Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014449.1 Kokia drynarioides strain JFW-HI SEQ_129488, 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: 101079
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 14 characters in sequence are not A, C, G, or T
Found at i:481 original size:30 final size:30
Alignment explanation
Indices: 445--547 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 30
435 CTGGAGGTCG
*
445 CTAAACTATCCAAAAATTACATTTTAACCC
1 CTAAACTTTCCAAAAATTACATTTTAACCC
* *
475 CTAAACTTTTC-AAAATTCCATTTTTAA-CC
1 CTAAACTTTCCAAAAATTACA-TTTTAACCC
* * * * *
504 CTGATCTTTTCATAAATTACATTTT-GCCC
1 CTAAACTTTCCAAAAATTACATTTTAACCC
*
533 TTAAACTTTCCAAAA
1 CTAAACTTTCCAAAA
548 TCTCATTTTT
Statistics
Matches: 57, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
29 35 0.61
30 22 0.39
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (30 bp):
CTAAACTTTCCAAAAATTACATTTTAACCC
Found at i:498 original size:29 final size:29
Alignment explanation
Indices: 457--556 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
447 AAACTATCCA
457 AAAATTACATTTTAACCCCTAAACTTTTC
1 AAAATTACATTTTAACCCCTAAACTTTTC
* * *
486 AAAATTCCATTTTTAA-CCCTGATCTTTTC
1 AAAATTACA-TTTTAACCCCTAAACTTTTC
* * *
515 ATAAATTACATTTT-GCCCTTAAACTTTCC
1 A-AAATTACATTTTAACCCCTAAACTTTTC
544 AAAATCT-CATTTT
1 AAAAT-TACATTTT
557 TGACCCTGAA
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
28 10 0.17
29 35 0.60
30 13 0.22
ACGTcount: A:0.33, C:0.23, G:0.02, T:0.42
Consensus pattern (29 bp):
AAAATTACATTTTAACCCCTAAACTTTTC
Found at i:579 original size:58 final size:59
Alignment explanation
Indices: 455--588 Score: 148
Period size: 58 Copynumber: 2.3 Consensus size: 59
445 CTAAACTATC
* * *
455 CAAAAATTACATTTTAACCCCTAAACTTTTCAAAATTCCATTTTTAACCCTGATCTTTT
1 CAAAAATTACATTTTAACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTGAACTTCT
* * * * *
514 CATAAATTACATTTT-GCCCTTAAACTTTCCAAAA-TCTCATTTTTGACCCTGAAAGTTCT
1 CAAAAATTACATTTTAACCCCTAAACTTTCCAAAATTC-CATTTTTAACCCTG-AACTTCT
573 -AAAAATTACCATTTTA
1 CAAAAATTA-CATTTTA
589 CCACCGGAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
57 2 0.03
58 36 0.58
59 24 0.39
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (59 bp):
CAAAAATTACATTTTAACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTGAACTTCT
Found at i:645 original size:59 final size:58
Alignment explanation
Indices: 573--881 Score: 329
Period size: 59 Copynumber: 5.3 Consensus size: 58
563 TGAAAGTTCT
**
573 AAAAATTACCATTTTACCACCGGAA-GTCTAAAAACTCTGTTTTTGATCTCGAACCTTCC
1 AAAAATTACCATTTTACC-CC-GAATGTCTAAAAACTCCATTTTTGATCTCGAACCTTCC
* * * * * *
632 AAAATTTATCATTTTACCCTCGAATGTCTAAAAACTCTATTTTTTATCCCGAACCTTCT
1 AAAAATTACCATTTTACCC-CGAATGTCTAAAAACTCCATTTTTGATCTCGAACCTTCC
*
691 AAAAATTACCATTTTACCCTCGAATGTCTAAAAATTCCATTTTTGATCTCGAACCTTCC
1 AAAAATTACCATTTTACCC-CGAATGTCTAAAAACTCCATTTTTGATCTCGAACCTTCC
* * * * *
750 -AAAATTACCATTTTACCCCCGAACT-TCCAAAAATTCCATTTTTGA-CCCTGAAACTTTC
1 AAAAATTACCATTTTA-CCCCGAA-TGTCTAAAAACTCCATTTTTGATCTC-GAACCTTCC
* * * * *
808 AAAAATTATCATTTTACCCCCGGATGTCCAAAAACTCCGTTTTTTATCTCGAACCTTCC
1 AAAAATTACCATTTTA-CCCCGAATGTCTAAAAACTCCATTTTTGATCTCGAACCTTCC
* *
867 TAAATTTACCATTTT
1 AAAAATTACCATTTT
882 TGAATCTATT
Statistics
Matches: 214, Mismatches: 28, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
57 2 0.01
58 50 0.23
59 160 0.75
60 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCGAATGTCTAAAAACTCCATTTTTGATCTCGAACCTTCC
Found at i:675 original size:29 final size:29
Alignment explanation
Indices: 643--798 Score: 103
Period size: 29 Copynumber: 5.3 Consensus size: 29
633 AAATTTATCA
* *
643 TTTTACCCTCGAATGTCTAAAAACTCTATT
1 TTTTACCCTCGAATGTCTAAAAATTCCA-T
*
673 TTTTATCC-CGAACCT-TCTAAAAATTACCA-
1 TTTTACCCTCGAA--TGTCTAAAAATT-CCAT
702 TTTTACCCTCGAATGTCTAAAAATTCCAT
1 TTTTACCCTCGAATGTCTAAAAATTCCAT
* *
731 TTTTGA-TCTCGAACCT-TC-CAAAATTACCA-
1 TTTT-ACCCTCGAA--TGTCTAAAAATT-CCAT
* *
760 TTTTACCCCCGAACT-TCCAAAAATTCCAT
1 TTTTACCCTCGAA-TGTCTAAAAATTCCAT
789 TTTTGACCCT
1 TTTT-ACCCT
799 GAAACTTTCA
Statistics
Matches: 102, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
28 12 0.12
29 56 0.55
30 30 0.29
31 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.37
Consensus pattern (29 bp):
TTTTACCCTCGAATGTCTAAAAATTCCAT
Found at i:691 original size:118 final size:117
Alignment explanation
Indices: 540--881 Score: 426
Period size: 117 Copynumber: 2.9 Consensus size: 117
530 CCCTTAAACT
* *
540 TTCCAAAATCT-CATTTTTGACCCTGAAAGTTCTAAAAATTACCATTTTACCACCGGAAGTCTAA
1 TTCCAAAAACTCCATTTTTGACCCTGAAACTTCTAAAAATTACCATTTTACC-CCGGAAGTCTAA
* * *
604 AAACTCTGTTTTTGATCTCGAACCTTCCAAAATTTATCATTTTACCCTCGAA-
65 AAACTCCGTTTTTGATCTCGAACCTTCCAAAATTTACCATTTTACCCCCGAAC
* * * *
656 TGTCTAAAAACTCTATTTTTTATCCC-GAACCTTCTAAAAATTACCATTTTACCCTC-GAATGTC
1 T-TCCAAAAACTCCATTTTTGA-CCCTGAAACTTCTAAAAATTACCATTTTACCC-CGGAA-GTC
* *
719 TAAAAATTCCATTTTTGATCTCGAACCTTCCAAAA-TTACCATTTTACCCCCGAAC
62 TAAAAACTCCGTTTTTGATCTCGAACCTTCCAAAATTTACCATTTTACCCCCGAAC
* * * *
774 TTCCAAAAATTCCATTTTTGACCCTGAAACTT-TCAAAAATTATCATTTTACCCCCGGATGTCCA
1 TTCCAAAAACTCCATTTTTGACCCTGAAACTTCT-AAAAATTACCATTTTA-CCCCGGAAGTCTA
* *
838 AAAACTCCGTTTTTTATCTCGAACCTTCCTAAATTTACCATTTT
64 AAAACTCCGTTTTTGATCTCGAACCTTCCAAAATTTACCATTTT
882 TGAATCTATT
Statistics
Matches: 192, Mismatches: 23, Indels: 20
0.82 0.10 0.09
Matches are distributed among these distances:
116 5 0.03
117 100 0.52
118 84 0.44
119 3 0.02
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (117 bp):
TTCCAAAAACTCCATTTTTGACCCTGAAACTTCTAAAAATTACCATTTTACCCCGGAAGTCTAAA
AACTCCGTTTTTGATCTCGAACCTTCCAAAATTTACCATTTTACCCCCGAAC
Found at i:811 original size:29 final size:29
Alignment explanation
Indices: 721--811 Score: 82
Period size: 29 Copynumber: 3.1 Consensus size: 29
711 CGAATGTCTA
* *
721 AAAATTCCATTTTTGA-TCTCGAACCTTCC
1 AAAATTCCATTTTTGACCCT-GAAACTTCC
*
750 AAAATTACCA-TTTT-ACCCCCG-AACTTCC
1 AAAATT-CCATTTTTGA-CCCTGAAACTTCC
*
778 AAAAATTCCATTTTTGACCCTGAAACTTTC
1 -AAAATTCCATTTTTGACCCTGAAACTTCC
808 AAAA
1 AAAA
812 ATTATCATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
28 10 0.20
29 29 0.58
30 11 0.22
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.33
Consensus pattern (29 bp):
AAAATTCCATTTTTGACCCTGAAACTTCC
Found at i:4365 original size:1 final size:1
Alignment explanation
Indices: 4359--4455 Score: 50
Period size: 1 Copynumber: 97.0 Consensus size: 1
4349 TTCAATGAAT
* * * * ** * * * * * *
4359 AAAAAAAAGAAAAAAGAAGAAGAAAAAGGAAAAACAAAAACAAAAAACAAAAAATAATAAAAATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
4424 ACAAAAAACAAAAACAAAAAAATAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4456 GAGAGGTCGA
Statistics
Matches: 66, Mismatches: 30, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.84, C:0.06, G:0.06, T:0.04
Consensus pattern (1 bp):
A
Found at i:4397 original size:13 final size:13
Alignment explanation
Indices: 4361--4457 Score: 60
Period size: 13 Copynumber: 7.6 Consensus size: 13
4351 CAATGAATAA
4361 AAAAAAGAAAAA-
1 AAAAAAGAAAAAC
* *
4373 AGAAGAAGAAAAAG
1 A-AAAAAGAAAAAC
* *
4387 GAAAAACAAAAAC
1 AAAAAAGAAAAAC
*
4400 AAAAAACAAAAA-
1 AAAAAAGAAAAAC
*
4412 ATAATAAA-AATAAC
1 A-AA-AAAGAAAAAC
*
4426 AAAAAACAAAAAC
1 AAAAAAGAAAAAC
*
4439 AAAAAA-ATAAA-
1 AAAAAAGAAAAAC
4450 AAAAAAGA
1 AAAAAAGA
4458 GAGGTCGAGG
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
11 6 0.09
12 10 0.14
13 49 0.71
14 4 0.06
ACGTcount: A:0.82, C:0.06, G:0.07, T:0.04
Consensus pattern (13 bp):
AAAAAAGAAAAAC
Found at i:4398 original size:7 final size:7
Alignment explanation
Indices: 4388--4444 Score: 59
Period size: 7 Copynumber: 8.7 Consensus size: 7
4378 AAGAAAAAGG
4388 AAAAAC-
1 AAAAACA
4394 AAAAACA
1 AAAAACA
4401 AAAAACA
1 AAAAACA
*
4408 AAAAA-T
1 AAAAACA
*
4414 AATAA-A
1 AAAAACA
*
4420 AATAACA
1 AAAAACA
4427 AAAAAC-
1 AAAAACA
4433 AAAAACA
1 AAAAACA
4440 AAAAA
1 AAAAA
4445 ATAAAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
6 21 0.48
7 23 0.52
ACGTcount: A:0.84, C:0.11, G:0.00, T:0.05
Consensus pattern (7 bp):
AAAAACA
Found at i:4410 original size:26 final size:26
Alignment explanation
Indices: 4381--4437 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
4371 AAAGAAGAAG
*
4381 AAAAAGGAA-AAACAAAAACAAAAAAC
1 AAAAAAGAATAAA-AAAAACAAAAAAC
* *
4407 AAAAAATAATAAAAATAACAAAAAAC
1 AAAAAAGAATAAAAAAAACAAAAAAC
4433 AAAAA
1 AAAAA
4438 CAAAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 24 0.89
27 3 0.11
ACGTcount: A:0.82, C:0.09, G:0.04, T:0.05
Consensus pattern (26 bp):
AAAAAAGAATAAAAAAAACAAAAAAC
Found at i:4411 original size:39 final size:39
Alignment explanation
Indices: 4361--4444 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 39
4351 CAATGAATAA
* **
4361 AAAAAAGAAAAAAGAAGAAGAAA-AAGGAAAAACAAAAAC
1 AAAAAACAAAAAAGAAGAA-AAATAACAAAAAACAAAAAC
* *
4400 AAAAAACAAAAAATAATAAAAATAACAAAAAACAAAAAC
1 AAAAAACAAAAAAGAAGAAAAATAACAAAAAACAAAAAC
4439 AAAAAA
1 AAAAAA
4445 ATAAAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 3 0.08
39 36 0.92
ACGTcount: A:0.82, C:0.07, G:0.07, T:0.04
Consensus pattern (39 bp):
AAAAAACAAAAAAGAAGAAAAATAACAAAAAACAAAAAC
Found at i:5510 original size:50 final size:48
Alignment explanation
Indices: 5366--5658 Score: 148
Period size: 51 Copynumber: 5.8 Consensus size: 48
5356 CTACAGGTCT
*
5366 CAGTACCACAAAGAGACAAAAGGGAAAGGTCTAAGTCACAACGGTAGGAC
1 CAGTACCACAAAGA-ACAAAAGGGAAAGGTCTAAGTCGCAACGGTA-GAC
* * * *
5416 CATGTACCTCAGAAG-ACATGAAGGGAAAGATTTAA-TCTGCAACGGTTA-ATC
1 CA-GTACCACA-AAGAACA-AAAGGGAAAGGTCTAAGTC-GCAACGG-TAGA-C
* * *
5467 CAGTACCACAAAGATACAAAAAGGAAAGGTCTAAGTCGTAACGGCAAGAC
1 CAGTACCACAAAGA-ACAAAAGGGAAAGGTCTAAGTCGCAACGG-TAGAC
* * * * * * *
5517 CGTGTACCTCAAAAGACACGAAA-GGAAAGATTTAAGCCGCAACGG-CGAATC
1 C-AGTACCAC-AAAGA-ACAAAAGGGAAAGGTCTAAGTCGCAACGGTAG-A-C
* ** * * * * *
5568 TAGTACCATGAAG-ACATGAAGGGAAAGATCTAAGACCGCAACGGCAAATC
1 CAGTACCACAAAGAACA-AAAGGGAAAGGTCTAAG-TCGCAACGGTAGA-C
* *
5618 CAGTACCACAAAGATACAAAAGGGAATGGTTTAAGTCGCAA
1 CAGTACCACAAAGA-ACAAAAGGGAAAGGTCTAAGTCGCAA
5659 TGGCGGGCCG
Statistics
Matches: 183, Mismatches: 40, Indels: 40
0.70 0.15 0.15
Matches are distributed among these distances:
47 2 0.01
48 2 0.01
49 19 0.10
50 69 0.38
51 73 0.40
52 18 0.10
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (48 bp):
CAGTACCACAAAGAACAAAAGGGAAAGGTCTAAGTCGCAACGGTAGAC
Found at i:5544 original size:101 final size:101
Alignment explanation
Indices: 5366--5575 Score: 285
Period size: 101 Copynumber: 2.1 Consensus size: 101
5356 CTACAGGTCT
* * * *
5366 CAGTACCACAAAGAGACAAAAGGGAAAGGTCTAAGTCACAACGGTAGGACCATGTACCTCAGAAG
1 CAGTACCACAAAGAGACAAAAAGGAAAGGTCTAAGTCACAACGGCAAGACCATGTACCTCAAAAG
* * * * **
5431 ACATGAAGGGAAAGATTTAATCTGCAACGGTTAATC
66 ACACGAAAGGAAAGATTTAAGCCGCAACGGCGAATC
* ** *
5467 CAGTACCACAAAGATACAAAAAGGAAAGGTCTAAGTCGTAACGGCAAGACCGTGTACCTCAAAAG
1 CAGTACCACAAAGAGACAAAAAGGAAAGGTCTAAGTCACAACGGCAAGACCATGTACCTCAAAAG
5532 ACACGAAAGGAAAGATTTAAGCCGCAACGGCGAATC
66 ACACGAAAGGAAAGATTTAAGCCGCAACGGCGAATC
*
5568 TAGTACCA
1 CAGTACCA
5576 TGAAGACATG
Statistics
Matches: 94, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
101 94 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.15
Consensus pattern (101 bp):
CAGTACCACAAAGAGACAAAAAGGAAAGGTCTAAGTCACAACGGCAAGACCATGTACCTCAAAAG
ACACGAAAGGAAAGATTTAAGCCGCAACGGCGAATC
Found at i:5611 original size:101 final size:100
Alignment explanation
Indices: 5366--5614 Score: 284
Period size: 101 Copynumber: 2.5 Consensus size: 100
5356 CTACAGGTCT
* * * *
5366 CAGTACCACAAAGAGACAAAAGGGAAAGGTCTAAGTCACAACGGTAGGACCATGTACCTCAGAAG
1 CAGTACCACAAAGA-ACAAAAGGGAAAGGTCTAAGTCGCAACGGCAAGACCATGTACCTCAAAAG
* * * * **
5431 ACATGAAGGGAAAGATTTAATCTGCAACGGTTAATC
65 ACACGAAAGGAAAGATTTAAGCCGCAACGGCGAATC
* * *
5467 CAGTACCACAAAGATACAAAAAGGAAAGGTCTAAGTCGTAACGGCAAGACCGTGTACCTCAAAAG
1 CAGTACCACAAAGA-ACAAAAGGGAAAGGTCTAAGTCGCAACGGCAAGACCATGTACCTCAAAAG
5532 ACACGAAAGGAAAGATTTAAGCCGCAACGGCGAATC
65 ACACGAAAGGAAAGATTTAAGCCGCAACGGCGAATC
* ** * * *
5568 TAGTACCATGAAG-ACATGAAGGGAAAGATCTAAGACCGCAACGGCAA
1 CAGTACCACAAAGAACA-AAAGGGAAAGGTCTAAG-TCGCAACGGCAA
5615 ATCCAGTACC
Statistics
Matches: 124, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
99 3 0.02
100 14 0.11
101 107 0.86
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (100 bp):
CAGTACCACAAAGAACAAAAGGGAAAGGTCTAAGTCGCAACGGCAAGACCATGTACCTCAAAAGA
CACGAAAGGAAAGATTTAAGCCGCAACGGCGAATC
Found at i:5724 original size:50 final size:50
Alignment explanation
Indices: 5419--5724 Score: 160
Period size: 50 Copynumber: 6.1 Consensus size: 50
5409 GTAGGACCAT
* * * * * ** *
5419 GTACCTCAGAAGACATGAAGGGAAAGATTTAATCTGCAACGGTTAATCCA
1 GTACCTCAAAAGAAAAGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTA
* * * * * * * *
5469 GTACCAC-AAAGATACAA-AAAGGAAAGGTCTAAGTCGTAACGGCAAGACCGT-
1 GTACCTCAAAAGA-A-AAGAAGGGAAAGATTTAAGCCGCAACGGCGA-ATC-TA
* * *
5520 GTACCTCAAAAGACACGAAAGGAAAGATTTAAGCCGCAACGGCGAATCTA
1 GTACCTCAAAAGAAAAGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTA
* * * * * *
5570 GTA-C-CATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCAAATCCA
1 GTACCTCA-AAAGAAAAGAAGGGAAAGATTTAAG-CCGCAACGGCGAATCTA
* * * * * ***
5620 GTACCAC-AAAGATACAA-AAGGGAATGGTTTAAGTCGCAATGGCGGGCCGT-
1 GTACCTCAAAAGA-A-AAGAAGGGAAAGATTTAAGCCGCAACGGCGAATC-TA
* *
5670 GTACCTCAAAAGAAAAGAAGGGAAAGATTTAAGCTGCAACGACGAATCTA
1 GTACCTCAAAAGAAAAGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTA
5720 GTACC
1 GTACC
5725 ACGAAGATTT
Statistics
Matches: 186, Mismatches: 53, Indels: 34
0.68 0.19 0.12
Matches are distributed among these distances:
48 2 0.01
49 30 0.16
50 96 0.52
51 51 0.27
52 7 0.04
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.16
Consensus pattern (50 bp):
GTACCTCAAAAGAAAAGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTA
Found at i:5774 original size:150 final size:151
Alignment explanation
Indices: 5427--5745 Score: 435
Period size: 150 Copynumber: 2.1 Consensus size: 151
5417 ATGTACCTCA
* * * **
5427 GAAGACATGAAGGGAAAGATTTAA-TCTGCAACGGTTAATCCAGTACCACAAAGATACAAAAAGG
1 GAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCAAATCCAGTACCACAAAGATACAAAAAGG
* * *
5491 AAAGGTCTAAGTCGTAACGGCAAGACCGTGTACCTCAAAAGACACGAAAGGAAAGATTTAAGCCG
66 AAAGGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAAAAGAAAAGAAAGGAAAGATTTAAGCCG
* *
5556 CAACGGCGAATCTAGTACCAT
131 CAACGACGAATCTAGTACCAC
*
5577 GAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCAAATCCAGTACCACAAAGATACAAAAGGG
1 GAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCAAATCCAGTACCACAAAGATACAAAAAGG
* * * * * * *
5642 AATGGTTTAAGTCGCAATGGC-GGGCCGTGTACCTCAAAAGAAAAGAAGGGAAAGATTTAAGCTG
66 AAAGGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAAAAGAAAAGAAAGGAAAGATTTAAGCCG
5706 CAACGACGAATCTAGTACCAC
131 CAACGACGAATCTAGTACCAC
**
5727 GAAGATTTGAAGGGGAAAG
1 GAAGACATGAA-GGGAAAG
5746 GTTTAAGTTG
Statistics
Matches: 147, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
150 88 0.60
151 59 0.40
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (151 bp):
GAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCAAATCCAGTACCACAAAGATACAAAAAGG
AAAGGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAAAAGAAAAGAAAGGAAAGATTTAAGCCG
CAACGACGAATCTAGTACCAC
Found at i:6032 original size:101 final size:101
Alignment explanation
Indices: 5868--6054 Score: 257
Period size: 101 Copynumber: 1.9 Consensus size: 101
5858 GGCAAATCTT
* * * * * *
5868 TATCTCTCTGAAGTTGCAGTAGGAGCAAAATGAAGCTTTAACGTCAATTCCTATCCTCTTGAAGT
1 TATCTCTCTGAAATTGCAGTAAGAGCAAAATGAAGCTTCAACATCAAATCCTATCCTCCTGAAGT
* *
5933 TGCAGTAAAGTTGGATTAAAAACAATTGTAAGTCTG
66 TGCAGCAAAGTTGGAATAAAAACAATTGTAAGTCTG
* * * *
5969 TATCTCTTTGAAATTGTAGTAAGAGCAAGATGAAGCTTCAACATCAAATCCTATCTTCCTGAAGT
1 TATCTCTCTGAAATTGCAGTAAGAGCAAAATGAAGCTTCAACATCAAATCCTATCCTCCTGAAGT
*
6034 TGCAGCGAAGTTGGAATAAAA
66 TGCAGCAAAGTTGGAATAAAA
6055 CTACAGCAGC
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 73 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (101 bp):
TATCTCTCTGAAATTGCAGTAAGAGCAAAATGAAGCTTCAACATCAAATCCTATCCTCCTGAAGT
TGCAGCAAAGTTGGAATAAAAACAATTGTAAGTCTG
Found at i:7242 original size:206 final size:206
Alignment explanation
Indices: 6299--7281 Score: 1367
Period size: 206 Copynumber: 4.8 Consensus size: 206
6289 CCGGCCTCTT
* * * * * ** * *
6299 GATATTGAGAAGTAGATCAAAGCAATAAAATAGTTAGCTTCCTGATGAGATATTGAGAAATGGAT
1 GATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACCGAGAAGTGGAC
* *
6364 CAAATTCGTCTTCCTGATGCGATACAGAGAAGCGGATTGAAACAAACGACACGGTCATCTTCCTG
66 CAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATACGGTCATCTTCCTG
* * * *
6429 ATGAGATATTGAGAAGAAGACCAAATCAAACTCACGCTTGATATGAGCAAATCTTCGAACCCTAG
131 ATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAATCTTCGAACCCCAG
*
6494 CTTCTTGATGA
196 CTTCCTGATGA
* *
6505 GATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGATGAGATTCCGAGAAGTGGAC
1 GATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACCGAGAAGTGGAC
** * * *
6570 CAAATTCGTCTTATTGATGAGATACAGAGAAGCGGATTGAAACAAACGATGCGATCGTCTTCCTG
66 CAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATACGGTCATCTTCCTG
* *
6635 ATAAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAAATCTTCGAACCCCAG
131 ATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAATCTTCGAACCCCAG
*
6700 CTTCTTGATGA
196 CTTCCTGATGA
* *
6711 GATACTGAGAAGTAGGTCGAAGTAATAAAATGGTTAGCTTCCTGATGAGATACCGAGAAGTGGAC
1 GATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACCGAGAAGTGGAC
* * * *
6776 CAAATTCGTCTTCCTGATGAGATACAGAGAAGAGGCTTGAAACAAACGACACGGTCATCTTCCTA
66 CAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATACGGTCATCTTCCTG
* *
6841 ATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTTG-ACCCCTA
131 ATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAATCTTCGAACCCC-A
*
6905 GCTTCCTAATGA
195 GCTTCCTGATGA
* * *
6917 GATACTAAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGAC
1 GATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACCGAGAAGTGGAC
* * * * *
6982 CAAATTCGTCTTCTTGATAAGATACAGAGAAGCGGATTGAAACAAGCAATACGGTCATCTTCATG
66 CAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATACGGTCATCTTCCTG
*
7047 ATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAG
131 ATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAATCTTCGAACCCCAG
7112 CTTCCTGATGA
196 CTTCCTGATGA
* * * * *
7123 GATACTGAGAAGCAAGTCGAAACAATAAAATGGTTAGCTTCCTTATGAGATACGGAGAAGTGAAC
1 GATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACCGAGAAGTGGAC
* * * * ** *** *
7188 CAAATTCATCTTCCTGATGAAACACAGAGAAGTGGATCAAAACAGGTGATACGGTCATCTT-CTT
66 CAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATACGGTCATCTTCCTG
* * * *
7252 AGTAAAATACTGAGAAGAAGGCCAAGTCAA
131 A-TGAGATACTGAGAAGAAGACCAAATCAA
7282 TGAAACCAAA
Statistics
Matches: 695, Mismatches: 79, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
205 7 0.01
206 683 0.98
207 5 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (206 bp):
GATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACCGAGAAGTGGAC
CAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGATACGGTCATCTTCCTG
ATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAATCTTCGAACCCCAG
CTTCCTGATGA
Found at i:9606 original size:29 final size:29
Alignment explanation
Indices: 9573--9697 Score: 105
Period size: 29 Copynumber: 4.3 Consensus size: 29
9563 AGAAATCTCA
*
9573 TTTTACCCTTGAAC-TTCAAAAATTACATT
1 TTTTACCCTCGAACTTTCAAAAATTACA-T
* *
9602 TTTTACCCT-GATCTTTTCATAAATTACAT
1 TTTTACCCTCGAAC-TTTCAAAAATTACAT
* * * *
9631 TTTTGCCCCCGAACTTTCCAAAATTCCAT
1 TTTTACCCTCGAACTTTCAAAAATTACAT
*
9660 TTTTAACCTCGAAAC-TTCAAAAAATTACCA-
1 TTTTACCCTCG-AACTTTC-AAAAATTA-CAT
9690 TTTTACCC
1 TTTTACCC
9698 CGGATGTCTA
Statistics
Matches: 76, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
28 3 0.04
29 40 0.53
30 31 0.41
31 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (29 bp):
TTTTACCCTCGAACTTTCAAAAATTACAT
Found at i:9722 original size:59 final size:58
Alignment explanation
Indices: 9659--10028 Score: 286
Period size: 59 Copynumber: 6.2 Consensus size: 58
9649 CAAAATTCCA
* *
9659 TTTTTAACCTCGAAACTTCAAAAAATTACCATTTTACCCCGGATGTCTAAAAACTCCTT
1 TTTTTAACCTCGAACCTTC-AAAAATTACCATTTTACCCCGAATGTCTAAAAACTCCTT
* * * * *
9718 TTTTTTATCTCGAACCTTCCAAAATTTACCATTTTACCCCCAAATGTTTAAAAACT--TT
1 TTTTTAACCTCGAACCTT-CAAAAATTACCATTTTA-CCCCGAATGTCTAAAAACTCCTT
* * * *
9776 ATTTTTGATCTCGAACCTTTCGAAAATTACCATTTTACCACCGAATGTCTAAAAACTCCAT
1 -TTTTTAACCTCGAACC-TTCAAAAATTACCATTTTACC-CCGAATGTCTAAAAACTCCTT
* * * * * ** * *
9837 TTTTGATCC-CGACCCTTCCAAAATTGCCATTTTACCCTCGAACT-TCCCCAAAATTCC-A
1 TTTTTAACCTCGAACCTTCAAAAATTACCATTTTACCC-CGAA-TGT-CTAAAAACTCCTT
* * * * *
9895 TTTTTGACCTCAAAACTTCCAAAAATTATCATTTTACCCCCGGATGTCTAAAAACTCCGTT
1 TTTTTAACCTCGAACCTT-CAAAAATTACCATTTTA-CCCCGAATGTCTAAAAACTCC-TT
* * * *
9956 TTTTTTATCTCGAACCTTCTAAAATTTACCATTTTTACCCTCGAATGTCT-AAAACTCC-A
1 TTTTTAACCTCGAACCTTC-AAAAATTACCA-TTTTACCC-CGAATGTCTAAAAACTCCTT
*
10015 TTTTTACCCTCGAA
1 TTTTTAACCTCGAA
10029 TGTCTAAAAC
Statistics
Matches: 243, Mismatches: 49, Indels: 38
0.74 0.15 0.12
Matches are distributed among these distances:
57 1 0.00
58 34 0.14
59 114 0.47
60 43 0.18
61 38 0.16
62 13 0.05
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.36
Consensus pattern (58 bp):
TTTTTAACCTCGAACCTTCAAAAATTACCATTTTACCCCGAATGTCTAAAAACTCCTT
Found at i:9802 original size:118 final size:118
Alignment explanation
Indices: 9650--10019 Score: 417
Period size: 118 Copynumber: 3.1 Consensus size: 118
9640 CGAACTTTCC
* * *
9650 AAAATTCCATTTTTAACCTCGAAACTTCAAAAAATTACCATTTTACCCCGGATGTCTAAAAACTC
1 AAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTACCATTTTACCCCGGATGTCTAAAAACTC
*
9715 CTTTTTTTTATCTCGAACCTTCCAAAATTTACCATTTTACCCCCAAATGTTTA
66 CTTTTTTTTATCTCGAACCTTCCAAAATTTACCATTTTACCCCCAAATGTCTA
* * * * * * *
9768 AAAACTT-TATTTTTGATCTCGAACCTTTCGAAAATTACCATTTTACCACCGAATGTCTAAAAAC
1 AAAA-TTCCATTTTTGACCTCAAAACTTCCAAAAATTACCATTTTACC-CCGGATGTCTAAAAAC
* * * * * * * **
9832 TCC-ATTTTTGATCCCGACCCTTCCAAAA-TTGCCATTTTACCCTCGAACT-TCCCC
64 TCCTTTTTTTTATCTCGAACCTTCCAAAATTTACCATTTTACCC-CCAAATGT-CTA
*
9886 AAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTATCATTTTACCCCCGGATGTCTAAAAACT
1 AAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTACCATTTTA-CCCCGGATGTCTAAAAACT
* * *
9951 CCGTTTTTTTTATCTCGAACCTTCTAAAATTTACCATTTTTACCCTCGAATGTCT-
65 CC-TTTTTTTTATCTCGAACCTTCCAAAATTTACCA-TTTTACCCCCAAATGTCTA
*
10006 AAAACTCCATTTTT
1 AAAATTCCATTTTT
10020 ACCCTCGAAT
Statistics
Matches: 203, Mismatches: 38, Indels: 20
0.78 0.15 0.08
Matches are distributed among these distances:
117 16 0.08
118 115 0.57
119 22 0.11
120 33 0.16
121 8 0.04
122 9 0.04
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.36
Consensus pattern (118 bp):
AAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTACCATTTTACCCCGGATGTCTAAAAACTC
CTTTTTTTTATCTCGAACCTTCCAAAATTTACCATTTTACCCCCAAATGTCTA
Found at i:9916 original size:29 final size:28
Alignment explanation
Indices: 9851--9933 Score: 71
Period size: 30 Copynumber: 2.8 Consensus size: 28
9841 GATCCCGACC
*
9851 CTTCCAAAATTGCCATTTTACCCTCGAA
1 CTTCCAAAATTGCCATTTTACCCTCAAA
9879 CTTCCCCAAAATT-CCATTTTTGA-CCTCAAAA
1 CTT--CCAAAATTGCCA-TTTT-ACCCTC-AAA
**
9910 CTTCCAAAAATTATCATTTTACCC
1 CTTCC-AAAATTGCCATTTTACCC
9934 CCGGATGTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
28 3 0.07
29 6 0.13
30 28 0.62
31 8 0.18
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.34
Consensus pattern (28 bp):
CTTCCAAAATTGCCATTTTACCCTCAAA
Found at i:10022 original size:28 final size:28
Alignment explanation
Indices: 9984--10047 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
9974 CTAAAATTTA
9984 CCATTTTTACCCTCGAATGTCTAAAACT
1 CCATTTTTACCCTCGAATGTCTAAAACT
10012 CCATTTTTACCCTCGAATGTCTAAAACT
1 CCATTTTTACCCTCGAATGTCTAAAACT
10040 CCATTTTT
1 CCATTTTT
10048 TATCCGAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.27, C:0.28, G:0.06, T:0.39
Consensus pattern (28 bp):
CCATTTTTACCCTCGAATGTCTAAAACT
Found at i:10074 original size:87 final size:89
Alignment explanation
Indices: 9749--10106 Score: 255
Period size: 87 Copynumber: 4.0 Consensus size: 89
9739 AAATTTACCA
* * ** * * *
9749 TTTTACCCCCAAATGTTTAAAAACT-TTATTTTTGATCTCGAACCTTTCGAAAATTACCATTTTA
1 TTTTACCCCCGAATGTCTAAAAACTCCGATTTTTTATCTCGAACCTTCCAAAAATTACCATTTTA
9813 CCAC-CGAATGTCTAAAAACTCCAT
66 CC-CTCGAATGTCTAAAAACTCCAT
* * * * * *
9837 TTTTGA-TCCCGACCCT-TC-CAAAATTGCC-A--TTTTACCCTCGAA-CTTCCCCAAAATT-CC
1 TTTT-ACCCCCGA--ATGTCTAAAAACT-CCGATTTTTTA-TCTCGAACCTT-CCAAAAATTACC
* * * *
9894 ATTTTTGA-CCTCAAAACT-TCCAAAAATTATCA-
60 A-TTTT-ACCCTC-GAA-TGTCTAAAAACT-CCAT
* * * *
9926 TTTTACCCCCGGATGTCTAAAAACTCCGTTTTTTTTATCTCGAACCTTCTAAAATTTACCATTTT
1 TTTTACCCCCGAATGTCTAAAAACTCCG-ATTTTTTATCTCGAACCTTCCAAAAATTACCA-TTT
9991 TACCCTCGAATGTCT-AAAACTCCAT
64 TACCCTCGAATGTCTAAAAACTCCAT
*
10016 TTTTACCCTCGAATGTCT-AAAACTCC-ATTTTTTATC-CGAAACCTTCCAAAAATTACCATTTT
1 TTTTACCCCCGAATGTCTAAAAACTCCGATTTTTTATCTCG-AACCTTCCAAAAATTACCATTTT
*
10078 ACCCTCGGATGTCTAAAAACTCCAT
65 ACCCTCGAATGTCTAAAAACTCCAT
10103 TTTT
1 TTTT
10107 TGATCCCGAA
Statistics
Matches: 208, Mismatches: 35, Indels: 55
0.70 0.12 0.18
Matches are distributed among these distances:
86 19 0.09
87 52 0.25
88 37 0.18
89 37 0.18
90 26 0.12
91 17 0.08
92 20 0.10
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (89 bp):
TTTTACCCCCGAATGTCTAAAAACTCCGATTTTTTATCTCGAACCTTCCAAAAATTACCATTTTA
CCCTCGAATGTCTAAAAACTCCAT
Found at i:10135 original size:60 final size:59
Alignment explanation
Indices: 10016--10201 Score: 232
Period size: 60 Copynumber: 3.1 Consensus size: 59
10006 AAAACTCCAT
10016 TTTTACCCTCGAATGTCT-AAAACTCCATTTTTTAT-CCGAAACCTTCCAAAAATTACCA
1 TTTTACCCTCGAATGTCTAAAAACTCCATTTTTTATCCCG-AACCTTCCAAAAATTACCA
*
10074 TTTTACCCTCGGATGTCTAAAAACTCCATTTTTTGATCCCGAACCTTCCAAAAATTACCA
1 TTTTACCCTCGAATGTCTAAAAACTCCATTTTTT-ATCCCGAACCTTCCAAAAATTACCA
* * * * * * * ** *
10134 TTTTACCCCCGAAAGTCCAAAAATTCTATTTTTTTACCCCAAAATTTCCCAAAATTACCA
1 TTTTACCCTCGAATGTCTAAAAACTCCA-TTTTTTATCCCGAACCTTCCAAAAATTACCA
10194 TTTTACCC
1 TTTTACCC
10202 CTCCAGAGTC
Statistics
Matches: 112, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
58 17 0.15
59 15 0.13
60 71 0.63
61 9 0.08
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.34
Consensus pattern (59 bp):
TTTTACCCTCGAATGTCTAAAAACTCCATTTTTTATCCCGAACCTTCCAAAAATTACCA
Found at i:10155 original size:29 final size:29
Alignment explanation
Indices: 10120--10221 Score: 84
Period size: 29 Copynumber: 3.4 Consensus size: 29
10110 TCCCGAACCT
*
10120 TCCAAAAATTACCATTTTACCCCCGAAAG
1 TCCAAAAATTACCATTTTACCCCCAAAAG
* *
10149 TCCAAAAATT-CTATTTTTTTA-CCCCAAAATT
1 TCCAAAAATTACCA---TTTTACCCCCAAAA-G
* * *
10180 TCCCAAAATTACCATTTTACCCCTCCAGAG
1 TCCAAAAATTACCATTTTACCCC-CAAAAG
10210 TCC-AAAATTACC
1 TCCAAAAATTACC
10222 GTTATGCCCC
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
28 2 0.03
29 24 0.41
30 13 0.22
31 17 0.29
32 2 0.03
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.30
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCCAAAAG
Found at i:10626 original size:96 final size:96
Alignment explanation
Indices: 10461--10645 Score: 259
Period size: 96 Copynumber: 1.9 Consensus size: 96
10451 AAAACTTTAA
* * ***
10461 AATCGAGGCAATATTTTTTCATTTCGAGTTTCGAAATTTTGTGCCTTAACTTACTAGGTGCATTT
1 AATCGAGGCAATATTTTTTCATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
*
10526 TTTCTTCAAATCGAAATAATCGAATACCTTT
66 TTTCTTCAAATCAAAATAATCGAATACCTTT
*
10557 AATCGAGGCAATGTTTTCTT-ATCTTCGA--TTCTGAAAATTTGCGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAATATTTT-TTCAT-TTCGAGTTTC-GAAAATTTGCGCCTTAACTTACTAGGTGCA
10619 ACCTTTCTTCAAATCAAAATAATCGAA
63 ACCTTTCTTCAAATCAAAATAATCGAA
10646 CATCCTTTTC
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
95 3 0.04
96 69 0.87
97 7 0.09
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (96 bp):
AATCGAGGCAATATTTTTTCATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
TTTCTTCAAATCAAAATAATCGAATACCTTT
Found at i:12570 original size:21 final size:21
Alignment explanation
Indices: 12503--12571 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 21
12493 AAATTTCGAA
* *
12503 TTTTTTA-TTTTTAAAATCAT
1 TTTTTTATTTTTTAATATAAT
* * *
12523 TTTTATTATTTTTT-TTTTCATAC
1 TTTT-TTATTTTTTAATAT-A-AT
12546 TTTTTTATTTTTTAATATAAT
1 TTTTTTATTTTTTAATATAAT
12567 TTTTT
1 TTTTT
12572 AAATTGTTAC
Statistics
Matches: 36, Mismatches: 8, Indels: 9
0.68 0.15 0.17
Matches are distributed among these distances:
20 4 0.11
21 10 0.28
22 15 0.42
23 7 0.19
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTTATTTTTTAATATAAT
Found at i:16836 original size:21 final size:21
Alignment explanation
Indices: 16791--16836 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
16781 AAAATATCTA
* *
16791 AACTGAAAAAATTTAAAACTG
1 AACTCAAAAAATTCAAAACTG
16812 AACTCAAAAAATTCAAAGACT-
1 AACTCAAAAAATTCAAA-ACTG
16833 AACT
1 AACT
16837 TGAATCCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.57, C:0.15, G:0.07, T:0.22
Consensus pattern (21 bp):
AACTCAAAAAATTCAAAACTG
Found at i:17267 original size:23 final size:22
Alignment explanation
Indices: 17227--17271 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
17217 AAAATTATTA
* *
17227 AATATTAAAATAATATAATATG
1 AATATTAAAAAAAAATAATATG
17249 AATATTTAAAAAAAAATAATATG
1 AATA-TTAAAAAAAAATAATATG
17272 GGCTGGTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
AATATTAAAAAAAAATAATATG
Found at i:17766 original size:17 final size:19
Alignment explanation
Indices: 17744--17778 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17734 TTAAAATTTA
17744 AAATAA-TAT-ATATTTTT
1 AAATAATTATAATATTTTT
17761 AAATAATTATAATATTTT
1 AAATAATTATAATATTTT
17779 ATTATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATAATTATAATATTTTT
Found at i:18500 original size:22 final size:22
Alignment explanation
Indices: 18474--18523 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
18464 TTATTAAAAT
*
18474 AAAAAATT-AGAATTACAGGGAC
1 AAAAAATTCA-AATTACAAGGAC
*
18496 CAAAAATTCAAATTACAAGGAC
1 AAAAAATTCAAATTACAAGGAC
18518 AAAAAA
1 AAAAAA
18524 AGACGAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (22 bp):
AAAAAATTCAAATTACAAGGAC
Found at i:25834 original size:18 final size:18
Alignment explanation
Indices: 25775--25854 Score: 63
Period size: 18 Copynumber: 4.3 Consensus size: 18
25765 TTTTTTATAA
25775 TTTTTTAAGTTTT-AATAT
1 TTTTTTAA-TTTTAAATAT
* * **
25793 ATTTTGAGATTTTTTATAT
1 TTTTTTA-ATTTTAAATAT
*
25812 TTTTTTATTTTTAAATAT
1 TTTTTTAATTTTAAATAT
* *
25830 TTTTTCAATTTTAAGTACT
1 TTTTTTAATTTTAAATA-T
25849 TTTTTT
1 TTTTTT
25855 TTAAAATTTT
Statistics
Matches: 47, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
18 31 0.66
19 16 0.34
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTTTAATTTTAAATAT
Found at i:26567 original size:23 final size:23
Alignment explanation
Indices: 26541--26584 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
26531 GAGATTTTTA
26541 TTTAAATATTTTTCTTTTCTTTC
1 TTTAAATATTTTTCTTTTCTTTC
* * *
26564 TTTACATGTTTTTTTTTTCTT
1 TTTAAATATTTTTCTTTTCTT
26585 AGAACTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.14, C:0.11, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTAAATATTTTTCTTTTCTTTC
Found at i:27552 original size:13 final size:13
Alignment explanation
Indices: 27536--27589 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
27526 TTAAGGCCAT
27536 AAATAATTAATTA
1 AAATAATTAATTA
27549 AAATAATATAA-TA
1 AAATAAT-TAATTA
27562 AAAT-ATT-ATTA
1 AAATAATTAATTA
* *
27573 TATTAATTAATTTA
1 AAATAATTAA-TTA
27587 AAA
1 AAA
27590 CGAAATTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
10 1 0.03
11 5 0.16
12 5 0.16
13 14 0.44
14 7 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATAATTAATTA
Found at i:29964 original size:25 final size:25
Alignment explanation
Indices: 29918--29965 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
29908 TAAAACTTTC
*
29918 AAAATATTTATTTAGAATTTTTTGA
1 AAAATATTTATTTAGAAATTTTTGA
29943 AAAATAATTTATTTA-AAATTTTT
1 AAAAT-ATTTATTTAGAAATTTTT
29966 AATTTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (25 bp):
AAAATATTTATTTAGAAATTTTTGA
Found at i:33371 original size:19 final size:20
Alignment explanation
Indices: 33331--33374 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
33321 ATGGTTTTTT
33331 TTTTTCTGAAGTATATAAAA
1 TTTTTCTGAAGTATATAAAA
*
33351 TTTTTCT-AA-TATAATACAA
1 TTTTTCTGAAGTAT-ATAAAA
33370 TTTTT
1 TTTTT
33375 ATTTTTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 12 0.55
20 7 0.32
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (20 bp):
TTTTTCTGAAGTATATAAAA
Found at i:42728 original size:17 final size:16
Alignment explanation
Indices: 42697--42730 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42687 ACTCGAAGCC
*
42697 ATTTCAAAAGCGAAAG
1 ATTTCAAAAGAGAAAG
42713 ATTTCAAAAGAAGAAAG
1 ATTTCAAAAG-AGAAAG
42730 A
1 A
42731 AAAACCTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.56, C:0.09, G:0.18, T:0.18
Consensus pattern (16 bp):
ATTTCAAAAGAGAAAG
Found at i:51692 original size:43 final size:43
Alignment explanation
Indices: 51585--51684 Score: 148
Period size: 43 Copynumber: 2.3 Consensus size: 43
51575 AATTGAAAAG
*
51585 TTTTCCCACAAACGCCGCTAAAGAAAATGGTCTTTAGCGGCAC
1 TTTTCCCACAAACGCCGCTAAAGAAAATGGTCTTTAGAGGCAC
* **
51628 -TTTCCTCACAAACGCCGCTAAAGAACATGGTCTTTAGAGGTGC
1 TTTTCC-CACAAACGCCGCTAAAGAAAATGGTCTTTAGAGGCAC
51671 TTTTCCCACAAACG
1 TTTTCCCACAAACG
51685 TAGCTAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
42 5 0.10
43 41 0.80
44 5 0.10
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
TTTTCCCACAAACGCCGCTAAAGAAAATGGTCTTTAGAGGCAC
Found at i:54920 original size:18 final size:18
Alignment explanation
Indices: 54897--54933 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
54887 GAAGAATGAA
*
54897 ATTAGGGATTTAAAAATG
1 ATTAGGAATTTAAAAATG
*
54915 ATTAGGAATTTAGAAATG
1 ATTAGGAATTTAAAAATG
54933 A
1 A
54934 AAGAGGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (18 bp):
ATTAGGAATTTAAAAATG
Found at i:55115 original size:41 final size:41
Alignment explanation
Indices: 55069--55237 Score: 160
Period size: 41 Copynumber: 4.1 Consensus size: 41
55059 TAATGCTCTA
* ** **
55069 GACCTTTTGCGGCATTTTTCAAATAAACGATGCAATTGCTT
1 GACCTTTAGCGGCATTTTTCCCATAAACGATGTTATTGCTT
* * * * **
55110 TACCTTTTGTGGTATTTTTCCCATAAACGCCGTTATTGCTT
1 GACCTTTAGCGGCATTTTTCCCATAAACGATGTTATTGCTT
* * *
55151 GACCTTTAGCTGCGTTTTTCCCATAAACGTTGTTATTGCTT
1 GACCTTTAGCGGCATTTTTCCCATAAACGATGTTATTGCTT
* * **
55192 GACCTTTAGCGGCATTTTTTCCACAAACG-TCACTATTGCTT
1 GACCTTTAGCGGCATTTTTCCCATAAACGAT-GTTATTGCTT
55233 GACCT
1 GACCT
55238 CTAATTTTCT
Statistics
Matches: 104, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
40 1 0.01
41 103 0.99
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (41 bp):
GACCTTTAGCGGCATTTTTCCCATAAACGATGTTATTGCTT
Found at i:56789 original size:22 final size:22
Alignment explanation
Indices: 56764--56812 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
56754 CATTTCCAAG
56764 TAAT-ATTAA-AAGTATCTTATAC
1 TAATCATTAACAA-TAT-TTATAC
56786 TAATCATTAACAATATTTATAC
1 TAATCATTAACAATATTTATAC
*
56808 CAATC
1 TAATC
56813 GAACTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 14 0.58
23 8 0.33
24 2 0.08
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (22 bp):
TAATCATTAACAATATTTATAC
Found at i:57226 original size:41 final size:41
Alignment explanation
Indices: 57181--57340 Score: 160
Period size: 41 Copynumber: 3.9 Consensus size: 41
57171 GCGGCGTTTT
* *
57181 GCTTCCTCATAAACATCACTAATGCTCTGACCTTTAGCGGC
1 GCTTCCTCATAAACGTCGCTAATGCTCTGACCTTTAGCGGC
* * * * **
57222 GCTTCCCCATAAATGTCGCTAATGCTTTGGCCTTTAGCGAT
1 GCTTCCTCATAAACGTCGCTAATGCTCTGACCTTTAGCGGC
* * * * *
57263 GCTTGCCT-ATAAAGGCCGCTAAAGCTTTGACCTTTAGTGGC
1 GCTT-CCTCATAAACGTCGCTAATGCTCTGACCTTTAGCGGC
* * *
57304 GCTTCCTCATAAGCGTCGCTAATACTCTAACCTTTAG
1 GCTTCCTCATAAACGTCGCTAATGCTCTGACCTTTAG
57341 TGTCGTTTTT
Statistics
Matches: 94, Mismatches: 23, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
40 3 0.03
41 89 0.95
42 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (41 bp):
GCTTCCTCATAAACGTCGCTAATGCTCTGACCTTTAGCGGC
Found at i:66065 original size:15 final size:16
Alignment explanation
Indices: 66045--66087 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
66035 TTGCTGTTAA
66045 AGTTTTAAAGAAC-TG
1 AGTTTTAAAGAACTTG
*
66060 AGTTTT-ATGAACTTG
1 AGTTTTAAAGAACTTG
*
66075 AATTTTAAAGAAC
1 AGTTTTAAAGAAC
66088 AAGAATTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.22
15 13 0.57
16 5 0.22
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (16 bp):
AGTTTTAAAGAACTTG
Found at i:76127 original size:40 final size:40
Alignment explanation
Indices: 76070--76161 Score: 175
Period size: 40 Copynumber: 2.3 Consensus size: 40
76060 CATATAAACT
*
76070 ATCGATTCAAAAGAAGAAGAAGCATTATTCCATCATAACA
1 ATCGATTCAAAAAAAGAAGAAGCATTATTCCATCATAACA
76110 ATCGATTCAAAAAAAGAAGAAGCATTATTCCATCATAACA
1 ATCGATTCAAAAAAAGAAGAAGCATTATTCCATCATAACA
76150 ATCGATTCAAAA
1 ATCGATTCAAAA
76162 GAAGCAGTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (40 bp):
ATCGATTCAAAAAAAGAAGAAGCATTATTCCATCATAACA
Found at i:77706 original size:30 final size:29
Alignment explanation
Indices: 77666--77823 Score: 88
Period size: 30 Copynumber: 5.2 Consensus size: 29
77656 TTAATATAAT
* *
77666 ATTTGGTACTTGAACTTGAAATTTTTT-TTA
1 ATTTGATACTTAAACTT--AATTTTTTATTA
*
77696 ATTTGATACTTAAACTT-TTTTTTTGATTCA
1 ATTTGATACTTAAACTTAATTTTTT-ATT-A
*
77726 ATTTGATACTCAAACTTAACACTTTTTT-TTA
1 ATTTGATACTTAAACTT-A-A-TTTTTTATTA
* * * **
77757 ATTTGGTACGTAAACTTGACTCTTTTTCCTA
1 ATTTGATACTTAAACTT-AAT-TTTTTATTA
* **
77788 ATTTGATACTTAATCTTTTTTTTTTATATTA
1 ATTTGATACTTAAAC-TTAATTTTT-TATTA
77819 ATTTG
1 ATTTG
77824 TTATGCATAA
Statistics
Matches: 99, Mismatches: 18, Indels: 21
0.72 0.13 0.15
Matches are distributed among these distances:
27 6 0.06
29 3 0.03
30 41 0.41
31 39 0.39
32 4 0.04
34 6 0.06
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.54
Consensus pattern (29 bp):
ATTTGATACTTAAACTTAATTTTTTATTA
Found at i:78045 original size:22 final size:21
Alignment explanation
Indices: 78004--78045 Score: 50
Period size: 22 Copynumber: 1.9 Consensus size: 21
77994 ATTGGATCCA
78004 AAAAAATTTAAGTATTAAATTT
1 AAAAAATTTAAG-ATTAAATTT
78026 AAAAAATGTTAA-ATTCAAAT
1 AAAAAAT-TTAAGATT-AAAT
78046 AATAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
21 3 0.17
22 11 0.61
23 4 0.22
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAAAATTTAAGATTAAATTT
Found at i:78103 original size:25 final size:26
Alignment explanation
Indices: 78036--78103 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 26
78026 AAAAAATGTT
* *
78036 AAATTCAAATAATAAATTAAGTAAAA
1 AAATTCAGATATTAAATTAAGTAAAA
* *
78062 AAATTGAGATATCAAATTAA-TAAAA
1 AAATTCAGATATTAAATTAAGTAAAA
*
78087 AAATGTCA-ATTTTAAAT
1 AAAT-TCAGATATTAAAT
78104 ACTAAATGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
25 16 0.47
26 18 0.53
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (26 bp):
AAATTCAGATATTAAATTAAGTAAAA
Found at i:78725 original size:23 final size:24
Alignment explanation
Indices: 78691--78735 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
78681 TCCTTTGTTG
*
78691 CCCTCCGACCCC-CACAATTCCAT
1 CCCTCCGACCCCTCAAAATTCCAT
*
78714 CCCTCCGCCCCCTCAAAATTCC
1 CCCTCCGACCCCTCAAAATTCC
78736 CGAAAATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.20, C:0.58, G:0.04, T:0.18
Consensus pattern (24 bp):
CCCTCCGACCCCTCAAAATTCCAT
Found at i:100344 original size:7 final size:7
Alignment explanation
Indices: 100332--100364 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
100322 TTCTTGTTGG
100332 GCACTGT
1 GCACTGT
100339 GCACTGT
1 GCACTGT
100346 GCACTGT
1 GCACTGT
100353 GCACTGT
1 GCACTGT
100360 GCACT
1 GCACT
100365 AGTGTGGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.30, G:0.27, T:0.27
Consensus pattern (7 bp):
GCACTGT
Done.