Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006960.1 Corchorus capsularis cultivar CVL-1 contig06981, 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: 23889
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:8479 original size:48 final size:48
Alignment explanation
Indices: 8407--8528 Score: 156
Period size: 49 Copynumber: 2.5 Consensus size: 48
8397 CGTGCCAATT
* * * *
8407 AATTTTGTCCAAAAATTGATAAAAA-GTGCAATGAAAAGTAAATATTC
1 AATTTTGTCTAAAAATTGAGAAAAAGGTGCAAGGAAAAGTAAAGATTC
* *
8454 AATTTTGTCATAAAAATTGAGAAAAAGGTGCAAGGAAAATTAAAGGTTC
1 AATTTTGTC-TAAAAATTGAGAAAAAGGTGCAAGGAAAAGTAAAGATTC
*
8503 AATTTTGTTGTAAAAATTGAGAAAAA
1 AATTTTG-TCTAAAAATTGAGAAAAA
8529 CTCCAGGAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
47 9 0.14
48 14 0.22
49 41 0.63
50 1 0.02
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.30
Consensus pattern (48 bp):
AATTTTGTCTAAAAATTGAGAAAAAGGTGCAAGGAAAAGTAAAGATTC
Found at i:11049 original size:30 final size:31
Alignment explanation
Indices: 10991--11049 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
10981 ATGTTTTTCG
* *
10991 ATTGTACCCTTATTTTTAAAATATATTTCCA
1 ATTGTACCCTTATTTTAAAAACATATTTCCA
*
11022 ATTGTACTCTT-TTTTAAAAACATATTTC
1 ATTGTACCCTTATTTTAAAAACATATTTC
11050 TAAATTGCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.49
Consensus pattern (31 bp):
ATTGTACCCTTATTTTAAAAACATATTTCCA
Found at i:11056 original size:31 final size:31
Alignment explanation
Indices: 10991--11056 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
10981 ATGTTTTTCG
* * *
10991 ATTGTACCCTTATTTTTAAAATATATTTCCA
1 ATTGTACCCTTATTTTAAAAACATATTTCAA
*
11022 ATTGTACTCTT-TTTTAAAAACATATTTCTAA
1 ATTGTACCCTTATTTTAAAAACATATTTC-AA
11053 ATTG
1 ATTG
11057 CCATTACTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (31 bp):
ATTGTACCCTTATTTTAAAAACATATTTCAA
Found at i:11367 original size:11 final size:11
Alignment explanation
Indices: 11351--11393 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
11341 TATACTATAT
11351 CTAATTAATAG
1 CTAATTAATAG
*
11362 CTAATTAATAT
1 CTAATTAATAG
11373 CTAATTAATAG
1 CTAATTAATAG
*
11384 TTAATTAATA
1 CTAATTAATA
11394 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:11375 original size:22 final size:22
Alignment explanation
Indices: 11347--11393 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
11337 CCATTATACT
11347 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
11369 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
11391 ATA
1 ATA
11394 ATGAATAAAT
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:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:12336 original size:20 final size:22
Alignment explanation
Indices: 12313--12366 Score: 76
Period size: 20 Copynumber: 2.5 Consensus size: 22
12303 AGGATTACTA
*
12313 AAATTTAATAGAAGG-TTATC-
1 AAATTTCATAGAAGGATTATCG
*
12333 AAATCTCATAGAAGGATTATCG
1 AAATTTCATAGAAGGATTATCG
12355 AAATTTCATAGA
1 AAATTTCATAGA
12367 GATCAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 13 0.45
21 5 0.17
22 11 0.38
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.31
Consensus pattern (22 bp):
AAATTTCATAGAAGGATTATCG
Found at i:12516 original size:21 final size:22
Alignment explanation
Indices: 12466--12519 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
12456 GAGGGGTCAA
* *
12466 CAAAATTTTATAAAGAGATTAT
1 CAAAATTTCATAAAAAGATTAT
*
12488 CAAAATTTCATAAAAAGGTTAT
1 CAAAATTTCATAAAAAGATTAT
*
12510 CAAATTTTCA
1 CAAAATTTCA
12520 AAATGTGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAAAAAGATTAT
Found at i:12530 original size:44 final size:44
Alignment explanation
Indices: 12415--12543 Score: 120
Period size: 44 Copynumber: 2.9 Consensus size: 44
12405 TATCAATGCG
* * * * * *
12415 AGGTTATCAAAATTACATAATGTGATTATCATAATTTCATAGAG
1 AGGTTATCAAATTTTCAAAATGTGATTATCAAAATTTCATAAAA
* * * *
12459 GGGTCAACAAAATTTT-ATAAA-GAGATTATCAAAATTTCATAAAA
1 AGGTTATC-AAATTTTCA-AAATGTGATTATCAAAATTTCATAAAA
12503 AGGTTATCAAATTTTCAAAATGTGATTA-CAAAAATTTCATA
1 AGGTTATCAAATTTTCAAAATGTGATTATC-AAAATTTCATA
12544 GTGGTATTTC
Statistics
Matches: 66, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
43 11 0.17
44 48 0.73
45 7 0.11
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (44 bp):
AGGTTATCAAATTTTCAAAATGTGATTATCAAAATTTCATAAAA
Found at i:12586 original size:22 final size:21
Alignment explanation
Indices: 12559--12807 Score: 85
Period size: 22 Copynumber: 12.0 Consensus size: 21
12549 ATTTCTGGGG
12559 AGGTTATCAAAATTTCATAGT
1 AGGTTATCAAAATTTCATAGT
* *
12580 ATGGTTA-CCAAA--T--TAGCA
1 A-GGTTATCAAAATTTCATAG-T
* *
12598 AGGTTATTAAAATTTTATTA-T
1 AGGTTATCAAAATTTCA-TAGT
* *
12619 GGAGTTATCAAAATTT--TAGGG
1 AG-GTTATCAAAATTTCATA-GT
*
12640 AGGATATCAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATAG--T
* **
12663 A-GTTTTCAAAATTTCATAAA
1 AGGTTATCAAAATTTCATAGT
*
12683 AGGGTTATCAAAATTTCATAGGG
1 A-GGTTATCAAAATTTCATA-GT
* * *
12706 AGATTAACAAAATTTCATAAT
1 AGGTTATCAAAATTTCATAGT
** *
12727 GAGGTTATCAAAAAATCATAGGG
1 -AGGTTATCAAAATTTCATA-GT
* *
12750 AGGTAATTAAAA-TT--T-GT
1 AGGTTATCAAAATTTCATAGT
* *
12767 A-GTTATCAAGATTTCATAAGA
1 AGGTTATCAAAATTTCAT-AGT
* *
12788 AAGTTATCAAAATTTTATAG
1 AGGTTATCAAAATTTCATAG
12808 GGAGGTTTAT
Statistics
Matches: 164, Mismatches: 38, Indels: 52
0.65 0.15 0.20
Matches are distributed among these distances:
16 7 0.04
17 12 0.07
18 4 0.02
19 5 0.03
20 14 0.09
21 13 0.08
22 105 0.64
23 4 0.02
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.36
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGT
Found at i:12746 original size:66 final size:64
Alignment explanation
Indices: 12622--12746 Score: 146
Period size: 66 Copynumber: 1.9 Consensus size: 64
12612 TTATTATGGA
* * * * **
12622 GTTATCAAAATTTTAGGGAGGATATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAAAAGG
1 GTTATCAAAATTTTAGGGAGGATAACAAAATTTCATAGATGAGTTATCAAAAAATCATAAAAGG
12686 GTTATCAAAATTTCATAGGGA-GATTAACAAAATTTCATA-ATGAGGTTATCAAAAAATCATA
1 GTTATCAAAATTT--TAGGGAGGA-TAACAAAATTTCATAGATGA-GTTATCAAAAAATCATA
12747 GGGAGGTAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
64 13 0.25
65 4 0.08
66 34 0.67
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (64 bp):
GTTATCAAAATTTTAGGGAGGATAACAAAATTTCATAGATGAGTTATCAAAAAATCATAAAAGG
Found at i:12762 original size:44 final size:44
Alignment explanation
Indices: 12669--12764 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
12659 GTTTAGTTTT
** *
12669 CAAAATTTCATAAAAGGGTTATCAAAATTTCATAGGGAGATTAA
1 CAAAATTTCATAAAAGGGTTATCAAAAAATCATAGGGAGAGTAA
*
12713 CAAAATTTCAT-AATGAGGTTATCAAAAAATCATAGGGAG-GTAA
1 CAAAATTTCATAAAAG-GGTTATCAAAAAATCATAGGGAGAGTAA
*
12756 TTAAAATTT
1 -CAAAATTT
12765 GTAGTTATCA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
43 6 0.13
44 39 0.87
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (44 bp):
CAAAATTTCATAAAAGGGTTATCAAAAAATCATAGGGAGAGTAA
Found at i:12823 original size:25 final size:25
Alignment explanation
Indices: 12792--12849 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
12782 ATAAGAAAGT
* *
12792 TATCAAAATTTTATAGGGAGGTTTA
1 TATCAAAATTTTATAGGAAGATTTA
12817 TATCAAAATTTTATAGGAAGATTTA
1 TATCAAAATTTTATAGGAAGATTTA
12842 T-T-AAAATT
1 TATCAAAATT
12850 CAATAGCGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 6 0.19
24 1 0.03
25 24 0.77
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.41
Consensus pattern (25 bp):
TATCAAAATTTTATAGGAAGATTTA
Found at i:12877 original size:22 final size:22
Alignment explanation
Indices: 12817--12896 Score: 58
Period size: 22 Copynumber: 3.6 Consensus size: 22
12807 GGGAGGTTTA
* *
12817 TATCAAAATTTTATAG-GAAGATT
1 TATCAAAATTTCATAGCGTA-A-T
*
12840 TATTAAAA-TTCAATAGCG-AGAT
1 TATCAAAATTTC-ATAGCGTA-AT
* *
12862 TATCATAATTTCATAGTGTAAT
1 TATCAAAATTTCATAGCGTAAT
12884 TATCAAAATTTCA
1 TATCAAAATTTCA
12897 GAGTGTGGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
22 28 0.60
23 18 0.38
24 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (22 bp):
TATCAAAATTTCATAGCGTAAT
Found at i:12901 original size:22 final size:22
Alignment explanation
Indices: 12860--12902 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12850 CAATAGCGAG
* *
12860 ATTATCATAATTTCATAGTGTA
1 ATTATCAAAATTTCAGAGTGTA
12882 ATTATCAAAATTTCAGAGTGT
1 ATTATCAAAATTTCAGAGTGT
12903 GGTTACTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (22 bp):
ATTATCAAAATTTCAGAGTGTA
Found at i:13081 original size:22 final size:22
Alignment explanation
Indices: 13041--13097 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
13031 TTGAGATGTT
* * *
13041 CAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATAAGAAGGTTAA
13063 CAAAATTTCATAAGAAGGTTAA
1 CAAAATTTCATAAGAAGGTTAA
*
13085 AAGAAATTT-ATAA
1 CA-AAATTTCATAA
13098 AAAAGTTCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 24 0.80
23 6 0.20
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (22 bp):
CAAAATTTCATAAGAAGGTTAA
Found at i:13918 original size:28 final size:28
Alignment explanation
Indices: 13878--13934 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
13868 TTAAGATTTA
13878 AGCTTAATTTAATAAATCCCTTCCATCG
1 AGCTTAATTTAATAAATCCCTTCCATCG
13906 AGCTTAATTTAATAAATCCCTTCCATCG
1 AGCTTAATTTAATAAATCCCTTCCATCG
13934 A
1 A
13935 CTTTGACAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (28 bp):
AGCTTAATTTAATAAATCCCTTCCATCG
Found at i:16615 original size:16 final size:15
Alignment explanation
Indices: 16578--16620 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
16568 AGGTGGGTAA
*
16578 AAAAAAGAAAAAATT
1 AAAAAATAAAAAATT
* *
16593 ATGAAATTAAAAAATT
1 A-AAAAATAAAAAATT
16609 AAAAAATAAAAA
1 AAAAAATAAAAA
16621 GTAAATTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (15 bp):
AAAAAATAAAAAATT
Found at i:20811 original size:152 final size:153
Alignment explanation
Indices: 20531--21247 Score: 1035
Period size: 152 Copynumber: 4.7 Consensus size: 153
20521 ATTAAGCCCA
* ** *
20531 AACAAAGCTTTTCTTTCAATTATTTACGGCCTAACTATAATTATTTTCATGAGGTTAGTCCATTG
1 AACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATTATTTTGGTGAGATTAGTCCATTG
* * ** *
20596 TGAAGTTTTTCGCTCATTCAGAACATTTTTTTTCTAGCCTTTCGTGGCCCATTAGTGCTGTTTTG
66 TGAAGTTTTTAGCTCATTCAGAACACTTTTTTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTG
*
20661 AATCGTCCTCGATTTGGCAAACC
131 AATCGTCTTCGATTTGGCAAACC
* * * *
20684 -ACGAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTG
1 AACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATTATTTTGGTGAGATTAGTCCATTG
*
20748 TGAAGTTTTTAGCTCATTCAGAACACTTTTTTTCGGGCCGTTCGGGGCCCATTAGTGCTGTTTTG
66 TGAAGTTTTTAGCTCATTCAGAACACTTTTTTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTG
*
20813 AATCGTCTTCGATTTGGGAAACC
131 AATCGTCTTCGATTTGGCAAACC
* * *
20836 -ACATAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
1 AACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATTATTTTGGTGAGATTAGTCCATTG
* * *
20900 TGAAGTTTTTAACTCATTCAAAACACTTGTTATTTCGGGCCTTTCGAGGCCCATTAGTGCTGTTT
66 TGAAGTTTTTAGCTCATTCAGAACACTT-TT-TTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTT
* * * *
20965 TAAATCGGCTTCAATTTGGC-TACC
129 TGAATCGTCTTCGATTTGGCAAACC
* *
20989 AACAAAGCTTTTCTTTCAATTGTTTACGACCTAACTATAATCATTTTGGTGAGATTAGTCCATTG
1 AACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATTATTTTGGTGAGATTAGTCCATTG
* * * *
21054 TGAATTTTTTTAGCTCATTCAGAACAATTGTTATTTCGGGCCATTCGGGACCCATTAGTGCTGTT
66 TGAA-GTTTTTAGCTCATTCAGAACACTT-TT-TTTCGGGCCTTTCGGGGCCCATTAGTGCTGTT
*
21119 TTGAATCGTCTTCGATTTGGCAATCC
128 TTGAATCGTCTTCGATTTGGCAAACC
* *
21145 AACAAAGCTTTTCTTTCAATTATTTACAGCCTAACTATAATTATTTTGGTGAGATTAGTCCATTG
1 AACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATTATTTTGGTGAGATTAGTCCATTG
*
21210 TGAAGTTTTTAGCTCATGCAGAACACTTTTTTTTCGGG
66 TGAAGTTTTTAGCTCATTCAGAACAC-TTTTTTTCGGG
21248 AGTTTCTGAT
Statistics
Matches: 506, Mismatches: 52, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
152 221 0.44
153 5 0.01
154 119 0.24
155 92 0.18
156 69 0.14
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (153 bp):
AACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATTATTTTGGTGAGATTAGTCCATTG
TGAAGTTTTTAGCTCATTCAGAACACTTTTTTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTG
AATCGTCTTCGATTTGGCAAACC
Found at i:22141 original size:33 final size:33
Alignment explanation
Indices: 22115--22243 Score: 170
Period size: 33 Copynumber: 3.9 Consensus size: 33
22105 GGCCGGTTGA
* *
22115 GGCCGGACATGTCC-ATGTCGCGTGGCCGGTGTT
1 GGCCGGACATCTCCGA-GTCACGTGGCCGGTGTT
*
22148 GGCCGGGCATCTCCGAGTCACGTGGCCGGTGTT
1 GGCCGGACATCTCCGAGTCACGTGGCCGGTGTT
*
22181 GGCCGGGCATCTCCGAGTCACGTGGCCGGTGTT
1 GGCCGGACATCTCCGAGTCACGTGGCCGGTGTT
* * * *
22214 GGCCGGACTTCTCCAAGTCGCATGGCCGGT
1 GGCCGGACATCTCCGAGTCACGTGGCCGGT
22244 CACTAGTGCT
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
33 86 0.99
34 1 0.01
ACGTcount: A:0.10, C:0.30, G:0.38, T:0.22
Consensus pattern (33 bp):
GGCCGGACATCTCCGAGTCACGTGGCCGGTGTT
Found at i:22753 original size:153 final size:152
Alignment explanation
Indices: 22354--23049 Score: 1006
Period size: 153 Copynumber: 4.6 Consensus size: 152
22344 TAGCGCATCA
22354 CTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTT
1 CTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTT
* * * *
22419 CCATTGTTTATGGCCTAACTATAATTATTTTGATGGGATTAGTCCATTGTGAAGTTTTCAGCTCA
66 CCATTGTTTACGGCCTAACTATAATCATTTT-ATGAGATTAGTCCATTGTGAAGTTTTTAGCTCA
22484 TTCAGAACAC-TTT-TTTCGGGC
130 TTCAGAACACTTTTATTTCGGGC
* *
22505 CGTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGGAAACCACAAAGCTTTTCTTT
1 CTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTT
* * * *
22570 CCATTGTTTATGGCCTAACTATAATTATTTTCATGAGATTAGTCCATTGTGAAGTTTTTCGCTGA
66 CCATTGTTTACGGCCTAACTATAATCATTTT-ATGAGATTAGTCCATTGTGAAGTTTTTAGCTCA
22635 TTCAGAACACTTGTTATTTCGGGC
130 TTCAGAACACTT-TTATTTCGGGC
* * * * *
22659 CTTTCGAGGCACATTAGTGCTGTTTTAAATCGGCTTCAATTT-GC-AACCAACAAAGCTTTTCTT
1 CTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACC-ACAAAGCTTTTCTT
* * *
22722 TCAATTGTTTACGACCTAACTATAATCATTTTAGTGAGATTAGTCCATTGTGAAGTTTTTAGTTC
65 TCCATTGTTTACGGCCTAACTATAATCATTTTA-TGAGATTAGTCCATTGTGAAGTTTTTAGCTC
* *
22787 ATTTAGAACACTTGTTATTTCGGAC
129 ATTCAGAACACTT-TTATTTCGGGC
* *
22812 ATTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGCAAACCACAAAGCTTTTCTTT
1 CTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTT
* * *
22877 CCATTGTTTAAGGCCTAACTATAATCATTTATGTGAGATTAGTCCATTGCGAAGTTTTTAGCTCA
66 CCATTGTTTACGGCCTAACTATAATCATTT-TATGAGATTAGTCCATTGTGAAGTTTTTAGCTCA
* *
22942 TTCAGAACACTTTTTTTTCGGGA
130 TTCAGAACACTTTTATTTCGGGC
* * *
22965 GTTTCGGGGCCCAGTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCAAAAAGC-TTTCATT
1 CTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTC-TT
*
23029 TCAATTGTTTACGGCCTAACT
65 TCCATTGTTTACGGCCTAACT
23050 TGATGCGGCA
Statistics
Matches: 492, Mismatches: 44, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
151 133 0.27
152 10 0.02
153 215 0.44
154 129 0.26
155 5 0.01
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (152 bp):
CTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTT
CCATTGTTTACGGCCTAACTATAATCATTTTATGAGATTAGTCCATTGTGAAGTTTTTAGCTCAT
TCAGAACACTTTTATTTCGGGC
Found at i:23023 original size:307 final size:305
Alignment explanation
Indices: 22353--23049 Score: 1028
Period size: 307 Copynumber: 2.3 Consensus size: 305
22343 TTAGCGCATC
*
22353 ACTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTT
1 ACTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCAAAAAGCTTTTCTT
* * * *
22418 TCCATTGTTTATGGCCTAACTATAATTATTTTGATGGGATTAGTCCATTGTGAAGTTTTCAGCTC
66 TCAATTGTTTACGGCCTAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTCAGCTC
* * *
22483 ATTCAGAACACTTTTTTCGGGCCGTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTG
131 ATTCAGAACACTTTTTTCGGACAGTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTG
* * *
22548 GGAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTCATGAGATTAGT
196 GCAAACCACAAAGCTTTTCTTTCCATTGTTTAAGGCCTAACTATAATCATTTTCATGAGATTAGT
* * *
22613 CCATTGTGAAGTTTTTCGCTGATTCAGAACACTTGTTATTTCGGG
261 CCATTGCGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGG
* * * * * *
22658 CCTTTCGAGGCACATTAGTGCTGTTTTAAATCGGCTTCAATTT-GC-AACCAACAAAGCTTTTCT
1 ACTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCAA-AAAGCTTTTCT
* * *
22721 TTCAATTGTTTACGACCTAACTATAATCATTTT-AGTGAGATTAGTCCATTGTGAAGTTTTTAGT
65 TTCAATTGTTTACGGCCTAACTATAATCATTTTGA-TGAGATTAGTCCATTGTGAAGTTTTCAGC
* *
22785 TCATTTAGAACACTTGTTATTTCGGACATTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCG
129 TCATTCAGAACAC-T-TT-TTTCGGACAGTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCG
*
22850 ATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTAAGGCCTAACTATAATCATTTAT-GTGAG
191 ATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTAAGGCCTAACTATAATCATTT-TCATGAG
*
22914 ATTAGTCCATTGCGAAGTTTTTAGCTCATTCAGAACACTT-TTTTTTCGGG
255 ATTAGTCCATTGCGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGG
* *
22964 AGTTTCGGGGCCCAGTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCAAAAAGC-TTTCAT
1 ACTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCAAAAAGCTTTTC-T
23028 TTCAATTGTTTACGGCCTAACT
65 TTCAATTGTTTACGGCCTAACT
23050 TGATGCGGCA
Statistics
Matches: 347, Mismatches: 36, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
303 6 0.02
304 80 0.23
305 38 0.11
306 50 0.14
307 166 0.48
308 7 0.02
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (305 bp):
ACTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCAAAAAGCTTTTCTT
TCAATTGTTTACGGCCTAACTATAATCATTTTGATGAGATTAGTCCATTGTGAAGTTTTCAGCTC
ATTCAGAACACTTTTTTCGGACAGTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTG
GCAAACCACAAAGCTTTTCTTTCCATTGTTTAAGGCCTAACTATAATCATTTTCATGAGATTAGT
CCATTGCGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGG
Found at i:23197 original size:33 final size:33
Alignment explanation
Indices: 23160--23272 Score: 118
Period size: 33 Copynumber: 3.4 Consensus size: 33
23150 AGCACTAGTG
* * *
23160 ACCGGCCATGCGACTTGGAGAAGTCCAGCTAAC
1 ACCGGCCATGCGACTCGGAGAAGCCCAGCCAAC
* * *
23193 ACCGGCCATGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCATGCGACTCGGAGAAGCCCAGCCAAC
* * * *
23226 ACCGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCATGCGACTCGGAGAAGCCCAGCCAAC
* *
23259 AACGGCCACGCGAC
1 ACCGGCCATGCGAC
23273 ATGGACATGT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.24, C:0.36, G:0.29, T:0.11
Consensus pattern (33 bp):
ACCGGCCATGCGACTCGGAGAAGCCCAGCCAAC
Found at i:23289 original size:33 final size:33
Alignment explanation
Indices: 23190--23299 Score: 107
Period size: 33 Copynumber: 3.3 Consensus size: 33
23180 AAGTCCAGCT
* * * *
23190 AACACCGGCCATGTGACTCGGAGATGCCCGGCC
1 AACAACGGCCACGCGACTCGGACATGCCCGGCC
* * *
23223 AACACCGGCCACGTGACTCGGAGATGCCCGGCC
1 AACAACGGCCACGCGACTCGGACATGCCCGGCC
* *
23256 AACAACGGCCACGCGACAT-GGACATGTCTGGCC
1 AACAACGGCCACGCGAC-TCGGACATGCCCGGCC
23289 -ACAACCGGCCA
1 AACAA-CGGCCA
23300 TCGCTAGGCG
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
32 4 0.06
33 64 0.93
34 1 0.01
ACGTcount: A:0.25, C:0.37, G:0.28, T:0.10
Consensus pattern (33 bp):
AACAACGGCCACGCGACTCGGACATGCCCGGCC
Done.