Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005700.1 Hibiscus syriacus cultivar Beakdansim tig00013330_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: 60731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1797 original size:13 final size:13
Alignment explanation
Indices: 1781--1812 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1771 CTCAATGCAC
1781 GTCATAAATGTGT
1 GTCATAAATGTGT
1794 GTCATAAATGTGT
1 GTCATAAATGTGT
1807 GTCATA
1 GTCATA
1813 GATTTATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (13 bp):
GTCATAAATGTGT
Found at i:21082 original size:25 final size:27
Alignment explanation
Indices: 21054--21105 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
21044 TTTGTAATTT
*
21054 TAAAATT-T-TATTTTAAATAAAAAAA
1 TAAAATTATATATTTTAAAGAAAAAAA
*
21079 TAAAATTATATATTTTTAAGAAAAAAA
1 TAAAATTATATATTTTAAAGAAAAAAA
21106 ACCCCAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 1 0.04
27 15 0.65
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
TAAAATTATATATTTTAAAGAAAAAAA
Found at i:24377 original size:5 final size:5
Alignment explanation
Indices: 24363--24395 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
24353 TTTATTTGAC
24363 AATA- AATAT AATAT AATAT AATAT AATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATA
24396 AAAATATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:24974 original size:16 final size:18
Alignment explanation
Indices: 24948--24980 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
24938 AATTAAAATT
24948 ACAAGACAC-AATTGAAA
1 ACAAGACACAAATTGAAA
24965 ACAA-ACACAAATTGAA
1 ACAAGACACAAATTGAA
24981 GGAACACGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.61, C:0.18, G:0.09, T:0.12
Consensus pattern (18 bp):
ACAAGACACAAATTGAAA
Found at i:26387 original size:20 final size:20
Alignment explanation
Indices: 26344--26387 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
26334 CCTTTTTTTG
* ***
26344 TTTGCAATTTCTTTTTTTTG
1 TTTGCAATTTCTTCTTTAAC
26364 TTTGCAATTTCTTCTTTAAC
1 TTTGCAATTTCTTCTTTAAC
26384 TTTG
1 TTTG
26388 ACCCCAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.09, T:0.64
Consensus pattern (20 bp):
TTTGCAATTTCTTCTTTAAC
Found at i:26387 original size:24 final size:20
Alignment explanation
Indices: 26328--26376 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
26318 ACAGGTTTTT
*
26328 CAATTTCCTTTTTTTGTTTG
1 CAATTTCTTTTTTTTGTTTG
26348 CAATTTCTTTTTTTTGTTTG
1 CAATTTCTTTTTTTTGTTTG
26368 CAATTTCTT
1 CAATTTCTT
26377 CTTTAACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.14, G:0.08, T:0.65
Consensus pattern (20 bp):
CAATTTCTTTTTTTTGTTTG
Found at i:27540 original size:17 final size:17
Alignment explanation
Indices: 27518--27554 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
27508 ATTCGAGTTT
27518 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
27535 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
27552 GAG
1 GAG
27555 CTCAAAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.27
Consensus pattern (17 bp):
GAGTTCGAGCTTGAATC
Found at i:27596 original size:24 final size:24
Alignment explanation
Indices: 27538--27604 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
27528 TTGAATCGAG
*
27538 TTCGAGCTTGAATCGAGCTCAAAA
1 TTCGAGCTTCAATCGAGCTCAAAA
*
27562 TT-GAGCTTCAATCGAGCTC-AAG
1 TTCGAGCTTCAATCGAGCTCAAAA
27584 TCTCGAGCTTCAATCGAGCTC
1 T-TCGAGCTTCAATCGAGCTC
27605 CTGAATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
22 3 0.08
23 17 0.44
24 19 0.49
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (24 bp):
TTCGAGCTTCAATCGAGCTCAAAA
Found at i:30087 original size:15 final size:15
Alignment explanation
Indices: 30067--30169 Score: 100
Period size: 15 Copynumber: 6.5 Consensus size: 15
30057 TAATAAGGTT
30067 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
30082 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
30097 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
30112 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
*
30131 TTGATTTATTTTTAAATA
1 ---ATTTATTTTAAAATA
30149 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
30163 ATTTATT
1 ATTTATT
30170 AGTATGGATT
Statistics
Matches: 74, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
14 12 0.16
15 43 0.58
16 4 0.05
17 2 0.03
18 1 0.01
19 1 0.01
20 2 0.03
21 3 0.04
22 6 0.08
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:30103 original size:30 final size:30
Alignment explanation
Indices: 30067--30126 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
30057 TAATAAGGTT
*
30067 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAAATTATTATAAAATA
30097 ATTTATTTTAAAATAAATTATTATAAAATA
1 ATTTATTTTAAAATAAATTATTATAAAATA
30127 TGGATTGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
ATTTATTTTAAAATAAATTATTATAAAATA
Found at i:30147 original size:22 final size:22
Alignment explanation
Indices: 30122--30216 Score: 68
Period size: 22 Copynumber: 4.2 Consensus size: 22
30112 AATTATTATA
30122 AAATATGGATTGATTTATTTTT
1 AAATATGGATTGATTTATTTTT
** * * *
30144 AAATAATTTATTTTAAATAATTTATT
1 AAAT-ATGGA--TTGATTTATTT-TT
* *
30170 -AGTATGGATTGATTTATTTTA
1 AAATATGGATTGATTTATTTTT
*
30191 AAATATGAATTGATTTA-TTTT
1 AAATATGGATTGATTTATTTTT
30212 AAATA
1 AAATA
30217 ACTTATTAGT
Statistics
Matches: 53, Mismatches: 15, Indels: 11
0.67 0.19 0.14
Matches are distributed among these distances:
21 9 0.17
22 26 0.49
23 3 0.06
24 3 0.06
25 10 0.19
26 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
AAATATGGATTGATTTATTTTT
Found at i:30159 original size:14 final size:14
Alignment explanation
Indices: 30134--30169 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
30124 ATATGGATTG
30134 ATTTATTTTTAAATA
1 ATTTA-TTTTAAATA
30149 ATTTATTTTAAATA
1 ATTTATTTTAAATA
30163 ATTTATT
1 ATTTATT
30170 AGTATGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:30187 original size:32 final size:31
Alignment explanation
Indices: 30149--30300 Score: 142
Period size: 32 Copynumber: 5.4 Consensus size: 31
30139 TTTTTAAATA
30149 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAA-TTATTAGTATGGATTG
30181 ATTTATTTT-AA-AA-TA-T-G-A---ATTG
1 ATTTATTTTAAATAATTATTAGTATGGATTG
30203 ATTTATTTTAAATAACTTATTAGTATGGATTG
1 ATTTATTTTAAATAA-TTATTAGTATGGATTG
*
30235 ATTTATTTT-AA-AA-TA-T-G-A---ACTG
1 ATTTATTTTAAATAATTATTAGTATGGATTG
30257 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAA-TTATTAGTATGGATTG
30289 ATTTATTTTAAA
1 ATTTATTTTAAA
30301 ATATGGATTA
Statistics
Matches: 98, Mismatches: 2, Indels: 40
0.70 0.01 0.29
Matches are distributed among these distances:
22 25 0.26
23 4 0.04
24 4 0.04
25 2 0.02
26 6 0.06
27 4 0.04
28 6 0.06
29 2 0.02
30 4 0.04
31 4 0.04
32 37 0.38
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (31 bp):
ATTTATTTTAAATAATTATTAGTATGGATTG
Found at i:30205 original size:69 final size:67
Alignment explanation
Indices: 30067--30224 Score: 185
Period size: 69 Copynumber: 2.3 Consensus size: 67
30057 TAATAAGGTT
* *
30067 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
1 ATTTATTTTTAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGAAT
30132 TG
66 TG
* ** * * * *
30134 ATTTATTTTTAAATAATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 ATTTATTTTTAAATAATTTATTATAAAATAATTTATT--T-TAAAATAAATTATTATAAAATATG
30198 AATTG
63 AATTG
*
30203 ATTTA-TTTTAAATAACTTATTA
1 ATTTATTTTTAAATAATTTATTA
30225 GTATGGATTG
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
66 13 0.17
67 21 0.27
68 16 0.21
69 27 0.35
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (67 bp):
ATTTATTTTTAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGAAT
TG
Found at i:30214 original size:54 final size:54
Alignment explanation
Indices: 30149--30846 Score: 324
Period size: 54 Copynumber: 12.8 Consensus size: 54
30139 TTTTTAAATA
30149 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
* *
30203 ATTTATTTTAAATAACTTATTAGTATGGATTGATTTATTTTAAAATATGAACTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
* *
30257 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
* * * **
30311 ATTTA--TT--AT--TGTAGTT-GTATTGATTAATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAAT-ATGAATT-G
** * ** * * * **
30360 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTT-AAATAATTTATTAG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGAATT-G
** ** * * * * ** *
30414 TATGGATTTT-TTTATTTTA-AAATATGGATTAATTTATTATTGTAGT-TGTACGGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT-TTAAAATATG-A---ATTG
* *
30471 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
* * * *
30525 ATTTATTTTAAATAATTTATTGGTATAGATTTATTTATTTT--AA-AT-AATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
* ** * * * *
30575 A-TTAGTATGGACTGATTTATTTTAAAATATGGTTTGATTTATTTTAAATAATTTATTAGTATGG
1 ATTTA-TTTTAAATAATTTA--TT--AGTATGGATTGATTTATTTT-AA-AA--TA-T-G-A---
*
30639 AATG
51 ATTG
* *
30643 TTTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
* *
30697 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT--AA-AT-AATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGAATTG
* * * * * * *** *
30741 ATTAGTATGGGTTGATTTATTT-TAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATT--TAT--TTTAAATAATTTAT-TAGTATGGATTGATTTA-T-TT-TA-AAATATGAATTG
30803 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
30847 TAATTTATTA
Statistics
Matches: 496, Mismatches: 86, Indels: 124
0.70 0.12 0.18
Matches are distributed among these distances:
44 6 0.01
45 2 0.00
46 4 0.01
47 4 0.01
48 47 0.09
49 7 0.01
50 22 0.04
51 3 0.01
52 10 0.02
53 1 0.00
54 252 0.51
55 10 0.02
56 13 0.03
57 13 0.03
58 46 0.09
59 2 0.00
60 5 0.01
61 3 0.01
62 9 0.02
63 2 0.00
64 18 0.04
65 1 0.00
66 2 0.00
68 11 0.02
69 3 0.01
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
Found at i:30356 original size:80 final size:80
Alignment explanation
Indices: 30257--30846 Score: 361
Period size: 80 Copynumber: 7.5 Consensus size: 80
30247 ATATGAACTG
*
30257 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
30322 TAGTTGTATTGATTA
66 TAGTTGTATTGATTA
30337 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT-TTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATT-
* * **
30401 AATAATT-TATTAGTATGG
65 -GTAGTTGTATT-G-ATTA
* * * *** *
30419 ATTT-TTTT--AT--TTTA-AAATATGGATTAATTTATTATTGTAGTTGTACGGATTGATTTATT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATATGGATTGATTTATT
* *
30478 -TTAAATAATT-TATT-AGTATA
62 ATT--GTAGTTGTATTGA-T-TA
* * * ** * * *
30498 GATTGA-TTT--AT--TTTA-AAATATGGATTGATTTATTTT-AAATAATTTATTGGTATA-GAT
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATTGATTTATTAT
* * * * *
30555 T-TATTTATTTTAAATA
64 TGTAGTTGTATTGATTA
* * * * *
30571 ATTTATTAGTATGGACTGATTTATTTTAAAATATGGTTTGATTTATTTT--AA-AT--A---ATT
1 ATTTATT--T-T-AAATAATTTA--TT--AGTATGGATTGATTTATTTTAAAATATGGATTGATT
* * * *
30628 TATTA--GTA--TGGAATGTTTT
58 TATTATTGTAGTTGTATTGATTA
30647 ATTT----TAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
* *
30708 TAGTTGTATGGATTG
66 TAGTTGTATTGATTA
*
30723 ATTTATTTTAAATAATTTATTAGTATGGGTTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
* *
30788 TAGTTGTATGGATTG
66 TAGTTGTATTGATTA
30803 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
30847 TAATTTATTA
Statistics
Matches: 407, Mismatches: 55, Indels: 96
0.73 0.10 0.17
Matches are distributed among these distances:
64 18 0.04
66 4 0.01
67 2 0.00
68 7 0.02
69 2 0.00
72 12 0.03
73 7 0.02
74 6 0.01
75 3 0.01
76 42 0.10
77 7 0.02
78 10 0.02
79 9 0.02
80 235 0.58
81 14 0.03
82 6 0.01
83 2 0.00
85 2 0.00
86 19 0.05
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (80 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
TAGTTGTATTGATTA
Found at i:30359 original size:134 final size:134
Alignment explanation
Indices: 30203--30568 Score: 633
Period size: 134 Copynumber: 2.7 Consensus size: 134
30193 ATATGAATTG
* * *
30203 ATTTATTTTAAATAACTTATTAGTATGGATTGATTTATTTTAAAATATGAACTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
* **
30268 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAGTTGTATTG
66 ATAATTTATTAGTATGGATTTATTTATTTTAAAATATGGATTAATTTATTATTGTAGTTGTACGG
30333 ATTA
131 ATTA
30337 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
*
30402 ATAATTTATTAGTATGGATTTTTTTATTTTAAAATATGGATTAATTTATTATTGTAGTTGTACGG
66 ATAATTTATTAGTATGGATTTATTTATTTTAAAATATGGATTAATTTATTATTGTAGTTGTACGG
*
30467 ATTG
131 ATTA
*
30471 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
* *
30536 ATAATTTATTGGTATAGATTTATTTATTTTAAA
66 ATAATTTATTAGTATGGATTTATTTATTTTAAA
30569 TAATTTATTA
Statistics
Matches: 220, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
134 220 1.00
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.53
Consensus pattern (134 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
ATAATTTATTAGTATGGATTTATTTATTTTAAAATATGGATTAATTTATTATTGTAGTTGTACGG
ATTA
Found at i:30375 original size:32 final size:32
Alignment explanation
Indices: 30327--30434 Score: 110
Period size: 32 Copynumber: 3.7 Consensus size: 32
30317 TATTGTAGTT
* *
30327 GTATTGATTAATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
30359 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
30382 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
**
30413 GTATGGATTTTTTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
30435 ATATGGATTA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
22 14 0.23
23 4 0.06
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.06
32 32 0.52
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:30376 original size:22 final size:22
Alignment explanation
Indices: 30360--30402 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
30350 AATTTATTAG
30360 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
30382 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
30403 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:30507 original size:32 final size:32
Alignment explanation
Indices: 30465--30686 Score: 232
Period size: 32 Copynumber: 7.6 Consensus size: 32
30455 GTAGTTGTAC
30465 GGATTGATTTATTTTAAATAATTTATTAGTAT
1 GGATTGATTTATTTTAAATAATTTATTAGTAT
*
30497 AGATTGATTTA-TTT---TAA---A--A-TAT
1 GGATTGATTTATTTTAAATAATTTATTAGTAT
*
30519 GGATTGATTTATTTTAAATAATTTATTGGTAT
1 GGATTGATTTATTTTAAATAATTTATTAGTAT
* *
30551 AGATTTATTTATTTTAAATAATTTATTAGTAT
1 GGATTGATTTATTTTAAATAATTTATTAGTAT
*
30583 GGACTGATTTA-TTT---TAA---A--A-TAT
1 GGATTGATTTATTTTAAATAATTTATTAGTAT
*
30605 GGTTTGATTTATTTTAAATAATTTATTAGTAT
1 GGATTGATTTATTTTAAATAATTTATTAGTAT
* *
30637 GGAATGTTTTATTTTAAATAATTTATTAGTAT
1 GGATTGATTTATTTTAAATAATTTATTAGTAT
30669 GGATTGATTTATTTTAAA
1 GGATTGATTTATTTTAAA
30687 ATATGGATTG
Statistics
Matches: 154, Mismatches: 16, Indels: 40
0.73 0.08 0.19
Matches are distributed among these distances:
22 25 0.16
23 8 0.05
25 2 0.01
26 6 0.04
28 6 0.04
29 2 0.01
31 7 0.05
32 98 0.64
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
GGATTGATTTATTTTAAATAATTTATTAGTAT
Found at i:30531 original size:188 final size:184
Alignment explanation
Indices: 30147--30783 Score: 580
Period size: 188 Copynumber: 3.3 Consensus size: 184
30137 TATTTTTAAA
30147 TAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTT
1 TAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTT
*
30212 AAATAACTTATTAGTATGGATTGATTTATTTTAAAATATGAACTGATTTATTTTAAATAATTTAT
66 AAATAACTTATTAGTATGGATTGATTTATTTTAAAATATG-A--GATTTAATTT-AATAATTTAT
* **
30277 TAGTATGGATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAGTTGTATTGAT
127 TAGTACGGATTGATTTATTTTAAAATATGGATTAATAGATTATTGTAGTTGTATTGAT
*
30335 TAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTT
1 TAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTT
* ** *
30400 AAATAATTTATTAGTATGGATTTTTTTATTTTAAAATATG-GA-TTAATTT-ATTATTGTAGTT-
66 AAATAACTTATTAGTATGGATTGATTTATTTTAAAATATGAGATTTAATTTAATAATT-TA-TTA
** *
30461 GTACGGATTGATTTATTTT-AAATAATTTATTAGTATAGATTGATT-TA-TTTTAAAATATGGAT
129 GTACGGATTGATTTATTTTAAAAT-ATGGATTA--ATAGATT-ATTGTAGTTGT---AT-T-GAT
* * * * *
30523 TGATTTATTTTAAATAATTTATTGGTATAGATTTATTTATTTTAAATAATTTATTAGTATGGACT
1 TAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-T-G-A---ATT
* * * * * *
30588 GATTTATTTT-AA-AA--TA-TGGT-TTGATTTATTTTAAATAATTTATTAGTATGGAATGTTTT
56 GATTTATTTTAAATAACTTATTAGTATGGATTGA-TTT--AT--TTTA-AAATAT-G-A-GATTT
* * * **
30647 ATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGT
112 AATTT-AATAATTTATTAGTACGGATTGATTTATTTTAAAATATGGATTAATAGATTATTGTAGT
*
30712 TGTATGGAT
176 TGTATTGAT
* * *
30721 TGATTTATTTTAAATAATTTATTAGTATGGGTTGATTTATTTTAAAATATGGATTGATTTATT
1 TAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATT
30784 ATTGTAGTTG
Statistics
Matches: 371, Mismatches: 40, Indels: 76
0.76 0.08 0.16
Matches are distributed among these distances:
181 9 0.02
182 26 0.07
183 11 0.03
184 9 0.02
185 3 0.01
186 2 0.01
187 1 0.00
188 153 0.41
189 2 0.01
190 2 0.01
192 9 0.02
193 8 0.02
194 5 0.01
195 2 0.01
196 4 0.01
197 8 0.02
198 58 0.16
199 1 0.00
200 2 0.01
201 3 0.01
202 8 0.02
203 11 0.03
204 25 0.07
205 9 0.02
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.53
Consensus pattern (184 bp):
TAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTTT
AAATAACTTATTAGTATGGATTGATTTATTTTAAAATATGAGATTTAATTTAATAATTTATTAGT
ACGGATTGATTTATTTTAAAATATGGATTAATAGATTATTGTAGTTGTATTGAT
Found at i:30544 original size:14 final size:14
Alignment explanation
Indices: 30525--30577 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
30515 ATATGGATTG
30525 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
30539 ATTTATTGGTATAGATTT
1 ATTTATT--T-TA-AATA
30557 ATTTATTTTAAATA
1 ATTTATTTTAAATA
30571 ATTTATT
1 ATTTATT
30578 AGTATGGACT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 16 0.52
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.29
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:30605 original size:22 final size:22
Alignment explanation
Indices: 30580--30622 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
30570 AATTTATTAG
30580 TATGGACTGATTTATTTTAAAA
1 TATGGACTGATTTATTTTAAAA
**
30602 TATGGTTTGATTTATTTTAAA
1 TATGGACTGATTTATTTTAAA
30623 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGACTGATTTATTTTAAAA
Found at i:30680 original size:18 final size:18
Alignment explanation
Indices: 30657--30704 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
30647 ATTTTAAATA
*
30657 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
30675 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
30697 ATTTATTA
1 ATTTATTA
30705 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:30782 original size:252 final size:246
Alignment explanation
Indices: 30382--30846 Score: 752
Period size: 252 Copynumber: 1.9 Consensus size: 246
30372 TATTTTAAAA
* **
30382 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTTTTTTATTTTAAAATATGGATTAAT
1 TATGGAATGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAAT
30447 TTATTATTGTAGTTGTACGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT
66 TTATTATTGTAGTTGTACGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT
* *
30512 AAAATATGGATTGATTTATTTTAAATAATTTA-TTGGTATAGATTTATTTATTTTAAATAATTTA
131 AAAATATGGATTGATTTA--TT--AT--TGTAGTT-GTATAGATTGATTTATTTTAAATAATTTA
30576 TTAGTATGGACTGATTTATTTTAAAATATGGTTTGATTTATTTTAAATAATTTATTAG
189 TTAGTATGGACTGATTTATTTTAAAATATGGTTTGATTTATTTTAAATAATTTATTAG
* *
30634 TATGGAATGTTTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGAATGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAAT
* * *
30699 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGGTTGATTTATTTT
66 TTATTATTGTAGTTGTACGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT
*
30764 AAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTAT
131 AAAATATGGATTGATTTATTATTGTAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTAT
*
30829 GGATTGATTTATTTTAAA
196 GGACTGATTTATTTTAAA
30847 TAATTTATTA
Statistics
Matches: 200, Mismatches: 12, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
246 54 0.27
247 2 0.01
248 2 0.01
250 2 0.01
252 140 0.70
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (246 bp):
TATGGAATGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAAT
TTATTATTGTAGTTGTACGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT
AAAATATGGATTGATTTATTATTGTAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTAT
GGACTGATTTATTTTAAAATATGGTTTGATTTATTTTAAATAATTTATTAG
Found at i:30834 original size:32 final size:32
Alignment explanation
Indices: 30793--30856 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
30783 TATTGTAGTT
30793 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
30825 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
30857 TTGTAGTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:30906 original size:31 final size:31
Alignment explanation
Indices: 30871--30929 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
30861 AGTTGTATGG
* *
30871 ATTATTTAAATTTCAATATTGTAAAACTAAA
1 ATTATTTAAATCTCAATATTGCAAAACTAAA
*
30902 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAATATTGCAAAACT
30930 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAATATTGCAAAACTAAA
Found at i:33646 original size:36 final size:36
Alignment explanation
Indices: 33551--33649 Score: 101
Period size: 38 Copynumber: 2.6 Consensus size: 36
33541 AACCGACTCG
* *
33551 AAAATATGTATCTTCTATCCGAATTCGATTCAATCCAA
1 AAAATATATATCTTC-ATCCG-ATTCGACTCAATCCAA
* * *
33589 AACAATTTATATCTTTCATCCGA-TCTGACTCGATCCGA
1 AA-AATATATATC-TTCATCCGATTC-GACTCAATCCAA
33627 AAAATATATATCTTCATCCGATT
1 AAAATATATATCTTCATCCGATT
33650 TCGGTCTAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
36 9 0.18
37 12 0.24
38 14 0.27
39 13 0.25
40 3 0.06
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.35
Consensus pattern (36 bp):
AAAATATATATCTTCATCCGATTCGACTCAATCCAA
Found at i:34790 original size:10 final size:10
Alignment explanation
Indices: 34777--34806 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
34767 AAAACAAAAA
34777 TCCCGGTTTT
1 TCCCGGTTTT
34787 TCCCGGTTTT
1 TCCCGGTTTT
*
34797 TTCCGGTTTT
1 TCCCGGTTTT
34807 CAGCCGGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.20, T:0.53
Consensus pattern (10 bp):
TCCCGGTTTT
Found at i:35031 original size:2 final size:2
Alignment explanation
Indices: 35024--35078 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
35014 TCTTTTGTTT
35024 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
35066 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
35079 TAATTTAGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44374 original size:126 final size:125
Alignment explanation
Indices: 44148--44400 Score: 382
Period size: 126 Copynumber: 2.0 Consensus size: 125
44138 GTTCCTACTG
* * **
44148 GTGTTACAGTATTGTTTTAAACTATCTAGTTGAACTATTTTGGAATTTAAATATTTTGGTCTTAA
1 GTGTTACAATATTATTTTAAACTATCTAGTTGAACTATTTTGGAATTTAAATATTTTGGTCAAAA
* * *
44213 ATCCAATGTGAGAAAAAGGGTATCGATACTAGAAACATGAGTATTGATATTGCCCCTCTA
66 ATCCAATGTCAAAAAAAGGGTATCGATACTAGAAACAGGAGTATTGATATTGCCCCTCTA
*
44273 GTGTTACAATATTATTTTAAACTATCT-GCTTGAATTATTTTTGGAATTTAAATATTTTGGTCAA
1 GTGTTACAATATTATTTTAAACTATCTAG-TTGAACTA-TTTTGGAATTTAAATATTTTGGTCAA
** *
44337 AAATCTGATGTCAAAAAAAGGGTATCGATACTGGAAACAGGAGTATTGATATTGCCCCTCTA
64 AAATCCAATGTCAAAAAAAGGGTATCGATACTAGAAACAGGAGTATTGATATTGCCCCTCTA
44399 GT
1 GT
44401 ATCAATACTG
Statistics
Matches: 115, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
124 1 0.01
125 32 0.28
126 82 0.71
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (125 bp):
GTGTTACAATATTATTTTAAACTATCTAGTTGAACTATTTTGGAATTTAAATATTTTGGTCAAAA
ATCCAATGTCAAAAAAAGGGTATCGATACTAGAAACAGGAGTATTGATATTGCCCCTCTA
Found at i:44415 original size:41 final size:41
Alignment explanation
Indices: 44358--44451 Score: 152
Period size: 41 Copynumber: 2.3 Consensus size: 41
44348 CAAAAAAAGG
44358 GTATCGATACTGGAAACAGGAGTATTGATATTGCCCCTCTA
1 GTATCGATACTGGAAACAGGAGTATTGATATTGCCCCTCTA
* * *
44399 GTATCAATACTGGAAACATGAGTATTGATATTGCTCCTCTA
1 GTATCGATACTGGAAACAGGAGTATTGATATTGCCCCTCTA
*
44440 ATATCGATACTG
1 GTATCGATACTG
44452 AGGGTACCTG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (41 bp):
GTATCGATACTGGAAACAGGAGTATTGATATTGCCCCTCTA
Found at i:49635 original size:25 final size:25
Alignment explanation
Indices: 49600--49658 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
49590 CAAGTGTTCT
49600 AGTT-AAATATTGGATGCTAAGATG
1 AGTTAAAATATTGGATGCTAAGATG
49624 AGTTAAAATATTGGATGCTAAGATG
1 AGTTAAAATATTGGATGCTAAGATG
49649 AGTTAAAATA
1 AGTTAAAATA
49659 ATATAAGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.12
25 30 0.88
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.32
Consensus pattern (25 bp):
AGTTAAAATATTGGATGCTAAGATG
Found at i:50238 original size:21 final size:21
Alignment explanation
Indices: 50214--50264 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
50204 ATGAGTCAAC
50214 GAGATAAGATTGATCAAGTAA
1 GAGATAAGATTGATCAAGTAA
50235 GAGATAAGATTGATCAAGTAA
1 GAGATAAGATTGATCAAGTAA
50256 GAGATAAGA
1 GAGATAAGA
50265 GTTATAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.49, C:0.04, G:0.25, T:0.22
Consensus pattern (21 bp):
GAGATAAGATTGATCAAGTAA
Found at i:50989 original size:18 final size:18
Alignment explanation
Indices: 50949--50991 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
50939 ATATCATTTC
* **
50949 ATTATCCTTATTATTATT
1 ATTATCATTATTAGCATT
*
50967 CTTATCATTATTAGCATT
1 ATTATCATTATTAGCATT
50985 ATTATCA
1 ATTATCA
50992 ATCATATCTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTATCATTATTAGCATT
Found at i:56139 original size:17 final size:16
Alignment explanation
Indices: 56109--56143 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
56099 ACATGAATAA
*
56109 ATACTAATTTCATATC
1 ATACTAATTACATATC
56125 ATACATAATTACATATC
1 ATAC-TAATTACATATC
56142 AT
1 AT
56144 CTCTTATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (16 bp):
ATACTAATTACATATC
Found at i:56423 original size:18 final size:18
Alignment explanation
Indices: 56400--56470 Score: 106
Period size: 18 Copynumber: 3.9 Consensus size: 18
56390 ACGTAGAATT
*
56400 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
56418 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
*
56436 TGTCCCAAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
56454 TGTCTCGAAGGACCACT
1 TGTCCCGAAGGACCACT
56471 CTTTAAGAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:57402 original size:20 final size:20
Alignment explanation
Indices: 57367--57404 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57357 TTCCCATTGA
*
57367 AGTGCATCGGTACATTATAC
1 AGTGCATCGATACATTATAC
*
57387 AGTGCATCGATGCATTAT
1 AGTGCATCGATACATTAT
57405 TTAACATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTATAC
Found at i:59716 original size:45 final size:43
Alignment explanation
Indices: 59674--59795 Score: 163
Period size: 45 Copynumber: 2.7 Consensus size: 43
59664 GCATTTGATG
*
59674 CATCGATGCACAGCCATGCATCGATGCACTCTGGCTATTTTGAAA
1 CATCGATGCACTG--ATGCATCGATGCACTCTGGCTATTTTGAAA
* *
59719 CATCAAATGCATTTGATGCATCGATGCACTCTGGCTATTTTGAAA
1 CATC-GATGCA-CTGATGCATCGATGCACTCTGGCTATTTTGAAA
59764 CATCGAATGCACTTGATGCATCGATGCACTCT
1 CATCG-ATGCAC-TGATGCATCGATGCACTCT
59796 TAGTGCACCG
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
45 62 0.91
46 5 0.07
47 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (43 bp):
CATCGATGCACTGATGCATCGATGCACTCTGGCTATTTTGAAA
Found at i:59792 original size:17 final size:19
Alignment explanation
Indices: 59764--59812 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
59754 TATTTTGAAA
59764 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
59782 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
59801 CACCGATGCACT
1 CATCGATGCACT
59813 AAGGCTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Done.