Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013821.1 Kokia drynarioides strain JFW-HI SEQ_128849, 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: 41120
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:4485 original size:58 final size:55
Alignment explanation
Indices: 4403--4555 Score: 170
Period size: 55 Copynumber: 2.7 Consensus size: 55
4393 ATATATTATG
*
4403 ATTTTTATT-AATTCATATTTTAATAATAATTATATTAAAA-ATGTTATTAAATTATAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAACATG--ATTAAAATATAT
* *
4460 ACTATTTTATTAAATTGA-ATTTAATAATAATCA-AGTTAAAACATGATTAAAATATTT
1 A-T-TTTTATTAAATT-ATATTTAATAATAATTATA-TTAAAACATGATTAAAATATAT
*
4517 ATTTTTATTAAATTATATTTAATAATAATTTTATTAAAA
1 ATTTTTATTAAATTATATTTAATAATAATTATATTAAAA
4556 TTTAACAACA
Statistics
Matches: 83, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
54 1 0.01
55 31 0.37
56 2 0.02
57 13 0.16
58 20 0.24
59 11 0.13
60 5 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (55 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAACATGATTAAAATATAT
Found at i:4743 original size:16 final size:16
Alignment explanation
Indices: 4722--4781 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
4712 TGAAATATTG
*
4722 ATTACAG-TCTTATTCC
1 ATTACAGCTC-TATTAC
4738 ATTACAGCTCTATTAC
1 ATTACAGCTCTATTAC
*
4754 ATTACAGCTCTATTTC
1 ATTACAGCTCTATTAC
*
4770 ATTACAGTTCTA
1 ATTACAGCTCTA
4782 CTCTATTACA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
16 38 0.95
17 2 0.05
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.42
Consensus pattern (16 bp):
ATTACAGCTCTATTAC
Found at i:4790 original size:32 final size:33
Alignment explanation
Indices: 4722--4793 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 33
4712 TGAAATATTG
*
4722 ATTACAG-TCTTATTCCATTACAGCTCTATTAC
1 ATTACAGCTCTTATTCCATTACAGCTCTACTAC
* *
4754 ATTACAGCTC-TATTTCATTACAGTTCTACT-C
1 ATTACAGCTCTTATTCCATTACAGCTCTACTAC
4785 TATTACAGC
1 -ATTACAGC
4794 GTACCAAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 1 0.03
32 32 0.91
33 2 0.06
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (33 bp):
ATTACAGCTCTTATTCCATTACAGCTCTACTAC
Found at i:5437 original size:25 final size:23
Alignment explanation
Indices: 5392--5437 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
5382 CATAGAGATA
* *
5392 ATGAATAACATTTGTTTATTTTC
1 ATGAATAACATTTGATCATTTTC
5415 ATGAATAATCAATTTGATCATTT
1 ATGAATAA-C-ATTTGATCATTT
5438 CAGTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 1 0.05
25 10 0.53
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (23 bp):
ATGAATAACATTTGATCATTTTC
Found at i:8689 original size:29 final size:28
Alignment explanation
Indices: 8644--8873 Score: 126
Period size: 29 Copynumber: 7.8 Consensus size: 28
8634 AAATGGTAAC
8644 TTTTTGGAAGTGTCGGGGTCAAAAAAGAGA
1 TTTTTGGAAGT-TCGGGGT-AAAAAAGAGA
* **
8674 TTTTTGGAAATTCGGGGGTAAAATGGTA-A
1 TTTTTGGAAGTTC-GGGGTAAAAAAG-AGA
*
8703 TTTTTGGAAGTTTCGAGGTAAAAAATGAGA
1 TTTTTGGAAG-TTCGGGGTAAAAAA-GAGA
*
8733 TTTTTGGAAGTTCGGGGGT-AAAATGTTA-A
1 TTTTTGGAAGTTC-GGGGTAAAAAAG--AGA
* * * *
8762 TTTTAGGAAGTTTCGAGGTTAAAAATGGGA
1 TTTTTGGAAG-TTCG-GGGTAAAAAAGAGA
* ** **
8792 TTTTTGGAAATTTAAGGGTAAAATTGTA-A
1 TTTTTGG-AAGTTCGGGGTAAAAAAG-AGA
* * * *
8821 TTTTAGGAAGTTTCGAGGTCAAAAATGGGA
1 TTTTTGGAAG-TTCGGGGT-AAAAAAGAGA
8851 TTTTTGGAAGTTCGAGGGTAAAA
1 TTTTTGGAAGTTCG-GGGTAAAA
8874 TGGTAATTTT
Statistics
Matches: 154, Mismatches: 28, Indels: 37
0.70 0.13 0.17
Matches are distributed among these distances:
28 3 0.02
29 73 0.47
30 70 0.45
31 8 0.05
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (28 bp):
TTTTTGGAAGTTCGGGGTAAAAAAGAGA
Found at i:8727 original size:59 final size:59
Alignment explanation
Indices: 8631--8893 Score: 355
Period size: 59 Copynumber: 4.4 Consensus size: 59
8621 ACATCTGGGA
* * * *
8631 GTAAAATGGTAACTTTTTGGAAGTGTCGGGGTCAAAAAAGAGATTTTTGGAAATTCGGGG
1 GTAAAATGGTAA-TTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAAATTCGAGG
* * *
8691 GTAAAATGGTAATTTTTGGAAGTTTCGAGGTAAAAAATGAGATTTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAAATTCGAGG
* * * * **
8750 GTAAAATGTTAATTTTAGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAATTTAAGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAAATTCGAGG
* * * *
8809 GTAAAATTGTAATTTTAGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAAATTCGAGG
8868 GTAAAATGGTAATTTTTGGATAGTTT
1 GTAAAATGGTAATTTTTGGA-AGTTT
8894 AGGGAACTCC
Statistics
Matches: 181, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
59 164 0.91
60 17 0.09
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.35
Consensus pattern (59 bp):
GTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAAATTCGAGG
Found at i:9302 original size:11 final size:12
Alignment explanation
Indices: 9275--9303 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
9265 CTAAGTCCAA
9275 TCGGGTCGGATT
1 TCGGGTCGGATT
9287 TCGGGTCGGA-T
1 TCGGGTCGGATT
9298 TCGGGT
1 TCGGGT
9304 AATTACTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.07, C:0.17, G:0.45, T:0.31
Consensus pattern (12 bp):
TCGGGTCGGATT
Found at i:10617 original size:6 final size:6
Alignment explanation
Indices: 10596--10658 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
10586 TTTTGGACTT
* *
10596 TTTAAC TTTGAA TTTAAA TTTAAA -TTAAA TTTAAA TTTAAGA -TT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA
*
10642 TTTAAA -TTCAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
10659 AAAAAAGGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 1 0.02
5 12 0.26
6 33 0.70
7 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:10625 original size:11 final size:12
Alignment explanation
Indices: 10596--10658 Score: 62
Period size: 11 Copynumber: 5.5 Consensus size: 12
10586 TTTTGGACTT
* *
10596 TTTAACTTTGAA
1 TTTAAATTTAAA
10608 TTTAAATTTAAA
1 TTTAAATTTAAA
10620 -TTAAATTTAAA
1 TTTAAATTTAAA
10631 TTTAAGA-TT-AA
1 TTTAA-ATTTAAA
*
10642 TTTAAA-TTCAA
1 TTTAAATTTAAA
10653 TTTAAA
1 TTTAAA
10659 AAAAAAGGCC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
10 3 0.07
11 26 0.57
12 16 0.35
13 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:10628 original size:17 final size:17
Alignment explanation
Indices: 10606--10649 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
10596 TTTAACTTTG
10606 AATTTAAATTTAA-ATT
1 AATTTAAATTTAAGATT
10622 AAATTTAAATTTAAGATT
1 -AATTTAAATTTAAGATT
10640 AATTTAAATT
1 AATTTAAATT
10650 CAATTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 23 0.88
18 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
AATTTAAATTTAAGATT
Found at i:11241 original size:204 final size:202
Alignment explanation
Indices: 10890--11492 Score: 964
Period size: 204 Copynumber: 3.0 Consensus size: 202
10880 GGTTTTATCG
* *
10890 ATTT-GGTCTTCTTCTCAGTAT-TTCATTAGGAAGATGA-CTACATCG--TTTGTTTCAATTCGC
1 ATTTAGGTCTTCTTCTCAGTGTCTT-ATCAGGAAGATGATC-ACATCGCTTTTGTTTCAATTCGC
* *
10950 TTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATAAGGAAGCTAACC
64 TCCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACC
* * *
11015 TTTTATTGCTTCAACCTGCTTCTCATTGTTTCATCAGGAAGCTGAGGTTTGAAGATTTTGCTCGT
129 TTTTATTGCTTCGACCTGCTTCTCAGTGTTTCATCAGGAAGCTG-GGTTCGAAGATTTTGCTCGT
11080 TTTGAGCCTC
193 TTTGAGCCTC
11090 ATTTAGGTCTTCTTCTCAGTGTCTTATCAGGAAGATGATCACATCGCTATTTGTTTCAATTCGCT
1 ATTTAGGTCTTCTTCTCAGTGTCTTATCAGGAAGATGATCACATCGCT-TTTGTTTCAATTCGCT
*
11155 CCTCTGTATCTCATCAGGAAGACAAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCT
65 CCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCT
11220 TTTATTGCTTCGACCTGCTTCTCAGTGTTTCATCAGGAAGCTGGGATTCGAAGATTTTGCTCGTT
130 TTTATTGCTTCGACCTGCTTCTCAGTGTTTCATCAGGAAGCTGGG-TTCGAAGATTTTGCTCGTT
*
11285 TCGAGCCTC
194 TTGAGCCTC
*
11294 ATTTAGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCGCT
1 ATTTAGGTCTTCTTCTCAGTGTCTTATCAGGAAGATGATCACATCGCT-TTTGTTTCAATTCGCT
*
11359 CCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCT
65 CCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCT
* * * * *
11424 TTTATTGCTTCGACCTGCGTCTCAGTGTCTGATCATGAAGCTGGGGTTCGAAGATTTTGCTCGCT
130 TTTATTGCTTCGACCTGCTTCTCAGTGTTTCATCAGGAAGCT-GGGTTCGAAGATTTTGCTCGTT
11489 TTGA
194 TTGA
11493 CCGTGGATTT
Statistics
Matches: 376, Mismatches: 19, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
200 4 0.01
201 34 0.09
202 3 0.01
203 2 0.01
204 330 0.88
205 3 0.01
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (202 bp):
ATTTAGGTCTTCTTCTCAGTGTCTTATCAGGAAGATGATCACATCGCTTTTGTTTCAATTCGCTC
CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTT
TTATTGCTTCGACCTGCTTCTCAGTGTTTCATCAGGAAGCTGGGTTCGAAGATTTTGCTCGTTTT
GAGCCTC
Found at i:19263 original size:59 final size:59
Alignment explanation
Indices: 19170--19549 Score: 483
Period size: 59 Copynumber: 6.4 Consensus size: 59
19160 ACATCTGGGA
* * * * *
19170 GTAAAATGGTAATTTTTAGGAAGTGTCGAGGTCAAAAATGGGATTTTTGGAAATTTGGGG
1 GTAAAATGGTAA-TTTTAGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
*
19230 GTAAAATGGTAATTTTATGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTAGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
* ***
19289 GTAAAATGGTAATTTTAGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTTAGG
1 GTAAAATGGTAATTTTAGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
** * * * * *
19348 GTAAAATGGTAATTTTTTGAAG-GTTCGGGTCAAAAATGAGATTTTTAGAAGTTCGTGG
1 GTAAAATGGTAATTTTAGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
** * * * *
19406 GTAAAATGGTAATTTTTTGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAATTCGGGG
1 GTAAAATGGTAATTTTAGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
* * * *
19465 GTAAAATGGTAATTTTAGGAAGTTTTGGGTTCGAAAATGGGATTTTTGGAAGGTCAGGG
1 GTAAAATGGTAATTTTAGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
*
19524 GTAAAATGGTAATTTTTGGATAGTTT
1 GTAAAATGGTAATTTTAGGA-AGTTT
19550 AGGGACCTTC
Statistics
Matches: 277, Mismatches: 41, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
58 50 0.18
59 210 0.76
60 17 0.06
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (59 bp):
GTAAAATGGTAATTTTAGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
Found at i:19393 original size:176 final size:178
Alignment explanation
Indices: 19170--19540 Score: 552
Period size: 176 Copynumber: 2.1 Consensus size: 178
19160 ACATCTGGGA
* * *
19170 GTAAAATGGTAATTTTTAGGAAGTGTCGAGGTCAAAAATGGGATTTTTGGAAATTTGGGGGTAAA
1 GTAAAATGGTAATTTTTAGGAAGTGTCGAGGTCAAAAATGAGATTTTTAGAAATTCGGGGGTAAA
* * *
19235 ATGGTAATTTTATGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTA
66 ATGGTAATTTTATGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAATTCGGGGGTAAAATGGTA
* *
19300 ATTTTAGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTTA-GG
131 ATTTTAGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAG-GTCAGGG
* * *
19348 GTAAAATGGTAATTTTT-TGAAG-GTTCG-GGTCAAAAATGAGATTTTTAGAAGTTCGTGGGTAA
1 GTAAAATGGTAATTTTTAGGAAGTG-TCGAGGTCAAAAATGAGATTTTTAGAAATTCGGGGGTAA
* *
19410 AATGGTAATTTTTTGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAATTCGGGGGTAAAATGGT
65 AATGGTAATTTTATGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAATTCGGGGGTAAAATGGT
* * *
19475 AATTTTAGGAAGTTTTGGGTTCGAAAATGGGATTTTTGGAAGGTCAGGG
130 AATTTTAGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGGTCAGGG
19524 GTAAAATGGTAATTTTT
1 GTAAAATGGTAATTTTT
19541 GGATAGTTTA
Statistics
Matches: 175, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
175 2 0.01
176 149 0.85
177 7 0.04
178 17 0.10
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (178 bp):
GTAAAATGGTAATTTTTAGGAAGTGTCGAGGTCAAAAATGAGATTTTTAGAAATTCGGGGGTAAA
ATGGTAATTTTATGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAATTCGGGGGTAAAATGGTA
ATTTTAGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGGTCAGGG
Found at i:20596 original size:25 final size:24
Alignment explanation
Indices: 20555--20607 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
20545 GAATACTTTT
20555 TTATTATTAATAATTAAAAAATTTA
1 TTATTATTAATAATT-AAAAATTTA
* * *
20580 TTATTATTATTATTTAAACATTTA
1 TTATTATTAATAATTAAAAATTTA
20604 TTAT
1 TTAT
20608 AAAAAAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TTATTATTAATAATTAAAAATTTA
Found at i:20607 original size:24 final size:25
Alignment explanation
Indices: 20555--20607 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
20545 GAATACTTTT
20555 TTATTATTAATAATTAAAAAATTTA
1 TTATTATTAATAATTAAAAAATTTA
* * *
20580 TTATTATT-ATTATTTAAACATTTA
1 TTATTATTAATAATTAAAAAATTTA
20604 TTAT
1 TTAT
20608 AAAAAAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TTATTATTAATAATTAAAAAATTTA
Found at i:21303 original size:6 final size:6
Alignment explanation
Indices: 21282--21356 Score: 86
Period size: 6 Copynumber: 13.0 Consensus size: 6
21272 TTTTGGACTT
* *
21282 TTTAAC TTTGAA TTTAAA TTTAAA -TTAAA TTTAAA TTTAAGA -TT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA
*
21328 TTTAAA TTCAAA TTTAAA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
21357 AAAAAGGCCC
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
4 1 0.02
5 13 0.22
6 44 0.75
7 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:21314 original size:17 final size:17
Alignment explanation
Indices: 21292--21356 Score: 89
Period size: 17 Copynumber: 3.8 Consensus size: 17
21282 TTTAACTTTG
21292 AATTTAAATTTAAATTA
1 AATTTAAATTTAAATTA
21309 AATTTAAATTTAAGATT-
1 AATTTAAATTTAA-ATTA
*
21326 AATTTAAATTCAAATTTA
1 AATTTAAATTTAAA-TTA
21344 AA-TTAAATTTAAA
1 AATTTAAATTTAAA
21357 AAAAAGGCCC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.02
17 37 0.86
18 5 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
AATTTAAATTTAAATTA
Found at i:21353 original size:23 final size:23
Alignment explanation
Indices: 21292--21356 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 23
21282 TTTAACTTTG
*
21292 AATTTAAATTTAAA-TTAAATTTA
1 AATTTAAA-TTAAATTTAAATTCA
21315 AATTTAAGATT-AATTTAAATTCA
1 AATTTAA-ATTAAATTTAAATTCA
21338 AATTTAAATTAAATTTAAA
1 AATTTAAATTAAATTTAAA
21357 AAAAAGGCCC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
22 5 0.13
23 32 0.84
24 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
AATTTAAATTAAATTTAAATTCA
Found at i:22770 original size:41 final size:41
Alignment explanation
Indices: 22712--23013 Score: 344
Period size: 41 Copynumber: 7.4 Consensus size: 41
22702 TTGAAAAGTA
* *
22712 AAGCATTAGCGGTGCTTATGGGAAAGCGCCGCTAAAGGTC-
1 AAGCATTAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCG
* * *
22752 AGAGCATTAGCGGCGCTTATG-G-GAGCACCGCTAAAAGTCG
1 A-AGCATTAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCG
**
22792 GGGCATTAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCG
1 AAGCATTAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCG
* * * *
22833 AAGCATTAGCGGCACTTAT-AGAACAGCACCGTTAAAAGTCG
1 AAGCATTAGCGGCGCTTATGAGAA-AGCGCCGCTAAAGGTCG
* *
22874 AATCATTAGCAGCGCTTATGAGAAAGCGCCGCTAAAGGTCG
1 AAGCATTAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCG
* * * *
22915 AAGCATTAGCGACGCTTAT-AGAAAAGTGCCGCTAAAAGTCA
1 AAGCATTAGCGGCGCTTATGAG-AAAGCGCCGCTAAAGGTCG
* * *
22956 AAGCATTAACGGCGCTTATGAAAAAGCGCTGCTAAAGGTCG
1 AAGCATTAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCG
* *
22997 AAGCATTTGCGACGCTT
1 AAGCATTAGCGGCGCTT
23014 TCTAATAAAC
Statistics
Matches: 217, Mismatches: 37, Indels: 15
0.81 0.14 0.06
Matches are distributed among these distances:
39 32 0.15
40 9 0.04
41 171 0.79
42 5 0.02
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.20
Consensus pattern (41 bp):
AAGCATTAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCG
Found at i:22897 original size:82 final size:82
Alignment explanation
Indices: 22712--23013 Score: 394
Period size: 82 Copynumber: 3.7 Consensus size: 82
22702 TTGAAAAGTA
* * *
22712 AAGCATTAGCGGTGCTTATGGGAAAGCGCCGCTAAAGGTC-AGAGCATTAGCGGCGCTTAT-G-G
1 AAGCATTAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCGA-AGCATTAGCGGCGCTTATAGAA
*
22774 GAGCACCGCTAAAAGTCG
65 AAGCACCGCTAAAAGTCG
** * *
22792 GGGCATTAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCGAAGCATTAGCGGCACTTATAGAAC
1 AAGCATTAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCGAAGCATTAGCGGCGCTTATAGAAA
*
22857 AGCACCGTTAAAAGTCG
66 AGCACCGCTAAAAGTCG
* * *
22874 AATCATTAGCAGCGCTTATGAGAAAGCGCCGCTAAAGGTCGAAGCATTAGCGACGCTTATAGAAA
1 AAGCATTAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCGAAGCATTAGCGGCGCTTATAGAAA
** *
22939 AGTGCCGCTAAAAGTCA
66 AGCACCGCTAAAAGTCG
* * * * *
22956 AAGCATTAACGGCGCTTATGAAAAAGCGCTGCTAAAGGTCGAAGCATTTGCGACGCTT
1 AAGCATTAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCGAAGCATTAGCGGCGCTT
23014 TCTAATAAAC
Statistics
Matches: 194, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
80 53 0.27
81 2 0.01
82 139 0.72
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.20
Consensus pattern (82 bp):
AAGCATTAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCGAAGCATTAGCGGCGCTTATAGAAA
AGCACCGCTAAAAGTCG
Found at i:27279 original size:43 final size:43
Alignment explanation
Indices: 27226--27439 Score: 277
Period size: 43 Copynumber: 5.0 Consensus size: 43
27216 AGTTTTAGTG
*
27226 GCGTTTGTGGGAAAAGTGCCGCTAAAGACCATGTTCTTTAGCA
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCA
* * * * * * *
27269 GTGTTGGTGGGAAAAACACCGCTAAAGACCATGTTATCTAGCG
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCA
* *
27312 GCGTTTGTGGGAAAAGCGCCGTTAAAGACCATGTTCTTTAGCG
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCA
* *
27355 GCGTTTTTGAGG-TAAGCGCCGCTAAAGACCATGTTCTTTAGCA
1 GCGTTTGTG-GGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCA
* * *
27398 GCGTTTGAGGGAAAAGCGCTGCTAAAGACCATGTTCTATAGC
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGC
27440 GGCATTTTTC
Statistics
Matches: 145, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
42 2 0.01
43 141 0.97
44 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (43 bp):
GCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCA
Found at i:31080 original size:31 final size:30
Alignment explanation
Indices: 31037--31095 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
31027 AGCTTACTCA
31037 CGAACTTTAGTAGCAAAATTCAATCAAAACT
1 CGAACTTTAGTAGCAAAATTCAAT-AAAACT
* * *
31068 CGAATTTTAGTAGTAAAGTTCAATAAAA
1 CGAACTTTAGTAGCAAAATTCAATAAAA
31096 TAAAAGTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.29
Consensus pattern (30 bp):
CGAACTTTAGTAGCAAAATTCAATAAAACT
Found at i:36339 original size:25 final size:24
Alignment explanation
Indices: 36286--36330 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
36276 AGGAAAATTA
36286 TTTTTT-AT-TATAAATAAGAGGC
1 TTTTTTAATATATAAATAAGAGGC
36308 TTTTTTAGATATATAAATAAGAG
1 TTTTTTA-ATATATAAATAAGAG
36331 TTTAGTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
24 2 0.10
25 12 0.60
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.44
Consensus pattern (24 bp):
TTTTTTAATATATAAATAAGAGGC
Found at i:36819 original size:47 final size:47
Alignment explanation
Indices: 36759--36856 Score: 153
Period size: 47 Copynumber: 2.1 Consensus size: 47
36749 ACTCCCCTGT
* * *
36759 TAAATGGTAATAAAAACTAGCGGTGCATTTTCACATTAATCACTCTA
1 TAAATGGTAATAAAAACTAACGGTCCATTTCCACATTAATCACTCTA
*
36806 TAAATGGTAATAAAGACTAACGGTCCATTTCCACATTAATCACTCTA
1 TAAATGGTAATAAAAACTAACGGTCCATTTCCACATTAATCACTCTA
36853 -AAAT
1 TAAAT
36857 TAGGGTAAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
46 4 0.09
47 43 0.91
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (47 bp):
TAAATGGTAATAAAAACTAACGGTCCATTTCCACATTAATCACTCTA
Found at i:38123 original size:19 final size:18
Alignment explanation
Indices: 38087--38126 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
38077 AAAGTAATAG
38087 AAATTTATTTCTTAGAAT
1 AAATTTATTTCTTAGAAT
* *
38105 AAATTCTATTTTTTGGAAT
1 AAATT-TATTTCTTAGAAT
38124 AAA
1 AAA
38127 AATTTCTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (18 bp):
AAATTTATTTCTTAGAAT
Found at i:40886 original size:68 final size:68
Alignment explanation
Indices: 40777--40912 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
40767 GCCTCCTTTT
40777 AGTATGTGACCACCTTCATTTCTTTCTCCTTTTTTTCAATGATTTTTTGTTTTATGGAGTCAACT
1 AGTATGTGACCACCTTCATTTCTTTCTCCTTTTTTTCAATGATTTTTTGTTTTATGGAGTCAACT
40842 TGC
66 TGC
*
40845 AGTATGTGACCATCTTCATTTCTTTCTCCTTTTTTTCAATGATTTTTTGTTTTATGGAGTCAACT
1 AGTATGTGACCACCTTCATTTCTTTCTCCTTTTTTTCAATGATTTTTTGTTTTATGGAGTCAACT
40910 TGC
66 TGC
40913 TTGTCATGCT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (68 bp):
AGTATGTGACCACCTTCATTTCTTTCTCCTTTTTTTCAATGATTTTTTGTTTTATGGAGTCAACT
TGC
Done.