Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003736.1 Hibiscus syriacus cultivar Beakdansim tig00007994_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: 86356
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:859 original size:16 final size:18
Alignment explanation
Indices: 833--872 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
823 AATATTATAA
833 ATATTAATATAT-ATTAT
1 ATATTAATATATCATTAT
*
850 -TATTAGTATATCATTAT
1 ATATTAATATATCATTAT
867 ATATTA
1 ATATTA
873 TTACATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 10 0.50
17 5 0.25
18 5 0.25
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATATTAATATATCATTAT
Found at i:4379 original size:13 final size:13
Alignment explanation
Indices: 4361--4386 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4351 AGAAAATCTA
4361 TATATATATATAT
1 TATATATATATAT
4374 TATATATATATAT
1 TATATATATATAT
4387 CGTAAGAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:12592 original size:28 final size:27
Alignment explanation
Indices: 12544--12598 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
12534 AAATTTCCGA
* *
12544 TAAAAAATAATATTTTATCAAAAATAT
1 TAAAAAATAATAATATATCAAAAATAT
* *
12571 TAAAAAATACTAATATATTCAATAATAT
1 TAAAAAATAATAATATA-TCAAAAATAT
12599 ATTTTTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAAAAATAATAATATATCAAAAATAT
Found at i:15274 original size:19 final size:19
Alignment explanation
Indices: 15250--15286 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
15240 ATGACCAACA
*
15250 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
15269 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
15287 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:15335 original size:20 final size:20
Alignment explanation
Indices: 15312--15424 Score: 122
Period size: 20 Copynumber: 5.6 Consensus size: 20
15302 GTTTCCAGAT
*
15312 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
15332 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
*
15352 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
*
15372 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
*
15393 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
15413 TCGCAACGCGAT
1 TCGCAACGCGAT
15425 AATACAAAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
19 3 0.04
20 55 0.72
21 16 0.21
22 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:15438 original size:21 final size:20
Alignment explanation
Indices: 15349--15439 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
15339 GCGAATATGT
**
15349 AAATCGCAACGCGATTCTGAC
1 AAATCGCAACGCGATAAT-AC
*
15370 -TATCGCAACGCGATAATAC
1 AAATCGCAACGCGATAATAC
**
15389 ATAATCGCAACGCGATTCTGAC
1 A-AATCGCAACGCGATAAT-AC
*
15411 -TATCGCAACGCGATAATAC
1 AAATCGCAACGCGATAATAC
15430 AAAATCGCAA
1 -AAATCGCAA
15440 TACGATTTTC
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
19 4 0.07
20 28 0.51
21 21 0.38
22 2 0.04
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGATAATAC
Found at i:15446 original size:41 final size:41
Alignment explanation
Indices: 15312--15439 Score: 188
Period size: 41 Copynumber: 3.1 Consensus size: 41
15302 GTTTCCAGAT
* * **
15312 TCGCAACGCGATTTTGACTATCGCAATGCG--AATATGTAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATA-CAAAA
*
15352 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAA
15393 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAA
15434 TCGCAA
1 TCGCAA
15440 TACGATTTTC
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
40 28 0.35
41 48 0.60
42 4 0.05
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (41 bp):
TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAA
Found at i:15615 original size:22 final size:22
Alignment explanation
Indices: 15590--15640 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
15580 CTACGGCGAC
15590 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
15612 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
15634 ATCCGTC
1 ATCCGTC
15641 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:15788 original size:25 final size:26
Alignment explanation
Indices: 15758--15813 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
15748 TTATTATTAG
15758 GTTTTTCATATTGAAATTGATAATAA
1 GTTTTTCATATTGAAATTGATAATAA
*
15784 GTTTTTCATATTGAAATTGATGATAA
1 GTTTTTCATATTGAAATTGATAATAA
15810 GTTT
1 GTTT
15814 ACTGGTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.34, C:0.04, G:0.14, T:0.48
Consensus pattern (26 bp):
GTTTTTCATATTGAAATTGATAATAA
Found at i:16058 original size:20 final size:20
Alignment explanation
Indices: 16033--16076 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
16023 AAAATCGCAA
16033 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
** *
16053 CGATAGTCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
16073 CGAT
1 CGAT
16077 TTTAAGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
CGATAGTCAAATTCGCGTTG
Found at i:18045 original size:20 final size:19
Alignment explanation
Indices: 17987--18055 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 19
17977 CGAAACTTAA
17987 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* *
18007 ATCGTAATGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
*
18027 ATCGCAACGCGAAGTTGACT
1 ATCGCAACGCGAA-ATGACT
18047 ATCGCAACG
1 ATCGCAACG
18056 GGATAATCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:18213 original size:20 final size:20
Alignment explanation
Indices: 18185--18252 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
18175 CGATTATCCT
*
18185 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAATTTCGC
*
18205 GTTGTGATAGTC-ATTTCCGC
1 GTTGCGATAGTCAATTT-CGC
*
18225 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAATTTCGC
18245 GTTGCGAT
1 GTTGCGAT
18253 TTGAGTTTCG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCAATTTCGC
Found at i:18281 original size:20 final size:19
Alignment explanation
Indices: 18239--18281 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
18229 CGATAGTCAT
*
18239 TTTCGCGTTGCGATTTGAG
1 TTTCGCGTTGCGATTTAAG
*
18258 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGA-TTTAAG
18278 TTTC
1 TTTC
18282 AGAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.49
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTAAG
Found at i:18852 original size:21 final size:21
Alignment explanation
Indices: 18757--18864 Score: 110
Period size: 21 Copynumber: 5.1 Consensus size: 21
18747 GCCCGACTCA
18757 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
18778 TCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* ** *
18799 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
* *
18820 CCTCTCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
18841 CCTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
18862 CCT
1 CCT
18865 CCCACTATTC
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 1 0.01
21 67 0.97
22 1 0.01
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.25
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:18865 original size:42 final size:42
Alignment explanation
Indices: 18757--18879 Score: 126
Period size: 42 Copynumber: 2.9 Consensus size: 42
18747 GCCCGACTCA
*
18757 CCTGTCATCGTTCAAGAGG--CCTCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGTCCCTCT-C-ACCGTTCAAGAGGCC
* **
18799 CCTATCATCCCTCAAGA-GTCCCCTCTCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGT-CCCTCTCACCGTTCAAGAGGCC
* * **
18841 CCTGTCATCGTTGAAGAGGTCCCTCCCACTATTCAAGAG
1 CCTGTCATCGTTCAAGAGGTCCCTCTCACCGTTCAAGAG
18880 CCCGATTCAT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
41 1 0.02
42 57 0.86
43 3 0.05
44 5 0.08
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGGTCCCTCTCACCGTTCAAGAGGCC
Found at i:20286 original size:14 final size:14
Alignment explanation
Indices: 20264--20325 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
20254 TTTCTTGTTT
20264 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
20278 AATTTATTTGTAAA
1 AATTGATTTGTAAA
* *
20292 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
20307 TATTGATGTGTAAA
1 AATTGATTTGTAAA
20321 TAATT
1 -AATT
20326 CTTATTTGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
14 24 0.65
15 13 0.35
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:20526 original size:20 final size:20
Alignment explanation
Indices: 20501--20690 Score: 143
Period size: 20 Copynumber: 9.8 Consensus size: 20
20491 CAATTTTCTC
*
20501 GTTGCGATAGTCAAATACCA
1 GTTGCGATAGTCAAATTCCA
*
20521 GTTGCGATAATCAAATT-CA
1 GTTGCGATAGTCAAATTCCA
**
20540 CGTTGCGATAGTCAAATTCGT
1 -GTTGCGATAGTCAAATTCCA
20561 GTTGCGATAGTCAAATTCGC-
1 GTTGCGATAGTCAAATTC-CA
*
20581 GTTGCGATAGTCATATTCGC-
1 GTTGCGATAGTCAAATTC-CA
**
20601 GTTTTGATAGTCAAATTCGC-
1 GTTGCGATAGTCAAATTC-CA
**
20621 GTTGCGAT--T----TTTGA
1 GTTGCGATAGTCAAATTCCA
*
20635 GTTGCGATAATCAAATTCGC-
1 GTTGCGATAGTCAAATTC-CA
20655 GTTGCGATAGTCAAATTCGC-
1 GTTGCGATAGTCAAATTC-CA
*
20675 GTTGCGATATTCAAAT
1 GTTGCGATAGTCAAAT
20691 GAATGTGTAA
Statistics
Matches: 141, Mismatches: 18, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
14 10 0.07
16 1 0.01
18 1 0.01
19 2 0.01
20 127 0.90
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCCA
Found at i:20544 original size:40 final size:39
Alignment explanation
Indices: 20500--20690 Score: 203
Period size: 40 Copynumber: 4.9 Consensus size: 39
20490 GCAATTTTCT
* *
20500 CGTTGCGATAGTCAAATACCAGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCC-GTTGCGATAATCAAATTCG
* *
20540 CGTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTC-CGTTGCGATAATCAAATTCG
* ** *
20580 CGTTGCGATAGTCATATTCGCGTTTTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTC-CGTTGCGATAATCAAATTCG
* **
20620 CGTTGCGAT--T---TTTGAGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCCGTTGCGATAATCAAATTCG
*
20654 CGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAATTC-CGTTGCGATAATCAAAT
20691 GAATGTGTAA
Statistics
Matches: 126, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
34 25 0.20
35 2 0.02
36 1 0.01
38 1 0.01
39 2 0.02
40 95 0.75
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (39 bp):
CGTTGCGATAGTCAAATTCCGTTGCGATAATCAAATTCG
Found at i:20574 original size:60 final size:60
Alignment explanation
Indices: 20500--20690 Score: 234
Period size: 60 Copynumber: 3.3 Consensus size: 60
20490 GCAATTTTCT
* *
20500 CGTTGCGATAGTCAAATACCAGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCCAGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCG
* * * **
20560 TGTTGCGATAGTCAAATTCGC-GTTGCGATAGTCATATTCGCGTTTTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTC-CAGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCG
**
20620 CGTTGCGAT--T----TTTGAGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCCAGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCG
*
20674 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
20691 GAATGTGTAA
Statistics
Matches: 109, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
54 46 0.42
56 1 0.01
58 1 0.01
60 60 0.55
61 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (60 bp):
CGTTGCGATAGTCAAATTCCAGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCG
Found at i:20876 original size:12 final size:12
Alignment explanation
Indices: 20858--20897 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
20848 GTGAAGCCGG
**
20858 TTGTGATTGAGA
1 TTGTGATTTTGA
*
20870 TTTTGATTTTGA
1 TTGTGATTTTGA
20882 TTGTGATTTTGA
1 TTGTGATTTTGA
20894 TTGT
1 TTGT
20898 CTTTTTCTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.25, T:0.57
Consensus pattern (12 bp):
TTGTGATTTTGA
Found at i:20884 original size:18 final size:18
Alignment explanation
Indices: 20861--20895 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20851 AAGCCGGTTG
20861 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
20879 TGATTGTGATTTTGATT
1 TGATTGAGATTTTGATT
20896 GTCTTTTTCT
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:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:23224 original size:24 final size:24
Alignment explanation
Indices: 23173--23224 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
23163 ATCTGAGTAT
** *
23173 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
23197 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
23221 TGAC
1 TGAC
23225 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:24091 original size:21 final size:21
Alignment explanation
Indices: 24065--24263 Score: 207
Period size: 21 Copynumber: 9.7 Consensus size: 21
24055 GATAGTCAGA
24065 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
24086 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
**
24107 ATCGCGTTGCGA-TA-GTCAGA
1 ATCGCGTTGCGATTATGT-ATT
*
24127 ATCGCTTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
**
24148 ATCGCGTTGCGA-TA-GTCAGA
1 ATCGCGTTGCGATTATGT-ATT
*
24168 ATCGCGTTACGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
**
24189 ATCGCGTTGCGA-TA-GTCAGA
1 ATCGCGTTGCGATTATGT-ATT
24209 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
* **
24230 ATCACGTTGCGA-TA-GTCAGA
1 ATCGCGTTGCGATTATGT-ATT
24250 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
24264 TACATATTCG
Statistics
Matches: 147, Mismatches: 20, Indels: 22
0.78 0.11 0.12
Matches are distributed among these distances:
19 8 0.05
20 57 0.39
21 76 0.52
22 6 0.04
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:24121 original size:62 final size:62
Alignment explanation
Indices: 24045--24263 Score: 277
Period size: 62 Copynumber: 3.5 Consensus size: 62
24035 GACAGTCAGA
*
24045 ATCGCGCTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGATTATGTATT
* **
24107 ATCGCGTTGCGATAGTCAGAATCGCTTTGCGATTATGTATTATCGCGTTGCGA-TA-GTCAGA
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGATTATGT-ATT
* ** **
24168 ATCGCGTTACGATTATGT-ATTATCGCGTTGCGA-TA-GTCAGAATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGA-TA-GTCAGAATCGCGTTGCGATTATGT-ATTATCGCGTTGCGATTATGTATT
*
24230 ATCACGTTGCGATAGTCAGAATCGCGTTGCGATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATT
24264 TACATATTCG
Statistics
Matches: 133, Mismatches: 16, Indels: 16
0.81 0.10 0.10
Matches are distributed among these distances:
60 6 0.05
61 44 0.33
62 79 0.59
63 4 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (62 bp):
ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGATTATGTATT
Found at i:24131 original size:41 final size:41
Alignment explanation
Indices: 24030--24263 Score: 339
Period size: 41 Copynumber: 5.7 Consensus size: 41
24020 GAAATTCAGT
* * **
24030 GTTGCGACAGTCAGAATCGCGCTGCGA-TA-GTCAGAATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATGT-ATTATCGC
**
24070 GTTGCGATTATGT-ATTATCGCGTTGCGATTATGTATTATCGC
1 GTTGCGA-TA-GTCAGAATCGCGTTGCGATTATGTATTATCGC
*
24112 GTTGCGATAGTCAGAATCGCTTTGCGATTATGTATTATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGC
*
24153 GTTGCGATAGTCAGAATCGCGTTACGATTATGTATTATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGC
*
24194 GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCAC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGC
24235 GTTGCGATAGTCAGAATCGCGTTGCGATT
1 GTTGCGATAGTCAGAATCGCGTTGCGATT
24264 TACATATTCG
Statistics
Matches: 176, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
40 9 0.05
41 148 0.84
42 17 0.10
43 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (41 bp):
GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGC
Found at i:24295 original size:21 final size:20
Alignment explanation
Indices: 24249--24296 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
24239 CGATAGTCAG
* * *
24249 AATCGCGTTGCGATTTACAT
1 AATCGCATTGCAATTTACAA
*
24269 ATTCGCATTGCAATTTTACAA
1 AATCGCATTGCAA-TTTACAA
24290 AATCGCA
1 AATCGCA
24297 ATACGATAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (20 bp):
AATCGCATTGCAATTTACAA
Found at i:24372 original size:19 final size:19
Alignment explanation
Indices: 24348--24384 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
24338 TGCGATACTG
*
24348 GAGATCGCGTTGCAATTTA
1 GAGATCGCATTGCAATTTA
24367 GAGATCGCATTGCAATTT
1 GAGATCGCATTGCAATTT
24385 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCAATTTA
Found at i:32483 original size:14 final size:14
Alignment explanation
Indices: 32464--32490 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
32454 ACTGTTTTCT
32464 TTTGGATGTCATGC
1 TTTGGATGTCATGC
32478 TTTGGATGTCATG
1 TTTGGATGTCATG
32491 TTAATTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.11, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTGGATGTCATGC
Found at i:38806 original size:30 final size:30
Alignment explanation
Indices: 38772--38872 Score: 202
Period size: 30 Copynumber: 3.4 Consensus size: 30
38762 GGTAGACCAC
38772 ATTTTCAAATTGTTTCTTTTAATTTTATAT
1 ATTTTCAAATTGTTTCTTTTAATTTTATAT
38802 ATTTTCAAATTGTTTCTTTTAATTTTATAT
1 ATTTTCAAATTGTTTCTTTTAATTTTATAT
38832 ATTTTCAAATTGTTTCTTTTAATTTTATAT
1 ATTTTCAAATTGTTTCTTTTAATTTTATAT
38862 ATTTTCAAATT
1 ATTTTCAAATT
38873 TTAGATAAGA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (30 bp):
ATTTTCAAATTGTTTCTTTTAATTTTATAT
Found at i:45063 original size:9 final size:8
Alignment explanation
Indices: 44960--45064 Score: 57
Period size: 9 Copynumber: 12.1 Consensus size: 8
44950 CATAAATATG
*
44960 AAAATAAT
1 AAAAAAAT
*
44968 AAATAAAAC
1 AAA-AAAAT
44977 AAAAAAAT
1 AAAAAAAT
* **
44985 AACAAAGG
1 AAAAAAAT
44993 AAAAATAAT
1 AAAAA-AAT
45002 AAAATAAAT
1 AAAA-AAAT
*
45011 AAAAATAAA
1 AAAAA-AAT
45020 AAACCAAAAT
1 AAA--AAAAT
45030 AAATAAAAT
1 AAA-AAAAT
***
45039 GGTAAAAT
1 AAAAAAAT
45047 AAAAAAAT
1 AAAAAAAT
45055 AAGAAAAAT
1 AA-AAAAAT
45064 A
1 A
45065 TGATGATAAT
Statistics
Matches: 72, Mismatches: 18, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
8 29 0.40
9 35 0.49
10 6 0.08
11 2 0.03
ACGTcount: A:0.76, C:0.04, G:0.05, T:0.15
Consensus pattern (8 bp):
AAAAAAAT
Found at i:45076 original size:3 final size:3
Alignment explanation
Indices: 45070--45148 Score: 81
Period size: 3 Copynumber: 26.3 Consensus size: 3
45060 AAATATGATG
* ** * *
45070 ATA ATA ATA ATA ATA ATA ACT- ATA ATA ATA AGA A-A CCA AAA CAGA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA -ATA
45115 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
45149 ATGAAAAAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
2 2 0.03
3 61 0.92
4 3 0.05
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:45174 original size:15 final size:15
Alignment explanation
Indices: 45114--45174 Score: 55
Period size: 12 Copynumber: 4.5 Consensus size: 15
45104 ACCAAAACAG
45114 AATAATAAT-AAT--
1 AATAATAATAAATGA
45126 AATAATAAT-AAT--
1 AATAATAATAAATGA
45138 AATAATAATAAATGA
1 AATAATAATAAATGA
*
45153 AAAAATAA-AAATGA
1 AATAATAATAAATGA
45167 AACTAATA
1 AA-TAATA
45175 TATTAATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
12 21 0.49
13 3 0.07
14 8 0.19
15 11 0.26
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (15 bp):
AATAATAATAAATGA
Found at i:46310 original size:16 final size:16
Alignment explanation
Indices: 46279--46317 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
46269 AGAATAAAAT
46279 TAAAAAT-ATAACATA
1 TAAAAATAATAACATA
* *
46294 TAATAATAATAATATA
1 TAAAAATAATAACATA
46310 TAAAAATA
1 TAAAAATA
46318 GTTCCCAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAAATAATAACATA
Found at i:46378 original size:36 final size:35
Alignment explanation
Indices: 46325--46601 Score: 233
Period size: 38 Copynumber: 7.6 Consensus size: 35
46315 ATAGTTCCCA
*
46325 AAAACT-TATATAATATATATTTTCAAAAATATTTT
1 AAAACTATATATTATATATATTTTC-AAAATATTTT
* *
46360 AAAACTATATATTATATATATTTT-AAAAAATATTC
1 AAAACTATATATTATATATATTTTCAAAATAT-TTT
* *
46395 AAAACTATATACTATATA-AGCTTTTTCAAAATGTTTT
1 AAAACTATATATTATATATA---TTTTCAAAATATTTT
* *
46432 CAAAA--ACTATATTATATATATATTTCAAATTTTTTT
1 -AAAACTA-TATATTATATATAT-TTTCAAAATATTTT
*
46468 AAAACTATATATTATATATATGTTTCCAAAATGTTTT
1 AAAACTATATATTATATATAT-TTT-CAAAATATTTT
* * * *
46505 AAAAACTATATAATATATATGTTTTCAAAATGCTTTC
1 -AAAACTATATATTATATATATTTTCAAAAT-ATTTT
*
46542 ATAAACTATATATTATATATATAGTTCAAAA-ATCATTT
1 A-AAACTATATATTATATATAT-TTTCAAAATAT--TTT
*
46580 ACAAACTATATAATATATATAT
1 A-AAACTATATATTATATATAT
46602 AAATAAAATA
Statistics
Matches: 199, Mismatches: 24, Indels: 35
0.77 0.09 0.14
Matches are distributed among these distances:
34 7 0.04
35 30 0.15
36 54 0.27
37 50 0.25
38 58 0.29
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (35 bp):
AAAACTATATATTATATATATTTTCAAAATATTTT
Found at i:46425 original size:73 final size:72
Alignment explanation
Indices: 46325--46601 Score: 278
Period size: 75 Copynumber: 3.8 Consensus size: 72
46315 ATAGTTCCCA
* *
46325 AAAACT-TATATAATATATA-TTTTCAAAAATATTTT-AAAACTATATATTATATATATTTTAAA
1 AAAACTATATATTATATATATTTTTCAAAAATATTTTAAAAACTATATAATATATATATTTT-AA
*
46387 AAATATTC
65 AAATTTTC
* * * *
46395 AAAACTATATACTATATA-AGCTTTTTC-AAAATGTTTTCAAAAACTATATTATATATATATTTC
1 AAAACTATATATTATATATA--TTTTTCAAAAATATTTT-AAAAACTATATAATATATATATTTT
** *
46458 AAATTTTTTT
63 AAAAATTTTC
* * * * *
46468 AAAACTATATATTATATATATGTTTCCAAAATGTTTTAAAAACTATATAATATATATGTTTTCAA
1 AAAACTATATATTATATATATTTTTCAAAAATATTTTAAAAACTATATAATATATATATTTTAAA
46533 AATGCTTTC
66 AAT--TTTC
** *
46542 ATAAACTATATATTATATATATAGTTCAAAAATCA-TTTACAAACTATATAATATATATAT
1 A-AAACTATATATTATATATATTTTTCAAAAAT-ATTTTAAAAACTATATAATATATATAT
46602 AAATAAAATA
Statistics
Matches: 170, Mismatches: 25, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
70 7 0.04
71 9 0.05
72 39 0.23
73 38 0.22
74 26 0.15
75 51 0.30
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (72 bp):
AAAACTATATATTATATATATTTTTCAAAAATATTTTAAAAACTATATAATATATATATTTTAAA
AATTTTC
Found at i:46510 original size:38 final size:38
Alignment explanation
Indices: 46324--46601 Score: 226
Period size: 36 Copynumber: 7.6 Consensus size: 38
46314 AATAGTTCCC
* * *
46324 AAAAACT-TATATAATATATAT-TTTCAAAAATATTTT
1 AAAAACTATATATTATATATATGTTTCCAAAATGTTTT
** *
46360 -AAAACTATATATTATATATAT-TTT--AAAAAATATT
1 AAAAACTATATATTATATATATGTTTCCAAAATGTTTT
* * *
46394 CAAAACTATATACTATATA-A-GCTTTTTCAAAATGTTTT
1 AAAAACTATATATTATATATATG--TTTCCAAAATGTTTT
* *
46432 CAAAAAC--TATATTATATATATATTT-C-AAATTTTTT
1 -AAAAACTATATATTATATATATGTTTCCAAAATGTTTT
*
46467 TAAAACTATATATTATATATATGTTTCCAAAATGTTTT
1 AAAAACTATATATTATATATATGTTTCCAAAATGTTTT
* *
46505 AAAAACTATATA--ATATATATGTTTTCAAAATGCTTTC
1 AAAAACTATATATTATATATATGTTTCCAAAATG-TTTT
* * **
46542 ATAAACTATATATTATATATATAG-TTCAAAAATCATTT
1 AAAAACTATATATTATATATAT-GTTTCCAAAATGTTTT
* *
46580 ACAAACTATATAATATATATAT
1 AAAAACTATATATTATATATAT
46602 AAATAAAATA
Statistics
Matches: 199, Mismatches: 25, Indels: 34
0.77 0.10 0.13
Matches are distributed among these distances:
34 14 0.07
35 31 0.16
36 56 0.28
37 28 0.14
38 49 0.25
39 20 0.10
40 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (38 bp):
AAAAACTATATATTATATATATGTTTCCAAAATGTTTT
Found at i:47120 original size:85 final size:85
Alignment explanation
Indices: 46976--47637 Score: 777
Period size: 85 Copynumber: 7.8 Consensus size: 85
46966 ACGTGTCATC
* * * * **** *
46976 GAGCTGAGTGGAATCGAACTCGATAGTTTTTTGTTGACAGATAGTTTTTCTCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
* *
47041 CTGTAAATTTGATGTGCCTCT
65 CTGTAAATTTGATATGCCTTT
* *
47062 GAGCTGAATGTAATCGAACTCGATGGTCTTTATTGACAGATAACCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
* *
47127 TGTAAATTTGATGTGCCTCT
66 TGTAAATTTGATATGCCTTT
* * * * * *
47147 GAGCTTAATGTAATCGAACTCGAAGGTCTTTATTGACAAATAACCCTTCTTGCCTTGAGCTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
47212 TGTAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* ** * ** *** * *
47232 GAGCTGAATGTAATCGAACTCAAAAATCTTCGTTGACAGATAGA-TTTTCTTAACTTAAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATA-ACCCTTCTCGCCTTGAGTTATG
* *
47296 TTGTAAATTTGATATGTCTTT
65 CTGTAAATTTGATATGCCTTT
* * * * * * *
47317 GAGCTAAATGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTATCGCCTTAAGTTACGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
*
47382 TGCAAAATTTGATATGCCTTT
66 TG-TAAATTTGATATGCCTTT
* * *
47403 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
47468 TGTAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * * * *
47488 GAGTTGAGTGTAATCGAACTCAAAGGTCTTGGTTGACAAATAACCCTTATCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
*
47553 TGCAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * * *
47573 GAGCTGAGTGTAATCGAACTTGAAGGTCTTGGTTGACAGATAACCCTTCTTGCCTTGAGATATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
47638 CACCAATAGT
Statistics
Matches: 502, Mismatches: 71, Indels: 7
0.87 0.12 0.01
Matches are distributed among these distances:
85 405 0.81
86 97 0.19
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
TGTAAATTTGATATGCCTTT
Found at i:47817 original size:86 final size:86
Alignment explanation
Indices: 47710--47879 Score: 250
Period size: 86 Copynumber: 2.0 Consensus size: 86
47700 TCCAGGTCGT
* *
47710 TCCCCTTAACGAGTCTGAACCAAGTGAGATGATATTTGGATGACTCCCCTTCACGGGAAAACCAT
1 TCCCCTTAACGAGTCTAAACCAAGTGAGATGATATTTGGATGACTACCCTTCACGGGAAAACCAT
*
47775 GTGGTATGTTCTTCAAGTGGA
66 GTGATATGTTCTTCAAGTGGA
* * * * * *
47796 TCCCCTTAGCGGGTCTAAACCAAGTGAGATGATCTTTGGATGACTACCCTTTATGGGAAAGCCAT
1 TCCCCTTAACGAGTCTAAACCAAGTGAGATGATATTTGGATGACTACCCTTCACGGGAAAACCAT
*
47861 GTGATATGTTCTTCGAGTG
66 GTGATATGTTCTTCAAGTG
47880 ACTCCTCTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 74 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.29
Consensus pattern (86 bp):
TCCCCTTAACGAGTCTAAACCAAGTGAGATGATATTTGGATGACTACCCTTCACGGGAAAACCAT
GTGATATGTTCTTCAAGTGGA
Found at i:67524 original size:35 final size:34
Alignment explanation
Indices: 67479--67580 Score: 145
Period size: 35 Copynumber: 3.0 Consensus size: 34
67469 ATATTCTAGC
67479 AACTCTCTATATTATATTAATATTAATGCTTAACA
1 AACTCTCTATATTAT-TTAATATTAATGCTTAACA
* *
67514 AACTCTCTATATTATGTTAATATGAATGCTAAACA
1 AACTCTCTATATTAT-TTAATATTAATGCTTAACA
*
67549 AACTCTCTATA-T-TCTAATATTAATGCTTAACA
1 AACTCTCTATATTATTTAATATTAATGCTTAACA
67581 TTCACCCTAC
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
32 16 0.26
33 1 0.02
34 1 0.02
35 43 0.70
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.40
Consensus pattern (34 bp):
AACTCTCTATATTATTTAATATTAATGCTTAACA
Found at i:72071 original size:42 final size:43
Alignment explanation
Indices: 71960--72073 Score: 178
Period size: 42 Copynumber: 2.7 Consensus size: 43
71950 CGGATTCTCG
* *
71960 TGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTCACGA
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCACAA
*
72003 -GTTTGTTTCACGAAATTCGTTTTCCGGAAAATGTTTTC-CAA
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCACAA
*
72044 TGTTTGTTTCACGTAATTAGTTTTCCGGAA
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAA
72074 CGTAATTATT
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 2 0.03
42 63 0.97
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.44
Consensus pattern (43 bp):
TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCACAA
Found at i:72291 original size:22 final size:23
Alignment explanation
Indices: 72261--72304 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
72251 TTTATTTATT
72261 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
72284 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
72305 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:72298 original size:31 final size:31
Alignment explanation
Indices: 72253--72311 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
72243 AAATATTATT
72253 TATTTATTTATTAATATT-TATAATAATATAA
1 TATTTATTTATTAATATTATATAA-AATATAA
72284 TATTATATTT-TTAATATTATATAAAATA
1 TATT-TATTTATTAATATTATATAAAATA
72312 ATCAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
TATTTATTTATTAATATTATATAAAATATAA
Found at i:72321 original size:30 final size:32
Alignment explanation
Indices: 72257--72329 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 32
72247 ATTATTTATT
* *
72257 TATTTATTAATATTTATAATAATATAATATTA
1 TATTTATTAATATTTATAATAAAATAATAATA
72289 TATTT-TTAATA-TTAT-ATAAAATAATCAATA
1 TATTTATTAATATTTATAATAAAATAAT-AATA
72319 TA-TTA-TAATAT
1 TATTTATTAATAT
72330 ATAAGATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
29 16 0.44
30 9 0.25
31 6 0.17
32 5 0.14
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
TATTTATTAATATTTATAATAAAATAATAATA
Found at i:72383 original size:30 final size:28
Alignment explanation
Indices: 72316--72418 Score: 79
Period size: 28 Copynumber: 3.6 Consensus size: 28
72306 AAAATAATCA
* *
72316 ATATATTATAAT-ATATAAGATATATATTTT
1 ATATATT-TAATAATATAATA-AAAT-TTTT
72346 -TAT-TTTAATAATATATATAAAATGTTTT
1 ATATATTTAATAATATA-ATAAAAT-TTTT
* *
72374 ATATATTTAATAAT-GAATAATATTATTT
1 ATATATTTAATAATATAATAAAATT-TTT
72402 ATATATTTAAATAATAT
1 ATATATTT-AATAATAT
72419 TTTAGTAAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
27 5 0.08
28 31 0.52
29 15 0.25
30 9 0.15
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
ATATATTTAATAATATAATAAAATTTTT
Found at i:72660 original size:16 final size:17
Alignment explanation
Indices: 72559--72665 Score: 53
Period size: 16 Copynumber: 6.2 Consensus size: 17
72549 ATTAATAAAA
*
72559 TTATAA-AAAT-ACTAT
1 TTATAATAAATAATTAT
72574 TTAATAATAAATAAATTATTT
1 TT-ATAATAAAT-AATTA--T
*
72595 TTAATAATAAATAAGT-T
1 TT-ATAATAAATAATTAT
*
72612 TTATGATAAATAATATTAT
1 TTATAATAAAT-A-ATTAT
** **
72631 TTATTGTATTTAA-TAT
1 TTATAATAAATAATTAT
72647 TTATAATAAATAATT-T
1 TTATAATAAATAATTAT
72663 TTA
1 TTA
72666 AAAAACTCTT
Statistics
Matches: 70, Mismatches: 12, Indels: 19
0.69 0.12 0.19
Matches are distributed among these distances:
15 2 0.03
16 28 0.40
17 10 0.14
18 3 0.04
19 11 0.16
20 3 0.04
21 13 0.19
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.49
Consensus pattern (17 bp):
TTATAATAAATAATTAT
Found at i:72835 original size:15 final size:15
Alignment explanation
Indices: 72815--72865 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
72805 CATTTTCCAG
*
72815 AATTCAAATTACAGT
1 AATTCAAATTTCAGT
**
72830 AATTCATTTTTCAGT
1 AATTCAAATTTCAGT
72845 AATTCAAATTTCAGT
1 AATTCAAATTTCAGT
72860 AATTCA
1 AATTCA
72866 TTTTCCGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (15 bp):
AATTCAAATTTCAGT
Found at i:72849 original size:30 final size:29
Alignment explanation
Indices: 72799--72871 Score: 119
Period size: 30 Copynumber: 2.5 Consensus size: 29
72789 TTCCAGAAAT
72799 GTAATTCATTTTCCAGAATTCAAATTACA
1 GTAATTCATTTTCCAGAATTCAAATTACA
* *
72828 GTAATTCATTTTTCAGTAATTCAAATTTCA
1 GTAATTCATTTTCCAG-AATTCAAATTACA
72858 GTAATTCATTTTCC
1 GTAATTCATTTTCC
72872 GAAAAACCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTACA
Found at i:79812 original size:23 final size:22
Alignment explanation
Indices: 79786--79843 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
79776 GGCCCTTCGA
79786 TGCATTTCTATGTGGCACTACGG
1 TGCATTTCTATG-GGCACTACGG
* * *
79809 TGCAATTCTACGGGCACTTCGG
1 TGCATTTCTATGGGCACTACGG
*
79831 TGCAATTTATATG
1 TGC-ATTTCTATG
79844 AGCTGTGGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (22 bp):
TGCATTTCTATGGGCACTACGG
Found at i:79831 original size:22 final size:23
Alignment explanation
Indices: 79775--79837 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
79765 CAACCTTATA
* * * *
79775 TGGCCCTTCGATGCATTTCTATG
1 TGGCACTTCGGTGCAATTCTACG
*
79798 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
79821 -GGCACTTCGGTGCAATT
1 TGGCACTTCGGTGCAATT
79838 TATATGAGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:84842 original size:23 final size:23
Alignment explanation
Indices: 84779--84843 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
84769 TAACCTTATA
*
84779 TGGCACTTTCGGTGCATTTCTACG
1 TGGCAC-TTCGGTGCAATTCTACG
* *
84803 CGGCACTAT-GGTTCAATTCTACG
1 TGGCACT-TCGGTGCAATTCTACG
84826 TGGCACTTCGGTGCAATT
1 TGGCACTTCGGTGCAATT
84844 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
22 1 0.03
23 27 0.79
24 6 0.18
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.34
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Done.