Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020345.1 Corchorus olitorius cultivar O-4 contig20378, 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: 45815
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--28 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1 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
29 CCTACCTATT
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:700 original size:41 final size:41
Alignment explanation
Indices: 655--747 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
645 TCCTCCATTG
*
655 TTGAAGGATATTAAAGAATATATTTTTTAAAGGATTTATTT
1 TTGAAGGATATTAAAGAATATATTTCTTAAAGGATTTATTT
* *
696 TTGAAGGATATTTAAGAATGTATTTCTTAAAGGATTTATTT
1 TTGAAGGATATTAAAGAATATATTTCTTAAAGGATTTATTT
*
737 TTTAAGGATAT
1 TTGAAGGATAT
748 ATTATGATGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.37, C:0.01, G:0.16, T:0.46
Consensus pattern (41 bp):
TTGAAGGATATTAAAGAATATATTTCTTAAAGGATTTATTT
Found at i:702 original size:15 final size:15
Alignment explanation
Indices: 678--750 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
668 AAGAATATAT
678 TTTTTAAAGGATTTA
1 TTTTTAAAGGATTTA
*
693 TTTTTGAAGGA--TA
1 TTTTTAAAGGATTTA
* *
706 --TTT-AAGAATGTA
1 TTTTTAAAGGATTTA
718 TTTCTTAAAGGATTTA
1 TTT-TTAAAGGATTTA
* *
734 TTTTTTAAGGATATA
1 TTTTTAAAGGATTTA
749 TT
1 TT
751 ATGATGATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
10 4 0.09
11 3 0.07
12 2 0.04
13 2 0.04
14 1 0.02
15 24 0.52
16 10 0.22
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.51
Consensus pattern (15 bp):
TTTTTAAAGGATTTA
Found at i:2320 original size:355 final size:355
Alignment explanation
Indices: 1669--2380 Score: 1280
Period size: 355 Copynumber: 2.0 Consensus size: 355
1659 AGGCCCCTTT
1669 TGAGGATCGATGAGGAGGCTCCATTTGAACTTTTGTTGTCCTTTTCTGTCTTTTCTCACTTGCCA
1 TGAGGATCGATGAGGAGGCTCCATTTGAACTTTTGTTGTCCTTTTCTGTCTTTTCTCACTTGCCA
*
1734 AATTACTAAGAAGACCCTAGCTTAGTTTCTAGCCAGTTCTTACCCTTGAGCCATTTTTTGTAATT
66 AATTACTAAGAAGACCCTAGCTTAGTTTCTAGCCAGTTCTTACCCTTGAGCCATTTGTTGTAATT
*
1799 ATCCTTTCTTTTCACATAAATGTTATAATAACTCCTATCCCCCTTAATTATCTAGAATTGTAACC
131 ATCCTTTCTTTTCACATAAATGTTATAATAAATCCTATCCCCCTTAATTATCTAGAATTGTAACC
1864 TCTCTCCAGACCTTTCATGTCCATATGAAGAAGAGAGTAAACTTAGTTTTTGTTTAAGTACTACA
196 TCTCTCCAGACCTTTCATGTCCATATGAAGAAGAGAGTAAACTTAGTTTTTGTTTAAGTACTACA
* * *
1929 CACTTTAGAGGAGGAAATAAAATTGAAGTTATTGCACCTATCCATGTACAAACTAATATTTTTAA
261 CACTTTAGAAGAGGAAACAAAATTGAAGCTATTGCACCTATCCATGTACAAACTAATATTTTTAA
1994 TTTATTGCTAACTTTAGGGCATATACTCAA
326 TTTATTGCTAACTTTAGGGCATATACTCAA
* *
2024 TGAGGATCGATGAGGAGGCTCCATTTGAACTTTTTTTGTCTTTTTCTGTCTTTTCTCACTTGCCA
1 TGAGGATCGATGAGGAGGCTCCATTTGAACTTTTGTTGTCCTTTTCTGTCTTTTCTCACTTGCCA
* * *
2089 AATTACTAAGAAGACTCTAGGTTAGTTTCTAGCCAGTTCTTACCCTTGAGCCCTTTGTTGTAATT
66 AATTACTAAGAAGACCCTAGCTTAGTTTCTAGCCAGTTCTTACCCTTGAGCCATTTGTTGTAATT
2154 ATCCTTTCTTTTCACATAAATGTTATAATAAATCCTATCCCCCTTAATTATCTAGAATTGTAACC
131 ATCCTTTCTTTTCACATAAATGTTATAATAAATCCTATCCCCCTTAATTATCTAGAATTGTAACC
* * * *
2219 TCTTTTCAGGCCTTTCATGTCCATATGAAGAAGAGAGTAAACTTAGTTTTTGTTTAAGTGCTACA
196 TCTCTCCAGACCTTTCATGTCCATATGAAGAAGAGAGTAAACTTAGTTTTTGTTTAAGTACTACA
* *
2284 CACTTTAGAAGAGGAAACAAAATTGAAGCTATTGCACTTGTCCATGTACAAACTAATATTTTTAA
261 CACTTTAGAAGAGGAAACAAAATTGAAGCTATTGCACCTATCCATGTACAAACTAATATTTTTAA
2349 TTTATTGCTAACTTTAGGGCATATACTCAA
326 TTTATTGCTAACTTTAGGGCATATACTCAA
2379 TG
1 TG
2381 TTAATAGTAT
Statistics
Matches: 341, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
355 341 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (355 bp):
TGAGGATCGATGAGGAGGCTCCATTTGAACTTTTGTTGTCCTTTTCTGTCTTTTCTCACTTGCCA
AATTACTAAGAAGACCCTAGCTTAGTTTCTAGCCAGTTCTTACCCTTGAGCCATTTGTTGTAATT
ATCCTTTCTTTTCACATAAATGTTATAATAAATCCTATCCCCCTTAATTATCTAGAATTGTAACC
TCTCTCCAGACCTTTCATGTCCATATGAAGAAGAGAGTAAACTTAGTTTTTGTTTAAGTACTACA
CACTTTAGAAGAGGAAACAAAATTGAAGCTATTGCACCTATCCATGTACAAACTAATATTTTTAA
TTTATTGCTAACTTTAGGGCATATACTCAA
Found at i:4041 original size:2 final size:2
Alignment explanation
Indices: 4034--4061 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4024 GTACTTTTTA
4034 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
4062 TAGTATCATC
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:8919 original size:132 final size:133
Alignment explanation
Indices: 8712--8977 Score: 364
Period size: 132 Copynumber: 2.0 Consensus size: 133
8702 CATTGTTTAA
*
8712 ACTTTTATAGTTTTATTCAACTAAAAACTCTATTTTTATCTAATTAAATCTAATATCCTTATAAC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATCTAATTAAATCTAATATCCTTATAAC
* ** *
8777 TATTTAATTTTTACCATTTTACT-AT-TTTAATT-AAAAACTTTTATATATTA-AAATTTTTTAA
66 TATTTAATTTTTACCACTTTACTAATATTTAATTAAAAAACTTAGATATATTAGAAA-TTTTAAA
8838 ATAT
130 ATAT
*
8842 ACTTTTATA-TTATTACTCAACTAAAAACTCTATTTTTTATTTAAATTAAATCTAATATCCTTAT
1 ACTTTTATAGTT-TTACTCAACTAAAAACTCTA-TTTTTATCT-AATTAAATCTAATATCCTTAT
* **
8906 -ACATATTTTATTTTTATTACTTTACTAATATTTAATTAAAAAACTTAGATATATTAGAAATTTT
63 AAC-TATTTAATTTTTACCACTTTACTAATATTTAATTAAAAAACTTAGATATATTAGAAATTTT
8970 AAAATAT
127 AAAATAT
8977 A
1 A
8978 TTTCTTAAAT
Statistics
Matches: 119, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
129 2 0.02
130 28 0.24
131 10 0.08
132 40 0.34
133 2 0.02
134 7 0.06
135 27 0.23
136 3 0.03
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (133 bp):
ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATCTAATTAAATCTAATATCCTTATAAC
TATTTAATTTTTACCACTTTACTAATATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAA
TAT
Found at i:10374 original size:19 final size:21
Alignment explanation
Indices: 10341--10380 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
10331 TCCTAGAAAC
10341 AATTGTTTTCTTCTAGTTTTT
1 AATTGTTTTCTTCTAGTTTTT
10362 AATT-TTTTC-TCTAGTTTTT
1 AATTGTTTTCTTCTAGTTTTT
10381 GAAGGGGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 5 0.26
21 4 0.21
ACGTcount: A:0.15, C:0.10, G:0.07, T:0.68
Consensus pattern (21 bp):
AATTGTTTTCTTCTAGTTTTT
Found at i:11258 original size:16 final size:18
Alignment explanation
Indices: 11226--11258 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
11216 TTTGATTTAG
11226 TTTTGCTTTATTAATTGC
1 TTTTGCTTTATTAATTGC
11244 TTTT-CTTTA-TAATTG
1 TTTTGCTTTATTAATTG
11259 GTATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (18 bp):
TTTTGCTTTATTAATTGC
Found at i:12300 original size:30 final size:30
Alignment explanation
Indices: 12246--12330 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
12236 GGCCTAGACG
* * * * *
12246 TTCGTCGTTCCGTTCCCAAGGTCCTGGACG
1 TTCGTCATTCCTTTGCCAAAGTCCTGGACA
* * *
12276 TTTGTCCTTCCTTTGTCAAAGTCCTGGACA
1 TTCGTCATTCCTTTGCCAAAGTCCTGGACA
*
12306 TTCGTCATTCCTTTGCCAAGGTCCT
1 TTCGTCATTCCTTTGCCAAAGTCCT
12331 CAAAATCGGA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.13, C:0.31, G:0.20, T:0.36
Consensus pattern (30 bp):
TTCGTCATTCCTTTGCCAAAGTCCTGGACA
Found at i:13782 original size:15 final size:15
Alignment explanation
Indices: 13762--13793 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
13752 GCCGGTTGCT
13762 AGTACCTTTATTAGC
1 AGTACCTTTATTAGC
13777 AGTACCTTTATTAGC
1 AGTACCTTTATTAGC
13792 AG
1 AG
13794 CTCAAAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (15 bp):
AGTACCTTTATTAGC
Found at i:15216 original size:29 final size:29
Alignment explanation
Indices: 15174--15232 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
15164 TGTATTGTGG
15174 TGGGTTGGGTAGGTTTTGGAAGCAGAGCT
1 TGGGTTGGGTAGGTTTTGGAAGCAGAGCT
15203 TGGGTTGGGTAGGTTTTGGAAGCAGAGCT
1 TGGGTTGGGTAGGTTTTGGAAGCAGAGCT
15232 T
1 T
15233 TTCAAGTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.07, G:0.44, T:0.32
Consensus pattern (29 bp):
TGGGTTGGGTAGGTTTTGGAAGCAGAGCT
Found at i:15528 original size:201 final size:201
Alignment explanation
Indices: 15183--15585 Score: 806
Period size: 201 Copynumber: 2.0 Consensus size: 201
15173 GTGGGTTGGG
15183 TAGGTTTTGGAAGCAGAGCTTGGGTTGGGTAGGTTTTGGAAGCAGAGCTTTTCAAGTGTGTGAAA
1 TAGGTTTTGGAAGCAGAGCTTGGGTTGGGTAGGTTTTGGAAGCAGAGCTTTTCAAGTGTGTGAAA
15248 AACAAGTACGGAGAAGGTTAGGAAGGTTTCATGATGAGTAAGCTTGTTCCTGTGGTGAGAAATAT
66 AACAAGTACGGAGAAGGTTAGGAAGGTTTCATGATGAGTAAGCTTGTTCCTGTGGTGAGAAATAT
15313 TAGCCAATCTGACTTGGGATGGAACAAGACAAGACTTAGCTTAGCTATAGCAATCAAGGAAAATG
131 TAGCCAATCTGACTTGGGATGGAACAAGACAAGACTTAGCTTAGCTATAGCAATCAAGGAAAATG
15378 TTCACA
196 TTCACA
15384 TAGGTTTTGGAAGCAGAGCTTGGGTTGGGTAGGTTTTGGAAGCAGAGCTTTTCAAGTGTGTGAAA
1 TAGGTTTTGGAAGCAGAGCTTGGGTTGGGTAGGTTTTGGAAGCAGAGCTTTTCAAGTGTGTGAAA
15449 AACAAGTACGGAGAAGGTTAGGAAGGTTTCATGATGAGTAAGCTTGTTCCTGTGGTGAGAAATAT
66 AACAAGTACGGAGAAGGTTAGGAAGGTTTCATGATGAGTAAGCTTGTTCCTGTGGTGAGAAATAT
15514 TAGCCAATCTGACTTGGGATGGAACAAGACAAGACTTAGCTTAGCTATAGCAATCAAGGAAAATG
131 TAGCCAATCTGACTTGGGATGGAACAAGACAAGACTTAGCTTAGCTATAGCAATCAAGGAAAATG
15579 TTCACA
196 TTCACA
15585 T
1 T
15586 CACTACAACA
Statistics
Matches: 202, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 202 1.00
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.28
Consensus pattern (201 bp):
TAGGTTTTGGAAGCAGAGCTTGGGTTGGGTAGGTTTTGGAAGCAGAGCTTTTCAAGTGTGTGAAA
AACAAGTACGGAGAAGGTTAGGAAGGTTTCATGATGAGTAAGCTTGTTCCTGTGGTGAGAAATAT
TAGCCAATCTGACTTGGGATGGAACAAGACAAGACTTAGCTTAGCTATAGCAATCAAGGAAAATG
TTCACA
Found at i:15654 original size:34 final size:34
Alignment explanation
Indices: 15616--15686 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
15606 TGCATAAGTA
15616 TATGCCTCTGAAAATTAATTATGGTTGCTAAATC
1 TATGCCTCTGAAAATTAATTATGGTTGCTAAATC
15650 TATGCCTCTGAAAATTAATTATGGTTGCTAAATC
1 TATGCCTCTGAAAATTAATTATGGTTGCTAAATC
15684 TAT
1 TAT
15687 TTAGAGGCAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (34 bp):
TATGCCTCTGAAAATTAATTATGGTTGCTAAATC
Found at i:19410 original size:24 final size:24
Alignment explanation
Indices: 19383--19435 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
19373 AGCGATGTGT
*
19383 TTTTTATGGATATTTAAGAATGTA
1 TTTTTAAGGATATTTAAGAATGTA
*
19407 TTTTGAAGGATATTTAAGAATGTA
1 TTTTTAAGGATATTTAAGAATGTA
19431 TTTTT
1 TTTTT
19436 TAAAGGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
TTTTTAAGGATATTTAAGAATGTA
Found at i:19452 original size:41 final size:41
Alignment explanation
Indices: 19407--19484 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
19397 TAAGAATGTA
19407 TTTTGAAGGATATTTAAGAATGTATTTTTTAAAGGATTTAG
1 TTTTGAAGGATATTTAAGAATGTATTTTTTAAAGGATTTAG
19448 TTTTGAAGGATATTTAAGAATGTATTTTTTAAAGGAT
1 TTTTGAAGGATATTTAAGAATGTATTTTTTAAAGGAT
19485 ATATATACTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (41 bp):
TTTTGAAGGATATTTAAGAATGTATTTTTTAAAGGATTTAG
Found at i:20726 original size:32 final size:32
Alignment explanation
Indices: 20690--20753 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
20680 AAACTCCAGA
20690 AGATTAAACCCCCTACAACACCCTCCACATAG
1 AGATTAAACCCCCTACAACACCCTCCACATAG
*
20722 AGATTAAACCCCCTGCAACACCCTCCACATAG
1 AGATTAAACCCCCTACAACACCCTCCACATAG
20754 CCACCGCCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.41, G:0.08, T:0.16
Consensus pattern (32 bp):
AGATTAAACCCCCTACAACACCCTCCACATAG
Found at i:28965 original size:2 final size:2
Alignment explanation
Indices: 28958--28988 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28948 GAGACTTCAA
28958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28989 ATGTAATGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34697 original size:18 final size:19
Alignment explanation
Indices: 34673--34739 Score: 77
Period size: 18 Copynumber: 3.6 Consensus size: 19
34663 TTAAATATAT
34673 ATTATTATTTATT-TTTAA
1 ATTATTATTTATTATTTAA
*
34691 CTTATTATTTATTATTTAA
1 ATTATTATTTATTATTTAA
*
34710 AATA-TATTTATTATTT-A
1 ATTATTATTTATTATTTAA
*
34727 TTTATTTATTTAT
1 ATTA-TTATTTAT
34740 AGTAAAACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
17 3 0.07
18 24 0.59
19 14 0.34
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTATTATTTATTATTTAA
Found at i:34702 original size:7 final size:7
Alignment explanation
Indices: 34674--34736 Score: 51
Period size: 7 Copynumber: 8.7 Consensus size: 7
34664 TAAATATATA
34674 TTATTAT
1 TTATTAT
34681 TTATT-T
1 TTATTAT
*
34687 TTA--AC
1 TTATTAT
34692 TTATTAT
1 TTATTAT
34699 TTATTAT
1 TTATTAT
34706 TTAAAATATAT
1 TT---AT-TAT
34717 TTATTAT
1 TTATTAT
34724 TTATTTAT
1 TTA-TTAT
34732 TTATT
1 TTATT
34737 TATAGTAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
5 3 0.07
6 4 0.09
7 23 0.50
8 9 0.20
10 2 0.04
11 5 0.11
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (7 bp):
TTATTAT
Found at i:34740 original size:25 final size:25
Alignment explanation
Indices: 34667--34740 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
34657 TAGTAATTAA
*
34667 ATATATATTA-TTATTTA-TT-TTT
1 ATATTTATTATTTATTTATTTATTT
* **
34689 A-ACTTATTATTTA-TTATTTAAAAT
1 ATATTTATTATTTATTTATTT-ATTT
34713 ATATTTATTATTTATTTATTTATTT
1 ATATTTATTATTTATTTATTTATTT
34738 ATA
1 ATA
34741 GTAAAACTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
21 9 0.23
22 6 0.15
24 2 0.05
25 16 0.41
26 6 0.15
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (25 bp):
ATATTTATTATTTATTTATTTATTT
Found at i:36665 original size:13 final size:13
Alignment explanation
Indices: 36647--36671 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36637 TATAAATTCC
36647 AAATAATATTTAT
1 AAATAATATTTAT
36660 AAATAATATTTA
1 AAATAATATTTA
36672 GAACATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:37612 original size:29 final size:29
Alignment explanation
Indices: 37569--37649 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
37559 CTTCAGCCAG
* *
37569 AAAAAAAGTAGTAATTAATCACT-TTGGCC
1 AAAAAAAGTACTAATTAATCACTCCT-GCC
*
37598 AAAAAAAGTACTAATTAATAACTCCTGCC
1 AAAAAAAGTACTAATTAATCACTCCTGCC
37627 AGAAAAAAGTACTAATTAATCAC
1 A-AAAAAAGTACTAATTAATCAC
37650 AAAAGGAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 25 0.54
30 21 0.46
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.25
Consensus pattern (29 bp):
AAAAAAAGTACTAATTAATCACTCCTGCC
Found at i:37901 original size:19 final size:19
Alignment explanation
Indices: 37877--37932 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
37867 CTTATTTGTA
*
37877 ACCGTTTCACCATCGTTTG
1 ACCGTTTCACCACCGTTTG
37896 ACCGTTTCACCACCGTTTG
1 ACCGTTTCACCACCGTTTG
*
37915 ACCGTTTCACCACTGTTT
1 ACCGTTTCACCACCGTTT
37933 TGGGTCCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.16, C:0.34, G:0.14, T:0.36
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Found at i:38008 original size:21 final size:19
Alignment explanation
Indices: 37983--38040 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
37973 GCTGCTCTAA
37983 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* * *
38004 TAATCTAATTTGTACAGTG
1 TAATCTCATCTGTACAGTC
38023 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
38041 TGCTAAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:39259 original size:21 final size:21
Alignment explanation
Indices: 39234--39276 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39224 ATGTTGAAAA
**
39234 TTTGGTGGGCCAAGTTTTAAT
1 TTTGGTGAACCAAGTTTTAAT
*
39255 TTTGGTGAACCCAGTTTTAAT
1 TTTGGTGAACCAAGTTTTAAT
39276 T
1 T
39277 ATATACAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.23, T:0.44
Consensus pattern (21 bp):
TTTGGTGAACCAAGTTTTAAT
Found at i:44789 original size:2 final size:2
Alignment explanation
Indices: 44782--44828 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
44772 GAGAATTTGG
* *
44782 TA TA TA TA TA CA TA TA TA TA TA TA TA TA AA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44822 TA -A TA TA
1 TA TA TA TA
44829 ATACCATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:45368 original size:13 final size:13
Alignment explanation
Indices: 45334--45373 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
45324 TAATCAAATC
45334 ATAA-TTTTTTA-
1 ATAATTTTTTTAT
45345 A-AATTTATTTTAT
1 ATAATTT-TTTTAT
45358 ATAATTTTTTTAT
1 ATAATTTTTTTAT
45371 ATA
1 ATA
45374 TAATTAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.08
11 3 0.12
12 5 0.20
13 10 0.40
14 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATAATTTTTTTAT
Found at i:45575 original size:22 final size:22
Alignment explanation
Indices: 45544--45585 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
45534 AGAGACAAGA
*
45544 AATTGTCAACTATGAAAGTCGC
1 AATTGACAACTATGAAAGTCGC
45566 AATTGACAACTATGAAAGTC
1 AATTGACAACTATGAAAGTC
45586 ACAGTGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (22 bp):
AATTGACAACTATGAAAGTCGC
Done.