Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006151.1 Hibiscus syriacus cultivar Beakdansim tig00014612_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: 72574
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:8928 original size:32 final size:31
Alignment explanation
Indices: 8867--8929 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 31
8857 ACATGTAATC
*
8867 TTATTTCTAAGGAATTCAGGATTCAAAAAAAA
1 TTATTTCTAAGGAATTCAGAATT-AAAAAAAA
*
8899 TTATTTTTAAGGAATTCAAGAAATTAAAAAA
1 TTATTTCTAAGGAATTC-AG-AATTAAAAAA
8930 TAGGCATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 16 0.59
33 8 0.30
34 3 0.11
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.33
Consensus pattern (31 bp):
TTATTTCTAAGGAATTCAGAATTAAAAAAAA
Found at i:10298 original size:13 final size:13
Alignment explanation
Indices: 10280--10329 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
10270 TGTTTGGCTT
*
10280 TGCTTTTGAAAAG
1 TGCTTTTGAAAAA
*
10293 TGCTTTGGAAAAA
1 TGCTTTTGAAAAA
10306 TGCTTTT-AAGAAA
1 TGCTTTTGAA-AAA
10319 TGCTTTTGAAA
1 TGCTTTTGAAA
10330 CGAGTAGGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 2 0.06
13 28 0.88
14 2 0.06
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAA
Found at i:13032 original size:18 final size:19
Alignment explanation
Indices: 13004--13044 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
12994 ATAAAATCTA
13004 ATTTCCCCTCTTTTTCTTC-
1 ATTTCCCCTC-TTTTCTTCT
13023 ATTT-CCCTCTTTTCTTCT
1 ATTTCCCCTCTTTTCTTCT
13041 ATTT
1 ATTT
13045 TTTCTTCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 9 0.43
19 4 0.19
ACGTcount: A:0.07, C:0.32, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTCCCCTCTTTTCTTCT
Found at i:14065 original size:31 final size:31
Alignment explanation
Indices: 14030--14100 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
14020 ATATATATAT
14030 TCACTAAATTATAAGAATGGTTTTATTTTGA
1 TCACTAAATTATAAGAATGGTTTTATTTTGA
14061 TCACTAAATTATAAGAATGGTTTTATTTTGA
1 TCACTAAATTATAAGAATGGTTTTATTTTGA
*
14092 TCACGAAAT
1 TCACTAAAT
14101 CAAAAATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (31 bp):
TCACTAAATTATAAGAATGGTTTTATTTTGA
Found at i:14532 original size:10 final size:10
Alignment explanation
Indices: 14517--14556 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
14507 TTTATCACAC
14517 CAAATTCTCT
1 CAAATTCTCT
14527 CAAATTCTCT
1 CAAATTCTCT
14537 -AAATTTCTCT
1 CAAA-TTCTCT
*
14547 CAAATACTCT
1 CAAATTCTCT
14557 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:20087 original size:2 final size:2
Alignment explanation
Indices: 20080--20105 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20070 TTTTAAGTGA
20080 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
20106 TCATCACGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28036 original size:22 final size:21
Alignment explanation
Indices: 28006--28048 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
27996 CCGGAAATAT
*
28006 TAAAAAATATTGATTTTAGGTA
1 TAAAAAATAATG-TTTTAGGTA
*
28028 TAAATAATAATGTTTTAGGTA
1 TAAAAAATAATGTTTTAGGTA
28049 ATTTTTACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (21 bp):
TAAAAAATAATGTTTTAGGTA
Found at i:28196 original size:24 final size:25
Alignment explanation
Indices: 28169--28237 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
28159 AACATCAAAT
28169 ACAATAA-AATAATATTATTTATTA
1 ACAATAAGAATAATATTATTTATTA
*
28193 ACAA-AATAATAATATTATTT-TTA
1 ACAATAAGAATAATATTATTTATTA
28216 A-AATATTAGAATAAT-TTATTTA
1 ACAATA--AGAATAATATTATTTA
28238 ATATTATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.05
23 7 0.18
24 23 0.59
25 7 0.18
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (25 bp):
ACAATAAGAATAATATTATTTATTA
Found at i:28399 original size:33 final size:28
Alignment explanation
Indices: 28340--28402 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 28
28330 ATTATAAATT
*
28340 ATATATATTATTTATTATAATAAGAATA
1 ATATATATTATTTATCATAATAAGAATA
28368 ATATATCATTAATTATATCATAATGAGAGAATA
1 ATATAT-ATT-ATT-TATCATAAT-A-AGAATA
28401 AT
1 AT
28403 GAAACATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 6 0.21
29 3 0.10
30 3 0.10
31 8 0.28
32 1 0.03
33 8 0.28
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.41
Consensus pattern (28 bp):
ATATATATTATTTATCATAATAAGAATA
Found at i:28930 original size:24 final size:23
Alignment explanation
Indices: 28892--28948 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
28882 ATTTGCAATG
28892 TTTTATT-TTAAAAATAATATTA
1 TTTTATTGTTAAAAATAATATTA
28914 TTATT-TTGTTAATAAATAATATTA
1 TT-TTATTGTTAA-AAATAATATTA
28938 TTTTATTGTTA
1 TTTTATTGTTA
28949 TCCTTTGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.13
23 8 0.26
24 19 0.61
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTTATTGTTAAAAATAATATTA
Found at i:29654 original size:21 final size:20
Alignment explanation
Indices: 29568--29725 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
29558 AAATGACCAA
**
29568 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
29587 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
29607 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
29627 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
29648 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
29669 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
29689 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
29710 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
29726 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:29716 original size:20 final size:20
Alignment explanation
Indices: 29692--29905 Score: 243
Period size: 20 Copynumber: 10.7 Consensus size: 20
29682 CGATTTTCCA
* ** *
29692 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
29712 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
29732 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
29752 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
29772 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
**
29792 AAATCGCAACGCGTATGTGT
1 AAATCGCAACGCGTATCCGT
*
29812 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
29832 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
29852 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
29872 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
29893 AAATCGCAACGCG
1 AAATCGCAACGCG
29906 ATATTTAAAG
Statistics
Matches: 165, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 145 0.88
21 17 0.10
22 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:30326 original size:33 final size:33
Alignment explanation
Indices: 30287--30357 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
30277 TTCACTTAGA
* *
30287 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
30320 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
30353 TTTCA
1 TTTCA
30358 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:30463 original size:21 final size:20
Alignment explanation
Indices: 30437--30542 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
30427 TGCAGAAGAG
30437 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
30458 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
30478 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
30499 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
30513 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
30532 TCGCAACGAGA
1 TCGCAACGAGA
30543 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:30481 original size:20 final size:21
Alignment explanation
Indices: 30435--30513 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
30425 TTTGCAGAAG
*
30435 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
30457 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
30476 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
30498 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
30514 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:30494 original size:41 final size:38
Alignment explanation
Indices: 30430--30546 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
30420 TTCAATTTGC
* *
30430 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
30468 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
30509 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
30542 AGAAT
1 AGAAT
30547 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:30519 original size:14 final size:14
Alignment explanation
Indices: 30500--30553 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
30490 AAATGAAAAG
30500 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
30514 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
30533 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
30547 CGCAACG
1 CGCAACG
30554 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:30529 original size:33 final size:33
Alignment explanation
Indices: 30489--30558 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
30479 CGCAACGAGA
30489 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
30522 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
30555 GAAA
1 GAAA
30559 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:30565 original size:33 final size:33
Alignment explanation
Indices: 30495--30569 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
30485 GAGAGAAATG
* **
30495 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
30528 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
30561 AAAATCGCA
1 AAAATCGCA
30570 TTGGGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:30596 original size:19 final size:19
Alignment explanation
Indices: 30574--30662 Score: 72
Period size: 19 Copynumber: 5.2 Consensus size: 19
30564 ATCGCATTGG
30574 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
*
30593 GA--TTC-TAT--CGTTGC
1 GATTTTCATTTCGCGTTGC
30607 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
*
30626 GA--TTC---TCTCGTTGC
1 GATTTTCATTTCGCGTTGC
* *
30640 GATTGTCATCTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
30659 GATT
1 GATT
30663 CTCTCGTTGC
Statistics
Matches: 55, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
14 18 0.33
16 7 0.13
17 8 0.15
19 22 0.40
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
GATTTTCATTTCGCGTTGC
Found at i:30606 original size:14 final size:14
Alignment explanation
Indices: 30587--30676 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
30577 TTTCATTTCG
*
30587 CGTTGCGATTCTAT
1 CGTTGCGATTCTCT
*
30601 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
30620 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
30634 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
30651 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
30667 CGTTGCGATT
1 CGTTGCGATT
30677 TTCATTTCAA
Statistics
Matches: 63, Mismatches: 3, Indels: 20
0.73 0.03 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 17 0.27
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:30616 original size:33 final size:33
Alignment explanation
Indices: 30574--30684 Score: 195
Period size: 33 Copynumber: 3.4 Consensus size: 33
30564 ATCGCATTGG
*
30574 GATTTTCATTTCGCGTTGCGATTCTATCGTTGC
1 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
30607 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
* *
30640 GATTGTCATCTCGCGTTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
30673 GATTTTCATTTC
1 GATTTTCATTTC
30685 AACCAAAAGA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
Found at i:32533 original size:93 final size:93
Alignment explanation
Indices: 32374--32754 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
32364 TAGATTGCTT
*
32374 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32439 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
32467 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32532 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
32560 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32625 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
32653 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32718 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
32746 AGTAAATTT
1 AGTAAATTT
32755 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 285 1.00
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:32823 original size:20 final size:20
Alignment explanation
Indices: 32798--32863 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
32788 TAGTTTACTT
* *
32798 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
32818 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
*
32837 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTCAAAA
32856 TCGCAACG
1 TCGCAACG
32864 ACAGAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.45, C:0.27, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:32838 original size:19 final size:19
Alignment explanation
Indices: 32798--32899 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
32788 TAGTTTACTT
* *
32798 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
32818 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
32837 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
32856 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
**
32870 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
32889 TCGCAATGCGA
1 TCGCAACGCGA
32900 TTTTCATTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.59
20 13 0.19
ACGTcount: A:0.45, C:0.25, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:32911 original size:19 final size:19
Alignment explanation
Indices: 32889--32953 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
32879 GAAATGAAAA
*
32889 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
32908 TCGCGTTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
32924 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
32941 TCGCATTGCGATT
1 TCGCATTGCGATT
32954 CTGTCGTTGC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 6 0.15
16 8 0.21
17 8 0.21
19 17 0.44
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:32930 original size:14 final size:14
Alignment explanation
Indices: 32911--32967 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
32901 TTTCATTTCG
32911 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
32925 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
32942 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
32958 CGTTGCGATT
1 CGTTGCGATT
32968 TTGGTTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:32937 original size:33 final size:33
Alignment explanation
Indices: 32895--32986 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
32885 AAAATCGCAA
*
32895 TGCGATTTTCATTTCGCGTTGCGATTCTTTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
*
32928 TGCGATTTTCATTTCGCATTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
**
32961 TGCGATTTTGGTTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCGTTGCGATT
32987 TTAAGTTTCG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
Found at i:32982 original size:19 final size:20
Alignment explanation
Indices: 32958--33004 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
32948 GCGATTCTGT
*
32958 CGTTGCGATTTT-GGTTTCG
1 CGTTGCGATTTTAAGTTTCG
32977 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTAAGTTTCG
*
32997 TGTTGCGA
1 CGTTGCGA
33005 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.11, C:0.15, G:0.30, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTAAGTTTCG
Found at i:34949 original size:14 final size:14
Alignment explanation
Indices: 34930--34965 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
34920 ATTGTTTAAT
34930 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
34944 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
34958 TGATTTGT
1 TGATTTGT
34966 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:35096 original size:19 final size:19
Alignment explanation
Indices: 35072--35169 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
35062 AAAATTGACT
35072 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
35091 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
35110 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
35124 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
35143 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
35163 ATCGCAA
1 ATCGCAA
35170 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:35201 original size:53 final size:53
Alignment explanation
Indices: 35072--35191 Score: 233
Period size: 53 Copynumber: 2.3 Consensus size: 53
35062 AAAATTGACT
35072 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
35124 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
35177 ATCGCAATGCGAAAT
1 ATCGCAATGCGAAAT
35192 TCATTTCGCA
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 29 0.43
53 38 0.57
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:37509 original size:12 final size:12
Alignment explanation
Indices: 37492--37516 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37482 TCTTCGGGGA
37492 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37504 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37516 C
1 C
37517 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:37725 original size:24 final size:24
Alignment explanation
Indices: 37691--37737 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
37681 CTGAAACATC
37691 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
37715 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
37738 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:38448 original size:20 final size:20
Alignment explanation
Indices: 38420--38669 Score: 241
Period size: 20 Copynumber: 12.5 Consensus size: 20
38410 AAATTTCAGT
* * *
38420 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
38440 GTTGCGATTTATGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
38460 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
38480 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* **
38500 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACGGATTCGC
*
38520 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
38540 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
38560 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
38580 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
38600 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
38620 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
38640 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
38660 GTTGCGATTT
1 GTTGCGATTT
38670 TGGAAAATCG
Statistics
Matches: 198, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:38686 original size:21 final size:21
Alignment explanation
Indices: 38656--38738 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
38646 ATTTTCATAT
*
38656 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
38677 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
38698 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
38719 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
38739 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:38729 original size:42 final size:43
Alignment explanation
Indices: 38636--38734 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
38626 ATTTATGTGT
* *
38636 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
38677 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
38719 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
38735 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:38927 original size:23 final size:23
Alignment explanation
Indices: 38879--38928 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
38869 TTTCTCTTTA
* *
38879 TTATATAAGCGCTATCTATTACG
1 TTATATAAGCGCTACCTAATACG
*
38902 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
38925 TTAT
1 TTAT
38929 TGTGCTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:39015 original size:23 final size:23
Alignment explanation
Indices: 38965--39009 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
38955 AACATATTTT
* * *
38965 ATTATATAAGTGTTAGCTATTAC
1 ATTATATAAGTGATACCTAATAC
38988 ATTATATAAGTGATACCTAATA
1 ATTATATAAGTGATACCTAATA
39010 TGTTATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (23 bp):
ATTATATAAGTGATACCTAATAC
Found at i:39021 original size:87 final size:87
Alignment explanation
Indices: 38875--39086 Score: 325
Period size: 87 Copynumber: 2.4 Consensus size: 87
38865 CGATTTTCTC
* * *
38875 TTTATTATATAAGCGCTATCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATA
1 TTTATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTGCTTGATA
*
38940 ATGTTTCCAGTAATTAACATAT
66 ATGTTTCCAGTAATTAACATAA
* * * *
38962 TTTATTATATAAGTGTTAGCTATTACATTATATAAGTGATACCTAATATGTTATTGTGCTTGATA
1 TTTATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTGCTTGATA
*
39027 ATGTTTCCAGTAATTAACCTAA
66 ATGTTTCCAGTAATTAACATAA
**
39049 TTTATTATATAAGCGCTACCTATTTTATTATATAAGCG
1 TTTATTATATAAGCGCTACCTATTACATTATATAAGCG
39087 CTACATATTA
Statistics
Matches: 111, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 111 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (87 bp):
TTTATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTGCTTGATA
ATGTTTCCAGTAATTAACATAA
Found at i:39069 original size:23 final size:23
Alignment explanation
Indices: 39043--39115 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
39033 CCAGTAATTA
39043 ACCTAATTTATTATATAAGCGCT
1 ACCTAATTTATTATATAAGCGCT
*
39066 ACCTATTTTATTATATAAGCGCT
1 ACCTAATTTATTATATAAGCGCT
* * *
39089 ACAT-ATTACATTATATAAGCGTT
1 ACCTAATT-TATTATATAAGCGCT
39112 ACCT
1 ACCT
39116 TATATGTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 2 0.05
23 41 0.95
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.40
Consensus pattern (23 bp):
ACCTAATTTATTATATAAGCGCT
Found at i:39096 original size:110 final size:110
Alignment explanation
Indices: 38959--39196 Score: 352
Period size: 110 Copynumber: 2.2 Consensus size: 110
38949 GTAATTAACA
* * *
38959 TATTTTATTATATAAGTGTTAGCTATTACATTATATAAGTGATACCTAATATGTTATTGTGCTTG
1 TATTTTATTATATAAGCGCTAGCTATTACATTATATAAGCGATACCTAATATGTTATTGTGCTTG
*
39024 ATAATGTTTCCAGTAATTAACCTAATTTATTATATAAGCGCTACC
66 ATAATGTTTCCAGTAATTAACCTAATTTATTATATAAGCGATACC
* * *
39069 TATTTTATTATATAAGCGCTA-CATATTACATTATATAAGCGTTACCTTATATGTTATTGTGTTT
1 TATTTTATTATATAAGCGCTAGC-TATTACATTATATAAGCGATACCTAATATGTTATTGTGCTT
* * *
39133 GATAATGTTTCTAGTAATTAACCTATTTTATTATATAAGTGATACC
65 GATAATGTTTCCAGTAATTAACCTAATTTATTATATAAGCGATACC
**
39179 TATTACATTATATAAGCG
1 TATTTTATTATATAAGCG
39197 ATATCTAATA
Statistics
Matches: 115, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
109 1 0.01
110 114 0.99
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (110 bp):
TATTTTATTATATAAGCGCTAGCTATTACATTATATAAGCGATACCTAATATGTTATTGTGCTTG
ATAATGTTTCCAGTAATTAACCTAATTTATTATATAAGCGATACC
Found at i:39164 original size:87 final size:86
Alignment explanation
Indices: 39066--39302 Score: 375
Period size: 87 Copynumber: 2.7 Consensus size: 86
39056 TATAAGCGCT
* * *
39066 ACCTATTTTATTATATAAGCGCTACATATTACATTATATAAGCGTTACCTTATATGTTATTGTGT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCG-TACCTAATATGTTATTGTGC
*
39131 TTGATAATGTTTCTAGTAATTA
65 TTAATAATGTTTCTAGTAATTA
* * * *
39153 ACCTATTTTATTATATAAGTGATACCTATTACATTATATAAGCGATATCTAATATATTATTGTGC
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCG-TACCTAATATGTTATTGTGC
39218 TTAATAATGTTTCTAGTAATTA
65 TTAATAATGTTTCTAGTAATTA
39240 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCAGTACCTAATATGTTATTGT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGC-GTACCTAATATGTTATTGT
39303 ACTTGGTAAT
Statistics
Matches: 136, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
87 135 0.99
88 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (86 bp):
ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGTACCTAATATGTTATTGTGCT
TAATAATGTTTCTAGTAATTA
Found at i:39188 original size:23 final size:23
Alignment explanation
Indices: 39153--39199 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
39143 CTAGTAATTA
** *
39153 ACCTATTTTATTATATAAGTGAT
1 ACCTATTACATTATATAAGCGAT
39176 ACCTATTACATTATATAAGCGAT
1 ACCTATTACATTATATAAGCGAT
39199 A
1 A
39200 TCTAATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGAT
Found at i:39211 original size:23 final size:23
Alignment explanation
Indices: 39161--39212 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
39151 TAACCTATTT
* *
39161 TATTATATAAGTGATACCTATTA
1 TATTATATAAGCGATACCTAATA
* *
39184 CATTATATAAGCGATATCTAATA
1 TATTATATAAGCGATACCTAATA
39207 TATTAT
1 TATTAT
39213 TGTGCTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (23 bp):
TATTATATAAGCGATACCTAATA
Found at i:39215 original size:197 final size:197
Alignment explanation
Indices: 38875--39282 Score: 656
Period size: 197 Copynumber: 2.1 Consensus size: 197
38865 CGATTTTCTC
*
38875 TTTATTATATAAGCGCTATCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATA
1 TTTATTATATAAGCGCTATCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATA
* * *
38940 ATGTTTCCAGTAATTAACATATTTTATTATATAAGTGTTAGCTATTACATTATATAAGTGATACC
66 ATGTTTCCAGTAATTAACATATTTTATTATATAAGTGATACCTATTACATTATATAAGCGATACC
* *
39005 TAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAACCTAATTTATTATATAAGCGCTACCT
131 TAATATATTATTGTGCTTAATAATGTTTCCAGTAATTAACCTAATTTATTATATAAGCGCTACCT
39070 AT
196 AT
* * *
39072 TTTATTATATAAGCGCTA-CATATTACATTATATAAGCGTTACCTTATATGTTATTGTGTTTGAT
1 TTTATTATATAAGCGCTATC-TATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGAT
* * *
39136 AATGTTTCTAGTAATTAACCTATTTTATTATATAAGTGATACCTATTACATTATATAAGCGATAT
65 AATGTTTCCAGTAATTAACATATTTTATTATATAAGTGATACCTATTACATTATATAAGCGATAC
* *
39201 CTAATATATTATTGTGCTTAATAATGTTTCTAGTAATTAACCTATTTTATTATATAAGCGCTACC
130 CTAATATATTATTGTGCTTAATAATGTTTCCAGTAATTAACCTAATTTATTATATAAGCGCTACC
39266 TAT
195 TAT
**
39269 TACATTATATAAGC
1 TTTATTATATAAGC
39283 AGTACCTAAT
Statistics
Matches: 194, Mismatches: 16, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
196 1 0.01
197 193 0.99
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (197 bp):
TTTATTATATAAGCGCTATCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATA
ATGTTTCCAGTAATTAACATATTTTATTATATAAGTGATACCTATTACATTATATAAGCGATACC
TAATATATTATTGTGCTTAATAATGTTTCCAGTAATTAACCTAATTTATTATATAAGCGCTACCT
AT
Found at i:39275 original size:23 final size:23
Alignment explanation
Indices: 39240--39290 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
39230 CTAGTAATTA
**
39240 ACCTATTTTATTATATAAGC-GCT
1 ACCTATTACATTATATAAGCAG-T
39263 ACCTATTACATTATATAAGCAGT
1 ACCTATTACATTATATAAGCAGT
39286 ACCTA
1 ACCTA
39291 ATATGTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCAGT
Found at i:40420 original size:12 final size:12
Alignment explanation
Indices: 40403--40436 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40393 TAAGGGAGAT
*
40403 TTTTTTATTTTA
1 TTTTTTATTGTA
40415 TTTTTTATTGTA
1 TTTTTTATTGTA
40427 TTTATTTATT
1 TTT-TTTATT
40437 CCTTTCACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTTTTATTGTA
Found at i:45256 original size:13 final size:13
Alignment explanation
Indices: 45238--45263 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45228 TTTGAATGTC
45238 CAAGTTATAAGCA
1 CAAGTTATAAGCA
45251 CAAGTTATAAGCA
1 CAAGTTATAAGCA
45264 TGAGATGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
CAAGTTATAAGCA
Found at i:46131 original size:26 final size:25
Alignment explanation
Indices: 46075--46125 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
46065 AATATTAATT
*
46075 AAATTTAATAGTGTTTTAACTTTCAA
1 AAATTTAACAGTGTTTT-ACTTTCAA
*
46101 AAATTTAACAGTGTTTT-TTTTCAA
1 AAATTTAACAGTGTTTTACTTTCAA
46125 A
1 A
46126 CAAATTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
26 16 0.70
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (25 bp):
AAATTTAACAGTGTTTTACTTTCAA
Found at i:49866 original size:16 final size:16
Alignment explanation
Indices: 49845--49875 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49835 AAATTAATCA
49845 AATGATAAAATAAATG
1 AATGATAAAATAAATG
*
49861 AATGATCAAATAAAT
1 AATGATAAAATAAAT
49876 AGGTTATTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.10, T:0.26
Consensus pattern (16 bp):
AATGATAAAATAAATG
Found at i:49963 original size:15 final size:14
Alignment explanation
Indices: 49943--49993 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
49933 TTTCGGAAAA
49943 TGAATTACTAGAATT
1 TGAATTACT-GAATT
**
49958 TGAATTACTGAAAAA
1 TGAATTACTG-AATT
49973 TGAATTACTGGAATT
1 TGAATTACT-GAATT
49988 TGAATT
1 TGAATT
49994 CTGGAAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (14 bp):
TGAATTACTGAATT
Found at i:49971 original size:29 final size:29
Alignment explanation
Indices: 49937--50009 Score: 119
Period size: 30 Copynumber: 2.5 Consensus size: 29
49927 TTGGTTTTTC
49937 GGAAAATGAATTACTAGAATTTGAATTACT
1 GGAAAATGAATTACTAGAATTTGAATT-CT
* *
49967 GAAAAATGAATTACTGGAATTTGAATTCT
1 GGAAAATGAATTACTAGAATTTGAATTCT
49996 GGAAAATGAATTAC
1 GGAAAATGAATTAC
50010 ATTTCTGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.32
Consensus pattern (29 bp):
GGAAAATGAATTACTAGAATTTGAATTCT
Found at i:50391 original size:23 final size:23
Alignment explanation
Indices: 50342--50404 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
50332 GTGTTATATT
**
50342 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
50365 ATATTTTAAATATTTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
50388 ATATTATTAAAATATAT
1 ATATT-TTAAAA-ATAT
50405 AAATAATATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
23 23 0.74
24 5 0.16
25 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:50396 original size:11 final size:11
Alignment explanation
Indices: 50380--50417 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
50370 TTAAATATTT
50380 TTATTAAAATA
1 TTATTAAAATA
50391 TTATTAAAATA
1 TTATTAAAATA
*
50402 -TATAAATAATA
1 TTATTAA-AATA
50413 TTATT
1 TTATT
50418 CATTATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 5 0.22
11 15 0.65
12 3 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTATTAAAATA
Found at i:50432 original size:19 final size:20
Alignment explanation
Indices: 50380--50432 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
50370 TTAAATATTT
50380 TTATTAAA-ATATTATTAAA
1 TTATTAAATATATTATTAAA
* *
50399 ATATATAAATAATATTATT-CA
1 TTAT-TAAAT-ATATTATTAAA
50420 TTATTAAATATAT
1 TTATTAAATATAT
50433 AAATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 4 0.14
22 8 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATTAAATATATTATTAAA
Found at i:50446 original size:24 final size:28
Alignment explanation
Indices: 50389--50544 Score: 78
Period size: 26 Copynumber: 5.5 Consensus size: 28
50379 TTTATTAAAA
50389 TATTATTAAAATATATAAATAATATTATT
1 TATTATTAAAATATATAAAT-ATATTATT
* * *
50418 CATTATT-AAATATATAAATTTTTTTATTATA
1 TATTATTAAAATATATAAA----TATATTATT
*
50449 TATTATTAAAATA-A-AAATATAATATCT
1 TATTATTAAAATATATAAATATATTAT-T
**
50476 TA-TATTATTATA-ATATAAT-TGATTA-T
1 TATTATTAAAATATATA-AATAT-ATTATT
* *
50502 T-TTATATAAAAT-TAAAAATATAATATT
1 TATTAT-TAAAATATATAAATATATTATT
50529 ATATTATTATAAATAT
1 -TATTATTA-AAATAT
50545 TAATAAATTA
Statistics
Matches: 95, Mismatches: 14, Indels: 35
0.66 0.10 0.24
Matches are distributed among these distances:
26 26 0.27
27 12 0.13
28 20 0.21
29 14 0.15
30 4 0.04
31 13 0.14
32 6 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
TATTATTAAAATATATAAATATATTATT
Found at i:50471 original size:60 final size:60
Alignment explanation
Indices: 50371--50553 Score: 163
Period size: 60 Copynumber: 3.1 Consensus size: 60
50361 TAGTATATTT
* * *
50371 TAAATATTTTTATTAAAATATTATTAAAATATATAA-ATAATATTAT-TCATTATTAAATATA
1 TAAATTTTTTTATT-ATATATTATTAAAATA-AAAATATAATATTATAT-ATTATTAAATATA
*
50432 TAAATTTTTTTATTATATATTATTAAAATAAAAATATAATATCT-TATATTATTATA-ATA
1 TAAATTTTTTTATTATATATTATTAAAATAAAAATATAATAT-TATATATTATTAAATATA
**
50491 T-AA-TTGATTATT-T-TA-TA-TAAAATTAAAAATATAATATTATATTATTA-TAAATATTAA
1 TAAATTTTTTTATTATATATTATTAAAA-TAAAAATATAATATTATA-TATTATTAAATA-T-A
50548 TAAATT
1 TAAATT
50554 AATAAATAAT
Statistics
Matches: 104, Mismatches: 7, Indels: 24
0.77 0.05 0.18
Matches are distributed among these distances:
53 6 0.06
54 21 0.20
55 8 0.08
56 2 0.02
57 9 0.09
58 4 0.04
59 8 0.08
60 31 0.30
61 15 0.14
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (60 bp):
TAAATTTTTTTATTATATATTATTAAAATAAAAATATAATATTATATATTATTAAATATA
Found at i:50523 original size:31 final size:33
Alignment explanation
Indices: 50477--50556 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 33
50467 ATAATATCTT
* *
50477 ATATTATTATAATATAATTGATTATTTTA-TATAA
1 ATATTAATA-AATATAATT-ATTATATTATTATAA
50511 A-ATTAA-AAATATAA-TATTATATTATTATAA
1 ATATTAATAAATATAATTATTATATTATTATAA
50541 ATATTAATAAAT-TAAT
1 ATATTAATAAATATAAT
50557 AAATAATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
29 8 0.20
30 7 0.17
31 15 0.38
32 5 0.12
33 4 0.10
34 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (33 bp):
ATATTAATAAATATAATTATTATATTATTATAA
Found at i:50531 original size:22 final size:23
Alignment explanation
Indices: 50506--50549 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
50496 GATTATTTTA
50506 TATAAAATTAAAAATA-TAATAT
1 TATAAAATTAAAAATATTAATAT
** *
50528 TATATTATTATAAATATTAATA
1 TATAAAATTAAAAATATTAATA
50550 AATTAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAAAATTAAAAATATTAATAT
Found at i:50800 original size:42 final size:42
Alignment explanation
Indices: 50741--50860 Score: 161
Period size: 42 Copynumber: 2.9 Consensus size: 42
50731 ATGAATTACG
*
50741 TTCCGGAAAACGAATTACGTGAAATAAATAC-AGGAAAATATT
1 TTCCGAAAAACGAATTACGTGAAATAAATACGA-GAAAATATT
* * *
50783 TTCCGAAAAACAAATTACGTGAAACAAACACGAGAAAATATT
1 TTCCGAAAAACGAATTACGTGAAATAAATACGAGAAAATATT
* * *
50825 TTCTGAAAAATGAATTACGTGAAATAAATACTAGAA
1 TTCCGAAAAACGAATTACGTGAAATAAATACGAGAA
50861 TTCGAGAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
42 66 0.99
43 1 0.01
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.23
Consensus pattern (42 bp):
TTCCGAAAAACGAATTACGTGAAATAAATACGAGAAAATATT
Found at i:53188 original size:72 final size:72
Alignment explanation
Indices: 53104--53304 Score: 246
Period size: 72 Copynumber: 2.7 Consensus size: 72
53094 ATTGTGCCTG
53104 CCATCATGATCACC-TGTACCATGGACATAAACATGCTCATAGTCATAGTCATGAAAACCATGAT
1 CCATCATGATCACCATG-ACCATGGACATAAACATGCTCAT-GTCATAGTCATGAAAACCATGAT
*
53168 TTTGCCCA-
64 TATGCCCAC
* * * *
53176 CCATCATGATCACCATGACCATGGACATGATCATGCTCATG-CTTATGCTCATGACAACCATGAT
1 CCATCATGATCACCATGACCATGGACATAAACATGCTCATGTCATA-G-TCATGAAAACCATGAT
53240 TATGCCCAC
64 TATGCCCAC
* * *
53249 CATCATCATGATCACCATGACCATGGACCTAAACATGATCATGCTCGTAGTCATGA
1 C--CATCATGATCACCATGACCATGGACATAAACATGCTCATG-TCATAGTCATGA
53305 CCACCATCAT
Statistics
Matches: 111, Mismatches: 10, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
70 3 0.03
71 2 0.02
72 57 0.51
73 3 0.03
75 42 0.38
76 1 0.01
77 3 0.03
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (72 bp):
CCATCATGATCACCATGACCATGGACATAAACATGCTCATGTCATAGTCATGAAAACCATGATTA
TGCCCAC
Found at i:54354 original size:22 final size:21
Alignment explanation
Indices: 54313--54354 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
54303 TTCGGTATTT
*
54313 AGCCCAACTTTTTTTTAATAG
1 AGCCCAACTTTTTTTAAATAG
54334 AGCCCAACTTATTTTTAAATA
1 AGCCCAACTT-TTTTTAAATA
54355 CAATTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.40
Consensus pattern (21 bp):
AGCCCAACTTTTTTTAAATAG
Found at i:55782 original size:14 final size:14
Alignment explanation
Indices: 55763--55790 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55753 AAATATATGA
55763 AAAGAACTTCAGGT
1 AAAGAACTTCAGGT
55777 AAAGAACTTCAGGT
1 AAAGAACTTCAGGT
55791 CGGACATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AAAGAACTTCAGGT
Found at i:61753 original size:14 final size:14
Alignment explanation
Indices: 61717--61745 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
61707 GCTCACAAAA
61717 GATACGGTGGGATG
1 GATACGGTGGGATG
61731 GATACGGTGGGATG
1 GATACGGTGGGATG
61745 G
1 G
61746 GAACGGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.52, T:0.21
Consensus pattern (14 bp):
GATACGGTGGGATG
Found at i:62302 original size:6 final size:7
Alignment explanation
Indices: 62287--62311 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
62277 TGAATATTGC
62287 TTTTCTT
1 TTTTCTT
62294 TTTTCTT
1 TTTTCTT
62301 TTTTCTT
1 TTTTCTT
62308 TTTT
1 TTTT
62312 TTGGGTTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:72534 original size:21 final size:21
Alignment explanation
Indices: 72495--72534 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
72485 CAATCTTCTG
*
72495 TTGTACATTATAATGATTATA
1 TTGTACATTATAATAATTATA
* *
72516 TTGTATATTATATTAATTA
1 TTGTACATTATAATAATTA
72535 ATTTCATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (21 bp):
TTGTACATTATAATAATTATA
Done.