--345759 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
345669 AATCAAAAAA
*
345679 CTATGGGGACAGAACTTTTTGCTTTTGACAGTTAACTAATG
1 CTATGGGGACAGAACTTTATGCTTTTGACAGTTAACTAATG
345720 CTATGGGGACAGAACTTTATGCTTTTGACAGTTAACTAAT
1 CTATGGGGACAGAACTTTATGCTTTTGACAGTTAACTAAT
345760 ACTTAACATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (41 bp):
CTATGGGGACAGAACTTTATGCTTTTGACAGTTAACTAATG
Found at i:345742 original size:21 final size:21
Alignment explanation
Indices: 345679--345742 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
345669 AATCAAAAAA
*
345679 CTATGGGGACAGAACTTTTTG
1 CTATGGGGACAGAACTTTATG
** *
345700 CT-T-TTGACAGTTAAC-TAATG
1 CTATGGGGACAG--AACTTTATG
345720 CTATGGGGACAGAACTTTATG
1 CTATGGGGACAGAACTTTATG
345741 CT
1 CT
345743 TTTGACAGTT
Statistics
Matches: 31, Mismatches: 7, Indels: 10
0.65 0.15 0.21
Matches are distributed among these distances:
19 5 0.16
20 9 0.29
21 12 0.39
22 5 0.16
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (21 bp):
CTATGGGGACAGAACTTTATG
Found at i:345756 original size:21 final size:21
Alignment explanation
Indices: 345691--345756 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
345681 ATGGGGACAG
*
345691 AACTTTTTGCTTTTGACAGTT
1 AACTTTATGCTTTTGACAGTT
* **
345712 AAC-TAATGCTATGGGGACAG--
1 AACTTTATGCT-T-TTGACAGTT
345732 AACTTTATGCTTTTGACAGTT
1 AACTTTATGCTTTTGACAGTT
345753 AACT
1 AACT
345757 AATACTTAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
19 5 0.15
20 9 0.27
21 14 0.42
22 5 0.15
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.39
Consensus pattern (21 bp):
AACTTTATGCTTTTGACAGTT
Found at i:351145 original size:21 final size:23
Alignment explanation
Indices: 351111--351156 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
351101 AAATAATACC
*
351111 TTTCTTCTCTATTTT-TTAAATT
1 TTTCTTCTCAATTTTCTTAAATT
351133 TTTC-TCTCAATTTTCTTAAATT
1 TTTCTTCTCAATTTTCTTAAATT
351155 TT
1 TT
351157 AATAGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTCTTCTCAATTTTCTTAAATT
Found at i:358568 original size:44 final size:44
Alignment explanation
Indices: 358520--358698 Score: 108
Period size: 44 Copynumber: 4.2 Consensus size: 44
358510 AATAATATCC
* *
358520 AAACAACA-AAAATAACAACCAAAACAGA-AGCAAAAATAACAGCA
1 AAACAACATAAAA-AACAACAAAAACA-ACAACAAAAATAACAGCA
* * *
358564 AAACAATATTAAAAACAACAAAAATAACAACAAAAATAACAGCAA
1 AAACAACATAAAAAACAACAAAAACAACAACAAAAATAACAGC-A
* * * * *
358609 AAACAATAT-TAAAACAACAATCAA-AACAATAAAAA-AAGCACCA
1 AAACAACATAAAAAACAACAA-AAACAACAACAAAAATAA-CAGCA
* ** * *
358652 AAACAA-A-AAACAAC-ACAAAAA-AAGTA-AAAAACAACACCA
1 AAACAACATAAAAAACAACAAAAACAACAACAAAAATAACAGCA
358691 AAACAACA
1 AAACAACA
358699 ATATAATTTT
Statistics
Matches: 113, Mismatches: 14, Indels: 20
0.77 0.10 0.14
Matches are distributed among these distances:
39 16 0.14
40 8 0.07
41 4 0.04
42 5 0.04
43 10 0.09
44 55 0.49
45 15 0.13
ACGTcount: A:0.70, C:0.19, G:0.03, T:0.07
Consensus pattern (44 bp):
AAACAACATAAAAAACAACAAAAACAACAACAAAAATAACAGCA
Found at i:358623 original size:56 final size:56
Alignment explanation
Indices: 358520--358643 Score: 142
Period size: 56 Copynumber: 2.2 Consensus size: 56
358510 AATAATATCC
* * * *
358520 AAACAACAAAAATAACAACCAAAACAGAAGCAAAAATAACAGCAAAACAATATTAA
1 AAACAACAAAAATAACAACAAAAACAGAAGCAAAAACAACAGCAAAACAACAATAA
* * ** *
358576 AAACAACAAAAATAACAACAAAAATA-ACAGCAAAAACAATATTAAAACAACAATCA
1 AAACAACAAAAATAACAACAAAAACAGA-AGCAAAAACAACAGCAAAACAACAATAA
*
358632 AAACAATAAAAA
1 AAACAACAAAAA
358644 AAGCACCAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
55 1 0.02
56 56 0.98
ACGTcount: A:0.70, C:0.17, G:0.03, T:0.10
Consensus pattern (56 bp):
AAACAACAAAAATAACAACAAAAACAGAAGCAAAAACAACAGCAAAACAACAATAA
Found at i:358633 original size:24 final size:23
Alignment explanation
Indices: 358563--358639 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
358553 AAATAACAGC
358563 AAAACAATATTAAAAACAACAA-A
1 AAAACAATATT-AAAACAACAACA
* * *
358586 AATAACAACA--AAAATAACAGCA
1 AA-AACAATATTAAAACAACAACA
358608 AAAACAATATTAAAACAACAATC-
1 AAAACAATATTAAAACAACAA-CA
358631 AAAACAATA
1 AAAACAATA
358640 AAAAAAGCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
21 14 0.33
22 3 0.07
23 19 0.44
24 7 0.16
ACGTcount: A:0.70, C:0.16, G:0.01, T:0.13
Consensus pattern (23 bp):
AAAACAATATTAAAACAACAACA
Found at i:358641 original size:20 final size:20
Alignment explanation
Indices: 358618--358696 Score: 60
Period size: 20 Copynumber: 4.0 Consensus size: 20
358608 AAAACAATAT
*
358618 TAAAACAACAATCAAAACAA
1 TAAAACAACAACCAAAACAA
*
358638 TAAAAAAAGC-ACCAAAACAA
1 TAAAACAA-CAACCAAAACAA
*
358658 -AAAACAAC-A-CAAAAAAA
1 TAAAACAACAACCAAAACAA
358675 GTAAAA-AACAACACCAAAACAA
1 -TAAAACAAC-A-ACCAAAACAA
358697 CAATATAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
17 7 0.15
18 5 0.11
19 10 0.21
20 16 0.34
21 2 0.04
22 7 0.15
ACGTcount: A:0.72, C:0.20, G:0.03, T:0.05
Consensus pattern (20 bp):
TAAAACAACAACCAAAACAA
Found at i:361658 original size:6 final size:6
Alignment explanation
Indices: 361647--361713 Score: 134
Period size: 6 Copynumber: 11.2 Consensus size: 6
361637 GGGAAGAAGG
361647 AGGCAA AGGCAA AGGCAA AGGCAA AGGCAA AGGCAA AGGCAA AGGCAA
1 AGGCAA AGGCAA AGGCAA AGGCAA AGGCAA AGGCAA AGGCAA AGGCAA
361695 AGGCAA AGGCAA AGGCAA A
1 AGGCAA AGGCAA AGGCAA A
361714 AACAAAGTCC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.51, C:0.16, G:0.33, T:0.00
Consensus pattern (6 bp):
AGGCAA
Found at i:368053 original size:21 final size:21
Alignment explanation
Indices: 368027--368068 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
368017 TGATAAAGTA
368027 CTCTTAACCAAAAACAGCCTG
1 CTCTTAACCAAAAACAGCCTG
368048 CTCTTAACCAAAAACAGCCTG
1 CTCTTAACCAAAAACAGCCTG
368069 GCCCAATCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.33, G:0.10, T:0.19
Consensus pattern (21 bp):
CTCTTAACCAAAAACAGCCTG
Found at i:373809 original size:19 final size:19
Alignment explanation
Indices: 373785--373828 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
373775 CCTCCTTCGG
* *
373785 ATTTTACTTCTTATTTTAT
1 ATTTTACTTATTATTTTAA
* *
373804 ATTTTATTTATTTTTTTAA
1 ATTTTACTTATTATTTTAA
373823 ATTTTA
1 ATTTTA
373829 TTGCATTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTTACTTATTATTTTAA
Found at i:376732 original size:15 final size:14
Alignment explanation
Indices: 376712--376761 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
376702 ACAATTTTGC
376712 TAAAAATATTTAATT
1 TAAAAATATTTAA-T
376727 TAAAAATACATTTAA-
1 TAAAAAT--ATTTAAT
376742 -AAAAATATTT-AT
1 TAAAAATATTTAAT
376754 TAAAAATA
1 TAAAAATA
376762 AGTTGAGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
11 1 0.03
12 4 0.13
13 7 0.23
14 6 0.19
15 7 0.23
17 6 0.19
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAAATATTTAAT
Found at i:396072 original size:7 final size:7
Alignment explanation
Indices: 396060--396084 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
396050 TAATTATTAT
396060 TAAAAAA
1 TAAAAAA
396067 TAAAAAA
1 TAAAAAA
396074 TAAAAAA
1 TAAAAAA
396081 TAAA
1 TAAA
396085 TTAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:396167 original size:42 final size:44
Alignment explanation
Indices: 396119--396211 Score: 145
Period size: 42 Copynumber: 2.2 Consensus size: 44
396109 TTATAAATTA
396119 TAAAATTCAAAAAATTGAATATAT-AAAAAATAAAAAA-AAAGT
1 TAAAATTCAAAAAATTGAATATATAAAAAAATAAAAAATAAAGT
* * *
396161 TAAAATTTAAAAATTTGAATATATAAAAAAATAAAAAATTAAGT
1 TAAAATTCAAAAAATTGAATATATAAAAAAATAAAAAATAAAGT
396205 TAAAATT
1 TAAAATT
396212 TAACATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 22 0.48
43 13 0.28
44 11 0.24
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (44 bp):
TAAAATTCAAAAAATTGAATATATAAAAAAATAAAAAATAAAGT
Found at i:396592 original size:19 final size:19
Alignment explanation
Indices: 396570--396631 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
396560 TTTTAACTAA
396570 ATTTTTAATTTTTATATTT
1 ATTTTTAATTTTTATATTT
*
396589 ATTTTCAATTTTTATATATT
1 ATTTTTAATTTTTATAT-TT
* *
396609 TTTTTTGAAGTTTTATAATTT
1 ATTTTT-AATTTTTAT-ATTT
396630 AT
1 AT
396632 ATATACTTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.46
20 6 0.17
21 11 0.31
22 2 0.06
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (19 bp):
ATTTTTAATTTTTATATTT
Found at i:396608 original size:21 final size:20
Alignment explanation
Indices: 396570--396631 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
396560 TTTTAACTAA
*
396570 ATTTTTAATTTT-TATATTT
1 ATTTTCAATTTTATATATTT
396589 ATTTTCAATTTTTATATATTT
1 ATTTTCAA-TTTTATATATTT
* *
396610 TTTTTGAAGTTTTATA-ATTT
1 ATTTTCAA-TTTTATATATTT
396630 AT
1 AT
396632 ATATACTTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.19
20 9 0.25
21 20 0.56
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (20 bp):
ATTTTCAATTTTATATATTT
Found at i:401315 original size:14 final size:14
Alignment explanation
Indices: 401296--401326 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
401286 ATAATAGATT
401296 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
401310 TTTAATTAATTAAA
1 TTTAATTAAATAAA
401324 TTT
1 TTT
401327 TGTAAACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:401596 original size:3 final size:3
Alignment explanation
Indices: 401588--401643 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
401578 AGTAAAAAAG
* * * *
401588 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAT GAA GAT GAA GAT GAA GAT
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
401636 GAA GAA GA
1 GAA GAA GA
401644 GAGGTGTGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.07
Consensus pattern (3 bp):
GAA
Found at i:406639 original size:3 final size:3
Alignment explanation
Indices: 406631--406655 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
406621 ATTCAACAAA
406631 CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC C
406656 CACAATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:414690 original size:26 final size:26
Alignment explanation
Indices: 414635--414689 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
414625 TAAATTTGAG
** *
414635 AAAACATGAATAATCATATAAAGAAA
1 AAAACATGAATAAGAAAATAAAGAAA
414661 AAAACATGAATAAGAAAAT-AAGAAA
1 AAAACATGAATAAGAAAATAAAGAAA
414686 AAAA
1 AAAA
414690 AATATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.71, C:0.05, G:0.09, T:0.15
Consensus pattern (26 bp):
AAAACATGAATAAGAAAATAAAGAAA
Found at i:426969 original size:22 final size:23
Alignment explanation
Indices: 426944--426993 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
426934 AATGCACAAA
* *
426944 TAAACAGAAAGTACA-AACGTGC
1 TAAACAGAAAGCACACAAAGTGC
* *
426966 TAAACGGAGAGCACACAAAGTGC
1 TAAACAGAAAGCACACAAAGTGC
426989 TAAAC
1 TAAAC
426994 GAAGAGCGCG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (23 bp):
TAAACAGAAAGCACACAAAGTGC
Found at i:426989 original size:23 final size:24
Alignment explanation
Indices: 426956--427000 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
426946 AACAGAAAGT
*
426956 ACAAACGTGCTAAACGGAGAGCAC
1 ACAAACGTGCTAAACGAAGAGCAC
426980 ACAAA-GTGCTAAACGAAGAGC
1 ACAAACGTGCTAAACGAAGAGC
427001 GCGCTAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.09
Consensus pattern (24 bp):
ACAAACGTGCTAAACGAAGAGCAC
Found at i:429502 original size:43 final size:43
Alignment explanation
Indices: 429436--429519 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
429426 TTTTTCCATT
*
429436 GCTTGTATTTTACTAGCCTTTAACTTCCTGTTGTGTCTTTATA
1 GCTTGTATTTTACTAGCCTTTAACTCCCTGTTGTGTCTTTATA
429479 GCTTGTATTTTTACTAGCC-TTAACTCCCTGTTGTGTCTTTA
1 GCTTGTA-TTTTACTAGCCTTTAACTCCCTGTTGTGTCTTTA
429520 CTGCCATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.15, C:0.20, G:0.14, T:0.50
Consensus pattern (43 bp):
GCTTGTATTTTACTAGCCTTTAACTCCCTGTTGTGTCTTTATA
Found at i:434865 original size:30 final size:29
Alignment explanation
Indices: 434829--434885 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
434819 TATTTGAATG
**
434829 TTTAATTTGGTAATTAAATTTGTTTTTTTT
1 TTTAATTTAATAATTAAATTT-TTTTTTTT
*
434859 TTTAATTTAATATTTAAATTTTTTTTT
1 TTTAATTTAATAATTAAATTTTTTTTT
434886 AATATACTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (29 bp):
TTTAATTTAATAATTAAATTTTTTTTTTT
Found at i:435313 original size:22 final size:23
Alignment explanation
Indices: 435287--435331 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
435277 TTGAAAATTA
*
435287 TTTTTAAAAAG-TAATTTTTTTT
1 TTTTTAAAAAGTTAATATTTTTT
*
435309 TTTTTAAAATGTTAATATTTTTT
1 TTTTTAAAAAGTTAATATTTTTT
435332 AGTGTTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (23 bp):
TTTTTAAAAAGTTAATATTTTTT
Found at i:435371 original size:33 final size:32
Alignment explanation
Indices: 435334--435396 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
435324 TATTTTTTAG
* **
435334 TGTTTGAATGAATTTATGTAAAATATTTTATGT
1 TGTTTG-ATAAATTTATAAAAAATATTTTATGT
*
435367 TGTTTGATAAATTTTTAAAAAATATTTTAT
1 TGTTTGATAAATTTATAAAAAATATTTTAT
435397 AAAAGTTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 20 0.77
33 6 0.23
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (32 bp):
TGTTTGATAAATTTATAAAAAATATTTTATGT
Found at i:435734 original size:94 final size:95
Alignment explanation
Indices: 435552--435734 Score: 251
Period size: 94 Copynumber: 1.9 Consensus size: 95
435542 CATGACTACC
* * * *
435552 AATGTGACATCAATAAAATTGACAAAAAAATTTAATAATGTCAATAATTGGACTTGATTTTCAAA
1 AATGTGACATCAACAAAATTGACAAAAAAATTTAACAAGGTCAACAATTGGACTTGATTTTCAAA
* *
435617 TCTAAAAAGTAGAGGGACGAAATTGATAAA
66 TCTAAAAAGTAGAAGGACAAAATTGATAAA
* *
435647 AATGTGATATCAACAAAATTGAC-AAATAATTTAACAAGGTCAACAATTGGACTTGATTTTCAAA
1 AATGTGACATCAACAAAATTGACAAAAAAATTTAACAAGGTCAACAATTGGACTTGATTTTCAAA
* * * *
435711 TTTGAAAAGTATAAGGATAAAATT
66 TCTAAAAAGTAGAAGGACAAAATT
435735 CTTGAAAATG
Statistics
Matches: 76, Mismatches: 12, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
94 55 0.72
95 21 0.28
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.30
Consensus pattern (95 bp):
AATGTGACATCAACAAAATTGACAAAAAAATTTAACAAGGTCAACAATTGGACTTGATTTTCAAA
TCTAAAAAGTAGAAGGACAAAATTGATAAA
Found at i:435840 original size:15 final size:15
Alignment explanation
Indices: 435820--435874 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
435810 ATATTACAAA
435820 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
435835 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
435852 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
435869 ATATTT
1 ATATTT
435875 TCAATAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 15 0.45
16 1 0.03
17 7 0.21
18 1 0.03
19 9 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:437007 original size:9 final size:9
Alignment explanation
Indices: 436993--437028 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
436983 CAACCTTTTT
436993 TTTTTTTAA
1 TTTTTTTAA
437002 TTTTTTTAA
1 TTTTTTTAA
437011 TTTTTTTTAA
1 -TTTTTTTAA
437021 TTTTTTTA
1 TTTTTTTA
437029 GTATTAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:437007 original size:10 final size:10
Alignment explanation
Indices: 436992--437027 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
436982 GCAACCTTTT
436992 TTTTTTTTAA
1 TTTTTTTTAA
437002 -TTTTTTTAA
1 TTTTTTTTAA
437011 TTTTTTTTAA
1 TTTTTTTTAA
437021 TTTTTTT
1 TTTTTTT
437028 AGTATTAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:437016 original size:19 final size:19
Alignment explanation
Indices: 436992--437028 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
436982 GCAACCTTTT
436992 TTTTTTTTAATTTTTTTAA
1 TTTTTTTTAATTTTTTTAA
437011 TTTTTTTTAATTTTTTTA
1 TTTTTTTTAATTTTTTTA
437029 GTATTAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTTTAATTTTTTTAA
Found at i:439555 original size:18 final size:19
Alignment explanation
Indices: 439516--439556 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
439506 GTTATTTAGA
*
439516 TATTGTATAATTTTTGTTT
1 TATTGTATAATTTTTGTAT
439535 TATTGT-TAATTTTAT-TAT
1 TATTGTATAATTTT-TGTAT
439553 TATT
1 TATT
439557 TTAGAGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (19 bp):
TATTGTATAATTTTTGTAT
Found at i:447548 original size:2 final size:2
Alignment explanation
Indices: 447541--447565 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
447531 AATGAAAAGC
447541 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
447566 CCGGGCTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:450845 original size:20 final size:21
Alignment explanation
Indices: 450822--450865 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
450812 TCCTTTTTTT
*
450822 TTTCATT-TTTATTTTTTGGA
1 TTTCATTCTTTATTTTTAGGA
*
450842 TTTCATTCTTTCTTTTTAGGA
1 TTTCATTCTTTATTTTTAGGA
450863 TTT
1 TTT
450866 TTTGTTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.68
Consensus pattern (21 bp):
TTTCATTCTTTATTTTTAGGA
Found at i:471218 original size:3 final size:3
Alignment explanation
Indices: 471210--471247 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
471200 AAACTCGAGG
471210 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
471248 AGTGAAGCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:474250 original size:31 final size:31
Alignment explanation
Indices: 474215--474280 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
474205 AAAAAAAATT
*
474215 AATAATCCAGTAACTTAAATAAAAATTTTCG
1 AATAATCCAATAACTTAAATAAAAATTTTCG
** * * *
474246 AATAATTTAATAATTTAAATGAAAATTTTCT
1 AATAATCCAATAACTTAAATAAAAATTTTCG
474277 AATA
1 AATA
474281 TTTCAATGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.38
Consensus pattern (31 bp):
AATAATCCAATAACTTAAATAAAAATTTTCG
Done.