Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011798.1 Corchorus capsularis cultivar CVL-1 contig11819, 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: 47225
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:116 original size:45 final size:46
Alignment explanation
Indices: 49--150 Score: 118
Period size: 46 Copynumber: 2.3 Consensus size: 46
39 TAATACTTTC
* *
49 AAATTTTGAT-AATCACACTATAAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCACACTATAAAATTGTAATAAACCTCGCTATA
*** * *
93 AAATTTTGATAAATCTTTCTATAAAATTTTAATAAACCTCTCTATA
1 AAATTTTGATAAATCACACTATAAAATTGTAATAAACCTCGCTATA
*
139 AAAGTTTGATAA
1 AAATTTTGATAA
151 CTTTCTTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 10 0.21
45 17 0.35
46 21 0.44
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (46 bp):
AAATTTTGATAAATCACACTATAAAATTGTAATAAACCTCGCTATA
Found at i:119 original size:23 final size:22
Alignment explanation
Indices: 49--346 Score: 111
Period size: 22 Copynumber: 13.7 Consensus size: 22
39 TAATACTTTC
* * *
49 AAATTTTGATAATCACACTATA
1 AAATTTTGATAACCTCTCTATA
* * *
71 AAATTGTGATAACCTCGCTATG
1 AAATTTTGATAACCTCTCTATA
* *
93 AAATTTTGATAAATCTTTCTATA
1 AAATTTTGAT-AACCTCTCTATA
*
116 AAATTTTAATAAACCTCTCTATA
1 AAATTTTGAT-AACCTCTCTATA
* * *
139 AAAGTTTGATAA-CTTTCTTATG
1 AAATTTTGATAACCTCTC-TATA
* *
161 AAATCTTGATAA-----CTA-C
1 AAATTTTGATAACCTCTCTATA
* * *
177 AAATTTTGATAAGCTCCCTATG
1 AAATTTTGATAACCTCTCTATA
**
199 ATTTTTTGATAACCTCAT-TATGA
1 AAATTTTGATAACCTC-TCTAT-A
* * * * *
222 AAA-TTTGTTAATCTCCCCATG
1 AAATTTTGATAACCTCTCTATA
* * * *
243 AAATTTTGATCTACAT-ACTATG
1 AAATTTTGAT-AACCTCTCTATA
*
265 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTCTC-TATA
**
287 AAATTTTGATAA-CTAAACTATGA
1 AAATTTTGATAACCT-CTCTAT-A
*
310 AAA-TTTGATAACCT-TCATATG
1 AAATTTTGATAACCTCTC-TATA
*
331 AAATTTTGATATCCTC
1 AAATTTTGATAACCTC
347 ACTGAATTTT
Statistics
Matches: 205, Mismatches: 49, Indels: 43
0.69 0.16 0.14
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
18 1 0.00
21 18 0.09
22 128 0.62
23 45 0.22
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACCTCTCTATA
Found at i:250 original size:44 final size:43
Alignment explanation
Indices: 181--349 Score: 146
Period size: 44 Copynumber: 3.8 Consensus size: 43
171 AACTACAAAT
** *
181 TTTGATAAGCTCCCTATGATTTTTTGATAACCTCATTATGAAAA
1 TTTGATAA-CTCCCTATGAAATTTTGATAACCTCACTATGAAAA
* * * * *
225 TTTGTTAATCTCCCCATGAAATTTTGATCTACAT-ACTATGAAAT
1 TTTGATAA-CTCCCTATGAAATTTTGAT-AACCTCACTATGAAAA
*
269 TTTGATAAC-CCTCTTATGAAATTTTGATAA-CTAAACTATGAAAA
1 TTTGATAACTCC-C-TATGAAATTTTGATAACCT-CACTATGAAAA
* * *
313 TTTGATAACCTTCATATGAAATTTTGATATCCTCACT
1 TTTGATAA-CTCCCTATGAAATTTTGATAACCTCACT
350 GAATTTTGAT
Statistics
Matches: 99, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 86 0.87
45 6 0.06
46 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (43 bp):
TTTGATAACTCCCTATGAAATTTTGATAACCTCACTATGAAAA
Found at i:395 original size:20 final size:19
Alignment explanation
Indices: 332--398 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
322 CTTCATATGA
332 AATTTTGATATCC-TCACTG
1 AATTTTGATATCCTTC-CTG
*
351 AATTTTGATATCCTCCCTG
1 AATTTTGATATCCTTCCTG
*
370 AATTTTGGTATCCTTCCTG
1 AATTTTGATATCCTTCCTG
389 AAATTTTGAT
1 -AATTTTGAT
399 TACTCCATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 33 0.79
20 9 0.21
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (19 bp):
AATTTTGATATCCTTCCTG
Found at i:529 original size:22 final size:22
Alignment explanation
Indices: 504--628 Score: 119
Period size: 22 Copynumber: 5.7 Consensus size: 22
494 AATCAGATTT
*
504 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
*
526 TGAAATTTTGATAACATCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
548 TAAAATTTT-ATTGACCCCTCTA
1 TGAAATTTTGA-TAACCTCTTTA
* * *
570 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
592 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
614 TGAAATTTTGATAAC
1 TGAAATTTTGATAAC
629 AACACTATGG
Statistics
Matches: 82, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
21 1 0.01
22 78 0.95
23 3 0.04
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:599 original size:44 final size:43
Alignment explanation
Indices: 479--649 Score: 139
Period size: 44 Copynumber: 3.9 Consensus size: 43
469 AAAAATACCA
* * * * *
479 CTATGAAATTTTTG-TAATCAGATTTTGAAAATTTGATAACCTCT
1 CTATGAAA-TTTTGATAA-CACATTATGAAATTTTGATAACCCCG
* * * * *
523 TTATGAAATTTTGATAACATCTTTATAAAATTTT-ATTGACCCCT
1 CTATGAAATTTTGATAACA-CATTATGAAATTTTGA-TAACCCCG
* *
567 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAA-CACATTATGAAATTTTGATAACCCCG
* * *
611 CTTTGAAATTTTGATAACAACACTATGGAATTTTGATAA
1 CTATGAAATTTTGATAAC-ACATTATGAAATTTTGATAA
650 TCTTCATATA
Statistics
Matches: 103, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
43 9 0.09
44 91 0.88
45 3 0.03
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (43 bp):
CTATGAAATTTTGATAACACATTATGAAATTTTGATAACCCCG
Found at i:642 original size:22 final size:21
Alignment explanation
Indices: 567--649 Score: 85
Period size: 22 Copynumber: 3.8 Consensus size: 21
557 ATTGACCCCT
567 CTATGAAATTTTGATAATCACA
1 CTATGAAATTTTGATAA-CACA
* * * *
589 TTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAA-CACA
*
611 CTTTGAAATTTTGATAACAACA
1 CTATGAAATTTTGATAAC-ACA
*
633 CTATGGAATTTTGATAA
1 CTATGAAATTTTGATAA
650 TCTTCATATA
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
21 1 0.02
22 47 0.98
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (21 bp):
CTATGAAATTTTGATAACACA
Found at i:785 original size:22 final size:22
Alignment explanation
Indices: 504--787 Score: 76
Period size: 22 Copynumber: 12.7 Consensus size: 22
494 AATCAGATTT
* *
504 TGAAAATTTGATAACC-TCTTTA
1 TGAAATTTTGATAACCTTC-ATA
526 TGAAATTTTGATAACATCTT--TA
1 TGAAATTTTGATAAC--CTTCATA
* * *
548 TAAAATTTT-ATTGACCCCTC-TA
1 TGAAATTTTGA-T-AACCTTCATA
* *
570 TGAAATTTTGATAATC-ACATTA
1 TGAAATTTTGATAACCTTCA-TA
* * *
592 TGTAATTTTGATAACC-TCGCTT
1 TGAAATTTTGATAACCTTC-ATA
**
614 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAACCTTCA-TA
* *
636 TGGAATTTTGATAATCTTCATA
1 TGAAATTTTGATAACCTTCATA
* * *
658 T-AAATTTTGATGATCATATCTTTA
1 TGAAATTTTGAT-AACCT-TC-ATA
*
682 TGAAATTTCGATAATCAC-TC-TA
1 TGAAATTTTGATAA-C-CTTCATA
* *
704 TGAGA-TTGGATAACCTTC-TA
1 TGAAATTTTGATAACCTTCATA
* * *
724 TCAAATTTTGGTACTCCTT-ATGAAA
1 TGAAATTTTGATA-ACCTTCAT---A
*
749 TTGAGACTTTT-ATAACCTTCATA
1 -TGA-AATTTTGATAACCTTCATA
772 TGAAATTTTGATAACC
1 TGAAATTTTGATAACC
788 ACACTAACCT
Statistics
Matches: 192, Mismatches: 40, Indels: 60
0.66 0.14 0.21
Matches are distributed among these distances:
19 1 0.01
20 9 0.05
21 32 0.17
22 107 0.56
23 9 0.05
24 7 0.04
25 16 0.08
26 6 0.03
27 5 0.03
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:1054 original size:22 final size:22
Alignment explanation
Indices: 1026--1110 Score: 134
Period size: 22 Copynumber: 3.9 Consensus size: 22
1016 TAACCTGATC
*
1026 CTATGAAATTTTGGTAACCACT
1 CTATGAAATTTTGGTAACCACA
*
1048 CTATGAAATTTTGGTAACTACA
1 CTATGAAATTTTGGTAACCACA
1070 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* *
1092 CTATGGAATTTTGATAACC
1 CTATGAAATTTTGGTAACC
1111 TCCTCATGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:1119 original size:22 final size:22
Alignment explanation
Indices: 1026--1133 Score: 101
Period size: 22 Copynumber: 4.9 Consensus size: 22
1016 TAACCTGATC
* * *
1026 CTATGAAATTTTGGTAACCACT
1 CTATGGAATTTTGATAACCACA
* * *
1048 CTATGAAATTTTGGTAACTACA
1 CTATGGAATTTTGATAACCACA
* *
1070 CTATGAAATTTTGGTAACCACA
1 CTATGGAATTTTGATAACCACA
*
1092 CTATGGAATTTTGATAACCTC-
1 CTATGGAATTTTGATAACCACA
* *
1113 CTCATGGAATTATAATAACCA
1 CT-ATGGAATTTTGATAACCA
1134 AAGTAAAATA
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
21 2 0.03
22 74 0.97
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (22 bp):
CTATGGAATTTTGATAACCACA
Found at i:1280 original size:31 final size:31
Alignment explanation
Indices: 1223--1289 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 31
1213 TGATAATTTA
*
1223 GAAATATGTTTTTTAAAAAAAGGGTACAATTG
1 GAAATATG-TTTTTAAAAAAAGGGTACAATCG
1255 GAAATATG-TTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTTAAAAA-AAGGGTACAATCG
1286 GAAA
1 GAAA
1290 ACATAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 9 0.27
31 16 0.48
32 8 0.24
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.30
Consensus pattern (31 bp):
GAAATATGTTTTTAAAAAAAGGGTACAATCG
Found at i:1325 original size:2 final size:2
Alignment explanation
Indices: 1318--1360 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
1308 TTCGTACTTT
*
1318 TA TA TA TA GTG TA TA 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 TA TA TA TA TA TA TA
1361 ACAATCGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 37 0.97
3 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1390 original size:82 final size:82
Alignment explanation
Indices: 1279--1431 Score: 297
Period size: 82 Copynumber: 1.9 Consensus size: 82
1269 AAATAAGGGT
1279 ACAATCGGAAAACATAAAGTTTCCCCTTATTCGTACTTTTATATATAGTGTATATATATATATAT
1 ACAATCGGAAAACATAAAGTTTCCCCTTATTCGTACTTTTATATATAGTGTATATATATATATAT
1344 ATATATATATATATATA
66 ATATATATATATATATA
*
1361 ACAATCGGAAAACATAAAGTTTCCTCTTATTCGTACTTTTATATATAGTGTATATATATATATAT
1 ACAATCGGAAAACATAAAGTTTCCCCTTATTCGTACTTTTATATATAGTGTATATATATATATAT
1426 ATATAT
66 ATATAT
1432 GTGTGTGTAT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 70 1.00
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (82 bp):
ACAATCGGAAAACATAAAGTTTCCCCTTATTCGTACTTTTATATATAGTGTATATATATATATAT
ATATATATATATATATA
Found at i:11277 original size:18 final size:18
Alignment explanation
Indices: 11254--11292 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
11244 ATATAGGCAC
* *
11254 ATAGATACATCGCTATAA
1 ATAGATACATCACCATAA
11272 ATAGATACATCACCATAA
1 ATAGATACATCACCATAA
11290 ATA
1 ATA
11293 TAAGGGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.26
Consensus pattern (18 bp):
ATAGATACATCACCATAA
Found at i:13610 original size:16 final size:16
Alignment explanation
Indices: 13589--13621 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
13579 GATTTGTCTT
13589 AGGGCCAAAGGCAGTG
1 AGGGCCAAAGGCAGTG
13605 AGGGCCAAAGGCAGTG
1 AGGGCCAAAGGCAGTG
13621 A
1 A
13622 TTAAAAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.42, T:0.06
Consensus pattern (16 bp):
AGGGCCAAAGGCAGTG
Found at i:14339 original size:14 final size:14
Alignment explanation
Indices: 14320--14349 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
14310 AAAAGGCCGA
14320 ACCGACCGAAACCG
1 ACCGACCGAAACCG
*
14334 ACCGACCGCAACCG
1 ACCGACCGAAACCG
14348 AC
1 AC
14350 ATAGCACCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.47, G:0.20, T:0.00
Consensus pattern (14 bp):
ACCGACCGAAACCG
Found at i:16677 original size:11 final size:12
Alignment explanation
Indices: 16661--16690 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16651 ATAAAAATTC
16661 AAACCGA-TAAA
1 AAACCGACTAAA
16672 AAACCGACTAAA
1 AAACCGACTAAA
16684 AAACCGA
1 AAACCGA
16691 AAATCGACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.60, C:0.23, G:0.10, T:0.07
Consensus pattern (12 bp):
AAACCGACTAAA
Found at i:16806 original size:19 final size:19
Alignment explanation
Indices: 16782--16818 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
16772 TTTTTAATAA
16782 TTTTTTTT--GCCAGACCT
1 TTTTTTTTGGGCCAGACCT
16799 TTTTTTTTGGGCCAGACCT
1 TTTTTTTTGGGCCAGACCT
16818 T
1 T
16819 AATAAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.11, C:0.22, G:0.16, T:0.51
Consensus pattern (19 bp):
TTTTTTTTGGGCCAGACCT
Found at i:18762 original size:14 final size:14
Alignment explanation
Indices: 18743--18769 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18733 ATGGATGATG
18743 GATGCCTATTAACA
1 GATGCCTATTAACA
18757 GATGCCTATTAAC
1 GATGCCTATTAAC
18770 CATGAGCTTT
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:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
GATGCCTATTAACA
Found at i:23965 original size:3 final size:3
Alignment explanation
Indices: 23957--23991 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
23947 TTTTATTTAT
23957 TTA TTA TTA TTA TATA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA T
23992 ATTCTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:24050 original size:34 final size:34
Alignment explanation
Indices: 24006--24073 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
23996 TTTTTACTAC
*
24006 TCATGACATTGAAATGAGTTACACAATAAAAAGT
1 TCATGACATTGAAATGAATTACACAATAAAAAGT
* *
24040 TCATGGCATTGAAATGAATTACACAGTAAAAAGT
1 TCATGACATTGAAATGAATTACACAATAAAAAGT
24074 AGTTCTCTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (34 bp):
TCATGACATTGAAATGAATTACACAATAAAAAGT
Found at i:24102 original size:24 final size:24
Alignment explanation
Indices: 24070--24119 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
24060 ACACAGTAAA
24070 AAGTAGTTCTCTCATTTTTCCCAT
1 AAGTAGTTCTCTCATTTTTCCCAT
24094 AAGTAGTTCTCTCATTTTTCCCAT
1 AAGTAGTTCTCTCATTTTTCCCAT
24118 AA
1 AA
24120 TCCCCCCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (24 bp):
AAGTAGTTCTCTCATTTTTCCCAT
Found at i:40867 original size:78 final size:79
Alignment explanation
Indices: 40730--40890 Score: 288
Period size: 78 Copynumber: 2.1 Consensus size: 79
40720 TGCATCGTTG
* *
40730 TGCCTTTAACTGCACATTAATAATTCCCACAAACCAACTTTACTCGGAGGCACCATTATACCTTG
1 TGCCTCTAACTGCACATTAAGAATTCCCACAAACCAACTTTACTCGGAGGCACCATTATACCTTG
40795 ATGTATAATAGGAA
66 ATGTATAATAGGAA
*
40809 TGCCTCTAACTGCATATTAAGAATTCCCAC-AACCAACTTTACTCGGAGGCACCATTATACCTTG
1 TGCCTCTAACTGCACATTAAGAATTCCCACAAACCAACTTTACTCGGAGGCACCATTATACCTTG
40873 ATGTATAATAGGAA
66 ATGTATAATAGGAA
40887 TGCC
1 TGCC
40891 ATGTTACACG
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 52 0.66
79 27 0.34
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.29
Consensus pattern (79 bp):
TGCCTCTAACTGCACATTAAGAATTCCCACAAACCAACTTTACTCGGAGGCACCATTATACCTTG
ATGTATAATAGGAA
Found at i:41022 original size:52 final size:54
Alignment explanation
Indices: 40913--41054 Score: 163
Period size: 52 Copynumber: 2.7 Consensus size: 54
40903 TTAAATATTT
*
40913 ATTTGCACCATTACACCTTT-ACTA-TGTAATAGGAATGCACTGTATAACTTTTG
1 ATTTGCACCATTACACCTTTAAC-AGTGTAATAGGAATGCACTGTATAACTTCTG
* *
40966 -TTTGCACCATTACACCTTTAACAGTGTAATAGGAATGCA-TTTATGAC-TCTG
1 ATTTGCACCATTACACCTTTAACAGTGTAATAGGAATGCACTGTATAACTTCTG
* * * *
41017 ATTTGCACCACTATACC-TTAA-TGTATAATAGGAATGCA
1 ATTTGCACCATTACACCTTTAACAGTGTAATAGGAATGCA
41055 ACGTTGTGCC
Statistics
Matches: 79, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
50 15 0.19
51 7 0.09
52 40 0.51
53 17 0.22
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (54 bp):
ATTTGCACCATTACACCTTTAACAGTGTAATAGGAATGCACTGTATAACTTCTG
Found at i:41654 original size:88 final size:88
Alignment explanation
Indices: 41470--41682 Score: 243
Period size: 88 Copynumber: 2.4 Consensus size: 88
41460 ACTTCAACTT
* * * *
41470 GGCACCACTATACCCTTTATGTATAATAGGAATGCCACCTTTGCGCCTTTTACAGCATATTAAGA
1 GGCACCATTATA-CCTTGATGTATAATAGGAATG-CACCTTTGCGCCTTTAACAGCATAATAAGA
* *
41535 ATTTTCGTTACCAACTTTTATTTGAA
64 A-TTTCCTTACCAACTTTTATTAGAA
* * * * *
41561 TGCACCATTATACCTTGATGTATAATAGGAATGCA-TTATTGTGCCTTTAACTGTATAATAAGAA
1 GGCACCATTATACCTTGATGTATAATAGGAATGCACCT-TTGCGCCTTTAACAGCATAATAAGAA
*
41625 -TTCCTATTCCAACTTTTATTCAG-A
65 TTTCCT-TACCAACTTTTATT-AGAA
41649 GGCACCATTATACCTTGATGTATAATAGGAATGC
1 GGCACCATTATACCTTGATGTATAATAGGAATGC
41683 CATGTTACAC
Statistics
Matches: 106, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
87 4 0.04
88 48 0.45
89 24 0.23
90 20 0.19
91 10 0.09
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (88 bp):
GGCACCATTATACCTTGATGTATAATAGGAATGCACCTTTGCGCCTTTAACAGCATAATAAGAAT
TTCCTTACCAACTTTTATTAGAA
Found at i:46742 original size:2 final size:2
Alignment explanation
Indices: 46735--46761 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46725 TCACCAAATA
46735 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 A
46762 CATAATTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.