Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009603.1 Kokia drynarioides strain JFW-HI SEQ_124319, 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: 152098
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:8538 original size:50 final size:50
Alignment explanation
Indices: 8479--8575 Score: 194
Period size: 50 Copynumber: 1.9 Consensus size: 50
8469 TTAATCTTTT
8479 ACATTTTTAATTAGAGATAGCCATGCATTTAAATAAGCTCGAACACATTC
1 ACATTTTTAATTAGAGATAGCCATGCATTTAAATAAGCTCGAACACATTC
8529 ACATTTTTAATTAGAGATAGCCATGCATTTAAATAAGCTCGAACACA
1 ACATTTTTAATTAGAGATAGCCATGCATTTAAATAAGCTCGAACACA
8576 CAACTTTCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (50 bp):
ACATTTTTAATTAGAGATAGCCATGCATTTAAATAAGCTCGAACACATTC
Found at i:23980 original size:29 final size:30
Alignment explanation
Indices: 23930--23986 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
23920 TTAGAGGTTA
*
23930 CTCGTGTAAGAGTCAAACCTTT-CAAAATG
1 CTCGTATAAGAGTCAAACCTTTACAAAATG
* * *
23959 CTCGTATAAGGGTCTAATCTTTACAAAA
1 CTCGTATAAGAGTCAAACCTTTACAAAA
23987 GTGACTTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (30 bp):
CTCGTATAAGAGTCAAACCTTTACAAAATG
Found at i:26823 original size:259 final size:260
Alignment explanation
Indices: 26362--26881 Score: 997
Period size: 259 Copynumber: 2.0 Consensus size: 260
26352 TTAAGTAAAG
*
26362 TGACAAAACTCAAGTTTTTTTAATATTATTGATAAAAAAAAAAAAAGATGATGTCGAAGGAGATA
1 TGACAAAACTCAAGTTTATTTAATATTATTGAT-AAAAAAAAAAAAGATGATGTCGAAGGAGATA
26427 ACGATTCACACAATAACAAACCGTAAAGTTTTGATTTAGTAGAAAAGTATTTTCCTCTAATGGAG
65 ACGATTCACACAATAACAAACCGTAAAGTTTTGATTTAGTAGAAAAGTATTTTCCTCTAATGGAG
26492 AGGAGGGAGGTACTTATAGTAAAGGTTTGGCTACCAGCCACCCTTAGCCCTCGACACGTGTCCAA
130 AGGAGGGAGGTACTTATAGTAAAGGTTTGGCTACCAGCCACCCTTAGCCCTCGACACGTGTCCAA
26557 GAGGTTCTCGTCTAAGTAGGCATGTGAATTGCATTTAATAGAGTTTCACATGTTATTCAACCTAG
195 GAGGTTCTCGTCTAAGTAGGCATGTGAATTGCATTTAATAGAGTTTCACATGTTATTCAACCTAG
26622 A
260 A
*
26623 TGACAAAACTCAAGTTTATTTAATATTATTGAT-AAAAAAAAAAGGATGATGTCGAAGGAGATAA
1 TGACAAAACTCAAGTTTATTTAATATTATTGATAAAAAAAAAAAAGATGATGTCGAAGGAGATAA
*
26687 CGATTCACACAATAGCAAACCGTAAAGTTTTGATTTAGTAGAAAAGTATTTTCCTCTAATGGAGA
66 CGATTCACACAATAACAAACCGTAAAGTTTTGATTTAGTAGAAAAGTATTTTCCTCTAATGGAGA
26752 GGAGGGAGGTACTTATAGTAAAGGTTTGGCTACCAGCCACCCTTAGCCCTCGACACGTGTCCAAG
131 GGAGGGAGGTACTTATAGTAAAGGTTTGGCTACCAGCCACCCTTAGCCCTCGACACGTGTCCAAG
26817 AGGTTCTCGTCTAAGTAGGCATGTGAATTGCATTTAATAGAGTTTCACATGTTATTCAACCTAGA
196 AGGTTCTCGTCTAAGTAGGCATGTGAATTGCATTTAATAGAGTTTCACATGTTATTCAACCTAGA
26882 AGAAGACTTA
Statistics
Matches: 256, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
259 224 0.88
261 32 0.12
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (260 bp):
TGACAAAACTCAAGTTTATTTAATATTATTGATAAAAAAAAAAAAGATGATGTCGAAGGAGATAA
CGATTCACACAATAACAAACCGTAAAGTTTTGATTTAGTAGAAAAGTATTTTCCTCTAATGGAGA
GGAGGGAGGTACTTATAGTAAAGGTTTGGCTACCAGCCACCCTTAGCCCTCGACACGTGTCCAAG
AGGTTCTCGTCTAAGTAGGCATGTGAATTGCATTTAATAGAGTTTCACATGTTATTCAACCTAGA
Found at i:29557 original size:3 final size:3
Alignment explanation
Indices: 29549--29581 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
29539 ATGCATGTGT
29549 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29582 TTGACGGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:31606 original size:64 final size:63
Alignment explanation
Indices: 31538--31665 Score: 177
Period size: 64 Copynumber: 2.0 Consensus size: 63
31528 TTTTTCTAAG
* * * * *
31538 TCATTTTCATTTTGAAGAAAACCACATTT-ATTTTCAAATGATTTTATTTTTTCCATTTTCGTTT
1 TCATTTTAATTTTGAAGAAAACCAC-TTTCATTTCCAAATGA-TTTAATTTCTCCATTTTCATTT
*
31602 TCATTTTAATTTTGGAGAAAACCACTTTCATTTCCAAATGATTTAATTTCTCCATTTTCATTT
1 TCATTTTAATTTTGAAGAAAACCACTTTCATTTCCAAATGATTTAATTTCTCCATTTTCATTT
31665 T
1 T
31666 GGAAAAAACC
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
63 23 0.40
64 34 0.60
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (63 bp):
TCATTTTAATTTTGAAGAAAACCACTTTCATTTCCAAATGATTTAATTTCTCCATTTTCATTT
Found at i:36473 original size:114 final size:115
Alignment explanation
Indices: 36273--36595 Score: 366
Period size: 114 Copynumber: 2.7 Consensus size: 115
36263 ATCTATACAG
* * *
36273 AACAAGAAGCACAGGCAGAGAAGCAAATTCACATGAATAACATTTTAAAACCAAACTTATCTCGG
1 AACAAGAAGCACAGGCAGAGAAGCAAACTCACATGAATAACATTTTAAAA-CGAACTTATCTCGA
*
36338 AAGCTAAAGATTGTTCAAACATGTAATCAG-C-TAGAGTAAGCAAATA-CTA
65 AAGCTAAAGATTGTTCAAACATGTAATC-GCCTTAGAGTAAGCAAATACCGA
*** * * * * *
36387 AACAAGAAGCATTTGCAGAGATGCAAACTCGCATGCATAACATTTTAAAATTGAACTTATCTCAA
1 AACAAGAAGCACAGGCAGAGAAGCAAACTCACATGAATAACATTTTAAAA-CGAACTTATCTCGA
*
36452 AAACTAAAGATTGTTCAAACATGTAATCGCCTCAATTTTAGAGTAAGCAAATACCGA
65 AAGCTAAAGATTGTTCAAACATGTAATCG-C-C----TTAGAGTAAGCAAATACCGA
* *
36509 AA-AAGAAGCACAGGCAGAGAAGCAAACTCACATGTATAACATTTTAAGAAGGAACTTATCTCGA
1 AACAAGAAGCACAGGCAGAGAAGCAAACTCACATGAATAACATTTTAA-AACGAACTTATCTCGA
**
36573 AAGCTAAAAGATCATTCAAACAT
65 AAGCT-AAAGATTGTTCAAACAT
36596 TACCTCGATT
Statistics
Matches: 173, Mismatches: 25, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
113 1 0.01
114 80 0.46
116 1 0.01
121 70 0.40
122 21 0.12
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.23
Consensus pattern (115 bp):
AACAAGAAGCACAGGCAGAGAAGCAAACTCACATGAATAACATTTTAAAACGAACTTATCTCGAA
AGCTAAAGATTGTTCAAACATGTAATCGCCTTAGAGTAAGCAAATACCGA
Found at i:53412 original size:61 final size:61
Alignment explanation
Indices: 53311--53429 Score: 145
Period size: 61 Copynumber: 2.0 Consensus size: 61
53301 TTGACCTCTT
* * *
53311 CAAAATTTTGAAAAATTTTGATTTTCTATTTGAGTGTTTTAGAATATTTTATTTAGGTTTC
1 CAAAATTTTGAAAAATTTTGATTTTCTATTTGAGTGTTTTAGAAAATTTCAATTAGGTTTC
* *
53372 CAAAATTTTTG-AAAATTTTTATTTT-TTTCTTGAAGT-TTTTAGAAAATTTCAATTAGGT
1 CAAAA-TTTTGAAAAATTTTGATTTTCTAT-TTG-AGTGTTTTAGAAAATTTCAATTAGGT
53430 CCCCTCAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
60 2 0.04
61 40 0.80
62 8 0.16
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (61 bp):
CAAAATTTTGAAAAATTTTGATTTTCTATTTGAGTGTTTTAGAAAATTTCAATTAGGTTTC
Found at i:55340 original size:19 final size:19
Alignment explanation
Indices: 55310--55357 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
55300 AAAAATATTA
55310 ATTATATTTATTGTTTAAAT
1 ATTAT-TTTATTGTTTAAAT
* *
55330 TTTATTTTATTTTTTAAAT
1 ATTATTTTATTGTTTAAAT
55349 ATT-TTTTAT
1 ATTATTTTAT
55358 CTATTATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 6 0.24
19 15 0.60
20 4 0.16
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
ATTATTTTATTGTTTAAAT
Found at i:55397 original size:12 final size:12
Alignment explanation
Indices: 55380--55412 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
55370 AATGCCATCG
55380 AGAAAGAAAAAA
1 AGAAAGAAAAAA
55392 AGAAAGAAAAAA
1 AGAAAGAAAAAA
55404 A-AAA-AAAAA
1 AGAAAGAAAAA
55413 GGTCTTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 5 0.24
11 3 0.14
12 13 0.62
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAAA
Found at i:55405 original size:16 final size:16
Alignment explanation
Indices: 55380--55413 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55370 AATGCCATCG
* *
55380 AGAAAGAAAAAAAGAA
1 AGAAAAAAAAAAAAAA
55396 AGAAAAAAAAAAAAAA
1 AGAAAAAAAAAAAAAA
55412 AG
1 AG
55414 GTCTTATTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAAAAAAAA
Found at i:56227 original size:46 final size:46
Alignment explanation
Indices: 56177--56273 Score: 115
Period size: 46 Copynumber: 2.1 Consensus size: 46
56167 ATATTTGTAC
* *
56177 TTATTCGAATTTT-ATGTCGATATTGATTGTGATTTTTTATTTAGGG
1 TTATTCG-ATTTTGATGTCGATATTGATTGTGATATTTGATTTAGGG
* * * * *
56223 TTATTCGATTTTGATTTTGATTTTGATTTTTATATTTGATTTAGGG
1 TTATTCGATTTTGATGTCGATATTGATTGTGATATTTGATTTAGGG
56269 TTATT
1 TTATT
56274 TCGGTTTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 5 0.12
46 38 0.88
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.59
Consensus pattern (46 bp):
TTATTCGATTTTGATGTCGATATTGATTGTGATATTTGATTTAGGG
Found at i:56240 original size:6 final size:6
Alignment explanation
Indices: 56229--56264 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
56219 AGGGTTATTC
*
56229 GATTTT GATTTT GATTTT GATTTT TATATTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GAT-TTT GATTT
56265 AGGGTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67
Consensus pattern (6 bp):
GATTTT
Found at i:56501 original size:30 final size:31
Alignment explanation
Indices: 56434--56504 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
56424 ACTGTTAATC
* *
56434 AGTGATTGTTTTGGCACTTTTCAATAACGTT
1 AGTGACTGTTTTGCCACTTTTCAATAACGTT
56465 AGTGACTGTTTTGCCACATTTTC-A-AA-GTT
1 AGTGACTGTTTTGCCAC-TTTTCAATAACGTT
56494 GAGTGACTGTT
1 -AGTGACTGTT
56505 GTGTTAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 3 0.08
30 12 0.33
31 16 0.44
32 5 0.14
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (31 bp):
AGTGACTGTTTTGCCACTTTTCAATAACGTT
Found at i:69353 original size:18 final size:19
Alignment explanation
Indices: 69312--69353 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
69302 AAAATAAAAT
*
69312 AATT-ATTTAATAAATACG
1 AATTAATTTAATAAATACA
69330 AA-TAATTTAA-AAATACA
1 AATTAATTTAATAAATACA
69347 AATTAAT
1 AATTAAT
69354 CTAGAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (19 bp):
AATTAATTTAATAAATACA
Found at i:70649 original size:137 final size:133
Alignment explanation
Indices: 70492--70761 Score: 486
Period size: 137 Copynumber: 2.0 Consensus size: 133
70482 TTTTATTTGA
*
70492 TTCATGATTATTTTTAATTGTTTATGGTATAAAAATAATTATTTTATAATAGTGAACATAATTTA
1 TTCATGATTATTTTTAATTGTTTATGGTATAAAAATAAATATTTTATAATAGTGAACATAATTTA
*
70557 AAATTTTTATATATATATATTAGATTTTATCACATCTATATAATGGGTAAAATTAAAATTATTTA
66 AAA--TTT-T-TATATATATTAGATTTTATCACATCTATATAATGGATAAAATTAAAATTATTTA
70622 ATCACGG
127 ATCACGG
70629 TTCATGATTATTTTTAATTGTTTATGGTATAAAAATAAATATTTTATAATAGTGAACATAATTTA
1 TTCATGATTATTTTTAATTGTTTATGGTATAAAAATAAATATTTTATAATAGTGAACATAATTTA
70694 AAATTTTTATATATATTAGATTTTATCACATCTATATAATGGATAAAATTAAAATTATTTAATCA
66 AAATTTTTATATATATTAGATTTTATCACATCTATATAATGGATAAAATTAAAATTATTTAATCA
70759 CGG
131 CGG
70762 GAGTTAAGTG
Statistics
Matches: 131, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
133 60 0.46
134 1 0.01
135 3 0.02
137 67 0.51
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.46
Consensus pattern (133 bp):
TTCATGATTATTTTTAATTGTTTATGGTATAAAAATAAATATTTTATAATAGTGAACATAATTTA
AAATTTTTATATATATTAGATTTTATCACATCTATATAATGGATAAAATTAAAATTATTTAATCA
CGG
Found at i:72701 original size:27 final size:29
Alignment explanation
Indices: 72664--72732 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
72654 CTATATAAAA
*
72664 ATATAACATAAATAGAAA-A-A-TAAATAT
1 ATATGACATAAATA-AAATACAGTAAATAT
72691 ATATGACATAAATAAAATATCAGTAAATAT
1 ATATGACATAAATAAAATA-CAGTAAATAT
*
72721 ATATGAAATAAA
1 ATATGACATAAA
72733 AATTGTGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
26 3 0.08
27 14 0.39
29 1 0.03
30 18 0.50
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (29 bp):
ATATGACATAAATAAAATACAGTAAATAT
Found at i:72703 original size:15 final size:15
Alignment explanation
Indices: 72683--72732 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
72673 AAATAGAAAA
72683 ATAAATATATATGAC
1 ATAAATATATATGAC
*
72698 ATAAATA-AAAT-ATC
1 ATAAATATATATGA-C
*
72712 AGTAAATATATATGAA
1 A-TAAATATATATGAC
72728 ATAAA
1 ATAAA
72733 AATTGTGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
13 1 0.04
14 5 0.18
15 17 0.61
16 4 0.14
17 1 0.04
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (15 bp):
ATAAATATATATGAC
Found at i:74438 original size:30 final size:30
Alignment explanation
Indices: 74395--74465 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 30
74385 AAATTATATT
74395 TTATGTTTTTATTA-A-AAAATAGATAAATTAA
1 TTAT-TTTTTATTAGATAAAA-AG-TAAATTAA
*
74426 TT-TTTTTATATTAGATAAAAAGTAAATTAG
1 TTATTTTT-TATTAGATAAAAAGTAAATTAA
74456 TTATTTTTTA
1 TTATTTTTTA
74466 ATATTTACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
29 4 0.11
30 17 0.49
31 10 0.29
32 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (30 bp):
TTATTTTTTATTAGATAAAAAGTAAATTAA
Found at i:77317 original size:28 final size:28
Alignment explanation
Indices: 77278--77339 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
77268 AATTCGAACA
*
77278 ATAAAACTAAATTCTTAAA-A-ATAAAATT
1 ATAAAACTAAATT-TCAAATATATAAAA-T
*
77306 ATAAAATTAAATTTCAAATATATAAAAT
1 ATAAAACTAAATTTCAAATATATAAAAT
77334 ATAAAA
1 ATAAAA
77340 ACCTAAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 4 0.13
28 20 0.67
29 6 0.20
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAAAACTAAATTTCAAATATATAAAAT
Found at i:81857 original size:48 final size:48
Alignment explanation
Indices: 81786--81880 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
81776 TTTTGACAGT
81786 TAATTGAATCAAACTTGCTAATCCTCTAACCTTTGTATATGTGATTGC
1 TAATTGAATCAAACTTGCTAATCCTCTAACCTTTGTATATGTGATTGC
*
81834 TAATTGGATCAAACTTGCTAATCCTCTAACCTTTGTATATGTGATTG
1 TAATTGAATCAAACTTGCTAATCCTCTAACCTTTGTATATGTGATTG
81881 AATAGAAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (48 bp):
TAATTGAATCAAACTTGCTAATCCTCTAACCTTTGTATATGTGATTGC
Found at i:85485 original size:33 final size:33
Alignment explanation
Indices: 85443--85578 Score: 132
Period size: 33 Copynumber: 4.4 Consensus size: 33
85433 TTACCTCTAC
*
85443 TCTGTATTTGCTACACTTAGTTCATTAAATCAT
1 TCTGTATTTGCTACACTTAGTTCGTTAAATCAT
*
85476 TCTGTATTTGCT--AC-----TCCTTAAATCAT
1 TCTGTATTTGCTACACTTAGTTCGTTAAATCAT
*
85502 TCTG---TCGCTACACTTAGTTCGTTAAATCAT
1 TCTGTATTTGCTACACTTAGTTCGTTAAATCAT
* * *
85532 T-TTTCTGTCGCTACACTTAGTTCGTTAAATCAT
1 TCTGTAT-TTGCTACACTTAGTTCGTTAAATCAT
85565 TCTGTATTTGCTAC
1 TCTGTATTTGCTAC
85579 TCCTTGAGCT
Statistics
Matches: 84, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
23 4 0.05
25 2 0.02
26 15 0.18
29 1 0.01
30 12 0.14
31 2 0.02
33 45 0.54
34 3 0.04
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (33 bp):
TCTGTATTTGCTACACTTAGTTCGTTAAATCAT
Found at i:106523 original size:18 final size:19
Alignment explanation
Indices: 106483--106523 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
106473 TTTACCCTTA
*
106483 CATTTTTCAAACAATTAAT
1 CATTTTGCAAACAATTAAT
*
106502 -ATTTTGCAAAC-ATTATT
1 CATTTTGCAAACAATTAAT
106519 CATTT
1 CATTT
106524 ATTATTGGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (19 bp):
CATTTTGCAAACAATTAAT
Found at i:109430 original size:42 final size:42
Alignment explanation
Indices: 109347--109437 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
109337 TGATCCAATC
* * *
109347 GAAAGCTAACGGTGTTTGGTGGCCTCGGCGTCATCGAAAATG
1 GAAAGCTAACGGTGTTTGGAGGCCTCGCCGCCATCGAAAATG
* * *
109389 GAAAGCTAACGGTGTTTGGAGGGCTCGCCGCCATTGGAAATG
1 GAAAGCTAACGGTGTTTGGAGGCCTCGCCGCCATCGAAAATG
*
109431 GGAAGCT
1 GAAAGCT
109438 GTTGAGTGCT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (42 bp):
GAAAGCTAACGGTGTTTGGAGGCCTCGCCGCCATCGAAAATG
Found at i:110262 original size:20 final size:20
Alignment explanation
Indices: 110239--110291 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
110229 TATGAATTAA
*
110239 TTATTAACTTTTCTAAAATT
1 TTATTAAATTTTCTAAAATT
* **
110259 TTATTGAAATTTTTTATTATT
1 TTATT-AAATTTTCTAAAATT
110280 TTATTAAATTTT
1 TTATTAAATTTT
110292 TATAAATTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (20 bp):
TTATTAAATTTTCTAAAATT
Found at i:113803 original size:29 final size:30
Alignment explanation
Indices: 113771--113829 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
113761 TATGGTTTAA
*
113771 TGTGCAA-TTATATACAT-GAATTTTGATTT
1 TGTGCAAGTT-TATACATAAAATTTTGATTT
113800 TGTGCAAGTTTATACATAAAATTTTGATTT
1 TGTGCAAGTTTATACATAAAATTTTGATTT
113830 GATCTAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (30 bp):
TGTGCAAGTTTATACATAAAATTTTGATTT
Found at i:114084 original size:29 final size:27
Alignment explanation
Indices: 114018--114084 Score: 64
Period size: 31 Copynumber: 2.3 Consensus size: 27
114008 GAATTTAATG
*
114018 TGTATAATTGCATCATATTAAAGTTCA
1 TGTATAATTGCATCATATTAAAATTCA
*
114045 CGTATACAATTGCA-CATTAAATTAAAATTCA
1 TGTAT--AATTGCATCA-T--ATTAAAATTCA
114076 TGTATAATT
1 TGTATAATT
114085 TTGAGATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
27 4 0.12
28 2 0.06
29 12 0.38
31 14 0.44
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (27 bp):
TGTATAATTGCATCATATTAAAATTCA
Found at i:118865 original size:13 final size:15
Alignment explanation
Indices: 118834--118867 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
118824 TATTCGGTTT
118834 ATTCGAATAATTCAA
1 ATTCGAATAATTCAA
118849 ATTCGAA-AATT-AA
1 ATTCGAATAATTCAA
118862 ATTCGA
1 ATTCGA
118868 TTCGAACTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 4 0.21
15 7 0.37
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (15 bp):
ATTCGAATAATTCAA
Found at i:120174 original size:20 final size:20
Alignment explanation
Indices: 120145--120185 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
120135 GTTGCTGCAG
*
120145 ATTGATTGGCCAAGAGCTGT
1 ATTGAGTGGCCAAGAGCTGT
*
120165 ATTGAGTGGCCGAGAGCTGT
1 ATTGAGTGGCCAAGAGCTGT
120185 A
1 A
120186 ATAATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.27
Consensus pattern (20 bp):
ATTGAGTGGCCAAGAGCTGT
Found at i:134344 original size:17 final size:15
Alignment explanation
Indices: 134322--134356 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 15
134312 AGCTTTCAAG
134322 TTTGAATTTTATTTTTA
1 TTTGAA-TTT-TTTTTA
134339 TTTGAATTTTTTTTA
1 TTTGAATTTTTTTTA
134354 TTT
1 TTT
134357 AAGTTTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 3 0.17
17 6 0.33
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTGAATTTTTTTTA
Found at i:134648 original size:84 final size:84
Alignment explanation
Indices: 134487--134650 Score: 192
Period size: 84 Copynumber: 2.0 Consensus size: 84
134477 TTTAAAATAG
* ** * * *
134487 AAAATTTTCATTTAAATTTTTTATAATTTATAAAATTTTAAATTAATAATGATAAAATTACATTT
1 AAAATTTTCATTTAAATTTTTTATAATTTATAAAAATACAAATTAAAAATGAAAAAAATACATTT
*
134552 TAATTCTCTAAAAATTCTA
66 TAATTATCTAAAAATTCTA
*
134571 AAAATTTT-ATTT-AATTTTTTAATAA-TTATAAAAATACAAATTATTAAAATGAAAAAAATATA
1 AAAATTTTCATTTAAATTTTTT-ATAATTTATAAAAATACAAATTA--AAAATGAAAAAAATACA
134633 TTTT-ATTATCATAAAAAT
63 TTTTAATTATC-TAAAAAT
134651 ATATAATTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
82 23 0.34
83 13 0.19
84 32 0.47
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (84 bp):
AAAATTTTCATTTAAATTTTTTATAATTTATAAAAATACAAATTAAAAATGAAAAAAATACATTT
TAATTATCTAAAAATTCTA
Found at i:135171 original size:24 final size:24
Alignment explanation
Indices: 135115--135176 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 24
135105 TATTCTATAA
*
135115 GAATTAAAAATTA-ATAATATTTTT
1 GAATTAAAAA-TAGATAATAATTTT
*
135139 G--TTACAAAATAGATCATAATTTT
1 GAATTA-AAAATAGATAATAATTTT
*
135162 GAATTAAAAACAGAT
1 GAATTAAAAATAGAT
135177 TGTATATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
22 5 0.16
23 14 0.45
24 9 0.29
25 3 0.10
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (24 bp):
GAATTAAAAATAGATAATAATTTT
Found at i:140464 original size:29 final size:30
Alignment explanation
Indices: 140432--140488 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
140422 TGGTTTAATA
*
140432 TGTAATTATATACA-ATAATTTTGATTTTG
1 TGTAATTATATACATAAAATTTTGATTTTG
*
140461 TGTAATTTTATACATAAAATTTTGATTT
1 TGTAATTATATACATAAAATTTTGATTT
140489 GATCAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.53
Consensus pattern (30 bp):
TGTAATTATATACATAAAATTTTGATTTTG
Found at i:140783 original size:30 final size:30
Alignment explanation
Indices: 140744--140822 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
140734 ATATAATATA
140744 GTAATTAAATTAAATTAATTATTATATAAT
1 GTAATTAAATTAAATTAATTATTATATAAT
* * * * *
140774 GTGATTAAATAAAATAAAATATTATATGAT
1 GTAATTAAATTAAATTAATTATTATATAAT
*
140804 GTAATTACATTAAATTAAT
1 GTAATTAAATTAAATTAAT
140823 AATGAAGTTC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (30 bp):
GTAATTAAATTAAATTAATTATTATATAAT
Found at i:142869 original size:23 final size:22
Alignment explanation
Indices: 142839--142942 Score: 100
Period size: 23 Copynumber: 4.5 Consensus size: 22
142829 ACACTAGCGC
*
142839 GCTCTCTGTTTAGCACGTCTTGT
1 GCTCTCTGTTTAGCACGT-GTGT
*
142862 GCTCTCTGTTATTAGCATTGTGTGT
1 GCTCTCTG-T-TTAGCA-CGTGTGT
* * *
142887 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCAC-GTGTGT
*
142910 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCAC-GTGTGT
142933 GCTCTCTGTT
1 GCTCTCTGTT
142943 ACCCAGCACT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
23 46 0.70
24 1 0.02
25 17 0.26
26 2 0.03
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (22 bp):
GCTCTCTGTTTAGCACGTGTGT
Found at i:142959 original size:71 final size:69
Alignment explanation
Indices: 142840--142989 Score: 205
Period size: 71 Copynumber: 2.1 Consensus size: 69
142830 CACTAGCGCG
* ** * *
142840 CTCTCTGTTTAGCACGTCTTGTGCTCTCTGTTATTAGCATTGTGTGTGCTCTCTGATTAGTACTT
1 CTCTCTGTTTAGCACGTCGTGTGCTCTCTGTTACCAGCACTGTATGTGCTCTCTG-TTAGTACTT
142905 TGTGTA
65 TG-GTA
142911 CTCTCTGTTTAGCACTGT-GTGTGCTCTCTGTTACCCAGCACT-TATGTGCTCTCTGTTAGTACT
1 CTCTCTGTTTAGCAC-GTCGTGTGCTCTCTGTTA-CCAGCACTGTATGTGCTCTCTGTTAGTACT
142974 TTGGTA
64 TTGGTA
142980 CTCTCTGTTT
1 CTCTCTGTTT
142990 GTTCAGTATA
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
69 13 0.18
70 11 0.15
71 41 0.57
72 7 0.10
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (69 bp):
CTCTCTGTTTAGCACGTCGTGTGCTCTCTGTTACCAGCACTGTATGTGCTCTCTGTTAGTACTTT
GGTA
Found at i:142974 original size:21 final size:20
Alignment explanation
Indices: 142839--142988 Score: 84
Period size: 23 Copynumber: 6.5 Consensus size: 20
142829 ACACTAGCGC
142839 GCTCTCTGTTTAGCACGTCTTGT
1 GCTCTCTG-TTAGCAC-T-TTGT
*
142862 GCTCTCTGTTATTAGCATTGTGTGT
1 GCTCTCTG---TTAGCACT-T-TGT
*
142887 GCTCTCTGATTAGTACTTTGT
1 GCTCTCTG-TTAGCACTTTGT
142908 GTACTCTCTGTTTAGCACTGTGTGT
1 G--CTCTCTG-TTAGCACT-T-TGT
142933 GCTCTCTGTTACCCAGCACTTATGT
1 GCTCTCTGTT----AGCACTT-TGT
*
142958 GCTCTCTGTTAGTACTTTGGT
1 GCTCTCTGTTAGCACTTT-GT
*
142979 ACTCTCTGTT
1 GCTCTCTGTT
142989 TGTTCAGTAT
Statistics
Matches: 105, Mismatches: 10, Indels: 26
0.74 0.07 0.18
Matches are distributed among these distances:
20 1 0.01
21 21 0.20
22 3 0.03
23 36 0.34
24 3 0.03
25 35 0.33
26 6 0.06
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (20 bp):
GCTCTCTGTTAGCACTTTGT
Found at i:151399 original size:24 final size:24
Alignment explanation
Indices: 151371--151424 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
151361 TCCCGGTGAA
*
151371 GGTGGCTTCACGATAGGAGGCGTT
1 GGTGGCTTCACGATAGGAGGCGAT
151395 GGTGGCTTCACGATAGGAGGCGAT
1 GGTGGCTTCACGATAGGAGGCGAT
151419 GGTGGC
1 GGTGGC
151425 GGTAGAATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.44, T:0.22
Consensus pattern (24 bp):
GGTGGCTTCACGATAGGAGGCGAT
Found at i:151464 original size:24 final size:24
Alignment explanation
Indices: 151371--151462 Score: 87
Period size: 24 Copynumber: 3.8 Consensus size: 24
151361 TCCCGGTGAA
*
151371 GGTGGCTTCACGATAGGAGGCGTT
1 GGTGGCTTCACAATAGGAGGCGTT
* *
151395 GGTGGCTTCACGATAGGAGGCGAT
1 GGTGGCTTCACAATAGGAGGCGTT
* * * * *
151419 GGTGGCGGT-AGAATCGGCGGTGTT
1 GGTGGC-TTCACAATAGGAGGCGTT
*
151443 GGTGGATTCACAATAGGAGG
1 GGTGGCTTCACAATAGGAGG
151463 TGGCAGAATA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
23 1 0.02
24 51 0.96
25 1 0.02
ACGTcount: A:0.20, C:0.14, G:0.43, T:0.23
Consensus pattern (24 bp):
GGTGGCTTCACAATAGGAGGCGTT
Found at i:151477 original size:39 final size:39
Alignment explanation
Indices: 151428--151604 Score: 318
Period size: 39 Copynumber: 4.5 Consensus size: 39
151418 TGGTGGCGGT
151428 AGAATCGGCGGTGTTGGTGGATTCACAATAGGAGGTGGC
1 AGAATCGGCGGTGTTGGTGGATTCACAATAGGAGGTGGC
*
151467 AGAATAGGCGGTGTTGGTGGATTCACAATAGGAGGTGGC
1 AGAATCGGCGGTGTTGGTGGATTCACAATAGGAGGTGGC
151506 AGAATCGGCGGTGTTGGTGGATTCACAATAGGAGGTGGC
1 AGAATCGGCGGTGTTGGTGGATTCACAATAGGAGGTGGC
* *
151545 AGAATCGGCGGTATTGGTGGGTTCACAATAGGAGGTGGC
1 AGAATCGGCGGTGTTGGTGGATTCACAATAGGAGGTGGC
*
151584 AGAATCGGCGGTATTGGTGGA
1 AGAATCGGCGGTGTTGGTGGA
151605 CTGGGGTAGA
Statistics
Matches: 133, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 133 1.00
ACGTcount: A:0.24, C:0.12, G:0.41, T:0.23
Consensus pattern (39 bp):
AGAATCGGCGGTGTTGGTGGATTCACAATAGGAGGTGGC
Found at i:151734 original size:33 final size:33
Alignment explanation
Indices: 151692--151819 Score: 123
Period size: 33 Copynumber: 3.8 Consensus size: 33
151682 TGTATGTGGC
*
151692 GGAGGCTTCACAACAGGTGGTTTGGGTGTATAT
1 GGAGGCTTCACAACAGGTGGTTTGGGTGCATAT
*
151725 GGAGGCTTCACAACCGGTGGTTTGGGTGCATACGGT
1 GGAGGCTTCACAACAGGTGGTTTGGGTGCATA---T
* * * * * * *
151761 GGAGGCTTTACAATAGGAGGCTTAGGTACATAG
1 GGAGGCTTCACAACAGGTGGTTTGGGTGCATAT
*
151794 GGAGGCTTTC-CAGCAGGTGGTTTGGG
1 GGAGGC-TTCACAACAGGTGGTTTGGG
151820 AGGATGCGGT
Statistics
Matches: 75, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
33 47 0.63
34 2 0.03
36 26 0.35
ACGTcount: A:0.20, C:0.15, G:0.38, T:0.27
Consensus pattern (33 bp):
GGAGGCTTCACAACAGGTGGTTTGGGTGCATAT
Found at i:151898 original size:42 final size:42
Alignment explanation
Indices: 151839--151969 Score: 174
Period size: 42 Copynumber: 3.1 Consensus size: 42
151829 TGGTTGTTTT
*
151839 GGTGGTTCAGGGTGATACGGGGGTTTCACCACCGGAGGCTTA
1 GGTGGTTTAGGGTGATACGGGGGTTTCACCACCGGAGGCTTA
* * * *
151881 GGTGGTTTAGGGTGATACGGTGGCTTCACCACCGGTGGCTTC
1 GGTGGTTTAGGGTGATACGGGGGTTTCACCACCGGAGGCTTA
* * *
151923 GGCGGTTTAGGGTGATATGGTGGGTTT-ACCACTGGAGGCTTA
1 GGTGGTTTAGGGTGATACGG-GGGTTTCACCACCGGAGGCTTA
151965 GGTGG
1 GGTGG
151970 CTTTGGAGGA
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
42 71 0.95
43 4 0.05
ACGTcount: A:0.15, C:0.17, G:0.41, T:0.27
Consensus pattern (42 bp):
GGTGGTTTAGGGTGATACGGGGGTTTCACCACCGGAGGCTTA
Found at i:152036 original size:93 final size:93
Alignment explanation
Indices: 151913--152098 Score: 363
Period size: 93 Copynumber: 2.0 Consensus size: 93
151903 GCTTCACCAC
151913 CGGTGGCTTCGGCGGTTTAGGGTGATATGGTGGGTTTACCACTGGAGGCTTAGGTGGCTTTGGAG
1 CGGTGGCTTCGGCGGTTTAGGGTGATATGGTGGGTTTACCACTGGAGGCTTAGGTGGCTTTGGAG
151978 GATGATGAATTGGAGGTTTAGGGTGATA
66 GATGATGAATTGGAGGTTTAGGGTGATA
*
152006 CGGTGGCTTCGGTGGTTTAGGGTGATATGGTGGGTTTACCACTGGAGGCTTAGGTGGCTTTGGAG
1 CGGTGGCTTCGGCGGTTTAGGGTGATATGGTGGGTTTACCACTGGAGGCTTAGGTGGCTTTGGAG
152071 GATGATGAATTGGAGGTTTAGGGTGATA
66 GATGATGAATTGGAGGTTTAGGGTGATA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.17, C:0.09, G:0.42, T:0.32
Consensus pattern (93 bp):
CGGTGGCTTCGGCGGTTTAGGGTGATATGGTGGGTTTACCACTGGAGGCTTAGGTGGCTTTGGAG
GATGATGAATTGGAGGTTTAGGGTGATA
Done.