Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013845.1 Kokia drynarioides strain JFW-HI SEQ_128873, 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: 54051
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:597 original size:59 final size:57
Alignment explanation
Indices: 534--751 Score: 208
Period size: 59 Copynumber: 3.7 Consensus size: 57
524 AAAATGATAA
* * * * *
534 TTTTGGATTCTCGGGGGTGAAACGGTAATTTTGGGAAAATTT-GAGGTTAAAAATGGGAT
1 TTTTGGATT-TCGGGGGTAAAATGG-GATTTTTGG-AAGTTTCGAGGTTAAAAATGGGAT
* *
593 TTTTGAAAGTTT-GGGGG-AAAATGGGATTTTTGGAAGTTTCGAGGTCAAAAATGGGAT
1 TTTTG-GA-TTTCGGGGGTAAAATGGGATTTTTGGAAGTTTCGAGGTTAAAAATGGGAT
* *
650 TTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGTTAAAAATGGGAT
1 TTTTGG-ATTTCGGGGGT-AAAATGGGATTTTTGGAAGTTTCGAGGTTAAAAATGGGAT
* **
709 TTTTGGAAGTTCGGGGGGTAAAAATTAGATTTTTGGACAGTTT
1 TTTTGG-ATTTC-GGGGGT-AAAATGGGATTTTTGGA-AGTTT
752 AGGGACCTTC
Statistics
Matches: 137, Mismatches: 13, Indels: 16
0.83 0.08 0.10
Matches are distributed among these distances:
56 7 0.05
57 34 0.25
58 5 0.04
59 60 0.44
60 24 0.18
61 7 0.05
ACGTcount: A:0.28, C:0.04, G:0.33, T:0.35
Consensus pattern (57 bp):
TTTTGGATTTCGGGGGTAAAATGGGATTTTTGGAAGTTTCGAGGTTAAAAATGGGAT
Found at i:646 original size:30 final size:30
Alignment explanation
Indices: 576--751 Score: 200
Period size: 30 Copynumber: 6.0 Consensus size: 30
566 GGGAAAATTT
*
576 GAGGTTAAAAATGGGATTTTTGAAAGTTT-
1 GAGGTTAAAAATGGGATTTTTGGAAGTTTC
**
605 G-GG-GGAAAATGGGATTTTTGGAAGTTTC
1 GAGGTTAAAAATGGGATTTTTGGAAGTTTC
*
633 GAGGTCAAAAATGGGATTTTTGGAAG-TTC
1 GAGGTTAAAAATGGGATTTTTGGAAGTTTC
* *
662 GGGGGTAAAAATGGGATTTTTGGAAGTTTC
1 GAGGTTAAAAATGGGATTTTTGGAAGTTTC
*
692 GGGGTTAAAAATGGGATTTTTGGAAG-TTC
1 GAGGTTAAAAATGGGATTTTTGGAAGTTTC
* * **
721 GGGGGGTAAAAATTAGATTTTTGGACAGTTT
1 -GAGGTTAAAAATGGGATTTTTGGA-AGTTT
752 AGGGACCTTC
Statistics
Matches: 128, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
27 21 0.16
28 3 0.02
29 32 0.25
30 68 0.53
31 2 0.02
32 2 0.02
ACGTcount: A:0.29, C:0.03, G:0.34, T:0.34
Consensus pattern (30 bp):
GAGGTTAAAAATGGGATTTTTGGAAGTTTC
Found at i:2691 original size:6 final size:6
Alignment explanation
Indices: 2677--2725 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
2667 ATTTGGAAAA
* *
2677 TAAATT TAAACT TAAA-T TAAATT TAAATT CGAAA-- TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT TAAATT
2723 TAA
1 TAA
2726 TATAATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
4 3 0.08
5 5 0.14
6 25 0.69
7 3 0.08
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:2699 original size:17 final size:16
Alignment explanation
Indices: 2677--2737 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 16
2667 ATTTGGAAAA
2677 TAAATTTAAACTTAAAT
1 TAAATTTAAA-TTAAAT
2694 TAAATTTAAATTCGAAA-
1 TAAATTTAAATT--AAAT
*
2711 TAAATTTAAATTTAAT
1 TAAATTTAAATTAAAT
*
2727 ATAATTTTAAA
1 -TAAATTTAAA
2738 CTTCTACACA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 2 0.05
16 2 0.05
17 31 0.82
18 3 0.08
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (16 bp):
TAAATTTAAATTAAAT
Found at i:4315 original size:59 final size:57
Alignment explanation
Indices: 4252--4469 Score: 208
Period size: 59 Copynumber: 3.7 Consensus size: 57
4242 AAAATGATAA
* * * * *
4252 TTTTGGATTCTCGGGGGTGAAACGGTAATTTTGGGAAAATTT-GAGGTTAAAAATGGGAT
1 TTTTGGATT-TCGGGGGTAAAATGG-GATTTTTGG-AAGTTTCGAGGTTAAAAATGGGAT
* *
4311 TTTTGAAAGTTT-GGGGG-AAAATGGGATTTTTGGAAGTTTCGAGGTCAAAAATGGGAT
1 TTTTG-GA-TTTCGGGGGTAAAATGGGATTTTTGGAAGTTTCGAGGTTAAAAATGGGAT
* *
4368 TTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGTTAAAAATGGGAT
1 TTTTGG-ATTTCGGGGGT-AAAATGGGATTTTTGGAAGTTTCGAGGTTAAAAATGGGAT
* **
4427 TTTTGGAAGTTCGGGGGGTAAAAATTAGATTTTTGGACAGTTT
1 TTTTGG-ATTTC-GGGGGT-AAAATGGGATTTTTGGA-AGTTT
4470 AGGGACCTTC
Statistics
Matches: 137, Mismatches: 13, Indels: 16
0.83 0.08 0.10
Matches are distributed among these distances:
56 7 0.05
57 34 0.25
58 5 0.04
59 60 0.44
60 24 0.18
61 7 0.05
ACGTcount: A:0.28, C:0.04, G:0.33, T:0.35
Consensus pattern (57 bp):
TTTTGGATTTCGGGGGTAAAATGGGATTTTTGGAAGTTTCGAGGTTAAAAATGGGAT
Found at i:4364 original size:30 final size:30
Alignment explanation
Indices: 4294--4469 Score: 200
Period size: 30 Copynumber: 6.0 Consensus size: 30
4284 GGGAAAATTT
*
4294 GAGGTTAAAAATGGGATTTTTGAAAGTTT-
1 GAGGTTAAAAATGGGATTTTTGGAAGTTTC
**
4323 G-GG-GGAAAATGGGATTTTTGGAAGTTTC
1 GAGGTTAAAAATGGGATTTTTGGAAGTTTC
*
4351 GAGGTCAAAAATGGGATTTTTGGAAG-TTC
1 GAGGTTAAAAATGGGATTTTTGGAAGTTTC
* *
4380 GGGGGTAAAAATGGGATTTTTGGAAGTTTC
1 GAGGTTAAAAATGGGATTTTTGGAAGTTTC
*
4410 GGGGTTAAAAATGGGATTTTTGGAAG-TTC
1 GAGGTTAAAAATGGGATTTTTGGAAGTTTC
* * **
4439 GGGGGGTAAAAATTAGATTTTTGGACAGTTT
1 -GAGGTTAAAAATGGGATTTTTGGA-AGTTT
4470 AGGGACCTTC
Statistics
Matches: 128, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
27 21 0.16
28 3 0.02
29 32 0.25
30 68 0.53
31 2 0.02
32 2 0.02
ACGTcount: A:0.29, C:0.03, G:0.34, T:0.34
Consensus pattern (30 bp):
GAGGTTAAAAATGGGATTTTTGGAAGTTTC
Found at i:6409 original size:6 final size:6
Alignment explanation
Indices: 6395--6443 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
6385 ATTTGGAAAA
* *
6395 TAAATT TAAACT TAAA-T TAAATT TAAATT CGAAA-- TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT TAAATT
6441 TAA
1 TAA
6444 TATAATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
4 3 0.08
5 5 0.14
6 25 0.69
7 3 0.08
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:6417 original size:17 final size:16
Alignment explanation
Indices: 6395--6455 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 16
6385 ATTTGGAAAA
6395 TAAATTTAAACTTAAAT
1 TAAATTTAAA-TTAAAT
6412 TAAATTTAAATTCGAAA-
1 TAAATTTAAATT--AAAT
*
6429 TAAATTTAAATTTAAT
1 TAAATTTAAATTAAAT
*
6445 ATAATTTTAAA
1 -TAAATTTAAA
6456 CTTCTACACA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 2 0.05
16 2 0.05
17 31 0.82
18 3 0.08
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (16 bp):
TAAATTTAAATTAAAT
Found at i:7284 original size:206 final size:206
Alignment explanation
Indices: 6827--7490 Score: 910
Period size: 206 Copynumber: 3.2 Consensus size: 206
6817 TTTCGTTGAC
* * **
6827 TTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGGCCGCATCACTTGTTTTGATCCAG-TTCTCT
1 TTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCC-GCTTCTCT
* * * * * * * * * *
6891 GTGTTTCATCAAGAAGACGGATTTGGTTCACTCCTCCGTATCTCATCAGGGAGCTATCCATTTTA
65 GTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACC-GTTTA
* * * * * * * *
6956 TTACTTCGACCTGCTTCTCAGTATCTTATGAGGAAGTTGGGGTTCGAAGGTTTATTCATCG---T
129 TTGCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTT-TGC-TCGCTTT
** *
7018 --GCGTGGGTTTGGT
192 GAGCGTGGGCCTGAT
* *
7031 TCGGCCTTCTTCTCAGTATCTTATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTG
1 TTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTG
7096 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTTTATT
66 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTTTATT
*
7161 GCTTCGACCTGCTTCTCGGTGTCTCATTAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAGC
131 GCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAGC
7226 GTGGGCCTGAT
196 GTGGGCCTGAT
* * * *
7237 TTGGTCTTGTTCTCAGTATCTCATTAGGAAGATGACCGCATCGCTTGTTTCAATCAGCTTCTCTG
1 TTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTG
7302 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTTTATT
66 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTTTATT
7367 GCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAGC
131 GCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAGC
7432 GTGGGCCTGAT
196 GTGGGCCTGAT
* * * *
7443 TTGGTCTTCTTCTTAGTATCTCA-CTAGGAAGATGACCGCGTCGTTTGT
1 TTGGCCTTCTTCTCAGTATCTCATC-AGGAAGATGACCGCATCGCTTGT
7491 GGGTATCGCA
Statistics
Matches: 414, Mismatches: 39, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
201 3 0.01
202 2 0.00
203 51 0.12
204 107 0.26
206 251 0.61
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.36
Consensus pattern (206 bp):
TTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTG
TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTTTATT
GCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAGC
GTGGGCCTGAT
Found at i:19242 original size:29 final size:28
Alignment explanation
Indices: 19195--19268 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 28
19185 ATCGGAGTTC
* *
19195 AAAATGAGACTTTTCGGATTAC-CGGGGGCA
1 AAAATGATAATTTT-GGATT-CTCGGGGG-A
*
19225 AAAATGATAATTTTGGATTCTCGGGGGT
1 AAAATGATAATTTTGGATTCTCGGGGGA
* *
19253 GAAACGATAATTTTGG
1 AAAATGATAATTTTGG
19269 GAAAATTCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
28 15 0.39
29 11 0.29
30 12 0.32
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (28 bp):
AAAATGATAATTTTGGATTCTCGGGGGA
Found at i:19325 original size:59 final size:59
Alignment explanation
Indices: 19282--19548 Score: 322
Period size: 59 Copynumber: 4.4 Consensus size: 59
19272 AATTCATGGT
*
19282 TAAAAATGGGATTTTTGGGAGTTTTAGGGTC-AAAATGGGATTTTTGGAAGTTCGGGGG
1 TAAAAATGGGATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
* *
19340 TAAAAATGGGATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGG
1 TAAAAATGGGATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
* *
19399 TAAAAATGGGATTTTTGGATGTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGG
1 TAAAAAT--G------GGAT-TTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTTGGAAGTTCGG
19464 GGG
57 GGG
* * * ** *
19467 TAAAAATGAGATTTTTGGAAGTTTCAGGGTCAAAAAT-AGATTTTTTTCAAGTTCGAGGG
1 TAAAAATGGGATTTTTGGAAGTTTTAGGGTCAAAAATGGGA-TTTTTGGAAGTTCGGGGG
*
19526 TAAAATTGGGATTTTTGGAAGTT
1 TAAAAATGGGATTTTTGGAAGTT
19549 CGGGGGTAAA
Statistics
Matches: 185, Mismatches: 13, Indels: 21
0.84 0.06 0.10
Matches are distributed among these distances:
58 31 0.17
59 91 0.49
60 3 0.02
61 1 0.01
66 1 0.01
67 4 0.02
68 54 0.29
ACGTcount: A:0.28, C:0.03, G:0.32, T:0.37
Consensus pattern (59 bp):
TAAAAATGGGATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
Found at i:19377 original size:30 final size:29
Alignment explanation
Indices: 19282--19579 Score: 276
Period size: 29 Copynumber: 9.8 Consensus size: 29
19272 AATTCATGGT
* **
19282 TAAAAATGGGATTTTTGGGAGTTTTAGGG
1 TAAAAATGGGATTTTTGGAAGTTTGGGGG
* *
19311 TCAAAATGGGATTTTTGGAAGTTCGGGGG
1 TAAAAATGGGATTTTTGGAAGTTTGGGGG
*
19340 TAAAAATGGGATTTTTGGAAGTTTTGGGG
1 TAAAAATGGGATTTTTGGAAGTTTGGGGG
19369 TCAAAAATGGGATTTTTGGAAGTTTGGGGG
1 T-AAAAATGGGATTTTTGGAAGTTTGGGGG
*
19399 TAAAAATGGGATTTTTGGATGTTTTGGAAGTTTTGGGG
1 TAAAAAT--G------GGAT-TTTTGGAAGTTTGGGGG
*
19437 TCAAAAATGGGATTTTTGGAAGTTTGGGGG
1 TAAAAA-TGGGATTTTTGGAAGTTTGGGGG
* **
19467 TAAAAATGAGATTTTTGGAAGTTTCAGGG
1 TAAAAATGGGATTTTTGGAAGTTTGGGGG
* ** * *
19496 TCAAAAAT-AGATTTTTTTCAAGTTCGAGGG
1 T-AAAAATGGGA-TTTTTGGAAGTTTGGGGG
* *
19526 TAAAATTGGGATTTTTGGAAGTTCGGGGG
1 TAAAAATGGGATTTTTGGAAGTTTGGGGG
*
19555 TAAAAACT-AGATTTTTGGATAGTTT
1 TAAAAA-TGGGATTTTTGGA-AGTTT
19580 AGGGACCTTC
Statistics
Matches: 225, Mismatches: 28, Indels: 31
0.79 0.10 0.11
Matches are distributed among these distances:
29 116 0.52
30 77 0.34
31 5 0.02
37 5 0.02
38 21 0.09
39 1 0.00
ACGTcount: A:0.28, C:0.03, G:0.32, T:0.37
Consensus pattern (29 bp):
TAAAAATGGGATTTTTGGAAGTTTGGGGG
Found at i:19431 original size:68 final size:68
Alignment explanation
Indices: 19348--19490 Score: 261
Period size: 68 Copynumber: 2.1 Consensus size: 68
19338 GGTAAAAATG
*
19348 GGAT-TTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGGATT
1 GGATGTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGAGATT
19412 TTT
66 TTT
19415 GGATGTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGAGATT
1 GGATGTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGAGATT
19480 TTT
66 TTT
*
19483 GGAAGTTT
1 GGATGTTT
19491 CAGGGTCAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 4 0.05
68 69 0.95
ACGTcount: A:0.26, C:0.01, G:0.34, T:0.38
Consensus pattern (68 bp):
GGATGTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGAGATT
TTT
Found at i:19445 original size:39 final size:38
Alignment explanation
Indices: 19378--19461 Score: 134
Period size: 39 Copynumber: 2.2 Consensus size: 38
19368 GTCAAAAATG
19378 GGAT-TTTTGGAAGTTTGGGGGTAAAAATGGGATTTTT
1 GGATGTTTTGGAAGTTTGGGGGTAAAAATGGGATTTTT
*
19415 GGATGTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTT
1 GGATGTTTTGGAAGTTTGGGGGT-AAAAATGGGATTTTT
*
19454 GGAAGTTT
1 GGATGTTT
19462 GGGGGTAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
37 4 0.09
38 17 0.40
39 22 0.51
ACGTcount: A:0.24, C:0.01, G:0.35, T:0.40
Consensus pattern (38 bp):
GGATGTTTTGGAAGTTTGGGGGTAAAAATGGGATTTTT
Found at i:21545 original size:18 final size:19
Alignment explanation
Indices: 21522--21558 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
21512 AAATTTAAAC
21522 TTAAA-TTAATAATGAAAT
1 TTAAATTTAATAATGAAAT
21540 TTAAATTTAATAATGAAAT
1 TTAAATTTAATAATGAAAT
21559 AACATTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
TTAAATTTAATAATGAAAT
Found at i:22547 original size:20 final size:20
Alignment explanation
Indices: 22522--22571 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
22512 ATTTGTCTCT
22522 AGTGTCGTGAAATCCAAGTC
1 AGTGTCGTGAAATCCAAGTC
22542 AGTGTCGTGAAATCCAAGTC
1 AGTGTCGTGAAATCCAAGTC
22562 AGTGTCGTGA
1 AGTGTCGTGA
22572 CATTCGAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (20 bp):
AGTGTCGTGAAATCCAAGTC
Found at i:33103 original size:27 final size:27
Alignment explanation
Indices: 33052--33103 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
33042 AGCTGAATAT
*
33052 TTTAGGTATCAAAATAGAACAAAAAAA
1 TTTAGGTATCAAAATAGAAAAAAAAAA
*
33079 TTTAGGTATCAAAATA-AAAATAAAA
1 TTTAGGTATCAAAATAGAAAAAAAAA
33104 TAAGTATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.60, C:0.06, G:0.10, T:0.25
Consensus pattern (27 bp):
TTTAGGTATCAAAATAGAAAAAAAAAA
Found at i:33238 original size:52 final size:52
Alignment explanation
Indices: 33174--33284 Score: 197
Period size: 52 Copynumber: 2.2 Consensus size: 52
33164 ACCGAAATAC
33174 TATT-TAATAATAAAAATTATATTTAAATTTAATTATTAAAATATATTATAA
1 TATTATAATAATAAAAATTATATTTAAATTTAATTATTAAAATATATTATAA
* *
33225 TATTATAATAATAATAATTATATTTAAATTTAATTATTAAAATATATTATAT
1 TATTATAATAATAAAAATTATATTTAAATTTAATTATTAAAATATATTATAA
33277 TATTATAA
1 TATTATAA
33285 AAGTATTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 4 0.07
52 53 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (52 bp):
TATTATAATAATAAAAATTATATTTAAATTTAATTATTAAAATATATTATAA
Found at i:40930 original size:27 final size:28
Alignment explanation
Indices: 40865--40919 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
40855 ATCGAAGTTG
* * *
40865 AAAATGAGATTTTTGGATACTCGGGGGC
1 AAAATGATAATTTTGGACACTCGGGGGC
40893 AAAATGATAATTTTGGACACTCGGGGG
1 AAAATGATAATTTTGGACACTCGGGGG
40920 GAAATGGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.27
Consensus pattern (28 bp):
AAAATGATAATTTTGGACACTCGGGGGC
Found at i:40935 original size:27 final size:28
Alignment explanation
Indices: 40877--40935 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
40867 AATGAGATTT
* *
40877 TTGGATACTCGGGGGCAAAATGATAATT
1 TTGGACACTCGGGGGCAAAATGATAATG
* *
40905 TTGGACACTCGGGGG-GAAATGGTAATG
1 TTGGACACTCGGGGGCAAAATGATAATG
40932 TTGG
1 TTGG
40936 GAAAATTCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.27, C:0.10, G:0.36, T:0.27
Consensus pattern (28 bp):
TTGGACACTCGGGGGCAAAATGATAATG
Found at i:40982 original size:29 final size:29
Alignment explanation
Indices: 40951--41051 Score: 93
Period size: 29 Copynumber: 3.4 Consensus size: 29
40941 TTCAGGGTCA
40951 AAAATGGAATTTTTAGACATTCGAGGG-T
1 AAAATGGAATTTTTAGACATTCGAGGGTT
* *
40979 AAAATGATAATTTTTAGAAAGTGT-G-GGGTTT
1 AAAATG-GAATTTTTAGACA-T-TCGAGGG-TT
* *
41010 AAAACGAAATTTTTAGACATTCGA-GGTT
1 AAAATGGAATTTTTAGACATTCGAGGGTT
41038 AAAATGGTAATTTT
1 AAAATGG-AATTTT
41052 GGGAAAAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
28 14 0.24
29 24 0.41
30 13 0.22
31 7 0.12
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTAGACATTCGAGGGTT
Found at i:41126 original size:28 final size:30
Alignment explanation
Indices: 41095--41238 Score: 90
Period size: 29 Copynumber: 4.9 Consensus size: 30
41085 AGAAGTTTGG
41095 GGGT-AAATGGTAATTTTTGGAAAAATC-A
1 GGGTAAAATGGTAATTTTTGGAAAAATCGA
** *
41123 GGGTCAATAATGG-AATTTTTGG-AAGTTCGG
1 GGGT-AA-AATGGTAATTTTTGGAAAAATCGA
41153 GGGTAAAATGGTAA-TTTTGGAAAAAAATC-A
1 GGGTAAAATGGTAATTTTTGG--AAAAATCGA
* * **
41183 TGGTCAAAAAT-G-AAATTTTGGAAAGTTCGA
1 GGGT--AAAATGGTAATTTTTGGAAAAATCGA
* *
41213 GGGTTAAAT-GTAATTTTTAGAAAAAT
1 GGGTAAAATGGTAATTTTTGGAAAAAT
41239 TGGGGTTAAA
Statistics
Matches: 88, Mismatches: 15, Indels: 25
0.69 0.12 0.20
Matches are distributed among these distances:
28 20 0.23
29 24 0.27
30 23 0.26
31 16 0.18
32 5 0.06
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGTAAAATGGTAATTTTTGGAAAAATCGA
Found at i:41209 original size:60 final size:58
Alignment explanation
Indices: 41037--41229 Score: 198
Period size: 60 Copynumber: 3.3 Consensus size: 58
41027 CATTCGAGGT
* * * *
41037 TAAAATGGTAATTTTGGGAAAAAAAAAACGAGGTC-AAAATGGAATTTTAGAAGTTTGGGGG
1 TAAAATGGTAATTTT-GG--AAAAAAATC-AGGTCAAAAATGAAATTTTGGAAGTTCGGGGG
* *
41098 T-AAATGGTAATTTTTGG--AAAAATCAGGGTCAATAATGGAATTTTTGGAAGTTCGGGGG
1 TAAAATGGTAA-TTTTGGAAAAAAATCA-GGTCAAAAAT-GAAATTTTGGAAGTTCGGGGG
*
41156 TAAAATGGTAATTTTGGAAAAAAATCATGGTCAAAAATGAAATTTTGGAAAGTTCGAGGG
1 TAAAATGGTAATTTTGGAAAAAAATCA-GGTCAAAAATGAAATTTTGG-AAGTTCGGGGG
*
41216 TTAAAT-GTAATTTT
1 TAAAATGGTAATTTT
41230 TAGAAAAATT
Statistics
Matches: 113, Mismatches: 11, Indels: 18
0.80 0.08 0.13
Matches are distributed among these distances:
55 1 0.01
56 10 0.09
57 4 0.04
58 24 0.21
59 26 0.23
60 43 0.38
61 5 0.04
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.31
Consensus pattern (58 bp):
TAAAATGGTAATTTTGGAAAAAAATCAGGTCAAAAATGAAATTTTGGAAGTTCGGGGG
Found at i:41236 original size:60 final size:58
Alignment explanation
Indices: 41029--41259 Score: 191
Period size: 60 Copynumber: 3.9 Consensus size: 58
41019 TTTTTAGACA
* * ** * *
41029 TTCGAGGTTAAAATGGTAATTTTGGGAAAAAAAAAACGAGGTC-AAAATGGAATTTTAGAAG
1 TTCGGGGTT-AAATGGTAATTTT-TGAAAAAAATCA-G-GGTCAAAAATGAAATTTTGGAAG
* * * * *
41090 TTTGGGGGTAAATGGTAATTTTTG-GAAAAATCAGGGTCAATAATGGAATTTTTGGAAG
1 TTCGGGGTTAAATGGTAATTTTTGAAAAAAATCAGGGTCAAAAAT-GAAATTTTGGAAG
* * *
41148 TTCGGGGGTAAAATGGTAATTTTGGAAAAAAATCATGGTCAAAAATGAAATTTTGGAAAG
1 TTC-GGGGTTAAATGGTAATTTTTGAAAAAAATCAGGGTCAAAAATGAAATTTTGG-AAG
* ** * *
41208 TTCGAGGGTTAAAT-GTAATTTTT-AGAAAAATTGGGGTTAAAAATAAAATTTT
1 TTCG-GGGTTAAATGGTAATTTTTGAAAAAAATCAGGGTCAAAAATGAAATTTT
41260 TGAAAAGTTT
Statistics
Matches: 137, Mismatches: 27, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
56 4 0.03
57 5 0.04
58 41 0.30
59 37 0.27
60 44 0.32
61 6 0.04
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.32
Consensus pattern (58 bp):
TTCGGGGTTAAATGGTAATTTTTGAAAAAAATCAGGGTCAAAAATGAAATTTTGGAAG
Found at i:41261 original size:59 final size:60
Alignment explanation
Indices: 40921--41292 Score: 237
Period size: 59 Copynumber: 6.3 Consensus size: 60
40911 ACTCGGGGGG
* ** * * * *
40921 AAATGGTAATGTTGGGAAAATTCAGGGTCAAAAATGGAATTTTTAGACA-TTCGAGGGTA
1 AAATGGTAATTTTTAGAAAAATCAGGGTCAAAAATGAAATTTTTGGAAAGTTCGAGGGTA
* * ** ** * * * *
40980 AAATGATAATTTTTAG-AAAGTGTGGGGTTTAAAACGAAATTTTTAGACA-TTCGAGGTTA
1 AAATGGTAATTTTTAGAAAAAT-CAGGGTCAAAAATGAAATTTTTGGAAAGTTCGAGGGTA
* * ** * * * *
41039 AAATGGTAATTTTGGGAAAAAAAAAACGAGGTC-AAAATGGAA-TTTTAG-AAGTTTGGGGGT-
1 AAATGGTAATTTT--TAGAAAAATCA-G-GGTCAAAAATGAAATTTTTGGAAAGTTCGAGGGTA
* * * *
41099 AAATGGTAATTTTTGGAAAAATCAGGGTCAATAATGGAATTTTTGG-AAGTTCGGGGGTA
1 AAATGGTAATTTTTAGAAAAATCAGGGTCAAAAATGAAATTTTTGGAAAGTTCGAGGGTA
* * * *
41158 AAATGGTAATTTTGGAAAAAAATCATGGTCAAAAATGAAA-TTTTGGAAAGTTCGAGGGTT
1 AAATGGTAATTTT-TAGAAAAATCAGGGTCAAAAATGAAATTTTTGGAAAGTTCGAGGGTA
** * * * *
41218 AAAT-GTAATTTTTAGAAAAATTGGGGTTAAAAATAAAATTTTTGAAAAGTT-TAGGGGTA
1 AAATGGTAATTTTTAGAAAAATCAGGGTCAAAAATGAAATTTTTGGAAAGTTCGA-GGGTA
*
41277 AAAT-ATAATTTTTAGA
1 AAATGGTAATTTTTAGA
41293 TAGTTTAGGG
Statistics
Matches: 246, Mismatches: 53, Indels: 28
0.75 0.16 0.09
Matches are distributed among these distances:
56 4 0.02
57 9 0.04
58 46 0.19
59 111 0.45
60 49 0.20
61 13 0.05
62 11 0.04
63 3 0.01
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (60 bp):
AAATGGTAATTTTTAGAAAAATCAGGGTCAAAAATGAAATTTTTGGAAAGTTCGAGGGTA
Found at i:41275 original size:119 final size:118
Alignment explanation
Indices: 40921--41288 Score: 299
Period size: 119 Copynumber: 3.1 Consensus size: 118
40911 ACTCGGGGGG
* * * * * *
40921 AAATGGTAATGTTGG-GAAAATTCAGGGTCAAAAATGGAATTTTTAGACA-TTCGAGGGTAAAAT
1 AAATGGTAATTTTGGAAAAAAATCA-GGTCAAAAAT-GAAATTTTAGAAAGTTCGAGGGTTAAAT
* * * * * *
40984 GATAATTTTTAG-AAAGTGTGGGGTTTAAAACGAAATTTTT-AGACA--TTCGAGGTTA
64 G-TAATTTTTAGAAAAAT-TGGGGTTAAAAATGAAATTTTTGA-AAAGTTTAG-GGGTA
* * * *
41039 AAATGGTAATTTTGGGAAAAAAAAAACGAGGTC-AAAATGGAATTTTAG-AAGTTTG-GGGGTAA
1 AAATGGTAATTTT-GG--AAAAAAATC-AGGTCAAAAATGAAATTTTAGAAAGTTCGAGGGTTAA
* ** * * * * **
41101 ATGGTAATTTTTGGAAAAATCAGGGTCAATAATGGAATTTTTG-GAAGTTCGGGGGTA
62 AT-GTAATTTTTAGAAAAATTGGGGTTAAAAATGAAATTTTTGAAAAGTTTAGGGGTA
*
41158 AAATGGTAATTTTGGAAAAAAATCATGGTCAAAAATGAAATTTTGGAAAGTTCGAGGGTTAAATG
1 AAATGGTAATTTTGGAAAAAAATCA-GGTCAAAAATGAAATTTTAGAAAGTTCGAGGGTTAAATG
*
41223 TAATTTTTAGAAAAATTGGGGTTAAAAATAAAATTTTTGAAAAGTTTAGGGGTA
65 TAATTTTTAGAAAAATTGGGGTTAAAAATGAAATTTTTGAAAAGTTTAGGGGTA
*
41277 AAAT-ATAATTTT
1 AAATGGTAATTTT
41289 TAGATAGTTT
Statistics
Matches: 194, Mismatches: 40, Indels: 32
0.73 0.15 0.12
Matches are distributed among these distances:
115 1 0.01
116 12 0.06
117 13 0.07
118 61 0.31
119 74 0.38
120 18 0.09
121 5 0.03
122 9 0.05
123 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (118 bp):
AAATGGTAATTTTGGAAAAAAATCAGGTCAAAAATGAAATTTTAGAAAGTTCGAGGGTTAAATGT
AATTTTTAGAAAAATTGGGGTTAAAAATGAAATTTTTGAAAAGTTTAGGGGTA
Found at i:41279 original size:29 final size:29
Alignment explanation
Indices: 41224--41302 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
41214 GGTTAAATGT
**
41224 AATTTTTAGAAAAATT-GGGGTTAAAAATAA
1 AATTTTTAGAAAGTTTAGGGG-T-AAAATAA
*
41254 AATTTTT-GAAAAGTTTAGGGGTAAAATAT
1 AATTTTTAG-AAAGTTTAGGGGTAAAATAA
*
41283 AATTTTTAGATAGTTTAGGG
1 AATTTTTAGAAAGTTTAGGG
41303 ACCTTTAGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 24 0.57
30 14 0.33
31 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (29 bp):
AATTTTTAGAAAGTTTAGGGGTAAAATAA
Found at i:42466 original size:12 final size:13
Alignment explanation
Indices: 42449--42491 Score: 63
Period size: 12 Copynumber: 3.5 Consensus size: 13
42439 TTTCACTTTC
*
42449 TTTATTATTTAT-
1 TTTATTATTAATA
42461 TTTATTATTAATA
1 TTTATTATTAATA
42474 TTT-TTATTAATA
1 TTTATTATTAATA
42486 TTTATT
1 TTTATT
42492 GTCGAAACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 23 0.82
13 5 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTATTATTAATA
Found at i:42470 original size:15 final size:15
Alignment explanation
Indices: 42450--42491 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
42440 TTCACTTTCT
42450 TTATTATTTATTTTA
1 TTATTATTTATTTTA
*
42465 TTATTA-ATATTTTTA
1 TTATTATTTA-TTTTA
*
42480 TTAATATTTATT
1 TTATTATTTATT
42492 GTCGAAACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATTATTTATTTTA
Found at i:43133 original size:97 final size:97
Alignment explanation
Indices: 42948--43141 Score: 239
Period size: 97 Copynumber: 2.0 Consensus size: 97
42938 CACTTTTTAA
* * * **
42948 AAGGATGTTCGATTATTTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTTAGGTACAAATTTTC
1 AAGGATATTCGATTATTCCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGACACAAATTTTC
* *
43013 AGAATCAGAGATAAGAAACATTGCCTCGATTT
66 AGAATCAGAAATAAAAAACATTGCCTCGATTT
* **
43045 AAGGATATTCGATTATTCCGATTTGAAGAAAAA-TCGTGCCTAGTAAGTTAAGACACAAATTTTC
1 AAGGATATTCGATTATTCCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGACACAAATTTTC
** *
43109 A-AGATTTGAAATAAAAGAATATTGCCTCGATTT
66 AGA-ATCAGAAATAAAA-AACATTGCCTCGATTT
43142 TAAAGTTTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
95 1 0.01
96 36 0.44
97 45 0.55
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (97 bp):
AAGGATATTCGATTATTCCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGACACAAATTTTC
AGAATCAGAAATAAAAAACATTGCCTCGATTT
Found at i:43585 original size:30 final size:29
Alignment explanation
Indices: 43538--43798 Score: 140
Period size: 30 Copynumber: 8.9 Consensus size: 29
43528 AAATCGATGT
*
43538 TAAAAATGGAA-TTTTGGAAAGTTAAGGGG
1 TAAAAATGTAATTTTTGGAAAGTT-AGGGG
* *
43567 TAAAAATGTAATTTTTGG-AAGTTCGAGG
1 TAAAAATGTAATTTTTGGAAAGTTAGGGG
* * * **
43595 TCAAAAATAG-AATTTTT-AAAAGATCGATAG
1 T-AAAAAT-GTAATTTTTGGAAAGTTAG-GGG
* * * *
43625 TAAAAATGTAATATATGGAAAGTTCGAGG
1 TAAAAATGTAATTTTTGGAAAGTTAGGGG
* *
43654 TCAAAAATATAA-TTTTGGAAAGTTTAAGGG
1 T-AAAAATGTAATTTTTGGAAAG-TTAGGGG
*** * *
43684 TAAAAATGTAATTTTAAAAAAGTTCAAGTG
1 TAAAAATGTAATTTTTGGAAAGTT-AGGGG
* * * *
43714 TAAAAGTGTAATTTTTGAAAAGTTCGAGGT
1 TAAAAATGTAATTTTTGGAAAGTTAG-GGG
*
43744 TAAAAATATAA-TTTTGGAGAAGTTTAGGGG
1 TAAAAATGTAATTTTTGGA-AAG-TTAGGGG
* *
43774 TTAAAATATAATTTTT-GAATAGTTA
1 TAAAAATGTAATTTTTGGAA-AGTTA
43799 AGGAACTTTA
Statistics
Matches: 179, Mismatches: 37, Indels: 32
0.72 0.15 0.13
Matches are distributed among these distances:
28 5 0.03
29 76 0.42
30 91 0.51
31 7 0.04
ACGTcount: A:0.43, C:0.03, G:0.21, T:0.34
Consensus pattern (29 bp):
TAAAAATGTAATTTTTGGAAAGTTAGGGG
Found at i:43706 original size:59 final size:60
Alignment explanation
Indices: 43380--43759 Score: 263
Period size: 59 Copynumber: 6.4 Consensus size: 60
43370 ATTTTAGACA
* *
43380 TTCGAGGGT-AAAATGGTAATTCTTGAAAAAA-ATCGAGATC-AAAATGGAATTTTAGG-AAG
1 TTCGAGGGTAAAAAT-GTAATT-TTGAAAAAAGTTCGAGGTCAAAAATGGAATTTT-GGAAAG
* * *
43439 TTTGGGGGTAAAAATATAATTTTGGGAAAAAA--T-GAGGTCAAAAATGGAATTTTAGG-AAG
1 TTCGAGGGTAAAAATGTAATTTT--GAAAAAAGTTCGAGGTCAAAAATGGAATTTT-GGAAAG
** * *
43498 TTCGAGGGT-AAAATGTAATTTTTGGAAAAAAAATCGATGTTAAAAATGGAATTTTGGAAAG
1 TTCGAGGGTAAAAATGTAA-TTTT-GAAAAAAGTTCGAGGTCAAAAATGGAATTTTGGAAAG
* * * **
43559 TT-AAGGGGTAAAAATGTAATTTTTG---GAAGTTCGAGGTCAAAAATAGAATTTTTAAAAG
1 TTCGA-GGGTAAAAATGTAA-TTTTGAAAAAAGTTCGAGGTCAAAAATGGAATTTTGGAAAG
* ** * * **
43617 ATCGATAGTAAAAATGTAATATATG--GAAAGTTCGAGGTCAAAAATATAATTTTGGAAAG
1 TTCGAGGGTAAAAATGTAAT-TTTGAAAAAAGTTCGAGGTCAAAAATGGAATTTTGGAAAG
** * * * *
43676 TTTAAGGGTAAAAATGTAATTTT-AAAAAAGTTCAAGTGT-AAAAGTGTAATTTTTGAAAAG
1 TTCGAGGGTAAAAATGTAATTTTGAAAAAAGTTCGAG-GTCAAAAATGGAA-TTTTGGAAAG
* *
43736 TTCGAGGTTAAAAATATAATTTTG
1 TTCGAGGGTAAAAATGTAATTTTG
43760 GAGAAGTTTA
Statistics
Matches: 260, Mismatches: 42, Indels: 36
0.77 0.12 0.11
Matches are distributed among these distances:
57 1 0.00
58 66 0.25
59 105 0.40
60 46 0.18
61 28 0.11
62 14 0.05
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.31
Consensus pattern (60 bp):
TTCGAGGGTAAAAATGTAATTTTGAAAAAAGTTCGAGGTCAAAAATGGAATTTTGGAAAG
Found at i:43749 original size:89 final size:90
Alignment explanation
Indices: 43624--43788 Score: 251
Period size: 89 Copynumber: 1.8 Consensus size: 90
43614 AAGATCGATA
*
43624 GTAAAAATGTAATATATGGAAAGTTCGAGGTCAAAAATATAATTTTGGA-AAGTTTAAGGGTAAA
1 GTAAAAATGTAATATATGAAAAGTTCGAGGTCAAAAATATAATTTTGGAGAAGTTTAAGGGTAAA
*
43688 AATGTAATTTTAAAAAAGTTCAAGT
66 AATATAATTTTAAAAAAGTTCAAGT
* * * * * *
43713 GTAAAAGTGTAATTTTTGAAAAGTTCGAGGTTAAAAATATAATTTTGGAGAAGTTTAGGGGTTAA
1 GTAAAAATGTAATATATGAAAAGTTCGAGGTCAAAAATATAATTTTGGAGAAGTTTAAGGGTAAA
43778 AATATAATTTT
66 AATATAATTTT
43789 TGAATAGTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
89 44 0.66
90 23 0.34
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (90 bp):
GTAAAAATGTAATATATGAAAAGTTCGAGGTCAAAAATATAATTTTGGAGAAGTTTAAGGGTAAA
AATATAATTTTAAAAAAGTTCAAGT
Found at i:45732 original size:17 final size:17
Alignment explanation
Indices: 45712--45815 Score: 96
Period size: 17 Copynumber: 6.4 Consensus size: 17
45702 TTTTTTAATA
* *
45712 TTAAGTTTTAAATCAAT
1 TTAAATTTTAAATAAAT
*
45729 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
45746 TTAAA-TTTAAGATAAAT
1 TTAAATTTTAA-ATAAAT
45763 TTAAA-TTT-AA-AAA-
1 TTAAATTTTAAATAAAT
45776 -TAAA-TTTAAGATAAAT
1 TTAAATTTTAA-ATAAAT
*
45792 TTAAATTTAAAAATAAAT
1 TTAAATTT-TAAATAAAT
45810 TTAAAT
1 TTAAAT
45816 CAATTTAAAC
Statistics
Matches: 74, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
12 7 0.09
13 1 0.01
14 4 0.05
15 4 0.05
16 6 0.08
17 36 0.49
18 14 0.19
19 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:45745 original size:11 final size:11
Alignment explanation
Indices: 45729--45798 Score: 61
Period size: 11 Copynumber: 6.2 Consensus size: 11
45719 TTAAATCAAT
*
45729 TTAAATTTTAA
1 TTAAATTTAAA
45740 TTAAATTTAAA
1 TTAAATTTAAA
* **
45751 TTTAAGATAAA
1 TTAAATTTAAA
45762 TTTAAATTTAAAA
1 -TTAAATTT-AAA
*
45775 ATAAATTTAAGA
1 TTAAATTTAA-A
45787 -TAAATTTAAA
1 TTAAATTTAAA
45797 TT
1 TT
45799 TAAAAATAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
10 1 0.02
11 30 0.64
12 13 0.28
13 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:45749 original size:6 final size:6
Alignment explanation
Indices: 45726--45815 Score: 82
Period size: 6 Copynumber: 15.5 Consensus size: 6
45716 GTTTTAAATC
*
45726 AATTTA AATTTT AA-TTA AATTTA AATTTA AGA--TA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA A-ATTTA AATTTA AATTTA
** **
45772 AAAATA AATTTA AGA--TA AATTTA AATTTA AAAATA AATTTA AAT
1 AATTTA AATTTA A-ATTTA AATTTA AATTTA AATTTA AATTTA AAT
45816 CAATTTAAAC
Statistics
Matches: 67, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
4 2 0.03
5 10 0.15
6 53 0.79
7 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:45781 original size:29 final size:29
Alignment explanation
Indices: 45730--45824 Score: 140
Period size: 29 Copynumber: 3.3 Consensus size: 29
45720 TAAATCAATT
* **
45730 TAAATTTTAA-TTAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAAAATAAATTTAAGA
45758 TAAATTTAAATTTAAAAATAAATTTAAGA
1 TAAATTTAAATTTAAAAATAAATTTAAGA
45787 TAAATTTAAATTTAAAAATAAATTTAA-A
1 TAAATTTAAATTTAAAAATAAATTTAAGA
*
45815 TCAATTTAAA
1 TAAATTTAAA
45825 CCCAACTTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
28 19 0.31
29 43 0.69
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (29 bp):
TAAATTTAAATTTAAAAATAAATTTAAGA
Found at i:45820 original size:10 final size:10
Alignment explanation
Indices: 45747--45824 Score: 51
Period size: 11 Copynumber: 8.0 Consensus size: 10
45737 TAATTAAATT
45747 TAAATTTAAGA
1 TAAATTTAA-A
45758 TAAATTTAAA
1 TAAATTTAAA
*
45768 T---TTAAAAA
1 TAAATT-TAAA
45776 TAAATTTAAGA
1 TAAATTTAA-A
45787 TAAATTTAAA
1 TAAATTTAAA
*
45797 T---TTAAAAA
1 TAAATT-TAAA
45805 TAAATTTAAA
1 TAAATTTAAA
*
45815 TCAATTTAAA
1 TAAATTTAAA
45825 CCCAACTTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 19
0.69 0.06 0.25
Matches are distributed among these distances:
7 4 0.08
8 8 0.15
10 18 0.34
11 23 0.43
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:46625 original size:17 final size:17
Alignment explanation
Indices: 46602--46665 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
46592 GTTTTTATTT
46602 ATTTAAATTTATAATAA
1 ATTTAAATTTATAATAA
* *
46619 TTTTAAATTTAAAAATAA
1 ATTTAAATTT-ATAATAA
* * *
46637 ATTTAAACTTACATTAA
1 ATTTAAATTTATAATAA
46654 ATTTAAATTTAT
1 ATTTAAATTTAT
46666 TTAAAATAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
17 24 0.63
18 14 0.37
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTAAATTTATAATAA
Found at i:46629 original size:6 final size:6
Alignment explanation
Indices: 46602--46664 Score: 51
Period size: 6 Copynumber: 10.8 Consensus size: 6
46592 GTTTTTATTT
* ** * *
46602 ATTTAA ATTTATA A--TAA TTTTAA ATTTAA AAATAA ATTTAA ACTTAC
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
46649 A-TTAA ATTTAA ATTTA
1 ATTTAA ATTTAA ATTTA
46665 TTTAAAATAA
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
4 1 0.02
5 6 0.14
6 35 0.80
7 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (6 bp):
ATTTAA
Found at i:46672 original size:17 final size:18
Alignment explanation
Indices: 46650--46695 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
46640 TAAACTTACA
*
46650 TTAAATTTAAATTT-AT-
1 TTAAAATTAAATTTGATC
46666 TTAAAA-TAAATTTGATC
1 TTAAAATTAAATTTGATC
46683 TTAAAA-TAAATTT
1 TTAAAATTAAATTT
46696 AAAATGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 7 0.26
16 7 0.26
17 13 0.48
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
TTAAAATTAAATTTGATC
Found at i:46693 original size:38 final size:35
Alignment explanation
Indices: 46602--46698 Score: 104
Period size: 38 Copynumber: 2.7 Consensus size: 35
46592 GTTTTTATTT
* * *
46602 ATTTAAATTTATAATAATTTTAAATTTAAAAATAA
1 ATTTAAACTTAAAATAAATTTAAATTTAAAAATAA
* *
46637 ATTTAAACTTACATTAAATTTAAATTTATTTAAAATAA
1 ATTTAAACTTAAAATAAATTTAAATTTA---AAAATAA
* *
46675 ATTTGATCTTAAAATAAATTTAAA
1 ATTTAAACTTAAAATAAATTTAAA
46699 ATGAATTTGG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
35 24 0.47
38 27 0.53
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (35 bp):
ATTTAAACTTAAAATAAATTTAAATTTAAAAATAA
Found at i:51744 original size:13 final size:13
Alignment explanation
Indices: 51726--51752 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
51716 CTAAGAATGC
51726 CAAAGTATTGTCT
1 CAAAGTATTGTCT
51739 CAAAGTATTGTCT
1 CAAAGTATTGTCT
51752 C
1 C
51753 GAGGTCTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (13 bp):
CAAAGTATTGTCT
Found at i:52986 original size:59 final size:59
Alignment explanation
Indices: 52887--53529 Score: 882
Period size: 59 Copynumber: 11.0 Consensus size: 59
52877 ACGGAGTGGC
* * * ** *
52887 AAAATGGT-AGTTTTGGAATGTTCGGAATCAAAAATAGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTGATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * *
52945 AGAATGGTAATTTTTAGAAAGTTCAGGGTCAAAAATGGGA-TTTTGGAAGTTCGGGGGT
1 AAAATGGTGATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
53003 AAAATGGTTATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTGATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * *
53062 AAAATGGTGATTTTTTGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTTGGGGGT
1 AAAATGGTGATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
53121 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGTGT
1 AAAATGGTGATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
53180 AAAATGGTGA-TTTTAGGAAGGTTCGGGGTCAAAATTGGGATTTTTTGAAGTTCGGGGGT
1 AAAATGGTGATTTTTA-GAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
53239 AAAATGGTGATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTTGAAGTTCGGGGGT
1 AAAATGGTGATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * *
53298 AAAATGATAATTTTTAGAAGGTTAGGGGTC-AAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTGATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* ** * **
53356 AAAATGGTGATTTTTGGAAGGTTTAGGGTCAAAAATAGGATTTTTGGAAGTTTAGGGGT
1 AAAATGGTGATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
53415 AAAATGGTAATTTTTAGAAGGTTTGGGGTC-AAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTGATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
53473 AAAATGGTGATTTTTGGAAGGTTCGGGGTCAAAAATAGGATTTTTGAAAGTTCGGGG
1 AAAATGGTGATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
53530 ACTTTCGGAG
Statistics
Matches: 519, Mismatches: 60, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
58 166 0.32
59 349 0.67
60 4 0.01
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (59 bp):
AAAATGGTGATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:53104 original size:117 final size:118
Alignment explanation
Indices: 52887--53529 Score: 913
Period size: 117 Copynumber: 5.5 Consensus size: 118
52877 ACGGAGTGGC
* * * *
52887 AAAATGGT-AGTTTTGGAATGTTCG-GAATCAAAAATAGGATTTTTGGAAGTTCGGGGGTAGAAT
1 AAAATGGTGATTTTTGGAAGGTTCGAG-GTCAAAAATAGGATTTTTGGAAGTTCGGGGGTAAAAT
* *
52950 GGTAATTTTTAGAAAGTTCAGGGTCAAAAATGGGA-TTTTGGAAGTTCGGGGGT
65 GGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
53003 AAAATGGTTATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATG
1 AAAATGGTGATTTTTGGAAGGTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCGGGGGTAAAATG
* * * * *
53068 GTGATTTTTTGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTTGGGGGT
66 GTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * * *
53121 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGTGTAAAATG
1 AAAATGGTGATTTTTGGAAGGTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCGGGGGTAAAATG
* * *
53186 GTGA-TTTTAGGAAGGTTCGGGGTCAAAATTGGGATTTTTTGAAGTTCGGGGGT
66 GTAATTTTTA-GAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
53239 AAAATGGTGATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTTGAAGTTCGGGGGTAAAATG
1 AAAATGGTGATTTTTGGAAGGTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCGGGGGTAAAATG
* * *
53304 ATAATTTTTAGAAGGTTAGGGGTC-AAAATGGGATTTTTGGAAGTTCGAGGGT
66 GTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* **
53356 AAAATGGTGATTTTTGGAAGGTT-TAGGGTCAAAAATAGGATTTTTGGAAGTTTAGGGGTAAAAT
1 AAAATGGTGATTTTTGGAAGGTTCGA-GGTCAAAAATAGGATTTTTGGAAGTTCGGGGGTAAAAT
* *
53420 GGTAATTTTTAGAAGGTTTGGGGTC-AAAATGGGATTTTTGGAAGTTCGAGGGT
65 GGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
53473 AAAATGGTGATTTTTGGAAGGTTCGGGGTCAAAAATAGGATTTTTGAAAGTTCGGGG
1 AAAATGGTGATTTTTGGAAGGTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCGGGG
53530 ACTTTCGGAG
Statistics
Matches: 475, Mismatches: 45, Indels: 13
0.89 0.08 0.02
Matches are distributed among these distances:
116 9 0.02
117 265 0.56
118 196 0.41
119 5 0.01
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (118 bp):
AAAATGGTGATTTTTGGAAGGTTCGAGGTCAAAAATAGGATTTTTGGAAGTTCGGGGGTAAAATG
GTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
Done.