Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006174.1 Kokia drynarioides strain JFW-HI SEQ_120738, 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: 204875
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Warning! 140 characters in sequence are not A, C, G, or T
Found at i:11338 original size:16 final size:15
Alignment explanation
Indices: 11316--11357 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
11306 CATTACTAAT
11316 TTAAAATTTTATAAA
1 TTAAAATTTTATAAA
*
11331 TTATAAATGGTT-TAAA
1 TTA-AAAT-TTTATAAA
11347 TTAAAATTTTA
1 TTAAAATTTTA
11358 CCATTTTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
14 2 0.09
15 7 0.32
16 11 0.50
17 2 0.09
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (15 bp):
TTAAAATTTTATAAA
Found at i:14120 original size:47 final size:47
Alignment explanation
Indices: 14066--14159 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
14056 TTCTCCCTTA
14066 AAACTTAGGCAGTAAGCACAACTTGTTTCCTCTCTCAAATGCTCACT
1 AAACTTAGGCAGTAAGCACAACTTGTTTCCTCTCTCAAATGCTCACT
14113 AAACTTAGGCAGTAAGCACAACTTGTTTCCTCTCTCAAATGCTCACT
1 AAACTTAGGCAGTAAGCACAACTTGTTTCCTCTCTCAAATGCTCACT
14160 CAAAAATACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.30
Consensus pattern (47 bp):
AAACTTAGGCAGTAAGCACAACTTGTTTCCTCTCTCAAATGCTCACT
Found at i:28883 original size:29 final size:29
Alignment explanation
Indices: 28829--28902 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
28819 TAGGTATGTT
* *
28829 ATATTATATTATTTGATTTATTTAATTAGA
1 ATATAATATTATTTGATTTATCTAA-TAGA
*
28859 ATATAATATT-TTTTATTTATCTAATAGA
1 ATATAATATTATTTGATTTATCTAATAGA
* * *
28887 ATGTAAAATTACTTGA
1 ATATAATATTATTTGA
28903 AAGTAATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 12 0.33
29 15 0.42
30 9 0.25
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (29 bp):
ATATAATATTATTTGATTTATCTAATAGA
Found at i:40433 original size:27 final size:27
Alignment explanation
Indices: 40403--40481 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 27
40393 GTACGATTTC
40403 ATTAGGATTGATGAATTGAGATTTTAA
1 ATTAGGATTGATGAATTGAGATTTTAA
* * * * *
40430 ATTA-AAAT-AT-TA-GGA-ATTTT-C
1 ATTAGGATTGATGAATTGAGATTTTAA
40451 ATTAGGATTGATGAATTGAGATTTTAA
1 ATTAGGATTGATGAATTGAGATTTTAA
40478 ATTA
1 ATTA
40482 AAATATTAGG
Statistics
Matches: 36, Mismatches: 10, Indels: 12
0.62 0.17 0.21
Matches are distributed among these distances:
21 4 0.11
22 7 0.19
23 4 0.11
24 2 0.06
25 4 0.11
26 7 0.19
27 8 0.22
ACGTcount: A:0.39, C:0.01, G:0.18, T:0.42
Consensus pattern (27 bp):
ATTAGGATTGATGAATTGAGATTTTAA
Found at i:40451 original size:48 final size:48
Alignment explanation
Indices: 40399--40498 Score: 200
Period size: 48 Copynumber: 2.1 Consensus size: 48
40389 AATTGTACGA
40399 TTTCATTAGGATTGATGAATTGAGATTTTAAATTAAAATATTAGGAAT
1 TTTCATTAGGATTGATGAATTGAGATTTTAAATTAAAATATTAGGAAT
40447 TTTCATTAGGATTGATGAATTGAGATTTTAAATTAAAATATTAGGAAT
1 TTTCATTAGGATTGATGAATTGAGATTTTAAATTAAAATATTAGGAAT
40495 TTTC
1 TTTC
40499 TACTTAATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (48 bp):
TTTCATTAGGATTGATGAATTGAGATTTTAAATTAAAATATTAGGAAT
Found at i:40523 original size:48 final size:46
Alignment explanation
Indices: 40399--40514 Score: 146
Period size: 48 Copynumber: 2.4 Consensus size: 46
40389 AATTGTACGA
*
40399 TTTCATTAGGATTGATGAATTGAGATTTTAAATTAAAATATTAGGAAT
1 TTTCATTA-GATT-ATAAATTGAGATTTTAAATTAAAATATTAGGAAT
*
40447 TTTCATTAGGATTGATGAATTGAGATTTTAAATTAAAATATTAGGAAT
1 TTTCATTA-GATT-ATAAATTGAGATTTTAAATTAAAATATTAGGAAT
40495 TTTCTACTTA-ATT-TAAATTG
1 TTTC-A-TTAGATTATAAATTG
40515 TAATATTTTC
Statistics
Matches: 65, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
46 6 0.09
48 55 0.85
49 1 0.02
50 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (46 bp):
TTTCATTAGATTATAAATTGAGATTTTAAATTAAAATATTAGGAAT
Found at i:41583 original size:16 final size:16
Alignment explanation
Indices: 41558--41597 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
41548 CATTTTATCT
* * *
41558 TTGATCTTGATTTTCA
1 TTGATATTGATCTCCA
41574 TTGATATTGATCTCCA
1 TTGATATTGATCTCCA
41590 TTGATATT
1 TTGATATT
41598 AAGTATAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (16 bp):
TTGATATTGATCTCCA
Found at i:49149 original size:51 final size:51
Alignment explanation
Indices: 49094--49190 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
49084 AAATTCAAAT
* * *
49094 ATAAATTTAAATCACAATTAGAGTTTCACTATAGTTGAATCAAATTTTAAA
1 ATAAATTTAAATCACAATTAAAATTTCACTATAATTGAATCAAATTTTAAA
* *
49145 ATAAATTTGAATCACAATTAAAATTTCATTATAATTGAATCAAATT
1 ATAAATTTAAATCACAATTAAAATTTCACTATAATTGAATCAAATT
49191 AAAATTCATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.38
Consensus pattern (51 bp):
ATAAATTTAAATCACAATTAAAATTTCACTATAATTGAATCAAATTTTAAA
Found at i:49194 original size:27 final size:26
Alignment explanation
Indices: 49151--49203 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
49141 TAAAATAAAT
49151 TTGAATCACAATTAAAATTTCATTATAA
1 TTGAATCACAATTAAAA-TTCA-TATAA
49179 TTGAATCA-AATTAAAATTCATATAA
1 TTGAATCACAATTAAAATTCATATAA
49204 ACTATTACGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 5 0.20
26 4 0.16
27 8 0.32
28 8 0.32
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (26 bp):
TTGAATCACAATTAAAATTCATATAA
Found at i:67926 original size:20 final size:21
Alignment explanation
Indices: 67897--67948 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
67887 AGAGTTAAGT
*
67897 AATTTAAATAATT-TTTT-TA
1 AATTTTAATAATTATTTTGTA
67916 ATATTTTAATAATTATTTTGTA
1 A-ATTTTAATAATTATTTTGTA
67938 AATTATTAATA
1 AATT-TTAATA
67949 GTTTAATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.04
20 11 0.39
21 7 0.25
22 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AATTTTAATAATTATTTTGTA
Found at i:76209 original size:30 final size:30
Alignment explanation
Indices: 76173--76231 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
76163 TACATTTCAG
76173 TCCCTCAACTTTAAAAATATGACAAAACAA
1 TCCCTCAACTTTAAAAATATGACAAAACAA
* *
76203 TCCCTCAACTTTGAAAATGTGACAAAACA
1 TCCCTCAACTTTAAAAATATGACAAAACA
76232 GTCCTTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.24
Consensus pattern (30 bp):
TCCCTCAACTTTAAAAATATGACAAAACAA
Found at i:76359 original size:30 final size:31
Alignment explanation
Indices: 76323--76391 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
76313 CGGTTATATT
*
76323 TAACAAAACAATCACTCAACTT-T-GAAAATG
1 TAACAAAACAATCACTAAACTTATCGAAAA-G
*
76353 TAACAAAACAATCACTAAAGTTATCGAAAAG
1 TAACAAAACAATCACTAAACTTATCGAAAAG
76384 TAACAAAA
1 TAACAAAA
76392 TAGTCCTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 20 0.57
31 10 0.29
32 5 0.14
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.20
Consensus pattern (31 bp):
TAACAAAACAATCACTAAACTTATCGAAAAG
Found at i:77379 original size:30 final size:31
Alignment explanation
Indices: 77320--77386 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
77310 AAGAGGATTA
*
77320 TTTTGTCACTTTTCGATAACTTTAGTGACTG
1 TTTTGTCACTTTTCGATAACTTGAGTGACTG
*
77351 TTTTGTCACATTTTC-A-AAGTTGAGTGACTG
1 TTTTGTCAC-TTTTCGATAACTTGAGTGACTG
77381 TTTTGT
1 TTTTGT
77387 AAACCAGGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 18 0.55
31 10 0.30
32 5 0.15
ACGTcount: A:0.19, C:0.13, G:0.18, T:0.49
Consensus pattern (31 bp):
TTTTGTCACTTTTCGATAACTTGAGTGACTG
Found at i:80176 original size:8 final size:8
Alignment explanation
Indices: 80163--80188 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
80153 ATAAGCATTG
80163 TACATGAA
1 TACATGAA
80171 TACATGAA
1 TACATGAA
80179 TACATGAA
1 TACATGAA
80187 TA
1 TA
80189 AAAATGAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.27
Consensus pattern (8 bp):
TACATGAA
Found at i:85846 original size:46 final size:47
Alignment explanation
Indices: 85789--85877 Score: 128
Period size: 47 Copynumber: 1.9 Consensus size: 47
85779 CTCAGTAAAA
* *
85789 CAATTATTAAAAATATATTT-TT-TATAAAATAACGAAACATTAATGG
1 CAATTACTAAAAATAT-TTTCTTCTATAAAATAACAAAACATTAATGG
*
85835 CAATTACTAAAAATATTTTCTTCTATAAAATAATAAAACATTA
1 CAATTACTAAAAATATTTTCTTCTATAAAATAACAAAACATTA
85878 CCATGGAGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
45 3 0.08
46 17 0.45
47 18 0.47
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (47 bp):
CAATTACTAAAAATATTTTCTTCTATAAAATAACAAAACATTAATGG
Found at i:86004 original size:12 final size:12
Alignment explanation
Indices: 85987--86011 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
85977 CATAATTAAA
85987 ATTTCATTTTAT
1 ATTTCATTTTAT
85999 ATTTCATTTTAT
1 ATTTCATTTTAT
86011 A
1 A
86012 AATATATACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTCATTTTAT
Found at i:86666 original size:59 final size:61
Alignment explanation
Indices: 86548--86667 Score: 217
Period size: 59 Copynumber: 2.0 Consensus size: 61
86538 TTATATGTCA
86548 CATCATATCAATAAAATTAAAAAATAATTAATTTTTTTTATTTATTTTCAAATGATTTAAC
1 CATCATATCAATAAAATTAAAAAATAATTAATTTTTTTTATTTATTTTCAAATGATTTAAC
*
86609 CATCATATCAATAAAGTT-AAAAATAATTAA-TTTTTTTATTTATTTTCAAATGATTTAAC
1 CATCATATCAATAAAATTAAAAAATAATTAATTTTTTTTATTTATTTTCAAATGATTTAAC
86668 AAATGGTACA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
59 29 0.50
60 12 0.21
61 17 0.29
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (61 bp):
CATCATATCAATAAAATTAAAAAATAATTAATTTTTTTTATTTATTTTCAAATGATTTAAC
Found at i:87682 original size:18 final size:18
Alignment explanation
Indices: 87658--87727 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
87648 TAACTATCCC
87658 TAAAATAATAGCAAAATT
1 TAAAATAATAGCAAAATT
*
87676 TACAATAA-AGCAAAAATT
1 TAAAATAATAGC-AAAATT
**
87694 ATAAAAT-ATCCCAAAA-T
1 -TAAAATAATAGCAAAATT
87711 TAAAATAATAGCAAAAT
1 TAAAATAATAGCAAAAT
87728 AAAAATAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
16 6 0.15
17 11 0.27
18 18 0.44
19 6 0.15
ACGTcount: A:0.61, C:0.10, G:0.04, T:0.24
Consensus pattern (18 bp):
TAAAATAATAGCAAAATT
Found at i:87727 original size:17 final size:17
Alignment explanation
Indices: 87658--87735 Score: 70
Period size: 17 Copynumber: 4.5 Consensus size: 17
87648 TAACTATCCC
87658 TAAAATAATAGCAAAATT
1 TAAAATAATAGCAAAA-T
*
87676 TACAATAA-AGCAAAAAT
1 TAAAATAATAGC-AAAAT
**
87693 TATAAA-ATATCCCAAAAT
1 TA-AAATA-ATAGCAAAAT
87711 TAAAATAATAGCAAAAT
1 TAAAATAATAGCAAAAT
*
87728 AAAAATAA
1 TAAAATAA
87736 AATAATTTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
17 25 0.52
18 22 0.46
19 1 0.02
ACGTcount: A:0.64, C:0.09, G:0.04, T:0.23
Consensus pattern (17 bp):
TAAAATAATAGCAAAAT
Found at i:87727 original size:35 final size:34
Alignment explanation
Indices: 87669--87734 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
87659 AAAATAATAG
*
87669 CAAAATTTACAATAAAGCAAAAATTATAAAATATCC
1 CAAAATTTAAAATAAAGCAAAAA-TA-AAAATATCC
87705 CAAAA-TTAAAATAATAGC-AAAATAAAAATA
1 CAAAATTTAAAATAA-AGCAAAAATAAAAATA
87735 AAATAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 6 0.21
34 2 0.07
35 12 0.43
36 8 0.29
ACGTcount: A:0.64, C:0.11, G:0.03, T:0.23
Consensus pattern (34 bp):
CAAAATTTAAAATAAAGCAAAAATAAAAATATCC
Found at i:90577 original size:16 final size:18
Alignment explanation
Indices: 90546--90578 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
90536 GTCGATTTCA
90546 GAAAGAATAGAAAATTAC
1 GAAAGAATAGAAAATTAC
90564 GAAA-AATA-AAAATTA
1 GAAAGAATAGAAAATTA
90579 AATTAAATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.67, C:0.03, G:0.12, T:0.18
Consensus pattern (18 bp):
GAAAGAATAGAAAATTAC
Found at i:90734 original size:27 final size:24
Alignment explanation
Indices: 90680--90734 Score: 56
Period size: 27 Copynumber: 2.2 Consensus size: 24
90670 TTAATTTGTT
* *
90680 ATTTTTTATATAATAATAAATTTT
1 ATTTTTTATATAATAATAAATATA
*
90704 ATTTTTTAATATATATATATATATATA
1 ATTTTTT-ATATA-ATA-ATAAATATA
90731 ATTT
1 ATTT
90735 AGATATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 7 0.28
25 5 0.20
26 3 0.12
27 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTTTTATATAATAATAAATATA
Found at i:91374 original size:61 final size:61
Alignment explanation
Indices: 91275--91390 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 61
91265 TCTTGGCTAC
* ** * *
91275 CCAAAATGAAATCTTTGCAATTTTGTCCTCTTAATCTTATGACGCTTTCATTTTAATCACA
1 CCAAAATGAAATCTTTGCAATTTTCTCAACATAATCTTAAGACGCTTTCATTTTAATCACA
* * *
91336 CCAAAATGAAATCTTTGCAATTTTCTCAACATACTCTTAAGGCGCTTTTATTTTA
1 CCAAAATGAAATCTTTGCAATTTTCTCAACATAATCTTAAGACGCTTTCATTTTA
91391 GTCATTTAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.41
Consensus pattern (61 bp):
CCAAAATGAAATCTTTGCAATTTTCTCAACATAATCTTAAGACGCTTTCATTTTAATCACA
Found at i:95027 original size:22 final size:23
Alignment explanation
Indices: 94996--95051 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
94986 TGGGACGTTG
*
94996 AATATATTGAAAATGTTTTA-ATT
1 AATAT-TTGAAAATGTTTTATAAT
* *
95019 ATTATTTGAAAATTTTTTATAAT
1 AATATTTGAAAATGTTTTATAAT
95042 AATATTTGAA
1 AATATTTGAA
95052 TTGATAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (23 bp):
AATATTTGAAAATGTTTTATAAT
Found at i:107175 original size:20 final size:20
Alignment explanation
Indices: 107150--107211 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
107140 ATATATATGC
107150 TTGTTTTAAAGTCTTAGTCT
1 TTGTTTTAAAGTCTTAGTCT
* *
107170 TTG-TTT-GAGTC--AATGC-
1 TTGTTTTAAAGTCTTAGT-CT
107186 TTGTTTTAAAGTCTTAGTCT
1 TTGTTTTAAAGTCTTAGTCT
107206 TTGTTT
1 TTGTTT
107212 GAGTCAATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 5 0.16
17 4 0.12
18 8 0.25
19 4 0.12
20 11 0.34
ACGTcount: A:0.18, C:0.10, G:0.18, T:0.55
Consensus pattern (20 bp):
TTGTTTTAAAGTCTTAGTCT
Found at i:107193 original size:36 final size:36
Alignment explanation
Indices: 107146--107219 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
107136 AAGTATATAT
107146 ATGCTTGTTTTAAAGTCTTAGTCTTTGTTTGAGTCA
1 ATGCTTGTTTTAAAGTCTTAGTCTTTGTTTGAGTCA
107182 ATGCTTGTTTTAAAGTCTTAGTCTTTGTTTGAGTCA
1 ATGCTTGTTTTAAAGTCTTAGTCTTTGTTTGAGTCA
107218 AT
1 AT
107220 CTTAGAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.50
Consensus pattern (36 bp):
ATGCTTGTTTTAAAGTCTTAGTCTTTGTTTGAGTCA
Found at i:111987 original size:59 final size:59
Alignment explanation
Indices: 111894--112013 Score: 204
Period size: 59 Copynumber: 2.0 Consensus size: 59
111884 GATGTCTAAA
* * *
111894 TGGGCTAAAAAGTGTGCAATCGGTTTACATGTAGTCACTTAGGCACCTGACGGAGTGCG
1 TGGGCTAAAAAGTGTGCAATCGGCTTACACGTAGTCACTTAGACACCTGACGGAGTGCG
*
111953 TGGGCTAAAGAGTGTGCAATCGGCTTACACGTAGTCACTTAGACACCTGACGGAGTGCG
1 TGGGCTAAAAAGTGTGCAATCGGCTTACACGTAGTCACTTAGACACCTGACGGAGTGCG
112012 TG
1 TG
112014 ATGTTTTATT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (59 bp):
TGGGCTAAAAAGTGTGCAATCGGCTTACACGTAGTCACTTAGACACCTGACGGAGTGCG
Found at i:113244 original size:25 final size:26
Alignment explanation
Indices: 113196--113246 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
113186 TAATTTAATA
**
113196 ATTAATAATTTTATATTTTTTTATTT
1 ATTAATAATTTTATATTTAATTATTT
113222 ATTAA-AATTTTATATTTAATTATTT
1 ATTAATAATTTTATATTTAATTATTT
113247 TAACATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
ATTAATAATTTTATATTTAATTATTT
Found at i:115487 original size:13 final size:13
Alignment explanation
Indices: 115469--115494 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
115459 GACATTATTT
115469 AAAAAAAAACAAA
1 AAAAAAAAACAAA
115482 AAAAAAAAACAAA
1 AAAAAAAAACAAA
115495 TATGATTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACAAA
Found at i:126680 original size:32 final size:31
Alignment explanation
Indices: 126618--126697 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
126608 ATAAAATGTT
* *
126618 TAATTAATCAATATGAGTTATCAAAATTAAG
1 TAATTAATTAATATAAGTTATCAAAATTAAG
*
126649 TAATTAATTAATCATAAGTTA-CTAAATTTAAG
1 TAATTAATTAAT-ATAAGTTATC-AAAATTAAG
*
126681 TAATCAATT--TATAAGTT
1 TAATTAATTAATATAAGTT
126698 TATGGTGTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
29 7 0.16
30 1 0.02
31 12 0.28
32 23 0.53
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.40
Consensus pattern (31 bp):
TAATTAATTAATATAAGTTATCAAAATTAAG
Found at i:127472 original size:6 final size:6
Alignment explanation
Indices: 127461--127487 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
127451 GACAAATCCG
127461 ACCCGA ACCCGA ACCCGA ACCCGA ACC
1 ACCCGA ACCCGA ACCCGA ACCCGA ACC
127488 AATCTAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCCGA
Found at i:128419 original size:18 final size:18
Alignment explanation
Indices: 128379--128421 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
128369 ATTCAAGTAG
128379 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
128397 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
128415 TAATTAA
1 TAATTAA
128422 AAACTTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:134771 original size:16 final size:16
Alignment explanation
Indices: 134750--134782 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
134740 ATTTAAATGC
134750 ATTTAT-AATATATAAA
1 ATTTATAAAT-TATAAA
134766 ATTTATAAATTATAAA
1 ATTTATAAATTATAAA
134782 A
1 A
134783 AATTAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTATAAATTATAAA
Found at i:135134 original size:22 final size:22
Alignment explanation
Indices: 135088--135134 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
135078 CTGCCCATAT
*
135088 TTTTTAAATTATATTTATATTA
1 TTTTTAAATTATATTTATATAA
*
135110 TTTTTAATTTAATATTTA-ATAA
1 TTTTTAAATT-ATATTTATATAA
135132 TTT
1 TTT
135135 ATATATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTTAAATTATATTTATATAA
Found at i:135142 original size:23 final size:23
Alignment explanation
Indices: 135098--135142 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
135088 TTTTTAAATT
* *
135098 ATATTTATATTATTTTTAATTTA
1 ATATTTATATAATTTATAATTTA
135121 ATATTTA-ATAATTTATATATTT
1 ATATTTATATAATTTATA-ATTT
135143 TATGTTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATATTTATATAATTTATAATTTA
Found at i:143997 original size:31 final size:30
Alignment explanation
Indices: 143949--144060 Score: 100
Period size: 31 Copynumber: 3.6 Consensus size: 30
143939 CCTGGTCCCA
* *
143949 AAAAGTTTGGAAAATTTTGATTAAATCCTTT
1 AAAATTTTTGAAAATTTT-ATTAAATCCTTT
* * *
143980 AAAATTTTTAAAAATTTTAATCAAAT-ATTCT
1 AAAATTTTTGAAAATTTT-ATTAAATCCTT-T
* * *
144011 AAAAGTTTTGAAAATTTTAGTTAAACCCCTT
1 AAAATTTTTGAAAATTTTA-TTAAATCCTTT
*
144042 AAAGTTTTTGAAAATTTTA
1 AAAATTTTTGAAAATTTTA
144061 AATAAACCCC
Statistics
Matches: 64, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
30 3 0.05
31 60 0.94
32 1 0.02
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (30 bp):
AAAATTTTTGAAAATTTTATTAAATCCTTT
Found at i:144048 original size:30 final size:31
Alignment explanation
Indices: 144012--144070 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
144002 AAATATTCTA
**
144012 AAAG-TTTTGAAAATTTTAGTTAAACCCCTT
1 AAAGTTTTTGAAAATTTTAAATAAACCCCTT
144042 AAAGTTTTTGAAAATTTTAAATAAACCCC
1 AAAGTTTTTGAAAATTTTAAATAAACCCC
144071 AAAACACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (31 bp):
AAAGTTTTTGAAAATTTTAAATAAACCCCTT
Found at i:145183 original size:20 final size:20
Alignment explanation
Indices: 145139--145176 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
145129 ATGTTTAATG
**
145139 ATTTAGATAATGCTTTTACT
1 ATTTAGATAATGCTTGGACT
145159 ATTTAGATAATGCTTGGA
1 ATTTAGATAATGCTTGGA
145177 TCTTTTACGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (20 bp):
ATTTAGATAATGCTTGGACT
Found at i:147431 original size:23 final size:21
Alignment explanation
Indices: 147401--147447 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
147391 ATACTTTAAT
*
147401 TTTTTAAAAATTAAAAATATAAA
1 TTTTTAAAAAAT-AAAATA-AAA
147424 TTTTTAAAAAATAAAATAAAA
1 TTTTTAAAAAATAAAATAAAA
147445 TTT
1 TTT
147448 ATTATTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.26
22 6 0.26
23 11 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTTTAAAAAATAAAATAAAA
Found at i:148948 original size:2 final size:2
Alignment explanation
Indices: 148943--148974 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
148933 ATACACAGAA
148943 AT AT AT 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 AT AT AT
148975 TATTTCAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:153578 original size:6 final size:6
Alignment explanation
Indices: 153548--153576 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
153538 TTTAAGCTTG
153548 GTTTTT GTTTTT GTTTTT GTTTTT -TTTTT
1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT
153577 TTGTATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
GTTTTT
Found at i:167317 original size:22 final size:23
Alignment explanation
Indices: 167277--167319 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
167267 ATTTATTTCA
*
167277 AATATATAATTTTATATATTTGC
1 AATAAATAATTTTATATATTTGC
*
167300 AATAAATATTTTTA-ATATTT
1 AATAAATAATTTTATATATTT
167320 AAAATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
AATAAATAATTTTATATATTTGC
Found at i:167325 original size:22 final size:23
Alignment explanation
Indices: 167270--167325 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
167260 CATTAAAATT
* *
167270 TATTTCAAATATATAATTTTATA
1 TATTTAAAATAAATAATTTTATA
** *
167293 TATTTGCAATAAATATTTTTA-A
1 TATTTAAAATAAATAATTTTATA
167315 TATTTAAAATA
1 TATTTAAAATA
167326 TAATTTATAC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (23 bp):
TATTTAAAATAAATAATTTTATA
Found at i:169261 original size:18 final size:19
Alignment explanation
Indices: 169224--169265 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
169214 TAAATATTAT
*
169224 ATAAAATAATATTTTAAAA
1 ATAAAATAATATTATAAAA
169243 ATAAAATAATA-TATAAAA
1 ATAAAATAATATTATAAAA
169261 ATAAA
1 ATAAA
169266 TTTAAATAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAAATAATATTATAAAA
Found at i:177791 original size:31 final size:31
Alignment explanation
Indices: 177724--177784 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
177714 TACAAAATTA
*** *
177724 TCACTAAATTAATCAAAAGTTATCGTTTAAC
1 TCACTAAATTAATCAAAAAAAATCATTTAAC
*
177755 TCACTAAATTAATCAAAAAAAATTATTTAA
1 TCACTAAATTAATCAAAAAAAATCATTTAA
177785 ACCACTAGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.34
Consensus pattern (31 bp):
TCACTAAATTAATCAAAAAAAATCATTTAAC
Found at i:184877 original size:2 final size:2
Alignment explanation
Indices: 184870--184917 Score: 73
Period size: 2 Copynumber: 24.5 Consensus size: 2
184860 TGAATTCGAT
184870 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
184912 -A TA TA T
1 TA TA TA T
184918 TTTATATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.05
2 39 0.91
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:184999 original size:24 final size:25
Alignment explanation
Indices: 184869--184986 Score: 78
Period size: 26 Copynumber: 4.6 Consensus size: 25
184859 ATGAATTCGA
*
184869 TTATATATAT-ATATATATATATATAT
1 TTATATATATAATAT-TA-ATATATTT
* *
184895 ATATATATATGATATTAATATATTT
1 TTATATATATAATATTAATATATTT
* * * * * *
184920 TATATTTATTTAATTTTGATTTGATTCG
1 T-TATATATATAATATTAATAT-ATT-T
**
184948 AAATATATATAATATTAATATATTT
1 TTATATATATAATATTAATATATTT
184973 TTATAT-TATAATAT
1 TTATATATATAATAT
184987 ATAGATTATT
Statistics
Matches: 68, Mismatches: 20, Indels: 10
0.69 0.20 0.10
Matches are distributed among these distances:
24 8 0.12
25 11 0.16
26 28 0.41
27 21 0.31
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (25 bp):
TTATATATATAATATTAATATATTT
Found at i:198632 original size:2 final size:2
Alignment explanation
Indices: 198627--198652 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
198617 ACCAAGTACA
198627 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
198653 AGAGAGAGAG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:200410 original size:3 final size:3
Alignment explanation
Indices: 200404--200442 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
200394 ATACCCTCCT
* * *
200404 CCA CCA CCG CCA CCA CCT CCG CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
200443 TAGCCCCTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.26, C:0.67, G:0.05, T:0.03
Consensus pattern (3 bp):
CCA
Found at i:200425 original size:12 final size:12
Alignment explanation
Indices: 200404--200442 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
200394 ATACCCTCCT
200404 CCACCACCGCCA
1 CCACCACCGCCA
*
200416 CCACCTCCGCCA
1 CCACCACCGCCA
*
200428 CCACCACCACCA
1 CCACCACCGCCA
200440 CCA
1 CCA
200443 TAGCCCCTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.26, C:0.67, G:0.05, T:0.03
Consensus pattern (12 bp):
CCACCACCGCCA
Found at i:204762 original size:6 final size:6
Alignment explanation
Indices: 204751--204784 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
204741 GTGGTCTCCC
204751 CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT CCTC
1 CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT CCTC
204785 CAGCTCGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (6 bp):
CCTCTT
Done.