Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000842.1 Hibiscus syriacus cultivar Beakdansim tig00001625_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: 83399
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5554 original size:20 final size:20
Alignment explanation
Indices: 5529--5575 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
5519 CAGTTTCAAT
5529 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
5549 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
5569 TCGCAAC
1 TCGCAAC
5576 ACATAAGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:5592 original size:20 final size:20
Alignment explanation
Indices: 5569--5694 Score: 125
Period size: 20 Copynumber: 6.3 Consensus size: 20
5559 AATCTGTAAA
5569 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
5589 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
*
5609 CCGCAACACA-AAGTCAAAT
1 TCGCAACACATAAGTCAAAT
* * *
5628 TCGCAACACAAAAGTTAAAC
1 TCGCAACACATAAGTCAAAT
*
5648 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
*
5668 T-GCAACACATAATTTCAAAT
1 TCGCAACACATAA-GTCAAAT
*
5688 TCACAAC
1 TCGCAAC
5695 GCGAAACACA
Statistics
Matches: 86, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
18 2 0.02
19 25 0.29
20 52 0.60
21 7 0.08
ACGTcount: A:0.43, C:0.26, G:0.12, T:0.19
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:5623 original size:39 final size:40
Alignment explanation
Indices: 5549--5634 Score: 124
Period size: 39 Copynumber: 2.2 Consensus size: 40
5539 AATCTGTAAA
*
5549 TCGCAACGCGAATCTGTAAATCGCAACACATAAGTCAAAT
1 TCGCAACGCGAATCAGTAAATCGCAACACATAAGTCAAAT
5589 TCGCAACGCG-AT-AGTCAAATCCGCAACACA-AAGTCAAAT
1 TCGCAACGCGAATCAGT-AAAT-CGCAACACATAAGTCAAAT
5628 TCGCAAC
1 TCGCAAC
5635 ACAAAAGTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
38 2 0.05
39 22 0.51
40 19 0.44
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.17
Consensus pattern (40 bp):
TCGCAACGCGAATCAGTAAATCGCAACACATAAGTCAAAT
Found at i:5652 original size:59 final size:60
Alignment explanation
Indices: 5569--5694 Score: 175
Period size: 59 Copynumber: 2.1 Consensus size: 60
5559 AATCTGTAAA
* *
5569 TCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAATCCGCAACACA-AA-GTCAAAT
1 TCGCAACACAAAAGTCAAACTCGCAACGCGATAGTCAAAT-CGCAACACATAATGTCAAAT
* * *
5628 TCGCAACACAAAAGTTAAACTCGCAACGCGATAGTCAAATTGCAACACATAATTTCAAAT
1 TCGCAACACAAAAGTCAAACTCGCAACGCGATAGTCAAATCGCAACACATAATGTCAAAT
*
5688 TCACAAC
1 TCGCAAC
5695 GCGAAACACA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 8 0.14
59 39 0.66
60 12 0.20
ACGTcount: A:0.43, C:0.26, G:0.12, T:0.19
Consensus pattern (60 bp):
TCGCAACACAAAAGTCAAACTCGCAACGCGATAGTCAAATCGCAACACATAATGTCAAAT
Found at i:5653 original size:39 final size:38
Alignment explanation
Indices: 5565--5676 Score: 127
Period size: 39 Copynumber: 2.9 Consensus size: 38
5555 CGCGAATCTG
* * *
5565 TAAATCGCAACACATAAGTCAAATTCGCAACGCGATAGT
1 TAAATCGCAACACA-AAGTCAAATTCGCAACACAAAAGT
*
5604 CAAATCCGCAACACAAAGTCAAATTCGCAACACAAAAGT
1 TAAAT-CGCAACACAAAGTCAAATTCGCAACACAAAAGT
* *
5643 TAAACTCGCAACGCGATAGTCAAATT-GCAACACA
1 TAAA-TCGCAACAC-AAAGTCAAATTCGCAACACA
5677 TAATTTCAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
39 43 0.68
40 20 0.32
ACGTcount: A:0.44, C:0.26, G:0.13, T:0.17
Consensus pattern (38 bp):
TAAATCGCAACACAAAGTCAAATTCGCAACACAAAAGT
Found at i:6229 original size:20 final size:20
Alignment explanation
Indices: 6187--6229 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
6177 GCGATTTTAG
* * * *
6187 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGAATTTAAGT
6207 TTCGCATTGCGAATTTAAGT
1 TTCGCATTGCGAATTTAAGT
6227 TTC
1 TTC
6230 AGAAACTACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.47
Consensus pattern (20 bp):
TTCGCATTGCGAATTTAAGT
Found at i:10236 original size:17 final size:18
Alignment explanation
Indices: 10214--10248 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
10204 AAGCCGGTTG
*
10214 TGATTGGGA-TTTGATTT
1 TGATTGCGATTTTGATTT
10231 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
10249 CCTTTTGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:12519 original size:23 final size:24
Alignment explanation
Indices: 12486--12538 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
12476 CCATCACATC
12486 ATCAAAATCCA-GAATTGACCAAG
1 ATCAAAATCCAGGAATTGACCAAG
* *
12509 ATCAAAGTCCAGGTATTGACCAAG
1 ATCAAAATCCAGGAATTGACCAAG
12533 ATCAAA
1 ATCAAA
12539 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (24 bp):
ATCAAAATCCAGGAATTGACCAAG
Found at i:13531 original size:19 final size:20
Alignment explanation
Indices: 13490--13541 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
13480 TTAAATTCGT
* *
13490 GTTGTAAATTCGAAAATCTA
1 GTTGTGAATTTGAAAATCTA
*
13510 GTTGTGAATTTGAAATTC-A
1 GTTGTGAATTTGAAAATCTA
*
13529 GTTGCGAATTTGA
1 GTTGTGAATTTGA
13542 CTATCGCGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (20 bp):
GTTGTGAATTTGAAAATCTA
Found at i:13598 original size:20 final size:20
Alignment explanation
Indices: 13573--13615 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
13563 TTATGTGTTA
13573 CGATTTACAAATTCGCGTTG
1 CGATTTACAAATTCGCGTTG
* *
13593 CGATTTATAGATTCGCGTTG
1 CGATTTACAAATTCGCGTTG
13613 CGA
1 CGA
13616 ATTTGACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (20 bp):
CGATTTACAAATTCGCGTTG
Found at i:13660 original size:40 final size:40
Alignment explanation
Indices: 13593--13700 Score: 139
Period size: 40 Copynumber: 2.7 Consensus size: 40
13583 ATTCGCGTTG
* * *
13593 CGATTTATAGATTCGCGTTGCGAATTTGACTTTTGTGTTA
1 CGATTTACAGATTCGCGTTGCGAATTTGACTTCTGTGCTA
* *
13633 CGAATTTGAC-TA-TCGCGTTGCGAATTTGACTTCTGTGCTG
1 CG-ATTT-ACAGATTCGCGTTGCGAATTTGACTTCTGTGCTA
13673 CGATTTACAGATTCGCGTTGCGAATTTG
1 CGATTTACAGATTCGCGTTGCGAATTTG
13701 GAAAATCGCA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
38 2 0.03
39 5 0.09
40 45 0.78
41 5 0.09
42 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (40 bp):
CGATTTACAGATTCGCGTTGCGAATTTGACTTCTGTGCTA
Found at i:13674 original size:20 final size:20
Alignment explanation
Indices: 13609--13675 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
13599 ATAGATTCGC
*
13609 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
* *
13629 GTTACGAATTTGACTATC-GC
1 GTTGCGAATTTGACT-TCTGT
13649 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
*
13669 GCTGCGA
1 GTTGCGA
13676 TTTACAGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.05
20 36 0.92
21 1 0.03
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.40
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:13675 original size:60 final size:59
Alignment explanation
Indices: 13529--13665 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 59
13519 TTGAAATTCA
*
13529 GTTGCGAATTTGACTATCGCGTTGCAAATTTAACTTATGTGTTACGATTTACAAATTCGC
1 GTTGCGAATTTGACT-TCGCGTTGCGAATTTAACTTATGTGTTACGATTTACAAATTCGC
* * * *
13589 GTTGCGATTTATAGA-TTCGCGTTGCGAATTTGACTTTTGTGTTACGAATTTGAC-TA-TCGC
1 GTTGCGAATT-T-GACTTCGCGTTGCGAATTTAACTTATGTGTTACG-ATTT-ACAAATTCGC
13649 GTTGCGAATTTGACTTC
1 GTTGCGAATTTGACTTC
13666 TGTGCTGCGA
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
58 2 0.03
59 4 0.06
60 49 0.74
61 7 0.11
62 4 0.06
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (59 bp):
GTTGCGAATTTGACTTCGCGTTGCGAATTTAACTTATGTGTTACGATTTACAAATTCGC
Found at i:13737 original size:20 final size:20
Alignment explanation
Indices: 13671--13737 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
13661 ACTTCTGTGC
* *
13671 TGCGATTTACAGATTCGCGT
1 TGCGAATTACAAATTCGCGT
** * **
13691 TGCGAATTTGGAAAATCGCAA
1 TGCGAA-TTACAAATTCGCGT
*
13712 TGCGAATTACATATTCGCGT
1 TGCGAATTACAAATTCGCGT
13732 TGCGAA
1 TGCGAA
13738 ATTGGAAATT
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (20 bp):
TGCGAATTACAAATTCGCGT
Found at i:13753 original size:20 final size:20
Alignment explanation
Indices: 13685--13777 Score: 80
Period size: 20 Copynumber: 4.6 Consensus size: 20
13675 ATTTACAGAT
*
13685 TCGCGTTGCGAATTTGGAAAA
1 TCGCGTTGCGAAATTGG-AAA
** ** *
13706 TCGCAATGCG-AATTACATAT
1 TCGCGTTGCGAAATTGGA-AA
13726 TCGCGTTGCGAAATTGGAAA
1 TCGCGTTGCGAAATTGGAAA
* * *
13746 TTGGGTTGCGAAATTGGAGA
1 TCGCGTTGCGAAATTGGAAA
13766 TCGCGTTGCGAA
1 TCGCGTTGCGAA
13778 TTATTGGTCA
Statistics
Matches: 54, Mismatches: 16, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
19 1 0.02
20 40 0.74
21 13 0.24
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (20 bp):
TCGCGTTGCGAAATTGGAAA
Found at i:16433 original size:31 final size:31
Alignment explanation
Indices: 16312--16437 Score: 173
Period size: 31 Copynumber: 4.0 Consensus size: 31
16302 AGGGTCGAGG
*
16312 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
16343 GTTTTACCTATGTTATTCGGGACATATGGACT
1 G-TTTACCTATGTTCTTCGGGACATATGGACT
* *
16375 CTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
16406 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
16437 G
1 G
16438 GTCATTCGGG
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
31 55 0.65
32 29 0.35
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:17352 original size:19 final size:19
Alignment explanation
Indices: 17307--17353 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
17297 TGTTCACAAT
17307 ACTGTTCATACAGTATATA
1 ACTGTTCATACAGTATATA
* *
17326 ACTATTCATACCGTATAGTA
1 ACTGTTCATACAGTATA-TA
17346 A-TGTTCAT
1 ACTGTTCAT
17354 GAAAAACGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (19 bp):
ACTGTTCATACAGTATATA
Found at i:26422 original size:24 final size:23
Alignment explanation
Indices: 26378--26441 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
26368 TAAATTATAA
* *
26378 ATAAAAATAA-ATATCTTTGTATT
1 ATAAAAATAAGTTAT-TTTGTAGT
*
26401 GTAAAAATAAGTTATTTGTGTAGT
1 ATAAAAATAAGTTATTT-TGTAGT
26425 ATAAAAATAAGTTATTT
1 ATAAAAATAAGTTATTT
26442 ATATATTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.31
24 24 0.69
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (23 bp):
ATAAAAATAAGTTATTTTGTAGT
Found at i:26665 original size:31 final size:30
Alignment explanation
Indices: 26628--26768 Score: 80
Period size: 31 Copynumber: 4.7 Consensus size: 30
26618 ACTTTTAAAT
26628 ATTCTAATTTCATCCTTAAATTATGATTCTC
1 ATTCTAATTTCATCCTTAAATTATGA-TCTC
* * *
26659 ATTCTAAATTT-GTCCTTAAACTTTTGA--AC
1 ATTCT-AATTTCATCCTTAAA-TTATGATCTC
* ** *
26688 ATTCAAATTTCATCCCCAAACTATGAATCTC
1 ATTCTAATTTCATCCTTAAATTATG-ATCTC
* * *
26719 ATTCTAAATTGAT-CTTAAACTTTTAGATCT-
1 ATTCTAATTTCATCCTTAAA-TTAT-GATCTC
*
26749 -TTC-AATTTCATCCTCAAATT
1 ATTCTAATTTCATCCTTAAATT
26769 CATCAAGATA
Statistics
Matches: 81, Mismatches: 20, Indels: 21
0.66 0.16 0.17
Matches are distributed among these distances:
28 16 0.20
29 20 0.25
30 4 0.05
31 30 0.37
32 11 0.14
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (30 bp):
ATTCTAATTTCATCCTTAAATTATGATCTC
Found at i:26713 original size:60 final size:58
Alignment explanation
Indices: 26618--26766 Score: 174
Period size: 60 Copynumber: 2.5 Consensus size: 58
26608 ATTAATCCTT
* * * * *
26618 ACTTTTAAATATTCTAATTTCATCCTTAAATTATGATTCTCATTCTAAATTTG-TCCTTAA
1 ACTTTTGAACATTC-AATTTCATCCTCAAACTATGAATCTCATTCTAAA-TTGAT-CTTAA
*
26678 ACTTTTGAACATTCAAATTTCATCCCCAAACTATGAATCTCATTCTAAATTGATCTTAA
1 ACTTTTGAACATTC-AATTTCATCCTCAAACTATGAATCTCATTCTAAATTGATCTTAA
* *
26737 ACTTTTAGATCTTTCAATTTCATCCTCAAA
1 ACTTTT-GAACATTCAATTTCATCCTCAAA
26767 TTCATCAAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
59 28 0.36
60 49 0.64
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (58 bp):
ACTTTTGAACATTCAATTTCATCCTCAAACTATGAATCTCATTCTAAATTGATCTTAA
Found at i:27016 original size:60 final size:62
Alignment explanation
Indices: 26883--27019 Score: 144
Period size: 60 Copynumber: 2.3 Consensus size: 62
26873 GTATATATGA
* * *
26883 ATAA-TTTAGAAT-AAAATTAAAATATTCAAAAAGTTTGGGGACCAATTTAGAATGAAGATC
1 ATAACTTTAGGATGAAAATTAAAATATTCAAAAAGTTTGAGGACCAATTTAGAATGAAAATC
* *
26943 ATAACTTTGGGATGAAAA-TAAAAT-TTCCAAAAA-TTTGAGGACTAATTTAGAAT-AATAATC
1 ATAACTTTAGGATGAAAATTAAAATATT-CAAAAAGTTTGAGGACCAATTTAGAATGAA-AATC
*
27003 AT-AGTTTAAGGATGAAA
1 ATAACTTT-AGGATGAAA
27020 TTGAAATGCT
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
59 6 0.09
60 37 0.57
61 18 0.28
62 4 0.06
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (62 bp):
ATAACTTTAGGATGAAAATTAAAATATTCAAAAAGTTTGAGGACCAATTTAGAATGAAAATC
Found at i:27509 original size:14 final size:13
Alignment explanation
Indices: 27479--27530 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
27469 TAAAACATAT
*
27479 TAAATAATAAATAA
1 TAAAT-ATAATTAA
27493 TAAATATAATTATA
1 TAAATATAATTA-A
*
27507 TAACTATAATTAA
1 TAAATATAATTAA
* *
27520 AAAATAAAATT
1 TAAATATAATT
27531 GGGGCTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
13 15 0.47
14 17 0.53
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
TAAATATAATTAA
Found at i:44215 original size:19 final size:19
Alignment explanation
Indices: 44179--44215 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44169 TTTATAGCGA
*
44179 AAATTTAAAATTTAAATTG
1 AAATTTAAAAATTAAATTG
*
44198 AAATTTAAAAATTCAATT
1 AAATTTAAAAATTAAATT
44216 CAAAATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (19 bp):
AAATTTAAAAATTAAATTG
Found at i:44335 original size:27 final size:27
Alignment explanation
Indices: 44305--44394 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 27
44295 GAAAAAAAAG
44305 ATAAAAATAATATAAAAAATGAAATAA
1 ATAAAAATAATATAAAAAATGAAATAA
* * *
44332 ATAAAAGAGAAAAAATAAAAATGTTAAATAA
1 ATAAAA-ATAATATA-AAAAATG--AAATAA
*
44363 A-AAAAATAATAAGTAATAAAT-AAATAA
1 ATAAAAATAAT-A-TAAAAAATGAAATAA
44390 ATAAA
1 ATAAA
44395 TAAAATAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
27 13 0.27
28 8 0.16
29 10 0.20
30 10 0.20
31 8 0.16
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (27 bp):
ATAAAAATAATATAAAAAATGAAATAA
Found at i:53447 original size:63 final size:63
Alignment explanation
Indices: 53348--53471 Score: 221
Period size: 63 Copynumber: 2.0 Consensus size: 63
53338 AACAAATGTC
* *
53348 ATTTTGAATTAACAATATCAATCTCAAAAGAGAAAAACAAAATGAAAACCTGTTAGAAAGCTT
1 ATTTTGAATCAACAATATCAATCTCAAAAGAGAAAAACAAAAGGAAAACCTGTTAGAAAGCTT
*
53411 ATTTTGAATCAACAATATCAATCTCAAAAGGGAAAAACAAAAGGAAAACCTGTTAGAAAGC
1 ATTTTGAATCAACAATATCAATCTCAAAAGAGAAAAACAAAAGGAAAACCTGTTAGAAAGC
53472 AGCCACATCC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.51, C:0.14, G:0.13, T:0.23
Consensus pattern (63 bp):
ATTTTGAATCAACAATATCAATCTCAAAAGAGAAAAACAAAAGGAAAACCTGTTAGAAAGCTT
Found at i:53643 original size:31 final size:31
Alignment explanation
Indices: 53601--53659 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
53591 GGATTCAACG
*
53601 TAAAATTTTAAAAATTTTAGA-GTTTTAAGT
1 TAAAATTTTAAAAATTTTAAAGGTTTTAAGT
53631 TAAAATCTTTAAAAATTTTAAAGGTTTTA
1 TAAAAT-TTTAAAAATTTTAAAGGTTTTA
53660 TTTATACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 6 0.23
31 14 0.54
32 6 0.23
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (31 bp):
TAAAATTTTAAAAATTTTAAAGGTTTTAAGT
Found at i:54624 original size:3 final size:3
Alignment explanation
Indices: 54618--54643 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54608 AATCAAGACA
54618 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
54644 GGAAAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:54694 original size:13 final size:13
Alignment explanation
Indices: 54674--54746 Score: 55
Period size: 12 Copynumber: 5.9 Consensus size: 13
54664 AAATAAATTG
54674 AAAA-AATAAATA
1 AAAATAATAAATA
* * *
54686 AAAAGAATAAGTC
1 AAAATAATAAATA
54699 AAAATAAT-AATA
1 AAAATAATAAATA
*
54711 ATAATAATAAATA
1 AAAATAATAAATA
* *
54724 AGAAT-AGAAATA
1 AAAATAATAAATA
*
54736 AGAA-AATAAAT
1 AAAATAATAAAT
54747 TAAGGAACAA
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
12 28 0.57
13 21 0.43
ACGTcount: A:0.71, C:0.01, G:0.07, T:0.21
Consensus pattern (13 bp):
AAAATAATAAATA
Found at i:54722 original size:19 final size:20
Alignment explanation
Indices: 54678--54729 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
54668 AAATTGAAAA
*
54678 AATAAATAAAAAGAATAAGT
1 AATAAATAAAAATAATAAGT
* *
54698 CA-AAATAATAATAATAA-T
1 AATAAATAAAAATAATAAGT
*
54716 AATAAATAAGAATA
1 AATAAATAAAAATA
54730 GAAATAAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 2 0.08
19 23 0.88
20 1 0.04
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (20 bp):
AATAAATAAAAATAATAAGT
Found at i:56190 original size:4 final size:4
Alignment explanation
Indices: 56181--56235 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
56171 AATAATAAGT
* *
56181 AATA AATA AATA AATA AA-A ATGTA GA-A AATA AATA AATA AATA TAATA
1 AATA AATA AATA AATA AATA A-ATA AATA AATA AATA AATA AATA -AATA
*
56229 AAAA AAT
1 AATA AAT
56236 TCCAAAACTA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
3 4 0.10
4 32 0.78
5 5 0.12
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:56232 original size:23 final size:23
Alignment explanation
Indices: 56170--56232 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 23
56160 AAAAAAGAAA
56170 AAATAATAAGTAATAAATAAATAAAT
1 AAAT-ATAA-TAA-AAATAAATAAAT
* *
56196 AAAAAT-GTAGAAAATAAATAAAT
1 AAATATAATA-AAAATAAATAAAT
56219 AAATATAATAAAAA
1 AAATATAATAAAAA
56233 AATTCCAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
23 23 0.74
24 3 0.10
25 2 0.06
26 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (23 bp):
AAATATAATAAAAATAAATAAAT
Found at i:56297 original size:27 final size:28
Alignment explanation
Indices: 56252--56329 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 28
56242 ACTATATAAT
**
56252 ATATATATATTTTTTAAAAA-TTCTAAA
1 ATATATATATTTTAAAAAAATTTCTAAA
56279 ATATATATATTTTAAAAAAATAATTTTCTAAA
1 ATATATATATTTT--AAAAA-AA-TTTCTAAA
*
56311 CTATATATATTTTAAAAAA
1 ATATATATATTTTAAAAAA
56330 TAATTTTTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
27 13 0.30
29 4 0.09
30 7 0.16
32 19 0.44
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (28 bp):
ATATATATATTTTAAAAAAATTTCTAAA
Found at i:56319 original size:36 final size:34
Alignment explanation
Indices: 56279--56392 Score: 110
Period size: 36 Copynumber: 3.3 Consensus size: 34
56269 AAATTCTAAA
56279 ATATATATATTTTAAAAAAATAATTTTCTAAAC---
1 ATATATATATTTT-AAAAAATAATTTT-TAAACTAT
56312 -TATATATATTTTAAAAAATAATTTTTAGAACTAT
1 ATATATATATTTTAAAAAATAATTTTTA-AACTAT
* ** *
56346 ATAATATATATTTTCAAAAATTGTTTTAAAAACTAT
1 AT-ATATATATTTTAAAAAATAATTTT-TAAACTAT
56382 ATATTATATAT
1 ATA-TATATAT
56393 ATATTTTCAA
Statistics
Matches: 69, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
30 2 0.03
31 16 0.23
32 12 0.17
35 2 0.03
36 36 0.52
37 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (34 bp):
ATATATATATTTTAAAAAATAATTTTTAAACTAT
Found at i:56331 original size:31 final size:32
Alignment explanation
Indices: 56272--56348 Score: 122
Period size: 31 Copynumber: 2.4 Consensus size: 32
56262 TTTTTAAAAA
*
56272 TTCTAAAATATATATATTTTAAAAAAATAATT
1 TTCTAAACTATATATATTTTAAAAAAATAATT
56304 TTCTAAACTATATATATTTT-AAAAAATAATT
1 TTCTAAACTATATATATTTTAAAAAAATAATT
56335 TT-TAGAACTATATA
1 TTCTA-AACTATATA
56349 ATATATATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
30 2 0.05
31 22 0.51
32 19 0.44
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.44
Consensus pattern (32 bp):
TTCTAAACTATATATATTTTAAAAAAATAATT
Found at i:56467 original size:2 final size:2
Alignment explanation
Indices: 56460--56520 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
56450 TTTTAAAAAC
56460 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56502 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
56521 GTGTGTGTGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56469 original size:41 final size:40
Alignment explanation
Indices: 56343--56478 Score: 204
Period size: 42 Copynumber: 3.4 Consensus size: 40
56333 TTTTTAGAAC
56343 TATATA-ATATATATTTTCAAAAATTGTTTTAAAAACTATA
1 TATATATATATATATTTTCAAAAA-TGTTTTAAAAACTATA
56383 TAT-TATATATATATTTTCAAAAATGTTTTAAAAACTATA
1 TATATATATATATATTTTCAAAAATGTTTTAAAAACTATA
* **
56422 TAATATACATATATATGTTTTTAAAATGTTTTAAAAACTATA
1 T-ATATATATATATAT-TTTCAAAAATGTTTTAAAAACTATA
56464 TATATATATATATAT
1 TATATATATATATAT
56479 ATATATATAT
Statistics
Matches: 88, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
39 19 0.22
40 22 0.25
41 23 0.26
42 24 0.27
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (40 bp):
TATATATATATATATTTTCAAAAATGTTTTAAAAACTATA
Found at i:56525 original size:2 final size:2
Alignment explanation
Indices: 56520--56558 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
56510 TATATATATA
56520 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
56559 TTTCAAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:56633 original size:73 final size:73
Alignment explanation
Indices: 56556--56702 Score: 235
Period size: 73 Copynumber: 2.0 Consensus size: 73
56546 TGTGTGTGTG
*
56556 TGTTTTCAAAATGTTTTAAAATACTATATATTATATAT-TTTT-AAATTGTTTTAAAAACTATAT
1 TGTTTTCAAAATGTTTTAAAA-ACTATATATTATATATATTTTCAAAATG-TTTAAAAACTATAT
56619 AATATACATA
64 AATATACATA
*
56629 TGTTTTCAAAATGTTTTAAAAACTATTTATTATATATATTTTCAAAATGTTTAAAAACTATATAA
1 TGTTTTCAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATGTTTAAAAACTATATAA
*
56694 TATATATA
66 TATACATA
56702 T
1 T
56703 ATATATATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
72 15 0.22
73 49 0.71
74 5 0.07
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (73 bp):
TGTTTTCAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATGTTTAAAAACTATATAA
TATACATA
Found at i:56689 original size:35 final size:36
Alignment explanation
Indices: 56558--56702 Score: 197
Period size: 35 Copynumber: 4.0 Consensus size: 36
56548 TGTGTGTGTG
56558 TTTTCAAAATGTTTTAAAATACTATATATTATATAT-
1 TTTTCAAAATGTTTTAAAA-ACTATATATTATATATA
* * *
56594 TTTT-AAATTGTTTTAAAAACTATATAATATACATATG
1 TTTTCAAAATGTTTTAAAAACTATAT-AT-TATATATA
*
56631 TTTTCAAAATGTTTTAAAAACTATTTATTATATATA
1 TTTTCAAAATGTTTTAAAAACTATATATTATATATA
*
56667 TTTTCAAAATG-TTTAAAAACTATATAATATATATA
1 TTTTCAAAATGTTTTAAAAACTATATATTATATATA
56702 T
1 T
56703 ATATATATAT
Statistics
Matches: 97, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
34 7 0.07
35 38 0.39
36 27 0.28
37 6 0.06
38 19 0.20
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (36 bp):
TTTTCAAAATGTTTTAAAAACTATATATTATATATA
Found at i:56698 original size:2 final size:2
Alignment explanation
Indices: 56687--56719 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
56677 GTTTAAAAAC
56687 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56720 ATAAGAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:57466 original size:84 final size:84
Alignment explanation
Indices: 57380--58435 Score: 1450
Period size: 84 Copynumber: 12.6 Consensus size: 84
57370 AGTGTAATCA
* ** * * * * * * *
57380 AACTTGAAGGTCTTCAGTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
* * * *
57445 TTTGAGCTGAGTGTAATCA
66 TTGGAGCTGAGCGTAGTCG
* *
57464 AACTCGAAGGTC-TTTGATTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGC
1 AACTCGAAGGTCTTTTG-TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGC
*
57528 CTTTGAGCTGAGCGTAGTCG
65 CTTGGAGCTGAGCGTAGTCG
* * * * * *
57548 AACTCAAAGGTCTTTTGGTGGCAGATAGCCCTTTTAGCCTTGAGCTATGCTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
57613 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* *
57632 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGATATGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
57697 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * * * *
57716 AACTCGAAGGTCTTTTGGTGGCAGATAGCCTTTCTAGCCTTGAGCTATGCTACAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
*
57781 TTGGAGCTGAGCGTAGTCT
66 TTGGAGCTGAGCGTAGTCG
* * *
57800 AACTCGAAGGTCTTTGGCTGGCAGATAACCTTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
*
57865 TTGGAGCTGAGCGTAATCG
66 TTGGAGCTGAGCGTAGTCG
* * * *
57884 AACTCGAAGGTCTTTTGGTGGCAGATATCCCTTCTAGCCTTGAGATATGCTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
57949 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * *
57968 AACTCGAATGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
58033 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * * * * * *
58052 AACTCGAAGGTATTTTGGTGGAAGGTAGCCCTTCTAGCCTTCAGCTATGCTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
* *
58117 TTGGAGCTGAACGTAGTCA
66 TTGGAGCTGAGCGTAGTCG
* * *
58136 AACTCGAAGGTCTTTGGTTGGAAGAAAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
58201 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * *
58220 AACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
*
58285 TTGGAGCTGAGCGTAATCG
66 TTGGAGCTGAGCGTAGTCG
* * *
58304 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCCGCAAATGATATGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
* *
58369 TTGGAGCTGGGCGTGGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * * *
58388 AACTCGAAGGTC-TTGGCTGACAGATAACCATTCTCGCCTTGAGTTATG
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
58436 TTGCCGATAG
Statistics
Matches: 862, Mismatches: 108, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
83 34 0.04
84 824 0.96
85 4 0.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (84 bp):
AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCC
TTGGAGCTGAGCGTAGTCG
Found at i:57600 original size:168 final size:168
Alignment explanation
Indices: 57400--58435 Score: 1653
Period size: 168 Copynumber: 6.2 Consensus size: 168
57390 TCTTCAGTTA
* * * * * * *
57400 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAA
1 GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* * *
57465 ACTCGAAGGTCTTTGATTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCT
66 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
* *
57530 TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTG
131 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
*
57568 GCAGATAGCCCTTTTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
*
57633 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGATATGCCT
66 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
57698 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
131 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
* * *
57736 GCAGATAGCCTTTCTAGCCTTGAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCTA
1 GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* *
57801 ACTCGAAGGTCTTTGGCTGGCAGATAACCTTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
66 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
*
57866 TGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGTG
131 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
* *
57904 GCAGATATCCCTTCTAGCCTTGAGATATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* *
57969 ACTCGAATGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCT
66 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
*
58034 TGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTGGTG
131 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
* * * * *
58072 GAAGGTAGCCCTTCTAGCCTTCAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCAA
1 GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* *
58137 ACTCGAAGGTCTTTGGTTGGAAGAAAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
66 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
58202 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
131 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
* * *
58240 GCAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAATCGA
1 GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* *
58305 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCCGCAAATGATATGCCT
66 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
* *
58370 TGGAGCTGGGCGTGGTCGAACTCGAAGGTC--TTGGCTG
131 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TG
* * * * *
58407 ACAGATAACCATTCTCGCCTTGAGTTATG
1 GCAGATAGCCCTTCTAGCCTTGAGCTATG
58436 TTGCCGATAG
Statistics
Matches: 804, Mismatches: 63, Indels: 3
0.92 0.07 0.00
Matches are distributed among these distances:
166 4 0.00
167 27 0.03
168 773 0.96
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (168 bp):
GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTG
Found at i:59414 original size:23 final size:23
Alignment explanation
Indices: 59388--59433 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
59378 AAGAACCAAG
*
59388 ATAAA-CTTAAATATACCATTAAA
1 ATAAAGCTTAAACAT-CCATTAAA
*
59411 ATAAAGTTTAAACATCCATTAAA
1 ATAAAGCTTAAACATCCATTAAA
59434 CCAACCACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (23 bp):
ATAAAGCTTAAACATCCATTAAA
Found at i:71690 original size:100 final size:98
Alignment explanation
Indices: 71469--71728 Score: 369
Period size: 100 Copynumber: 2.6 Consensus size: 98
71459 GGCTAGCTGA
** * * *
71469 ATCCATAAAGCTAGGGCGTTTAACCAATTACTCTAGAGGGACATCTCAA-TATCATTGTATAGAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAACT-TTATTGTATAGAT
71533 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
65 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
* *
71567 ATCCATAAAGCCGGGGCGTTTAACTAATTGCTCTAGAGGTACAACTCAAGCTTTATTGTATAGAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA-CTTTATTGTATAGAT
* *
71632 ATTATGATCACCTTTATCAGGCTTAGCTGAATCTT
65 ATTATAATCACCTTTATCAGGC-TAGCTGAATATT
** *
71667 ATCCATAAAGCCGGGGTATTTAACCAATTGCTCTAGAGGGATAACTCAATCTTTATTGTATA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA-CTTTATTGTATA
71729 TTATAATATT
Statistics
Matches: 144, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
98 43 0.30
99 33 0.23
100 68 0.47
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (98 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAACTTTATTGTATAGATA
TTATAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:78518 original size:14 final size:14
Alignment explanation
Indices: 78486--78518 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
78476 AAATAATATT
78486 GAAAACTTGAACTC
1 GAAAACTTGAACTC
78500 GAAAAGCTTGAACTC
1 GAAAA-CTTGAACTC
78515 -AAAA
1 GAAAA
78519 AAAATTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (14 bp):
GAAAACTTGAACTC
Found at i:79830 original size:12 final size:12
Alignment explanation
Indices: 79796--79838 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
79786 AAATTATGTA
*
79796 TTAATTCTAATCC
1 TTAATTATAAT-C
79809 TTATATTATAATC
1 TTA-ATTATAATC
79822 TTAATTATAATC
1 TTAATTATAATC
79834 ATTAA
1 -TTAA
79839 ATTAATTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 9 0.33
13 11 0.41
14 7 0.26
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (12 bp):
TTAATTATAATC
Found at i:80367 original size:2 final size:2
Alignment explanation
Indices: 80351--80398 Score: 60
Period size: 2 Copynumber: 23.5 Consensus size: 2
80341 TTTAATCTTC
* * *
80351 TA TA TA CA TA CA TA TA TA CTA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
80394 TA TA T
1 TA TA T
80399 GCATCATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:80428 original size:8 final size:8
Alignment explanation
Indices: 80358--80468 Score: 61
Period size: 8 Copynumber: 13.8 Consensus size: 8
80348 TTCTATATAC
80358 ATACATAT
1 ATACATAT
*
80366 ATAC-TAC
1 ATACATAT
*
80373 ATATATAT
1 ATACATAT
*
80381 ATATATAT
1 ATACATAT
*
80389 ATATATAT
1 ATACATAT
*
80397 ATGCATCATAA
1 AT--A-CATAT
*
80408 ATACAT-C
1 ATACATAT
80415 ATACATAT
1 ATACATAT
80423 ATACATGA-
1 ATACAT-AT
*
80431 ATCATATAT
1 AT-ACATAT
80440 ATACATAT
1 ATACATAT
*
80448 CTA-AGTAT
1 ATACA-TAT
80456 A-ACATAT
1 ATACATAT
80463 ATACAT
1 ATACAT
80469 GCATCTTATC
Statistics
Matches: 81, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
7 17 0.21
8 51 0.63
9 7 0.09
10 1 0.01
11 5 0.06
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.37
Consensus pattern (8 bp):
ATACATAT
Found at i:80545 original size:18 final size:17
Alignment explanation
Indices: 80516--80554 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
80506 TATATATACA
80516 TATAAGTATAACATATG
1 TATAAGTATAACATATG
*
80533 TATAAGTTATAACATGTG
1 TATAAG-TATAACATATG
80551 TATA
1 TATA
80555 TAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (17 bp):
TATAAGTATAACATATG
Found at i:80776 original size:4 final size:4
Alignment explanation
Indices: 80767--80812 Score: 78
Period size: 4 Copynumber: 12.0 Consensus size: 4
80757 TTTCATGCAT
80767 CATA CATA CAT- CATA CATA CATA CATA CATA -ATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
80813 TATAATATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 6 0.15
4 34 0.85
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:80791 original size:19 final size:19
Alignment explanation
Indices: 80767--80819 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
80757 TTTCATGCAT
*
80767 CATACATACATCATACATA
1 CATACATACATAATACATA
80786 CATACATACATAATACATA
1 CATACATACATAATACATA
*
80805 CATACATATATAATA
1 CATACATACATAATA
80820 TACTTATGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (19 bp):
CATACATACATAATACATA
Found at i:80812 original size:15 final size:16
Alignment explanation
Indices: 80767--80812 Score: 78
Period size: 15 Copynumber: 3.0 Consensus size: 16
80757 TTTCATGCAT
80767 CATACATACAT-CATA
1 CATACATACATACATA
80782 CATACATACATACATA
1 CATACATACATACATA
80798 -ATACATACATACATA
1 CATACATACATACATA
80813 TATAATATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 26 0.87
16 4 0.13
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (16 bp):
CATACATACATACATA
Found at i:82829 original size:37 final size:38
Alignment explanation
Indices: 82763--82837 Score: 134
Period size: 37 Copynumber: 2.0 Consensus size: 38
82753 ATTAAAGTGT
82763 CAAGGGTATAATTGATTTTGGGACACTTCGATATATGC
1 CAAGGGTATAATTGATTTTGGGACACTTCGATATATGC
*
82801 CAAGGGTATAATTGA-TTTGGGACACTTCGATTTATGC
1 CAAGGGTATAATTGATTTTGGGACACTTCGATATATGC
82838 AGTGTTTTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 21 0.58
38 15 0.42
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (38 bp):
CAAGGGTATAATTGATTTTGGGACACTTCGATATATGC
Done.