Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012625.1 Corchorus capsularis cultivar CVL-1 contig12646, 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: 85974
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:9150 original size:22 final size:23
Alignment explanation
Indices: 9105--9150 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
9095 TTTAGACTTC
* *
9105 ATTTATAAAGAATATGGATTAAT
1 ATTTACAAAGAATATGAATTAAT
9128 ATTTACAAAGAA-ATGAATTAAT
1 ATTTACAAAGAATATGAATTAAT
9150 A
1 A
9151 ACTACAGCAT
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:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (23 bp):
ATTTACAAAGAATATGAATTAAT
Found at i:9156 original size:22 final size:23
Alignment explanation
Indices: 9111--9156 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
9101 CTTCATTTAT
* **
9111 AAAGAATATGGATTAATATTTAC
1 AAAGAATATGAATTAATAACTAC
9134 AAAGAA-ATGAATTAATAACTAC
1 AAAGAATATGAATTAATAACTAC
9156 A
1 A
9157 GCATCCAGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (23 bp):
AAAGAATATGAATTAATAACTAC
Found at i:11095 original size:107 final size:104
Alignment explanation
Indices: 10868--11130 Score: 375
Period size: 107 Copynumber: 2.5 Consensus size: 104
10858 AATTTTTCTA
* ** *
10868 ACCCTTAAAATAAAATTTTAATTTTAATTTGGGCTAAACGTAGTG-AATTAATTATATATTTTAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAATTATATATTTTAT
*
10932 TTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
66 TTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
* * * *
10971 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGAATAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGG-CTAAACTTAGTGAAATTAATTATATATTTTA
* *
11036 TTTCTAAAACCCTATTACAATAAATTATTAATTTTGAAATTT
65 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT
*
11078 ACCCTTAAAATAAAAATAAAATTTTAGTTTGGGGCTAAACTTAGTGAAATTAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTT-GGGCTAAACTTAGTGAAATTAA
11131 GGCTAAACTT
Statistics
Matches: 141, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
103 30 0.21
104 10 0.07
105 35 0.25
107 63 0.45
108 3 0.02
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (104 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAATTATATATTTTAT
TTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:11179 original size:17 final size:17
Alignment explanation
Indices: 11141--11180 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
11131 GGCTAAACTT
11141 AAGAAAAAAATAAAAAA
1 AAGAAAAAAATAAAAAA
*
11158 TAGAAAAAAA-AAAAAGA
1 AAGAAAAAAATAAAAA-A
11175 AAGAAA
1 AAGAAA
11181 GAGAGAAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (17 bp):
AAGAAAAAAATAAAAAA
Found at i:12384 original size:2 final size:2
Alignment explanation
Indices: 12377--12404 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12367 CAAACTCAGA
12377 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
12405 TGTGATGTAA
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:19683 original size:24 final size:25
Alignment explanation
Indices: 19623--19681 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
19613 TTCAAACCCT
*
19623 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACATCTTC
19648 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
19672 AAA-TTCATTT
1 AAACTTCATTT
19682 TCCTTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 18 0.55
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.41
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:19720 original size:26 final size:26
Alignment explanation
Indices: 19691--19758 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
19681 TTCCTTCATT
19691 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
19717 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
19743 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
19759 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:19782 original size:52 final size:51
Alignment explanation
Indices: 19691--19808 Score: 122
Period size: 52 Copynumber: 2.4 Consensus size: 51
19681 TTCCTTCATT
* *
19691 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTAGATACTAA
1 TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTA-AAACTAA
* * *
19743 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
1 TTAAACATAAACTAATTAAA-T-ACTAATTAATAATAAACTAATTAAAACTAA
19794 -T---CATAAACTAATTAA
1 TTAAACATAAACTAATTAA
19809 TATTAAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
47 10 0.17
48 3 0.05
50 1 0.02
51 10 0.17
52 28 0.48
53 6 0.10
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (51 bp):
TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTAAAACTAA
Found at i:20735 original size:31 final size:30
Alignment explanation
Indices: 20697--20799 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 30
20687 TAATTTGGCT
*
20697 AAATAAGGGCCTAACATTATCTAAAATGCTC
1 AAATAAGGGCCTAAC-TTATCGAAAATGCTC
* * **
20728 AAATAAGGGCATGATCTT-T-GAATTTGAC-C
1 AAATAAGGGCCT-AACTTATCGAAAATG-CTC
20757 AAATAAGGGCCTAACGTTATCGAAAATGCTC
1 AAATAAGGGCCTAAC-TTATCGAAAATGCTC
20788 AAATAAGGGCCT
1 AAATAAGGGCCT
20800 GATGTCTGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
28 2 0.04
29 18 0.32
30 4 0.07
31 31 0.54
32 2 0.04
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.25
Consensus pattern (30 bp):
AAATAAGGGCCTAACTTATCGAAAATGCTC
Found at i:20796 original size:60 final size:58
Alignment explanation
Indices: 20636--20802 Score: 190
Period size: 60 Copynumber: 2.8 Consensus size: 58
20626 GCTAATTGCT
* * * * * * * *
20636 CAAATAAGAGTCTAACGTTTGTCAAAATACTCAAATAAGGACTCGATGTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-TTATCAAAATGCTCAAATAAGGGCT-GATCTTTGAATTTGAC
* *
20696 TAAATAAGGGCCTAACATTATCTAAAATGCTCAAATAAGGGCATGATCTTTGAATTTGAC
1 CAAATAAGGGCCTAACGTTATC-AAAATGCTCAAATAAGGGC-TGATCTTTGAATTTGAC
20756 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCTGAT
1 CAAATAAGGGCCTAACGTTATC-AAAATGCTCAAATAAGGG-CTGAT
20803 GTCTGTTTGG
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
59 4 0.04
60 85 0.93
61 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (58 bp):
CAAATAAGGGCCTAACGTTATCAAAATGCTCAAATAAGGGCTGATCTTTGAATTTGAC
Found at i:20865 original size:31 final size:30
Alignment explanation
Indices: 20830--20934 Score: 106
Period size: 31 Copynumber: 3.5 Consensus size: 30
20820 GTGAGACAGA
20830 CCCTTATTTGAGCATTTTGGCAAACATTAGG
1 CCCTTATTTGAGCATTTT-GCAAACATTAGG
** * * * *
20861 CCCTTATTTG-GCCAAATT-AAAAGATCAGA
1 CCCTTATTTGAG-CATTTTGCAAACATTAGG
*
20890 CCCTTATTTGAGCATTTTGACAAACGTTAGG
1 CCCTTATTTGAGCATTTTG-CAAACATTAGG
20921 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
20935 ATTAACCTAT
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
29 21 0.37
30 2 0.04
31 34 0.60
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTGCAAACATTAGG
Found at i:22508 original size:13 final size:13
Alignment explanation
Indices: 22490--22524 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
22480 ACTTTTCATG
22490 AATAATATATATA
1 AATAATATATATA
*
22503 AATAATAAATATA
1 AATAATATATATA
*
22516 AATGATATA
1 AATAATATA
22525 AGAATAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (13 bp):
AATAATATATATA
Found at i:23293 original size:21 final size:21
Alignment explanation
Indices: 23269--23312 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
23259 ATAAGGGCCC
23269 TAAAACACA-ATTTAAATAAAT
1 TAAAACACATATTT-AATAAAT
* *
23290 TAAAATACATATTTAGTAAAT
1 TAAAACACATATTTAATAAAT
23311 TA
1 TA
23313 TGACATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAAACACATATTTAATAAAT
Found at i:23668 original size:22 final size:22
Alignment explanation
Indices: 23641--23687 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
23631 ATATATGTAG
23641 TATATTTGTATTAATTTATTAA
1 TATATTTGTATTAATTTATTAA
*
23663 TATATTTGTATTAGTTTATTAA
1 TATATTTGTATTAATTTATTAA
23685 TAT
1 TAT
23688 CAATTCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (22 bp):
TATATTTGTATTAATTTATTAA
Found at i:24009 original size:13 final size:13
Alignment explanation
Indices: 23991--24016 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23981 ACAATTTAAT
23991 ATAATTATTGAAA
1 ATAATTATTGAAA
24004 ATAATTATTGAAA
1 ATAATTATTGAAA
24017 TTTATTGAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
ATAATTATTGAAA
Found at i:28392 original size:20 final size:20
Alignment explanation
Indices: 28367--28407 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
28357 CTACACTGTC
28367 TCTGGATTAATAGATGAGGT
1 TCTGGATTAATAGATGAGGT
28387 TCTGGATTAATAGATGAGGT
1 TCTGGATTAATAGATGAGGT
28407 T
1 T
28408 GATGAGACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.37
Consensus pattern (20 bp):
TCTGGATTAATAGATGAGGT
Found at i:33084 original size:15 final size:17
Alignment explanation
Indices: 33046--33087 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
33036 AAAAAAATCT
33046 GAATCCGAAAAAGTTCA
1 GAATCCGAAAAAGTTCA
*
33063 -AACCCGAAAAA-TT-A
1 GAATCCGAAAAAGTTCA
33077 GAATCCGAAAA
1 GAATCCGAAAA
33088 TTCTAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 1 0.05
15 11 0.50
16 10 0.45
ACGTcount: A:0.52, C:0.19, G:0.14, T:0.14
Consensus pattern (17 bp):
GAATCCGAAAAAGTTCA
Found at i:33385 original size:32 final size:32
Alignment explanation
Indices: 33341--33416 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
33331 ACCTAACCCA
* *
33341 AAATTGAA-CCGAAATCGAATCAA-CTTGACAC
1 AAATTTAACCCGAAATCAAATCAATC-TGACAC
* *
33372 AAATTTAACCCGAACTCAAATCAATCTGACCC
1 AAATTTAACCCGAAATCAAATCAATCTGACAC
33404 AAATTTAACCCGA
1 AAATTTAACCCGA
33417 CTCAAACCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
31 7 0.18
32 31 0.79
33 1 0.03
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.21
Consensus pattern (32 bp):
AAATTTAACCCGAAATCAAATCAATCTGACAC
Found at i:42010 original size:5 final size:5
Alignment explanation
Indices: 42000--42028 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
41990 GAGAGCTATC
42000 CAAAA CAAAA CAAAA CAAAA CAAAA -AAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA
42029 GGGAAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:43421 original size:28 final size:29
Alignment explanation
Indices: 43388--43458 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
43378 CAATTTTGAT
*
43388 AGTTTAGGAGTAAAAAT-TCCAAAT-TAAA
1 AGTTTAGGA-AAAAAATGTCCAAATCTAAA
* *
43416 AGTTTAGCAAAAAAATGTCCATATCCTAAA
1 AGTTTAGGAAAAAAATGTCCAAAT-CTAAA
43446 AGTTTAGGAAAAA
1 AGTTTAGGAAAAA
43459 CAATTAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.17
28 14 0.39
30 16 0.44
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (29 bp):
AGTTTAGGAAAAAAATGTCCAAATCTAAA
Found at i:43678 original size:20 final size:20
Alignment explanation
Indices: 43653--43691 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
43643 CGGAATTTAT
43653 AATTTGTTTATTTATGTATA
1 AATTTGTTTATTTATGTATA
43673 AATTTGTTTATTTATGTAT
1 AATTTGTTTATTTATGTAT
43692 TTGGTAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (20 bp):
AATTTGTTTATTTATGTATA
Found at i:52290 original size:8 final size:9
Alignment explanation
Indices: 52279--52324 Score: 53
Period size: 8 Copynumber: 5.3 Consensus size: 9
52269 CGTCAACATC
52279 TAAT-TATA
1 TAATATATA
52287 TAATATATA
1 TAATATATA
52296 T-ATATATA
1 TAATATATA
52304 T-ATATATA
1 TAATATATA
*
52312 TATTCATATA
1 TAAT-ATATA
52322 TAA
1 TAA
52325 ATTTATGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 20 0.61
9 6 0.18
10 7 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (9 bp):
TAATATATA
Found at i:52294 original size:2 final size:2
Alignment explanation
Indices: 52283--52323 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
52273 AACATCTAAT
52283 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T- TCA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
52324 AATTTATGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.06
2 33 0.92
3 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:58591 original size:3 final size:3
Alignment explanation
Indices: 58583--58612 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
58573 ACATACTCTT
*
58583 ATA ATA ATA ATA ATA ATA TTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
58613 TATTTAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:64120 original size:23 final size:24
Alignment explanation
Indices: 64070--64120 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
64060 ACATATATAT
*
64070 AATGGTAATTATTTTTTTTTATAACA
1 AATGGTAATTA--TTTTCTTATAACA
*
64096 AATGGTAATTA-TTTCTTATACCA
1 AATGGTAATTATTTTCTTATAACA
64119 AA
1 AA
64121 GATGGCCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 12 0.52
26 11 0.48
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (24 bp):
AATGGTAATTATTTTCTTATAACA
Found at i:65186 original size:20 final size:20
Alignment explanation
Indices: 65163--65210 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
65153 AAAAATTCAG
*
65163 AAAAAAGAAATTCCTTAATAA
1 AAAAAAGAAATTCATTAA-AA
*
65184 AAAATTA-AAATTCATTAAAA
1 AAAA-AAGAAATTCATTAAAA
65204 AAAAAAG
1 AAAAAAG
65211 GACTAGAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
19 1 0.05
20 6 0.27
21 14 0.64
22 1 0.05
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.23
Consensus pattern (20 bp):
AAAAAAGAAATTCATTAAAA
Found at i:65668 original size:13 final size:13
Alignment explanation
Indices: 65650--65678 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
65640 CTTTGCTAAA
65650 TTCTGATCTGGGT
1 TTCTGATCTGGGT
65663 TTCTGATCTGGGT
1 TTCTGATCTGGGT
65676 TTC
1 TTC
65679 AAGTTATCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.17, G:0.28, T:0.48
Consensus pattern (13 bp):
TTCTGATCTGGGT
Found at i:66058 original size:20 final size:21
Alignment explanation
Indices: 66015--66057 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
66005 GGATTTTTAA
*
66015 TTTAATGAATTTTGTTTTATT
1 TTTAATGAATTTTGTTTAATT
66036 TTTAA-GAATTTT-TTTAATT
1 TTTAATGAATTTTGTTTAATT
66055 TTT
1 TTT
66058 TTATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 7 0.33
21 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (21 bp):
TTTAATGAATTTTGTTTAATT
Found at i:68866 original size:155 final size:151
Alignment explanation
Indices: 68571--69129 Score: 500
Period size: 155 Copynumber: 3.6 Consensus size: 151
68561 GTAGACCATT
* *
68571 TTGGCTAAGTTTCATCTCAAACGGACTTA-AGATGAAAAACTTATTCA-AGTTTTTCAGTTAAGG
1 TTGGC-AAGTTTCATCTC-AACAGACTTAGA-ATGAAAAACTTA-TGATAGTTTTTCAGTTAAGG
* * * * *
68634 ACAGTTTGGGGTGAGAAACCACTTCATCATGATAGGGAGTTCGGTTTTACTTAGAATTTTTTCCA
62 ACAGTTTGGGGTGAGAAACAAGTTCACCATCA-AGGGAGCTCGGTTTTACTTAGAATTTTTTCCA
*
68699 TAAGTTTTTGGAGATAATCTAAGTCTC
126 T-AGTTTATGGAGATAATCTAAGTCTC
68726 TTGGCCAAGTTTCATCTCAGACAGACTTAGAATGAAAAACTTATGATAGTTTTTCAGTTAAGGAC
1 TTGG-CAAGTTTCATCTCA-ACAGACTTAGAATGAAAAACTTATGATAGTTTTTCAGTTAAGGAC
* * **** * * * *
68791 AATTTGAGGTGAGAAGTTGGTTCACCACCAAGGAGAACTCGGCTTTACTTAGAATTTTTTTCATA
64 AGTTTGGGGTGAGAAACAAGTTCACCATCAAGG-GAGCTCGGTTTTACTTAGAATTTTTTCCATA
*
68856 GTCTTATGGAGATAATCTAAGCCTAC
128 GT-TTATGGAGATAATCTAAGTCT-C
** * * *** * *
68882 TGGTGG-AA-AATCAGCCTTATTGGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGA
1 T--TGGCAAGTTTCA-TCTCAACAGACTTAGAATGAAAAACTTATGATAGTTTTTCAGTTAAGGA
* * * *
68945 CAG-TTAGGGAGAGAAACCAAGTTCACCATCAACGGGAGGTCGGTTTTACTTGGAATTTTTTCCA
63 CAGTTTGGGGTGAGAAA-CAAGTTCACCATCAA-GGGAGCTCGGTTTTACTTAGAATTTTTTCCA
* * *
69009 TAGTATTATAGAGATAGTCTATGTCTC
126 TAGT-TTATGGAGATAATCTAAGTCTC
* * * * *
69036 ATGGAAAAGTTTCATCTCATTCAGACTTAGAATGAAAAACTTATGCT-GATTTTTCATTTAAGGA
1 TTGG-CAAGTTTCATCTCA-ACAGACTTAGAATGAAAAACTTATGATAG-TTTTTCAGTTAAGGA
* * *
69100 CAGTTTGGGGTGTGAGACCTAGTTCACCAT
63 CAGTTTGGGGTGAGA-AACAAGTTCACCAT
69130 GAAGAAGGGC
Statistics
Matches: 327, Mismatches: 58, Indels: 37
0.77 0.14 0.09
Matches are distributed among these distances:
152 3 0.01
154 25 0.08
155 265 0.81
156 30 0.09
157 1 0.00
158 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (151 bp):
TTGGCAAGTTTCATCTCAACAGACTTAGAATGAAAAACTTATGATAGTTTTTCAGTTAAGGACAG
TTTGGGGTGAGAAACAAGTTCACCATCAAGGGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTT
TATGGAGATAATCTAAGTCTC
Found at i:77201 original size:129 final size:129
Alignment explanation
Indices: 77049--77313 Score: 523
Period size: 129 Copynumber: 2.1 Consensus size: 129
77039 TCTATACTAT
77049 ATTAAA-AAGTACGTTCAGCTGTAAAACTTTTGAATCGCCTATTATACCCTTATTTGTTAAATAT
1 ATTAAATAAGTACGTTCAGCTGTAAAACTTTTGAATCGCCTATTATACCCTTATTTGTTAAATAT
77113 ATTTCTAAATTGCCATTGCTAGGTTTTTATAGTTTTACTGAACTAAAAACTCTATTTTTATTTA
66 ATTTCTAAATTGCCATTGCTAGGTTTTTATAGTTTTACTGAACTAAAAACTCTATTTTTATTTA
77177 ATTAAATAAGTACGTTCAGCTGTAAAACTTTTGAATCGCCTATTATACCCTTATTTGTTAAATAT
1 ATTAAATAAGTACGTTCAGCTGTAAAACTTTTGAATCGCCTATTATACCCTTATTTGTTAAATAT
77242 ATTTCTAAATTGCCATTGCTAGGTTTTTATAGTTTTACTGAACTAAAAACTCTATTTTTATTTA
66 ATTTCTAAATTGCCATTGCTAGGTTTTTATAGTTTTACTGAACTAAAAACTCTATTTTTATTTA
77306 ATTAAATA
1 ATTAAATA
77314 TAATATCTTT
Statistics
Matches: 136, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
128 6 0.04
129 130 0.96
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.44
Consensus pattern (129 bp):
ATTAAATAAGTACGTTCAGCTGTAAAACTTTTGAATCGCCTATTATACCCTTATTTGTTAAATAT
ATTTCTAAATTGCCATTGCTAGGTTTTTATAGTTTTACTGAACTAAAAACTCTATTTTTATTTA
Found at i:77348 original size:70 final size:70
Alignment explanation
Indices: 77266--77496 Score: 293
Period size: 70 Copynumber: 3.2 Consensus size: 70
77256 ATTGCTAGGT
* * *
77266 TTTTA-TAGTTTTACTGAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATT
77330 ATTTTA
65 ATTTTA
77336 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTT-T-A-TA
*
77401 TTATATTTTACCA
62 AT-TATTTT---A
* * *
77414 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
*
77479 TTATA
66 TTTTA
*
77484 TTTTACAATTTTA
1 TTTTACTATTTTA
77497 GTTAAAAAAA
Statistics
Matches: 142, Mismatches: 10, Indels: 18
0.84 0.06 0.11
Matches are distributed among these distances:
70 61 0.43
71 5 0.04
72 1 0.01
73 6 0.04
74 5 0.04
75 7 0.05
76 1 0.01
77 2 0.01
78 54 0.38
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.49
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
TTTTA
Found at i:77348 original size:78 final size:76
Alignment explanation
Indices: 77266--77496 Score: 323
Period size: 78 Copynumber: 3.1 Consensus size: 76
77256 ATTGCTAGGT
* * *
77266 TTTTATAGTTTTACTGAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-T-A-TA
1 TTTTATA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
*
77327 AT-TATTTT--A
65 TTATATTTTACA
77336 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTA-TATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
77401 TTATATTTTACCA
65 TTATATTTTA-CA
*
77414 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTA-TATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
77479 TTATATTTTACAA
65 TTATATTTTAC-A
77492 TTTTA
1 TTTTA
77497 GTTAAAAAAA
Statistics
Matches: 146, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
70 48 0.33
71 5 0.03
72 1 0.01
73 1 0.01
74 3 0.02
75 6 0.04
77 1 0.01
78 81 0.55
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.49
Consensus pattern (76 bp):
TTTTATATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTAT
TATATTTTACA
Found at i:81229 original size:2 final size:2
Alignment explanation
Indices: 81222--81249 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
81212 TAACCTTTAT
81222 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
81250 CTTTAAAATA
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):
TA
Found at i:84448 original size:166 final size:166
Alignment explanation
Indices: 84003--84461 Score: 587
Period size: 171 Copynumber: 2.7 Consensus size: 166
83993 CCACACCCCG
* * * * * * * * *
84003 GATTAATGAGGAGCAAGAGAATTAATTTTTTTCATCTTTTCCCACTTTACCGATTACTTAAATGT
1 GATTGATGATGAGCTAGAGAACTAATTTTTTTCGTCTTTACCTACTTGACAGATTACTTAAATGT
* * * *
84068 CCTAACTTTTGATTATTGAGGTGATTAAATAACTAGACTTTTTGGTCATTTCTCAATTGACTTTA
66 CCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATGGACTTTA
* * * * *
84133 ATAGAATAGTGGAATTACTAAATGATCCCTACCAAG
131 ATAGAATAGTAGAATTAATAAAAGATCCCCACCAAA
* * ** * * * *
84169 GCTTGCTTTTGGAGCTAGAGAACTTAA-TTTTTTGGTCTTTACCTACTTGGCATATTATTTAAAT
1 GATTGATGAT-GAGCTAGAGAAC-TAATTTTTTTCGTCTTTACCTACTTGACAGATTA-CT---T
* * *
84233 AAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAAGTAATCTTTTTGATCATTTCTCAATGG
60 AAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATGG
*
84298 ACTTTAATAGAATAGTAGAATTAATAAAAGATCCCCATCAAA
125 ACTTTAATAGAATAGTAGAATTAATAAAAGATCCCCACCAAA
84340 GATTGATGATGAGCTAGAGAACTAATTTTTTTCGTCTTTACCTACTTGACAGATTACTTAAATGT
1 GATTGATGATGAGCTAGAGAACTAATTTTTTTCGTCTTTACCTACTTGACAGATTACTTAAATGT
84405 CCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
66 CCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
84462 TGACAAATGA
Statistics
Matches: 245, Mismatches: 41, Indels: 14
0.82 0.14 0.05
Matches are distributed among these distances:
166 65 0.27
167 32 0.13
168 4 0.02
169 4 0.02
170 39 0.16
171 101 0.41
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.39
Consensus pattern (166 bp):
GATTGATGATGAGCTAGAGAACTAATTTTTTTCGTCTTTACCTACTTGACAGATTACTTAAATGT
CCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATGGACTTTA
ATAGAATAGTAGAATTAATAAAAGATCCCCACCAAA
Done.