Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001508.1 Hibiscus syriacus cultivar Beakdansim tig00002953_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: 98425
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1107 original size:228 final size:227
Alignment explanation
Indices: 684--1195 Score: 589
Period size: 228 Copynumber: 2.3 Consensus size: 227
674 GGAAATTCCC
* * * *
684 TTTTTACTTTTTAAAAACTTCAA-TTTCAGATTTAAATGAGAAAC-TTTCTTATTTTTTTGGAAA
1 TTTTTACTTTTCAAAAATTTCAATTTTCAGATTT-AATGAGAAACTTTTCTCA--TTTTTCG-AA
*
747 AAAACATGTGAAACTCATGCCCGAAGATCTTATGGATGCCCGAAAGACTTACCATCTTGCTCGAA
62 AAAACATATGAAACTCATGCCCGAAGATCTTATGGATGCCCGAAAGACTTACCATCTTGCTCGAA
* * * * *
812 AGGCTTATAGATACCCAAAAGATTTATGCATCATGCTTGAAAGACTTACTGATGGCCGAATGACT
127 AGACTTACAGATACCCAAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCGAAGGACT
* * * **
877 TAC-CA-TTTGGGAATATTTTACTAGGTAAGAAACTT
192 TACTAATTTTGGAAATAGTTTACTAAATAAGAAAC-T
* *
912 TTTTTACTTTTCAAAAATTTCAATTTTCAGATTTAAGTGAGAAACTTTTCTCATTTTTCG-AGAG
1 TTTTTACTTTTCAAAAATTTCAATTTTCAGATTTAA-TGAGAAACTTTTCTCATTTTTCGAAAAA
* * *
976 ACATATGATAACATCCT-CCCAGAAGGTCTTATGGATGCCCGAATA-ACTTATCATCTTGCTCGA
65 ACATATGA-AAC-TCATGCCC-GAAGATCTTATGGATGCCCGAA-AGACTTACCATCTTGCTCGA
* * *
1039 AA-ACTTACATATGACCCAAATGATTTAAGCTTCATGCTCG-AAGACTTACTGATGGCCCGAAGG
126 AAGACTTACAGAT-ACCCAAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGG-CCGAAGG
1102 ACTTACTAATTTTGGAAATAGTTTACTAAATAAGAAACT
189 ACTTACTAATTTTGGAAATAGTTTACTAAATAAGAAACT
* * *
1141 TTATTACTTTTC--AAATTTTAATATTT-AGATTTAATGAGAAATTTTTCTCATTTTT
1 TTTTTACTTTTCAAAAATTTCAAT-TTTCAGATTTAATGAGAAACTTTTCTCATTTTT
1196 AACCTATAAA
Statistics
Matches: 246, Mismatches: 26, Indels: 26
0.83 0.09 0.09
Matches are distributed among these distances:
226 29 0.12
227 45 0.18
228 110 0.45
229 32 0.13
230 30 0.12
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (227 bp):
TTTTTACTTTTCAAAAATTTCAATTTTCAGATTTAATGAGAAACTTTTCTCATTTTTCGAAAAAA
CATATGAAACTCATGCCCGAAGATCTTATGGATGCCCGAAAGACTTACCATCTTGCTCGAAAGAC
TTACAGATACCCAAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCGAAGGACTTACT
AATTTTGGAAATAGTTTACTAAATAAGAAACT
Found at i:3688 original size:16 final size:17
Alignment explanation
Indices: 3655--3690 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3645 TTTAAAATTT
3655 TAATTATTTTGTAAAAG
1 TAATTATTTTGTAAAAG
*
3672 TAATTGTTTTG-AAAAG
1 TAATTATTTTGTAAAAG
3688 TAA
1 TAA
3691 ATGTGATACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (17 bp):
TAATTATTTTGTAAAAG
Found at i:9789 original size:12 final size:13
Alignment explanation
Indices: 9766--9795 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
9756 ATAAGTGATA
9766 TATATATATATGT
1 TATATATATATGT
9779 TATAT-TATATGT
1 TATATATATATGT
9791 TATAT
1 TATAT
9796 GATCCATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (13 bp):
TATATATATATGT
Found at i:10686 original size:16 final size:17
Alignment explanation
Indices: 10653--10686 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
10643 TTTAAAATTT
*
10653 TAATTATTTTGTAAAAG
1 TAATCATTTTGTAAAAG
10670 TAATCATTTTG-AAAAG
1 TAATCATTTTGTAAAAG
10686 T
1 T
10687 GAATGTGACA
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:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (17 bp):
TAATCATTTTGTAAAAG
Found at i:12502 original size:12 final size:12
Alignment explanation
Indices: 12481--12557 Score: 52
Period size: 12 Copynumber: 6.4 Consensus size: 12
12471 GTTCTCTTTC
*
12481 TTCTTTTATTTT
1 TTCTTCTATTTT
12493 TTCTTCTATTTT
1 TTCTTCTATTTT
*
12505 TTCCTTTTA-TTT
1 TT-CTTCTATTTT
12517 TTCTT-T-TTGTT
1 TTCTTCTATT-TT
* *
12528 GTCTTCTCTTTTT
1 TTCTTCT-ATTTT
* *
12541 TTCATCTTTTTT
1 TTCTTCTATTTT
12553 TTCTT
1 TTCTT
12558 TTCCATTCTT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
10 2 0.04
11 9 0.17
12 28 0.53
13 12 0.23
14 2 0.04
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.77
Consensus pattern (12 bp):
TTCTTCTATTTT
Found at i:12515 original size:13 final size:12
Alignment explanation
Indices: 12481--12523 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
12471 GTTCTCTTTC
12481 TTCTTTTATTTT
1 TTCTTTTATTTT
*
12493 TTCTTCTATTTT
1 TTCTTTTATTTT
12505 TTCCTTTTA-TTT
1 TT-CTTTTATTTT
12517 TTCTTTT
1 TTCTTTT
12524 TGTTGTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 5 0.18
12 18 0.64
13 5 0.18
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (12 bp):
TTCTTTTATTTT
Found at i:12572 original size:48 final size:48
Alignment explanation
Indices: 12489--12604 Score: 112
Period size: 49 Copynumber: 2.4 Consensus size: 48
12479 TCTTCTTTTA
* * * * *
12489 TTTTTTCTTCTATTTTTTCCTTTTATTTTTCTTTTTGT-TGTCTT-CTCT
1 TTTTTTCATCT-TTTTTTTCTTTTATTCTTCTTTTTATCTCT-TTCCTCT
12537 TTTTTTCATCTTTTTTTTCTTTTCCATTCTT-TTTTTATCTCTTTCCTCT
1 TTTTTTCATCTTTTTTTTCTTTT--ATTCTTCTTTTTATCTCTTTCCTCT
* *
12586 TTCTTTCCTCTTTTTTTTC
1 TTTTTTCATCTTTTTTTTC
12605 GAATATGAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
47 11 0.19
48 18 0.32
49 28 0.49
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.73
Consensus pattern (48 bp):
TTTTTTCATCTTTTTTTTCTTTTATTCTTCTTTTTATCTCTTTCCTCT
Found at i:12586 original size:19 final size:17
Alignment explanation
Indices: 12539--12587 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
12529 TCTTCTCTTT
*
12539 TTTTCATCTTTTTTTTC
1 TTTTCCTCTTTTTTTTC
12556 TTTTCCATTCTTTTTTTATC
1 TTTTCC--TCTTTTTTT-TC
12576 TCTTTCCTCTTT
1 T-TTTCCTCTTT
12588 CTTTCCTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.19
19 14 0.52
20 3 0.11
21 5 0.19
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCCTCTTTTTTTTC
Found at i:20259 original size:54 final size:54
Alignment explanation
Indices: 20196--20409 Score: 333
Period size: 54 Copynumber: 4.0 Consensus size: 54
20186 TCTGTGGTTT
*
20196 TTGCACACATAGTGCTAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
1 TTGCACACATAGTGCTAATACAGTAATTCACAAACTCATTATGAATTACTTAGG
*
20250 TTGCACACATAGTGCCAATACAGTAATTCACAAACTCATTATGAATTACTTAGG
1 TTGCACACATAGTGCTAATACAGTAATTCACAAACTCATTATGAATTACTTAGG
* * *
20304 TTTCACACATAGTG-TCAATACGGTAATTCACAAACTCAATATGAATTACTTAGG
1 TTGCACACATAGTGCT-AATACAGTAATTCACAAACTCATTATGAATTACTTAGG
* *
20358 TTGCACACATAGTGGC-AATACAATAATTCACAAAGTCATTATGAATTACTTA
1 TTGCACACATAGT-GCTAATACAGTAATTCACAAACTCATTATGAATTACTTA
20410 AAAACTCATT
Statistics
Matches: 146, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
54 145 0.99
55 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (54 bp):
TTGCACACATAGTGCTAATACAGTAATTCACAAACTCATTATGAATTACTTAGG
Found at i:20388 original size:108 final size:108
Alignment explanation
Indices: 20199--20409 Score: 370
Period size: 108 Copynumber: 2.0 Consensus size: 108
20189 GTGGTTTTTG
*
20199 CACACATAGTGCTAATACGGTAATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTG
1 CACACATAGTGCTAATACGGTAATTCACAAACTCAATATGAATTACTTAGGTTGCACACATAGTG
*
20264 CCAATACAGTAATTCACAAACTCATTATGAATTACTTAGGTTT
66 CCAATACAATAATTCACAAACTCATTATGAATTACTTAGGTTT
20307 CACACATAGTG-TCAATACGGTAATTCACAAACTCAATATGAATTACTTAGGTTGCACACATAGT
1 CACACATAGTGCT-AATACGGTAATTCACAAACTCAATATGAATTACTTAGGTTGCACACATAGT
* *
20371 GGCAATACAATAATTCACAAAGTCATTATGAATTACTTA
65 GCCAATACAATAATTCACAAACTCATTATGAATTACTTA
20410 AAAACTCATT
Statistics
Matches: 98, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
107 1 0.01
108 97 0.99
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (108 bp):
CACACATAGTGCTAATACGGTAATTCACAAACTCAATATGAATTACTTAGGTTGCACACATAGTG
CCAATACAATAATTCACAAACTCATTATGAATTACTTAGGTTT
Found at i:22072 original size:21 final size:21
Alignment explanation
Indices: 22048--22104 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
22038 TTTTACACTT
*
22048 AGGGAACCAATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
22069 AGGGAACCGATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
*
22090 AGGGTACCGATTCCC
1 AGGGAACCGATTCCC
22105 CCACGCTCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGAACCGATTCCCTATGAG
Found at i:22436 original size:32 final size:33
Alignment explanation
Indices: 22340--22438 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
22330 AACTCAACAT
* * *
22340 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
22373 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
22406 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
22438 A
1 A
22439 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:22457 original size:21 final size:21
Alignment explanation
Indices: 22433--22474 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
22423 ACTTCAAGTT
22433 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
22454 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
22475 AAAAATAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:24940 original size:26 final size:28
Alignment explanation
Indices: 24904--24960 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
24894 AAAAAACCGG
24904 TTTTTCCC-AAATCCGG-T-TTCGGATTT
1 TTTTTCCCAAAAT-CGGATATTCGGATTT
*
24930 TTTTTCGCAAAATCGGATATTCGGATTT
1 TTTTTCCCAAAATCGGATATTCGGATTT
24958 TTT
1 TTT
24961 GTGCACCCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 10 0.37
27 5 0.19
28 12 0.44
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.47
Consensus pattern (28 bp):
TTTTTCCCAAAATCGGATATTCGGATTT
Found at i:26177 original size:60 final size:58
Alignment explanation
Indices: 26022--26196 Score: 154
Period size: 60 Copynumber: 2.9 Consensus size: 58
26012 ATAGTTCGGA
* * * * * * *
26022 ATGAAATTGAAACATTTAAAATTTTGGAGACTTATTTAGAATGAGGGTCTTAGTTTGGCG
1 ATGAAATTAAAATATTTAAAAATTT-GAGACTAATTTA-AATGAGAGTCATAATTTGGCG
* * ** * *
26082 ATGAAATTAAAATGTTCAAAAGGTTGATGATTAATTTATAATGAGAGTCATAATTTATG-G
1 ATGAAATTAAAATATTTAAAAATTTGA-GACTAATTTA-AATGAGAGTCATAATTT-GGCG
* *
26142 ATGAAATTAAAATATTTAAAAATTTAGAGACTAATTTAAATAAGAATCATAATTT
1 ATGAAATTAAAATATTTAAAAATTT-GAGACTAATTTAAATGAGAGTCATAATTT
26197 TAAAATATGT
Statistics
Matches: 92, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
59 17 0.18
60 72 0.78
61 3 0.03
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.37
Consensus pattern (58 bp):
ATGAAATTAAAATATTTAAAAATTTGAGACTAATTTAAATGAGAGTCATAATTTGGCG
Found at i:26473 original size:19 final size:19
Alignment explanation
Indices: 26434--26488 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
26424 TTAAAAATTT
*
26434 TAAATTTTTATATAGTTTAAA
1 TAAA-TTTTATAT-TTTTAAA
26455 TAAATTTTATATTTTTAAA
1 TAAATTTTATATTTTTAAA
* **
26474 TTAATAATATATTTT
1 TAAATTTTATATTTT
26489 CTTTCCTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 18 0.60
20 8 0.27
21 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TAAATTTTATATTTTTAAA
Found at i:37036 original size:6 final size:6
Alignment explanation
Indices: 37025--37064 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
37015 AGTACATACA
37025 GGGGTG GGGGTG GGGGTG GGGGTG GGGGTG GGGGTG GGGG
1 GGGGTG GGGGTG GGGGTG GGGGTG GGGGTG GGGGTG GGGG
37065 AGGGAGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.85, T:0.15
Consensus pattern (6 bp):
GGGGTG
Found at i:37292 original size:31 final size:31
Alignment explanation
Indices: 37236--37297 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
37226 ATATATATAT
*
37236 ATATCCTTACAAGAAGACAATGTGAACTAAA
1 ATATCCTTACAAGAAGACAACGTGAACTAAA
* *
37267 ATATCCTTACAAGAAGACGACGTGAATTAAA
1 ATATCCTTACAAGAAGACAACGTGAACTAAA
37298 TAATAGGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.23
Consensus pattern (31 bp):
ATATCCTTACAAGAAGACAACGTGAACTAAA
Found at i:38551 original size:26 final size:27
Alignment explanation
Indices: 38513--38569 Score: 98
Period size: 26 Copynumber: 2.1 Consensus size: 27
38503 GATTTTTGTT
38513 TCGACTCTATCATGAAGTGGATACTGA
1 TCGACTCTATCATGAAGTGGATACTGA
*
38540 TCGA-TCTCTCATGAAGTGGATACTGA
1 TCGACTCTATCATGAAGTGGATACTGA
38566 TCGA
1 TCGA
38570 ATAGCTACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (27 bp):
TCGACTCTATCATGAAGTGGATACTGA
Found at i:43475 original size:221 final size:220
Alignment explanation
Indices: 43092--43491 Score: 526
Period size: 221 Copynumber: 1.8 Consensus size: 220
43082 CTCCCTATTC
* * *
43092 TTTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTTTGGTCCCTATTCATTCACGGAG
1 TTTCAGGGAGTATAAGACTCGAACAATCTTCA-CAAAAGTGTTTGCTCACTATTCATTCACGGAG
* * * *
43157 TATAAGAATCGAACAATCTTCAGCAAACGTGTTCGCTCCCTATTCTTTCAGGGAGTATAAGACTT
65 TATAAGAATCGAACAATCTTCAGAAAACGGGTTCGCTCACTATTCTTTCAGGGAGTATAAGACTC
* *
43222 GAACAATCTTCAGCAAACGGGTCTGCTCCCTATTCTTTTAGGGAGTATAAGACTCGAACAATCTT
130 GAACAATCTTCAGAAAACGGGTCTGCTCCCTATTCTTTTAGAGAGTATAAGACTCGAACAATCTT
43287 CAACAAACGAGTCCGCTCTCTATTTT
195 CAACAAACGAGTCCGCTCTCTATTTT
* * * *
43313 TTTCAGGGATTAT-AGAACTCGAACAATCTTTTA-AAAAGTGGTTTGCTCACTATTCTTTCAGGG
1 TTTCAGGGAGTATAAG-ACTCGAACAATC-TTCACAAAAGT-GTTTGCTCACTATTCATTCACGG
* * *
43376 AGTATATA-ACTCGAACCATCTTCTA-AAAATGGGTTCGCTCACTATTCTTTCAGGGAGTAT-AG
63 AGTATA-AGAATCGAACAATCTTC-AGAAAACGGGTTCGCTCACTATTCTTTCAGGGAGTATAAG
43438 AACTCGAACAATCTTCTA-AAAACGGGT-TCGCTCCCTATTCTTTTAGAGAGTATA
126 -ACTCGAACAATCTTC-AGAAAACGGGTCT-GCTCCCTATTCTTTTAGAGAGTATA
43492 GAACCCGATC
Statistics
Matches: 155, Mismatches: 16, Indels: 16
0.83 0.09 0.09
Matches are distributed among these distances:
220 10 0.06
221 139 0.90
222 6 0.04
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (220 bp):
TTTCAGGGAGTATAAGACTCGAACAATCTTCACAAAAGTGTTTGCTCACTATTCATTCACGGAGT
ATAAGAATCGAACAATCTTCAGAAAACGGGTTCGCTCACTATTCTTTCAGGGAGTATAAGACTCG
AACAATCTTCAGAAAACGGGTCTGCTCCCTATTCTTTTAGAGAGTATAAGACTCGAACAATCTTC
AACAAACGAGTCCGCTCTCTATTTT
Found at i:43492 original size:55 final size:54
Alignment explanation
Indices: 43081--43495 Score: 437
Period size: 55 Copynumber: 7.5 Consensus size: 54
43071 TTACAGGTCT
* * *
43081 GCTCCCTATTCTTTCAGGGAGTATA-AGACTCGAACAATCTTCAGCAAACGTGTTT
1 GCTCCCTATTCTTTCAGGGAGTATAGA-ACTCGAACAATCTTCA-AAAACGGGTTC
* * * * *
43136 GGTCCCTATTCATTCACGGAGTATAAGAA-TCGAACAATCTTCAGCAAACGTGTTC
1 GCTCCCTATTCTTTCAGGGAGTAT-AGAACTCGAACAATCTTCA-AAAACGGGTTC
* *
43191 GCTCCCTATTCTTTCAGGGAGTATA-AGACTTGAACAATCTTCAGCAAACGGG-TC
1 GCTCCCTATTCTTTCAGGGAGTATAGA-ACTCGAACAATCTTCA-AAAACGGGTTC
* * *
43245 TGCTCCCTATTCTTTTAGGGAGTATA-AGACTCGAACAATCTTCAACAAACGAGTCC
1 -GCTCCCTATTCTTTCAGGGAGTATAGA-ACTCGAACAATCTTCAA-AAACGGGTTC
* * * * *
43301 GCTCTCTATTTTTTTCAGGGATTATAGAACTCGAACAATCTTTTAAAAA-GTGGTTT
1 GCTCCCTA-TTCTTTCAGGGAGTATAGAACTCGAACAATC-TTCAAAAACG-GGTTC
* * * *
43357 GCTCACTATTCTTTCAGGGAGTATATAACTCGAACCATCTTCTAAAAATGGGTTC
1 GCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTC-AAAAACGGGTTC
*
43412 GCTCACTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTAAAAACGGGTTC
1 GCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTC-AAAAACGGGTTC
* *
43467 GCTCCCTATTCTTTTAGAGAGTATAGAAC
1 GCTCCCTATTCTTTCAGGGAGTATAGAAC
43496 CCGATCTTGA
Statistics
Matches: 312, Mismatches: 35, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
53 1 0.00
54 6 0.02
55 257 0.82
56 42 0.13
57 6 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (54 bp):
GCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCAAAAACGGGTTC
Found at i:43588 original size:36 final size:36
Alignment explanation
Indices: 43511--43645 Score: 200
Period size: 36 Copynumber: 3.7 Consensus size: 36
43501 CTTGATTTGT
43511 TTCACTACTCTTCCGTGAAGGCTTATAGATAATTTTC
1 TTCACTACTCTTCCGTGAAGGCTTA-AGATAATTTTC
* *
43548 TTCACTACTCTTCTGAGAAGGCTTAAGATAATTTGT-
1 TTCACTACTCTTCCGTGAAGGCTTAAGATAATTT-TC
* * *
43584 TTCACTACACTTCTGTGAAGGCTTAAGATGATTTTC
1 TTCACTACTCTTCCGTGAAGGCTTAAGATAATTTTC
43620 TTCACTACTCTTCCGTGAAGGCTTAA
1 TTCACTACTCTTCCGTGAAGGCTTAA
43646 TATTGATTTG
Statistics
Matches: 89, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
35 1 0.01
36 64 0.72
37 24 0.27
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.39
Consensus pattern (36 bp):
TTCACTACTCTTCCGTGAAGGCTTAAGATAATTTTC
Found at i:43641 original size:72 final size:73
Alignment explanation
Indices: 43505--43645 Score: 230
Period size: 72 Copynumber: 1.9 Consensus size: 73
43495 CCCGATCTTG
* *
43505 ATTTGTTTCACTACTCTTCCGTGAAGGCTTATAGATAATTTTCTTCACTACTCTTCTGAGAAGGC
1 ATTTGTTTCACTACACTTCCGTGAAGGCTTATAGATAATTTTCTTCACTACTCTTCCGAGAAGGC
43570 TTAAGATA
66 TTAAGATA
* * *
43578 ATTTGTTTCACTACACTTCTGTGAAGGCTTA-AGATGATTTTCTTCACTACTCTTCCGTGAAGGC
1 ATTTGTTTCACTACACTTCCGTGAAGGCTTATAGATAATTTTCTTCACTACTCTTCCGAGAAGGC
43642 TTAA
66 TTAA
43646 TATTGATTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
72 34 0.54
73 29 0.46
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.40
Consensus pattern (73 bp):
ATTTGTTTCACTACACTTCCGTGAAGGCTTATAGATAATTTTCTTCACTACTCTTCCGAGAAGGC
TTAAGATA
Found at i:45970 original size:101 final size:101
Alignment explanation
Indices: 45795--45987 Score: 287
Period size: 101 Copynumber: 1.9 Consensus size: 101
45785 TTGTAATTTT
* * *
45795 CCTTTATCAGGCTAGTTTAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCTCCAGAGGGA
1 CCTTTATCAGGCTAGCTAAATCTTATCCATAAAGCCGGGGCGTTAAACCAATTGCTCCAGAGGGA
* * *
45860 CAGTTCAAGCTTTATTGTATATATATATTATAATCA
66 CAGCTCAAGCTTTATTATATACATATATTATAATCA
** * **
45896 CCTTTATCAGGCTAGCTAAATCTTATCCATAATTCTGGGGCGTTAAACCAATTGCTTTAGAGGGA
1 CCTTTATCAGGCTAGCTAAATCTTATCCATAAAGCCGGGGCGTTAAACCAATTGCTCCAGAGGGA
45961 CAGCTCAAGCTTTATTATATACATATA
66 CAGCTCAAGCTTTATTATATACATATA
45988 ACATTATAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 81 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (101 bp):
CCTTTATCAGGCTAGCTAAATCTTATCCATAAAGCCGGGGCGTTAAACCAATTGCTCCAGAGGGA
CAGCTCAAGCTTTATTATATACATATATTATAATCA
Found at i:46555 original size:13 final size:13
Alignment explanation
Indices: 46539--46573 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
46529 AAAGATGAGA
46539 AAGTTCAAAAAAC
1 AAGTTCAAAAAAC
46552 AAGTTCAAAAAAC
1 AAGTTCAAAAAAC
46565 AAGTTCAAA
1 AAGTTCAAA
46574 CAAGATATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.60, C:0.14, G:0.09, T:0.17
Consensus pattern (13 bp):
AAGTTCAAAAAAC
Found at i:51083 original size:32 final size:33
Alignment explanation
Indices: 51031--51095 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 33
51021 AAAAAATACG
*
51031 CCTAAATTTTGAGGACCTAAA-GCTAATTTACC
1 CCTAAATTTTGAGGACCTAAACCCTAATTTACC
51063 CCTAAATTTATG-GTGA-CTAAACCCTAATTTACC
1 CCTAAATTT-TGAG-GACCTAAACCCTAATTTACC
51096 TAAAAGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (33 bp):
CCTAAATTTTGAGGACCTAAACCCTAATTTACC
Found at i:73869 original size:268 final size:262
Alignment explanation
Indices: 73247--74089 Score: 1244
Period size: 268 Copynumber: 3.2 Consensus size: 262
73237 TTCTTACTTT
* * *
73247 GTAAGTCTTTCGGACCATCAGTAAGTCTTTCGAA-CATGATGATTAAATCCTTCTGGTCATATGT
1 GTAAGTCCTTCGGACCATCAGTAAGTC-TTCCAAGCATGATGATTAAATCCTTCGGGTCATATGT
* * *
73311 CAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGTCATCTATAAGACCTT-TGGACATGATGTTTT
65 CAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGG-CAAGATGTTTT
73375 CACATGATGTTTGTGAAAAATGAGAAAAGCAATTTTCAAAATTTCTCATTTTAATGTTTTCAGAA
129 CACATGATGTTTGTGAAAAATGAGAAAAGCAATTTTCAAAATTTCTCATTTTAATGTTTTCAGAA
* *
73440 AATGAAATTTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCGAGTAAACTATTTCCTA
194 AATG-AATTTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAA
73505 AATTG
258 AATTG
* * * * * *
73510 GTAAGTCCTTTGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
1 GTAAGTCCTTCGGACCATCAGTAAGTCTTCCAAGCATGATGATTAAATCCTTCGGGTCATATGTC
* **
73575 AATCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCGGGATGTTTTCA
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCAAGATGTTTTCA
* *
73640 CATGATATTTGTGAAAAATGAGAAAAGCAATTTTCAAAATTTCTCATTTTGATGTTTTCAGAAAA
131 CATGATGTTTGTGAAAAATGAGAAAAGCAATTTTCAAAATTTCTCATTTTAATGTTTTCAGAAAA
* * * **
73705 TGATTTTTTTTAAAAAAAAAAATAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTC
196 TGA-ATTTTTT-----GAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTC
*
73770 CAAAATCG
255 CAAAATTG
* *
73778 GTAAGTCCTTCGGGA-CATCAGTAAGTCTTCCAAGCATGATGATTAAATCATTCGGGTCATTTGT
1 GTAAGTCCTTC-GGACCATCAGTAAGTCTTCCAAGCATGATGATTAAATCCTTCGGGTCATATGT
* * *
73842 CAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTACAAGACCTTCGGGCAAGATGATTTC
65 CAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCAAGATGTTTTC
* *
73907 ACGTGATGTTTGTGAAAAATGAGAAAAGTAATTTTCAAAATTTCTCATTTTAATGTTTTCAGAAA
130 ACATGATGTTTGTGAAAAATGAGAAAAGCAATTTTCAAAATTTCTCATTTTAATGTTTTCAGAAA
* *
73972 ATGAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTT-TTACCTAGTAAACTATTTTCAAAA
195 ATGAATTTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAA
74036 TTG
260 TTG
* *
74039 GTAAGTCCTTCGGACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCT
1 GTAAGTCCTTCGGACCATCAGTAAGTCTTCCAAGCATGATGATTAAATCCT
74090 CCAGATTATC
Statistics
Matches: 518, Mismatches: 52, Indels: 22
0.88 0.09 0.04
Matches are distributed among these distances:
260 3 0.01
261 69 0.13
262 29 0.06
263 180 0.35
264 2 0.00
267 5 0.01
268 228 0.44
269 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (262 bp):
GTAAGTCCTTCGGACCATCAGTAAGTCTTCCAAGCATGATGATTAAATCCTTCGGGTCATATGTC
AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCAAGATGTTTTCA
CATGATGTTTGTGAAAAATGAGAAAAGCAATTTTCAAAATTTCTCATTTTAATGTTTTCAGAAAA
TGAATTTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAT
TG
Found at i:74236 original size:3 final size:3
Alignment explanation
Indices: 74228--74334 Score: 110
Period size: 3 Copynumber: 36.0 Consensus size: 3
74218 TTTGTCTGAG
* *
74228 TTA TTA TTA TTA ATA TTTA TTA TTA TTA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
74274 CTA ATA ATA TTA -TA TTA TTA TTA TTA CTA ATA ATA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
74320 TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA
74335 GACTAATTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
2 4 0.04
3 83 0.93
4 2 0.02
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:74296 original size:26 final size:26
Alignment explanation
Indices: 74254--74328 Score: 132
Period size: 26 Copynumber: 2.8 Consensus size: 26
74244 TTATTATTAT
*
74254 TATTATTATTAATATTATTACTAATAA
1 TATTA-TATTATTATTATTACTAATAA
74281 TATTATATTATTATTATTACTAATAA
1 TATTATATTATTATTATTACTAATAA
74307 TATTATATTATTATTATTACTA
1 TATTATATTATTATTATTACTA
74329 TTATTAGACT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
26 42 0.89
27 5 0.11
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
TATTATATTATTATTATTACTAATAA
Found at i:75997 original size:14 final size:15
Alignment explanation
Indices: 75954--75998 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
75944 AACTTTTAAA
* *
75954 TTTAATGTTTAATAT
1 TTTAATTTTTATTAT
*
75969 TTTAGTTTTTATTAT
1 TTTAATTTTTATTAT
75984 TTTAATTTTT-TTAT
1 TTTAATTTTTATTAT
75998 T
1 T
75999 CCAACACTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (15 bp):
TTTAATTTTTATTAT
Found at i:76063 original size:29 final size:30
Alignment explanation
Indices: 76031--76101 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
76021 TTTATTTTTT
*
76031 TGCCCTTTAATTTTC-ATCATTTACATTTC
1 TGCCCTTTAATTTTCTATCATTTACATTCC
* *
76060 TGCCCTTTAA-TTTCTGTTATTTACATTCC
1 TGCCCTTTAATTTTCTATCATTTACATTCC
*
76089 TACCCTTTAATTT
1 TGCCCTTTAATTT
76102 ATGTTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 4 0.11
29 30 0.83
30 2 0.06
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.52
Consensus pattern (30 bp):
TGCCCTTTAATTTTCTATCATTTACATTCC
Found at i:76106 original size:29 final size:29
Alignment explanation
Indices: 76049--76110 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
76039 AATTTTCATC
* * *
76049 ATTTACATTTCTGCCCTTTAATTTCTGTT
1 ATTTACATTCCTACCCTTTAATTTATGTT
76078 ATTTACATTCCTACCCTTTAATTTATGTT
1 ATTTACATTCCTACCCTTTAATTTATGTT
76107 ATTT
1 ATTT
76111 TAATTTCAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.21, C:0.19, G:0.05, T:0.55
Consensus pattern (29 bp):
ATTTACATTCCTACCCTTTAATTTATGTT
Found at i:79123 original size:21 final size:21
Alignment explanation
Indices: 79090--79137 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
79080 AGTGCCCAAC
79090 AATAAT-A-AAAATCGATAGAA
1 AATAATAACAAAATCGATA-AA
79110 AA-AATAACAAAATCGATAAA
1 AATAATAACAAAATCGATAAA
79130 AATAATAA
1 AATAATAA
79138 TATTTTCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 3 0.12
20 7 0.28
21 15 0.60
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (21 bp):
AATAATAACAAAATCGATAAA
Found at i:93204 original size:3 final size:3
Alignment explanation
Indices: 93196--93225 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
93186 AAATAAGAGA
93196 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
93226 TATAAATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.