Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013543.1 Corchorus capsularis cultivar CVL-1 contig13564, 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: 10034
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Found at i:5236 original size:19 final size:19
Alignment explanation
Indices: 5214--5252 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5204 GGAAAAAATG
*
5214 AAAAAAAATGAAAAAAGAA
1 AAAAAAAAGGAAAAAAGAA
* *
5233 AAAAGAAAGGAAAAGAGAA
1 AAAAAAAAGGAAAAAAGAA
5252 A
1 A
5253 GAGCAACGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (19 bp):
AAAAAAAAGGAAAAAAGAA
Found at i:5310 original size:45 final size:44
Alignment explanation
Indices: 5261--5404 Score: 191
Period size: 45 Copynumber: 3.2 Consensus size: 44
5251 AAGAGCAACG
*
5261 ATGGTTTTCAAAAAATAGTCATGGCTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTCAAAAAA-AGTCATGGTTTTCAAAAGGTTTTGATAAA
* *
5306 ATGGTTTTCAAAAAGAGTCGTGGTTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTCAAAAAAAGTCATGGTTTTCAAAAGGTTTTGATAAA
* *
5350 ATGTTTTTTCAAGAAAAA-TCATGGTTTTCAAGAGGGTTTTGATAAA
1 ATG-GTTTTCAA-AAAAAGTCATGGTTTTCAA-AAGGTTTTGATAAA
*
5396 AGGGTTTTC
1 ATGGTTTTC
5405 CAAAGTTACA
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
44 30 0.34
45 38 0.44
46 19 0.22
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.38
Consensus pattern (44 bp):
ATGGTTTTCAAAAAAAGTCATGGTTTTCAAAAGGTTTTGATAAA
Found at i:5336 original size:44 final size:43
Alignment explanation
Indices: 5261--5404 Score: 180
Period size: 44 Copynumber: 3.2 Consensus size: 43
5251 AAGAGCAACG
*
5261 ATGGTTTTCAAAAAATAGTCATGGCTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTC-AAAAA-AGTCATGGTTTTCAAAAGGTTTTGATAAA
*
5306 ATGGTTTTCAAAAAGAGTCGTGGTTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTCAAAAA-AGTCATGGTTTTCAAAAGGTTTTGATAAA
* * *
5350 ATGTTTTTTCAAGAAAAATCATGGTTTTCAAGAGGGTTTTGATAAA
1 ATG-GTTTTCAA-AAAAGTCATGGTTTTCAA-AAGGTTTTGATAAA
*
5396 AGGGTTTTC
1 ATGGTTTTC
5405 CAAAGTTACA
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
44 35 0.40
45 34 0.39
46 18 0.21
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.38
Consensus pattern (43 bp):
ATGGTTTTCAAAAAAGTCATGGTTTTCAAAAGGTTTTGATAAA
Found at i:6188 original size:24 final size:19
Alignment explanation
Indices: 6173--6218 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 19
6163 GAAAAATGAT
6173 GAAAGAAGAGAAAAGAAAAAA
1 GAAA-AAGA-AAAAGAAAAAA
6194 GAAAAAGAAAAAGAAAAAA
1 GAAAAAGAAAAAGAAAAAA
6213 GAAAAA
1 GAAAAA
6219 TGAATGATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 17 0.68
20 4 0.16
21 4 0.16
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
GAAAAAGAAAAAGAAAAAA
Found at i:6193 original size:7 final size:7
Alignment explanation
Indices: 6173--6218 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
6163 GAAAAATGAT
*
6173 GAAAGAA
1 GAAAAAA
*
6180 GAGAAAA
1 GAAAAAA
6187 GAAAAAA
1 GAAAAAA
6194 G-AAAAA
1 GAAAAAA
6200 G-AAAAA
1 GAAAAAA
6206 GAAAAAA
1 GAAAAAA
6213 GAAAAA
1 GAAAAA
6219 TGAATGATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
6 12 0.34
7 23 0.66
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:6198 original size:6 final size:6
Alignment explanation
Indices: 6173--6218 Score: 56
Period size: 6 Copynumber: 7.0 Consensus size: 6
6163 GAAAAATGAT
6173 GAAAGAA GAGAAAA GAAAAAA GAAAAA GAAAAA GAAAAAA GAAAAA
1 GAAA-AA GA-AAAA G-AAAAA GAAAAA GAAAAA G-AAAAA GAAAAA
6219 TGAATGATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
6 17 0.47
7 16 0.44
8 3 0.08
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:7322 original size:35 final size:35
Alignment explanation
Indices: 7247--7417 Score: 124
Period size: 35 Copynumber: 5.0 Consensus size: 35
7237 GTTAATGTTT
* *
7247 ATTGATCTAAGGCGATCTTTCTTCAGTTAA-TT--
1 ATTGATCCAGGGCGATCTTTCTTCAGTTAATTTCA
*
7279 A--G-TTCAGGGCGATCTTTCTTCAGTTAATTTCA
1 ATTGATCCAGGGCGATCTTTCTTCAGTTAATTTCA
* * * *
7311 ATTGATCCAGGGCGATATTTTTTTTGAGTTTATTTCA
1 ATTGATCCAGGGCG--ATCTTTCTTCAGTTAATTTCA
* * *
7348 GTTGACCCAGGGCGGTCTTTCTTCAGCTT-ATTTCA
1 ATTGATCCAGGGCGATCTTTCTTCAG-TTAATTTCA
* * * *
7383 ATTGACCCAGGGTGGTCTTTC-TCTAGTTTATTTCA
1 ATTGATCCAGGGCGATCTTTCTTC-AGTTAATTTCA
7418 TAATGATCGA
Statistics
Matches: 112, Mismatches: 16, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
29 22 0.20
30 3 0.03
32 2 0.02
34 5 0.04
35 49 0.44
36 2 0.02
37 29 0.26
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (35 bp):
ATTGATCCAGGGCGATCTTTCTTCAGTTAATTTCA
Found at i:7521 original size:52 final size:53
Alignment explanation
Indices: 7441--7543 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 53
7431 AGTCGACCTA
*
7441 GGGCGGTCTTTCTTTAGTAGCTTCCAAGTTTA-TCCAAGTTTATGTTAGAACG
1 GGGCGGTCTTTCTTTAGTAGCTTCCAAGTTTATTCCAAGTTTATGTCAGAACG
* * * **
7493 GGGCGGTCTTTCTTCT-GTTGTTTTCAAGTTTATTTGAAGTTTATGTCAGAA
1 GGGCGGTCTTTCTT-TAGTAGCTTCCAAGTTTATTCCAAGTTTATGTCAGAA
7544 TGATCGATTC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
52 27 0.63
53 16 0.37
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (53 bp):
GGGCGGTCTTTCTTTAGTAGCTTCCAAGTTTATTCCAAGTTTATGTCAGAACG
Found at i:7634 original size:70 final size:70
Alignment explanation
Indices: 7493--8094 Score: 733
Period size: 70 Copynumber: 8.5 Consensus size: 70
7483 TGTTAGAACG
* * **
7493 GGGCGGTCTTTCTTCTGTTGTTTTCAAGTTTATTTGAAGTTTATGTCAGAATGATCGATTC-GAT
1 GGGCGGTCTTTCTTCAGTTGTTTCCAAGTTTA-TCCAAGTTTATGTCAGAATGATCGATTCAG-T
7557 CGACCCA
64 CGACCCA
* * * * * * *
7564 GGGTGGTCTTTCTTTAGTAGCTTCCAAGTTTATCCAAGTTTATGTTAGAACGATCAATTCAGTCG
1 GGGCGGTCTTTCTTCAGTTGTTTCCAAGTTTATCCAAGTTTATGTCAGAATGATCGATTCAGTCG
7629 ACCCA
66 ACCCA
* * * *
7634 GGGCGGTCTCTCTTCAAG-TGTTTTCAAGTTTATTCAAAGTTTTATATCAGAATGATCGATTCAG
1 GGGCGGTCTTTCTTC-AGTTGTTTCCAAGTTTA-TCCAAG-TTTATGTCAGAATGATCGATTCAG
7698 TCGACCCA
63 TCGACCCA
* *
7706 GGGCGGTCTTTCTTCAGTTGTTTTCAAGTTTATTCAAAGTTTTATGTCAGAATGATCGATTCAGT
1 GGGCGGTCTTTCTTCAGTTGTTTCCAAGTTTA-TCCAAG-TTTATGTCAGAATGATCGATTCAGT
*
7771 GGACCCA
64 CGACCCA
* * * *
7778 GGGTGGTCTTTCTTTAGTTGTTTTCAAGTTTATCCAAGTTTATGTCAGAATGATCGATTAAGTCG
1 GGGCGGTCTTTCTTCAGTTGTTTCCAAGTTTATCCAAGTTTATGTCAGAATGATCGATTCAGTCG
*
7843 ACCTA
66 ACCCA
* * * * *
7848 GGGCGGTCTTTCTTCAGTTGTTTCCAAGTTTATCCAAGTTTATGTTAAAACGATCAATTCAATCG
1 GGGCGGTCTTTCTTCAGTTGTTTCCAAGTTTATCCAAGTTTATGTCAGAATGATCGATTCAGTCG
7913 ACCCA
66 ACCCA
* *
7918 GGGCGGTCTTTCTTCAGTTGTTTTCAAAGATTATTCCAAGTTTATGTCAGAATGATCGATTCAGT
1 GGGCGGTCTTTCTTCAGTTG-TTTCCAAGTTTA-TCCAAGTTTATGTCAGAATGATCGATTCAGT
*
7983 AGACCCA
64 CGACCCA
* * * * * *
7990 GGGTGGTCTTTCTTCAGTAGTTTCCACGTTTATCCAATTTTATGTTAGAATGATCGATTCAGTTG
1 GGGCGGTCTTTCTTCAGTTGTTTCCAAGTTTATCCAAGTTTATGTCAGAATGATCGATTCAGTCG
8055 ACCCA
66 ACCCA
* * * *
8060 GGGCGGTTTTTCATAAGTTGTTTCC-AGTTGATCCA
1 GGGCGGTCTTTCTTCAGTTGTTTCCAAGTTTATCCA
8095 GGGTGGTCTA
Statistics
Matches: 460, Mismatches: 64, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
69 8 0.02
70 218 0.47
71 60 0.13
72 174 0.38
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (70 bp):
GGGCGGTCTTTCTTCAGTTGTTTCCAAGTTTATCCAAGTTTATGTCAGAATGATCGATTCAGTCG
ACCCA
Found at i:7820 original size:142 final size:141
Alignment explanation
Indices: 7493--8082 Score: 790
Period size: 142 Copynumber: 4.2 Consensus size: 141
7483 TGTTAGAACG
** **
7493 GGGCGGTCTTTCTTCTGTTGTTTTCAAGTTTATTTGAAGTTTATGTCAGAATGATCGATTC-GAT
1 GGGCGGTCTTTCTTAAGTTGTTTTCAAGTTTATTCCAAGTTTATGTCAGAATGATCGATTCAG-T
* * *
7557 CGACCCAGGGTGGTCTTTCTTTAGTAGCTTCCAAGTTTATCCAAGTTTATGTTAGAACGATCAAT
65 CGACCCAGGGCGGTCTTTCTTCAGTAGTTTCCAAGTTTATCCAAGTTTATGTTAGAACGATCAAT
7622 TCAGTCGACCCA
130 TCAGTCGACCCA
* * *
7634 GGGCGGTCTCTCTTCAAG-TGTTTTCAAGTTTATTCAAAGTTTTATATCAGAATGATCGATTCAG
1 GGGCGGTCTTTCTT-AAGTTGTTTTCAAGTTTATTCCAAG-TTTATGTCAGAATGATCGATTCAG
* * * * *
7698 TCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTTATTCAAAGTTTTATGTCAGAATGATC
64 TCGACCCAGGGCGGTCTTTCTTCAGTAGTTTCCAAGTTTA-TCCAAG-TTTATGTTAGAACGATC
* *
7763 GATTCAGTGGACCCA
127 AATTCAGTCGACCCA
* * *
7778 GGGTGGTCTTTCTTTAGTTGTTTTCAAGTTTA-TCCAAGTTTATGTCAGAATGATCGATTAAGTC
1 GGGCGGTCTTTCTTAAGTTGTTTTCAAGTTTATTCCAAGTTTATGTCAGAATGATCGATTCAGTC
* * *
7842 GACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTTATCCAAGTTTATGTTAAAACGATCAATT
66 GACCCAGGGCGGTCTTTCTTCAGTAGTTTCCAAGTTTATCCAAGTTTATGTTAGAACGATCAATT
*
7907 CAATCGACCCA
131 CAGTCGACCCA
* *
7918 GGGCGGTCTTTCTTCAGTTGTTTTCAAAGATTATTCCAAGTTTATGTCAGAATGATCGATTCAGT
1 GGGCGGTCTTTCTTAAGTTGTTTTC-AAGTTTATTCCAAGTTTATGTCAGAATGATCGATTCAGT
* * * * * *
7983 AGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTTTATCCAATTTTATGTTAGAATGATCGAT
65 CGACCCAGGGCGGTCTTTCTTCAGTAGTTTCCAAGTTTATCCAAGTTTATGTTAGAACGATCAAT
*
8048 TCAGTTGACCCA
130 TCAGTCGACCCA
* *
8060 GGGCGGTTTTTCATAAGTTGTTT
1 GGGCGGTCTTTCTTAAGTTGTTT
8083 CCAGTTGATC
Statistics
Matches: 392, Mismatches: 49, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
140 49 0.12
141 43 0.11
142 233 0.59
143 13 0.03
144 54 0.14
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (141 bp):
GGGCGGTCTTTCTTAAGTTGTTTTCAAGTTTATTCCAAGTTTATGTCAGAATGATCGATTCAGTC
GACCCAGGGCGGTCTTTCTTCAGTAGTTTCCAAGTTTATCCAAGTTTATGTTAGAACGATCAATT
CAGTCGACCCA
Found at i:8188 original size:40 final size:40
Alignment explanation
Indices: 8144--8219 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
8134 GTCTTCGTCA
*
8144 AAGATTCATTACTTTATCAGTTAGTTTCAGAATCCTGTTC
1 AAGATTCATTACTTTATCAGTTAGTCTCAGAATCCTGTTC
** * *
8184 AAGATTGTTTACTTTATCAGTTGGTCTCAGGATCCT
1 AAGATTCATTACTTTATCAGTTAGTCTCAGAATCCT
8220 ATTTGAGGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (40 bp):
AAGATTCATTACTTTATCAGTTAGTCTCAGAATCCTGTTC
Found at i:8350 original size:65 final size:61
Alignment explanation
Indices: 8250--8851 Score: 252
Period size: 58 Copynumber: 9.9 Consensus size: 61
8240 TGAATTTCTT
* * * * ** *
8250 TTTAAAATCCTGTTTTAGGTCTCT-GTTCGAAAGTTTTGATTCAAAATCCTATTTGAGAGTTTCA
1 TTTAAAATCCTGCTTGAGGTCTCTAG-TCGAGAGTTTTGATTC-AAATCCAAAATCA-AG-TTCA
* * * *
8314 TTCTAAAATCCTGCTTGAGGGCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCATGTTCA
1 TT-TAAAATCCTGCTTGAGGTCTCTAGTCGAGAG-TT-TTGATTCAAATCCAAAATCAAGTTCA
* * *
8378 TTTCAAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATATCATGTTC
1 TTT-AAAATCCTGCTTGAGGTCTCTAGTCGAGAG-TT-TTGATTCAAATCC-AAA-ATCAAGTTC
8443 A
61 A
* ** **
8444 TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTG-TT----T-CAATGTCTTGTTTCA
1 TTTAAAATCCTGCTTGAGGTCTCTAGTCGAGAG-TT-TTGATTCAAATCCAAAATCAAG-TTCA
* ** **
8502 TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTG-TT----T-CAATGTCTTGTTTCA
1 TTTAAAATCCTGCTTGAGGTCTCTAGTCGAGAG-TT-TTGATTCAAATCCAAAATCAAG-TTCA
* * *** **
8560 TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTATTTC-AATTTTAAATCTTG-TC-
1 TTTAAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTT-TGA-TTCAAATCCAAAATCAAGTTCA
** ** * * **
8620 TTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTATTTC-AATCCAAAATCTTGTTTCA
1 TTTAAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTT-TGA-TTCAAATCCAAAATCAAG-TTCA
* * * * **
8683 TTTTAAATCCTGCTTGAGGTCTCTAGTCGAGAG--TT-A-TC-AATTCTAAGTCCTGTTTCA
1 TTTAAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTGATTCAAATCCAAAATCAAG-TTCA
* * * * * **
8740 TTTTCAAATCCTACTCGAGGTCTCTAATCGAGAG--TT--TTC-AACCCAAAATCTTGTTTCA
1 -TTTAAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTGATTCAAATCCAAAATCAAG-TTCA
* * * * *
8798 TTTTAAATCCTGCTTGAGATCTCTAGCCGAGAGTTTCTGTTTC-AATCTAAAATC
1 TTTAAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTT-TGATTCAAATCCAAAATC
8852 TTGCTCGAGA
Statistics
Matches: 459, Mismatches: 54, Indels: 52
0.81 0.10 0.09
Matches are distributed among these distances:
56 1 0.00
57 51 0.11
58 144 0.31
59 5 0.01
60 54 0.12
61 3 0.01
62 15 0.03
63 35 0.08
64 56 0.12
65 65 0.14
66 24 0.05
67 6 0.01
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.41
Consensus pattern (61 bp):
TTTAAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTGATTCAAATCCAAAATCAAGTTCA
Found at i:8508 original size:58 final size:58
Alignment explanation
Indices: 8440--8843 Score: 426
Period size: 58 Copynumber: 6.9 Consensus size: 58
8430 AAATATCATG
*
8440 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATGTCTTGT
1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATGTCTTGT
*
8498 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATGTCTTGT
1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATGTCTTGT
* *
8556 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTATTTCAAT-TTTAAATCT
1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATGTCT---TGT
* ** * *
8616 TGTC-TTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATCCAAAATCTTGT
1 T-TCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTATTTCAAT-----GTCTTGT
* * *
8679 TTCATTTTAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTATC--AATTCTAA-GTCCTGT
1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTT-TCTTATTTC-AATGTCTTGT
* * * * *** **
8736 TTCATTTTCAAATCCTACTCGAGGTCTCTAATCGAGAGTTT-TCAACCCAAAATCTTGT
1 TTCA-TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATGTCTTGT
* * * *
8794 TTCATTTTAAATCCTGCTTGAGATCTCTAGCCGAGAGTTTC-TGTTTCAAT
1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTATTTCAAT
8844 CTAAAATCTT
Statistics
Matches: 291, Mismatches: 37, Indels: 37
0.80 0.10 0.10
Matches are distributed among these distances:
57 47 0.16
58 151 0.52
60 46 0.16
61 2 0.01
62 6 0.02
63 35 0.12
64 2 0.01
66 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (58 bp):
TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATGTCTTGT
Found at i:8547 original size:123 final size:121
Alignment explanation
Indices: 8308--8843 Score: 561
Period size: 123 Copynumber: 4.4 Consensus size: 121
8298 CTATTTGAGA
* *
8308 GTTTCATTCTAAAATCCTGCTTGAGGGCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCAT
1 GTTTCATT-TCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATT-C----T-AT
* *
8373 G-TTCATTTCAAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATATC
59 GTTTCATTTC-AAATCCTACTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TCC-AAA-ATC
*
8437 AT
120 TT
8439 G-TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATGTCT-TGTTTCA
1 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAAT-TCTATGTTTCA
* * *
8502 TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAAT-----GTCTT
65 TTTCAAATCCTACTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAATCTT
* * *
8554 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATTTTAAATCTTGT
1 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCT--ATGTT-T
* * *
8619 C-TTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATCCAAAATCTT
63 CATTTCAAATCCTACTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAATCTT
* ** * *
8677 GTTTCATTTTAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTATC--AATTCTAAGTC-CTGTTTC
1 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTT-TCTTGTTTC-AATTCTATGTTTC
* *
8739 ATTTTCAAATCCTACTCGAGGTCTCTAATCGAGAG-----T-TTTCAACCCAAAATCTT
64 A-TTTCAAATCCTACTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAATCTT
* * *
8792 GTTTCATTTTAAATCCTGCTTGAGATCTCTAGCCGAGAGTTTC-TGTTTCAAT
1 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAAT
8844 CTAAAATCTT
Statistics
Matches: 360, Mismatches: 28, Indels: 51
0.82 0.06 0.12
Matches are distributed among these distances:
114 4 0.01
115 64 0.18
116 51 0.14
118 45 0.12
119 4 0.01
120 3 0.01
121 30 0.08
122 5 0.01
123 91 0.25
124 10 0.03
125 1 0.00
129 44 0.12
130 7 0.02
131 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (121 bp):
GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCTATGTTTCAT
TTCAAATCCTACTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAATCTT
Found at i:8679 original size:181 final size:180
Alignment explanation
Indices: 8308--8776 Score: 542
Period size: 181 Copynumber: 2.6 Consensus size: 180
8298 CTATTTGAGA
*
8308 GTTTCATTCTAAAATCCTGCTTGAGGGCTCTAGTCGAGAGTTTCTTGTTTCAAT-TCCAAAATCA
1 GTTTCATT-TAAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATGT-C----T--
*
8372 TG-TTCATTTCAAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATAT
58 TGTTTCATTTC-AAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATT-CAAAATAT
* ** * * *
8436 CATGTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATGTCTT
121 CATGTTCATTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATATCTT
*
8496 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATGTCTTGTTTCAT
1 GTTTCATTTAAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATGTCTTGTTTCAT
** *
8561 TTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATT-TTAA-ATCTTG-TC-TT
66 TTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATTCAAAATATCATGTTCATT
8622 CCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATCCAAAATCTT
131 CCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTATTTCAAT-----ATCTT
* ** *
8677 GTTTCATTTTAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTATC--AATTCTAA-GTCCTGTTTC
1 GTTTCATTTAAAATCCTGCTTGAGGTCTCTAGTCGAGAGTT-TCTTGTTTC-AATGTCTTGTTTC
* * *
8739 ATTTTCAAATCCTACTCGAGGTCTCTAATCGAGAGTTT
64 A-TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTT
8777 TCAACCCAAA
Statistics
Matches: 252, Mismatches: 19, Indels: 27
0.85 0.06 0.09
Matches are distributed among these distances:
176 42 0.17
177 2 0.01
178 5 0.02
179 2 0.01
180 13 0.05
181 124 0.49
182 10 0.04
183 1 0.00
187 44 0.17
188 9 0.04
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (180 bp):
GTTTCATTTAAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATGTCTTGTTTCAT
TTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATTCAAAATATCATGTTCATT
CCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATATCTT
Found at i:8833 original size:57 final size:57
Alignment explanation
Indices: 8308--8833 Score: 369
Period size: 58 Copynumber: 8.7 Consensus size: 57
8298 CTATTTGAGA
* * *
8308 GTTTCATTCTAAAATCCTGCTTGAGGGCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCAT
1 GTTTCATT-TTAAATCCTGCTTGAGGTCTCTAGTCGAGAG-----T-TTTCAA-TCCAAAATCTT
*
8373 G-TTCATTTCAAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATATC
1 GTTTCATTT-TAAATCCTGCTTGAGGTCTCTAGTCGAGAG-----T-TTTCAA-TCC-AAA-ATC
*
8437 AT
56 TT
* *** * **
8439 G-TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATGTCTT
1 GTTTCATTTTAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTT-TCAATCCAAAATCTT
* *** * **
8496 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATGTCTT
1 GTTTCATTTTAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTT-TCAATCCAAAATCTT
* ***
8554 GTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATTTTAAATCTT
1 GTTTCATTTTAAATCCTGCTTGAGGTCTCTAGTCGAGAG-----T-TTTCAATCCAAAATCTT
** ** *
8617 G--TC-TTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTATTTCAATCCAAAATCTT
1 GTTTCATTTTAAATCCTGCTTGAGGTCTCTAGTCGAGAG-----T-TTTCAATCCAAAATCTT
* * * * *
8677 GTTTCATTTTAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTATCAATTCTAAGTCCT
1 GTTTCATTTTAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTCAATCCAAAATCTT
* * * *
8734 GTTTCATTTTCAAATCCTACTCGAGGTCTCTAATCGAGAGTTTTCAACCCAAAATCTT
1 GTTTCATTTT-AAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTCAATCCAAAATCTT
* *
8792 GTTTCATTTTAAATCCTGCTTGAGATCTCTAGCCGAGAGTTT
1 GTTTCATTTTAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTT
8834 CTGTTTCAAT
Statistics
Matches: 399, Mismatches: 47, Indels: 38
0.82 0.10 0.08
Matches are distributed among these distances:
57 53 0.13
58 146 0.37
59 4 0.01
60 53 0.13
61 2 0.01
62 2 0.01
63 39 0.10
64 54 0.14
65 33 0.08
66 13 0.03
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (57 bp):
GTTTCATTTTAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTCAATCCAAAATCTT
Done.