Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012375.1 Kokia drynarioides strain JFW-HI SEQ_127379, 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: 126766
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:1453 original size:27 final size:28
Alignment explanation
Indices: 1422--1476 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
1412 AAAATTTTAT
1422 TAAAA-TA-ATAACTTTATTTTATATCAG
1 TAAAATTACATAA-TTTATTTTATATCAG
*
1449 TAAAATTAGCATAATTTTTTTTATATCA
1 TAAAATTA-CATAATTTATTTTATATCA
1477 AATATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.21
28 2 0.08
29 13 0.54
30 4 0.17
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (28 bp):
TAAAATTACATAATTTATTTTATATCAG
Found at i:4034 original size:16 final size:16
Alignment explanation
Indices: 4013--4043 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4003 GTGTGCTTTT
*
4013 TGATTGGTTGAAAATA
1 TGATTGATTGAAAATA
4029 TGATTGATTGAAAAT
1 TGATTGATTGAAAAT
4044 TCTCTTTGTT
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:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (16 bp):
TGATTGATTGAAAATA
Found at i:6412 original size:121 final size:121
Alignment explanation
Indices: 6198--6435 Score: 424
Period size: 121 Copynumber: 2.0 Consensus size: 121
6188 CTTCGGGGCC
* * *
6198 TATATTCGAAGTCGAAATGTCAGACAAACATAAAACATGCAGATAAACCCCAAGACTGAGCAACC
1 TATATTCGAAGTCGAAATGTCAGACAAAAAGAAAACATGCAGATAAACCCCAAGAATGAGCAACC
*
6263 AAACACACTGAAGCCTCAAGAAGCAATGTTATTGTTGTGAAATGACCATACAATGT
66 AAACACACTGAAGCCTCAAGAAGCAATGTTATTATTGTGAAATGACCATACAATGT
6319 TATATTCGAAGTCGAAATGTCAGGA-AAAAAGAAAACATGCAGATAAACCCCAAGAATGAGCAAC
1 TATATTCGAAGTCGAAATGTCA-GACAAAAAGAAAACATGCAGATAAACCCCAAGAATGAGCAAC
6383 CAAACACACTGAAGCCTCAAGAAGCAATGTTATTATTGTGAAATGACCATACA
65 CAAACACACTGAAGCCTCAAGAAGCAATGTTATTATTGTGAAATGACCATACA
6436 TACATTGACA
Statistics
Matches: 112, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
121 110 0.98
122 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.20
Consensus pattern (121 bp):
TATATTCGAAGTCGAAATGTCAGACAAAAAGAAAACATGCAGATAAACCCCAAGAATGAGCAACC
AAACACACTGAAGCCTCAAGAAGCAATGTTATTATTGTGAAATGACCATACAATGT
Found at i:8778 original size:13 final size:13
Alignment explanation
Indices: 8747--8776 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
8737 CGCAAATTAT
8747 AATTTATATTTTA
1 AATTTATATTTTA
8760 AATTTAT-TTTTA
1 AATTTATATTTTA
8772 AATTT
1 AATTT
8777 TAAAATGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
AATTTATATTTTA
Found at i:17201 original size:16 final size:14
Alignment explanation
Indices: 17179--17231 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
17169 AGGTTTTAGG
17179 TTAAATTTTTTTTT
1 TTAAATTTTTTTTT
**
17193 TTCATAATTTTTTACT
1 TT-A-AATTTTTTTTT
17209 TTAAATTTTTTTTT
1 TTAAATTTTTTTTT
*
17223 ATAAATTTT
1 TTAAATTTT
17232 ATATAAAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.59
15 2 0.06
16 11 0.34
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (14 bp):
TTAAATTTTTTTTT
Found at i:28969 original size:15 final size:14
Alignment explanation
Indices: 28946--28989 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
28936 ATTTAAATTC
28946 AATACTTAAATTTTT
1 AATACTT-AATTTTT
*
28961 AATATTTAATTTTT
1 AATACTTAATTTTT
*
28975 CAACACTTAATTTTT
1 -AATACTTAATTTTT
28990 TAGCACTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (14 bp):
AATACTTAATTTTT
Found at i:37237 original size:24 final size:26
Alignment explanation
Indices: 37209--37256 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
37199 ATTATTTTAT
*
37209 TATAT-AAATA-ATTTTAAAATATGA
1 TATATCAAATACATTTAAAAATATGA
37233 TATATCAAATACATTTAAAAATAT
1 TATATCAAATACATTTAAAAATAT
37257 TAAAACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (26 bp):
TATATCAAATACATTTAAAAATATGA
Found at i:37266 original size:12 final size:12
Alignment explanation
Indices: 37251--37276 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
37241 ATACATTTAA
37251 AAATATTAAAAC
1 AAATATTAAAAC
37263 AAATATTAAAAC
1 AAATATTAAAAC
37275 AA
1 AA
37277 CAAATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:38003 original size:22 final size:23
Alignment explanation
Indices: 37972--38014 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
37962 ATTTAATCAT
*
37972 TATTACAAATAAAAA-AAAATAG
1 TATTAAAAATAAAAATAAAATAG
37994 TATTAAAAATAAAAATAAAAT
1 TATTAAAAATAAAAATAAAAT
38015 TATTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (23 bp):
TATTAAAAATAAAAATAAAATAG
Found at i:45502 original size:240 final size:240
Alignment explanation
Indices: 45079--45556 Score: 875
Period size: 240 Copynumber: 2.0 Consensus size: 240
45069 CATTATTGTG
* * *
45079 AAAAAAGGATGTAAATTTTGTAGACATATGAAGTACCATGGATGTTGGTGCTGCAAGCTTTGGAT
1 AAAAAAGAATGTAAAATTTGCAGACATATGAAGTACCATGGATGTTGGTGCTGCAAGCTTTGGAT
*
45144 AAACCAGAGCTCAGAGGATAAAGGGTATCATCCACATCTGATAATAAAACATATATCAATCAGAA
66 AAACCAGAGCTCAGAGGATAAAGGGCATCATCCACATCTGATAATAAAACATATATCAATCAGAA
* *
45209 ATGTTAATCAGATTAAGGGAACCCCAAAGGGTCTGATATACTGCAGAAAGACACACTTACTAAAG
131 ATGTTAATCACATTAAGAGAACCCCAAAGGGTCTGATATACTGCAGAAAGACACACTTACTAAAG
45274 AGAAGATAGTCATATTTTGGTGCTGCAATATGCTGATACTGGTAA
196 AGAAGATAGTCATATTTTGGTGCTGCAATATGCTGATACTGGTAA
*
45319 AAAAAAGAATGTAAAATTTGCAGACATATGAAGTACCTTGGATGTTGGTGCTGCAAGCTTTGGAT
1 AAAAAAGAATGTAAAATTTGCAGACATATGAAGTACCATGGATGTTGGTGCTGCAAGCTTTGGAT
*
45384 AAACCAGAGCTCAGAGGATAAAGGGCATCATCTACATCTGATAATAAAACATATATCAATCAGAA
66 AAACCAGAGCTCAGAGGATAAAGGGCATCATCCACATCTGATAATAAAACATATATCAATCAGAA
*
45449 ATGTTAATCACATTAAGAGAACTCCAAAGGGTCTGATATACTGCAGAAAGACACACTTACTAAAG
131 ATGTTAATCACATTAAGAGAACCCCAAAGGGTCTGATATACTGCAGAAAGACACACTTACTAAAG
45514 AGAAGATAGTCATATTTTGGTGCTGCAATATGCTGATACTGGT
196 AGAAGATAGTCATATTTTGGTGCTGCAATATGCTGATACTGGT
45557 TTTCATATCC
Statistics
Matches: 229, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
240 229 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (240 bp):
AAAAAAGAATGTAAAATTTGCAGACATATGAAGTACCATGGATGTTGGTGCTGCAAGCTTTGGAT
AAACCAGAGCTCAGAGGATAAAGGGCATCATCCACATCTGATAATAAAACATATATCAATCAGAA
ATGTTAATCACATTAAGAGAACCCCAAAGGGTCTGATATACTGCAGAAAGACACACTTACTAAAG
AGAAGATAGTCATATTTTGGTGCTGCAATATGCTGATACTGGTAA
Found at i:46230 original size:22 final size:22
Alignment explanation
Indices: 46198--46241 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
46188 TTCTCATTAA
46198 CGTTACATAACAATTCCCGTTC
1 CGTTACATAACAATTCCCGTTC
* *
46220 CGTTACGTAACAATTCCTGTTC
1 CGTTACATAACAATTCCCGTTC
46242 TTTCTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
CGTTACATAACAATTCCCGTTC
Found at i:46471 original size:2 final size:2
Alignment explanation
Indices: 46464--46496 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
46454 TTTGTTCCAC
46464 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
46497 AGGCATCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:65166 original size:23 final size:22
Alignment explanation
Indices: 65134--65229 Score: 93
Period size: 23 Copynumber: 4.2 Consensus size: 22
65124 GCTGGGGAAA
*
65134 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
65156 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * * *
65179 CAGTAGGCGCACATAGCGTAAAT
1 CAGTAGGCACACACAGTG-CAAT
* * *
65202 CAGCAGGCACACAAAGTGCGAAA
1 CAGTAGGCACACACAGTGC-AAT
65225 CAGTA
1 CAGTA
65230 AGCGCGCTAG
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
22 15 0.25
23 44 0.75
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:67704 original size:23 final size:23
Alignment explanation
Indices: 67674--67761 Score: 101
Period size: 23 Copynumber: 3.8 Consensus size: 23
67664 GCTGGGGAAA
67674 CAGTAAGCACACACAGTGC-AAT
1 CAGTAAGCACACACAGTGCAAAT
*
67696 CCAGTAAGCACACATAGTGCAAAT
1 -CAGTAAGCACACACAGTGCAAAT
* *
67720 CAGTAGGCATACGA-AGTGCGAAA-
1 CAGTAAGCACAC-ACAGTGC-AAAT
67743 CAGTAAGCACACACAGTGC
1 CAGTAAGCACACACAGTGC
67762 TGAACAATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
22 1 0.02
23 48 0.86
24 7 0.12
ACGTcount: A:0.40, C:0.25, G:0.22, T:0.14
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:67767 original size:23 final size:21
Alignment explanation
Indices: 67672--67773 Score: 80
Period size: 23 Copynumber: 4.5 Consensus size: 21
67662 GTGCTGGGGA
67672 AACAGTAAGCACACACAGTGC-
1 AACAGTAAGCACACA-AGTGCG
*
67693 AATCCAGTAAGCACACATAGTGCA
1 AA--CAGTAAGCACACA-AGTGCG
* *
67717 AATCAGTAGGCATACGAAGTGCG
1 AA-CAGTAAGCACAC-AAGTGCG
67740 AAACAGTAAGCACACACAGTGCTG
1 -AACAGTAAGCACACA-AGTGC-G
*
67764 AACAATAAGC
1 AACAGTAAGC
67774 GCACTAGCGT
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
21 2 0.03
22 1 0.02
23 57 0.86
24 6 0.09
ACGTcount: A:0.42, C:0.24, G:0.21, T:0.14
Consensus pattern (21 bp):
AACAGTAAGCACACAAGTGCG
Found at i:68404 original size:11 final size:11
Alignment explanation
Indices: 68377--68405 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
68367 TCAGTCTCTA
68377 ATAATTTTTCT
1 ATAATTTTTCT
68388 AT-ATTTTTCT
1 ATAATTTTTCT
68398 ATAATTTT
1 ATAATTTT
68406 CCAAAGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (11 bp):
ATAATTTTTCT
Found at i:69140 original size:29 final size:29
Alignment explanation
Indices: 69098--69218 Score: 172
Period size: 29 Copynumber: 4.1 Consensus size: 29
69088 TTTTATTCAC
*
69098 TATCTTGAAGAAATTTGGAAGAAAATAAT
1 TATCTTGAAAAAATTTGGAAGAAAATAAT
69127 TATCTTGAAAAAATTTGGAAGAAAATAAT
1 TATCTTGAAAAAATTTGGAAGAAAATAAT
**
69156 TAAATAT-AATTAGAAATTTGGAAGAAAATAAT
1 TATCT-TGAA--A-AAATTTGGAAGAAAATAAT
69188 TATCTTGAAAAAATTTGGAAGAAAATAAT
1 TATCTTGAAAAAATTTGGAAGAAAATAAT
69217 TA
1 TA
69219 AATATAATTA
Statistics
Matches: 82, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
29 54 0.66
30 2 0.02
31 2 0.02
32 24 0.29
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.31
Consensus pattern (29 bp):
TATCTTGAAAAAATTTGGAAGAAAATAAT
Found at i:69201 original size:61 final size:61
Alignment explanation
Indices: 69106--69228 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
69096 ACTATCTTGA
69106 AGAAATTTGGAAGAAAATAATTATCTTGAAAAAATTTGGAAGAAAATAATTAAATATAATT
1 AGAAATTTGGAAGAAAATAATTATCTTGAAAAAATTTGGAAGAAAATAATTAAATATAATT
69167 AGAAATTTGGAAGAAAATAATTATCTTGAAAAAATTTGGAAGAAAATAATTAAATATAATT
1 AGAAATTTGGAAGAAAATAATTATCTTGAAAAAATTTGGAAGAAAATAATTAAATATAATT
69228 A
1 A
69229 TAATTATATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.54, C:0.02, G:0.13, T:0.31
Consensus pattern (61 bp):
AGAAATTTGGAAGAAAATAATTATCTTGAAAAAATTTGGAAGAAAATAATTAAATATAATT
Found at i:70555 original size:21 final size:21
Alignment explanation
Indices: 70531--70570 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
70521 AAAATGATCT
70531 AAAA-TATTAATAATTAAATTG
1 AAAATTATT-ATAATTAAATTG
*
70552 AAAATTATTATAGTTAAAT
1 AAAATTATTATAATTAAAT
70571 AATCAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
AAAATTATTATAATTAAATTG
Found at i:71197 original size:17 final size:16
Alignment explanation
Indices: 71172--71219 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
71162 TTCTGGATGT
71172 AATTATTCTTGAACAAC
1 AATTATTC-TGAACAAC
* *
71189 AATTGTTCTGATCAAC
1 AATTATTCTGAACAAC
* *
71205 AACTATTCTAAACAA
1 AATTATTCTGAACAA
71220 GAGTTGTTGT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (16 bp):
AATTATTCTGAACAAC
Found at i:75292 original size:2 final size:2
Alignment explanation
Indices: 75285--75316 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
75275 TTAATTATGT
75285 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
75317 ATTTATACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:83519 original size:2 final size:2
Alignment explanation
Indices: 83512--83538 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
83502 CACCCTCTTA
83512 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
83539 AAGAGACGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:83793 original size:17 final size:16
Alignment explanation
Indices: 83768--83819 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
83758 AAGTTCCACT
83768 ATTATAAATATACTAC
1 ATTATAAATATACTAC
*
83784 ATTCATAAATATAATAC
1 ATT-ATAAATATACTAC
* *
83801 AATACAAATATAC-AC
1 ATTATAAATATACTAC
83816 ATTA
1 ATTA
83820 CCAACTATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 5 0.17
16 11 0.37
17 14 0.47
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTATAAATATACTAC
Found at i:88057 original size:2 final size:2
Alignment explanation
Indices: 88050--88076 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
88040 TGCTGTCCAT
88050 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 T
88077 TAATTTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:88541 original size:19 final size:19
Alignment explanation
Indices: 88505--88553 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
88495 AAAAGGTTAA
*
88505 TAAGACAAATA-A-ATATT
1 TAAGAAAAATATACATATT
*
88522 TAATAAAAATATACATATT
1 TAAGAAAAATATACATATT
*
88541 TAAGAAATATATA
1 TAAGAAAAATATA
88554 TTGGTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 9 0.35
18 1 0.04
19 16 0.62
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (19 bp):
TAAGAAAAATATACATATT
Found at i:88581 original size:81 final size:82
Alignment explanation
Indices: 88447--88612 Score: 325
Period size: 81 Copynumber: 2.0 Consensus size: 82
88437 TATAAGTTCT
88447 AATATACATATTTAAGAAATATATATTGGTTTTTTTTTTTTTATGTTTAAAAGGTTAATAAGACA
1 AATATACATATTTAAGAAATATATATTGGTTTTTTTTTTTTTATGTTTAAAAGGTTAATAAGACA
88512 AATAAATATTTAATAAA
66 AATAAATATTTAATAAA
88529 AATATACATATTTAAGAAATATATATTGG-TTTTTTTTTTTTATGTTTAAAAGGTTAATAAGACA
1 AATATACATATTTAAGAAATATATATTGGTTTTTTTTTTTTTATGTTTAAAAGGTTAATAAGACA
88593 AATAAATATTTAATAAA
66 AATAAATATTTAATAAA
88610 AAT
1 AAT
88613 GAGGTTACTA
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 55 0.65
82 29 0.35
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (82 bp):
AATATACATATTTAAGAAATATATATTGGTTTTTTTTTTTTTATGTTTAAAAGGTTAATAAGACA
AATAAATATTTAATAAA
Found at i:89749 original size:44 final size:44
Alignment explanation
Indices: 89695--89784 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 44
89685 CAATTGTAAC
*
89695 TTAAAATATAATTATTTTTAAAAA-ATTAATTATCAGAACTTCTA
1 TTAAAATATAATTATTATTAAAAATA-TAATTATCAGAACTTCTA
* * * *
89739 TTAAATTATAATTATTATTAAATATATAATTATCATAACTTTTA
1 TTAAAATATAATTATTATTAAAAATATAATTATCAGAACTTCTA
89783 TT
1 TT
89785 TTATTTTAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 39 0.98
45 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.48
Consensus pattern (44 bp):
TTAAAATATAATTATTATTAAAAATATAATTATCAGAACTTCTA
Found at i:89768 original size:18 final size:17
Alignment explanation
Indices: 89737--89771 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
89727 TCAGAACTTC
89737 TATTAAATTATAATTAT
1 TATTAAATTATAATTAT
89754 TATTAAATATATAATTAT
1 TATTAAAT-TATAATTAT
89772 CATAACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTAAATTATAATTAT
Found at i:99883 original size:56 final size:56
Alignment explanation
Indices: 99797--99908 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
99787 TAAGAAGCTG
99797 TATATGTCTTGATCAAATTCAACAGGTACAAATTTGGATTAATCAGGTGGATATCA
1 TATATGTCTTGATCAAATTCAACAGGTACAAATTTGGATTAATCAGGTGGATATCA
99853 TATATGTCTTGATCAAATTCAACAGGTACAAATTTGGATTAATCAGGTGGATATCA
1 TATATGTCTTGATCAAATTCAACAGGTACAAATTTGGATTAATCAGGTGGATATCA
99909 ATTTTCCTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (56 bp):
TATATGTCTTGATCAAATTCAACAGGTACAAATTTGGATTAATCAGGTGGATATCA
Found at i:101050 original size:21 final size:20
Alignment explanation
Indices: 101016--101056 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
101006 TAAAAGATAT
* *
101016 TATATTTATTTTTATATTTA
1 TATATTTATATTTAAATTTA
101036 TATATCTTATATTTAAATTTA
1 TATAT-TTATATTTAAATTTA
101057 AAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TATATTTATATTTAAATTTA
Found at i:103013 original size:18 final size:18
Alignment explanation
Indices: 102966--103024 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
102956 TCGGGCAATA
102966 AAAGAAACAGAATAATAAAAG
1 AAAGAAA-AGAA-AA-AAAAG
102987 -AAGAAAAGAAAAAAAAG
1 AAAGAAAAGAAAAAAAAG
* *
103004 AAAGAGAAGAAGAAAAAG
1 AAAGAAAAGAAAAAAAAG
103022 AAA
1 AAA
103025 AAGATGAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 5 0.14
18 20 0.57
19 4 0.11
20 6 0.17
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (18 bp):
AAAGAAAAGAAAAAAAAG
Found at i:103017 original size:26 final size:25
Alignment explanation
Indices: 102984--103051 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 25
102974 AGAATAATAA
102984 AAGAAGAAAAGAAAAAAAAGAAAGAG
1 AAGAAGAAAAGAAAAAAAAG-AAGAG
* *
103010 AAGAAGAAAAAGAAAAAGATGAAGAG
1 AAGAAG-AAAAGAAAAAAAAGAAGAG
* *
103036 GAGAA-AAGAGAAAAAA
1 AAGAAGAAAAGAAAAAA
103052 TCTAGAGTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 9 0.25
26 15 0.42
27 12 0.33
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (25 bp):
AAGAAGAAAAGAAAAAAAAGAAGAG
Found at i:103033 original size:18 final size:18
Alignment explanation
Indices: 102982--103034 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
102972 ACAGAATAAT
* *
102982 AAAAGAAGAA-AAGAAAA
1 AAAAGAAAAAGAAGAAGA
*
102999 AAAAGAAAGAGAAGAAGA
1 AAAAGAAAAAGAAGAAGA
*
103017 AAAAGAAAAAGATGAAGA
1 AAAAGAAAAAGAAGAAGA
103035 GGAGAAAAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 8 0.27
18 22 0.73
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAGAAGAAGA
Found at i:103058 original size:23 final size:23
Alignment explanation
Indices: 103014--103058 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
103004 AAAGAGAAGA
*
103014 AGAAAAAGAAAAAGATGAAGAGG
1 AGAAAAAGAAAAAGATCAAGAGG
*
103037 AGAAAAGAGAAAAA-ATCTAGAG
1 AGAAAA-AGAAAAAGATCAAGAG
103059 TGGTTCAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.64, C:0.02, G:0.27, T:0.07
Consensus pattern (23 bp):
AGAAAAAGAAAAAGATCAAGAGG
Found at i:104922 original size:19 final size:19
Alignment explanation
Indices: 104893--104931 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
104883 ACGTTGATAA
104893 TGATTTTTG-TTTTAATTT
1 TGATTTTTGTTTTTAATTT
104911 TGATTGTTTGTTTTTAATTT
1 TGATT-TTTGTTTTTAATTT
104931 T
1 T
104932 TAAATCTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 4 0.21
20 10 0.53
ACGTcount: A:0.15, C:0.00, G:0.13, T:0.72
Consensus pattern (19 bp):
TGATTTTTGTTTTTAATTT
Found at i:105074 original size:27 final size:29
Alignment explanation
Indices: 105026--105088 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
105016 TCTTTTACAA
* *
105026 ATATTAAATTATTTATATAATTTTATTAT
1 ATATTATATTATTTATAGAATTTTATTAT
*
105055 ATATTATATT-TTTA-AGAATTTTATTTT
1 ATATTATATTATTTATAGAATTTTATTAT
*
105082 CTATTAT
1 ATATTAT
105089 TTTCAATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 17 0.57
28 4 0.13
29 9 0.30
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (29 bp):
ATATTATATTATTTATAGAATTTTATTAT
Found at i:113649 original size:49 final size:49
Alignment explanation
Indices: 113577--113674 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
113567 CAGATTTGTG
113577 GTTTGGAGCTTCATCGCCAAATCAGCATCCATACTTCCAAATATCTCAT
1 GTTTGGAGCTTCATCGCCAAATCAGCATCCATACTTCCAAATATCTCAT
113626 GTTTGGAGCTTCATCGCCAAATCAGCATCCATACTTCCAAATATCTCAT
1 GTTTGGAGCTTCATCGCCAAATCAGCATCCATACTTCCAAATATCTCAT
113675 TCTTTTCTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (49 bp):
GTTTGGAGCTTCATCGCCAAATCAGCATCCATACTTCCAAATATCTCAT
Found at i:115279 original size:17 final size:17
Alignment explanation
Indices: 115259--115302 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
115249 TTTATAAACT
115259 AGAAAAATAATTATGAA
1 AGAAAAATAATTATGAA
* *
115276 AGAAGAATAATTATTAA
1 AGAAAAATAATTATGAA
*
115293 A-ACAAATAAT
1 AGAAAAATAAT
115303 ATAAAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (17 bp):
AGAAAAATAATTATGAA
Found at i:119283 original size:19 final size:19
Alignment explanation
Indices: 119239--119283 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
119229 ATAAAAAATA
119239 TTTAAGATGTTAAAAAACCT
1 TTTAA-ATGTTAAAAAACCT
*
119259 TATAAATGTTCAAAAAA-CT
1 TTTAAATGTT-AAAAAACCT
119278 TTTAAA
1 TTTAAA
119284 AATTGTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.36
Consensus pattern (19 bp):
TTTAAATGTTAAAAAACCT
Found at i:122279 original size:28 final size:29
Alignment explanation
Indices: 122245--122309 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
122235 TATTTTATAC
* *
122245 TATTTTTTAAATATTTTTATGAATTT-TT
1 TATTTTTTAAATATTTTTATAAATTTAAT
* *
122273 TATTTTTTGAATATTTTTTTAAATTTAAT
1 TATTTTTTAAATATTTTTATAAATTTAAT
122302 TATTTTTT
1 TATTTTTT
122310 GCGAATAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 23 0.72
29 9 0.28
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (29 bp):
TATTTTTTAAATATTTTTATAAATTTAAT
Found at i:122283 original size:16 final size:18
Alignment explanation
Indices: 122256--122290 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
122246 ATTTTTTAAA
122256 TATTTTTATGAAT-TTTT
1 TATTTTTATGAATATTTT
122273 TATTTTT-TGAATATTTT
1 TATTTTTATGAATATTTT
122290 T
1 T
122291 TTAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (18 bp):
TATTTTTATGAATATTTT
Found at i:123784 original size:22 final size:23
Alignment explanation
Indices: 123725--123784 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
123715 GGTGTTATTT
123725 AAAATATTATAAAAATTATAAAAG
1 AAAATATTA-AAAAATTATAAAAG
* *
123749 AAAATTATTTAAAAATTATAACA-
1 AAAA-TATTAAAAAATTATAAAAG
*
123772 AAAACATTAAAAA
1 AAAATATTAAAAA
123785 TGGTAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 7 0.23
23 4 0.13
24 16 0.52
25 4 0.13
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAATATTAAAAAATTATAAAAG
Found at i:124173 original size:10 final size:10
Alignment explanation
Indices: 124140--124182 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
124130 TTTTACGAAA
*
124140 TTATAATAAT
1 TTATAATTAT
*
124150 TTATAATTGTT
1 TTATAATT-AT
*
124161 TTATGATTAT
1 TTATAATTAT
124171 TTATAATTAT
1 TTATAATTAT
124181 TT
1 TT
124183 TTAGAATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (10 bp):
TTATAATTAT
Done.