Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006346.1 Corchorus capsularis cultivar CVL-1 contig06367, 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: 31616
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Found at i:9530 original size:38 final size:38
Alignment explanation
Indices: 9488--10202 Score: 1162
Period size: 38 Copynumber: 18.8 Consensus size: 38
9478 TAATTAAGAG
* * * * * *
9488 TAAGAATCAAAGTAGTAATAACCAGCAAAATTGGTAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
* *
9526 TAAGAGTCAAAATAATAGTAATCAGTATAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
*
9564 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAC
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
* *
9602 TAAGTGCCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
* * * *
9640 TGAGAGTCAAAGTAAGAATAATCAGTAAAATCGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
* * *
9678 TAAGAGTCAAAGTAAGAATAATCAGTAAAATCGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
*
9716 TAAGAGTCAAAGTAATAGTAATCAGTAAAATCGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
*
9754 TAAGAGTCAAAGTAATAGTAATCAGTAAAATCGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
* *
9792 TAAGAGTCCAAGTAATAGTAATCAGTAAAATCGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
9830 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
9868 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
*
9906 TGAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
*
9944 TGAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
9982 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
10020 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
10058 TAAGAGTCAAAGTAATAGTAATCAGT-AAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
*
10095 TAAGAGTCAAAGTAATAGTAATCAATAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
10133 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
*
10171 TAAGAGTCAAGGTAAAAATAGTAATCAGTAAA
1 TAAGAGTCAAAGT---AATAGTAATCAGTAAA
10203 TCAGTAATTA
Statistics
Matches: 642, Mismatches: 31, Indels: 5
0.95 0.05 0.01
Matches are distributed among these distances:
37 36 0.06
38 590 0.92
41 16 0.02
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (38 bp):
TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
Found at i:10339 original size:33 final size:32
Alignment explanation
Indices: 10270--10344 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 32
10260 AAGAGTAACT
*
10270 AGTAATTAAGAAAGGAAGTGAAAAAATTAATC
1 AGTAATTAAGAAAGGAAGTGAAAAAACTAATC
10302 AGTAATTAAGAAAGGAAGT-AAAAAGGACTAATC
1 AGTAATTAAGAAAGGAAGTGAAAAA--ACTAATC
10335 AGTAAATTAA
1 AGT-AATTAA
10345 TAATTAAGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
31 5 0.13
32 19 0.49
33 9 0.23
34 6 0.15
ACGTcount: A:0.56, C:0.04, G:0.19, T:0.21
Consensus pattern (32 bp):
AGTAATTAAGAAAGGAAGTGAAAAAACTAATC
Found at i:10614 original size:21 final size:21
Alignment explanation
Indices: 10572--10613 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
10562 GTAAGCTAAG
10572 AGTAATCAGTAAAAAGGTAAA
1 AGTAATCAGTAAAAAGGTAAA
10593 AGTAATCAGTAAAAA-GTAAA
1 AGTAATCAGTAAAAAGGTAAA
10613 A
1 A
10614 ATGGCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.60, C:0.05, G:0.17, T:0.19
Consensus pattern (21 bp):
AGTAATCAGTAAAAAGGTAAA
Found at i:10760 original size:26 final size:26
Alignment explanation
Indices: 10708--10759 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
10698 AAAATGGTGT
10708 AGAGTAAAAAAATGGTATTAAGTAAA
1 AGAGTAAAAAAATGGTATTAAGTAAA
* *
10734 AGAGT-AAAATATGGTATTAATTAAA
1 AGAGTAAAAAAATGGTATTAAGTAAA
10759 A
1 A
10760 AATGGTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.27
Consensus pattern (26 bp):
AGAGTAAAAAAATGGTATTAAGTAAA
Found at i:10834 original size:16 final size:16
Alignment explanation
Indices: 10781--10834 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
10771 GCAAATGGGT
**
10781 TAAAAATGGTATCCAG
1 TAAAAATGGTATTAAG
* *
10797 TAAGAGATGGTATTAAA
1 TAA-AAATGGTATTAAG
*
10814 CAAAAATGGTATTAAG
1 TAAAAATGGTATTAAG
10830 TAAAA
1 TAAAA
10835 GAGTAAGAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 18 0.62
17 11 0.38
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.26
Consensus pattern (16 bp):
TAAAAATGGTATTAAG
Found at i:14726 original size:16 final size:13
Alignment explanation
Indices: 14694--14729 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
14684 ACATATATAT
14694 ATAATAATAATAA
1 ATAATAATAATAA
14707 ATAATAATAATAA
1 ATAATAATAATAA
* *
14720 GTGATAATAA
1 ATAATAATAA
14730 CAATTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (13 bp):
ATAATAATAATAA
Found at i:24278 original size:38 final size:38
Alignment explanation
Indices: 24236--24997 Score: 1185
Period size: 38 Copynumber: 20.1 Consensus size: 38
24226 TAATTAAGAG
* * * * * *
24236 TAAGAATCAAAGTAGTAATAACCAGCAAAATTGGTAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
* *
24274 TAAGAGTCAAAATAATAGTAATCAGTATAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
24312 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
* *
24350 TAAGAGCCAAAGTAATAGTAATCAGAAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
* * * *
24388 TCAGAGTCAAAGTAAGAATAATCAGTAAAATCGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
* * *
24426 TAAGAGTCAAAGTAAGAATAATCAGTAAAATCGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
* *
24464 TAAGAGTCAAAGTAATAGTAATCAATAAAATCGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
*
24502 TAAGAGTCAAAGTAATAGTAATCAGTAAAATCGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
*
24540 TAAGAGTCAAAGTAATAGTAATCAGTAAAATCGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
24578 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
24616 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
24654 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
24692 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
24730 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
24768 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
24806 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
24844 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
* *
24882 TAAGAGTCAAAGTAAAAATAATCAGTAAAATTGATAAT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
* * *
24920 CAAGAGTCAAGGTAAAAATAGTAATCAGT-AAA-TCAGTAAT
1 TAAGAGTCAAAGT---AATAGTAATCAGTAAAATTGA-TAAT
** *
24960 TAAGAGTC-AAGGGAT--TAATCAGT-AAATTGATACT
1 TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
24994 TAAG
1 TAAG
24998 GGAGAGAGTA
Statistics
Matches: 682, Mismatches: 37, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
34 18 0.03
35 2 0.00
36 2 0.00
38 631 0.93
39 4 0.01
40 14 0.02
41 11 0.02
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (38 bp):
TAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAAT
Found at i:24408 original size:22 final size:22
Alignment explanation
Indices: 24383--24447 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
24373 AGAAAAATTG
24383 ATAATTCAGAGTCAAAGTAAGA
1 ATAATTCAGAGTCAAAGTAAGA
* *
24405 ATAA-TC--AGT-AAAAT-CG-
1 ATAATTCAGAGTCAAAGTAAGA
*
24421 ATAATTAAGAGTCAAAGTAAGA
1 ATAATTCAGAGTCAAAGTAAGA
24443 ATAAT
1 ATAAT
24448 CAGTAAAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 12
0.65 0.10 0.24
Matches are distributed among these distances:
16 4 0.12
17 2 0.06
18 4 0.12
19 6 0.19
20 4 0.12
21 3 0.09
22 9 0.28
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (22 bp):
ATAATTCAGAGTCAAAGTAAGA
Found at i:25042 original size:32 final size:32
Alignment explanation
Indices: 25006--25093 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 32
24996 AGGGAGAGAG
* *
25006 TAAAAGAGTAACCAGTAATTAAGAAAGGAAGT
1 TAAAAGACTAATCAGTAATTAAGAAAGGAAGT
* * *
25038 TAAAAAATTAATCTGTAATTAAGAAAGGAAGT
1 TAAAAGACTAATCAGTAATTAAGAAAGGAAGT
*
25070 AAAAAGGACTAATCAGTAAATTAA
1 TAAAA-GACTAATCAGT-AATTAA
25094 TAATTAAGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 32 0.70
33 8 0.17
34 6 0.13
ACGTcount: A:0.55, C:0.06, G:0.17, T:0.23
Consensus pattern (32 bp):
TAAAAGACTAATCAGTAATTAAGAAAGGAAGT
Found at i:25417 original size:14 final size:14
Alignment explanation
Indices: 25398--25427 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
25388 AGTAGTAAAA
25398 AAGTAATCAGTAAG
1 AAGTAATCAGTAAG
25412 AAGTAATCAGTAAG
1 AAGTAATCAGTAAG
25426 AA
1 AA
25428 TGTCAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (14 bp):
AAGTAATCAGTAAG
Found at i:25539 original size:17 final size:17
Alignment explanation
Indices: 25517--25549 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25507 AGTAAAAGAG
25517 TAAAAAATGGTATTAAT
1 TAAAAAATGGTATTAAT
*
25534 TAAAAAATGGTGTTAA
1 TAAAAAATGGTATTAA
25550 GCAAAAGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (17 bp):
TAAAAAATGGTATTAAT
Found at i:25539 original size:26 final size:26
Alignment explanation
Indices: 25487--25538 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
25477 AAAATGGTGT
25487 AGAGTAAAAAAATGGTATTAAGTAAA
1 AGAGTAAAAAAATGGTATTAAGTAAA
*
25513 AGAGT-AAAAAATGGTATTAATTAAA
1 AGAGTAAAAAAATGGTATTAAGTAAA
25538 A
1 A
25539 AATGGTGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (26 bp):
AGAGTAAAAAAATGGTATTAAGTAAA
Found at i:25586 original size:42 final size:42
Alignment explanation
Indices: 25432--25597 Score: 138
Period size: 42 Copynumber: 3.9 Consensus size: 42
25422 TAAGAATGTC
* * * *
25432 AAAAATGGTATCAAGTGAAATATGGTATTGAGTAAGAAG-GTCAA
1 AAAAATGGTATCAAGTAAAAAATGGTATTAAGCAA-AAGAGT--A
* *
25476 AAAAATGGTGT-AGAGTAAAAAAATGGTATTAAGTAAAAGAGTA
1 AAAAATGGTATCA-AGT-AAAAAATGGTATTAAGCAAAAGAGTA
* * * * *
25519 AAAAATGGTATTAATTAAAAAATGGTGTTAAGCAAAAGGGTT
1 AAAAATGGTATCAAGTAAAAAATGGTATTAAGCAAAAGAGTA
* * * *
25561 AAAAATGGTATCCAGTAAGAGATGGTATTAAACAAAA
1 AAAAATGGTATCAAGTAAAAAATGGTATTAAGCAAAA
25598 ATGGTATTAA
Statistics
Matches: 101, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 52 0.51
43 14 0.14
44 17 0.17
45 18 0.18
ACGTcount: A:0.49, C:0.04, G:0.22, T:0.25
Consensus pattern (42 bp):
AAAAATGGTATCAAGTAAAAAATGGTATTAAGCAAAAGAGTA
Found at i:25613 original size:16 final size:16
Alignment explanation
Indices: 25560--25613 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
25550 GCAAAAGGGT
**
25560 TAAAAATGGTATCCAG
1 TAAAAATGGTATTAAG
* *
25576 TAAGAGATGGTATTAAA
1 TAA-AAATGGTATTAAG
*
25593 CAAAAATGGTATTAAG
1 TAAAAATGGTATTAAG
25609 TAAAA
1 TAAAA
25614 GAGTAAGAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 18 0.62
17 11 0.38
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.26
Consensus pattern (16 bp):
TAAAAATGGTATTAAG
Found at i:27527 original size:35 final size:34
Alignment explanation
Indices: 27481--27827 Score: 453
Period size: 35 Copynumber: 9.9 Consensus size: 34
27471 GGTGAATCAG
27481 TAATAAGTAACTTAATTCAGGGTAATTAAGTAAGT
1 TAATAAGTAACTTAATTCAGGGTAATTAAGT-AGT
*
27516 TAATAAGTAACTTAATTCAGGGTAATAAAGTAGT
1 TAATAAGTAACTTAATTCAGGGTAATTAAGTAGT
* *
27550 TCAATGAGTAACTTAATTCAGGGTAATTAAGCAAGT
1 T-AATAAGTAACTTAATTCAGGGTAATTAAG-TAGT
*** * *
27586 CGGTAAGCAACTTAATTCAGGGCAATTAAGTGAGT
1 TAATAAGTAACTTAATTCAGGGTAATTAAGT-AGT
* *
27621 CAGTAA-TCAACCTTAATTCAGGGTAATTAAGTGAGT
1 TAATAAGT-AA-CTTAATTCAGGGTAATTAAGT-AGT
* * *
27657 TAATAATTAACTAAATTTAGGGTAATTAAGTAGT
1 TAATAAGTAACTTAATTCAGGGTAATTAAGTAGT
27691 TCAATAAGTAACTTAATTCAGGGTAATTAAGTGAGT
1 T-AATAAGTAACTTAATTCAGGGTAATTAAGT-AGT
27727 TAATAAGTAACTTAATTCAGGGTAATTAAGTAGT
1 TAATAAGTAACTTAATTCAGGGTAATTAAGTAGT
* *
27761 TCAATAAGTAACATAATTCAAGGTAATTAAGTAGT
1 T-AATAAGTAACTTAATTCAGGGTAATTAAGTAGT
27796 TCAATAAGTAACTTAATTCAGGGTAATTAAGT
1 T-AATAAGTAACTTAATTCAGGGTAATTAAGT
27828 TTAGTAAGAA
Statistics
Matches: 278, Mismatches: 25, Indels: 18
0.87 0.08 0.06
Matches are distributed among these distances:
34 12 0.04
35 228 0.82
36 37 0.13
37 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.33
Consensus pattern (34 bp):
TAATAAGTAACTTAATTCAGGGTAATTAAGTAGT
Found at i:27745 original size:141 final size:139
Alignment explanation
Indices: 27482--27827 Score: 489
Period size: 141 Copynumber: 2.5 Consensus size: 139
27472 GTGAATCAGT
*
27482 AATAAGTAACTTAATTCAGGGTAATTAAGTAAGTTAATAAGTAACTTAATTCAGGGTAATAAAGT
1 AATAAGTAACTTAATTCAGGGTAATTAAGT-AGTTAATAAGTAACTTAATTCAGGGTAATTAAGT
* **
27547 AGTTCAATGAGTAACTTAATTCAGGGTAATTAAGCAAGTCGGTAAGCAACTTAATTCAGGGCAAT
65 AGTTCAATAAGTAACTTAATTCAGGGTAATTAAGCAAGTCAATAAGCAACTTAATTCAGGGCAAT
27612 TAAGTGAG-TC
130 TAAGT-AGTTC
* * * *
27622 AGTAA-TCAACCTTAATTCAGGGTAATTAAGTGAGTTAATAATTAACTAAATTTAGGGTAATTAA
1 AATAAGT-AA-CTTAATTCAGGGTAATTAAGT-AGTTAATAAGTAACTTAATTCAGGGTAATTAA
** * * *
27686 GTAGTTCAATAAGTAACTTAATTCAGGGTAATTAAGTGAGTTAATAAGTAACTTAATTCAGGGTA
63 GTAGTTCAATAAGTAACTTAATTCAGGGTAATTAAGCAAGTCAATAAGCAACTTAATTCAGGGCA
27751 ATTAAGTAGTTC
128 ATTAAGTAGTTC
* *
27763 AATAAGTAACATAATTCAAGGTAATTAAGTAGTTCAATAAGTAACTTAATTCAGGGTAATTAAGT
1 AATAAGTAACTTAATTCAGGGTAATTAAGTAGTT-AATAAGTAACTTAATTCAGGGTAATTAAGT
27828 TTAGTAAGAA
Statistics
Matches: 181, Mismatches: 20, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
139 5 0.03
140 54 0.30
141 121 0.67
142 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (139 bp):
AATAAGTAACTTAATTCAGGGTAATTAAGTAGTTAATAAGTAACTTAATTCAGGGTAATTAAGTA
GTTCAATAAGTAACTTAATTCAGGGTAATTAAGCAAGTCAATAAGCAACTTAATTCAGGGCAATT
AAGTAGTTC
Found at i:28706 original size:33 final size:33
Alignment explanation
Indices: 28669--28750 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 33
28659 TGACTTGGAG
*
28669 ATGCCCGACCA-ACACCGGTCACGCGACATGACC
1 ATGCCCGACCACA-ACCGGCCACGCGACATGACC
*
28702 ATGCCCGGCCACAACCGGCCACGCGACATGACC
1 ATGCCCGACCACAACCGGCCACGCGACATGACC
*
28735 ATGCCCGGCCACAACC
1 ATGCCCGACCACAACC
28751 AGTTACATGA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 45 0.98
34 1 0.02
ACGTcount: A:0.26, C:0.45, G:0.22, T:0.07
Consensus pattern (33 bp):
ATGCCCGACCACAACCGGCCACGCGACATGACC
Found at i:29710 original size:8 final size:8
Alignment explanation
Indices: 29697--29730 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
29687 CACCTTCTTG
29697 AAAAATTC
1 AAAAATTC
29705 AAAAATTC
1 AAAAATTC
*
29713 AGAAACTTC
1 A-AAAATTC
29722 AAAAATTC
1 AAAAATTC
29730 A
1 A
29731 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Done.