Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009480.1 Corchorus capsularis cultivar CVL-1 contig09501, 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: 112019
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1477 original size:31 final size:31
Alignment explanation
Indices: 1434--1492 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1424 AGTTAGGCTT
*
1434 AATGCACAATTTGCACCATAAATTATAAGCA
1 AATGCACAATTTGCACCATAAACTATAAGCA
* *
1465 AATGGACAATTTGCACCCTAAACTATAA
1 AATGCACAATTTGCACCATAAACTATAA
1493 CTTACAGACA
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:0.44, C:0.20, G:0.10, T:0.25
Consensus pattern (31 bp):
AATGCACAATTTGCACCATAAACTATAAGCA
Found at i:1673 original size:28 final size:30
Alignment explanation
Indices: 1618--1692 Score: 102
Period size: 28 Copynumber: 2.6 Consensus size: 30
1608 CCGTCCAATT
*
1618 GGGTGCAAATTGTTCATAAATTATAGTTTA
1 GGGTGCAAATTGTTCATAAATTAAAGTTTA
1648 GGGTGC-AATTG-TC-TAAAATTAAAGTTTA
1 GGGTGCAAATTGTTCAT-AAATTAAAGTTTA
*
1676 GAGTGCAAATTGTTCAT
1 GGGTGCAAATTGTTCAT
1693 TTGCTTATAG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 1 0.03
28 19 0.49
29 10 0.26
30 8 0.21
31 1 0.03
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.37
Consensus pattern (30 bp):
GGGTGCAAATTGTTCATAAATTAAAGTTTA
Found at i:2955 original size:2 final size:2
Alignment explanation
Indices: 2948--2993 Score: 74
Period size: 2 Copynumber: 22.0 Consensus size: 2
2938 TTATCAATTA
2948 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT
2992 AT
1 AT
2994 TATTTTTAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 38 0.90
3 4 0.10
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3757 original size:78 final size:78
Alignment explanation
Indices: 3659--3812 Score: 236
Period size: 78 Copynumber: 2.0 Consensus size: 78
3649 AATATCTTTA
* * * *
3659 TTCAATCAGTTAATCAAGCACCACTCTAAAACAAAGAATGCCCGTAGCGCTAGCGCGGGCTAATA
1 TTCAATCAGTTAATCAAGCACCACTCTAAAACAAAGAACGCCCGTAACGCCAGCGCGGACTAATA
*
3724 TGACTTGTATAAT
66 TAACTTGTATAAT
* * *
3737 TTCAATCAGTTAATCAAGCACCACTCTAAAATAAAGAACGTCCGTAACGCCAGTGCGGACTAATA
1 TTCAATCAGTTAATCAAGCACCACTCTAAAACAAAGAACGCCCGTAACGCCAGCGCGGACTAATA
3802 TAACTTGTATA
66 TAACTTGTATA
3813 TAGTTAATTA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 68 1.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (78 bp):
TTCAATCAGTTAATCAAGCACCACTCTAAAACAAAGAACGCCCGTAACGCCAGCGCGGACTAATA
TAACTTGTATAAT
Found at i:3961 original size:13 final size:13
Alignment explanation
Indices: 3943--3972 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3933 TCCTTTTTAA
3943 TTGTCCATTTCCC
1 TTGTCCATTTCCC
3956 TTGTCCATTTCCC
1 TTGTCCATTTCCC
3969 TTGT
1 TTGT
3973 TCCTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.07, C:0.33, G:0.10, T:0.50
Consensus pattern (13 bp):
TTGTCCATTTCCC
Found at i:5102 original size:29 final size:30
Alignment explanation
Indices: 5069--5134 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
5059 CGCCAACGGT
* * *
5069 CAAATAAGTTCTTAAACT-TCAATTTTGGC
1 CAAATAAGTCCCTAAACTACCAATTTTGGC
*
5098 CAAATAAGTCCCTGAACTACCAATTTTGGC
1 CAAATAAGTCCCTAAACTACCAATTTTGGC
*
5128 CAGATAA
1 CAAATAA
5135 ACCCTTCTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (30 bp):
CAAATAAGTCCCTAAACTACCAATTTTGGC
Found at i:5449 original size:29 final size:30
Alignment explanation
Indices: 5408--5465 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
5398 TTATCTGGCC
*
5408 AAAATTGGTAGTTCAGGAGCTTATTTGACA
1 AAAATTGGAAGTTCAGGAGCTTATTTGACA
** *
5438 AAAATT-GAAGTTTGGGGGCTTATTTGAC
1 AAAATTGGAAGTTCAGGAGCTTATTTGAC
5466 GTTGATGGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (30 bp):
AAAATTGGAAGTTCAGGAGCTTATTTGACA
Found at i:7256 original size:6 final size:6
Alignment explanation
Indices: 7245--7278 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
7235 TTTGAGTATG
7245 TATAAA TATAAA TATAAA TATAAA TATAAA TATA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATA
7279 TTTAATTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TATAAA
Found at i:8806 original size:107 final size:106
Alignment explanation
Indices: 8656--8913 Score: 380
Period size: 107 Copynumber: 2.5 Consensus size: 106
8646 AGTTTAGCCT
* *
8656 TAATTTCACTAAGTTTAGCTCCAAATTAAAATTTTATTTTTATTTTAAAGG-TAAATTTCAAAAT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAAGGATAAATTCCAAAAT
8720 TAATAATTTATTATTATAGGGTTTTAGAAATAAAATACAAAAC
66 TAATAA--TATTATTATAGGGTTTTAGAAATAAAATACAAAAC
*
8763 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTT-AAGGATAAATTCCATAAT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAAGGATAAATTCCAAAAT
* * *
8827 TAATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 TAATAATATTATTATAGGGTTTTAGAAATAAAATACAAAAC
* ** *
8868 TAA-TTCACTGAGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTAA
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAA
8914 GGGTTAGAAA
Statistics
Matches: 139, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
103 24 0.17
104 14 0.10
105 35 0.25
106 4 0.03
107 62 0.45
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (106 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAAGGATAAATTCCAAAAT
TAATAATATTATTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:15868 original size:3 final size:3
Alignment explanation
Indices: 15860--15913 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
15850 GCTATCATCT
* *
15860 TTA TTA TTA TTA TCA TTA TATA TTA TTA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
15906 TTA TTA TT
1 TTA TTA TT
15914 CCCTGTTTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:15949 original size:28 final size:28
Alignment explanation
Indices: 15917--15970 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
15907 TATTATTCCC
* *
15917 TGTTTACTCCCCTTCATTTCTTATCCTT
1 TGTTTACTCCACTTCATTTCTCATCCTT
* *
15945 TGTTTACTTCATTTCATTTCTCATCC
1 TGTTTACTCCACTTCATTTCTCATCC
15971 ATTTCCTCCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.13, C:0.30, G:0.04, T:0.54
Consensus pattern (28 bp):
TGTTTACTCCACTTCATTTCTCATCCTT
Found at i:18862 original size:35 final size:35
Alignment explanation
Indices: 18816--19150 Score: 469
Period size: 35 Copynumber: 9.6 Consensus size: 35
18806 AGTAATAAGC
18816 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATT
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATT
*
18851 AACTTAATTCAGGGTAATTAAGTAATTCGGTAATT
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATT
*
18886 AACTTAATTCAGGGTAATTAAGTAATTCGGTAATT
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATT
18921 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATT
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATT
*
18956 AACTTAATTCAGGGTAATTAAGTAATTCGGTAATT
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATT
* * *
18991 AACTTAATTCAGGGTAATTAAGTGAGTCAATAATT
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATT
*
19026 AACTTAATAT-AGGGTAATTAAGTAATTCGGTAATT
1 AACTTAAT-TCAGGGTAATTAAGTAATTCAGTAATT
* * * *
19061 AACTTAATTCAAGGTAATTAAGTGAGTT-AATAATC
1 AACTTAATTCAGGGTAATTAAGT-AATTCAGTAATT
* * * *
19096 AACTTAATTTAGGG-AAGTTAAGTAGTTCAATAAGT
1 AACTTAATTCAGGGTAA-TTAAGTAATTCAGTAATT
* *
19131 AACCTAATTCAGGGAAATTA
1 AACTTAATTCAGGGTAATTA
19151 TGTTTAGTAA
Statistics
Matches: 272, Mismatches: 22, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
34 7 0.03
35 259 0.95
36 6 0.02
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (35 bp):
AACTTAATTCAGGGTAATTAAGTAATTCAGTAATT
Found at i:20048 original size:29 final size:29
Alignment explanation
Indices: 20006--20064 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
19996 AGAAACAGTC
20006 ACAAGCAGCCTTTTGCAACCTCCACCTTG
1 ACAAGCAGCCTTTTGCAACCTCCACCTTG
20035 ACAAGCAGCCTTTTGCAACCTCCACCTTG
1 ACAAGCAGCCTTTTGCAACCTCCACCTTG
20064 A
1 A
20065 TTAGCTCTAG
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:0.25, C:0.37, G:0.14, T:0.24
Consensus pattern (29 bp):
ACAAGCAGCCTTTTGCAACCTCCACCTTG
Found at i:22221 original size:21 final size:21
Alignment explanation
Indices: 22180--22221 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
22170 CCGTTTGGCA
* *
22180 TTGTTGCCATTTTTATTTTTT
1 TTGTTGCCATTTTCATGTTTT
22201 TTGTTGCCATTTTCATGTTTT
1 TTGTTGCCATTTTCATGTTTT
22222 GAAAACAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.12, G:0.12, T:0.67
Consensus pattern (21 bp):
TTGTTGCCATTTTCATGTTTT
Found at i:23822 original size:11 final size:11
Alignment explanation
Indices: 23806--23844 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
23796 ACAGCGTAAT
*
23806 AAAAACGAAAC
1 AAAAACAAAAC
23817 AAAAACAAAAC
1 AAAAACAAAAC
23828 AAAAACAAAAAC
1 AAAAAC-AAAAC
23840 AAAAA
1 AAAAA
23845 ACAAGAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.82, C:0.15, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:23848 original size:7 final size:6
Alignment explanation
Indices: 23813--23844 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
23803 AATAAAAACG
23813 AAACAA AAAC-A AAACAA AAACAA AAACAA AAA
1 AAACAA AAACAA AAACAA AAACAA AAACAA AAA
23845 ACAAGAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACAA
Found at i:31525 original size:24 final size:24
Alignment explanation
Indices: 31494--31571 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
31484 GTCTTTTTGA
*
31494 ACGACCACTATGTGGCCGAATCTC
1 ACGACCACCATGTGGCCGAATCTC
* * *
31518 ACGGCCACCATGTGGTCGAATTTC
1 ACGACCACCATGTGGCCGAATCTC
*
31542 ACGACTACCA--TGGCCGAATCTC
1 ACGACCACCATGTGGCCGAATCTC
31564 ACGACCAC
1 ACGACCAC
31572 TATAGCTTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 17 0.38
24 28 0.62
ACGTcount: A:0.26, C:0.35, G:0.21, T:0.19
Consensus pattern (24 bp):
ACGACCACCATGTGGCCGAATCTC
Found at i:39959 original size:37 final size:37
Alignment explanation
Indices: 39868--39962 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 37
39858 ATCTAAGCCC
*
39868 AAATAGGACGTTGGAGACAAAGACAAAAAGCAAAATT
1 AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
** * * *
39905 AAATACAACATTAGAAACAATGAC-AAAAGTCAAAATT
1 AAATAGGACGTTGGAAACAAAGACAAAAAG-CAAAATT
39942 AAATAGGACGTTGGAAACAAA
1 AAATAGGACGTTGGAAACAAA
39963 AAGCAAAAGT
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
36 5 0.11
37 41 0.89
ACGTcount: A:0.56, C:0.12, G:0.17, T:0.16
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
Found at i:40117 original size:31 final size:31
Alignment explanation
Indices: 40082--40148 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
40072 ATGGCAATTT
40082 AGAAATATGTTTTAAGAA-AAAGGGTACAATC
1 AGAAATATGTTTTAA-AACAAAGGGTACAATC
40113 AGAAATATGTTTTAAAACAAAGGGTACAATC
1 AGAAATATGTTTTAAAACAAAGGGTACAATC
*
40144 GGAAA
1 AGAAA
40149 ATATAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.24
Consensus pattern (31 bp):
AGAAATATGTTTTAAAACAAAGGGTACAATC
Found at i:40202 original size:10 final size:10
Alignment explanation
Indices: 40180--40209 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
40170 GTACTTTTAT
40180 ATATAGTATAG
1 ATATAG-ATAG
40191 ATATAGATAG
1 ATATAGATAG
40201 ATATAGATA
1 ATATAGATA
40210 TATTTCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (10 bp):
ATATAGATAG
Found at i:41580 original size:393 final size:382
Alignment explanation
Indices: 40856--41622 Score: 1248
Period size: 393 Copynumber: 2.0 Consensus size: 382
40846 TGATGCGGAG
*
40856 CATTCCTATTGGTCATGTTGGATCCTAATTAATGAGGATAATCTAAATTTCCATTATTTTAATAA
1 CATTCCTATTGGTCATGTTGGATCCTAATTAATGAGAATAATCTAAATTTCCATTATTTTAATAA
* **
40921 TGGAATAATTAAAATATTTTTAATAATGACAATTTAGAAATATATTTGGAAAAAAAGGGGTGCAA
66 TGGAATAATTAAAATATTTTTAATAATGACAATTTAGAAATATATTTGAAAAAAAAGAAGTGCAA
* *
40986 TTTTCCCTTAATTCGTACTTTTATATATAGTATTATAGATATAGATAGATAATATGAATATTCTT
131 GTTTCCCTTAATTCGTACTTTTATATATAGTACTATAGATATAGATAGATAATATGAATATTCTT
* *
41051 AAATGTATAAAAAAATAAAAAATTTACATATAAAAAGTACACAAGCTCGATTAGGCTCACGAGCT
196 AAATGCATAAAAAAATAAAAAAATTACATATAAAAAGTACACAAGCTCGATTAGGCTCACGAGCT
* *
41116 GCTCGAGCTCGGCTTGACTAACTACTCAAGTAGCTCGAGATCGAGTTCGGCTTGAGAAAAAAGAG
261 GCTCGAGCTCGACTTGACTAACTACTCAAGTAGCTCGAGATCGAGTTCGACTTGAGAAAAAAGAG
*
41181 TCAAACTCGAGTATTCATTAAATCAAGGCCGAGTAGCTCACGTGTAGTGATGTGAAA
326 TCAAACTCGAGTATTCATCAAATCAAGGCCGAGTAGCTCACGTGTAGTGATGTGAAA
41238 CATTCCTATTGGTCATGTTGGATCCTAATTAATGAGAATAATCTAAATTTCCATTATTTTAATAA
1 CATTCCTATTGGTCATGTTGGATCCTAATTAATGAGAATAATCTAAATTTCCATTATTTTAATAA
*
41303 TGGAATAATTAAAATATTTTTAATAATGACAATTTAGAAATATATTTGAAAAAAAAGTACAATTA
66 TGGAATAATTAAAATATTTTTAATAATGACAATTTAGAAATATATTTGAAAAAAAAG---AAGT-
*
41368 GAAAACATAAAGTTTCCCTTTATTCGTACTTTTATATATAGTACTATAGATATAGATAGATAATA
127 G----C---AAGTTTCCCTTAATTCGTACTTTTATATATAGTACTATAGATATAGATAGATAATA
*
41433 TGAATTTTCTTAAATGCAT-AAAAAATAAAAAAAATTACATATAAAAAGTACACAAGCTCGATTA
185 TGAATATTCTTAAATGCATAAAAAAAT-AAAAAAATTACATATAAAAAGTACACAAGCTCGATTA
* *
41497 GGCTCACGAGCTGCTCGAGCTCGACTTGACTAACTACTCGAGTAGCTCGAGCTCGAGTTCGACTT
249 GGCTCACGAGCTGCTCGAGCTCGACTTGACTAACTACTCAAGTAGCTCGAGATCGAGTTCGACTT
* * *
41562 GAGAAAAGAGATTCAAACTCGAGTATTCATCAAATCGAGGCCGAGTAGCTCACGTGTAGTG
314 GAGAAAAAAGAGTCAAACTCGAGTATTCATCAAATCAAGGCCGAGTAGCTCACGTGTAGTG
41623 TCGTCTCATT
Statistics
Matches: 354, Mismatches: 19, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
382 120 0.34
385 1 0.00
386 1 0.00
390 1 0.00
392 7 0.02
393 224 0.63
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (382 bp):
CATTCCTATTGGTCATGTTGGATCCTAATTAATGAGAATAATCTAAATTTCCATTATTTTAATAA
TGGAATAATTAAAATATTTTTAATAATGACAATTTAGAAATATATTTGAAAAAAAAGAAGTGCAA
GTTTCCCTTAATTCGTACTTTTATATATAGTACTATAGATATAGATAGATAATATGAATATTCTT
AAATGCATAAAAAAATAAAAAAATTACATATAAAAAGTACACAAGCTCGATTAGGCTCACGAGCT
GCTCGAGCTCGACTTGACTAACTACTCAAGTAGCTCGAGATCGAGTTCGACTTGAGAAAAAAGAG
TCAAACTCGAGTATTCATCAAATCAAGGCCGAGTAGCTCACGTGTAGTGATGTGAAA
Found at i:42421 original size:16 final size:17
Alignment explanation
Indices: 42397--42429 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
42387 CACCTCACAC
*
42397 CCCTCACATA-TGATCA
1 CCCTAACATAGTGATCA
42413 CCCTAACATAGTGATCA
1 CCCTAACATAGTGATCA
42430 GGCCGCCCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.33, C:0.33, G:0.09, T:0.24
Consensus pattern (17 bp):
CCCTAACATAGTGATCA
Found at i:46866 original size:18 final size:18
Alignment explanation
Indices: 46843--46881 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
46833 TTAAAATTAA
46843 AATCTGAAGTATACTACT
1 AATCTGAAGTATACTACT
46861 AATCTGAAGTATACTACT
1 AATCTGAAGTATACTACT
46879 AAT
1 AAT
46882 TTTATCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (18 bp):
AATCTGAAGTATACTACT
Found at i:48404 original size:15 final size:15
Alignment explanation
Indices: 48384--48416 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
48374 CTCGTACTTT
48384 TATATATAGTATAGA
1 TATATATAGTATAGA
48399 TATATATAGTATAGA
1 TATATATAGTATAGA
48414 TAT
1 TAT
48417 GCTTGATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (15 bp):
TATATATAGTATAGA
Found at i:55921 original size:11 final size:10
Alignment explanation
Indices: 55896--55920 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55886 TTAGTTTTCG
55896 TTTTTCTTTT
1 TTTTTCTTTT
55906 TTTTTCTTTT
1 TTTTTCTTTT
55916 TTTTT
1 TTTTT
55921 TATAATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:66640 original size:25 final size:25
Alignment explanation
Indices: 66591--66640 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
66581 AAAGAAATCA
*
66591 AAGTGAAACCATATGTTTTGGCAAT
1 AAGTGAAACCATATGTTTAGGCAAT
* *
66616 AAGTGATACCATATGTTTAGTCAAT
1 AAGTGAAACCATATGTTTAGGCAAT
66641 GAAAACAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (25 bp):
AAGTGAAACCATATGTTTAGGCAAT
Found at i:82487 original size:17 final size:17
Alignment explanation
Indices: 82465--82498 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
82455 AATTTTCTCA
82465 GTTCTT-TTTTTCTTTTT
1 GTTCTTCTTTTT-TTTTT
82482 GTTCTTCTTTTTTTTTT
1 GTTCTTCTTTTTTTTTT
82499 TTTTTGCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (17 bp):
GTTCTTCTTTTTTTTTT
Found at i:90992 original size:3 final size:3
Alignment explanation
Indices: 90984--91020 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
90974 CATTCTAAAA
90984 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
91021 TAGATAGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:91799 original size:51 final size:51
Alignment explanation
Indices: 91723--91826 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
91713 TTAATCTTAT
91723 TTAGGAACACCCAAATTAATGGTGTATCAATTTCTTGAAATCAACTCTAAC
1 TTAGGAACACCCAAATTAATGGTGTATCAATTTCTTGAAATCAACTCTAAC
*
91774 TTAGGAACACCCAAATTAATGGTGTATCAATTTCTTGAAATCAACTTTAAC
1 TTAGGAACACCCAAATTAATGGTGTATCAATTTCTTGAAATCAACTCTAAC
91825 TT
1 TT
91827 TATTAAAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34
Consensus pattern (51 bp):
TTAGGAACACCCAAATTAATGGTGTATCAATTTCTTGAAATCAACTCTAAC
Found at i:92058 original size:31 final size:31
Alignment explanation
Indices: 92020--92084 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
92010 TTGGGTTATC
92020 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
92051 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
92082 AGT
1 AGT
92085 TTGTTCAGTT
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:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (31 bp):
AGTCTCCAGATCTTTAGATCTTGGATGTTTG
Found at i:92439 original size:105 final size:105
Alignment explanation
Indices: 92257--92466 Score: 420
Period size: 105 Copynumber: 2.0 Consensus size: 105
92247 CACAGAAGCG
92257 AAAACAAAGAGGTGTCGCGCGTGCTAGAGACTCATGGGAAAGGTTCGAAACTCCAATTCAAAGGA
1 AAAACAAAGAGGTGTCGCGCGTGCTAGAGACTCATGGGAAAGGTTCGAAACTCCAATTCAAAGGA
92322 TTCAGATCACGATGCCAAATCCAGATCAAGACCTTGATGA
66 TTCAGATCACGATGCCAAATCCAGATCAAGACCTTGATGA
92362 AAAACAAAGAGGTGTCGCGCGTGCTAGAGACTCATGGGAAAGGTTCGAAACTCCAATTCAAAGGA
1 AAAACAAAGAGGTGTCGCGCGTGCTAGAGACTCATGGGAAAGGTTCGAAACTCCAATTCAAAGGA
92427 TTCAGATCACGATGCCAAATCCAGATCAAGACCTTGATGA
66 TTCAGATCACGATGCCAAATCCAGATCAAGACCTTGATGA
92467 TGAAATTCAA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (105 bp):
AAAACAAAGAGGTGTCGCGCGTGCTAGAGACTCATGGGAAAGGTTCGAAACTCCAATTCAAAGGA
TTCAGATCACGATGCCAAATCCAGATCAAGACCTTGATGA
Found at i:96293 original size:7 final size:7
Alignment explanation
Indices: 96281--96313 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
96271 GTGCAAGTGA
96281 AGTGACT
1 AGTGACT
96288 AGTGACT
1 AGTGACT
96295 AGTGACT
1 AGTGACT
96302 AGTGACT
1 AGTGACT
96309 AGTGA
1 AGTGA
96314 GTGGTGCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.27
Consensus pattern (7 bp):
AGTGACT
Found at i:102238 original size:9 final size:8
Alignment explanation
Indices: 102226--102254 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
102216 CAAAAAACGC
102226 AAAAAAAT
1 AAAAAAAT
102234 AAAAAAAT
1 AAAAAAAT
102242 -AAAAAAT
1 AAAAAAAT
102249 AAAAAA
1 AAAAAA
102255 GAAGAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:110214 original size:14 final size:14
Alignment explanation
Indices: 110195--110235 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
110185 TTTTTTTTTG
110195 AAATTTCGAATTTC
1 AAATTTCGAATTTC
* *
110209 AAATTTTGAAATTC
1 AAATTTCGAATTTC
110223 AAATTTCGAATTT
1 AAATTTCGAATTT
110236 TGGCGGGCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (14 bp):
AAATTTCGAATTTC
Found at i:110229 original size:21 final size:22
Alignment explanation
Indices: 110190--110237 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
110180 TGTTTTTTTT
*
110190 TTTTGAAATTTCGAATTTCAAA
1 TTTTGAAATTTCAAATTTCAAA
*
110212 TTTTGAAA-TTCAAATTTCGAA
1 TTTTGAAATTTCAAATTTCAAA
110233 TTTTG
1 TTTTG
110238 GCGGGCTGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.48
Consensus pattern (22 bp):
TTTTGAAATTTCAAATTTCAAA
Done.