Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008053.1 Hibiscus syriacus cultivar Beakdansim tig00110548_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: 6772376
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 32 of 32
Found at i:6727219 original size:14 final size:14
Alignment explanation
Indices: 6727196--6727228 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
6727186 GCTTGTTTAA
*
6727196 TTGATTTGTAAAAG
1 TTGATCTGTAAAAG
6727210 TTGATCTGTAAAAG
1 TTGATCTGTAAAAG
6727224 TTGAT
1 TTGAT
6727229 TTGTTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.42
Consensus pattern (14 bp):
TTGATCTGTAAAAG
Found at i:6727413 original size:20 final size:20
Alignment explanation
Indices: 6727388--6727434 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
6727378 GATTTTCTCG
6727388 TTGCGATAATCAAATTCCCA
1 TTGCGATAATCAAATTCCCA
* *
6727408 TTGCGATAATCAAATTCGCG
1 TTGCGATAATCAAATTCCCA
6727428 TTGCGAT
1 TTGCGAT
6727435 TTTTGCGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (20 bp):
TTGCGATAATCAAATTCCCA
Found at i:6727455 original size:34 final size:34
Alignment explanation
Indices: 6727411--6727542 Score: 140
Period size: 34 Copynumber: 3.7 Consensus size: 34
6727401 ATTCCCATTG
*
6727411 CGATAATCAAATTCGCGTTGCGATTTT-TGCGTTA
1 CGATAGTCAAATTCGCGTTGCGATTTTCT-CGTTA
* *
6727445 CGATAGTCAAATGCGCTTTGCGATTTTCTCGTTA
1 CGATAGTCAAATTCGCGTTGCGATTTTCTCGTTA
* * *
6727479 CGATAGTCAAATTCCCGTTGCGATAATCAAATTCACGTTG
1 CGATAGTCAAATTCGCGTTGCGAT--T----TTCTCGTTA
6727519 CGATAGTCAAATTCGCGTTGCGAT
1 CGATAGTCAAATTCGCGTTGCGAT
6727543 ATTCAAATGA
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
34 50 0.61
35 1 0.01
36 1 0.01
40 30 0.37
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (34 bp):
CGATAGTCAAATTCGCGTTGCGATTTTCTCGTTA
Found at i:6727466 original size:54 final size:54
Alignment explanation
Indices: 6727363--6727468 Score: 133
Period size: 54 Copynumber: 2.0 Consensus size: 54
6727353 GTTGCTATTG
* * *
6727363 TCAAATACGCTTTGCGATTTTCTCGTTGCGATAATCAAATTCCCATTGCGATAA
1 TCAAATACGCGTTGCGATTTTCTCGTTACGATAATCAAATGCCCATTGCGATAA
* * * *
6727417 TCAAATTCGCGTTGCGATTTT-TGCGTTACGATAGTCAAATGCGCTTTGCGAT
1 TCAAATACGCGTTGCGATTTTCT-CGTTACGATAATCAAATGCCCATTGCGAT
6727469 TTTCTCGTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.02
54 43 0.98
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (54 bp):
TCAAATACGCGTTGCGATTTTCTCGTTACGATAATCAAATGCCCATTGCGATAA
Found at i:6727483 original size:88 final size:88
Alignment explanation
Indices: 6727362--6727522 Score: 277
Period size: 88 Copynumber: 1.8 Consensus size: 88
6727352 CGTTGCTATT
* *
6727362 GTCAAATACGCTTTGCGATTTTCTCGTTGCGATAATCAAATTCCCATTGCGATAATCAAATTCGC
1 GTCAAATACGCTTTGCGATTTTCTCGTTACGATAATCAAATTCCCATTGCGATAATCAAATTCAC
6727427 GTTGCGATTTTTGCGTTACGATA
66 GTTGCGATTTTTGCGTTACGATA
* * *
6727450 GTCAAATGCGCTTTGCGATTTTCTCGTTACGATAGTCAAATTCCCGTTGCGATAATCAAATTCAC
1 GTCAAATACGCTTTGCGATTTTCTCGTTACGATAATCAAATTCCCATTGCGATAATCAAATTCAC
6727515 GTTGCGAT
66 GTTGCGAT
6727523 AGTCAAATTC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 68 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (88 bp):
GTCAAATACGCTTTGCGATTTTCTCGTTACGATAATCAAATTCCCATTGCGATAATCAAATTCAC
GTTGCGATTTTTGCGTTACGATA
Found at i:6727502 original size:20 final size:20
Alignment explanation
Indices: 6727474--6727550 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
6727464 GCGATTTTCT
* *
6727474 CGTTACGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCA
*
6727494 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
6727514 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
*
6727534 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
6727551 GAATGTGTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:6727744 original size:18 final size:18
Alignment explanation
Indices: 6727721--6727755 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6727711 AAGTCGGTTG
*
6727721 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
6727739 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
6727756 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:6729810 original size:14 final size:14
Alignment explanation
Indices: 6729791--6729827 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
6729781 TCCCGTGGCA
6729791 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
6729805 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
6729819 TTCTTCTTC
1 TT-TTCTTC
6729828 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:6730051 original size:24 final size:24
Alignment explanation
Indices: 6730017--6730070 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
6730007 CTGAAACATC
6730017 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
6730041 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
6730065 ATCAAA
1 ATCAAA
6730071 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:6730084 original size:24 final size:24
Alignment explanation
Indices: 6730017--6730084 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
6730007 CTGAAACATC
* * *
6730017 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
6730041 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
6730065 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
6730085 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:6730750 original size:17 final size:17
Alignment explanation
Indices: 6730724--6730761 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
6730714 CGGAAGGGGA
*
6730724 AGGATTTCGTTGGATAT
1 AGGATGTCGTTGGATAT
6730741 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
6730758 AGGA
1 AGGA
6730762 ACGGATGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.34, T:0.34
Consensus pattern (17 bp):
AGGATGTCGTTGGATAT
Found at i:6730960 original size:20 final size:20
Alignment explanation
Indices: 6730928--6731055 Score: 105
Period size: 20 Copynumber: 6.3 Consensus size: 20
6730918 GAAATTCAGT
6730928 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* * * *
6730948 GTTGTGATGGTCAAAATCAC
1 GTTGCGATAGTCAGAATCGC
6730968 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* * *
6730988 GTTGCGAT-TTACATATTCGC
1 GTTGCGATAGT-CAGAATCGC
** *
6731008 GTTGCGATTTTCCAAAATCGC
1 GTTGCGATAGT-CAGAATCGC
** *
6731029 AATGCGATAGTCAAAATCGC
1 GTTGCGATAGTCAGAATCGC
*
6731049 GTCGCGA
1 GTTGCGA
6731056 ATCTGGAAAC
Statistics
Matches: 85, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
19 1 0.01
20 68 0.80
21 16 0.19
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:6734646 original size:15 final size:15
Alignment explanation
Indices: 6734626--6734658 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
6734616 CATTATTCTC
*
6734626 TTTCGAGCACTTATA
1 TTTCGAGCACTTACA
6734641 TTTCGAGCACTTACA
1 TTTCGAGCACTTACA
6734656 TTT
1 TTT
6734659 TAGTCACAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.42
Consensus pattern (15 bp):
TTTCGAGCACTTACA
Found at i:6734962 original size:421 final size:416
Alignment explanation
Indices: 6733990--6735226 Score: 2109
Period size: 421 Copynumber: 3.0 Consensus size: 416
6733980 GAGAGGGAGA
*
6733990 GAACCTTGAGAGCATATTTTCTCTCTGTTTTAAGGAAGAGGGGAGGATGTGAGAAATGAGAATAA
1 GAACCTTGAGA--ATATTTTCTCTCTGTTTTAAAGAAGAGGGGAGGATGTGAGAAATGAGAATAA
*
6734055 TAAACCTATTTTGGCTTAGGTGAAAAATATATATAGCATAGTCGAAATGGTGTCGTTTAAGGGGG
64 TAAACCTATTTTGGCTTAGGTGAAAAATATATATAGCATAGTCGAAATGGTGTCGTTTAAGGAGG
*
6734120 CCTTCAGCGTGTTTTCTGGGATGGGTTAATAGCCCTTTAAGTCTCTGCTCCTTAGTAATCTTACC
129 CCTTCAGCGTGTTTTCTGGGATGGGTTAATAGCCCTTTAAGTCTCTGCTCCTTTGTAATCTTACC
6734185 TTTTAGCCATATAATGAAGTTTTTCATTA-T-TC--T------CTTTCGAGCACTTACATTTTAG
194 TTTTAGCCATATAATGAAGTTTTTCATTATTCTCTTTCGAGCACTTTCGAGCACTTACATTTTAG
*
6734240 TCACAAGTAGCATGTTTTATGTATTTTTTCTAACATTCGAATTTGACCCTGTGATTTATGTATTT
259 TCACAAGTAGCATGTGTTATGTATTTTTTCTAACATTCGAATTTGACCCTGTGATTTATGTATTT
*
6734305 TTCATTTTAGTCGCTACCTTGCATATGGTTTAATTATCATTTAGTCCTTCATGTTTCTGGTTTAA
324 TTCATTTTAGTCACTACCTTGCATATGGTTTAATTATCATTTAGTCCTTCATGTTTCTGGTTTAA
* *
6734370 TTTATTTTTAGACATTTATATTATTTATG
389 TTTA-TTTTAGTCCTTTATATTATTTATG
* *
6734399 GAACCTTGAGAATATTTTCTCTCTGTTTTAAGGAAGAGGGGAGGTTGTGAGAAATGAGAATAATA
1 GAACCTTGAGAATATTTTCTCTCTGTTTTAAAGAAGAGGGGAGGATGTGAGAAATGAGAATAATA
*
6734464 AACCTATTTTGGCTTATGTGAAAAATATATATAGCATAGTCGAAATGGTGTCGTTTAAGGAGGCC
66 AACCTATTTTGGCTTAGGTGAAAAATATATATAGCATAGTCGAAATGGTGTCGTTTAAGGAGGCC
*
6734529 TTCAGCGTGTTTTCTGGGATGGGTTAATAGCCCTTTAAGTTTCTGCTCCTTTGTAATCTTACCTT
131 TTCAGCGTGTTTTCTGGGATGGGTTAATAGCCCTTTAAGTCTCTGCTCCTTTGTAATCTTACCTT
*
6734594 TTAGCTATATAATGAAGTTTTTCATTATTCTCTTTCGAGCACTTATATTTCGAGCACTTACATTT
196 TTAGCCATATAATGAAGTTTTTCATTATTCTCTTTCGAGCAC-----TTTCGAGCACTTACATTT
*
6734659 TAGTCACAAGTAGCATGTGTTATGTATTTTTTCTAACATTCGAATTTGACCCTGTGATTTATCTA
256 TAGTCACAAGTAGCATGTGTTATGTATTTTTTCTAACATTCGAATTTGACCCTGTGATTTATGTA
*
6734724 TTTTTCATTTTAGTCACTGCCTTGCATATGGTTTAATTATCATTTAGTCCTTCATGTTTCTGGTT
321 TTTTTCATTTTAGTCACTACCTTGCATATGGTTTAATTATCATTTAGTCCTTCATGTTTCTGGTT
6734789 TAATTTATTTTAGTCCTTTATATTATTTATG
386 TAATTTATTTTAGTCCTTTATATTATTTATG
6734820 GAACCTTGAGAATATTTTCTCTCTGTTTTAAAGAAGAGGGGAGGATGTGAGAAATGAGAATAATA
1 GAACCTTGAGAATATTTTCTCTCTGTTTTAAAGAAGAGGGGAGGATGTGAGAAATGAGAATAATA
* *
6734885 AACCTATTTTGGCTTAGGTGAAAAATATATATAGCATAGTCGAAATGGTGTTGTTTAAGGGGGCC
66 AACCTATTTTGGCTTAGGTGAAAAATATATATAGCATAGTCGAAATGGTGTCGTTTAAGGAGGCC
6734950 TTCAGCGTGTTTTCTGGGATGGGTTAATAGCCCTTTAAGTCTCTGCTCCTTTGTAATCTTACCTT
131 TTCAGCGTGTTTTCTGGGATGGGTTAATAGCCCTTTAAGTCTCTGCTCCTTTGTAATCTTACCTT
6735015 TTAGCCATATAATGAAGTTTTTCATTATTCTCTTTCGAGCAC-TT-----A--T--ATTTTAGTC
196 TTAGCCATATAATGAAGTTTTTCATTATTCTCTTTCGAGCACTTTCGAGCACTTACATTTTAGTC
*
6735070 ACAAGTAGCATGTGTTATGTATTTTTTTTAACATTCGAATTTGACCCTGTGATTTATGTATTTTT
261 ACAAGTAGCATGTGTTATGTATTTTTTCTAACATTCGAATTTGACCCTGTGATTTATGTATTTTT
6735135 CATTTTAGTCACTACCTTGCATATGGTTTAATTATCATTTAGTCCTTCATGTTTCTGGTTTAATT
326 CATTTTAGTCACTACCTTGCATATGGTTTAATTATCATTTAGTCCTTCATGTTTCTGGTTTAATT
6735200 TATTTTAGTCCTTTATATTATTTATG
391 TATTTTAGTCCTTTATATTATTTATG
6735226 G
1 G
6735227 GTTATTTTTG
Statistics
Matches: 791, Mismatches: 22, Indels: 33
0.93 0.03 0.04
Matches are distributed among these distances:
406 163 0.21
407 205 0.26
408 2 0.00
409 13 0.02
410 1 0.00
411 1 0.00
415 2 0.00
417 1 0.00
421 252 0.32
422 151 0.19
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (416 bp):
GAACCTTGAGAATATTTTCTCTCTGTTTTAAAGAAGAGGGGAGGATGTGAGAAATGAGAATAATA
AACCTATTTTGGCTTAGGTGAAAAATATATATAGCATAGTCGAAATGGTGTCGTTTAAGGAGGCC
TTCAGCGTGTTTTCTGGGATGGGTTAATAGCCCTTTAAGTCTCTGCTCCTTTGTAATCTTACCTT
TTAGCCATATAATGAAGTTTTTCATTATTCTCTTTCGAGCACTTTCGAGCACTTACATTTTAGTC
ACAAGTAGCATGTGTTATGTATTTTTTCTAACATTCGAATTTGACCCTGTGATTTATGTATTTTT
CATTTTAGTCACTACCTTGCATATGGTTTAATTATCATTTAGTCCTTCATGTTTCTGGTTTAATT
TATTTTAGTCCTTTATATTATTTATG
Found at i:6735343 original size:30 final size:31
Alignment explanation
Indices: 6735304--6735371 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
6735294 ATTGTCCATC
*
6735304 CCTTCAAATTTCTA-TTTTTGCTATTTTAGT
1 CCTTTAAATTTCTAGTTTTTGCTATTTTAGT
*
6735334 CCTTTAAATTTCTAGTTTTTGCTATTTTATT
1 CCTTTAAATTTCTAGTTTTTGCTATTTTAGT
6735365 CCTTTAA
1 CCTTTAA
6735372 GTTTATGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 13 0.37
31 22 0.63
ACGTcount: A:0.21, C:0.16, G:0.06, T:0.57
Consensus pattern (31 bp):
CCTTTAAATTTCTAGTTTTTGCTATTTTAGT
Found at i:6742271 original size:19 final size:16
Alignment explanation
Indices: 6742245--6742288 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 16
6742235 ACTAAAAAAA
6742245 TGTGTTTTGATTTTAAAT
1 TGTGTTTTGA-TTT-AAT
6742263 TGTTGTTTTTGATTTAAT
1 TG-TG-TTTTGATTTAAT
6742281 TGTGTTTT
1 TGTGTTTT
6742289 TAAAACTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 4 0.17
17 2 0.08
18 7 0.29
19 5 0.21
20 6 0.25
ACGTcount: A:0.16, C:0.00, G:0.18, T:0.66
Consensus pattern (16 bp):
TGTGTTTTGATTTAAT
Found at i:6742283 original size:18 final size:19
Alignment explanation
Indices: 6742245--6742289 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
6742235 ACTAAAAAAA
6742245 TGTG-TTTTGATTTTAAAT
1 TGTGTTTTTGATTTTAAAT
6742263 TGTTGTTTTTGA-TTT-AAT
1 TG-TGTTTTTGATTTTAAAT
6742281 TGTGTTTTT
1 TGTGTTTTT
6742290 AAAACTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 7 0.28
18 7 0.28
19 5 0.20
20 6 0.24
ACGTcount: A:0.16, C:0.00, G:0.18, T:0.67
Consensus pattern (19 bp):
TGTGTTTTTGATTTTAAAT
Found at i:6743454 original size:29 final size:29
Alignment explanation
Indices: 6743422--6743477 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
6743412 TAGGATTTAT
*
6743422 TGTTTTAATATTTTGAATGTTTGAATTTG
1 TGTTTTAAGATTTTGAATGTTTGAATTTG
** *
6743451 TGTTTTTGGATTTTGGATGTTTGAATT
1 TGTTTTAAGATTTTGAATGTTTGAATT
6743478 GTTTGTTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.21, T:0.59
Consensus pattern (29 bp):
TGTTTTAAGATTTTGAATGTTTGAATTTG
Found at i:6750705 original size:41 final size:41
Alignment explanation
Indices: 6750617--6750773 Score: 118
Period size: 42 Copynumber: 3.8 Consensus size: 41
6750607 AATTGATACT
* * * *
6750617 TTAGCGGCGTTTTTAGTAAAAACGCTGCAATAGAGTTGACA
1 TTAGCGGCGTTTTTAGCAAAAACGCCGCAATAGAGTGGAAA
* *
6750658 TATAGCGGCGTTTTTA-CAAAAATGCCGCAATAGGGTGGCAAA
1 T-TAGCGGCGTTTTTAGCAAAAACGCCGCAATAGAGTGG-AAA
* * * * * * ***
6750700 TTAGCGGCGTTTATACCACAAACGCCACAATAAAATAGTTCA
1 TTAGCGGCGTTTTTAGCAAAAACGCCGCAATAGAGT-GGAAA
* **
6750742 TTTGCGGCGTTTTTATTAAAAACGCCGCAATA
1 TTAGCGGCGTTTTTAGCAAAAACGCCGCAATA
6750774 TTCTGATATA
Statistics
Matches: 90, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
41 31 0.34
42 58 0.64
43 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (41 bp):
TTAGCGGCGTTTTTAGCAAAAACGCCGCAATAGAGTGGAAA
Found at i:6752699 original size:28 final size:28
Alignment explanation
Indices: 6752668--6752721 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
6752658 TTATGAGTGC
6752668 ATATAATAT-TTGTCATGGAAGTTTATCA
1 ATAT-ATATCTTGTCATGGAAGTTTATCA
* *
6752696 ATATTTCTCTTGTCATGGAAGTTTAT
1 ATATATATCTTGTCATGGAAGTTTAT
6752722 ATTTTCTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (28 bp):
ATATATATCTTGTCATGGAAGTTTATCA
Found at i:6759278 original size:21 final size:21
Alignment explanation
Indices: 6759260--6759345 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
6759250 ATGAAGCAAG
*
6759260 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
6759281 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
6759302 GGAAGCAGAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
6759323 GGCAGCACAGAGAG-AGGCAGC
1 GGAAGCAGAGAGAGCA-GCAGC
6759344 GG
1 GG
6759346 CAGAACAGAG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 1 0.02
21 55 0.98
ACGTcount: A:0.37, C:0.20, G:0.42, T:0.01
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:6759346 original size:21 final size:21
Alignment explanation
Indices: 6759268--6759360 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
6759258 AGGGAAACAG
* *
6759268 AGAGAGCAGCAGCGGAAGCAGC
1 AGAGAGAAGCAGCGGCAGCA-C
* * * *
6759290 -TAGAGCAGCAGCGGAAGCAG
1 AGAGAGAAGCAGCGGCAGCAC
6759310 AGAGAGAAGCAGCGGCAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
* *
6759331 AGAGAGAGGCAGCGGCAGAAC
1 AGAGAGAAGCAGCGGCAGCAC
6759352 AGAGAGAAG
1 AGAGAGAAG
6759361 TAATGTATCA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.39, C:0.19, G:0.41, T:0.01
Consensus pattern (21 bp):
AGAGAGAAGCAGCGGCAGCAC
Found at i:6759899 original size:43 final size:41
Alignment explanation
Indices: 6759697--6759921 Score: 137
Period size: 43 Copynumber: 5.2 Consensus size: 41
6759687 CATACATTTA
* * * * *
6759697 GCGGCGTTTTTGATAAAAACGCCGCAAAATCTCAATACATATTCT
1 GCGGCG-TTTT-ATGAAAACGCCGCTAAATATCAAAACCTA-T-T
* * * * ** *
6759742 GCGGCGTTTTTAGGAAAACGCCGGTAAAAATAAAAATTTACT
1 GCGGCG-TTTTATGAAAACGCCGCTAAATATCAAAACCTATT
* * * *
6759784 GCGGCATTTTGGAAGAAAACGCCGCTAAACATCAACGA-CTATT
1 GCGGCGTTTT--ATGAAAACGCCGCTAAATATCAA-AACCTATT
* * * *
6759827 GCGGCGTTTGTCTGCCAAATGCCGTTAAATATCAAAACCTATT
1 GCGGCGTTT-TATG-AAAACGCCGCTAAATATCAAAACCTATT
* *
6759870 GCGGCGTTTTAATGATAAACGCCGCTAAATATCAATACCTTTT
1 GCGGCGTTTT-ATGA-AAACGCCGCTAAATATCAAAACCTATT
6759913 GCGGCGTTT
1 GCGGCGTTT
6759922 ACTTTTGCTG
Statistics
Matches: 139, Mismatches: 33, Indels: 18
0.73 0.17 0.09
Matches are distributed among these distances:
41 4 0.03
42 9 0.06
43 94 0.68
44 21 0.15
45 11 0.08
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTTATGAAAACGCCGCTAAATATCAAAACCTATT
Found at i:6761649 original size:21 final size:21
Alignment explanation
Indices: 6761623--6761666 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
6761613 ATTTCTGGGT
* *
6761623 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
6761644 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
6761665 AA
1 AA
6761667 ACGAACAACA
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:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:6763057 original size:14 final size:14
Alignment explanation
Indices: 6763038--6763065 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6763028 GAAAAGAAGC
6763038 TATGTGATACGTGA
1 TATGTGATACGTGA
6763052 TATGTGATACGTGA
1 TATGTGATACGTGA
6763066 ATTACAAGTT
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:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:6763436 original size:149 final size:149
Alignment explanation
Indices: 6763166--6763480 Score: 542
Period size: 149 Copynumber: 2.1 Consensus size: 149
6763156 GAGTCGATGG
* *
6763166 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
6763231 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
6763296 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
6763315 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAATATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
* **
6763380 ACTTGATCTCTAGTATATGTATATAATTCTTAAGGAATAATATGTGGTCCTTATGGACATTTTTA
66 ACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
6763445 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
6763464 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
6763481 TGCAATTATA
Statistics
Matches: 157, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
148 1 0.01
149 156 0.99
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:6763481 original size:23 final size:23
Alignment explanation
Indices: 6763448--6763492 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
6763438 ATTTTTATAT
*
6763448 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
6763471 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
6763493 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:6764868 original size:103 final size:103
Alignment explanation
Indices: 6764689--6764895 Score: 405
Period size: 103 Copynumber: 2.0 Consensus size: 103
6764679 GCGTCCATGA
6764689 TGACAACAATTGACAAATCTTCAACAAAACATCGTCGAAATCTATTTGTGTGAGGATCCCTTGTA
1 TGACAACAATTGACAAATCTTCAACAAAACATCGTCGAAATCTATTTGTGTGAGGATCCCTTGTA
6764754 TCTTTATCTAGTATTATGAAAATCTAATATTATAATTT
66 TCTTTATCTAGTATTATGAAAATCTAATATTATAATTT
*
6764792 TGACAACAATTGACAAATCTTCAACAAAACATTGTCGAAATCTATTTGTGTGAGGATCCCTTGTA
1 TGACAACAATTGACAAATCTTCAACAAAACATCGTCGAAATCTATTTGTGTGAGGATCCCTTGTA
6764857 TCTTTATCTAGTATTATGAAAATCTAATATTATAATTT
66 TCTTTATCTAGTATTATGAAAATCTAATATTATAATTT
6764895 T
1 T
6764896 ACTAAAGAAT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.38
Consensus pattern (103 bp):
TGACAACAATTGACAAATCTTCAACAAAACATCGTCGAAATCTATTTGTGTGAGGATCCCTTGTA
TCTTTATCTAGTATTATGAAAATCTAATATTATAATTT
Found at i:6770282 original size:15 final size:15
Alignment explanation
Indices: 6770264--6770296 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
6770254 TAAAATTCTA
*
6770264 AAAGGTAATTGATTT
1 AAAGGTAAATGATTT
6770279 AAAGGTAAATGATTT
1 AAAGGTAAATGATTT
6770294 AAA
1 AAA
6770297 ATAAGTGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.33
Consensus pattern (15 bp):
AAAGGTAAATGATTT
Done.