Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005838.1 Hibiscus syriacus cultivar Beakdansim tig00013687_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: 146289
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1585 original size:16 final size:16
Alignment explanation
Indices: 1555--1689 Score: 245
Period size: 16 Copynumber: 8.5 Consensus size: 16
1545 AGTGATTAGG
*
1555 ATGATT-AAGCGTTGA
1 ATGATTCAAACGTTGA
1570 ATGATTCAAACGTTGA
1 ATGATTCAAACGTTGA
1586 ATGATTCAAACGTTGA
1 ATGATTCAAACGTTGA
1602 ATGATTCAAACGTTGA
1 ATGATTCAAACGTTGA
1618 ATGATTCAAACGTTGA
1 ATGATTCAAACGTTGA
1634 ATGATTCAAACGTTGA
1 ATGATTCAAACGTTGA
*
1650 ATGATTTAAACGTTGA
1 ATGATTCAAACGTTGA
1666 ATGATTCAAACGTTGA
1 ATGATTCAAACGTTGA
1682 ATGATTCA
1 ATGATTCA
1690 GAGACTCTGT
Statistics
Matches: 116, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
15 6 0.05
16 110 0.95
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (16 bp):
ATGATTCAAACGTTGA
Found at i:3180 original size:2 final size:2
Alignment explanation
Indices: 3173--3222 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
3163 TGGATATACA
3173 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3215 AT AT AT AT
1 AT AT AT AT
3223 TATTTTTCCG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3927 original size:24 final size:24
Alignment explanation
Indices: 3899--3945 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3889 TTTTTATATA
*
3899 TAATAATATTACATATTTAATTAT
1 TAATAATATTACATATTAAATTAT
* *
3923 TAATAATTTTATATATTAAATTA
1 TAATAATATTACATATTAAATTA
3946 AACTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATAATATTACATATTAAATTAT
Found at i:4043 original size:20 final size:21
Alignment explanation
Indices: 3996--4044 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
3986 GTATGTTTAA
**
3996 TAATTAATATAATATTTTGTT
1 TAATTAATATAATACGTTGTT
*
4017 TAA-TAATATAGTACGTT-TT
1 TAATTAATATAATACGTTGTT
4036 TAATTAATA
1 TAATTAATA
4045 ATTTGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.21
20 16 0.67
21 3 0.12
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (21 bp):
TAATTAATATAATACGTTGTT
Found at i:4501 original size:4 final size:4
Alignment explanation
Indices: 4492--4600 Score: 65
Period size: 4 Copynumber: 25.8 Consensus size: 4
4482 GGAGGTAATT
* * *
4492 TTTA TTTA TTTA TTTA CTTTGA ATTA TTTA TTTA TGTA TTCA TTTA TTTCGA
1 TTTA TTTA TTTA TTTA -TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTT--A
* * * * * * * *
4544 ATAA ATTA GTGA TTTA TTTA TTTA TTTAA TTCAA ATAA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TT-TA TTTA TTTA TTTA TTTA
4594 TTTA TTT
1 TTTA TTT
4601 GAAGGGGTAT
Statistics
Matches: 82, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
4 69 0.84
5 10 0.12
6 3 0.04
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (4 bp):
TTTA
Found at i:4526 original size:30 final size:29
Alignment explanation
Indices: 4492--4600 Score: 110
Period size: 30 Copynumber: 3.5 Consensus size: 29
4482 GGAGGTAATT
*
4492 TTTATTTATTTATTTACTTTGAATTATTTA
1 TTTATTTATTTATTTA-TTTGAATAATTTA
* *
4522 TTTATGTATTCATTTATTTCGAATAAATTAGTGA
1 TTTATTTATTTATTTATTT-GAAT-AATT--T-A
**
4556 TTTATTTATTTATTTAATTCAAATAATTTA
1 TTTATTTATTTATTT-ATTTGAATAATTTA
4586 TTTATTTATTTATTT
1 TTTATTTATTTATTT
4601 GAAGGGGTAT
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
29 3 0.05
30 34 0.52
31 4 0.06
33 5 0.08
34 17 0.26
35 3 0.05
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (29 bp):
TTTATTTATTTATTTATTTGAATAATTTA
Found at i:4600 original size:34 final size:34
Alignment explanation
Indices: 4513--4600 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 34
4503 ATTTACTTTG
* * * *
4513 AATTATTTATTTATGTATTCATTTATTTCGAATA
1 AATTATTTATTTATTTATTTATTTAATTCAAATA
* *
4547 AATTAGTGATTTATTTATTTATTTAATTCAAATA
1 AATTATTTATTTATTTATTTATTTAATTCAAATA
*
4581 ATTTATTTATTTATTTATTT
1 AATTATTTATTTATTTATTT
4601 GAAGGGGTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (34 bp):
AATTATTTATTTATTTATTTATTTAATTCAAATA
Found at i:8351 original size:21 final size:23
Alignment explanation
Indices: 8300--8361 Score: 83
Period size: 21 Copynumber: 2.7 Consensus size: 23
8290 GAATGTTAAA
*
8300 ATGGTATCGATACTACTTAGTGT
1 ATGGTACCGATACTACTTAGTGT
*
8323 AGTAGTACCGATACT-CTTAGT-T
1 A-TGGTACCGATACTACTTAGTGT
8345 ATGGTACCGATACTACT
1 ATGGTACCGATACTACT
8362 CCTTTTGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 12 0.35
22 4 0.12
23 7 0.21
24 11 0.32
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (23 bp):
ATGGTACCGATACTACTTAGTGT
Found at i:25427 original size:18 final size:18
Alignment explanation
Indices: 25404--25457 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
25394 ATAATTTTAA
25404 AAAATTTATTTAAAATTT
1 AAAATTTATTTAAAATTT
* *
25422 AAAATTATATATATAATTTT
1 AAAATT-TATTTA-AAATTT
*
25442 AAATATATATTTAAAA
1 AAA-ATTTATTTAAAA
25458 GAAAACACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 6 0.21
19 7 0.25
20 13 0.46
21 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATTTATTTAAAATTT
Found at i:25439 original size:19 final size:19
Alignment explanation
Indices: 25404--25457 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
25394 ATAATTTTAA
*
25404 AAAATT-TATTTAAAATTT
1 AAAATTATATATAAAATTT
*
25422 AAAATTATATATATAATTT
1 AAAATTATATATAAAATTT
* *
25441 TAAATATATATTTAAAA
1 AAAAT-TATATATAAAA
25458 GAAAACACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
18 6 0.21
19 14 0.48
20 9 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAATTATATATAAAATTT
Found at i:25450 original size:20 final size:20
Alignment explanation
Indices: 25394--25451 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
25384 TCATAACCTA
* * *
25394 ATAATTTTAAAAAATTTATTT
1 ATAATTTT-AAATATATATAT
* *
25415 AAAATTTAAAAT-TATATAT
1 ATAATTTTAAATATATATAT
25434 ATAATTTTAAATATATAT
1 ATAATTTTAAATATATAT
25452 TTAAAAGAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 15 0.52
20 8 0.28
21 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAATTTTAAATATATATAT
Found at i:25481 original size:18 final size:19
Alignment explanation
Indices: 25460--25495 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
25450 ATTTAAAAGA
25460 AAACAC-AAATTTTGAAAT
1 AAACACAAAATTTTGAAAT
*
25478 AAACCCAAAATTTTGAAA
1 AAACACAAAATTTTGAAA
25496 ACATTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.25
Consensus pattern (19 bp):
AAACACAAAATTTTGAAAT
Found at i:26033 original size:29 final size:30
Alignment explanation
Indices: 25982--26043 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
25972 TTGAATTACG
* *
25982 AAATGAAACGTTAGGCACCAAACT-AGAATA
1 AAATGAAACATTAGACACCAAACTGA-AATA
*
26012 AAAT-AAACATTAGACACTAAACTGAAATA
1 AAATGAAACATTAGACACCAAACTGAAATA
26041 AAA
1 AAA
26044 AACATACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.56, C:0.15, G:0.11, T:0.18
Consensus pattern (30 bp):
AAATGAAACATTAGACACCAAACTGAAATA
Found at i:26340 original size:29 final size:29
Alignment explanation
Indices: 26272--26329 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
26262 TATTAATTTG
**
26272 ATATTAATTTAAAATAATTTAATATAATAGT
1 ATATTAA--TAAAATAAAATAATATAATAGT
*
26303 CTATTAATAAAATAAAATAATATAATA
1 ATATTAATAAAATAAAATAATATAATA
26330 TATGTCTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.75
31 6 0.25
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (29 bp):
ATATTAATAAAATAAAATAATATAATAGT
Found at i:31914 original size:29 final size:28
Alignment explanation
Indices: 31881--31969 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 28
31871 CAAATTTTGG
31881 TTAGTGATTAAAATATAAGTTTTAAAAGT
1 TTAGTGATTAAAATATAA-TTTTAAAAGT
* *
31910 TTAGTTG-TTAAAGTATAAATTTTTAAAAAT
1 TTAG-TGATTAAAATAT-AA-TTTTAAAAGT
* **
31940 TTAGGGACAAAAAATATAATTTTAAAAGT
1 TTAGTGA-TTAAAATATAATTTTAAAAGT
31969 T
1 T
31970 ATATTTTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
29 23 0.48
30 19 0.40
31 6 0.12
ACGTcount: A:0.46, C:0.01, G:0.12, T:0.40
Consensus pattern (28 bp):
TTAGTGATTAAAATATAATTTTAAAAGT
Found at i:35410 original size:140 final size:140
Alignment explanation
Indices: 35243--35501 Score: 369
Period size: 140 Copynumber: 1.9 Consensus size: 140
35233 TAGAAATGTG
* * * * * *
35243 GGCTCTAATATTAATCATAATTGATTTTGACCAATTATTGAAGCTAATAATCGATGAAAACTCTA
1 GGCTCTAATAATAATCATAATTCATTTTAACCAATTATTGAAACAAATAATCGATGAAAACCCTA
35308 GGGCATTTTAATGAGAGAGCCAAATCAAATTA-TTCCTTAAATTTAAAGACTAAGTGTAGTTCTG
66 GGGCATTTTAATGAGAGAGCCAAATCAAATTATTTCC-TAAATTTAAAGACTAAGTGTAGTTCTG
35372 CCTAAAATGGA
130 CCTAAAATGGA
*
35383 GGCTCTAATTAATAA-CTTAATTCATTTTAACCAATTATTGAAACAAATAATCGATGAAAACCCT
1 GGCTCTAA-TAATAATCATAATTCATTTTAACCAATTATTGAAACAAATAATCGATGAAAACCCT
* * * * * *
35447 CGGGTATTTTAATGCGAGAGTCAAATCGAATTATTTCCTAAGTTTAAAGACTAAG
65 AGGGCATTTTAATGAGAGAGCCAAATCAAATTATTTCCTAAATTTAAAGACTAAG
35502 GTTCGAGAAC
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
140 95 0.91
141 9 0.09
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (140 bp):
GGCTCTAATAATAATCATAATTCATTTTAACCAATTATTGAAACAAATAATCGATGAAAACCCTA
GGGCATTTTAATGAGAGAGCCAAATCAAATTATTTCCTAAATTTAAAGACTAAGTGTAGTTCTGC
CTAAAATGGA
Found at i:36350 original size:19 final size:19
Alignment explanation
Indices: 36326--36363 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
36316 AACCGTTTTC
36326 TTAAAACTAAATACTATTT
1 TTAAAACTAAATACTATTT
*
36345 TTAAAACTATATACTATTT
1 TTAAAACTAAATACTATTT
36364 ACTGTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAAACTAAATACTATTT
Found at i:36382 original size:13 final size:13
Alignment explanation
Indices: 36364--36388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36354 TATACTATTT
36364 ACTGTTTTCAAAA
1 ACTGTTTTCAAAA
36377 ACTGTTTTCAAA
1 ACTGTTTTCAAA
36389 CCGTATACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
ACTGTTTTCAAAA
Found at i:36600 original size:20 final size:20
Alignment explanation
Indices: 36546--36605 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
36536 CCCGAAATCA
36546 CAGTTTTCGAATTCGCAAC-
1 CAGTTTTCGAATTCGCAACT
* * *
36565 AAGAATTTAC-ATTTCGCAACT
1 CAG--TTTTCGAATTCGCAACT
*
36586 CAGTTTTCGAATTCGTAACT
1 CAGTTTTCGAATTCGCAACT
36606 TGAATATGGA
Statistics
Matches: 30, Mismatches: 7, Indels: 7
0.68 0.16 0.16
Matches are distributed among these distances:
19 6 0.20
20 18 0.60
21 6 0.20
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (20 bp):
CAGTTTTCGAATTCGCAACT
Found at i:36619 original size:40 final size:40
Alignment explanation
Indices: 36546--36625 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
36536 CCCGAAATCA
*
36546 CAGTTTTCGAATTCGCAACAAGAATTTACATTTCGCAACT
1 CAGTTTTCGAATTCGCAACAAGAATATACATTTCGCAACT
* ** **
36586 CAGTTTTCGAATTCGTAACTTGAATATGGATTTCGCAACT
1 CAGTTTTCGAATTCGCAACAAGAATATACATTTCGCAACT
36626 TGAAAATCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (40 bp):
CAGTTTTCGAATTCGCAACAAGAATATACATTTCGCAACT
Found at i:36640 original size:20 final size:20
Alignment explanation
Indices: 36592--36725 Score: 117
Period size: 20 Copynumber: 6.7 Consensus size: 20
36582 AACTCAGTTT
* *
36592 TCGAATTCGTAACTTGAATA
1 TCGAATTCGCAACTTGAAAA
* *
36612 TGGATTTCGCAACTTGAAAA
1 TCGAATTCGCAACTTGAAAA
* * *
36632 TCGAATTCGCATCTCGAAAT
1 TCGAATTCGCAACTTGAAAA
* * *
36652 TCAAATTCGCAACTCGAAAC
1 TCGAATTCGCAACTTGAAAA
** *
36672 TTAAATTCGCAACTTGAAAT
1 TCGAATTCGCAACTTGAAAA
*
36692 TCGAATTCGCAAC-TCAAAA
1 TCGAATTCGCAACTTGAAAA
*
36711 TTCGAATTCGTAACT
1 -TCGAATTCGCAACT
36726 CGATTTTCAT
Statistics
Matches: 92, Mismatches: 20, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
19 4 0.04
20 88 0.96
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (20 bp):
TCGAATTCGCAACTTGAAAA
Found at i:36659 original size:60 final size:60
Alignment explanation
Indices: 36577--36728 Score: 171
Period size: 60 Copynumber: 2.5 Consensus size: 60
36567 GAATTTACAT
*** * * * *
36577 TTCGCAACTCAGTTTTCGAATTCGTAACTTGAATA-TGGATTTCGCAACTTGAAAATCGAA
1 TTCGCAACTCAAAATTCAAATTCGTAACTCGAA-ACTGAAATTCGCAACTTGAAAATCGAA
* * * * *
36637 TTCGCATCTCGAAATTCAAATTCGCAACTCGAAACTTAAATTCGCAACTTGAAATTCGAA
1 TTCGCAACTCAAAATTCAAATTCGTAACTCGAAACTGAAATTCGCAACTTGAAAATCGAA
*
36697 TTCGCAACTCAAAATTCGAATTCGTAACTCGA
1 TTCGCAACTCAAAATTCAAATTCGTAACTCGA
36729 TTTTCATTTT
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
59 1 0.01
60 74 0.99
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (60 bp):
TTCGCAACTCAAAATTCAAATTCGTAACTCGAAACTGAAATTCGCAACTTGAAAATCGAA
Found at i:36931 original size:20 final size:20
Alignment explanation
Indices: 36908--36993 Score: 61
Period size: 20 Copynumber: 4.3 Consensus size: 20
36898 ACTCGCATTA
36908 CGAATTAGAAAATCGAGTTG
1 CGAATTAGAAAATCGAGTTG
* * * *
36928 CGAA-AACGAAACTCGTGTTA
1 CGAATTA-GAAAATCGAGTTG
36948 CGAATTTA-AAAATCGAGTTG
1 CGAA-TTAGAAAATCGAGTTG
* * *
36968 CGAA-AAAAAAATTCGTGTTG
1 CGAATTAGAAAA-TCGAGTTG
36988 CGAATT
1 CGAATT
36994 CGGAAACTGT
Statistics
Matches: 49, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
18 1 0.02
19 5 0.10
20 42 0.86
22 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (20 bp):
CGAATTAGAAAATCGAGTTG
Found at i:36984 original size:40 final size:41
Alignment explanation
Indices: 36896--36993 Score: 128
Period size: 40 Copynumber: 2.4 Consensus size: 41
36886 GTGTTAATTG
** **
36896 AAACTCGCATTACGAA-TTAGAAAATCGAGTTGCGAAAACG
1 AAACTCGTGTTACGAATTTAGAAAATCGAGTTGCGAAAAAA
36936 AAACTCGTGTTACGAATTTA-AAAATCGAGTTGCGAAAAAA
1 AAACTCGTGTTACGAATTTAGAAAATCGAGTTGCGAAAAAA
* *
36976 AAATTCGTGTTGCGAATT
1 AAACTCGTGTTACGAATT
36994 CGGAAACTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
40 48 0.94
41 3 0.06
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (41 bp):
AAACTCGTGTTACGAATTTAGAAAATCGAGTTGCGAAAAAA
Found at i:37159 original size:25 final size:23
Alignment explanation
Indices: 37117--37168 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
37107 TTATTTTCTC
*
37117 TTTTTAAAACTATATATATATACTA
1 TTTTCAAAACTATATATATA-A-TA
* *
37142 TTTTCAAAATTATGTATATAATA
1 TTTTCAAAACTATATATATAATA
37165 TTTT
1 TTTT
37169 ACCTTTATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.25
24 1 0.04
25 17 0.71
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTTCAAAACTATATATATAATA
Found at i:38613 original size:2 final size:2
Alignment explanation
Indices: 38606--38657 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
38596 AACTAAACGT
38606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38648 TA TA TA TA TA
1 TA TA TA TA TA
38658 AATGAAATTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41297 original size:2 final size:2
Alignment explanation
Indices: 41290--41321 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41280 CTATTTCTCA
41290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41322 TTAATATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43072 original size:2 final size:2
Alignment explanation
Indices: 43065--43091 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43055 ATAATTAGCC
43065 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
43092 TGCTTATTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44210 original size:17 final size:17
Alignment explanation
Indices: 44188--44221 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
44178 TTACACATTA
44188 GGTACATAAACTATCAT
1 GGTACATAAACTATCAT
44205 GGTACATAAACTATCAT
1 GGTACATAAACTATCAT
44222 TTTTTAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (17 bp):
GGTACATAAACTATCAT
Found at i:47364 original size:17 final size:17
Alignment explanation
Indices: 47342--47378 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
47332 CTAATTAGAT
* *
47342 ATTAAATTTATTATTAA
1 ATTAAAATTATGATTAA
47359 ATTAAAATTATGATTAA
1 ATTAAAATTATGATTAA
47376 ATT
1 ATT
47379 GAAAGAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
ATTAAAATTATGATTAA
Found at i:50666 original size:37 final size:37
Alignment explanation
Indices: 50594--50668 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
50584 GTTGGAAAAT
* *
50594 ATTTATATATTTTCTTTAAAAAATTTAAATTTATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAATATATAAA
* *
50631 ATTTATATAATTTTTTTTACAAAATTGAAA-ATATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAATATATAAA
50668 A
1 A
50669 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAATATATAAA
Found at i:54008 original size:2 final size:2
Alignment explanation
Indices: 54001--54039 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
53991 TTCAAAAGAA
54001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54040 AAATAATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54394 original size:102 final size:104
Alignment explanation
Indices: 54196--54399 Score: 331
Period size: 102 Copynumber: 1.9 Consensus size: 104
54186 ATAGACACCA
*
54196 ACAACACATTAAATTTCATCCTAATATAAATATAAAATGCAATGCAATGAATTTTATTTTAATTT
1 ACAACACATTAAATTTCATCCTAATATAAATATAAAATGCAATGC----AATTTTACTTTAATTT
*
54261 AATTTTTAAAATTATAATTACAATAATAACTAATCACGTATGC
62 AATTTTTAAAATTATAATTACAATAAGAACTAATCACGTATGC
54304 ACAACACATTAAATTTCATCCTAATATAAATATAAAATGCAATGC-A-TTTACTTTAATTTAATT
1 ACAACACATTAAATTTCATCCTAATATAAATATAAAATGCAATGCAATTTTACTTTAATTTAATT
*
54367 TTTAAAATTATTATTACAATAAGAACTAATCAC
66 TTTAAAATTATAATTACAATAAGAACTAATCAC
54400 TTATACACCA
Statistics
Matches: 93, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
102 47 0.51
103 1 0.01
108 45 0.48
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.38
Consensus pattern (104 bp):
ACAACACATTAAATTTCATCCTAATATAAATATAAAATGCAATGCAATTTTACTTTAATTTAATT
TTTAAAATTATAATTACAATAAGAACTAATCACGTATGC
Found at i:61596 original size:29 final size:29
Alignment explanation
Indices: 61559--61643 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
61549 AGGGATCGGC
61559 GGACGAATTTGAATTTATAAAATTTTAGA
1 GGACGAATTTGAATTTATAAAATTTTAGA
* *
61588 TGATGAATTTGAATTTATAAAATTTTAGA
1 GGACGAATTTGAATTTATAAAATTTTAGA
*
61617 GGACGAATTTGAACTTATAAAATTTTA
1 GGACGAATTTGAATTTATAAAATTTTA
61644 AAGAGGATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.40
Consensus pattern (29 bp):
GGACGAATTTGAATTTATAAAATTTTAGA
Found at i:64941 original size:17 final size:16
Alignment explanation
Indices: 64905--64942 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
64895 GGATTTATGG
64905 TATATTTTTTAAATTA
1 TATATTTTTTAAATTA
*
64921 -ATATTATTTTAATTTA
1 TATATT-TTTTAAATTA
64937 TATATT
1 TATATT
64943 CTCGAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 5 0.26
16 9 0.47
17 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATTTTTTAAATTA
Found at i:66513 original size:114 final size:114
Alignment explanation
Indices: 66313--66538 Score: 452
Period size: 114 Copynumber: 2.0 Consensus size: 114
66303 GCCACTGTTC
66313 TGCTCAGTGACTGCTTATATGAATTTTCCCTTTGGGTTTTCACTTAGATTTTGCCTCAGTCCTTC
1 TGCTCAGTGACTGCTTATATGAATTTTCCCTTTGGGTTTTCACTTAGATTTTGCCTCAGTCCTTC
66378 TTTGTTTTTGCCTACATTTTCAAAACCTTCAAACCAAGGCCTCCTTCTT
66 TTTGTTTTTGCCTACATTTTCAAAACCTTCAAACCAAGGCCTCCTTCTT
66427 TGCTCAGTGACTGCTTATATGAATTTTCCCTTTGGGTTTTCACTTAGATTTTGCCTCAGTCCTTC
1 TGCTCAGTGACTGCTTATATGAATTTTCCCTTTGGGTTTTCACTTAGATTTTGCCTCAGTCCTTC
66492 TTTGTTTTTGCCTACATTTTCAAAACCTTCAAACCAAGGCCTCCTTC
66 TTTGTTTTTGCCTACATTTTCAAAACCTTCAAACCAAGGCCTCCTTC
66539 AACTGGCTTC
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 112 1.00
ACGTcount: A:0.19, C:0.26, G:0.13, T:0.42
Consensus pattern (114 bp):
TGCTCAGTGACTGCTTATATGAATTTTCCCTTTGGGTTTTCACTTAGATTTTGCCTCAGTCCTTC
TTTGTTTTTGCCTACATTTTCAAAACCTTCAAACCAAGGCCTCCTTCTT
Found at i:67726 original size:73 final size:74
Alignment explanation
Indices: 67596--67736 Score: 221
Period size: 73 Copynumber: 1.9 Consensus size: 74
67586 TCACTATGTC
* *** *
67596 GTTAAATTGTTAACGGCATTAAAAACGACGCCGTTTTAAAAGAATAAAATTTTCACCAAAACAAC
1 GTTAAATTGTTAACGACATTAAAAACGACGAAATTTTAAAAGAACAAAATTTTCACCAAAACAAC
67661 ATCATTGTT
66 ATCATTGTT
*
67670 GTTAAATTGTTAACGACATTAAAAA-GATGAAATTTTAAAAGAACAAAATTTTCACCAAAACAAC
1 GTTAAATTGTTAACGACATTAAAAACGACGAAATTTTAAAAGAACAAAATTTTCACCAAAACAAC
67734 ATC
66 ATC
67737 GTTTTGCATA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 37 0.61
74 24 0.39
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (74 bp):
GTTAAATTGTTAACGACATTAAAAACGACGAAATTTTAAAAGAACAAAATTTTCACCAAAACAAC
ATCATTGTT
Found at i:70750 original size:22 final size:22
Alignment explanation
Indices: 70722--70782 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
70712 GTTTTTATTA
*
70722 TTTAATTTTTCTTATTGTTTA-T
1 TTTAATTTTT-TTATTATTTAGT
70744 TTTAATTGTTTTTATTATTTAGT
1 TTTAATT-TTTTTATTATTTAGT
*
70767 TTATAATGTTTTTATT
1 TT-TAATTTTTTTATT
70783 TAATTTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 16 0.47
23 14 0.41
24 4 0.12
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.70
Consensus pattern (22 bp):
TTTAATTTTTTTATTATTTAGT
Found at i:70780 original size:23 final size:21
Alignment explanation
Indices: 70722--70804 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 21
70712 GTTTTTATTA
* *
70722 TTTAATTTTTCTTATTGTTTAT
1 TTTAATGTTT-TTATTATTTAT
70744 TTTAATTGTTTTTATTATTTAGT
1 TTTAA-TGTTTTTATTATTTA-T
70767 TTATAATGTTTTTATTTAATTT-T
1 TT-TAATGTTTTTA-TT-ATTTAT
* *
70790 CTTAATGTATTTATT
1 TTTAATGTTTTTATT
70805 GTTTCTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
21 2 0.04
22 24 0.46
23 17 0.33
24 5 0.10
25 4 0.08
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTAATGTTTTTATTATTTAT
Found at i:76834 original size:60 final size:60
Alignment explanation
Indices: 76761--77008 Score: 478
Period size: 60 Copynumber: 4.1 Consensus size: 60
76751 TCCATTTATT
*
76761 ACTCAAACTTTGACAACTTCCCAAAATAGTCAAATTTCACATTCTAACTTCAAATTCATC
1 ACTCAAACTTTGACAACTTCCCAAAATAGTCAAATTTCACATTCTAACATCAAATTCATC
76821 ACTCAAACTTTGACAACTTCCCAAAATAGTCAAATTTCACATTCTAACATCAAATTCATC
1 ACTCAAACTTTGACAACTTCCCAAAATAGTCAAATTTCACATTCTAACATCAAATTCATC
76881 ACTCAAACTTTGACAACTTCCCAAAATAGTCAAATTTCACATTCTAACATCAAATTCATC
1 ACTCAAACTTTGACAACTTCCCAAAATAGTCAAATTTCACATTCTAACATCAAATTCATC
*
76941 ACTCAAACTTTGACAACTTCTCAAAATAGTCAAATTTCACATTCTAACATCAAATTCATC
1 ACTCAAACTTTGACAACTTCCCAAAATAGTCAAATTTCACATTCTAACATCAAATTCATC
77001 ACTCAAAC
1 ACTCAAAC
77009 ATTAATTTTC
Statistics
Matches: 186, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 186 1.00
ACGTcount: A:0.40, C:0.27, G:0.03, T:0.30
Consensus pattern (60 bp):
ACTCAAACTTTGACAACTTCCCAAAATAGTCAAATTTCACATTCTAACATCAAATTCATC
Found at i:78288 original size:29 final size:30
Alignment explanation
Indices: 78245--78301 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
78235 TCCATGAACT
*
78245 TTTCTAAATTTTATATTTTAATCACTAAAC
1 TTTCTAAAATTTATATTTTAATCACTAAAC
**
78275 TTTC-AAAATTTATATTTTGGTCACTAA
1 TTTCTAAAATTTATATTTTAATCACTAA
78302 CCAAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.49
Consensus pattern (30 bp):
TTTCTAAAATTTATATTTTAATCACTAAAC
Found at i:84498 original size:30 final size:30
Alignment explanation
Indices: 84435--84500 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
84425 GAAAAGTCAC
*
84435 AAATCGATCACTAACATTATCGTTTGTTACA
1 AAAT-GATCACTAACATTATCGTATGTTACA
*
84466 AAATGATCACTAACGTTATCGTATGTTACA
1 AAATGATCACTAACATTATCGTATGTTACA
84496 AAATG
1 AAATG
84501 GTCGCTCGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 29 0.88
31 4 0.12
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (30 bp):
AAATGATCACTAACATTATCGTATGTTACA
Found at i:94278 original size:21 final size:21
Alignment explanation
Indices: 94249--94299 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
94239 TTCGAACTTA
*
94249 TCAAGTCAAGTTAAACTTTAT
1 TCAACTCAAGTTAAACTTTAT
*
94270 TCAACTCAAGTTAAATTTTAT
1 TCAACTCAAGTTAAACTTTAT
94291 TCAACTCAA
1 TCAACTCAA
94300 CTCGTTAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (21 bp):
TCAACTCAAGTTAAACTTTAT
Found at i:101914 original size:15 final size:15
Alignment explanation
Indices: 101890--101920 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
101880 GGATTAGAAG
101890 CTCTCGATCTCTACT
1 CTCTCGATCTCTACT
*
101905 CTCTCTATCTCTACT
1 CTCTCGATCTCTACT
101920 C
1 C
101921 GCCATCACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.42, G:0.03, T:0.42
Consensus pattern (15 bp):
CTCTCGATCTCTACT
Found at i:103380 original size:5 final size:5
Alignment explanation
Indices: 103370--103396 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
103360 AGTCATATAT
103370 TCGGG TCGGG TCGGG TCGGG TCGGG TC
1 TCGGG TCGGG TCGGG TCGGG TCGGG TC
103397 ACGGGTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.22, G:0.56, T:0.22
Consensus pattern (5 bp):
TCGGG
Found at i:105156 original size:121 final size:118
Alignment explanation
Indices: 104928--105226 Score: 330
Period size: 121 Copynumber: 2.5 Consensus size: 118
104918 TAAATTATAT
* * * * * *
104928 ATTTAGTACCTAAACTATCAATTTTAGTC-TATATTAGTACGTAAACTTCTATTTTTTTTAAATC
1 ATTTAGTACCT-AACTATCAATTTGACTCGT-T-TTAGTACCTAAACTTC-AATTTTTTCAAACC
* ** * *
104992 ATACCTAACGTTTAGTTTTCATTTCATTTTTGCATTTCGCCATTTAAAACCTAATAC
62 ATACCTAACGTTTAGTTTTCATTTCATTTTAGCATACCACCATTTAAAACCTAACAC
105049 ATTTAGTACCTAACTATCAATATTGACTCGTTTTAGTACCTAAACCTTCAATTTTTTCAAACCAT
1 ATTTAGTACCTAACTATCAAT-TTGACTCGTTTTAGTACCTAAA-CTTCAATTTTTTCAAACCAT
* * * * * *
105114 GCCTGACGTTTAGTTTTTCATTTCATTTTAGTATACCACCATTTAAAACTTAGCGC
64 ACCTAACGTTTAG-TTTTCATTTCATTTTAGCATACCACCATTTAAAACCTAACAC
* * *
105170 ATTTAGTACCTAACTATCAATTATGATTCGTTTTATTACCTAAATTTTCAATTTTTT
1 ATTTAGTACCTAACTATCAATT-TGACTCGTTTTAGTACCTAAA-CTTCAATTTTTT
105227 TAAATTTAAC
Statistics
Matches: 152, Mismatches: 21, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
120 46 0.30
121 105 0.69
122 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.44
Consensus pattern (118 bp):
ATTTAGTACCTAACTATCAATTTGACTCGTTTTAGTACCTAAACTTCAATTTTTTCAAACCATAC
CTAACGTTTAGTTTTCATTTCATTTTAGCATACCACCATTTAAAACCTAACAC
Found at i:107816 original size:45 final size:45
Alignment explanation
Indices: 107760--107996 Score: 266
Period size: 45 Copynumber: 5.3 Consensus size: 45
107750 TGTCCTTCCG
107760 AAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTTCATCCA
1 AAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTTCATCCA
* * * * *
107805 AAACTGTATCAT--TTTCGGATGGAACATCGATCCTCTCTTCATCCA
1 AAACAGTATCATCATTT--GATGCAAGATCAATCCTCTTTTCATCCA
* * * ***
107850 AAACTGTATCAT--TTTCGGATGGAATATTGGTCCTCTTTTCATCCA
1 AAACAGTATCATCATTT--GATGCAAGATCAATCCTCTTTTCATCCA
* * * *
107895 AAACTGTATCATCATTTGATGCAAAATCAATTCTCTTTTCTTCCA
1 AAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTTCATCCA
*
107940 AAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTTCTTCCA
1 AAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTTCATCCA
107985 AAACAGTATCAT
1 AAACAGTATCAT
107997 TTTCTGATAC
Statistics
Matches: 169, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
43 3 0.02
45 163 0.96
47 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (45 bp):
AAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTTCATCCA
Found at i:107942 original size:22 final size:22
Alignment explanation
Indices: 107916--107987 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
107906 TCATTTGATG
107916 CAAAATCAATTCTCTTTTCTTC
1 CAAAATCAATTCTCTTTTCTTC
* * ** *
107938 CAAAA-CAGTATCATCATTTGATG
1 CAAAATCAAT-TC-TCTTTTCTTC
* *
107961 CAAGATCAATCCTCTTTTCTTC
1 CAAAATCAATTCTCTTTTCTTC
107983 CAAAA
1 CAAAA
107988 CAGTATCATT
Statistics
Matches: 34, Mismatches: 13, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
21 3 0.09
22 17 0.50
23 11 0.32
24 3 0.09
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (22 bp):
CAAAATCAATTCTCTTTTCTTC
Found at i:107974 original size:90 final size:89
Alignment explanation
Indices: 107754--108032 Score: 296
Period size: 90 Copynumber: 3.1 Consensus size: 89
107744 GTGCTATGTC
*
107754 CTTCCGAAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTTCATCCAAAACTGTATCATTT
1 CTTCCAAAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTTCATCCAAAACTGTATCATTT
* * *
107819 TCGGATGGAACATCGATCCTCTCTT
66 TC-GATGCAAAATCAATCCTCTCTT
* * * * ***
107844 CATCCAAAACTGTATCAT--TTTCGGATGGAATATTGGTCCTCTTTTCATCCAAAACTGTATCAT
1 CTTCCAAAACAGTATCATCATTT--GATGCAAGATCAATCCTCTTTTCATCCAAAACTGTATCAT
* *
107907 CATTT-GATGCAAAATCAATTCTCTTTT
64 --TTTCGATGCAAAATCAATCCTCTCTT
* *
107934 CTTCCAAAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTTCTTCCAAAACAGTATCATTT
1 CTTCCAAAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTTCATCCAAAACTGTATCATTT
* * * *
107999 TCTGATACAATATTAATCTTCT-TT
66 TC-GATGCAAAATCAATCCTCTCTT
108023 GCTTCCAAAA
1 -CTTCCAAAA
108033 GAACCTCGTC
Statistics
Matches: 153, Mismatches: 27, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
88 6 0.04
89 2 0.01
90 139 0.91
92 6 0.04
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (89 bp):
CTTCCAAAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTTCATCCAAAACTGTATCATTT
TCGATGCAAAATCAATCCTCTCTT
Found at i:108011 original size:135 final size:134
Alignment explanation
Indices: 107760--108012 Score: 346
Period size: 135 Copynumber: 1.9 Consensus size: 134
107750 TGTCCTTCCG
* *
107760 AAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTTCATCCAAAACTGTATCATTTTCGGAT
1 AAACAGTATCATCATTTGATGCAAAATCAATCCTCTTTTCATCCAAAACAGTATCATTTTC-GAT
* * * **
107825 GGAACATCGATCCTCTCTTCATCCAAAACTGTATCATTTTCGGATGGAATATTGGTCCTCTTTTC
65 GCAACATCAATCCTCTCTTCATCCAAAACAGTATCATTTTCGGATACAATATTGGTCCTCTTTTC
107890 ATCCA
130 ATCCA
* * *
107895 AAACTGTATCATCATTTGATGCAAAATCAATTCTCTTTTCTTCCAAAACAGTATCATCATTT-GA
1 AAACAGTATCATCATTTGATGCAAAATCAATCCTCTTTTCATCCAAAACAGTATCAT--TTTCGA
* * * *
107959 TGCAAGATCAATCCTCTTTTCTTCCAAAACAGTATCATTTTCTGATACAATATT
64 TGCAACATCAATCCTCTCTTCATCCAAAACAGTATCATTTTCGGATACAATATT
108013 AATCTTCTTT
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
135 99 0.97
137 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (134 bp):
AAACAGTATCATCATTTGATGCAAAATCAATCCTCTTTTCATCCAAAACAGTATCATTTTCGATG
CAACATCAATCCTCTCTTCATCCAAAACAGTATCATTTTCGGATACAATATTGGTCCTCTTTTCA
TCCA
Found at i:108022 original size:45 final size:45
Alignment explanation
Indices: 107754--108032 Score: 262
Period size: 45 Copynumber: 6.2 Consensus size: 45
107744 GTGCTATGTC
*
107754 CTTCCGAAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTT
1 CTTCCAAAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTT
* * * * * *
107799 CATCCAAAACTGTATCAT--TTTCGGATGGAACATCGATCCTCTCTT
1 CTTCCAAAACAGTATCATCATTT--GATGCAAGATCAATCCTCTTTT
* * * * ***
107844 CATCCAAAACTGTATCAT--TTTCGGATGGAATATTGGTCCTCTTTT
1 CTTCCAAAACAGTATCATCATTT--GATGCAAGATCAATCCTCTTTT
* * * *
107889 CATCCAAAACTGTATCATCATTTGATGCAAAATCAATTCTCTTTT
1 CTTCCAAAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTT
107934 CTTCCAAAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTT
1 CTTCCAAAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTT
* * * * * *
107979 CTTCCAAAACAGTATCAT-TTTCTGATACAATATTAATCTTCTTTG
1 CTTCCAAAACAGTATCATCATT-TGATGCAAGATCAATCCTCTTTT
108024 CTTCCAAAA
1 CTTCCAAAA
108033 GAACCTCGTC
Statistics
Matches: 202, Mismatches: 27, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
43 3 0.01
44 2 0.01
45 194 0.96
47 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (45 bp):
CTTCCAAAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTT
Found at i:111072 original size:38 final size:39
Alignment explanation
Indices: 110997--111072 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 39
110987 TTTTATTTCT
**
110997 TTTTAATACCTACCATTAAAAACTTTAATTTTTGTTTTA
1 TTTTAATACCTACCATTAAAAACTTTAATTTAAGTTTTA
*
111036 TTTTAATA-CTACCATTCAAAA-TTTAATATTAAGTTTT
1 TTTTAATACCTACCATTAAAAACTTTAAT-TTAAGTTTT
111073 GAAATATTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 6 0.18
38 19 0.58
39 8 0.24
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.50
Consensus pattern (39 bp):
TTTTAATACCTACCATTAAAAACTTTAATTTAAGTTTTA
Found at i:112482 original size:21 final size:22
Alignment explanation
Indices: 112436--112482 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
112426 CACACATGTA
* * *
112436 TTAATGAAGAAAACTTTGAGTT
1 TTAAAGAAGAAAACTTAGAATT
112458 TTAAAGAAGAAAA-TTAGAATT
1 TTAAAGAAGAAAACTTAGAATT
112479 TTAA
1 TTAA
112483 GAAATTCCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.49, C:0.02, G:0.15, T:0.34
Consensus pattern (22 bp):
TTAAAGAAGAAAACTTAGAATT
Found at i:117410 original size:20 final size:21
Alignment explanation
Indices: 117371--117410 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
117361 GTTGGAACGG
*
117371 ATTTAAAAACCACGATAAAAA
1 ATTTAAAAACCACGAGAAAAA
117392 ATTTAAAAACCACG-GAAAA
1 ATTTAAAAACCACGAGAAAA
117411 GGGCCAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.60, C:0.15, G:0.07, T:0.17
Consensus pattern (21 bp):
ATTTAAAAACCACGAGAAAAA
Found at i:119311 original size:20 final size:21
Alignment explanation
Indices: 119274--119312 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
119264 ATTGGACAAA
119274 AAATATTAAATAAAAATATAT
1 AAATATTAAATAAAAATATAT
*
119295 AAATATT-AATAATAATAT
1 AAATATTAAATAAAAATAT
119313 TTTAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATATTAAATAAAAATATAT
Found at i:119883 original size:44 final size:44
Alignment explanation
Indices: 119835--119975 Score: 140
Period size: 44 Copynumber: 3.2 Consensus size: 44
119825 TTTTTTGTGA
* * * * *
119835 AAACGGCGCAATAGGTCTGGTATTTAACGGCGTTTTTAGGGTAC
1 AAACGCCGCGATAGGTCTGGAATATAACGGCGTTTTTAGGATAC
* * *
119879 AAACGCCGCGATAGGACTGGAATATAGCGTCGTTTTTAGGATAC
1 AAACGCCGCGATAGGTCTGGAATATAACGGCGTTTTTAGGATAC
* * * * **
119923 AAACACCGCGATAGGTCT-TATATATAGCGGCATTTTTTTGATAC
1 AAACGCCGCGATAGGTCTGGA-ATATAACGGCGTTTTTAGGATAC
119967 AAACGCCGC
1 AAACGCCGC
119976 TAAATAACAC
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
43 1 0.01
44 79 0.99
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (44 bp):
AAACGCCGCGATAGGTCTGGAATATAACGGCGTTTTTAGGATAC
Found at i:123387 original size:13 final size:13
Alignment explanation
Indices: 123369--123393 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
123359 TCAAACCAAA
123369 GGAGAAATAAAGC
1 GGAGAAATAAAGC
123382 GGAGAAATAAAG
1 GGAGAAATAAAG
123394 AAATAAGAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.32, T:0.08
Consensus pattern (13 bp):
GGAGAAATAAAGC
Found at i:123891 original size:39 final size:40
Alignment explanation
Indices: 123778--123931 Score: 132
Period size: 41 Copynumber: 3.8 Consensus size: 40
123768 ATATTAAATT
* * * * * *
123778 TATTGCTGCATTTGTATAAAAACGCCACTAATGTCCA-AA
1 TATTGCGGCGTTTGTGTAAAAACGCCACTAAAGTACACAC
* *
123817 TATTTTGCGGCGTTTTTGTTTAAAAACGACACTAAAGTA-ACAC
1 TA--TTGCGGCG--TTTGTGTAAAAACGCCACTAAAGTACACAC
* * *
123860 TATTGCGGCGTTTGTGTAAAAACGCCGCTAAATTACCACTC
1 TATTGCGGCGTTTGTGTAAAAACGCCACTAAAGTA-CACAC
*
123901 TATTGCGGCGTTTGTTGAAAAAACGCCACTA
1 TATTGCGGCGTTTG-TGTAAAAACGCCACTA
123932 TAAACATCTC
Statistics
Matches: 93, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
39 23 0.25
41 31 0.33
42 15 0.16
43 24 0.26
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (40 bp):
TATTGCGGCGTTTGTGTAAAAACGCCACTAAAGTACACAC
Found at i:123904 original size:41 final size:41
Alignment explanation
Indices: 123859--124017 Score: 146
Period size: 41 Copynumber: 3.8 Consensus size: 41
123849 TAAAGTAACA
*
123859 CTATTGCGGCGTTTGTGTAAAAACGCCGCTAAATTACCACT
1 CTATTACGGCGTTTGTGTAAAAACGCCGCTAAATTACCACT
* * *
123900 CTATTGCGGCGTTTGTTGAAAAAACGCCACTATAA--A-CATCT
1 CTATTACGGCGTTTG-TGTAAAAACGCCGCTA-AATTACCA-CT
* * *
123941 CTATTACGGCGTTT-TAGCTATAAATGCTGCTAAATTACCACT
1 CTATTACGGCGTTTGT-G-TAAAAACGCCGCTAAATTACCACT
* *
123983 CTATTACGGCTTTTGTTTAAAAAAACGCCGCTAAA
1 CTATTACGGCGTTTGTGT--AAAAACGCCGCTAAA
124018 GTATCATTTT
Statistics
Matches: 94, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
39 1 0.01
40 5 0.05
41 41 0.44
42 30 0.32
43 17 0.18
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.31
Consensus pattern (41 bp):
CTATTACGGCGTTTGTGTAAAAACGCCGCTAAATTACCACT
Found at i:125129 original size:13 final size:14
Alignment explanation
Indices: 125106--125141 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
125096 CCACGACACG
125106 ATTCAAATTATTTT
1 ATTCAAATTATTTT
125120 ATTC-AATTATTTT
1 ATTCAAATTATTTT
*
125133 ATTTAAATT
1 ATTCAAATT
125142 GTTATGTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTCAAATTATTTT
Found at i:130602 original size:41 final size:41
Alignment explanation
Indices: 130557--130651 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
130547 TGCTTTTTGA
*
130557 ACAAACACCGC-AAAAGACTCTTACTTTAGAGGCGTTTGTAT
1 ACAAACACCGCTAAAA-ACTCATACTTTAGAGGCGTTTGTAT
* * * * * *
130598 ACAAACACTGCTAAAAACTCATATTTTTGTGGTGTTTTTAT
1 ACAAACACCGCTAAAAACTCATACTTTAGAGGCGTTTGTAT
*
130639 ACAAACGCCGCTA
1 ACAAACACCGCTA
130652 TATGATTGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 40 0.91
42 4 0.09
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (41 bp):
ACAAACACCGCTAAAAACTCATACTTTAGAGGCGTTTGTAT
Done.