Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016352.1 Corchorus capsularis cultivar CVL-1 contig16373, 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: 12029
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Found at i:3400 original size:33 final size:33
Alignment explanation
Indices: 3363--3425 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
3353 AGTTAACGGA
3363 TCATGTGACC-GGTTGTGGCCGGGCATGGCCGAG
1 TCATGTGACCTGG-TGTGGCCGGGCATGGCCGAG
*
3396 TCATGTGGCCTGGTGTGGCCGGGCATGGCC
1 TCATGTGACCTGGTGTGGCCGGGCATGGCC
3426 ATGTCGCGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.10, C:0.25, G:0.43, T:0.22
Consensus pattern (33 bp):
TCATGTGACCTGGTGTGGCCGGGCATGGCCGAG
Found at i:3437 original size:33 final size:32
Alignment explanation
Indices: 3371--3507 Score: 141
Period size: 33 Copynumber: 4.2 Consensus size: 32
3361 GATCATGTGA
* **
3371 CCGGTTGTGGCCGGGCATGGCCGA-GTCATGTGG
1 CCGG-TGTGGCCGGGCATCGCC-ATGTCGCGTGG
*
3404 CCTGGTGTGGCCGGGCATGGCCATGTCGCGTGG
1 CC-GGTGTGGCCGGGCATCGCCATGTCGCGTGG
* *
3437 CCGGTGATGGCCGGGCATCTCCATGTCGCATGG
1 CCGGTG-TGGCCGGGCATCGCCATGTCGCGTGG
* * *
3470 CCGGTGTTGCGCGGGCATCTCCAAGTCGCGTGG
1 CCGGTGTGGC-CGGGCATCGCCATGTCGCGTGG
3503 CCGGT
1 CCGGT
3508 CACAAGTGCT
Statistics
Matches: 92, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
32 8 0.09
33 82 0.89
34 2 0.02
ACGTcount: A:0.09, C:0.28, G:0.42, T:0.21
Consensus pattern (32 bp):
CCGGTGTGGCCGGGCATCGCCATGTCGCGTGG
Found at i:4700 original size:159 final size:159
Alignment explanation
Indices: 3618--4699 Score: 1603
Period size: 159 Copynumber: 6.8 Consensus size: 159
3608 TGGCGCATCA
*
3618 AACAGGCTCATCTCACTCCGACACAAGGCTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAA
1 AACAGGCTCATCTCACTCCTACACAAGGCTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAA
*
3683 TGGAGCCTTTCGCTAAGAACGATGTTTTGCACACAAACGCGCGTTGTTGAGGCTTTGGGCTTCAA
66 T-GAGCCTTTCGATAAGAACGATGTTTTGCACACAAACGCGCGTTGTTGAGGCTTTGGGCTTCAA
*
3748 GGAGAGCTTTGTTTTTGCACAAGGCTGTCC
130 GGAGAGCTTTGTTTTTGCACAGGGCTGTCC
* * *
3778 AACAGGCTCATCTCACTCCAACACAAGGCTTTTGAGCACACGTTGCGCAAAAAATAGCTTCTAGA
1 AACAGGCTCATCTCACTCCTACACAAGGCTTTTGAGCACTCGTTGCGCAAAAAAT-GCTTCTGGA
** ** *
3843 ATGAGCCTTTCGATAAGAACGATGTTTTGCACACAAACGCGCAATGCAGAGGATTTGGGCTTCAA
65 ATGAGCCTTTCGATAAGAACGATGTTTTGCACACAAACGCGCGTTGTTGAGGCTTTGGGCTTCAA
3908 GGAGAGCTTTGTTTTTGCACAGGGCTGTCC
130 GGAGAGCTTTGTTTTTGCACAGGGCTGTCC
* * * * ** * *
3938 AAAAAGCTCTTCTTACT-CTGATGCAAGACTTTTGAGCACTCGTTGCACAAAAAATGCTTCTGGA
1 AACAGGCTCATCTCACTCCT-ACACAAGGCTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGA
** ** ** *
4002 ATGAGCCTTTCTCTAAGAACGATGTTTTGCACACAAACGCGCAATGCAGAGGATTTGGGCTTCAA
65 ATGAGCCTTTCGATAAGAACGATGTTTTGCACACAAACGCGCGTTGTTGAGGCTTTGGGCTTCAA
* *
4067 GGACATCTTTGTTTTTGCACAGGGCTGTCC
130 GGAGAGCTTTGTTTTTGCACAGGGCTGTCC
* * *
4097 AACAGGCTCATCTCACT-CTGACACAAGGCTTTTGAGCACTCGTTGTGCAAAAAAAGCTTCTGGG
1 AACAGGCTCATCTCACTCCT-ACACAAGGCTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGA
* *
4161 ATGAGCCTTTCGATAAGAACAATGTTTTGCACACAAACGCGCTTTGTTGAGGCTTTGGGCTTCAA
65 ATGAGCCTTTCGATAAGAACGATGTTTTGCACACAAACGCGCGTTGTTGAGGCTTTGGGCTTCAA
*
4226 GGAGAGCTTTGTTTTTGCACGGGGCTGTCC
130 GGAGAGCTTTGTTTTTGCACAGGGCTGTCC
* * *
4256 AACAGGCTCATCTCACTCCGACACAAGACTTTTGAGCACTCGTTGCGCAAAAACTGCTTCTGGAA
1 AACAGGCTCATCTCACTCCTACACAAGGCTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAA
* *
4321 TGAGCCTTTCGCTAAGAACGATGTTTTGCACACAAACGCGCGTTGTTGAGGCTTTGGGCTTGAAG
66 TGAGCCTTTCGATAAGAACGATGTTTTGCACACAAACGCGCGTTGTTGAGGCTTTGGGCTTCAAG
*
4386 GAGAGCTTTGTTATTGCACAGGGCTGTCC
131 GAGAGCTTTGTTTTTGCACAGGGCTGTCC
*
4415 AACAGGCTCATCTCACT-CTAACACAAGGCTTTTGAGCACTCATTGCGCAAAAAATGCTTCTGGA
1 AACAGGCTCATCTCACTCCT-ACACAAGGCTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGA
** * ** *
4479 ATGTTCCTTTCGATAAGAACAATGTTTTGCACACAAACGCGCCATGTTGAGGCTTTGGGCTTGAA
65 ATGAGCCTTTCGATAAGAACGATGTTTTGCACACAAACGCGCGTTGTTGAGGCTTTGGGCTTCAA
* *
4544 GAAGAGCTTTGTTTTTGCTCAGGGCTGTCC
130 GGAGAGCTTTGTTTTTGCACAGGGCTGTCC
* * *
4574 AACAAGCTCATCTCACTCCTACACAAGACTTTTGAGCACTCGTTGCGCAAAAAATGCTTTTGGAA
1 AACAGGCTCATCTCACTCCTACACAAGGCTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAA
* * *
4639 CGAGCCTTTCGTTAAGAACGATGTTTTGCACACAAATGCGCGTTGTTGAGGCTTTGGGCTT
66 TGAGCCTTTCGATAAGAACGATGTTTTGCACACAAACGCGCGTTGTTGAGGCTTTGGGCTT
4700 GTAGACACCC
Statistics
Matches: 833, Mismatches: 84, Indels: 11
0.90 0.09 0.01
Matches are distributed among these distances:
158 1 0.00
159 637 0.76
160 185 0.22
161 10 0.01
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (159 bp):
AACAGGCTCATCTCACTCCTACACAAGGCTTTTGAGCACTCGTTGCGCAAAAAATGCTTCTGGAA
TGAGCCTTTCGATAAGAACGATGTTTTGCACACAAACGCGCGTTGTTGAGGCTTTGGGCTTCAAG
GAGAGCTTTGTTTTTGCACAGGGCTGTCC
Found at i:8536 original size:13 final size:13
Alignment explanation
Indices: 8520--8545 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8510 TTAATTAGGC
8520 CTTGCTATTATCT
1 CTTGCTATTATCT
8533 CTTGCTATTATCT
1 CTTGCTATTATCT
8546 TGATTTATGT
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:0.15, C:0.23, G:0.08, T:0.54
Consensus pattern (13 bp):
CTTGCTATTATCT
Found at i:8742 original size:3 final size:3
Alignment explanation
Indices: 8734--8758 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
8724 CCATATTTAT
8734 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
8759 GCCATGTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9158 original size:20 final size:20
Alignment explanation
Indices: 9133--9192 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
9123 AAAAGAGTAA
9133 AATGGTAATCAGTAAAAAGG
1 AATGGTAATCAGTAAAAAGG
* * *
9153 AATGGTAATTAGTGAAAAGT
1 AATGGTAATCAGTAAAAAGG
*
9173 AAAGAGTAATCAGTAAAAAG
1 AATG-GTAATCAGTAAAAAG
9193 TAAAATGGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 20 0.61
21 13 0.39
ACGTcount: A:0.52, C:0.03, G:0.23, T:0.22
Consensus pattern (20 bp):
AATGGTAATCAGTAAAAAGG
Found at i:9181 original size:21 final size:21
Alignment explanation
Indices: 9137--9196 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
9127 GAGTAAAATG
* *
9137 GTAATCAGTAAAAAGGAATG-
1 GTAATCAGTAAAAAGTAAAGA
* *
9157 GTAATTAGTGAAAAGTAAAGA
1 GTAATCAGTAAAAAGTAAAGA
9178 GTAATCAGTAAAAAGTAAA
1 GTAATCAGTAAAAAGTAAA
9197 ATGGTAAAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.53, C:0.03, G:0.22, T:0.22
Consensus pattern (21 bp):
GTAATCAGTAAAAAGTAAAGA
Found at i:9232 original size:36 final size:36
Alignment explanation
Indices: 9170--9710 Score: 523
Period size: 36 Copynumber: 15.2 Consensus size: 36
9160 ATTAGTGAAA
*
9170 AGTAAAGAGTAATCAGTAAAAAGTAAAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAG
* * *
9206 AGTACAGAGTAATCAGCAAA-ACGTAAAATGGTAAAA
1 AGTAAAGAGTAATCAGTAAAGA-GTAAAATGGTAAAG
* *
9242 AGAAAACAGTAATCAGTAAATG-GTAAAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAA-GAGTAAAATGGTAAAG
*
9278 AGTAAAGAGTAATCAGTAGAA-AGTAAAATAGTAAAAAG
1 AGTAAAGAGTAATCAGTA-AAGAGTAAAATGGT--AAAG
*
9316 TAATGGTAATCAGTACTAATCAGTAAAGAGTAAAATGGTAAA-
1 --A--GTAA--AG-AGTAATCAGTAAAGAGTAAAATGGTAAAG
* *
9358 ACATAAAGAGTAATCAGTAAATAGTAAAATGGTAAAG
1 A-GTAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAG
* *
9395 GGTAAAGAGTAATCAGTAAAGAGCAAAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAG
9431 AGTAAAGAGTAATCAGTAAAGAGTAAAA---T---G
1 AGTAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAG
* *
9461 -GTAAAGAGTAAT-AGTAAAGAGTAAAAGGGTAAAA
1 AGTAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAG
*
9495 AGTAAAGAGTAATCAGTAAATAGTAAAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAG
* * **
9531 GGTAAAGAGTAATCAGCAAAGAACAAAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAG
9567 AGTAAAGAGTAATCAGTAAAGAGTAAAA---T---G
1 AGTAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAG
* * *
9597 -GTAAAGAGTAAT-AGTAAAGAGTAGAACGGTAAAA
1 AGTAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAG
* * **
9631 AGTAAAGAATAATCAGTAATCA-AGTAAAATGATAGGG
1 AGTAAAGAGTAATCAGTAA--AGAGTAAAATGGTAAAG
* * **
9668 AGTAAATAGTAATCAGTAAAGTG-AAAATGGTAATC
1 AGTAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAG
9703 AGTAAAGA
1 AGTAAAGA
9711 AGAATAAAAA
Statistics
Matches: 417, Mismatches: 53, Indels: 71
0.77 0.10 0.13
Matches are distributed among these distances:
28 27 0.06
29 24 0.06
30 2 0.00
31 2 0.00
33 2 0.00
35 40 0.10
36 249 0.60
37 30 0.07
38 5 0.01
39 3 0.01
40 2 0.00
42 4 0.01
43 3 0.01
44 4 0.01
45 20 0.05
ACGTcount: A:0.53, C:0.05, G:0.23, T:0.20
Consensus pattern (36 bp):
AGTAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAG
Found at i:9288 original size:29 final size:29
Alignment explanation
Indices: 9256--9506 Score: 102
Period size: 29 Copynumber: 8.2 Consensus size: 29
9246 AACAGTAATC
9256 AGTAAATGGTAAAATGGTAAAGAGTAAAG
1 AGTAAATGGTAAAATGGTAAAGAGTAAAG
* * *
9285 AGT-AATCAGTAGAAA--GTAAAATAGTAAAA
1 AGTAAAT-GGTA-AAATGGT-AAAGAGTAAAG
* ** **
9314 AGT-AATGGTAATCAGTACTAATCAGTAAAG
1 AGTAAATGGTAA--AATGGTAAAGAGTAAAG
** **
9344 AGTAAAATGGTAAAA-CATAAAGAGTAATC
1 AGT-AAATGGTAAAATGGTAAAGAGTAAAG
* *
9373 AGTAAATAGTAAAATGGTAAAGGGTAAAG
1 AGTAAATGGTAAAATGGTAAAGAGTAAAG
*
9402 AGTAATCAGTAAAGAGCAAAATGGTAAAGAGTAAAG
1 AGTAA--A-T---G-GTAAAATGGTAAAGAGTAAAG
*
9438 AGTAATCAGTAAAGAGTAAAATGGTAAAGAGT-AAT
1 AGTAA--A-T---G-GTAAAATGGTAAAGAGTAAAG
* *
9473 AGTAAA-GAGTAAAAGGGTAAAAAGTAAAG
1 AGTAAATG-GTAAAATGGTAAAGAGTAAAG
9502 AGTAA
1 AGTAA
9507 TCAGTAAATA
Statistics
Matches: 174, Mismatches: 30, Indels: 36
0.73 0.12 0.15
Matches are distributed among these distances:
27 1 0.01
28 35 0.20
29 54 0.31
30 15 0.09
31 2 0.01
32 9 0.05
33 1 0.01
35 7 0.04
36 50 0.29
ACGTcount: A:0.53, C:0.04, G:0.23, T:0.20
Consensus pattern (29 bp):
AGTAAATGGTAAAATGGTAAAGAGTAAAG
Found at i:9312 original size:8 final size:7
Alignment explanation
Indices: 9167--9318 Score: 54
Period size: 7 Copynumber: 21.1 Consensus size: 7
9157 GTAATTAGTG
9167 AAAAGTA
1 AAAAGTA
*
9174 AAGAGTA
1 AAAAGTA
**
9181 ATCAGTA
1 AAAAGTA
9188 AAAAGTA
1 AAAAGTA
*
9195 AAATGGTA
1 AAA-AGTA
*
9203 AAGAGTA
1 AAAAGTA
* *
9210 CAGAGTA
1 AAAAGTA
** *
9217 ATCAGCA
1 AAAAGTA
*
9224 AAACGTA
1 AAAAGTA
*
9231 AAATGGTA
1 AAA-AGTA
9239 AAAAG-A
1 AAAAGTA
9245 AAACAGTA
1 AAA-AGTA
**
9253 ATCAGTA
1 AAAAGTA
**
9260 AATGGTA
1 AAAAGTA
*
9267 AAATGGTA
1 AAA-AGTA
*
9275 AAGAGTA
1 AAAAGTA
*
9282 AAGAGTA
1 AAAAGTA
**
9289 ATCAGTA
1 AAAAGTA
*
9296 GAAAGTA
1 AAAAGTA
9303 AAATAGTA
1 AAA-AGTA
9311 AAAAGTA
1 AAAAGTA
9318 A
1 A
9319 TGGTAATCAG
Statistics
Matches: 106, Mismatches: 33, Indels: 12
0.70 0.22 0.08
Matches are distributed among these distances:
6 4 0.04
7 76 0.72
8 26 0.25
ACGTcount: A:0.56, C:0.05, G:0.20, T:0.18
Consensus pattern (7 bp):
AAAAGTA
Found at i:9339 original size:45 final size:46
Alignment explanation
Indices: 9287--9376 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 46
9277 GAGTAAAGAG
*
9287 TAATCAGTAGAA-AGTAAAATAGTAAAA-AGTAATG-GTAATCAGTAC
1 TAATCAGTA-AAGAGTAAAATAGTAAAACA-TAAAGAGTAATCAGTAC
*
9332 TAATCAGTAAAGAGTAAAATGGTAAAACATAAAGAGTAATCAGTA
1 TAATCAGTAAAGAGTAAAATAGTAAAACATAAAGAGTAATCAGTA
9377 AATAGTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
44 2 0.05
45 27 0.68
46 11 0.28
ACGTcount: A:0.52, C:0.07, G:0.18, T:0.23
Consensus pattern (46 bp):
TAATCAGTAAAGAGTAAAATAGTAAAACATAAAGAGTAATCAGTAC
Found at i:9355 original size:153 final size:153
Alignment explanation
Indices: 9179--9613 Score: 464
Period size: 153 Copynumber: 3.0 Consensus size: 153
9169 AAGTAAAGAG
* *
9179 TAATCAGTAAAAAGTAAAATGGTAAAGA-GTACAGAGTAATCAGCAAA-ACGTAAAATGGTAAAA
1 TAATCAGTAAAAAGTAAAATGGTAAA-ACATAAAGAGTAATCAGCAAATA-GTAAAATGGTAAAA
*
9242 AGAAAACAGTAATCAGTAAATG-GTAAAATGGTAAAGAGTAAAGAGTAATCAGTAGAA-AGTAAA
64 AGAAAACAGTAATCAGTAAA-GAGCAAAATGGTAAAGAGTAAAGAGTAATCAGTA-AAGAGTAAA
*
9305 ATAGTAAAAAGTAATGGTAATCAGTAC
127 ATAGTAAAAAGTAATAGTAATCAGTAC
* * **
9332 TAATCAGTAAAGAGTAAAATGGTAAAACATAAAGAGTAATCAGTAAATAGTAAAATGGTAAAGGG
1 TAATCAGTAAAAAGTAAAATGGTAAAACATAAAGAGTAATCAGCAAATAGTAAAATGGTAAAAAG
* * *
9397 TAAAGAGTAATCAGTAAAGAGCAAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAGTAAAATGG
66 AAAACAGTAATCAGTAAAGAGCAAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAGTAAAATAG
9462 T--AAAG----AGTAAT-AGTA-
131 TAAAAAGTAATAGTAATCAGTAC
* * * * **
9477 -AA-GAGTAAAAGGGT---A----AAAA-GTAAAGAGTAATCAGTAAATAGTAAAATGGTAAAGG
1 TAATCAGTAAAA-AGTAAAATGGTAAAACATAAAGAGTAATCAGCAAATAGTAAAATGGTAAAAA
* * * * *
9532 GTAAAGAGTAATCAGCAAAGAACAAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAGTAAAATG
65 GAAAACAGTAATCAGTAAAGAGCAAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAGTAAAATA
*
9597 GTAAAGAGTAATAGTAA
130 GTAAAAAGTAATAGTAA
9614 AGAGTAGAAC
Statistics
Matches: 253, Mismatches: 18, Indels: 33
0.83 0.06 0.11
Matches are distributed among these distances:
136 100 0.40
137 4 0.02
138 3 0.01
141 1 0.00
142 5 0.02
143 6 0.02
144 4 0.02
146 4 0.02
147 5 0.02
151 4 0.02
152 4 0.02
153 112 0.44
154 1 0.00
ACGTcount: A:0.53, C:0.05, G:0.22, T:0.20
Consensus pattern (153 bp):
TAATCAGTAAAAAGTAAAATGGTAAAACATAAAGAGTAATCAGCAAATAGTAAAATGGTAAAAAG
AAAACAGTAATCAGTAAAGAGCAAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAGTAAAATAG
TAAAAAGTAATAGTAATCAGTAC
Found at i:9383 original size:7 final size:7
Alignment explanation
Indices: 9361--9638 Score: 133
Period size: 7 Copynumber: 38.9 Consensus size: 7
9351 TGGTAAAACA
9361 TAAAGAG
1 TAAAGAG
**
9368 TAATCAG
1 TAAAGAG
*
9375 TAAATAG
1 TAAAGAG
9382 TAAA-ATGG
1 TAAAGA--G
*
9390 TAAAGGG
1 TAAAGAG
9397 TAAAGAG
1 TAAAGAG
**
9404 TAATCAG
1 TAAAGAG
9411 TAAAGAG
1 TAAAGAG
*
9418 CAAA-ATGG
1 TAAAGA--G
9426 TAAAGAG
1 TAAAGAG
9433 TAAAGAG
1 TAAAGAG
**
9440 TAATCAG
1 TAAAGAG
9447 TAAAGAG
1 TAAAGAG
9454 TAAA-ATGG
1 TAAAGA--G
9462 TAAAGAG
1 TAAAGAG
*
9469 T-AATAG
1 TAAAGAG
9475 TAAAGAG
1 TAAAGAG
*
9482 TAAAAGGG
1 T-AAAGAG
*
9490 TAAAAAG
1 TAAAGAG
9497 TAAAGAG
1 TAAAGAG
**
9504 TAATCAG
1 TAAAGAG
*
9511 TAAATAG
1 TAAAGAG
9518 TAAA-ATGG
1 TAAAGA--G
*
9526 TAAAGGG
1 TAAAGAG
9533 TAAAGAG
1 TAAAGAG
**
9540 TAATCAG
1 TAAAGAG
* *
9547 CAAAGAA
1 TAAAGAG
*
9554 CAAA-ATGG
1 TAAAGA--G
9562 TAAAGAG
1 TAAAGAG
9569 TAAAGAG
1 TAAAGAG
**
9576 TAATCAG
1 TAAAGAG
9583 TAAAGAG
1 TAAAGAG
9590 TAAA-ATGG
1 TAAAGA--G
9598 TAAAGAG
1 TAAAGAG
*
9605 T-AATAG
1 TAAAGAG
9611 TAAAGAG
1 TAAAGAG
9618 TAGAACG-G
1 TA-AA-GAG
*
9626 TAAAAAG
1 TAAAGAG
9633 TAAAGA
1 TAAAGA
9639 ATAATCAGTA
Statistics
Matches: 203, Mismatches: 44, Indels: 48
0.69 0.15 0.16
Matches are distributed among these distances:
6 16 0.08
7 144 0.71
8 38 0.19
9 5 0.02
ACGTcount: A:0.53, C:0.04, G:0.24, T:0.19
Consensus pattern (7 bp):
TAAAGAG
Found at i:9501 original size:136 final size:136
Alignment explanation
Indices: 9332--9710 Score: 577
Period size: 136 Copynumber: 2.8 Consensus size: 136
9322 TAATCAGTAC
*
9332 TAATCAGTAAAGAGTAAAATGGTAAAACA-TAAAGAGTAATCAGTAAATAGTAAAATGGTAAAGG
1 TAAT-AGTAAAGAGTAAAACGGTAAAA-AGTAAAGAGTAATCAGTAAATAGTAAAATGGTAAAGG
9396 GTAAAGAGTAATCAGTAAAGAGCAAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAGTAAAATG
64 GTAAAGAGTAATCAGTAAAGAGCAAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAGTAAAATG
9461 GTAAAGAG
129 GTAAAGAG
*
9469 TAATAGTAAAGAGTAAAAGGGTAAAAAGTAAAGAGTAATCAGTAAATAGTAAAATGGTAAAGGGT
1 TAATAGTAAAGAGTAAAACGGTAAAAAGTAAAGAGTAATCAGTAAATAGTAAAATGGTAAAGGGT
* *
9534 AAAGAGTAATCAGCAAAGAACAAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAGTAAAATGGT
66 AAAGAGTAATCAGTAAAGAGCAAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAGTAAAATGGT
9599 AAAGAG
131 AAAGAG
* * * *
9605 TAATAGTAAAGAGTAGAACGGTAAAAAGTAAAGAATAATCAGT-AATCAAGTAAAATGAT-AGGG
1 TAATAGTAAAGAGTAAAACGGTAAAAAGTAAAGAGTAATCAGTAAAT--AGTAAAATGGTAAAGG
* * **
9668 AGTAAATAGTAATCAGTAAAGTG-AAAATGGTAATCAGTAAAGA
64 -GTAAAGAGTAATCAGTAAAGAGCAAAATGGTAAAGAGTAAAGA
9711 AGAATAAAAA
Statistics
Matches: 224, Mismatches: 14, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
135 4 0.02
136 188 0.84
137 32 0.14
ACGTcount: A:0.53, C:0.04, G:0.23, T:0.20
Consensus pattern (136 bp):
TAATAGTAAAGAGTAAAACGGTAAAAAGTAAAGAGTAATCAGTAAATAGTAAAATGGTAAAGGGT
AAAGAGTAATCAGTAAAGAGCAAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAGTAAAATGGT
AAAGAG
Found at i:9769 original size:29 final size:27
Alignment explanation
Indices: 9691--10064 Score: 178
Period size: 28 Copynumber: 13.9 Consensus size: 27
9681 CAGTAAAGTG
*
9691 AAAATGGTAATCAGTAAAGAAGAATAA
1 AAAATGGTAATCAGTAAAAAAGAATAA
* *
9718 AAAATGGTATTCAGTAAAAAAAAGAGTAA
1 AAAATGGTAATCAGT--AAAAAAGAATAA
* *
9747 GAAGTGGTAATCAGT----AAG--T-A
1 AAAATGGTAATCAGTAAAAAAGAATAA
* *
9767 AAAATGGTATTCAGTAGTAAAAAGAGT-A
1 AAAATGGTAATCAGTA--AAAAAGAATAA
* *
9795 AAAATGGTATTCAGTAAAGTAAA-AAAAGTA
1 AAAATGGTAATCAGTAAA--AAAGAATA--A
** *
9825 AAAATGGTGTTCAGTAGTAAAAAGAGT-A
1 AAAATGGTAATCAGTA--AAAAAGAATAA
* * *
9853 AAAATGGTATTCAGT-AAAAA-AAGAG
1 AAAATGGTAATCAGTAAAAAAGAATAA
*
9878 AAAATGGTAATCAGT--AAAA-AA-AG
1 AAAATGGTAATCAGTAAAAAAGAATAA
*
9901 AAAATGGTAATCAGTAGAAAAGAATAAA
1 AAAATGGTAATCAGTAAAAAAGAAT-AA
*
9929 AAAATGGTATTCAGTAAAAAAG--TAA
1 AAAATGGTAATCAGTAAAAAAGAATAA
*
9954 GAAAAGGGTAATCAGTAAAAAAAAAAGAATAGTAA
1 -AAAATGGTAATCAGT----AAAAAAG-A-A-TAA
* * *
9989 GAAAAGGGTAATAAGTAAAAAAGAGT-A
1 -AAAATGGTAATCAGTAAAAAAGAATAA
* *
10016 AAAATAGTAATCAGT-AAAAAGAGTAA
1 AAAATGGTAATCAGTAAAAAAGAATAA
* *
10042 GAAA-GGTAATTAGTAAAAGAAGA
1 AAAATGGTAATCAGTAAAA-AAGA
10065 GGTAGAAAAT
Statistics
Matches: 278, Mismatches: 32, Indels: 74
0.72 0.08 0.19
Matches are distributed among these distances:
20 13 0.05
21 1 0.00
23 20 0.07
24 7 0.03
25 42 0.15
26 40 0.14
27 20 0.07
28 58 0.21
29 22 0.08
30 27 0.10
31 8 0.03
32 2 0.01
35 18 0.06
ACGTcount: A:0.56, C:0.03, G:0.20, T:0.20
Consensus pattern (27 bp):
AAAATGGTAATCAGTAAAAAAGAATAA
Found at i:9773 original size:49 final size:49
Alignment explanation
Indices: 9717--9819 Score: 154
Period size: 49 Copynumber: 2.1 Consensus size: 49
9707 AAGAAGAATA
*
9717 AAAAATGGTATTCAGTAAAAAAAAGAGTAAGAAGTGGTAATCAGT-AAGT
1 AAAAATGGTATTCAGTAAAAAAAAGAGTAA-AAATGGTAATCAGTAAAGT
** *
9766 AAAAATGGTATTCAGTAGTAAAAAGAGTAAAAATGGTATTCAGTAAAGT
1 AAAAATGGTATTCAGTAAAAAAAAGAGTAAAAATGGTAATCAGTAAAGT
9815 AAAAA
1 AAAAA
9820 AAGTAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 12 0.24
49 37 0.76
ACGTcount: A:0.52, C:0.04, G:0.20, T:0.23
Consensus pattern (49 bp):
AAAAATGGTATTCAGTAAAAAAAAGAGTAAAAATGGTAATCAGTAAAGT
Found at i:9787 original size:19 final size:20
Alignment explanation
Indices: 9751--9789 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9741 GAGTAAGAAG
9751 TGGTAATCAGTAAGTAAAAA
1 TGGTAATCAGTAAGTAAAAA
*
9771 TGGTATTCAGT-AGTAAAAA
1 TGGTAATCAGTAAGTAAAAA
9790 GAGTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.28
Consensus pattern (20 bp):
TGGTAATCAGTAAGTAAAAA
Found at i:9795 original size:28 final size:28
Alignment explanation
Indices: 9763--9944 Score: 204
Period size: 28 Copynumber: 6.7 Consensus size: 28
9753 GTAATCAGTA
9763 AGTAAAAATGGTATTCAGTAGTAAAAAG
1 AGTAAAAATGGTATTCAGTAGTAAAAAG
*
9791 AGTAAAAATGGTATTCAGTAAAGTAAAAAA
1 AGTAAAAATGGTATTCAGT--AGTAAAAAG
*
9821 AGTAAAAATGGTGTTCAGTAGTAAAAAG
1 AGTAAAAATGGTATTCAGTAGTAAAAAG
*
9849 AGTAAAAATGGTATTCAGTA-AAAAAAG
1 AGTAAAAATGGTATTCAGTAGTAAAAAG
*
9876 AG--AAAATGGTAATCAGTA--AAAAA-
1 AGTAAAAATGGTATTCAGTAGTAAAAAG
*
9899 AG--AAAATGGTAATCAGTAG--AAAAG
1 AGTAAAAATGGTATTCAGTAGTAAAAAG
*
9923 AATAAAAAAATGGTATTCAGTA
1 AGT--AAAAATGGTATTCAGTA
9945 AAAAAGTAAG
Statistics
Matches: 138, Mismatches: 8, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
23 22 0.16
24 6 0.04
25 15 0.11
27 8 0.06
28 61 0.44
30 26 0.19
ACGTcount: A:0.54, C:0.04, G:0.20, T:0.23
Consensus pattern (28 bp):
AGTAAAAATGGTATTCAGTAGTAAAAAG
Found at i:9907 original size:76 final size:75
Alignment explanation
Indices: 9691--9976 Score: 228
Period size: 76 Copynumber: 3.6 Consensus size: 75
9681 CAGTAAAGTG
* * * *
9691 AAAATGGTAATCAGTAAAGAAGAATAAAAAATGGTATTCAGTAAAAAAAAGAGTAAGAAGTGGTA
1 AAAATGGTATTCAGTAAA-AA-AAGAGAAAATGGTAATCAGT-AAAAAAAGA--AA-AA-TGGTA
9756 ATCAGT-----A-AGTA
59 ATCAGTAGAAAAGAGTA
* *
9767 AAAATGGTATTCAGTAGTAAAAAGAGTAAAAATGGTATTCAGTAAAGTAAAAAAAGTAAAAATGG
1 AAAATGGTATTCAGTA-AAAAAAGAG--AAAATGGTA---A-T-CAGTAAAAAAAG-AAAAATGG
**
9832 TGTTCAGTAGTAAAAAGAGTA
57 TAATCAGTAG--AAAAGAGTA
9853 AAAATGGTATTCAGTAAAAAAAGAGAAAATGGTAATCAGTAAAAAAAG-AAAATGGTAATCAGTA
1 AAAATGGTATTCAGTAAAAAAAGAGAAAATGGTAATCAGTAAAAAAAGAAAAATGGTAATCAGTA
*
9917 GAAAAGAATAAA
66 GAAAAGAGT--A
*
9929 AAAATGGTATTCAGT-AAAAAAGTAAGAAAAGGGTAATCAGTAAAAAAA
1 AAAATGGTATTCAGTAAAAAAAG--AGAAAATGGTAATCAGTAAAAAAA
9977 AAAGAATAGT
Statistics
Matches: 175, Mismatches: 14, Indels: 41
0.76 0.06 0.18
Matches are distributed among these distances:
74 7 0.04
75 10 0.06
76 48 0.27
77 33 0.19
78 20 0.11
79 3 0.02
80 3 0.02
81 9 0.05
82 4 0.02
83 9 0.05
85 9 0.05
86 20 0.11
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.21
Consensus pattern (75 bp):
AAAATGGTATTCAGTAAAAAAAGAGAAAATGGTAATCAGTAAAAAAAGAAAAATGGTAATCAGTA
GAAAAGAGTA
Found at i:9976 original size:18 final size:17
Alignment explanation
Indices: 9949--10010 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
9939 TCAGTAAAAA
*
9949 AGTAAGAAAAGGGTAAT
1 AGTAAAAAAAGGGTAAT
**
9966 CAGTAAAAAAAAAAG-AAT
1 -AGT-AAAAAAAGGGTAAT
*
9984 AGTAAGAAAAGGGTAAT
1 AGTAAAAAAAGGGTAAT
10001 AAGTAAAAAA
1 -AGTAAAAAA
10011 GAGTAAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
16 7 0.21
17 6 0.18
18 14 0.41
19 7 0.21
ACGTcount: A:0.63, C:0.02, G:0.21, T:0.15
Consensus pattern (17 bp):
AGTAAAAAAAGGGTAAT
Found at i:10001 original size:17 final size:18
Alignment explanation
Indices: 9948--10016 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 18
9938 TTCAGTAAAA
*
9948 AAGTAAGAAAAGGGTAAT
1 AAGTAAGAAAAGAGTAAT
* * *
9966 CAGTAAAAAAAAAAG-AAT
1 AAGT-AAGAAAAGAGTAAT
*
9984 -AGTAAGAAAAGGGTAAT
1 AAGTAAGAAAAGAGTAAT
10001 AAGTAA-AAAAGAGTAA
1 AAGTAAGAAAAGAGTAA
10017 AAATAGTAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
16 7 0.17
17 15 0.38
18 11 0.28
19 7 0.17
ACGTcount: A:0.62, C:0.01, G:0.22, T:0.14
Consensus pattern (18 bp):
AAGTAAGAAAAGAGTAAT
Found at i:10034 original size:25 final size:25
Alignment explanation
Indices: 9984--10059 Score: 82
Period size: 25 Copynumber: 2.9 Consensus size: 25
9974 AAAAAAGAAT
9984 AGTAAGAAAAGGGTAATAAGTAAAAAAG
1 AGTAAGAAAA--GTAATAAGT-AAAAAG
*
10012 AGTAA-AAATAGTAATCAGTAAAAAG
1 AGTAAGAAA-AGTAATAAGTAAAAAG
* *
10037 AGTAAGAAAGGTAATTAGTAAAA
1 AGTAAGAAAAGTAATAAGTAAAA
10060 GAAGAGGTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
25 23 0.53
26 11 0.26
27 3 0.07
28 6 0.14
ACGTcount: A:0.59, C:0.01, G:0.21, T:0.18
Consensus pattern (25 bp):
AGTAAGAAAAGTAATAAGTAAAAAG
Found at i:10329 original size:42 final size:42
Alignment explanation
Indices: 10281--10364 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
10271 CATGGGACGC
*
10281 CGCACGGGACATCGCACAAGCCATCCGGCCACAACCGGCCAT
1 CGCACGGGACAACGCACAAGCCATCCGGCCACAACCGGCCAT
* *** *
10323 CGCACGGGCCAACGCATGCGCCATCCGGGCACAACCGGCCAT
1 CGCACGGGACAACGCACAAGCCATCCGGCCACAACCGGCCAT
10365 TCGACCCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.24, C:0.43, G:0.26, T:0.07
Consensus pattern (42 bp):
CGCACGGGACAACGCACAAGCCATCCGGCCACAACCGGCCAT
Found at i:11833 original size:8 final size:8
Alignment explanation
Indices: 11820--11853 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
11810 CACCTTCTTG
11820 AAAAATTC
1 AAAAATTC
11828 AAAAATTC
1 AAAAATTC
*
11836 AGAAACTTC
1 A-AAAATTC
11845 AAAAATTC
1 AAAAATTC
11853 A
1 A
11854 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.