Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 1 of 199
Found at i:163 original size:32 final size:32
Alignment explanation
Indices: 127--212 Score: 127
Period size: 32 Copynumber: 2.7 Consensus size: 32
117 AATCCAGGTT
*
127 GGGATATCCTAAGAATGGGATAAATCCAAACC
1 GGGATATCCTCAGAATGGGATAAATCCAAACC
* * *
159 GGGATAACCGCAGAATGGGATAAATCTAAACC
1 GGGATATCCTCAGAATGGGATAAATCCAAACC
*
191 GGGATATCCTCCGAATGGGATA
1 GGGATATCCTCAGAATGGGATA
213 TCCCTACCTG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.19
Consensus pattern (32 bp):
GGGATATCCTCAGAATGGGATAAATCCAAACC
Found at i:1537 original size:17 final size:17
Alignment explanation
Indices: 1511--1546 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1501 ACCTGAACTT
1511 ACTAACATTGTTAAAAA
1 ACTAACATTGTTAAAAA
*
1528 ACTAATATTGTTAAAAA
1 ACTAACATTGTTAAAAA
1545 AC
1 AC
1547 CGAAATCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.31
Consensus pattern (17 bp):
ACTAACATTGTTAAAAA
Found at i:2540 original size:19 final size:20
Alignment explanation
Indices: 2505--2552 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
2495 CAAACAACCC
*
2505 AAAACAGAAATGAATAAGCA
1 AAAACAAAAATGAATAAGCA
2525 AAAACAAAAATG-ATAAGCA
1 AAAACAAAAATGAATAAGCA
2544 AAAA-AAAAA
1 AAAACAAAAA
2553 CACACAGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 5 0.19
19 11 0.41
20 11 0.41
ACGTcount: A:0.73, C:0.08, G:0.10, T:0.08
Consensus pattern (20 bp):
AAAACAAAAATGAATAAGCA
Found at i:5369 original size:14 final size:14
Alignment explanation
Indices: 5350--5394 Score: 90
Period size: 14 Copynumber: 3.2 Consensus size: 14
5340 ACGGATATAC
5350 CAGAACCGGGATAT
1 CAGAACCGGGATAT
5364 CAGAACCGGGATAT
1 CAGAACCGGGATAT
5378 CAGAACCGGGATAT
1 CAGAACCGGGATAT
5392 CAG
1 CAG
5395 CGTGACAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.36, C:0.22, G:0.29, T:0.13
Consensus pattern (14 bp):
CAGAACCGGGATAT
Found at i:5543 original size:31 final size:31
Alignment explanation
Indices: 5495--5566 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
5485 GGATTTGAAG
5495 GGGATA-CCCCGCAATAGCTTATACCGGACA
1 GGGATATCCCCGCAATAGCTTATACCGGACA
5525 GGGATATCCGCCG-AATAGCTTATACCGGACA
1 GGGATATCC-CCGCAATAGCTTATACCGGACA
5556 GGGATATCCCC
1 GGGATATCCCC
5567 TTATATTCGT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
30 8 0.20
31 29 0.73
32 3 0.08
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.18
Consensus pattern (31 bp):
GGGATATCCCCGCAATAGCTTATACCGGACA
Found at i:6167 original size:15 final size:15
Alignment explanation
Indices: 6147--6175 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6137 AAGGTGAGAA
6147 AAAATTTTAATGATT
1 AAAATTTTAATGATT
6162 AAAATTTTAATGAT
1 AAAATTTTAATGAT
6176 CAAGAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (15 bp):
AAAATTTTAATGATT
Found at i:6748 original size:518 final size:516
Alignment explanation
Indices: 5733--6698 Score: 1587
Period size: 518 Copynumber: 1.9 Consensus size: 516
5723 GGGCAAAAAC
*
5733 AAAATCAGCTTTATAATATATTATATTTATCTGAGTGTGTTCTGTACTATATATTTAAAATAAAT
1 AAAATCAGCTTCATAATATATTATATTTATCTGAGTGTGTTCTGTACTATATATTTAAAATAAAT
* * * * *
5798 AGGTAAACCCGAAACAATTGTTGGCTTTGTTTAAAGCCCTCCATTCATTATTTTGACGGATTATT
66 AGGTAAACCCGAAAAAACTGTTGGCTTTGTCTAAAGCCCTCCATTCATTAGTTTAACGGATTATT
*
5863 AACTTGAAAGCTTCAAAAGCTTGGTTATTCGAGGTGATTTCTCCAAAACTCCTGAAAAGGTATTT
131 AACTTGAAAGCTTCAAAAGCTTGGTTATTCGAGGTGATTTCTCCAAAACTCCTGAAAAGGTACTT
* *
5928 TTCCTGAACTCGAATAATCCTAAACTGGCCTATCACATGCCGGACGCTGTAACATCATCAAAACT
196 TTCCTGAACTAGAATAATCCTAAACTGGCCTATCACATACCGGACGCTGTAACATCATCAAAACT
* *
5993 GAGTGGGACAAGGTAAATAGAAAACTCTTTACCCTTTTTAAGCAATGAAGCAGGAGAATCCCTGG
261 GAGTGGGACAAGGTAAATAGAAAACTCTTTACCCTTTTGAAGCAATGAAACAGGAGAATCCCTGG
*
6058 AGTCCGATGCATTATCAAGAACATAAGATCTAGCAATCCCAAGAAAGATACAGTCTGAGGATCAT
326 AGTCCAATGCATTATCAAGAACATAAGATCTAGCAATCCCAAGAAAGATACAGTCTGAGGATCAT
* *** *
6123 GGGGAGAACCTACAAAGGTGAGAAAAAATTTTAATGATTAAAATTTTAATGATCAAGAACATAAG
391 GGGGAGAACCTACAAAGGTGAG-AAAAATTTTAATAATTAAAATGGAAATGAGCAAGAACA-AAG
*
6188 ATCTAGCAATCCCAACAATACTCTGCTGAGCAAGAAATAAAAAGATCTGACAAAAACTCACCG
454 ATCTAGCAAACCCAACAATACTCTGCTGAGCAAGAAATAAAAAGATCTGACAAAAACTCACCG
*
6251 AAAATCAGCTTCATAATATATTATATTTATCTGAGTGTGTTCTGTATTATATATTTAAAATAAAT
1 AAAATCAGCTTCATAATATATTATATTTATCTGAGTGTGTTCTGTACTATATATTTAAAATAAAT
6316 AGGTAAACCCGAAAAAACTGTTGGCTTTGTCTAAAGCCCTCCATTCATTAGTTTAACGGATTATT
66 AGGTAAACCCGAAAAAACTGTTGGCTTTGTCTAAAGCCCTCCATTCATTAGTTTAACGGATTATT
* *
6381 GACTTGAAAGCTTCAAAAGCTTGGTTATTTGAGGTGATTTCTCCAAAACTCCTGAAAAGGT-CTT
131 AACTTGAAAGCTTCAAAAGCTTGGTTATTCGAGGTGATTTCTCCAAAACTCCTGAAAAGGTACTT
* *
6445 TTCCTGAACTAGAATAATCCTAAACTGGCCTATCCCATACCGGACGCTGTAACGTCATCAAAACT
196 TTCCTGAACTAGAATAATCCTAAACTGGCCTATCACATACCGGACGCTGTAACATCATCAAAACT
* *
6510 GAGTGGGACAAGGTAAATAGAAAACTCTTTACCCTTTTGAGGCAATGAAACAGGAGTATCCCTGG
261 GAGTGGGACAAGGTAAATAGAAAACTCTTTACCCTTTTGAAGCAATGAAACAGGAGAATCCCTGG
*
6575 AGTCCAATGCATTATCAAGAACATAAGGAAGATCTAGCAATTCCAAGAAAGATACAGTCTGAGGA
326 AGTCCAATGCATTATCAAGAACAT----AAGATCTAGCAATCCCAAGAAAGATACAGTCTGAGGA
* *
6640 TTATGGGGAGAACCTGCACAAGGTGAG-AAAATTTTAATAATTAAAA-GGAAATCGAGCAA
387 TCATGGGGAGAACCTACA-AAGGTGAGAAAAATTTTAATAATTAAAATGGAAAT-GAGCAA
6699 AATCAAATTG
Statistics
Matches: 415, Mismatches: 27, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
517 147 0.35
518 182 0.44
519 3 0.01
520 23 0.06
521 52 0.13
522 8 0.02
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (516 bp):
AAAATCAGCTTCATAATATATTATATTTATCTGAGTGTGTTCTGTACTATATATTTAAAATAAAT
AGGTAAACCCGAAAAAACTGTTGGCTTTGTCTAAAGCCCTCCATTCATTAGTTTAACGGATTATT
AACTTGAAAGCTTCAAAAGCTTGGTTATTCGAGGTGATTTCTCCAAAACTCCTGAAAAGGTACTT
TTCCTGAACTAGAATAATCCTAAACTGGCCTATCACATACCGGACGCTGTAACATCATCAAAACT
GAGTGGGACAAGGTAAATAGAAAACTCTTTACCCTTTTGAAGCAATGAAACAGGAGAATCCCTGG
AGTCCAATGCATTATCAAGAACATAAGATCTAGCAATCCCAAGAAAGATACAGTCTGAGGATCAT
GGGGAGAACCTACAAAGGTGAGAAAAATTTTAATAATTAAAATGGAAATGAGCAAGAACAAAGAT
CTAGCAAACCCAACAATACTCTGCTGAGCAAGAAATAAAAAGATCTGACAAAAACTCACCG
Found at i:12984 original size:16 final size:16
Alignment explanation
Indices: 12963--12995 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12953 TCAAAACCCT
12963 CCTACTTTCCCTTTTG
1 CCTACTTTCCCTTTTG
12979 CCTACTTTCCCTTTTG
1 CCTACTTTCCCTTTTG
12995 C
1 C
12996 TTTGCTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.39, G:0.06, T:0.48
Consensus pattern (16 bp):
CCTACTTTCCCTTTTG
Found at i:15886 original size:15 final size:15
Alignment explanation
Indices: 15842--15891 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
15832 ACCCCTAGAC
15842 CCCAAGCCGGGATAT
1 CCCAAGCCGGGATAT
***
15857 CCCTAAATTGGGATAT
1 CCC-AAGCCGGGATAT
15873 CCCAAGCCGGGATAT
1 CCCAAGCCGGGATAT
15888 CCCA
1 CCCA
15892 TTCTTGGGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.18
Consensus pattern (15 bp):
CCCAAGCCGGGATAT
Found at i:15979 original size:21 final size:21
Alignment explanation
Indices: 15949--16005 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
15939 CAAACACGTT
* *
15949 AAAAAT-CTGAACCGGTCACC
1 AAAAATACTGAACCGGCCACA
* *
15969 AAAACTGCTGAACCGGCCACA
1 AAAAATACTGAACCGGCCACA
15990 AAAAATACTGAACCGG
1 AAAAATACTGAACCGG
16006 GACGGGATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 5 0.16
21 26 0.84
ACGTcount: A:0.42, C:0.28, G:0.18, T:0.12
Consensus pattern (21 bp):
AAAAATACTGAACCGGCCACA
Found at i:19523 original size:78 final size:78
Alignment explanation
Indices: 19394--19544 Score: 248
Period size: 78 Copynumber: 1.9 Consensus size: 78
19384 GTAAACAAAG
* * *
19394 TCCATGGTGATCGCTATCAACATGATCACCAACTCTCCTAGCTGATGAGATCAAGGGATCATGGT
1 TCCATGGTGATCACTATCAACATGATCACCAACTCTCCCAGCTGATAAGATCAAGGGATCATGGT
19459 TTAATGGTCGAAC
66 TTAATGGTCGAAC
* * *
19472 TCCATGGTGATCATTATCAACATGATCACCGACTCTCCCAGCTGGTAAGATCAAGGGATCATGGT
1 TCCATGGTGATCACTATCAACATGATCACCAACTCTCCCAGCTGATAAGATCAAGGGATCATGGT
19537 TTAATGGT
66 TTAATGGT
19545 AGAATATGAG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 67 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (78 bp):
TCCATGGTGATCACTATCAACATGATCACCAACTCTCCCAGCTGATAAGATCAAGGGATCATGGT
TTAATGGTCGAAC
Found at i:21162 original size:15 final size:15
Alignment explanation
Indices: 21142--21175 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
21132 GAAAAGGTCA
21142 TTGAAAAAGGTTCTG
1 TTGAAAAAGGTTCTG
21157 TTG--AAAGGTTCTG
1 TTGAAAAAGGTTCTG
21170 TTGAAA
1 TTGAAA
21176 CCTTGATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
13 13 0.76
15 4 0.24
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (15 bp):
TTGAAAAAGGTTCTG
Found at i:21163 original size:13 final size:13
Alignment explanation
Indices: 21147--21175 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
21137 GGTCATTGAA
21147 AAAGGTTCTGTTG
1 AAAGGTTCTGTTG
21160 AAAGGTTCTGTTG
1 AAAGGTTCTGTTG
21173 AAA
1 AAA
21176 CCTTGATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (13 bp):
AAAGGTTCTGTTG
Found at i:25651 original size:31 final size:31
Alignment explanation
Indices: 25615--25679 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
25605 TTAAGGTTAG
*
25615 AATATCATTCACAAATCTCAAAATAAGTAGA
1 AATATCATTCACAAATCTCAAAATAAATAGA
*
25646 AATATCATTCACAAATCTGAAAATAAATAGA
1 AATATCATTCACAAATCTCAAAATAAATAGA
25677 AAT
1 AAT
25680 CACAACTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (31 bp):
AATATCATTCACAAATCTCAAAATAAATAGA
Found at i:26461 original size:26 final size:26
Alignment explanation
Indices: 26411--26461 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
26401 TATAAAATTT
*
26411 CAAATATATATTCAGAAATATAAAAG
1 CAAATATATATTCAAAAATATAAAAG
*
26437 CAAATATATGTTACAAAAATA-AAAA
1 CAAATATATATT-CAAAAATATAAAA
26462 TAAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.25
Consensus pattern (26 bp):
CAAATATATATTCAAAAATATAAAAG
Found at i:26467 original size:26 final size:26
Alignment explanation
Indices: 26412--26468 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
26402 ATAAAATTTC
* *
26412 AAATATATATTCAGAAATATAAAAGC
1 AAATATATATTCAAAAATATAAAAGA
* *
26438 AAATATATGTTACAAAAATA-AAAATA
1 AAATATATATT-CAAAAATATAAAAGA
26464 AAATA
1 AAATA
26469 AAAAATGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (26 bp):
AAATATATATTCAAAAATATAAAAGA
Found at i:26557 original size:135 final size:135
Alignment explanation
Indices: 26404--26655 Score: 495
Period size: 135 Copynumber: 1.9 Consensus size: 135
26394 AAAAATATAT
26404 AAAATTTCAAATATATATTCAGAAATATAAAAGCAAATATATGTTACAAAAATAAAAATAAAATA
1 AAAATTTCAAATATATATTCAGAAATATAAAAGCAAATATATGTTACAAAAATAAAAATAAAATA
26469 AAAAATGTGTTTTTTATTGTTCGGGTCATGTTTGGATTAAATTTAAATTTGAATAAATTATAATT
66 AAAAATGTGTTTTTTATTGTTCGGGTCATGTTTGGATTAAATTTAAATTTGAATAAATTATAATT
26534 ATTCA
131 ATTCA
26539 AAAATTTCAAATATATATTCAGAAATATAAAAGCAAATATATGTTACAAAAATAAAAATAAAATA
1 AAAATTTCAAATATATATTCAGAAATATAAAAGCAAATATATGTTACAAAAATAAAAATAAAATA
*
26604 AAAAATGTGTTTTTTATTGTTCGGGTCATGTTTGGATTGAATTTAAATTTGA
66 AAAAATGTGTTTTTTATTGTTCGGGTCATGTTTGGATTAAATTTAAATTTGA
26656 TGTTTTCTAT
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 116 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (135 bp):
AAAATTTCAAATATATATTCAGAAATATAAAAGCAAATATATGTTACAAAAATAAAAATAAAATA
AAAAATGTGTTTTTTATTGTTCGGGTCATGTTTGGATTAAATTTAAATTTGAATAAATTATAATT
ATTCA
Found at i:26596 original size:26 final size:26
Alignment explanation
Indices: 26546--26596 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
26536 TCAAAAATTT
*
26546 CAAATATATATTCAGAAATATAAAAG
1 CAAATATATATTCAAAAATATAAAAG
*
26572 CAAATATATGTTACAAAAATA-AAAA
1 CAAATATATATT-CAAAAATATAAAA
26597 TAAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.25
Consensus pattern (26 bp):
CAAATATATATTCAAAAATATAAAAG
Found at i:26602 original size:26 final size:26
Alignment explanation
Indices: 26547--26603 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
26537 CAAAAATTTC
* *
26547 AAATATATATTCAGAAATATAAAAGC
1 AAATATATATTCAAAAATATAAAAGA
* *
26573 AAATATATGTTACAAAAATA-AAAATA
1 AAATATATATT-CAAAAATATAAAAGA
26599 AAATA
1 AAATA
26604 AAAAATGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (26 bp):
AAATATATATTCAAAAATATAAAAGA
Found at i:32010 original size:12 final size:13
Alignment explanation
Indices: 31995--32043 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
31985 TATTTTCAAA
31995 AAATA-TAATAAT
1 AAATATTAATAAT
32007 AAATATTAAT-AT
1 AAATATTAATAAT
*
32019 TAATATTAA-AAT
1 AAATATTAATAAT
32031 AATTATATTAATA
1 AA--ATATTAATA
32044 TTAATTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
12 18 0.60
13 4 0.13
14 7 0.23
15 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATATTAATAAT
Found at i:41707 original size:14 final size:15
Alignment explanation
Indices: 41674--41708 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
41664 AAATTTAAGA
41674 AAAAATGAATATTGT
1 AAAAATGAATATTGT
* *
41689 AAAAATGAATGTTTT
1 AAAAATGAATATTGT
41704 AAAAA
1 AAAAA
41709 AACTTAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.31
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:46942 original size:9 final size:9
Alignment explanation
Indices: 46930--47024 Score: 145
Period size: 9 Copynumber: 10.6 Consensus size: 9
46920 TCAATTTGGT
46930 TAATTCGGG
1 TAATTCGGG
*
46939 TAATTCGGT
1 TAATTCGGG
*
46948 TAGTTCGGG
1 TAATTCGGG
46957 TAATTCGGG
1 TAATTCGGG
46966 TAATTCGGG
1 TAATTCGGG
46975 TAATTCGGG
1 TAATTCGGG
46984 TAATTCGGG
1 TAATTCGGG
*
46993 TAATTCGGT
1 TAATTCGGG
*
47002 TAATTCGGT
1 TAATTCGGG
*
47011 TAATTCGGT
1 TAATTCGGG
47020 TAATT
1 TAATT
47025 TTTAACCAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 81 1.00
ACGTcount: A:0.22, C:0.11, G:0.28, T:0.39
Consensus pattern (9 bp):
TAATTCGGG
Found at i:46948 original size:18 final size:18
Alignment explanation
Indices: 46922--47024 Score: 161
Period size: 18 Copynumber: 5.7 Consensus size: 18
46912 GTAGTGGTTC
*
46922 AATTTGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
46940 AATTCGGTTAGTTCGGGT
1 AATTCGGTTAATTCGGGT
*
46958 AATTCGGGTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
46976 AATTCGGGTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
46994 AATTCGGTTAATTCGGTT
1 AATTCGGTTAATTCGGGT
47012 AATTCGGTTAATT
1 AATTCGGTTAATT
47025 TTTAACCAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 79 1.00
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.40
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:56040 original size:2 final size:2
Alignment explanation
Indices: 56035--56062 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
56025 TTTTGTGGAA
56035 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56063 TTAAACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75119 original size:73 final size:74
Alignment explanation
Indices: 75000--75142 Score: 180
Period size: 73 Copynumber: 1.9 Consensus size: 74
74990 CAAACAAGTT
* * * * * * * * *
75000 TAACTTTGAACCTCGACTCTCATAGGTGTCAAGGTTCGTTTAATATTTTTATTATTTTC-TTCTT
1 TAACTTTGAACATCGACTCTCAAAGATGCCAAGGTCCATTTAATATTTTTACTACTTTCTTTATT
75064 TTTAATGTC
66 TTTAATGTC
* *
75073 TAACTTTGAACATTGACTCTCAAAGATGCCGAGGTCCATTTAATATTTTTACTACTTTCTTTATT
1 TAACTTTGAACATCGACTCTCAAAGATGCCAAGGTCCATTTAATATTTTTACTACTTTCTTTATT
75138 TTTAA
66 TTTAA
75143 GTTTGACTTC
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
73 49 0.84
74 9 0.16
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (74 bp):
TAACTTTGAACATCGACTCTCAAAGATGCCAAGGTCCATTTAATATTTTTACTACTTTCTTTATT
TTTAATGTC
Found at i:82293 original size:13 final size:13
Alignment explanation
Indices: 82277--82303 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
82267 TTCTTTATTT
82277 TTTTAATAGATCC
1 TTTTAATAGATCC
82290 TTTTAATAGATCC
1 TTTTAATAGATCC
82303 T
1 T
82304 CACTAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (13 bp):
TTTTAATAGATCC
Found at i:87118 original size:57 final size:57
Alignment explanation
Indices: 87050--87161 Score: 179
Period size: 57 Copynumber: 2.0 Consensus size: 57
87040 AATAAGAACC
* * * *
87050 ATTGGTAGAGGCTATCATGGTTTGGTTTTGTTCAGTTAGAAGGTCTACCTTCGTAAG
1 ATTGGTAGAGGCTATCAAGGTTTGGTTTTGTTCAGCTAGAAGATCTACATTCGTAAG
*
87107 ATTGGTAGAGGCTGTCAAGGTTTGGTTTTGTTCAGCTAGAAGATCTACATTCGTA
1 ATTGGTAGAGGCTATCAAGGTTTGGTTTTGTTCAGCTAGAAGATCTACATTCGTA
87162 TCTACCAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (57 bp):
ATTGGTAGAGGCTATCAAGGTTTGGTTTTGTTCAGCTAGAAGATCTACATTCGTAAG
Found at i:92465 original size:16 final size:16
Alignment explanation
Indices: 92444--92476 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
92434 AATAAAAGGG
92444 TAAAAGAAAGTCAAGA
1 TAAAAGAAAGTCAAGA
92460 TAAAAGAAAGTCAAGA
1 TAAAAGAAAGTCAAGA
92476 T
1 T
92477 CTACTTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
TAAAAGAAAGTCAAGA
Found at i:93211 original size:18 final size:18
Alignment explanation
Indices: 93185--93227 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
93175 CATTTTCTAG
93185 TTTTCCTTTCTCCTTTTT
1 TTTTCCTTTCTCCTTTTT
* * *
93203 TTTTTCTTTTTTCTTTTT
1 TTTTCCTTTCTCCTTTTT
93221 TTTTCCT
1 TTTTCCT
93228 GATGACGGCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTCCTTTCTCCTTTTT
Found at i:96689 original size:17 final size:17
Alignment explanation
Indices: 96667--96701 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
96657 AATAGAAGGG
96667 TACGGTGCATAAAATGT
1 TACGGTGCATAAAATGT
96684 TACGGTGCATAAAATGT
1 TACGGTGCATAAAATGT
96701 T
1 T
96702 CAACCTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.31
Consensus pattern (17 bp):
TACGGTGCATAAAATGT
Found at i:102844 original size:2 final size:2
Alignment explanation
Indices: 102837--102875 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
102827 GCAATTTTGA
102837 AT AT AT 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 AT AT AT A
102876 AACATCAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:105139 original size:18 final size:18
Alignment explanation
Indices: 105093--105150 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
105083 CATTTATAAC
105093 TTTATAAATTTGTAATTT
1 TTTATAAATTTGTAATTT
* *
105111 TTTTTATATTTGTGAA-TT
1 TTTATAAATTTGT-AATTT
* *
105129 TTTATAAATTTATAATGT
1 TTTATAAATTTGTAATTT
105147 TTTA
1 TTTA
105151 AATTTTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
17 2 0.06
18 28 0.88
19 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (18 bp):
TTTATAAATTTGTAATTT
Found at i:110366 original size:84 final size:84
Alignment explanation
Indices: 110262--110429 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
110252 TGTTTGCTAA
110262 CTGGAGGTTTTTTTTTTTTGAGTAATATATAGGAATAGTAAGCTGACATGTAAGTCTCCCTAAAA
1 CTGGAGGTTTTTTTTTTTTGAGTAATATATAGGAATAGTAAGCTGACATGTAAGTCTCCCTAAAA
110327 TAGAAAATTATTGTTTTAG
66 TAGAAAATTATTGTTTTAG
110346 CTGGAGGTTTTTTTTTTTTGAGTAATATATAGGAATAGTAAGCTGACATGTAAGTCTCCCTAAAA
1 CTGGAGGTTTTTTTTTTTTGAGTAATATATAGGAATAGTAAGCTGACATGTAAGTCTCCCTAAAA
110411 TAGAAAATTATTGTTTTAG
66 TAGAAAATTATTGTTTTAG
110430 TCCCCCGAAG
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.40
Consensus pattern (84 bp):
CTGGAGGTTTTTTTTTTTTGAGTAATATATAGGAATAGTAAGCTGACATGTAAGTCTCCCTAAAA
TAGAAAATTATTGTTTTAG
Found at i:112543 original size:51 final size:51
Alignment explanation
Indices: 112467--112567 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
112457 TAAATGGGAG
*
112467 AAAAAAAAACAACTTAGGACTATCAAAACATGCCTTGTTCTTCAAGGCATT
1 AAAAAAAAACAACTTAGGACTATCAAAACATGCCTTGTTCTTCAACGCATT
*
112518 AAAAAACAACAACTTAGGACTATCAAAACATGCCTTGTTCTTCAACGCAT
1 AAAAAAAAACAACTTAGGACTATCAAAACATGCCTTGTTCTTCAACGCAT
112568 ATTCAAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.43, C:0.22, G:0.11, T:0.25
Consensus pattern (51 bp):
AAAAAAAAACAACTTAGGACTATCAAAACATGCCTTGTTCTTCAACGCATT
Found at i:113706 original size:4 final size:4
Alignment explanation
Indices: 113699--113746 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
113689 ATCAAATAAA
* * * *
113699 TATG TATG TATG TAAG TATG TAAG TATG TAAG TATG TAAG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
113747 ACCTATTACA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (4 bp):
TATG
Found at i:113712 original size:8 final size:8
Alignment explanation
Indices: 113699--113744 Score: 83
Period size: 8 Copynumber: 5.8 Consensus size: 8
113689 ATCAAATAAA
*
113699 TATGTATG
1 TATGTAAG
113707 TATGTAAG
1 TATGTAAG
113715 TATGTAAG
1 TATGTAAG
113723 TATGTAAG
1 TATGTAAG
113731 TATGTAAG
1 TATGTAAG
113739 TATGTA
1 TATGTA
113745 TGACCTATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (8 bp):
TATGTAAG
Found at i:128171 original size:30 final size:29
Alignment explanation
Indices: 128119--128193 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 29
128109 ACATGAAAGG
* *
128119 TTTAATTGATTTTTTATATTTTACA-ATGA
1 TTTAATTGATTTTTAATATTTTA-AGAGGA
128148 TTTAATTGATTTTTAATTATTTTAAGAGGA
1 TTTAATTGATTTTTAA-TATTTTAAGAGGA
* *
128178 CTTAATTGACTTTTAA
1 TTTAATTGATTTTTAA
128194 AATGGTATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 16 0.40
30 24 0.60
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (29 bp):
TTTAATTGATTTTTAATATTTTAAGAGGA
Found at i:128271 original size:31 final size:32
Alignment explanation
Indices: 128236--128305 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 32
128226 TTTTAATTTT
*
128236 TAATTGTTTTT-AATAATTTGTAT-ATA-TTTCA
1 TAATTGTTTTTGAA-AATTT-TATAATATTTTAA
128267 TAATT-TTTTTGAAAATTTTATAATATTTTAA
1 TAATTGTTTTTGAAAATTTTATAATATTTTAA
128298 TAATTGTT
1 TAATTGTT
128306 AAAACTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
29 3 0.09
30 13 0.38
31 16 0.47
32 2 0.06
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (32 bp):
TAATTGTTTTTGAAAATTTTATAATATTTTAA
Found at i:129170 original size:31 final size:31
Alignment explanation
Indices: 129117--129175 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
129107 ATAAGCATTT
*
129117 TCGTTACATAATTCTATTATTTTAGTCACTG
1 TCGTTACATAATTCTATCATTTTAGTCACTG
* * *
129148 TCGTTATATACTTTTATCATTTTAGTCA
1 TCGTTACATAATTCTATCATTTTAGTCA
129176 TAAAACGCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.51
Consensus pattern (31 bp):
TCGTTACATAATTCTATCATTTTAGTCACTG
Found at i:129871 original size:5 final size:5
Alignment explanation
Indices: 129856--129925 Score: 86
Period size: 5 Copynumber: 13.8 Consensus size: 5
129846 AGAATAATGC
* * *
129856 TTATCA TTATA TTATA TTATA TTATA TTATA TTATA TTATA GTGTA TCATA
1 TTAT-A TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* *
129907 TTACA TTACA TTATA TTAT
1 TTATA TTATA TTATA TTAT
129926 TTAAATATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
5 52 0.93
6 4 0.07
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (5 bp):
TTATA
Found at i:135849 original size:16 final size:16
Alignment explanation
Indices: 135828--135858 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
135818 CGAAAGTGGT
135828 ACTGTGTATATCTATC
1 ACTGTGTATATCTATC
135844 ACTGTGTATATCTAT
1 ACTGTGTATATCTAT
135859 TTGAGGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (16 bp):
ACTGTGTATATCTATC
Found at i:143183 original size:22 final size:22
Alignment explanation
Indices: 143131--143183 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
143121 TTCGCTTCAT
*
143131 TTCATTGAAAAACACTGAAAAA
1 TTCATAGAAAAACACTGAAAAA
* * * * *
143153 TTGAGAGAAAAACATTGTAAGA
1 TTCATAGAAAAACACTGAAAAA
143175 TTCATAGAA
1 TTCATAGAA
143184 TTTTGCTCTT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (22 bp):
TTCATAGAAAAACACTGAAAAA
Found at i:149982 original size:16 final size:17
Alignment explanation
Indices: 149961--149993 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
149951 ATTGATTGAT
*
149961 AAAATT-ATTTAGTTAA
1 AAAATTAATTTAATTAA
149977 AAAATTAATTTAATTAA
1 AAAATTAATTTAATTAA
149994 TTAAATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
AAAATTAATTTAATTAA
Found at i:151804 original size:26 final size:26
Alignment explanation
Indices: 151769--151859 Score: 78
Period size: 26 Copynumber: 3.5 Consensus size: 26
151759 CTGATTGATA
*
151769 TTATCTATTTTAAATTGTTTCATATT
1 TTATTTATTTTAAATTGTTTCATATT
**
151795 TTATTTATTTCGAATTGCTTTC-TATT
1 TTATTTATTTTAAATTG-TTTCATATT
* * * *
151821 AT-TTTATCTTAAACTGTTTCATGTATA
1 TTATTTATTTTAAATTGTTTCA--TATT
151848 TTATTTATTTTA
1 TTATTTATTTTA
151860 GATTTTTACG
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
24 4 0.08
25 10 0.20
26 19 0.39
27 8 0.16
28 8 0.16
ACGTcount: A:0.25, C:0.09, G:0.05, T:0.60
Consensus pattern (26 bp):
TTATTTATTTTAAATTGTTTCATATT
Found at i:156589 original size:6 final size:6
Alignment explanation
Indices: 156580--156629 Score: 73
Period size: 6 Copynumber: 7.8 Consensus size: 6
156570 CAGAAAACAG
156580 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAATAAA ATCAAAA ATAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT-A-AAA AT-AAAA ATAAA
156630 TTACAAACCC
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
6 29 0.71
7 6 0.15
8 6 0.15
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:172344 original size:17 final size:17
Alignment explanation
Indices: 172310--172352 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
172300 TAAAATAAAC
*
172310 TAAAATTATTTAATTTA
1 TAAAATTATATAATTTA
172327 TAAATATTATATAA-TTA
1 TAAA-ATTATATAATTTA
172344 TAATAATTA
1 TAA-AATTA
172353 ATTAGCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAATTATATAATTTA
Found at i:174273 original size:2 final size:2
Alignment explanation
Indices: 174268--174314 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
174258 TATTATAAAC
174268 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
174310 AT AT A
1 AT AT A
174315 AGTTTTAGGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:175814 original size:24 final size:24
Alignment explanation
Indices: 175780--175831 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
175770 TTTTTAGAAG
* **
175780 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAACATAATAT
175804 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATTAACATAATAT
175828 ATTT
1 ATTT
175832 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAACATAATAT
Found at i:193474 original size:2 final size:2
Alignment explanation
Indices: 193467--193493 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
193457 GGTTAACAAG
193467 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 T
193494 TGACAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:203672 original size:3 final size:3
Alignment explanation
Indices: 203666--203706 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
203656 ATTCTCTTTG
203666 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TGTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC TT
203707 TTCAATTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 1 0.03
3 34 0.94
4 1 0.03
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:203746 original size:117 final size:116
Alignment explanation
Indices: 203555--203799 Score: 341
Period size: 117 Copynumber: 2.1 Consensus size: 116
203545 CTCTGCTGCA
* * * *
203555 TCTT-TTCTTTTTCTTTTCTTCTTTTTCTTCTTTTCAGTTTCATCCTCAGCCCCTGCATCAATTG
1 TCTTCTTCTTCTTCTTTTCTTCTTTGTCTTCTTTTCAATTTCATCCT---CCCCTACATCAATTG
* * * *
203619 CACCGTCAACAACAGCAATAGCCTCAATAGCCTCCTCATTCTCTTTGTTCTTCT
63 CACCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTCTCATTGCTCTTCT
*
203673 TCTTCTTCTTCTTCTTCTTCTTCTTTGTCTTCTTTTCAATTTCATCACT-CTCTACATCAATTGC
1 TCTTCTTCTTCTTCTT-TTCTTCTTTGTCTTCTTTTCAATTTCATC-CTCCCCTACATCAATTGC
*
203737 ACCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTCT
64 ACCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTCTCATTGCTCTTCT
203790 TCTTCTTCTT
1 TCTTCTTCTT
203800 TTCAATTTCA
Statistics
Matches: 114, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
117 71 0.62
118 4 0.04
119 10 0.09
120 27 0.24
121 2 0.02
ACGTcount: A:0.18, C:0.31, G:0.06, T:0.45
Consensus pattern (116 bp):
TCTTCTTCTTCTTCTTTTCTTCTTTGTCTTCTTTTCAATTTCATCCTCCCCTACATCAATTGCAC
CATCAACAACAGCAATAGCCTCAATAGCATCCTCATTCTCATTGCTCTTCT
Found at i:203836 original size:117 final size:116
Alignment explanation
Indices: 203610--203827 Score: 271
Period size: 117 Copynumber: 1.9 Consensus size: 116
203600 TCAGCCCCTG
* * * *
203610 CATCAATTGCACCGTCAACAACAGCAATAGCCTCAATAGCCTCCTCATTCTCTTTGTTCTTCTTC
1 CATCAATTGCACCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTCTCATTGCTCTTCTTC
* * ** ** * * *
203675 TTCTTCTTCTTCTTCTTCTTCTTTGTCTTCTTTTCAATTTCATCACTCTCTA
66 TTCTTCTTCTTCATCTTCATCACTCCCTAC-TATCAATTCCATCACTCTCTA
*
203727 CATCAATTGCACCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTCTTC
1 CATCAATTGCACCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTCTCATTGCTCTTCTTC
203792 TTCTTCTT-TTCAAT-TTCATCACTCCCTAC-ATCAATT
66 TTCTTCTTCTTC-ATCTTCATCACTCCCTACTATCAATT
203828 GCACCATCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
114 6 0.07
116 12 0.14
117 69 0.79
ACGTcount: A:0.22, C:0.32, G:0.06, T:0.41
Consensus pattern (116 bp):
CATCAATTGCACCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTCTCATTGCTCTTCTTC
TTCTTCTTCTTCATCTTCATCACTCCCTACTATCAATTCCATCACTCTCTA
Found at i:203954 original size:99 final size:93
Alignment explanation
Indices: 203691--203991 Score: 480
Period size: 93 Copynumber: 3.2 Consensus size: 93
203681 TTCTTCTTCT
*
203691 TCTTCTT-TGTCTTCTTTTCAATTTCATCACTCTCTACATCAATTGCACCATCAACAACAGCAAT
1 TCTTCTTCT-TCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAAT
203755 AGCCTCAATAGCATCCTCATTTTCATTGC
65 AGCCTCAATAGCATCCTCATTTTCATTGC
203784 TCTTCTTCTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAATA
1 TCTTCTTCTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAATA
203849 GCCTCAATAGCATCCTCATTTTCATTGC
66 GCCTCAATAGCATCCTCATTTTCATTGC
* *
203877 TCTTCTTCTTCTTCTTTTCAATTTCATTACTCCCTACATCAATTGCACTATCAACAACAGCAACA
1 TCTTCTTCTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCAC---CATC-A-A-CAACA
*
203942 GCAATAGCCTCAATAGCAT-CTACATTCTCATTGC
60 GCAATAGCCTCAATAGCATCCT-CATTTTCATTGC
203976 TCTTCTTCTTCTTCTT
1 TCTTCTTCTTCTTCTT
203992 ATTTTTCTTT
Statistics
Matches: 196, Mismatches: 4, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
93 137 0.70
94 1 0.01
96 3 0.02
97 1 0.01
98 3 0.02
99 51 0.26
ACGTcount: A:0.25, C:0.31, G:0.06, T:0.38
Consensus pattern (93 bp):
TCTTCTTCTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAATA
GCCTCAATAGCATCCTCATTTTCATTGC
Found at i:204200 original size:12 final size:12
Alignment explanation
Indices: 204179--204211 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
204169 CTCTTTATTC
204179 TTCTTCTTCTTT
1 TTCTTCTTCTTT
*
204191 TTCTTTTTCTTT
1 TTCTTCTTCTTT
204203 TTCTTCTTC
1 TTCTTCTTC
204212 ACTTGAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:208811 original size:234 final size:233
Alignment explanation
Indices: 208512--209182 Score: 827
Period size: 234 Copynumber: 2.9 Consensus size: 233
208502 CAACAAATTC
* * *
208512 AATTC-AATTCATTTTCAGCAACTTTTCATTCACTTTCTCACCAACCAAAAAACAGATCAAACCA
1 AATTCAAATTCATTTTCCGCAACTTTTCCTTCACTTTCTCACCAACCAAACAACAGATCAAACCA
* * *
208576 AAAAGAAAAGCAGATGAAATTTTGACTTCGCAAAAACATGACCATGCAAGCTTAAGGATCTTTAA
66 AAAAGAAAAACAGATGAAATTTAGACTT-GCAAAAACATGA-CATGTAAGCTTAAGGATCTTTAA
* *
208641 GATCAAATTCCCGTTTGTTGACCGAGAAAACGGATGACAAGAAGTATTTACTACTCATACATGTA
129 GATCAAATTCCCGTTTGTTTACCGAGAAAACGGATGAAAAGAAGT-TTTACTACTCATACATGTA
* *
208706 AACCTAACATCGT-ATTCATATTTTAATTTTACATC-AATA
193 AACCTAACATCATAATTCATATTTTAATGTTACATCAAATA
** *
208745 AATTCAAATTCAAATTCCGCAACTTTCCCTTCACTTTCTCACCAACCAAACAACAGATCAAACCA
1 AATTCAAATTCATTTTCCGCAACTTTTCCTTCACTTTCTCACCAACCAAACAACAGATCAAACCA
* * * * *
208810 AAAAGAAAAACAGATGAAATTTAGACTTTGCAAATACATAATCATATAAGCTTAAAGACCTTTAA
66 AAAAGAAAAACAGATGAAATTTAGAC-TTGCAAAAACATGA-CATGTAAGCTTAAGGATCTTTAA
* *
208875 GATCAAATTCCCGTTTATTTATCGAGAAAACGGATGAAAAGAAGCTTTTACTACTCATACATGTA
129 GATCAAATTCCCGTTTGTTTACCGAGAAAACGGATGAAAAGAAG-TTTTACTACTCATACATGTA
*
208940 AACCTAACATCATAATTTATATTTTAATGTTACATCAATTAATA
193 AACCTAACATCATAATTCATATTTTAATGTTACATC-A--AATA
*
208984 AATTCAAATTCATTTTCCGCAACTTTTCCTTCACTTTTTCACCAACC-AACAACAGATCAAGCAA
1 AATTCAAATTCATTTTCCGCAACTTTTCCTTCACTTTCTCACCAACCAAACAACAGATC-A--AA
** * * * ** **** *
209048 AAAAAAAAAAAAAAAGAAGGAAA-ACAGA--TG-AAACTTTTGACTTGTAAGCTTAAGGATCTTT
63 CCAAAAAGAAAAACAG-ATGAAATTTAGACTTGCAAAAACATGACATGTAAGCTTAAGGATCTTT
* *
209109 AAGATCAAATTCCCGTTTGTTTACCGAGAAAATGGATGAAAAGAAGTTTTTACTCCTCATACATG
127 AAGATCAAATTCCCGTTTGTTTACCGAGAAAACGGATGAAAAGAAG-TTTTACTACTCATACATG
*
209174 TTAACCTAA
191 TAAACCTAA
209183 TAAATTCAAA
Statistics
Matches: 378, Mismatches: 48, Indels: 21
0.85 0.11 0.05
Matches are distributed among these distances:
233 5 0.01
234 177 0.47
235 23 0.06
236 85 0.22
237 5 0.01
238 13 0.03
239 48 0.13
241 17 0.04
242 5 0.01
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (233 bp):
AATTCAAATTCATTTTCCGCAACTTTTCCTTCACTTTCTCACCAACCAAACAACAGATCAAACCA
AAAAGAAAAACAGATGAAATTTAGACTTGCAAAAACATGACATGTAAGCTTAAGGATCTTTAAGA
TCAAATTCCCGTTTGTTTACCGAGAAAACGGATGAAAAGAAGTTTTACTACTCATACATGTAAAC
CTAACATCATAATTCATATTTTAATGTTACATCAAATA
Found at i:211552 original size:17 final size:17
Alignment explanation
Indices: 211532--211564 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
211522 TATATTTTTA
*
211532 TTTTTAATCAAATATAC
1 TTTTCAATCAAATATAC
211549 TTTTCAATCAAATATA
1 TTTTCAATCAAATATA
211565 TATTAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTCAATCAAATATAC
Found at i:212195 original size:13 final size:13
Alignment explanation
Indices: 212177--212208 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
212167 TCGTGGGCCC
212177 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
212190 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
*
212203 GTCTTT
1 TTCTTT
212209 CAGCAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (13 bp):
TTCTTTTTTCTTT
Found at i:220045 original size:18 final size:18
Alignment explanation
Indices: 220022--220060 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
220012 TTGATACGAG
220022 AAAATATATAATAAAAAT
1 AAAATATATAATAAAAAT
* *
220040 AAAATATATATTTAAAAT
1 AAAATATATAATAAAAAT
220058 AAA
1 AAA
220061 TGATAAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATATATAATAAAAAT
Found at i:220129 original size:21 final size:21
Alignment explanation
Indices: 220105--220145 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
220095 TAAACTTTAA
220105 TTTTGTACAAATTTATATATGT
1 TTTTGTA-AAATTTATATATGT
*
220127 TTTTTTAAAATTTATATAT
1 TTTTGTAAAATTTATATAT
220146 ATGGAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTGTAAAATTTATATATGT
Found at i:222546 original size:3 final size:3
Alignment explanation
Indices: 222538--222587 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
222528 AAGGGTCGCT
222538 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
222586 TT
1 TT
222588 TTTCCTCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:225313 original size:14 final size:14
Alignment explanation
Indices: 225294--225339 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
225284 AAGAAAAATC
225294 ATGATAAACAAGTT
1 ATGATAAACAAGTT
* *
225308 ATGATAGA-AA-TC
1 ATGATAAACAAGTT
225320 ATGATAAACAAGTT
1 ATGATAAACAAGTT
225334 ATGATA
1 ATGATA
225340 GCTTGCGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 8 0.31
13 4 0.15
14 14 0.54
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (14 bp):
ATGATAAACAAGTT
Found at i:225323 original size:26 final size:26
Alignment explanation
Indices: 225289--225340 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
225279 AAAGAAAGAA
225289 AAATCATGATAAACAAGTTATGATAG
1 AAATCATGATAAACAAGTTATGATAG
225315 AAATCATGATAAACAAGTTATGATAG
1 AAATCATGATAAACAAGTTATGATAG
225341 CTTGCGTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (26 bp):
AAATCATGATAAACAAGTTATGATAG
Found at i:234109 original size:17 final size:17
Alignment explanation
Indices: 234087--234120 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
234077 CTAATGAATA
*
234087 GATTGATGTAAGTACTT
1 GATTGATATAAGTACTT
*
234104 GATTGATATGAGTACTT
1 GATTGATATAAGTACTT
234121 CAAGGATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (17 bp):
GATTGATATAAGTACTT
Found at i:235111 original size:18 final size:17
Alignment explanation
Indices: 235067--235115 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
235057 TATACTTATT
235067 AAAATTATAAAAGTATATA
1 AAAATTATAAAA--ATATA
*
235086 AAAA-TATAAAAATCTA
1 AAAATTATAAAAATATA
235102 ATAAATTATAAAAA
1 A-AAATTATAAAAA
235116 GAATTATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 5 0.19
17 3 0.11
18 15 0.56
19 4 0.15
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAATTATAAAAATATA
Found at i:235155 original size:29 final size:28
Alignment explanation
Indices: 235065--235186 Score: 83
Period size: 29 Copynumber: 4.3 Consensus size: 28
235055 TATATACTTA
235065 TTAAAATT-ATAAAAGTATATAAAA-AT
1 TTAAAATTAATAAAAGTATATAAAATAT
* * * *
235091 ATAAAAATCTAAT-AAATTATA-AAAAGAA
1 -TTAAAAT-TAATAAAAGTATATAAAATAT
*
235119 TTATAAATTAATAAAACTTATATAAAATAT
1 TTA-AAATTAATAAAA-GTATATAAAATAT
* * *
235149 TTAAAATTAAAAAAACGTAT-TAGAATTT
1 TTAAAATTAATAAAA-GTATATAAAATAT
235177 TTATAAATTA
1 TTA-AAATTA
235187 CATATTTTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
27 16 0.21
28 25 0.32
29 28 0.36
30 8 0.10
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.35
Consensus pattern (28 bp):
TTAAAATTAATAAAAGTATATAAAATAT
Found at i:238356 original size:130 final size:130
Alignment explanation
Indices: 238118--238372 Score: 456
Period size: 130 Copynumber: 2.0 Consensus size: 130
238108 CATCTCTAGA
*
238118 TTGTAAAGGGGAGACAACCAAGCAAATCTAAGTTCAGATTATTGTTAGTGTCCTTTGAAATTGCT
1 TTGTAAAGGGGAGACAACCAAGCAAATCTAAGTCCAGATTATTGTTAGTGTCCTTTGAAATTGCT
*
238183 AACATTTACGTTTATCGAAACTAGTTATCACCGACACACGAAATGCGTATCAGTGATATTGTTAG
66 AACATTTACGTTTATCGAAACTAGTTATCACCGACACACGAAATGCATATCAGTGATATTGTTAG
* *
238248 TTGTAAAGGGGAGACAACCAAGCAAATCTAAGTCCATATTATTGTTAGTGTCCTTTGGAATTGCT
1 TTGTAAAGGGGAGACAACCAAGCAAATCTAAGTCCAGATTATTGTTAGTGTCCTTTGAAATTGCT
* *
238313 AACATTTATGTTTATCGAAACTAGTTATCACCGACACATGAAATGCATATCAGTGATATT
66 AACATTTACGTTTATCGAAACTAGTTATCACCGACACACGAAATGCATATCAGTGATATT
238373 ACATCTGAAA
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 119 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (130 bp):
TTGTAAAGGGGAGACAACCAAGCAAATCTAAGTCCAGATTATTGTTAGTGTCCTTTGAAATTGCT
AACATTTACGTTTATCGAAACTAGTTATCACCGACACACGAAATGCATATCAGTGATATTGTTAG
Found at i:240822 original size:2 final size:2
Alignment explanation
Indices: 240817--240841 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
240807 TTTAAATAGC
240817 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
240842 TACCGGCGAG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:246102 original size:3 final size:3
Alignment explanation
Indices: 246094--246158 Score: 85
Period size: 3 Copynumber: 21.7 Consensus size: 3
246084 AGGAGACTCA
* * *
246094 GAT GAT GAT GAT GAT GGT GAT GAT GAT GAT GAT AAT GAT GGT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
246142 GGT GAT GAT GGT GAT GA
1 GAT GAT GAT GAT GAT GA
246159 AGGTGAGGCT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:250774 original size:25 final size:26
Alignment explanation
Indices: 250745--250799 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
250735 TATTTTTACA
*
250745 AATTATACATAT-AAAATTTTGCTTT
1 AATTATACATATGAAAATTTTACTTT
* * *
250770 AATTATATATGTGAAAATTTTATTTT
1 AATTATACATATGAAAATTTTACTTT
250796 AATT
1 AATT
250800 CGATTATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (26 bp):
AATTATACATATGAAAATTTTACTTT
Found at i:255144 original size:24 final size:24
Alignment explanation
Indices: 255112--255164 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
255102 ATAATAAAAA
* *
255112 TATAATTTTATTATTTTAATAGTT
1 TATAATTTTATCATTTTAAAAGTT
* *
255136 TATATTTTTATCATTTTAAAATTT
1 TATAATTTTATCATTTTAAAAGTT
255160 TATAA
1 TATAA
255165 AATTTTAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (24 bp):
TATAATTTTATCATTTTAAAAGTT
Found at i:283621 original size:28 final size:28
Alignment explanation
Indices: 283590--283645 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
283580 ACAAAATTTT
* *
283590 ATTTAATTTAATGTCACGTCAGTCGTTG
1 ATTTAATTTAATGTCACATCAGTAGTTG
*
283618 ATTTGATTTAATGTCACATCAGTAGTTG
1 ATTTAATTTAATGTCACATCAGTAGTTG
283646 TTAAGACAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (28 bp):
ATTTAATTTAATGTCACATCAGTAGTTG
Found at i:289063 original size:40 final size:40
Alignment explanation
Indices: 289019--289126 Score: 189
Period size: 40 Copynumber: 2.7 Consensus size: 40
289009 AATACCTATC
* *
289019 TTCTCTGTAACTCTTCTCATTCATCAATTAAATATCCATT
1 TTCTCTGTAACTCTTCTCATTCATCAATAAAATATCCAAT
289059 TTCTCTGTAACTCTTCTCATTCATCAATAAAATATCCAAT
1 TTCTCTGTAACTCTTCTCATTCATCAATAAAATATCCAAT
*
289099 TTCTCTGTAACTCTTCTTATTCATCAAT
1 TTCTCTGTAACTCTTCTCATTCATCAAT
289127 CACCTTCTTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.28, C:0.25, G:0.03, T:0.44
Consensus pattern (40 bp):
TTCTCTGTAACTCTTCTCATTCATCAATAAAATATCCAAT
Found at i:299955 original size:21 final size:20
Alignment explanation
Indices: 299917--299960 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
299907 AACTTTGCTT
* *
299917 AAATTTAAGATAACAAAGCA
1 AAATTTAAGATAAAAAAGAA
*
299937 AAATTTATGAATAAAAAAGAA
1 AAATTTAAG-ATAAAAAAGAA
299958 AAA
1 AAA
299961 GAGTCCTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.66, C:0.05, G:0.09, T:0.20
Consensus pattern (20 bp):
AAATTTAAGATAAAAAAGAA
Found at i:299959 original size:20 final size:20
Alignment explanation
Indices: 299917--299959 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
299907 AACTTTGCTT
*
299917 AAATTTAAGATAACAAAGCA
1 AAATTTAAGATAAAAAAGCA
*
299937 AAATTTATGAATAAAAAAG-A
1 AAATTTAAG-ATAAAAAAGCA
299957 AAA
1 AAA
299960 AGAGTCCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.65, C:0.05, G:0.09, T:0.21
Consensus pattern (20 bp):
AAATTTAAGATAAAAAAGCA
Found at i:306045 original size:11 final size:11
Alignment explanation
Indices: 306029--306057 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
306019 TTAAGTTCGA
306029 GATTGGCACAT
1 GATTGGCACAT
306040 GATTGGCACAT
1 GATTGGCACAT
306051 GATTGGC
1 GATTGGC
306058 CAAGGCATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (11 bp):
GATTGGCACAT
Found at i:312151 original size:12 final size:12
Alignment explanation
Indices: 312130--312162 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
312120 AAAGGGTAAG
312130 AGAT-AATAAAT
1 AGATAAATAAAT
312141 AGATAAATAAAT
1 AGATAAATAAAT
*
312153 AAATAAATAA
1 AGATAAATAA
312163 TATATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (12 bp):
AGATAAATAAAT
Found at i:312209 original size:23 final size:24
Alignment explanation
Indices: 312183--312227 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
312173 GAAATCTATA
312183 AAGGGTCGAAA-T-TAAATAAAATT
1 AAGGG-CGAAATTGTAAATAAAATT
*
312206 AAGGGCTAAATTGTAAATAAAA
1 AAGGGCGAAATTGTAAATAAAA
312228 AAAGCAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 6 0.32
24 9 0.47
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.24
Consensus pattern (24 bp):
AAGGGCGAAATTGTAAATAAAATT
Found at i:315302 original size:18 final size:17
Alignment explanation
Indices: 315274--315312 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
315264 TTCTTTTCTT
*
315274 ATTAGATTAAAGTAGAA
1 ATTAGATTAAAATAGAA
*
315291 ATTAGTATTAAAATAGAG
1 ATTAG-ATTAAAATAGAA
315309 ATTA
1 ATTA
315313 TGCACAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (17 bp):
ATTAGATTAAAATAGAA
Found at i:323233 original size:19 final size:19
Alignment explanation
Indices: 323211--323248 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
323201 TGTAACTTTA
323211 TAATA-ATTTTATAATTTTT
1 TAATATATTTTA-AATTTTT
323230 TAATATATTTTAAATTTTT
1 TAATATATTTTAAATTTTT
323249 AAAAAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TAATATATTTTAAATTTTT
Found at i:323588 original size:11 final size:11
Alignment explanation
Indices: 323573--323635 Score: 72
Period size: 11 Copynumber: 5.4 Consensus size: 11
323563 AAAATTAAAA
323573 AAAAAGTATTTT
1 AAAAA-TATTTT
323585 AAAAATATTTT
1 AAAAATATTTT
* *
323596 AAAATTAAAAATTT
1 -AAA--AATATTTT
323610 AAAAATATTTT
1 AAAAATATTTT
323621 AAAAATATTTT
1 AAAAATATTTT
323632 AAAA
1 AAAA
323636 TTAAAAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
11 27 0.61
12 8 0.18
13 3 0.07
14 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:323599 original size:25 final size:24
Alignment explanation
Indices: 323548--323635 Score: 78
Period size: 25 Copynumber: 3.8 Consensus size: 24
323538 TAATAAATAC
* *
323548 TAAAAAATTATTTT-AAAA-ATTA
1 TAAAAAAATATTTTAAAAATATTT
*
323570 AAAAAAAAGTATTTTAAAAATATTT
1 TAAAAAAA-TATTTTAAAAATATTT
*
323595 TAAAATTAAA-AATTTAAAAATATTT
1 TAAAA--AAATATTTTAAAAATATTT
323620 T--AAAAATATTTTAAAA
1 TAAAAAAATATTTTAAAA
323636 TTAAAAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
21 3 0.06
22 14 0.26
23 8 0.15
24 4 0.07
25 22 0.41
27 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (24 bp):
TAAAAAAATATTTTAAAAATATTT
Found at i:323614 original size:15 final size:16
Alignment explanation
Indices: 323586--323692 Score: 55
Period size: 16 Copynumber: 6.6 Consensus size: 16
323576 AAGTATTTTA
*
323586 AAAATATTTTAAAATT
1 AAAATATTTAAAAATT
323602 AAAA-ATTTAAAAATATTTT
1 AAAATATTT-AAAA-A--TT
*
323621 AAAAATATTTTAAAATT
1 -AAAATATTTAAAAATT
* *
323638 AAAA-A--TAATAA-G
1 AAAATATTTAAAAATT
*
323650 AAAATATTTTAAAATT
1 AAAATATTTAAAAATT
*
323666 AAAAAAATTTAAAAA-T
1 -AAAATATTTAAAAATT
323682 AAATATATTTA
1 AAA-ATATTTA
323693 TTATATCGGG
Statistics
Matches: 68, Mismatches: 11, Indels: 24
0.66 0.11 0.23
Matches are distributed among these distances:
12 4 0.06
13 5 0.07
15 12 0.18
16 18 0.26
17 15 0.22
19 3 0.04
20 7 0.10
21 4 0.06
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (16 bp):
AAAATATTTAAAAATT
Found at i:323619 original size:36 final size:35
Alignment explanation
Indices: 323550--323663 Score: 142
Period size: 36 Copynumber: 3.1 Consensus size: 35
323540 ATAAATACTA
*
323550 AAAAATTATTTTAAAAATTAAAAA--AAAAGTATTTT
1 AAAAA-TATTTT-AAAATTAAAAATTAAAAATATTTT
323585 AAAAATATTTTAAAATTAAAAATTTAAAAATATTTT
1 AAAAATATTTTAAAATTAAAAA-TTAAAAATATTTT
323621 AAAAATATTTTAAAATTAAAAATAATAAGAAAATATTTT
1 AAAAATATTTTAAAATTAAAAAT--T-A-AAAATATTTT
323660 AAAA
1 AAAA
323664 TTAAAAAAAT
Statistics
Matches: 71, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
33 11 0.15
34 6 0.08
35 6 0.08
36 32 0.45
37 1 0.01
38 1 0.01
39 14 0.20
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (35 bp):
AAAAATATTTTAAAATTAAAAATTAAAAATATTTT
Found at i:325161 original size:24 final size:25
Alignment explanation
Indices: 325125--325175 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
325115 CCCATTTTTT
*
325125 AATAAACATTAAAAAAT-TATTTTAA
1 AATAAACAATAAAAAATAT-TTTTAA
325150 AATAAA-AATAAAAAATATTTTTAA
1 AATAAACAATAAAAAATATTTTTAA
325174 AA
1 AA
325176 GTATTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
AATAAACAATAAAAAATATTTTTAA
Found at i:344630 original size:5 final size:5
Alignment explanation
Indices: 344612--344658 Score: 64
Period size: 5 Copynumber: 10.0 Consensus size: 5
344602 CAACAACAAC
*
344612 AAAGA AAAGC AAA-A AAA-A AAA-A AAAGA AAAGA AAAGA AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
344659 GGAAGGGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
4 11 0.28
5 28 0.72
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:344637 original size:22 final size:21
Alignment explanation
Indices: 344612--344656 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
344602 CAACAACAAC
344612 AAAGAAAAGCAAAAAAAAAAAA
1 AAAGAAAAG-AAAAAAAAAAAA
* *
344634 AAAGAAAAGAAAAGAAAAGAA
1 AAAGAAAAGAAAAAAAAAAAA
344655 AA
1 AA
344657 GAGGAAGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.84, C:0.02, G:0.13, T:0.00
Consensus pattern (21 bp):
AAAGAAAAGAAAAAAAAAAAA
Found at i:351948 original size:23 final size:24
Alignment explanation
Indices: 351914--351966 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 24
351904 TCAAGGTTCG
351914 TTTC-TTTTCTACCAAACA-GGTT
1 TTTCTTTTTCTACCAAACAGGGTT
351936 TTTCTTTTTCTACCAAACAGGGTT
1 TTTCTTTTTCTACCAAACAGGGTT
351960 TGTTCTT
1 T-TTCTT
351967 ATACTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 4 0.14
23 14 0.50
24 5 0.18
25 5 0.18
ACGTcount: A:0.19, C:0.21, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTCTTTTTCTACCAAACAGGGTT
Found at i:354033 original size:22 final size:22
Alignment explanation
Indices: 353986--354038 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
353976 AATAATATTA
* * *
353986 ATAAATCATAATATTAATATGC
1 ATAAATAATAATATGAAAATGC
354008 ATAAATAATAATTATGAAAATG-
1 ATAAATAATAA-TATGAAAATGC
354030 ATAATATAA
1 ATAA-ATAA
354039 ATAACAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.34
Consensus pattern (22 bp):
ATAAATAATAATATGAAAATGC
Found at i:354087 original size:16 final size:15
Alignment explanation
Indices: 354030--354076 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
354020 TATGAAAATG
* *
354030 ATAATATAAATAACA
1 ATAACATAAATAATA
*
354045 ATAACAATATATAATA
1 ATAAC-ATAAATAATA
354061 ATAACATAAATAATA
1 ATAACATAAATAATA
354076 A
1 A
354077 ATAATCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAACATAAATAATA
Found at i:354271 original size:18 final size:18
Alignment explanation
Indices: 354248--354283 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
354238 TTAAAAATTG
354248 AAAATAAATAAAT-AAATA
1 AAAAT-AATAAATGAAATA
354266 AAAATAATAAATGAAATA
1 AAAATAATAAATGAAATA
354284 GTTTAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (18 bp):
AAAATAATAAATGAAATA
Found at i:356949 original size:28 final size:28
Alignment explanation
Indices: 356917--356976 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
356907 CAAAAAATAA
356917 ATAATTTACTTTCGATAAATACATGTGT
1 ATAATTTACTTTCGATAAATACATGTGT
*
356945 ATAATTTACTTTCGGTAAATACATGTGT
1 ATAATTTACTTTCGATAAATACATGTGT
356973 ATAA
1 ATAA
356977 ATAAAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.42
Consensus pattern (28 bp):
ATAATTTACTTTCGATAAATACATGTGT
Found at i:361939 original size:17 final size:17
Alignment explanation
Indices: 361912--361957 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
361902 CCGATATAAT
* * *
361912 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
*
361929 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
361946 AAATATTTTTAA
1 AAATATTTTTAA
361958 AATATTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:361987 original size:22 final size:21
Alignment explanation
Indices: 361931--361988 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
361921 TATTTTTTAA
361931 ATTTTTTTAA--TTTTAAAAT
1 ATTTTTTTAATTTTTTAAAAT
**
361950 ATTTTTAAAATATTTTTAAAAT
1 ATTTTTTTAAT-TTTTTAAAAT
361972 ACTTTTTTTAATTTTTT
1 A-TTTTTTTAATTTTTT
361989 TTAATTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 8 0.26
22 15 0.48
23 8 0.26
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTTTTAATTTTTTAAAAT
Found at i:364896 original size:55 final size:56
Alignment explanation
Indices: 364788--364900 Score: 167
Period size: 55 Copynumber: 2.0 Consensus size: 56
364778 TATTGTTTGG
*
364788 TAAGAAAGTCGATTGATGAATGAGAAGAATTTATGAGAAAATGGATATTTATAGTTT
1 TAAGAAAGTCGATTGATGAATGAGAAGAATTCAT-AGAAAATGGATATTTATAGTTT
* *
364845 TAAGAAGGT-GATTGATGAATGAGAAGAGTCTCAT-GAAAATGGATATTTATAGTTT
1 TAAGAAAGTCGATTGATGAATGAGAAGAAT-TCATAGAAAATGGATATTTATAGTTT
364900 T
1 T
364901 GCAGATTAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
55 22 0.42
56 19 0.37
57 11 0.21
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.34
Consensus pattern (56 bp):
TAAGAAAGTCGATTGATGAATGAGAAGAATTCATAGAAAATGGATATTTATAGTTT
Found at i:368222 original size:2 final size:2
Alignment explanation
Indices: 368215--368241 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
368205 TATTTATGCA
368215 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 A
368242 AATTTAGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:369548 original size:29 final size:26
Alignment explanation
Indices: 369504--369558 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 26
369494 TTTGATTCTT
369504 TTTAATATAGGGACTAA-ATTGATCCA
1 TTTAATATAGGGACTAACA-TGATCCA
369530 TTTAATAATAGAGGTACTAACATGATCCA
1 TTTAAT-ATAG-GG-ACTAACATGATCCA
369559 GCCCCTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 6 0.24
27 4 0.16
28 2 0.08
29 12 0.48
30 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (26 bp):
TTTAATATAGGGACTAACATGATCCA
Found at i:373606 original size:93 final size:93
Alignment explanation
Indices: 373445--373635 Score: 355
Period size: 93 Copynumber: 2.1 Consensus size: 93
373435 TATTTGTTCA
*
373445 GTAAAGGAGACAAAATGCAATTTAAATCTTAGTATATTTTAATATAAAGGCCTCCATGATGCTCT
1 GTAAAGGAGACAAAATACAATTTAAATCTTAGTATATTTTAATATAAAGGCCTCCATGATGCTCT
373510 TACCACCGAAGAATAATGAGAAGACACT
66 TACCACCGAAGAATAATGAGAAGACACT
* *
373538 GTAAAGGAGACAAAATACAATTTAAATCTTAGTATATTTTAATATAAAGGTCTCCATGATGCTTT
1 GTAAAGGAGACAAAATACAATTTAAATCTTAGTATATTTTAATATAAAGGCCTCCATGATGCTCT
373603 TACCACCGAAGAATAATGAGAAGACACT
66 TACCACCGAAGAATAATGAGAAGACACT
373631 GTAAA
1 GTAAA
373636 ACCATAAATC
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 95 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.28
Consensus pattern (93 bp):
GTAAAGGAGACAAAATACAATTTAAATCTTAGTATATTTTAATATAAAGGCCTCCATGATGCTCT
TACCACCGAAGAATAATGAGAAGACACT
Found at i:378938 original size:17 final size:18
Alignment explanation
Indices: 378899--378944 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
378889 AAAAAAATTA
378899 TTTTTTAGAATTTCAACT
1 TTTTTTAGAATTTCAACT
* *
378917 ATTTTTA-AATTTCTA-T
1 TTTTTTAGAATTTCAACT
378933 TTTTTT-GAATTT
1 TTTTTTAGAATTT
378945 ATATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 11 0.46
17 7 0.29
18 6 0.25
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (18 bp):
TTTTTTAGAATTTCAACT
Found at i:378949 original size:2 final size:2
Alignment explanation
Indices: 378944--378968 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
378934 TTTTTGAATT
378944 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
378969 TACACTTTTC
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:389041 original size:2 final size:2
Alignment explanation
Indices: 389034--389070 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
389024 TTCTAACATG
389034 TA TA TA TA TA 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
389071 TAGATTCTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:389541 original size:17 final size:17
Alignment explanation
Indices: 389515--389548 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
389505 GAGTGAATTT
*
389515 CAAAAGATCATCAAAAG
1 CAAAACATCATCAAAAG
389532 CAAAACATCATCAAAAG
1 CAAAACATCATCAAAAG
389549 ATAAGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.59, C:0.21, G:0.09, T:0.12
Consensus pattern (17 bp):
CAAAACATCATCAAAAG
Found at i:396436 original size:20 final size:19
Alignment explanation
Indices: 396390--396428 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
396380 NNNTTTTTAA
396390 AATATTTAAAATATTTTTT
1 AATATTTAAAATATTTTTT
*
396409 AATTTTTAAAATAATTTTTT
1 AATATTTAAAAT-ATTTTTT
396429 GGTATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATATTTAAAATATTTTTT
Found at i:399597 original size:14 final size:16
Alignment explanation
Indices: 399566--399595 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
399556 AAAAAATTAG
399566 TATATATATTTTTAAA
1 TATATATATTTTTAAA
399582 TATATA-ATTTTTAA
1 TATATATATTTTTAA
399596 TAATTTACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATATATTTTTAAA
Found at i:410033 original size:14 final size:14
Alignment explanation
Indices: 410014--410053 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
410004 TTGATAGCCA
410014 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
410028 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
410042 GGAAAATGTTTT
1 GTAAAATGTTTT
410054 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:410062 original size:20 final size:20
Alignment explanation
Indices: 410037--410076 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
410027 CGTAAAATGA
*
410037 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
410057 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
410077 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:410066 original size:34 final size:35
Alignment explanation
Indices: 410022--410088 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
410012 CAGTAAAATG
*
410022 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
410056 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
410089 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:410092 original size:14 final size:15
Alignment explanation
Indices: 410016--410092 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
410006 GATAGCCAGT
* *
410016 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
410030 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
410044 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
410064 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
410079 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
410093 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:413912 original size:12 final size:12
Alignment explanation
Indices: 413895--413920 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
413885 TAGAACTACT
413895 CATAGCCCCTCC
1 CATAGCCCCTCC
413907 CATAGCCCCTCC
1 CATAGCCCCTCC
413919 CA
1 CA
413921 ACCCTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.58, G:0.08, T:0.15
Consensus pattern (12 bp):
CATAGCCCCTCC
Found at i:417420 original size:17 final size:17
Alignment explanation
Indices: 417398--417439 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
417388 TGGACATATT
*
417398 TTTATATTTATATTGTA
1 TTTATAATTATATTGTA
417415 TTTATAATTATATTGTA
1 TTTATAATTATATTGTA
*
417432 TTTGTAAT
1 TTTATAAT
417440 CGTAATTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (17 bp):
TTTATAATTATATTGTA
Found at i:420885 original size:2 final size:2
Alignment explanation
Indices: 420878--420908 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
420868 TAAATTTCAA
420878 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
420909 AAGATTTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:421275 original size:2 final size:2
Alignment explanation
Indices: 421268--421295 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
421258 TCGAAAAATG
421268 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
421296 ATGTTGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:425043 original size:14 final size:13
Alignment explanation
Indices: 425020--425055 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
425010 TATATTTTAA
425020 AATTATTAAATCT
1 AATTATTAAATCT
425033 AATTAATTAAATCT
1 AATT-ATTAAATCT
425047 AATTTATTA
1 AA-TTATTA
425056 TAAAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.19
14 15 0.71
15 2 0.10
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTATTAAATCT
Found at i:426850 original size:2 final size:2
Alignment explanation
Indices: 426843--426879 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
426833 TCCATTTGTT
426843 TA TA TA TA TA 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
426880 TTAAGGTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:429087 original size:6 final size:6
Alignment explanation
Indices: 429076--429110 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
429066 TTTTGTTACT
* *
429076 TGGCAG TGGCAG TGGCAG TGGCAA TGGCAA TGGCA
1 TGGCAG TGGCAG TGGCAG TGGCAG TGGCAG TGGCA
429111 ATGGGGGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.23, C:0.17, G:0.43, T:0.17
Consensus pattern (6 bp):
TGGCAG
Found at i:429093 original size:12 final size:12
Alignment explanation
Indices: 429076--429114 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
429066 TTTTGTTACT
*
429076 TGGCAGTGGCAG
1 TGGCAGTGGCAA
429088 TGGCAGTGGCAA
1 TGGCAGTGGCAA
*
429100 TGGCAATGGCAA
1 TGGCAGTGGCAA
429112 TGG
1 TGG
429115 GGGTTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.23, C:0.15, G:0.44, T:0.18
Consensus pattern (12 bp):
TGGCAGTGGCAA
Found at i:429111 original size:6 final size:6
Alignment explanation
Indices: 429076--429114 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
429066 TTTTGTTACT
* * *
429076 TGGCAG TGGCAG TGGCAG TGGCAA TGGCAA TGGCAA TGG
1 TGGCAA TGGCAA TGGCAA TGGCAA TGGCAA TGGCAA TGG
429115 GGGTTTCACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.23, C:0.15, G:0.44, T:0.18
Consensus pattern (6 bp):
TGGCAA
Found at i:431689 original size:51 final size:51
Alignment explanation
Indices: 431607--431822 Score: 346
Period size: 51 Copynumber: 4.3 Consensus size: 51
431597 ACTTCTGATC
*
431607 AGTGATAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
*
431658 AGTGGA-AAGTGATAAGTAGTAGCTTCAGCTACACTTATCTAATCAGTGACA
1 AGT-GACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
*
431709 AATGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
* * *
431760 AGTGGCAAGTGATAAGTGGTAGCTT-AGCTACACTTATCTGATCAATGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
*
431810 AGTGATAAGTGAT
1 AGTGACAAGTGAT
431823 CATACGTAAG
Statistics
Matches: 154, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
50 37 0.24
51 115 0.75
52 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
Found at i:438132 original size:25 final size:26
Alignment explanation
Indices: 438079--438132 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
438069 CATACTAAGG
438079 AAGATTTTCTTAGCCTGATTTTCTTT
1 AAGATTTTCTTAGCCTGATTTTCTTT
*
438105 AAGATTTTCTTGGCCTGA-TTTCTTT
1 AAGATTTTCTTAGCCTGATTTTCTTT
438130 AAG
1 AAG
438133 TATTCTACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (26 bp):
AAGATTTTCTTAGCCTGATTTTCTTT
Found at i:438650 original size:55 final size:55
Alignment explanation
Indices: 438566--438675 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
438556 AGATAACTAG
438566 TATATTTTTCCCTTTATTCCTTGTTTTGTGGATTA-TATAACGAATATTGATGTAC
1 TATATTTTTCCCTTTATTCCTTGTTTTGTGGATTACT-TAACGAATATTGATGTAC
*
438621 TATATTTTTCTCTTTATTCCTTGTTTTGTGGATTACTTAACGAATATTGATGTAC
1 TATATTTTTCCCTTTATTCCTTGTTTTGTGGATTACTTAACGAATATTGATGTAC
438676 GATAATGTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
55 52 0.98
56 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.52
Consensus pattern (55 bp):
TATATTTTTCCCTTTATTCCTTGTTTTGTGGATTACTTAACGAATATTGATGTAC
Found at i:455439 original size:18 final size:18
Alignment explanation
Indices: 455416--455475 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
455406 AGATGTTCGA
455416 CTTGGATTTCTCCGAAAC
1 CTTGGATTTCTCCGAAAC
* * *
455434 CTTGGACTTC-CTTGAGAC
1 CTTGGATTTCTC-CGAAAC
455452 CTTGGATTTCTCCGAAAC
1 CTTGGATTTCTCCGAAAC
455470 CTTGGA
1 CTTGGA
455476 GATCCTCACA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 1 0.03
18 32 0.94
19 1 0.03
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (18 bp):
CTTGGATTTCTCCGAAAC
Done.