Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007866.1 Hibiscus syriacus cultivar Beakdansim tig00110238_pilon, 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: 49304
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:606 original size:28 final size:29
Alignment explanation
Indices: 554--679 Score: 146
Period size: 30 Copynumber: 4.2 Consensus size: 29
544 GGTCGAGGGT
* * *
554 TTACCTATTTCTTCTGGACATATGGACTGT
1 TTACCTA-TGCTTCGGGACATATGGACTGA
584 TTACCTATG-TTCGGGACATATGGACTGA
1 TTACCTATGCTTCGGGACATATGGACTGA
* * * *
612 TTACCTATGTTCTCGGAACATACGGACTGT
1 TTACCTATGCT-TCGGGACATATGGACTGA
642 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATG--CTTCGGGACATATGGACTGA
673 TTACCTA
1 TTACCTA
680 GGTTCTTCGG
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
28 26 0.32
29 2 0.02
30 31 0.38
31 22 0.27
32 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (29 bp):
TTACCTATGCTTCGGGACATATGGACTGA
Found at i:644 original size:58 final size:60
Alignment explanation
Indices: 554--691 Score: 203
Period size: 58 Copynumber: 2.3 Consensus size: 60
544 GGTCGAGGGT
*
554 TTACCTAT-TTCTTCTGG-ACATATGGACTGTTTACCTATG-TTCGGGACATATGGACTGA
1 TTACCTATGTTCTTC-GGAACATACGGACTGTTTACCTATGCTTCGGGACATATGGACTGA
612 TTACCTATGTTC-TCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATG--CTTCGGGACATATGGACTGA
*
673 TTACCTAGGTTCTTCGGAA
1 TTACCTATGTTCTTCGGAA
692 TCTATGGACT
Statistics
Matches: 72, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
57 2 0.03
58 31 0.43
59 3 0.04
61 30 0.42
62 6 0.08
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (60 bp):
TTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGCTTCGGGACATATGGACTGA
Found at i:670 original size:31 final size:31
Alignment explanation
Indices: 552--702 Score: 179
Period size: 31 Copynumber: 5.0 Consensus size: 31
542 AGGGTCGAGG
*
552 GTTTACCTAT-TTCTTCTGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
582 GTTTACCTATG---TTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
610 GATTACCTATGTTC-TCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
640 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
671 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
702 G
1 G
703 GTCCTTCGGG
Statistics
Matches: 103, Mismatches: 12, Indels: 11
0.82 0.10 0.09
Matches are distributed among these distances:
28 26 0.25
30 36 0.35
31 40 0.39
32 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:3514 original size:21 final size:21
Alignment explanation
Indices: 3488--3532 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3478 GATTTCTGGG
* *
3488 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3509 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3530 CAA
1 CAA
3533 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4388 original size:31 final size:31
Alignment explanation
Indices: 4350--4505 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
4340 AGGGTCGAGG
*
4350 GTTTACCTATGTTCTTCTGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4381 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
4412 GATTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
4443 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
4474 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
4505 G
1 G
4506 GTCCTTCGGG
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
31 111 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4504 original size:62 final size:62
Alignment explanation
Indices: 4352--4505 Score: 249
Period size: 62 Copynumber: 2.5 Consensus size: 62
4342 GGTCGAGGGT
*
4352 TTACCTATGTTCTTCTGG-ACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTC-GGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
4414 TTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
4476 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
4506 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
61 2 0.02
62 83 0.97
63 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
Found at i:11373 original size:21 final size:20
Alignment explanation
Indices: 11347--11393 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
11337 GAACGCTGGA
11347 AACCGGTTTTGACCGGTTTTG
1 AACCGGTTTTGACCGG-TTTG
11368 AACCGGTTTTGACCGGTTTG
1 AACCGGTTTTGACCGGTTTG
11388 -ACCGGT
1 AACCGGT
11394 CACGACCCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 6 0.23
20 4 0.15
21 16 0.62
ACGTcount: A:0.15, C:0.21, G:0.30, T:0.34
Consensus pattern (20 bp):
AACCGGTTTTGACCGGTTTG
Found at i:11374 original size:11 final size:10
Alignment explanation
Indices: 11348--11393 Score: 76
Period size: 10 Copynumber: 4.6 Consensus size: 10
11338 AACGCTGGAA
11348 ACCGGTTTTG
1 ACCGGTTTTG
11358 ACCGGTTTTG
1 ACCGGTTTTG
11368 AACCGGTTTTG
1 -ACCGGTTTTG
11379 ACCGG-TTTG
1 ACCGGTTTTG
11388 ACCGGT
1 ACCGGT
11394 CACGACCCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.26
10 15 0.44
11 10 0.29
ACGTcount: A:0.13, C:0.22, G:0.30, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:11447 original size:13 final size:13
Alignment explanation
Indices: 11406--11436 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
11396 CGACCCGTTT
*
11406 ACCCGTTTACCCG
1 ACCCGTTGACCCG
11419 ACCCGTTGACCCG
1 ACCCGTTGACCCG
11432 ACCCG
1 ACCCG
11437 ACCCGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:18597 original size:11 final size:11
Alignment explanation
Indices: 18565--18603 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
18555 CGCTGGAAAT
18565 CGGTTTTG-AC
1 CGGTTTTGAAC
18575 CGG-TTT-AAC
1 CGGTTTTGAAC
18584 CGGTTTTGAAC
1 CGGTTTTGAAC
18595 CGGTTTTGA
1 CGGTTTTGA
18604 CTGGTTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.31
10 6 0.23
11 12 0.46
ACGTcount: A:0.15, C:0.18, G:0.28, T:0.38
Consensus pattern (11 bp):
CGGTTTTGAAC
Found at i:18644 original size:21 final size:18
Alignment explanation
Indices: 18620--18667 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 18
18610 TGACCGGTCA
18620 CGACCCGTTTACCCGTTTACC
1 CGACCCGTTTACCCG---ACC
18641 CGACCCGTTTACCCGACC
1 CGACCCGTTTACCCGACC
18659 CGACCCGTT
1 CGACCCGTT
18668 GACCGTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 12 0.44
21 15 0.56
ACGTcount: A:0.15, C:0.46, G:0.17, T:0.23
Consensus pattern (18 bp):
CGACCCGTTTACCCGACC
Found at i:18671 original size:13 final size:13
Alignment explanation
Indices: 18630--18660 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
18620 CGACCCGTTT
18630 ACCCGTTTACCCG
1 ACCCGTTTACCCG
18643 ACCCGTTTACCCG
1 ACCCGTTTACCCG
18656 ACCCG
1 ACCCG
18661 ACCCGTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.19
Consensus pattern (13 bp):
ACCCGTTTACCCG
Found at i:18740 original size:29 final size:29
Alignment explanation
Indices: 18679--18754 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
18669 ACCGTTGACC
*** *
18679 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
18708 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
18737 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
18755 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.21, C:0.09, G:0.28, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:22655 original size:42 final size:42
Alignment explanation
Indices: 22594--22714 Score: 161
Period size: 42 Copynumber: 2.9 Consensus size: 42
22584 CTTAGTAAGA
* *
22594 CCTTCGGGTCATCAATAAGTCTTTTGAGCATGATGATTAAAT
1 CCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAAT
* * * *
22636 CCTTCGCGTTATCAGTAAGTCTTTCAATCATGATGATTAAAT
1 CCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAAT
* * *
22678 CCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGAT
1 CCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGAT
22715 AAGTTCTCTG
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (42 bp):
CCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAAT
Found at i:22777 original size:37 final size:37
Alignment explanation
Indices: 22733--22840 Score: 153
Period size: 37 Copynumber: 2.9 Consensus size: 37
22723 TGGGCTATCT
*
22733 TAAGCCTTCACGGAAGAGTCGTGAAGCAAATCAATCA
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCA
* * * *
22770 TAAGCCTTCACGAAAGAGTATTGAAACAAATCAATCT
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCA
**
22807 TAAGCCTTCACGGAAGAAAAGTGAAGCAAATCAA
1 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAA
22841 GATCGAGTCC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (37 bp):
TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCA
Found at i:22917 original size:55 final size:55
Alignment explanation
Indices: 22843--23260 Score: 480
Period size: 55 Copynumber: 7.6 Consensus size: 55
22833 CAAATCAAGA
** * *
22843 TCGAGTCCTATAC-CGTCTGAAAGAATAGGGAGTTGACATGTTTGATGAAGATTG-
1 TCGAGTCCTATACTC-TCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
22897 TCTGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
1 TC-GAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
* * *
22953 TCGTGTCCTATACTCTCTGAAAGAATAGGGAGTAGACATGTTTGCTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
* * *
23008 TCGAGTCCTATACTCTTTGAAAGAATAGGGAGCAGACACGTTCGTTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
* * * * * *
23063 TTGAGTCCTATACTCCCCGAAAGATTAGGAAGCAGATACGTTTGCTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
* * * * * * * *
23118 TTGAGTCTTGTACTCCCTGAAATAATAGGGAGCGGATACGTTTACTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
* * * * * * * *
23173 TCGAGTCCTATACTCCCTGAAAAAATAGGGAGCATACCCATTTTCCGAAGATTATT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATT-GT
* * *
23229 TCAAGTCATATACTCCCTGAAAGAATAGGGAG
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAG
23261 AGAACCCGTT
Statistics
Matches: 315, Mismatches: 45, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
54 2 0.01
55 280 0.89
56 33 0.10
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (55 bp):
TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
Found at i:27022 original size:7 final size:7
Alignment explanation
Indices: 27010--27039 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
27000 AAATTAACTT
27010 AATAAAA
1 AATAAAA
27017 AATAAAA
1 AATAAAA
*
27024 GATAAAA
1 AATAAAA
27031 AATAAAA
1 AATAAAA
27038 AA
1 AA
27040 AATGTAATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (7 bp):
AATAAAA
Found at i:28720 original size:21 final size:21
Alignment explanation
Indices: 28694--28756 Score: 56
Period size: 27 Copynumber: 2.7 Consensus size: 21
28684 ACCCAAAGGT
28694 CAATATCGATACTATGAGGCA
1 CAATATCGATACTATGAGGCA
28715 CAATATCAGTACCGATACTATGAGGCA
1 C-A-AT-A-T--CGATACTATGAGGCA
28742 CAATATC-AGTACTAT
1 CAATATCGA-TACTAT
28757 CGTCATGAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
20 1 0.03
21 8 0.23
22 1 0.03
23 3 0.09
24 2 0.06
25 3 0.09
26 1 0.03
27 16 0.46
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (21 bp):
CAATATCGATACTATGAGGCA
Found at i:28766 original size:27 final size:27
Alignment explanation
Indices: 28700--28753 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
28690 AGGTCAATAT
28700 CGATACTATGAGGCACAATATCAGTAC
1 CGATACTATGAGGCACAATATCAGTAC
28727 CGATACTATGAGGCACAATATCAGTAC
1 CGATACTATGAGGCACAATATCAGTAC
28754 TATCGTCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (27 bp):
CGATACTATGAGGCACAATATCAGTAC
Found at i:31214 original size:21 final size:21
Alignment explanation
Indices: 31188--31229 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
31178 GTTCTTTTGG
31188 TTTGGCTCTATATTTTTGTTT
1 TTTGGCTCTATATTTTTGTTT
*
31209 TTTGGCTCTCTATTTTTGTTT
1 TTTGGCTCTATATTTTTGTTT
31230 CGGTTTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.12, G:0.14, T:0.67
Consensus pattern (21 bp):
TTTGGCTCTATATTTTTGTTT
Found at i:32527 original size:134 final size:134
Alignment explanation
Indices: 32308--32768 Score: 628
Period size: 134 Copynumber: 3.5 Consensus size: 134
32298 CTATTTCTGC
* * *
32308 AGGGAAGATCAGA-TCGAG-AAACTTTGATTCA-TTCCACTGTTCTTCATGGAAGATTGAATCGG
1 AGGG-AGATCAGAGTCGAGAAAACTTTGATCCACTT-CACTGTTCTTCAGGGAAGATTGAATCAG
** **
32370 AATCGATTTGCTTCACTAATCTTCAGGAAGACCAAATATGAAAGAAGAAGAATCTGCTCCACTAC
64 AATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGCGTCTGCTCCACTAC
32435 TCTTTA
129 TCTTTA
* * *
32441 TGGGAGATCAGAGTCGAGAAAACTTTGATCCACTTCACTATTCTTCAGGGAAGATTGAATTAGAA
1 AGGGAGATCAGAGTCGAGAAAACTTTGATCCACTTCACTGTTCTTCAGGGAAGATTGAATCAGAA
* *
32506 TCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTCTGCTTCACTACTC
66 TCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGCGTCTGCTCCACTACTC
32571 TTTA
131 TTTA
* * * * * *
32575 GGGGATATCACAGTCAAGAAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCAGA
1 AGGGAGATCAGAGTCGAG-AAAACTTTGATCCACTTCACTGTTCTTCAGGGAAGATTGAATCAGA
* * *
32640 TTTGATTTGCTTCACTGCTCTTTAGGAAGACCAAATATG-AAGAAGAAGCGTCTGCTCCACTACT
65 ATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGCGTCTGCTCCACTACT
32704 -TTTA
130 CTTTA
* * *
32708 AGGGAGATCAAACTCGAGAAATCTTTGATCCACTTCACT-TCTCTTCAGGGAAGATTGAATC
1 AGGGAGATCAGAGTCGAGAAAACTTTGATCCACTTCACTGT-TCTTCAGGGAAGATTGAATC
32769 TGAAAATCAA
Statistics
Matches: 290, Mismatches: 33, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
132 47 0.16
133 25 0.09
134 139 0.48
135 79 0.27
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (134 bp):
AGGGAGATCAGAGTCGAGAAAACTTTGATCCACTTCACTGTTCTTCAGGGAAGATTGAATCAGAA
TCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGCGTCTGCTCCACTACTC
TTTA
Found at i:33399 original size:45 final size:45
Alignment explanation
Indices: 33306--33644 Score: 276
Period size: 45 Copynumber: 7.6 Consensus size: 45
33296 TACCGAAAAG
* ** * * *
33306 TTGACTCATCTCCGCGAGAAAAACAAA-ATGGACAACACCAAAAGA
1 TTGACTCATCTTCGCGAGAAAGTCAAAGA-AGACAACACTAAAATA
* * * *
33351 TTGACTCATCTTGGCGAGAATGTCAAGGAAGACAGCACTAAAATA
1 TTGACTCATCTTCGCGAGAAAGTCAAAGAAGACAACACTAAAATA
** * *
33396 TTGACTCATCTTCATGAGAAAGT-AAAGGAAGACAACACTGAAAGA
1 TTGACTCATCTTCGCGAGAAAGTCAAA-GAAGACAACACTAAAATA
* *
33441 TTGACTCCTCTTTGCGAGAAAGTC-AAGAAGGACAACACTAAAATA
1 TTGACTCATCTTCGCGAGAAAGTCAAAGAA-GACAACACTAAAATA
* * * * * * *
33486 TTGAATCCTCTTTGCGAAAAAATCAAAAAAGGACAACACTGAAATA
1 TTGACTCATCTTCGCGAGAAAGTCAAAGAA-GACAACACTAAAATA
* * * * * *
33532 TTGAATCCTCTTCGCAAGAAAGTCAAAAAAGACAATACTGAAATA
1 TTGACTCATCTTCGCGAGAAAGTCAAAGAAGACAACACTAAAATA
* * * * * *
33577 TTGACTTATCTTCACAAGAAAGTC-AAGAATA-AA-ACTGAAAGA
1 TTGACTCATCTTCGCGAGAAAGTCAAAGAAGACAACACTAAAATA
*
33619 TTGACTCCTCTTCGCGAGAAAGTCAA
1 TTGACTCATCTTCGCGAGAAAGTCAA
33645 GAATAACAAA
Statistics
Matches: 243, Mismatches: 45, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
42 28 0.12
43 3 0.01
44 10 0.04
45 156 0.64
46 46 0.19
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (45 bp):
TTGACTCATCTTCGCGAGAAAGTCAAAGAAGACAACACTAAAATA
Found at i:33668 original size:38 final size:38
Alignment explanation
Indices: 33576--34521 Score: 759
Period size: 38 Copynumber: 23.9 Consensus size: 38
33566 ATACTGAAAT
* * *
33576 ATTGACTTATCTTCACAAGAAAGTCAAGAATAAAACTGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAAT--AAC--AAAG
* * *
33618 ATTGACTCCTCTTCGCGAGAAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * * * * *
33656 ATCGAGTTCTCTTCATGAGGAAGTTAATAATAAAAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * *
33694 ATCGACTTCTCTTTATGAGGAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * ** *
33732 ATTAATTTCTCGCCACGAGGATGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
33770 ATTAATTGA-TTCCTCTTCGCGAGGGAGTCAAGAATAACAAAG
1 ----ATTGACTT-CTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
33812 ATTGACTTCTCTTCATGAAGAAGTCAAGAATAACAAAGATTG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC-AA-A--G
* ** *
33854 ATTGACTCCTCTTTGCGAGGGAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
*
33892 ATTGACCTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC-AA-A--G
* *
33934 ATTGACTCCTCTTCACGAGGGAGTCAAGAATAA-AATAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA-AG
* *
33972 AATGACTTCTCTTCACGAGGAAGTCAAGAATAACAGAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
34010 ATTGACCTCTCTTCACGAGGAAATCAAGAATAACATTGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAAG
* * * * *
34052 ATTTACTCCTCTTCGCGAGGGAGTCAAGAACAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * * *
34090 ATTAACTTATCTTCACGAGGAAGTCAATAATAACATTGAAAAA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC-----AAAG
* * * * *
34133 ATTGACTCCTCTTCGCGAGGGAGTCAAGAATAATATAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * * **
34171 ATTGACTTCACTTCATGAGGAATTCAAGGTTAATATTGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAA-G--AATA-ACAAAG
* * * * * * *
34213 ATTGACTCCTCTTCGCAAGGGATTCAGGAATAGCAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * *
34251 ATTAACTTCTCTTCACGAGGAAGTCAAGAATAACAGAT
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
*
34289 ATTGACTTCTCTTCATGAGGAAGTCAAGAATAACATTGAA-
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACA---AAG
* * * *
34329 ATGTTGACTCCTCTTCGCGAGGGAGTCAAGAACAACAAAG
1 A--TTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
34369 ATTGACTTCTCTTCAAGAGGAAGTTAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
34407 ATTGATTTCTCTTCACGAGGATGTCAATG-ATAACATTGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAA-GAATAAC----AAAG
* ** * *
34449 ATTGACTCCTCTTCTTGA-GAGAGTCAGGAGTAACAAAG
1 ATTGACTTCTCTTCACGAGGA-AGTCAAGAATAACAAAG
* *
34487 ATTAACTTTTCTTCACGAGGAAGTCAAGAATAACA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACA
34522 TTGAAAGATT
Statistics
Matches: 719, Mismatches: 143, Indels: 88
0.76 0.15 0.09
Matches are distributed among these distances:
38 424 0.59
39 17 0.02
40 11 0.02
41 13 0.02
42 224 0.31
43 30 0.04
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (38 bp):
ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
Found at i:34442 original size:118 final size:118
Alignment explanation
Indices: 33576--34556 Score: 817
Period size: 118 Copynumber: 8.2 Consensus size: 118
33566 ATACTGAAAT
* ** * * **
33576 ATTGACTTATCTTCACAAGAAAGTCAAGAATAAAACT-GAAAGATTGACTCCTCTTCGCGAGAAA
1 ATTGACTTCTCTTCATGAGGAAGTCAAGAATAACA-TAGAAAGATTGACTCCTCTTCGCGAGGGA
* * * * * *
33640 GTCAAGAATAACAAAGATCGAGTTCTCTTCATGAGGAAGTTAATAATAAAAAAG
65 GTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * * * * ** *
33694 ATCGACTTCTCTTTATGAGGAAGTCAAGAATAAC----AAAGATTAATTTCTCGCCACGA-GGAT
1 ATTGACTTCTCTTCATGAGGAAGTCAAGAATAACATAGAAAGATTGACTCCTCTTCGCGAGGGA-
* *
33754 GTCAAGAATAACAAAGATTAATTGA-TTCCTCTTCGCGAGGGAGTCAAGAATAACAAAG
65 GTCAAGAATAACAAAG----ATTGACTT-CTCTTCACGAGGAAGTCAAGAATAACAAAG
* * ** *
33812 ATTGACTTCTCTTCATGAAGAAGTCAAGAATAACAAAGATTGATTGACTCCTCTTTGCGAGGGAG
1 ATTGACTTCTCTTCATGAGGAAGTCAAGAATAACATAGAAAGATTGACTCCTCTTCGCGAGGGAG
*
33877 TCAAGAATAACAAAGATTGACCTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTG
66 TCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC-AA-A--G
* * * * * * *
33934 ATTGACTCCTCTTCACGAGGGAGTCAAGAATAAAATAG--A-A-TGACTTCTCTTCACGAGGAAG
1 ATTGACTTCTCTTCATGAGGAAGTCAAGAATAACATAGAAAGATTGACTCCTCTTCGCGAGGGAG
* * *
33995 TCAAGAATAACAGAGATTGACCTCTCTTCACGAGGAAATCAAGAATAACATTGAAAG
66 TCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAAG
* * ** * * * ** * *
34052 ATTTACTCCTCTTCGCGAGGGAGTCAAG---AACA-ACAAAGATTAACTTATCTTCACGAGGAAG
1 ATTGACTTCTCTTCATGAGGAAGTCAAGAATAACATAGAAAGATTGACTCCTCTTCGCGAGGGAG
* * * * * * *
34113 TCAATAATAACATTGAAAAAATTGACTCCTCTTCGCGAGGGAGTCAAGAATAATATAG
66 TCAAGAATAAC-----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * ** * * * *
34171 ATTGACTTCACTTCATGAGGAATTCAAGGTTAATATTGAAAGATTGACTCCTCTTCGCAAGGGAT
1 ATTGACTTCTCTTCATGAGGAAGTCAAGAATAACATAGAAAGATTGACTCCTCTTCGCGAGGGAG
* * * * *
34236 TCAGGAATAGCAAAGATTAACTTCTCTTCACGAGGAAGTCAAGAATAACAGAT
66 TCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
*
34289 ATTGACTTCTCTTCATGAGGAAGTCAAGAATAACATTGAAATG-TTGACTCCTCTTCGCGAGGGA
1 ATTGACTTCTCTTCATGAGGAAGTCAAGAATAACATAGAAA-GATTGACTCCTCTTCGCGAGGGA
* * *
34353 GTCAAGAACAACAAAGATTGACTTCTCTTCAAGAGGAAGTTAAGAATAACAAAG
65 GTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * * * ** *
34407 ATTGATTTCTCTTCACGAGGATGTCAATG-ATAACATTGAAAGATTGACTCCTCTTCTTGAGAGA
1 ATTGACTTCTCTTCATGAGGAAGTCAA-GAATAACATAGAAAGATTGACTCCTCTTCGCGAGGGA
* * * *
34471 GTCAGGAGTAACAAAGATTAACTTTTCTTCACGAGGAAGTCAAGAATAACATTGAAAG
65 GTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAAG
* * *
34529 ATTGACTCCTCTTTATGAGGGAGTCAAG
1 ATTGACTTCTCTTCATGAGGAAGTCAAG
34557 TTGAAGCTTC
Statistics
Matches: 695, Mismatches: 129, Indels: 75
0.77 0.14 0.08
Matches are distributed among these distances:
113 1 0.00
114 33 0.05
115 3 0.00
116 1 0.00
117 4 0.01
118 467 0.67
119 30 0.04
120 2 0.00
121 3 0.00
122 90 0.13
123 61 0.09
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (118 bp):
ATTGACTTCTCTTCATGAGGAAGTCAAGAATAACATAGAAAGATTGACTCCTCTTCGCGAGGGAG
TCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
Found at i:34449 original size:80 final size:78
Alignment explanation
Indices: 33571--34556 Score: 757
Period size: 80 Copynumber: 12.4 Consensus size: 78
33561 AGACAATACT
* * * * * *
33571 GAAATATTGACTTATCTTCACAAGAAAGTCAAGAATAAAACTGAAAGATTGACTCCTCTTCGCGA
1 GAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT--AAC--AAAGATTGACTTCTCTTCACGA
*
33636 GAAAGTCAAGAATAAC-
62 GGAAGTCAAGAATAACA
* * * * * * * * *
33652 -AAAGATCGAGTTCTCTTCATGAGGAAGTTAATAATAAAAAAGATCGACTTCTCTTTATGAGGAA
1 GAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAA
33716 GTCAAGAATAAC-
66 GTCAAGAATAACA
* * ** * *
33728 -AAAGATTAATTTCTCGCCACGAGGATGTCAAGAATAACAAAGATTAATTGA-TTCCTCTTCGCG
1 GAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG----ATTGACTT-CTCTTCACG
*
33791 AGGGAGTCAAGAATAAC-
61 AGGAAGTCAAGAATAACA
* * * **
33808 -AAAGATTGACTTCTCTTCATGAAGAAGTCAAGAATAACAAAGATTGATTGACTCCTCTTTGCGA
1 GAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC-AA-A--GATTGACTTCTCTTCACGA
*
33872 GGGAGTCAAGAATAAC-
62 GGAAGTCAAGAATAACA
* *
33888 -AAAGATTGACCTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGATTGACTCCTCTTCACGA
1 GAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC-AA-A--GATTGACTTCTCTTCACGA
*
33952 GGGAGTCAAGAATAA-A
62 GGAAGTCAAGAATAACA
* * * *
33968 -ATAGAATGACTTCTCTTCACGAGGAAGTCAAGAATAACAGAGATTGACCTCTCTTCACGAGGAA
1 GAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAA
*
34032 ATCAAGAATAACA
66 GTCAAGAATAACA
* * * * * * *
34045 TTGAAAGATTTACTCCTCTTCGCGAGGGAGTCAAGAACAACAAAGATTAACTTATCTTCACGAGG
1 --GAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGG
*
34110 AAGTCAATAATAACA
64 AAGTCAAGAATAACA
* * * * * * * *
34125 TTGAAAAAATTGACTCCTCTTCGCGAGGGAGTCAAGAATAATATAGATTGACTTCACTTCATGAG
1 --G-AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAG
* ** *
34190 GAATTCAAGGTTAATA
63 GAAGTCAAGAATAACA
* * * * * * * *
34206 TTGAAAGATTGACTCCTCTTCGCAAGGGATTCAGGAATAGCAAAGATTAACTTCTCTTCACGAGG
1 --GAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGG
34271 AAGTCAAGAATAACA
64 AAGTCAAGAATAACA
* * * *
34286 G--ATATTGACTTCTCTTCATGAGGAAGTCAAGAATAACATTGAA-ATGTTGACTCCTCTTCGCG
1 GAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACA---AAGA--TTGACTTCTCTTCACG
* *
34348 AGGGAGTCAAGAACAAC-
61 AGGAAGTCAAGAATAACA
* * * *
34365 -AAAGATTGACTTCTCTTCAAGAGGAAGTTAAGAATAACAAAGATTGATTTCTCTTCACGAGGAT
1 GAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAA
34429 GTCAATG-ATAACA
66 GTCAA-GAATAACA
* ** * * * *
34442 TTGAAAGATTGACTCCTCTTCTTGA-GAGAGTCAGGAGTAACAAAGATTAACTTTTCTTCACGAG
1 --GAAAGATTGACTTCTCTTCACGAGGA-AGTCAAGAATAACAAAGATTGACTTCTCTTCACGAG
34506 GAAGTCAAGAATAACA
63 GAAGTCAAGAATAACA
* * * *
34522 TTGAAAGATTGACTCCTCTTTATGAGGGAGTCAAG
1 --GAAAGATTGACTTCTCTTCACGAGGAAGTCAAG
34557 TTGAAGCTTC
Statistics
Matches: 742, Mismatches: 131, Indels: 65
0.79 0.14 0.07
Matches are distributed among these distances:
76 147 0.20
77 4 0.01
78 6 0.01
79 8 0.01
80 505 0.68
81 70 0.09
82 1 0.00
84 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (78 bp):
GAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAA
GTCAAGAATAACA
Found at i:36383 original size:17 final size:18
Alignment explanation
Indices: 36361--36451 Score: 66
Period size: 18 Copynumber: 5.1 Consensus size: 18
36351 AAATACTTGA
36361 TTTATTTTCTCTCA-TTT-
1 TTTATTTTCT-TCATTTTC
*
36378 TTTATTTTCTTTATTTTC
1 TTTATTTTCTTCATTTTC
**
36396 TTTATTTTCTTTTTTTTTTC
1 TTTATTTTC--TTCATTTTC
*
36416 TTCT-TTTTCTTCTTTTTC
1 TT-TATTTTCTTCATTTTC
36434 TTCT-TTTTCTTC-TTTTC
1 TT-TATTTTCTTCATTTTC
36451 T
1 T
36452 CTCGTTTTTC
Statistics
Matches: 66, Mismatches: 3, Indels: 10
0.84 0.04 0.13
Matches are distributed among these distances:
16 2 0.03
17 19 0.29
18 29 0.44
20 15 0.23
21 1 0.02
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTATTTTCTTCATTTTC
Found at i:36392 original size:9 final size:9
Alignment explanation
Indices: 36361--36411 Score: 63
Period size: 9 Copynumber: 5.9 Consensus size: 9
36351 AAATACTTGA
36361 TTTATTTTC
1 TTTATTTTC
*
36370 TCTCA-TTT-
1 T-TTATTTTC
36378 TTTATTTTC
1 TTTATTTTC
36387 TTTATTTTC
1 TTTATTTTC
36396 TTTATTTTC
1 TTTATTTTC
36405 TTT-TTTT
1 TTTATTTT
36412 TTTCTTCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
7 2 0.05
8 8 0.22
9 25 0.68
10 2 0.05
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTATTTTC
Found at i:36412 original size:9 final size:9
Alignment explanation
Indices: 36377--36510 Score: 81
Period size: 9 Copynumber: 14.2 Consensus size: 9
36367 TTCTCTCATT
36377 TTTTATTTTC
1 TTTT-TTTTC
*
36387 TTTATTTTC
1 TTTTTTTTC
*
36396 TTTATTTTCTT
1 TTT-TTTT-TC
36407 TTTTTTTTC
1 TTTTTTTTC
*
36416 TTCTTTTTC
1 TTTTTTTTC
*
36425 TTCTTTTTC
1 TTTTTTTTC
*
36434 TTCTTTTTC
1 TTTTTTTTC
36443 TTCTTTTCTCTC
1 TT-TTTT-T-TC
*
36455 GTTTTTCTTC
1 -TTTTTTTTC
*
36465 TTATTTTTC
1 TTTTTTTTC
* *
36474 TATCTTTTC
1 TTTTTTTTC
* **
36483 TCTTTCAT-
1 TTTTTTTTC
*
36491 TTTTTTATC
1 TTTTTTTTC
36500 TTTTTTTTC
1 TTTTTTTTC
36509 TT
1 TT
36511 CTCTCTCCTT
Statistics
Matches: 98, Mismatches: 19, Indels: 15
0.74 0.14 0.11
Matches are distributed among these distances:
8 6 0.06
9 64 0.65
10 15 0.15
11 6 0.06
12 5 0.05
13 2 0.02
ACGTcount: A:0.05, C:0.17, G:0.01, T:0.77
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:36428 original size:12 final size:12
Alignment explanation
Indices: 36393--36479 Score: 65
Period size: 12 Copynumber: 7.2 Consensus size: 12
36383 TTTCTTTATT
36393 TTCTTTATT-TTC
1 TTCTTT-TTCTTC
*
36405 TT-TTTTTTTTC
1 TTCTTTTTCTTC
36416 TTCTTTTTCTTC
1 TTCTTTTTCTTC
*
36428 TT-TTTCTTCTTT
1 TTCTTT-TTCTTC
*
36440 TTCTTCTT-TTC
1 TTCTTTTTCTTC
36451 TCTCGTTTTTCTTC
1 T-TC-TTTTTCTTC
*
36465 TTATTTTTCTATC
1 TTCTTTTTCT-TC
36478 TT
1 TT
36480 TTCTCTTTCA
Statistics
Matches: 61, Mismatches: 6, Indels: 15
0.74 0.07 0.18
Matches are distributed among these distances:
10 2 0.03
11 14 0.23
12 30 0.49
13 11 0.18
14 4 0.07
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (12 bp):
TTCTTTTTCTTC
Found at i:36486 original size:23 final size:21
Alignment explanation
Indices: 36400--36508 Score: 90
Period size: 18 Copynumber: 5.4 Consensus size: 21
36390 ATTTTCTTTA
**
36400 TTTTCTTTTTTTTTTCT-TCT
1 TTTTCTTTCATTTTTCTATCT
36420 TTTTC-TTC-TTTTTCT-TCT
1 TTTTCTTTCATTTTTCTATCT
*
36438 TTTTC-TTC--TTTTCTCTCGT
1 TTTTCTTTCATTTTTCTATC-T
*
36457 TTTTCTTCTTATTTTTCTATCT
1 TTTTCTT-TCATTTTTCTATCT
*
36479 TTTCTCTTTCATTTTTTTATCT
1 TTT-TCTTTCATTTTTCTATCT
36501 TTTT-TTTC
1 TTTTCTTTC
36509 TTCTCTCTCC
Statistics
Matches: 77, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
17 6 0.08
18 20 0.26
19 8 0.10
20 10 0.13
21 2 0.03
22 19 0.25
23 12 0.16
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (21 bp):
TTTTCTTTCATTTTTCTATCT
Found at i:36522 original size:29 final size:29
Alignment explanation
Indices: 36480--36535 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
36470 TTTCTATCTT
* *
36480 TTCTCTTTCATTTTTTTATCTTTTTTTTC
1 TTCTCTCTCATTTTTATATCTTTTTTTTC
* *
36509 TTCTCTCTCCTTTTTATCTCTTTTTTT
1 TTCTCTCTCATTTTTATATCTTTTTTT
36536 ATGAATTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.73
Consensus pattern (29 bp):
TTCTCTCTCATTTTTATATCTTTTTTTTC
Found at i:42872 original size:21 final size:21
Alignment explanation
Indices: 42848--42907 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
42838 GTTCTTTAAG
42848 TTTGGCTCTCTATTTTTGTTT
1 TTTGGCTCTCTATTTTTGTTT
* *
42869 TTTGGCTCTCTA-TTTCG--G
1 TTTGGCTCTCTATTTTTGTTT
*
42887 TTTGTCTCTCTATTTTTGTTT
1 TTTGGCTCTCTATTTTTGTTT
42908 CGATTTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 11 0.35
19 4 0.13
20 4 0.13
21 12 0.39
ACGTcount: A:0.05, C:0.17, G:0.15, T:0.63
Consensus pattern (21 bp):
TTTGGCTCTCTATTTTTGTTT
Found at i:42907 original size:18 final size:18
Alignment explanation
Indices: 42847--42907 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 18
42837 CGTTCTTTAA
42847 GTTTGGCTCTCTATTTTT
1 GTTTGGCTCTCTATTTTT
**
42865 GTTTTTTGGCTCTCTATTTCG
1 G---TTTGGCTCTCTATTTTT
*
42886 GTTTGTCTCTCTATTTTT
1 GTTTGGCTCTCTATTTTT
42904 GTTT
1 GTTT
42908 CGATTTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 19 0.54
21 16 0.46
ACGTcount: A:0.05, C:0.16, G:0.16, T:0.62
Consensus pattern (18 bp):
GTTTGGCTCTCTATTTTT
Found at i:43086 original size:233 final size:233
Alignment explanation
Indices: 42678--43105 Score: 716
Period size: 233 Copynumber: 1.8 Consensus size: 233
42668 GCTTCTTTCC
* * *
42678 TTTTAAACTCGATCGTCCACTGTCGGATCTTCTCCAAACAGAGATATGTGGCTCCTTTCGTCTCC
1 TTTTAAACTCGATCGTCCACCGTCGGATCTTCTCCAAACAGAGATATGTGGCTCCCTTCATCTCC
*
42743 GCGCGTCCCCATACCGTTCGAATCGTAGATCCGACACTCCGAAGGCCGACAAGGAACCTTGGCTC
66 GCGCGTCCCCACACCGTTCGAATCGTAGATCCGACACTCCGAAGGCCGACAAGGAACCTTGGCTC
42808 AAGGTAGTCTCTTCATCCCTTTTCTTTTTCGTTCTTTAAGTTTGGCTCTCTATTTTTGTTTTTTG
131 AAGGTAGTCTCTTCATCCCTTTTCTTTTTCGTTCTTTAAGTTTGGCTCTCTATTTTTGTTTTTTG
42873 GCTCTCTATTTCGGTTTGTCTCTCTATTTTTGTTTCGA
196 GCTCTCTATTTCGGTTTGTCTCTCTATTTTTGTTTCGA
*
42911 TTTTAAACTCGATTGTCCACCGTCGGATCTTCTCCAAAC-GAAGATATGTGGCTCCCTTCATCTC
1 TTTTAAACTCGATCGTCCACCGTCGGATCTTCTCCAAACAG-AGATATGTGGCTCCCTTCATCTC
* * * * *
42975 CGCGCGTCCCCACACCGTTTGGATTGTAGATCTGACACTCTGAAGGCCGACAAGGAACCTTGGC-
65 CGCGCGTCCCCACACCGTTCGAATCGTAGATCCGACACTCCGAAGGCCGACAAGGAACCTTGGCT
**
43039 CGAAGGTAGTCTCTTCATCCCTTTTCTTTTTCGTTCTTTTGGTTTGGCTCTCTATTTTTGTTTTT
130 C-AAGGTAGTCTCTTCATCCCTTTTCTTTTTCGTTCTTTAAGTTTGGCTCTCTATTTTTGTTTTT
43104 TG
194 TG
43106 TTTCGGTTTT
Statistics
Matches: 181, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
232 2 0.01
233 179 0.99
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.38
Consensus pattern (233 bp):
TTTTAAACTCGATCGTCCACCGTCGGATCTTCTCCAAACAGAGATATGTGGCTCCCTTCATCTCC
GCGCGTCCCCACACCGTTCGAATCGTAGATCCGACACTCCGAAGGCCGACAAGGAACCTTGGCTC
AAGGTAGTCTCTTCATCCCTTTTCTTTTTCGTTCTTTAAGTTTGGCTCTCTATTTTTGTTTTTTG
GCTCTCTATTTCGGTTTGTCTCTCTATTTTTGTTTCGA
Done.