Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014843.1 Corchorus olitorius cultivar O-4 contig14876, 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: 65793
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:297 original size:34 final size:34
Alignment explanation
Indices: 233--299 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
223 AAAAGAAGAT
* ** *
233 TATATATTTTTTATGTTATACGTTATAAATTAAA
1 TATATATATTTTATGTTATACACTACAAATTAAA
*
267 TATATATATTTTATGTTATATACTACAAATTAA
1 TATATATATTTTATGTTATACACTACAAATTAA
300 TGTAATTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (34 bp):
TATATATATTTTATGTTATACACTACAAATTAAA
Found at i:958 original size:14 final size:14
Alignment explanation
Indices: 939--965 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
929 ATTTTAAGAG
939 AAGTAATTACCAAC
1 AAGTAATTACCAAC
953 AAGTAATTACCAA
1 AAGTAATTACCAA
966 AAACTCAACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (14 bp):
AAGTAATTACCAAC
Found at i:3230 original size:141 final size:141
Alignment explanation
Indices: 2972--3265 Score: 419
Period size: 141 Copynumber: 2.1 Consensus size: 141
2962 TCTTCCCATG
* ** ** * * *
2972 TCTTCAGGCAACTCAACAAGCTCTTGACATTGATATAATTTTAATGTTCGCAAGTTTTGCAATGT
1 TCTTCAGGCAACACAACAAGCTCTCCACATCCATATAATTTTAATGTTCGCAAATTATACAATGT
3037 ACACAAAGAGCTTGGCAACCACTCAATAGAAGTTCTAGAGAGATCCAAATATCTCAAATGCCTCA
66 ACACAAAGAGCTTGGCAACCACTCAATAGAAGTTCTAGAGAGATCCAAATATCTCAAATGCCTCA
*
3102 ATTTACCAATT
131 ATTCACCAATT
*
3113 TCTTCAGGCAACACAACAAGCTCTCCACATCCATATAATTTTAATGTTTGCAAATTATACAATGT
1 TCTTCAGGCAACACAACAAGCTCTCCACATCCATATAATTTTAATGTTCGCAAATTATACAATGT
* * * * * **
3178 ACGCAAAGAGCTTGGCAACCTCTTAAT-GTAAGTTTTAGAGAGATCCAGATATCTCAAATGTTTC
66 ACACAAAGAGCTTGGCAACCACTCAATAG-AAGTTCTAGAGAGATCCAAATATCTCAAATGCCTC
3242 AATTCACCAATT
130 AATTCACCAATT
3254 TCTTCAGGCAAC
1 TCTTCAGGCAAC
3266 TCATTGATAT
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
140 1 0.01
141 134 0.99
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (141 bp):
TCTTCAGGCAACACAACAAGCTCTCCACATCCATATAATTTTAATGTTCGCAAATTATACAATGT
ACACAAAGAGCTTGGCAACCACTCAATAGAAGTTCTAGAGAGATCCAAATATCTCAAATGCCTCA
ATTCACCAATT
Found at i:5048 original size:12 final size:12
Alignment explanation
Indices: 5031--5055 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5021 GCGCTTGCCA
5031 TTTTTTCTTTTT
1 TTTTTTCTTTTT
5043 TTTTTTCTTTTT
1 TTTTTTCTTTTT
5055 T
1 T
5056 CTGGTATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:5758 original size:21 final size:21
Alignment explanation
Indices: 5732--5772 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5722 TGTTTGTGAT
5732 TAATTACAA-AACATTTTTAAC
1 TAATTA-AAGAACATTTTTAAC
5753 TAATTAAAGAACATTTTTAA
1 TAATTAAAGAACATTTTTAA
5773 TTTATGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (21 bp):
TAATTAAAGAACATTTTTAAC
Found at i:6689 original size:26 final size:26
Alignment explanation
Indices: 6635--6690 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
6625 GTAGAGTAAC
* *
6635 AAAATGTGAAATTTATTATCTCAAAA
1 AAAATGTGAAATTTATGATCTAAAAA
*
6661 AAAATGTGAAATTTATGAT-TAAAAG
1 AAAATGTGAAATTTATGATCTAAAAA
6686 AAAAT
1 AAAAT
6691 TATTTAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.32
Consensus pattern (26 bp):
AAAATGTGAAATTTATGATCTAAAAA
Found at i:8506 original size:20 final size:19
Alignment explanation
Indices: 8468--8517 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
8458 AATACTAACA
8468 AATACATAATAAATAATAAT
1 AATAC-TAATAAATAATAAT
*
8488 AATACTAATAATATTATAAT
1 AATACTAATAA-ATAATAAT
8508 AATACTAATA
1 AATACTAATA
8518 CTTCCAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (19 bp):
AATACTAATAAATAATAAT
Found at i:8573 original size:13 final size:13
Alignment explanation
Indices: 8557--8581 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8547 TAACATAAAA
8557 AATTATTTTTTAT
1 AATTATTTTTTAT
8570 AATTATTTTTTA
1 AATTATTTTTTA
8582 AAAAAATTGA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
AATTATTTTTTAT
Found at i:10693 original size:2 final size:2
Alignment explanation
Indices: 10686--10765 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
10676 TCTTAATATT
10686 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
10728 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
10766 AGTAAGAAAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:22822 original size:18 final size:18
Alignment explanation
Indices: 22799--22942 Score: 146
Period size: 18 Copynumber: 8.4 Consensus size: 18
22789 AAGGGCTAAA
22799 AAACAGGACCGAAAGGTC
1 AAACAGGACCGAAAGGTC
22817 AAACAGGACCGAAAGGTC
1 AAACAGGACCGAAAGGTC
22835 AAACAGGACCGAAAGGTC
1 AAACAGGACCGAAAGGTC
22853 AAACAGGACC-AAGAGGTC
1 AAACAGGACCGAA-AGGTC
* * *
22871 GAACA--A--G-CA-G-A
1 AAACAGGACCGAAAGGTC
22882 AAACAGGACC-AAAGAGTC
1 AAACAGGACCGAAAG-GTC
*
22900 AAACAGGACCAAAAGGTC
1 AAACAGGACCGAAAGGTC
22918 AAACAGGACC-AAGAGGTC
1 AAACAGGACCGAA-AGGTC
*
22936 TAACAGG
1 AAACAGG
22943 CAGAAAATAG
Statistics
Matches: 107, Mismatches: 7, Indels: 24
0.78 0.05 0.17
Matches are distributed among these distances:
11 4 0.04
12 1 0.01
13 2 0.02
15 1 0.01
16 1 0.01
17 5 0.05
18 89 0.83
19 4 0.04
ACGTcount: A:0.47, C:0.22, G:0.26, T:0.06
Consensus pattern (18 bp):
AAACAGGACCGAAAGGTC
Found at i:22839 original size:36 final size:36
Alignment explanation
Indices: 22799--22942 Score: 162
Period size: 36 Copynumber: 4.2 Consensus size: 36
22789 AAGGGCTAAA
22799 AAACAGGACCGAAAGGTCAAACAGGACCGAA-AGGTC
1 AAACAGGACCGAAAGGTCAAACAGGACC-AAGAGGTC
22835 AAACAGGACCGAAAGGTCAAACAGGACCAAGAGGTC
1 AAACAGGACCGAAAGGTCAAACAGGACCAAGAGGTC
* * *
22871 GAACA--A--G-CA-G-AAAACAGGACCAA-AGAGTC
1 AAACAGGACCGAAAGGTCAAACAGGACCAAGAG-GTC
*
22900 AAACAGGACCAAAAGGTCAAACAGGACCAAGAGGTC
1 AAACAGGACCGAAAGGTCAAACAGGACCAAGAGGTC
*
22936 TAACAGG
1 AAACAGG
22943 CAGAAAATAG
Statistics
Matches: 90, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
28 2 0.02
29 19 0.21
30 1 0.01
31 2 0.02
32 1 0.01
34 2 0.02
35 3 0.03
36 58 0.64
37 2 0.02
ACGTcount: A:0.47, C:0.22, G:0.26, T:0.06
Consensus pattern (36 bp):
AAACAGGACCGAAAGGTCAAACAGGACCAAGAGGTC
Found at i:22903 original size:65 final size:64
Alignment explanation
Indices: 22817--22975 Score: 239
Period size: 65 Copynumber: 2.5 Consensus size: 64
22807 CCGAAAGGTC
*
22817 AAACAGGACCGAAAGGTCAAACAGGACCGAAAGGTCAAACAGGACCAAGAGGTCGAACAAGCAGA
1 AAACAGGACC-AAAGGTCAAACAGGACCAAAAGGTCAAACAGGACCAAGAGGTCGAACAAGCAGA
* *
22882 AAACAGGACCAAAGAGTCAAACAGGACCAAAAGGTCAAACAGGACCAAGAGGTCTAACAGGCAGA
1 AAACAGGACCAAAG-GTCAAACAGGACCAAAAGGTCAAACAGGACCAAGAGGTCGAACAAGCAGA
* * *
22947 AAATAGGACGAAAGGTCAAAC-GGAGCAAA
1 AAACAGGACCAAAGGTCAAACAGGACCAAA
22976 CTTCTTCATC
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
63 7 0.08
64 11 0.13
65 69 0.79
ACGTcount: A:0.48, C:0.20, G:0.26, T:0.06
Consensus pattern (64 bp):
AAACAGGACCAAAGGTCAAACAGGACCAAAAGGTCAAACAGGACCAAGAGGTCGAACAAGCAGA
Found at i:23098 original size:13 final size:13
Alignment explanation
Indices: 23077--23115 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
23067 GAGGTCAAAG
23077 TCAACAGTCAACTC
1 TCAA-AGTCAACTC
**
23091 TCAAAGTCAACGG
1 TCAAAGTCAACTC
23104 TCAAAGTCAACT
1 TCAAAGTCAACT
23116 AGATGATGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.21
Consensus pattern (13 bp):
TCAAAGTCAACTC
Found at i:23200 original size:13 final size:13
Alignment explanation
Indices: 23182--23206 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23172 TGGTCAACGG
23182 ATGATGTGGCAGC
1 ATGATGTGGCAGC
23195 ATGATGTGGCAG
1 ATGATGTGGCAG
23207 GTTGACTCGG
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:0.24, C:0.12, G:0.40, T:0.24
Consensus pattern (13 bp):
ATGATGTGGCAGC
Found at i:23269 original size:49 final size:49
Alignment explanation
Indices: 23175--23270 Score: 120
Period size: 49 Copynumber: 2.0 Consensus size: 49
23165 GGTTGACTGG
* ** * *
23175 TCAACGGATGATGTGGCAGCATGATGTGGCAGGTTGACTCGGTCAACGA
1 TCAACGGATGACGTGGCAGCATGACATGGCAAGTTGACTCAGTCAACGA
* * *
23224 TCAATGGATGACGTGGCAGGATGACATGGCAAGTTGACTTAGTCAAC
1 TCAACGGATGACGTGGCAGCATGACATGGCAAGTTGACTCAGTCAAC
23271 AGTGATGACG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (49 bp):
TCAACGGATGACGTGGCAGCATGACATGGCAAGTTGACTCAGTCAACGA
Found at i:23277 original size:77 final size:78
Alignment explanation
Indices: 23108--23277 Score: 170
Period size: 77 Copynumber: 2.2 Consensus size: 78
23098 CAACGGTCAA
* * *
23108 AGTCAACTAGATGATGTGGCATGTTGACCCAGTCAACGGTCAACGAATGACGTGGCAGGTTGACT
1 AGTCAAC-AG-TGATGTGGCAGGTTGACCCAGTCAACGATCAACGAATGACGTGGCAGGATGACT
23173 GGTCAACGGATGATGT
64 GGTCAAC-GATGATGT
* * * * * *
23189 -GGCAGCA-TGATGTGGCAGGTTGACTCGGTCAACGATCAATGGATGACGTGGCAGGATGACATG
1 AGTCAACAGTGATGTGGCAGGTTGACCCAGTCAACGATCAACGAATGACGTGGCAGGATGAC-TG
*
23252 G-CAA-GTTGACT-T
65 GTCAACGATGA-TGT
23264 AGTCAACAGTGATG
1 AGTCAACAGTGATG
23278 ACGTGGCAGC
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
75 5 0.07
76 6 0.08
77 54 0.74
78 3 0.04
79 1 0.01
80 4 0.05
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (78 bp):
AGTCAACAGTGATGTGGCAGGTTGACCCAGTCAACGATCAACGAATGACGTGGCAGGATGACTGG
TCAACGATGATGT
Found at i:31248 original size:28 final size:28
Alignment explanation
Indices: 31208--31266 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
31198 TTTGTAAACT
31208 AGTGCTTAATCTAATCTGTCAGTTTCCC
1 AGTGCTTAATCTAATCTGTCAGTTTCCC
31236 AGTGCTTAATCTAATCTGTCAGTTTCCC
1 AGTGCTTAATCTAATCTGTCAGTTTCCC
31264 AGT
1 AGT
31267 TTCTATCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (28 bp):
AGTGCTTAATCTAATCTGTCAGTTTCCC
Found at i:37148 original size:351 final size:352
Alignment explanation
Indices: 36483--37183 Score: 1070
Period size: 351 Copynumber: 2.0 Consensus size: 352
36473 TCCAAAACAT
* * *
36483 TCTCCAAGTCGGTTTAGGAGAAGATCAATTCTGTCCAGAAATTTCAAAGGCAAAATCGTCCACTA
1 TCTCCAAATCGGTTTAGGAGAAGATCAATTCTATCCAGAAATTTCAAAGGCAAAATCGTCCACGA
* * *
36548 GAACTGCAGAATTAGGTCTCAAGGTAAACATAAAAGTTGTAAATCTTGGAATCCTCTTTCCAATG
66 GAACTACAGAATTAGGTCTCAAGGTAAACATAAAAGTTGTAAATCTTGGAATCCTCTGTCCAACG
* *
36613 GTATCTCATTTGCATTTTTTCTGAGCTCTAGATGAAAAATTATAAATTTTTTTCCAAAACTGCTC
131 GTATCTCATTTGCATTTTTTCTGAGCTCTAGATCAAAAATTATAAATTTTCTTCCAAAACTGCTC
* *
36678 TTGTAAAGTCCTTTTTTGAATATGATTTAACAATGCTGCATCGGGACTGAACCATTACTGCATCA
196 TTGTAAAGTCCTTCTTTGAATATGATTTAACAATGCTGCATAGGGACTGAACCATTACTGCATCA
* * *
36743 TAATTACTGATTGGACTTGGACTCCTTCTTTGGTCTTCCATATTAACGAATTGGGTCTAAGAATA
261 TAATTACTGATTGGACTTGAACTCCTTCTTTGGGCTTCCATATTAACAAATTGGGTCTAAGAATA
** *
36808 TCAGATTTAGGTTTCAAGACATCTGGC
326 TCAGATTTAGACTTCAAAACATCTGGC
* * *
36835 TCTCCAAATCGGTTTAGGAGAAGATCAATTCTATCTAGAAATTTCAAGGGCAAAATCGTCTACCG
1 TCTCCAAATCGGTTTAGGAGAAGATCAATTCTATCCAGAAATTTCAAAGGCAAAATCGTCCA-CG
* * *
36900 A-AACTACAGAATTAGGTCTCAAGGTAAACATAAAAGTTGTAGATCTTGGAATTCTCTGTCTAAC
65 AGAACTACAGAATTAGGTCTCAAGGTAAACATAAAAGTTGTAAATCTTGGAATCCTCTGTCCAAC
* *
36964 GGTATCTCATTTGCA-TTTTTCTGAGCTCTGGATCAAAAGTTATGAAA-TTTCTTCCAAAACTGC
130 GGTATCTCATTTGCATTTTTTCTGAGCTCTAGATCAAAAATTAT-AAATTTTCTTCCAAAACTGC
*
37027 TCTTGTAAAGT-CTTCCTTTGAATATGATTTAACAATGCTGCATTAGGG-CTGAATCATTACTGC
194 TCTTGTAAAGTCCTT-CTTTGAATATGATTTAACAATGCTGCA-TAGGGACTGAACCATTACTGC
** *
37090 ATCATAATTACTGATTGGTTTTGAACTCCTTCTTTGGGCTTCTATATTAACAAATTGGGTCTAAG
257 ATCATAATTACTGATTGGACTTGAACTCCTTCTTTGGGCTTCCATATTAACAAATTGGGTCTAAG
*
37155 ATTATCAGATTTAGACTTCAAAACATCTG
322 AATATCAGATTTAGACTTCAAAACATCTG
37184 ACTTGCCAAT
Statistics
Matches: 316, Mismatches: 29, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
350 3 0.01
351 175 0.55
352 136 0.43
353 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (352 bp):
TCTCCAAATCGGTTTAGGAGAAGATCAATTCTATCCAGAAATTTCAAAGGCAAAATCGTCCACGA
GAACTACAGAATTAGGTCTCAAGGTAAACATAAAAGTTGTAAATCTTGGAATCCTCTGTCCAACG
GTATCTCATTTGCATTTTTTCTGAGCTCTAGATCAAAAATTATAAATTTTCTTCCAAAACTGCTC
TTGTAAAGTCCTTCTTTGAATATGATTTAACAATGCTGCATAGGGACTGAACCATTACTGCATCA
TAATTACTGATTGGACTTGAACTCCTTCTTTGGGCTTCCATATTAACAAATTGGGTCTAAGAATA
TCAGATTTAGACTTCAAAACATCTGGC
Found at i:37774 original size:17 final size:17
Alignment explanation
Indices: 37752--37787 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
37742 CAGTACCATC
37752 CTATACCAACATGATTA
1 CTATACCAACATGATTA
37769 CTATACCAACATGATTA
1 CTATACCAACATGATTA
37786 CT
1 CT
37788 CAGGCTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.31
Consensus pattern (17 bp):
CTATACCAACATGATTA
Found at i:39309 original size:19 final size:21
Alignment explanation
Indices: 39281--39320 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
39271 ATATAATAAT
*
39281 TTAATTATTT-AATT-TTTTA
1 TTAATAATTTCAATTATTTTA
39300 TTAATAATTTCAATTATTTTA
1 TTAATAATTTCAATTATTTTA
39321 ATATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 4 0.22
21 5 0.28
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
TTAATAATTTCAATTATTTTA
Found at i:39309 original size:27 final size:30
Alignment explanation
Indices: 39274--39328 Score: 89
Period size: 27 Copynumber: 1.9 Consensus size: 30
39264 CAATACAATA
39274 TAATAATTT-AATTA-TTTAAT-TTTTTAT
1 TAATAATTTCAATTATTTTAATATTTTTAT
39301 TAATAATTTCAATTATTTTAATATTTTT
1 TAATAATTTCAATTATTTTAATATTTTT
39329 TTTATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 9 0.36
28 5 0.20
29 6 0.24
30 5 0.20
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
TAATAATTTCAATTATTTTAATATTTTTAT
Found at i:39718 original size:65 final size:65
Alignment explanation
Indices: 39614--39741 Score: 220
Period size: 65 Copynumber: 2.0 Consensus size: 65
39604 TAAGTTGTCC
39614 AATTGTCTTGTTAAGTTTGCAATAAATTAGAAATAGTTTAACCAACAAGTGGTTGATTCAAGTCT
1 AATTGTCTTGTTAAGTTTGCAATAAATTAGAAATAGTTTAACCAACAAGTGGTTGATTCAAGTCT
* * * *
39679 AATTGTGTTGTTAAGTTTGCAATAGATTGGAAATAGTTTAATCAACAAGTGGTTGATTCAAGT
1 AATTGTCTTGTTAAGTTTGCAATAAATTAGAAATAGTTTAACCAACAAGTGGTTGATTCAAGT
39742 GGTTTGACAC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.38
Consensus pattern (65 bp):
AATTGTCTTGTTAAGTTTGCAATAAATTAGAAATAGTTTAACCAACAAGTGGTTGATTCAAGTCT
Found at i:40602 original size:17 final size:17
Alignment explanation
Indices: 40580--40620 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
40570 GAGAGGATTT
40580 TTTTTTTCAA-TGATCTA
1 TTTTTTTCAATTG-TCTA
40597 TTTTTTTCAATTGTCTA
1 TTTTTTTCAATTGTCTA
40614 TTTTTTT
1 TTTTTTT
40621 GGCAGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 21 0.91
18 2 0.09
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTTTTTCAATTGTCTA
Found at i:41775 original size:29 final size:30
Alignment explanation
Indices: 41732--41800 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
41722 GTTTGTACGG
* *
41732 TTTGCCCCATAAACTCCAATTTT-GGACAT
1 TTTGCCCCCTGAACTCCAATTTTGGGACAT
* * *
41761 TTTGTCCCCTGAACTTCAATTTTGGGACGT
1 TTTGCCCCCTGAACTCCAATTTTGGGACAT
41791 TTTGCCCCCT
1 TTTGCCCCCT
41801 CAAGCTAACG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.19, C:0.29, G:0.14, T:0.38
Consensus pattern (30 bp):
TTTGCCCCCTGAACTCCAATTTTGGGACAT
Found at i:44757 original size:2 final size:2
Alignment explanation
Indices: 44750--44807 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
44740 TCATAACAAT
44750 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
44792 CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA
44808 TATATATATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:44812 original size:2 final size:2
Alignment explanation
Indices: 44807--44835 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44797 ACACACACAC
44807 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 A
44836 ACATCTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49720 original size:22 final size:22
Alignment explanation
Indices: 49676--49749 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
49666 AATTTATTAC
* * *
49676 AATTTTATA-GGTAATTATAAA
1 AATTTCATAGGGTGATTATCAA
* *
49697 AATTTCATATGGTGGTTATCAA
1 AATTTCATAGGGTGATTATCAA
* *
49719 AATTTAATAGGGTGATTATCGA
1 AATTTCATAGGGTGATTATCAA
49741 AATTTCATA
1 AATTTCATA
49750 AAAATATTCA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 8 0.19
22 35 0.81
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (22 bp):
AATTTCATAGGGTGATTATCAA
Found at i:51711 original size:23 final size:27
Alignment explanation
Indices: 51659--51708 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
51649 TTATGTTCGT
51659 TTATATTATATATTATATATATAATAA
1 TTATATTATATATTATATATATAATAA
*
51686 TTATATT-TTTATT-TATATA-AATA
1 TTATATTATATATTATATATATAATA
51709 TTAAAATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 6 0.27
26 5 0.23
27 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTATATTATATATTATATATATAATAA
Found at i:51757 original size:40 final size:41
Alignment explanation
Indices: 51673--51759 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 41
51663 ATTATATATT
* *
51673 ATATATATAATAATTATATTTTTATTTATATAAATATTAAA
1 ATATATATAATAATTATATTTTTATTCATATAAATATAAAA
*
51714 ATATGTAT-ATAATTATA-TTTTATTCCATAT-AATATAAATA
1 ATATATATAATAATTATATTTTTATT-CATATAAATATAAA-A
51754 ATATAT
1 ATATAT
51760 TTATTCCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 14 0.35
40 19 0.47
41 7 0.17
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (41 bp):
ATATATATAATAATTATATTTTTATTCATATAAATATAAAA
Found at i:52516 original size:28 final size:28
Alignment explanation
Indices: 52459--52516 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
52449 TTTTCTTGCG
* *
52459 ATAATAATATAATTGATAATATTTGATA
1 ATAATAATATAATTAATAATATATGATA
52487 ATAATAATATAATTAATTAATATATG-TA
1 ATAATAATATAATTAA-TAATATATGATA
52515 AT
1 AT
52517 CGTGTTAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (28 bp):
ATAATAATATAATTAATAATATATGATA
Found at i:59510 original size:21 final size:21
Alignment explanation
Indices: 59486--59526 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
59476 TCTCACCGTA
59486 TGTGAGTTTTGTGCCACTTTG
1 TGTGAGTTTTGTGCCACTTTG
* *
59507 TGTGGGTTTTGTGCCCCTTT
1 TGTGAGTTTTGTGCCACTTT
59527 ATATGGGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.17, G:0.29, T:0.49
Consensus pattern (21 bp):
TGTGAGTTTTGTGCCACTTTG
Found at i:59533 original size:21 final size:21
Alignment explanation
Indices: 59491--59533 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
59481 CCGTATGTGA
* *
59491 GTTTTGTGCCACTTTGTGTGG
1 GTTTTGTGCCACTTTATATGG
*
59512 GTTTTGTGCCCCTTTATATGG
1 GTTTTGTGCCACTTTATATGG
59533 G
1 G
59534 CTTAATTAGT
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:0.07, C:0.16, G:0.30, T:0.47
Consensus pattern (21 bp):
GTTTTGTGCCACTTTATATGG
Done.