Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002445.1 Hibiscus syriacus cultivar Beakdansim tig00005006_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: 60232
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:605 original size:14 final size:15
Alignment explanation
Indices: 586--616 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
576 GATTGGATAG
586 AAAATTATTT-AATT
1 AAAATTATTTAAATT
600 AAAATTATTTAAATT
1 AAAATTATTTAAATT
615 AA
1 AA
617 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATTATTTAAATT
Found at i:4023 original size:14 final size:16
Alignment explanation
Indices: 4006--4038 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
3996 AGACTAAATA
4006 TTAAAAT-AAT-TTAT
1 TTAAAATAAATATTAT
4020 TTAAAATAAATATTAT
1 TTAAAATAAATATTAT
4036 TTA
1 TTA
4039 TTATATACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 3 0.18
16 7 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAAATAAATATTAT
Found at i:5434 original size:18 final size:18
Alignment explanation
Indices: 5402--5437 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
5392 CTGTAATTAT
5402 TATTTTTAATAATATTTA
1 TATTTTTAATAATATTTA
5420 TATTATTTAAT-ATATTTA
1 TATT-TTTAATAATATTTA
5438 ATAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTTTAATAATATTTA
Found at i:5442 original size:3 final size:3
Alignment explanation
Indices: 5436--5527 Score: 152
Period size: 3 Copynumber: 31.3 Consensus size: 3
5426 TTAATATATT
*
5436 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
5483 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA T-A TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5528 GATATGGGTA
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
2 4 0.05
3 79 0.95
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:6094 original size:113 final size:113
Alignment explanation
Indices: 5850--6627 Score: 1366
Period size: 113 Copynumber: 6.9 Consensus size: 113
5840 AGAATTATGC
* * * *
5850 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
5915 TATGAAC-TTCTCCGG-AAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGT
5961 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
6026 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGT
6074 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
6139 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGT
6187 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**
6252 TATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGAC
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGT
6300 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
6365 TATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCA-G-
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGT
6411 ACAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 A-AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
**
6476 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGAC
65 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGT
6525 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
6590 TATGAACTTTCTCTGGAAAAAATAATCCATCAATTGAT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGAT
6628 AGATTTGAAT
Statistics
Matches: 645, Mismatches: 17, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
111 69 0.11
112 116 0.18
113 459 0.71
114 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.37
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGT
Found at i:7489 original size:83 final size:83
Alignment explanation
Indices: 7355--8306 Score: 1644
Period size: 83 Copynumber: 11.5 Consensus size: 83
7345 GTTCCTACCA
* ** *
7355 AACCAGATCAGATAACTCAAAG-A-ATTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
*
7418 CAATGATTGGTTCTG-CC
66 CAATGATTGATTCTGTCC
** *
7435 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAAT
1 -AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
7500 TCAATGATTGATTCTGTCC
65 TCAATGATTGATTCTGTCC
7519 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
* *
7584 CAGTGATTGATTCTGTCT
66 CAATGATTGATTCTGTCC
** *
7602 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTC-CAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
7666 CAATGATTGATTCTGTCC
66 CAATGATTGATTCTGTCC
7684 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
* * *
7749 CAGTGATTGATTCTATCT
66 CAATGATTGATTCTGTCC
** *
7767 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
7832 CAATGATTGATTCTGTCC
66 CAATGATTGATTCTGTCC
** *
7850 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
7915 CAATGATTGATTCTGTCC
66 CAATGATTGATTCTGTCC
7933 AACCAGATCAGATAACTCAAAGAACACTTCCAG-AGATGCTATTAACAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
7997 CAATGATTGATTCTGTCC
66 CAATGATTGATTCTGTCC
8015 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
8080 CAATGATTGATTCTGTCC
66 CAATGATTGATTCTGTCC
8098 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
* *
8163 CAGTGATTGATTCTGTCT
66 CAATGATTGATTCTGTCC
8181 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
8246 CAATGATTGATTCTGTCC
66 CAATGATTGATTCTGTCC
8264 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
8307 GAGTATATTG
Statistics
Matches: 835, Mismatches: 31, Indels: 8
0.96 0.04 0.01
Matches are distributed among these distances:
81 22 0.03
82 157 0.19
83 654 0.78
84 2 0.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.28
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
CAATGATTGATTCTGTCC
Found at i:7819 original size:248 final size:249
Alignment explanation
Indices: 7355--8306 Score: 1698
Period size: 248 Copynumber: 3.8 Consensus size: 249
7345 GTTCCTACCA
*
7355 AACCAGATCAGATAACTCAAAG-A-ATTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
* **
7418 CAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGG
66 CAATGATTGATTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAA
*
7482 CAAATTCATCTTCCAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
130 CAAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
* *
7547 TCCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAGTGATTGATTCTGTCT
195 TCCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGATTCTGTCC
7602 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCC-AATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
7666 CAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAC
66 CAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAC
* * *
7731 AAATTCATCTTCTAAATTCAGTGATTGATTCTATCTAACCAGATCAGATAACTCAAAGAACACTT
131 AAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
** *
7796 CCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGATTCTGTCC
196 CCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGATTCTGTCC
7850 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
7915 CAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAG-AGATGCTATTAAC
66 CAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAC
7979 AAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
131 AAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
8044 CCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGATTCTGTCC
196 CCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGATTCTGTCC
** *
8098 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
* *
8163 CAGTGATTGATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAC
66 CAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAC
8228 AAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
131 AAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
8293 CCAGAAGATGCTAT
196 CCAGAAGATGCTAT
8307 GAGTATATTG
Statistics
Matches: 676, Mismatches: 24, Indels: 8
0.95 0.03 0.01
Matches are distributed among these distances:
247 22 0.03
248 471 0.70
249 183 0.27
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.28
Consensus pattern (249 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
CAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAC
AAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
CCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGATTCTGTCC
Found at i:7999 original size:331 final size:331
Alignment explanation
Indices: 7355--8306 Score: 1667
Period size: 331 Copynumber: 2.9 Consensus size: 331
7345 GTTCCTACCA
* ** *
7355 AACCAGATCAGATAACTCAAAG-A-ATTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
* *
7418 CAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
66 CAATGATTGATTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
7483 AAATTCATCTTCCAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
131 AAATTCATCTTCCAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
* *
7548 CCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAGTGATTGATTCTGTCTAACCAGATCAG
196 CCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAACCAGATCAG
** *
7613 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAATTCAATGATTGATT
261 ATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCAAATTCAATGATTGATT
7678 CTGTCC
326 CTGTCC
7684 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
* * *
7749 CAGTGATTGATTCTATCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
66 CAATGATTGATTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
7814 AAATTCATCTTCCAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
131 AAATTCATCTTCCAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
** *
7879 CCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGATTCTGTCCAACCAGATCAG
196 CCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAACCAGATCAG
7944 ATAACTCAAAGAACACTTCCAG-AGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGAT
261 ATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTC-AAATTCAATGATTGAT
8008 TCTGTCC
325 TCTGTCC
8015 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
* **
8080 CAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAC
66 CAATGATTGATTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
* * *
8145 AAATTCATCTTCTAAATTCAGTGATTGATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTT
131 AAATTCATCTTCCAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
8210 CCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAACCAGATCAG
196 CCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAACCAGATCAG
8275 ATAACTCAAAGAACACTTCCAGAAGATGCTAT
261 ATAACTCAAAGAACACTTCCAGAAGATGCTAT
8307 GAGTATATTG
Statistics
Matches: 591, Mismatches: 28, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
329 22 0.04
330 24 0.04
331 536 0.91
332 9 0.02
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.28
Consensus pattern (331 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
CAATGATTGATTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
AAATTCATCTTCCAAATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
CCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGATTCTGTCCAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCAAATTCAATGATTGATT
CTGTCC
Found at i:9474 original size:12 final size:12
Alignment explanation
Indices: 9457--9518 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
9447 TGACCCCTCA
9457 TTTTTTTTTCTT
1 TTTTTTTTTCTT
*
9469 TTTTTTCTTC--
1 TTTTTTTTTCTT
*
9479 TCTTTTTTTCTT
1 TTTTTTTTTCTT
*
9491 TTTCTTTTTCTT
1 TTTTTTTTTCTT
* *
9503 TTCTTTTCTCTT
1 TTTTTTTTTCTT
9515 TTTT
1 TTTT
9519 CTTCAAGTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
10 8 0.21
12 31 0.79
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:9484 original size:22 final size:21
Alignment explanation
Indices: 9458--9522 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 21
9448 GACCCCTCAT
9458 TTTTTTTTCTTTTTTTTCTTC
1 TTTTTTTTCTTTTTTTTCTTC
9479 TCTTTTTTTCTTTTTCTTT-TTC
1 T-TTTTTTTCTTTTT-TTTCTTC
*
9501 TTTTCTTTTCTCTTTTTTCTTC
1 TTTT-TTTTCTTTTTTTTCTTC
9523 AAGTATAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 7 0.18
22 29 0.74
23 3 0.08
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTTTTCTTTTTTTTCTTC
Found at i:9498 original size:25 final size:24
Alignment explanation
Indices: 9457--9518 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
9447 TGACCCCTCA
9457 TTTTTTT-TTCTTTTTTTTCTTCTC
1 TTTTTTTCTT-TTTTTTTTCTTCTC
*
9481 TTTTTTTCTTTTTCTTTTTCTTTTC
1 TTTTTTTCTTTTT-TTTTTCTTCTC
*
9506 -TTTTCTCTTTTTT
1 TTTTTTTCTTTTTT
9519 CTTCAAGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 1 0.03
24 21 0.62
25 12 0.35
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (24 bp):
TTTTTTTCTTTTTTTTTTCTTCTC
Found at i:21753 original size:15 final size:15
Alignment explanation
Indices: 21712--21753 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
21702 CCTCGGTAAG
*
21712 TTTCTTTTCTTCCTT
1 TTTCTTTTCTTTCTT
*
21727 TTTCTTTCCTTTC-T
1 TTTCTTTTCTTTCTT
21741 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
21754 GCTGAGTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTCTTTTCTTTCTT
Found at i:22319 original size:3 final size:3
Alignment explanation
Indices: 22311--22383 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
22301 TTAATATATT
*
22311 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
22359 TGA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
22384 GATATGGGTA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:22499 original size:19 final size:22
Alignment explanation
Indices: 22451--22505 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
22441 TTTTTTGTGT
22451 TTTTATATAAAATGATAGTATAA
1 TTTTATATAAAAT-ATAGTATAA
22474 TTATTATATAAAAT-TA-TA-AA
1 TT-TTATATAAAATATAGTATAA
22494 TTTTATTATAAA
1 TTTTA-TATAAA
22506 TGCAGGTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.10
20 10 0.33
21 2 0.07
22 2 0.07
23 2 0.07
24 11 0.37
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTTATATAAAATATAGTATAA
Found at i:22811 original size:15 final size:15
Alignment explanation
Indices: 22791--22823 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
22781 TGGTTGTATT
22791 GGGGGATGACAGTGA
1 GGGGGATGACAGTGA
*
22806 GGGGGATGACGGTGA
1 GGGGGATGACAGTGA
22821 GGG
1 GGG
22824 AAAACAGAGT
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:0.21, C:0.06, G:0.61, T:0.12
Consensus pattern (15 bp):
GGGGGATGACAGTGA
Found at i:28937 original size:21 final size:21
Alignment explanation
Indices: 28881--28970 Score: 110
Period size: 21 Copynumber: 4.2 Consensus size: 21
28871 GGGAATCGAC
*
28881 CCCCCCTGA-GGGAACCGATT
1 CCCCCCAGAGGGGAACCGATT
**
28901 CCCCCTTTGAAGGGGAACCGATT
1 CCCCC-CAG-AGGGGAACCGATT
28924 CCCCCCAGAGGGGAACCGATT
1 CCCCCCAGAGGGGAACCGATT
* *
28945 CCCCCCAGAGGGGAATCGATA
1 CCCCCCAGAGGGGAACCGATT
28966 CCCCC
1 CCCCC
28971 TAAGGTTATG
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.08
21 39 0.63
22 2 0.03
23 16 0.26
ACGTcount: A:0.22, C:0.39, G:0.26, T:0.13
Consensus pattern (21 bp):
CCCCCCAGAGGGGAACCGATT
Found at i:31581 original size:22 final size:22
Alignment explanation
Indices: 31556--31598 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
31546 AACAATTTCA
* *
31556 AAATAATTTTACAAAGTATTCC
1 AAATAATTTAACAAAGCATTCC
*
31578 AAATGATTTAACAAAGCATTC
1 AAATAATTTAACAAAGCATTC
31599 ATAGACTCGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.33
Consensus pattern (22 bp):
AAATAATTTAACAAAGCATTCC
Found at i:33452 original size:200 final size:199
Alignment explanation
Indices: 33052--33778 Score: 763
Period size: 201 Copynumber: 3.6 Consensus size: 199
33042 ACCTAAATAT
* * *
33052 GTGTCGATACATTT-TATACAAGTATCGA-CCCAAAAAATATCAAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTATATAAAAGTATCGATCCC-AAAAACATCAAAACCGATAATTATAATGTAA
* * * * * * *
33115 TAGGTAAATTAACAATATAACCGGTATAAATATACCGG-TTAATTAGAAAACATGTCAACATAAT
65 TAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCATCATAAT
* * *
33179 GTATCGACACTTGTGTAATTTGTGTCGATACTTATTGTCCAGGATGAATGCACAAACGAGGTGC-
130 GTATCGACACTTGT-TAATTTGTGTCGATACTT-TTGTCCAGAATGAATACACAAA-AAGGTGCA
33243 ACGCATAAA
192 AC-CATAAA
*
33252 GTGTCGATACATTTAT-TAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTATT
1 GTGTCGATACATTTATATAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAAT
* * * * *
33316 AGGTAAATTTACAATGTAACCGATAAAAATATACCAGTTTTATGATAAAATAGGTCATCATAAAG
66 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCATCATAATG
* *
33381 TATCGACACTTGATAAATTTGTGTTGATACTTTTGGTCCAGAATGAATAC-CAAAAATGGTGCAA
131 TATCGACACTTG-TTAATTTGTGTCGATACTTTT-GTCCAGAATGAATACACAAAAA-GGTGCAA
33445 CCATAAA
193 CCATAAA
* * * * * * * * *
33452 GTGTTGATACATTTATAAAAAAGTAACGATCCCGAAAATATCGAAACCCATAAGTATAATATAAT
1 GTGTCGATACATTTATATAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAAT
* * *
33517 AGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTC-TAAATAAT
66 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAT-CATAAT
* * * **
33581 GTATCGACACGTTGTTAGTTTGTGTCGATACTTTTTTCCAGAATGAAATATGAATGCTCAACCAG
130 GTATCGACAC-TTGTTAATTTGTGTCGATACTTTTGTCCAGAATG--A-AT--A--CACAAAAAG
*
33646 GTGCAAGCATAAA
187 GTGCAACCATAAA
** * ** ** *
33659 GTGTCGATACATTTA-A-AATTGTATTGATCTAAAAAACATCGTAACCGATAATAATAATGTAAT
1 GTGTCGATACATTTATATAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAAT
* * **
33722 AGGTAAATTTGCAATGTTACCGGTATAAATATACCGG-TTTACTTTGAAAATAGGTCA
66 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTA-TGAGAAAATAGGTCA
33779 ATATAAGCGC
Statistics
Matches: 442, Mismatches: 65, Indels: 34
0.82 0.12 0.06
Matches are distributed among these distances:
199 1 0.00
200 128 0.29
201 188 0.43
202 5 0.01
203 2 0.00
204 4 0.01
205 81 0.18
206 1 0.00
207 28 0.06
208 4 0.01
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (199 bp):
GTGTCGATACATTTATATAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAAT
AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCATCATAATG
TATCGACACTTGTTAATTTGTGTCGATACTTTTGTCCAGAATGAATACACAAAAAGGTGCAACCA
TAAA
Found at i:33867 original size:64 final size:64
Alignment explanation
Indices: 33799--33918 Score: 213
Period size: 64 Copynumber: 1.9 Consensus size: 64
33789 TACCTATTAC
*
33799 ATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCCTATTTT
1 ATTATATAAGAGCTACCTAATATGTTATTATACTTGATAATATTTCCGGTTAAATGCCTATTTT
* *
33863 ATTATATAAGCGCTACCTAATATGTTATTATACTTGTTAATATTTCCGGTTAAATG
1 ATTATATAAGAGCTACCTAATATGTTATTATACTTGATAATATTTCCGGTTAAATG
33919 ATATAACATT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (64 bp):
ATTATATAAGAGCTACCTAATATGTTATTATACTTGATAATATTTCCGGTTAAATGCCTATTTT
Found at i:34514 original size:14 final size:14
Alignment explanation
Indices: 34495--34543 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
34485 GAATATTTAC
34495 AATATTTAATTATT
1 AATATTTAATTATT
*
34509 AATATTTAATTAAT
1 AATATTTAATTATT
*
34523 AA-A-TTAAATATT
1 AATATTTAATTATT
*
34535 AATAATTAA
1 AATATTTAA
34544 ATAAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 9 0.30
13 2 0.07
14 19 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATTTAATTATT
Found at i:34534 original size:26 final size:26
Alignment explanation
Indices: 34500--34552 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
34490 TTTACAATAT
* * * *
34500 TTAATTATTAATATTTAATTAATAAA
1 TTAAATATTAATAATTAAATAAAAAA
34526 TTAAATATTAATAATTAAATAAAAAA
1 TTAAATATTAATAATTAAATAAAAAA
34552 T
1 T
34553 AAGAATAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TTAAATATTAATAATTAAATAAAAAA
Found at i:34570 original size:16 final size:16
Alignment explanation
Indices: 34551--34593 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
34541 TAAATAAAAA
*
34551 ATAAGAATAAT-ATTTG
1 ATAA-AATAATAATTCG
34567 ATAAAATTAATAATTCG
1 ATAAAA-TAATAATTCG
34584 ATAAAATAAT
1 ATAAAATAAT
34594 TTACAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 12 0.50
17 10 0.42
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (16 bp):
ATAAAATAATAATTCG
Found at i:36552 original size:32 final size:30
Alignment explanation
Indices: 36492--36583 Score: 100
Period size: 32 Copynumber: 3.1 Consensus size: 30
36482 GTTTTTATAT
* *
36492 TTTTTATT-AATATAATTATATAAATATTA
1 TTTTTATTAAATATATTTATATAATTATTA
36521 TTTTTATTAAAATAATATTTATATAATTATTA
1 TTTTTATT-AAAT-ATATTTATATAATTATTA
* * *
36553 TTTAT-TTAAATTTATTAAT-TAATTATTA
1 TTTTTATTAAATATATTTATATAATTATTA
36581 TTT
1 TTT
36584 GTGCTAAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
28 12 0.22
29 14 0.25
30 4 0.07
31 5 0.09
32 20 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTTTATTAAATATATTTATATAATTATTA
Found at i:36577 original size:25 final size:24
Alignment explanation
Indices: 36537--36583 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
36527 TTAAAATAAT
36537 ATTTATATAATTATTATTTATTTAA
1 ATTTATATAATTATTA-TTATTTAA
36562 ATTTAT-TAATTAATTATTATTT
1 ATTTATATAATT-ATTATTATTT
36584 GTGCTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTATATAATTATTATTATTTAA
Found at i:38317 original size:21 final size:21
Alignment explanation
Indices: 38227--38317 Score: 94
Period size: 21 Copynumber: 4.3 Consensus size: 21
38217 GCCATCTATG
* *
38227 CAGGGTTACATTCCTAGCCCA
1 CAGGGTTACATACCCAGCCCA
*
38248 CAGGAG-TACATACCCAGCCTA
1 CAGG-GTTACATACCCAGCCCA
*
38269 CAGGGGTACATACCCAGCCCA
1 CAGGGTTACATACCCAGCCCA
* * * *
38290 CAAGGTTACATGCCTAGCCCG
1 CAGGGTTACATACCCAGCCCA
38311 CAGGGTT
1 CAGGGTT
38318 TTATGACACC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
20 1 0.02
21 56 0.97
22 1 0.02
ACGTcount: A:0.26, C:0.33, G:0.23, T:0.18
Consensus pattern (21 bp):
CAGGGTTACATACCCAGCCCA
Found at i:38867 original size:46 final size:46
Alignment explanation
Indices: 38778--38867 Score: 103
Period size: 46 Copynumber: 2.0 Consensus size: 46
38768 TACAACAATA
* * ***
38778 TTTTTAAAATTTAAATTCAAATTCAACATTAAATGTTTGTTAAATG
1 TTTTTAAAATGTAAATCCAAATTCAACATTAAATGTCAATTAAATG
38824 TTTTTAAAATGTAAATCCAAATTCAAC-TTAATAT-TCCAATTAAA
1 TTTTTAAAATGTAAATCCAAATTCAACATTAA-ATGT-CAATTAAA
38868 ATTTAAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
45 5 0.14
46 32 0.86
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.42
Consensus pattern (46 bp):
TTTTTAAAATGTAAATCCAAATTCAACATTAAATGTCAATTAAATG
Found at i:39183 original size:13 final size:13
Alignment explanation
Indices: 39152--39176 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39142 TGACACTCTA
39152 ACATAAATTTCAG
1 ACATAAATTTCAG
39165 ACATAAATTTCA
1 ACATAAATTTCA
39177 AGTATAATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (13 bp):
ACATAAATTTCAG
Found at i:40212 original size:138 final size:137
Alignment explanation
Indices: 39951--40475 Score: 705
Period size: 138 Copynumber: 3.9 Consensus size: 137
39941 TGTTTTCAAC
39951 AAATTATAACATATTCTCTGACAAAATAATGGAAG-GCGCATCCCCTGAAACGCGCTTT---CAC
1 AAATTATAACATATTCTCTGACAAAATAATGGAAGTGCGC--CCCCTGAAACGCGCTTTCACCAC
*
40012 TTTGCTGCGTCCCCTCAAACATGATATGTACTGACATGAATAGTGCCCCGGGGGACATGAGTGAC
64 TTTGCTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCGGGGGACATGAGTGAC
*
40077 ACAATAGGG
129 ATAATAGGG
* * *
40086 AAATTATAACATATTCTATGACAAAATAATGGAAGGTGTGCCCCCTGAAATGCGCTTTCACCACT
1 AAATTATAACATATTCTCTGACAAAATAATGGAA-GTGCGCCCCCTGAAACGCGCTTTCACCACT
* * * * *
40151 TTGTTGCGTCCCCTCAAACATAATAGGTAATGACATAAATAGTGCCCCGGGGGATATGAGTGACA
65 TTGCTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCGGGGGACATGAGTGACA
40216 TAATAGGG
130 TAATAGGG
* *
40224 CAATTATAACATATTCTCTGACAAAATAATGG-A-TACGCCCCCT-AAA--CGCTTTCACCACTT
1 AAATTATAACATATTCTCTGACAAAATAATGGAAGTGCGCCCCCTGAAACGCGCTTTCACCACTT
* *
40284 TGCT--GTCCCCTCAAACATGATAGTTACTAACATGAATAGTGCCCCGGGGGACATGAGTGACAT
66 TGCTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCGGGGGACATGAGTGACAT
40347 AATAGGG
131 AATAGGG
* * * * *
40354 TAATTATAACATATTATCTGACAAAATAATGGAAG-GTGCCCCTTGAAACGTGCTTTCACCACTT
1 AAATTATAACATATTCTCTGACAAAATAATGGAAGTGCGCCCCCTGAAACGCGCTTTCACCACTT
* ** * * *
40418 TGTTGCACCCCCTCAAACATGATAAGTACTGATATGAATAATGCCCCCGGGGGACATG
66 TGCTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTG-CCCCGGGGGACATG
40476 TGTAACACCC
Statistics
Matches: 342, Mismatches: 35, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
130 90 0.26
131 7 0.02
132 20 0.06
134 19 0.06
135 57 0.17
136 31 0.09
137 18 0.05
138 100 0.29
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (137 bp):
AAATTATAACATATTCTCTGACAAAATAATGGAAGTGCGCCCCCTGAAACGCGCTTTCACCACTT
TGCTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCGGGGGACATGAGTGACAT
AATAGGG
Found at i:41934 original size:3 final size:3
Alignment explanation
Indices: 41926--41957 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41916 CTCACATATA
41926 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
41958 AGAAAGAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:48394 original size:31 final size:31
Alignment explanation
Indices: 48337--48403 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 31
48327 TAAAAAATTT
*
48337 AAATTTAAAAGTTAGAGTGATTAAATTAGAAA
1 AAATTTAAAAGTTAGAGTAATTAAATTA-AAA
*
48369 TAATTTAAAAGTTA-AGTAATTAAATTAAAA
1 AAATTTAAAAGTTAGAGTAATTAAATTAAAA
48399 AAATT
1 AAATT
48404 AAACTTCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 7 0.22
31 12 0.38
32 13 0.41
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34
Consensus pattern (31 bp):
AAATTTAAAAGTTAGAGTAATTAAATTAAAA
Found at i:48968 original size:41 final size:42
Alignment explanation
Indices: 48918--49026 Score: 188
Period size: 41 Copynumber: 2.7 Consensus size: 42
48908 GACTATCGCA
*
48918 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATT-CAAATTTG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCG
48959 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCG
49001 TTGCGATAGTCCAAGTT--CGTTGCGAT
1 TTGCGATAGTCCAAGTTCGCGTTGCGAT
49027 AGTCCAAGTT
Statistics
Matches: 66, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
40 9 0.14
41 33 0.50
42 24 0.36
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCG
Found at i:49034 original size:61 final size:61
Alignment explanation
Indices: 48958--49075 Score: 227
Period size: 61 Copynumber: 1.9 Consensus size: 61
48948 ATTCAAATTT
48958 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTC
*
49019 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAA
49076 AATCGCAACG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (61 bp):
GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTC
Found at i:49907 original size:21 final size:21
Alignment explanation
Indices: 49883--49933 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
49873 ATTTTAGACT
*
49883 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
49904 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
49925 ATCGCAACG
1 ATCGCAACG
49934 TGATGTTCGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:53476 original size:45 final size:45
Alignment explanation
Indices: 53424--53524 Score: 193
Period size: 45 Copynumber: 2.2 Consensus size: 45
53414 CTAAAGTTCA
*
53424 CGGCGTTTGTTAACGAAAAATGCCGTAATAGGTTCTGATATTTAG
1 CGGCGTTTGTTAACGAAAAATGCCGCAATAGGTTCTGATATTTAG
53469 CGGCGTTTGTTAACGAAAAATGCCGCAATAGGTTCTGATATTTAG
1 CGGCGTTTGTTAACGAAAAATGCCGCAATAGGTTCTGATATTTAG
53514 CGGCGTTTGTT
1 CGGCGTTTGTT
53525 TTAAAACAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (45 bp):
CGGCGTTTGTTAACGAAAAATGCCGCAATAGGTTCTGATATTTAG
Found at i:53741 original size:44 final size:44
Alignment explanation
Indices: 53553--53818 Score: 246
Period size: 44 Copynumber: 6.2 Consensus size: 44
53543 TTTTGAGATT
* **
53553 TAGCGGCGTTTTT-GGATACAAACCCCGCTAAAGGTCTGGTATA
1 TAGCGGCGTTTTTAGAATACAAATGCCGCTAAAGGTCTGGTATA
* * *
53596 TAGCGGCGTTTTT---A-A-AAACGCCGCTAAAGTTTTGGTATA
1 TAGCGGCGTTTTTAGAATACAAATGCCGCTAAAGGTCTGGTATA
* * * * * *
53635 TAACGACGCTTTCAGTATATAAACT-CCGCTAAAGGTCTGG--TA
1 TAGCGGCGTTTTTAGAATACAAA-TGCCGCTAAAGGTCTGGTATA
* *
53677 TAGCGGCGTTTTTAGAATACAAATACCGCTAAAGATCTGGTATA
1 TAGCGGCGTTTTTAGAATACAAATGCCGCTAAAGGTCTGGTATA
* * * * *
53721 TAGCGTCCTTTTTAGGATACAAATGTCGTTAAAGGTCTGGTATA
1 TAGCGGCGTTTTTAGAATACAAATGCCGCTAAAGGTCTGGTATA
* * *
53765 TAACGGCGTTTTTAGAATACAAACGCCGCTAAAGGT-TGATATA
1 TAGCGGCGTTTTTAGAATACAAATGCCGCTAAAGGTCTGGTATA
*
53808 TAGCGACGTTT
1 TAGCGGCGTTT
53819 GTTAATAAAA
Statistics
Matches: 180, Mismatches: 34, Indels: 18
0.78 0.15 0.08
Matches are distributed among these distances:
39 30 0.17
40 1 0.01
41 2 0.01
42 34 0.19
43 29 0.16
44 84 0.47
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (44 bp):
TAGCGGCGTTTTTAGAATACAAATGCCGCTAAAGGTCTGGTATA
Found at i:59996 original size:26 final size:24
Alignment explanation
Indices: 59937--60000 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 24
59927 TCATAATAAG
59937 TTTGTCTCTTAAAACAATACTTCA
1 TTTGTCTCTTAAAACAATACTTCA
*
59961 TTTGTCTCTTAAAAC-ACACTTCATTA
1 TTTGTCTCTTAAAACAATACTTC---A
59987 TTTGTCTCTTAAAA
1 TTTGTCTCTTAAAA
60001 ACAACATTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
23 6 0.17
24 15 0.42
26 15 0.42
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (24 bp):
TTTGTCTCTTAAAACAATACTTCA
Done.