Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 29
Found at i:197302 original size:20 final size:21
Alignment explanation
Indices: 197274--197313 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
197264 TATTTATAAA
197274 ATTAATTTTT-AAAATTTTAT
1 ATTAATTTTTAAAAATTTTAT
*
197294 ATTATTTTTTAAAAATTTTA
1 ATTAATTTTTAAAAATTTTA
197314 AAATTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTAATTTTTAAAAATTTTAT
Found at i:197319 original size:19 final size:19
Alignment explanation
Indices: 197279--197354 Score: 52
Period size: 21 Copynumber: 3.9 Consensus size: 19
197269 ATAAAATTAA
*
197279 TTTTT-AAAATTTTATATTAT
1 TTTTTAAAAATTTTA-A-AAT
197299 TTTTTAAAAATTTTAAAATT
1 TTTTTAAAAATTTTAAAA-T
*
197319 TTATTTAATAA--TT-AAAT
1 TT-TTTAAAAATTTTAAAAT
*
197336 TTTTTAAATATTATTAAAA
1 TTTTTAAAAATT-TTAAAA
197355 ATATAAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
16 6 0.13
17 3 0.07
18 3 0.07
19 5 0.11
20 12 0.27
21 16 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTTAAAAATTTTAAAAT
Found at i:197325 original size:21 final size:21
Alignment explanation
Indices: 197272--197331 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
197262 ATTATTTATA
197272 AAATTAATT-TTT-AAAATTTT
1 AAATT-ATTATTTAAAAATTTT
* *
197292 ATATTATTTTTTAAAAATTTT
1 AAATTATTATTTAAAAATTTT
*
197313 AAAATT-TTATTTAATAATT
1 -AAATTATTATTTAAAAATT
197332 AAATTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 3 0.09
20 7 0.21
21 19 0.58
22 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATTATTATTTAAAAATTTT
Found at i:197339 original size:27 final size:27
Alignment explanation
Indices: 197263--197350 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
197253 AAAATTAAAA
*
197263 TTATTTATAAAATT-AATTTTTAAAATT
1 TTATTTA-ATAATTAAATTTTTAAAATT
* ** *
197290 TTATATTATTTTTTAAAAATTTTAAAATT
1 TTAT-TTAATAATT-AAATTTTTAAAATT
* *
197319 TTATTTAATAATTAAATTTTTTAAATA
1 TTATTTAATAATTAAATTTTTAAAATT
197346 TTATT
1 TTATT
197351 AAAAATATAA
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
27 22 0.47
28 9 0.19
29 16 0.34
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTATTTAATAATTAAATTTTTAAAATT
Found at i:197361 original size:27 final size:27
Alignment explanation
Indices: 197262--197361 Score: 69
Period size: 27 Copynumber: 3.6 Consensus size: 27
197252 AAAAATTAAA
197262 ATTATTTATAAAATT-AATTTTTAAAAT
1 ATTATTTA-AAAATTAAATTTTTAAAAT
* **** *
197289 TTTATATTATTTTTTAAAAATTTTAAAAT
1 ATTAT-TTAAAAATT-AAATTTTTAAAAT
* * *
197318 TTTATTTAATAATTAAATTTTTTAAAT
1 ATTATTTAAAAATTAAATTTTTAAAAT
197345 ATTA-TTAAAAATATAAA
1 ATTATTTAAAAAT-TAAA
197362 AAAAACATTG
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
26 7 0.12
27 24 0.43
28 9 0.16
29 16 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTATTTAAAAATTAAATTTTTAAAAT
Found at i:197485 original size:27 final size:27
Alignment explanation
Indices: 197455--197520 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
197445 GTATTATTAG
*
197455 AATAATAAAAATAT-TTTTAAAAATATA
1 AATAATAAAAA-ATCCTTTAAAAATATA
* *
197482 AATATTAAAAAATCCTTTCAAAATATA
1 AATAATAAAAAATCCTTTAAAAATATA
*
197509 AAAAATAAAAAA
1 AATAATAAAAAA
197521 AAATATTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 2 0.06
27 31 0.94
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (27 bp):
AATAATAAAAAATCCTTTAAAAATATA
Found at i:197765 original size:27 final size:28
Alignment explanation
Indices: 197735--197798 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 28
197725 TAAATATTTT
197735 TTATATTTTTTTA-AATATAGTTTC-TG-A
1 TTATATTTTTTTAGAA-ATA-TTTCATGTA
*
197762 TTAT-TTTTTTTAGAAATATTTCATGTT
1 TTATATTTTTTTAGAAATATTTCATGTA
197789 TTATATTTTT
1 TTATATTTTT
197799 AATATTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
25 4 0.12
26 13 0.41
27 10 0.31
28 5 0.16
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (28 bp):
TTATATTTTTTTAGAAATATTTCATGTA
Found at i:197808 original size:18 final size:19
Alignment explanation
Indices: 197787--197827 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
197777 ATATTTCATG
*
197787 TTTTATAT-TTTTAATATT
1 TTTTATATATTATAATATT
197805 TTTTATATAATTATAATATT
1 TTTTATAT-ATTATAATATT
197825 TTT
1 TTT
197828 AGTTAGATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTATATATTATAATATT
Found at i:198060 original size:14 final size:14
Alignment explanation
Indices: 198038--198078 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
198028 TCGATTATAT
*
198038 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
198052 GTTCATTTATGTTC
1 GTTCATTTATGTTC
198066 GTTCA-TTATGTTC
1 GTTCATTTATGTTC
198079 AAACAGATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 8 0.31
14 18 0.69
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.56
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:200351 original size:22 final size:22
Alignment explanation
Indices: 200310--200351 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
200300 GGTTGCATCG
*
200310 AAAACATTACACTATCAAACCT
1 AAAACATTACACAATCAAACCT
200332 AAAACATTACACCAAT-AAAC
1 AAAACATTACA-CAATCAAAC
200352 TTTGTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (22 bp):
AAAACATTACACAATCAAACCT
Found at i:207583 original size:31 final size:29
Alignment explanation
Indices: 207531--207590 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 29
207521 ACTTCAAATG
207531 AAATATCATTTTTACCTTTGAACTTTAGATA
1 AAATATCATTTTTACCTTTGAA-TTT-GATA
207562 AAATATCATTTTGGT-CC-TTGAATTTGATA
1 AAATATCATTTT--TACCTTTGAATTTGATA
207591 GAAGCATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
29 4 0.15
30 3 0.11
31 17 0.63
32 2 0.07
33 1 0.04
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (29 bp):
AAATATCATTTTTACCTTTGAATTTGATA
Found at i:207799 original size:23 final size:23
Alignment explanation
Indices: 207773--207833 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
207763 AGTGTGCGCT
* **
207773 AACATGTTCATTTAATTTTCATG
1 AACATATTCATTTAACGTTCATG
* *
207796 AACATATTTATTTAACGTTCGTG
1 AACATATTCATTTAACGTTCATG
*
207819 AACATTTTCATTTAA
1 AACATATTCATTTAA
207834 AGTCCATTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (23 bp):
AACATATTCATTTAACGTTCATG
Found at i:211399 original size:19 final size:18
Alignment explanation
Indices: 211359--211401 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
211349 TTAAAGTTTA
*
211359 TAAA-TTTAAAATTAATT
1 TAAATTTTAAAATGAATT
*
211376 AAAATTTTAAATATGAATT
1 TAAATTTTAAA-ATGAATT
211395 TAAATTT
1 TAAATTT
211402 ACTCAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 3 0.14
18 6 0.29
19 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TAAATTTTAAAATGAATT
Found at i:214476 original size:18 final size:18
Alignment explanation
Indices: 214450--214484 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
214440 ATTCCAAGTT
*
214450 TGTGCCTGAGGCTGTGTC
1 TGTGCCTGAGCCTGTGTC
*
214468 TGTGTCTGAGCCTGTGT
1 TGTGCCTGAGCCTGTGT
214485 AGTGGGTGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.20, G:0.37, T:0.37
Consensus pattern (18 bp):
TGTGCCTGAGCCTGTGTC
Found at i:223676 original size:44 final size:44
Alignment explanation
Indices: 223613--223741 Score: 240
Period size: 44 Copynumber: 2.9 Consensus size: 44
223603 AAACGTTTTC
223613 ATGAACATTACCGTGAACATTAATGAACAATACTGTGAACATTA
1 ATGAACATTACCGTGAACATTAATGAACAATACTGTGAACATTA
223657 ATGAACATTACCGTGAACATTAATGAACAATACTGTGAACATTA
1 ATGAACATTACCGTGAACATTAATGAACAATACTGTGAACATTA
* *
223701 ATGAACATTACCGTGAACAGTAATGAACAATACCGTGAACA
1 ATGAACATTACCGTGAACATTAATGAACAATACTGTGAACA
223742 GTACCGAATG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 83 1.00
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (44 bp):
ATGAACATTACCGTGAACATTAATGAACAATACTGTGAACATTA
Found at i:223744 original size:22 final size:22
Alignment explanation
Indices: 223613--223741 Score: 204
Period size: 22 Copynumber: 5.9 Consensus size: 22
223603 AAACGTTTTC
*
223613 ATGAACATTACCGTGAACATTA
1 ATGAACAATACCGTGAACATTA
*
223635 ATGAACAATACTGTGAACATTA
1 ATGAACAATACCGTGAACATTA
*
223657 ATGAACATTACCGTGAACATTA
1 ATGAACAATACCGTGAACATTA
*
223679 ATGAACAATACTGTGAACATTA
1 ATGAACAATACCGTGAACATTA
* *
223701 ATGAACATTACCGTGAACAGTA
1 ATGAACAATACCGTGAACATTA
223723 ATGAACAATACCGTGAACA
1 ATGAACAATACCGTGAACA
223742 GTACCGAATG
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 97 1.00
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (22 bp):
ATGAACAATACCGTGAACATTA
Found at i:224327 original size:35 final size:33
Alignment explanation
Indices: 224269--224333 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
224259 ATCTTATTCC
224269 TTATCATTATCCTATTATTATCATTAATACCTT
1 TTATCATTATCCTATTATTATCATTAATACCTT
*
224302 TTATCATATAT-CTATATACTTATCATTTATAC
1 TTATCAT-TATCCTAT-TA-TTATCATTAATAC
224334 ACATCATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 11 0.39
34 5 0.18
35 12 0.43
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (33 bp):
TTATCATTATCCTATTATTATCATTAATACCTT
Found at i:224680 original size:22 final size:22
Alignment explanation
Indices: 224650--224695 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
224640 AGCATGTGAA
*
224650 ATTTATCCCGAATGACCTATGT
1 ATTTATCCCGAAGGACCTATGT
* *
224672 ATTTTTCCCGAAGGACCTCTGT
1 ATTTATCCCGAAGGACCTATGT
224694 AT
1 AT
224696 ATGTGTAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (22 bp):
ATTTATCCCGAAGGACCTATGT
Found at i:225452 original size:10 final size:9
Alignment explanation
Indices: 225428--225461 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
225418 AAAGCTGGAA
*
225428 ACCGGTTTA
1 ACCGGTTTG
225437 ACCGGTTTTG
1 ACCGG-TTTG
225447 ACCGGTTTG
1 ACCGGTTTG
225456 ACCGGT
1 ACCGGT
225462 CACGACCCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.32
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:225483 original size:13 final size:13
Alignment explanation
Indices: 225465--225517 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
225455 GACCGGTCAC
225465 GACCCGACCCGTT
1 GACCCGACCCGTT
225478 GACCCGACCCGTT
1 GACCCGACCCGTT
*
225491 AACCCGACCC--T
1 GACCCGACCCGTT
225502 -ACCCGACCCGTT
1 GACCCGACCCGTT
225514 GACC
1 GACC
225518 GACTTGACCC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
12 1 0.03
13 25 0.69
ACGTcount: A:0.19, C:0.49, G:0.19, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:226422 original size:453 final size:453
Alignment explanation
Indices: 225576--226482 Score: 1697
Period size: 453 Copynumber: 2.0 Consensus size: 453
225566 ATTTTGGTGA
*
225576 TATTCTGGGAATTAATTCGAAAAGGGGTGCTATTTCTGTAAAATGGTTGACAGTTTGTTGACCTC
1 TATTCTGGGAATTAATTCGAAAAGGGGTGCTATTTCTGTAAAATGGTTAACAGTTTGTTGACCTC
225641 ATTTGACCAGAACTTTGACCGGCTTTGACCGGCTATTAAACTATCGTTAATCTTTTCCGAGAATA
66 ATTTGACCAGAACTTTGACCGGCTTTGACCGGCTATTAAACTATCGTTAATCTTTTCCGAGAATA
* * **
225706 CCTATCCTGACAATTTTTGACGTCCCGAATCCGTTTTTGGGGTCTGTTTCACCAAATTCGAACCT
131 CCTATCCTGACAATTTTCGACATCCCGAATCCGTTTTTGGGGTCCATTTCACCAAATTCGAACCT
225771 GAAAGTCTCCAAATCGTCAGTCAAACCCGTTGACTTTGATTTTGACCAAGAATTCAAATTTTCAG
196 GAAAGTCTCCAAATCGTCAGTCAAACCCGTTGACTTTGATTTTGACCAAGAATTCAAATTTTCAG
225836 AAAGTCATACTTTATGTTTTTCGACGTCCTGAATCTGATTCCGAAGTCCGTTTTGCCAAATTCTG
261 AAAGTCATACTTTATGTTTTTCGACGTCCTGAATCTGATTCCGAAGTCCGTTTTGCCAAATTCTG
* *
225901 ACCCGAAATTCCCGAATCGAGCTTGTAAACACATAAGGCTTAATATTTTAATATTTTGATTATTT
326 ACCCAAAATTCCCGAATCGAGCTTGTAAACACAAAAGGCTTAATATTTTAATATTTTGATTATTT
225966 AATTGAGATTTGGTCAAGGATTTATTCAATAAAAATATTTTATGAAGGTACTCGTGTTTCACC
391 AATTGAGATTTGGTCAAGGATTTATTCAATAAAAATATTTTATGAAGGTACTCGTGTTTCACC
*
226029 TATTCTGGGAATTAATTCTAAAAGGGGTGCTATTTCTGTAAAATGGTTAACAGTTTGTTGACCTC
1 TATTCTGGGAATTAATTCGAAAAGGGGTGCTATTTCTGTAAAATGGTTAACAGTTTGTTGACCTC
*
226094 ATTTGACCAGAACTTTGATCGGCTTTGACCGGCTATTAAACTATCGTTAATCTTTTCCGAGAATA
66 ATTTGACCAGAACTTTGACCGGCTTTGACCGGCTATTAAACTATCGTTAATCTTTTCCGAGAATA
* *
226159 CCTATCCTGACAGTTTTCGACATCTCGAATCCGTTTTTGGGGTCCATTTCACCAAATTCGAACCT
131 CCTATCCTGACAATTTTCGACATCCCGAATCCGTTTTTGGGGTCCATTTCACCAAATTCGAACCT
226224 GAAAGTCTCCAAATCGTCAGTCAAACCCGTTGACTTTGATTTTGACCAAGAATTCAAATTTTCAG
196 GAAAGTCTCCAAATCGTCAGTCAAACCCGTTGACTTTGATTTTGACCAAGAATTCAAATTTTCAG
226289 AAAGTCATACTTTATGTTTTTCGACGTCCTGAATCTGATTCCGAAGTCCGTTTTGCCAAATTCTG
261 AAAGTCATACTTTATGTTTTTCGACGTCCTGAATCTGATTCCGAAGTCCGTTTTGCCAAATTCTG
*
226354 ACCCAAAATTCCCGAATCGAGCTTGTAAACCCAAAAGGCTTAATATTTTAATATTTTGATTATTT
326 ACCCAAAATTCCCGAATCGAGCTTGTAAACACAAAAGGCTTAATATTTTAATATTTTGATTATTT
*
226419 AATTGAGATTTGGTCAAGGATTTATTCAATAAAAATATTTTATGAATGTACTCGTGTTTCACC
391 AATTGAGATTTGGTCAAGGATTTATTCAATAAAAATATTTTATGAAGGTACTCGTGTTTCACC
226482 T
1 T
226483 GAGCAAGAAT
Statistics
Matches: 441, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
453 441 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (453 bp):
TATTCTGGGAATTAATTCGAAAAGGGGTGCTATTTCTGTAAAATGGTTAACAGTTTGTTGACCTC
ATTTGACCAGAACTTTGACCGGCTTTGACCGGCTATTAAACTATCGTTAATCTTTTCCGAGAATA
CCTATCCTGACAATTTTCGACATCCCGAATCCGTTTTTGGGGTCCATTTCACCAAATTCGAACCT
GAAAGTCTCCAAATCGTCAGTCAAACCCGTTGACTTTGATTTTGACCAAGAATTCAAATTTTCAG
AAAGTCATACTTTATGTTTTTCGACGTCCTGAATCTGATTCCGAAGTCCGTTTTGCCAAATTCTG
ACCCAAAATTCCCGAATCGAGCTTGTAAACACAAAAGGCTTAATATTTTAATATTTTGATTATTT
AATTGAGATTTGGTCAAGGATTTATTCAATAAAAATATTTTATGAAGGTACTCGTGTTTCACC
Found at i:233129 original size:9 final size:9
Alignment explanation
Indices: 233115--233164 Score: 73
Period size: 9 Copynumber: 5.3 Consensus size: 9
233105 TGGAAACTGA
233115 TTTAACCAG
1 TTTAACCAG
233124 TTTAACCAG
1 TTTAACCAG
*
233133 TTTTGAACCGG
1 -TTT-AACCAG
233144 TTTAACCAG
1 TTTAACCAG
233153 TTTAACCAG
1 TTTAACCAG
233162 TTT
1 TTT
233165 TGAACCGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
9 26 0.70
10 6 0.16
11 5 0.14
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (9 bp):
TTTAACCAG
Found at i:233157 original size:29 final size:29
Alignment explanation
Indices: 233115--233175 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
233105 TGGAAACTGA
233115 TTTAACCAGTTTAACCAGTTTTGAACCGG
1 TTTAACCAGTTTAACCAGTTTTGAACCGG
233144 TTTAACCAGTTTAACCAGTTTTGAACCGG
1 TTTAACCAGTTTAACCAGTTTTGAACCGG
233173 TTT
1 TTT
233176 GACCGGTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (29 bp):
TTTAACCAGTTTAACCAGTTTTGAACCGG
Found at i:233170 original size:20 final size:18
Alignment explanation
Indices: 233115--233164 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 18
233105 TGGAAACTGA
233115 TTTAACCAGTTTAACCAG
1 TTTAACCAGTTTAACCAG
*
233133 TTTTGAACCGGTTTAACCAG
1 -TTT-AACCAGTTTAACCAG
233153 TTTAACCAGTTT
1 TTTAACCAGTTT
233165 TGAACCGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 8 0.29
19 6 0.21
20 14 0.50
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (18 bp):
TTTAACCAGTTTAACCAG
Found at i:233212 original size:18 final size:18
Alignment explanation
Indices: 233185--233230 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
233175 TGACCGGTCA
* * *
233185 CGACCTGACCCTTTGACC
1 CGACCCGACCCGTTAACC
233203 CGACCCGACCCGTTAACC
1 CGACCCGACCCGTTAACC
*
233221 CGACTCGACC
1 CGACCCGACC
233231 TGTTGACCGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.48, G:0.17, T:0.15
Consensus pattern (18 bp):
CGACCCGACCCGTTAACC
Found at i:236577 original size:30 final size:30
Alignment explanation
Indices: 236525--236615 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 30
236515 ACCCATTTGT
*
236525 AACTTTTTAAAA-TTATATTTTGGTCCCTA
1 AACTTTTTAAAATTTATAATTTGGTCCCTA
*
236554 AACTTTTTAAAATTTATACTTTGGTCACC-A
1 AACTTTTTAAAATTTATAATTTGGTC-CCTA
* ** *
236584 ATCTTTTCCAAATTTATAATTTGGTCACTA
1 AACTTTTTAAAATTTATAATTTGGTCCCTA
236614 AA
1 AA
236616 TAAATCCATT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 13 0.25
30 37 0.71
31 2 0.04
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (30 bp):
AACTTTTTAAAATTTATAATTTGGTCCCTA
Found at i:238773 original size:14 final size:13
Alignment explanation
Indices: 238722--238761 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
238712 GCCGAGTATA
* *
238722 TATATTTAAATTA
1 TATATATAAATTT
*
238735 AATATATAAATTT
1 TATATATAAATTT
238748 TATATATAAATTT
1 TATATATAAATTT
238761 T
1 T
238762 TTAATTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATATAAATTT
Found at i:238778 original size:19 final size:19
Alignment explanation
Indices: 238725--238785 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
238715 GAGTATATAT
* *
238725 ATTTAAATTAAATATATAA
1 ATTTAAATTAAATTTATTA
* *
238744 ATTTTATATATAAATTTTTTA
1 A-TTTAAAT-TAAATTTATTA
238765 ATTTAAATTAAATTTATTA
1 ATTTAAATTAAATTTATTA
238784 AT
1 AT
238786 GTTATATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 13 0.38
20 12 0.35
21 9 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTAAATTAAATTTATTA
Found at i:239403 original size:23 final size:23
Alignment explanation
Indices: 239377--239427 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
239367 CGTTGCATGC
239377 CATAGCTCCGAGATTCCTGCAAT
1 CATAGCTCCGAGATTCCTGCAAT
* *
239400 CATAGCTGCGAGATTCCTGCAGT
1 CATAGCTCCGAGATTCCTGCAAT
239423 CATAG
1 CATAG
239428 TTGCATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (23 bp):
CATAGCTCCGAGATTCCTGCAAT
Found at i:246487 original size:64 final size:64
Alignment explanation
Indices: 246364--246508 Score: 159
Period size: 64 Copynumber: 2.2 Consensus size: 64
246354 GTGCACCAAG
* * * * * * *
246364 TGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGCCTGAGTGTATCGGTGCATTGCT
1 TGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCATGAGTGCATCGATGCATGGAT
** *
246428 TGTGCATCGATGCATGAAATGCATTCGATG-TTCAATGTATTCAATG-GTGCATCGATGCATGGA
1 TGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATA-GC-ATGAGTGCATCGATGCATGGA
246491 T
64 T
246492 TGATGCATCGATGCATG
1 TG-TGCATCGATGCATG
246509 CCTTTGAAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
63 6 0.09
64 46 0.68
65 16 0.24
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (64 bp):
TGTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCATGAGTGCATCGATGCATGGAT
Found at i:249090 original size:44 final size:44
Alignment explanation
Indices: 249001--249097 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
248991 GCTCTTGTGC
* *
249001 ATCGATGCACATTCAAGGGCGTGCATCGGTGCATCAGTTGATGT
1 ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGTTAATGT
* *
249045 ATTGATGCACATTCAAAGGG-ATGCATCGGTGCA-CTGTTAAGTGT
1 ATCGATGCACATTC-AAGGGCATGCATCGGTGCATCAGTTAA-TGT
249089 ATCGATGCA
1 ATCGATGCA
249098 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 5 0.11
44 36 0.78
45 5 0.11
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGTTAATGT
Found at i:254819 original size:21 final size:21
Alignment explanation
Indices: 254793--254841 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
254783 GGGAGCGTCG
254793 GTGCATCGATGCATGACTATA
1 GTGCATCGATGCATGACTATA
254814 GTGCATCGATGCATGACTATA
1 GTGCATCGATGCATGACTATA
254835 GTGCATC
1 GTGCATC
254842 AGTGTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (21 bp):
GTGCATCGATGCATGACTATA
Found at i:254917 original size:19 final size:19
Alignment explanation
Indices: 254880--254918 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
254870 GGAACACTTA
* *
254880 GTGCATCGGTGCACCAAAT
1 GTGCATCGATGCACAAAAT
*
254899 GTGCATCGATGCATAAAAT
1 GTGCATCGATGCACAAAAT
254918 G
1 G
254919 CATTCTATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.23
Consensus pattern (19 bp):
GTGCATCGATGCACAAAAT
Found at i:255375 original size:45 final size:49
Alignment explanation
Indices: 255290--255383 Score: 124
Period size: 49 Copynumber: 2.0 Consensus size: 49
255280 GTTTTCAACA
* * *
255290 AGTTTGTTAGTTTAAGTTATATATTATATTATATAAAAATTAGTTAATT
1 AGTTTGTTAGTTTAAGTTATATATTATAGTATAAAAAAATTAATTAATT
*
255339 AGTTTTTTAGTTTAAGTTAT-TA-TA-AGTA-AAAAAAATTAATTAATT
1 AGTTTGTTAGTTTAAGTTATATATTATAGTATAAAAAAATTAATTAATT
255384 TGTTAGTGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 15 0.37
46 3 0.07
47 2 0.05
48 2 0.05
49 19 0.46
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (49 bp):
AGTTTGTTAGTTTAAGTTATATATTATAGTATAAAAAAATTAATTAATT
Found at i:255765 original size:17 final size:17
Alignment explanation
Indices: 255743--255803 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
255733 ATTTATTCTC
255743 GTTTAAAAAAATATTGT
1 GTTTAAAAAAATATTGT
*
255760 GTTTAAAAATATTTATTGTT
1 GTTTAAAAA-A-ATATTG-T
*
255780 GTTTTAAAAAAATATTTT
1 G-TTTAAAAAAATATTGT
255798 GTTTAA
1 GTTTAA
255804 TTTGAATTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 14 0.38
18 3 0.08
19 9 0.24
20 3 0.08
21 8 0.22
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (17 bp):
GTTTAAAAAAATATTGT
Found at i:256611 original size:26 final size:26
Alignment explanation
Indices: 256582--256678 Score: 76
Period size: 26 Copynumber: 3.7 Consensus size: 26
256572 ATAATAAATA
256582 ATTATTAGTAATCATTATTAAATCAT
1 ATTATTAGTAATCATTATTAAATCAT
*
256608 ATTATTATTAAATCATTAAATATCAAATCAT
1 ATTATTAGT-AATCATT--AT-T-AAATCAT
* * *
256639 -TAGATTAATAATAATTATTAAATC--
1 AT-TATTAGTAATCATTATTAAATCAT
256663 ATTATTAGTAAT-ATTA
1 ATTATTAGTAATCATTA
256679 GTAATCAATC
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
23 4 0.07
24 8 0.14
25 1 0.02
26 13 0.22
27 8 0.14
28 2 0.03
29 2 0.03
30 8 0.14
31 12 0.21
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (26 bp):
ATTATTAGTAATCATTATTAAATCAT
Found at i:259289 original size:44 final size:40
Alignment explanation
Indices: 259225--259347 Score: 135
Period size: 44 Copynumber: 3.0 Consensus size: 40
259215 ATATAACTTA
* *
259225 AATATTTAACTAAC-TACAAACTAATTAAATATTTTTTAT
1 AATATATAACTAACAAACAAACTAATTAAATATTTTTTAT
*
259264 -ATATAACTAACGACTAACAAACAAACTAATTAATTATTTTTT-T
1 AATAT-A-T-A--ACTAACAAACAAACTAATTAAATATTTTTTAT
*
259307 AATATATAACTATCAAACAAACTAATTAAATAATTTTTTAT
1 AATATATAACTAACAAACAAACTAATTAAAT-ATTTTTTAT
259348 TTATGTATGA
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
38 4 0.06
39 21 0.30
40 8 0.11
41 3 0.04
42 1 0.01
43 8 0.11
44 25 0.36
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.40
Consensus pattern (40 bp):
AATATATAACTAACAAACAAACTAATTAAATATTTTTTAT
Found at i:259325 original size:39 final size:43
Alignment explanation
Indices: 259240--259347 Score: 136
Period size: 39 Copynumber: 2.6 Consensus size: 43
259230 TTAACTAACT
259240 ACAAACTAATTAAATATTTTTTATATATAACTAACGACTAACAA
1 ACAAACTAATTAAATATTTTTTATATATAACTAAC-ACTAACAA
* *
259284 ACAAACTAATTAATTATTTTTT-TA-AT-A-TATA-ACTATCAA
1 ACAAACTAATTAAATATTTTTTATATATAACTA-ACACTAACAA
259323 ACAAACTAATTAAATAATTTTTTAT
1 ACAAACTAATTAAAT-ATTTTTTAT
259348 TTATGTATGA
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
39 21 0.36
40 9 0.16
41 3 0.05
42 2 0.03
43 2 0.03
44 21 0.36
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.40
Consensus pattern (43 bp):
ACAAACTAATTAAATATTTTTTATATATAACTAACACTAACAA
Found at i:259410 original size:21 final size:21
Alignment explanation
Indices: 259357--259396 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
259347 TTTATGTATG
259357 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
259378 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
259397 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:259715 original size:23 final size:23
Alignment explanation
Indices: 259667--259753 Score: 120
Period size: 23 Copynumber: 3.7 Consensus size: 23
259657 CAACAATAAT
*
259667 TGCTGCATGAAGCAGCGAAAATGA
1 TGCTGCATAAAGCAGCG-AAATGA
*
259691 TGATGCATAAAGCAGCGAAATGA
1 TGCTGCATAAAGCAGCGAAATGA
*
259714 TGCTGCATGAAGCAGCGAAATGA
1 TGCTGCATAAAGCAGCGAAATGA
*
259737 TGCTGCAATAATGCAGC
1 TGCTGC-ATAAAGCAGC
259754 TATTAAAGCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
23 33 0.59
24 23 0.41
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCTGCATAAAGCAGCGAAATGA
Found at i:264695 original size:28 final size:26
Alignment explanation
Indices: 264655--264709 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 26
264645 AAACTACACA
264655 TTTAGTACCTAAACTATCAATTTTGTTT
1 TTTAGTACCTAAACTATC-A-TTTGTTT
*
264683 TTTAGTACCTAAACTTTCATTTGTTT
1 TTTAGTACCTAAACTATCATTTGTTT
264709 T
1 T
264710 AAAATCATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 8 0.31
27 1 0.04
28 17 0.65
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (26 bp):
TTTAGTACCTAAACTATCATTTGTTT
Found at i:282689 original size:59 final size:59
Alignment explanation
Indices: 282567--282712 Score: 177
Period size: 59 Copynumber: 2.5 Consensus size: 59
282557 ATTCTCATTT
* * * * * * *
282567 TAAATTGTCATTACACTTTTGAATATTCTAATTTCATCCTCAGACTATGACTCTAATTA
1 TAAATTGTCCTTAAACTTTTAAACATTCCAATTTCATCCTCAAACTATGACCCTAATTA
* *
282626 TAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCATCC-CAAACTATGACCCTTATTC
1 TAAATT-GTCCTTAAACTTTTAAACATTCCAATTTCATCCTCAAACTATGACCCTAATTA
*
282685 TAAATTGATCCTCAAACTTTTAAACATT
1 TAAATTG-TCCTTAAACTTTTAAACATT
282713 TCAAATTCTT
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
58 1 0.01
59 46 0.61
60 28 0.37
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (59 bp):
TAAATTGTCCTTAAACTTTTAAACATTCCAATTTCATCCTCAAACTATGACCCTAATTA
Found at i:283834 original size:18 final size:19
Alignment explanation
Indices: 283799--283835 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
283789 CCCGGAATGT
283799 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
283819 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
283836 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:291843 original size:29 final size:28
Alignment explanation
Indices: 291809--291886 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 28
291799 CGGTGATTAG
* *
291809 TATATTTATCGATCTAACACCGATTAGAT
1 TATATTT-TCGATCTAACACAGATCAGAT
* *
291838 TATATTTTTCTATCTAACACAGGTCAGAT
1 TATA-TTTTCGATCTAACACAGATCAGAT
291867 TATATTTTCTGATCTAACAC
1 TATATTTTC-GATCTAACAC
291887 TCGTAGCAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.12
29 34 0.81
30 3 0.07
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (28 bp):
TATATTTTCGATCTAACACAGATCAGAT
Found at i:294125 original size:3 final size:3
Alignment explanation
Indices: 294117--294147 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
294107 TAATTGTTAG
294117 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
294148 TTTTTAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:295405 original size:42 final size:43
Alignment explanation
Indices: 295334--295467 Score: 137
Period size: 44 Copynumber: 3.1 Consensus size: 43
295324 TCGCAAAAGG
* * * * *
295334 TAGCGGCGTTTTTCGTTCACAAACGCCGCTGAAGGTGATGT-TTTT
1 TAGCGGCATTTTT--TTTACAAACGCCGCTAAAGGTAAT-TATATT
295379 TAGCGGC-TTTTTTTTACAAACGCCGCTAAAGGTAATTATATT
1 TAGCGGCATTTTTTTTACAAACGCCGCTAAAGGTAATTATATT
* * * *
295421 TAACGGCATTTTTTATTACAAACGCCGCTAAATGTTATGATATT
1 TAGCGGCATTTTTT-TTACAAACGCCGCTAAAGGTAATTATATT
295465 TAG
1 TAG
295468 TGGCGTATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
41 1 0.01
42 30 0.39
43 6 0.08
44 33 0.43
45 7 0.09
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.37
Consensus pattern (43 bp):
TAGCGGCATTTTTTTTACAAACGCCGCTAAAGGTAATTATATT
Found at i:295447 original size:44 final size:42
Alignment explanation
Indices: 295352--295466 Score: 133
Period size: 42 Copynumber: 2.7 Consensus size: 42
295342 TTTTTCGTTC
* * * *
295352 ACAAACGCCGCTGAAGGTGATGT-TTTTTAGCGGCTTTTTTTT
1 ACAAACGCCGCTAAAGGTAAT-TATATTTAACGGCTTTTTTTT
295394 ACAAACGCCGCTAAAGGTAATTATATTTAACGGCATTTTTTATT
1 ACAAACGCCGCTAAAGGTAATTATATTTAACGGC-TTTTTT-TT
* * *
295438 ACAAACGCCGCTAAATGTTATGATATTTA
1 ACAAACGCCGCTAAAGGTAATTATATTTA
295467 GTGGCGTATT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
41 1 0.02
42 28 0.44
43 6 0.10
44 28 0.44
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (42 bp):
ACAAACGCCGCTAAAGGTAATTATATTTAACGGCTTTTTTTT
Found at i:295764 original size:21 final size:20
Alignment explanation
Indices: 295740--295798 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
295730 ATTATCCAAT
*
295740 AAACTTAACATCCATAACAAC
1 AAACTTAA-ATCTATAACAAC
*
295761 AAACTTGAAATCTATAACAAG
1 AAACTT-AAATCTATAACAAC
*
295782 ATACTTAAAATCTATAA
1 AAACTT-AAATCTATAA
295799 TAATAAATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.25
Consensus pattern (20 bp):
AAACTTAAATCTATAACAAC
Found at i:297109 original size:22 final size:22
Alignment explanation
Indices: 297084--297143 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
297074 AAAAATATTA
* *
297084 AAAATATAATTGACACCCCTTT
1 AAAATATAATTGACACCACTCT
297106 AAAATA-ATATTGACACCACTCT
1 AAAATATA-ATTGACACCACTCT
*
297128 AAAA-ATAAATGACACC
1 AAAATATAATTGACACC
297144 GTACTATAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 10 0.30
22 23 0.70
ACGTcount: A:0.48, C:0.22, G:0.05, T:0.25
Consensus pattern (22 bp):
AAAATATAATTGACACCACTCT
Found at i:299745 original size:19 final size:21
Alignment explanation
Indices: 299713--299751 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
299703 GAAAAAATGA
299713 CAATCAAGCAAGAGC-GAAAC
1 CAATCAAGCAAGAGCAGAAAC
299733 CAATCAA-CAAGAGCAGAAA
1 CAATCAAGCAAGAGCAGAAA
299752 TAGCAAGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.54, C:0.23, G:0.18, T:0.05
Consensus pattern (21 bp):
CAATCAAGCAAGAGCAGAAAC
Found at i:300277 original size:41 final size:41
Alignment explanation
Indices: 300186--300614 Score: 397
Period size: 41 Copynumber: 10.4 Consensus size: 41
300176 TTATGTTTAC
* * ** *
300186 AAACGCCGCTAAAGTACGAGTCTATAGTAGCGTTTTTATACA
1 AAACGCCACTAAAGTACGTGTCTATAGCGGCGTTTGTATA-A
* * *
300228 CAAACGCCACTAAAGTAAGAGTCTATAGCGGCGTTTATATAA
1 -AAACGCCACTAAAGTACGTGTCTATAGCGGCGTTTGTATAA
*
300270 AAACGCCACTAAAGTACATGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGTGTCTATAGCGGCGTTTGTATAA
* * *
300311 AAACACCGCTAAATTACGTGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGTGTCTATAGCGGCGTTTGTATAA
* *
300352 AAACGCCACTAAATTACGTGTCTATAGCGGCATTTGTATAA
1 AAACGCCACTAAAGTACGTGTCTATAGCGGCGTTTGTATAA
** *
300393 AAACGCCACTAACTTACGTGTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGTGTCTATAGCGGCGTTTGTATAA
* * * *
300434 AAACGCCGCTAAAGTAC-TACTCTTTTGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGT-GTCTATAGCGGCGTTTGTATAA
* * *
300475 AAACGCCGCTAAAGTAC-T-ACTAT-GTCATGGCGTTTGTTTAAA
1 AAACGCCACTAAAGTACGTGTCTATAG-C--GGCGTTTGTAT-AA
* * * * *
300517 AAATGCCACT-ATGGA--TGAACATATTGCGGCGTTTGTATAAA
1 AAACGCCACTAAAGTACGTG-TC-TATAGCGGCGTTTGTAT-AA
* * *
300558 AAACGCCACTAAAGTAC-TACTCTGTTGCGGCGTTTTGTATAA
1 AAACGCCACTAAAGTACGT-GTCTATAGCGGCG-TTTGTATAA
*
300600 AAACGCCGCTAAAGT
1 AAACGCCACTAAAGT
300615 TACCAAATTG
Statistics
Matches: 332, Mismatches: 41, Indels: 27
0.83 0.10 0.07
Matches are distributed among these distances:
38 1 0.00
39 4 0.01
40 2 0.01
41 235 0.71
42 41 0.12
43 48 0.14
44 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGTGTCTATAGCGGCGTTTGTATAA
Found at i:306304 original size:21 final size:20
Alignment explanation
Indices: 306277--306375 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
306267 AATCAGTTTC
306277 CAAAATCGCAATGCGATTCTT
1 CAAAATCGCAATGCGATT-TT
* * *
306298 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAATGCGAT-TTT
* *
306319 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAATGCGATTTT
* * *
306339 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAATGCGATTTT
* *
306360 GAAAATCGCAACGCGA
1 CAAAATCGCAATGCGA
306376 ACACATAAAT
Statistics
Matches: 62, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
20 16 0.26
21 46 0.74
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
CAAAATCGCAATGCGATTTT
Found at i:306404 original size:20 final size:20
Alignment explanation
Indices: 306342--306535 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
306332 CGATTTTCCA
* ** *
306342 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
306362 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
306382 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
306402 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
306422 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
* *
306442 AAATCGCAATGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
306462 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
306482 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
306502 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
306523 AAATCGCAACGCG
1 AAATCGCAACGCG
306536 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:306426 original size:60 final size:60
Alignment explanation
Indices: 306342--306535 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
306332 CGATTTTCCA
* ** * *
306342 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** * *
306402 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
306462 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
306523 AAATCGCAACGCG
1 AAATCGCAACGCG
306536 ATATTTAAAG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 80 0.73
61 30 0.27
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:306957 original size:33 final size:33
Alignment explanation
Indices: 306918--306988 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
306908 TTCACTTAGA
*
306918 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
306951 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
306984 TTTCA
1 TTTCA
306989 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:307112 original size:20 final size:20
Alignment explanation
Indices: 307068--307177 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
307058 TGCAGAAGAG
*
307068 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
307089 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
307109 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
307130 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
307144 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
307163 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
307178 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:307125 original size:41 final size:38
Alignment explanation
Indices: 307061--307177 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
307051 TTCAATTTGC
* *
307061 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
307099 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
307140 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
307173 AGAAT
1 AGAAT
307178 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:307147 original size:14 final size:14
Alignment explanation
Indices: 307128--307184 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
307118 GAGAAATGAA
307128 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
307142 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
307161 AATCGCAACGAGAG
1 AATCGCAACGAGAG
307175 AATCGCAACG
1 AATCGCAACG
307185 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:307160 original size:33 final size:33
Alignment explanation
Indices: 307120--307200 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
307110 CGCAACGAGA
307120 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
307153 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
307186 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
307201 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:307218 original size:19 final size:19
Alignment explanation
Indices: 307196--307293 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
307186 GAAACCAAAA
*
307196 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
307215 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
307229 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
307248 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
307262 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
307281 TCGCGTTGCGATT
1 TCGCGTTGCGATT
307294 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:307237 original size:14 final size:14
Alignment explanation
Indices: 307218--307307 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
307208 TTTCATTTCG
307218 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
307232 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
307251 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
307265 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
307284 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
307298 CGTTGCGATT
1 CGTTGCGATT
307308 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:307243 original size:33 final size:33
Alignment explanation
Indices: 307201--307315 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
307191 CAAAATCGCA
307201 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
307234 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
307267 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
307300 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
307316 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:309173 original size:93 final size:93
Alignment explanation
Indices: 309014--309389 Score: 736
Period size: 93 Copynumber: 4.1 Consensus size: 93
309004 TAGATTGCTT
*
309014 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
309079 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
309107 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
309172 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
309200 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
309265 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
309293 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
309358 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
309385 AGTAA
1 AGTAA
309390 TGCAATCCAT
Statistics
Matches: 282, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 6 0.02
93 276 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:309557 original size:19 final size:19
Alignment explanation
Indices: 309437--309551 Score: 132
Period size: 19 Copynumber: 6.3 Consensus size: 19
309427 TAGTTTACTT
* *
309437 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
309457 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* **
309476 TTGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
309495 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
309514 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
309528 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
309547 TCGCA
1 TCGCA
309552 TTGCGATTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 51 0.64
20 13 0.16
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:309569 original size:19 final size:19
Alignment explanation
Indices: 309547--309681 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
309537 GAAACCAAAA
*
309547 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
309566 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
309582 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
309599 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
309615 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
309632 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
309651 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
309671 TCGTGTTGCGA
1 TCGCGTTGCGA
309682 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:309588 original size:14 final size:14
Alignment explanation
Indices: 309569--309625 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
309559 TTTCATTTCG
309569 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
309583 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
309600 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
309616 CGTTGCGATT
1 CGTTGCGATT
309626 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:309594 original size:33 final size:33
Alignment explanation
Indices: 309552--309644 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
309542 CAAAATCGCA
*
309552 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
309585 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
309618 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
309645 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:311751 original size:19 final size:19
Alignment explanation
Indices: 311735--311832 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
311725 AAAAATGACT
311735 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
311754 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
311773 ATCGCAACGCG--A-G--A
1 ATCGCAATGCGAAATGAAA
311787 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
311806 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
311826 ATCGCAA
1 ATCGCAA
311833 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.15
16 2 0.03
17 2 0.03
19 40 0.56
20 16 0.23
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:311864 original size:53 final size:53
Alignment explanation
Indices: 311735--311850 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
311725 AAAAATGACT
*
311735 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGCGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
311787 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
311840 ATCGCAATGCG
1 ATCGCAATGCG
311851 TTTATAATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:311894 original size:33 final size:33
Alignment explanation
Indices: 311857--312009 Score: 159
Period size: 33 Copynumber: 4.5 Consensus size: 33
311847 TGCGTTTATA
311857 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
311890 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
311930 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
311961 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
311994 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
312010 TTCATTTCGC
Statistics
Matches: 97, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 52 0.54
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:311903 original size:19 final size:19
Alignment explanation
Indices: 311879--312095 Score: 249
Period size: 19 Copynumber: 12.4 Consensus size: 19
311869 GATTCTCTCG
311879 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
311898 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
311917 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
311931 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
311950 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
311969 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
311983 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
312002 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
312021 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
312035 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
312055 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
312069 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
312088 TTGCGATT
1 TTGCGATT
312096 CTCTCGTTGC
Statistics
Matches: 169, Mismatches: 8, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 29 0.17
16 23 0.14
17 20 0.12
18 3 0.02
19 82 0.49
20 12 0.07
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:311914 original size:52 final size:52
Alignment explanation
Indices: 311857--312067 Score: 413
Period size: 52 Copynumber: 4.0 Consensus size: 52
311847 TGCGTTTATA
311857 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
311909 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
311961 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
312013 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
312066 AT
1 AT
312068 GTTGGGATTT
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 141 0.89
53 17 0.11
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:312039 original size:33 final size:33
Alignment explanation
Indices: 311898--312128 Score: 236
Period size: 33 Copynumber: 6.8 Consensus size: 33
311888 TCATTTCGCA
311898 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
311931 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
311967 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
312002 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
312035 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
312069 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* * *
312102 TTGCGATTGTAATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTT-CGCATTGCGAT
312129 AGTCAAATGC
Statistics
Matches: 164, Mismatches: 19, Indels: 29
0.77 0.09 0.14
Matches are distributed among these distances:
31 9 0.05
32 6 0.04
33 78 0.48
34 39 0.24
35 6 0.04
36 4 0.02
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.05
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:314626 original size:24 final size:24
Alignment explanation
Indices: 314592--314638 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
314582 CTGAAACATC
314592 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
314616 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
314639 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:315349 original size:20 final size:20
Alignment explanation
Indices: 315321--315550 Score: 230
Period size: 20 Copynumber: 11.5 Consensus size: 20
315311 AAATTTCAGT
* * *
315321 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
315341 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
315361 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
315381 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
315401 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
315421 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
315441 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
315461 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
315481 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
315501 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
**
315521 GTTGCGATTTTA-ATATTCGC
1 GTTGCGA-TTTACGGATTCGC
315541 GTTGCGATTT
1 GTTGCGATTT
315551 TGGAAAATCG
Statistics
Matches: 183, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
19 3 0.02
20 175 0.96
21 5 0.03
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:315551 original size:20 final size:20
Alignment explanation
Indices: 315517--315614 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
315507 ATTTATGTGT
*
315517 TCGCGTTGCGATTTTAATAT
1 TCGCGTTGCGATTTTAATAA
315537 TCGCGTTGCGATTTTGGAA-AA
1 TCGCGTTGCGATTTT--AATAA
** *
315558 TCGCAATGCGAATTTGTACT-A
1 TCGCGTTGCG-ATTT-TAATAA
* *
315579 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTT-AATAA
315600 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
315615 GGAAACTGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 20 0.32
21 35 0.56
22 6 0.10
23 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTAATAA
Found at i:315610 original size:42 final size:43
Alignment explanation
Indices: 315517--315615 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
315507 ATTTATGTGT
* *
315517 TCGCGTTGCG-ATTT-TAATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
** *
315558 TCGCAATGCGAATTTGTACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAA-AA
*
315600 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
315616 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 10 0.21
42 33 0.70
43 4 0.09
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
Found at i:316187 original size:27 final size:27
Alignment explanation
Indices: 316141--316233 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 27
316131 TATAATTGAG
*
316141 GCCCATCAAT-AAGTATTACTACTAAA
1 GCCCATAAATCAAGTATTACTACTAAA
*
316167 GCCCATAAATCAAGTGA-TACTACTAAG
1 GCCCATAAATCAAGT-ATTACTACTAAA
* ** * * *
316194 GCCCATTAATCAAACACTACTAATAAG
1 GCCCATAAATCAAGTATTACTACTAAA
*
316221 GCCCATAAGTCAA
1 GCCCATAAATCAA
316234 ACACCATTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
26 10 0.18
27 45 0.80
28 1 0.02
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.23
Consensus pattern (27 bp):
GCCCATAAATCAAGTATTACTACTAAA
Found at i:316234 original size:27 final size:27
Alignment explanation
Indices: 316184--316237 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
316174 AATCAAGTGA
*
316184 TACTACTAAGGCCCATTAATCAAACAC
1 TACTAATAAGGCCCATTAATCAAACAC
316211 TACTAATAAGGCCCA-TAAGTCAAACAC
1 TACTAATAAGGCCCATTAA-TCAAACAC
316238 CATTATTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.43, C:0.28, G:0.09, T:0.20
Consensus pattern (27 bp):
TACTAATAAGGCCCATTAATCAAACAC
Found at i:316247 original size:27 final size:27
Alignment explanation
Indices: 316185--316259 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
316175 ATCAAGTGAT
* *
316185 ACTACTAAGGCCCATTAATCAAACACT
1 ACTAATAAGGCCCATTAATCAAACACC
316212 ACTAATAAGGCCCA-TAAGTCAAACACC
1 ACTAATAAGGCCCATTAA-TCAAACACC
* * **
316239 ATTATTAAGGCCTGTTAATCA
1 ACTAATAAGGCCCATTAATCA
316260 TAGAATTCGT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 3 0.08
27 34 0.85
28 3 0.08
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.24
Consensus pattern (27 bp):
ACTAATAAGGCCCATTAATCAAACACC
Found at i:317435 original size:22 final size:23
Alignment explanation
Indices: 317396--317440 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
317386 TTGTTGGGAG
* *
317396 CATATGGGTACCGGTACT-CCTT
1 CATAGGGGTACCGATACTACCTT
*
317418 CATAGGGGTATCGATACTACCTT
1 CATAGGGGTACCGATACTACCTT
317441 TATAAAATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (23 bp):
CATAGGGGTACCGATACTACCTT
Found at i:319803 original size:81 final size:81
Alignment explanation
Indices: 319707--319868 Score: 270
Period size: 81 Copynumber: 2.0 Consensus size: 81
319697 CTACTAAACT
* * * *
319707 AACAAAATATAAAATACAATATTCTTAGTAATTCTATTCTCTAATAATCTTTTATTCTTACTGAT
1 AACAAAATACAAAATACAATATTCTTAATAATTATATTCTCTAATAATCTTTTATTCTTACTAAT
* *
319772 AATCTTATATTCCGTG
66 AATATTATATTACGTG
319788 AACAAAATACAAAATACAATATTCTTAATAATTATATTCTCTAATAATCTTTTATTCTTACTAAT
1 AACAAAATACAAAATACAATATTCTTAATAATTATATTCTCTAATAATCTTTTATTCTTACTAAT
319853 AATATTATATTACGTG
66 AATATTATATTACGTG
319869 TACTAAACGC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.43
Consensus pattern (81 bp):
AACAAAATACAAAATACAATATTCTTAATAATTATATTCTCTAATAATCTTTTATTCTTACTAAT
AATATTATATTACGTG
Found at i:319834 original size:16 final size:15
Alignment explanation
Indices: 319806--319858 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
319796 ACAAAATACA
319806 ATATTCTTAATAATT
1 ATATTCTTAATAATT
319821 ATATTCTCTAATAATCTT
1 ATATTCT-TAATAA--TT
* * *
319839 TTATTCTTACTAATA
1 ATATTCTTAATAATT
319854 ATATT
1 ATATT
319859 ATATTACGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 12 0.39
16 6 0.19
17 5 0.16
18 8 0.26
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTCTTAATAATT
Found at i:319863 original size:20 final size:18
Alignment explanation
Indices: 319806--319863 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 18
319796 ACAAAATACA
319806 ATATTCT-TAAT-A-ATT
1 ATATTCTCTAATAATATT
*
319821 ATATTCTCTAATAATCTT
1 ATATTCTCTAATAATATT
*
319839 TTATTCTTACTAATAATATT
1 ATATTC-T-CTAATAATATT
319859 ATATT
1 ATATT
319864 ACGTGTACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
15 7 0.21
16 4 0.12
17 1 0.03
18 7 0.21
19 1 0.03
20 14 0.41
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTCTCTAATAATATT
Found at i:323337 original size:108 final size:108
Alignment explanation
Indices: 323186--323425 Score: 261
Period size: 108 Copynumber: 2.2 Consensus size: 108
323176 ATAAGATGAT
* * * ** * *
323186 TATAATA--TAATATATATTTATAATTTTTTTATACTTTCGATAATCTATACATACTTTACGTAC
1 TATAATATTTAATATATATTAATAA--TTTTTAGAATTTTTATAATCTACACATACTCTACGTAC
* * *
323249 ATGTC-GCTGCTCGAATATTAGACTTTAATAGATAAAAGAAAAGAG
64 ATG-CAGCTGCTCAAACATTAAACTTTAATAGATAAAAGAAAAGAG
* *
323294 TATAATATTTAATGTATATTAATAATTTTTAGAATTTTTATAATGTACACATACTCTACGTACAT
1 TATAATATTTAATATATATTAATAATTTTTAGAATTTTTATAATCTACACATACTCTACGTACAT
* * * * *
323359 GCAGTTGTTCAAACCTTAAACTTTAATGGGTAAAAGAAAAGAG
66 GCAGCTGCTCAAACATTAAACTTTAATAGATAAAAGAAAAGAG
* *
323402 TATGATGTTTAATATATATTAATA
1 TATAATATTTAATATATATTAATA
323426 TAAATATAAT
Statistics
Matches: 109, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
107 1 0.01
108 94 0.86
110 14 0.13
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.40
Consensus pattern (108 bp):
TATAATATTTAATATATATTAATAATTTTTAGAATTTTTATAATCTACACATACTCTACGTACAT
GCAGCTGCTCAAACATTAAACTTTAATAGATAAAAGAAAAGAG
Found at i:324876 original size:14 final size:14
Alignment explanation
Indices: 324857--324886 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
324847 TAGTTATGAT
*
324857 TTTAGTTTGGTTAG
1 TTTAGTTTGATTAG
324871 TTTAGTTTGATTAG
1 TTTAGTTTGATTAG
324885 TT
1 TT
324887 GAATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (14 bp):
TTTAGTTTGATTAG
Found at i:329000 original size:40 final size:40
Alignment explanation
Indices: 328944--329038 Score: 172
Period size: 40 Copynumber: 2.4 Consensus size: 40
328934 GCGATTTTCA
*
328944 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAACGCGAATATGTAAATCGCAATGCGAGTAT
*
328984 GACTATCGCAACGCGAATATGTAAATCGCAATGCGATTAT
1 GACTATCGCAACGCGAATATGTAAATCGCAATGCGAGTAT
329024 GACTATCGCAACGCG
1 GACTATCGCAACGCG
329039 TATTATTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (40 bp):
GACTATCGCAACGCGAATATGTAAATCGCAATGCGAGTAT
Found at i:329031 original size:20 final size:20
Alignment explanation
Indices: 328944--329034 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
328934 GCGATTTTCA
328944 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGAATAT
* *
328964 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAATGCGAATAT
*
328984 GACTATCGCAACGCGAATAT
1 GACTATCGCAATGCGAATAT
* *
329004 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGAATAT
329024 GACTATCGCAA
1 GACTATCGCAA
329035 CGCGTATTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
19 2 0.03
20 54 0.93
21 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (20 bp):
GACTATCGCAATGCGAATAT
Found at i:329210 original size:22 final size:22
Alignment explanation
Indices: 329185--329226 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
329175 GGCGACATCC
329185 GTCCCCATCTCCGACGAAATTA
1 GTCCCCATCTCCGACGAAATTA
*
329207 GTCCCCATCTCCGGCGAAAT
1 GTCCCCATCTCCGACGAAAT
329227 CCATCTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATTA
Found at i:329678 original size:20 final size:20
Alignment explanation
Indices: 329613--329680 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
329603 AGAATCGCAA
* *
329613 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGTGT
** *
329632 TGCGATAGTCATTTTCGTAT
1 TGCGATTTTCATTTTCGTGT
329652 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
329672 TGCGATTTT
1 TGCGATTTT
329681 AAGTTTCAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 7 0.17
20 33 0.82
ACGTcount: A:0.13, C:0.15, G:0.22, T:0.50
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGTGT
Found at i:331618 original size:20 final size:19
Alignment explanation
Indices: 331593--331660 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 19
331583 TAGTTTACTT
331593 TCGCAACGCAGAAATGACTA
1 TCGCAACGC-GAAATGACTA
*
331613 TCGCAACGCGGAAATAACTA
1 TCGCAACGC-GAAATGACTA
* *
331633 TCGCAATGCGAATTTGACTA
1 TCGCAACGCGAA-ATGACTA
331653 TCGCAACG
1 TCGCAACG
331661 AAAGAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.07
20 38 0.93
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:332280 original size:18 final size:19
Alignment explanation
Indices: 332241--332282 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
332231 CTCACCTGTC
332241 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
332262 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
332280 ATC
1 ATC
332283 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:333798 original size:36 final size:30
Alignment explanation
Indices: 333718--333783 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
333708 ATAAGAGTTG
*
333718 ATTTATTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
333748 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
333778 ATTTGT
1 ATTTGT
333784 GCTTGTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTCTT
Found at i:333958 original size:20 final size:20
Alignment explanation
Indices: 333933--334210 Score: 243
Period size: 20 Copynumber: 14.8 Consensus size: 20
333923 GCGATTTTCT
* *
333933 CGTTGCTATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
333953 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
333973 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
*
333992 CGTTGCGAT--T---A-TCT
1 CGTTGCGATAGTCAAATTCG
334006 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
334026 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
334046 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
334066 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
*
334080 CGTTGCAATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
334100 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
334120 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
334134 CGTTGCGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
334154 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
334174 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
334194 CGTTGCGATAGTTAAAT
1 CGTTGCGATAGTCAAAT
334211 GAATGTGCAA
Statistics
Matches: 209, Mismatches: 31, Indels: 36
0.76 0.11 0.13
Matches are distributed among these distances:
14 30 0.14
16 3 0.01
17 1 0.00
18 2 0.01
19 17 0.08
20 156 0.75
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:334021 original size:53 final size:54
Alignment explanation
Indices: 333953--334054 Score: 170
Period size: 53 Copynumber: 1.9 Consensus size: 54
333943 GTCAAATTCC
* *
333953 CGTTGCGATAATCAAATTCGCGTTGCGATAG-TCATTTCGCGTTGCGATTATCT
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGATTATCT
*
334006 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGAT
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGAT
334055 AGTCATTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 30 0.67
54 15 0.33
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.34
Consensus pattern (54 bp):
CGTTGCGATAATCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGATTATCT
Found at i:334084 original size:54 final size:54
Alignment explanation
Indices: 334026--334182 Score: 253
Period size: 54 Copynumber: 2.9 Consensus size: 54
334016 GTCAAATTCG
334026 CGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
* *
334080 CGTTGCAATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
* * *
334134 CGTTGCGATA-TTCAAATTCACGTTGCGATAGTCATATTCGCGTTGCGAT
1 CGTTGCGATAGTT-AAATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT
334183 AGTCATATTC
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 1 0.01
54 94 0.99
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (54 bp):
CGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
Found at i:334097 original size:74 final size:73
Alignment explanation
Indices: 333921--334205 Score: 333
Period size: 74 Copynumber: 3.9 Consensus size: 73
333911 CTAATACACT
* * * *
333921 TTGCGATTTTCTCGTTGCTATAGTCAAATTCCCGTTGCGATAATCAAATTCGCGTTGCGATAGTC
1 TTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTC
*
333986 ATTTCGCG
66 ATTTCGCA
*
333994 TTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGATAGTC
1 TTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTC
334059 ATTTTCGCA
66 A-TTTCGCA
* * ** *
334068 TTGCGATTATCCCGTTGCAATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA-T
1 TTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGA-TAGT
**
334132 CCCGTT-GCGA
65 -CATTTCGC-A
* * * * * *
334142 TATTCAAAT-TCACGTTGCGATAGTCATATTCGCGTTGCGATAGTCATATTCGCGTTGCGATAGT
1 T-TGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGT
334206 TAAATGAATG
Statistics
Matches: 184, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
73 65 0.35
74 112 0.61
75 7 0.04
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (73 bp):
TTGCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTC
ATTTCGCA
Found at i:334408 original size:18 final size:18
Alignment explanation
Indices: 334385--334419 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
334375 AAGCCGGTTG
*
334385 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
334403 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
334420 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:336700 original size:24 final size:24
Alignment explanation
Indices: 336666--336719 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
336656 CTAAAACATC
336666 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
336690 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
336714 ATCAAA
1 ATCAAA
336720 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:337587 original size:20 final size:20
Alignment explanation
Indices: 337538--337728 Score: 147
Period size: 20 Copynumber: 9.4 Consensus size: 20
337528 TTGAAATTCA
* *
337538 GCATTGCGACAGTCAGAATC
1 GCATTGCGATAGTCATAATC
337558 GCATTGCGATAGTCATAATC
1 GCATTGCGATAGTCATAATC
* *
337578 GCATTGCGAT-TTACATATTC
1 GCATTGCGATAGT-CATAATC
* *
337598 GCGTTGCGATAGTCATACTC
1 GCATTGCGATAGTCATAATC
* *
337618 GCGTTGCGATAGTCATACTC
1 GCATTGCGATAGTCATAATC
* *
337638 GCATTGCGAT-TTACATATTC
1 GCATTGCGATAGT-CATAATC
*
337658 GCATTGCGATAGTCGGAAAATC
1 GCATTGCGATAGTC--ATAATC
** * *
337680 GCAACGCGA-ATTTGGA-AATC
1 GCATTGCGATA-GT-CATAATC
* *
337700 GCAATGCGATAGTCAGAATC
1 GCATTGCGATAGTCATAATC
337720 GCATTGCGA
1 GCATTGCGA
337729 ATCTGGAAAT
Statistics
Matches: 140, Mismatches: 21, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 5 0.04
22 12 0.09
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (20 bp):
GCATTGCGATAGTCATAATC
Found at i:337612 original size:60 final size:60
Alignment explanation
Indices: 337533--337671 Score: 215
Period size: 60 Copynumber: 2.3 Consensus size: 60
337523 CGAATTTGAA
*
337533 ATTCAGCATTGCGACAGTCAGAATCGCATTGCGATAGTCATAATCGCATTGCGATTTACAT
1 ATTC-GCATTGCGATAGTCAGAATCGCATTGCGATAGTCATAATCGCATTGCGATTTACAT
* * * * *
337594 ATTCGCGTTGCGATAGTCATACTCGCGTTGCGATAGTCATACTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATAGTCAGAATCGCATTGCGATAGTCATAATCGCATTGCGATTTACAT
337654 ATTCGCATTGCGATAGTC
1 ATTCGCATTGCGATAGTC
337672 GGAAAATCGC
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
60 67 0.94
61 4 0.06
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (60 bp):
ATTCGCATTGCGATAGTCAGAATCGCATTGCGATAGTCATAATCGCATTGCGATTTACAT
Found at i:337736 original size:40 final size:41
Alignment explanation
Indices: 337656--337738 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 41
337646 ATTTACATAT
* *
337656 TCGCATTGCGATAGTCGGAAAATCGCAACGCGAATTTGGAAA
1 TCGCAATGCGATAGTC-GAAAATCGCAACGCGAATCTGGAAA
* **
337698 TCGCAATGCGATAGTC-AGAATCGCATTGCGAATCTGGAAA
1 TCGCAATGCGATAGTCGAAAATCGCAACGCGAATCTGGAAA
337738 T
1 T
337739 TGATTTGCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
40 21 0.58
42 15 0.42
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (41 bp):
TCGCAATGCGATAGTCGAAAATCGCAACGCGAATCTGGAAA
Found at i:340385 original size:13 final size:13
Alignment explanation
Indices: 340367--340392 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
340357 TATATACGCA
340367 CATATGAAGACTG
1 CATATGAAGACTG
340380 CATATGAAGACTG
1 CATATGAAGACTG
340393 TTCAACTATG
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:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
CATATGAAGACTG
Found at i:344934 original size:58 final size:59
Alignment explanation
Indices: 344851--344980 Score: 158
Period size: 61 Copynumber: 2.2 Consensus size: 59
344841 GATTATTAAG
* * **
344851 AACATACACATACGCAAACGAATAACTGCATACTTA-AAAA-AGGA-AAAAAAAACAAA
1 AACAAACACATACGAAAACGAATAACTGCATACTTAGAAAAGAAAAGAAAAAAAACAAA
* * *
344907 AACAGACACATACGAAATTACGAATAACTGTATACTTAGAAAAGAAAAGAAAAAAAACAAG
1 AACAAACACATACGAAA--ACGAATAACTGCATACTTAGAAAAGAAAAGAAAAAAAACAAA
344968 AACAAACACATAC
1 AACAAACACATAC
344981 ACACGAATTG
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
56 15 0.24
58 18 0.29
59 4 0.06
60 2 0.03
61 23 0.37
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.13
Consensus pattern (59 bp):
AACAAACACATACGAAAACGAATAACTGCATACTTAGAAAAGAAAAGAAAAAAAACAAA
Found at i:345474 original size:21 final size:21
Alignment explanation
Indices: 345448--345487 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
345438 TATAATGTAA
* *
345448 ATTTCAGAATAATTAAATTAG
1 ATTTCAAAATAAATAAATTAG
345469 ATTTCAAAATAAATAAATT
1 ATTTCAAAATAAATAAATT
345488 TAATTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTTCAAAATAAATAAATTAG
Found at i:350859 original size:19 final size:19
Alignment explanation
Indices: 350826--350879 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
350816 AACTTTTCTC
*
350826 ATCTCATACATAATTATAA
1 ATCTCATACAAAATTATAA
350845 ATCGT-ATACAAAATTATAA
1 ATC-TCATACAAAATTATAA
*
350864 ATCTCATAAAAAATTA
1 ATCTCATACAAAATTA
350880 ACCCTACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 1 0.03
19 29 0.94
20 1 0.03
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (19 bp):
ATCTCATACAAAATTATAA
Found at i:352119 original size:24 final size:24
Alignment explanation
Indices: 352092--352180 Score: 69
Period size: 23 Copynumber: 3.8 Consensus size: 24
352082 AGCTCGTATA
352092 AATTTGCACCGAAGTGCCACGTAG
1 AATTTGCACCGAAGTGCCACGTAG
* * * *
352116 AATTTATC-CCGAAAG-ACCGCATAG
1 AATTT-GCACCG-AAGTGCCACGTAG
352140 AA-TTGCACCGAAGTGCCACGTA-
1 AATTTGCACCGAAGTGCCACGTAG
** *
352162 AAAATGCACCGTAGTGCCA
1 AATTTGCACCGAAGTGCCA
352181 TATAAGATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 11
0.70 0.14 0.15
Matches are distributed among these distances:
22 6 0.12
23 24 0.48
24 16 0.32
25 4 0.08
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (24 bp):
AATTTGCACCGAAGTGCCACGTAG
Found at i:352356 original size:24 final size:24
Alignment explanation
Indices: 352294--352362 Score: 111
Period size: 24 Copynumber: 2.9 Consensus size: 24
352284 AATACATATA
* * *
352294 TGTCCCGAATGACCACATAGAATT
1 TGTCCCGAAGGACCGCGTAGAATT
352318 TGTCCCGAAGGACCGCGTAGAATT
1 TGTCCCGAAGGACCGCGTAGAATT
352342 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCGAAGGACCGCGTAGA
352363 CCCTCTACTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (24 bp):
TGTCCCGAAGGACCGCGTAGAATT
Found at i:354861 original size:18 final size:18
Alignment explanation
Indices: 354838--354876 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
354828 TCCTCCTCAT
354838 TTCCTCCATATTTTCTTC
1 TTCCTCCATATTTTCTTC
354856 TTCCTCCATATTTTCTTC
1 TTCCTCCATATTTTCTTC
354874 TTC
1 TTC
354877 ATATTTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.33, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCCATATTTTCTTC
Found at i:361439 original size:17 final size:19
Alignment explanation
Indices: 361414--361452 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
361404 ATATCTGTAT
361414 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
361432 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
361451 TA
1 TA
361453 AGTTGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:361779 original size:2 final size:2
Alignment explanation
Indices: 361772--361799 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
361762 TGCCATGTTA
361772 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
361800 TTGTGAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:384534 original size:31 final size:31
Alignment explanation
Indices: 384496--384559 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
384486 CAATGTGTCA
384496 ATTTGGTACCGATATTTTCCTATTGATACCT
1 ATTTGGTACCGATATTTTCCTATTGATACCT
*
384527 ATTTGGTATCGATATTTTCCTATTGATACCT
1 ATTTGGTACCGATATTTTCCTATTGATACCT
384558 AT
1 AT
384560 ATGTAAAAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.47
Consensus pattern (31 bp):
ATTTGGTACCGATATTTTCCTATTGATACCT
Found at i:386249 original size:19 final size:19
Alignment explanation
Indices: 386225--386262 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
386215 TCAAAATAGG
*
386225 AAATATCTTA-AATTATAAT
1 AAATAT-TTACAATCATAAT
386244 AAATATTTACAATCATAAT
1 AAATATTTACAATCATAAT
386263 CGTAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATATTTACAATCATAAT
Found at i:386673 original size:23 final size:23
Alignment explanation
Indices: 386647--386706 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
386637 TCAAACGACC
386647 GAAAAACGTG-C-TAAAATACAAAA
1 GAAAAACGTGTCAT-AAATAC-AAA
*
386670 GAAAAA-GTGTCATACATACAAA
1 GAAAAACGTGTCATAAATACAAA
386692 GAAAAACGTGTCATA
1 GAAAAACGTGTCATA
386707 CATGCAGACT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 12 0.36
23 20 0.61
24 1 0.03
ACGTcount: A:0.55, C:0.13, G:0.15, T:0.17
Consensus pattern (23 bp):
GAAAAACGTGTCATAAATACAAA
Found at i:386707 original size:23 final size:23
Alignment explanation
Indices: 386662--386709 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
386652 ACGTGCTAAA
386662 ATACAAAAGAAAAAGTGTCATAC
1 ATACAAAAGAAAAAGTGTCATAC
386685 ATAC-AAAGAAAAACGTGTCATAC
1 ATACAAAAGAAAAA-GTGTCATAC
386708 AT
1 AT
386710 GCAGACTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.19
Consensus pattern (23 bp):
ATACAAAAGAAAAAGTGTCATAC
Found at i:387989 original size:6 final size:6
Alignment explanation
Indices: 387978--388015 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
387968 AACCTGATTC
* *
387978 ATATAT ATATAT ATATAA ATATAA ATATAA ATATAA AT
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA AT
388016 GTATAAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAA
Found at i:389637 original size:16 final size:16
Alignment explanation
Indices: 389618--389648 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
389608 ATAAAAATAT
*
389618 ATTATTTTTAAAAAAA
1 ATTATGTTTAAAAAAA
389634 ATTATGTTTAAAAAA
1 ATTATGTTTAAAAAA
389649 TTACGTTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTATGTTTAAAAAAA
Found at i:390799 original size:2 final size:2
Alignment explanation
Indices: 390792--390823 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
390782 AAATATTGAC
390792 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
390824 CCTAGAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:393339 original size:23 final size:24
Alignment explanation
Indices: 393289--393339 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
393279 ACTTCTTTTA
*
393289 TGTTTAGGGTTTTAGTGATTTAGG
1 TGTTTAGGGTTTTAGTAATTTAGG
393313 -GTTTAGGGTTTT-G-AATTTAAGG
1 TGTTTAGGGTTTTAGTAATTT-AGG
393335 TGTTT
1 TGTTT
393340 TTTTTATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.17
22 4 0.17
23 16 0.67
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (24 bp):
TGTTTAGGGTTTTAGTAATTTAGG
Found at i:397220 original size:11 final size:12
Alignment explanation
Indices: 397204--397235 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
397194 GATTTGTTAA
397204 TTAGTTAGTA-G
1 TTAGTTAGTACG
397215 TTAGTTAG-ACG
1 TTAGTTAGTACG
397226 TTAGTTAGTA
1 TTAGTTAGTA
397236 TGCTAGCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 17 0.89
12 1 0.05
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.44
Consensus pattern (12 bp):
TTAGTTAGTACG
Done.