Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009407.1 Kokia drynarioides strain JFW-HI SEQ_124114, 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: 174649
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:432 original size:25 final size:24
Alignment explanation
Indices: 404--457 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
394 TACCTTGAGA
404 AATAAAAAAATTAAAAAATTAGGTT
1 AATAAAAAAA-TAAAAAATTAGGTT
* **
429 AATAATAAAATATGAAATTAGGTT
1 AATAAAAAAATAAAAAATTAGGTT
*
453 GATAA
1 AATAA
458 GAACCCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (24 bp):
AATAAAAAAATAAAAAATTAGGTT
Found at i:5347 original size:23 final size:24
Alignment explanation
Indices: 5315--5363 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
5305 ACTACCATTT
5315 TCTAAATAAAATAATAAT-AAATA
1 TCTAAATAAAATAATAATAAAATA
* *
5338 TCTAAGTAAAATATTAATAAAATA
1 TCTAAATAAAATAATAATAAAATA
5362 TC
1 TC
5364 ATCAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (24 bp):
TCTAAATAAAATAATAATAAAATA
Found at i:5362 original size:11 final size:11
Alignment explanation
Indices: 5319--5362 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
5309 CCATTTTCTA
*
5319 AATAAAATAAT
1 AATAAAATATT
5330 AAT-AAATATCT
1 AATAAAATAT-T
5341 AAGTAAAATATT
1 AA-TAAAATATT
5353 AATAAAATAT
1 AATAAAATAT
5363 CATCAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 5 0.17
11 14 0.48
12 4 0.14
13 6 0.21
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (11 bp):
AATAAAATATT
Found at i:20567 original size:43 final size:43
Alignment explanation
Indices: 20506--20589 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
20496 GTTCCAGACC
*
20506 GTGTTTCTGTGTGAAAAATAATCACACGGTCGTGTCACAGATT
1 GTGTTTCTGTGCGAAAAATAATCACACGGTCGTGTCACAGATT
20549 GTGTTTCTGTGCGAAAAATAATCACACGGTCGTGTCACAGA
1 GTGTTTCTGTGCGAAAAATAATCACACGGTCGTGTCACAGA
20590 CCGTGTGACA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (43 bp):
GTGTTTCTGTGCGAAAAATAATCACACGGTCGTGTCACAGATT
Found at i:21547 original size:26 final size:26
Alignment explanation
Indices: 21513--21562 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
21503 ATTCATTCGA
21513 GCCAAGTACAGAGTATAGCTCATTTT
1 GCCAAGTACAGAGTATAGCTCATTTT
* *
21539 GCCATGTACAGAGTATTGCTCATT
1 GCCAAGTACAGAGTATAGCTCATT
21563 CAGGCCAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (26 bp):
GCCAAGTACAGAGTATAGCTCATTTT
Found at i:21590 original size:27 final size:28
Alignment explanation
Indices: 21566--21658 Score: 102
Period size: 27 Copynumber: 3.4 Consensus size: 28
21556 GCTCATTCAG
*
21566 GCCAGAAATAGAGTAGCACT-TATTCGA
1 GCCAGAAACAGAGTAGCACTCTATTCGA
* *
21593 GCTAGAAACAGAGTATCACTCT-TTCGA
1 GCCAGAAACAGAGTAGCACTCTATTCGA
* * *
21620 GCCAGAAACAGAGTATCGCTCT-TTCAA
1 GCCAGAAACAGAGTAGCACTCTATTCGA
*
21647 GCCAAAAACAGA
1 GCCAGAAACAGA
21659 TTATTACCCT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 57 0.98
28 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (28 bp):
GCCAGAAACAGAGTAGCACTCTATTCGA
Found at i:28058 original size:153 final size:153
Alignment explanation
Indices: 27776--28058 Score: 349
Period size: 153 Copynumber: 1.8 Consensus size: 153
27766 TTTTGGGGGG
* * ** * * *
27776 TTTGATTTTGGGTTTCTCGAGAAACAAATAAAAAATTGCACTGAGTCACAAAGTGTTGTTCTTGG
1 TTTGATATTGGGTTTCTCGAGAAACAAACAAAAAATTGCACAAACTAACAAAGTATTGTTCTTGG
* *
27841 TGTCGATTTGGAGAGAAAGGAAAGAAGCCCAAGTGTTGAAATCGTTAGTCCTTCAAGTATAAAGA
66 TGTCGATTTGAAGAGAAAGGAAAGAAGCCCAAGTGTTGAAATCGTTAGTCCTTCAAGTAAAAAGA
27906 AAAAAAGAAGCCCCAAAGTTGTT
131 AAAAAAGAAGCCCCAAAGTTGTT
**
27929 TTTGATATTGGGTTTCTCGAGAAACAAACAAAAAACTT-CACAAACTAAGGAAGTATTGCTT-TT
1 TTTGATATTGGGTTTCTCGAGAAACAAACAAAAAA-TTGCACAAACTAACAAAGTATTG-TTCTT
* * * * **
27992 GGTGTCTATTTGAAGGGAAAGGAAAGATA--TCTAGATGTTGAAATCGTTAGTTGTTCAAGTAAA
64 GGTGTCGATTTGAAGAGAAAGGAAAGA-AGCCCAAG-TGTTGAAATCGTTAGTCCTTCAAGTAAA
28055 AAGA
127 AAGA
28059 GGAAATTTTC
Statistics
Matches: 109, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
152 3 0.03
153 101 0.93
154 5 0.05
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (153 bp):
TTTGATATTGGGTTTCTCGAGAAACAAACAAAAAATTGCACAAACTAACAAAGTATTGTTCTTGG
TGTCGATTTGAAGAGAAAGGAAAGAAGCCCAAGTGTTGAAATCGTTAGTCCTTCAAGTAAAAAGA
AAAAAAGAAGCCCCAAAGTTGTT
Found at i:28349 original size:158 final size:155
Alignment explanation
Indices: 28078--28392 Score: 506
Period size: 158 Copynumber: 2.0 Consensus size: 155
28068 CCGTTCAAGA
**
28078 AAAAGGTAAAGCAAAATTAGACGGGTTTTGTATTTTCATGAGAAACAAACAGAAAACTTCACAAA
1 AAAAGGTAAAGCAAAATTAGACGGGTTTCATATTTTCATGAGAAACAAACAGAAAACTTCACAAA
28143 CTCAGATTATTCATGATTAGATGCAAATGGACAAAGAGAAATGGATTTT-GAATTCACCAGTTGA
66 CTCAGATTATTCATGATTAGATGCAAATGGACAAAGAGAAATGGATTTTAG-ATTCA--A-TTGA
*
28207 AGAAGAGAAGCCAAATTACATTGAATTTC
127 AGAAGAGAAGCCAAATTAAATTGAATTTC
* *
28236 AAAAGGTAAAGCAAAATTAGATGGGTTTCATATTTTCCTGAGAAACAAACAGAAAACTTCACAAA
1 AAAAGGTAAAGCAAAATTAGACGGGTTTCATATTTTCATGAGAAACAAACAGAAAACTTCACAAA
* * * *
28301 CTCATATTCTTCATGATTTGATGCAAATGGACAGAGAGAAATGGATTTTAGATTCAATTGAAGAA
66 CTCAGATTATTCATGATTAGATGCAAATGGACAAAGAGAAATGGATTTTAGATTCAATTGAAGAA
28366 GAGAAGCCAAATTAAATTGAATTTC
131 GAGAAGCCAAATTAAATTGAATTTC
28391 AA
1 AA
28393 GGTTTAACAA
Statistics
Matches: 147, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
155 34 0.23
156 1 0.01
158 111 0.76
159 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (155 bp):
AAAAGGTAAAGCAAAATTAGACGGGTTTCATATTTTCATGAGAAACAAACAGAAAACTTCACAAA
CTCAGATTATTCATGATTAGATGCAAATGGACAAAGAGAAATGGATTTTAGATTCAATTGAAGAA
GAGAAGCCAAATTAAATTGAATTTC
Found at i:30365 original size:6 final size:6
Alignment explanation
Indices: 30356--30420 Score: 59
Period size: 6 Copynumber: 11.3 Consensus size: 6
30346 GTCCAACAAG
* *
30356 ATTTAA ATTT-A TTTTAA AATTAA ATTT-- ATTTAA ATTTAA ATTT--
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
30399 ATTATAA ATTTAAA ATTTAA AT
1 ATT-TAA ATTT-AA ATTTAA AT
30421 CTATTTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
4 7 0.15
5 5 0.10
6 27 0.56
7 9 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:30380 original size:17 final size:17
Alignment explanation
Indices: 30356--30417 Score: 90
Period size: 17 Copynumber: 3.6 Consensus size: 17
30346 GTCCAACAAG
30356 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
*
30373 AATTAAATTTA-TTTAA
1 ATTTAAATTTATTTTAA
*
30389 ATTTAAATTTATTATAA
1 ATTTAAATTTATTTTAA
30406 ATTTAAAATTTA
1 ATTT-AAATTTA
30418 AATCTATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
16 15 0.38
17 18 0.45
18 7 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:30419 original size:24 final size:22
Alignment explanation
Indices: 30383--30430 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 22
30373 AATTAAATTT
*
30383 ATTTAAATTTAAATTTATTATAA
1 ATTTAAATTTAAATCTATT-TAA
30406 ATTTAAAATTTAAATCTATTTAA
1 ATTT-AAATTTAAATCTATTTAA
30429 AT
1 AT
30431 CAAGTCCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTAAATTTAAATCTATTTAA
Found at i:31131 original size:3 final size:3
Alignment explanation
Indices: 31123--31182 Score: 75
Period size: 3 Copynumber: 19.0 Consensus size: 3
31113 CTGATAGCAT
**
31123 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAAA TAAA TAA TTG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA T-AA T-AA TAA TAA TAA
31171 TAA TAA TAA TAA
1 TAA TAA TAA TAA
31183 AAGAAACGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 41 0.79
4 11 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:32176 original size:29 final size:29
Alignment explanation
Indices: 32133--32513 Score: 253
Period size: 29 Copynumber: 13.0 Consensus size: 29
32123 CTAAACTGTT
* * *
32133 CAAAAATTACA-TTTTGCCATCTAAC-TC
1 CAAAAATTCCATTTTTACCCTCTAACTTC
* *
32160 CTAAAAATTCCATTTTTACCCCCGAACTTC
1 C-AAAAATTCCATTTTTACCCTCTAACTTC
* ** *
32190 CAAAAATTCCATTTTCGACCCTAAAATTTC
1 CAAAAATTCCATTTT-TACCCTCTAACTTC
32220 CAAAAATTCCATTTTTACCCTCTAACTTC
1 CAAAAATTCCATTTTTACCCTCTAACTTC
* **
32249 CAAAAATTCCATTTTAACCCTAAAACTTC
1 CAAAAATTCCATTTTTACCCTCTAACTTC
*
32278 C-AAAATTCCATTTTTACCC-CCAATCTTC
1 CAAAAATTCCATTTTTACCCTCTAA-CTTC
* ** *
32306 TAAAAATTCCATTTTTAACACC-GAAACTTT
1 CAAAAATTCCATTTTT-AC-CCTCTAACTTC
* * *
32336 CAAAAATTACATTTTTACCCTCGAACATC
1 CAAAAATTCCATTTTTACCCTCTAACTTC
* * * *
32365 CAAAATTTCCATTTTTGCCCTCGAAACTTT
1 CAAAAATTCCATTTTTACCCTC-TAACTTC
* *
32395 CAAAAATTACCA-TTTTACCC-CCAAATATC
1 CAAAAATT-CCATTTTTACCCTCTAACT-TC
* * * *
32424 CAAAAACTCTATTTTCGA-CCTCGAAAC-TC
1 CAAAAATTCCATTTT-TACCCTC-TAACTTC
*
32453 CAAGAATTCCATTTTTTACCC-CTGAA-TATC
1 CAAAAATTCCA-TTTTTACCCTCT-AACT-TC
* * *
32483 TAAAAATTCCATCTTTTAACCTCGAACTTC
1 CAAAAATTCCAT-TTTTACCCTCTAACTTC
32513 C
1 C
32514 CCAAAATTAC
Statistics
Matches: 274, Mismatches: 56, Indels: 45
0.73 0.15 0.12
Matches are distributed among these distances:
27 3 0.01
28 37 0.14
29 129 0.47
30 94 0.34
31 11 0.04
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCTCTAACTTC
Found at i:32234 original size:59 final size:59
Alignment explanation
Indices: 32162--32494 Score: 301
Period size: 59 Copynumber: 5.7 Consensus size: 59
32152 TCTAACTCCT
32162 AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTCGACCCTAAAATTTCC
1 AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTCGACCCTAAAATTTCC
* * * *
32221 AAAAATTCCATTTTTACCCTCTAACTTCCAAAAATTCCATTTT-AACCCTAAAACTTCC
1 AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTCGACCCTAAAATTTCC
* ** * *
32279 -AAAATTCCATTTTTACCCCC-AATCTTCTAAAAATTCCATTTTTAACACCGAAACTTT-C
1 AAAAATTCCATTTTTACCCCCGAA-CTTCCAAAAATTCCATTTTCGAC-CCTAAAATTTCC
* * * * * *
32337 AAAAATTACATTTTTACCCTCGAACATCCAAAATTTCCATTTTTG-CCCTCGAAACTTT-C
1 AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTCGACCCT--AAAATTTCC
* * * * *
32396 AAAAATTACCA-TTTTACCCCC-AAATATCCAAAAACTCTATTTTCGA-CCTCGAAA-CTCC
1 AAAAATT-CCATTTTTACCCCCGAACT-TCCAAAAATTCCATTTTCGACCCT-AAAATTTCC
* * *
32454 AAGAATTCCATTTTTTACCCCTGAA-TATCTAAAAATTCCAT
1 AAAAATTCCA-TTTTTACCCCCGAACT-TCCAAAAATTCCAT
32495 CTTTTAACCT
Statistics
Matches: 227, Mismatches: 33, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
56 2 0.01
57 43 0.19
58 29 0.13
59 147 0.65
60 6 0.03
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (59 bp):
AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTCGACCCTAAAATTTCC
Found at i:32340 original size:116 final size:117
Alignment explanation
Indices: 32162--32503 Score: 347
Period size: 116 Copynumber: 2.9 Consensus size: 117
32152 TCTAACTCCT
* *
32162 AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTCGACCCTAAAATTTCCAAAAAT
1 AAAAATTCCATTTTTACCCCC-AACTTCCAAAAATTCCATTTTCAACCCGAAAATTTCCAAAAAT
* * *
32227 TCCATTTTTACCCTCTAACTTCCAAAAATTCCATTTTAACCCT-AAAAC-TTC
65 TACATTTTTACCCTCGAACATCCAAAAATTCCATTTTAACCCTCAAAACTTTC
* * * *
32278 CAAAATTCCATTTTTACCCCCAATCTTCTAAAAATTCCATTTTTAACACCGAAACTTT-CAAAAA
1 AAAAATTCCATTTTTACCCCCAA-CTTCCAAAAATTCCATTTTCAAC-CCGAAAATTTCCAAAAA
* ** *
32342 TTACATTTTTACCCTCGAACATCCAAAATTTCCATTTTTGCCCTCGAAACTTTC
64 TTACATTTTTACCCTCGAACATCCAAAAATTCCATTTTAACCCTCAAAACTTTC
* * * * * *
32396 AAAAATTACCA-TTTTACCCCCAAATATCCAAAAACTCTATTTTCGACCTCG-AAA-CTCCAAGA
1 AAAAATT-CCATTTTTACCCCCAACT-TCCAAAAATTCCATTTTCAACC-CGAAAATTTCCAAAA
* * *
32458 ATTCCATTTTTTACCC-CTGAATATCTAAAAATTCCATCTTTTAACC
63 ATTACA-TTTTTACCCTC-GAACATCCAAAAATTCCA--TTTTAACC
32504 TCGAACTTCC
Statistics
Matches: 185, Mismatches: 29, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
115 2 0.01
116 85 0.46
117 26 0.14
118 63 0.34
119 3 0.02
120 6 0.03
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (117 bp):
AAAAATTCCATTTTTACCCCCAACTTCCAAAAATTCCATTTTCAACCCGAAAATTTCCAAAAATT
ACATTTTTACCCTCGAACATCCAAAAATTCCATTTTAACCCTCAAAACTTTC
Found at i:32601 original size:39 final size:39
Alignment explanation
Indices: 32547--32627 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
32537 AAGACCAAAG
32547 TTACCATTTTGCCCCCGGTATCCAAAGTCTCATTTTTTT
1 TTACCATTTTGCCCCCGGTATCCAAAGTCTCATTTTTTT
32586 TTACCATTTTGCCCCCGGTATCCAAAGTCTCATTTTTTT
1 TTACCATTTTGCCCCCGGTATCCAAAGTCTCATTTTTTT
32625 TTA
1 TTA
32628 TCTTCAATTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.19, C:0.27, G:0.10, T:0.44
Consensus pattern (39 bp):
TTACCATTTTGCCCCCGGTATCCAAAGTCTCATTTTTTT
Found at i:40625 original size:2 final size:2
Alignment explanation
Indices: 40618--40643 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40608 GCTTCATTTA
40618 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
40644 GTGGGGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45731 original size:6 final size:6
Alignment explanation
Indices: 45720--45744 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
45710 TTAATAATAC
45720 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
45745 AAATTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:47253 original size:31 final size:31
Alignment explanation
Indices: 47215--47281 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
47205 TTGGTATATG
*
47215 AACTTGACACTTTTTTTT-AATTTAGTACTTA
1 AACTTGACA-TTTTTTTTCAAGTTAGTACTTA
* *
47246 AACTTGACATTTTTTTTCAAGTTGGTTCTTA
1 AACTTGACATTTTTTTTCAAGTTAGTACTTA
47277 AACTT
1 AACTT
47282 TTTGGGGTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (31 bp):
AACTTGACATTTTTTTTCAAGTTAGTACTTA
Found at i:47675 original size:59 final size:61
Alignment explanation
Indices: 47483--47678 Score: 161
Period size: 59 Copynumber: 3.3 Consensus size: 61
47473 AATATTTAAT
* * * * * *
47483 AAATTTAAGTACCAAATTGAATC-TAAAAACACTTAAG-TACCGAATTAAG-AAAAATGAT-
1 AAATTCAAGTACCAAATTGAATCAAAAAAAAAGTTTAGATACCAAATTAAGAAAAAAT-ATC
* * * *
47541 AAGTTTAGGTACCAAATTGAATCCAAAAAAAAAGTTTAGATACCACATTAAGAAAAAATATC
1 AAATTCAAGTACCAAATTGAAT-CAAAAAAAAAGTTTAGATACCAAATTAAGAAAAAATATC
* * * * * * *
47603 AAATTCAAATACCAAATTGAGT-AAAATAAAA-TTTAGATATCAAATTAAGAAGACATGTC
1 AAATTCAAGTACCAAATTGAATCAAAAAAAAAGTTTAGATACCAAATTAAGAAAAAATATC
* *
47662 GAGTTCAAGTACCAAAT
1 AAATTCAAGTACCAAAT
47679 ATTATATTAA
Statistics
Matches: 111, Mismatches: 22, Indels: 9
0.78 0.15 0.06
Matches are distributed among these distances:
58 20 0.18
59 38 0.34
60 18 0.16
61 12 0.11
62 23 0.21
ACGTcount: A:0.51, C:0.12, G:0.11, T:0.26
Consensus pattern (61 bp):
AAATTCAAGTACCAAATTGAATCAAAAAAAAAGTTTAGATACCAAATTAAGAAAAAATATC
Found at i:47768 original size:8 final size:8
Alignment explanation
Indices: 47755--47786 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
47745 TATTTCGTTT
47755 TATAAAAA
1 TATAAAAA
47763 TATAAAAA
1 TATAAAAA
47771 TATAAAAA
1 TATAAAAA
47779 TA-AAAAA
1 TATAAAAA
47786 T
1 T
47787 TGTGACATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
TATAAAAA
Found at i:48374 original size:118 final size:117
Alignment explanation
Indices: 48159--48414 Score: 306
Period size: 118 Copynumber: 2.2 Consensus size: 117
48149 GAGGAGAAAG
* * ** *
48159 AAATGTGATAGGAACTTGTCATTGAACAAGTATATCTGACCGTATCTGGATATGGGTACGAGGAT
1 AAATGTGATAGGAACTTGTCATTGAACAAGTATATCTAACCGAATCCAGATATGGATACGAGGAT
* * * *
48224 ATGTCCTCTGAGGATTCCCGGAATACAGAAAAGATGAGAAAGAGACTCCAAC
66 ATGTCCTCCGAGGACTCCCGAAATACAGAAAAGAGGAGAAAGAGACTCCAAC
* *
48276 AAATGTGATAGGAATTTAG-CATTGAACAAGTATATCTAACCTGAATCCAGATATGGATATGAGG
1 AAATGTGATAGGAACTT-GTCATTGAACAAGTATATCTAACC-GAATCCAGATATGGATACGAGG
* *
48340 ATATGTCCTCCGAGGACTCTCC-AAATAC-GTAAAAGAGGAGAAAGAGA--CGAAT
64 ATATGTCCTCCGAGGACTC-CCGAAATACAG-AAAAGAGGAGAAAGAGACTCCAAC
*
48392 AAATTGTAATAGGAACTTGTCAT
1 AAA-TGTGATAGGAACTTGTCAT
48415 CTAGCACATG
Statistics
Matches: 118, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
116 7 0.06
117 53 0.45
118 56 0.47
119 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (117 bp):
AAATGTGATAGGAACTTGTCATTGAACAAGTATATCTAACCGAATCCAGATATGGATACGAGGAT
ATGTCCTCCGAGGACTCCCGAAATACAGAAAAGAGGAGAAAGAGACTCCAAC
Found at i:60568 original size:11 final size:11
Alignment explanation
Indices: 60504--60572 Score: 57
Period size: 11 Copynumber: 5.6 Consensus size: 11
60494 CCACATGAAC
*
60504 AAATGATTTTA
1 AAATTATTTTA
*
60515 AAATTAATTTA
1 AAATTATTTTA
60526 AAATTATTTTTTA
1 AAATTA--TTTTA
60539 AAATATAAATTTATTA
1 AAAT-T--A-TT-TTA
60555 AAATTATTTTA
1 AAATTATTTTA
60566 AAATTAT
1 AAATTAT
60573 AATCATCATC
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
11 25 0.51
12 2 0.04
13 9 0.18
14 1 0.02
15 4 0.08
16 8 0.16
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:61553 original size:28 final size:25
Alignment explanation
Indices: 61493--61541 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
61483 AAATGAAATT
* *
61493 AAAATTATTTAATAATTTTATATTA
1 AAAATAATATAATAATTTTATATTA
61518 AAAATAATATAATAATTTTATATT
1 AAAATAATATAATAATTTTATATT
61542 TTAAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAATAATATAATAATTTTATATTA
Found at i:89134 original size:28 final size:27
Alignment explanation
Indices: 89080--89157 Score: 65
Period size: 28 Copynumber: 2.9 Consensus size: 27
89070 TTTAGGATTT
89080 TGTT-TTG-TTTTAATTTAAATTTTAAA
1 TGTTGTTGATTTTAATTT-AATTTTAAA
*
89106 TTTTGTTGATTTTAATTT-ATTTTAAAAA
1 TGTTGTTGATTTTAATTTAATTTT--AAA
* *
89134 TGTTGTTTG-GTATAATTTAATTTT
1 TGTTG-TTGATTTTAATTTAATTTT
89158 TGATTAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
26 8 0.19
27 3 0.07
28 23 0.55
29 8 0.19
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (27 bp):
TGTTGTTGATTTTAATTTAATTTTAAA
Found at i:89238 original size:18 final size:18
Alignment explanation
Indices: 89198--89240 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
89188 GTTTATAGTG
89198 TTTATATTTTTATGTGTT
1 TTTATATTTTTATGTGTT
* *
89216 ATTATATTTTT-TTTGTT
1 TTTATATTTTTATGTGTT
89233 TTT-TATTT
1 TTTATATTT
89241 ATTTTATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 5 0.23
17 7 0.32
18 10 0.45
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (18 bp):
TTTATATTTTTATGTGTT
Found at i:89245 original size:18 final size:21
Alignment explanation
Indices: 89202--89245 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 21
89192 ATAGTGTTTA
89202 TATTTTTATGTGTTATTATAT
1 TATTTTTATGTGTTATTATAT
*
89223 T-TTTTT-TGT-TTTTTAT-T
1 TATTTTTATGTGTTATTATAT
89240 TATTTT
1 TATTTT
89246 ATAAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
17 2 0.10
18 10 0.48
19 3 0.14
20 5 0.24
21 1 0.05
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (21 bp):
TATTTTTATGTGTTATTATAT
Found at i:89385 original size:14 final size:15
Alignment explanation
Indices: 89357--89389 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
89347 TAATTTAAAT
*
89357 ATTTTTTTTGTATTA
1 ATTTTGTTTGTATTA
89372 ATTTTGTTTG-ATTA
1 ATTTTGTTTGTATTA
89386 ATTT
1 ATTT
89390 AAAGAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (15 bp):
ATTTTGTTTGTATTA
Found at i:93446 original size:4 final size:4
Alignment explanation
Indices: 93432--93463 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
93422 ATAAATGAAA
*
93432 GTAT ATAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
93464 TTATTAATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:95094 original size:24 final size:24
Alignment explanation
Indices: 95066--95118 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
95056 CGATGTTCCT
95066 GGAGTTGTGGTTGTCCCCGTTGGA
1 GGAGTTGTGGTTGTCCCCGTTGGA
*
95090 GGAGTTGTGGTTGTCCCGGTTGGA
1 GGAGTTGTGGTTGTCCCCGTTGGA
95114 GGAGT
1 GGAGT
95119 CATGGTAGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.09, C:0.13, G:0.45, T:0.32
Consensus pattern (24 bp):
GGAGTTGTGGTTGTCCCCGTTGGA
Found at i:95124 original size:24 final size:24
Alignment explanation
Indices: 95073--95146 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 24
95063 CCTGGAGTTG
* **
95073 TGGTTGTCCCCGTTGGAGGAGTTG
1 TGGTTGTCCCGGTTGGAGGAGTCA
95097 TGGTTGTCCCGGTTGGAGGAGTCA
1 TGGTTGTCCCGGTTGGAGGAGTCA
* ** *
95121 TGGTAGGGCCGGTCGGAGGAGTCA
1 TGGTTGTCCCGGTTGGAGGAGTCA
95145 TG
1 TG
95147 ATAGGACCGG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.12, C:0.16, G:0.45, T:0.27
Consensus pattern (24 bp):
TGGTTGTCCCGGTTGGAGGAGTCA
Found at i:95151 original size:24 final size:24
Alignment explanation
Indices: 95105--95162 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
95095 TGTGGTTGTC
* * *
95105 CCGGTTGGAGGAGTCATGGTAGGG
1 CCGGTCGGAGGAGTCATGATAGGA
95129 CCGGTCGGAGGAGTCATGATAGGA
1 CCGGTCGGAGGAGTCATGATAGGA
*
95153 CCGGTGGGAG
1 CCGGTCGGAG
95163 TCGGATTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.19, C:0.16, G:0.48, T:0.17
Consensus pattern (24 bp):
CCGGTCGGAGGAGTCATGATAGGA
Found at i:95191 original size:27 final size:27
Alignment explanation
Indices: 95159--95238 Score: 133
Period size: 27 Copynumber: 3.0 Consensus size: 27
95149 AGGACCGGTG
*
95159 GGAGTCGGATTTGTGTCTGGTAATGTT
1 GGAGTCGGATTTGTGTCTGGTGATGTT
95186 GGAGTCGGATTTGTGTCTGGTGATGTT
1 GGAGTCGGATTTGTGTCTGGTGATGTT
* *
95213 GGAGTCGGATTAGTGTCCGGTGATGT
1 GGAGTCGGATTTGTGTCTGGTGATGT
95239 CGGGGTAGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.14, C:0.09, G:0.40, T:0.38
Consensus pattern (27 bp):
GGAGTCGGATTTGTGTCTGGTGATGTT
Found at i:99872 original size:19 final size:20
Alignment explanation
Indices: 99850--99892 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
99840 TATTTTAACC
99850 TTTATAGTAATTTT-TTATT
1 TTTATAGTAATTTTATTATT
*
99869 TTTATATTAATTTTAATTATT
1 TTTATAGTAATTTT-ATTATT
99890 TTT
1 TTT
99893 CTTATACGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.62
21 8 0.38
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTATAGTAATTTTATTATT
Found at i:102312 original size:42 final size:42
Alignment explanation
Indices: 102250--102334 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
102240 TGACTTGATT
* * *
102250 AACTTAAACCTACATTATTTTACGTGTAAACAATCAGATCAA
1 AACTTAAACATACATGATTTTACATGTAAACAATCAGATCAA
*
102292 AACTTAAATATACATGATTTTACATGTAAACAATCAGATCAA
1 AACTTAAACATACATGATTTTACATGTAAACAATCAGATCAA
102334 A
1 A
102335 CATAATGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (42 bp):
AACTTAAACATACATGATTTTACATGTAAACAATCAGATCAA
Found at i:107918 original size:19 final size:19
Alignment explanation
Indices: 107894--107930 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
107884 GCTTTTCCAC
107894 TTCCTTATAGCATGTTTTT
1 TTCCTTATAGCATGTTTTT
* *
107913 TTCCTTATGGTATGTTTT
1 TTCCTTATAGCATGTTTT
107931 CGTCTACTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (19 bp):
TTCCTTATAGCATGTTTTT
Found at i:109959 original size:22 final size:22
Alignment explanation
Indices: 109925--109968 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
109915 TAGTTTAATC
* *
109925 ATAAGTCTTTATTTAAACAAAT
1 ATAAATCTGTATTTAAACAAAT
109947 ATAAATCTGTATTTAAACAAAT
1 ATAAATCTGTATTTAAACAAAT
109969 TAAGTCAGGT
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:0.48, C:0.09, G:0.05, T:0.39
Consensus pattern (22 bp):
ATAAATCTGTATTTAAACAAAT
Found at i:111731 original size:2 final size:2
Alignment explanation
Indices: 111724--111748 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
111714 TTTTATATTT
111724 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
111749 GTTCCTATTT
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:113846 original size:30 final size:31
Alignment explanation
Indices: 113806--113863 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
113796 TAGATTTGTT
* *
113806 TTATTGTCATGTTGTATT-ATGCTTTTATTA
1 TTATTGTCATGTTATATTCATGCATTTATTA
*
113836 TTATTTTCATGTTATATTCATGCATTTA
1 TTATTGTCATGTTATATTCATGCATTTA
113864 GGGAGTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.22, C:0.09, G:0.10, T:0.59
Consensus pattern (31 bp):
TTATTGTCATGTTATATTCATGCATTTATTA
Found at i:119639 original size:17 final size:17
Alignment explanation
Indices: 119614--119652 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
119604 TATTCGGTTC
119614 TTATTTTTTT-T-ATATT
1 TTATTTTTTTCTAAT-TT
119630 TTATTTTTTTCTAATTT
1 TTATTTTTTTCTAATTT
119647 TTATTT
1 TTATTT
119653 GTTTGTGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.48
17 9 0.43
18 2 0.10
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (17 bp):
TTATTTTTTTCTAATTT
Found at i:122337 original size:18 final size:19
Alignment explanation
Indices: 122314--122353 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
122304 TTTACTAATT
*
122314 TTATAT-TTTTGTTAGATA
1 TTATATATTTGGTTAGATA
122332 TTATATCATTTGGTTAGATA
1 TTATAT-ATTTGGTTAGATA
122352 TT
1 TT
122354 CCAAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
20 13 0.68
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (19 bp):
TTATATATTTGGTTAGATA
Found at i:128782 original size:21 final size:21
Alignment explanation
Indices: 128757--128799 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
128747 CGCAGAGGCT
128757 TTTGCACATCTAAAGAAACCC
1 TTTGCACATCTAAAGAAACCC
128778 TTTGCACATCTAAAGAAACCC
1 TTTGCACATCTAAAGAAACCC
128799 T
1 T
128800 AATACGACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.28, G:0.09, T:0.26
Consensus pattern (21 bp):
TTTGCACATCTAAAGAAACCC
Found at i:148776 original size:3 final size:3
Alignment explanation
Indices: 148768--148793 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
148758 GAGAGTAGTT
148768 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
148794 TTGGCCAAAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:149159 original size:20 final size:21
Alignment explanation
Indices: 149120--149159 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
149110 TAGCTTTATA
149120 TTTTTATTTTTAAGATTTTTT
1 TTTTTATTTTTAAGATTTTTT
* *
149141 TTTTTTTTTTTCAGATTTT
1 TTTTTATTTTTAAGATTTT
149160 ATTTAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTTTATTTTTAAGATTTTTT
Found at i:171532 original size:11 final size:11
Alignment explanation
Indices: 171510--171540 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
171500 CATTTTTCCC
171510 TTCTTTTC-TT
1 TTCTTTTCTTT
171520 TTCTTTTCTTT
1 TTCTTTTCTTT
171531 TTCTTTTCTT
1 TTCTTTTCTT
171541 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTCTTTTCTTT
Found at i:171534 original size:6 final size:5
Alignment explanation
Indices: 171510--171554 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
171500 CATTTTTCCC
* *
171510 TTCTT TTCTT TTCTT TTCTTT TTCTT TTCTT AT-TT TTATT TTCTT
1 TTCTT TTCTT TTCTT TTC-TT TTCTT TTCTT TTCTT TTCTT TTCTT
171555 CCGTTTCTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
4 3 0.09
5 27 0.77
6 5 0.14
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (5 bp):
TTCTT
Done.