Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007780.1 Hibiscus syriacus cultivar Beakdansim tig00110063_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: 764298
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:812 original size:56 final size:56
Alignment explanation
Indices: 744--849 Score: 203
Period size: 56 Copynumber: 1.9 Consensus size: 56
734 CTTGGAAGAA
*
744 CAAATATTTCTAAATTATATGGATGTGTATATGAACAACTAAAATTAATATAATAC
1 CAAATATTTCTAAATTATATCGATGTGTATATGAACAACTAAAATTAATATAATAC
800 CAAATATTTCTAAATTATATCGATGTGTATATGAACAACTAAAATTAATA
1 CAAATATTTCTAAATTATATCGATGTGTATATGAACAACTAAAATTAATA
850 ACACAGAGAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.36
Consensus pattern (56 bp):
CAAATATTTCTAAATTATATCGATGTGTATATGAACAACTAAAATTAATATAATAC
Found at i:3685 original size:31 final size:31
Alignment explanation
Indices: 3647--3712 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
3637 ATCATTTGTT
* * *
3647 AAAATAAATCGAAGTTGAAACTAAAT-ATTAA
1 AAAATAAAACGAAATT-AAAATAAATAATTAA
*
3678 AAAATAAAACGAAATTAAAATAGATAATTAA
1 AAAATAAAACGAAATTAAAATAAATAATTAA
3709 AAAA
1 AAAA
3713 ATCAAAGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.65, C:0.05, G:0.08, T:0.23
Consensus pattern (31 bp):
AAAATAAAACGAAATTAAAATAAATAATTAA
Found at i:10358 original size:16 final size:16
Alignment explanation
Indices: 10326--10361 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
10316 CGAATAAAAA
10326 TATATTTATATAAATG
1 TATATTTATATAAATG
* *
10342 TATATTTATTTAGATG
1 TATATTTATATAAATG
10358 TATA
1 TATA
10362 AATAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (16 bp):
TATATTTATATAAATG
Found at i:10423 original size:16 final size:18
Alignment explanation
Indices: 10391--10424 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
10381 TATTAATGTA
10391 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
10409 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
10425 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:10643 original size:25 final size:25
Alignment explanation
Indices: 10615--10673 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
10605 ACAATTTATC
*
10615 AAATATAATATTTTTTATTGTAAAA
1 AAATATAATATTTTCTATTGTAAAA
*
10640 AAATATTATATTTTCTATTGTAAAA
1 AAATATAATATTTTCTATTGTAAAA
10665 AAATATAAT
1 AAATATAAT
10674 TTTCCCATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (25 bp):
AAATATAATATTTTCTATTGTAAAA
Found at i:11121 original size:130 final size:130
Alignment explanation
Indices: 10917--11164 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
10907 AATTTTATTC
* *
10917 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATAATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATAATGTGCTAACACATGTCAGAT
** *
10982 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
11047 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATAATGTGCTAACACATGTCAGAT
11112 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
11165 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATAATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:11599 original size:35 final size:35
Alignment explanation
Indices: 11560--11635 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
11550 AATTGAATTT
* *
11560 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
11595 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
11630 AATTGA
1 AATTGA
11636 GGTATGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:16079 original size:25 final size:25
Alignment explanation
Indices: 16045--16095 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
16035 GGTCCACATT
16045 TATGTTCCAAAAGACCAAATATATG
1 TATGTTCCAAAAGACCAAATATATG
* * *
16070 TATGTTCCAAAGGATCACATATATG
1 TATGTTCCAAAAGACCAAATATATG
16095 T
1 T
16096 CCCGGAGGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (25 bp):
TATGTTCCAAAAGACCAAATATATG
Found at i:23030 original size:21 final size:21
Alignment explanation
Indices: 23006--23129 Score: 79
Period size: 21 Copynumber: 5.8 Consensus size: 21
22996 TATCCCGAAT
*
23006 GACCACATATATGTCCCATCG
1 GACCACATATATGTCCCATAG
* * *
23027 GACCCCATAGAATTGTCCCGTAG
1 GACCACATA-TA-TGTCCCATAG
* * *
23050 GACCACATATATGTTCCAAAT
1 GACCACATATATGTCCCATAG
* * * *
23071 GACCAAATATATGTCCAAAAAA
1 GACCACATATATGTCC-CATAG
* *
23093 GACCGA-ATATATGTTCCAAAG
1 GACC-ACATATATGTCCCATAG
*
23114 GATCACATATATGTCC
1 GACCACATATATGTCC
23130 TGAAGGACCA
Statistics
Matches: 79, Mismatches: 19, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
20 1 0.01
21 43 0.54
22 18 0.23
23 17 0.22
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (21 bp):
GACCACATATATGTCCCATAG
Found at i:24439 original size:52 final size:52
Alignment explanation
Indices: 24367--24470 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
24357 GTTTCTATAA
*
24367 ACTTTTCTAATGCTTCATCAATCAAAAGCACTCATGAATTGCAAGAATAAAC
1 ACTTTCCTAATGCTTCATCAATCAAAAGCACTCATGAATTGCAAGAATAAAC
24419 ACTTTCCTAATGCTTCATCAATCAAAAGCACTCATGAATTGCAAGAATAAAC
1 ACTTTCCTAATGCTTCATCAATCAAAAGCACTCATGAATTGCAAGAATAAAC
24471 CAGCTGTAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (52 bp):
ACTTTCCTAATGCTTCATCAATCAAAAGCACTCATGAATTGCAAGAATAAAC
Found at i:24565 original size:7 final size:7
Alignment explanation
Indices: 24553--24581 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
24543 AGAAATATAT
24553 CTTTTCC
1 CTTTTCC
24560 CTTTTCC
1 CTTTTCC
24567 CTTTTCC
1 CTTTTCC
24574 CTTTTCC
1 CTTTTCC
24581 C
1 C
24582 CTAGCTCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (7 bp):
CTTTTCC
Found at i:29643 original size:27 final size:27
Alignment explanation
Indices: 29611--29666 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
29601 TACAGTCGCT
**
29611 TACTCCAAGCCTAGGGTATTCCCTAAA
1 TACTCCAAGCCTAGGAAATTCCCTAAA
*
29638 TACTCCAAGCCTTGGAAATTCCCTAAA
1 TACTCCAAGCCTAGGAAATTCCCTAAA
29665 TA
1 TA
29667 ATCTTATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (27 bp):
TACTCCAAGCCTAGGAAATTCCCTAAA
Found at i:39990 original size:20 final size:20
Alignment explanation
Indices: 39965--40011 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
39955 GCATTAAGTT
39965 TTCTCTTTCAATTTCTTTAA
1 TTCTCTTTCAATTTCTTTAA
39985 TTCTCTTTCAATTTCTTTAA
1 TTCTCTTTCAATTTCTTTAA
40005 TTCTCTT
1 TTCTCTT
40012 GGTATATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (20 bp):
TTCTCTTTCAATTTCTTTAA
Found at i:39991 original size:10 final size:11
Alignment explanation
Indices: 39965--40011 Score: 66
Period size: 10 Copynumber: 4.6 Consensus size: 11
39955 GCATTAAGTT
39965 TTCTCTTTCAA
1 TTCTCTTTCAA
39976 TT-TCTTT-AA
1 TTCTCTTTCAA
39985 TTCTCTTTCAA
1 TTCTCTTTCAA
39996 TT-TCTTT-AA
1 TTCTCTTTCAA
40005 TTCTCTT
1 TTCTCTT
40012 GGTATATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
9 8 0.24
10 19 0.58
11 6 0.18
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (11 bp):
TTCTCTTTCAA
Found at i:45069 original size:7 final size:6
Alignment explanation
Indices: 45044--45086 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
45034 ATCCACAAAT
* *
45044 AATATA AATAAA AATAAA AATAAAA AATAAA GATAAA ATATAA
1 AATAAA AATAAA AATAAA AAT-AAA AATAAA AATAAA A-ATAA
45087 GTTCATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
6 22 0.69
7 10 0.31
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (6 bp):
AATAAA
Found at i:45071 original size:13 final size:13
Alignment explanation
Indices: 45044--45086 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
45034 ATCCACAAAT
*
45044 AATATAAAT-AAA
1 AATAAAAATAAAA
45056 AATAAAAATAAAA
1 AATAAAAATAAAA
*
45069 AATAAAGATAAAA
1 AATAAAAATAAAA
*
45082 TATAA
1 AATAA
45087 GTTCATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 8 0.30
13 19 0.70
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (13 bp):
AATAAAAATAAAA
Found at i:52260 original size:21 final size:21
Alignment explanation
Indices: 52234--52276 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
52224 GATGAACTAC
52234 GGCTTTGCAA-AAGTGTTTCTT
1 GGCTTTGCAACAAGT-TTTCTT
*
52255 GGCTTTGTAACAAGTTTTCTT
1 GGCTTTGCAACAAGTTTTCTT
52276 G
1 G
52277 ATTTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.44
Consensus pattern (21 bp):
GGCTTTGCAACAAGTTTTCTT
Found at i:61503 original size:21 final size:21
Alignment explanation
Indices: 61478--61601 Score: 117
Period size: 21 Copynumber: 5.7 Consensus size: 21
61468 TTTTCGTAAG
61478 AGTACTTTGTGTACTTGGAGT
1 AGTACTTTGTGTACTTGGAGT
* *
61499 AGTACTTTTTATACTATGGTAAG-
1 AGTACTTTGTGTACT-TGG--AGT
* *
61522 ATTACTTTGTGCACTTGGAGT
1 AGTACTTTGTGTACTTGGAGT
* *
61543 AGTACTTTTTGTACTATTGCAAG-
1 AGTACTTTGTGTAC--TTG-GAGT
*
61566 AGTACTTTGTGTACTTGTAGT
1 AGTACTTTGTGTACTTGGAGT
61587 AGTACTTTGTGTACT
1 AGTACTTTGTGTACT
61602 ATGGCACTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
20 4 0.05
21 42 0.51
22 6 0.07
23 27 0.33
24 4 0.05
ACGTcount: A:0.23, C:0.11, G:0.22, T:0.44
Consensus pattern (21 bp):
AGTACTTTGTGTACTTGGAGT
Found at i:61538 original size:44 final size:44
Alignment explanation
Indices: 61473--61605 Score: 203
Period size: 44 Copynumber: 3.0 Consensus size: 44
61463 TTGAATTTTC
*
61473 GTAAGAGTACTTTGTGTACTTGGAGTAGTACTTTTTATACTATG
1 GTAAGAGTACTTTGTGTACTTGGAGTAGTACTTTTTGTACTATG
* * *
61517 GTAAGATTACTTTGTGCACTTGGAGTAGTACTTTTTGTACTATT
1 GTAAGAGTACTTTGTGTACTTGGAGTAGTACTTTTTGTACTATG
* * *
61561 GCAAGAGTACTTTGTGTACTTGTAGTAGTACTTTGTGTACTATG
1 GTAAGAGTACTTTGTGTACTTGGAGTAGTACTTTTTGTACTATG
61605 G
1 G
61606 CACTTTGTGT
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 79 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (44 bp):
GTAAGAGTACTTTGTGTACTTGGAGTAGTACTTTTTGTACTATG
Found at i:67460 original size:54 final size:54
Alignment explanation
Indices: 67373--67705 Score: 432
Period size: 54 Copynumber: 6.2 Consensus size: 54
67363 GATTATCAAA
* *
67373 TCGGCACTAAGTGTGCATTTCGCGGAATTCATCCTATGTGGAAGAATAACCGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
* * *
67427 TCGGTACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACTGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
* *
67481 TCGGCACTAAGTGTGCATTTTACGGAAGTCATCCTATGTGGATGAATAACCGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
** * * *
67535 TCGATACTAAGTGTGCATTTCATGGAATTCATCCTATGTAGATGTATAACCGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
* * ***
67589 TCGACACTAAGTGTGCATTACACGGAATTCATCCTATGTGGATGAATAATTATT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
* * * * * * * *
67643 TCAGCAATAAGTGTGCCTTTCACGAAATTCATCCTTTATGGATGAATAGCCATT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
*
67697 TCGACACTA
1 TCGGCACTA
67706 TGGGTACAAA
Statistics
Matches: 240, Mismatches: 39, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 240 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (54 bp):
TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
Found at i:73601 original size:20 final size:20
Alignment explanation
Indices: 73557--73607 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
73547 TCTGCTAGGT
**
73557 AGTATCGATACCTAAGGGGG
1 AGTATCGATACCTAAGGAAG
73577 AGTATCGATACCTAAGGTAAG
1 AGTATCGATACCTAAGG-AAG
73598 -GTATCGATAC
1 AGTATCGATAC
73608 TATTCAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (20 bp):
AGTATCGATACCTAAGGAAG
Found at i:73693 original size:22 final size:22
Alignment explanation
Indices: 73650--73703 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
73640 TACCATAGCA
*
73650 TAGTATCGGTACCATAGAATGG
1 TAGTATCGATACCATAGAATGG
* *
73672 TAGTATCGATACCATGGTATGG
1 TAGTATCGATACCATAGAATGG
73694 --GTATCGATAC
1 TAGTATCGATAC
73704 TGAGGGACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 10 0.34
22 19 0.66
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (22 bp):
TAGTATCGATACCATAGAATGG
Found at i:74119 original size:54 final size:54
Alignment explanation
Indices: 74025--74411 Score: 551
Period size: 54 Copynumber: 7.1 Consensus size: 54
74015 GATTACCATA
* * *
74025 TCAGCACTAAGTGTGTATTTCACGGAATTTATCCTTTGTGGATGAATAACCGTT
1 TCAGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
* * *
74079 TCGGTACTAAGTGTGCATTTCACGGAATTCATCTTATGTGGATGAATAACCGTT
1 TCAGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
* *
74133 TCAGCATTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTT
1 TCAGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
* * *
74187 TCGGCACTAAGTGTGCATTTCACGAAATT-ATCCTATGTGAATGAATAACCGTT
1 TCAGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
* * **
74240 TCAACACACTAAGTATGCATTTCACATAATTCATCCTATGTGGATGAATAACCGTT
1 TC-A-GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
* * * * *
74296 TCAGCACTAAGTGTGCATTTCACGAAATTCATCTTATTTGGATGAATAATCATT
1 TCAGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
*
74350 TCAGCACTAAGTGTGCATTACACGGAATTCATCCTATGTGGATGAATAACCGTT
1 TCAGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
*
74404 TCGGCACT
1 TCAGCACT
74412 CTGGGTACAA
Statistics
Matches: 293, Mismatches: 37, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
53 25 0.09
54 220 0.75
55 23 0.08
56 25 0.09
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (54 bp):
TCAGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
Found at i:77375 original size:21 final size:21
Alignment explanation
Indices: 77350--77473 Score: 144
Period size: 21 Copynumber: 5.7 Consensus size: 21
77340 ATTTCGTAAG
*
77350 AGTACTTTGTGTAATTGGAGT
1 AGTACTTTGTGTACTTGGAGT
77371 AGTACTTTGTGTACTATGGTAAG-
1 AGTACTTTGTGTACT-TGG--AGT
* *
77394 AGTACGTTGTCTACTTGGAGT
1 AGTACTTTGTGTACTTGGAGT
77415 AGTACTTTGTGTACTATGGAAAG-
1 AGTACTTTGTGTACT-TGG--AGT
*
77438 AGTACTTTGTGTACTTGTAGT
1 AGTACTTTGTGTACTTGGAGT
77459 AGTACTTTGTGTACT
1 AGTACTTTGTGTACT
77474 ATGGCACTTT
Statistics
Matches: 89, Mismatches: 6, Indels: 16
0.80 0.05 0.14
Matches are distributed among these distances:
20 4 0.04
21 42 0.47
22 11 0.12
23 28 0.31
24 4 0.04
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.41
Consensus pattern (21 bp):
AGTACTTTGTGTACTTGGAGT
Found at i:77412 original size:44 final size:44
Alignment explanation
Indices: 77345--77477 Score: 221
Period size: 44 Copynumber: 3.0 Consensus size: 44
77335 TTGCAATTTC
*
77345 GTAAGAGTACTTTGTGTAATTGGAGTAGTACTTTGTGTACTATG
1 GTAAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTGTACTATG
* *
77389 GTAAGAGTACGTTGTCTACTTGGAGTAGTACTTTGTGTACTATG
1 GTAAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTGTACTATG
* *
77433 GAAAGAGTACTTTGTGTACTTGTAGTAGTACTTTGTGTACTATG
1 GTAAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTGTACTATG
77477 G
1 G
77478 CACTTTGTGT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 82 1.00
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.40
Consensus pattern (44 bp):
GTAAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTGTACTATG
Found at i:81639 original size:28 final size:28
Alignment explanation
Indices: 81583--81641 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
81573 CTTGGAGGTC
**
81583 TTTTGGGTCATTTTACACTTCAGGGGTA
1 TTTTGGGTCATTTTACACTTCAGCAGTA
81611 TTTTGGGTCATTTT-C-CTTCAGTCCAGTA
1 TTTTGGGTCATTTTACACTTCAG--CAGTA
81639 TTT
1 TTT
81642 CCAGTTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 6 0.22
27 1 0.04
28 20 0.74
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.47
Consensus pattern (28 bp):
TTTTGGGTCATTTTACACTTCAGCAGTA
Found at i:82541 original size:17 final size:17
Alignment explanation
Indices: 82521--82562 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
82511 CAACGATCAT
82521 GTCAATGGCTAGTCAAA
1 GTCAATGGCTAGTCAAA
82538 GTCAATGGCTAGTCAAA
1 GTCAATGGCTAGTCAAA
82555 GTCAATGG
1 GTCAATGG
82563 GTTGACTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (17 bp):
GTCAATGGCTAGTCAAA
Found at i:82598 original size:14 final size:14
Alignment explanation
Indices: 82579--82616 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
82569 TCTGTTCAAG
82579 TTGACTCAACTGGC
1 TTGACTCAACTGGC
82593 TTGACTCAACTGGC
1 TTGACTCAACTGGC
82607 TTGACTCAAC
1 TTGACTCAAC
82617 GAGTTGAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (14 bp):
TTGACTCAACTGGC
Found at i:85641 original size:20 final size:21
Alignment explanation
Indices: 85612--85672 Score: 90
Period size: 20 Copynumber: 3.0 Consensus size: 21
85602 ATCAGATTGT
*
85612 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
85633 CCA-GGGGTACCGATT-CCCC
1 CCAGGGGGTACCGATTCCCCC
*
85652 CTAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
85673 TGTTTAACGG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.17
20 23 0.64
21 7 0.19
ACGTcount: A:0.16, C:0.39, G:0.28, T:0.16
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:86286 original size:23 final size:23
Alignment explanation
Indices: 86260--86315 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
86250 CCTAAACATA
* *
86260 AAACTGTTCTGACCCCTCTTTAC
1 AAACCGTTCCGACCCCTCTTTAC
* *
86283 AAACCATTCCGACCCCTCTTTGC
1 AAACCGTTCCGACCCCTCTTTAC
86306 AAACCGTTCC
1 AAACCGTTCC
86316 AGTTGTCAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.23, C:0.39, G:0.09, T:0.29
Consensus pattern (23 bp):
AAACCGTTCCGACCCCTCTTTAC
Found at i:90277 original size:27 final size:27
Alignment explanation
Indices: 90232--90302 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
90222 AGGGCTTGGA
*
90232 GGTATTTTGGGTCATTTTA-CACTTTAGG
1 GGTATTTT-GGTCATTTTACCA-TTTAAG
90260 GGTATTTTGGTCATTTTACCATTTAAG
1 GGTATTTTGGTCATTTTACCATTTAAG
*
90287 GGTATTTTAGTCATTT
1 GGTATTTTGGTCATTT
90303 CCTTCAGTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 30 0.75
28 10 0.25
ACGTcount: A:0.20, C:0.10, G:0.21, T:0.49
Consensus pattern (27 bp):
GGTATTTTGGTCATTTTACCATTTAAG
Found at i:91133 original size:16 final size:17
Alignment explanation
Indices: 91112--91144 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
91102 TGTCAAAATA
91112 CATAAAA-ATGACTTTT
1 CATAAAATATGACTTTT
*
91128 CATAAAATTTGACTTTT
1 CATAAAATATGACTTTT
91145 TGGTCAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (17 bp):
CATAAAATATGACTTTT
Found at i:93687 original size:24 final size:24
Alignment explanation
Indices: 93650--93697 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
93640 CAAGTTTTCC
93650 TGATGTATAAAACATCTATGTACA
1 TGATGTATAAAACATCTATGTACA
* * *
93674 TGATGTTTATAACATTTATGTACA
1 TGATGTATAAAACATCTATGTACA
93698 ATGTCATGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (24 bp):
TGATGTATAAAACATCTATGTACA
Found at i:101813 original size:23 final size:23
Alignment explanation
Indices: 101780--101845 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
101770 GGTTCTACGT
* * *
101780 GGTCTTTCGGGACATTTTTACAG
1 GGTCCTTCGGGACATTTCTACAC
*
101803 GGTTCTTCGGGACATTTCTACAC
1 GGTCCTTCGGGACATTTCTACAC
* *
101826 GGTCCTTTGGGGCATTTCTA
1 GGTCCTTCGGGACATTTCTA
101846 TGTGTCCTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (23 bp):
GGTCCTTCGGGACATTTCTACAC
Found at i:103384 original size:30 final size:31
Alignment explanation
Indices: 103316--103384 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 31
103306 AACCATTCAC
* * * **
103316 AATTTTTCTAAATTTAACAAATTGGTCCCTT
1 AATTTTTCAAAAATTAACAAAATGGTCCCAA
*
103347 AACTTTTCAAAAATT-ACAAAATGGTCCCAA
1 AATTTTTCAAAAATTAACAAAATGGTCCCAA
103377 AATTTTTC
1 AATTTTTC
103385 TAAGGCTTGT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (31 bp):
AATTTTTCAAAAATTAACAAAATGGTCCCAA
Found at i:108399 original size:9 final size:9
Alignment explanation
Indices: 108379--108412 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
108369 CATTTAGAGA
108379 GAGAGAAAAT
1 GAGAG-AAAT
108389 GAGAGAAAT
1 GAGAGAAAT
*
108398 GAGATAAAT
1 GAGAGAAAT
108407 GAGAGA
1 GAGAGA
108413 GTTTGCCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.32, T:0.12
Consensus pattern (9 bp):
GAGAGAAAT
Found at i:108834 original size:18 final size:19
Alignment explanation
Indices: 108795--108834 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
108785 TTATCATTAA
108795 TTATTATATGATTAAGTAT
1 TTATTATATGATTAAGTAT
108814 TTATT-TAT-ATTAAGTTAT
1 TTATTATATGATTAAG-TAT
108832 TTA
1 TTA
108835 AATTTAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 9 0.45
19 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (19 bp):
TTATTATATGATTAAGTAT
Found at i:109534 original size:22 final size:22
Alignment explanation
Indices: 109509--109552 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
109499 TATGGGATAG
109509 GGGACCTTTCTTTGAACTCACA
1 GGGACCTTTCTTTGAACTCACA
109531 GGGACCTTTCTTTGAACTCACA
1 GGGACCTTTCTTTGAACTCACA
109553 CCTTATGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (22 bp):
GGGACCTTTCTTTGAACTCACA
Found at i:114403 original size:39 final size:39
Alignment explanation
Indices: 114349--114426 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
114339 GACATTGAGA
*
114349 GTTGGGACATCTTGAAGGCTCACATCAG-CATGAAATAAT
1 GTTGGGACATCTTGAAAGCTCACATCAGACA-GAAATAAT
* * *
114388 GTTGGGGCATGTTGAAAGCTCATATCAGACAGAAATAAT
1 GTTGGGACATCTTGAAAGCTCACATCAGACAGAAATAAT
114427 CTATGTGGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (39 bp):
GTTGGGACATCTTGAAAGCTCACATCAGACAGAAATAAT
Found at i:116045 original size:88 final size:87
Alignment explanation
Indices: 115932--116101 Score: 261
Period size: 88 Copynumber: 1.9 Consensus size: 87
115922 GCAAGATCAA
* * * * *
115932 AATTCGCTCTCCACGAAAGAGTAGTGGAACGGATTTTTCAGCAAAGTATGAAATCTTCACGGAAG
1 AATTCGCTCTCCAAGAAAGAATAGTGGAAAGGATTTTTCAGCAAAGTATGAAACCTTCACAG-AG
*
115997 AGTAGTGAAGTAATCCAACCTCG
65 AATAGTGAAGTAATCCAACCTCG
116020 AATTCGCTCTCCATAG-AAGAATAGTGGAAAGGATTTTTCAGCAAAGTATGAAACCTTCACAGAG
1 AATTCGCTCTCCA-AGAAAGAATAGTGGAAAGGATTTTTCAGCAAAGTATGAAACCTTCACAGAG
116084 AATAGTGAAGTAATCCAA
65 AATAGTGAAGTAATCCAA
116102 TTGTGAGTCT
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
87 19 0.25
88 55 0.73
89 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (87 bp):
AATTCGCTCTCCAAGAAAGAATAGTGGAAAGGATTTTTCAGCAAAGTATGAAACCTTCACAGAGA
ATAGTGAAGTAATCCAACCTCG
Found at i:122401 original size:27 final size:27
Alignment explanation
Indices: 122344--122414 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
122334 AGGGCTTTGA
* *
122344 GGTATTTTGGGTCATTTTACACTTCAGG
1 GGTATTTT-GATCATTTTACACTTCAAG
*
122372 GGTATTTTGATCATTTTAC-CATTTAAG
1 GGTATTTTGATCATTTTACAC-TTCAAG
* *
122399 GGTATTATAATCATTT
1 GGTATTTTGATCATTT
122415 CCTTTAGTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.03
27 28 0.76
28 8 0.22
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.46
Consensus pattern (27 bp):
GGTATTTTGATCATTTTACACTTCAAG
Found at i:122443 original size:18 final size:17
Alignment explanation
Indices: 122412--122445 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
122402 ATTATAATCA
122412 TTTCCTTTAGTTCAGTC
1 TTTCCTTTAGTTCAGTC
*
122429 TTTCCATTTATTTCAGT
1 TTTCC-TTTAGTTCAGT
122446 TATTTCAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.21, G:0.09, T:0.56
Consensus pattern (17 bp):
TTTCCTTTAGTTCAGTC
Found at i:123165 original size:17 final size:17
Alignment explanation
Indices: 123134--123167 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
123124 CGTCAAAATA
*
123134 CATAAAATATGACTTTT
1 CATAAAATATAACTTTT
*
123151 CATAAAATTTAACTTTT
1 CATAAAATATAACTTTT
123168 TGGTTAAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (17 bp):
CATAAAATATAACTTTT
Found at i:123282 original size:13 final size:13
Alignment explanation
Indices: 123266--123310 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
123256 CAATCGGTGA
123266 ACTCAACAAGTTG
1 ACTCAACAAGTTG
* *
123279 ACTCAATTAGGTTG
1 ACTCAA-CAAGTTG
123293 ACTCAACAAGTTG
1 ACTCAACAAGTTG
123306 ACTCA
1 ACTCA
123311 GCTCGATCGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (13 bp):
ACTCAACAAGTTG
Found at i:123304 original size:27 final size:26
Alignment explanation
Indices: 123246--123310 Score: 96
Period size: 27 Copynumber: 2.5 Consensus size: 26
123236 TAACTCTGTT
*
123246 CAAGTTGACTCAATCGGTGAACTCAA
1 CAAGTTGACTCAATAGGTGAACTCAA
123272 CAAGTTGACTCAATTAGGTTG-ACTCAA
1 CAAGTTGACTCAA-TAGG-TGAACTCAA
123299 CAAGTTGACTCA
1 CAAGTTGACTCA
123311 GCTCGATCGG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 13 0.36
27 21 0.58
28 2 0.06
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (26 bp):
CAAGTTGACTCAATAGGTGAACTCAA
Found at i:127894 original size:21 final size:21
Alignment explanation
Indices: 127870--127915 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
127860 GTAGTTTTAC
127870 GCGCATTATCGGAGTGTGATG
1 GCGCATTATCGGAGTGTGATG
127891 GCGCATTATCGGAGTGTGATG
1 GCGCATTATCGGAGTGTGATG
127912 GCGC
1 GCGC
127916 GTGCAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.17, G:0.39, T:0.26
Consensus pattern (21 bp):
GCGCATTATCGGAGTGTGATG
Found at i:129364 original size:17 final size:18
Alignment explanation
Indices: 129337--129370 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
129327 TTAATATACT
129337 ATTTATAATTAATTTAAG
1 ATTTATAATTAATTTAAG
*
129355 ATTT-TAATTATTTTAA
1 ATTTATAATTAATTTAA
129371 ATTAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
ATTTATAATTAATTTAAG
Found at i:129396 original size:27 final size:29
Alignment explanation
Indices: 129327--129397 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 29
129317 GCTAAAAAAA
*
129327 TTAATATACTATTTATAATTAATTTAAGATT
1 TTAAT-TA-TATTTATAATTAAATTAAGATT
129358 TTAATTAT-TTTA-AATTAAATTAA-A-T
1 TTAATTATATTTATAATTAAATTAAGATT
*
129383 TTATTTTATATTTAT
1 TTA-ATTATATTTAT
129398 CTATTAAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
25 4 0.11
26 5 0.14
27 14 0.40
28 4 0.11
29 1 0.03
30 2 0.06
31 5 0.14
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (29 bp):
TTAATTATATTTATAATTAAATTAAGATT
Found at i:129621 original size:19 final size:21
Alignment explanation
Indices: 129588--129662 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 21
129578 GACTCGACCC
129588 AAAATAATATATTTAATTAA-
1 AAAATAATATATTTAATTAAT
* *
129608 AAAATATTAT-TTTATTTAAT
1 AAAATAATATATTTAATTAAT
**
129628 AAAAGTAA-GGATTTAATTTAAAT
1 AAAA-TAATATATTTAA-TT-AAT
129651 AAAATAATATAT
1 AAAATAATATAT
129663 AAAGGGTTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
19 8 0.20
20 13 0.32
21 6 0.15
22 5 0.12
23 9 0.22
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
AAAATAATATATTTAATTAAT
Found at i:131332 original size:42 final size:42
Alignment explanation
Indices: 131260--131349 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
131250 ATGGTTACGA
* * *
131260 ATGATTCATCACTTTTAATTTAAATAAAAAATATTGCAGTTG
1 ATGATTCATCACTTTTAATTTAAATAAAAAAAATTACAATTG
*
131302 ATGATTCATCATTTTTAATTTAAATAAAAAAAATTACAATTG
1 ATGATTCATCACTTTTAATTTAAATAAAAAAAATTACAATTG
131344 ATGATT
1 ATGATT
131350 AGATTATCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (42 bp):
ATGATTCATCACTTTTAATTTAAATAAAAAAAATTACAATTG
Found at i:132199 original size:31 final size:31
Alignment explanation
Indices: 132164--132223 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
132154 ATGATTTTAA
132164 AAAATT-AAAAGTTTAAATATTAAAACATATC
1 AAAATTGAAAA-TTTAAATATTAAAACATATC
*
132195 AAAATTGATAATTTAAATATTAAAACATA
1 AAAATTGAAAATTTAAATATTAAAACATA
132224 ATTTAAATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.33
Consensus pattern (31 bp):
AAAATTGAAAATTTAAATATTAAAACATATC
Found at i:132226 original size:19 final size:19
Alignment explanation
Indices: 132202--132238 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
132192 ATCAAAATTG
*
132202 ATAATTTAAATATTAAAAC
1 ATAATTTAAATACTAAAAC
132221 ATAATTTAAATACTAAAA
1 ATAATTTAAATACTAAAA
132239 ATTAAAAGTT
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:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAATTTAAATACTAAAAC
Found at i:134589 original size:17 final size:17
Alignment explanation
Indices: 134564--134602 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
134554 CCCCATAAAA
*
134564 ATTTAAATTTATCATAT
1 ATTTTAATTTATCATAT
* *
134581 ATTTTAATTTTTTATAT
1 ATTTTAATTTATCATAT
134598 ATTTT
1 ATTTT
134603 CTATTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTAATTTATCATAT
Found at i:146881 original size:6 final size:6
Alignment explanation
Indices: 146865--146896 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
146855 TCTCGTCTCG
146865 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
146897 GATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:147061 original size:42 final size:42
Alignment explanation
Indices: 146979--147061 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
146969 CGTGATTTTG
* *
146979 GACTATCGCAACGAATTTAGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTAGAATAAATCGCAACACAAACTTC
*
147021 GACTATCGCAACGAATTTGGAATAAATCGCAACACAAACTT
1 GACTATCGCAACGAATTTAGAATAAATCGCAACACAAACTT
147062 GGAATAAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTAGAATAAATCGCAACACAAACTTC
Found at i:147067 original size:23 final size:23
Alignment explanation
Indices: 146989--147214 Score: 176
Period size: 23 Copynumber: 10.5 Consensus size: 23
146979 GACTATCGCA
* *
146989 ACGAATTTAGAATAAATCGCAAC
1 ACGAACTTGGAATAAATCGCAAC
* * *
147012 GCGAACTTCGACT--ATCGC-A-
1 ACGAACTTGGAATAAATCGCAAC
*
147031 ACGAATTTGGAATAAATCGCAAC
1 ACGAACTTGGAATAAATCGCAAC
*
147054 ACAAACTTGGAATAAATCGCAAC
1 ACGAACTTGGAATAAATCGCAAC
* * *
147077 ACGAACTTCGACT--ATCAC-A-
1 ACGAACTTGGAATAAATCGCAAC
* *
147096 ACGAATTTGGAATAAATCGTAAC
1 ACGAACTTGGAATAAATCGCAAC
*
147119 GCGAACTTGGAATAAATCGC-A-
1 ACGAACTTGGAATAAATCGCAAC
*
147140 A-GAATTTGGAATAAATCGCAAC
1 ACGAACTTGGAATAAATCGCAAC
* * *
147162 GCGAACTTCGACT--ATCGC-A-
1 ACGAACTTGGAATAAATCGCAAC
*
147181 ACGAACTTTGAATAAATCGCAAC
1 ACGAACTTGGAATAAATCGCAAC
*
147204 GCGAACTTGGA
1 ACGAACTTGGA
147215 CTATCGCAAT
Statistics
Matches: 155, Mismatches: 33, Indels: 30
0.71 0.15 0.14
Matches are distributed among these distances:
19 29 0.19
20 20 0.13
21 28 0.18
22 4 0.03
23 74 0.48
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (23 bp):
ACGAACTTGGAATAAATCGCAAC
Found at i:147075 original size:65 final size:65
Alignment explanation
Indices: 146989--147223 Score: 250
Period size: 65 Copynumber: 3.7 Consensus size: 65
146979 GACTATCGCA
* *
146989 ACGAATTTAGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAAC
1 ACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAAC
* * * *
147054 ACAAACTTGGAATAAATCGCAACACGAACTTCGACTATCACAACGAATTTGGAATAAATCGTAAC
1 ACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAAC
* * * * * * *
147119 GCGAACTTGGAATAAATCGCAA---GAATTTGGAATAAATCGCAACGCGAACTTCGACT--ATCG
1 ACGAACTTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAA--CGAATTTGGAATAAATCG
147179 C-A-
62 CAAC
* *
147181 ACGAACTTTGAATAAATCGCAACGCGAACTTGGACTATCGCAA
1 ACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
147224 TGCGAATATG
Statistics
Matches: 143, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
62 28 0.20
63 8 0.06
64 10 0.07
65 88 0.62
66 9 0.06
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (65 bp):
ACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAAC
Found at i:147109 original size:42 final size:42
Alignment explanation
Indices: 147060--147223 Score: 233
Period size: 42 Copynumber: 3.9 Consensus size: 42
147050 CAACACAAAC
* *
147060 TTGGAATAAATCGCAACACGAACTTCGACTATCACAACGAAT
1 TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAT
* * *
147102 TTGGAATAAATCGTAACGCGAACTTGGAATAAATCGCAA-GAAT
1 TTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAACGAAT
147145 TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACT
1 TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAA-T
*
147188 TT-GAATAAATCGCAACGCGAACTTGGACTATCGCAA
1 TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
147224 TGCGAATATG
Statistics
Matches: 109, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
41 7 0.06
42 62 0.57
43 34 0.31
44 6 0.06
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.22
Consensus pattern (42 bp):
TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAT
Found at i:147167 original size:85 final size:88
Alignment explanation
Indices: 147025--147214 Score: 275
Period size: 85 Copynumber: 2.2 Consensus size: 88
147015 AACTTCGACT
*
147025 ATCGCAA--CGAATTTGGAATAAATCGCAACACAAACTTGGAATAAATCGCAACACGAACTTCGA
1 ATCGCAACGCGAACTTGGAATAAATCGCAACACAAACTTGGAATAAATCGCAACACGAACTTCGA
147088 CTATCACAACGAA-TTTGGAATAA
66 CTATCACAACGAACTTT-GAATAA
* * * *
147111 ATCGTAACGCGAACTTGGAATAAATCGC-A-A-GAATTTGGAATAAATCGCAACGCGAACTTCGA
1 ATCGCAACGCGAACTTGGAATAAATCGCAACACAAACTTGGAATAAATCGCAACACGAACTTCGA
*
147173 CTATCGCAACGAACTTTGAATAA
66 CTATCACAACGAACTTTGAATAA
147196 ATCGCAACGCGAACTTGGA
1 ATCGCAACGCGAACTTGGA
147215 CTATCGCAAT
Statistics
Matches: 94, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
85 65 0.69
86 10 0.11
87 1 0.01
88 18 0.19
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (88 bp):
ATCGCAACGCGAACTTGGAATAAATCGCAACACAAACTTGGAATAAATCGCAACACGAACTTCGA
CTATCACAACGAACTTTGAATAA
Found at i:153908 original size:19 final size:20
Alignment explanation
Indices: 153871--153915 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
153861 TTAATTGCGA
* *
153871 AAATTAAAAAATTTAGATTG
1 AAATTAAAAAATCTAGATTC
*
153891 AAATTTAAAAATCT-GATTC
1 AAATTAAAAAATCTAGATTC
153910 AAATTA
1 AAATTA
153916 CTTACCTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (20 bp):
AAATTAAAAAATCTAGATTC
Found at i:154185 original size:3 final size:3
Alignment explanation
Indices: 154174--154234 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
154164 TTTTTTATCG
** *
154174 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
154219 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
154235 CATATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:154229 original size:29 final size:30
Alignment explanation
Indices: 154167--154229 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
154157 TCCGGTTTTT
*
154167 TTTATCGTTATTTTATTATTATTATTATTA
1 TTTATCGTTATCTTATTATTATTATTATTA
154197 -TTATCGTTATCTTATTATT-TTATTATTA
1 TTTATCGTTATCTTATTATTATTATTATTA
154225 TTTAT
1 TTTAT
154230 TATTACATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (30 bp):
TTTATCGTTATCTTATTATTATTATTATTA
Found at i:154240 original size:28 final size:28
Alignment explanation
Indices: 154180--154245 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
154170 ATCGTTATTT
* *
154180 TATTATTATTATTATTATTATCGTTATCT
1 TATTATT-TTATTATTATTATCATTATCA
*
154209 TATTATTTTATTATTATTTATTATTA-CA
1 TATTATTTTATTATTA-TTATCATTATCA
*
154237 TATTTTTTT
1 TATTATTTT
154246 TGCAGGCCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (28 bp):
TATTATTTTATTATTATTATCATTATCA
Found at i:161975 original size:36 final size:35
Alignment explanation
Indices: 161892--162021 Score: 106
Period size: 36 Copynumber: 3.7 Consensus size: 35
161882 AAAAAATAAT
* *
161892 AACAAAGTTGATCTCACTTGAGATC-GTTTCTC-AAA
1 AACAAATTTG-TCTCACTTGAGA-CAATTTCTCTAAA
* *
161927 AACGAACTTTGTCTCGCTTGAGACAATTTCTCTAAA
1 AAC-AAATTTGTCTCACTTGAGACAATTTCTCTAAA
* * *
161963 AACAAATGTTGTCTCATTTGAGACTATATCT-T-AA
1 AACAAAT-TTGTCTCACTTGAGACAATTTCTCTAAA
* *
161997 AGCAAATTTCGTCTCGCTTGAGACA
1 AACAAATTT-GTCTCACTTGAGACA
162022 TCATTTTCTC
Statistics
Matches: 77, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
33 2 0.03
34 21 0.27
35 24 0.31
36 30 0.39
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (35 bp):
AACAAATTTGTCTCACTTGAGACAATTTCTCTAAA
Found at i:162334 original size:59 final size:58
Alignment explanation
Indices: 162272--162383 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 58
162262 TTTCTCTTGA
162272 AAAAAATCTTTGAG-TTAGTTCCTTTT-AAATAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAAATCTTTGAGATT-GTTCCTTTTGAAA-AAAATCTTGGAGTTTGTTCCTTTTGAAT
* * *
162330 AAAAAATCTTTGAGATTGTTTCTTTTGGAAAAAAATCTTTGAGTTTGTTTCTTT
1 AAAAAATCTTTGAGATTGTTCCTTTT-GAAAAAAATCTTGGAGTTTGTTCCTTT
162384 GGAAACAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
58 22 0.46
59 23 0.48
60 3 0.06
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.46
Consensus pattern (58 bp):
AAAAAATCTTTGAGATTGTTCCTTTTGAAAAAAATCTTGGAGTTTGTTCCTTTTGAAT
Found at i:162372 original size:29 final size:29
Alignment explanation
Indices: 162261--162398 Score: 151
Period size: 28 Copynumber: 4.8 Consensus size: 29
162251 TCTTGAGACA
* *
162261 GTTTCTCTT-GAAAAAAATCTTTGAGTTA
1 GTTTCTTTTGGAAAAAAATCTTTGAGTTT
* *
162289 GTTCCTTTT--AAATAAAATCTTGGAGTTT
1 GTTTCTTTTGGAAA-AAAATCTTTGAGTTT
* * *
162317 GTTCCTTTTGAATAAAAAATCTTTGAGATT
1 GTTTCTTTTGGA-AAAAAATCTTTGAGTTT
162347 GTTTCTTTTGGAAAAAAATCTTTGAGTTT
1 GTTTCTTTTGGAAAAAAATCTTTGAGTTT
162376 GTTTC-TTTGGAAACAAAAT-TTTG
1 GTTTCTTTTGGAAA-AAAATCTTTG
162399 TCTCTCTTAA
Statistics
Matches: 96, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
27 3 0.03
28 41 0.43
29 26 0.27
30 24 0.25
31 2 0.02
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.45
Consensus pattern (29 bp):
GTTTCTTTTGGAAAAAAATCTTTGAGTTT
Found at i:162426 original size:37 final size:37
Alignment explanation
Indices: 162376--162492 Score: 115
Period size: 37 Copynumber: 3.4 Consensus size: 37
162366 CTTTGAGTTT
162376 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* * * *
162413 GTTTCTTTTGAAACAAAA------ATCT-TTGAG-TCT
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT-A
162443 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* *
162480 ATTTCTTTTGAAA
1 GTTTCTTTGGAAA
162493 AAATCTTTGA
Statistics
Matches: 61, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
29 1 0.02
30 21 0.34
31 3 0.05
36 3 0.05
37 32 0.52
38 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (37 bp):
GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
Found at i:162548 original size:63 final size:65
Alignment explanation
Indices: 162342--162573 Score: 274
Period size: 67 Copynumber: 3.6 Consensus size: 65
162332 AAAATCTTTG
* * *
162342 AGATTGTTTCTTTTGGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTT
1 AGATAGTTTCTTTT-GAAAAAAATCTTTGAATCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTT
162407 A
65 A
*
162408 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTTG-AA-AAAAATCTTTGAATCTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
162473 TA
64 TA
* * *
162475 AGATAATTTCTTTTG-AAAAAATCTTTGAATCTGTTT-TTCT-TAAA-ATAAATTTTGTATCTCT
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAATCTGTTTCTT-TGGAAACA-AAATTTTGTCTCTCT
*
162536 TG
64 TA
* * ** *
162538 AGACAGTTTCTCTTGAAGTAAATCTTTGAATATGTT
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAATCTGTT
162574 CATTTTGAAA
Statistics
Matches: 148, Mismatches: 13, Indels: 12
0.86 0.08 0.07
Matches are distributed among these distances:
62 1 0.01
63 32 0.22
64 37 0.25
65 2 0.01
66 15 0.10
67 61 0.41
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (65 bp):
AGATAGTTTCTTTTGAAAAAAATCTTTGAATCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
Found at i:162749 original size:63 final size:62
Alignment explanation
Indices: 162651--162768 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 62
162641 GAAACAAAAC
* *
162651 AAACATCTTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCATTCGAGACAGTTTTCCTTT
1 AAACATCTTTGAGATCATTTCCATTTAAACAAATTTTGTCTCATTCGAGACAGTTTTCCTTT
* *
162713 AAACAATCTTTGAG-TCATTT-CATTTGAAACAAAATTTTGTCTCTTTTGAGACAGTT
1 AAAC-ATCTTTGAGATCATTTCCATTT-AAAC-AAATTTTGTCTCATTCGAGACAGTT
162769 GCTTTTGAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
61 4 0.08
62 14 0.29
63 31 0.63
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.42
Consensus pattern (62 bp):
AAACATCTTTGAGATCATTTCCATTTAAACAAATTTTGTCTCATTCGAGACAGTTTTCCTTT
Found at i:163056 original size:40 final size:41
Alignment explanation
Indices: 162997--163235 Score: 157
Period size: 40 Copynumber: 5.7 Consensus size: 41
162987 TCAGCCGTCC
* * *
162997 TCATCATGTAGGAACCGTGTCATCCCCAG-ACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCATCCCCAGAACCAGATCTCT
* * * *
163037 TCATCACGTATGAGTCGTGTCA-CCCTAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATCCCCAG--AACCAGATC-TCT
* * * * *
163079 TCATCACGTAGGAACCGTGTTATCACCTTTAGATAGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTCATC-CC--CAGA-A-CCAGATCTCT
*
163125 TCATCACGTATGAGTCGTGTCATTCCCC-G-ACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCA-TCCCCAGAACCAGATCTCT
* *
163165 TCATCACGTATGAGCCGTGTCA-CCCTTAGATGACCAGACCTCT
1 TCATCACGTATGAGCCGTGTCATCCC-CAGA--ACCAGATCTCT
** * *
163208 TCATTGCGTATGAGCAGTGTCGTCCCCA
1 TCATCACGTATGAGCCGTGTCATCCCCA
163236 CCAACAGAAC
Statistics
Matches: 154, Mismatches: 27, Indels: 33
0.72 0.13 0.15
Matches are distributed among these distances:
38 3 0.02
39 5 0.03
40 49 0.32
41 2 0.01
42 25 0.16
43 31 0.20
44 6 0.04
45 1 0.01
46 29 0.19
47 3 0.02
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (41 bp):
TCATCACGTATGAGCCGTGTCATCCCCAGAACCAGATCTCT
Found at i:163081 original size:82 final size:86
Alignment explanation
Indices: 162988--163146 Score: 236
Period size: 82 Copynumber: 1.9 Consensus size: 86
162978 TTTAGATGGT
* *
162988 CAGCCGTCCTCATCATGTAGGAACCGTGTCATC-CC-CAG-A-CCAGATCTCTTCATCACGTATG
1 CAGCCGTCCTCATCACGTAGGAACCGTGTCATCACCTCAGAAGCCAGAACTCTTCATCACGTATG
163049 AGTCGTGTCACCCTAGATAAC
66 AGTCGTGTCACCCTAGATAAC
* *
163070 CAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATAGCCAGAACTCTTCATCACGTA
1 CAGCCGTCCTCATCACGTAGGAACCGTGTCATCACC-TCAGA-AGCCAGAACTCTTCATCACGTA
163135 TGAGTCGTGTCA
64 TGAGTCGTGTCA
163147 TTCCCCGACC
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
82 31 0.46
83 2 0.03
85 2 0.03
87 1 0.01
88 31 0.46
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (86 bp):
CAGCCGTCCTCATCACGTAGGAACCGTGTCATCACCTCAGAAGCCAGAACTCTTCATCACGTATG
AGTCGTGTCACCCTAGATAAC
Found at i:163100 original size:128 final size:129
Alignment explanation
Indices: 162846--163201 Score: 513
Period size: 128 Copynumber: 2.8 Consensus size: 129
162836 AACCATAACT
* *
162846 CCTTTAGAT-GACCAGATCTCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCCTC
1 CCTTTAGATAG-CCAGAACTCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTC
* *
162910 ATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATC
65 ATCACGTATGAGCCGTGTC-ACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATC
162975 A
129 A
* * * * * *
162976 CCTTTAGATGGTCAG-CCGTCCTCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTC
1 CCTTTAGATAGCCAGAAC-TCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTC
* *
163039 ATCACGTATGAGTCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
65 ATCACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCA
* *
163104 CCTTTAGATAGCCAGAACTCTTCATCACGTATGAGTCGTGTCATTCCCC-GACCAGATCTCTTCA
1 CCTTTAGATAGCCAGAACTCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTCA
*
163168 TCACGTATGAGCCGTGTCACCCTTAGATGACCAG
66 TCACGTATGAGCCGTGTCACCC-TAGATAACCAG
163202 ACCTCTTCAT
Statistics
Matches: 201, Mismatches: 20, Indels: 11
0.87 0.09 0.05
Matches are distributed among these distances:
128 113 0.56
129 53 0.26
130 34 0.17
131 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (129 bp):
CCTTTAGATAGCCAGAACTCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTCA
TCACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCA
Found at i:163134 original size:46 final size:45
Alignment explanation
Indices: 162905--163118 Score: 171
Period size: 46 Copynumber: 4.9 Consensus size: 45
162895 AGACCAGATC
* * * *
162905 TCCTCATCACGTAGGAGCCGTGTCA--ACCATAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTTATCACCTTAGATAGCCAGCCG
* * *
162948 TCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGTCAGCCG
1 TCCTCATCACGTAGGAACCGTGTTATCACC-TTAGATAGCCAGCCG
* * * *
162994 TCCTCATCATGTAGGAACCGTGTCATC-CC-CAG--A-CCAGATC-
1 TCCTCATCACGTAGGAACCGTGTTATCACCTTAGATAGCCAG-CCG
* * ** * *
163034 TCTTCATCACGTATGAGTCGTG---TCACCCTAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTTATCACCTTAGATAGCCAGCCG
163076 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATAGCCAG
1 TCCTCATCACGTAGGAACCGTGTTATCACC-TTAGATAGCCAG
163119 AACTCTTCAT
Statistics
Matches: 130, Mismatches: 27, Indels: 25
0.71 0.15 0.14
Matches are distributed among these distances:
37 2 0.02
38 2 0.02
39 2 0.02
40 20 0.15
41 3 0.02
42 22 0.17
43 24 0.18
45 10 0.08
46 45 0.35
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (45 bp):
TCCTCATCACGTAGGAACCGTGTTATCACCTTAGATAGCCAGCCG
Found at i:163396 original size:3 final size:3
Alignment explanation
Indices: 163385--163445 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
163375 TTTTTTATCG
** *
163385 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
163430 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
163446 CATATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:163440 original size:29 final size:30
Alignment explanation
Indices: 163378--163440 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
163368 TCCGGTTTTT
*
163378 TTTATCGTTATTTTATTATTATTATTATTA
1 TTTATCGTTATCTTATTATTATTATTATTA
163408 -TTATCGTTATCTTATTATT-TTATTATTA
1 TTTATCGTTATCTTATTATTATTATTATTA
163436 TTTAT
1 TTTAT
163441 TATTACATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (30 bp):
TTTATCGTTATCTTATTATTATTATTATTA
Found at i:163451 original size:28 final size:28
Alignment explanation
Indices: 163391--163456 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
163381 ATCGTTATTT
* *
163391 TATTATTATTATTATTATTATCGTTATCT
1 TATTATT-TTATTATTATTATCATTATCA
*
163420 TATTATTTTATTATTATTTATTATTA-CA
1 TATTATTTTATTATTA-TTATCATTATCA
*
163448 TATTTTTTT
1 TATTATTTT
163457 TGCAGGCCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (28 bp):
TATTATTTTATTATTATTATCATTATCA
Found at i:167429 original size:23 final size:23
Alignment explanation
Indices: 167398--167461 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
167388 GCTATATAAT
* * **
167398 TATAGTATATAACATAGTATGTA
1 TATATTATATAACATAATACATA
167421 TATATTATATAACATAATACATA
1 TATATTATATAACATAATACATA
* *
167444 TACATTATATACCATAAT
1 TATATTATATAACATAAT
167462 TAATAACACA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (23 bp):
TATATTATATAACATAATACATA
Found at i:168569 original size:106 final size:106
Alignment explanation
Indices: 168397--168976 Score: 901
Period size: 106 Copynumber: 5.5 Consensus size: 106
168387 TGCTGTTTCA
* * * * *
168397 AGTCCAATATCATTCGCCGTGAAGTTGAAATTAGATCTGAAACTAGAAAGTTGTTTGTTGACAAC
1 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAAC
* *
168462 CAATCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGACTTG
66 CAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTG
* * *
168503 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATTTGAAACTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAAC
* *
168568 CAATCGCCCCTTCGTTGTGAAGTTGAGTTTGTGTTGTCTTG
66 CAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTG
*
168609 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAAC
* *
168674 CAGTCGCCCCTTCATTGTCAAGTTGAGCTTGTGTTGTCTTG
66 CAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTG
168715 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAAC
* *
168780 CAGTCACCCATTCGTTGTGAAGTTGAGCTTGTGTTGTCTTG
66 CAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTG
* * *
168821 AGTCTAATATTC-TTCACTGTGAAGTTGAAATTGGCTCTGAAACTGAGAAGTTGTTTGTTGACAA
1 AGTCCAATA-TCATTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAA
* * * *
168885 CCAGTCGCCCTTTCGTTATGAAGTTGAGCTTGTTTTGTCTTA
65 CCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTG
* * *
168927 AGTCCAATATTATTCGTTGTGAAGTTGAAATTGGCTCTAAAACTGGGAAG
1 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAG
168977 CCCTTTCGTC
Statistics
Matches: 439, Mismatches: 33, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
105 1 0.00
106 436 0.99
107 2 0.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (106 bp):
AGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAAC
CAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTG
Found at i:171275 original size:18 final size:20
Alignment explanation
Indices: 171248--171285 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
171238 AAGAGACAAA
171248 AATATCTTGA-TAG-CTTCT
1 AATATCTTGACTAGTCTTCT
*
171266 AATATGTTGACTAGTCTTCT
1 AATATCTTGACTAGTCTTCT
171286 GCCTTCGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (20 bp):
AATATCTTGACTAGTCTTCT
Found at i:191612 original size:19 final size:20
Alignment explanation
Indices: 191588--191625 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
191578 AAAACATTCA
*
191588 AACAAACAAGA-AAAACAAC
1 AACAAAAAAGAGAAAACAAC
191607 AACAAAAAAGAGAAAACAA
1 AACAAAAAAGAGAAAACAA
191626 GATTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.76, C:0.16, G:0.08, T:0.00
Consensus pattern (20 bp):
AACAAAAAAGAGAAAACAAC
Found at i:197184 original size:3 final size:3
Alignment explanation
Indices: 197176--197255 Score: 87
Period size: 3 Copynumber: 27.7 Consensus size: 3
197166 TCCGAGTTGA
* *
197176 TAT TAT TA- TAT TAT TAC TAT TAT TAT TAT TA- TAT TAT TA- TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
197221 TA- TAT TAT TAT ATAT TAA TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA
197256 AATAATATTA
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
2 8 0.12
3 54 0.83
4 3 0.05
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:197188 original size:8 final size:8
Alignment explanation
Indices: 197175--197255 Score: 105
Period size: 8 Copynumber: 10.1 Consensus size: 8
197165 GTCCGAGTTG
197175 ATATTATT
1 ATATTATT
197183 ATATTATT
1 ATATTATT
197191 ACTATTA-T
1 A-TATTATT
197199 -TATTATT
1 ATATTATT
197206 ATATTATT
1 ATATTATT
*
197214 ATATTACT
1 ATATTATT
197222 ATATTATT
1 ATATTATT
197230 ATA-TATT
1 ATATTATT
197237 AATATTATT
1 -ATATTATT
197246 AATATTATT
1 -ATATTATT
197255 A
1 A
197256 AATAATATTA
Statistics
Matches: 66, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
6 5 0.08
7 5 0.08
8 38 0.58
9 18 0.27
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (8 bp):
ATATTATT
Found at i:197264 original size:46 final size:47
Alignment explanation
Indices: 197175--197266 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 47
197165 GTCCGAGTTG
* * * *
197175 ATATTATTATATTATTACTATTATTATTATTATATTATTATATTACT
1 ATATTATTATATTATTAATATTATTAATATTATATAATAATATTACT
197222 ATATTATTATA-TATTAATATTATTAATATTAT-TAAATAATATTAC
1 ATATTATTATATTATTAATATTATTAATATTATAT-AATAATATTAC
197267 AAAATCGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 1 0.03
46 28 0.70
47 11 0.28
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (47 bp):
ATATTATTATATTATTAATATTATTAATATTATATAATAATATTACT
Found at i:204838 original size:44 final size:45
Alignment explanation
Indices: 204772--205048 Score: 416
Period size: 44 Copynumber: 6.2 Consensus size: 45
204762 GTGCAATATT
*
204772 TTACCATTTAATACCATAAGCTCGTAAGATTATTTTACCAATACAC
1 TTACCATTTAA-ACCATAAGCTCGTAAGCTTATTTTACCAATACAC
204818 TTACCATTT-AACCATAAGCTCGTAAGCTTATTTTACCAATACAC
1 TTACCATTTAAACCATAAGCTCGTAAGCTTATTTTACCAATACAC
*
204862 TTACCATTTAATACCATAAGCTCGTAAGCTTATTTTA-CAATATAC
1 TTACCATTTAA-ACCATAAGCTCGTAAGCTTATTTTACCAATACAC
* ***
204907 TTGCCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATACAC
1 TTACCATTTAAACCATAAGCTCGTAAGCTTATTTTACCAATACAC
*
204952 TTACCATTT-AACCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTAAACCATAAGCTCGTAAGCTTATTTTACCAATACAC
***
204996 TTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATACAC
1 TTACCATTTAAACCATAAGCTCGTAAGCTTATTTTACCAATACAC
*
205041 TTGCCATT
1 TTACCATT
205049 ATTCCATAGC
Statistics
Matches: 212, Mismatches: 15, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
44 107 0.50
45 71 0.33
46 34 0.16
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (45 bp):
TTACCATTTAAACCATAAGCTCGTAAGCTTATTTTACCAATACAC
Found at i:204895 original size:90 final size:91
Alignment explanation
Indices: 204772--205048 Score: 472
Period size: 90 Copynumber: 3.1 Consensus size: 91
204762 GTGCAATATT
* * **
204772 TTACCATTTAATACCATAAGCTCGTAAGATTATTTTACCAATACACTTACCATTT-AACCATAAG
1 TTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAG
204836 CTCGTAAGCTTATTTTACCAATACAC
66 CTCGTAAGCTTATTTTACCAATACAC
*
204862 TTACCATTTAATACCATAAGCTCGTAAGCTTATTTTA-CAATATACTTGCCATTTGTTCCATAAG
1 TTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAG
204926 CTCGTAAGCTTATTTTACCAATACAC
66 CTCGTAAGCTTATTTTACCAATACAC
204952 TTACCATTT-A-ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAG
1 TTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAG
205015 CTCGTAAGCTTATTTTACCAATACAC
66 CTCGTAAGCTTATTTTACCAATACAC
*
205041 TTGCCATT
1 TTACCATT
205049 ATTCCATAGC
Statistics
Matches: 178, Mismatches: 7, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
88 25 0.14
89 75 0.42
90 78 0.44
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (91 bp):
TTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAG
CTCGTAAGCTTATTTTACCAATACAC
Found at i:205037 original size:134 final size:133
Alignment explanation
Indices: 204785--205056 Score: 465
Period size: 134 Copynumber: 2.0 Consensus size: 133
204775 CCATTTAATA
204785 CCATAAGCTCGTAAGATTATTTTACCAATACACTTACCATTTAACCATAAGCTCGTAAGCTTATT
1 CCATAAGCTCGTAAGATTATTTTACCAATACACTTACCATTTAACCATAAGCTCGTAAGCTTATT
*
204850 TTACCAATACACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACAATATACTTGCCATT
66 TTACCAATACACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACAATACACTTGCCA-T
*
204915 TGTT
130 TATT
*
204919 CCATAAGCTCGTAAGCTTATTTTACCAATACACTTACCATTTAACCATAAGCTCGTAAGCTTATT
1 CCATAAGCTCGTAAGATTATTTTACCAATACACTTACCATTTAACCATAAGCTCGTAAGCTTATT
* * *
204984 TTACCAATATACTTACCATTT-GTTCCATAAGCTCGTAAGCTTATTTTACCAATACACTTGCCAT
66 TTACCAATACACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTA-CAATACACTTGCCAT
205048 TATT
130 TATT
205052 CCATA
1 CCATA
205057 GCCATAAACC
Statistics
Matches: 131, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
133 34 0.26
134 97 0.74
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (133 bp):
CCATAAGCTCGTAAGATTATTTTACCAATACACTTACCATTTAACCATAAGCTCGTAAGCTTATT
TTACCAATACACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACAATACACTTGCCATT
ATT
Found at i:205056 original size:89 final size:89
Alignment explanation
Indices: 204772--205056 Score: 441
Period size: 89 Copynumber: 3.2 Consensus size: 89
204762 GTGCAATATT
* * **
204772 TTACCATTTAATACCATAAGCTCGTAAGATTATTTTACCAATACACTTACCATTT-AACCATAAG
1 TTACCA-TT-ATACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAG
204836 CTCGTAAGCTTATTTTACCAATACAC
64 CTCGTAAGCTTATTTTACCAATACAC
*
204862 TTACCATTTAATACCATAAGCTCGTAAGCTTATTTTA-CAATATACTTGCCATTTGTTCCATAAG
1 TTACCA-TT-ATACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAG
204926 CTCGTAAGCTTATTTTACCAATACAC
64 CTCGTAAGCTTATTTTACCAATACAC
204952 TTACCATT-TAACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAGC
1 TTACCATTAT-ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAGC
205016 TCGTAAGCTTATTTTACCAATACAC
65 TCGTAAGCTTATTTTACCAATACAC
* *
205041 TTGCCATTATTCCATA
1 TTACCATTATACCATA
205057 GCCATAAACC
Statistics
Matches: 183, Mismatches: 8, Indels: 9
0.92 0.04 0.05
Matches are distributed among these distances:
87 1 0.01
88 25 0.14
89 81 0.44
90 76 0.42
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (89 bp):
TTACCATTATACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTTCCATAAGCT
CGTAAGCTTATTTTACCAATACAC
Found at i:207415 original size:43 final size:42
Alignment explanation
Indices: 207367--207452 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 42
207357 CATAAAAGGT
* * *
207367 TGGGGTATGCTGAAGGCCCATTTTCAGTCAAAAATAATCTATG
1 TGGGGTATGCCGAAGGCCCATTTT-AGACAAAAATAATCCATG
*
207410 TGGGGTATGCCGAAGGCCCATTTTAGACAAAAATGATCCATG
1 TGGGGTATGCCGAAGGCCCATTTTAGACAAAAATAATCCATG
207452 T
1 T
207453 AGGATATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 16 0.41
43 23 0.59
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (42 bp):
TGGGGTATGCCGAAGGCCCATTTTAGACAAAAATAATCCATG
Found at i:208942 original size:120 final size:119
Alignment explanation
Indices: 208693--209097 Score: 652
Period size: 120 Copynumber: 3.4 Consensus size: 119
208683 TTTCCCACGA
*
208693 ATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAAGATGTTTTCACATGAAAATGAGGA
1 ATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAAGATGTTTTCGCATGAAAATGAGGA
* *
208758 AGCAA-TTTCAAATTTTCTTATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
66 AGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
**
208811 ATTTGTAAAACCTCTAGGTCATCTGTAAAACCTCAGGGTAAGATGTTTTCGCATGAAAATGAGGA
1 ATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAAGATGTTTTCGCATGAAAATGAGGA
*
208876 AACAATTTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
66 AGCAA-TTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
* * *
208931 ATTTGTAAAACCTTCGGGTCATCTGTAAAACCTCAAGGTAGGATGTTTTCGCATGAAAATGAGGA
1 ATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAAGATGTTTTCGCATGAAAATGAGGA
* *
208996 AGCGATTTTCAAAGTTTCTCATTTAATGTTATAGAAAATTAAATCCTCCGGGTG
66 AGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
* * * *
209050 ATTTGTAAAGCCTCCGGGTCACCTGTAAAACCTTA-GGTATGATGTTTT
1 ATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAAGATGTTTT
209098 TAATTTTGAT
Statistics
Matches: 266, Mismatches: 19, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
118 78 0.29
119 79 0.30
120 109 0.41
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (119 bp):
ATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAAGATGTTTTCGCATGAAAATGAGGA
AGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
Found at i:209238 original size:3 final size:3
Alignment explanation
Indices: 209230--209312 Score: 93
Period size: 3 Copynumber: 28.7 Consensus size: 3
209220 TCCGAGTTGA
* *
209230 TAT TAT TA- TAT TAT TAC TAT TAT TA- TAT TAT TA- TAT TAT TAC TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
209274 TAT TAT TAT TAT TAT ATAT TAA TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA
209313 AATAATATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
2 8 0.12
3 57 0.84
4 3 0.04
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:209263 original size:25 final size:25
Alignment explanation
Indices: 209229--209312 Score: 127
Period size: 25 Copynumber: 3.4 Consensus size: 25
209219 GTCCGAGTTG
209229 ATATTATTATATTATTACTATTATT
1 ATATTATTATATTATTACTATTATT
209254 ATATTATTATATTATTACTA-TATT
1 ATATTATTATATTATTACTATTATT
*
209278 ATTATTATTATA-TATTAATATTATT
1 A-TATTATTATATTATTACTATTATT
209303 AATATTATTA
1 -ATATTATTA
209313 AATAATATTA
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
24 12 0.22
25 42 0.76
26 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATTATTATATTATTACTATTATT
Found at i:209318 original size:22 final size:22
Alignment explanation
Indices: 209254--209322 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
209244 TACTATTATT
*
209254 ATATTATT-ATATTATT-ACT-
1 ATATTATTAATATTATTAAATA
* *
209273 ATATTATTATTATTA-TATATTA
1 ATATTATTAATATTATTA-AATA
209295 ATATTATTAATATTATTAAATA
1 ATATTATTAATATTATTAAATA
209317 ATATTA
1 ATATTA
209323 CAAAATCAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
19 9 0.22
20 5 0.12
21 2 0.05
22 23 0.56
23 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATTATTAATATTATTAAATA
Found at i:212600 original size:36 final size:35
Alignment explanation
Indices: 212560--212684 Score: 111
Period size: 36 Copynumber: 3.7 Consensus size: 35
212550 TTGACAAACT
*
212560 TTGAGACTGTTTCTCTTGAAACAAATGTTGTCTCTC
1 TTGAGACAGTTTCTCTTGAAACAAA-GTTGTCTCTC
212596 TTGAGACAGTTTCTCTTGAAACACAA------TCT-
1 TTGAGACAGTTTCTCTTGAAACA-AAGTTGTCTCTC
* ** * *
212625 TTGAGTCTTTTTCTCTTAAAACAAAAGTTTGTCTTTC
1 TTGAGACAGTTTCTCTTGAAAC-AAAG-TTGTCTCTC
212662 TTGAGACAGTTTCTCTTGAAACA
1 TTGAGACAGTTTCTCTTGAAACA
212685 CAATTTTGAG
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
29 20 0.29
30 4 0.06
36 25 0.36
37 20 0.29
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (35 bp):
TTGAGACAGTTTCTCTTGAAACAAAGTTGTCTCTC
Found at i:212675 original size:66 final size:66
Alignment explanation
Indices: 212553--212781 Score: 295
Period size: 65 Copynumber: 3.5 Consensus size: 66
212543 AACAAAATTG
* * * * * *
212553 ACAAACTTTGAGACTGTTTCTCTTGAAACAAATG-TTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 ACAATCTTTGAGTCTTTTTCTCTTAAAACAAAAGTTTGTCTTTCTTGAGACAGTTTCTCTTGAAA
212617 C
66 C
212618 ACAATCTTTGAGTCTTTTTCTCTTAAAACAAAAGTTTGTCTTTCTTGAGACAGTTTCTCTTGAAA
1 ACAATCTTTGAGTCTTTTTCTCTTAAAACAAAAGTTTGTCTTTCTTGAGACAGTTTCTCTTGAAA
212683 C
66 C
* * **
212684 ACAAT-TTTGAGTTTTTTTCTCTTAAAACAAAAATTTGTCTTTCTTGAGACAACTTCTCTTGAAA
1 ACAATCTTTGAGTCTTTTTCTCTTAAAACAAAAGTTTGTCTTTCTTGAGACAGTTTCTCTTGAAA
212748 C
66 C
* *
212749 A-ATCATCTTTGAGT-TTATTTCCCTTGAAACAAA
1 ACA--ATCTTTGAGTCTT-TTTCTCTTAAAACAAA
212782 TACCTAAAGA
Statistics
Matches: 147, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
64 1 0.01
65 86 0.59
66 39 0.27
67 21 0.14
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (66 bp):
ACAATCTTTGAGTCTTTTTCTCTTAAAACAAAAGTTTGTCTTTCTTGAGACAGTTTCTCTTGAAA
C
Found at i:213253 original size:3 final size:3
Alignment explanation
Indices: 213239--213271 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
213229 GTTCTACATT
213239 TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TT
213272 TTACATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:213435 original size:21 final size:23
Alignment explanation
Indices: 213396--213441 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
213386 ATCACTTAAC
* *
213396 CCGACCCTATTAGAGACCC-GAA
1 CCGACCCTATTACAAACCCAGAA
213418 CCGACCC-ATTACAAACCCAGAA
1 CCGACCCTATTACAAACCCAGAA
213440 CC
1 CC
213442 CATATTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.35, C:0.41, G:0.13, T:0.11
Consensus pattern (23 bp):
CCGACCCTATTACAAACCCAGAA
Found at i:214369 original size:5 final size:5
Alignment explanation
Indices: 214316--214384 Score: 52
Period size: 5 Copynumber: 13.6 Consensus size: 5
214306 TTGCTTTACG
* ** *
214316 TTTA- TTTAT TTTGAT TTTTT TTTA- CCTAT TTTCAT TTTCAT TTTGT
1 TTTAT TTTAT TTT-AT TTTAT TTTAT TTTAT TTT-AT TTT-AT TTTAT
*
214362 TTTAT TTTAG TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTT
214385 TGTGAAAAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
4 6 0.12
5 29 0.57
6 16 0.31
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:216889 original size:12 final size:12
Alignment explanation
Indices: 216868--216900 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
216858 AGGTATGTTC
216868 AATA-AATTTTT
1 AATATAATTTTT
*
216879 AATTTAATTTTT
1 AATATAATTTTT
216891 AATATAATTT
1 AATATAATTT
216901 CATATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 3 0.16
12 16 0.84
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
AATATAATTTTT
Found at i:218326 original size:18 final size:19
Alignment explanation
Indices: 218305--218343 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
218295 TGTTATAGCT
*
218305 TTAATTAATGTTAT-AATA
1 TTAATTAATGGTATAAATA
*
218323 TTAATTATTGGTATAAATA
1 TTAATTAATGGTATAAATA
218342 TT
1 TT
218344 TGTTAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (19 bp):
TTAATTAATGGTATAAATA
Found at i:222189 original size:21 final size:21
Alignment explanation
Indices: 222151--222190 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
222141 GAGTATTGGG
*
222151 CACGTGTACTTCCGTCCATTT
1 CACGTGTACTTCCCTCCATTT
222172 CACGTG-ACTTCCCCTCCAT
1 CACGTGTACTT-CCCTCCAT
222191 GCTTGCATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.15, C:0.40, G:0.12, T:0.33
Consensus pattern (21 bp):
CACGTGTACTTCCCTCCATTT
Found at i:232199 original size:3 final size:3
Alignment explanation
Indices: 232191--232240 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
232181 TTTTTATCCA
*
232191 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
232239 TA
1 TA
232241 AATATATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:232267 original size:14 final size:15
Alignment explanation
Indices: 232239--232273 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
232229 TTATTATTAT
232239 TAAATATATATTAAA
1 TAAATATATATTAAA
232254 TAAATATATA-TAAA
1 TAAATATATATTAAA
232268 TAAATA
1 TAAATA
232274 ATTACAGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:234353 original size:6 final size:7
Alignment explanation
Indices: 234332--234356 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
234322 TGTCTCCATT
234332 AATTAAA
1 AATTAAA
234339 AATTAAA
1 AATTAAA
234346 AATTAAA
1 AATTAAA
234353 AATT
1 AATT
234357 TATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:234430 original size:22 final size:23
Alignment explanation
Indices: 234396--234439 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
234386 CAAAATCTTT
234396 ATATTTACTTATTAT-TTTTATA
1 ATATTTACTTATTATATTTTATA
*
234418 ATATTTA-TATATTGTATTTTAT
1 ATATTTACT-TATTATATTTTAT
234440 TTGCAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 1 0.05
22 12 0.63
23 6 0.32
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
ATATTTACTTATTATATTTTATA
Found at i:235956 original size:8 final size:7
Alignment explanation
Indices: 235932--235973 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
235922 TTTTCATACA
235932 TGCA-TT
1 TGCATTT
235938 TGCATTT
1 TGCATTT
235945 TGCATCTT
1 TGCAT-TT
235953 TGCATTT
1 TGCATTT
* *
235960 TTCATTG
1 TGCATTT
235967 TGCATTT
1 TGCATTT
235974 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:235956 original size:15 final size:14
Alignment explanation
Indices: 235932--235973 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
235922 TTTTCATACA
235932 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
235945 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
235960 TTCATTGTGCATTT
1 TGCATTTTGCATTT
235974 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:236060 original size:26 final size:26
Alignment explanation
Indices: 236031--236089 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
236021 CATTCACATA
*
236031 TTTACATTTGAATTTGCATTTGCATT
1 TTTACATTTGAATTTACATTTGCATT
* * *
236057 TTTACGTTTGTATTTACATTTTCATT
1 TTTACATTTGAATTTACATTTGCATT
236083 TTTACAT
1 TTTACAT
236090 AATTACATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (26 bp):
TTTACATTTGAATTTACATTTGCATT
Found at i:238075 original size:13 final size:12
Alignment explanation
Indices: 238035--238069 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
238025 TCCAGCAAAG
238035 AAAGAAGAAAAAA
1 AAAGAA-AAAAAA
238048 AAAGGAAAAAAAA
1 AAA-GAAAAAAAA
238061 AAAGAAAAA
1 AAAGAAAAA
238070 GGAAAATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.29
13 12 0.57
14 3 0.14
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:240416 original size:83 final size:83
Alignment explanation
Indices: 240288--241074 Score: 1267
Period size: 83 Copynumber: 9.5 Consensus size: 83
240278 GAATGTGCCA
240288 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
*
240353 CGGAACATGAATGTGTTC
66 CGGAAGATGAATGTGTTC
* * *
240371 ATAGCATCTTCTGGAAGTGTCCTTTGAGTTATTTGATCTGGTTTGGCAGAACCAAACATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
** * *
240436 TAGAAGATGAATTTG-CC
66 CGGAAGATGAATGTGTTC
240453 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
*
240518 TCGGAACATGAATGTGTTC
65 TCGGAAGATGAATGTGTTC
*
240537 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
** * *
240602 TAGAAGATGAATTTG-CC
66 CGGAAGATGAATGTGTTC
*
240619 AATAGCATCTTCTTGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
*
240684 TCGGAACATGAATGTGTTC
65 TCGGAAGATGAATGTGTTC
*
240703 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
** * *
240768 TAGAAGATGAATTTG-CC
66 CGGAAGATGAATGTGTTC
240785 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
*
240850 TCGGAACATGAATGTGTTC
65 TCGGAAGATGAATGTGTTC
*
240869 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
** * *
240934 TAGAAGATGAATTTG-CC
66 CGGAAGATGAATGTGTTC
240951 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
241016 TCGGAAGATGAATGTGTTC
65 TCGGAAGATGAATGTGTTC
241035 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
241075 ATTCAGTAGG
Statistics
Matches: 643, Mismatches: 53, Indels: 16
0.90 0.07 0.02
Matches are distributed among these distances:
82 4 0.01
83 635 0.99
84 4 0.01
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
CGGAAGATGAATGTGTTC
Found at i:240564 original size:166 final size:166
Alignment explanation
Indices: 240272--241074 Score: 1516
Period size: 166 Copynumber: 4.8 Consensus size: 166
240262 TAAGCATAGT
* *
240272 GAAGCTGAATGTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
*
240337 AACCAATCATTGAATTCGGAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTA
66 AACCAATCATTGAATTCGGAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
* *
240402 TTTGATCTGGTTTGGCAGAACCAAACATTGAATTTA
131 TCTGATCTGGTTTGGCAGAACCAATCATTGAATTTA
240438 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
240503 AACCAATCATTGAATTCGGAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
66 AACCAATCATTGAATTCGGAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
*
240568 TTTGATCTGGTTTGGCAGAACCAATCATTGAATTTA
131 TCTGATCTGGTTTGGCAGAACCAATCATTGAATTTA
*
240604 GAAGATGAATTTGCCAATAGCATCTTCTTGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
240669 AACCAATCATTGAATTCGGAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
66 AACCAATCATTGAATTCGGAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
*
240734 TCTGATCTGGTTTGGCAGAACCAATCATTGAGTTTA
131 TCTGATCTGGTTTGGCAGAACCAATCATTGAATTTA
240770 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
240835 AACCAATCATTGAATTCGGAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
66 AACCAATCATTGAATTCGGAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
*
240900 TCTGATCTGGTTTGGCAGAACCAATCATTGAGTTTA
131 TCTGATCTGGTTTGGCAGAACCAATCATTGAATTTA
240936 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
*
241001 AACCAATCATTGAATTCGGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
66 AACCAATCATTGAATTCGGAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
241066 TCTGATCTG
131 TCTGATCTG
241075 ATTCAGTAGG
Statistics
Matches: 628, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 628 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (166 bp):
GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
AACCAATCATTGAATTCGGAACATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
TCTGATCTGGTTTGGCAGAACCAATCATTGAATTTA
Found at i:242117 original size:116 final size:113
Alignment explanation
Indices: 241710--242347 Score: 828
Period size: 116 Copynumber: 5.6 Consensus size: 113
241700 TCGAATCCAC
* *
241710 TTGATGGATCAGTC-TTTCCAGAGAAG-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 TTGATGGATCA-TCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
* * * * ** *
241773 GAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCCGAA-TC--CAC
64 GAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
* * *
241820 TTGATGGATCAGTC-TTTCCAAAGAAG-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 TTGATGGATCA-TCATTGCC-AGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
* * * *
241883 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-TTCTGAATTCATCAAA
64 GAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCT-TGAATTCATC-AT
* *
241934 TTGATGGATTATCTTTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGA
1 TTGATGGATCATCATTGCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGA
241999 AGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
63 AGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
*
242050 TTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGA
1 TTGATGGATCATCATTGCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGA
242115 AGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
63 AGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
*
242166 TTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGA
1 TTGATGGATCATCATTGCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGA
242231 AGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
63 AGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
** * * *
242282 TTGATGGATCATCATCCCCAGCAG-AAAGTTCATAATAAGAAGAACTCATCTGAAGAAAG-AGAA
1 TTGATGGATCATCATTGCCAG--GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
242345 GAA
64 GAA
242348 TTTATTCAAT
Statistics
Matches: 491, Mismatches: 23, Indels: 25
0.91 0.04 0.05
Matches are distributed among these distances:
110 97 0.20
111 3 0.01
113 14 0.03
114 45 0.09
115 1 0.00
116 249 0.51
117 80 0.16
118 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (113 bp):
TTGATGGATCATCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
Found at i:242498 original size:3 final size:3
Alignment explanation
Indices: 242490--242543 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
242480 TCCATATTTT
*
242490 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
242538 TTA TTA
1 TTA TTA
242544 AATATATATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:242570 original size:14 final size:15
Alignment explanation
Indices: 242542--242576 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
242532 TTATTATTAT
242542 TAAATATATATTAAA
1 TAAATATATATTAAA
242557 TAAATATATA-TAAA
1 TAAATATATATTAAA
242571 TAAATA
1 TAAATA
242577 ATTACAGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:246147 original size:20 final size:20
Alignment explanation
Indices: 246122--246172 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
246112 AATACTTCTC
246122 TTCTTTCTTCTATAATTCAT
1 TTCTTTCTTCTATAATTCAT
246142 TTCTTTCTTCTATAATTCAT
1 TTCTTTCTTCTATAATTCAT
246162 TTCTTTCTTCT
1 TTCTTTCTTCT
246173 TCCTTCTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.63
Consensus pattern (20 bp):
TTCTTTCTTCTATAATTCAT
Found at i:250720 original size:21 final size:21
Alignment explanation
Indices: 250660--250721 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
250650 TAACACTTGA
*
250660 AAATTTGAAGCAAATT-AAAAT
1 AAATTTGAA-CAATTTCAAAAT
* *
250681 AAATTTGAACAGTTTTCAAAGT
1 AAATTTGAACA-ATTTCAAAAT
250703 AAATTTGAACAATTTCAAA
1 AAATTTGAACAATTTCAAA
250722 TTTAAAAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.06
21 18 0.51
22 15 0.43
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (21 bp):
AAATTTGAACAATTTCAAAAT
Found at i:250727 original size:22 final size:22
Alignment explanation
Indices: 250680--250721 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
250670 CAAATTAAAA
*
250680 TAAATTTGAACAGTTTTCAAAG
1 TAAATTTGAACAGATTTCAAAG
250702 TAAATTTGAACA-ATTTCAAA
1 TAAATTTGAACAGATTTCAAA
250722 TTTAAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (22 bp):
TAAATTTGAACAGATTTCAAAG
Found at i:255431 original size:26 final size:26
Alignment explanation
Indices: 255401--255463 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
255391 TTGGTTCATG
255401 TAAATATTTAAATTTAAAATTTTTAT
1 TAAATATTTAAATTTAAAATTTTTAT
*
255427 TAAATATTTAAATTTAAATTTTTTAT
1 TAAATATTTAAATTTAAAATTTTTAT
255453 TAAATATTTAA
1 TAAATATTTAA
255464 TCAAGTAGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TAAATATTTAAATTTAAAATTTTTAT
Found at i:257019 original size:21 final size:21
Alignment explanation
Indices: 256995--257048 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
256985 ACTAATTTCC
256995 CAAATTGGCCATTT-AATATTT
1 CAAATTGGCCATTTAAAT-TTT
** *
257016 CAAATTTTCCTTTTAAATTTT
1 CAAATTGGCCATTTAAATTTT
*
257037 CGAATTGGCCAT
1 CAAATTGGCCAT
257049 GCATTTTAGC
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (21 bp):
CAAATTGGCCATTTAAATTTT
Found at i:259704 original size:20 final size:19
Alignment explanation
Indices: 259679--259746 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
259669 TTTCAAAGAT
259679 GGTATCGATACCGTCCTTCA
1 GGTATCGATACCGTCCTT-A
*
259699 GGTATCGGTACC--CCTTA
1 GGTATCGATACCGTCCTTA
* * *
259716 -GTATCAATACTGTTCTTA
1 GGTATCGATACCGTCCTTA
259734 GGGTATCGATACC
1 -GGTATCGATACC
259747 TCATGAATGG
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
16 8 0.22
17 1 0.03
18 8 0.22
20 20 0.54
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (19 bp):
GGTATCGATACCGTCCTTA
Found at i:272913 original size:19 final size:19
Alignment explanation
Indices: 272871--272917 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
272861 AAACACGTAT
* *
272871 TTATGAACATTACTATATG
1 TTATGAACAGTACTATAAG
272890 TTATGAACAGTACTATACAG
1 TTATGAACAGTACTATA-AG
272910 -TATGAACA
1 TTATGAACA
272918 ATACCTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 24 0.96
20 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (19 bp):
TTATGAACAGTACTATAAG
Done.