Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014690.1 Kokia drynarioides strain JFW-HI SEQ_129729, 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: 321489
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 39 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:202970 original size:24 final size:23
Alignment explanation
Indices: 202928--202972 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
202918 TTTTAGTCCT
* *
202928 TGTTTTTTAATTTTATTTTAATA
1 TGTTTTTTAAATATATTTTAATA
202951 TGTTTTTTAAATATAGTTTTAA
1 TGTTTTTTAAATATA-TTTTAA
202973 ATCTTTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (23 bp):
TGTTTTTTAAATATATTTTAATA
Found at i:202979 original size:23 final size:23
Alignment explanation
Indices: 202930--202979 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
202920 TTAGTCCTTG
* * *
202930 TTTTTTAATTTTATTTTAATATG
1 TTTTTTAAATATATTTTAATATC
202953 TTTTTTAAATATAGTTTTAA-ATC
1 TTTTTTAAATATA-TTTTAATATC
202976 TTTT
1 TTTT
202980 GATTTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (23 bp):
TTTTTTAAATATATTTTAATATC
Found at i:218338 original size:26 final size:27
Alignment explanation
Indices: 218288--218341 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
218278 ATTCAATTTA
218288 TCAATTCCAACCCCTTTTATAACATCC
1 TCAATTCCAACCCCTTTTATAACATCC
*
218315 TCAATTCCAA-CCTTTTTATAACATCC
1 TCAATTCCAACCCCTTTTATAACATCC
218341 T
1 T
218342 ATAATAGGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (27 bp):
TCAATTCCAACCCCTTTTATAACATCC
Found at i:221802 original size:2 final size:2
Alignment explanation
Indices: 221795--221822 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
221785 GATACCCACA
221795 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
221823 TATCACACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:222004 original size:25 final size:25
Alignment explanation
Indices: 221970--222022 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
221960 TTATATAAAA
221970 AATAAAAAAATGAAAA-TAATTTT-AT
1 AATAAAAAAAT-AAAAGT-ATTTTAAT
*
221995 AATAATAAAATAAAAGTATTTTAAT
1 AATAAAAAAATAAAAGTATTTTAAT
222020 AAT
1 AAT
222023 TTCACACCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (25 bp):
AATAAAAAAATAAAAGTATTTTAAT
Found at i:223019 original size:30 final size:30
Alignment explanation
Indices: 222978--223043 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
222968 ATTTTATCAT
* *
222978 TTTTATAATTTTTAAATAATTAAATTAAAA
1 TTTTATAATTTTTAAAGAATTAAAATAAAA
* * *
223008 TTTTATTATTTTTAAAGGATTAAAATATAA
1 TTTTATAATTTTTAAAGAATTAAAATAAAA
223038 TTTTAT
1 TTTTAT
223044 CATTAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (30 bp):
TTTTATAATTTTTAAAGAATTAAAATAAAA
Found at i:226809 original size:29 final size:28
Alignment explanation
Indices: 226748--226810 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
226738 AAAATATCCC
* * *
226748 CAAAAAATTTCACTAATCCTATTTCGTT
1 CAAAAAATTTCACGAACCCTATTTCATT
*
226776 CAAAAAATTTGACGAACCCTATTTCATT
1 CAAAAAATTTCACGAACCCTATTTCATT
226804 CAAAAAA
1 CAAAAAA
226811 AAATTCACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.32
Consensus pattern (28 bp):
CAAAAAATTTCACGAACCCTATTTCATT
Found at i:233706 original size:10 final size:10
Alignment explanation
Indices: 233689--233747 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
233679 ATCGACAGAT
233689 TAATTAAATA
1 TAATTAAATA
* *
233699 TTATTAAAAA
1 TAATTAAATA
233709 TAATTAAATTA
1 TAATTAAA-TA
233720 TAA--AAATA
1 TAATTAAATA
* *
233728 AAAATAAA-A
1 TAATTAAATA
233737 TAATTAAATA
1 TAATTAAATA
233747 T
1 T
233748 TTTCTATAAC
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
8 4 0.11
9 10 0.26
10 20 0.53
11 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TAATTAAATA
Found at i:233809 original size:21 final size:23
Alignment explanation
Indices: 233755--233823 Score: 92
Period size: 22 Copynumber: 3.1 Consensus size: 23
233745 TATTTTCTAT
233755 AACCATTAATTTAAAATACCCTAA
1 AACC-TTAATTTAAAATACCCTAA
*
233779 ACCCTT-ATTTAAAATA-CC-AA
1 AACCTTAATTTAAAATACCCTAA
233799 AACCTTAATTTAAAA-ACCCTAA
1 AACCTTAATTTAAAATACCCTAA
233821 AAC
1 AAC
233824 TAAATAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 8 0.20
21 12 0.30
22 15 0.38
23 2 0.05
24 3 0.08
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (23 bp):
AACCTTAATTTAAAATACCCTAA
Found at i:233923 original size:30 final size:30
Alignment explanation
Indices: 233872--233932 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 30
233862 CAAAATAGCA
233872 AAATTTAGATATATTGTTTTG-AATTTTAG
1 AAATTTAGATATATTGTTTTGAAATTTTAG
*
233901 AAATTTAGATATGTTAGTTTTGAAATTTTAG
1 AAATTTAGATATATT-GTTTTGAAATTTTAG
233932 A
1 A
233933 CGTTAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 14 0.48
30 6 0.21
31 9 0.31
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (30 bp):
AAATTTAGATATATTGTTTTGAAATTTTAG
Found at i:234398 original size:3 final size:3
Alignment explanation
Indices: 234390--234415 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
234380 TAATAAACCC
234390 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
234416 CAATTTTACT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:239159 original size:19 final size:19
Alignment explanation
Indices: 239137--239173 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
239127 GACAGTCAAA
239137 GTCAAAGCCAACGAGTTAG
1 GTCAAAGCCAACGAGTTAG
* *
239156 GTCAAAGTCAACGGGTTA
1 GTCAAAGCCAACGAGTTA
239174 ACGGGTCGGT
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:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (19 bp):
GTCAAAGCCAACGAGTTAG
Found at i:256344 original size:14 final size:15
Alignment explanation
Indices: 256325--256353 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
256315 GCATGAGGTA
256325 AAACTTA-GATGCTT
1 AAACTTATGATGCTT
256339 AAACTTATGATGCTT
1 AAACTTATGATGCTT
256354 GTAAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (15 bp):
AAACTTATGATGCTT
Found at i:261754 original size:28 final size:28
Alignment explanation
Indices: 261688--261761 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
261678 TATGATTGAA
**
261688 AGGGTTGATG-AATTTTTTGAAGTAAAG
1 AGGGTTGATGAAATTTTTTGAACAAAAG
* * *
261715 AGAGTTGTTGAAATTTTTTGAACAAAAT
1 AGGGTTGATGAAATTTTTTGAACAAAAG
*
261743 AGGGTTCATGAAATTTTTT
1 AGGGTTGATGAAATTTTTT
261762 AGGGATATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 8 0.21
28 30 0.79
ACGTcount: A:0.34, C:0.03, G:0.23, T:0.41
Consensus pattern (28 bp):
AGGGTTGATGAAATTTTTTGAACAAAAG
Found at i:270227 original size:17 final size:17
Alignment explanation
Indices: 270198--270245 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
270188 TCTCATCTTA
* **
270198 CTCATTTCTTTTTTTTT
1 CTCATCTCTTTTCCTTT
270215 CTCACTCTCTTTTCCTTT
1 CTCA-TCTCTTTTCCTTT
270233 CTCATCTCTTTTC
1 CTCATCTCTTTTC
270246 TCACTACTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.06, C:0.31, G:0.00, T:0.62
Consensus pattern (17 bp):
CTCATCTCTTTTCCTTT
Found at i:273864 original size:16 final size:16
Alignment explanation
Indices: 273843--273874 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
273833 TGATGTACCA
273843 TTTTTTTCCC-TCTTT
1 TTTTTTTCCCTTCTTT
273858 TTTTTTTCCCTTCTTT
1 TTTTTTTCCCTTCTTT
273874 T
1 T
273875 CCATATTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTTCCCTTCTTT
Found at i:274551 original size:24 final size:24
Alignment explanation
Indices: 274522--274567 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
274512 ATTCTAATTT
*
274522 TTATATTAATATTAAGTAAAATAA
1 TTATATTAATATTAAATAAAATAA
274546 TTATATTAATATTAAATAAAAT
1 TTATATTAATATTAAATAAAAT
274568 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TTATATTAATATTAAATAAAATAA
Found at i:274971 original size:25 final size:24
Alignment explanation
Indices: 274896--274971 Score: 61
Period size: 25 Copynumber: 3.1 Consensus size: 24
274886 TAGGTTTTTA
*
274896 TTTTATTTAATATTAATATAATTATT
1 TTTTA-TTAATATTAATATAA-AATT
*
274922 TTTTGA-TAA-A-TAATAT-AATTAT
1 TTTT-ATTAATATTAATATAAAAT-T
274944 TTTTATTCAATATTAATATAAAATT
1 TTTTATT-AATATTAATATAAAATT
274969 TTT
1 TTT
274972 GTTTATTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 15
0.69 0.05 0.26
Matches are distributed among these distances:
21 2 0.05
22 7 0.17
23 8 0.20
24 2 0.05
25 13 0.32
26 7 0.17
27 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (24 bp):
TTTTATTAATATTAATATAAAATT
Found at i:276052 original size:13 final size:15
Alignment explanation
Indices: 276023--276055 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
276013 GGTGAAGAAA
276023 ATAAATATTTGATAT
1 ATAAATATTTGATAT
276038 ATAAATA-TT-ATAT
1 ATAAATATTTGATAT
276051 ATAAA
1 ATAAA
276056 AAAAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 2 0.11
15 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
ATAAATATTTGATAT
Found at i:276223 original size:97 final size:98
Alignment explanation
Indices: 276093--276292 Score: 303
Period size: 97 Copynumber: 2.0 Consensus size: 98
276083 TTTTTAAAAT
* *
276093 AAAATATATTTAACATAATGATAAATATCAAATATATATTTTTATTATATAATTATATAATTATT
1 AAAATATATTTAACATAATGAT-AATATCAAATATATATTTTTATTATATAATTACACAATTATT
* * *
276158 AATTTATTTATATAAATAAAGGAGCTATTAATTA
65 AATTTAGTTATATAAATAAAAGAACTATTAATTA
* *
276192 AAAATATTTTTAACATAATGAT-ATATCAAATATATATTTTTATTATATAATTACACACTTATTA
1 AAAATATATTTAACATAATGATAATATCAAATATATATTTTTATTATATAATTACACAATTATTA
* *
276256 TTTTAGTTATATAAATAAAAGAATTATTAATTA
66 ATTTAGTTATATAAATAAAAGAACTATTAATTA
276289 AAAA
1 AAAA
276293 ATGAATTAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
97 71 0.77
99 21 0.23
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (98 bp):
AAAATATATTTAACATAATGATAATATCAAATATATATTTTTATTATATAATTACACAATTATTA
ATTTAGTTATATAAATAAAAGAACTATTAATTA
Found at i:276320 original size:97 final size:97
Alignment explanation
Indices: 276117--276326 Score: 235
Period size: 97 Copynumber: 2.2 Consensus size: 97
276107 ATAATGATAA
* * * * * *
276117 ATATCAAATATATATTTTTATTATATAATTATATAATTATTAATTTATTTATATAAATAAAGGAG
1 ATATAAAATATATATTTTTATTATATAATTACACAATTATTAATTTAGTTATATAAATAAAAGAA
** * **
276182 CTATTAATTAAAAATATTTTTAACATAATGAT
66 CTATTAATTAAAAATATAATTAAAATAAAAAT
* * *
276214 ATATCAAATATATATTTTTATTATATAATTACACACTTATTATTTTAGTTATATAAATAAAAGAA
1 ATATAAAATATATATTTTTATTATATAATTACACAATTATTAATTTAGTTATATAAATAAAAGAA
*
276279 TTATTAATTAAAAA-ATGAATTAAAATAAAAA-
66 CTATTAATTAAAAATAT-AATTAAAATAAAAAT
*
276310 ATTTAAAAATAATATAT
1 ATAT-AAAAT-ATATAT
276327 CTATTAATTA
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
96 5 0.05
97 84 0.88
98 6 0.06
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (97 bp):
ATATAAAATATATATTTTTATTATATAATTACACAATTATTAATTTAGTTATATAAATAAAAGAA
CTATTAATTAAAAATATAATTAAAATAAAAAT
Found at i:277245 original size:16 final size:16
Alignment explanation
Indices: 277224--277255 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
277214 AGACGTCTTT
*
277224 AAAAATAATTTTTTTC
1 AAAAATAATTTATTTC
277240 AAAAATAATTTATTTC
1 AAAAATAATTTATTTC
277256 TCTAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAAATAATTTATTTC
Found at i:278016 original size:17 final size:17
Alignment explanation
Indices: 277987--278056 Score: 72
Period size: 16 Copynumber: 4.2 Consensus size: 17
277977 TCATATTTAT
*
277987 TTTTTATA-TTTAATAA
1 TTTTTATAGGTTAATAA
*
278003 TTTTGATAGGTTAAT-A
1 TTTTTATAGGTTAATAA
* **
278019 TTTTTAAAATTTAAATAA
1 TTTTTATAGGTT-AATAA
278037 TTTTTATAGGTTAATAA
1 TTTTTATAGGTTAATAA
278054 TTT
1 TTT
278057 GTGTTATATA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
16 16 0.38
17 16 0.38
18 10 0.24
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (17 bp):
TTTTTATAGGTTAATAA
Found at i:278046 original size:34 final size:33
Alignment explanation
Indices: 277984--278052 Score: 102
Period size: 34 Copynumber: 2.1 Consensus size: 33
277974 TAATCATATT
* *
277984 TATTTTTTATATTTAATAATTTTGATAGGTTAA
1 TATTTTTAAAATTTAATAATTTTGATAGGTTAA
*
278017 TATTTTTAAAATTTAAATAATTTTTATAGGTTAA
1 TATTTTTAAAATTT-AATAATTTTGATAGGTTAA
278051 TA
1 TA
278053 ATTTGTGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 12 0.38
34 20 0.62
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (33 bp):
TATTTTTAAAATTTAATAATTTTGATAGGTTAA
Found at i:278301 original size:14 final size:15
Alignment explanation
Indices: 278261--278324 Score: 69
Period size: 14 Copynumber: 4.3 Consensus size: 15
278251 TAATTGATAA
* *
278261 AATTAATTAAATTAAA
1 AATTAATTAAAAT-AT
278277 AATTAATTAAAATAT
1 AATTAATTAAAATAT
*
278292 -ATTTATTAAAA-AT
1 AATTAATTAAAATAT
278305 AATTAATTAAAATATT
1 AATTAATTAAAATA-T
278321 AATT
1 AATT
278325 TAATGAGATA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
13 2 0.05
14 20 0.49
15 2 0.05
16 17 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTAATTAAAATAT
Found at i:284090 original size:28 final size:29
Alignment explanation
Indices: 284050--284106 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
284040 AAAATAGGAT
*
284050 TTTAAATTTTTTAAAAATTGA-AAAAAAA
1 TTTAAATTATTTAAAAATTGATAAAAAAA
* *
284078 TTTAGATTATTTAAAAGTTGATAAAAAAA
1 TTTAAATTATTTAAAAATTGATAAAAAAA
284107 ATTATTTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (29 bp):
TTTAAATTATTTAAAAATTGATAAAAAAA
Found at i:284158 original size:28 final size:27
Alignment explanation
Indices: 284063--284159 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 27
284053 AAATTTTTTA
* *
284063 AAAATTGAAAAAAAATTTAGATTA-TTT
1 AAAATTGAAAAAAAAATTAGA-TACCTT
**
284090 AAAAGTTGATAAAAAAAATTATTTGACCTT
1 AAAA-TTGA-AAAAAAAATTAGAT-ACCTT
* *
284120 AAAGTTAAAAAAAAAATTAGATACCTT
1 AAAATTGAAAAAAAAATTAGATACCTT
284147 ACAAATTGAAAAA
1 A-AAATTGAAAAA
284160 TAATATTTTA
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
27 10 0.18
28 26 0.47
29 14 0.25
30 5 0.09
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (27 bp):
AAAATTGAAAAAAAAATTAGATACCTT
Found at i:286940 original size:103 final size:103
Alignment explanation
Indices: 286758--286962 Score: 374
Period size: 103 Copynumber: 2.0 Consensus size: 103
286748 TTCAGTGACT
286758 ATGCAAACTCAAGTCTAATACACTTGGACTCTTGAGATCCATTTATCTGAAATTTGAAGAAACGC
1 ATGCAAACTCAAGTCTAATACACTTGGACTCTTGAGATCCATTTATCTGAAATTTGAAGAAACGC
286823 ATAACTTGGATATGATTTTGTTTTACAGCTCAAAGACC
66 ATAACTTGGATATGATTTTGTTTTACAGCTCAAAGACC
* * *
286861 ATGCAAACTCAAGTCTAATACTCTTGGACTCTTGAGATCCATTTGTCTGAAATTTGAAGAAATGC
1 ATGCAAACTCAAGTCTAATACACTTGGACTCTTGAGATCCATTTATCTGAAATTTGAAGAAACGC
*
286926 ATAACTTGGCTATGATTTTGTTTTACAGCTCAAAGAC
66 ATAACTTGGATATGATTTTGTTTTACAGCTCAAAGAC
286963 TTCAGCTTGC
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (103 bp):
ATGCAAACTCAAGTCTAATACACTTGGACTCTTGAGATCCATTTATCTGAAATTTGAAGAAACGC
ATAACTTGGATATGATTTTGTTTTACAGCTCAAAGACC
Found at i:290607 original size:51 final size:50
Alignment explanation
Indices: 290524--290677 Score: 193
Period size: 51 Copynumber: 3.0 Consensus size: 50
290514 AAAAGTCAAT
*
290524 ACCTTTATTGCATATGCATTCATACATTCATAAAGTTTTACAACGCATTTC
1 ACCTTT-TTGCATATGCATTCATACGTTCATAAAGTTTTACAACGCATTTC
* * * *
290575 ACCTTTCTTCCATATGCATTCATACGTCCATAAAG-TTTATCAATGCATTTA
1 ACCTTT-TTGCATATGCATTCATACGTTCATAAAGTTTTA-CAACGCATTTC
* * *
290626 ACCTCTTTTGCATATTCATTCATACGTTCATAAAGTTTTGCATCGCATTTC
1 ACCT-TTTTGCATATGCATTCATACGTTCATAAAGTTTTACAACGCATTTC
290677 A
1 A
290678 TGCATTAAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
50 4 0.05
51 78 0.90
52 5 0.06
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (50 bp):
ACCTTTTTGCATATGCATTCATACGTTCATAAAGTTTTACAACGCATTTC
Found at i:296001 original size:30 final size:30
Alignment explanation
Indices: 295965--296025 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
295955 CTTGAGGATT
295965 ATAAGCCATTAGATTTCGATTTCCCAAATG
1 ATAAGCCATTAGATTTCGATTTCCCAAATG
295995 ATAAGCCATTAGATTTCGATTTCCCAAATG
1 ATAAGCCATTAGATTTCGATTTCCCAAATG
296025 A
1 A
296026 AGATCTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (30 bp):
ATAAGCCATTAGATTTCGATTTCCCAAATG
Found at i:298925 original size:49 final size:50
Alignment explanation
Indices: 298765--298923 Score: 205
Period size: 50 Copynumber: 3.2 Consensus size: 50
298755 CAAAACAACT
* * *
298765 AATCTTATACACCTAAAGCTGTAGAGGAGCAGATTGAAGTCGTAATGGTG
1 AATCTTATACACCTAAAGCTGTAGAGGAGCAGATTGAAGCCGTAAAGGCG
* * *
298815 AATCTTATACACCTAAAGTTGTAGAGGAGCAGATTGAAGCTGT-AAGAGCT
1 AATCTTATACACCTAAAGCTGTAGAGGAGCAGATTGAAGCCGTAAAG-GCG
* * * *
298865 AATCCTATAC-TCTAAAGCTGTAGAGGGGCAAATTGAAGCCGTAAAGGCG
1 AATCTTATACACCTAAAGCTGTAGAGGAGCAGATTGAAGCCGTAAAGGCG
298914 AATCTTATAC
1 AATCTTATAC
298924 TCCTGATTCT
Statistics
Matches: 93, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
49 40 0.43
50 53 0.57
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (50 bp):
AATCTTATACACCTAAAGCTGTAGAGGAGCAGATTGAAGCCGTAAAGGCG
Found at i:298950 original size:99 final size:100
Alignment explanation
Indices: 298763--298978 Score: 231
Period size: 99 Copynumber: 2.2 Consensus size: 100
298753 GACAAAACAA
* * * * *
298763 CTAATCTTATACACCTAAAGCTGTAGAGGAGCAGATTGAAGTCGTAATGGTGAATCTTATACACC
1 CTAATCCTATACACCTAAAGCTGTAGAGGAGCAAATTGAAGCCGTAAAGGCGAATCTTATACACC
* * * **
298828 TAAAGTTGTAGAGGAGCAGATTGAAGCTGTAAGAG
66 TAAAGTTGAAAAGGAGCAAATTGAAGCTACAAGAG
* * *
298863 CTAATCCTATAC-TCTAAAGCTGTAGAGGGGCAAATTGAAGCCGTAAAGGCGAATCTTATACTCC
1 CTAATCCTATACACCTAAAGCTGTAGAGGAGCAAATTGAAGCCGTAAAGGCGAATCTTATACACC
* *
298927 T-GATTCTGGAAAAGG-GCAAATTGAAGCTACAAGAG
66 TAAAGT-T-GAAAAGGAGCAAATTGAAGCTACAAGAG
* * *
298962 CAAATCCTGTACCCCTA
1 CTAATCCTATACACCTA
298979 GAATTGTAGA
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
98 2 0.02
99 74 0.78
100 19 0.20
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (100 bp):
CTAATCCTATACACCTAAAGCTGTAGAGGAGCAAATTGAAGCCGTAAAGGCGAATCTTATACACC
TAAAGTTGAAAAGGAGCAAATTGAAGCTACAAGAG
Found at i:300134 original size:27 final size:26
Alignment explanation
Indices: 300104--300159 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
300094 ATTACATATA
300104 TATATATATTA-TTTATTTTATCTATTC
1 TATATATATTATTTTATTTTAT-T-TTC
*
300131 TATATATCTTATTTTATTTTATTTTC
1 TATATATATTATTTTATTTTATTTTC
300157 TAT
1 TAT
300160 TTCAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 6 0.22
27 11 0.41
28 10 0.37
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (26 bp):
TATATATATTATTTTATTTTATTTTC
Found at i:303006 original size:21 final size:21
Alignment explanation
Indices: 302981--303029 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
302971 TATGTATTAT
*
302981 ATTAAAATATTTTTAATCAA-A
1 ATTAAAATATTTTAAAT-AACA
*
303002 ATTAACATTATTTTAAATAACA
1 ATTAA-AATATTTTAAATAACA
303024 ATTAAA
1 ATTAAA
303030 CATAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAAAATATTTTAAATAACA
Found at i:303958 original size:39 final size:39
Alignment explanation
Indices: 303912--304010 Score: 171
Period size: 39 Copynumber: 2.5 Consensus size: 39
303902 TTAAATAGGG
303912 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
*
303951 TTTTAATGTGTCTTATTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
* *
303990 TTTTAAGGTGTCTAAGTTTGA
1 TTTTAATGTGTCTTAGTTTGA
304011 AACAAATTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.54
Consensus pattern (39 bp):
TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
Found at i:304092 original size:32 final size:32
Alignment explanation
Indices: 304056--304118 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
304046 AGCCGAAATT
* *
304056 AATTAGCTGATTAATGTGTTTCAGGTACATGC
1 AATTAGCTGATTAATATATTTCAGGTACATGC
* *
304088 AATTAGTTGATTAATATATTTTAGGTACATG
1 AATTAGCTGATTAATATATTTCAGGTACATG
304119 TATGGATGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (32 bp):
AATTAGCTGATTAATATATTTCAGGTACATGC
Found at i:304533 original size:17 final size:17
Alignment explanation
Indices: 304511--304545 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
304501 GCCAGAGAAG
304511 GTTCAAGGAAGTTTCCA
1 GTTCAAGGAAGTTTCCA
304528 GTTCAAGGAAGTTTCCA
1 GTTCAAGGAAGTTTCCA
304545 G
1 G
304546 CTCCATTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (17 bp):
GTTCAAGGAAGTTTCCA
Found at i:305671 original size:31 final size:30
Alignment explanation
Indices: 305636--305709 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
305626 AAAATTATAA
* *
305636 ATAAACTTTAATTAAATGTGTAATTTGATAC
1 ATAAACTTTAATTAAA-GTGCAATTTAATAC
* *
305667 ATAAATTTTAATT-TAGTGCAATTTAATAC
1 ATAAACTTTAATTAAAGTGCAATTTAATAC
*
305696 ATAAACTTTGATTA
1 ATAAACTTTAATTA
305710 TGATTTAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 23 0.64
30 1 0.03
31 12 0.33
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (30 bp):
ATAAACTTTAATTAAAGTGCAATTTAATAC
Found at i:319118 original size:12 final size:12
Alignment explanation
Indices: 319101--319142 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
319091 TATCTTCTTG
*
319101 TTTTTCATTTCC
1 TTTTTCATTTTC
*
319113 TTTTTC-TTCTTG
1 TTTTTCATT-TTC
319125 TTTTTCATTTTC
1 TTTTTCATTTTC
319137 TTTTTC
1 TTTTTC
319143 CTCTTGAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTTCATTTTC
Found at i:319125 original size:24 final size:24
Alignment explanation
Indices: 319093--319148 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
319083 TGTATGGGTA
319093 TCTTCTTGTTTTTCATTTCCTTTT
1 TCTTCTTGTTTTTCATTTCCTTTT
*
319117 TCTTCTTGTTTTTCATTTTCTTTT
1 TCTTCTTGTTTTTCATTTCCTTTT
*
319141 TCCTCTTG
1 TCTTCTTG
319149 AGAACTCTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.04, C:0.21, G:0.05, T:0.70
Consensus pattern (24 bp):
TCTTCTTGTTTTTCATTTCCTTTT
Found at i:320772 original size:19 final size:20
Alignment explanation
Indices: 320739--320777 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
320729 ATCCACAGAA
*
320739 TATTTTTTTTATTTTTCTCG
1 TATTTTTCTTATTTTTCTCG
320759 TATTTTTCTT-TTTTTCTCG
1 TATTTTTCTTATTTTTCTCG
320778 ACTTTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.08, C:0.13, G:0.05, T:0.74
Consensus pattern (20 bp):
TATTTTTCTTATTTTTCTCG
Done.