Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014710.1 Corchorus capsularis cultivar CVL-1 contig14731, 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: 16072
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Found at i:2843 original size:47 final size:47
Alignment explanation
Indices: 2771--2889 Score: 204
Period size: 47 Copynumber: 2.5 Consensus size: 47
2761 GAGGGATCCA
*
2771 AGTTGAAAACTCACAAAGGGGGGCTTGGATCCATTGGGGGTCACTTG
1 AGTTGAAAACTCACAAAGGGCGGCTTGGATCCATTGGGGGTCACTTG
2818 AGTTGAAAACTCACAAAGGGCGGCTTGGATCCATTGGGGGTCACTTG
1 AGTTGAAAACTCACAAAGGGCGGCTTGGATCCATTGGGGGTCACTTG
*
2865 AGTTGAAAACCCGA-AAAGGGCGGCT
1 AGTTGAAAACTC-ACAAAGGGCGGCT
2890 CAAGTGAAGG
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
47 68 0.99
48 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.33, T:0.21
Consensus pattern (47 bp):
AGTTGAAAACTCACAAAGGGCGGCTTGGATCCATTGGGGGTCACTTG
Found at i:3364 original size:15 final size:15
Alignment explanation
Indices: 3343--3379 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 15
3333 AATTATTTGG
3343 AAAAAAAAGAAGAGAGA
1 AAAAAAAAG-A-AGAGA
3360 AAAAAAAAGAAGAGA
1 AAAAAAAAGAAGAGA
3375 AAAAA
1 AAAAA
3380 GCAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.50
16 1 0.05
17 9 0.45
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAGAGA
Found at i:3365 original size:17 final size:16
Alignment explanation
Indices: 3343--3379 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
3333 AATTATTTGG
3343 AAAAAAAAGAAGAGAGA
1 AAAAAAAAGAAGAGA-A
3360 AAAAAAAAGAAGAGAA
1 AAAAAAAAGAAGAGAA
3376 AAAA
1 AAAA
3380 GCAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAGAGAA
Found at i:3377 original size:12 final size:12
Alignment explanation
Indices: 3362--3406 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
3352 AAGAGAGAAA
3362 AAAAAAGAAGAG
1 AAAAAAGAAGAG
* *
3374 AAAAAAGCAAAAA
1 AAAAAAG-AAGAG
3387 AAAAAGAGAAGAG
1 AAAAA-AGAAGAG
3400 AAAAAAG
1 AAAAAAG
3407 GATAAAGCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 9 0.33
13 16 0.59
14 2 0.07
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAGAG
Found at i:4837 original size:107 final size:107
Alignment explanation
Indices: 4614--4845 Score: 254
Period size: 107 Copynumber: 2.2 Consensus size: 107
4604 CTTCAATGAC
* * * * *
4614 CCAGGGTGGTCTATTCTTCAGTTCAGTTCAGAATGATCGAGGGTGGTCGTTGTTCAGCTTATTTC
1 CCAGGGTGGTC-GTTCTTTAATTCAGTTCAGAATGATCGAGGGAGGTCGTTCTTCAGCTTATTTC
* * *
4679 AGTTAACCCAGGGCGGTCTTTCTCCAGTTTGAGTCGGAACGAT
65 AGTTAACCCAGGGCGGTCATTCTCCAGTTTCAGTAGGAACGAT
* *
4722 CGAGGGTGGTCGTTCTTTAATTCAGTTCGGAATGATCGAGGGAGGTCGTTCTTCAGTCTGT-TTT
1 CCAGGGTGGTCGTTCTTTAATTCAGTTCAGAATGATCGAGGGAGGTCGTTCTTCAG-CT-TATTT
* ** * *
4786 -AGTTGAACCCAGGGTGGTCATTCTTTA-TTTCAGTAGGGATGAT
64 CAGTT-AACCCAGGGCGGTCATTCTCCAGTTTCAGTAGGAACGAT
* *
4829 CCATGGTGGTCTTTCTT
1 CCAGGGTGGTCGTTCTT
4846 CAGTTACTTA
Statistics
Matches: 103, Mismatches: 18, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
107 69 0.67
108 33 0.32
109 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (107 bp):
CCAGGGTGGTCGTTCTTTAATTCAGTTCAGAATGATCGAGGGAGGTCGTTCTTCAGCTTATTTCA
GTTAACCCAGGGCGGTCATTCTCCAGTTTCAGTAGGAACGAT
Found at i:5486 original size:13 final size:13
Alignment explanation
Indices: 5468--5493 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5458 TGGTAGCCTG
5468 TGTTCATTAAGCA
1 TGTTCATTAAGCA
5481 TGTTCATTAAGCA
1 TGTTCATTAAGCA
5494 CTTTCCGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTTCATTAAGCA
Found at i:9000 original size:26 final size:26
Alignment explanation
Indices: 8970--9074 Score: 122
Period size: 26 Copynumber: 4.0 Consensus size: 26
8960 AATTGGTAAT
*
8970 CAGTAATCAATAAAAAGAGTAAGAAA
1 CAGTAATCAGTAAAAAGAGTAAGAAA
*
8996 CAGTATTCAGTAAAAAGAGTAAGAAAA
1 CAGTAATCAGTAAAAAGAGTAAG-AAA
* * * *
9023 GAGTCATCAGTGAAAAGAGTAGGAAA
1 CAGTAATCAGTAAAAAGAGTAAGAAA
*
9049 CAAT-ATCCAGTAAAAAGAGTAAGAAA
1 CAGTAAT-CAGTAAAAAGAGTAAGAAA
9075 AGAGCAATAA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
25 2 0.03
26 43 0.65
27 21 0.32
ACGTcount: A:0.55, C:0.09, G:0.20, T:0.16
Consensus pattern (26 bp):
CAGTAATCAGTAAAAAGAGTAAGAAA
Found at i:9174 original size:22 final size:22
Alignment explanation
Indices: 9136--9474 Score: 113
Period size: 22 Copynumber: 15.4 Consensus size: 22
9126 GGCAATCAGT
** *
9136 AAGAGTAAAATAATAATTAGAA
1 AAGAGTAAAATGGTAATCAGAA
9158 AAGAGTAAAATGGTAATCAGTAA
1 AAGAGTAAAATGGTAATCAG-AA
*
9181 AA-AGTAAAA-GAGTAATCAGCA
1 AAGAGTAAAATG-GTAATCAGAA
* *
9202 AAGA--AAAATGGTGAA-GAGTA
1 AAGAGTAAAATGGT-AATCAGAA
*
9222 AAGAGTAGAGTAAAGAGTAATCA-ATA
1 AAGAGTA-A--AATG-GTAATCAGA-A
*
9248 AAG-G--AAATGGTAATTAGTAAAGA
1 AAGAGTAAAATGGTAATCAG---A-A
* *
9271 AAAAGTAAAA-GAGTAAAAT-AGTA
1 AAGAGTAAAATG-GT--AATCAGAA
** *
9294 ATCAGTAAAA-GGTAATCA-AT
1 AAGAGTAAAATGGTAATCAGAA
* * **
9314 AGGAGTAAAATAGTAATC-GGT
1 AAGAGTAAAATGGTAATCAGAA
* *** *
9335 AAGAGCAAAACAATAATCAGTA
1 AAGAGTAAAATGGTAATCAGAA
**
9357 AAGAGTAAAATAATAATCAGCAA
1 AAGAGTAAAATGGTAATCAG-AA
*
9380 AA-AGTAAGAA-GGTAATCAGTA
1 AAGAGTAA-AATGGTAATCAGAA
*
9401 AAGAGTAAAATAGTAATCAGTAA
1 AAGAGTAAAATGGTAATCAG-AA
*
9424 AA-AGTAAGAA-GGTAATCAGTA
1 AAGAGTAA-AATGGTAATCAGAA
*
9445 AAGAGTAAAATAGTAATCAGTAA
1 AAGAGTAAAATGGTAATCAG-AA
9468 AAG-GTAA
1 AAGAGTAA
9475 TCAGTAAGAG
Statistics
Matches: 241, Mismatches: 40, Indels: 72
0.68 0.11 0.20
Matches are distributed among these distances:
19 6 0.02
20 27 0.11
21 39 0.16
22 111 0.46
23 33 0.14
24 1 0.00
25 7 0.03
26 12 0.05
27 2 0.01
28 3 0.01
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.19
Consensus pattern (22 bp):
AAGAGTAAAATGGTAATCAGAA
Found at i:9233 original size:12 final size:12
Alignment explanation
Indices: 9216--9240 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9206 AAAATGGTGA
9216 AGAGTAAAGAGT
1 AGAGTAAAGAGT
9228 AGAGTAAAGAGT
1 AGAGTAAAGAGT
9240 A
1 A
9241 ATCAATAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (12 bp):
AGAGTAAAGAGT
Found at i:9282 original size:45 final size:46
Alignment explanation
Indices: 9179--9286 Score: 123
Period size: 45 Copynumber: 2.4 Consensus size: 46
9169 GGTAATCAGT
*
9179 AAAAAGTAAAAGAGTAATCAGCAAAGAAAAATGGTGAAGAGTAAAG
1 AAAAAGTAAAAGAGTAATCAACAAAGAAAAATGGTGAAGAGTAAAG
* * * * *
9225 AGTAGAGT-AAAGAGTAATCAATAAAG-GAAATGGT-AATTAGTAAAG
1 A-AAAAGTAAAAGAGTAATCAACAAAGAAAAATGGTGAA-GAGTAAAG
9270 AAAAAGTAAAAGAGTAA
1 AAAAAGTAAAAGAGTAA
9287 AATAGTAATC
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
44 6 0.12
45 24 0.47
46 17 0.33
47 4 0.08
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17
Consensus pattern (46 bp):
AAAAAGTAAAAGAGTAATCAACAAAGAAAAATGGTGAAGAGTAAAG
Found at i:9349 original size:35 final size:35
Alignment explanation
Indices: 9281--9349 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
9271 AAAAGTAAAA
** *
9281 GAGTAAAATAGTAATCAGTAAAAGGTAATCAATAG
1 GAGTAAAATAGTAATCAGTAAAAGCAAAACAATAG
* *
9316 GAGTAAAATAGTAATCGGTAAGAGCAAAACAATA
1 GAGTAAAATAGTAATCAGTAAAAGCAAAACAATA
9350 ATCAGTAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.20
Consensus pattern (35 bp):
GAGTAAAATAGTAATCAGTAAAAGCAAAACAATAG
Found at i:9458 original size:166 final size:165
Alignment explanation
Indices: 9278--9575 Score: 440
Period size: 166 Copynumber: 1.8 Consensus size: 165
9268 AGAAAAAGTA
* *
9278 AAAGAGTAAAATAGTAATCAGTAAAAGGTAATCAATAGGAGTAAAATAGTAATCGGTAAGAGCAA
1 AAAGAGTAAAATAGTAATCAGTAAAAGGTAATCAATAAGAGTAAAATAGTAATCAGTAAGAGCAA
9343 AACAATAATCAGTAAAGAGTAAAATAATAATCAGCAAAA-AGTAAGAA-GGTAATCAG-TAAAGA
66 AACAATAATCAG-AAAGAGTAAAATAATAATCAG-AAAAGAGTAA-AATGGTAATCAGTTAAA-A
9405 GTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAGT
127 GTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAGT
* *
9444 AAAGAGTAAAATAGTAATCAGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATCATTAAGAGCAA
1 AAAGAGTAAAATAGTAATCAGTAAAAGGTAATCAATAAGAGTAAAATAGTAATCAGTAAGAGCAA
*** * * * *
9509 AATGGTAATTAGCAAGAGTAAAATAGTAATTAGAAAAGAGTAAAATGGTAATCAGTTAAAAGTAA
66 AACAATAATCAGAAAGAGTAAAATAATAATCAGAAAAGAGTAAAATGGTAATCAGTTAAAAGTAA
9574 AA
131 AA
9576 AAAGAGAGTC
Statistics
Matches: 118, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
164 6 0.05
165 39 0.33
166 73 0.62
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (165 bp):
AAAGAGTAAAATAGTAATCAGTAAAAGGTAATCAATAAGAGTAAAATAGTAATCAGTAAGAGCAA
AACAATAATCAGAAAGAGTAAAATAATAATCAGAAAAGAGTAAAATGGTAATCAGTTAAAAGTAA
AATAGTAATCAGTAAAAAGTAAGAAGGTAATCAGT
Found at i:9491 original size:35 final size:37
Alignment explanation
Indices: 9426--9504 Score: 135
Period size: 35 Copynumber: 2.2 Consensus size: 37
9416 ATCAGTAAAA
9426 AGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATC
1 AGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATC
9463 AGTAA-AAGGTAATCAGT-AAGAGTAAAATAGTAATC
1 AGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATC
*
9498 ATTAAGA
1 AGTAAGA
9505 GCAAAATGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 22 0.55
36 13 0.32
37 5 0.12
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (37 bp):
AGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATC
Found at i:9503 original size:21 final size:22
Alignment explanation
Indices: 9482--9682 Score: 98
Period size: 22 Copynumber: 9.4 Consensus size: 22
9472 TAATCAGTAA
9482 GAGTAAAATAGTAATCA-TTAA
1 GAGTAAAATAGTAATCAGTTAA
* * * *
9503 GAGCAAAATGGTAATTAG-CAA
1 GAGTAAAATAGTAATCAGTTAA
* **
9524 GAGTAAAATAGTAATTAGAAAA
1 GAGTAAAATAGTAATCAGTTAA
*
9546 GAGTAAAATGGTAATCAGTTAA
1 GAGTAAAATAGTAATCAGTTAA
* *
9568 AAGTAAAAAAAG-AGAGTCAG-TAA
1 GAGT-AAAATAGTA-A-TCAGTTAA
* * * *
9591 GGGTAAAATGGTAATTAGTAAA
1 GAGTAAAATAGTAATCAGTTAA
* **
9613 GAGTAAAGT-GATAATCAGGAAA
1 GAGTAAAATAG-TAATCAGTTAA
*
9635 GAGT--AATAGAAATCAG-TAA
1 GAGTAAAATAGTAATCAGTTAA
* *
9654 GAAGT--AATAGTAAACAGTAAA
1 G-AGTAAAATAGTAATCAGTTAA
*
9675 AAGTAAAA
1 GAGTAAAA
9683 AGGTAAAAAG
Statistics
Matches: 136, Mismatches: 31, Indels: 25
0.71 0.16 0.13
Matches are distributed among these distances:
19 3 0.02
20 24 0.18
21 39 0.29
22 54 0.40
23 12 0.09
24 4 0.03
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.21
Consensus pattern (22 bp):
GAGTAAAATAGTAATCAGTTAA
Found at i:9618 original size:22 final size:22
Alignment explanation
Indices: 9463--9640 Score: 136
Period size: 21 Copynumber: 8.2 Consensus size: 22
9453 AATAGTAATC
9463 AGTAAAA-GGTAATCAGT-AAG
1 AGTAAAATGGTAATCAGTAAAG
* *
9483 AGTAAAATAGTAATCA-TTAAG
1 AGTAAAATGGTAATCAGTAAAG
* * *
9504 AGCAAAATGGTAATTAG-CAAG
1 AGTAAAATGGTAATCAGTAAAG
* * *
9525 AGTAAAATAGTAATTAGAAAAG
1 AGTAAAATGGTAATCAGTAAAG
9547 AGTAAAATGGTAATCAGTTAAA-
1 AGTAAAATGGTAATCAG-TAAAG
* *
9569 AGTAAAAAAAGAG-AGTCAGT-AAG
1 AGT--AAAATG-GTAATCAGTAAAG
* *
9592 GGTAAAATGGTAATTAGTAAAG
1 AGTAAAATGGTAATCAGTAAAG
* * *
9614 AGTAAAGTGATAATCAGGAAAG
1 AGTAAAATGGTAATCAGTAAAG
9636 AGTAA
1 AGTAA
9641 TAGAAATCAG
Statistics
Matches: 125, Mismatches: 22, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
20 9 0.07
21 51 0.41
22 48 0.38
23 6 0.05
24 10 0.08
25 1 0.01
ACGTcount: A:0.52, C:0.04, G:0.22, T:0.22
Consensus pattern (22 bp):
AGTAAAATGGTAATCAGTAAAG
Found at i:9630 original size:166 final size:166
Alignment explanation
Indices: 9278--9619 Score: 437
Period size: 166 Copynumber: 2.1 Consensus size: 166
9268 AGAAAAAGTA
* *
9278 AAAGAGTAAAATAGTAATCAGTAAAAGGTAATCAATAGGAGTAAAATAGTAATCGGTAAGAGCAA
1 AAAGAGTAAAATAGTAATCAGTAAAAGGTAATCAATAAGAGTAAAATAGTAATCAGTAAGAGCAA
9343 AACAATAATCAGTAAAGAGTAAAATAATAATCAGCAAAAAGTAAGAAGGTAATCAGTAAAGAGTA
66 AACAATAATCAGTAAAGAGTAAAATAATAATCAGCAAAAAGTAAGAAGGTAATCAGTAAAGAGTA
*
9408 AAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAGT
131 AAAAAGTAATCAGTAAAAAGTAAGAAGGTAATCAGT
* *
9444 AAAGAGTAAAATAGTAATCAGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATCATTAAGAGCAA
1 AAAGAGTAAAATAGTAATCAGTAAAAGGTAATCAATAAGAGTAAAATAGTAATCAGTAAGAGCAA
*** * * * *
9509 AATGGTAATTAG-CAAGAGTAAAATAGTAATTAG-AAAAGAGTAA-AATGGTAATCAGTTAAA-A
66 AACAATAATCAGTAAAGAGTAAAATAATAATCAGCAAAA-AGTAAGAA-GGTAATCAG-TAAAGA
** *
9570 GTAAAAAAAG-AGAGTCAGT-AAGGGTAA-AATGGTAATTAGT
128 GT-AAAAAAGTA-A-TCAGTAAAAAGTAAGAA-GGTAATCAGT
9610 AAAGAGTAAA
1 AAAGAGTAAA
9620 GTGATAATCA
Statistics
Matches: 154, Mismatches: 15, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
164 6 0.04
165 38 0.25
166 105 0.68
167 5 0.03
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (166 bp):
AAAGAGTAAAATAGTAATCAGTAAAAGGTAATCAATAAGAGTAAAATAGTAATCAGTAAGAGCAA
AACAATAATCAGTAAAGAGTAAAATAATAATCAGCAAAAAGTAAGAAGGTAATCAGTAAAGAGTA
AAAAAGTAATCAGTAAAAAGTAAGAAGGTAATCAGT
Found at i:9672 original size:7 final size:7
Alignment explanation
Indices: 9649--9718 Score: 54
Period size: 7 Copynumber: 10.0 Consensus size: 7
9639 AATAGAAATC
*
9649 AGTAAGA
1 AGTAAAA
*
9656 AGT-AAT
1 AGTAAAA
*
9662 AGTAAAC
1 AGTAAAA
9669 AGTAAAA
1 AGTAAAA
9676 AGTAAAA
1 AGTAAAA
9683 AGGTAAAA
1 A-GTAAAA
9691 AG-AAAA
1 AGTAAAA
**
9697 GAGTAATC
1 -AGTAAAA
9705 AGTAAAA
1 AGTAAAA
*
9712 GGTAAAA
1 AGTAAAA
9719 TGGTAATTAG
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
6 8 0.16
7 33 0.66
8 9 0.18
ACGTcount: A:0.61, C:0.03, G:0.20, T:0.16
Consensus pattern (7 bp):
AGTAAAA
Found at i:9690 original size:15 final size:14
Alignment explanation
Indices: 9670--9718 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
9660 ATAGTAAACA
9670 GTAAAAAGTAAAAAG
1 GTAAAAAGT-AAAAG
9685 GTAAAAAG-AAAAG
1 GTAAAAAGTAAAAG
**
9698 AGTAATCAGTAAAAG
1 -GTAAAAAGTAAAAG
9713 GTAAAA
1 GTAAAA
9719 TGGTAATTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
13 5 0.18
14 10 0.36
15 13 0.46
ACGTcount: A:0.63, C:0.02, G:0.20, T:0.14
Consensus pattern (14 bp):
GTAAAAAGTAAAAG
Found at i:9724 original size:22 final size:22
Alignment explanation
Indices: 9699--9750 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
9689 AAAGAAAAGA
*
9699 GTAATCAGTAAA-AGGTAAAATG
1 GTAATCAGTAAAGA-GCAAAATG
* *
9721 GTAATTAGTAAAGAGCAATATG
1 GTAATCAGTAAAGAGCAAAATG
9743 GTAATCAG
1 GTAATCAG
9751 AGTAAAGGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.25
Consensus pattern (22 bp):
GTAATCAGTAAAGAGCAAAATG
Found at i:9805 original size:26 final size:26
Alignment explanation
Indices: 9774--9860 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 26
9764 GAAATCAGTA
9774 AATCAGTAATTAAGTGAAAAGAGATT
1 AATCAGTAATTAAGTGAAAAGAGATT
* ** *
9800 AATCAGAGTCAAGGTAA-TGATAATCAG-TA
1 AATC--AGT-AA-TTAAGTGA-AAAGAGATT
*
9829 AATCAGTAATTAAGTGAAAAGAAATT
1 AATCAGTAATTAAGTGAAAAGAGATT
9855 AATCAG
1 AATCAG
9861 AGTCAAGGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
25 6 0.13
26 16 0.36
27 3 0.07
28 3 0.07
29 10 0.22
30 7 0.16
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.25
Consensus pattern (26 bp):
AATCAGTAATTAAGTGAAAAGAGATT
Found at i:9956 original size:55 final size:55
Alignment explanation
Indices: 9744--9957 Score: 313
Period size: 55 Copynumber: 3.9 Consensus size: 55
9734 AGCAATATGG
* * *
9744 TAATCAGAGTAAAGGTAATAGAAATCAGTAAATCAGTAATTAAGTGAAAAGAGAT
1 TAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
* *
9799 TAATCAGAGTCAAGGTAAT-GATAATCAGTAAATCAGTAATTAAGTGAAAAGAAAT
1 TAATCAGAGTCAAGGTAATAG-TAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
* *
9854 TAATCAGAGTCAAGGTAATGGTAATCAGTAAATCAGCAATTAAGTAAAAAGAGAT
1 TAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
* * * *
9909 TAATCAGAGTCGAGGTAATAGTAATCAGTAAATCAATAATCAGGTAAAA
1 TAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAA
9958 GATAGTAATC
Statistics
Matches: 145, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
54 1 0.01
55 143 0.99
56 1 0.01
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.24
Consensus pattern (55 bp):
TAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
Found at i:9988 original size:70 final size:70
Alignment explanation
Indices: 9909--10131 Score: 263
Period size: 71 Copynumber: 3.2 Consensus size: 70
9899 AAAAAGAGAT
*
9909 TAATC-AGAGTCGAGGTAATAGTAATCAGTAAATCAATAATCAGGTAAAAGATAGTAATCAGTAA
1 TAATCAAGAGTCAAGGTAATAGTAATCAGTAAATCAATAATCAGGTAAAAGATAGTAATCAGTAA
9973 ATTGA
66 ATTGA
* * *
9978 TAATCAAGAGTCCAGATAATAGTAATCAGTAAATCAGTAATCAGGTAAAAAGATAGTAATCAGTA
1 TAATCAAGAGTCAAGGTAATAGTAATCAGTAAATCAATAATCAGGT-AAAAGATAGTAATCAGTA
10043 AATTGA
65 AATTGA
* * * * * **
10049 TAA-CTAAGAGTCAAGGTAAGAGATTAATGAGTAATTAAAGAGCCTAGGTAAAA-ATAGTAATCA
1 TAATC-AAGAGTCAAGGTAATAG--TAATCAGTAAATCAATAATC-AGGTAAAAGATAGTAATCA
*
10112 GTAAATCGA
62 GTAAATTGA
*
10121 TAATTAAGAGT
1 TAATCAAGAGT
10132 TAAAATGATC
Statistics
Matches: 132, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
69 5 0.04
70 38 0.29
71 41 0.31
72 27 0.20
73 17 0.13
74 4 0.03
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.26
Consensus pattern (70 bp):
TAATCAAGAGTCAAGGTAATAGTAATCAGTAAATCAATAATCAGGTAAAAGATAGTAATCAGTAA
ATTGA
Found at i:12237 original size:157 final size:158
Alignment explanation
Indices: 12041--12327 Score: 366
Period size: 157 Copynumber: 1.8 Consensus size: 158
12031 CATTTTCTGT
* * * *
12041 GCAACGAGTGCTCAAATGTCGTGCGTCAAATTGCGATGAGATTGTTGGACTA-CCCTGTGCACAA
1 GCAACGAGTGCTCAAAAGTCGTGCGTCAAATTGAGATGAGATTGTTAGAC-AGCCCTATGCACAA
* * * * *
12105 ACAAAGCTTTC-ACGAATTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAA-ACATAGTTCTTA
65 ACAAAGCTCTCTACGAAGTCCAAAGCATCAACTTTGCGCGTTTGTATGC-AACACATAGTTCTTA
12168 GCAAAACTCTTTCTGGATGCGTTTTTTCGC
129 GCAAAACTCTTTCTGGATGCGTTTTTTCGC
* * * *
12198 GCAACGAGTGCTCAAAAGTCGTGTGTCGGAA-TGAGATGAGCTTGTTAGACAGCGCTATGCACAA
1 GCAACGAGTGCTCAAAAGTCGTGCGTC-AAATTGAGATGAGATTGTTAGACAGCCCTATGCACAA
* * * *
12262 ACAAAGCTCTCTTCGAAGTCCAAAGCATCAAGTTTGCGGGTTTGTATGCAACACATCGTTCTTAG
65 ACAAAGCTCTCTACGAAGTCCAAAGCATCAACTTTGCGCGTTTGTATGCAACACATAGTTCTTAG
12327 C
130 C
12328 GGTTTGTCGG
Statistics
Matches: 109, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
156 1 0.01
157 63 0.58
158 45 0.41
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (158 bp):
GCAACGAGTGCTCAAAAGTCGTGCGTCAAATTGAGATGAGATTGTTAGACAGCCCTATGCACAAA
CAAAGCTCTCTACGAAGTCCAAAGCATCAACTTTGCGCGTTTGTATGCAACACATAGTTCTTAGC
AAAACTCTTTCTGGATGCGTTTTTTCGC
Found at i:12396 original size:111 final size:111
Alignment explanation
Indices: 12221--12432 Score: 255
Period size: 111 Copynumber: 1.9 Consensus size: 111
12211 AAAAGTCGTG
* * * * * *
12221 TGTCGGAATGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCTTCGAAGTCCAAA
1 TGTCGGAATGAGATGAACTTGTTAGACAGCGCCATCCACAAACAAAGCTCTCCTAGAAGCCCAAA
* * ** * *
12286 GCATCAAGTTTGCGGGTTTGTATGCAACACATCGTTCTTAGCGGTT
66 ACATCAACTTTAAGCGTTTGTATGCAAAACATCGTTCTTAGCGGTT
* * *
12332 TGTCGGAATGAGATGAACTTTTTGGACAGC-CCAGTCCACAAACAAAGCTTTCCTAGAAGCCCAA
1 TGTCGGAATGAGATGAACTTGTTAGACAGCGCCA-TCCACAAACAAAGCTCTCCTAGAAGCCCAA
* *
12396 AACCTCAACTTTAAGCGTTTGTGTGCAAAACATCGTT
65 AACATCAACTTTAAGCGTTTGTATGCAAAACATCGTT
12433 TTGAGGAACA
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
110 2 0.02
111 81 0.98
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (111 bp):
TGTCGGAATGAGATGAACTTGTTAGACAGCGCCATCCACAAACAAAGCTCTCCTAGAAGCCCAAA
ACATCAACTTTAAGCGTTTGTATGCAAAACATCGTTCTTAGCGGTT
Found at i:13372 original size:270 final size:269
Alignment explanation
Indices: 12879--13440 Score: 786
Period size: 270 Copynumber: 2.1 Consensus size: 269
12869 TTCCAACAAG
* * * *
12879 GAGTGCTCAAAAGGCATGTGTCGGAGTGAGATGAGCTTATTAGACAACACTATGCACAAACAAAG
1 GAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTATCAGACAACACTATGCACAAACAAAG
*** **
12944 CTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGTTTGTTTGCAACAAATCGTTCTTAGCGGTGT
66 CTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGTAACTTACCAACAAATCGTTCTTAGCGGTGT
* *
13009 GTTGGTGTGAGATGAGCTTCCTGAACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAAA
131 GTCGGAGTGAGATGAGCTTCCTGAACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAAA
* * *
13074 TCTCAACTTTGAGCAGTTCTATGCAAAACATCATTTTTACCGAAAGGCTCATTCCAGATGCATTT
196 CCTCAACTTTGAGCAGTTCTAAGCAAAACATCATTTTTACCGAAAGGCTCATTCCAGATGAATTT
13139 TTCACGCAAC
261 TT-ACGCAAC
* * **
13149 GAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTCAGACAGCGTTATGCACAAACAAAG
1 GAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTATCAGACAACACTATGCACAAACAAAG
* *
13214 CTCTCCTCGAAGTCCAAAGCATCAATTTTGCGCGTAACTATACCAA-ACATCGTTCTTAGCGGTG
66 CTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGTAACT-TACCAACAAATCGTTCTTAGCGGTG
* * * * *
13278 TGTCGGAGTGAGATGTGCTAT-TTGGACAGCCCTGTGCACAAACAAAGCTTTCTTAGAAGCCCAA
130 TGTCGGAGTGAGATGAGCT-TCCTGAACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAA
* * * *
13342 AGCCTCAACTTTGAGCGGTTGTAAGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGAAT
194 AACCTCAACTTTGAGCAGTTCTAAGCAAAACATCATTTTTACCGAAAGGCTCATTCCAGATGAAT
* *
13407 TTTTGCGCAAT
259 TTTTACGCAAC
* *
13418 GAGTGCTCAAATGTCGTGCGTCG
1 GAGTGCTCAAAAGTCGTGTGTCG
13441 AATTGCTATA
Statistics
Matches: 257, Mismatches: 33, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
269 26 0.10
270 226 0.88
271 5 0.02
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (269 bp):
GAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTATCAGACAACACTATGCACAAACAAAG
CTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGTAACTTACCAACAAATCGTTCTTAGCGGTGT
GTCGGAGTGAGATGAGCTTCCTGAACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAAA
CCTCAACTTTGAGCAGTTCTAAGCAAAACATCATTTTTACCGAAAGGCTCATTCCAGATGAATTT
TTACGCAAC
Found at i:13921 original size:157 final size:158
Alignment explanation
Indices: 13574--13969 Score: 384
Period size: 158 Copynumber: 2.5 Consensus size: 158
13564 GTTCTTAGCA
* * * * * *
13574 GTTTGTCGGAGTGAGATGAACTTT-TTGGATAGCCATGTGCACAAACAAAGCTTTCCTAGAAGTT
1 GTTTGTCGGAATGAGATG-AGTTTGTTGGACAGCCCTGTGCACAAACAAAGCTTT-CAAGAAGTC
* * * *
13638 CAAAACCTCAACTTTGAGCGGTTCTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATG
64 CAAAGCCTCAACTTTGAGCGGTTCTATGCAAAACATAATTCTTAGCGAAAGACTCATTCCAGATG
* *
13703 CAATTTTTGCGCAACGAATGCTCAAATGTC
129 CAATTTTTGCGAAACGAATGCTCAAAAGTC
** * * * * **
13733 GTGCGTTGCATTGCGATGAGAATGTTGGACAGCCCTGTGCACAAACAAAGCTTTCAAGAAGTCCA
1 GTTTGTCGGAATGAGATGAGTTTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCAAGAAGTCCA
* * * * * * ** *
13798 AAGCCTCAACTTTGTGCGTTTTTGTGCTAAACATAATTCTTAGC-AAA-ACTCTTTCTGGATGCG
66 AAGCCTCAACTTTGAGCGGTTCTATGCAAAACATAATTCTTAGCGAAAGACTCATTCCAGATGCA
* *
13861 TTTTTTCGCGAAACGAGTGCTCAAAAGTC
131 ATTTTT-GCGAAACGAATGCTCAAAAGTC
* * * * ** *
13890 GTTTGTCGGAATGAGATGAGTTTGTTAGACAGCGCTATACACAAACAAAGCCCTCATCGAAGTCC
1 GTTTGTCGGAATGAGATGAGTTTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCA-AGAAGTCC
*
13955 AAAGCATCAACTTTG
65 AAAGCCTCAACTTTG
13970 CGTGTTTGTA
Statistics
Matches: 188, Mismatches: 46, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
156 16 0.09
157 64 0.34
158 68 0.36
159 40 0.21
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (158 bp):
GTTTGTCGGAATGAGATGAGTTTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCAAGAAGTCCA
AAGCCTCAACTTTGAGCGGTTCTATGCAAAACATAATTCTTAGCGAAAGACTCATTCCAGATGCA
ATTTTTGCGAAACGAATGCTCAAAAGTC
Found at i:14068 original size:111 final size:111
Alignment explanation
Indices: 13890--14104 Score: 252
Period size: 111 Copynumber: 1.9 Consensus size: 111
13880 CTCAAAAGTC
* * * *
13890 GTTTGTCGGAATGAGATGAGTTTGTTAGACAGCGCTATACACAAACAAAGCCCTCATCGAAGTCC
1 GTTTGTCGGAATGAGATGACTTTGTTAGACAGCCCTATACACAAACAAAGCCCTCATAGAAGCCC
* * *** *
13955 AAAGCATCAACTTTGCGTGTTTGTATGCAACACATCGTTCTTAGCG
66 AAAACATAAACTTTGAACGTTTGTATGCAAAACATCGTTCTTAGCG
* * * ** *
14001 GTTTGTCGGAATGAGATGAACTTT-TTGGACAGCCCTTTGCACAAACAAAGCTTTCCTAGAAGCC
1 GTTTGTCGGAATGAGATG-ACTTTGTTAGACAGCCCTATACACAAACAAAGCCCTCATAGAAGCC
* *
14065 CAAAACCTAAACTTTGAACGTTTGTGTGCAAAACATCGTT
65 CAAAACATAAACTTTGAACGTTTGTATGCAAAACATCGTT
14105 TTGAGGAACA
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
111 81 0.95
112 4 0.05
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.28
Consensus pattern (111 bp):
GTTTGTCGGAATGAGATGACTTTGTTAGACAGCCCTATACACAAACAAAGCCCTCATAGAAGCCC
AAAACATAAACTTTGAACGTTTGTATGCAAAACATCGTTCTTAGCG
Found at i:14337 original size:178 final size:178
Alignment explanation
Indices: 14012--14337 Score: 417
Period size: 178 Copynumber: 1.8 Consensus size: 178
14002 TTTGTCGGAA
* * *
14012 TGAGATGAACTTTTTGGACAGCCCTTTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTAAAC
1 TGAGATGAACTTTTTGAACACCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTAAAC
* * * *
14077 TTTGAACGTTTGTGTGCAAAACATCGTTTTGAGGAACAACCTCATTCCAGATGCGTTTTTTGCGC
66 TTTGAACGTTTATGTGCAAAACATCATTTTGAGCAACAACCTCATTCCAGATGCATTTTTTGCGC
* *
14142 AATGAGTGCTTAAATGTCATGTGTCGGAGTGAGTTGAGCATGTTGGAG
131 AACGAGTGATTAAATGTCATGTGTCGGAGTGAGTTGAGCATGTTGGAG
* * * * * *
14190 TGAGATGAGCTTTTTGAACACCCCTATGCACAAATAAAGGTTTCCTGGAAGCCCAAAATCTCAAC
1 TGAGATGAACTTTTTGAACACCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTAAAC
* * * *
14255 TTTGAGCAGTTCTATG-G-AAAACATTATTTTTAGCAA-AAGGCTCATTCCAGATGCATTTTTTG
66 TTTGAAC-GTT-TATGTGCAAAACATCATTTTGAGCAACAA-CCTCATTCCAGATGCATTTTTTG
14317 CGCAACGAGT-ATTCAAATGTC
128 CGCAACGAGTGATT-AAATGTC
14338 GTGCGTCGAG
Statistics
Matches: 125, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
177 4 0.03
178 114 0.91
179 4 0.03
180 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (178 bp):
TGAGATGAACTTTTTGAACACCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTAAAC
TTTGAACGTTTATGTGCAAAACATCATTTTGAGCAACAACCTCATTCCAGATGCATTTTTTGCGC
AACGAGTGATTAAATGTCATGTGTCGGAGTGAGTTGAGCATGTTGGAG
Found at i:14366 original size:178 final size:179
Alignment explanation
Indices: 14003--14366 Score: 409
Period size: 178 Copynumber: 2.0 Consensus size: 179
13993 TCTTAGCGGT
* * * *
14003 TTGTCGGAATGAGATGAACTTTTTGGACAGCCCTTTGCACAAACAAAGCTTTCCTAGAAGCCCAA
1 TTGTTGGAATGAGATGAACTTTTTGAACACCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAA
* * * *
14068 AACCTAAACTTTGAACGTTTGTGTGCAAAACATCGTTTTGAGGAACAACCTCATTCCAGATGCGT
66 AACCTAAACTTTGAACGTTTATGTGCAAAACATCATTTTGAGCAACAACCTCATTCCAGATGCAT
* * * *
14133 TTTTTGCGCAATGAGTGCTTAAATGTCATGTGTCGGAGTGAGTTGAGCA
131 TTTTTGCGCAACGAGTGATTAAATGTCATGCGTCGGAGTGAGATGAGCA
* * * * *
14182 -TGTTGGAGTGAGATGAGCTTTTTGAACACCCCTATGCACAAATAAAGGTTTCCTGGAAGCCCAA
1 TTGTTGGAATGAGATGAACTTTTTGAACACCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAA
* * * * * *
14246 AATCTCAACTTTGAGCAGTTCTATG-G-AAAACATTATTTTTAGCAA-AAGGCTCATTCCAGATG
66 AACCTAAACTTTGAAC-GTT-TATGTGCAAAACATCATTTTGAGCAACAA-CCTCATTCCAGATG
* *
14308 CATTTTTTGCGCAACGAGT-ATTCAAATGTCGTGCGTC-GAGTTGCGATGAG-A
128 CATTTTTTGCGCAACGAGTGATT-AAATGTCATGCGTCGGAG-TGAGATGAGCA
14359 TTGTTGGA
1 TTGTTGGA
14367 CAGCCCTGTG
Statistics
Matches: 154, Mismatches: 25, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
177 8 0.05
178 139 0.90
179 4 0.03
180 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (179 bp):
TTGTTGGAATGAGATGAACTTTTTGAACACCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAA
AACCTAAACTTTGAACGTTTATGTGCAAAACATCATTTTGAGCAACAACCTCATTCCAGATGCAT
TTTTTGCGCAACGAGTGATTAAATGTCATGCGTCGGAGTGAGATGAGCA
Found at i:14743 original size:605 final size:605
Alignment explanation
Indices: 13581--14764 Score: 1859
Period size: 605 Copynumber: 2.0 Consensus size: 605
13571 GCAGTTTGTC
* * * * **
13581 GGAGTGAGATGAACTTTTTGGATAGCCATGTGCACAAACAAAGCTTTCCTAGAAGTTCAAAACCT
1 GGAGTGAGATGAACTTTTTGAACACCCATATGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCT
* *
13646 CAACTTTGAGCGGTTCTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCAATTTTT
66 CAACTTTGAGCAGTTCTATGCAAAACATCATTTTTAGCAAAAGGCTCATTCCAGATGCAATTTTT
* *
13711 GCGCAACGAATGCTCAAATGTCGTGCGTTGCATTGCGATGAGAATGTTGGACAGCCCTGTGCACA
131 GCGCAACGAATACTCAAATGTCGTGCGTCGCATTGCGATGAGAATGTTGGACAGCCCTGTGCACA
*
13776 AACAAAGCTTTCAAGAAGTCCAAAGCCTCAACTTTGTGCGTTTTTGTGCTAAACATAATTCTTAG
196 AACAAAGCTTTCAAGAAGTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAACATAATTCTTAG
* *
13841 CAAAACTCTTTCTGGATGCGTTTTTTCGCGAAACGAGTGCTCAAAAGTCGTTTGTCGGAATGAGA
261 CAAAACTCTTTCTGGATGCGTTTTTTCGCGAAACGAGTGCTCAAAAGTCGTGTATCGGAATGAGA
*
13906 TGAGTTTGTTAGACAGCGCTATACACAAACAAAGCCCTCATCGAAGTCCAAAGCATCAACTTTGC
326 TGAGCTTGTTAGACAGCGCTATACACAAACAAAGCCCTCATCGAAGTCCAAAGCATCAACTTTGC
* *
13971 GTGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAATGAGATGAACTTTTTGGACAGCCC
391 GCGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAATGAGATGAACATTTTGGACAGCCC
* *
14036 TTTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTAAACTTTGAACGTTTGTGTGCAAAACAT
456 TGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTAAACTTTGAACATTTGTGTGCAAAACAT
* * * *
14101 CGTTTTGAGGAACAACCTCATTCCAGATGCGTTTTTTGCGCAATGAGTGCTTAAATGTCATGTGT
521 CATTTTGAGGAACAACCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCATGTGT
14166 CGGAGTGAGTTGAGCATGTT
586 CGGAGTGAGTTGAGCATGTT
* * * * * *
14186 GGAGTGAGATGAGCTTTTTGAACACCCCTATGCACAAATAAAGGTTTCCTGGAAGCCCAAAATCT
1 GGAGTGAGATGAACTTTTTGAACACCCATATGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCT
* * *
14251 CAACTTTGAGCAGTTCTATGGAAAACATTATTTTTAGCAAAAGGCTCATTCCAGATGCATTTTTT
66 CAACTTTGAGCAGTTCTATGCAAAACATCATTTTTAGCAAAAGGCTCATTCCAGATGCAATTTTT
* * *
14316 GCGCAACGAGTATTCAAATGTCGTGCGTCG-AGTTGCGATGAGATTGTTGGACAGCCCTGTGCAC
131 GCGCAACGAATACTCAAATGTCGTGCGTCGCA-TTGCGATGAGAATGTTGGACAGCCCTGTGCAC
* * * * * *
14380 AAACAAAGCTTTCACGAATTCCAAGGCGTCAACTTTGCGCGTTTTTGTGCTAATCATAGTTCTTA
195 AAACAAAGCTTTCAAGAAGTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAACATAATTCTTA
*
14445 GCAAAACTCTTTCTGGATGCGTTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTATCGGAATGAG
260 GCAAAACTCTTTCTGGATGCGTTTTTTCGCGAAACGAGTGCTCAAAAGTCGTGTATCGGAATGAG
* * * * *
14510 ATGAGCTTGTTAGCCAGGGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTG
325 ATGAGCTTGTTAGACAGCGCTATACACAAACAAAGCCCTCATCGAAGTCCAAAGCATCAACTTTG
14575 CGCGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAATGAGATGAACATTTTGGACAGCC
390 CGCGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAATGAGATGAACATTTTGGACAGCC
* *
14640 CTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCATTTGTGTGCAAAACA
455 CTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTAAACTTTGAACATTTGTGTGCAAAACA
* ** * *
14705 TCATTTTTAGCGAA-AGGCTCATTCTAGATGCATTTTTTGCGCAACGAGTGGTCAAATGTC
520 TCATTTTGAG-GAACAACCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTC
14765 GTGCGTTGAA
Statistics
Matches: 524, Mismatches: 53, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
604 1 0.00
605 520 0.99
606 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (605 bp):
GGAGTGAGATGAACTTTTTGAACACCCATATGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCT
CAACTTTGAGCAGTTCTATGCAAAACATCATTTTTAGCAAAAGGCTCATTCCAGATGCAATTTTT
GCGCAACGAATACTCAAATGTCGTGCGTCGCATTGCGATGAGAATGTTGGACAGCCCTGTGCACA
AACAAAGCTTTCAAGAAGTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAACATAATTCTTAG
CAAAACTCTTTCTGGATGCGTTTTTTCGCGAAACGAGTGCTCAAAAGTCGTGTATCGGAATGAGA
TGAGCTTGTTAGACAGCGCTATACACAAACAAAGCCCTCATCGAAGTCCAAAGCATCAACTTTGC
GCGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAATGAGATGAACATTTTGGACAGCCC
TGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTAAACTTTGAACATTTGTGTGCAAAACAT
CATTTTGAGGAACAACCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCATGTGT
CGGAGTGAGTTGAGCATGTT
Found at i:14940 original size:157 final size:157
Alignment explanation
Indices: 14615--14973 Score: 395
Period size: 157 Copynumber: 2.3 Consensus size: 157
14605 GGTTTGTCGG
*
14615 AATGAGATGAACATT-TTGGACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTC
1 AATGAGATG-AGATTGTT-GACAGCCCTGTGCACAAACAAAGCTTTCC-AGAAGCCCAAAACCTC
* * *
14679 AACTTTGAGCATTTGTGTGCAAAACATCATTTTTAGCGAAAGGCTCATTCTAGATGCATTTTTTG
63 AACTTTGAGCATTTGTCTGCAAAACATCATTCTTAGCGAAAGACTCATTCTAGATGCATTTTTTG
* * * *
14744 CGCAACGAGTGGTCAAATGTCGTGCGTTGA
128 CGCAACGAGTGCTCAAAAGTCGTGCATCGA
* * ** *
14774 ATTGCGATGAGATTGTTGTACAGCCCTGTGCACAAACAAAGCTTT-CACGAATTCCAAAGCCTCA
1 AATGAGATGAGATTGTTG-ACAGCCCTGTGCACAAACAAAGCTTTCCA-GAAGCCCAAAACCTCA
* * * * * *
14838 ACTTTGCGCATTTTTCTGCTAAACAT-AGTTCTTAGC-AAA-ACTCTTTCTGGATGCGTTTTTTC
64 ACTTTGAGCATTTGTCTGCAAAACATCA-TTCTTAGCGAAAGACTCATTCTAGATGCATTTTTT-
*
14900 GCGCAACGAGTGCTCAAAAGTCGTGTATCGA
127 GCGCAACGAGTGCTCAAAAGTCGTGCATCGA
* * * *
14931 AATGAGATGAGCTTGTTAGCCAGCGCTATGCACAAACAAAGCT
1 AATGAGATGAGATTGTT-GACAGCCCTGTGCACAAACAAAGCT
14974 CTCCTCAAAG
Statistics
Matches: 168, Mismatches: 26, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
156 18 0.11
157 66 0.39
158 49 0.29
159 35 0.21
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (157 bp):
AATGAGATGAGATTGTTGACAGCCCTGTGCACAAACAAAGCTTTCCAGAAGCCCAAAACCTCAAC
TTTGAGCATTTGTCTGCAAAACATCATTCTTAGCGAAAGACTCATTCTAGATGCATTTTTTGCGC
AACGAGTGCTCAAAAGTCGTGCATCGA
Found at i:14993 original size:427 final size:426
Alignment explanation
Indices: 14190--15479 Score: 2067
Period size: 427 Copynumber: 3.0 Consensus size: 426
14180 CATGTTGGAG
* * * *
14190 TGAGATGAGCTTTTTGAACACCCCTATGCACAAATAAAGGTTTCCTGGAAGCCCAAAATCTCAAC
1 TGAGATGAGC-TTTTGAACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAAATCTCAAC
* * * *
14255 TTTGAGCAGTTCTATGGAAAACATTATTTTTAGCAAAAGGCTCATTCCAGATGCATTTTTTGCGC
65 TTTGAGCAGTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGC
** *
14320 AACGAGTATTCAAATGTCGTGCGTCGAGTTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACA
130 AACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACA
* * *
14385 AAGCTTTCACGAATTCCAAGGCGTCAACTTTGCGCGTTTTTGTGCTAATCATAGTTCTTAGCAAA
195 AAGCTTTCACGAATTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAACATAGTTCTTAGCAAA
14450 ACTCTTTCTGGATGCGTTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTATCGGAATGAGATGAG
260 ACTCTTTCTGGATGCGTTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTATCGGAATGAGATGAG
* *
14515 CTTGTTAGCCAGGGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGT
325 CTTGTTAGCCAGGGCTATGCACAAACAAAGCTCTCCTCAAAGTCGAAAGCATCAACTTTGCGCGT
14580 TTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAA
390 TTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAA
* * * *
14617 TGAGATGAACATTTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAAC
1 TGAGATGAGC-TTTTGAACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAAATCTCAAC
* * *
14682 TTTGAGCATTTGTGTGCAAAACATCATTTTTAGCGAAAGGCTCATTCTAGATGCATTTTTTGCGC
65 TTTGAGCAGTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGC
* * *
14747 AACGAGTGGTCAAATGTCGTGCGTTGAATTGCGATGAGATTGTTGTACAGCCCTGTGCACAAACA
130 AACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACA
* *
14812 AAGCTTTCACGAATTCCAAAGCCTCAACTTTGCGCATTTTTCTGCTAAACATAGTTCTTAGCAAA
195 AAGCTTTCACGAATTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAACATAGTTCTTAGCAAA
*
14877 ACTCTTTCTGGATGCGTTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTATCGAAATGAGATGAG
260 ACTCTTTCTGGATGCGTTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTATCGGAATGAGATGAG
* *
14942 CTTGTTAGCCAGCGCTATGCACAAACAAAGCTCTCCTCAAAGTCGAAAGCATCAATTTTGCGCGT
325 CTTGTTAGCCAGGGCTATGCACAAACAAAGCTCTCCTCAAAGTCGAAAGCATCAACTTTGCGCGT
* * * *
15007 TTGTTTGCAACACATCGTTCTTAGCGGTGTGTTGGAG
390 TTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAA
* *
15044 TGAGATGAGCTTTCTGAACCGCCCTATGCACAAACAAAGCTTCCCTAGAAGCCCAAAATCTCAAC
1 TGAGATGAGCTTT-TGAACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAAATCTCAAC
*
15109 TTTGAGCGGTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGC
65 TTTGAGCAGTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGC
*
15174 AAAGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACA
130 AACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACA
* * *
15239 AAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCGTGTTTTTGTGCTAAACATAGTTCTTATCAAA
195 AAGCTTTCACGAATTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAACATAGTTCTTAGCAAA
* * * *
15304 ACTATTTTTGGATGCGTTTTTTCGCGCAATGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAG
260 ACTCTTTCTGGATGCGTTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTATCGGAATGAGATGAG
* * * * * **
15369 CTTGTCAGACAGGGTTATGCAAAAACAAAGCTTTCCTCAAAGTCGAAAGCATCAACTTTGCAAGT
325 CTTGTTAGCCAGGGCTATGCACAAACAAAGCTCTCCTCAAAGTCGAAAGCATCAACTTTGCGCGT
*
15434 TTGTATGCAATACATCGTTCTTAGCGGTTTGTCGGAA
390 TTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAA
15471 TGAGATGAG
1 TGAGATGAG
15480 TGCTAAAAAG
Statistics
Matches: 789, Mismatches: 73, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
426 3 0.00
427 786 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (426 bp):
TGAGATGAGCTTTTGAACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAAATCTCAACT
TTGAGCAGTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCA
ACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAA
AGCTTTCACGAATTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAACATAGTTCTTAGCAAAA
CTCTTTCTGGATGCGTTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTATCGGAATGAGATGAGC
TTGTTAGCCAGGGCTATGCACAAACAAAGCTCTCCTCAAAGTCGAAAGCATCAACTTTGCGCGTT
TGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAA
Found at i:15991 original size:571 final size:570
Alignment explanation
Indices: 14956--16049 Score: 1810
Period size: 571 Copynumber: 1.9 Consensus size: 570
14946 TTAGCCAGCG
* *
14956 CTATGCACAAACAAAGCTCTCCTCAAAGTCGAAAGCATCAATTTTGCGCGTTTGTTTGCAACACA
1 CTATGCACAAACAAAGCTCTCCTCAAAGTCGAAAGCATAAATTTTGCGCGTTTATTTGCAACACA
* *
15021 TCGTTCTTAGCGGTGTGTTGGAGTGAGATGAGCTTTCTGAACCGCCCTATGCACAAACAAAGCTT
66 TCGTTCTTAGCGGTGCGTTGGAGTGAGATGAGCTTTCTGAACAGCCCTATGCACAAACAAAGCTT
* * * *
15086 CCCTAGAAGCCCAAAATCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTAGCGAAAGGCT
131 CCCTAGAAGCCCAAAATCTCAACTTAGAGCAGTTCTATGCAAAACATCATTTTTAGCGAAAGACT
* *
15151 CATTCCAGATGCATTTTTTGCGCAAAGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTG
196 CATTCAAGATGCATTTTTTGCGCAAAGAGTGCTCAAATGTCGTGCATCGAATTGCGATGAGATTG
* * *
15216 TTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCGTGTTTTTG
261 TTGGACAACCCTGTGCACAAACAAAGCTTTCACAAAGTCCAAAGCCTCAACTTTGCGCGTTTTTG
* * * *
15281 TGCTAAACATAGTTCTTATCAAAACTATTTTTGGATGCGTTTTTTCGCGCAATGAGTGCTCAAAA
326 TGATAAACATAGTTCTTAGCAAAACTATTTCTGGATGCGTTTTTTCGCGCAACGAGTGCTCAAAA
* * *
15346 GTCGTGTGTCGGAATGAGATGAGCTTGTCAGACAGGGTTATGCAAAAACAAAGCTTTCCTCAAAG
391 GTCGTGTGTCGGAATGAGATGAGCTTGTCAGACAGCGCTATGCAAAAACAAAGCTCTCCTCAAAG
* *
15411 TCGAAAGCATCAACTTTGCAAGTTTGTATGCAATACATCGTTCTTAGCGGTTTGTCGGAATGAGA
456 TCCAAAGCATCAACTTTGCAAGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAATGAGA
15476 TGAGTGCTAAAAAGTCGTTTGTCAGAGTGAGAGGAGCAAGATGGACAACC
521 TGAGTGCTAAAAAGTCGTTTGTCAGAGTGAGAGGAGCAAGATGGACAACC
* *
15526 CTATGCACAAACAAAGCTCTCCTCGAAGTCGACAGCATAAATTTTGCGCGTTTATTTGCAACACA
1 CTATGCACAAACAAAGCTCTCCTCAAAGTCGAAAGCATAAATTTTGCGCGTTTATTTGCAACACA
* *
15591 TCGTTCTTAGCGGTGCGTTGGAGTGAGATGAGCTTTTTTGAACAGTCCTATGCACAAACAAAGCT
66 TCGTTCTTAGCGGTGCGTTGGAGTGAGATGAGC-TTTCTGAACAGCCCTATGCACAAACAAAGCT
* * *
15656 TTCCTGGAAGCCCAAAATCTCAACTTAGAGCATTTCTATGCAAAACATCATTTTTAGCGAAAGAC
130 TCCCTAGAAGCCCAAAATCTCAACTTAGAGCAGTTCTATGCAAAACATCATTTTTAGCGAAAGAC
* *
15721 TTATTCAAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCATCGAATTGCGATGAGATT
195 TCATTCAAGATGCATTTTTTGCGCAAAGAGTGCTCAAATGTCGTGCATCGAATTGCGATGAGATT
15786 GTTGGACAACCCTGTGCACAAACAAAGCTTTCACAAAGTCCAAAGCCTCAACTTTGCGCGTTTTT
260 GTTGGACAACCCTGTGCACAAACAAAGCTTTCACAAAGTCCAAAGCCTCAACTTTGCGCGTTTTT
* *
15851 GTGATAAACATAGTTCTTAGCAAAATTCTTTCTGGATGCGTTTTTTCGCGCAACGAGTGCTCAAA
325 GTGATAAACATAGTTCTTAGCAAAACTATTTCTGGATGCGTTTTTTCGCGCAACGAGTGCTCAAA
* * * * *
15916 AGTCGTGTGTTGGAATGATATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAA
390 AGTCGTGTGTCGGAATGAGATGAGCTTGTCAGACAGCGCTATGCAAAAACAAAGCTCTCCTCAAA
** *
15981 GTCCAAAGCATCAACTTTGCGCGTTTGTTTGCAACACATCGTTCTTAGCGGTTTGTCGGAATGAG
455 GTCCAAAGCATCAACTTTGCAAGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAATGAG
16046 ATGA
520 ATGA
16050 ACTTTTTGGA
Statistics
Matches: 482, Mismatches: 41, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
570 93 0.19
571 389 0.81
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (570 bp):
CTATGCACAAACAAAGCTCTCCTCAAAGTCGAAAGCATAAATTTTGCGCGTTTATTTGCAACACA
TCGTTCTTAGCGGTGCGTTGGAGTGAGATGAGCTTTCTGAACAGCCCTATGCACAAACAAAGCTT
CCCTAGAAGCCCAAAATCTCAACTTAGAGCAGTTCTATGCAAAACATCATTTTTAGCGAAAGACT
CATTCAAGATGCATTTTTTGCGCAAAGAGTGCTCAAATGTCGTGCATCGAATTGCGATGAGATTG
TTGGACAACCCTGTGCACAAACAAAGCTTTCACAAAGTCCAAAGCCTCAACTTTGCGCGTTTTTG
TGATAAACATAGTTCTTAGCAAAACTATTTCTGGATGCGTTTTTTCGCGCAACGAGTGCTCAAAA
GTCGTGTGTCGGAATGAGATGAGCTTGTCAGACAGCGCTATGCAAAAACAAAGCTCTCCTCAAAG
TCCAAAGCATCAACTTTGCAAGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAATGAGA
TGAGTGCTAAAAAGTCGTTTGTCAGAGTGAGAGGAGCAAGATGGACAACC
Done.