Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 167 of 196
Found at i:48988890 original size:39 final size:39
Alignment explanation
Indices: 48988836--48988914 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
48988826 AAGTAGATTC
*
48988836 CATAACTATCCACCTATTACTCTACCATGTTCTGAAACA
1 CATAACTATCCACCTATTACTCTACCATGTTCAGAAACA
*
48988875 CATAACTATCCACCTATTACTCTTCCATGTTCAGAAACA
1 CATAACTATCCACCTATTACTCTACCATGTTCAGAAACA
48988914 C
1 C
48988915 TTAGCACTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (39 bp):
CATAACTATCCACCTATTACTCTACCATGTTCAGAAACA
Found at i:48989701 original size:21 final size:21
Alignment explanation
Indices: 48989677--48989722 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
48989667 GCGTCGGGGG
* *
48989677 TTTGGGTA-GAAGGAGTGTCGT
1 TTTGGGGAGGAAGG-GTATCGT
48989698 TTTGGGGAGGAAGGGTATCGT
1 TTTGGGGAGGAAGGGTATCGT
48989719 TTTG
1 TTTG
48989723 AGGTGGGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.17, C:0.04, G:0.43, T:0.35
Consensus pattern (21 bp):
TTTGGGGAGGAAGGGTATCGT
Found at i:48998513 original size:25 final size:24
Alignment explanation
Indices: 48998485--48998544 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
48998475 CAATTTACAA
48998485 CTCGTATGAGCTTACCG-TTATTCAG
1 CTCGTATGAGCTTACCGTTTA-TC-G
* *
48998510 CTCGAAGGAGCTTACCGTTTATCG
1 CTCGTATGAGCTTACCGTTTATCG
*
48998534 CTTGTATGAGC
1 CTCGTATGAGC
48998545 ATACATGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 9 0.31
25 17 0.59
26 3 0.10
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (24 bp):
CTCGTATGAGCTTACCGTTTATCG
Found at i:49001690 original size:3 final size:3
Alignment explanation
Indices: 49001677--49001719 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
49001667 GTGGAATCTA
*
49001677 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG -AG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
49001720 GGTTGATTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:49004354 original size:39 final size:39
Alignment explanation
Indices: 49004310--49004444 Score: 182
Period size: 39 Copynumber: 3.5 Consensus size: 39
49004300 AGTGCTGATA
49004310 ATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCGGTG
1 ATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCGGTG
* * * *
49004349 ATTATTCAGGCTATGTGCCTAGCAGGATGTGTACCGGTA
1 ATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCGGTG
* * * *
49004388 ATTATTCGAGCTATGCGCCTAGTAGGCTTTGTGCCGGTG
1 ATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCGGTG
*
49004427 -TTATTCGGGCTCTGTGCC
1 ATTATTCGGGCTATGTGCC
49004445 GGTGTATTGA
Statistics
Matches: 81, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
38 15 0.19
39 66 0.81
ACGTcount: A:0.16, C:0.21, G:0.31, T:0.33
Consensus pattern (39 bp):
ATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCGGTG
Found at i:49006907 original size:21 final size:23
Alignment explanation
Indices: 49006865--49006909 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
49006855 ATTTTTTCCA
*
49006865 AATATGTGTATTGGACTGAATTG
1 AATATGTGTATTGGACTAAATTG
*
49006888 AATATG-G-ATTGTACTAAATTG
1 AATATGTGTATTGGACTAAATTG
49006909 A
1 A
49006910 GCTAAATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 1 0.05
23 6 0.30
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (23 bp):
AATATGTGTATTGGACTAAATTG
Found at i:49007138 original size:20 final size:20
Alignment explanation
Indices: 49007096--49007137 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
49007086 TGAAAAATAA
49007096 TTTCTAGAAAATGATTTACT
1 TTTCTAGAAAATGATTTACT
49007116 TTTCT-GAAAATGATTTACT
1 TTTCTAGAAAATGATTTACT
49007135 TTT
1 TTT
49007138 TTGGTGTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTAGAAAATGATTTACT
Found at i:49010553 original size:25 final size:26
Alignment explanation
Indices: 49010525--49010574 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
49010515 AAAAGGTTTT
49010525 GGGGAATAAAAGGTT-GAGGGAAAAG
1 GGGGAATAAAAGGTTGGAGGGAAAAG
* **
49010550 GGGGAGTAAAATTTTGGAGGGAAAA
1 GGGGAATAAAAGGTTGGAGGGAAAA
49010575 TATTAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.42, T:0.16
Consensus pattern (26 bp):
GGGGAATAAAAGGTTGGAGGGAAAAG
Found at i:49010660 original size:31 final size:30
Alignment explanation
Indices: 49010625--49010684 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
49010615 GGAGGTGGGA
*
49010625 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
49010656 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
49010685 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:49011760 original size:24 final size:24
Alignment explanation
Indices: 49011672--49011812 Score: 101
Period size: 25 Copynumber: 5.8 Consensus size: 24
49011662 TTTCTGTTAT
*
49011672 TTGGCTCTCACGAGCTTC-CTGATAA
1 TTGGCTCTCATGAGCTTCTC-GAT-A
49011697 TTGGCTCTCATGAGCTTCTCGATTA
1 TTGGCTCTCATGAGCTTCTCGA-TA
*
49011722 ATGGCTCTC-TAGAGCTTCTCGATA
1 TTGGCTCTCAT-GAGCTTCTCGATA
** *
49011746 TTGGCTAGCATGAGCTTCCCGAT-
1 TTGGCTCTCATGAGCTTCTCGATA
* * *
49011769 TACGGCTCTTATGAGCTT-TCCGTTA
1 T-TGGCTCTCATGAGCTTCT-CGATA
* *
49011794 CATGGCTCACATGAGCTTC
1 -TTGGCTCTCATGAGCTTC
49011813 CCGTTACATG
Statistics
Matches: 91, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
23 1 0.01
24 35 0.38
25 53 0.58
26 2 0.02
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.34
Consensus pattern (24 bp):
TTGGCTCTCATGAGCTTCTCGATA
Found at i:49011761 original size:49 final size:50
Alignment explanation
Indices: 49011673--49011815 Score: 131
Period size: 49 Copynumber: 2.9 Consensus size: 50
49011663 TTCTGTTATT
** *
49011673 TGGCTCTC-ACGAGCTTCCTGATAATTGGCTCTCATGAGCTTCTCGATTAA
1 TGGCTCTCTACGAGCTTCCTGATAATTGGCTAGCATGAGCTTCCCGATT-A
49011723 TGGCTCTCTA-GAGCTT-CTCGAT-ATTGGCTAGCATGAGCTTCCCGATTA
1 TGGCTCTCTACGAGCTTCCT-GATAATTGGCTAGCATGAGCTTCCCGATTA
* * *
49011771 CGGCTCT-TATGAGCTTTCC-GTTACA-TGGCTCA-CATGAGCTTCCCG
1 TGGCTCTCTACGAGC-TTCCTGATA-ATTGGCT-AGCATGAGCTTCCCG
49011816 TTACATGGCT
Statistics
Matches: 80, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
47 2 0.03
48 13 0.16
49 44 0.55
50 20 0.25
51 1 0.01
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.33
Consensus pattern (50 bp):
TGGCTCTCTACGAGCTTCCTGATAATTGGCTAGCATGAGCTTCCCGATTA
Found at i:49011800 original size:25 final size:25
Alignment explanation
Indices: 49011698--49011827 Score: 101
Period size: 25 Copynumber: 5.3 Consensus size: 25
49011688 TCCTGATAAT
* *
49011698 TGGCTCTCATGAGCTTCTCGATTA-A
1 TGGCTCACATGAGCTTCCCG-TTACA
* * * *
49011723 TGGCTCTC-TAGAGCTTCTCGATA-T
1 TGGCTCACAT-GAGCTTCCCGTTACA
49011747 TGGCT-AGCATGAGCTTCCCGATTAC-
1 TGGCTCA-CATGAGCTTCCCG-TTACA
** *
49011772 -GGCTCTTATGAGCTTTCCGTTACA
1 TGGCTCACATGAGCTTCCCGTTACA
49011796 TGGCTCACATGAGCTTCCCGTTACA
1 TGGCTCACATGAGCTTCCCGTTACA
49011821 TGGCTCA
1 TGGCTCA
49011828 GAAAAGCTTC
Statistics
Matches: 86, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
23 4 0.05
24 33 0.38
25 49 0.57
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.33
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCCCGTTACA
Found at i:49011835 original size:25 final size:25
Alignment explanation
Indices: 49011782--49011848 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
49011772 GGCTCTTATG
* **
49011782 AGCTTTCCGTTACATGGCTCACATG
1 AGCTTCCCGTTACATGGCTCACAAA
*
49011807 AGCTTCCCGTTACATGGCTCAGAAA
1 AGCTTCCCGTTACATGGCTCACAAA
*
49011832 AGCTTCCTGTTTACATG
1 AGCTTCCCG-TTACATG
49011849 CTCGTATGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 29 0.81
26 7 0.19
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.31
Consensus pattern (25 bp):
AGCTTCCCGTTACATGGCTCACAAA
Found at i:49016522 original size:125 final size:125
Alignment explanation
Indices: 49016317--49016714 Score: 532
Period size: 125 Copynumber: 3.2 Consensus size: 125
49016307 CGTTCCCTCC
* * * *
49016317 TGGATGCGTTTTTGCTACAGTTGGTCTTGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAAT
1 TGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAAT
* *
49016382 AGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAGAATTTGTTAAATCACGCCCACG
66 AGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAGAATTTGTAAAATCGCGCCCACG
* * * * * *
49016442 TGGACGTGCTTTTGCTACAGTAGGTCCT-GAAAAAATTATCTCGAGTTGACGTTTCTGAGAAAAT
1 TGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAAT
* * * * *
49016506 AGTACAAAAAAT-GCTTCAAGCAGGATGCTATT-TGAGAAGAATTTCTAAAATCGCGCCCTCG
66 AGT--ATAAAATCGCTTCTACCAGGATGCT-TTATGAGAAGAATTTGTAAAATCGCGCCCACG
* * * *
49016567 TGGACGCGCTTTTGCTATAGTTGGTTCTGGAAGAAATAATTTTGAGTTGACGTTTTTGAGCAAAT
1 TGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAAT
* * *
49016632 AGTATAAAATCGCTTCTACCAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGTCCACG
66 AGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAGAATTTGTAAAATCGCGCCCACG
49016692 TGGACGCGCTTTTGCTACAGTAG
1 TGGACGCGCTTTTGCTACAGTAG
49016715 CATGCTTGGG
Statistics
Matches: 230, Mismatches: 37, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
124 42 0.18
125 147 0.64
126 41 0.18
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (125 bp):
TGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAAT
AGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAGAATTTGTAAAATCGCGCCCACG
Found at i:49019844 original size:25 final size:24
Alignment explanation
Indices: 49019818--49019915 Score: 87
Period size: 25 Copynumber: 4.2 Consensus size: 24
49019808 AAAATAACTC
49019818 AAAAAAATTTCTATTTTATTACAT
1 AAAAAAATTTCTATTTTATTACAT
* *
49019842 CAAATAAACTTCTATTTTATTACAT
1 -AAAAAAATTTCTATTTTATTACAT
* * ** *
49019867 AAAATAATATC-A--AAATAAC-T
1 AAAAAAATTTCTATTTTATTACAT
49019887 GAAAAAAATTTCTATTTTATTACAT
1 -AAAAAAATTTCTATTTTATTACAT
49019912 AAAA
1 AAAA
49019916 TAATATCAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
20 1 0.02
21 13 0.24
22 1 0.02
23 1 0.02
24 15 0.28
25 23 0.43
ACGTcount: A:0.50, C:0.10, G:0.01, T:0.39
Consensus pattern (24 bp):
AAAAAAATTTCTATTTTATTACAT
Found at i:49019872 original size:70 final size:70
Alignment explanation
Indices: 49019788--49019918 Score: 235
Period size: 70 Copynumber: 1.9 Consensus size: 70
49019778 TAAGCTCATG
* *
49019788 TTATTACATCAAATAATATCAAAATAACTCAAAAAAATTTCTATTTTATTACATCAAATAAACTT
1 TTATTACATAAAATAATATCAAAATAACTCAAAAAAATTTCTATTTTATTACATAAAATAAACTT
49019853 CTATT
66 CTATT
*
49019858 TTATTACATAAAATAATATCAAAATAACTGAAAAAAATTTCTATTTTATTACATAAAATAA
1 TTATTACATAAAATAATATCAAAATAACTCAAAAAAATTTCTATTTTATTACATAAAATAA
49019919 TATCAAAATA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.50, C:0.11, G:0.01, T:0.37
Consensus pattern (70 bp):
TTATTACATAAAATAATATCAAAATAACTCAAAAAAATTTCTATTTTATTACATAAAATAAACTT
CTATT
Found at i:49020371 original size:18 final size:18
Alignment explanation
Indices: 49020348--49020387 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
49020338 GACTCGAAAA
*
49020348 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
49020366 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
49020384 AGGA
1 AGGA
49020388 AACGCACCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:49022198 original size:10 final size:10
Alignment explanation
Indices: 49022185--49022209 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49022175 TTGAAAAAAA
49022185 TAAAATTATT
1 TAAAATTATT
49022195 TAAAATTATT
1 TAAAATTATT
49022205 TAAAA
1 TAAAA
49022210 ATAGGGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TAAAATTATT
Found at i:49022263 original size:51 final size:51
Alignment explanation
Indices: 49022208--49022305 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
49022198 AATTATTTAA
49022208 AAATAGGGATTTAAGAGAAATTTAAGAA-GAACTTGAGAGCAAATTGAAATT
1 AAATAGGGATTTAAGAGAAATTT-AGAAGGAACTTGAGAGCAAATTGAAATT
* * * * *
49022259 AAATATGGATTTGAGATAAATTTTGAAGGAATTTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGA
49022306 GAGGAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
50 3 0.07
51 38 0.93
ACGTcount: A:0.46, C:0.03, G:0.22, T:0.29
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAAATT
Found at i:49022305 original size:11 final size:12
Alignment explanation
Indices: 49022288--49022320 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
49022278 ATTTTGAAGG
49022288 AATTTGAGAGCA
1 AATTTGAGAGCA
*
49022300 AA-TTGAGAGGA
1 AATTTGAGAGCA
49022311 AATTTGAGAG
1 AATTTGAGAG
49022321 AGGATTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.42, C:0.03, G:0.30, T:0.24
Consensus pattern (12 bp):
AATTTGAGAGCA
Found at i:49025709 original size:13 final size:13
Alignment explanation
Indices: 49025691--49025715 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49025681 AACGAATATC
49025691 AAATAAAATAAAT
1 AAATAAAATAAAT
49025704 AAATAAAATAAA
1 AAATAAAATAAA
49025716 ATTAGTAACC
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:49026626 original size:3 final size:3
Alignment explanation
Indices: 49026618--49026643 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
49026608 AATATTTTAA
49026618 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
49026644 CAAAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:49043638 original size:41 final size:41
Alignment explanation
Indices: 49043593--49043672 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
49043583 CTGAAATGCA
*
49043593 TCACCGACATTAAGCCTGCTAGACGTAAAGTCTGTATTATT
1 TCACCGACATCAAGCCTGCTAGACGTAAAGTCTGTATTATT
**
49043634 TCACCGGTATCAAGCCTGCTAGACGTAAAGTCTGTATTA
1 TCACCGACATCAAGCCTGCTAGACGTAAAGTCTGTATTA
49043673 CATTCGATCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (41 bp):
TCACCGACATCAAGCCTGCTAGACGTAAAGTCTGTATTATT
Found at i:49043947 original size:12 final size:12
Alignment explanation
Indices: 49043930--49043984 Score: 65
Period size: 12 Copynumber: 4.3 Consensus size: 12
49043920 AAAAACTTAT
49043930 ATATATATATAC
1 ATATATATATAC
*
49043942 ATATATATATTC
1 ATATATATATAC
*
49043954 GAGTATTATACATAC
1 -A-TA-TATATATAC
49043969 ATATATATATAC
1 ATATATATATAC
49043981 ATAT
1 ATAT
49043985 CTTTGACTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 23 0.64
13 3 0.08
14 3 0.08
15 7 0.19
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (12 bp):
ATATATATATAC
Found at i:49048229 original size:23 final size:23
Alignment explanation
Indices: 49048203--49048261 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
49048193 CAGCTCGTAT
* *
49048203 GAGCTTACCGTTTCAGCTCTACG
1 GAGCTTACCGTTTCAGCTCAACA
*
49048226 GAGCTTACCGTTTCAGCTCAATA
1 GAGCTTACCGTTTCAGCTCAACA
49048249 GAGCTTACCGTTT
1 GAGCTTACCGTTT
49048262 ATCAGCTCGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.32
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGCTCAACA
Found at i:49056903 original size:53 final size:53
Alignment explanation
Indices: 49056792--49056903 Score: 199
Period size: 52 Copynumber: 2.1 Consensus size: 53
49056782 AAAACTGATG
*
49056792 TAATTTATATTATCTTTTTTCATGACAGTCGAAGGGCCCATCACAACCTAACT
1 TAATTTATATTATCTTTTTTCATGACAGTCGAAGAGCCCATCACAACCTAACT
49056845 TAATTTATATTATCTTTTTTCAT-ACAGTCGAAGAGCCCATCACAACCTAACT
1 TAATTTATATTATCTTTTTTCATGACAGTCGAAGAGCCCATCACAACCTAACT
49056897 TCAATTT
1 T-AATTT
49056904 GAACCACTTG
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 29 0.51
53 28 0.49
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (53 bp):
TAATTTATATTATCTTTTTTCATGACAGTCGAAGAGCCCATCACAACCTAACT
Found at i:49058782 original size:25 final size:25
Alignment explanation
Indices: 49058754--49058818 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
49058744 TACGAACTGT
*
49058754 ATATTGGGAAGCTC-TTGCGAGCCAA
1 ATATTGGGAAGCTCATT-AGAGCCAA
* *
49058779 ATATCGAGAAGCTCATTAGAGCCAA
1 ATATTGGGAAGCTCATTAGAGCCAA
* *
49058804 GTATTGGGAAACTCA
1 ATATTGGGAAGCTCA
49058819 AGAGAGCTGT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
25 30 0.94
26 2 0.06
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (25 bp):
ATATTGGGAAGCTCATTAGAGCCAA
Found at i:49059173 original size:16 final size:15
Alignment explanation
Indices: 49059133--49059175 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
49059123 TATATGAATG
* *
49059133 AATTTAACTCAATTT
1 AATTTAATTCAATTC
*
49059148 AATATAATTCATATTC
1 AATTTAATTCA-ATTC
49059164 AATTTAATTCAA
1 AATTTAATTCAA
49059176 CATGCATCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTTAATTCAATTC
Found at i:49064410 original size:2 final size:2
Alignment explanation
Indices: 49064403--49064434 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
49064393 CAACCAAATG
49064403 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49064435 ATCCGTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49071644 original size:35 final size:35
Alignment explanation
Indices: 49071599--49071684 Score: 156
Period size: 36 Copynumber: 2.5 Consensus size: 35
49071589 ATTAGCAGCG
49071599 TTTTTT-GAAAAACGCTGCTAAATGAGCATTGGCA
1 TTTTTTGGAAAAACGCTGCTAAATGAGCATTGGCA
49071633 TTTTTTGGAAAAAACGCTGCTAAATGAGCATTGGCA
1 TTTTTTGG-AAAAACGCTGCTAAATGAGCATTGGCA
49071669 TTTTTTGGAAAAACGC
1 TTTTTTGGAAAAACGC
49071685 CGCAAAAAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
34 6 0.12
35 9 0.18
36 35 0.70
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (35 bp):
TTTTTTGGAAAAACGCTGCTAAATGAGCATTGGCA
Found at i:49071804 original size:40 final size:41
Alignment explanation
Indices: 49071727--49071842 Score: 132
Period size: 40 Copynumber: 2.9 Consensus size: 41
49071717 TTGATCTTTT
* *
49071727 GGGGCTTTAGCGGCATTTTTGAAAAAGCGCCTCTAATGCTC
1 GGGGCTTTAACAGCATTTTTGAAAAAGCGCCTCTAATGCTC
*
49071768 GGGGCTTTAACAGCGTTTTTG-AAAAGCGCCGT-TAATGCTC
1 GGGGCTTTAACAGCATTTTTGAAAAAGCGCC-TCTAATGCTC
* * *
49071808 GGGGATTTAGC-GACA-TTTTGAAAAAGCGCCGCTAA
1 GGGGCTTTAACAG-CATTTTTGAAAAAGCGCCTCTAA
49071843 AAACATTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
39 6 0.09
40 39 0.61
41 19 0.30
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (41 bp):
GGGGCTTTAACAGCATTTTTGAAAAAGCGCCTCTAATGCTC
Found at i:49072517 original size:15 final size:15
Alignment explanation
Indices: 49072499--49072541 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
49072489 ACTATTTTAA
*
49072499 GGTTTATGGATTATG
1 GGTTTATGGATTATC
*
49072514 GGTTTAGGGATTA-C
1 GGTTTATGGATTATC
*
49072528 GGTTTATGGTTTAT
1 GGTTTATGGATTAT
49072542 TGTTTAAGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.47
Consensus pattern (15 bp):
GGTTTATGGATTATC
Found at i:49072540 original size:7 final size:7
Alignment explanation
Indices: 49072431--49072604 Score: 52
Period size: 7 Copynumber: 24.4 Consensus size: 7
49072421 TTAATTATAA
*
49072431 TTATAGT
1 TTATGGT
*
49072438 TTAAGGT
1 TTATGGT
*
49072445 TTAGGGT
1 TTATGGT
*
49072452 TTAGGGT
1 TTATGGT
*
49072459 ATATGGT
1 TTATGGT
* *
49072466 GTAGGGT
1 TTATGGT
*
49072473 TTAAGGT
1 TTATGGT
*
49072480 TTAAGAGT
1 TTATG-GT
49072488 TACTAT--T
1 T--TATGGT
*
49072495 TTAAGGT
1 TTATGGT
*
49072502 TTATGGA
1 TTATGGT
49072509 TTATGGGT
1 TTAT-GGT
* *
49072517 TTAGGGA
1 TTATGGT
*
49072524 TTACGGT
1 TTATGGT
49072531 TTATGGT
1 TTATGGT
*
49072538 TTATTGT
1 TTATGGT
*
49072545 TTAAGAG-
1 TTATG-GT
49072552 TTA-GGAT
1 TTATGG-T
*
49072559 TTAAGGT
1 TTATGGT
* *
49072566 TCAGGGGT
1 TTA-TGGT
*
49072574 TTA-GGAG
1 TTATGG-T
*
49072581 TTATGTT
1 TTATGGT
49072588 TTATGGT
1 TTATGGT
49072595 TTATGGT
1 TTATGGT
49072602 TTA
1 TTA
49072605 GGGGTTTAGA
Statistics
Matches: 125, Mismatches: 29, Indels: 26
0.69 0.16 0.14
Matches are distributed among these distances:
5 3 0.02
6 3 0.02
7 100 0.80
8 17 0.14
10 2 0.02
ACGTcount: A:0.23, C:0.02, G:0.30, T:0.45
Consensus pattern (7 bp):
TTATGGT
Found at i:49079626 original size:48 final size:48
Alignment explanation
Indices: 49079547--49079688 Score: 232
Period size: 48 Copynumber: 3.0 Consensus size: 48
49079537 AGGGAATTCT
* * **
49079547 GTTGAATCCTTTATTGTTGCGAGTT-GAGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCTTTATAGGTGAAAGTTAG-GCTGACTTAGGCGTTTTTACG
49079595 GTTGAATCCTTTATAGGTGAAAGTTAGGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCTTTATAGGTGAAAGTTAGGCTGACTTAGGCGTTTTTACG
49079643 GTTGAATCCTTTATAGGTGAAAGTTAGGCTGACTTAGGCGTTTTTA
1 GTTGAATCCTTTATAGGTGAAAGTTAGGCTGACTTAGGCGTTTTTA
49079689 AGCCAAGAAA
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
48 88 0.99
49 1 0.01
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.39
Consensus pattern (48 bp):
GTTGAATCCTTTATAGGTGAAAGTTAGGCTGACTTAGGCGTTTTTACG
Found at i:49080819 original size:16 final size:16
Alignment explanation
Indices: 49080788--49080824 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
49080778 ATATGAAGAA
49080788 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
49080804 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
49080820 TATTA
1 TATTA
49080825 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:49080863 original size:16 final size:16
Alignment explanation
Indices: 49080844--49080878 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
49080834 TGAAATATTA
*
49080844 AATAATTTATTAAAAT
1 AATAAATTATTAAAAT
*
49080860 AATAAATTATTAATAT
1 AATAAATTATTAAAAT
49080876 AAT
1 AAT
49080879 TTATTATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATAAATTATTAAAAT
Found at i:49080884 original size:16 final size:15
Alignment explanation
Indices: 49080839--49080885 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 15
49080829 AAAATTGAAA
49080839 TATTAAATAATTTAT
1 TATTAAATAATTTAT
**
49080854 TA--AAATAATAAAT
1 TATTAAATAATTTAT
49080867 TATTAATATAATTTAT
1 TATTAA-ATAATTTAT
49080883 TAT
1 TAT
49080886 ATGATTAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
13 11 0.44
15 4 0.16
16 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTAAATAATTTAT
Found at i:49085948 original size:12 final size:12
Alignment explanation
Indices: 49085921--49085967 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
49085911 AATTTAAAGC
49085921 ATATATACATAA-
1 ATATATACA-AAT
*
49085933 ATATTTACAAAT
1 ATATATACAAAT
*
49085945 ATATATACAAGT
1 ATATATACAAAT
49085957 ATAGTATACAA
1 ATA-TATACAA
49085968 GTAAACTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 2 0.07
12 21 0.70
13 7 0.23
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (12 bp):
ATATATACAAAT
Found at i:49086610 original size:12 final size:12
Alignment explanation
Indices: 49086595--49086633 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
49086585 GATAGAGATG
*
49086595 ATGATAGTAATA
1 ATGATAATAATA
49086607 ATGATAATATATA
1 ATGATAATA-ATA
49086620 AT-ATAATAATA
1 ATGATAATAATA
49086631 ATG
1 ATG
49086634 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 5 0.21
12 14 0.58
13 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (12 bp):
ATGATAATAATA
Found at i:49088211 original size:45 final size:44
Alignment explanation
Indices: 49088156--49088245 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
49088146 AAGACTTGTA
* * **
49088156 TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCA-CACCAATACAGGAAGACAAGATCTGCTT
* *
49088201 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTT
49088245 T
1 T
49088246 TTCAATCGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 24 0.62
45 15 0.38
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (44 bp):
TCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTT
Found at i:49088491 original size:44 final size:44
Alignment explanation
Indices: 49088441--49088924 Score: 315
Period size: 45 Copynumber: 10.9 Consensus size: 44
49088431 ACCAATATAG
* * *
49088441 GAAGACAAGACCTACTATCTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCAGTACAT
* * * * * ***
49088485 GAAGACACGATCTGTTTTCTTCGACCTAC-TCTACCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTTGATCTACTTC-A-CGCCAGTACAT
*
49088530 GGAGACAAGATCTG-TTTCTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCAGTACAT
* * ***
49088573 GAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTTGATCTACTTCA-CGCCAGTACAT
* *
49088618 GGAGACAAGATCTG-TTGACTTTGATCTACTTCACGCC-GATACAT
1 GAAGACAAGATCTGCTT-TCTTTGATCTACTTCACGCCAG-TACAT
* ***
49088662 GAAGACAAGATCTGCTTTCTTTGATCTAC-TCTACCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTTGATCTACTTC-A-CGCCAGTACAT
* * *
49088707 GGAGACAAGATCTG-TTGACTTTGATCTACTTCACG-CTGATACAT
1 GAAGACAAGATCTGCTT-TCTTTGATCTACTTCACGCCAG-TACAT
* * * * * *
49088751 GAAGACAATATCTACTTTCTTTCGATCTGCTTCGCCACCAGTATGA-
1 GAAGACAAGATCTGCTTTCTTT-GATCTACTTC-ACGCCAGTA-CAT
* * * * * *
49088797 GAAGGCGAGATCTG-TATATTCGATCTACTTCACGCTAGTACAT
1 GAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCAGTACAT
* * * * ***
49088840 GAAGACAAGATCTG-TATTCCTTCGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCT-TT-CTTTGATCTACTTC-ACGCCAGTACAT
***
49088886 GAAGGTGAGATCTG-TTATCTTTGATCTACTTCACGCCAG
1 GAAGACAAGATCTGCTT-TCTTTGATCTACTTCACGCCAG
49088925 AAGACAAGAT
Statistics
Matches: 332, Mismatches: 84, Indels: 48
0.72 0.18 0.10
Matches are distributed among these distances:
42 1 0.00
43 46 0.14
44 120 0.36
45 127 0.38
46 35 0.11
47 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
GAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCAGTACAT
Found at i:49088678 original size:89 final size:88
Alignment explanation
Indices: 49088459--49088924 Score: 580
Period size: 89 Copynumber: 5.2 Consensus size: 88
49088449 GACCTACTAT
* * * * *
49088459 CTTTGATCTACTTCACGCCAGTACATGAAGACACGATCTGTTTTCTTCGACCTACTCTACCACCA
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACCA
*
49088524 GTATGGGGAGACAAGATCTGTTT
66 GTATGGGGAGACAAGATCTGTTA
49088547 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACCA
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACCA
49088612 GTATGGGGAGACAAGATCTGTTGA
66 GTATGGGGAGACAAGATCTGTT-A
*
49088636 CTTTGATCTACTTCACGCC-GATACATGAAGACAAGATCTGCTTTCTTTGATCTACTCTACCACC
1 CTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACC
49088700 AGTATGGGGAGACAAGATCTGTTGA
65 AGTATGGGGAGACAAGATCTGTT-A
* * * * * *
49088725 CTTTGATCTACTTCACG-CTGATACATGAAGACAATATCTACTTTCTTTCGATCTGCTTCGCCAC
1 CTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTGCTTTCTTT-GATCTACTCCACCAC
* * * *
49088789 CAGTATGAGAAGGCGAGATCTGTATA
64 CAGTATGGGGAGACAAGATCTGT-TA
* * * * * *
49088815 -TTCGATCTACTTCACGCTAGTACATGAAGACAAGATCTG-TATTCCTTCGATCTGCTTCGCCAC
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT-TT-CTTTGATCTACTCCACCAC
* ***
49088878 CAGTATGGGAAGGTGAGATCTGTTA
64 CAGTATGGGGAGACAAGATCTGTTA
49088903 TCTTTGATCTACTTCACGCCAG
1 -CTTTGATCTACTTCACGCCAG
49088925 AAGACAAGAT
Statistics
Matches: 341, Mismatches: 27, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
88 87 0.26
89 200 0.59
90 53 0.16
91 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (88 bp):
CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACCA
GTATGGGGAGACAAGATCTGTTA
Found at i:49088778 original size:45 final size:43
Alignment explanation
Indices: 49088441--49088852 Score: 216
Period size: 44 Copynumber: 9.3 Consensus size: 43
49088431 ACCAATATAG
* *
49088441 GAAGACAAGACCTACTATCTTTGATCTACTTCACGCCAG-TACAT
1 GAAGACAAGATCT-CTTTCTTTGATCTACTTCACG-CAGATACAT
* * * * ***
49088485 GAAGACACGATCTGTTTTCTTCGACCTACTCTACCAC-CAG-TATGG
1 GAAGACAAGATCT-CTTTCTTTGATCTACT-T--CACGCAGATACAT
* *
49088530 GGAGACAAGATCTGTTTCTTTGATCTACTTCACGCCAG-TACAT
1 GAAGACAAGATCTCTTTCTTTGATCTACTTCACG-CAGATACAT
* * ***
49088573 GAAGACAAGATCTGCTTTCTTTGATCTACTCCAC-CACCAGTATGG
1 GAAGACAAGATCT-CTTTCTTTGATCTACTTCACGCA-GA-TACAT
* * * *
49088618 GGAGACAAGATCTGTTGACTTTGATCTACTTCACGCCGATACAT
1 GAAGACAAGATCTCTT-TCTTTGATCTACTTCACGCAGATACAT
***
49088662 GAAGACAAGATCTGCTTTCTTTGATCTACTCTACCAC-CAG-TATGG
1 GAAGACAAGATCT-CTTTCTTTGATCTACT-T--CACGCAGATACAT
* * * *
49088707 GGAGACAAGATCTGTTGACTTTGATCTACTTCACGCTGATACAT
1 GAAGACAAGATCTCTT-TCTTTGATCTACTTCACGCAGATACAT
* * *
49088751 GAAGACAATATCTACTTTCTTTCGATCTGCTTCGCCAC-CAG-TATGA-
1 GAAGACAAGATCT-CTTTCTTT-GATCTACTT---CACGCAGATA-CAT
* * * * * *
49088797 GAAGGCGAGATCTGTATATTCGATCTACTTCACGCTAG-TACAT
1 GAAGACAAGATCTCTTTCTTTGATCTACTTCACGC-AGATACAT
49088840 GAAGACAAGATCT
1 GAAGACAAGATCT
49088853 GTATTCCTTC
Statistics
Matches: 275, Mismatches: 66, Indels: 55
0.69 0.17 0.14
Matches are distributed among these distances:
41 6 0.02
42 7 0.03
43 35 0.13
44 110 0.40
45 90 0.33
46 15 0.05
47 9 0.03
48 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (43 bp):
GAAGACAAGATCTCTTTCTTTGATCTACTTCACGCAGATACAT
Found at i:49090344 original size:49 final size:51
Alignment explanation
Indices: 49090285--49090411 Score: 143
Period size: 49 Copynumber: 2.5 Consensus size: 51
49090275 CCTTTGGTCT
*
49090285 AAGGCGCCCTTTGCGA-GTTTTCACCTTAGCCTCTC-CATTTTTTTT-ACTC
1 AAGGCGCCCTTTG-GAGGGTTTCACCTTAGCCTCTCTCATTTTTTTTGACTC
* * * * *
49090334 AAGGCTCCCTTTGTAGGGTTTCACCTTGGTCTCTCTCTTTTTTTTTGACTC
1 AAGGCGCCCTTTGGAGGGTTTCACCTTAGCCTCTCTCATTTTTTTTGACTC
* * *
49090385 AAAGCGCCCTTTGTAGGCTTTCACCTT
1 AAGGCGCCCTTTGGAGGGTTTCACCTT
49090412 GGTCCCACGT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
48 1 0.02
49 28 0.42
50 9 0.14
51 28 0.42
ACGTcount: A:0.13, C:0.28, G:0.17, T:0.42
Consensus pattern (51 bp):
AAGGCGCCCTTTGGAGGGTTTCACCTTAGCCTCTCTCATTTTTTTTGACTC
Found at i:49090395 original size:51 final size:49
Alignment explanation
Indices: 49090303--49090415 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 49
49090293 CTTTGCGAGT
* * * * *
49090303 TTTCACCTTAGCCTCTCCATTTTTTTTACTCAAGGCTCCCTTTGTAGGG
1 TTTCACCTTGGTCTCTCCATTTTTTTTACTCAAAGCGCCCTTTGTAGGC
*
49090352 TTTCACCTTGGTCTCTCTCTTTTTTTTTGACTCAAAGCGCCCTTTGTAGGC
1 TTTCACCTTGGTCTCTC-CATTTTTTTT-ACTCAAAGCGCCCTTTGTAGGC
49090403 TTTCACCTTGGTC
1 TTTCACCTTGGTC
49090416 CCACGTTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
49 15 0.27
50 9 0.16
51 32 0.57
ACGTcount: A:0.12, C:0.28, G:0.15, T:0.44
Consensus pattern (49 bp):
TTTCACCTTGGTCTCTCCATTTTTTTTACTCAAAGCGCCCTTTGTAGGC
Found at i:49090426 original size:51 final size:50
Alignment explanation
Indices: 49090322--49090427 Score: 142
Period size: 51 Copynumber: 2.1 Consensus size: 50
49090312 AGCCTCTCCA
* * * * *
49090322 TTTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCTTGGTCTCTCTCT
1 TTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTCCCACTCT
*
49090372 TTTTTTTTGACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTCCCAC-GT
1 TTTTTTTT-ACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTCCCACTCT
49090422 TTTTTT
1 TTTTTT
49090428 AAGCAGAGTA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
50 15 0.31
51 34 0.69
ACGTcount: A:0.11, C:0.25, G:0.16, T:0.47
Consensus pattern (50 bp):
TTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTCCCACTCT
Found at i:49093142 original size:20 final size:20
Alignment explanation
Indices: 49093113--49093152 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
49093103 TAAAGGTCTT
* *
49093113 TAATGCATATGATGTGATGC
1 TAATGAATATGATGCGATGC
49093133 TAATGAATATGATGCGATGC
1 TAATGAATATGATGCGATGC
49093153 ATGAGGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.33
Consensus pattern (20 bp):
TAATGAATATGATGCGATGC
Found at i:49097049 original size:2 final size:2
Alignment explanation
Indices: 49097044--49097077 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
49097034 AATATAAAAG
49097044 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49097078 AGTTGAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49097268 original size:12 final size:12
Alignment explanation
Indices: 49097253--49097291 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
49097243 GATAGAGATG
*
49097253 ATGATAGTAATA
1 ATGATAATAATA
49097265 ATGATAATATATA
1 ATGATAATA-ATA
49097278 AT-ATAATAATA
1 ATGATAATAATA
49097289 ATG
1 ATG
49097292 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 5 0.21
12 14 0.58
13 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (12 bp):
ATGATAATAATA
Found at i:49097822 original size:11 final size:11
Alignment explanation
Indices: 49097806--49097833 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
49097796 TGAGAAAGGC
49097806 GCACCGTGGCG
1 GCACCGTGGCG
49097817 GCACCGTGGCG
1 GCACCGTGGCG
49097828 GCACCG
1 GCACCG
49097834 GTAAGCGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.11, C:0.39, G:0.43, T:0.07
Consensus pattern (11 bp):
GCACCGTGGCG
Found at i:49099794 original size:15 final size:14
Alignment explanation
Indices: 49099758--49099797 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
49099748 TATCTTATTG
49099758 AAAT-TTTAAAAAA
1 AAATATTTAAAAAA
*
49099771 AAATATTTATAAAA
1 AAATATTTAAAAAA
49099785 AAATACTTTAAAA
1 AAATA-TTTAAAA
49099798 CTTAATCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 4 0.17
14 13 0.57
15 6 0.26
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATTTAAAAAA
Found at i:49100819 original size:98 final size:98
Alignment explanation
Indices: 49100647--49100841 Score: 318
Period size: 98 Copynumber: 2.0 Consensus size: 98
49100637 ACAATAAAAT
*
49100647 TTTAAAAGAACATCCACTTATCAAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACTTATCAAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
49100712 TCTAGAATCCCAAACTCAGAATATTTCATTTAC
66 TCTAAAATCCCAAACTCAGAATATTTCATTTAC
* *
49100745 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCT
1 TTTAAAAGAACATCCACTTATCAAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
* * * *
49100810 TTTAAAATCCCAAATTCGGAATATTTCCTTTA
66 TCTAAAATCCCAAACTCAGAATATTTCATTTA
49100842 TTGTTTTTAG
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTTATCAAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TCTAAAATCCCAAACTCAGAATATTTCATTTAC
Found at i:49102318 original size:22 final size:23
Alignment explanation
Indices: 49102276--49102318 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
49102266 AATTTAAATC
49102276 TCTAAGATTACAAAATCATATAT
1 TCTAAGATTACAAAATCATATAT
*
49102299 TCTAAGATTAC-ATATCATAT
1 TCTAAGATTACAAAATCATAT
49102319 CTAATATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (23 bp):
TCTAAGATTACAAAATCATATAT
Found at i:49104252 original size:2 final size:2
Alignment explanation
Indices: 49104245--49104273 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49104235 ACTAGTATCC
49104245 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
49104274 GCTCCCCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:49114857 original size:21 final size:20
Alignment explanation
Indices: 49114821--49115012 Score: 78
Period size: 19 Copynumber: 9.3 Consensus size: 20
49114811 TTTTTATTTT
*
49114821 AAAAAT-TTTAAAAAATTAA
1 AAAAATATTTTAAAAATTAA
**
49114840 AAAAAGTATTTTAAAAATATTT
1 AAAAA-TATTTTAAAAAT-TAA
*
49114862 TAAAATATTTT-AAAATT--
1 AAAAATATTTTAAAAATTAA
*
49114879 AAAAATTTTTTAAAAAAAGTATTTTAA
1 AAAAATATTTT---AAAA--A--TTAA
*
49114906 AAAAGTATTTT-AAAATTAA
1 AAAAATATTTTAAAAATTAA
** *
49114925 AAAAA-ATTAAAAAAGTATTTA
1 AAAAATATTTTAAAA--ATTAA
*
49114946 AAAAATATTTT-AAAATTTA
1 AAAAATATTTTAAAAATTAA
** *
49114965 AAAAA-ATTAAAAAAAGTATGTA
1 AAAAATATTTTAAAAA-T-T-AA
49114987 AAAAATATTTT-AAAATTAA
1 AAAAATATTTTAAAAATTAA
49115006 AAAAATA
1 AAAAATA
49115013 AATATATTTA
Statistics
Matches: 132, Mismatches: 19, Indels: 44
0.68 0.10 0.23
Matches are distributed among these distances:
17 9 0.07
18 6 0.05
19 39 0.30
20 8 0.06
21 33 0.25
22 19 0.14
23 7 0.05
25 2 0.02
27 9 0.07
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
AAAAATATTTTAAAAATTAA
Found at i:49114877 original size:41 final size:40
Alignment explanation
Indices: 49114815--49115010 Score: 200
Period size: 41 Copynumber: 4.7 Consensus size: 40
49114805 GGCCTATTTT
*
49114815 TATTTTAAAA-ATTTTAAAAAATTAAAAAAAGTATTTTAAAAA-
1 TATTTTAAAATATTTT--AAAATTAAAAAAA--ATTTAAAAAAG
***
49114857 TATTTTAAAATATTTTAAAATTAAAAATTTTTTAAAAAAAG
1 TATTTTAAAATATTTTAAAATTAAAAAAAATTT-AAAAAAG
49114898 TATTTTAAAAAAGTATTTTAAAATTAAAAAAAA-TTAAAAAAG
1 TATTTT--AAAA-TATTTTAAAATTAAAAAAAATTTAAAAAAG
* * *
49114940 TATTTAAAAAATATTTTAAAATTTAAAAAAATTAAAAAAAG
1 TATTT-TAAAATATTTTAAAATTAAAAAAAATTTAAAAAAG
**
49114981 TATGTAAAAAATATTTTAAAATTAAAAAAA
1 TAT-TTTAAAATATTTTAAAATTAAAAAAA
49115011 TAAATATATT
Statistics
Matches: 133, Mismatches: 12, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
39 3 0.02
40 24 0.18
41 55 0.41
42 23 0.17
43 11 0.08
44 17 0.13
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (40 bp):
TATTTTAAAATATTTTAAAATTAAAAAAAATTTAAAAAAG
Found at i:49114893 original size:10 final size:10
Alignment explanation
Indices: 49114815--49114877 Score: 65
Period size: 10 Copynumber: 6.1 Consensus size: 10
49114805 GGCCTATTTT
49114815 TATTTTAAAA
1 TATTTTAAAA
49114825 -ATTTTAAAA
1 TATTTTAAAA
* **
49114834 AATTAAAAAAA
1 TATT-TTAAAA
49114845 GTATTTTAAAAA
1 -TATTTT-AAAA
49114857 TATTTTAAAA
1 TATTTTAAAA
49114867 TATTTTAAAA
1 TATTTTAAAA
49114877 T
1 T
49114878 TAAAAATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
9 9 0.20
10 18 0.41
11 10 0.23
12 7 0.16
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:49114907 original size:12 final size:13
Alignment explanation
Indices: 49114839--49114960 Score: 69
Period size: 12 Copynumber: 9.3 Consensus size: 13
49114829 TAAAAAATTA
49114839 AAAAAAGTATTTT
1 AAAAAAGTATTTT
49114852 -AAAAA-TATTTT
1 AAAAAAGTATTTT
49114863 --AAAA-TATTTT
1 AAAAAAGTATTTT
* *
49114873 AAAATTAAAAATTTTTT
1 --AA--AAAAGTATTTT
49114890 AAAAAAAGTATTTT
1 -AAAAAAGTATTTT
49114904 AAAAAAGTATTTT
1 AAAAAAGTATTTT
** **
49114917 AAAATTAAAAAAAATT
1 -AAA--AAAGTATTTT
49114933 AAAAAAGTA-TTT
1 AAAAAAGTATTTT
49114945 AAAAAA-TATTTT
1 AAAAAAGTATTTT
49114957 AAAA
1 AAAA
49114961 TTTAAAAAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
10 10 0.11
11 8 0.09
12 20 0.23
13 17 0.19
14 12 0.14
15 3 0.03
16 13 0.15
17 5 0.06
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
AAAAAAGTATTTT
Found at i:49114931 original size:54 final size:54
Alignment explanation
Indices: 49114836--49114960 Score: 152
Period size: 54 Copynumber: 2.4 Consensus size: 54
49114826 TTTTAAAAAA
*** * *
49114836 TTAAAAAAAGTATTTT-AAAAATATTTTAAAATATTTTAAAATT-AAAAATTTT
1 TTAAAAAAAGTATTTTAAAAAATATTTTAAAATATAAAAAAATTAAAAAAGTAT
49114888 TTAAAAAAAGTATTTTAAAAAAGTATTTTAAAAT-TAAAAAAAATTAAAAAAGTAT
1 TTAAAAAAAGTATTTTAAAAAA-TATTTTAAAATAT-AAAAAAATTAAAAAAGTAT
49114943 TT-AAAAAA-TATTTTAAAA
1 TTAAAAAAAGTATTTTAAAA
49114961 TTTAAAAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
52 16 0.25
53 16 0.25
54 23 0.36
55 9 0.14
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (54 bp):
TTAAAAAAAGTATTTTAAAAAATATTTTAAAATATAAAAAAATTAAAAAAGTAT
Found at i:49114990 original size:94 final size:96
Alignment explanation
Indices: 49114815--49115001 Score: 236
Period size: 94 Copynumber: 2.0 Consensus size: 96
49114805 GGCCTATTTT
** * **
49114815 TATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATATTTTAAAATTA
1 TATTTTAAAAATTAAAAAAAATTAAAAAAAGTATTTAAAAAATATTTTAAAATATTAAAAAATTA
*** * *
49114880 AAAATTTTTTAAAAAAAGTATTTTAAAAAAG
66 AAAAAAGTATAAAAAAAATATTTTAAAAAAG
49114911 TATTTT-AAAATTAAAAAAAATT-AAAAAAGTATTTAAAAAATATTTTAAAAT-TTAAAAAAATT
1 TATTTTAAAAATTAAAAAAAATTAAAAAAAGTATTTAAAAAATATTTTAAAATATT-AAAAAATT
**
49114973 AAAAAAAGTATGTAAAAAATATTTTAAAA
65 AAAAAAAGTATAAAAAAAATATTTTAAAA
49115002 TTAAAAAAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
93 2 0.03
94 56 0.72
95 14 0.18
96 6 0.08
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (96 bp):
TATTTTAAAAATTAAAAAAAATTAAAAAAAGTATTTAAAAAATATTTTAAAATATTAAAAAATTA
AAAAAAGTATAAAAAAAATATTTTAAAAAAG
Found at i:49120656 original size:2 final size:2
Alignment explanation
Indices: 49120649--49120674 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
49120639 TTTAATTTTA
49120649 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
49120675 TGTTTCAGGA
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:49123286 original size:25 final size:27
Alignment explanation
Indices: 49123256--49123319 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 27
49123246 TAATTTTTGA
*
49123256 ATTTGATGATGATTTTGTG-TTT-TGCT
1 ATTTGATGAT-AGTTTGTGATTTCTGCT
*
49123282 A-TTGATGATAGTTTGTGATTTCTGTT
1 ATTTGATGATAGTTTGTGATTTCTGCT
49123308 ATTTGATGATAG
1 ATTTGATGATAG
49123320 AAAATAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
24 7 0.21
25 11 0.33
26 5 0.15
27 10 0.30
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.53
Consensus pattern (27 bp):
ATTTGATGATAGTTTGTGATTTCTGCT
Found at i:49126646 original size:23 final size:22
Alignment explanation
Indices: 49126603--49126646 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
49126593 TTCTAAGTAG
49126603 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
49126626 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
49126647 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:49126806 original size:51 final size:51
Alignment explanation
Indices: 49126742--49126881 Score: 165
Period size: 51 Copynumber: 2.7 Consensus size: 51
49126732 TGTTCAGTTT
* * *
49126742 ACATACTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATAC
1 ACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCGATAC
* * * * *
49126793 ACGTAGTAGCCTGCACATAGTACTATACACGTGATCGA-AACTATCCGGTAC
1 ACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAACCATCCGATAC
** *
49126844 GTATAGTAGCTTGCACATAGTACTACACACGTGACCAT
1 ACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
49126882 CACTTTCACT
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
50 2 0.03
51 69 0.95
52 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (51 bp):
ACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCGATAC
Found at i:49131730 original size:3 final size:3
Alignment explanation
Indices: 49131722--49131747 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
49131712 CTTTTTGTTT
49131722 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
49131748 GTAAACTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:49134035 original size:11 final size:11
Alignment explanation
Indices: 49134021--49134109 Score: 63
Period size: 11 Copynumber: 8.9 Consensus size: 11
49134011 ATTTTTTAAA
49134021 TTTTAAAATAT
1 TTTTAAAATAT
49134032 TTTTAAAATACT
1 TTTTAAAATA-T
***
49134044 TTTT-TTTTAT
1 TTTTAAAATAT
49134054 TTTT---A-AT
1 TTTTAAAATAT
49134061 -TTTAAAATAT
1 TTTTAAAATAT
*
49134071 TTTAAAAATAT
1 TTTTAAAATAT
49134082 TTTT--AA-A-
1 TTTTAAAATAT
49134089 TTTTAAAATAT
1 TTTTAAAATAT
49134100 TTTTAAAATA
1 TTTTAAAATA
49134110 CATTTTTTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
6 3 0.05
7 6 0.10
8 1 0.02
9 5 0.08
10 8 0.13
11 34 0.55
12 5 0.08
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:49134062 original size:39 final size:38
Alignment explanation
Indices: 49134013--49134127 Score: 122
Period size: 39 Copynumber: 3.2 Consensus size: 38
49134003 TTTTTTAAAT
49134013 TTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTTTA
1 TTTTT-AATTTTAAAATATTTTTAAAATAC-TTTTTTTTA
*
49134053 TTTTTAATTTTAAAATA-TTTTAAAA-A--TATTTTTA
1 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTA
*
49134087 -----AATTTTAAAATATTTTTAAAATACATTTTTTTAA
1 TTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTTTA
49134121 TTTTTAA
1 TTTTTAA
49134128 AATAAAATTT
Statistics
Matches: 62, Mismatches: 3, Indels: 21
0.72 0.03 0.24
Matches are distributed among these distances:
29 12 0.19
30 8 0.13
31 1 0.02
34 13 0.21
37 1 0.02
38 8 0.13
39 14 0.23
40 5 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (38 bp):
TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTA
Found at i:49134085 original size:29 final size:32
Alignment explanation
Indices: 49134053--49134131 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 32
49134043 TTTTTTTTTA
*
49134053 TTTTTAATTTTAAAATA-TTTTAAAA-ATA-T
1 TTTTTAATTTTAAAATATTTTTAAAATACATT
*
49134082 TTTTAAATTTTAAAATATTTTTAAAATACATT
1 TTTTTAATTTTAAAATATTTTTAAAATACATT
49134114 TTTTTAATTTTTAAAATA
1 TTTTTAA-TTTTAAAATA
49134132 AAATTTTGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 16 0.37
30 8 0.19
31 2 0.05
32 7 0.16
33 10 0.23
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (32 bp):
TTTTTAATTTTAAAATATTTTTAAAATACATT
Found at i:49134093 original size:19 final size:18
Alignment explanation
Indices: 49134069--49134106 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
49134059 ATTTTAAAAT
49134069 ATTTTAAAAATATTTTTAA
1 ATTTT-AAAATATTTTTAA
49134088 ATTTTAAAATATTTTTAA
1 ATTTTAAAATATTTTTAA
49134106 A
1 A
49134107 ATACATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTAAAATATTTTTAA
Found at i:49134145 original size:22 final size:21
Alignment explanation
Indices: 49134097--49134152 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
49134087 AATTTTAAAA
* **
49134097 TATTTTTAAAATACATTTTTT
1 TATTTTTAAAATAAATTTTGG
49134118 TAATTTTTAAAATAAAATTTTGG
1 T-ATTTTTAAAAT-AAATTTTGG
49134141 TATTTATTAAAA
1 TATTT-TTAAAA
49134153 AATAGGCCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.03
22 15 0.52
23 13 0.45
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTGG
Found at i:49134880 original size:22 final size:23
Alignment explanation
Indices: 49134855--49134898 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
49134845 GTTTTTATTT
49134855 TAATAATAAATTTTAAA-AATAA
1 TAATAATAAATTTTAAATAATAA
**
49134877 TAATTTTAAATTTTAAATAATA
1 TAATAATAAATTTTAAATAATA
49134899 TTCTCCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATAATAAATTTTAAATAATAA
Found at i:49134883 original size:15 final size:16
Alignment explanation
Indices: 49134856--49134886 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
49134846 TTTTTATTTT
49134856 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
49134872 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
49134887 TTTTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:49140023 original size:24 final size:24
Alignment explanation
Indices: 49139996--49140042 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
49139986 ATTGAAATGG
49139996 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
49140020 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
49140043 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:49140040 original size:15 final size:15
Alignment explanation
Indices: 49140020--49140068 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 15
49140010 TGATGAATTT
49140020 ATTGAATTTATATTG
1 ATTGAATTTATATTG
49140035 ATTGAATTGGTATATAT-
1 ATTGAATT--TATAT-TG
49140052 ATTGAA--TATATTG
1 ATTGAATTTATATTG
49140065 ATTG
1 ATTG
49140069 TTTTAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
12 1 0.03
13 9 0.30
15 8 0.27
17 11 0.37
18 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:49140818 original size:18 final size:18
Alignment explanation
Indices: 49140795--49140831 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
49140785 GTTATATACA
49140795 TATAAATATATGTTTATG
1 TATAAATATATGTTTATG
49140813 TATAAATATATGTTTATG
1 TATAAATATATGTTTATG
49140831 T
1 T
49140832 TTGAGGTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (18 bp):
TATAAATATATGTTTATG
Found at i:49150023 original size:27 final size:28
Alignment explanation
Indices: 49149974--49150027 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
49149964 AATTATGGTA
**
49149974 AAAATTTAATAATATAATTATACTAAATC
1 AAAATTTAATAATATAAAAATAC-AAATC
49150003 AAAATTT-AT-ATATAAAAATACAAAT
1 AAAATTTAATAATATAAAAATACAAAT
49150028 TAGATAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 4 0.17
27 10 0.43
28 2 0.09
29 7 0.30
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (28 bp):
AAAATTTAATAATATAAAAATACAAATC
Found at i:49150868 original size:13 final size:15
Alignment explanation
Indices: 49150839--49150871 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
49150829 CGTGAAGAAA
49150839 ATAAATATTTGACAT
1 ATAAATATTTGACAT
49150854 ATAAATA-TT-ACAT
1 ATAAATATTTGACAT
49150867 ATAAA
1 ATAAA
49150872 GAAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 2 0.11
15 7 0.39
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (15 bp):
ATAAATATTTGACAT
Found at i:49153457 original size:118 final size:118
Alignment explanation
Indices: 49153315--49153531 Score: 328
Period size: 118 Copynumber: 1.8 Consensus size: 118
49153305 TGTATGTTGA
* * * *
49153315 TTTTATTTTTTAATGATAATTTGTATAGTTTT-AAATATAACATTGATCATTATATTTTTGATCG
1 TTTTATATTATAATAATAATTTGTATA-TTTTAAAATATAACATTGAACATTATATTTTTGATCG
* *
49153379 AATGATTAGACTTATGTTGAAAGTAATATTAAGATTCGTTTGACTAGTGTATTT
65 AATAATTAGACTTATGTTGAAAATAATATTAAGATTCGTTTGACTAGTGTATTT
* *
49153433 TTTTATATTATAATAATAATTTGTATATTTTAAAATATAACATTGAACATTATATTTTTGTTTGA
1 TTTTATATTATAATAATAATTTGTATATTTTAAAATATAACATTGAACATTATATTTTTGATCGA
* *
49153498 ATAATTAGATTTGTGTTGAAAATAATATTAAGAT
66 ATAATTAGACTTATGTTGAAAATAATATTAAGAT
49153532 ACTTTTTATA
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
117 4 0.05
118 84 0.95
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.49
Consensus pattern (118 bp):
TTTTATATTATAATAATAATTTGTATATTTTAAAATATAACATTGAACATTATATTTTTGATCGA
ATAATTAGACTTATGTTGAAAATAATATTAAGATTCGTTTGACTAGTGTATTT
Found at i:49158475 original size:19 final size:19
Alignment explanation
Indices: 49158451--49158572 Score: 59
Period size: 19 Copynumber: 6.3 Consensus size: 19
49158441 ATTTTCTATA
49158451 TTTTAATATTTTTAATAAT
1 TTTTAATATTTTTAATAAT
49158470 TTTTAAAATTATTTTTAA-AAT
1 TTTT--AA-TATTTTTAATAAT
** * *
49158491 TTAAAATATATTT-ATATT
1 TTTTAATATTTTTAATAAT
* ** *
49158509 TTTTATAAATTTAAAATATT
1 TTTTA-ATATTTTTAATAAT
* * *
49158529 TTTTTATATTTTTTTATCAT
1 TTTTAATA-TTTTTAATAAT
* * *
49158549 TTTTATTAATTTTAATAGT
1 TTTTAATATTTTTAATAAT
49158568 TTTTA
1 TTTTA
49158573 TCATTTTTGC
Statistics
Matches: 73, Mismatches: 23, Indels: 14
0.66 0.21 0.13
Matches are distributed among these distances:
17 1 0.01
18 11 0.15
19 24 0.33
20 21 0.29
21 7 0.10
22 9 0.12
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (19 bp):
TTTTAATATTTTTAATAAT
Found at i:49158519 original size:28 final size:28
Alignment explanation
Indices: 49158481--49158542 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 28
49158471 TTTAAAATTA
49158481 TTTTTAAAATTTAAAATA-TATTTATAT
1 TTTTTAAAATTTAAAATATTATTTATAT
*
49158508 TTTTTATAAATTTAAAATATTTTTTTATAT
1 TTTTTA-AAATTTAAAATA-TTATTTATAT
49158538 TTTTT
1 TTTTT
49158543 TATCATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
27 6 0.19
28 12 0.39
30 13 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTTTAAAATTTAAAATATTATTTATAT
Found at i:49160669 original size:3 final size:3
Alignment explanation
Indices: 49160663--49160706 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
49160653 TTTAGCCACT
*
49160663 TTA TTA TT- TTG TTTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49160707 GCTATTTGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
2 4 0.11
3 31 0.84
4 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:49161267 original size:16 final size:16
Alignment explanation
Indices: 49161248--49161278 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49161238 TACACCCATA
*
49161248 TATATGTACATATTTT
1 TATATATACATATTTT
49161264 TATATATACATATTT
1 TATATATACATATTT
49161279 ATCGTTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATATACATATTTT
Found at i:49162802 original size:19 final size:21
Alignment explanation
Indices: 49162775--49162842 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
49162765 CGAATACGCC
*
49162775 AACAAAAGCTCG-AA-AGCTT
1 AACAGAAGCTCGTAAGAGCTT
**
49162794 AACAGAAGCTCGTAAGATTTT
1 AACAGAAGCTCGTAAGAGCTT
* *
49162815 AACAGAAGCTCGTAAGAACTA
1 AACAGAAGCTCGTAAGAGCTT
49162836 AACAGAA
1 AACAGAA
49162843 AGTAAAACAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.27
20 2 0.05
21 28 0.68
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTT
Found at i:49162818 original size:21 final size:21
Alignment explanation
Indices: 49162792--49162831 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
49162782 GCTCGAAAGC
49162792 TTAACAGAAGCTCGTAAGATT
1 TTAACAGAAGCTCGTAAGATT
49162813 TTAACAGAAGCTCGTAAGA
1 TTAACAGAAGCTCGTAAGA
49162832 ACTAAACAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (21 bp):
TTAACAGAAGCTCGTAAGATT
Found at i:49164053 original size:13 final size:13
Alignment explanation
Indices: 49164035--49164059 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49164025 ATTTACGGCT
49164035 CGGTTTATAGAAA
1 CGGTTTATAGAAA
49164048 CGGTTTATAGAA
1 CGGTTTATAGAA
49164060 GCATAATCTT
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:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (13 bp):
CGGTTTATAGAAA
Found at i:49166625 original size:21 final size:21
Alignment explanation
Indices: 49166601--49166640 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
49166591 ACATTTTCTA
*
49166601 AAGTTAAAAGTCAAAACTATT
1 AAGTTAAAAGGCAAAACTATT
49166622 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGGCAAAACTA
49166641 CGTTGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATT
Found at i:49166635 original size:70 final size:67
Alignment explanation
Indices: 49166557--49166689 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 67
49166547 TCTGAATATG
* ** *
49166557 AAAAGGCAAAACTACGTCATTTTGATAAATGTTTACATTTTCTAAAGTTAAAAGTCAAAACTATT
1 AAAAGGCAAAACTACGTCATTTTGATAAATATTTAC-TCAT-TAAA-TTAAAAGGCAAAACTATT
49166622 AAGTT
63 AAGTT
**
49166627 AAAAGGCAAAACTACGTTGTTTTGATAAATATTTACTCATTAAATTAAAAGGCAAAACTATTA
1 AAAAGGCAAAACTACGTCATTTTGATAAATATTTACTCATTAAATTAAAAGGCAAAACTATTA
49166690 TATTGTTTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 18 0.32
68 4 0.07
69 2 0.04
70 33 0.58
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (67 bp):
AAAAGGCAAAACTACGTCATTTTGATAAATATTTACTCATTAAATTAAAAGGCAAAACTATTAAG
TT
Found at i:49168922 original size:30 final size:30
Alignment explanation
Indices: 49168882--49168946 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
49168872 ATATATTTAT
* * *
49168882 TTTTTTAATTTTAAAATATTTTTTACATAC
1 TTTTTAAATTTTAAAATATTTTTAAAATAC
49168912 TTTTTAAATTTTAAAATATTTTTAAAATAC
1 TTTTTAAATTTTAAAATATTTTTAAAATAC
49168942 TTTTT
1 TTTTT
49168947 TTTAATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTTAAATTTTAAAATATTTTTAAAATAC
Found at i:49168935 original size:41 final size:40
Alignment explanation
Indices: 49168890--49169052 Score: 204
Period size: 41 Copynumber: 4.0 Consensus size: 40
49168880 ATTTTTTTAA
*
49168890 TTTTAAAATA-TTTTTTACATACTTTTTAAATTTTAAAATAT
1 TTTTAAAATACTTTTTTA-AT-TTTTTTAAATTTTAAAATAT
*
49168931 TTTTAAAATACTTTTTTTTAATTTTTTT-AATTTTAAAACAT
1 TTTTAAAATAC--TTTTTTAATTTTTTTAAATTTTAAAATAT
* * *
49168972 TTTAAAAATATTTTTTTAATTTTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTTAATTTTTTTAAATTTTAAAATAT
*
49169012 TTTTAAAATACTTTTTTTAATTTTTTAAAATTTTTAAAATA
1 TTTTAAAATAC-TTTTTTAATTTTTTTAAA-TTTTAAAATA
49169053 AAAATGGGCC
Statistics
Matches: 107, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
39 15 0.14
40 21 0.20
41 47 0.44
42 15 0.14
43 2 0.02
44 7 0.07
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (40 bp):
TTTTAAAATACTTTTTTAATTTTTTTAAATTTTAAAATAT
Found at i:49169030 original size:31 final size:30
Alignment explanation
Indices: 49168970--49169052 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 30
49168960 ATTTTAAAAC
**
49168970 ATTTTAAAAATATTTTTTTAAT-TTTTTTTA
1 ATTTT-AAAATATTTTTAAAATATTTTTTTA
49169000 ATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTAAAATATTTTTAAAATA-TTTTTTTA
*
49169031 ATTTTTTAAA-ATTTTTAAAATA
1 A-TTTTAAAATATTTTTAAAATA
49169053 AAAATGGGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
29 14 0.30
30 5 0.11
31 21 0.45
32 7 0.15
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (30 bp):
ATTTTAAAATATTTTTAAAATATTTTTTTA
Found at i:49169044 original size:81 final size:82
Alignment explanation
Indices: 49168889--49169050 Score: 242
Period size: 81 Copynumber: 2.0 Consensus size: 82
49168879 TATTTTTTTA
49168889 ATTTTAAAATATTTTTTACATACTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTTAATT
1 ATTTTAAAATATTTTTTACATACTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTTAATT
*
49168954 TTTTTAA-TTTTAAAAC
66 TTTTAAATTTTTAAAAC
* *
49168970 ATTTTAAAAATATTTTTTTA-AT-TTTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTTAA
1 ATTTT-AAAATA-TTTTTTACATACTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTTAA
49169032 TTTTTTAAAATTTTTAAAA
64 TTTTTT-AAATTTTTAAAA
49169051 TAAAAATGGG
Statistics
Matches: 74, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
80 15 0.20
81 36 0.49
82 16 0.22
83 7 0.09
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (82 bp):
ATTTTAAAATATTTTTTACATACTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTTAATT
TTTTAAATTTTTAAAAC
Found at i:49170555 original size:41 final size:41
Alignment explanation
Indices: 49170510--49170671 Score: 236
Period size: 41 Copynumber: 4.0 Consensus size: 41
49170500 TTGTATAAAA
* * * * * *
49170510 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGATACATTC
1 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATACATTT
49170551 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATACATTT
1 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATACATTT
49170592 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATACATTT
1 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATACATTT
* *
49170633 CACCGGCATC-AAGCCTGCTAGACGTAAAGTCTGAAACAT
1 CACCGGCA-CAAAGCCTGCTAGACATAAAGTCTGATACAT
49170672 CTTATTTTCA
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
41 111 0.99
42 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (41 bp):
CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATACATTT
Found at i:49171344 original size:16 final size:17
Alignment explanation
Indices: 49171323--49171357 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
49171313 ATCTAATAAT
49171323 TTATACAT-GTATATAC
1 TTATACATCGTATATAC
*
49171339 TTATACATCGTTTATAC
1 TTATACATCGTATATAC
49171356 TT
1 TT
49171358 CAACTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (17 bp):
TTATACATCGTATATAC
Found at i:49176339 original size:15 final size:15
Alignment explanation
Indices: 49176287--49176340 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
49176277 GAAAATTTAT
49176287 GTTTTCCATCCTTCTA
1 GTTTT-CATCCTTCTA
*
49176303 GTTTTCTACGCCTTCTA
1 GTTTTC-A-TCCTTCTA
* *
49176320 TTTTTCATCCTTCTG
1 GTTTTCATCCTTCTA
49176335 GTTTTC
1 GTTTTC
49176341 TTTCCACTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 12 0.39
16 7 0.23
17 12 0.39
ACGTcount: A:0.09, C:0.28, G:0.09, T:0.54
Consensus pattern (15 bp):
GTTTTCATCCTTCTA
Found at i:49186610 original size:14 final size:15
Alignment explanation
Indices: 49186563--49186600 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
49186553 AGAAAACAAA
49186563 TTTTGAAAAAATTGT
1 TTTTGAAAAAATTGT
49186578 TTTTGAAAAAATTGT
1 TTTTGAAAAAATTGT
49186593 TTTTGAAA
1 TTTTGAAA
49186601 TATTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
TTTTGAAAAAATTGT
Found at i:49187450 original size:31 final size:31
Alignment explanation
Indices: 49187414--49187472 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
49187404 ATTAAGAACA
*
49187414 AAATCTTTTCGAAAGTGCTCAAATAAGGACT
1 AAATCTTTTCAAAAGTGCTCAAATAAGGACT
*
49187445 AAATCTTTTTAAAAGTGCTCAAATAAGG
1 AAATCTTTTCAAAAGTGCTCAAATAAGG
49187473 GCTTCTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (31 bp):
AAATCTTTTCAAAAGTGCTCAAATAAGGACT
Found at i:49187722 original size:24 final size:24
Alignment explanation
Indices: 49187694--49187742 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
49187684 GGATGAGAGG
49187694 AGAGAGTGAAAAAGTTGAAAGAAA
1 AGAGAGTGAAAAAGTTGAAAGAAA
49187718 AGAGAGTGAAAAAGTTGAAAGAAA
1 AGAGAGTGAAAAAGTTGAAAGAAA
49187742 A
1 A
49187743 TAAATTTTGA
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:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (24 bp):
AGAGAGTGAAAAAGTTGAAAGAAA
Found at i:49197056 original size:39 final size:37
Alignment explanation
Indices: 49196989--49197081 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
49196979 ACCAGAATGG
* *
49196989 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
49197028 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
49197065 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
49197082 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:49197445 original size:3 final size:3
Alignment explanation
Indices: 49197437--49197484 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
49197427 ATTCCCACTC
* * * *
49197437 ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA CTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
49197485 CTTACCTCAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:49197485 original size:18 final size:18
Alignment explanation
Indices: 49197438--49197486 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
49197428 TTCCCACTCA
*
49197438 TAATAATAATAATAATAC
1 TAATAATAATACTAATAC
49197456 TAATAATAATACTAATAC
1 TAATAATAATACTAATAC
*
49197474 TAATATTAATACT
1 TAATAATAATACT
49197487 TACCTCACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAATAATACTAATAC
Found at i:49197486 original size:12 final size:12
Alignment explanation
Indices: 49197437--49197484 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
49197427 ATTCCCACTC
*
49197437 ATAATAATAATA
1 ATAATACTAATA
49197449 ATAATACTAATA
1 ATAATACTAATA
49197461 ATAATACTAATA
1 ATAATACTAATA
* *
49197473 CTAATATTAATA
1 ATAATACTAATA
49197485 CTTACCTCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATACTAATA
Found at i:49198225 original size:20 final size:20
Alignment explanation
Indices: 49198191--49198230 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
49198181 TTCTATTCTG
*
49198191 TTTCTTTTCTGTTTTGTTTC
1 TTTCTTTTCTGTTTTATTTC
49198211 TTTCTTTTTCT-TTTTATTTC
1 TTTC-TTTTCTGTTTTATTTC
49198231 CTTTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTCTTTTCTGTTTTATTTC
Found at i:49198397 original size:31 final size:28
Alignment explanation
Indices: 49198361--49198428 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
49198351 TTGTCTTTAT
**
49198361 TTAATTTATTTCTTAATATAATATTTATAA
1 TTAATTTATTTAATAATAT-A-ATTTATAA
* *
49198391 TGTAATTAATTTAATAATATACTTTATAA
1 T-TAATTTATTTAATAATATAATTTATAA
49198420 TTAATTTAT
1 TTAATTTAT
49198429 ATATTTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 8 0.25
30 2 0.06
31 15 0.47
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATTTATTTAATAATATAATTTATAA
Found at i:49198445 original size:21 final size:20
Alignment explanation
Indices: 49198407--49198445 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
49198397 TAATTTAATA
*
49198407 ATATACTTTATAATTAATTT
1 ATATACTTTATAAATAATTT
*
49198427 ATATATTTATATAAATAAT
1 ATATACTT-TATAAATAAT
49198446 AATATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATACTTTATAAATAATTT
Found at i:49203388 original size:21 final size:21
Alignment explanation
Indices: 49203346--49203388 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
49203336 TTCACTATAC
*
49203346 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
49203367 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
49203388 A
1 A
49203389 ATCTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:49204501 original size:39 final size:37
Alignment explanation
Indices: 49204434--49204526 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
49204424 ACCAGAATGG
* *
49204434 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
49204473 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
49204510 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
49204527 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:49204888 original size:3 final size:3
Alignment explanation
Indices: 49204880--49204927 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
49204870 ATTCCCACTC
* * * *
49204880 ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA CTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
49204928 CTTACCTCAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:49204928 original size:18 final size:18
Alignment explanation
Indices: 49204881--49204929 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
49204871 TTCCCACTCA
*
49204881 TAATAATAATAATAATAC
1 TAATAATAATACTAATAC
49204899 TAATAATAATACTAATAC
1 TAATAATAATACTAATAC
*
49204917 TAATATTAATACT
1 TAATAATAATACT
49204930 TACCTCACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAATAATACTAATAC
Found at i:49204929 original size:12 final size:12
Alignment explanation
Indices: 49204880--49204927 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
49204870 ATTCCCACTC
*
49204880 ATAATAATAATA
1 ATAATACTAATA
49204892 ATAATACTAATA
1 ATAATACTAATA
49204904 ATAATACTAATA
1 ATAATACTAATA
* *
49204916 CTAATATTAATA
1 ATAATACTAATA
49204928 CTTACCTCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATACTAATA
Found at i:49205667 original size:20 final size:20
Alignment explanation
Indices: 49205633--49205672 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
49205623 TTCTATTCTG
*
49205633 TTTCTTTTCTGTTTTGTTTC
1 TTTCTTTTCTGTTTTATTTC
49205653 TTTCTTTTTCT-TTTTATTTC
1 TTTC-TTTTCTGTTTTATTTC
49205673 CTTTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTCTTTTCTGTTTTATTTC
Found at i:49225293 original size:16 final size:16
Alignment explanation
Indices: 49225266--49225305 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
49225256 TCGTATATAT
49225266 TTGTATAA-AATAGTA
1 TTGTATAAGAATAGTA
* *
49225281 TTGTGTAAGAATATTA
1 TTGTATAAGAATAGTA
49225297 TTGTATAAG
1 TTGTATAAG
49225306 TCTTTAAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.42
Consensus pattern (16 bp):
TTGTATAAGAATAGTA
Found at i:49227932 original size:102 final size:103
Alignment explanation
Indices: 49227658--49228013 Score: 590
Period size: 102 Copynumber: 3.4 Consensus size: 103
49227648 GGGTAGCTGT
* * * *
49227658 GTGCTGATTCCCCGATTCATTGGTGGTACTATGTGCG-TGATCCACCATATCTTTGAAATGTGAA
1 GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCGTATCTTTGAAATG-AAA
49227722 AGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
64 AGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
*
49227762 GTACTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAA
1 GTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAA
49227827 GGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
65 GGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
*
49227866 GTGCTGATT-CCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAAG
1 GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAAG
49227930 GGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
66 GGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
* * *
49227968 GTGCTGATTCCCCGATTCAGTGCTGGTGCTAAGTGCGAGATCCACC
1 GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
49228014 AATAACGGTT
Statistics
Matches: 238, Mismatches: 11, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
102 97 0.41
103 36 0.15
104 64 0.27
105 40 0.17
106 1 0.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (103 bp):
GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTTGAAATGAAAAG
GGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
Found at i:49230636 original size:20 final size:22
Alignment explanation
Indices: 49230589--49230629 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
49230579 TAACGGTACA
*
49230589 ATAATATTAAATATATTAAAAT
1 ATAATAATAAATATATTAAAAT
*
49230611 AAAATAATAAATAT-TTAAA
1 ATAATAATAAATATATTAAA
49230630 TGTAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAATAATAAATATATTAAAAT
Found at i:49231256 original size:13 final size:13
Alignment explanation
Indices: 49231240--49231264 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49231230 TTCTCCTTCC
49231240 CTTTCCCCTACCT
1 CTTTCCCCTACCT
49231253 CTTTCCCCTACC
1 CTTTCCCCTACC
49231265 CCTTCCCCGT
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:0.56, G:0.00, T:0.36
Consensus pattern (13 bp):
CTTTCCCCTACCT
Found at i:49232911 original size:13 final size:13
Alignment explanation
Indices: 49232893--49232917 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49232883 ATTATTAATA
49232893 TTATTTTGTGTGT
1 TTATTTTGTGTGT
49232906 TTATTTTGTGTG
1 TTATTTTGTGTG
49232918 CATTTGATTG
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:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:49234618 original size:41 final size:41
Alignment explanation
Indices: 49234573--49234734 Score: 218
Period size: 41 Copynumber: 4.0 Consensus size: 41
49234563 AAATTATTCA
*
49234573 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCG
* * * * *
49234614 GACTATATGTCTAGCAGGATAAATGTCGGTGAATTGAATCG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCG
*
49234655 GACTATACATCTAGCAGGCTAAGTGCCGGTGAACTGAATCAG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATC-G
* * *
49234697 G-CTACAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAAT
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAAT
49234735 TAAACTATAA
Statistics
Matches: 106, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 104 0.98
42 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (41 bp):
GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCG
Found at i:49234747 original size:41 final size:41
Alignment explanation
Indices: 49234570--49234769 Score: 215
Period size: 41 Copynumber: 4.9 Consensus size: 41
49234560 GTGAAATTAT
* *
49234570 TCAGACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAA
1 TCAGACTATAAGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * * * * *
49234611 TCGGACTATATGTCTAGCAGGATAAATGTCGGTGAATTGAA
1 TCAGACTATAAGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
*
49234652 TCGGACTATACA-TCTAGCAGGCTAAGTGCCGGTGAACTGAA
1 TCAGACTATA-AGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * *
49234693 TCAGGCTACAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
1 TCAGACTATAAGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * * * *
49234734 TTAAACTATAAGCCTATCAGG-TGAAGTGCCAGTGAA
1 TCAGACTATAAGTCTAGCAGGCT-AAGTGCCGGTGAA
49234770 TCTGTTTAAA
Statistics
Matches: 136, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 2 0.01
41 134 0.99
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (41 bp):
TCAGACTATAAGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
Found at i:49236689 original size:34 final size:35
Alignment explanation
Indices: 49236635--49236701 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
49236625 CAAACACCAG
*
49236635 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
49236670 AAAACATTTTCTAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
49236702 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:49238346 original size:4 final size:4
Alignment explanation
Indices: 49238339--49238467 Score: 90
Period size: 4 Copynumber: 32.0 Consensus size: 4
49238329 GAAGGAGAGG
* *
49238339 GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA G-AA -AAA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
* * *
49238387 -AAG GAAA G-GA GAAGA GAAA AAAA GAAA GAAA G-AA G-AA GAAAA GGAAA
1 GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA
* *
49238434 TGAGAA GAAA AAAA GAAA GAAA GAAG GAAA GAAA
1 -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
49238468 AGGAAAGGAG
Statistics
Matches: 99, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
3 14 0.14
4 64 0.65
5 17 0.17
6 4 0.04
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:49238404 original size:19 final size:19
Alignment explanation
Indices: 49238382--49238485 Score: 72
Period size: 20 Copynumber: 5.4 Consensus size: 19
49238372 AAAGAAGGAA
49238382 AGAAAAAGGAAAGGAGAAG
1 AGAAAAAGGAAAGGAGAAG
* *
49238401 AGAAAAAAAGAAAGAAAGAAG
1 AG-AAAAAGGAAAG-GAGAAG
*
49238422 A-AGAAAAGGAAATGAGAAG
1 AGA-AAAAGGAAAGGAGAAG
* *
49238441 A-AAAAAAGAAAGAAAGAAGG
1 AGAAAAAGGAAAG-GAGAA-G
*
49238461 AAAGAAAAGGAAAGGAG--G
1 AGA-AAAAGGAAAGGAGAAG
49238479 AGAAAAA
1 AGAAAAA
49238486 AAAAAGAAGA
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
17 4 0.06
18 11 0.16
19 14 0.21
20 20 0.30
21 9 0.13
22 9 0.13
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (19 bp):
AGAAAAAGGAAAGGAGAAG
Done.