Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015928.1 Corchorus capsularis cultivar CVL-1 contig15949, 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: 67114
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1177 original size:27 final size:28
Alignment explanation
Indices: 1147--1216 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 28
1137 ACCCAAGGGT
*
1147 ATTTTGGTCATTTTTTGCAC-CAGGGGC
1 ATTTTGGTCATTTTTTGCACTAAGGGGC
*
1174 ATTTTGGTCA-TTTCTGCACTAAGGGGC
1 ATTTTGGTCATTTTTTGCACTAAGGGGC
*
1201 ATTTTAGTCATTTTTT
1 ATTTTGGTCATTTTTT
1217 AAGTTCACCT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 8 0.22
27 25 0.68
28 4 0.11
ACGTcount: A:0.17, C:0.16, G:0.21, T:0.46
Consensus pattern (28 bp):
ATTTTGGTCATTTTTTGCACTAAGGGGC
Found at i:2453 original size:38 final size:38
Alignment explanation
Indices: 2402--2481 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 38
2392 AAGGTCAAAC
* * *
2402 AAGACTTGTTTTTCAACATCTAAGCACAAGCTCAAGTA
1 AAGACTTGCTTTTCAACATCCAAGCACAAGCCCAAGTA
2440 AAGACTTGCTTTTCAACATCCAAGCACAAGCCCAAGTA
1 AAGACTTGCTTTTCAACATCCAAGCACAAGCCCAAGTA
2478 AAGA
1 AAGA
2482 TCAACTCAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (38 bp):
AAGACTTGCTTTTCAACATCCAAGCACAAGCCCAAGTA
Found at i:4230 original size:50 final size:50
Alignment explanation
Indices: 4155--4473 Score: 419
Period size: 50 Copynumber: 6.4 Consensus size: 50
4145 GAACTTTGGT
* * * *
4155 ATAACAAGATTGAATTTTCACGTAATTAGTAAATAAAAATGTCATCTTTGA
1 ATAA-AAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCACCTTTGA
* *
4206 ATAAAAGGTTGAATTTTTAAGTAATTGGTAAGTAAAAATGTCACCTTTGA
1 ATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCACCTTTGA
* * *
4256 ATAAAAGATTGAATTTTTAAATAATTGGTAAATAAAGATGTAACCTTTGA
1 ATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCACCTTTGA
*
4306 ATAAAAGGTTGAATTTTTTAAGTAATTGGTAAATAAAAATGTCACCTTTGA
1 ATAAAAGATTGAA-TTTTTAAGTAATTGGTAAATAAAAATGTCACCTTTGA
** * **
4357 GCAAAAGATTGAATTTTTAAGTAATTAGTAAATAAGGATGT-ACCCTTTGA
1 ATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCA-CCTTTGA
*
4407 ATAAAAGATTGAATTTTTAAGTAATTGGCAAAT-AAAATGTCA-CTTTGA
1 ATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCACCTTTGA
* * *
4455 ATTAAAGTTTGAACTTTTA
1 ATAAAAGATTGAATTTTTA
4474 GGCCATTAGT
Statistics
Matches: 235, Mismatches: 30, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
48 22 0.09
49 6 0.03
50 159 0.68
51 48 0.20
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (50 bp):
ATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCACCTTTGA
Found at i:4372 original size:101 final size:100
Alignment explanation
Indices: 4160--4473 Score: 443
Period size: 101 Copynumber: 3.1 Consensus size: 100
4150 TTGGTATAAC
* * * * *
4160 AAGATTGAATTTTCACGTAATTAGTAAATAAAAATGTCATCTTTGAATAAAAGGTTGAATTTTTA
1 AAGATTGAATTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTGAATAAAAGGTTGAATTTTTA
* *
4225 AGTAATTGGTAAGTAAAAATGTCACCTTTGAATAA
66 AGTAATTGGTAAATAAAAATGTCACCTTTGAACAA
* *
4260 AAGATTGAATTTTTAAATAATTGGTAAATAAAGATGTAACCTTTGAATAAAAGGTTGAATTTTTT
1 AAGATTGAATTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTGAATAAAAGGTTGAA-TTTTT
*
4325 AAGTAATTGGTAAATAAAAATGTCACCTTTGAGCAA
65 AAGTAATTGGTAAATAAAAATGTCACCTTTGAACAA
* * *
4361 AAGATTGAATTTTTAAGTAATTAGTAAATAAGGATGTACCCTTTGAATAAAAGATTGAATTTTTA
1 AAGATTGAATTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTGAATAAAAGGTTGAATTTTTA
* **
4426 AGTAATTGGCAAAT-AAAATGTCA-CTTTGAATTA
66 AGTAATTGGTAAATAAAAATGTCACCTTTGAACAA
* *
4459 AAGTTTGAACTTTTA
1 AAGATTGAATTTTTA
4474 GGCCATTAGT
Statistics
Matches: 192, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
98 20 0.10
99 9 0.05
100 71 0.37
101 92 0.48
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (100 bp):
AAGATTGAATTTTTAAGTAATTAGTAAATAAAGATGTAACCTTTGAATAAAAGGTTGAATTTTTA
AGTAATTGGTAAATAAAAATGTCACCTTTGAACAA
Found at i:5313 original size:55 final size:55
Alignment explanation
Indices: 5253--5814 Score: 846
Period size: 55 Copynumber: 10.4 Consensus size: 55
5243 AAAAAGGAAC
* * *
5253 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGACAAGGTGATAGTAATCAATA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* * *
5308 AATCAGTAATTAAGTGAAAAGAGATTAATCGGAGTCAAGGTAATGGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* * *
5363 AATCAGTAATTAAGTAAAAAGAGATTAATCAAAGACAAGGTAATGGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* *
5418 AACCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
5473 AATCAGTAATTAAGT----A-A-A-T--T-AGAGTCGAA-GTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC-AAGGTAATAGTAATCAGTA
*
5518 AATCAGTAATTGAGTAAAAAGAGATTAATCAGAGTCGAA-GTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC-AAGGTAATAGTAATCAGTA
*
5573 AATCAGTAATTGAGTAAAAAGAGATTAATCAGAGTCGAA-GTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC-AAGGTAATAGTAATCAGTA
5628 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCGAA-GTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC-AAGGTAATAGTAATCAGTA
*
5683 AATTAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
5738 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* *
5793 AATCAGTAATCAGGTAAAAAGA
1 AATCAGTAATTAAGTAAAAAGA
5815 TAATAATTAG
Statistics
Matches: 473, Mismatches: 22, Indels: 24
0.91 0.04 0.05
Matches are distributed among these distances:
45 36 0.08
46 3 0.01
48 1 0.00
49 2 0.00
50 2 0.00
51 2 0.00
52 1 0.00
54 3 0.01
55 423 0.89
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
Found at i:5467 original size:21 final size:21
Alignment explanation
Indices: 5443--5515 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 21
5433 AAAAAGAGAT
5443 TAATCAGAGTCAAAGTAATAG
1 TAATCAGAGTCAAAGTAATAG
*
5464 TAATC--AGTAAATCAGTAATTAAG
1 TAATCAGAGTCAA--AGTAA-T-AG
* *
5487 TAAATTAGAGTCGAAGTAATAG
1 T-AATCAGAGTCAAAGTAATAG
5509 TAATCAG
1 TAATCAG
5516 TAAATCAGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 14
0.68 0.08 0.24
Matches are distributed among these distances:
19 5 0.12
21 15 0.38
22 4 0.10
23 4 0.10
24 8 0.20
26 4 0.10
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (21 bp):
TAATCAGAGTCAAAGTAATAG
Found at i:5490 original size:16 final size:16
Alignment explanation
Indices: 5469--5535 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
5459 AATAGTAATC
5469 AGTAAATCAGTAATTA
1 AGTAAATCAGTAATTA
* * *
5485 AGTAAATTAG-AGTCGA
1 AGTAAATCAGTAAT-TA
*
5501 AGT-AAT-AGTAA-TC
1 AGTAAATCAGTAATTA
*
5514 AGTAAATCAGTAATTG
1 AGTAAATCAGTAATTA
5530 AGTAAA
1 AGTAAA
5536 AAGAGATTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
13 3 0.08
14 5 0.13
15 11 0.28
16 20 0.51
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (16 bp):
AGTAAATCAGTAATTA
Found at i:5728 original size:265 final size:265
Alignment explanation
Indices: 5253--5755 Score: 832
Period size: 265 Copynumber: 1.9 Consensus size: 265
5243 AAAAAGGAAC
*
5253 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGACAAGGTGATAGTAATCAATAAATCAGTAAT
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGACAAGGTAATAGTAATCAATAAATCAGTAAT
* * *
5318 TAAGTGAAAAGAGATTAATCGGAGTCAAGGTAATGGTAATCAGTAAATCAGTAATTAAGTAAAAA
66 TAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAA
*
5383 GAGATTAATCAAAGACAAGGTAATGGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATC
131 GAGATTAATCAAAGACAAGGTAATAGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATC
5448 AGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAATTAGAGTCGAAGTAATAGTAAT
196 AGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAATTAGAGTCGAAGTAATAGTAAT
5513 CAGTA
261 CAGTA
* * *
5518 AATCAGTAATTGAGTAAAAAGAGATTAATCAGAGTCGAA-GTAATAGTAATCAGTAAATCAGTAA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGAC-AAGGTAATAGTAATCAATAAATCAGTAA
*
5582 TTGAGTAAAAAGAGATTAATCAGAGTCGAA-GTAATAGTAATCAGTAAATCAGTAATTAAGTAAA
65 TTAAGTAAAAAGAGATTAATCAGAGTC-AAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAA
* * **
5646 AAGAGATTAATCAGAGTCGAA-GTAATAGTAATCAGTAAATTAGTAATTAAGTAAAAAGAGATTA
129 AAGAGATTAATCAAAGAC-AAGGTAATAGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTA
*
5710 ATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAA
193 ATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAA
5756 AAGAGATTAA
Statistics
Matches: 221, Mismatches: 14, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
265 215 0.97
266 6 0.03
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (265 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGACAAGGTAATAGTAATCAATAAATCAGTAAT
TAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAA
GAGATTAATCAAAGACAAGGTAATAGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATC
AGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAATTAGAGTCGAAGTAATAGTAAT
CAGTA
Found at i:5780 original size:26 final size:26
Alignment explanation
Indices: 5696--5780 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
5686 TAGTAATTAA
5696 GTAAAAAGAGATTAATCAGAGTCAAG
1 GTAAAAAGAGATTAATCAGAGTCAAG
* * * *
5722 GTAATAGTAATCAG-TAAATCAGTAATTAA-
1 GTAA-A--AA-GAGATTAATCAG-AGTCAAG
5751 GTAAAAAGAGATTAATCAGAGTCAAG
1 GTAAAAAGAGATTAATCAGAGTCAAG
5777 GTAA
1 GTAA
5781 TAGTAATCAG
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 6 0.14
26 17 0.39
27 1 0.02
28 1 0.02
29 13 0.30
30 6 0.14
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (26 bp):
GTAAAAAGAGATTAATCAGAGTCAAG
Found at i:6132 original size:21 final size:22
Alignment explanation
Indices: 6101--6445 Score: 158
Period size: 21 Copynumber: 16.0 Consensus size: 22
6091 AAGGTGTCTG
* * *
6101 AAAGGGTAAAATGGTAATTAGT
1 AAAGAGTAAAATAGTAATCAGT
*
6123 AAAGAGAAAAATAGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* *
6145 AAAAAGTAAGAA-GGTAATCA--
1 AAAGAGTAA-AATAGTAATCAGT
*
6165 ACAAGAGTAAAATAGTAGTCAGT
1 A-AAGAGTAAAATAGTAATCAGT
*
6188 AAAAAGT-AAATAGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* *
6209 -AAGAGTAAAATGGTAATAAGT
1 AAAGAGTAAAATAGTAATCAGT
* *
6230 AAA-AG-GAAATCAGTAA-GAGT
1 AAAGAGTAAAAT-AGTAATCAGT
* *
6250 AAA-AG------GGTGATCAGT
1 AAAGAGTAAAATAGTAATCAGT
6265 AAAGAGTAAAA-AGCTAATCA--
1 AAAGAGTAAAATAG-TAATCAGT
*
6285 ACAAGAAGTAAAA-AGTAGTCAGT
1 A-AAG-AGTAAAATAGTAATCAGT
* * * *
6308 AAAAAGCAAAA-GGCAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
* *
6329 AAAAAGTAAAAGAGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
*
6351 AAAAAAAGAGCAGAAAATAGTAATCAGT
1 ----AAAGAG--TAAAATAGTAATCAGT
*
6379 AAAAGAGTAAAATGGTAATCAGT
1 -AAAGAGTAAAATAGTAATCAGT
* * **
6402 AAAAAGTAAGAGGGTAATCA--
1 AAAGAGTAAAATAGTAATCAGT
*
6422 ACAAGAGTAAAATGGTAATCAGT
1 A-AAGAGTAAAATAGTAATCAGT
6445 A
1 A
6446 CAAAGTGAAG
Statistics
Matches: 250, Mismatches: 43, Indels: 59
0.71 0.12 0.17
Matches are distributed among these distances:
14 3 0.01
15 6 0.02
16 2 0.01
20 22 0.09
21 92 0.37
22 80 0.32
23 19 0.08
25 7 0.03
26 5 0.02
28 14 0.06
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.19
Consensus pattern (22 bp):
AAAGAGTAAAATAGTAATCAGT
Found at i:6177 original size:43 final size:43
Alignment explanation
Indices: 6124--6457 Score: 155
Period size: 43 Copynumber: 7.8 Consensus size: 43
6114 GTAATTAGTA
*
6124 AAGAGAAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
* **
6167 AAGAGTAAAATAGTAGTCAGTAAAAAGTAA-ATA-GTAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGA-AGGTAATCAAC
* * * * **
6209 AAGAGTAAAATGGTAATAAGTAAAAGGAAATCA-GTAAGAGT-AA-
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGT-A-A-TCAAC
* * * *
6252 AAGGGT--GATCAGTAA--AG-----AGTAAAAAGCTAATCAAC
1 AAGAGTAAAAT-AGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
* * *
6287 AAGAAGTAAAA-AGTAGTCAGTAAAAAGCAA-AAGGCAATCAGTA-
1 AAG-AGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCA--AC
* * * *
6330 AAAAGTAAAAGAGTAATCAGTAAAAAAAG-AGCAGAAAATAGTAATCAGTAA
1 AAGAGTAAAATAGTAATCAGT--AAAAAGTA--AG--AA-GGTAATCA--AC
* *
6381 AAGAGTAAAATGGTAATCAGTAAAAAGTAAGAGGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
* *
6424 AAGAGTAAAATGGTAATCAGTACAAAGTGAAGAA
1 AAGAGTAAAATAGTAATCAGTAAAAAGT-AAGAA
6458 TAATCAGTAA
Statistics
Matches: 221, Mismatches: 37, Indels: 65
0.68 0.11 0.20
Matches are distributed among these distances:
33 1 0.00
34 3 0.01
35 8 0.04
36 7 0.03
38 3 0.01
40 2 0.01
41 2 0.01
42 55 0.25
43 78 0.35
44 8 0.04
45 14 0.06
46 2 0.01
48 2 0.01
49 8 0.04
50 10 0.05
51 18 0.08
ACGTcount: A:0.55, C:0.07, G:0.21, T:0.18
Consensus pattern (43 bp):
AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
Found at i:6199 original size:64 final size:63
Alignment explanation
Indices: 6074--6469 Score: 262
Period size: 64 Copynumber: 6.2 Consensus size: 63
6064 AATAGCATGC
* * * * * * *
6074 AATCAGTAAAAAGTAAAAAGGT-GTCTGA-AAGGGTAAAATGGTAATTAGTAAAGAGAAAAATAG
1 AATCAGTAAAAAGT-AAAAGGTAATC-AACAAGAGTAAAATAGTAATCAGTAAAAAG-TAAATAG
6137 T
63 T
*
6138 AATCAGTAAAAAGTAAGAAGGTAATCAACAAGAGTAAAATAGTAGTCAGTAAAAAGTAAATAGT
1 AATCAGTAAAAAGTAA-AAGGTAATCAACAAGAGTAAAATAGTAATCAGTAAAAAGTAAATAGT
* * * *
6202 AATCAGT-AAGAGTAAAATGGTAAT-----A-AGTAAAA-GGAAATCAGT-AAGAGTAAA-AGGG
1 AATCAGTAAAAAGTAAAA-GGTAATCAACAAGAGTAAAATAGTAATCAGTAAAAAGTAAATA--G
6257 T
63 T
* * * * *
6258 GATCAGTAAAGAGTAAAAAGCTAATCAACAAGAAGTAAAA-AGTAGTCAGTAAAAAGCAAA-AGG
1 AATCAGTAAAAAGT-AAAAGGTAATCAACAAG-AGTAAAATAGTAATCAGTAAAAAGTAAATA-G
*
6321 C
63 T
* *
6322 AATCAGTAAAAAGTAAAAGAGTAATCAGTAAAAAAAGAGCAGAAAATAGTAATCAGTAAAAGAGT
1 AATCAGTAAAAAGTAAAAG-GTAATC-----AACAAGAG--TAAAATAGTAATCAGTAAAA-AGT
*
6387 AAAATGGT
57 -AAATAGT
* * * * * *
6395 AATCAGTAAAAAGTAAGAGGGTAATCAACAAGAGTAAAATGGTAATCAGTACAAAGTGAAGAAT
1 AATCAGTAAAAAGTAA-AAGGTAATCAACAAGAGTAAAATAGTAATCAGTAAAAAGTAAATAGT
6459 AATCAGTAAAA
1 AATCAGTAAAA
6470 TAGTGTTGGT
Statistics
Matches: 264, Mismatches: 39, Indels: 58
0.73 0.11 0.16
Matches are distributed among these distances:
54 1 0.00
55 8 0.03
56 15 0.06
57 18 0.07
58 5 0.02
62 3 0.01
63 20 0.08
64 81 0.31
65 35 0.13
66 17 0.06
68 9 0.03
69 5 0.02
70 4 0.02
71 13 0.05
72 2 0.01
73 26 0.10
74 2 0.01
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.19
Consensus pattern (63 bp):
AATCAGTAAAAAGTAAAAGGTAATCAACAAGAGTAAAATAGTAATCAGTAAAAAGTAAATAGT
Found at i:6230 original size:35 final size:34
Alignment explanation
Indices: 6186--6273 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 34
6176 ATAGTAGTCA
* *
6186 GTAAAAAGTAAATAGTAATCAGTAAGAGTAAAATG
1 GTAATAAGTAAA-AGTAATCAGTAAGAGTAAAAGG
*
6221 GTAATAAGTAAAAGGAAATCAGTAAGAGTAAAAGG
1 GTAATAAGTAAAA-GTAATCAGTAAGAGTAAAAGG
* *
6256 GTGATCAGTAAAGAGTAA
1 GTAATAAGTAAA-AGTAA
6274 AAAGCTAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 1 0.02
35 43 0.96
36 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.24, T:0.20
Consensus pattern (34 bp):
GTAATAAGTAAAAGTAATCAGTAAGAGTAAAAGG
Found at i:6351 original size:15 final size:15
Alignment explanation
Indices: 6333--6388 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
6323 ATCAGTAAAA
6333 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* *
6348 AGTAAAA-A-AAGAGC
1 AGTAAAAGAGTA-ATC
*
6362 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
6376 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
6389 AATGGTAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 17 0.53
ACGTcount: A:0.59, C:0.05, G:0.20, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:7068 original size:63 final size:63
Alignment explanation
Indices: 6929--7147 Score: 250
Period size: 63 Copynumber: 3.5 Consensus size: 63
6919 AAACATGGCT
* * *
6929 AAACTGACCCTTTGTCCGAAAGGGTATTTTGAGAA-A-TAGGA-TCTAAGTGCAGGAATGTGAAC
1 AAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAATACTA-AACT-TAAATGCAGGAATGTG-AC
6991 -
63 G
* * * *
6991 AAACTGACCGTTTGTCTGAAAGGGTATTTTGGGAATACTAACCTTAAATGTAGGAATGTGACG
1 AAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAATACTAAACTTAAATGCAGGAATGTGACG
* * * *
7054 AAACTGACCCTTTGTCTGAAAGGGTGTTTTGGGAATACTAAACTTAAATGCAAGAAGGTGACG
1 AAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAATACTAAACTTAAATGCAGGAATGTGACG
* *
7117 AAGC-CATCCCTTTGTCCGAAAGGGTATTTTG
1 AAACTGA-CCCTTTGTCCGAAAGGGTATTTTG
7148 AGAAAAAGCG
Statistics
Matches: 135, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
62 35 0.26
63 97 0.72
64 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (63 bp):
AAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAATACTAAACTTAAATGCAGGAATGTGACG
Found at i:7389 original size:48 final size:47
Alignment explanation
Indices: 7318--7433 Score: 171
Period size: 48 Copynumber: 2.4 Consensus size: 47
7308 CTTCCATATG
*
7318 GGAA-GGGCGTTTTGGAAAAAAGAAATGCAAACGGTGACCTTCCGACCA
1 GGAAGGGGC-TTTTGG-AATAAGAAATGCAAACGGTGACCTTCCGACCA
* *
7366 GGAAGGGGCTTTTTGGAATAAGAAATGCAAACTGTGACCTTCCGACCG
1 GGAAGGGGC-TTTTGGAATAAGAAATGCAAACGGTGACCTTCCGACCA
7414 GGAAGGGGCTTTTGGAATAA
1 GGAAGGGGCTTTTGGAATAA
7434 AAAAAATGCA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
47 11 0.17
48 42 0.67
49 10 0.16
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.21
Consensus pattern (47 bp):
GGAAGGGGCTTTTGGAATAAGAAATGCAAACGGTGACCTTCCGACCA
Found at i:7454 original size:48 final size:48
Alignment explanation
Indices: 7318--7456 Score: 122
Period size: 48 Copynumber: 2.9 Consensus size: 48
7308 CTTCCATATG
* * ****
7318 GGAA-GGGCGTTTTGGAAAAAAGAAATGCAAACGGTGACCTTCCGACCA
1 GGAAGGGGCTTTTTGGAATAAA-AAATGCAAACTAACACCTTCCGACCA
* *** *
7366 GGAAGGGGCTTTTTGGAATAAGAAATGCAAACTGTGACCTTCCGACCG
1 GGAAGGGGCTTTTTGGAATAAAAAATGCAAACTAACACCTTCCGACCA
*
7414 GGAAGGGGC-TTTTGGAATAAAAAAAATGCAGAC-AACACCTTCC
1 GGAAGGGGCTTTTTGGAAT--AAAAAATGCAAACTAACACCTTCC
7457 AGTGAGGAAG
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
47 9 0.12
48 44 0.56
49 25 0.32
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (48 bp):
GGAAGGGGCTTTTTGGAATAAAAAATGCAAACTAACACCTTCCGACCA
Found at i:7507 original size:41 final size:41
Alignment explanation
Indices: 7445--7603 Score: 180
Period size: 41 Copynumber: 3.9 Consensus size: 41
7435 AAAAATGCAG
* * *
7445 ACAACACCTTCC-AGTGAGGAAGGGCAAGATAGGAAAACTAA
1 ACAACACCTTCCGA-TGGGGAAGGGCAAAACAGGAAAACTAA
* **
7486 ACAACACCTTCCGATGGGGAAGGGC-AAACTGGGAAATTTAA
1 ACAACACCTTCCGATGGGGAAGGGCAAAAC-AGGAAAACTAA
* *
7527 ACAACACCTTCCGGTGGGGAAGGGCAAAACAAGAAAACTAA
1 ACAACACCTTCCGATGGGGAAGGGCAAAACAGGAAAACTAA
* *
7568 ACAACAGCTTCCGACGAGGG-AGGGCAAAACAGGAAA
1 ACAACACCTTCCGATG-GGGAAGGGCAAAACAGGAAA
7604 TTAGACAAAG
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 2 0.02
41 89 0.90
42 8 0.08
ACGTcount: A:0.42, C:0.21, G:0.26, T:0.11
Consensus pattern (41 bp):
ACAACACCTTCCGATGGGGAAGGGCAAAACAGGAAAACTAA
Found at i:7592 original size:82 final size:82
Alignment explanation
Indices: 7445--7595 Score: 223
Period size: 82 Copynumber: 1.8 Consensus size: 82
7435 AAAAATGCAG
* * * *
7445 ACAACACCTTCCAGTGAGGAAGGGCAAGATAGGAAAACTAAACAACACCTTCCGATGGGGAAGGG
1 ACAACACCTTCCAGTGAGGAAGGGCAAAACAAGAAAACTAAACAACACCTTCCGACGGGGAAGGG
7510 CAAACTGGGAAATTTAA
66 CAAACTGGGAAATTTAA
* * *
7527 ACAACACCTTCCGGTGGGGAAGGGCAAAACAAGAAAACTAAACAACAGCTTCCGACGAGGG-AGG
1 ACAACACCTTCCAGTGAGGAAGGGCAAAACAAGAAAACTAAACAACACCTTCCGACG-GGGAAGG
7591 GCAAA
65 GCAAA
7596 ACAGGAAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
82 58 0.95
83 3 0.05
ACGTcount: A:0.40, C:0.21, G:0.26, T:0.12
Consensus pattern (82 bp):
ACAACACCTTCCAGTGAGGAAGGGCAAAACAAGAAAACTAAACAACACCTTCCGACGGGGAAGGG
CAAACTGGGAAATTTAA
Found at i:17139 original size:84 final size:84
Alignment explanation
Indices: 17009--17253 Score: 416
Period size: 84 Copynumber: 3.0 Consensus size: 84
16999 AAATTATTCT
**
17009 TGTGTTTTTATTATGAGTTTGAGTAGCTAAATCCTTAATTAGGGTTTAGGGTGTAGTCAATTGGG
1 TGTGTTTTTATTATGAGCCTGAGTAGCTAAATCCTTAATTAGGGTTTAGGGTGTAGTCAATTGGG
17074 AATTATTGTTTAATTTATG
66 AATTATTGTTTAATTTATG
17093 TGTGTTTTTATTATGAGCCTGAGTAGCTAAATCCTTAATTAGGGTTTAGGGTGTAGTCAATTGGG
1 TGTGTTTTTATTATGAGCCTGAGTAGCTAAATCCTTAATTAGGGTTTAGGGTGTAGTCAATTGGG
17158 AATTATTGTTTAATTTATG
66 AATTATTGTTTAATTTATG
17177 TGTGTTTTTATTATGAGCCTGAGTAGCTAAATCCTTAATTAGGG--T----T-TAGTCAATTGGG
1 TGTGTTTTTATTATGAGCCTGAGTAGCTAAATCCTTAATTAGGGTTTAGGGTGTAGTCAATTGGG
17235 AATTATTGTTTAA-TTATG
66 AATTATTGTTTAATTTATG
17253 T
1 T
17254 TTTGAATTAT
Statistics
Matches: 159, Mismatches: 2, Indels: 8
0.94 0.01 0.05
Matches are distributed among these distances:
76 6 0.04
77 25 0.16
78 1 0.01
82 1 0.01
84 126 0.79
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (84 bp):
TGTGTTTTTATTATGAGCCTGAGTAGCTAAATCCTTAATTAGGGTTTAGGGTGTAGTCAATTGGG
AATTATTGTTTAATTTATG
Found at i:26287 original size:28 final size:28
Alignment explanation
Indices: 26255--26339 Score: 143
Period size: 28 Copynumber: 3.0 Consensus size: 28
26245 ATTTGATTCC
* *
26255 TTTCTTTTTGTAGTTGGAAAACATGTGT
1 TTTCTATTTGGAGTTGGAAAACATGTGT
*
26283 TTTCTATTTGGAGTTGGAAAATATGTGT
1 TTTCTATTTGGAGTTGGAAAACATGTGT
26311 TTTCTATTTGGAGTTGGAAAACATGTGT
1 TTTCTATTTGGAGTTGGAAAACATGTGT
26339 T
1 T
26340 GTAAACATGG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (28 bp):
TTTCTATTTGGAGTTGGAAAACATGTGT
Found at i:28473 original size:2 final size:2
Alignment explanation
Indices: 28466--28540 Score: 63
Period size: 2 Copynumber: 39.0 Consensus size: 2
28456 GGATAGTAGC
*
28466 TA TA TA TA TG TA TA -A TA TA TA TA TA TA TA TA -A TGA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
*
28506 -A TA TA TA TGA TA GTA -A CA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA TA TA
28541 ATAATGATCA
Statistics
Matches: 62, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
1 6 0.10
2 50 0.81
3 6 0.10
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (2 bp):
TA
Found at i:28488 original size:17 final size:17
Alignment explanation
Indices: 28466--28543 Score: 69
Period size: 15 Copynumber: 4.8 Consensus size: 17
28456 GGATAGTAGC
*
28466 TATATATAT-GTATA-A
1 TATATATATAATATATA
28481 TATATATAT-ATATATA
1 TATATATATAATATATA
28497 -ATGATA-ATAATATATA
1 TAT-ATATATAATATATA
*
28513 TGATAGTA-ACAATATATA
1 T-ATA-TATATAATATATA
28531 TATATATATAATA
1 TATATATATAATA
28544 ATGATCATGC
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
15 17 0.32
16 13 0.25
17 9 0.17
18 14 0.26
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.42
Consensus pattern (17 bp):
TATATATATAATATATA
Found at i:35204 original size:49 final size:49
Alignment explanation
Indices: 35144--35319 Score: 210
Period size: 49 Copynumber: 3.6 Consensus size: 49
35134 TTTGTTCGGA
* * **
35144 AAGGGCATTTTAAGAAAAAGCGAGTAAAAATTAACGCCTTCCGTCCGGG
1 AAGGGCGTTTTAAGAAAAAGCAAGTAAAAATTAGTGCCTTCCGTCCGGG
* * * ** *
35193 AAGGGTGTTTT-AGGAAAAGCAAGTAAAAAATAGTATCTTCCGTCCGAG
1 AAGGGCGTTTTAAGAAAAAGCAAGTAAAAATTAGTGCCTTCCGTCCGGG
* *
35241 AATGGCGTTTTAGGAAAAAGCAAGTAAAAATTAGTGCCTTCCGTCCGGG
1 AAGGGCGTTTTAAGAAAAAGCAAGTAAAAATTAGTGCCTTCCGTCCGGG
** *
35290 AAGGGCGTTTTGGGAAATAGCAAGTAAAAA
1 AAGGGCGTTTTAAGAAAAAGCAAGTAAAAA
35320 CTGAAAATTG
Statistics
Matches: 105, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
48 38 0.36
49 67 0.64
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (49 bp):
AAGGGCGTTTTAAGAAAAAGCAAGTAAAAATTAGTGCCTTCCGTCCGGG
Found at i:38288 original size:17 final size:17
Alignment explanation
Indices: 38236--38291 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
38226 AAGAGAATCA
*
38236 AATGGACCAAAGAAATG
1 AATGAACCAAAGAAATG
*
38253 AATTAA--AAATGAAATG
1 AATGAACCAAA-GAAATG
*
38269 AATGAACCAAAGAAAGG
1 AATGAACCAAAGAAATG
38286 AATGAA
1 AATGAA
38292 ATGATTTGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 3 0.09
16 11 0.34
17 15 0.47
18 3 0.09
ACGTcount: A:0.59, C:0.07, G:0.20, T:0.14
Consensus pattern (17 bp):
AATGAACCAAAGAAATG
Found at i:38676 original size:29 final size:29
Alignment explanation
Indices: 38631--38686 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
38621 CAAGCCCAAA
* *
38631 TCAAGTTAAAAATGAAATGGTTCAATTTT
1 TCAAGTTAAAAAAGAAATGATTCAATTTT
38660 TCAAGTTAAAAAAGAAATGATTCAATT
1 TCAAGTTAAAAAAGAAATGATTCAATT
38687 AACAATTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (29 bp):
TCAAGTTAAAAAAGAAATGATTCAATTTT
Found at i:40092 original size:16 final size:16
Alignment explanation
Indices: 40073--40127 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
40063 GAACCTGAAT
40073 CCGAAAAAACCCGAAC
1 CCGAAAAAACCCGAAC
* * *
40089 CCGAAAAAGCTCAAAC
1 CCGAAAAAACCCGAAC
*
40105 CCGAAAAAACCCGAAT
1 CCGAAAAAACCCGAAC
40121 CCGAAAA
1 CCGAAAA
40128 TTTATGAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.51, C:0.33, G:0.13, T:0.04
Consensus pattern (16 bp):
CCGAAAAAACCCGAAC
Found at i:40311 original size:32 final size:32
Alignment explanation
Indices: 40265--40382 Score: 175
Period size: 32 Copynumber: 3.7 Consensus size: 32
40255 TCTGGCCAAA
**
40265 ACCCAAATAGAACCCGAACCCGAATTAACCTG
1 ACCCAAATTCAACCCGAACCCGAATTAACCTG
*
40297 ACCCAAATTCAACCCGAGCCCGAATTAACCTG
1 ACCCAAATTCAACCCGAACCCGAATTAACCTG
* *
40329 ACCCAAATT-AACCCGAGCCCGAATTAACTTG
1 ACCCAAATTCAACCCGAACCCGAATTAACCTG
*
40360 ACCCAAATCCAACCCGAACCCGA
1 ACCCAAATTCAACCCGAACCCGA
40383 CTCAAGCCCA
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 29 0.37
32 50 0.63
ACGTcount: A:0.37, C:0.37, G:0.12, T:0.14
Consensus pattern (32 bp):
ACCCAAATTCAACCCGAACCCGAATTAACCTG
Found at i:42740 original size:16 final size:17
Alignment explanation
Indices: 42719--42752 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
42709 AAAAATATTA
42719 AAAATAAT-AAAAAAAT
1 AAAATAATGAAAAAAAT
42735 AAAATAATGAAAAAAAT
1 AAAATAATGAAAAAAAT
42752 A
1 A
42753 TTTAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAATAATGAAAAAAAT
Found at i:49341 original size:18 final size:17
Alignment explanation
Indices: 49314--49349 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
49304 TTTCTCTTCA
*
49314 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCAAGT
49331 TCTAGTTTTTCTTCAAGT
1 TCTA-TTTTTCTTCAAGT
49349 T
1 T
49350 TTAGGTTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.14, C:0.17, G:0.08, T:0.61
Consensus pattern (17 bp):
TCTATTTTTCTTCAAGT
Found at i:50647 original size:21 final size:23
Alignment explanation
Indices: 50603--50647 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
50593 CTTTGGTGAC
* *
50603 TTTCGACCCTTTGCAGAGGTTGA
1 TTTCGACCCATTCCAGAGGTTGA
50626 TTTCGACCCATTCCA-A-GTTGA
1 TTTCGACCCATTCCAGAGGTTGA
50647 T
1 T
50648 GCAGGACACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 1 0.05
23 13 0.65
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (23 bp):
TTTCGACCCATTCCAGAGGTTGA
Found at i:64609 original size:21 final size:21
Alignment explanation
Indices: 64567--64625 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
64557 AAACTAAAGC
*
64567 AAAT-TAT-AAAGAAAAC-CT
1 AAATATATAAAAGAAACCTCT
64585 AAATATATAAAAGAAACCTCT
1 AAATATATAAAAGAAACCTCT
*
64606 AAATATA-AATAAGATACCTC
1 AAATATATAA-AAGAAACCTC
64626 CAACATAGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 4 0.11
19 3 0.09
20 10 0.29
21 18 0.51
ACGTcount: A:0.58, C:0.14, G:0.05, T:0.24
Consensus pattern (21 bp):
AAATATATAAAAGAAACCTCT
Done.