Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010040.1 Kokia drynarioides strain JFW-HI SEQ_124808, 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: 95481
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2346 original size:29 final size:29
Alignment explanation
Indices: 2286--2608 Score: 318
Period size: 30 Copynumber: 11.0 Consensus size: 29
2276 CGGACATCTG
*
2286 GGGGT-AAAAGGGTAATTTTTGGAAGTTTC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTC
* * *
2315 GAGGTCAAAAATGGGATTTTTGGAAG-ATC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTC
* *
2344 GAGGGTAAAAATGGAAATTTTGGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTC
*
2374 GGGGTTAAAAATGGGATTTTTGGAAG-TTC
1 GGGG-TAAAAATGGAATTTTTGGAAGTTTC
*
2403 GGGGGTAAAAATGGAATTTTTGGAAGTTTT
1 -GGGGTAAAAATGGAATTTTTGGAAGTTTC
* * *
2433 GGTGTGAAAAATGGGATTTTTGGAAGTTTA
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTC
2463 GGGGTAAAAATGGAATTTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
** *
2492 ATGGTAAAAAATGCG-ATTATTT-GAAGTTTG
1 GGGGT-AAAAATG-GAATT-TTTGGAAGTTTC
* *
2522 GGGGTAAAAATTGAATTTTTGGATAGTTTA
1 GGGGTAAAAATGGAATTTTTGGA-AGTTTC
* *
2552 GGGGTCAAAATTGG-ATTATTGGAAG-TTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTC
*
2580 AGGGTAAAAATGGAATTTTTGGACAGTTT
1 GGGGTAAAAATGGAATTTTTGGA-AGTTT
2609 AGGGACCTTC
Statistics
Matches: 242, Mismatches: 34, Indels: 35
0.78 0.11 0.11
Matches are distributed among these distances:
27 7 0.03
28 18 0.07
29 94 0.39
30 107 0.44
31 16 0.07
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTC
Found at i:2350 original size:59 final size:59
Alignment explanation
Indices: 2299--2608 Score: 362
Period size: 59 Copynumber: 5.3 Consensus size: 59
2289 GTAAAAGGGT
*
2299 AATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGATCGAGGGTAAAAATGG
1 AATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
* * * * *
2358 AAATTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGG
1 AATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
* * *
2417 AATTTTTGGAAGTTTTG-GTGTGAAAAATGGGATTTTTGGAAGTT-TAGGGGTAAAAATGG
1 AATTTTTGGAAGTTTCGAG-GTCAAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAAATGG
* * * * *
2476 AATTTTTGGAAGTTTC-ATGGTAAAAAATGCGATTATTT-GAAGTTTGGGGGTAAAAATTG
1 AATTTTTGGAAGTTTCGA-GGTCAAAAATGGGATT-TTTGGAAGTTCGAGGGTAAAAATGG
* * * *
2535 AATTTTTGGATAGTTTAGGGGTC-AAAATTGGATTATTGGAAGTTC-AGGGTAAAAATGG
1 AATTTTTGGA-AGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
2593 AATTTTTGGACAGTTT
1 AATTTTTGGA-AGTTT
2609 AGGGACCTTC
Statistics
Matches: 216, Mismatches: 26, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
58 29 0.13
59 175 0.81
60 12 0.06
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (59 bp):
AATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
Found at i:4396 original size:12 final size:11
Alignment explanation
Indices: 4393--4453 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
4383 AATTTTGAAA
4393 TTAAATTTAAAT
1 TTAAA-TTAAAT
*
4405 TTAGATT-AAT
1 TTAAATTAAAT
4415 TTAAATTTAAA-
1 TTAAA-TTAAAT
*
4426 ATAAATCTAAAT
1 TTAAAT-TAAAT
*
4438 TTAAAATAAAT
1 TTAAATTAAAT
4449 TTAAA
1 TTAAA
4454 AGGGGGCCCG
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
10 8 0.20
11 22 0.55
12 10 0.25
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:4438 original size:17 final size:17
Alignment explanation
Indices: 4380--4453 Score: 87
Period size: 17 Copynumber: 4.4 Consensus size: 17
4370 TGGAATTTTT
* *
4380 TTTAATTTTGAAATTAAA
1 TTTAAATTT-AAAATAAA
* *
4398 TTTAAATTT-AGATTAA
1 TTTAAATTTAAAATAAA
4414 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
4431 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
4448 TTTAAA
1 TTTAAA
4454 AGGGGGCCCG
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
16 13 0.28
17 26 0.55
18 8 0.17
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:4444 original size:7 final size:6
Alignment explanation
Indices: 4380--4453 Score: 59
Period size: 6 Copynumber: 13.0 Consensus size: 6
4370 TGGAATTTTT
* *
4380 TTTAAT TTTGAAA -TTAAA TTTAAA TTTAGA -TT-AA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
4426 -ATAAA TCTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
4454 AGGGGGCCCG
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
4 1 0.02
5 15 0.28
6 36 0.67
7 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:7921 original size:20 final size:22
Alignment explanation
Indices: 7893--7937 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
7883 AAATTATTTT
7893 ATTTAATTTT-AAATATAAAAA
1 ATTTAATTTTGAAATATAAAAA
* *
7914 ATTT-ATTTTGTATTATAAAAA
1 ATTTAATTTTGAAATATAAAAA
7935 ATT
1 ATT
7938 ATATATCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTTAATTTTGAAATATAAAAA
Found at i:10594 original size:24 final size:24
Alignment explanation
Indices: 10566--10640 Score: 116
Period size: 24 Copynumber: 3.1 Consensus size: 24
10556 ATTTTGACTC
10566 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
10590 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
* *
10614 AAA-AAATTAAACAGAGTTTAACTG
1 AAACAAA-TAAACAAAGTTTAATTG
10638 AAA
1 AAA
10641 GATTATTTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 3 0.06
24 45 0.94
ACGTcount: A:0.59, C:0.08, G:0.09, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAATTG
Found at i:11045 original size:27 final size:26
Alignment explanation
Indices: 11015--11067 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
11005 TAAGACACAT
11015 AGAATGAATGA-GAAAAAGAAAGAAAAA
1 AGAA-GAATGATGAAAAAGAAA-AAAAA
* *
11042 AGAAGATTGATGAACAAGAAAAAAAA
1 AGAAGAATGATGAAAAAGAAAAAAAA
11068 GTGGACGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.68, C:0.02, G:0.21, T:0.09
Consensus pattern (26 bp):
AGAAGAATGATGAAAAAGAAAAAAAA
Found at i:14960 original size:36 final size:36
Alignment explanation
Indices: 14920--15048 Score: 117
Period size: 36 Copynumber: 3.7 Consensus size: 36
14910 TATTTTTATT
*
14920 AAATAAATAATTTTTAAATAGTATTTATGTCAAATA
1 AAATAAATAATTTTTAAATATTATTTATGTCAAATA
* * *** *
14956 AAATAAAT-ATTTGT--ATTTTATTTAAT-TTTTATT
1 AAATAAATAATTTTTAAATATTATTT-ATGTCAAATA
*
14989 AAATAAATAATCTTTAAATATTATTTATGTCAAATA
1 AAATAAATAATTTTTAAATATTATTTATGTCAAATA
* *
15025 AAATTAAT-ATTTTT-TATATTATTT
1 AAATAAATAATTTTTAAATATTATTT
15049 TACTAAATAA
Statistics
Matches: 71, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
33 18 0.25
34 15 0.21
35 12 0.17
36 26 0.37
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (36 bp):
AAATAAATAATTTTTAAATATTATTTATGTCAAATA
Found at i:15067 original size:69 final size:69
Alignment explanation
Indices: 14911--15058 Score: 207
Period size: 69 Copynumber: 2.2 Consensus size: 69
14901 TGTTAGGGTT
* * *
14911 ATTTTTATTAAATAAATAATTTTTAAATAGTATTTATGTCAAATAAAATAAATATTTGTATTTTA
1 ATTTTTACTAAATAAATAATCTTTAAATAGTATTTATGTCAAATAAAATAAATATTTGTATTATA
14976 TTTA
66 TTTA
* * *
14980 ATTTTTATTAAATAAATAATCTTTAAATATTATTTATGTCAAATAAAATTAATATTT-T-TTATA
1 ATTTTTACTAAATAAATAATCTTTAAATAGTATTTATGTCAAATAAAATAAATATTTGTATTATA
15043 -TT-
66 TTTA
15045 A-TTTTACTAAATAA
1 ATTTTTACTAAATAA
15059 CCCTAATAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
64 12 0.16
65 1 0.01
66 2 0.03
67 4 0.05
68 1 0.01
69 54 0.73
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (69 bp):
ATTTTTACTAAATAAATAATCTTTAAATAGTATTTATGTCAAATAAAATAAATATTTGTATTATA
TTTA
Found at i:16477 original size:21 final size:21
Alignment explanation
Indices: 16451--16491 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16441 GATTACCAAG
* *
16451 TCTTCATGGATGGTTTGGGCA
1 TCTTCATGAACGGTTTGGGCA
16472 TCTTCATGAACGGTTTGGGC
1 TCTTCATGAACGGTTTGGGC
16492 TCATTCCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.17, G:0.32, T:0.37
Consensus pattern (21 bp):
TCTTCATGAACGGTTTGGGCA
Found at i:20438 original size:28 final size:28
Alignment explanation
Indices: 20404--20472 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
20394 TAAAATGACG
20404 ATATAAAAATTTTCAATAAATAAAA-AAA
1 ATATAAAAATTTTCAAT-AATAAAATAAA
* *
20432 ATAT-AAAATTATTTAATATTAAAATAAA
1 ATATAAAAATT-TTCAATAATAAAATAAA
20460 ATA-AAATAATTTT
1 ATATAAA-AATTTT
20473 TTTAAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
27 12 0.34
28 19 0.54
29 4 0.11
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (28 bp):
ATATAAAAATTTTCAATAATAAAATAAA
Found at i:30969 original size:62 final size:62
Alignment explanation
Indices: 30902--31275 Score: 372
Period size: 62 Copynumber: 6.1 Consensus size: 62
30892 TTTTTCAGAA
* *
30902 AAAAAAATTTGAAATTTTTTTATCCGAGAACAGGGGGAGTCGGCCATTGCATGACCAACACC
1 AAAAAAATTTGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC
* * * *
30964 AAAAAAATTTGAAATTTTTTTATTCGAGAAAAGGGGGTGTCGGCCATTGCATAATCAATA-C
1 AAAAAAATTTGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC
* * * * *
31025 AAAAAAATTTTGAAATTTTTTT-TCTGAAAAAAAGGGGTGTCGACCATTGCATGGCCAACACC
1 AAAAAAA-TTTGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC
* * *
31087 -CAAAAA--TGCAATTTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGGCCAACACC
1 AAAAAAATTTG-AAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC
* * * ** * * *
31147 AAAAAATTTTGAAATTTTTTTTTCTGA-AAAAGAAGGTGTCTGTCATCGCATGACCAACACC
1 AAAAAAATTTGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC
* ** * * * * **
31208 -CAAAAA-TACAATTTTTTTTATCAGATAAATA-GGGGTGTCGGCCATTGTATGGGCAACA-C
1 AAAAAAATTTGAAATTTTTTTATCCGAGAAA-AGGGGGTGTCGGCCATTGCATGACCAACACC
31267 AAAAAAATT
1 AAAAAAATT
31276 GTATTTTTTA
Statistics
Matches: 253, Mismatches: 48, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
58 2 0.01
59 24 0.09
60 67 0.26
61 76 0.30
62 82 0.32
63 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (62 bp):
AAAAAAATTTGAAATTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC
Found at i:31157 original size:121 final size:120
Alignment explanation
Indices: 30902--31306 Score: 428
Period size: 121 Copynumber: 3.3 Consensus size: 120
30892 TTTTTCAGAA
* * * * * * *
30902 AAAAAAATTTGAAATTTTTTTATCCGAGAACAGGGGGAGTCGGCCATTGCATGACCAACACCAAA
1 AAAAAATTTTGAAATTTTTTT-TCTGAAAAAAAGGGGTGTC-GCCATTGCATGACCAACACC-CA
* * *** * *
30967 AAAATTTG-AAATTTTTTTATTCGAGAAAAGGGGGTGTCGGCCATTGCATAATCAATACA
63 AAAA--TGCAATTTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGGCCAACACC
*
31026 AAAAAATTTTGAAATTTTTTTTCTGAAAAAAAGGGGTGTCGACCATTGCATGGCCAACACCCAAA
1 AAAAAATTTTGAAATTTTTTTTCTGAAAAAAAGGGGTGTCG-CCATTGCATGACCAACACCCAAA
31091 AATGCAATTTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGGCCAACACC
65 AATGCAATTTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGGCCAACACC
* *
31147 AAAAAATTTTGAAATTTTTTTTTCTGAAAAAGAA--GGTGTCTGTCATCGCATGACCAACACCCA
1 AAAAAATTTTGAAA-TTTTTTTTCTGAAAAA-AAGGGGTGTC-GCCATTGCATGACCAACACCCA
* * * * *
31210 AAAATACAATTTTTTTTATCAGATAAATA-GGGGTGTCGGCCATTGTATGGGCAACA-C
63 AAAATGCAATTTTTTTTATCCGAGAAA-AGGGGGTGTCGGCCATTGCATGGCCAACACC
* * * *
31267 AAAAAA-ATTG-TATTTTTTATCTAACAAAAAAGGGGTGTCG
1 AAAAAATTTTGAAATTTTTTTTCTGA-AAAAAAGGGGTGTCG
31307 GCCACCAAAT
Statistics
Matches: 245, Mismatches: 27, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
117 12 0.05
118 6 0.02
119 9 0.04
120 9 0.04
121 131 0.53
122 24 0.10
123 34 0.14
124 20 0.08
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (120 bp):
AAAAAATTTTGAAATTTTTTTTCTGAAAAAAAGGGGTGTCGCCATTGCATGACCAACACCCAAAA
ATGCAATTTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGGCCAACACC
Found at i:31185 original size:61 final size:62
Alignment explanation
Indices: 30902--31275 Score: 356
Period size: 61 Copynumber: 6.1 Consensus size: 62
30892 TTTTTCAGAA
* * * *
30902 AAAAAAATTTGAAATTTTTTTATCCGAGAACAGGGGGAGTCGGCCATTGCATGACCAACACC
1 AAAAAATTTTGAAATTTTTTTTTCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC
* * * * *
30964 AAAAAAATTTGAAATTTTTTTATT-CGAGAAAAGGGGGTGTCGGCCATTGCATAATCAATACA
1 AAAAAATTTTGAAATTTTTTT-TTCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC
* * * * *
31026 AAAAAATTTTGAAA-TTTTTTTTCTGAAAAAAAGGGGTGTCGACCATTGCATGGCCAACACC
1 AAAAAATTTTGAAATTTTTTTTTCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC
* * *
31087 CAAAAA---TGCAATTTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGGCCAACACC
1 AAAAAATTTTGAAATTTTTTTT-TCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC
* ** * * *
31147 AAAAAATTTTGAAATTTTTTTTTCTGA-AAAAGAAGGTGTCTGTCATCGCATGACCAACACC
1 AAAAAATTTTGAAATTTTTTTTTCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC
* * * * ** *
31208 CAAAAA---T-ACAATTTTTTTTATCAGATAAATA-GGGGTGTCGGCCATTGTATGGGCAACACA
1 AAAAAATTTTGA-AATTTTTTTT-TCCGAGAAA-AGGGGGTGTCGGCCATTGCATGACCAACACC
31268 AAAAAATT
1 AAAAAATT
31276 GTATTTTTTA
Statistics
Matches: 255, Mismatches: 44, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
57 1 0.00
58 15 0.06
59 11 0.04
60 71 0.28
61 74 0.29
62 70 0.27
63 13 0.05
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (62 bp):
AAAAAATTTTGAAATTTTTTTTTCCGAGAAAAGGGGGTGTCGGCCATTGCATGACCAACACC
Found at i:31282 original size:60 final size:58
Alignment explanation
Indices: 30902--31310 Score: 311
Period size: 60 Copynumber: 6.7 Consensus size: 58
30892 TTTTTCAGAA
* * * *
30902 AAAAAAATTTGAAATTTTTTTATCCGAGAACAGGGGGAGTCGGCCATTGCATGACCAACACC
1 AAAAAAA-TTGAATTTTTTTTAT-C-AGAAAAAGGGGTGTCGGCCATTGCATGACCAACA-C
* * * * *
30964 AAAAAAATTTGAAATTTTTTTATTCGAGAAAAGGGGGTGTCGGCCATTGCATAATCAATAC
1 AAAAAAA-TTGAATTTTTTTTA-TC-AGAAAAAGGGGTGTCGGCCATTGCATGACCAACAC
* * * * *
31025 AAAAAAATTTTGAAATTTTTTTTCTGAAAAAAAGGGGTGTCGACCATTGCATGGCCAACAC
1 AAAAAAA--TTG-AATTTTTTTTATCAGAAAAAGGGGTGTCGGCCATTGCATGACCAACAC
** * *
31086 CCAAAAA-TGCAATTTTTTTTATCCGAGAAAAGGGGGTGTCGGCCATTGCATGGCCAACACC
1 AAAAAAATTG-AATTTTTTTTAT-C-AGAAAAAGGGGTGTCGGCCATTGCATGACCAACA-C
* * * * * *
31147 AAAAAATTTTGAAATTTTTTTT-TCTGAAAAAGAAGGTGTCTGTCATCGCATGACCAACAC
1 AAAAAA-ATTG-AATTTTTTTTATCAGAAAAAG-GGGTGTCGGCCATTGCATGACCAACAC
** ** * **
31207 CCAAAAATACAATTTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGTATGGGCAACAC
1 AAAAAAATTGAATTTTTTTTATCAGA-AAA-AGGGGTGTCGGCCATTGCATGACCAACAC
* *
31267 AAAAAAATTGTATTTTTTATCTAACA-AAAAAGGGGTGTCGGCCA
1 AAAAAAATTGAATTTTTT-T-TATCAGAAAAAGGGGTGTCGGCCA
31311 CCAAATTTTT
Statistics
Matches: 280, Mismatches: 53, Indels: 31
0.77 0.15 0.09
Matches are distributed among these distances:
58 23 0.08
59 19 0.07
60 81 0.29
61 72 0.26
62 63 0.22
63 22 0.08
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (58 bp):
AAAAAAATTGAATTTTTTTTATCAGAAAAAGGGGTGTCGGCCATTGCATGACCAACAC
Found at i:32118 original size:30 final size:30
Alignment explanation
Indices: 32082--32141 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
32072 AATGTCTGGG
*
32082 CCATACTCCCATTTTCCTGGTTGATACATA
1 CCATACTCCCATTTTCCTGGCTGATACATA
32112 CCATACTCCCATTTTCCTGGCTGATACATA
1 CCATACTCCCATTTTCCTGGCTGATACATA
32142 TTAATGGAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.23, C:0.32, G:0.10, T:0.35
Consensus pattern (30 bp):
CCATACTCCCATTTTCCTGGCTGATACATA
Found at i:36087 original size:24 final size:22
Alignment explanation
Indices: 36060--36116 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
36050 TTTTGAGCAA
36060 TTTAATTTTTTCTTTTTATGTTCT
1 TTTAATTTTTTCTTTTT-T-TTCT
36084 TTTAA-TTTTTCTTTTTTTTCT
1 TTTAATTTTTTCTTTTTTTTCT
**
36105 TTTTTTTTTTTC
1 TTTAATTTTTTC
36117 ATTCTCTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 7 0.23
22 7 0.23
23 11 0.37
24 5 0.17
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTAATTTTTTCTTTTTTTTCT
Found at i:36121 original size:17 final size:15
Alignment explanation
Indices: 36065--36115 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 15
36055 AGCAATTTAA
*
36065 TTTTTTCTTTTTATGT
1 TTTTTTCTTTTTCT-T
**
36081 TCTTTTAATTTTTCTT
1 T-TTTTTCTTTTTCTT
36097 TTTTTTCTTTTT-TT
1 TTTTTTCTTTTTCTT
36111 TTTTT
1 TTTTT
36116 CATTCTCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 7 0.24
15 9 0.31
16 3 0.10
17 10 0.34
ACGTcount: A:0.06, C:0.08, G:0.02, T:0.84
Consensus pattern (15 bp):
TTTTTTCTTTTTCTT
Found at i:37086 original size:21 final size:21
Alignment explanation
Indices: 37060--37116 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 21
37050 TAAAAAATTG
37060 GAAAATTTGAAAAAATTCAAA
1 GAAAATTTGAAAAAATTCAAA
* *
37081 GAAAA-TAG-GAAAATTCAAA
1 GAAAATTTGAAAAAATTCAAA
* * *
37100 AAAAATCTCAAAAAATT
1 GAAAATTTGAAAAAATT
37117 TAAAAATTCG
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
19 14 0.52
20 2 0.07
21 11 0.41
ACGTcount: A:0.63, C:0.07, G:0.09, T:0.21
Consensus pattern (21 bp):
GAAAATTTGAAAAAATTCAAA
Found at i:37115 original size:29 final size:28
Alignment explanation
Indices: 37051--37114 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
37041 AGAAATCTTT
* **
37051 AAAAAATTGGAAAATTTGAAAAAATTCA
1 AAAAAATAGGAAAATTAAAAAAAATTCA
37079 AAGAAAATAGGAAAATTCAAAAAAAATCTCA
1 AA-AAAATAGGAAAATT-AAAAAAAAT-TCA
37110 AAAAA
1 AAAAA
37115 TTTAAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 2 0.07
29 13 0.43
30 10 0.33
31 5 0.17
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.19
Consensus pattern (28 bp):
AAAAAATAGGAAAATTAAAAAAAATTCA
Found at i:37121 original size:18 final size:18
Alignment explanation
Indices: 37100--37141 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
37090 AAAATTCAAA
*
37100 AAAAATCTC-AAAAAATTT
1 AAAAAT-TCGAAAAAATAT
*
37118 AAAAATTCGGAAAAATAT
1 AAAAATTCGAAAAAATAT
37136 AAAAAT
1 AAAAAT
37142 ATTATGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.24
Consensus pattern (18 bp):
AAAAATTCGAAAAAATAT
Found at i:45119 original size:16 final size:16
Alignment explanation
Indices: 45100--45134 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
45090 GAACTCTGAT
*
45100 TTTGCTGAATTCTTGA
1 TTTGATGAATTCTTGA
*
45116 TTTGATGTATTCTTGA
1 TTTGATGAATTCTTGA
45132 TTT
1 TTT
45135 CTTTTTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.09, G:0.17, T:0.57
Consensus pattern (16 bp):
TTTGATGAATTCTTGA
Found at i:49114 original size:47 final size:47
Alignment explanation
Indices: 49034--49125 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 47
49024 AAGGTGAAAG
49034 AAGTGGCAGTTTATCTGCAAAAGTGATGACTTGTCCACAATATTACA
1 AAGTGGCAGTTTATCTGCAAAAGTGATGACTTGTCCACAATATTACA
* * * *
49081 AAGTGGCAGTTTATTTGCAAATGTGGTGGCTTGTCCACAATATTA
1 AAGTGGCAGTTTATCTGCAAAAGTGATGACTTGTCCACAATATTA
49126 TTGAGTGACA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (47 bp):
AAGTGGCAGTTTATCTGCAAAAGTGATGACTTGTCCACAATATTACA
Found at i:49141 original size:47 final size:47
Alignment explanation
Indices: 49034--49146 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 47
49024 AAGGTGAAAG
* * *
49034 AAGTGGCAGTTTATCTGCAAAAGTGATGACTTGTCCACAATATTACA
1 AAGTGACAATTTATTTGCAAAAGTGATGACTTGTCCACAATATTACA
* * * * * **
49081 AAGTGGCAGTTTATTTGCAAATGTGGTGGCTTGTCCACAATATTATT
1 AAGTGACAATTTATTTGCAAAAGTGATGACTTGTCCACAATATTACA
*
49128 GAGTGACAATTTATTTGCA
1 AAGTGACAATTTATTTGCA
49147 TTACTGTGAC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (47 bp):
AAGTGACAATTTATTTGCAAAAGTGATGACTTGTCCACAATATTACA
Found at i:49272 original size:24 final size:23
Alignment explanation
Indices: 49233--49277 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
49223 GATAGGTAGG
49233 ATGTTTTAAAAGAAATTTGCATAT
1 ATGTTTTAAAAGAAA-TTGCATAT
49257 ATGTTTTACAAA-AAATTGCAT
1 ATGTTTTA-AAAGAAATTGCAT
49278 TGTTGTGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 6 0.30
24 11 0.55
25 3 0.15
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (23 bp):
ATGTTTTAAAAGAAATTGCATAT
Found at i:51233 original size:56 final size:56
Alignment explanation
Indices: 51155--51343 Score: 265
Period size: 56 Copynumber: 3.4 Consensus size: 56
51145 AGGGTATTAG
* * * *
51155 GATATTATTATGCGATATTATCTCTTAGCAATTTAATTCTTAATGAGATATTATAA
1 GATATTATTATGAGATATTATCTCTTAACAATTTGATTCATAATGAGATATTATAA
*
51211 GATATTATTATGAGATATTATCTCTTAACAATTTGATTCATAATGGGATATTAT-A
1 GATATTATTATGAGATATTATCTCTTAACAATTTGATTCATAATGAGATATTATAA
* * *
51266 GAATATTATTATGGGATATCATCT-TTAAACAATTTGATTCCTAATGAGATATTATAA
1 G-ATATTATTATGAGATATTATCTCTT-AACAATTTGATTCATAATGAGATATTATAA
*
51323 GATATTATTATGAAATATTAT
1 GATATTATTATGAGATATTAT
51344 TTTTTAGAAA
Statistics
Matches: 118, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
55 4 0.03
56 112 0.95
57 2 0.02
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (56 bp):
GATATTATTATGAGATATTATCTCTTAACAATTTGATTCATAATGAGATATTATAA
Found at i:51359 original size:112 final size:112
Alignment explanation
Indices: 51156--51360 Score: 297
Period size: 112 Copynumber: 1.8 Consensus size: 112
51146 GGGTATTAGG
* * *
51156 ATATTATTATGCGATATTATCTCTTAGCAATTTAATTCTTAATGAGATATTATAAGATATTATTA
1 ATATTATTATGCGATATCATCTCTTAACAATTTAATTCCTAATGAGATATTATAAGATATTATTA
* *
51221 TGAGATATTATCTCTTAACAATTTGATTCATAATGGGATATTATAGA
66 TGAAATATTATCTCTTAACAAATTGATTCATAATGGGATATTATAGA
* *
51268 ATATTATTATGGGATATCATCT-TTAAACAATTTGATTCCTAATGAGATATTATAAGATATTATT
1 ATATTATTATGCGATATCATCTCTT-AACAATTTAATTCCTAATGAGATATTATAAGATATTATT
* *
51332 ATGAAATATTATTTTTTAGA-AAATTGATT
65 ATGAAATATTATCTCTTA-ACAAATTGATT
51361 TCTATGTACT
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
111 2 0.02
112 79 0.96
113 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (112 bp):
ATATTATTATGCGATATCATCTCTTAACAATTTAATTCCTAATGAGATATTATAAGATATTATTA
TGAAATATTATCTCTTAACAAATTGATTCATAATGGGATATTATAGA
Found at i:51987 original size:5 final size:5
Alignment explanation
Indices: 51979--52032 Score: 90
Period size: 5 Copynumber: 10.8 Consensus size: 5
51969 TCAATTTAAT
* *
51979 TCGAC TCGAC TCGAC TCGAC TCAAC TCGAC TCGAC TCGAC TCAAC TCGAC
1 TCGAC TCGAC TCGAC TCGAC TCGAC TCGAC TCGAC TCGAC TCGAC TCGAC
52029 TCGA
1 TCGA
52033 ACAAATATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.24, C:0.39, G:0.17, T:0.20
Consensus pattern (5 bp):
TCGAC
Found at i:52005 original size:20 final size:20
Alignment explanation
Indices: 51982--52032 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
51972 ATTTAATTCG
51982 ACTCGACTCGACTCGACTCA
1 ACTCGACTCGACTCGACTCA
52002 ACTCGACTCGACTCGACTCA
1 ACTCGACTCGACTCGACTCA
52022 ACTCGACTCGA
1 ACTCGACTCGA
52033 ACAAATATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.39, G:0.16, T:0.20
Consensus pattern (20 bp):
ACTCGACTCGACTCGACTCA
Found at i:52295 original size:3 final size:3
Alignment explanation
Indices: 52287--52330 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
52277 GAGACTGACG
* *
52287 CTT CTT CTT CTT CTT CTT CTT CTC CTT CTT CTT CTT CCT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
52331 CCCTCTCCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:52953 original size:126 final size:126
Alignment explanation
Indices: 52802--53053 Score: 495
Period size: 126 Copynumber: 2.0 Consensus size: 126
52792 TTTGGAGGAA
52802 AGGGTTTTGGTATCTTGTACACCAAGAAACCGATCATCAATGACATGAACAATTTTTCTTTTGCT
1 AGGGTTTTGGTATCTTGTACACCAAGAAACCGATCATCAATGACATGAACAATTTTTCTTTTGCT
*
52867 CGGATTTGTTTGGTAGCAAGAATAGAAAGTGGAAATGATGATTGAAACTTTCAGTCTATGT
66 CGGATTTGTTTGGTAGCAAGAATAGAAAGTGGAAATGATGATTGAAACTTTCAGTCAATGT
52928 AGGGTTTTGGTATCTTGTACACCAAGAAACCGATCATCAATGACATGAACAATTTTTCTTTTGCT
1 AGGGTTTTGGTATCTTGTACACCAAGAAACCGATCATCAATGACATGAACAATTTTTCTTTTGCT
52993 CGGATTTGTTTGGTAGCAAGAATAGAAAGTGGAAATGATGATTGAAACTTTCAGTCAATGT
66 CGGATTTGTTTGGTAGCAAGAATAGAAAGTGGAAATGATGATTGAAACTTTCAGTCAATGT
53054 TCTTATATAA
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 125 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (126 bp):
AGGGTTTTGGTATCTTGTACACCAAGAAACCGATCATCAATGACATGAACAATTTTTCTTTTGCT
CGGATTTGTTTGGTAGCAAGAATAGAAAGTGGAAATGATGATTGAAACTTTCAGTCAATGT
Found at i:59276 original size:20 final size:21
Alignment explanation
Indices: 59230--59283 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
59220 AATTAATTTT
59230 TTTTTTACTATTTTTAAATAA
1 TTTTTTACTATTTTTAAATAA
*
59251 TATTTTA-TATTTTT-AATAAA
1 TTTTTTACTATTTTTAAAT-AA
*
59271 TTTTTTACAATTT
1 TTTTTTACTATTT
59284 ATACATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 3 0.11
20 15 0.54
21 10 0.36
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTTTACTATTTTTAAATAA
Found at i:63206 original size:99 final size:99
Alignment explanation
Indices: 62997--63875 Score: 668
Period size: 99 Copynumber: 8.9 Consensus size: 99
62987 TAAGATTTAT
* * * * * * * * *
62997 CATTGTGGCTTCAATCTTTCCCGTCACAT-TTCTAAGGT-GCTAGGTTCGTCATTGCGGCTTCAA
1 CATTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATC-GGGTTCGCCGTTGCGGCCTCAA
* * * *
63060 CCTTTCCCTTCATATCTTCATCGTATCGGCTTCGT
65 CCTTTCCCTTCATATCTTCATGGTACCGGATTCGC
* * * * * * *
63095 CGTTGCGACCTCAATCC-TTCTCATCGCATATTCTAAGGTACCGGGTTCACCGTTGCGGCCTCAA
1 CATTGCGGCCTCAA-CCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAA
* * *
63159 TCTTTCCCTTCATATCTTCGTGGTACCGGATTCGT
65 CCTTTCCCTTCATATCTTCATGGTACCGGATTCGC
* * * * *
63194 CATTACGGCCTCAACCTTTCCCATTACATCTTCTTAGGTATCGGGTTTGTCGTTGCGGCCTCAAC
1 CATTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAAC
* * *
63259 CTTTCCCTTCGTATCTTCATTGTACCGGGTTCGC
66 CTTTCCCTTCATATCTTCATGGTACCGGATTCGC
* *** ** * * * *
63293 CGTTATAGCCTCAACCTTTCTTATC-CTATC-TCCATGGTACCGGGTTCGCTGTTGCGGCCTCAA
1 CATTGCGGCCTCAACCTTTCCCATCAC-ATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAA
* * * * *
63356 CCTTTCCCATAATATCTTCTTAGGTACTGGGTTCGC
65 CCTTTCCCTTCATATCTTCAT-GGTACCGGATTCGC
* * * * * * * * *
63392 CATCGAGGCCTCAATCC-TTCCCTTCAAATTTTC-ATGGTATCGGGTTCGTCGTTGTGGCCTTAA
1 CATTGCGGCCTCAA-CCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAA
* * * * *
63455 CCTTTGCCATCACATCTTCTTAGGTACC-GAGTTTG-
65 CCTTTCCCTTCATATCTTCAT-GGTACCGGA-TTCGC
* * * * *
63490 CAGTTGCGGCCTCAACCTTTCCTATCACATCTTCTAAGGTATCGGGTTCGACATTGCGACCTTAA
1 CA-TTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAA
* *
63555 CCTTTCCCTTCGTATCTTCATGGTACCGGGTTCGC
65 CCTTTCCCTTCATATCTTCATGGTACCGGATTCGC
* ** * ** ** *
63590 CGTTGCAACCTCAACCTTTCCCATCACATCTTCTAAGGTACCGAATTCGCTATTGCGACCTCAAT
1 CATTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAA-
* **
63655 CC-TTCCCTTCAAATCTTCATGGTA-TTGAGTTCGC
65 CCTTTCCCTTCATATCTTCATGGTACCGGA-TTCGC
* * * * * * * * * *
63689 CGTTGCGACCTCAACCTTTCCCATCAGATCTTCTAAGATATTGGATTTGCTGTCGCGGTCTCAAT
1 CATTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAA-
* *
63754 CC-TTCCCTTCAAATCTTCATGGTACCGGATTCAC
65 CCTTTCCCTTCATATCTTCATGGTACCGGATTCGC
* * * * * * *
63788 CATTGCGGCCTCAATCATTCCCTTCAAATCTTC-ATGGTATCGAGTTCGCCGTTGCGACCTCAAC
1 CATTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAAC
* *
63852 CTTTCCCTTTATATCTTCAGGGTA
66 CTTTCCCTTCATATCTTCATGGTA
63876 TTAGATTTGT
Statistics
Matches: 619, Mismatches: 143, Indels: 38
0.77 0.18 0.05
Matches are distributed among these distances:
97 2 0.00
98 110 0.18
99 455 0.74
100 52 0.08
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (99 bp):
CATTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAAC
CTTTCCCTTCATATCTTCATGGTACCGGATTCGC
Found at i:63284 original size:148 final size:146
Alignment explanation
Indices: 63041--63875 Score: 677
Period size: 148 Copynumber: 5.6 Consensus size: 146
63031 AGGTGCTAGG
* * * * *
63041 TTCGTCATTGCGGCTTCAACCTTTCCCTTCATATCTTCATCGTATCGGCTTCGTCGTTGCGACCT
1 TTCG-CATTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATCGGGTTCGCCGTTGCGACCT
* * * * * * *
63106 CAATCC-TTCTCATCGCATATTCTAAGGTACCGGGTTCACCGTTGCGGCCTCAATCTTTCCCTTC
65 CAA-CCTTTCCCTTCGTATCTTC-ATGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTC
* *
63170 ATATCTTCGTGGTACCGGA
128 ACATCTTCATGGTACCGGA
* * * * * *
63189 TTCGTCATTACGGCCTCAACCTTTCCCATT-ACATCTTCTTAGGTATCGGGTTTGTCGTTGCGGC
1 TTCG-CATTGCGGCCTCAACCTTTCCC-TTCAAATCTTCAT-GGTATCGGGTTCGCCGTTGCGAC
* *** *
63253 CTCAACCTTTCCCTTCGTATCTTCATTGTACCGGGTTCGCCGTTATAGCCTCAACCTTT-CTTAT
63 CTCAACCTTTCCCTTCGTATCTTCATGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCT-T
* *
63317 C-CTATCTCCATGGTACCGGG
127 CAC-ATCTTCATGGTACCGGA
* * * * * * *
63337 TTCGCTGTTGCGGCCTCAACCTTTCCCAT-AATATCTTCTTAGGTA-CTGGGTTCGCCATCGAGG
1 TTCGC-ATTGCGGCCTCAACCTTTCCCTTCAA-ATCTTCAT-GGTATC-GGGTTCGCCGTTGCGA
** * * * * * * *
63400 CCTCAATCC-TTCCCTTCAAATTTTCATGGTATCGGGTTCGTCGTTGTGGCCTTAACCTTTGCCA
62 CCTCAA-CCTTTCCCTTCGTATCTTCATGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCT
*
63464 TCACATCTTCTTAGGTACC-GA
126 TCACATCTTCAT-GGTACCGGA
* * * * *
63485 GTTTGCAGTTGCGGCCTCAACCTTT-CCTATCACATCTTCTAAGGTATCGGGTTCGACATTGCGA
1 -TTCGCA-TTGCGGCCTCAACCTTTCCCT-TCAAATCTTC-ATGGTATCGGGTTCGCCGTTGCGA
* ** *
63549 CCTTAACCTTTCCCTTCGTATCTTCATGGTACCGGGTTCGCCGTTGCAACCTCAACCTTTCCCAT
62 CCTCAACCTTTCCCTTCGTATCTTCATGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTT
* *
63614 CACATCTTCTAAGGTACCGAA
127 CACATCTTC-ATGGTACCGGA
* * *
63635 TTCGCTATTGCGACCTCAATCC-TTCCCTTCAAATCTTCATGGTATTGAGTTCGCCGTTGCGACC
1 TTCGC-ATTGCGGCCTCAA-CCTTTCCCTTCAAATCTTCATGGTATCGGGTTCGCCGTTGCGACC
* * * ** * * * * *
63699 TCAACCTTTCCCATCAG-ATCTTCTAAGATATTGGATTTGCTGTCGCGGTCTCAATCC-TTCCCT
64 TCAACCTTTCCCTTC-GTATCTTC-ATGGTACCGGGTTCGCCGTTGCGGCCTCAA-CCTTTCCCT
*
63762 TCAAATCTTCATGGTACCGGA
126 TCACATCTTCATGGTACCGGA
* * * *
63783 TTCACCATTGCGGCCTCAATCATTCCCTTCAAATCTTCATGGTATCGAGTTCGCCGTTGCGACCT
1 TTC-GCATTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATCGGGTTCGCCGTTGCGACCT
** *
63848 CAACCTTTCCCTTTATATCTTCAGGGTA
65 CAACCTTTCCCTTCGTATCTTCATGGTA
63876 TTAGATTTGT
Statistics
Matches: 552, Mismatches: 105, Indels: 61
0.77 0.15 0.08
Matches are distributed among these distances:
147 11 0.02
148 311 0.56
149 219 0.40
150 11 0.02
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.35
Consensus pattern (146 bp):
TTCGCATTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATCGGGTTCGCCGTTGCGACCTC
AACCTTTCCCTTCGTATCTTCATGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCACA
TCTTCATGGTACCGGA
Found at i:63876 original size:49 final size:49
Alignment explanation
Indices: 63039--63875 Score: 590
Period size: 49 Copynumber: 16.9 Consensus size: 49
63029 TAAGGTGCTA
* * * * *
63039 GGTTCGTCATTGCGGCTTCAACCTTTCCCTTCATATCTTCATCGTATCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCG
* * * * * ** * *
63088 GCTTCGTCGTTGCGACCTCAATCC-TTCTCATCGCATATTCTAAGGTACCG
1 GGTTCGCCGTTGCGGCCTCAA-CCTTTCCCTTCATATCTTC-ATGGTACCG
* * *
63138 GGTTCACCGTTGCGGCCTCAATCTTTCCCTTCATATCTTCGTGGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCG
* * * * * * *
63187 GATTCGTCATTACGGCCTCAACCTTTCCCATT-ACATCTTCTTAGGTATCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCC-TTCATATCTTCAT-GGTACCG
* * * *
63237 GGTTTGTCGTTGCGGCCTCAACCTTTCCCTTCGTATCTTCATTGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCG
*** * * *
63286 GGTTCGCCGTTATAGCCTCAACCTTT-CTTATCCTATCTCCATGGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCT-TCATATCTTCATGGTACCG
* * * * *
63335 GGTTCGCTGTTGCGGCCTCAACCTTTCCCATAATATCTTCTTAGGTACTG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCAT-GGTACCG
* * * * * *
63385 GGTTCGCCATCGAGGCCTCAATCC-TTCCCTTCAAATTTTCATGGTATCG
1 GGTTCGCCGTTGCGGCCTCAA-CCTTTCCCTTCATATCTTCATGGTACCG
* * * * * * *
63434 GGTTCGTCGTTGTGGCCTTAACCTTTGCCATCACATCTTCTTAGGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCAT-GGTACCG
* * * * * *
63484 AGTTTGCAGTTGCGGCCTCAACCTTT-CCTATCACATCTTCTAAGGTATCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCT-TCATATCTTC-ATGGTACCG
* * * * *
63534 GGTTCGACATTGCGACCTTAACCTTTCCCTTCGTATCTTCATGGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCG
** * * *
63583 GGTTCGCCGTTGCAACCTCAACCTTTCCCATCACATCTTCTAAGGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTC-ATGGTACCG
** ** * * **
63633 AATTCGCTATTGCGACCTCAATCC-TTCCCTTCAAATCTTCATGGTATTG
1 GGTTCGCCGTTGCGGCCTCAA-CCTTTCCCTTCATATCTTCATGGTACCG
* * * * * * **
63682 AGTTCGCCGTTGCGACCTCAACCTTTCCCATCAGATCTTCTAAGATATTG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTC-ATGGTACCG
* * * * * *
63732 GATTTGCTGTCGCGGTCTCAATCC-TTCCCTTCAAATCTTCATGGTACCG
1 GGTTCGCCGTTGCGGCCTCAA-CCTTTCCCTTCATATCTTCATGGTACCG
* * * * * * *
63781 GATTCACCATTGCGGCCTCAATCATTCCCTTCAAATCTTCATGGTATCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCG
* * * *
63830 AGTTCGCCGTTGCGACCTCAACCTTTCCCTTTATATCTTCAGGGTA
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTA
63876 TTAGATTTGT
Statistics
Matches: 606, Mismatches: 161, Indels: 42
0.75 0.20 0.05
Matches are distributed among these distances:
48 7 0.01
49 335 0.55
50 255 0.42
51 9 0.01
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.35
Consensus pattern (49 bp):
GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCG
Found at i:64698 original size:41 final size:41
Alignment explanation
Indices: 64640--64720 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
64630 TTTGGTTTCA
* *
64640 AGACGCCCTTTATGGGTTTTCATCTCGATCCCTTTTTTTTG
1 AGACGCCCTTTACGGGTTTTCATCTCAATCCCTTTTTTTTG
* *
64681 AGACGCCGTTTACGGGTTTTCATCTCAATCCTTTTTTTTT
1 AGACGCCCTTTACGGGTTTTCATCTCAATCCCTTTTTTTT
64721 AGGTAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (41 bp):
AGACGCCCTTTACGGGTTTTCATCTCAATCCCTTTTTTTTG
Found at i:72122 original size:30 final size:30
Alignment explanation
Indices: 72082--72344 Score: 232
Period size: 30 Copynumber: 8.9 Consensus size: 30
72072 AAGCATTTGT
*
72082 GGTCAAAATGTAAGTTTGGAAAAGTTTAGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTAGG
* * * *
72112 CGTAAAAATGTGATTTTGGGAAAGTTT-GG
1 GGTCAAAATGTAATTTTGGAAAAGTTTAGG
* * * *
72141 GGTCAAAATGCAATGTTAGAAAAGTTTAGA
1 GGTCAAAATGTAATTTTGGAAAAGTTTAGG
* * *
72171 AGTTAAAATGTTATTTTAGG-AAAGTTTAGG
1 GGTCAAAATGTAATTTT-GGAAAAGTTTAGG
*
72201 GGTCAAAATGTAA-TTTGGAAAAGTTTAAG
1 GGTCAAAATGTAATTTTGGAAAAGTTTAGG
* * * *
72230 GG-CTAAAATATGATTTTGG-GAAGTAT-GG
1 GGTC-AAAATGTAATTTTGGAAAAGTTTAGG
* *
72258 GATCAAAATGCAATTTTGGAAAAGTTTAGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTAGG
* * **
72288 GGTTAAAATGTATTTTTTAAGAAAGTTTAGG
1 GGTCAAAATGTAATTTTGGA-AAAGTTTAGG
* *
72319 GGTTAAAATGTAATTTTAGAAAAGTT
1 GGTCAAAATGTAATTTTGGAAAAGTT
72345 CAAGGGCTAA
Statistics
Matches: 180, Mismatches: 44, Indels: 18
0.74 0.18 0.07
Matches are distributed among these distances:
28 17 0.09
29 54 0.30
30 81 0.45
31 28 0.16
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (30 bp):
GGTCAAAATGTAATTTTGGAAAAGTTTAGG
Found at i:72163 original size:59 final size:57
Alignment explanation
Indices: 72077--72378 Score: 263
Period size: 59 Copynumber: 5.1 Consensus size: 57
72067 TTTTGAAGCA
*
72077 TTTGTGGTCAAAATGTAA-GTTTGGAAAAGTTTAGGCGTAAAAATGTGATTTTGGGAAAG
1 TTTGGGGTCAAAATGTAATG-TTGGAAAAGTTTAGG-GT-AAAATGTGATTTTGGGAAAG
* * * * *
72136 TTTGGGGTCAAAATGCAATGTTAGAAAAGTTTAGAAGTTAAAATGTTATTTTAGGAAAG
1 TTTGGGGTCAAAATGTAATGTTGGAAAAGTTTAG--GGTAAAATGTGATTTTGGGAAAG
*
72195 TTTAGGGGTCAAAATGTAAT-TTGGAAAAGTTTAAGGGCTAAAATATGATTTTGGG-AAG
1 TTT-GGGGTCAAAATGTAATGTTGGAAAAGTTT-AGGG-TAAAATGTGATTTTGGGAAAG
* * * * **
72253 TATGGGATCAAAATGCAATTTTGGAAAAGTTTAGGGGTTAAAATGT-ATTTTTTAAGAAAG
1 TTTGGGGTCAAAATGTAATGTTGGAAAAGTTTA-GGG-TAAAATGTGA--TTTTGGGAAAG
* * * * *
72313 TTTAGGGGTTAAAATGTAATTTTAGAAAAGTTCAAGGGCTAAAATATGATTTTGGG-AAG
1 TTT-GGGGTCAAAATGTAATGTTGGAAAAGTT-TAGGG-TAAAATGTGATTTTGGGAAAG
*
72372 TGTGGGG
1 TTTGGGG
72379 AACTACTGGG
Statistics
Matches: 199, Mismatches: 30, Indels: 29
0.77 0.12 0.11
Matches are distributed among these distances:
57 16 0.08
58 32 0.16
59 85 0.43
60 29 0.15
61 35 0.18
62 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (57 bp):
TTTGGGGTCAAAATGTAATGTTGGAAAAGTTTAGGGTAAAATGTGATTTTGGGAAAG
Found at i:72238 original size:118 final size:119
Alignment explanation
Indices: 72082--72378 Score: 413
Period size: 118 Copynumber: 2.5 Consensus size: 119
72072 AAGCATTTGT
* *
72082 GGTCAAAATGTAAGTTTGGAAAAGTTT-A-GGCGTAAAAATGTGATTTTGGGAAAGTTTGGGGTC
1 GGTCAAAATGTAAGTTTGGAAAAGTTTAAGGGC-T-AAAATATGATTTTGGG-AAGTATGGGGTC
*
72145 AAAATGCAATGTTAGAAAAGTTTAGAAGTTAAAATGT-TATTTTAGGAAAGTTTAGG
63 AAAATGCAATGTTAGAAAAGTTTAGAAGTTAAAATGTATATTTTAAGAAAGTTTAGG
*
72201 GGTCAAAATGTAA-TTTGGAAAAGTTTAAGGGCTAAAATATGATTTTGGGAAGTATGGGATCAAA
1 GGTCAAAATGTAAGTTTGGAAAAGTTTAAGGGCTAAAATATGATTTTGGGAAGTATGGGGTCAAA
* * ** *
72265 ATGCAATTTTGGAAAAGTTTAGGGGTTAAAATGTATTTTTTAAGAAAGTTTAGG
66 ATGCAATGTTAGAAAAGTTTAGAAGTTAAAATGTATATTTTAAGAAAGTTTAGG
* * * * *
72319 GGTTAAAATGTAATTTTAGAAAAGTTCAAGGGCTAAAATATGATTTTGGGAAGTGTGGGG
1 GGTCAAAATGTAAGTTTGGAAAAGTTTAAGGGCTAAAATATGATTTTGGGAAGTATGGGG
72379 AACTACTGGG
Statistics
Matches: 160, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
117 43 0.27
118 57 0.36
119 57 0.36
120 3 0.02
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (119 bp):
GGTCAAAATGTAAGTTTGGAAAAGTTTAAGGGCTAAAATATGATTTTGGGAAGTATGGGGTCAAA
ATGCAATGTTAGAAAAGTTTAGAAGTTAAAATGTATATTTTAAGAAAGTTTAGG
Found at i:73769 original size:7 final size:7
Alignment explanation
Indices: 73770--73796 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
73760 TTTAAAATTT
73770 ATTTTAA
1 ATTTTAA
73777 ATTTTAA
1 ATTTTAA
73784 ATTTTAA
1 ATTTTAA
73791 ATTTTA
1 ATTTTA
73797 TTTTTGGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTTTAA
Found at i:78944 original size:34 final size:34
Alignment explanation
Indices: 78905--79020 Score: 162
Period size: 34 Copynumber: 3.4 Consensus size: 34
78895 ATTACAATGT
*
78905 CATTTGGTGTGCTGGATGGATTGGCTCATACGAG
1 CATTTGGTGTGCTGGATGGACTGGCTCATACGAG
* *
78939 CATTTGGTATGCT-GATGGACTGGCTCATATGAG
1 CATTTGGTGTGCTGGATGGACTGGCTCATACGAG
* *
78972 CATTTGATGTGCTAGATGGACTGGCTCATACGAG
1 CATTTGGTGTGCTGGATGGACTGGCTCATACGAG
* *
79006 CATATGGTGTTCTGG
1 CATTTGGTGTGCTGG
79021 TTGGTTAACA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
33 29 0.41
34 42 0.59
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.33
Consensus pattern (34 bp):
CATTTGGTGTGCTGGATGGACTGGCTCATACGAG
Found at i:84380 original size:22 final size:22
Alignment explanation
Indices: 84331--84380 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
84321 AGCGGTTAAA
* *
84331 ATTAAAATGTAATTTTTATAAT
1 ATTAAAATGTAATTTTTAAAAG
*
84353 AATAAAAT-TATATTTTTAAAAG
1 ATTAAAATGTA-ATTTTTAAAAG
84375 ATTAAA
1 ATTAAA
84381 TTAAAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (22 bp):
ATTAAAATGTAATTTTTAAAAG
Found at i:89551 original size:21 final size:21
Alignment explanation
Indices: 89527--89566 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
89517 TTTTCTAAAA
* *
89527 TTAAAAGTCAAAGTCATTAAG
1 TTAAAAGACAAAATCATTAAG
89548 TTAAAAGACAAAATCATTA
1 TTAAAAGACAAAATCATTA
89567 TATTGTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.28
Consensus pattern (21 bp):
TTAAAAGACAAAATCATTAAG
Found at i:92343 original size:26 final size:26
Alignment explanation
Indices: 92301--92421 Score: 109
Period size: 27 Copynumber: 4.3 Consensus size: 26
92291 GGGTTTAAAT
* * *
92301 TTTTTATTTTTATTTTTAAGGGGCCCAA
1 TTTTT-TTTTAATTTTTAA-GGTCCAAA
*
92329 TTTTTTTTTAATTTTTATAGGTCAAAA
1 TTTTTTTTTAATTTTTA-AGGTCCAAA
*
92356 TTTTGTTTTTATTAATTTTTAAGGTCCTCAA
1 --TT-TTTTT-TTAATTTTTAAGGTCC-AAA
92387 -TTTTTTTTAATTTTTAAGGGTCCAAA
1 TTTTTTTTTAATTTTTAA-GGTCCAAA
92413 TTTTTTTTT
1 TTTTTTTTT
92422 TACCAACTTT
Statistics
Matches: 78, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
26 13 0.17
27 34 0.44
28 7 0.09
29 2 0.03
30 10 0.13
31 12 0.15
ACGTcount: A:0.23, C:0.07, G:0.10, T:0.60
Consensus pattern (26 bp):
TTTTTTTTTAATTTTTAAGGTCCAAA
Found at i:92389 original size:31 final size:30
Alignment explanation
Indices: 92329--92421 Score: 83
Period size: 26 Copynumber: 3.2 Consensus size: 30
92319 AGGGGCCCAA
92329 TTTTTTT-TTAATTTTTATAGGTCAAAATT
1 TTTTTTTATTAATTTTTATAGGTCAAAATT
**
92358 TTGTTTTTATTAATTTTTA-AGGTCCTCAA--
1 TT-TTTTTATTAATTTTTATAGGT-CAAAATT
*
92387 -TTTTTT-TTAATTTTTA-AGGGTCCAAATT
1 TTTTTTTATTAATTTTTATA-GGTCAAAATT
92415 TTTTTTT
1 TTTTTTT
92422 TACCAACTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
26 14 0.26
27 8 0.15
28 1 0.02
29 8 0.15
30 9 0.17
31 13 0.25
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.61
Consensus pattern (30 bp):
TTTTTTTATTAATTTTTATAGGTCAAAATT
Found at i:92422 original size:57 final size:57
Alignment explanation
Indices: 92297--92423 Score: 163
Period size: 57 Copynumber: 2.2 Consensus size: 57
92287 AAAAGGGTTT
*
92297 AAATTTTTTATTT-TTATTTTTAAGGGGCCCAATTTTTTTTTAATTTTTATAGGTCA
1 AAATTTTTTTTTTATTATTTTTAAGGGGCCCAATTTTTTTTTAATTTTTATAGGTCA
* * *
92353 AAATTTTGTTTTTATTAATTTTTAA-GGTCCTCAA-TTTTTTTTAATTTTTA-AGGGTCC
1 AAATTTTTTTTTTATT-ATTTTTAAGGGGCC-CAATTTTTTTTTAATTTTTATA-GGTCA
92410 AAATTTTTTTTTTA
1 AAATTTTTTTTTTA
92424 CCAACTTTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
56 12 0.19
57 39 0.63
58 11 0.18
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.58
Consensus pattern (57 bp):
AAATTTTTTTTTTATTATTTTTAAGGGGCCCAATTTTTTTTTAATTTTTATAGGTCA
Found at i:92433 original size:57 final size:59
Alignment explanation
Indices: 92330--92453 Score: 155
Period size: 57 Copynumber: 2.1 Consensus size: 59
92320 GGGGCCCAAT
** * * *
92330 TTTTTTTTAATTTTTATAGGTCAAAATTTTGTTTTTATTAATTTTTAAG-GTCCT-CAA
1 TTTTTTTTAATTTTTATAGGTCAAAATTTTGTTTTTACCAACTTTTAAGAGACCTAAAA
* *
92387 TTTTTTTTAATTTTTA-AGGGTCCAAATTTTTTTTTTACCAACTTTTAAGAGACCTAAAA
1 TTTTTTTTAATTTTTATA-GGTCAAAATTTTGTTTTTACCAACTTTTAAGAGACCTAAAA
92446 TTTTTTTT
1 TTTTTTTT
92454 CTACAACTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
56 1 0.02
57 42 0.74
58 4 0.07
59 10 0.18
ACGTcount: A:0.27, C:0.09, G:0.08, T:0.56
Consensus pattern (59 bp):
TTTTTTTTAATTTTTATAGGTCAAAATTTTGTTTTTACCAACTTTTAAGAGACCTAAAA
Found at i:94160 original size:29 final size:29
Alignment explanation
Indices: 94128--94219 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
94118 AAAATGAGAC
* *
94128 TTTTCAGATACTCGAGGGTAAAATGGTAA
1 TTTTCAGAAATTCGAGGGTAAAATGGTAA
** * *
94157 TTTTGGGAAAATTTGAGGTTAAAAAT-GTAA
1 TTTTCAG-AAATTCGAGGGT-AAAATGGTAA
* * *
94187 TTTTTAGACATTCGAGGGTAAAAGGGTAA
1 TTTTCAGAAATTCGAGGGTAAAATGGTAA
94216 TTTT
1 TTTT
94220 GAGAGTTTTG
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
28 4 0.08
29 22 0.46
30 17 0.35
31 5 0.10
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (29 bp):
TTTTCAGAAATTCGAGGGTAAAATGGTAA
Found at i:94232 original size:29 final size:29
Alignment explanation
Indices: 94141--94238 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 29
94131 TCAGATACTC
* *
94141 GAGGGTAAAATGGTAATTTTGGGAAAATTT
1 GAGGGTAAAAAGGTAATTTTGAG-AAATTT
* * * * *
94171 GAGGTTAAAAATGTAATTTTTAGACATTC
1 GAGGGTAAAAAGGTAATTTTGAGAAATTT
* **
94200 GAGGGTAAAAGGGTAATTTTGAGAGTTTT
1 GAGGGTAAAAAGGTAATTTTGAGAAATTT
94229 GA-GGTAAAAA
1 GAGGGTAAAAA
94239 ATGGAGTCTT
Statistics
Matches: 53, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
28 7 0.13
29 28 0.53
30 18 0.34
ACGTcount: A:0.38, C:0.02, G:0.28, T:0.33
Consensus pattern (29 bp):
GAGGGTAAAAAGGTAATTTTGAGAAATTT
Found at i:94264 original size:58 final size:58
Alignment explanation
Indices: 94140--94301 Score: 171
Period size: 59 Copynumber: 2.8 Consensus size: 58
94130 TTCAGATACT
* ** * * * * *
94140 CGAGGGTAAAATGGTAATTTTGGGAAAATTTGAGGTTAAAAATGTAATTTTTAGACATT
1 CGAGGGTAAAATGGTAATTTTGAG-AGTTTTGAGGTAAAAAATGGAATCTTCAGACATC
* * *
94199 CGAGGGTAAAAGGGTAATTTTGAGAGTTTTGAGGTAAAAAATGGAGTCTTCGGACATC
1 CGAGGGTAAAATGGTAATTTTGAGAGTTTTGAGGTAAAAAATGGAATCTTCAGACATC
* * * *
94257 CGGGGGTAAAATGGTATTTGTTGAGAGTTTCGAGGTCAAAAATGG
1 CGAGGGTAAAATGGTAATT-TTGAGAGTTTTGAGGTAAAAAATGG
94302 TATTTTTAGA
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
58 41 0.48
59 45 0.52
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.31
Consensus pattern (58 bp):
CGAGGGTAAAATGGTAATTTTGAGAGTTTTGAGGTAAAAAATGGAATCTTCAGACATC
Found at i:94325 original size:59 final size:57
Alignment explanation
Indices: 94168--94632 Score: 426
Period size: 59 Copynumber: 7.9 Consensus size: 57
94158 TTTGGGAAAA
* ** * *
94168 TTTGAGGTTAAAAATGTAATTTTTAGACA-TTCGAGGGT-AAAAGGGTAA-TTTTGAGAGT
1 TTTGAGGTCAAAAATGGGATTTTTGGA-AGTTCG-GGGTAAAAATGG-AATTTTTG-GAGT
* * * * *
94226 TTTGAGGTAAAAAAT-GGAGTCTTCGGACA-TCCGGGGGT-AAAATGGTATTTGTTGAGAGT
1 TTTGAGGTCAAAAATGGGA-TTTTTGGA-AGTTC-GGGGTAAAAATGGAATTT-TTG-GAGT
* * * *
94285 TTCGAGGTCAAAAATGGTATTTTTAGAAGTTCGGGAGTAAAAATGGAATTTTTGAAAGT
1 TTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGG-GTAAAAATGGAATTTTTG-GAGT
* ** *
94344 TTTGGGGTCAAAAATGGGATTTTTGGAAGTTCAATGGTAAAAATGGAATCTTTGGAGT
1 TTTGAGGTCAAAAATGGGATTTTTGGAAGTTC-GGGGTAAAAATGGAATTTTTGGAGT
* * *
94402 ATT-AGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGAAATTTTTGGAAGT
1 TTTGA-GGTCAAAAATGGGATTTTTGGAAG-TTCGGGGTAAAAATGGAATTTTTGG-AGT
*
94461 TTT-AGAGTCAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGT
1 TTTGAG-GTCAAAAATGGGATTTTTGGAAGTTCG-GGGTAAAAATGGAATTTTTGG-AGT
* * * *
94520 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGACGGTAAAAATGGAATTTTTGGAAGTT
1 TTTGAGGTCAAAAATGGGATTTTTGGAAGTTCG-GGGTAAAAATGGAATTTTTGG-AG-T
*
94580 TTTG-GGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTG
1 TTTGAGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGTAAAAATGGAATTTTTG
94633 AATAGTTTAG
Statistics
Matches: 348, Mismatches: 42, Indels: 33
0.82 0.10 0.08
Matches are distributed among these distances:
57 2 0.01
58 90 0.26
59 233 0.67
60 23 0.07
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (57 bp):
TTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGTAAAAATGGAATTTTTGGAGT
Found at i:94351 original size:88 final size:87
Alignment explanation
Indices: 94258--94632 Score: 413
Period size: 88 Copynumber: 4.3 Consensus size: 87
94248 TCGGACATCC
* * * *
94258 GGGGGT-AAAATGGTATTTGTT-GAGAGTTTCGA-GGTCAAAAATGGTATTTTTAGAAGTTCGGG
1 GGGGGTAAAAATGGAATTT-TTGGA-AGTTT-GACGGT-AAAAATGGAATTTTTGGAAGTTTGGG
*
94320 AGT-AAAAATGGAATTTTTGAAAGTTT
62 -GTCAAAAATGGAATTTTTGGAAGTTT
* * ** * * *
94346 TGGGGTCAAAAATGGGATTTTTGGAAGTTCAATGGTAAAAATGGAATCTTTGG-AGTATTAGGGT
1 GGGGGT-AAAAATGGAATTTTTGGAAGTTTGACGGTAAAAATGGAATTTTTGGAAGT-TTGGGGT
*
94410 CAAAAATGGGATTTTTGGAAGTTT
64 CAAAAATGGAATTTTTGGAAGTTT
* * *
94434 GGGGGTAAAAATGAAATTTTTGGAAGTTTTA-GAGTCAAAAATGGGATTTTTGGAAGTTTGAGGG
1 GGGGGTAAAAATGGAATTTTTGGAAGTTTGACG-GT-AAAAATGGAATTTTTGGAAGTTTG-GGG
94498 T-AAAAATGGAATTTTTGGAAGTTTT
63 TCAAAAATGGAATTTTTGGAAG-TTT
* * *
94523 GGGGTTAAAAATGGGATTTTTGGAAGTTTGACGGTAAAAATGGAATTTTTGGAAGTTTTTGGGTC
1 GGGGGTAAAAATGGAATTTTTGGAAGTTTGACGGTAAAAATGGAATTTTTGGAAG-TTTGGGGTC
*
94588 AAAAATGGGATTTTTGGAAGTTT
65 AAAAATGGAATTTTTGGAAGTTT
94611 GGGGGTAAAAATGGAATTTTTG
1 GGGGGTAAAAATGGAATTTTTG
94633 AATAGTTTAG
Statistics
Matches: 244, Mismatches: 29, Indels: 28
0.81 0.10 0.09
Matches are distributed among these distances:
86 1 0.00
87 28 0.11
88 131 0.54
89 70 0.29
90 14 0.06
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (87 bp):
GGGGGTAAAAATGGAATTTTTGGAAGTTTGACGGTAAAAATGGAATTTTTGGAAGTTTGGGGTCA
AAAATGGAATTTTTGGAAGTTT
Found at i:94359 original size:30 final size:29
Alignment explanation
Indices: 94259--94632 Score: 373
Period size: 29 Copynumber: 12.7 Consensus size: 29
94249 CGGACATCCG
* *
94259 GGGGT-AAAATGGTATTTGTT-GAGAGTTTC
1 GGGGTAAAAATGGAATTT-TTGGA-AGTTTT
* * * *
94288 GAGGTCAAAAATGGTATTTTTAGAAG-TTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
*
94317 GGGAGTAAAAATGGAATTTTTGAAAGTTTT
1 GGG-GTAAAAATGGAATTTTTGGAAGTTTT
* **
94347 GGGGTCAAAAATGGGATTTTTGGAAGTTCA
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
** * *
94377 ATGGTAAAAATGGAATCTTTGG-AGTATT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
* * *
94405 AGGGTCAAAAATGGGATTTTTGGAAGTTTG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
*
94435 GGGGTAAAAATGAAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
* * *
94464 AGAGTCAAAAATGGGATTTTTGGAAG-TTT
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
94493 GAGGGTAAAAATGGAATTTTTGGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTT
*
94523 GGGGTTAAAAATGGGATTTTTGGAAG-TTT
1 GGGG-TAAAAATGGAATTTTTGGAAGTTTT
*
94552 GACGGTAAAAATGGAATTTTTGGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTT
* * *
94582 TGGGTCAAAAATGGGATTTTTGGAAGTTTG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
94612 GGGGTAAAAATGGAATTTTTG
1 GGGGTAAAAATGGAATTTTTG
94633 AATAGTTTAG
Statistics
Matches: 288, Mismatches: 42, Indels: 30
0.80 0.12 0.08
Matches are distributed among these distances:
28 7 0.02
29 149 0.52
30 118 0.41
31 14 0.05
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.36
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTT
Done.