Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010962.1 Kokia drynarioides strain JFW-HI SEQ_125930, 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: 61800
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:194 original size:17 final size:17
Alignment explanation
Indices: 151--196 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
141 TGGTTTCACA
151 TGTCAAGAATTAAAATT
1 TGTCAAGAATTAAAATT
168 TG-CAAG-----AAATT
1 TGTCAAGAATTAAAATT
179 TGTCAAGAATTAAAATT
1 TGTCAAGAATTAAAATT
196 T
1 T
197 TCGAATCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 12
0.66 0.00 0.34
Matches are distributed among these distances:
11 7 0.30
12 4 0.17
16 4 0.17
17 8 0.35
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.35
Consensus pattern (17 bp):
TGTCAAGAATTAAAATT
Found at i:1972 original size:51 final size:49
Alignment explanation
Indices: 1872--1972 Score: 121
Period size: 49 Copynumber: 2.0 Consensus size: 49
1862 AAACAAACTA
* * * *
1872 TGCAAGCAAACTACTTAATCAAAAAGAAATGAAGCAAAACAAACAACAT
1 TGCAAGCAAACTACTAAATAAAAAAAAAATCAAGCAAAACAAACAACAT
* * *
1921 TGCAAGCAAACTACTAAATAAAAAAAAAAATTCAAGCCACAGAAACAACAT
1 TGCAAGCAAACTACTAAAT-AAAAAAAAAA-TCAAGCAAAACAAACAACAT
1972 T
1 T
1973 ATAAAGATGA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 18 0.42
50 8 0.19
51 17 0.40
ACGTcount: A:0.57, C:0.19, G:0.09, T:0.15
Consensus pattern (49 bp):
TGCAAGCAAACTACTAAATAAAAAAAAAATCAAGCAAAACAAACAACAT
Found at i:2610 original size:353 final size:352
Alignment explanation
Indices: 1763--2816 Score: 1629
Period size: 353 Copynumber: 3.0 Consensus size: 352
1753 TCGAATTCGA
* *
1763 GTGGCAGGCAAAGGGAAAAGGCTAGCTTTGTTCAACATATACG-AAGAGTTCCTTCCAAAAGTTA
1 GTGGTAGGCAAA-GGAAAAGGCTAGCTTTGTTCAACAAATACGAAAGAGTTCCTTCCAAAAGTTA
* *
1827 TTAGTAAATAACATCTTGGTCAGTAACGATGG-TTCAAACAAACTATGCAAGCAAACTACTTAAT
65 TTAGTAAATAACATCTTGGTCAGTAACAATGGATTCAAACAAACTATGCAAGCAAACAACTTAAT
* * *
1891 CAAAAAGAAATGAAGCAAAACAAACAACATTGCAAGCAAACTACTAAATAAAAAAAAAAATTCAA
130 CAAAAAGAATTGAAGC-AAACAAACAACATTGCAAGCAAACTACT-AAT-TAAAAAAGAATTCAA
* * * *
1956 GCCACAGAAACAACATTATAAAGATGAGAAAGAGCAACAAAACAATCATACTAGGAAAAATAATC
192 GCCACAAAAACAACATTATAAGGATGAGAAAGA--AATAAAATAATCATACTAGGAAAAATAATC
* *
2021 AACCATCACAAAGAGATATATCGACAGTCGATATTAAAGCATATTTAAAAGATCAGTCTTAAGGG
255 AACCATCACAAA-A-AGATATCGACAGTCGATATTAAAGCCTATTTAAAAGAT-AGTCTTAAGGG
*
2086 ATTTAAACCTAAACAATCTTATCCCTTAACATTGGG
317 ATTTAAATCTAAACAATCTTATCCCTTAACATTGGG
*
2122 GTGGTAGACAAAGGAAAAGGCTAGCTTTGTTCAACAAATACGAAAGAG----TTCCAAAAGTTAT
1 GTGGTAGGCAAAGGAAAAGGCTAGCTTTGTTCAACAAATACGAAAGAGTTCCTTCCAAAAGTTAT
2183 TAGTAAATAACATCTTGGTCAGTAACAATGGATTCAAACAAACTATGCAAGCAAACAACTTAATC
66 TAGTAAATAACATCTTGGTCAGTAACAATGGATTCAAACAAACTATGCAAGCAAACAACTTAATC
*
2248 AAAAAGAATTGAAGCAAACAAACAACATTGCAAGCAAACTACTAATTAAAAAAGAATTCAAGCCC
131 AAAAAGAATTGAAGCAAACAAACAACATTGCAAGCAAACTACTAATTAAAAAAGAATTCAAGCCA
*
2313 CAAAAACAACATTACAAGGATGAGAAAGAAATAAAATAATCATACTAGGAAAAATAATCAACCAT
196 CAAAAACAACATTATAAGGATGAGAAAGAAATAAAATAATCATACTAGGAAAAATAATCAACCAT
2378 CACAAAAAGATATCGACAGTCGATATTAAAGCCTATTTAAAAGAGTAGTCTTAAGGGATTTAAAT
261 CACAAAAAGATATCGACAGTCGATATTAAAGCCTATTTAAAAGA-TAGTCTTAAGGGATTTAAAT
* *
2443 CTAAACAATCTTATTCCTTAAGATTGGG
325 CTAAACAATCTTATCCCTTAACATTGGG
* *
2471 GTGGTAGGCAAAGGAAAAGGCTAGCTTTGTTCAACAAATATGAAAGAGTTCCTTCCAAAAGTTTT
1 GTGGTAGGCAAAGGAAAAGGCTAGCTTTGTTCAACAAATACGAAAGAGTTCCTTCCAAAAGTTAT
* *
2536 TAGTAAATAACATCTAGGTCAGTAACAATGGATTCAAACAAACTATGCAAGCAAAAAACTTAATC
66 TAGTAAATAACATCTTGGTCAGTAACAATGGATTCAAACAAACTATGCAAGCAAACAACTTAATC
* * * *
2601 AAAAAGAATTGAAGCAAACAAACAAAATAGCAAGCAAACTACTAAATAAAAAAGAATTCAAGACA
131 AAAAAGAATTGAAGCAAACAAACAACATTGCAAGCAAACTACTAATTAAAAAAGAATTCAAGCCA
* * * * *
2666 CAAAAACAACATTATAAGGATGAGAAAGGGTAATAAAATGATCTTACTAGGAAAAACATTCAACC
196 CAAAAACAACATTATAAGGATGAGAAA--GAAATAAAATAATCATACTAGGAAAAATAATCAACC
* *
2731 ATCACAAAGAGATATCGACATTCGATATTAAAGCC-ATTTAAAAGATTAGTCTTAAGGGATTTAA
259 ATCACAAAAAGATATCGACAGTCGATATTAAAGCCTATTTAAAAGA-TAGTCTTAAGGGATTTAA
2795 ATCTAAACAATCTT-TCCCTTAA
323 ATCTAAACAATCTTATCCCTTAA
2817 TTATAAATAA
Statistics
Matches: 647, Mismatches: 39, Indels: 24
0.91 0.05 0.03
Matches are distributed among these distances:
349 125 0.19
350 2 0.00
351 40 0.06
353 210 0.32
354 45 0.07
355 135 0.21
356 46 0.07
358 29 0.04
359 15 0.02
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.23
Consensus pattern (352 bp):
GTGGTAGGCAAAGGAAAAGGCTAGCTTTGTTCAACAAATACGAAAGAGTTCCTTCCAAAAGTTAT
TAGTAAATAACATCTTGGTCAGTAACAATGGATTCAAACAAACTATGCAAGCAAACAACTTAATC
AAAAAGAATTGAAGCAAACAAACAACATTGCAAGCAAACTACTAATTAAAAAAGAATTCAAGCCA
CAAAAACAACATTATAAGGATGAGAAAGAAATAAAATAATCATACTAGGAAAAATAATCAACCAT
CACAAAAAGATATCGACAGTCGATATTAAAGCCTATTTAAAAGATAGTCTTAAGGGATTTAAATC
TAAACAATCTTATCCCTTAACATTGGG
Found at i:4298 original size:409 final size:406
Alignment explanation
Indices: 3540--4358 Score: 1548
Period size: 409 Copynumber: 2.0 Consensus size: 406
3530 TTAAAAAAAA
** *
3540 AACTATCATTTATTGTACCTGAGAGACCAGCCTGTTGAGATTAGTGTAAGCAGGCCTCTCAATAT
1 AACTATCATTTATTGTACCCAAGAGACCAGCCTGTTGAGATTAGTGTAAGCAGGCCTCACAATAT
3605 TACTTAGAGATCTGACGGTTGGAGAAAGAAAAAACACTAATTACTTACTTGTGTAGTGGCCTCTG
66 TACTTAGAGATCTGACGGTTGGAGAAAGAAAAAACACTAATTACTTACTTGTGTAGTGGCCTCTG
* *
3670 GCAAAGTTATTTGTAGCATCTTCTTTGCCCCTAATAATCTGTTCTGGGTGGAATAATTGATTTCC
131 GCAAAGTTATTTGTAGCATCTTCTTTGCCCCTAATAAGCTGCTCTGGGTGGAATAATTGATTTCC
3735 AGCGCCGGTTTCACTGAAAAAGGTGTTGAAAGCATCATCTCCACCTGCGACTGTTTTGTCACCCA
196 AGCGCCGGTTTCACTGAAAAAGGTGTTGAAAGCATCATCTCCACCTGCGACTGTTTTGTCACCCA
3800 TCATTTGTCCATCAGGCTACTTCCGAAAACAAGAAAGAAGATTAAATACCCAACTTGAAGGAAAT
261 TCATTTGTCCATCAGGCTACTTCCGAAAACAAGAAAGAAGATTAAATACCCAACTTGAAGGAAAT
3865 ATTGAGTTAATATGGTAAAAAGAACACAAAAAAAAAAACTGAATGCCATGTTCAAGACAGTAGAG
326 ATTGAGTTAATATGGTAAAAAGAACAC--AAAAAAAAACTGAATGCCATGTTCAAGACAGTAGAG
*
3930 TTCCTAACAGACGTTACC
389 TTCCCAACAGACGTTACC
3948 AACTATCATTTATTGTACCCAAGAGACCAGCCTGTTGAGATTAGTGTAAGCAGGCCTCACAATAT
1 AACTATCATTTATTGTACCCAAGAGACCAGCCTGTTGAGATTAGTGTAAGCAGGCCTCACAATAT
4013 TACTTAGAGATCTGACGGTTGGAGAAAGAAAAAAACACTAATTACTTACTTGTGTAGTGGCCTCT
66 TACTTAGAGATCTGACGGTTGGAGAAAG-AAAAAACACTAATTACTTACTTGTGTAGTGGCCTCT
4078 GGCAAAGTTATTTGTAGCATCTTCTTTGCCCCTAATAAGCTGCTCTGGGTGGAATAATTGATTTC
130 GGCAAAGTTATTTGTAGCATCTTCTTTGCCCCTAATAAGCTGCTCTGGGTGGAATAATTGATTTC
4143 CAGCGCCGGTTTCACTGAAAAAGGTGTTGAAAGCATCATCTCCACCTGCGACTGTTTTGTCACCC
195 CAGCGCCGGTTTCACTGAAAAAGGTGTTGAAAGCATCATCTCCACCTGCGACTGTTTTGTCACCC
4208 ATCATTTGTCCATCAGGCTACTTCCGAAAACAAGAAAGAAGATTAAATACCCAACTTGAAGGAAA
260 ATCATTTGTCCATCAGGCTACTTCCGAAAACAAGAAAGAAGATTAAATACCCAACTTGAAGGAAA
*
4273 TATTGAGTTAATATGGTAAAAAGAACACAAAAAAAACCTGAATGCCATGTTCAAGACAGTAGAGT
325 TATTGAGTTAATATGGTAAAAAGAACACAAAAAAAAACTGAATGCCATGTTCAAGACAGTAGAGT
4338 TCCCAACAGACGTTACC
390 TCCCAACAGACGTTACC
4355 AACT
1 AACT
4359 TAGATACCAG
Statistics
Matches: 403, Mismatches: 7, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
407 56 0.14
408 90 0.22
409 257 0.64
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (406 bp):
AACTATCATTTATTGTACCCAAGAGACCAGCCTGTTGAGATTAGTGTAAGCAGGCCTCACAATAT
TACTTAGAGATCTGACGGTTGGAGAAAGAAAAAACACTAATTACTTACTTGTGTAGTGGCCTCTG
GCAAAGTTATTTGTAGCATCTTCTTTGCCCCTAATAAGCTGCTCTGGGTGGAATAATTGATTTCC
AGCGCCGGTTTCACTGAAAAAGGTGTTGAAAGCATCATCTCCACCTGCGACTGTTTTGTCACCCA
TCATTTGTCCATCAGGCTACTTCCGAAAACAAGAAAGAAGATTAAATACCCAACTTGAAGGAAAT
ATTGAGTTAATATGGTAAAAAGAACACAAAAAAAAACTGAATGCCATGTTCAAGACAGTAGAGTT
CCCAACAGACGTTACC
Found at i:4517 original size:67 final size:68
Alignment explanation
Indices: 4409--4556 Score: 262
Period size: 69 Copynumber: 2.2 Consensus size: 68
4399 AAGAAGGAGA
*
4409 TAACCGTTGGAGCGTTTGAAAACTTAAAATTTGAAT-AAAAAAATAAAAGTAACCGTTGGAGTGA
1 TAACCGTTGGAGCGTCTGAAAACTTAAAATTTGAATAAAAAAAATAAAAGTAACCGTTGGAGTGA
4473 AAG
66 AAG
4476 TAACCGTTGGAGCGTCTGAAAACTTAAAATTTGAATAAAAAAAAATAAAAGTAACCGTTGGAGTG
1 TAACCGTTGGAGCGTCTGAAAACTTAAAATTTGAAT-AAAAAAAATAAAAGTAACCGTTGGAGTG
*
4541 TAAG
65 AAAG
4545 TAACCGTTGGAG
1 TAACCGTTGGAG
4557 TGTAAGTAAC
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
67 35 0.45
69 42 0.55
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (68 bp):
TAACCGTTGGAGCGTCTGAAAACTTAAAATTTGAATAAAAAAAATAAAAGTAACCGTTGGAGTGA
AAG
Found at i:4547 original size:18 final size:18
Alignment explanation
Indices: 4524--4574 Score: 102
Period size: 18 Copynumber: 2.8 Consensus size: 18
4514 AAAAAAATAA
4524 AAGTAACCGTTGGAGTGT
1 AAGTAACCGTTGGAGTGT
4542 AAGTAACCGTTGGAGTGT
1 AAGTAACCGTTGGAGTGT
4560 AAGTAACCGTTGGAG
1 AAGTAACCGTTGGAG
4575 CATTTGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.25
Consensus pattern (18 bp):
AAGTAACCGTTGGAGTGT
Found at i:4552 original size:87 final size:89
Alignment explanation
Indices: 4455--4625 Score: 274
Period size: 87 Copynumber: 1.9 Consensus size: 89
4445 AAAAAAATAA
*
4455 AAGTAACCGTTGGAGTGAAAGTAACCGTTGGAGCGTCTGAAAACTTAAAATTTGAATAAAAA-AA
1 AAGTAACCGTTGGAGTGAAAGTAACCGTTGGAGCATCTGAAAACTTAAAATTTGAATAAAAAGAA
*
4519 AATAA-AAGTAACCGTTGGAGTGT
66 AAAAAGAAGTAACCGTTGGAGTGT
* * *
4542 AAGTAACCGTTGGAGTGTAAGTAACCGTTGGAGCATTTGAAAACTTAAATTTTGAATAAAAAGGA
1 AAGTAACCGTTGGAGTGAAAGTAACCGTTGGAGCATCTGAAAACTTAAAATTTGAATAAAAA-GA
4607 AAAAAAGAAGTAACCGTTG
65 AAAAAAGAAGTAACCGTTG
4626 TAGCGTTTGA
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
87 58 0.76
89 6 0.08
90 12 0.16
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.25
Consensus pattern (89 bp):
AAGTAACCGTTGGAGTGAAAGTAACCGTTGGAGCATCTGAAAACTTAAAATTTGAATAAAAAGAA
AAAAAGAAGTAACCGTTGGAGTGT
Found at i:4721 original size:55 final size:52
Alignment explanation
Indices: 4560--4722 Score: 220
Period size: 54 Copynumber: 3.0 Consensus size: 52
4550 GTTGGAGTGT
* *
4560 AAGTAACCGTTGGAGCATTTGAAAACTTAAATTTTGAATAAAAAGGAAAAAAA
1 AAGTAACCGTTGGAGCGTTTGAAAACTTAAATTTTGAATAAAAA-GAAAATAA
*
4613 GAAGTAACCGTTGTAGCGTTTGAAAACTTAAAATTTT-AATAAAAAGAAAATAA
1 -AAGTAACCGTTGGAGCGTTTGAAAACTT-AAATTTTGAATAAAAAGAAAATAA
* *
4666 AAGTAACCGTTGGAGAGCGTTTGAAAATTTAAACTTTTGAATAAAAAGAAGATAA
1 AAGTAACCGTT-G-GAGCGTTTGAAAACTTAAA-TTTTGAATAAAAAGAAAATAA
4721 AA
1 AA
4723 ATACTAAAAT
Statistics
Matches: 98, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
52 11 0.11
53 11 0.11
54 52 0.53
55 24 0.24
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.26
Consensus pattern (52 bp):
AAGTAACCGTTGGAGCGTTTGAAAACTTAAATTTTGAATAAAAAGAAAATAA
Found at i:5574 original size:25 final size:24
Alignment explanation
Indices: 5546--5594 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
5536 AAATTTCAAA
* *
5546 TTAAATTTAAAAAAGATTAAAATAT
1 TTAAAATTAAAAAAGA-AAAAATAT
*
5571 TTAAAATTATAAAAGAAAAAATAT
1 TTAAAATTAAAAAAGAAAAAATAT
5595 GTTTGTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
TTAAAATTAAAAAAGAAAAAATAT
Found at i:7602 original size:52 final size:52
Alignment explanation
Indices: 7539--7731 Score: 251
Period size: 52 Copynumber: 3.7 Consensus size: 52
7529 ATAAACAAAG
*
7539 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTATGGATTAAA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAA
* * * * * *
7591 AGGTCCAATGACTAAGTGTCATTGTGAGTATATGGATCCTTTACGGATTAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAA
* * * * ** *
7643 AGGTCCGATGACTCTATGTCATCGTGAGTATACGAATCCCTCGTGGATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAA
*
7695 AGGTCCGATGGCTATGTGTCATCGTGAGTATATGAAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT
7732 GAAGTGAAAT
Statistics
Matches: 117, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 117 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAA
Found at i:7716 original size:104 final size:104
Alignment explanation
Indices: 7536--7728 Score: 278
Period size: 104 Copynumber: 1.9 Consensus size: 104
7526 GCCATAAACA
* * * *
7536 AAGAGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTATGGATTAAAAGGTCCAATG
1 AAGAGGTCCGATGACTATATGTCATCATGAGTATACGAATCCCTCATGGATTAAAAGGTCCAATG
*
7601 ACTAAGTGTCATTGTGAGTATATGGATCCTTTACGGATT
66 ACTAAGTGTCATCGTGAGTATATGGATCCTTTACGGATT
* * * * *
7640 AAGAGGTCCGATGACTCTATGTCATCGTGAGTATACGAATCCCTCGTGGATTATAAGGTCCGATG
1 AAGAGGTCCGATGACTATATGTCATCATGAGTATACGAATCCCTCATGGATTAAAAGGTCCAATG
* *
7705 GCTATGTGTCATCGTGAGTATATG
66 ACTAAGTGTCATCGTGAGTATATG
7729 AATGAAGTGA
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
104 77 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (104 bp):
AAGAGGTCCGATGACTATATGTCATCATGAGTATACGAATCCCTCATGGATTAAAAGGTCCAATG
ACTAAGTGTCATCGTGAGTATATGGATCCTTTACGGATT
Found at i:9545 original size:2 final size:2
Alignment explanation
Indices: 9538--9562 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9528 CCATACATTC
9538 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
9563 GTCTATAATT
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:10852 original size:18 final size:18
Alignment explanation
Indices: 10811--10846 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
10801 CTTGGTTCAC
10811 TTGGTTTAGATGTTGGGT
1 TTGGTTTAGATGTTGGGT
10829 TTGGTTTA-AT-TTGGGT
1 TTGGTTTAGATGTTGGGT
10845 TT
1 TT
10847 AGGGTTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 2 0.11
18 8 0.44
ACGTcount: A:0.11, C:0.00, G:0.33, T:0.56
Consensus pattern (18 bp):
TTGGTTTAGATGTTGGGT
Found at i:21955 original size:22 final size:22
Alignment explanation
Indices: 21902--21966 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
21892 GTAACAATAT
*
21902 AATAACAAAATGACAACAAAAC
1 AATAACAAAATGACAGCAAAAC
* **
21924 AACAGTAAAATGACAGCAAAAC
1 AATAACAAAATGACAGCAAAAC
* **
21946 AGTAACAAAACAACAGCAAAA
1 AATAACAAAATGACAGCAAAA
21967 AAAAATTTAA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.65, C:0.18, G:0.09, T:0.08
Consensus pattern (22 bp):
AATAACAAAATGACAGCAAAAC
Found at i:27654 original size:4 final size:4
Alignment explanation
Indices: 27645--27670 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
27635 TAACACTCCT
27645 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
27671 GTATATATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:28603 original size:10 final size:10
Alignment explanation
Indices: 28590--28627 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
28580 CTTTTTGTAT
28590 TTTTTAAATA
1 TTTTTAAATA
28600 TTTTTAAATA
1 TTTTTAAATA
28610 -TTTTAAATTA
1 TTTTTAAA-TA
28620 TTTGTTAA
1 TTT-TTAA
28628 CATGGTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 7 0.28
10 12 0.48
11 2 0.08
12 4 0.16
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:29421 original size:21 final size:22
Alignment explanation
Indices: 29397--29446 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
29387 TTGTTTATCC
*
29397 ATATTATATATT-ATAAAAATA
1 ATATTATATATTCATAAAAAAA
*
29418 ATATAAT-TATTCATAAAAAAA
1 ATATTATATATTCATAAAAAAA
29439 ATATTATA
1 ATATTATA
29447 ATTTTTTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATTATATATTCATAAAAAAA
Found at i:30951 original size:2 final size:2
Alignment explanation
Indices: 30946--30975 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30936 GTGTTTTTTA
30946 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
30976 TATCAATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32222 original size:374 final size:374
Alignment explanation
Indices: 31533--32262 Score: 1343
Period size: 374 Copynumber: 2.0 Consensus size: 374
31523 TCTTCCTCTT
31533 CGATGTCGTAGCTCCGACATTGACATCATCACCAGTTTTTATCTGTTCTTCTACCCGTCGGTGGC
1 CGATGTCGTAGCTCCGACATTGACATCATCACCAGTTTTTATCTGTTCTTCTACCCGTCGGTGGC
* *
31598 CACCATTCCAACGTCGTGATCTCTCAAAATTGCTTTGGATGTCTCCAAGTTCGTGGTTTGCCGAA
66 CACCATTCCAACGTCATGATCTCTCAAAATTGCTTTGGATGTCTCCAAGTCCGTGGTTTGCCGAA
31663 GGTGAGTGCTTTTTATAGTTGTTTTGGTTGTAATATGGTTTGGCTTGAGTCGGGTGGGGTAGTAG
131 GGTGAGTGCTTTTTATAGTTGTTTTGGTTGTAATATGGTTTGGCTTGAGTCGGGTGGGGTAGTAG
* *
31728 TGGGACAGGAAATTTGGATCATAGAGTCAAATTTTGGAAAATAACTCAAAGAAAAGGTAAATGAA
196 CGGGACAGGAAATTTGGATCATAGAGTCAAATTTTGGAAAATAACTAAAAGAAAAGGTAAATGAA
*
31793 ATGAATTTCAATAGTTTGTACACTTTTCACAATTGCCCACAATGTTTTATCATATATTAAAATCA
261 ATAAATTTCAATAGTTTGTACACTTTTCACAATTGCCCACAATGTTTTATCATATATTAAAATCA
31858 TTGAATTATCTTCGCTCTGCAATATTGTAAAATTTTAACGGATAACGGA
326 TTGAATTATCTTCGCTCTGCAATATTGTAAAATTTTAACGGATAACGGA
*
31907 CGATGTCGTAGCTCCGACATTGACATCATCGCCAGTTTTTATCTGTTCTTCTACCCGTCGGTGGC
1 CGATGTCGTAGCTCCGACATTGACATCATCACCAGTTTTTATCTGTTCTTCTACCCGTCGGTGGC
*
31972 CACCATTCCAACGTCATGATCTCTCAAATTTGCTTTGGATGTCTCCAAGTCCGTGGTTTGCCGAA
66 CACCATTCCAACGTCATGATCTCTCAAAATTGCTTTGGATGTCTCCAAGTCCGTGGTTTGCCGAA
*
32037 GGTGAGTGCTTTTTATAGTTGTTTTGGTTGTAATATGGTTTGGCTTGAGTTGGGTGGGGTAGTAG
131 GGTGAGTGCTTTTTATAGTTGTTTTGGTTGTAATATGGTTTGGCTTGAGTCGGGTGGGGTAGTAG
*
32102 CGGGTCAGGAAATTTGGATCATAGAGTCAAATTTTGGAAAATAACTAAAAGAAAAGGTAAATGAA
196 CGGGACAGGAAATTTGGATCATAGAGTCAAATTTTGGAAAATAACTAAAAGAAAAGGTAAATGAA
* * *
32167 GTAAATTTCAATAGTTTGTACATTTTTCACAATTGCCCACAATGTTTTCTCATATATTAAAATCA
261 ATAAATTTCAATAGTTTGTACACTTTTCACAATTGCCCACAATGTTTTATCATATATTAAAATCA
*
32232 TTGAATTATCTTCGCTCTGTAATATTGTAAA
326 TTGAATTATCTTCGCTCTGCAATATTGTAAA
32263 CTCGGATAAC
Statistics
Matches: 343, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
374 343 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (374 bp):
CGATGTCGTAGCTCCGACATTGACATCATCACCAGTTTTTATCTGTTCTTCTACCCGTCGGTGGC
CACCATTCCAACGTCATGATCTCTCAAAATTGCTTTGGATGTCTCCAAGTCCGTGGTTTGCCGAA
GGTGAGTGCTTTTTATAGTTGTTTTGGTTGTAATATGGTTTGGCTTGAGTCGGGTGGGGTAGTAG
CGGGACAGGAAATTTGGATCATAGAGTCAAATTTTGGAAAATAACTAAAAGAAAAGGTAAATGAA
ATAAATTTCAATAGTTTGTACACTTTTCACAATTGCCCACAATGTTTTATCATATATTAAAATCA
TTGAATTATCTTCGCTCTGCAATATTGTAAAATTTTAACGGATAACGGA
Found at i:33393 original size:20 final size:20
Alignment explanation
Indices: 33357--33394 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33347 CCAGAGCAAA
* *
33357 CTTCCCCTTCTCTCTTCCCT
1 CTTCCCCTTCCCCCTTCCCT
33377 CTTCCCCTTCCCCCTTCC
1 CTTCCCCTTCCCCCTTCC
33395 TTGCCAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (20 bp):
CTTCCCCTTCCCCCTTCCCT
Found at i:33536 original size:13 final size:13
Alignment explanation
Indices: 33518--33548 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
33508 CCAGATCAAA
*
33518 CTTCCCCTTCCCT
1 CTTCCCCTTCCCC
33531 CTTCCCCTTCCCC
1 CTTCCCCTTCCCC
33544 CTTCC
1 CTTCC
33549 TTGCCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (13 bp):
CTTCCCCTTCCCC
Found at i:38852 original size:52 final size:52
Alignment explanation
Indices: 38771--38954 Score: 244
Period size: 52 Copynumber: 3.5 Consensus size: 52
38761 ATTTCATTTA
* * * *
38771 ATACTCACGACGACACATAGTCATTGGACCTCTTGTTCCGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCTTATTCCGTAAAGGATTCAT
* * *
38823 ACACTCACGATGACACATAGTTATCGGACCTCATAATT-CGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTC-TTATTCCGTAAAGGATTCAT
* * * * *
38875 ATACTCATGATGACACAGAATCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCTTATTCCGTAAAGGATTCAT
38927 ATACTCACGATGACACATAGTCATCGGA
1 ATACTCACGATGACACATAGTCATCGGA
38955 TCTTAGTCAT
Statistics
Matches: 112, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
51 2 0.02
52 107 0.96
53 3 0.03
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCTTATTCCGTAAAGGATTCAT
Found at i:40263 original size:12 final size:13
Alignment explanation
Indices: 40237--40266 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
40227 TCGGACCCGT
40237 AAATATTTAATGA
1 AAATATTTAATGA
40250 AAATATTT-ATGA
1 AAATATTTAATGA
40262 AAATA
1 AAATA
40267 AATCATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
AAATATTTAATGA
Found at i:43045 original size:21 final size:21
Alignment explanation
Indices: 43019--43069 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
43009 TGGAGTTTGA
43019 TAAGTTCAAGCTTGAAATTGG
1 TAAGTTCAAGCTTGAAATTGG
* *
43040 TAAGTTCAAGTTTGAATTTGG
1 TAAGTTCAAGCTTGAAATTGG
43061 TAAGTTCAA
1 TAAGTTCAA
43070 TCAAGTCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (21 bp):
TAAGTTCAAGCTTGAAATTGG
Found at i:44903 original size:20 final size:21
Alignment explanation
Indices: 44865--44903 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44855 GGAACTTATA
*
44865 GTTTCGGTAGATGGATAGGAT
1 GTTTCGATAGATGGATAGGAT
44886 GTTTCGATAGAT-GATAGG
1 GTTTCGATAGATGGATAGG
44904 GGTTGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.26, C:0.05, G:0.36, T:0.33
Consensus pattern (21 bp):
GTTTCGATAGATGGATAGGAT
Found at i:46021 original size:27 final size:27
Alignment explanation
Indices: 45969--46025 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
45959 TAATTCTAAA
* ** *
45969 AATTTTCATGAAATGTTTTTTGAATAT
1 AATTTTCAAGAAATGTTTGATAAATAT
45996 AATTTTCAAGAAATGTTTGATAAATAT
1 AATTTTCAAGAAATGTTTGATAAATAT
46023 AAT
1 AAT
46026 AAATAAAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.46
Consensus pattern (27 bp):
AATTTTCAAGAAATGTTTGATAAATAT
Found at i:47917 original size:16 final size:18
Alignment explanation
Indices: 47899--47931 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
47889 ACTTTAAAAA
47899 TTTTAAA-AAATAAATAT
1 TTTTAAAGAAATAAATAT
47916 TTTTAAAGAAA-AAATA
1 TTTTAAAGAAATAAATA
47932 AATAATTGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TTTTAAAGAAATAAATAT
Found at i:50334 original size:18 final size:18
Alignment explanation
Indices: 50311--50348 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
50301 GTAATAAAGT
50311 ATGCATAATAAA-ATTAAA
1 ATGCATAA-AAATATTAAA
50329 ATGCATAAAAATATTAAA
1 ATGCATAAAAATATTAAA
50347 AT
1 AT
50349 AAACTTTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (18 bp):
ATGCATAAAAATATTAAA
Found at i:51832 original size:17 final size:19
Alignment explanation
Indices: 51810--51855 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
51800 ATATTACGTC
51810 AATAAATA-ATTAAAAA-A
1 AATAAATATATTAAAAACA
*
51827 AATAAACATATTAAAAACA
1 AATAAATATATTAAAAACA
*
51846 AAAAAATATA
1 AATAAATATA
51856 AAAAATCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 7 0.29
18 8 0.33
19 9 0.38
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (19 bp):
AATAAATATATTAAAAACA
Found at i:51860 original size:10 final size:9
Alignment explanation
Indices: 51811--51878 Score: 61
Period size: 9 Copynumber: 7.8 Consensus size: 9
51801 TATTACGTCA
*
51811 ATAAATAAT
1 ATAAAAAAT
*
51820 -TAAAAAAA
1 ATAAAAAAT
*
51828 AT-AAACAT
1 ATAAAAAAT
* *
51836 ATTAAAAAC
1 ATAAAAAAT
51845 A-AAAAAAT
1 ATAAAAAAT
51853 ATAAAAAAT
1 ATAAAAAAT
51862 CATAAAAAAT
1 -ATAAAAAAT
51872 ATAAAAA
1 ATAAAAA
51879 TAACATGAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
8 18 0.38
9 20 0.43
10 9 0.19
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:51870 original size:19 final size:17
Alignment explanation
Indices: 51820--51878 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
51810 AATAAATAAT
*
51820 TAAAAAA-AATAAACATA
1 TAAAAAACAA-AAAAATA
*
51837 TTAAAAACAAAAAAATA
1 TAAAAAACAAAAAAATA
51854 TAAAAAATCATAAAAAATA
1 TAAAAAA-CA-AAAAAATA
51873 TAAAAA
1 TAAAAA
51879 TAACATGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 18 0.50
18 4 0.11
19 14 0.39
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (17 bp):
TAAAAAACAAAAAAATA
Found at i:61603 original size:19 final size:20
Alignment explanation
Indices: 61561--61602 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
61551 TTATTGTATG
61561 AAACGAGCCATTTTAAAAAA
1 AAACGAGCCATTTTAAAAAA
61581 AAACGAGCCATTTTAAAAAA
1 AAACGAGCCATTTTAAAAAA
61601 AA
1 AA
61603 CAAAATTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.14, G:0.10, T:0.19
Consensus pattern (20 bp):
AAACGAGCCATTTTAAAAAA
Done.