Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002435.1 Hibiscus syriacus cultivar Beakdansim tig00004980_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: 104052
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2857 original size:6 final size:6
Alignment explanation
Indices: 2848--2872 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2838 GCGAAGGAGT
2848 ACGAGG ACGAGG ACGAGG ACGAGG A
1 ACGAGG ACGAGG ACGAGG ACGAGG A
2873 AGAAGAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.48, T:0.00
Consensus pattern (6 bp):
ACGAGG
Found at i:6425 original size:81 final size:81
Alignment explanation
Indices: 6287--6445 Score: 237
Period size: 81 Copynumber: 2.0 Consensus size: 81
6277 AGTCTCTTGC
* * * *
6287 ACAACTGGCTCGGTAGCTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGT
1 ACAACCGGCTCAGTAACTTCCTGCTCTACACCTATGTGAGAGCTTGTCGATCCGCCATTTCGTGT
6352 GCGAACCATTCTCGGT
66 GCGAACCATTCTCGGT
* * * *
6368 ACAACCGGCTCAGTAACTTCCTGCTCTACACCTATGTGCGAGCTTGTTGCTCTGCCATTTCGTGT
1 ACAACCGGCTCAGTAACTTCCTGCTCTACACCTATGTGAGAGCTTGTCGATCCGCCATTTCGTGT
*
6433 GTGAACCATTCTC
66 GCGAACCATTCTC
6446 TGTAACTCGC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 69 1.00
ACGTcount: A:0.17, C:0.31, G:0.21, T:0.31
Consensus pattern (81 bp):
ACAACCGGCTCAGTAACTTCCTGCTCTACACCTATGTGAGAGCTTGTCGATCCGCCATTTCGTGT
GCGAACCATTCTCGGT
Found at i:6772 original size:112 final size:113
Alignment explanation
Indices: 6562--6772 Score: 307
Period size: 112 Copynumber: 1.9 Consensus size: 113
6552 AATTAACGAT
** * *
6562 TGAGCACCTCTGTGCTTCAATTGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTAACACCTCTGTGTAGCCAAAAGCGATTGAGCACCTC
* * *
6627 TTTGCTTCAATCGATAACTGACACCTCTGTGCAGTTAAAAAAAATGAC
66 TATGCTTCAATCGAGAACTGACACCTCTATGCAGTTAAAAAAAATGAC
* * * *
6675 TGAGCACCTCTGTGCTTCAGCCGGGAGCTAACACCTCTGTGTAGCTAAGA-CGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTAACACCTCTGTGTAGCCAAAAGCGATTGAGCACCTC
*
6739 TATGCTTCAATCGAGGACTGACACCTCTATGCAG
66 TATGCTTCAATCGAGAACTGACACCTCTATGCAG
6773 CCAAAATGAC
Statistics
Matches: 86, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
112 43 0.50
113 43 0.50
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (113 bp):
TGAGCACCTCTGTGCTTCAACCGAGAGCTAACACCTCTGTGTAGCCAAAAGCGATTGAGCACCTC
TATGCTTCAATCGAGAACTGACACCTCTATGCAGTTAAAAAAAATGAC
Found at i:6787 original size:54 final size:55
Alignment explanation
Indices: 6562--6804 Score: 233
Period size: 54 Copynumber: 4.4 Consensus size: 55
6552 AATTAACGAT
* * *
6562 TGAGCACCTCTGTGCTTCAATTGA-GAGCTGACACCTCTGTGTAGCCAAAAGTGAT
1 TGAGCACCTCTGTGCTTCAATCGAGGAGCTGACACCTCTGTGCAGCCAAAA-TGAC
* * * **
6617 TGAGCACCTCTTTGCTTCAATCGA-TAACTGACACCTCTGTGCAGTTAAAAAAAATGAC
1 TGAGCACCTCTGTGCTTCAATCGAGGAGCTGACACCTCTGTGCAG----CCAAAATGAC
** * * * * * *
6675 TGAGCACCTCTGTGCTTCAGCCG-GGAGCTAACACCTCTGTGTAGCTAAGACGAT
1 TGAGCACCTCTGTGCTTCAATCGAGGAGCTGACACCTCTGTGCAGCCAAAATGAC
* *
6729 TGAGCACCTCTATGCTTCAATCGAGGA-CTGACACCTCTATGCAGCCAAAATGAC
1 TGAGCACCTCTGTGCTTCAATCGAGGAGCTGACACCTCTGTGCAGCCAAAATGAC
* *
6783 TGAGCACCTTTGTGTTTCAATC
1 TGAGCACCTCTGTGCTTCAATC
6805 TAAAATCTAG
Statistics
Matches: 149, Mismatches: 33, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
54 64 0.43
55 42 0.28
58 39 0.26
59 4 0.03
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (55 bp):
TGAGCACCTCTGTGCTTCAATCGAGGAGCTGACACCTCTGTGCAGCCAAAATGAC
Found at i:22299 original size:32 final size:32
Alignment explanation
Indices: 22254--22314 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
22244 GTGCTACCCC
*
22254 ATCTGGAGGACTTTTAGAGGCTCTTCCTAGCA
1 ATCTGGAGGACTTTTAGAGGCACTTCCTAGCA
*
22286 ATCTGGAGTACTTTTAGAGGCACTTCCTA
1 ATCTGGAGGACTTTTAGAGGCACTTCCTA
22315 ATAAGATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (32 bp):
ATCTGGAGGACTTTTAGAGGCACTTCCTAGCA
Found at i:24482 original size:16 final size:17
Alignment explanation
Indices: 24449--24482 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
24439 ATTAAACTAA
24449 AAATATATAATCTTGAT
1 AAATATATAATCTTGAT
*
24466 AAATATATTAT-TTGAT
1 AAATATATAATCTTGAT
24482 A
1 A
24483 TATTCACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (17 bp):
AAATATATAATCTTGAT
Found at i:25764 original size:17 final size:18
Alignment explanation
Indices: 25734--25767 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
25724 AAAAACACAC
*
25734 ATTACATTATTAAAATAA
1 ATTACATTAGTAAAATAA
25752 ATTA-ATTAGTAAAATA
1 ATTACATTAGTAAAATA
25768 TAATCGACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
ATTACATTAGTAAAATAA
Found at i:28110 original size:3 final size:3
Alignment explanation
Indices: 28088--28165 Score: 79
Period size: 3 Copynumber: 26.0 Consensus size: 3
28078 ATGTAAAATT
* * *
28088 ATA ATA TTA ATA AAA ATA ATA AT- ATA A-A TATA AAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
**
28132 ATAA ATA ATA ATA ATA ATA ACG ATA ATA ATA ATA
1 AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28166 TACAAAAAAG
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
2 3 0.05
3 54 0.89
4 4 0.07
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:28621 original size:129 final size:132
Alignment explanation
Indices: 28363--28704 Score: 453
Period size: 129 Copynumber: 2.6 Consensus size: 132
28353 CGTCTAAGGG
* * * * *
28363 TGACATGGTTCCTACGTGATGAGGAAATCTAGTC-GAGGGATGACACTGCTCATACATGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTG-GGGATGACACGGCTCATACATGATGAAG
* * *
28427 AGTTCTGGTCATCTTTAGGAGGAGTGATAACACGATTCCTACGTGATAAGGATGGCTGGTTATCT
65 AGTTCTGGCCATC-TTA-GAAGAGTGATAACACGATTCCTACGTGATAAGGACGGCTGGTTATCT
28492 A-GGC
128 ATGGC
*
28496 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGG-ATGACACGGCTCATACATGATGAAG
* *
28561 AGTTCTGGCCATC-TA-AAG-GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAT
65 AGTTCTGGCCATCTTAGAAGAGTGATAACACGATTCCTACGTGATAAGGACGGCTGGTTATCTAT
*
28623 GGT
130 GGC
* * *
28626 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGCTCATACATGATGAAGA
*
28691 CG-GCTGGCCATCTT
66 -GTTCTGGCCATCTT
28705 TAGGAGTTAT
Statistics
Matches: 187, Mismatches: 17, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
129 71 0.38
130 45 0.24
132 2 0.01
133 33 0.18
134 36 0.19
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (132 bp):
TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGCTCATACATGATGAAGA
GTTCTGGCCATCTTAGAAGAGTGATAACACGATTCCTACGTGATAAGGACGGCTGGTTATCTATG
GC
Found at i:28756 original size:28 final size:28
Alignment explanation
Indices: 28716--28778 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
28706 AGGAGTTATG
* *
28716 GTTTCAAGAGAAACCA-AATTAAAGATTT
1 GTTTCAAAAGAAA-CAGAATCAAAGATTT
*
28744 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGAATCAAAGATTT
28772 GTTTCAA
1 GTTTCAA
28779 GAAAACAAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGAATCAAAGATTT
Found at i:28807 original size:30 final size:28
Alignment explanation
Indices: 28736--28811 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 28
28726 AAACCAAATT
28736 AAAGATTTGTTTCAAAAGAAACAGACTC
1 AAAGATTTGTTTCAAAAGAAACAGACTC
*
28764 AAAGATTTGTTTCAAGA-AAACA-AGCTC
1 AAAGATTTGTTTCAAAAGAAACAGA-CTC
28791 AAAGATAATGTGTTTCAAAAG
1 AAAGAT--T-TGTTTCAAAAG
28812 CAACTGTCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.02
27 14 0.34
28 16 0.39
29 1 0.02
30 9 0.22
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAGACTC
Found at i:29045 original size:37 final size:36
Alignment explanation
Indices: 28989--29115 Score: 106
Period size: 37 Copynumber: 3.6 Consensus size: 36
28979 GAAACATATT
*
28989 CAAAGATTTT-TTTCAAAAGAAATTATCTTAAGATAGA
1 CAAA-ATTTTGTTTCAAAAGAAACTATCTTAAGA-AGA
* * * *
29026 CAAAATTTTGTTTCCAAAGAAACAAAC-TCA-AAG-
1 CAAAATTTTGTTTCAAAAGAAACTATCTTAAGAAGA
* *
29059 ---ATTTTTGTTTTAAAAGAAACTATCTTAAGAGAGA
1 CAAAATTTTGTTTCAAAAGAAACTATCTTAAGA-AGA
*
29093 CAAAATTTTGTTTCCAAAGAAAC
1 CAAAATTTTGTTTCAAAAGAAAC
29116 AAACTCAAAG
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
30 19 0.28
31 2 0.03
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 7 0.10
37 34 0.50
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (36 bp):
CAAAATTTTGTTTCAAAAGAAACTATCTTAAGAAGA
Found at i:29094 original size:67 final size:66
Alignment explanation
Indices: 28978--29147 Score: 256
Period size: 67 Copynumber: 2.6 Consensus size: 66
28968 TCATTTTAAG
* * * *
28978 AGAAACATATTCAAAGA-TTTTTTTCAAAAGAAATTATCTTAAGATAGACAAAATTTTGTTTCCA
1 AGAAACAAACTCAAAGATTTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCA
29042 A
66 A
*
29043 AGAAACAAACTCAAAGATTTTTGTTTTAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTT-TTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCC
29108 AA
65 AA
*
29110 AGAAACAAACTCAAAGA--TTTTTTCAAAAGAAACAATCT
1 AGAAACAAACTCAAAGATTTTTTTTCAAAAGAAACTATCT
29148 CAAAGATTTT
Statistics
Matches: 96, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
64 16 0.17
65 18 0.19
66 4 0.04
67 58 0.60
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (66 bp):
AGAAACAAACTCAAAGATTTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCA
A
Found at i:29157 original size:26 final size:27
Alignment explanation
Indices: 29103--29159 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
29093 CAAAATTTTG
*
29103 TTTCCAAAGAAACAAACTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
*
29130 TTTCAAAAGAAACAATCTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
29157 TTT
1 TTT
29160 TCACAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.32
Consensus pattern (27 bp):
TTTCAAAAGAAACAAACTCAAAGATTT
Found at i:29221 original size:52 final size:53
Alignment explanation
Indices: 29146--29249 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
29136 AAGAAACAAT
29146 CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
29200 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
29250 CAATAAATAG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 41 0.84
54 8 0.16
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:29289 original size:25 final size:26
Alignment explanation
Indices: 29260--29338 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 26
29250 CAATAAATAG
29260 ACTCAAAGATTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTTCAAAAGAAACAA
*
29285 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAG--ATTT-TTCAAAAGAAACAA
*
29314 ACTCAAAGATTTTTTCAAGAGAAAC
1 ACTCAAAGA-TTTTTCAAAAGAAAC
29339 TGTCTCAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
25 8 0.17
27 15 0.33
28 14 0.30
29 9 0.20
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.25
Consensus pattern (26 bp):
ACTCAAAGATTTTTCAAAAGAAACAA
Found at i:29346 original size:27 final size:26
Alignment explanation
Indices: 29260--29338 Score: 106
Period size: 28 Copynumber: 3.0 Consensus size: 26
29250 CAATAAATAG
29260 ACTCAAAGA-TTTTTCAAAAGAAACA
1 ACTCAAAGATTTTTTCAAAAGAAACA
*
29285 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTT-TTCAAAAGAAAC-A
*
29314 ACTCAAAGATTTTTTCAAGAGAAAC
1 ACTCAAAGATTTTTTCAAAAGAAAC
29339 TGTCTCAAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 9 0.19
27 13 0.28
28 14 0.30
29 11 0.23
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.25
Consensus pattern (26 bp):
ACTCAAAGATTTTTTCAAAAGAAACA
Found at i:29620 original size:34 final size:34
Alignment explanation
Indices: 29574--29673 Score: 112
Period size: 34 Copynumber: 2.9 Consensus size: 34
29564 ATTATGATAG
29574 AAGATGATGTCTCAAGCGAGACAAAATTTG-CTTT
1 AAGAT-ATGTCTCAAGCGAGACAAAATTTGTCTTT
** *
29608 AAGATATAGTCTCAAATGAGACAAAATTTGTTTTT
1 AAGATAT-GTCTCAAGCGAGACAAAATTTGTCTTT
* *
29643 AGAGAAATTGTCTCAAGCGAGACAAAGTTTG
1 A-AGATA-TGTCTCAAGCGAGACAAAATTTG
29674 AGAAAACGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
33 2 0.04
34 25 0.45
35 4 0.07
36 23 0.42
37 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (34 bp):
AAGATATGTCTCAAGCGAGACAAAATTTGTCTTT
Found at i:29665 original size:36 final size:34
Alignment explanation
Indices: 29581--29673 Score: 114
Period size: 36 Copynumber: 2.7 Consensus size: 34
29571 TAGAAGATGA
*
29581 TGTCTCAAGCGAGACAAAATTTGCTTTAAGATAT
1 TGTCTCAAGCGAGACAAAATTTGCTTTAAGAAAT
* ** *
29615 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTG-CTTTA-AGAAAT
*
29651 TGTCTCAAGCGAGACAAAGTTTG
1 TGTCTCAAGCGAGACAAAATTTG
29674 AGAAAACGAT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
34 20 0.42
35 4 0.08
36 24 0.50
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (34 bp):
TGTCTCAAGCGAGACAAAATTTGCTTTAAGAAAT
Found at i:29838 original size:37 final size:35
Alignment explanation
Indices: 29763--29881 Score: 139
Period size: 36 Copynumber: 3.3 Consensus size: 35
29753 AGTGAGGCGG
29763 AATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAA
1 AATTTGTTTTT-AAGAAATTGTCTCAAACGAGACAA
* * * *
29799 ATTTTGTTTTTTAGAAAGCTGTCTCAATCGAGACAA
1 AATTTGTTTTTAAGAAA-TTGTCTCAAACGAGACAA
** *
29835 AATTTGCTTTGAAAGAAATTGTCTCAAGCGAGACAAA
1 AATTTG-TTTTTAAGAAATTGTCTCAAACGAGAC-AA
29872 AATTTGTTTT
1 AATTTGTTTT
29882 AAAATTCTCA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
35 5 0.07
36 48 0.70
37 16 0.23
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (35 bp):
AATTTGTTTTTAAGAAATTGTCTCAAACGAGACAA
Found at i:30438 original size:4 final size:4
Alignment explanation
Indices: 30429--30498 Score: 81
Period size: 4 Copynumber: 18.0 Consensus size: 4
30419 TTTATGTATC
* *
30429 ATGT ATGT A--T ATGT ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATAT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
30475 ACGT ATAT ACGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT
30499 GTATACTCTT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 2 0.04
4 52 0.96
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:31706 original size:12 final size:12
Alignment explanation
Indices: 31685--31735 Score: 79
Period size: 12 Copynumber: 4.4 Consensus size: 12
31675 GTTCTTTGCT
*
31685 TTTTTCCTTTGA
1 TTTTTGCTTTGA
31697 TTTTTGCTTTGA
1 TTTTTGCTTTGA
31709 TTTTT-CTTTG-
1 TTTTTGCTTTGA
31719 TTTTTGCTTTGA
1 TTTTTGCTTTGA
31731 TTTTT
1 TTTTT
31736 TTTCTCTCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
10 5 0.14
11 10 0.28
12 21 0.58
ACGTcount: A:0.06, C:0.10, G:0.12, T:0.73
Consensus pattern (12 bp):
TTTTTGCTTTGA
Found at i:31712 original size:11 final size:11
Alignment explanation
Indices: 31686--31734 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
31676 TTCTTTGCTT
*
31686 TTTTCCTTTGA
1 TTTTGCTTTGA
31697 TTTTTGCTTTGA
1 -TTTTGCTTTGA
* *
31709 TTTTTCTTTGT
1 TTTTGCTTTGA
31720 TTTTGCTTTGA
1 TTTTGCTTTGA
31731 TTTT
1 TTTT
31735 TTTTCTCTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.06, C:0.10, G:0.12, T:0.71
Consensus pattern (11 bp):
TTTTGCTTTGA
Found at i:31764 original size:12 final size:12
Alignment explanation
Indices: 31670--31794 Score: 53
Period size: 11 Copynumber: 10.4 Consensus size: 12
31660 CTTTATCCTC
31670 TTTTTGTTCTTTG
1 TTTTT-TTCTTTG
*
31683 CTTTTTTCCTTTG
1 -TTTTTTTCTTTG
* *
31696 ATTTTTGCTTTG
1 TTTTTTTCTTTG
*
31708 -ATTTTTCTTTG
1 TTTTTTTCTTTG
*
31719 -TTTTTGCTTTG
1 TTTTTTTCTTTG
*
31730 ATTTTTTT-TCT-
1 -TTTTTTTCTTTG
* * **
31741 CTCTGCTCTTTG
1 TTTTTTTCTTTG
31753 TTTTTTTCTTTG
1 TTTTTTTCTTTG
*
31765 CTCTTTTCTCTTTG
1 -T-TTTTTTCTTTG
* *
31779 -ATTTTTCCTTG
1 TTTTTTTCTTTG
31790 TTTTT
1 TTTTT
31795 GATTGGATCT
Statistics
Matches: 81, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
10 3 0.04
11 28 0.35
12 23 0.28
13 12 0.15
14 15 0.19
ACGTcount: A:0.03, C:0.15, G:0.10, T:0.71
Consensus pattern (12 bp):
TTTTTTTCTTTG
Found at i:31766 original size:19 final size:21
Alignment explanation
Indices: 31732--31770 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31722 TTGCTTTGAT
31732 TTTTTTTCTCTCTGCTCTTTG
1 TTTTTTTCTCTCTGCTCTTTG
31753 TTTTTTTCT-T-TGCTCTTT
1 TTTTTTTCTCTCTGCTCTTT
31771 TCTCTTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 1 0.06
21 9 0.50
ACGTcount: A:0.00, C:0.21, G:0.08, T:0.72
Consensus pattern (21 bp):
TTTTTTTCTCTCTGCTCTTTG
Found at i:32434 original size:26 final size:24
Alignment explanation
Indices: 32399--32469 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 24
32389 CAAAGTGGAA
*
32399 AGAATGTTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
*
32423 AGGGAATATTTCAAGG--TCGAA-A-
1 A--GAATATTTCAAGGTCTCAAAGAG
32445 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
32469 A
1 A
32470 TAGAATGTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
20 13 0.34
22 5 0.13
23 2 0.05
24 6 0.16
26 12 0.32
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (24 bp):
AGAATATTTCAAGGTCTCAAAGAG
Found at i:32474 original size:26 final size:26
Alignment explanation
Indices: 32396--32475 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
32386 TTTCAAAGTG
*
32396 GAAAGAATGTTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
**
32422 GAGGGAATATTTCAAGG--TC---GA
1 GAAAGAATATTTCAAGGTCTCAAAGA
32443 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
*
32468 GATAGAAT
1 GAAAGAAT
32476 GTCAAAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
20 14 0.33
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 20 0.48
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (26 bp):
GAAAGAATATTTCAAGGTCTCAAAGA
Found at i:36473 original size:17 final size:18
Alignment explanation
Indices: 36443--36476 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
36433 AAAAACACAC
*
36443 ATTACATTATTAAAATAA
1 ATTACATTAGTAAAATAA
36461 ATTA-ATTAGTAAAATA
1 ATTACATTAGTAAAATA
36477 TAATCGACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
ATTACATTAGTAAAATAA
Found at i:38825 original size:17 final size:17
Alignment explanation
Indices: 38803--38886 Score: 93
Period size: 17 Copynumber: 4.9 Consensus size: 17
38793 CAAAAATATG
* *
38803 TAAAATTATAATATTAA
1 TAAAATAATAATAATAA
38820 TAAAATAATAAT-ATAAA
1 TAAAATAATAATAAT-AA
38837 TATAAA-AATAATAATAA
1 TA-AAATAATAATAATAA
38854 T-AAATAATAATAATAA
1 TAAAATAATAATAATAA
*
38870 TAACGATAATAATAATA
1 TAA-AATAATAATAATA
38887 TACAAAAAAG
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.05
16 13 0.22
17 25 0.43
18 17 0.29
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (17 bp):
TAAAATAATAATAATAA
Found at i:38831 original size:3 final size:3
Alignment explanation
Indices: 38810--38886 Score: 79
Period size: 3 Copynumber: 26.0 Consensus size: 3
38800 ATGTAAAATT
* *
38810 ATA ATA TTA ATA A-A ATA ATA AT- ATA A-A TATA AAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
**
38853 ATAA ATA ATA ATA ATA ATA ACG ATA ATA ATA ATA
1 AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
38887 TACAAAAAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.08
3 52 0.85
4 4 0.07
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:47862 original size:43 final size:43
Alignment explanation
Indices: 47799--47885 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
47789 CAATTGTCTA
*
47799 TTGCATCAAAAATGGGTAAATTATACAAATGGTCACTTATGTT
1 TTGCATCAAAAATGGATAAATTATACAAATGGTCACTTATGTT
47842 TTGCATCAAAAATGGATAAATTATACAAATGGTCACTTATGTT
1 TTGCATCAAAAATGGATAAATTATACAAATGGTCACTTATGTT
47885 T
1 T
47886 GAGTAAGTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (43 bp):
TTGCATCAAAAATGGATAAATTATACAAATGGTCACTTATGTT
Found at i:50177 original size:4 final size:4
Alignment explanation
Indices: 50168--50194 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
50158 TTCAACTATG
50168 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
50195 ACATGCATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:61592 original size:6 final size:6
Alignment explanation
Indices: 61581--61613 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
61571 TATGCCTTCC
61581 ACCCAT ACCCAT ACCCAT ACCCAT ACCCAT ACC
1 ACCCAT ACCCAT ACCCAT ACCCAT ACCCAT ACC
61614 AATGGAGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.00, T:0.15
Consensus pattern (6 bp):
ACCCAT
Found at i:62107 original size:15 final size:14
Alignment explanation
Indices: 62072--62105 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
62062 CTAAATGATC
*
62072 ATTTTTAGTTATAT
1 ATTTTTAGTTATAA
*
62086 ATTTTTAGTTTTAA
1 ATTTTTAGTTATAA
62100 ATTTTT
1 ATTTTT
62106 TATGTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (14 bp):
ATTTTTAGTTATAA
Found at i:65691 original size:30 final size:30
Alignment explanation
Indices: 65655--65711 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
65645 ATCCAGTCAG
*
65655 TCAATTAATCAATTGTAATAATTAAGTCGC
1 TCAATTAATCAATTGTAACAATTAAGTCGC
**
65685 TCAATTAATTGATTGTAACAATTAAGT
1 TCAATTAATCAATTGTAACAATTAAGT
65712 TATGTGTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (30 bp):
TCAATTAATCAATTGTAACAATTAAGTCGC
Found at i:66015 original size:15 final size:15
Alignment explanation
Indices: 65997--66072 Score: 77
Period size: 15 Copynumber: 5.3 Consensus size: 15
65987 GTGAAATTCT
65997 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
66012 AATTATTTATATAAA
1 AATTATTTAAATAAA
* *
66027 AATT-TATCAAT-AA
1 AATTATTTAAATAAA
*
66040 TA-TATTTAAATAAA
1 AATTATTTAAATAAA
**
66054 AATTATTTTTATAAA
1 AATTATTTAAATAAA
66069 AATT
1 AATT
66073 CATCGATAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
12 1 0.02
13 8 0.17
14 7 0.15
15 32 0.67
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:66047 original size:42 final size:42
Alignment explanation
Indices: 65996--66087 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
65986 AGTGAAATTC
*
65996 TAAT-TATTTAAATAAAAATTATTTATATAAAAATTTATCAA
1 TAATATATTTAAATAAAAATTATTTATATAAAAATTCATCAA
* *
66037 TAATATATTTAAATAAAAATTATTTTTATAAAAATTCATCGA
1 TAATATATTTAAATAAAAATTATTTATATAAAAATTCATCAA
66079 TAATATATT
1 TAATATATT
66088 ATTTTATTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (42 bp):
TAATATATTTAAATAAAAATTATTTATATAAAAATTCATCAA
Found at i:69899 original size:73 final size:73
Alignment explanation
Indices: 69787--69934 Score: 260
Period size: 73 Copynumber: 2.0 Consensus size: 73
69777 GCATTTCATC
*
69787 TTAGACCCAACCTCAATTCTCTCCAGTACTCTTGCAGTTTTCAGTATAGCCTTACGCACATGTAC
1 TTAGACCCAACCTCAATTCTCTCCAGTACTCTTGCAGTTTTCAGTATAGCCTTAAGCACATGTAC
69852 TCTTGCAT
66 TCTTGCAT
* * *
69860 TTAGACCCAAGCTCAATTCTCTCCGGTACTCTTGCAGTTTTCAGTATAGCCTTAAGGACATGTAC
1 TTAGACCCAACCTCAATTCTCTCCAGTACTCTTGCAGTTTTCAGTATAGCCTTAAGCACATGTAC
69925 TCTTGCAT
66 TCTTGCAT
69933 TT
1 TT
69935 CAGGTGAGTA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (73 bp):
TTAGACCCAACCTCAATTCTCTCCAGTACTCTTGCAGTTTTCAGTATAGCCTTAAGCACATGTAC
TCTTGCAT
Found at i:76290 original size:3 final size:3
Alignment explanation
Indices: 76284--76308 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
76274 ACTTCTTCTA
76284 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
76309 GGAGTTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:78474 original size:22 final size:23
Alignment explanation
Indices: 78446--78502 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 23
78436 AAATTAATAA
78446 TATATTATGTAAAATG-TTCGAT
1 TATATTATGTAAAATGTTTCGAT
78468 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
78491 TATA--ATGTAAAA
1 TATATTATGTAAAA
78503 ATTATAACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.24
22 16 0.47
23 10 0.29
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (23 bp):
TATATTATGTAAAATGTTTCGAT
Found at i:78545 original size:13 final size:13
Alignment explanation
Indices: 78516--78550 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
78506 ATAACTAATA
*
78516 ATATTAAAT-ATT
1 ATATTAAATAAAT
78528 ATATTAAATAAAT
1 ATATTAAATAAAT
78541 ATATTAAATA
1 ATATTAAATA
78551 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:81552 original size:8 final size:8
Alignment explanation
Indices: 81539--81579 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
81529 CTCATTTTCA
81539 GAGAATTT
1 GAGAATTT
81547 GAGAATTT
1 GAGAATTT
*
81555 -AGAGTTT
1 GAGAATTT
*
81562 GGGAATTT
1 GAGAATTT
81570 GAGAATTT
1 GAGAATTT
81578 GA
1 GA
81580 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:81877 original size:126 final size:126
Alignment explanation
Indices: 81647--82249 Score: 1174
Period size: 126 Copynumber: 4.8 Consensus size: 126
81637 CTATAATCGG
81647 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
81712 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGTACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
81773 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
81838 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
81899 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
81964 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
82025 TTCACTATTCACGTGAAGGCGCGTTCCC-GGGG-GCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
82088 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
82149 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
82214 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
82250 ATAACTTAAA
Statistics
Matches: 473, Mismatches: 2, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
124 120 0.25
125 8 0.02
126 345 0.73
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
Found at i:82216 original size:250 final size:252
Alignment explanation
Indices: 81647--82249 Score: 1174
Period size: 250 Copynumber: 2.4 Consensus size: 252
81637 CTATAATCGG
81647 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
81712 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGTACACTAGATATATCAGTACCTATTATTTCA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTATTTCA
81777 CTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
131 CTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
81842 TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
196 TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
81899 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
81964 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTATTTCA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTATTTCA
82029 CTATTCACGTGAAGGCGCGTTCCC-GGGG-GCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
131 CTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
82092 TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
196 TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
82149 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
82214 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
82250 ATAACTTAAA
Statistics
Matches: 349, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
250 193 0.55
251 4 0.01
252 152 0.44
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (252 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTATTTCA
CTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
Found at i:82730 original size:33 final size:32
Alignment explanation
Indices: 82627--82731 Score: 131
Period size: 33 Copynumber: 3.2 Consensus size: 32
82617 TAAGTTGAAA
*
82627 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAAT-TTAAATTTCGAATAATATAATTT-TAT
*
82661 TTTAAATTTAAATTT-GAATAATATTATTTTATT
1 TTT-AATTTAAATTTCGAATAATATAATTTTA-T
*
82694 TTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTAAATTTCGAATAATATAATTT-TAT
82727 TTTAA
1 TTTAA
82732 AAACATTATC
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
32 12 0.19
33 34 0.55
34 13 0.21
35 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (32 bp):
TTTAATTTAAATTTCGAATAATATAATTTTAT
Found at i:83337 original size:21 final size:21
Alignment explanation
Indices: 83249--83342 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
83239 TATGGTATAA
*
83249 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
83270 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
83291 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
83312 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
83333 AACCCTGCGG
1 AACCCTGCGG
83343 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:85158 original size:18 final size:21
Alignment explanation
Indices: 85118--85157 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
85108 TCTAAATAAA
*
85118 TAATAATTATAAATATTATTT
1 TAATAATTATAAATAATATTT
85139 TAATAA-TA-AAATAATATTT
1 TAATAATTATAAATAATATTT
85158 ACATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 2 0.11
21 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATAATTATAAATAATATTT
Found at i:92148 original size:18 final size:19
Alignment explanation
Indices: 92110--92149 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
92100 GTGATTATTA
* *
92110 ATTATCTTTTTTTTTTCAT
1 ATTATCCTTTATTTTTCAT
92129 ATTATCCTTTATTTTT-AT
1 ATTATCCTTTATTTTTCAT
92147 ATT
1 ATT
92150 TTTTTCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTATCCTTTATTTTTCAT
Found at i:93950 original size:97 final size:100
Alignment explanation
Indices: 93772--93957 Score: 297
Period size: 97 Copynumber: 1.9 Consensus size: 100
93762 CTTTGCAAGT
* *
93772 AAACCTCGCTCAATAAGCAAACCTTGTTCCCCCCTTCTTATTACTGTTAATCCATTTCAGAAGGG
1 AAACCTCGCTCAATAAGCAAACCTTGTTCCCCCCTGC-T-TCACTGTTAATCCATTTCAGAAGGG
93837 AGCGTACAAAAACTGTGGCGTAAAGTGGGAGCAGCAG
64 AGCGTACAAAAACTGTGGCGTAAAGTGGGAGCAGCAG
*
93874 AAACCTCGCTCAATAAGCAAACCTTGTTGCCCCC-GC-TCA-TGTTAATCCATTTCAGAAGGGAG
1 AAACCTCGCTCAATAAGCAAACCTTGTTCCCCCCTGCTTCACTGTTAATCCATTTCAGAAGGGAG
*
93936 CGTACAAAAGCTGTGGCGTAAA
66 CGTACAAAAACTGTGGCGTAAA
93958 CCAGGAAAAT
Statistics
Matches: 80, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
97 44 0.55
98 2 0.03
101 1 0.01
102 33 0.41
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (100 bp):
AAACCTCGCTCAATAAGCAAACCTTGTTCCCCCCTGCTTCACTGTTAATCCATTTCAGAAGGGAG
CGTACAAAAACTGTGGCGTAAAGTGGGAGCAGCAG
Done.