Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012874.1 Kokia drynarioides strain JFW-HI SEQ_127888, 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: 182654
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Warning! 152 characters in sequence are not A, C, G, or T
Found at i:337 original size:16 final size:16
Alignment explanation
Indices: 316--366 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
306 TGAATTACTG
*
316 ATTACAGCTCTATTCC
1 ATTACAGTTCTATTCC
* * *
332 ATTACAATTCTTTTCT
1 ATTACAGTTCTATTCC
*
348 GTTACAGTTCTATTCC
1 ATTACAGTTCTATTCC
364 ATT
1 ATT
367 GCCGCCCCAT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.47
Consensus pattern (16 bp):
ATTACAGTTCTATTCC
Found at i:14357 original size:23 final size:23
Alignment explanation
Indices: 14325--14479 Score: 156
Period size: 23 Copynumber: 6.7 Consensus size: 23
14315 AGGAACAATA
14325 GTGTGCTCTCTGTTTAGCAC-GT
1 GTGTGCTCTCTGTTTAGCACTGT
*
14347 CTCGTGCTCTCTGTTATTAGCACTGT
1 GT-GTGCTCTCTG-T-TTAGCACTGT
* *
14373 GTGTGCTCTCTGATTAGCACTTT
1 GTGTGCTCTCTGTTTAGCACTGT
14396 GTGTGCTCTCTGTTTAGCACTGT
1 GTGTGCTCTCTGTTTAGCACTGT
*
14419 GTGTGCTCTCTGTTGCACGGCACT-T
1 GTGTGCTCTCTGTT-TA--GCACTGT
* * *
14444 ATGTGCTCTCTG-TTAGTACTTT
1 GTGTGCTCTCTGTTTAGCACTGT
*
14466 G-GTACTCTCTGTTT
1 GTGTGCTCTCTGTTT
14480 GTTCCGTATA
Statistics
Matches: 112, Mismatches: 12, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
21 13 0.12
22 4 0.04
23 55 0.49
24 3 0.03
25 29 0.26
26 8 0.07
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.43
Consensus pattern (23 bp):
GTGTGCTCTCTGTTTAGCACTGT
Found at i:14413 original size:71 final size:69
Alignment explanation
Indices: 14325--14479 Score: 190
Period size: 71 Copynumber: 2.2 Consensus size: 69
14315 AGGAACAATA
* *
14325 GTGTGCTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGTT-ATTAGCACTGTGTGTGCTCTCTGATT
1 GTGTGCTCTCTGTTTAGCACTGTCT-GTGCTCTCTGTTCA-CAGCACT-TATGTGCTCTCTG-TT
14388 AGCACTTT
62 AGCACTTT
* * *
14396 GTGTGCTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTGCACGGCACTTATGTGCTCTCTGTTAGT
1 GTGTGCTCTCTGTTTAGCACTGTCTGTGCTCTCTGTT-CACAGCACTTATGTGCTCTCTGTTAGC
14461 ACTTT
65 ACTTT
*
14466 G-GTACTCTCTGTTT
1 GTGTGCTCTCTGTTT
14480 GTTCCGTATA
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
69 12 0.16
70 10 0.13
71 44 0.59
72 8 0.11
73 1 0.01
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.43
Consensus pattern (69 bp):
GTGTGCTCTCTGTTTAGCACTGTCTGTGCTCTCTGTTCACAGCACTTATGTGCTCTCTGTTAGCA
CTTT
Found at i:14416 original size:46 final size:48
Alignment explanation
Indices: 14325--14437 Score: 155
Period size: 48 Copynumber: 2.4 Consensus size: 48
14315 AGGAACAATA
*
14325 GTGTGCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGT
1 GTGTGCTCTCTGATTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGT
* *
14373 GTGTGCTCTCTGATTAGCAC-TTTGTGTGCTCTCTG-T-TTAGCACTGT
1 GTGTGCTCTCTGATTAGCACGTCT-CGTGCTCTCTGTTATTAGCACTGT
14419 GTGTGCTCTCTG-TT-GCACG
1 GTGTGCTCTCTGATTAGCACG
14438 GCACTTATGT
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
44 4 0.07
45 2 0.03
46 22 0.37
47 3 0.05
48 29 0.48
ACGTcount: A:0.10, C:0.24, G:0.25, T:0.42
Consensus pattern (48 bp):
GTGTGCTCTCTGATTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGT
Found at i:14449 original size:48 final size:45
Alignment explanation
Indices: 14325--14478 Score: 145
Period size: 48 Copynumber: 3.3 Consensus size: 45
14315 AGGAACAATA
* *
14325 GTGTGCTCTCTGTTTAGCACGTCT-CGTGCTCTCTGTTATTAGCACTGT
1 GTGTGCTCTCTG-TTAGCAC-TTTATGTGCTCTCTG-T-TTAGCACTGT
*
14373 GTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTTAGCACTGT
1 GTGTGCTCTCTG-TTAGCACTTTATGTGCTCTCTGTTTAGCACTGT
* *
14419 GTGTGCTCTCTGTTGCACGGCAC-TTATGTGCTCTCTG-TTAGTACTTT
1 GTGTGCTCTCTGTT--A--GCACTTTATGTGCTCTCTGTTTAGCACTGT
*
14466 G-GTACTCTCTGTT
1 GTGTGCTCTCTGTT
14479 TGTTCCGTAT
Statistics
Matches: 94, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
45 2 0.02
46 33 0.35
47 13 0.14
48 42 0.45
49 4 0.04
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.43
Consensus pattern (45 bp):
GTGTGCTCTCTGTTAGCACTTTATGTGCTCTCTGTTTAGCACTGT
Found at i:15752 original size:24 final size:24
Alignment explanation
Indices: 15723--15773 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
15713 AGAAATAATC
*
15723 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
15747 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
15771 TTT
1 TTT
15774 GAGTCAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:16244 original size:15 final size:16
Alignment explanation
Indices: 16217--16259 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
16207 AATAAACATC
16217 TAAAATTAA-TTTA-AA
1 TAAAA-TAATTTTACAA
16232 TAAAATAATTTTACAA
1 TAAAATAATTTTACAA
*
16248 TTAAATAATTTT
1 TAAAATAATTTT
16260 TTAACTCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 3 0.12
15 9 0.36
16 13 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAATAATTTTACAA
Found at i:22873 original size:17 final size:17
Alignment explanation
Indices: 22796--22871 Score: 68
Period size: 16 Copynumber: 4.6 Consensus size: 17
22786 ATAATCAATT
**
22796 AATATTTTTTATATCCA
1 AATATTTTTTATATTTA
*
22813 AA-ATTATTTA-ATTTA
1 AATATTTTTTATATTTA
* **
22828 ATTCATTTGGTATATTTA
1 AAT-ATTTTTTATATTTA
22846 AATATTTTTTATA-TTA
1 AATATTTTTTATATTTA
22862 AATATTTTTT
1 AATATTTTTT
22872 TAAAATAATA
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
15 4 0.09
16 20 0.43
17 15 0.33
18 7 0.15
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.58
Consensus pattern (17 bp):
AATATTTTTTATATTTA
Found at i:24742 original size:3 final size:3
Alignment explanation
Indices: 24734--24762 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
24724 AGTCAATTCA
24734 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
24763 ATTGATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:26122 original size:30 final size:31
Alignment explanation
Indices: 26088--26154 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
26078 GTTACATTTA
*
26088 ACAAAACAATCACTCAACTT-T-GAAAATGTG
1 ACAAAACAATCACTAAACTTATCGAAAA-GTG
* *
26118 ACAAAACAGTCACTAAATTTATCGAAAAGTG
1 ACAAAACAATCACTAAACTTATCGAAAAGTG
26149 ACAAAA
1 ACAAAA
26155 TATTCCTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 17 0.53
31 10 0.31
32 5 0.16
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.21
Consensus pattern (31 bp):
ACAAAACAATCACTAAACTTATCGAAAAGTG
Found at i:26257 original size:348 final size:348
Alignment explanation
Indices: 25620--26312 Score: 1298
Period size: 348 Copynumber: 2.0 Consensus size: 348
25610 CCCTAAATTT
* *
25620 TAAAAATGTGACAAAACAGTCATTTTTCATGTATTCCATCACAGACATCATGGAACAGTGACATG
1 TAAAAATGTGACAAAACAGTCATTTTTCATGTATTCCATCACAAACATCACGGAACAGTGACATG
25685 GCAGTTGACGGCGTCTAAGGAGTGTGAAAAACATCTAGCTGGCCAGTTACATTTAACAAAACAAT
66 GCAGTTGACGGCGTCTAAGGAGTGTGAAAAACATCTAGCTGGCCAGTTACATTTAACAAAACAAT
25750 CACTCAACTTTGAAAATGTGACAAAACAGTCACTAATGTTATCGAAAAGTGACAAAATAGTCCTC
131 CACTCAACTTTGAAAATGTGACAAAACAGTCACTAATGTTATCGAAAAGTGACAAAATAGTCCTC
25815 TACTTACTATTCATTTTTCTCCCTTGAATTTTCTCGAAAAATTTTGGTAAAAGCCTTGTGAGATG
196 TACTTACTATTCATTTTTCTCCCTTGAATTTTCTCGAAAAATTTTGGTAAAAGCCTTGTGAGATG
25880 TGAAAGGAAAGGGAAGTCTAGGTGTTGTTCTGTTTGACTCCAAAAATGGCTTCTTTGTACTGCAA
261 TGAAAGGAAAGGGAAGTCTAGGTGTTGTTCTGTTTGACTCCAAAAATGGCTTCTTTGTACTGCAA
25945 TAATCAGGTAAGAGATTCTTTGG
326 TAATCAGGTAAGAGATTCTTTGG
* * *
25968 TAAAAATGTGACAAAACAGTCCTTTTTCATGTATTCCGTCACAAACGTCACGGAACAGTGACATG
1 TAAAAATGTGACAAAACAGTCATTTTTCATGTATTCCATCACAAACATCACGGAACAGTGACATG
*
26033 GCAGTTGACGGCGTCTAAGGAGTGTGAAAAACATCTAGTTGGCCAGTTACATTTAACAAAACAAT
66 GCAGTTGACGGCGTCTAAGGAGTGTGAAAAACATCTAGCTGGCCAGTTACATTTAACAAAACAAT
*
26098 CACTCAACTTTGAAAATGTGACAAAACAGTCACTAAAT-TTATCGAAAAGTGACAAAATATTCCT
131 CACTCAACTTTGAAAATGTGACAAAACAGTCACT-AATGTTATCGAAAAGTGACAAAATAGTCCT
26162 CTACTTACTATTCATTTTTCTCCCTTGAATTTTCTCGAAAAATTTTGGTAAAAGCCTTGTGAGAT
195 CTACTTACTATTCATTTTTCTCCCTTGAATTTTCTCGAAAAATTTTGGTAAAAGCCTTGTGAGAT
*
26227 GTGAAAGGAAAGGGAAGTCTAGGTGTTGTTCTGTTTGACTCCAAAAATTGCTTCTTTGTACTGCA
260 GTGAAAGGAAAGGGAAGTCTAGGTGTTGTTCTGTTTGACTCCAAAAATGGCTTCTTTGTACTGCA
26292 ATAATCAGGTAAGAGATTCTT
325 ATAATCAGGTAAGAGATTCTT
26313 GTTTTACCAA
Statistics
Matches: 336, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
348 333 0.99
349 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (348 bp):
TAAAAATGTGACAAAACAGTCATTTTTCATGTATTCCATCACAAACATCACGGAACAGTGACATG
GCAGTTGACGGCGTCTAAGGAGTGTGAAAAACATCTAGCTGGCCAGTTACATTTAACAAAACAAT
CACTCAACTTTGAAAATGTGACAAAACAGTCACTAATGTTATCGAAAAGTGACAAAATAGTCCTC
TACTTACTATTCATTTTTCTCCCTTGAATTTTCTCGAAAAATTTTGGTAAAAGCCTTGTGAGATG
TGAAAGGAAAGGGAAGTCTAGGTGTTGTTCTGTTTGACTCCAAAAATGGCTTCTTTGTACTGCAA
TAATCAGGTAAGAGATTCTTTGG
Found at i:39347 original size:60 final size:61
Alignment explanation
Indices: 39273--39387 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
39263 TTTAATATAA
* * * *
39273 AATTTGGTACTTGAACTTGAT-ACTT-TTTCTTAATTTGGTATCTAAACTTTTTTTGGACCC
1 AATTTAGTACTTGAACCTG-TCACTTGTTTCCTAATTTGGTACCTAAACTTTTTTTGGACCC
* *
39333 AATTTAGTACTTGAACCTGTCATTTGTTTCCTAATTTGGTACCTAAGCTTTTTTT
1 AATTTAGTACTTGAACCTGTCACTTGTTTCCTAATTTGGTACCTAAACTTTTTTT
39388 AAAATTCAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 1 0.02
60 20 0.43
61 26 0.55
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.49
Consensus pattern (61 bp):
AATTTAGTACTTGAACCTGTCACTTGTTTCCTAATTTGGTACCTAAACTTTTTTTGGACCC
Found at i:39666 original size:89 final size:89
Alignment explanation
Indices: 39573--39737 Score: 212
Period size: 89 Copynumber: 1.9 Consensus size: 89
39563 CCAAAAGAGC
* *
39573 CAAGTTCAG-GTACCAAATTGGACCCCAAAAAA-TTTA-AGTACCAACTTAA-AAAAACTGTCAA
1 CAAGTT-AGAGTACCAAATTGGA-CCAAAAAAAGTTTAGA-TACCAAATTAATAAAAACTGTCAA
*
39634 GTTTAGGTACCAAATTAGGAAAAATTAT
63 GTTCAGGTA-CAAATTAGGAAAAATTAT
* * *
39662 CAAGTTTGAGTATCAAATTGGACCAAAAAAAGTTTAGATACCAAATTAATAAAAAGTGTCAAGTT
1 CAAGTTAGAGTACCAAATTGGACCAAAAAAAGTTTAGATACCAAATTAATAAAAACTGTCAAGTT
39727 CAGGTACAAAT
66 CAGGTACAAAT
39738 GTTATATTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
88 9 0.14
89 37 0.56
90 20 0.30
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (89 bp):
CAAGTTAGAGTACCAAATTGGACCAAAAAAAGTTTAGATACCAAATTAATAAAAACTGTCAAGTT
CAGGTACAAATTAGGAAAAATTAT
Found at i:40753 original size:16 final size:17
Alignment explanation
Indices: 40717--40756 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 17
40707 TTATGTTAAT
40717 AAATAATTTAAAATTATAA
1 AAAT-ATTTAAAA-TATAA
40736 AAATATTTAAAA-ATAA
1 AAATATTTAAAATATAA
40752 AAATA
1 AAATA
40757 AAAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
18 8 0.38
19 4 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATATTTAAAATATAA
Found at i:43008 original size:23 final size:23
Alignment explanation
Indices: 42964--43008 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
42954 AATATATAAA
*
42964 ATATAAACTTCAAAAAAGAATAT
1 ATATAAACTTCAAAAAAAAATAT
*
42987 ATATAAA-TTGAAAATAAAAATA
1 ATATAAACTTCAAAA-AAAAATA
43009 ACAAATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (23 bp):
ATATAAACTTCAAAAAAAAATAT
Found at i:46537 original size:20 final size:20
Alignment explanation
Indices: 46512--46552 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
46502 AATAAGCATA
*
46512 TTATGATGTATTTGAGACAT
1 TTATGATGTACTTGAGACAT
46532 TTATGATGTACTTGAGACAT
1 TTATGATGTACTTGAGACAT
46552 T
1 T
46553 GTTTGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (20 bp):
TTATGATGTACTTGAGACAT
Found at i:56121 original size:18 final size:18
Alignment explanation
Indices: 56098--56132 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56088 CTCTTTTTTG
*
56098 ATATTTTATATTTTAAAT
1 ATATTTTATAATTTAAAT
*
56116 ATATTTTTTAATTTAAA
1 ATATTTTATAATTTAAA
56133 AATAAAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATTTTATAATTTAAAT
Found at i:56129 original size:26 final size:25
Alignment explanation
Indices: 56066--56129 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 25
56056 ATTTCAATTT
*
56066 TTTTTTAATTTTATTATTAAAACTC
1 TTTTTTAATTTTATTATTAAAACTA
*
56091 TTTTTTGATATTTTATATTTTAAATA-TA
1 TTTTTT-A-ATTTTAT-TATTAAA-ACTA
56119 TTTTTTAATTT
1 TTTTTTAATTT
56130 AAAAATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
25 6 0.18
26 5 0.15
27 8 0.24
28 13 0.39
29 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (25 bp):
TTTTTTAATTTTATTATTAAAACTA
Found at i:76796 original size:18 final size:18
Alignment explanation
Indices: 76769--76803 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
76759 TGAATGGAGC
*
76769 AATTTAAAAATTCTTCAA
1 AATTTAAAAATTATTCAA
*
76787 AATTTCAAAATTATTCA
1 AATTTAAAAATTATTCA
76804 TCCAAACACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTTAAAAATTATTCAA
Found at i:87228 original size:15 final size:15
Alignment explanation
Indices: 87208--87236 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
87198 AAAAAGAGCC
87208 TGGATAATTTCAGTG
1 TGGATAATTTCAGTG
87223 TGGATAATTTCAGT
1 TGGATAATTTCAGT
87237 ATGATATGAA
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:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (15 bp):
TGGATAATTTCAGTG
Found at i:98907 original size:20 final size:18
Alignment explanation
Indices: 98853--98908 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
98843 TGGAAAATAA
* * *
98853 TAAAATAATATATTAAAT
1 TAAAAAAATAAATTAATT
*
98871 TAAAAAAATAACTTAATT
1 TAAAAAAATAAATTAATT
98889 TAAAGAAAATAAATGTAATT
1 TAAA-AAAATAAAT-TAATT
98909 ATCTTTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 18 0.58
19 8 0.26
20 5 0.16
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (18 bp):
TAAAAAAATAAATTAATT
Found at i:110242 original size:23 final size:23
Alignment explanation
Indices: 110199--110243 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
110189 ATTTGGTAAA
* *
110199 AAAAAATTTGACTTTTAAAAATT
1 AAAAAATATGACCTTTAAAAATT
110222 AAAAAATATGAACCTTTAAAAA
1 AAAAAATATG-ACCTTTAAAAA
110244 CTGGAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (23 bp):
AAAAAATATGACCTTTAAAAATT
Found at i:112271 original size:29 final size:28
Alignment explanation
Indices: 112190--112268 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
112180 TTAATTAAGC
* **
112190 CTAAATTTTGAAATATCAAAAGTAGAGTGA
1 CTAAATTTT-AAATAT-AAAAATAGAGAAA
* * *
112220 TTAAAATTCTAAAAATAAAAATAGAGAAA
1 CT-AAATTTTAAATATAAAAATAGAGAAA
112249 CTAAATTTTAAATATAAAAA
1 CTAAATTTTAAATATAAAAA
112269 ATATATAGAG
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
28 16 0.41
29 11 0.28
30 6 0.15
31 6 0.15
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.29
Consensus pattern (28 bp):
CTAAATTTTAAATATAAAAATAGAGAAA
Found at i:112736 original size:24 final size:24
Alignment explanation
Indices: 112674--112736 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
112664 AAAATCAATC
*
112674 ATTTAATAAATAT-TAATTTACAT
1 ATTTAATAAATATAAAATTTACAT
** * *
112697 ATCGAATCAATTTAAAATTTACAT
1 ATTTAATAAATATAAAATTTACAT
112721 ATTTAATAAATATAAA
1 ATTTAATAAATATAAA
112737 TATATTATTA
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
23 9 0.30
24 21 0.70
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (24 bp):
ATTTAATAAATATAAAATTTACAT
Found at i:113510 original size:3 final size:3
Alignment explanation
Indices: 113466--113490 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
113456 TGGCTTCAAA
113466 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
113491 TTGACAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:113601 original size:41 final size:41
Alignment explanation
Indices: 113543--113625 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
113533 AGAAGTCGCA
* *
113543 TTTTTAATTTATTTTCTTAAGTAACGTTCAAACTGTATTAT
1 TTTTTAATGTATATTCTTAAGTAACGTTCAAACTGTATTAT
*
113584 TTTTTAATGTATATTCTTAAGTGACGTTCAAACTGTATTAT
1 TTTTTAATGTATATTCTTAAGTAACGTTCAAACTGTATTAT
113625 T
1 T
113626 GTTAGGGAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (41 bp):
TTTTTAATGTATATTCTTAAGTAACGTTCAAACTGTATTAT
Found at i:122753 original size:42 final size:42
Alignment explanation
Indices: 122706--122842 Score: 152
Period size: 42 Copynumber: 3.3 Consensus size: 42
122696 ACATGTCAGT
* * * *
122706 AAAAGCTCGTTTAACTGAACGTGCTTTCTTGCCAACTATGC-
1 AAAAGCTCGTCTAGCTGAACGAGCTTTCTTGACAACTATGCG
* * *
122747 AGAAAGCTCGTCCAGCTGAACGAGTTTTCTTGACAACTGTGCG
1 A-AAAGCTCGTCTAGCTGAACGAGCTTTCTTGACAACTATGCG
* * *
122790 AAAAGCTCGCCTAGCTGAACGAGCTTTCCTGACAA-TAATGTG
1 AAAAGCTCGTCTAGCTGAACGAGCTTTCTTGACAACT-ATGCG
122832 AAAAGCTCGTC
1 AAAAGCTCGTC
122843 AACTGGACAC
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.03
42 76 0.96
43 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Consensus pattern (42 bp):
AAAAGCTCGTCTAGCTGAACGAGCTTTCTTGACAACTATGCG
Found at i:127486 original size:26 final size:25
Alignment explanation
Indices: 127449--127497 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
127439 CCCTAAATAG
127449 TATTTATGATTATATTATGTAAAAT
1 TATTTATGATTATATTATGTAAAAT
* *
127474 TATTATATTATTATTTTATGTAAA
1 TATT-TATGATTATATTATGTAAA
127498 TTTTGGTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (25 bp):
TATTTATGATTATATTATGTAAAAT
Found at i:136152 original size:31 final size:32
Alignment explanation
Indices: 136126--136196 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
136116 AATAAAAATG
*
136126 AATAAAATT-ATTAAATATTATAATAAAATAA
1 AATAAAATTAAATAAATATTATAATAAAATAA
* **
136157 AATAAAATTAAATAAATATTCTTTTAAAATAA
1 AATAAAATTAAATAAATATTATAATAAAATAA
*
136189 TATAAAAT
1 AATAAAAT
136197 AATGTTAAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 9 0.26
32 25 0.74
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (32 bp):
AATAAAATTAAATAAATATTATAATAAAATAA
Found at i:141474 original size:17 final size:17
Alignment explanation
Indices: 141448--141481 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
141438 GCTGATGTTT
141448 AGAAAAAAAAAAAAGAA
1 AGAAAAAAAAAAAAGAA
* *
141465 AGAAATAAAACAAAGAA
1 AGAAAAAAAAAAAAGAA
141482 GTTTCAAGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (17 bp):
AGAAAAAAAAAAAAGAA
Found at i:152899 original size:27 final size:27
Alignment explanation
Indices: 152868--152921 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
152858 AAACCTAAAA
*
152868 CCAAATCTTTATATATAATAGGTTAGT
1 CCAAATCATTATATATAATAGGTTAGT
* *
152895 CCAAATCATTGTATATACTAGGTTAGT
1 CCAAATCATTATATATAATAGGTTAGT
152922 TAAAAAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (27 bp):
CCAAATCATTATATATAATAGGTTAGT
Found at i:153947 original size:3 final size:3
Alignment explanation
Indices: 153941--153967 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
153931 ATAAAAAAAA
153941 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
153968 TTGAAGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:156126 original size:130 final size:131
Alignment explanation
Indices: 155885--156130 Score: 467
Period size: 130 Copynumber: 1.9 Consensus size: 131
155875 AATAAGTGAT
155885 TTATTTTTCTGATATAACATATTGAATCTATGTTGCTCCAACTCTTCATTTTTCTTAAAAGTACC
1 TTATTTTTCTGATATAACATATTGAATCTATGTTGCTCCAACTCTTCATTTTTCTTAAAAGTACC
155950 TATATCTAACACTAGTATCCGACACATGATTATGGGGACATAAGCTTCAAGTACCTATATCTAAC
66 TATATCTAACACTAGTATCCGACACATGATTATGGGGACATAAGCTTCAAGTACCTATATCTAAC
156015 A
131 A
156016 TTATTTTTCTGATATAACATATTGAATCTATGTTGCTCCAACTCTTCA-TTTTCTTAAAAGTACC
1 TTATTTTTCTGATATAACATATTGAATCTATGTTGCTCCAACTCTTCATTTTTCTTAAAAGTACC
* *
156080 TATATCTAACACTAGTATCCGACACATGATTATGGGGATATGAGCTTCAAG
66 TATATCTAACACTAGTATCCGACACATGATTATGGGGACATAAGCTTCAAG
156131 GACCCTTCAC
Statistics
Matches: 113, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
130 65 0.58
131 48 0.42
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (131 bp):
TTATTTTTCTGATATAACATATTGAATCTATGTTGCTCCAACTCTTCATTTTTCTTAAAAGTACC
TATATCTAACACTAGTATCCGACACATGATTATGGGGACATAAGCTTCAAGTACCTATATCTAAC
A
Found at i:158321 original size:29 final size:30
Alignment explanation
Indices: 158271--158329 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
158261 ATGCTATAAA
*
158271 CAAATTAAAAATGATATTAAAATA-ATTATT
1 CAAATTAAAAATGAAATTAAAA-ACATTATT
*
158301 CAAATTATAAAT-AAATTAAAAACATTATT
1 CAAATTAAAAATGAAATTAAAAACATTATT
158330 AAAACAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 1 0.04
29 14 0.54
30 11 0.42
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (30 bp):
CAAATTAAAAATGAAATTAAAAACATTATT
Found at i:158322 original size:41 final size:41
Alignment explanation
Indices: 158265--158349 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
158255 ATAAGCATGC
* * *
158265 TATAAACAAATTAAAAATGA-TATTAAAATAATTATTCAAAT
1 TATAAACAAATTAAAAA-CATTATTAAAACAAATATTCAAAT
* *
158306 TATAAATAAATTAAAAACATTATTAAAACAAATCTTCAAAT
1 TATAAACAAATTAAAAACATTATTAAAACAAATATTCAAAT
158347 TAT
1 TAT
158350 TATAAGTCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.58, C:0.07, G:0.01, T:0.34
Consensus pattern (41 bp):
TATAAACAAATTAAAAACATTATTAAAACAAATATTCAAAT
Found at i:160034 original size:86 final size:86
Alignment explanation
Indices: 159860--160023 Score: 283
Period size: 86 Copynumber: 1.9 Consensus size: 86
159850 GCAACCAGAC
*
159860 ATTAGGTCTTGTAACCATTTCTAAGTCAAAACAAAATCAGGGAAGTAAGAACTACATGAGGAGAA
1 ATTAGGTCTTGTAACAATTTCTAAGTCAAAACAAAATCAGGGAAGTAAGAACTACATGAGGAGAA
**
159925 GCAGGGGGAGAAGCGCTGTAA
66 GCAACGGGAGAAGCGCTGTAA
*
159946 ATTAGGTCTTGTAATAATTTCTAAGTCAAAACAAAATCAGGGAAGTAAGAACTACATGAGGAGAA
1 ATTAGGTCTTGTAACAATTTCTAAGTCAAAACAAAATCAGGGAAGTAAGAACTACATGAGGAGAA
*
160011 GCAACTGGAGAAG
66 GCAACGGGAGAAG
160024 TGTCGTAAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 73 1.00
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.21
Consensus pattern (86 bp):
ATTAGGTCTTGTAACAATTTCTAAGTCAAAACAAAATCAGGGAAGTAAGAACTACATGAGGAGAA
GCAACGGGAGAAGCGCTGTAA
Found at i:172012 original size:9 final size:9
Alignment explanation
Indices: 171978--172021 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 9
171968 CTTTATAATT
171978 TTTAAAAAA
1 TTTAAAAAA
171987 -TTAAATTAAA
1 TTTAAA--AAA
171997 TTTTAAAAAA
1 -TTTAAAAAA
172007 TTTAAAAAA
1 TTTAAAAAA
172016 TTTAAA
1 TTTAAA
172022 TAAAAACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 5 0.16
9 15 0.48
10 6 0.19
12 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:175258 original size:15 final size:15
Alignment explanation
Indices: 175240--175280 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
175230 TTTAAAATTT
*
175240 TTAAAATCTTAAATA
1 TTAAAATCTTAAAAA
175255 TTAAAAT-TTAAAAA
1 TTAAAATCTTAAAAA
*
175269 CTAAAATCTTAA
1 TTAAAATCTTAA
175281 CACTAATGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAAATCTTAAAAA
Found at i:175275 original size:22 final size:22
Alignment explanation
Indices: 175239--175280 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
175229 TTTTAAAATT
* *
175239 TTTAAAATCTTAAATATTAAAA
1 TTTAAAAACTAAAATATTAAAA
*
175261 TTTAAAAACTAAAATCTTAA
1 TTTAAAAACTAAAATATTAA
175281 CACTAATGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAAACTAAAATATTAAAA
Found at i:176973 original size:283 final size:283
Alignment explanation
Indices: 176466--177034 Score: 1111
Period size: 283 Copynumber: 2.0 Consensus size: 283
176456 CATTTGAGGC
176466 TTCTGGAATAAGCCAACAAGCAAAAACAAATACAACCAATTTGCAATATTAACATCCATGTATAG
1 TTCTGGAATAAGCCAACAAGCAAAAACAAATACAACCAATTTGCAATATTAACATCCATGTATAG
*
176531 GATCTTTTAAAATTCTCATTCGAACCCAAATTATACTCCAGAATCAATGGAATCGTGTTCCACTC
66 GATCTTTTAAAATTCTCATTCGAACCCAAATTATACTCCAGAATCAATGGAATCGTATTCCACTC
176596 CTAATCGGAAGACCTTCCACCCACAAGTCATGGGTGGATTCTGCATCACTGTCAAAGCCAGAGCA
131 CTAATCGGAAGACCTTCCACCCACAAGTCATGGGTGGATTCTGCATCACTGTCAAAGCCAGAGCA
* *
176661 TTTGGTAGAGATCAACTAAGTTAACAATTTAAACTGGGAAAAATTGGTGGATCATTCAGTTTTGC
196 TTTGGGAGAGATCAACTAAGTTAACAATTTAAACTGGGAAAAATTGGCGGATCATTCAGTTTTGC
176726 AGAATACAATGATCAAGGGGAAA
261 AGAATACAATGATCAAGGGGAAA
176749 TTCTGGAATAAGCCAACAAGCAAAAACAAATACAACCAATTTGCAATATTAACATCCATGTATAG
1 TTCTGGAATAAGCCAACAAGCAAAAACAAATACAACCAATTTGCAATATTAACATCCATGTATAG
176814 GATCTTTTAAAATTCTCATTCGAACCCAAATTATACTCCAGAATCAATGGAATCGTATTCCACTC
66 GATCTTTTAAAATTCTCATTCGAACCCAAATTATACTCCAGAATCAATGGAATCGTATTCCACTC
176879 CTAATCGGAAGACCTTCCACCCACAAGTCATGGGTGGATTCTGCATCACTGTCAAAGCCAGAGCA
131 CTAATCGGAAGACCTTCCACCCACAAGTCATGGGTGGATTCTGCATCACTGTCAAAGCCAGAGCA
176944 TTTGGGAGAGATCAACTAAGTTAACAATTTAAACTGGGAAAAATTGGCGGATCATTCAGTTTTGC
196 TTTGGGAGAGATCAACTAAGTTAACAATTTAAACTGGGAAAAATTGGCGGATCATTCAGTTTTGC
177009 AGAATACAATGATCAAGGGGAAA
261 AGAATACAATGATCAAGGGGAAA
177032 TTC
1 TTC
177035 CTTGTTCTCC
Statistics
Matches: 283, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
283 283 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (283 bp):
TTCTGGAATAAGCCAACAAGCAAAAACAAATACAACCAATTTGCAATATTAACATCCATGTATAG
GATCTTTTAAAATTCTCATTCGAACCCAAATTATACTCCAGAATCAATGGAATCGTATTCCACTC
CTAATCGGAAGACCTTCCACCCACAAGTCATGGGTGGATTCTGCATCACTGTCAAAGCCAGAGCA
TTTGGGAGAGATCAACTAAGTTAACAATTTAAACTGGGAAAAATTGGCGGATCATTCAGTTTTGC
AGAATACAATGATCAAGGGGAAA
Done.