Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008129.1 Hibiscus syriacus cultivar Beakdansim tig00110684_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: 2577775
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:238538 original size:96 final size:95
Alignment explanation
Indices: 238343--238543 Score: 212
Period size: 96 Copynumber: 2.1 Consensus size: 95
238333 CCCCTTCCTG
* *
238343 GTATCGATACCAAAATTATGTTCGATGTTTCATGGTATCGATACCCTTTACGTGGTATCGATACT
1 GTATCGATACCAAAATTATGTTCGATGTTGCATGGTATCGATACCCTTTACATGGTATCGATACT
* * * * *
238408 ACCCTTCTATGGTACCGATACTCCTTTACG
66 ACCCTTCAACGGTACCGATACTCATTAACA
* *
238438 GTATCGATACCAAAATTA-GATTCGATGTATGCTTGGTATCGATACCCTTT-CAATGGTATTGAT
1 GTATCGATACCAAAATTATG-TTCGATGT-TGCATGGTATCGATACCCTTTAC-ATGGTATCGAT
** * *
238501 A-TTGCC-TCAACGGTATCGATACTGATTGAATCA
63 ACTACCCTTCAACGGTACCGATACTCATT-AA-CA
238534 GTATCGATAC
1 GTATCGATAC
238544 TACCCAAAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
94 17 0.19
95 31 0.35
96 40 0.45
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (95 bp):
GTATCGATACCAAAATTATGTTCGATGTTGCATGGTATCGATACCCTTTACATGGTATCGATACT
ACCCTTCAACGGTACCGATACTCATTAACA
Found at i:243918 original size:45 final size:42
Alignment explanation
Indices: 243869--244013 Score: 117
Period size: 45 Copynumber: 3.5 Consensus size: 42
243859 CTTTTATGTT
*
243869 GATAATGCACCCATATGCATTTCAACAATGGCATCCTTTCATGCC
1 GATAATGCACCCATATACATTTC-AC-ATGGCATCCTTT-ATGCC
* *
243914 GATAATGCACCCATATACA-TT---AT--TAT--TTTATGCT
1 GATAATGCACCCATATACATTTCACATGGCATCCTTTATGCC
* *
243948 GACAATGTACCCATATACATTTCAGCTATGGCATCCTTTTATGCC
1 GATAATGCACCCATATACATTTCA-C-ATGGCATCC-TTTATGCC
* *
243993 AATAATGCACCCATATGCATT
1 GATAATGCACCCATATACATT
244014 ATTCTTTTAT
Statistics
Matches: 78, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
34 21 0.27
35 5 0.06
37 2 0.03
39 2 0.03
40 2 0.03
42 2 0.03
44 2 0.03
45 42 0.54
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (42 bp):
GATAATGCACCCATATACATTTCACATGGCATCCTTTATGCC
Found at i:243992 original size:79 final size:79
Alignment explanation
Indices: 243859--244181 Score: 466
Period size: 79 Copynumber: 4.1 Consensus size: 79
243849 CTAAAATATA
* * * * * * *
243859 CTTTTATGTTGATAATGCACCCATATGCATTTCAACAATGGCATCCTTTCATGCCGATAATGCAC
1 CTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCAC
*
243924 CCATATACATTATT
66 CCATATGCATTATT
* *
243938 ATTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCATCCTTTTATGCCAATAATGCAC
1 CTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCAC
244003 CCATATGCATTATT
66 CCATATGCATTATT
* * * *
244017 CTTTTATGCTAACAATGTACCCATATACATTTTAGCTACGACATCCTTTCATGCCAATAATGCAC
1 CTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCAC
244082 CCATATGCATTATT
66 CCATATGCATTATT
* * * * *
244096 CTTTTATGTTGACAATGTATCTATATGCATTTCAGCTATGGCATCATTTCATGCCAATAATGCAC
1 CTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCAC
*
244161 CCATATGCATGATT
66 CCATATGCATTATT
244175 CTTTTAT
1 CTTTTAT
244182 TCGTTTTAGA
Statistics
Matches: 218, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 218 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (79 bp):
CTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCAC
CCATATGCATTATT
Found at i:244039 original size:34 final size:34
Alignment explanation
Indices: 243983--244047 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
243973 CTATGGCATC
* *
243983 CTTTTATGCCAATAATGCACCCATATGCATTATT
1 CTTTTATGCCAACAATGCACCCATATACATTATT
* *
244017 CTTTTATGCTAACAATGTACCCATATACATT
1 CTTTTATGCCAACAATGCACCCATATACATT
244048 TTAGCTACGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (34 bp):
CTTTTATGCCAACAATGCACCCATATACATTATT
Found at i:244609 original size:20 final size:20
Alignment explanation
Indices: 244581--244622 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
244571 CTGATTCCAA
* *
244581 AGTATCGATACTACTACCCT
1 AGTACCGATACTACTACACT
*
244601 AGTACCGATACTTCTACACT
1 AGTACCGATACTACTACACT
244621 AG
1 AG
244623 GGTACCAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (20 bp):
AGTACCGATACTACTACACT
Found at i:253170 original size:36 final size:36
Alignment explanation
Indices: 253130--253315 Score: 134
Period size: 36 Copynumber: 5.2 Consensus size: 36
253120 ATTAAATTCA
* *
253130 TATCTTTTTAAATATTCTAAACTAAAAGATATTTAT
1 TATCTTTTTAAATATTCGAAATTAAAAGATATTTAT
* ** * *
253166 TATCTCTTTAAAT-TT-GAATATTGATCAGATAATT-G
1 TATCTTTTTAAATATTCGAA-ATT-AAAAGATATTTAT
* * *
253201 TATCCTTTCAAATA-TCTTAAATTAAAAGATATTTAT
1 TATCTTTTTAAATATTC-GAAATTAAAAGATATTTAT
* * *
253237 TATCTTTTTAAAT-TT-GAATATTAAAATATA-TCAA
1 TATCTTTTTAAATATTCGAA-ATTAAAAGATATTTAT
* * *
253271 TATCTTTTTGAATATTTCAAAATTAAAGGATATTTAT
1 TATCTTTTTAAATA-TTCGAAATTAAAAGATATTTAT
253308 TATCTTTT
1 TATCTTTT
253316 AAACTTGAAT
Statistics
Matches: 111, Mismatches: 27, Indels: 23
0.69 0.17 0.14
Matches are distributed among these distances:
34 18 0.16
35 33 0.30
36 46 0.41
37 14 0.13
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (36 bp):
TATCTTTTTAAATATTCGAAATTAAAAGATATTTAT
Found at i:253277 original size:34 final size:34
Alignment explanation
Indices: 253237--253399 Score: 122
Period size: 36 Copynumber: 4.7 Consensus size: 34
253227 AGATATTTAT
253237 TATCTTTTTAAATTTGAATATTAAAATATATCAA
1 TATCTTTTTAAATTTGAATATTAAAATATATCAA
* * * *
253271 TATCTTTTTGAATATTTCAAAATTAAAGGATAT-TTAT
1 TATCTTTTT-AA-ATTTGAATATTAAA--ATATATCAA
* * *
253308 TATC-TTTTAAACTTGAATACTAAAAAGATATCAA
1 TATCTTTTTAAATTTGAATA-TTAAAATATATCAA
* *
253342 TATCTTTTTTTATTATTTCAA-ATTAAAATATAT---
1 TATC--TTTTTA-AATTTGAATATTAAAATATATCAA
253375 TATCTTTTTAAAGTTTGAATATTAA
1 TATCTTTTTAAA-TTTGAATATTAA
253400 TGAATAAAAT
Statistics
Matches: 99, Mismatches: 18, Indels: 26
0.69 0.13 0.18
Matches are distributed among these distances:
30 1 0.01
31 11 0.11
32 5 0.05
33 7 0.07
34 21 0.21
35 8 0.08
36 25 0.25
37 12 0.12
38 9 0.09
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (34 bp):
TATCTTTTTAAATTTGAATATTAAAATATATCAA
Found at i:253294 original size:71 final size:70
Alignment explanation
Indices: 253129--253399 Score: 272
Period size: 71 Copynumber: 3.9 Consensus size: 70
253119 AATTAAATTC
* *
253129 ATATCTTTTTAAATA-TTCTAAACTAAAAGATATTTATTATCTCTTTAAATTTGAATATTGATCA
1 ATATCTTTTTAAATATTTC-AAATTAAAAGATATTTATTATCTTTTTAAATTTGAATATT-A--A
* *
253193 GATA-AT-T
62 AATATATCA
* * *
253200 GTATCCTTTCAAATATCTT-AAATTAAAAGATATTTATTATCTTTTTAAATTTGAATATTAAAAT
1 ATATCTTTTTAAATAT-TTCAAATTAAAAGATATTTATTATCTTTTTAAATTTGAATATTAAAAT
253264 ATATCA
65 ATATCA
* * * *
253270 ATATCTTTTTGAATATTTCAAAATTAAAGGATATTTATTATC-TTTTAAACTTGAATACTAAAAA
1 ATATCTTTTTAAATATTTC-AAATTAAAAGATATTTATTATCTTTTTAAATTTGAATA-TTAAAA
*
253334 GATATCA
64 TATATCA
* *
253341 ATATCTTTTTTTATTATTTCAAATT-AAA-ATA--TATTATCTTTTTAAAGTTTGAATATTAA
1 ATATC-TTTTTAAATATTTCAAATTAAAAGATATTTATTATCTTTTTAAA-TTTGAATATTAA
253400 TGAATAAAAT
Statistics
Matches: 170, Mismatches: 20, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
67 7 0.04
68 14 0.08
69 14 0.08
70 29 0.17
71 92 0.54
72 12 0.07
73 2 0.01
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (70 bp):
ATATCTTTTTAAATATTTCAAATTAAAAGATATTTATTATCTTTTTAAATTTGAATATTAAAATA
TATCA
Found at i:254502 original size:44 final size:42
Alignment explanation
Indices: 254446--254560 Score: 146
Period size: 42 Copynumber: 2.7 Consensus size: 42
254436 ATATTTTAAA
*
254446 AATAATTAAAATAATAAATTTATAATAATATTTATTATATTT-T
1 AATAATTAAAATAATATATTT-TAATAATATTT-TTATATTTAT
*
254489 AATCTATTAAAATAATATATTTT-ATAATAATTTTTATATTTAT
1 AAT-AATTAAAATAATATATTTTAATAAT-ATTTTTATATTTAT
*
254532 AATAATT-AAAGAATATATTTTAATAATAT
1 AATAATTAAAATAATATATTTTAATAATAT
254561 AAAAATAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
41 15 0.23
42 21 0.33
43 12 0.19
44 16 0.25
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (42 bp):
AATAATTAAAATAATATATTTTAATAATATTTTTATATTTAT
Found at i:254555 original size:21 final size:22
Alignment explanation
Indices: 254523--254567 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
254513 TAATAATTTT
254523 TATATTTATAATAAT-TAAAGAA
1 TATATTTATAATAATATAAA-AA
254545 TATATTT-TAATAATATAAAAA
1 TATATTTATAATAATATAAAAA
254566 TA
1 TA
254568 AAATCCCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TATATTTATAATAATATAAAAA
Found at i:262006 original size:17 final size:17
Alignment explanation
Indices: 261980--262013 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
261970 AGTGATGTGA
*
261980 GTGTTAAATGTCGAATG
1 GTGTTAAATGTCAAATG
*
261997 GTGTTCAATGTCAAATG
1 GTGTTAAATGTCAAATG
262014 TTGGAGAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.35
Consensus pattern (17 bp):
GTGTTAAATGTCAAATG
Found at i:264622 original size:29 final size:28
Alignment explanation
Indices: 264588--264642 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
264578 TAAATTTTGG
*
264588 TTAGTGATCAAAATGTAAAATTTGAAAGC
1 TTAGTGATCAAAATATAAAA-TTGAAAGC
*
264617 TTAGTGATCAAAGTATAAAATTGAAA
1 TTAGTGATCAAAATATAAAATTGAAA
264643 AAGTTTAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.31
Consensus pattern (28 bp):
TTAGTGATCAAAATATAAAATTGAAAGC
Found at i:267234 original size:14 final size:14
Alignment explanation
Indices: 267211--267255 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
267201 GAATTTTTAG
*
267211 ATAAAGATAAAAAA
1 ATAAAAATAAAAAA
* *
267225 ATAAGAATAAAATA
1 ATAAAAATAAAAAA
*
267239 ATAAAAATAAATAA
1 ATAAAAATAAAAAA
267253 ATA
1 ATA
267256 TAATTCGTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (14 bp):
ATAAAAATAAAAAA
Found at i:267244 original size:20 final size:20
Alignment explanation
Indices: 267211--267248 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
267201 GAATTTTTAG
267211 ATAAAGATAAAAAAATAAGA
1 ATAAAGATAAAAAAATAAGA
267231 ATAAA-ATAATAAAAATAA
1 ATAAAGATAA-AAAAATAA
267249 ATAAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (20 bp):
ATAAAGATAAAAAAATAAGA
Found at i:267294 original size:8 final size:8
Alignment explanation
Indices: 267282--267314 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
267272 GAACATAAGG
*
267282 ATAAAATG
1 ATAAAATA
267290 ATAAAATA
1 ATAAAATA
267298 ATAAAATA
1 ATAAAATA
267306 AT-AAATA
1 ATAAAATA
267313 AT
1 AT
267315 GATAAGGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (8 bp):
ATAAAATA
Found at i:276707 original size:24 final size:24
Alignment explanation
Indices: 276680--276725 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
276670 GTGGAAGAGG
*
276680 TAGAGGCCAAAGT-GGCCAACGAGA
1 TAGAGGCAAAAGTAGG-CAACGAGA
276704 TAGAGGCAAAAGTAGGCAACGA
1 TAGAGGCAAAAGTAGGCAACGA
276726 CCACAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.41, C:0.17, G:0.33, T:0.09
Consensus pattern (24 bp):
TAGAGGCAAAAGTAGGCAACGAGA
Found at i:279410 original size:110 final size:110
Alignment explanation
Indices: 279236--279507 Score: 306
Period size: 110 Copynumber: 2.5 Consensus size: 110
279226 ACATAGTGCC
* * * *
279236 TATACGA-TAGTTCATCAACTCAT-AGTGAATTAC-GTGG-GTTGCACATATCGTG-CATGTATA
1 TATACGATTA-TTCATCAACTCATGA-TGAATT-CTATGGATTTGCACACATAGTGTC-TGTATA
* *
279296 GTTATTCCTCAACTCATGATGAAATCCGTGGATTTGCACAAATAATGT-C-
62 GTTATTCATCAACTCATGATGAAATCCGTAGATTTGCACAAAT-A-GTACA
* * * * *
279345 TGTACGGTTATTCATCAACTCATGATGAGTTCTGTGGATTTGCACACATAGTGTCTGTATGGTTA
1 TATACGATTATTCATCAACTCATGATGAATTCTATGGATTTGCACACATAGTGTCTGTATAGTTA
* *
279410 TTCATCAACTCATGATGAATTCCGTAGATTTGCACACATAGTACA
66 TTCATCAACTCATGATGAAATCCGTAGATTTGCACAAATAGTACA
* *
279455 TATACTATTATTCATCAACTCATGATGAATTCTATGGATTTGTACACATAGTG
1 TATACGATTATTCATCAACTCATGATGAATTCTATGGATTTGCACACATAGTG
279508 CATGTACTAC
Statistics
Matches: 139, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
108 3 0.02
109 29 0.21
110 106 0.76
111 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (110 bp):
TATACGATTATTCATCAACTCATGATGAATTCTATGGATTTGCACACATAGTGTCTGTATAGTTA
TTCATCAACTCATGATGAAATCCGTAGATTTGCACAAATAGTACA
Found at i:279502 original size:55 final size:55
Alignment explanation
Indices: 279246--279516 Score: 252
Period size: 55 Copynumber: 4.9 Consensus size: 55
279236 TATACGATAG
* * * *
279246 TTCATCAACTCAT-AGTGAATTAC-GTGG-GTTGCACATATCGTGCATGTA-TAGTTA
1 TTCATCAACTCATGA-TGAATT-CTGTGGATTTGCACACATAGTACATGTACTA-TTA
* * * * **
279300 TTCCTCAACTCATGATGAAATCCGTGGATTTGCACAAATAATGT-C-TGTACGGTTA
1 TTCATCAACTCATGATGAATTCTGTGGATTTGCACACAT-A-GTACATGTACTATTA
* * *
279355 TTCATCAACTCATGATGAGTTCTGTGGATTTGCACACATAGTGTC-TGTA-TGGTTA
1 TTCATCAACTCATGATGAATTCTGTGGATTTGCACACATAGT-ACATGTACT-ATTA
* * *
279410 TTCATCAACTCATGATGAATTCCGTAGATTTGCACACATAGTACATATACTATTA
1 TTCATCAACTCATGATGAATTCTGTGGATTTGCACACATAGTACATGTACTATTA
* * *
279465 TTCATCAACTCATGATGAATTCTATGGATTTGTACACATAGTGCATGTACTA
1 TTCATCAACTCATGATGAATTCTGTGGATTTGCACACATAGTACATGTACTA
279517 CACTTAGTAC
Statistics
Matches: 181, Mismatches: 25, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
53 3 0.02
54 23 0.13
55 151 0.83
56 2 0.01
57 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (55 bp):
TTCATCAACTCATGATGAATTCTGTGGATTTGCACACATAGTACATGTACTATTA
Found at i:286070 original size:55 final size:55
Alignment explanation
Indices: 285957--286123 Score: 196
Period size: 55 Copynumber: 3.1 Consensus size: 55
285947 GTAATGCTTA
* * * * **
285957 TACGGT-AGTTCATCAACTCATAATGAATTTCGTGG-GTTGCACATATCA-TGAATG
1 TACGGTCA-TTCATCAACTCATGATGAATTCCGTGGATTTGCACACAT-AGTGCCTG
* * * * *
286011 TACGGTTATTCCTCAACTCATGATGAATTCTGTGGATTTGCACATATAGTTCCTG
1 TACGGTCATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCCTG
286066 TACGGTCATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCCTG
1 TACGGTCATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCCTG
286121 TAC
1 TAC
286124 TACACTTAGT
Statistics
Matches: 97, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
54 30 0.31
55 67 0.69
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (55 bp):
TACGGTCATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCCTG
Found at i:303200 original size:15 final size:15
Alignment explanation
Indices: 303180--303208 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
303170 AAAATAATCA
303180 ATGTTCACCATTAAG
1 ATGTTCACCATTAAG
303195 ATGTTCACCATTAA
1 ATGTTCACCATTAA
303209 AATATTCCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (15 bp):
ATGTTCACCATTAAG
Found at i:304592 original size:15 final size:15
Alignment explanation
Indices: 304549--304594 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
304539 ATATTTAGTT
*
304549 GGGCGGGCGGATGAG
1 GGGCGGGCGGATGCG
*
304564 GAGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
*
304579 GGGCGGGTGGATGCG
1 GGGCGGGCGGATGCG
304594 G
1 G
304595 TGTGGATGCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.11, C:0.15, G:0.65, T:0.09
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:306252 original size:15 final size:15
Alignment explanation
Indices: 306232--306261 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
306222 CTAACAGATT
306232 TCAATTCCTTCACAG
1 TCAATTCCTTCACAG
306247 TCAATTCCTTCACAG
1 TCAATTCCTTCACAG
306262 ATTCCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.07, T:0.33
Consensus pattern (15 bp):
TCAATTCCTTCACAG
Found at i:312063 original size:20 final size:20
Alignment explanation
Indices: 312038--312087 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
312028 AACAACCCCC
312038 ACACGGATGGACCAAGCTAA
1 ACACGGATGGACCAAGCTAA
312058 ACACGGATGGACCAAGCTAA
1 ACACGGATGGACCAAGCTAA
312078 ACACGGATGG
1 ACACGGATGG
312088 CGCACGACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.24, G:0.28, T:0.10
Consensus pattern (20 bp):
ACACGGATGGACCAAGCTAA
Found at i:314199 original size:45 final size:45
Alignment explanation
Indices: 314138--314357 Score: 316
Period size: 45 Copynumber: 4.9 Consensus size: 45
314128 ACCATTATAC
*
314138 ACTTTTCTGTTGATAATGCACCCATATACACTTCAACTATAGTAT
1 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTAT
* *
314183 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATATTAT
1 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTAT
* * * * *
314228 ACTCTTT-AGTTGATAATGCACTCATATGCATCTCAACTATAGCAT
1 ACT-TTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTAT
*
314273 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTAT
1 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTAT
* * *
314318 ATTTTTCTGTTGATAATGTACCCGTATACATTTCAACTAT
1 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTAT
314358 GGCATCCTTT
Statistics
Matches: 155, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
44 3 0.02
45 149 0.96
46 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (45 bp):
ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTAT
Found at i:314264 original size:90 final size:90
Alignment explanation
Indices: 314141--314395 Score: 300
Period size: 90 Copynumber: 2.8 Consensus size: 90
314131 ATTATACACT
* * *
314141 TTTCTGTTGATAATGCACCCATATACACTTCAACTATAGTATACTTTTCTGTTGATAATGTACCC
1 TTTCAGTTGATAATGCACCCATATACACTTCAACTATAGCATACTTTTCTGTTGATAATGCACCC
*
314206 ATATACATTTCAACTATATTATACTC
66 ATATACATTTCAACTATAGTATA-TC
* *
314232 TTT-AGTTGATAATGCACTCATATGCA-TCTCAACTATAGCATACTTTTCTGTTGATAATGCACC
1 TTTCAGTTGATAATGCACCCATATACACT-TCAACTATAGCATACTTTTCTGTTGATAATGCACC
* *
314295 CATATGCATTTCAACTATAGTATATT
65 CATATACATTTCAACTATAGTATATC
* * * * * * **
314321 TTTCTGTTGATAATGTACCCGTATACATTTCAACTATGGCAT-CCTTTCAATGCCGATAATGCAC
1 TTTCAGTTGATAATGCACCCATATACACTTCAACTATAGCATACTTTTC--TGTTGATAATGCAC
*
314385 CCATATGCATT
64 CCATATACATT
314396 ATTATTTTCA
Statistics
Matches: 142, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
89 10 0.07
90 105 0.74
91 27 0.19
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (90 bp):
TTTCAGTTGATAATGCACCCATATACACTTCAACTATAGCATACTTTTCTGTTGATAATGCACCC
ATATACATTTCAACTATAGTATATC
Found at i:314413 original size:135 final size:134
Alignment explanation
Indices: 314138--314394 Score: 374
Period size: 135 Copynumber: 1.9 Consensus size: 134
314128 ACCATTATAC
314138 ACTTTTCTGTTGATAATGCACCCATATACACTTCAACTATAGTATACTTTTCTGTTGATAATGTA
1 ACTTTTCTGTTGATAATGCACCCATATACACTTCAACTATAGTATACTTTTCTGTTGATAATGTA
** ** *
314203 CCCATATACATTTCAACTATATTATACTCTTTAGTTGATAATGCACTCATATGCATCTCAACTAT
66 CCCATATACATTTCAACTATAGCATACTCTTTAGCCGATAATGCACCCATATGCATCT-AACTAT
314268 AGCAT
130 AGCAT
* * *
314273 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATATTTTTCTGTTGATAATGTA
1 ACTTTTCTGTTGATAATGCACCCATATACACTTCAACTATAGTATACTTTTCTGTTGATAATGTA
* *
314338 CCCGTATACATTTCAACTATGGCAT-C-CTTTCAATGCCGATAATGCACCCATATGCAT
66 CCCATATACATTTCAACTATAGCATACTCTTT--A-GCCGATAATGCACCCATATGCAT
314395 TATTATTTTC
Statistics
Matches: 109, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
133 4 0.04
134 1 0.01
135 84 0.77
136 20 0.18
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.39
Consensus pattern (134 bp):
ACTTTTCTGTTGATAATGCACCCATATACACTTCAACTATAGTATACTTTTCTGTTGATAATGTA
CCCATATACATTTCAACTATAGCATACTCTTTAGCCGATAATGCACCCATATGCATCTAACTATA
GCAT
Found at i:314972 original size:95 final size:93
Alignment explanation
Indices: 314804--315046 Score: 249
Period size: 95 Copynumber: 2.6 Consensus size: 93
314794 TCTGGCCCTT
* * * * *
314804 CAGTATTGATACCCCTACCATGGTATCGATACTACCATAC-ATTGGTATCGATACCCCCTTCCAG
1 CAGTATCGATACCCTTACCATGGTATCGATACTACTATACTA-TGGTACCGATA-CCCCTTACAG
*
314868 TACCAATACCAAAATTAGATTCGATGTGGCC
64 TACCAATACCAAAATTAGATTCGATGT-GAC
* **
314899 CAGTATCGATACCCTTACCATGGTATCAATACTACTATACTATGGTACCGATACCCCTATATGGT
1 CAGTATCGATACCCTTACCATGGTATCGATACTACTATACTATGGTACCGATACCCCT-TACAGT
* * * *
314964 ATCGATACCAAAATTAGGTTCGATGTTAC
65 ACCAATACCAAAATTAGATTCGATGTGAC
* * * * *
314993 CAGGTATCGGTACCCTCACCATGATATCGATACCACT-TAGT-TAGGTACCGATAC
1 CA-GTATCGATACCCTTACCATGGTATCGATACTACTATACTAT-GGTACCGATAC
315047 TGATTGAATT
Statistics
Matches: 125, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
93 1 0.01
94 22 0.18
95 101 0.81
96 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (93 bp):
CAGTATCGATACCCTTACCATGGTATCGATACTACTATACTATGGTACCGATACCCCTTACAGTA
CCAATACCAAAATTAGATTCGATGTGAC
Found at i:319758 original size:19 final size:20
Alignment explanation
Indices: 319722--319772 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
319712 AACCCCTTTA
319722 AAAATACATGATTTTTTTAATG
1 AAAATACATGA--TTTTTAATG
319744 AAAATACATGA-TTTTAATG
1 AAAATACATGATTTTTAATG
*
319763 AAGATACATG
1 AAAATACATG
319773 CTCTTGGCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 17 0.61
22 11 0.39
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (20 bp):
AAAATACATGATTTTTAATG
Found at i:319971 original size:22 final size:22
Alignment explanation
Indices: 319940--319993 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
319930 TGCTTGAATG
319940 ATGCACATGGAAGCCTACATGA
1 ATGCACATGGAAGCCTACATGA
* *
319962 ATGCATATGGCAGCCTACATGA
1 ATGCACATGGAAGCCTACATGA
*
319984 ATGTACATGG
1 ATGCACATGG
319994 GTCTTCTTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.22
Consensus pattern (22 bp):
ATGCACATGGAAGCCTACATGA
Found at i:322896 original size:14 final size:14
Alignment explanation
Indices: 322863--322897 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
322853 TCCGACTTTC
*
322863 CATTATAAATTCCA
1 CATTATAAATACCA
322877 -ATTATAAATACCA
1 CATTATAAATACCA
322890 CATTATAA
1 CATTATAA
322898 CCACCCAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (14 bp):
CATTATAAATACCA
Found at i:337420 original size:2 final size:2
Alignment explanation
Indices: 337413--337672 Score: 441
Period size: 2 Copynumber: 130.5 Consensus size: 2
337403 TTGTATAAAC
337413 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
337455 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
337497 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* *
337539 GA GA GA GA GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA GG
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * *
337581 GA GA GA GA GG GA GA GA GG GA GA GA GG GA GA GA GA GA GG GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* *
337623 GA GA GA G- GA GA GA GA GA GG GA GA GA GA GG GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
337664 GA GA GA GA G
1 GA GA GA GA G
337673 GAATAAATTA
Statistics
Matches: 241, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
1 1 0.00
2 240 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:338793 original size:7 final size:7
Alignment explanation
Indices: 338781--338812 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
338771 TTGATGATAT
338781 TTTTCCC
1 TTTTCCC
338788 TTTTCCC
1 TTTTCCC
338795 TTTTCCC
1 TTTTCCC
338802 TTTTCCC
1 TTTTCCC
338809 TTTT
1 TTTT
338813 TAAATTCGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTCCC
Found at i:344290 original size:38 final size:38
Alignment explanation
Indices: 344239--344324 Score: 127
Period size: 38 Copynumber: 2.3 Consensus size: 38
344229 TACGATTCCA
* *
344239 AAATTTACATGCATCGGAATTCGTACCAGTATGATATG
1 AAATTTACGTGCATCAGAATTCGTACCAGTATGATATG
* **
344277 AAATTTACGTGCATCATAATTCGTACTGGTATGATATG
1 AAATTTACGTGCATCAGAATTCGTACCAGTATGATATG
344315 AAATTTACGT
1 AAATTTACGT
344325 TCATAAGATG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (38 bp):
AAATTTACGTGCATCAGAATTCGTACCAGTATGATATG
Found at i:345261 original size:20 final size:19
Alignment explanation
Indices: 345235--345291 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 19
345225 TACTACAACC
345235 CTCAGTATCGATACCAAGA
1 CTCAGTATCGATACCAAGA
* *
345254 GGTCAGTATCGATACCAATA
1 -CTCAGTATCGATACCAAGA
345274 CTCTAGTATCGATACCAA
1 CTC-AGTATCGATACCAA
345292 AGCCCTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (19 bp):
CTCAGTATCGATACCAAGA
Found at i:347385 original size:15 final size:17
Alignment explanation
Indices: 347342--347399 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
347332 AAAATGAAAC
*
347342 TAAAAGAAATAAT-ACAA
1 TAAAAGATAT-ATCACAA
347359 TAAAAGATATATCACAA
1 TAAAAGATATATCACAA
* * *
347376 TAAAATATATATTATAA
1 TAAAAGATATATCACAA
347393 TAAAAGA
1 TAAAAGA
347400 AATAGTACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
16 2 0.06
17 33 0.94
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (17 bp):
TAAAAGATATATCACAA
Found at i:355939 original size:26 final size:26
Alignment explanation
Indices: 355903--355954 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
355893 GGTAGACTGC
355903 CTAGTGCCCTAACTATTTAGGCTAGG
1 CTAGTGCCCTAACTATTTAGGCTAGG
*
355929 CTAGTTCCCTAACTATTTAGGCTAGG
1 CTAGTGCCCTAACTATTTAGGCTAGG
355955 TACTGTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (26 bp):
CTAGTGCCCTAACTATTTAGGCTAGG
Found at i:356055 original size:20 final size:20
Alignment explanation
Indices: 356030--356094 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
356020 TCCCTAGCCC
356030 CGATCGTGCCCTCCCTTCAT
1 CGATCGTGCCCTCCCTTCAT
* *
356050 CGATCGTGGCATCCCTTCAT
1 CGATCGTGCCCTCCCTTCAT
* *
356070 CGATCGTGCCCTCTCTTAAT
1 CGATCGTGCCCTCCCTTCAT
356090 CGATC
1 CGATC
356095 ACCTTTCGGC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.14, C:0.38, G:0.17, T:0.31
Consensus pattern (20 bp):
CGATCGTGCCCTCCCTTCAT
Found at i:356648 original size:14 final size:13
Alignment explanation
Indices: 356627--356669 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
356617 TTTAGTCAAC
356627 CCATTGACTTTGA
1 CCATTGACTTTGA
*
356640 CCTATTGACTTTAA
1 CC-ATTGACTTTGA
*
356654 CCGTTGACTTTGA
1 CCATTGACTTTGA
356667 CCA
1 CCA
356670 AAAAAGTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (13 bp):
CCATTGACTTTGA
Found at i:357967 original size:18 final size:18
Alignment explanation
Indices: 357921--357967 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
357911 CGCTAAAATA
* *
357921 GTATCGATACCGAAGTGG
1 GTATCGATACTGAAATGG
*
357939 GTATCGGTACTGAAATGG
1 GTATCGATACTGAAATGG
357957 GTATCGATACT
1 GTATCGATACT
357968 ATAGAAGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (18 bp):
GTATCGATACTGAAATGG
Found at i:357985 original size:22 final size:20
Alignment explanation
Indices: 357957--358011 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
357947 ACTGAAATGG
357957 GTATCGATACTATAGAAGAGAA
1 GTATCGATACTATAG--GAGAA
* **
357979 GTATCGATACCATAGGAGGG
1 GTATCGATACTATAGGAGAA
357999 GTATCGATACTAT
1 GTATCGATACTAT
358012 TCAGTCTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 15 0.52
22 14 0.48
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.25
Consensus pattern (20 bp):
GTATCGATACTATAGGAGAA
Found at i:358004 original size:20 final size:21
Alignment explanation
Indices: 357955--358008 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
357945 GTACTGAAAT
*
357955 GGGTATCGATACTATAGAAGAG
1 GGGTATCGATACCATAG-AGAG
**
357977 AAGTATCGATACCATAG-GAG
1 GGGTATCGATACCATAGAGAG
357997 GGGTATCGATAC
1 GGGTATCGATAC
358009 TATTCAGTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 13 0.48
22 14 0.52
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.22
Consensus pattern (21 bp):
GGGTATCGATACCATAGAGAG
Found at i:358405 original size:54 final size:54
Alignment explanation
Indices: 358318--358609 Score: 359
Period size: 54 Copynumber: 5.4 Consensus size: 54
358308 ATGTTACATT
** * *
358318 TTACCGTATTAACACTATGTGTGTACCCCACGTAATTCATAACGAGTTTGTGAA
1 TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTGTGAA
* * *
358372 TTTCTGTATTGGCGCTATGTGTGCACCCCACGTAATTCATAATGAGTTTGTGAA
1 TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTGTGAA
* * *
358426 TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTTATAACGAGTTTGTAAA
1 TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTGTGAA
* * * * *
358480 TTACCGTATTCGCACTATGTATGCATCCCATGTAATTCATAATGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTGTGAA
* * * ** *
358534 TTACCGTATTTGAATTATGTGTGCAATCCACATAATTCATAATGAGTTTGTGAA
1 TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTGTGAA
* * **
358588 CTACCTTATCAGCACTATGTGT
1 TTACCGTATTGGCACTATGTGT
358610 TCAAAACCGC
Statistics
Matches: 202, Mismatches: 36, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 202 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (54 bp):
TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTGTGAA
Found at i:358585 original size:162 final size:162
Alignment explanation
Indices: 358318--358609 Score: 395
Period size: 162 Copynumber: 1.8 Consensus size: 162
358308 ATGTTACATT
* * * * *
358318 TTACCGTATTAACACTATGTGTGTACCCCACGTAATTCATAACGAGTTTGTGAATTTCTGTATTG
1 TTACCGTATTAACACTATGTATGCACCCCACGTAATTCATAACGAGTTTATGAATTACCGTATTG
** * * * **
358383 GCGCTATGTGTGCACCCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCACTATGTGT
66 GAACTATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAACTACCGTATCAGCACTATGTGT
358448 GCACCCCACGTAATTTATAACGAGTTTGTAAA
131 GCACCCCACGTAATTTATAACGAGTTTGTAAA
** * * * *
358480 TTACCGTATTCGCACTATGTATGCATCCCATGTAATTCATAATGAGTTTATGAATTACCGTATTT
1 TTACCGTATTAACACTATGTATGCACCCCACGTAATTCATAACGAGTTTATGAATTACCGTATTG
* * *
358545 GAATTATGTGTGCAATCCACATAATTCATAATGAGTTTGTGAACTACCTTATCAGCACTATGTGT
66 GAACTATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAACTACCGTATCAGCACTATGTGT
358610 TCAAAACCGC
Statistics
Matches: 109, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
162 109 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (162 bp):
TTACCGTATTAACACTATGTATGCACCCCACGTAATTCATAACGAGTTTATGAATTACCGTATTG
GAACTATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAACTACCGTATCAGCACTATGTGT
GCACCCCACGTAATTTATAACGAGTTTGTAAA
Found at i:360790 original size:20 final size:20
Alignment explanation
Indices: 360761--360809 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
360751 CAAGCTGGTA
*
360761 ATTCCTTTCGGACCCAAGGC
1 ATTCCCTTCGGACCCAAGGC
360781 ATTCCCTTCGGACCCAAGGC
1 ATTCCCTTCGGACCCAAGGC
360801 ATTCCCTTC
1 ATTCCCTTC
360810 TGTTGGCTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.39, G:0.16, T:0.27
Consensus pattern (20 bp):
ATTCCCTTCGGACCCAAGGC
Found at i:362222 original size:7 final size:7
Alignment explanation
Indices: 362210--362340 Score: 228
Period size: 7 Copynumber: 18.7 Consensus size: 7
362200 TTTGCATGAC
362210 ATTTCTA
1 ATTTCTA
362217 ATTTCTA
1 ATTTCTA
362224 ATTTCTA
1 ATTTCTA
362231 ATTTCTA
1 ATTTCTA
362238 A-TTCTTA
1 ATTTC-TA
362245 ATTTCTA
1 ATTTCTA
362252 ATTTCTA
1 ATTTCTA
*
362259 ATTCCTA
1 ATTTCTA
362266 ATTTCTA
1 ATTTCTA
362273 ATTTCTA
1 ATTTCTA
*
362280 ATTCCTA
1 ATTTCTA
362287 ATTTCTA
1 ATTTCTA
362294 ATTTCTA
1 ATTTCTA
362301 ATTTCTA
1 ATTTCTA
362308 ATTTCTA
1 ATTTCTA
362315 ATTTCTA
1 ATTTCTA
362322 ATTTCTA
1 ATTTCTA
362329 ATTTCTA
1 ATTTCTA
362336 ATTTC
1 ATTTC
362341 AACCACTAAA
Statistics
Matches: 118, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
6 3 0.03
7 112 0.95
8 3 0.03
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTTCTA
Found at i:370780 original size:39 final size:39
Alignment explanation
Indices: 370673--370785 Score: 154
Period size: 39 Copynumber: 2.9 Consensus size: 39
370663 TAGTTCATAC
* * * **
370673 GGTGGACGCAATCTTATACGTAAGCACTTCAGTGCAAAT
1 GGTGGACGCAACCTTATGCGTAAGAACTTTGGTGCAAAT
** *
370712 GGTGGACAAAACCTTATGCGTAAGAACTTTGGTGTAAAT
1 GGTGGACGCAACCTTATGCGTAAGAACTTTGGTGCAAAT
370751 GGTGGACGCAACCTTATGCGTAAGAACTTTGGTGC
1 GGTGGACGCAACCTTATGCGTAAGAACTTTGGTGC
370786 GACTCAAATA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (39 bp):
GGTGGACGCAACCTTATGCGTAAGAACTTTGGTGCAAAT
Found at i:374873 original size:46 final size:46
Alignment explanation
Indices: 374806--374946 Score: 219
Period size: 46 Copynumber: 3.1 Consensus size: 46
374796 ACCACTGCAT
*
374806 ATTTTCATTTATGGCATCCTTTCATTCCAATTATGTACTGTTATAC
1 ATTTTCATTTATGGCATCCTTTCATTCCAATTATGCACTGTTATAC
* * *
374852 ATTTTCAATTATGGCATCCTTTCATGCCAATTATGCATTGTTATAC
1 ATTTTCATTTATGGCATCCTTTCATTCCAATTATGCACTGTTATAC
* * *
374898 ATTTTCATTTATGTCATCCTTTCATTCTAATTATGCACTATTATAC
1 ATTTTCATTTATGGCATCCTTTCATTCCAATTATGCACTGTTATAC
374944 ATT
1 ATT
374947 AGTCTTTTAT
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.48
Consensus pattern (46 bp):
ATTTTCATTTATGGCATCCTTTCATTCCAATTATGCACTGTTATAC
Found at i:375535 original size:24 final size:24
Alignment explanation
Indices: 375491--375539 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
375481 AGATTGAAGA
375491 AAATGGGTTTTTGAGTGATATGTTG
1 AAATGGGTTTTTGAGTGATAT-TTG
375516 AAATGGGTTTTATG-GT-ATATTTG
1 AAATGGGTTTT-TGAGTGATATTTG
375539 A
1 A
375540 CTTGACATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.17
24 4 0.17
25 13 0.57
26 2 0.09
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.45
Consensus pattern (24 bp):
AAATGGGTTTTTGAGTGATATTTG
Found at i:376832 original size:95 final size:94
Alignment explanation
Indices: 376669--376845 Score: 232
Period size: 95 Copynumber: 1.9 Consensus size: 94
376659 ATATCTACGA
* * * *
376669 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGCAACATCGAATCTAAAATCGATATTGA
1 GGTAGTATCGATACCATGGTAACGGTATCGATACCAGGAAACATCAAATCTAAAATCGATATCGA
*
376734 TACCATAAGGGGGTATCGGTACCATAGTAG
66 TACCAGAA-GGGGTATCGGTACCATAGTAG
* * *
376764 GGTAGTATCGATATCATGGTAACGGTGTCGATACCAGGAAACATCAAAGT-TAAAACTTG-TATC
1 GGTAGTATCGATACCATGGTAACGGTATCGATACCAGGAAACATCAAA-TCTAAAA-TCGATATC
*
376827 GATACCGGAAGGGGTATCG
64 GATACCAGAAGGGGTATCG
376846 ATATCATGAT
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
94 9 0.13
95 59 0.83
96 3 0.04
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.24
Consensus pattern (94 bp):
GGTAGTATCGATACCATGGTAACGGTATCGATACCAGGAAACATCAAATCTAAAATCGATATCGA
TACCAGAAGGGGTATCGGTACCATAGTAG
Found at i:377401 original size:26 final size:26
Alignment explanation
Indices: 377327--377568 Score: 110
Period size: 26 Copynumber: 10.2 Consensus size: 26
377317 GCATGAACAT
*
377327 ATGCCATAATTAAAAATGCATGAAATG
1 ATGCCATAATT-AAAATGCATGAAAGG
* * *
377354 ATG---T-ATT--AAGGCATGTACGG
1 ATGCCATAATTAAAATGCATGAAAGG
*
377374 ATGCCATAATTAAAATGCATAAAAGG
1 ATGCCATAATTAAAATGCATGAAAGG
* * *
377400 AT---A-CATT--AAGGCATGAATGG
1 ATGCCATAATTAAAATGCATGAAAGG
377420 ATGCCATAATTAAAATGCATGAAAGG
1 ATGCCATAATTAAAATGCATGAAAGG
* * *
377446 ATG-C---ATT--AAGGCGTGAACGG
1 ATGCCATAATTAAAATGCATGAAAGG
377466 ATGCCATAATTAAAATGCATG-AA--
1 ATGCCATAATTAAAATGCATGAAAGG
*
377489 ATG--ATACATT--AAGGCATGAAAGG
1 ATGCCATA-ATTAAAATGCATGAAAGG
377512 ATGCCATAAACTGT-AAA-GCATGAAAGG
1 ATGCCAT-AA-T-TAAAATGCATGAAAGG
377539 ATGCCATAAACTT--AATGCATGAAAGG
1 ATGCCAT-AA-TTAAAATGCATGAAAGG
377565 ATGC
1 ATGC
377569 ATCAAAGCAT
Statistics
Matches: 164, Mismatches: 22, Indels: 59
0.67 0.09 0.24
Matches are distributed among these distances:
20 44 0.27
21 6 0.04
22 9 0.05
23 12 0.07
24 10 0.06
25 7 0.04
26 48 0.29
27 26 0.16
28 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (26 bp):
ATGCCATAATTAAAATGCATGAAAGG
Found at i:377408 original size:46 final size:46
Alignment explanation
Indices: 377231--377542 Score: 376
Period size: 46 Copynumber: 6.7 Consensus size: 46
377221 TGTATAGAAA
* * *
377231 GGATACCATAATTAAAATTGCATGAAAGGATGCAATAAGACATGAAC
1 GGATGCCATAATTAAAA-TGCATGAAAGGATGCATTAAGGCATGAAC
* ** * *
377278 GGAAGCCATAATTAAAAATTTAGGAAATGATGCATTAAGGCATGAAC
1 GGATGCCATAATT-AAAATGCATGAAAGGATGCATTAAGGCATGAAC
** * * *
377325 ATATGCCATAATTAAAAATGCATGAAATGATGTATTAAGGCATGTAC
1 GGATGCCATAATT-AAAATGCATGAAAGGATGCATTAAGGCATGAAC
* * *
377372 GGATGCCATAATTAAAATGCATAAAAGGATACATTAAGGCATGAAT
1 GGATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAC
*
377418 GGATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCGTGAAC
1 GGATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAC
* * *
377464 GGATGCCATAATTAAAATGCATGAAATGATACATTAAGGCATGAAA
1 GGATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAC
377510 GGATGCCATAAACTGT-AAA-GCATGAAAGGATGC
1 GGATGCCAT-AA-T-TAAAATGCATGAAAGGATGC
377543 CATAAACTTA
Statistics
Matches: 227, Mismatches: 34, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
46 120 0.53
47 98 0.43
48 8 0.04
49 1 0.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (46 bp):
GGATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAC
Found at i:377540 original size:27 final size:26
Alignment explanation
Indices: 377497--377568 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 26
377487 AAATGATACA
*
377497 TTAAGGCATGAAAGGATGCCATAAAC
1 TTAAAGCATGAAAGGATGCCATAAAC
377523 TGTAAAGCATGAAAGGATGCCATAAAC
1 T-TAAAGCATGAAAGGATGCCATAAAC
*
377550 TTAATGCATGAAAGGATGC
1 TTAAAGCATGAAAGGATGC
377569 ATCAAAGCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
26 18 0.42
27 25 0.58
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.21
Consensus pattern (26 bp):
TTAAAGCATGAAAGGATGCCATAAAC
Found at i:383640 original size:20 final size:20
Alignment explanation
Indices: 383591--383644 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 20
383581 TACCGTAAGG
* *
383591 GGGTATCGGTACCATGGTAG
1 GGGTATCGATACCATGGTAA
383611 GGTAGTATCGATACCATGGTAA
1 GG--GTATCGATACCATGGTAA
383633 GGGTATCGATAC
1 GGGTATCGATAC
383645 TAGGAAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (20 bp):
GGGTATCGATACCATGGTAA
Found at i:383642 original size:95 final size:94
Alignment explanation
Indices: 383516--383699 Score: 282
Period size: 95 Copynumber: 1.9 Consensus size: 94
383506 ATACCTACGA
383516 GGTAGTATCGATACCATGGTAAGGGTATCGATAGC-AGGAAACA-TCAAATCTAAAATTGGTATC
1 GGTAGTATCGATACCATGGTAAGGGTATCGATA-CTAGGAAACATTCAAAT-TAAAATTGGTATC
* * *
383579 GATACCGTAAGGGGGTATCGGTACCATGGTAG
64 GATACCGGAA-GCGGTATCAGTACCATGGTAG
* *
383611 GGTAGTATCGATACCATGGTAAGGGTATCGATACTAGGAAACATTGAAGTTAAAATTGGTATCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACTAGGAAACATTCAAATTAAAATTGGTATCGA
383676 TACCGGAAGCGGTATCAGTACCAT
66 TACCGGAAGCGGTATCAGTACCAT
383700 AATTTAGAAG
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
94 15 0.18
95 63 0.77
96 4 0.05
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (94 bp):
GGTAGTATCGATACCATGGTAAGGGTATCGATACTAGGAAACATTCAAATTAAAATTGGTATCGA
TACCGGAAGCGGTATCAGTACCATGGTAG
Found at i:384089 original size:46 final size:46
Alignment explanation
Indices: 384026--384196 Score: 209
Period size: 46 Copynumber: 3.7 Consensus size: 46
384016 TGCATTAACA
* *
384026 GCATGAAATGATGCATTAAGGCTTGAACGGATGCCATAATTAAAAT
1 GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
* * * *
384072 GCATTAAATCATGCATTAAGGCATGAATGAATGCCATAATTAAAAT
1 GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
* * **
384118 GCATGAAATGATGCATTAA-GCATGAAAGGATACCATAAACTGTAAT
1 GCATGAAATGATGCATTAAGGCATGAAAGGATGCCAT-AATTAAAAT
* * *
384164 GCATGAAAGGATGCATTAAAGCATGAATGGATG
1 GCATGAAATGATGCATTAAGGCATGAAAGGATG
384197 TGTTAATATG
Statistics
Matches: 107, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
45 14 0.13
46 82 0.77
47 11 0.10
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (46 bp):
GCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
Found at i:384131 original size:26 final size:26
Alignment explanation
Indices: 384055--384131 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
384045 GGCTTGAACG
*
384055 GATGCCATAATTAAAATGCATTAAAT
1 GATGCCATAATTAAAATGCATGAAAT
* *
384081 CATG-C---ATT--AAGGCATG-AAT
1 GATGCCATAATTAAAATGCATGAAAT
384100 GAATGCCATAATTAAAATGCATGAAAT
1 G-ATGCCATAATTAAAATGCATGAAAT
384127 GATGC
1 GATGC
384132 ATTAAGCATG
Statistics
Matches: 38, Mismatches: 5, Indels: 16
0.64 0.08 0.27
Matches are distributed among these distances:
19 3 0.08
20 9 0.24
21 1 0.03
22 3 0.08
24 3 0.08
25 1 0.03
26 14 0.37
27 4 0.11
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (26 bp):
GATGCCATAATTAAAATGCATGAAAT
Found at i:385596 original size:54 final size:54
Alignment explanation
Indices: 385336--385574 Score: 343
Period size: 54 Copynumber: 4.4 Consensus size: 54
385326 TTACCAAATA
* * *
385336 GGCACTAAGTGTGCATTTCACAGAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
385390 GACACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
385444 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGAATGAATAACCTTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
385498 GGAACTAATTGTGAATTTCACGGAATTCATCCTATGTGTATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
385552 GGCACTGAGTGTACATTTCACGG
1 GGCACTAAGTGTGCATTTCACGG
385575 GTTTCATAAT
Statistics
Matches: 164, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 164 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:391036 original size:13 final size:13
Alignment explanation
Indices: 391002--391028 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
390992 ATTTTAAAAA
391002 TGGTCATTAATTT
1 TGGTCATTAATTT
391015 TGGTCATTAATTT
1 TGGTCATTAATTT
391028 T
1 T
391029 TGTTATTATA
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:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (13 bp):
TGGTCATTAATTT
Found at i:392172 original size:21 final size:23
Alignment explanation
Indices: 392137--392184 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
392127 ATTTTTCAAC
*
392137 TTCCCTCCAAATAAAATT-TATA
1 TTCCCTCCAAATAAAATTGAATA
*
392159 TTCCCT-CTAATAAAATTGAATA
1 TTCCCTCCAAATAAAATTGAATA
392181 TTCC
1 TTCC
392185 TTATACATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.38
Consensus pattern (23 bp):
TTCCCTCCAAATAAAATTGAATA
Found at i:393488 original size:18 final size:19
Alignment explanation
Indices: 393465--393507 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
393455 ACTCTTGATA
*
393465 TTTATTATAAAAT-TTATT
1 TTTATTATAAAATGTAATT
* *
393483 TTTATTTTAAAGTGTAATT
1 TTTATTATAAAATGTAATT
393502 TTTATT
1 TTTATT
393508 TTTGAAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTATTATAAAATGTAATT
Found at i:395942 original size:95 final size:95
Alignment explanation
Indices: 395818--396005 Score: 295
Period size: 95 Copynumber: 2.0 Consensus size: 95
395808 ACCAATGAGG
* * * *
395818 TAGTATCAATACCATGGTAAGGGTATCGATACCAAGCAACATCGAATCTAAATTTGGTATCGATA
1 TAGTATCAATACCATGGTAAGGGTATCGATACCAAGAAACATCAAACCTAAATTTGATATCGATA
*
395883 CTGAAAGGGGGTATCGGTACCATAGTATTT
66 CCGAAAGGGGGTATCGGTACCATAGTATTT
* * *
395913 TAGTATCGATACCATGGTAAGGGTATCGATTCCAGGAAACATCAAACCTAAATTTGATATCGATA
1 TAGTATCAATACCATGGTAAGGGTATCGATACCAAGAAACATCAAACCTAAATTTGATATCGATA
*
395978 CCGAAATGGGGTATCGGTACCATAGTAT
66 CCGAAAGGGGGTATCGGTACCATAGTAT
396006 AGAAGTATCG
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 84 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (95 bp):
TAGTATCAATACCATGGTAAGGGTATCGATACCAAGAAACATCAAACCTAAATTTGATATCGATA
CCGAAAGGGGGTATCGGTACCATAGTATTT
Found at i:396013 original size:95 final size:95
Alignment explanation
Indices: 395819--396039 Score: 291
Period size: 95 Copynumber: 2.3 Consensus size: 95
395809 CCAATGAGGT
* * * * *
395819 AGTATCAATACCATGGTAAGGGTATCGATACCAAGCAACATCGAATCTAAATTTGGTATCGATAC
1 AGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAACCTAAATTTGATATCGATAC
* ***
395884 TGAAAGGGGGTATCGGTACCATAGTATTTT
66 CGAAAGGGGGTATCGGTACCATAGTATAGA
* *
395914 AGTATCGATACCATGGTAAGGGTATCGATTCCAGGAAACATCAAACCTAAATTTGATATCGATAC
1 AGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAACCTAAATTTGATATCGATAC
*
395979 CGAAATGGGGTATCGGTACCATAGTATAGA
66 CGAAAGGGGGTATCGGTACCATAGTATAGA
* * *
396009 AGTATCGGTACCAGGGT-AGTAGTATCGATAC
1 AGTATCGATACCATGGTAAG-GGTATCGATAC
396040 TATATAGCTA
Statistics
Matches: 109, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
94 2 0.02
95 107 0.98
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (95 bp):
AGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAACCTAAATTTGATATCGATAC
CGAAAGGGGGTATCGGTACCATAGTATAGA
Found at i:396838 original size:54 final size:54
Alignment explanation
Indices: 396362--396816 Score: 613
Period size: 54 Copynumber: 8.4 Consensus size: 54
396352 TTACCAAATT
* * **
396362 GGCACTAAGTGTTCATTTCATGGAATTCATCCTATGTGGATGAATAACTATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
396416 GGTACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
396470 GGTACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGTTGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
396524 GGCACTAAGTGTGCATTTAACGGAATTCATCCTATGTTGATGAATAATCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
** * * * * *
396578 GAAACTAAGTGTGCTTTTTACGGAATTCATTCTATATGGATGAGTAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * **
396632 GGCACTAAGTGTGCATTTTACGGAATTCATCCTATATGGATGAATAACATTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * **
396686 GACAGTAAGTGTGCATTTCACGGAATTCATCCTACATGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
396740 GACACTAAGTTTTCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
396794 GGCACTGAGTGTGCATTTCACGG
1 GGCACTAAGTGTGCATTTCACGG
396817 GTTTCATAAT
Statistics
Matches: 351, Mismatches: 50, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 351 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:397524 original size:54 final size:54
Alignment explanation
Indices: 397466--398201 Score: 891
Period size: 54 Copynumber: 13.8 Consensus size: 54
397456 CATTACGGAA
* * * * **
397466 ATTCATAAACTTATTATGAATTCCGTGAATTGCACCCTTAGTGTCGAAACAATT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
* * * *
397520 ATTCATCAACATATGATGAATTTC--G---TG---A-TTAGTACCGAAATGGTT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
* * * * *
397565 ATTCATCTACTTATGATTAATTCTGTGAATTGCACACTTAGTACCAAAACGGTT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
* * * * * *
397619 ATTCATCAACTTATGATGAATTCCATGAATTGCACTCTTAATGTCAAAATAGG-T
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAA-CGGTT
** *
397673 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCAAAAACAGTT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
* * * * *
397727 ATTTATCAACTTATGATGAATTCTGTGAATTGCACACATAGTCCCGAAAAC-GTC
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCG-AAACGGTT
*
397781 ATTCATCAACTTATGATGAATTCCGTGACTTGCACACTTAGTGCCGAAACGGTT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
** *
397835 ATTCATCAACTTATGATGAATTTTGTGAATTACACACTTAGTGCCGAAACGGTT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
* * * *
397889 ATTCATCAACTTATGATGAATTTCGTGAATTGCACAATTAGTGTCGAAACAGTT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
* * * *
397943 ATTCATCAACTTATGATGAATTCTGTGAATTGCACAGTTAGTGCCAAAACCTGTT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAA-CGGTT
** * *
397998 ATTCATCAACTTATGATGAATTTTGTGAATTACACACTTAGTGCCGAAATGGTT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
* * * *
398052 ATTCATCAACTTATGATGAATTTCGTGAATTGCACAATTAGTGTCGAAATGGTT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
* *
398106 ATTCATCAACTTATGATGAATTCCGTGAATTGCACAGTTAGTGCCGAAACGATT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
* *
398160 ATTCATCAACTTATGATGAATTCAGTAAATTGCACACTTAGT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGT
398202 ACCTATTTGG
Statistics
Matches: 589, Mismatches: 79, Indels: 28
0.85 0.11 0.04
Matches are distributed among these distances:
45 31 0.05
47 1 0.00
49 2 0.00
50 2 0.00
52 1 0.00
53 6 0.01
54 491 0.83
55 55 0.09
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (54 bp):
ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTT
Found at i:397846 original size:27 final size:27
Alignment explanation
Indices: 397816--397901 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
397806 TGACTTGCAC
397816 ACTTAGTGCCGAAACGGTTATTCATCA
1 ACTTAGTGCCGAAACGGTTATTCATCA
** *** *
397843 ACTTA-TGATGAATTTTGTGAATT-A-CA
1 ACTTAGTGCCGAA-ACGGT-TATTCATCA
397869 CACTTAGTGCCGAAACGGTTATTCATCA
1 -ACTTAGTGCCGAAACGGTTATTCATCA
397897 ACTTA
1 ACTTA
397902 TGATGAATTT
Statistics
Matches: 41, Mismatches: 12, Indels: 12
0.63 0.18 0.18
Matches are distributed among these distances:
26 10 0.24
27 21 0.51
28 10 0.24
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (27 bp):
ACTTAGTGCCGAAACGGTTATTCATCA
Found at i:398063 original size:27 final size:27
Alignment explanation
Indices: 398033--398118 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
398023 TGAATTACAC
*
398033 ACTTAGTGCCGAAATGGTTATTCATCA
1 ACTTAGTGACGAAATGGTTATTCATCA
* * * *
398060 ACTTA-TGATGAATTTCGTGAATTGCA-CA
1 ACTTAGTGACGAA-ATGGT-TATT-CATCA
*
398088 A-TTAGTGTCGAAATGGTTATTCATCA
1 ACTTAGTGACGAAATGGTTATTCATCA
398114 ACTTA
1 ACTTA
398119 TGATGAATTC
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
25 2 0.05
26 11 0.26
27 17 0.40
28 11 0.26
29 2 0.05
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36
Consensus pattern (27 bp):
ACTTAGTGACGAAATGGTTATTCATCA
Found at i:403382 original size:54 final size:54
Alignment explanation
Indices: 403246--403722 Score: 661
Period size: 54 Copynumber: 8.8 Consensus size: 54
403236 CAATACGAAA
* * *
403246 ATTCATAAACTTACT-ATGAATTCCGTGAATTGCACCCTTAGTGCCGAAAACGGTT
1 ATTCATCAACTTA-TGATGAATTCCGTGAATTGCACACTTAGTGCCG-AAACAGTT
* * * *
403301 ATTCATCAACATATGATGAATTTCGTGAATTGCACACTTAGTGCCAAAATAGTT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
* ** *
403355 ATTCATCAACTTATGATGAATTCCGTGAATTGTACACTTAGTATCGAAATAGTT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
* * * *
403409 ATTCATCAACTTTTGATGAATTTCATGAATTGCACACTTAGTGCCGAAACGGTT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
403463 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
* *
403517 ATTCATCAACTTATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAATT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
* * * * * *
403571 ATTCATTAACTTAGGATGAATTCCATGAATTGCTCACTTAGAGCCGAAACGGTT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
* * *
403625 ATTCTTCAACTTATGATGAATTCAGTGATTTGCACACTTAGTGCCGAAACAGTT
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
* * *
403679 ATTCATCAACTTATGATTAATTACGTAAATTG-ACACTTAGTGCC
1 ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCC
403723 TATTTGGTAA
Statistics
Matches: 371, Mismatches: 50, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
53 12 0.03
54 320 0.86
55 39 0.11
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (54 bp):
ATTCATCAACTTATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACAGTT
Found at i:403501 original size:27 final size:27
Alignment explanation
Indices: 403471--403556 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
403461 TTATTCATCA
*
403471 ACTTATGATGAATTCCGTGAATTGCAC
1 ACTTATGATGAATTCAGTGAATTGCAC
** * *
403498 ACTTAGTGCCGAA-ACAGT-TATT-CATC
1 ACTTA-TGATGAATTCAGTGAATTGCA-C
*
403524 AACTTATGATGAATTCTGTGAATTGCAC
1 -ACTTATGATGAATTCAGTGAATTGCAC
403552 ACTTA
1 ACTTA
403557 GTGCCGAAAC
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
25 2 0.05
26 9 0.21
27 21 0.49
28 9 0.21
29 2 0.05
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (27 bp):
ACTTATGATGAATTCAGTGAATTGCAC
Found at i:408053 original size:2 final size:2
Alignment explanation
Indices: 408048--408082 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
408038 ATTTATTTTC
*
408048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
408083 GTTATTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:411722 original size:92 final size:92
Alignment explanation
Indices: 411557--411736 Score: 324
Period size: 92 Copynumber: 2.0 Consensus size: 92
411547 AAGACCATGG
* * *
411557 CAATATGATAAGAGGACCATCCATGATTTTTTTACCAATCAATATTCGTTCAACTATGGAGGGAT
1 CAATATGATAAGAGGACCATCCATGATTGTTTTACCAATCAATATTCGTTCAACCATGGAGGGAA
*
411622 GAAGATTATCCTAACACCTTTGACACC
66 GAAAATTATCCTAACACCTTTGACACC
411649 CAATATGATAAGAGGACCATCCATGATTGTTTTACCAATCAATATTCGTTCAACCATGGAGGGAA
1 CAATATGATAAGAGGACCATCCATGATTGTTTTACCAATCAATATTCGTTCAACCATGGAGGGAA
411714 GAAAATTATCCTAACACCTTTGA
66 GAAAATTATCCTAACACCTTTGA
411737 TTCCTAAACA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 84 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (92 bp):
CAATATGATAAGAGGACCATCCATGATTGTTTTACCAATCAATATTCGTTCAACCATGGAGGGAA
GAAAATTATCCTAACACCTTTGACACC
Found at i:413732 original size:22 final size:21
Alignment explanation
Indices: 413701--413745 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
413691 TATCTTCATT
413701 TCATCATCAACACCA-ACAACA
1 TCATCATCAACACCATA-AACA
*
413722 TCATCTATCAAGACCATAAACA
1 TCATC-ATCAACACCATAAACA
413744 TC
1 TC
413746 TTCTCAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 15 0.71
23 1 0.05
ACGTcount: A:0.44, C:0.33, G:0.02, T:0.20
Consensus pattern (21 bp):
TCATCATCAACACCATAAACA
Found at i:417415 original size:34 final size:34
Alignment explanation
Indices: 417327--417393 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
417317 TTAGAATATT
417327 TATA-ATATATATATATAATGGATAGTACCTATA
1 TATATATATATATATATAATGGATAGTACCTATA
417360 TATATATATATATATATAATGGATAGTACC-ATA
1 TATATATATATATATATAATGGATAGTACCTATA
417393 T
1 T
417394 TACTACTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 8 0.24
34 25 0.76
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (34 bp):
TATATATATATATATATAATGGATAGTACCTATA
Found at i:423900 original size:30 final size:30
Alignment explanation
Indices: 423861--423919 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
423851 AGTAAAACAC
*
423861 TCAATAAAATCAAAGAAA-AATAATTAAAAT
1 TCAAGAAAATCAAAGAAATAA-AATTAAAAT
*
423891 TCAAGAAAATTAAAGAAATAAAATTAAAA
1 TCAAGAAAATCAAAGAAATAAAATTAAAA
423920 ATGGGTTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (30 bp):
TCAAGAAAATCAAAGAAATAAAATTAAAAT
Found at i:434727 original size:12 final size:12
Alignment explanation
Indices: 434710--434736 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
434700 AACTTCCAAG
434710 GAGTTAGTATTA
1 GAGTTAGTATTA
434722 GAGTTAGTATTA
1 GAGTTAGTATTA
434734 GAG
1 GAG
434737 GAAGAAGTTG
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:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (12 bp):
GAGTTAGTATTA
Found at i:446839 original size:2 final size:2
Alignment explanation
Indices: 446832--446858 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
446822 AAATAAATAC
446832 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
446859 AAACATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:455887 original size:16 final size:16
Alignment explanation
Indices: 455866--455905 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
455856 TGAACAAAAT
455866 ATTTTACCCTTTTCCA
1 ATTTTACCCTTTTCCA
455882 ATTTTACCCTTTTCCA
1 ATTTTACCCTTTTCCA
455898 ATTTTACC
1 ATTTTACC
455906 AAGCAACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTACCCTTTTCCA
Found at i:465490 original size:16 final size:17
Alignment explanation
Indices: 465465--465498 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
465455 AATATATATG
465465 AATATATTATA-ATAAA
1 AATATATTATATATAAA
*
465481 AATATCTTATATATAAA
1 AATATATTATATATAAA
465498 A
1 A
465499 TTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AATATATTATATATAAA
Found at i:466285 original size:35 final size:35
Alignment explanation
Indices: 466232--466300 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
466222 ACTTAATTAT
*
466232 TTGTTCATAAATATAATCACAAACATCTTCATTTA
1 TTGTTCATAAATAGAATCACAAACATCTTCATTTA
* * * *
466267 TTGTTTATGAATAGAATCATAAACATCTTTATTT
1 TTGTTCATAAATAGAATCACAAACATCTTCATTT
466301 GATGTTGGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (35 bp):
TTGTTCATAAATAGAATCACAAACATCTTCATTTA
Found at i:467272 original size:2 final size:2
Alignment explanation
Indices: 467265--467289 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
467255 ACAAGTTCTT
467265 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
467290 GATGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:468164 original size:46 final size:46
Alignment explanation
Indices: 468111--468205 Score: 138
Period size: 46 Copynumber: 2.1 Consensus size: 46
468101 AAAGCAAACG
** *
468111 GGTGCATTATTGTTGCAATAAATGACCT-CTGAAAAGTTGTTAAAAT
1 GGTGCATTATTACTGCAATAAATGACCTAC-GAAAAGTAGTTAAAAT
*
468157 GGTGCATTATTACTGCAATAAATGACCTACGAAAAGTAGTTGAAAT
1 GGTGCATTATTACTGCAATAAATGACCTACGAAAAGTAGTTAAAAT
468203 GGT
1 GGT
468206 ACAATAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 43 0.98
47 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.32
Consensus pattern (46 bp):
GGTGCATTATTACTGCAATAAATGACCTACGAAAAGTAGTTAAAAT
Found at i:470391 original size:12 final size:12
Alignment explanation
Indices: 470374--470403 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
470364 AACATCTTCC
470374 CCATTACCTTAG
1 CCATTACCTTAG
470386 CCATTACCTTAG
1 CCATTACCTTAG
470398 CCATTA
1 CCATTA
470404 TAAAAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.33, G:0.07, T:0.33
Consensus pattern (12 bp):
CCATTACCTTAG
Found at i:473570 original size:25 final size:25
Alignment explanation
Indices: 473542--473596 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
473532 AGAATATGAA
473542 CAGCCCTTGGTTTGAATGATTAAAT
1 CAGCCCTTGGTTTGAATGATTAAAT
*
473567 CAGCCCTTGGTTTGGATGATTAAAT
1 CAGCCCTTGGTTTGAATGATTAAAT
473592 CAGCC
1 CAGCC
473597 TTGAATGCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (25 bp):
CAGCCCTTGGTTTGAATGATTAAAT
Found at i:474021 original size:17 final size:17
Alignment explanation
Indices: 473999--474066 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
473989 AATTAAGAGT
473999 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
474016 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
* *
474033 TAGTTTAATTAATGAGC
1 TAGTTTAATAAATGAAC
* *
474050 TAACTTTATTAAATGAA
1 T-AGTTTAATAAATGAA
474067 GTAGATGCAT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 30 0.73
18 11 0.27
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:474079 original size:17 final size:17
Alignment explanation
Indices: 474059--474121 Score: 67
Period size: 17 Copynumber: 3.7 Consensus size: 17
474049 CTAACTTTAT
474059 TAAATGAAGTAGATGCA
1 TAAATGAAGTAGATGCA
* *
474076 TAAATGAAGTAGCT-TA
1 TAAATGAAGTAGATGCA
*
474092 CTAAAT-AATCTAGATGCA
1 -TAAATGAA-GTAGATGCA
474110 TAAATGAAGTAG
1 TAAATGAAGTAG
474122 CTTACTAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
16 3 0.08
17 30 0.83
18 3 0.08
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (17 bp):
TAAATGAAGTAGATGCA
Found at i:474082 original size:35 final size:33
Alignment explanation
Indices: 474068--474175 Score: 121
Period size: 34 Copynumber: 3.2 Consensus size: 33
474058 TTAAATGAAG
*
474068 TAGATGCATAAATGAAGTAGCTTACTAAATAATC
1 TAGATGCATAAATG-AGTAACTTACTAAATAATC
*
474102 TAGATGCATAAATGAAGTAGCTTACTAAATAATC
1 TAGATGCATAAATG-AGTAACTTACTAAATAATC
* *
474136 TAAATGCATAAATGA-TATACTTCCCTAAATGAA-C
1 TAGATGCATAAATGAGTA-ACTT-ACTAAAT-AATC
474170 TAGATG
1 TAGATG
474176 ATTTAAATAA
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
32 2 0.03
33 4 0.06
34 59 0.88
35 2 0.03
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.30
Consensus pattern (33 bp):
TAGATGCATAAATGAGTAACTTACTAAATAATC
Found at i:474106 original size:34 final size:34
Alignment explanation
Indices: 474068--474150 Score: 157
Period size: 34 Copynumber: 2.4 Consensus size: 34
474058 TTAAATGAAG
474068 TAGATGCATAAATGAAGTAGCTTACTAAATAATC
1 TAGATGCATAAATGAAGTAGCTTACTAAATAATC
474102 TAGATGCATAAATGAAGTAGCTTACTAAATAATC
1 TAGATGCATAAATGAAGTAGCTTACTAAATAATC
*
474136 TAAATGCATAAATGA
1 TAGATGCATAAATGA
474151 TATACTTCCC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (34 bp):
TAGATGCATAAATGAAGTAGCTTACTAAATAATC
Found at i:474130 original size:17 final size:17
Alignment explanation
Indices: 474076--474131 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
474066 AGTAGATGCA
474076 TAAATGAAGTAGCTTAC
1 TAAATGAAGTAGCTTAC
* * *
474093 TAAAT-AATCTAG-ATGC
1 TAAATGAA-GTAGCTTAC
474109 ATAAATGAAGTAGCTTAC
1 -TAAATGAAGTAGCTTAC
474127 TAAAT
1 TAAAT
474132 AATCTAAATG
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
16 4 0.14
17 21 0.72
18 4 0.14
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (17 bp):
TAAATGAAGTAGCTTAC
Found at i:478416 original size:2 final size:2
Alignment explanation
Indices: 478411--478471 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
478401 TATGCATAAT
478411 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
478453 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
478472 GCAACTGATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:480063 original size:31 final size:31
Alignment explanation
Indices: 480036--480097 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
480026 TTACAAATTT
* *
480036 GTCACTAATATTATCGATTTAAAACAAAATG
1 GTCACTAACATTATAGATTTAAAACAAAATG
* *
480067 GTCACTAACATTTTAGATTTATAACAAAATG
1 GTCACTAACATTATAGATTTAAAACAAAATG
480098 AGCACTCTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (31 bp):
GTCACTAACATTATAGATTTAAAACAAAATG
Found at i:482281 original size:4 final size:4
Alignment explanation
Indices: 482272--482298 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
482262 AAGAAACATG
482272 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
482299 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:482303 original size:2 final size:2
Alignment explanation
Indices: 482296--482329 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
482286 ACATACATAC
482296 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
482330 CATGTAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:482654 original size:13 final size:14
Alignment explanation
Indices: 482620--482656 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
482610 TTAAAAGATT
482620 GAAATTTAAAGGAAA
1 GAAA-TTAAAGGAAA
482635 GAAATTAAAGGAAA
1 GAAATTAAAGGAAA
482649 -AAATTAAA
1 GAAATTAAA
482657 ATAACAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.36
14 10 0.45
15 4 0.18
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (14 bp):
GAAATTAAAGGAAA
Found at i:486305 original size:38 final size:38
Alignment explanation
Indices: 486263--486343 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
486253 AAGATTTGTG
486263 GCTTTTCAAATGATGGCTTAAGTAGGTGGATAATGCTC
1 GCTTTTCAAATGATGGCTTAAGTAGGTGGATAATGCTC
*
486301 GCTTTTCAAATGATGGCTTAAGTAGGTGGATAATGCTT
1 GCTTTTCAAATGATGGCTTAAGTAGGTGGATAATGCTC
486339 GCTTT
1 GCTTT
486344 ATCTCCTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (38 bp):
GCTTTTCAAATGATGGCTTAAGTAGGTGGATAATGCTC
Found at i:490442 original size:240 final size:241
Alignment explanation
Indices: 490007--490449 Score: 728
Period size: 240 Copynumber: 1.8 Consensus size: 241
489997 AATAAGAAAT
* * *
490007 GTAAACAAGAAAGCCTCACAAAGGTAGGTGTTTACAAGAATTGATATCACATGAATGGATGCAAA
1 GTAAACAAGAAAGCCTCACAAAGGTAGGTGTTTACAAGAATTGAGATCACAAGAATGAATGCAAA
* *
490072 AGATAGACAATTAGGCTCAAACACTTGTGTACAAGAGAAAAAAGAAAATAAAGAGTGAAAGAGTT
66 AGATAGACAATTAGGCTCAAACACTTATGTACAACAGAAAAAAGAAAATAAAGAGTGAAAGAGTT
* ** * * *
490137 TTTCTCTTGATCTCTATTACTTGGATAGGTGTTGTAACCTTCTTCAAGTGTCCTTAGAGTGTTTT
131 TTTCTCTTAATCTAAATTACTTGGATAGGTGTTGTAACCTTCTTCAAGTGTCCCTAAAATGTTTT
490202 TATTGTGTAAAATAAGTTTATATCCATTTACGACAATTTGGGATGA
196 TATTGTGTAAAATAAGTTTATATCCATTTACGACAATTTGGGATGA
* *
490248 GTAAACAAGAAAGCCTCACAAAGTTAGGTGTTTACAAGAATTGAGCTCACAAGAAT-AATGCAAA
1 GTAAACAAGAAAGCCTCACAAAGGTAGGTGTTTACAAGAATTGAGATCACAAGAATGAATGCAAA
490312 AGATAGACAATT-GAGCTCAAACACTTATGTACAACAGAAAAAAGAAAATAAAGAGTGAAAGAGT
66 AGATAGACAATTAG-GCTCAAACACTTATGTACAACAGAAAAAAGAAAATAAAGAGTGAAAGAGT
**
490376 TTTTCTCTTAATCTAAATTGTTTGGATAGGTGTTGTAACCTTCTTCAAGTGTCCCTAAAATGTTT
130 TTTTCTCTTAATCTAAATTACTTGGATAGGTGTTGTAACCTTCTTCAAGTGTCCCTAAAATGTTT
490441 TTATTGTGT
195 TTATTGTGT
490450 GGAATGAGTT
Statistics
Matches: 186, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
239 1 0.01
240 133 0.72
241 52 0.28
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (241 bp):
GTAAACAAGAAAGCCTCACAAAGGTAGGTGTTTACAAGAATTGAGATCACAAGAATGAATGCAAA
AGATAGACAATTAGGCTCAAACACTTATGTACAACAGAAAAAAGAAAATAAAGAGTGAAAGAGTT
TTTCTCTTAATCTAAATTACTTGGATAGGTGTTGTAACCTTCTTCAAGTGTCCCTAAAATGTTTT
TATTGTGTAAAATAAGTTTATATCCATTTACGACAATTTGGGATGA
Found at i:490702 original size:11 final size:11
Alignment explanation
Indices: 490686--490722 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
490676 ATTTTAAAAG
490686 TTTTAAACACA
1 TTTTAAACACA
490697 TTTTAAACAC-
1 TTTTAAACACA
*
490707 -TTTAAACATA
1 TTTTAAACACA
490717 TTTTAA
1 TTTTAA
490723 TTAACTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 8 0.35
11 15 0.65
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (11 bp):
TTTTAAACACA
Found at i:494240 original size:3 final size:3
Alignment explanation
Indices: 494227--494280 Score: 90
Period size: 3 Copynumber: 17.7 Consensus size: 3
494217 TACTTAGTAT
494227 TAA TCAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
494273 TAG TAA TA
1 TAA TAA TA
494281 GTAAATGATT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:496905 original size:158 final size:157
Alignment explanation
Indices: 496233--497082 Score: 967
Period size: 157 Copynumber: 5.4 Consensus size: 157
496223 CCTGATTTCA
* * * * * * * * * *
496233 TTATTTCTTCAATTC-CCCTTCATTTTAAGTCTATTTTTACCATATTAGAATCATATGCTCTTAA
1 TTATTTCTTCAATTCATCATTTATTTTAAGTATTTTTTTACCAAATTTGAACCACATGCTCCTAA
* *
496297 ACCATCGTAGAATACATGTGTACTTTCAATTCCTCCTTTTGATAATAAATTTTCTA-TTTTCAAT
66 ACCATCATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAAATTTTCTATTTTTCAAT
* * *
496361 TTAGTCCCT-ATATTTTTCATGTTTTCC
131 TTAGTCCCTCA-ACTTTTCATATCTTCC
* * * * * *
496388 ATATTTCTTGAATTCATTATTTATTTTAAGTCCCCCTTTTTTTTTTACCAAATTTAAATCACATG
1 TTATTTCTTCAATTCATCATTTATTTTAAG-------TATTTTTTTACCAAATTTGAACCACATG
* * * *
496453 CTCCTAAACCATCATATAATACATGTATACTTTCAATTCCTCTTTTTGAGAATAAACTTTCTATT
59 CTCCTAAACCATCATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAAATTTTCTATT
* * * *
496518 TTTCAATTTAATCCTTAAACTTTTTATATCTTCC
124 TTTCAATTTAGTCCCTCAACTTTTCATATCTTCC
* * *
496552 TTATTTCTCCAATTCATCCTTTATTTTAAGTATTTTTTTACCAAATTTGAACCACATGCTTCTAA
1 TTATTTCTTCAATTCATCATTTATTTTAAGTATTTTTTTACCAAATTTGAACCACATGCTCCTAA
* * *
496617 ACCATTGA-ATAATACATGTGTACTTTCAATTCCTATTTTTGATAATAAATTTTCTATTTTTCAA
66 ACCA-TCATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAAATTTTCTATTTTTCAA
* * *
496681 TTTTGTTCCTCAACTTTCCATATCTTCC
130 TTTAGTCCCTCAACTTTTCATATCTTCC
*
496709 TTATTTCTTCAATTCATCCTTTATTTTAAGTATCTTTTTTACCAAATTTGAACCACATGCTCCT-
1 TTATTTCTTCAATTCATCATTTATTTTAAGTAT-TTTTTTACCAAATTTGAACCACATGCTCCTA
* *
496773 AACAATCATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAAATTTTCTATTTTTAAA
65 AACCATCATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAAATTTTCTATTTTTCAA
*
496838 TTTAGTCCCTCAACTTTTTTATATCTTCC
130 TTTAGTCCCTCAAC-TTTTCATATCTTCC
* * * * *
496867 TTATTTCTTTAATTCATCATTTATTTTAAGTATGTTTTTACCAAAGTTGAACCACGT-ATCCGTA
1 TTATTTCTTCAATTCATCATTTATTTTAAGTATTTTTTTACCAAATTTGAACCACATGCTCC-TA
* * * * * ** *
496931 ATCCATTATAGAATACATGTGTCCTTTTAATTTCTCTTGCTGATAATAAAAATTT-TATTTTTCA
65 AACCATCATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAAT-AAATTTTCTATTTTTCA
*
496995 ATTTAGTCCCTCAACTTTTCATATATTCC
129 ATTTAGTCCCTCAACTTTTCATATCTTCC
* * * **
497024 TTATTTCTACAATTCAACATTTATTTTAAGTCCCTTTTTTTAATAAATTTGAACCACAT
1 TTATTTCTTCAATTCATCATTTATTTTAAGT--ATTTTTTTACCAAATTTGAACCACAT
497083 TCTCATATAT
Statistics
Matches: 592, Mismatches: 84, Indels: 34
0.83 0.12 0.05
Matches are distributed among these distances:
155 13 0.02
156 15 0.03
157 271 0.46
158 136 0.23
159 26 0.04
163 78 0.13
164 52 0.09
165 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.47
Consensus pattern (157 bp):
TTATTTCTTCAATTCATCATTTATTTTAAGTATTTTTTTACCAAATTTGAACCACATGCTCCTAA
ACCATCATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAAATTTTCTATTTTTCAAT
TTAGTCCCTCAACTTTTCATATCTTCC
Found at i:496907 original size:315 final size:316
Alignment explanation
Indices: 496254--497082 Score: 990
Period size: 315 Copynumber: 2.6 Consensus size: 316
496244 ATTCCCCTTC
* * * * * * * *
496254 ATTTTAAGTCTATTTTTACCATATTAGAATCATATGC-TCTTAAACCATCGTAGAATACATGTGT
1 ATTTTAAGTATATTTTTACCAAATTTGAACCACATGCTTCGTAAACCATTGAAGAATACATGTGT
* *
496318 ACTTTCAATTCCTCCTTTTGATAATAAATTTTCTA-TTTTCAATTTAGTCCCT-ATATTTTTCAT
66 ACTTTCAATTCCTCTTTTTGATAATAAATTTTCTATTTTTCAATTTAGTCCCTCA-ACTTTTCAT
* * * * * * * *
496381 GTTTTCCATATTTCTTGAATTCATTATTTATTTTAAGTCCCCCTTTTTTTTTTACCAAATTTAAA
130 ATATTCCTTATTTCTTCAATTCATCATTTATTTTAAG------TATCTTTTTTACCAAATTTGAA
* * *
496446 TCACATGCTCCTAAACCATCATATAATACATGTATACTTTCAATTCCTCTTTTTGAGAATAAACT
189 CCACATGCTCCTAAACAATCATAGAATACATGTATACTTTCAATTCCTCTTTTTGAGAATAAACT
* * *
496511 TTCTATTTTTCAATTTAATCCTTAAACTTTTTATATCTTCCTTATTTCTCCAATTCATCCTTT
254 TTCTATTTTTAAATTTAATCCCTAAACTTTTTATATCTTCCTTATTTCTCCAATTCATCATTT
* *
496574 ATTTTAAGTATTTTTTTACCAAATTTGAACCACATGCTTC-TAAACCATTGAATAATACATGTGT
1 ATTTTAAGTATATTTTTACCAAATTTGAACCACATGCTTCGTAAACCATTGAAGAATACATGTGT
* * * *
496638 ACTTTCAATTCCTATTTTTGATAATAAATTTTCTATTTTTCAATTTTGTTCCTCAACTTTCCATA
66 ACTTTCAATTCCTCTTTTTGATAATAAATTTTCTATTTTTCAATTTAGTCCCTCAACTTTTCATA
* *
496703 TCTTCCTTATTTCTTCAATTCATCCTTTATTTTAAGTATCTTTTTTACCAAATTTGAACCACATG
131 TATTCCTTATTTCTTCAATTCATCATTTATTTTAAGTATCTTTTTTACCAAATTTGAACCACATG
* * *
496768 CTCCT-AACAATCATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAATAAATTTTCTATT
196 CTCCTAAACAATCATAGAATACATGTATACTTTCAATTCCTCTTTTTGAGAATAAACTTTCTATT
* * **
496832 TTTAAATTTAGTCCCTCAACTTTTTTATATCTTCCTTATTTCTTTAATTCATCATTT
261 TTTAAATTTAATCCCTAAAC-TTTTTATATCTTCCTTATTTCTCCAATTCATCATTT
* * * * * *
496889 ATTTTAAGTATGTTTTTACCAAAGTTGAACCACGT-ATCCGTAATCCATT-ATAGAATACATGTG
1 ATTTTAAGTATATTTTTACCAAATTTGAACCACATGCTTCGTAAACCATTGA-AGAATACATGTG
* * * ** *
496952 TCCTTTTAATTTCTCTTGCTGATAATAAAAATTT-TATTTTTCAATTTAGTCCCTCAACTTTTCA
65 TACTTTCAATTCCTCTTTTTGATAAT-AAATTTTCTATTTTTCAATTTAGTCCCTCAACTTTTCA
* * ** **
497016 TATATTCCTTATTTCTACAATTCAACATTTATTTTAAGTCCCTTTTTTTAATAAATTTGAACCAC
129 TATATTCCTTATTTCTTCAATTCATCATTTATTTTAAGTATC-TTTTTTACCAAATTTGAACCAC
497081 AT
193 AT
497083 TCTCATATAT
Statistics
Matches: 439, Mismatches: 62, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
314 73 0.17
315 197 0.45
316 28 0.06
320 85 0.19
321 55 0.13
322 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (316 bp):
ATTTTAAGTATATTTTTACCAAATTTGAACCACATGCTTCGTAAACCATTGAAGAATACATGTGT
ACTTTCAATTCCTCTTTTTGATAATAAATTTTCTATTTTTCAATTTAGTCCCTCAACTTTTCATA
TATTCCTTATTTCTTCAATTCATCATTTATTTTAAGTATCTTTTTTACCAAATTTGAACCACATG
CTCCTAAACAATCATAGAATACATGTATACTTTCAATTCCTCTTTTTGAGAATAAACTTTCTATT
TTTAAATTTAATCCCTAAACTTTTTATATCTTCCTTATTTCTCCAATTCATCATTT
Found at i:497931 original size:60 final size:60
Alignment explanation
Indices: 497849--498039 Score: 197
Period size: 60 Copynumber: 3.1 Consensus size: 60
497839 AAAACAAACG
* * *
497849 TACTTACACCAATATAATTATGTGTTTATTTTTTGGTACCAAGATAATAGGAGCTGTACA
1 TACTTACACCAGTATAAGTATGTGTTTATTTTTTGGTACCAAGATAATAGGAGATGTACA
* * * * * *
497909 TACTTATACTAGTGTAAGTATGTGTTTATTTTTAT-GTACCAAGAT-ATTGGAAAATGTGCA
1 TACTTACACCAGTATAAGTATGTGTTTATTTTT-TGGTACCAAGATAATAGG-AGATGTACA
* * * * * *
497969 TACTTACACCGGTATAAGTATGTGTTTGTTTTTAGGTACCATGTTATTGAGAGAGATGTACA
1 TACTTACACCAGTATAAGTATGTGTTTATTTTTTGGTACCAAGATAAT-AG-GAGATGTACA
498031 TACTTACAC
1 TACTTACAC
498040 TGATGTTAAT
Statistics
Matches: 104, Mismatches: 21, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
59 4 0.04
60 80 0.77
61 2 0.02
62 17 0.16
63 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (60 bp):
TACTTACACCAGTATAAGTATGTGTTTATTTTTTGGTACCAAGATAATAGGAGATGTACA
Found at i:499356 original size:24 final size:24
Alignment explanation
Indices: 499329--499378 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
499319 AGACATAATT
499329 TTAGATAACATTATTATTGATTTA
1 TTAGATAACATTATTATTGATTTA
*
499353 TTAGATAACGTTATTATTGATTTA
1 TTAGATAACATTATTATTGATTTA
499377 TT
1 TT
499379 TTGTTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.04, G:0.10, T:0.52
Consensus pattern (24 bp):
TTAGATAACATTATTATTGATTTA
Found at i:501319 original size:40 final size:39
Alignment explanation
Indices: 501247--501323 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
501237 AAGAAACAAG
*
501247 ATTAAAGACAACAAAAATAATGGTAATAAAATTGAGAAAA
1 ATTAAAGACAACAAAAATAAGGGTAATAAAATT-AGAAAA
* *
501287 ATTAGAGACAAGAGAAAATAAGGGTAAT-AAATTAGAA
1 ATTAAAGACAACA-AAAATAAGGGTAATAAAATTAGAA
501324 CATAAGACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 16 0.48
41 13 0.39
ACGTcount: A:0.60, C:0.04, G:0.17, T:0.19
Consensus pattern (39 bp):
ATTAAAGACAACAAAAATAAGGGTAATAAAATTAGAAAA
Found at i:509445 original size:2 final size:2
Alignment explanation
Indices: 509438--509471 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
509428 TGTGTATTTA
509438 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
509472 TTGTGTGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:514172 original size:24 final size:24
Alignment explanation
Indices: 514139--514199 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
514129 TGATCAATGT
514139 AATT-AACATGCAATCGAATTTTC
1 AATTAAACATGCAATCGAATTTTC
514162 AATTAAACATGCAATCGAATTTTC
1 AATTAAACATGCAATCGAATTTTC
514186 AATTAAACATGCAA
1 AATTAAACATGCAA
514200 ACATTGTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.11
24 33 0.89
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.31
Consensus pattern (24 bp):
AATTAAACATGCAATCGAATTTTC
Found at i:526860 original size:21 final size:21
Alignment explanation
Indices: 526802--526852 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
526792 CCTTTACCTT
526802 AAGGGATCGATCCTTTTGAGA
1 AAGGGATCGATCCTTTTGAGA
526823 AAGGGATCGATCCTTTTGAGA
1 AAGGGATCGATCCTTTTGAGA
526844 AAGGGATCG
1 AAGGGATCG
526853 GTCTTTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.25
Consensus pattern (21 bp):
AAGGGATCGATCCTTTTGAGA
Found at i:529036 original size:16 final size:17
Alignment explanation
Indices: 529015--529051 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
529005 CAAATTTAAA
*
529015 ATTTATTTTTTTAA-TT
1 ATTTATATTTTTAATTT
529031 ATTTATATTTTTAATTT
1 ATTTATATTTTTAATTT
529048 ATTT
1 ATTT
529052 TCAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTATATTTTTAATTT
Found at i:531500 original size:3 final size:3
Alignment explanation
Indices: 531492--531550 Score: 82
Period size: 3 Copynumber: 19.3 Consensus size: 3
531482 TATTTTTAAA
* * *
531492 ATT ATT ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT ATT AAAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
531538 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
531551 CAGGCCCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
3 47 0.96
4 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:532850 original size:2 final size:2
Alignment explanation
Indices: 532843--532904 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
532833 CTTTTTAGTC
532843 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
532885 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
532905 TTTAGAGTAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:537023 original size:229 final size:227
Alignment explanation
Indices: 536618--537066 Score: 783
Period size: 229 Copynumber: 2.0 Consensus size: 227
536608 GTAAATTATC
* * *
536618 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
536683 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
536748 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
536813 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
* *
536846 TATCATTTTTATAAAAGTGTCCATACTTATTTTACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
536911 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-ATAAT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT-AT
* *
536975 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
537040 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
537067 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
228 41 0.20
229 169 0.80
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:537155 original size:20 final size:19
Alignment explanation
Indices: 537132--537177 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
537122 CGATATACCA
537132 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
537152 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
537172 GGTAAA
1 GGTAAA
537178 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:537321 original size:20 final size:20
Alignment explanation
Indices: 537298--537345 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
537288 CGATATAACA
*
537298 GGTAAAATTATGATAAAACC
1 GGTAAAATAATGATAAAACC
537318 GGTAACAA-AATGATAAAACC
1 GGTAA-AATAATGATAAAACC
537338 GGTAAAAT
1 GGTAAAAT
537346 GATACCGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 21 0.84
21 2 0.08
ACGTcount: A:0.52, C:0.10, G:0.17, T:0.21
Consensus pattern (20 bp):
GGTAAAATAATGATAAAACC
Found at i:539618 original size:21 final size:21
Alignment explanation
Indices: 539571--539635 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
539561 AAGACAATCA
* *
539571 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
539593 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
539613 AGAGTCGAAGA-AACACTCGAG
1 AGAGTCGAAGAGAA-ACTCGAG
539634 AG
1 AG
539636 GAATAAGGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 3 0.08
21 33 0.89
22 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.29, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:539709 original size:32 final size:32
Alignment explanation
Indices: 539668--539728 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
539658 AAATAGATGG
*
539668 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
* *
539700 AGTGGTGAAAGAAGTTGGGGTGTTAAGGG
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGG
539729 GTGATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.48, T:0.23
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
Found at i:541549 original size:19 final size:19
Alignment explanation
Indices: 541525--541573 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
541515 AATGTCGAGT
541525 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
541544 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
541563 TATTTTTGTAT
1 TAATTTTGTAT
541574 GTCAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:542228 original size:198 final size:198
Alignment explanation
Indices: 541692--543254 Score: 3026
Period size: 198 Copynumber: 7.9 Consensus size: 198
541682 CAATATGGCC
* *
541692 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
541757 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
541822 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
541887 TGGAA
195 TGG-A
*
541892 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCCAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
541957 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
542022 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
542087 GGA
196 GGA
542090 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
542155 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
542220 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
542285 GGA
196 GGA
542288 AACAAGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
542351 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
542416 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
542481 GGA
196 GGA
542484 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
542549 CAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
542613 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
542678 GGA
196 GGA
542681 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
542746 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
542811 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
542876 GGA
196 GGA
542879 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
542944 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCAGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
543009 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
543074 GGAA
196 GG-A
543078 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
543142 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
543207 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
543255 AATTTAAATA
Statistics
Matches: 1351, Mismatches: 8, Indels: 10
0.99 0.01 0.01
Matches are distributed among these distances:
196 195 0.14
197 196 0.15
198 730 0.54
199 196 0.15
200 34 0.03
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (198 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGA
Found at i:542971 original size:593 final size:595
Alignment explanation
Indices: 541692--543254 Score: 3037
Period size: 593 Copynumber: 2.6 Consensus size: 595
541682 CAATATGGCC
* *
541692 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
541757 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
541822 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
541887 TGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
195 TGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
*
541952 CAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
260 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
542017 GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAA
325 GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAA
542082 TGAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
390 TGAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
542147 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
455 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
542212 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCA
520 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCA
542277 GAATGAATGGA
585 GAATGAATGGA
542288 AACAAGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
542351 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
542416 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
542481 GG-AAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
542545 AACCCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
542609 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
542674 GAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCA
391 GAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCA
542739 TCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
456 TCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
542804 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAG
521 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAG
542869 AATGAATGGA
586 AATGAATGGA
542879 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
542944 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCAGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
543009 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
543074 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
543138 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
543203 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
543255 AATTTAAATA
Statistics
Matches: 957, Mismatches: 6, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
591 336 0.35
592 88 0.09
593 376 0.39
594 129 0.13
596 28 0.03
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (595 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
GAATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCA
TCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAG
AATGAATGGA
Found at i:544693 original size:3 final size:3
Alignment explanation
Indices: 544685--544756 Score: 65
Period size: 3 Copynumber: 24.0 Consensus size: 3
544675 TCTTTTAACA
* * ** * *
544685 GAT GAT GAT GAT GAC GAT GA- AACT GGC GAT GAA GAT GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GA-T GAT GAT GAT GAT GAT GAT GAT
*
544730 GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
544757 CCAAACAAGT
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
2 1 0.02
3 52 0.98
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:546290 original size:183 final size:182
Alignment explanation
Indices: 545955--546380 Score: 746
Period size: 183 Copynumber: 2.3 Consensus size: 182
545945 CAAAGTTTTC
* * * * *
545955 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
546020 AAAAAAGTGTCGATTGAAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATA
66 AAAAAAGTGTCGATT--AAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATA
546085 TAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
129 TAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
546139 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
* *
546204 AAAAAAGTGTCGACATT-TACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATA
66 AAAAAAGTGTCG--ATTAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATA
546268 TAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
129 TAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
546322 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATA
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATA
546381 GGATGTGGCA
Statistics
Matches: 233, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
183 158 0.68
184 72 0.31
186 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (182 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGATTAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATA
ACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
Found at i:546621 original size:23 final size:23
Alignment explanation
Indices: 546590--546652 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
546580 ATAGGTAAAC
*
546590 ATATGATGTAATAGGTACCCCTT
1 ATATAATGTAATAGGTACCCCTT
* **
546613 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTACCCCTT
546636 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
546653 GTGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTACCCCTT
Found at i:546660 original size:23 final size:23
Alignment explanation
Indices: 546590--546662 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
546580 ATAGGTAAAC
* * **
546590 ATATGATGTAATAGGTACCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
546613 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
546636 ATATAATGTAATAGGTAGT-GGTT
1 ATATAATGTAATAGGTA-TCGGTT
546659 ATAT
1 ATAT
546663 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 43 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:546959 original size:24 final size:25
Alignment explanation
Indices: 546927--546976 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
546917 ACAACAAATC
*
546927 AATTAAACATTG-TGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
546951 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
546976 A
1 A
546977 TTTGGATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Done.