Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007728.1 Corchorus capsularis cultivar CVL-1 contig07749, 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: 66559
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2226 original size:30 final size:30
Alignment explanation
Indices: 2192--2250 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2182 ATTCTTGCTC
*
2192 CTTGAAATAATTCTTCAA-TGATCTTCAATT
1 CTTGAAATAA-TCTTCAATTAATCTTCAATT
*
2222 CTTGAAATTATCTTCAATTAATCTTCAAT
1 CTTGAAATAATCTTCAATTAATCTTCAAT
2251 CACAAACTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.34, C:0.17, G:0.05, T:0.44
Consensus pattern (30 bp):
CTTGAAATAATCTTCAATTAATCTTCAATT
Found at i:3303 original size:11 final size:11
Alignment explanation
Indices: 3287--3339 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
3277 GAATTACCAG
3287 GTGTACCACAA
1 GTGTACCACAA
*
3298 GTGTA-CACAG
1 GTGTACCACAA
*
3308 GTATACCACAA
1 GTGTACCACAA
*
3319 ATGTA-CACAA
1 GTGTACCACAA
*
3329 GTTTACCACAA
1 GTGTACCACAA
3340 CGGATGTACC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.21
Consensus pattern (11 bp):
GTGTACCACAA
Found at i:3314 original size:21 final size:21
Alignment explanation
Indices: 3284--3339 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
3274 TCAGAATTAC
* *
3284 CAGGTGTACCACAAGTGTACA
1 CAGGTATACCACAAATGTACA
3305 CAGGTATACCACAAATGTACA
1 CAGGTATACCACAAATGTACA
* *
3326 CAAGTTTACCACAA
1 CAGGTATACCACAA
3340 CGGATGTACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (21 bp):
CAGGTATACCACAAATGTACA
Found at i:3529 original size:17 final size:17
Alignment explanation
Indices: 3507--3559 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
3497 ATCACCACCC
3507 AGATCACCAGTGATCTT
1 AGATCACCAGTGATCTT
* *
3524 AGATCACCATTGATGC-A
1 AGATCACCAGTGAT-CTT
**
3541 AGATCACTGGTGATCTT
1 AGATCACCAGTGATCTT
3558 AG
1 AG
3560 TCAATTCCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
16 1 0.04
17 26 0.93
18 1 0.04
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (17 bp):
AGATCACCAGTGATCTT
Found at i:3961 original size:3 final size:3
Alignment explanation
Indices: 3953--3998 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3943 GATTTGTATG
3953 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3999 ATATATATAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4221 original size:2 final size:2
Alignment explanation
Indices: 4214--4240 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4204 ATATCATTAT
4214 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4241 CTACTATCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4224 original size:34 final size:34
Alignment explanation
Indices: 4154--4222 Score: 106
Period size: 32 Copynumber: 2.1 Consensus size: 34
4144 GAAAAATGAG
*
4154 TATTTCAATTTTGGGGAGAAATCATTATTATATA
1 TATTTCAATTTTGGGCAGAAATCATTATTATATA
*
4188 TATTTCAA-TTTGGGCA-ATATCATTATTATATA
1 TATTTCAATTTTGGGCAGAAATCATTATTATATA
4220 TAT
1 TAT
4223 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 18 0.55
33 7 0.21
34 8 0.24
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (34 bp):
TATTTCAATTTTGGGCAGAAATCATTATTATATA
Found at i:5478 original size:112 final size:111
Alignment explanation
Indices: 5281--5493 Score: 372
Period size: 112 Copynumber: 1.9 Consensus size: 111
5271 GAATTACACA
*
5281 ATGTGCTCAAGTATTATACTACTTCCGTCTCATATTATCTGTACCTTTTGGGTCAAACCAATCAT
1 ATGTGCTCAAGTATTATACTACTTCCATCTCATATTATCTGTACCTTTTGGGTCAAACCAATCAT
5346 ACATTTGACTTAAAATTTTTAAAAAATTATATTTTGATTAAGTTAAG
66 ACATTTGACTTAAAATTTTTAAAAAA-TATATTTTGATTAAGTTAAG
* * *
5393 ATGTGCTCAAGTATTATACTACTTTCATCTCATATTATTTGTCCCTTTTGGGTCAAACCAATCAT
1 ATGTGCTCAAGTATTATACTACTTCCATCTCATATTATCTGTACCTTTTGGGTCAAACCAATCAT
*
5458 ACATTTGACTTAAAATTTTTAAAAAATATGTTTTGA
66 ACATTTGACTTAAAATTTTTAAAAAATATATTTTGA
5494 AAAGTTTAAA
Statistics
Matches: 96, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
111 9 0.09
112 87 0.91
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (111 bp):
ATGTGCTCAAGTATTATACTACTTCCATCTCATATTATCTGTACCTTTTGGGTCAAACCAATCAT
ACATTTGACTTAAAATTTTTAAAAAATATATTTTGATTAAGTTAAG
Found at i:6117 original size:3 final size:3
Alignment explanation
Indices: 6111--6136 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6101 AAAAAAAAAA
6111 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
6137 CAATTGTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:7096 original size:2 final size:2
Alignment explanation
Indices: 7084--7118 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
7074 GCACTTGCAC
7084 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7119 GAAAAGCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24602 original size:46 final size:46
Alignment explanation
Indices: 24535--24622 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
24525 ACCGATGGGA
*
24535 GTGACCTGGCCTACCCTTACCTCTTCAGGAAAATACCACTGTTACC
1 GTGACCTGGCCTACCCTTACCTCTTCAGAAAAATACCACTGTTACC
* *
24581 GTGACGTGGCTTACCCTTACCTCTTCAGAAAAATACCACTGT
1 GTGACCTGGCCTACCCTTACCTCTTCAGAAAAATACCACTGT
24623 CACCATAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (46 bp):
GTGACCTGGCCTACCCTTACCTCTTCAGAAAAATACCACTGTTACC
Found at i:27690 original size:6 final size:6
Alignment explanation
Indices: 27680--27759 Score: 71
Period size: 6 Copynumber: 14.0 Consensus size: 6
27670 AAGTTCAGTC
* * *
27680 ACAAAA CCAAAA AAAAAA AC-AAA ACAAAA AC-AAC AC-AAA ACAAAA
1 ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA
* *
27725 ACAAAA GCAAAAA ACAAAA A-GAAA ACAAAA A-AAAA
1 ACAAAA AC-AAAA ACAAAA ACAAAA ACAAAA ACAAAA
27760 CATATGTTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
5 21 0.35
6 34 0.57
7 5 0.08
ACGTcount: A:0.81, C:0.16, G:0.03, T:0.00
Consensus pattern (6 bp):
ACAAAA
Found at i:27703 original size:11 final size:11
Alignment explanation
Indices: 27688--27759 Score: 74
Period size: 11 Copynumber: 6.5 Consensus size: 11
27678 TCACAAAACC
27688 AAAAAA-AAAA
1 AAAAAACAAAA
*
27698 ACAAAACAAAA
1 AAAAAACAAAA
* *
27709 ACAACACAAAA
1 AAAAAACAAAA
*
27720 CAAAAACAAAA
1 AAAAAACAAAA
27731 GCAAAAAACAAAA
1 --AAAAAACAAAA
*
27744 AGAAAACAAAA
1 AAAAAACAAAA
27755 AAAAA
1 AAAAA
27760 CATATGTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
10 5 0.10
11 36 0.71
13 10 0.20
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:27737 original size:40 final size:39
Alignment explanation
Indices: 27680--27761 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 39
27670 AAGTTCAGTC
* * *
27680 ACAAAACCAAAAAAAAAAACAAAACA-AAAACAACACAAA
1 ACAAAAACAAAAAAAAAAACAAAA-AGAAAACAAAAAAAA
*
27719 ACAAAAACAAAAGCAAAAAACAAAAAGAAAACAAAAAAAA
1 ACAAAAACAAAA-AAAAAAACAAAAAGAAAACAAAAAAAA
27759 ACA
1 ACA
27762 TATGTTTACA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 12 0.32
40 25 0.68
ACGTcount: A:0.80, C:0.17, G:0.02, T:0.00
Consensus pattern (39 bp):
ACAAAAACAAAAAAAAAAACAAAAAGAAAACAAAAAAAA
Found at i:27794 original size:28 final size:29
Alignment explanation
Indices: 27769--27861 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 29
27759 ACATATGTTT
27769 ACATATACAACAACAATGGCCTATGTCGCC
1 ACATATACAACAACAATGGCCTATGTC-CC
*
27799 ATATATACAACAACAATGGCCTATGTCGCC
1 ACATATACAACAACAATGGCCTATGTC-CC
* **
27829 -CATATA-TATTA-AATGGCCTATGTCGCC
1 ACATATACAACAACAATGGCCTATGTC-CC
27856 ACATAT
1 ACATAT
27862 CATGTACTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
27 16 0.28
28 7 0.12
29 5 0.09
30 29 0.51
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (29 bp):
ACATATACAACAACAATGGCCTATGTCCC
Found at i:27807 original size:30 final size:31
Alignment explanation
Indices: 27771--27836 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 31
27761 ATATGTTTAC
27771 ATATACAACAACAATGGCCTATGTCG-CCAT
1 ATATACAACAACAATGGCCTATGTCGCCCAT
27801 ATATACAACAACAATGGCCTATGTCGCCCAT
1 ATATACAACAACAATGGCCTATGTCGCCCAT
27832 ATATA
1 ATATA
27837 TTAAATGGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 26 0.74
31 9 0.26
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (31 bp):
ATATACAACAACAATGGCCTATGTCGCCCAT
Found at i:27886 original size:35 final size:35
Alignment explanation
Indices: 27842--27927 Score: 145
Period size: 35 Copynumber: 2.5 Consensus size: 35
27832 ATATATTAAA
*
27842 TGGCCTATGTCGCCACATATCATGTACTATTACCT
1 TGGCCTATGTCGCCACATATCATGAACTATTACCT
*
27877 TGGCTTATGTCGCCACATATCATGAACTATTACCT
1 TGGCCTATGTCGCCACATATCATGAACTATTACCT
*
27912 TGGCCTATGACGCCAC
1 TGGCCTATGTCGCCAC
27928 TCCATATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.31
Consensus pattern (35 bp):
TGGCCTATGTCGCCACATATCATGAACTATTACCT
Found at i:27975 original size:29 final size:29
Alignment explanation
Indices: 27912--28016 Score: 129
Period size: 29 Copynumber: 3.5 Consensus size: 29
27902 ACTATTACCT
* * *
27912 TGGCCTATGACGCCACTCCATATATACAAAAA
1 TGGCCTATGATGCCAC-ACATATAT--AATAA
27944 TGGCCTATGATGCCACACATATATAATAA
1 TGGCCTATGATGCCACACATATATAATAA
*
27973 TGGCCTATGATGCCACATATATATAATAA
1 TGGCCTATGATGCCACACATATATAATAA
* *
28002 TGGCTTATGTTGCCA
1 TGGCCTATGATGCCA
28017 AACACTTAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
29 45 0.67
31 7 0.10
32 15 0.22
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (29 bp):
TGGCCTATGATGCCACACATATATAATAA
Found at i:28204 original size:88 final size:87
Alignment explanation
Indices: 28083--28492 Score: 504
Period size: 88 Copynumber: 4.6 Consensus size: 87
28073 TTAAAAAATA
* * * *
28083 TTTTCATTGCCGCTAATCAAAGCGAGCTAAATATCTAAATGTTCCCTCCAACTAGCAGAATCTTT
1 TTTT-ATTGCCGCTAA-CAAAGCGAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTT
*
28148 TCTCCTTGTAGAGGTCGAAAGCAC
64 TCTCCTTGTAGAGGTTGAAAGCAC
* *
28172 TTTTATTGCTGCTAACAAAGGCAAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTTT
1 TTTTATTGCCGCTAACAAA-GCGAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTTT
28237 CTCCTTGTAGAGGTTGAAAGCAC
65 CTCCTTGTAGAGGTTGAAAGCAC
* *
28260 TTTTATTGCTGCTAACAAAG-GCAGCCTCAATATCTAAATGCTCCCTCCGAGTAGTAGAATCTTT
1 TTTTATTGCCGCTAACAAAGCG-AG-CTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTT
*
28324 TCTCCATGTAGAGGTTGAAAGCAC
64 TCTCCTTGTAGAGGTTGAAAGCAC
* *
28348 TTTTATTTGCCGCTAATCAAAGCGAGCTTAATATCTATATGCTCCCTCCAAGTAGTAGAATCATT
1 TTTTA-TTGCCGCTAA-CAAAGCGAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATC---
28413 TTTTTTTCTCCTTTGTAGAGGTTGAAAGCAC
61 ---TTTTCTCC-TTGTAGAGGTTGAAAGCAC
* * *
28444 TTTCT-TTGCAGCTATCAAAGCGAGCT-TATCATCTAAATG-TCTCCTCCAA
1 TTT-TATTGCCGCTAACAAAGCGAGCTCAAT-ATCTAAATGCTC-CCTCCAA
28493 AATGAACTTC
Statistics
Matches: 286, Mismatches: 19, Indels: 27
0.86 0.06 0.08
Matches are distributed among these distances:
87 7 0.02
88 157 0.55
89 46 0.16
90 7 0.02
91 1 0.00
93 4 0.01
94 26 0.09
95 16 0.06
96 21 0.07
97 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (87 bp):
TTTTATTGCCGCTAACAAAGCGAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTTTC
TCCTTGTAGAGGTTGAAAGCAC
Found at i:29352 original size:27 final size:27
Alignment explanation
Indices: 29322--29374 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
29312 GTGACGTGAA
29322 AAATAGAAAGGGGGCATGGTATATAAC
1 AAATAGAAAGGGGGCATGGTATATAAC
*
29349 AAATAGAAAGGGGGCATGGTGTATAA
1 AAATAGAAAGGGGGCATGGTATATAA
29375 AAAACGAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.06, G:0.32, T:0.19
Consensus pattern (27 bp):
AAATAGAAAGGGGGCATGGTATATAAC
Found at i:29477 original size:2 final size:2
Alignment explanation
Indices: 29470--29496 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29460 AGCTTGGCAG
29470 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
29497 AAATATAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30061 original size:31 final size:31
Alignment explanation
Indices: 30009--30079 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
29999 CCTCTGCTAC
* *
30009 AGGTAATA-TCCACGTGGTTACACATGTTAA
1 AGGTAATACCCCACGTGGTTACACACGTTAA
* *
30039 AGGTAATACCCCACTTGGTTACACACGTTAC
1 AGGTAATACCCCACGTGGTTACACACGTTAA
30070 AGGTAATACC
1 AGGTAATACC
30080 TTGTGACTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 8 0.22
31 28 0.78
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (31 bp):
AGGTAATACCCCACGTGGTTACACACGTTAA
Found at i:30720 original size:46 final size:46
Alignment explanation
Indices: 30653--30740 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
30643 ACCGATGGGA
*
30653 GTGACGTGGCCTACCCTTACCTCTTCAGGAAAATACCACTGTTACC
1 GTGACGTGGCCTACCCTTACCTCTTCAGAAAAATACCACTGTTACC
* *
30699 GTGACGTGGCTTACCCTTACCTTTTCAGAAAAATACCACTGT
1 GTGACGTGGCCTACCCTTACCTCTTCAGAAAAATACCACTGT
30741 CACCATAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (46 bp):
GTGACGTGGCCTACCCTTACCTCTTCAGAAAAATACCACTGTTACC
Found at i:30876 original size:41 final size:41
Alignment explanation
Indices: 30803--30945 Score: 126
Period size: 50 Copynumber: 3.2 Consensus size: 41
30793 ATGTTTATGG
*
30803 GATAATTATGGTGATTATA-TAATTAACCATATTATCCATAGA
1 GATAATTAT-G-GATTATATTTATTAACCATATTATCCATAGA
30845 GATAATTATGGATTATATTTATTAACCATATTATCTACATAAATATTAGA
1 GATAATTATGGATTATATTTATTAACCATATTATC--C------A-TAGA
** ** *
30895 GATAATTATGGATTATATTTATTAGTCATATTATCTTTAAA
1 GATAATTATGGATTATATTTATTAACCATATTATCCATAGA
30936 GATAATTATG
1 GATAATTATG
30946 ACAATTATCA
Statistics
Matches: 85, Mismatches: 6, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
40 7 0.08
41 30 0.35
42 9 0.11
43 1 0.01
49 1 0.01
50 37 0.44
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (41 bp):
GATAATTATGGATTATATTTATTAACCATATTATCCATAGA
Found at i:37429 original size:29 final size:29
Alignment explanation
Indices: 37387--37479 Score: 107
Period size: 29 Copynumber: 3.1 Consensus size: 29
37377 TTGAAAGAAA
* *
37387 AAAAAACTACAACGTTTTGCCCTGTTTTG
1 AAAAAACGATAACGTTTTGCCCTGTTTTG
37416 AAAAAACGATAACGTTTTGCCC-GTTTTTG
1 AAAAAACGATAACGTTTTGCCCTG-TTTTG
* *
37445 AAAAAAAAATGATAACGTTTTGCCCTTTTTTG
1 ---AAAAAACGATAACGTTTTGCCCTGTTTTG
37477 AAA
1 AAA
37480 TCATGCGCTT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
28 1 0.02
29 28 0.51
32 26 0.47
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (29 bp):
AAAAAACGATAACGTTTTGCCCTGTTTTG
Found at i:37452 original size:32 final size:31
Alignment explanation
Indices: 37383--37479 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 31
37373 TTTTTTGAAA
* *
37383 GAAAAAAAAACTACAACGTTTTGCCCTGTTTT
1 GAAAAAAAAACGATAACGTTTTGCCCT-TTTT
37415 G---AAAAAACGATAACGTTTTGCCCGTTTTT
1 GAAAAAAAAACGATAACGTTTTGCCC-TTTTT
*
37444 GAAAAAAAAATGATAACGTTTTGCCCTTTTTT
1 GAAAAAAAAACGATAACGTTTTGCCC-TTTTT
37476 GAAA
1 GAAA
37480 TCATGCGCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
29 25 0.44
30 1 0.02
32 31 0.54
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (31 bp):
GAAAAAAAAACGATAACGTTTTGCCCTTTTT
Found at i:40179 original size:26 final size:27
Alignment explanation
Indices: 40131--40186 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
40121 GTGAGGAAAG
*
40131 AGTAAAATTACAGGCTTAGTGTTACCA
1 AGTAAAATTACAGGCTCAGTGTTACCA
*
40158 AGTAAAATTA-TGGCTCAGTGTTACCA
1 AGTAAAATTACAGGCTCAGTGTTACCA
40184 AGT
1 AGT
40187 GTGACATAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (27 bp):
AGTAAAATTACAGGCTCAGTGTTACCA
Found at i:41676 original size:27 final size:26
Alignment explanation
Indices: 41645--41715 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 26
41635 GGTCACCTAG
41645 GGGCATTTCGGTCATTTTCACATTCATA
1 GGGCATTT-GGTCATTTTCACATTCA-A
*
41673 -GGCATTT-GTCATTTTCGCATTCAA
1 GGGCATTTGGTCATTTTCACATTCAA
41697 GGGGCATTTTGGTCATTTT
1 -GGGCA-TTTGGTCATTTT
41716 GAGTCCATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
24 1 0.03
25 15 0.39
26 4 0.11
27 10 0.26
28 8 0.21
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (26 bp):
GGGCATTTGGTCATTTTCACATTCAA
Found at i:41970 original size:34 final size:34
Alignment explanation
Indices: 41927--41995 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
41917 AGTCAATTCT
*
41927 TAAGTTTAAGAATATTTAGGTAATTTAGTTCACA
1 TAAGTTTAAGAATATTTAGATAATTTAGTTCACA
41961 TAAGTTTAAGAATATTTAGATAATTTAGTTCACA
1 TAAGTTTAAGAATATTTAGATAATTTAGTTCACA
41995 T
1 T
41996 GGGATTAGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (34 bp):
TAAGTTTAAGAATATTTAGATAATTTAGTTCACA
Found at i:42035 original size:4 final size:4
Alignment explanation
Indices: 42026--42086 Score: 83
Period size: 4 Copynumber: 16.0 Consensus size: 4
42016 AAAATACAAA
*
42026 AAAT AAAT AAAT AAAT AAAT AAGT AAAT AAAT AAAT AAA- AAAT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
42072 AAAT -AAT ATAT AAAT
1 AAAT AAAT AAAT AAAT
42087 TGGAAATCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
3 9 0.18
4 41 0.82
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:45709 original size:14 final size:13
Alignment explanation
Indices: 45665--45696 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
45655 GAAGGAAAAT
45665 AAAAAAAATGAAA
1 AAAAAAAATGAAA
45678 AAGAAAAAATGAAA
1 AA-AAAAAATGAAA
45692 AAAAA
1 AAAAA
45697 TGGAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.06
Consensus pattern (13 bp):
AAAAAAAATGAAA
Found at i:45716 original size:24 final size:24
Alignment explanation
Indices: 45660--45709 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
45650 AATTTGAAGG
45660 AAAAT-AAAAAAAATGAAAAAGAA
1 AAAATGAAAAAAAATGAAAAAGAA
*
45683 AAAATGAAAAAAAATGGAAAA-AA
1 AAAATGAAAAAAAATGAAAAAGAA
45706 AAAA
1 AAAA
45710 CAGAAAAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (24 bp):
AAAATGAAAAAAAATGAAAAAGAA
Found at i:49946 original size:29 final size:29
Alignment explanation
Indices: 49904--49962 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
49894 AGGAATCTAA
49904 CATCCATATTATGAGAGATTGCCCACTTG
1 CATCCATATTATGAGAGATTGCCCACTTG
49933 CATCCATATTATGAGAGATTGCCCACTTG
1 CATCCATATTATGAGAGATTGCCCACTTG
49962 C
1 C
49963 TGTTGGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (29 bp):
CATCCATATTATGAGAGATTGCCCACTTG
Found at i:53632 original size:21 final size:21
Alignment explanation
Indices: 53608--53656 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
53598 ATAGTTTAGA
* *
53608 TTTAATTTACTTTGTTTTATT
1 TTTAATTTAATTTCTTTTATT
* *
53629 TTTAGTTTAATTTCTTTTCTT
1 TTTAATTTAATTTCTTTTATT
*
53650 TATAATT
1 TTTAATT
53657 GCTAATTTTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTAATTTAATTTCTTTTATT
Found at i:54987 original size:15 final size:16
Alignment explanation
Indices: 54967--54996 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54957 GATCTTGCAA
54967 TCTTAAGTT-TTTATT
1 TCTTAAGTTGTTTATT
54982 TCTTAAGTTGTTTAT
1 TCTTAAGTTGTTTAT
54997 ATTGTTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (16 bp):
TCTTAAGTTGTTTATT
Found at i:55169 original size:82 final size:82
Alignment explanation
Indices: 55033--55244 Score: 390
Period size: 82 Copynumber: 2.6 Consensus size: 82
55023 AATAATATTG
* *
55033 AAAATTACC-TTGACACCAGAAGTTGTCATTTTGGTAAATTAAAATTACTGCTGACACTATAAGT
1 AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATTAAAATTACTGCTGACACTAGAAGT
55097 TGTCACCTTGGCAAATT
66 TGTCACCTTGGCAAATT
55114 AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATTAAAATTACTGCTGACACTAGAAGT
1 AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATTAAAATTACTGCTGACACTAGAAGT
55179 TGTCACCTTGGCAAATT
66 TGTCACCTTGGCAAATT
*
55196 AAAATTACCTTTGACACCAGAAATTGTCACTTTGGTAAATTAAAATTAC
1 AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATTAAAATTAC
55245 CTTTGAAGTG
Statistics
Matches: 127, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
81 9 0.07
82 118 0.93
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (82 bp):
AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATTAAAATTACTGCTGACACTAGAAGT
TGTCACCTTGGCAAATT
Found at i:55245 original size:41 final size:41
Alignment explanation
Indices: 55033--55250 Score: 298
Period size: 41 Copynumber: 5.3 Consensus size: 41
55023 AATAATATTG
*
55033 AAAATTACC-TTGACACCAGAAGTTGTCATTTTGGTAAATT
1 AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATT
* * * * *
55073 AAAATTA-CTGCTGACACTATAAGTTGTCACCTTGGCAAATT
1 AAAATTACCT-TTGACACCAGAAGTTGTCACTTTGGTAAATT
55114 AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATT
1 AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATT
* * * *
55155 AAAATTA-CTGCTGACACTAGAAGTTGTCACCTTGGCAAATT
1 AAAATTACCT-TTGACACCAGAAGTTGTCACTTTGGTAAATT
*
55196 AAAATTACCTTTGACACCAGAAATTGTCACTTTGGTAAATT
1 AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATT
55237 AAAATTACCTTTGA
1 AAAATTACCTTTGA
55251 AGTGGTACTC
Statistics
Matches: 153, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.01
40 9 0.06
41 139 0.91
42 4 0.03
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (41 bp):
AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATT
Found at i:63034 original size:104 final size:106
Alignment explanation
Indices: 62845--63076 Score: 276
Period size: 104 Copynumber: 2.2 Consensus size: 106
62835 AAAAATAAAA
* * * *
62845 TTTTAATTTGGGGCTAAATTTAATGAAATTAGTTTTGTATTTTATTTCTAAAACCCTATAACTAT
1 TTTTAATTTTGGGCTAAACTTAATGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACTAA
** * * *
62910 AAATTATTAAATTTGAAATTTACCCTT-AAAA-TAATTTTT
66 AAAACATTAAATTTCAAATTTACCCTTAAAAATTAAGTTTC
* *
62949 TTTTAATTTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACTCTATAA-TAA
1 TTTTAATTTTGGGCTAAACTTAATGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACTAA
* * * *
63013 AAAACCTTTAATTTCATAATTTTCTCTTAAAAATTAAGTTTC
66 AAAACATTAAATTTCA-AATTTACCCTTAAAAATTAAGTTTC
*
63055 TTTT-ATTGT-GGCTAAACTTAAT
1 TTTTAATTTTGGGCTAAACTTAAT
63077 ACAAACTAAA
Statistics
Matches: 108, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
103 13 0.12
104 77 0.71
105 8 0.07
106 10 0.09
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.47
Consensus pattern (106 bp):
TTTTAATTTTGGGCTAAACTTAATGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACTAA
AAAACATTAAATTTCAAATTTACCCTTAAAAATTAAGTTTC
Found at i:64253 original size:109 final size:110
Alignment explanation
Indices: 64066--64272 Score: 362
Period size: 109 Copynumber: 1.9 Consensus size: 110
64056 TCTTAATTTG
*
64066 CTTGTGAAGTCTACAAACCCCATTGACAGTGTAATAAATAATAATAATTTTTTAAAATAAAAGTA
1 CTTGTGAAGTCTACAAACCCCATTGACAGTGTAATAAATAATAATAATTTTTTAAAATAAAAGAA
*
64131 CTATCTATCCGAAAAATTACATATC-TTTAGTAATTTTTAATCCC
66 CTATATATCCGAAAAATTACATATCTTTTAGTAATTTTTAATCCC
* *
64175 CTTGTGGAGTCTACAAACGCCATTGACAGTGTAATAAATAATAATAATTTTTTAAAATAAAAGAA
1 CTTGTGAAGTCTACAAACCCCATTGACAGTGTAATAAATAATAATAATTTTTTAAAATAAAAGAA
*
64240 CTATATATTCGAAAAATTACATATCTTTTAGTA
66 CTATATATCCGAAAAATTACATATCTTTTAGTA
64273 TTTAATTTTT
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
109 85 0.92
110 7 0.08
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.35
Consensus pattern (110 bp):
CTTGTGAAGTCTACAAACCCCATTGACAGTGTAATAAATAATAATAATTTTTTAAAATAAAAGAA
CTATATATCCGAAAAATTACATATCTTTTAGTAATTTTTAATCCC
Done.