Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012620.1 Kokia drynarioides strain JFW-HI SEQ_127629, 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: 231457
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:689 original size:2 final size:2
Alignment explanation
Indices: 682--707 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
672 TTTGACTTTA
682 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
708 TTCATTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4980 original size:3 final size:3
Alignment explanation
Indices: 4950--5008 Score: 63
Period size: 3 Copynumber: 21.0 Consensus size: 3
4940 TATCGGTATT
* * *
4950 GAA GCA GAA AAA G-A GAA -AA GAA -AA GAA GAA GGA -AA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
4994 GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA
5009 AAAGTTATCC
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 7 0.15
3 39 0.85
ACGTcount: A:0.68, C:0.02, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5006 original size:12 final size:12
Alignment explanation
Indices: 4950--5008 Score: 63
Period size: 11 Copynumber: 5.2 Consensus size: 12
4940 TATCGGTATT
* *
4950 GAAGCAGAAAAA
1 GAAGAAGAAGAA
4962 G-AGAA-AAGAA
1 GAAGAAGAAGAA
*
4972 -AAGAAGAAGGA
1 GAAGAAGAAGAA
4983 -AAGAAGAAGAA
1 GAAGAAGAAGAA
4994 GAAGAAGAAGAA
1 GAAGAAGAAGAA
5006 GAA
1 GAA
5009 AAAGTTATCC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 8 0.20
11 17 0.43
12 15 0.38
ACGTcount: A:0.68, C:0.02, G:0.31, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAGAA
Found at i:9072 original size:123 final size:123
Alignment explanation
Indices: 8928--9186 Score: 446
Period size: 123 Copynumber: 2.1 Consensus size: 123
8918 GCTATCTTTT
* *
8928 CCTTTTATCTAATATCTCATATTAAAATGGAAATATTCCTTTAGAGAAATATATGGAAGGTTTAT
1 CCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAGAGAAATATATGGAAGGGTTAT
* *
8993 TAAGACAATATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTG
66 TAAAACAATATATCCTCTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTG
*
9051 CCTTTTATATAATATCTCATATTAAAATGGATATATTCCTTTAGAGAAATATATGGAAGGGTTAT
1 CCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAGAGAAATATATGGAAGGGTTAT
* * *
9116 TAAAACATTATATCCTCTCCAAAAGGATATTAACTTTCATGTTTTTAATATTCAATTT
66 TAAAACAATATATCCTCTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTG
9174 CCTTTTATATAAT
1 CCTTTTATATAAT
9187 CTATGGAAGG
Statistics
Matches: 128, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 128 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (123 bp):
CCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAGAGAAATATATGGAAGGGTTAT
TAAAACAATATATCCTCTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTG
Found at i:9231 original size:86 final size:86
Alignment explanation
Indices: 9102--9272 Score: 297
Period size: 86 Copynumber: 2.0 Consensus size: 86
9092 TAGAGAAATA
*
9102 TATGGAAGGGTTATTAAAACATTATATCCTCTCCAAAAGGATATTAACTTTCATGTTTTTAATAT
1 TATGGAAGGGTTATTAAAACATTATATCCTCTCCAAAAGGATATTAACTTCCATGTTTTTAATAT
*
9167 TCAATTTCCTTTTATATAATC
66 TCAATTTCCCTTTATATAATC
* * *
9188 TATGGAAGGTTTATTAAAATATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATAT
1 TATGGAAGGGTTATTAAAACATTATATCCTCTCCAAAAGGATATTAACTTCCATGTTTTTAATAT
9253 TCAATTTCCCTTTATATAAT
66 TCAATTTCCCTTTATATAAT
9273 ATCTCATATT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (86 bp):
TATGGAAGGGTTATTAAAACATTATATCCTCTCCAAAAGGATATTAACTTCCATGTTTTTAATAT
TCAATTTCCCTTTATATAATC
Found at i:9327 original size:209 final size:208
Alignment explanation
Indices: 8979--9375 Score: 659
Period size: 209 Copynumber: 1.9 Consensus size: 208
8969 TAGAGAAATA
*
8979 TATGGAAGGTTTATTAAGACAATATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATAT
1 TATGGAAGGTTTATTAAAACAATATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATAT
* * *
9044 TCAATTGCCTTTTATATAATATCTCATATTAAAATGGATATATTCCTTTAGAGAAATATATGGAA
66 TCAATTGCCCTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAA
* * *
9109 GGGTTATTAAAACATTATATCCTCTCCAAAAGGATATTAACTTTCATGTTTTTAATATTCAATTT
131 GAGTTATTAAAACATTATATCATCTCCAAAAGGATATTAACTTCCATG-TTTTAATATTCAATTT
9174 CCTTTTATATAATC
195 CCTTTTATATAATC
* *
9188 TATGGAAGGTTTATTAAAATATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATAT
1 TATGGAAGGTTTATTAAAACAATATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATAT
* *
9253 TCAATTTCCCTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATTTATGGAA
66 TCAATTGCCCTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAA
* * *
9318 GATTTATTAAAACATTATATCATTTCCAAAAGGATATTTACTTCCATGTTTTAATATT
131 GAGTTATTAAAACATTATATCATCTCCAAAAGGATATTAACTTCCATGTTTTAATATT
9376 TAACGAAACC
Statistics
Matches: 174, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
208 10 0.06
209 164 0.94
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (208 bp):
TATGGAAGGTTTATTAAAACAATATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATAT
TCAATTGCCCTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAA
GAGTTATTAAAACATTATATCATCTCCAAAAGGATATTAACTTCCATGTTTTAATATTCAATTTC
CTTTTATATAATC
Found at i:11364 original size:21 final size:21
Alignment explanation
Indices: 11338--11398 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
11328 GGCGATGTCA
*
11338 CAACACACATGAGTCGTGTTG
1 CAACACACAGGAGTCGTGTTG
11359 CAACACACAGGAGTCGTGTTG
1 CAACACACAGGAGTCGTGTTG
11380 CAACACACAGGAGTCGTGT
1 CAACACACAGGAGTCGTGT
11399 CATGACGAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.20
Consensus pattern (21 bp):
CAACACACAGGAGTCGTGTTG
Found at i:19265 original size:28 final size:28
Alignment explanation
Indices: 19223--19297 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
19213 CACTAAGTTA
* * *
19223 CTGAAATGTGGAAGCCTTTATGGCTATT
1 CTGATATGTGAAAGCCTTTATAGCTATT
*
19251 CTGATATGTGAAAGCCTTTGTAGCTATT
1 CTGATATGTGAAAGCCTTTATAGCTATT
* *
19279 TTGATATGTCAAAGCCTTT
1 CTGATATGTGAAAGCCTTT
19298 GTGGTTGTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (28 bp):
CTGATATGTGAAAGCCTTTATAGCTATT
Found at i:19320 original size:28 final size:28
Alignment explanation
Indices: 19289--19362 Score: 130
Period size: 28 Copynumber: 2.6 Consensus size: 28
19279 TTGATATGTC
19289 AAAGCCTTTGTGGTTGTTCTCTAATATG
1 AAAGCCTTTGTGGTTGTTCTCTAATATG
* *
19317 AAAGTCTTTGTGGTTGTTCTCTGATATG
1 AAAGCCTTTGTGGTTGTTCTCTAATATG
19345 AAAGCCTTTGTGGTTGTT
1 AAAGCCTTTGTGGTTGTT
19363 TTCTGTTATA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.45
Consensus pattern (28 bp):
AAAGCCTTTGTGGTTGTTCTCTAATATG
Found at i:19367 original size:28 final size:28
Alignment explanation
Indices: 19249--19367 Score: 125
Period size: 28 Copynumber: 4.2 Consensus size: 28
19239 TTTATGGCTA
* * *
19249 TTCTGATATGTGAAAGCCTTTGTAGCT-AT
1 TTCTGATA--TGAAAGCCTTTGTGGTTGTT
19278 TT-TGATATGTCAAAGCCTTTGTGGTTGTT
1 TTCTGATATG--AAAGCCTTTGTGGTTGTT
* * *
19307 CTCTAATATGAAAGTCTTTGTGGTTGTT
1 TTCTGATATGAAAGCCTTTGTGGTTGTT
*
19335 CTCTGATATGAAAGCCTTTGTGGTTGTT
1 TTCTGATATGAAAGCCTTTGTGGTTGTT
19363 TTCTG
1 TTCTG
19368 TTATATGCGA
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
26 2 0.03
28 65 0.84
29 4 0.05
30 6 0.08
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.45
Consensus pattern (28 bp):
TTCTGATATGAAAGCCTTTGTGGTTGTT
Found at i:20597 original size:15 final size:15
Alignment explanation
Indices: 20577--20607 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20567 GAAACTATAT
20577 GGGTTAAACTGTAAA
1 GGGTTAAACTGTAAA
*
20592 GGGTTAAATTGTAAA
1 GGGTTAAACTGTAAA
20607 G
1 G
20608 ATTTCAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.29, T:0.29
Consensus pattern (15 bp):
GGGTTAAACTGTAAA
Found at i:26459 original size:18 final size:19
Alignment explanation
Indices: 26428--26470 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
26418 GAAAATTTAG
26428 AAAAATAAAAGAATCTTGT
1 AAAAATAAAAGAATCTTGT
* * *
26447 AAAAA-AAATGAATGTTTT
1 AAAAATAAAAGAATCTTGT
26465 AAAAAT
1 AAAAAT
26471 CTTAATTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.28
Consensus pattern (19 bp):
AAAAATAAAAGAATCTTGT
Found at i:29494 original size:20 final size:21
Alignment explanation
Indices: 29465--29516 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
29455 TTGGAGTTGC
*
29465 GGTATAGATACCTAAT-AAAA
1 GGTATCGATACCTAATGAAAA
* **
29485 GGTATCGATACTTGTTGAAAA
1 GGTATCGATACCTAATGAAAA
29506 GGTATCGATAC
1 GGTATCGATAC
29517 TTTTTGTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (21 bp):
GGTATCGATACCTAATGAAAA
Found at i:31338 original size:15 final size:15
Alignment explanation
Indices: 31318--31373 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
31308 ATGAATTAAA
31318 CAATTTAATTTTTAT
1 CAATTTAATTTTTAT
31333 CAATTTTAAATTTTTTAAT
1 CAA-TTT-AA-TTTTT-AT
*
31352 -AATTTAATTCTTAT
1 CAATTTAATTTTTAT
31366 CAATTTAA
1 CAATTTAA
31374 AATACCAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 2 0.06
15 14 0.40
16 5 0.14
17 5 0.14
18 7 0.20
19 2 0.06
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
CAATTTAATTTTTAT
Found at i:34970 original size:28 final size:28
Alignment explanation
Indices: 34938--34993 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
34928 AAGGTTTTAA
34938 TGAGGCACATTATCTTCCAATGGATATC
1 TGAGGCACATTATCTTCCAATGGATATC
34966 TGAGGCACATTATCTTCCAATGGATATC
1 TGAGGCACATTATCTTCCAATGGATATC
34994 CAAAGGGGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (28 bp):
TGAGGCACATTATCTTCCAATGGATATC
Found at i:38219 original size:58 final size:58
Alignment explanation
Indices: 38140--38258 Score: 136
Period size: 58 Copynumber: 2.0 Consensus size: 58
38130 TCATTTTTCA
* * *
38140 TTTTCATTTTCATTTTGGAGAAAGCCACTT-TCATTTCCAAATGATTT-C-ATTTATCCAT
1 TTTTCATTTTCACTTTCGAGAAA-AC-CTTATCATTTCCAAATG-TTTCCTATTTATCCAT
* *
38198 TTTTCATTTTCGCTTTCGAGAAAACCTTAATCATTTCCAAATGTTTCCTATTTCTCCAT
1 TTTTCATTTTCACTTTCGAGAAAACCTT-ATCATTTCCAAATGTTTCCTATTTATCCAT
38257 TT
1 TT
38259 CTCCATTTCT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
56 3 0.06
57 4 0.08
58 34 0.65
59 11 0.21
ACGTcount: A:0.24, C:0.21, G:0.08, T:0.47
Consensus pattern (58 bp):
TTTTCATTTTCACTTTCGAGAAAACCTTATCATTTCCAAATGTTTCCTATTTATCCAT
Found at i:40761 original size:10 final size:10
Alignment explanation
Indices: 40736--40770 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
40726 GTATAATTAT
40736 TTTATTTTATC
1 TTTATTTTA-C
40747 TTTTATTTTAC
1 -TTTATTTTAC
40758 TTTATTTTAC
1 TTTATTTTAC
40768 TTT
1 TTT
40771 TGGGTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 1 0.04
12 9 0.39
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTATTTTAC
Found at i:50653 original size:28 final size:28
Alignment explanation
Indices: 50507--51003 Score: 348
Period size: 29 Copynumber: 17.2 Consensus size: 28
50497 GTTTCAAAGT
* * *
50507 GTTTGGGGTTAAAACGTAA-TTTTGGAAA
1 GTTTAGGGTAAAAATGTAATTTTTGG-AA
* * *
50535 GTTTTAAGGGTAAAAATGTCACTTTGGGAAA
1 G-TTT-AGGGTAAAAATGTAATTTTTGG-AA
*
50566 G-TTCGGGATAAAAACT-TAA-TTTTGGAAA
1 GTTTAGGG-TAAAAA-TGTAATTTTTGG-AA
* *
50594 GTTTTAGGGGT-AAAATGTTATTTTGGGAAA
1 G-TTTA-GGGTAAAAATGTAATTTTTGG-AA
* *
50624 GTTTAGGGTAAAAAGGTGATTTTTGGAA
1 GTTTAGGGTAAAAATGTAATTTTTGGAA
* *
50652 GTTCGAGGGTAAAATTGTAATTTTTGAGAA
1 GTT-TAGGGTAAAAATGTAATTTTTG-GAA
* * *
50682 TTTTAAGGGTAAAAATGTGATTGTTGGAA
1 GTTT-AGGGTAAAAATGTAATTTTTGGAA
* **
50711 GTTTAAGGGCAAAAATGTAATTTTTAAAA
1 GTTT-AGGGTAAAAATGTAATTTTTGGAA
**
50740 GTTCGGGGTAAAAATGTAATTTTTGGAA
1 GTTTAGGGTAAAAATGTAATTTTTGGAA
* *
50768 GTTTAGGG-GAAAATGTAA-TTTTAGAA
1 GTTTAGGGTAAAAATGTAATTTTTGGAA
*
50794 GTTTGAGGG-AAAAATGTAATTTTTGAAA
1 GTTT-AGGGTAAAAATGTAATTTTTGGAA
* * *
50822 GTTCAAGGGTTAAAATGTGATTTTTGGAA
1 GTT-TAGGGTAAAAATGTAATTTTTGGAA
**
50851 GTTTAAGGG-AAAAATGTAATTTTTAAAA
1 GTTT-AGGGTAAAAATGTAATTTTTGGAA
50879 GTTTAGGGGTAAAAATGTAATTTTTGAGAA
1 GTTTA-GGGTAAAAATGTAATTTTTG-GAA
* * * *
50909 GTTTAAGGGTTAAAATGTGATTTTAGAAAA
1 GTTT-AGGGTAAAAATGTAATTTTTG-GAA
* *
50939 GTTTAGATGTTAAAATGTAA-TTTTGGAAAA
1 GTTTAG-GGTAAAAATGTAATTTTTGG--AA
* * *
50969 GTTTAGGGGTTAAAATATGATTTTTGGATA
1 GTTTA-GGGTAAAAATGTAATTTTTGGA-A
50999 GTTTA
1 GTTTA
51004 AGGACCTTTT
Statistics
Matches: 377, Mismatches: 63, Indels: 56
0.76 0.13 0.11
Matches are distributed among these distances:
26 11 0.03
27 23 0.06
28 84 0.22
29 128 0.34
30 111 0.29
31 20 0.05
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (28 bp):
GTTTAGGGTAAAAATGTAATTTTTGGAA
Found at i:50932 original size:30 final size:30
Alignment explanation
Indices: 50512--51006 Score: 365
Period size: 30 Copynumber: 17.1 Consensus size: 30
50502 AAAGTGTTTG
* * *
50512 GGGTTAAAACGTAATTTTGGA-AAGTTTTAA
1 GGGTAAAAATGTAATTTTTGAGAAG-TTTAA
* * * *
50542 GGGTAAAAATGTCA-CTTTGGGAAAG-TT-C
1 GGGTAAAAATGTAATTTTTGAG-AAGTTTAA
* *
50570 GGGATAAAAACT-TAATTTTGGA-AAGTTTTAG
1 GGG-TAAAAA-TGTAATTTTTGAGAAG-TTTAA
* *
50601 GGGT-AAAATGTTA-TTTTGGGAAAGTTT-A
1 GGGTAAAAATGTAATTTTTGAG-AAGTTTAA
* * **
50629 GGGTAAAAAGGTGATTTTTG-GAAGTTCGA
1 GGGTAAAAATGTAATTTTTGAGAAGTTTAA
* *
50658 GGGTAAAATTGTAATTTTTGAGAATTTTAA
1 GGGTAAAAATGTAATTTTTGAGAAGTTTAA
* *
50688 GGGTAAAAATGTGATTGTTG-GAAGTTTAA
1 GGGTAAAAATGTAATTTTTGAGAAGTTTAA
* * **
50717 GGGCAAAAATGTAATTTTT-AAAAG-TTCG
1 GGGTAAAAATGTAATTTTTGAGAAGTTTAA
50745 GGGTAAAAATGTAATTTTTG-GAAGTTT-A
1 GGGTAAAAATGTAATTTTTGAGAAGTTTAA
* *
50773 GGG-GAAAATGTAA-TTTT-AGAAGTTTGA
1 GGGTAAAAATGTAATTTTTGAGAAGTTTAA
*
50800 GGG-AAAAATGTAATTTTTGA-AAGTTCAA
1 GGGTAAAAATGTAATTTTTGAGAAGTTTAA
* *
50828 GGGTTAAAATGTGATTTTTG-GAAGTTTAA
1 GGGTAAAAATGTAATTTTTGAGAAGTTTAA
* *
50857 GGG-AAAAATGTAATTTTT-AAAAGTTTAG
1 GGGTAAAAATGTAATTTTTGAGAAGTTTAA
50885 GGGTAAAAATGTAATTTTTGAGAAGTTTAA
1 GGGTAAAAATGTAATTTTTGAGAAGTTTAA
* * * *
50915 GGGTTAAAATGTGATTTTAGAAAAGTTT-A
1 GGGTAAAAATGTAATTTTTGAGAAGTTTAA
* * * * *
50944 GATGTTAAAATGTAATTTTGGAAAAGTTTAG
1 G-GGTAAAAATGTAATTTTTGAGAAGTTTAA
* * *
50975 GGGTTAAAATATGATTTTTG-GATAGTTTAA
1 GGGTAAAAATGTAATTTTTGAGA-AGTTTAA
51005 GG
1 GG
51007 ACCTTTTGGG
Statistics
Matches: 370, Mismatches: 65, Indels: 60
0.75 0.13 0.12
Matches are distributed among these distances:
26 11 0.03
27 22 0.06
28 82 0.22
29 120 0.32
30 128 0.35
31 7 0.02
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.36
Consensus pattern (30 bp):
GGGTAAAAATGTAATTTTTGAGAAGTTTAA
Found at i:52764 original size:6 final size:6
Alignment explanation
Indices: 52747--52870 Score: 94
Period size: 6 Copynumber: 20.8 Consensus size: 6
52737 GGACTTTTAA
* * *
52747 TTAAATT TTAAAT TTAAAT TCAAA- ATAAAT TTAAAT TTAAA- ATAAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * * * *
52794 TTAAAT TCAAAA ATAAGT TTAAAT TTAAA- ATAAAT TTAAAC TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
52840 ATAAAT TAAAAT TTAAAAT TTAAAAT TTAAA
1 TTAAAT TTAAAT TT-AAAT TT-AAAT TTAAA
52871 ATTGGGTTCA
Statistics
Matches: 91, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
5 15 0.16
6 58 0.64
7 18 0.20
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:52775 original size:17 final size:17
Alignment explanation
Indices: 52755--52858 Score: 154
Period size: 17 Copynumber: 6.1 Consensus size: 17
52745 AATTAAATTT
*
52755 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
52772 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
52789 TAAATTTAAATTCAAAAA
1 TAAATTTAAATT-TAAAA
*
52807 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
52824 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
52841 TAAATTAAAATTTAAAA
1 TAAATTTAAATTTAAAA
52858 T
1 T
52859 TTAAAATTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
17 63 0.81
18 15 0.19
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:52817 original size:52 final size:52
Alignment explanation
Indices: 52759--52857 Score: 162
Period size: 52 Copynumber: 1.9 Consensus size: 52
52749 AAATTTTAAA
* *
52759 TTTAAATTCAAAATAAATTTAAATTTAAAATAAATTTAAATTCAAAAATAAG
1 TTTAAATTCAAAATAAATTTAAACTTAAAATAAATTAAAATTCAAAAATAAG
* *
52811 TTTAAATTTAAAATAAATTTAAACTTAAAATAAATTAAAATTTAAAA
1 TTTAAATTCAAAATAAATTTAAACTTAAAATAAATTAAAATTCAAAA
52858 TTTAAAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (52 bp):
TTTAAATTCAAAATAAATTTAAACTTAAAATAAATTAAAATTCAAAAATAAG
Found at i:52864 original size:14 final size:14
Alignment explanation
Indices: 52845--52873 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
52835 TTAAAATAAA
52845 TTAAAATTTAAAAT
1 TTAAAATTTAAAAT
52859 TTAAAATTTAAAAT
1 TTAAAATTTAAAAT
52873 T
1 T
52874 GGGTTCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAAATTTAAAAT
Found at i:57545 original size:19 final size:19
Alignment explanation
Indices: 57521--57557 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
57511 TAATCGAACA
57521 GACCCGAACCCGTTGACCC
1 GACCCGAACCCGTTGACCC
57540 GACCCGAACCCGTTGACC
1 GACCCGAACCCGTTGACC
57558 ATTGACAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.46, G:0.22, T:0.11
Consensus pattern (19 bp):
GACCCGAACCCGTTGACCC
Found at i:57575 original size:21 final size:21
Alignment explanation
Indices: 57549--57611 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
57539 CGACCCGAAC
57549 CCGTTGACCATTGA-CAGTTGA
1 CCGTTGACCATTGATC-GTTGA
57570 CCGTTGACCATTGATCGTTGA
1 CCGTTGACCATTGATCGTTGA
* *
57591 CCGTTGA-CTTTGATCATTGA
1 CCGTTGACCATTGATCGTTGA
57611 C
1 C
57612 TTTTTTAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
20 12 0.31
21 26 0.67
22 1 0.03
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (21 bp):
CCGTTGACCATTGATCGTTGA
Found at i:57583 original size:14 final size:14
Alignment explanation
Indices: 57549--57598 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
57539 CGACCCGAAC
*
57549 CCGTTGACCATTGA
1 CCGTTGACCGTTGA
*
57563 CAGTTGACCGTTGA
1 CCGTTGACCGTTGA
* *
57577 CCATTGATCGTTGA
1 CCGTTGACCGTTGA
57591 CCGTTGAC
1 CCGTTGAC
57599 TTTGATCATT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (14 bp):
CCGTTGACCGTTGA
Found at i:59270 original size:14 final size:14
Alignment explanation
Indices: 59250--59289 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
59240 ATCTTCAAGT
59250 ATATTTATTATGAT-
1 ATATTTATTAT-ATC
*
59264 TTATTTATTATATC
1 ATATTTATTATATC
59278 ATATTTATTATA
1 ATATTTATTATA
59290 ATTAGAGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (14 bp):
ATATTTATTATATC
Found at i:64173 original size:16 final size:17
Alignment explanation
Indices: 64152--64185 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
64142 ACCCTAATTT
*
64152 TTTTTTATAAAT-ATAG
1 TTTTTTACAAATAATAG
64168 TTTTTTACAAATAATAG
1 TTTTTTACAAATAATAG
64185 T
1 T
64186 AATTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (17 bp):
TTTTTTACAAATAATAG
Found at i:68993 original size:2 final size:2
Alignment explanation
Indices: 68986--69016 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
68976 ATAGATGTTA
68986 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69017 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69626 original size:340 final size:340
Alignment explanation
Indices: 69006--69648 Score: 1214
Period size: 340 Copynumber: 1.9 Consensus size: 340
68996 ATATATATAT
*
69006 ATATATATATAGAGAGAGAGAGAGAGAGATTTCCTTCTTTAGCATTCAAAGTAAAATCAGATGGT
1 ATATATAAATAGAGAGAGAGAGAGAGAGATTTCCTTCTTTAGCATTCAAAGTAAAATCAGATGGT
*
69071 AAAAAATGTATGAAAAGATAACGGAACAATGTCGTGTTAAGTGTCAAAGGAAAGGTTAGGGTAGG
66 AAAAAATGAATGAAAAGATAACGGAACAATGTCGTGTTAAGTGTCAAAGGAAAGGTTAGGGTAGG
69136 GCAGGGGTTTTGCCTCTACATTCTCGGCATTTCACTGTCTGACCAATTATATAATCTTTAAGTAA
131 GCAGGGGTTTTGCCTCTACATTCTCGGCATTTCACTGTCTGACCAATTATATAATCTTTAAGTAA
*
69201 CTAACTCCTACCTGTATGCATACACACGCAGACACAGACATACACAAAACCATACACACCATGCA
196 CAAACTCCTACCTGTATGCATACACACGCAGACACAGACATACACAAAACCATACACACCATGCA
69266 AACTCATTAAATCCAACAATACCCTGTGGATTCTGCAACTGCTTGTGGAAGTTGTATTAAACAAT
261 AACTCATTAAATCCAACAATACCCTGTGGATTCTGCAACTGCTTGTGGAAGTTGTATTAAACAAT
69331 CCAGCCTGGATATTA
326 CCAGCCTGGATATTA
* *
69346 ATATATAAATATATAGAGAGAGAGAGAGATTTCCTTCTTTAGCATTCAAAGTAAAATCAGATGGT
1 ATATATAAATAGAGAGAGAGAGAGAGAGATTTCCTTCTTTAGCATTCAAAGTAAAATCAGATGGT
*
69411 AAAAAATGAATGAAAAGATAACGGAACAATGTCGTGTTAAGTGTCAAATGAAAGGTTAGGGTAGG
66 AAAAAATGAATGAAAAGATAACGGAACAATGTCGTGTTAAGTGTCAAAGGAAAGGTTAGGGTAGG
69476 GCAGGGGTTTTGCCTCTACATTCTCGGCATTTCACTGTCTGACCAATTATATAATCTTTAAGTAA
131 GCAGGGGTTTTGCCTCTACATTCTCGGCATTTCACTGTCTGACCAATTATATAATCTTTAAGTAA
*
69541 CAAACTCCTACCTGTATGCTTACACACGCAGACACAGACATACACAAAACCATACACACCATGCA
196 CAAACTCCTACCTGTATGCATACACACGCAGACACAGACATACACAAAACCATACACACCATGCA
*
69606 AACTCATTAAATCCAACAATACCCTGTGGATTCTGCAATTGCT
261 AACTCATTAAATCCAACAATACCCTGTGGATTCTGCAACTGCT
69649 GATTATCAAA
Statistics
Matches: 295, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
340 295 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (340 bp):
ATATATAAATAGAGAGAGAGAGAGAGAGATTTCCTTCTTTAGCATTCAAAGTAAAATCAGATGGT
AAAAAATGAATGAAAAGATAACGGAACAATGTCGTGTTAAGTGTCAAAGGAAAGGTTAGGGTAGG
GCAGGGGTTTTGCCTCTACATTCTCGGCATTTCACTGTCTGACCAATTATATAATCTTTAAGTAA
CAAACTCCTACCTGTATGCATACACACGCAGACACAGACATACACAAAACCATACACACCATGCA
AACTCATTAAATCCAACAATACCCTGTGGATTCTGCAACTGCTTGTGGAAGTTGTATTAAACAAT
CCAGCCTGGATATTA
Found at i:80086 original size:12 final size:12
Alignment explanation
Indices: 80069--80093 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
80059 AATATTAATA
80069 TTAAAATAAGAT
1 TTAAAATAAGAT
80081 TTAAAATAAGAT
1 TTAAAATAAGAT
80093 T
1 T
80094 ATATTGGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TTAAAATAAGAT
Found at i:82033 original size:10 final size:9
Alignment explanation
Indices: 82018--82044 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
82008 ATAATCTCTG
82018 AAAAAAATA
1 AAAAAAATA
82027 AAAAAAATA
1 AAAAAAATA
82036 AAAAAAATA
1 AAAAAAATA
82045 CTTCATCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAATA
Found at i:87253 original size:27 final size:25
Alignment explanation
Indices: 87223--87283 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
87213 AAAGAAAAAG
*
87223 AGAAAAAAATAGTATTTGAAGATG-ATA
1 AGAAAAAAATA--AATTGAA-ATGAATA
*
87250 AGAAAAATATAAATTGAAATGAATA
1 AGAAAAAAATAAATTGAAATGAATA
87275 AGAAAAAAA
1 AGAAAAAAA
87284 ATTTATGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 3 0.10
25 17 0.57
27 10 0.33
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (25 bp):
AGAAAAAAATAAATTGAAATGAATA
Found at i:87334 original size:28 final size:28
Alignment explanation
Indices: 87303--87398 Score: 76
Period size: 27 Copynumber: 3.5 Consensus size: 28
87293 ATAAAGAAAT
87303 AAAAGAAAGAGGAAATGAATAGATAAAA
1 AAAAGAAAGAGGAAATGAATAGATAAAA
* * **
87331 AAAAGAAA-AGAAAAAGAAATTAG-T-AGG
1 AAAAGAAAGAGGAAATG-AA-TAGATAAAA
87358 AAAAGAAAGA-GAAATGAATAGA-AATAA
1 AAAAGAAAGAGGAAATGAATAGATAA-AA
* *
87385 AAAAAAAATAGGAA
1 AAAAGAAAGAGGAA
87399 GAAAAATGTG
Statistics
Matches: 51, Mismatches: 10, Indels: 14
0.68 0.13 0.19
Matches are distributed among these distances:
25 3 0.06
26 3 0.06
27 27 0.53
28 15 0.29
29 3 0.06
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (28 bp):
AAAAGAAAGAGGAAATGAATAGATAAAA
Found at i:89990 original size:45 final size:45
Alignment explanation
Indices: 89939--90071 Score: 146
Period size: 45 Copynumber: 3.0 Consensus size: 45
89929 CATGCTTTCA
* * * *
89939 CATGATGTCATAGCATCTTTTAACTATGGTCTTGCTCAT-TTCTCT
1 CATGATGTCATAACATCTTTTAGCTATGGTCTTACTCATCTT-TAT
* *
89984 CATGATG-CTATAACGTCTTTCAGCTATGGTCTTACTCATCTTTAT
1 CATGATGTC-ATAACATCTTTTAGCTATGGTCTTACTCATCTTTAT
* * *
90029 CATGACGTCATAACATCTTTTAGCTATGATCTTAATCAT-TTTA
1 CATGATGTCATAACATCTTTTAGCTATGGTCTTACTCATCTTTA
90072 GGCATATAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
44 5 0.07
45 66 0.89
46 3 0.04
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (45 bp):
CATGATGTCATAACATCTTTTAGCTATGGTCTTACTCATCTTTAT
Found at i:94279 original size:71 final size:71
Alignment explanation
Indices: 94163--94314 Score: 286
Period size: 71 Copynumber: 2.1 Consensus size: 71
94153 TATCTTATTG
94163 CATTAATTTTTTACATATAATAGTTTTCAAACATAAACAAGTCACAACATTAAGGTTTTAATTCA
1 CATTAATTTTTTACATATAATAGTTTTCAAACATAAACAAGTCACAACATTAAGGTTTTAATTCA
94228 TTTCGC
66 TTTCGC
94234 CATTAATTTTTTACATATAATAGTTTTCAAACATAAACAAGTCACAACATTAAGGTTTTAATTCA
1 CATTAATTTTTTACATATAATAGTTTTCAAACATAAACAAGTCACAACATTAAGGTTTTAATTCA
94299 TTTCGC
66 TTTCGC
* *
94305 CCTTCATTTT
1 CATTAATTTT
94315 ATTCAATTTC
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 79 1.00
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (71 bp):
CATTAATTTTTTACATATAATAGTTTTCAAACATAAACAAGTCACAACATTAAGGTTTTAATTCA
TTTCGC
Found at i:94370 original size:53 final size:53
Alignment explanation
Indices: 94307--94413 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
94297 CATTTCGCCC
* *
94307 TTCATTTTATTCAATTTCAATCATAGCAATTTACATTCACAATCAAATGTTAT
1 TTCATTTTATTCAATTTCAATCATAACAATTTACATTCACAATCAAATCTTAT
94360 TTCATTTTATTCAATTTCAATCATAACAATTTACATTCACAATCAAATCTTAT
1 TTCATTTTATTCAATTTCAATCATAACAATTTACATTCACAATCAAATCTTAT
94413 T
1 T
94414 GGCAATGTCT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.44
Consensus pattern (53 bp):
TTCATTTTATTCAATTTCAATCATAACAATTTACATTCACAATCAAATCTTAT
Found at i:100253 original size:73 final size:72
Alignment explanation
Indices: 100134--100287 Score: 274
Period size: 73 Copynumber: 2.1 Consensus size: 72
100124 TATTTTTGTT
100134 ATTATTAATCCCCTTATCTTATTCAGATATTTATTTATTTTATATTATTTATATAAAAAAACCCT
1 ATTATTAATCCCCTTATCTTATTCAGATATTTATTTATTTTATATTATTTATAT-AAAAAACCCT
100199 AAAAAATC
65 AAAAAATC
* *
100207 ATTATTAATCCTCTTATCTTATTCTGATATTTATTTATTTTATATTATTTATATAAAAAACCCTA
1 ATTATTAATCCCCTTATCTTATTCAGATATTTATTTATTTTATATTATTTATATAAAAAACCCTA
100272 AAAAATC
66 AAAAATC
100279 ATTA-TAATC
1 ATTATTAATC
100288 AATAGTATCT
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
71 5 0.06
72 22 0.28
73 52 0.66
ACGTcount: A:0.39, C:0.13, G:0.01, T:0.47
Consensus pattern (72 bp):
ATTATTAATCCCCTTATCTTATTCAGATATTTATTTATTTTATATTATTTATATAAAAAACCCTA
AAAAATC
Found at i:101504 original size:14 final size:14
Alignment explanation
Indices: 101485--101522 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
101475 TCTTAATATA
*
101485 ATTTAAAATTATTT
1 ATTTAAAATAATTT
101499 ATTT-AAATAATTT
1 ATTTAAAATAATTT
*
101512 AATTAAAATAA
1 ATTTAAAATAA
101523 AATATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTTAAAATAATTT
Found at i:102468 original size:18 final size:17
Alignment explanation
Indices: 102425--102469 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
102415 TATTTATCAA
*
102425 AATAAAATTAAATATAG
1 AATAAAATTAAATAGAG
102442 ATCATAAAATTAAATACGAG
1 A--ATAAAATTAAATA-GAG
102462 AATAAAAT
1 AATAAAAT
102470 ACAATATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 7 0.29
19 13 0.54
20 3 0.12
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (17 bp):
AATAAAATTAAATAGAG
Found at i:105476 original size:28 final size:28
Alignment explanation
Indices: 105417--105502 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 28
105407 GATATTTTTC
* *
105417 ATTTGAAATTAATTAAGTTTATGAA--TGA
1 ATTTGAAATTAATTATGTTTA--AATTTGT
105445 ATTTGAAATTAATTATGTTTAAATTTGT
1 ATTTGAAATTAATTATGTTTAAATTTGT
* * **
105473 ATTT--AATTAATAATTTTTATGTTTGT
1 ATTTGAAATTAATTATGTTTAAATTTGT
105499 ATTT
1 ATTT
105503 TGGTTTAGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
26 24 0.48
28 26 0.52
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.53
Consensus pattern (28 bp):
ATTTGAAATTAATTATGTTTAAATTTGT
Found at i:105491 original size:26 final size:26
Alignment explanation
Indices: 105451--105502 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
105441 ATGAATTTGA
*
105451 AATTAATTATGTTTAAATTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
* **
105477 AATTAATAATTTTTATGTTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
105503 TGGTTTAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (26 bp):
AATTAATAATGTTTAAATTTGTATTT
Found at i:105678 original size:17 final size:16
Alignment explanation
Indices: 105656--105705 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
105646 CGGTTCATGG
*
105656 TTTAAGGTTTATAATT
1 TTTAAGGTTTAGAATT
* *
105672 ATTTAAGATTTAGGATT
1 -TTTAAGGTTTAGAATT
*
105689 TTTAAGGTTTAGGATT
1 TTTAAGGTTTAGAATT
105705 T
1 T
105706 AAAAGTTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (16 bp):
TTTAAGGTTTAGAATT
Found at i:105694 original size:16 final size:16
Alignment explanation
Indices: 105673--105705 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
105663 TTTATAATTA
105673 TTTAAGATTTAGGATT
1 TTTAAGATTTAGGATT
*
105689 TTTAAGGTTTAGGATT
1 TTTAAGATTTAGGATT
105705 T
1 T
105706 AAAAGTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (16 bp):
TTTAAGATTTAGGATT
Found at i:106833 original size:43 final size:43
Alignment explanation
Indices: 106768--106864 Score: 149
Period size: 43 Copynumber: 2.3 Consensus size: 43
106758 AATTGCACAA
* *
106768 TTAATAACATGTCACGATATTAATAAGAGTAAAGTAATATAAT
1 TTAATAACATGCCACGATATTAACAAGAGTAAAGTAATATAAT
* * *
106811 TTAGTAACATGCCACGATATTAACATGAGTCAAGTAATATAAT
1 TTAATAACATGCCACGATATTAACAAGAGTAAAGTAATATAAT
106854 TTAATAACATG
1 TTAATAACATG
106865 TCAATGAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.32
Consensus pattern (43 bp):
TTAATAACATGCCACGATATTAACAAGAGTAAAGTAATATAAT
Found at i:108289 original size:23 final size:24
Alignment explanation
Indices: 108250--108300 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
108240 TAATAGGGAT
108250 TTTCAATTTACAATTCA-TATCAC
1 TTTCAATTTACAATTCACTATCAC
* *
108273 TTTCAA-TTCCAATTTCACTTTCAC
1 TTTCAATTTACAA-TTCACTATCAC
108297 TTTC
1 TTTC
108301 GCTTTCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 10 0.42
24 9 0.38
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTCAATTTACAATTCACTATCAC
Found at i:110748 original size:21 final size:21
Alignment explanation
Indices: 110724--110779 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
110714 TAGTGTAGAC
*
110724 TTCTACCGATACAAGTGACAA
1 TTCTACCGATACAAGTAACAA
* **
110745 TTCTACCGATATAAGTAACTC
1 TTCTACCGATACAAGTAACAA
*
110766 TTCTATCGATACAA
1 TTCTACCGATACAA
110780 ATCTTGCTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAGTAACAA
Found at i:111612 original size:52 final size:52
Alignment explanation
Indices: 111534--111719 Score: 304
Period size: 52 Copynumber: 3.6 Consensus size: 52
111524 TTCTCATTTA
*
111534 ATACTCACGATGACACATTGTCATCGGACCTCATAATCTGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGAATCAT
* *
111586 ATACTCACGATGACACATAGTCATCGGACCTCATCAT-TCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCT-GTAAAGGAATCAT
*
111638 ATACTCACGATGACACATAGTCATTGGACCTCATAATCTGTAAAGG-ATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGAATCAT
*
111689 ATACTCACGATGACACATAGTCATTGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
111720 TTTTCATTTA
Statistics
Matches: 126, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
51 36 0.29
52 89 0.71
53 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGAATCAT
Found at i:115594 original size:20 final size:20
Alignment explanation
Indices: 115571--115638 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
115561 CATATCATGG
*
115571 TATCGATATTTTTCAAATCT
1 TATCGATATTTTTCAAATAT
* ** *
115591 TATCGATA-CTTAAAAATAGG
1 TATCGATATTTTTCAAATA-T
*
115611 TATCAATATTTTTCAAATAT
1 TATCGATATTTTTCAAATAT
115631 TATCGATA
1 TATCGATA
115639 CCTTTGAATG
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
19 6 0.17
20 22 0.63
21 7 0.20
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (20 bp):
TATCGATATTTTTCAAATAT
Found at i:115613 original size:40 final size:39
Alignment explanation
Indices: 115529--115667 Score: 138
Period size: 40 Copynumber: 3.5 Consensus size: 39
115519 TTTGAAAGAG
* * * **
115529 GGTATCGATATTATACAAA-CATTATCGATACTCATATCAT
1 GGTATCGATATTTTTCAAATC-TTATCGATACTTA-AAAAT
115569 GGTATCGATATTTTTCAAATCTTATCGATACTTAAAAAT
1 GGTATCGATATTTTTCAAATCTTATCGATACTTAAAAAT
* * **
115608 AGGTATCAATATTTTTCAAATATTATCGATACCTT-TGAAT
1 -GGTATCGATATTTTTCAAATCTTATCGATA-CTTAAAAAT
115648 GGGTATCGATATTTTTCAAA
1 -GGTATCGATATTTTTCAAA
115668 CGTTTAAAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 3 0.04
40 78 0.92
41 4 0.05
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (39 bp):
GGTATCGATATTTTTCAAATCTTATCGATACTTAAAAAT
Found at i:118192 original size:21 final size:20
Alignment explanation
Indices: 118140--118192 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
118130 TCGATACTTA
*
118140 AAAACTGGTATCGATATTTTT
1 AAAA-TGGTATCAATATTTTT
* **
118161 AGAATAATATCAATATTTTTT
1 AAAATGGTATCAATA-TTTTT
118182 AAAATGGTATC
1 AAAATGGTATC
118193 GTTACCAAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.42
Consensus pattern (20 bp):
AAAATGGTATCAATATTTTT
Found at i:120882 original size:89 final size:89
Alignment explanation
Indices: 120730--120907 Score: 338
Period size: 89 Copynumber: 2.0 Consensus size: 89
120720 GACTAATACA
* *
120730 ATGTTCATTGCAAAAGTTATTAAAACCAAGGTTTTCAAATTCTTTTCCATGACCACTTTTTACAC
1 ATGTTCATTGCAAAAGTTATTAAAACCAAGATTTTCAAATTCTTTTCCATGACCACTTCTTACAC
120795 TTGAAATCATATATCCCACTTGAT
66 TTGAAATCATATATCCCACTTGAT
120819 ATGTTCATTGCAAAAGTTATTAAAACCAAGATTTTCAAATTCTTTTCCATGACCACTTCTTACAC
1 ATGTTCATTGCAAAAGTTATTAAAACCAAGATTTTCAAATTCTTTTCCATGACCACTTCTTACAC
120884 TTGAAATCATATATCCCACTTGAT
66 TTGAAATCATATATCCCACTTGAT
120908 TTTGAATCAT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (89 bp):
ATGTTCATTGCAAAAGTTATTAAAACCAAGATTTTCAAATTCTTTTCCATGACCACTTCTTACAC
TTGAAATCATATATCCCACTTGAT
Found at i:124398 original size:40 final size:41
Alignment explanation
Indices: 124313--124413 Score: 127
Period size: 40 Copynumber: 2.5 Consensus size: 41
124303 TTTTGAAAGA
* * *
124313 GGGTATCGATATTATACAAACATTATCGATACTCATATCAT
1 GGGTATCGATATTTTTCAAACATTATCGATACTCATATAAT
* *
124354 -GGTATCGATATTTTTCAAATATTATCGATAC-C-TTTGAAT
1 GGGTATCGATATTTTTCAAACATTATCGATACTCATAT-AAT
124393 GGGTATCGATATTTTTCAAAC
1 GGGTATCGATATTTTTCAAAC
124414 GTTTCAAAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
38 2 0.04
39 3 0.06
40 47 0.90
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (41 bp):
GGGTATCGATATTTTTCAAACATTATCGATACTCATATAAT
Found at i:124970 original size:3 final size:3
Alignment explanation
Indices: 124964--124989 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
124954 GATGATGATG
124964 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
124990 GTTTATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:125877 original size:11 final size:12
Alignment explanation
Indices: 125853--125879 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
125843 AAATACACTT
125853 AAAAACATTAAA
1 AAAAACATTAAA
125865 AAAAACATTAAA
1 AAAAACATTAAA
125877 AAA
1 AAA
125880 TTAATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAACATTAAA
Found at i:126051 original size:12 final size:12
Alignment explanation
Indices: 126034--126149 Score: 69
Period size: 12 Copynumber: 9.9 Consensus size: 12
126024 ATAACATCCA
*
126034 AACAACAAAAAT
1 AACAACAAAAAC
126046 AACAACAAAAAC
1 AACAACAAAAAC
* * *
126058 AGCAGCAAAAAT
1 AACAACAAAAAC
**
126070 AAC-AGTAAAAC
1 AACAACAAAAAC
**
126081 AACATTAAAAAC
1 AACAACAAAAAC
* *
126093 AACAGCAAAAAT
1 AACAACAAAAAC
* *
126105 AAC-ACGAAAAT
1 AACAACAAAAAC
*
126116 AGCAATC-AAAAC
1 AACAA-CAAAAAC
*
126128 AATAA-AAAAAC
1 AACAACAAAAAC
126139 AACAACAAAAA
1 AACAACAAAAA
126150 ACAGTAAAAA
Statistics
Matches: 77, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
11 24 0.31
12 52 0.68
13 1 0.01
ACGTcount: A:0.69, C:0.18, G:0.05, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:126103 original size:24 final size:24
Alignment explanation
Indices: 126034--126116 Score: 71
Period size: 23 Copynumber: 3.5 Consensus size: 24
126024 ATAACATCCA
* *
126034 AACAACAAAAATAACAACAAAAAC
1 AACAGCAAAAATAACAGCAAAAAC
* *
126058 AGCAGCAAAAATAACAG-TAAAAC
1 AACAGCAAAAATAACAGCAAAAAC
** * *
126081 AACATTAAAAACAACAGCAAAAAT
1 AACAGCAAAAATAACAGCAAAAAC
*
126105 AACA-CGAAAATA
1 AACAGCAAAAATA
126117 GCAATCAAAA
Statistics
Matches: 45, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
23 23 0.51
24 22 0.49
ACGTcount: A:0.67, C:0.18, G:0.06, T:0.08
Consensus pattern (24 bp):
AACAGCAAAAATAACAGCAAAAAC
Found at i:126129 original size:35 final size:35
Alignment explanation
Indices: 126041--126108 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
126031 CCAAACAACA
* * *
126041 AAAATAACAACAAAAACAGCAGCAAAAATAACAGT
1 AAAACAACAATAAAAACAACAGCAAAAATAACAGT
*
126076 AAAACAACATTAAAAACAACAGCAAAAATAACA
1 AAAACAACAATAAAAACAACAGCAAAAATAACA
126109 CGAAAATAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.68, C:0.18, G:0.06, T:0.09
Consensus pattern (35 bp):
AAAACAACAATAAAAACAACAGCAAAAATAACAGT
Found at i:127239 original size:16 final size:16
Alignment explanation
Indices: 127218--127252 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
127208 AACATAATAT
127218 AATAAACATATT-TAAA
1 AATAAACAT-TTATAAA
127234 AATAAACATTTATAAA
1 AATAAACATTTATAAA
127250 AAT
1 AAT
127253 TTAATTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAAACATTTATAAA
Found at i:132696 original size:24 final size:24
Alignment explanation
Indices: 132664--132709 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
132654 GATGTTTAAC
132664 TTTTCATTTTATTTAA-CTTTCAAT
1 TTTTCATTTT-TTTAATCTTTCAAT
*
132688 TTTTTATTTTTTTAATCTTTCA
1 TTTTCATTTTTTTAATCTTTCA
132710 TGTAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTCATTTTTTTAATCTTTCAAT
Found at i:137875 original size:2 final size:2
Alignment explanation
Indices: 137868--137905 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
137858 GGAGTAAATT
137868 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
137906 TATATATATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:138116 original size:24 final size:24
Alignment explanation
Indices: 138065--138117 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
138055 TAAATGGATG
* * *
138065 TTTAACCTTTCATCTCCCTTGACT
1 TTTAACCTTCCATCTCCCTTAACA
* *
138089 TTTAACCTTCCATCTTCTTTAACA
1 TTTAACCTTCCATCTCCCTTAACA
138113 TTTAA
1 TTTAA
138118 TATTTTTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.23, C:0.28, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTAACCTTCCATCTCCCTTAACA
Found at i:138907 original size:18 final size:18
Alignment explanation
Indices: 138872--138905 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
138862 GGTTTTTAAT
138872 TAAATTTCTAATAATTTA
1 TAAATTTCTAATAATTTA
*
138890 TAAATTT-TAATTATTT
1 TAAATTTCTAATAATTT
138906 TAATGATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TAAATTTCTAATAATTTA
Found at i:139056 original size:22 final size:22
Alignment explanation
Indices: 139031--139072 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
139021 TTTTTAAATA
139031 ATTTAAAATATTTTTATTTTTT
1 ATTTAAAATATTTTTATTTTTT
** *
139053 ATTTTTATTATTTTTATTTT
1 ATTTAAAATATTTTTATTTT
139073 ATTGAGTGGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (22 bp):
ATTTAAAATATTTTTATTTTTT
Found at i:139057 original size:13 final size:15
Alignment explanation
Indices: 139039--139072 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
139029 TAATTTAAAA
139039 TATTTTTA-T-TTTT
1 TATTTTTATTATTTT
139052 TATTTTTATTATTTT
1 TATTTTTATTATTTT
139067 TATTTT
1 TATTTT
139073 ATTGAGTGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 1 0.05
15 10 0.53
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TATTTTTATTATTTT
Found at i:140861 original size:14 final size:14
Alignment explanation
Indices: 140842--140879 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
140832 TGTTTTACTG
140842 AAAATGACTTCCGA
1 AAAATGACTTCCGA
* *
140856 AAAATGATTTCTGA
1 AAAATGACTTCCGA
140870 AAAATGACTT
1 AAAATGACTT
140880 ATTTTTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (14 bp):
AAAATGACTTCCGA
Found at i:141471 original size:13 final size:14
Alignment explanation
Indices: 141433--141474 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
141423 TATGTGAAGA
141433 ATATTATTTAAAATT
1 ATATTA-TTAAAATT
*
141448 ATCATTTTTAAAATT
1 AT-ATTATTAAAATT
141463 -TATTATTAAAAT
1 ATATTATTAAAAT
141475 AAAATTGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 10 0.42
16 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTATTAAAATT
Found at i:141530 original size:16 final size:16
Alignment explanation
Indices: 141484--141533 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
141474 TAAAATTGAC
141484 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
**
141501 -TA--AATAATAAATT
1 ATATTAATAATTTATT
141514 ATATTAATAATTTATT
1 ATATTAATAATTTATT
141530 ATAT
1 ATAT
141534 GTCTAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 9 0.35
14 2 0.08
16 15 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:142317 original size:17 final size:16
Alignment explanation
Indices: 142280--142343 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
142270 TCTATATTAC
142280 AATAAATCATAAAATA
1 AATAAATCATAAAATA
*
142296 GATAATATCA-AAAACTA
1 AATAA-ATCATAAAA-TA
142313 AAT-AA-C-TAAAATA
1 AATAAATCATAAAATA
142326 AATAAA-CAATAAAATA
1 AATAAATC-ATAAAATA
142342 AA
1 AA
142344 CAAACAACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
13 5 0.12
14 8 0.20
15 1 0.03
16 18 0.45
17 8 0.20
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.22
Consensus pattern (16 bp):
AATAAATCATAAAATA
Found at i:142340 original size:16 final size:16
Alignment explanation
Indices: 142319--142350 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
142309 ACTAAATAAC
*
142319 TAAAATAAATAAACAA
1 TAAAATAAACAAACAA
142335 TAAAATAAACAAACAA
1 TAAAATAAACAAACAA
142351 CTAAGCCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (16 bp):
TAAAATAAACAAACAA
Found at i:147518 original size:19 final size:20
Alignment explanation
Indices: 147472--147522 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
147462 AATGCCCAAC
* *
147472 CTGACCCATTGACCCGTTAA
1 CTGACCTATTGACCCATTAA
147492 CTGACCTATTGACCCATTAA
1 CTGACCTATTGACCCATTAA
147512 C-GACCTATTGA
1 CTGACCTATTGA
147523 TTTGACCGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.27
Consensus pattern (20 bp):
CTGACCTATTGACCCATTAA
Found at i:150463 original size:41 final size:41
Alignment explanation
Indices: 150406--150489 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
150396 ATAGTGCACT
150406 TAACAAAAATACCCAGTTCCATAGATACAGTACTAGCTATA
1 TAACAAAAATACCCAGTTCCATAGATACAGTACTAGCTATA
150447 TAACAAAAATACCCAGTTCCATAGATACAGTACTAGCTATA
1 TAACAAAAATACCCAGTTCCATAGATACAGTACTAGCTATA
150488 TA
1 TA
150490 GGAATAAGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (41 bp):
TAACAAAAATACCCAGTTCCATAGATACAGTACTAGCTATA
Found at i:160627 original size:5 final size:5
Alignment explanation
Indices: 160617--160642 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
160607 ACATATATCT
160617 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
160643 CTTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:161244 original size:17 final size:18
Alignment explanation
Indices: 161212--161251 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
161202 ACTAAATTCT
*
161212 AATGACAAATGGAAATGC
1 AATGACAAATGCAAATGC
161230 AATGAC-AATGCAAATGC
1 AATGACAAATGCAAATGC
161247 AATGA
1 AATGA
161252 TAGTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.50, C:0.12, G:0.20, T:0.17
Consensus pattern (18 bp):
AATGACAAATGCAAATGC
Found at i:165244 original size:25 final size:25
Alignment explanation
Indices: 165193--165356 Score: 186
Period size: 25 Copynumber: 6.5 Consensus size: 25
165183 CAATGTTTAG
*
165193 CTCTTACGAGCCCAGATAGAATATCA
1 CTCTTACGAG-CCAGACAGAATATCA
*
165219 CTCTTACGAGCCAAACAGAATATCA
1 CTCTTACGAGCCAGACAGAATATCA
*
165244 CTCTTACAAGCCAGACA-AGATATCA
1 CTCTTACGAGCCAGACAGA-ATATCA
* * *
165269 CTCTTACGAGCCAGATAGGATATCG
1 CTCTTACGAGCCAGACAGAATATCA
* **
165294 CTCTTACGAGCCAGACAGGATATTG
1 CTCTTACGAGCCAGACAGAATATCA
* * *
165319 CTCTTACGAGCCATATAGAATATCG
1 CTCTTACGAGCCAGACAGAATATCA
*
165344 CTCTTATGAGCCA
1 CTCTTACGAGCCA
165357 AAGTTAAGAA
Statistics
Matches: 121, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
24 1 0.01
25 110 0.91
26 10 0.08
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (25 bp):
CTCTTACGAGCCAGACAGAATATCA
Found at i:165348 original size:75 final size:75
Alignment explanation
Indices: 165192--165356 Score: 206
Period size: 75 Copynumber: 2.2 Consensus size: 75
165182 ACAATGTTTA
165192 GCTCTTACGAGCCCAGATAGAATATCACTCTTACGAGCCAAACAGAATATCACTCTTACAAGCCA
1 GCTCTTACGAG-CCAGATAGAATATCACTCTTACGAGCCAAACAGAATATCACTCTTACAAGCCA
165257 GACAAGATATC
65 GACAAGATATC
* * * * * ** * *
165268 ACTCTTACGAGCCAGATAGGATATCGCTCTTACGAGCCAGACAGGATATTGCTCTTACGAGCCAT
1 GCTCTTACGAGCCAGATAGAATATCACTCTTACGAGCCAAACAGAATATCACTCTTACAAGCCAG
*
165333 A-TAGAATATC
66 ACAAG-ATATC
*
165343 GCTCTTATGAGCCA
1 GCTCTTACGAGCCA
165357 AAGTTAAGAA
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
74 2 0.03
75 64 0.84
76 10 0.13
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.24
Consensus pattern (75 bp):
GCTCTTACGAGCCAGATAGAATATCACTCTTACGAGCCAAACAGAATATCACTCTTACAAGCCAG
ACAAGATATC
Found at i:165355 original size:50 final size:50
Alignment explanation
Indices: 165192--165356 Score: 213
Period size: 50 Copynumber: 3.3 Consensus size: 50
165182 ACAATGTTTA
* * *
165192 GCTCTTACGAGCCCAGATAGAATATCACTCTTACGAGCCAAACAGAATATC
1 GCTCTTACGAG-CCAGACAGGATATCACTCTTACGAGCCAAATAGAATATC
* * * * *
165243 ACTCTTACAAGCCAGACAAGATATCACTCTTACGAGCCAGATAGGATATC
1 GCTCTTACGAGCCAGACAGGATATCACTCTTACGAGCCAAATAGAATATC
** *
165293 GCTCTTACGAGCCAGACAGGATATTGCTCTTACGAGCCATATAGAATATC
1 GCTCTTACGAGCCAGACAGGATATCACTCTTACGAGCCAAATAGAATATC
*
165343 GCTCTTATGAGCCA
1 GCTCTTACGAGCCA
165357 AAGTTAAGAA
Statistics
Matches: 98, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 89 0.91
51 9 0.09
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.24
Consensus pattern (50 bp):
GCTCTTACGAGCCAGACAGGATATCACTCTTACGAGCCAAATAGAATATC
Found at i:168228 original size:18 final size:18
Alignment explanation
Indices: 168194--168229 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
168184 AAGCCCAATC
*
168194 AACCCAACCCATTGACCG
1 AACCCAACCCATAGACCG
*
168212 AACCCAACCCGTAGACCG
1 AACCCAACCCATAGACCG
168230 TTGACTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.44, G:0.14, T:0.08
Consensus pattern (18 bp):
AACCCAACCCATAGACCG
Found at i:171201 original size:36 final size:36
Alignment explanation
Indices: 171154--171225 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
171144 TATTGGTTGA
171154 AGGATCTTCAGAGATTGTTTGTGGAGATGAACTATC
1 AGGATCTTCAGAGATTGTTTGTGGAGATGAACTATC
171190 AGGATCTTCAGAGATTGTTTGTGGAGATGAACTATC
1 AGGATCTTCAGAGATTGTTTGTGGAGATGAACTATC
171226 CTGCTGGGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (36 bp):
AGGATCTTCAGAGATTGTTTGTGGAGATGAACTATC
Found at i:177187 original size:13 final size:13
Alignment explanation
Indices: 177171--177195 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
177161 TAAATTTATT
177171 TTATTTTATTTTA
1 TTATTTTATTTTA
177184 TTATTTTATTTT
1 TTATTTTATTTT
177196 TGGGTTATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:177941 original size:13 final size:13
Alignment explanation
Indices: 177923--177950 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
177913 ATATATAAAA
177923 ATGTTTTACAATC
1 ATGTTTTACAATC
177936 ATGTTTTACAATC
1 ATGTTTTACAATC
177949 AT
1 AT
177951 TTTAGATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.46
Consensus pattern (13 bp):
ATGTTTTACAATC
Found at i:180480 original size:25 final size:25
Alignment explanation
Indices: 180430--180548 Score: 121
Period size: 25 Copynumber: 4.7 Consensus size: 25
180420 TCCAAAAATT
* * *
180430 TAGCTCATATGAGCCTAGACAGAATA
1 TAGCTCTTACGAGCC-AGATAGAATA
*
180456 TAGCTCTTACGAGTCAGATAGAATA
1 TAGCTCTTACGAGCCAGATAGAATA
* * * *
180481 TCGCTCTTATGAGCTAGATAGTATA
1 TAGCTCTTACGAGCCAGATAGAATA
* * *
180506 TCGCTCTTATGAGCCAGACAGAATA
1 TAGCTCTTACGAGCCAGATAGAATA
*
180531 TAGTTCTTACGAGCCAGA
1 TAGCTCTTACGAGCCAGA
180549 GTTCAAAAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
25 66 0.85
26 12 0.15
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (25 bp):
TAGCTCTTACGAGCCAGATAGAATA
Found at i:182134 original size:14 final size:15
Alignment explanation
Indices: 182115--182147 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
182105 ACTAACTTTT
182115 AATTCAATAATT-AA
1 AATTCAATAATTCAA
*
182129 AATTCACTAATTCAA
1 AATTCAATAATTCAA
182144 AATT
1 AATT
182148 TCATATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
AATTCAATAATTCAA
Found at i:184070 original size:12 final size:12
Alignment explanation
Indices: 184053--184082 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
184043 CCGTCATTGC
184053 CATCATTGCCAT
1 CATCATTGCCAT
*
184065 CATCATTTCCAT
1 CATCATTGCCAT
184077 CATCAT
1 CATCAT
184083 CGTTGTCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.33, G:0.03, T:0.37
Consensus pattern (12 bp):
CATCATTGCCAT
Found at i:187725 original size:25 final size:25
Alignment explanation
Indices: 187697--187977 Score: 292
Period size: 25 Copynumber: 11.2 Consensus size: 25
187687 AATTTCTGAA
* * *
187697 GTCTGACTCGTATGAGCGATATTTT
1 GTCTGGCTCGTAAGAGCGATATTCT
187722 GTCTGGCTCGTAAGAGCGATATTCT
1 GTCTGGCTCGTAAGAGCGATATTCT
* *
187747 GTCTGGCTCGTAAGAGTGATATCCT
1 GTCTGGCTCGTAAGAGCGATATTCT
* * * *
187772 ATCTGGCTCATAAGAGTGATATCCT
1 GTCTGGCTCGTAAGAGCGATATTCT
* * *
187797 ATCTAGCTCGTAAGAGCGATACTCT
1 GTCTGGCTCGTAAGAGCGATATTCT
* * *
187822 GTCTAGCTCGTAAGAGTGATATCCT
1 GTCTGGCTCGTAAGAGCGATATTCT
* * *
187847 ATCTGGCTCGTAAGAGCAATACTCT
1 GTCTGGCTCGTAAGAGCGATATTCT
* * *
187872 GTCTGGCTCGTAAAAACGATATTTT
1 GTCTGGCTCGTAAGAGCGATATTCT
*
187897 GTTTGGCTCGTAAGAGCGATATTCT
1 GTCTGGCTCGTAAGAGCGATATTCT
* * *
187922 ATTTGGATCGTAAGAGCGATATTCT
1 GTCTGGCTCGTAAGAGCGATATTCT
* * * **
187947 GTCTAGCTCGTACGGGTAATATTCT
1 GTCTGGCTCGTAAGAGCGATATTCT
187972 GTCTGG
1 GTCTGG
187978 GCTCATATGA
Statistics
Matches: 213, Mismatches: 43, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 213 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (25 bp):
GTCTGGCTCGTAAGAGCGATATTCT
Found at i:188960 original size:17 final size:18
Alignment explanation
Indices: 188935--188968 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
188925 TTAGTTTGCT
188935 GTAAATGTA-TGAAATTC
1 GTAAATGTATTGAAATTC
*
188952 GTAATTGTATTGAAATT
1 GTAAATGTATTGAAATT
188969 TGTATTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (18 bp):
GTAAATGTATTGAAATTC
Found at i:190530 original size:52 final size:52
Alignment explanation
Indices: 190448--190583 Score: 184
Period size: 52 Copynumber: 2.6 Consensus size: 52
190438 ATGCATTTTT
* * * * *
190448 TATACTCACAATGACACAGAGTCATCGGACCT-TTAATCCGTATTAGGAATCC
1 TATACTCACGATGACACATAGTCATCGGACCTCTTAATCCATA-AAGGAATCA
* * *
190500 TATACTGACGATGACACATAGTCATTGGACCTCTTAATCCATAAAGGATTCA
1 TATACTCACGATGACACATAGTCATCGGACCTCTTAATCCATAAAGGAATCA
190552 TATACTCACGATGACACATAGTCATCGGACCT
1 TATACTCACGATGACACATAGTCATCGGACCT
190584 ATTTCATTCA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
52 64 0.88
53 9 0.12
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (52 bp):
TATACTCACGATGACACATAGTCATCGGACCTCTTAATCCATAAAGGAATCA
Found at i:192184 original size:9 final size:9
Alignment explanation
Indices: 192167--192207 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
192157 TTTAGGGTTT
192167 AAAAA-AAG
1 AAAAAGAAG
192175 AAAAAGAAG
1 AAAAAGAAG
192184 -AAAAGAAG
1 AAAAAGAAG
*
192192 AAAAATAAG
1 AAAAAGAAG
*
192201 AAGAAGA
1 AAAAAGA
192208 GGAGAAGGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
8 13 0.46
9 15 0.54
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:192192 original size:17 final size:17
Alignment explanation
Indices: 192167--192207 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
192157 TTTAGGGTTT
*
192167 AAAAAAAGAAAAAGAAG
1 AAAAGAAGAAAAAGAAG
*
192184 AAAAGAAGAAAAATAAG
1 AAAAGAAGAAAAAGAAG
192201 AAGAAGA
1 AA-AAGA
192208 GGAGAAGGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAAGAAGAAAAAGAAG
Found at i:192875 original size:30 final size:31
Alignment explanation
Indices: 192810--192875 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
192800 TGTTAATCAA
* *
192810 TGACTGTTTTGTCACTTTTTGATAACGTTAG
1 TGACTATTTTGTCACTTTTTCATAACGTTAG
192841 TGACTATTTTGTCACTTTTTCA-AA-GTTGAG
1 TGACTATTTTGTCACTTTTTCATAACGTT-AG
192871 TGACT
1 TGACT
192876 GAAATGAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 3 0.09
30 9 0.28
31 20 0.62
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (31 bp):
TGACTATTTTGTCACTTTTTCATAACGTTAG
Found at i:196569 original size:72 final size:72
Alignment explanation
Indices: 196347--196603 Score: 383
Period size: 72 Copynumber: 3.6 Consensus size: 72
196337 CAATGTTAAA
*
196347 CTAGTTTTATCAGTAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
196412 GTGCAAT
66 GTGCAAT
* * * *
196419 CTAGCTTTATCAATAGTT-ATGATGAGTATGGTTTTTGGATATTGAATTTATGTTCTACTTATTT
1 CTAGTTTTATCAATAGTTGTTTAT--GTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTT
196483 ATGTGCAAT
64 ATGTGCAAT
* * *
196492 CTAGTTTTATCAACAATTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTTTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
196557 GTGCAAT
66 GTGCAAT
* * *
196564 TTAGTTTTATCAATAGTTGTTTATATTT-GATTTTGGATAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATAT
196604 AAAATTTGTT
Statistics
Matches: 165, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
71 14 0.08
72 86 0.52
73 62 0.38
74 3 0.02
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.53
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
GTGCAAT
Found at i:198753 original size:11 final size:11
Alignment explanation
Indices: 198737--198761 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
198727 GATTAATTTT
198737 TTAAAATAAAA
1 TTAAAATAAAA
198748 TTAAAATAAAA
1 TTAAAATAAAA
198759 TTA
1 TTA
198762 TCAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TTAAAATAAAA
Found at i:204008 original size:14 final size:14
Alignment explanation
Indices: 203989--204033 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
203979 AATTTGAATT
203989 TCGAGTTAAATGAA
1 TCGAGTTAAATGAA
204003 TCGAGTT--AT---
1 TCGAGTTAAATGAA
204012 TCGAGTTAAATGAA
1 TCGAGTTAAATGAA
204026 TCGAGTTA
1 TCGAGTTA
204034 TTCGAGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
9 7 0.27
11 2 0.08
12 2 0.08
14 15 0.58
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (14 bp):
TCGAGTTAAATGAA
Found at i:204018 original size:23 final size:23
Alignment explanation
Indices: 203988--204043 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
203978 AAATTTGAAT
203988 TTCGAGTTAAATGAATCGAGTTA
1 TTCGAGTTAAATGAATCGAGTTA
204011 TTCGAGTTAAATGAATCGAGTTA
1 TTCGAGTTAAATGAATCGAGTTA
204034 TTCGAGTTAA
1 TTCGAGTTAA
204044 TTCATTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (23 bp):
TTCGAGTTAAATGAATCGAGTTA
Found at i:205484 original size:13 final size:13
Alignment explanation
Indices: 205466--205494 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
205456 GGTGAGCTTC
205466 TTAGATACACCCA
1 TTAGATACACCCA
205479 TTAGATACACCCA
1 TTAGATACACCCA
205492 TTA
1 TTA
205495 AAGTTGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.28
Consensus pattern (13 bp):
TTAGATACACCCA
Found at i:209785 original size:17 final size:17
Alignment explanation
Indices: 209747--209785 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
209737 AGGTGGAGAA
* *
209747 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
*
209764 TTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
209781 CTTGT
1 CTTGT
209786 CAAGGTGAAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:209832 original size:41 final size:41
Alignment explanation
Indices: 209775--209870 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
209765 TTGTTCGTAG
* * *
209775 AGAATTCTTGTCAAGGTGAAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGAAGATTATTAGAATTGAGTGACT
209816 AGAATTCTTGTTAAGGTGAAGATTATTAGAATTGAGTGACT
1 AGAATTCTTGTTAAGGTGAAGATTATTAGAATTGAGTGACT
*
209857 ATAATTCTTGTTAA
1 AGAATTCTTGTTAA
209871 AATAAAATTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGAAGATTATTAGAATTGAGTGACT
Found at i:209881 original size:17 final size:18
Alignment explanation
Indices: 209859--209896 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
209849 GAGTGACTAT
*
209859 AATTCT-TGTTAAAATAA
1 AATTCTGTGGTAAAATAA
*
209876 AATTCTGTGGTAACATAA
1 AATTCTGTGGTAAAATAA
209894 AAT
1 AAT
209897 AAAAGTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.37
Consensus pattern (18 bp):
AATTCTGTGGTAAAATAA
Found at i:214155 original size:12 final size:12
Alignment explanation
Indices: 214138--214162 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
214128 TAAATATATC
214138 AAGTTAGGTGCA
1 AAGTTAGGTGCA
214150 AAGTTAGGTGCA
1 AAGTTAGGTGCA
214162 A
1 A
214163 GTTGAGGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.32, T:0.24
Consensus pattern (12 bp):
AAGTTAGGTGCA
Found at i:220693 original size:38 final size:38
Alignment explanation
Indices: 220651--220737 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
220641 ACTGAACTGA
220651 CTTGTAAGAGCAATATTGGCTCGTAAGAGCGATACTAG
1 CTTGTAAGAGCAATATTGGCTCGTAAGAGCGATACTAG
** * *
220689 CTTGTGAA-AGTGATATTGGTTCGTGAGAGCGATACTAG
1 CTTGT-AAGAGCAATATTGGCTCGTAAGAGCGATACTAG
*
220727 CTCGTAAGAGC
1 CTTGTAAGAGC
220738 GATTTACTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
37 2 0.05
38 37 0.90
39 2 0.05
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.28
Consensus pattern (38 bp):
CTTGTAAGAGCAATATTGGCTCGTAAGAGCGATACTAG
Found at i:220731 original size:19 final size:19
Alignment explanation
Indices: 220654--220740 Score: 77
Period size: 19 Copynumber: 4.6 Consensus size: 19
220644 GAACTGACTT
* * *
220654 GTAAGAGCAATATTGGCTC
1 GTAAGAGCGATACTAGCTC
*
220673 GTAAGAGCGATACTAGCTT
1 GTAAGAGCGATACTAGCTC
* * * *
220692 GTGAA-AGTGATATTGGTTC
1 GT-AAGAGCGATACTAGCTC
*
220711 GTGAGAGCGATACTAGCTC
1 GTAAGAGCGATACTAGCTC
220730 GTAAGAGCGAT
1 GTAAGAGCGAT
220741 TTACTGACTG
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
18 1 0.02
19 48 0.94
20 2 0.04
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (19 bp):
GTAAGAGCGATACTAGCTC
Found at i:227055 original size:14 final size:14
Alignment explanation
Indices: 227036--227062 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
227026 AAGCGATTCA
227036 TCCTCATCGTTCCC
1 TCCTCATCGTTCCC
227050 TCCTCATCGTTCC
1 TCCTCATCGTTCC
227063 TCCCTACTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.48, G:0.07, T:0.37
Consensus pattern (14 bp):
TCCTCATCGTTCCC
Found at i:227547 original size:21 final size:21
Alignment explanation
Indices: 227523--227566 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
227513 CATTTAAATA
*
227523 TAATGACATTTATCA-ATTAAT
1 TAATGAAATTTAT-ATATTAAT
*
227544 TAATTAAATTTATATATTAAT
1 TAATGAAATTTATATATTAAT
227565 TA
1 TA
227567 CTATAATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (21 bp):
TAATGAAATTTATATATTAAT
Found at i:228036 original size:13 final size:13
Alignment explanation
Indices: 228018--228050 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
228008 TTTTAAAGTT
228018 AAAAAATAATTAA
1 AAAAAATAATTAA
*
228031 AAAAAATAGTTAA
1 AAAAAATAATTAA
228044 AAAAAAT
1 AAAAAAT
228051 TTGGGGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (13 bp):
AAAAAATAATTAA
Found at i:229865 original size:24 final size:24
Alignment explanation
Indices: 229833--229891 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
229823 GGAATATTAT
* *
229833 GGTGATGGTAATGAAGGTGGTGAG
1 GGTGATGGTAATAAAGGTGGTGAA
229857 GGTGATGGTAATAAAGGTGGTGAA
1 GGTGATGGTAATAAAGGTGGTGAA
*
229881 GGTGAGGGTAA
1 GGTGATGGTAA
229892 GGGTGAGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.47, T:0.24
Consensus pattern (24 bp):
GGTGATGGTAATAAAGGTGGTGAA
Found at i:229950 original size:30 final size:30
Alignment explanation
Indices: 229916--229998 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 30
229906 GGGTTGTTTG
*
229916 CAGTAAAGGTGATGAGGGTGAGGATGCTAA
1 CAGTAAAGGTGGTGAGGGTGAGGATGCTAA
* *
229946 CAGT-AAGAGTGGTAAGGGTGAGGATGCTAG
1 CAGTAAAG-GTGGTGAGGGTGAGGATGCTAA
*
229976 CAGTAAGGGTGGTGAGGGTGAGG
1 CAGTAAAGGTGGTGAGGGTGAGG
229999 GAGATGGTGG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 3 0.07
30 41 0.89
31 2 0.04
ACGTcount: A:0.29, C:0.06, G:0.46, T:0.19
Consensus pattern (30 bp):
CAGTAAAGGTGGTGAGGGTGAGGATGCTAA
Done.