Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 182 of 279
Found at i:59612443 original size:12 final size:12
Alignment explanation
Indices: 59612426--59612451 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
59612416 AGGATTGGCG
59612426 CGGCCTAGCACA
1 CGGCCTAGCACA
59612438 CGGCCTAGCACA
1 CGGCCTAGCACA
59612450 CG
1 CG
59612452 AACGTGTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.42, G:0.27, T:0.08
Consensus pattern (12 bp):
CGGCCTAGCACA
Found at i:59613768 original size:12 final size:13
Alignment explanation
Indices: 59613740--59613772 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
59613730 TATTTTCTTT
59613740 TTCTCCATCTACC
1 TTCTCCATCTACC
*
59613753 TTCTCC-TCTTCC
1 TTCTCCATCTACC
59613765 TTCTCCAT
1 TTCTCCAT
59613773 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:59614875 original size:28 final size:28
Alignment explanation
Indices: 59614843--59614907 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
59614833 ATTTACTAGA
*
59614843 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
59614871 ATACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
59614899 ATACCCCTA
1 ATACCCCTA
59614908 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:59615071 original size:27 final size:27
Alignment explanation
Indices: 59615013--59615102 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
59615003 AGGAAGCGTC
59615013 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
59615041 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
59615068 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
59615097 CTGGTG
1 CTGGTG
59615103 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:59615121 original size:55 final size:56
Alignment explanation
Indices: 59615013--59615127 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
59615003 AGGAAGCGTC
* *
59615013 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
59615068 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
59615124 CTGG
1 CTGG
59615128 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.58
56 21 0.40
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:59615590 original size:19 final size:19
Alignment explanation
Indices: 59615566--59615604 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
59615556 TTTTAATTAT
* *
59615566 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
59615585 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
59615604 T
1 T
59615605 ATGATGAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:59620749 original size:33 final size:33
Alignment explanation
Indices: 59620647--59620750 Score: 81
Period size: 33 Copynumber: 3.2 Consensus size: 33
59620637 TCATTGGGTG
59620647 TTATCGGGTTTTGAAGCGAGTAGGCCCAGTGGC
1 TTATCGGGTTTTGAAGCGAGTAGGCCCAGTGGC
* * **** *
59620680 TTATC-AG-TTGGAATTGCCTCCA-GACCA-TGGGCC
1 TTATCGGGTTTTGAA--GCGAGTAGGCCCAGT-GG-C
59620713 TTATCGGGTTTTGAAGCGAGTAGGCCCAGTGGC
1 TTATCGGGTTTTGAAGCGAGTAGGCCCAGTGGC
59620746 TTATC
1 TTATC
59620751 AGTTGGAATT
Statistics
Matches: 49, Mismatches: 14, Indels: 16
0.62 0.18 0.20
Matches are distributed among these distances:
31 6 0.12
32 7 0.14
33 23 0.47
34 7 0.14
35 6 0.12
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (33 bp):
TTATCGGGTTTTGAAGCGAGTAGGCCCAGTGGC
Found at i:59621650 original size:13 final size:13
Alignment explanation
Indices: 59621634--59621658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59621624 GAAATTCTGA
59621634 TCATCTTTTCTTC
1 TCATCTTTTCTTC
59621647 TCATCTTTTCTT
1 TCATCTTTTCTT
59621659 TATTTTCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (13 bp):
TCATCTTTTCTTC
Found at i:59621697 original size:12 final size:13
Alignment explanation
Indices: 59621669--59621701 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
59621659 TATTTTCTTT
59621669 TTCTCCATCTACC
1 TTCTCCATCTACC
*
59621682 TTCTCC-TCTTCC
1 TTCTCCATCTACC
59621694 TTCTCCAT
1 TTCTCCAT
59621702 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:59622804 original size:28 final size:28
Alignment explanation
Indices: 59622772--59622836 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
59622762 ATTTACTAGA
*
59622772 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
59622800 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
59622828 ATACCCCTA
1 ATACCCCTA
59622837 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:59623000 original size:27 final size:27
Alignment explanation
Indices: 59622942--59623031 Score: 137
Period size: 28 Copynumber: 3.2 Consensus size: 27
59622932 AGGAAGCGTC
59622942 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
59622970 CTGGTGGCACTGCCACAAATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
59622997 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
59623026 CTGGTG
1 CTGGTG
59623032 ACTCTGTCAC
Statistics
Matches: 59, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
27 25 0.42
28 27 0.46
29 7 0.12
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.31
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:59623050 original size:55 final size:56
Alignment explanation
Indices: 59622942--59623056 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
59622932 AGGAAGCGTC
* *
59622942 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCACTGCCACAAATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACACTGCCACAAATATCTGTAT
* * * *
59622997 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCAC-ATTTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACACTGCCACAAATATCTGTAT
59623053 CTGG
1 CTGG
59623057 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 31 0.61
56 19 0.37
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACACTGCCACAAATATCTGTAT
Found at i:59623281 original size:19 final size:19
Alignment explanation
Indices: 59623257--59623295 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
59623247 TTTTAATTAT
* *
59623257 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
59623276 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
59623295 T
1 T
59623296 ATGATGAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:59630689 original size:46 final size:46
Alignment explanation
Indices: 59630622--59630714 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
59630612 ACACGGGTTA
*
59630622 GACACACGGGTGTGTGGTTGGCTGTGTAACCCAAGTCAGTATGTAT
1 GACACACGGGTGTGTGGTTGGCCGTGTAACCCAAGTCAGTATGTAT
59630668 GACACACGGGTGTGTGGTTGGCCGTGTAACCCAAGTCAGTATGTAT
1 GACACACGGGTGTGTGGTTGGCCGTGTAACCCAAGTCAGTATGTAT
59630714 G
1 G
59630715 CCCTGTTTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (46 bp):
GACACACGGGTGTGTGGTTGGCCGTGTAACCCAAGTCAGTATGTAT
Found at i:59637392 original size:23 final size:23
Alignment explanation
Indices: 59637362--59637406 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
59637352 ATTATAAAAC
59637362 AAAAAAAGGAAAAACAAACTAAA
1 AAAAAAAGGAAAAACAAACTAAA
59637385 AAAAAAAGGAAAAACAAACTAA
1 AAAAAAAGGAAAAACAAACTAA
59637407 GTTATTGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.78, C:0.09, G:0.09, T:0.04
Consensus pattern (23 bp):
AAAAAAAGGAAAAACAAACTAAA
Found at i:59644257 original size:18 final size:17
Alignment explanation
Indices: 59644230--59644263 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
59644220 TCATCAATAA
*
59644230 CTTTGACTCAGAATTTT
1 CTTTGACTCAAAATTTT
59644247 CTTTCGACTCAAAATTT
1 CTTT-GACTCAAAATTT
59644264 GTGGGTACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (17 bp):
CTTTGACTCAAAATTTT
Found at i:59665355 original size:2 final size:2
Alignment explanation
Indices: 59665348--59665384 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
59665338 GATCTTATTT
59665348 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
59665385 TTGCGTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:59667572 original size:24 final size:24
Alignment explanation
Indices: 59667544--59667596 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
59667534 AAGTTTTGAA
59667544 ATTAAAATATACA-TGATATATAAT
1 ATTAAAATATA-ATTGATATATAAT
* *
59667568 ATTAAAATTTAATTTATATATAAT
1 ATTAAAATATAATTGATATATAAT
59667592 ATTAA
1 ATTAA
59667597 CAATTTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTAAAATATAATTGATATATAAT
Found at i:59675830 original size:24 final size:24
Alignment explanation
Indices: 59675803--59675858 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
59675793 GAAAATATAC
* *
59675803 AGGGACTTGATTAGCAATTAACCA
1 AGGGACTTAATGAGCAATTAACCA
** *
59675827 AGGGACTTAATGATTATTTAACCA
1 AGGGACTTAATGAGCAATTAACCA
59675851 AGGGACTT
1 AGGGACTT
59675859 TTAATTAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (24 bp):
AGGGACTTAATGAGCAATTAACCA
Found at i:59677925 original size:47 final size:47
Alignment explanation
Indices: 59677800--59677927 Score: 168
Period size: 47 Copynumber: 2.7 Consensus size: 47
59677790 AATTGATAAG
* * * * * *
59677800 TACCTATACCATGACCTGTAGCCAAATCAAGCTAACTTATTCCAGAG
1 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATTCCAAAA
*
59677847 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTC-CTCTCAAAA
1 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATTC-CAAAA
*
59677894 TACCTATATCATGGCCCGTAGCCAAATCAAGGTA
1 TACCTATACCATGGCCCGTAGCCAAATCAAGGTA
59677928 TTATTTGCAC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
46 2 0.03
47 70 0.97
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (47 bp):
TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATTCCAAAA
Found at i:59684762 original size:33 final size:33
Alignment explanation
Indices: 59684725--59684791 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
59684715 TAGGTAAATC
59684725 ACACTATGAACGTCACAAGTGAATTGATTCACA
1 ACACTATGAACGTCACAAGTGAATTGATTCACA
59684758 ACACTATGAACGTCACAAGTGAATTGATTCACA
1 ACACTATGAACGTCACAAGTGAATTGATTCACA
59684791 A
1 A
59684792 ACAGATTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (33 bp):
ACACTATGAACGTCACAAGTGAATTGATTCACA
Found at i:59694402 original size:2 final size:2
Alignment explanation
Indices: 59694395--59694437 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
59694385 AAAGAAGAGG
59694395 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
59694437 T
1 T
59694438 AGATATACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:59695807 original size:18 final size:18
Alignment explanation
Indices: 59695781--59695822 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
59695771 GATGAAATTT
59695781 TAATATAATTTATT-TAAA
1 TAATATAA-TTATTGTAAA
*
59695799 TAATGTAATTATTGTAAA
1 TAATATAATTATTGTAAA
59695817 TTAATA
1 -TAATA
59695823 CTTAACCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (18 bp):
TAATATAATTATTGTAAA
Found at i:59697750 original size:6 final size:6
Alignment explanation
Indices: 59697740--59697773 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
59697730 GCCTTGACCG
* *
59697740 TTCTAG TTCTAG TTCTAC TTCTAC TTCTAC TTCT
1 TTCTAC TTCTAC TTCTAC TTCTAC TTCTAC TTCT
59697774 CTGAATGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.26, G:0.06, T:0.53
Consensus pattern (6 bp):
TTCTAC
Found at i:59702591 original size:87 final size:87
Alignment explanation
Indices: 59702435--59702594 Score: 259
Period size: 87 Copynumber: 1.8 Consensus size: 87
59702425 AAAGAGTTGG
* *
59702435 TGGTGCTAACATGATTTGAAAGCAATGCATATACGAATCAAGTACATAATTTAGTTATCCAAATA
1 TGGTGCTAACATGATTTGAAAGCAATGCATATACAAATCAAGTACATAAATTAGTTATCCAAATA
59702500 ATTTATAAGCAAAAGAGCTCAA
66 ATTTATAAGCAAAAGAGCTCAA
* *
59702522 TGGTTCTAACATGATTTGAAAGCAATGCATATACAAATCAAGTGTCA-AAATTAGTTATCCAAAT
1 TGGTGCTAACATGATTTGAAAGCAATGCATATACAAATCAAGT-ACATAAATTAGTTATCCAAAT
*
59702586 GATTTATAA
65 AATTTATAA
59702595 ACATGCTATT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
87 65 0.97
88 2 0.03
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (87 bp):
TGGTGCTAACATGATTTGAAAGCAATGCATATACAAATCAAGTACATAAATTAGTTATCCAAATA
ATTTATAAGCAAAAGAGCTCAA
Found at i:59705431 original size:16 final size:16
Alignment explanation
Indices: 59705410--59705440 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59705400 CTTGAAATTA
*
59705410 ATATAAATTTTATAAT
1 ATATAAACTTTATAAT
59705426 ATATAAACTTTATAA
1 ATATAAACTTTATAA
59705441 AAAATATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATAAACTTTATAAT
Found at i:59706433 original size:16 final size:16
Alignment explanation
Indices: 59706412--59706445 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59706402 TGTATTTATG
*
59706412 TATTTAAAATTTATTT
1 TATTTAAAATTTAATT
*
59706428 TATTTATAATTTAATT
1 TATTTAAAATTTAATT
59706444 TA
1 TA
59706446 GTTTTTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTAAAATTTAATT
Found at i:59712157 original size:18 final size:18
Alignment explanation
Indices: 59712130--59712164 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
59712120 ACTAACTGAA
59712130 TAACCATTTGAAATACAT
1 TAACCATTTGAAATACAT
*
59712148 TAACCTTTTGAAATACA
1 TAACCATTTGAAATACA
59712165 CGAATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (18 bp):
TAACCATTTGAAATACAT
Found at i:59721925 original size:43 final size:43
Alignment explanation
Indices: 59721771--59721930 Score: 151
Period size: 44 Copynumber: 3.7 Consensus size: 43
59721761 CGAAGGCAAC
* *
59721771 GACCTTTAACCCCCTAAGCAGTAGGGTAACAAGCTAAAGTTCATA
1 GACC-TTAACCCCCTAAGCAGTAGGGTAACAAGCCAAA-TTAATA
* * * * * * *
59721816 GATCTTATCACCCTAAGCAGTAGGGAAACAGATCGAAAATAAT-
1 GACCTTAACCCCCTAAGCAGTAGGGTAACA-AGCCAAATTAATA
* * *
59721859 GAGCTTTAACCTCCTAAGCAGTAGGGTAACAAGCCAAATTTATA
1 GA-CCTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTAATA
* *
59721903 GACCTTAACCCCCTCAGTAGTAGGGTAA
1 GACCTTAACCCCCTAAGCAGTAGGGTAA
59721931 TAGGCTGAAA
Statistics
Matches: 90, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
43 32 0.36
44 50 0.56
45 8 0.09
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (43 bp):
GACCTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTAATA
Found at i:59722112 original size:44 final size:44
Alignment explanation
Indices: 59722047--59722373 Score: 249
Period size: 44 Copynumber: 7.5 Consensus size: 44
59722037 AGATCTCAAC
*
59722047 CCCCTAAGCAGTAGGGAAACAGATTGAAGATGATGAGTCTTAAA
1 CCCCTAAGCAGTAGGGTAACAGATTGAAGATGATGAGTCTTAAA
** * * * * *
59722091 CCCCTAAGCAGTAGGGTAACAGGCT-AA-AT-TTACAGACCTCAAC
1 CCCCTAAGCAGTAGGGTAACAGATTGAAGATGAT-GAG-TCTTAAA
59722134 CCCCTAAGCAGTAGGG-AAGCAGATTGAAGATGATGAGTCTTAAA
1 CCCCTAAGCAGTAGGGTAA-CAGATTGAAGATGATGAGTCTTAAA
* * * * *
59722178 ACCCTAAGCAGTAGGGTAACAGACT-AA-AT-TTACAGATCTTAAC
1 CCCCTAAGCAGTAGGGTAACAGATTGAAGATGAT-GAG-TCTTAAA
* * ** *
59722221 CCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAGCCTTAAA
1 CCCCTAAGCAGTAGGGTAACAGATTGAAGATGATGAGTCTTAAA
* ** * **
59722265 CCCCTAAGCAGTAGGGTAACAGGTTG-ATTTTACAAGATCTTAAA
1 CCCCTAAGCAGTAGGGTAACAGATTGAAGATGATGAG-TCTTAAA
* * * ** * *
59722309 CCTCTAAGCAGTAGGGAAACAGA-TCAATGATGACAAGCCTTAAC
1 CCCCTAAGCAGTAGGGTAACAGATTGAA-GATGATGAGTCTTAAA
59722353 CCCCTAAGCAGTAGGGTAACA
1 CCCCTAAGCAGTAGGGTAACA
59722374 AGTTGAAAAT
Statistics
Matches: 217, Mismatches: 51, Indels: 30
0.73 0.17 0.10
Matches are distributed among these distances:
41 2 0.01
42 10 0.05
43 60 0.28
44 129 0.59
45 14 0.06
46 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (44 bp):
CCCCTAAGCAGTAGGGTAACAGATTGAAGATGATGAGTCTTAAA
Found at i:59722132 original size:87 final size:87
Alignment explanation
Indices: 59722031--59722373 Score: 481
Period size: 87 Copynumber: 3.9 Consensus size: 87
59722021 CAGATTGAAG
*
59722031 ATTTACAGATCTCAACCCCCTAAGCAGTAGGGAAACAGATTGAAGATGATGAGTCTTAAACCCCT
1 ATTTACAGATCTCAACCCCCTAAGCAGTAGGGAAACAGATTGAAGATGATGAGCCTTAAACCCCT
59722096 AAGCAGTAGGGTAACAGGCTAA
66 AAGCAGTAGGGTAACAGGCTAA
* * * *
59722118 ATTTACAGACCTCAACCCCCTAAGCAGTAGGGAAGCAGATTGAAGATGATGAGTCTTAAAACCCT
1 ATTTACAGATCTCAACCCCCTAAGCAGTAGGGAAACAGATTGAAGATGATGAGCCTTAAACCCCT
*
59722183 AAGCAGTAGGGTAACAGACTAA
66 AAGCAGTAGGGTAACAGGCTAA
* * **
59722205 ATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAGCCTTAAACCCCT
1 ATTTACAGATCTCAACCCCCTAAGCAGTAGGGAAACAGATTGAAGATGATGAGCCTTAAACCCCT
* *
59722270 AAGCAGTAGGGTAACAGGTTGA
66 AAGCAGTAGGGTAACAGGCTAA
* * * * * ** *
59722292 TTTTACAAGATCTTAAACCTCTAAGCAGTAGGGAAACAGA-TCAATGATGACAAGCCTTAACCCC
1 ATTTAC-AGATCTCAACCCCCTAAGCAGTAGGGAAACAGATTGAA-GATGATGAGCCTTAAACCC
59722356 CTAAGCAGTAGGGTAACA
64 CTAAGCAGTAGGGTAACA
59722374 AGTTGAAAAT
Statistics
Matches: 229, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
87 166 0.72
88 63 0.28
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (87 bp):
ATTTACAGATCTCAACCCCCTAAGCAGTAGGGAAACAGATTGAAGATGATGAGCCTTAAACCCCT
AAGCAGTAGGGTAACAGGCTAA
Found at i:59722504 original size:68 final size:68
Alignment explanation
Indices: 59722390--59722660 Score: 470
Period size: 68 Copynumber: 4.0 Consensus size: 68
59722380 AAATCAAATA
*
59722390 TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGAAGATCTCCTTGAAGTTTCAGTGG
1 TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGG
59722455 ATC
66 ATC
*
59722458 TCTTTTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGG
1 TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGG
59722523 ATC
66 ATC
* * * *
59722526 TCTTCTCCCTGATATGGTGTTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGTGA
1 TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGG
59722591 ATC
66 ATC
* *
59722594 TCTTCTCCCTGAAATGGCGTTGGAGCAGCTAAAAGCCACAGCAGATTTCCTTGAAGTTTCAGTGG
1 TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGG
59722659 AT
66 AT
59722661 TAATCGAAGC
Statistics
Matches: 190, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 190 1.00
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (68 bp):
TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGG
ATC
Found at i:59722688 original size:41 final size:42
Alignment explanation
Indices: 59722626--59722711 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 42
59722616 GAGCAGCTAA
* *
59722626 AAGCCACAGCAGATTTCCTTGAAGTTTCAGTGG-ATTAATCG
1 AAGCCACAGCAAATCTCCTTGAAGTTTCAGTGGAATTAATCG
* * *
59722667 AAGCTACAGCAAATCTCCTTGAAGTTTTAGTGGAATTAATTG
1 AAGCCACAGCAAATCTCCTTGAAGTTTCAGTGGAATTAATCG
59722709 AAG
1 AAG
59722712 TCATGTGTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 29 0.74
42 10 0.26
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (42 bp):
AAGCCACAGCAAATCTCCTTGAAGTTTCAGTGGAATTAATCG
Found at i:59726311 original size:44 final size:44
Alignment explanation
Indices: 59726252--59726555 Score: 203
Period size: 43 Copynumber: 7.0 Consensus size: 44
59726242 CCTTTATTTT
* * * *
59726252 AATCCGCTTCACTGTAATCTTAGGGTGATAAGATCTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
* ** * *
59726296 AATCTGCTCCGCTGTAATCTCAATGAGATAAGATCTGAAAT-TCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT---CTGGCTTC
* * * ** *
59726342 GATCTGTTCCACTGTAATCTCAGGGAAATAAGAT-AGTGTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
* *
59726385 AATCTGCTCCACTGTAATCTCAGGGAGATAAGA-C-CT-GATGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
* * * * *** *
59726426 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGATC-CTTTATTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTC-TGGCTTC
* * * *
59726470 AATCCGCTCCACTGTAA-CTTCAGGGAGATAGGAT-TATGTCTTC
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTCTGGCTTC
* * *
59726513 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTT
59726556 TAGTTTGCCC
Statistics
Matches: 199, Mismatches: 49, Indels: 24
0.73 0.18 0.09
Matches are distributed among these distances:
40 1 0.01
41 29 0.15
42 4 0.02
43 67 0.34
44 65 0.33
46 32 0.16
47 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
Found at i:59726398 original size:43 final size:43
Alignment explanation
Indices: 59726207--59726546 Score: 217
Period size: 44 Copynumber: 7.8 Consensus size: 43
59726197 AGACCTAATA
* * * * * *
59726207 CAATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTT
1 CAATCTGCTCCACTGTAATC-TCAGGGAGATAAGATACTGT-CTT
* * * * * * *
59726251 TAATCCGCTTCACTGTAATCTTAGGGTGATAAGATCTCTGGCTT
1 CAATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-ACTGTCTT
* **
59726295 CAATCTGCTCCGCTGTAATCTCAATGAGATAAGAT-CTGAAATTCTT
1 CAATCTGCTCCACTGTAATCTCAGGGAGATAAGATACTG----TCTT
* * * *
59726341 CGATCTGTTCCACTGTAATCTCAGGGAAATAAGATAGTGTCTT
1 CAATCTGCTCCACTGTAATCTCAGGGAGATAAGATACTGTCTT
* * *
59726384 CAATCTGCTCCACTGTAATCTCAGGGAGATAAGA-CCTG-ATG
1 CAATCTGCTCCACTGTAATCTCAGGGAGATAAGATACTGTCTT
* * * * * * *
59726425 CGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTT
1 CAATCTGCTCCACTGTAATC-TCAGGGAGATAAGATACTGT-CTT
* * *
59726469 TAATCCGCTCCACTGTAA-CTTCAGGGAGATAGGATTA-TGTCTT
1 CAATCTGCTCCACTGTAATC-TCAGGGAGATAAGA-TACTGTCTT
* *
59726512 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
1 CAATCTGCTCCACTGTAATCTCAGGGAGATAAGAT
59726547 TTCTGGCTTT
Statistics
Matches: 226, Mismatches: 57, Indels: 28
0.73 0.18 0.09
Matches are distributed among these distances:
40 1 0.00
41 29 0.13
42 9 0.04
43 64 0.28
44 85 0.38
45 4 0.02
46 32 0.14
47 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (43 bp):
CAATCTGCTCCACTGTAATCTCAGGGAGATAAGATACTGTCTT
Found at i:59726839 original size:86 final size:86
Alignment explanation
Indices: 59726744--59727588 Score: 1225
Period size: 86 Copynumber: 9.8 Consensus size: 86
59726734 AGCTTCAATG
** * * * *
59726744 CAACCGATGGAGGCAAGGCTTTGT-T-TTTGATCTGCTTTGCTGTTAATACAGGAAGGCAAGATC
1 CAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC
* * * *
59726807 TGCTTCTTTAACTAGCTCCA-CTG
65 T-TTTCTTTAACCAGCTCTATC-A
* ** * * *
59726830 CAATCGATGGATGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATC
1 CAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC
* *
59726893 TGCTTCTTTAACCAGCTCCA-CTA
65 T-TTTCTTTAACCAGCTCTATC-A
* * *
59726916 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC-
*
59726981 TTTGTCTTCAACCAGCTCTATCA
65 TTT-TCTTTAACCAGCTCTATCA
*
59727004 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
59727069 TTTCTTTAACCAGCTCTATCA
66 TTTCTTTAACCAGCTCTATCA
*
59727090 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
59727155 TTTCTTTAACCAGCTCTATCA
66 TTTCTTTAACCAGCTCTATCA
*
59727176 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
59727241 TTTCTTTAACCAGCTCTATCA
66 TTTCTTTAACCAGCTCTATCA
*
59727262 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
59727327 TTTCTTTAACCAGCTCTATCA
66 TTTCTTTAACCAGCTCTATCA
* *
59727348 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC-
*
59727413 TTTGTCTTCAACCAGCTCTATCA
65 TTT-TCTTTAACCAGCTCTATCA
* *
59727436 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC-
*
59727501 TTTGTCTTCAACCAGCTCTATCA
65 TTT-TCTTTAACCAGCTCTATCA
* * *
59727524 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTATCAATGCAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
59727589 GTAACTTCAT
Statistics
Matches: 721, Mismatches: 31, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
85 5 0.01
86 428 0.59
87 42 0.06
88 245 0.34
89 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (86 bp):
CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
TTTCTTTAACCAGCTCTATCA
Found at i:59731901 original size:19 final size:20
Alignment explanation
Indices: 59731872--59731920 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
59731862 CACTTCGTGA
* *
59731872 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
59731891 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
59731911 AAATG-AATGC
1 AAATGTAATGC
59731921 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:59733657 original size:87 final size:87
Alignment explanation
Indices: 59733549--59733929 Score: 334
Period size: 87 Copynumber: 4.4 Consensus size: 87
59733539 GATAAGATCC
*
59733549 TTTAATCCGCTCCACTGTAACTTCGGGGAGATAAGATAGTGTCTTCGATCTGCTCCGCTATAATC
1 TTTAATCCGCTCCACTGTAACTTCAGGGAGATAAGATAGTGTCTTCGATCTGCTCCGCTATAATC
59733614 TCAGGGAGATAAGATCTCTTAT
66 TCAGGGAGATAAGATCTCTTAT
* *
59733636 TTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATC
1 TTTAATCCGCTCCACTGTAACTTCAGGGAGATAAGATAGTGTCTTCGATCTGCTCCGCTATAATC
***
59733701 TCAGGGAGATAAGATCTGAAATT
66 TCAGGGAGATAAGATCTCTTA-T
** * * ** * * ** *
59733724 CTTTGGTCTGTTCCACTGTAA-TCTCAGGGAGATAAGA-CCTGAT-GT-GATCTTCTCTACTGTA
1 -TTTAATCCGCTCCACTGTAACT-TCAGGGAGATAAGATAGTG-TCTTCGATCTGCTCCGCTATA
*
59733785 A-CTTCAGAGAGATAAGATC-C----
63 ATC-TCAGGGAGATAAGATCTCTTAT
* * * * * * *
59733805 TTTAATCCGCTCCATTGTAA-TCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAA
1 TTTAATCCGCTCCACTGTAACT-TCAGGGAGATAAGA-TAGTGTCTTCGATCTGCTCCGCTATAA
***
59733869 TCTCAGGGAGATAAGATCTCTGGC
64 TCTCAGGGAGATAAGATCTCTTAT
* * * *
59733893 TTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGAT
1 TTTAATCCGCTCCACTGTAACTTCAGGGAGATAAGAT
59733930 CTGAAATTCT
Statistics
Matches: 238, Mismatches: 40, Indels: 32
0.77 0.13 0.10
Matches are distributed among these distances:
80 29 0.12
81 1 0.00
82 3 0.01
83 29 0.12
84 2 0.01
86 1 0.00
87 110 0.46
88 33 0.14
89 30 0.13
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (87 bp):
TTTAATCCGCTCCACTGTAACTTCAGGGAGATAAGATAGTGTCTTCGATCTGCTCCGCTATAATC
TCAGGGAGATAAGATCTCTTAT
Found at i:59733749 original size:46 final size:43
Alignment explanation
Indices: 59733524--59733974 Score: 283
Period size: 44 Copynumber: 10.5 Consensus size: 43
59733514 ATCTACTCTG
* * * *
59733524 CTGTAACCTCAGAGAGATAAGATC----CTTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGATCTATTCTTTGATCTGCTCCA
* * *
59733563 CTGTAA-CTTCGGGGAGATAAGA--TAGTGTCTTCGATCTGCTCCG
1 CTGTAATC-TCAGGGAGATAAGATCTA-T-TCTTTGATCTGCTCCA
* * * * *
59733606 CTATAATCTCAGGGAGATAAGATCTCTTATTTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGATCTATT-CTTTGATCTGCTCCA
* * *
59733650 CTGTAA-CTTCAGGGAGATAGGA--TAGTGTCTTCGATCTGCTCCG
1 CTGTAATC-TCAGGGAGATAAGATCTA-T-TCTTTGATCTGCTCCA
* *
59733693 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCA
1 CTGTAATCTCAGGGAGATAAGATCT---ATTCTTTGATCTGCTCCA
* * * *
59733739 CTGTAATCTCAGGGAGATAAGACCTGA---TGTGATCTTCTCTA
1 CTGTAATCTCAGGGAGATAAGATCT-ATTCTTTGATCTGCTCCA
* * *
59733780 CTGTAA-CTTCAGAGAGATAAGATC----CTTTAATCCGCTCCA
1 CTGTAATC-TCAGGGAGATAAGATCTATTCTTTGATCTGCTCCA
* * * *
59733819 TTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGATCTA-T-TCTTTGATCTGCTCCA
* * ** *
59733863 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGATCTAT-TCTTTGATCTGCTCCA
* * *
59733907 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCA
1 CTGTAATCTCAGGGAGATAAGATCT---ATTCTTTGATCTGCTCCA
59733953 CTGTAATCTCAGGGAGATAAGA
1 CTGTAATCTCAGGGAGATAAGA
59733975 CCTGTATAAT
Statistics
Matches: 314, Mismatches: 65, Indels: 59
0.72 0.15 0.13
Matches are distributed among these distances:
38 1 0.00
39 44 0.14
40 2 0.01
41 29 0.09
42 1 0.00
43 61 0.19
44 103 0.33
45 3 0.01
46 67 0.21
47 2 0.01
48 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (43 bp):
CTGTAATCTCAGGGAGATAAGATCTATTCTTTGATCTGCTCCA
Found at i:59742695 original size:46 final size:45
Alignment explanation
Indices: 59742627--59742718 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 45
59742617 AAACTTAATA
*
59742627 GATCAGCCTGAACTGCTAGAGTTTGCAGATGATCAGCTACTTCGC
1 GATCAGCCTGAACCGCTAGAGTTTGCAGATGATCAGCTACTTCGC
59742672 GNATCAGCCTGAACCGCTAGAGTTTGCAGATGATCAGCTACTTCGC
1 G-ATCAGCCTGAACCGCTAGAGTTTGCAGATGATCAGCTACTTCGC
59742718 G
1 G
59742719 CACTTGAGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 1 0.02
46 44 0.98
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.25
Consensus pattern (45 bp):
GATCAGCCTGAACCGCTAGAGTTTGCAGATGATCAGCTACTTCGC
Found at i:59745391 original size:15 final size:15
Alignment explanation
Indices: 59745371--59745402 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
59745361 ACATATGTGG
*
59745371 AAAATAAAATAAGAT
1 AAAATAAAATAACAT
59745386 AAAATAAAATAACAT
1 AAAATAAAATAACAT
59745401 AA
1 AA
59745403 TATATAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (15 bp):
AAAATAAAATAACAT
Found at i:59745658 original size:3 final size:3
Alignment explanation
Indices: 59745643--59745789 Score: 285
Period size: 3 Copynumber: 49.0 Consensus size: 3
59745633 AATAGTAAGG
*
59745643 ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
59745691 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
59745739 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
59745787 ATA
1 ATA
59745790 CTAAACAACA
Statistics
Matches: 142, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
3 142 1.00
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:59751461 original size:131 final size:129
Alignment explanation
Indices: 59751251--59751707 Score: 402
Period size: 131 Copynumber: 3.5 Consensus size: 129
59751241 ACACTTGGTT
* * * *** * *
59751251 ATTCGTGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCATTTACCCAAAGTAATCGAAGGT
1 ATTCG-GGAATCATGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGTTCAAAATAATCGAATGT
* * * * * * * *
59751316 CCCTTTAGAATTTCACTCATGTCTTCCAAAAATCCTTTAAAACGAAGGTAATACTCGGTGTTTGA
65 TCC-TTAGGATTTCATTCATGTCTTCTAAAAA-CCTTTAAAACGAAGGAAATATTCGATGTTTGG
*
59751381 TA
128 CA
* **
59751383 ATTCGGGAATCATACCCTATCGTGCTGGGTTGTGATTTCTCATTTGTTCAAAATAATCGAATGTT
1 ATTCGGGAATCATGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGTTCAAAATAATCGAATGTT
* * ** ** * **
59751448 CCTTCAGGTTTTCATTCATGT-TTATTAAAAACCTTCCGAAACGAAGGCGATTTTAAATGTTTGG
66 CCTT-AGGATTTCATTCATGTCTT-CTAAAAACCTT-TAAAACGAAGGAAATATTCGATGTTTGG
*
59751512 CG
128 CA
* * * * * *
59751514 ATTTGAGAATCGTGCCCTATCGTGCTGGGTTGCATATTT-TCGTTTGTTCAAAACAATC-AAAGA
1 ATTCGGGAATCATGCCCTATCGTGCTGGGTTGCA-ATTTCTCATTTGTTCAAAATAATCGAATG-
* * *
59751577 CTCCTTAGGAATTTCATTCATG-CTTTCTAAAAACCCTTTAAAACGAAAGAAATGTTCGATGTTT
64 TTCCTTAGG-ATTTCATTCATGTC-TTCTAAAAA-CCTTTAAAACGAAGGAAATATTCGATGTTT
59751641 GGCA
126 GGCA
*
59751645 ATTCGGTGAAT-AGTGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAATAATCGAAT
1 ATTCGG-GAATCA-TGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGTTCAAAATAATCGAAT
59751708 ATATCTTCGG
Statistics
Matches: 257, Mismatches: 55, Indels: 25
0.76 0.16 0.07
Matches are distributed among these distances:
130 14 0.05
131 182 0.71
132 59 0.23
133 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (129 bp):
ATTCGGGAATCATGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGTTCAAAATAATCGAATGTT
CCTTAGGATTTCATTCATGTCTTCTAAAAACCTTTAAAACGAAGGAAATATTCGATGTTTGGCA
Found at i:59757914 original size:21 final size:22
Alignment explanation
Indices: 59757874--59757914 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
59757864 ATTTTAAAAA
*
59757874 ATTTTCTTTTCGAAATTTTTAG
1 ATTTTCTTTTCGAAAATTTTAG
*
59757896 ATTTTTTTTTC-AAAATTTT
1 ATTTTCTTTTCGAAAATTTT
59757915 GGAATTAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.63
Consensus pattern (22 bp):
ATTTTCTTTTCGAAAATTTTAG
Found at i:59775232 original size:28 final size:29
Alignment explanation
Indices: 59775196--59775252 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
59775186 TTATTTGGGG
*
59775196 TTTCTGGTTGTAATTTTGGAC-TTTGAACT
1 TTTCTGGTTGTAATTTCGG-CTTTTGAACT
*
59775225 TTTC-GGTTTTAATTTCGGCTTTTGAACT
1 TTTCTGGTTGTAATTTCGGCTTTTGAACT
59775253 GTGGATGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 1 0.04
28 20 0.80
29 4 0.16
ACGTcount: A:0.16, C:0.12, G:0.19, T:0.53
Consensus pattern (29 bp):
TTTCTGGTTGTAATTTCGGCTTTTGAACT
Found at i:59778988 original size:21 final size:21
Alignment explanation
Indices: 59778962--59779003 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
59778952 TAGCAGCACA
59778962 GCCGTAATTACCTAATTATGT
1 GCCGTAATTACCTAATTATGT
59778983 GCCGTAATTACCTAATTATGT
1 GCCGTAATTACCTAATTATGT
59779004 ACCACATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (21 bp):
GCCGTAATTACCTAATTATGT
Found at i:59780495 original size:15 final size:15
Alignment explanation
Indices: 59780475--59780504 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
59780465 TATCTTGTTA
59780475 GTACAAAACTCCGGT
1 GTACAAAACTCCGGT
59780490 GTACAAAACTCCGGT
1 GTACAAAACTCCGGT
59780505 AAGGAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (15 bp):
GTACAAAACTCCGGT
Found at i:59789912 original size:22 final size:22
Alignment explanation
Indices: 59789842--59789913 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
59789832 TGCACCAGTA
* *
59789842 TATGAGAGCCCTTTAAGGGACG
1 TATGAGAGCCCTTTATGAGACG
* * *
59789864 TTTGAGAGCCCCTTGTGTAGGACG
1 TATGAGAGCCCTTTATG-A-GACG
*
59789888 TATGAAAGCCCTTTATGAGACG
1 TATGAGAGCCCTTTATGAGACG
59789910 TATG
1 TATG
59789914 GAAGACCATG
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
22 21 0.54
23 1 0.03
24 17 0.44
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (22 bp):
TATGAGAGCCCTTTATGAGACG
Found at i:59789973 original size:28 final size:28
Alignment explanation
Indices: 59789942--59790036 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 28
59789932 AATATATAAT
*
59789942 ATGTGGGAAGTCCATCAGGACTATTTAA
1 ATGTGGGAAGTCCATCAAGACTATTTAA
* * * * *
59789970 ATGTGGGGAGCCCTTCAAGACTGTCTAA
1 ATGTGGGAAGTCCATCAAGACTATTTAA
* * * *
59789998 ATGTAGGCAGTCCGTCAAGACGATCTTAA
1 ATGTGGGAAGTCCATCAAGACTAT-TTAA
59790027 ATGT-GGAAGT
1 ATGTGGGAAGT
59790037 TGTCCAAGAC
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
28 45 0.87
29 7 0.13
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.26
Consensus pattern (28 bp):
ATGTGGGAAGTCCATCAAGACTATTTAA
Found at i:59790044 original size:28 final size:29
Alignment explanation
Indices: 59789995--59790069 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
59789985 CAAGACTGTC
* * *
59789995 TAAATGTAGGCAGTCCGT-CAAGACGATCT
1 TAAATG-AGGAAGTCTGTCCAAGACAATCT
*
59790024 TAAATGTGGAAGT-TGTCCAAGACAATCT
1 TAAATGAGGAAGTCTGTCCAAGACAATCT
59790052 TAAATGAGGAAGTCTGTC
1 TAAATGAGGAAGTCTGTC
59790070 TAAATGTTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
27 2 0.05
28 27 0.69
29 10 0.26
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (29 bp):
TAAATGAGGAAGTCTGTCCAAGACAATCT
Found at i:59803842 original size:22 final size:22
Alignment explanation
Indices: 59803804--59803847 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
59803794 TTGCCCGGGC
* *
59803804 CCAAAACCAGACACAAATAAAA
1 CCAAAACCAAACACAAAAAAAA
59803826 CCAAAACCAAA-ACCAAAAAAAA
1 CCAAAACCAAACA-CAAAAAAAA
59803848 AAACAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.68, C:0.27, G:0.02, T:0.02
Consensus pattern (22 bp):
CCAAAACCAAACACAAAAAAAA
Found at i:59805061 original size:16 final size:17
Alignment explanation
Indices: 59805029--59805065 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
59805019 TATTCTTATT
59805029 TTTATTTCTCGTTGCTTA
1 TTTATTTCTC-TTGCTTA
59805047 TTTATTTCT-TTGCTTA
1 TTTATTTCTCTTGCTTA
59805063 TTT
1 TTT
59805066 TTACACTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.11, C:0.14, G:0.08, T:0.68
Consensus pattern (17 bp):
TTTATTTCTCTTGCTTA
Found at i:59805068 original size:18 final size:19
Alignment explanation
Indices: 59805023--59805068 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
59805013 CGTCATTATT
59805023 CTTATTTTTATTTCTCGTTG
1 CTTATTTTTATTTCTC-TTG
59805043 CTTA--TTTATTTCT-TTG
1 CTTATTTTTATTTCTCTTG
59805059 CTTATTTTTA
1 CTTATTTTTA
59805069 CACTTTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 7 0.29
18 13 0.54
20 4 0.17
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (19 bp):
CTTATTTTTATTTCTCTTG
Found at i:59806782 original size:87 final size:87
Alignment explanation
Indices: 59806632--59806832 Score: 357
Period size: 87 Copynumber: 2.3 Consensus size: 87
59806622 TGAATTCAAT
59806632 CCTATTCAGATGGACTTGATGAATTCATTGATATGTGAGGTTGAGTTTCTTACTCTTAATGAGTT
1 CCTATTCAGATGGACTTGATGAATTCATTGATATGTGAGGTTGAGTTTCTTACTCTTAATGAGTT
59806697 CATATCCCAGAGTTTGGATGGA
66 CATATCCCAGAGTTTGGATGGA
*
59806719 CCTATTCAGATGGACTTGATGAATTCATTGATATGTGAGGTTGAGTTTCTTACTCTTAGTGAGTT
1 CCTATTCAGATGGACTTGATGAATTCATTGATATGTGAGGTTGAGTTTCTTACTCTTAATGAGTT
*
59806784 CATATCCCAGAGTTTGGATGGT
66 CATATCCCAGAGTTTGGATGGA
* * *
59806806 CCTATTGAGACGAACTTGATGAATTCA
1 CCTATTCAGATGGACTTGATGAATTCA
59806833 CCGAATTTAA
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 109 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.37
Consensus pattern (87 bp):
CCTATTCAGATGGACTTGATGAATTCATTGATATGTGAGGTTGAGTTTCTTACTCTTAATGAGTT
CATATCCCAGAGTTTGGATGGA
Found at i:59810656 original size:3 final size:3
Alignment explanation
Indices: 59810650--59810677 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
59810640 TCATCAAACC
59810650 CAG CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG C
59810678 TTCAAGTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:59816599 original size:28 final size:28
Alignment explanation
Indices: 59816551--59816604 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
59816541 TTTTGGGCTC
*
59816551 AAATTAAATTATATATTTTTACTAGTAA
1 AAATTAAATTATATATTTTTAATAGTAA
59816579 AAATATAAATT-TATCA-TTTTAATAGT
1 AAAT-TAAATTATAT-ATTTTTAATAGT
59816605 TTATATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (28 bp):
AAATTAAATTATATATTTTTAATAGTAA
Found at i:59819166 original size:18 final size:19
Alignment explanation
Indices: 59819126--59819170 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
59819116 CAGTCGGTAA
59819126 CAATCAATTATTCAATAAT
1 CAATCAATTATTCAATAAT
* *
59819145 -AATCAGTTATTCAGT-AT
1 CAATCAATTATTCAATAAT
59819162 CAATCAATT
1 CAATCAATT
59819171 GATCGGTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (19 bp):
CAATCAATTATTCAATAAT
Found at i:59819180 original size:26 final size:27
Alignment explanation
Indices: 59819150--59819206 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 27
59819140 ATAATAATCA
*
59819150 GTTATTC-AGTATCAATCAATTGATCG
1 GTTATTCTAGTAACAATCAATTGATCG
59819176 GTTA-TCTAGTAACAATCAATTGATCG
1 GTTATTCTAGTAACAATCAATTGATCG
59819202 GTTAT
1 GTTAT
59819207 CCAATAGCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 2 0.07
26 26 0.93
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (27 bp):
GTTATTCTAGTAACAATCAATTGATCG
Found at i:59819207 original size:26 final size:26
Alignment explanation
Indices: 59819157--59819207 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
59819147 TCAGTTATTC
*
59819157 AGTATCAATCAATTGATCGGTTATCT
1 AGTAACAATCAATTGATCGGTTATCT
59819183 AGTAACAATCAATTGATCGGTTATC
1 AGTAACAATCAATTGATCGGTTATC
59819208 CAATAGCAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (26 bp):
AGTAACAATCAATTGATCGGTTATCT
Found at i:59819220 original size:26 final size:26
Alignment explanation
Indices: 59819162--59819222 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
59819152 TATTCAGTAT
* *
59819162 CAATCAATTGATCGGTTATCTAGTAA
1 CAATCAATTGATCGGTTATCCAATAA
*
59819188 CAATCAATTGATCGGTTATCCAATAG
1 CAATCAATTGATCGGTTATCCAATAA
*
59819214 CAGTCAATT
1 CAATCAATT
59819223 ATTCAGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (26 bp):
CAATCAATTGATCGGTTATCCAATAA
Found at i:59819238 original size:18 final size:18
Alignment explanation
Indices: 59819217--59819254 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
59819207 CCAATAGCAG
*
59819217 TCAATTATTCAGTAAAAA
1 TCAAATATTCAGTAAAAA
*
59819235 TCAAATATTCAGTAACAA
1 TCAAATATTCAGTAAAAA
59819253 TC
1 TC
59819255 GATCTTTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (18 bp):
TCAAATATTCAGTAAAAA
Found at i:59819496 original size:12 final size:12
Alignment explanation
Indices: 59819479--59819503 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59819469 AGTGCCGAAT
59819479 CGGTAACAGTAA
1 CGGTAACAGTAA
59819491 CGGTAACAGTAA
1 CGGTAACAGTAA
59819503 C
1 C
59819504 AGTAGTTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:59820595 original size:5 final size:5
Alignment explanation
Indices: 59820587--59820625 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
59820577 TTCTTTAGTT
59820587 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
59820626 GTTAAAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:59821474 original size:36 final size:35
Alignment explanation
Indices: 59821409--59821476 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
59821399 AAAATAATAG
*
59821409 CAAAAATAACAATAAAACAAGAGTCATATAATATC
1 CAAAAATAACAATAAAACAAGAGTAATATAATATC
*
59821444 CAAACAATAACAATAAAA-TAGTAGTAATATAAT
1 CAAA-AATAACAATAAAACAAG-AGTAATATAAT
59821477 GATGAAATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
35 6 0.21
36 23 0.79
ACGTcount: A:0.60, C:0.12, G:0.06, T:0.22
Consensus pattern (35 bp):
CAAAAATAACAATAAAACAAGAGTAATATAATATC
Found at i:59824013 original size:26 final size:26
Alignment explanation
Indices: 59823982--59824036 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
59823972 TTGCAAAAGT
* *
59823982 AAAAC-TACATATATAAACAAGACTAA
1 AAAACTTACAGATAAAAACAAGA-TAA
*
59824008 AAAACTTATAGATAAAAACAAGATAA
1 AAAACTTACAGATAAAAACAAGATAA
59824034 AAA
1 AAA
59824037 CTTTCAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.65, C:0.11, G:0.05, T:0.18
Consensus pattern (26 bp):
AAAACTTACAGATAAAAACAAGATAA
Found at i:59826341 original size:13 final size:13
Alignment explanation
Indices: 59826325--59826349 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59826315 TTTATTTTCC
59826325 ACGGTGGCCGGCA
1 ACGGTGGCCGGCA
59826338 ACGGTGGCCGGC
1 ACGGTGGCCGGC
59826350 GGTGGTGACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.32, G:0.48, T:0.08
Consensus pattern (13 bp):
ACGGTGGCCGGCA
Found at i:59827120 original size:22 final size:22
Alignment explanation
Indices: 59827095--59827194 Score: 94
Period size: 22 Copynumber: 4.3 Consensus size: 22
59827085 ATTATGCATA
**
59827095 TATATATTAATATTATATTATG
1 TATATATTTTTATTATATTATG
*
59827117 TATATTATTTTT-TTAAATATTATA
1 TATA-TATTTTTATT--ATATTATG
*
59827141 TATATGTATTTTTTTATATATTATG
1 TATA--TATTTTTAT-TATATTATG
*
59827166 TATATATTTTTAATATATTATG
1 TATATATTTTTATTATATTATG
59827188 TATATAT
1 TATATAT
59827195 ATTATGTACA
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
22 22 0.34
23 12 0.18
24 11 0.17
25 18 0.28
26 1 0.02
27 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
TATATATTTTTATTATATTATG
Found at i:59827156 original size:25 final size:24
Alignment explanation
Indices: 59827109--59827197 Score: 112
Period size: 25 Copynumber: 3.7 Consensus size: 24
59827099 TATTAATATT
59827109 ATATTATGTATATTATTTTTTTAA
1 ATATTATGTATATTATTTTTTTAA
* *
59827133 ATATTATATATATGTATTTTTTTAT
1 ATATTATGTATAT-TATTTTTTTAA
59827158 ATATTATGTATA-TA--TTTTTAA
1 ATATTATGTATATTATTTTTTTAA
59827179 TATATTATGTATATATATT
1 -ATATTATGTATAT-TATT
59827198 ATGTACATAC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
21 6 0.11
22 12 0.22
23 2 0.04
24 14 0.25
25 21 0.38
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
ATATTATGTATATTATTTTTTTAA
Found at i:59827230 original size:11 final size:11
Alignment explanation
Indices: 59827095--59827258 Score: 73
Period size: 11 Copynumber: 15.2 Consensus size: 11
59827085 ATTATGCATA
*
59827095 TATATATTA-A
1 TATATATTATG
59827105 TATTATATTATG
1 TA-TATATTATG
*
59827117 TATATTATT-TT
1 TATA-TATTATG
* *
59827128 TTTA-AATAT-
1 TATATATTATG
59827137 TATATA-TATG
1 TATATATTATG
*
59827147 TAT-T-TT-TT
1 TATATATTATG
59827155 TATATATTATG
1 TATATATTATG
*
59827166 TATATATT-TT
1 TATATATTATG
59827176 TAATATATTATG
1 T-ATATATTATG
59827188 TATATATATTATG
1 --TATATATTATG
*
59827201 TACATACTTAT-
1 TATATA-TTATG
*
59827212 AATATTATTATG
1 TATA-TATTATG
* *
59827224 TATTTATTCT-
1 TATATATTATG
59827234 TA-ATATATATG
1 TATATAT-TATG
59827245 TATATATTTATG
1 TATATA-TTATG
59827257 TA
1 TA
59827259 GTATTATTAA
Statistics
Matches: 116, Mismatches: 17, Indels: 40
0.67 0.10 0.23
Matches are distributed among these distances:
8 4 0.03
9 14 0.12
10 15 0.13
11 47 0.41
12 24 0.21
13 11 0.09
14 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (11 bp):
TATATATTATG
Found at i:59827360 original size:24 final size:24
Alignment explanation
Indices: 59827306--59827401 Score: 86
Period size: 25 Copynumber: 3.8 Consensus size: 24
59827296 CTAATATGTA
59827306 TATATTATGTAAATATTTTTAATAC
1 TATATTATGTAAATATTTTT-ATAC
*
59827331 TATATTATGTATATATTTTT-TAC
1 TATATTATGTAAATATTTTTATAC
* * *
59827354 ATGTATTATGTACATATTTTCAATAAC
1 -TATATTATGTAAATATTTT-TAT-AC
*
59827381 TATATCATATGTATATATTTT
1 TATAT--TATGTAAATATTTT
59827402 ATGTACATAC
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
23 3 0.05
24 17 0.29
25 19 0.32
26 5 0.08
27 2 0.03
28 13 0.22
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.53
Consensus pattern (24 bp):
TATATTATGTAAATATTTTTATAC
Found at i:59827363 original size:198 final size:194
Alignment explanation
Indices: 59827102--59827546 Score: 531
Period size: 204 Copynumber: 2.2 Consensus size: 194
59827092 ATATATATAT
* * * * *
59827102 TAATAT-TATATTATGTATATTATTTTTTTAAATATTATATATATGTATTTTTTTATATATTATG
1 TAATATATATATTATGTA-AATATTTTTATATATATTATGTATA--TATTTTTTCATATATTATG
*
59827166 TATATATTTT-TAA-TATAT-TATGTATATATATTATGTACATACTTATAATATTATTATGTATT
63 TACATATTTTATAACTATATATATGTATATATATTATGTACATACTTATAATATTATTATGTATT
* * *
59827228 TATTCTTAATATATATGTATATATTTATGTAGTATTATTAATAGTT-GCTTTTAATATTATTATT
128 TATTCTTAATATATA--TATATATATATGTA-TATTATTAATAGTTAGCTTTTAACATTATTATC
59827292 ATTTC
190 ATTTC
*
59827297 TAATATGTATATATTATGTAAATATTTTTAATACTATATTATGTATATATTTTTTACATGTATTA
1 TAATA--TATATATTATGTAAATATTTTT-ATA-TATATTATGTATATATTTTTT-CATATATTA
* *
59827362 TGTACATATTTTCAATAACTATATCATATGTATATATTTTATGTACATACTTTTAATATTATTAT
61 TGTACATATTTT--ATAACTATAT-ATATGTATATATATTATGTACATACTTATAATATTATTAT
* * * **
59827427 GTATTTATTTTTAATATATATATGTATATATTTATATTATTAATAGTTATTTTTTAACATTATTA
123 GTATTTATTCTTAATATATATATATATATATGTATATTATTAATAGTTAGCTTTTAACATTATTA
59827492 TCATTTC
188 TCATTTC
* * *
59827499 TAATATATATGTGTATCGTATATGTTTTTATATATATTATGTATATAT
1 TAATATATATAT-TAT-GTAAATATTTTTATATATATTATGTATATAT
59827547 CTTTAGTATT
Statistics
Matches: 215, Mismatches: 20, Indels: 25
0.83 0.08 0.10
Matches are distributed among these distances:
195 5 0.02
197 17 0.08
198 31 0.14
199 11 0.05
200 22 0.10
201 23 0.11
202 50 0.23
204 56 0.26
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (194 bp):
TAATATATATATTATGTAAATATTTTTATATATATTATGTATATATTTTTTCATATATTATGTAC
ATATTTTATAACTATATATATGTATATATATTATGTACATACTTATAATATTATTATGTATTTAT
TCTTAATATATATATATATATATGTATATTATTAATAGTTAGCTTTTAACATTATTATCATTTC
Found at i:59827427 original size:88 final size:87
Alignment explanation
Indices: 59827299--59827459 Score: 220
Period size: 88 Copynumber: 1.8 Consensus size: 87
59827289 ATTATTTCTA
* *
59827299 ATATGTATATATTATGTAAATATTTTTAATACTATATTATGTATATATTTTTTACATGTAT-TAT
1 ATATGTATATATTATGTAAATACTTTTAATACTATATTATGTATATA-TTTTTA-ATATATATAT
59827363 GTACATATTTTCAATAACTATATC
64 GTACATATTTTCAATAACTATATC
* *
59827387 ATATGTATATATTTTATGTACATACTTTTAATA-T-TATTATGTATTTATTTTTAATATATATAT
1 ATATGTATATA--TTATGTAAATACTTTTAATACTATATTATGTATATATTTTTAATATATATAT
*
59827450 GTATATATTT
64 GTACATATTT
59827460 ATATTATTAA
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
86 5 0.08
87 18 0.28
88 23 0.35
89 1 0.02
90 18 0.28
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (87 bp):
ATATGTATATATTATGTAAATACTTTTAATACTATATTATGTATATATTTTTAATATATATATGT
ACATATTTTCAATAACTATATC
Found at i:59827544 original size:23 final size:23
Alignment explanation
Indices: 59827178--59827401 Score: 92
Period size: 23 Copynumber: 9.4 Consensus size: 23
59827168 TATATTTTTA
*
59827178 ATATATTATGTATATATATTATGT
1 ATATATT-TTTATATATATTATGT
* * *
59827202 ACATACTTATA-ATATTATTATGT
1 ATATATTTTTATATA-TATTATGT
* *
59827225 ATTTATTCTTA-ATATA-TATGT
1 ATATATTTTTATATATATTATGT
*
59827246 ATATA--TTTATGTAGTATTAT-T
1 ATATATTTTTATATA-TATTATGT
59827267 A-ATAGTTGCTTT-TA-ATATTAT-T
1 ATATA-TT--TTTATATATATTATGT
59827289 AT-TATTTCTAATATGTATATATTATGT
1 ATATATTT-T--TA--TATATATTATGT
*
59827316 AAATATTTTTAATACTATATTATGT
1 ATATATTTTT-ATA-TATATTATGT
* *
59827341 ATATATTTTTTACATGTATTATGT
1 ATATA-TTTTTATATATATTATGT
* *
59827365 ACATATTTTCAATAACTATATCATATGT
1 ATATATTTT-TAT-A-TATAT--TATGT
59827393 ATATATTTT
1 ATATATTTT
59827402 ATGTACATAC
Statistics
Matches: 152, Mismatches: 21, Indels: 50
0.68 0.09 0.22
Matches are distributed among these distances:
19 4 0.03
20 6 0.04
21 15 0.10
22 19 0.12
23 25 0.16
24 22 0.14
25 23 0.15
26 17 0.11
27 3 0.02
28 18 0.12
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (23 bp):
ATATATTTTTATATATATTATGT
Found at i:59827551 original size:23 final size:22
Alignment explanation
Indices: 59827155--59827868 Score: 111
Period size: 24 Copynumber: 31.5 Consensus size: 22
59827145 TGTATTTTTT
* * *
59827155 TATATATTATGTATATATT-TT
1 TATATATTTTATATATATTATG
59827176 TAATATATTATGTATATATATTATG
1 T-ATATATT-T-TATATATATTATG
* *
59827201 TACATA-CTTATAATATTATTATG
1 TATATATTTTAT-ATA-TATTATG
*
59827224 TATTTATTCTTA-ATATA-TATG
1 TATATATT-TTATATATATTATG
*
59827245 TATATA-TTTATGTAGTATTAT-
1 TATATATTTTATATA-TATTATG
*
59827266 TA-ATAGTTGCTTTTA-ATATTAT-
1 TATATA-TT--TTATATATATTATG
59827288 TAT-TATTTCTAATATGTATATATTATG
1 TATATA-TT-T--TA--TATATATTATG
*
59827315 TAAATATTTTTAATACTATATTATG
1 TATATA-TTTT-ATA-TATATTATG
* *
59827340 TATATATTTTTTACATGTATTATG
1 TATATA--TTTTATATATATTATG
*
59827364 TACATATTTTCAATAACTATATCATATG
1 TATATATTTT--AT-A-TATAT--TATG
* *
59827392 TATATATTTTATGTACA-TACT-
1 TATATATTTTATATATATTA-TG
* * *
59827413 TTTA-ATATTAT-TAT-GTAT-
1 TATATATTTTATATATATTATG
* *
59827431 T-TATTTTTAATATATA-TATG
1 TATATATTTTATATATATTATG
59827451 TATATA-TTTATAT-TATTAATAG
1 TATATATTTTATATATATT-AT-G
*
59827473 T-TAT-TTTT-TA-ACATTAT-
1 TATATATTTTATATATATTATG
*
59827490 TATCAT-TTCTAATATATATGTGTATCG
1 TAT-ATATT-T--TATATATAT-TAT-G
*
59827517 TATATGTTTTTATATATATTATG
1 TATAT-ATTTTATATATATTATG
59827540 TATATATCTTTAGTAT-TATTA-G
1 TATATAT-TTTA-TATATATTATG
* *
59827562 TTATATGTTTTTTATACTATTTCATG
1 -TATATATTTTATATA-TA-TT-ATG
*
59827588 TATATATTTTTATATTATCCTTAT-
1 TATATA-TTTTATA-TAT-ATTATG
59827612 TAT-TATTATTAT-TAATATTA-G
1 TATATATT-TTATAT-ATATTATG
* *
59827633 TATGTGTTTTAT-TATA--A-G
1 TATATATTTTATATATATTATG
59827651 TATATATCTTTA-ATATA-TATG
1 TATATAT-TTTATATATATTATG
*
59827672 TATATA-TTTATGTAATATTAT-
1 TATATATTTTATAT-ATATTATG
* * * *
59827693 TAATAGTTGTTTTTTAAAACATTAT-
1 T-ATA--TATTTTAT-ATATATTATG
59827718 TAT-TATTTCTAATATGTATATACTATG
1 TATATATTT-T-ATA--TATAT--TATG
*
59827745 TAAATATTTTAATACTATATTATG
1 TATATATTTT-ATA-TATATTATG
* *
59827769 TATACATTTTTTATATATATTACG
1 TAT--ATATTTTATATATATTATG
59827793 TATATATATCTT-T-T-TGA-TAT-
1 TATATAT-T-TTATATAT-ATTATG
* *
59827813 TGTAT-TTTTATATATGTTATG
1 TATATATTTTATATATATTATG
*
59827834 TATATATCTTTAATACTATATTATT
1 TATATAT-TTT-ATA-TATATTATG
*
59827859 TTTATATTTT
1 TATATATTTT
59827869 CTATTTTTCA
Statistics
Matches: 519, Mismatches: 69, Indels: 207
0.65 0.09 0.26
Matches are distributed among these distances:
17 5 0.01
18 16 0.03
19 35 0.07
20 39 0.08
21 72 0.14
22 63 0.12
23 53 0.10
24 79 0.15
25 71 0.14
26 45 0.09
27 16 0.03
28 25 0.05
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (22 bp):
TATATATTTTATATATATTATG
Found at i:59827922 original size:57 final size:54
Alignment explanation
Indices: 59827815--59827922 Score: 119
Period size: 57 Copynumber: 1.9 Consensus size: 54
59827805 TTTGATATTG
* * *
59827815 TATTTTTATATATGTTATGTATATATCTTTAATACTATATTATTTTTATATTTTC
1 TATTTTTATATATCTTACGTATATATCTTTAATACTATATTA-TTGTATATTTTC
* *
59827870 TATTTTTCATATTATCTTACGTATATATTTTTTAATAACTGTATTA-TGTATAT
1 TATTTTT-ATA-TATCTTACGTATATA-TCTTTAAT-ACTATATTATTGTATAT
59827923 ACTATTACTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
55 7 0.16
56 3 0.07
57 19 0.43
58 7 0.16
59 8 0.18
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.59
Consensus pattern (54 bp):
TATTTTTATATATCTTACGTATATATCTTTAATACTATATTATTGTATATTTTC
Found at i:59830285 original size:21 final size:20
Alignment explanation
Indices: 59830200--59830288 Score: 72
Period size: 21 Copynumber: 4.2 Consensus size: 20
59830190 AGACATATGA
*
59830200 AAATGATACTATTTATAAAAAT
1 AAAT-ATACTA-TAATAAAAAT
*
59830222 ATATATACGTATAAT-AAAAT
1 AAATATAC-TATAATAAAAAT
* * *
59830242 ATATATACTAATATTAATAAT
1 AAATATACT-ATAATAAAAAT
*
59830263 AAATATACTAGGAATAAAAAT
1 AAATATACTA-TAATAAAAAT
59830284 AAATA
1 AAATA
59830289 AAATAATAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
19 1 0.02
20 18 0.33
21 31 0.56
22 5 0.09
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (20 bp):
AAATATACTATAATAAAAAT
Found at i:59830825 original size:22 final size:23
Alignment explanation
Indices: 59830787--59830845 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
59830777 ATATACACGA
* *
59830787 AATAGTATAAAAAATATATA-ACT
1 AATAATATATAAAATATATACA-T
59830810 AATAATAT-TAAAATATATACAT
1 AATAATATATAAAATATATACAT
*
59830832 GATAATATATAAAA
1 AATAATATATAAAA
59830846 AATGATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (23 bp):
AATAATATATAAAATATATACAT
Found at i:59830964 original size:2 final size:2
Alignment explanation
Indices: 59830951--59831022 Score: 53
Period size: 2 Copynumber: 38.0 Consensus size: 2
59830941 TTGCATAAAC
* * * *
59830951 AT AT AC AT AT AT AT AT -T AA AG AT AT AT AT AT AT AC AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
59830991 AT AT AT A- AA AT AT AT AC A- AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59831023 TGGAAATGAA
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
1 4 0.07
2 51 0.93
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (2 bp):
AT
Found at i:59830977 original size:13 final size:13
Alignment explanation
Indices: 59830957--59831006 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 13
59830947 AAACATATAC
59830957 ATATATATATTAAA
1 ATATATATA-TAAA
*
59830971 GATATATATATATAC
1 -ATATATATATA-AA
59830986 ATAATATATATAAA
1 AT-ATATATATAAA
59831000 ATATATA
1 ATATATA
59831007 CAATATATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 7 0.23
15 19 0.61
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATATATATAAA
Found at i:59830992 original size:11 final size:11
Alignment explanation
Indices: 59830978--59831019 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
59830968 AAAGATATAT
59830978 ATATATACATA
1 ATATATACATA
* *
59830989 ATATATATAAA
1 ATATATACATA
59831000 ATATATAC--A
1 ATATATACATA
59831009 ATATATACATA
1 ATATATACATA
59831020 TATTGGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 9 0.35
11 17 0.65
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (11 bp):
ATATATACATA
Found at i:59831155 original size:21 final size:21
Alignment explanation
Indices: 59831111--59831155 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
59831101 ATAGTGTTAG
* *
59831111 AAATATACAATATAATATTAA
1 AAATATACAATACAATAGTAA
59831132 AAATATAC-ATACAATAGTATA
1 AAATATACAATACAATAGTA-A
59831153 AAA
1 AAA
59831156 GATGTATATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (21 bp):
AAATATACAATACAATAGTAA
Found at i:59843171 original size:26 final size:26
Alignment explanation
Indices: 59843140--59843289 Score: 246
Period size: 26 Copynumber: 5.8 Consensus size: 26
59843130 TGAAATGCCC
59843140 ATCATGGAACATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAATCCATT
*
59843166 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAATCCATT
* *
59843192 ATCATGGAATATTTACCTAATCCATC
1 ATCATGGAACATTTACCTAATCCATT
*
59843218 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAATCCATT
* *
59843244 ATCATGGAATATTTACCTAATCCATC
1 ATCATGGAACATTTACCTAATCCATT
59843270 ATCATGGAACATTTACCTAA
1 ATCATGGAACATTTACCTAA
59843290 CCGTTGTGAG
Statistics
Matches: 113, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 113 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAATCCATT
Found at i:59843212 original size:52 final size:52
Alignment explanation
Indices: 59843140--59843291 Score: 286
Period size: 52 Copynumber: 2.9 Consensus size: 52
59843130 TGAAATGCCC
* *
59843140 ATCATGGAACATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATCATCATGGAACATTTACCTAACCCATT
59843192 ATCATGGAATATTTACCTAATCCATCATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATCATCATGGAACATTTACCTAACCCATT
59843244 ATCATGGAATATTTACCTAATCCATCATCATGGAACATTTACCTAACC
1 ATCATGGAATATTTACCTAATCCATCATCATGGAACATTTACCTAACC
59843292 GTTGTGAGCA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 98 1.00
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.32
Consensus pattern (52 bp):
ATCATGGAATATTTACCTAATCCATCATCATGGAACATTTACCTAACCCATT
Found at i:59850892 original size:29 final size:29
Alignment explanation
Indices: 59850833--59850892 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
59850823 AGTTATAATA
* *
59850833 ATCACTCAACTGTTTAATTTTATTTTTTT
1 ATCACTCAACTGTTTAATTTTATATTCTT
* *
59850862 ATCACTCAA-TTTTTAATTATTCTATTCTT
1 ATCACTCAACTGTTTAATT-TTATATTCTT
59850891 AT
1 AT
59850893 GTTATCATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.27, C:0.15, G:0.02, T:0.57
Consensus pattern (29 bp):
ATCACTCAACTGTTTAATTTTATATTCTT
Found at i:59852106 original size:17 final size:17
Alignment explanation
Indices: 59852075--59852108 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
59852065 AGTTTAATAT
* *
59852075 ATATTATTCATATTTAA
1 ATATTATTAAAATTTAA
59852092 ATATTATTAAAATTTAA
1 ATATTATTAAAATTTAA
59852109 CTAATTCAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTATTAAAATTTAA
Found at i:59853591 original size:7 final size:7
Alignment explanation
Indices: 59853581--59853611 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
59853571 AAAATAAATA
59853581 TTATATT
1 TTATATT
59853588 TTATATT
1 TTATATT
59853595 TTATATT
1 TTATATT
59853602 TTATATT
1 TTATATT
59853609 TTA
1 TTA
59853612 AAATTCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATATT
Found at i:59874245 original size:27 final size:27
Alignment explanation
Indices: 59874207--59874260 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
59874197 CCACTCTCAG
59874207 ATTCCTGTACTTTAAGGTAGTTGAGAA
1 ATTCCTGTACTTTAAGGTAGTTGAGAA
59874234 ATTCCTGTACTTTAAGGTAGTTGAGAA
1 ATTCCTGTACTTTAAGGTAGTTGAGAA
59874261 GATTTTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (27 bp):
ATTCCTGTACTTTAAGGTAGTTGAGAA
Found at i:59874272 original size:27 final size:27
Alignment explanation
Indices: 59874215--59874273 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
59874205 AGATTCCTGT
**
59874215 ACTTTAAGGTAGTTGAGAAATTCCTGT
1 ACTTTAAGGTAGTTGAGAAATTCCTAA
*
59874242 ACTTTAAGGTAGTTGAGAAGATT-TTAA
1 ACTTTAAGGTAGTTGAGAA-ATTCCTAA
59874269 ACTTT
1 ACTTT
59874274 TTTCAATTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.39
Consensus pattern (27 bp):
ACTTTAAGGTAGTTGAGAAATTCCTAA
Found at i:59881317 original size:40 final size:40
Alignment explanation
Indices: 59881271--59881422 Score: 187
Period size: 40 Copynumber: 4.0 Consensus size: 40
59881261 GAATATTTTA
*
59881271 TTTTATCTTTTAGTAGTTGAATAGAATAAAGGAATTATTT
1 TTTTATCTTTTAGTAGTTGATTAGAATAAAGGAATTATTT
* * *
59881311 TTTTATCTTTTATTAGTTTATTAGAATAAGGGAATTATTT
1 TTTTATCTTTTAGTAGTTGATTAGAATAAAGGAATTATTT
59881351 TTTTATC--TT--TA---G--TAGAATAAAGGAATTATTT
1 TTTTATCTTTTAGTAGTTGATTAGAATAAAGGAATTATTT
* *
59881382 TTTTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTT
1 TTTTATCTTTTAGTAGTTGATTAGAATAAAGGAATTATTT
59881422 T
1 T
59881423 CCCAATTAGG
Statistics
Matches: 95, Mismatches: 8, Indels: 18
0.79 0.07 0.15
Matches are distributed among these distances:
31 25 0.26
33 2 0.02
35 2 0.02
36 2 0.02
38 2 0.02
40 62 0.65
ACGTcount: A:0.32, C:0.03, G:0.14, T:0.51
Consensus pattern (40 bp):
TTTTATCTTTTAGTAGTTGATTAGAATAAAGGAATTATTT
Found at i:59881368 original size:31 final size:32
Alignment explanation
Indices: 59881327--59881397 Score: 117
Period size: 31 Copynumber: 2.2 Consensus size: 32
59881317 CTTTTATTAG
* *
59881327 TTTATTAGAATAAGGGAATTATTTTTTTATC-
1 TTTAGTAGAATAAAGGAATTATTTTTTTATCT
59881358 TTTAGTAGAATAAAGGAATTATTTTTTTATCT
1 TTTAGTAGAATAAAGGAATTATTTTTTTATCT
59881390 TTTAGTAG
1 TTTAGTAG
59881398 TTTATTAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
31 29 0.78
32 8 0.22
ACGTcount: A:0.32, C:0.03, G:0.14, T:0.51
Consensus pattern (32 bp):
TTTAGTAGAATAAAGGAATTATTTTTTTATCT
Found at i:59887716 original size:3 final size:3
Alignment explanation
Indices: 59887708--59887738 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
59887698 CAACCAATAA
59887708 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
59887739 ACTAAACAAA
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:59888461 original size:29 final size:30
Alignment explanation
Indices: 59888413--59888480 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
59888403 TTTTTATAGT
59888413 TTAT-ATTTTTATAATTTTTAAAAAATTAA
1 TTATAATTTTTATAATTTTTAAAAAATTAA
* *
59888442 TTCA-AATTTTTATAA-TTTTAAGAGATTAA
1 TT-ATAATTTTTATAATTTTTAAAAAATTAA
59888471 TTATAATTTT
1 TTATAATTTT
59888481 ATCTTTACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 1 0.03
29 22 0.65
30 11 0.32
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TTATAATTTTTATAATTTTTAAAAAATTAA
Found at i:59890374 original size:48 final size:48
Alignment explanation
Indices: 59890302--59890489 Score: 243
Period size: 48 Copynumber: 3.9 Consensus size: 48
59890292 TAGGGAATTT
* * *
59890302 ATTGATTTGGCTTCAAGACC-TGATATTGGCACTTCGGGTGTGAGCTTC
1 ATTGATTTGGCTTC-GGGCCATGATATTGGCACTTCGGGTGCGAGCTTC
* *
59890350 ATTGATTTGGCTTCGGGCCATGATATTGGCACTTCTGGTGCAAGCTTC
1 ATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCGAGCTTC
* * * *
59890398 ATTGATTTGGCTTCGGGCCATAATATTAGCCCTTCGGGTGCGAGCTAC
1 ATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCGAGCTTC
* * * *
59890446 ATTGATTTGGCTTCGAGCCATGATATTGACACTTAGGGTACGAG
1 ATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCGAG
59890490 ACTCTCGAGT
Statistics
Matches: 121, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
47 3 0.02
48 118 0.98
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (48 bp):
ATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCGAGCTTC
Found at i:59895046 original size:28 final size:28
Alignment explanation
Indices: 59895012--59895091 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
59895002 TTTGAATTTG
59895012 CGACCACAAAAGTTTAAAGTATATTTAC
1 CGACCACAAAAGTTTAAAGTATATTTAC
* * *
59895040 CGACCACGGAGAAGTGT-CA-TATATTTAC
1 CGACCAC--AAAAGTTTAAAGTATATTTAC
59895068 CGACCACAAAAGTTTAAAGTATAT
1 CGACCACAAAAGTTTAAAGTATAT
59895092 AATGACTCAG
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
26 6 0.14
27 1 0.02
28 28 0.67
29 1 0.02
30 6 0.14
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (28 bp):
CGACCACAAAAGTTTAAAGTATATTTAC
Found at i:59895632 original size:18 final size:18
Alignment explanation
Indices: 59895609--59895649 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
59895599 GATTTGTCAG
59895609 CAAGTTAAAGCTAAACAT
1 CAAGTTAAAGCTAAACAT
59895627 CAAGTTAAAGCTAAACAT
1 CAAGTTAAAGCTAAACAT
59895645 CAAGT
1 CAAGT
59895650 ACCTTCGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (18 bp):
CAAGTTAAAGCTAAACAT
Found at i:59913038 original size:47 final size:47
Alignment explanation
Indices: 59912955--59913044 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 47
59912945 CTTGGGTAAC
* *
59912955 TATGCATAATATTAAAAACATAAGGTTCAGTATGGTGGTTGCTTAAT
1 TATGCATAATATCAAAAACATAAGGTTCAGTATGGTGATTGCTTAAT
* * * *
59913002 TATGTATAATATCAAAATCATAAGGTAT-GGTGTGGTGATTGCT
1 TATGCATAATATCAAAAACATAAGGT-TCAGTATGGTGATTGCT
59913045 CACCTTGTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
47 35 0.97
48 1 0.03
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (47 bp):
TATGCATAATATCAAAAACATAAGGTTCAGTATGGTGATTGCTTAAT
Found at i:59913757 original size:53 final size:53
Alignment explanation
Indices: 59913699--59913806 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
59913689 TCTCTTTTAC
*
59913699 AAGGAAAAATTAAAATTAATTTTTTTTAAAAATTAAGAAAATTAAGAAATTAA
1 AAGGAAAAACTAAAATTAATTTTTTTTAAAAATTAAGAAAATTAAGAAATTAA
59913752 AAGGAAAAACTAAAATTAATTTTTTTTAAAAATTAAGAAAATTAAGAAATTAA
1 AAGGAAAAACTAAAATTAATTTTTTTTAAAAATTAAGAAAATTAAGAAATTAA
59913805 AA
1 AA
59913807 AGATAATATG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.32
Consensus pattern (53 bp):
AAGGAAAAACTAAAATTAATTTTTTTTAAAAATTAAGAAAATTAAGAAATTAA
Found at i:59915770 original size:38 final size:38
Alignment explanation
Indices: 59915719--59915795 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
59915709 CATTATGATA
*
59915719 TACAATTAAATCTAAAACTAATTTGAGCTTACGAATGC
1 TACAATTAAATCTAAAACTAATTCGAGCTTACGAATGC
*
59915757 TACAATTAAATCTAAGACTAATTCGAGCTTACGAATGC
1 TACAATTAAATCTAAAACTAATTCGAGCTTACGAATGC
59915795 T
1 T
59915796 TTTTATAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (38 bp):
TACAATTAAATCTAAAACTAATTCGAGCTTACGAATGC
Found at i:59917357 original size:22 final size:22
Alignment explanation
Indices: 59917332--59917374 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
59917322 TATCCAAATA
59917332 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
59917354 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
59917375 AATAGGAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:59917378 original size:11 final size:11
Alignment explanation
Indices: 59917339--59917379 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
59917329 ATAATAACAA
59917339 CAAAATAGTAG
1 CAAAATAGTAG
* *
59917350 CAACATAATAG
1 CAAAATAGTAG
*
59917361 TAAAATAGTAG
1 CAAAATAGTAG
59917372 CAAAATAG
1 CAAAATAG
59917380 GAAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:59918587 original size:22 final size:24
Alignment explanation
Indices: 59918559--59918602 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
59918549 ACTTTGTTCA
59918559 ACTTTAACTT-TTAT-TCAAAACC
1 ACTTTAACTTGTTATATCAAAACC
*
59918581 ACTTTAATTTGTTATATCAAAA
1 ACTTTAACTTGTTATATCAAAA
59918603 TATATGATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (24 bp):
ACTTTAACTTGTTATATCAAAACC
Found at i:59923070 original size:15 final size:14
Alignment explanation
Indices: 59923046--59923086 Score: 64
Period size: 15 Copynumber: 2.8 Consensus size: 14
59923036 TAAATTCAAC
59923046 ACTTAAATTTTTAAT
1 ACTT-AATTTTTAAT
59923061 ACTTATATTTTTAAT
1 ACTTA-ATTTTTAAT
59923076 ACTTAATTTTT
1 ACTTAATTTTT
59923087 CAGTTTATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
ACTTAATTTTTAAT
Found at i:59923996 original size:51 final size:52
Alignment explanation
Indices: 59923899--59924001 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 52
59923889 AGAATAAGGC
*
59923899 AAGTCCTACATTCTTGTTGGATGTTGTACTGTTTTTAGGTAAAAATAGACAACA
1 AAGTCCTACACTCTTGTTGGA--TTGTACTGTTTTTAGGTAAAAATAGACAACA
59923953 AAGTCCTACACTCTTGTTGGA-TGTACTGTTTTTAGGTAAAAATAGACAA
1 AAGTCCTACACTCTTGTTGGATTGTACTGTTTTTAGGTAAAAATAGACAA
59924002 AAATAATAGT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
51 28 0.58
54 20 0.42
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (52 bp):
AAGTCCTACACTCTTGTTGGATTGTACTGTTTTTAGGTAAAAATAGACAACA
Found at i:59925933 original size:22 final size:22
Alignment explanation
Indices: 59925905--59925951 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
59925895 TAAATTATAA
59925905 TAAAATGATAATGATACTACTT
1 TAAAATGATAATGATACTACTT
*
59925927 TAAAATGATAATGGTACTACTT
1 TAAAATGATAATGATACTACTT
59925949 TAA
1 TAA
59925952 TGTAGCCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.36
Consensus pattern (22 bp):
TAAAATGATAATGATACTACTT
Found at i:59948619 original size:20 final size:20
Alignment explanation
Indices: 59948594--59948635 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
59948584 TTTCATGTAC
59948594 GTGGTATTGTAATGTAAGTT
1 GTGGTATTGTAATGTAAGTT
59948614 GTGGTATTGTAATGTAAGTT
1 GTGGTATTGTAATGTAAGTT
59948634 GT
1 GT
59948636 AGATGTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (20 bp):
GTGGTATTGTAATGTAAGTT
Found at i:59948647 original size:7 final size:7
Alignment explanation
Indices: 59948637--59948662 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
59948627 GTAAGTTGTA
59948637 GATGTTT
1 GATGTTT
59948644 GATGTTT
1 GATGTTT
59948651 GATGTTT
1 GATGTTT
59948658 GATGT
1 GATGT
59948663 GCCTAGCAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (7 bp):
GATGTTT
Found at i:59951767 original size:15 final size:17
Alignment explanation
Indices: 59951743--59951779 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
59951733 CGTGTACTCT
59951743 ATTTTGATAT-TTTT-A
1 ATTTTGATATCTTTTGA
*
59951758 ATTTTTATATCTTTTGA
1 ATTTTGATATCTTTTGA
59951775 ATTTT
1 ATTTT
59951780 AAAGTTTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 9 0.47
16 4 0.21
17 6 0.32
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (17 bp):
ATTTTGATATCTTTTGA
Found at i:59959032 original size:16 final size:18
Alignment explanation
Indices: 59959011--59959045 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
59959001 ATAAATATTA
59959011 ATATTATAT-T-ATTTTT
1 ATATTATATGTCATTTTT
59959027 ATATTATATGTCATTTTT
1 ATATTATATGTCATTTTT
59959045 A
1 A
59959046 AATAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
ATATTATATGTCATTTTT
Found at i:59976440 original size:25 final size:25
Alignment explanation
Indices: 59976379--59976440 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
59976369 TTTGCTTGAA
*
59976379 AATTTATGTGATAGGAAAATCGTATG
1 AATTTA-GTGATAGGAAAATCGTATC
** * **
59976405 AAAATATTGATAGGAAAATTTTATC
1 AATTTAGTGATAGGAAAATCGTATC
59976430 AATTTAGTGAT
1 AATTTAGTGAT
59976441 TAGTTAGAAA
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (25 bp):
AATTTAGTGATAGGAAAATCGTATC
Found at i:59980334 original size:50 final size:50
Alignment explanation
Indices: 59980259--59980359 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
59980249 ACTTTTTTCT
*
59980259 GTCTATCATTACGATACTCTAATCTAATGGTATTAATTTCTAGCATTGGA
1 GTCTATCATTACGATACTCTAATCTAATGGTATTAATTTCTAACATTGGA
*
59980309 GTCTATCATTACGGTACTCTAATCTAATGGTATTAATTTCTAACATTGGA
1 GTCTATCATTACGATACTCTAATCTAATGGTATTAATTTCTAACATTGGA
59980359 G
1 G
59980360 AACACTAACC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.40
Consensus pattern (50 bp):
GTCTATCATTACGATACTCTAATCTAATGGTATTAATTTCTAACATTGGA
Found at i:59980810 original size:20 final size:19
Alignment explanation
Indices: 59980773--59980821 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
59980763 AAAATTCTCC
59980773 CTTTATTTTTTTTCTCTTT
1 CTTTATTTTTTTTCTCTTT
* *
59980792 CTTTCTTTTCTTTTTTCTTT
1 CTTTATTTT-TTTTCTCTTT
*
59980812 -TTAATTTTTT
1 CTTTATTTTTT
59980822 CTTCCCAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 2 0.08
19 14 0.56
20 9 0.36
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (19 bp):
CTTTATTTTTTTTCTCTTT
Found at i:59996974 original size:15 final size:15
Alignment explanation
Indices: 59996954--59997028 Score: 75
Period size: 15 Copynumber: 5.2 Consensus size: 15
59996944 GGCATTGTTT
* *
59996954 ATGATGAAGATGAAG
1 ATGATGGAGATGATG
*
59996969 ATGATGGGGATGATG
1 ATGATGGAGATGATG
*
59996984 ATGATGGTGATGATG
1 ATGATGGAGATGATG
59996999 ATGATGGA-A-G-TG
1 ATGATGGAGATGATG
* *
59997011 ATGATGGTGATGGTG
1 ATGATGGAGATGATG
59997026 ATG
1 ATG
59997029 CATGCAACAC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
12 9 0.18
13 2 0.04
14 2 0.04
15 38 0.75
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (15 bp):
ATGATGGAGATGATG
Found at i:59996986 original size:6 final size:6
Alignment explanation
Indices: 59996954--59997028 Score: 62
Period size: 6 Copynumber: 12.5 Consensus size: 6
59996944 GGCATTGTTT
* * ** *
59996954 ATGATG AAGATG AAGATG ATGGGG ATGATG ATGATG GTGATG ATGATG
1 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG
* * *
59997002 ATGGAAG -TGATG ATGGTG ATGGTG ATG
1 AT-GATG ATGATG ATGATG ATGATG ATG
59997029 CATGCAACAC
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
5 3 0.05
6 50 0.89
7 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (6 bp):
ATGATG
Found at i:59997003 original size:9 final size:9
Alignment explanation
Indices: 59996954--59997028 Score: 62
Period size: 9 Copynumber: 8.3 Consensus size: 9
59996944 GGCATTGTTT
*
59996954 ATGATGAAG
1 ATGATGATG
*
59996963 ATGAAGATG
1 ATGATGATG
**
59996972 ATGGGGATG
1 ATGATGATG
59996981 ATGATGATG
1 ATGATGATG
*
59996990 GTGATGATG
1 ATGATGATG
*
59996999 ATGATGGAAG
1 ATGAT-GATG
59997009 -TGATGATG
1 ATGATGATG
* *
59997017 GTGATGGTG
1 ATGATGATG
59997026 ATG
1 ATG
59997029 CATGCAACAC
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
8 3 0.06
9 46 0.88
10 3 0.06
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (9 bp):
ATGATGATG
Found at i:59997011 original size:18 final size:16
Alignment explanation
Indices: 59996962--59997028 Score: 77
Period size: 15 Copynumber: 4.2 Consensus size: 16
59996952 TTATGATGAA
*
59996962 GATGAAGATGATGGG-
1 GATGATGATGATGGGT
59996977 GATGATGATGAT-GGT
1 GATGATGATGATGGGT
59996992 GATGATGATGATGGAAGT
1 GATGATGATGATGG--GT
*
59997010 GATGATGGTGAT-GGT
1 GATGATGATGATGGGT
59997025 GATG
1 GATG
59997029 CATGCAACAC
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.04
15 29 0.63
16 1 0.02
17 1 0.02
18 13 0.28
ACGTcount: A:0.28, C:0.00, G:0.43, T:0.28
Consensus pattern (16 bp):
GATGATGATGATGGGT
Found at i:60017517 original size:39 final size:39
Alignment explanation
Indices: 60017463--60017582 Score: 186
Period size: 39 Copynumber: 3.1 Consensus size: 39
60017453 CCGGGTACCA
* *
60017463 TTCCAGCACGTAGCCTGCAGACTTCAAGTCCAGATATAT
1 TTCCAGCACATAGCCTGCGGACTTCAAGTCCAGATATAT
*
60017502 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT
1 TTCCAGCACATAGCCTGCGGACTTCAAGTCCAGATATAT
* * *
60017541 TTCCAGCATATAGCCTGCGGACCTCATGTCCAGATATAT
1 TTCCAGCACATAGCCTGCGGACTTCAAGTCCAGATATAT
60017580 TTC
1 TTC
60017583 AAATACCATG
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACTTCAAGTCCAGATATAT
Found at i:60018887 original size:21 final size:21
Alignment explanation
Indices: 60018862--60018902 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
60018852 CGACAATTTC
60018862 AATTCATACTT-TTCAACCATG
1 AATTC-TACTTATTCAACCATG
60018883 AATTCTACTTATTCAACCAT
1 AATTCTACTTATTCAACCAT
60018903 CATTTAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTCTACTTATTCAACCATG
Found at i:60020269 original size:24 final size:25
Alignment explanation
Indices: 60020241--60020292 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
60020231 AGAGAAAAGG
* *
60020241 AAAAATGTGCTACAAAACGGAAAAA
1 AAAAACGTGCTACAAAACAGAAAAA
*
60020266 AAAAACGTGCTACAAAGCAGAAAAA
1 AAAAACGTGCTACAAAACAGAAAAA
60020291 AA
1 AA
60020293 CACTATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.62, C:0.13, G:0.15, T:0.10
Consensus pattern (25 bp):
AAAAACGTGCTACAAAACAGAAAAA
Found at i:60020290 original size:26 final size:26
Alignment explanation
Indices: 60020227--60020292 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
60020217 TGAAACTAGA
** *
60020227 ACAAAG-AGAAAAGGAAAAATGTGCT
1 ACAAAGCAGAAAAAAAAAAACGTGCT
* *
60020252 ACAAAAC-GGAAAAAAAAAACGTGCT
1 ACAAAGCAGAAAAAAAAAAACGTGCT
60020277 ACAAAGCAGAAAAAAA
1 ACAAAGCAGAAAAAAA
60020293 CACTATTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
25 25 0.78
26 7 0.22
ACGTcount: A:0.62, C:0.12, G:0.18, T:0.08
Consensus pattern (26 bp):
ACAAAGCAGAAAAAAAAAAACGTGCT
Found at i:60021351 original size:14 final size:14
Alignment explanation
Indices: 60021321--60021354 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
60021311 TCAGAAATGT
*
60021321 AAATTATTTTTTAA
1 AAATTATTTTTCAA
*
60021335 AAATTATTTTTCGA
1 AAATTATTTTTCAA
60021349 AAATTA
1 AAATTA
60021355 CTTTCAGTAA
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:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (14 bp):
AAATTATTTTTCAA
Done.