Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007512.1 Hibiscus syriacus cultivar Beakdansim tig00020895_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: 90093
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2451 original size:15 final size:15
Alignment explanation
Indices: 2431--2461 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2421 AAAATATAAC
2431 ATTTCTAATAATCTT
1 ATTTCTAATAATCTT
*
2446 ATTTCTGATAATCTT
1 ATTTCTAATAATCTT
2461 A
1 A
2462 CATTTTTCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTCTAATAATCTT
Found at i:6434 original size:12 final size:12
Alignment explanation
Indices: 6417--6455 Score: 78
Period size: 12 Copynumber: 3.2 Consensus size: 12
6407 GGAGTTTGGT
6417 TATGTAAAATGA
1 TATGTAAAATGA
6429 TATGTAAAATGA
1 TATGTAAAATGA
6441 TATGTAAAATGA
1 TATGTAAAATGA
6453 TAT
1 TAT
6456 AAAAAGAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (12 bp):
TATGTAAAATGA
Found at i:24054 original size:22 final size:21
Alignment explanation
Indices: 24014--24054 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
24004 AAAAATAATA
* *
24014 TTAAAAAGATTACTTTATATT
1 TTAAAAAAATTACTCTATATT
24035 TTAAAAAAATTACTCCTATA
1 TTAAAAAAATTACT-CTATA
24055 ATTTCACCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (21 bp):
TTAAAAAAATTACTCTATATT
Found at i:27622 original size:20 final size:20
Alignment explanation
Indices: 27599--27650 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
27589 TGGTTCACGT
* *
27599 AATATAAGATTATCAGTAGG
1 AATAAAAGATTATAAGTAGG
27619 AATAAAAGATTATAAGTAGG
1 AATAAAAGATTATAAGTAGG
27639 AATAAAAGATTA
1 AATAAAAGATTA
27651 CTAGGGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (20 bp):
AATAAAAGATTATAAGTAGG
Found at i:29251 original size:23 final size:25
Alignment explanation
Indices: 29202--29255 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
29192 AAATGAGGAG
29202 TATTATTGATATAAATAATTATGAAA
1 TATTATTGATATAAATAATTA-GAAA
* *
29228 TATTATTTATATCAAT-ATTA-AAA
1 TATTATTGATATAAATAATTAGAAA
29251 TATTA
1 TATTA
29256 AAAAAATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 8 0.31
25 4 0.15
26 14 0.54
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
TATTATTGATATAAATAATTAGAAA
Found at i:29731 original size:2 final size:2
Alignment explanation
Indices: 29724--29752 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29714 CAATTATCCA
29724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29753 CTAAATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33701 original size:24 final size:20
Alignment explanation
Indices: 33648--33705 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
33638 TTCCCCTTGA
*
33648 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
33668 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
33691 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
33706 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:33780 original size:64 final size:63
Alignment explanation
Indices: 33693--33854 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 63
33683 TCTTTAACAT
* * *
33693 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCA-TTTTAA-GG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAATGG
* * ***
33755 GCTTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGTATTCGATGTTTCCATTTTTAATG
1 G--TGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAATG
33820 G
63 G
*
33821 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
33855 CTGAACAATT
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 68 0.82
65 9 0.11
66 3 0.04
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAATGG
Found at i:35219 original size:34 final size:35
Alignment explanation
Indices: 35180--35245 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 35
35170 TTCGAAATGG
* *
35180 AGTGCATGGATGTACT-CATGGTGCATCGATGCAT
1 AGTGCATGGATGCACTACAGGGTGCATCGATGCAT
*
35214 AGTGCATGGATGCACTACAGGGTGCATGGATG
1 AGTGCATGGATGCACTACAGGGTGCATCGATG
35246 TACTTTGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 15 0.54
35 13 0.46
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (35 bp):
AGTGCATGGATGCACTACAGGGTGCATCGATGCAT
Found at i:35602 original size:21 final size:21
Alignment explanation
Indices: 35547--35605 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
35537 TGTTTAATGA
35547 AAAAT-ATACCAATTGTTAAC
1 AAAATGATACCAATTGTTAAC
35567 AAAATGA-ACCAATTGTTAAC
1 AAAATGATACCAATTGTTAAC
*
35587 AAAATGATATCAATTGTTA
1 AAAATGATACCAATTGTTA
35606 CCAATTGTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 25 0.69
21 11 0.31
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (21 bp):
AAAATGATACCAATTGTTAAC
Found at i:38767 original size:34 final size:34
Alignment explanation
Indices: 38727--38793 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
38717 TTCGAAATGG
38727 AGTGCATAGATGCAC-CCAGGGTGCATCGATGCAT
1 AGTGCATAGATGCACTCCA-GGTGCATCGATGCAT
* * *
38761 AGTGCATGGATGCACTGCAGGTGCATGGATGCA
1 AGTGCATAGATGCACTCCAGGTGCATCGATGCA
38794 CTATAGGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.21
Consensus pattern (34 bp):
AGTGCATAGATGCACTCCAGGTGCATCGATGCAT
Found at i:38786 original size:19 final size:20
Alignment explanation
Indices: 38762--38811 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
38752 TCGATGCATA
*
38762 GTGCATGGATGCACTGCA-G
1 GTGCATGGATGCACTACAGG
*
38781 GTGCATGGATGCACTATAGG
1 GTGCATGGATGCACTACAGG
38801 GTGCATGGATG
1 GTGCATGGATG
38812 TACTTTTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.24
Consensus pattern (20 bp):
GTGCATGGATGCACTACAGG
Found at i:42079 original size:7 final size:7
Alignment explanation
Indices: 42057--42102 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
42047 TATTAAAATA
*
42057 TAATTTT
1 TAATATT
42064 TAATCATT
1 TAAT-ATT
42072 TAATATT
1 TAATATT
42079 TAATACTT
1 TAATA-TT
*
42087 AAATATT
1 TAATATT
42094 TAATATT
1 TAATATT
42101 TA
1 TA
42103 TGATACTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 22 0.65
8 12 0.35
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (7 bp):
TAATATT
Found at i:42082 original size:22 final size:22
Alignment explanation
Indices: 42069--42123 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
42059 ATTTTTAATC
42069 ATTTAATATTTAATACTTAAAT
1 ATTTAATATTTAATACTTAAAT
42091 ATTTAATATTTATGATAC-TAAA-
1 ATTTAATATTTA--ATACTTAAAT
*
42113 ATCTAATATTT
1 ATTTAATATTT
42124 TAAAAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 22 0.73
23 4 0.13
24 4 0.13
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTTAATATTTAATACTTAAAT
Found at i:43526 original size:31 final size:31
Alignment explanation
Indices: 43448--43527 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 31
43438 ATATAATATT
*
43448 TATTTTAT-AGTA-TTTAGATAAATTTATTAA
1 TATTTTATAAGTATTTTA-ATAAATTTAATAA
*
43478 TAATTTTATAA-TCTTTTAATAAATTTAATAA
1 T-ATTTTATAAGTATTTTAATAAATTTAATAA
43509 GTATTTTATAAGT-TTTTAA
1 -TATTTTATAAGTATTTTAA
43528 ACTTTATTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
30 1 0.02
31 35 0.81
32 7 0.16
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (31 bp):
TATTTTATAAGTATTTTAATAAATTTAATAA
Found at i:44273 original size:20 final size:20
Alignment explanation
Indices: 44248--44328 Score: 71
Period size: 20 Copynumber: 4.0 Consensus size: 20
44238 TAAAGTTTAA
44248 AAATTTA-TAAAATACTTATT
1 AAATTTATTAAAATA-TTATT
44268 AAATTTATTAAAATATTA-T
1 AAATTTATTAAAATATTATT
*
44287 AAAATTATTAATAA-ATTTATCT
1 AAATTTATTAA-AATA-TTAT-T
44309 AAATTCTA-TAAAATAATTAT
1 AAATT-TATTAAAAT-ATTAT
44329 ATTATCAACT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
19 12 0.24
20 15 0.29
21 9 0.18
22 12 0.24
23 3 0.06
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTTATTAAAATATTATT
Found at i:44280 original size:31 final size:29
Alignment explanation
Indices: 44247--44328 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 29
44237 ATAAAGTTTA
44247 AAAATTTATAAAATACTTATTAAATTTATT
1 AAAATTTATAAAATA-TTATTAAATTTATT
*
44277 AAAATATTATAAAATTATTAATAAATTTATCT
1 AAAAT-TTATAAAA-TATTATTAAATTTAT-T
44309 -AAATTCTATAAAATAATTAT
1 AAAATT-TATAAAAT-ATTAT
44329 ATTATCAACT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
30 7 0.16
31 35 0.78
32 3 0.07
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (29 bp):
AAAATTTATAAAATATTATTAAATTTATT
Found at i:44294 original size:19 final size:21
Alignment explanation
Indices: 44247--44297 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
44237 ATAAAGTTTA
44247 AAAATT-TATAAAATACTTATT
1 AAAATTAT-TAAAATACTTATT
*
44268 AAATTTATTAAAATA-TTA-T
1 AAAATTATTAAAATACTTATT
44287 AAAATTATTAA
1 AAAATTATTAA
44298 TAAATTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 11 0.41
20 3 0.11
21 12 0.44
22 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATTATTAAAATACTTATT
Found at i:44361 original size:20 final size:21
Alignment explanation
Indices: 44321--44362 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
44311 ATTCTATAAA
44321 ATAATTATATTATCAACTTTT
1 ATAATTATATTATCAACTTTT
44342 ATAATT-TATTA-CAACATTTT
1 ATAATTATATTATCAAC-TTTT
44362 A
1 A
44363 GTGACTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 10 0.50
21 6 0.30
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAATTATATTATCAACTTTT
Found at i:47483 original size:13 final size:13
Alignment explanation
Indices: 47465--47492 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
47455 ATTTAGCCGC
47465 GACGGTCGATAAA
1 GACGGTCGATAAA
47478 GACGGTCGATAAA
1 GACGGTCGATAAA
47491 GA
1 GA
47493 ACAAAATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.32, T:0.14
Consensus pattern (13 bp):
GACGGTCGATAAA
Found at i:48799 original size:152 final size:152
Alignment explanation
Indices: 48523--48831 Score: 595
Period size: 152 Copynumber: 2.0 Consensus size: 152
48513 TTAATGAGCT
48523 AGATGTACAGCTTCTGGAAGGCATACTTAGCAGCTTGAACGGGGTTCGGCAATTTTGTTTTGACA
1 AGATGTACAGCTTCTGGAAGGCATACTTAGCAGCTTGAACGGGGTTCGGCAATTTTGTTTTGACA
48588 GAACTTCTGGAGAACTTGAAGTTCTTTTTGATCTGAAGTTGTCAGTTCAAGATCCTTGGTTGGTG
66 GAACTTCTGGAGAACTTGAAGTTCTTTTTGATCTGAAGTTGTCAGTTCAAGATCCTTGGTTGGTG
48653 GAATTGAAGGAGGAAGTAAAGG
131 GAATTGAAGGAGGAAGTAAAGG
48675 AGATGTACAGCTTCTGGAAGGCATACTTAGCAGCTTGAA-GGGGTTCGGCAATTTTGTTTTGACA
1 AGATGTACAGCTTCTGGAAGGCATACTTAGCAGCTTGAACGGGGTTCGGCAATTTTGTTTTGACA
48739 GAACTTCTGGAGAACTTGAAGTTCTTTTTGATCCTGAAGTTGTCAGTTCAAGATCCTTGGTTGGT
66 GAACTTCTGGAGAACTTGAAGTTCTTTTTGAT-CTGAAGTTGTCAGTTCAAGATCCTTGGTTGGT
48804 GGAATTGAAGGAGGAAGTAAAGG
130 GGAATTGAAGGAGGAAGTAAAGG
48827 -GATGT
1 AGATGT
48832 TCAACTGCAT
Statistics
Matches: 156, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
151 62 0.40
152 94 0.60
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (152 bp):
AGATGTACAGCTTCTGGAAGGCATACTTAGCAGCTTGAACGGGGTTCGGCAATTTTGTTTTGACA
GAACTTCTGGAGAACTTGAAGTTCTTTTTGATCTGAAGTTGTCAGTTCAAGATCCTTGGTTGGTG
GAATTGAAGGAGGAAGTAAAGG
Found at i:65690 original size:22 final size:22
Alignment explanation
Indices: 65673--65739 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
65663 CTCGTATAAA
65673 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
65695 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
65717 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
65739 T
1 T
65740 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:66000 original size:30 final size:31
Alignment explanation
Indices: 65959--66018 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
65949 TAGACATAGT
*
65959 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
65989 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
66019 AACTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:66076 original size:29 final size:29
Alignment explanation
Indices: 66034--66103 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
66024 TTCTGCATAA
**
66034 TCATGTCATGTAATACATATAATATGAAT
1 TCATGTCATGTAATACATATAATACAAAT
*
66063 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACATATAATACAAAT
66092 TCATGTCATGTA
1 TCATGTCATGTA
66104 TCATAATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (29 bp):
TCATGTCATGTAATACATATAATACAAAT
Found at i:66554 original size:67 final size:68
Alignment explanation
Indices: 66407--66558 Score: 198
Period size: 68 Copynumber: 2.2 Consensus size: 68
66397 TTTTCTCATG
* * * *
66407 GGGGAATCGGTTCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAGTCTGGAATTTCATATACGA
1 GGGGTATCGGTT-CCCCCCATAGGGGTAACGATTCCCCTCAAGCAGTCTGGAATATCATATACGA
*
66472 TGAG
65 TGAA
* * * * *
66476 GGGGTATCGGTTCCCCCCATGGGGGTAACGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTTCCCCCCATAGGGGTAACGATTCCCCTCAAGCAGTCTGGAATATCATATACGAT
66540 GAA
66 GAA
66543 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
66559 TTGAATGGGT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
67 27 0.37
68 35 0.48
69 11 0.15
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.27
Consensus pattern (68 bp):
GGGGTATCGGTTCCCCCCATAGGGGTAACGATTCCCCTCAAGCAGTCTGGAATATCATATACGAT
GAA
Found at i:66568 original size:21 final size:21
Alignment explanation
Indices: 66538--66580 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
66528 ATCATATTCG
* *
66538 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
66559 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
66580 T
1 T
66581 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:72623 original size:22 final size:22
Alignment explanation
Indices: 72606--72672 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
72596 CTCGTATAAA
72606 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
72628 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
72650 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
72672 T
1 T
72673 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:72933 original size:30 final size:31
Alignment explanation
Indices: 72892--72951 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
72882 TAGACATAGT
*
72892 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
72922 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
72952 AACTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:73009 original size:29 final size:29
Alignment explanation
Indices: 72967--73036 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
72957 TTCTGCATAA
**
72967 TCATGTCATGTAATACATATAATATGAAT
1 TCATGTCATGTAATACATATAATACAAAT
*
72996 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACATATAATACAAAT
73025 TCATGTCATGTA
1 TCATGTCATGTA
73037 TCATAATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (29 bp):
TCATGTCATGTAATACATATAATACAAAT
Found at i:73457 original size:67 final size:67
Alignment explanation
Indices: 73340--73490 Score: 196
Period size: 67 Copynumber: 2.2 Consensus size: 67
73330 TTTTCTCATG
* * * *
73340 GGGGAATCGGTTCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAGTCTGGAATTTCATATACGA
1 GGGGTATCGGTT-CCCCCCATAGGGGTAACGATTCCCCTCAAGCAGTCTGGAA-ATCATATACGA
73405 TG-A
64 TGAA
* * * * *
73408 GGGGTATCGGTTCCCCCCATGGGGGTAACGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTG
1 GGGGTATCGGTTCCCCCCATAGGGGTAACGATTCCCCTCAAGCAGTCTGGAAATCATATACGATG
73473 AA
66 AA
73475 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
73491 TTGAATGGGT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
66 10 0.14
67 52 0.71
68 11 0.15
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.27
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCATAGGGGTAACGATTCCCCTCAAGCAGTCTGGAAATCATATACGATG
AA
Found at i:73500 original size:21 final size:21
Alignment explanation
Indices: 73470--73512 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
73460 ATCATATTCG
* *
73470 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
73491 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
73512 T
1 T
73513 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:75861 original size:15 final size:15
Alignment explanation
Indices: 75843--75871 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
75833 ATTGAAAGCA
75843 TATAAGTTGAAGTTT
1 TATAAGTTGAAGTTT
75858 TATAAGTTGAAGTT
1 TATAAGTTGAAGTT
75872 CTCCCTCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (15 bp):
TATAAGTTGAAGTTT
Found at i:84217 original size:2 final size:2
Alignment explanation
Indices: 84210--84235 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
84200 AAATGAATAA
84210 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
84236 GCATACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85817 original size:54 final size:55
Alignment explanation
Indices: 85758--86234 Score: 459
Period size: 55 Copynumber: 8.9 Consensus size: 55
85748 TGGCGGGTAG
* * * *** *
85758 GCTCCCTATTCTTTCAGTGAGTATA-AGACTCAAACAATCTTCGGCAAACGTGT-T
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAAAAAACGTGTCC
** * * *
85812 GCTCCCTATTCAGTCAGGGAGTATA-AGACTTGAACAATCTTCAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAA-AAAACGTGTCC
* * *
85868 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGGAA-AATCTTCAATAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC-GAACAATCTTCAAAAAACGTGTCC
* * * *
85923 GCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAAACGTGTCC
* ** *
85978 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTC-AACGACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAAACGTGTCC
**
86032 GCTCCCTATTCCTTCAGAGAGTATA-AGACT----CAATCTTCAACGAAC-TGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAAAAAACGTGTCC
* * * *
86082 GCTCCCTATTCCTTC--AGAGTATAGGACT----CAATCTTTAACAAA-GTGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAAACGTGTCC
* * * * *
86130 GCTCCCTATTCTTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAATGAGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAAACGTGTCC
* *
86185 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAAACG
86235 AGTTGCTTCA
Statistics
Matches: 355, Mismatches: 52, Indels: 31
0.81 0.12 0.07
Matches are distributed among these distances:
48 41 0.12
50 40 0.11
51 3 0.01
53 1 0.00
54 85 0.24
55 148 0.42
56 33 0.09
57 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAAACGTGTCC
Found at i:86133 original size:48 final size:48
Alignment explanation
Indices: 86012--86148 Score: 177
Period size: 48 Copynumber: 2.8 Consensus size: 48
86002 AGAACTCGAA
*
86012 CAATCTTCAAC-GACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACT
1 CAATCTTCAACAAAC-TGTCCGCTCCCTATTCCTTC--AGAGTATAAGACT
* *
86062 CAATCTTCAACGAACTGTCCGCTCCCTATTCCTTCAGAGTATAGGACT
1 CAATCTTCAACAAACTGTCCGCTCCCTATTCCTTCAGAGTATAAGACT
* * * *
86110 CAATCTTTAACAAAGTGTTCGCTCCCTATTCTTTCAGAG
1 CAATCTTCAACAAACTGTCCGCTCCCTATTCCTTCAGAG
86149 AGTATAGAAC
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
48 46 0.58
50 31 0.39
51 2 0.03
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (48 bp):
CAATCTTCAACAAACTGTCCGCTCCCTATTCCTTCAGAGTATAAGACT
Found at i:86284 original size:36 final size:36
Alignment explanation
Indices: 86237--86341 Score: 140
Period size: 36 Copynumber: 2.9 Consensus size: 36
86227 AACAAACGAG
*
86237 TTGCTTCACTACTCTTTCGTGAAGGCTTAAGATGAT
1 TTGCTTCACTACTCTTTCGTGAAGGCTTAAGATGAA
* * *
86273 TTGCTTCACTACTCTTCCGTTAAGGCTTAAGTTTGAA
1 TTGCTTCACTACTCTTTCGTGAAGGCTTAAG-ATGAA
* *
86310 TTGCTTCACTGCTC-TTCATGAAGGCTTAAGAT
1 TTGCTTCACTACTCTTTCGTGAAGGCTTAAGAT
86342 TGACCTGTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
35 1 0.02
36 42 0.71
37 16 0.27
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (36 bp):
TTGCTTCACTACTCTTTCGTGAAGGCTTAAGATGAA
Found at i:87623 original size:15 final size:16
Alignment explanation
Indices: 87600--87637 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
87590 ACCCTCCTTT
*
87600 ATTTCTCTTTTTTT-C
1 ATTTTTCTTTTTTTCC
87615 ATTTTTCTTTTTTTCC
1 ATTTTTCTTTTTTTCC
87631 ATTTTTC
1 ATTTTTC
87638 ATTTCCTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTTCTTTTTTTCC
Found at i:87628 original size:16 final size:17
Alignment explanation
Indices: 87601--87637 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
87591 CCCTCCTTTA
*
87601 TTTCTCTTTTTTTCATT
1 TTTCTCTTTTTTCCATT
87618 TTTCT-TTTTTTCCATT
1 TTTCTCTTTTTTCCATT
87634 TTTC
1 TTTC
87638 ATTTCCTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCTCTTTTTTCCATT
Found at i:87695 original size:18 final size:19
Alignment explanation
Indices: 87674--87724 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
87664 TTTTTTTTTC
87674 TTTTCATTTTTTC-CATCAT
1 TTTTCATTTTTTCTCAT-AT
87693 TTTTC-TTTTTTCTCAT-T
1 TTTTCATTTTTTCTCATAT
87710 TTTTCATTTTTTCTC
1 TTTTCATTTTTTCTC
87725 TTTTATTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.20
18 16 0.53
19 8 0.27
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTCATTTTTTCTCATAT
Found at i:87721 original size:25 final size:25
Alignment explanation
Indices: 87596--87728 Score: 91
Period size: 25 Copynumber: 5.3 Consensus size: 25
87586 TTGAACCCTC
*
87596 CTTTATTTCTCTTTTTTTCA-TTTTT
1 CTTT-TTTCTCATTTTTTCATTTTTT
*
87621 CTTTTTT-TCCA-TTTTTCATTTCCTT
1 CTTTTTTCT-CATTTTTTCATTT-TTT
** *
87646 CCCTTTTC-CCTTTTTCTC-TTTTTT
1 CTTTTTTCTCATTTTT-TCATTTTTT
87670 -TTTCTTT-TCATTTTTTCCATCATTTTT
1 CTTT-TTTCTCATTTTTT-CAT--TTTTT
87697 CTTTTTTCTCATTTTTTCATTTTTT
1 CTTTTTTCTCATTTTTTCATTTTTT
*
87722 CTCTTTT
1 CTTTTTT
87729 ATTCTTCTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
23 10 0.12
24 19 0.23
25 30 0.36
26 2 0.02
27 11 0.13
28 12 0.14
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (25 bp):
CTTTTTTCTCATTTTTTCATTTTTT
Done.