Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012633.1 Corchorus capsularis cultivar CVL-1 contig12654, 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: 92118
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:1101 original size:31 final size:31
Alignment explanation
Indices: 1066--1130 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
1056 AACTGAACAA
1066 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1097 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1128 ACT
1 ACT
1131 GATAACCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAGATCTGGAG
Found at i:3769 original size:2 final size:2
Alignment explanation
Indices: 3762--3793 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
3752 CTCTCAGGTA
3762 AT AT AT AT ACT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A
3794 AAAGTACGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3965 original size:27 final size:27
Alignment explanation
Indices: 3935--3988 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
3925 AATGACCTAG
*
3935 CAACATAGTATTACATAAATTTGGATT
1 CAACATACTATTACATAAATTTGGATT
*
3962 CAACGTACTATTACATAAATTTGGATT
1 CAACATACTATTACATAAATTTGGATT
3989 TGATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (27 bp):
CAACATACTATTACATAAATTTGGATT
Found at i:8425 original size:18 final size:18
Alignment explanation
Indices: 8375--8431 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
8365 ATTAATCGTA
*
8375 AATAAACTAATTAAAACT
1 AATAAACTAATTAACACT
* *
8393 AATAAAATAATTAACCCT
1 AATAAACTAATTAACACT
* *
8411 AATAAACTATTTAACAAT
1 AATAAACTAATTAACACT
8429 AAT
1 AAT
8432 TAATCTTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAAACTAATTAACACT
Found at i:8577 original size:31 final size:30
Alignment explanation
Indices: 8542--8599 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
8532 TCAAAATTTA
*
8542 AATTAAGAATTTCA-TAATTTAAATTAATAAT
1 AATTAA-AATTTAATTAA-TTAAATTAATAAT
*
8573 AATTAATATTTAATTAATTAAATTAAT
1 AATTAAAATTTAATTAATTAAATTAAT
8600 TAAAAAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (30 bp):
AATTAAAATTTAATTAATTAAATTAATAAT
Found at i:8881 original size:30 final size:30
Alignment explanation
Indices: 8845--8909 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
8835 TTGAAGAAAA
*
8845 TGAAGTAAATATTTAAATTTGAAGGTTGTT
1 TGAAGTAAAGATTTAAATTTGAAGGTTGTT
* *
8875 TGAAGTAAAGATTTTAGTTTGAAGGTTGTT
1 TGAAGTAAAGATTTAAATTTGAAGGTTGTT
8905 TGAAG
1 TGAAG
8910 GTTTTAAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.42
Consensus pattern (30 bp):
TGAAGTAAAGATTTAAATTTGAAGGTTGTT
Found at i:11192 original size:45 final size:45
Alignment explanation
Indices: 11141--11230 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
11131 TAATAGAGTA
11141 GTGGAATTACTAAAAGATCCCTA-CTCCAGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTATC-CCAGATTAATGATGAGCTGG
*
11186 GTGGAATTACTAAAAGATCCCTATCCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTATCCCAGATTAATGATGAGCTGG
11231 AGAAGTAATC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
45 42 0.98
46 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTATCCCAGATTAATGATGAGCTGG
Found at i:11692 original size:8 final size:8
Alignment explanation
Indices: 11676--11705 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
11666 AATTCCATAA
*
11676 TTCCATAT
1 TTCCTTAT
11684 TTCCTTAT
1 TTCCTTAT
11692 TTCCTTAT
1 TTCCTTAT
11700 TTCCTT
1 TTCCTT
11706 TATATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.13, C:0.27, G:0.00, T:0.60
Consensus pattern (8 bp):
TTCCTTAT
Found at i:14121 original size:23 final size:23
Alignment explanation
Indices: 14095--14140 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
14085 CTTATGGTGG
14095 TTTCAAGGGAGCAGTATGTTTCT
1 TTTCAAGGGAGCAGTATGTTTCT
*
14118 TTTCAGGGGAGCAGTATGTTTCT
1 TTTCAAGGGAGCAGTATGTTTCT
14141 AGACATGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.39
Consensus pattern (23 bp):
TTTCAAGGGAGCAGTATGTTTCT
Found at i:14674 original size:159 final size:159
Alignment explanation
Indices: 14424--14710 Score: 484
Period size: 159 Copynumber: 1.8 Consensus size: 159
14414 TCCAAGAAGA
* * *
14424 AAGTGATAGCCGTGGATATTGGCGAGTTTGGGATGGCTGTTGTTGATGCTTTGTCGAGTGAAAGA
1 AAGTGATAGACGTGGATATTGGCGAGTTTGGGATCGCTGTTGTTGATGCTTTATCGAGTGAAAGA
* *
14489 GCAAAAATGGTCAAAGAATCTGAGGCCATGAAAATAAAGGGGCGCAAACGAAATTCCAAGAAGTG
66 GCAAAAATGGTCAAAAAATCTGAGGCCATGAAAATAAAGGGGCGCAAACAAAATTCCAAGAAGTG
14554 ACAGACGTGGATATTTGCCAACTTGTGGG
131 ACAGACGTGGATATTTGCCAACTTGTGGG
* *
14583 AAGTGATAGACGTGGATATTGGCGAGTTTGGGATCGCTGTTTTTGATGTTTTATCGAGTGAAAGA
1 AAGTGATAGACGTGGATATTGGCGAGTTTGGGATCGCTGTTGTTGATGCTTTATCGAGTGAAAGA
* * *
14648 GCGAAAATGGTCAAAAAATTTGAGGCCATGAAAATAAAGGGGTGCAAACAAAATTCCAAGAAG
66 GCAAAAATGGTCAAAAAATCTGAGGCCATGAAAATAAAGGGGCGCAAACAAAATTCCAAGAAG
14711 AAAGTTGCAA
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
159 118 1.00
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.25
Consensus pattern (159 bp):
AAGTGATAGACGTGGATATTGGCGAGTTTGGGATCGCTGTTGTTGATGCTTTATCGAGTGAAAGA
GCAAAAATGGTCAAAAAATCTGAGGCCATGAAAATAAAGGGGCGCAAACAAAATTCCAAGAAGTG
ACAGACGTGGATATTTGCCAACTTGTGGG
Found at i:20120 original size:20 final size:21
Alignment explanation
Indices: 20087--20125 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
20077 GACTATGTAA
20087 AAAACCGATCAAACCGGTCAT
1 AAAACCGATCAAACCGGTCAT
20108 AAAACCG-TCAAACCGGTC
1 AAAACCGATCAAACCGGTC
20126 GGTTGAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.41, C:0.31, G:0.15, T:0.13
Consensus pattern (21 bp):
AAAACCGATCAAACCGGTCAT
Found at i:20238 original size:182 final size:170
Alignment explanation
Indices: 20029--20384 Score: 568
Period size: 182 Copynumber: 2.0 Consensus size: 170
20019 GTTCAATTCT
20029 TACCATTTACAAATTTTTTTTATTTTTTTAAAAATGTATTAAAATTTTGACTATGTAAAAAACCG
1 TACCATTTACAAATTTTTTTTATTTTTTTAAAAATGTATTAAAATTTTGACTATGTAAAAAACCG
20094 ATCAAACCGGTCATAAAACCGTCAAACCGGTCGGTTGAACCACGGTTGAACCGGGTCAACGTCGG
66 ATCAAACCGGTCATAAAACCGTCAAA----TC-G--G---C-CGGTTGAACCGGGTCAACGTCGG
* *
20159 TACTTTGACTGGACGATTTTATACATGTGCCGTTACCAGATTGACCACCGA
120 TACGTTGACTGGACGATTTTATACATGTACCGTTACCAGATTGACCACCGA
*
20210 TACCATTTACAAATATTTTTTTATTTTTTTAAAAATGTATTAAAATTTTGACTATGTAAAGAACC
1 TACCATTTACAAAT-TTTTTTTATTTTTTTAAAAATGTATTAAAATTTTGACTATGTAAAAAACC
20275 GATCAAACCGGTCATAAAACCGTCAAATCGGCCGGTTGAACCGGGTCAACGTCGGTACGTTGACT
65 GATCAAACCGGTCATAAAACCGTCAAATCGGCCGGTTGAACCGGGTCAACGTCGGTACGTTGACT
*
20340 GGACGATTTTATCCATGTACCGTTACCAGATTGACCACCGA
130 GGACGATTTTATACATGTACCGTTACCAGATTGACCACCGA
20381 TACC
1 TACC
20385 CGGTTAAACC
Statistics
Matches: 170, Mismatches: 4, Indels: 12
0.91 0.02 0.06
Matches are distributed among these distances:
171 75 0.44
172 1 0.01
175 1 0.01
177 1 0.01
178 2 0.01
181 14 0.08
182 76 0.45
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (170 bp):
TACCATTTACAAATTTTTTTTATTTTTTTAAAAATGTATTAAAATTTTGACTATGTAAAAAACCG
ATCAAACCGGTCATAAAACCGTCAAATCGGCCGGTTGAACCGGGTCAACGTCGGTACGTTGACTG
GACGATTTTATACATGTACCGTTACCAGATTGACCACCGA
Found at i:34011 original size:13 final size:13
Alignment explanation
Indices: 33993--34020 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
33983 GCCGCTGACA
33993 GCACCCATGCCAT
1 GCACCCATGCCAT
34006 GCACCCATGCCAT
1 GCACCCATGCCAT
34019 GC
1 GC
34021 CGATGTCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.46, G:0.18, T:0.14
Consensus pattern (13 bp):
GCACCCATGCCAT
Found at i:35694 original size:6 final size:6
Alignment explanation
Indices: 35686--35715 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
35676 CATTGCATGC
*
35686 ATTTGC ATTTGT ATTTGT ATTTGT ATTTGT
1 ATTTGT ATTTGT ATTTGT ATTTGT ATTTGT
35716 TCTATTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.63
Consensus pattern (6 bp):
ATTTGT
Found at i:40781 original size:38 final size:38
Alignment explanation
Indices: 40739--40816 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
40729 TTTCAACAAA
*
40739 TTCAACTATCTCAAATTCTTACTTAATACTTT-ACATTT
1 TTCAACAATCTCAAATTCTTACTTAATACTTTGA-ATTT
* * *
40777 TTCAACAATTTTACATTCTTACTTAATACTTTGAATTT
1 TTCAACAATCTCAAATTCTTACTTAATACTTTGAATTT
40815 TT
1 TT
40817 GGTAATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 34 0.97
39 1 0.03
ACGTcount: A:0.31, C:0.18, G:0.01, T:0.50
Consensus pattern (38 bp):
TTCAACAATCTCAAATTCTTACTTAATACTTTGAATTT
Found at i:42746 original size:18 final size:18
Alignment explanation
Indices: 42723--42763 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
42713 ATTCGGTAAC
42723 TTTATTACCAAAATATAT
1 TTTATTACCAAAATATAT
42741 TTTATTACCAAAATATAT
1 TTTATTACCAAAATATAT
*
42759 GTTAT
1 TTTAT
42764 AGAAATGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.46
Consensus pattern (18 bp):
TTTATTACCAAAATATAT
Found at i:43804 original size:20 final size:19
Alignment explanation
Indices: 43770--43807 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
43760 ACTACTAAAA
*
43770 AAAACAATTAGAGGTTATC
1 AAAACAATTAAAGGTTATC
43789 AAAACAATTATAAGGTTAT
1 AAAACAATTA-AAGGTTAT
43808 TAATAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAACAATTAAAGGTTATC
Found at i:46385 original size:16 final size:19
Alignment explanation
Indices: 46370--46438 Score: 62
Period size: 16 Copynumber: 4.0 Consensus size: 19
46360 TTGTATAATA
*
46370 ATATGATAT-GATA-ATAT
1 ATATGATATAGATAGATAG
46387 ATAT-ATATAGATAGATAG
1 ATATGATATAGATAGATAG
*
46405 ATA-GATAT--ATAGATAT
1 ATATGATATAGATAGATAG
*
46421 ATA-GATATAGATATATAG
1 ATATGATATAGATAGATAG
46439 CAGTTAAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
16 19 0.44
17 8 0.19
18 16 0.37
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.36
Consensus pattern (19 bp):
ATATGATATAGATAGATAG
Found at i:46394 original size:8 final size:8
Alignment explanation
Indices: 46385--46438 Score: 67
Period size: 8 Copynumber: 7.0 Consensus size: 8
46375 ATATGATAAT
*
46385 ATATATAT
1 ATATATAG
*
46393 ATAGATAG
1 ATATATAG
*
46401 ATAGATAG
1 ATATATAG
46409 ATATATAG
1 ATATATAG
46417 ATATATAG
1 ATATATAG
46425 --ATATAG
1 ATATATAG
46431 ATATATAG
1 ATATATAG
46439 CAGTTAAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
6 6 0.15
8 35 0.85
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (8 bp):
ATATATAG
Found at i:46408 original size:12 final size:12
Alignment explanation
Indices: 46393--46427 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
46383 ATATATATAT
46393 ATAGATAGATAG
1 ATAGATAGATAG
*
46405 ATAGATATATAG
1 ATAGATAGATAG
*
46417 ATATATAGATA
1 ATAGATAGATA
46428 TAGATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.31
Consensus pattern (12 bp):
ATAGATAGATAG
Found at i:46667 original size:36 final size:36
Alignment explanation
Indices: 46612--46692 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
46602 AATTGATCAA
*
46612 AAGTTATAATTTTAAATTTGTTATTGATAAGAATATT
1 AAGTT-TAAATTTAAATTTGTTATTGATAAGAATATT
46649 AAGTTTAAATTTAAATTTGTTATTGATAAGAATATT
1 AAGTTTAAATTTAAATTTGTTATTGATAAGAATATT
46685 AAGTTTAA
1 AAGTTTAA
46693 GTGTTATACC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 38 0.88
37 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (36 bp):
AAGTTTAAATTTAAATTTGTTATTGATAAGAATATT
Found at i:57420 original size:7 final size:7
Alignment explanation
Indices: 57408--57432 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
57398 TGTTTGCATG
57408 TTTCAAT
1 TTTCAAT
57415 TTTCAAT
1 TTTCAAT
57422 TTTCAAT
1 TTTCAAT
57429 TTTC
1 TTTC
57433 TGATTGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTCAAT
Found at i:60932 original size:1 final size:1
Alignment explanation
Indices: 60928--60966 Score: 60
Period size: 1 Copynumber: 39.0 Consensus size: 1
60918 ATTTTTCTGG
**
60928 TTTTTTTTTTTTAATTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
60967 GTGTAAGGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.05, C:0.00, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:60939 original size:23 final size:23
Alignment explanation
Indices: 60913--60962 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
60903 CATAATTGCA
60913 TTTTAATTTTTCTGGTTTTTTTT
1 TTTTAATTTTTCTGGTTTTTTTT
* **
60936 TTTTAATTTTTTTTTTTTTTTTT
1 TTTTAATTTTTCTGGTTTTTTTT
60959 TTTT
1 TTTT
60963 TTTTGTGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.08, C:0.02, G:0.04, T:0.86
Consensus pattern (23 bp):
TTTTAATTTTTCTGGTTTTTTTT
Found at i:63791 original size:13 final size:14
Alignment explanation
Indices: 63766--63799 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
63756 ATATGGGAAA
63766 CAAATCATGTTAAC
1 CAAATCATGTTAAC
63780 CAAATC-TGTTAAC
1 CAAATCATGTTAAC
63793 CAAATCA
1 CAAATCA
63800 GTAAAGGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (14 bp):
CAAATCATGTTAAC
Found at i:64498 original size:28 final size:28
Alignment explanation
Indices: 64458--64524 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
64448 TTCTTCTAAA
64458 ATGATTTTGATACAAGTGAAATGTCAAC
1 ATGATTTTGATACAAGTGAAATGTCAAC
64486 ATGATTTTGATACAAGTGAAATGTCAAC
1 ATGATTTTGATACAAGTGAAATGTCAAC
64514 ATGATTTTGAT
1 ATGATTTTGAT
64525 GATGTATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (28 bp):
ATGATTTTGATACAAGTGAAATGTCAAC
Found at i:76274 original size:72 final size:75
Alignment explanation
Indices: 76181--76444 Score: 259
Period size: 85 Copynumber: 3.3 Consensus size: 75
76171 GACATAATTT
*
76181 GAGACAATTTTTGCAGGGATTCCTTC-ATAA-T-TTGGCTTTCTCTTCATCCAATGAGTCAGCTT
1 GAGACAATTTTTGCAGAGATTCCTTCAATAATTATTGGCTTTCTCTTCATCCAATGAGTCAGCTT
76243 TGCATTATTG
66 TGCATTATTG
*
76253 GAGACAATTTTTGCAGAGATT-CTTCATGATAACTTTGCAGACCATTGGCTTTCTCTTCATCTAA
1 GAGACAATTTTTGCAGAGATTCCTTCA--ATAA--TT-------ATTGGCTTTCTCTTCATCCAA
76317 TGAGTCAGCTTTGCATTATTG
55 TGAGTCAGCTTTGCATTATTG
* *
76338 GAGACAATTTTTGCAGAGATT-CTTTATGATAACTTTACAGACCATTGGCTTTCTCTTCATCTAA
1 GAGACAATTTTTGCAGAGATTCCTTCA--ATAA--TT-------ATTGGCTTTCTCTTCATCCAA
76402 TGAGTCAGCTTTGCATTATTG
55 TGAGTCAGCTTTGCATTATTG
76423 GAGACAATTTTTGCAGAGATTC
1 GAGACAATTTTTGCAGAGATTC
76445 TTTATAATTG
Statistics
Matches: 173, Mismatches: 4, Indels: 16
0.90 0.02 0.08
Matches are distributed among these distances:
71 4 0.02
72 20 0.12
74 4 0.02
77 1 0.01
85 144 0.83
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (75 bp):
GAGACAATTTTTGCAGAGATTCCTTCAATAATTATTGGCTTTCTCTTCATCCAATGAGTCAGCTT
TGCATTATTG
Found at i:76447 original size:85 final size:85
Alignment explanation
Indices: 76212--76449 Score: 449
Period size: 85 Copynumber: 2.8 Consensus size: 85
76202 CCTTCATAAT
*
76212 TTGGCTTTCTCTTCATCCAATGAGTCAGCTTTGCATTATTGGAGACAATTTTTGCAGAGATTCTT
1 TTGGCTTTCTCTTCATCTAATGAGTCAGCTTTGCATTATTGGAGACAATTTTTGCAGAGATTCTT
* *
76277 CATGATAACTTTGCAGACCA
66 TATGATAACTTTACAGACCA
76297 TTGGCTTTCTCTTCATCTAATGAGTCAGCTTTGCATTATTGGAGACAATTTTTGCAGAGATTCTT
1 TTGGCTTTCTCTTCATCTAATGAGTCAGCTTTGCATTATTGGAGACAATTTTTGCAGAGATTCTT
76362 TATGATAACTTTACAGACCA
66 TATGATAACTTTACAGACCA
76382 TTGGCTTTCTCTTCATCTAATGAGTCAGCTTTGCATTATTGGAGACAATTTTTGCAGAGATTCTT
1 TTGGCTTTCTCTTCATCTAATGAGTCAGCTTTGCATTATTGGAGACAATTTTTGCAGAGATTCTT
76447 TAT
66 TAT
76450 AATTGGGATA
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 150 1.00
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.40
Consensus pattern (85 bp):
TTGGCTTTCTCTTCATCTAATGAGTCAGCTTTGCATTATTGGAGACAATTTTTGCAGAGATTCTT
TATGATAACTTTACAGACCA
Found at i:84161 original size:31 final size:31
Alignment explanation
Indices: 84125--84183 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
84115 AGTTTTGTAA
84125 AACTTTTGAAACACCTATTATACCCTTATTT
1 AACTTTTGAAACACCTATTATACCCTTATTT
** *
84156 AACTTTTGAAATGCCTATTATATCCTTA
1 AACTTTTGAAACACCTATTATACCCTTA
84184 CTTGTTCAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.42
Consensus pattern (31 bp):
AACTTTTGAAACACCTATTATACCCTTATTT
Found at i:86380 original size:22 final size:22
Alignment explanation
Indices: 86355--86890 Score: 145
Period size: 22 Copynumber: 24.6 Consensus size: 22
86345 ATGATCCCAT
86355 TATGAAATTTTGATAACCTACC
1 TATGAAATTTTGATAACCTACC
* **
86377 TATGAAATTTTAATAATGATA-C
1 TATGAAATTTTGATAA-CCTACC
* * * ***
86399 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTACC
** * *
86421 TAT-AAATTTTTTTAAACCTTCT
1 TATGAAATTTTGAT-AACCTACC
* * *
86443 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTACC
* * * *
86465 TAAGGAATTTTGA-AGAGCT-CAA
1 TATGAAATTTTGATA-ACCTAC-C
* *
86487 TATGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCTACC
* *
86509 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTAC-C
*
86532 TAT-AAGATGTTGATAACCT-CC
1 TATGAA-ATTTTGATAACCTACC
* * * **
86553 ATAAGATATATTGATAACC-ATGT
1 -TATGAAATTTTGATAACCTA-CC
* * *
86576 TATGAAAATTTT-AAAACCTTCA
1 TATG-AAATTTTGATAACCTACC
*
86598 TATG-AATTGTTGGTAATCAC-ACC
1 TATGAAATT-TTGATAA-C-CTACC
* *
86621 -CTGAAATTGTGATAA--TATCAC
1 TATGAAATTTTGATAACCTA-C-C
* *
86642 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTACC
* *
86665 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTACC
* * * *
86688 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTACC
*
86710 TATGAAATCTTGATAA-CTA-C
1 TATGAAATTTTGATAACCTACC
*
86730 ----AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTACC
** * *
86748 TATGATTTTTTGACAACCT-CAT
1 TATGAAATTTTGATAACCTAC-C
* *
86770 TATGAAATTTTGTTAATCT-CC
1 TATGAAATTTTGATAACCTACC
** * *
86791 TTATGAAATTTTGATCTGCATA-T
1 -TATGAAATTTTGAT-AACCTACC
*
86814 TATGAAATTTTGATAACACT-CT
1 TATGAAATTTTGATAAC-CTACC
* *
86836 TATGAAATTTTGA-AA-TTAAAC
1 TATGAAATTTTGATAACCT-ACC
*
86857 TATGAAATTTTGATATCCT-CC
1 TATGAAATTTTGATAACCTACC
*
86878 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
86891 TACTCTATAA
Statistics
Matches: 371, Mismatches: 99, Indels: 90
0.66 0.18 0.16
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
19 2 0.01
20 17 0.05
21 31 0.08
22 226 0.61
23 78 0.21
24 2 0.01
25 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTACC
Found at i:86458 original size:23 final size:22
Alignment explanation
Indices: 86413--86458 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
86403 GAATTTCGAG
* *
86413 AACCTTTTTATAAATTTTTTTA
1 AACCTTCTTATAAATTTTGTTA
86435 AACCTTCTTATGAAATTTTGTTA
1 AACCTTCTTAT-AAATTTTGTTA
86458 A
1 A
86459 TCTCCCTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.52
Consensus pattern (22 bp):
AACCTTCTTATAAATTTTGTTA
Found at i:86672 original size:23 final size:23
Alignment explanation
Indices: 86641--86725 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
86631 GATAATATCA
*
86641 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
86664 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
86687 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
86709 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
86726 CTACAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:86679 original size:45 final size:44
Alignment explanation
Indices: 86624--86725 Score: 107
Period size: 45 Copynumber: 2.3 Consensus size: 44
86614 TCACACCCTG
* *
86624 AAATTGTGATAATA-TCACTATGAAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAA-ACTCACTATAAAATTTTGATAAAT-TTCCTATA
* * * *
86669 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCTTATG
1 AAATTTTGATAAA-CTCACTATAAAATTTTGATAAATTTCCTATA
*
86714 AAATCTTGATAA
1 AAATTTTGATAA
86726 CTACAAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
44 1 0.02
45 28 0.58
46 19 0.40
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (44 bp):
AAATTTTGATAAACTCACTATAAAATTTTGATAAATTTCCTATA
Found at i:87021 original size:22 final size:22
Alignment explanation
Indices: 86992--87047 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
86982 TTGTAATCAC
86992 ATTT-TGAAAATTTGATAACCT
1 ATTTATGAAAATTTGATAACCT
* *
87013 ATTTATGAAATTTTGTTAACCT
1 ATTTATGAAAATTTGATAACCT
*
87035 CTTTAT-AAAATTT
1 ATTTATGAAAATTT
87048 TGTTGACCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (22 bp):
ATTTATGAAAATTTGATAACCT
Found at i:87048 original size:22 final size:22
Alignment explanation
Indices: 86998--87051 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
86988 TCACATTTTG
*
86998 AAAA-TTTGATAACCTATTTAT
1 AAAATTTTGTTAACCTATTTAT
* *
87019 GAAATTTTGTTAACCTCTTTAT
1 AAAATTTTGTTAACCTATTTAT
87041 AAAATTTTGTT
1 AAAATTTTGTT
87052 GACCCCTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.48
Consensus pattern (22 bp):
AAAATTTTGTTAACCTATTTAT
Found at i:87067 original size:22 final size:22
Alignment explanation
Indices: 87016--87137 Score: 75
Period size: 22 Copynumber: 5.5 Consensus size: 22
87006 ATAACCTATT
* *
87016 TATGAAATTTTGTTAACCTCTT
1 TATGAAATTTTGTTAACCCCTC
* *
87038 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGTTAACCCCTC
* * * *
87060 TATGAAATTCTGATAATCACAT-
1 TATGAAATTTTGTTAA-CCCCTC
* * * *
87082 TATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGTTAACCCCTC
* * ** *
87104 TTTGAAATTTTGATAACAACAC
1 TATGAAATTTTGTTAACCCCTC
87126 TATGAAATTTTG
1 TATGAAATTTTG
87138 ATAATCTTCC
Statistics
Matches: 76, Mismatches: 22, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
21 1 0.01
22 72 0.95
23 3 0.04
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGTTAACCCCTC
Found at i:87091 original size:44 final size:44
Alignment explanation
Indices: 87042--87141 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 44
87032 CCTCTTTATA
* * * *
87042 AAATTTTGTTGACCCCTCTATGAAATTCTGATAATC-ACATTATG
1 AAATTTTGATAACCCCGCTATGAAATTCTGATAA-CAACACTATG
* * * *
87086 TAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACACTATG
1 AAATTTTGATAACCCCGCTATGAAATTCTGATAACAACACTATG
87130 AAATTTTGATAA
1 AAATTTTGATAA
87142 TCTTCCTATA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
43 1 0.02
44 45 0.98
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (44 bp):
AAATTTTGATAACCCCGCTATGAAATTCTGATAACAACACTATG
Found at i:87112 original size:66 final size:66
Alignment explanation
Indices: 87015--87143 Score: 152
Period size: 66 Copynumber: 2.0 Consensus size: 66
87005 GATAACCTAT
* * * * ** *
87015 TTATGAAATTTTGTTAACCTCTTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCAC
1 TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
87080 A
66 A
* * *
87081 TTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACACTATGAAATTTTGATAATC
1 TTATGAAATTTTGATAACCTC-CTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATC
87144 TTCCTATAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 50 0.96
67 2 0.04
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
A
Found at i:87134 original size:88 final size:88
Alignment explanation
Indices: 86972--87137 Score: 192
Period size: 88 Copynumber: 1.9 Consensus size: 88
86962 AAAATACCAT
* * * * ** *
86972 TATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTATTTATGAAATTTTGTTAACCTCT
1 TATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTACTTATGAAATTTTGATAACAACA
*
87037 TTATAAAATTTTGTTGACCCCTC
66 CTATAAAATTTTGTTGACCCCTC
* * *
87060 TATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAA
1 TATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACCT-ACTTATGAAATTTTGATAACAA
*
87123 CACTATGAAATTTTG
64 CACTATAAAATTTTG
87138 ATAATCTTCC
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
87 4 0.06
88 58 0.91
89 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (88 bp):
TATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTACTTATGAAATTTTGATAACAACA
CTATAAAATTTTGTTGACCCCTC
Found at i:87138 original size:22 final size:21
Alignment explanation
Indices: 87059--87141 Score: 85
Period size: 22 Copynumber: 3.8 Consensus size: 21
87049 GTTGACCCCT
*
87059 CTATGAAATTCTGATAATCACA
1 CTATGAAATTTTGATAA-CACA
* * * *
87081 TTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAA-CACA
*
87103 CTTTGAAATTTTGATAACAACA
1 CTATGAAATTTTGATAAC-ACA
87125 CTATGAAATTTTGATAA
1 CTATGAAATTTTGATAA
87142 TCTTCCTATA
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
21 1 0.02
22 47 0.98
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (21 bp):
CTATGAAATTTTGATAACACA
Found at i:87150 original size:22 final size:23
Alignment explanation
Indices: 87059--87189 Score: 83
Period size: 22 Copynumber: 5.8 Consensus size: 23
87049 GTTGACCCCT
* *
87059 CTATGAAATTCTGATAATC-ACA
1 CTATGAAATTTTGATAATCTTCA
* * * *
87081 TTATGTAATTTTGATAA-CCTCG
1 CTATGAAATTTTGATAATCTTCA
* **
87103 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATCTTCA
87125 CTATGAAATTTTGATAATCTTC-
1 CTATGAAATTTTGATAATCTTCA
* ** *
87147 CTAT-AAAATTCAATAATCTGATCT
1 CTATGAAATTTTGATAATCT--TCA
*
87171 CTATGAAATTTCGATAATC
1 CTATGAAATTTTGATAATC
87190 ACTCTATGAG
Statistics
Matches: 84, Mismatches: 19, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
21 13 0.15
22 51 0.61
23 4 0.05
24 4 0.05
25 12 0.14
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCTTCA
Found at i:87197 original size:22 final size:22
Alignment explanation
Indices: 87057--87208 Score: 82
Period size: 22 Copynumber: 6.9 Consensus size: 22
87047 TTGTTGACCC
87057 CTCTATGAAA-TTCTGATAATCA
1 CTCTATGAAATTTC-GATAATCA
* * * *
87079 CAT-TATGTAATTTTGATAACCT
1 C-TCTATGAAATTTCGATAATCA
* * *
87101 CGCTTTGAAATTTTGATAA-CAA
1 CTCTATGAAATTTCGATAATC-A
* *
87123 CACTATGAAATTTTGATAATC-
1 CTCTATGAAATTTCGATAATCA
* * *
87144 TTCCTAT-AAAATTCAATAATCTGA
1 CT-CTATGAAATTTCGATAATC--A
87168 TCTCTATGAAATTTCGATAATCA
1 -CTCTATGAAATTTCGATAATCA
*
87191 CTCTATGAGATTT-GATAA
1 CTCTATGAAATTTCGATAA
87209 CCTTCTATCA
Statistics
Matches: 100, Mismatches: 19, Indels: 23
0.70 0.13 0.16
Matches are distributed among these distances:
21 17 0.17
22 61 0.61
23 5 0.05
24 4 0.04
25 13 0.13
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
CTCTATGAAATTTCGATAATCA
Found at i:87277 original size:22 final size:21
Alignment explanation
Indices: 87248--87387 Score: 88
Period size: 22 Copynumber: 6.4 Consensus size: 21
87238 AAATTGAGAC
87248 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
87269 TTTTGATAACCGCACTATAAAA
1 TTTTGATAACCTCA-TATGAAA
**
87291 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
* *
87313 TATT-AGTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCAT-ATGAAA
** *
87335 TTTTTTTAACCACACTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
87357 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-ATATGAAA
87379 TTTTGATAA
1 TTTTGATAA
87388 TCTCTTTGAT
Statistics
Matches: 93, Mismatches: 16, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
21 11 0.12
22 78 0.84
23 4 0.04
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:87336 original size:44 final size:44
Alignment explanation
Indices: 87263--87387 Score: 112
Period size: 44 Copynumber: 2.8 Consensus size: 44
87253 TAACCTTCAT
* * * * *
87263 ATGAAATT-TTGATAACCGCACTATAAAATTTTGATAACCTCCCC
1 ATGAAATTATT-ATAACCTCGCTATGAAATTTTGATAACCACACC
** *
87307 ATGAAA-TATTAGTAACCTC-CTAATGAAATTTTTTTAACCACACT
1 ATGAAATTATTA-TAACCTCGCT-ATGAAATTTTGATAACCACACC
* *
87351 ATGAAATTCTTATAACCTCGCTATGACATTTTGATAA
1 ATGAAATTATTATAACCTCGCTATGAAATTTTGATAA
87388 TCTCTTTGAT
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
43 4 0.06
44 55 0.85
45 6 0.09
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (44 bp):
ATGAAATTATTATAACCTCGCTATGAAATTTTGATAACCACACC
Found at i:87484 original size:24 final size:22
Alignment explanation
Indices: 87423--87606 Score: 106
Period size: 22 Copynumber: 8.3 Consensus size: 22
87413 TTGTGAAAAT
* * *
87423 TAACCACCCTATGGAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
87445 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
87467 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
*
87491 TAACC-ACACTATGAAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
**
87513 TAA-CAACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* **
87535 TAACC-ACACTATGGAATTTCGA
1 TAACCAAC-CTATGAAATTTTAA
* * *
87557 TAGCC-TCCTCATGAAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * * *
87579 TAATCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
87601 TAACCA
1 TAACCA
87607 CATAGAGACA
Statistics
Matches: 129, Mismatches: 26, Indels: 14
0.76 0.15 0.08
Matches are distributed among these distances:
21 4 0.03
22 103 0.80
23 4 0.03
24 18 0.14
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:87495 original size:46 final size:45
Alignment explanation
Indices: 87445--87545 Score: 120
Period size: 44 Copynumber: 2.3 Consensus size: 45
87435 GGAATTTCAA
*
87445 TAACCAAC-CTAAGAAATTTTAATAACCTGATC-CTATGAAATTTTGG
1 TAACCAACACTAAGAAATTTTAATAA-C--AACACTATGAAATTTTGG
* *
87491 TAACC-ACACTATGAAATTTTGATAACAACACTATGAAATTTTGG
1 TAACCAACACTAAGAAATTTTAATAACAACACTATGAAATTTTGG
87535 TAACC-ACACTA
1 TAACCAACACTA
87546 TGGAATTTCG
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
43 2 0.04
44 25 0.50
45 3 0.06
46 20 0.40
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.31
Consensus pattern (45 bp):
TAACCAACACTAAGAAATTTTAATAACAACACTATGAAATTTTGG
Found at i:87505 original size:22 final size:22
Alignment explanation
Indices: 87477--87553 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
87467 TAACCTGATC
87477 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* *
87499 CTATGAAATTTTGATAACAACA
1 CTATGAAATTTTGGTAACCACA
87521 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
*
87543 CTATGGAATTT
1 CTATGAAATTT
87554 CGATAGCCTC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:87571 original size:44 final size:43
Alignment explanation
Indices: 87474--87574 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 43
87464 TAATAACCTG
*
87474 ATCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAAC
1 ATCCTATGAAATTTTGGTAACCACACTATGAAATTTCGATAAC
* * *
87517 AACACTATGAAATTTTGGTAACCACACTATGGAATTTCGATAGC
1 ATC-CTATGAAATTTTGGTAACCACACTATGAAATTTCGATAAC
*
87561 CTCCTCATGAAATT
1 ATCCT-ATGAAATT
87575 ATAATAATCA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
43 4 0.08
44 46 0.92
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.33
Consensus pattern (43 bp):
ATCCTATGAAATTTTGGTAACCACACTATGAAATTTCGATAAC
Found at i:88124 original size:87 final size:87
Alignment explanation
Indices: 87950--88114 Score: 269
Period size: 87 Copynumber: 1.9 Consensus size: 87
87940 TCTAATAATT
* *
87950 AATAATGGAATAATTAAAATATTATTTAGTAATGACAATTTAGAAATATGTTTTAAAAAAGGATA
1 AATAATAGAACAATTAAAATATTATTTAGTAATGACAATTTAGAAATATGTTTTAAAAAAGGATA
**
88015 CAATTGGAATTTATAATTAAAA
66 CAATTGGAAAATATAATTAAAA
* *
88037 AATAATAGAACAATTAAAATATTATTTAGTAATGGCAATTTAGAAATATGTTTTAAAAAAGGGTA
1 AATAATAGAACAATTAAAATATTATTTAGTAATGACAATTTAGAAATATGTTTTAAAAAAGGATA
88102 CAATT-GAAAATAT
66 CAATTGGAAAATAT
88115 GTTTTAAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 6 0.08
87 66 0.92
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (87 bp):
AATAATAGAACAATTAAAATATTATTTAGTAATGACAATTTAGAAATATGTTTTAAAAAAGGATA
CAATTGGAAAATATAATTAAAA
Done.