Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015187.1 Kokia drynarioides strain JFW-HI SEQ_130231, 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: 325226
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 148 characters in sequence are not A, C, G, or T
Found at i:28 original size:18 final size:18
Alignment explanation
Indices: 5--48 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
1 AAAT
*
5 AAATTTAAATTTTTAAAC
1 AAATTTAAATTTTAAAAC
*
23 AAATTT-AATTTTAAAAT
1 AAATTTAAATTTTAAAAC
40 AAATTTAAA
1 AAATTTAAA
49 GGGAGTATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTTAAATTTTAAAAC
Found at i:339 original size:21 final size:21
Alignment explanation
Indices: 301--340 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
291 TGCTCTGCAC
*
301 TTCTACCGATACATGTATGAG
1 TTCTACCGATACAAGTATGAG
322 TTCTACCGGA-ACAAGTATG
1 TTCTACC-GATACAAGTATG
341 CAGATTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAGTATGAG
Found at i:950 original size:42 final size:42
Alignment explanation
Indices: 890--1085 Score: 293
Period size: 42 Copynumber: 4.6 Consensus size: 42
880 TATGCTCTAG
** * *
890 CCGAGACATAAGTCTTCCTTTAAACATAATCTCATGATTATC
1 CCGAGACACGAGTCTTCCTTTAAACATAATCTCATGCTCATC
* *
932 TCGAGTCACGAGTCTTCCTTTAAACATAATCTCATGCTCATC
1 CCGAGACACGAGTCTTCCTTTAAACATAATCTCATGCTCATC
* *
974 TCGAGTCACGAGTCTTCCTTTAAACATAATCTCATGCTCATC
1 CCGAGACACGAGTCTTCCTTTAAACATAATCTCATGCTCATC
*
1016 CCGAGACATGAGTCTTCCTTTAAACATAATCTCATGCTCATC
1 CCGAGACACGAGTCTTCCTTTAAACATAATCTCATGCTCATC
*
1058 CCGAGACACGAGTCTTCCATTTATACAT
1 CCGAGACACGAGTCTTCC-TTTAAACAT
1086 CAAGTGATTC
Statistics
Matches: 142, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
42 134 0.94
43 8 0.06
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.32
Consensus pattern (42 bp):
CCGAGACACGAGTCTTCCTTTAAACATAATCTCATGCTCATC
Found at i:6556 original size:16 final size:16
Alignment explanation
Indices: 6535--6570 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6525 TAAATTATTA
*
6535 ATTATAGCTCTATTCC
1 ATTATAACTCTATTCC
*
6551 ATTATAATTCTATTCC
1 ATTATAACTCTATTCC
6567 ATTA
1 ATTA
6571 CAGTTCAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (16 bp):
ATTATAACTCTATTCC
Found at i:11305 original size:11 final size:11
Alignment explanation
Indices: 11289--11329 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
11279 TTATTCTAGC
11289 CTTTTCTTATG
1 CTTTTCTTATG
11300 CTTTTCTTATG
1 CTTTTCTTATG
* *
11311 CTTTTCTTTTC
1 CTTTTCTTATG
11322 CTTTTCTT
1 CTTTTCTT
11330 GGTAGGAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.05, C:0.22, G:0.05, T:0.68
Consensus pattern (11 bp):
CTTTTCTTATG
Found at i:26657 original size:29 final size:29
Alignment explanation
Indices: 26615--26674 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
26605 GCTATACCAG
*
26615 CTTTCCATGGTTCCTTCTCACAATAAAAC
1 CTTTCCATGGTTCCTTCTCACAACAAAAC
26644 CTTTCCATGGTTCCTTCTCACAACAAAAC
1 CTTTCCATGGTTCCTTCTCACAACAAAAC
26673 CT
1 CT
26675 ACCTAGATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.33, G:0.07, T:0.33
Consensus pattern (29 bp):
CTTTCCATGGTTCCTTCTCACAACAAAAC
Found at i:31402 original size:28 final size:28
Alignment explanation
Indices: 31209--31463 Score: 152
Period size: 28 Copynumber: 9.1 Consensus size: 28
31199 TTTGACATAG
* *
31209 ATAGCCATAAAGGCATCC-TTGAACAAA
1 ATAGCCACAAAGGCATCCATTTAACAAA
* **
31236 GATAG-CAAAAGAGGTGTCCATTT-ACAAAA
1 -ATAGCCACAA-AGGCATCCATTTAAC-AAA
* *
31265 ATAACCACAAAGGCGTCCATTT-ACAAAA
1 ATAGCCACAAAGGCATCCATTTAAC-AAA
* * * *
31293 ATAGCCACAAAGACGTAC-TTTCACAAA
1 ATAGCCACAAAGGCATCCATTTAACAAA
* *
31320 GATAGTCACAAAGGCATCC-TTTCACAAA
1 -ATAGCCACAAAGGCATCCATTTAACAAA
* * *
31348 GATAGTCACAAAGGCATCC-TTTCATAAA
1 -ATAGCCACAAAGGCATCCATTTAACAAA
* *
31376 TATAGTCACAAAGGC-TCCATTTAATAAA
1 -ATAGCCACAAAGGCATCCATTTAACAAA
* * *
31404 ATAAACCATAAAGGC-TCACATTTAACAGA
1 AT-AGCCACAAAGGCATC-CATTTAACAAA
31433 ATCAGCCACAAAGGC-TCACATTTAACAAA
1 AT-AGCCACAAAGGCATC-CATTTAACAAA
31462 AT
1 AT
31464 CAACCATAAA
Statistics
Matches: 192, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
27 15 0.08
28 132 0.69
29 45 0.23
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.21
Consensus pattern (28 bp):
ATAGCCACAAAGGCATCCATTTAACAAA
Found at i:31425 original size:29 final size:29
Alignment explanation
Indices: 31385--31486 Score: 134
Period size: 29 Copynumber: 3.6 Consensus size: 29
31375 ATATAGTCAC
* *
31385 AAAGGCTC-CATTTAATAAAATAAACCAT
1 AAAGGCTCACATTTAACAAAATCAACCAT
* * *
31413 AAAGGCTCACATTTAACAGAATCAGCCAC
1 AAAGGCTCACATTTAACAAAATCAACCAT
31442 AAAGGCTCACATTTAACAAAATCAACCAT
1 AAAGGCTCACATTTAACAAAATCAACCAT
* *
31471 AAAGACTCATATTTAA
1 AAAGGCTCACATTTAA
31487 GAGGTGCACG
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
28 8 0.13
29 55 0.87
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.23
Consensus pattern (29 bp):
AAAGGCTCACATTTAACAAAATCAACCAT
Found at i:40013 original size:38 final size:40
Alignment explanation
Indices: 39919--40015 Score: 135
Period size: 40 Copynumber: 2.5 Consensus size: 40
39909 AAATTCCCCA
* *
39919 GTATTTATTGAGCTTAGTGCCTAGCAGGCTTCATGCTAGT
1 GTATTTATCGGGCTTAGTGCCTAGCAGGCTTCATGCTAGT
* *
39959 GTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTG-TCG-
1 GTATTTATCGGGCTTAGTGCCTAGCAGGCTTCATGCTAGT
*
39997 GTGTTTATCGGGCTTAGTG
1 GTATTTATCGGGCTTAGTG
40016 TTTGTGTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
38 18 0.35
39 2 0.04
40 32 0.62
ACGTcount: A:0.15, C:0.18, G:0.30, T:0.37
Consensus pattern (40 bp):
GTATTTATCGGGCTTAGTGCCTAGCAGGCTTCATGCTAGT
Found at i:40042 original size:62 final size:63
Alignment explanation
Indices: 39957--40079 Score: 203
Period size: 62 Copynumber: 2.0 Consensus size: 63
39947 CTTCATGCTA
*
39957 GTGTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGTCGGTG-TTTATCGGGCTTAGTGTTT
1 GTGTATTTATCGGGCTTAGTGCCTAGCAAGCTTCGTGTCGGTGATTTATCGGGCTTAGTGTTT
* *
40019 GTGTATTTATTGGGCTTAGTGCCTAGCAAGCTTGGTGTCGGTGTATTTATCGGGCTTAGTG
1 GTGTATTTATCGGGCTTAGTGCCTAGCAAGCTTCGTGTCGGTG-ATTTATCGGGCTTAGTG
40080 CCTAGCGGGC
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 40 0.71
64 16 0.29
ACGTcount: A:0.13, C:0.15, G:0.33, T:0.40
Consensus pattern (63 bp):
GTGTATTTATCGGGCTTAGTGCCTAGCAAGCTTCGTGTCGGTGATTTATCGGGCTTAGTGTTT
Found at i:40074 original size:40 final size:40
Alignment explanation
Indices: 40019--40138 Score: 132
Period size: 40 Copynumber: 3.0 Consensus size: 40
40009 CTTAGTGTTT
*
40019 GTGTATTTATTGGGCTTAGTGCCTAGCAAGCTTGGTGTCG
1 GTGTATTTATCGGGCTTAGTGCCTAGCAAGCTTGGTGTCG
** * *
40059 GTGTATTTATCGGGCTTAGTGCCTAGCGGGCTTTGTGCCG
1 GTGTATTTATCGGGCTTAGTGCCTAGCAAGCTTGGTGTCG
* * * * *
40099 GTGTATACTATCAGGCTTTTGAGCCTAGCAAGTTTGGTGT
1 GTGTAT-TTATCGGGC-TTAGTGCCTAGCAAGCTTGGTGT
40139 TGATGTATAT
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
40 41 0.64
41 7 0.11
42 16 0.25
ACGTcount: A:0.15, C:0.17, G:0.32, T:0.37
Consensus pattern (40 bp):
GTGTATTTATCGGGCTTAGTGCCTAGCAAGCTTGGTGTCG
Found at i:40101 original size:102 final size:102
Alignment explanation
Indices: 39919--40102 Score: 280
Period size: 102 Copynumber: 1.8 Consensus size: 102
39909 AAATTCCCCA
*
39919 GTATTTATTGAGCTTAGTGCCTAGCAGGCTTCATGCTAGTGTATTTATCGGGCTTAGTGCCTAGC
1 GTATTTATTGAGCTTAGTGCCTAGCAAGCTTCATGCTAGTGTATTTATCGGGCTTAGTGCCTAGC
*
39984 AGGCTTCGTGTCGGTGTTTATCGGGCTTAGTGTTTGT
66 AGGCTTCGTGCCGGTGTTTATCGGGCTTAGTGTTTGT
* ** *
40021 GTATTTATTGGGCTTAGTGCCTAGCAAGCTTGGTG-TCGGTGTATTTATCGGGCTTAGTGCCTAG
1 GTATTTATTGAGCTTAGTGCCTAGCAAGCTTCATGCT-AGTGTATTTATCGGGCTTAGTGCCTAG
* *
40085 CGGGCTTTGTGCCGGTGT
65 CAGGCTTCGTGCCGGTGT
40103 ATACTATCAG
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 1 0.01
102 72 0.99
ACGTcount: A:0.14, C:0.17, G:0.32, T:0.38
Consensus pattern (102 bp):
GTATTTATTGAGCTTAGTGCCTAGCAAGCTTCATGCTAGTGTATTTATCGGGCTTAGTGCCTAGC
AGGCTTCGTGCCGGTGTTTATCGGGCTTAGTGTTTGT
Found at i:45163 original size:20 final size:21
Alignment explanation
Indices: 45138--45192 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
45128 CTAGGCATGG
45138 GGATGAGA-AAATGAGAGAAA
1 GGATGAGAGAAATGAGAGAAA
*
45158 GGATGAGAGAATTGAGAG-AA
1 GGATGAGAGAAATGAGAGAAA
*
45178 -GAAGAGAG-AATGAGA
1 GGATGAGAGAAATGAGA
45193 ATGTGAAGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 6 0.19
19 7 0.23
20 10 0.32
21 8 0.26
ACGTcount: A:0.51, C:0.00, G:0.38, T:0.11
Consensus pattern (21 bp):
GGATGAGAGAAATGAGAGAAA
Found at i:48932 original size:24 final size:25
Alignment explanation
Indices: 48905--48976 Score: 85
Period size: 24 Copynumber: 2.9 Consensus size: 25
48895 TTCATTGCGT
48905 TTTACGCTCGTCAGCTTGCACAT-G
1 TTTACGCTCGTCAGCTTGCACATCG
** *
48929 TTTACGCTCGTCAGCTTATATATGCG
1 TTTACGCTCGTCAGCTTGCACAT-CG
48955 TTTACGCTCG-CTAGCTTGCACA
1 TTTACGCTCGTC-AGCTTGCACA
48977 CATTCGAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 20 0.51
25 1 0.03
26 18 0.46
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (25 bp):
TTTACGCTCGTCAGCTTGCACATCG
Found at i:54039 original size:6 final size:6
Alignment explanation
Indices: 54002--54037 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
53992 CCGGAAGAAA
*
54002 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC ACTTCC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC
54038 ACCGCGGTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (6 bp):
TCTTCC
Found at i:55519 original size:16 final size:17
Alignment explanation
Indices: 55498--55540 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
55488 TTTGAACTTT
55498 TTTTAAATATATAT-TG
1 TTTTAAATATATATGTG
55514 TTTTAAAT-T-TATGTG
1 TTTTAAATATATATGTG
55529 TTTT-AATATATA
1 TTTTAAATATATA
55541 ATTAGTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 6 0.25
15 8 0.33
16 10 0.42
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (17 bp):
TTTTAAATATATATGTG
Found at i:57836 original size:22 final size:20
Alignment explanation
Indices: 57786--57844 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
57776 TCAAGTTTAG
57786 GTATCAAATTAAAAAAAAAA
1 GTATCAAATTAAAAAAAAAA
*
57806 TTATCAAATTAAAAAAAATTAA
1 GTATCAAATTAAAAAAAA--AA
57828 GTA-CTAAATTAAAAAAA
1 GTATC-AAATTAAAAAAA
57845 TATGTTAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 17 0.50
21 1 0.03
22 16 0.47
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.25
Consensus pattern (20 bp):
GTATCAAATTAAAAAAAAAA
Found at i:64560 original size:4 final size:4
Alignment explanation
Indices: 64551--64592 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
64541 ACATATCTAA
64551 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
64593 TCTGCTTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:66531 original size:41 final size:41
Alignment explanation
Indices: 66467--66547 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
66457 CATTTTGTCG
*
66467 TTAAATTCTATTATTTCCCTAACGGCAATATTACGTGACAA
1 TTAAATTCTATTATCTCCCTAACGGCAATATTACGTGACAA
* *
66508 TTAAATTCTATTATCTCCTTAACGGTAATATTACGTGACA
1 TTAAATTCTATTATCTCCCTAACGGCAATATTACGTGACA
66548 GTCTAAATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (41 bp):
TTAAATTCTATTATCTCCCTAACGGCAATATTACGTGACAA
Found at i:69297 original size:59 final size:59
Alignment explanation
Indices: 69093--69312 Score: 273
Period size: 59 Copynumber: 3.7 Consensus size: 59
69083 TTGAGAATTT
* * * * *
69093 GGGGTCAAAATGTAA-TTTATGTAAAATTTAGGGGTTAAAATGTAATTTTTGGAAAGGTTC
1 GGGGTCAAAATGTAATTTTA-GGAAAGTTTAAGGGTTAAAATGTAA-TTTTGGAAAGTTTA
*
69153 GAGGGTTAAAATGTAATTTTAGGAAAGTTTAAGGGTTAAAATGTAATTTTAGGAAAGTTTA
1 G-GGGTCAAAATGTAATTTTAGGAAAGTTTAAGGGTTAAAATGTAATTTT-GGAAAGTTTA
* * * * *
69214 AGGGTTAAAATGTAATTTT-GGAAAGTTTAAGGGTAAAAATGTAGTTTTGGGAAGTTTA
1 GGGGTCAAAATGTAATTTTAGGAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAGTTTA
* *
69272 GGGGTCAAAATGTAATTTTAAGAAAGTTTAGGGGTTAAAAT
1 GGGGTCAAAATGTAATTTTAGGAAAGTTTAAGGGTTAAAAT
69313 AAAATTTTAG
Statistics
Matches: 141, Mismatches: 15, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
58 26 0.18
59 45 0.32
60 23 0.16
61 43 0.30
62 4 0.03
ACGTcount: A:0.37, C:0.01, G:0.26, T:0.35
Consensus pattern (59 bp):
GGGGTCAAAATGTAATTTTAGGAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAGTTTA
Found at i:69321 original size:30 final size:29
Alignment explanation
Indices: 69093--69312 Score: 269
Period size: 30 Copynumber: 7.4 Consensus size: 29
69083 TTGAGAATTT
* * *
69093 GGGGTCAAAATGTAATTTATGTAAAATTTA
1 GGGGTTAAAATGTAATTT-TGGAAAGTTTA
* *
69123 GGGGTTAAAATGTAATTTTTGGAAAGGTTC
1 GGGGTTAAAATGTAA-TTTTGGAAAGTTTA
69153 GAGGGTTAAAATGTAATTTTAGGAAAGTTTA
1 G-GGGTTAAAATGTAATTTT-GGAAAGTTTA
*
69184 AGGGTTAAAATGTAATTTTAGGAAAGTTTA
1 GGGGTTAAAATGTAATTTT-GGAAAGTTTA
*
69214 AGGGTTAAAATGTAATTTTGGAAAGTTTA
1 GGGGTTAAAATGTAATTTTGGAAAGTTTA
* * * *
69243 AGGGTAAAAATGTAGTTTTGGGAAGTTTA
1 GGGGTTAAAATGTAATTTTGGAAAGTTTA
* *
69272 GGGGTCAAAATGTAATTTTAAGAAAGTTTA
1 GGGGTTAAAATGTAATTTT-GGAAAGTTTA
69302 GGGGTTAAAAT
1 GGGGTTAAAAT
69313 AAAATTTTAG
Statistics
Matches: 169, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
29 52 0.31
30 92 0.54
31 25 0.15
ACGTcount: A:0.37, C:0.01, G:0.26, T:0.35
Consensus pattern (29 bp):
GGGGTTAAAATGTAATTTTGGAAAGTTTA
Found at i:69341 original size:22 final size:22
Alignment explanation
Indices: 69315--69358 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
69305 GTTAAAATAA
69315 AATTTTAGAAAAA-TTTGAGGGT
1 AATTTTA-AAAAAGTTTGAGGGT
69337 AATTTTAAAAAAGTTTGAGGGT
1 AATTTTAAAAAAGTTTGAGGGT
69359 TAAAACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (22 bp):
AATTTTAAAAAAGTTTGAGGGT
Found at i:69371 original size:30 final size:30
Alignment explanation
Indices: 69337--69393 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
69327 ATTTGAGGGT
69337 AATTTTAAAAAAGTTTGAGGG-TTAAAACAA
1 AATTTTAAAAAAGTTT-AGGGCTTAAAACAA
* *
69367 AATTTTAGAGAAGTTTAGGGCTTAAAA
1 AATTTTAAAAAAGTTTAGGGCTTAAAA
69394 TGTAATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.32
Consensus pattern (30 bp):
AATTTTAAAAAAGTTTAGGGCTTAAAACAA
Found at i:69401 original size:30 final size:30
Alignment explanation
Indices: 69335--69402 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
69325 AAATTTGAGG
69335 GTAATTTTAAAAAAGTTTGAGGGTTAAAAC
1 GTAATTTTAAAAAAGTTTGAGGGTTAAAAC
** * * *
69365 AAAATTTTAGAGAAGTTT-AGGGCTTAAAAT
1 GTAATTTTAAAAAAGTTTGAGGG-TTAAAAC
69395 GTAATTTT
1 GTAATTTT
69403 GAAAGAATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.37
Consensus pattern (30 bp):
GTAATTTTAAAAAAGTTTGAGGGTTAAAAC
Found at i:70200 original size:2 final size:2
Alignment explanation
Indices: 70193--70266 Score: 103
Period size: 2 Copynumber: 37.0 Consensus size: 2
70183 ATAAACATGC
* ** *
70193 AT AT AT AT AT AT AT AC GG GT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
70235 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70267 GTATTAATAT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:71268 original size:39 final size:39
Alignment explanation
Indices: 71220--71673 Score: 255
Period size: 39 Copynumber: 11.7 Consensus size: 39
71210 GATAACTGCA
*
71220 ATCTGCCCCATGATCTGGGTAAGAGATTGGATTACTGTG
1 ATCTGCCCCATGATCTGGGTAAGAGATTGGATGACTGTG
* * * * * * **
71259 ATCTACCCCATGGTCGGGGTAAAAGATCGGGTGGTTGTG
1 ATCTGCCCCATGATCTGGGTAAGAGATTGGATGACTGTG
* * * **
71298 ATCTGCCTCATGAT-TGGGGTAAGAGATCGAAT-AGCTGCA
1 ATCTGCCCCATGATCT-GGGTAAGAGATTGGATGA-CTGTG
* * *
71337 ATCTGCCTCATGATC-GAGGTAAGAGATTGAATGGCTGTG
1 ATCTGCCCCATGATCTG-GGTAAGAGATTGGATGACTGTG
* * * **
71376 ATCTGCCCCATGATCAGGGTAAGAGATCGGATGGCTGCA
1 ATCTGCCCCATGATCTGGGTAAGAGATTGGATGACTGTG
*** * ** *
71415 ATCCATCCCATGATCTGGGTAAGAGATCGGATGGTTATG
1 ATCTGCCCCATGATCTGGGTAAGAGATTGGATGACTGTG
* * * * *
71454 ATTTGCCCTATGATCGGGGTAAGAGA-TCGA-GTAGTTGTG
1 ATCTGCCCCATGATCTGGGTAAGAGATTGGATG-A-CTGTG
* **
71493 ATCTGCCCCATGATCTGGGTAAGAGATCGGATGA-TGCA
1 ATCTGCCCCATGATCTGGGTAAGAGATTGGATGACTGTG
** *
71531 ATCTGCCCCATGATAGGGGTAAGAGATTGGAT-AGTTGTG
1 ATCTGCCCCATGATCTGGGTAAGAGATTGGATGA-CTGTG
* * * * **
71570 ATCTACCCCAAGATC-GTTGTAAGAGATCGGATGA-TGCA
1 ATCTGCCCCATGATCTG-GGTAAGAGATTGGATGACTGTG
* * * *
71608 ATCTACCCC-TG-TCGTGGGGTAAAAGATTGGCTGACGGTG
1 ATCTGCCCCATGATC-T-GGGTAAGAGATTGGATGACTGTG
* * * * *
71647 ATCTACCCTATTATCGGGGTAAAAGAT
1 ATCTGCCCCATGATCTGGGTAAGAGAT
71674 CATATGGTTG
Statistics
Matches: 318, Mismatches: 77, Indels: 40
0.73 0.18 0.09
Matches are distributed among these distances:
36 2 0.01
37 3 0.01
38 59 0.19
39 245 0.77
40 6 0.02
41 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.27
Consensus pattern (39 bp):
ATCTGCCCCATGATCTGGGTAAGAGATTGGATGACTGTG
Found at i:71358 original size:78 final size:77
Alignment explanation
Indices: 71220--71557 Score: 324
Period size: 78 Copynumber: 4.4 Consensus size: 77
71210 GATAACTGCA
* * * ** * * * *
71220 ATCTGCCCCATGATCTGGGTAAGAGATTGGATTA-CTGTGATCTACCCCATGGTCGGGGTAAAAG
1 ATCTGCCCCATGATCGGGGTAAGAGA-TCGAATAGCTGCAATCT-GCCCATGATCTGGGTAAGAG
*
71284 ATCGGGTGGTTGTG
64 ATCGGATGGTTGTG
* *
71298 ATCTGCCTCATGATTGGGGTAAGAGATCGAATAGCTGCAATCTGCCTCATGATC-GAGGTAAGAG
1 ATCTGCCCCATGATCGGGGTAAGAGATCGAATAGCTGCAATCTGCC-CATGATCTG-GGTAAGAG
* * *
71362 ATTGAATGGCTGTG
64 ATCGGATGGTTGTG
* * *
71376 ATCTGCCCCATGATCAGGGTAAGAGATCGGATGGCTGCAATCCAT-CCCATGATCTGGGTAAGAG
1 ATCTGCCCCATGATCGGGGTAAGAGATCGAATAGCTGCAAT-C-TGCCCATGATCTGGGTAAGAG
*
71440 ATCGGATGGTTATG
64 ATCGGATGGTTGTG
* * * * **
71454 ATTTGCCCTATGATCGGGGTAAGAGATCGAGTAGTTGTGATCTGCCCCATGATCTGGGTAAGAGA
1 ATCTGCCCCATGATCGGGGTAAGAGATCGAATAGCTGCAATCTG-CCCATGATCTGGGTAAGAGA
* **
71519 TCGGAT-GATGCA
65 TCGGATGGTTGTG
*
71531 ATCTGCCCCATGATAGGGGTAAGAGAT
1 ATCTGCCCCATGATCGGGGTAAGAGAT
71558 TGGATAGTTG
Statistics
Matches: 213, Mismatches: 39, Indels: 17
0.79 0.14 0.06
Matches are distributed among these distances:
76 1 0.00
77 35 0.16
78 172 0.81
79 4 0.02
80 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.26
Consensus pattern (77 bp):
ATCTGCCCCATGATCGGGGTAAGAGATCGAATAGCTGCAATCTGCCCATGATCTGGGTAAGAGAT
CGGATGGTTGTG
Found at i:71427 original size:117 final size:114
Alignment explanation
Indices: 71215--71557 Score: 327
Period size: 117 Copynumber: 2.9 Consensus size: 114
71205 TTTTGGATAA
* * * *
71215 CTGCAATCTGCCCCATGATCTGGGTAAGAGATTGGATTA-CTGTGATCTACCCCATGGTCGGGGT
1 CTGCAATCTG-CCCATGATC-GGGTAAGAGATT-GAATAGCTGTGATCTGCCCCATGATCAGGGT
* * * **
71279 AAAAGATCGGGTGGTTGTGAT-CTGCCTCATGATTGGGGTAAGAGATCGAATAG
63 AAGAGATCGGATGGATGCAATCCT-CC-CATGATTGGGGTAAGAGATCGAATAG
*
71332 CTGCAATCTGCCTCATGATCGAGGTAAGAGATTGAATGGCTGTGATCTGCCCCATGATCAGGGTA
1 CTGCAATCTGCC-CATGATCG-GGTAAGAGATTGAATAGCTGTGATCTGCCCCATGATCAGGGTA
* * *
71397 AGAGATCGGATGGCTGCAATCCATCCCATGATCT-GGGTAAGAGATCGGATGG
64 AGAGATCGGATGGATGCAATCC-TCCCATGAT-TGGGGTAAGAGATCGAATAG
* *** * * * * *
71449 TTATGATTTGCCCTATGATCGGGGTAAGAGATCGAGTAGTTGTGATCTGCCCCATGATCTGGGTA
1 CTGCAATCTGCCC-ATGATC-GGGTAAGAGATTGAATAGCTGTGATCTGCCCCATGATCAGGGTA
*
71514 AGAGATCGGAT-GATGCAAT-CTGCCCCATGATAGGGGTAAGAGAT
64 AGAGATCGGATGGATGCAATCCT--CCCATGATTGGGGTAAGAGAT
71558 TGGATAGTTG
Statistics
Matches: 191, Mismatches: 24, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
114 1 0.01
115 1 0.01
116 33 0.17
117 150 0.79
118 5 0.03
119 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.26
Consensus pattern (114 bp):
CTGCAATCTGCCCATGATCGGGTAAGAGATTGAATAGCTGTGATCTGCCCCATGATCAGGGTAAG
AGATCGGATGGATGCAATCCTCCCATGATTGGGGTAAGAGATCGAATAG
Found at i:71635 original size:77 final size:77
Alignment explanation
Indices: 71421--71637 Score: 212
Period size: 77 Copynumber: 2.8 Consensus size: 77
71411 TGCAATCCAT
* * * * * * *
71421 CCCATGATCTGGGTAAGAGATCGGATGGTTATG--ATTTGCCCTATGATCGGGGTAAGAGA-TCG
1 CCCAAGATCTGGGTAAGAGATCGGAT-G--ATGCAATCTACCCCATGATAGGGGTAAAAGATTGG
*
71483 AGTAGTTGTGATCTGC
63 A-TAGTTGTGATCTAC
* * *
71499 CCCATGATCTGGGTAAGAGATCGGATGATGCAATCTGCCCCATGATAGGGGTAAGAGATTGGATA
1 CCCAAGATCTGGGTAAGAGATCGGATGATGCAATCTACCCCATGATAGGGGTAAAAGATTGGATA
71564 GTTGTGATCTAC
66 GTTGTGATCTAC
* *
71576 CCCAAGATC-GTTGTAAGAGATCGGATGATGCAATCTACCCC-TG-TCGTGGGGTAAAAGATTGG
1 CCCAAGATCTG-GGTAAGAGATCGGATGATGCAATCTACCCCATGAT--AGGGGTAAAAGATTGG
71638 CTGACGGTGA
Statistics
Matches: 123, Mismatches: 10, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
75 4 0.03
76 3 0.02
77 87 0.71
78 29 0.24
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (77 bp):
CCCAAGATCTGGGTAAGAGATCGGATGATGCAATCTACCCCATGATAGGGGTAAAAGATTGGATA
GTTGTGATCTAC
Found at i:71884 original size:78 final size:78
Alignment explanation
Indices: 71490--71871 Score: 319
Period size: 78 Copynumber: 4.9 Consensus size: 78
71480 TCGAGTAGTT
* * * * * *
71490 GTGATCTGCCCCATGATCTGGGTAAGAGATCGGAT-GATGCAATCTGCCCC-AT-GATAGGGGTA
1 GTGATGTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCTATCG--CGGGGTA
*
71552 AGAGATTGGAT-A-G
64 AGAGATTGGCTGACG
* * * ** * * * * * *
71565 TTGTGATCTACCCCAAGATCGTTGTAAGAGATCGGAT-GATGCAATCTACCCCTGTCGTGGGGTA
1 --GTGATGTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCTATCGCGGGGTA
*
71629 AAAGATTGGCTGACG
64 AGAGATTGGCTGACG
* * * * * *
71644 GTGATCTACCCTATTATCGGGGTAAAAGATC-ATATGGTTGCAATTTACCCCTATCGCGGGGTAA
1 GTGATGTGCCCCATGATCGGGGTAAAAGATCGA-ATGGTTGCAATCTGCCCCTATCGCGGGGTAA
*
71708 GAGATTTGCTGACG
65 GAGATTGGCTGACG
* * * ** * * * *
71722 GTGATCTGCCCCATTATCGGGATAAAAGATCGAATCATTGCAATCTGCCTCTGTCACGTGGTAAG
1 GTGATGTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCTATCGCGGGGTAAG
*
71787 AGATTGGCTAACG
66 AGATTGGCTGACG
** *
71800 GTGATGTGTTCCATGATCGGGGTAAAAGATCGAATGGTTGTAATCTGCCCCTATCGCGGGGTAAG
1 GTGATGTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCTATCGCGGGGTAAG
71865 AGATTGG
66 AGATTGG
71872 ATGGTTGTGA
Statistics
Matches: 250, Mismatches: 48, Indels: 13
0.80 0.15 0.04
Matches are distributed among these distances:
77 86 0.34
78 161 0.64
79 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.27
Consensus pattern (78 bp):
GTGATGTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCTATCGCGGGGTAAG
AGATTGGCTGACG
Found at i:84005 original size:59 final size:59
Alignment explanation
Indices: 83813--84074 Score: 264
Period size: 59 Copynumber: 4.4 Consensus size: 59
83803 GTTTTGGGAA
* * * * *
83813 TTTGA-GGTTAAAATGTAA-TTTATGGAAAATTTAGGGGTTAAAATGTAATTTTTGGAAAGG
1 TTTGAGGGTAAAAATGTAATTTTA-GG-AAGTTTAAGGGTTAAAATGTAA-TTTAGGAAAAG
* *
83873 TTTGAGGGTAAAAATGTAATTTTGGGAATGTTTGAGGGTTAAAATGTAATTTAGG-AAAG
1 TTTGAGGGTAAAAATGTAATTTTAGGAA-GTTTAAGGGTTAAAATGTAATTTAGGAAAAG
* * * *
83932 TTT-AGGGGTCAAAATGTAATTTTAAGGAAGTTTAAAGG-TAAAATGTAATTTTGGAAAAT
1 TTTGA-GGGTAAAAATGTAATTTT-AGGAAGTTTAAGGGTTAAAATGTAATTTAGGAAAAG
* * *** *
83991 TTTGAGGGTAAAAATGTAATTTTAGAAAGTTTAGGGGTTAAAACAAAATTTAGAAAAAG
1 TTTGAGGGTAAAAATGTAATTTTAGGAAGTTTAAGGGTTAAAATGTAATTTAGGAAAAG
* *
84050 TTTAAGGGTTAAAATGTAATTTTAG
1 TTTGAGGGTAAAAATGTAATTTTAG
84075 AAGAGTTCAA
Statistics
Matches: 169, Mismatches: 25, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
58 27 0.16
59 91 0.54
60 17 0.10
61 31 0.18
62 3 0.02
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.36
Consensus pattern (59 bp):
TTTGAGGGTAAAAATGTAATTTTAGGAAGTTTAAGGGTTAAAATGTAATTTAGGAAAAG
Found at i:84087 original size:30 final size:29
Alignment explanation
Indices: 83818--84087 Score: 231
Period size: 30 Copynumber: 9.1 Consensus size: 29
83808 GGGAATTTGA
* * *
83818 GGTTAAAATGTAATTTATGGAAAATTTAGG
1 GGTTAAAATGTAATTT-TAGAAAGTTTAAG
* *
83848 GGTTAAAATGTAATTTTTGGAAAGGTTTGAG
1 GGTTAAAATGTAA-TTTTAGAAA-GTTTAAG
* * * *
83879 GGTAAAAATGTAATTTTGGGAATGTTTGAG
1 GGTTAAAATGTAATTTT-AGAAAGTTTAAG
*
83909 GGTTAAAATGTAA-TTTAGGAAAGTTTAGG
1 GGTTAAAATGTAATTTTA-GAAAGTTTAAG
* * *
83938 GGTCAAAATGTAATTTTAAGGAAGTTTAAA
1 GGTTAAAATGTAATTTT-AGAAAGTTTAAG
* * *
83968 GG-TAAAATGTAATTTTGGAAAATTTTGAG
1 GGTTAAAATGTAATTTTAG-AAAGTTTAAG
* *
83997 GGTAAAAATGTAATTTTAGAAAGTTTAGG
1 GGTTAAAATGTAATTTTAGAAAGTTTAAG
** *
84026 GGTTAAAA-CAAAATTTAGAAAAAGTTTAAG
1 GGTTAAAATGTAATTTTAG--AAAGTTTAAG
*
84056 GGTTAAAATGTAATTTTAGAAGAGTTCAAG
1 GGTTAAAATGTAATTTTAGAA-AGTTTAAG
84086 GG
1 GG
84088 CTCTTTTATG
Statistics
Matches: 194, Mismatches: 34, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
28 8 0.04
29 60 0.31
30 95 0.49
31 31 0.16
ACGTcount: A:0.40, C:0.01, G:0.25, T:0.34
Consensus pattern (29 bp):
GGTTAAAATGTAATTTTAGAAAGTTTAAG
Found at i:85566 original size:20 final size:20
Alignment explanation
Indices: 85517--85556 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
85507 GGAAGACCCT
*
85517 TAAAACCTTATCAAATTACA
1 TAAAACATTATCAAATTACA
85537 TAAAACATTATCAAATTACA
1 TAAAACATTATCAAATTACA
85557 AAATTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAACATTATCAAATTACA
Found at i:89572 original size:22 final size:22
Alignment explanation
Indices: 89540--89585 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
89530 TTTTCTCTCA
89540 TTTTCTCTCTTGTC-AAACACCAT
1 TTTTCTCTC-T-TCAAAACACCAT
89563 TTTTCT-TCTTCAAAACACCAT
1 TTTTCTCTCTTCAAAACACCAT
89584 TT
1 TT
89586 ATAAAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.09
21 12 0.55
22 2 0.09
23 6 0.27
ACGTcount: A:0.24, C:0.28, G:0.02, T:0.46
Consensus pattern (22 bp):
TTTTCTCTCTTCAAAACACCAT
Found at i:97023 original size:22 final size:22
Alignment explanation
Indices: 96991--97034 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
96981 GAAGGAATGT
*
96991 GTAACTTTGTAAATCCTACTAA
1 GTAACTATGTAAATCCTACTAA
97013 GTAACTATGTAAATCCTACTAA
1 GTAACTATGTAAATCCTACTAA
97035 CACAAGAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (22 bp):
GTAACTATGTAAATCCTACTAA
Found at i:98211 original size:25 final size:24
Alignment explanation
Indices: 98183--98256 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 24
98173 TAAAATTGAA
98183 AAATAATCTAATCTTAAAGTGATCC
1 AAATAA-CTAATCTTAAAGTGATCC
* * *
98208 AAAT-A--AA-CTAAAATTGA--A
1 AAATAACTAATCTTAAAGTGATCC
98226 AAATAAACTAATCTTAAAGTGATCC
1 AAAT-AACTAATCTTAAAGTGATCC
98251 AAATAA
1 AAATAA
98257 ACTTCAGTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 15
0.63 0.11 0.26
Matches are distributed among these distances:
18 4 0.11
20 9 0.25
21 2 0.06
22 2 0.06
23 8 0.22
24 3 0.08
25 8 0.22
ACGTcount: A:0.54, C:0.12, G:0.07, T:0.27
Consensus pattern (24 bp):
AAATAACTAATCTTAAAGTGATCC
Found at i:98269 original size:43 final size:43
Alignment explanation
Indices: 98169--98259 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
98159 AGATTGGGCC
*
98169 AAACTAAAATTGAAAAATAATCTAATCTTAAAGTGATCCAAAT
1 AAACTAAAATTGAAAAATAAACTAATCTTAAAGTGATCCAAAT
98212 AAACTAAAATTGAAAAATAAACTAATCTTAAAGTGATCCAAAT
1 AAACTAAAATTGAAAAATAAACTAATCTTAAAGTGATCCAAAT
98255 AAACT
1 AAACT
98260 TCAGTTGAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.26
Consensus pattern (43 bp):
AAACTAAAATTGAAAAATAAACTAATCTTAAAGTGATCCAAAT
Found at i:98903 original size:17 final size:17
Alignment explanation
Indices: 98881--98913 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
98871 TTAAAAAATA
98881 ATAATAA-ATTTATTAAC
1 ATAATAATA-TTATTAAC
98898 ATAATAATATTATTAA
1 ATAATAATATTATTAA
98914 AATTTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATAATATTATTAAC
Found at i:99020 original size:51 final size:52
Alignment explanation
Indices: 98939--99036 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 52
98929 TCGTTCCTCC
** *
98939 GTTAAATTATTAATGATGATTTTTTTTATTTAGCATAATAATAAATTTATCT
1 GTTAAATTATTAATGATGAACTTTTTTATTTAGCATAATAAAAAATTTATCT
* *
98991 GTTAAATTATTAATGGT-AACTTTTTTATTTAGTATAATAAAAAATT
1 GTTAAATTATTAATGATGAACTTTTTTATTTAGCATAATAAAAAATT
99037 CAAAGATCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
51 25 0.61
52 16 0.39
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (52 bp):
GTTAAATTATTAATGATGAACTTTTTTATTTAGCATAATAAAAAATTTATCT
Found at i:99140 original size:24 final size:24
Alignment explanation
Indices: 99113--99158 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
99103 TTTATCATTC
* *
99113 TTAAAAATTAAAAATTAAAAAACT
1 TTAAAAAATAAAAAATAAAAAACT
99137 TTAAAAAATAAAAAATAAAAAA
1 TTAAAAAATAAAAAATAAAAAA
99159 TATTTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (24 bp):
TTAAAAAATAAAAAATAAAAAACT
Found at i:99164 original size:25 final size:24
Alignment explanation
Indices: 99116--99166 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
99106 ATCATTCTTA
* * *
99116 AAAATTAAAAATTAAAAAACTTTA
1 AAAAATAAAAAATAAAAAAATTTA
99140 AAAAATAAAAAATAAAAAATATTTA
1 AAAAATAAAAAATAAAAAA-ATTTA
99165 AA
1 AA
99167 TTTTCATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAAATAAAAAATAAAAAAATTTA
Found at i:103987 original size:28 final size:27
Alignment explanation
Indices: 103956--104009 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
103946 ATATTTTTAT
*
103956 ATAATTTATAATA-ATATTATTATAATTC
1 ATAATATATAATATATA-TA-TATAATTC
103984 ATAATATATAATATATATATATAATT
1 ATAATATATAATATATATATATAATT
104010 ATGAAAAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 7 0.29
28 14 0.58
29 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
ATAATATATAATATATATATATAATTC
Found at i:104000 original size:21 final size:20
Alignment explanation
Indices: 103953--104000 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
103943 TTTATATTTT
* *
103953 TATATAATTTATAATAATAT
1 TATATAATTCATAATAATAA
103973 TATTATAATTCATAATATATAA
1 TA-TATAATTCATAATA-ATAA
103995 TATATA
1 TATATA
104001 TATATAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 17 0.71
22 5 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TATATAATTCATAATAATAA
Found at i:112869 original size:2 final size:2
Alignment explanation
Indices: 112862--112894 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
112852 TTATTCACCA
112862 AT 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 AT A
112895 AATCCAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:113613 original size:91 final size:90
Alignment explanation
Indices: 113426--113619 Score: 250
Period size: 90 Copynumber: 2.1 Consensus size: 90
113416 ATTAAAAAAA
* **
113426 TTAGGTACCAAATTAGGAAAAAGAGTGAAGTTCAAGTATCAAATTGGACCCCAAAAAGTTTAAGT
1 TTAGGTACCAAATTAGGAAAAAGAGTGAAGTTCAAGTACCAAATTGGACCAAAAAAAGTTTAAGT
*
113491 ACCAACTTAAAAAAAAGTGTCAAGT
66 ACCAAATTAAAAAAAAGTGTCAAGT
* * *
113516 TTAGGTATCAAATTAGGAAAAA-ATGTTAAGTTCGAGTACCAAATTGGACCAAAAAAAAGTTT-A
1 TTAGGTACCAAATTAGGAAAAAGA-GTGAAGTTCAAGTACCAAATTGGACC-AAAAAAAGTTTAA
* *
113579 GATACTAAATTAGAAAAAAA-TTTCAAGT
64 G-TACCAAATTA-AAAAAAAGTGTCAAGT
113607 TTAGGTACCAAAT
1 TTAGGTACCAAAT
113620 GTTATATTAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
89 1 0.01
90 46 0.51
91 36 0.40
92 7 0.08
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.26
Consensus pattern (90 bp):
TTAGGTACCAAATTAGGAAAAAGAGTGAAGTTCAAGTACCAAATTGGACCAAAAAAAGTTTAAGT
ACCAAATTAAAAAAAAGTGTCAAGT
Found at i:121967 original size:21 final size:20
Alignment explanation
Indices: 121917--121967 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
121907 ACAAGAATAT
*
121917 TAAAAATTATAAAAAATTTA
1 TAAAAATTATAAAAAAATTA
*
121937 TGAAACATTATAAAAATAATTA
1 T-AAAAATTATAAAAA-AATTA
121959 -AAAATATTA
1 TAAAA-ATTA
121968 ATAGTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 4 0.16
21 17 0.68
22 4 0.16
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
TAAAAATTATAAAAAAATTA
Found at i:129080 original size:18 final size:18
Alignment explanation
Indices: 129057--129095 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
129047 ATTTATTTGC
129057 ATTTTTTA-AAAAATATAT
1 ATTTTTTACAAAAATA-AT
*
129075 ATTTTTTACAAAGATAAT
1 ATTTTTTACAAAAATAAT
129093 ATT
1 ATT
129096 ATGTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTTTTTACAAAAATAAT
Found at i:130025 original size:25 final size:25
Alignment explanation
Indices: 129996--130045 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
129986 AAGTTACAAC
129996 AATAGAAATTGAAGAAGTTCAGAAG
1 AATAGAAATTGAAGAAGTTCAGAAG
130021 AATAGAAATTGAAGAAGTTCAGAAG
1 AATAGAAATTGAAGAAGTTCAGAAG
130046 GTATAAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.24, T:0.20
Consensus pattern (25 bp):
AATAGAAATTGAAGAAGTTCAGAAG
Found at i:133060 original size:6 final size:6
Alignment explanation
Indices: 133051--133104 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
133041 GCGGGGTTGA
* * * * *
133051 GGTTAT GGTTCT AGTTCT AGTTTT GGTTCT GGTTGT GGTTCT GGTTCT
1 GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT
133099 GGTTCT
1 GGTTCT
133105 TGTTGTAGTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.06, C:0.11, G:0.31, T:0.52
Consensus pattern (6 bp):
GGTTCT
Found at i:134990 original size:19 final size:21
Alignment explanation
Indices: 134943--135014 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 21
134933 TCGGATATTC
* *
134943 AAATAAAAAGTATACAAAAT-
1 AAATAAAAATTATAAAAAATG
* *
134963 TAAT-TAAATTAT-AAAAATG
1 AAATAAAAATTATAAAAAATG
134982 AAAT-AAAA-TATTAAAAAATG
1 AAATAAAAATTA-TAAAAAATG
135002 AAATAAAAATTAT
1 AAATAAAAATTAT
135015 TAACAAATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
18 7 0.17
19 13 0.32
20 14 0.34
21 5 0.12
22 2 0.05
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (21 bp):
AAATAAAAATTATAAAAAATG
Found at i:135000 original size:20 final size:20
Alignment explanation
Indices: 134968--135014 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
134958 AAAATTAATT
134968 AAATTATAAAAATGAAATAA
1 AAATTATAAAAATGAAATAA
134988 AATATTA-AAAAATGAAATAA
1 AA-ATTATAAAAATGAAATAA
135008 AAATTAT
1 AAATTAT
135015 TAACAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.16
20 17 0.68
21 4 0.16
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (20 bp):
AAATTATAAAAATGAAATAA
Found at i:158140 original size:27 final size:26
Alignment explanation
Indices: 158083--158168 Score: 82
Period size: 27 Copynumber: 3.2 Consensus size: 26
158073 TGCGAACCAA
* * *
158083 GTTCGCCAATTGGTTTAGCTAACTAGA
1 GTTCGCCAATTGGTTT-GCGAACTGGG
* *
158110 GTTCGCCAATAGGTTTGGCGAATTGGG
1 GTTCGCCAATTGGTTT-GCGAACTGGG
* * *
158137 GTTCACCAGTTGGTTTGAGAACTGGG
1 GTTCGCCAATTGGTTTGCGAACTGGG
158163 GTTCGC
1 GTTCGC
158169 TAGTGTAAGT
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
26 13 0.28
27 34 0.72
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.31
Consensus pattern (26 bp):
GTTCGCCAATTGGTTTGCGAACTGGG
Found at i:158685 original size:21 final size:21
Alignment explanation
Indices: 158656--158697 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
158646 CTTTTCTATA
* *
158656 GACTTTGTTTTCAAGATATGT
1 GACTATGTTTTAAAGATATGT
158677 GACTATGTTTTAAAGATATGT
1 GACTATGTTTTAAAGATATGT
158698 TTTATGCGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.45
Consensus pattern (21 bp):
GACTATGTTTTAAAGATATGT
Found at i:159237 original size:18 final size:17
Alignment explanation
Indices: 159211--159260 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
159201 CTATGTTGTT
*
159211 ACCTGTGTTAGTATGCGA
1 ACCTATGTT-GTATGCGA
*
159229 ACCTATGTTGTTATGTGA
1 ACCTATGTTG-TATGCGA
*
159247 ACATATGTTGTATG
1 ACCTATGTTGTATG
159261 AAGTATGCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (17 bp):
ACCTATGTTGTATGCGA
Found at i:170119 original size:27 final size:29
Alignment explanation
Indices: 170089--170142 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
170079 AAGGAGGAAG
170089 ATGTGGC-ATTTT-TGGCAAATATGTGAT
1 ATGTGGCTATTTTATGGCAAATATGTGAT
*
170116 ATGTGGCTATTTTATGGCGAATATGTG
1 ATGTGGCTATTTTATGGCAAATATGTG
170143 GCAGTTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.29
28 5 0.21
29 12 0.50
ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41
Consensus pattern (29 bp):
ATGTGGCTATTTTATGGCAAATATGTGAT
Found at i:170677 original size:20 final size:19
Alignment explanation
Indices: 170639--170681 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
170629 TGATTTGGAC
170639 TTTGAGGATTTTACTTGTT
1 TTTGAGGATTTTACTTGTT
*
170658 ATTTGA-GATTTTATTATGTT
1 -TTTGAGGATTTTACT-TGTT
170678 TTTG
1 TTTG
170682 TTTATGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.19, C:0.02, G:0.19, T:0.60
Consensus pattern (19 bp):
TTTGAGGATTTTACTTGTT
Found at i:172585 original size:17 final size:17
Alignment explanation
Indices: 172563--172601 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
172553 ATGTTAAGAT
*
172563 AATTTTAATAAAAATAA
1 AATTTTAAGAAAAATAA
* *
172580 AATTTTGAGAGAAATAA
1 AATTTTAAGAAAAATAA
172597 AATTT
1 AATTT
172602 GAGTGAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (17 bp):
AATTTTAAGAAAAATAA
Found at i:172611 original size:17 final size:18
Alignment explanation
Indices: 172573--172611 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
172563 AATTTTAATA
172573 AAAATAAAATTTTGAGAG
1 AAAATAAAATTTTGAGAG
*
172591 -AAATAAAA-TTTGAGTG
1 AAAATAAAATTTTGAGAG
172607 AAAAT
1 AAAAT
172612 TTATCAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.28
Consensus pattern (18 bp):
AAAATAAAATTTTGAGAG
Found at i:173846 original size:6 final size:6
Alignment explanation
Indices: 173835--173862 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
173825 TATAGAACCC
173835 ATTTGA ATTTGA ATTTGA ATTTGA ATTT
1 ATTTGA ATTTGA ATTTGA ATTTGA ATTT
173863 TGACAGTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (6 bp):
ATTTGA
Found at i:174897 original size:5 final size:5
Alignment explanation
Indices: 174887--174920 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
174877 TCAGGGTTAA
174887 AAATC AAATC AAATC AAATC AAATC AAATC AAAT
1 AAATC AAATC AAATC AAATC AAATC AAATC AAAT
174921 GAGGGTGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.62, C:0.18, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATC
Found at i:177457 original size:6 final size:6
Alignment explanation
Indices: 177446--177515 Score: 58
Period size: 6 Copynumber: 12.2 Consensus size: 6
177436 GGACCCAACA
* * * *
177446 AAATTT AAATTT -ATTTT AAAATT AAGTTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
177492 --ATTAT AAATTT AAAATT AAATTT A
1 AAATT-T AAATTT AAATTT AAATTT A
177516 TTTAAACAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
4 3 0.06
5 9 0.18
6 35 0.70
7 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:177475 original size:17 final size:17
Alignment explanation
Indices: 177445--177505 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
177435 CGGACCCAAC
177445 AAAATTTAAATTTATTTT
1 AAAA-TTAAATTTATTTT
*
177463 AAAATTAAGTTTATTTT
1 AAAATTAAATTTATTTT
* *
177480 AAATTTAAATTTATTAT
1 AAAATTAAATTTATTTT
*
177497 AAATTTAAA
1 AAAATTAAA
177506 ATTAAATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 35 0.90
18 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AAAATTAAATTTATTTT
Found at i:177486 original size:23 final size:22
Alignment explanation
Indices: 177460--177518 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 22
177450 TTAAATTTAT
177460 TTTAAAATTAAGTTTATTTTAAA
1 TTTAAAATTAA-TTTATTTTAAA
*
177483 TTT---A--AATTTATTATAAA
1 TTTAAAATTAATTTATTTTAAA
177500 TTTAAAATTAAATTTATTT
1 TTTAAAATT-AATTTATTT
177519 AAACAATGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
17 13 0.46
18 2 0.07
20 2 0.07
23 11 0.39
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTAAAATTAATTTATTTTAAA
Found at i:179378 original size:29 final size:30
Alignment explanation
Indices: 179324--179837 Score: 176
Period size: 29 Copynumber: 17.6 Consensus size: 30
179314 TCTTAAACTG
* *
179324 TCCAAAAATTA-TA-TTTTGACTTTCGAA-C
1 TCCAAAAATTACCATTTTTGAC-CTCGAATC
*
179352 TCCTAAAAATTA-CATTTTTGACCTCGAATG
1 TCC-AAAAATTACCATTTTTGACCTCGAATC
* * *
179382 TCCAAAAA-TACAATTTTTGACCTCAAACTT
1 TCCAAAAATTACCATTTTTGACCTCGAA-TC
* *
179412 TCCAAAAATTACCA-TTTT-ACCCTCAAATA
1 TCCAAAAATTACCATTTTTGA-CCTCGAATC
* *
179441 TCCAAAAATT-CTATTTTTGACCGT-GAATTT
1 TCCAAAAATTACCATTTTTGACC-TCGAA-TC
* * *
179471 TCTAAAAATTACCA-TTTTGATCTCGAATG
1 TCCAAAAATTACCATTTTTGACCTCGAATC
* * * *
179500 TCCAAAAA-TATCATTTTTAATCTCGAACTT
1 TCCAAAAATTACCATTTTTGACCTCGAA-TC
* *
179530 TCCAAAAATTATCA-TTTT-A---C-AATG
1 TCCAAAAATTACCATTTTTGACCTCGAATC
* * *
179554 TCTAACAATT-CCA-TTTTGACCTCGAAAC
1 TCCAAAAATTACCATTTTTGACCTCGAATC
** * * * *
179582 TTTTAAAAATTACCA-TTAT-ACCCTTGGATG
1 -TCCAAAAATTACCATTTTTGA-CCTCGAATC
* * * *
179612 TCC-AAAATTTCCATTTTTAACCACGAAAC
1 TCCAAAAATTACCATTTTTGACCTCGAATC
* * * *
179641 TTCTAAAAATTACCATTTTAT-TCCT-GGATA
1 -TCCAAAAATTACCATTTT-TGACCTCGAATC
* * *
179671 TCCAAAAATTA-CATTTTTGACCCCAAAAC
1 TCCAAAAATTACCATTTTTGACCTCGAATC
* *
179700 TTCTAAAAATTTA-CA-TTTT-ACCCTCGAATG
1 -TCCAAAAA-TTACCATTTTTGA-CCTCGAATC
* * *
179730 TCC-AAAATTACCATTTTTTACCTCAAACTTT
1 TCCAAAAATTACCATTTTTGACCTCGAA--TC
* *
179761 TCAAAAAATTACCA-TTTT-ACCCTCGAATG
1 TCCAAAAATTACCATTTTTGA-CCTCGAATC
* * *
179790 TTCAAAAATT-CCATTTTTCACCAT-GAAATT
1 TCCAAAAATTACCATTTTTGACC-TCG-AATC
*
179820 TCAAAAAATTACCATTTT
1 TCCAAAAATTACCATTTT
179838 ACCCCTAAAA
Statistics
Matches: 369, Mismatches: 71, Indels: 89
0.70 0.13 0.17
Matches are distributed among these distances:
23 6 0.02
24 10 0.03
25 2 0.01
26 1 0.00
27 5 0.01
28 39 0.11
29 132 0.36
30 112 0.30
31 51 0.14
32 11 0.03
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.37
Consensus pattern (30 bp):
TCCAAAAATTACCATTTTTGACCTCGAATC
Found at i:179423 original size:59 final size:59
Alignment explanation
Indices: 179354--179841 Score: 416
Period size: 59 Copynumber: 8.4 Consensus size: 59
179344 TTTCGAACTC
*
179354 CTAAAAATTA-CATTTTTGA-CCTCGAATGTCCAAAAATACAATTTTTGACCTCAAACTTT
1 CTAAAAATTACCA-TTTT-ACCCTCGAATGTCCAAAAATACCATTTTTGACCTCAAACTTT
* * * * * * *
179413 CCAAAAATTACCATTTTACCCTCAAATATCCAAAAATTCTATTTTTGACCGT-GAATTTT
1 CTAAAAATTACCATTTTACCCTCGAATGTCCAAAAATACCATTTTTGACC-TCAAACTTT
* * * * *
179472 CTAAAAATTACCATTTTGA-TCTCGAATGTCCAAAAATATCATTTTTAATCTCGAACTTT
1 CTAAAAATTACCATTTT-ACCCTCGAATGTCCAAAAATACCATTTTTGACCTCAAACTTT
* * * * *
179531 CCAAAAATTATCATTTTA----C-AATGTCTAACAATTCCA-TTTTGACCTCGAAACTTT
1 CTAAAAATTACCATTTTACCCTCGAATGTCCAAAAATACCATTTTTGACCTC-AAACTTT
* * * * * * *
179585 -TAAAAATTACCATTATACCCTTGGATGTCCAAAATTTCCATTTTTAACCACGAAAC-TT
1 CTAAAAATTACCATTTTACCCTCGAATGTCCAAAAATACCATTTTTGACCTC-AAACTTT
* * * *
179643 CTAAAAATTACCATTTTATTCCT-GGATATCCAAAAATTA-CATTTTTGACCCCAAAAC-TT
1 CTAAAAATTACCATTTTA-CCCTCGAATGTCCAAAAA-TACCATTTTTGACCTC-AAACTTT
* *
179702 CTAAAAATTTA-CATTTTACCCTCGAATGTCCAAAATTACCATTTTTTACCTCAAACTTTT
1 CTAAAAA-TTACCATTTTACCCTCGAATGTCCAAAAATACCATTTTTGACCTCAAAC-TTT
* * * * *
179762 CAAAAAATTACCATTTTACCCTCGAATGTTCAAAAATTCCATTTTTCACCATGAAA-TTT
1 CTAAAAATTACCATTTTACCCTCGAATGTCCAAAAATACCATTTTTGACC-TCAAACTTT
*
179821 CAAAAAATTACCATTTTACCC
1 CTAAAAATTACCATTTTACCC
179842 CTAAAATGTC
Statistics
Matches: 351, Mismatches: 56, Indels: 44
0.78 0.12 0.10
Matches are distributed among these distances:
53 22 0.06
54 19 0.05
55 1 0.00
58 27 0.08
59 224 0.64
60 54 0.15
61 4 0.01
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.36
Consensus pattern (59 bp):
CTAAAAATTACCATTTTACCCTCGAATGTCCAAAAATACCATTTTTGACCTCAAACTTT
Found at i:179531 original size:118 final size:117
Alignment explanation
Indices: 179354--179841 Score: 466
Period size: 118 Copynumber: 4.2 Consensus size: 117
179344 TTTCGAACTC
*
179354 CTAAAAATTA-CATTTTTGA-CCTCGAATGTCCAAAAATA-CAATTTTTGACCTCAAACTTTCCA
1 CTAAAAATTACCA-TTTT-ACCCTCGAATGTCCAAAAATATC-ATTTTTAACCTCAAACTTTCCA
* * *
179416 AAAATTACCATTTTACCCTCAAATATCCAAAAATTCTATTTTTGACCGTGAATTTT
63 AAAATTACCATTTTACCCTCGAATATCCAAAAATTCCATTTTTGACC-TGAAATTT
* * *
179472 CTAAAAATTACCATTTTGA-TCTCGAATGTCCAAAAATATCATTTTTAATCTCGAACTTTCCAAA
1 CTAAAAATTACCATTTT-ACCCTCGAATGTCCAAAAATATCATTTTTAACCTCAAACTTTCCAAA
* * * *
179536 AATTATCATTTTA----C-AATGTCTAACAATTCCA-TTTTGACCTCGAAACTTT
65 AATTACCATTTTACCCTCGAATATCCAAAAATTCCATTTTTGACCT-GAAA-TTT
* * * * * *
179585 -TAAAAATTACCATTATACCCTTGGATGTCC-AAAATTTCCATTTTTAACCACGAAAC-TTCTAA
1 CTAAAAATTACCATTTTACCCTCGAATGTCCAAAAATAT-CATTTTTAACCTC-AAACTTTCCAA
* * * ** *
179647 AAATTACCATTTTATTCCT-GGATATCCAAAAATTACATTTTTGACCCCAAAACTT
64 AAATTACCATTTTA-CCCTCGAATATCCAAAAATTCCATTTTTGA-CCTGAAATTT
* * * *
179702 CTAAAAATTTA-CATTTTACCCTCGAATGTCCAAAATTACCATTTTTTACCTCAAACTTTTCAAA
1 CTAAAAA-TTACCATTTTACCCTCGAATGTCCAAAAATATCATTTTTAACCTCAAAC-TTTCCAA
* * *
179766 AAATTACCATTTTACCCTCGAATGTTCAAAAATTCCATTTTTCACCATGAAATTT
64 AAATTACCATTTTACCCTCGAATATCCAAAAATTCCATTTTTGACC-TGAAATTT
*
179821 CAAAAAATTACCATTTTACCC
1 CTAAAAATTACCATTTTACCC
179842 CTAAAATGTC
Statistics
Matches: 300, Mismatches: 47, Indels: 45
0.77 0.12 0.11
Matches are distributed among these distances:
111 8 0.03
112 64 0.21
113 19 0.06
114 1 0.00
117 18 0.06
118 118 0.39
119 72 0.24
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.36
Consensus pattern (117 bp):
CTAAAAATTACCATTTTACCCTCGAATGTCCAAAAATATCATTTTTAACCTCAAACTTTCCAAAA
ATTACCATTTTACCCTCGAATATCCAAAAATTCCATTTTTGACCTGAAATTT
Found at i:179859 original size:29 final size:29
Alignment explanation
Indices: 179673--179871 Score: 99
Period size: 30 Copynumber: 6.7 Consensus size: 29
179663 CCTGGATATC
179673 CAAAAATTA-CATTTTTGACCCC-AAAACT-T
1 CAAAAATTACCA-TTTT-ACCCCTAAAA-TGT
**
179702 CTAAAAATTTA-CATTTTA-CCCTCGAATGT
1 C-AAAAA-TTACCATTTTACCCCTAAAATGT
* * * *
179731 CCAAAATTACCATTTTTTACCTC-AAACTTTT
1 CAAAAATTACCA--TTTTACCCCTAAA-ATGT
**
179762 CAAAAAATTACCATTTTA-CCCTCGAATGTT
1 C-AAAAATTACCATTTTACCCCTAAAATG-T
* * * *
179792 CAAAAATT-CCATTTTTCACCATGAAATTT
1 CAAAAATTACCATTTTAC-CCCTAAAATGT
179821 CAAAAAATTACCATTTTACCCCTAAAATGT
1 C-AAAAATTACCATTTTACCCCTAAAATGT
* * *
179851 CTAAAATTATCGTTTTACCCC
1 CAAAAATTACCATTTTACCCC
179872 CGGGCATCCA
Statistics
Matches: 128, Mismatches: 26, Indels: 32
0.69 0.14 0.17
Matches are distributed among these distances:
27 3 0.02
28 17 0.13
29 35 0.27
30 45 0.35
31 18 0.14
32 10 0.08
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.36
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCCTAAAATGT
Found at i:180230 original size:97 final size:97
Alignment explanation
Indices: 180121--180314 Score: 275
Period size: 97 Copynumber: 2.0 Consensus size: 97
180111 AAAACCTTTA
* *
180121 AAATCGAGGCAATA-TTCTTTTAT-TTTGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCG
1 AAATCGAGGCAATATTTC-TTTATCTTTGA-TTCTGAAAATTTGTGCCTTAACTTACTAGGCGCA
* *
180184 ATTTTTCTTCAAATCGAAATAATCGAATACCCTT
64 ACTTTTCTTCAAATCGAAATAATCAAATACCCTT
* * *
180218 AAATCGAGGCAATGTTTCTTTATCTTTGATTCTGAAAATTTGTTCCTTAACTTACTAGGTGCAAC
1 AAATCGAGGCAATATTTCTTTATCTTTGATTCTGAAAATTTGTGCCTTAACTTACTAGGCGCAAC
* *
180283 TTTTCTTCAAATCGAGATAATCAAATATCCTT
66 TTTTCTTCAAATCGAAATAATCAAATACCCTT
180315 TTCCAAGGTT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
97 78 0.91
98 8 0.09
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (97 bp):
AAATCGAGGCAATATTTCTTTATCTTTGATTCTGAAAATTTGTGCCTTAACTTACTAGGCGCAAC
TTTTCTTCAAATCGAAATAATCAAATACCCTT
Found at i:194592 original size:20 final size:20
Alignment explanation
Indices: 194555--194615 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
194545 TTAATAAAAA
*
194555 TTATAAAAGAATTCAAAATAT
1 TTATAAAA-AATTTAAAATAT
*
194576 TTTTAAAAAATTTAAAATAT
1 TTATAAAAAATTTAAAATAT
*
194596 TTATAAAAATTTTAAAATAT
1 TTATAAAAAATTTAAAATAT
194616 ATATTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 29 0.81
21 7 0.19
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
TTATAAAAAATTTAAAATAT
Found at i:195034 original size:2 final size:2
Alignment explanation
Indices: 195029--195063 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
195019 TTTTTATTTT
195029 TA TA TA -A T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
195064 TTTAAACATG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:195246 original size:27 final size:25
Alignment explanation
Indices: 195190--195247 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 25
195180 GAGGATTTTG
*
195190 ATTTTAGAAATAGAGGGAAAGTAAAT
1 ATTTTAGAAATAGAGGGAAAG-AAAA
195216 ATTTTAGGAAATAGAGAGGAACA-AAAA
1 ATTTTA-GAAATAGAG-GGAA-AGAAAA
195243 ATTTT
1 ATTTT
195248 GATTTTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 6 0.21
27 17 0.61
28 4 0.14
29 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.21, T:0.28
Consensus pattern (25 bp):
ATTTTAGAAATAGAGGGAAAGAAAA
Found at i:195502 original size:32 final size:33
Alignment explanation
Indices: 195437--195503 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
195427 CATCAAATCA
*
195437 AATTTTAATCATCCCTAATCAAACCAACTCTAC
1 AATTTTAATCATCCATAATCAAACCAACTCTAC
*
195470 AATTTTAATCATCCATAATCTAA-CAACTCTAC
1 AATTTTAATCATCCATAATCAAACCAACTCTAC
195502 AA
1 AA
195504 GCGGTTTACG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 11 0.34
33 21 0.66
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (33 bp):
AATTTTAATCATCCATAATCAAACCAACTCTAC
Found at i:216019 original size:30 final size:30
Alignment explanation
Indices: 215956--216052 Score: 144
Period size: 30 Copynumber: 3.2 Consensus size: 30
215946 AATTTCAGTA
215956 ACTGTTTTGTCAC-TTTTCAATAACGTT-AGTG
1 ACTGTTTTGTCACATTTTC-A-AA-GTTGAGTG
215987 ACTGTTTTGTCACATTTTCAAAGTTGAGTG
1 ACTGTTTTGTCACATTTTCAAAGTTGAGTG
*
216017 ACTGTTATGTCACATTTTCAAAGTTGAGTG
1 ACTGTTTTGTCACATTTTCAAAGTTGAGTG
216047 ACTGTT
1 ACTGTT
216053 GTGTTAAATG
Statistics
Matches: 63, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
29 3 0.05
30 41 0.65
31 14 0.22
32 5 0.08
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (30 bp):
ACTGTTTTGTCACATTTTCAAAGTTGAGTG
Found at i:222723 original size:28 final size:30
Alignment explanation
Indices: 222678--222738 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
222668 AAACTAGCGA
*
222678 TTTAATTGATTTTATAAA-ATTT-ATGATT
1 TTTAATTGATTTTATAAAGATTTAATCATT
*
222706 TTTAATT-ATTTATTTAAAGATTTAATCATT
1 TTTAATTGATTT-TATAAAGATTTAATCATT
222736 TTT
1 TTT
222739 TAGGTCTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.14
28 12 0.43
29 4 0.14
30 8 0.29
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (30 bp):
TTTAATTGATTTTATAAAGATTTAATCATT
Found at i:235214 original size:36 final size:35
Alignment explanation
Indices: 235167--235254 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 35
235157 AATAATAACT
* * *
235167 AACCTCAGCTGAATCTCTATGATCAAGAAAAAAAAA
1 AACCTCAGCTGAAACTCAATGAACAA-AAAAAAAAA
*
235203 AACCTTAGCTGAAACTCAATGAAC--AAAAAAAAA
1 AACCTCAGCTGAAACTCAATGAACAAAAAAAAAAA
235236 AACCTCAGCTGAAACTCAA
1 AACCTCAGCTGAAACTCAA
235255 GCGATAATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
33 27 0.57
36 20 0.43
ACGTcount: A:0.51, C:0.22, G:0.10, T:0.17
Consensus pattern (35 bp):
AACCTCAGCTGAAACTCAATGAACAAAAAAAAAAA
Found at i:238346 original size:27 final size:26
Alignment explanation
Indices: 238316--238377 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
238306 CTAACACAGA
238316 TGGAGGGTTTTAAAGTGACAACATCCT
1 TGGAGGGTTTTAAAGTGACAACA-CCT
* * *
238343 TGGAGAGTTTTGAAGTGACGACACCT
1 TGGAGGGTTTTAAAGTGACAACACCT
238369 T--AGGGTTTT
1 TGGAGGGTTTT
238378 TTGCCACTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 7 0.23
26 4 0.13
27 20 0.65
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (26 bp):
TGGAGGGTTTTAAAGTGACAACACCT
Found at i:241631 original size:13 final size:12
Alignment explanation
Indices: 241612--241655 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 12
241602 GAATTTACTC
241612 AATTAAATAAAA
1 AATTAAATAAAA
*
241624 ACATTAAATAACA
1 A-ATTAAATAAAA
*
241637 AATT-AATTAAA
1 AATTAAATAAAA
241648 AATTAAAT
1 AATTAAAT
241656 TAAACAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 9 0.33
12 7 0.26
13 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (12 bp):
AATTAAATAAAA
Found at i:241656 original size:12 final size:12
Alignment explanation
Indices: 241612--241659 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
241602 GAATTTACTC
*
241612 AATTAAATAAAA
1 AATTAAATTAAA
241624 ACATTAAA-TAACA
1 A-ATTAAATTAA-A
241637 AATT-AATTAAA
1 AATTAAATTAAA
241648 AATTAAATTAAA
1 AATTAAATTAAA
241660 CAAAACAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
11 7 0.23
12 16 0.52
13 8 0.26
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (12 bp):
AATTAAATTAAA
Found at i:245806 original size:22 final size:21
Alignment explanation
Indices: 245774--245819 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
245764 TAATTTGATA
245774 TTTTTTGAATTTATA-AGTAT
1 TTTTTTGAATTTATATAGTAT
*
245794 TTTTTTGCAAATTTATATATTAT
1 TTTTTTG--AATTTATATAGTAT
245817 TTT
1 TTT
245820 GATTTTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
22 8 0.36
23 7 0.32
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTTTTGAATTTATATAGTAT
Found at i:245814 original size:20 final size:22
Alignment explanation
Indices: 245781--245820 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
245771 ATATTTTTTG
*
245781 AATTTATAAGTATTTTTTTGCA
1 AATTTATAAGTATTATTTTGCA
245803 AATTTAT-A-TATTATTTTG
1 AATTTATAAGTATTATTTTG
245821 ATTTTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 1 0.06
22 7 0.41
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (22 bp):
AATTTATAAGTATTATTTTGCA
Found at i:251347 original size:2 final size:2
Alignment explanation
Indices: 251342--251366 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
251332 ATGTTTTGAT
251342 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
251367 TTGAGATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:255416 original size:17 final size:17
Alignment explanation
Indices: 255390--255425 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
255380 GAGCATTACC
* *
255390 AGGGATGTAGATAGAGA
1 AGGGAAGTAGAGAGAGA
255407 AGGGAAGTAGAGAGAGA
1 AGGGAAGTAGAGAGAGA
255424 AG
1 AG
255426 AGAAAAAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.11
Consensus pattern (17 bp):
AGGGAAGTAGAGAGAGA
Found at i:257006 original size:20 final size:20
Alignment explanation
Indices: 256957--257009 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
256947 AGACCATGTC
256957 TGATATTGCTCGATGCTCCT
1 TGATATTGCTCGATGCTCCT
* * *
256977 TGGTACTGCTCGATGCTTCT
1 TGATATTGCTCGATGCTCCT
*
256997 TGATGTTGCTCGA
1 TGATATTGCTCGA
257010 CGCATGCTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.40
Consensus pattern (20 bp):
TGATATTGCTCGATGCTCCT
Found at i:261500 original size:20 final size:21
Alignment explanation
Indices: 261471--261511 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
261461 AGACCATGTC
*
261471 TGGTATTGCTCGATGC-TCCT
1 TGGTACTGCTCGATGCGTCCT
261491 TGGTACTGCTCGATGCGTCCT
1 TGGTACTGCTCGATGCGTCCT
261512 AATGTTGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.10, C:0.27, G:0.27, T:0.37
Consensus pattern (21 bp):
TGGTACTGCTCGATGCGTCCT
Found at i:261533 original size:20 final size:20
Alignment explanation
Indices: 261497--261535 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
261487 TCCTTGGTAC
*
261497 TGCTCGATGCGTCCTAATGT
1 TGCTCGATGCATCCTAATGT
*
261517 TGCTCGATGCATGCTAATG
1 TGCTCGATGCATCCTAATG
261536 CAGTTGTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (20 bp):
TGCTCGATGCATCCTAATGT
Found at i:262281 original size:22 final size:22
Alignment explanation
Indices: 262242--262283 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
262232 AGCAAAAAGG
***
262242 ATATTTTTCAATTTTTAAAAAA
1 ATATTTTTCAAAAGTTAAAAAA
262264 ATATTTTTCAAAAGTTAAAA
1 ATATTTTTCAAAAGTTAAAA
262284 TCTTTTTTAA
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:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATTTTTCAAAAGTTAAAAAA
Found at i:262289 original size:19 final size:20
Alignment explanation
Indices: 262261--262304 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
262251 AATTTTTAAA
*
262261 AAAATATTTTTCAAA-AGTT
1 AAAATATTTTTCAAATAATT
* *
262280 AAAATCTTTTTTAAATAATT
1 AAAATATTTTTCAAATAATT
262300 AAAAT
1 AAAAT
262305 GTATATAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (20 bp):
AAAATATTTTTCAAATAATT
Found at i:264819 original size:8 final size:8
Alignment explanation
Indices: 264806--264833 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
264796 CTTACCATTT
264806 AAAAAAAG
1 AAAAAAAG
264814 AAAAAAAG
1 AAAAAAAG
264822 AAAAAAAG
1 AAAAAAAG
264830 AAAA
1 AAAA
264834 CTACATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:266625 original size:47 final size:47
Alignment explanation
Indices: 266574--266671 Score: 196
Period size: 47 Copynumber: 2.1 Consensus size: 47
266564 GAAGGTAAAG
266574 TTATGTACTTCTACTCTTTGAATTACAAGCAGCTATCAAAACACAAT
1 TTATGTACTTCTACTCTTTGAATTACAAGCAGCTATCAAAACACAAT
266621 TTATGTACTTCTACTCTTTGAATTACAAGCAGCTATCAAAACACAAT
1 TTATGTACTTCTACTCTTTGAATTACAAGCAGCTATCAAAACACAAT
266668 TTAT
1 TTAT
266672 TACATAAAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (47 bp):
TTATGTACTTCTACTCTTTGAATTACAAGCAGCTATCAAAACACAAT
Found at i:276227 original size:11 final size:11
Alignment explanation
Indices: 276211--276249 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
276201 AATGATTTAA
276211 ATTTTTGTTGT
1 ATTTTTGTTGT
*
276222 ATTTTTTTTGGT
1 ATTTTTGTT-GT
276234 AATTTTTGTTGT
1 -ATTTTTGTTGT
276246 ATTT
1 ATTT
276250 ATTAAGCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 12 0.50
12 4 0.17
13 8 0.33
ACGTcount: A:0.13, C:0.00, G:0.15, T:0.72
Consensus pattern (11 bp):
ATTTTTGTTGT
Found at i:279410 original size:18 final size:17
Alignment explanation
Indices: 279389--279436 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
279379 AAATTACAAA
*
279389 AAAAATAAAATAATTTTT
1 AAAAATAAAAT-ATTTAT
*
279407 AAAATTTAAAATATTTAT
1 AAAA-ATAAAATATTTAT
279425 AAAAATCAAAAT
1 AAAAAT-AAAAT
279437 TATATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 18 0.72
19 6 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAATAAAATATTTAT
Found at i:279488 original size:10 final size:10
Alignment explanation
Indices: 279451--279509 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
279441 TTTTTTTAAT
279451 AATTTT-AAA
1 AATTTTAAAA
*
279460 AATTCTAAAGA
1 AATTTTAAA-A
279471 ATATTTTAAAA
1 A-ATTTTAAAA
279482 AATTTT--AA
1 AATTTTAAAA
*
279490 ATTTTTAAAA
1 AATTTTAAAA
*
279500 AATTCTAAAA
1 AATTTTAAAA
279510 TAATAATTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
8 7 0.17
9 5 0.12
10 17 0.43
11 4 0.10
12 7 0.17
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (10 bp):
AATTTTAAAA
Found at i:279497 original size:18 final size:18
Alignment explanation
Indices: 279474--279508 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
279464 CTAAAGAATA
*
279474 TTTTAAAAAATTTTAAAT
1 TTTTAAAAAATTCTAAAT
279492 TTTTAAAAAATTCTAAA
1 TTTTAAAAAATTCTAAA
279509 ATAATAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTAAAAAATTCTAAAT
Found at i:279625 original size:16 final size:16
Alignment explanation
Indices: 279606--279636 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
279596 TTGAAGAATT
279606 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
279622 TTTCAAATTTATATG
1 TTTCAAATATATATG
279637 TTCTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:281730 original size:15 final size:16
Alignment explanation
Indices: 281710--281745 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
281700 TAGTTATATT
281710 TATTTTT-TATTTATA
1 TATTTTTATATTTATA
281725 TATTTTTAATATTTATA
1 TATTTTT-ATATTTATA
281742 TATT
1 TATT
281746 AAAAAGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
17 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTTTATATTTATA
Found at i:282380 original size:25 final size:25
Alignment explanation
Indices: 282352--282405 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
282342 AGCAACTACT
*
282352 CAACTAAGAATAAGG-AAGCAGCTAA
1 CAACT-AGAATAAGGAAAACAGCTAA
*
282377 CAACTAGAATCAGGAAAACAGCTAA
1 CAACTAGAATAAGGAAAACAGCTAA
282402 CAAC
1 CAAC
282406 CTCCAGTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.52, C:0.20, G:0.17, T:0.11
Consensus pattern (25 bp):
CAACTAGAATAAGGAAAACAGCTAA
Found at i:291394 original size:14 final size:14
Alignment explanation
Indices: 291375--291405 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
291365 CTAATATATA
*
291375 TATATGTATGTGTG
1 TATATGTAGGTGTG
291389 TATATGTAGGTGTG
1 TATATGTAGGTGTG
291403 TAT
1 TAT
291406 TTAGAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (14 bp):
TATATGTAGGTGTG
Found at i:292220 original size:21 final size:21
Alignment explanation
Indices: 292177--292266 Score: 67
Period size: 22 Copynumber: 4.2 Consensus size: 21
292167 AAAATTTATA
**
292177 TTATTGTTTTGG-TGCTTCCTT
1 TTATTGTTTTGGTTG-TTGTTT
292198 TTATTGTTTTGGTTGTTGTTTT
1 TTATTGTTTTGGTTGTTG-TTT
* * *
292220 TTACTGTTTTGGTTTTTTTTTT
1 TTATTGTTTTGG-TTGTTGTTT
* *
292242 TTACTGTTTT-GATGTTGTTAT
1 TTATTGTTTTGGTTGTTGTT-T
292263 TTAT
1 TTAT
292267 GTTGCTGTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
20 5 0.09
21 19 0.34
22 28 0.50
23 4 0.07
ACGTcount: A:0.08, C:0.06, G:0.18, T:0.69
Consensus pattern (21 bp):
TTATTGTTTTGGTTGTTGTTT
Found at i:292227 original size:22 final size:22
Alignment explanation
Indices: 292196--292269 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 22
292186 TGGTGCTTCC
*
292196 TTTTATTGTTTTGGTTGTTGTT
1 TTTTACTGTTTTGGTTGTTGTT
* *
292218 TTTTACTGTTTTGGTTTTTTTT
1 TTTTACTGTTTTGGTTGTTGTT
*
292240 TTTTACTGTTTT-GATGTTGTT
1 TTTTACTGTTTTGGTTGTTGTT
*
292261 ATTTA-TGTT
1 TTTTACTGTT
292270 GCTGTTTTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.09
21 10 0.22
22 31 0.69
ACGTcount: A:0.08, C:0.03, G:0.18, T:0.72
Consensus pattern (22 bp):
TTTTACTGTTTTGGTTGTTGTT
Found at i:292287 original size:24 final size:25
Alignment explanation
Indices: 292245--292293 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
292235 TTTTTTTTTA
*
292245 CTGTTTTGATGTTGTTATTTATGTTG
1 CTGTTTT-ATGTTGCTATTTATGTTG
*
292271 CTGTTTT-TGTTGCTATTTTTGTT
1 CTGTTTTATGTTGCTATTTATGTT
292294 ATTTTACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
26 7 0.33
ACGTcount: A:0.08, C:0.06, G:0.20, T:0.65
Consensus pattern (25 bp):
CTGTTTTATGTTGCTATTTATGTTG
Found at i:292315 original size:32 final size:35
Alignment explanation
Indices: 292275--292340 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
292265 ATGTTGCTGT
292275 TTTTGTTGCT-ATTT-TTGTTATTTTA-CTGTTAA
1 TTTTGTTGCTGATTTGTTGTTATTTTAGCTGTTAA
*
292307 TTTTGTTGCTGTTTTGGTTGTTATTTTAGCTGTT
1 TTTTGTTGCTGATTT-GTTGTTATTTTAGCTGTT
292341 TGGATGTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 10 0.34
33 3 0.10
35 11 0.38
36 5 0.17
ACGTcount: A:0.11, C:0.06, G:0.18, T:0.65
Consensus pattern (35 bp):
TTTTGTTGCTGATTTGTTGTTATTTTAGCTGTTAA
Found at i:292349 original size:44 final size:44
Alignment explanation
Indices: 292257--292342 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
292247 GTTTTGATGT
* * * *
292257 TGTT-ATTTATGTTGCTGTTTTTGTTGCTATTTTTGTTATTTTAC
1 TGTTAATTT-TGTTGCTGTTTTGGTTGCTATTTTAGCTATTTGAC
* *
292301 TGTTAATTTTGTTGCTGTTTTGGTTGTTATTTTAGCTGTTTG
1 TGTTAATTTTGTTGCTGTTTTGGTTGCTATTTTAGCTATTTG
292343 GATGTTATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 31 0.89
45 4 0.11
ACGTcount: A:0.10, C:0.06, G:0.20, T:0.64
Consensus pattern (44 bp):
TGTTAATTTTGTTGCTGTTTTGGTTGCTATTTTAGCTATTTGAC
Found at i:292355 original size:21 final size:21
Alignment explanation
Indices: 292314--292353 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
292304 TAATTTTGTT
*
292314 GCTGTTTTGGTTGTTATTTTA
1 GCTGTTTTGGATGTTATTTTA
292335 GCTG-TTTGGATGTTATTTT
1 GCTGTTTTGGATGTTATTTT
292354 TATGCGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.10, C:0.05, G:0.25, T:0.60
Consensus pattern (21 bp):
GCTGTTTTGGATGTTATTTTA
Found at i:292547 original size:38 final size:38
Alignment explanation
Indices: 292465--292548 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 38
292455 ATATAAAGAA
* * *
292465 TTTTTAATGTATTTTAAATTTATTTATTTTTTAATGTT
1 TTTTTAATGTATTTTAAATTTATTTATATATTAATGAT
*
292503 TGTTTTAATGT-TTTTAAGTTTATTTGATATATTATAT-AT
1 T-TTTTAATGTATTTTAAATTTATTT-ATATATTA-ATGAT
292542 TTTTTAA
1 TTTTTAA
292549 ATTTGTTGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
38 20 0.51
39 17 0.44
40 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.65
Consensus pattern (38 bp):
TTTTTAATGTATTTTAAATTTATTTATATATTAATGAT
Found at i:294633 original size:20 final size:20
Alignment explanation
Indices: 294608--294648 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
294598 CTTGAAAATT
294608 TATATCATAAAAATAATTTA
1 TATATCATAAAAATAATTTA
294628 TATATCATAAAAATAATTTA
1 TATATCATAAAAATAATTTA
294648 T
1 T
294649 GTATTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATCATAAAAATAATTTA
Found at i:302922 original size:28 final size:28
Alignment explanation
Indices: 302891--302958 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
302881 TTTAATAATT
*
302891 AATTATTTAATTCTCTCTCTTTTTCCCA
1 AATTAATTAATTCTCTCTCTTTTTCCCA
302919 AATTAATTAATTCTCTCTCTTTTTCCCA
1 AATTAATTAATTCTCTCTCTTTTTCCCA
302947 AATTAATTAATT
1 AATTAATTAATT
302959 AATTAATTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.28, C:0.21, G:0.00, T:0.51
Consensus pattern (28 bp):
AATTAATTAATTCTCTCTCTTTTTCCCA
Found at i:302959 original size:32 final size:31
Alignment explanation
Indices: 302887--302962 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 31
302877 CCAATTTAAT
*
302887 AATTAATTATTTAATTCTCTCTCTTTTTCCC
1 AATTAATTAATTAATTCTCTCTCTTTTTCCC
302918 -A--AATTAATTAATTCTCTCTCTTTTTCCC
1 AATTAATTAATTAATTCTCTCTCTTTTTCCC
302946 AAATTAATTAATTAATT
1 -AATTAATTAATTAATT
302963 AATTAAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 26 0.65
30 2 0.05
32 12 0.30
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.51
Consensus pattern (31 bp):
AATTAATTAATTAATTCTCTCTCTTTTTCCC
Found at i:304267 original size:25 final size:25
Alignment explanation
Indices: 304239--304287 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
304229 ACGGAGACGT
304239 TAGTTGATTGATCAACGAATTATCC
1 TAGTTGATTGATCAACGAATTATCC
304264 TAGTTGATTGATCAACGAATTATC
1 TAGTTGATTGATCAACGAATTATC
304288 TTATGTGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (25 bp):
TAGTTGATTGATCAACGAATTATCC
Found at i:304918 original size:31 final size:31
Alignment explanation
Indices: 304883--304947 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
304873 GTGAAAAAAG
304883 ATAGTACCAATGGTAATGTTAAGGAAGACAA
1 ATAGTACCAATGGTAATGTTAAGGAAGACAA
*
304914 ATAGTACTAATGGTAATGTTAAGGAAGACAA
1 ATAGTACCAATGGTAATGTTAAGGAAGACAA
304945 ATA
1 ATA
304948 AAATAGTAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.46, C:0.08, G:0.22, T:0.25
Consensus pattern (31 bp):
ATAGTACCAATGGTAATGTTAAGGAAGACAA
Found at i:306165 original size:2 final size:2
Alignment explanation
Indices: 306153--306187 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
306143 TCATTGCACA
*
306153 AT AT AT GT 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 AT AT A
306188 GTTTAGATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:317040 original size:15 final size:15
Alignment explanation
Indices: 317020--317070 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
317010 TTGTCTCGTA
317020 TTATATTTTAATTAT
1 TTATATTTTAATTAT
* *
317035 TTATATTTAAAATA-
1 TTATATTTTAATTAT
* * *
317049 TTAAATTTTACTCAT
1 TTATATTTTAATTAT
317064 TTATATT
1 TTATATT
317071 GTCGTTTTAT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATTTTAATTAT
Found at i:321413 original size:2 final size:2
Alignment explanation
Indices: 321395--321452 Score: 91
Period size: 2 Copynumber: 29.0 Consensus size: 2
321385 TTTATGTAAA
*
321395 AT AT -T AT AT AA ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
321437 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
321453 TCAGTCATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 1 0.02
2 50 0.96
3 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:321830 original size:19 final size:19
Alignment explanation
Indices: 321802--321864 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
321792 AGAGCAGATT
321802 ATGTTGAATCGTGCTTGTA
1 ATGTTGAATCGTGCTTGTA
* * * *
321821 ATGTTTAATCAGAG-TAGATT
1 ATGTTGAATC-GTGCTTG-TA
*
321841 ATGTTGAATCGTGCTTCTA
1 ATGTTGAATCGTGCTTGTA
321860 ATGTT
1 ATGTT
321865 TATTATATAC
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.43
Consensus pattern (19 bp):
ATGTTGAATCGTGCTTGTA
Found at i:321840 original size:39 final size:39
Alignment explanation
Indices: 321792--321866 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
321782 TTTCTCAATT
*
321792 AGAGCAGATTATGTTGAATCGTGCTTGTAATGTTTAATC
1 AGAGCAGATTATGTTGAATCGTGCTTCTAATGTTTAATC
*
321831 AGAGTAGATTATGTTGAATCGTGCTTCTAATGTTTA
1 AGAGCAGATTATGTTGAATCGTGCTTCTAATGTTTA
321867 TTATATACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (39 bp):
AGAGCAGATTATGTTGAATCGTGCTTCTAATGTTTAATC
Done.