Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014038.1 Corchorus capsularis cultivar CVL-1 contig14059, 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: 97839
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:9158 original size:60 final size:59
Alignment explanation
Indices: 9061--9184 Score: 230
Period size: 60 Copynumber: 2.1 Consensus size: 59
9051 CACAATTTAC
*
9061 AAATGCCTTTACAAAACAAATATTGCATGTAATGAATTTTTAAATGAGGCAAAAAGATA
1 AAATGCCTTTACAAAACAAATATTGCATATAATGAATTTTTAAATGAGGCAAAAAGATA
9120 AAATGCCTTTACAAAACAAAATATTGCATATAATGAATTTTTAAATGAGGCAAAAAGATA
1 AAATGCCTTTACAAAAC-AAATATTGCATATAATGAATTTTTAAATGAGGCAAAAAGATA
9180 AAATG
1 AAATG
9185 GAATAAAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 17 0.27
60 46 0.73
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (59 bp):
AAATGCCTTTACAAAACAAATATTGCATATAATGAATTTTTAAATGAGGCAAAAAGATA
Found at i:9643 original size:3 final size:3
Alignment explanation
Indices: 9635--9661 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9625 GATTACCCAT
9635 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
9662 GTGTAGATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10511 original size:20 final size:21
Alignment explanation
Indices: 10488--10531 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
10478 TGCAAATCGT
10488 AAATATGAA-AGTCAAACCCC
1 AAATATGAATAGTCAAACCCC
* *
10508 AAATATTAATGGTCAAACCCC
1 AAATATGAATAGTCAAACCCC
10529 AAA
1 AAA
10532 GCATCCATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.50, C:0.23, G:0.09, T:0.18
Consensus pattern (21 bp):
AAATATGAATAGTCAAACCCC
Found at i:10524 original size:21 final size:21
Alignment explanation
Indices: 10498--10590 Score: 71
Period size: 21 Copynumber: 4.3 Consensus size: 21
10488 AAATATGAAA
10498 GTCAAACCCCAAATATTAATG
1 GTCAAACCCCAAATATTAATG
* ** *
10519 GTCAAACCCCAAAGCATCCATT
1 GTCAAACCCCAAA-TATTAATG
* * *
10541 GTGAAACCTCAAATTTTAATG
1 GTCAAACCCCAAATATTAATG
**
10562 GTCAAACTACAAATCATGT-ATG
1 GTCAAACCCCAAAT-AT-TAATG
10584 GTCAAAC
1 GTCAAAC
10591 TGTAAAGCAC
Statistics
Matches: 54, Mismatches: 15, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
21 27 0.50
22 26 0.48
23 1 0.02
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.25
Consensus pattern (21 bp):
GTCAAACCCCAAATATTAATG
Found at i:10650 original size:21 final size:23
Alignment explanation
Indices: 10615--10658 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
10605 ACCCCTACTA
*
10615 GTAATGGGATCAAACCTCAAATC
1 GTAATGGGATCAAACCCCAAATC
10638 GTAAT-GG-TCAAACCCCAAATC
1 GTAATGGGATCAAACCCCAAATC
10659 ATGTATAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 2 0.10
23 5 0.25
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (23 bp):
GTAATGGGATCAAACCCCAAATC
Found at i:10723 original size:87 final size:87
Alignment explanation
Indices: 10601--11056 Score: 664
Period size: 87 Copynumber: 5.3 Consensus size: 87
10591 TGTAAAGCAC
* *
10601 GCAAACCCCTACTAGTAATGGGATCAAACCTCAAATCGTAATGGTCAAACCCCAAATCATGTATA
1 GCAAACCCTTACTAGTAATGGGATCAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATA
10666 GTGAAATTTAAAGCATGATTAG
66 GTGAAATTTAAAGCATGATTAG
** * *
10688 ATAAACACTTACTAGTAATGGGATCAAACCCCAAATTGTAATGGTCAAACCCCAAATCATGTATA
1 GCAAACCCTTACTAGTAATGGGATCAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATA
*
10753 ATG-AATTTAAAGCATGATTAG
66 GTGAAATTTAAAGCATGATTAG
* * * * * *
10774 ACAAACCCCTACTAGTAATGGGATCAAACCTCAAACCGTGATGGTCAAACCCCAAATCATGTATG
1 GCAAACCCTTACTAGTAATGGGATCAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATA
10839 GTGAAATTTAAAGCATGATTAG
66 GTGAAATTTAAAGCATGATTAG
* *
10861 GTAAACCCTTACTAGTAATGGGATCAAACCCCAAATCGTAATGGTCAAAACCCAAATCATGTATA
1 GCAAACCCTTACTAGTAATGGGATCAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATA
10926 GTGAAATTTAAAGCATGATTAG
66 GTGAAATTTAAAGCATGATTAG
* * * ** *
10948 GCAAACCCCTACTAGTAATGTGATCAAACCCCAAAGCGTAATGGTCAAACCTAAAATCATGTATG
1 GCAAACCCTTACTAGTAATGGGATCAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATA
***
11013 GTGAAACCGAAAGCATGATTAG
66 GTGAAATTTAAAGCATGATTAG
*
11035 GCAAA-TCTCTACTAGTAATGGG
1 GCAAACCCT-TACTAGTAATGGG
11057 GCTAAATAAT
Statistics
Matches: 329, Mismatches: 38, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
86 78 0.24
87 251 0.76
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (87 bp):
GCAAACCCTTACTAGTAATGGGATCAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATA
GTGAAATTTAAAGCATGATTAG
Found at i:10750 original size:23 final size:23
Alignment explanation
Indices: 10702--10744 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
10692 ACACTTACTA
10702 GTAATGGGATCAAACCCCAAATT
1 GTAATGGGATCAAACCCCAAATT
10725 GTAAT-GG-TCAAACCCCAAAT
1 GTAATGGGATCAAACCCCAAAT
10745 CATGTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.65
22 2 0.10
23 5 0.25
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (23 bp):
GTAATGGGATCAAACCCCAAATT
Found at i:10845 original size:173 final size:174
Alignment explanation
Indices: 10602--11056 Score: 716
Period size: 173 Copynumber: 2.6 Consensus size: 174
10592 GTAAAGCACG
* *
10602 CAAACCCCTACTAGTAATGGGATCAAACCTCAAATCGTAATGGTCAAACCCCAAATCATGTATAG
1 CAAACCCCTACTAGTAATGGGATCAAACCTCAAACCGTAATGGTCAAACCCCAAATCATGTATGG
* *
10667 TGAAATTTAAAGCATGATTAGATAAACACTTACTAGTAATGGGATCAAACCCCAAATTGTAATGG
66 TGAAATTTAAAGCATGATTAGGTAAACACTTACTAGTAATGGGATCAAACCCCAAATCGTAATGG
*
10732 TCAAACCCCAAATCATGTATAATG-AATTTAAAGCATGATTAGA
131 TCAAAACCCAAATCATGTATAATGAAATTTAAAGCATGATTAGA
*
10775 CAAACCCCTACTAGTAATGGGATCAAACCTCAAACCGTGATGGTCAAACCCCAAATCATGTATGG
1 CAAACCCCTACTAGTAATGGGATCAAACCTCAAACCGTAATGGTCAAACCCCAAATCATGTATGG
*
10840 TGAAATTTAAAGCATGATTAGGTAAACCCTTACTAGTAATGGGATCAAACCCCAAATCGTAATGG
66 TGAAATTTAAAGCATGATTAGGTAAACACTTACTAGTAATGGGATCAAACCCCAAATCGTAATGG
* *
10905 TCAAAACCCAAATCATGTATAGTGAAATTTAAAGCATGATTAGG
131 TCAAAACCCAAATCATGTATAATGAAATTTAAAGCATGATTAGA
* * * **
10949 CAAACCCCTACTAGTAATGTGATCAAACCCCAAAGCGTAATGGTCAAACCTAAAATCATGTATGG
1 CAAACCCCTACTAGTAATGGGATCAAACCTCAAACCGTAATGGTCAAACCCCAAATCATGTATGG
*** * *
11014 TGAAACCGAAAGCATGATTAGGCAAA-TCTCTACTAGTAATGGG
66 TGAAATTTAAAGCATGATTAGGTAAACACT-TACTAGTAATGGG
11057 GCTAAATAAT
Statistics
Matches: 260, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
173 148 0.57
174 112 0.43
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (174 bp):
CAAACCCCTACTAGTAATGGGATCAAACCTCAAACCGTAATGGTCAAACCCCAAATCATGTATGG
TGAAATTTAAAGCATGATTAGGTAAACACTTACTAGTAATGGGATCAAACCCCAAATCGTAATGG
TCAAAACCCAAATCATGTATAATGAAATTTAAAGCATGATTAGA
Found at i:10914 original size:21 final size:23
Alignment explanation
Indices: 10875--10918 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
10865 ACCCTTACTA
*
10875 GTAATGGGATCAAACCCCAAATC
1 GTAATGGGATCAAAACCCAAATC
10898 GTAAT-GG-TCAAAACCCAAATC
1 GTAATGGGATCAAAACCCAAATC
10919 ATGTATAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 2 0.10
23 5 0.25
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (23 bp):
GTAATGGGATCAAAACCCAAATC
Found at i:12129 original size:2 final size:2
Alignment explanation
Indices: 12118--12154 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
12108 GATTCTTAGA
12118 AT AT -T 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 AT AT AT
12155 TTTGAAGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12545 original size:31 final size:31
Alignment explanation
Indices: 12510--12574 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
12500 AACTGAACTA
*
12510 ACTCAAACATCCAAGATCTAAAGATCTGAAG
1 ACTCAAACATCCAAGATCTAAAAATCTGAAG
*
12541 ACTCAAACATCCAAGATCTAAAAATCTGGAG
1 ACTCAAACATCCAAGATCTAAAAATCTGAAG
12572 ACT
1 ACT
12575 GATAATCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.23, G:0.12, T:0.20
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAAATCTGAAG
Found at i:18099 original size:30 final size:30
Alignment explanation
Indices: 18041--18112 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
18031 TTTGCCCATG
* * *
18041 GAACT-TCAATTCTGGATATCTTGTCCCCT
1 GAACTCTCAATTTTGGACATCTTGCCCCCT
*
18070 GAACTCTCAATTTTGGACATTTTGCCCCCT
1 GAACTCTCAATTTTGGACATCTTGCCCCCT
**
18100 GAAAACTCAATTT
1 GAACTCTCAATTT
18113 GAGCCTCTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 5 0.14
30 31 0.86
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.36
Consensus pattern (30 bp):
GAACTCTCAATTTTGGACATCTTGCCCCCT
Found at i:19264 original size:31 final size:31
Alignment explanation
Indices: 19208--19278 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
19198 AAATAAGTCC
* * *
19208 CCGAATTTTGTGATACATCTCAAATCAGGAT
1 CCGAACTTTGCGATAAATCTCAAATCAGGAT
* *
19239 CCGAACTTTGCGATAAATCTTAAATCTGGAT
1 CCGAACTTTGCGATAAATCTCAAATCAGGAT
19270 CCGAACTTT
1 CCGAACTTT
19279 CGAAAAGGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (31 bp):
CCGAACTTTGCGATAAATCTCAAATCAGGAT
Found at i:24634 original size:25 final size:25
Alignment explanation
Indices: 24606--24659 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
24596 TTTTAAACAA
* *
24606 AAAATTTTC-AATATTTCTCATCGAG
1 AAAATTTACAAAT-TTTCTCATCAAG
24631 AAAA-TTACAAATTTTCTCATCAAG
1 AAAATTTACAAATTTTCTCATCAAG
24655 AAAAT
1 AAAAT
24660 ATACCACCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (25 bp):
AAAATTTACAAATTTTCTCATCAAG
Found at i:33296 original size:1 final size:1
Alignment explanation
Indices: 33290--33323 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
33280 CTAGGCTGCC
33290 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33324 AAATAACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:35329 original size:12 final size:12
Alignment explanation
Indices: 35312--35337 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35302 CCAAAGCCTC
35312 ATGCTTGTGAGT
1 ATGCTTGTGAGT
35324 ATGCTTGTGAGT
1 ATGCTTGTGAGT
35336 AT
1 AT
35338 TCAGATTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (12 bp):
ATGCTTGTGAGT
Found at i:37446 original size:152 final size:152
Alignment explanation
Indices: 37165--37448 Score: 514
Period size: 152 Copynumber: 1.9 Consensus size: 152
37155 TGGGGTAAAG
* * *
37165 CTCTTTCAAGAATAGTTTTCTCCATTTACAAGATTCACCCGAGATCAGGGGAACAAGTGATGAAT
1 CTCTCTCAAGAATAGTTTTCTCCATTTACAAGACTCACCCAAGATCAGGGGAACAAGTGATGAAT
*
37230 CACTCGAATCAGCCACTTGTTGGTTTGACTCTATCTTATTTGTATTATTCTTTGGTATATTTACA
66 CACTCGAATCAGCCACTTGTTGGTTTAACTCTATCTTATTTGTATTATTCTTTGGTATATTTACA
37295 AGTTAAACTCCGAGTTGATATA
131 AGTTAAACTCCGAGTTGATATA
37317 CTCTCTCAAGAATAGTTTTCTCCATTTACAAGACTCACCCAAGATCAGGGGAACAAGTGATGAAT
1 CTCTCTCAAGAATAGTTTTCTCCATTTACAAGACTCACCCAAGATCAGGGGAACAAGTGATGAAT
* *
37382 CACTTGAATCAGCCACTTGTTGGTTTAACTCTATCTTATTTGTATTATTTTTTGGTATATTTACA
66 CACTCGAATCAGCCACTTGTTGGTTTAACTCTATCTTATTTGTATTATTCTTTGGTATATTTACA
37447 AG
131 AG
37449 CTAATCTTGT
Statistics
Matches: 126, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
152 126 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (152 bp):
CTCTCTCAAGAATAGTTTTCTCCATTTACAAGACTCACCCAAGATCAGGGGAACAAGTGATGAAT
CACTCGAATCAGCCACTTGTTGGTTTAACTCTATCTTATTTGTATTATTCTTTGGTATATTTACA
AGTTAAACTCCGAGTTGATATA
Found at i:42936 original size:6 final size:6
Alignment explanation
Indices: 42914--42968 Score: 64
Period size: 6 Copynumber: 9.5 Consensus size: 6
42904 GTACTTTTTA
42914 ATATA- ATATAG --ATAG ATATAG AT-TAG ATATAG TCATATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG --ATATAG ATATAG
42960 ATATAG ATA
1 ATATAG ATA
42969 AATAAATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
4 4 0.09
5 10 0.23
6 24 0.55
8 6 0.14
ACGTcount: A:0.49, C:0.02, G:0.15, T:0.35
Consensus pattern (6 bp):
ATATAG
Found at i:47140 original size:31 final size:32
Alignment explanation
Indices: 47105--47178 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 32
47095 TTAAAAATAT
*
47105 TTTCTTA-AGAAAAAACTTTCTAGTTTTAAAC
1 TTTCTTATAGAAAAAACTTTCTACTTTTAAAC
**
47136 TTTC-TATAGAAAAAACTTTCTACTTTTTTAC
1 TTTCTTATAGAAAAAACTTTCTACTTTTAAAC
47167 TTTC-TATAGAAA
1 TTTCTTATAGAAA
47179 CTTCCAAACG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 2 0.05
31 37 0.95
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (32 bp):
TTTCTTATAGAAAAAACTTTCTACTTTTAAAC
Found at i:47297 original size:15 final size:15
Alignment explanation
Indices: 47277--47308 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
47267 ATGGGAAGAA
47277 TAATTCCGCGTCTCC
1 TAATTCCGCGTCTCC
*
47292 TAATTCCGCTTCTCC
1 TAATTCCGCGTCTCC
47307 TA
1 TA
47309 CACTTGGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.38, G:0.09, T:0.38
Consensus pattern (15 bp):
TAATTCCGCGTCTCC
Found at i:49428 original size:27 final size:27
Alignment explanation
Indices: 49390--49444 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
49380 GCCACACGAA
49390 GATCAACGAGTCTTATTGCATGGAACT
1 GATCAACGAGTCTTATTGCATGGAACT
49417 GATCAACGAGTCTTATTGCATGGAACT
1 GATCAACGAGTCTTATTGCATGGAACT
49444 G
1 G
49445 CTAAGGGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (27 bp):
GATCAACGAGTCTTATTGCATGGAACT
Found at i:50649 original size:21 final size:22
Alignment explanation
Indices: 50605--50646 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
50595 TAAATGACTA
50605 AAAAGAATATATACTTAATAAT
1 AAAAGAATATATACTTAATAAT
*
50627 AAAAGTAT-TATACTATAATA
1 AAAAGAATATATACT-TAATA
50647 TAATCCTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (22 bp):
AAAAGAATATATACTTAATAAT
Found at i:50742 original size:5 final size:5
Alignment explanation
Indices: 50732--50777 Score: 69
Period size: 5 Copynumber: 9.6 Consensus size: 5
50722 AGATATGCTT
*
50732 ATAAG ATAAG ATAAG AT-AG -TAAG ATAAG TTAAG ATAAG ATAAG ATA
1 ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATA
50778 TATTCCCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 1 0.03
4 4 0.11
5 32 0.86
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.24
Consensus pattern (5 bp):
ATAAG
Found at i:53249 original size:59 final size:59
Alignment explanation
Indices: 53157--53274 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
53147 TTTTCTCTGT
53157 AGGTGAATTGGGTGTCTTCAATCTTCAACTTAAAGAGTGGACTATGCTAACTCTAGAGG
1 AGGTGAATTGGGTGTCTTCAATCTTCAACTTAAAGAGTGGACTATGCTAACTCTAGAGG
53216 AGGTGAATTGGGTGTCTTCAATCTTCAACTTAAAGAGTGGACTATGCTAACTCTAGAGG
1 AGGTGAATTGGGTGTCTTCAATCTTCAACTTAAAGAGTGGACTATGCTAACTCTAGAGG
53275 GGCTACCAGG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (59 bp):
AGGTGAATTGGGTGTCTTCAATCTTCAACTTAAAGAGTGGACTATGCTAACTCTAGAGG
Found at i:56339 original size:43 final size:43
Alignment explanation
Indices: 56291--56380 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
56281 ATATTGCTTG
56291 AGAAATCAAACAAGTTGTATTTGGGATACAACTAAGCCACTTA
1 AGAAATCAAACAAGTTGTATTTGGGATACAACTAAGCCACTTA
56334 AGAAATCAAACAAGTTGTATTTGGGATACAACTAAGCCACTTA
1 AGAAATCAAACAAGTTGTATTTGGGATACAACTAAGCCACTTA
56377 AGAA
1 AGAA
56381 CATCCAAGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (43 bp):
AGAAATCAAACAAGTTGTATTTGGGATACAACTAAGCCACTTA
Found at i:58104 original size:61 final size:58
Alignment explanation
Indices: 58009--58148 Score: 201
Period size: 61 Copynumber: 2.4 Consensus size: 58
57999 CAAATATATA
58009 AAACCTAGAGCCATTGGGATTGAGATTTGGTTGTGCCGTAGTTAAC-ACTACAAGTAGTCTG
1 AAACCTAGAGCCATTGGGATTGAGATTTGGTTGTGCCGTAGTT-ACGACTAC-A--AGTCTG
* * * *
58070 AAACCTAAAGCCATTGGGATTGGGATTTGGTTGTGCCGTAGTTCCGACTGCAAGTCTG
1 AAACCTAGAGCCATTGGGATTGAGATTTGGTTGTGCCGTAGTTACGACTACAAGTCTG
58128 AAACCTAGAGCCATTGGGATT
1 AAACCTAGAGCCATTGGGATT
58149 TGGTTGTGGA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
58 26 0.36
60 2 0.03
61 45 0.62
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (58 bp):
AAACCTAGAGCCATTGGGATTGAGATTTGGTTGTGCCGTAGTTACGACTACAAGTCTG
Found at i:64747 original size:23 final size:22
Alignment explanation
Indices: 64720--64764 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
64710 TTTCCCAAGT
*
64720 AAAGTTAACTTCTCAAGTTTTTG
1 AAAGTGAACTTCT-AAGTTTTTG
* *
64743 AAAGTGAATTTCTAATTTTTTG
1 AAAGTGAACTTCTAAGTTTTTG
64765 GTCATCCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (22 bp):
AAAGTGAACTTCTAAGTTTTTG
Found at i:69289 original size:17 final size:17
Alignment explanation
Indices: 69267--69301 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
69257 GCTCTTGAAA
69267 AATAACTAGTTAAGATT
1 AATAACTAGTTAAGATT
69284 AATAACTAGTTAAGATT
1 AATAACTAGTTAAGATT
69301 A
1 A
69302 CTCTGCTTGT
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:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (17 bp):
AATAACTAGTTAAGATT
Found at i:69454 original size:2 final size:2
Alignment explanation
Indices: 69447--69474 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
69437 ATGGCAATAA
69447 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
69475 TAAATATTAA
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:69648 original size:42 final size:42
Alignment explanation
Indices: 69566--69648 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
69556 GGGCTCAGGC
* **
69566 TCACCCAAATTGGCTTTTGCCCAAATATTGGCTCCAAAATTT
1 TCACCCAAATTGGCTTTGGCCCAAATATTGGAGCCAAAATTT
*
69608 TCACCCAAATTGGAC-TTGGCCCAAATATTGGAGCCCAAATT
1 TCACCCAAATTGG-CTTTGGCCCAAATATTGGAGCCAAAATT
69649 AAAAGTCCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (42 bp):
TCACCCAAATTGGCTTTGGCCCAAATATTGGAGCCAAAATTT
Found at i:69889 original size:10 final size:11
Alignment explanation
Indices: 69860--69902 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
69850 CATCTGGTTT
69860 TGCCGTGTCCA
1 TGCCGTGTCCA
69871 TGCCGTGTCCA
1 TGCCGTGTCCA
* *
69882 -GGCGTGTCCC
1 TGCCGTGTCCA
*
69892 TCCCGTGTCCA
1 TGCCGTGTCCA
69903 CCACATTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.07, C:0.40, G:0.28, T:0.26
Consensus pattern (11 bp):
TGCCGTGTCCA
Found at i:69889 original size:21 final size:21
Alignment explanation
Indices: 69863--69902 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
69853 CTGGTTTTGC
*
69863 CGTGTCCATGCCGTGTCCAGG
1 CGTGTCCATCCCGTGTCCAGG
*
69884 CGTGTCCCTCCCGTGTCCA
1 CGTGTCCATCCCGTGTCCA
69903 CCACATTTTT
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:0.07, C:0.40, G:0.28, T:0.25
Consensus pattern (21 bp):
CGTGTCCATCCCGTGTCCAGG
Found at i:72913 original size:13 final size:13
Alignment explanation
Indices: 72895--72921 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
72885 AAAGTAGATA
72895 TTCGAGTTTTGTG
1 TTCGAGTTTTGTG
72908 TTCGAGTTTTGTG
1 TTCGAGTTTTGTG
72921 T
1 T
72922 ATAAAGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.30, T:0.56
Consensus pattern (13 bp):
TTCGAGTTTTGTG
Found at i:73746 original size:21 final size:22
Alignment explanation
Indices: 73697--73752 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
73687 AACACACTAT
73697 AATATTAACTTTATATAAAAAATA
1 AATA-TAA-TTTATATAAAAAATA
* *
73721 AATATGATTTATTTAAAAAAT-
1 AATATAATTTATATAAAAAATA
*
73742 TATATAATTTA
1 AATATAATTTA
73753 ATGATATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 9 0.32
22 13 0.46
23 2 0.07
24 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
AATATAATTTATATAAAAAATA
Found at i:78605 original size:16 final size:17
Alignment explanation
Indices: 78586--78721 Score: 161
Period size: 17 Copynumber: 8.2 Consensus size: 17
78576 TATTGTATTG
*
78586 GGTGAGTATCT-CACCA
1 GGTGAGTATTTGCACCA
78602 GGTGAGTA-TTGCACCA
1 GGTGAGTATTTGCACCA
*
78618 GGTGAGCA-TTGCACCA
1 GGTGAGTATTTGCACCA
*
78634 GGTGAGTGTTTGCACCA
1 GGTGAGTATTTGCACCA
* *
78651 GGTGAGTGTTTGTACCA
1 GGTGAGTATTTGCACCA
*
78668 GGTGAGTATTTGTACCA
1 GGTGAGTATTTGCACCA
**
78685 GGTGAGTATTTATACCA
1 GGTGAGTATTTGCACCA
* *
78702 GGTGAGTGTTTGTACCA
1 GGTGAGTATTTGCACCA
78719 GGT
1 GGT
78722 ACCAGGTGAG
Statistics
Matches: 109, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
15 1 0.01
16 34 0.31
17 74 0.68
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (17 bp):
GGTGAGTATTTGCACCA
Found at i:78927 original size:12 final size:12
Alignment explanation
Indices: 78906--78957 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
78896 TATATTATTG
*
78906 TTATTGTATATA
1 TTATTATATATA
78918 TTATTATATATA
1 TTATTATATATA
78930 -TACGTTGATTATATA
1 TTA--TT-A-TATATA
78945 TTATTATATATA
1 TTATTATATATA
78957 T
1 T
78958 ACGTTGATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
11 2 0.06
12 18 0.53
13 3 0.09
14 3 0.09
15 6 0.18
16 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (12 bp):
TTATTATATATA
Found at i:78952 original size:25 final size:27
Alignment explanation
Indices: 78912--78969 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
78902 ATTGTTATTG
78912 TATATATTATTATATATATACGTTGAT
1 TATATATTATTATATATATACGTTGAT
78939 TATATATTATTATATATATACGTTGAT
1 TATATATTATTATATATATACGTTGAT
78966 TATA
1 TATA
78970 CGATTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (27 bp):
TATATATTATTATATATATACGTTGAT
Found at i:78984 original size:27 final size:26
Alignment explanation
Indices: 78925--78985 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
78915 ATATTATTAT
* *
78925 ATATATACGTTGATTATATATTATTAT
1 ATATATACGTTGATTATAGATTA-TAA
78952 ATATATACGTTGATTATACGATTA-AA
1 ATATATACGTTGATTATA-GATTATAA
78978 ATCATATA
1 AT-ATATA
78986 TTAAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 3 0.10
27 23 0.77
28 4 0.13
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (26 bp):
ATATATACGTTGATTATAGATTATAA
Found at i:80224 original size:18 final size:18
Alignment explanation
Indices: 80197--80279 Score: 112
Period size: 18 Copynumber: 4.6 Consensus size: 18
80187 AAAAAATTCT
80197 TCTTCTTCCTCGGATGAC
1 TCTTCTTCCTCGGATGAC
* *
80215 TCTTCGTCCTCGGATGAT
1 TCTTCTTCCTCGGATGAC
* *
80233 TATTCTTCTTCGGATGAC
1 TCTTCTTCCTCGGATGAC
* *
80251 TCTTCCTCCTCGGATGAT
1 TCTTCTTCCTCGGATGAC
80269 TCTTCTTCCTC
1 TCTTCTTCCTC
80280 CTCGGAATCG
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.11, C:0.31, G:0.16, T:0.42
Consensus pattern (18 bp):
TCTTCTTCCTCGGATGAC
Found at i:80246 original size:36 final size:36
Alignment explanation
Indices: 80199--80279 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
80189 AAAATTCTTC
*
80199 TTCTTCCTCGGATGACTCTTCGTCCTCGGATGATTA
1 TTCTTCCTCGGATGACTCTTCCTCCTCGGATGATTA
* *
80235 TTCTTCTTCGGATGACTCTTCCTCCTCGGATGATTC
1 TTCTTCCTCGGATGACTCTTCCTCCTCGGATGATTA
80271 TTCTTCCTC
1 TTCTTCCTC
80280 CTCGGAATCG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.11, C:0.31, G:0.16, T:0.42
Consensus pattern (36 bp):
TTCTTCCTCGGATGACTCTTCCTCCTCGGATGATTA
Found at i:80352 original size:15 final size:16
Alignment explanation
Indices: 80327--80357 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
80317 GATGATGATT
80327 CTTCTTCCTCGGATGA
1 CTTCTTCCTCGGATGA
80343 CTTC-TCCTCGGATGA
1 CTTCTTCCTCGGATGA
80358 TTTTTCTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.13, C:0.32, G:0.19, T:0.35
Consensus pattern (16 bp):
CTTCTTCCTCGGATGA
Found at i:80376 original size:93 final size:92
Alignment explanation
Indices: 80227--80405 Score: 263
Period size: 93 Copynumber: 1.9 Consensus size: 92
80217 TTCGTCCTCG
*
80227 GATGATTATTCTTCTTCGGATGACTCTTCCTCCTCGGATGATTCTTCTTCCTCCTCGGAATCGGA
1 GATGATTATTCTTCCTCGGATGAC-CTTCCTCCTCGGATGATTCTTCTTCCTCCTCGGAATCGGA
80292 TGATCCCATTTCGGAGGATTCGGATGAT
65 TGATCCCATTTCGGAGGATTCGGATGAT
* *
80320 GATGATTCTTCTTCCTCGGATGA-CTT-CTCCTCGGATGATTTTTCTTCTACTTCCTCGGAATCG
1 GATGATTATTCTTCCTCGGATGACCTTCCTCCTCGGATGATTCTTCTTC--C-TCCTCGGAATCG
* *
80383 GATGATCCTATTTCGGATGATTC
63 GATGATCCCATTTCGGAGGATTC
80406 TTCTTCGGAT
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
90 20 0.26
91 3 0.04
92 1 0.01
93 54 0.69
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.39
Consensus pattern (92 bp):
GATGATTATTCTTCCTCGGATGACCTTCCTCCTCGGATGATTCTTCTTCCTCCTCGGAATCGGAT
GATCCCATTTCGGAGGATTCGGATGAT
Found at i:80400 original size:15 final size:15
Alignment explanation
Indices: 80380--80418 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
80370 TTCCTCGGAA
80380 TCGGATGATCCTAT-T
1 TCGGATGATCCT-TCT
*
80395 TCGGATGATTCTTCT
1 TCGGATGATCCTTCT
80410 TCGGATGAT
1 TCGGATGAT
80419 GATTGCTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.05
15 21 0.95
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (15 bp):
TCGGATGATCCTTCT
Found at i:80417 original size:93 final size:92
Alignment explanation
Indices: 80206--80418 Score: 241
Period size: 93 Copynumber: 2.3 Consensus size: 92
80196 TTCTTCTTCC
* *
80206 TCGGATGACTCTTCGTCCTCGGATGATTATTCTTCTTCGGATGACTCTTCCTCCTCGGATGATTC
1 TCGGATGATTCTTC-T--TCGGATGATTATTCTTCCTCGGATGAC-CTTCCTCCTCGGATGATTC
80271 TTCTTCCTCCTCGGAATCGGATGATCCCATT
62 TTCTTCCTCCTCGGAATCGGATGATCCCATT
* *** *** * *
80302 TCGGAGGATTCGGATGATGATGATTCTTCTTCCTCGGATGA-CTT-CTCCTCGGATGATTTTTCT
1 TCGGATGATTCTTCTTCGGATGATTATTCTTCCTCGGATGACCTTCCTCCTCGGATGATTCTTCT
*
80365 TCTACTTCCTCGGAATCGGATGATCCTATT
66 TC--C-TCCTCGGAATCGGATGATCCCATT
80395 TCGGATGATTCTTCTTCGGATGAT
1 TCGGATGATTCTTCTTCGGATGAT
80419 GATTGCTCTT
Statistics
Matches: 95, Mismatches: 19, Indels: 9
0.77 0.15 0.07
Matches are distributed among these distances:
90 20 0.21
91 3 0.03
92 1 0.01
93 61 0.64
95 1 0.01
96 9 0.09
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (92 bp):
TCGGATGATTCTTCTTCGGATGATTATTCTTCCTCGGATGACCTTCCTCCTCGGATGATTCTTCT
TCCTCCTCGGAATCGGATGATCCCATT
Found at i:84785 original size:29 final size:29
Alignment explanation
Indices: 84725--84792 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
84715 ACCAAACCGT
* **** *
84725 CAAATAAGCCCCTAAACTTTTATTTTGGC
1 CAAATAAGCCCCTAAACTCTTAAAAAGAC
84754 CAAATAAGCCCCTAAACTCTTAAAAAGAC
1 CAAATAAGCCCCTAAACTCTTAAAAAGAC
84783 CAAATAAGCC
1 CAAATAAGCC
84793 ATGTTGCCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (29 bp):
CAAATAAGCCCCTAAACTCTTAAAAAGAC
Found at i:85281 original size:33 final size:33
Alignment explanation
Indices: 85244--85314 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
85234 AGAGTACTCA
85244 CTAAATAAATATTTATAAAATCATTAAAAAGAT
1 CTAAATAAATATTTATAAAATCATTAAAAAGAT
85277 CTAAATAAATATTTATAAAATCATTAAAAAGAT
1 CTAAATAAATATTTATAAAATCATTAAAAAGAT
85310 CTAAA
1 CTAAA
85315 GAGTACTGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (33 bp):
CTAAATAAATATTTATAAAATCATTAAAAAGAT
Found at i:85657 original size:12 final size:12
Alignment explanation
Indices: 85640--85664 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
85630 TGGGGTTGAC
85640 TCAATAGGGTAG
1 TCAATAGGGTAG
85652 TCAATAGGGTAG
1 TCAATAGGGTAG
85664 T
1 T
85665 ATAAAAGGCT
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:0.32, C:0.08, G:0.32, T:0.28
Consensus pattern (12 bp):
TCAATAGGGTAG
Found at i:86585 original size:53 final size:53
Alignment explanation
Indices: 86505--86610 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
86495 CTCCGTATAA
86505 CCACTCGGTAATCTGAATTTAATTTGGACTCTCATGAATCACTTGCATCATGC
1 CCACTCGGTAATCTGAATTTAATTTGGACTCTCATGAATCACTTGCATCATGC
*
86558 CCACTCGGTAATCTGAATTTAATTTGGACTCTCATGCATCACTTGCATCATGC
1 CCACTCGGTAATCTGAATTTAATTTGGACTCTCATGAATCACTTGCATCATGC
86611 ATTTATTTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (53 bp):
CCACTCGGTAATCTGAATTTAATTTGGACTCTCATGAATCACTTGCATCATGC
Found at i:88125 original size:15 final size:16
Alignment explanation
Indices: 88098--88127 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
88088 AACAATAAAG
88098 AAAATAATGAAGAATA
1 AAAATAATGAAGAATA
88114 AAAATAAT-AAGAAT
1 AAAATAATGAAGAAT
88128 TAGTATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (16 bp):
AAAATAATGAAGAATA
Found at i:88254 original size:15 final size:15
Alignment explanation
Indices: 88234--88262 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
88224 TTTATTGAAT
88234 AAAAATTATATTTCG
1 AAAAATTATATTTCG
88249 AAAAATTATATTTC
1 AAAAATTATATTTC
88263 AATAAAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (15 bp):
AAAAATTATATTTCG
Found at i:93959 original size:51 final size:51
Alignment explanation
Indices: 93879--93981 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
93869 TATAAAGTTC
93879 ACCAAATAAGCAATATTCAATACAAATTTTATCCCTCCATTAAACTTTTTT
1 ACCAAATAAGCAATATTCAATACAAATTTTATCCCTCCATTAAACTTTTTT
*
93930 ACCAAATAAGCAATATTCAATACAGATTTTATCCCTCCATTAAACTTTTTT
1 ACCAAATAAGCAATATTCAATACAAATTTTATCCCTCCATTAAACTTTTTT
93981 A
1 A
93982 GTTAGTGCCA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.37
Consensus pattern (51 bp):
ACCAAATAAGCAATATTCAATACAAATTTTATCCCTCCATTAAACTTTTTT
Found at i:96480 original size:6 final size:6
Alignment explanation
Indices: 96469--96507 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
96459 ACTTCTAGGT
*
96469 TTTCAA TTTCAA TTTTCAT TTTCAA TTTCAA TTTCAA TT
1 TTTCAA TTTCAA -TTTCAA TTTCAA TTTCAA TTTCAA TT
96508 ATGACCATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTCAA
Found at i:96486 original size:13 final size:13
Alignment explanation
Indices: 96468--96507 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
96458 CACTTCTAGG
96468 TTTTCAATTTCAA
1 TTTTCAATTTCAA
*
96481 TTTTCATTTTCAA
1 TTTTCAATTTCAA
96494 -TTTCAATTTCAA
1 TTTTCAATTTCAA
96506 TT
1 TT
96508 ATGACCATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTCAATTTCAA
Found at i:96720 original size:36 final size:36
Alignment explanation
Indices: 96649--96780 Score: 207
Period size: 36 Copynumber: 3.8 Consensus size: 36
96639 CAACACAAGG
* *
96649 AGTAGAAGTGGGAGCCCCAT---CCGTCGCCCTATA
1 AGTAGAAGTAGGAGCCCCATCCACCGCCGCCCTATA
*
96682 AGTAGAAGTAGGAGCCCTATCCACCGCCGCCCTATA
1 AGTAGAAGTAGGAGCCCCATCCACCGCCGCCCTATA
*
96718 AGTAGAAGTAGGAGCCCTATCCACCGCCGCCCTATA
1 AGTAGAAGTAGGAGCCCCATCCACCGCCGCCCTATA
96754 AGTAGAAGTAGGAGCCCCATCCACCGC
1 AGTAGAAGTAGGAGCCCCATCCACCGC
96781 TTCCGCTTCT
Statistics
Matches: 92, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
33 18 0.20
36 74 0.80
ACGTcount: A:0.27, C:0.33, G:0.24, T:0.16
Consensus pattern (36 bp):
AGTAGAAGTAGGAGCCCCATCCACCGCCGCCCTATA
Found at i:97144 original size:6 final size:6
Alignment explanation
Indices: 97135--97159 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
97125 GAAGAGGAGG
97135 AGCCGC AGCCGC AGCCGC AGCCGC A
1 AGCCGC AGCCGC AGCCGC AGCCGC A
97160 TCGCACCAGA
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:0.48, G:0.32, T:0.00
Consensus pattern (6 bp):
AGCCGC
Done.