Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003539.1 Hibiscus syriacus cultivar Beakdansim tig00007467_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: 76220
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2359 original size:12 final size:12
Alignment explanation
Indices: 2342--2366 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2332 GTTACAGTCG
2342 GAGGAGATGAAC
1 GAGGAGATGAAC
2354 GAGGAGATGAAC
1 GAGGAGATGAAC
2366 G
1 G
2367 GGGAAGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.44, T:0.08
Consensus pattern (12 bp):
GAGGAGATGAAC
Found at i:7665 original size:164 final size:163
Alignment explanation
Indices: 7392--7882 Score: 631
Period size: 164 Copynumber: 3.0 Consensus size: 163
7382 AACTAAGTTA
* * * *
7392 ATTTGATGCCATTTTGTTGCATTTTTTAAGGAGTAT-GTTATGTATCAAATTAGATGAATGGTTC
1 ATTTGATGCCCTTTTGTTGCA-TTTTTATGGAGTATGGTCATGTATCGAATTAGATGAATGGTTC
* * * * * *
7456 AACCTGTTCACGAAATTTTAGTTCATTGAATGTATTTATTGTCTGTTCTTGTCATGTGGATAATC
65 GACGTGTTCAC-AAATTTTAGTTCATTGAATGCATTTAGTGTCTGTTCTTGTTATGTCGATAATC
* * *
7521 ACGTATCGATTGAATGATGGCGTTGCTAACTTGCT
129 ACATATCGATTGAAAGATGGCGTTACTAACTTGCT
*
7556 GTTTGATGCCCTTTTGTTGCATTTTTATGGAGTATGGTCATGTATCGAATTAGATGAATGGTTCG
1 ATTTGATGCCCTTTTGTTGCATTTTTATGGAGTATGGTCATGTATCGAATTAGATGAATGGTTCG
* *
7621 ACGTGTTCACAAAATTTTAGTTCATTGAATGCATTTAGTGTCTGTTCTTGTTGTGTCAATAATCA
66 ACGTGTTCAC-AAATTTTAGTTCATTGAATGCATTTAGTGTCTGTTCTTGTTATGTCGATAATCA
*
7686 CATATCGATCGAACA-ATGGCGTTACTAACTTGCT
130 CATATCGATTGAA-AGATGGCGTTACTAACTTGCT
* *
7720 ATTTGATGCCCTTTTCTTGCGTTTTTTATGGAGTATGGTCATGTATCGAATTAGATGAATGGTTC
1 ATTTGATGCCCTTTTGTTGC-ATTTTTATGGAGTATGGTCATGTATCGAATTAGATGAATGGTTC
* * * * *
7785 GATGTGCTCAC--A----AGTGCATT-AAGTGCATTTAGTGTCTGTTCTTTTTATGTCGATAATT
65 GACGTGTTCACAAATTTTAGTTCATTGAA-TGCATTTAGTGTCTGTTCTTGTTATGTCGATAATC
* *
7843 ACATATCGATTGAAAGATGACGTTACTAACTCGCT
129 ACATATCGATTGAAAGATGGCGTTACTAACTTGCT
7878 ATTTG
1 ATTTG
7883 TAATCAATAT
Statistics
Matches: 291, Mismatches: 31, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
157 3 0.01
158 73 0.25
162 1 0.00
163 13 0.04
164 149 0.51
165 52 0.18
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (163 bp):
ATTTGATGCCCTTTTGTTGCATTTTTATGGAGTATGGTCATGTATCGAATTAGATGAATGGTTCG
ACGTGTTCACAAATTTTAGTTCATTGAATGCATTTAGTGTCTGTTCTTGTTATGTCGATAATCAC
ATATCGATTGAAAGATGGCGTTACTAACTTGCT
Found at i:9993 original size:6 final size:6
Alignment explanation
Indices: 9984--10028 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
9974 CACAGGGAGG
* * *
9984 GGCCGG GGCCGG GGCCGA GGTCGA GGCCGA GGCCGA GGCCGA GGC
1 GGCCGA GGCCGA GGCCGA GGCCGA GGCCGA GGCCGA GGCCGA GGC
10029 AGCTATCCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.11, C:0.31, G:0.56, T:0.02
Consensus pattern (6 bp):
GGCCGA
Found at i:23383 original size:18 final size:17
Alignment explanation
Indices: 23346--23384 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
23336 TATGGAATTG
* *
23346 GATTTTAATTCCTGACA
1 GATTTCAATTCCTCACA
23363 GATTTCAATTCCTTCACA
1 GATTTCAATTCC-TCACA
23381 GATT
1 GATT
23385 CTAATCCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (17 bp):
GATTTCAATTCCTCACA
Found at i:25978 original size:14 final size:14
Alignment explanation
Indices: 25959--25986 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25949 CGCTGGGCAT
25959 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
25973 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
25987 ATGAGCTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:26146 original size:20 final size:20
Alignment explanation
Indices: 26093--26147 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
26083 TCATAGCTCG
**
26093 TTCGGATGGCCTCAAATGCT
1 TTCGGATGGCCTCGGATGCT
*
26113 CTCGGATGGCCTCGGATGCT
1 TTCGGATGGCCTCGGATGCT
26133 TTCGGATGGCCTCGG
1 TTCGGATGGCCTCGG
26148 TCGGATGGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (20 bp):
TTCGGATGGCCTCGGATGCT
Found at i:26153 original size:14 final size:14
Alignment explanation
Indices: 26134--26171 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
26124 TCGGATGCTT
26134 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
26148 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
26162 TCGGATGGCC
1 TCGGATGGCC
26172 AGCGAGTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.08, C:0.29, G:0.42, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:27806 original size:16 final size:16
Alignment explanation
Indices: 27785--27833 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
27775 TATTATAGTG
27785 ATAAAATAATTATTTT
1 ATAAAATAATTATTTT
* * *
27801 ATAAAAAAATTAATTA
1 ATAAAATAATTATTTT
**
27817 ATTTAATAATTATTTT
1 ATAAAATAATTATTTT
27833 A
1 A
27834 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAAATAATTATTTT
Found at i:27814 original size:20 final size:20
Alignment explanation
Indices: 27755--27821 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
27745 TATCATTAAA
27755 TTTATCAAAAAAATTATAATTAT
1 TTTAT-AAAAAAA-T-TAATTAT
* * *
27778 TATAGTGATAAAA-TAATTAT
1 TTTA-TAAAAAAATTAATTAT
*
27798 TTTATAAAAAAATTAATTAA
1 TTTATAAAAAAATTAATTAT
27818 TTTA
1 TTTA
27822 ATAATTATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
19 6 0.17
20 20 0.57
23 8 0.23
24 1 0.03
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (20 bp):
TTTATAAAAAAATTAATTAT
Found at i:30586 original size:20 final size:20
Alignment explanation
Indices: 30561--30615 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
30551 GGCTGCTGGA
*
30561 AACCGGTT-TAACCAGTTTTC
1 AACCGGTTCTAACC-GGTTTC
*
30581 AACCGGTTCTGACCGGTTTC
1 AACCGGTTCTAACCGGTTTC
*
30601 AACCGGTTCGAACCG
1 AACCGGTTCTAACCG
30616 TTTGTTGTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (20 bp):
AACCGGTTCTAACCGGTTTC
Found at i:30652 original size:16 final size:15
Alignment explanation
Indices: 30629--30662 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
30619 GTTGTCTGAC
30629 CCGACCGACCGTTGA
1 CCGACCGACCGTTGA
30644 CCGACCCGACCGTTGA
1 CCGA-CCGACCGTTGA
30660 CCG
1 CCG
30663 TTGACCGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.18, C:0.44, G:0.26, T:0.12
Consensus pattern (15 bp):
CCGACCGACCGTTGA
Found at i:32942 original size:18 final size:18
Alignment explanation
Indices: 32914--32952 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
32904 CAAATATTAA
32914 ATATAATAAAC-AATATT
1 ATATAATAAACTAATATT
32931 ATATACATAAACTTAATATT
1 ATATA-ATAAAC-TAATATT
32951 AT
1 AT
32953 TATTCTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
20 8 0.42
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATAATAAACTAATATT
Found at i:33114 original size:23 final size:22
Alignment explanation
Indices: 33086--33131 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
33076 TTACATTATA
33086 TTTAAAAATATTAATTAGAATAT
1 TTTAAAAATATTAATTA-AATAT
* * *
33109 TTTAAATATCTTTATTAAATAT
1 TTTAAAAATATTAATTAAATAT
33131 T
1 T
33132 ATATTAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTAAAAATATTAATTAAATAT
Found at i:33156 original size:17 final size:18
Alignment explanation
Indices: 33121--33160 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
33111 TAAATATCTT
*
33121 TATTAAATATTATATTAA
1 TATTAAATATTATAATAA
33139 TATTAAATA-TATAATAA
1 TATTAAATATTATAATAA
33156 TATTA
1 TATTA
33161 TTCATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATATTATAATAA
Found at i:33383 original size:24 final size:21
Alignment explanation
Indices: 33327--33410 Score: 61
Period size: 24 Copynumber: 3.9 Consensus size: 21
33317 TTAAAAATAT
33327 AATATTATTATTAGAA-ATATTAA
1 AATATT-TTATTA-AATAT-TTAA
33350 AATA--TT-TTAAATATTTAATA
1 AATATTTTATTAAATATTT-A-A
33370 AATATTTTAATTAAATGATATTAA
1 AATATTTT-ATTAAAT-AT-TTAA
33394 AATATTTTATT-AATATT
1 AATATTTTATTAAATATT
33411 AAATTCATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 21
0.71 0.00 0.29
Matches are distributed among these distances:
18 4 0.08
19 6 0.12
20 8 0.15
21 2 0.04
22 5 0.10
23 7 0.13
24 15 0.29
25 3 0.06
26 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AATATTTTATTAAATATTTAA
Found at i:34667 original size:29 final size:30
Alignment explanation
Indices: 34612--34668 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 30
34602 CTTGATTCAT
34612 AAATCACTCAATTATCATAAAATTATAAAC
1 AAATCACTCAATTATCATAAAATTATAAAC
34642 AAATCA-TCGAATT-TCA-AAACATTATAA
1 AAATCACTC-AATTATCATAAA-ATTATAA
34669 TGAGCCACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 3 0.12
29 12 0.48
30 10 0.40
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.30
Consensus pattern (30 bp):
AAATCACTCAATTATCATAAAATTATAAAC
Found at i:35227 original size:16 final size:18
Alignment explanation
Indices: 35185--35229 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
35175 TCATTGAATG
35185 TAAGATTACCAGTAGAAA
1 TAAGATTACCAGTAGAAA
35203 TAAAAGATTACCAGT-G-AA
1 T--AAGATTACCAGTAGAAA
35221 TAAGATTAC
1 TAAGATTAC
35230 TGTGAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 4 0.16
19 1 0.04
20 12 0.48
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (18 bp):
TAAGATTACCAGTAGAAA
Found at i:37358 original size:18 final size:18
Alignment explanation
Indices: 37335--37384 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
37325 TTTCGATTCT
*
37335 TTCGACCGATTAAACCGG
1 TTCGACCGATTAAACCGA
* *
37353 TTCGACCAATTAGACCGA
1 TTCGACCGATTAAACCGA
*
37371 TTCAACCGATTAAA
1 TTCGACCGATTAAA
37385 TTAATAAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (18 bp):
TTCGACCGATTAAACCGA
Found at i:38667 original size:14 final size:14
Alignment explanation
Indices: 38650--38676 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38640 AAACACAGAT
38650 TGCAAAGTACAACA
1 TGCAAAGTACAACA
38664 TGCAAAGTACAAC
1 TGCAAAGTACAAC
38677 CTACAAAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.22, G:0.15, T:0.15
Consensus pattern (14 bp):
TGCAAAGTACAACA
Found at i:39850 original size:20 final size:20
Alignment explanation
Indices: 39827--39897 Score: 133
Period size: 20 Copynumber: 3.5 Consensus size: 20
39817 CACGGAATGT
39827 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
39847 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
*
39867 AAGATTACCAATGGGAATAA
1 AAGATTACCAGTGGGAATAA
39887 AAGATTACCAG
1 AAGATTACCAG
39898 GGAATAGGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:44455 original size:30 final size:29
Alignment explanation
Indices: 44360--44457 Score: 115
Period size: 29 Copynumber: 3.3 Consensus size: 29
44350 ACTCGACCCA
* *
44360 GTGACATTTTGGGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTTAAAAAG
* *
44389 GTGACATTTTGGGAATTATTTGTAAAACG
1 GTGACATTTTGGGAATTATTTTTAAAAAG
* * *
44418 ATGATATTTTGGTAATTATTTTTAATAAAG
1 GTGACATTTTGGGAATTATTTTTAA-AAAG
*
44448 GTGATATTTT
1 GTGACATTTT
44458 TGTAATTTTC
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
29 46 0.79
30 12 0.21
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (29 bp):
GTGACATTTTGGGAATTATTTTTAAAAAG
Found at i:47920 original size:12 final size:14
Alignment explanation
Indices: 47907--47956 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
47897 TATGTTTAAT
47907 TATTATTAT-TAT-
1 TATTATTATATATA
47919 TATTATTATATATA
1 TATTATTATATATA
47933 TA-TATATATATATA
1 TATTAT-TATATATA
47947 TATATATTAT
1 TAT-TATTAT
47957 TAGTAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
12 9 0.27
13 6 0.18
14 12 0.36
15 3 0.09
16 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTATTATATATA
Found at i:47932 original size:2 final size:2
Alignment explanation
Indices: 47925--47953 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
47915 TTATTATTAT
47925 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47954 TATTAGTAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49302 original size:14 final size:14
Alignment explanation
Indices: 49283--49312 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
49273 TACTTTCCAT
49283 TTCATCCATTTTAA
1 TTCATCCATTTTAA
49297 TTCATCCATTTTAA
1 TTCATCCATTTTAA
49311 TT
1 TT
49313 ATAAGAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (14 bp):
TTCATCCATTTTAA
Found at i:49502 original size:16 final size:15
Alignment explanation
Indices: 49460--49505 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
49450 TATATTATAG
*
49460 TTTTAATTTTATTTA
1 TTTTAATATTATTTA
*
49475 TTTTATTCATTATTTA
1 TTTTAAT-ATTATTTA
49491 TTTGTAATATTATTT
1 TTT-TAATATTATTT
49506 TATTATTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 6 0.23
16 17 0.65
17 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTTAATATTATTTA
Found at i:49503 original size:12 final size:11
Alignment explanation
Indices: 49488--49562 Score: 73
Period size: 12 Copynumber: 6.6 Consensus size: 11
49478 TATTCATTAT
49488 TTATTTGTAATA
1 TTATTT-TAATA
*
49500 TTATTTTATTA
1 TTATTTTAATA
49511 TTACTTTTAATA
1 TTA-TTTTAATA
49523 -TATTTTAATTA
1 TTATTTTAA-TA
*
49534 TTACTTTAATTA
1 TTATTTTAA-TA
*
49546 TTATTTTATTA
1 TTATTTTAATA
49557 TT-TTTT
1 TTATTTT
49563 TTATCTTAGT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
10 10 0.18
11 15 0.27
12 30 0.55
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:49521 original size:23 final size:22
Alignment explanation
Indices: 49495--49558 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 22
49485 TATTTATTTG
49495 TAATATTATTTTATTATTACTTT
1 TAATATTATTTTATTATTAC-TT
49518 TAATA-TATTTTAATTATTACTT
1 TAATATTATTTT-ATTATTACTT
49540 TAATTATTATTTTATTATT
1 TAA-TATTATTTTATTATT
49559 TTTTTTATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.29
23 21 0.55
24 6 0.16
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (22 bp):
TAATATTATTTTATTATTACTT
Found at i:49536 original size:34 final size:33
Alignment explanation
Indices: 49489--49562 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 33
49479 ATTCATTATT
*
49489 TATTTGTAATATTA-TTTTATTATTACTTTTAATA
1 TATTT-TAATATTACTTTAATTATTA-TTTTAATA
*
49523 TATTTTAATTATTACTTTAATTATTATTTTATTA
1 TATTTTAA-TATTACTTTAATTATTATTTTAATA
*
49557 TTTTTT
1 TATTTT
49563 TTATCTTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 3 0.09
34 22 0.63
35 10 0.29
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (33 bp):
TATTTTAATATTACTTTAATTATTATTTTAATA
Found at i:49859 original size:21 final size:19
Alignment explanation
Indices: 49835--49882 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
49825 ATATTCTTAA
49835 ATAAATAAATATCTTACTTTT
1 ATAAATAAATATC-TA-TTTT
*
49856 ATAAAT-TATATCTATTTT
1 ATAAATAAATATCTATTTT
49874 -TAAATAAAT
1 ATAAATAAAT
49883 GTTTTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 5 0.21
18 6 0.25
19 2 0.08
20 5 0.21
21 6 0.25
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAAATAAATATCTATTTT
Found at i:50911 original size:27 final size:25
Alignment explanation
Indices: 50840--50913 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 25
50830 ATAATAATGG
*
50840 AAATAAAT-AAATAAATAGAAATTC
1 AAATAAATAAAATAAATAAAAATTC
*
50864 AAGTAAATAAAA-AATATTAAATAATTC
1 AAATAAATAAAATAA-A-TAAA-AATTC
*
50891 AAAATAAATAAAATAAGTAAAAA
1 -AAATAAATAAAATAAATAAAAA
50914 ATGACTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
24 9 0.22
25 4 0.10
26 5 0.12
27 9 0.22
28 11 0.28
29 2 0.05
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (25 bp):
AAATAAATAAAATAAATAAAAATTC
Found at i:50913 original size:19 final size:20
Alignment explanation
Indices: 50848--50913 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 20
50838 GGAAATAAAT
*
50848 AAATAAATAGAAATTCAAGTAA
1 AAATAAATATAAA-T-AAGTAA
* * *
50870 ATAAAAAATATTAAATAATTCA
1 A-AATAAATA-TAAATAAGTAA
50892 AAATAAATA-AAATAAGTAA
1 AAATAAATATAAATAAGTAA
50911 AAA
1 AAA
50914 ATGACTAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
19 11 0.31
21 7 0.20
22 6 0.17
23 8 0.23
24 3 0.09
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (20 bp):
AAATAAATATAAATAAGTAA
Found at i:50944 original size:14 final size:15
Alignment explanation
Indices: 50910--50943 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
50900 AAAATAAGTA
*
50910 AAAAATGACTAAATT
1 AAAAATGACTAAACT
*
50925 AAAAATGATTAAACT
1 AAAAATGACTAAACT
50940 AAAA
1 AAAA
50944 TAACATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAAATGACTAAACT
Found at i:56714 original size:24 final size:24
Alignment explanation
Indices: 56582--56700 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
56572 TTCGATTTGA
*
56582 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
56606 ATTGTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
*
56630 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* *
56654 ATTCTGATATAATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
*
56678 ATTTTGATATGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
56701 AATTATGTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 82 0.98
25 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:56877 original size:43 final size:43
Alignment explanation
Indices: 56816--56953 Score: 251
Period size: 43 Copynumber: 3.2 Consensus size: 43
56806 GGGCTTTACT
*
56816 TGGTGTGTTGGTGGGTGTATGGTTTTGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
56859 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
56902 TGGTGTGTTGGTGGGTGTATGGTTCT-GGGAAGCCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAA-CCTACACATTA
56945 TGGTGTGTT
1 TGGTGTGTT
56954 CGGTTGGAGG
Statistics
Matches: 93, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
42 5 0.05
43 88 0.95
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.37
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
Found at i:59113 original size:18 final size:18
Alignment explanation
Indices: 59090--59131 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
59080 ATTCTTGATG
59090 AGGAAGATAAGGTGCTTC
1 AGGAAGATAAGGTGCTTC
59108 AGGAAGATAAGGTGCTTC
1 AGGAAGATAAGGTGCTTC
59126 AGGAAG
1 AGGAAG
59132 TGTATTTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.10, G:0.36, T:0.19
Consensus pattern (18 bp):
AGGAAGATAAGGTGCTTC
Found at i:62608 original size:38 final size:38
Alignment explanation
Indices: 62527--62611 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 38
62517 TAATAATTAT
*
62527 TATATATATATAATATTAATAAATTTAATTTAATTTAA
1 TATATATATATAATATTAATAAATTTAATTTAATATAA
* * *
62565 AATATATATATAATATTTATATATTTAATTTAA-AT-A
1 TATATATATATAATATTAATAAATTTAATTTAATATAA
62601 TATATATATAT
1 TATATATATAT
62612 CCAGCCCGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 11 0.26
37 1 0.02
38 30 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (38 bp):
TATATATATATAATATTAATAAATTTAATTTAATATAA
Found at i:65485 original size:21 final size:21
Alignment explanation
Indices: 65461--65527 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
65451 AGATTTAAGC
* *
65461 TTTAGGGTTTATAGATTAGGA
1 TTTAGGGTTTAGAGATTATGA
**
65482 TTTAATGTTTAGAGATTATGA
1 TTTAGGGTTTAGAGATTATGA
*
65503 TTT-GGGATTTAGAGTTTATGA
1 TTTAGGG-TTTAGAGATTATGA
65524 TTTA
1 TTTA
65528 AAATTTAGGG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 1 0.03
21 36 0.97
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (21 bp):
TTTAGGGTTTAGAGATTATGA
Found at i:65500 original size:28 final size:28
Alignment explanation
Indices: 65445--65513 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
65435 TATAGTTTGG
* * *
65445 GATTTAAGATTTAAGCTTTAGGGTTTAT
1 GATTTAGGATTTAAGCTTTAGAGATTAT
65473 AGA-TTAGGATTTAATG-TTTAGAGATTAT
1 -GATTTAGGATTTAA-GCTTTAGAGATTAT
*
65501 GATTTGGGATTTA
1 GATTTAGGATTTA
65514 GAGTTTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 2 0.06
28 29 0.85
29 3 0.09
ACGTcount: A:0.30, C:0.01, G:0.23, T:0.45
Consensus pattern (28 bp):
GATTTAGGATTTAAGCTTTAGAGATTAT
Found at i:65533 original size:21 final size:21
Alignment explanation
Indices: 65480--65540 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
65470 TATAGATTAG
** *
65480 GATTTAATGTTTAGAGATTAT
1 GATTTAAAATTTAGAGTTTAT
***
65501 GATTTGGGATTTAGAGTTTAT
1 GATTTAAAATTTAGAGTTTAT
*
65522 GATTTAAAATTTAGGGTTT
1 GATTTAAAATTTAGAGTTT
65541 GATATTTGGG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.48
Consensus pattern (21 bp):
GATTTAAAATTTAGAGTTTAT
Found at i:72224 original size:20 final size:20
Alignment explanation
Indices: 72188--72268 Score: 60
Period size: 20 Copynumber: 3.9 Consensus size: 20
72178 TTTTGGTGCA
*
72188 GAGGGAATCGATACCCCC-AT
1 GAGGGAA-CGATTCCCCCTAT
*
72208 GAGGGAACAGATTCCCCCTTT
1 GAGGGAAC-GATTCCCCCTAT
72229 GAAGGGGAACTGATTCCCCCTA-
1 G-A-GGGAAC-GATTCCCCCTAT
*
72251 G-GGGAATCGATACCCCCT
1 GAGGGAA-CGATTCCCCCT
72269 GGGGTTCTGG
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
19 15 0.29
20 16 0.31
21 2 0.04
22 2 0.04
23 16 0.31
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.19
Consensus pattern (20 bp):
GAGGGAACGATTCCCCCTAT
Found at i:72266 original size:19 final size:19
Alignment explanation
Indices: 72231--72272 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
72221 CCCCCTTTGA
*
72231 AGGGGAACTGATTCCCCCT
1 AGGGGAACTGATACCCCCT
72250 AGGGGAA-TCGATACCCCCT
1 AGGGGAACT-GATACCCCCT
72269 -GGGG
1 AGGGG
72273 TTCTGGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.21, C:0.29, G:0.33, T:0.17
Consensus pattern (19 bp):
AGGGGAACTGATACCCCCT
Found at i:73224 original size:28 final size:29
Alignment explanation
Indices: 73192--73246 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
73182 GTGGAAATTT
73192 TAAAC-TTTTGATCTTGAACCTATTATGA
1 TAAACTTTTTGATCTTGAACCTATTATGA
73220 TAAACTTTTTGATCTTGAACCTATTAT
1 TAAACTTTTTGATCTTGAACCTATTAT
73247 CTACCATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (29 bp):
TAAACTTTTTGATCTTGAACCTATTATGA
Found at i:75703 original size:49 final size:49
Alignment explanation
Indices: 75604--75798 Score: 141
Period size: 51 Copynumber: 3.9 Consensus size: 49
75594 ACAATATTTC
* *
75604 TAATAATATAATA-TTAT-TTTAATTTTATAATAAAATAATCAATTATATTATA
1 TAATAATATAATATTTATATTTAATTTAATAAT-ATATAAT-AA--A-ATTATA
* *
75656 TAATAATATAAGATTTATATTTTATTTAATAATATATAATAAAATTATAA
1 TAATAATATAATATTTATATTTAATTTAATAATATATAATAAAATTAT-A
* * ** * *
75706 TAA-AATTTATATATTTATTAATTTCATAGAA-AATATATTATTAAATTATTA
1 TAATAATATA-ATATTTA-T-ATTTAATTTAATAATATATAATAAAATTA-TA
*
75757 TAATGAATAT-ATTTTTATATTTAATATTAATAATA-ATAATAA
1 TAAT-AATATAATATTTATATTTAAT-TTAATAATATATAATAA
75799 TTTTAATAAA
Statistics
Matches: 114, Mismatches: 18, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
49 16 0.14
50 19 0.17
51 30 0.26
52 23 0.20
53 14 0.12
54 12 0.11
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (49 bp):
TAATAATATAATATTTATATTTAATTTAATAATATATAATAAAATTATA
Found at i:75826 original size:22 final size:22
Alignment explanation
Indices: 75801--75885 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 22
75791 AATAATAATT
75801 TTAATAAATA-TTTTAAAATATA
1 TTAATAAATATTTTTAAAA-ATA
*
75823 TTAATTAATATTTTTAAAAATA
1 TTAATAAATATTTTTAAAAATA
*
75845 TAATATAACACTATTACTTTAATAAATAA
1 TTA-ATAA-A-TATT--TTTAA-AAAT-A
75874 TTAAT-AATATTT
1 TTAATAAATATTT
75886 ATAATATTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
22 14 0.27
23 12 0.24
24 1 0.02
25 8 0.16
26 1 0.02
27 6 0.12
28 6 0.12
29 3 0.06
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAATAAATATTTTTAAAAATA
Found at i:76164 original size:34 final size:35
Alignment explanation
Indices: 76105--76179 Score: 107
Period size: 34 Copynumber: 2.1 Consensus size: 35
76095 CAAACATCAT
* *
76105 AAAACGTTTTCGAGAAAAATGTAATTCATTTTACGG
1 AAAACGTTTTCCAG-AAAATGTAATTCATTTTACAG
*
76141 AAAACGTTTTCCAG-AAATGTAATTCATTTTCCAG
1 AAAACGTTTTCCAGAAAATGTAATTCATTTTACAG
76175 AAAAC
1 AAAAC
76180 CAATTACAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 23 0.64
36 13 0.36
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (35 bp):
AAAACGTTTTCCAGAAAATGTAATTCATTTTACAG
Done.