Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014743.1 Kokia drynarioides strain JFW-HI SEQ_129782, whole genome shotgun sequence
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: 141020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 193 characters in sequence are not A, C, G, or T
Found at i:5102 original size:23 final size:23
Alignment explanation
Indices: 5076--5171 Score: 117
Period size: 23 Copynumber: 4.2 Consensus size: 23
5066 ACATTAGCGC
5076 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
5099 GCTCTCT-ATTTAGCAC-GTCTCGT
1 GCTCTCTGA-TTAGCACTGTGT-GT
*
5122 GCTCTTTGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
5145 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
5168 GCTC
1 GCTC
5172 AGTACTTTGT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
22 4 0.06
23 56 0.89
24 3 0.05
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:5170 original size:46 final size:46
Alignment explanation
Indices: 5076--5235 Score: 126
Period size: 46 Copynumber: 3.7 Consensus size: 46
5066 ACATTAGCGC
* * *
5076 GCTCTCTGATTAGCACTGT-GTGTGCTCTCT-ATTTAGCACGTCT-CGT
1 GCTCTCTGATTAGCACT-TCGTGTACTCTCTGA-TTAGCAC-TTTGTGT
* *
5122 GCTCTTTGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTCGTGTACTCTCTGATTAGCACTTTGTGT
* * *
5168 G--CTC-----AGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTCGTGTACTCTCTGATTAGCACTTTGTGT
* *
5207 GCTCTCTGTTTAGTACTTCG-GTACTCTCT
1 GCTCTCTGATTAGCACTTCGTGTACTCTCT
5236 ATTTGTTCCG
Statistics
Matches: 95, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
39 32 0.34
41 3 0.03
44 2 0.02
45 12 0.13
46 45 0.47
47 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTTCGTGTACTCTCTGATTAGCACTTTGTGT
Found at i:5189 original size:39 final size:39
Alignment explanation
Indices: 5136--5210 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
5126 TTTGATTAGC
*
5136 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
5175 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
5211 TCTGTTTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:5205 original size:23 final size:23
Alignment explanation
Indices: 5175--5235 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
5165 TGTGCTCAGT
5175 ACTTTGTGTACTCTCTGTTTAGC
1 ACTTTGTGTACTCTCTGTTTAGC
* *
5198 ACTTTGTGTGCTCTCTGTTTAGT
1 ACTTTGTGTACTCTCTGTTTAGC
*
5221 ACTTCG-GTACTCTCT
1 ACTTTGTGTACTCTCT
5236 ATTTGTTCCG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 8 0.24
23 26 0.76
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (23 bp):
ACTTTGTGTACTCTCTGTTTAGC
Found at i:6849 original size:23 final size:23
Alignment explanation
Indices: 6801--6949 Score: 151
Period size: 23 Copynumber: 6.5 Consensus size: 23
6791 TATACGAAAC
* * *
6801 AAACAGAGAGTA-TCAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
6823 -AACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
6845 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
6868 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
6891 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
6914 AATAACAGAGAGCACA-AGACGTGCT
1 -A-AACAGAGAGCACACA-AAGTGCT
*
6939 AACCAGAGAGC
1 AAACAGAGAGC
6950 GCGCTAGTGT
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
21 10 0.09
22 7 0.07
23 70 0.65
24 3 0.03
25 17 0.16
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:6889 original size:46 final size:46
Alignment explanation
Indices: 6801--6948 Score: 176
Period size: 46 Copynumber: 3.2 Consensus size: 46
6791 TATACGAAAC
* *
6801 AAACAGAGAGTA-TCAAAGTACTAA-CAGAGAGCACACACAGTGCT
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
6845 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
* * * * *
6891 AATCAGAGAGCACACACAGTGCTAATAACAGAGAGCACA-AGACGTGCT
1 AAACAGAGAGTACACAAAGTACTAAT--CAGAGAGCACACA-AAGTGCT
*
6939 AACCAGAGAG
1 AAACAGAGAG
6949 CGCGCTAGTG
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
44 12 0.13
45 11 0.12
46 41 0.45
47 1 0.01
48 26 0.29
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (46 bp):
AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
Found at i:14195 original size:32 final size:32
Alignment explanation
Indices: 14158--14223 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
14148 GCCTAAGTAA
14158 TTCTACTGGACAAGCTTCATCTTACAATATTC
1 TTCTACTGGACAAGCTTCATCTTACAATATTC
14190 TTCTACTGGACAAGCTTCATCTTACAATATTC
1 TTCTACTGGACAAGCTTCATCTTACAATATTC
14222 TT
1 TT
14224 TCTTTTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.39
Consensus pattern (32 bp):
TTCTACTGGACAAGCTTCATCTTACAATATTC
Found at i:21560 original size:23 final size:23
Alignment explanation
Indices: 21534--21629 Score: 117
Period size: 23 Copynumber: 4.2 Consensus size: 23
21524 ACATTAGCGC
21534 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
21557 GCTCTCT-ATTTAGCAC-GTCTCGT
1 GCTCTCTGA-TTAGCACTGTGT-GT
*
21580 GCTCTTTGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
21603 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
21626 GCTC
1 GCTC
21630 AGTACTTTGT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
22 4 0.06
23 56 0.89
24 3 0.05
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:21628 original size:46 final size:46
Alignment explanation
Indices: 21534--21693 Score: 126
Period size: 46 Copynumber: 3.7 Consensus size: 46
21524 ACATTAGCGC
* * *
21534 GCTCTCTGATTAGCACTGT-GTGTGCTCTCT-ATTTAGCACGTCT-CGT
1 GCTCTCTGATTAGCACT-TCGTGTACTCTCTGA-TTAGCAC-TTTGTGT
* *
21580 GCTCTTTGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTCGTGTACTCTCTGATTAGCACTTTGTGT
* * *
21626 G--CTC-----AGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTCGTGTACTCTCTGATTAGCACTTTGTGT
* *
21665 GCTCTCTGTTTAGTACTTCG-GTACTCTCT
1 GCTCTCTGATTAGCACTTCGTGTACTCTCT
21694 ATTTGTTCCG
Statistics
Matches: 95, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
39 32 0.34
41 3 0.03
44 2 0.02
45 12 0.13
46 45 0.47
47 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTTCGTGTACTCTCTGATTAGCACTTTGTGT
Found at i:21647 original size:39 final size:39
Alignment explanation
Indices: 21594--21668 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
21584 TTTGATTAGC
*
21594 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
21633 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
21669 TCTGTTTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:21663 original size:23 final size:23
Alignment explanation
Indices: 21633--21693 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
21623 TGTGCTCAGT
21633 ACTTTGTGTACTCTCTGTTTAGC
1 ACTTTGTGTACTCTCTGTTTAGC
* *
21656 ACTTTGTGTGCTCTCTGTTTAGT
1 ACTTTGTGTACTCTCTGTTTAGC
*
21679 ACTTCG-GTACTCTCT
1 ACTTTGTGTACTCTCT
21694 ATTTGTTCCG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 8 0.24
23 26 0.76
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (23 bp):
ACTTTGTGTACTCTCTGTTTAGC
Found at i:23307 original size:23 final size:23
Alignment explanation
Indices: 23259--23407 Score: 151
Period size: 23 Copynumber: 6.5 Consensus size: 23
23249 TATACGAAAC
* * *
23259 AAACAGAGAGTA-TCAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
23281 -AACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
23303 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
23326 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
23349 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
23372 AATAACAGAGAGCACA-AGACGTGCT
1 -A-AACAGAGAGCACACA-AAGTGCT
*
23397 AACCAGAGAGC
1 AAACAGAGAGC
23408 GCGCTAGTGT
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
21 10 0.09
22 7 0.07
23 70 0.65
24 3 0.03
25 17 0.16
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:23347 original size:46 final size:46
Alignment explanation
Indices: 23259--23406 Score: 176
Period size: 46 Copynumber: 3.2 Consensus size: 46
23249 TATACGAAAC
* *
23259 AAACAGAGAGTA-TCAAAGTACTAA-CAGAGAGCACACACAGTGCT
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
23303 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
* * * * *
23349 AATCAGAGAGCACACACAGTGCTAATAACAGAGAGCACA-AGACGTGCT
1 AAACAGAGAGTACACAAAGTACTAAT--CAGAGAGCACACA-AAGTGCT
*
23397 AACCAGAGAG
1 AAACAGAGAG
23407 CGCGCTAGTG
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
44 12 0.13
45 11 0.12
46 41 0.45
47 1 0.01
48 26 0.29
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (46 bp):
AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
Found at i:30653 original size:32 final size:32
Alignment explanation
Indices: 30616--30681 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
30606 GCCTAAGTAA
30616 TTCTACTGGACAAGCTTCATCTTACAATATTC
1 TTCTACTGGACAAGCTTCATCTTACAATATTC
30648 TTCTACTGGACAAGCTTCATCTTACAATATTC
1 TTCTACTGGACAAGCTTCATCTTACAATATTC
30680 TT
1 TT
30682 TCTTTTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.39
Consensus pattern (32 bp):
TTCTACTGGACAAGCTTCATCTTACAATATTC
Found at i:34108 original size:56 final size:56
Alignment explanation
Indices: 34022--34135 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
34012 TTATACAGAG
34022 GTTGAGTTGCTTCAGATATTATTGGTTTAAATTTCAAGTGATTTGTGTGGCATTGT
1 GTTGAGTTGCTTCAGATATTATTGGTTTAAATTTCAAGTGATTTGTGTGGCATTGT
34078 GTTGAGTTGCTTCAGATATTATTGGTTTAAATTTCAAGTGATTTGTGTGGCATTGT
1 GTTGAGTTGCTTCAGATATTATTGGTTTAAATTTCAAGTGATTTGTGTGGCATTGT
34134 GT
1 GT
34136 AACTATTATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (56 bp):
GTTGAGTTGCTTCAGATATTATTGGTTTAAATTTCAAGTGATTTGTGTGGCATTGT
Found at i:35653 original size:40 final size:41
Alignment explanation
Indices: 35609--35689 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 41
35599 TGTTCCAAAA
35609 GTACATAGCATATTGACATGTTA-GTTTGCAATTTCTAAAT
1 GTACATAGCATATTGACATGTTATGTTTGCAATTTCTAAAT
* *
35649 GTACATGGCATATTGACATGTTATTTTTGCAATTTCTAAAT
1 GTACATAGCATATTGACATGTTATGTTTGCAATTTCTAAAT
35690 TGCAGGATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 22 0.58
41 16 0.42
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (41 bp):
GTACATAGCATATTGACATGTTATGTTTGCAATTTCTAAAT
Found at i:40161 original size:3 final size:3
Alignment explanation
Indices: 40155--40189 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
40145 AGAAGAAGAA
40155 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
40190 GGGGCTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:41328 original size:19 final size:18
Alignment explanation
Indices: 41299--41335 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
41289 GGAGAATTTT
41299 CTTTTTCTTTTACCTTTG
1 CTTTTTCTTTTACCTTTG
*
41317 CTTTTTCGTTTTTCCTTTG
1 CTTTTTC-TTTTACCTTTG
41336 TGGATGGCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.03, C:0.22, G:0.08, T:0.68
Consensus pattern (18 bp):
CTTTTTCTTTTACCTTTG
Found at i:43011 original size:12 final size:10
Alignment explanation
Indices: 42985--43031 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
42975 ATATAATTAA
42985 AATATTTTTT
1 AATATTTTTT
42995 AATATTGTTTT
1 AATATT-TTTT
43006 -ATATATTTTT
1 AATAT-TTTTT
43016 AA-ATTTTTT
1 AATATTTTTT
43025 AA-ATTTT
1 AATATTTT
43032 AAAAAATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 12 0.35
10 16 0.47
11 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (10 bp):
AATATTTTTT
Found at i:43023 original size:9 final size:9
Alignment explanation
Indices: 42988--43031 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
42978 TAATTAAAAT
42988 ATTTTTTAA
1 ATTTTTTAA
*
42997 TATTGTTTTAT
1 -ATT-TTTTAA
43008 ATATTTTTAA
1 AT-TTTTTAA
43018 ATTTTTTAA
1 ATTTTTTAA
43027 ATTTT
1 ATTTT
43032 AAAAAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 12 0.40
10 12 0.40
11 6 0.20
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:46340 original size:12 final size:12
Alignment explanation
Indices: 46325--46354 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
46315 TTAAAATGCA
46325 AAAAAAAAAAAG
1 AAAAAAAAAAAG
46337 AAAAAAAAAAAG
1 AAAAAAAAAAAG
46349 AAAAAA
1 AAAAAA
46355 GGGAAAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:59925 original size:31 final size:31
Alignment explanation
Indices: 59890--60030 Score: 121
Period size: 31 Copynumber: 4.5 Consensus size: 31
59880 TTAATATAAC
* *
59890 ATTTGATACCTAAACTTGATACTTTTTTCTA
1 ATTTGGTACCTAAACTTGACACTTTTTTCTA
* *
59921 ATTTGGTACCTAAAC---A-ATTTTTTTAGTCCA
1 ATTTGGTACCTAAACTTGACA-CTTTTT--TCTA
* *
59951 ATTTGGTA-CTCAAACTTGACACGTTTTCCTA
1 ATTTGGTACCT-AAACTTGACACTTTTTTCTA
*
59982 ATTTGGTACCTAAACTTGACACTTTTTTTTTA
1 ATTTGGTACCTAAACTTGACAC-TTTTTTCTA
* *
60014 AGTTGGTACTTAAACTT
1 ATTTGGTACCTAAACTT
60031 TTTGGAGTCC
Statistics
Matches: 88, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
27 1 0.01
28 6 0.07
29 2 0.02
30 15 0.17
31 35 0.40
32 23 0.26
33 5 0.06
34 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.45
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTTCTA
Found at i:60028 original size:32 final size:31
Alignment explanation
Indices: 59953--60030 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 31
59943 TTAGTCCAAT
* *
59953 TTGGTACTCAAACTTGACACGTTTTCCTAAT
1 TTGGTACTTAAACTTGACACGTTTTCCTAAG
* * **
59984 TTGGTACCTAAACTTGACACTTTTTTTTTAAG
1 TTGGTACTTAAACTTGACAC-GTTTTCCTAAG
60016 TTGGTACTTAAACTT
1 TTGGTACTTAAACTT
60031 TTTGGAGTCC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 18 0.46
32 21 0.54
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.44
Consensus pattern (31 bp):
TTGGTACTTAAACTTGACACGTTTTCCTAAG
Found at i:60069 original size:91 final size:91
Alignment explanation
Indices: 59890--60081 Score: 235
Period size: 91 Copynumber: 2.1 Consensus size: 91
59880 TTAATATAAC
* * * **
59890 ATTTGATACCTAAACTTGATACTTTTTTCTAATTTGGTACCTAAACAATTTTTTTAGTCCAATTT
1 ATTTGGTACCTAAACTTGACACTTTTTTCTAAGTTGGTACCTAAAC-ATTTTTGGAGTCCAATTT
* *
59955 GGTACTCAAACTTGACACGTTTTCCTA
65 GATACTCAAACTAGACACGTTTTCCTA
* *
59982 ATTTGGTACCTAAACTTGACACTTTTTTTTTAAGTTGGTACTTAAAC-TTTTTGGAGTCCAATTT
1 ATTTGGTACCTAAACTTGACAC-TTTTTTCTAAGTTGGTACCTAAACATTTTTGGAGTCCAATTT
* * *
60046 GATAC-CTGAACTAGACTCTTTTTCCTA
65 GATACTC-AAACTAGACACGTTTTCCTA
60073 ATTTGGTAC
1 ATTTGGTAC
60082 ATAATTTTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
90 1 0.01
91 44 0.51
92 20 0.23
93 21 0.24
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.44
Consensus pattern (91 bp):
ATTTGGTACCTAAACTTGACACTTTTTTCTAAGTTGGTACCTAAACATTTTTGGAGTCCAATTTG
ATACTCAAACTAGACACGTTTTCCTA
Found at i:60336 original size:31 final size:32
Alignment explanation
Indices: 60257--60336 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
60247 TCTAAAAAAG
*
60257 AGTTTAGGTGCTAAATTAAGAAAAAAATGTCA
1 AGTTTAGGTACTAAATTAAGAAAAAAATGTCA
* * *
60289 AGTTTAAGTA-TCAAATT-AGGAAAAAGTGTCA
1 AGTTTAGGTACT-AAATTAAGAAAAAAATGTCA
*
60320 AGTTCAGGTACTAAATT
1 AGTTTAGGTACTAAATT
60337 GGGTCAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
31 26 0.65
32 14 0.35
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (32 bp):
AGTTTAGGTACTAAATTAAGAAAAAAATGTCA
Found at i:64123 original size:15 final size:15
Alignment explanation
Indices: 64089--64139 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
64079 TGTAAAGTAA
*
64089 ATTCCTCAGTAATCAC
1 ATTCCT-AGCAATCAC
*
64105 ATTCCTAGCAATCAT
1 ATTCCTAGCAATCAC
* *
64120 ATTCCAAGGAATCAC
1 ATTCCTAGCAATCAC
64135 ATTCC
1 ATTCC
64140 ATTGGAATCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 24 0.80
16 6 0.20
ACGTcount: A:0.33, C:0.29, G:0.08, T:0.29
Consensus pattern (15 bp):
ATTCCTAGCAATCAC
Found at i:65906 original size:58 final size:59
Alignment explanation
Indices: 65815--65979 Score: 149
Period size: 59 Copynumber: 2.8 Consensus size: 59
65805 ACTAATTTGG
* * * * * * **
65815 ACAAAAAAAAA-TCAATCTCTAAATGTAGAAACAATTACTAAATTCAGA-GATTAACTTGG
1 ACAAAAAAAAATTCAAACCCT-AATATAAAAACAATTA-TAAATTCAGACAATTAAATTAA
* *
65874 AC-AAAAAAAATTCAAACCCTATTATAACAACAATTATCAAATTCA-ACAATTAAATTAA
1 ACAAAAAAAAATTCAAACCCTAATATAAAAACAATTAT-AAATTCAGACAATTAAATTAA
** *
65932 ACAAAAAAAAATTCAAACTTTAATATAAAAATAATTATTAAATTCAGA
1 ACAAAAAAAAATTCAAACCCTAATATAAAAACAATTA-TAAATTCAGA
65980 TCATAAAAAA
Statistics
Matches: 85, Mismatches: 15, Indels: 11
0.77 0.14 0.10
Matches are distributed among these distances:
57 2 0.02
58 36 0.42
59 45 0.53
60 2 0.02
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.27
Consensus pattern (59 bp):
ACAAAAAAAAATTCAAACCCTAATATAAAAACAATTATAAATTCAGACAATTAAATTAA
Found at i:75529 original size:15 final size:14
Alignment explanation
Indices: 75482--75529 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
75472 GAATTTTATA
75482 AATTAAAAAATAATT
1 AATT-AAAAATAATT
*
75497 ATATTAAAAATAAAT
1 A-ATTAAAAATAATT
*
75512 AATGTAAAAATATTT
1 AAT-TAAAAATAATT
75527 AAT
1 AAT
75530 AAGAATATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 2 0.07
15 23 0.82
16 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
AATTAAAAATAATT
Found at i:84304 original size:21 final size:20
Alignment explanation
Indices: 84246--84305 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 20
84236 CTTTATAATT
* *
84246 TATAAAAATTTAAATTAATAA
1 TATAAAAATTT-ATTTAAAAA
*
84267 TGATAAAACATCT-TTTAAAAA
1 T-ATAAAA-ATTTATTTAAAAA
84288 TATAAAAATTTGATTTAA
1 TATAAAAATTT-ATTTAA
84306 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
19 3 0.10
20 6 0.19
21 13 0.42
22 6 0.19
23 3 0.10
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
TATAAAAATTTATTTAAAAA
Found at i:87933 original size:20 final size:21
Alignment explanation
Indices: 87889--87933 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
87879 TCCAAATCCA
87889 TTTTTCTTCTTCTTCTTCTCC
1 TTTTTCTTCTTCTTCTTCTCC
*
87910 -TTTTCTTATTTCTT-TTC-CC
1 TTTTTCTT-CTTCTTCTTCTCC
87929 TTTTT
1 TTTTT
87934 TAATCCCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
19 2 0.10
20 14 0.67
21 5 0.24
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTCTTCTTCTTCTTCTCC
Found at i:88528 original size:17 final size:18
Alignment explanation
Indices: 88498--88531 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
88488 TCAGAAATAC
*
88498 TTTTGATATGAAAAGTAT
1 TTTTGATATAAAAAGTAT
88516 TTTTGA-ATAAAAAGTA
1 TTTTGATATAAAAAGTA
88532 ATGCTAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (18 bp):
TTTTGATATAAAAAGTAT
Found at i:91744 original size:11 final size:11
Alignment explanation
Indices: 91728--91772 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
91718 TAACCATTTA
91728 TAATAAAATAT
1 TAATAAAATAT
*
91739 TAATAACATATCT
1 TAATAA-A-ATAT
*
91752 TATTAAAATAT
1 TAATAAAATAT
91763 TAATAAAATA
1 TAATAAAATA
91773 ATTATTATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 18 0.64
12 2 0.07
13 8 0.29
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:93052 original size:18 final size:19
Alignment explanation
Indices: 93029--93071 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
93019 AATCATTAAA
*
93029 AAAAATCTATAAAA-TAGT
1 AAAAATATATAAAATTAGT
* *
93047 AAAAATATTTAAAATTATT
1 AAAAATATATAAAATTAGT
93066 AAAAAT
1 AAAAAT
93072 TTAAATAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAATATATAAAATTAGT
Found at i:93088 original size:37 final size:37
Alignment explanation
Indices: 93047--93125 Score: 92
Period size: 37 Copynumber: 2.1 Consensus size: 37
93037 ATAAAATAGT
*
93047 AAAAATATTTA-AAAT-TATTAAAAATT-TAAATAACTAA
1 AAAAATATATACAAATAT-TTAAAAATTATAAATAA--AA
*
93084 AAAAATGTATACAAATATTTAAAAATTATAAATAAAA
1 AAAAATATATACAAATATTTAAAAATTATAAATAAAA
93121 AAAAA
1 AAAAA
93126 CTCAAAATCC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
37 16 0.43
38 13 0.35
39 8 0.22
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (37 bp):
AAAAATATATACAAATATTTAAAAATTATAAATAAAA
Found at i:93284 original size:9 final size:9
Alignment explanation
Indices: 93270--93312 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
93260 AAATAACTGA
93270 AAAAATTTT
1 AAAAATTTT
*
93279 AAAAATTTA
1 AAAAATTTT
93288 AACAAATATTT
1 AA-AAAT-TTT
*
93299 AAAAATTAT
1 AAAAATTTT
93308 AAAAA
1 AAAAA
93313 AACCCAAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 17 0.59
10 8 0.28
11 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAAATTTT
Found at i:93301 original size:20 final size:20
Alignment explanation
Indices: 93272--93310 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
93262 ATAACTGAAA
93272 AAATTTTAAAAATT-TAAAC
1 AAATTTTAAAAATTATAAAC
93291 AAATATTTAAAAATTATAAA
1 AAAT-TTTAAAAATTATAAA
93311 AAAACCCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATTTTAAAAATTATAAAC
Found at i:93539 original size:188 final size:187
Alignment explanation
Indices: 93084--93627 Score: 768
Period size: 188 Copynumber: 2.9 Consensus size: 187
93074 AAATAACTAA
* * * *
93084 AAAAATGTATACAAATATTTAAAAATTATAAATAAAAAAAAACTCAAAATCCAAATCTAAAACTT
1 AAAAATGTAAACAAATATTTAAAAA-T-T--AT--AAAAAAACCCAAGATCCAAACCTAAAACTT
* * *
93149 GGCAAATTTTATTAAAATAGCTCAACAACTAAACAAAAATACACGGCCGCGTTTACAAGTAATTT
60 GGCAAATTTTATTGAAATAGCTCAACAACTAAACAAAAAT-CGCGTCCGCGTTTACAAGTAATTT
* * *
93214 CCCAATAATTATTAAAAAAAAAAAAAACAAAACA-CTTAGCAAATTTAAATAACTGAAAAAATTT
124 CCCAATAATTATT--AAACAAAAAAATCAAAACAGCTTAGCAAATTAAAATAACTGAAAAAATTT
93278 T
187 T
*
93279 AAAAATTTAAACAAATATTTAAAAATTATAAAAAAACCCAAGATCCAAACCTAAAACTTGGCAAA
1 AAAAATGTAAACAAATATTTAAAAATTATAAAAAAACCCAAGATCCAAACCTAAAACTTGGCAAA
* * *
93344 TTTTATTGAAATAGCTCAACAACTAAACAGAAATCTGCGTCTGCGTTTACAAGTAATTTCCCTAG
66 TTTTATTGAAATAGCTCAACAACTAAACAAAAATC-GCGTCCGCGTTTACAAGTAATTTCCC-AA
** *
93409 TAATTATTAAACAAAAAAATTTAAACAGCTTCGCAAATTAAAATAACTGAAAAAA-TTT
129 TAATTATTAAACAAAAAAATCAAAACAGCTTAGCAAATTAAAATAACTGAAAAAATTTT
* *
93467 AAAAATGTAAACAAATATTTAAAAATTATAGAAAAACCCAAGATCCAAGCCTAAAACTTGGCAAA
1 AAAAATGTAAACAAATATTTAAAAATTATAAAAAAACCCAAGATCCAAACCTAAAACTTGGCAAA
*
93532 TTTTATTGAAATAGCTCAATAACTAAACAAAAATCCGCGTCCGCGTTTACAAGTAATTTCCCCAA
66 TTTTATTGAAATAGCTCAACAACTAAACAAAAAT-CGCGTCCGCGTTTACAAGTAATTT-CCCAA
*
93597 TAATTATTAAACAAAAAAATCGAAACAGCTT
129 TAATTATTAAACAAAAAAATCAAAACAGCTT
93628 GGCCAATCCT
Statistics
Matches: 318, Mismatches: 26, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
188 165 0.52
189 117 0.37
190 9 0.03
191 2 0.01
193 1 0.00
194 1 0.00
195 23 0.07
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.26
Consensus pattern (187 bp):
AAAAATGTAAACAAATATTTAAAAATTATAAAAAAACCCAAGATCCAAACCTAAAACTTGGCAAA
TTTTATTGAAATAGCTCAACAACTAAACAAAAATCGCGTCCGCGTTTACAAGTAATTTCCCAATA
ATTATTAAACAAAAAAATCAAAACAGCTTAGCAAATTAAAATAACTGAAAAAATTTT
Found at i:97018 original size:74 final size:76
Alignment explanation
Indices: 96818--97043 Score: 411
Period size: 76 Copynumber: 3.0 Consensus size: 76
96808 AAACAAAGAG
96818 AACACAATTTAAAAAACATAACATGTCAGTACAATTTAAAATCCCTCTTTATATTTTTCGGTTTT
1 AACACAATTTAAAAAACATAACATGTCAGTACAATTTAAAATCCCTCTTTATATTTTTCGGTTTT
*
96883 AGGGTTTCGGT
66 AGGGTTTCAGT
96894 AACACAATTTAAAAAACATAACATGTCAGTACAATTTAAAATCCCTCTTTATATTTTTCGGTTTT
1 AACACAATTTAAAAAACATAACATGTCAGTACAATTTAAAATCCCTCTTTATATTTTTCGGTTTT
96959 AGGGTTTCAGT
66 AGGGTTTCAGT
**
96970 -A-ACAATTTAAAAAACATAACATGTCAGTACAATTTAAAATCCCTCTTTATATTTTTTAGTTTT
1 AACACAATTTAAAAAACATAACATGTCAGTACAATTTAAAATCCCTCTTTATATTTTTCGGTTTT
97033 AGGGTTTCAGT
66 AGGGTTTCAGT
97044 TTTAGGGTTT
Statistics
Matches: 147, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
74 71 0.48
75 1 0.01
76 75 0.51
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (76 bp):
AACACAATTTAAAAAACATAACATGTCAGTACAATTTAAAATCCCTCTTTATATTTTTCGGTTTT
AGGGTTTCAGT
Found at i:97046 original size:14 final size:14
Alignment explanation
Indices: 97027--97092 Score: 91
Period size: 14 Copynumber: 4.9 Consensus size: 14
97017 TATATTTTTT
97027 AGTTTTAGGGTTTC
1 AGTTTTAGGGTTTC
97041 AGTTTTAGGGTTTC
1 AGTTTTAGGGTTTC
*
97055 AG-TTCAGGGTTT-
1 AGTTTTAGGGTTTC
*
97067 TGTTTTAGGGTTTC
1 AGTTTTAGGGTTTC
*
97081 ATTTTTAGGGTT
1 AGTTTTAGGGTT
97093 ATGGTTTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
12 1 0.02
13 18 0.40
14 26 0.58
ACGTcount: A:0.14, C:0.06, G:0.29, T:0.52
Consensus pattern (14 bp):
AGTTTTAGGGTTTC
Found at i:97106 original size:20 final size:20
Alignment explanation
Indices: 97083--97299 Score: 146
Period size: 20 Copynumber: 11.2 Consensus size: 20
97073 AGGGTTTCAT
* **
97083 TTTTAGGGTTATGGTTTTAA
1 TTTTAGGGTTAGGGTTTTGG
** *
97103 TTTTATTGTTAGTGTTTT-G
1 TTTTAGGGTTAGGGTTTTGG
*
97122 ATTTAGGGTTAGGGTTTT-G
1 TTTTAGGGTTAGGGTTTTGG
*
97141 ATTTAGGGTTAGGGTTTTGG
1 TTTTAGGGTTAGGGTTTTGG
* *
97161 TGTTATGGTTAGGGTTTTGG
1 TTTTAGGGTTAGGGTTTTGG
**
97181 TTTTAGGGTTAATGTTTTGG
1 TTTTAGGGTTAGGGTTTTGG
*
97201 TTTTAAGGTTA--G----GG
1 TTTTAGGGTTAGGGTTTTGG
** * **
97215 TTTTAGGGCCATGGTTTTAA
1 TTTTAGGGTTAGGGTTTTGG
* * * *
97235 TTTTAGGGTCAAGGTTTCAGT
1 TTTTAGGGTTAGGGTTT-TGG
*
97256 TTTTAGGG-TAGGGTTTTAG
1 TTTTAGGGTTAGGGTTTTGG
*
97275 TTTTAGGGTTAGGTTTTTGG
1 TTTTAGGGTTAGGGTTTTGG
97295 TTTTA
1 TTTTA
97300 AGATTATGGT
Statistics
Matches: 154, Mismatches: 34, Indels: 18
0.75 0.17 0.09
Matches are distributed among these distances:
14 10 0.06
16 1 0.01
18 1 0.01
19 41 0.27
20 93 0.60
21 8 0.05
ACGTcount: A:0.16, C:0.02, G:0.31, T:0.51
Consensus pattern (20 bp):
TTTTAGGGTTAGGGTTTTGG
Found at i:97186 original size:14 final size:14
Alignment explanation
Indices: 97142--97191 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
97132 AGGGTTTTGA
*
97142 TTTAGGGTTAGGGT
1 TTTAGGGTTATGGT
97156 TTT-GGTGTTATGG-
1 TTTAGG-GTTATGGT
*
97169 -TTAGGGTTTTGGT
1 TTTAGGGTTATGGT
97182 TTTAGGGTTA
1 TTTAGGGTTA
97192 ATGTTTTGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
12 8 0.28
13 4 0.14
14 17 0.59
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (14 bp):
TTTAGGGTTATGGT
Found at i:97378 original size:21 final size:20
Alignment explanation
Indices: 97341--97397 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
97331 AAGGTAAATG
**
97341 TTTAGGGTTAGCATTTCAAT
1 TTTAGGGTTAGGGTTTCAAT
97361 TTTAGGGTTTAGGGTTTCAAT
1 TTTAGGG-TTAGGGTTTCAAT
*
97382 TTTAAGGTTAGGGTTT
1 TTTAGGGTTAGGGTTT
97398 AAGGTTTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.47
Consensus pattern (20 bp):
TTTAGGGTTAGGGTTTCAAT
Found at i:97383 original size:27 final size:26
Alignment explanation
Indices: 97340--97404 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
97330 TAAGGTAAAT
* **
97340 GTTTAGGGTTAGCATTTCAATTTTAGG
1 GTTTAGGGTT-TCATTTCAAGGTTAGG
*
97367 GTTTAGGGTTTCAATTTTAAGGTTAGG
1 GTTTAGGGTTTC-ATTTCAAGGTTAGG
*
97394 GTTTAAGGTTT
1 GTTTAGGGTTT
97405 ATGGTTTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 1 0.03
27 31 0.97
ACGTcount: A:0.22, C:0.05, G:0.28, T:0.46
Consensus pattern (26 bp):
GTTTAGGGTTTCATTTCAAGGTTAGG
Found at i:97405 original size:20 final size:20
Alignment explanation
Indices: 97340--97410 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
97330 TAAGGTAAAT
* **
97340 GTTTAGGGTTAGCATTTCAA
1 GTTTAAGGTTAGGGTTTCAA
* *
97360 TTTTAGGGTTTAGGGTTTCAA
1 GTTTAAGG-TTAGGGTTTCAA
*
97381 TTTTAAGGTTAGGGTTT-AA
1 GTTTAAGGTTAGGGTTTCAA
*
97400 GGTTTATGGTT
1 -GTTTAAGGTT
97411 TTTGTTATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
19 2 0.05
20 24 0.56
21 17 0.40
ACGTcount: A:0.21, C:0.04, G:0.28, T:0.46
Consensus pattern (20 bp):
GTTTAAGGTTAGGGTTTCAA
Found at i:97482 original size:20 final size:20
Alignment explanation
Indices: 97426--97475 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
97416 TATAATTTCT
*
97426 ATTTTAGGGTTAGGGTTTTG
1 ATTTTAGGGTTAGGGTTATG
* *
97446 GTTTTAGAGTTAGGGTTATG
1 ATTTTAGGGTTAGGGTTATG
97466 ATTTTAGGGT
1 ATTTTAGGGT
97476 CAAGGTTTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (20 bp):
ATTTTAGGGTTAGGGTTATG
Found at i:97516 original size:14 final size:13
Alignment explanation
Indices: 97488--97539 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
97478 AGGTTTCAAT
**
97488 TTTTAGGTTAGGA
1 TTTTAGGTTTTGA
97501 TTTTAGTGTTTTGA
1 TTTTAG-GTTTTGA
*
97515 TTTTAGGTTTTTGG
1 TTTTAGG-TTTTGA
97529 TTTTATGGTTT
1 TTTTA-GGTTT
97540 CAATATTAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 7 0.21
14 24 0.73
15 2 0.06
ACGTcount: A:0.13, C:0.00, G:0.25, T:0.62
Consensus pattern (13 bp):
TTTTAGGTTTTGA
Found at i:97624 original size:14 final size:14
Alignment explanation
Indices: 97605--97631 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
97595 GTGTTTTATT
97605 TTTTAGGGTTTTGG
1 TTTTAGGGTTTTGG
97619 TTTTAGGGTTTTG
1 TTTTAGGGTTTTG
97632 ATTTAAGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.00, G:0.33, T:0.59
Consensus pattern (14 bp):
TTTTAGGGTTTTGG
Found at i:97782 original size:20 final size:21
Alignment explanation
Indices: 97759--97802 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
97749 AGGTTTAGAG
*
97759 TTTAAGG-TTTTAGTTTCGGT
1 TTTAAGGACTTTAGTTTCGGT
*
97779 TTT-AGGACTTTGGTTTCGGT
1 TTTAAGGACTTTAGTTTCGGT
97799 TTTA
1 TTTA
97803 GTGTCAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.14, C:0.07, G:0.25, T:0.55
Consensus pattern (21 bp):
TTTAAGGACTTTAGTTTCGGT
Found at i:101805 original size:15 final size:14
Alignment explanation
Indices: 101787--101817 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
101777 TAAAAAATGT
*
101787 AAAATAGAAAAAAA
1 AAAAAAGAAAAAAA
101801 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
101815 AAA
1 AAA
101818 GAGAACATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.06, T:0.03
Consensus pattern (14 bp):
AAAAAAGAAAAAAA
Found at i:102794 original size:15 final size:15
Alignment explanation
Indices: 102769--102803 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
102759 TATATTTTCA
102769 ATTTATTAAAATTAAT
1 ATTT-TTAAAATTAAT
102785 ATTTTTAAAATTAAT
1 ATTTTTAAAATTAAT
102800 -TTTT
1 ATTTT
102804 ATATAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 11 0.58
16 4 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTTAAAATTAAT
Found at i:103801 original size:15 final size:15
Alignment explanation
Indices: 103781--103809 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
103771 AGACTACAAA
103781 TGCAAAAACAGAAAT
1 TGCAAAAACAGAAAT
103796 TGCAAAAACAGAAA
1 TGCAAAAACAGAAA
103810 ACATGACCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.10
Consensus pattern (15 bp):
TGCAAAAACAGAAAT
Found at i:104627 original size:16 final size:16
Alignment explanation
Indices: 104608--104638 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
104598 ATCTAAACAT
*
104608 AAAAAAATATTATTTA
1 AAAAAAAAATTATTTA
104624 AAAAAAAAATTATTT
1 AAAAAAAAATTATTT
104639 TTCAAAAACT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAAAAAATTATTTA
Found at i:104632 original size:19 final size:19
Alignment explanation
Indices: 104608--104646 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
104598 ATCTAAACAT
104608 AAAAAAATATTATTT-AAAA
1 AAAAAAATATT-TTTCAAAA
*
104627 AAAAAATTATTTTTCAAAA
1 AAAAAAATATTTTTCAAAA
104646 A
1 A
104647 CTACTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAAAATATTTTTCAAAA
Found at i:104645 original size:14 final size:14
Alignment explanation
Indices: 104628--104661 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
104618 TATTTAAAAA
*
104628 AAAAATTATTTTTC
1 AAAAATTACTTTTC
*
104642 AAAAACTACTTTTC
1 AAAAATTACTTTTC
104656 AAAAAT
1 AAAAAT
104662 ACAAAATCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAAATTACTTTTC
Found at i:105284 original size:13 final size:13
Alignment explanation
Indices: 105253--105277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
105243 AAAAATATAC
105253 ACACAAAAAAAAA
1 ACACAAAAAAAAA
105266 ACACAAAAAAAA
1 ACACAAAAAAAA
105278 TCCACAATAA
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:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (13 bp):
ACACAAAAAAAAA
Found at i:122634 original size:24 final size:24
Alignment explanation
Indices: 122605--122658 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
122595 TCTTTCTAAA
*
122605 ATATTTAATATTTATTAATATAAT
1 ATATTTAACATTTATTAATATAAT
* *
122629 ATATTTTACATTTATTAGTATAAT
1 ATATTTAACATTTATTAATATAAT
*
122653 TTATTT
1 ATATTT
122659 GACTTGCGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
ATATTTAACATTTATTAATATAAT
Found at i:134870 original size:14 final size:14
Alignment explanation
Indices: 134791--134871 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
134781 AAACTTGCAC
**
134791 CTTTAAATTTTGGA
1 CTTTAAATTTTAAA
* * *
134805 CTTCAAATTCTATA
1 CTTTAAATTTTAAA
** *
134819 CTTTAAATTCCAAC
1 CTTTAAATTTTAAA
*
134833 CTCTTAAATCTTAAA
1 CT-TTAAATTTTAAA
134848 CTTTAAATTTTAAA
1 CTTTAAATTTTAAA
*
134862 CTTTTAATTT
1 CTTTAAATTT
134872 AGGGTACAAG
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
14 42 0.81
15 10 0.19
ACGTcount: A:0.35, C:0.16, G:0.02, T:0.47
Consensus pattern (14 bp):
CTTTAAATTTTAAA
Found at i:135655 original size:2 final size:2
Alignment explanation
Indices: 135648--135682 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
135638 ATTTTCTGTA
135648 CT CT CT 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 CT CT CT C
135683 GCAATTATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:140963 original size:2 final size:2
Alignment explanation
Indices: 140956--140986 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
140946 ACAATCACTT
140956 TA TA TA 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 TA TA TA T
140987 GATCTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.