Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold468
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: 1127621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:320188 original size:71 final size:71
Alignment explanation
Indices: 320091--320258 Score: 248
Period size: 71 Copynumber: 2.4 Consensus size: 71
320081 ATAATTATTC
* * * *
320091 AATGTATTGATACATCTAGGTAAAAAGACAGAATGTATCGATACATTCATA-CATGTATCGATAT
1 AATGTATTGATACATCTAGGTAAAAAGACAGAATGTATCGACACATT-AAAGAATGTATCGATAC
320155 ATTGAAA
65 ATTGAAA
*
320162 AATGTATTGATACATCTAGGTAAAAAGATAGAATGTATCGACACATTAAAGAATGTATCGATACA
1 AATGTATTGATACATCTAGGTAAAAAGACAGAATGTATCGACACATTAAAGAATGTATCGATACA
320227 TTGAAA
66 TTGAAA
* * *
320233 AATGTATCGATACATTTGGGTAAAAA
1 AATGTATTGATACATCTAGGTAAAAA
320259 TGTGACTTTT
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
70 2 0.02
71 86 0.98
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (71 bp):
AATGTATTGATACATCTAGGTAAAAAGACAGAATGTATCGACACATTAAAGAATGTATCGATACA
TTGAAA
Found at i:320216 original size:20 final size:21
Alignment explanation
Indices: 320191--320248 Score: 93
Period size: 20 Copynumber: 2.9 Consensus size: 21
320181 GTAAAAAGAT
*
320191 AGAATGTATCGACACATT-AA
1 AGAATGTATCGATACATTGAA
320211 AGAATGTATCGATACATTGAA
1 AGAATGTATCGATACATTGAA
320232 A-AATGTATCGATACATT
1 AGAATGTATCGATACATT
320249 TGGGTAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 33 0.92
21 3 0.08
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
AGAATGTATCGATACATTGAA
Found at i:321360 original size:11 final size:11
Alignment explanation
Indices: 321344--321374 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
321334 ACCAGGCACT
*
321344 CCACTGCTTGC
1 CCACTGCCTGC
321355 CCACTGCCTGC
1 CCACTGCCTGC
321366 CCACTGCCT
1 CCACTGCCT
321375 ACCCTTCCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.52, G:0.16, T:0.23
Consensus pattern (11 bp):
CCACTGCCTGC
Found at i:322387 original size:21 final size:21
Alignment explanation
Indices: 322357--322397 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
322347 CCCTACTAAC
*
322357 ATTCATGGGATGTTTGCATCA
1 ATTCAGGGGATGTTTGCATCA
322378 ATTCAGGGGATGTTTGCATC
1 ATTCAGGGGATGTTTGCATC
322398 CATCTTCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.37
Consensus pattern (21 bp):
ATTCAGGGGATGTTTGCATCA
Found at i:331854 original size:9 final size:9
Alignment explanation
Indices: 331840--331865 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
331830 TGACGAGGAG
331840 GAAGATGAA
1 GAAGATGAA
331849 GAAGATGAA
1 GAAGATGAA
331858 GAAGATGA
1 GAAGATGA
331866 TCTAAATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.35, T:0.12
Consensus pattern (9 bp):
GAAGATGAA
Found at i:335758 original size:368 final size:370
Alignment explanation
Indices: 335030--336135 Score: 1494
Period size: 368 Copynumber: 3.0 Consensus size: 370
335020 CATAGAAATT
*
335030 TAATGGGTTCGTGAAGATGTTGATGAAGACATTTATGAACATTGATGAATAAAGTAAATTTAGTA
1 TAATGGGTTCGTGAAGATGTTGATGAAGATATTTATGAACATTGATGAATAAAGTAAATTTAGTA
* *
335095 AGATTATTGCATGACATTGATTTGTTATATTTATATA-A-ATATATATTTTGTTGTATGATACAT
66 AGATTATTGCATGACATTGATTTGTTATATTTATATATATATTTTTATTTTGTTGTATGATACAT
335158 ATTGCATTTTACTATGAC----ACTACTTTTATTAACTTAAAATTGTTGCAGATAATATGCCAAG
131 ATTGCATTTTACTATGACTAATACTACTTTTATTAACTTAAAATTGTTGCAGATAATATGCCAAG
* * **
335219 GAAAAGATTAAAAGGTTTGAATATTGTTCACACTCGTTCAGAATCAAAGCCCATTGATGCTTCAA
196 GAGAAGATTAAAA----TG---A--G----CACTCGTTCAGAATCAGAGCCTGTTGATGCTTCAA
* * * *
335284 CTACATCTTCTATGGTAATCCCAAATATGCTTTTAACAAATATGACTACAAAGAATGCAATTCAT
248 CTACACCTTCTATGGTAATCCCAAATATGCTTTTAAGAAATACGACTACAGAGAATGCAATTCAT
* * *
335349 AGTAATTTGAACACATGTATTGTTAAATGCCATAAAAGTTGTTAAATGCAATTCATAG
313 AGTAATTTGAACACATGTATTGTTAAATGCCATAGAAGTTGTTAAATACAATTCATAA
*
335407 TAATAGGTTCGTGAAGATGTTGATGAAGATATTTATGAACATTGATGAATAAAGTAAATTTAGTA
1 TAATGGGTTCGTGAAGATGTTGATGAAGATATTTATGAACATTGATGAATAAAGTAAATTTAGTA
*
335472 AGATTATTACATGACATTGATTTGTTATATATATATATATATATTTTTATTTTGTTGTATGATAC
66 AGATTATTGCATGACATTGATTTGTTATAT-T-TATATATATATTTTTATTTTGTTGTATGATAC
*
335537 ATATTGCATTTTACTATGACTAATACTACTTTTATTAACTTAAAATTGTTACAGATAATATGCCA
129 ATATTGCATTTTACTATGACTAATACTACTTTTATTAACTTAAAATTGTTGCAGATAATATGCCA
* *
335602 AGGAGAAGATT-AAA-G-G-ACTCATTCAAAATCAGAGCCTGTTGATGCTTCAACTACACCCTT-
194 AGGAGAAGATTAAAATGAGCACTCGTTCAGAATCAGAGCCTGTTGATGCTTCAACTACA-CCTTC
* * * *
335662 TACGGTTATCCCAGATATGCTTTTAAGAAATACGACTACAGAGAATGCAATTCCTAGTAATTTGA
258 TATGGTAATCCCAAATATGCTTTTAAGAAATACGACTACAGAGAATGCAATTCATAGTAATTTGA
*
335727 AAACATGTATTGTTAAATGCCATAGAAGTTGTTAAATACAATTCATAA
323 ACACATGTATTGTTAAATGCCATAGAAGTTGTTAAATACAATTCATAA
* *
335775 TAATGGGTTCGTGAAGATATTGATGAAGATATTTATGAACATTAATGAATAAAGTAAATTTAGTA
1 TAATGGGTTCGTGAAGATGTTGATGAAGATATTTATGAACATTGATGAATAAAGTAAATTTAGTA
* * *
335840 AGATTATTGCATGACATT-A--T-TT-T-GTTATATATATA-TTTTATTTTGTTTTATGATATAT
66 AGATTATTGCATGACATTGATTTGTTATATTTATATATATATTTTTATTTTGTTGTATGATACAT
*
335898 ATTGCATTTTACTATGACTAATACTACTTTTATTAACTTAAAATTGTTGCAGATAATATGCCAAA
131 ATTGCATTTTACTATGACTAATACTACTTTTATTAACTTAAAATTGTTGCAGATAATATGCCAAG
335963 GAGAAGATTAAAAGGTTTGAATATTGTTCACACTCGTTCAGAATCAGAG-CTCGTTGATGCTTCA
196 GAGAAGATTAAAA----TG---A--G----CACTCGTTCAGAATCAGAGCCT-GTTGATGCTTCA
* * * *
336027 ACTACACCTTCTATGATAATCCCAAATATGCTCTTAAGAAATACGACTACAGGGAATGCTATTCA
247 ACTACACCTTCTATGGTAATCCCAAATATGCTTTTAAGAAATACGACTACAGAGAATGCAATTCA
*
336092 TAGTAATTTGAACGCATGTATTGTTAAATGCCATAGAAGTTGTT
312 TAGTAATTTGAACACATGTATTGTTAAATGCCATAGAAGTTGTT
336136 GTCTTTTATT
Statistics
Matches: 656, Mismatches: 45, Indels: 57
0.87 0.06 0.08
Matches are distributed among these distances:
359 93 0.14
360 13 0.02
361 1 0.00
363 1 0.00
364 2 0.00
365 2 0.00
367 1 0.00
368 215 0.33
369 3 0.00
371 1 0.00
373 1 0.00
375 6 0.01
376 122 0.19
377 92 0.14
378 1 0.00
379 7 0.01
380 1 0.00
381 41 0.06
384 3 0.00
385 50 0.08
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (370 bp):
TAATGGGTTCGTGAAGATGTTGATGAAGATATTTATGAACATTGATGAATAAAGTAAATTTAGTA
AGATTATTGCATGACATTGATTTGTTATATTTATATATATATTTTTATTTTGTTGTATGATACAT
ATTGCATTTTACTATGACTAATACTACTTTTATTAACTTAAAATTGTTGCAGATAATATGCCAAG
GAGAAGATTAAAATGAGCACTCGTTCAGAATCAGAGCCTGTTGATGCTTCAACTACACCTTCTAT
GGTAATCCCAAATATGCTTTTAAGAAATACGACTACAGAGAATGCAATTCATAGTAATTTGAACA
CATGTATTGTTAAATGCCATAGAAGTTGTTAAATACAATTCATAA
Found at i:335880 original size:21 final size:22
Alignment explanation
Indices: 335856--335897 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
335846 TTGCATGACA
335856 TTATTTTGTTATAT-ATATATT
1 TTATTTTGTTATATGATATATT
*
335877 TTATTTTGTTTTATGATATAT
1 TTATTTTGTTATATGATATAT
335898 ATTGCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
TTATTTTGTTATATGATATATT
Found at i:341209 original size:79 final size:79
Alignment explanation
Indices: 341122--341386 Score: 249
Period size: 79 Copynumber: 3.4 Consensus size: 79
341112 TGGTGTTCTG
* **
341122 GAAATAAAATCGGGGTTGGAGGATCCCCTCAGAAATAACAGGGTTGGAGTATCCCTGATTGTAGA
1 GAAATAAAATCGGGGTTGGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCTGATTGTAGA
341187 AAATCGACGCTTT-
66 AAATCGACGCTTTA
* ** *
341200 GAAAATAAAATCAGGGTTGGAGTAAACCCTC-GAAAATAATGGGGTTGGAGTAT-CTTCGATTGT
1 G-AAATAAAATCGGGGTTGGAGTATCCCCTCAG-AAATAATGGGGTTGGAGTATCCCT-GATTGT
*
341263 -GAAAAATCGATGCTTTA
63 AG-AAAATCGACGCTTTA
* * * *
341280 GAAATAAGACCGGGGTTGGAGTATCCCCGCCA-AAATAATGGGGTTAGAGTATTCCC-GATTGTG
1 GAAATAAAATCGGGGTTGGAGTATCCCC-TCAGAAATAATGGGGTTGGAGTA-TCCCTGATTGT-
* * * *
341343 AGAAATTAG-TGTTTTA
63 AGAAAATCGACGCTTTA
*
341359 GAAATAAAA-CAGGGGTTGAAGTATCCCC
1 GAAATAAAATC-GGGGTTGGAGTATCCCC
341387 AATTATGAGA
Statistics
Matches: 154, Mismatches: 21, Indels: 23
0.78 0.11 0.12
Matches are distributed among these distances:
78 6 0.04
79 138 0.90
80 8 0.05
81 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (79 bp):
GAAATAAAATCGGGGTTGGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCTGATTGTAGA
AAATCGACGCTTTA
Found at i:341396 original size:51 final size:51
Alignment explanation
Indices: 341319--341485 Score: 219
Period size: 51 Copynumber: 3.3 Consensus size: 51
341309 CCAAAATAAT
* * *
341319 GGGGTTAGAGTATTCCCGATTGTGAGAAATTAGTGTTTTAGAAATAAAACA
1 GGGGTTAGAGTATCCCCAATTGTGAGAAATTAGTGTTTTAGAAATAAAACC
* * *
341370 GGGGTT-GAAGTATCCCCAATTATGAGAAATTGGTGTTTTAAAAATAAAACC
1 GGGGTTAG-AGTATCCCCAATTGTGAGAAATTAGTGTTTTAGAAATAAAACC
* * * * *
341421 GGAGTTAGAGTATCCCCAATTGTGAGAAATCAATATTTTAGAAATAAAGCC
1 GGGGTTAGAGTATCCCCAATTGTGAGAAATTAGTGTTTTAGAAATAAAACC
341472 GGGGTTAGAGTATC
1 GGGGTTAGAGTATC
341486 TCCTCGAAAA
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
50 1 0.01
51 97 0.98
52 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (51 bp):
GGGGTTAGAGTATCCCCAATTGTGAGAAATTAGTGTTTTAGAAATAAAACC
Found at i:341530 original size:130 final size:129
Alignment explanation
Indices: 341378--341614 Score: 359
Period size: 130 Copynumber: 1.8 Consensus size: 129
341368 CAGGGGTTGA
* * *
341378 AGTATCCCCAATTATGAGAAATTGGTGTTTTAAAAATAAAACCGGAGTTAGAGTATCCCCAATTG
1 AGTATCCCCAATTATAAAAAATTGATGTTTTAAAAATAAAACCGGAGTTAGAGTATCCCCAA--G
* *
341443 -TGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTAGAGTATCTCCTCGAAAATAACAGGATTG
64 ATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTAGAGTATCTCCTCGAAAATAACAGGATTG
341507 G
129 G
* * * *
341508 AGTATCCCCAATTATAAAAAATTGATGTTTTAGAAATAAAATCGGGGTTAGAGTATCCCCGAGAT
1 AGTATCCCCAATTATAAAAAATTGATGTTTTAAAAATAAAACCGGAGTTAGAGTATCCCCAAGAT
*
341573 GAAAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTATC
66 GAAAAATCAATATTTTAGAAATAAAACCGGGGTTAGAGTATC
341615 CCCGAGATAA
Statistics
Matches: 96, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
128 1 0.01
129 40 0.42
130 55 0.57
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (129 bp):
AGTATCCCCAATTATAAAAAATTGATGTTTTAAAAATAAAACCGGAGTTAGAGTATCCCCAAGAT
GAAAAATCAATATTTTAGAAATAAAACCGGGGTTAGAGTATCTCCTCGAAAATAACAGGATTGG
Found at i:341565 original size:181 final size:180
Alignment explanation
Indices: 341258--341617 Score: 404
Period size: 181 Copynumber: 2.0 Consensus size: 180
341248 AGTATCTTCG
* * * ** *
341258 ATTGTGAAAAATCGATGCTTTAGAAATAAGACCGGGGTTGGAGTATCCCCGCCAAAATAATGGGG
1 ATTGTGAAAAATCAATACTTTAGAAATAAGACCGGGGTTAGAGTATCCCCGCCAAAATAACAGGA
* * * * *
341323 TTAGAGTATTCCCGATTGTGAGAAATTAGTGTTTTAGAAATAAAACAGGGGTTGAAGTATCCCCA
66 TTAGAGTATCCCCAATTATAAAAAATTAGTGTTTTAGAAATAAAACAGGGGTTGAAGTATCCCCA
* * *** *
341388 ATTATGAGAAATTGGTGTTTTAAAAATAAAACCGGAGTTAGAGTATCCCCA
131 A-GATGAAAAATCAATATTTTAAAAATAAAACCGGAGTTAGAGTATCCCCA
* * * * *
341439 ATTGTGAGAAATCAATATTTTAGAAATAA-AGCCGGGGTTAGAGTATCTCCTCGAAAATAACAGG
1 ATTGTGAAAAATCAATACTTTAGAAATAAGA-CCGGGGTTAGAGTATCCCCGCCAAAATAACAGG
*
341503 ATTGGAGTATCCCCAATTATAAAAAATT-GATGTTTTAGAAATAAAATC-GGGGTT-AGAGTATC
65 ATTAGAGTATCCCCAATTATAAAAAATTAG-TGTTTTAGAAATAAAA-CAGGGGTTGA-AGTATC
* * * *
341565 CCCGAGATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
127 CCCAAGATGAAAAATCAATATTTTAAAAATAAAACCGGAGTTAGAGTATCCCC
341618 GAGATAAAAA
Statistics
Matches: 148, Mismatches: 27, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
180 42 0.28
181 105 0.71
182 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (180 bp):
ATTGTGAAAAATCAATACTTTAGAAATAAGACCGGGGTTAGAGTATCCCCGCCAAAATAACAGGA
TTAGAGTATCCCCAATTATAAAAAATTAGTGTTTTAGAAATAAAACAGGGGTTGAAGTATCCCCA
AGATGAAAAATCAATATTTTAAAAATAAAACCGGAGTTAGAGTATCCCCA
Found at i:341593 original size:50 final size:50
Alignment explanation
Indices: 341507--341630 Score: 167
Period size: 50 Copynumber: 2.5 Consensus size: 50
341497 AACAGGATTG
* * ** * *
341507 GAGTATCCCCAATTATAAAAAATTGATGTTTTAGAAATAAAATCGGGGTTA
1 GAGTATCCCCGA-GATAAAAAATCAATATTTTAGAAATAAAACCGGGGTTA
* *
341558 GAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTG
1 GAGTATCCCCGAGATAAAAAATCAATATTTTAGAAATAAAACCGGGGTTA
341608 GAGTATCCCCGAGATAAAAAATC
1 GAGTATCCCCGAGATAAAAAATC
341631 TAGAAATTCA
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
50 53 0.83
51 11 0.17
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (50 bp):
GAGTATCCCCGAGATAAAAAATCAATATTTTAGAAATAAAACCGGGGTTA
Found at i:345149 original size:13 final size:13
Alignment explanation
Indices: 345131--345155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
345121 CATATTGCTT
345131 TGTATCGATACAA
1 TGTATCGATACAA
345144 TGTATCGATACA
1 TGTATCGATACA
345156 TGTTCTTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:345259 original size:13 final size:13
Alignment explanation
Indices: 345222--345284 Score: 69
Period size: 13 Copynumber: 4.9 Consensus size: 13
345212 AACTTACTCA
*
345222 GTATCGATACAGT
1 GTATCGATACATT
345235 GTATCGATACATT
1 GTATCGATACATT
345248 GTATCGATACA-T
1 GTATCGATACATT
*
345260 G-GT-GATACATCAT
1 GTATCGATACAT--T
345273 GTATCGATACAT
1 GTATCGATACAT
345285 GGTAAAATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
10 6 0.14
11 1 0.02
12 2 0.05
13 25 0.60
14 1 0.02
15 7 0.17
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:345281 original size:25 final size:24
Alignment explanation
Indices: 345222--345287 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 24
345212 AACTTACTCA
*
345222 GTATCGATACAGTGTATCGATACATT
1 GTATCGATACA-TG-GTCGATACATT
345248 GTATCGATACATGGT-GATACATCAT
1 GTATCGATACATGGTCGATACAT--T
345273 GTATCGATACATGGT
1 GTATCGATACATGGT
345288 AAAATGTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 7 0.19
24 1 0.03
25 18 0.49
26 11 0.30
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Consensus pattern (24 bp):
GTATCGATACATGGTCGATACATT
Found at i:345789 original size:36 final size:33
Alignment explanation
Indices: 345743--345835 Score: 109
Period size: 36 Copynumber: 2.8 Consensus size: 33
345733 CTAAGTAATT
* *
345743 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGGG
1 GAGAGCTTCTATCTTAGCC-TTGAAAAAGAT-GAG
345778 AGAGAGCTTCTATCTTAG-CTTGTAAAAAGATGAG
1 -GAGAGCTTCTATCTTAGCCTTG-AAAAAGATGAG
*
345812 GAGA-TTTCTATCTTAGCCTTGAAA
1 GAGAGCTTCTATCTTAGCCTTGAAA
345836 GATAGTGTTG
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
32 14 0.27
33 8 0.15
34 5 0.10
35 9 0.17
36 16 0.31
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (33 bp):
GAGAGCTTCTATCTTAGCCTTGAAAAAGATGAG
Found at i:346707 original size:12 final size:12
Alignment explanation
Indices: 346690--346716 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
346680 CCTATCCAAA
346690 CAAGAAAATCCT
1 CAAGAAAATCCT
346702 CAAGAAAATCCT
1 CAAGAAAATCCT
346714 CAA
1 CAA
346717 TAGCCTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.07, T:0.15
Consensus pattern (12 bp):
CAAGAAAATCCT
Found at i:347400 original size:21 final size:22
Alignment explanation
Indices: 347376--347431 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
347366 GAACTAGAGG
347376 AGAAAATGAATGAGTTACAA-A
1 AGAAAATGAATGAGTTACAAGA
*
347397 AGAAAA-GAAATGAGTTGCAAGA
1 AGAAAATG-AATGAGTTACAAGA
*
347419 TGAAAAT-AATGAG
1 AGAAAATGAATGAG
347432 CTAACTAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 1 0.03
21 23 0.77
22 6 0.20
ACGTcount: A:0.55, C:0.04, G:0.23, T:0.18
Consensus pattern (22 bp):
AGAAAATGAATGAGTTACAAGA
Found at i:348769 original size:33 final size:34
Alignment explanation
Indices: 348732--348800 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
348722 GTTACAAGCT
348732 ATGTATCGATACATT-T-CTTCATGTATCGATA-AA
1 ATGTATCGATACATTGTAC--CATGTATCGATACAA
348765 ATGTATCGATACATTGTACCATGTATCGATACAA
1 ATGTATCGATACATTGTACCATGTATCGATACAA
348799 AT
1 AT
348801 AGTGATAGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
33 27 0.82
34 5 0.15
35 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (34 bp):
ATGTATCGATACATTGTACCATGTATCGATACAA
Found at i:348853 original size:21 final size:19
Alignment explanation
Indices: 348827--348900 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
348817 TTGCCAGTTT
**
348827 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
348848 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* *
348867 CATGTATCGATACAAAGCAG
1 CATGTATCGATACAATG-AA
348887 CATGTATCGATACA
1 CATGTATCGATACA
348901 TCTGGGTGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
19 18 0.38
20 15 0.31
21 15 0.31
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:349502 original size:42 final size:39
Alignment explanation
Indices: 349421--349503 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
349411 GTTTTCATTT
* *
349421 TTCTCCCCCTTAAACGATTATCTCCTCCTTTATAAAAAA
1 TTCTCCCCCTTAAACGATTATCTCCCCCCTTATAAAAAA
* * *
349460 TTCTCCCCCTTTAACTATTATCTTCTCCCCCTTATGTAAAAA
1 TTCTCCCCCTTAAACGATTATC-TC-CCCCCTTAT-AAAAAA
349502 TT
1 TT
349504 TATTTTCACA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 20 0.56
40 2 0.06
41 7 0.19
42 7 0.19
ACGTcount: A:0.27, C:0.31, G:0.02, T:0.40
Consensus pattern (39 bp):
TTCTCCCCCTTAAACGATTATCTCCCCCCTTATAAAAAA
Found at i:351350 original size:13 final size:13
Alignment explanation
Indices: 351332--351360 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
351322 AAATAGTACC
351332 CAATGTATCGATA
1 CAATGTATCGATA
351345 CAATGTATCGATA
1 CAATGTATCGATA
351358 CAA
1 CAA
351361 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:357560 original size:33 final size:33
Alignment explanation
Indices: 357518--357581 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 33
357508 ATTACAAGCT
357518 ATGTATCGATACATT-T-CTTCATGTATCGATATA
1 ATGTATCGATACATTGTAC--CATGTATCGATATA
357551 ATGTATCGATACATTGTACCATGTATCGATA
1 ATGTATCGATACATTGTACCATGTATCGATA
357582 CAAATAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATATA
Found at i:361198 original size:3 final size:3
Alignment explanation
Indices: 361190--361223 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
361180 CGAGTCAACT
*
361190 TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
361224 TGATGGTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:363516 original size:634 final size:634
Alignment explanation
Indices: 362308--363565 Score: 2507
Period size: 634 Copynumber: 2.0 Consensus size: 634
362298 TTTACCTTTT
362308 AGGTAAAGGTACAACCTTACAACACTTATCTTTTCAAGGCTAAGATAATAACCTCTCAATCTCTC
1 AGGTAAAGGTACAACCTTACAACACTTATCTTTTCAAGGCTAAGATAATAACCTCTCAATCTCTC
362373 CAAGAATTATACCTCAAATTCTTAAGAGATTGTACACCAAGGTTGAATACAACCTTTATGACACA
66 CAAGAATTATACCTCAAATTCTTAAGAGATTGTACACCAAGGTTGAATACAACCTTTATGACACA
362438 AAGAGATTTTATAAACGAGAAATGCCTCTAAGTAGGCTGGTGTTTGTGAAGGTATAAGCACAAAA
131 AAGAGATTTTATAAACGAGAAATGCCTCTAAGTAGGCTGGTGTTTGTGAAGGTATAAGCACAAAA
362503 GAATACAAATGAGCTTCAAAGAATAACAGCCATGAATATAAAAGCTCTTACAAATATAGAAAATG
196 GAATACAAATGAGCTTCAAAGAATAACAGCCATGAATATAAAAGCTCTTACAAATATAGAAAATG
362568 ATAAAACTTTAAATGCTTGGATTTTTTGATGTTTCTTGTTGGTTCTTGTTGTTCTTTAGCTATTG
261 ATAAAACTTTAAATGCTTGGATTTTTTGATGTTTCTTGTTGGTTCTTGTTGTTCTTTAGCTATTG
362633 AAAACTCATATTTATAGGCTAGAATGTTGACATAATCATTGGAGGTTGAATGATTGTGTTTGTAG
326 AAAACTCATATTTATAGGCTAGAATGTTGACATAATCATTGGAGGTTGAATGATTGTGTTTGTAG
362698 CTGTTGTTGACTTGTTTGGAGCTTATTTTCGCACATTCACGCTCCTATGTATCGATACTTATCAT
391 CTGTTGTTGACTTGTTTGGAGCTTATTTTCGCACATTCACGCTCCTATGTATCGATACTTATCAT
362763 AATGTATTGATACATGCATTTGAAATTTATAGCCGTTGGGTTCAATGTATCGATATATTTCACCA
456 AATGTATTGATACATGCATTTGAAATTTATAGCCGTTGGGTTCAATGTATCGATATATTTCACCA
362828 TGTATCGATACAATGTATTGATACACTATATCAATACTAAGTGAGTTTAGCTATTACCAATTTTA
521 TGTATCGATACAATGTATTGATACACTATATCAATACTAAGTGAGTTTAGCTATTACCAATTTTA
362893 GTATCGATGCAGTTCAGTGTGTATCGATATCAAGAACATACCAAGGTAA
586 GTATCGATGCAGTTCAGTGTGTATCGATATCAAGAACATACCAAGGTAA
*
362942 AGGTAAAGGTACAACCTTACAACACTTATCTTTTCATGGCTAAGATAATAACCTCTCAATCTCTC
1 AGGTAAAGGTACAACCTTACAACACTTATCTTTTCAAGGCTAAGATAATAACCTCTCAATCTCTC
363007 CAAGAATTATACCTCAAATTCTTAAGAGATTGTACACCAAGGTTGAATACAACCTTTATGACACA
66 CAAGAATTATACCTCAAATTCTTAAGAGATTGTACACCAAGGTTGAATACAACCTTTATGACACA
363072 AAGAGATTTTATAAACGAGAAATGCCTCTAAGTAGGCTGGTGTTTGTGAAGGTATAAGCACAAAA
131 AAGAGATTTTATAAACGAGAAATGCCTCTAAGTAGGCTGGTGTTTGTGAAGGTATAAGCACAAAA
363137 GAATACAAATGAGCTTCAAAGAATAACAGCCATGAATATAAAAGCTCTTACAAATATAGAAAATG
196 GAATACAAATGAGCTTCAAAGAATAACAGCCATGAATATAAAAGCTCTTACAAATATAGAAAATG
363202 ATAAAACTTTAAATGCTTGGATTTTTTGATGTTTCTTGTTGGTTCTTGTTGTTCTTTAGCTATTG
261 ATAAAACTTTAAATGCTTGGATTTTTTGATGTTTCTTGTTGGTTCTTGTTGTTCTTTAGCTATTG
363267 AAAACTCATATTTATAGGCTAGAATGTTGACATAATCATTGGAGGTTGAATGATTGTGTTTGTAG
326 AAAACTCATATTTATAGGCTAGAATGTTGACATAATCATTGGAGGTTGAATGATTGTGTTTGTAG
363332 CTGTTGTTGACTTGTTTGGAGCTTATTTTCGCACATTCACGCTCCTATGTATCGATACTTATCAT
391 CTGTTGTTGACTTGTTTGGAGCTTATTTTCGCACATTCACGCTCCTATGTATCGATACTTATCAT
363397 AATGTATTGATACATGCATTTGAAATTTATAGCCGTTGGGTTCAATGTATCGATATATTTCACCA
456 AATGTATTGATACATGCATTTGAAATTTATAGCCGTTGGGTTCAATGTATCGATATATTTCACCA
363462 TGTATCGATACAATGTATTGATACACTATATCAATACTAAGTGAGTTTAGCTATTACCAATTTTA
521 TGTATCGATACAATGTATTGATACACTATATCAATACTAAGTGAGTTTAGCTATTACCAATTTTA
363527 GTATCGATGCAGTTCAGTGTGTATCGATATCAAGAACAT
586 GTATCGATGCAGTTCAGTGTGTATCGATATCAAGAACAT
363566 GTATCGATAC
Statistics
Matches: 623, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
634 623 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (634 bp):
AGGTAAAGGTACAACCTTACAACACTTATCTTTTCAAGGCTAAGATAATAACCTCTCAATCTCTC
CAAGAATTATACCTCAAATTCTTAAGAGATTGTACACCAAGGTTGAATACAACCTTTATGACACA
AAGAGATTTTATAAACGAGAAATGCCTCTAAGTAGGCTGGTGTTTGTGAAGGTATAAGCACAAAA
GAATACAAATGAGCTTCAAAGAATAACAGCCATGAATATAAAAGCTCTTACAAATATAGAAAATG
ATAAAACTTTAAATGCTTGGATTTTTTGATGTTTCTTGTTGGTTCTTGTTGTTCTTTAGCTATTG
AAAACTCATATTTATAGGCTAGAATGTTGACATAATCATTGGAGGTTGAATGATTGTGTTTGTAG
CTGTTGTTGACTTGTTTGGAGCTTATTTTCGCACATTCACGCTCCTATGTATCGATACTTATCAT
AATGTATTGATACATGCATTTGAAATTTATAGCCGTTGGGTTCAATGTATCGATATATTTCACCA
TGTATCGATACAATGTATTGATACACTATATCAATACTAAGTGAGTTTAGCTATTACCAATTTTA
GTATCGATGCAGTTCAGTGTGTATCGATATCAAGAACATACCAAGGTAA
Found at i:363580 original size:13 final size:13
Alignment explanation
Indices: 363564--363588 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
363554 TATCAAGAAC
363564 ATGTATCGATACA
1 ATGTATCGATACA
363577 ATGTATCGATAC
1 ATGTATCGATAC
363589 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:363587 original size:32 final size:33
Alignment explanation
Indices: 363546--363609 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
363536 CAGTTCAGTG
363546 TGTATCGATA-TCAAG-AACATGTATCGATACAA
1 TGTATCGATACT-AAGCAACATGTATCGATACAA
*
363578 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACTAAGCAACATGTATCGATACA
363610 TCTAGGTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (33 bp):
TGTATCGATACTAAGCAACATGTATCGATACAA
Found at i:364618 original size:156 final size:155
Alignment explanation
Indices: 364353--365204 Score: 550
Period size: 156 Copynumber: 5.5 Consensus size: 155
364343 CATCGGCAAT
* * * * * * ** ** * *
364353 CTTTTTAAGTCCATTAGTGGTATTGGGAACTTTTAAGTC-AAAGGTATCCCCTAAAGGCATTTTC
1 CTTTTTAAGTCCTTTAGGGGTATCGAGTACTTTTACGTCGAAA-GTATCCTTTAGGGGTATTTTT
* * * * * * * * * * *
364417 GTAATTTTTCAAAATCGAGTCCTAGGTTGTTACTGAGTTCACTTTTTATGCGAGAGGTAGATATT
65 GTAATTTTTTAGAAGCAAGTCCTAGGTTGTCACCGAGTCCGC-TTTTATGCGAAAGGTGGGTATT
* *
364482 TAGGATAGGTTCATCTCATCTATTATC
129 TAGGATAGGTTCATCCCATCTATAATC
* *
364509 CTTTTTAAGTCCTATAGGGGTATCGAGTACTTTTACGTCGAAAATATCCTTTAGGGGTATTTTTG
1 CTTTTTAAGTCCTTTAGGGGTATCGAGTACTTTTACGTCGAAAGTATCCTTTAGGGGTATTTTTG
* ** * * *
364574 TAATTTTTTAGAA-CAAACTCCTAGGTTGTCGTCGGGTCCGCTTTTACAT-C-AAAGGT-GGCAG
66 TAATTTTTTAGAAGC-AAGTCCTAGGTTGTCACCGAGTCCGCTTTT--ATGCGAAAGGTGGGTAT
*
364635 TTAGGATAGGTTCATCCCAT-T-TCAAAC
128 TTAGGATAGGTTCATCCCATCTAT-AATC
* * * * * * * *
364662 ATTTTTTAGTCCTTTAGAGGTA-CTAGGTACTTGTACGTC-AAAGGTAT-CTCCTAAGGATATTT
1 CTTTTTAAGTCCTTTAGGGGTATCGA-GTACTTTTACGTCGAAA-GTATCCT-TTAGGGGTATTT
* * * * * *
364724 TTGTAATTTTTTA-AAGCTGAGTCTTAGGTTGTCACCGAGTCTGCTTTTATGCTG-TAGGTTGAT
63 TTGTAATTTTTTAGAAGC-AAGTCCTAGGTTGTCACCGAGTCCGCTTTTATGC-GAAAGGTGGGT
* * *
364787 ATTTAGGGTAGGTTCATCCCAGTTTA-AATT
126 ATTTAGGATAGGTTCATCCCA-TCTATAATC
* * * * * *
364817 CTTTTTAAGTTCTTTAGGGTTGTCGAGATACTTTTACGTCG-AAGATATACATATAGGGGCATTT
1 CTTTTTAAGTCCTTTAGGGGTATCGAG-TACTTTTACGTCGAAAG-TAT-CCTTTAGGGGTATTT
* * * * * * * * *
364881 TTGTTATTTTTTATAATCAAGTTCTAGGTTGTTACCGGGTCCGCTTTTATGCCAAAGGGGGGCAT
63 TTGTAATTTTTTAGAAGCAAGTCCTAGGTTGTCACCGAGTCCGCTTTTATGCGAAAGGTGGGTAT
* *
364946 TTAGGATAGGTTCATCCCATCTCTAGT-
128 TTAGGATAGGTTCATCCCATCTATAATC
* *** * ** ** *
364973 CTTTTCAAGTCCTTTAGTATTATCGGGGTACTTTTACGTC-AAAGGTATACCCGTAAAGGTACTT
1 CTTTTTAAGTCCTTTAGGGGTATC-GAGTACTTTTACGTCGAAA-GTAT-CCTTTAGGGGTATTT
* * * * *
365037 TTGTAATTTTCTAGAACCAAGTCCTAAGTTGTCACCAAGTCCGCTTTGATGCTG-AAGGTGGGTA
63 TTGTAATTTTTTAGAAGCAAGTCCTAGGTTGTCACCGAGTCCGCTTTTATGC-GAAAGGTGGGTA
* *
365101 TTTAGGATAGTTTCAGCCCCATCTATAATC
127 TTTAGGATAGGTTCA-TCCCATCTATAATC
* * ** * * * * **
365131 ATTTTTAAGTCCTTTAGGGGTATCAAAAACTTTTACGTTGAAGGTATCCCTTAGGGGCATTTTCA
1 CTTTTTAAGTCCTTTAGGGGTATCGAGTACTTTTACGTCGAAAGTATCCTTTAGGGGTATTTTTG
365196 TAATTTTTT
66 TAATTTTTT
365205 TTAAACTTAG
Statistics
Matches: 527, Mismatches: 137, Indels: 64
0.72 0.19 0.09
Matches are distributed among these distances:
151 2 0.00
152 11 0.02
153 86 0.16
154 41 0.08
155 31 0.06
156 225 0.43
157 106 0.20
158 25 0.05
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (155 bp):
CTTTTTAAGTCCTTTAGGGGTATCGAGTACTTTTACGTCGAAAGTATCCTTTAGGGGTATTTTTG
TAATTTTTTAGAAGCAAGTCCTAGGTTGTCACCGAGTCCGCTTTTATGCGAAAGGTGGGTATTTA
GGATAGGTTCATCCCATCTATAATC
Found at i:365168 original size:313 final size:306
Alignment explanation
Indices: 364471--365204 Score: 753
Period size: 313 Copynumber: 2.4 Consensus size: 306
364461 TTTATGCGAG
* * * * * *
364471 AGGTAGATATTTAGGATAGGTTCATCTCATCTATTATCCTTTTTAAGTCCTATAGGGGTATCGAG
1 AGGTGGATATTTAGGATAGGTTCATCCCATCTATAAT-CTTTTTAAGTCCTTTAGGGGTATCAAA
* *
364536 TACTTTTACGTCGAAAATATCCTTTAGGGGTATTTTTGTAATTTTTTAGAACAAACTCCTAGGTT
65 TACTTTTACGTCGAAGATATCC-TTAGGGGCATTTTTGTAATTTTTTAGAACAAACTCCTAGGTT
** * * *
364601 GTCGTCGGGTCCGCTTTTACATCAAAGGTGGCAGTTAGGATAGGTTCATCCCATTTCAAACATTT
129 GTCACCGGGTCCGCTTTTACACCAAAGGGGGCAGTTAGGATAGGTTCATCCCATCTCAAACATTT
** * *
364666 TTTAGTCCTTTAGAGGTACTAGGTACTTGTACGTCAAAGGTATCTCCTAAGGATATTTTTGTAAT
194 TCAAGTCCTTTAGAGGTACGAGGTACTTGTACGTCAAAGGTATCTCCTAAGGATACTTTTGTAAT
* ** * * * * * *
364731 TTTTTAAAGCTGAGTCTTAGGTTGTCACCGAGTCTGCTTTTATGCTGT
259 TTTCTAAAGCCAAGTCCTAAGTTGTCACCAAGTCCGCTTTGATGCTGA
* * * * * *
364779 AGGTTGATATTTAGGGTAGGTTCATCCCAGTTTA-AATTCTTTTTAAGTTCTTTAGGGTTGTCGA
1 AGGTGGATATTTAGGATAGGTTCATCCCA-TCTATAA-TCTTTTTAAGTCCTTTAGGGGTATC-A
* * * * * *
364843 GATACTTTTACGTCGAAGATATACATATAGGGGCATTTTTGTTATTTTTTATAATC-AAGTTCTA
63 AATACTTTTACGTCGAAGATAT-CCT-TAGGGGCATTTTTGTAATTTTTTAGAA-CAAACTCCTA
* ** * *
364907 GGTTGTTACCGGGTCCGCTTTTATGCCAAAGGGGGGCATTTAGGATAGGTTCATCCCATCTCTAG
125 GGTTGTCACCGGGTCCGCTTTTACACCAAA-GGGGGCAGTTAGGATAGGTTCATCCCATCTC-AA
* * * *
364972 TC-TTTTCAAGTCCTTTAGTA-TTATCGGGGTACTTTTACGTCAAAGGTATAC-CCGTAAAGG-T
188 ACATTTTCAAGTCCTTTAG-AGGTA-CGAGGTACTTGTACGTCAAAGGTAT-CTCC-T-AAGGAT
365033 ACTTTTGTAATTTTCTAGAA-CCAAGTCCTAAGTTGTCACCAAGTCCGCTTTGATGCTGA
248 ACTTTTGTAATTTTCTA-AAGCCAAGTCCTAAGTTGTCACCAAGTCCGCTTTGATGCTGA
* * *
365092 AGGTGGGTATTTAGGATAGTTTCAGCCCCATCTATAATCATTTTTAAGTCCTTTAGGGGTATCAA
1 AGGTGGATATTTAGGATAGGTTCA-TCCCATCTATAATC-TTTTTAAGTCCTTTAGGGGTATCAA
* * * **
365157 AAACTTTTACGTTGAAGGTATCCCTTAGGGGCATTTTCATAATTTTTT
64 ATACTTTTACGTCGAAGATAT-CCTTAGGGGCATTTTTGTAATTTTTT
365205 TTAAACTTAG
Statistics
Matches: 345, Mismatches: 64, Indels: 30
0.79 0.15 0.07
Matches are distributed among these distances:
308 47 0.14
309 24 0.07
310 55 0.16
311 45 0.13
312 47 0.14
313 95 0.28
314 32 0.09
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (306 bp):
AGGTGGATATTTAGGATAGGTTCATCCCATCTATAATCTTTTTAAGTCCTTTAGGGGTATCAAAT
ACTTTTACGTCGAAGATATCCTTAGGGGCATTTTTGTAATTTTTTAGAACAAACTCCTAGGTTGT
CACCGGGTCCGCTTTTACACCAAAGGGGGCAGTTAGGATAGGTTCATCCCATCTCAAACATTTTC
AAGTCCTTTAGAGGTACGAGGTACTTGTACGTCAAAGGTATCTCCTAAGGATACTTTTGTAATTT
TCTAAAGCCAAGTCCTAAGTTGTCACCAAGTCCGCTTTGATGCTGA
Found at i:376033 original size:17 final size:18
Alignment explanation
Indices: 376013--376056 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
376003 AAATTAAAAC
376013 TAAATAAAAGAAAAT-AA
1 TAAATAAAAGAAAATAAA
376030 TAAAT-AAAGAAAATAAA
1 TAAATAAAAGAAAATAAA
*
376047 AAAATAAAAG
1 TAAATAAAAG
376057 CTTAAGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 9 0.38
17 11 0.46
18 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (18 bp):
TAAATAAAAGAAAATAAA
Found at i:376037 original size:21 final size:21
Alignment explanation
Indices: 376013--376054 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
376003 AAATTAAAAC
* *
376013 TAAATAAAAGAAAATAATAAA
1 TAAAGAAAAGAAAAAAATAAA
*
376034 TAAAGAAAATAAAAAAATAAA
1 TAAAGAAAAGAAAAAAATAAA
376055 AGCTTAAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (21 bp):
TAAAGAAAAGAAAAAAATAAA
Found at i:382050 original size:3 final size:3
Alignment explanation
Indices: 382042--382069 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
382032 TCAACCATCA
382042 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
382070 AGTTGACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:383804 original size:22 final size:22
Alignment explanation
Indices: 383776--383818 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
383766 TATTCAAAAT
383776 GAAAAAGGTTACTCTTTATCTC
1 GAAAAAGGTTACTCTTTATCTC
383798 GAAAAAGGTTACTCTTTATCT
1 GAAAAAGGTTACTCTTTATCT
383819 AATATAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (22 bp):
GAAAAAGGTTACTCTTTATCTC
Found at i:384955 original size:13 final size:13
Alignment explanation
Indices: 384937--384962 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
384927 CAATTTTTTG
384937 TGTATCGATACAT
1 TGTATCGATACAT
384950 TGTATCGATACAT
1 TGTATCGATACAT
384963 ACTTGCTGTA
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:385047 original size:20 final size:20
Alignment explanation
Indices: 385022--385094 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
385012 CAACTTTTTT
385022 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
385042 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
385063 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
385083 ATGTATCGATAC
1 ATGTATCGATAC
385095 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:385060 original size:41 final size:41
Alignment explanation
Indices: 385001--385094 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
384991 CTGCCAAGAA
*
385001 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
385042 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
385083 ATGTATCGATAC
1 ATGTATCGATAC
385095 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:385076 original size:21 final size:21
Alignment explanation
Indices: 385001--385076 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
384991 CTGCCAAGAA
* *
385001 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
385022 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
385042 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
385063 ATGTATCGATACAT
1 ATGTATCGATACAT
385077 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:386106 original size:83 final size:83
Alignment explanation
Indices: 385967--386136 Score: 340
Period size: 83 Copynumber: 2.0 Consensus size: 83
385957 TTCTTCAATA
385967 TTTTCAATTTCTTCCTTTATAACAAATAATCAATTCTATTTCTCTACGAATTCTCCCCCATTGTG
1 TTTTCAATTTCTTCCTTTATAACAAATAATCAATTCTATTTCTCTACGAATTCTCCCCCATTGTG
386032 AAACATCTTTTTCCCCCT
66 AAACATCTTTTTCCCCCT
386050 TTTTCAATTTCTTCCTTTATAACAAATAATCAATTCTATTTCTCTACGAATTCTCCCCCATTGTG
1 TTTTCAATTTCTTCCTTTATAACAAATAATCAATTCTATTTCTCTACGAATTCTCCCCCATTGTG
386115 AAACATCTTTTTCCCCCT
66 AAACATCTTTTTCCCCCT
386133 TTTT
1 TTTT
386137 ATCAGGCCAA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 87 1.00
ACGTcount: A:0.25, C:0.27, G:0.04, T:0.45
Consensus pattern (83 bp):
TTTTCAATTTCTTCCTTTATAACAAATAATCAATTCTATTTCTCTACGAATTCTCCCCCATTGTG
AAACATCTTTTTCCCCCT
Found at i:390514 original size:13 final size:13
Alignment explanation
Indices: 390496--390520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
390486 CAATTTTTTG
390496 TGTATCGATACAT
1 TGTATCGATACAT
390509 TGTATCGATACA
1 TGTATCGATACA
390521 AGTTTGGCTA
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:390587 original size:20 final size:20
Alignment explanation
Indices: 390562--390634 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
390552 CAACTTTTTT
390562 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
390582 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
390603 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
390623 ATGTATCGATAC
1 ATGTATCGATAC
390635 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:390600 original size:41 final size:41
Alignment explanation
Indices: 390541--390634 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
390531 CTGCCAAGAA
*
390541 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
390582 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
390623 ATGTATCGATAC
1 ATGTATCGATAC
390635 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:390616 original size:21 final size:21
Alignment explanation
Indices: 390541--390616 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
390531 CTGCCAAGAA
* *
390541 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
390562 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
390582 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
390603 ATGTATCGATACAT
1 ATGTATCGATACAT
390617 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:394711 original size:19 final size:19
Alignment explanation
Indices: 394687--394743 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
394677 TGTATCGATA
* *
394687 CATTGTATCAATACATGTT
1 CATTGTATCGATACATGAT
394706 CATTGTATCGATACATGGAT
1 CATTGTATCGATACAT-GAT
*
394726 AATTGTATCGATACATGA
1 CATTGTATCGATACATGA
394744 AACTAGCAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:394732 original size:20 final size:20
Alignment explanation
Indices: 394683--394742 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
394673 GCTTTGTATC
*
394683 GATACATTGTATCAATACAT-
1 GATA-ATTGTATCGATACATG
* *
394703 GTTCATTGTATCGATACATG
1 GATAATTGTATCGATACATG
394723 GATAATTGTATCGATACATG
1 GATAATTGTATCGATACATG
394743 AAACTAGCAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 14 0.41
20 20 0.59
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (20 bp):
GATAATTGTATCGATACATG
Found at i:398947 original size:13 final size:13
Alignment explanation
Indices: 398929--398955 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
398919 ACATTATGCT
398929 TTGTATCGATACA
1 TTGTATCGATACA
398942 TTGTATCGATACA
1 TTGTATCGATACA
398955 T
1 T
398956 GTTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:398985 original size:20 final size:19
Alignment explanation
Indices: 398939--398995 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
398929 TTGTATCGAT
*
398939 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
398958 TCATTGTATCAATACATGG
1 ACATTGTATCGATACATGG
398977 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
398996 AAACTAGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:399058 original size:13 final size:13
Alignment explanation
Indices: 399040--399070 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
399030 CGATACATGG
399040 TACATTATATCGA
1 TACATTATATCGA
*
399053 TACATTGTATCGA
1 TACATTATATCGA
399066 TACAT
1 TACAT
399071 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (13 bp):
TACATTATATCGA
Found at i:399064 original size:33 final size:33
Alignment explanation
Indices: 399024--399092 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
399014 CTACCATTGT
*
399024 TTGTATCGATACATGGT-ACATTATATCGATACA
1 TTGTATCGATACATGATGA-ATTATATCGATACA
*
399057 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTATATCGATACA
399090 TTG
1 TTG
399093 CTTTTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTATATCGATACA
Found at i:407175 original size:22 final size:22
Alignment explanation
Indices: 407150--407191 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
407140 AATTTTTTGA
*
407150 TTTGACAAAGGGGGAGAAATGC
1 TTTGACAAAGGGGGAAAAATGC
407172 TTTGACAAAGGGGGAAAAAT
1 TTTGACAAAGGGGGAAAAAT
407192 ATGTTTATCT
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:0.40, C:0.07, G:0.33, T:0.19
Consensus pattern (22 bp):
TTTGACAAAGGGGGAAAAATGC
Found at i:407803 original size:13 final size:13
Alignment explanation
Indices: 407785--407811 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
407775 ACATTATGCT
407785 TTGTATCGATACA
1 TTGTATCGATACA
407798 TTGTATCGATACA
1 TTGTATCGATACA
407811 T
1 T
407812 ATTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:407826 original size:32 final size:33
Alignment explanation
Indices: 407766--407830 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
407756 CACATCCAGA
*
407766 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATTATGCATTGTATCGATACAT
*
407799 TGTATCGATACA-TATTCATTGTATCGATACAT
1 TGTATCGATACATTATGCATTGTATCGATACAT
407831 GGACAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTATGCATTGTATCGATACAT
Found at i:407841 original size:20 final size:19
Alignment explanation
Indices: 407795--407851 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
407785 TTGTATCGAT
**
407795 ACATTGTATCGATACATAT
1 ACATTGTATCGATACATGG
*
407814 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
407833 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
407852 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:407914 original size:13 final size:13
Alignment explanation
Indices: 407896--407948 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
407886 CGATACATGG
*
407896 TACATTGTATCTA
1 TACATTGTATCGA
407909 TACATTGTATCGA
1 TACATTGTATCGA
407922 TACA-TG-AT-G-
1 TACATTGTATCGA
407931 -A-ATTGTATCGA
1 TACATTGTATCGA
407942 TACATTG
1 TACATTG
407949 CTTGTAACGA
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 20 0.61
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:407921 original size:33 final size:33
Alignment explanation
Indices: 407883--407948 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
407873 TCATTGTTTA
* *
407883 TATCGATACATGGT-ACATTGTATCTATACATTG
1 TATCGATACATGATGA-ATTGTATCGATACATTG
407916 TATCGATACATGATGAATTGTATCGATACATTG
1 TATCGATACATGATGAATTGTATCGATACATTG
407949 CTTGTAACGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (33 bp):
TATCGATACATGATGAATTGTATCGATACATTG
Found at i:410853 original size:13 final size:13
Alignment explanation
Indices: 410828--410857 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
410818 GATATAAATG
410828 TAATTTAATTTTT
1 TAATTTAATTTTT
410841 TAATTATAATTTTT
1 TAATT-TAATTTTT
410855 TAA
1 TAA
410858 AAGTTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TAATTTAATTTTT
Found at i:425962 original size:2 final size:2
Alignment explanation
Indices: 425955--426009 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
425945 CATGAGGAGG
425955 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
425997 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
426010 GCAGATAGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:429066 original size:17 final size:17
Alignment explanation
Indices: 429044--429184 Score: 63
Period size: 17 Copynumber: 8.5 Consensus size: 17
429034 TTGTATAATT
429044 TTTATATTATTATTATA
1 TTTATATTATTATTATA
*
429061 TTTATA--A-AATTATA
1 TTTATATTATTATTATA
* *
429075 TTTTTA-TA-TA-AAT-
1 TTTATATTATTATTATA
*
429088 TTTGATATAATT-TTAATA
1 TTT-ATATTATTATT-ATA
*
429106 TTTATATTATTTTTA-A
1 TTTATATTATTATTATA
429122 TATTATATTA-TATTATA
1 T-TTATATTATTATTATA
*
429139 TAATTAT-TTTTATATTATA
1 T--TTATATTAT-TATTATA
*
429158 TTTATGTTATATATT-TA
1 TTTATATTAT-TATTATA
429175 TATTATATTA
1 T-TTATATTA
429185 AATATTATCA
Statistics
Matches: 97, Mismatches: 12, Indels: 29
0.70 0.09 0.21
Matches are distributed among these distances:
13 3 0.03
14 15 0.15
15 4 0.04
16 7 0.07
17 35 0.36
18 25 0.26
19 8 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (17 bp):
TTTATATTATTATTATA
Found at i:429107 original size:56 final size:55
Alignment explanation
Indices: 429033--429141 Score: 143
Period size: 56 Copynumber: 2.0 Consensus size: 55
429023 TATTGATATC
*
429033 TTTGTATAATTTTTATA-TTATTATTATATTTATAAAATTATATT-T-TTATATAAAT
1 TTTGTATAATTTTAATATTTA-TATTAT-TTT-TAAAATTATATTATATTATATAAAT
*
429088 TTTGATATAATTTTAATATTTATATTATTTTTAATATTATATTATATTATATAA
1 TTTG-TATAATTTTAATATTTATATTATTTTTAAAATTATATTATATTATATAA
429142 TTATTTTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
54 11 0.23
55 8 0.17
56 26 0.54
57 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (55 bp):
TTTGTATAATTTTAATATTTATATTATTTTTAAAATTATATTATATTATATAAAT
Found at i:429154 original size:29 final size:29
Alignment explanation
Indices: 429069--429184 Score: 102
Period size: 29 Copynumber: 4.1 Consensus size: 29
429059 TATTTATAAA
*
429069 ATTATATT-T-TTATATAA--ATTTTGAT
1 ATTATATTATATTATATAATTATTTTTAT
* *
429094 ATAATTTTAATATT-TAT-ATTATTTTTAAT
1 ATTATATT-ATATTATATAATTATTTTT-AT
429123 ATTATATTATATTATATAATTATTTTTAT
1 ATTATATTATATTATATAATTATTTTTAT
* * *
429152 ATTATATTTATGTTATATATTTA-TATTAT
1 ATTATA-TTATATTATATAATTATTTTTAT
429181 ATTA
1 ATTA
429185 AATATTATCA
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
25 6 0.08
26 1 0.01
27 4 0.05
28 12 0.16
29 28 0.38
30 23 0.31
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTATATTATATTATATAATTATTTTTAT
Found at i:429156 original size:24 final size:25
Alignment explanation
Indices: 429107--429201 Score: 94
Period size: 24 Copynumber: 4.0 Consensus size: 25
429097 ATTTTAATAT
*
429107 TTATATTAT-TTTTA-ATA-TTATA
1 TTATATTATATATTATATATTTATA
429129 TTATATTATATAATTAT-T-TTTATA
1 TTATATTATAT-ATTATATATTTATA
*
429153 TTATATT-TATGTTATATATTTATA
1 TTATATTATATATTATATATTTATA
* *
429177 TTATATTAAATATTATCAAATTTAT
1 TTATATTATATATTAT-ATATTTAT
429202 TAAACGAAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
22 13 0.22
23 5 0.08
24 29 0.48
25 6 0.10
26 7 0.12
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (25 bp):
TTATATTATATATTATATATTTATA
Found at i:429320 original size:2 final size:2
Alignment explanation
Indices: 429313--429341 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
429303 CATCTTATTT
429313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
429342 TTTTTTTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:430075 original size:34 final size:35
Alignment explanation
Indices: 430041--430106 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
430031 TTCAAGATTA
*
430041 AAATATAT-CATAGATTT-TTAAAAA-AATTATATT
1 AAATATATAAATAG-TTTATTAAAAATAATTATATT
*
430074 AAATTTATAAATAGTTTATTAAAAATAATTATA
1 AAATATATAAATAGTTTATTAAAAATAATTATA
430107 AATAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 10 0.36
34 11 0.39
35 7 0.25
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (35 bp):
AAATATATAAATAGTTTATTAAAAATAATTATATT
Found at i:431314 original size:25 final size:24
Alignment explanation
Indices: 431284--431380 Score: 74
Period size: 25 Copynumber: 4.0 Consensus size: 24
431274 TTTAATTTTT
*
431284 ATTTATTATTAAAATATTAAAAAT
1 ATTTATTATTAAAATATTAAAAAA
* *
431308 ATGTTA-TATTAATATTTTTAAAAAA
1 AT-TTATTATTAA-AATATTAAAAAA
*
431333 ATTTATAATTAAAATA--AGAAAAA
1 ATTTATTATTAAAATATTA-AAAAA
* *
431356 ATTTATTTAATATAAATAGTAAAAA
1 ATTTA-TTATTA-AAATATTAAAAA
431381 TTAGACTTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
22 1 0.02
23 10 0.18
24 17 0.30
25 24 0.42
26 4 0.07
27 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (24 bp):
ATTTATTATTAAAATATTAAAAAA
Found at i:431365 original size:21 final size:22
Alignment explanation
Indices: 431328--431370 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
431318 AATATTTTTA
431328 AAAAAATTTATAATTAAAATAAG
1 AAAAAATTTAT-ATTAAAATAAG
*
431351 AAAAAATTTAT-TTAATATAA
1 AAAAAATTTATATTAAAATAA
431371 ATAGTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAAAATTTATATTAAAATAAG
Found at i:432855 original size:20 final size:20
Alignment explanation
Indices: 432830--432883 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
432820 CTCTAAAAGG
432830 GCCCTTGTGTATCCATACAA
1 GCCCTTGTGTATCCATACAA
** *
432850 GCCCTTTGTGCCTTCATACAA
1 GCCC-TTGTGTATCCATACAA
*
432871 GCCTTTTGTGTAT
1 GCC-CTTGTGTAT
432884 GTTGGAGTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.37
Consensus pattern (20 bp):
GCCCTTGTGTATCCATACAA
Found at i:438664 original size:13 final size:13
Alignment explanation
Indices: 438646--438670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
438636 CAAAGATCAG
438646 TGTATCGATACAA
1 TGTATCGATACAA
438659 TGTATCGATACA
1 TGTATCGATACA
438671 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:438735 original size:19 final size:19
Alignment explanation
Indices: 438711--438777 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
438701 TAGTAGCTAA
438711 TTATGTATCGATACAACAC
1 TTATGTATCGATACAACAC
438730 TTATGTATCGAT---ACA-
1 TTATGTATCGATACAACAC
438745 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAACAC
438762 TTATGTATCGATACAA
1 TTATGTATCGATACAA
438778 ATCGTTGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.21
14 1 0.02
16 6 0.14
18 1 0.02
19 25 0.60
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (19 bp):
TTATGTATCGATACAACAC
Found at i:438751 original size:13 final size:13
Alignment explanation
Indices: 438733--438757 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
438723 ACAACACTTA
438733 TGTATCGATACAT
1 TGTATCGATACAT
438746 TGTATCGATACA
1 TGTATCGATACA
438758 ACACTTATGT
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:438755 original size:32 final size:32
Alignment explanation
Indices: 438714--438776 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
438704 TAGCTAATTA
438714 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
438746 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
438777 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:439543 original size:52 final size:51
Alignment explanation
Indices: 439465--439656 Score: 199
Period size: 49 Copynumber: 3.7 Consensus size: 51
439455 AAAAGGATGT
* ** * * *
439465 CAATGTGCTGATTCACGGTTAGCAACATTAGACTTGAAGATGAGAAGAATGC
1 CAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAGAAG-GTGC
* **
439517 CAATGTGCTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCAACATT-GGACTTAAAGATGA-GAAGGTGC
* * * *
439570 CAATATGCTAATTCAAGGCCAGCGATATTGGACTTAAAGAT--GAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAGAAGGTGC
* * *
439619 CAATGTACTGATTCAAGGCCAGCGACATTGGTCTTAAA
1 CAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAA
439657 AACAATTTGT
Statistics
Matches: 117, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
49 41 0.35
52 35 0.30
53 37 0.32
54 4 0.03
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (51 bp):
CAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAGAAGGTGC
Found at i:439584 original size:53 final size:52
Alignment explanation
Indices: 439465--439649 Score: 182
Period size: 53 Copynumber: 3.6 Consensus size: 52
439455 AAAAGGATGT
* ** * * *
439465 CAATGTGCTGATTCACGGTTAGCAACATT-AGACTTGAAGATGA-GAAGAATGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGGACTT-AAGATGATGAAG-GTGC
* * **
439517 CAATGTGCTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGGACTT-AAGATGATGAAGGTGC
* * *
439570 CAATATGCTAATTCAAGGCCAGCGATATT-GGACTTAA-A-GATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGGACTTAAGATGATGAAGGTGC
*
439619 CAATGTACTGATTCAAGGCCAGCGACATTGG
1 CAATGTGCTGATTCAAGGCCAGCGACATTGG
439650 TCTTAAAAAC
Statistics
Matches: 110, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
49 36 0.33
50 2 0.02
51 2 0.02
52 29 0.26
53 37 0.34
54 4 0.04
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGGACTTAAGATGATGAAGGTGC
Found at i:447842 original size:20 final size:20
Alignment explanation
Indices: 447817--447886 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
447807 ACCCTGAAAA
*
447817 GTATCGATACATATTTAAAT
1 GTATCGATACATATTCAAAT
* *
447837 GTATCGATACAGATTGC-ATT
1 GTATCGATACATATT-CAAAT
*
447857 GTATCGATACATGA-CCAAAT
1 GTATCGATACAT-ATTCAAAT
447877 GTATCGATAC
1 GTATCGATAC
447887 TTGAAAAAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 39 0.95
21 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (20 bp):
GTATCGATACATATTCAAAT
Found at i:447901 original size:21 final size:20
Alignment explanation
Indices: 447856--447908 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
447846 CAGATTGCAT
**
447856 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
*
447876 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAA-A
447897 TGTATCGATACA
1 TGTATCGATACA
447909 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:447977 original size:13 final size:13
Alignment explanation
Indices: 447959--447985 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
447949 TACACACAAT
447959 TTGTATCGATACA
1 TTGTATCGATACA
447972 TTGTATCGATACA
1 TTGTATCGATACA
447985 T
1 T
447986 CCTAAAATGT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:449596 original size:9 final size:9
Alignment explanation
Indices: 449582--449612 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
449572 CATCAAGAAC
449582 GATGAAGAT
1 GATGAAGAT
449591 GATGAAGAT
1 GATGAAGAT
*
449600 GATGATGAT
1 GATGAAGAT
449609 GATG
1 GATG
449613 GTGACTCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (9 bp):
GATGAAGAT
Found at i:453956 original size:8 final size:8
Alignment explanation
Indices: 453943--453968 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
453933 ATTTGATTAA
453943 ATTTTGTG
1 ATTTTGTG
453951 ATTTTGTG
1 ATTTTGTG
453959 ATTTTGTG
1 ATTTTGTG
453967 AT
1 AT
453969 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:454188 original size:13 final size:13
Alignment explanation
Indices: 454170--454194 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
454160 CAGCATTCTT
454170 TGTATCGATACAG
1 TGTATCGATACAG
454183 TGTATCGATACA
1 TGTATCGATACA
454195 AGGAGATTAT
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:456636 original size:20 final size:20
Alignment explanation
Indices: 456588--456644 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
456578 GTCAAAACCC
* *
456588 TGAAAAGTATCGATACATAT
1 TGAAATGTATCGATACAGAT
*
456608 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACAGAT
* * *
456628 TGCATTGTATTGATACA
1 TGAAATGTATCGATACA
456645 TTGTATCGAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAATGTATCGATACAGAT
Found at i:456671 original size:20 final size:21
Alignment explanation
Indices: 456646--456698 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
456636 ATTGATACAT
**
456646 TGTATCGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
*
456666 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
456687 TGTATCGATACA
1 TGTATCGATACA
456699 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:457967 original size:28 final size:28
Alignment explanation
Indices: 457927--457998 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
457917 GGAATAAAGC
** *
457927 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
457955 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
457983 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
457999 TCGATTATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:458056 original size:52 final size:52
Alignment explanation
Indices: 457987--458424 Score: 301
Period size: 51 Copynumber: 8.3 Consensus size: 52
457977 AAATAACGAG
*
457987 GTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* * ** * *
458039 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
*
458092 -TTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* * * * * * * *
458143 ATTGGAGTATCCCCGATTAAAGGAGAAATTGGT-GTTGTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* * * * *
458196 GTTGGAGTATCCCCGATTATGAAAAATCGATA-TTTTGAAAATAAAGTCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* **** * * *
458247 GTTGGAGTATCCCC--TCA-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTATGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
* * *
458302 GTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
*
458356 GTTGGAGTATCCCCGATTAT-AGAAAATT--AATGTTTT-GAAAGTAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTGGTAT-TTTTGGAAA-TAAAATCGGA
* *
458407 GTTGGAATATCCTCGATT
1 GTTGGAGTATCCCCGATT
458425 GTGGAGAATT
Statistics
Matches: 300, Mismatches: 58, Indels: 57
0.72 0.14 0.14
Matches are distributed among these distances:
48 4 0.01
49 4 0.01
50 5 0.02
51 81 0.27
52 81 0.27
53 61 0.20
54 35 0.12
55 17 0.06
56 3 0.01
57 3 0.01
58 5 0.02
59 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:458119 original size:104 final size:104
Alignment explanation
Indices: 457988--458427 Score: 435
Period size: 104 Copynumber: 4.2 Consensus size: 104
457978 AATAACGAGG
* *
457988 TTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
1 TTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
* *
458053 GATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
66 GATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGA
*
458092 TTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCC
1 TTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
* *
458157 GATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGGGG
66 GATTAAAGGA-AAATTGGTGTTTTGAAAATAAAACCGGGA
* * * * * *
458197 TTGGAGTATCCCCGATTATGAAAAATCGATA-TTTTGAAAATAAAGTCGGGGTTGGAGTATCCCC
1 TTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTAT-CCC
* * ** * ** ** * *
458261 TCAGAAATAACGG--GGTTGGAGTATCCCCGATGAT-TAA-CGGGG
65 -C-G-ATTAAAGGAAAATTGGTGT-T--TTGAAAATAAAACCGGGA
* *
458303 TTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 TTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
* ** * *
458368 CCGATTATA-GAAAATTAATGTTTTGAAAGTAAAATC-GGA
64 CCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGA
* *
458407 GTTGGAATATCCTCGATTGTG
1 -TTGGAGTATCCCCGATTGTG
458428 GAGAATTAAG
Statistics
Matches: 270, Mismatches: 50, Indels: 31
0.77 0.14 0.09
Matches are distributed among these distances:
103 3 0.01
104 102 0.38
105 84 0.31
106 32 0.12
107 10 0.04
108 13 0.05
109 26 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (104 bp):
TTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
GATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGA
Found at i:458306 original size:27 final size:28
Alignment explanation
Indices: 458243--458318 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
458233 AAAATAAAGT
*
458243 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
458271 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
458298 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
458319 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:460801 original size:13 final size:13
Alignment explanation
Indices: 460783--460808 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
460773 ACAAAGATCC
460783 ATGTATCGATACA
1 ATGTATCGATACA
460796 ATGTATCGATACA
1 ATGTATCGATACA
460809 CAGAAAAATG
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:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:460804 original size:33 final size:33
Alignment explanation
Indices: 460762--460828 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
460752 AAAATTTCCA
***
460762 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
460795 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
460828 A
1 A
460829 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:460872 original size:19 final size:18
Alignment explanation
Indices: 460848--460915 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
460838 CAGTAGCTAA
460848 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
460867 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
460882 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
460899 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
460916 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:460888 original size:13 final size:13
Alignment explanation
Indices: 460870--460894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
460860 ACAATACTTA
460870 TGTATCGATACAT
1 TGTATCGATACAT
460883 TGTATCGATACA
1 TGTATCGATACA
460895 AAACTTATGT
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:460892 original size:32 final size:32
Alignment explanation
Indices: 460851--460913 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
460841 TAGCTAATTA
*
460851 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
460883 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
460914 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:464638 original size:13 final size:13
Alignment explanation
Indices: 464620--464645 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
464610 TACACAAAGT
464620 ATGTATCGATACA
1 ATGTATCGATACA
464633 ATGTATCGATACA
1 ATGTATCGATACA
464646 CCAAAACATG
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:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:464643 original size:32 final size:33
Alignment explanation
Indices: 464602--464665 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
464592 TAGCCAAACT
**
464602 TGTATCGATACA-CAAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAACATGTATCGATACAA
464634 TGTATCGATACACCAAAACATGTATCGATACA
1 TGTATCGATACACCAAAACATGTATCGATACA
464666 TTAGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACACCAAAACATGTATCGATACAA
Found at i:468014 original size:13 final size:13
Alignment explanation
Indices: 467996--468021 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
467986 CAATTTTTTG
467996 TGTATCGATACAT
1 TGTATCGATACAT
468009 TGTATCGATACAT
1 TGTATCGATACAT
468022 ACTTGCTGTA
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:468105 original size:20 final size:20
Alignment explanation
Indices: 468060--468132 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
468050 CTGCTAAGAA
***
468060 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGAATC
468081 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
468101 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
468121 ATGTATCGATAC
1 ATGTATCGATAC
468133 TTTTAAGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.64
21 14 0.31
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:468133 original size:20 final size:20
Alignment explanation
Indices: 468080--468135 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
468070 ACATCTTTTT
*
468080 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
468100 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
468119 TTATGTATCGATACTTT
1 -CATGTATCGATACTTT
468136 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:468820 original size:27 final size:27
Alignment explanation
Indices: 468782--468837 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
468772 TAATCAAGTA
468782 ATTCATATCAAAAATTTATTTGCACAT
1 ATTCATATCAAAAATTTATTTGCACAT
468809 ATTCATATCAAAAATTTATTTGCACAT
1 ATTCATATCAAAAATTTATTTGCACAT
468836 AT
1 AT
468838 CTATTTTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (27 bp):
ATTCATATCAAAAATTTATTTGCACAT
Found at i:470448 original size:21 final size:21
Alignment explanation
Indices: 470424--470470 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
470414 TTTGATGCTG
470424 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
470444 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
470465 ATTTTG
1 ATTTTG
470471 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:470609 original size:13 final size:13
Alignment explanation
Indices: 470591--470629 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
470581 ATAATCACCC
*
470591 TGTATCGATACAG
1 TGTATCGATACAA
470604 TGTATCGATACAA
1 TGTATCGATACAA
470617 TGTATCGATACAA
1 TGTATCGATACAA
470630 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:470640 original size:20 final size:20
Alignment explanation
Indices: 470615--470693 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
470605 GTATCGATAC
470615 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
470635 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
470660 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
470680 CATGTATCGATACA
1 AATGTATCGATACA
470694 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:472729 original size:15 final size:15
Alignment explanation
Indices: 472709--472739 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
472699 ATTTCGTTTG
*
472709 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
472724 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
472739 G
1 G
472740 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:474571 original size:21 final size:21
Alignment explanation
Indices: 474542--474586 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
474532 AAGTTTTCAT
*
474542 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
474562 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
474584 TTT
1 TTT
474587 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:476823 original size:13 final size:13
Alignment explanation
Indices: 476805--476830 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
476795 CAATTTTTTG
476805 TGTATCGATACAT
1 TGTATCGATACAT
476818 TGTATCGATACAT
1 TGTATCGATACAT
476831 ACTTGCTGTA
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:479417 original size:20 final size:20
Alignment explanation
Indices: 479394--479468 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
479384 AAATACCTAG
479394 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
** * * *
479414 ATGTATTAATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
479434 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
479454 ATGTATCGATACATT
1 ATGTATCGATACATT
479469 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:479466 original size:40 final size:39
Alignment explanation
Indices: 479394--479471 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
479384 AAATACCTAG
* *
479394 ATGTATCGATACATTTTTCAATGTATTAATACATGTATGA
1 ATGTATCGATACATTCTTCAATGTATCAATACAT-TATGA
*
479434 ATGTATCGATACATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATGTATCAATACATTATG
479472 TCTTTTTACT
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:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATGTATCAATACATTATGA
Found at i:479510 original size:51 final size:51
Alignment explanation
Indices: 479434--479569 Score: 229
Period size: 51 Copynumber: 2.7 Consensus size: 51
479424 ACATGTATGA
479434 ATGTATCGATACATTCTTCAATGTATCGATACATTATGTCTTTTTA-CTCAG
1 ATGTATCGATACATTCTTCAATGTATCGATACATTATGTCTTTTTACCT-AG
*
479485 ATGTATCGATACATTCTTCAATGTATCGATACATTTTGTCTTTTTACCTAG
1 ATGTATCGATACATTCTTCAATGTATCGATACATTATGTCTTTTTACCTAG
* *
479536 ATGTATCGATATATTTTTCAATGTATCGATACAT
1 ATGTATCGATACATTCTTCAATGTATCGATACAT
479570 CTAGTTAAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
51 79 0.98
52 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (51 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATTATGTCTTTTTACCTAG
Found at i:479526 original size:24 final size:20
Alignment explanation
Indices: 479394--479519 Score: 92
Period size: 20 Copynumber: 5.8 Consensus size: 20
479384 AAATACCTAG
*
479394 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
** * *
479414 ATGTATTAATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
479434 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
479454 ATGTATCGATACATTATGTCTTTTTACTCA
1 ATGTATCGATAC---AT-TC----T--TCA
479484 GATGTATCGATACATTCTTCA
1 -ATGTATCGATACATTCTTCA
479505 ATGTATCGATACATT
1 ATGTATCGATACATT
479520 TTGTCTTTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
19 1 0.01
20 55 0.65
21 4 0.05
23 3 0.04
24 2 0.02
27 2 0.02
28 3 0.04
30 3 0.04
31 12 0.14
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:484827 original size:19 final size:19
Alignment explanation
Indices: 484803--484844 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
484793 TTATATAAAT
*
484803 AATTTA-TTAAATAATTATA
1 AATTTATTTAAA-AACTATA
484822 AATTTATTTAAAAACTATA
1 AATTTATTTAAAAACTATA
484841 AATT
1 AATT
484845 ACAACAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTTATTTAAAAACTATA
Found at i:493064 original size:79 final size:79
Alignment explanation
Indices: 492896--493260 Score: 314
Period size: 79 Copynumber: 4.6 Consensus size: 79
492886 CTTGGAATAT
* * *
492896 GGGGTTGGAGTATCCCCGAGATGAAAAATTTAATATTTTT-GAAATTAAAAAATGAGGTTGGAGT
1 GGGGTTGGAGTATCCCTGAGATGAAAAA-TTAATATTTTTGGAAA-T-AAAAACGGGGTTGGAGT
*
492960 ATCTCCTCTG-AAATAAC
63 ATCCCCTC-GAAAATAAC
* * ** *
492977 GGGATTGGAGTATCTCTGAGATGAAAAATCGATATTTTTGGAAATAAAAACGGGGCTGGAGTATC
1 GGGGTTGGAGTATCCCTGAGATGAAAAATTAATATTTTTGGAAATAAAAACGGGGTTGGAGTATC
493042 CCCTCGAAAATAAC
66 CCCTCGAAAATAAC
* * *
493056 GGGGTTGGAGTA-CCCTTA-A-GAAAAATTTAATA-TTTTGAAAATAAAAACGGAGTTGGAGTAT
1 GGGGTTGGAGTATCCCTGAGATGAAAAA-TTAATATTTTTGGAAATAAAAACGGGGTTGGAGTAT
* * *
493117 CCCCTCGAAATTGAT
65 CCCCTCGAAAATAAC
* * * * * * * * **
493132 AGAGTTAGAGTATCCCCGAGATGAAAATTTTAATATTTTT-GAAACAAAAATGGTGTTAAAGTAT
1 GGGGTTGGAGTATCCCTGAGATGAAAA-ATTAATATTTTTGGAAATAAAAACGGGGTTGGAGTAT
* *
493196 CCTCTCAAAAATAAC
65 CCCCTCGAAAATAAC
* * * ** *
493211 GGGGTTAGAATAT-CTTCGAGATGAAAAATCGATATTTTTGGAAAGAAAAA
1 GGGGTTGGAGTATCCCT-GAGATGAAAAATTAATATTTTTGGAAATAAAAA
493261 ATTAGAAATT
Statistics
Matches: 228, Mismatches: 46, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
76 53 0.23
77 9 0.04
78 16 0.07
79 107 0.47
80 14 0.06
81 29 0.13
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.29
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCTGAGATGAAAAATTAATATTTTTGGAAATAAAAACGGGGTTGGAGTATC
CCCTCGAAAATAAC
Found at i:493144 original size:155 final size:157
Alignment explanation
Indices: 492918--493216 Score: 349
Period size: 155 Copynumber: 1.9 Consensus size: 157
492908 TCCCCGAGAT
* * * *
492918 GAAAAATTTAATATTTTTGAAATTAAAAAATGAGGTTGGAGTATCTCCTCTGAAATAACGGGATT
1 GAAAAATTTAATATTTTTGAAAATAAAAAAGGAGGTTGGAGTATCCCCTCTGAAATAACGAGATT
* * * * * **
492983 GGAGTATCTCTGAGATGAAAA-ATCGATATTTTTGGAAATAAAAACGGGGCTGGAGTATCCCCTC
66 AGAGTATCCCCGAGATGAAAATATCAATATTTTT-GAAACAAAAACGGGGCTAAAGTATCCCCTC
*
493047 GAAAATAACGGGGTTGGAGTACCCTTAA
130 AAAAATAACGGGGTTGGAGTACCCTTAA
*
493075 GAAAAATTTAATA-TTTTGAAAATAAAAACGGA-GTTGGAGTATCCCCTC-GAAATTGATA-GAG
1 GAAAAATTTAATATTTTTGAAAATAAAAAAGGAGGTTGGAGTATCCCCTCTGAAA-T-A-ACGAG
* * * * * *
493136 -TTAGAGTATCCCCGAGATGAAAATTTTAATATTTTTGAAACAAAAATGGTGTTAAAGTATCCTC
63 ATTAGAGTATCCCCGAGATGAAAATATCAATATTTTTGAAACAAAAACGGGGCTAAAGTATCCCC
493200 TCAAAAATAACGGGGTT
128 TCAAAAATAACGGGGTT
493217 AGAATATCTT
Statistics
Matches: 119, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
154 4 0.03
155 73 0.61
156 28 0.24
157 14 0.12
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (157 bp):
GAAAAATTTAATATTTTTGAAAATAAAAAAGGAGGTTGGAGTATCCCCTCTGAAATAACGAGATT
AGAGTATCCCCGAGATGAAAATATCAATATTTTTGAAACAAAAACGGGGCTAAAGTATCCCCTCA
AAAATAACGGGGTTGGAGTACCCTTAA
Found at i:495678 original size:20 final size:20
Alignment explanation
Indices: 495653--495690 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
495643 TGTAAGCATA
*
495653 TATCGATACATTTTCTTATG
1 TATCGATACATTTCCTTATG
495673 TATCGATACATTTCCTTA
1 TATCGATACATTTCCTTA
495691 GCATCATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.47
Consensus pattern (20 bp):
TATCGATACATTTCCTTATG
Found at i:495758 original size:20 final size:21
Alignment explanation
Indices: 495733--495783 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
495723 TTTAGACATA
495733 TATCGATACATTCACT-CATG
1 TATCGATACATTCACTGCATG
* **
495753 TATCGATACATTTACTGTTTG
1 TATCGATACATTCACTGCATG
495774 TATCGATACA
1 TATCGATACA
495784 AATTATAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (21 bp):
TATCGATACATTCACTGCATG
Found at i:502193 original size:2 final size:2
Alignment explanation
Indices: 502186--502215 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
502176 TAGATTAAAC
502186 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
502216 CTTCATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:502491 original size:2 final size:2
Alignment explanation
Indices: 502486--502515 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
502476 TAAAAAAAGT
502486 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
502516 AAAGAGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:521452 original size:18 final size:20
Alignment explanation
Indices: 521431--521474 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
521421 ATAATTATAG
521431 ATATAAATA-TAATATTT-T
1 ATATAAATAGTAATATTTAT
* *
521449 ATATAATTAGTAATGTTTAT
1 ATATAAATAGTAATATTTAT
521469 ATATAA
1 ATATAA
521475 TTTTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 7 0.32
20 7 0.32
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
ATATAAATAGTAATATTTAT
Found at i:521473 original size:20 final size:18
Alignment explanation
Indices: 521377--521498 Score: 69
Period size: 19 Copynumber: 6.8 Consensus size: 18
521367 CAAAAAAAAA
521377 TTTATATAATTAGATAAT-T
1 TTTATATAATT--ATAATAT
* *
521396 TTATATGTAACTGATAATAT
1 TT-TATATAA-TTATAATAT
*
521416 TTTATATAATTAT-AGA-
1 TTTATATAATTATAATAT
521432 --TATA-AA-TATAATAT
1 TTTATATAATTATAATAT
*
521446 TTTATATAATTAGTAATGT
1 TTTATATAATTA-TAATAT
* *
521465 TTATATATAATTTTTAATTT
1 TT-TATATAA-TTATAATAT
*
521485 TTTATATTATTATA
1 TTTATATAATTATA
521499 CAAAAAGCTA
Statistics
Matches: 80, Mismatches: 11, Indels: 25
0.69 0.09 0.22
Matches are distributed among these distances:
12 3 0.04
13 4 0.05
14 4 0.05
16 4 0.05
17 4 0.05
18 9 0.11
19 26 0.32
20 23 0.29
21 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTATATAATTATAATAT
Found at i:521488 original size:69 final size:66
Alignment explanation
Indices: 521377--521564 Score: 198
Period size: 69 Copynumber: 2.8 Consensus size: 66
521367 CAAAAAAAAA
* * *
521377 TTTATATAATTAGATAATTTTATATGTAACTGATAATATTTTATATAATTATAGATATAAATATA
1 TTTATATAATTAG-TAATTTTATATATAACTGATAATATTTTATATAATTATACA-A-AAAGATA
521442 ATAT
63 ATAT
* ** * * *
521446 TTTATATAATTAGTAATGTTTATATATAATTTTTAATTTTTTATATTATTATACAAAAAGCTAAT
1 TTTATATAATTAGTAAT-TTTATATATAACTGATAATATTTTATATAATTATACAAAAAGATAAT
521511 AT
65 AT
* * *
521513 TTTATATAACTTA-TAATTTGTATATATAAATGGTAATATTTATATGTAATTA
1 TTTATATAA-TTAGTAATTT-TATATATAACTGATAATATTT-TATATAATTA
521565 ATAATATTTT
Statistics
Matches: 100, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
66 2 0.02
67 39 0.39
68 16 0.16
69 43 0.43
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (66 bp):
TTTATATAATTAGTAATTTTATATATAACTGATAATATTTTATATAATTATACAAAAAGATAATA
T
Found at i:521540 original size:87 final size:86
Alignment explanation
Indices: 521438--521748 Score: 251
Period size: 87 Copynumber: 3.6 Consensus size: 86
521428 TAGATATAAA
* * * * ** * * *
521438 TATAATATTT-TATATAATTAGTAATGTTTATATATAATTTTTAATTTTTTATATTATTATA-CA
1 TATAATGTTTATATATAAATAGTAATATTTATATGTAATTAATAATATTTTATATAACTATATCA
521501 AAAAGCTAATATTTTATATAACT
66 AAAAG-TAAT-TTTTATATAACT
* * *
521524 TATAAT-TTGTATATATAAATGGTAATATTTATATGTAATTAATAATATTTTATGTAACTATATG
1 TATAATGTT-TATATATAAATAGTAATATTTATATGTAATTAATAATATTTTATATAACTATATC
* *
521588 TAAAAGTAATTTTTATGTAACT
65 AAAAAGTAATTTTTATATAACT
* * **
521610 TATAATGTTTATA-CTAACTAGTAATATTTATATGTAATTGGTAATATTTTATGTAATAAC-ATA
1 TATAATGTTTATATATAAATAGTAATATTTATATGTAATTAATAATATTTTA--T-ATAACTATA
* *
521673 T-AAATA-TAATGTTATTATATAATT
63 TCAAAAAGTAAT-TT-TTATATAACT
* * * * * * *
521697 TGTAATGTTT-TATGTAATTAGAAATATTTAAATGTAATTAGTAATGTTTTAT
1 TATAATGTTTATATATAAATAGTAATATTTATATGTAATTAATAATATTTTAT
521749 GAAATTAAAT
Statistics
Matches: 185, Mismatches: 30, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
85 40 0.22
86 35 0.19
87 101 0.55
88 9 0.05
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (86 bp):
TATAATGTTTATATATAAATAGTAATATTTATATGTAATTAATAATATTTTATATAACTATATCA
AAAAGTAATTTTTATATAACT
Found at i:521556 original size:20 final size:20
Alignment explanation
Indices: 521507--521573 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
521497 TACAAAAAGC
* *
521507 TAATATTT-TATATAACTTA
1 TAATATTTATATATAAATGA
*
521526 TAAT-TTGTATATATAAATGG
1 TAATATT-TATATATAAATGA
* * *
521546 TAATATTTATATGTAATTAA
1 TAATATTTATATATAAATGA
521566 TAATATTT
1 TAATATTT
521574 TATGTAACTA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
18 2 0.05
19 5 0.13
20 29 0.76
21 2 0.05
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (20 bp):
TAATATTTATATATAAATGA
Found at i:521606 original size:27 final size:28
Alignment explanation
Indices: 521553--521609 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 28
521543 TGGTAATATT
521553 TATATGTAATTAATAATATTTTATGTAAC
1 TATATGTAA-TAATAATATTTTATGTAAC
521582 TATATGTAA-AAGTAAT-TTTTATGTAAC
1 TATATGTAATAA-TAATATTTTATGTAAC
521609 T
1 T
521610 TATAATGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 14 0.52
28 4 0.15
29 9 0.33
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (28 bp):
TATATGTAATAATAATATTTTATGTAAC
Found at i:521704 original size:20 final size:19
Alignment explanation
Indices: 521679--521748 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 19
521669 CATATAAATA
521679 TAATGTTATTATATAATTTG
1 TAATGTT-TTATATAATTTG
* *
521699 TAATGTTTTATGTAATTAG
1 TAATGTTTTATATAATTTG
* * * * *
521718 AAATATTTAAATGTAATTAG
1 TAATGTTT-TATATAATTTG
521738 TAATGTTTTAT
1 TAATGTTTTAT
521749 GAAATTAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 18 0.44
20 23 0.56
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (19 bp):
TAATGTTTTATATAATTTG
Found at i:521993 original size:19 final size:20
Alignment explanation
Indices: 521965--522127 Score: 88
Period size: 19 Copynumber: 8.0 Consensus size: 20
521955 ACATTTAAAA
*
521965 ATAATGTTT-TATGTAATTT
1 ATAATATTTATATGTAATTT
*
521984 ATAATATTT-TATATAA-TT
1 ATAATATTTATATGTAATTT
* *
522002 AGTAATGTTTATATGTTA-TT
1 A-TAATATTTATATGTAATTT
* *
522022 AGTAATATTTATATAATTATTTTT
1 A-TAATATTTATAT--GTA-ATTT
*
522046 AAAAGTAATATTTGTATGTAATTT
1 ---A-TAATATTTATATGTAATTT
* * *
522070 ATAATGTTT-TATATAATTA
1 ATAATATTTATATGTAATTT
*
522089 ATAATGTTTATATGTAATTGT
1 ATAATATTTATATGTAATT-T
522110 -TAATATTTA-ATGTAATTT
1 ATAATATTTATATGTAATTT
522128 TATGTAAAAG
Statistics
Matches: 115, Mismatches: 18, Indels: 23
0.74 0.12 0.15
Matches are distributed among these distances:
18 4 0.03
19 46 0.40
20 43 0.37
21 1 0.01
22 1 0.01
24 5 0.04
25 2 0.02
27 13 0.11
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (20 bp):
ATAATATTTATATGTAATTT
Found at i:522014 original size:18 final size:18
Alignment explanation
Indices: 521972--522040 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 18
521962 AAAATAATGT
*
521972 TTTATGTAATTTA-TAATA
1 TTTATATAA-TTAGTAATA
*
521990 TTTTATATAATTAGTAATG
1 -TTTATATAATTAGTAATA
*
522009 TTTATATGTTATTAGTAATA
1 TTTATA--TAATTAGTAATA
522029 TTTATATAATTA
1 TTTATATAATTA
522041 TTTTTAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
18 14 0.33
19 12 0.29
20 16 0.38
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
TTTATATAATTAGTAATA
Done.