Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011293.1 Corchorus capsularis cultivar CVL-1 contig11314, 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: 4448
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Found at i:179 original size:14 final size:14
Alignment explanation
Indices: 142--181 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
132 GATGGTAAAG
*
142 AGTAAAGAATAATC
1 AGTAAAGAGTAATC
* *
156 AGTAAGGAGTAATT
1 AGTAAAGAGTAATC
170 AGTAAAGAGTAA
1 AGTAAAGAGTAA
182 AATGATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.23
Consensus pattern (14 bp):
AGTAAAGAGTAATC
Found at i:240 original size:35 final size:36
Alignment explanation
Indices: 163--283 Score: 115
Period size: 35 Copynumber: 3.4 Consensus size: 36
153 ATCAGTAAGG
* * *
163 AGTAATTAGTAAAGAGTAA-AATGATAAAAAAGTAAAG
1 AGTAATCAGTAAA-AGAAAGAATGAT-AAAAAGTAAAA
*
200 GGTAATCAGTAAAAG-AAGAATGATAAAAAGTAAAA
1 AGTAATCAGTAAAAGAAAGAATGATAAAAAGTAAAA
* *
235 AGTAATCAGT-AAAGAAAGAATGGTAAAGAG-AAAA
1 AGTAATCAGTAAAAGAAAGAATGATAAAAAGTAAAA
* *
269 GGGTAATCGGTAAAA
1 -AGTAATCAGTAAAA
284 AGTAAAAAGA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
34 8 0.11
35 42 0.58
36 11 0.15
37 11 0.15
ACGTcount: A:0.57, C:0.02, G:0.22, T:0.18
Consensus pattern (36 bp):
AGTAATCAGTAAAAGAAAGAATGATAAAAAGTAAAA
Found at i:318 original size:121 final size:120
Alignment explanation
Indices: 114--360 Score: 268
Period size: 121 Copynumber: 2.0 Consensus size: 120
104 AATTCAAGAG
* ** ** *
114 AGTAATCAGTAAAGGAAAGATGGTAAAGAGTAAAGAATAATCAGTAAGGAGTAATTAGTAAAGAG
1 AGTAATCAGTAAAGGAAAGATGGTAAAGAGAAAAGAATAATCAGTAAAAAGTAAAAAGTAAACAG
*
179 TAAAATGATAAAAAAGTAAAGGGTAAT-CAGTAAAAGAAG-AATGATAAAAAGTAAAA
66 TAAAA-GATAAAAAAGTAAAAGGTAATCCA-TAAAA-AAGTAATGATAAAAAGTAAAA
** * *
235 AGTAATCAGTAAA-GAAAGAATGGTAAAGAGAAAAGGGTAATCGGTAAAAAGTAAAAAGATAATC
1 AGTAATCAGTAAAGGAAAG-ATGGTAAAGAGAAAAGAATAATCAGTAAAAAGTAAAAAG-TAAAC
* * **
299 AGT-AAAGAATGAAATAGTAAAAGGTAATCCATAAAAAAGTAATGATAATCAGTAAAA
64 AGTAAAAG-ATAAAAAAGTAAAAGGTAATCCATAAAAAAGTAATGATAAAAAGTAAAA
*
356 GGTAA
1 AGTAA
361 AATAGTAATC
Statistics
Matches: 105, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
120 9 0.09
121 88 0.84
122 8 0.08
ACGTcount: A:0.56, C:0.04, G:0.21, T:0.19
Consensus pattern (120 bp):
AGTAATCAGTAAAGGAAAGATGGTAAAGAGAAAAGAATAATCAGTAAAAAGTAAAAAGTAAACAG
TAAAAGATAAAAAAGTAAAAGGTAATCCATAAAAAAGTAATGATAAAAAGTAAAA
Found at i:333 original size:29 final size:33
Alignment explanation
Indices: 288--360 Score: 75
Period size: 35 Copynumber: 2.3 Consensus size: 33
278 GTAAAAAGTA
*
288 AAAAGATAATCAGT-AAAG-AATGA-AAT-AGT
1 AAAAGGTAATCAGTAAAAGTAATGATAATCAGT
317 AAAAGGTAATCCA-TAAAAAAGTAATGATAATCAGT
1 AAAAGGTAAT-CAGT--AAAAGTAATGATAATCAGT
352 AAAAGGTAA
1 AAAAGGTAA
361 AATAGTAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
29 10 0.28
30 2 0.06
32 4 0.11
33 5 0.14
34 3 0.08
35 12 0.33
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (33 bp):
AAAAGGTAATCAGTAAAAGTAATGATAATCAGT
Found at i:372 original size:22 final size:22
Alignment explanation
Indices: 344--508 Score: 103
Period size: 22 Copynumber: 7.6 Consensus size: 22
334 AAAGTAATGA
344 TAATCAGTAAAAGGTAAAATAG
1 TAATCAGTAAAAGGTAAAATAG
* *
366 TAATCAGTAAGA-GCAAAAT-G
1 TAATCAGTAAAAGGTAAAATAG
* * *
386 ATAATCAATGAGAAGG--AAATGG
1 -TAATCAGT-AAAAGGTAAAATAG
* * * * *
408 TAATCAATGAGA-GCAAAATGG
1 TAATCAGTAAAAGGTAAAATAG
429 TAATCAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
* * *
451 TAATCATTAAAAAGTAAGAA-GG
1 TAATCAGTAAAAGGTAA-AATAG
473 TAATCAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
*
495 TAATCAGCAAAAGG
1 TAATCAGTAAAAGG
509 CAATCAGTAA
Statistics
Matches: 111, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
19 1 0.01
20 4 0.04
21 43 0.39
22 53 0.48
23 10 0.09
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.21
Consensus pattern (22 bp):
TAATCAGTAAAAGGTAAAATAG
Found at i:390 original size:21 final size:21
Alignment explanation
Indices: 339--456 Score: 80
Period size: 21 Copynumber: 5.5 Consensus size: 21
329 ATAAAAAAGT
* *
339 AATGATAATCAGTAAAAGGTAA
1 AATGATAATCAGTAAGA-GCAA
361 AAT-AGTAATCAGTAAGAGCAA
1 AATGA-TAATCAGTAAGAGCAA
* * *
382 AATGATAATCAATGAGAAG-GA
1 AATGATAATCAGTAAG-AGCAA
* * *
403 AATGGTAATCAATGAGAGCAA
1 AATGATAATCAGTAAGAGCAA
* *
424 AATGGTAATCAGTAAAGAGTAA
1 AATGATAATCAGT-AAGAGCAA
446 AAT-AGTAATCA
1 AATGA-TAATCA
457 TTAAAAAGTA
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
20 2 0.03
21 45 0.57
22 32 0.41
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.21
Consensus pattern (21 bp):
AATGATAATCAGTAAGAGCAA
Found at i:514 original size:36 final size:35
Alignment explanation
Indices: 467--608 Score: 203
Period size: 35 Copynumber: 4.0 Consensus size: 35
457 TTAAAAAGTA
*
467 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGC
1 AGAAGGTAATCAGT-AAGAGTAAAATAGTAATCAGT
* *
503 AAAAGGCAATCAGTAAGAGTAAAATAGTAATCAGT
1 AGAAGGTAATCAGTAAGAGTAAAATAGTAATCAGT
*
538 AGAAGGTAATCAGTAAAAAGTAAAATAGTAATCAGT
1 AGAAGGTAATCAGT-AAGAGTAAAATAGTAATCAGT
* * *
574 AGAAGATAATCAGTAAGAGTAAAACAGTAACCAGT
1 AGAAGGTAATCAGTAAGAGTAAAATAGTAATCAGT
609 GAGAGCAAAG
Statistics
Matches: 95, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
35 50 0.53
36 45 0.47
ACGTcount: A:0.51, C:0.08, G:0.20, T:0.20
Consensus pattern (35 bp):
AGAAGGTAATCAGTAAGAGTAAAATAGTAATCAGT
Found at i:545 original size:71 final size:71
Alignment explanation
Indices: 467--608 Score: 221
Period size: 71 Copynumber: 2.0 Consensus size: 71
457 TTAAAAAGTA
* * *
467 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGGCAATCAGTAAGAGTAAAATAGTA
1 AGAAGGTAATCAGTAAAAAGTAAAATAGTAATCAGCAAAAGACAATCAGTAAGAGTAAAACAGTA
*
532 ATCAGT
66 ACCAGT
* * *
538 AGAAGGTAATCAGTAAAAAGTAAAATAGTAATCAGTAGAAGATAATCAGTAAGAGTAAAACAGTA
1 AGAAGGTAATCAGTAAAAAGTAAAATAGTAATCAGCAAAAGACAATCAGTAAGAGTAAAACAGTA
603 ACCAGT
66 ACCAGT
609 GAGAGCAAAG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.51, C:0.08, G:0.20, T:0.20
Consensus pattern (71 bp):
AGAAGGTAATCAGTAAAAAGTAAAATAGTAATCAGCAAAAGACAATCAGTAAGAGTAAAACAGTA
ACCAGT
Found at i:560 original size:14 final size:14
Alignment explanation
Indices: 520--560 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
510 AATCAGTAAG
520 AGTAAAATAGTAATC
1 AGTAAAA-AGTAATC
* *
535 AGTAGAAGGTAATC
1 AGTAAAAAGTAATC
549 AGTAAAAAGTAA
1 AGTAAAAAGTAA
561 AATAGTAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.22
Consensus pattern (14 bp):
AGTAAAAAGTAATC
Found at i:608 original size:21 final size:21
Alignment explanation
Indices: 580--790 Score: 104
Period size: 21 Copynumber: 9.5 Consensus size: 21
570 CAGTAGAAGA
*
580 TAATCAGTAAGAGTAAAACAG
1 TAATCAGTAAGAGTAAAATAG
* * * * *
601 TAACCAGTGAGAGCAAAGTGG
1 TAATCAGTAAGAGTAAAATAG
* * *
622 TAATTAGTAAAAGTCAAATAG
1 TAATCAGTAAGAGTAAAATAG
*
643 TAATCAGTAAGAAGTAAAAGAG
1 TAATCAGTAAG-AGTAAAATAG
* *
665 TAATCTGTAAAAAAAGAGCAGAAAATAG
1 TAATCAGT-----AAGAG--TAAAATAG
*
693 TAATAAGTAAAAGAGTAAAATAG
1 TAATCAGT--AAGAGTAAAATAG
* *
716 TAATCAGTAAAAAGTAAGAA-GG
1 TAATCAGT-AAGAGTAA-AATAG
**
738 TAAATCAACAAGAGTAAAATAG
1 T-AATCAGTAAGAGTAAAATAG
*
760 TAATCAGTACAAAGTAAAGA-A-
1 TAATCAGTA-AGAGTAAA-ATAG
781 TAATCAGTAA
1 TAATCAGTAA
791 AATAGTGATG
Statistics
Matches: 143, Mismatches: 34, Indels: 27
0.70 0.17 0.13
Matches are distributed among these distances:
20 1 0.01
21 54 0.38
22 42 0.29
23 22 0.15
25 7 0.05
26 2 0.01
27 3 0.02
28 12 0.08
ACGTcount: A:0.54, C:0.07, G:0.19, T:0.20
Consensus pattern (21 bp):
TAATCAGTAAGAGTAAAATAG
Found at i:715 original size:23 final size:22
Alignment explanation
Indices: 686--732 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
676 AAAAGAGCAG
686 AAAATAGTAATAAGTAAAAGAGT
1 AAAATAGTAATAAGTAAAA-AGT
*
709 AAAATAGTAATCAGTAAAAAGT
1 AAAATAGTAATAAGTAAAAAGT
731 AA
1 AA
733 GAAGGTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.62, C:0.02, G:0.15, T:0.21
Consensus pattern (22 bp):
AAAATAGTAATAAGTAAAAAGT
Found at i:2410 original size:2 final size:2
Alignment explanation
Indices: 2403--2442 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
2393 GAGTCTTGTA
*
2403 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
2443 AAAGTACGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2515 original size:31 final size:32
Alignment explanation
Indices: 2466--2535 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
2456 GGAGAAACTT
*
2466 TATATTTTCCGATTGTACCCTTATT-TTTAAAA
1 TATATTTTCCAATTGTA-CCTTATTCTTTAAAA
*
2498 TATATTTT-CAATTGTACCTTTTTCTTTAAAA
1 TATATTTTCCAATTGTACCTTATTCTTTAAAA
*
2529 CATATTT
1 TATATTT
2536 CGAAATTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 6 0.18
31 20 0.59
32 8 0.24
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (32 bp):
TATATTTTCCAATTGTACCTTATTCTTTAAAA
Found at i:2744 original size:19 final size:20
Alignment explanation
Indices: 2717--2754 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2707 TACTATTATT
2717 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
2737 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
2755 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:2948 original size:22 final size:21
Alignment explanation
Indices: 2920--3116 Score: 139
Period size: 22 Copynumber: 9.0 Consensus size: 21
2910 TGTCTCTATG
2920 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCAT-AGA
* *
2942 TGGTTATTATAATTTC-TGAGA
1 TGGTTATCAAAATTTCAT-AGA
* *
2963 AGGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATTTCATAG-A
* *
2985 TGGTTACCGAAATTTCATAGTA
1 TGGTTATCAAAATTTCATAG-A
* *
3007 TGGTTATCGAAATTCCATAG-
1 TGGTTATCAAAATTTCATAGA
*
3027 TGTAGTTACCAAAATTTCATAGTA
1 TG--GTTATCAAAATTTCATAG-A
3051 TGGTTA-CTAAAATTTCATAGGA
1 TGGTTATC-AAAATTTCATA-GA
* * *
3073 TCAGGTTATTAAAATCTCTTAGA
1 T--GGTTATCAAAATTTCATAGA
**
3096 TTGGTTATTGAAATTTCATAG
1 -TGGTTATCAAAATTTCATAG
3117 GGTGGTTAAT
Statistics
Matches: 141, Mismatches: 22, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
20 2 0.01
21 20 0.14
22 99 0.70
23 3 0.02
24 17 0.12
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (21 bp):
TGGTTATCAAAATTTCATAGA
Found at i:3026 original size:44 final size:44
Alignment explanation
Indices: 2964--3070 Score: 153
Period size: 44 Copynumber: 2.4 Consensus size: 44
2954 TTTCTGAGAA
* * *
2964 GGTTATCAAAATTTCATAGTGTGGTTACCGAAATTTCATAGTAT
1 GGTTATCAAAATTCCATAGTGTAGTTACCAAAATTTCATAGTAT
*
3008 GGTTATCGAAATTCCATAGTGTAGTTACCAAAATTTCATAGTAT
1 GGTTATCAAAATTCCATAGTGTAGTTACCAAAATTTCATAGTAT
*
3052 GGTTA-CTAAAATTTCATAG
1 GGTTATC-AAAATTCCATAG
3071 GATCAGGTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 1 0.02
44 55 0.98
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (44 bp):
GGTTATCAAAATTCCATAGTGTAGTTACCAAAATTTCATAGTAT
Found at i:3123 original size:112 final size:109
Alignment explanation
Indices: 2922--3124 Score: 241
Period size: 112 Copynumber: 1.8 Consensus size: 109
2912 TCTCTATGTG
* * * *
2922 GTTATCAAAATTTCATAAGATGGTTATTATAATTTCTGAGAAGGTTATCAAAATTTCATAGTGTG
1 GTTACCAAAATTTCATAAGATGGTTACTAAAATTTCTGAGAAGGTTATCAAAATCTCATAGTGTG
*
2987 GTTACCGAAATTTCATAGTATGGTTATCGAAATTCCATAGTGTA
66 GTTACCGAAATTTCATAGGATGGTTATCGAAATTCCATAGTGTA
* *
3031 GTTACCAAAATTTCAT-AGTATGGTTACTAAAATTTCAT-AGGATCAGGTTATTAAAATCTCTTA
1 GTTACCAAAATTTCATAAG-ATGGTTACTAAAATTTC-TGA-GA--AGGTTATCAAAATCTCATA
** *
3094 GAT-TGGTTATTGAAATTTCATAGGGTGGTTA
61 G-TGTGGTTACCGAAATTTCATAGGATGGTTA
3125 ATTATCACAA
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
108 2 0.03
109 31 0.40
110 3 0.04
112 41 0.53
113 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (109 bp):
GTTACCAAAATTTCATAAGATGGTTACTAAAATTTCTGAGAAGGTTATCAAAATCTCATAGTGTG
GTTACCGAAATTTCATAGGATGGTTATCGAAATTCCATAGTGTA
Found at i:3283 original size:22 final size:22
Alignment explanation
Indices: 3224--3289 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
3214 TTCATTAAAT
* *
3224 ATTTCATGGGGAGGTTATCAAA
1 ATTTCATAGTGAGGTTATCAAA
* *
3246 ATTTTATAGTGTGGTTATCAAA
1 ATTTCATAGTGAGGTTATCAAA
3268 ATTTCATA-TGAAGGTTAT-AAA
1 ATTTCATAGTG-AGGTTATCAAA
3289 A
1 A
3290 GTCTTAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 6 0.16
22 31 0.84
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (22 bp):
ATTTCATAGTGAGGTTATCAAA
Found at i:3465 original size:22 final size:22
Alignment explanation
Indices: 3394--3565 Score: 95
Period size: 22 Copynumber: 7.8 Consensus size: 22
3384 TTTATAGAAA
*
3394 GATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATAATG-T
* * * *
3417 G-TTATCGAAATTTCAAAACGA
1 GATTATCAAAATTTCATAATGT
* *
3438 GGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCATAATGT
*
3460 GATTAT-AAGAATTTCATAGA-GG
1 GATTATCAA-AATTTCATA-ATGT
* * * * * *
3482 GGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCATAATGT
*
3504 GGTTATCAAAATTTCATAAATAG-
1 GATTATCAAAATTTCAT-AAT-GT
* *
3527 G-TTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCATAATGT
3548 GATTA-CAAAAATTTCATA
1 GATTATC-AAAATTTCATA
3566 GTGGTATTTC
Statistics
Matches: 113, Mismatches: 26, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
20 1 0.01
21 9 0.08
22 95 0.84
23 7 0.06
24 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.35
Consensus pattern (22 bp):
GATTATCAAAATTTCATAATGT
Found at i:3538 original size:21 final size:22
Alignment explanation
Indices: 3375--3541 Score: 126
Period size: 22 Copynumber: 7.6 Consensus size: 22
3365 AGAGATCAAA
*
3375 TTATCAAAATTT-ATAGAA-AGA
1 TTATCAAAATTTCATA-AAGAGG
** **
3396 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAAAGAGG
*
3418 TTATCGAAATTTCA-AAACGAGG
1 TTATCAAAATTTCATAAA-GAGG
* * * *
3440 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAAGAGG
* *
3462 TTAT-AAGAATTTCATAGAGGGG
1 TTATCAA-AATTTCATAAAGAGG
* * *
3484 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
*
3506 TTATCAAAATTTCATAAATAGG
1 TTATCAAAATTTCATAAAGAGG
*
3528 TTATCAAATTTTCA
1 TTATCAAAATTTCA
3542 AAATGTGATT
Statistics
Matches: 110, Mismatches: 30, Indels: 11
0.73 0.20 0.07
Matches are distributed among these distances:
21 15 0.14
22 91 0.83
23 4 0.04
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:3541 original size:66 final size:66
Alignment explanation
Indices: 3375--3541 Score: 157
Period size: 66 Copynumber: 2.5 Consensus size: 66
3365 AGAGATCAAA
* * ** * * *
3375 TTATCAAAATTT-ATAGAA-AGATTATCAAAATTTCATAGTGTTGTTATCGAAATTTCAAAACGA
1 TTATCAAAATTTCATA-AATAGGTTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAACGA
3438 GG
65 GG
* *
3440 TTATCAAAATTACAT-AAT-GTGATTAT-AAGAATTTCATAGAGGGGTCAACAAAATTTTATAAA
1 TTATCAAAATTTCATAAATAG-G-TTATCAA-AATTTCATAGAGGGGTCAACAAAATTTCA-AAA
3502 -GAGG
62 CGAGG
*
3506 TTATCAAAATTTCATAAATAGGTTATCAAATTTTCA
1 TTATCAAAATTTCATAAATAGGTTATCAAAATTTCA
3542 AAATGTGATT
Statistics
Matches: 82, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
64 3 0.04
65 13 0.16
66 56 0.68
67 9 0.11
68 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (66 bp):
TTATCAAAATTTCATAAATAGGTTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAACGAG
G
Found at i:3679 original size:19 final size:19
Alignment explanation
Indices: 3647--3694 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
3637 TTATGAAGTA
3647 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
3667 ATCAAAATTCAAGGAGGAT
1 ATCAAAATTCAAGGAGGAT
3686 ATCAAAATT
1 ATCAAAATT
3695 TCATATGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:3713 original size:22 final size:22
Alignment explanation
Indices: 3618--4246 Score: 175
Period size: 22 Copynumber: 29.0 Consensus size: 22
3608 ACCAAATTAG
* * *
3618 GAAGGTTATTAAACTTTTATTAT
1 GAAGGTTATCAAAATTTCA-TAT
*
3641 GAA-GTAATCAAAATTTCA-A-
1 GAAGGTTATCAAAATTTCATAT
* *
3660 GGAGGATATCAAAA-TTCA-A-
1 GAAGGTTATCAAAATTTCATAT
* *
3679 GGAGGATATCAAAATTTCATAT
1 GAAGGTTATCAAAATTTCATAT
3701 GAAGGTTATCAAAATTTCATAGT
1 GAAGGTTATCAAAATTTCATA-T
** * * * *
3724 TTA-GTTTTCAAAATATCACAA
1 GAAGGTTATCAAAATTTCATAT
3745 G-AGAGTTATCAAAATTTCATA-
1 GAAG-GTTATCAAAATTTCATAT
* * * *
3766 GTATGTAGATCAAAATTTCATAG
1 GAAGGT-TATCAAAATTTCATAT
* * *
3789 GGAGATTAACAAACA-TTCATAAT
1 GAAGGTTATCAAA-ATTTCAT-AT
**
3812 G-AGGTTATCAAAAAATCATAGT
1 GAAGGTTATCAAAATTTCATA-T
3834 G-AGGTTATCAAAA--T--T-T
1 GAAGGTTATCAAAATTTCATAT
* * *
3850 GTA-GTTATCAAGATTTCATAA
1 GAAGGTTATCAAAATTTCATAT
* * *
3871 GAAAGTTATCAAAATTTTATAG
1 GAAGGTTATCAAAATTTCATAT
* * * * *
3893 GGAGATTTATCTAAATTTTATAG
1 GAAG-GTTATCAAAATTTCATAT
*
3916 GAAGATTTATCAAAATTTCATA-
1 GAAG-GTTATCAAAATTTCATAT
* *
3938 GCGAGGTTATCACAATTTCATAGT
1 G-AAGGTTATCAAAATTTCATA-T
* * *
3962 G-TGATTATCAAAATTTCAGAGT
1 GAAGGTTATCAAAATTTCATA-T
* *
3984 G-TGATTA-CTAACAA-TTCATAT
1 GAAGGTTATC-AA-AATTTCATAT
* * * * *
4005 GGAGGTTTTTAAATTTTCATAAC
1 GAAGGTTATCAAAATTTCAT-AT
* * *
4028 G-TGGTTATCAATATATCATAT
1 GAAGGTTATCAAAATTTCATAT
* * *
4049 GGAGGTTATCAACATCTCATAGT
1 GAAGGTTATCAAAATTTCATA-T
**
4072 GTTGGTTATCAAAATTTCAT-T
1 GAAGGTTATCAAAATTTCATAT
*
4093 GGGAA-GTTATCAAAATTTCATGTT
1 --GAAGGTTATCAAAATTTCAT-AT
* * * *
4117 G-AGGTCT-TCGAAATTCCTTAG
1 GAAGGT-TATCAAAATTTCATAT
* * * *
4138 GGAGGTTAACCAAATTTCATAA
1 GAAGGTTATCAAAATTTCATAT
** *
4160 GAAGGTTAAAAGAAATTT-ATAA
1 GAAGGTTATCA-AAATTTCATAT
* * * *
4182 AAAGGTTCTCGAAATTCCATA-
1 GAAGGTTATCAAAATTTCATAT
** * *
4203 GTATCGTTATTAAAATTTCATAG
1 G-AAGGTTATCAAAATTTCATAT
4226 GAAGGTTATCAAAATTTCATA
1 GAAGGTTATCAAAATTTCATA
4247 ATGGGATCAT
Statistics
Matches: 459, Mismatches: 102, Indels: 91
0.70 0.16 0.14
Matches are distributed among these distances:
16 11 0.02
17 1 0.00
18 2 0.00
19 21 0.05
20 16 0.03
21 23 0.05
22 305 0.66
23 78 0.17
24 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
GAAGGTTATCAAAATTTCATAT
Found at i:3908 original size:23 final size:23
Alignment explanation
Indices: 3854--3938 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
3844 AAATTTGTAG
* * * *
3854 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
*
3876 TTATCAAAATTTTATAGGGAGAT
1 TTATCAAAATTTTATAGGAAGAT
*
3899 TTATCTAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
*
3922 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
3939 CGAGGTTATC
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:4069 original size:44 final size:45
Alignment explanation
Indices: 3999--4106 Score: 105
Period size: 45 Copynumber: 2.4 Consensus size: 45
3989 TACTAACAAT
* * * *
3999 TCATATGGAGGTTTTTAAATTTTCATAACG-TGGTTATCAATATA
1 TCATATGGAGGTTATCAAATTCTCATAACGTTGGTTATCAAAATA
** *
4043 TCATATGGAGGTTATCAACA-TCTCATAGTGTTGGTTATCAAAATT
1 TCATATGGAGGTTATCAA-ATTCTCATAACGTTGGTTATCAAAATA
*
4088 TCAT-TGGGAAGTTATCAAA
1 TCATAT-GGAGGTTATCAAA
4107 ATTTCATGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
44 25 0.47
45 28 0.53
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (45 bp):
TCATATGGAGGTTATCAAATTCTCATAACGTTGGTTATCAAAATA
Found at i:4289 original size:22 final size:22
Alignment explanation
Indices: 4261--4304 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4251 GATCATAAAA
4261 AATAGAGTA-ATTATCATAATTT
1 AATAGAG-AGATTATCATAATTT
*
4283 AATAGAGAGGTTATCATAATTT
1 AATAGAGAGATTATCATAATTT
4305 CATATGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.39
Consensus pattern (22 bp):
AATAGAGAGATTATCATAATTT
Done.