Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014097.1 Corchorus capsularis cultivar CVL-1 contig14118, 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: 5140
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Found at i:357 original size:36 final size:36
Alignment explanation
Indices: 311--1057 Score: 837
Period size: 36 Copynumber: 21.1 Consensus size: 36
301 TAATCAGTAC
* * *
311 TAATCAGTAAAGAGTAAAAT-GCTGAAGAGTCAAGAG
1 TAATCAGTAAAGAGTAAAATAG-TAAAAAGTAAAGAG
* * * *
347 TAATTAGTAAAGAATAAAATAGTGAAAAGTAAAGAC
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
* * *
383 TAATCAGTAAA-AGGTAAAATGGTAAAGAGTCAAGAG
1 TAATCAGTAAAGA-GTAAAATAGTAAAAAGTAAAGAG
* *
419 CAATCAGTAAAGAGTAGAATAGT----A--AAA-AG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
* * **
448 TAATCTGTAAAGAGTAAAATAGTAAAGAGTCGAGAG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
* * *
484 CAATCAGTAAAGAGTAGAATAGTAAAAAGTAAAAAG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
* *
520 TAATCAGTAAAG-GTAAAATGGTAAAGAGTAAAGAG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
* * *
555 TAATCAGTAAAAAGTAGAATAGTAAAAAGTAAAAAG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
* * *
591 TAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGAG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
627 TAATCAGTAAAGAGTAAAATAGTAAAAAG-AAAGAG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
*
662 TAATCAAT-AAGAGGTAAAAT-GATAAAAAGTAAAGAG
1 TAATCAGTAAAGA-GTAAAATAG-TAAAAAGTAAAGAG
* * *
698 TAATCAGTAAAAAGTAGAATAGTAAAAAGTAAAAAG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
* * *
734 TAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGAG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
770 TAATCAGTAAAGAGTAAAATAGTAAAAAG-AAAGAG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
805 TAATCAGT-AAGAGGTAAAAT-GATAAAAAGTAAAGAG
1 TAATCAGTAAAGA-GTAAAATAG-TAAAAAGTAAAGAG
* * *
841 TAATCAGTAAAAAGTAGAATAGTAAAAAGTAAAAAG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
* * * *
877 TAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGTG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
*
913 TAATCAGTCAAGAGTAAAATAGTAAAAAG-AAAGAG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
*
948 TAATCAGT-AAGAGGTAAAATGGTAAAAAGTAAAGAG
1 TAATCAGTAAAGA-GTAAAATAGTAAAAAGTAAAGAG
* * * *
984 TAATCAGTAAAAAGTAAAATGGTAAAAAGTAAAAAA
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
* * * * *
1020 TAATCAGCAAAAAGTAAAATGGTAAAGAGTAAATAG
1 TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
1056 TA
1 TA
1058 GTAAAGTGAA
Statistics
Matches: 603, Mismatches: 84, Indels: 48
0.82 0.11 0.07
Matches are distributed among these distances:
29 22 0.04
30 2 0.00
32 1 0.00
33 1 0.00
34 14 0.02
35 112 0.19
36 438 0.73
37 13 0.02
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.19
Consensus pattern (36 bp):
TAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
Found at i:452 original size:29 final size:28
Alignment explanation
Indices: 420--894 Score: 149
Period size: 29 Copynumber: 16.6 Consensus size: 28
410 AGTCAAGAGC
420 AATCAGTAAAGAGTAGAATAGTAAAAAGT
1 AATCAGTAAAGAGTA-AATAGTAAAAAGT
* *
449 AATCTGTAAAGAGTAAAATAGTAAAGAGTCGAGAGC
1 AATCAGTAAAGAGT-AAATAGT-AA-A----A-AGT
485 AATCAGTAAAGAGTAGAATAGTAAAAAGT
1 AATCAGTAAAGAGTA-AATAGTAAAAAGT
** ** * *
514 AAAAAGTAATCAGTAAA-GGTAAAATGGT
1 AATCAGTAAAGAGTAAATAGTAAAA-AGT
**
542 AAAGAGTAAAGAGT-AATCAGTAAAAAGT
1 AATCAGTAAAGAGTAAAT-AGTAAAAAGT
* * **
570 AGAAT-AGTAAAAAGTAAAAAGTAATCAGT
1 --AATCAGTAAAGAGTAAATAGTAAAAAGT
** * * *
599 AAAGAGTAAA-ATGGTAAAGAGTCAAGAGT
1 AATCAGTAAAGA--GTAAATAGTAAAAAGT
628 AATCAGTAAAGAGTAAAATAGTAAAAAG-
1 AATCAGTAAAGAGT-AAATAGTAAAAAGT
** ** * * *
656 AAAGAGTAATCAATAAGA-GGTAAAATGAT
1 AATCAGTAAAGAGTAA-ATAGTAAAAAG-T
**
685 AAAAAGTAAAGAGT-AATCAGTAAAAAGT
1 AATCAGTAAAGAGTAAAT-AGTAAAAAGT
* * **
713 AGAAT-AGTAAAAAGTAAAAAGTAATCAGT
1 --AATCAGTAAAGAGTAAATAGTAAAAAGT
** * * *
742 AAAGAGTAAA-ATGGTAAAGAGTCAAGAGT
1 AATCAGTAAAGA--GTAAATAGTAAAAAGT
771 AATCAGTAAAGAGTAAAATAGTAAAAAG-
1 AATCAGTAAAGAGT-AAATAGTAAAAAGT
** ** * *
799 AAAGAGTAATCAGTAAGA-GGTAAAATGAT
1 AATCAGTAAAGAGTAA-ATAGTAAAAAG-T
**
828 AAAAAGTAAAGAGT-AATCAGTAAAAAG-
1 AATCAGTAAAGAGTAAAT-AGTAAAAAGT
* *
855 --T-AG--AATAGTAAAAAGTAAAAAGT
1 AATCAGTAAAGAGTAAATAGTAAAAAGT
878 AATCAGTAAAGAGTAAA
1 AATCAGTAAAGAGTAAA
895 ATGGTAAAGA
Statistics
Matches: 328, Mismatches: 73, Indels: 91
0.67 0.15 0.18
Matches are distributed among these distances:
22 14 0.04
23 2 0.01
24 2 0.01
25 1 0.00
26 2 0.01
27 34 0.10
28 65 0.20
29 167 0.51
30 14 0.04
31 1 0.00
34 1 0.00
35 4 0.01
36 21 0.06
ACGTcount: A:0.56, C:0.04, G:0.21, T:0.19
Consensus pattern (28 bp):
AATCAGTAAAGAGTAAATAGTAAAAAGT
Found at i:483 original size:22 final size:23
Alignment explanation
Indices: 424--806 Score: 105
Period size: 22 Copynumber: 17.5 Consensus size: 23
414 AAGAGCAATC
*
424 AGTAAAGAGTAGAATAGTAAAA-
1 AGTAAAGAGTAGAAGAGTAAAAT
***
446 AGTAATCTGTA-AAGAGTAAAAT
1 AGTAAAGAGTAGAAGAGTAAAAT
* *
468 AGTAAAGAGTCG-AGAG--CAAT
1 AGTAAAGAGTAGAAGAGTAAAAT
*
488 CAGTAAAGAGTAGAATAGTAAAA-
1 -AGTAAAGAGTAGAAGAGTAAAAT
*
511 AGTAAAAAGTA-ATCAGTAAAGGTAAAAT
1 AGTAAAGAGTAGA--AG---A-GTAAAAT
*
539 GGTAAAGAGTA-AAGAGT--AAT
1 AGTAAAGAGTAGAAGAGTAAAAT
* *
559 CAGTAAAAAGTAGAATAGTAAAA-
1 -AGTAAAGAGTAGAAGAGTAAAAT
* ** *
582 AGTAAAAAGTA-ATCAGT-AAAG
1 AGTAAAGAGTAGAAGAGTAAAAT
* *
603 AGTAAA-ATGGTA-AAGAGT-CAAG
1 AGTAAAGA--GTAGAAGAGTAAAAT
**
625 AGTAATCAGTA-AAGAGTAAAAT
1 AGTAAAGAGTAGAAGAGTAAAAT
*
647 AGTAAAAAG-A-AAGAGT--AAT
1 AGTAAAGAGTAGAAGAGTAAAAT
* *
666 CAAT-AAGAGGTAAAATGA-TAAAA-
1 -AGTAAAGA-GTAGAA-GAGTAAAAT
**
689 AGTAAAGAGTA-ATCAGTAAAA-
1 AGTAAAGAGTAGAAGAGTAAAAT
* *
710 AGTAGAATAGTA-AAAAGTAAAA-
1 AGTA-AAGAGTAGAAGAGTAAAAT
**
732 AGTAATCAGTA-AAGAGTAAAAT
1 AGTAAAGAGTAGAAGAGTAAAAT
* *
754 GGTAAAGAGT-CAAGAGT--AAT
1 AGTAAAGAGTAGAAGAGTAAAAT
* *
774 CAGTAAAGAGTAAAATAGTAAAA-
1 -AGTAAAGAGTAGAAGAGTAAAAT
797 AG-AAAGAGTA
1 AGTAAAGAGTA
807 ATCAGTAAGA
Statistics
Matches: 277, Mismatches: 46, Indels: 77
0.69 0.12 0.19
Matches are distributed among these distances:
19 6 0.02
20 17 0.06
21 98 0.35
22 120 0.43
23 9 0.03
24 8 0.03
26 3 0.01
27 6 0.02
28 10 0.04
ACGTcount: A:0.56, C:0.04, G:0.21, T:0.19
Consensus pattern (23 bp):
AGTAAAGAGTAGAAGAGTAAAAT
Found at i:576 original size:107 final size:107
Alignment explanation
Indices: 311--1057 Score: 795
Period size: 107 Copynumber: 7.0 Consensus size: 107
301 TAATCAGTAC
* * * * * *
311 TAATCAGTAAAGAGTAAAATGCTGAAGAGTCAAGAGTAATTAGTAAAGAA-TAAAATAGTGAAAA
1 TAATCAGTAAAG-GTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAA-AAGTAAAATAGTAAAAA
* * * *
375 GTAAAGACTAATCAGTAAA-AGGTAAAATGGTAAAGAGTCAAGAG
64 GTAAAGAGTAATCAGTAAAGA-GTAAAATAGTAAAAAGTAAAGAG
* * * * * *
419 CAATCAGTAAA-G----A--GTAGAATAGTAAAAAGTAATCTGTAAAGAGTAAAATAGTAAAGAG
1 TAATCAGTAAAGGTAAAATGGTA-AAAAGTAAAGAGTAATCAGTAAAAAGTAAAATAGTAAAAAG
** * * *
477 TCGAGAGCAATCAGTAAAGAGTAGAATAGTAAAAAGTAAAAAG
65 TAAAGAGTAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
* *
520 TAATCAGTAAAGGTAAAATGGTAAAGAGTAAAGAGTAATCAGTAAAAAGTAGAATAGTAAAAAGT
1 TAATCAGTAAAGGTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGTAAAATAGTAAAAAGT
* * * *
585 AAAAAGTAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGAG
66 AAAGAGTAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
* * * *
627 TAATCAGTAAAGAGTAAAATAGTAAAAAG-AAAGAGTAATCAATAAGAGGTAAAAT-GATAAAAA
1 TAATCAGTAAAG-GTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGTAAAATAG-TAAAAA
* * *
690 GTAAAGAGTAATCAGTAAAAAGTAGAATAGTAAAAAGTAAAAAG
64 GTAAAGAGTAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
* * *
734 TAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGAGTAATCAGTAAAGAGTAAAATAGTAAAAAG
1 TAATCAGTAAAG-GTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGTAAAATAGTAAAAAG
799 -AAAGAGTAATCAGT-AAGAGGTAAAAT-GATAAAAAGTAAAGAG
65 TAAAGAGTAATCAGTAAAGA-GTAAAATAG-TAAAAAGTAAAGAG
* * * * * * *
841 TAATCAGTAAAAAGTAGAATAGTAAAAAGTAAAAAGTAATCAGTAAAGAGTAAAATGGTAAAGAG
1 TAATCAGT-AAAGGTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGTAAAATAGTAAAAAG
* * *
906 TCAAGTGTAATCAGTCAAGAGTAAAATAGTAAAAAG-AAAGAG
65 TAAAGAGTAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
*
948 TAATCAGTAAGAGGTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGTAAAATGGTAAAAAG
1 TAATCAGTAA-AGGTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGTAAAATAGTAAAAAG
* * * * * * *
1013 TAAAAAATAATCAGCAAAAAGTAAAATGGTAAAGAGTAAATAG
65 TAAAGAGTAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
1056 TA
1 TA
1058 GTAAAGTGAA
Statistics
Matches: 532, Mismatches: 85, Indels: 44
0.80 0.13 0.07
Matches are distributed among these distances:
100 2 0.00
101 73 0.14
102 3 0.01
106 9 0.02
107 348 0.65
108 91 0.17
109 6 0.01
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.19
Consensus pattern (107 bp):
TAATCAGTAAAGGTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGTAAAATAGTAAAAAGT
AAAGAGTAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAG
Found at i:641 original size:143 final size:143
Alignment explanation
Indices: 311--1049 Score: 1152
Period size: 143 Copynumber: 5.2 Consensus size: 143
301 TAATCAGTAC
* * * * *
311 TAATCAGTAAAGAGTAAAATGCTGAAGAGTCAAGAGTAATTAGTAAAGAATAAAATAGTGAAAAG
1 TAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGAGTAATCAGTAAAGAGTAAAATAGTAAAAAG
* * * * *
376 TAAAGACTAATCAGTAAAAGGTAAAATGGTAAAGAGTCAAGAGCAATCAGT--AAAG-AG--TAG
66 -AAAGAGTAATCAGTAAGAGGTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGTAGAATAG
*
436 --AATAGTAAAAAG
130 TAAAAAGTAAAAAG
* * * * *
448 TAATCTGTAAAGAGTAAAATAGTAAAGAGTCGAGAGCAATCAGTAAAGAGTAGAATAGTAAAAAG
1 TAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGAGTAATCAGTAAAGAGTAAAATAGTAAAAAG
* *
513 TAAAAAGTAATCAGTAA-AGGTAAAATGGTAAAGAGTAAAGAGTAATCAGTAAAAAGTAGAATAG
66 -AAAGAGTAATCAGTAAGAGGTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGTAGAATAG
577 TAAAAAGTAAAAAG
130 TAAAAAGTAAAAAG
591 TAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGAGTAATCAGTAAAGAGTAAAATAGTAAAAAG
1 TAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGAGTAATCAGTAAAGAGTAAAATAGTAAAAAG
* *
656 AAAGAGTAATCAATAAGAGGTAAAATGATAAAAAGTAAAGAGTAATCAGTAAAAAGTAGAATAGT
66 AAAGAGTAATCAGTAAGAGGTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGTAGAATAGT
721 AAAAAGTAAAAAG
131 AAAAAGTAAAAAG
734 TAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGAGTAATCAGTAAAGAGTAAAATAGTAAAAAG
1 TAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGAGTAATCAGTAAAGAGTAAAATAGTAAAAAG
*
799 AAAGAGTAATCAGTAAGAGGTAAAATGATAAAAAGTAAAGAGTAATCAGTAAAAAGTAGAATAGT
66 AAAGAGTAATCAGTAAGAGGTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGTAGAATAGT
864 AAAAAGTAAAAAG
131 AAAAAGTAAAAAG
* *
877 TAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGTGTAATCAGTCAAGAGTAAAATAGTAAAAAG
1 TAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGAGTAATCAGTAAAGAGTAAAATAGTAAAAAG
* *
942 AAAGAGTAATCAGTAAGAGGTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGTAAAATGGT
66 AAAGAGTAATCAGTAAGAGGTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGTAGAATAGT
*
1007 AAAAAGTAAAAAA
131 AAAAAGTAAAAAG
* *
1020 TAATCAGCAAAAAGTAAAATGGTAAAGAGT
1 TAATCAGTAAAGAGTAAAATGGTAAAGAGT
1050 AAATAGTAGT
Statistics
Matches: 561, Mismatches: 33, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
136 31 0.06
137 70 0.12
138 4 0.01
139 2 0.00
141 3 0.01
142 14 0.02
143 437 0.78
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.19
Consensus pattern (143 bp):
TAATCAGTAAAGAGTAAAATGGTAAAGAGTCAAGAGTAATCAGTAAAGAGTAAAATAGTAAAAAG
AAAGAGTAATCAGTAAGAGGTAAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGTAGAATAGT
AAAAAGTAAAAAG
Found at i:1008 original size:22 final size:21
Alignment explanation
Indices: 489--1057 Score: 245
Period size: 21 Copynumber: 27.5 Consensus size: 21
479 GAGAGCAATC
* * *
489 AGTAAAGAGTAGAATAGTAAAA
1 AGTAAAAAGTA-AAAAGTAAAG
**
511 AGTAAAAAGTAATCAGTAAAG
1 AGTAAAAAGTAAAAAGTAAAG
*** ** *
532 GTAAAATGGTAAAGAGTAAAG
1 AGTAAAAAGTAAAAAGTAAAG
** *
553 AGTAATCAGTAAAAAGTAGAAT
1 AGTAAAAAGTAAAAAGTA-AAG
**
575 AGTAAAAAGTAAAAAGTAATC
1 AGTAAAAAGTAAAAAGTAAAG
* *
596 AGTAAAGAGTAAAATGGTAAAG
1 AGTAAAAAGTAAAA-AGTAAAG
* * **
618 AGTCAAGAGTAATCAGTAAAG
1 AGTAAAAAGTAAAAAGTAAAG
639 AGTAAAATAGTAAAAAG-AAAG
1 AGTAAAA-AGTAAAAAGTAAAG
*
660 AGT---AA-T--CAA-TAAGAG
1 AGTAAAAAGTAAAAAGTAA-AG
*
675 -GTAAAATGATAAAAAGTAAAG
1 AGTAAAAAG-TAAAAAGTAAAG
** *
696 AGTAATCAGTAAAAAGTAGAAT
1 AGTAAAAAGTAAAAAGTA-AAG
**
718 AGTAAAAAGTAAAAAGTAATC
1 AGTAAAAAGTAAAAAGTAAAG
* *
739 AGTAAAGAGTAAAATGGTAAAG
1 AGTAAAAAGTAAAA-AGTAAAG
* * **
761 AGTCAAGAGTAATCAGTAAAG
1 AGTAAAAAGTAAAAAGTAAAG
782 AGTAAAATAGTAAAAAG-AAAG
1 AGTAAAA-AGTAAAAAGTAAAG
**
803 AGTAATCAGT---AAG---AG
1 AGTAAAAAGTAAAAAGTAAAG
*
818 -GTAAAATGATAAAAAGTAAAG
1 AGTAAAAAG-TAAAAAGTAAAG
** *
839 AGTAATCAGTAAAAAGTAGAAT
1 AGTAAAAAGTAAAAAGTA-AAG
**
861 AGTAAAAAGTAAAAAGTAATC
1 AGTAAAAAGTAAAAAGTAAAG
* *
882 AGTAAAGAGTAAAATGGTAAAG
1 AGTAAAAAGTAAAA-AGTAAAG
* ** ** *
904 AGTCAAGTGTAATCAGTCAAG
1 AGTAAAAAGTAAAAAGTAAAG
925 AGTAAAATAGTAAAAAG-AAAG
1 AGTAAAA-AGTAAAAAGTAAAG
**
946 AGTAATCAGT---AAG---AG
1 AGTAAAAAGTAAAAAGTAAAG
*
961 -GTAAAATGGTAAAAAGTAAAG
1 AGTAAAA-AGTAAAAAGTAAAG
**
982 AGTAATCAGTAAAAAGTAAAATG
1 AGTAAAAAGTAAAAAGT-AAA-G
* **
1005 -GTAAAAAGTAAAAAATAATC
1 AGTAAAAAGTAAAAAGTAAAG
* *
1025 AGCAAAAAGTAAAATGGTAAAG
1 AGTAAAAAGTAAAA-AGTAAAG
*
1047 AGTAAATAGTA
1 AGTAAAAAGTA
1058 GTAAAGTGAA
Statistics
Matches: 400, Mismatches: 107, Indels: 80
0.68 0.18 0.14
Matches are distributed among these distances:
14 15 0.04
15 9 0.02
16 1 0.00
17 8 0.02
18 7 0.02
19 1 0.00
20 6 0.01
21 179 0.45
22 173 0.43
23 1 0.00
ACGTcount: A:0.57, C:0.04, G:0.21, T:0.19
Consensus pattern (21 bp):
AGTAAAAAGTAAAAAGTAAAG
Found at i:1147 original size:24 final size:25
Alignment explanation
Indices: 1087--1147 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
1077 CAGTAAAGTA
*
1087 AAAAAG-GTAAAATTGGTATTCAGT
1 AAAAAGTGTAAAATTGATATTCAGT
*
1111 AGTAAAGTG-AAAA-TGATATTCAGT
1 A-AAAAGTGTAAAATTGATATTCAGT
1135 AAAAAGTGTAAAA
1 AAAAAGTGTAAAA
1148 ATGGTTCAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.19
24 16 0.52
25 8 0.26
26 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.20, T:0.26
Consensus pattern (25 bp):
AAAAAGTGTAAAATTGATATTCAGT
Found at i:1225 original size:25 final size:24
Alignment explanation
Indices: 1162--1226 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
1152 TTCAGTAAAG
1162 TAAA-AAAAAGGTTAAAAATGGTAT
1 TAAACAAAAAGG-TAAAAATGGTAT
1186 TAAAC-AAAAGAGTAAAAATGGTAT
1 TAAACAAAAAG-GTAAAAATGGTAT
*
1210 TAAGCAAAAATGGTAAA
1 TAAACAAAAA-GGTAAA
1227 GTAAAAAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
24 25 0.69
25 10 0.28
26 1 0.03
ACGTcount: A:0.58, C:0.03, G:0.17, T:0.22
Consensus pattern (24 bp):
TAAACAAAAAGGTAAAAATGGTAT
Found at i:1265 original size:26 final size:26
Alignment explanation
Indices: 1214--1283 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 26
1204 TGGTATTAAG
1214 CAAAAATGGTA--AAGTAAAAAAAGT
1 CAAAAATGGTATCAAGTAAAAAAAGT
* **
1238 CAAAAATGGTATCAAGTAAATAGGGT
1 CAAAAATGGTATCAAGTAAAAAAAGT
1264 CAAAAATGGTATCAAGTAAA
1 CAAAAATGGTATCAAGTAAA
1284 GTATGGTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 11 0.27
26 30 0.73
ACGTcount: A:0.54, C:0.07, G:0.19, T:0.20
Consensus pattern (26 bp):
CAAAAATGGTATCAAGTAAAAAAAGT
Found at i:1312 original size:43 final size:43
Alignment explanation
Indices: 1243--1326 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
1233 AAAGTCAAAA
1243 ATGGTATCAAGTAAATAGGGTCAAAAATGGTATCAAGTAAAGT
1 ATGGTATCAAGTAAATAGGGTCAAAAATGGTATCAAGTAAAGT
* *
1286 ATGGTATTAAGTAAGA-A-GGTCAAAAAATGGTATTAAGTAAA
1 ATGGTATCAAGTAA-ATAGGGTC-AAAAATGGTATCAAGTAAA
1327 AGAGTAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 4 0.11
43 32 0.86
44 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.23, T:0.26
Consensus pattern (43 bp):
ATGGTATCAAGTAAATAGGGTCAAAAATGGTATCAAGTAAAGT
Found at i:1322 original size:26 final size:27
Alignment explanation
Indices: 1286--1353 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 27
1276 CAAGTAAAGT
*
1286 ATGGTATTAAGTAAGAAG-GTCA-AAAA
1 ATGGTATTAAGTAA-AAGAGTAAGAAAA
1312 ATGGTATTAAGTAAAAGAGTAAGAAAA
1 ATGGTATTAAGTAAAAGAGTAAGAAAA
*
1339 ATGGTA-AAAGTAAAA
1 ATGGTATTAAGTAAAA
1354 ATGATAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 3 0.08
26 25 0.66
27 10 0.26
ACGTcount: A:0.54, C:0.01, G:0.22, T:0.22
Consensus pattern (27 bp):
ATGGTATTAAGTAAAAGAGTAAGAAAA
Found at i:1355 original size:15 final size:15
Alignment explanation
Indices: 1335--1365 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1325 AAAGAGTAAG
*
1335 AAAAATGGTAAAAGT
1 AAAAATGATAAAAGT
1350 AAAAATGATAAAAGT
1 AAAAATGATAAAAGT
1365 A
1 A
1366 GCAAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (15 bp):
AAAAATGATAAAAGT
Found at i:2735 original size:33 final size:33
Alignment explanation
Indices: 2689--2753 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
2679 ATCCTCACAC
2689 TTTTTATGCTTTATGCTATTTAATCATTTACAT
1 TTTTTATGCTTTATGCTATTTAATCATTTACAT
* *
2722 TTTTTATGTTTTATGCTATTTAATCCTTTACA
1 TTTTTATGCTTTATGCTATTTAATCATTTACA
2754 ATTATGGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.12, G:0.06, T:0.58
Consensus pattern (33 bp):
TTTTTATGCTTTATGCTATTTAATCATTTACAT
Found at i:3232 original size:40 final size:41
Alignment explanation
Indices: 3187--3325 Score: 167
Period size: 41 Copynumber: 3.4 Consensus size: 41
3177 TTTAATCACC
*
3187 ATCTCTCTTAGGGTTTAGCTTGATTTT-GAGGGTTTGTTTT
1 ATCTCTCTTAGGGTTTAGCTTGATTTTAGGGGGTTTGTTTT
* * *
3227 ATCTCTCCTATGGTTTAGCTTTG-TTTTAGGGGTGTTTGATTT
1 ATCTCTCTTAGGGTTTAGC-TTGATTTTAGGGG-GTTTGTTTT
* *
3269 CTCTCTTTTAGGGTTTAGCTT-ATTTTAGGGGGTTATGTTTT
1 ATCTCTCTTAGGGTTTAGCTTGATTTTAGGGGGTT-TGTTTT
*
3310 ATCTTTCTTAGGGTTT
1 ATCTCTCTTAGGGTTT
3326 GGGCTTACTT
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
40 24 0.29
41 35 0.43
42 23 0.28
ACGTcount: A:0.12, C:0.11, G:0.24, T:0.53
Consensus pattern (41 bp):
ATCTCTCTTAGGGTTTAGCTTGATTTTAGGGGGTTTGTTTT
Found at i:3263 original size:38 final size:40
Alignment explanation
Indices: 3187--3325 Score: 106
Period size: 40 Copynumber: 3.4 Consensus size: 40
3177 TTTAATCACC
* *
3187 ATCTCTCTTAGGGTTTAGCTTGATTTTGAGGGTTTGTTTT
1 ATCTCTCCTAGGGTTTAGCTTGATTTTGAGGGTGTGTTTT
*
3227 ATCTCTCCTATGGTTTAGCTTTG-TTTT-AGGG-GTGTTTGAT
1 ATCTCTCCTAGGGTTTAGC-TTGATTTTGAGGGTGTGTTT--T
* * * *
3267 TTCTCTCTTTTAGGGTTTAGCTT-ATTTTAGGGGGTTATGTTTT
1 ATCTCTC--CTAGGGTTTAGCTTGATTTT-GAGGG-TGTGTTTT
* *
3310 ATCTTTCTTAGGGTTT
1 ATCTCTCCTAGGGTTT
3326 GGGCTTACTT
Statistics
Matches: 79, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
38 5 0.06
39 4 0.05
40 28 0.35
41 18 0.23
42 10 0.13
43 9 0.11
45 5 0.06
ACGTcount: A:0.12, C:0.11, G:0.24, T:0.53
Consensus pattern (40 bp):
ATCTCTCCTAGGGTTTAGCTTGATTTTGAGGGTGTGTTTT
Found at i:4153 original size:2 final size:2
Alignment explanation
Indices: 4146--4175 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4136 AGGTAAATCT
4146 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
4176 GTTTTTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4529 original size:55 final size:55
Alignment explanation
Indices: 4364--4517 Score: 299
Period size: 55 Copynumber: 2.8 Consensus size: 55
4354 TTTGTCTTTT
*
4364 TAGCTCTTAGGATAATTGATATTATGTTGATATGGATATAATTGGTACCCGCAAG
1 TAGCTCTTAGGATAATTGATTTTATGTTGATATGGATATAATTGGTACCCGCAAG
4419 TAGCTCTTAGGATAATTGATTTTATGTTGATATGGATATAATTGGTACCCGCAAG
1 TAGCTCTTAGGATAATTGATTTTATGTTGATATGGATATAATTGGTACCCGCAAG
4474 TAGCTCTTAGGATAATTGATTTTATGTTGATATGGATATAATTG
1 TAGCTCTTAGGATAATTGATTTTATGTTGATATGGATATAATTG
4518 ATATCAGCAA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 98 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (55 bp):
TAGCTCTTAGGATAATTGATTTTATGTTGATATGGATATAATTGGTACCCGCAAG
Done.