Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000026.1 Hibiscus syriacus cultivar Beakdansim tig00000044_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: 105645
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:5093 original size:22 final size:21
Alignment explanation
Indices: 5068--5111 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
5058 ATCTCTTTTC
5068 TTTTCATTTCAAGTTTTCATTT
1 TTTTCATTTCAAGTTTT-ATTT
* *
5090 TTTTTATTTTAAGTTTTATTT
1 TTTTCATTTCAAGTTTTATTT
5111 T
1 T
5112 CAAATATGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTCATTTCAAGTTTTATTT
Found at i:6526 original size:21 final size:21
Alignment explanation
Indices: 6500--6540 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
6490 AGATCGAAGC
6500 ACGAGCACGAAGAATCCACGT
1 ACGAGCACGAAGAATCCACGT
6521 ACGAGCACGAAGAATCCACG
1 ACGAGCACGAAGAATCCACG
6541 CACAAACGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.29, G:0.24, T:0.07
Consensus pattern (21 bp):
ACGAGCACGAAGAATCCACGT
Found at i:9411 original size:21 final size:21
Alignment explanation
Indices: 9385--9431 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
9375 AAAAATGACT
9385 TTTTCTTGTCCCTTCGGTACA
1 TTTTCTTGTCCCTTCGGTACA
9406 TTTTCTTGTCCCTTCGGTACA
1 TTTTCTTGTCCCTTCGGTACA
9427 TTTTC
1 TTTTC
9432 ATATAGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.09, C:0.28, G:0.13, T:0.51
Consensus pattern (21 bp):
TTTTCTTGTCCCTTCGGTACA
Found at i:11782 original size:15 final size:14
Alignment explanation
Indices: 11762--11822 Score: 68
Period size: 15 Copynumber: 4.2 Consensus size: 14
11752 TTTTGAAAAC
11762 TTTATTTCATTTTAA
1 TTTATTTCA-TTTAA
*
11777 TTTATTTCATTTCA
1 TTTATTTCATTTAA
*
11791 TTTCATTTCATTCAA
1 TTT-ATTTCATTTAA
* *
11806 TTTATTTTATTTTA
1 TTTATTTCATTTAA
11820 TTT
1 TTT
11823 TATCAAATGC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
14 18 0.46
15 21 0.54
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTCATTTAA
Found at i:11825 original size:5 final size:5
Alignment explanation
Indices: 11762--11850 Score: 54
Period size: 5 Copynumber: 17.6 Consensus size: 5
11752 TTTTGAAAAC
* * * * * * * *
11762 TTTAT TTCAT TTTAA TTTAT TTCAT TTCAT TTCAT TTCA- TTCAA TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
***
11811 TTTAT TTTAT TTTAT CAAAT GCTTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT --TTTAT TTTAT TTTAT TTT
11851 TCTCTGAATA
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
4 4 0.06
5 62 0.91
7 2 0.03
ACGTcount: A:0.24, C:0.09, G:0.01, T:0.66
Consensus pattern (5 bp):
TTTAT
Found at i:18822 original size:16 final size:16
Alignment explanation
Indices: 18801--18838 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
18791 AATCATAACA
*
18801 TGAACACCAATGATGC
1 TGAACACCAACGATGC
*
18817 TGAACACCAACGATGT
1 TGAACACCAACGATGC
18833 TGAACA
1 TGAACA
18839 TTGGTACACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (16 bp):
TGAACACCAACGATGC
Found at i:20325 original size:519 final size:518
Alignment explanation
Indices: 19342--20380 Score: 1900
Period size: 519 Copynumber: 2.0 Consensus size: 518
19332 CAAACTAAAT
*
19342 CATATTTCTCAACATGATTTCAAGTTTTCCAACATACTTATAAATTCCCAAAAATATTTACTTTT
1 CATACTTCTCAACATGATTTCAAGTTTTCCAACATACTTATAAATTCCCAAAAATATTTACTTTT
*
19407 CATTATTCATCCTTCAACCTTTACTTATTTCATAATCCACCACTAAATTATGAATTCTTTTTAGA
66 CATTATTCATCCTTCAACCTTTACTTACTTCATAATCCACCACTAAATTATGAATTCTTTTTAGA
**
19472 ATTCATATCAACTTTCCCCTTTAATTCATAGTGGTCCTTCACCATTATGATCATTTCACATTAAT
131 ATTCATATCAACTTTCCCCTTTAATTCATAGTGACCCTTCACCATTATGATCATTTCACATTAAT
*
19537 TACATAAAATTTTAAGAATGACAATAAAATATTCAAATCAACACTTAAAAATTCAAAATCTTGCA
196 TACATAAAATTTTAAGAATGACAATAAAATATTCAAATCAACACTTAAAAATTCAAAAGCTTGCA
*
19602 AATTCATCCTAAATTTTCTTAAACTTTGTCAATTCAACCTCCAATCTCTGTAAACTTGTAATTTA
261 AATTAATCCTAAATTTTCTTAAACTTTGTCAATTCAACCTCCAATCTCTGTAAACTTGTAATTTA
19667 TTTCAAACTTAATAATCAAACAAAAATTTCAGCAAGCTTCCAAAATTTCCAAATTGTCCTAATTT
326 TTTCAAACTTAATAATCAAACAAAAATTTCAGCAAGCTTCCAAAATTTCCAAATTGTCCTAATTT
*
19732 ACCCAAATGATACTTCTACATTTACTAACTTGCAAACAAGTCCCCATTTTCTTAGGACCTTTCTA
391 ACCCAAATGATACTTCTACATTTACTAACTTGCAAACAAGTCCCCATTTTCTTAGGACCTTTCGA
19797 ATTCCAACCCAAACTTCTACCAAATTTACAATTTGGTTCCAATAGCTTTCCAACTTAATTTTC
456 ATTCCAACCCAAACTTCTACCAAATTTACAATTTGGTTCCAATAGCTTTCCAACTTAATTTTC
*
19860 CATACTTCTCAACATGATTTCAAGTTTTCCAACATACTTATAAATTCCTAAAAATATTTACTTTT
1 CATACTTCTCAACATGATTTCAAGTTTTCCAACATACTTATAAATTCCCAAAAATATTTACTTTT
19925 CATTATTCATCCTTCAACCTTTACTTACTTCATAATCCAACCACTAAATTATGAATTCTTTTTAG
66 CATTATTCATCCTTCAACCTTTACTTACTTCATAATCC-ACCACTAAATTATGAATTCTTTTTAG
*
19990 AATTCATATCAACTTTCCCCTTTAATTCATAGTGACCCTTCACCATTATTATCATTTCACATTAA
130 AATTCATATCAACTTTCCCCTTTAATTCATAGTGACCCTTCACCATTATGATCATTTCACATTAA
* * *
20055 TTACATAAAATTTTCAGAATGTCAATAAAATATTCAAATCAACACTTAAACATTCAAAAGCTTGC
195 TTACATAAAATTTTAAGAATGACAATAAAATATTCAAATCAACACTTAAAAATTCAAAAGCTTGC
*
20120 AAATTAATCTTAAATTTTCTTAAACTTTGTCAATTCAACCTCCAATCTCTGTAAACTTGTAATTT
260 AAATTAATCCTAAATTTTCTTAAACTTTGTCAATTCAACCTCCAATCTCTGTAAACTTGTAATTT
* * *
20185 ATTTCAAACTTAATAATTAAACAAAAATTTCAGCAATCTTCCAGAATTTCCAGAATTGTCCTAAT
325 ATTTCAAACTTAATAATCAAACAAAAATTTCAGCAAGCTTCCAAAATTTCCA-AATTGTCCTAAT
*
20250 TTA-CCAAATGATACTTCTACATTTACTAACTTGCAAACAAGTCCCCATTTTCTTTGGACCTTTC
389 TTACCCAAATGATACTTCTACATTTACTAACTTGCAAACAAGTCCCCATTTTCTTAGGACCTTTC
20314 GAATTCCAACCCAAACTTCTACCAAATTTACAATTTGGTTCCAATAGCTTTCCAACTTAATTTTC
454 GAATTCCAACCCAAACTTCTACCAAATTTACAATTTGGTTCCAATAGCTTTCCAACTTAATTTTC
20379 CA
1 CA
20381 GCATCTCAAT
Statistics
Matches: 502, Mismatches: 17, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
518 100 0.20
519 387 0.77
520 15 0.03
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (518 bp):
CATACTTCTCAACATGATTTCAAGTTTTCCAACATACTTATAAATTCCCAAAAATATTTACTTTT
CATTATTCATCCTTCAACCTTTACTTACTTCATAATCCACCACTAAATTATGAATTCTTTTTAGA
ATTCATATCAACTTTCCCCTTTAATTCATAGTGACCCTTCACCATTATGATCATTTCACATTAAT
TACATAAAATTTTAAGAATGACAATAAAATATTCAAATCAACACTTAAAAATTCAAAAGCTTGCA
AATTAATCCTAAATTTTCTTAAACTTTGTCAATTCAACCTCCAATCTCTGTAAACTTGTAATTTA
TTTCAAACTTAATAATCAAACAAAAATTTCAGCAAGCTTCCAAAATTTCCAAATTGTCCTAATTT
ACCCAAATGATACTTCTACATTTACTAACTTGCAAACAAGTCCCCATTTTCTTAGGACCTTTCGA
ATTCCAACCCAAACTTCTACCAAATTTACAATTTGGTTCCAATAGCTTTCCAACTTAATTTTC
Found at i:24468 original size:27 final size:26
Alignment explanation
Indices: 24412--24472 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
24402 TTCATTTGCT
*
24412 AAAATTAACTAACATTATTAATTCAA
1 AAAATTAACTAACATAATTAATTCAA
24438 AAAATTAA-TAACATAAATATAA-TCATA
1 AAAATTAACTAACAT-AAT-TAATTCA-A
24465 AAAATTAA
1 AAAATTAA
24473 ATTTAAGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 6 0.19
26 13 0.42
27 12 0.39
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAATTAACTAACATAATTAATTCAA
Found at i:29380 original size:24 final size:24
Alignment explanation
Indices: 29307--29408 Score: 72
Period size: 26 Copynumber: 4.4 Consensus size: 24
29297 AATTAAATAA
* * *
29307 TATTTTTAT-AAT-ATTACAAATA
1 TATTTTTATAAATAATTATATATT
*
29329 TATTTTT-TATAATGATT-T-TATT
1 TATTTTTATA-AATAATTATATATT
29351 TA-TTTTATAAATAATTATATATT
1 TATTTTTATAAATAATTATATATT
* * *
29374 TATTTTTATAAAATATATTTTTTAGT
1 TATTTTTAT-AAATA-ATTATATATT
29400 TATTTTTAT
1 TATTTTTAT
29409 TTATAAATAA
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
21 11 0.17
22 14 0.22
23 9 0.14
24 9 0.14
25 5 0.08
26 16 0.25
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (24 bp):
TATTTTTATAAATAATTATATATT
Found at i:29407 original size:26 final size:24
Alignment explanation
Indices: 29344--29408 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 24
29334 TTTATAATGA
29344 TTTTATTTA-TTTTATAAATAATT
1 TTTTATTTATTTTTATAAATAATT
* *
29367 ATATATTTATTTTTATAAAATATATT
1 TTTTATTTATTTTTAT-AAATA-ATT
*
29393 TTTTAGTTATTTTTAT
1 TTTTATTTATTTTTAT
29409 TTATAAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 7 0.21
24 6 0.18
25 5 0.15
26 16 0.47
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTTATTTATTTTTATAAATAATT
Found at i:33532 original size:5 final size:5
Alignment explanation
Indices: 33524--33597 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
33514 CTTTATCTTA
* * *
33524 TTTTC TTTTTA TTTTC -TTTC ATTTC TTTTC CTTTC TTTTC -TTTC -TTTC
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
*
33572 TTTTC TTTTC GTTTTTC CTTTC TTTT
1 TTTTC TTTTC --TTTTC TTTTC TTTT
33598 TATCAACTCA
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
4 12 0.21
5 36 0.63
6 4 0.07
7 5 0.09
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:33598 original size:18 final size:17
Alignment explanation
Indices: 33549--33597 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
33539 CTTTCATTTC
*
33549 TTTTCCTTTCTTTTCTT
1 TTTTCCTTTCTTTTCGT
*
33566 TCTTTCTTTTCTTTTCGT
1 T-TTTCCTTTCTTTTCGT
33584 TTTTCCTTTCTTTT
1 TTTTCCTTTCTTTT
33598 TATCAACTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTCCTTTCTTTTCGT
Found at i:46613 original size:27 final size:27
Alignment explanation
Indices: 46583--46640 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
46573 GCAACACTCA
46583 GCAGTGCAAATCTGTTTGTTCCTGTAT
1 GCAGTGCAAATCTGTTTGTTCCTGTAT
*
46610 GCAGTGCAAATCTTTTTGTTCCTGTAT
1 GCAGTGCAAATCTGTTTGTTCCTGTAT
46637 GCAG
1 GCAG
46641 ATTGACCTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (27 bp):
GCAGTGCAAATCTGTTTGTTCCTGTAT
Found at i:50138 original size:15 final size:15
Alignment explanation
Indices: 50126--50156 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
50116 AACTAGAATG
50126 TGTGAAATGAGAAAC
1 TGTGAAATGAGAAAC
50141 TGTGAAATGAGAAAC
1 TGTGAAATGAGAAAC
50156 T
1 T
50157 AAAGAAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (15 bp):
TGTGAAATGAGAAAC
Found at i:53034 original size:5 final size:5
Alignment explanation
Indices: 53010--53058 Score: 80
Period size: 5 Copynumber: 9.8 Consensus size: 5
53000 GTCCGTCCGT
* *
53010 CTCGT CTCGG CTCGG CTCGG CTCGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
53059 TGGTCGTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.02, C:0.41, G:0.37, T:0.20
Consensus pattern (5 bp):
CTCGG
Found at i:53067 original size:6 final size:6
Alignment explanation
Indices: 53056--53182 Score: 191
Period size: 6 Copynumber: 21.2 Consensus size: 6
53046 TCGGCTCGGC
* * * *
53056 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
* * *
53104 TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
53152 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
53183 AATACGTGTC
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 119 1.00
ACGTcount: A:0.06, C:0.17, G:0.50, T:0.28
Consensus pattern (6 bp):
TCGTGG
Found at i:53448 original size:12 final size:12
Alignment explanation
Indices: 53431--53455 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53421 TGTACAAAGG
53431 AGACAAGCTGTT
1 AGACAAGCTGTT
53443 AGACAAGCTGTT
1 AGACAAGCTGTT
53455 A
1 A
53456 ATATCAGGAG
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:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (12 bp):
AGACAAGCTGTT
Found at i:53494 original size:22 final size:22
Alignment explanation
Indices: 53469--53523 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
53459 TCAGGAGTTA
* *
53469 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
53491 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
53513 CGGGAGTTATA
1 CAGGAGTTATA
53524 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:59064 original size:5 final size:5
Alignment explanation
Indices: 59050--59088 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
59040 GTCCGTCCGT
* * *
59050 CTCGT CTCGG CTCGG CACGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
59089 TGGTCGTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.05, C:0.41, G:0.36, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:59097 original size:6 final size:6
Alignment explanation
Indices: 59086--59146 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
59076 TCGGCTCGGC
* * *
59086 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
59134 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
59147 AATACGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.05, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:59445 original size:22 final size:22
Alignment explanation
Indices: 59420--59474 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
59410 TCAGGAGTTA
* *
59420 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
59442 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
59464 CGGGAGTTATA
1 CAGGAGTTATA
59475 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:61302 original size:21 final size:20
Alignment explanation
Indices: 61216--61373 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
61206 AAATGACCAA
**
61216 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
61235 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
61255 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
61275 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
61296 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
61317 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
61337 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
61358 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
61374 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:61435 original size:20 final size:20
Alignment explanation
Indices: 61341--61533 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
61331 GATTTTCCAG
* ** *
61341 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
61361 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
61381 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
61401 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
61421 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
61441 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
61461 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
61481 AATCGCAATGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
61502 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
61522 AATCGCAACGCG
1 AATCGCAACGCG
61534 ATTTTTAAAG
Statistics
Matches: 149, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
19 1 0.01
20 130 0.87
21 18 0.12
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:61952 original size:33 final size:33
Alignment explanation
Indices: 61913--61983 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
61903 TTCACTTAGA
61913 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
61946 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
61979 TTTCA
1 TTTCA
61984 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:62089 original size:21 final size:21
Alignment explanation
Indices: 62063--62139 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
62053 TGCAGAAGAG
62063 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
62084 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
*
62104 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
62126 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
62140 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.19
21 29 0.62
22 9 0.19
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:62143 original size:14 final size:14
Alignment explanation
Indices: 62124--62180 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
62114 GAAAAATGAA
62124 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
62138 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
62157 AATCGCAACGAGAG
1 AATCGCAACGAGAG
62171 AATCGCAACG
1 AATCGCAACG
62181 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:62155 original size:33 final size:33
Alignment explanation
Indices: 62117--62196 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
62107 GCAACGAGAA
62117 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
62150 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
62183 AAACCAAAATCGCA
1 AAATGAAAATCGCA
62197 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:62214 original size:19 final size:19
Alignment explanation
Indices: 62192--62317 Score: 69
Period size: 19 Copynumber: 7.1 Consensus size: 19
62182 GAAACCAAAA
*
62192 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
62211 TCGCGTTACGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
62225 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
62244 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
62258 T--CGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
62276 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
62296 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
62316 TC
1 TC
62318 AACCAAAAGA
Statistics
Matches: 82, Mismatches: 11, Indels: 28
0.68 0.09 0.23
Matches are distributed among these distances:
12 8 0.10
14 13 0.16
16 3 0.04
17 6 0.07
19 22 0.27
20 19 0.23
21 11 0.13
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:62263 original size:31 final size:33
Alignment explanation
Indices: 62197--62317 Score: 138
Period size: 33 Copynumber: 3.5 Consensus size: 33
62187 CAAAATCGCA
62197 TTGCGATTTTCATTTCGCGTTACGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTACGATTCTCTCG
*
62230 TTGCGATTTTCATTTCGCGTTGCGA-T-TCTCG
1 TTGCGATTTTCATTTCGCGTTACGATTCTCTCG
*
62261 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT---AC-G--ATTCTCTCG
62302 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
62318 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
31 17 0.23
32 3 0.04
33 30 0.40
36 1 0.01
37 1 0.01
39 3 0.04
40 3 0.04
41 17 0.23
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTACGATTCTCTCG
Found at i:62281 original size:21 final size:21
Alignment explanation
Indices: 62256--62317 Score: 90
Period size: 20 Copynumber: 3.0 Consensus size: 21
62246 GCGTTGCGAT
62256 TCTCGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTC
***
62277 TCTCGTTGCGACAGTCA-TTC
1 TCTCGTTGCGATTTTCATTTC
62297 TCTCGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTC
62318 AACCAAAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.11, C:0.26, G:0.16, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTC
Found at i:66553 original size:15 final size:15
Alignment explanation
Indices: 66541--66571 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
66531 AACTAGAATG
66541 TGTGAAATGAGAAAC
1 TGTGAAATGAGAAAC
66556 TGTGAAATGAGAAAC
1 TGTGAAATGAGAAAC
66571 T
1 T
66572 AAAGAAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (15 bp):
TGTGAAATGAGAAAC
Found at i:69454 original size:5 final size:5
Alignment explanation
Indices: 69435--69493 Score: 82
Period size: 5 Copynumber: 11.8 Consensus size: 5
69425 GTCCGTCCGT
* * * *
69435 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
69485 CTCGG CTCG
1 CTCGG CTCG
69494 TGGTCGTGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.05, C:0.41, G:0.37, T:0.17
Consensus pattern (5 bp):
CTCGG
Found at i:69502 original size:6 final size:6
Alignment explanation
Indices: 69491--69606 Score: 187
Period size: 6 Copynumber: 19.3 Consensus size: 6
69481 TCGGCTCGGC
* * * *
69491 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
*
69539 TCGAGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
69587 TCGTGG TCGTGG TCGTGG TC
1 TCGTGG TCGTGG TCGTGG TC
69607 ATACGTGTCT
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 108 1.00
ACGTcount: A:0.04, C:0.17, G:0.49, T:0.29
Consensus pattern (6 bp):
TCGTGG
Found at i:69905 original size:22 final size:22
Alignment explanation
Indices: 69880--69934 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
69870 TCAGGAGTTA
* *
69880 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
69902 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
69924 CGGGAGTTATA
1 CAGGAGTTATA
69935 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:75665 original size:93 final size:93
Alignment explanation
Indices: 75506--75821 Score: 614
Period size: 93 Copynumber: 3.4 Consensus size: 93
75496 TAGATTGCTT
* *
75506 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTCTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
75571 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
75599 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
75664 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
75692 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
75757 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
75785 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
75822 AATACCCTGA
Statistics
Matches: 221, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 221 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:75956 original size:14 final size:14
Alignment explanation
Indices: 75937--75993 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
75927 CGAAACTTAA
75937 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
75951 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
75970 AATCGCAACGACAG
1 AATCGCAACGAGAG
75984 AATCGCAACG
1 AATCGCAACG
75994 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:75975 original size:19 final size:18
Alignment explanation
Indices: 75951--76042 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
75941 GCAACGAGAG
75951 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
75970 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
75984 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
76003 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
76017 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
76036 AATCGCA
1 AATCGCA
76043 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:75977 original size:33 final size:33
Alignment explanation
Indices: 75919--76042 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
75909 TAGTTTACTT
* * *
75919 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
75953 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
75986 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
76019 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
76043 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:76019 original size:14 final size:14
Alignment explanation
Indices: 75968--76026 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
75958 ACGCGAAATG
75968 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
75982 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
76001 AAAATCGCAACGAC
1 AAAATCGCAACGAC
76015 AAAATCGCAACG
1 AAAATCGCAACG
76027 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:76060 original size:19 final size:19
Alignment explanation
Indices: 76038--76194 Score: 127
Period size: 19 Copynumber: 8.8 Consensus size: 19
76028 GAAACCAAAA
*
76038 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
76057 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
76071 TCTCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
* * *
76090 TCGCATAGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
76106 T--AGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
76123 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
76142 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
76161 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
76180 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
76195 AAGTTTTGTG
Statistics
Matches: 107, Mismatches: 21, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
14 15 0.14
16 7 0.07
17 7 0.07
19 78 0.73
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:76085 original size:33 final size:33
Alignment explanation
Indices: 76043--76135 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
76033 CAAAATCGCA
*
76043 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
* * * *
76076 TTGCGATTTTTATTTCGCATAGCGATTCTGTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
76109 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
76136 TTGGTTTCGC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
Found at i:76168 original size:38 final size:38
Alignment explanation
Indices: 76038--76194 Score: 136
Period size: 33 Copynumber: 4.4 Consensus size: 38
76028 GAAACCAAAA
*
76038 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* * * *
76073 T--CGTTGCGATTTTTATTTCGCATAGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* * **
76106 T--AGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
76142 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
76180 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
76195 AAGTTTTGTG
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 47 0.48
34 1 0.01
35 2 0.02
36 2 0.02
38 43 0.44
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:78151 original size:14 final size:14
Alignment explanation
Indices: 78132--78167 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
78122 ATTGTTTAAT
78132 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
78146 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
78160 TGATTTGT
1 TGATTTGT
78168 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:78290 original size:19 final size:18
Alignment explanation
Indices: 78274--78389 Score: 113
Period size: 19 Copynumber: 6.7 Consensus size: 18
78264 AAAAATGACT
78274 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
78293 ATCGCAATGCAAAATGAA
1 ATCGCAATGCGAAATGAA
*
78311 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
78325 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
78344 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATG-AA
*
78364 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
78378 ATCGCAATGCGA
1 ATCGCAATGCGA
78390 TTTTCATTTC
Statistics
Matches: 84, Mismatches: 5, Indels: 19
0.78 0.05 0.18
Matches are distributed among these distances:
14 16 0.19
15 1 0.01
16 11 0.13
17 4 0.05
18 10 0.12
19 26 0.31
20 16 0.19
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:78350 original size:51 final size:53
Alignment explanation
Indices: 78274--78389 Score: 209
Period size: 51 Copynumber: 2.2 Consensus size: 53
78264 AAAAATGACT
78274 ATCGCAATGCGAAATGAAAATCGCAATGC-AAAATG-AAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
78325 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
78378 ATCGCAATGCGA
1 ATCGCAATGCGA
78390 TTTTCATTTC
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
51 29 0.47
52 5 0.08
53 28 0.45
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:78466 original size:72 final size:70
Alignment explanation
Indices: 78380--78674 Score: 277
Period size: 72 Copynumber: 4.2 Consensus size: 70
78370 ACGAGAGAAT
*
78380 CGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
1 CGCATTGCGATTTTCATTTCG--TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
78445 TTCATTT-
63 TTCATTTC
* * * * *
78452 CGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCG
1 CGCATTGCGATTTTCATTT-CG--TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCG
78514 ATTTTCATTTC
60 ATTTTCATTTC
* *
78525 CGCATTGCGA--TTC-TCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA
1 CGCATTGCGATTTTCATTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGA
78587 TTTTCATTTC
61 TTTTCATTTC
* * *
78597 CGCATTGCGATTTTCA--T-GTTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTA
1 CGCATTGCGATTTTCATTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
78659 ATTTC
66 ATTTC
**
78664 CGTGTTGCGAT
1 CGCATTGCGAT
78675 AGTCAAATGC
Statistics
Matches: 188, Mismatches: 19, Indels: 37
0.77 0.08 0.15
Matches are distributed among these distances:
65 9 0.05
66 3 0.02
67 31 0.16
68 2 0.01
69 6 0.03
70 7 0.04
71 3 0.02
72 87 0.46
73 27 0.14
74 9 0.05
75 4 0.02
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (70 bp):
CGCATTGCGATTTTCATTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
ATTTC
Found at i:78670 original size:53 final size:53
Alignment explanation
Indices: 78385--78655 Score: 421
Period size: 53 Copynumber: 5.1 Consensus size: 53
78375 AGAATCGCAA
78385 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
78438 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
78491 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
78544 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA--TTC-TCT-CG--T
*
78602 TGCGATTTTCA--T-G--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
78649 TGCGATT
1 TGCGATT
78656 GTAATTTCCG
Statistics
Matches: 209, Mismatches: 3, Indels: 18
0.91 0.01 0.08
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.01
52 10 0.05
53 163 0.78
54 3 0.01
55 3 0.01
56 3 0.01
58 12 0.06
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:80954 original size:12 final size:12
Alignment explanation
Indices: 80939--80963 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
80929 TTTTCGGGGA
80939 CTTTTTCTTCTT
1 CTTTTTCTTCTT
80951 CTTTTTCTTCTT
1 CTTTTTCTTCTT
80963 C
1 C
80964 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:81171 original size:24 final size:24
Alignment explanation
Indices: 81137--81183 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
81127 CTGAAACATC
81137 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
81161 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
81184 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:81904 original size:20 final size:20
Alignment explanation
Indices: 81876--82104 Score: 226
Period size: 20 Copynumber: 11.4 Consensus size: 20
81866 AAATTTCAGT
* * *
81876 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
81896 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
81916 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
81936 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
81956 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
81976 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
81996 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
82016 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* * *
82036 GTTACGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
82056 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
82076 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
82096 GTTGCGATT
1 GTTGCGATT
82105 CTGAAAAATC
Statistics
Matches: 179, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 178 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:83733 original size:17 final size:17
Alignment explanation
Indices: 83713--83746 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
83703 ATTACACGGA
83713 ATATTATATATTATAAT
1 ATATTATATATTATAAT
83730 ATATTATATATTATAAT
1 ATATTATATATTATAAT
83747 GGATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTATATATTATAAT
Found at i:88309 original size:12 final size:13
Alignment explanation
Indices: 88292--88320 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
88282 TATTCTTATT
88292 AAAAAACAAA-AG
1 AAAAAACAAAGAG
88304 AAAAAACAAAGAG
1 AAAAAACAAAGAG
88317 AAAA
1 AAAA
88321 GAGAACACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAGAG
Found at i:94757 original size:15 final size:15
Alignment explanation
Indices: 94737--94788 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
94727 TTTTTATGGA
* *
94737 TCCTCATCTTCCTCC
1 TCCTCATCATCATCC
*
94752 TCCTCATCATCATCG
1 TCCTCATCATCATCC
* * *
94767 TCCTCATCCTCTTCT
1 TCCTCATCATCATCC
94782 TCCTCAT
1 TCCTCAT
94789 TGCCACCATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.12, C:0.46, G:0.02, T:0.40
Consensus pattern (15 bp):
TCCTCATCATCATCC
Found at i:96941 original size:8 final size:7
Alignment explanation
Indices: 96929--97041 Score: 56
Period size: 8 Copynumber: 15.6 Consensus size: 7
96919 AGTTTTTAAT
96929 TAAATAA
1 TAAATAA
96936 TCAAATAA
1 T-AAATAA
96944 TAAATAA
1 TAAATAA
*
96951 -ATA-AA
1 TAAATAA
*
96956 TAAATAC
1 TAAATAA
96963 TAAAATAA
1 T-AAATAA
96971 T-AATAA
1 TAAATAA
96977 T-AATAA
1 TAAATAA
96983 TAAACTAA
1 TAAA-TAA
* *
96991 TTAATTACT
1 -TAAATA-A
97000 TAAATAA
1 TAAATAA
97007 TAAA-AA
1 TAAATAA
*
97013 TTTTAATGAA
1 --TAAAT-AA
97023 TAAAATAA
1 T-AAATAA
*
97031 TAAATTA
1 TAAATAA
97038 TAAA
1 TAAA
97042 AACAATTATA
Statistics
Matches: 82, Mismatches: 11, Indels: 26
0.69 0.09 0.22
Matches are distributed among these distances:
5 2 0.02
6 18 0.22
7 24 0.29
8 30 0.37
9 6 0.07
10 2 0.02
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.32
Consensus pattern (7 bp):
TAAATAA
Found at i:96952 original size:35 final size:36
Alignment explanation
Indices: 96885--96954 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 36
96875 TGCCTTCCAA
* * *
96885 TTTTTAACTGTAATTAATAAATATTAACTAAATAAG
1 TTTTTAACTGTAAATAATAAATAATAAATAAATAAG
96921 TTTTTAA-T-TAAATAATCAAATAATAAATAAATAA
1 TTTTTAACTGTAAATAAT-AAATAATAAATAAATAA
96955 ATAAATACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
34 7 0.23
35 16 0.53
36 7 0.23
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (36 bp):
TTTTTAACTGTAAATAATAAATAATAAATAAATAAG
Found at i:97904 original size:17 final size:17
Alignment explanation
Indices: 97873--97905 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
97863 TATTATATTA
97873 TTAAATATAAAAATAAT
1 TTAAATATAAAAATAAT
97890 TTAAA-ATAAATAATAA
1 TTAAATATAAA-AATAA
97906 AACATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAATATAAAAATAAT
Found at i:99185 original size:18 final size:19
Alignment explanation
Indices: 99148--99185 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
99138 TCTTAAATTT
* *
99148 TCTATTATTTTATTATAAA
1 TCTAATATTTTATAATAAA
99167 TCTAATATTTT-TAATAAA
1 TCTAATATTTTATAATAAA
99185 T
1 T
99186 TATCAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TCTAATATTTTATAATAAA
Done.