Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009362.1 Kokia drynarioides strain JFW-HI SEQ_124069, 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: 68342
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:12058 original size:42 final size:42
Alignment explanation
Indices: 11999--12079 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
11989 ATGACCACTT
* * *
11999 TAACCCAACCACTGATGGTGGGGGTTGGGTCATTATCTACTG
1 TAACCCAACCACTGATGGTGGGGATTAGGCCATTATCTACTG
12041 TAACCCAACCACTGATGGTGGGGATTAGGCCATTATCTA
1 TAACCCAACCACTGATGGTGGGGATTAGGCCATTATCTA
12080 ATCTGTGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (42 bp):
TAACCCAACCACTGATGGTGGGGATTAGGCCATTATCTACTG
Found at i:13376 original size:20 final size:21
Alignment explanation
Indices: 13329--13376 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
13319 AACTCGAACC
* *
13329 TCAAATCTCAAACCTCAAACT
1 TCAAACCTTAAACCTCAAACT
**
13350 TTGAACCTTAAACCT-AAACT
1 TCAAACCTTAAACCTCAAACT
13370 TCAAACC
1 TCAAACC
13377 CCAAATTTGA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.42, C:0.31, G:0.02, T:0.25
Consensus pattern (21 bp):
TCAAACCTTAAACCTCAAACT
Found at i:13914 original size:20 final size:21
Alignment explanation
Indices: 13867--13914 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
13857 AACTCGAATC
* *
13867 TCAAATCTCAAACCTCAAACT
1 TCAAACCTTAAACCTCAAACT
**
13888 TTGAACCTTAAACCT-AAACT
1 TCAAACCTTAAACCTCAAACT
13908 TCAAACC
1 TCAAACC
13915 CCAAATTTGA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.42, C:0.31, G:0.02, T:0.25
Consensus pattern (21 bp):
TCAAACCTTAAACCTCAAACT
Found at i:13920 original size:538 final size:538
Alignment explanation
Indices: 12903--13979 Score: 2136
Period size: 538 Copynumber: 2.0 Consensus size: 538
12893 ATCCGATTCG
12903 ATTCAAAAAAATTTTAAATTGAATTTGGTTGCCAAAATAGGATTCATCAACTCGATTAACTCAAA
1 ATTCAAAAAAATTTTAAATTGAATTTGGTTGCCAAAATAGGATTCATCAACTCGATTAACTCAAA
12968 ATTTTTTGACTCGATTCAACTCGACTCGATCGAATACTCACCCTAGTGATATGTTTATGTCATGC
66 ATTTTTTGACTCGATTCAACTCGACTCGATCGAATACTCACCCTAGTGATATGTTTATGTCATGC
13033 TTTGATGATGCATCGACTGTAGGAGAGTCTTGATGATTTGGACTCGTGTGCTTTAATCCAACAAT
131 TTTGATGATGCATCGACTGTAGGAGAGTCTTGATGATTTGGACTCGTGTGCTTTAATCCAACAAT
13098 TCTAGTTTCTTCATAAATTTATTTTGTTTTAGGAGTGTGCATTATTTGTTGAAGGGTTTTGTAAT
196 TCTAGTTTCTTCATAAATTTATTTTGTTTTAGGAGTGTGCATTATTTGTTGAAGGGTTTTGTAAT
13163 AAATGATAAAGGGAAAGATTGTTAGAAATTTGGGAGAAATTATTTTATGGACTTTTCACATAAAA
261 AAATGATAAAGGGAAAGATTGTTAGAAATTTGGGAGAAATTATTTTATGGACTTTTCACATAAAA
13228 TTATTTGTGGTTTATTTTTAATTATTTAATAATATTTCAATAATTTTTTTAAAGTAATTGATAAA
326 TTATTTGTGGTTTATTTTTAATTATTTAATAATATTTCAATAATTTTTTTAAAGTAATTGATAAA
13293 TGATTTTGGTTATTTTTTGAACTCCGAACTCGAACCTCAAATCTCAAACCTCAAACTTTGAACCT
391 TGATTTTGGTTATTTTTTGAACTCCGAACTCGAACCTCAAATCTCAAACCTCAAACTTTGAACCT
*
13358 TAAACCTAAACTTCAAACCCCAAATTTGAAGTATAAACCTTAGCTAAAAGTTCAGGATTTAAGGT
456 TAAACCTAAACTTCAAACCCCAAATTTGAAGTATAAACCTTAACTAAAAGTTCAGGATTTAAGGT
13423 TTAGGTTATAAAAAAATT
521 TTAGGTTATAAAAAAATT
13441 ATTCAAAAAAATTTTAAATTGAATTTGGTTGCCAAAATAGGATTCATCAACTCGATTAACTCAAA
1 ATTCAAAAAAATTTTAAATTGAATTTGGTTGCCAAAATAGGATTCATCAACTCGATTAACTCAAA
13506 ATTTTTTGACTCGATTCAACTCGACTCGATCGAATACTCACCCTAGTGATATGTTTATGTCATGC
66 ATTTTTTGACTCGATTCAACTCGACTCGATCGAATACTCACCCTAGTGATATGTTTATGTCATGC
13571 TTTGATGATGCATCGACTGTAGGAGAGTCTTGATGATTTGGACTCGTGTGCTTTAATCCAACAAT
131 TTTGATGATGCATCGACTGTAGGAGAGTCTTGATGATTTGGACTCGTGTGCTTTAATCCAACAAT
13636 TCTAGTTTCTTCATAAATTTATTTTGTTTTAGGAGTGTGCATTATTTGTTGAAGGGTTTTGTAAT
196 TCTAGTTTCTTCATAAATTTATTTTGTTTTAGGAGTGTGCATTATTTGTTGAAGGGTTTTGTAAT
13701 AAATGATAAAGGGAAAGATTGTTAGAAATTTGGGAGAAATTATTTTATGGACTTTTCACATAAAA
261 AAATGATAAAGGGAAAGATTGTTAGAAATTTGGGAGAAATTATTTTATGGACTTTTCACATAAAA
13766 TTATTTGTGGTTTATTTTTAATTATTTAATAATATTTCAATAATTTTTTTAAAGTAATTGATAAA
326 TTATTTGTGGTTTATTTTTAATTATTTAATAATATTTCAATAATTTTTTTAAAGTAATTGATAAA
*
13831 TGATTTTGGTTATTTTTTGAACTCCGAACTCGAATCTCAAATCTCAAACCTCAAACTTTGAACCT
391 TGATTTTGGTTATTTTTTGAACTCCGAACTCGAACCTCAAATCTCAAACCTCAAACTTTGAACCT
13896 TAAACCTAAACTTCAAACCCCAAATTTGAAGTATAAACCTTAACTAAAAGTTCAGGATTTAAGGT
456 TAAACCTAAACTTCAAACCCCAAATTTGAAGTATAAACCTTAACTAAAAGTTCAGGATTTAAGGT
13961 TTAGGTTATAAAAAAATT
521 TTAGGTTATAAAAAAATT
13979 A
1 A
13980 CCGAAATTAT
Statistics
Matches: 537, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
538 537 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.39
Consensus pattern (538 bp):
ATTCAAAAAAATTTTAAATTGAATTTGGTTGCCAAAATAGGATTCATCAACTCGATTAACTCAAA
ATTTTTTGACTCGATTCAACTCGACTCGATCGAATACTCACCCTAGTGATATGTTTATGTCATGC
TTTGATGATGCATCGACTGTAGGAGAGTCTTGATGATTTGGACTCGTGTGCTTTAATCCAACAAT
TCTAGTTTCTTCATAAATTTATTTTGTTTTAGGAGTGTGCATTATTTGTTGAAGGGTTTTGTAAT
AAATGATAAAGGGAAAGATTGTTAGAAATTTGGGAGAAATTATTTTATGGACTTTTCACATAAAA
TTATTTGTGGTTTATTTTTAATTATTTAATAATATTTCAATAATTTTTTTAAAGTAATTGATAAA
TGATTTTGGTTATTTTTTGAACTCCGAACTCGAACCTCAAATCTCAAACCTCAAACTTTGAACCT
TAAACCTAAACTTCAAACCCCAAATTTGAAGTATAAACCTTAACTAAAAGTTCAGGATTTAAGGT
TTAGGTTATAAAAAAATT
Found at i:14436 original size:155 final size:154
Alignment explanation
Indices: 14135--14446 Score: 500
Period size: 155 Copynumber: 2.0 Consensus size: 154
14125 TTAGGCCCGA
* * * * * *
14135 AATTTAGAAGGGTTTGGGCAAAAAAATTAGGCCCGTTATCTGAACCCAACCTGACCTGACTCATT
1 AATTTAAAAGGATTTGGGAAAAAAAATTAGGCCCATTATCTGAACCCAACCTGACCCGACTCAAT
*
14200 TTAAATTTATAATACTTTATATTATTTTATTTTTATATATTACATAATTTAAAATGCATAAAATA
66 TTAAATTTATAATACTTTATATTATTTTATTTTTATATATTACATAATTCAAAATGCATAAAATA
14265 ATAAACCTATATTAAATATATAAT
131 ATAAACCTATATTAAATATATAAT
* *
14289 AATTTAAAAGGATTTGGGTAAAAAAAATTAGGCCCATTA-CTTGAACTCGACCTGACCCGACTCA
1 AATTTAAAAGGATTTGGG-AAAAAAAATTAGGCCCATTATC-TGAACCCAACCTGACCCGACTCA
*
14353 ATTTAAATTTATAATACTTTATATTATTTTATTTTTATATATTATATAATTCAAAATGCATAAAA
64 ATTTAAATTTATAATACTTTATATTATTTTATTTTTATATATTACATAATTCAAAATGCATAAAA
*
14418 TAATAAATCTATATTAAATATATAAT
129 TAATAAACCTATATTAAATATATAAT
14444 AAT
1 AAT
14447 ACTATAATGT
Statistics
Matches: 145, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
154 17 0.12
155 128 0.88
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (154 bp):
AATTTAAAAGGATTTGGGAAAAAAAATTAGGCCCATTATCTGAACCCAACCTGACCCGACTCAAT
TTAAATTTATAATACTTTATATTATTTTATTTTTATATATTACATAATTCAAAATGCATAAAATA
ATAAACCTATATTAAATATATAAT
Found at i:14442 original size:22 final size:25
Alignment explanation
Indices: 14417--14469 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 25
14407 AATGCATAAA
14417 ATAATAAAT-CTAT-AT-TAAATAT
1 ATAATAAATACTATAATGTAAATAT
14439 ATAAT-AATACTATAATGTAAATAT
1 ATAATAAATACTATAATGTAAATAT
14463 -TAATAAA
1 ATAATAAA
14470 ATAGATGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 3 0.11
22 9 0.33
23 6 0.22
24 9 0.33
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATAATAAATACTATAATGTAAATAT
Found at i:14735 original size:19 final size:19
Alignment explanation
Indices: 14697--14735 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
14687 TAAAAAATTT
*
14697 ATAAAATTATTAAAATAAA
1 ATAAAATTATTAAAAAAAA
14716 ATAAATATT-TTAAAAAAAA
1 ATAAA-ATTATTAAAAAAAA
14735 A
1 A
14736 GTTAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAAATTATTAAAAAAAA
Found at i:16224 original size:18 final size:17
Alignment explanation
Indices: 16203--16247 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
16193 TAGATTAATT
* *
16203 TTTAGATTTATTTCTAAA
1 TTTAAATTTACTT-TAAA
16221 TTTAAATTTACTTTAAA
1 TTTAAATTTACTTTAAA
16238 TTTAAATTTA
1 TTTAAATTTA
16248 AATTTACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:16226 original size:6 final size:6
Alignment explanation
Indices: 16217--16314 Score: 80
Period size: 6 Copynumber: 16.7 Consensus size: 6
16207 GATTTATTTC
* *
16217 TAAATT TAAATT T-ACTT TAAATT TAAATT TAAATT T-ACTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
** * *
16263 TAAATT T-TGTT TAAATT TGAAA-- TAATTT TAAACTT TAAACTT TAAAAT
1 TAAATT TAAATT TAAATT T-AAATT TAAATT TAAA-TT TAAA-TT TAAATT
16311 TAAA
1 TAAA
16315 CCCAAAATAA
Statistics
Matches: 74, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
4 2 0.03
5 12 0.16
6 44 0.59
7 16 0.22
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (6 bp):
TAAATT
Found at i:16237 original size:11 final size:11
Alignment explanation
Indices: 16221--16264 Score: 70
Period size: 11 Copynumber: 3.9 Consensus size: 11
16211 TATTTCTAAA
16221 TTTAAATTTAC
1 TTTAAATTTAC
*
16232 TTTAAATTTAAA
1 TTTAAATTT-AC
16244 TTTAAATTTAC
1 TTTAAATTTAC
16255 TTTAAATTTA
1 TTTAAATTTA
16265 AATTTTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAC
Found at i:16239 original size:17 final size:17
Alignment explanation
Indices: 16238--16285 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
16228 TTACTTTAAA
16238 TTTAAATTTAAATTTAC
1 TTTAAATTTAAATTTAC
**
16255 TTTAAATTTAAATTTTG
1 TTTAAATTTAAATTTAC
16272 TTTAAATTTGAAAT
1 TTTAAATTT-AAAT
16286 AATTTTAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 24 0.86
18 4 0.14
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAC
Found at i:16243 original size:23 final size:23
Alignment explanation
Indices: 16217--16269 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
16207 GATTTATTTC
16217 TAAATTTAAATTTACTTTAAATT
1 TAAATTTAAATTTACTTTAAATT
16240 TAAATTTAAATTTACTTTAAATT
1 TAAATTTAAATTTACTTTAAATT
16263 TAAATTT
1 TAAATTT
16270 TGTTTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAATTTAAATTTACTTTAAATT
Found at i:18203 original size:59 final size:58
Alignment explanation
Indices: 18106--18281 Score: 237
Period size: 59 Copynumber: 3.0 Consensus size: 58
18096 CCTTGGAGGT
* * *
18106 CCCTAAACTGTCCACAAATTCCA-TTTTGACCTCAAAACTTCCAAGAATTATATTTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTGA-CTCAAAACTTCCAAAAATTACATTTTTAC
*
18165 CCCTAAACTTCCAAAAATTCCATTTTTGACATCGAAACTTCCAAAAATTACATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTGAC-TCAAAACTTCCAAAAATTACATTTTTAC
** * *
18224 CCCCGAACTTCCAAAAATTCCATTTTTTACTCCAAAACTTTCAAAAATTACATTTTTA
1 CCCTAAACTTCCAAAAATTCCATTTTTGACT-CAAAACTTCCAAAAATTACATTTTTA
18282 TCGCCGAACC
Statistics
Matches: 105, Mismatches: 9, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
58 14 0.13
59 91 0.87
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (58 bp):
CCCTAAACTTCCAAAAATTCCATTTTTGACTCAAAACTTCCAAAAATTACATTTTTAC
Found at i:18205 original size:30 final size:29
Alignment explanation
Indices: 18110--18281 Score: 166
Period size: 29 Copynumber: 5.8 Consensus size: 29
18100 GGAGGTCCCT
* * *
18110 AAACTGTCCACAAATTCCATTTTGACCTCA
1 AAACT-TCCAAAAATTACATTTTTACCTCA
* * * *
18140 AAACTTCCAAGAATTATATTTTTACCCCT
1 AAACTTCCAAAAATTACATTTTTACCTCA
* * *
18169 AAACTTCCAAAAATTCCATTTTTGACATCG
1 AAACTTCCAAAAATTACATTTTT-ACCTCA
* *
18199 AAACTTCCAAAAATTACATTTTTACCCCC
1 AAACTTCCAAAAATTACATTTTTACCTCA
* *
18228 GAACTTCCAAAAATTCCATTTTTTA-CTCCA
1 AAACTTCCAAAAATTACA-TTTTTACCT-CA
*
18258 AAACTTTCAAAAATTACATTTTTA
1 AAACTTCCAAAAATTACATTTTTA
18282 TCGCCGAACC
Statistics
Matches: 115, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
29 63 0.55
30 52 0.45
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTACCTCA
Found at i:18289 original size:59 final size:56
Alignment explanation
Indices: 18111--18422 Score: 233
Period size: 59 Copynumber: 5.4 Consensus size: 56
18101 GAGGTCCCTA
* * * *
18111 AACTGTCCACAAATTCCATTTTGACCTCAAAACTTCCAAGAATTATATTTTTACCCCTA
1 AACT-TCCAAAAATTCCATTTTGACC-CAAAACTTCCAAAAATTACATTTTTACCCC-G
* *
18170 AACTTCCAAAAATTCCATTTTTGACATCGAAACTTCCAAAAATTACATTTTTACCCCCG
1 AACTTCCAAAAATTCCA-TTTTGAC-CCAAAACTTCCAAAAATTACATTTTTA-CCCCG
* * *
18229 AACTTCCAAAAATTCCATTTTTTACTCCAAAACTTTCAAAAATTACATTTTTATCGCCG
1 AACTTCCAAAAATTCCA-TTTTGAC-CCAAAACTTCCAAAAATTACATTTTTA-CCCCG
* * * * **
18288 AACCT-CAAAAATTCTATTTTTACCCTTAAACTTTTAAAAATTACCA-TTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTGACCC-AAAACTTCCAAAAATTA-CATTTTTA-CCCCG
* ** * *
18345 AA-TGTCCAAAACTT-TGTTTTGACCTCGAAAC-TCAAAAAAATTACCATTTTT-CCCTCG
1 AACT-TCCAAAAATTCCATTTTGACC-CAAAACTTC-CAAAAATTA-CATTTTTACCC-CG
18402 AA-TGTCCAAAAATTCCATTTT
1 AACT-TCCAAAAATTCCATTTT
18423 TTATCTCGAT
Statistics
Matches: 212, Mismatches: 29, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
56 6 0.03
57 72 0.34
58 40 0.19
59 90 0.42
60 4 0.02
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (56 bp):
AACTTCCAAAAATTCCATTTTGACCCAAAACTTCCAAAAATTACATTTTTACCCCG
Found at i:18298 original size:29 final size:27
Alignment explanation
Indices: 18141--18309 Score: 99
Period size: 29 Copynumber: 5.8 Consensus size: 27
18131 TTGACCTCAA
* * * *
18141 AACTTCCAAGAATTATATTTTTACCCCTA
1 AACTT-CAAAAATTACATTTTTATCCC-G
* *
18170 AACTTCCAAAAATTCCATTTTTGA-CATCG
1 AACTT-CAAAAATTACATTTTT-ATC-CCG
*
18199 AAACTTCCAAAAATTACATTTTTACCCCCG
1 -AACTT-CAAAAATTACATTTTTA-TCCCG
* **
18229 AACTTCCAAAAATTCCATTTTTTACTCCAA
1 AACTT-CAAAAATTACA-TTTTTA-TCCCG
18259 AACTTTCAAAAATTACATTTTTATCGCCG
1 AAC-TTCAAAAATTACATTTTTATC-CCG
*
18288 AACCTCAAAAATT-CTATTTTTA
1 AACTTCAAAAATTAC-ATTTTTA
18310 CCCTTAAACT
Statistics
Matches: 116, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
27 1 0.01
28 18 0.16
29 47 0.41
30 47 0.41
31 3 0.03
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (27 bp):
AACTTCAAAAATTACATTTTTATCCCG
Found at i:18355 original size:29 final size:29
Alignment explanation
Indices: 18323--18518 Score: 102
Period size: 30 Copynumber: 6.8 Consensus size: 29
18313 TTAAACTTTT
*
18323 AAAAATTACCATTTTACCCCCGAATGTCC
1 AAAAATTACCATTTTACCCTCGAATGTCC
* ** ** *
18352 AAAACTT--TGTTTTGA-CCTCGAAACTCAA
1 AAAAATTACCATTTT-ACCCTCGAATGTC-C
*
18380 AAAAATTACCATTTTTCCCTCGAATGTCC
1 AAAAATTACCATTTTACCCTCGAATGTCC
* * * *
18409 AAAAATT-CCATTTTTTA-TCTCGATTTTTCT
1 AAAAATTACCA--TTTTACCCTCGA-ATGTCC
*
18439 AAAAATTACCGTTTTACCCTCGAATGT-C
1 AAAAATTACCATTTTACCCTCGAATGTCC
* * * *
18467 TAAAATT-TCATTTTAAACCC-CAAAATTTCC
1 AAAAATTACCATTTT--ACCCTC-GAATGTCC
*
18497 AAAAATTACCATTTTACGCTCG
1 AAAAATTACCATTTTACCCTCG
18519 GGTATCCAAA
Statistics
Matches: 118, Mismatches: 33, Indels: 32
0.64 0.18 0.17
Matches are distributed among these distances:
27 17 0.14
28 17 0.14
29 36 0.31
30 40 0.34
31 8 0.07
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.36
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTCGAATGTCC
Found at i:23823 original size:18 final size:18
Alignment explanation
Indices: 23776--23824 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
23766 TATAAATAAA
* *
23776 TAAAAATATCAATGAATG
1 TAAAAATATAAATGAAGG
*
23794 AATAAAAT-TAAATGAAGG
1 TA-AAAATATAAATGAAGG
23812 TAAAAATATAAAT
1 TAAAAATATAAAT
23825 AACATTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.27
Consensus pattern (18 bp):
TAAAAATATAAATGAAGG
Found at i:23825 original size:28 final size:24
Alignment explanation
Indices: 23794--23858 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 24
23784 TCAATGAATG
23794 AATAAAATTAAATGAAGGTAAAAATATA
1 AATAAAATTAAAT-AA--TAAAAA-ATA
*
23822 AATAACATT-AA-AATAAAAAATA
1 AATAAAATTAAATAATAAAAAATA
23844 AATAAAATTAAATAA
1 AATAAAATTAAATAA
23859 AAGTGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
22 11 0.33
23 8 0.24
24 2 0.06
25 2 0.06
27 2 0.06
28 8 0.24
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.25
Consensus pattern (24 bp):
AATAAAATTAAATAATAAAAAATA
Found at i:24052 original size:33 final size:31
Alignment explanation
Indices: 23991--24056 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
23981 ATTTAATGAT
23991 AAATAAATAAATAAACAAAAAAAGATAATAA
1 AAATAAATAAATAAACAAAAAAAGATAATAA
*
24022 AAATAAATGCAAATTAAATAAAAAAA-ATAATAA
1 AAATAAAT--AAA-TAAACAAAAAAAGATAATAA
24055 AA
1 AA
24057 GAGATAACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 8 0.26
33 12 0.39
34 11 0.35
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (31 bp):
AAATAAATAAATAAACAAAAAAAGATAATAA
Found at i:24104 original size:22 final size:21
Alignment explanation
Indices: 24079--24131 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
24069 AAATGACATG
24079 AAAATAAATAAC-AATTAAATA
1 AAAATAAA-AACAAATTAAATA
*
24100 AAAAAACAAAACAAATTAAATA
1 AAAATA-AAAACAAATTAAATA
24122 AAAATAAAAA
1 AAAATAAAAA
24132 TTAAATGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (21 bp):
AAAATAAAAACAAATTAAATA
Found at i:24132 original size:17 final size:17
Alignment explanation
Indices: 24112--24170 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 17
24102 AAAACAAAAC
24112 AAATTAAATAAAAATAA
1 AAATTAAATAAAAATAA
*
24129 AAATTAAATGCTAAAATAA
1 AAATTAAAT--AAAAATAA
* *
24148 ACAAATATATAAACAATAA
1 A-AATTAAATAAA-AATAA
24167 AAAT
1 AAAT
24171 AATTGGGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
17 9 0.27
18 4 0.12
19 14 0.42
20 6 0.18
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (17 bp):
AAATTAAATAAAAATAA
Found at i:24230 original size:25 final size:25
Alignment explanation
Indices: 24191--24246 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
24181 AGGCATGAAA
*
24191 ATAAATGACAAATAAATAAATAAAT
1 ATAAATGACAAATAAACAAATAAAT
* *
24216 -TAAATGTCGAAATAAACAAGTAAAT
1 ATAAATGAC-AAATAAACAAATAAAT
24241 ATAAAT
1 ATAAAT
24247 AATAATGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 7 0.27
25 14 0.54
26 5 0.19
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (25 bp):
ATAAATGACAAATAAACAAATAAAT
Found at i:26281 original size:22 final size:21
Alignment explanation
Indices: 26243--26290 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
26233 GTCATTAATG
*
26243 AGAAGTTGATGAATTAGGCTT
1 AGAAATTGATGAATTAGGCTT
26264 -GAAATTGATAGATATTAGGCTT
1 AGAAATTGAT-GA-ATTAGGCTT
26286 AGAAA
1 AGAAA
26291 ATGAAAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 8 0.35
21 2 0.09
22 9 0.39
23 4 0.17
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (21 bp):
AGAAATTGATGAATTAGGCTT
Found at i:28323 original size:33 final size:33
Alignment explanation
Indices: 28281--28346 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
28271 TGTTTAATTC
28281 ATTCTAATACTTGTGACGAATTGCATAATTGTT
1 ATTCTAATACTTGTGACGAATTGCATAATTGTT
28314 ATTCTAATACTTGTGACGAATTGCATAATTGTT
1 ATTCTAATACTTGTGACGAATTGCATAATTGTT
28347 TATGTCGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (33 bp):
ATTCTAATACTTGTGACGAATTGCATAATTGTT
Found at i:37958 original size:3 final size:3
Alignment explanation
Indices: 37950--37980 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
37940 GAGTTTTTCC
37950 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
37981 TGATAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:54073 original size:29 final size:29
Alignment explanation
Indices: 54049--54267 Score: 177
Period size: 29 Copynumber: 7.4 Consensus size: 29
54039 AAAACTTTTG
*
54049 AAAATTACATTTTTACCCCCAAACTTTCA
1 AAAATTACATTTTTACCCCCAAACTTCCA
* * * *
54078 AAAATTCCATTCTTAACCCCAAAGCTTCAA
1 AAAATTACATTTTTACCCCCAAA-CTTCCA
* *
54108 AAAATTACATTTTTACCCTCGAACTTCCA
1 AAAATTACATTTTTACCCCCAAACTTCCA
* ** * *
54137 AAAATTCCATTTTTACCCATAAATTTCAA
1 AAAATTACATTTTTACCCCCAAACTTCCA
* * ** **
54166 AAAATTCCATTTTGGACCCTTAAACTTTGA
1 AAAATTACATTTT-TACCCCCAAACTTCCA
* * * *
54196 AAATTTCCATTTTTACCCTCGAACTTCCA
1 AAAATTACATTTTTACCCCCAAACTTCCA
* * *
54225 AAAATTTCATTTTTGACCTCGAAACTTCCA
1 AAAATTACATTTTT-ACCCCCAAACTTCCA
*
54255 AAAATTACGTTTT
1 AAAATTACATTTT
54268 ATCCTCGAAC
Statistics
Matches: 151, Mismatches: 36, Indels: 5
0.79 0.19 0.03
Matches are distributed among these distances:
29 84 0.56
30 67 0.44
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCCAAACTTCCA
Found at i:54080 original size:59 final size:59
Alignment explanation
Indices: 54009--54260 Score: 215
Period size: 59 Copynumber: 4.3 Consensus size: 59
53999 GGAGGTCCCT
* ***
54009 AAACTATCCAAAAATTCCATTTTTAACATCAAAACTTTTGAAAATTACATTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTAACACCAAAACTTCAAAAAATTACATTTTTACCCCC
* * * * *
54069 AAACTTTCAAAAATTCCATTCTTAACCCCAAAGCTTCAAAAAATTACATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTAACACCAAAACTTCAAAAAATTACATTTTTACCCCC
* * * * **
54128 GAACTTCCAAAAATTCCATTTTT-AC-CCATAAATTTCAAAAAATTCCATTTTGGACCCTT
1 AAACTTCCAAAAATTCCATTTTTAACACCA-AAACTTCAAAAAATTACATTTT-TACCCCC
** * ** * * * *
54187 AAACTTTGAAAATTTCCATTTTT-AC-CCTCGAACTTCCAAAAATTTCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTAACACC-AAAACTTCAAAAAATTACATTTTT-ACCCCC
54246 AAACTTCCAAAAATT
1 AAACTTCCAAAAATT
54261 ACGTTTTATC
Statistics
Matches: 155, Mismatches: 33, Indels: 9
0.79 0.17 0.05
Matches are distributed among these distances:
57 3 0.02
58 21 0.14
59 126 0.81
60 5 0.03
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTAACACCAAAACTTCAAAAAATTACATTTTTACCCCC
Found at i:54169 original size:88 final size:88
Alignment explanation
Indices: 54049--54260 Score: 243
Period size: 88 Copynumber: 2.4 Consensus size: 88
54039 AAAACTTTTG
*
54049 AAAATTACATTTTTACCCCCAAACTTTCAAAAATTCCATTCTT-AACCC-CAAAGCTTCAAAAAA
1 AAAATTACATTTTTACCCACAAACTTTCAAAAATTCCATT-TTGAACCCTCAAA-CTTCAAAAAA
54112 TTACATTTTTACCCTCGAACTTCCA
64 TTACATTTTTACCCTCGAACTTCCA
* * * * ** *
54137 AAAATTCCATTTTTACCCATAAA-TTTCAAAAAATTCCATTTTGGACCCTTAAACTTTGAAAATT
1 AAAATTACATTTTTACCCACAAACTTTC-AAAAATTCCATTTTGAACCCTCAAACTTCAAAAAAT
*
54201 TCCATTTTTACCCTCGAACTTCCA
65 TACATTTTTACCCTCGAACTTCCA
* * *
54225 AAAATTTCATTTTTGACCTC-GAAACTTCCAAAAATT
1 AAAATTACATTTTT-ACC-CACAAACTTTCAAAAATT
54261 ACGTTTTATC
Statistics
Matches: 106, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
87 6 0.06
88 80 0.75
89 16 0.15
90 4 0.04
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (88 bp):
AAAATTACATTTTTACCCACAAACTTTCAAAAATTCCATTTTGAACCCTCAAACTTCAAAAAATT
ACATTTTTACCCTCGAACTTCCA
Found at i:54296 original size:29 final size:28
Alignment explanation
Indices: 54010--54296 Score: 173
Period size: 29 Copynumber: 9.8 Consensus size: 28
54000 GAGGTCCCTA
* *
54010 AACTATCCAAAAATTCCATTTTTAACATCAA
1 AACT-TCCAAAAATTCCATTTTT-ACCTC-G
*** * * *
54041 AACTTTTGAAAATTACATTTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTA-CCTCG
* * * *
54070 AACTTTCAAAAATTCCATTCTTAACCCCA
1 AACTTCCAAAAATTCCATT-TTTACCTCG
* *
54099 AAGCTTCAAAAAATTACATTTTTACCCTCG
1 AA-CTTCCAAAAATTCCATTTTTA-CCTCG
*
54129 AACTTCCAAAAATTCCATTTTTACC-CATA
1 AACTTCCAAAAATTCCATTTTTACCTC--G
* * * **
54158 AATTTCAAAAAATTCCATTTTGGACCCTTA
1 AACTTCCAAAAATTCCATTTT-TA-CCTCG
** *
54188 AACTTTGAAAATTTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTA-CCTCG
*
54217 AACTTCCAAAAATTTCATTTTTGACCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCTCG
* *
54246 AAACTTCCAAAAATTAC-GTTTTATCCTCG
1 -AACTTCCAAAAATTCCATTTTTA-CCTCG
* *
54275 AACCTCCAAAAATCCCATTTTT
1 AACTTCCAAAAATTCCATTTTT
54297 GACCCTAAAA
Statistics
Matches: 203, Mismatches: 40, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.00
28 16 0.08
29 107 0.53
30 73 0.36
31 6 0.03
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTTACCTCG
Found at i:54317 original size:58 final size:58
Alignment explanation
Indices: 54165--54330 Score: 156
Period size: 58 Copynumber: 2.8 Consensus size: 58
54155 ATAAATTTCA
* * * * * *
54165 AAAAATTCCATTTTGGACCCTTAAACTTTGAAAATTTCCATTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTGACCCTAAAATTTTGAAAA-TTACAGTTTTACCCTCGAACCTCC
* * * *** *
54224 AAAAATTTCATTTTTGACCTCGAAACTTCCAAAAATTAC-GTTTTATCCTCGAACCTCC
1 AAAAATTCCATTTTTGACC-CTAAAATTTTGAAAATTACAGTTTTACCCTCGAACCTCC
*
54282 AAAAATCCCATTTTTGACCCTAAAATTTTTGAAAATTACCA-TTTTACCC
1 AAAAATTCCATTTTTGACCCTAAAA-TTTTGAAAATTA-CAGTTTTACCC
54331 CTAAATGTCC
Statistics
Matches: 82, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
57 4 0.05
58 42 0.51
59 28 0.34
60 8 0.10
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (58 bp):
AAAAATTCCATTTTTGACCCTAAAATTTTGAAAATTACAGTTTTACCCTCGAACCTCC
Found at i:54354 original size:59 final size:58
Alignment explanation
Indices: 54137--54355 Score: 167
Period size: 59 Copynumber: 3.7 Consensus size: 58
54127 CGAACTTCCA
* * * * *
54137 AAAATT-CCATTTTTACCCATAAATTTCAAAAAATTCCATTTTGGACCCTTAAACTTTG
1 AAAATTACCATTTTTACCCCTAAA-TTCCAAAAATTCCATTTTTGACCCTAAAATTTTG
* * * * * * ***
54195 AAAATTTCCATTTTTACCCTCGAACTTCCAAAAATTTCATTTTTGACCTCGAAACTTCCA
1 AAAATTACCATTTTTACCC-CTAAATTCCAAAAATTCCATTTTTGACC-CTAAAATTTTG
* * * ** *
54255 AAAATTA-C-GTTTTATCCTCGAACCTCCAAAAATCCCATTTTTGACCCTAAAATTTTTG
1 AAAATTACCATTTTTA-CCCCTAAATTCCAAAAATTCCATTTTTGACCCTAAAA-TTTTG
*
54313 AAAATTACCA-TTTTACCCCTAAATGTCCAAAAATTCTATTTTT
1 AAAATTACCATTTTTACCCCTAAAT-TCCAAAAATTCCATTTTT
54356 TACCTCGATT
Statistics
Matches: 123, Mismatches: 30, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
57 4 0.03
58 50 0.41
59 57 0.46
60 12 0.10
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.37
Consensus pattern (58 bp):
AAAATTACCATTTTTACCCCTAAATTCCAAAAATTCCATTTTTGACCCTAAAATTTTG
Found at i:54401 original size:28 final size:27
Alignment explanation
Indices: 54353--54412 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
54343 AAATTCTATT
* *
54353 TTTTACCTCGATTTTCTTAAAATTACCG
1 TTTTACCTCGAATTTCTTAAAATT-CCA
54381 TTTTACCTTCGAATTTC-TAAAATTCCA
1 TTTTACC-TCGAATTTCTTAAAATTCCA
54408 TTTTA
1 TTTTA
54413 AACCCCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 7 0.24
28 14 0.48
29 8 0.28
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (27 bp):
TTTTACCTCGAATTTCTTAAAATTCCA
Found at i:67295 original size:58 final size:58
Alignment explanation
Indices: 67174--67298 Score: 155
Period size: 58 Copynumber: 2.2 Consensus size: 58
67164 ATATCAAGTT
* * * *
67174 ATCAAAACTTGTTTCTAAAGAAAGTTACCATCCGATCTTGTTCAAATGAGAAAAGGTG
1 ATCAAAATTTGTTTCTAAAAAAAGTCACCATCCGATCTTGTTCAAATGAGAAAAGGAG
* * *
67232 GTCAAAATTTGTTTCTAAAAAAAGTCACCATCCGATCTTGCTT-AACTGA-AAGAATGAG
1 ATCAAAATTTGTTTCTAAAAAAAGTCACCATCCGATCTTG-TTCAAATGAGAA-AAGGAG
67290 ATCAAAATT
1 ATCAAAATT
67299 CATTTCAAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
57 2 0.04
58 53 0.93
59 2 0.04
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (58 bp):
ATCAAAATTTGTTTCTAAAAAAAGTCACCATCCGATCTTGTTCAAATGAGAAAAGGAG
Found at i:68234 original size:9 final size:9
Alignment explanation
Indices: 68212--68248 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
68202 AAAGAAAGAA
68212 AGAAGAA-G
1 AGAAGAAGG
68220 -GAAGAAGG
1 AGAAGAAGG
68228 AGAAGAAGG
1 AGAAGAAGG
*
68237 GGAAGAAGG
1 AGAAGAAGG
68246 AGA
1 AGA
68249 GGAAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
7 6 0.24
8 1 0.04
9 18 0.72
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (9 bp):
AGAAGAAGG
Done.