Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011830.1 Kokia drynarioides strain JFW-HI SEQ_126826, 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: 140540
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:120 original size:9 final size:9
Alignment explanation
Indices: 108--175 Score: 58
Period size: 9 Copynumber: 8.1 Consensus size: 9
98 AAACACATTA
108 CCTTTCTTT
1 CCTTTCTTT
117 CC-TTC-TT
1 CCTTTCTTT
124 -CTTTCTTT
1 CCTTTCTTT
* *
132 CCTCTCATT
1 CCTTTCTTT
141 -C-TTCTTT
1 CCTTTCTTT
*
148 -CTTTCCTCT
1 CCTTT-CTTT
157 CCTTTCTTT
1 CCTTTCTTT
166 CCTTTCTTT
1 CCTTTCTTT
175 C
1 C
176 TTTACCGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
6 1 0.02
7 10 0.21
8 8 0.17
9 24 0.51
10 4 0.09
ACGTcount: A:0.01, C:0.37, G:0.00, T:0.62
Consensus pattern (9 bp):
CCTTTCTTT
Found at i:129 original size:4 final size:4
Alignment explanation
Indices: 109--178 Score: 54
Period size: 4 Copynumber: 17.0 Consensus size: 4
99 AACACATTAC
* * * *
109 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CATT C-TT CTTT CTTT CCTCTC
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT -CT-TT
158 CTTT CTTT CCTTT CTTT CTTT
1 CTTT CTTT -CTTT CTTT CTTT
179 ACCGTTTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
3 6 0.11
4 36 0.67
5 11 0.20
6 1 0.02
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.64
Consensus pattern (4 bp):
CTTT
Found at i:144 original size:20 final size:20
Alignment explanation
Indices: 119--157 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
109 CTTTCTTTCC
119 TTCTTCTTTCTTTCCTCTCA
1 TTCTTCTTTCTTTCCTCTCA
139 TTCTTCTTTCTTTCCTCTC
1 TTCTTCTTTCTTTCCTCTC
158 CTTTCTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.03, C:0.36, G:0.00, T:0.62
Consensus pattern (20 bp):
TTCTTCTTTCTTTCCTCTCA
Found at i:163 original size:14 final size:13
Alignment explanation
Indices: 108--178 Score: 69
Period size: 11 Copynumber: 5.7 Consensus size: 13
98 AAACACATTA
108 CCTTTCTTTCCTT
1 CCTTTCTTTCCTT
*
121 -C-TTCTTTCTTT
1 CCTTTCTTTCCTT
* *
132 CCTCTCATT-CTT
1 CCTTTCTTTCCTT
144 -CTTTCTTTCCTCT
1 CCTTTCTTTCCT-T
157 CCTTTCTTTCCTT
1 CCTTTCTTTCCTT
*
170 TCTTTCTTT
1 CCTTTCTTT
179 ACCGTTTATT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
11 15 0.33
12 6 0.13
13 14 0.30
14 11 0.24
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.63
Consensus pattern (13 bp):
CCTTTCTTTCCTT
Found at i:167 original size:34 final size:35
Alignment explanation
Indices: 109--177 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 35
99 AACACATTAC
*
109 CTTTCTTTCCTTCTTCTTTCTTTCCTCTCATTCTT
1 CTTTCTTTCCTTCTCCTTTCTTTCCTCTCATTCTT
* *
144 CTTTCTTTCC-TCTCCTTTCTTTCCTTTCTTTCTT
1 CTTTCTTTCCTTCTCCTTTCTTTCCTCTCATTCTT
178 TACCGTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 21 0.68
35 10 0.32
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (35 bp):
CTTTCTTTCCTTCTCCTTTCTTTCCTCTCATTCTT
Found at i:1615 original size:20 final size:21
Alignment explanation
Indices: 1590--1631 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1580 GTGTTTTGGT
1590 AAAAAA-GAAAAGGAGAGAAA
1 AAAAAAGGAAAAGGAGAGAAA
1610 AAAAAAGGGAAAAGGAGAGAAA
1 AAAAAA-GGAAAAGGAGAGAAA
1632 GAGGGAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (21 bp):
AAAAAAGGAAAAGGAGAGAAA
Found at i:2832 original size:14 final size:14
Alignment explanation
Indices: 2813--2841 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2803 TGTAGTCAAG
2813 TGGTTTTGTTGTAC
1 TGGTTTTGTTGTAC
2827 TGGTTTTGTTGTAC
1 TGGTTTTGTTGTAC
2841 T
1 T
2842 TTTACCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.28, T:0.59
Consensus pattern (14 bp):
TGGTTTTGTTGTAC
Found at i:2901 original size:16 final size:17
Alignment explanation
Indices: 2876--2908 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2866 AAAACTTTAT
*
2876 TTTCATATTTTTTTACA
1 TTTCATATTTTATTACA
2893 TTTCA-ATTTTATTACA
1 TTTCATATTTTATTACA
2909 AATTGTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTCATATTTTATTACA
Found at i:3981 original size:20 final size:20
Alignment explanation
Indices: 3956--3993 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3946 CGACACTTTA
3956 TGGTGTGTAGGGTTGGATAT
1 TGGTGTGTAGGGTTGGATAT
*
3976 TGGTGTGTTGGGTTGGAT
1 TGGTGTGTAGGGTTGGAT
3994 GAAGATGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.47, T:0.42
Consensus pattern (20 bp):
TGGTGTGTAGGGTTGGATAT
Found at i:8989 original size:40 final size:40
Alignment explanation
Indices: 8945--9048 Score: 118
Period size: 40 Copynumber: 2.6 Consensus size: 40
8935 GACACTATTG
* * *
8945 AACTGGTAGTGACACTGTGAACACTGCAGTATTATTACTA
1 AACTGGCAGTGACACTGTAAACACTGCAATATTATTACTA
* * *
8985 AACTGGCAGTGTCACTGTAAACATTGCAATATTATTACTG
1 AACTGGCAGTGACACTGTAAACACTGCAATATTATTACTA
* * * *
9025 GATTGACTGTGACACTGTAAACAC
1 AACTGGCAGTGACACTGTAAACAC
9049 AACTAGGCTT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (40 bp):
AACTGGCAGTGACACTGTAAACACTGCAATATTATTACTA
Found at i:15130 original size:62 final size:60
Alignment explanation
Indices: 15013--15130 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 60
15003 CGTTTCAATT
* * *
15013 TTCATTTAATACTCACGATGACACAAAGTCATCGGACCTTTAATCTGCAATGGATTTCAC
1 TTCATTCAATACTCACGATGACACAAAGCCATCGGACCTTTAATCTGCAAGGGATTTCAC
* *
15073 TTCATTCATATACTCATGATGACACATAGCCATCGGACCTTTTAATCTGCAAGGGATT
1 TTCATTCA-ATACTCACGATGACACAAAGCCATCGGACC-TTTAATCTGCAAGGGATT
15131 CATATACTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 7 0.14
61 27 0.53
62 17 0.33
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (60 bp):
TTCATTCAATACTCACGATGACACAAAGCCATCGGACCTTTAATCTGCAAGGGATTTCAC
Found at i:15164 original size:52 final size:52
Alignment explanation
Indices: 15076--15319 Score: 294
Period size: 52 Copynumber: 4.7 Consensus size: 52
15066 ATTTCACTTC
* * * * * *
15076 ATTCATATACTCATGATGACACATAGCCATCGGACCTTTTAATCTGCAAGGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCGTTTAATCCGTAAAGG
* * * * *
15128 ATTCATATACTCACGATGACACAGAGTCAACAGACC-TCTTAATCTGTAAATG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCGT-TTAATCCGTAAAGG
* * *
15180 A-TCTATATACTCATGATGACACTTAGTCATCGGACCGTTTAATCCGTAAATG
1 ATTC-ATATACTCACGATGACACATAGTCATCGGACCGTTTAATCCGTAAAGG
* *
15232 ATTCATATACTCACGATGACACTTAGTCATCCGACCGTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCGTTTAATCCGTAAAGG
* *
15284 ATTCATATACTCACGATGACTCATAATCATCGGACC
1 ATTCATATACTCACGATGACACATAGTCATCGGACC
15320 TCTTCATTTA
Statistics
Matches: 167, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
51 3 0.02
52 161 0.96
53 3 0.02
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGTCATCGGACCGTTTAATCCGTAAAGG
Found at i:22619 original size:27 final size:27
Alignment explanation
Indices: 22589--22641 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
22579 GCCCAGAATC
* * * *
22589 AGAATAATGCTTTTTCTAGCCAAAATT
1 AGAATAACGCTCTTTCGAGCAAAAATT
22616 AGAATAACGCTCTTTCGAGCAAAAAT
1 AGAATAACGCTCTTTCGAGCAAAAAT
22642 CAGATTACTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (27 bp):
AGAATAACGCTCTTTCGAGCAAAAATT
Found at i:30093 original size:21 final size:21
Alignment explanation
Indices: 30050--30091 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
30040 GTAAAGATTG
*
30050 ATTGTGTGATTAATTGGTGAA
1 ATTGTGTGATTAATTGGAGAA
*
30071 ATTGTG-GATTAATTTGAGAA
1 ATTGTGTGATTAATTGGAGAA
30091 A
1 A
30092 ATAAAGGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.40
Consensus pattern (21 bp):
ATTGTGTGATTAATTGGAGAA
Found at i:30305 original size:47 final size:47
Alignment explanation
Indices: 30246--30357 Score: 122
Period size: 47 Copynumber: 2.4 Consensus size: 47
30236 ACACTAGCGC
*
30246 GCTCTCTATTTAGCACTACGT-GTGCTCTCT-AT-TTAGCACTATGAAGT
1 GCTCTCTGTTTAGCACT-C-TCGTGCTCTCTGATATTAGCACTATG-AGT
* * *
30293 GCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTTTGCGT
1 GCTCTCTGTTTAGCAC-TCTCGTGCTCTCTGATATTAGCACTATGAGT
*
30341 GCTCTCTGATTAGCACT
1 GCTCTCTGTTTAGCACT
30358 TTATGTGCTC
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
46 1 0.02
47 26 0.46
48 19 0.34
49 10 0.18
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (47 bp):
GCTCTCTGTTTAGCACTCTCGTGCTCTCTGATATTAGCACTATGAGT
Found at i:30321 original size:23 final size:23
Alignment explanation
Indices: 30246--30357 Score: 102
Period size: 23 Copynumber: 4.7 Consensus size: 23
30236 ACACTAGCGC
* *
30246 GCTCTCTATTTAGCACTAC-GTGT
1 GCTCTCTGTTTAGCACT-CTGCGT
* * *
30269 GCTCTCTATTTAGCACTATGAAGT
1 GCTCTCTGTTTAGCACTCTG-CGT
30293 GCTCTCTGTTTAGCACGTCT-CGT
1 GCTCTCTGTTTAGCAC-TCTGCGT
*
30316 GCTCTCTGTTATTAGCACTTTGCGT
1 GCTCTCTG-T-TTAGCACTCTGCGT
*
30341 GCTCTCTGATTAGCACT
1 GCTCTCTGTTTAGCACT
30358 TTATGTGCTC
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
23 36 0.47
24 20 0.26
25 20 0.26
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTCTGCGT
Found at i:30367 original size:48 final size:47
Alignment explanation
Indices: 30266--30356 Score: 112
Period size: 48 Copynumber: 1.9 Consensus size: 47
30256 TAGCACTACG
*
30266 TGTGCTCTCTATTTAGCACTATGAAGTGCTCTCTGTTTAGCACGTCT
1 TGTGCTCTCTATTTAGCACTATGAAGTGCTCTCTGATTAGCACGTCT
* * * *
30313 CGTGCTCTCTGTTATTAGCACTTTG-CGTGCTCTCTGATTAGCAC
1 TGTGCTCTCT-AT-TTAGCACTATGAAGTGCTCTCTGATTAGCAC
30357 TTTATGTGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
47 9 0.24
48 18 0.49
49 10 0.27
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (47 bp):
TGTGCTCTCTATTTAGCACTATGAAGTGCTCTCTGATTAGCACGTCT
Found at i:30386 original size:39 final size:39
Alignment explanation
Indices: 30332--30406 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
30322 TGTTATTAGC
*
30332 ACTTTGCGTGCTCTCTGA-TTAGCACTTTATGTGCTCAGT
1 ACTTTGCGTACTCTCT-ATTTAGCACTTTATGTGCTCAGT
* *
30371 ACTTTGTGTACTCTCTATTTAGCACTTTGTGTGCTC
1 ACTTTGCGTACTCTCTATTTAGCACTTTATGTGCTC
30407 TCTGTGGCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.44
Consensus pattern (39 bp):
ACTTTGCGTACTCTCTATTTAGCACTTTATGTGCTCAGT
Found at i:32388 original size:38 final size:38
Alignment explanation
Indices: 32333--32408 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
32323 CAAGTTGAAG
*
32333 AACATATTTTTAACTTCATTTTCAATCATCGGTATCAC
1 AACATATTTTTAACTTCATTTTCAATCATCGATATCAC
*
32371 AACATATTTTTAGCTTCATTTTCAATCATCGATATCAC
1 AACATATTTTTAACTTCATTTTCAATCATCGATATCAC
32409 GGGTACACCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (38 bp):
AACATATTTTTAACTTCATTTTCAATCATCGATATCAC
Found at i:33584 original size:18 final size:18
Alignment explanation
Indices: 33563--33612 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
33553 AATGCTCTTC
**
33563 CGAGCCAGTATGCTTTAA
1 CGAGCCAGTATGCTCAAA
33581 CGAGCCAGTATGCTCAAA
1 CGAGCCAGTATGCTCAAA
33599 CGAGCCAGTATGCT
1 CGAGCCAGTATGCT
33613 AATTCTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (18 bp):
CGAGCCAGTATGCTCAAA
Found at i:37587 original size:15 final size:15
Alignment explanation
Indices: 37567--37607 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
37557 TATTAGACAC
37567 ATATATTAATAGGAA
1 ATATATTAATAGGAA
*
37582 ATATATCAATAGGAA
1 ATATATTAATAGGAA
37597 ATATACTTAAT
1 ATATA-TTAAT
37608 TGCATCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (15 bp):
ATATATTAATAGGAA
Found at i:38598 original size:40 final size:40
Alignment explanation
Indices: 38507--38606 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
38497 TATACTGCGA
* * * **
38507 TGTTTACAGTATCACCGCCAATTCAGCTATAATGTTGCAG
1 TGTTTACAGTGTCACTGTCAATTCAGCTATAATGTCACAG
*
38547 TGTTTACAGTGTCACTGTCAATTCAGTTATAATGTCACAG
1 TGTTTACAGTGTCACTGTCAATTCAGCTATAATGTCACAG
* *
38587 TGTTTATAGTGTCATTGTCA
1 TGTTTACAGTGTCACTGTCA
38607 GTTATAATCG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (40 bp):
TGTTTACAGTGTCACTGTCAATTCAGCTATAATGTCACAG
Found at i:39763 original size:12 final size:12
Alignment explanation
Indices: 39746--39770 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39736 CAAAATCAAA
39746 AAATAAAATAAT
1 AAATAAAATAAT
39758 AAATAAAATAAT
1 AAATAAAATAAT
39770 A
1 A
39771 TAAATAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:39767 original size:17 final size:18
Alignment explanation
Indices: 39745--39778 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39735 TCAAAATCAA
39745 AAAATAAAAT-AATAAAT
1 AAAATAAAATAAATAAAT
*
39762 AAAATAATATAAATAAA
1 AAAATAAAATAAATAAA
39779 ACATATATTC
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATAAAATAAATAAAT
Found at i:44568 original size:26 final size:26
Alignment explanation
Indices: 44539--44663 Score: 142
Period size: 26 Copynumber: 4.8 Consensus size: 26
44529 AAATGTATGT
* * *
44539 TCATGTTGGCGAGCGTAAACACATAA
1 TCATGCTGACGAGCGTAAACGCATAA
* *
44565 TCATGCTGACGAGCGTAAACGTATAT
1 TCATGCTGACGAGCGTAAACGCATAA
* * *
44591 TCATGCTAACGAGCGTAAACGTATAT
1 TCATGCTGACGAGCGTAAACGCATAA
**
44617 TCATGCTGGTGAGCGTAAACGCATAA
1 TCATGCTGACGAGCGTAAACGCATAA
* *
44643 TCATGCTGATGAGCGTTAACG
1 TCATGCTGACGAGCGTAAACG
44664 TGTTGTCTAA
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 86 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (26 bp):
TCATGCTGACGAGCGTAAACGCATAA
Found at i:44604 original size:52 final size:52
Alignment explanation
Indices: 44524--44658 Score: 153
Period size: 52 Copynumber: 2.6 Consensus size: 52
44514 GAACTCTAGT
* * * *
44524 AGCGTAAATGTATGTTCATGTTGGCGAGCGTAAACACATAATCATGCTGACG
1 AGCGTAAACGTATATTCATGCTGACGAGCGTAAACACATAATCATGCTGACG
* ** * **
44576 AGCGTAAACGTATATTCATGCTAACGAGCGTAAACGTATATTCATGCTGGTG
1 AGCGTAAACGTATATTCATGCTGACGAGCGTAAACACATAATCATGCTGACG
* * *
44628 AGCGTAAACGCATAATCATGCTGATGAGCGT
1 AGCGTAAACGTATATTCATGCTGACGAGCGT
44659 TAACGTGTTG
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (52 bp):
AGCGTAAACGTATATTCATGCTGACGAGCGTAAACACATAATCATGCTGACG
Found at i:54536 original size:40 final size:40
Alignment explanation
Indices: 54464--54643 Score: 180
Period size: 40 Copynumber: 4.5 Consensus size: 40
54454 GTCGTATACT
* * * * * *
54464 GCAGTTTTTACAGTATCACCGCCAGTTTAGTTATAATGTC
1 GCAGTGTTTACAGTGTCACTGCCAGTTCAGTAATAATATC
* * * **
54504 GCAGTGCTTACAGTGTCACTGCTAGTTCAGTTATAACGTC
1 GCAGTGTTTACAGTGTCACTGCCAGTTCAGTAATAATATC
* * * * *
54544 CCAATGTTTGCAGTGTCACTGCCAGTTCGGTAATATTATC
1 GCAGTGTTTACAGTGTCACTGCCAGTTCAGTAATAATATC
** *
54584 ATAGTGTTTACAGTGTCACTGCCAGTTCGGTAATAATATC
1 GCAGTGTTTACAGTGTCACTGCCAGTTCAGTAATAATATC
*
54624 GTAGTGTTTACAGTGTCACT
1 GCAGTGTTTACAGTGTCACT
54644 TGCAGTTATA
Statistics
Matches: 117, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 117 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.36
Consensus pattern (40 bp):
GCAGTGTTTACAGTGTCACTGCCAGTTCAGTAATAATATC
Found at i:58629 original size:39 final size:39
Alignment explanation
Indices: 58521--58632 Score: 134
Period size: 39 Copynumber: 2.9 Consensus size: 39
58511 TGAAATGATA
* * * *
58521 TACTAAACTGAGAGTGACACTGGAAACACTACAACGATT
1 TACTAAACTGACAGTGACACTGTAAACACTGCAACGACT
* *
58560 TACTAAACTGATAGTGACATTGTAAACACTGCAACGACT
1 TACTAAACTGACAGTGACACTGTAAACACTGCAACGACT
* * **
58599 TATTGAACTTCCAGTGACACTGTAAACACTGCAA
1 TACTAAACTGACAGTGACACTGTAAACACTGCAA
58633 TGCTATATTG
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 62 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24
Consensus pattern (39 bp):
TACTAAACTGACAGTGACACTGTAAACACTGCAACGACT
Found at i:58654 original size:39 final size:39
Alignment explanation
Indices: 58533--58666 Score: 128
Period size: 39 Copynumber: 3.4 Consensus size: 39
58523 CTAAACTGAG
* * * * * *
58533 AGTGACACTGGAAACACTACAACGATTTACTAAACTGAT
1 AGTGACACTGTAAACACTGCAACGACTTATTGAACTGCT
* * *
58572 AGTGACATTGTAAACACTGCAACGACTTATTGAACTTCC
1 AGTGACACTGTAAACACTGCAACGACTTATTGAACTGCT
* *
58611 AGTGACACTGTAAACACTGCAATG-CTATATTGAA-TGGGT
1 AGTGACACTGTAAACACTGCAACGACT-TATTGAACT-GCT
*
58650 AGTGATACTGTAAACAC
1 AGTGACACTGTAAACAC
58667 CGTAACTTTA
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
38 3 0.04
39 75 0.96
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (39 bp):
AGTGACACTGTAAACACTGCAACGACTTATTGAACTGCT
Found at i:66495 original size:17 final size:17
Alignment explanation
Indices: 66464--66512 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
66454 AAATACAATG
* *
66464 AAAATGTGATAACAAGT
1 AAAATGTCATGACAAGT
*
66481 AAAATG-CAATGACAATT
1 AAAATGTC-ATGACAAGT
66498 AAAATGTCATGACAA
1 AAAATGTCATGACAA
66513 CTAGAGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 26 0.96
18 1 0.04
ACGTcount: A:0.53, C:0.10, G:0.14, T:0.22
Consensus pattern (17 bp):
AAAATGTCATGACAAGT
Found at i:66913 original size:3 final size:3
Alignment explanation
Indices: 66905--66960 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
66895 GTCGGGACAA
*
66905 CTT CTT CTT CTT TTT CCTT C-T CTT CTT -TT CCTT CTT CTT -TT CTT
1 CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT
66949 -TT C-T CTT CTT CT
1 CTT CTT CTT CTT CT
66961 GTTTCAATAC
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
2 10 0.23
3 30 0.68
4 4 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:68770 original size:24 final size:24
Alignment explanation
Indices: 68725--68771 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
68715 TGCAAAAACT
68725 AAAGAAACAAATTAAAGTAAAATA
1 AAAGAAACAAATTAAAGTAAAATA
68749 AAAGACAA-AAATTAACAG-AAAAT
1 AAAGA-AACAAATTAA-AGTAAAAT
68772 TTTTTGCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.70, C:0.06, G:0.09, T:0.15
Consensus pattern (24 bp):
AAAGAAACAAATTAAAGTAAAATA
Found at i:77351 original size:39 final size:39
Alignment explanation
Indices: 77308--77460 Score: 191
Period size: 39 Copynumber: 3.9 Consensus size: 39
77298 ACTTTTCTGA
* * *
77308 AATGATATACTAAACTGGAAGTGACACTATAAACACTGC
1 AATGATATACTGAACTGGCAGTGACACTGTAAACACTGC
* * *
77347 AATGATTTATTGAACTGGCAGTGACACTGTAAACACAGC
1 AATGATATACTGAACTGGCAGTGACACTGTAAACACTGC
* *
77386 AACGATATACTGAACTGGCAGTGACACTGTAAACACTAC
1 AATGATATACTGAACTGGCAGTGACACTGTAAACACTGC
* * *
77425 AATGCTATACTGAA-TGGGCGGTGAGACTGTAAACAC
1 AATGATATACTGAACT-GGCAGTGACACTGTAAACAC
77461 CGTAACTTTA
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
38 1 0.01
39 97 0.99
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (39 bp):
AATGATATACTGAACTGGCAGTGACACTGTAAACACTGC
Found at i:93472 original size:3 final size:3
Alignment explanation
Indices: 93464--93489 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
93454 GACTCACCTT
93464 CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CA
93490 TCGCCACCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:97879 original size:42 final size:42
Alignment explanation
Indices: 97815--97897 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
97805 GTTATTATAC
* *
97815 ACAAACTTGGCTAAAGGTAGGTGATCATCCCAGCTACCCCTG
1 ACAAACTTGGATAAAGGTAGGTGATCATCCCAACTACCCCTG
* * *
97857 ACAACCTTGGATAATGGTAGGTGATCCTCCCAACTACCCCT
1 ACAAACTTGGATAAAGGTAGGTGATCATCCCAACTACCCCT
97898 AAAATTAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (42 bp):
ACAAACTTGGATAAAGGTAGGTGATCATCCCAACTACCCCTG
Found at i:109591 original size:175 final size:175
Alignment explanation
Indices: 109300--109641 Score: 675
Period size: 175 Copynumber: 2.0 Consensus size: 175
109290 AGTATATATG
109300 ATGCATTTCTCACAATACAAGTAATGCCTCAAGATTTTCAACGTAAACACGAACACAACTAACTC
1 ATGCATTTCTCACAATACAAGTAATGCCTCAAGATTTTCAACGTAAACACGAACACAACTAACTC
109365 CAGGTCATGAGTAGGATAATTCCCCTCGTGCACCTTAAGCTATCGAGACACATACGCTACCACTT
66 CAGGTCATGAGTAGGATAATTCCCCTCGTGCACCTTAAGCTATCGAGACACATACGCTACCACTT
109430 TCTCTCTTGTATCAAGACACATCCCAAACCTACATGTCATGAGTA
131 TCTCTCTTGTATCAAGACACATCCCAAACCTACATGTCATGAGTA
*
109475 ATGCATTTCTCACAATACAAGTAATGCCTCAAGATTTTCAATGTAAACACGAACACAACTAACTC
1 ATGCATTTCTCACAATACAAGTAATGCCTCAAGATTTTCAACGTAAACACGAACACAACTAACTC
109540 CAGGTCATGAGTAGGATAATTCCCCTCGTGCACCTTAAGCTATCGAGACACATACGCTACCACTT
66 CAGGTCATGAGTAGGATAATTCCCCTCGTGCACCTTAAGCTATCGAGACACATACGCTACCACTT
109605 TCTCTCTTGTATCAAGACACATCCCAAACCTACATGT
131 TCTCTCTTGTATCAAGACACATCCCAAACCTACATGT
109642 GATGCATCAC
Statistics
Matches: 166, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 166 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (175 bp):
ATGCATTTCTCACAATACAAGTAATGCCTCAAGATTTTCAACGTAAACACGAACACAACTAACTC
CAGGTCATGAGTAGGATAATTCCCCTCGTGCACCTTAAGCTATCGAGACACATACGCTACCACTT
TCTCTCTTGTATCAAGACACATCCCAAACCTACATGTCATGAGTA
Found at i:111286 original size:28 final size:28
Alignment explanation
Indices: 111237--111292 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
111227 CCTTTGTCCG
*
111237 GTGTCCCATGACCACTACTAGAGCTCAT
1 GTGTCCCACGACCACTACTAGAGCTCAT
*
111265 GTGTCCCACGATCC-CTATTAGAGCTCAT
1 GTGTCCCACGA-CCACTACTAGAGCTCAT
111293 ACTCCCCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (28 bp):
GTGTCCCACGACCACTACTAGAGCTCAT
Found at i:112026 original size:39 final size:39
Alignment explanation
Indices: 111925--112155 Score: 212
Period size: 39 Copynumber: 5.9 Consensus size: 39
111915 AAAACAGGGT
* * *
111925 AATTTTGTATAGTGTCGTAGTGTTTACAGTGTCACTACC
1 AATTTAGTATAGTATCGTAGTGTTTACAGTGTCACTGCC
* ** * *
111964 CATTTCAGTATACCATCATAGTGTTTACAGTGTCACTACC
1 AATTT-AGTATAGTATCGTAGTGTTTACAGTGTCACTGCC
* * * * *
112004 AATTTTGTATAGTATTGCAGTGTTTATAATGTCACTGCC
1 AATTTAGTATAGTATCGTAGTGTTTACAGTGTCACTGCC
** * * *
112043 AATTTAGTATAGTGCCTTAGTGTTTATAGTATCACTGCC
1 AATTTAGTATAGTATCGTAGTGTTTACAGTGTCACTGCC
* * * *
112082 AATTCAGTATAGTGTCATAGTGTTTATAGTGTCACTGCC
1 AATTTAGTATAGTATCGTAGTGTTTACAGTGTCACTGCC
* * *
112121 AATTCAATATAGCTA-CGCAGTGTTTACAGTGTCAC
1 AATTTAGTATAG-TATCGTAGTGTTTACAGTGTCAC
112156 AGTCAGCTCA
Statistics
Matches: 157, Mismatches: 33, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
39 123 0.78
40 34 0.22
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (39 bp):
AATTTAGTATAGTATCGTAGTGTTTACAGTGTCACTGCC
Found at i:112132 original size:117 final size:118
Alignment explanation
Indices: 111925--112155 Score: 277
Period size: 117 Copynumber: 2.0 Consensus size: 118
111915 AAAACAGGGT
* * * *
111925 AATTTTGTATAGTGTCGTAGTGTTTACAGTGTCACTACCCATTTCAGTATACCATCATAGTGTTT
1 AATTTAGTATAGTGCCGTAGTGTTTACAGTATCACTACCCAATTCAGTATACCATCATAGTGTTT
*** * *
111990 ACAGTGTCACTACCAATTTTGTATAG-TATTGCAGTGTTTATAATGTCACTGCC
66 ACAGTGTCACTACCAATTCAATATAGCTA-CGCAGTGTTTACAATGTCACTGCC
* * * ***
112043 AATTTAGTATAGTGCCTTAGTGTTTATAGTATCACT-GCCAATTCAGTATAGTGTCATAGTGTTT
1 AATTTAGTATAGTGCCGTAGTGTTTACAGTATCACTACCCAATTCAGTATACCATCATAGTGTTT
* * *
112107 ATAGTGTCACTGCCAATTCAATATAGCTACGCAGTGTTTACAGTGTCAC
66 ACAGTGTCACTACCAATTCAATATAGCTACGCAGTGTTTACAATGTCAC
112156 AGTCAGCTCA
Statistics
Matches: 94, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
117 61 0.65
118 33 0.35
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (118 bp):
AATTTAGTATAGTGCCGTAGTGTTTACAGTATCACTACCCAATTCAGTATACCATCATAGTGTTT
ACAGTGTCACTACCAATTCAATATAGCTACGCAGTGTTTACAATGTCACTGCC
Found at i:113169 original size:3 final size:3
Alignment explanation
Indices: 113161--113206 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
113151 TGTTTAACTA
* * *
113161 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT ATT AAT ATT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
113207 TCAATATCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:113207 original size:6 final size:6
Alignment explanation
Indices: 113161--113218 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
113151 TGTTTAACTA
* * * * *
113161 AATAAT AATAAT AATAAT AATAAT AATATT AATATT AATATT AATATC
1 AATATT AATATT AATATT AATATT AATATT AATATT AATATT AATATT
*
113209 AATATC AATA
1 AATATT AATA
113219 ATAGTAACAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (6 bp):
AATATT
Found at i:113207 original size:12 final size:12
Alignment explanation
Indices: 113161--113221 Score: 70
Period size: 12 Copynumber: 5.1 Consensus size: 12
113151 TGTTTAACTA
*
113161 AATAATAATAAT
1 AATATTAATAAT
*
113173 AATAATAATAAT
1 AATATTAATAAT
*
113185 AATATTAATATT
1 AATATTAATAAT
113197 AATATTAAT-AT
1 AATATTAATAAT
*
113208 CAATATCAATAAT
1 -AATATTAATAAT
113221 A
1 A
113222 GTAACACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
11 1 0.02
12 40 0.93
13 2 0.05
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATTAATAAT
Found at i:113207 original size:18 final size:18
Alignment explanation
Indices: 113161--113221 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
113151 TGTTTAACTA
* *
113161 AATAATAATAATAATAAT
1 AATAATAATATTAATATT
113179 AATAATAATATTAATATT
1 AATAATAATATTAATATT
* * *
113197 AATATTAATATCAATATC
1 AATAATAATATTAATATT
113215 AATAATA
1 AATAATA
113222 GTAACACCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAATAATATTAATATT
Found at i:118730 original size:39 final size:39
Alignment explanation
Indices: 118687--119009 Score: 330
Period size: 39 Copynumber: 8.3 Consensus size: 39
118677 TGCAATGGCC
* *
118687 ACAGTGTCACTGCCAGA-TCAGTGTAGTATTGTAGTGTTT
1 ACAGTGTCACTGCCA-ATTCAGTATAGTATCGTAGTGTTT
* * *
118726 ACAGTGTCACTGCCAATTTAGTATAGTGTTGTAGTGTTT
1 ACAGTGTCACTGCCAATTCAGTATAGTATCGTAGTGTTT
* * * * *
118765 ATAGTGTCACTACCCATTTCAGCATAGCATCGTAGTGTTT
1 ACAGTGTCACT-GCCAATTCAGTATAGTATCGTAGTGTTT
* *
118805 ACAATGTCACTGCCAATTCAGTATAGTATCGTATTGTTT
1 ACAGTGTCACTGCCAATTCAGTATAGTATCGTAGTGTTT
* * * *
118844 ACAGTGTCACTGTCAATTCAATATAGTGTCATAGTGCTTT
1 ACAGTGTCACTGCCAATTCAGTATAGTATCGTAGTG-TTT
* *
118884 -CAGTGTCATTGCCAATTCAGTATAGTGTCGTAGTGTTT
1 ACAGTGTCACTGCCAATTCAGTATAGTATCGTAGTGTTT
* * **
118922 ACAGTGCCACTGCCAATTCAATATAGT-TACAAAGTGTTT
1 ACAGTGTCACTGCCAATTCAGTATAGTAT-CGTAGTGTTT
* * **
118961 ACAGTGTCACTGTCAGTTCAGTA-AGGTATTATAGTGTTT
1 ACAGTGTCACTGCCAATTCAGTATA-GTATCGTAGTGTTT
*
119000 GCAGTGTCAC
1 ACAGTGTCAC
119010 CATCAGTTCA
Statistics
Matches: 237, Mismatches: 40, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
38 6 0.03
39 197 0.83
40 34 0.14
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (39 bp):
ACAGTGTCACTGCCAATTCAGTATAGTATCGTAGTGTTT
Found at i:119327 original size:64 final size:63
Alignment explanation
Indices: 119209--119327 Score: 150
Period size: 63 Copynumber: 1.9 Consensus size: 63
119199 GGGCCCAGAC
* * *
119209 CGTGTAACTCACTGTTTCTGGTTCTATGACACACGGTCCAAACACACGCCCGTGTTCTCAAGA
1 CGTGTAACTCACTGTTTCTGATGCTATGACACACGGACCAAACACACGCCCGTGTTCTCAAGA
* * * *
119272 CGTGTAACTCACTGTTTCTTATGCATATGGCACAC-GACCTAGACACACGCTCGTGT
1 CGTGTAACTCACTGTTTCTGATGC-TATGACACACGGACC-AAACACACGCCCGTGT
119328 GTTCGCCCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
63 24 0.51
64 23 0.49
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (63 bp):
CGTGTAACTCACTGTTTCTGATGCTATGACACACGGACCAAACACACGCCCGTGTTCTCAAGA
Found at i:122796 original size:19 final size:21
Alignment explanation
Indices: 122759--122798 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
122749 TATTTAACTT
122759 TATTATTAATGTCACAAAAAAA
1 TATTATTAATG-CACAAAAAAA
122781 TATTATTAATG-A-AAAAAA
1 TATTATTAATGCACAAAAAA
122799 CCTTATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
22 11 0.61
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
TATTATTAATGCACAAAAAAA
Found at i:122883 original size:2 final size:2
Alignment explanation
Indices: 122876--122900 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
122866 AGTCAAAGTT
122876 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
122901 TCTCATACCT
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:124723 original size:19 final size:18
Alignment explanation
Indices: 124695--124730 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
124685 TTATTGTATG
124695 CTATTTTTAAACACATAC
1 CTATTTTTAAACACATAC
*
124713 CTATATTTTAAATACATA
1 CTAT-TTTTAAACACATA
124731 ATTTCTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (18 bp):
CTATTTTTAAACACATAC
Found at i:125878 original size:22 final size:22
Alignment explanation
Indices: 125853--125898 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
125843 ATACTAGTAA
125853 AACTTCCAAATAAATTATCTAG
1 AACTTCCAAATAAATTATCTAG
125875 AACTTCCAAATAAATTATCTAG
1 AACTTCCAAATAAATTATCTAG
125897 AA
1 AA
125899 TTCACAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.30
Consensus pattern (22 bp):
AACTTCCAAATAAATTATCTAG
Found at i:128480 original size:23 final size:23
Alignment explanation
Indices: 128438--128481 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
128428 ATTTTAAACT
** *
128438 TTATTATTAATGTCACAAAAAAA
1 TTATTATTAATGGAAAAAAAAAA
128461 TTATTATTAATGGAAAAAAAA
1 TTATTATTAATGGAAAAAAAA
128482 TCTTATTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (23 bp):
TTATTATTAATGGAAAAAAAAAA
Found at i:128566 original size:2 final size:2
Alignment explanation
Indices: 128559--128603 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
128549 ACTCAAAGTT
128559 TA TA 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 TA TA
128601 TA T
1 TA T
128604 TATCATACCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:128683 original size:2 final size:2
Alignment explanation
Indices: 128676--128700 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
128666 ACTCAAAGTT
128676 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
128701 TCTCATACCT
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:134081 original size:22 final size:20
Alignment explanation
Indices: 134044--134093 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
134034 TTATGTTATT
*
134044 TTTAATGAAAATTTATTTTA
1 TTTAATTAAAATTTATTTTA
134064 TTTAATTAAAATAATTATTTTA
1 TTTAATTAAAAT--TTATTTTA
*
134086 TTTTATTA
1 TTTAATTA
134094 TCTGTGTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 11 0.42
22 15 0.58
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTAATTAAAATTTATTTTA
Found at i:134591 original size:33 final size:33
Alignment explanation
Indices: 134554--134618 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
134544 AAATAGGAAC
*
134554 TATACTCAATTGCAATAATATAACCCTTATAAA
1 TATACTCAATTGCAATAATATAACCCTAATAAA
134587 TATACTCAATTGCAATAATATAACCCTAATAA
1 TATACTCAATTGCAATAATATAACCCTAATAA
134619 TATTTATAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.32
Consensus pattern (33 bp):
TATACTCAATTGCAATAATATAACCCTAATAAA
Done.