Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 125 of 144
Found at i:30144132 original size:16 final size:17
Alignment explanation
Indices: 30144105--30144137 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
30144095 GCACACTGAT
*
30144105 TTTTCGATGTTTTTGCA
1 TTTTCGATGTTTCTGCA
30144122 TTTTC-ATGTTTCTGCA
1 TTTTCGATGTTTCTGCA
30144138 ATTGCAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.58
Consensus pattern (17 bp):
TTTTCGATGTTTCTGCA
Found at i:30144340 original size:265 final size:267
Alignment explanation
Indices: 30143865--30144374 Score: 721
Period size: 265 Copynumber: 1.9 Consensus size: 267
30143855 TTGACGTGGG
* *
30143865 TCTGCAATTGCAAAATCTCTCAATTTTTGATCCACAATAAGAAAAACATAGCTATCTGAGAAATC
1 TCTGCAATTGCAAAATCTCCCAATTTTTGATCCACAATAAGAAAAACATAGCTATCTAAGAAATC
* * ** * * *
30143930 CGTATTGTAGTCCATGCAACGTTTTTTGGGTTTATGTTACCAATAAAGCTTCTTGGGTTTCACAA
66 CATATGGTAGTCCATGCAACGTTTCCTGGGTTTATCTTACCAAAAAAGCTTCTTGGGTTTCAAAA
30143995 CTTATAATCGCACTCTTATAGTTATGCAAGTAGTTTACTTAAAATGTACAAAAACAAGAGGCTTA
131 CTTATAATCGCACTCTTATAGTTATGCAAGTAGTTTACTTAAAA-GTACAAAAACAAGAGGCTTA
* *
30144060 GAGTTGGTTTTAGGAGTTTCCTTGGATATAAGTTGGCA-CACTGATTTTTCGATGTTTTTGCATT
195 AAGTTGGTTTTAGGAGTTTCCTGGGATATAAGTTGGCACCACTGATTTTTCGATGTTTTTGCATT
30144124 TTCATGTT
260 TTCATGTT
* *
30144132 TCTGCAATTGCAAAA-CTCCCAATTTTTTATCCACAATAAG-AAAACATAGTTATGCTAAGAAAT
1 TCTGCAATTGCAAAATCTCCCAATTTTTGATCCACAATAAGAAAAACATAGCTAT-CTAAGAAAT
* *
30144195 CCATATGGTAGTTCATGCAAGGTTTCCTGGGTTTATCTTACCAAAAAATGCTTCTTGGGTTTCAA
65 CCATATGGTAGTCCATGCAACGTTTCCTGGGTTTATCTTACCAAAAAA-GCTTCTTGGGTTTC-A
* ** *
30144260 AAACTTATAATTGCA-TGC-T-T-GTTATTTAAGTAGTTTACTTGGAAAA-TACAAAAACAGGAG
128 AAACTTATAATCGCACT-CTTATAGTTATGCAAGTAGTTTACTT--AAAAGTACAAAAACAAGAG
*
30144320 GCTTAAAGTTGGTTTTAGGAGTTTCCTGGGATATAAGTTGGCACCACTGGTTTTT
190 GCTTAAAGTTGGTTTTAGGAGTTTCCTGGGATATAAGTTGGCACCACTGATTTTT
30144375 TCATATTTCT
Statistics
Matches: 216, Mismatches: 20, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
265 84 0.39
266 82 0.38
267 35 0.16
268 15 0.07
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (267 bp):
TCTGCAATTGCAAAATCTCCCAATTTTTGATCCACAATAAGAAAAACATAGCTATCTAAGAAATC
CATATGGTAGTCCATGCAACGTTTCCTGGGTTTATCTTACCAAAAAAGCTTCTTGGGTTTCAAAA
CTTATAATCGCACTCTTATAGTTATGCAAGTAGTTTACTTAAAAGTACAAAAACAAGAGGCTTAA
AGTTGGTTTTAGGAGTTTCCTGGGATATAAGTTGGCACCACTGATTTTTCGATGTTTTTGCATTT
TCATGTT
Found at i:30162710 original size:12 final size:13
Alignment explanation
Indices: 30162687--30162723 Score: 58
Period size: 12 Copynumber: 2.8 Consensus size: 13
30162677 TTGATTCTTA
30162687 AAAAAATCAAAATT
1 AAAAAAT-AAAATT
30162701 AAAAAA-AAAATT
1 AAAAAATAAAATT
30162713 AAAAAATAAAA
1 AAAAAATAAAA
30162724 AATTATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.55
13 4 0.18
14 6 0.27
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAATAAAATT
Found at i:30162710 original size:19 final size:19
Alignment explanation
Indices: 30162686--30162725 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
30162676 CTTGATTCTT
* *
30162686 AAAAAAATCAAAATTAAAA
1 AAAAAAATAAAAAATAAAA
*
30162705 AAAAAATTAAAAAATAAAA
1 AAAAAAATAAAAAATAAAA
30162724 AA
1 AA
30162726 TTATTTAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAAAAATAAAAAATAAAA
Found at i:30173980 original size:128 final size:128
Alignment explanation
Indices: 30173747--30174003 Score: 381
Period size: 128 Copynumber: 2.0 Consensus size: 128
30173737 AGGCTAGCAC
** *
30173747 CGATACGAAATAGAATGATGCTGATAATATCACCAAGGCTAATGATCTTTATTTGACTTTCAAAT
1 CGATACGAAATAGAAAAATGCTGATAATATCACCAAGGCCAATGATCTTTATTTGACTTTCAAAT
* *
30173812 GGCAAGCATGATCTCATAAAAACTAAGGCACATTACAATATCACTGATAATGATGAGCTGCAA
66 GCCAAGCATGATCTCATAAAAACCAAGGCACATTACAATATCACTGATAATGATGAGCTGCAA
* * *
30173875 CGATACTAAATAGAAAAATGTTGATAATATCACCAAGGCCAATGATCTTTATTTGA-TGTTCAAT
1 CGATACGAAATAGAAAAATGCTGATAATATCACCAAGGCCAATGATCTTTATTTGACT-TTCAAA
** * * *
30173939 TGCCTGGCATGATCTCATAAAACCCAAGGCACATTATAATATCATTGATAATGATGAGCTGCAA
65 TGCCAAGCATGATCTCATAAAAACCAAGGCACATTACAATATCACTGATAATGATGAGCTGCAA
30174003 C
1 C
30174004 AATTTACCTT
Statistics
Matches: 115, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
127 1 0.01
128 114 0.99
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (128 bp):
CGATACGAAATAGAAAAATGCTGATAATATCACCAAGGCCAATGATCTTTATTTGACTTTCAAAT
GCCAAGCATGATCTCATAAAAACCAAGGCACATTACAATATCACTGATAATGATGAGCTGCAA
Found at i:30185131 original size:10 final size:10
Alignment explanation
Indices: 30185098--30185140 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
30185088 TCCCAAAAAA
*
30185098 TTTGAATTTT
1 TTTGAATTAT
*
30185108 TTTAAATTAT
1 TTTGAATTAT
30185118 TTTGAATTAT
1 TTTGAATTAT
*
30185128 TTTGTATT-T
1 TTTGAATTAT
30185137 TTTG
1 TTTG
30185141 TTGAGAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 5 0.17
10 24 0.83
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.67
Consensus pattern (10 bp):
TTTGAATTAT
Found at i:30185746 original size:29 final size:28
Alignment explanation
Indices: 30185696--30185756 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 28
30185686 TGTGGTAATT
* *
30185696 AAAATAAAAACATTAAATTTAAAT-TTA
1 AAAATAAAAAAACTAAATTTAAATATTA
30185723 AAAATAAAAAAACTATAATATTAAATATTA
1 AAAATAAAAAAACTA-AAT-TTAAATATTA
30185753 AAAA
1 AAAA
30185757 ATACCTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 13 0.45
28 3 0.10
29 6 0.21
30 7 0.24
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (28 bp):
AAAATAAAAAAACTAAATTTAAATATTA
Found at i:30187960 original size:45 final size:45
Alignment explanation
Indices: 30187861--30187986 Score: 139
Period size: 45 Copynumber: 2.8 Consensus size: 45
30187851 ATTGGTAAGG
* * * * *
30187861 CTTCAAATAGCATAGTATTTAT-AGTTTATGGTTTAAGGTTTAGGA
1 CTTCAAATAACATAGTGTTTATGA-TTTAGGGTTTAAGGATCAGGA
*
30187906 CTTCAAATAATATAGTGTTTATGATTTAGGGTTTAAGGATCATGG-
1 CTTCAAATAACATAGTGTTTATGATTTAGGGTTTAAGGATCA-GGA
* * *
30187951 CTTCGAATAACGTAGGGTTTATGATTTAGGGTTTAA
1 CTTCAAATAACATAGTGTTTATGATTTAGGGTTTAA
30187987 AAATTATGAC
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
45 66 0.96
46 3 0.04
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.40
Consensus pattern (45 bp):
CTTCAAATAACATAGTGTTTATGATTTAGGGTTTAAGGATCAGGA
Found at i:30188011 original size:45 final size:45
Alignment explanation
Indices: 30187885--30188061 Score: 158
Period size: 45 Copynumber: 3.9 Consensus size: 45
30187875 GTATTTATAG
* ** * * *
30187885 TTTATGGTTTAAGGTTTAGGACTTCAAATAATATAGTGTTTATGA
1 TTTAGGGTTTAAGAATTATGACTTCAAATAATGTAGGGTTTATGA
* * * * *
30187930 TTTAGGGTTTAAGGATCATGGCTTCGAATAACGTAGGGTTTATGA
1 TTTAGGGTTTAAGAATTATGACTTCAAATAATGTAGGGTTTATGA
* * *
30187975 TTTAGGGTTTAAAAATTATGACTTTAAAAAATGTAGGGTTTAATG-
1 TTTAGGGTTTAAGAATTATGACTTCAAATAATGTAGGGTTT-ATGA
* * ** * *
30188020 TTCAGGGTTTATGAATTATGACTTTGAATAACGTAAGGTTTA
1 TTTAGGGTTTAAGAATTATGACTTCAAATAATGTAGGGTTTA
30188062 AGGTTTTGTT
Statistics
Matches: 107, Mismatches: 24, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
44 1 0.01
45 103 0.96
46 3 0.03
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.40
Consensus pattern (45 bp):
TTTAGGGTTTAAGAATTATGACTTCAAATAATGTAGGGTTTATGA
Found at i:30194765 original size:19 final size:19
Alignment explanation
Indices: 30194743--30194781 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
30194733 AAGGAGTTTC
*
30194743 ATATCAATATATTCCAATT
1 ATATCAAGATATTCCAATT
*
30194762 ATATCAAGATGTTCCAATT
1 ATATCAAGATATTCCAATT
30194781 A
1 A
30194782 ATGTTTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (19 bp):
ATATCAAGATATTCCAATT
Found at i:30196452 original size:29 final size:29
Alignment explanation
Indices: 30196417--30196486 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
30196407 ATTATAAGGC
* *
30196417 ATAGATCAAATTAGTCCCT-TCACTGTTAA
1 ATAGATCAAATTAATCCCTGT-ACTATTAA
*
30196446 ATAGATCAATTTAATCCCTGTACTATTAA
1 ATAGATCAAATTAATCCCTGTACTATTAA
*
30196475 AAAGAATCAAAT
1 ATAG-ATCAAAT
30196487 AATACCAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 27 0.79
30 7 0.21
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (29 bp):
ATAGATCAAATTAATCCCTGTACTATTAA
Found at i:30198543 original size:12 final size:12
Alignment explanation
Indices: 30198526--30198558 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
30198516 AGAGCCAGAT
30198526 TCATCTTCATCC
1 TCATCTTCATCC
*
30198538 TCATCTTCGTCC
1 TCATCTTCATCC
30198550 TCATCTTCA
1 TCATCTTCA
30198559 AACTTCTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.39, G:0.03, T:0.42
Consensus pattern (12 bp):
TCATCTTCATCC
Found at i:30205144 original size:12 final size:12
Alignment explanation
Indices: 30205127--30205159 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
30205117 AGAGCCAGAT
30205127 TCATCTTCATCC
1 TCATCTTCATCC
*
30205139 TCATCTTCGTCC
1 TCATCTTCATCC
30205151 TCATCTTCA
1 TCATCTTCA
30205160 AACTTCTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.39, G:0.03, T:0.42
Consensus pattern (12 bp):
TCATCTTCATCC
Found at i:30206650 original size:27 final size:29
Alignment explanation
Indices: 30206619--30206678 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
30206609 TTCTATACAT
30206619 TTTTTACATTTAA-AATTTAATTTA-TTA
1 TTTTTACATTTAAGAATTTAATTTATTTA
** *
30206646 TTTTTATTTTTAAGATTTTAATTTATTTA
1 TTTTTACATTTAAGAATTTAATTTATTTA
30206675 TTTT
1 TTTT
30206679 CAGATCTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 11 0.39
28 10 0.36
29 7 0.25
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (29 bp):
TTTTTACATTTAAGAATTTAATTTATTTA
Found at i:30207614 original size:19 final size:19
Alignment explanation
Indices: 30207590--30207637 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
30207580 TTTTGGTTTT
*
30207590 TGTTTAGAA-TAAAATGAAA
1 TGTTTAAAACTAAAA-GAAA
30207609 TGTTTAAAACTTAAAAGAAA
1 TGTTTAAAAC-TAAAAGAAA
*
30207629 TGTTCAAAA
1 TGTTTAAAA
30207638 TCACATCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 8 0.32
20 12 0.48
21 5 0.20
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.31
Consensus pattern (19 bp):
TGTTTAAAACTAAAAGAAA
Found at i:30207630 original size:20 final size:21
Alignment explanation
Indices: 30207599--30207637 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
30207589 TTGTTTAGAA
*
30207599 TAAAATGAAATGTTTAAAACT
1 TAAAATGAAATGTTCAAAACT
30207620 TAAAA-GAAATGTTCAAAA
1 TAAAATGAAATGTTCAAAA
30207638 TCACATCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.28
Consensus pattern (21 bp):
TAAAATGAAATGTTCAAAACT
Found at i:30208107 original size:247 final size:245
Alignment explanation
Indices: 30207671--30208163 Score: 677
Period size: 247 Copynumber: 2.0 Consensus size: 245
30207661 CTACGTTGTA
* * *
30207671 ATGTGCATATATGTAAAGCCAAAAGTTCAAATTTGACAAATAGACAGTCACGTTACAACTTACCT
1 ATGTGCATATATGCAAAGCCAAAAGTTCAAATTTGACAAATAGACAGTCACATCACAACTTACCT
* * *
30207736 TATCTCTACGTTGCAATATGCATATATGCAAAGCCAAAAGTATTCCAACCAAATGATCACATCGC
66 TATCTATACGTTACAATATGCATAAATGCAAAGCCAAAAGTATTCCAACCAAATGATCACATCGC
* *
30207801 AACTTCATAGGAAAGAATGTCGCAACATAGTTTTGAAATGTTGAGACTTCAATTGTCATTTACTT
131 AACTTCATAGGAAAGAATGTCGCAACATAGATTTGAAATGCTGAGACTTCAATTGTCATTT--TT
* ** *
30207866 CGCGGCTTTCCATTTTAGAAAAAAAAAACATGAACACACTCCGACTTGTGCC
194 CGCGACTCACCATTTTAGAAAAAAAAAACACGAACACACTCCGACTTGTGCC
* * ** *
30207918 ATGTGCATATATGCAAAGCCAAAGGTTCAAATTTTACAAATAGATGGTCACATCACATCTTACCT
1 ATGTGCATATATGCAAAGCCAAAAGTTCAAATTTGACAAATAGACAGTCACATCACAACTTACCT
* *
30207983 TATCTATACGTTACAATGTGCATAAATGCAAAG-TAAAAGGTGA-TCCAACCAAATGATCACATC
66 TATCTATACGTTACAATATGCATAAATGCAAAGCCAAAA-GT-ATTCCAACCAAATGATCACATC
* * * *
30208046 GCAACTTTATA-GAAGATAATGTCGCAACATGGATTTGGAATGCTGAGACTTCAATTGTCATTTT
129 GCAACTTCATAGGAA-AGAATGTCGCAACATAGATTTGAAATGCTGAGACTTCAATTGTCATTTT
* * * *
30208110 TCGCGACTCACCGTTTTAGAAAAAGAAAATACGAACACACTGCGACTTGTGCC
193 TCGCGACTCACCATTTTAGAAAAAAAAAACACGAACACACTCCGACTTGTGCC
30208163 A
1 A
30208164 ATGAGATTTC
Statistics
Matches: 216, Mismatches: 27, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
245 47 0.22
246 7 0.03
247 161 0.75
248 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (245 bp):
ATGTGCATATATGCAAAGCCAAAAGTTCAAATTTGACAAATAGACAGTCACATCACAACTTACCT
TATCTATACGTTACAATATGCATAAATGCAAAGCCAAAAGTATTCCAACCAAATGATCACATCGC
AACTTCATAGGAAAGAATGTCGCAACATAGATTTGAAATGCTGAGACTTCAATTGTCATTTTTCG
CGACTCACCATTTTAGAAAAAAAAAACACGAACACACTCCGACTTGTGCC
Found at i:30216654 original size:22 final size:23
Alignment explanation
Indices: 30216616--30216658 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
30216606 CTTGTATGAA
*
30216616 CTTATATAGTTTATATAGTTTAT
1 CTTATATAGCTTATATAGTTTAT
30216639 CTTATAT-GCTTATATAGTTT
1 CTTATATAGCTTATATAGTTT
30216659 GTTTTCCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.56
Consensus pattern (23 bp):
CTTATATAGCTTATATAGTTTAT
Found at i:30221973 original size:31 final size:33
Alignment explanation
Indices: 30221938--30222009 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 33
30221928 AAGTTTTTAT
30221938 AAAATATTTT-TAGAAAATTTAT-CAAACAAT-A
1 AAAATATTTTATA-AAAATTTATCCAAACAATAA
* **
30221969 AAAATATTTTATACAAATTTATCCGCACAATAA
1 AAAATATTTTATAAAAATTTATCCAAACAATAA
30222002 AAAATATT
1 AAAATATT
30222010 AATTTATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 18 0.51
32 8 0.23
33 9 0.26
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.35
Consensus pattern (33 bp):
AAAATATTTTATAAAAATTTATCCAAACAATAA
Found at i:30223696 original size:26 final size:27
Alignment explanation
Indices: 30223641--30223696 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
30223631 GAACCTTTTC
*
30223641 TTTTTTGCTACAAATTACTATATATAT
1 TTTTTTGCTACAAATTACTATAAATAT
* *
30223668 TTTTTTG-TACAATTTCATTATAAAT-T
1 TTTTTTGCTACAAATT-ACTATAAATAT
30223694 TTT
1 TTT
30223697 AATCATATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (27 bp):
TTTTTTGCTACAAATTACTATAAATAT
Found at i:30225173 original size:33 final size:32
Alignment explanation
Indices: 30225106--30225178 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 32
30225096 CATTTTAAGC
*
30225106 AAAATATTTTAAAAAAATTTATTAAACAATAA
1 AAAATATTTTAAAAAAATTCATTAAACAATAA
* *
30225138 AAAATATTTTACACAAATTCATCTAAAC-ATAA
1 AAAATATTTTAAAAAAATTCAT-TAAACAATAA
30225170 AAAAGTATT
1 AAAA-TATT
30225179 AATTTTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 27 0.75
33 9 0.25
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.33
Consensus pattern (32 bp):
AAAATATTTTAAAAAAATTCATTAAACAATAA
Found at i:30240721 original size:2 final size:2
Alignment explanation
Indices: 30240714--30240748 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
30240704 AGGCACTAAA
30240714 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
30240749 TTTATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30245767 original size:25 final size:25
Alignment explanation
Indices: 30245733--30245783 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
30245723 GGCATTCGGA
30245733 TCTTTTACTGCCACAGACATAACCT
1 TCTTTTACTGCCACAGACATAACCT
*
30245758 TCTTTTACTGCCACATACATAACCT
1 TCTTTTACTGCCACAGACATAACCT
30245783 T
1 T
30245784 TAAGTTACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.31, G:0.06, T:0.35
Consensus pattern (25 bp):
TCTTTTACTGCCACAGACATAACCT
Found at i:30252385 original size:12 final size:12
Alignment explanation
Indices: 30252368--30252393 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30252358 GAGTCTTAGA
30252368 GCACAAGTAAGT
1 GCACAAGTAAGT
30252380 GCACAAGTAAGT
1 GCACAAGTAAGT
30252392 GC
1 GC
30252394 TGAGTTCAAC
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:0.38, C:0.19, G:0.27, T:0.15
Consensus pattern (12 bp):
GCACAAGTAAGT
Found at i:30252442 original size:29 final size:29
Alignment explanation
Indices: 30252400--30252457 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
30252390 GTGCTGAGTT
30252400 CAACTGCACTGTCATTTATTCTACAATAC
1 CAACTGCACTGTCATTTATTCTACAATAC
30252429 CAACTGCACTGTCATTTATTCTACAATAC
1 CAACTGCACTGTCATTTATTCTACAATAC
30252458 TTAAGGTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (29 bp):
CAACTGCACTGTCATTTATTCTACAATAC
Found at i:30254748 original size:15 final size:16
Alignment explanation
Indices: 30254730--30254759 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30254720 TTTTAATTTT
30254730 TTTAA-TTTTAAACCG
1 TTTAATTTTTAAACCG
30254745 TTTAATTTTTAAACC
1 TTTAATTTTTAAACC
30254760 ATATTTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.13, G:0.03, T:0.50
Consensus pattern (16 bp):
TTTAATTTTTAAACCG
Found at i:30254756 original size:44 final size:44
Alignment explanation
Indices: 30254700--30254817 Score: 141
Period size: 44 Copynumber: 2.6 Consensus size: 44
30254690 GGTATAAAAT
* *
30254700 TTTAATATTTTAAATCTACATTTTAATTTTTTTAATTTTAAACCG
1 TTTAAT-TTTTAAATCTACATTTTAATTTTTTTAATATTAAACCA
* *
30254745 TTTAATTTTTAAA-CCATATTTTAACTTTTTTTAATATTAAACCA
1 TTTAATTTTTAAATCTACATTTTAA-TTTTTTTAATATTAAACCA
30254789 TTTAATTTTTCTATAAT-TACATTTTAATT
1 TTTAA-TTTT-TA-AATCTACATTTTAATT
30254818 AAAAAATAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
43 9 0.15
44 29 0.47
45 10 0.16
46 4 0.06
47 10 0.16
ACGTcount: A:0.34, C:0.09, G:0.01, T:0.56
Consensus pattern (44 bp):
TTTAATTTTTAAATCTACATTTTAATTTTTTTAATATTAAACCA
Found at i:30259039 original size:4 final size:4
Alignment explanation
Indices: 30259030--30259056 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
30259020 TTCGACAAGT
30259030 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
30259057 ATTTAAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:30279736 original size:2 final size:2
Alignment explanation
Indices: 30279729--30279754 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30279719 TAAGATTCAT
30279729 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
30279755 AGTTTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:30283177 original size:8 final size:8
Alignment explanation
Indices: 30283166--30283207 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
30283156 ATTAATTTTT
30283166 TAAAATTA
1 TAAAATTA
*
30283174 TAAAAATA
1 TAAAATTA
30283182 T-AAATTA
1 TAAAATTA
*
30283189 TTAAAATGA
1 -TAAAATTA
30283198 TAAAATTA
1 TAAAATTA
30283206 TA
1 TA
30283208 TTTTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 5 0.18
8 18 0.64
9 5 0.18
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (8 bp):
TAAAATTA
Found at i:30283188 original size:15 final size:17
Alignment explanation
Indices: 30283166--30283207 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
30283156 ATTAATTTTT
30283166 TAAAATTATAAAAAT-A
1 TAAAATTATAAAAATGA
*
30283182 T-AAATTATTAAAATGA
1 TAAAATTATAAAAATGA
30283198 TAAAATTATA
1 TAAAATTATA
30283208 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 3 0.14
17 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TAAAATTATAAAAATGA
Found at i:30283200 original size:24 final size:24
Alignment explanation
Indices: 30283137--30283207 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
30283127 ACTTTGATCT
* *
30283137 TTAAAATGATTAAAAAATAATTAATTTT
1 TTAAAATGA-T-AAAAAT-A-TAAATTA
*
30283165 TTAAAATTATAAAAATATAAATTA
1 TTAAAATGATAAAAATATAAATTA
*
30283189 TTAAAATGATAAAATTATA
1 TTAAAATGATAAAAATATA
30283208 TTTTTATTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
24 22 0.58
25 1 0.03
26 6 0.16
27 1 0.03
28 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (24 bp):
TTAAAATGATAAAAATATAAATTA
Found at i:30284580 original size:15 final size:14
Alignment explanation
Indices: 30284534--30284586 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
30284524 TAAAACATGT
30284534 TATTATA-TT-AAA
1 TATTATATTTAAAA
30284546 -ATTATATTTAAAA
1 TATTATATTTAAAA
*
30284559 TATTTATACTTAAATA
1 TA-TTATATTTAAA-A
30284575 TATTATATTTAA
1 TATTATATTTAA
30284587 GCCGAAATCC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
11 6 0.18
12 2 0.06
13 3 0.09
14 1 0.03
15 19 0.56
16 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTATATTTAAAA
Found at i:30285394 original size:20 final size:19
Alignment explanation
Indices: 30285342--30285406 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
30285332 TTTTGATAAA
30285342 TTAAATAATTATA-ATTTA-
1 TTAAAT-ATTATATATTTAT
30285360 TTAAAT-TT-TAT-TTTATT
1 TTAAATATTATATATTTA-T
30285377 TTAAATATTATATATTTAT
1 TTAAATATTATATATTTAT
*
30285396 ATTAATTATTA
1 -TTAAATATTA
30285407 ATTCAAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 6 0.15
16 2 0.05
17 6 0.15
18 8 0.21
19 4 0.10
20 13 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTAAATATTATATATTTAT
Found at i:30288386 original size:29 final size:28
Alignment explanation
Indices: 30288353--30288411 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
30288343 AATTGTTTTT
30288353 ATTTATAA-TTTATTATAAATTTTTAAAAA
1 ATTTA-AATTTTA-TATAAATTTTTAAAAA
* **
30288382 ATTTAAGTTTTATATATTTTTTTAAAAA
1 ATTTAAATTTTATATAAATTTTTAAAAA
30288410 AT
1 AT
30288412 AAATATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
ATTTAAATTTTATATAAATTTTTAAAAA
Found at i:30299803 original size:6 final size:6
Alignment explanation
Indices: 30299792--30299819 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
30299782 AAGATGATCA
30299792 TCAGGC TCAGGC TCAGGC TCAGGC TCAG
1 TCAGGC TCAGGC TCAGGC TCAGGC TCAG
30299820 CAGCTGCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.32, T:0.18
Consensus pattern (6 bp):
TCAGGC
Found at i:30301291 original size:23 final size:23
Alignment explanation
Indices: 30301240--30301292 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
30301230 TGATCTAAAC
*
30301240 AAATACTCATATTTATATAATTA
1 AAATATTCATATTTATATAATTA
*
30301263 AAATATTCATATTT-TATACTATA
1 AAATATTCATATTTATATAAT-TA
30301286 AAATATT
1 AAATATT
30301293 TATTATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATATTCATATTTATATAATTA
Found at i:30303723 original size:17 final size:18
Alignment explanation
Indices: 30303683--30303724 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
30303673 TAGTCTTAAT
30303683 AATTTTTTGAATTAATCGA
1 AATTTTTTGAATT-ATCGA
* *
30303702 TATTTTTTGAATT-TTGA
1 AATTTTTTGAATTATCGA
30303719 AATTTT
1 AATTTT
30303725 AAACAGTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 8 0.40
19 12 0.60
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (18 bp):
AATTTTTTGAATTATCGA
Found at i:30306077 original size:29 final size:30
Alignment explanation
Indices: 30306027--30306084 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
30306017 ACTTATATTT
30306027 TTAAAATAAAAATTAAAAAAAATAAATTCC
1 TTAAAATAAAAATTAAAAAAAATAAATTCC
30306057 TTAAAAT-AAAA-TAAAATAAAATAAATTC
1 TTAAAATAAAAATTAAAA-AAAATAAATTC
30306085 GAAATGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 5 0.19
29 15 0.56
30 7 0.26
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (30 bp):
TTAAAATAAAAATTAAAAAAAATAAATTCC
Found at i:30306509 original size:66 final size:67
Alignment explanation
Indices: 30306424--30306550 Score: 166
Period size: 66 Copynumber: 1.9 Consensus size: 67
30306414 TTTTTAATTA
* * * *
30306424 TTTTTCGCATATATGTTTATAACGTAATTTCTAGTTTCGTGATAAATTGTATATA-TATTTAAAG
1 TTTTTCACATATATATTTATAACGTAATTTCTAGTTTCGTAATAAATTATATATATTATTTAAAG
30306488 AT
66 AT
** * * *
30306490 TTTTTCACATATATATTTATAATTTAGTTTGTAGTTTCTTAATAAATTATATATATTATTT
1 TTTTTCACATATATATTTATAACGTAATTTCTAGTTTCGTAATAAATTATATATATTATTT
30306551 TTGTATACAC
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
66 46 0.90
67 5 0.10
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (67 bp):
TTTTTCACATATATATTTATAACGTAATTTCTAGTTTCGTAATAAATTATATATATTATTTAAAG
AT
Found at i:30312525 original size:16 final size:16
Alignment explanation
Indices: 30312481--30312526 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
30312471 TAAACTAATA
30312481 ATTATTCAATAAAATT
1 ATTATTCAATAAAATT
30312497 -TTGA-T-AA-AAAATT
1 ATT-ATTCAATAAAATT
30312510 ATTATTCAATAAAATT
1 ATTATTCAATAAAATT
30312526 A
1 A
30312527 ATTTGTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
13 7 0.28
14 5 0.20
15 5 0.20
16 8 0.32
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (16 bp):
ATTATTCAATAAAATT
Found at i:30314033 original size:21 final size:22
Alignment explanation
Indices: 30314004--30314046 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
30313994 ATTACTTAAA
*
30314004 TTTTAAAATGATTGG-TAATTT
1 TTTTAAAATGATCGGTTAATTT
*
30314025 TTTTTAAATGATCGGTTAATTT
1 TTTTAAAATGATCGGTTAATTT
30314047 CTATTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.53
Consensus pattern (22 bp):
TTTTAAAATGATCGGTTAATTT
Found at i:30314503 original size:13 final size:13
Alignment explanation
Indices: 30314487--30314511 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30314477 AACACACATT
30314487 TCTAAAATATAAA
1 TCTAAAATATAAA
30314500 TCTAAAATATAA
1 TCTAAAATATAA
30314512 TTTATATATA
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
TCTAAAATATAAA
Found at i:30323072 original size:2 final size:2
Alignment explanation
Indices: 30323065--30323107 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
30323055 ACAAGCTTAT
30323065 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
30323107 T
1 T
30323108 TCCCCTGCAC
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:30326904 original size:3 final size:3
Alignment explanation
Indices: 30326896--30326924 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
30326886 AAACATTTGC
30326896 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
30326925 AGAGGATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:30329604 original size:16 final size:16
Alignment explanation
Indices: 30329578--30329630 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
30329568 ATACAGCTGT
30329578 ATTTAATAATTTTA-TA
1 ATTT-ATAATTTTATTA
30329594 GATTTATAATTTTATTA
1 -ATTTATAATTTTATTA
*
30329611 ATTAATAA-TTTATTA
1 ATTTATAATTTTATTA
*
30329626 TTTTA
1 ATTTA
30329631 AAAGATGTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 10 0.31
16 16 0.50
17 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
ATTTATAATTTTATTA
Found at i:30329631 original size:16 final size:16
Alignment explanation
Indices: 30329580--30329625 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
30329570 ACAGCTGTAT
30329580 TTAATAATTTTA-TAGA
1 TTAATAATTTTATTA-A
*
30329596 TTTATAATTTTATTAA
1 TTAATAATTTTATTAA
30329612 TTAATAA-TTTATTA
1 TTAATAATTTTATTA
30329626 TTTTAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 7 0.26
16 18 0.67
17 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TTAATAATTTTATTAA
Found at i:30330004 original size:25 final size:26
Alignment explanation
Indices: 30329976--30330037 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
30329966 TAAGATGACT
30329976 ATATAAAAAATTTAATAAATA-AAAA
1 ATATAAAAAATTTAATAAATATAAAA
* * *
30330001 ATATATAAAA-TTATTAAATATTAAA
1 ATATAAAAAATTTAATAAATATAAAA
30330026 ATAATAAAAAAT
1 AT-ATAAAAAAT
30330038 ATATTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 9 0.30
25 14 0.47
26 7 0.23
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (26 bp):
ATATAAAAAATTTAATAAATATAAAA
Found at i:30334773 original size:39 final size:37
Alignment explanation
Indices: 30334714--30334799 Score: 127
Period size: 39 Copynumber: 2.3 Consensus size: 37
30334704 AAAAAAACGG
*
30334714 GAAAAAAAACACACAAATTTTACGTGAAAACCCTTTC
1 GAAAAAAAACACACAAATTTTACATGAAAACCCTTTC
*
30334751 GAAAAAAAACACACACAGATTTTATATGAAAACCCTTTC
1 GAAAAAAAACACACA-A-ATTTTACATGAAAACCCTTTC
*
30334790 GAGAAAAAAC
1 GAAAAAAAAC
30334800 CACGGGCAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 15 0.34
38 1 0.02
39 28 0.64
ACGTcount: A:0.51, C:0.20, G:0.09, T:0.20
Consensus pattern (37 bp):
GAAAAAAAACACACAAATTTTACATGAAAACCCTTTC
Found at i:30335113 original size:41 final size:41
Alignment explanation
Indices: 30335046--30335141 Score: 158
Period size: 41 Copynumber: 2.3 Consensus size: 41
30335036 GAATTTTATT
*
30335046 TTAATAAGAATTCTAGTCATCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCATCCAATTCTAACAATCTCCACC
30335087 TTAACAAGAATTCTAGTCA-CCTAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCATCC-AATTCTAACAATCTCCACC
*
30335128 TTGACAAGAATTCT
1 TTAACAAGAATTCT
30335142 CTATGAACAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
40 2 0.04
41 50 0.96
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.31
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCATCCAATTCTAACAATCTCCACC
Found at i:30340346 original size:21 final size:21
Alignment explanation
Indices: 30340322--30340361 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30340312 TTGTATGCCT
30340322 ACAATTACATCCTCGTTAGGC
1 ACAATTACATCCTCGTTAGGC
* *
30340343 ACAATTTCATTCTCGTTAG
1 ACAATTACATCCTCGTTAG
30340362 CCAAAATATC
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:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (21 bp):
ACAATTACATCCTCGTTAGGC
Found at i:30344319 original size:18 final size:18
Alignment explanation
Indices: 30344284--30344322 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
30344274 TATACCTTTT
**
30344284 TTTCACTTTAGTTTTTAA
1 TTTCACTTTAGTACTTAA
*
30344302 TTTCATTTTAGTACTTAA
1 TTTCACTTTAGTACTTAA
30344320 TTT
1 TTT
30344323 AGTATATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTCACTTTAGTACTTAA
Found at i:30344497 original size:23 final size:22
Alignment explanation
Indices: 30344454--30344500 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
30344444 TTTATTACTG
* * *
30344454 AAATTAAATTATATGTTTTAAA
1 AAATTAAATAATATATATTAAA
30344476 AAATTAAATAAATATATATTAAA
1 AAATTAAAT-AATATATATTAAA
30344499 AA
1 AA
30344501 TAAAAAATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATTAAATAATATATATTAAA
Found at i:30348610 original size:24 final size:24
Alignment explanation
Indices: 30348578--30348623 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
30348568 TATTTTTAAC
30348578 AATTAATAAAAATGT-AAAATTCAA
1 AATTAATAAAAAT-TCAAAATTCAA
*
30348602 AATTAATAATAATTCAAAATTC
1 AATTAATAAAAATTCAAAATTC
30348624 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (24 bp):
AATTAATAAAAATTCAAAATTCAA
Found at i:30369786 original size:23 final size:24
Alignment explanation
Indices: 30369755--30369800 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
30369745 AAAATATGAA
*
30369755 AAATATAAATTTAA-AAACTAAAAC
1 AAATATAAA-TAAATAAACTAAAAC
30369779 AAAT-TAAATAAATAAACTAAAA
1 AAATATAAATAAATAAACTAAAA
30369801 TAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 13 0.65
24 4 0.20
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.24
Consensus pattern (24 bp):
AAATATAAATAAATAAACTAAAAC
Found at i:30383591 original size:286 final size:286
Alignment explanation
Indices: 30383073--30383647 Score: 1089
Period size: 286 Copynumber: 2.0 Consensus size: 286
30383063 ACACCCAATG
30383073 TGACTAAACTATTAGCAAATTTACAGTATAGTCACTCATCATCAATAAGTTATAAAATGGTCACT
1 TGACTAAACTATTAGCAAATTTACAGTATAGTCACTCATCATCAATAAGTTATAAAATGGTCACT
*
30383138 GAAATATTCAAAAGTTTTCATTTACGTCTTTAGGCTATTAAAACCGTTGTTCTCTGGTTTTCTCT
66 GAAATATTCAAAAGTTTTCATTTACGTCTTTAGGCTATTAAAACCGTTGTTCTCTGGTCTTCTCT
* *
30383203 ATTTGCACTAGCTGCTCTAATCGAAAACTTTCTTTTTCTTTCTCTTTTACAAATTAGTTCTTTTT
131 ATTTGCACTAGCTGCTCTAATCGAAAACTCTCATTTTCTTTCTCTTTTACAAATTAGTTCTTTTT
*
30383268 TCATGAAACAATTTTAAACATCACAAATCTACGAATCAAAATCCAAACATATTTATTCTTTGATC
196 TCATGAAACAATTTTAAACATCACAAATCTACGAATCAAAATCCAAACATATTTATTCTTCGATC
30383333 TTCGATATTGACCGTCAAATTGACTT
261 TTCGATATTGACCGTCAAATTGACTT
30383359 TGACTAAACTATTAGCAAATTTACAGTATAGTCACTCATCATCAATAAGTTATAAAATGGTCACT
1 TGACTAAACTATTAGCAAATTTACAGTATAGTCACTCATCATCAATAAGTTATAAAATGGTCACT
30383424 GAAATATTCAAAAGTTTTCATTTACGTCTTTAGGCTATTAAAACCGTTGTTCTCTGGTCTTCTCT
66 GAAATATTCAAAAGTTTTCATTTACGTCTTTAGGCTATTAAAACCGTTGTTCTCTGGTCTTCTCT
30383489 ATTTGCACT-GCCTGCTCTAATCGAAAACTCTCATTTTCTTTCTCTTTTACAAATTAGTTCTTTT
131 ATTTGCACTAG-CTGCTCTAATCGAAAACTCTCATTTTCTTTCTCTTTTACAAATTAGTTCTTTT
*
30383553 TTCATGAAACAATTTTAAACATCACAAATCTGCGAATCAAAATCCAAACATATTTATTCTTCGAT
195 TTCATGAAACAATTTTAAACATCACAAATCTACGAATCAAAATCCAAACATATTTATTCTTCGAT
30383618 CTTCGATATTGACCGTCAAATTGACTT
260 CTTCGATATTGACCGTCAAATTGACTT
30383645 TGA
1 TGA
30383648 TCAAAGGTTT
Statistics
Matches: 283, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
285 1 0.00
286 282 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (286 bp):
TGACTAAACTATTAGCAAATTTACAGTATAGTCACTCATCATCAATAAGTTATAAAATGGTCACT
GAAATATTCAAAAGTTTTCATTTACGTCTTTAGGCTATTAAAACCGTTGTTCTCTGGTCTTCTCT
ATTTGCACTAGCTGCTCTAATCGAAAACTCTCATTTTCTTTCTCTTTTACAAATTAGTTCTTTTT
TCATGAAACAATTTTAAACATCACAAATCTACGAATCAAAATCCAAACATATTTATTCTTCGATC
TTCGATATTGACCGTCAAATTGACTT
Found at i:30385112 original size:17 final size:17
Alignment explanation
Indices: 30385060--30385112 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 17
30385050 TCCTTTTATA
30385060 ATTTTTTAATTTAATA-
1 ATTTTTTAATTTAATAT
*
30385076 AATTTTTAATTGTTAAATAT
1 ATTTTTTAA-T-TT-AATAT
*
30385096 TTTTTTTAATTTAATAT
1 ATTTTTTAATTTAATAT
30385113 GGATAATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
16 8 0.27
17 6 0.20
18 4 0.13
19 5 0.17
20 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
ATTTTTTAATTTAATAT
Found at i:30387075 original size:19 final size:20
Alignment explanation
Indices: 30387053--30387100 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
30387043 TCACGTCAGT
30387053 ATTTAATTAAAAT-TTAAAA
1 ATTTAATTAAAATATTAAAA
*
30387072 ATTT--TAAAAATATTAAAA
1 ATTTAATTAAAATATTAAAA
*
30387090 AATTAATTAAA
1 ATTTAATTAAA
30387101 TGTTAGATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
17 6 0.26
18 9 0.39
19 4 0.17
20 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTAATTAAAATATTAAAA
Found at i:30390351 original size:16 final size:16
Alignment explanation
Indices: 30390332--30390368 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
30390322 CTAATTTAAA
30390332 TTTTAAAATATTTATT
1 TTTTAAAATATTTATT
*
30390348 TTTT--AATATTTTTT
1 TTTTAAAATATTTATT
30390362 TTTTAAA
1 TTTTAAA
30390369 TTTAAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
14 13 0.72
16 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTAAAATATTTATT
Found at i:30390371 original size:13 final size:14
Alignment explanation
Indices: 30390338--30390372 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
30390328 TAAATTTTAA
30390338 AATATTTATTTTTT
1 AATATTTATTTTTT
*
30390352 AATATTTTTTTTTT
1 AATATTTATTTTTT
30390366 AA-ATTTA
1 AATATTTA
30390373 AATATGAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
AATATTTATTTTTT
Found at i:30397726 original size:15 final size:16
Alignment explanation
Indices: 30397693--30397745 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
30397683 TGTCCGATCC
*
30397693 ATTTTAAGT-TTATAAT
1 ATTTT-AGTATTATATT
30397709 ATTTTA-TATTATATT
1 ATTTTAGTATTATATT
30397724 ATTTTTATGTATTATATT
1 A-TTTTA-GTATTATATT
30397742 ATTT
1 ATTT
30397746 AAAACACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
14 1 0.03
15 8 0.25
16 10 0.31
17 3 0.09
18 10 0.31
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (16 bp):
ATTTTAGTATTATATT
Found at i:30398899 original size:24 final size:24
Alignment explanation
Indices: 30398871--30398919 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
30398861 GGGTTATATA
30398871 TTACCCAGGGATGGGTATAGGAGC
1 TTACCCAGGGATGGGTATAGGAGC
30398895 TTACCCAGGGATGGGTATAGGAGC
1 TTACCCAGGGATGGGTATAGGAGC
30398919 T
1 T
30398920 ATGTAAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.37, T:0.22
Consensus pattern (24 bp):
TTACCCAGGGATGGGTATAGGAGC
Found at i:30402019 original size:15 final size:16
Alignment explanation
Indices: 30401986--30402038 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
30401976 TGTCCGATCC
*
30401986 ATTTTAAGT-TTATAAT
1 ATTTT-AGTATTATATT
30402002 ATTTTA-TATTATATT
1 ATTTTAGTATTATATT
30402017 ATTTTTATGTATTATATT
1 A-TTTTA-GTATTATATT
30402035 ATTT
1 ATTT
30402039 AAAACACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
14 1 0.03
15 8 0.25
16 10 0.31
17 3 0.09
18 10 0.31
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (16 bp):
ATTTTAGTATTATATT
Found at i:30403192 original size:24 final size:24
Alignment explanation
Indices: 30403164--30403212 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
30403154 GGGTTATATA
30403164 TTACCCAGGGATGGGTATAGGAGC
1 TTACCCAGGGATGGGTATAGGAGC
30403188 TTACCCAGGGATGGGTATAGGAGC
1 TTACCCAGGGATGGGTATAGGAGC
30403212 T
1 T
30403213 ATGTAAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.37, T:0.22
Consensus pattern (24 bp):
TTACCCAGGGATGGGTATAGGAGC
Found at i:30406313 original size:15 final size:16
Alignment explanation
Indices: 30406280--30406332 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
30406270 TGTCCGATCC
*
30406280 ATTTTAAGT-TTATAAT
1 ATTTT-AGTATTATATT
30406296 ATTTTA-TATTATATT
1 ATTTTAGTATTATATT
30406311 ATTTTTATGTATTATATT
1 A-TTTTA-GTATTATATT
30406329 ATTT
1 ATTT
30406333 AAAACACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
14 1 0.03
15 8 0.25
16 10 0.31
17 3 0.09
18 10 0.31
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (16 bp):
ATTTTAGTATTATATT
Found at i:30407486 original size:24 final size:24
Alignment explanation
Indices: 30407458--30407506 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
30407448 GGGTTATATA
30407458 TTACCCAGGGATGGGTATAGGAGC
1 TTACCCAGGGATGGGTATAGGAGC
30407482 TTACCCAGGGATGGGTATAGGAGC
1 TTACCCAGGGATGGGTATAGGAGC
30407506 T
1 T
30407507 ATGTAAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.37, T:0.22
Consensus pattern (24 bp):
TTACCCAGGGATGGGTATAGGAGC
Found at i:30410603 original size:15 final size:16
Alignment explanation
Indices: 30410570--30410622 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
30410560 TGTCCGATCC
*
30410570 ATTTTAAGT-TTATAAT
1 ATTTT-AGTATTATATT
30410586 ATTTTA-TATTATATT
1 ATTTTAGTATTATATT
30410601 ATTTTTATGTATTATATT
1 A-TTTTA-GTATTATATT
30410619 ATTT
1 ATTT
30410623 AAAACACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
14 1 0.03
15 8 0.25
16 10 0.31
17 3 0.09
18 10 0.31
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (16 bp):
ATTTTAGTATTATATT
Found at i:30411774 original size:24 final size:24
Alignment explanation
Indices: 30411746--30411794 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
30411736 GGGTTATATA
30411746 TTACCCAGGGATGGGTATAGGAGC
1 TTACCCAGGGATGGGTATAGGAGC
30411770 TTACCCAGGGATGGGTATAGGAGC
1 TTACCCAGGGATGGGTATAGGAGC
30411794 T
1 T
30411795 ATGTAAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.37, T:0.22
Consensus pattern (24 bp):
TTACCCAGGGATGGGTATAGGAGC
Found at i:30416071 original size:23 final size:25
Alignment explanation
Indices: 30416027--30416075 Score: 84
Period size: 23 Copynumber: 2.0 Consensus size: 25
30416017 GGGTTATATA
30416027 TTACCCAGGGATGAGGTATAGGAGC
1 TTACCCAGGGATGAGGTATAGGAGC
30416052 TTACCCA-GGATG-GGTATAGGAGC
1 TTACCCAGGGATGAGGTATAGGAGC
30416075 T
1 T
30416076 ATGTAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 12 0.50
24 5 0.21
25 7 0.29
ACGTcount: A:0.27, C:0.16, G:0.35, T:0.22
Consensus pattern (25 bp):
TTACCCAGGGATGAGGTATAGGAGC
Found at i:30420608 original size:26 final size:26
Alignment explanation
Indices: 30420579--30420629 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
30420569 AAAACTCGAA
30420579 AGCTTCCAATGGAACTGAACTATTAT
1 AGCTTCCAATGGAACTGAACTATTAT
*
30420605 AGCTTCCAGTGGAACTGAACTATTA
1 AGCTTCCAATGGAACTGAACTATTA
30420630 CAACAAGTCA
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:0.20, G:0.18, T:0.29
Consensus pattern (26 bp):
AGCTTCCAATGGAACTGAACTATTAT
Found at i:30427233 original size:24 final size:24
Alignment explanation
Indices: 30427206--30427254 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
30427196 TGTTTTACAT
30427206 AGCTCCTATACCCATCCCTGGGTA
1 AGCTCCTATACCCATCCCTGGGTA
30427230 AGCTCCTATACCCATCCCTGGGTA
1 AGCTCCTATACCCATCCCTGGGTA
30427254 A
1 A
30427255 TATATAACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.37, G:0.16, T:0.24
Consensus pattern (24 bp):
AGCTCCTATACCCATCCCTGGGTA
Found at i:30427339 original size:20 final size:20
Alignment explanation
Indices: 30427302--30427339 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30427292 TTCAAAGTAT
*
30427302 ACATGAAATTCATTGAAACA
1 ACATGAAATTCATAGAAACA
30427322 ACATGAGAATTCA-AGAAA
1 ACATGA-AATTCATAGAAA
30427340 ACAAGTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (20 bp):
ACATGAAATTCATAGAAACA
Found at i:30428417 original size:15 final size:17
Alignment explanation
Indices: 30428380--30428415 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
30428370 AATGTGTTTT
30428380 AAATAATATAATACATAA
1 AAATAATATAATA-ATAA
30428398 AAATAATATAAT-ATAA
1 AAATAATATAATAATAA
30428414 AA
1 AA
30428416 TATTATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
18 12 0.67
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATAATATAATAATAA
Found at i:30438234 original size:20 final size:20
Alignment explanation
Indices: 30438203--30438240 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
30438193 AAATCGTTGG
30438203 TTAAATGTTTTTTTAAACATT
1 TTAAATG-TTTTTTAAACATT
30438224 TTAAA-GTTTTTTAAACA
1 TTAAATGTTTTTTAAACA
30438241 ATGAGATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 1 0.06
21 5 0.29
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (20 bp):
TTAAATGTTTTTTAAACATT
Found at i:30441831 original size:48 final size:48
Alignment explanation
Indices: 30441761--30441853 Score: 143
Period size: 48 Copynumber: 1.9 Consensus size: 48
30441751 AAGTTTTCTA
* *
30441761 TTTGTTTCTTGGGAAAAAACTCTATTTGTTTCTGGGGAAAATACTTTG
1 TTTGTTTCTTCGGAAAAAACTCTATTTGTTTCTCGGGAAAATACTTTG
*
30441809 TTTGTTT-TTCGGAAAAATACTCTGTTTGTTTCTCGGGAAAATACT
1 TTTGTTTCTTCGGAAAAA-ACTCTATTTGTTTCTCGGGAAAATACT
30441854 AAACCCATCT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 9 0.22
48 32 0.78
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (48 bp):
TTTGTTTCTTCGGAAAAAACTCTATTTGTTTCTCGGGAAAATACTTTG
Found at i:30441850 original size:24 final size:24
Alignment explanation
Indices: 30441761--30441853 Score: 123
Period size: 24 Copynumber: 3.9 Consensus size: 24
30441751 AAGTTTTCTA
* * *
30441761 TTTGTTTCTTGGGAAAAAACTCTA
1 TTTGTTTCTCGGGAAAATACTCTG
* *
30441785 TTTGTTTCTGGGGAAAATACTTTG
1 TTTGTTTCTCGGGAAAATACTCTG
* *
30441809 TTTGTTTTTCGGAAAAATACTCTG
1 TTTGTTTCTCGGGAAAATACTCTG
30441833 TTTGTTTCTCGGGAAAATACT
1 TTTGTTTCTCGGGAAAATACT
30441854 AAACCCATCT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (24 bp):
TTTGTTTCTCGGGAAAATACTCTG
Found at i:30443387 original size:29 final size:28
Alignment explanation
Indices: 30443342--30443396 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
30443332 GACAGAACAC
*
30443342 AAGTTTAAGGGCCAACTAGGTCCAAAAA
1 AAGTTTAAGGGCCAACTAGGTACAAAAA
*
30443370 AAGTTTTAGGGACCAACTAGGTACAAA
1 AAGTTTAAGGG-CCAACTAGGTACAAA
30443397 TGGATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (28 bp):
AAGTTTAAGGGCCAACTAGGTACAAAAA
Found at i:30453837 original size:6 final size:6
Alignment explanation
Indices: 30453828--30453899 Score: 53
Period size: 6 Copynumber: 12.2 Consensus size: 6
30453818 GGTTTTTATT
*
30453828 ATTTAA ATTTAGA A--TAA ATTTAA ATTTAA ATTTTTAA A--CAA ATTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA A--TTTAA ATTTAA ATTTAA
* **
30453875 ACTTAA AAATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA A
30453900 ATCAATTCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
4 5 0.10
5 2 0.04
6 37 0.71
7 2 0.04
8 6 0.12
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:30453872 original size:18 final size:18
Alignment explanation
Indices: 30453849--30453900 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
30453839 GAATAAATTT
**
30453849 AAATTTAAATTTTTAAAC
1 AAATTTAAATTTAAAAAC
* *
30453867 AAATTTAAACTTAAAAAT
1 AAATTTAAATTTAAAAAC
30453885 AAATTTAAATTTAAAA
1 AAATTTAAATTTAAAA
30453901 TCAATTCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATTTAAATTTAAAAAC
Found at i:30454524 original size:49 final size:49
Alignment explanation
Indices: 30454438--30454579 Score: 169
Period size: 49 Copynumber: 2.9 Consensus size: 49
30454428 CCTTTGCCTT
** *
30454438 CATATCTTCGCGGTACTGGATTTGCCGCTGCGGCTTAAATCTTTCCCTA-
1 CATATCTTCATGGTACTGGATTTGCCGTTGCGGCTTAAATCTTTCCC-AG
* * * * *
30454487 CGTATCTTTATGGTTCTGGATTTGTCGTTGCGACTTAAATCTTTCCCAG
1 CATATCTTCATGGTACTGGATTTGCCGTTGCGGCTTAAATCTTTCCCAG
* * *
30454536 CATATCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTT
1 CATATCTTCATGGTACTGGATTTGCCGTTGCGGCTTAAATCTTT
30454580 TCCTTCATGT
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
48 1 0.01
49 75 0.99
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (49 bp):
CATATCTTCATGGTACTGGATTTGCCGTTGCGGCTTAAATCTTTCCCAG
Found at i:30454600 original size:49 final size:49
Alignment explanation
Indices: 30454514--30455033 Score: 360
Period size: 49 Copynumber: 10.4 Consensus size: 49
30454504 GGATTTGTCG
* ** * * * * *
30454514 TTGCGACTTAAATCTTTCCCAGCATATCTTCGTGGTACTGGATTCGCCA
1 TTGCGACTTAGATCTTTCCCTTCATGTTTTTGAGGTACTGGATCCGCCA
* * * *
30454563 TTGCGGCTTAAATCTTTTCCTTCATGTTTTTGAGGTACATGG-TCCGCCG
1 TTGCGACTTAGATCTTTCCCTTCATGTTTTTGAGGTAC-TGGATCCGCCA
* * * * **
30454612 TTGCGACTTATACCTTTCCCTTTA-GTATATTTGTGGTACTGGATATGCCA
1 TTGCGACTTAGATCTTTCCCTTCATGT-T-TTTGAGGTACTGGATCCGCCA
* * * *
30454662 TTGCGGTCTTAGATCTTTCCCTTCATGTTTCTGAGGTACACGG-TCCGCCG
1 TTGC-GACTTAGATCTTTCCCTTCATGTTTTTGAGGTAC-TGGATCCGCCA
* * * * *
30454712 TTGCGACTTAGACCTTTCCCTTTA-GTATCTTTGTGGTACTAGATCCGTCA
1 TTGCGACTTAGATCTTTCCCTTCATGT-T-TTTGAGGTACTGGATCCGCCA
** * *
30454762 TTGCGGTTTTAGATCTTTCCCTTCATGTTTCTGAGGTACACGG-TCCGCCA
1 TTGC-GACTTAGATCTTTCCCTTCATGTTTTTGAGGTAC-TGGATCCGCCA
* * * * * *
30454812 TTGTGACTTAGA-CTTTTCCCTTTAATATCTTTGCGGTACTGGATCCACCA
1 TTGCGACTTAGATC-TTTCCC-TTCATGTTTTTGAGGTACTGGATCCGCCA
* * * * *
30454862 TTGCAGTCTTAGATCTTTCCCTT-TTGTATCTTT--TGTACTGGATTCGTCA
1 TTGC-GACTTAGATCTTTCCCTTCATGT-T-TTTGAGGTACTGGATCCGCCA
* *
30454911 TTGCGATCTTAGATCTTTCCCTTCATGTTTCTAAGGTACATGG-TCCGCCA
1 TTGCGA-CTTAGATCTTTCCCTTCATGTTTTTGAGGTAC-TGGATCCGCCA
* * *
30454961 TTGCGACTTAGACCTTTCCCTT-TTGTATCTTTGCGGTACTGGATCCGCCA
1 TTGCGACTTAGATCTTTCCCTTCATGT-T-TTTGAGGTACTGGATCCGCCA
*
30455011 TTGCTGTCTTAGATCTTTCCCTT
1 TTGC-GACTTAGATCTTTCCCTT
30455034 TATGCTTCTA
Statistics
Matches: 363, Mismatches: 79, Indels: 56
0.73 0.16 0.11
Matches are distributed among these distances:
48 11 0.03
49 145 0.40
50 130 0.36
51 72 0.20
52 5 0.01
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (49 bp):
TTGCGACTTAGATCTTTCCCTTCATGTTTTTGAGGTACTGGATCCGCCA
Found at i:30454614 original size:98 final size:98
Alignment explanation
Indices: 30454344--30454884 Score: 414
Period size: 100 Copynumber: 5.5 Consensus size: 98
30454334 GGCTATAATG
* * * * * *
30454344 TCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATTTTTTCCTTCGTGCTTTCGTGATGTA-A-
1 TCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATG-TTTC-TGAGGTACAC
* * * * **
30454407 GGTTCGCCATTGCGACTCAAACCTTTGCCTTCATA
64 GGTCCGCCGTTGCGACTTAAACCTTTCCCAGCATA
* * ** * * * * *
30454442 TCTTCGCGGTACTGGATTTGCCGCTGCGGCTTAAATCTTTCCC-T-ACGTATCTTTATGGTTC-T
1 TCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTTTC-TGA-GGTACAC
** * *
30454504 GGATTTGTCGTTGCGACTTAAATCTTTCCCAGCATA
64 GG-TCCGCCGTTGCGACTTAAACCTTTCCCAGCATA
* * *
30454540 TCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTTCCTTCATGTTTTTGAGGTACATGG
1 TCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACACGG
* *
30454605 TCCGCCGTTGCGACTTATACCTTTCCCTTTAGTATA
66 TCCGCCGTTGCGACTTAAACCTTTCCC---AGCATA
*
30454641 T-TT-GTGGTACTGGATAT-GCCATTGCGGTCTTAGATCTTTCCCTTCATGTTTCTGAGGTACAC
1 TCTTCGTGGTACTGGAT-TCGCCATTGCGG-CTTAAATCTTTCCCTTCATGTTTCTGAGGTACAC
* ***
30454703 GGTCCGCCGTTGCGACTTAGACCTTTCCCTTTAGTA
64 GGTCCGCCGTTGCGACTTAAACCTTTCCCAGCA-TA
* * * * * *
30454739 TCTTTGTGGTACTAGATCCGTCATTGCGGTTTTAGATCTTTCCCTTCATGTTTCTGAGGTACACG
1 TCTTCGTGGTACTGGATTCGCCATTGCGG-CTTAAATCTTTCCCTTCATGTTTCTGAGGTACACG
* * * * ***
30454804 GTCCGCCATTGTGACTTAGACTTTTCCCTTTAATA
65 GTCCGCCGTTGCGACTTAAACCTTTCCC-AGCATA
* * * * * *
30454839 TCTTTGCGGTACTGGATCCACCATTGCAGTCTTAGATCTTTCCCTT
1 TCTTCGTGGTACTGGATTCGCCATTGC-GGCTTAAATCTTTCCCTT
30454885 TTGTATCTTT
Statistics
Matches: 367, Mismatches: 58, Indels: 34
0.80 0.13 0.07
Matches are distributed among these distances:
95 5 0.01
96 3 0.01
97 5 0.01
98 129 0.35
99 30 0.08
100 185 0.50
101 10 0.03
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.39
Consensus pattern (98 bp):
TCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACACGG
TCCGCCGTTGCGACTTAAACCTTTCCCAGCATA
Found at i:30454707 original size:100 final size:100
Alignment explanation
Indices: 30454512--30454884 Score: 493
Period size: 100 Copynumber: 3.8 Consensus size: 100
30454502 CTGGATTTGT
* * * *
30454512 CGTTGCGACTTAAATCTTTCCC---AGCATATCTTCGTGGTACTGGATTCGCCATTGCGG-CTTA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATAT-TT-GTGGTACTGGATCCGCCATTGCGGTCTTA
* * * *
30454573 AATCTTTTCCTTCATGTTTTTGAGGTACATGGTCCGC
64 GATCTTTCCCTTCATGTTTCTGAGGTACACGGTCCGC
* **
30454610 CGTTGCGACTTATACCTTTCCCTTTAGTATATTTGTGGTACTGGATATGCCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATATTTGTGGTACTGGATCCGCCATTGCGGTCTTAGA
30454675 TCTTTCCCTTCATGTTTCTGAGGTACACGGTCCGC
66 TCTTTCCCTTCATGTTTCTGAGGTACACGGTCCGC
* * * *
30454710 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGTGGTACTAGATCCGTCATTGCGGTTTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATATTTGTGGTACTGGATCCGCCATTGCGGTCTTAGA
30454775 TCTTTCCCTTCATGTTTCTGAGGTACACGGTCCGC
66 TCTTTCCCTTCATGTTTCTGAGGTACACGGTCCGC
* * * * * * * *
30454810 CATTGTGACTTAGACTTTTCCCTTTAATATCTTTGCGGTACTGGATCCACCATTGCAGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATATTTGTGGTACTGGATCCGCCATTGCGGTCTTAGA
30454875 TCTTTCCCTT
66 TCTTTCCCTT
30454885 TTGTATCTTT
Statistics
Matches: 245, Mismatches: 26, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
98 20 0.08
99 22 0.09
100 197 0.80
101 6 0.02
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.39
Consensus pattern (100 bp):
CGTTGCGACTTAGACCTTTCCCTTTAGTATATTTGTGGTACTGGATCCGCCATTGCGGTCTTAGA
TCTTTCCCTTCATGTTTCTGAGGTACACGGTCCGC
Found at i:30454830 original size:149 final size:148
Alignment explanation
Indices: 30454658--30455035 Score: 422
Period size: 149 Copynumber: 2.5 Consensus size: 148
30454648 TACTGGATAT
* * * * *
30454658 GCCATTGCGGTCTTAGA-TCTTTCCCTTCATGT-TTCTGAGGTACACGG-TCCGCCGTTGC-GAC
1 GCCATTGC-GACTTAGACT-TTTCCCTTAATATCTT-TGAGGTAC-CGGATCCACCATTGCAGAC
* *
30454719 TTAGACCTTTCCCTTTAGTATCTTTGTGGTACTAGATCCGTCATTGCGGTTTTAGATCTTTCCCT
62 TTAGACCTTTCCCTTTAGTATCTTT-T-GTACTAGATCCGTCATTGCGATCTTAGATCTTTCCCT
*
30454784 TCATGTTTCTGAGGTACACGGTCC
125 TCATGTTTCTAAGGTACACGGTCC
* * * *
30454808 GCCATTGTGACTTAGACTTTTCCCTTTAATATCTTTGCGGTACTGGATCCACCATTGCAGTCTTA
1 GCCATTGCGACTTAGACTTTTCCC-TTAATATCTTTGAGGTACCGGATCCACCATTGCAGACTTA
* * * *
30454873 GATCTTTCCCTTTTGTATCTTTTGTACTGGATTCGTCATTGCGATCTTAGATCTTTCCCTTCATG
65 GACCTTTCCCTTTAGTATCTTTTGTACTAGATCCGTCATTGCGATCTTAGATCTTTCCCTTCATG
*
30454938 TTTCTAAGGTACATGGTCC
130 TTTCTAAGGTACACGGTCC
* ** * * * * *
30454957 GCCATTGCGACTTAGACCTTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCTGTCTTA
1 GCCATTGCGACTTAGACTTTTCCC-TTAATATCTTTGAGGTACCGGATCCACCATTGCAGACTTA
*
30455022 GATCTTTCCCTTTA
65 GACCTTTCCCTTTA
30455036 TGCTTCTAAG
Statistics
Matches: 199, Mismatches: 24, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
149 142 0.71
150 30 0.15
151 27 0.14
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (148 bp):
GCCATTGCGACTTAGACTTTTCCCTTAATATCTTTGAGGTACCGGATCCACCATTGCAGACTTAG
ACCTTTCCCTTTAGTATCTTTTGTACTAGATCCGTCATTGCGATCTTAGATCTTTCCCTTCATGT
TTCTAAGGTACACGGTCC
Found at i:30454923 original size:249 final size:251
Alignment explanation
Indices: 30454625--30455091 Score: 699
Period size: 249 Copynumber: 1.9 Consensus size: 251
30454615 CGACTTATAC
*
30454625 CTTTCCCTTTAGTATATTTGTGGTACTGGATATGCCATTGCGGTCTTAGATCTTTCCCTTCATGT
1 CTTTCCCTTTAGTATATTTGTGGTACTGGATATGCCATTGCGATCTTAGATCTTTCCCTTCATGT
* * *
30454690 TTCTGAGGTACACGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGTGGTACTAGA
66 TTCTAAGGTACACGGTCCGCCATTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTAGA
* * * * *
30454755 TCCGTCATTGCGGTTTTAGATCTTTCCCTTCATGTTTCTGAGGTACACGGTCCGCCATTGTGACT
131 TCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGCTTCTAAGGTACAAGGTCCGCCATTGTGACT
* *
30454820 TAGA-CTTTTCCCTTTAATATCTTTGCGGTACTGGATCCACCATTGCAGTCTTAGAT
196 TAAACCTTTTCCCTTCAA-ATCTTTGCGGTACTGGATCCACCATTGCAGTCTTAGAT
* * *
30454876 CTTTCCCTTTTGTATCTTT-T-GTACTGGAT-TCGTCATTGCGATCTTAGATCTTTCCCTTCATG
1 CTTTCCCTTTAGTATATTTGTGGTACTGGATAT-GCCATTGCGATCTTAGATCTTTCCCTTCATG
* * *
30454938 TTTCTAAGGTACATGGTCCGCCATTGCGACTTAGACCTTTCCCTTTTGTATCTTTGCGGTACTGG
65 TTTCTAAGGTACACGGTCCGCCATTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTAG
* * * *
30455003 ATCCGCCATTGCTGTCTTAGATCTTTCCCTTTATGCTTCTAAGGTACAAGGTTCGCCGTTGTGAC
130 ATCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGCTTCTAAGGTACAAGGTCCGCCATTGTGAC
30455068 TTAAACCTTTTCCCTTCAAATCTT
195 TTAAACCTTTTCCCTTCAAATCTT
30455092 CGTTTTTCTT
Statistics
Matches: 193, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
248 1 0.01
249 162 0.84
250 13 0.07
251 17 0.09
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.40
Consensus pattern (251 bp):
CTTTCCCTTTAGTATATTTGTGGTACTGGATATGCCATTGCGATCTTAGATCTTTCCCTTCATGT
TTCTAAGGTACACGGTCCGCCATTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTAGA
TCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGCTTCTAAGGTACAAGGTCCGCCATTGTGACT
TAAACCTTTTCCCTTCAAATCTTTGCGGTACTGGATCCACCATTGCAGTCTTAGAT
Found at i:30454930 original size:100 final size:100
Alignment explanation
Indices: 30454537--30455035 Score: 467
Period size: 100 Copynumber: 5.0 Consensus size: 100
30454527 CTTTCCCAGC
* * * * * *
30454537 ATATCTTCGTGGTACTGGATTCGCCATTGCGG-CTTAAATCTTTTCCTTCATGTTTTTGAGGTAC
1 ATATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGTATCTGAGGTAC
* * *
30454601 ATGGTCCGCCGTTGCGACTTATACCTTTCCCTTTA
66 ACGGTCCGCCATTGCGACTTAGACCTTTCCCTTTA
* * ** *
30454636 GTATATTTGTGGTACTGGATATGCCATTGCGGTCTTAGATCTTTCCCTTCATGTTTCTGAGGTAC
1 ATATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGTATCTGAGGTAC
*
30454701 ACGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTA
66 ACGGTCCGCCATTGCGACTTAGACCTTTCCCTTTA
* * * * *
30454736 GTATCTTTGTGGTACTAGATCCGTCATTGCGGTTTTAGATCTTTCCCTTCATGTTTCTGAGGTAC
1 ATATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGTATCTGAGGTAC
* *
30454801 ACGGTCCGCCATTGTGACTTAGACTTTTCCCTTTA
66 ACGGTCCGCCATTGCGACTTAGACCTTTCCCTTTA
* * * * ***
30454836 ATATCTTTGCGGTACTGGATCCACCATTGCAGTCTTAGATCTTTCCCTT-TTGTATCTTTTGTAC
1 ATATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGTATCTGAGGTAC
* * * * *
30454900 -TGGATTCGTCATTGCGATCTTAGATCTTTCCC-TTC
66 ACGG-TCCGCCATTGCGA-CTTAGACCTTTCCCTTTA
* ** * * * *
30454935 ATGT-TTCTAAGGTACATGG-TCCGCCATTGC-GACTTAGACCTTTCCCTT-TTGTATCTTTGCG
1 ATATCTT-TGTGGTAC-TGGATCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGTATC--TGAG
* * *
30454996 GTAC-TGGATCCGCCATTGCTGTCTTAGATCTTTCCCTTTA
62 GTACACGG-TCCGCCATTGC-GACTTAGACCTTTCCCTTTA
30455036 TGCTTCTAAG
Statistics
Matches: 340, Mismatches: 51, Indels: 16
0.84 0.13 0.04
Matches are distributed among these distances:
98 27 0.08
99 68 0.20
100 242 0.71
101 3 0.01
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.40
Consensus pattern (100 bp):
ATATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCTTCATGTATCTGAGGTAC
ACGGTCCGCCATTGCGACTTAGACCTTTCCCTTTA
Found at i:30454931 original size:200 final size:197
Alignment explanation
Indices: 30454344--30455035 Score: 551
Period size: 200 Copynumber: 3.5 Consensus size: 197
30454334 GGCTATAATG
* * * * * *
30454344 TCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATTTTTTCCTTCGTGCTTTCGTGATGTA-A-
1 TCTTCGTGGTACTAGATCCGCCATTGCGGCTTAAATCTTTCCCTTCATG-TTTC-TGAGGTACAC
* * * * * * * *** **
30454407 GGTTCGCCATTGCGACTCAAACCTTTGCC-TTCATATCTTCGCGGTACTGGATTTGCCGCTGC-G
64 GGTCCGCCATTGCGACTTAGACCTTTCCCTTTAATATATTTGCGGTACTGGATACACCATTGCAG
* * * * * *
30454470 GCTTAAATCTTTCCC-TACGTATCTTTATGGTTCTGGATTTGTCGTTGCGACTTAAATCTTTCCC
129 TCTTAGATCTTTCCCTTATGTATCTTT-T-GTACTGGATTCGTCGTTGCGACTTAGATCTTTCCC
**
30454534 AGCATA
192 TTCATA
* * * * *
30454540 TCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTTCCTTCATGTTTTTGAGGTACATGG
1 TCTTCGTGGTACTAGATCCGCCATTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACACGG
* * * * ** *
30454605 TCCGCCGTTGCGACTTATACCTTTCCCTTTAGTATATTTGTGGTACTGGATATGCCATTGCGGTC
66 TCCGCCATTGCGACTTAGACCTTTCCCTTTAATATATTTGCGGTACTGGATACACCATTGCAGTC
* *** * * * *
30454670 TTAGATCTTTCCCTTCATGTTTCTGAGGTACACGG-TCCGCCGTTGCGACTTAGACCTTTCCCTT
131 TTAGATCTTTCCCTT-ATGTATCTTTTGTAC-TGGATTCGTCGTTGCGACTTAGATCTTTCCCTT
*
30454734 TAGTA
194 CA-TA
* * * *
30454739 TCTTTGTGGTACTAGATCCGTCATTGCGGTTTTAGATCTTTCCCTTCATGTTTCTGAGGTACACG
1 TCTTCGTGGTACTAGATCCGCCATTGCGG-CTTAAATCTTTCCCTTCATGTTTCTGAGGTACACG
* * * *
30454804 GTCCGCCATTGTGACTTAGACTTTTCCCTTTAATATCTTTGCGGTACTGGATCCACCATTGCAGT
65 GTCCGCCATTGCGACTTAGACCTTTCCCTTTAATATATTTGCGGTACTGGATACACCATTGCAGT
* *
30454869 CTTAGATCTTTCCCTTTTGTATCTTTTGTACTGGATTCGTCATTGCGATCTTAGATCTTTCCCTT
130 CTTAGATCTTTCCCTTATGTATCTTTTGTACTGGATTCGTCGTTGCGA-CTTAGATCTTTCCCTT
*
30454934 CATG
194 CATA
* * * * * * *
30454938 T-TTC-TAAGGTAC-ATGGTCCGCCATTGCGACTTAGACCTTTCCCTT-TTGTATCTTTGCGGTA
1 TCTTCGT--GGTACTA-GATCCGCCATTGCGGCTTAAATCTTTCCCTTCATGT-T-TCTGAGGTA
* * *
30454999 C-TGGATCCGCCATTGCTGTCTTAGATCTTTCCCTTTA
61 CACGG-TCCGCCATTGC-GACTTAGACCTTTCCCTTTA
30455036 TGCTTCTAAG
Statistics
Matches: 396, Mismatches: 82, Indels: 32
0.78 0.16 0.06
Matches are distributed among these distances:
194 6 0.02
195 4 0.01
196 69 0.17
197 29 0.07
198 62 0.16
199 87 0.22
200 139 0.35
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (197 bp):
TCTTCGTGGTACTAGATCCGCCATTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACACGG
TCCGCCATTGCGACTTAGACCTTTCCCTTTAATATATTTGCGGTACTGGATACACCATTGCAGTC
TTAGATCTTTCCCTTATGTATCTTTTGTACTGGATTCGTCGTTGCGACTTAGATCTTTCCCTTCA
TA
Found at i:30455043 original size:100 final size:98
Alignment explanation
Indices: 30454846--30455083 Score: 291
Period size: 100 Copynumber: 2.4 Consensus size: 98
30454836 ATATCTTTGC
* * * * * *
30454846 GGTAC-TGGATCCACCATTGCAGTCTTAGATCTTTCCCTTTTGTATCTTTTGTACTGGATTCGTC
1 GGTACATGG-TCCGCCATTGC-GACTTAGACCTTTCCCTTTTGTATCTTTGGTACTGGATCCGCC
*
30454910 ATTGCGATCTTAGATCTTTCCCTTCATGTTTCTAA
64 ATTGCGATCTTAGATCTTTCCCTTCATGCTTCTAA
30454945 GGTACATGGTCCGCCATTGCGACTTAGACCTTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCC
1 GGTACATGGTCCGCCATTGCGACTTAGACCTTTCCCTTTTGTATCTTT--GGTACTGGATCCGCC
*
30455010 ATTGCTG-TCTTAGATCTTTCCCTTTATGCTTCTAA
64 ATTGC-GATCTTAGATCTTTCCCTTCATGCTTCTAA
* * * * *
30455045 GGTACAAGGTTCGCCGTTGTGACTTAAACCTTTTCCCTT
1 GGTACATGGTCCGCCATTGCGACTTAGACC-TTTCCCTT
30455084 CAAATCTTCG
Statistics
Matches: 121, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
98 26 0.21
99 15 0.12
100 71 0.59
101 9 0.07
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.40
Consensus pattern (98 bp):
GGTACATGGTCCGCCATTGCGACTTAGACCTTTCCCTTTTGTATCTTTGGTACTGGATCCGCCAT
TGCGATCTTAGATCTTTCCCTTCATGCTTCTAA
Found at i:30459154 original size:2 final size:2
Alignment explanation
Indices: 30459147--30459172 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30459137 TAATGATTTA
30459147 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
30459173 GTTTAAAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30459930 original size:23 final size:22
Alignment explanation
Indices: 30459879--30459931 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
30459869 GACATTATTC
30459879 AAATAAATTTAAATTTAAATTT
1 AAATAAATTTAAATTTAAATTT
* *
30459901 ATGATAAATTTAAATTTTCAATTT
1 A-AATAAATTTAAA-TTTAAATTT
30459925 AAATAAA
1 AAATAAA
30459932 AATCATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 16 0.62
24 9 0.35
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATAAATTTAAATTTAAATTT
Found at i:30475148 original size:6 final size:6
Alignment explanation
Indices: 30475137--30475183 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
30475127 GGAGAGGAGT
** * *
30475137 TGGAAG TGGAAG TGGAAG TGGAAG TGGATC TGGATG TGGATG TGGAA
1 TGGAAG TGGAAG TGGAAG TGGAAG TGGAAG TGGAAG TGGAAG TGGAA
30475184 ATGGGGGGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.28, C:0.02, G:0.47, T:0.23
Consensus pattern (6 bp):
TGGAAG
Found at i:30476738 original size:46 final size:46
Alignment explanation
Indices: 30476671--30476759 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
30476661 CATAAGATTT
30476671 TTAAATGTCATGAAATCAAGTCCTACAGTTGAAATAATGGAGGTTG
1 TTAAATGTCATGAAATCAAGTCCTACAGTTGAAATAATGGAGGTTG
30476717 TTAAATGTCATGAAATCAAGTCCTACAGTTGAAATAATGGAGG
1 TTAAATGTCATGAAATCAAGTCCTACAGTTGAAATAATGGAGG
30476760 CCAAGCTCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.29
Consensus pattern (46 bp):
TTAAATGTCATGAAATCAAGTCCTACAGTTGAAATAATGGAGGTTG
Found at i:30480360 original size:3 final size:3
Alignment explanation
Indices: 30480352--30480387 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
30480342 ATACAGATAA
*
30480352 GAG GAG GAG GAG GAG GAG GAG GTG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
30480388 AGAGAATAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.67, T:0.03
Consensus pattern (3 bp):
GAG
Found at i:30481231 original size:7 final size:7
Alignment explanation
Indices: 30481219--30481247 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
30481209 TAATTAAAAA
30481219 ATATAAT
1 ATATAAT
30481226 ATATAAT
1 ATATAAT
30481233 ATATAA-
1 ATATAAT
30481239 ATATAAT
1 ATATAAT
30481246 AT
1 AT
30481248 TTGTCGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
ATATAAT
Found at i:30482410 original size:20 final size:20
Alignment explanation
Indices: 30482373--30482411 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30482363 TGTTGTTTGA
*
30482373 TAAATTAAATAATTAAATAG
1 TAAATTAAATAATAAAATAG
* *
30482393 TAAATTTAATGATAAAATA
1 TAAATTAAATAATAAAATA
30482412 TCTTTAACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (20 bp):
TAAATTAAATAATAAAATAG
Found at i:30492278 original size:2 final size:2
Alignment explanation
Indices: 30492271--30492342 Score: 117
Period size: 2 Copynumber: 36.0 Consensus size: 2
30492261 TTATATTGTG
30492271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
30492313 AT AT AT AG AT AT AG AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30492343 TTATTAAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:30495908 original size:109 final size:108
Alignment explanation
Indices: 30495750--30495948 Score: 251
Period size: 109 Copynumber: 1.8 Consensus size: 108
30495740 TTTTTTTTCC
* * *
30495750 TTTTTCAGAATTAATTTTAGTTTTTAGTAAGAGGGAAAAACTTAGGGTTTTAC-AAGAAGTACCT
1 TTTTTCAGAATTAATTCTAGTTTTTAGTAAAAAGGAAAAACTTAGGG-TTTACAAAGAAGTACCT
* * *
30495814 AAGTTTTTATAGGAAAAAT-CATTTTATTTTTTAATTTCTTTTA
65 AAATTTTTACAAGAAAAATACATTTTATTTTTTAATTTCTTTTA
* * *
30495857 TTTTTTAGAATTAATTCTAGATTTTTCAGTAAAAAGG-AAAATTTGAGGGTTTACAAAGAATTAC
1 TTTTTCAGAATTAATTCTAG-TTTTT-AGTAAAAAGGAAAAACTT-AGGGTTTACAAAGAAGTAC
*
30495921 TTAAATTTTTACAAGAAAAATACATTTT
63 CTAAATTTTTACAAGAAAAATACATTTT
30495949 TATATGAAAT
Statistics
Matches: 77, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
107 18 0.23
108 16 0.21
109 37 0.48
110 6 0.08
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (108 bp):
TTTTTCAGAATTAATTCTAGTTTTTAGTAAAAAGGAAAAACTTAGGGTTTACAAAGAAGTACCTA
AATTTTTACAAGAAAAATACATTTTATTTTTTAATTTCTTTTA
Found at i:30498171 original size:19 final size:20
Alignment explanation
Indices: 30498122--30498162 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
30498112 AAAAATATAT
30498122 TAAAAATAT-TTT-ATAAAA
1 TAAAAATATATTTAATAAAA
30498140 TAAAAATATATTTAAT-AAA
1 TAAAAATATATTTAATAAAA
30498159 TAAA
1 TAAA
30498163 TTTATATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.43
19 10 0.48
20 2 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAATATATTTAATAAAA
Found at i:30501063 original size:26 final size:26
Alignment explanation
Indices: 30501011--30501069 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
30501001 CATTTTCTTG
*
30501011 AAATTTTACCAAGGACAAAATCGTCA
1 AAATTTTACCAAGGACAAAATCATCA
* ** *
30501037 AAATTTTATCAAGGGTAAAATTATCA
1 AAATTTTACCAAGGACAAAATCATCA
*
30501063 AACTTTT
1 AAATTTT
30501070 TTTGGGAGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (26 bp):
AAATTTTACCAAGGACAAAATCATCA
Found at i:30501685 original size:20 final size:19
Alignment explanation
Indices: 30501660--30501705 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
30501650 ACCTAGTAAG
30501660 TTACGATACGATCTTTCAAA
1 TTACGA-ACGATCTTTCAAA
* *
30501680 TTACGAAGGTTCTTTCAAA
1 TTACGAACGATCTTTCAAA
30501699 TTACGAA
1 TTACGAA
30501706 GGAACGTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (19 bp):
TTACGAACGATCTTTCAAA
Found at i:30501695 original size:19 final size:19
Alignment explanation
Indices: 30501671--30501707 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
30501661 TACGATACGA
30501671 TCTTTCAAATTACGAAGGT
1 TCTTTCAAATTACGAAGGT
30501690 TCTTTCAAATTACGAAGG
1 TCTTTCAAATTACGAAGG
30501708 AACGTACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
TCTTTCAAATTACGAAGGT
Found at i:30514297 original size:13 final size:13
Alignment explanation
Indices: 30514279--30514305 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30514269 AGAAACATGA
30514279 AAGATTTATTTTC
1 AAGATTTATTTTC
30514292 AAGATTTATTTTC
1 AAGATTTATTTTC
30514305 A
1 A
30514306 TGGCATCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (13 bp):
AAGATTTATTTTC
Found at i:30518476 original size:3 final size:3
Alignment explanation
Indices: 30518468--30518508 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
30518458 ACGTTTTAAT
30518468 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
30518509 TTGTTTACTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:30526253 original size:39 final size:39
Alignment explanation
Indices: 30526210--30526287 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
30526200 CTCTCCCTGT
30526210 TGCGAACTTTCAATCGGCAACTCTTAGAGCATCTCTAAA
1 TGCGAACTTTCAATCGGCAACTCTTAGAGCATCTCTAAA
30526249 TGCGAACTTTCAATCGGCAACTCTTAGAGCATCTCTAAA
1 TGCGAACTTTCAATCGGCAACTCTTAGAGCATCTCTAAA
30526288 AACTTAGGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (39 bp):
TGCGAACTTTCAATCGGCAACTCTTAGAGCATCTCTAAA
Found at i:30526873 original size:18 final size:19
Alignment explanation
Indices: 30526836--30526874 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
30526826 TTAAAAAAAT
*
30526836 AATTAAAAATAATTTTTAA
1 AATTAAAAATAATTTATAA
*
30526855 AATTCAAAAT-ATTTATAA
1 AATTAAAAATAATTTATAA
30526873 AA
1 AA
30526875 ACTCCAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTAAAAATAATTTATAA
Found at i:30533908 original size:93 final size:91
Alignment explanation
Indices: 30533698--30533952 Score: 252
Period size: 93 Copynumber: 2.8 Consensus size: 91
30533688 TGTAAGGATG
* * ** * *
30533698 TAAAAGCCCTCAAAC-TTTTTCAAAAAAAAGTAATTAAGTTTTTGCTTTTATTTTGTACTCACTT
1 TAAAAGCTCTCAAACTTTTTTCAAAAAAAAGCAATTAAGACTTT-CTTTTATTTTGCACTCAATT
*
30533762 GGATACTTGAACTTTCAAAACGCATTA
65 GGATACTTGAACTTTCAAAACGCATCA
* *** *
30533789 TAAAAGCTCTCAAACTCTATAAAAAAAAAAAGCAATTAAGCCCTTTCTTTTATTTTGCACTCAAT
1 TAAAAGCTCTCAAACT-TTTTTCAAAAAAAAGCAATTAAG-ACTTTCTTTTATTTTGCACTCAAT
* * *
30533854 TGGGTATTTGAACTTTCAAAATGCATCA
64 TGGATACTTGAACTTTCAAAACGCATCA
** *
30533882 -AAAAGGCTCTCAATTTTTTTTC-AAAAAAAGCAATTAA-ACTCTC-TTT-TTTTGCACTCAATT
1 TAAAA-GCTCTCAAACTTTTTTCAAAAAAAAGCAATTAAGACTTTCTTTTATTTTGCACTCAATT
**
30533942 AAATACTTGAA
65 GGATACTTGAA
30533953 TCATCCCTAA
Statistics
Matches: 134, Mismatches: 26, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
87 21 0.16
88 3 0.02
89 4 0.03
91 29 0.22
92 6 0.04
93 68 0.51
94 3 0.02
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.36
Consensus pattern (91 bp):
TAAAAGCTCTCAAACTTTTTTCAAAAAAAAGCAATTAAGACTTTCTTTTATTTTGCACTCAATTG
GATACTTGAACTTTCAAAACGCATCA
Found at i:30534911 original size:69 final size:69
Alignment explanation
Indices: 30534820--30534964 Score: 290
Period size: 69 Copynumber: 2.1 Consensus size: 69
30534810 ATTATAATAC
30534820 GATAAAAAATAATAAAATACGAATATATTAATTTAATATCACTTGCTTAAATTATGTCAGTTAAA
1 GATAAAAAATAATAAAATACGAATATATTAATTTAATATCACTTGCTTAAATTATGTCAGTTAAA
30534885 TATA
66 TATA
30534889 GATAAAAAATAATAAAATACGAATATATTAATTTAATATCACTTGCTTAAATTATGTCAGTTAAA
1 GATAAAAAATAATAAAATACGAATATATTAATTTAATATCACTTGCTTAAATTATGTCAGTTAAA
30534954 TATA
66 TATA
30534958 GATAAAA
1 GATAAAA
30534965 TTTTAAAAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 76 1.00
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.35
Consensus pattern (69 bp):
GATAAAAAATAATAAAATACGAATATATTAATTTAATATCACTTGCTTAAATTATGTCAGTTAAA
TATA
Found at i:30537781 original size:23 final size:23
Alignment explanation
Indices: 30537725--30537900 Score: 149
Period size: 23 Copynumber: 7.4 Consensus size: 23
30537715 CGGAGTACTG
*
30537725 AACAGAGAGCAC-CATAAGTGCTGGGC
1 AACAGAGAGCACACA-AAGTGCT---A
*
30537751 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
30537774 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACAAAGTGCTA
* *
30537797 ATCAGAGAGCACACAAAGTACTA
1 AACAGAGAGCACACAAAGTGCTA
*
30537820 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
** * *
30537843 ATTAGAAAGCACACAAAGTGTTAA
1 AACAGAGAGCACACAAAGTGCT-A
* * *
30537867 TAACAAAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
30537891 AACAGAGAGC
1 AACAGAGAGC
30537901 GCGCTAGTGT
Statistics
Matches: 127, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
23 91 0.72
24 2 0.02
25 13 0.10
26 19 0.15
27 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:30537993 original size:27 final size:24
Alignment explanation
Indices: 30537963--30538011 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
30537953 TCTACATGGG
30537963 CATAATATCTTATATAACATCATTTCT
1 CATAAT-T-TTATATAACA-CATTTCT
*
30537990 CATAATTTTATATATCACATTT
1 CATAATTTTATATAACACATTT
30538012 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 9 0.43
26 1 0.05
27 6 0.29
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (24 bp):
CATAATTTTATATAACACATTTCT
Found at i:30540223 original size:9 final size:9
Alignment explanation
Indices: 30540209--30540309 Score: 60
Period size: 9 Copynumber: 10.7 Consensus size: 9
30540199 ACATGTGACA
30540209 AAAAAATAT
1 AAAAAATAT
*
30540218 AAAAAATAA
1 AAAAAATAT
*
30540227 AAAAAATTCT
1 AAAAAA-TAT
* **
30540237 TAAATTTATT
1 AAAAAATA-T
**
30540247 AAATTATAAT
1 AAAAAAT-AT
30540257 AAAAAAATAT
1 A-AAAAATAT
* *
30540267 AAAAATTGT
1 AAAAAATAT
30540276 AAAAAATAT
1 AAAAAATAT
30540285 AAAAAATTAT
1 AAAAAA-TAT
30540295 AAAATAA-AT
1 AAAA-AATAT
30540304 AAAAAA
1 AAAAAA
30540310 ATGCCCTTTA
Statistics
Matches: 70, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
8 2 0.03
9 40 0.57
10 21 0.30
11 7 0.10
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (9 bp):
AAAAAATAT
Found at i:30540278 original size:19 final size:19
Alignment explanation
Indices: 30540255--30540311 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 19
30540245 TTAAATTATA
30540255 ATAAAAAAATATAAAAATT
1 ATAAAAAAATATAAAAATT
*
30540274 GT-AAAAAATATAAAAAATT
1 ATAAAAAAATAT-AAAAATT
*
30540293 ATAAAATAAATAAAAAAAT
1 ATAAAA-AAATATAAAAAT
30540312 GCCCTTTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 9 0.28
19 9 0.28
20 9 0.28
21 5 0.16
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (19 bp):
ATAAAAAAATATAAAAATT
Found at i:30540507 original size:12 final size:11
Alignment explanation
Indices: 30540484--30540525 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
30540474 GATATGATAA
30540484 TTTTATAATTT
1 TTTTATAATTT
*
30540495 TTTTATAA--A
1 TTTTATAATTT
30540504 TTTTAT-ATTT
1 TTTTATAATTT
30540514 TTTTATAATTT
1 TTTTATAATTT
30540525 T
1 T
30540526 CTTACGACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
8 1 0.04
9 6 0.23
10 6 0.23
11 13 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:30540507 original size:20 final size:18
Alignment explanation
Indices: 30540480--30540525 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 18
30540470 TTTTGATATG
30540480 ATAATTTTATAATTTTTTT
1 ATAATTTTAT-ATTTTTTT
30540499 ATAAATTTTATATTTTTTT
1 AT-AATTTTATATTTTTTT
30540518 ATAATTTT
1 ATAATTTT
30540526 CTTACGACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.23
19 12 0.46
20 8 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATAATTTTATATTTTTTT
Found at i:30540578 original size:18 final size:18
Alignment explanation
Indices: 30540555--30540606 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
30540545 TTATAAATTT
30540555 ATTTTTATATATTTTTTA
1 ATTTTTATATATTTTTTA
**
30540573 ATTTTT-TAATATTTAATA
1 ATTTTTAT-ATATTTTTTA
* *
30540591 AATTTTAAATATTTTT
1 ATTTTTATATATTTTT
30540607 ATTAAAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTTATATATTTTTTA
Found at i:30540612 original size:20 final size:20
Alignment explanation
Indices: 30540579--30540628 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
30540569 TTTAATTTTT
* * *
30540579 TAATATTTAATAAATTTTAA
1 TAATTTTTATTAAAATTTAA
30540599 -ATATTTTTATTAAAATTTAA
1 TA-ATTTTTATTAAAATTTAA
30540619 TAATTTTTAT
1 TAATTTTTAT
30540629 AACTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 23 0.92
21 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATTTTTATTAAAATTTAA
Found at i:30540641 original size:15 final size:15
Alignment explanation
Indices: 30540621--30540650 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30540611 AAATTTAATA
30540621 ATTTTTATAACTTTT
1 ATTTTTATAACTTTT
*
30540636 ATTTTTATATCTTTT
1 ATTTTTATAACTTTT
30540651 TTATGTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTTATAACTTTT
Found at i:30543654 original size:2 final size:2
Alignment explanation
Indices: 30543647--30543686 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
30543637 CTTATTAGAA
30543647 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
30543687 ATATAACAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:30547163 original size:54 final size:54
Alignment explanation
Indices: 30547101--30547210 Score: 184
Period size: 54 Copynumber: 2.0 Consensus size: 54
30547091 AGTAACTTTA
* *
30547101 CAATATAAATTATATAAGATAATTACACTTATATAAACAAATATTTTATTTATT
1 CAATATAAATTATATAAAATAATAACACTTATATAAACAAATATTTTATTTATT
**
30547155 CAATATAAATTATATAAAATAATAACACTTATATAAACGCATATTTTATTTATT
1 CAATATAAATTATATAAAATAATAACACTTATATAAACAAATATTTTATTTATT
30547209 CA
1 CA
30547211 TATTTATTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (54 bp):
CAATATAAATTATATAAAATAATAACACTTATATAAACAAATATTTTATTTATT
Found at i:30553604 original size:23 final size:23
Alignment explanation
Indices: 30553578--30553625 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
30553568 AAGAAGTACT
30553578 GTGATTTTACGTCTATTGGTGTA
1 GTGATTTTACGTCTATTGGTGTA
30553601 GTGATTTTACGTCTATTGGTGTA
1 GTGATTTTACGTCTATTGGTGTA
30553624 GT
1 GT
30553626 AAAATGGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.08, G:0.27, T:0.48
Consensus pattern (23 bp):
GTGATTTTACGTCTATTGGTGTA
Found at i:30564501 original size:247 final size:244
Alignment explanation
Indices: 30564062--30564555 Score: 801
Period size: 247 Copynumber: 2.0 Consensus size: 244
30564052 CAAATCCAAA
* *
30564062 TCAAACTGAATCATTAAGGGTTAATTTGGCATTCTAAATGAAAATTTAGTACTTTTAAAGAATTT
1 TCAAACTGAATCATTAAGGGCTAATTTGGCATTCTAAATGAAAATTTAGTACTTTTAAAGAATCT
* * *
30564127 GTGGAACGGTTTATTAATTTGATGTTATTTAAAAAATATATTATTATTGATAATATAATAATTCA
66 GTGGAACGGTTTATTAATTTGATGTTATTTAAAAAAAACATTATTATTGATAAGATAATAATTCA
* * * *
30564192 ACACAGCATATCTTGAGCCTATTTGTAATTTTTTTTTGTTAAAATGGGGATTTAAAAATTGGTTT
131 ACAAAGCATACCTTGAGCCTATTCGTAATTTTTTTTTGTTAAAATAGGGATTTAAAAATTGGTTT
* *
30564257 GGTAGA-GAATTTCATGTAATGATTTGATGATTAAGAGTGTTTTATCGTC
196 AGTA-ATGAATTTCATGTAATGATTTGATGATTAAGAGTGTTTTATCATC
* *
30564306 TCAAATTGAATCATTAAGGGCTAATTTGGTATTCTAAATGAAAATTTAGAAGTACTTTTAAAGAA
1 TCAAACTGAATCATTAAGGGCTAATTTGGCATTCTAAATGAAAATTT---AGTACTTTTAAAGAA
30564371 TCTGTGGAACGGTTTATTAATTTGATGTTATTTAAAAAAAACATTATTATTGATAAGATAATAAT
63 TCTGTGGAACGGTTTATTAATTTGATGTTATTTAAAAAAAACATTATTATTGATAAGATAATAAT
* *
30564436 TTAACAAAGCATACCTTGAGCCTATTCGTATTTTTTTTTTGTTAAAATAGGGATTTAAAAATTGG
128 TCAACAAAGCATACCTTGAGCCTATTCGTAATTTTTTTTTGTTAAAATAGGGATTTAAAAATTGG
*
30564501 TTTAGTAATGAATTTCATGTAATGATTTGATGATTAAGGGTGTTTTATCATC
193 TTTAGTAATGAATTTCATGTAATGATTTGATGATTAAGAGTGTTTTATCATC
30564553 TCA
1 TCA
30564556 GGTATGATAT
Statistics
Matches: 230, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
244 44 0.19
246 1 0.00
247 185 0.80
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.41
Consensus pattern (244 bp):
TCAAACTGAATCATTAAGGGCTAATTTGGCATTCTAAATGAAAATTTAGTACTTTTAAAGAATCT
GTGGAACGGTTTATTAATTTGATGTTATTTAAAAAAAACATTATTATTGATAAGATAATAATTCA
ACAAAGCATACCTTGAGCCTATTCGTAATTTTTTTTTGTTAAAATAGGGATTTAAAAATTGGTTT
AGTAATGAATTTCATGTAATGATTTGATGATTAAGAGTGTTTTATCATC
Done.