Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000405.1 Hibiscus syriacus cultivar Beakdansim tig00000746_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: 95195
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:435 original size:21 final size:21
Alignment explanation
Indices: 411--455 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
401 CTTGTTCGTT
* *
411 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
432 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
453 TTG
1 TTG
456 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3646 original size:22 final size:22
Alignment explanation
Indices: 3605--3684 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
3595 CTCGTATAAA
3605 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
3628 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
3650 TGCACCGAAGTGCCCGTAGAA-
1 TGCACCGAAGTGCCCGTAGAAT
*
3671 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
3685 ATATAATGAT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
21 13 0.23
22 31 0.55
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:5389 original size:21 final size:21
Alignment explanation
Indices: 5365--5409 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5355 TCTTGTTCGT
* *
5365 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5386 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5407 TTG
1 TTG
5410 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:10521 original size:21 final size:21
Alignment explanation
Indices: 10470--10522 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
10460 ATTATGACTA
10470 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
10491 TCGCGTTGCGATTTTCTCAA-T
1 TCGCAATGCGATTTTC-CAATT
10512 TCGCAATGCGA
1 TCGCAATGCGA
10523 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:10537 original size:20 final size:21
Alignment explanation
Indices: 10512--10569 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
10502 TTTTCTCAAT
*
10512 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
10532 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
10553 TCGCAATGCGATATTAA
1 TCGCAATGCGA-ATTAA
10570 CTATCGCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 12 0.39
21 16 0.52
22 3 0.10
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:10598 original size:21 final size:21
Alignment explanation
Indices: 10549--10627 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
10539 GCGAATTTGG
* *
10549 AAAATCGCAATGCGATATTA-
1 AAAATCGCAACGCGATAATAC
**
10569 ACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATAATAC
10590 AAAATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATAATAC
10611 AAAATCGCAACGCGATA
1 AAAATCGCAACGCGATA
10628 CTAACTTTCG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 16 0.31
21 36 0.69
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.18
Consensus pattern (21 bp):
AAAATCGCAACGCGATAATAC
Found at i:10641 original size:20 final size:20
Alignment explanation
Indices: 10552--10687 Score: 101
Period size: 20 Copynumber: 6.7 Consensus size: 20
10542 AATTTGGAAA
* *
10552 ATCGCAATGCGATATTAACT
1 ATCGCAACGCGATACTAACT
* **
10572 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATACTA-ACT
* **
10593 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATACTA-ACT
10614 ATCGCAACGCGATACTAACT
1 ATCGCAACGCGATACTAACT
* * * *
10634 TTCGCAACGTGATTCTGACT
1 ATCGCAACGCGATACTAACT
* * * *
10654 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTAACT
*
10674 ATCGCAACGAGATA
1 ATCGCAACGCGATA
10688 ATACATAATT
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 63 0.62
21 38 0.38
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTAACT
Found at i:11258 original size:20 final size:20
Alignment explanation
Indices: 11233--11288 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
11223 CAACGGGGAA
11233 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
11253 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
11273 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
11289 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:11331 original size:14 final size:14
Alignment explanation
Indices: 11312--11365 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
11302 GAAAATCGCA
11312 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
11326 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
11343 CATTGCGATTCTCTCG
1 --TTGCGATTTTCTCG
11359 TTGCGAT
1 TTGCGAT
11366 AGTCAATTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:11331 original size:33 final size:33
Alignment explanation
Indices: 11294--11364 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
11284 AAAATCGCAA
*
11294 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
** ** **
11327 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
11360 TGCGA
1 TGCGA
11365 TAGTCAATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
Found at i:12977 original size:41 final size:42
Alignment explanation
Indices: 12923--13014 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
12913 CCTCTTCAAC
* *
12923 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
12964 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
13006 GATGACAGG
1 GATGACAGG
13015 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 20 0.44
42 25 0.56
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:12979 original size:21 final size:21
Alignment explanation
Indices: 12950--13010 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
12940 GAACGGTGGG
*
12950 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
12971 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
12992 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
13011 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:13376 original size:20 final size:20
Alignment explanation
Indices: 13351--13403 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
13341 GAATAATAGT
*
13351 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
13371 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* *
13391 TAACTATCGCAAC
1 TTACTTTCGCAAC
13404 GCGGAAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.25
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:13431 original size:19 final size:19
Alignment explanation
Indices: 13357--13443 Score: 84
Period size: 20 Copynumber: 4.4 Consensus size: 19
13347 TAGTTTACTT
* * *
13357 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAA-TGACTA
*
13377 TCGCAACGCGAAAATAACTA
1 TCGCAACGCG-AAATGACTA
*
13397 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACTA
**
13417 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
13436 TCGCAACG
1 TCGCAACG
13444 ACAAAATCTC
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
19 15 0.26
20 38 0.67
21 4 0.07
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:13451 original size:14 final size:14
Alignment explanation
Indices: 13432--13488 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
13422 ACGCGAAATG
13432 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
13446 AAAATCTCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
13465 AAAATCGCAACGAC
1 AAAATCGCAACGAC
13479 AAAATCGCAA
1 AAAATCGCAA
13489 TGCGAAACAC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.51, C:0.23, G:0.14, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:13506 original size:33 final size:33
Alignment explanation
Indices: 13416--13495 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
13406 GGAAATGGCT
*
13416 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
13449 ATCTCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
13482 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
13496 CACAAATCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:13524 original size:19 final size:19
Alignment explanation
Indices: 13502--13598 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
13492 GAAACACAAA
13502 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
13521 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
13537 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
13554 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
13570 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
13587 TCGCATTGCGAT
1 TCGCATTGCGAT
13599 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 12 0.19
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 23 0.37
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:13543 original size:14 final size:14
Alignment explanation
Indices: 13524--13582 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
13514 TTTCATTTCG
13524 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
13538 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
13555 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
13571 CGTTGCGATTTT
1 CGTTGCGATTTT
13583 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:13549 original size:33 final size:33
Alignment explanation
Indices: 13507--13598 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
13497 ACAAATCGCA
*
13507 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
13540 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
13573 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
13599 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:13605 original size:19 final size:20
Alignment explanation
Indices: 13583--13626 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
13573 TTGCGATTTT
13583 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
** *
13602 CATTTCCGTGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
13622 CATTT
1 CATTT
13627 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:13617 original size:20 final size:20
Alignment explanation
Indices: 13592--13637 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
13582 TCATTTCGCA
13592 TTGCGATAGCCATTTCCGTG
1 TTGCGATAGCCATTTCCGTG
* *
13612 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGTG
13632 TTGCGA
1 TTGCGA
13638 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.39
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGTG
Found at i:15575 original size:20 final size:20
Alignment explanation
Indices: 15527--15585 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
15517 AATAGTTTCT
* *
15527 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
15547 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
15567 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
15586 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:15861 original size:22 final size:22
Alignment explanation
Indices: 15834--15877 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
15824 GATGGAGATA
15834 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
15856 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
15878 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:16092 original size:20 final size:20
Alignment explanation
Indices: 16064--16134 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
16054 GATTATGTAT
* *
16064 TATCTCGTTACGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
16084 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
16104 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
16124 TATCGCGTTGC
1 TATCGCGTTGC
16135 AATTTTGTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:16166 original size:41 final size:41
Alignment explanation
Indices: 16044--16181 Score: 138
Period size: 41 Copynumber: 3.4 Consensus size: 41
16034 CGCTTTGAAA
* * * *
16044 ATCGCATTGCGATTATGTATTATCTCGTTACGAAAGTCAGT
1 ATCGCATTGCAATTTTGTATTATCACGTTGCGAAAGTCAGT
* * * *
16085 ATCGCGTTGCGAA---AGTAAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGC-AATTTTGT-ATTATCACGTTGCGAAAGTCAGT
* *
16125 ATCGCGTTGCAATTTTGTATTATCACGTTGCGATAGTCAGT
1 ATCGCATTGCAATTTTGTATTATCACGTTGCGAAAGTCAGT
*
16166 ATCGCATTGCGATTTT
1 ATCGCATTGCAATTTT
16182 CCCAATTCGC
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
39 4 0.05
40 30 0.38
41 43 0.54
42 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCAATTTTGTATTATCACGTTGCGAAAGTCAGT
Found at i:16175 original size:20 final size:20
Alignment explanation
Indices: 16064--16178 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
16054 GATTATGTAT
* * *
16064 TATCTCGTTACGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
16084 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
*
16104 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
16124 TATCGCGTTGCAATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
*
16145 TATCACGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
16165 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
16179 TTTCCCAATT
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
19 3 0.04
20 61 0.78
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:16195 original size:41 final size:41
Alignment explanation
Indices: 16104--16199 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
16094 CGAAAGTAAG
* * ** *
16104 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCAATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAA
* *
16145 TATCACGTTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTT-CCAA
16187 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
16200 TTACTTATTC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAA
Found at i:16260 original size:21 final size:22
Alignment explanation
Indices: 16208--16260 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
16198 ATTTACTTAT
16208 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
16229 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
16250 TCGCATTGCGA
1 TCGCATTGCGA
16261 TATTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:21170 original size:47 final size:47
Alignment explanation
Indices: 21116--21333 Score: 161
Period size: 47 Copynumber: 4.6 Consensus size: 47
21106 TGTTGGTTAG
* * *
21116 GATCCGATATCACTAATTATCATGTACTTTAACCACCGACCGGTTCA
1 GATCCGATATTATTAATTATCATGTACATTAACCACCGACCGGTTCA
* * ** ** *
21163 GATCCGATATTATTGATTACCATGTACATTAACCAATTG-GTGGTTCG
1 GATCCGATATTATTAATTATCATGTACATTAACC-ACCGACCGGTTCA
** * * * * ** *
21210 GATATGATATTGTTGATTTTCATGTACATTAACCACCAATTGGTTCG
1 GATCCGATATTATTAATTATCATGTACATTAACCACCGACCGGTTCA
** * * *
21257 GATTTGATATTATTAATTATCAAT-TACATTAACTACTGACCGGTTTA
1 GATCCGATATTATTAATTATC-ATGTACATTAACCACCGACCGGTTCA
* * *
21304 AATCCGATATCACTAATTATCATGTACATT
1 GATCCGATATTATTAATTATCATGTACATT
21334 GCAAGTTCAA
Statistics
Matches: 132, Mismatches: 35, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
46 3 0.02
47 125 0.95
48 4 0.03
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (47 bp):
GATCCGATATTATTAATTATCATGTACATTAACCACCGACCGGTTCA
Found at i:21480 original size:14 final size:13
Alignment explanation
Indices: 21432--21479 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
21422 TAAAAGACAA
*
21432 ATTTTATTATTAT
1 ATTTTATTTTTAT
*
21445 ATTTGTATTTGTAT
1 ATTT-TATTTTTAT
*
21459 TTTTTATATTTTAT
1 ATTTTAT-TTTTAT
21473 ATTTTAT
1 ATTTTAT
21480 ACAATCTTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 7 0.25
14 21 0.75
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (13 bp):
ATTTTATTTTTAT
Found at i:28139 original size:3 final size:3
Alignment explanation
Indices: 28124--28162 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
28114 GGGGTGATTT
* *
28124 GGA GGA AGA GGA GGA GGA GGA GGA GGA AGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
28163 AGAAGAAGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:28144 original size:15 final size:15
Alignment explanation
Indices: 28124--28190 Score: 71
Period size: 15 Copynumber: 4.3 Consensus size: 15
28114 GGGGTGATTT
* *
28124 GGAGGAAGAGGAGGA
1 GGAGGAGGAGGAAGA
28139 GGAGGAGGAGGAAGA
1 GGAGGAGGAGGAAGA
*
28154 GGAGGAGGAAGAAGA
1 GGAGGAGGAGGAAGA
*
28169 AGAGGAGATTGAGGAAGA
1 GGAGGAG---GAGGAAGA
28187 GGAG
1 GGAG
28191 TTAGAGGATG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
15 33 0.77
18 10 0.23
ACGTcount: A:0.42, C:0.00, G:0.55, T:0.03
Consensus pattern (15 bp):
GGAGGAGGAGGAAGA
Found at i:31192 original size:240 final size:240
Alignment explanation
Indices: 30782--31236 Score: 901
Period size: 240 Copynumber: 1.9 Consensus size: 240
30772 TTTCTAGCTC
*
30782 TCTCTTGACGGGGTCAAGAAAAGGTTGAGATAATCTTCGTTTACGTCTTCAACAACATGGCTGAC
1 TCTCTTGACGGAGTCAAGAAAAGGTTGAGATAATCTTCGTTTACGTCTTCAACAACATGGCTGAC
30847 AAGAAGATCGTTCATAGCTATATTCCAGTCCCTTGTAAAGCGAAGGAAGCATTGAGTTTTTATTA
66 AAGAAGATCGTTCATAGCTATATTCCAGTCCCTTGTAAAGCGAAGGAAGCATTGAGTTTTTATTA
30912 TTATTGAGTTGTACGGGTTTATGACCCCATTATTGGAAAGAACCAAAGGGAAGAAGAGAGTTGGG
131 TTATTGAGTTGTACGGGTTTATGACCCCATTATTGGAAAGAACCAAAGGGAAGAAGAGAGTTGGG
30977 GTTTTAACGGCTGACAACAATAATTTTATATTTAATTTCCCACTT
196 GTTTTAACGGCTGACAACAATAATTTTATATTTAATTTCCCACTT
31022 TCTCTTGACGGAGTCAAGAAAAGGTTGAGATAATCTTCGTTTACGTCTTCAACAACATGGCTGAC
1 TCTCTTGACGGAGTCAAGAAAAGGTTGAGATAATCTTCGTTTACGTCTTCAACAACATGGCTGAC
31087 AAGAAGATCGTTCATAGCTATATTCCAGTCCCTTGTAAAGCGAAGGAAGCATTGAGTTTTTATTA
66 AAGAAGATCGTTCATAGCTATATTCCAGTCCCTTGTAAAGCGAAGGAAGCATTGAGTTTTTATTA
31152 TTATTGAGTTGTACGGGTTTATGACCCCATTATTGGAAAGAACCAAAGGGAAGAAGAGAGTTGGG
131 TTATTGAGTTGTACGGGTTTATGACCCCATTATTGGAAAGAACCAAAGGGAAGAAGAGAGTTGGG
31217 GTTTTAACGGCTGACAACAA
196 GTTTTAACGGCTGACAACAA
31237 GATTCAATGG
Statistics
Matches: 214, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
240 214 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (240 bp):
TCTCTTGACGGAGTCAAGAAAAGGTTGAGATAATCTTCGTTTACGTCTTCAACAACATGGCTGAC
AAGAAGATCGTTCATAGCTATATTCCAGTCCCTTGTAAAGCGAAGGAAGCATTGAGTTTTTATTA
TTATTGAGTTGTACGGGTTTATGACCCCATTATTGGAAAGAACCAAAGGGAAGAAGAGAGTTGGG
GTTTTAACGGCTGACAACAATAATTTTATATTTAATTTCCCACTT
Found at i:35633 original size:66 final size:66
Alignment explanation
Indices: 35527--35855 Score: 577
Period size: 66 Copynumber: 5.0 Consensus size: 66
35517 CAGATCCCCG
* * * *
35527 GTTTCGTCAACAGATTCACCATTTTCTTCTTCACCTTGTTCCTCAATCATAACCTTGTTTTGATT
1 GTTTCATCAACAAATTCACCATTTTCTTCTTTACCTTGTTCCTCAATCATAACCTTGTTTTGCTT
35592 C
66 C
* * *
35593 GTTTCGTCAACAACTTCCCCATTTTCTTCTTTACCTTGTTCCTCAATCATAACCTTGTTTTGCTT
1 GTTTCATCAACAAATTCACCATTTTCTTCTTTACCTTGTTCCTCAATCATAACCTTGTTTTGCTT
35658 C
66 C
35659 GTTTCATCAACAAATTCACCATTTTCTTCTTTACCTTGTTCCTCAATCATAACCTTGTTTTGCTT
1 GTTTCATCAACAAATTCACCATTTTCTTCTTTACCTTGTTCCTCAATCATAACCTTGTTTTGCTT
35724 C
66 C
35725 GTTTCATCAACAAATTCACCATTTTCTTCTTTACCTTGTTCCTCAATCATAACCTTGTTTTGCTT
1 GTTTCATCAACAAATTCACCATTTTCTTCTTTACCTTGTTCCTCAATCATAACCTTGTTTTGCTT
35790 C
66 C
* *
35791 GTTTCATCAACAAATTCACCATTTTCTTCATTACCTTGTTCCTCAATCATATCCTTGTTTTGCTT
1 GTTTCATCAACAAATTCACCATTTTCTTCTTTACCTTGTTCCTCAATCATAACCTTGTTTTGCTT
35856 AAAAAAACTG
Statistics
Matches: 253, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 253 1.00
ACGTcount: A:0.20, C:0.28, G:0.07, T:0.45
Consensus pattern (66 bp):
GTTTCATCAACAAATTCACCATTTTCTTCTTTACCTTGTTCCTCAATCATAACCTTGTTTTGCTT
C
Found at i:38375 original size:25 final size:25
Alignment explanation
Indices: 38347--38397 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
38337 TAAAATATTC
*
38347 ATAATTAT-AATTAAGATGTATAATT
1 ATAATTATAAATT-AGATATATAATT
38372 ATAATTATAAATTAGATATATAATT
1 ATAATTATAAATTAGATATATAATT
38397 A
1 A
38398 GGATATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (25 bp):
ATAATTATAAATTAGATATATAATT
Found at i:39370 original size:29 final size:31
Alignment explanation
Indices: 39338--39400 Score: 103
Period size: 29 Copynumber: 2.1 Consensus size: 31
39328 ATTTTTTTCG
*
39338 CAAACTTTCTAAAATAAT-AATTAAGCCC-T
1 CAAACTTTCTAAAAAAATCAATTAAGCCCAT
39367 CAAACTTTCTAAAAAAATCAATTAAGCCCAT
1 CAAACTTTCTAAAAAAATCAATTAAGCCCAT
39398 CAA
1 CAA
39401 CCATGTTATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 17 0.55
30 10 0.32
31 4 0.13
ACGTcount: A:0.48, C:0.22, G:0.03, T:0.27
Consensus pattern (31 bp):
CAAACTTTCTAAAAAAATCAATTAAGCCCAT
Found at i:40143 original size:17 final size:15
Alignment explanation
Indices: 40105--40135 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40095 AAATTCTAAA
*
40105 TATTTAAATAAAAAT
1 TATTTATATAAAAAT
40120 TATTTATATAAAAAT
1 TATTTATATAAAAAT
40135 T
1 T
40136 CTATTTATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTATATAAAAAT
Found at i:46283 original size:32 final size:32
Alignment explanation
Indices: 46221--46309 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 32
46211 ATCTCAAGTC
* * *
46221 ATCACCTTTGATGACATG-TCCTATGACACGTT
1 ATCACCTTGGATGACATGATAC-ATGTCACGTT
* * *
46253 ATTATCTTGGATGATATGATACATGTCACGTT
1 ATCACCTTGGATGACATGATACATGTCACGTT
* *
46285 ATCACCTTGGGTGACATGGTACATG
1 ATCACCTTGGATGACATGATACATG
46310 CTATTTCATC
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
32 43 0.96
33 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (32 bp):
ATCACCTTGGATGACATGATACATGTCACGTT
Found at i:46713 original size:8 final size:8
Alignment explanation
Indices: 46700--47716 Score: 1674
Period size: 8 Copynumber: 127.1 Consensus size: 8
46690 TGAATAATAC
46700 ATGTATGT
1 ATGTATGT
46708 ATGTATGT
1 ATGTATGT
46716 ATGTATGT
1 ATGTATGT
46724 ATGTATGT
1 ATGTATGT
46732 ATGTATGT
1 ATGTATGT
46740 ATGTATGT
1 ATGTATGT
46748 ATGTATGT
1 ATGTATGT
46756 ATGTATGT
1 ATGTATGT
*
46764 ATGTATGC
1 ATGTATGT
* *
46772 GTGTATGC
1 ATGTATGT
46780 ATGTATGT
1 ATGTATGT
46788 ATGTATGT
1 ATGTATGT
46796 ATGTATGT
1 ATGTATGT
46804 ATGTATGT
1 ATGTATGT
46812 ATGTATGT
1 ATGTATGT
46820 ATGTATGT
1 ATGTATGT
46828 ATGTATGT
1 ATGTATGT
46836 ATGTATGT
1 ATGTATGT
**
46844 ATGCGTGT
1 ATGTATGT
*
46852 ATGCATGT
1 ATGTATGT
46860 ATGTATGT
1 ATGTATGT
46868 ATGTATGT
1 ATGTATGT
46876 ATGTATGT
1 ATGTATGT
46884 ATGTATGT
1 ATGTATGT
46892 ATGTATGT
1 ATGTATGT
46900 ATGTATGT
1 ATGTATGT
46908 ATGTATGT
1 ATGTATGT
*
46916 ATGTATGC
1 ATGTATGT
* *
46924 GTGTATGC
1 ATGTATGT
46932 ATGTATGT
1 ATGTATGT
46940 ATGTATGT
1 ATGTATGT
46948 ATGTATGT
1 ATGTATGT
46956 ATGTATGT
1 ATGTATGT
46964 ATGTATGT
1 ATGTATGT
46972 ATGTATGT
1 ATGTATGT
46980 ATGTATGT
1 ATGTATGT
46988 ATGTATGT
1 ATGTATGT
46996 ATGTATGT
1 ATGTATGT
47004 ATGTATGT
1 ATGTATGT
47012 ATGTATGT
1 ATGTATGT
47020 ATGTATGT
1 ATGTATGT
*
47028 ATGTATGC
1 ATGTATGT
*
47036 ATGTATGC
1 ATGTATGT
*
47044 ATGTATGC
1 ATGTATGT
*
47052 ATGTATGC
1 ATGTATGT
*
47060 ATGTATGC
1 ATGTATGT
*
47068 ATGTATGC
1 ATGTATGT
* *
47076 ATGCATGC
1 ATGTATGT
*
47084 ATGTATGC
1 ATGTATGT
* *
47092 ATGCATGC
1 ATGTATGT
*
47100 ATGTATGC
1 ATGTATGT
* *
47108 ATGCATGC
1 ATGTATGT
* *
47116 ATGCATGC
1 ATGTATGT
47124 ATGTATGT
1 ATGTATGT
47132 ATGTATGT
1 ATGTATGT
47140 ATGTATGT
1 ATGTATGT
*
47148 ATGTATGC
1 ATGTATGT
47156 ATGTATGT
1 ATGTATGT
*
47164 ATGTATGC
1 ATGTATGT
*
47172 ATGTATGC
1 ATGTATGT
*
47180 ATGTATGC
1 ATGTATGT
*
47188 ATGTATGC
1 ATGTATGT
*
47196 ATGTATGC
1 ATGTATGT
*
47204 ATGTATGC
1 ATGTATGT
*
47212 ATGTATGC
1 ATGTATGT
*
47220 ATGTATGC
1 ATGTATGT
47228 ATGTATGT
1 ATGTATGT
*
47236 ATGTATGC
1 ATGTATGT
47244 ATGTATGT
1 ATGTATGT
*
47252 ATGTATGC
1 ATGTATGT
*
47260 ATGTATGC
1 ATGTATGT
47268 ATGTATGT
1 ATGTATGT
47276 ATGTATGT
1 ATGTATGT
47284 ATGTATGT
1 ATGTATGT
47292 ATGTATGT
1 ATGTATGT
47300 ATGTATGT
1 ATGTATGT
47308 ATGTATGT
1 ATGTATGT
47316 ATGTATGT
1 ATGTATGT
47324 ATGTATGT
1 ATGTATGT
47332 ATGTATGT
1 ATGTATGT
47340 ATGTATGT
1 ATGTATGT
47348 ATGTATGT
1 ATGTATGT
47356 ATGTATGT
1 ATGTATGT
47364 ATGTATGT
1 ATGTATGT
*
47372 ATGCATGT
1 ATGTATGT
*
47380 ATGCATGT
1 ATGTATGT
*
47388 ATGCATGT
1 ATGTATGT
47396 ATGTATGT
1 ATGTATGT
47404 ATGTATGT
1 ATGTATGT
47412 ATGTATGT
1 ATGTATGT
47420 ATGTATGT
1 ATGTATGT
47428 ATGTATGT
1 ATGTATGT
47436 ATGTATGT
1 ATGTATGT
47444 ATGTATGT
1 ATGTATGT
47452 ATGTATGT
1 ATGTATGT
47460 ATGTATGT
1 ATGTATGT
47468 ATGTATGT
1 ATGTATGT
47476 ATGTATGT
1 ATGTATGT
47484 ATGTATGT
1 ATGTATGT
47492 ATGTATGT
1 ATGTATGT
47500 ATGTATGT
1 ATGTATGT
47508 ATGTATGT
1 ATGTATGT
47516 ATGTATGT
1 ATGTATGT
47524 ATGTATGT
1 ATGTATGT
47532 ATGTATGT
1 ATGTATGT
47540 ATGTATGT
1 ATGTATGT
47548 ATGTATGT
1 ATGTATGT
47556 ATGTATGT
1 ATGTATGT
47564 ATGTATGT
1 ATGTATGT
47572 ATGTATGT
1 ATGTATGT
47580 ATGTATGT
1 ATGTATGT
47588 ATGTATGT
1 ATGTATGT
47596 ATGTATGT
1 ATGTATGT
47604 ATGTATGT
1 ATGTATGT
47612 ATGTATGT
1 ATGTATGT
47620 ATGTATGT
1 ATGTATGT
47628 ATGTATGT
1 ATGTATGT
47636 ATGTATGT
1 ATGTATGT
47644 ATGTATGT
1 ATGTATGT
47652 ATGTATGT
1 ATGTATGT
47660 ATGTATGT
1 ATGTATGT
47668 ATGTATGT
1 ATGTATGT
47676 ATGTATGT
1 ATGTATGT
47684 ATGTATGT
1 ATGTATGT
47692 ATGTATGT
1 ATGTATGT
47700 ATGTATGT
1 ATGTATGT
47708 ATGTATGT
1 ATGTATGT
47716 A
1 A
47717 CATGAAGATT
Statistics
Matches: 979, Mismatches: 30, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 979 1.00
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (8 bp):
ATGTATGT
Found at i:48121 original size:10 final size:10
Alignment explanation
Indices: 48094--48123 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
48084 AAATTAAATA
48094 TATATTATTT
1 TATATTATTT
48104 TATAATTATTT
1 TAT-ATTATTT
48115 TATATTATT
1 TATATTATT
48124 CAAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TATATTATTT
Found at i:51705 original size:2 final size:2
Alignment explanation
Indices: 51668--51692 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
51658 ATTTTAATGT
51668 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 T
51693 TCGTGTCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53893 original size:72 final size:71
Alignment explanation
Indices: 53787--53923 Score: 195
Period size: 72 Copynumber: 1.9 Consensus size: 71
53777 AAATGGAGCC
* * * *
53787 CACTGAATTATCATATTTTCGAATTTTTTAAATAAAAAATGATGTTT-AAAATATTTTTTAATTA
1 CACTAAATTACCATATTTTCGAATATTTGAAAT-AAAAAT-ATGTTTAAAAATATTTTTTAATTA
53851 TTGAGTCA
64 TTGAGTCA
* *
53859 CACTAAATTACCATATTTTTGAATATTTGAAATAAAAATATTTTTAAAAATATTTTTTAATTATT
1 CACTAAATTACCATATTTTCGAATATTTGAAATAAAAATATGTTTAAAAATATTTTTTAATTATT
53924 AAACTTAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
70 5 0.09
71 25 0.43
72 28 0.48
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.47
Consensus pattern (71 bp):
CACTAAATTACCATATTTTCGAATATTTGAAATAAAAATATGTTTAAAAATATTTTTTAATTATT
GAGTCA
Found at i:53918 original size:13 final size:12
Alignment explanation
Indices: 53891--53915 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53881 ATATTTGAAA
53891 TAAAAATATTTT
1 TAAAAATATTTT
53903 TAAAAATATTTT
1 TAAAAATATTTT
53915 T
1 T
53916 TAATTATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAAATATTTT
Found at i:54118 original size:17 final size:17
Alignment explanation
Indices: 54096--54135 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
54086 TGTTATTTTG
54096 TCAAGTCTCACGACTAT
1 TCAAGTCTCACGACTAT
*
54113 TCAAGTCTCATGACTAT
1 TCAAGTCTCACGACTAT
*
54130 TAAAGT
1 TCAAGT
54136 TACAAAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (17 bp):
TCAAGTCTCACGACTAT
Found at i:60188 original size:37 final size:37
Alignment explanation
Indices: 60138--60212 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
60128 AGAAAGACGC
*
60138 ATGATGAAGTCAACGTCTTCTGTATGACCTGGGAAAG
1 ATGATGAACTCAACGTCTTCTGTATGACCTGGGAAAG
*
60175 ATGATGCACTCAACGTCTTCTGTATGACCTGGGAAAG
1 ATGATGAACTCAACGTCTTCTGTATGACCTGGGAAAG
60212 A
1 A
60213 CGCATGAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (37 bp):
ATGATGAACTCAACGTCTTCTGTATGACCTGGGAAAG
Found at i:60360 original size:12 final size:12
Alignment explanation
Indices: 60339--60369 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
60329 GTCTTCTCTT
60339 TTTCACTGTTCA
1 TTTCACTGTTCA
*
60351 TTTCATTGTTCA
1 TTTCACTGTTCA
60363 TTTCACT
1 TTTCACT
60370 CCAGTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.16, C:0.23, G:0.06, T:0.55
Consensus pattern (12 bp):
TTTCACTGTTCA
Found at i:60506 original size:16 final size:16
Alignment explanation
Indices: 60485--60517 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
60475 AAAATTTAAC
*
60485 ATTTTTAAATATTTTT
1 ATTTTTAAATATATTT
60501 ATTTTTAAATATATTT
1 ATTTTTAAATATATTT
60517 A
1 A
60518 AATAAGAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTTAAATATATTT
Found at i:61745 original size:31 final size:33
Alignment explanation
Indices: 61709--61774 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 33
61699 AAACATGAAA
* *
61709 AATAAGTTGGTCACCTACCAA-A-GAATTTTCC
1 AATAAGTTGGTCACCAACCAAGATGAAATTTCC
61740 AATAAGTTGGTCACCAACCAAGATGAAATTTCC
1 AATAAGTTGGTCACCAACCAAGATGAAATTTCC
61773 AA
1 AA
61775 CTTGTCAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 20 0.65
32 1 0.03
33 10 0.32
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (33 bp):
AATAAGTTGGTCACCAACCAAGATGAAATTTCC
Found at i:66387 original size:33 final size:33
Alignment explanation
Indices: 66323--66421 Score: 157
Period size: 33 Copynumber: 3.1 Consensus size: 33
66313 AAACATGAAA
* *
66323 AATAAGTTGGTCACCTACCAA-A-GAATTTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
66354 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
*
66387 AATAAGTTGGCCACCAACCAAGATGAAATTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
66420 AA
1 AA
66422 CTTGCCAACT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
31 19 0.30
32 1 0.02
33 43 0.68
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.24
Consensus pattern (33 bp):
AATAAGTTGGCCACCAACCAAGATGAATTTTCC
Found at i:70536 original size:9 final size:9
Alignment explanation
Indices: 70522--70548 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
70512 AACGTTAAGC
70522 ACCAAAATG
1 ACCAAAATG
70531 ACCAAAATG
1 ACCAAAATG
70540 ACCAAAATG
1 ACCAAAATG
70549 CCCTTATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.22, G:0.11, T:0.11
Consensus pattern (9 bp):
ACCAAAATG
Found at i:71921 original size:31 final size:31
Alignment explanation
Indices: 71850--71923 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
71840 CTAATGTGAC
* * *
71850 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCCGAAATCAT
*
71881 TCTCAGGTAGGCCCTGCGGCCCCGAAATC-T
1 TCTTAGGTAGGCCCTGCGGCCCCGAAATCAT
*
71911 ATCTTGGGTAGGC
1 -TCTTAGGTAGGC
71924 TCTAAGGCCC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCCGAAATCAT
Found at i:73408 original size:36 final size:36
Alignment explanation
Indices: 73368--73437 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
73358 TAATATTTTT
* *
73368 TATTATAATCGAAAATATTCA-AATATTAACATTTCC
1 TATTATAATAGAAAATATT-ATAAAATTAACATTTCC
*
73404 TATTATAATATAAAATATTATAAAATTAACATTT
1 TATTATAATAGAAAATATTATAAAATTAACATTT
73438 AAATTATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 1 0.03
36 29 0.97
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (36 bp):
TATTATAATAGAAAATATTATAAAATTAACATTTCC
Found at i:81313 original size:199 final size:197
Alignment explanation
Indices: 80960--81550 Score: 843
Period size: 199 Copynumber: 3.0 Consensus size: 197
80950 TTTCTCCACT
* * *
80960 TTCTTAGGTATGCAAGCTACTTTTCAAAATGCATAACTTAGATTTGAAA-CTATGTTGTTTCGTT
1 TTCTTAGGTATG-AAGCTACTTCTCAAAATGCATAACTTAGA-TTCAAATCTATGTTGTTTAGTT
* * *
81024 TCTTCATTTTTGTTAAATTATAGTGTTCGAAACTTGTGTTGCGACACTTGCATACGAGTCCGAGT
64 TCTTCATTTTTGTTGAATTATCGTGTTCGAAACTTATGTTGCGACACTTGCATACGAGTCCGAGT
*
81089 AAACACCTAGGACCCCAGACAAGAGGAAAATGATGAATGTTAATTTTATGCAGCACTGACCCTGT
129 AAACACCTAGGACCCCAGACAAGAGGAAAATGATGAATGTTAATTTTATGCAGGACTGACCCTGT
81154 GTCA
194 GTCA
* * * *
81158 TTCTTAAGTATGAGAGCTACTTGTCAAACTGCATAACTTAGATTCAAATCTATGTTGTCTAGTTT
1 TTCTTAGGTATGA-AGCTACTTCTCAAAATGCATAACTTAGATTCAAATCTATGTTGTTTAGTTT
* * *
81223 CTTCATATTTTCTTGAATTATCGTGTTCGGAACTTATGTTGCGACACTTGCATATGAGTCCGAGT
65 CTTCAT-TTTTGTTGAATTATCGTGTTCGAAACTTATGTTGCGACACTTGCATACGAGTCCGAGT
81288 AAACACCTAGGACCCCAGACAAGAGGAAAATGATGAATGTTAATTTTATGCAGGACTGACCCTGT
129 AAACACCTAGGACCCCAGACAAGAGGAAAATGATGAATGTTAATTTTATGCAGGACTGACCCTGT
*
81353 GTCT
194 GTCA
* * *
81357 TTCTTAGGTATACAAGCTACATCTCAAAATGCCA-AACTTAGATTCAAATCTATGTTGTTTTGTT
1 TTCTTAGGTAT-GAAGCTACTTCTCAAAATG-CATAACTTAGATTCAAATCTATGTTGTTTAGTT
* *
81421 TCTTGATTTTTTGTTGAATTATCGTGTTCGAAACTTATG-TGCAACACTTGCATACGAGTCCGAG
64 TCTTCA-TTTTTGTTGAATTATCGTGTTCGAAACTTATGTTGCGACACTTGCATACGAGTCCGAG
* ** * **
81485 TAAATACCTAGGATACCAGAC--GAGGAAAATGATGAATGTTAA-CTTATGCAGGGTTGACCCTG
128 TAAACACCTAGGACCCCAGACAAGAGGAAAATGATGAATGTTAATTTTATGCAGGACTGACCCTG
81547 TGTC
193 TGTC
81551 TTTTCTGGAA
Statistics
Matches: 355, Mismatches: 32, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
195 21 0.06
196 21 0.06
197 6 0.02
198 98 0.28
199 205 0.58
200 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (197 bp):
TTCTTAGGTATGAAGCTACTTCTCAAAATGCATAACTTAGATTCAAATCTATGTTGTTTAGTTTC
TTCATTTTTGTTGAATTATCGTGTTCGAAACTTATGTTGCGACACTTGCATACGAGTCCGAGTAA
ACACCTAGGACCCCAGACAAGAGGAAAATGATGAATGTTAATTTTATGCAGGACTGACCCTGTGT
CA
Done.