Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003066.1 Hibiscus syriacus cultivar Beakdansim tig00006391_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: 86112
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:1261 original size:28 final size:29
Alignment explanation
Indices: 1229--1288 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 29
1219 ATAGTTTTTA
1229 TATTTTTTATTAATATAAT-TATATA-AAT
1 TATTTTTTATTAA-ATAATATATATATAAT
*
1257 TA-TTTTTATTAAATAATATTTATATAAT
1 TATTTTTTATTAAATAATATATATATAAT
1285 TATT
1 TATT
1289 ATTATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.18
27 15 0.54
28 7 0.25
29 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TATTTTTTATTAAATAATATATATATAAT
Found at i:1304 original size:28 final size:28
Alignment explanation
Indices: 1235--1299 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
1225 TTTATATTTT
* *
1235 TTATT-AAT-ATAATTATATAAATTATTT
1 TTATTAAATAATATTTATAT-AATTATTA
1262 TTATTAAATAATATTTATATAATTATTA
1 TTATTAAATAATATTTATATAATTATTA
1290 TTATTTAAAT
1 TTA-TTAAAT
1300 TTATTAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 5 0.15
28 13 0.39
29 15 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TTATTAAATAATATTTATATAATTATTA
Found at i:1319 original size:23 final size:24
Alignment explanation
Indices: 1247--1309 Score: 65
Period size: 28 Copynumber: 2.5 Consensus size: 24
1237 ATTAATATAA
*
1247 TTATATAAATTATTTTTATTAAATAATAT
1 TTATAT-AATTATTATTATT---TAA-AT
1276 TTATATAATTATTATTATTTAAAT
1 TTATATAATTATTATTATTTAAAT
1300 TTAT-TAATTA
1 TTATATAATTA
1310 ATTTTTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 6 0.18
24 6 0.18
25 3 0.09
28 12 0.36
29 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATATAATTATTATTATTTAAAT
Found at i:1425 original size:21 final size:21
Alignment explanation
Indices: 1401--1448 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1391 TCTCCAGACA
1401 TTTTAGTAAT-ATGGTAATATT
1 TTTTA-TAATAATGGTAATATT
* *
1422 TTTTATATTAATGTTAATATT
1 TTTTATAATAATGGTAATATT
*
1443 TATTAT
1 TTTTAT
1449 TATTTTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (21 bp):
TTTTATAATAATGGTAATATT
Found at i:1481 original size:17 final size:17
Alignment explanation
Indices: 1453--1499 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1443 TATTATTATT
1453 TTAATT-TAAATTTAAA
1 TTAATTATAAATTTAAA
* * *
1469 TTTATTATGAATTTATA
1 TTAATTATAAATTTAAA
1486 TTAATTATAAATTT
1 TTAATTATAAATTT
1500 TTATAATGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAATTATAAATTTAAA
Found at i:1483 original size:28 final size:27
Alignment explanation
Indices: 1423--1514 Score: 91
Period size: 28 Copynumber: 3.3 Consensus size: 27
1413 GGTAATATTT
* *
1423 TTTATATTAATGTTAATATTTATTATTAT
1 TTTATATTAAT-TTAA-ATTTATTATGAA
1452 TTTA-ATTTAAATTTAAATTTATTATGAA
1 TTTATA-TT-AATTTAAATTTATTATGAA
1480 TTTATATTAATTATAAATTT-TTAT-AA
1 TTTATATTAATT-TAAATTTATTATGAA
*
1506 TGTATATTA
1 TTTATATTA
1515 TTGAGGAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
26 10 0.18
27 8 0.14
28 24 0.43
29 11 0.20
30 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (27 bp):
TTTATATTAATTTAAATTTATTATGAA
Found at i:3131 original size:21 final size:21
Alignment explanation
Indices: 3105--3165 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
3095 ATCTTCGCAG
*
3105 GGTTACATTCCTAGCCC-TCA
1 GGTTACATTCCTAGCCCGCCA
3125 TGGTTACATTCCTAGCCCGCCA
1 -GGTTACATTCCTAGCCCGCCA
*
3147 GGTTACATGCCTAGCCCGC
1 GGTTACATTCCTAGCCCGC
3166 AGAGTGTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.18, C:0.36, G:0.20, T:0.26
Consensus pattern (21 bp):
GGTTACATTCCTAGCCCGCCA
Found at i:3653 original size:57 final size:58
Alignment explanation
Indices: 3581--3721 Score: 159
Period size: 57 Copynumber: 2.5 Consensus size: 58
3571 TTTATCCATA
*
3581 CGTAAAAA-ATGTCGATGCTCATTCCATTAAAACC-A-ACTTATCACTTCATATTTATT
1 CGTAAAAACATGTCGATGCTCATTCCATT-AAACCGAGACTTATCACTTCACATTTATT
**
3637 CGTAAAAACATGTCGATGCTCATT---TTAGTCCTGAGTACTTATCACTTCACATTTATT
1 CGTAAAAACATGTCGATGCTCATTCCATTAAACC-GAG-ACTTATCACTTCACATTTATT
* * *
3694 CGTAAAAACATATCGATGTTTATTCCAT
1 CGTAAAAACATGTCGATGCTCATTCCAT
3722 ACAATTTCAA
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
53 3 0.04
54 2 0.03
55 1 0.01
56 8 0.11
57 56 0.79
60 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.37
Consensus pattern (58 bp):
CGTAAAAACATGTCGATGCTCATTCCATTAAACCGAGACTTATCACTTCACATTTATT
Found at i:3846 original size:63 final size:63
Alignment explanation
Indices: 3738--3858 Score: 206
Period size: 63 Copynumber: 1.9 Consensus size: 63
3728 TCAATGTCAC
* *
3738 AACCAACTTATCACTTCACATTTATTCAATTTATCTATAACATTTTATCCAATTTATTTAAAT
1 AACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTTAAAT
* *
3801 AACCAACTGATCACTTCACATTTATTCAATTTATCCATAATATTTTATCTAATTTATT
1 AACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATT
3859 CAAACTTCAC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.36, C:0.19, G:0.01, T:0.45
Consensus pattern (63 bp):
AACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTTAAAT
Found at i:4297 original size:128 final size:128
Alignment explanation
Indices: 3992--4584 Score: 760
Period size: 127 Copynumber: 4.8 Consensus size: 128
3982 CCATCCATCT
*
3992 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT-GACAAAATAA
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT-TACACAAAATAA
* *
4056 TGGAAGGCGCACCCCCAGGAACGAGCCTTCA-AGTCCCCTCAGAAATAATAGGTACTGACATGA
65 TGGAAGGCGCGCCCCCAGGAACGCGCCTTCACAGTCCCCTCAGAAATAATAGGTACTGACATGA
* * *
4119 ATAATTTCCCAGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
**
4184 GGAAGGCGCGCCCCTGGGAACGCGCCTTCACTA-TCCCCTCAGAAATAATAGGTACTGACATGA
66 GGAAGGCGCGCCCCCAGGAACGCGCCTTCAC-AGTCCCCTCAGAAATAATAGGTACTGACATGA
4247 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
* * * * *
4312 GGAAGGCGCG-TCCCTGAGAACGCGCCTTCA-AGTCCCCTAAGAAATATTAAGTACTGACATGA
66 GGAAGGCGCGCCCCCAG-GAACGCGCCTTCACAGTCCCCTCAGAAATAATAGGTACTGACATGA
*
4374 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTTTTACACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
* * * *
4439 TGAAGGCGCGCCCAC-GAAACGCGCCTTCACCA-T----T------T--TGGGTACTGACATGA
66 GGAAGGCGCGCCCCCAGGAACGCGCCTTCA-CAGTCCCCTCAGAAATAATAGGTACTGACATGA
* * * *
4489 ATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCT-GACAAAATA
1 ATAGT-TCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT-TACACAAAATA
* * *
4553 ATGAAAGGTGC-CCCCCAGGAACGCGCTTTCAC
64 ATGGAAGGCGCGCCCCCAGGAACGCGCCTTCAC
4585 GTGAATAGTG
Statistics
Matches: 421, Mismatches: 34, Indels: 34
0.86 0.07 0.07
Matches are distributed among these distances:
115 23 0.05
116 72 0.17
117 2 0.00
123 1 0.00
126 14 0.03
127 190 0.45
128 118 0.28
129 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (128 bp):
ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
GGAAGGCGCGCCCCCAGGAACGCGCCTTCACAGTCCCCTCAGAAATAATAGGTACTGACATGA
Found at i:4576 original size:116 final size:115
Alignment explanation
Indices: 4362--4584 Score: 317
Period size: 116 Copynumber: 1.9 Consensus size: 115
4352 GAAATATTAA
* * *
4362 GTACTGACATGAATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTTTT
1 GTACTGACATGAATAGTCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTTCT
*
4427 ACACAAAATAATTGAAGGCGCGCCCACGAAACGCGCCTTCACCATTTTGG
66 ACACAAAATAATTGAAGGCGCCCCCACGAAACGCGCCTTCACCATTTTGG
4477 GTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTAT
1 GTACTGACATGAATAGT-CCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATT-T
* * * *
4542 CT-GACAAAATAA-TGAAAGGTGCCCCC-CAGGAACGCGCTTTCAC
64 CTACACAAAATAATTG-AAGGCGCCCCCAC-GAAACGCGCCTTCAC
4585 GTGAATAGTG
Statistics
Matches: 96, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
115 20 0.21
116 74 0.77
117 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (115 bp):
GTACTGACATGAATAGTCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTTCT
ACACAAAATAATTGAAGGCGCCCCCACGAAACGCGCCTTCACCATTTTGG
Found at i:5350 original size:23 final size:23
Alignment explanation
Indices: 5324--5371 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
5314 ACCGAAATGT
5324 CACGTAGAATTGCACCGTAGTGC
1 CACGTAGAATTGCACCGTAGTGC
*
5347 CACGTAGAATTGCACTGTAGTGC
1 CACGTAGAATTGCACCGTAGTGC
5370 CA
1 CA
5372 TATAATATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (23 bp):
CACGTAGAATTGCACCGTAGTGC
Found at i:7029 original size:21 final size:21
Alignment explanation
Indices: 7003--7044 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6993 TTTTTATTCG
* *
7003 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
7024 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
7045 ATAGCCCATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:9208 original size:23 final size:23
Alignment explanation
Indices: 9182--9232 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
9172 CTATACTTCA
*
9182 ACTTCTCCACATATAACTAAACC
1 ACTTCTCCACATAGAACTAAACC
9205 ACTTCTCCACATAGAACTAAACC
1 ACTTCTCCACATAGAACTAAACC
9228 ACTTC
1 ACTTC
9233 ATCTAACTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.35, G:0.02, T:0.25
Consensus pattern (23 bp):
ACTTCTCCACATAGAACTAAACC
Found at i:10446 original size:23 final size:23
Alignment explanation
Indices: 10412--10472 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
10402 CTCATATAAA
* *
10412 TGCACCGAAGTGTCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
**
10435 TGCACCGTAGTGCCGTGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
10458 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
10473 TATAATAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:12177 original size:21 final size:21
Alignment explanation
Indices: 12151--12194 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12141 TTTTTATTCG
* *
12151 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
12172 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
12193 CT
1 CT
12195 AGCCCATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:20175 original size:13 final size:13
Alignment explanation
Indices: 20157--20183 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20147 GCGGTAGACT
20157 ATTATATAGGTAA
1 ATTATATAGGTAA
20170 ATTATATAGGTAA
1 ATTATATAGGTAA
20183 A
1 A
20184 ACATACGCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (13 bp):
ATTATATAGGTAA
Found at i:21994 original size:24 final size:24
Alignment explanation
Indices: 21961--22015 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
21951 GGAAACAATG
21961 AAAT-AAGTAAATAAG-ATAGATTAA
1 AAATAAAGTAAATAAGTA-AGA-TAA
21985 AAA-AAAGTAAATAAGTAAGATAA
1 AAATAAAGTAAATAAGTAAGATAA
22008 AAATAAAG
1 AAATAAAG
22016 GAAGGGAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 6 0.21
24 21 0.75
25 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (24 bp):
AAATAAAGTAAATAAGTAAGATAA
Found at i:22108 original size:22 final size:19
Alignment explanation
Indices: 22070--22124 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 19
22060 AATGCAGAAC
*
22070 ATAAGAATAATATAATAAACA
1 ATAAGAA-AATAAAATAAA-A
22091 AGTAAAGAAAATAAAATAAAA
1 A-T-AAGAAAATAAAATAAAA
22112 ATAA-AAAATAAAA
1 ATAAGAAAATAAAA
22125 ATGAAGATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 9 0.29
19 2 0.06
20 1 0.03
21 3 0.10
22 11 0.35
23 5 0.16
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (19 bp):
ATAAGAAAATAAAATAAAA
Found at i:22121 original size:18 final size:19
Alignment explanation
Indices: 22078--22162 Score: 75
Period size: 22 Copynumber: 4.2 Consensus size: 19
22068 ACATAAGAAT
*
22078 AATATAATAAACAAGTAAAGAA
1 AATAAAATAAA-AA-TAAAG-A
22100 AATAAAATAAAAATAAA-A
1 AATAAAATAAAAATAAAGA
22118 AATAAAAATGAAGATAATAAAGA
1 AAT-AAAAT-AA-A-AATAAAGA
*
22141 AATTAAAT-AAAATAAAGA
1 AATAAAATAAAAATAAAGA
22159 AATA
1 AATA
22163 GTATATATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
18 15 0.27
19 6 0.11
20 7 0.13
21 3 0.05
22 20 0.36
23 4 0.07
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (19 bp):
AATAAAATAAAAATAAAGA
Found at i:22134 original size:19 final size:18
Alignment explanation
Indices: 22098--22162 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 18
22088 ACAAGTAAAG
22098 AAAATAAAATAAAAATAA
1 AAAATAAAATAAAAATAA
22116 AAAATAAAAATGAAGATAATAA
1 AAAAT-AAAAT-AA-A-AATAA
*
22138 AGAAATTAAAT-AAAATAA
1 A-AAATAAAATAAAAATAA
22156 AGAAATA
1 A-AAATA
22163 GTATATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
18 16 0.40
19 6 0.15
20 3 0.08
21 1 0.03
22 10 0.25
23 4 0.10
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.18
Consensus pattern (18 bp):
AAAATAAAATAAAAATAA
Found at i:22197 original size:9 final size:9
Alignment explanation
Indices: 22181--22235 Score: 58
Period size: 9 Copynumber: 5.9 Consensus size: 9
22171 ATATATATAT
22181 AAATAATAA
1 AAATAATAA
*
22190 AGATAATAA
1 AAATAATAA
22199 AAATAA-AA
1 AAATAATAA
22207 AAATGAAATAA
1 AAAT--AATAA
*
22218 TAAATAATGA
1 -AAATAATAA
22228 AAATAATA
1 AAATAATA
22236 TACATACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 6 0.16
9 20 0.53
10 6 0.16
11 2 0.05
12 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (9 bp):
AAATAATAA
Found at i:22221 original size:16 final size:16
Alignment explanation
Indices: 22181--22235 Score: 62
Period size: 15 Copynumber: 3.5 Consensus size: 16
22171 ATATATATAT
22181 AAATAATAAAGATAAT-
1 AAATAATAAA-ATAATG
*
22197 AAA-AATAAAAAAATG
1 AAATAATAAAATAATG
22212 AAATAAT-AAATAATG
1 AAATAATAAAATAATG
22227 AAAATAATA
1 -AAATAATA
22236 TACATACATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 4 0.12
15 16 0.48
16 13 0.39
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (16 bp):
AAATAATAAAATAATG
Found at i:22326 original size:29 final size:30
Alignment explanation
Indices: 22280--22345 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
22270 AAAAAAAGTA
* *
22280 ATATATATATATGCATAATAGAGA-ATAAT
1 ATATATATATATACATAATAGAAACATAAT
* *
22309 ATATATATATATATATAATATAAACATAAT
1 ATATATATATATACATAATAGAAACATAAT
22339 ATA-ATAT
1 ATATATAT
22346 TTAACTGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (30 bp):
ATATATATATATACATAATAGAAACATAAT
Found at i:25082 original size:18 final size:18
Alignment explanation
Indices: 25059--25104 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
25049 TAGTTTTCAT
*
25059 TTTAAATTATCAAACATA
1 TTTAAAATATCAAACATA
25077 TTTAAAATATCAAACATA
1 TTTAAAATATCAAACATA
25095 TTTAAAATAT
1 TTTAAAATAT
25105 TTAAAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTAAAATATCAAACATA
Found at i:25104 original size:9 final size:9
Alignment explanation
Indices: 25074--25112 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
25064 ATTATCAAAC
25074 ATATTTAAA
1 ATATTTAAA
*
25083 ATA-TCAAA
1 ATATTTAAA
25091 CATATTTAAA
1 -ATATTTAAA
25101 ATATTTAAA
1 ATATTTAAA
25110 ATA
1 ATA
25113 ATTATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 4 0.15
9 18 0.69
10 4 0.15
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (9 bp):
ATATTTAAA
Found at i:27613 original size:105 final size:105
Alignment explanation
Indices: 27431--27645 Score: 376
Period size: 105 Copynumber: 2.0 Consensus size: 105
27421 GGTGGTGAGG
* *
27431 AAGCTATATTAAGAAACGATAATGCAGTTTCTGAGGAGGGTTATTCTGCAACTCCAATTGGGGAT
1 AAGCTATATTAAGAAACGATAATGCAGTTTCAGAGGAGGGTTATTCTGCAACTCCAATTGGGGAG
* *
27496 GAGGACCATTTTGAGTCTGTTTCTTTAGAAAATCAAGATA
66 GAGGACCATTTTGAGCCTGTTTCTTTAGAAAATCAAAATA
* *
27536 AAGCTATATTAAGAAACGATAATGCAGTTTCAGAGGAGGTTTATTCTGCAACTCCTATTGGGGAG
1 AAGCTATATTAAGAAACGATAATGCAGTTTCAGAGGAGGGTTATTCTGCAACTCCAATTGGGGAG
27601 GAGGACCATTTTGAGCCTGTTTCTTTAGAAAATCAAAATA
66 GAGGACCATTTTGAGCCTGTTTCTTTAGAAAATCAAAATA
27641 AAGCT
1 AAGCT
27646 TTTGAAGAGT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (105 bp):
AAGCTATATTAAGAAACGATAATGCAGTTTCAGAGGAGGGTTATTCTGCAACTCCAATTGGGGAG
GAGGACCATTTTGAGCCTGTTTCTTTAGAAAATCAAAATA
Found at i:33027 original size:18 final size:19
Alignment explanation
Indices: 33004--33068 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 19
32994 ATGGCTGCTG
33004 TTTCTGGTTTA-TGTTTCA
1 TTTCTGGTTTACTGTTTCA
* *
33022 TTTCTGTTTTACTTTTTTCA
1 TTTCTGGTTTAC-TGTTTCA
* *
33042 TTTCT--TTTCCTGTTTCC
1 TTTCTGGTTTACTGTTTCA
33059 TCTTCTGGTT
1 T-TTCTGGTT
33069 GCTTCCTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
17 6 0.16
18 18 0.49
20 13 0.35
ACGTcount: A:0.06, C:0.18, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTCTGGTTTACTGTTTCA
Found at i:51706 original size:10 final size:10
Alignment explanation
Indices: 51678--51711 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
51668 GGAGCCATGC
51678 TCTCTAGTAA
1 TCTCTAGTAA
51688 TCTCATAGTAA
1 TCTC-TAGTAA
51699 TCTCTAGT-A
1 TCTCTAGTAA
51708 TCTC
1 TCTC
51712 CATCTTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.22
10 8 0.35
11 10 0.43
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (10 bp):
TCTCTAGTAA
Found at i:56025 original size:45 final size:45
Alignment explanation
Indices: 55961--56049 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
55951 CTCCATAACG
* *
55961 TAGTTAAACATCTTAAATGGTTTAGGACCCAATTAACTTCGCAAC
1 TAGTTAAACATCCTAAATGGTTTACGACCCAATTAACTTCGCAAC
*
56006 TAGTTAAACATCCTAAATGGTTTACGACCCAATTAACTTTGCAA
1 TAGTTAAACATCCTAAATGGTTTACGACCCAATTAACTTCGCAA
56050 TTCTCCAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.31
Consensus pattern (45 bp):
TAGTTAAACATCCTAAATGGTTTACGACCCAATTAACTTCGCAAC
Found at i:58949 original size:22 final size:22
Alignment explanation
Indices: 58921--58963 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
58911 CAAACCATTC
58921 AGGGGGGAATCAGTACCCTCTT
1 AGGGGGGAATCAGTACCCTCTT
* *
58943 AGGGGGGAATCGGTTCCCTCT
1 AGGGGGGAATCAGTACCCTCT
58964 GAGCAATCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.23, G:0.35, T:0.23
Consensus pattern (22 bp):
AGGGGGGAATCAGTACCCTCTT
Found at i:61045 original size:21 final size:23
Alignment explanation
Indices: 60997--61045 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
60987 ATTCCCCTGT
60997 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
61020 AGGGGGAATCGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
61041 GGGGG
1 GGGGG
61046 CACCAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.33
22 3 0.12
23 13 0.54
ACGTcount: A:0.18, C:0.22, G:0.41, T:0.18
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:72069 original size:20 final size:19
Alignment explanation
Indices: 72037--72080 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
72027 TTGTTTGTAA
72037 ATTTTTTATTCTCATTAAT
1 ATTTTTTATTCTCATTAAT
*
72056 -TTTTTTATACTCTCGTTAAT
1 ATTTTTTAT--TCTCATTAAT
72076 ATTTT
1 ATTTT
72081 AACTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 8 0.38
20 9 0.43
21 4 0.19
ACGTcount: A:0.23, C:0.11, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTTATTCTCATTAAT
Found at i:72155 original size:19 final size:20
Alignment explanation
Indices: 72106--72163 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
72096 TTTTTAAAAT
* *
72106 ATAATATTATAAATATATTTT
1 ATAATATTA-AATTATATTTG
*
72127 ATAATTTTAAATTATATTTG
1 ATAATATTAAATTATATTTG
*
72147 AT-ATATTAAATAATATT
1 ATAATATTAAATTATATT
72164 ATATTATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 13 0.41
20 11 0.34
21 8 0.25
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATAATATTAAATTATATTTG
Found at i:72174 original size:19 final size:19
Alignment explanation
Indices: 72105--72180 Score: 50
Period size: 19 Copynumber: 3.9 Consensus size: 19
72095 TTTTTTAAAA
*
72105 TATAATATTATAAAT-ATAT
1 TATATTATT-TAAATAATAT
* * *
72124 TTTATAATTTTAAATTATAT
1 TATATTA-TTTAAATAATAT
72144 T-TGA-TATATTAAATAATAT
1 TAT-ATTAT-TTAAATAATAT
*
72163 TATATTATTTAAAGAATA
1 TATATTATTTAAATAATA
72181 CAAAGAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
18 1 0.02
19 32 0.71
20 12 0.27
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TATATTATTTAAATAATAT
Found at i:72446 original size:16 final size:16
Alignment explanation
Indices: 72425--72457 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
72415 CGCAGTGGAG
72425 TAAAAATACTAGGGTT
1 TAAAAATACTAGGGTT
72441 TAAAAATACTAGGGTT
1 TAAAAATACTAGGGTT
72457 T
1 T
72458 CAGCGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TAAAAATACTAGGGTT
Found at i:83676 original size:22 final size:20
Alignment explanation
Indices: 83651--83690 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
83641 GAGTTCACTG
83651 TGGATGCTTAAGTTTTTCTTAA
1 TGGATGCTT--GTTTTTCTTAA
*
83673 TGGATGGTTGTTTTTCTT
1 TGGATGCTTGTTTTTCTT
83691 TATGTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.15, C:0.07, G:0.23, T:0.55
Consensus pattern (20 bp):
TGGATGCTTGTTTTTCTTAA
Done.