Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 117 of 135
Found at i:39206516 original size:17 final size:16
Alignment explanation
Indices: 39206494--39206574 Score: 81
Period size: 17 Copynumber: 4.8 Consensus size: 16
39206484 ACTTGTCTTT
*
39206494 TTAAATTTATAATAATA
1 TTAAATTTAAAATAA-A
*
39206511 TTAAATTTAAATTAAAA
1 TTAAATTTAAAAT-AAA
*
39206528 TTGAATTTAAAATAAA
1 TTAAATTTAAAATAAA
*
39206544 TTTAAAATTAAAATAAA
1 -TTAAATTTAAAATAAA
*
39206561 TTTAATTTCAAAAT
1 TTAAATTT-AAAAT
39206575 GGTTTGGGCC
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
16 9 0.17
17 42 0.79
18 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (16 bp):
TTAAATTTAAAATAAA
Found at i:39206537 original size:12 final size:12
Alignment explanation
Indices: 39206494--39206555 Score: 60
Period size: 11 Copynumber: 5.4 Consensus size: 12
39206484 ACTTGTCTTT
*
39206494 TTAAATTTATAA
1 TTAAATTTAAAA
*
39206506 -T-AATATTAAAT
1 TTAAAT-TTAAAA
39206517 TTAAA-TTAAAA
1 TTAAATTTAAAA
*
39206528 TTGAATTTAAAA
1 TTAAATTTAAAA
39206540 -TAAATTTAAAA
1 TTAAATTTAAAA
39206551 TTAAA
1 TTAAA
39206556 ATAAATTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
10 3 0.08
11 24 0.60
12 11 0.28
13 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
TTAAATTTAAAA
Found at i:39206964 original size:92 final size:92
Alignment explanation
Indices: 39206827--39207417 Score: 841
Period size: 92 Copynumber: 6.4 Consensus size: 92
39206817 ATGTCGGGGT
* *
39206827 TTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTGCTACAACTTC
1 TTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
* *
39206892 AAGAGGATAGGGATTGATGTTTGATGC
66 AAGAGGATAGGAAATGATGTTTGATGC
* * *
39206919 TTCATCTTGCTCTTATTACAACTTCAGATAGATAAATACTTGCTATCCAACTTTACTACAACTTC
1 TTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
* *
39206984 ATGAGGATAGGAAATGAGGTTTGATGC
66 AAGAGGATAGGAAATGATGTTTGATGC
**
39207011 TTCATCTAACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
1 TTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
39207076 AAGAGGATAGGAAATGATG-TTGATGC
66 AAGAGGATAGGAAATGATGTTTGATGC
* *
39207102 TTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAGCTTTACTACAACTTC
1 TTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
39207167 AAGAGGATAGGAAATGATG-TTGATGC
66 AAGAGGATAGGAAATGATGTTTGATGC
* * * * *
39207193 TTCATCTAGCTCTTACTACAACTTCAAAGAGATAAAGGCTTGTTATCCAACTTTACTATAACTTC
1 TTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
* * ** *
39207258 AAGAGGATAAGAATTGCCGTTTGAAGC
66 AAGAGGATAGGAAATGATGTTTGATGC
* * *
39207285 TTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAG-GTT-CATTATCCAACTTTACTATAACT
1 TTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGC--TATCCAACTTTACTACAACT
* * *
39207348 TCAAGAGGATAAGAATTGAAT-TTTGAAGC
64 TCAAGAGGATAGGAAATG-ATGTTTGATGC
* *
39207377 TTTATCTTGCTCTTACTACAACTTCAGAGAGATAAAAACTT
1 TTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTT
39207418 TTCCCTTTTG
Statistics
Matches: 455, Mismatches: 39, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
91 173 0.38
92 280 0.62
93 2 0.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (92 bp):
TTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
AAGAGGATAGGAAATGATGTTTGATGC
Found at i:39207536 original size:50 final size:50
Alignment explanation
Indices: 39207417--39207717 Score: 207
Period size: 50 Copynumber: 5.9 Consensus size: 50
39207407 GATAAAAACT
* * * * * *
39207417 TTTCCCTTTTGTCTTTTTGCGGTACTAGATCTGCCGTTGCGGTCTTAGATC
1 TTTCCCTTTCGTGTTTTTGAGGTAC-AGGTCCGCCGTTGCGGACTTAGATC
* *
39207468 TTTCCC-GTCGTGTCTTTTGAGGTACACGGTCCGCCGTTGC-GACTTAGACC
1 TTTCCCTTTCGTGT-TTTTGAGGTACA-GGTCCGCCGTTGCGGACTTAGATC
* * * * * * *
39207518 TTTCCCTTTTGTGTTTTTGCGATACTAGATCCGTCGTTGCAGTCTTAGATC
1 TTTCCCTTTCGTGTTTTTGAGGTAC-AGGTCCGCCGTTGCGGACTTAGATC
* * * * *
39207569 TATCCC-GTCGTGTTTCTGAGGTACACGGTCCGCCGTTG-TGACTTAGACC
1 TTTCCCTTTCGTGTTTTTGAGGTACA-GGTCCGCCGTTGCGGACTTAGATC
* * * * * *
39207618 TTTCCCTTTTGTGTTTTTTTTGTGGTACTGGATCTGCCATTGCGGTCTTAGATC
1 TTTCCCTTTCGTG---TTTTTGAGGTACAGG-TCCGCCGTTGCGGACTTAGATC
* * *
39207672 TTTCCCTTCTCATGCTTCTGAGGTACATGGTCCGCCGTTGC-GACTT
1 TTTCCCTT-TCGTGTTTTTGAGGTACA-GGTCCGCCGTTGCGGACTT
39207718 TGAGAACTGA
Statistics
Matches: 189, Mismatches: 47, Indels: 28
0.72 0.18 0.11
Matches are distributed among these distances:
49 14 0.07
50 66 0.35
51 50 0.26
52 20 0.11
53 20 0.11
54 16 0.08
55 3 0.02
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (50 bp):
TTTCCCTTTCGTGTTTTTGAGGTACAGGTCCGCCGTTGCGGACTTAGATC
Found at i:39207636 original size:101 final size:100
Alignment explanation
Indices: 39207417--39207717 Score: 413
Period size: 101 Copynumber: 3.0 Consensus size: 100
39207407 GATAAAAACT
*
39207417 TTTCCCTTTTGTCTTTTTGCGGTACTAGATCTGCCGTTGCGGTCTTAGATCTTTCCCGTCGTGTC
1 TTTCCCTTTTGTGTTTTTGCGGTACTAGATCTGCCGTTGCGGTCTTAGATCTTTCCCGTCGTGT-
*
39207482 TTTTGAGGTACACGGTCCGCCGTTGCGACTTAGACC
65 TTCTGAGGTACACGGTCCGCCGTTGCGACTTAGACC
* * * * *
39207518 TTTCCCTTTTGTGTTTTTGCGATACTAGATCCGTCGTTGCAGTCTTAGATCTATCCCGTCGTGTT
1 TTTCCCTTTTGTGTTTTTGCGGTACTAGATCTGCCGTTGCGGTCTTAGATCTTTCCCGTCGTGTT
*
39207583 TCTGAGGTACACGGTCCGCCGTTGTGACTTAGACC
66 TCTGAGGTACACGGTCCGCCGTTGCGACTTAGACC
* * * *
39207618 TTTCCCTTTTGTGTTTTTTTTGTGGTACTGGATCTGCCATTGCGGTCTTAGATCTTTCCCTTCTC
1 TTTCCCTTTTGTG---TTTTTGCGGTACTAGATCTGCCGTTGCGGTCTTAGATCTTTCCC--GTC
* * *
39207683 ATGCTTCTGAGGTACATGGTCCGCCGTTGCGACTT
61 GTGTTTCTGAGGTACACGGTCCGCCGTTGCGACTT
39207718 TGAGAACTGA
Statistics
Matches: 174, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
100 47 0.27
101 58 0.33
103 36 0.21
105 33 0.19
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (100 bp):
TTTCCCTTTTGTGTTTTTGCGGTACTAGATCTGCCGTTGCGGTCTTAGATCTTTCCCGTCGTGTT
TCTGAGGTACACGGTCCGCCGTTGCGACTTAGACC
Found at i:39208888 original size:7 final size:7
Alignment explanation
Indices: 39208876--39208935 Score: 68
Period size: 7 Copynumber: 8.3 Consensus size: 7
39208866 CGACCTCTCC
39208876 TTTTCTTT
1 TTTTC-TT
39208884 TTTCTCTT
1 TTT-TCTT
39208892 TTTTCTT
1 TTTTCTT
*
39208899 TTTTATT
1 TTTTCTT
39208906 TTTTC-T
1 TTTTCTT
39208912 TTTTCTCT
1 TTTTCT-T
*
39208920 TCTTCTT
1 TTTTCTT
39208927 TTTTCTT
1 TTTTCTT
39208934 TT
1 TT
39208936 CTTTTATTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
6 6 0.13
7 23 0.51
8 14 0.31
9 2 0.04
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTCTT
Found at i:39208894 original size:15 final size:15
Alignment explanation
Indices: 39208871--39208932 Score: 74
Period size: 16 Copynumber: 4.2 Consensus size: 15
39208861 CACCTCGACC
*
39208871 TCTCCTTTTCTTTTT
1 TCTCTTTTTCTTTTT
39208886 TCTCTTTTTTCTTTTT
1 TCTC-TTTTTCTTTTT
*
39208902 TAT-TTTTTC-TTTT
1 TCTCTTTTTCTTTTT
*
39208915 TCTCTTCTTCTTTTT
1 TCTCTTTTTCTTTTT
39208930 TCT
1 TCT
39208933 TTTCTTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
13 6 0.15
14 11 0.28
15 11 0.28
16 12 0.30
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (15 bp):
TCTCTTTTTCTTTTT
Found at i:39208900 original size:21 final size:22
Alignment explanation
Indices: 39208875--39208932 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
39208865 TCGACCTCTC
39208875 CTTTTCTTTTTTCTCTTTTT-T
1 CTTTTCTTTTTTCTCTTTTTCT
*
39208896 CTTTT-TTATTTTTTCTTTTTCT
1 CTTTTCTT-TTTTCTCTTTTTCT
39208918 CTTCTTCTTTTTTCT
1 CTT-TTCTTTTTTCT
39208933 TTTCTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.52
22 4 0.13
23 7 0.23
24 2 0.06
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (22 bp):
CTTTTCTTTTTTCTCTTTTTCT
Found at i:39208933 original size:21 final size:20
Alignment explanation
Indices: 39208891--39208940 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
39208881 TTTTTTCTCT
39208891 TTTTTCTTTTTTATTTTTTC
1 TTTTTCTTTTTTATTTTTTC
* *
39208911 TTTTTCTCTTCTTCTTTTTTC
1 TTTTTCT-TTTTTATTTTTTC
39208932 -TTTTCTTTT
1 TTTTTCTTTT
39208941 ATTCATTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 2 0.08
20 13 0.50
21 11 0.42
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTCTTTTTTATTTTTTC
Found at i:39214687 original size:144 final size:145
Alignment explanation
Indices: 39214435--39214713 Score: 366
Period size: 144 Copynumber: 1.9 Consensus size: 145
39214425 TGGATGCCCG
* * *
39214435 GGGGAAAAATGGTAATTTTGGAAAAATTTAGGGTTAAAAATGATATTTTAGACACTTAAGAGTAA
1 GGGGAAAAATGGTAATTTTGAAAAAACTTAGGGTTAAAAATGACATTTTAGACACTTAAGAGTAA
* * * *
39214500 AATGATAATTTTCGGAAGAATCGGGATCAAAACGGGACTTTTTGGATGTCCGAGGGCAAAATGGT
66 AACGATAATTTTCGGAAAAATCGGGATCAAAACGAGACTTTTTGGATATCCGAGGGCAAAATGGT
*
39214565 GATTTTGGACTCTCA
131 AATTTTGGACTCTCA
* * * *
39214580 GGGGCAAAATGGTAATTTT-AAAAAACTTGGGGTT-AAAATGACATTTTAGACACTTGAGGGTAA
1 GGGGAAAAATGGTAATTTTGAAAAAACTTAGGGTTAAAAATGACATTTTAGACACTTAAGAGTAA
* * * * *
39214643 AACGATAATTTTTGGAAAAAATCGGGATCAAAAATGAGA-TTTTTGGATATTCGGGGGTAAAATG
66 AACGATAATTTTCGG-AAAAATCGGGATC-AAAACGAGACTTTTTGGATATCCGAGGGCAAAATG
39214707 GTAATTT
129 GTAATTT
39214714 CGAGAGTTTC
Statistics
Matches: 115, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
143 39 0.34
144 51 0.44
145 25 0.22
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (145 bp):
GGGGAAAAATGGTAATTTTGAAAAAACTTAGGGTTAAAAATGACATTTTAGACACTTAAGAGTAA
AACGATAATTTTCGGAAAAATCGGGATCAAAACGAGACTTTTTGGATATCCGAGGGCAAAATGGT
AATTTTGGACTCTCA
Found at i:39214828 original size:30 final size:29
Alignment explanation
Indices: 39214752--39214841 Score: 117
Period size: 29 Copynumber: 3.1 Consensus size: 29
39214742 TTTGGAAGTT
* *
39214752 ATGTAATTTTCAGAAGTTTTGGGGTCAAA
1 ATGTAATTTTAAGAAGTTTTAGGGTCAAA
* *
39214781 ATGTAATTTTTAGAAGTTTTAGGGTTAAA
1 ATGTAATTTTAAGAAGTTTTAGGGTCAAA
**
39214810 ATGTAATTTTGAAGAAGTTCGAGGGTCAAA
1 ATGTAATTTT-AAGAAGTTTTAGGGTCAAA
39214840 AT
1 AT
39214842 ACAATTTTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 36 0.68
30 17 0.32
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.38
Consensus pattern (29 bp):
ATGTAATTTTAAGAAGTTTTAGGGTCAAA
Found at i:39216200 original size:12 final size:12
Alignment explanation
Indices: 39216185--39216219 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
39216175 TTATCACTAT
*
39216185 TATTATTATTAA
1 TATTATTAATAA
39216197 TATTATTAATAA
1 TATTATTAATAA
*
39216209 TATAATTAATA
1 TATTATTAATA
39216220 TTCACATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TATTATTAATAA
Found at i:39216354 original size:22 final size:21
Alignment explanation
Indices: 39216328--39216369 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39216318 TGAAAACATA
*
39216328 AATGGCAGTTAAACATGCATTG
1 AATGGCAG-CAAACATGCATTG
*
39216350 AATGGTAGCAAACATGCATT
1 AATGGCAGCAAACATGCATT
39216370 AATACCTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.26
Consensus pattern (21 bp):
AATGGCAGCAAACATGCATTG
Found at i:39216818 original size:6 final size:6
Alignment explanation
Indices: 39216809--39216888 Score: 55
Period size: 6 Copynumber: 14.0 Consensus size: 6
39216799 GACTTTTCTT
*
39216809 TTTAAA TTTATAA --TAATA TT-AAA TTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTA-AA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
39216855 -TTAAA ATTGAA TTTAAA -ATAAA TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
39216889 ATGGTTTGGG
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
4 1 0.02
5 20 0.35
6 34 0.60
7 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:39216842 original size:11 final size:11
Alignment explanation
Indices: 39216826--39216881 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
39216816 TTATAATAAT
39216826 ATTAAATTTAA
1 ATTAAATTTAA
*
39216837 ATTAAATTCAA
1 ATTAAATTTAA
*
39216848 ATTTAAATTAAA
1 A-TTAAATTTAA
*
39216860 ATTGAATTTAA
1 ATTAAATTTAA
*
39216871 AATAAATTTAA
1 ATTAAATTTAA
39216882 TTTTAAAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 28 0.74
12 10 0.26
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:39216886 original size:17 final size:17
Alignment explanation
Indices: 39216809--39216890 Score: 85
Period size: 17 Copynumber: 4.8 Consensus size: 17
39216799 GACTTTTCTT
*
39216809 TTTAAATTTATAAT-AA
1 TTTAAATTTAAAATAAA
*
39216825 TATTAAATTTAAATTAAA
1 T-TTAAATTTAAAATAAA
* *
39216843 TTCAAATTTAAATTAAA
1 TTTAAATTTAAAATAAA
* *
39216860 ATTGAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
39216877 TTTAATTTTAAAAT
1 TTTAAATTTAAAAT
39216891 GGTTTGGGCC
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
16 1 0.02
17 50 0.93
18 3 0.06
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:39220461 original size:15 final size:14
Alignment explanation
Indices: 39220419--39220467 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
39220409 TTGATTAAAT
*
39220419 TTAATTAATCAAAA
1 TTAATTAATCAAAC
*
39220433 TTAATTAATTAAAC
1 TTAATTAATCAAAC
*
39220447 TCTAATTAACCAAACC
1 T-TAATTAATCAAA-C
39220463 TTAAT
1 TTAAT
39220468 CTTAATTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 13 0.45
15 14 0.48
16 2 0.07
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAATTAATCAAAC
Found at i:39221118 original size:2 final size:2
Alignment explanation
Indices: 39221111--39221140 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39221101 ATGTTTTTAA
39221111 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
39221141 TTCACACCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39221340 original size:23 final size:25
Alignment explanation
Indices: 39221314--39221367 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
39221304 AAATTAATAT
* *
39221314 ATTATGTTTAA-TCCTTTT-TAAAA
1 ATTATGTTCAACTCCTTTTAAAAAA
39221337 ATTATTGTTCAACTCCTTTTAAAAAA
1 ATTA-TGTTCAACTCCTTTTAAAAAA
39221363 ATTAT
1 ATTAT
39221368 AGATTTGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 4 0.15
24 6 0.23
25 8 0.31
26 8 0.31
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (25 bp):
ATTATGTTCAACTCCTTTTAAAAAA
Found at i:39236532 original size:22 final size:22
Alignment explanation
Indices: 39236499--39236553 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
39236489 TTGTAAGTTA
*
39236499 ATTTTAATTTTGAGAATTTTAGT
1 ATTTT-ATTTTGAGAATTTAAGT
* *
39236522 ATTTTATTTTGAGAGTTTAATT
1 ATTTTATTTTGAGAATTTAAGT
39236544 ATTTTATTTT
1 ATTTTATTTT
39236554 TAATTTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 24 0.83
23 5 0.17
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.62
Consensus pattern (22 bp):
ATTTTATTTTGAGAATTTAAGT
Found at i:39236866 original size:11 final size:11
Alignment explanation
Indices: 39236852--39236881 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39236842 ATTAGGTTTT
39236852 TTTATTTAAAG
1 TTTATTTAAAG
*
39236863 TTTATTTAAAT
1 TTTATTTAAAG
39236874 TTTATTTA
1 TTTATTTA
39236882 TTACTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
TTTATTTAAAG
Found at i:39237591 original size:7 final size:8
Alignment explanation
Indices: 39237567--39237609 Score: 50
Period size: 9 Copynumber: 4.9 Consensus size: 8
39237557 AATATTTTAA
39237567 TAATATTTT
1 TAAT-TTTT
39237576 TAATAATTTT
1 TAAT--TTTT
39237586 TAATTTTT
1 TAATTTTT
39237594 ATAATTTTT
1 -TAATTTTT
39237603 TAATTTT
1 TAATTTT
39237610 AATAAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 11 0.34
9 12 0.38
10 9 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TAATTTTT
Found at i:39237593 original size:17 final size:18
Alignment explanation
Indices: 39237571--39237614 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
39237561 TTTTAATAAT
39237571 ATTTTTAATAA-TTTTTA
1 ATTTTTAATAATTTTTTA
39237588 ATTTTT-ATAATTTTTTA
1 ATTTTTAATAATTTTTTA
39237605 A-TTTTAATAA
1 ATTTTTAATAA
39237615 ATTAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.32
17 17 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTAATAATTTTTTA
Found at i:39237617 original size:10 final size:11
Alignment explanation
Indices: 39237557--39237589 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
39237547 AAATTTAAAA
39237557 AATATTTTAAT
1 AATATTTTAAT
39237568 AATATTTTTAAT
1 AATA-TTTTAAT
39237580 AAT-TTTTAAT
1 AATATTTTAAT
39237590 TTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.33
11 4 0.19
12 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AATATTTTAAT
Found at i:39242835 original size:21 final size:21
Alignment explanation
Indices: 39242807--39242853 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
39242797 AGAAAGGTTT
39242807 TAAA-AATAAAAAACAAAAAA
1 TAAAGAATAAAAAACAAAAAA
* *
39242827 TAAAGAATAAAGAACAAAAGA
1 TAAAGAATAAAAAACAAAAAA
39242848 -AAAGAA
1 TAAAGAA
39242854 GGAGAAATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.79, C:0.04, G:0.09, T:0.09
Consensus pattern (21 bp):
TAAAGAATAAAAAACAAAAAA
Found at i:39243459 original size:29 final size:29
Alignment explanation
Indices: 39243410--39243629 Score: 98
Period size: 29 Copynumber: 7.8 Consensus size: 29
39243400 CCTAAACTAT
39243410 CCAAAAATTA-CATTTTGACCCCGATTTCA
1 CCAAAAATTACCATTTT-ACCCCGATTTCA
* *
39243439 CCAAAAATTACCATTTTACCCTCAAACCTT--
1 CCAAAAATTACCATTTTACCC-C-GA-TTTCA
**
39243469 CC-AAAATT-CCA---T--CCTAATTTCA
1 CCAAAAATTACCATTTTACCCCGATTTCA
* *
39243491 CCAAAAATTACCAATTTACCCCTAAACTTT--
1 CCAAAAATTACCATTTTACCCC--GA-TTTCA
39243521 CC-AAAATT-CCATTTTTAGCCCCGATTTCA
1 CCAAAAATTACCA-TTTTA-CCCCGATTTCA
* *
39243550 CCAAAAAATACCATTTTACTCCCGAACTT--
1 CCAAAAATTACCATTTTAC-CCCG-ATTTCA
* **
39243579 CC-AAAA-TCCCATTTTTAACCTTGATTTCA
1 CCAAAAATTACCA-TTTT-ACCCCGATTTCA
39243608 CCAAAAATTACCATTTTACCCC
1 CCAAAAATTACCATTTTACCCC
39243630 TAAACCTTCC
Statistics
Matches: 145, Mismatches: 16, Indels: 60
0.66 0.07 0.27
Matches are distributed among these distances:
20 2 0.01
21 2 0.01
22 2 0.01
23 8 0.06
24 3 0.02
25 1 0.01
27 11 0.08
28 17 0.12
29 44 0.30
30 37 0.26
31 13 0.09
32 5 0.03
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (29 bp):
CCAAAAATTACCATTTTACCCCGATTTCA
Found at i:39243511 original size:52 final size:52
Alignment explanation
Indices: 39243433--39243649 Score: 170
Period size: 58 Copynumber: 3.9 Consensus size: 52
39243423 TTTGACCCCG
*
39243433 ATTTCACCAAAAATTACCATTTTA-CCCTCAAACCTTCCAAAATTCCATCCTA
1 ATTTCACCAAAAATTACCAATTTACCCCT-AAACCTTCCAAAATTCCATCCTA
* **
39243485 ATTTCACCAAAAATTACCAATTTACCCCTAAACTTTCCAAAATTCCATTTTTAGCCCCG
1 ATTTCACCAAAAATTACCAATTTACCCCTAAACCTTCCAAAATTCCA----T---CCTA
* * * * *
39243544 ATTTCACCAAAAAATACCATTTTACTCCC-GAA-CTTCCAAAATCCCATTTTTAACCTTG
1 ATTTCACCAAAAATTACCAATTTAC-CCCTAAACCTTCCAAAATTCCA----T--CC-TA
* *
39243602 ATTTCACCAAAAATTACCATTTTACCCCTAAACCTTCCAAAATCCCAT
1 ATTTCACCAAAAATTACCAATTTACCCCTAAACCTTCCAAAATTCCAT
39243650 TTTTAACCCT
Statistics
Matches: 139, Mismatches: 14, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
52 40 0.29
53 4 0.03
55 1 0.01
56 1 0.01
57 5 0.04
58 44 0.32
59 41 0.29
60 3 0.02
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.31
Consensus pattern (52 bp):
ATTTCACCAAAAATTACCAATTTACCCCTAAACCTTCCAAAATTCCATCCTA
Found at i:39243564 original size:31 final size:30
Alignment explanation
Indices: 39243523--39243629 Score: 82
Period size: 31 Copynumber: 3.6 Consensus size: 30
39243513 TAAACTTTCC
*
39243523 AAAATTCCATTTTTAGCCCCGATTTCACCAA
1 AAAATACCATTTTTA-CCCCGATTTCACCAA
*
39243554 AAAATACCA-TTTTACTCCCGAACTT--CC--
1 AAAATACCATTTTTAC-CCCG-ATTTCACCAA
* **
39243581 AAAATCCCATTTTTAACCTTGATTTCACCAA
1 AAAATACCATTTTT-ACCCCGATTTCACCAA
*
39243612 AAATTACCA-TTTTACCCC
1 AAAATACCATTTTTACCCC
39243630 TAAACCTTCC
Statistics
Matches: 58, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
27 11 0.19
28 6 0.10
29 10 0.17
30 13 0.22
31 18 0.31
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAATACCATTTTTACCCCGATTTCACCAA
Found at i:39243670 original size:30 final size:30
Alignment explanation
Indices: 39243577--39243674 Score: 85
Period size: 30 Copynumber: 3.3 Consensus size: 30
39243567 ACTCCCGAAC
*
39243577 TTCCAAAATCCCATTTTTAACCTTG-ATTT
1 TTCCAAAATCCCATTTTTAACCCTGAATTT
** * * ***
39243606 CACCAAAAATTACCA-TTTTACCCCT-AAACC
1 TTCC-AAAA-TCCCATTTTTAACCCTGAATTT
39243636 TTCCAAAATCCCATTTTTAACCCTGAATTT
1 TTCCAAAATCCCATTTTTAACCCTGAATTT
39243666 TTCCAAAAT
1 TTCCAAAAT
39243675 TATATTTTGC
Statistics
Matches: 49, Mismatches: 15, Indels: 9
0.67 0.21 0.12
Matches are distributed among these distances:
28 4 0.08
29 15 0.31
30 26 0.53
31 4 0.08
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.36
Consensus pattern (30 bp):
TTCCAAAATCCCATTTTTAACCCTGAATTT
Found at i:39243676 original size:59 final size:59
Alignment explanation
Indices: 39243485--39243661 Score: 259
Period size: 59 Copynumber: 3.0 Consensus size: 59
39243475 TTCCATCCTA
* * * * *
39243485 ATTTCACCAAAAATTACCAATTTACCCCTAAACTTTCCAAAATTCCATTTTTAGCCCCG
1 ATTTCACCAAAAATTACCATTTTACCCCTAAACCTTCCAAAATCCCATTTTTAACCCTG
* * *
39243544 ATTTCACCAAAAAATACCATTTTACTCCC-GAA-CTTCCAAAATCCCATTTTTAACCTTG
1 ATTTCACCAAAAATTACCATTTTAC-CCCTAAACCTTCCAAAATCCCATTTTTAACCCTG
39243602 ATTTCACCAAAAATTACCATTTTACCCCTAAACCTTCCAAAATCCCATTTTTAACCCTG
1 ATTTCACCAAAAATTACCATTTTACCCCTAAACCTTCCAAAATCCCATTTTTAACCCTG
39243661 A
1 A
39243662 ATTTTTCCAA
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
57 3 0.03
58 47 0.45
59 51 0.49
60 3 0.03
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (59 bp):
ATTTCACCAAAAATTACCATTTTACCCCTAAACCTTCCAAAATCCCATTTTTAACCCTG
Found at i:39246002 original size:89 final size:90
Alignment explanation
Indices: 39245901--39246066 Score: 205
Period size: 89 Copynumber: 1.8 Consensus size: 90
39245891 TAAATTAAAA
* * *
39245901 AAAAAAAGTCAAGTTCAGA-TACCAAATAGGACTC-CAAAAAGTTTA-AGTACCAACTT-AGAAA
1 AAAAAAAGTCAAGTT-AGAGTACCAAATAGAAC-CAAAAAAAGTTTAGA-TACCAAATTAAGAAA
39245962 AAGTATCAAGTTTAGCTATCAAATTAGG
63 AAGTATCAAGTTTAGCTATCAAATTAGG
* * *
39245990 AAAAAATGTCAAGTTTGAGTACCAAATTGAACCAAAAAAAAGTTTAGATACCAAATTAAGAAAAA
1 AAAAAAAGTCAAGTTAGAGTACCAAATAGAACC-AAAAAAAGTTTAGATACCAAATTAAGAAAAA
*
39246055 GTGTCAAGTTTA
65 GTATCAAGTTTA
39246067 TGTACAAAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
88 3 0.05
89 25 0.38
90 18 0.28
91 19 0.29
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.24
Consensus pattern (90 bp):
AAAAAAAGTCAAGTTAGAGTACCAAATAGAACCAAAAAAAGTTTAGATACCAAATTAAGAAAAAG
TATCAAGTTTAGCTATCAAATTAGG
Found at i:39246016 original size:31 final size:29
Alignment explanation
Indices: 39245939--39246076 Score: 102
Period size: 31 Copynumber: 4.6 Consensus size: 29
39245929 GGACTCCAAA
* *
39245939 AAGTTTAAGTACCAACTTAGAAAAAGTATC
1 AAGTTT-AGTACCAAATTAGAAAAAATATC
* *
39245969 AAGTTTAGCTATCAAATTAGGAAAAAATGTC
1 AAGTTTAG-TACCAAATTA-GAAAAAATATC
*
39246000 AAGTTTGAGTACCAAATT-GAACCAAAA-A-A
1 AAGTTT-AGTACCAAATTAGAA--AAAATATC
* *
39246029 AAGTTTAGATACCAAATTAAGAAAAAGTGTC
1 AAGTTTAG-TACCAAATT-AGAAAAAATATC
*
39246060 AAGTTTATGTACAAAAT
1 AAGTTTA-GTACCAAAT
39246077 ATTATATTAA
Statistics
Matches: 86, Mismatches: 11, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
28 2 0.02
29 23 0.27
30 14 0.16
31 44 0.51
32 3 0.03
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (29 bp):
AAGTTTAGTACCAAATTAGAAAAAATATC
Found at i:39251445 original size:29 final size:28
Alignment explanation
Indices: 39251413--39251698 Score: 123
Period size: 29 Copynumber: 9.7 Consensus size: 28
39251403 TATGGATACC
*
39251413 CGGGGGCAAAATGGTAATTTTGGTGTAAT
1 CGGGGGAAAAATGG-AATTTTGGTGTAAT
* *** *
39251442 CGGGGTTTAAAAATGGAATTTTAAAAG-ATT
1 CGGGG--GAAAAATGGAATTTT-GGTGTAAT
* *
39251472 CGGGGGTAAAATGGCAATTTTTGGTGAAAT
1 CGGGGGAAAAATGG-AA-TTTTGGTGTAAT
* * **
39251502 CGGGGTTAAAAATGAAATTTTAGAAGCT--T
1 CGGGG-GAAAAATGGAATTTT-GGTG-TAAT
* * * *
39251531 CAGGGGTAAAATAGTAATTTTCGGTGAAAT
1 CGGGGGAAAAAT-GGAATTTT-GGTGTAAT
* * *
39251561 CGGGGTTAAAAATGGAATTTTGGAAGT-TT
1 CGGGG-GAAAAATGGAATTTTGG-TGTAAT
* *
39251590 CGGGGGTAAAATGGTAATTTTCGGTGAAAT
1 CGGGGGAAAAATGG-AATTTT-GGTGTAAT
** * *
39251620 CGGAGTTAAAAATGGAATTTTGGAAGT-TT
1 CGG-GGGAAAAATGGAATTTTGG-TGTAAT
*
39251649 CGGGGGTAAAATGGTAATTTTGGTGTAAT
1 CGGGGGAAAAATGG-AATTTTGGTGTAAT
*
39251678 TGGGGTGAAAAATGGAATTTT
1 CGGGG-GAAAAATGGAATTTT
39251699 AAAAGATTTA
Statistics
Matches: 184, Mismatches: 51, Indels: 44
0.66 0.18 0.16
Matches are distributed among these distances:
28 29 0.16
29 66 0.36
30 62 0.34
31 27 0.15
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (28 bp):
CGGGGGAAAAATGGAATTTTGGTGTAAT
Found at i:39251476 original size:59 final size:58
Alignment explanation
Indices: 39251413--39251728 Score: 425
Period size: 59 Copynumber: 5.4 Consensus size: 58
39251403 TATGGATACC
* * *
39251413 CGGGGGCAAAATGGTAATTTTGGTGTAATCGGGGTTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGG-TTAAAAATGGAATTTTAGAAGATT
* * *
39251472 CGGGGGTAAAATGGCAATTTTTGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
* * * *
39251531 CAGGGGTAAAATAGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTT
1 CGGGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
* * *
39251590 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGAGTTAAAAATGGAATTTTGGAAGTTT
1 CGGGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
* * * *
39251649 CGGGGGTAAAATGGTAATTTTGGTGTAATTGGGGTGAAAAATGGAATTTTAAAAGATTT
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGA-TT
*
39251708 AGGGGGTAAAATGGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
39251729 TGAAAGATTT
Statistics
Matches: 231, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
58 32 0.14
59 183 0.79
60 16 0.07
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (58 bp):
CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
Found at i:39251718 original size:29 final size:28
Alignment explanation
Indices: 39251686--39251757 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 28
39251676 ATTGGGGTGA
39251686 AAAATGGAATTTTAAAAGATTTAGGGGGT
1 AAAATGGAATTTTAAAAGATTTA-GGGGT
* *
39251715 AAAATGGTAATTTTTGAAAGATTTAGGGTT
1 AAAATGG-AA-TTTTAAAAGATTTAGGGGT
*
39251745 AAAATGTAATTTT
1 AAAATGGAATTTT
39251758 GGAAAAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 4 0.11
29 9 0.24
30 12 0.32
31 13 0.34
ACGTcount: A:0.40, C:0.00, G:0.22, T:0.38
Consensus pattern (28 bp):
AAAATGGAATTTTAAAAGATTTAGGGGT
Found at i:39251748 original size:30 final size:29
Alignment explanation
Indices: 39251686--39251882 Score: 141
Period size: 30 Copynumber: 6.6 Consensus size: 29
39251676 ATTGGGGTGA
* * *
39251686 AAAATGGAATTTT-AAAAGATTTAGGGGGT
1 AAAATGTAATTTTGGAAAGATTTA-GGGTT
*
39251715 AAAATGGTAATTTTTGAAAGATTTAGGGTT
1 AAAAT-GTAATTTTGGAAAGATTTAGGGTT
* *
39251745 AAAATGTAATTTTGGAAA-AGTTTTGGTGTC
1 AAAATGTAATTTTGGAAAGA-TTTAGG-GTT
* * *
39251775 AAAATATAATTTTGGAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGG-AAAGATTTAGGGTT
* * *
39251805 AAAATGTAATTCTGGAAA-AGTTTCGGGGTC
1 AAAATGTAATTTTGGAAAGA-TTT-AGGGTT
* * *
39251835 AAAATATAATTTTGGAAA-AGTTTCGGGGTC
1 AAAATGTAATTTTGGAAAGA-TTT-AGGGTT
*
39251865 AAAATATAATTTTGGAAA
1 AAAATGTAATTTTGGAAA
39251883 AGTTTTGAGG
Statistics
Matches: 144, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.01
29 28 0.19
30 98 0.68
31 17 0.12
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAGATTTAGGGTT
Found at i:39251883 original size:30 final size:30
Alignment explanation
Indices: 39251722--39251911 Score: 256
Period size: 30 Copynumber: 6.3 Consensus size: 30
39251712 GGTAAAATGG
* * * * *
39251722 TAATTTTTG-AAAGATTTAGGGTTAAAATG
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
*
39251751 TAATTTTGGAAAAGTTTTGGTGTCAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
* *
39251781 TAATTTTGGAAAAGTTTTGGGGTTAAAATG
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
* *
39251811 TAATTCTGGAAAAGTTTCGGGGTCAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
*
39251841 TAATTTTGGAAAAGTTTCGGGGTCAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
*
39251871 TAATTTTGGAAAAGTTTTGAGGTCAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
39251901 TAATTTCTGGA
1 TAATTT-TGGA
39251912 TTGTTTGGGG
Statistics
Matches: 143, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
29 8 0.06
30 131 0.92
31 4 0.03
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.37
Consensus pattern (30 bp):
TAATTTTGGAAAAGTTTTGGGGTCAAAATA
Found at i:39252299 original size:158 final size:162
Alignment explanation
Indices: 39252000--39252314 Score: 446
Period size: 158 Copynumber: 2.0 Consensus size: 162
39251990 ACCCATTTGA
*
39252000 AAACCTTGAAAAATTTTAGGACCAATTTTGTAATTAAATAAAAGTTGATTTAAGGATTAAATTAA
1 AAACCTTGAAAAATTTTAGGACCAATTTCGTAATTAAATAAAAGTTGATTTAAGGATTAAATTAA
*
39252065 AACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGACGACACGTGGCAACCTC
66 AACAAA-TAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGACGACACGTGGCAACCTA
*
39252130 TGGTGCAGTCAAACAGTCAAAGGACTAGTTTAT
130 TGGTACAGTCAAACAGTCAAAGGACTAGTTTAT
* *
39252163 AAACCTTGAAAAATTATT-GGGCCAA-TTCGTAATTAAA-ATAAAGTTGATTT-GGGATTAAATT
1 AAACCTTGAAAAATT-TTAGGACCAATTTCGTAATTAAATA-AAAGTTGATTTAAGGATTAAATT
* * * * *
39252224 AAAA-TAA-AAAAATAAAAAAGGACTAAATGCATAAATAATCCAAAAAG-TGACACGTGGCAGCC
64 AAAACAAATAAAAAT-AAAAAGGACTAAATACAGAAATAATCCAAAAAGACGACACGTGGCAACC
*
39252286 TATGGTACGGTCAAACAGTCAAAGGACTA
128 TATGGTACAGTCAAACAGTCAAAGGACTA
39252315 AATTGAAAAG
Statistics
Matches: 138, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
158 45 0.33
159 31 0.22
160 2 0.01
161 15 0.11
162 22 0.16
163 21 0.15
164 2 0.01
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (162 bp):
AAACCTTGAAAAATTTTAGGACCAATTTCGTAATTAAATAAAAGTTGATTTAAGGATTAAATTAA
AACAAATAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGACGACACGTGGCAACCTAT
GGTACAGTCAAACAGTCAAAGGACTAGTTTAT
Found at i:39253810 original size:6 final size:6
Alignment explanation
Indices: 39253794--39253882 Score: 89
Period size: 6 Copynumber: 15.0 Consensus size: 6
39253784 TTAAATTTGT
**
39253794 TTTATAA TTTAAA TTTAAA TTTAAA TTT-AA GGTAAA TTTAAA TAATTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
39253844 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA --TAAA TTTAAA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
39253883 ATCAATTTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
4 5 0.07
5 6 0.09
6 48 0.69
7 5 0.07
8 6 0.09
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:39253831 original size:11 final size:11
Alignment explanation
Indices: 39253815--39253865 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
39253805 AATTTAAATT
*
39253815 TAAATTTAAGG
1 TAAATTTAAGA
39253826 TAAATTTAA-A
1 TAAATTTAAGA
* **
39253836 T-AATTAAATT
1 TAAATTTAAGA
39253846 TAAATTTAAGA
1 TAAATTTAAGA
39253857 TAAATTTAA
1 TAAATTTAA
39253866 ATTTAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 24 0.75
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (11 bp):
TAAATTTAAGA
Found at i:39253867 original size:37 final size:38
Alignment explanation
Indices: 39253806--39253882 Score: 95
Period size: 37 Copynumber: 2.0 Consensus size: 38
39253796 TATAATTTAA
*
39253806 ATTTAAATTTAAATTTAAGGTAAATTTAAATAA-TTAA
1 ATTTAAATTTAAATTAAAGGTAAATTTAAATAATTTAA
**
39253843 ATTTAAATTTAAGA-TAAATTTAAATTTAAATAAATTTAA
1 ATTTAAATTTAA-ATTAAAGGTAAATTTAAAT-AATTTAA
39253882 A
1 A
39253883 ATCAATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 26 0.76
38 3 0.09
39 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (38 bp):
ATTTAAATTTAAATTAAAGGTAAATTTAAATAATTTAA
Found at i:39253884 original size:17 final size:16
Alignment explanation
Indices: 39253794--39253882 Score: 101
Period size: 17 Copynumber: 5.4 Consensus size: 16
39253784 TTAAATTTGT
39253794 TTTATAATTTAAATTTAAA
1 TTTA-AATTTAAA--TAAA
*
39253813 TTTAAATTTAAGGTAAA
1 TTTAAATTTAA-ATAAA
*
39253830 TTTAAA--TAATTAAA
1 TTTAAATTTAAATAAA
39253844 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
39253861 TTTAAATTTAAATAAA
1 TTTAAATTTAAATAAA
39253877 TTTAAA
1 TTTAAA
39253883 ATCAATTTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.16
15 3 0.05
16 14 0.22
17 25 0.40
18 7 0.11
19 4 0.06
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:39254226 original size:31 final size:31
Alignment explanation
Indices: 39254191--39254617 Score: 147
Period size: 37 Copynumber: 12.4 Consensus size: 31
39254181 CTATCCAACT
*
39254191 TTACTTCAATTTCAAGAGGATGACATTGCCC
1 TTACTTCAATTTCAAGAGGATGACGTTGCCC
* * *
39254222 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCAC
1 TTACTTCAATTTCA-AGAGGATGAC--GTT-GCC-C
* *
39254258 TCTACTTCAATTTCAAAGGGGATGACGTTGCTC
1 T-TACTTCAATTTC-AAGAGGATGACGTTGCCC
* * * *
39254291 TTACTTCAATTTCGGAGATGAAGACGTTTTATCCAC
1 TTACTTCAATTTC-AAGAGGATGACG--TT-GCC-C
* * * *
39254327 TCTACTTCAATTTCAAGGGGACG-TGTTATCCAC
1 T-TACTTCAATTTCAAGAGGATGACGTT-GCC-C
* * *
39254360 TCTACTTCAATTTCAAGGGGATGAGGTTGCTC
1 T-TACTTCAATTTCAAGAGGATGACGTTGCCC
* * * *
39254392 TTACTTCAATTTCGGAGATGAAGACCTGTTATCCAC
1 TTACTTCAATTTC-AAGAGGATGA-C-GTT-GCC-C
* *
39254428 TCTACTTCAATTTCAAGGGGATGAAGACGCGTTATCCAC
1 T-TACTTCAATTTCAAGAGGAT---GA--CGTT-GCC-C
* * * *
39254467 TCTACTTCAATTTCAGGGGGATGACATTGCTC
1 T-TACTTCAATTTCAAGAGGATGACGTTGCCC
* * *
39254499 TTACTTCAATTTCAGAGATGAAGACGTTTTATCCGC
1 TTACTTCAATTTCA-AGAGGATGACG--TT-GCC-C
*
39254535 TCTACTTCAATTTCAAG-GGATGAAGACGTGTTATCCAC
1 T-TACTTCAATTTCAAGAGGAT---GAC--GTT-GCC-C
* *
39254573 TCTACTTCAATTTCAAGGGGATGACGTTGCTC
1 T-TACTTCAATTTCAAGAGGATGACGTTGCCC
39254605 TTACTTCAATTTC
1 TTACTTCAATTTC
39254618 GGAGATGAAG
Statistics
Matches: 308, Mismatches: 53, Indels: 70
0.71 0.12 0.16
Matches are distributed among these distances:
31 51 0.17
32 46 0.15
33 35 0.11
34 19 0.06
35 11 0.04
36 24 0.08
37 56 0.18
38 28 0.09
39 36 0.12
40 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (31 bp):
TTACTTCAATTTCAAGAGGATGACGTTGCCC
Found at i:39254269 original size:68 final size:70
Alignment explanation
Indices: 39254182--39254771 Score: 423
Period size: 69 Copynumber: 8.4 Consensus size: 70
39254172 AAGACTTCGC
* *
39254182 TATCCAACTTTACTTCAATTTCAAGAGGATGACATTGCC-CT-TACTTCAATTTCAGAGATGAAG
1 TATCC-ACTCTACTTCAATTTCAAGAGGATGACGTTGCCACTCTACTTCAATTTCAGAGATGAAG
39254245 ACGTGT
65 ACGTGT
* * *
39254251 TATCCACTCTACTTCAATTTCAAAGGGGATGACGTTG-CTCT-TACTTCAATTTCGGAGATGAAG
1 TATCCACTCTACTTCAATTTC-AAGAGGATGACGTTGCCACTCTACTTCAATTTCAGAGATGAAG
*
39254314 ACGTTT
65 ACGTGT
* * * * ** *
39254320 TATCCACTCTACTTCAATTTCAAGGGGACG-TGTTATCCACTCTACTTCAATTTCA-AGGGGATG
1 TATCCACTCTACTTCAATTTCAAGAGGATGACGTT-GCCACTCTACTTCAATTTCAGAGATGAAG
39254383 A-G-G-
65 ACGTGT
* * * * * * *
39254386 T-TGCTCT-TACTTCAATTTCGGAGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGA
1 TATCCACTCTACTTCAATTTC-AAGAGGATGA-C-GTT-GCCACTCTACTTCAATTTC-A-GAGA
*
39254449 TGAAGACGCGT
60 TGAAGACGTGT
* * * *
39254460 TATCCACTCTACTTCAATTTCAGGGGGATGACATTG-CTCT-TACTTCAATTTCAGAGATGAAGA
1 TATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCCACTCTACTTCAATTTCAGAGATGAAGA
*
39254523 CGTTT
66 CGTGT
* * *
39254528 TATCCGCTCTACTTCAATTTCAAG-GGATGAAGACGTGTTATCCACTCTACTTCAATTTCA-AGG
1 TATCCACTCTACTTCAATTTCAAGAGGAT---GAC--GTT-GCCACTCTACTTCAATTTCAGAGA
* *
39254591 GGATGAC--G-
60 TGAAGACGTGT
* * * * * * * *
39254599 T-TGCTCT-TACTTCAATTTCGGAGATGAAGACCTGTTATCCACTCTACTCCAATTTCAAGGGGA
1 TATCCACTCTACTTCAATTTC-AAGAGGATGA-C-GTT-GCCACTCTACTTCAATTTC-A-GAGA
*
39254662 TGAAGACGCGT
60 TGAAGACGTGT
* * *
39254673 TATCCAACTCTACTTCACTTTCAAGAGGATGAGGTTG-CTCT-TACTTCAATTTCAGAGATGAAG
1 TATCC-ACTCTACTTCAATTTCAAGAGGATGACGTTGCCACTCTACTTCAATTTCAGAGATGAAG
39254736 ACGTGT
65 ACGTGT
*
39254742 TATCCAACTCTACTTCAATTTCGAGAGGAT
1 TATCC-ACTCTACTTCAATTTCAAGAGGAT
39254772 AAGGTTGATC
Statistics
Matches: 413, Mismatches: 71, Indels: 74
0.74 0.13 0.13
Matches are distributed among these distances:
64 12 0.03
65 9 0.02
66 1 0.00
67 7 0.02
68 107 0.26
69 133 0.32
70 34 0.08
71 28 0.07
72 6 0.01
73 4 0.01
74 16 0.04
75 24 0.06
76 21 0.05
77 11 0.03
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (70 bp):
TATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCCACTCTACTTCAATTTCAGAGATGAAGA
CGTGT
Found at i:39254517 original size:107 final size:106
Alignment explanation
Indices: 39254223--39254763 Score: 842
Period size: 106 Copynumber: 5.1 Consensus size: 106
39254213 ACATTGCCCT
*
39254223 TACTTCAATTTC-AGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGTT
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTC-AAGGGGATGACGTT
*
39254287 GCTCTTACTTCAATTTCGGAGATGAAGACGTTTTATCCACTC
65 GCTCTTACTTCAATTTCGGAGATGAAGACGTGTTATCCACTC
*
39254329 TACTTCAATTTCAA-GG--G--GACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAGGTTG
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
*
39254389 CTCTTACTTCAATTTCGGAGATGAAGACCTGTTATCCACTC
66 CTCTTACTTCAATTTCGGAGATGAAGACGTGTTATCCACTC
* * *
39254430 TACTTCAATTTCAAGGGGATGAAGACGCGTTATCCACTCTACTTCAATTTCAGGGGGATGACATT
1 TACTTCAATTTCAA-GGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTT
* * *
39254495 GCTCTTACTTCAATTTCAGAGATGAAGACGTTTTATCCGCTC
65 GCTCTTACTTCAATTTCGGAGATGAAGACGTGTTATCCACTC
39254537 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
*
39254602 CTCTTACTTCAATTTCGGAGATGAAGACCTGTTATCCACTC
66 CTCTTACTTCAATTTCGGAGATGAAGACGTGTTATCCACTC
* * * * *
39254643 TACTCCAATTTCAAGGGGATGAAGACGCGTTATCCAACTCTACTTCACTTTCAAGAGGATGAGGT
1 TACTTCAATTTCAA-GGGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACGT
*
39254708 TGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTC
64 TGCTCTTACTTCAATTTCGGAGATGAAGACGTGTTATCC-ACTC
39254752 TACTTCAATTTC
1 TACTTCAATTTC
39254764 GAGAGGATAA
Statistics
Matches: 398, Mismatches: 27, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
101 67 0.17
102 28 0.07
103 2 0.01
104 1 0.00
105 1 0.00
106 111 0.28
107 110 0.28
108 63 0.16
109 15 0.04
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (106 bp):
TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
CTCTTACTTCAATTTCGGAGATGAAGACGTGTTATCCACTC
Found at i:39254557 original size:38 final size:38
Alignment explanation
Indices: 39254500--39254763 Score: 233
Period size: 38 Copynumber: 7.3 Consensus size: 38
39254490 ACATTGCTCT
* * *
39254500 TACTTCAATTTC-AGAGATGAAGACGTTTTATCCGCTC
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
39254537 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
* * *
39254575 TACTTCAATTTCAAGGG--GATGAC--G-T-TGCTCT-
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
*
39254606 TACTTCAATTTC--GGAGATGAAGACCTGTTATCCACTC
1 TACTTCAATTTCAAGG-GATGAAGACGTGTTATCCACTC
* *
39254643 TACTCCAATTTCAAGGGGATGAAGACGCGTTATCCAACTC
1 TACTTCAATTTCAA-GGGATGAAGACGTGTTATCC-ACTC
* * *
39254683 TACTTCACTTTCAAGAGGAT---GA-G-G-T-TGCTCT-
1 TACTTCAATTTCAAG-GGATGAAGACGTGTTATCCACTC
*
39254714 TACTTCAATTTC-AGAGATGAAGACGTGTTATCCAACTC
1 TACTTCAATTTCAAGGGATGAAGACGTGTTATCC-ACTC
39254752 TACTTCAATTTC
1 TACTTCAATTTC
39254764 GAGAGGATAA
Statistics
Matches: 184, Mismatches: 20, Indels: 45
0.74 0.08 0.18
Matches are distributed among these distances:
29 5 0.03
30 3 0.02
31 23 0.12
32 13 0.07
33 4 0.02
34 4 0.02
35 3 0.02
36 12 0.07
37 27 0.15
38 51 0.28
39 17 0.09
40 22 0.12
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (38 bp):
TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
Found at i:39254627 original size:213 final size:208
Alignment explanation
Indices: 39254223--39254763 Score: 888
Period size: 213 Copynumber: 2.6 Consensus size: 208
39254213 ACATTGCCCT
* *
39254223 TACTTCAATTTC-A-GAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGT
1 TACTTCAATTTCAAGGGGATGAAGACGCGTTATCCACTCTACTTCAATTTC-AAGGGGATGACGT
*
39254286 TGCTCTTACTTCAATTTCGGAGATGAAGACGTTTTATCCACTCTACTTCAATTTCAAGGGGACGT
65 TGCTCTTACTTCAATTTCAGAGATGAAGACGTTTTATCCACTCTACTTCAATTTCAAGGGGACGT
*
39254351 GTTATCCACTCTACTTCAATTTCAAGGGGATGAGGTTGCTCTTACTTCAATTTCGGAGATGAAGA
130 GTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCGGAGATGAAGA
39254416 CCTGTTATCCACTC
195 CCTGTTATCCACTC
* *
39254430 TACTTCAATTTCAAGGGGATGAAGACGCGTTATCCACTCTACTTCAATTTCAGGGGGATGACATT
1 TACTTCAATTTCAAGGGGATGAAGACGCGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTT
*
39254495 GCTCTTACTTCAATTTCAGAGATGAAGACGTTTTATCCGCTCTACTTCAATTTCAAGGGATGAAG
66 GCTCTTACTTCAATTTCAGAGATGAAGACGTTTTATCCACTCTACTTCAATTTCAA-GG--G--G
39254560 ACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCGGAGATG
126 ACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCGGAGATG
39254625 AAGACCTGTTATCCACTC
191 AAGACCTGTTATCCACTC
* * * *
39254643 TACTCCAATTTCAAGGGGATGAAGACGCGTTATCCAACTCTACTTCACTTTCAAGAGGATGAGGT
1 TACTTCAATTTCAAGGGGATGAAGACGCGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACGT
*
39254708 TGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTC
65 TGCTCTTACTTCAATTTCAGAGATGAAGACGTTTTATCC-ACTCTACTTCAATTTC
39254764 GAGAGGATAA
Statistics
Matches: 310, Mismatches: 15, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
207 12 0.04
208 67 0.22
209 36 0.12
211 1 0.00
213 117 0.38
214 62 0.20
215 15 0.05
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (208 bp):
TACTTCAATTTCAAGGGGATGAAGACGCGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTT
GCTCTTACTTCAATTTCAGAGATGAAGACGTTTTATCCACTCTACTTCAATTTCAAGGGGACGTG
TTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCGGAGATGAAGAC
CTGTTATCCACTC
Found at i:39254683 original size:40 final size:39
Alignment explanation
Indices: 39254621--39254771 Score: 117
Period size: 40 Copynumber: 4.1 Consensus size: 39
39254611 CAATTTCGGA
*
39254621 GATGAAGACCTGTTATCCACTCTACTCCAATTTCAAGGG
1 GATGAAGACCTGTTATCCACTCTACTCCAATTTCAAGAG
* *
39254660 GATGAAGACGC-GTTATCCAACTCTACTTCACTTTCAAGAG
1 GATGAAGAC-CTGTTATCC-ACTCTACTCCAATTTCAAGAG
* * *
39254700 GATG-AG----G-T-TGCTCT-TACTTCAATTTC-AGA-
1 GATGAAGACCTGTTATCCACTCTACTCCAATTTCAAGAG
* * *
39254729 GATGAAGACGTGTTATCCAACTCTACTTCAATTTCGAGAG
1 GATGAAGACCTGTTATCC-ACTCTACTCCAATTTCAAGAG
39254769 GAT
1 GAT
39254772 AAGGTTGATC
Statistics
Matches: 91, Mismatches: 8, Indels: 25
0.73 0.06 0.20
Matches are distributed among these distances:
29 4 0.04
30 5 0.05
31 11 0.12
32 2 0.02
33 2 0.02
34 2 0.02
35 2 0.02
36 2 0.02
37 2 0.02
38 12 0.13
39 21 0.23
40 26 0.29
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (39 bp):
GATGAAGACCTGTTATCCACTCTACTCCAATTTCAAGAG
Found at i:39267004 original size:58 final size:59
Alignment explanation
Indices: 39266880--39267253 Score: 481
Period size: 58 Copynumber: 6.4 Consensus size: 59
39266870 TATGGATACC
* * *
39266880 CGGGGGCAAAATGGTAA-TTTTGGTGTAATCGGGGTTTAAAAATGGAATTTTA-AAATATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGG-TTAAAAATGGAATTTTAGAAGT-TT
* * ** * *
39266939 CGGGGGTAAAATGGCAATTTTTGGTAAAATTAGGGTT-AAAATGAAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTT
* * * *
39266997 CAGGGGTAAAACGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAGTTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTT
* * *
39267056 CGAGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTT-AAAATGGAATTTTGGAAGTTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTT
* * * *
39267114 CGGGGGTAAAATGGTAATTTTCGATGAAATCGGAGTTAAAAATGGAATTTTGGAAGTTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTT
* *
39267173 CGGGGGTAAAATGGTAA-TTTTGGTGTAATCGGGGTTAAAAATGGAATTTTAAAAGATTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAG-TTT
39267232 -GGGGGTAAAATGGTAATTTTTG
1 CGGGGGTAAAATGGTAATTTTTG
39267254 AAAGTTTTGG
Statistics
Matches: 276, Mismatches: 33, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
58 148 0.54
59 115 0.42
60 13 0.05
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTT
Found at i:39267031 original size:29 final size:30
Alignment explanation
Indices: 39266887--39267222 Score: 142
Period size: 30 Copynumber: 11.5 Consensus size: 30
39266877 ACCCGGGGGC
*
39266887 AAAATGGTAA-TTTTGGTGTAATCGGGGTTT
1 AAAATGGTAATTTTTGGTGAAATCGGGG-TT
** *
39266917 AAAAATGG-AA-TTTT--AAAATATTCGGGGGT
1 -AAAATGGTAATTTTTGGTGAA-A-TCGGGGTT
* * **
39266946 AAAATGGCAATTTTTGGTAAAATTAGGGTT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTT
* * ** **
39266976 AAAAT-GAAATTTTAGAAG-CTTCAGGGG-T
1 AAAATGGTAATTTTTGGTGAAATC-GGGGTT
*
39267004 AAAACGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTT
* *
39267034 AAAAATAG-AA-TTTT-G-GAAGTTTCGAGGG-T
1 -AAAATGGTAATTTTTGGTGAA--ATCG-GGGTT
*
39267063 AAAATGGTAATTTTCGGTGAAATCGGGGTT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTT
* *
39267093 AAAATGG-AA-TTTT-G-GAAGTTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAA--ATCGGGGTT
* * *
39267121 AAAATGGTAATTTTCGATGAAATCGGAGTT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTT
* *
39267151 AAAAATGG-AA-TTTT-G-GAAGTTTCGGGGGT
1 -AAAATGGTAATTTTTGGTGAA--ATCGGGGTT
*
39267180 AAAATGGTAA-TTTTGGTGTAATCGGGGTT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTT
39267209 AAAAATGG-AATTTT
1 -AAAATGGTAATTTT
39267223 AAAAGATTTG
Statistics
Matches: 226, Mismatches: 46, Indels: 67
0.67 0.14 0.20
Matches are distributed among these distances:
26 3 0.01
27 7 0.03
28 45 0.20
29 69 0.31
30 70 0.31
31 23 0.10
32 9 0.04
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTT
Found at i:39267045 original size:117 final size:117
Alignment explanation
Indices: 39266880--39267253 Score: 493
Period size: 117 Copynumber: 3.2 Consensus size: 117
39266870 TATGGATACC
* * * *
39266880 CGGGGGCAAAATGGTAA-TTTTGGTGTAATCGGGGTTTAAAAATGGAATTTT-AAAATATTCGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGG-TTAAAAATGGAATTTTGGAAGT-TTCGGG
* * ** * *
39266943 GGTAAAATGGCAATTTTTGGTAAAATTAGGGTTAAAATGAAATTTTAGAAGCTT
64 GGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTAGAAGATT
* * * *
39266997 CAGGGGTAAAACGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAGTTTCGAGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTTCGGGGG
* * *
39267062 TAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAATGGAATTTTGGAAGTTT
66 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTAGAAGATT
* * *
39267114 CGGGGGTAAAATGGTAATTTTCGATGAAATCGGAGTTAAAAATGGAATTTTGGAAGTTTCGGGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTTCGGGGG
* *
39267179 TAAAATGGTAA-TTTTGGTGTAATCGGGGTTAAAAATGGAATTTTAAAAGATT
66 TAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTAGAAGATT
*
39267231 TGGGGGTAAAATGGTAATTTTTG
1 CGGGGGTAAAATGGTAATTTTTG
39267254 AAAGTTTTGG
Statistics
Matches: 224, Mismatches: 30, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
116 17 0.08
117 188 0.84
118 19 0.08
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (117 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTTCGGGGG
TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTAGAAGATT
Found at i:39267235 original size:29 final size:30
Alignment explanation
Indices: 39267148--39267391 Score: 147
Period size: 30 Copynumber: 8.2 Consensus size: 30
39267138 TGAAATCGGA
* *
39267148 GTTAAAAATGGAATTTTG-GAAGTTTCGGG
1 GTTAAAAATGGAATTTTGAAAAGTTTTGGG
* ** * *
39267177 GGT-AAAATGGTAATTTTG--GTGTAATCGGG
1 GTTAAAAATGG-AATTTTGAAAAGT-TTTGGG
*
39267206 GTTAAAAATGGAATTTT-AAAAGATTTGGG
1 GTTAAAAATGGAATTTTGAAAAGTTTTGGG
*
39267235 GGT-AAAATGGTAATTTTTG-AAAGTTTTGGG
1 GTTAAAAATGG-AA-TTTTGAAAAGTTTTGGG
*
39267265 GTT-AAAATGTAATTTTGGAAAAGTTTTGGG
1 GTTAAAAATGGAATTTT-GAAAAGTTTTGGG
*
39267295 GTCAAAATAT--AATTTTGGAAAAGTTTTGGG
1 GTTAAAA-ATGGAATTTT-GAAAAGTTTTGGG
* *
39267325 GTTAAAATAT--AATTCTAGAAAAGTTTCGGG
1 GTTAAAA-ATGGAATT-TTGAAAAGTTTTGGG
* *
39267355 GTCAAAATAT--AATTTTGGAAAAGTTTTAGG
1 GTTAAAA-ATGGAATTTT-GAAAAGTTTTGGG
*
39267385 GTCAAAA
1 GTTAAAA
39267392 TATAATTTTT
Statistics
Matches: 179, Mismatches: 22, Indels: 27
0.79 0.10 0.12
Matches are distributed among these distances:
28 20 0.11
29 34 0.19
30 119 0.66
31 4 0.02
32 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (30 bp):
GTTAAAAATGGAATTTTGAAAAGTTTTGGG
Found at i:39267237 original size:30 final size:28
Alignment explanation
Indices: 39267087--39267332 Score: 113
Period size: 30 Copynumber: 8.4 Consensus size: 28
39267077 CGGTGAAATC
**
39267087 GGGGTTAAAATGGAATTTTGGAAGTTTCG
1 GGGGTTAAAATGGAATTTTAAAAGTTT-G
** * ** *
39267116 GGGG-TAAAATGGTAATTTTCGATGAAATC
1 GGGGTTAAAATGG-AATTTTAAAAG-TTTG
* **
39267145 GGAGTTAAAAATGGAATTTTGGAAGTTTCG
1 GGGGTT-AAAATGGAATTTTAAAAGTTT-G
*** * *
39267175 GGGG-TAAAATGGTAATTTT-GGTGTAATC
1 GGGGTTAAAATGG-AATTTTAAAAGT-TTG
39267203 GGGGTTAAAAATGGAATTTTAAAAGATTTG
1 GGGGTT-AAAATGGAATTTTAAAAG-TTTG
* *
39267233 GGGG-TAAAATGGTAATTTTTGAAAGTTTT
1 GGGGTTAAAATGG-AA-TTTTAAAAGTTTG
* *
39267262 GGGGTTAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTTAAAATGGAATTTT--AAAAGTTTG
* ** *
39267292 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTTAAAATGGAATTTT--AAAAGTTTG
39267322 GGGGTTAAAAT
1 GGGGTTAAAAT
39267333 ATAATTCTAG
Statistics
Matches: 173, Mismatches: 28, Indels: 31
0.75 0.12 0.13
Matches are distributed among these distances:
28 33 0.19
29 44 0.25
30 88 0.51
31 8 0.05
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.35
Consensus pattern (28 bp):
GGGGTTAAAATGGAATTTTAAAAGTTTG
Found at i:39267296 original size:59 final size:55
Alignment explanation
Indices: 39266881--39267315 Score: 383
Period size: 58 Copynumber: 7.5 Consensus size: 55
39266871 ATGGATACCC
* * * *
39266881 GGGGGCAAAATGGTAATTTTGGTGTAATCGGGGTTTAAAAATGGAATTTT-AAAATATT
1 GGGGGTAAAATGGTAATTTT-GTGAAATCGGGG-TT-AAAATGGAATTTTGGAAGT-TT
* * ** * * *
39266939 CGGGGGTAAAATGGCAATTTTTGGTAAAATTAGGGTTAAAATGAAATTTTAGAAGCTTC
1 -GGGGGTAAAATGGTAA-TTTT-GTGAAATCGGGGTTAAAATGGAATTTTGGAAG-TTT
* * *
39266998 AGGGGTAAAACGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAGTTT
1 GGGGGTAAAATGGTAA-TTTT-GTGAAATCGGGGTT-AAAATGGAATTTTGGAAGTTT
*
39267056 CGAGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAATGGAATTTTGGAAGTTT
1 -GGGGGTAAAATGGTAATTTT--GTGAAATCGGGGTTAAAATGGAATTTTGGAAGTTT
*
39267114 CGGGGGTAAAATGGTAATTTTCGATGAAATCGGAGTTAAAAATGGAATTTTGGAAGTTT
1 -GGGGGTAAAATGGTAATTTT-G-TGAAATCGGGGTT-AAAATGGAATTTTGGAAGTTT
* **
39267173 CGGGGGTAAAATGGTAATTTTGGTGTAATCGGGGTTAAAAATGGAATTTTAAAAGATTT
1 -GGGGGTAAAATGGTAATTTT-GTGAAATCGGGGTT-AAAATGGAATTTTGGAAG-TTT
* *
39267232 GGGGGTAAAATGGTAATTTT-TGAAAGTTTTGGGGTTAAAATGTAATTTTGGAAAAGTTT
1 GGGGGTAAAATGGTAATTTTGTGAAA---TCGGGGTTAAAATGGAATTTTGG--AAGTTT
* *
39267291 TGGGGTCAAAAT-ATAATTTTG-GAAA
1 GGGGGT-AAAATGGTAATTTTGTGAAA
39267316 AGTTTTGGGG
Statistics
Matches: 321, Mismatches: 39, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
56 4 0.01
57 1 0.00
58 160 0.50
59 134 0.42
60 22 0.07
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (55 bp):
GGGGGTAAAATGGTAATTTTGTGAAATCGGGGTTAAAATGGAATTTTGGAAGTTT
Found at i:39267296 original size:117 final size:111
Alignment explanation
Indices: 39266881--39267312 Score: 431
Period size: 117 Copynumber: 3.7 Consensus size: 111
39266871 ATGGATACCC
* * * *
39266881 GGGGGCAAAATGGTAATTTTGGTGTAATCGGGGTTTAAAAATGGAATTTT-AAAATATTCGGGGG
1 GGGGGTAAAATGGTAATTTT-GTGAAATCGGGG-TTAAAAAT-GAATTTTGGAAGT-TTC-GGGG
* * ** * *
39266945 TAAAATGGCAATTTTTGGTAAAATTAGGGTTAAAATGAAATTTTAGAAGCTTC
61 TAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAATGGAATTTTAGAAG-TTT
* *
39266998 AGGGGTAAAACGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAGTTTCGAGGGT
1 GGGGGTAAAATGGTAA-TTTT-GTGAAATCGGGGTTAAAAAT-GAATTTTGGAAGTTTCG-GGGT
*
39267063 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAATGGAATTTTGGAAGTTT
62 AAAATGGTAATTTT-GGTGAAATCGGGGTTAAAATGGAATTTTAGAAGTTT
*
39267114 CGGGGGTAAAATGGTAATTTTCGATGAAATCGGAGTTAAAAATGGAATTTTGGAAGTTTCGGGGG
1 -GGGGGTAAAATGGTAATTTT-G-TGAAATCGGGGTTAAAAAT-GAATTTTGGAAGTTTC-GGGG
* *
39267179 TAAAATGGTAATTTTGGTGTAATCGGGGTTAAAAATGGAATTTTAAAAGATTT
61 TAAAATGGTAATTTTGGTGAAATCGGGGTT-AAAATGGAATTTTAGAAG-TTT
* *
39267232 GGGGGTAAAATGGTAATTTT-TGAAAGTTTTGGGGTT-AAAATGTAATTTTGGAAAAGTTTTGGG
1 GGGGGTAAAATGGTAATTTTGTGAAA---TCGGGGTTAAAAATG-AATTTTGG--AAGTTTCGGG
*
39267295 GTCAAAAT-ATAATTTTGG
60 GT-AAAATGGTAATTTTGG
39267313 AAAAGTTTTG
Statistics
Matches: 273, Mismatches: 26, Indels: 32
0.82 0.08 0.10
Matches are distributed among these distances:
114 5 0.02
115 1 0.00
116 39 0.14
117 194 0.71
118 34 0.12
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (111 bp):
GGGGGTAAAATGGTAATTTTGTGAAATCGGGGTTAAAAATGAATTTTGGAAGTTTCGGGGTAAAA
TGGTAATTTTGGTGAAATCGGGGTTAAAATGGAATTTTAGAAGTTT
Found at i:39267333 original size:30 final size:30
Alignment explanation
Indices: 39267203--39267400 Score: 233
Period size: 30 Copynumber: 6.6 Consensus size: 30
39267193 TGGTGTAATC
*
39267203 GGGGTTAAAA-ATGGAATTTT--AAAAGATTT
1 GGGGTTAAAATAT--AATTTTGGAAAAGTTTT
* * *
39267232 GGGGGTAAAATGGTAATTTTTG-AAAGTTTT
1 GGGGTTAAAAT-ATAATTTTGGAAAAGTTTT
*
39267262 GGGGTTAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTTAAAATATAATTTTGGAAAAGTTTT
*
39267292 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTTAAAATATAATTTTGGAAAAGTTTT
* * *
39267322 GGGGTTAAAATATAATTCTAGAAAAGTTTC
1 GGGGTTAAAATATAATTTTGGAAAAGTTTT
*
39267352 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTTAAAATATAATTTTGGAAAAGTTTT
* *
39267382 AGGGTCAAAATATAATTTT
1 GGGGTTAAAATATAATTTT
39267401 TGGATTGTTT
Statistics
Matches: 148, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
29 24 0.16
30 123 0.83
31 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
GGGGTTAAAATATAATTTTGGAAAAGTTTT
Found at i:39267348 original size:90 final size:90
Alignment explanation
Indices: 39267223--39267400 Score: 259
Period size: 90 Copynumber: 2.0 Consensus size: 90
39267213 ATGGAATTTT
* * * * * *
39267223 AAAAGATTTGGGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTTAAAATGTAATTTTGGAAAAG
1 AAAAGATTTGGGGGTAAAATGATAATTCTAGAAAGTTTCGGGGTCAAAATATAATTTTGGAAAAG
*
39267288 TTTTGGGGTCAAAATATAATTTTGG
66 TTTTAGGGTCAAAATATAATTTTGG
* *
39267313 AAAAGTTTTGGGGTTAAAAT-ATAATTCTAGAAAAGTTTCGGGGTCAAAATATAATTTTGGAAAA
1 AAAAGATTTGGGGGTAAAATGATAATTCTAG-AAAGTTTCGGGGTCAAAATATAATTTTGGAAAA
39267377 GTTTTAGGGTCAAAATATAATTTT
65 GTTTTAGGGTCAAAATATAATTTT
39267401 TGGATTGTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
89 7 0.09
90 71 0.91
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (90 bp):
AAAAGATTTGGGGGTAAAATGATAATTCTAGAAAGTTTCGGGGTCAAAATATAATTTTGGAAAAG
TTTTAGGGTCAAAATATAATTTTGG
Found at i:39267754 original size:158 final size:161
Alignment explanation
Indices: 39267492--39267806 Score: 453
Period size: 157 Copynumber: 2.0 Consensus size: 161
39267482 GACCCATTTG
*
39267492 TAAACCTTGAAAAATTTTAGGACCAATTTTGTAATTAAATAAAAGTTGATTTAAGGATTAAATTA
1 TAAACCTTGAAAAATTTTAGGACCAATTTCGTAATTAAATAAAAGTTGATTTAAGGATTAAATTA
39267557 AAACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGATGACACGTGGCAACCT
66 AAACAAA-TAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAG-TGACACGTGGCAACCT
* *
39267622 CTGGTGCAATCAAACAGTCAAAGGACTAGTTTA
129 ATGGTACAATCAAACAGTCAAAGGACTAGTTTA
* *
39267655 TAAACCTTGAAAAATTATT-GGGCCAA-TTCGTAATTAAA-ATAAAGTTGATTT-GGGATTAAAT
1 TAAACCTTGAAAAATT-TTAGGACCAATTTCGTAATTAAATA-AAAGTTGATTTAAGGATTAAAT
* * * *
39267716 TAAAA-TAA-AAAAATAAAAAGGACTAAATGCATAAATAATCCAAAAAGTGACACGTGGCAGCCT
64 TAAAACAAATAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGTGACACGTGGCAACCT
**
39267779 ATGGTACGGTCAAACAGTCAAAGGACTA
129 ATGGTACAATCAAACAGTCAAAGGACTA
39267807 AATTGAAAAG
Statistics
Matches: 139, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
157 39 0.28
158 37 0.27
160 2 0.01
161 15 0.11
162 22 0.16
163 22 0.16
164 2 0.01
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (161 bp):
TAAACCTTGAAAAATTTTAGGACCAATTTCGTAATTAAATAAAAGTTGATTTAAGGATTAAATTA
AAACAAATAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGTGACACGTGGCAACCTAT
GGTACAATCAAACAGTCAAAGGACTAGTTTA
Found at i:39267828 original size:157 final size:160
Alignment explanation
Indices: 39267522--39267825 Score: 404
Period size: 158 Copynumber: 1.9 Consensus size: 160
39267512 GACCAATTTT
39267522 GTAATTAAATAAAAGTTGATTTAAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATA
1 GTAATTAAATAAAAGTTGATTTAAGGATTAAATTAAAACAAA-TAAAAATAAAAAGGACTAAATA
* * *
39267587 CAGAAATAATCCAAAAAGATGACACGTGGCAACCTCTGGTGCAATCAAACAGTCAAAGGACTAGT
65 CAGAAATAATCCAAAAAGATGACACGTGGCAACCTATGGTACAATCAAACAGTCAAAGGACTAAT
* *
39267652 TTATAAACCTTGAAAAATTATTGGGCCAATTC
130 TGATAAACATT-AAAAATTATTGGGCCAATTC
* * *
39267684 GTAATTAAA-ATAAAGTTGATTT-GGGATTAAATTAAAA-TAA-AAAAATAAAAAGGACTAAATG
1 GTAATTAAATA-AAAGTTGATTTAAGGATTAAATTAAAACAAATAAAAATAAAAAGGACTAAATA
* * **
39267745 CATAAATAATCCAAAAAG-TGACACGTGGCAGCCTATGGTACGGTCAAACAGTCAAAGGACTAAA
65 CAGAAATAATCCAAAAAGATGACACGTGGCAACCTATGGTACAATCAAACAGTCAAAGGACT-AA
39267809 TTGA-AAAGCAATTAAAA
129 TTGATAAA-C-ATTAAAA
39267826 TTACAGGGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
157 41 0.33
158 46 0.37
159 2 0.02
160 2 0.02
161 15 0.12
162 20 0.16
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.24
Consensus pattern (160 bp):
GTAATTAAATAAAAGTTGATTTAAGGATTAAATTAAAACAAATAAAAATAAAAAGGACTAAATAC
AGAAATAATCCAAAAAGATGACACGTGGCAACCTATGGTACAATCAAACAGTCAAAGGACTAATT
GATAAACATTAAAAATTATTGGGCCAATTC
Found at i:39269300 original size:6 final size:6
Alignment explanation
Indices: 39269284--39269405 Score: 118
Period size: 6 Copynumber: 21.0 Consensus size: 6
39269274 TTAAATTTGT
**
39269284 TTTATAA TTTAAA TTTAAA TTTAAA TTT-AA GGTAAA TTTAAA TAATTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
39269334 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA --TAAA TTTAAA TTTAAGA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
39269380 --TAAA TTTAAA TTTAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
39269406 ATCAATTTAA
Statistics
Matches: 98, Mismatches: 4, Indels: 27
0.76 0.03 0.21
Matches are distributed among these distances:
4 10 0.10
5 9 0.09
6 67 0.68
7 6 0.06
8 6 0.06
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:39269321 original size:11 final size:11
Alignment explanation
Indices: 39269305--39269388 Score: 59
Period size: 11 Copynumber: 7.8 Consensus size: 11
39269295 AATTTAAATT
*
39269305 TAAATTTAAGG
1 TAAATTTAAGA
39269316 TAAATTTAA-A
1 TAAATTTAAGA
* **
39269326 T-AATTAAATT
1 TAAATTTAAGA
39269336 TAAATTTAAGA
1 TAAATTTAAGA
39269347 TAAATTTAA-A
1 TAAATTTAAGA
* **
39269357 TTTAAA-TAAATT
1 --TAAATTTAAGA
39269369 TAAATTTAAGA
1 TAAATTTAAGA
39269380 TAAATTTAA
1 TAAATTTAA
39269389 ATTTAAATAA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
9 6 0.11
10 7 0.12
11 39 0.70
12 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (11 bp):
TAAATTTAAGA
Found at i:39269372 original size:33 final size:33
Alignment explanation
Indices: 39269284--39269405 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
39269274 TTAAATTTGT
*
39269284 TTTATAATTTAAATTTAAATTTAAATTTAAGGTAAA
1 TTTA-AATTTAAA--TAAATTTAAATTTAAGATAAA
*
39269320 TTTAAA--TAATTAAATTTAAATTTAAGATAAA
1 TTTAAATTTAAATAAATTTAAATTTAAGATAAA
39269351 TTTAAATTTAAATAAATTTAAATTTAAGATAAA
1 TTTAAATTTAAATAAATTTAAATTTAAGATAAA
39269384 TTTAAATTTAAATAAATTTAAA
1 TTTAAATTTAAATAAATTTAAA
39269406 ATCAATTTAA
Statistics
Matches: 81, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
31 26 0.32
33 49 0.60
35 2 0.02
36 4 0.05
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (33 bp):
TTTAAATTTAAATAAATTTAAATTTAAGATAAA
Found at i:39269407 original size:17 final size:16
Alignment explanation
Indices: 39269284--39269405 Score: 158
Period size: 17 Copynumber: 7.4 Consensus size: 16
39269274 TTAAATTTGT
39269284 TTTATAATTTAAATTTAAA
1 TTTA-AATTTAAA--TAAA
*
39269303 TTTAAATTTAAGGTAAA
1 TTTAAATTTAA-ATAAA
*
39269320 TTTAAA--TAATTAAA
1 TTTAAATTTAAATAAA
39269334 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
39269351 TTTAAATTTAAATAAA
1 TTTAAATTTAAATAAA
39269367 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
39269384 TTTAAATTTAAATAAA
1 TTTAAATTTAAATAAA
39269400 TTTAAA
1 TTTAAA
39269406 ATCAATTTAA
Statistics
Matches: 95, Mismatches: 3, Indels: 13
0.86 0.03 0.12
Matches are distributed among these distances:
14 10 0.11
15 3 0.03
16 30 0.32
17 41 0.43
18 7 0.07
19 4 0.04
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:39282108 original size:3 final size:3
Alignment explanation
Indices: 39282100--39282130 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
39282090 ATGGTATGAT
39282100 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
39282131 GTTATTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:39282603 original size:11 final size:11
Alignment explanation
Indices: 39282574--39282606 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
39282564 AACATTTGTG
39282574 TATGTATTTATT
1 TATGTATTT-TT
39282586 TAT-TATTTTT
1 TATGTATTTTT
39282596 TATGTATTTTT
1 TATGTATTTTT
39282607 CATGAACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 12 0.60
12 3 0.15
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (11 bp):
TATGTATTTTT
Found at i:39286697 original size:21 final size:20
Alignment explanation
Indices: 39286669--39286712 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
39286659 AATAAAAATT
*
39286669 AAAAAAAACCAAAATATAAA
1 AAAAAAAAACAAAATATAAA
**
39286689 AAAATAAAAATTAAATATAAA
1 AAAA-AAAAACAAAATATAAA
39286710 AAA
1 AAA
39286713 TTAAGGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAAAAAAACAAAATATAAA
Found at i:39286698 original size:16 final size:15
Alignment explanation
Indices: 39286658--39286716 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 15
39286648 CTACAAAGAC
39286658 AAATAAAAATTAAAA
1 AAATAAAAATTAAAA
39286673 AAA-ACCAAAATATAAAA
1 AAATA--AAAAT-TAAAA
*
39286690 AAATAAAAATTAAAT
1 AAATAAAAATTAAAA
*
39286705 ATA-AAAAATTAA
1 AAATAAAAATTAA
39286717 GGGGGAAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 10 0.26
15 9 0.24
16 10 0.26
17 8 0.21
18 1 0.03
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATAAAAATTAAAA
Found at i:39286894 original size:30 final size:30
Alignment explanation
Indices: 39286851--39286912 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
39286841 TAAATTTTAT
*
39286851 ATTTTAATAAAATGAATTAAACAAGATAAC
1 ATTTCAATAAAATGAATTAAACAAGATAAC
*
39286881 ATTTCAATCAAATGAATTAAACAAGATAAC
1 ATTTCAATAAAATGAATTAAACAAGATAAC
39286911 AT
1 AT
39286913 AACATATTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.55, C:0.10, G:0.06, T:0.29
Consensus pattern (30 bp):
ATTTCAATAAAATGAATTAAACAAGATAAC
Found at i:39291943 original size:14 final size:14
Alignment explanation
Indices: 39291924--39291951 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39291914 GTTTACCCAT
39291924 CAATCTTACTCATG
1 CAATCTTACTCATG
39291938 CAATCTTACTCATG
1 CAATCTTACTCATG
39291952 TAGTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (14 bp):
CAATCTTACTCATG
Found at i:39298211 original size:8 final size:9
Alignment explanation
Indices: 39298180--39298219 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
39298170 AAAAAATATA
39298180 TTTTAATTT
1 TTTTAATTT
39298189 TCATTTAATTT
1 T--TTTAATTT
*
39298200 TTTTTATTT
1 TTTTAATTT
39298209 TTTTAATTT
1 TTTTAATTT
39298218 TT
1 TT
39298220 GAACTTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 18 0.67
11 9 0.33
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTAATTT
Found at i:39298769 original size:29 final size:29
Alignment explanation
Indices: 39298715--39298793 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 29
39298705 TAAAAATATT
*
39298715 AAAAAT-ATTTT-ATAATTAATATATTTTT-
1 AAAAATAATTTTAATAATT-TTA-ATTTTTA
*
39298743 TAAAATAATTTTAATGAATTTTAATTTTTA
1 AAAAATAATTTTAAT-AATTTTAATTTTTA
* *
39298773 AAAAATAGTTTTTATAATTTT
1 AAAAATAATTTTAATAATTTT
39298794 TTGAATTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 5 0.12
29 17 0.40
30 16 0.38
31 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (29 bp):
AAAAATAATTTTAATAATTTTAATTTTTA
Found at i:39299022 original size:21 final size:19
Alignment explanation
Indices: 39298998--39299053 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
39298988 TTTAAAAGCA
39298998 TTTTATATAATTTTTATATT
1 TTTTATATAATTTTTA-ATT
*
39299018 TTTTTTAATAA-TTTTAATT
1 TTTTAT-ATAATTTTTAATT
* *
39299037 TTTAAAATAATTTTTAA
1 TTTTATATAATTTTTAA
39299054 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 4 0.13
19 12 0.40
20 10 0.33
21 4 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTATATAATTTTTAATT
Found at i:39300459 original size:30 final size:30
Alignment explanation
Indices: 39300419--39300475 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
39300409 GACATAGGCA
39300419 TTAAATCTTTAAAAATCA-AAAATTATTTT
1 TTAAATCTTTAAAAATCATAAAATTATTTT
*
39300448 TTAATATCTTTAAAAATTATAAAATTAT
1 TTAA-ATCTTTAAAAATCATAAAATTAT
39300476 AAATTAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 4 0.16
30 13 0.52
31 8 0.32
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (30 bp):
TTAAATCTTTAAAAATCATAAAATTATTTT
Found at i:39300483 original size:31 final size:30
Alignment explanation
Indices: 39300418--39300485 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
39300408 AGACATAGGC
**
39300418 ATTAA-ATCTTTAAAAATCAAAAATTATTT
1 ATTAATATCTTTAAAAATCAAAAATTATAA
* *
39300447 TTTAATATCTTTAAAAATTATAAAATTATAA
1 ATTAATATCTTTAAAAATCA-AAAATTATAA
39300478 ATTAATAT
1 ATTAATAT
39300486 AAGGATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 4 0.12
30 13 0.41
31 15 0.47
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (30 bp):
ATTAATATCTTTAAAAATCAAAAATTATAA
Found at i:39300896 original size:24 final size:23
Alignment explanation
Indices: 39300833--39300902 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
39300823 TTCATTTAAC
*
39300833 TTAATCGAACATATTCACAAACA
1 TTAATTGAACATATTCACAAACA
* * * * *
39300856 TTAAATGAATATTTTCATAAATA
1 TTAATTGAACATATTCACAAACA
* *
39300879 TATAATTGAACATGTTCACGAACA
1 T-TAATTGAACATATTCACAAACA
39300903 ATGTTAATGA
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
23 18 0.53
24 16 0.47
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (23 bp):
TTAATTGAACATATTCACAAACA
Found at i:39305319 original size:17 final size:17
Alignment explanation
Indices: 39305299--39305340 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
39305289 CTCCTTTGAC
*
39305299 CTTTAACCTTCCATCTT
1 CTTTAACCTTCCATATT
*
39305316 CTTTAACCTTTCATATT
1 CTTTAACCTTCCATATT
39305333 CTTATAAC
1 CTT-TAAC
39305341 TACTTTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTCCATATT
Found at i:39305603 original size:17 final size:17
Alignment explanation
Indices: 39305570--39305605 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
39305560 TACAACGTTC
39305570 TTGTTGAAGCAACAATG
1 TTGTTGAAGCAACAATG
39305587 TTGTTGAAGCAACAATG
1 TTGTTGAAGCAACAATG
39305604 TT
1 TT
39305606 AAGGTATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (17 bp):
TTGTTGAAGCAACAATG
Found at i:39307966 original size:33 final size:33
Alignment explanation
Indices: 39307923--39307994 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
39307913 ATGAATAACA
*
39307923 TATGAGATAGTGAAAAGAAGTTCATAGTGTTGG
1 TATGACATAGTGAAAAGAAGTTCATAGTGTTGG
39307956 TATGACATAGTGAAAAGAAGTTCATAGTGTTGG
1 TATGACATAGTGAAAAGAAGTTCATAGTGTTGG
39307989 TATGAC
1 TATGAC
39307995 CGGTTAGACC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.31
Consensus pattern (33 bp):
TATGACATAGTGAAAAGAAGTTCATAGTGTTGG
Found at i:39310726 original size:24 final size:24
Alignment explanation
Indices: 39310689--39310739 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
39310679 TAAATGGATG
39310689 TTTAACCTTTCATC-TCTCTTGACC
1 TTTAACCTTTCATCTTCT-TTGACC
39310713 TTTAA-CTTTCCATCTTCTTTGACC
1 TTTAACCTTT-CATCTTCTTTGACC
39310737 TTT
1 TTT
39310740 TATATTCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 4 0.16
24 18 0.72
25 3 0.12
ACGTcount: A:0.16, C:0.29, G:0.04, T:0.51
Consensus pattern (24 bp):
TTTAACCTTTCATCTTCTTTGACC
Found at i:39310872 original size:8 final size:8
Alignment explanation
Indices: 39310859--39310884 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
39310849 TGCAATACAA
39310859 ATTCTCAT
1 ATTCTCAT
39310867 ATTCTCAT
1 ATTCTCAT
39310875 ATTCTCAT
1 ATTCTCAT
39310883 AT
1 AT
39310885 CCATCATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTCTCAT
Found at i:39326337 original size:30 final size:30
Alignment explanation
Indices: 39326301--39326361 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 30
39326291 TTAGTATTGC
39326301 TTCTAAA-AAGCAGTTTTGGGACAAAAACAT
1 TTCTAAACAAGCAG-TTTGGGACAAAAACAT
39326331 TTCTAAACAAGCAGTTTGGGACAAAAACAT
1 TTCTAAACAAGCAGTTTGGGACAAAAACAT
39326361 T
1 T
39326362 CTTAAGCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (30 bp):
TTCTAAACAAGCAGTTTGGGACAAAAACAT
Found at i:39329304 original size:7 final size:7
Alignment explanation
Indices: 39329284--39329320 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
39329274 TCCGTTTATC
39329284 TTTA-GG
1 TTTAGGG
*
39329290 TTTCGGG
1 TTTAGGG
39329297 TTTAGGG
1 TTTAGGG
39329304 TTTAGGG
1 TTTAGGG
39329311 TTTAGGG
1 TTTAGGG
39329318 TTT
1 TTT
39329321 CCCATTGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
6 3 0.11
7 25 0.89
ACGTcount: A:0.11, C:0.03, G:0.38, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:39337990 original size:20 final size:20
Alignment explanation
Indices: 39337935--39337992 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
39337925 GCTTTTTTAA
39337935 TTTTTTAATGTTAAATTTGGAG
1 TTTTTT-AT-TTAAATTTGGAG
*** *
39337957 TTTACAATTT-AATTTTGAG
1 TTTTTTATTTAAATTTGGAG
39337976 TTTTTTATTTAAATTTG
1 TTTTTTATTTAAATTTG
39337993 ATTATTCAAT
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
19 15 0.56
20 7 0.26
21 2 0.07
22 3 0.11
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.59
Consensus pattern (20 bp):
TTTTTTATTTAAATTTGGAG
Found at i:39352070 original size:97 final size:97
Alignment explanation
Indices: 39351895--39352089 Score: 311
Period size: 97 Copynumber: 2.0 Consensus size: 97
39351885 CAACTTGAAG
* **
39351895 AAGACTAGTTTTAGACGGTAAAATCAGATGAGGACATGTGATTGTACTAAAAAAAAGAATAAGTA
1 AAGACTAGTCTTAGACGGTAAAATCAGACAAGGACATGTGATTGTACTAAAAAAAAGAATAAGTA
*
39351960 TATATATTTTTAGGGTAAACCAAATAAATGGC
66 TATATATTATTAGGGTAAACCAAATAAATGGC
* * *
39351992 AAGACTAGTCTTAGACGGTAAAATCAGACAATGACATGTGATTGTA-TTAAAAAAAGAATAATTA
1 AAGACTAGTCTTAGACGGTAAAATCAGACAAGGACATGTGATTGTACTAAAAAAAAGAATAAGTA
39352056 TATATATATATTAGGGTAAACCAAATAAATGGC
66 TATATAT-TATTAGGGTAAACCAAATAAATGGC
39352089 A
1 A
39352090 CTAAACTATT
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
96 23 0.26
97 67 0.74
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.28
Consensus pattern (97 bp):
AAGACTAGTCTTAGACGGTAAAATCAGACAAGGACATGTGATTGTACTAAAAAAAAGAATAAGTA
TATATATTATTAGGGTAAACCAAATAAATGGC
Found at i:39355658 original size:18 final size:18
Alignment explanation
Indices: 39355612--39355659 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
39355602 ATATAAAGAC
*
39355612 AATTATAATTACAATTTAT
1 AATTA-AATTATAATTTAT
*
39355631 ATATT-TATTATAATTTAT
1 A-ATTAAATTATAATTTAT
39355649 AATTAAATTAT
1 AATTAAATTAT
39355660 TTTAATTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
17 3 0.12
18 17 0.71
19 1 0.04
20 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTAAATTATAATTTAT
Found at i:39355683 original size:21 final size:21
Alignment explanation
Indices: 39355635--39355674 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39355625 ATTTATATAT
* *
39355635 TTATTATAATTTATAATTAAA
1 TTATTTTAATTCATAATTAAA
39355656 TTATTTTAATTCATAATTA
1 TTATTTTAATTCATAATTA
39355675 GAATGTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATTTTAATTCATAATTAAA
Found at i:39360107 original size:13 final size:14
Alignment explanation
Indices: 39360071--39360104 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39360061 TATTTCACTT
*
39360071 AAAATAATTTTCAG
1 AAAATAATTTTCAA
*
39360085 AAAATAATTTTTAA
1 AAAATAATTTTCAA
39360099 AAAATA
1 AAAATA
39360105 TTTATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (14 bp):
AAAATAATTTTCAA
Found at i:39360132 original size:18 final size:19
Alignment explanation
Indices: 39360091--39360133 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
39360081 TCAGAAAATA
*
39360091 ATTTTTAAAAAATATTTAT
1 ATTTTTAAAAAATATTAAT
* *
39360110 TTTTTTAGAAAA-ATTAAT
1 ATTTTTAAAAAATATTAAT
39360128 ATTTTT
1 ATTTTT
39360134 TTTATGTTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTTTAAAAAATATTAAT
Found at i:39361500 original size:21 final size:21
Alignment explanation
Indices: 39361471--39361511 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39361461 CTCTAAAAAA
*
39361471 TTTTACAAAAAAATTTAAATT
1 TTTTACAAAAAAATATAAATT
* *
39361492 TTTTTCAAAAATATATAAAT
1 TTTTACAAAAAAATATAAAT
39361512 GCAGAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTTACAAAAAAATATAAATT
Found at i:39374029 original size:41 final size:40
Alignment explanation
Indices: 39373984--39374060 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
39373974 ATTTTTAGGG
*
39373984 CGTTTGGACAAAAAACGTTGCAAAAGGTAAAGCAATAACGA
1 CGTTTGGAC-AAAAACGCTGCAAAAGGTAAAGCAATAACGA
** * *
39374025 CGTTTTTACATAAACGCTGCAAAAGGTAGAGCAATA
1 CGTTTGGACAAAAACGCTGCAAAAGGTAAAGCAATA
39374061 GCAGTGCTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 24 0.77
41 7 0.23
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.21
Consensus pattern (40 bp):
CGTTTGGACAAAAACGCTGCAAAAGGTAAAGCAATAACGA
Found at i:39375578 original size:41 final size:41
Alignment explanation
Indices: 39375514--39375669 Score: 154
Period size: 41 Copynumber: 3.8 Consensus size: 41
39375504 TGGGAAAGAG
* * * * *
39375514 CATTAGCGACGTTTGTGAGAAAGCGCCGTTAGAGGTCAGAA
1 CATTAGCGGCGTTTATGAAAAAGCGCCGCTAAAGGTCAGAA
*
39375555 CATTAGCGGCGTTTATGAAAAAGCGCCGCTAAAAGTCA-AA
1 CATTAGCGGCGTTTATGAAAAAGCGCCGCTAAAGGTCAGAA
* * *
39375595 GCATTAGCGGCGTTTATTAGAAAA-TGCCGCTAAAGGTCAGAG
1 -CATTAGCGGCGTTTATGA-AAAAGCGCCGCTAAAGGTCAGAA
** * **
39375637 CATTAGCAACGTTAATGAGTAAGCGCCGCTAAA
1 CATTAGCGGCGTTTATGAAAAAGCGCCGCTAAA
39375670 AGTTAAGTAA
Statistics
Matches: 94, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
40 4 0.04
41 85 0.90
42 5 0.05
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (41 bp):
CATTAGCGGCGTTTATGAAAAAGCGCCGCTAAAGGTCAGAA
Found at i:39375632 original size:82 final size:82
Alignment explanation
Indices: 39375512--39375672 Score: 205
Period size: 82 Copynumber: 2.0 Consensus size: 82
39375502 TATGGGAAAG
* * * * ** *
39375512 AGCATTAGCGACGTTTGTGAGAAAGCGCCGTTAGAGGTCAGAACATTAGCGGCGTTTATGAAAAA
1 AGCATTAGCGACGTTTATGAGAAAACGCCGCTAAAGGTCAGAACATTAGCAACGTTAATGAAAAA
39375577 GCGCCGCTAAAAGTCAA
66 GCGCCGCTAAAAGTCAA
* * * * **
39375594 AGCATTAGCGGCGTTTATTAGAAAATGCCGCTAAAGGTCAGAGCATTAGCAACGTTAATGAGTAA
1 AGCATTAGCGACGTTTATGAGAAAACGCCGCTAAAGGTCAGAACATTAGCAACGTTAATGAAAAA
39375659 GCGCCGCTAAAAGT
66 GCGCCGCTAAAAGT
39375673 TAAGTAATAG
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
82 66 1.00
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.22
Consensus pattern (82 bp):
AGCATTAGCGACGTTTATGAGAAAACGCCGCTAAAGGTCAGAACATTAGCAACGTTAATGAAAAA
GCGCCGCTAAAAGTCAA
Found at i:39375792 original size:27 final size:27
Alignment explanation
Indices: 39375762--39375844 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 27
39375752 ATTAACAATT
39375762 ATTTTAAAACTTATATAAACTAAAAAA
1 ATTTTAAAACTTATATAAACTAAAAAA
* * * **
39375789 ATTTTAAAA-TTTTAAAAAAATATTAAA
1 ATTTTAAAACTTAT-ATAAACTAAAAAA
*
39375816 ATTTT-AAACTTATATGAACTAAAAAA
1 ATTTTAAAACTTATATAAACTAAAAAA
39375842 ATT
1 ATT
39375845 AAATTATTTT
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
26 17 0.40
27 26 0.60
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (27 bp):
ATTTTAAAACTTATATAAACTAAAAAA
Found at i:39375830 original size:19 final size:19
Alignment explanation
Indices: 39375782--39375823 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
39375772 TTATATAAAC
*
39375782 TAAAAAAATTTTAAAATTT
1 TAAAAAAATATTAAAATTT
39375801 TAAAAAAATATTAAAATTT
1 TAAAAAAATATTAAAATTT
39375820 TAAA
1 TAAA
39375824 CTTATATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAAAATATTAAAATTT
Found at i:39378276 original size:19 final size:16
Alignment explanation
Indices: 39378252--39378295 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 16
39378242 TTTACAATTA
39378252 GATTTGAAGTTATTGATTG
1 GATTTGAA-TTA-TG-TTG
39378271 GATTTGAATTA-GTTG
1 GATTTGAATTATGTTG
39378286 GATTTGAATT
1 GATTTGAATT
39378296 TATAGGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 13 0.52
16 1 0.04
18 3 0.12
19 8 0.32
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (16 bp):
GATTTGAATTATGTTG
Found at i:39378516 original size:43 final size:42
Alignment explanation
Indices: 39378348--39378515 Score: 119
Period size: 43 Copynumber: 3.9 Consensus size: 42
39378338 AATTTTAGCA
* * * * *
39378348 ACGTTTGTGAAAAAACGTCGCTAAATATCATGTTCTTGAAT-
1 ACGTTTGTGAAAAAGCGTCGCTAAAGACCACGTTCTTTAATG
* * *
39378389 AGCGTTTGTGAGAAAAGCGTCACTAAAGATCACGTTCTTTAACG
1 A-CGTTTGTGA-AAAAGCGTCGCTAAAGACCACGTTCTTTAATG
* ** * *
39378433 ACGTTTACG-GCAACAA-CACCGTTAAAGACCACGTAT-TTTAGTG
1 ACGTTT--GTG-AAAAAGCGTCGCTAAAGACCACGT-TCTTTAATG
*
39378476 ACGTTTGTGGAAAAAGCGTCGCTAAAGACCATGTTCTTTA
1 ACGTTTGT-GAAAAAGCGTCGCTAAAGACCACGTTCTTTA
39378516 GCGGCATTTT
Statistics
Matches: 97, Mismatches: 19, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
41 2 0.02
42 14 0.14
43 73 0.75
44 6 0.06
45 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (42 bp):
ACGTTTGTGAAAAAGCGTCGCTAAAGACCACGTTCTTTAATG
Found at i:39390464 original size:25 final size:24
Alignment explanation
Indices: 39390426--39390475 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
39390416 TAAACTTAAC
*
39390426 ATTTTTTTTTAATTTGGTATCTAA
1 ATTTTTTTTCAATTTGGTATCTAA
*
39390450 ATTTTTTGTTCAATTTGGTATTTAA
1 ATTTTTT-TTCAATTTGGTATCTAA
39390475 A
1 A
39390476 CTTGACACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.26, C:0.04, G:0.10, T:0.60
Consensus pattern (24 bp):
ATTTTTTTTCAATTTGGTATCTAA
Found at i:39390511 original size:56 final size:56
Alignment explanation
Indices: 39390406--39390512 Score: 126
Period size: 56 Copynumber: 1.9 Consensus size: 56
39390396 ATAATATAAT
* ** *
39390406 ATTTGGTAGCTAAACTTAACATTTTTTTTTAATTTGGTATCTAAATTTTTTGTTCA
1 ATTTGGTAGCTAAACTTAACACTTTTTCCTAATTTGATATCTAAATTTTTTGTTCA
** * *
39390462 ATTTGGTATTTAAACTTGACACTTTTTCCTAATTTGAT-TCCTAATTTTTTT
1 ATTTGGTAGCTAAACTTAACACTTTTTCCTAATTTGATAT-CTAAATTTTTT
39390513 TAATATTAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
55 1 0.02
56 41 0.98
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.54
Consensus pattern (56 bp):
ATTTGGTAGCTAAACTTAACACTTTTTCCTAATTTGATATCTAAATTTTTTGTTCA
Found at i:39391009 original size:31 final size:31
Alignment explanation
Indices: 39390974--39391037 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
39390964 TTATAAAATG
*
39390974 GTCACTAAATTATGCAAAAGTTTTCATTTAA
1 GTCACTAAACTATGCAAAAGTTTTCATTTAA
* * *
39391005 GTCACTCAACTATTCAAAAGTTTTTATTTAA
1 GTCACTAAACTATGCAAAAGTTTTCATTTAA
39391036 GT
1 GT
39391038 TATTGGAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (31 bp):
GTCACTAAACTATGCAAAAGTTTTCATTTAA
Found at i:39397751 original size:25 final size:24
Alignment explanation
Indices: 39397703--39397751 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
39397693 TGTCGAACAA
*
39397703 TATTTTAAAAAATCAAAATATGGG
1 TATTTTAAAAAATCAAAAAATGGG
**
39397727 TATTTTAAATGATCGAAAAAATGGG
1 TATTTTAAAAAATC-AAAAAATGGG
39397752 AGTCGCCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (24 bp):
TATTTTAAAAAATCAAAAAATGGG
Found at i:39398746 original size:29 final size:29
Alignment explanation
Indices: 39398714--39399070 Score: 247
Period size: 29 Copynumber: 12.3 Consensus size: 29
39398704 AGCAAAACAA
*
39398714 TAATTTTTGTAAATTCGAGGGTAAAATAG
1 TAATTTTTGGAAATTCGAGGGTAAAATAG
* * * * *
39398743 TAA-TTTTGGACACTCGGGGGGTAAACTGG
1 TAATTTTTGGAAATTC-GAGGGTAAAATAG
* * *
39398772 TAATTTTTGGAAAGTTCTA-AGTCAAAATGG
1 TAATTTTTGGAAA-TTCGAGGGT-AAAATAG
39398802 TAATTTTTGGAAAGTTCG-GGGTAAAA-ATG
1 TAATTTTTGGAAA-TTCGAGGGTAAAATA-G
* *
39398831 TAATTTTTGGACATTTG-GGAGTAAAATAG
1 TAATTTTTGGAAATTCGAGG-GTAAAATAG
** *
39398860 TAATTTTTGGATGTTCGAGGGTAAAATGG
1 TAATTTTTGGAAATTCGAGGGTAAAATAG
* *
39398889 TAATTTTTGAAAAATTTG-GGGTCAAAA-ATG
1 TAATTTTTG-GAAATTCGAGGGT-AAAATA-G
* *
39398919 TAATTTTTGGATATTCGAGGGTAAAATGG
1 TAATTTTTGGAAATTCGAGGGTAAAATAG
** *
39398948 TAATTTTTGGATGTTCG-GGGTAAAATGG
1 TAATTTTTGGAAATTCGAGGGTAAAATAG
* * *
39398976 TAA-TTTTGCAAAATTCAAGGTTAAAA-ATG
1 TAATTTTTG-GAAATTCGAGGGTAAAATA-G
*
39399005 TAATTTTT-GAAAGTTTGAGGGTTAAAAT-G
1 TAATTTTTGGAAA-TTCGAGGG-TAAAATAG
*
39399034 TAATTTTTGGAAAGTT-TAGGGTTAAAAT-G
1 TAATTTTTGGAAA-TTCGAGGG-TAAAATAG
39399063 TAATTTTT
1 TAATTTTT
39399071 AGAAGTTTAG
Statistics
Matches: 264, Mismatches: 42, Indels: 44
0.75 0.12 0.13
Matches are distributed among these distances:
27 5 0.02
28 35 0.13
29 148 0.56
30 74 0.28
31 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (29 bp):
TAATTTTTGGAAATTCGAGGGTAAAATAG
Found at i:39398823 original size:59 final size:58
Alignment explanation
Indices: 39398761--39399070 Score: 232
Period size: 59 Copynumber: 5.3 Consensus size: 58
39398751 GACACTCGGG
* * *
39398761 GGGTAAACTGGTAATTTTTGGAAAGTTCTAAGTCAAAATGGTAATTTTTGGAAAGTTCG-
1 GGGTAAAATGGTAATTTTTGGAAAATT-TGAGTCAAAAT-GTAATTTTTGGAAAGTTCGA
* *
39398820 GGGTAAAAAT-GTAATTTTTGG-ACATTTGGGAGT-AAAATAGTAATTTTTGG-ATGTTCGA
1 GGGT-AAAATGGTAATTTTTGGAAAATTT--GAGTCAAAAT-GTAATTTTTGGAAAGTTCGA
* * *
39398878 GGGTAAAATGGTAATTTTTGAAAAATTTGGGGTCAAAAATGTAATTTTTGGATA-TTCGA
1 GGGTAAAATGGTAATTTTTGGAAAATTT-GAGTC-AAAATGTAATTTTTGGAAAGTTCGA
** * * * * *
39398937 GGGTAAAATGGTAATTTTTGG-ATGTTCGGGGT-AAAATGGTAA-TTTTGCAAAATTCAA
1 GGGTAAAATGGTAATTTTTGGAAAATT-TGAGTCAAAAT-GTAATTTTTGGAAAGTTCGA
* * * *
39398994 GGTTAAAAAT-GTAATTTTT-GAAAGTTTGAGGGTTAAAATGTAATTTTTGGAAAGTT-TA
1 GGGT-AAAATGGTAATTTTTGGAAAATTTGA--GTCAAAATGTAATTTTTGGAAAGTTCGA
39399052 GGGTTAAAAT-GTAATTTTT
1 GGG-TAAAATGGTAATTTTT
39399071 AGAAGTTTAG
Statistics
Matches: 206, Mismatches: 26, Indels: 39
0.76 0.10 0.14
Matches are distributed among these distances:
56 14 0.07
57 36 0.17
58 72 0.35
59 75 0.36
60 9 0.04
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.38
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGAAAATTTGAGTCAAAATGTAATTTTTGGAAAGTTCGA
Found at i:39398855 original size:88 final size:88
Alignment explanation
Indices: 39398714--39399099 Score: 350
Period size: 88 Copynumber: 4.4 Consensus size: 88
39398704 AGCAAAACAA
* ** * *
39398714 TAATTTTT-GTAAATTCGAGGGT-AAAATAGTAA-TTTTGGACACTCGGGGGGTAAACTGGTAAT
1 TAATTTTTGGAAAATTCG-GGGTAAAAAT-GTAATTTTTGGACACTTTGAGGGTAAAATGGTAAT
* *
39398776 TTTTGGAAAGTTCTA-AGTCAAAATGG
64 TTTTGG-AAGTTCGAGGGT-AAAATGG
* *
39398802 TAATTTTTGGAAAGTTCGGGGTAAAAATGTAATTTTTGGACA-TTTG-GGAGTAAAATAGTAATT
1 TAATTTTTGGAAAATTCGGGGTAAAAATGTAATTTTTGGACACTTTGAGG-GTAAAATGGTAATT
*
39398865 TTTGGATGTTCGAGGGTAAAATGG
65 TTTGGAAGTTCGAGGGTAAAATGG
* * * *
39398889 TAATTTTTGAAAAATTTGGGGTCAAAAATGTAATTTTTGGATA-TTCGAGGGTAAAATGGTAATT
1 TAATTTTTGGAAAATTCGGGGT-AAAAATGTAATTTTTGGACACTTTGAGGGTAAAATGGTAATT
*
39398953 TTTGGATGTTCG-GGGTAAAATGG
65 TTTGGAAGTTCGAGGGTAAAATGG
* * * * *
39398976 TAA-TTTTGCAAAATTCAAGGTTAAAAATGTAATTTTT-GAAAGTTTGAGGGTTAAAAT-GTAAT
1 TAATTTTTGGAAAATTC-GGGGTAAAAATGTAATTTTTGGACACTTTGAGGG-TAAAATGGTAAT
*
39399038 TTTTGGAAAGTT-TAGGGTTAAAAT-G
64 TTTTGG-AAGTTCGAGGG-TAAAATGG
* ** *
39399063 TAATTTTTAGAAGTTTAGGGGT-AAAATGATAATTTTT
1 TAATTTTTGGAAAATTCGGGGTAAAAATG-TAATTTTT
39399100 AAAGTTTGTG
Statistics
Matches: 253, Mismatches: 30, Indels: 31
0.81 0.10 0.10
Matches are distributed among these distances:
85 3 0.01
86 50 0.20
87 79 0.31
88 98 0.39
89 23 0.09
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (88 bp):
TAATTTTTGGAAAATTCGGGGTAAAAATGTAATTTTTGGACACTTTGAGGGTAAAATGGTAATTT
TTGGAAGTTCGAGGGTAAAATGG
Found at i:39398882 original size:58 final size:55
Alignment explanation
Indices: 39398714--39399099 Score: 275
Period size: 58 Copynumber: 6.6 Consensus size: 55
39398704 AGCAAAACAA
* * * * *
39398714 TAATTTTTGTAAATTCGAGGGTAAAATAGTAA-TTTTGGACA-CTCGGGGGGTAAACTGG
1 TAATTTTTGGAAATTTG-GGGTAAAAT-GTAATTTTTGGA-AGTTC-GAGGGTAAAAT-G
**
39398772 TAATTTTTGGAAAGTTCT-AAGTCAAAATGGTAATTTTTGGAAAGTTCG-GGGTAAAAATG
1 TAATTTTTGGAAA-TT-TGGGGT-AAAAT-GTAATTTTTGG-AAGTTCGAGGGT-AAAATG
* *
39398831 TAATTTTTGGACATTTGGGAGTAAAATAGTAATTTTTGGATGTTCGAGGGTAAAATGG
1 TAATTTTTGGAAATTTGGG-GTAAAAT-GTAATTTTTGGAAGTTCGAGGGTAAAAT-G
*
39398889 TAATTTTTGAAAAATTTGGGGTCAAAAATGTAATTTTTGGATA-TTCGAGGGTAAAATGG
1 TAATTTTTG-GAAATTTGGGGT--AAAATGTAATTTTTGGA-AGTTCGAGGGTAAAAT-G
** * * * * *
39398948 TAATTTTTGGATGTTCGGGGTAAAATGGTAA-TTTTGCAAAATTCAAGGTTAAAAATG
1 TAATTTTTGGAAATTTGGGGTAAAAT-GTAATTTTTG-GAAGTTCGAGGGT-AAAATG
*
39399005 TAATTTTT-GAAAGTTTGAGGGTTAAAATGTAATTTTTGGAAAGTT-TAGGGTTAAAATG
1 TAATTTTTGGAAA-TTTG-GGG-TAAAATGTAATTTTTGG-AAGTTCGAGGG-TAAAATG
* *
39399063 TAATTTTTAGAAGTTTAGGGGTAAAATGATAATTTTT
1 TAATTTTTGGAAATTT-GGGGTAAAATG-TAATTTTT
39399100 AAAGTTTGTG
Statistics
Matches: 270, Mismatches: 30, Indels: 56
0.76 0.08 0.16
Matches are distributed among these distances:
56 13 0.05
57 43 0.16
58 99 0.37
59 95 0.35
60 17 0.06
61 3 0.01
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (55 bp):
TAATTTTTGGAAATTTGGGGTAAAATGTAATTTTTGGAAGTTCGAGGGTAAAATG
Found at i:39399084 original size:29 final size:28
Alignment explanation
Indices: 39398760--39399135 Score: 229
Period size: 29 Copynumber: 13.0 Consensus size: 28
39398750 GGACACTCGG
*
39398760 GGGGTAAACTGGTAATTTTTGGAAAG-TTC
1 GGGGTAAAAT-GTAATTTTTGG-AAGTTTC
***
39398789 TAAGTCAAAATGGTAATTTTTGGAAAG-TTC
1 GGGGT-AAAAT-GTAATTTTTGG-AAGTTTC
39398819 GGGGTAAAAATGTAATTTTTGGACA-TTT-
1 GGGGT-AAAATGTAATTTTTGGA-AGTTTC
*
39398847 GGGAGTAAAATAGTAATTTTTGGATG-TTC
1 GGG-GTAAAAT-GTAATTTTTGGAAGTTTC
* *
39398876 GAGGGTAAAATGGTAATTTTTGAAAAATTT-
1 G-GGGTAAAAT-GTAATTTTTG-GAAGTTTC
39398906 GGGGTCAAAAATGTAATTTTTGG-A-TATTC
1 GGGGT--AAAATGTAATTTTTGGAAGT-TTC
*
39398935 GAGGGTAAAATGGTAATTTTTGGATG-TTC
1 G-GGGTAAAAT-GTAATTTTTGGAAGTTTC
* **
39398964 GGGGTAAAATGGTAA-TTTTGCAAAATTC
1 GGGGTAAAAT-GTAATTTTTGGAAGTTTC
* * *
39398992 AAGGTTAAAAATGTAATTTTTGAAAGTTT-
1 -GGGGT-AAAATGTAATTTTTGGAAGTTTC
*
39399021 GAGGGTTAAAATGTAATTTTTGGAAAGTTTA
1 G-GGG-TAAAATGTAATTTTTGG-AAGTTTC
* * *
39399052 GGGTTAAAATGTAATTTTTAGAAGTTTA
1 GGGGTAAAATGTAATTTTTGGAAGTTTC
*
39399080 GGGGTAAAATGATAATTTTT-AAAGTTT-
1 GGGGTAAAATG-TAATTTTTGGAAGTTTC
* * *
39399107 GTGGGCAAAAATATGATTTTTGGAAGTTT
1 G-GGG-TAAAATGTAATTTTTGGAAGTTT
39399136 GGAGACCTTC
Statistics
Matches: 283, Mismatches: 34, Indels: 60
0.75 0.09 0.16
Matches are distributed among these distances:
27 8 0.03
28 69 0.24
29 127 0.45
30 71 0.25
31 8 0.03
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (28 bp):
GGGGTAAAATGTAATTTTTGGAAGTTTC
Found at i:39400945 original size:11 final size:11
Alignment explanation
Indices: 39400931--39401026 Score: 54
Period size: 11 Copynumber: 8.6 Consensus size: 11
39400921 TTTAAGTTTT
39400931 AATTAAATTTA
1 AATTAAATTTA
*
39400942 AATTTAAA-ATA
1 AA-TTAAATTTA
39400953 AATTCAAATTTA
1 AATT-AAATTTA
* * *
39400965 AAATGAACTTA
1 AATTAAATTTA
*
39400976 AATTCAAA-ATA
1 AATT-AAATTTA
39400987 AATTAAATTTA
1 AATTAAATTTA
* * *
39400998 TACTAAATTCA
1 AATTAAATTTA
*
39401009 AACTTAAA-ATA
1 AA-TTAAATTTA
39401020 AATTAAA
1 AATTAAA
39401027 AATGGGTTCA
Statistics
Matches: 63, Mismatches: 16, Indels: 13
0.68 0.17 0.14
Matches are distributed among these distances:
10 10 0.16
11 37 0.59
12 16 0.25
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:39400954 original size:17 final size:17
Alignment explanation
Indices: 39400934--39401023 Score: 101
Period size: 17 Copynumber: 5.4 Consensus size: 17
39400924 AAGTTTTAAT
39400934 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
39400951 TAAATTCAAATTTAAAA
1 TAAATTTAAATTTAAAA
* * *
39400968 TGAACTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
* *
39400985 TAAA-TTAAATTTATAC
1 TAAATTTAAATTTAAAA
* *
39401001 TAAATTCAAACTTAAAA
1 TAAATTTAAATTTAAAA
39401018 TAAATT
1 TAAATT
39401024 AAAAATGGGT
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
16 13 0.22
17 46 0.78
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:39403156 original size:24 final size:24
Alignment explanation
Indices: 39403128--39403186 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
39403118 TAGACTAATA
*
39403128 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAT
* *
39403152 AGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAT
*
39403176 AGAATTTAACT
1 AGAGTTTAACT
39403187 GAAAGATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAT
Found at i:39403189 original size:24 final size:24
Alignment explanation
Indices: 39403140--39403190 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
39403130 AGTTTGACTC
* *
39403140 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAATAGAATTTAACTG
39403164 AAACAAATAAATAGAATTTAACTG
1 AAACAAATAAATAGAATTTAACTG
39403188 AAA
1 AAA
39403191 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.06, G:0.10, T:0.25
Consensus pattern (24 bp):
AAACAAATAAATAGAATTTAACTG
Found at i:39405144 original size:24 final size:24
Alignment explanation
Indices: 39405117--39405167 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
39405107 AGTTTGACTC
*
39405117 AAACAAATAAATA-AAGTTTAATTG
1 AAACAAATAAATAGAA-TTTAACTG
39405141 AAACAAATAAATAGAATTTAACTG
1 AAACAAATAAATAGAATTTAACTG
39405165 AAA
1 AAA
39405168 GATTATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.61, C:0.06, G:0.08, T:0.25
Consensus pattern (24 bp):
AAACAAATAAATAGAATTTAACTG
Found at i:39407482 original size:18 final size:18
Alignment explanation
Indices: 39407461--39407495 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
39407451 TTTTACTCCT
39407461 AAAAAATTCAAATTCAAC
1 AAAAAATTCAAATTCAAC
39407479 AAAAAATTCAAATTCAA
1 AAAAAATTCAAATTCAA
39407496 ATTTTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAAATTCAAATTCAAC
Found at i:39408915 original size:38 final size:38
Alignment explanation
Indices: 39408855--39408962 Score: 164
Period size: 38 Copynumber: 2.8 Consensus size: 38
39408845 AAAAAAGTAT
*
39408855 TTATATTAAAAAATCACCATAAATATAATAAATGGTTTA
1 TTATATTAAAAAATCA-AATAAATATAATAAATGGTTTA
*
39408894 TTATATTAAAAAATCAAATAAATATAATAAATGTTTTA
1 TTATATTAAAAAATCAAATAAATATAATAAATGGTTTA
*
39408932 TTGTATTAAAAACA-CAAATAAATATAATAAA
1 TTATATTAAAAA-ATCAAATAAATATAATAAA
39408963 ATTGTATTGT
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
38 48 0.74
39 17 0.26
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (38 bp):
TTATATTAAAAAATCAAATAAATATAATAAATGGTTTA
Found at i:39408971 original size:37 final size:37
Alignment explanation
Indices: 39408858--39408978 Score: 147
Period size: 38 Copynumber: 3.2 Consensus size: 37
39408848 AAAGTATTTA
* *
39408858 TATTAAAAAATCACCATAAATATAAT-AAATGGTTTATTA
1 TATTAAAAAATCA-AATAAATATAATAAAAT--TTTATTG
*
39408897 TATTAAAAAATCAAATAAATATAATAAATGTTTTATTG
1 TATTAAAAAATCAAATAAATATAATAAA-ATTTTATTG
*
39408935 TATTAAAAACA-CAAATAAATATAATAAAATTGTATTG
1 TATTAAAAA-ATCAAATAAATATAATAAAATTTTATTG
39408972 TATTAAA
1 TATTAAA
39408979 TATAGCTTTT
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
37 14 0.19
38 43 0.58
39 16 0.22
40 1 0.01
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (37 bp):
TATTAAAAAATCAAATAAATATAATAAAATTTTATTG
Found at i:39410466 original size:20 final size:21
Alignment explanation
Indices: 39410425--39410489 Score: 80
Period size: 20 Copynumber: 3.0 Consensus size: 21
39410415 TATATTATTG
*
39410425 TTTTGCTATTTTGTGTTGTTT
1 TTTTACTATTTTGTGTTGTTT
39410446 TTTTACTATTTTG-G-TGCTTT
1 TTTTACTATTTTGTGTTG-TTT
39410466 TTTTACTATTTTGATTGTTGTTT
1 TTTTACTATTTTG--TGTTGTTT
39410489 T
1 T
39410490 CATGTTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
19 2 0.05
20 17 0.45
21 12 0.32
23 5 0.13
24 2 0.05
ACGTcount: A:0.09, C:0.06, G:0.15, T:0.69
Consensus pattern (21 bp):
TTTTACTATTTTGTGTTGTTT
Found at i:39410726 original size:17 final size:18
Alignment explanation
Indices: 39410692--39410727 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
39410682 GTATTTTAAA
*
39410692 TTTGTTTATTTTTTAATG
1 TTTGTTTATTTTTAAATG
39410710 TTTGTTT-TTTTTAAATG
1 TTTGTTTATTTTTAAATG
39410727 T
1 T
39410728 ATTTGATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.72
Consensus pattern (18 bp):
TTTGTTTATTTTTAAATG
Found at i:39413818 original size:2 final size:2
Alignment explanation
Indices: 39413811--39413855 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
39413801 ATCTTGACAT
39413811 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39413853 TC T
1 TC T
39413856 TTTATATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:39421678 original size:94 final size:94
Alignment explanation
Indices: 39421506--39421678 Score: 312
Period size: 95 Copynumber: 1.8 Consensus size: 94
39421496 TAATTTTAAA
39421506 AGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTAAGTAAAAAACATTGTTCATATTTATTGA
1 AGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTAAGTAAAAAACATTGTTCATATTTATTGA
*
39421571 TTTAAAATTTAATAATGTTTAAAAAAATT
66 TTTAAAATATAATAATGTTTAAAAAAATT
*
39421600 AGTTAGTAATTTTATTTTGTTGTTAGTAAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTG
1 AGTTAGTAATTTTATTTTGTTGTTAGT-AGTAGTAGTAAGTAAAAAACATTGTTCATATTTATTG
39421665 ATTTAAAA-ATAATA
65 ATTTAAAATATAATA
39421679 TAATATTTTA
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
94 32 0.42
95 44 0.58
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (94 bp):
AGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTAAGTAAAAAACATTGTTCATATTTATTGA
TTTAAAATATAATAATGTTTAAAAAAATT
Found at i:39421909 original size:16 final size:16
Alignment explanation
Indices: 39421864--39421913 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
39421854 TAAACCTAGC
*
39421864 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
39421880 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
39421894 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
39421910 TAAT
1 TAAT
39421914 ACCCCTATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:39422029 original size:29 final size:29
Alignment explanation
Indices: 39421997--39422053 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
39421987 TGTGGATACT
* *
39421997 ATTTTGGTATATAAAATATATTTTGTATC
1 ATTTTAGTAAATAAAATATATTTTGTATC
* *
39422026 ATTTTAGTAAATAACATATTTTTTGTAT
1 ATTTTAGTAAATAAAATATATTTTGTAT
39422054 TTAATTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.53
Consensus pattern (29 bp):
ATTTTAGTAAATAAAATATATTTTGTATC
Found at i:39423292 original size:43 final size:43
Alignment explanation
Indices: 39423210--39423294 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
39423200 ATTAACATGT
* * *
39423210 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAACTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
39423253 TAAACTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAACTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
39423295 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (43 bp):
TAAACTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Done.