Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008572.1 Hibiscus syriacus cultivar Beakdansim tig00111498_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: 343468
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1672 original size:2 final size:2
Alignment explanation
Indices: 1622--1655 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1612 AATATGTACT
1622 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
1656 CACACACACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3049 original size:16 final size:18
Alignment explanation
Indices: 3028--3060 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3018 ACCCAACCCG
3028 ATCGGG-TA-TTTAAAAA
1 ATCGGGTTATTTTAAAAA
3044 ATCGGGTTATTTTAAAA
1 ATCGGGTTATTTTAAAA
3061 TTATAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (18 bp):
ATCGGGTTATTTTAAAAA
Found at i:5030 original size:168 final size:168
Alignment explanation
Indices: 4285--5121 Score: 1328
Period size: 168 Copynumber: 5.0 Consensus size: 168
4275 TTCATCGTTT
* * *
4285 TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCGAACATACTCTCCTTTAATTTCGTGCTCTC
1 TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTC
* *
4350 AGT-TTGACTTCCTCTAGAGATTCTTGCAGATAAATTACCTTAGATTCAACTTCCTTTAGGCTAT
66 AGTCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTAT
4414 CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
131 CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
* * * * *
4452 TCTTGAATGACACTCTGCAACTCA-TTTCTTTAGCCAACAACCTCTCGTCTAGTTTCATGCTCTC
1 TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTC
* * * * *
4516 GGCCTTGACTT-CTCTAGAGCTTCTTGCAGAT-AATCACTTTATA-TCAATTTCCTTTAGGCTAT
66 AGTCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTAT
4578 CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
131 CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
** * *
4616 TCCCGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTTTCC-TTAATTTCATGCTCCC
1 TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTC
*
4680 AGTCTTGACTTCCCCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTAT
66 AGTCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTAT
**
4745 CCTTCAACCGAGTTTCTTCCTCCTT-GACTTGGAAGCC
131 CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
* *
4782 TCTTGAATGACACTCCGCAACTCGGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTC
1 TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTC
*
4847 AGTCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCAAT
66 AGTCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTAT
* *
4912 CCTTCAACCGAGCTTCTTCCTCCTTGGACTCGGAAGCC
131 CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
* *
4950 TCTTGAATGACACTCCGCAACTCGGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTC
1 TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTC
*
5015 AGTCTTGAGTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTAT
66 AGTCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTAT
* * *
5080 CCTTCAACCGAGCTTCTTCCTCCTTGGACGCAGTAGCC
131 CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
5118 TCTT
1 TCTT
5122 CCTCAGATTG
Statistics
Matches: 616, Mismatches: 47, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
164 100 0.16
165 47 0.08
166 115 0.19
167 176 0.29
168 178 0.29
ACGTcount: A:0.22, C:0.29, G:0.13, T:0.35
Consensus pattern (168 bp):
TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTC
AGTCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTAT
CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
Found at i:8539 original size:60 final size:58
Alignment explanation
Indices: 8475--8598 Score: 149
Period size: 60 Copynumber: 2.1 Consensus size: 58
8465 TAAAGTACAC
* *
8475 AAATGATCCCCTAACTATGGGACATTATTTTGTTGAGTCTCATGACTATTAAAAGTTATG
1 AAATGATCCCCTAACTATAGGACATTATTTTGTTGAGTC-CAT-ACTATTAAAAGTTATA
* * * * * * *
8535 AAATGATCCCTTAATTGTAGGACATTGTTTTGTTGAGTCCCTCCTATTTAAAGTTATA
1 AAATGATCCCCTAACTATAGGACATTATTTTGTTGAGTCCATACTATTAAAAGTTATA
8593 AAATGA
1 AAATGA
8599 CTATTCGTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 19 0.35
59 2 0.04
60 34 0.62
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (58 bp):
AAATGATCCCCTAACTATAGGACATTATTTTGTTGAGTCCATACTATTAAAAGTTATA
Found at i:9344 original size:24 final size:25
Alignment explanation
Indices: 9302--9359 Score: 109
Period size: 24 Copynumber: 2.4 Consensus size: 25
9292 TACATCATCC
9302 AATAGTCTTAAAAAGATGTAAAACT
1 AATAGTCTTAAAAAGATGTAAAACT
9327 AATAGTCTTAAAAA-ATGTAAAACT
1 AATAGTCTTAAAAAGATGTAAAACT
9351 AATAGTCTT
1 AATAGTCTT
9360 GATTTAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 19 0.58
25 14 0.42
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (25 bp):
AATAGTCTTAAAAAGATGTAAAACT
Found at i:13460 original size:21 final size:21
Alignment explanation
Indices: 13436--13483 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
13426 AAGGGGTTGG
*
13436 TTGTTTGTCTCTTAATCGCGT
1 TTGTTTGCCTCTTAATCGCGT
13457 TTGTTTGCCTCTTAATCGCGT
1 TTGTTTGCCTCTTAATCGCGT
13478 TTGTTT
1 TTGTTT
13484 CGCACCTCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.08, C:0.19, G:0.19, T:0.54
Consensus pattern (21 bp):
TTGTTTGCCTCTTAATCGCGT
Found at i:27211 original size:5 final size:5
Alignment explanation
Indices: 27201--27225 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
27191 TTGGTTAAAG
27201 AGAAA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA
27226 GTTGATGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:27554 original size:32 final size:32
Alignment explanation
Indices: 27513--27593 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 32
27503 TTATTAATTC
*
27513 GTTTGATTTTAGTCTCTTAATTGTTAACTCAT
1 GTTTGATTTTAGTCCCTTAATTGTTAACTCAT
*
27545 GTTTGATTTTAATCCCTTAATTGTTAACTCAT
1 GTTTGATTTTAGTCCCTTAATTGTTAACTCAT
27577 GTTTGATTTTAGTCCCT
1 GTTTGATTTTAGTCCCT
27594 CAACTATATC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.21, C:0.15, G:0.12, T:0.52
Consensus pattern (32 bp):
GTTTGATTTTAGTCCCTTAATTGTTAACTCAT
Found at i:33693 original size:20 final size:21
Alignment explanation
Indices: 33668--33709 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
33658 AAAATAATAT
*
33668 TATTTA-TTATTAGTTAAAAA
1 TATTTATTTATGAGTTAAAAA
*
33688 TATTTATTTATGAGTTATAAA
1 TATTTATTTATGAGTTAAAAA
33709 T
1 T
33710 TGTAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (21 bp):
TATTTATTTATGAGTTAAAAA
Found at i:39694 original size:59 final size:58
Alignment explanation
Indices: 39609--39760 Score: 173
Period size: 59 Copynumber: 2.6 Consensus size: 58
39599 ATTCTTATTT
* * *
39609 TAAATTGGTCCTTAAACTTTTGAATATTTTAATTTCATCCCCAAACTATGACTTTCATTC
1 TAAATTGGTCCTTAAACTTTTGAATATTTCAATTCCATCCACAAACTATGAC--TCATTC
* * * *
39669 TAAATTAGTCCTTATA-TTTTTAATATTTCAATTCCATCCATAAACTATGACTCATTC
1 TAAATTGGTCCTTAAACTTTTGAATATTTCAATTCCATCCACAAACTATGACTCATTC
**
39726 TAAATTGGTCCCCCAAACTTTTGAAT-TTTCCAATT
1 TAAATTGGT-CCTTAAACTTTTGAATATTT-CAATT
39761 TTATCCCCAA
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
57 14 0.18
58 7 0.09
59 42 0.55
60 14 0.18
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (58 bp):
TAAATTGGTCCTTAAACTTTTGAATATTTCAATTCCATCCACAAACTATGACTCATTC
Found at i:40047 original size:59 final size:58
Alignment explanation
Indices: 39901--40039 Score: 145
Period size: 59 Copynumber: 2.4 Consensus size: 58
39891 CATATAGTTG
* * * * **
39901 GGATGAAATTGGAATATTAAAATTTAGGGACAAATTTAGAATGAAGATTATAGTTTGG
1 GGATGAAATTGGAATATTAAAATTTAAGGACAAATTCAGAATCAAGATCATAGTTTAA
* * * * * *
39959 GGAAGAAATTGAAATATTCAAATTTTAAGGACTAATTCA-TATCAATAGTCATAGTTTAA
1 GGATGAAATTGGAATATT-AAAATTTAAGGACAAATTCAGAATCAAGA-TCATAGTTTAA
40018 GGATGAAATTGGAATATTAAAA
1 GGATGAAATTGGAATATTAAAA
40040 AGTTAAGGTA
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
58 24 0.38
59 40 0.62
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.32
Consensus pattern (58 bp):
GGATGAAATTGGAATATTAAAATTTAAGGACAAATTCAGAATCAAGATCATAGTTTAA
Found at i:46103 original size:14 final size:14
Alignment explanation
Indices: 46084--46176 Score: 84
Period size: 14 Copynumber: 6.6 Consensus size: 14
46074 CTCGAGTACA
46084 TATTTAATAATAAT
1 TATTTAATAATAAT
*
46098 TATTTAA-ATTTAAT
1 TATTTAATA-ATAAT
*
46112 TATTTAACT-TTAAT
1 TATTTAA-TAATAAT
*
46126 GATTTAATAATAAT
1 TATTTAATAATAAT
*
46140 TATTTAACT-TTAAT
1 TATTTAA-TAATAAT
*
46154 GATTTAATAATAAT
1 TATTTAATAATAAT
46168 TACTTTAAT
1 TA-TTTAAT
46177 GATTTAACTT
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
13 3 0.05
14 54 0.84
15 7 0.11
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (14 bp):
TATTTAATAATAAT
Found at i:46118 original size:8 final size:8
Alignment explanation
Indices: 46094--46481 Score: 71
Period size: 8 Copynumber: 52.5 Consensus size: 8
46084 TATTTAATAA
46094 TAATTATT
1 TAATTATT
46102 TAA--ATT
1 TAATTATT
46108 TAATTATT
1 TAATTATT
*
46116 TAA--CTT
1 TAATTATT
*
46122 TAATGATT
1 TAATTATT
*
46130 TAA-TA-A
1 TAATTATT
46136 TAATTATT
1 TAATTATT
*
46144 TAA--CTT
1 TAATTATT
*
46150 TAATGATT
1 TAATTATT
*
46158 TAA-TA-A
1 TAATTATT
46164 TAATTACTT
1 TAATTA-TT
*
46173 TAATGATT
1 TAATTATT
*
46181 TAA--CTT
1 TAATTATT
*
46187 TAATGATT
1 TAATTATT
*
46195 TAA-TA-A
1 TAATTATT
46201 TAATTACTT
1 TAATTA-TT
* *
46210 TACTGATT
1 TAATTATT
46218 TAA-T-TT
1 TAATTATT
*
46224 TAATGATT
1 TAATTATT
*
46232 TAA-TA-A
1 TAATTATT
46238 TAATTACTT
1 TAATTA-TT
*
46247 TAATGATT
1 TAATTATT
46255 TAA-T-TT
1 TAATTATT
*
46261 TAATGATT
1 TAATTATT
*
46269 TAATGATT
1 TAATTATT
*
46277 TAA--CTT
1 TAATTATT
**
46283 TAATGCTT
1 TAATTATT
*
46291 TAA-TA-A
1 TAATTATT
46297 TAATTACTT
1 TAATTA-TT
*
46306 TAATGATT
1 TAATTATT
*
46314 TAA-TA-A
1 TAATTATT
*
46320 TAATGACTT
1 TAATTA-TT
*
46329 TAATGATT
1 TAATTATT
*
46337 TAA--CTT
1 TAATTATT
**
46343 TAATGCTT
1 TAATTATT
*
46351 TAA-TA-A
1 TAATTATT
46357 TAATTACTT
1 TAATTA-TT
*
46366 TAATGATT
1 TAATTATT
*
46374 TAATGATT
1 TAATTATT
*
46382 TAATGATT
1 TAATTATT
*
46390 TAATGATT
1 TAATTATT
**
46398 TAA-TAAA
1 TAATTATT
46405 TAATTACTT
1 TAATTA-TT
*
46414 TAATGATT
1 TAATTATT
46422 TAA-T-TT
1 TAATTATT
*
46428 TAATAATT
1 TAATTATT
*
46436 TAA-TA-A
1 TAATTATT
*
46442 TAATTACT
1 TAATTATT
46450 TAA-T-TT
1 TAATTATT
*
46456 TAATGATT
1 TAATTATT
46464 TAA-T-TT
1 TAATTATT
*
46470 TAATGATT
1 TAATTATT
46478 TAAT
1 TAAT
46482 AATAATTACT
Statistics
Matches: 276, Mismatches: 58, Indels: 92
0.65 0.14 0.22
Matches are distributed among these distances:
6 79 0.29
7 26 0.09
8 136 0.49
9 35 0.13
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.50
Consensus pattern (8 bp):
TAATTATT
Found at i:46175 original size:23 final size:23
Alignment explanation
Indices: 46085--46339 Score: 121
Period size: 23 Copynumber: 11.3 Consensus size: 23
46075 TCGAGTACAT
46085 ATTTAATAATAATTA-TTTAA--
1 ATTTAATAATAATTACTTTAATG
*
46105 ATTTAAT--TATTTAACTTTAATG
1 ATTTAATAATAATT-ACTTTAATG
46127 ATTTAATAATAATTATTTAACTTTAATG
1 ATTTAATAAT-A--A-TT-ACTTTAATG
46155 ATTTAATAATAATTACTTTAATG
1 ATTTAATAATAATTACTTTAATG
* * *
46178 ATTTAACT-TTAATGA-TTTAATA
1 ATTTAA-TAATAATTACTTTAATG
* * * *
46200 ATAATTACT-TTACTGA-TTTAAT-
1 AT--TTAATAATAATTACTTTAATG
* * * *
46222 -TTTAATGAT--TTAATAATAATT
1 ATTTAATAATAATTACT-TTAATG
* *
46243 ACTTTAATGAT--TTAATTTTAATG
1 A-TTTAATAATAATT-ACTTTAATG
*
46266 ATTTAATGAT--TTAACTTTAATG
1 ATTTAATAATAATT-ACTTTAATG
*
46288 CTTTAATAATAATTACTTTAATG
1 ATTTAATAATAATTACTTTAATG
*
46311 ATTTAATAATAATGACTTTAATG
1 ATTTAATAATAATTACTTTAATG
46334 ATTTAA
1 ATTTAA
46340 CTTTAATGCT
Statistics
Matches: 194, Mismatches: 19, Indels: 41
0.76 0.07 0.16
Matches are distributed among these distances:
18 6 0.03
19 6 0.03
20 17 0.09
21 1 0.01
22 43 0.22
23 85 0.44
24 11 0.06
25 2 0.01
27 1 0.01
28 22 0.11
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (23 bp):
ATTTAATAATAATTACTTTAATG
Found at i:46183 original size:37 final size:37
Alignment explanation
Indices: 46136--46393 Score: 329
Period size: 37 Copynumber: 6.7 Consensus size: 37
46126 GATTTAATAA
*
46136 TAATTATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
46173 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
* *
46210 TACTGATTTAATTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
* *
46247 TAATGATTTAATTTTAATGATTTAATGATTTAACTTTAATGCTT
1 TAATGATTTAACTTTAATGATTTAAT-A-ATAA--TT-A--CTT
* *
46291 TAATAATAATT-ACTTTAATGATTTAATAATAATGACTT
1 TAATGAT--TTAACTTTAATGATTTAATAATAATTACTT
*
46329 TAATGATTTAACTTTAATGCTTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
*
46366 TAATGATTTAATGATTTAATGATTTAAT
1 TAATGATTTAA--CTTTAATGATTTAAT
46394 GATTTAATAA
Statistics
Matches: 195, Mismatches: 14, Indels: 22
0.84 0.06 0.10
Matches are distributed among these distances:
36 2 0.01
37 132 0.68
38 10 0.05
39 16 0.08
40 1 0.01
41 3 0.02
42 1 0.01
43 3 0.02
44 10 0.05
45 15 0.08
46 2 0.01
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (37 bp):
TAATGATTTAACTTTAATGATTTAATAATAATTACTT
Found at i:46186 original size:14 final size:14
Alignment explanation
Indices: 46094--46512 Score: 180
Period size: 14 Copynumber: 32.0 Consensus size: 14
46084 TATTTAATAA
* *
46094 TAATTATTTAAATT
1 TAATGATTTAACTT
*
46108 TAATTATTTAACTT
1 TAATGATTTAACTT
*
46122 TAATGATTTAA-TAA
1 TAATGATTTAACT-T
*
46136 TAATTATTTAACTT
1 TAATGATTTAACTT
46150 TAATGATTTAA---
1 TAATGATTTAACTT
*
46161 TAAT-AATT-ACTT
1 TAATGATTTAACTT
46173 TAATGATTTAACTT
1 TAATGATTTAACTT
46187 TAATGATTTAA---
1 TAATGATTTAACTT
*
46198 TAAT-AATT-ACTT
1 TAATGATTTAACTT
* *
46210 TACTGATTTAATTT
1 TAATGATTTAACTT
46224 TAATGATTTAA---
1 TAATGATTTAACTT
*
46235 TAAT-AATT-ACTT
1 TAATGATTTAACTT
*
46247 TAATGATTTAATTT
1 TAATGATTTAACTT
46261 TAATG-----A-TT
1 TAATGATTTAACTT
46269 TAATGATTTAACTT
1 TAATGATTTAACTT
*
46283 TAATGCTTTAA---
1 TAATGATTTAACTT
*
46294 TAAT-AATT-ACTT
1 TAATGATTTAACTT
46306 TAATGATTTAA---
1 TAATGATTTAACTT
* *
46317 TAAT-A-ATGACTT
1 TAATGATTTAACTT
46329 TAATGATTTAACTT
1 TAATGATTTAACTT
*
46343 TAATGCTTTAA---
1 TAATGATTTAACTT
*
46354 TAAT-AATT-ACTT
1 TAATGATTTAACTT
*
46366 TAATGATTTAATGATT
1 TAATGATTTAA--CTT
*
46382 TAATGATTTAATGATT
1 TAATGATTTAA--CTT
*
46398 TAATAAATAATT-ACTT
1 TAAT-GAT--TTAACTT
*
46414 TAATGATTTAATTT
1 TAATGATTTAACTT
* *
46428 TAATAATTTAA-TAA
1 TAATGATTTAACT-T
* * *
46442 TAATTACTTAATTT
1 TAATGATTTAACTT
*
46456 TAATGATTTAATTT
1 TAATGATTTAACTT
*
46470 TAATGATTTAA-TAA
1 TAATGATTTAACT-T
* * *
46484 TAATTACTTGACTT
1 TAATGATTTAACTT
46498 TAATGATTTATACTT
1 TAATGATTTA-ACTT
46513 ACTGATATAA
Statistics
Matches: 308, Mismatches: 48, Indels: 97
0.68 0.11 0.21
Matches are distributed among these distances:
8 7 0.02
9 8 0.03
10 14 0.05
11 24 0.08
12 23 0.07
13 22 0.07
14 168 0.55
15 9 0.03
16 28 0.09
17 2 0.01
18 1 0.00
19 2 0.01
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (14 bp):
TAATGATTTAACTT
Found at i:46346 original size:23 final size:22
Alignment explanation
Indices: 46279--46385 Score: 101
Period size: 23 Copynumber: 4.7 Consensus size: 22
46269 TAATGATTTA
* * *
46279 ACTTTAATGCTTTAATAATAATT
1 ACTTTAATGATTTAAT-TTAATG
*
46302 ACTTTAATGATTTAATAATAATG
1 ACTTTAATGATTTAAT-TTAATG
46325 ACTTTAATGATTTAACTTTAATG
1 ACTTTAATGATTTAA-TTTAATG
* *
46348 -CTTTAATAATAATTACTTTAATG
1 ACTTTAATGAT--TTAATTTAATG
46371 A-TTTAATGATTTAAT
1 ACTTTAATGATTTAAT
46386 GATTTAATGA
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
21 4 0.05
22 9 0.12
23 56 0.77
24 4 0.05
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (22 bp):
ACTTTAATGATTTAATTTAATG
Found at i:46524 original size:42 final size:41
Alignment explanation
Indices: 46136--46527 Score: 280
Period size: 37 Copynumber: 9.7 Consensus size: 41
46126 GATTTAATAA
*
46136 TAATTATTTAACTTTAATGATTTAATAAT-A--A-TT-ACTT
1 TAATGATTTAA-TTTAATGATTTAATAATAATTACTTGACTT
46173 TAATGATTTAACTTTAATGATTTAATAAT-A--A-TT-ACTT
1 TAATGATTTAA-TTTAATGATTTAATAATAATTACTTGACTT
*
46210 TACTGATTTAATTTTAATGATTTAATAAT-A--A-TT-ACTT
1 TAATGATTTAA-TTTAATGATTTAATAATAATTACTTGACTT
* *
46247 TAATGATTTAATTTTAATGATTTAATGAT--TTAACTTTAATGCTT
1 TAATGATTTAA-TTTAATGATTTAATAATAATT-AC-TTGA--CTT
* *
46291 TAATAATAATTACTTTAATGATTTAATAAT-A--A--TGACTT
1 TAATGAT--TTAATTTAATGATTTAATAATAATTACTTGACTT
*
46329 TAATGATTTAACTTTAATGCTTTAATAATAATTACTTTAATGA-TT
1 TAATGATTTAA-TTTAATGATTTAATAATAATTAC--T--TGACTT
*
46374 TAATGATTTAATGATTTAATGATTTAAT-A-AA-TAATT-ACTT
1 TAATGATTT-A--ATTTAATGATTTAATAATAATTACTTGACTT
* * *
46414 TAATGATTTAATTTTAATAATTTAATAATAATTACTTAATTT
1 TAATGATTTAA-TTTAATGATTTAATAATAATTACTTGACTT
46456 TAATGATTTAATTTTAATGATTTAATAATAATTACTTGACTT
1 TAATGATTTAA-TTTAATGATTTAATAATAATTACTTGACTT
* * *
46498 TAATGATTTATACTTACTGATATAATAATA
1 TAATGATTTA-ATTTAATGATTTAATAATA
46528 GTAAATATAT
Statistics
Matches: 301, Mismatches: 23, Indels: 57
0.79 0.06 0.15
Matches are distributed among these distances:
36 3 0.01
37 115 0.38
38 23 0.08
39 4 0.01
40 17 0.06
41 6 0.02
42 69 0.23
43 2 0.01
44 11 0.04
45 29 0.10
46 8 0.03
47 13 0.04
48 1 0.00
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (41 bp):
TAATGATTTAATTTAATGATTTAATAATAATTACTTGACTT
Found at i:47033 original size:6 final size:6
Alignment explanation
Indices: 46981--47029 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
46971 GGTGAGAAGA
* * *
46981 ACTCCT ACTCCC ACTCCC ACTCCC GCTCCC ACTCCC ACTCCC AGTCCC
1 ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC
47029 A
1 A
47030 GTCCTTCTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.16, C:0.61, G:0.04, T:0.18
Consensus pattern (6 bp):
ACTCCC
Found at i:49053 original size:173 final size:173
Alignment explanation
Indices: 48760--49119 Score: 596
Period size: 173 Copynumber: 2.1 Consensus size: 173
48750 CATCAAATAT
* *
48760 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTTGCAATTTAATCACTAAATT
1 AAAATGATCCCTAATTACTAGTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
*
48825 TATAAATTCTTTCAAATTTAACCAATTAAGCATATTAATACTAAATTCAAGCATAGTATACCAAC
66 TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
* **
48890 TTTTTATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
131 TTTTAATAATTTACTCTAATTCCTTAAATTCCAAAAATTTTAC
*
48933 AAAATGATCCCTAATTACTAGTTGGTTCTCAACATTTTCAAACTTAGCAATTTAATC-CATAAAT
1 AAAATGATCCCTAATTACTAGTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCAC-TAAAT
* *
48997 TTATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATAGCAA
65 TTATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAA
*
49062 CTTTTAATAATTTACTCTTATTCCTTAAATTCCAAAAATTTTAC
130 CTTTTAATAATTTACTCTAATTCCTTAAATTCCAAAAATTTTAC
* *
49106 AAAACGGTCCCTAA
1 AAAATGATCCCTAA
49120 AACTTTACAA
Statistics
Matches: 174, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
172 1 0.01
173 173 0.99
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (173 bp):
AAAATGATCCCTAATTACTAGTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
TTTTAATAATTTACTCTAATTCCTTAAATTCCAAAAATTTTAC
Found at i:49418 original size:41 final size:41
Alignment explanation
Indices: 49361--49444 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
49351 TCCCTCTCAG
*
49361 GCTCTCACTGCTTCTGTAATTGTGAATTGCCTCAGCCCCGA
1 GCTCTCACTGCTTCTGTAATTGTGAATTACCTCAGCCCCGA
*
49402 GCTCTCACTGCTTCTGTAATTGTGAATTACCTCAGCCCTGA
1 GCTCTCACTGCTTCTGTAATTGTGAATTACCTCAGCCCCGA
49443 GC
1 GC
49445 AGTCTCTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.18, C:0.31, G:0.19, T:0.32
Consensus pattern (41 bp):
GCTCTCACTGCTTCTGTAATTGTGAATTACCTCAGCCCCGA
Found at i:49615 original size:23 final size:23
Alignment explanation
Indices: 49589--49632 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
49579 AATTGCATGC
49589 CCCCCACATGAAGACGTGCAGGA
1 CCCCCACATGAAGACGTGCAGGA
*
49612 CCCCCACATGCAGACGTGCAG
1 CCCCCACATGAAGACGTGCAG
49633 CCCCTGCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.39, G:0.25, T:0.09
Consensus pattern (23 bp):
CCCCCACATGAAGACGTGCAGGA
Found at i:49848 original size:30 final size:30
Alignment explanation
Indices: 49812--49868 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
49802 AAATTGCGTT
*
49812 AAAGACGCCGAGATATCCA-GCCTTCCATGC
1 AAAGACGCCGAGAGATCCACG-CTTCCATGC
49842 AAAGACGCCGAGAGATCCACGCTTCCA
1 AAAGACGCCGAGAGATCCACGCTTCCA
49869 CATCTGCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.32, C:0.33, G:0.21, T:0.14
Consensus pattern (30 bp):
AAAGACGCCGAGAGATCCACGCTTCCATGC
Found at i:56496 original size:2 final size:2
Alignment explanation
Indices: 56489--56524 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
56479 TACATTCTCA
56489 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
56525 TTCAGTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57410 original size:25 final size:25
Alignment explanation
Indices: 57378--57425 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
57368 ATCATATTTT
57378 AAATTCATATCCTAAGTTAATAATA
1 AAATTCATATCCTAAGTTAATAATA
* **
57403 AAATTCATTTGTTAAGTTAATAA
1 AAATTCATATCCTAAGTTAATAA
57426 AAGAATTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (25 bp):
AAATTCATATCCTAAGTTAATAATA
Found at i:57492 original size:24 final size:25
Alignment explanation
Indices: 57465--57517 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
57455 ATTTTTAAAG
*
57465 TTAAAATAAGAAT-AAAATAT-ATT
1 TTAAAATAAAAATAAAAATATAATT
*
57488 TTTAAATAAAAATAAAAATATAATT
1 TTAAAATAAAAATAAAAATATAATT
57513 TTAAA
1 TTAAA
57518 CTTAAGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.44
24 7 0.28
25 7 0.28
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (25 bp):
TTAAAATAAAAATAAAAATATAATT
Found at i:57495 original size:23 final size:24
Alignment explanation
Indices: 57468--57517 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
57458 TTTAAAGTTA
* *
57468 AAATAAGAAT-AAAATATATTTTT
1 AAATAAAAATAAAAATATAATTTT
57491 AAATAAAAATAAAAATATAATTTT
1 AAATAAAAATAAAAATATAATTTT
57515 AAA
1 AAA
57518 CTTAAGATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
AAATAAAAATAAAAATATAATTTT
Found at i:57500 original size:29 final size:30
Alignment explanation
Indices: 57448--57507 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
57438 TATATATAAC
* *
57448 AAAATATATTTTTAAAGTTAAAATAAGAAT
1 AAAATATATTTTTAAAGTAAAAATAAAAAT
57478 AAAATATATTTTTAAA-TAAAAATAAAAAT
1 AAAATATATTTTTAAAGTAAAAATAAAAAT
57507 A
1 A
57508 TAATTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATATATTTTTAAAGTAAAAATAAAAAT
Found at i:57531 original size:20 final size:18
Alignment explanation
Indices: 57497--57545 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
57487 TTTTAAATAA
*
57497 AAATAAAAATA-TAATTTT
1 AAATTAAAATATTAA-TTT
*
57515 AAACTTAAGATATTAATTT
1 AAA-TTAAAATATTAATTT
57534 AAATTAAAATAT
1 AAATTAAAATAT
57546 ATAAAATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 11 0.42
19 12 0.46
20 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
AAATTAAAATATTAATTT
Found at i:81401 original size:32 final size:32
Alignment explanation
Indices: 81364--81468 Score: 192
Period size: 32 Copynumber: 3.3 Consensus size: 32
81354 CAATGAAACC
81364 AAGACACACCCAGATGAGATAACTTGATGAAA
1 AAGACACACCCAGATGAGATAACTTGATGAAA
*
81396 AAGACACGCCCAGATGAGATAACTTGATGAAA
1 AAGACACACCCAGATGAGATAACTTGATGAAA
*
81428 AAGACACACCCAGATGAGAAAACTTGATGAAA
1 AAGACACACCCAGATGAGATAACTTGATGAAA
81460 AAGACACAC
1 AAGACACAC
81469 AAACCTTAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.48, C:0.20, G:0.19, T:0.13
Consensus pattern (32 bp):
AAGACACACCCAGATGAGATAACTTGATGAAA
Found at i:81936 original size:6 final size:6
Alignment explanation
Indices: 81922--82004 Score: 139
Period size: 6 Copynumber: 13.7 Consensus size: 6
81912 CCTCAATAGT
* *
81922 CAATGC CAATAC CAATAC CAATAC CAATAC CAATAC CAATAC CAATAT
1 CAATAC CAATAC CAATAC CAATAC CAATAC CAATAC CAATAC CAATAC
81970 CAATAC CAATAC CAATACC CAATAC CAATAC CAAT
1 CAATAC CAATAC CAATA-C CAATAC CAATAC CAAT
82005 GGATGTGGAG
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
6 67 0.92
7 6 0.08
ACGTcount: A:0.48, C:0.33, G:0.01, T:0.18
Consensus pattern (6 bp):
CAATAC
Found at i:84819 original size:16 final size:16
Alignment explanation
Indices: 84794--84828 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
84784 ACGATAGGGC
84794 AAAAAAAAAT-AATTG
1 AAAAAAAAATAAATTG
84809 AAAAAATAAATAAATTG
1 AAAAAA-AAATAAATTG
84826 AAA
1 AAA
84829 GACTACCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 4 0.22
17 8 0.44
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (16 bp):
AAAAAAAAATAAATTG
Found at i:105333 original size:6 final size:6
Alignment explanation
Indices: 105322--105358 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
105312 ACCTTTTCAA
105322 GGATAT GGATAT GGATAT GGATAT GGATAT GGATAT G
1 GGATAT GGATAT GGATAT GGATAT GGATAT GGATAT G
105359 AGTTTTATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (6 bp):
GGATAT
Found at i:105396 original size:12 final size:12
Alignment explanation
Indices: 105379--105440 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
105369 GGTTGATCAT
105379 GATGATGAAGAA
1 GATGATGAAGAA
105391 GATGATGCTGAAGAA
1 GATGA---TGAAGAA
* *
105406 GATTATGAAGAT
1 GATGATGAAGAA
* * *
105418 GATGTTGAACAG
1 GATGATGAAGAA
105430 GATGATGAAGA
1 GATGATGAAGA
105441 TTATTATGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
12 28 0.72
15 11 0.28
ACGTcount: A:0.42, C:0.03, G:0.32, T:0.23
Consensus pattern (12 bp):
GATGATGAAGAA
Found at i:105397 original size:15 final size:15
Alignment explanation
Indices: 105377--105413 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
105367 GGGGTTGATC
105377 ATGATGATGAAGAAG
1 ATGATGATGAAGAAG
*
105392 ATGATGCTGAAGAAG
1 ATGATGATGAAGAAG
*
105407 ATTATGA
1 ATGATGA
105414 AGATGATGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.30, T:0.24
Consensus pattern (15 bp):
ATGATGATGAAGAAG
Found at i:105418 original size:24 final size:24
Alignment explanation
Indices: 105382--105441 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
105372 TGATCATGAT
* *
105382 GATGAAGAAGATGATGCTGAAGAA
1 GATGATGAAGATGATGCTGAACAA
* * *
105406 GATTATGAAGATGATGTTGAACAG
1 GATGATGAAGATGATGCTGAACAA
105430 GATGATGAAGAT
1 GATGATGAAGAT
105442 TATTATGATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.42, C:0.03, G:0.32, T:0.23
Consensus pattern (24 bp):
GATGATGAAGATGATGCTGAACAA
Found at i:107897 original size:21 final size:21
Alignment explanation
Indices: 107873--107940 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
107863 TGCAACTAGT
107873 TATCCTCCACCTCTTGGAGCG
1 TATCCTCCACCTCTTGGAGCG
* * **** *
107894 TATCCGCCGCCTGCAACTA-CT
1 TATCCTCCACCT-CTTGGAGCG
107915 TATCCTCCACCTCTTGGAGCG
1 TATCCTCCACCTCTTGGAGCG
107936 TATCC
1 TATCC
107941 GCCGTATGGA
Statistics
Matches: 31, Mismatches: 14, Indels: 4
0.63 0.29 0.08
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.16, C:0.40, G:0.16, T:0.28
Consensus pattern (21 bp):
TATCCTCCACCTCTTGGAGCG
Found at i:107908 original size:42 final size:42
Alignment explanation
Indices: 107849--107944 Score: 183
Period size: 42 Copynumber: 2.3 Consensus size: 42
107839 GCCGGCAATG
*
107849 GCGTATCCGCCGCCTGCAACTAGTTATCCTCCACCTCTTGGA
1 GCGTATCCGCCGCCTGCAACTACTTATCCTCCACCTCTTGGA
107891 GCGTATCCGCCGCCTGCAACTACTTATCCTCCACCTCTTGGA
1 GCGTATCCGCCGCCTGCAACTACTTATCCTCCACCTCTTGGA
107933 GCGTATCCGCCG
1 GCGTATCCGCCG
107945 TATGGATACC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.16, C:0.40, G:0.20, T:0.25
Consensus pattern (42 bp):
GCGTATCCGCCGCCTGCAACTACTTATCCTCCACCTCTTGGA
Found at i:109879 original size:2 final size:2
Alignment explanation
Indices: 109872--109896 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
109862 ATATCATTAT
109872 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 T
109897 TGATAGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:110676 original size:23 final size:23
Alignment explanation
Indices: 110646--110709 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
110636 CTGAATGATT
*
110646 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGCTGAATGATTCAGCAAAA
110669 CAGTGCTGAATGATTCAGCAAAA
1 CAGTGCTGAATGATTCAGCAAAA
*
110692 CTGTGCTGAATGATTCAG
1 CAGTGCTGAATGATTCAG
110710 TACAGAAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (23 bp):
CAGTGCTGAATGATTCAGCAAAA
Found at i:110735 original size:27 final size:27
Alignment explanation
Indices: 110697--110763 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
110687 CAAAACTGTG
* *
110697 CTGAATGATTCAGTACAGAAGTACATT
1 CTGAATGATTCAGCACAGAAGTACAAT
*
110724 CTGAATGATTCAGCACAGAATTACAAT
1 CTGAATGATTCAGCACAGAAGTACAAT
*
110751 CTGAATCATTCAG
1 CTGAATGATTCAG
110764 AGTCAGTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.28
Consensus pattern (27 bp):
CTGAATGATTCAGCACAGAAGTACAAT
Found at i:110854 original size:15 final size:16
Alignment explanation
Indices: 110818--110855 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
110808 AGAGCCTCTA
110818 AATCATTCAGCATTTG
1 AATCATTCAGCATTTG
*
110834 AATCATTCAGCGTTT-
1 AATCATTCAGCATTTG
110849 AATCATT
1 AATCATT
110856 ATGAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (16 bp):
AATCATTCAGCATTTG
Found at i:111859 original size:16 final size:17
Alignment explanation
Indices: 111838--111881 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
111828 GCAAGAGCCC
*
111838 AGGGGTGGCATTT-TTT
1 AGGGGTGGCATTTGATT
*
111854 AGGGGTGACATTTGGATT
1 AGGGGTGGCATTT-GATT
111872 AGGGGTGGCA
1 AGGGGTGGCA
111882 CTTGTGGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 12 0.52
18 11 0.48
ACGTcount: A:0.18, C:0.07, G:0.43, T:0.32
Consensus pattern (17 bp):
AGGGGTGGCATTTGATT
Found at i:111988 original size:2 final size:2
Alignment explanation
Indices: 111981--112054 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
111971 GGTCCGCCCC
111981 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
112023 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
112055 CACTTGCATA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:112499 original size:74 final size:75
Alignment explanation
Indices: 112353--112501 Score: 169
Period size: 74 Copynumber: 2.0 Consensus size: 75
112343 AGAAGTATTT
* * * *
112353 TATTCTAAAATAAAATATTAGAATCAAAATGTTTTAAAAGTAATGAAGGATAAAGTACTTATTTA
1 TATTCTAAAATAAAATATTAGAATCAAAA-GTATTAAAAGTAATGAAAGATAAAATAATTATTTA
112418 ATCAAATGTTG
65 ATCAAATGTTG
* * *
112429 TATTTTAAAATAAAATGTTAAGAGTCAAAA-TATTAAAAG-AAT-AAAGATTAAAATAATTATTT
1 TATTCTAAAATAAAATATT-AGAATCAAAAGTATTAAAAGTAATGAAAGA-TAAAATAATTATTT
* *
112491 ATTTAAATGTT
64 AATCAAATGTT
112502 AAATATTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
73 4 0.06
74 24 0.39
75 8 0.13
76 17 0.27
77 9 0.15
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.37
Consensus pattern (75 bp):
TATTCTAAAATAAAATATTAGAATCAAAAGTATTAAAAGTAATGAAAGATAAAATAATTATTTAA
TCAAATGTTG
Found at i:115456 original size:29 final size:29
Alignment explanation
Indices: 115353--115448 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
115343 TATGATTCTC
* *
115353 ATTTTAAATTGATCCATAAACTTTTAAAT
1 ATTTTAAATTAATCCTTAAACTTTTAAAT
* * * * ** *
115382 GTTTTAATTTTATCTTTAAACTTGGACTATT
1 ATTTTAAATTAATCCTTAAACTTTTA--AAT
*
115413 ATTATAAATTAATCCTTAAACTTTTAAAT
1 ATTTTAAATTAATCCTTAAACTTTTAAAT
115442 ATTTTAA
1 ATTTTAA
115449 TTTCATCCCC
Statistics
Matches: 48, Mismatches: 17, Indels: 4
0.70 0.25 0.06
Matches are distributed among these distances:
29 27 0.56
31 21 0.44
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (29 bp):
ATTTTAAATTAATCCTTAAACTTTTAAAT
Found at i:115481 original size:60 final size:61
Alignment explanation
Indices: 115338--115482 Score: 145
Period size: 60 Copynumber: 2.4 Consensus size: 61
115328 TGTATGTTCT
* * * * * * **
115338 CAAATTATGAT-TCTCATTTTAAATTGATCCATAAACTTTTAAATGTTTTAATTTTATCTT
1 CAAACTATGATCTATCATTATAAATTAATCCATAAACTTTTAAATATTTTAATTTCATCCC
* * *
115398 TAAACT-TGGA-CTATTATTATAAATTAATCCTTAAACTTTTAAATATTTTAATTTCATCCC
1 CAAACTAT-GATCTATCATTATAAATTAATCCATAAACTTTTAAATATTTTAATTTCATCCC
*
115458 CAAACTATGATCT-TCATTCTAAATT
1 CAAACTATGATCTATCATTATAAATT
115483 GGTCTCCAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
59 1 0.01
60 63 0.94
61 3 0.04
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.46
Consensus pattern (61 bp):
CAAACTATGATCTATCATTATAAATTAATCCATAAACTTTTAAATATTTTAATTTCATCCC
Found at i:115712 original size:61 final size:60
Alignment explanation
Indices: 115645--115805 Score: 180
Period size: 60 Copynumber: 2.7 Consensus size: 60
115635 GGATGAATTT
* * **
115645 GGGATGAGATTGGAATGTTCAAAAAGTTTGGGGACTAATTTAGAATGA-AGATCATAGTTTG
1 GGGATGAAATTGGAATATTC-AAAAGTTTAAGGACTAATTTAGAATGAGAG-TCATAGTTTG
*** * *
115706 GGGATGAAATCAAAATCTTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTG
1 GGGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTG
** * *
115766 ATGATGAAATTGGAATATTCAAAAGTTTAAGAACCAATTT
1 GGGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTT
115806 GAAACAAGGG
Statistics
Matches: 82, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
60 66 0.80
61 16 0.20
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (60 bp):
GGGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTG
Found at i:124801 original size:24 final size:25
Alignment explanation
Indices: 124741--124801 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 25
124731 CTAACGTTAG
*
124741 GTTTTGAAAAAAATATTAATAGGAA
1 GTTTTGAAAAAAAAATTAATAGGAA
** *
124766 GTTTTGGGAAAAAAATT-GTAGGAA
1 GTTTTGAAAAAAAAATTAATAGGAA
*
124790 GTTTTTAAAAAA
1 GTTTTGAAAAAA
124802 TTGAAAGTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 15 0.52
25 14 0.48
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.33
Consensus pattern (25 bp):
GTTTTGAAAAAAAAATTAATAGGAA
Found at i:132164 original size:17 final size:18
Alignment explanation
Indices: 132144--132177 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
132134 TTTAAAATAT
132144 TTATTTATAT-TTTGTGG
1 TTATTTATATATTTGTGG
*
132161 TTATTTTTATATTTGTG
1 TTATTTATATATTTGTG
132178 TGGCATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.68
Consensus pattern (18 bp):
TTATTTATATATTTGTGG
Found at i:134223 original size:17 final size:18
Alignment explanation
Indices: 134203--134242 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
134193 TAATCTCACA
*
134203 TTATTTTTAG-TCTAATT
1 TTATTTTTAGTTATAATT
134220 TTA-TTTTAGTTATAATT
1 TTATTTTTAGTTATAATT
134237 TTATTT
1 TTATTT
134243 CTTATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 6 0.30
17 12 0.60
18 2 0.10
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (18 bp):
TTATTTTTAGTTATAATT
Found at i:139971 original size:32 final size:33
Alignment explanation
Indices: 139930--139992 Score: 110
Period size: 32 Copynumber: 1.9 Consensus size: 33
139920 TTCAAGTCAA
*
139930 TGTGATCTGAACCGATTTCAACCCG-TCCCCAG
1 TGTGATCTGAACCGATTTCAACACGTTCCCCAG
139962 TGTGATCTGAACCGATTTCAACACGTTCCCC
1 TGTGATCTGAACCGATTTCAACACGTTCCCC
139993 TTTGCATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 24 0.83
33 5 0.17
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.27
Consensus pattern (33 bp):
TGTGATCTGAACCGATTTCAACACGTTCCCCAG
Found at i:145264 original size:12 final size:12
Alignment explanation
Indices: 145247--145272 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
145237 CTACGGTTTT
145247 TGTTACTTCATA
1 TGTTACTTCATA
145259 TGTTACTTCATA
1 TGTTACTTCATA
145271 TG
1 TG
145273 ATTTTGCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (12 bp):
TGTTACTTCATA
Found at i:151066 original size:60 final size:58
Alignment explanation
Indices: 150962--151134 Score: 145
Period size: 60 Copynumber: 2.9 Consensus size: 58
150952 TCTATCATCC
* * * *
150962 TCATTTTAAATTAGTCCCTAATA-TTTTAAACATTTCAATCTCATCCTTAAATTATGA-CT
1 TCATTCTAAATTAGTCCC-AA-ACTTTTGAACATTTCATTTTCATCC-TAAATTATGATCT
* * **
151021 ATTATTCTAAATTAGTCCTCAAACTTTTGAACATTTCATTTTCATCCCCAAGCTATGATCT
1 -TCATTCTAAATTAGTCC-CAAACTTTTGAACATTTCATTTTCAT-CCTAAATTATGATCT
* **
151082 TCCTTCTAAATTAGTCCCCAAACTTTCTGAATGTTTCAATTTT-ATCCTAAATT
1 TCATTCTAAATTAGT-CCCAAACTTT-TGAACATTTC-ATTTTCATCCTAAATT
151135 GTTCGTATAT
Statistics
Matches: 91, Mismatches: 15, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
59 1 0.01
60 68 0.75
61 17 0.19
62 5 0.05
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.43
Consensus pattern (58 bp):
TCATTCTAAATTAGTCCCAAACTTTTGAACATTTCATTTTCATCCTAAATTATGATCT
Found at i:162458 original size:23 final size:23
Alignment explanation
Indices: 162428--162473 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
162418 GATCATTCGT
162428 TAAGAACGAAAGGAACCAAGAAC
1 TAAGAACGAAAGGAACCAAGAAC
162451 TAAGAACGAAAGGAACCAAGAAC
1 TAAGAACGAAAGGAACCAAGAAC
162474 AAACATGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.17, G:0.22, T:0.04
Consensus pattern (23 bp):
TAAGAACGAAAGGAACCAAGAAC
Found at i:165424 original size:21 final size:21
Alignment explanation
Indices: 165400--165451 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
165390 GCACGAAGAT
165400 GACGGGACGAACGGGAGAGAC
1 GACGGGACGAACGGGAGAGAC
* **
165421 GACGGGGCGAGGGGGAGAGAC
1 GACGGGACGAACGGGAGAGAC
*
165442 GGCGGGACGA
1 GACGGGACGA
165452 TCATGAGCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.17, G:0.56, T:0.00
Consensus pattern (21 bp):
GACGGGACGAACGGGAGAGAC
Found at i:165968 original size:60 final size:61
Alignment explanation
Indices: 165895--166030 Score: 145
Period size: 60 Copynumber: 2.3 Consensus size: 61
165885 ACTTTAGAGT
* * * * *
165895 AAAG-TACACAAATGGTCCCTT-GAGCATAGGGTATTGCTTTATTAAGTCCCTCGACTATTA
1 AAAGTTACA-AAATGGTCCATTCGAGCATAGAGTATTACTTTATTAAATCACTCGACTATTA
* ** * *
165955 AAAGTTACAAAATGAT-CATTCGATTATAGAGTGTTATTTTATTAAATCACTCGACTATTA
1 AAAGTTACAAAATGGTCCATTCGAGCATAGAGTATTACTTTATTAAATCACTCGACTATTA
166015 AAAGTT-CAAAATGGTC
1 AAAGTTACAAAATGGTC
166031 GTTCGACTAT
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
59 11 0.18
60 47 0.76
61 4 0.06
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (61 bp):
AAAGTTACAAAATGGTCCATTCGAGCATAGAGTATTACTTTATTAAATCACTCGACTATTA
Found at i:166350 original size:38 final size:38
Alignment explanation
Indices: 166299--166375 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
166289 CAAAACAACA
166299 CTCTATAGTTAAAAGACTATTTTGTAACTTTTCACAGT
1 CTCTATAGTTAAAAGACTATTTTGTAACTTTTCACAGT
166337 CTCTATAGTTAAAAGACTATTTTGTAACTTTTCACAGT
1 CTCTATAGTTAAAAGACTATTTTGTAACTTTTCACAGT
166375 C
1 C
166376 GAGAGATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (38 bp):
CTCTATAGTTAAAAGACTATTTTGTAACTTTTCACAGT
Found at i:179160 original size:37 final size:37
Alignment explanation
Indices: 179084--179160 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
179074 TTTTTATATT
*
179084 TTTAATTTTGTAAAAACAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAACAATTATATAAATATTATCAA
* *
179121 TTTAATTTTTTAAAGAA-AA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AACAATTATATAAATATTAT-CAA
179158 TTT
1 TTT
179161 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 20 0.57
38 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAACAATTATATAAATATTATCAA
Found at i:183926 original size:36 final size:36
Alignment explanation
Indices: 183864--183964 Score: 170
Period size: 35 Copynumber: 2.9 Consensus size: 36
183854 TTTTTATATT
* *
183864 TTTAATTTTGTAAA-AAATTATATAAATATTATGAA
1 TTTAATTTTTTAAAGAAAATATATAAATATTATGAA
183899 TTTAATTTTTTAAAGAAAATATATAAATATTATGAA
1 TTTAATTTTTTAAAGAAAATATATAAATATTATGAA
183935 TTTAA-TTTTTAAAGAAAATATATAAATATT
1 TTTAATTTTTTAAAGAAAATATATAAATATT
183965 TTACAATTTG
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 38 0.60
36 25 0.40
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.46
Consensus pattern (36 bp):
TTTAATTTTTTAAAGAAAATATATAAATATTATGAA
Found at i:196314 original size:16 final size:16
Alignment explanation
Indices: 196291--196331 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
196281 ACATAAAATA
196291 AAAT-AAATAATTTTT
1 AAATAAAATAATTTTT
196306 AAATAAAAT-A-TTTT
1 AAATAAAATAATTTTT
*
196320 ATATAAAATAAT
1 AAATAAAATAAT
196332 ATATTTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 12 0.55
15 6 0.27
16 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATAAAATAATTTTT
Found at i:196363 original size:33 final size:31
Alignment explanation
Indices: 196288--196364 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 31
196278 GACACATAAA
*
196288 ATAAAATAAATAATTTTTAAATAAAATATTTTAT
1 ATAAAAT-AATAATTTTTAAACAAAATA-TTT-T
* *
196322 ATAAAATAAT-ATATTT-AACAAAATTTATTT
1 ATAAAATAATAATTTTTAAACAAAATAT-TTT
196352 ATAAAATAATAAT
1 ATAAAATAATAAT
196365 CAGATCTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
30 12 0.32
31 11 0.29
32 5 0.13
33 3 0.08
34 7 0.18
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (31 bp):
ATAAAATAATAATTTTTAAACAAAATATTTT
Found at i:201038 original size:14 final size:15
Alignment explanation
Indices: 201019--201049 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
201009 GAACACCATT
201019 AATTT-AATTTATAA
1 AATTTAAATTTATAA
201033 AATTTAAATTTATAA
1 AATTTAAATTTATAA
201048 AA
1 AA
201050 GACTCAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTAAATTTATAA
Found at i:202763 original size:19 final size:19
Alignment explanation
Indices: 202739--202777 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
202729 CCATGAACTG
202739 ATAAATGAGAGATATGCTT
1 ATAAATGAGAGATATGCTT
202758 ATAAATGAGAGATATGCTT
1 ATAAATGAGAGATATGCTT
202777 A
1 A
202778 CATGTGGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (19 bp):
ATAAATGAGAGATATGCTT
Found at i:203927 original size:29 final size:28
Alignment explanation
Indices: 203870--203927 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
203860 AGTTGAAATG
**
203870 AAAATTAAAGTTCAATGCTATAATTGAT
1 AAAATTAAAGTTCAATGCTATAAACGAT
* *
203898 AAAATTGAAAGTTTAATGGTATAAACGAT
1 AAAATT-AAAGTTCAATGCTATAAACGAT
203927 A
1 A
203928 TAAAGCCTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (28 bp):
AAAATTAAAGTTCAATGCTATAAACGAT
Found at i:205583 original size:17 final size:18
Alignment explanation
Indices: 205553--205586 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
205543 ATTTCAAAAA
205553 AAAATATAAGTAATTTTT
1 AAAATATAAGTAATTTTT
*
205571 AAAA-ATAATTAATTTT
1 AAAATATAAGTAATTTT
205587 ATACATATAT
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:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
AAAATATAAGTAATTTTT
Found at i:206857 original size:29 final size:28
Alignment explanation
Indices: 206812--206869 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
206802 AGTTGAAATG
* *
206812 AAAATTAAAGTTCAATGTTATAATTGAT
1 AAAATTAAAGTTCAATGGTATAAATGAT
*
206840 AAAATTAAAAGTTTAATGGTATAAATGAT
1 AAAATT-AAAGTTCAATGGTATAAATGAT
206869 A
1 A
206870 CAACGATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (28 bp):
AAAATTAAAGTTCAATGGTATAAATGAT
Found at i:219371 original size:17 final size:17
Alignment explanation
Indices: 219349--219383 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
219339 GTGTGTGGAG
219349 CATTCTAGATAATTAAT
1 CATTCTAGATAATTAAT
219366 CATTCTAGATAATTAAT
1 CATTCTAGATAATTAAT
219383 C
1 C
219384 TCCACCCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (17 bp):
CATTCTAGATAATTAAT
Found at i:224780 original size:24 final size:25
Alignment explanation
Indices: 224753--224801 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
224743 GAAAATATGA
224753 ATATATT-TATGTTGA-ATTCATTTC
1 ATATATTCTAT-TTGATATTCATTTC
224777 ATATATTCGTATTTGATATTCATTT
1 ATATATTC-TATTTGATATTCATTT
224802 TGAATAGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.32
25 4 0.18
26 11 0.50
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (25 bp):
ATATATTCTATTTGATATTCATTTC
Found at i:225065 original size:29 final size:28
Alignment explanation
Indices: 225022--225078 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
225012 TTATTGAGTA
* *
225022 TTTTGATTATTAAAAATTATAAAATGAT
1 TTTTGATTATAAAAAATTAGAAAATGAT
225050 TTTTAGATTATAAAAAATTAGAAAATGAT
1 TTTT-GATTATAAAAAATTAGAAAATGAT
225079 CATATGACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (28 bp):
TTTTGATTATAAAAAATTAGAAAATGAT
Found at i:225858 original size:2 final size:2
Alignment explanation
Indices: 225851--225875 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
225841 TTATACTTGA
225851 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 A
225876 ATGTTTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:241838 original size:2 final size:2
Alignment explanation
Indices: 241831--241866 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
241821 ATATGATACA
241831 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
241867 TGTATATGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:242977 original size:31 final size:31
Alignment explanation
Indices: 242920--242978 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
242910 CGTCACTTCA
* **
242920 TTTCGTTTTAATTAACATGTGGTCATTTTCG
1 TTTCATTTTAATTAACATGTAATCATTTTCG
*
242951 TTTCATTTTAATTAAGATGTAATCATTT
1 TTTCATTTTAATTAACATGTAATCATTT
242979 ACCTTATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.53
Consensus pattern (31 bp):
TTTCATTTTAATTAACATGTAATCATTTTCG
Found at i:243456 original size:33 final size:33
Alignment explanation
Indices: 243419--243490 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
243409 CCACATTCCC
* *
243419 ATGTTTGGTTGGCCGAGAATCTCATTTCCGGTA
1 ATGTTTGGTTGGCCGAAAATCTCATTCCCGGTA
243452 ATGTTTGGTTGGCCGAAAATCTCATTCCCGGTA
1 ATGTTTGGTTGGCCGAAAATCTCATTCCCGGTA
243485 ATGTTT
1 ATGTTT
243491 TATTATCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (33 bp):
ATGTTTGGTTGGCCGAAAATCTCATTCCCGGTA
Found at i:244876 original size:9 final size:8
Alignment explanation
Indices: 244854--244887 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
244844 ATAGGGTTAT
244854 GATTTTTG
1 GATTTTTG
244862 GATTTTTG
1 GATTTTTG
244870 GATTTTT-
1 GATTTTTG
244877 GATTTTGTG
1 GATTTT-TG
244886 GA
1 GA
244888 GGTTATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.25
8 16 0.67
9 2 0.08
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (8 bp):
GATTTTTG
Found at i:249995 original size:491 final size:486
Alignment explanation
Indices: 249073--250052 Score: 1557
Period size: 491 Copynumber: 2.0 Consensus size: 486
249063 TAATTCGAAA
* *
249073 TTGCTTAGATATTCTAGCTTTTTAGCTTGTTTATTTGCGATTCGAATATAGAGTTGTTTCGATGT
1 TTGCTTAGATATTCTAGCTTTTTAGCTTGTTTATTTGCGATTCGAATATAGAATTGATTCGATGT
* *
249138 TATATTTTCATGAAGGTACTCGTGTTTCCCCCGACTGAGGTTCGATTCAATTCGATGCGACTCGT
66 TATATTTTCATGAAGGTACTCATGTTTCCCCCGACTGAGGTTCGATTCAATTCGATACGACTCGT
** *
249203 TGGACCGATCAGTCCGATGCACGTTCTCTGAGAGCTACCCGTAGGTTCCGTAACTTGTTAAATTA
131 ACGACCGATCAGTCCGATGCACGTTCTCTGAAAGCTACCCGTAGGTTCCGTAACTTGTTAAATTA
* * ** * * * * *
249268 TGATTTATTATTATTTTTCTATTATTTTAACCTAGTTTTCGATTCGTAGGATCTAGTGCTGCTGT
196 TGATTTATTATTATTTTGCCAGGATTTTAACCTAGTTTCCGATTCATAGGATCTAGCGATGCCGT
* * * *
249333 CGACCGTCCTAGGTAGATCCGTTAGTGGATTTTCATACCATACTACTCAGACTGGTTCAAGTGTG
261 CGACCATCCTAGGCAGATCCGCTAGTGGATTTCCATACCATACTACTCAGACTGGTTCAAGTGTG
* * *
249398 TTCATATAATGTTACAATTCCTTTTGAAATTGTTTGACTAATCGGATTTGAATTTTCTAATGATA
326 TTCATATAATGTTACAATTCCTTTTGAAACTGTTTGACTAAACGAATTTGAATTTTCTAATGATA
249463 TTAAATATTTTGAATTGCATGACATCTGTTTAAAATGCATGTTTTGACTTCTGATATCTGATTTC
391 TTAAATATTTTGAATTGCATGACATCTGTTTAAAATGCATGTTTTGACTTCTGATATC-----TC
249528 TGAATATTCTGATATGATCTCTGGTTACAACATTTC
451 TGAATATTCTGATATGATCTCTGGTTACAACATTTC
*
249564 TTGCTTAGATATTCTAGTTTTTTAGCTTGTTTATTTGCGATTCGAATATAGAATTGATTCGATGT
1 TTGCTTAGATATTCTAGCTTTTTAGCTTGTTTATTTGCGATTCGAATATAGAATTGATTCGATGT
*
249629 TATATTTTCATGAAGGTACTCATGTTTCCCCCGACTGAGGTTCGATTCAATTCGGTACGACTCGT
66 TATATTTTCATGAAGGTACTCATGTTTCCCCCGACTGAGGTTCGATTCAATTCGATACGACTCGT
*
249694 ACGACCGATCAGTCCGATGCACGTTCTCTGAAAGCTACTCGTAGGTTCCGTAACTTGTTAAATTA
131 ACGACCGATCAGTCCGATGCACGTTCTCTGAAAGCTACCCGTAGGTTCCGTAACTTGTTAAATTA
*
249759 TGATTTATTATTATTTTGCCAGGATTTTGACCTAGTTTCCGATTCATAGGATCTAGCGATGCCGT
196 TGATTTATTATTATTTTGCCAGGATTTTAACCTAGTTTCCGATTCATAGGATCTAGCGATGCCGT
* * * *
249824 TGACCATCCTAGGCAGATCTGCTAGTGGATTTCCATACCATACTACTTAGATTGGTTC-AGCTGT
261 CGACCATCCTAGGCAGATCCGCTAGTGGATTTCCATACCATACTACTCAGACTGGTTCAAG-TGT
* * * *
249888 GTTCATATAGTGTTATAATTCCTTTTTAAACTGTTTGACTAAACGAATTTTAATTTTCTAATGAT
325 GTTCATATAATGTTACAATTCCTTTTGAAACTGTTTGACTAAACGAATTTGAATTTTCTAATGAT
*
249953 ATTAAATATTTTGAATTGCATGACATCTGTTTAAAATGCATGTTTTGACTTTTGATATCTCTGAA
390 ATTAAATATTTTGAATTGCATGACATCTGTTTAAAATGCATGTTTTGACTTCTGATATCTCTGAA
* *
250018 TATTCTGATATGGTCTCTGGTTACAATATTTC
455 TATTCTGATATGATCTCTGGTTACAACATTTC
250050 TTG
1 TTG
250053 GTCTGATTCT
Statistics
Matches: 450, Mismatches: 38, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
486 39 0.09
490 2 0.00
491 409 0.91
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (486 bp):
TTGCTTAGATATTCTAGCTTTTTAGCTTGTTTATTTGCGATTCGAATATAGAATTGATTCGATGT
TATATTTTCATGAAGGTACTCATGTTTCCCCCGACTGAGGTTCGATTCAATTCGATACGACTCGT
ACGACCGATCAGTCCGATGCACGTTCTCTGAAAGCTACCCGTAGGTTCCGTAACTTGTTAAATTA
TGATTTATTATTATTTTGCCAGGATTTTAACCTAGTTTCCGATTCATAGGATCTAGCGATGCCGT
CGACCATCCTAGGCAGATCCGCTAGTGGATTTCCATACCATACTACTCAGACTGGTTCAAGTGTG
TTCATATAATGTTACAATTCCTTTTGAAACTGTTTGACTAAACGAATTTGAATTTTCTAATGATA
TTAAATATTTTGAATTGCATGACATCTGTTTAAAATGCATGTTTTGACTTCTGATATCTCTGAAT
ATTCTGATATGATCTCTGGTTACAACATTTC
Found at i:259577 original size:66 final size:66
Alignment explanation
Indices: 259435--259558 Score: 198
Period size: 66 Copynumber: 1.9 Consensus size: 66
259425 TTTAAATGGT
* *
259435 AAACACCTAAAAATATAATAGGAAAAACATTAAACACTTATTTTTAACAAAAAAAATAATATGTA
1 AAACACTTAAAAATATAATAGGAAAAACATTAAACACTTATTTATAACAAAAAAAATAATATGTA
259500 C
66 C
259501 AAACACTTAAAAATATAAT-GCGAGAAAACATTAAA-ACTTATTTATAACAAAAAAAATA
1 AAACACTTAAAAATATAATAG-GA-AAAACATTAAACACTTATTTATAACAAAAAAAATA
259559 TTTTTTTATA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
65 1 0.02
66 42 0.78
67 11 0.20
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (66 bp):
AAACACTTAAAAATATAATAGGAAAAACATTAAACACTTATTTATAACAAAAAAAATAATATGTA
C
Found at i:260421 original size:3 final size:3
Alignment explanation
Indices: 260413--260440 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
260403 AAATAGGGTT
260413 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
260441 CATTTTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:271991 original size:141 final size:140
Alignment explanation
Indices: 271722--272135 Score: 474
Period size: 141 Copynumber: 2.9 Consensus size: 140
271712 AATGTCCCAG
* *
271722 GCTCACAACATTGTTGTTGTCTGATTGTGATATAGGGAGTATTCCTGAAGGTTTCTTCAAGCATA
1 GCTCACAACGTTGTTGTTGTCTGATTGTGATATAGGGAGTATTCCAG-AGGTTTCTTCAAGCATA
* * * * *
271787 TGGGTGCACTTAAAATTCTTGATCTTTCCA-AAAACTCTATCAAGAGTCTTCCAAATTCTTTATC
65 TGGATGCACTTAAGATTCTTGATCTTTCTAGAAATC-CTATCAAGAGTCTTCCAAATTCCTTATC
*
271851 AAAGTGTTCCAA
129 AAACTGTTCCAA
* * * * *
271863 GTTGACAGCGTTGTTGTTGTCTGATTGTTATATAGGGAGTATTCCAGAGGCTTTTTTCAAGCATA
1 GCTCACAACGTTGTTGTTGTCTGATTGTGATATAGGGAGTATTCCAGAGG-TTTCTTCAAGCATA
* * * * * * * *
271928 TGAATGCACTTAAGGTTCTTGATCTTTCTAGGAATCCCATGAAGAATCTCCCAAACTCCTTATCA
65 TGGATGCACTTAAGATTCTTGATCTTTCTAGAAATCCTATCAAGAGTCTTCCAAATTCCTTATCA
** *
271993 AACTGTTTGAT
130 AACTGTTCCAA
* * **
272004 GCTCACAACTTTGTTGTTGTCTGATTGTGATATAGTGACCATTCCAGAAGAG-TTCTTCAAGCAT
1 GCTCACAACGTTGTTGTTGTCTGATTGTGATATAGGGAGTATTCCAG-AG-GTTTCTTCAAGCAT
* * *
272068 ATGGATGCACTCAAGATTCTTGAGCTTT-TCAGAAATCCTATCAAGAGTCTTCCACATTCCTTAT
64 ATGGATGCACTTAAGATTCTTGATCTTTCT-AGAAATCCTATCAAGAGTCTTCCAAATTCCTTAT
272132 CAAA
128 CAAA
272136 TTTGAAGAAT
Statistics
Matches: 224, Mismatches: 44, Indels: 10
0.81 0.16 0.04
Matches are distributed among these distances:
140 4 0.02
141 214 0.96
142 5 0.02
143 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (140 bp):
GCTCACAACGTTGTTGTTGTCTGATTGTGATATAGGGAGTATTCCAGAGGTTTCTTCAAGCATAT
GGATGCACTTAAGATTCTTGATCTTTCTAGAAATCCTATCAAGAGTCTTCCAAATTCCTTATCAA
ACTGTTCCAA
Found at i:276032 original size:13 final size:13
Alignment explanation
Indices: 276010--276062 Score: 67
Period size: 12 Copynumber: 4.2 Consensus size: 13
276000 CATATTGGAT
276010 TTTC-TTTTAAAC
1 TTTCTTTTTAAAC
276022 TTTCTTTTTAAA-
1 TTTCTTTTTAAAC
*
276034 TTTCTTTTTAATC
1 TTTCTTTTTAAAC
276047 TTT-TTTTTAAATC
1 TTTCTTTTTAAA-C
276060 TTT
1 TTT
276063 TTACCCTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
12 22 0.61
13 14 0.39
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTCTTTTTAAAC
Found at i:276063 original size:13 final size:13
Alignment explanation
Indices: 276009--276064 Score: 64
Period size: 13 Copynumber: 4.4 Consensus size: 13
275999 CCATATTGGA
276009 TTTTCTTTTAAA-C
1 TTTT-TTTTAAATC
276022 TTTCTTTTTAAAT-
1 TTT-TTTTTAAATC
*
276035 TTCTTTTT-AATC
1 TTTTTTTTAAATC
276047 TTTTTTTTAAATC
1 TTTTTTTTAAATC
276060 TTTTT
1 TTTTT
276065 ACCCTTACTC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
11 3 0.08
12 12 0.32
13 21 0.57
14 1 0.03
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTTTTAAATC
Found at i:284056 original size:11 final size:10
Alignment explanation
Indices: 284042--284094 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
284032 CTTAATAATT
284042 ATAATATAAAA
1 ATAAT-TAAAA
284053 ATAATTAAAA
1 ATAATTAAAA
*
284063 AT--TTTAAA
1 ATAATTAAAA
284071 ATAATTAAAA
1 ATAATTAAAA
*
284081 AT--TTTAAA
1 ATAATTAAAA
284089 ATAATT
1 ATAATT
284095 CAAAGACCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
8 14 0.40
10 16 0.46
11 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAATTAAAA
Found at i:284073 original size:18 final size:18
Alignment explanation
Indices: 284050--284094 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
284040 TTATAATATA
284050 AAAATAATTAAAAATTTT
1 AAAATAATTAAAAATTTT
284068 AAAATAATTAAAAATTTT
1 AAAATAATTAAAAATTTT
284086 AAAATAATT
1 AAAATAATT
284095 CAAAGACCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATAATTAAAAATTTT
Found at i:284576 original size:24 final size:24
Alignment explanation
Indices: 284524--284578 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
284514 CGTTAAAATG
* *
284524 ATAAACGAACATAAATGAACGAAC
1 ATAAACGAACACAAACGAACGAAC
* * *
284548 GTAAACGAACACAAACGAATGGAC
1 ATAAACGAACACAAACGAACGAAC
284572 ATAAACG
1 ATAAACG
284579 TACAAAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.18, G:0.16, T:0.11
Consensus pattern (24 bp):
ATAAACGAACACAAACGAACGAAC
Found at i:285662 original size:21 final size:21
Alignment explanation
Indices: 285597--285663 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
285587 TTTACGCCAT
* * *
285597 TGACCGTT-ACAGTATTGACT
1 TGACAGTTCACAGTGTTGACA
* *
285617 TGACAGTTCACAGTGCTAACA
1 TGACAGTTCACAGTGTTGACA
* * *
285638 TGACAGTTTACATTGTTGACG
1 TGACAGTTCACAGTGTTGACA
285659 TGACA
1 TGACA
285664 ATCCATCTGT
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 7 0.19
21 29 0.81
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.31
Consensus pattern (21 bp):
TGACAGTTCACAGTGTTGACA
Found at i:297053 original size:22 final size:23
Alignment explanation
Indices: 297016--297062 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
297006 AACCCTAAAT
297016 AAGCCCAAAAATCGTATCTGCTA
1 AAGCCCAAAAATCGTATCTGCTA
* *
297039 AAGCCC-AGAATCGTATCTTCTA
1 AAGCCCAAAAATCGTATCTGCTA
297061 AA
1 AA
297063 CTCGCGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (23 bp):
AAGCCCAAAAATCGTATCTGCTA
Found at i:309211 original size:226 final size:221
Alignment explanation
Indices: 308816--309257 Score: 733
Period size: 226 Copynumber: 2.0 Consensus size: 221
308806 GTAAATTATC
* *
308816 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATCTTTAGTTAA
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATATTTAGTTAA
**
308881 TATGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTG
66 TATGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTG
*
308946 TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAAC
131 TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAAAC
309011 ATAAATTACATAACTTTCAAAAAAGTA
196 ATAAATTACATAACTTT-AAAAAAGTA
* *
309038 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TG-AAA-ATATAT-TTATTATATTTAG
*
309103 TTAATATTGTTAAATTTAAATTCTAAATAATA-TTTATAAAATATCAAAACAATCAAATAAAATT
62 TTAATA-TGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
309167 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
126 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
309232 GAAACATAAATTACATAACTTTAAAA
191 GAAACATAAATTACATAACTTTAAAA
309258 GCAGTTTTAA
Statistics
Matches: 205, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
222 36 0.18
223 2 0.01
224 3 0.01
225 9 0.04
226 131 0.64
227 24 0.12
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (221 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATATTTAGTTAA
TATGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTG
TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAAAC
ATAAATTACATAACTTTAAAAAAGTA
Found at i:309346 original size:20 final size:19
Alignment explanation
Indices: 309323--309369 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
309313 CGATATACCA
309323 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
309343 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
309363 GGTAAAA
1 GGTAAAA
309370 TTAAAAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:309513 original size:20 final size:19
Alignment explanation
Indices: 309490--309536 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
309480 CGATATAACA
*
309490 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
309510 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
309530 GGTAAAA
1 GGTAAAA
309537 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:311877 original size:33 final size:33
Alignment explanation
Indices: 311835--311900 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
311825 AAATAGATGG
*
311835 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
311868 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
311901 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:313762 original size:19 final size:19
Alignment explanation
Indices: 313699--313761 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
313689 AATGTCGAGT
*
313699 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
313718 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
313737 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
313756 T-ATTTT
1 TAATTTT
313762 TTATGTGAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 5 0.12
19 38 0.88
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:314647 original size:197 final size:197
Alignment explanation
Indices: 313843--315251 Score: 2481
Period size: 198 Copynumber: 7.1 Consensus size: 197
313833 TTAAGGGTCA
*
313843 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTTTTACAAGGTGCATCAA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTTTTACAAGGTGCATCAA
313908 TAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 TAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
313973 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
130 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
314038 ATG
195 ATG
314041 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
314106 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
65 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
314171 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
130 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
314236 ATG
195 ATG
*** *
314239 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATT-TTTACAAGGTGCATC
*
314304 CATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
64 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
314368 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACTGGTTTTATGAGAGAATAAGTCTAAAT
129 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
314433 AATG
194 AATG
314437 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTTTTACAAGGTGCATCAA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTTTTACAAGGTGCATCAA
314502 TAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 TAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
314567 AATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATAAGTCTAAATA
130 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
314631 ATG
195 ATG
* * *** * *
314634 TGTCGACACTAATATAGTTTGTGTCGATATTTATTCCCAGAATGAATTAAAAACAAGGTGCACCC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATT-TTTACAAGGTGCATCA
314699 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAA-CCAAAAGTATAATGT
65 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
314763 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
130 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
314828 ATG
195 ATG
314831 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA-TTTTACAAGGTGCATCAA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTTTTACAAGGTGCATCAA
314895 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
66 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
314960 ATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATAAGTCTAAATAA
131 ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAA
315024 TG
196 TG
*** *
315026 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATT-TTTACAAGGTGCATC
*
315091 CATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
64 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
315155 TAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
129 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
315219 AATG
194 AATG
*
315223 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
315252 CTAATTTAAA
Statistics
Matches: 1160, Mismatches: 39, Indels: 25
0.95 0.03 0.02
Matches are distributed among these distances:
195 127 0.11
196 164 0.14
197 315 0.27
198 466 0.40
199 88 0.08
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (197 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTTTTACAAGGTGCATCAA
TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAA
TG
Found at i:316739 original size:18 final size:18
Alignment explanation
Indices: 316716--316777 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
316706 ATCGGTCGCA
* * *
316716 GAAGATGAAGCTGACGAT
1 GAAGATGACGATGATGAT
316734 GAAGATGACGATGATGAT
1 GAAGATGACGATGATGAT
*
316752 GATGATGACGATGATGAT
1 GAAGATGACGATGATGAT
316770 GAAGATGA
1 GAAGATGA
316778 TGATCCAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (18 bp):
GAAGATGACGATGATGAT
Found at i:316740 original size:6 final size:6
Alignment explanation
Indices: 316716--316777 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
316706 ATCGGTCGCA
* * * * * *
316716 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
*
316764 GATGAT GAAGAT GA
1 GAAGAT GAAGAT GA
316778 TGATCCAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:316751 original size:3 final size:3
Alignment explanation
Indices: 316731--316781 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
316721 TGAAGCTGAC
* * * *
316731 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAT GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
316779 GAT
1 GAT
316782 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:316778 original size:12 final size:12
Alignment explanation
Indices: 316719--316781 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
316709 GGTCGCAGAA
* *
316719 GATGAAGCTGAC
1 GATGAAGATGAT
*
316731 GATGAAGATGAC
1 GATGAAGATGAT
*
316743 GATGATGATGAT
1 GATGAAGATGAT
*
316755 GATGACGATGAT
1 GATGAAGATGAT
316767 GATGAAGATGAT
1 GATGAAGATGAT
316779 GAT
1 GAT
316782 CCAAACAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:318725 original size:184 final size:184
Alignment explanation
Indices: 318145--318998 Score: 1559
Period size: 184 Copynumber: 4.7 Consensus size: 184
318135 CTTTCAACAT
**
318145 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
318210 GGTCTACAACCTAAATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
318275 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
318329 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
318394 GGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
318458 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
318512 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
318577 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
318642 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
318696 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
**
318761 GGTCTACAACCGGTATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
318826 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
318880 ATTATAATGTAATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
**
318944 GGTCTACAACCGGTATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
318999 CCATTTAAAA
Statistics
Matches: 660, Mismatches: 9, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
183 283 0.43
184 377 0.57
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:318905 original size:367 final size:367
Alignment explanation
Indices: 318145--318998 Score: 1557
Period size: 367 Copynumber: 2.3 Consensus size: 367
318135 CTTTCAACAT
**
318145 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
318210 GGTCTACAACCTAAATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
318275 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
*
318340 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATAGGTCTACAACC
* *
318405 TATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATTGTGTCGATA
261 GATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATA
*
318470 TAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
326 CAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
318512 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
318577 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
318642 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
*
318707 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATAGGTCTACAACC
*
318772 GGTATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGAT
261 GATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGAT
318837 ACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
325 ACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
318880 ATTATAATGTAATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
**
318944 GGTCTACAACCGGTATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
318999 CCATTTAAAA
Statistics
Matches: 471, Mismatches: 15, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
367 358 0.76
368 113 0.24
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (367 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATAGGTCTACAACC
GATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATA
CAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:321583 original size:23 final size:23
Alignment explanation
Indices: 321552--321614 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
321542 ATAGGTAAAC
*
321552 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
321575 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
321598 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
321615 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:321622 original size:23 final size:23
Alignment explanation
Indices: 321552--321624 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
321542 ATAGGTAAAC
* * **
321552 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
321575 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
321598 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
321621 ATAT
1 ATAT
321625 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:322473 original size:15 final size:16
Alignment explanation
Indices: 322453--322486 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
322443 ATTTATTATT
322453 ATTATTT-AATATAAA
1 ATTATTTAAATATAAA
322468 ATTATTTAAAATATAAA
1 ATTATTT-AAATATAAA
322485 AT
1 AT
322487 AAAAATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTATTTAAATATAAA
Found at i:327908 original size:20 final size:20
Alignment explanation
Indices: 327883--327920 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
327873 CCTGACTTGT
*
327883 TTGGAAGACCTGTAAATCAG
1 TTGGAAGACCTGAAAATCAG
327903 TTGGAAGACCTGAAAATC
1 TTGGAAGACCTGAAAATC
327921 GGTTCCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (20 bp):
TTGGAAGACCTGAAAATCAG
Found at i:342954 original size:31 final size:31
Alignment explanation
Indices: 342911--342989 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
342901 TCATTTAAAT
*
342911 GAACGAATATGAACAAACTATACTCCTTAAG
1 GAACGAACATGAACAAACTATACTCCTTAAG
* * *
342942 GAACGAACATGAACAAGCTATATTCCTTAAT
1 GAACGAACATGAACAAACTATACTCCTTAAG
342973 GAACGAACATGAACAAA
1 GAACGAACATGAACAAA
342990 AATTTTTTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.20
Consensus pattern (31 bp):
GAACGAACATGAACAAACTATACTCCTTAAG
Done.