Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010762.1 Corchorus capsularis cultivar CVL-1 contig10783, 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: 24135
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:1294 original size:63 final size:62
Alignment explanation
Indices: 1227--1886 Score: 281
Period size: 63 Copynumber: 10.9 Consensus size: 62
1217 GTATTGGTGG
* *
1227 TGGTGGAGGTAGTGCTGGTGGAGCTTCAGGTTATGGAAGTGGAGGCGGCGAAGGAGGTGGAGC
1 TGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGG-GC
* * * * * *** * * * *
1290 TGGTGGTGCTGGAT-ATGGAGGAGCTGGGGGTTATGGAGGTGGTGGAGG-TAA-G-GGT-GGC
1 TGGTGGAGGTAG-TGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGGGC
* *
1348 -GGAGG-GGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGTGGCGAAGGAGGTGGTGC
1 TGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGG-GC
* *** ** * **** * * * * *
1409 TGGTGGTGCCGGTTATGGAGGAGCCGGGGGCTACGGAGGTGGTGG-AG-GAAAG-GGT-GGC
1 TGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGGGC
* * * *
1467 -GGCGGAGGTAGTGCTGGTGGAGCTTCTGGATATGGAGGTGGCGGCGGCGAAGGAGGTGGTGT
1 TGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGG-GC
* *** ** * *** * * * *
1529 TGGTGGTGCCGGTTATGGAGGAGCTGGGGGTTATGGAGGTGGTGGAGG-TAA--AGGT-GGC
1 TGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGGGC
* * * *
1587 -GGTGGGGGGTAGTGCTGGTGGAGCCTCAGGATATGGTGGTGGAGGCGGCGAAGGGGGTGGGGC
1 TGGT-GGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGT-GGGC
*** ** * **** * * * * *
1650 TGGTGGAGCCGGTTATGGAGGAGCAGGGGGCTATGGAGGTGGAGGTGGTGGAGGCAAAGG-CGGC
1 TGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGG---AGGTGGGC
1714 -GGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGGGGC
1 TGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGT-GGGC
* * * * * * **** * * * *
1776 TGGTGGTGCTGGTTAC-GGAGGAACAGGGGGGTATGGAGGTGGTGGAGGC-AA-G-GGT-AGC
1 TGGTGGAGGTAG-TGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGGGC
* *
1834 -GGTGGAGGTAGTGCTGGTGGAGCTTCTGGATATGGAGGTGGAGGAGGCGAAGG
1 TGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGG
1887 TGGCGGAGCT
Statistics
Matches: 415, Mismatches: 150, Indels: 68
0.66 0.24 0.11
Matches are distributed among these distances:
55 1 0.00
56 31 0.07
57 71 0.17
58 40 0.10
59 13 0.03
60 20 0.05
61 12 0.03
62 15 0.04
63 201 0.48
64 9 0.02
66 2 0.00
ACGTcount: A:0.17, C:0.09, G:0.54, T:0.20
Consensus pattern (62 bp):
TGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGGGC
Found at i:1336 original size:24 final size:24
Alignment explanation
Indices: 1282--1336 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 24
1272 CGGCGAAGGA
* * *
1282 GGTGGAGCTGGTGGTGCTGGATAT
1 GGTGGAGCTGGGGGTGATGGAGAT
* * *
1306 GGAGGAGCTGGGGGTTATGGAGGT
1 GGTGGAGCTGGGGGTGATGGAGAT
1330 GGTGGAG
1 GGTGGAG
1337 GTAAGGGTGG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.15, C:0.05, G:0.56, T:0.24
Consensus pattern (24 bp):
GGTGGAGCTGGGGGTGATGGAGAT
Found at i:1533 original size:120 final size:120
Alignment explanation
Indices: 1222--1989 Score: 943
Period size: 120 Copynumber: 6.3 Consensus size: 120
1212 AGGTGGTATT
* * *
1222 GGTGGTGGTGGAGGTAGTGCTGGTGGAGCTTCAGGTTATGGAAGTGGAGGCGGCGAAGGAGGTGG
1 GGTGGCGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGG
* * * * *
1287 AGCTGGTGGTGCTGGATATGGAGGAGCTGGGGGTTATGGAGGTGGTGGAGGTAAG
66 AGCTGGTGGTGCCGGTTATGGAGGAGCAGGGGGCTATGGAGGTGGTGGAGGAAAG
* *
1342 GGTGGCGGAGG-GGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGTGGCGAAGGAGGTGG
1 GGTGGCGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGG
* * *
1406 TGCTGGTGGTGCCGGTTATGGAGGAGCCGGGGGCTACGGAGGTGGTGGAGGAAAG
66 AGCTGGTGGTGCCGGTTATGGAGGAGCAGGGGGCTATGGAGGTGGTGGAGGAAAG
* * *
1461 GGTGGCGGCGGAGGTAGTGCTGGTGGAGCTTCTGGATATGGAGGTGGCGGCGGCGAAGGAGGTGG
1 GGTGGCGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGG
* * * *
1526 TGTTGGTGGTGCCGGTTATGGAGGAGCTGGGGGTTATGGAGGTGGTGGAGGTAAA-
66 AGCTGGTGGTGCCGGTTATGGAGGAGCAGGGGGCTATGGAGGTGGTGGAGG-AAAG
* * * *
1581 GGTGGCGGTGGGGGGTAGTGCTGGTGGAGCCTCAGGATATGGTGGTGGAGGCGGCGAAGGGGGTG
1 GGTGGCGGT-GGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTG
* *
1646 GGGCTGGTGGAGCCGGTTATGGAGGAGCAGGGGGCTATGGAGGTGGAGGTGGTGGAGGCAAA-
65 GAGCTGGTGGTGCCGGTTATGGAGGAGCAGGGGGC--T--A--TGGAGGTGGTGGAGG-AAAG
*
1708 GGCGGCGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGG
1 GGTGGCGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGG
* * * * * *
1773 GGCTGGTGGTGCTGGTTACGGAGGAACAGGGGGGTATGGAGGTGGTGGAGGCAAG
66 AGCTGGTGGTGCCGGTTATGGAGGAGCAGGGGGCTATGGAGGTGGTGGAGGAAAG
* * * * *
1828 GGTAGCGGTGGAGGTAGTGCTGGTGGAGCTTCTGGATATGGAGGTGGAGGAGGCGAAGGTGGCGG
1 GGTGGCGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGG
* * * * * * * * *
1893 AGCTGGCGGTGCTGGGTACGGAGGAGCCGGTGG-TCACGGAGGTGGTGGCGG-CAG
66 AGCTGGTGGTGCCGGTTATGGAGGAGCAGGGGGCT-ATGGAGGTGGTGGAGGAAAG
* * * *
1947 TGGAGGTGGAGGAGGTAGTGCTGGTGGAGCTTCTGGATATGGA
1 -GGTGGCGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGA
1990 AGCGGGGGTG
Statistics
Matches: 573, Mismatches: 63, Indels: 24
0.87 0.10 0.04
Matches are distributed among these distances:
119 113 0.20
120 267 0.47
121 82 0.14
122 1 0.00
123 1 0.00
124 1 0.00
125 1 0.00
126 81 0.14
127 26 0.05
ACGTcount: A:0.16, C:0.10, G:0.54, T:0.20
Consensus pattern (120 bp):
GGTGGCGGTGGAGGTAGTGCTGGTGGAGCTTCAGGATATGGAGGTGGAGGCGGCGAAGGAGGTGG
AGCTGGTGGTGCCGGTTATGGAGGAGCAGGGGGCTATGGAGGTGGTGGAGGAAAG
Found at i:1785 original size:57 final size:56
Alignment explanation
Indices: 1689--1907 Score: 138
Period size: 57 Copynumber: 3.7 Consensus size: 56
1679 GCTATGGAGG
* * * * *
1689 TGGAGGTGGTGGAGGCAAAGGCGGCGGTGG-AGGTAGTGCTGGTGGAGCTTCAGGATA
1 TGGAGGTGGAGGAGGCGAAGG-GGTGG-GGCTGGTGGTGCTGGTGGAGCTTCAGGATA
* *** *
1746 TGGAGGTGGAGGCGGCGAAGGAGGTGGGGCTGGTGGTGCTGGTTACGGAGGAACAGGGGGGTA
1 TGGAGGTGGAGGAGGCGAAGG-GGTGGGGCTGGTGGTGCTGG-T--GGAGCTTCA---GGATA
* ** * *
1809 TGGAGGTGGTGGAGGC-AA-GGGTAGCGGTGGAGGTAGTGCTGGTGGAGCTTCTGGATA
1 TGGAGGTGGAGGAGGCGAAGGGGT-G-GG-GCTGGTGGTGCTGGTGGAGCTTCAGGATA
* * *
1866 TGGAGGTGGAGGAGGCGAAGGTGGCGGAGCTGGCGGTGCTGG
1 TGGAGGTGGAGGAGGCGAAGG-GGTGGGGCTGGTGGTGCTGG
1908 GTACGGAGGA
Statistics
Matches: 121, Mismatches: 28, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
56 2 0.02
57 61 0.50
58 4 0.03
59 2 0.02
60 16 0.13
61 2 0.02
62 5 0.04
63 29 0.24
ACGTcount: A:0.17, C:0.10, G:0.54, T:0.18
Consensus pattern (56 bp):
TGGAGGTGGAGGAGGCGAAGGGGTGGGGCTGGTGGTGCTGGTGGAGCTTCAGGATA
Found at i:3098 original size:18 final size:17
Alignment explanation
Indices: 3077--3110 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3067 TTGAGTTGTT
3077 TTGAGTCAGTTTATTTTA
1 TTGAGTCAGTTT-TTTTA
3095 TTGAGTCAGTTTTTTT
1 TTGAGTCAGTTTTTTT
3111 CTAGTGTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.18, C:0.06, G:0.18, T:0.59
Consensus pattern (17 bp):
TTGAGTCAGTTTTTTTA
Found at i:8388 original size:24 final size:24
Alignment explanation
Indices: 8361--8407 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
8351 TTTAGGGTTT
8361 GGTGGGAATTTTCAATTTTGGGCC
1 GGTGGGAATTTTCAATTTTGGGCC
*
8385 GGTGGGAATTTTTAATTTTGGGC
1 GGTGGGAATTTTCAATTTTGGGC
8408 AAAACCTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.09, G:0.34, T:0.40
Consensus pattern (24 bp):
GGTGGGAATTTTCAATTTTGGGCC
Found at i:9360 original size:63 final size:64
Alignment explanation
Indices: 9241--9373 Score: 198
Period size: 63 Copynumber: 2.1 Consensus size: 64
9231 AAGTGTACTA
* * *
9241 ATTGCTGTGATGATTGCCCCAAGTCATGATGTGATTGTTGCAAGTGTAAATGCTGCACCAAGTGT
1 ATTGCAGTGATAATTGCCCCAAGTCA--ATGTGATTGTCGCAAGTGTAAATGCTGCACCAAGTGT
9306 G
64 G
9307 ATTGCAGTGATAATTGCCCCAAGTC-ATGTGATTGTCGCAAGTGT-AATGGCTGCACCAAGTGTG
1 ATTGCAGTGATAATTGCCCCAAGTCAATGTGATTGTCGCAAGTGTAAAT-GCTGCACCAAGTGTG
9370 ATTG
1 ATTG
9374 GTGTAATTGC
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
62 3 0.05
63 37 0.59
66 23 0.37
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (64 bp):
ATTGCAGTGATAATTGCCCCAAGTCAATGTGATTGTCGCAAGTGTAAATGCTGCACCAAGTGTG
Found at i:9371 original size:33 final size:31
Alignment explanation
Indices: 9270--9373 Score: 92
Period size: 33 Copynumber: 3.3 Consensus size: 31
9260 CAAGTCATGA
9270 TGTGATTGTTGCAAGTGTAAATGCTGCACCAAG
1 TGTGATTG-TGCAAGTGT-AATGCTGCACCAAG
*
9303 TGTGA-T-TGC-AGTGATAAT--TGCCCCAAG
1 TGTGATTGTGCAAGTG-TAATGCTGCACCAAG
9330 TCATGTGATTGTCGCAAGTGTAATGGCTGCACCAAG
1 ---TGTGATTGT-GCAAGTGTAAT-GCTGCACCAAG
9366 TGTGATTG
1 TGTGATTG
9374 GTGTAATTGC
Statistics
Matches: 58, Mismatches: 2, Indels: 22
0.71 0.02 0.27
Matches are distributed among these distances:
27 8 0.14
29 7 0.12
30 9 0.16
31 1 0.02
32 2 0.03
33 19 0.33
34 4 0.07
36 8 0.14
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (31 bp):
TGTGATTGTGCAAGTGTAATGCTGCACCAAG
Found at i:12660 original size:27 final size:27
Alignment explanation
Indices: 12622--12676 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
12612 TAAAGAGAGG
12622 TAATTGCTCTATTTTCATGTCCTAGTA
1 TAATTGCTCTATTTTCATGTCCTAGTA
12649 TAATTGCTCTATTTTCATGTCCTAGTA
1 TAATTGCTCTATTTTCATGTCCTAGTA
12676 T
1 T
12677 TTATAAATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (27 bp):
TAATTGCTCTATTTTCATGTCCTAGTA
Found at i:12753 original size:162 final size:162
Alignment explanation
Indices: 12486--12788 Score: 552
Period size: 162 Copynumber: 1.9 Consensus size: 162
12476 TCTTCAAAGA
* *
12486 ATAATTGCTCTATTTTCATGTCTTAGTATTTATAAATCCCTGCAAACAAAACACATCAGATTAAA
1 ATAATTGCTCTATTTTCATGTCCTAGTATTTATAAATCCCTGCAAACAAAACACACCAGATTAAA
12551 TGGGTCAAATAATCTTTGATAATCCTTGCTAATGAAAACTAAAATTCACTTTGAAAGAACCTAAA
66 TGGGTCAAATAATCTTTGATAATCCTTGCTAATGAAAACTAAAATTCACTTTGAAAGAACCTAAA
12616 GAGAGGTAATTGCTCTATTTTCATGTCCTAGT
131 GAGAGGTAATTGCTCTATTTTCATGTCCTAGT
* *
12648 ATAATTGCTCTATTTTCATGTCCTAGTATTTATAAATCCCTTCAAACAAAGCACACCAGATTAAA
1 ATAATTGCTCTATTTTCATGTCCTAGTATTTATAAATCCCTGCAAACAAAACACACCAGATTAAA
* *
12713 TGGGTCAACTAATCTTTGATAATCCTTGCTAGTGAAAACTAAAATTCACTTTGAAAGAACCTAAA
66 TGGGTCAAATAATCTTTGATAATCCTTGCTAATGAAAACTAAAATTCACTTTGAAAGAACCTAAA
12778 GAGAGGTAATT
131 GAGAGGTAATT
12789 TTTTTTATCA
Statistics
Matches: 135, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
162 135 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (162 bp):
ATAATTGCTCTATTTTCATGTCCTAGTATTTATAAATCCCTGCAAACAAAACACACCAGATTAAA
TGGGTCAAATAATCTTTGATAATCCTTGCTAATGAAAACTAAAATTCACTTTGAAAGAACCTAAA
GAGAGGTAATTGCTCTATTTTCATGTCCTAGT
Found at i:18627 original size:11 final size:12
Alignment explanation
Indices: 18585--18625 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
18575 TCCCTTTCAA
*
18585 TATAAAATAAAT
1 TATAAAATTAAT
*
18597 TATCAAA-TAAT
1 TATAAAATTAAT
18608 TATAAAATTAAT
1 TATAAAATTAAT
18620 TATAAA
1 TATAAA
18626 TTTGTTATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
TATAAAATTAAT
Found at i:18871 original size:16 final size:16
Alignment explanation
Indices: 18850--18880 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18840 TTCTTCTCCA
18850 TATTCTATTGTCTTTC
1 TATTCTATTGTCTTTC
*
18866 TATTCTCTTGTCTTT
1 TATTCTATTGTCTTT
18881 TTCATACTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.19, G:0.06, T:0.65
Consensus pattern (16 bp):
TATTCTATTGTCTTTC
Found at i:19352 original size:16 final size:17
Alignment explanation
Indices: 19331--19366 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
19321 TTCTTCTCCA
19331 TATTCTATTGTC-TTTC
1 TATTCTATTGTCTTTTC
*
19347 TATTCTCTTGTCTTTTC
1 TATTCTATTGTCTTTTC
19364 TAT
1 TAT
19367 ACTTCAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.11, C:0.19, G:0.06, T:0.64
Consensus pattern (17 bp):
TATTCTATTGTCTTTTC
Found at i:19705 original size:479 final size:481
Alignment explanation
Indices: 18806--19766 Score: 1847
Period size: 479 Copynumber: 2.0 Consensus size: 481
18796 AAATAAGATG
18806 AATGAGAACAATTTCTCACATTCTTTATATTTTCTTCTTCTCCATATTCTATTGTCTTTCTATTC
1 AATGAGAACAATTTCTCACATTCTTTATATTTTCTTCTTCTCCATATTCTATTGTCTTTCTATTC
18871 TCTTGTCTTTTTCATACTTCAATTTTACTCCATTGCTTTGTTTTGTTATCATTTCACAACAAAAT
66 TCTTGTCTTTTTCATACTTCAATTTTACTCCATTGCTTTGTTTTGTTATCATTTCACAACAAAAT
* *
18936 TTCATTTCTTAACTGAATTTTCTTAAAAGAAATTTTTTTTTAAAATAAAACAGCCGCACGCGAAG
131 GTCATTTCTTAACTGAATTTTCTTAAAAGAAATTTTTTTTAAAAATAAAACAGCCGCACGCGAAG
19001 CGCAGTCGGAAAGTTCTAGTATACATTATTATTACGTACGTTAAACTGTTAAAGTTTCATGATTG
196 CGCAGTCGGAAAGTTCTAGTATACATTATTATTACGTACGTTAAACTGTTAAAGTTTCATGATTG
19066 CCCTTATCTTGTATCATTATCATATAATTATGTACGTAGTATAGTGTAAAGTTTCTTCTAGTTAC
261 CCCTTATCTTGTATCATTATCATATAATTATGTACGTAGTATAGTGTAAAGTTTCTTCTAGTTAC
*
19131 TTAGATTGTAAACTTTAAAATTAATTTTATTCAATTTAAGTTTATGACCTCGAACAAATTAATAA
326 TTAGATTGTAAACTTTAAAATTAATTTTATTCAATTTAAGTTTATCACCTCGAACAAATTAATAA
19196 TTTTATAAGCAAGGTTCCCATTGAGAAACACATGGCATTTGATTTATTTGACAAGTGTCAATAGT
391 TTTTATAAGCAAGGTTCCCATTGAGAAACACATGGCATTTGATTTATTTGACAAGTGTCAATAGT
19261 TAATTTTCTAATATTTTGTTTATTAT
456 TAATTTTCTAATATTTTGTTTATTAT
19287 AATGAGAACAATTTCTCACATTCTTTATATTTTCTTCTTCTCCATATTCTATTGTCTTTCTATTC
1 AATGAGAACAATTTCTCACATTCTTTATATTTTCTTCTTCTCCATATTCTATTGTCTTTCTATTC
*
19352 TCTTGTC-TTTTCTATACTTCAATTTTACTCCATTGCTTTGTTTTGTTATTATTTCACAACAAAA
66 TCTTGTCTTTTTC-ATACTTCAATTTTACTCCATTGCTTTGTTTTGTTATCATTTCACAACAAAA
19416 TGTCATTTCTTAACTGAATTTTCTTAAAAG-AA-TTTTTTTAAAAATAAAACAGCCGCACGCGAA
130 TGTCATTTCTTAACTGAATTTTCTTAAAAGAAATTTTTTTTAAAAATAAAACAGCCGCACGCGAA
*
19479 GCGCGGTCGGAAAGTTCTAGTATACATTATTATTACGTACGTTAAACTGTTAAAGTTTCATGATT
195 GCGCAGTCGGAAAGTTCTAGTATACATTATTATTACGTACGTTAAACTGTTAAAGTTTCATGATT
19544 GCCCTTATCTTGTATCATTATCATATAATTATGTACGTAGTATAGTGTAAAGTTTCTTCTAGTTA
260 GCCCTTATCTTGTATCATTATCATATAATTATGTACGTAGTATAGTGTAAAGTTTCTTCTAGTTA
19609 CTTAGATTGTAAACTTTAAAATTAATTTTATTCAATTTAAGTTTATCACCTCGAACAAATTAATA
325 CTTAGATTGTAAACTTTAAAATTAATTTTATTCAATTTAAGTTTATCACCTCGAACAAATTAATA
19674 ATTTTATAAGCAAGGTTCCCATTGAGAAACACATGGCATTTGATTTATTTGACAAGTGTCAATAG
390 ATTTTATAAGCAAGGTTCCCATTGAGAAACACATGGCATTTGATTTATTTGACAAGTGTCAATAG
19739 TTAATTTTCTAATATTTTGTTTATTAT
455 TTAATTTTCTAATATTTTGTTTATTAT
19766 A
1 A
19767 TTTGTATTCA
Statistics
Matches: 474, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
479 316 0.67
480 7 0.01
481 151 0.32
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (481 bp):
AATGAGAACAATTTCTCACATTCTTTATATTTTCTTCTTCTCCATATTCTATTGTCTTTCTATTC
TCTTGTCTTTTTCATACTTCAATTTTACTCCATTGCTTTGTTTTGTTATCATTTCACAACAAAAT
GTCATTTCTTAACTGAATTTTCTTAAAAGAAATTTTTTTTAAAAATAAAACAGCCGCACGCGAAG
CGCAGTCGGAAAGTTCTAGTATACATTATTATTACGTACGTTAAACTGTTAAAGTTTCATGATTG
CCCTTATCTTGTATCATTATCATATAATTATGTACGTAGTATAGTGTAAAGTTTCTTCTAGTTAC
TTAGATTGTAAACTTTAAAATTAATTTTATTCAATTTAAGTTTATCACCTCGAACAAATTAATAA
TTTTATAAGCAAGGTTCCCATTGAGAAACACATGGCATTTGATTTATTTGACAAGTGTCAATAGT
TAATTTTCTAATATTTTGTTTATTAT
Found at i:19859 original size:11 final size:12
Alignment explanation
Indices: 19817--19857 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
19807 TCCCTTTCTA
*
19817 TATAAAATAAAT
1 TATAAAATTAAT
*
19829 TATCAAA-TAAT
1 TATAAAATTAAT
19840 TATAAAATTAAT
1 TATAAAATTAAT
19852 TATAAA
1 TATAAA
19858 TTTGTTATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
TATAAAATTAAT
Found at i:22826 original size:18 final size:20
Alignment explanation
Indices: 22790--22839 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
22780 GTGGAGAAGG
22790 TGGTGGTGGAGGCCGTGGAAA
1 TGGTGGTGGA-GCCGTGGAAA
*
22811 TGGTGGTGGAG-C-TGGATA
1 TGGTGGTGGAGCCGTGGAAA
*
22829 TGTTGGTGGAG
1 TGGTGGTGGAG
22840 GAGAGCATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 15 0.56
19 1 0.04
20 1 0.04
21 10 0.37
ACGTcount: A:0.16, C:0.06, G:0.52, T:0.26
Consensus pattern (20 bp):
TGGTGGTGGAGCCGTGGAAA
Found at i:22919 original size:9 final size:9
Alignment explanation
Indices: 22905--22982 Score: 61
Period size: 9 Copynumber: 8.7 Consensus size: 9
22895 TGGAGCTTCA
22905 GGTGGATAT
1 GGTGGATAT
22914 GGTGGATAT
1 GGTGGATAT
* *
22923 AGAGGATAT
1 GGTGGATAT
* *
22932 GGAGGTTCA-
1 GGTGGAT-AT
22941 GGTGGATAT
1 GGTGGATAT
*
22950 GGAGGATAT
1 GGTGGATAT
* *
22959 GGAGGTTCA-
1 GGTGGAT-AT
22968 GGTGGATAT
1 GGTGGATAT
22977 GGTGGA
1 GGTGGA
22983 GGTGGAAAAG
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
8 2 0.04
9 51 0.93
10 2 0.04
ACGTcount: A:0.26, C:0.03, G:0.45, T:0.27
Consensus pattern (9 bp):
GGTGGATAT
Found at i:22947 original size:18 final size:18
Alignment explanation
Indices: 22893--22954 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
22883 CGATTCTGGC
*
22893 TATGGAGCTTCAGGTGGA
1 TATGGAGGTTCAGGTGGA
* *
22911 TATGGTGGATAT-A-GAGGA
1 TATGGAGG-T-TCAGGTGGA
22929 TATGGAGGTTCAGGTGGA
1 TATGGAGGTTCAGGTGGA
22947 TATGGAGG
1 TATGGAGG
22955 ATATGGAGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 1 0.03
17 2 0.06
18 29 0.83
19 2 0.06
20 1 0.03
ACGTcount: A:0.26, C:0.05, G:0.42, T:0.27
Consensus pattern (18 bp):
TATGGAGGTTCAGGTGGA
Found at i:22957 original size:36 final size:36
Alignment explanation
Indices: 22893--22963 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
22883 CGATTCTGGC
*
22893 TATGGAGCTTCAGGTGGATATGGTGGATATAGAGGA
1 TATGGAGCTTCAGGTGGATATGGAGGATATAGAGGA
* *
22929 TATGGAGGTTCAGGTGGATATGGAGGATATGGAGG
1 TATGGAGCTTCAGGTGGATATGGAGGATATAGAGG
22964 TTCAGGTGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.27, C:0.04, G:0.42, T:0.27
Consensus pattern (36 bp):
TATGGAGCTTCAGGTGGATATGGAGGATATAGAGGA
Found at i:22977 original size:27 final size:27
Alignment explanation
Indices: 22914--22978 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
22904 AGGTGGATAT
*
22914 GGTGGATATAGAGGATATGGAGGTTCA
1 GGTGGATATGGAGGATATGGAGGTTCA
22941 GGTGGATATGGAGGATATGGAGGTTCA
1 GGTGGATATGGAGGATATGGAGGTTCA
22968 GGTGGATATGG
1 GGTGGATATGG
22979 TGGAGGTGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.26, C:0.03, G:0.45, T:0.26
Consensus pattern (27 bp):
GGTGGATATGGAGGATATGGAGGTTCA
Found at i:22988 original size:27 final size:27
Alignment explanation
Indices: 22914--22988 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
22904 AGGTGGATAT
* *
22914 GGTGGATATAGAGGATATGGAGGTTCA
1 GGTGGATATGGAGGAGATGGAGGTTCA
*
22941 GGTGGATATGGAGGATATGGAGGTTCA
1 GGTGGATATGGAGGAGATGGAGGTTCA
* *
22968 GGTGGATATGGTGGAGGTGGA
1 GGTGGATATGGAGGAGATGGA
22989 AAAGGTTCTG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.25, C:0.03, G:0.47, T:0.25
Consensus pattern (27 bp):
GGTGGATATGGAGGAGATGGAGGTTCA
Done.