Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold404
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: 638648
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 4
Found at i:186900 original size:6 final size:6
Alignment explanation
Indices: 186891--186964 Score: 73
Period size: 6 Copynumber: 12.7 Consensus size: 6
186881 TTTCTCTTTC
* *
186891 TCATTT TCATTT TCATTT TCATTT TCATTT TCTTTT TCTTTT TC-TTT
1 TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT
* * *
186938 TTATTC T-ATTTT TC-TTT TCTTTT TCAT
1 TCATTT TCA-TTT TCATTT TCATTT TCAT
186965 GCAAATTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
5 10 0.17
6 49 0.83
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (6 bp):
TCATTT
Found at i:186973 original size:23 final size:22
Alignment explanation
Indices: 186924--186977 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
186914 TTCATTTTCT
* * *
186924 TTTTCTTTTTCTTTTTATTCTAT
1 TTTTC-TTTTCTTTTTATGCAAA
186947 TTTTCTTTTCTTTTTCATGCAAA
1 TTTTCTTTTCTTTTT-ATGCAAA
186970 TTTT-TTTT
1 TTTTCTTTT
186978 AAAAATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTCTTTTCTTTTTATGCAAA
Found at i:187334 original size:31 final size:33
Alignment explanation
Indices: 187272--187334 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 33
187262 CTATTCTAAT
*
187272 AATTTTACTAATAAAAGGACCTAAATGATACAA
1 AATTTTACTAATAAAAGGACCTAAATAATACAA
* * *
187305 AATTTTA-TAATTAAATG-CCTAATTAATACA
1 AATTTTACTAATAAAAGGACCTAAATAATACA
187335 TTTTGAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 11 0.42
32 8 0.31
33 7 0.27
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.33
Consensus pattern (33 bp):
AATTTTACTAATAAAAGGACCTAAATAATACAA
Found at i:188367 original size:13 final size:13
Alignment explanation
Indices: 188348--188386 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
188338 ACTATTTATG
188348 ATGTATCGATACA
1 ATGTATCGATACA
*
188361 CTGTATCGATACA
1 ATGTATCGATACA
188374 ATGTATCGATACA
1 ATGTATCGATACA
188387 TGAATAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:188485 original size:22 final size:22
Alignment explanation
Indices: 188457--188513 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
188447 ACAGTGACCT
188457 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
188479 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
*
188501 ATGAACATTGATG
1 ATGAACAGTGATG
188514 AATAGTGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:188619 original size:53 final size:53
Alignment explanation
Indices: 188555--188691 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
188545 CTACTACCAA
188555 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
188608 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAGTGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
188661 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
188692 TATGCAATTT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 66 0.84
54 13 0.16
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:188724 original size:20 final size:20
Alignment explanation
Indices: 188661--188731 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
188651 GCCAGTGTCC
**
188661 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
188681 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
188701 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
188721 TGTATCGATAC
1 TGTATCGATAC
188732 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:188797 original size:21 final size:21
Alignment explanation
Indices: 188771--188811 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
188761 GTCAACTTTG
188771 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
188792 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
188812 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:189187 original size:19 final size:19
Alignment explanation
Indices: 189165--189214 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 19
189155 TATTATAATT
189165 TATATTAATTATTTAAAAA
1 TATATTAATTATTTAAAAA
*
189184 TATA--AATAATTTAAAAA
1 TATATTAATTATTTAAAAA
* *
189201 CATGTTAA-TATTTA
1 TATATTAATTATTTA
189215 TTTAAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
17 14 0.56
18 5 0.20
19 6 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
TATATTAATTATTTAAAAA
Found at i:191497 original size:24 final size:24
Alignment explanation
Indices: 191451--191524 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
191441 ATATTGCTAT
*
191451 TTATTTTGATTTA-ATTTATTTTACA
1 TTATTTT-ATTTATCTTTATTTTA-A
191476 -T-TTTTATTTTATCTTTATTTTAA
1 TTATTTTA-TTTATCTTTATTTTAA
* *
191499 TTATTTTATTTATTTTTATTTGAA
1 TTATTTTATTTATCTTTATTTTAA
191523 TT
1 TT
191525 GATAAAACCT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
22 1 0.02
23 9 0.21
24 27 0.64
25 5 0.12
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (24 bp):
TTATTTTATTTATCTTTATTTTAA
Found at i:195085 original size:41 final size:42
Alignment explanation
Indices: 194998--195095 Score: 130
Period size: 41 Copynumber: 2.4 Consensus size: 42
194988 CATGCCCACA
* *
194998 CCTTATCAAATAAGTGCTTTTGTTTTATTAACATGCTCACGT
1 CCTTATCAAATAAGAGCTTATGTTTTATTAACATGCTCACGT
*
195040 -CTTATCAAATAAGAGCTTATGTTTTATTAACGTGC-CTAC-T
1 CCTTATCAAATAAGAGCTTATGTTTTATTAACATGCTC-ACGT
*
195080 CCTTATCAAACAAGAG
1 CCTTATCAAATAAGAG
195096 TTTCTAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
40 2 0.04
41 48 0.96
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (42 bp):
CCTTATCAAATAAGAGCTTATGTTTTATTAACATGCTCACGT
Found at i:196109 original size:15 final size:15
Alignment explanation
Indices: 196091--196135 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
196081 AAAAAATTGA
196091 AAAATAAAAAAAAAG
1 AAAATAAAAAAAAAG
* *
196106 AAAAGAGAAAAAAAG
1 AAAATAAAAAAAAAG
196121 AAAATTGAAAAAAAA
1 AAAA-T-AAAAAAAA
196136 TTGAAAGGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 17 0.71
17 7 0.29
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (15 bp):
AAAATAAAAAAAAAG
Found at i:198179 original size:18 final size:18
Alignment explanation
Indices: 198128--198192 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
198118 ATTTTAATAT
* *
198128 ATTTATTTATTAAAATCTA
1 ATTTATTAAATAAAAT-TA
*
198147 TATTTA-TATATAAAATTA
1 -ATTTATTAAATAAAATTA
198165 ATTTATTAAATAAAATTA
1 ATTTATTAAATAAAATTA
198183 ATTT-TTAAAT
1 ATTTATTAAAT
198193 GATTTATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
17 11 0.28
18 17 0.43
19 7 0.17
20 5 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTATTAAATAAAATTA
Found at i:199050 original size:21 final size:21
Alignment explanation
Indices: 199026--199066 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
199016 AAAGCTCATG
199026 ATATAATTTACTTTT-GATAAT
1 ATATAATTTA-TTTTAGATAAT
199047 ATATAATTTATTTTAGATAA
1 ATATAATTTATTTTAGATAA
199067 ATTACTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
ATATAATTTATTTTAGATAAT
Found at i:200131 original size:20 final size:20
Alignment explanation
Indices: 200096--200147 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
200086 CAATAATTTG
* *
200096 TATCGATGCAATAAGTGAACA
1 TATCGATAC-ATAAGTAAACA
**
200117 TATCGATACATAAGTAAATG
1 TATCGATACATAAGTAAACA
200137 TATCGATACAT
1 TATCGATACAT
200148 GTTTGAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (20 bp):
TATCGATACATAAGTAAACA
Found at i:200267 original size:51 final size:52
Alignment explanation
Indices: 200206--200307 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 52
200196 AAATGAAAAT
* * *
200206 GTATCGATACATTTTTCATTATATCGATACATTCT-AGGTTTTGACCTAAAC
1 GTATCAATACATTCTTCATTATATCGATACATTCTGAGGTTTTGACATAAAC
* * *
200257 GTATCAATACATTCTTGATTGTATCGATACATTCTGAGTTTTTGACATAAA
1 GTATCAATACATTCTTCATTATATCGATACATTCTGAGGTTTTGACATAAA
200308 TATATTGATG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 31 0.70
52 13 0.30
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (52 bp):
GTATCAATACATTCTTCATTATATCGATACATTCTGAGGTTTTGACATAAAC
Found at i:201418 original size:20 final size:20
Alignment explanation
Indices: 201393--201449 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
201383 TTTTTACAAT
201393 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
201413 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
201433 TTGTATCGATACATTGT
1 TTGTATCGATACATTGT
201450 ATCGATACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:201447 original size:13 final size:13
Alignment explanation
Indices: 201431--201460 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
201421 ATACATTGCT
201431 CATTGTATCGATA
1 CATTGTATCGATA
201444 CATTGTATCGATA
1 CATTGTATCGATA
201457 CATT
1 CATT
201461 CTGGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:201530 original size:20 final size:19
Alignment explanation
Indices: 201476--201582 Score: 84
Period size: 20 Copynumber: 5.7 Consensus size: 19
201466 TTTACCCAGA
201476 TGTATCGATACATTTTGT-AT
1 TGTATCGATACA--TTGTCAT
*
201496 TGTATCGATATATTGCTCAT
1 TGTATCGATACATTG-TCAT
201516 TGTATCGAT--A----CAT
1 TGTATCGATACATTGTCAT
201529 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTG-TCAT
* * *
201549 TGTATCAATACATTTTACAA
1 TGTATCGATACATTGT-CAT
201569 TGTATCGATACATT
1 TGTATCGATACATT
201583 CAGGCATTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
13 12 0.17
15 1 0.01
18 4 0.06
19 2 0.03
20 53 0.74
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATTGTCAT
Found at i:201536 original size:33 final size:33
Alignment explanation
Indices: 201494--201562 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
201484 TACATTTTGT
* *
201494 ATTGTATCGATATATTGCTCATTGTATCGATAC
1 ATTGTATCGATACATTGCTCATTGTATCAATAC
201527 ATTGTATCGATACATTGCTCATTGTATCAATAC
1 ATTGTATCGATACATTGCTCATTGTATCAATAC
201560 ATT
1 ATT
201563 TTACAATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (33 bp):
ATTGTATCGATACATTGCTCATTGTATCAATAC
Found at i:201551 original size:53 final size:52
Alignment explanation
Indices: 201476--201582 Score: 128
Period size: 53 Copynumber: 2.0 Consensus size: 52
201466 TTTACCCAGA
* * *
201476 TGTATCGATACATTTTGTATTGTATCGATATATTGCT-CATTGTATCGATACAT
1 TGTATCGATACA-TTTGTATTGTATCAATACATT-CTACAATGTATCGATACAT
*
201529 TGTATCGATACA-TTGCTCATTGTATCAATACATTTTACAATGTATCGATACAT
1 TGTATCGATACATTTG-T-ATTGTATCAATACATTCTACAATGTATCGATACAT
201582 T
1 T
201583 CAGGCATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
51 3 0.06
52 2 0.04
53 42 0.89
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (52 bp):
TGTATCGATACATTTGTATTGTATCAATACATTCTACAATGTATCGATACAT
Found at i:201562 original size:13 final size:13
Alignment explanation
Indices: 201513--201543 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
201503 ATATATTGCT
201513 CATTGTATCGATA
1 CATTGTATCGATA
201526 CATTGTATCGATA
1 CATTGTATCGATA
201539 CATTG
1 CATTG
201544 CTCATTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:203961 original size:51 final size:51
Alignment explanation
Indices: 203906--204029 Score: 158
Period size: 51 Copynumber: 2.4 Consensus size: 51
203896 TCTCGGTTCC
* **
203906 ATTTCCAAAACGTCAATTTTTCTTAATCGGGGATACCCCAACTCCGATTTT
1 ATTTCCAAAACATCAATTTTTCGCAATCGGGGATACCCCAACTCCGATTTT
* * ** *
203957 ATTTCTAAAGCATCAATTTACCGCAATCGGGGATACTCCAACTCCGATTTT
1 ATTTCCAAAACATCAATTTTTCGCAATCGGGGATACCCCAACTCCGATTTT
* *
204008 ATTTTCAAAACAACAATTTTTC
1 ATTTCCAAAACATCAATTTTTC
204030 ATTGGGGATA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (51 bp):
ATTTCCAAAACATCAATTTTTCGCAATCGGGGATACCCCAACTCCGATTTT
Found at i:204150 original size:28 final size:28
Alignment explanation
Indices: 204111--204183 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
204101 TTTTTTTATA
204111 ATCGGAGG-TACTCCAACCCCATTATTTC
1 ATCGG-GGATACTCCAACCCCATTATTTC
* *
204139 ATCGGGGATACTCCAATCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCATTATTTC
*
204167 -TGAGGGGATACTCCAAC
1 AT-CGGGGATACTCCAAC
204184 GCCGATTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 3 0.08
28 36 0.92
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCATTATTTC
Found at i:204243 original size:50 final size:50
Alignment explanation
Indices: 204172--204280 Score: 132
Period size: 50 Copynumber: 2.2 Consensus size: 50
204162 ATTTCTGAGG
* * *
204172 GGATACTCCAACGCCGATTTTA-TTTCTAAAATACCAATTTTTCGCAATCG-
1 GGATACT-CAACGCCGATTTTATTTTC-AAAACACCAATTTCTCACAATCGA
* *
204222 GTGATACTCAACTCTGATTTTATTTTCAAAACACCAATTTCTCACAATCGA
1 G-GATACTCAACGCCGATTTTATTTTCAAAACACCAATTTCTCACAATCGA
204273 GGATACTC
1 GGATACTC
204281 CAACCCCGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
50 40 0.78
51 11 0.22
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (50 bp):
GGATACTCAACGCCGATTTTATTTTCAAAACACCAATTTCTCACAATCGA
Found at i:204246 original size:109 final size:109
Alignment explanation
Indices: 204026--204230 Score: 261
Period size: 109 Copynumber: 1.9 Consensus size: 109
204016 AACAACAATT
* *
204026 TTTCATTGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATATCTA
1 TTTCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATATCTA
** * * * *
204091 AAAATATTATTTTTTTTATAATCGGAGGTACTCCAACCCCATTA
66 AAAATACCATATTTTTCACAATCGGAGATACTCCAACCCCATTA
* * * * *
204135 TTTCATCGGGGATACTCCAATCCCGTTATTTCTGAGGGGATACTCCAACGCCGATTTTATTTCT-
1 TTTCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATATCTA
* *
204199 AAAATACCA-ATTTTTCGCAATCGGTGATACTC
66 AAAATACCATATTTTTCACAATCGGAGATACTC
204231 AACTCTGATT
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
107 17 0.21
108 7 0.09
109 57 0.70
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (109 bp):
TTTCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATATCTA
AAAATACCATATTTTTCACAATCGGAGATACTCCAACCCCATTA
Found at i:204322 original size:79 final size:79
Alignment explanation
Indices: 204224--204436 Score: 227
Period size: 79 Copynumber: 2.7 Consensus size: 79
204214 CGCAATCGGT
*
204224 GATACT-CAACTCTGATTTTATTTTCAAAACACCAA-TTTCTCACAATC-GAGGATACTCCAACC
1 GATACTCCAACCCTGATTTTATTTTCAAAACACCAATTTTCT-ACAATCAG-GGATACTCCAACC
*
204286 CCGTTATTTTCGCGGG
64 CCGTTATTTTCGAGGG
* * ** * **
204302 GATACTCCAACCCCGATTTTATTTTCAAAATACTGATTTTCTATAATCAGGGATACTCCAACCTT
1 GATACTCCAACCCTGATTTTATTTTCAAAACACCAATTTTCTACAATCAGGGATACTCCAACCCC
204367 GTTATTTTCGAGGG
66 GTTATTTTCGAGGG
* * * * * *
204381 GATACTCCAATCCTGATTTT-TATTTCTAGAACACCGATTTTCCATAATCGGGGATA
1 GATACTCCAACCCTGATTTTAT-TTTC-AAAACACCAATTTTCTACAATCAGGGATA
204437 TTCTGGCCCC
Statistics
Matches: 114, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
78 7 0.06
79 77 0.68
80 30 0.26
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (79 bp):
GATACTCCAACCCTGATTTTATTTTCAAAACACCAATTTTCTACAATCAGGGATACTCCAACCCC
GTTATTTTCGAGGG
Found at i:204349 original size:236 final size:235
Alignment explanation
Indices: 203934--204364 Score: 582
Period size: 236 Copynumber: 1.8 Consensus size: 235
203924 TTTCTTAATC
* * *
203934 GGGGATACCCCAACTCCGATTTTATTTCTAAAGCATCAATTTACCGCAATCGGGGATACTCCAAC
1 GGGGATACCCCAACGCCGATTTTATTTCTAAAACACCAATTTACCGCAATCGGGGATACTCCAAC
* * *
203999 TCCGATTTTATTTTCAAAACAACAATTTTTCATTGGGGATACTCCAACCCCGTTATTTCCGAGGG
66 TCCGATTTTATTTTCAAAACAACAATTTTACATCGAGGATACTCCAACCCCGTTATTTCCGAGGG
* * * *
204064 GATACTCCAACCCCGGCTTTATATCTAAAAATATTATTTTTTTTATAATC-GGAGGTACTCCAAC
131 GATACTCCAACCCCGACTTTATATCTAAAAATATGA-TTTTTCTATAATCAGG-GATACTCCAAC
204128 CCCATTATTTCATCGGGGATACTCCAATCCCGTTATTTCTGA
194 CCCATTATTTCATCGGGGATACTCCAATCCCGTTATTTCTGA
* * ** *
204170 GGGGATACTCCAACGCCGATTTTATTTCTAAAATACCAATTTTTCGCAATCGGTGATACT-CAAC
1 GGGGATACCCCAACGCCGATTTTATTTCTAAAACACCAATTTACCGCAATCGGGGATACTCCAAC
* * * *
204234 TCTGATTTTATTTTCAAAACACCAATTTCTCACAATCGAGGATACTCCAACCCCGTTATTTTCGC
66 TCCGATTTTATTTTCAAAACAACAATTT-T-AC-ATCGAGGATACTCCAACCCCGTTATTTCCGA
* * *
204299 GGGGATACTCCAACCCCGATTTTAT-TTTCAAAATACTGA-TTTTCTATAATCAGGGATACTCCA
128 GGGGATACTCCAACCCCGACTTTATATCTAAAAATA-TGATTTTTCTATAATCAGGGATACTCCA
204362 ACC
192 ACC
204365 TTGTTATTTT
Statistics
Matches: 168, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
235 30 0.18
236 75 0.45
237 11 0.07
238 52 0.31
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (235 bp):
GGGGATACCCCAACGCCGATTTTATTTCTAAAACACCAATTTACCGCAATCGGGGATACTCCAAC
TCCGATTTTATTTTCAAAACAACAATTTTACATCGAGGATACTCCAACCCCGTTATTTCCGAGGG
GATACTCCAACCCCGACTTTATATCTAAAAATATGATTTTTCTATAATCAGGGATACTCCAACCC
CATTATTTCATCGGGGATACTCCAATCCCGTTATTTCTGA
Found at i:205972 original size:23 final size:24
Alignment explanation
Indices: 205923--205975 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
205913 CGGCTGTCCT
* *
205923 TACCGGACGGAGGAACGATTCGGA
1 TACCGAACGGAGGAACGATTCGAA
*
205947 TACCGAACGGAGG-ATGATTCGAA
1 TACCGAACGGAGGAACGATTCGAA
205970 TACCGA
1 TACCGA
205976 TTTAGGCGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.32, C:0.21, G:0.32, T:0.15
Consensus pattern (24 bp):
TACCGAACGGAGGAACGATTCGAA
Found at i:216848 original size:1 final size:1
Alignment explanation
Indices: 216844--216915 Score: 54
Period size: 1 Copynumber: 72.0 Consensus size: 1
216834 CATTCTTTTT
* * * * * * * * * *
216844 AAAAAAAAAAACAAAAACAACAAAAAAACAAAAAAACAAAAAACAAAACAAAGAAAAAAGAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
216909 AAAAAAA
1 AAAAAAA
216916 GAAGAATCTG
Statistics
Matches: 51, Mismatches: 20, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:216868 original size:8 final size:8
Alignment explanation
Indices: 216844--216912 Score: 79
Period size: 9 Copynumber: 8.5 Consensus size: 8
216834 CATTCTTTTT
216844 AAAA-AAA
1 AAAACAAA
216851 AAAACAAA
1 AAAACAAA
216859 AACAACAAA
1 AA-AACAAA
216868 AAAACAAA
1 AAAACAAA
216876 AAAAC-AA
1 AAAACAAA
216883 AAAACAAA
1 AAAACAAA
*
216891 ACAAAGAAA
1 A-AAACAAA
*
216900 AAAGAGAAA
1 AAA-ACAAA
216909 AAAA
1 AAAA
216913 AAAGAAGAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 9
0.85 0.02 0.14
Matches are distributed among these distances:
7 11 0.20
8 22 0.39
9 23 0.41
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (8 bp):
AAAACAAA
Found at i:216870 original size:16 final size:16
Alignment explanation
Indices: 216844--216912 Score: 79
Period size: 17 Copynumber: 4.2 Consensus size: 16
216834 CATTCTTTTT
216844 AAAA-AAAAAAACAAA
1 AAAACAAAAAAACAAA
216859 AACAACAAAAAAACAAA
1 AA-AACAAAAAAACAAA
216876 AAAAC-AAAAAACAAA
1 AAAACAAAAAAACAAA
* *
216891 ACAAAGAAAAAAGAGAAA
1 A-AAACAAAAAA-ACAAA
216909 AAAA
1 AAAA
216913 AAAGAAGAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
15 13 0.28
16 8 0.17
17 21 0.45
18 5 0.11
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (16 bp):
AAAACAAAAAAACAAA
Found at i:216890 original size:32 final size:30
Alignment explanation
Indices: 216844--216915 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 30
216834 CATTCTTTTT
216844 AAAAAAAAAAACAAAAACAACA-AAAAAACAA
1 AAAAAAAAAAAC-AAAACAA-AGAAAAAACAA
* *
216875 AAAAACAAAAAACAAAACAAAGAAAAAAGAG
1 AAAAA-AAAAAACAAAACAAAGAAAAAACAA
216906 AAAAAAAAAA
1 AAAAAAAAAA
216916 GAAGAATCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 6 0.16
31 24 0.65
32 7 0.19
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (30 bp):
AAAAAAAAAAACAAAACAAAGAAAAAACAA
Found at i:217995 original size:99 final size:94
Alignment explanation
Indices: 217874--218058 Score: 239
Period size: 94 Copynumber: 1.9 Consensus size: 94
217864 ATCTAAACTT
* * ** *
217874 TCTCCTTTCACTTTTCAGTCCTCAAATAGCAGGATGCTTTTTCTTTTAAAGCCCACACAAGTTGG
1 TCTCCTTTCACCTTTCAGTCCTCAAAGAGCAGGA--C---ACCTTTCAAAGCCCACACAAGTTGG
217939 TGGCA-CTTTCTAGTCCTCAAAGAGCAGGACTCTC
61 TGGCACCTTTC-AGTCCTCAAAGAGCAGGACTCTC
*
217973 TCTCCTTTCACCCTTT-AGTCCTCAAAGAGTAGGACACCTTTCAAAGCCCACACAAGTTGGTGGC
1 TCTCCTTTCA-CCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGC
218037 ACCTTTCAGTCCTCAAAGAGCA
65 ACCTTTCAGTCCTCAAAGAGCA
218059 TGACGCCTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
94 42 0.54
95 5 0.06
97 1 0.01
99 26 0.33
100 4 0.05
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (94 bp):
TCTCCTTTCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
CCTTTCAGTCCTCAAAGAGCAGGACTCTC
Found at i:218049 original size:55 final size:55
Alignment explanation
Indices: 217989--218302 Score: 389
Period size: 55 Copynumber: 5.5 Consensus size: 55
217979 TTCACCCTTT
* * *
217989 AGTCCTCAAAGAGTAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTCCC
* * * *
218044 AGTCCTCAAAGAGCATGACGCCTTTCAAAGCCCAGACGAGTTGGTGGCAC-CCTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTC-CC
218099 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCC--TTTC----AAAGCCCACACAAGTTGGTGGCACTTCCC
218160 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCC
* *
218215 AATCCTCAAAAAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGTTGGTGGCACTTCCC
*
218276 AGTCCTCAAAGAGCACGACGCTCTTTC
1 AGTCCTCAAAGAGCAGGACGC-CTTTC
218303 CTTTCACCCT
Statistics
Matches: 227, Mismatches: 16, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
54 1 0.00
55 115 0.51
56 3 0.01
57 5 0.02
59 4 0.02
60 1 0.00
61 96 0.42
62 2 0.01
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCC
Found at i:218165 original size:61 final size:60
Alignment explanation
Indices: 218010--218301 Score: 365
Period size: 61 Copynumber: 5.0 Consensus size: 60
218000 AGTAGGACAC
* *
218010 CTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TCAGTCCTCAAAGAGCATGACGCC--TTT
1 CTTT-AAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTT
* * *
218069 C---AAAGCCCAGACGAGTTGGTGGCAC-CCTCCAGTCCTCAAAGAGCAGGACGCCTTTTT
1 CTTTAAAGCCCACACAAGTTGGTGGCACTTC-CCAGTCCTCAAAGAGCAGGACGCCTTTTT
218126 CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCC--TTT
1 C-TTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTT
* * *
218185 C---AAAGCCCACACAAGTTGGTGGCACTTCCCAATCCTCAAAAAGCAGGACGCCTTTTC
1 CTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTT
*
218242 CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCACGACGCTCTTT
1 C-TTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGC-CTTT
218302 CCTTTCACCC
Statistics
Matches: 203, Mismatches: 14, Indels: 29
0.83 0.06 0.12
Matches are distributed among these distances:
54 1 0.00
55 92 0.45
57 7 0.03
59 5 0.02
61 93 0.46
62 5 0.02
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.23
Consensus pattern (60 bp):
CTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTT
Found at i:218180 original size:116 final size:116
Alignment explanation
Indices: 218009--218302 Score: 457
Period size: 116 Copynumber: 2.5 Consensus size: 116
217999 GAGTAGGACA
* * *
218009 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TCAGTCCTCAAAGAGCATGACGCCTTTCAAA
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCACGACGCCTTTCAAA
* * * *
218073 GCCCAGACGAGTTGGTGGCACC-CTCCAGTCCTCAAAGAGCAGGACGCCTTTT
65 GCCCACACAAGTTGGTGGCACCTC-CCAATCCTCAAAAAGCAGGACGCCTTTT
* *
218125 TCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCACGACGCCTTTCAAAG
*
218190 CCCACACAAGTTGGTGGCACTTCCCAATCCTCAAAAAGCAGGACGCCTTTT
66 CCCACACAAGTTGGTGGCACCTCCCAATCCTCAAAAAGCAGGACGCCTTTT
218241 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCACGACGCTCTTTC
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCACGACGC-CTTTC
218303 CTTTCACCCT
Statistics
Matches: 164, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
115 3 0.02
116 155 0.95
117 6 0.04
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (116 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCACGACGCCTTTCAAAG
CCCACACAAGTTGGTGGCACCTCCCAATCCTCAAAAAGCAGGACGCCTTTT
Found at i:218419 original size:272 final size:265
Alignment explanation
Indices: 218038--218566 Score: 738
Period size: 272 Copynumber: 2.0 Consensus size: 265
218028 GTTGGTGGCA
* * * *
218038 CCTTTCAGTCCTCAAAGAGCATGACGCCTTTCAAAGCCCAGACGAGTTGGTGGCACCCTCCAGTC
1 CCTTTCAGTCCTCAAAGAGCAGGACGCATTTCAAAGCCCACACAAGTTGGTGGCACCCTCCAGTC
* *
218103 CTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCA
66 CTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACTTCACAGTCCTCA
218168 AAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAATCCTCAAAAAGCAGGA
131 AAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAATCCTCAAAAAGC-GG-
* * * *
218233 CGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCACGACGC
194 -G---ATGCCTTTAAAAGCCCACACAAGTTGGTGGCACCTT-CCAGTCCTCAAAGAGCAAGACGC
218297 TCTTTCCTTTCAC
254 -CTTTCCTTTCAC
* * ** *
218310 CCTTT-AGTCCTCAAAGAGTAGGACGCATTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGT
1 CCTTTCAGTCCTCAAAGAGCAGGACGCATTTCAAAGCCCACACAAGTTGGTGGCAC-CCTCCAGT
* * * * *
218374 CCTCAAAGAGTAGGATGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTACAGTCTTC
65 CCTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACTTCACAGTCCTC
* * * *
218439 AAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCGGG
130 AAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAATCCTCAAAAAGCGGG
*
218504 ATGCCTTTAAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACGCCTTT
195 ATGCCTTTAAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAAGACGCCTTT
218567 TAAAGCCCAC
Statistics
Matches: 230, Mismatches: 25, Indels: 11
0.86 0.09 0.04
Matches are distributed among these distances:
265 4 0.02
266 50 0.22
267 3 0.01
269 1 0.00
271 46 0.20
272 126 0.55
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (265 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGCATTTCAAAGCCCACACAAGTTGGTGGCACCCTCCAGTC
CTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACTTCACAGTCCTCA
AAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAATCCTCAAAAAGCGGGA
TGCCTTTAAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAAGACGCCTTTCCT
TTCAC
Found at i:218443 original size:156 final size:155
Alignment explanation
Indices: 218160--218446 Score: 430
Period size: 156 Copynumber: 1.8 Consensus size: 155
218150 GGCACTTCCC
*
218160 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAATCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCATTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAATCCTCAAA
* *
218225 AAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGC
66 AAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCACAGTCCTCAAAGAGC
218290 ACGACGCTCTTTCCTTTCACCCTTT
131 ACGACGCTCTTTCCTTTCACCCTTT
* * * * *
218315 AGTCCTCAAAGAGTAGGACGCATTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACGCATTTCAAAGCCCACACAAGTTGGTGGCAC-TTCCCAATCCTCAA
* * * * * * *
218380 AGAGTAGGATGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTACAGTCTTCAAAGAG
65 AAAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCACAGTCCTCAAAGAG
218445 CA
130 CA
218447 GGATGCCTTT
Statistics
Matches: 116, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
155 47 0.41
156 69 0.59
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (155 bp):
AGTCCTCAAAGAGCAGGACGCATTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAATCCTCAAA
AAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCACAGTCCTCAAAGAGC
ACGACGCTCTTTCCTTTCACCCTTT
Found at i:218617 original size:55 final size:55
Alignment explanation
Indices: 218315--218617 Score: 365
Period size: 55 Copynumber: 5.4 Consensus size: 55
218305 TTCACCCTTT
* * *
218315 AGTCCTCAAAGAGTAGGACGCATTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
1 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCC
* * * *
218371 AGTCCTCAAAGAGTAGGATGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTAC
1 AGTCCTCAAAGAGCAGGACGCC----T-TTT-AAAGCCCACACAAGTTGGTGGCACTTTCC
* * * *
218432 AGTCTTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCC
* * * *
218487 AATCCTCAAAGAGCGGGATGCCTTTAAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCC
* * *
218542 AGTCCTCAAAGAGCAAGACGCCTTTTAAAGCCCACACGAGTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCC
218597 AGTCCTCAAAGAGCAGGACGC
1 AGTCCTCAAAGAGCAGGACGC
218618 TCTCTCCTTT
Statistics
Matches: 217, Mismatches: 22, Indels: 17
0.85 0.09 0.07
Matches are distributed among these distances:
54 3 0.01
55 138 0.64
56 25 0.12
57 1 0.00
60 1 0.00
61 26 0.12
62 23 0.11
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCC
Found at i:219079 original size:20 final size:20
Alignment explanation
Indices: 219034--219085 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
219024 GTAGCCAAAC
**
219034 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
219054 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
219073 TTGTATCGATACA
1 TTGTATCGATACA
219086 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:227822 original size:13 final size:13
Alignment explanation
Indices: 227777--227829 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
227767 TAGCCAAACT
227777 TGTATCGATACAA
1 TGTATCGATACAA
* *
227790 TGTATAC-ACAAAGTA
1 TGTAT-CGATACA--A
227805 TGTATCGATACAA
1 TGTATCGATACAA
227818 TGTATCGATACA
1 TGTATCGATACA
227830 CAAAAAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 21 0.66
14 2 0.06
15 9 0.28
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:231462 original size:20 final size:19
Alignment explanation
Indices: 231433--231507 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
231423 AAAAAGACAT
231433 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
231452 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
231473 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
231493 AATGTATCGATACAT
1 AATGTATCGATACAT
231508 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:231490 original size:40 final size:39
Alignment explanation
Indices: 231430--231507 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
231420 GGTAAAAAGA
*
231430 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
231469 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
231508 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:233610 original size:21 final size:21
Alignment explanation
Indices: 233586--233626 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
233576 TTTTCTCATA
*
233586 TGCTAGGAAAATGATTTTTTC
1 TGCTAGAAAAATGATTTTTTC
*
233607 TGCTCGAAAAATGATTTTTT
1 TGCTAGAAAAATGATTTTTT
233627 AGGATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (21 bp):
TGCTAGAAAAATGATTTTTTC
Found at i:234111 original size:28 final size:28
Alignment explanation
Indices: 234072--234148 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
234062 TTTTTTCATA
*
234072 ATCGGGGGTACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
* * *
234100 ATCGGGGATACTCCAATCCTGTTATTTT
1 ATCGGGGATACTCCAACCCCGTTATTTC
* *
234128 TTAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
234149 ATTTTATTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.30
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:234197 original size:51 final size:51
Alignment explanation
Indices: 234134--234299 Score: 253
Period size: 51 Copynumber: 3.3 Consensus size: 51
234124 TTTTTTAGGG
234134 GATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCGTAATCGGT
1 GATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCGTAATCGGT
*
234185 GATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTCGTAATCGGT
1 GATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCGTAATCGGT
* * * * ** *
234236 GATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGG
1 GATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCGTAATCGGT
234287 GATACT-CAACCCC
1 GATACTCCAACCCC
234300 ATTATTTTCG
Statistics
Matches: 105, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
50 6 0.06
51 99 0.94
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.34
Consensus pattern (51 bp):
GATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCGTAATCGGT
Found at i:234330 original size:78 final size:77
Alignment explanation
Indices: 234236--234451 Score: 279
Period size: 78 Copynumber: 2.7 Consensus size: 77
234226 CGTAATCGGT
* * *
234236 GATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGGATACTCAACCCCA
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCGATTT-TCATAATCGGGGATACTCAACCCCA
*
234301 TTATTTTCGCGGG
65 TTATTTTCGAGGG
* * * * *
234314 GATACTCCAACCCCGATTTTATTTTCAAAATACTGATTTTCTATAATCAGGGATACTCCAACCCT
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTC-ATAATCGGGGATACT-CAACCCC
*
234379 GTTATTTTCGAGGG
64 ATTATTTTCGAGGG
* *
234393 GATACTCCAACCCCGATGTTTATTTCTAGAACACCGATTTTCCATAATCGGGGATACTC
1 GATACTCCAACCCCGAT-TTTATTTCCAAAACACCGATTTT-CATAATCGGGGATACTC
234452 TAGCCCCGTT
Statistics
Matches: 118, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
77 2 0.02
78 47 0.40
79 36 0.31
80 32 0.27
81 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (77 bp):
GATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTCATAATCGGGGATACTCAACCCCAT
TATTTTCGAGGG
Found at i:234402 original size:79 final size:78
Alignment explanation
Indices: 234236--234451 Score: 265
Period size: 79 Copynumber: 2.7 Consensus size: 78
234226 CGTAATCGGT
* * * * *
234236 GATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGGATACT-CAACCCC
1 GATACTCCAACCCCGATTTTATTTTCAAAACACGATTTTCT-ATAATCGGGGATACTCCAACCCC
*
234300 ATTATTTTCGCGGG
65 ATTATTTTCGAGGG
* * *
234314 GATACTCCAACCCCGATTTTATTTTCAAAATACTGATTTTCTATAATCAGGGATACTCCAACCCT
1 GATACTCCAACCCCGATTTTATTTTCAAAACAC-GATTTTCTATAATCGGGGATACTCCAACCCC
*
234379 GTTATTTTCGAGGG
65 ATTATTTTCGAGGG
* *
234393 GATACTCCAACCCCGATGTTTA-TTTCTAGAACACCGATTTTCCATAATCGGGGATACTC
1 GATACTCCAACCCCGAT-TTTATTTTC-AAAACA-CGATTTTCTATAATCGGGGATACTC
234452 TAGCCCCGTT
Statistics
Matches: 119, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
78 43 0.36
79 45 0.38
80 30 0.25
81 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (78 bp):
GATACTCCAACCCCGATTTTATTTTCAAAACACGATTTTCTATAATCGGGGATACTCCAACCCCA
TTATTTTCGAGGG
Found at i:241289 original size:58 final size:58
Alignment explanation
Indices: 241227--241433 Score: 200
Period size: 58 Copynumber: 3.6 Consensus size: 58
241217 CAAATCACGA
* * * *
241227 AAAATTACCTAAATGACATTAAAATGCATAAAATGATATAAAAGTCCTTAGATCATGG
1 AAAATGACCTAAATGACATCAAAATGCACAAAATGATATAAAAGTCCCTAGATCATGG
* ** ** * * *
241285 AAAATGACCCAAATGGGATCAAAATTAACAAAATTACATATAAGTCCCTAGATCATGG
1 AAAATGACCTAAATGACATCAAAATGCACAAAATGATATAAAAGTCCCTAGATCATGG
* * * * ** * * **
241343 TAAATGACCAAAACGATATC-AAATGCATGAAATGGTATAAAAGTCCCTAAATCATAA
1 AAAATGACCTAAATGACATCAAAATGCACAAAATGATATAAAAGTCCCTAGATCATGG
*
241400 AAAATGACCTAAATGACATCAAAATTCACAAAAT
1 AAAATGACCTAAATGACATCAAAATGCACAAAAT
241434 TACATCCAAT
Statistics
Matches: 113, Mismatches: 35, Indels: 2
0.75 0.23 0.01
Matches are distributed among these distances:
57 42 0.37
58 71 0.63
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (58 bp):
AAAATGACCTAAATGACATCAAAATGCACAAAATGATATAAAAGTCCCTAGATCATGG
Found at i:245928 original size:20 final size:21
Alignment explanation
Indices: 245903--245955 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
245893 TTCAACAATT
245903 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAAGTGAAA
***
245923 TGTATCGATACATGCTTGAAA
1 TGTATCGATACATAAGTGAAA
245944 TGTATCGATACA
1 TGTATCGATACA
245956 GCGCCATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (21 bp):
TGTATCGATACATAAGTGAAA
Found at i:247890 original size:19 final size:19
Alignment explanation
Indices: 247858--247913 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
247848 TGTATCGATA
* * *
247858 CATTGCATCAATACATGTT
1 CATTGTATCGATACATGCT
*
247877 CATTGTATCGATACATACT
1 CATTGTATCGATACATGCT
247896 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
247914 AAACGACAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:247975 original size:13 final size:13
Alignment explanation
Indices: 247957--247986 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
247947 GATACGTGGG
*
247957 ACATTGTATTGAT
1 ACATTGTATCGAT
247970 ACATTGTATCGAT
1 ACATTGTATCGAT
247983 ACAT
1 ACAT
247987 GGTACAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:248162 original size:30 final size:31
Alignment explanation
Indices: 248111--248169 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
248101 ACAAGACAAT
*
248111 AACAGCTACAAACATAATCATTCAACCTTTA
1 AACAGCTACAAACAAAATCATTCAACCTTTA
248142 AACAGCTACAAA-AAAATCATTCAACCTT
1 AACAGCTACAAACAAAATCATTCAACCTT
248170 CAACGAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.24
Consensus pattern (31 bp):
AACAGCTACAAACAAAATCATTCAACCTTTA
Found at i:266407 original size:23 final size:23
Alignment explanation
Indices: 266378--266421 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
266368 TAGTGTTAGT
*
266378 TTTAGTTATTTTTAGTTTTTAAC
1 TTTAGTTATTTTTAATTTTTAAC
266401 TTTAGTTATTTTTAATTTTTA
1 TTTAGTTATTTTTAATTTTTA
266422 GGTTTTATTT
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:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (23 bp):
TTTAGTTATTTTTAATTTTTAAC
Found at i:267133 original size:9 final size:9
Alignment explanation
Indices: 267119--267143 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
267109 AGGTATAGTG
267119 AAAAAAATA
1 AAAAAAATA
267128 AAAAAAATA
1 AAAAAAATA
267137 AAAAAAA
1 AAAAAAA
267144 ATAGAGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATA
Found at i:267604 original size:5 final size:5
Alignment explanation
Indices: 267594--267623 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
267584 ATGTTGGATG
267594 AATCA AATCA AATCA AATCA AATCA AATCA
1 AATCA AATCA AATCA AATCA AATCA AATCA
267624 TTACCATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
AATCA
Found at i:268059 original size:2 final size:2
Alignment explanation
Indices: 268052--268080 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
268042 CAATGCACAA
268052 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
268081 CACATTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:270647 original size:13 final size:13
Alignment explanation
Indices: 270629--270654 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
270619 CAATTTTTTG
270629 TGTATCGATACAT
1 TGTATCGATACAT
270642 TGTATCGATACAT
1 TGTATCGATACAT
270655 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:270669 original size:32 final size:33
Alignment explanation
Indices: 270609--270672 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
270599 TACAAGCCAA
** *
270609 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
270642 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
270673 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:272446 original size:13 final size:13
Alignment explanation
Indices: 272428--272452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
272418 ACTGAAGCAA
272428 TGTATCGATACAT
1 TGTATCGATACAT
272441 TGTATCGATACA
1 TGTATCGATACA
272453 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:276087 original size:13 final size:13
Alignment explanation
Indices: 276069--276094 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
276059 CAATTTTTTG
276069 TGTATCGATACAT
1 TGTATCGATACAT
276082 TGTATCGATACAT
1 TGTATCGATACAT
276095 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:276109 original size:32 final size:33
Alignment explanation
Indices: 276049--276112 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
276039 TACAAGCCAA
** *
276049 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
276082 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
276113 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:280158 original size:14 final size:15
Alignment explanation
Indices: 280139--280167 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
280129 TAGCTCAATA
280139 AAAAGAAAAA-AAAG
1 AAAAGAAAAAGAAAG
280153 AAAAGAAAAAGAAAG
1 AAAAGAAAAAGAAAG
280168 CTCACCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAGAAAG
Found at i:280244 original size:24 final size:23
Alignment explanation
Indices: 280217--280274 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 23
280207 AAAATTGATT
* *
280217 TTAATTAATTTATTTAAATTATAA
1 TTAATTAATTTAGTAAAATT-TAA
280241 TTAATTAATTTTAGTAAAATTTAA
1 TTAATTAA-TTTAGTAAAATTTAA
280265 TTAAATTAAT
1 TT-AATTAAT
280275 GAATGTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 14 0.47
25 16 0.53
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTAATTTAGTAAAATTTAA
Found at i:280568 original size:26 final size:26
Alignment explanation
Indices: 280525--280575 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
280515 TTTAAATTTT
280525 TTTATCAAATTCAATCAATCTTTTAAG
1 TTTATCAAATTCAATCAAT-TTTTAAG
* *
280552 TTTATC-AATTTATTCAATTTTTAA
1 TTTATCAAATTCAATCAATTTTTAA
280576 AATTTTACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 10 0.45
27 6 0.27
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTATCAAATTCAATCAATTTTTAAG
Found at i:282832 original size:17 final size:18
Alignment explanation
Indices: 282812--282859 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
282802 TATTTTTTTG
282812 ATTTTATAATTTATAT-T
1 ATTTTATAATTTATATAT
282829 ATTTT-TATATTTATATAT
1 ATTTTATA-ATTTATATAT
*
282847 ATTATATAATTTA
1 ATTTTATAATTTA
282860 ATCATATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 2 0.07
17 13 0.48
18 10 0.37
19 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTATAATTTATATAT
Found at i:282845 original size:26 final size:26
Alignment explanation
Indices: 282792--282858 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
282782 AGTTTGAATT
*
282792 TAATTTGAT-TTATTTTTTTGATTTTA
1 TAATTT-ATATTATTTTTATGATTTTA
282818 TAATTTATATTATTTTTAT-A-TTTA
1 TAATTTATATTATTTTTATGATTTTA
*
282842 TATATATTATATAATTT
1 TA-AT-TTATATTATTT
282859 AATCATATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
24 6 0.17
25 5 0.14
26 25 0.69
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (26 bp):
TAATTTATATTATTTTTATGATTTTA
Found at i:282866 original size:18 final size:18
Alignment explanation
Indices: 282816--282886 Score: 60
Period size: 17 Copynumber: 4.1 Consensus size: 18
282806 TTTTTGATTT
282816 TATAATTTATAT-TATT-
1 TATAATTTATATATATTA
*
282832 TTTATATTTATATATATTA
1 TATA-ATTTATATATATTA
282851 TATAATTTA-ATCATATTA
1 TATAATTTATAT-ATATTA
* **
282869 AAT-ATAAATATATATTA
1 TATAATTTATATATATTA
282886 T
1 T
282887 TATAGTGTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
16 3 0.07
17 19 0.43
18 19 0.43
19 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (18 bp):
TATAATTTATATATATTA
Found at i:283544 original size:27 final size:25
Alignment explanation
Indices: 283510--283560 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
283500 AAGAAAATTT
* *
283510 TAATTTATTTTTTTAAGAATTGTTAAA
1 TAATTTATGTTATTAA-AATT-TTAAA
283537 TAATTTATGTTATTAAAATTTTAA
1 TAATTTATGTTATTAAAATTTTAA
283561 TGAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 4 0.18
27 14 0.64
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (25 bp):
TAATTTATGTTATTAAAATTTTAAA
Found at i:283767 original size:45 final size:45
Alignment explanation
Indices: 283668--283755 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
283658 TAAAAAATAT
*
283668 AAAAAAATTATTATATTAATTGTCAATAGAGTTTTTAAATTCTTA
1 AAAAAAATTATTATATTAATTGTCAATAGAATTTTTAAATTCTTA
283713 AAAAAAATTATTATATTAATTGTCAATAGAATTTTTAAATTCT
1 AAAAAAATTATTATATTAATTGTCAATAGAATTTTTAAATTCT
283756 AGAAGTAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (45 bp):
AAAAAAATTATTATATTAATTGTCAATAGAATTTTTAAATTCTTA
Found at i:284790 original size:19 final size:19
Alignment explanation
Indices: 284766--284803 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
284756 AAAAGGAACT
284766 TAGTCGATCTTCCATTAAA
1 TAGTCGATCTTCCATTAAA
*
284785 TAGTCGATCTTCTATTAAA
1 TAGTCGATCTTCCATTAAA
284804 CTTGAGACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (19 bp):
TAGTCGATCTTCCATTAAA
Found at i:286093 original size:22 final size:22
Alignment explanation
Indices: 286051--286093 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
286041 AGTTTCAATT
* *
286051 TAACACACTTTAATTATAAAAA
1 TAACACACTTAAATTAAAAAAA
*
286073 TAACA-ACTTAAATTCAAAAAA
1 TAACACACTTAAATTAAAAAAA
286094 GTTGAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (22 bp):
TAACACACTTAAATTAAAAAAA
Found at i:287271 original size:16 final size:16
Alignment explanation
Indices: 287252--287284 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
287242 ACTATTATAA
287252 ATTTATATAAATTTTT
1 ATTTATATAAATTTTT
*
287268 ATTTATATATATTTTT
1 ATTTATATAAATTTTT
287284 A
1 A
287285 CACGTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTATATAAATTTTT
Found at i:287765 original size:21 final size:21
Alignment explanation
Indices: 287741--287784 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
287731 CAAATAAAAA
*
287741 TATTTGAATGTAAATGTCATT
1 TATTTGAATATAAATGTCATT
*
287762 TATTTGAATATGAATGTCATT
1 TATTTGAATATAAATGTCATT
287783 TA
1 TA
287785 GACTTGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.48
Consensus pattern (21 bp):
TATTTGAATATAAATGTCATT
Found at i:287903 original size:16 final size:16
Alignment explanation
Indices: 287884--287958 Score: 78
Period size: 16 Copynumber: 4.7 Consensus size: 16
287874 AGGTTTGTGG
*
287884 CATTTTGGGTTCGGAT
1 CATTTTGGGTTCGGGT
* *
287900 CATTTCGGGTTCAGGT
1 CATTTTGGGTTCGGGT
* *
287916 CACTTTGGATTCGGGT
1 CATTTTGGGTTCGGGT
* * *
287932 CATTTCGGATTTGGGT
1 CATTTTGGGTTCGGGT
287948 CATTTTGGGTT
1 CATTTTGGGTT
287959 GGAGTTTTTT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.12, C:0.15, G:0.31, T:0.43
Consensus pattern (16 bp):
CATTTTGGGTTCGGGT
Found at i:287955 original size:32 final size:32
Alignment explanation
Indices: 287884--287955 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
287874 AGGTTTGTGG
* *
287884 CATTTTGGGTTCGGATCATTTCGGGTTCAGGT
1 CATTTTGGATTCGGATCATTTCGGATTCAGGT
* * **
287916 CACTTTGGATTCGGGTCATTTCGGATTTGGGT
1 CATTTTGGATTCGGATCATTTCGGATTCAGGT
287948 CATTTTGG
1 CATTTTGG
287956 GTTGGAGTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.12, C:0.15, G:0.31, T:0.42
Consensus pattern (32 bp):
CATTTTGGATTCGGATCATTTCGGATTCAGGT
Found at i:287991 original size:16 final size:16
Alignment explanation
Indices: 287949--287992 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
287939 GATTTGGGTC
*
287949 ATTTTGGGTTGGAGTT
1 ATTTTGGGTTTGAGTT
*
287965 TTTTTGGGTTTGAGTT
1 ATTTTGGGTTTGAGTT
*
287981 ATTTTAGGTTTG
1 ATTTTGGGTTTG
287993 GGTCAATCGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.11, C:0.00, G:0.32, T:0.57
Consensus pattern (16 bp):
ATTTTGGGTTTGAGTT
Found at i:289106 original size:32 final size:32
Alignment explanation
Indices: 289052--289147 Score: 97
Period size: 32 Copynumber: 3.0 Consensus size: 32
289042 AATTATTCAG
* *
289052 GTCATTTCAGG-TTCAGGACATTTC-GAGTTTGA
1 GTCATTTC-GGATTCAGGTCATTTCGGA-TTCGA
*
289084 GTCATTTCGGATTCATGTCATTTCGGATTCGA
1 GTCATTTCGGATTCAGGTCATTTCGGATTCGA
* * *
289116 ATCATTTTGGATTCAGGGTCATTTCGGGTTCG
1 GTCATTTCGGATTCA-GGTCATTTCGGATTCG
289148 GACTAGTTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
31 2 0.04
32 36 0.67
33 16 0.30
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.40
Consensus pattern (32 bp):
GTCATTTCGGATTCAGGTCATTTCGGATTCGA
Found at i:289108 original size:16 final size:15
Alignment explanation
Indices: 289046--289142 Score: 70
Period size: 16 Copynumber: 6.0 Consensus size: 15
289036 CGAGTTAATT
289046 ATTCAGGTCATTTCAGG
1 ATTCA-GTCATTTC-GG
*
289063 -TTCAGGACATTTCGAG
1 ATTCA-GTCATTTCG-G
* *
289079 TTTGAGTCATTTCGG
1 ATTCAGTCATTTCGG
289094 ATTCATGTCATTTCGG
1 ATTCA-GTCATTTCGG
* *
289110 ATTCGAATCATTTTGG
1 ATTC-AGTCATTTCGG
289126 ATTCAGGGTCATTTCGG
1 ATTCA--GTCATTTCGG
289143 GTTCGGACTA
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
15 6 0.09
16 47 0.72
17 12 0.18
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (15 bp):
ATTCAGTCATTTCGG
Found at i:292243 original size:23 final size:22
Alignment explanation
Indices: 292185--292234 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
292175 CCAAAAAAAA
*
292185 AAAAAAACTTTTGATTTTGAGGG
1 AAAAAAAC-TTTGATTTTGAGAG
292208 AAAAAAACTTTGATTTTGA-AG
1 AAAAAAACTTTGATTTTGAGAG
292229 AAAAAA
1 AAAAAA
292235 TGGCTTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 7 0.27
22 11 0.42
23 8 0.31
ACGTcount: A:0.50, C:0.04, G:0.16, T:0.30
Consensus pattern (22 bp):
AAAAAAACTTTGATTTTGAGAG
Found at i:296572 original size:20 final size:20
Alignment explanation
Indices: 296547--296613 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
296537 ATTTGAAGCA
296547 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATC
296567 ATGTATCGAT---A--CAT-
1 ATGTATCGATACAATTCATC
296581 -TGTATCGATACAATGTC-TC
1 ATGTATCGATACAAT-TCATC
296600 ATGTATCGATACAA
1 ATGTATCGATACAA
296614 ACAGTGGTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
13 9 0.23
15 3 0.08
16 1 0.03
17 1 0.03
18 1 0.03
19 1 0.03
20 23 0.59
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTCATC
Found at i:296586 original size:13 final size:13
Alignment explanation
Indices: 296568--296592 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
296558 CAATTCATCA
296568 TGTATCGATACAT
1 TGTATCGATACAT
296581 TGTATCGATACA
1 TGTATCGATACA
296593 ATGTCTCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:296590 original size:33 final size:33
Alignment explanation
Indices: 296548--296612 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
296538 TTTGAAGCAA
296548 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATGTC-TCATGTATCGATACAT
296581 TGTATCGATACAATGTCTCATGTATCGATACA
1 TGTATCGATACAATGTCTCATGTATCGATACA
296613 AACAGTGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTCTCATGTATCGATACAT
Found at i:296667 original size:20 final size:20
Alignment explanation
Indices: 296642--296696 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
296632 CTGCCAGTTT
**
296642 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
*
296662 CATGTATCGATATAA-TGAA
1 CATGTATCGATACAATTGAA
*
296681 CATATATCGATACAAT
1 CATGTATCGATACAAT
296697 GTATCGATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:297331 original size:22 final size:21
Alignment explanation
Indices: 297286--297331 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
297276 GGCTCTCGTT
**
297286 TAAAAAATTTCTCCCTTTTAA
1 TAAAAAATTTCTCCCCCTTAA
*
297307 TAAAAAATTTTCTCCCCCTTGA
1 TAAAAAA-TTTCTCCCCCTTAA
297329 TAA
1 TAA
297332 TCGTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAAAAATTTCTCCCCCTTAA
Found at i:299070 original size:20 final size:21
Alignment explanation
Indices: 299045--299084 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
299035 TTTGTTAATA
299045 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAA-GAAGT
299065 ATTTTGAAGTGAAAAAGAAG
1 ATTTTGAAGTGAAAAAGAAG
299085 AAATTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAAGAAGT
Found at i:299230 original size:13 final size:13
Alignment explanation
Indices: 299212--299236 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
299202 TAGTAACCTA
299212 TGTATCGATACAT
1 TGTATCGATACAT
299225 TGTATCGATACA
1 TGTATCGATACA
299237 AAGAATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:305433 original size:13 final size:13
Alignment explanation
Indices: 305415--305439 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
305405 CAATTCATCA
305415 TGTATCGATACAT
1 TGTATCGATACAT
305428 TGTATCGATACA
1 TGTATCGATACA
305440 ATGTCCCACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:305437 original size:33 final size:33
Alignment explanation
Indices: 305395--305459 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
305385 TTTGAAGCAA
* *
305395 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATGTC-CCACGTATCGATACAT
305428 TGTATCGATACAATGTCCCACGTATCGATACA
1 TGTATCGATACAATGTCCCACGTATCGATACA
305460 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAATGTCCCACGTATCGATACAT
Found at i:305547 original size:13 final size:13
Alignment explanation
Indices: 305529--305555 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
305519 TACAATGAAC
305529 ATGTATCGATACA
1 ATGTATCGATACA
305542 ATGTATCGATACA
1 ATGTATCGATACA
305555 A
1 A
305556 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:305730 original size:21 final size:22
Alignment explanation
Indices: 305683--305734 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
305673 ATTTTTACTT
*
305683 AAAAACATTTGATTTAAAGTTC
1 AAAAACATTTGATTTAAAGCTC
305705 AAAAACATTTG-TTTATAA-CTC
1 AAAAACATTTGATTTA-AAGCTC
*
305726 TAAAACATT
1 AAAAACATT
305735 CATTGATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.37
Consensus pattern (22 bp):
AAAAACATTTGATTTAAAGCTC
Found at i:309217 original size:29 final size:29
Alignment explanation
Indices: 309162--309217 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
309152 AAAAATTTTT
* **
309162 AAAAAGAAAAAGAAGAATGAAGGAATAAG
1 AAAAAGAAAAAGAAGAAAGAAAAAATAAG
309191 AAAAAGAAAAA-AAGAAAAGAAAAAATA
1 AAAAAGAAAAAGAAG-AAAGAAAAAATA
309218 TTATATCAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (29 bp):
AAAAAGAAAAAGAAGAAAGAAAAAATAAG
Found at i:310547 original size:16 final size:16
Alignment explanation
Indices: 310526--310557 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
310516 TTGTGTGTAG
310526 ATGGTTTGTAACTTTA
1 ATGGTTTGTAACTTTA
310542 ATGGTTTGTAACTTTA
1 ATGGTTTGTAACTTTA
310558 CATATGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (16 bp):
ATGGTTTGTAACTTTA
Found at i:316448 original size:11 final size:11
Alignment explanation
Indices: 316427--316468 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
316417 ATATTTATAA
316427 TAATGAATAAAT
1 TAAT-AATAAAT
316439 TAATAATAAATT
1 TAATAATAAA-T
*
316451 TACTAATAAAT
1 TAATAATAAAT
316462 TAATAAT
1 TAATAAT
316469 TTATAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 13 0.48
12 14 0.52
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (11 bp):
TAATAATAAAT
Found at i:318240 original size:21 final size:20
Alignment explanation
Indices: 318216--318259 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
318206 ATATTTTATA
318216 ATTAAATTTAAATAAAAATAT
1 ATTAAATTTAAATAAAAAT-T
* *
318237 ATT-ATTTTAATTAAAAATT
1 ATTAAATTTAAATAAAAATT
318256 ATTA
1 ATTA
318260 TTGCAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
19 4 0.20
20 13 0.65
21 3 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAAATTTAAATAAAAATT
Found at i:318251 original size:20 final size:19
Alignment explanation
Indices: 318222--318261 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
318212 TATAATTAAA
318222 TTTAAATAAAAATATATTAT
1 TTTAAATAAAAAT-TATTAT
*
318242 TTTAATTAAAAATTATTAT
1 TTTAAATAAAAATTATTAT
318261 T
1 T
318262 GCAAATGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAAATAAAAATTATTAT
Found at i:319032 original size:21 final size:20
Alignment explanation
Indices: 318987--319030 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
318977 AATGTATTAT
318987 ATTTATTAATTTTAAAAAAA
1 ATTTATTAATTTTAAAAAAA
* *
319007 ATTTATTAATTTTTAATAAA
1 ATTTATTAATTTTAAAAAAA
319027 ATTT
1 ATTT
319031 TAAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTATTAATTTTAAAAAAA
Found at i:323247 original size:14 final size:14
Alignment explanation
Indices: 323230--323258 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
323220 AGAAGTCAAG
323230 TTTTTAATGGTATA
1 TTTTTAATGGTATA
323244 TTTTTAATGGTATA
1 TTTTTAATGGTATA
323258 T
1 T
323259 CTAAAGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (14 bp):
TTTTTAATGGTATA
Found at i:323412 original size:63 final size:63
Alignment explanation
Indices: 323341--323682 Score: 227
Period size: 63 Copynumber: 5.4 Consensus size: 63
323331 GCCAAGCTGG
* * * * *
323341 TTTGTTTTAAGTTAAACTTGTTTTCAAGGAATGAGTTAAACTTTGAGTCAATGTTTAGGTC-T
1 TTTGTTTTAAGTCAAACTTGTTTTCAAGGAATGAGTTAAACCTCGAGTCAATGTTGAGATCAT
* * *
323403 TTTGGTTTTAAGTCAAACTTGTTTTTAAGGAATGAGTCAAGCCTCGAGTCAATGTTGAGATCAT
1 TTT-GTTTTAAGTCAAACTTGTTTTCAAGGAATGAGTTAAACCTCGAGTCAATGTTGAGATCAT
* * * * * * * *
323467 TTTATTTTAAGTCGAACTTGTTTTCAAGGAATGAATTAATTCCT-GAATTAATGTTAAGATCTT
1 TTTGTTTTAAGTCAAACTTGTTTTCAAGGAATGAGTTAA-ACCTCGAGTCAATGTTGAGATCAT
* * * * * * * *
323530 TTTGTTTTCAAGTCGAACCTATTTTCAAGAAACT-AATTGAACGTCGA-TCAATTTTGATG-TCT
1 TTTGTTTT-AAGTCAAACTTGTTTTCAAGGAA-TGAGTTAAACCTCGAGTCAATGTTGA-GATC-
*
323592 TT
62 AT
* * * * * *
323594 TTTGTTTTAAGTAAAACTT-TCTTTCAA-GAACT-AGGTTGAGCCTTGAGTCAATGTTAAGGTC-
1 TTTGTTTTAAGTCAAACTTGT-TTTCAAGGAA-TGA-GTTAAACCTCGAGTCAATGTTGAGATCA
323655 T
63 T
** *
323656 CAT-TTTTAAGTCGAACTTGTTTTCAAG
1 TTTGTTTTAAGTCAAACTTGTTTTCAAG
323683 AAACAAAACA
Statistics
Matches: 224, Mismatches: 42, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
61 19 0.08
62 12 0.05
63 137 0.61
64 55 0.25
65 1 0.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (63 bp):
TTTGTTTTAAGTCAAACTTGTTTTCAAGGAATGAGTTAAACCTCGAGTCAATGTTGAGATCAT
Found at i:326104 original size:63 final size:63
Alignment explanation
Indices: 326026--326151 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
326016 TTCCAACCCT
*
326026 TTCCAGAACCTGAAATAGCCTAAAGTAAATGGAATCTAGTTTCATATTCTTCCAATGGCTGAC
1 TTCCAGAACCTGAAATAGCCTAAAGTAAATGGAAGCTAGTTTCATATTCTTCCAATGGCTGAC
** *
326089 TTCCAGAACCTGAAATAGCCTAAAGTATTTGGAAGCTAGTTTCATATTCTTCCTATGGCTGAC
1 TTCCAGAACCTGAAATAGCCTAAAGTAAATGGAAGCTAGTTTCATATTCTTCCAATGGCTGAC
326152 AGTAAGCTGC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (63 bp):
TTCCAGAACCTGAAATAGCCTAAAGTAAATGGAAGCTAGTTTCATATTCTTCCAATGGCTGAC
Found at i:328329 original size:25 final size:25
Alignment explanation
Indices: 328297--328385 Score: 70
Period size: 25 Copynumber: 3.3 Consensus size: 25
328287 AATCAAAATC
328297 ATAACAACCATATTGGATTTAACAA
1 ATAACAACCATATTGGATTTAACAA
* * * * **
328322 ATAACAACTAAATCAGAAAATAATCAAAA
1 ATAACAACCATAT-TGGATTTAA-C--AA
328351 TCATAACAACCATATTGGATTTAACAA
1 --ATAACAACCATATTGGATTTAACAA
328378 ATAACAAC
1 ATAACAAC
328386 TAAATCAGAA
Statistics
Matches: 46, Mismatches: 12, Indels: 12
0.66 0.17 0.17
Matches are distributed among these distances:
25 19 0.41
26 5 0.11
27 3 0.07
29 3 0.07
30 5 0.11
31 11 0.24
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.24
Consensus pattern (25 bp):
ATAACAACCATATTGGATTTAACAA
Found at i:328353 original size:56 final size:56
Alignment explanation
Indices: 328287--328479 Score: 368
Period size: 56 Copynumber: 3.4 Consensus size: 56
328277 GCTAACAACA
328287 AATCAAAATCATAACAACCATATTGGATTTAACAAATAACAACTAAATCAGAAAAT
1 AATCAAAATCATAACAACCATATTGGATTTAACAAATAACAACTAAATCAGAAAAT
328343 AATCAAAATCATAACAACCATATTGGATTTAACAAATAACAACTAAATCAGAAAAT
1 AATCAAAATCATAACAACCATATTGGATTTAACAAATAACAACTAAATCAGAAAAT
* *
328399 AATCAAAATCATAACAACCATATTGGATTTAAAAAATAACAACTAAATCAAAAAAT
1 AATCAAAATCATAACAACCATATTGGATTTAACAAATAACAACTAAATCAGAAAAT
328455 AATCAAAATCATAACAACCATATTG
1 AATCAAAATCATAACAACCATATTG
328480 AATTAAATGC
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 135 1.00
ACGTcount: A:0.56, C:0.16, G:0.05, T:0.23
Consensus pattern (56 bp):
AATCAAAATCATAACAACCATATTGGATTTAACAAATAACAACTAAATCAGAAAAT
Found at i:328357 original size:31 final size:31
Alignment explanation
Indices: 328322--328472 Score: 101
Period size: 31 Copynumber: 5.3 Consensus size: 31
328312 GATTTAACAA
328322 ATAACAACTAAATCAGAAAATAATCAAAATC
1 ATAACAACTAAATCAGAAAATAATCAAAATC
* * * * **
328353 ATAACAACCATAT-TGGATTTAA-C--AA--
1 ATAACAACTAAATCAGAAAATAATCAAAATC
328378 ATAACAACTAAATCAGAAAATAATCAAAATC
1 ATAACAACTAAATCAGAAAATAATCAAAATC
* * * * * *
328409 ATAACAACCATAT-TG--GAT--TTAAAA-A
1 ATAACAACTAAATCAGAAAATAATCAAAATC
*
328434 ATAACAACTAAATCAAAAAATAATCAAAATC
1 ATAACAACTAAATCAGAAAATAATCAAAATC
328465 ATAACAAC
1 ATAACAAC
328473 CATATTGAAT
Statistics
Matches: 83, Mismatches: 25, Indels: 24
0.63 0.19 0.18
Matches are distributed among these distances:
25 22 0.27
26 10 0.12
27 3 0.04
28 4 0.05
29 3 0.04
30 11 0.13
31 30 0.36
ACGTcount: A:0.58, C:0.16, G:0.04, T:0.22
Consensus pattern (31 bp):
ATAACAACTAAATCAGAAAATAATCAAAATC
Found at i:337449 original size:2 final size:2
Alignment explanation
Indices: 337442--337466 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
337432 AAAATCAATT
337442 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
337467 TTATTTATTT
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:337862 original size:16 final size:17
Alignment explanation
Indices: 337843--337875 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
337833 TGATCCAAAT
*
337843 TCAAAATTACTT-AAAC
1 TCAAAATAACTTGAAAC
337859 TCAAAATAACTTGAAAC
1 TCAAAATAACTTGAAAC
337876 AACTAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.27
Consensus pattern (17 bp):
TCAAAATAACTTGAAAC
Found at i:337950 original size:17 final size:17
Alignment explanation
Indices: 337909--337953 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
337899 TGATTGAAAA
*
337909 TTACTTATTAATTAAAT
1 TTACTTAATAATTAAAT
*
337926 TTATTTAATAATTAAAT
1 TTACTTAATAATTAAAT
337943 CTT-CTTAATAA
1 -TTACTTAATAA
337954 AAACTAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 22 0.92
18 2 0.08
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (17 bp):
TTACTTAATAATTAAAT
Found at i:338591 original size:20 final size:21
Alignment explanation
Indices: 338547--338600 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
338537 TTCTACAATT
* *
338547 TGTATCGATACAAACAGTAAA
1 TGTATTGATACATACAGTAAA
*
338568 TGTATTGATACATA-AGTGAA
1 TGTATTGATACATACAGTAAA
338588 TGTATTGATACAT
1 TGTATTGATACAT
338601 GCCCGAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (21 bp):
TGTATTGATACATACAGTAAA
Found at i:342117 original size:17 final size:17
Alignment explanation
Indices: 342088--342143 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
342078 CGTCGTGAAA
*
342088 AATATTATTAAAATATT
1 AATATTTTTAAAATATT
342105 GAAT-TTTTTAAAATATT
1 -AATATTTTTAAAATATT
*
342122 CATATTTTTAAATATATT
1 AATATTTTTAAA-ATATT
342140 AATA
1 AATA
342144 AAATATAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 2 0.06
17 20 0.61
18 11 0.33
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
AATATTTTTAAAATATT
Found at i:342348 original size:20 final size:18
Alignment explanation
Indices: 342323--342365 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
342313 TAATATTTCT
*
342323 ATATTTTATGAATTATAATA
1 ATATTTAAT-AATTATAA-A
*
342343 ATATTTAATAATTTTAAA
1 ATATTTAATAATTATAAA
342361 ATATT
1 ATATT
342366 CAATGTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 7 0.33
20 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
ATATTTAATAATTATAAA
Found at i:342416 original size:16 final size:18
Alignment explanation
Indices: 342356--342417 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
342346 TTTAATAATT
*
342356 TTAAAATATTCA-ATGTCA
1 TTAAAATATTCATAT-TTA
* * *
342374 TTATAATTTTAATATTTA
1 TTAAAATATTCATATTTA
342392 TTAAAATATTCATATTT-
1 TTAAAATATTCATATTTA
342409 TT-AAATATT
1 TTAAAATATT
342418 ATTAAAATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
16 7 0.19
17 2 0.06
18 25 0.69
19 2 0.06
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (18 bp):
TTAAAATATTCATATTTA
Found at i:342436 original size:28 final size:28
Alignment explanation
Indices: 342376--342436 Score: 92
Period size: 27 Copynumber: 2.2 Consensus size: 28
342366 CAATGTCATT
342376 ATAA-TTTTAATATTTATTAAAATATTC
1 ATAATTTTTAATATTTATTAAAATATTC
342403 AT-ATTTTTAA-ATATTATTAAAATATTC
1 ATAATTTTTAATAT-TTATTAAAATATTC
342430 ATAATTT
1 ATAATTT
342437 AAAGTATGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 3 0.10
27 24 0.77
28 4 0.13
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (28 bp):
ATAATTTTTAATATTTATTAAAATATTC
Found at i:342468 original size:11 final size:11
Alignment explanation
Indices: 342448--342486 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
342438 AAGTATGCTA
342448 TTAA-ATATTT
1 TTAATATATTT
342458 TTAATATATTT
1 TTAATATATTT
*
342469 TTATTATATTT
1 TTAATATATTT
342480 TTAATAT
1 TTAATAT
342487 TAATATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 4 0.15
11 22 0.85
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTAATATATTT
Found at i:342557 original size:54 final size:52
Alignment explanation
Indices: 342499--342601 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 52
342489 ATATTAAAAC
* * * *
342499 AATATTATTAAATATTATT-TTCAAAATGTTTCAATGTATTATTAAAATATTTTT
1 AATATTACTAAATATAATTATT-AAAATATTT-AATATATTATT-AAATATTTTT
*
342553 AATATTGCTAAATATAATTATTAAAATATTTAATATATTATTAAATATT
1 AATATTACTAAATATAATTATTAAAATATTTAATATATTATTAAATATT
342602 GTATACATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
52 7 0.16
53 10 0.23
54 24 0.56
55 2 0.05
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (52 bp):
AATATTACTAAATATAATTATTAAAATATTTAATATATTATTAAATATTTTT
Found at i:342591 original size:33 final size:33
Alignment explanation
Indices: 342536--342600 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
342526 GTTTCAATGT
* *
342536 ATTATTAAAATATTTTTAATATTGCTAAATATA
1 ATTATTAAAATATTTATAATATTACTAAATATA
*
342569 ATTATTAAAATATTTA-ATATATTATTAAATAT
1 ATTATTAAAATATTTATA-ATATTACTAAATAT
342601 TGTATACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (33 bp):
ATTATTAAAATATTTATAATATTACTAAATATA
Found at i:342600 original size:19 final size:20
Alignment explanation
Indices: 342553--342616 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 20
342543 AAATATTTTT
342553 AATATTGCTAAATATAATTATTAA
1 AATATTG-T-AATAT-ATTATT-A
342577 AATATT-TAATATATTATTA
1 AATATTGTAATATATTATTA
*
342596 AATATTGT-ATACATTATTA
1 AATATTGTAATATATTATTA
342615 AA
1 AA
342617 AAATTATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
19 19 0.50
20 7 0.18
21 5 0.13
22 1 0.03
24 6 0.16
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
AATATTGTAATATATTATTA
Found at i:342747 original size:34 final size:33
Alignment explanation
Indices: 342693--342797 Score: 103
Period size: 34 Copynumber: 3.2 Consensus size: 33
342683 TTAAATGTAG
*
342693 TATTAAATACTATTATTAAAATATTGTAATATAT
1 TATT-AATATTATTATTAAAATATTGTAATATAT
* * *
342727 TATTTAATATTATTACTAAAATAATTG-AGTATAC
1 TA-TTAATATTATTATTAAAAT-ATTGTAATATAT
*
342761 TATT-AT-TCA--ATTAAAATATTGTAATATAT
1 TATTAATATTATTATTAAAATATTGTAATATAT
342790 TATTAATA
1 TATTAATA
342798 ATATGAGATA
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
28 4 0.07
29 16 0.28
30 2 0.03
31 2 0.03
32 2 0.03
33 2 0.03
34 24 0.41
35 6 0.10
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (33 bp):
TATTAATATTATTATTAAAATATTGTAATATAT
Found at i:347622 original size:6 final size:6
Alignment explanation
Indices: 347599--347646 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
347589 AAATCTTCAC
* *
347599 TTTTCT TTTTTT TATTTAT TTTTATT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT T-TTTAT TTTTA-T TTTTAT TTTTAT TTTTAT TTTT
347647 TTTACAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 27 0.71
7 11 0.29
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:347626 original size:19 final size:19
Alignment explanation
Indices: 347599--347650 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
347589 AAATCTTCAC
*
347599 TTTTCTTTTTTTTATTTAT
1 TTTTATTTTTTTTATTTAT
347618 TTTTATTTTTTATT-TTTAT
1 TTTTATTTTTT-TTATTTAT
347637 TTTTATTTTTTTTA
1 TTTTATTTTTTTTA
347651 CAATTTCCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 2 0.07
19 26 0.87
20 2 0.07
ACGTcount: A:0.13, C:0.02, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTATTTTTTTTATTTAT
Found at i:347647 original size:13 final size:13
Alignment explanation
Indices: 347599--347646 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
347589 AAATCTTCAC
*
347599 TTTTCTTTTT-TT
1 TTTTATTTTTATT
347611 TATTTATTTTTATT
1 T-TTTATTTTTATT
347625 TTTTATTTTTA-T
1 TTTTATTTTTATT
347637 TTTTATTTTT
1 TTTTATTTTT
347647 TTTACAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
12 12 0.36
13 18 0.55
14 3 0.09
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTATTTTTATT
Done.