Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold15
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: 4011073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11440 characters in sequence are not A, C, G, or T
File 20 of 25
Found at i:3160924 original size:33 final size:33
Alignment explanation
Indices: 3160887--3160953 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3160877 TTCAACGATT
3160887 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
3160920 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
3160953 T
1 T
3160954 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:3160925 original size:13 final size:13
Alignment explanation
Indices: 3160907--3160931 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3160897 CATAAAATGT
3160907 TGTATCGATACAA
1 TGTATCGATACAA
3160920 TGTATCGATACA
1 TGTATCGATACA
3160932 TATTTTTTTG
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3161015 original size:13 final size:13
Alignment explanation
Indices: 3160997--3161021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3160987 ATTACTCACA
3160997 TGTATCGATACAT
1 TGTATCGATACAT
3161010 TGTATCGATACA
1 TGTATCGATACA
3161022 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3161158 original size:52 final size:52
Alignment explanation
Indices: 3161030--3161150 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
3161020 CACTGATCTT
*
3161030 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
3161082 TGTATCGATACATGCCGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3161134 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
3161151 ATAAATTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:3167880 original size:21 final size:21
Alignment explanation
Indices: 3167856--3167902 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3167846 ACCAACTTGC
3167856 AATTCAATTATCTTCTTTTCA
1 AATTCAATTATCTTCTTTTCA
* * *
3167877 AATTCACTTATTTTCTTTTCT
1 AATTCAATTATCTTCTTTTCA
3167898 AATTC
1 AATTC
3167903 TTCTTCTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTCAATTATCTTCTTTTCA
Found at i:3169514 original size:23 final size:24
Alignment explanation
Indices: 3169479--3169523 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
3169469 ACCTCTCAAT
3169479 TTCTTCAAGAATTAT-ACCCAAAA
1 TTCTTCAAGAATTATAACCCAAAA
*
3169502 TTCTT-AAGAAATTGTAACCCAA
1 TTCTTCAAG-AATTATAACCCAA
3169524 GGTTGAATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 3 0.16
23 10 0.53
24 6 0.32
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (24 bp):
TTCTTCAAGAATTATAACCCAAAA
Found at i:3169947 original size:20 final size:18
Alignment explanation
Indices: 3169922--3169992 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 18
3169912 GTTGGGCACA
3169922 ATGTATCGATACAATGTATC
1 ATGTATCGATACAA-G-ATC
*
3169942 ATGTATCGATGCCAAGATC
1 ATGTATCGAT-ACAAGATC
3169961 ATGTATCGATACAAAGCAAT-
1 ATGTATCGATAC-AAG--ATC
3169981 ATGTATCGATAC
1 ATGTATCGATAC
3169993 TTTTGGGTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
18 1 0.02
19 16 0.36
20 23 0.51
21 5 0.11
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (18 bp):
ATGTATCGATACAAGATC
Found at i:3170754 original size:48 final size:47
Alignment explanation
Indices: 3170583--3171188 Score: 459
Period size: 48 Copynumber: 12.7 Consensus size: 47
3170573 TCTTTTTTTG
* * * *
3170583 TTTGACTGTATTAGTATTAGAGCCTGGTCAAACTCTTTCATCCTTCA
1 TTTGACTGTATTGGTGTTAGGGCCTGGTCAAACTTTTTCATCCTTCA
* * * * * * *
3170630 TTTGATTGTATTGGTGTTAAGGCCTAGTTAAACTCTTTCATCCCTCG
1 TTTGACTGTATTGGTGTTAGGGCCTGGTCAAACTTTTTCATCCTTCA
* * * * **
3170677 TTTGACT-TATTAGTTTTAGGGCCTAGTCAAACTTTTATCTTTTTTCA
1 TTTGACTGTATTGGTGTTAGGGCCTGGTCAAACTTTT-TCATCCTTCA
* *
3170724 TTTGATTGTATTGGTGTTAGGGCCTGGTCAAACTCTTTTGAT-C-TCTA
1 TTTGACTGTATTGGTGTTAGGGCCTGGTCAAACT-TTTTCATCCTTC-A
* * * * * * *
3170771 GTTTGACTATATTGGTGTTAGAGTCTGGTTAAACTCTTATCTTCTTTCA
1 -TTTGACTGTATTGGTGTTAGGGCCTGGTCAAACT-TTTTCATCCTTCA
* ** * * * * *
3170820 TTTGACTGTATTAGTGTTAAAGCCTAGTTAAACTCTTATC-TTCTCCA
1 TTTGACTGTATTGGTGTTAGGGCCTGGTCAAACT-TTTTCATCCTTCA
* * * * *
3170867 GTTTGACTGCATTAGTGTTAGGGCTTGGTCAAACTCTTTCATCACTT-G
1 -TTTGACTGTATTGGTGTTAGGGCCTGGTCAAACTTTTTCATC-CTTCA
* ** * *
3170915 TTTGATTGTATTGGTGTTAAAGCCTGATCAAACTCTTTTCATCCTTCG
1 TTTGACTGTATTGGTGTTAGGGCCTGGTCAAACT-TTTTCATCCTTCA
* *** * *
3170963 TTTGACTGTATTGGTGTTAAGGCCTAAACAAACTCTTTTCATCATTCG
1 TTTGACTGTATTGGTGTTAGGGCCTGGTCAAACT-TTTTCATCCTTCA
* * *
3171011 TTTGACTATATTGGTGTTAGAGCTTGGTCAAACTCTTTTCATCCTTCA
1 TTTGACTGTATTGGTGTTAGGGCCTGGTCAAACT-TTTTCATCCTTCA
* * *
3171059 TTTGACTATATTGGTGTTAGGGCTTCGTCAAACTTTTTTCATCCTTCA
1 TTTGACTGTATTGGTGTTAGGGCCTGGTCAAAC-TTTTTCATCCTTCA
* * * * *
3171107 TTTAACTATATTGGTCTTAGGACCTGGTCAAACTCTTTTCATCCCTT-G
1 TTTGACTGTATTGGTGTTAGGGCCTGGTCAAACT-TTTTCAT-CCTTCA
* * * *
3171155 TTTGATTGTAGTGGTGTTAGGACTTGGTCAAACT
1 TTTGACTGTATTGGTGTTAGGGCCTGGTCAAACT
3171189 CTTCTCATTT
Statistics
Matches: 453, Mismatches: 91, Indels: 29
0.79 0.16 0.05
Matches are distributed among these distances:
46 26 0.06
47 94 0.21
48 320 0.71
49 11 0.02
50 2 0.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (47 bp):
TTTGACTGTATTGGTGTTAGGGCCTGGTCAAACTTTTTCATCCTTCA
Found at i:3171000 original size:239 final size:238
Alignment explanation
Indices: 3170583--3171173 Score: 654
Period size: 239 Copynumber: 2.5 Consensus size: 238
3170573 TCTTTTTTTG
* * *
3170583 TTTGACTGTATTAGTATTAGAGCCTGGTCAAACTCTTTCATCCTTCATTTGATTGTATTGGTGTT
1 TTTGACTGTATTAGTGTTAGAGCCTAGTCAAACTCTTTCATCCTTCATTTGACTGTATTGGTGTT
* * * * * * * **
3170648 AAGGCCTAGTTAAACTCTTTCATCCCTCGTTTGACT-TATTAGTTTTAGGGCCTAGTCAAACTTT
66 AGGGCCTGGTCAAACTCTTTCATCCCTTGTTTGATTGTATTGGTGTTAAAGCCTAGTCAAACTTT
* ** * * *** *
3170712 TATCTTTTTTCATTTGATTGTATTGGTGTTAGGGCCTGGTCAAACTCTTTTGATC-TCTAGTTTG
131 TATCATCCTTCATTTGACTGTATTGGTGTTAAGGCCTAAACAAACTCTTTTCATCAT-TAGTTTG
* * *
3170776 ACTATATTGGTGTTAGAG-TCTGGTTAAACTCTTATCTTCTTTCA
195 ACTATATTGGTGTTAGAGCT-TGGTCAAACTCTTATCATCCTTCA
* * * * * *
3170820 TTTGACTGTATTAGTGTTAAAGCCTAGTTAAACTCTTATC-TTCTCCAGTTTGACTGCATTAGTG
1 TTTGACTGTATTAGTGTTAGAGCCTAGTCAAACTCTT-TCATCCTTCA-TTTGACTGTATTGGTG
* *
3170884 TTAGGGCTTGGTCAAACTCTTTCATCACTTGTTTGATTGTATTGGTGTTAAAGCCT-GATCAAAC
64 TTAGGGCCTGGTCAAACTCTTTCATCCCTTGTTTGATTGTATTGGTGTTAAAGCCTAG-TCAAAC
* *
3170948 TCTTT-TCATCCTTCGTTTGACTGTATTGGTGTTAAGGCCTAAACAAACTCTTTTCATCATTCGT
128 T-TTTATCATCCTTCATTTGACTGTATTGGTGTTAAGGCCTAAACAAACTCTTTTCATCATTAGT
*
3171012 TTGACTATATTGGTGTTAGAGCTTGGTCAAACTCTTTTCATCCTTCA
192 TTGACTATATTGGTGTTAGAGCTTGGTCAAACTCTTATCATCCTTCA
* * * * * * * * *
3171059 TTTGACTATATTGGTGTTAGGGCTTCGTCAAACTTTTTTCATCCTTCATTTAACTATATTGGTCT
1 TTTGACTGTATTAGTGTTAGAGCCTAGTCAAAC-TCTTTCATCCTTCATTTGACTGTATTGGTGT
* *
3171124 TAGGACCTGGTCAAACTCTTTTCATCCCTTGTTTGATTGTAGTGGTGTTA
65 TAGGGCCTGGTCAAACTC-TTTCATCCCTTGTTTGATTGTATTGGTGTTA
3171174 GGACTTGGTC
Statistics
Matches: 290, Mismatches: 54, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
237 38 0.13
238 47 0.16
239 163 0.56
240 42 0.14
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (238 bp):
TTTGACTGTATTAGTGTTAGAGCCTAGTCAAACTCTTTCATCCTTCATTTGACTGTATTGGTGTT
AGGGCCTGGTCAAACTCTTTCATCCCTTGTTTGATTGTATTGGTGTTAAAGCCTAGTCAAACTTT
TATCATCCTTCATTTGACTGTATTGGTGTTAAGGCCTAAACAAACTCTTTTCATCATTAGTTTGA
CTATATTGGTGTTAGAGCTTGGTCAAACTCTTATCATCCTTCA
Found at i:3171139 original size:144 final size:142
Alignment explanation
Indices: 3170582--3171196 Score: 534
Period size: 144 Copynumber: 4.3 Consensus size: 142
3170572 ATCTTTTTTT
* * * * *
3170582 GTTTGACTGTATTAGTATTAGAGCCTGGTCAAACTC-TTTCATCCTTCATTTGATTGTATTGGTG
1 GTTTGACTGTATTGGTGTTAGAGCTTGGTCAAACTCTTTTCATCCTTCATTTGACTATATTGGTG
* * * * * *
3170646 TTAAGGCCTAGTTAAACTC-TTTCATCCCTCGTTTGACT-TATTAGTTTTAGGGCCTAGTCAAAC
66 TTAAAGCCT-GTCAAACTCTTTTCATCCTTCATTTGACTGTATTAGTGTTAGGACCTAGTCAAAC
* *
3170709 T-TTTATCTTTTTTC
130 TCTTT-TC-ATCTTC
* * * * *
3170723 ATTTGATTGTATTGGTGTTAGGGCCTGGTCAAACTCTTTTGAT-C-TCTAGTTTGACTATATTGG
1 GTTTGACTGTATTGGTGTTAGAGCTTGGTCAAACTCTTTTCATCCTTC-A-TTTGACTATATTGG
* * * * * * * *
3170786 TGTTAGAGTCTGGTTAAACTCTTATCTTCTTTCATTTGACTGTATTAGTGTTA-AAGCCTAGTTA
64 TGTTAAAGCCT-GTCAAACTCTTTTCATCCTTCATTTGACTGTATTAGTGTTAGGA-CCTAGTCA
* * *
3170850 AACTCTTATCTTCTCC
127 AACTCTTTTCATCTTC
* * * * * *
3170866 AGTTTGACTGCATTAGTGTTAGGGCTTGGTCAAACTC-TTTCATCACTT-GTTTGATTGTATTGG
1 -GTTTGACTGTATTGGTGTTAGAGCTTGGTCAAACTCTTTTCATC-CTTCATTTGACTATATTGG
* * **
3170929 TGTTAAAGCCTGATCAAACTCTTTTCATCCTTCGTTTGACTGTATTGGTGTTAAGG-CCTAAACA
64 TGTTAAAGCCTG-TCAAACTCTTTTCATCCTTCATTTGACTGTATTAGTGTT-AGGACCTAGTCA
3170993 AACTCTTTTCATCATTC
127 AACTCTTTTCATC-TTC
*
3171010 GTTTGACTATATTGGTGTTAGAGCTTGGTCAAACTCTTTTCATCCTTCATTTGACTATATTGGTG
1 GTTTGACTGTATTGGTGTTAGAGCTTGGTCAAACTCTTTTCATCCTTCATTTGACTATATTGGTG
** * * * * * * *
3171075 TTAGGGCTTCGTCAAACTTTTTTCATCCTTCATTTAACTATATTGGTCTTAGGACCTGGTCAAAC
66 TTAAAGCCT-GTCAAACTCTTTTCATCCTTCATTTGACTGTATTAGTGTTAGGACCTAGTCAAAC
3171140 TCTTTTCATCCCTT-
130 TCTTTTCAT--CTTC
* * *
3171154 GTTTGATTGTAGTGGTGTTAG-GACTTGGTCAAACTCTTCTCAT
1 GTTTGACTGTATTGGTGTTAGAG-CTTGGTCAAACTCTTTTCAT
3171197 TTTAGTGTGA
Statistics
Matches: 382, Mismatches: 70, Indels: 41
0.77 0.14 0.08
Matches are distributed among these distances:
140 2 0.01
141 33 0.09
142 35 0.09
143 132 0.35
144 172 0.45
145 6 0.02
146 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (142 bp):
GTTTGACTGTATTGGTGTTAGAGCTTGGTCAAACTCTTTTCATCCTTCATTTGACTATATTGGTG
TTAAAGCCTGTCAAACTCTTTTCATCCTTCATTTGACTGTATTAGTGTTAGGACCTAGTCAAACT
CTTTTCATCTTC
Found at i:3171674 original size:169 final size:170
Alignment explanation
Indices: 3171423--3171731 Score: 494
Period size: 169 Copynumber: 1.8 Consensus size: 170
3171413 ACTTAGTCCC
* * * * * *
3171423 AGGTAAACTTCTTTACCCTTTTTGTTGACTTATCAGTTCAGCCCTGGTTGACGTTTTATCCCTTG
1 AGGTAAACTCCTTTACCCCTATTATTGACTTATCAGTTCAGCCCTGGTTGACCTTTTATCCCCTG
* * *
3171488 TTTACCTGCCGGCTTAGTCCCGGATAAATTTCTTTATCTTTTGTTGACTTGTCGATTTTAT-CCA
66 TTTACCTGCCGGCTTAGTCCCGGATAAATTTCTTTATCCTTTGTTGACTTGTCAAATTTATCCCA
3171552 GTCAACCATTATACTATTTATCTACTTGTCGACCAATTCA
131 GTCAACCATTATACTATTTATCTACTTGTCGACCAATTCA
*
3171592 AGGTAAACTCCTTTACCCCTATTATTGACTTATCGGTTCAGCCCTGGTTGACCTTTTATCCCCTG
1 AGGTAAACTCCTTTACCCCTATTATTGACTTATCAGTTCAGCCCTGGTTGACCTTTTATCCCCTG
* * *
3171657 TTTACCTGCCGGCTTAGTCCTGGGTAAATTTCTTTATCCTTTGTTGATTTGTCAAATTTATCCCA
66 TTTACCTGCCGGCTTAGTCCCGGATAAATTTCTTTATCCTTTGTTGACTTGTCAAATTTATCCCA
3171722 GTCAACCATT
131 GTCAACCATT
3171732 GTAATATTCG
Statistics
Matches: 126, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
169 113 0.90
170 13 0.10
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (170 bp):
AGGTAAACTCCTTTACCCCTATTATTGACTTATCAGTTCAGCCCTGGTTGACCTTTTATCCCCTG
TTTACCTGCCGGCTTAGTCCCGGATAAATTTCTTTATCCTTTGTTGACTTGTCAAATTTATCCCA
GTCAACCATTATACTATTTATCTACTTGTCGACCAATTCA
Found at i:3175972 original size:51 final size:51
Alignment explanation
Indices: 3175910--3176025 Score: 151
Period size: 51 Copynumber: 2.3 Consensus size: 51
3175900 AAATAACGAG
* * *
3175910 GTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGGA
1 GTTGGAATATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGGA
* * * *
3175961 GTTGGAATATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAATCGGG
1 GTTGGAATATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGGA
* *
3176012 GTTCGAGTATCCCC
1 GTTGGAATATCCCC
3176026 TCGAAAATAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (51 bp):
GTTGGAATATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGGA
Found at i:3176021 original size:130 final size:131
Alignment explanation
Indices: 3175869--3176104 Score: 313
Period size: 130 Copynumber: 1.8 Consensus size: 131
3175859 CAATATTTGA
* * *
3175869 AAATAAAGCCGGGGTTGGAGTAT-CCC-CGATGAAATAACGAGG-TTGGAGTAT-CCTCGATTGT
1 AAATAAAACCGGGGTTCGAGTATCCCCTCGA--AAATAAC-AGGATTGGAGTATCCCT-GATTAT
* *
3175930 GAAAAATT-AGTGTTTTGGAAATAAAATCG-GAGTTGGAATATCCCCGATTGTGGAGAATTGGTG
62 GAAAAATTGA-TGTTTTAGAAATAAAACCGAGAGTTGGAATATCCCCGATTGTGGAGAATTGGTG
3175993 TTTTAG
126 TTTTAG
*
3175999 AAATAAAATCGGGGTTCGAGTATCCCCTCGAAAATAACAGGATTGGAGTATCCCTGATTATGAAA
1 AAATAAAACCGGGGTTCGAGTATCCCCTCGAAAATAACAGGATTGGAGTATCCCTGATTATGAAA
* *
3176064 AATTGATGTTTTAGAAATAAAACCGAGGGTTGGAGTATCCC
66 AATTGATGTTTTAGAAATAAAACCGAGAGTTGGAATATCCC
3176105 TTCGAAAATA
Statistics
Matches: 92, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
129 3 0.03
130 66 0.72
131 20 0.22
132 3 0.03
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (131 bp):
AAATAAAACCGGGGTTCGAGTATCCCCTCGAAAATAACAGGATTGGAGTATCCCTGATTATGAAA
AATTGATGTTTTAGAAATAAAACCGAGAGTTGGAATATCCCCGATTGTGGAGAATTGGTGTTTTA
G
Found at i:3176051 original size:79 final size:80
Alignment explanation
Indices: 3175962--3176136 Score: 244
Period size: 80 Copynumber: 2.2 Consensus size: 80
3175952 AAAATCGGAG
* * * * * *
3175962 TTGGAATATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAATCG-GGGTTCGAGTATCCCC
1 TTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGGTTCGAGTATCCCC
3176026 TCGAAAATAACAGGA
66 TCGAAAATAACAGGA
* * *
3176041 TTGGAGTATCCCTGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGGTTGGAGTATCCCT
1 TTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGGTTCGAGTATCCCC
* *
3176106 TCGAAAATAACGGGG
66 TCGAAAATAACAGGA
3176121 TTGGAGTATCCCCGAT
1 TTGGAGTATCCCCGAT
3176137 GATTAACGGG
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
79 41 0.49
80 42 0.51
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (80 bp):
TTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGGTTCGAGTATCCCC
TCGAAAATAACAGGA
Found at i:3176104 original size:52 final size:51
Alignment explanation
Indices: 3176041--3176382 Score: 241
Period size: 51 Copynumber: 6.6 Consensus size: 51
3176031 AATAACAGGA
3176041 TTGGAGTATCCCTGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGG
1 TTGGAGTATCCCTGATTATGAAAAATTGATGTTTTAGAAATAAAACCG-GGG
** *** *** * *
3176093 TTGGAGTATCCCTTCGAAAAT-AACGGGGTTGGA-GTATCCCCGATGAT-TAA-CGGGG
1 TTGGAGTATCCC-T-GATTATGAA--AAATT-GATGT-T-TTAGA-AATAAAACCGGGG
* * * *
3176148 TTGGAGTATCCCTGATTGTGAAAAATT-AGTGTTTTTGGAAATAAAATCGGAG
1 TTGGAGTATCCCTGATTATGAAAAATTGA-TG-TTTTAGAAATAAAACCGGGG
* * * *
3176200 TTGGAGTATCCCTGATTAAGGGAAAATTGGTGTTTT-GAAAATAAAACCGGGA
1 TTGGAGTATCCCTGATT-ATGAAAAATTGATGTTTTAG-AAATAAAACCGGGG
* * * * * * *
3176252 TTGGAGTATCCCCGATTGTGGAAAATTGGTG-TTTCGAAAATAAAATCGGAG
1 TTGGAGTATCCCTGATTATGAAAAATTGATGTTTTAG-AAATAAAACCGGGG
* * *
3176303 TTGGAGTATCCCCGATTATGGAAAATT-AGTGTTTTAGAAATAAAACTGGGG
1 TTGGAGTATCCCTGATTATGAAAAATTGA-TGTTTTAGAAATAAAACCGGGG
3176354 TTGGAGTATCCCTGATTATGAAAAATTGA
1 TTGGAGTATCCCTGATTATGAAAAATTGA
3176383 GAAACTTAAC
Statistics
Matches: 226, Mismatches: 43, Indels: 42
0.73 0.14 0.14
Matches are distributed among these distances:
50 6 0.03
51 94 0.42
52 73 0.32
53 16 0.07
54 7 0.03
55 19 0.08
56 5 0.02
57 4 0.02
58 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.30
Consensus pattern (51 bp):
TTGGAGTATCCCTGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGG
Found at i:3176122 original size:28 final size:28
Alignment explanation
Indices: 3176090--3176160 Score: 101
Period size: 27 Copynumber: 2.6 Consensus size: 28
3176080 ATAAAACCGA
3176090 GGGTTGGAGTATCCCTTCGA-AAATAACG
1 GGGTTGGAGTATCCC-TCGATAAATAACG
* *
3176118 GGGTTGGAGTATCCC-CGATGATTAACG
1 GGGTTGGAGTATCCCTCGATAAATAACG
3176145 GGGTTGGAGTATCCCT
1 GGGTTGGAGTATCCCT
3176161 GATTGTGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 3 0.08
27 21 0.54
28 15 0.38
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (28 bp):
GGGTTGGAGTATCCCTCGATAAATAACG
Found at i:3176280 original size:51 final size:51
Alignment explanation
Indices: 3176143--3176381 Score: 261
Period size: 51 Copynumber: 4.6 Consensus size: 51
3176133 CGATGATTAA
* * * * *
3176143 CGGGGTTGGAGTATCCCTGATTGTGAAAAATTAGTGTTTTTGGAAATAAAAT
1 CGGGATTGGAGTATCCCTGATTGTGGAAAATTGGTG-TTTTGAAAATAAAAC
3176195 C-GGAGTTGGAGTATCCCTGATTAAG-GGAAAATTGGTGTTTTGAAAATAAAAC
1 CGGGA-TTGGAGTATCCCTGATT--GTGGAAAATTGGTGTTTTGAAAATAAAAC
* * *
3176247 CGGGATTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTCGAAAATAAAAT
1 CGGGATTGGAGTATCCCTGATTGTGGAAAATTGGTGTTTTGAAAATAAAAC
* * *
3176298 C-GGAGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTT-AGAAATAAAAC
1 CGGGA-TTGGAGTATCCCTGATTGTGGAAAATTGGTGTTTTGA-AAATAAAAC
* * * *
3176349 TGGGGTTGGAGTATCCCTGATTATGAAAAATTG
1 CGGGATTGGAGTATCCCTGATTGTGGAAAATTG
3176382 AGAAACTTAA
Statistics
Matches: 162, Mismatches: 17, Indels: 17
0.83 0.09 0.09
Matches are distributed among these distances:
50 5 0.03
51 93 0.57
52 50 0.31
53 13 0.08
54 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.31
Consensus pattern (51 bp):
CGGGATTGGAGTATCCCTGATTGTGGAAAATTGGTGTTTTGAAAATAAAAC
Found at i:3176360 original size:102 final size:104
Alignment explanation
Indices: 3176143--3176381 Score: 349
Period size: 102 Copynumber: 2.3 Consensus size: 104
3176133 CGATGATTAA
* * *
3176143 CGGGGTTGGAGTATCCCTGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGGAGTTGGAGTA
1 CGGGGTTGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTCGAAAATAAAATCGGAGTTGGAGTA
* *
3176208 TCCCTGATTAAGGGAAAATTGGTGTTTTGAAAATAAAAC
66 TCCCCGATTAAGGGAAAATTAGTGTTTTGAAAATAAAAC
* * *
3176247 CGGGATTGGAGTATCCCCGATTGTGGAAAATTGGTG-TTTCGAAAATAAAATCGGAGTTGGAGTA
1 CGGGGTTGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTCGAAAATAAAATCGGAGTTGGAGTA
*
3176311 TCCCCGATT-ATGGAAAATTAGTGTTTT-AGAAATAAAAC
66 TCCCCGATTAAGGGAAAATTAGTGTTTTGA-AAATAAAAC
* *
3176349 TGGGGTTGGAGTATCCCTGATTATGAAAAATTG
1 CGGGGTTGGAGTATCCCTGATTGTGAAAAATTG
3176382 AGAAACTTAA
Statistics
Matches: 120, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
101 1 0.01
102 53 0.44
103 34 0.28
104 32 0.27
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.31
Consensus pattern (104 bp):
CGGGGTTGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTCGAAAATAAAATCGGAGTTGGAGTA
TCCCCGATTAAGGGAAAATTAGTGTTTTGAAAATAAAAC
Found at i:3178807 original size:19 final size:21
Alignment explanation
Indices: 3178783--3178834 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3178773 AGCGATACAC
*
3178783 TGTATCGATACA-TTACT-TA
1 TGTATCGATACATTTACTGAA
3178802 TGTATCGATACATTTACTGAA
1 TGTATCGATACATTTACTGAA
3178823 TGTATCGATACA
1 TGTATCGATACA
3178835 AATTATTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTACTGAA
Found at i:3179145 original size:13 final size:12
Alignment explanation
Indices: 3179125--3179162 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3179115 GAAATTTTCA
3179125 AAAATAAAAAAT
1 AAAATAAAAAAT
3179137 --AATAATAAAAT
1 AAAATAA-AAAAT
3179148 AAAATAAAAAAT
1 AAAATAAAAAAT
3179160 AAA
1 AAA
3179163 TTCTTTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 5 0.22
11 5 0.22
12 8 0.35
13 5 0.22
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:3186028 original size:13 final size:13
Alignment explanation
Indices: 3186010--3186035 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3186000 CAGGGTAGCT
3186010 TTGTATCGATACA
1 TTGTATCGATACA
3186023 TTGTATCGATACA
1 TTGTATCGATACA
3186036 ACACTCATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3189957 original size:51 final size:52
Alignment explanation
Indices: 3189898--3190033 Score: 213
Period size: 52 Copynumber: 2.6 Consensus size: 52
3189888 TCTGGAAAGA
* *
3189898 AAATGTATCGATACATTTTTCATTGTATCGATACGTTTT-GGGTTTTGA-CC
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTTTAGGGTTTTGACCC
3189948 AAATTGTATCGATACATTCTTCATTGTATCGATACATTTTAGGGTTTTGACCC
1 AAA-TGTATCGATACATTCTTCATTGTATCGATACATTTTAGGGTTTTGACCC
* *
3190001 AAATGTATTGATACATTCTTCAATGTATCGATA
1 AAATGTATCGATACATTCTTCATTGTATCGATA
3190034 TATTCAGGCA
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
50 3 0.04
51 34 0.43
52 37 0.47
53 5 0.06
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (52 bp):
AAATGTATCGATACATTCTTCATTGTATCGATACATTTTAGGGTTTTGACCC
Found at i:3196330 original size:29 final size:29
Alignment explanation
Indices: 3196298--3196358 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
3196288 TTTAGAGATA
* * * *
3196298 TTAAGAATTTTTTTGTCATTTCATTCATT
1 TTAAGAATTTATATGTCATTCCATGCATT
*
3196327 TTAAGGATTTATATGTCATTCCATGCATT
1 TTAAGAATTTATATGTCATTCCATGCATT
3196356 TTA
1 TTA
3196359 GTGAATACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.52
Consensus pattern (29 bp):
TTAAGAATTTATATGTCATTCCATGCATT
Found at i:3196500 original size:29 final size:28
Alignment explanation
Indices: 3196468--3196558 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 28
3196458 TTTCAAACAT
*
3196468 TTTAGGGTTATTCTAGTAATTTGCCATGA
1 TTTAAGGTTATTCTAGTAATTT-CCATGA
* *
3196497 TTTAAGATTATT-TATGCAATTT-CATGCA
1 TTTAAGGTTATTCTA-GTAATTTCCATG-A
** *
3196525 TTTTAAGGTCCTTCTAATAATTTTCCATGA
1 -TTTAAGGTTATTCTAGTAA-TTTCCATGA
3196555 TTTA
1 TTTA
3196559 GGACCATTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
27 4 0.08
28 3 0.06
29 31 0.65
30 6 0.12
31 4 0.08
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.47
Consensus pattern (28 bp):
TTTAAGGTTATTCTAGTAATTTCCATGA
Found at i:3196528 original size:58 final size:58
Alignment explanation
Indices: 3196465--3196589 Score: 169
Period size: 58 Copynumber: 2.2 Consensus size: 58
3196455 TTATTTCAAA
* * * **
3196465 CATTTTAGGGTTATTCTAGTAATTTGCCATGATTTAAGATTATTTATGCAATTTCATG
1 CATTTTAAGGTCATTCTAATAATTTGCCATGATTTAAGACCATTTATGCAATTTCATG
* * *
3196523 CATTTTAAGGTCCTTCTAATAATTTTCCATGATTTAGGACCATTTATGCAATTTCATG
1 CATTTTAAGGTCATTCTAATAATTTGCCATGATTTAAGACCATTTATGCAATTTCATG
*
3196581 CATCTTAAG
1 CATTTTAAG
3196590 CCCATTTTAG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (58 bp):
CATTTTAAGGTCATTCTAATAATTTGCCATGATTTAAGACCATTTATGCAATTTCATG
Found at i:3196654 original size:58 final size:58
Alignment explanation
Indices: 3196486--3196676 Score: 165
Period size: 58 Copynumber: 3.3 Consensus size: 58
3196476 TATTCTAGTA
* * ** * * *
3196486 ATTTGCCATGATTTAAGATTATTTATGCAATTTCATGCATTTTAAGGTCCTTCTA-AT
1 ATTTTCCATGATTTAGGACCATTTATGCAATTTCATGCATTTTAAGGTCATTTTAGGT
* **
3196543 AATTTTCCATGATTTAGGACCATTTATGCAATTTCATGCATCTTAAGCCCATTTTAGGT
1 -ATTTTCCATGATTTAGGACCATTTATGCAATTTCATGCATTTTAAGGTCATTTTAGGT
* ** * **
3196602 ATTTTCCAT-TTTTAGGGACTTTTTATACAATTTTTTGCATTTTAAGGTCA-TTTAGGT
1 ATTTTCCATGATTTA-GGACCATTTATGCAATTTCATGCATTTTAAGGTCATTTTAGGT
*
3196659 -TATTTCACATGATCTAGG
1 AT-TTTC-CATGATTTAGG
3196677 GGCACTTTAG
Statistics
Matches: 107, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
56 1 0.01
57 15 0.14
58 87 0.81
59 4 0.04
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (58 bp):
ATTTTCCATGATTTAGGACCATTTATGCAATTTCATGCATTTTAAGGTCATTTTAGGT
Found at i:3196939 original size:76 final size:75
Alignment explanation
Indices: 3196859--3197047 Score: 211
Period size: 76 Copynumber: 2.5 Consensus size: 75
3196849 TATGTTGAAG
* * *
3196859 CATGTCTATTAAGATTATTTTGGTAATAGTACTTTAAATATGAGTCTAGGG-TCATATGAGAA-C
1 CATGTCTATTAAGGTTATTTTGGTAATAGTACTTTAAAT-TGAGTCT-GGGATAATACGAGAATC
3196922 TTTCAAGTCAAAA
64 -TTCAAGTCAAAA
* * * *
3196935 CATGTCTATTAAGGTTATTTAGGTAATAGTGCCTTGAAATTGAGTCTGGGATAATACGGGAATCT
1 CATGTCTATTAAGGTTATTTTGGTAATAGT-ACTTTAAATTGAGTCTGGGATAATACGAGAATCT
** *
3197000 TCGTGTCGAAA
65 TCAAGTCAAAA
* * *
3197011 CATGTCTATTAAGGTTACTTTAGTAATAGTACCTTAA
1 CATGTCTATTAAGGTTATTTTGGTAATAGTACTTTAA
3197048 GGCCAATACT
Statistics
Matches: 94, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
75 7 0.07
76 79 0.84
77 8 0.09
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (75 bp):
CATGTCTATTAAGGTTATTTTGGTAATAGTACTTTAAATTGAGTCTGGGATAATACGAGAATCTT
CAAGTCAAAA
Found at i:3199200 original size:18 final size:18
Alignment explanation
Indices: 3199177--3199212 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3199167 TGGCATTAAA
3199177 ATTAGGCTACCAAAAGCT
1 ATTAGGCTACCAAAAGCT
3199195 ATTAGGCTACCAAAAGCT
1 ATTAGGCTACCAAAAGCT
3199213 GAGTACTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (18 bp):
ATTAGGCTACCAAAAGCT
Found at i:3200997 original size:91 final size:90
Alignment explanation
Indices: 3200872--3201158 Score: 308
Period size: 91 Copynumber: 3.2 Consensus size: 90
3200862 CATTAAAAAT
* * * * * * * *
3200872 TTTTATTTTAGGAAAACTCCATCTCCACTACTCCGAGGGGATACTCGAACCCCATTCT-CCTAAA
1 TTTTATTTTGGGGAAACTCTATCCCCACTACTCCGAGGAGATACTCCAAACCCATTCTAAC-AAA
**
3200936 A-AATTGGAATTTACCCTTCCTATTAG
65 ATAATTCAAATTTACCCTTCCTA-TAG
** *
3200962 TTTTATTTTGGGGGAAACTCTATCCCCACTACTCCGAGGAGATACTCCAAACCTTTTTTAACAAA
1 TTTTATTTT-GGGGAAACTCTATCCCCACTACTCCGAGGAGATACTCCAAACCCATTCTAACAAA
* * *
3201027 ATATTTCAAATTTACCTTTCGTATAG
65 ATAATTCAAATTTACCCTTCCTATAG
* ** *
3201053 TTTTATTTTTGGGGAAAGTCTATCCCCACTACTCCGAGGAGATACTCCAAACCTTTTTTAACAAA
1 TTTTA-TTTTGGGGAAACTCTATCCCCACTACTCCGAGGAGATACTCCAAACCCATTCTAACAAA
* * *
3201118 ATATTTCAAATTTACCTTTCGTATAG
65 ATAATTCAAATTTACCCTTCCTATAG
3201144 TTTTATTCTTGGGGA
1 TTTTATT-TTGGGGA
3201159 TATTCTAACC
Statistics
Matches: 175, Mismatches: 17, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
90 11 0.06
91 143 0.82
92 21 0.12
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (90 bp):
TTTTATTTTGGGGAAACTCTATCCCCACTACTCCGAGGAGATACTCCAAACCCATTCTAACAAAA
TAATTCAAATTTACCCTTCCTATAG
Found at i:3202375 original size:21 final size:21
Alignment explanation
Indices: 3202342--3202381 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3202332 TATTTAGATA
*
3202342 TAATCTTCTTTTTTTATGTAC
1 TAATCTTCTTTTTCTATGTAC
3202363 TAATCTT-TATTTTCTATGT
1 TAATCTTCT-TTTTCTATGT
3202382 TTTGTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.62
Consensus pattern (21 bp):
TAATCTTCTTTTTCTATGTAC
Found at i:3203421 original size:20 final size:20
Alignment explanation
Indices: 3203393--3203430 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3203383 GTTGGGCTCA
*
3203393 ATGTATCGATACAATTCACC
1 ATGTATCGATAAAATTCACC
*
3203413 ATGTGTCGATAAAATTCA
1 ATGTATCGATAAAATTCA
3203431 ATTATGAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (20 bp):
ATGTATCGATAAAATTCACC
Found at i:3206098 original size:32 final size:32
Alignment explanation
Indices: 3206043--3206103 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
3206033 ATAATCAAAA
*
3206043 TGTATCGATACAATTTTAATGTATTGATACAT
1 TGTATCGATACAATTTTAATGTATCGATACAT
*
3206075 TGTATCGATACAATTTCT-TTGTATCGATA
1 TGTATCGATACAATTT-TAATGTATCGATA
3206104 GATCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 25 0.96
33 1 0.04
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (32 bp):
TGTATCGATACAATTTTAATGTATCGATACAT
Found at i:3210957 original size:13 final size:13
Alignment explanation
Indices: 3210939--3210963 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3210929 CAAAGATCAG
3210939 TGTATCGATACAA
1 TGTATCGATACAA
3210952 TGTATCGATACA
1 TGTATCGATACA
3210964 TTTGAGTAAT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3211024 original size:13 final size:13
Alignment explanation
Indices: 3211002--3211091 Score: 54
Period size: 13 Copynumber: 6.0 Consensus size: 13
3210992 GGCAGTAGCT
*
3211002 TTGTAGCGATACA
1 TTGTATCGATACA
3211015 TTGTATCGATACAAAA
1 TTGTATCGATAC---A
*
3211031 CTTATGTATCCATACA
1 --T-TGTATCGATACA
3211047 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
3211063 CTTATGTATCGATACA
1 --T-TGTATCGATACA
3211079 TTGTATCGATACA
1 TTGTATCGATACA
3211092 ACACTTTATG
Statistics
Matches: 62, Mismatches: 3, Indels: 24
0.70 0.03 0.27
Matches are distributed among these distances:
13 31 0.50
14 2 0.03
16 8 0.13
18 2 0.03
19 19 0.31
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3211040 original size:19 final size:18
Alignment explanation
Indices: 3211016--3211113 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
3211006 AGCGATACAT
3211016 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
*
3211035 TGTATCCATAC--A--T-
1 TGTATCGATACAAACTTA
3211048 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
3211067 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
3211080 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
3211100 TGTATCGATACAAA
1 TGTATCGATACAAA
3211114 TCATTGAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 23 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:3211051 original size:32 final size:32
Alignment explanation
Indices: 3211003--3211111 Score: 182
Period size: 32 Copynumber: 3.4 Consensus size: 32
3210993 GCAGTAGCTT
* *
3211003 TGTAGCGATACATTGTATCGATACAAAACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
*
3211035 TGTATCCATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
3211067 TGTATCGATACATTGTATCGATACAACACTTTA
1 TGTATCGATACATTGTATCGATACAACAC-TTA
3211100 TGTATCGATACA
1 TGTATCGATACA
3211112 AATCATTGAA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 57 0.79
33 15 0.21
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:3214008 original size:13 final size:13
Alignment explanation
Indices: 3213990--3214016 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3213980 ACATTATGCT
3213990 TTGTATCGATACA
1 TTGTATCGATACA
3214003 TTGTATCGATACA
1 TTGTATCGATACA
3214016 T
1 T
3214017 GATAGTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3214013 original size:33 final size:32
Alignment explanation
Indices: 3213971--3214035 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
3213961 CACACCCAGA
*
3213971 TGTATCGATACATTAT-GCTTTGTATCGATACAT
1 TGTATCGATACATGATAG--TTGTATCGATACAT
3214004 TGTATCGATACATGATAGTTGTATCGATACAT
1 TGTATCGATACATGATAGTTGTATCGATACAT
3214036 GAACAATTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGATAGTTGTATCGATACAT
Found at i:3214020 original size:20 final size:20
Alignment explanation
Indices: 3213997--3214057 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
3213987 GCTTTGTATC
3213997 GATACATTGTATCGATACAT
1 GATACATTGTATCGATACAT
*
3214017 GATA-GTTGTATCGATACAT
1 GATACATTGTATCGATACAT
*
3214036 GA-ACAATTGCATCGATACAT
1 GATAC-ATTGTATCGATACAT
3214056 GA
1 GA
3214058 GATTGGCAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 1 0.03
19 16 0.44
20 19 0.53
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (20 bp):
GATACATTGTATCGATACAT
Found at i:3214027 original size:19 final size:19
Alignment explanation
Indices: 3214002--3214057 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
3213992 GTATCGATAC
*
3214002 ATTGTATCGATACATGATA
1 ATTGTATCGATACATGACA
*
3214021 GTTGTATCGATACATGAACA
1 ATTGTATCGATACATG-ACA
*
3214041 ATTGCATCGATACATGA
1 ATTGTATCGATACATGA
3214058 GATTGGCAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:3233307 original size:52 final size:51
Alignment explanation
Indices: 3233222--3233345 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
3233212 ATATGAAAAG
* *
3233222 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
3233273 CTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
3233325 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
3233346 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:3233372 original size:13 final size:13
Alignment explanation
Indices: 3233354--3233378 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3233344 CAAAGATCAG
3233354 TGTATCGATACAA
1 TGTATCGATACAA
3233367 TGTATCGATACA
1 TGTATCGATACA
3233379 TTTGAGTAAT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3233456 original size:33 final size:33
Alignment explanation
Indices: 3233419--3233485 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3233409 AGTAGCTTAA
3233419 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3233452 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3233485 A
1 A
3233486 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3233459 original size:13 final size:13
Alignment explanation
Indices: 3233441--3233465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3233431 CAAAAAAATA
3233441 TGTATCGATACAT
1 TGTATCGATACAT
3233454 TGTATCGATACA
1 TGTATCGATACA
3233466 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3234518 original size:28 final size:28
Alignment explanation
Indices: 3234463--3234892 Score: 520
Period size: 28 Copynumber: 14.9 Consensus size: 28
3234453 AAAAAAAAAA
*
3234463 GGTGCCACTAACTTGTGTGGTCTTTGAAAG
1 GGTGCCACTGACTTGTG-GG-CTTTGAAAG
*
3234493 GGTGCCATTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
3234521 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
3234549 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3234577 GATGCCACTGACTCGTGGGCTTTGAAAGGTTG
1 GGTGCCACTGACTTGTGGGCTTTGAAA----G
*
3234609 AAAGGATGCCACTGACTCGTGGGCTTTGAAAG
1 ---GG-TGCCACTGACTTGTGGGCTTTGAAAG
* **
3234641 GATGCCACTGACTCATGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* ** *
3234669 AGTGCCACTGACTCATGGGCTTTGAAGG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
3234697 GGTGCCACTGACTCGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
3234725 GATGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3234753 GGTACCACTGACTTGCGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3234781 GATACCACAGACTTGTGTGGCTTTGAAA-
1 GGTGCCACTGACTTGTG-GGCTTTGAAAG
*
3234809 GGTGCCACAGACTTGCGTGGGCTTTGAAAG
1 GGTGCCACTGACTT--GTGGGCTTTGAAAG
* *
3234839 GGTGCCACTGACTTGTGGGCTTTAAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3234867 GGTGCTACTAACTTGTGGGCTTTGAA
1 GGTGCCACTGACTTGTGGGCTTTGAA
3234893 GAGATGAACG
Statistics
Matches: 358, Mismatches: 30, Indels: 26
0.86 0.07 0.06
Matches are distributed among these distances:
28 276 0.77
29 23 0.06
30 31 0.09
32 2 0.01
35 1 0.00
36 25 0.07
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:3234617 original size:36 final size:36
Alignment explanation
Indices: 3234570--3234641 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
3234560 CTTGTGGGCT
3234570 TTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGG
1 TTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGG
3234606 TTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGG
1 TTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGG
3234642 ATGCCACTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (36 bp):
TTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGG
Found at i:3236146 original size:9 final size:9
Alignment explanation
Indices: 3236124--3236177 Score: 65
Period size: 9 Copynumber: 5.9 Consensus size: 9
3236114 TTTTTTGCTA
3236124 TTTTTTCTTGG
1 TTTTTT-TT-G
3236135 TTTTTTTTG
1 TTTTTTTTG
*
3236144 TTTTTTAT-
1 TTTTTTTTG
*
3236152 TTTTTTTGG
1 TTTTTTTTG
3236161 TTTTTTTTG
1 TTTTTTTTG
3236170 TTTTTTTT
1 TTTTTTTT
3236178 TTGGTATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
8 6 0.16
9 24 0.63
10 2 0.05
11 6 0.16
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:3236154 original size:26 final size:25
Alignment explanation
Indices: 3236124--3236179 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 25
3236114 TTTTTTGCTA
3236124 TTTTTTCTTGGTTTTTTTTGTTTTT
1 TTTTTTCTTGGTTTTTTTTGTTTTT
*
3236149 TATTTTTTTTGGTTTTTTTTGTTTTT
1 T-TTTTTCTTGGTTTTTTTTGTTTTT
3236175 TTTTT
1 TTTTT
3236180 GGTATAAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.86
Consensus pattern (25 bp):
TTTTTTCTTGGTTTTTTTTGTTTTT
Found at i:3236168 original size:21 final size:22
Alignment explanation
Indices: 3236139--3236182 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
3236129 TCTTGGTTTT
3236139 TTTTGTTTT-TTATTTTTTTTGG
1 TTTTGTTTTGTT-TTTTTTTTGG
3236161 TTTT-TTTTGTTTTTTTTTTGG
1 TTTTGTTTTGTTTTTTTTTTGG
3236182 T
1 T
3236183 ATAAAGGACG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.84
Consensus pattern (22 bp):
TTTTGTTTTGTTTTTTTTTTGG
Found at i:3240580 original size:20 final size:19
Alignment explanation
Indices: 3240557--3240630 Score: 87
Period size: 19 Copynumber: 3.7 Consensus size: 19
3240547 CACACCCAGA
*
3240557 TGTATCGATACATGCTGCTT
1 TGTATCGATACATG-TGCAT
*
3240577 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTGCAT
3240596 TGTATCGATACATG-GACAAAT
1 TGTATCGATACATGTG-C--AT
3240617 TGTATCGATACATG
1 TGTATCGATACATG
3240631 AAACTGGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.38
20 14 0.29
21 16 0.33
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATGTGCAT
Found at i:3240685 original size:20 final size:19
Alignment explanation
Indices: 3240660--3240712 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
3240650 TATCACTATT
3240660 TGTATCGATACATG-GTACAA
1 TGTATCGATACATGAG-A-AA
3240680 TGTATCGATACATGAAGAAA
1 TGTATCGATACATG-AGAAA
3240700 TGTATCGATACAT
1 TGTATCGATACAT
3240713 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 29 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (19 bp):
TGTATCGATACATGAGAAA
Found at i:3246679 original size:19 final size:19
Alignment explanation
Indices: 3246641--3246692 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
3246631 TTGAATGAAT
3246641 TTTG-ATGATTG--TTATG
1 TTTGTATGATTGAATTATG
3246657 -TTGTATGATTGAATTATG
1 TTTGTATGATTGAATTATG
*
3246675 TTTGTTTGATATGAATTA
1 TTTGTATGAT-TGAATTA
3246693 GGGTCTATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 3 0.10
16 7 0.23
18 5 0.17
19 8 0.27
20 7 0.23
ACGTcount: A:0.25, C:0.00, G:0.21, T:0.54
Consensus pattern (19 bp):
TTTGTATGATTGAATTATG
Found at i:3248679 original size:18 final size:18
Alignment explanation
Indices: 3248647--3248681 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3248637 AAATTTTTAT
* *
3248647 ATATAAAAGGGGGAGAAG
1 ATATAAAAAGAGGAGAAG
3248665 ATATAAAAAGAGGAGAA
1 ATATAAAAAGAGGAGAA
3248682 TTTTTTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.31, T:0.11
Consensus pattern (18 bp):
ATATAAAAAGAGGAGAAG
Found at i:3249290 original size:13 final size:13
Alignment explanation
Indices: 3249272--3249298 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3249262 ACATGTTGCT
3249272 TTGTATCGATACA
1 TTGTATCGATACA
3249285 TTGTATCGATACA
1 TTGTATCGATACA
3249298 T
1 T
3249299 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3249295 original size:33 final size:32
Alignment explanation
Indices: 3249253--3249317 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 32
3249243 CACACACAGA
*
3249253 TGTATCGATACATGTTGCTTTGTATCGATACAT
1 TGTATCGATACATGTT-CATTGTATCGATACAT
3249286 TGTATCGATACATGTTCATTGTATCGATACAT
1 TGTATCGATACATGTTCATTGTATCGATACAT
3249318 GGACAAATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATGTTCATTGTATCGATACAT
Found at i:3249329 original size:21 final size:19
Alignment explanation
Indices: 3249282--3249339 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
3249272 TTGTATCGAT
*
3249282 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
3249301 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
3249320 ACAAATTGTATCGATACATG
1 AC--ATTGTATCGATACATG
3249340 AAACTAGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.53
21 16 0.47
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:3264415 original size:23 final size:23
Alignment explanation
Indices: 3264385--3264428 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3264375 CACTTTTAAT
*
3264385 AGAAGCCACTTTTCTAAATAGGG
1 AGAAGCCACTTTTATAAATAGGG
3264408 AGAAGCCACTTTTATAAATAG
1 AGAAGCCACTTTTATAAATAG
3264429 CGAGTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (23 bp):
AGAAGCCACTTTTATAAATAGGG
Found at i:3266020 original size:15 final size:15
Alignment explanation
Indices: 3266000--3266033 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3265990 ACATAAGTTC
3266000 ACTATAGTTTTTCAA
1 ACTATAGTTTTTCAA
* *
3266015 ACTATATTTTTTCAT
1 ACTATAGTTTTTCAA
3266030 ACTA
1 ACTA
3266034 AATGAGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (15 bp):
ACTATAGTTTTTCAA
Found at i:3267929 original size:2 final size:2
Alignment explanation
Indices: 3267922--3267946 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3267912 TTAATTCTAC
3267922 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3267947 GAGATTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3269296 original size:37 final size:37
Alignment explanation
Indices: 3269246--3269321 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
3269236 CTCATAAGTT
*
3269246 AGTTTCCATTTTATAAAGACAAGATTTTCTGTGAGAG
1 AGTTTCCATTTTATAAAGACAAGATTTTCTCTGAGAG
3269283 AGTTTCCATTTTATAAAGACAAGATTTTCTCTGAGAG
1 AGTTTCCATTTTATAAAGACAAGATTTTCTCTGAGAG
3269320 AG
1 AG
3269322 ACAATTTGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (37 bp):
AGTTTCCATTTTATAAAGACAAGATTTTCTCTGAGAG
Found at i:3270298 original size:19 final size:20
Alignment explanation
Indices: 3270268--3270306 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3270258 TCCTTTATGT
3270268 ATATAGTATATAACTATATA
1 ATATAGTATATAACTATATA
*
3270288 ATATA-TATATATCTATATA
1 ATATAGTATATAACTATATA
3270307 TTTGAGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (20 bp):
ATATAGTATATAACTATATA
Found at i:3276410 original size:18 final size:19
Alignment explanation
Indices: 3276368--3276403 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3276358 TGAAAGTCTG
3276368 AATTATTGTTTATATTAAA
1 AATTATTGTTTATATTAAA
3276387 AATTATT-TTTATATTAA
1 AATTATTGTTTATATTAA
3276404 TATTTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
AATTATTGTTTATATTAAA
Found at i:3278815 original size:20 final size:20
Alignment explanation
Indices: 3278790--3278862 Score: 114
Period size: 20 Copynumber: 3.6 Consensus size: 20
3278780 GTTACAAGCT
3278790 ATGTATCGATACATT-T-CTTC
1 ATGTATCGATACATTGTAC--C
3278810 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
3278830 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
3278850 ATGTATCGATACA
1 ATGTATCGATACA
3278863 AATAGTGATA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
20 49 0.96
21 1 0.02
22 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGTACC
Found at i:3278937 original size:19 final size:19
Alignment explanation
Indices: 3278892--3278946 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
3278882 CTGCCAATTT
**
3278892 CATGTATCGATACAATTTGTC
1 CATGTATCGATAC-A-TTGAA
3278913 CATGTATCGATACATTGAA
1 CATGTATCGATACATTGAA
3278932 CATGTATCGATACAT
1 CATGTATCGATACAT
3278947 CTGGGTGTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 18 0.56
20 1 0.03
21 13 0.41
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (19 bp):
CATGTATCGATACATTGAA
Found at i:3279489 original size:18 final size:19
Alignment explanation
Indices: 3279466--3279534 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
3279456 GTTTTCGTTT
3279466 TTCT-CCCCTTAAAAAATA
1 TTCTCCCCCTTAAAAAATA
**
3279484 TTCTCCCCCTTAAACGAT-
1 TTCTCCCCCTTAAAAAATA
* *
3279502 TATCT-CCTCTTAAAAAAAA
1 T-TCTCCCCCTTAAAAAATA
3279521 TTCTCCCCCTTAAA
1 TTCTCCCCCTTAAA
3279535 CGATTATCTT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
18 17 0.43
19 23 0.57
ACGTcount: A:0.33, C:0.32, G:0.01, T:0.33
Consensus pattern (19 bp):
TTCTCCCCCTTAAAAAATA
Found at i:3279517 original size:37 final size:37
Alignment explanation
Indices: 3279467--3279543 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
3279457 TTTTCGTTTT
*
3279467 TCTCCCCTTAAAAAATATTCTCCCCCTTAAACGATTA
1 TCTCCCCTTAAAAAAAATTCTCCCCCTTAAACGATTA
*
3279504 TCTCCTCTTAAAAAAAATTCTCCCCCTTAAACGATTA
1 TCTCCCCTTAAAAAAAATTCTCCCCCTTAAACGATTA
3279541 TCT
1 TCT
3279544 TCTCCCCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.31, G:0.03, T:0.34
Consensus pattern (37 bp):
TCTCCCCTTAAAAAAAATTCTCCCCCTTAAACGATTA
Found at i:3279562 original size:18 final size:19
Alignment explanation
Indices: 3279539--3279578 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3279529 CTTAAACGAT
3279539 TATCTTCT-CCCCTTTTTA
1 TATCTTCTCCCCCTTTTTA
*
3279557 TATCTTTTCCCCCTTTTTA
1 TATCTTCTCCCCCTTTTTA
3279576 TAT
1 TAT
3279579 AAAAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.12, C:0.30, G:0.00, T:0.57
Consensus pattern (19 bp):
TATCTTCTCCCCCTTTTTA
Found at i:3285970 original size:9 final size:9
Alignment explanation
Indices: 3285944--3285973 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3285934 TTCATCCGAG
*
3285944 TCACCATCG
1 TCACCATCA
3285953 TCACCATCA
1 TCACCATCA
3285962 TCACCATCA
1 TCACCATCA
3285971 TCA
1 TCA
3285974 TCATTGTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.30, C:0.43, G:0.03, T:0.23
Consensus pattern (9 bp):
TCACCATCA
Found at i:3286202 original size:21 final size:21
Alignment explanation
Indices: 3286178--3286234 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3286168 AATTTATCCA
3286178 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
3286199 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
3286220 AATGTATCGATACAT
1 AATGTATCGATACAT
3286235 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:3286314 original size:19 final size:19
Alignment explanation
Indices: 3286290--3286354 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
3286280 AATTCAACAA
3286290 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3286309 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3286324 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3286341 TTTGTATCGATACA
1 TTTGTATCGATACA
3286355 ATGTATCGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 25 0.62
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3286329 original size:13 final size:13
Alignment explanation
Indices: 3286311--3286367 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
3286301 ACATAAGTTT
3286311 TGTATCGATACAA
1 TGTATCGATACAA
3286324 TGTATCGATACATAA
1 TGTATCGATAC--AA
3286339 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
3286356 TGTATCGATACA
1 TGTATCGATACA
3286368 TAATTAGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3286333 original size:32 final size:32
Alignment explanation
Indices: 3286292--3286370 Score: 158
Period size: 32 Copynumber: 2.5 Consensus size: 32
3286282 TTCAACAATT
3286292 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
3286324 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
3286356 TGTATCGATACATAA
1 TGTATCGATACATAA
3286371 TTAGCTACTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:3286428 original size:13 final size:13
Alignment explanation
Indices: 3286410--3286435 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3286400 TATTTTTCTG
3286410 TGTATCGATACAT
1 TGTATCGATACAT
3286423 TGTATCGATACAT
1 TGTATCGATACAT
3286436 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3289014 original size:53 final size:51
Alignment explanation
Indices: 3288928--3289099 Score: 168
Period size: 52 Copynumber: 3.3 Consensus size: 51
3288918 TTATTTTTGA
* * * *
3288928 GGGGATACTCCAACCCCAGTTTTATTGCTAAAACACTAATTTTTTCCACAATC
1 GGGGATACTCCAA-CCCGGTTTTATTTCCAAAACACCAA-TTTTTCCACAATC
* * **
3288981 GGGGATACTCCAACCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACCC-GGTTTTATTTCCAAAACACCAATTTTTCC-ACAATC
* *
3289033 GGGGATACTCCAACTCCGATTTTATTTCCAAAATTACCAATTTTT-CACAATC
1 GGGGATACTCCAAC-CCGGTTTTATTTCCAAAA-CACCAATTTTTCCACAATC
* *
3289085 GAGGATACTCTAACC
1 GGGGATACTCCAACC
3289100 TCCTTATTTC
Statistics
Matches: 98, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
51 7 0.07
52 51 0.52
53 36 0.37
54 4 0.04
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCGGTTTTATTTCCAAAACACCAATTTTTCCACAATC
Found at i:3291737 original size:33 final size:33
Alignment explanation
Indices: 3291699--3291765 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 33
3291689 GTTACAAGCT
3291699 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
*
3291732 ATGTATTGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
3291765 A
1 A
3291766 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:3291819 original size:21 final size:21
Alignment explanation
Indices: 3291794--3291849 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 21
3291784 CTGCTAATTT
**
3291794 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGAA
3291815 CATGTATCGATAC-A-TTGAA
1 CATGTATCGATACAATTTGAA
3291834 CATGTATCGATACAAT
1 CATGTATCGATACAAT
3291850 GTATGGATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 16 0.52
20 2 0.06
21 13 0.42
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (21 bp):
CATGTATCGATACAATTTGAA
Found at i:3292489 original size:26 final size:26
Alignment explanation
Indices: 3292455--3292507 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3292445 ATTTTTAAAG
**
3292455 AAGATTTCAAAGTTGAAATAATTCTT
1 AAGATTTCAAAGAAGAAATAATTCTT
* *
3292481 AAGATTTCATAGAAGAAATATTTCTT
1 AAGATTTCAAAGAAGAAATAATTCTT
3292507 A
1 A
3292508 TTTTCCCTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (26 bp):
AAGATTTCAAAGAAGAAATAATTCTT
Found at i:3292879 original size:41 final size:41
Alignment explanation
Indices: 3292828--3292956 Score: 249
Period size: 41 Copynumber: 3.1 Consensus size: 41
3292818 ATAATACATG
3292828 GTTTGTATGTTGGAATATTTTTAAAATAATAAGAATGGTTAT
1 GTTT-TATGTTGGAATATTTTTAAAATAATAAGAATGGTTAT
3292870 GTTTTATGTTGGAATATTTTTAAAATAATAAGAATGGTTAT
1 GTTTTATGTTGGAATATTTTTAAAATAATAAGAATGGTTAT
3292911 GTTTTATGTTGGAATATTTTTAAAATAATAAGAATGGTTAT
1 GTTTTATGTTGGAATATTTTTAAAATAATAAGAATGGTTAT
3292952 GTTTT
1 GTTTT
3292957 GAATAATCAT
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
41 83 0.95
42 4 0.05
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (41 bp):
GTTTTATGTTGGAATATTTTTAAAATAATAAGAATGGTTAT
Found at i:3296690 original size:10 final size:10
Alignment explanation
Indices: 3296655--3296702 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
3296645 ATAGAAAATG
3296655 ATAAATTTTAA
1 ATAAATTTT-A
*
3296666 ATAAA-ATTA
1 ATAAATTTTA
* *
3296675 AAAAATTTTT
1 ATAAATTTTA
3296685 ATAAATTTTA
1 ATAAATTTTA
3296695 ATAAATTT
1 ATAAATTT
3296703 ATCTCAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
9 5 0.17
10 20 0.67
11 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
ATAAATTTTA
Found at i:3298326 original size:1 final size:1
Alignment explanation
Indices: 3298293--3298317 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3298283 ACTAGACCTT
3298293 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
3298318 AATTCCCCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:3298959 original size:2 final size:2
Alignment explanation
Indices: 3298952--3298989 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3298942 AACAAACATT
3298952 TA TA 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 TA TA
3298990 ATTTTATACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3299872 original size:9 final size:9
Alignment explanation
Indices: 3299858--3299887 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
3299848 TAATAACGAT
3299858 ATAAATTAA
1 ATAAATTAA
3299867 ATAAATTAA
1 ATAAATTAA
3299876 ATTAAATTAA
1 A-TAAATTAA
3299886 AT
1 AT
3299888 TTTAAATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
ATAAATTAA
Found at i:3299876 original size:5 final size:5
Alignment explanation
Indices: 3299859--3299888 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
3299849 AATAACGATA
3299859 TAAAT TAAA- TAAAT TAAAT TAAAT TAAAT T
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT T
3299889 TTAAATTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:3314094 original size:1 final size:1
Alignment explanation
Indices: 3314088--3314190 Score: 53
Period size: 1 Copynumber: 103.0 Consensus size: 1
3314078 TCCTTCGTAT
* * *** * * * * *
3314088 AAAAAAAAACAAAAAAAGAAAAAACCCAAGAAAAAAAACAAAAAAAGAAACAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * * * *
3314153 ACCAAGAAAAAAAACAAAAAAACAAACAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3314191 GGGGTCTAGA
Statistics
Matches: 74, Mismatches: 28, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:3314121 original size:29 final size:29
Alignment explanation
Indices: 3314089--3314191 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 29
3314079 CCTTCGTATA
**
3314089 AAAAAAAACAAAAAAAGAAA-AAACCCAAG
1 AAAAAAAACAAAAAAAGAAACAAA-AAAAG
3314118 AAAAAAAACAAAAAAAGAAACAAAAAAAG
1 AAAAAAAACAAAAAAAGAAACAAAAAAAG
*
3314147 AAAAAAACCAAGAAAAA-AAACAAAAAAA-
1 AAAAAAAACAA-AAAAAGAAACAAAAAAAG
* * *
3314175 CAAACAAAGAAAAAAAG
1 AAAAAAAACAAAAAAAG
3314192 GGGTCTAGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.08
28 7 0.11
29 44 0.69
30 8 0.12
ACGTcount: A:0.83, C:0.11, G:0.07, T:0.00
Consensus pattern (29 bp):
AAAAAAAACAAAAAAAGAAACAAAAAAAG
Found at i:3314133 original size:12 final size:12
Alignment explanation
Indices: 3314088--3314190 Score: 73
Period size: 13 Copynumber: 7.8 Consensus size: 12
3314078 TCCTTCGTAT
3314088 AAAAAAAAACAA-
1 AAAAAAAAA-AAC
3314100 AAAAAGAAAAAACCC
1 AAAAA-AAAAAA--C
*
3314115 AAGAAAAAAAAC
1 AAAAAAAAAAAC
*
3314127 AAAAAAAGAAACAAA
1 -AAAAAA-AAA-AAC
3314142 AAAAGAAAAAAACC
1 AAAA-AAAAAAA-C
*
3314156 AAGAAAAAAAAC
1 AAAAAAAAAAAC
*
3314168 AAAAAAACAAAC
1 AAAAAAAAAAAC
3314180 AAAGAAAAAAA
1 AAA-AAAAAAA
3314191 GGGGTCTAGA
Statistics
Matches: 73, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
12 22 0.30
13 24 0.33
14 19 0.26
15 8 0.11
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:3314139 original size:41 final size:40
Alignment explanation
Indices: 3314088--3314187 Score: 164
Period size: 41 Copynumber: 2.4 Consensus size: 40
3314078 TCCTTCGTAT
*
3314088 AAAAAAAAACAAAAAAAGAAAAAACCCAAGAAAAAAAACA
1 AAAAAAAAACAAAAAAAGAAAAAAACCAAGAAAAAAAACA
3314128 AAAAAAGAAACAAAAAAAGAAAAAAACCAAGAAAAAAAACA
1 AAAAAA-AAACAAAAAAAGAAAAAAACCAAGAAAAAAAACA
3314169 AAAAAACAAACAAAGAAAA
1 AAAAAA-AAACAAA-AAAA
3314188 AAAGGGGTCT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
40 6 0.11
41 46 0.82
42 4 0.07
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (40 bp):
AAAAAAAAACAAAAAAAGAAAAAAACCAAGAAAAAAAACA
Found at i:3315467 original size:28 final size:28
Alignment explanation
Indices: 3315433--3315868 Score: 433
Period size: 28 Copynumber: 15.5 Consensus size: 28
3315423 CGTTCATCTC
3315433 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
3315461 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
3315489 TTCAAAGCCCACAAGTCAGTAGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
3315517 TTTAAAGCCCACAAGTCAGTGGCA-CCGTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC--T
*
3315546 TTCAAAGCCCATAAGT-A--GGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* * *
3315571 TTCATAGCCCATAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
3315599 TTCAAAGTCCACAAGTTAGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* * * *
3315628 TTCAAAGGCCACAAATTAGTGACA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* *
3315656 TTCAAAGCCCACAAGTCATTAGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
3315683 CTTCAAAGCCCACAAGTCAGTGGCATCCT
1 -TTCAAAGCCCACAAGTCAGTGGCATCCT
* **
3315712 TCCAAAGCCCATGAGAT-AGTGGCATCCT
1 TTCAAAGCCCACAAG-TCAGTGGCATCCT
3315740 TTCAAAGCCCACAAGTCAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
3315767 CTTCAAAGCCCACAAGTCAGAGGCA-CAT
1 -TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
3315795 TCTTAAAACCCACAAGTTATTGGCATCCT
1 T-TCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
3315824 TTTAAAGCCCACACAAGTCGGTGGCAACTTT
1 TTCAAAG-CC-CACAAGTCAGTGGCATC-CT
3315855 TTCTAAAGCCCACA
1 TTC-AAAGCCCACA
3315869 CAAGTTGGTG
Statistics
Matches: 346, Mismatches: 42, Indels: 38
0.81 0.10 0.09
Matches are distributed among these distances:
25 17 0.05
26 7 0.02
27 7 0.02
28 242 0.70
29 47 0.14
30 17 0.05
31 5 0.01
32 4 0.01
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:3316670 original size:20 final size:20
Alignment explanation
Indices: 3316645--3316802 Score: 120
Period size: 20 Copynumber: 7.8 Consensus size: 20
3316635 TTTTACCCAG
3316645 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* **
3316665 ATGTATTGATACA-TTACCTA
1 ATGTATCGATACATTTTTC-A
* * * *
3316685 GATATATCTATACATCTTCCA
1 -ATGTATCGATACATTTTTCA
* ***
3316706 ATGTATCGATAAATTACCCA
1 ATGTATCGATACATTTTTCA
*
3316726 GATGTATCGATACATCTTTCA
1 -ATGTATCGATACATTTTTCA
* ** * *
3316747 ATGTATCAATACACGTATGA
1 ATGTATCGATACATTTTTCA
3316767 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
*
3316787 ATGTATCAATACATTT
1 ATGTATCGATACATTT
3316803 GTCCTTTTAC
Statistics
Matches: 104, Mismatches: 30, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
19 3 0.03
20 72 0.69
21 26 0.25
22 3 0.03
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:3316698 original size:41 final size:41
Alignment explanation
Indices: 3316637--3316793 Score: 174
Period size: 41 Copynumber: 3.9 Consensus size: 41
3316627 AGTCACATTT
* * *
3316637 TTACCCAGATGTATCGATACATTTTTCAATGTATTGATACA
1 TTACCCAGATGTATCGATACATCTTTCAATGTATCGATAAA
* * * *
3316678 TTACCTAGATATATCTATACATCTTCCAATGTATCGATAAA
1 TTACCCAGATGTATCGATACATCTTTCAATGTATCGATAAA
* *
3316719 TTACCCAGATGTATCGATACATCTTTCAATGTATCAATACAC
1 TTACCCAGATGTATCGATACATCTTTCAATGTATCGATA-AA
* ** *
3316761 GTA-TGA-ATGTATCGATACATTTTTCAATGTATC
1 TTACCCAGATGTATCGATACATCTTTCAATGTATC
3316794 AATACATTTG
Statistics
Matches: 98, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
40 26 0.27
41 69 0.70
42 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (41 bp):
TTACCCAGATGTATCGATACATCTTTCAATGTATCGATAAA
Found at i:3322029 original size:20 final size:20
Alignment explanation
Indices: 3322004--3322061 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
3321994 TCCCGTGTGA
3322004 ATGTATCGATACAATTTTTG
1 ATGTATCGATACAATTTTTG
*
3322024 ATGTATCAATACAATTTTTG
1 ATGTATCGATACAATTTTTG
*
3322044 ATGTATTGATACATATTT
1 ATGTATCGATACA-ATTT
3322062 GAAAATATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 30 0.88
21 4 0.12
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.47
Consensus pattern (20 bp):
ATGTATCGATACAATTTTTG
Found at i:3322121 original size:20 final size:20
Alignment explanation
Indices: 3322096--3322147 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
3322086 TACAAGCCAA
**
3322096 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
3322116 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
3322135 TGTATCGATACAA
1 TGTATCGATACAA
3322148 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:3322226 original size:20 final size:20
Alignment explanation
Indices: 3322177--3322250 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
3322167 ATCTTAATGA
***
3322177 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGAAT
*
3322198 CAAGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
3322218 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
*
3322238 TATGTATCGATAC
1 CATGTATCGATAC
3322251 TTTTAAGGGT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.05
20 28 0.64
21 14 0.32
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:3322251 original size:20 final size:20
Alignment explanation
Indices: 3322201--3322253 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3322191 TCTTTTTCAA
*
3322201 GTATCGATACATTGCAACAT
1 GTATCGATACTTTGCAACAT
*
3322221 GTATCGATACTTTG-AATTAT
1 GTATCGATACTTTGCAA-CAT
3322241 GTATCGATACTTT
1 GTATCGATACTTT
3322254 TAAGGGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
GTATCGATACTTTGCAACAT
Found at i:3324252 original size:21 final size:20
Alignment explanation
Indices: 3324223--3324265 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
3324213 GACTAGTGTG
* *
3324223 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
3324244 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
3324264 GG
1 GG
3324266 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:3330891 original size:20 final size:20
Alignment explanation
Indices: 3330866--3330917 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
3330856 TACAAGCCAA
**
3330866 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
3330886 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
3330905 TGTATCGATACAA
1 TGTATCGATACAA
3330918 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:3331973 original size:2 final size:2
Alignment explanation
Indices: 3331960--3331989 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3331950 CGCGAGCAAC
*
3331960 AT AT AA 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
3331990 TAAATTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3332060 original size:18 final size:18
Alignment explanation
Indices: 3332027--3332070 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3332017 TTATTTTTAT
**
3332027 TTAAAAAATTTGTATTAC
1 TTAAAAAATTAATATTAC
*
3332045 TTAAAAAATTAATATTTC
1 TTAAAAAATTAATATTAC
*
3332063 GTAAAAAA
1 TTAAAAAA
3332071 ATAAAGAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (18 bp):
TTAAAAAATTAATATTAC
Found at i:3333046 original size:18 final size:18
Alignment explanation
Indices: 3333008--3333045 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3332998 ATTACATTTC
*
3333008 TTTATTTTTTATTTTTAT
1 TTTATTTTTTATTATTAT
3333026 TTTATTTTTT-TTATTAT
1 TTTATTTTTTATTATTAT
3333043 TTT
1 TTT
3333046 TTTGATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTATTTTTTATTATTAT
Found at i:3333048 original size:12 final size:11
Alignment explanation
Indices: 3333012--3333048 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
3333002 CATTTCTTTA
3333012 TTTTTTATTTT
1 TTTTTTATTTT
*
3333023 TATTTTATTTT
1 TTTTTTATTTT
3333034 TTTTATTATTTT
1 TTTT-TTATTTT
3333046 TTT
1 TTT
3333049 GATATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:3333282 original size:27 final size:27
Alignment explanation
Indices: 3333251--3333343 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
3333241 TAATACTCTT
* *
3333251 TGGCACAGGTACTTTAGCATAAATACC
1 TGGCACAGGTACTTTGGCATAAGTACC
3333278 TGGCACAGGTACTTTGGCATAAGTACC
1 TGGCACAGGTACTTTGGCATAAGTACC
* * * *
3333305 TGACACAAGTGCTTTGGCATAAGTACT
1 TGGCACAGGTACTTTGGCATAAGTACC
*
3333332 TGGCATAGGTAC
1 TGGCACAGGTAC
3333344 CTAGCACAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (27 bp):
TGGCACAGGTACTTTGGCATAAGTACC
Found at i:3333303 original size:14 final size:14
Alignment explanation
Indices: 3333248--3333343 Score: 63
Period size: 14 Copynumber: 7.1 Consensus size: 14
3333238 CCATAATACT
* *
3333248 CTTTGGCACAGGTA
1 CTTTGGCATAAGTA
* *
3333262 CTTTAGCATAAATA
1 CTTTGGCATAAGTA
* * *
3333276 C-CTGGCACAGGTA
1 CTTTGGCATAAGTA
3333289 CTTTGGCATAAGTA
1 CTTTGGCATAAGTA
* * * *
3333303 C-CTGACACAAGTG
1 CTTTGGCATAAGTA
3333316 CTTTGGCATAAGTA
1 CTTTGGCATAAGTA
*
3333330 C-TTGGCATAGGTA
1 CTTTGGCATAAGTA
3333343 C
1 C
3333344 CTAGCACAGA
Statistics
Matches: 59, Mismatches: 21, Indels: 5
0.69 0.25 0.06
Matches are distributed among these distances:
13 29 0.49
14 30 0.51
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (14 bp):
CTTTGGCATAAGTA
Found at i:3333336 original size:13 final size:13
Alignment explanation
Indices: 3333267--3333343 Score: 55
Period size: 13 Copynumber: 5.8 Consensus size: 13
3333257 AGGTACTTTA
* *
3333267 GCATAAATACCTG
1 GCATAAGTACTTG
* *
3333280 GCACAGGTACTTTG
1 GCATAAGTAC-TTG
*
3333294 GCATAAGTACCTG
1 GCATAAGTACTTG
* * *
3333307 ACACAAGTGCTTTG
1 GCATAAGTAC-TTG
3333321 GCATAAGTACTTG
1 GCATAAGTACTTG
*
3333334 GCATAGGTAC
1 GCATAAGTAC
3333344 CTAGCACAGA
Statistics
Matches: 47, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
13 28 0.60
14 19 0.40
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (13 bp):
GCATAAGTACTTG
Found at i:3333344 original size:40 final size:40
Alignment explanation
Indices: 3333278--3333380 Score: 111
Period size: 40 Copynumber: 2.5 Consensus size: 40
3333268 CATAAATACC
* *
3333278 TGGCACAGGTACTTTGGCATAAGTACCT-GACACA-AGTGCTT
1 TGGCACAAGTAC-TTGGCATAGGTACCTAG-CACAGA-TGCTT
*
3333319 TGGCATAAGTACTTGGCATAGGTACCTAGCACAGATGCTT
1 TGGCACAAGTACTTGGCATAGGTACCTAGCACAGATGCTT
* * *
3333359 TGGTACAAGTACCTGGTATAGG
1 TGGCACAAGTACTTGGCATAGG
3333381 CGTTTTGGCA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
40 41 0.77
41 12 0.23
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (40 bp):
TGGCACAAGTACTTGGCATAGGTACCTAGCACAGATGCTT
Found at i:3333433 original size:15 final size:15
Alignment explanation
Indices: 3333410--3333456 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
3333400 AGCACAAGCA
*
3333410 CTTTGGCATAGGTAT
1 CTTTGGCATAGGTAC
* *
3333425 CTTTAGCATAGATAC
1 CTTTGGCATAGGTAC
3333440 CTTTGGCATAGGTAC
1 CTTTGGCATAGGTAC
3333455 CT
1 CT
3333457 GGCATAGTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (15 bp):
CTTTGGCATAGGTAC
Found at i:3334674 original size:16 final size:16
Alignment explanation
Indices: 3334655--3334690 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
3334645 TAAATTTGTT
3334655 TTTTAATAAATGAAAC
1 TTTTAATAAATGAAAC
3334671 TTTTAATAAATGAAAC
1 TTTTAATAAATGAAAC
3334687 TTTT
1 TTTT
3334691 GCTGGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (16 bp):
TTTTAATAAATGAAAC
Found at i:3335209 original size:16 final size:16
Alignment explanation
Indices: 3335190--3335236 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
3335180 AAATTACTCA
3335190 AACTCGAAATAGCCCG
1 AACTCGAAATAGCCCG
*
3335206 AACTCGAGATAGCCCG
1 AACTCGAAATAGCCCG
* * *
3335222 AGCCCAAAATAGCCC
1 AACTCGAAATAGCCC
3335237 AAACCTGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.36, C:0.34, G:0.19, T:0.11
Consensus pattern (16 bp):
AACTCGAAATAGCCCG
Found at i:3335272 original size:16 final size:16
Alignment explanation
Indices: 3335248--3335294 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
3335238 AACCTGAAAA
3335248 AACCCGAACCCGAGAG
1 AACCCGAACCCGAGAG
** *
3335264 AACTTGAACTCGAGAG
1 AACCCGAACCCGAGAG
3335280 AACCCGAACCCGAGA
1 AACCCGAACCCGAGA
3335295 CTGACCCAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.38, C:0.32, G:0.23, T:0.06
Consensus pattern (16 bp):
AACCCGAACCCGAGAG
Found at i:3336748 original size:15 final size:16
Alignment explanation
Indices: 3336719--3336748 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3336709 CCGAATAAAT
3336719 TCAAATTCGAAAAAGC
1 TCAAATTCGAAAAAGC
3336735 TCAAATTC-AAAAAG
1 TCAAATTCGAAAAAG
3336749 TCTGAACCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.20
Consensus pattern (16 bp):
TCAAATTCGAAAAAGC
Found at i:3339698 original size:17 final size:16
Alignment explanation
Indices: 3339657--3339707 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
3339647 GATTGACTCG
* *
3339657 AATTCAAAATAATTAA
1 AATTTAAAATAATTTA
3339673 AATTTAAAATAATTTA
1 AATTTAAAATAATTTA
3339689 AATTTAAAAATAATTTA
1 AATTT-AAAATAATTTA
3339706 AA
1 AA
3339708 AATTTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 19 0.59
17 13 0.41
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTTAAAATAATTTA
Found at i:3339724 original size:26 final size:27
Alignment explanation
Indices: 3339673--3339733 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
3339663 AAATAATTAA
*
3339673 AATTTAAAATAATTTAAATTTAAAAAT
1 AATTTAAAATAATTTAAACTTAAAAAT
*
3339700 AATTTAAAA-ATTTTAAAACTT-AAAAT
1 AATTTAAAATAATTT-AAACTTAAAAAT
3339726 AATTTAAA
1 AATTTAAA
3339734 GTTACGATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 17 0.55
27 14 0.45
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (27 bp):
AATTTAAAATAATTTAAACTTAAAAAT
Found at i:3342943 original size:21 final size:20
Alignment explanation
Indices: 3342905--3342942 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3342895 TATATTGACG
*
3342905 AAAAAATTGGTAATTTTTGA
1 AAAAAATAGGTAATTTTTGA
3342925 AAAAAATAAGGT-ATTTTT
1 AAAAAAT-AGGTAATTTTT
3342943 TATAAAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (20 bp):
AAAAAATAGGTAATTTTTGA
Found at i:3343723 original size:13 final size:13
Alignment explanation
Indices: 3343705--3343730 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3343695 TACACAAAGT
3343705 ATGTATCGATACA
1 ATGTATCGATACA
3343718 ATGTATCGATACA
1 ATGTATCGATACA
3343731 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3343749 original size:34 final size:32
Alignment explanation
Indices: 3343687--3343751 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
3343677 TAGCCAAACT
**
3343687 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
3343719 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
3343752 TTGTCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:3346439 original size:42 final size:43
Alignment explanation
Indices: 3346375--3346466 Score: 114
Period size: 42 Copynumber: 2.1 Consensus size: 43
3346365 GGATGTATTA
* *
3346375 ATACATTTAAGCCTAATGTATCGATATATCACCAAAATGTATCG
1 ATACA-TTAAGCCTAATATATCGATACATCACCAAAATGTATCG
* * * *
3346419 ATACATT-AGCCTAATATATCGATGCATCACTAATATGTATTG
1 ATACATTAAGCCTAATATATCGATACATCACCAAAATGTATCG
3346461 ATACAT
1 ATACAT
3346467 CATGTTGTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 35 0.83
43 2 0.05
44 5 0.12
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (43 bp):
ATACATTAAGCCTAATATATCGATACATCACCAAAATGTATCG
Found at i:3349918 original size:13 final size:13
Alignment explanation
Indices: 3349900--3349925 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3349890 CAATTTTTTG
3349900 TGTATCGATACAT
1 TGTATCGATACAT
3349913 TGTATCGATACAT
1 TGTATCGATACAT
3349926 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3352302 original size:21 final size:21
Alignment explanation
Indices: 3352278--3352324 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3352268 TTTAATGCTG
3352278 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
3352298 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
3352319 ATTTTG
1 ATTTTG
3352325 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:3352463 original size:13 final size:13
Alignment explanation
Indices: 3352445--3352483 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3352435 ATAATCACCC
*
3352445 TGTATCGATACAG
1 TGTATCGATACAA
3352458 TGTATCGATACAA
1 TGTATCGATACAA
3352471 TGTATCGATACAA
1 TGTATCGATACAA
3352484 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3352494 original size:20 final size:20
Alignment explanation
Indices: 3352469--3352507 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3352459 GTATCGATAC
3352469 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
3352489 AATGTATCGATACATAGAA
1 AATGTATCGATACAAAGAA
3352508 TTTCCAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.23
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:3352567 original size:13 final size:13
Alignment explanation
Indices: 3352551--3352576 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3352541 TATTAACAGC
3352551 ATCCTACGAACCT
1 ATCCTACGAACCT
3352564 ATCCTACGAACCT
1 ATCCTACGAACCT
3352577 TAACTTACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.38, G:0.08, T:0.23
Consensus pattern (13 bp):
ATCCTACGAACCT
Done.