Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009576.1 Hibiscus syriacus cultivar Beakdansim tig00116944_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: 1684752
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1430206 original size:84 final size:84
Alignment explanation
Indices: 1430092--1430298 Score: 287
Period size: 84 Copynumber: 2.5 Consensus size: 84
1430082 GCAACTTAGT
* * * *
1430092 CAACTCAGGAACCTTT-GGAAGTTCTGGCTTTGGCAACTCGGGCACTTTTGGAAACTCAGGTACC
1 CAACTCATGAA-CTTTAGGAAGTTCAGGCTTTGGCAACTCGGGCACTGTTGGAAACTCAGGAACC
*
1430156 TTAGGTAATTCTA-GCTTTGG
65 TTAGGCAATTC-AGGCTTTGG
*
1430176 CAACTCATGAACTTTAGGAAGTTCAGGCTTTGGCAACTCTGGCACTGTTGGAAACTCAGGAACCT
1 CAACTCATGAACTTTAGGAAGTTCAGGCTTTGGCAACTCGGGCACTGTTGGAAACTCAGGAACCT
1430241 TAGGCAATTCAGGCTTTGG
66 TAGGCAATTCAGGCTTTGG
*
1430260 CAACTC-TGGAACTTTAGGTAA-TTCAGGCTTAGGCAACTC
1 CAACTCAT-GAACTTTAGG-AAGTTCAGGCTTTGGCAACTC
1430299 AGGTATTTTA
Statistics
Matches: 112, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
83 6 0.05
84 104 0.93
85 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (84 bp):
CAACTCATGAACTTTAGGAAGTTCAGGCTTTGGCAACTCGGGCACTGTTGGAAACTCAGGAACCT
TAGGCAATTCAGGCTTTGG
Found at i:1430232 original size:51 final size:51
Alignment explanation
Indices: 1430172--1430268 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
1430162 AATTCTAGCT
* * *
1430172 TTGGCAACTCATGAACTTTAGG-AAGTTCAGGCTTTGGCAACTCTGGCACTG
1 TTGGAAACTCAGGAACCTTAGGCAA-TTCAGGCTTTGGCAACTCTGGCACTG
1430223 TTGGAAACTCAGGAACCTTAGGCAATTCAGGCTTTGGCAACTCTGG
1 TTGGAAACTCAGGAACCTTAGGCAATTCAGGCTTTGGCAACTCTGG
1430269 AACTTTAGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
51 40 0.95
52 2 0.05
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.28
Consensus pattern (51 bp):
TTGGAAACTCAGGAACCTTAGGCAATTCAGGCTTTGGCAACTCTGGCACTG
Found at i:1430300 original size:15 final size:15
Alignment explanation
Indices: 1430239--1430301 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
1430229 ACTCAGGAAC
*
1430239 CTTAGGCAATTCAGG
1 CTTAGGCAACTCAGG
* *
1430254 CTTTGGCAACTCTGG
1 CTTAGGCAACTCAGG
* *
1430269 AACTTTAGGTAATTCAGG
1 --C-TTAGGCAACTCAGG
1430287 CTTAGGCAACTCAGG
1 CTTAGGCAACTCAGG
1430302 TATTTTAGGT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
15 24 0.67
16 1 0.03
17 1 0.03
18 10 0.28
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (15 bp):
CTTAGGCAACTCAGG
Found at i:1430309 original size:33 final size:33
Alignment explanation
Indices: 1430228--1430317 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
1430218 CACTGTTGGA
* * *
1430228 AACTCAGGAACCTTAGGCAATTCAGGCTTTGGC
1 AACTCAGGAACTTTAGGTAATTCAGGCTTAGGC
*
1430261 AACTCTGGAACTTTAGGTAATTCAGGCTTAGGC
1 AACTCAGGAACTTTAGGTAATTCAGGCTTAGGC
* * *
1430294 AACTCAGGTATTTTAGGTATTTCA
1 AACTCAGGAACTTTAGGTAATTCA
1430318 AGTTTTGAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (33 bp):
AACTCAGGAACTTTAGGTAATTCAGGCTTAGGC
Found at i:1431316 original size:82 final size:82
Alignment explanation
Indices: 1431220--1431379 Score: 284
Period size: 82 Copynumber: 2.0 Consensus size: 82
1431210 AACGTAATAT
1431220 AACCTTTGACATATAATATAATACAGATGCCTATTAATTGATCGAATAGTCAAAAATATTTATGT
1 AACCTTTGACATATAATATAATACAGATGCCTATTAATTGATCGAATAGTCAAAAATATTTATGT
1431285 CGTATCAATTTGTATAC
66 CGTATCAATTTGTATAC
* * *
1431302 AACCTTTGGCATATAATATAATACAGATGTCTATTAATTGATCGAATATTCAAAAATATTTATGT
1 AACCTTTGACATATAATATAATACAGATGCCTATTAATTGATCGAATAGTCAAAAATATTTATGT
*
1431367 TGTATCAATTTGT
66 CGTATCAATTTGT
1431380 GTACGTTCGA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (82 bp):
AACCTTTGACATATAATATAATACAGATGCCTATTAATTGATCGAATAGTCAAAAATATTTATGT
CGTATCAATTTGTATAC
Found at i:1434117 original size:33 final size:34
Alignment explanation
Indices: 1434080--1434191 Score: 133
Period size: 33 Copynumber: 3.4 Consensus size: 34
1434070 ATTCCTACCT
* * *
1434080 GATTAACCTGGCTAGTCC-GCGTAGGCTCAGG-CA
1 GATTAACCTGGCTCG-CCTGGGTAGGCTCCGGCCA
* *
1434113 GATTAACCTGGCTCGCCTGGGTACGTTCCGGCCA
1 GATTAACCTGGCTCGCCTGGGTAGGCTCCGGCCA
*
1434147 -ATTAACCTGGCTCGCCTGGGTAGGCTCCGGTC-
1 GATTAACCTGGCTCGCCTGGGTAGGCTCCGGCCA
1434179 GATTAACCTGGCT
1 GATTAACCTGGCT
1434192 TGTCCGTGTA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
32 2 0.03
33 64 0.94
34 2 0.03
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.24
Consensus pattern (34 bp):
GATTAACCTGGCTCGCCTGGGTAGGCTCCGGCCA
Found at i:1434509 original size:48 final size:48
Alignment explanation
Indices: 1434435--1434666 Score: 261
Period size: 48 Copynumber: 4.8 Consensus size: 48
1434425 TTTCTTTGGG
* * * *
1434435 CGGCGTTTGCATAAACAGCGTTTGCGTTTCTTTCGGAGGTGGAGGTGC
1 CGGCGGTTGCATAAACAGCGTCTGCGTTTCTTTCGGAGGCGGAGGCGC
* ** *
1434483 CGGCGGTTGCATAAATAGCGTCTGCGTTTCTTTATGATGCGGAGGCGC
1 CGGCGGTTGCATAAACAGCGTCTGCGTTTCTTTCGGAGGCGGAGGCGC
* * * * *
1434531 CGGTGGCTGCATAAACAGAGGT-TGCGTTTCTTTCGGAGGCGGATGCGT
1 CGGCGGTTGCATAAACAG-CGTCTGCGTTTCTTTCGGAGGCGGAGGCGC
*
1434579 CGGCGGTTGCATAAACAGCGTCTGCGTTTCTTTAGGAGGCGGAGGCGC
1 CGGCGGTTGCATAAACAGCGTCTGCGTTTCTTTCGGAGGCGGAGGCGC
* * * * *
1434627 TGGTGGTTGCATTAAA-AGAGTTTGCGTCTCTTTCGGAGGC
1 CGGCGGTTGCA-TAAACAGCGTCTGCGTTTCTTTCGGAGGC
1434667 TGTTGCATGA
Statistics
Matches: 152, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
47 2 0.01
48 144 0.95
49 6 0.04
ACGTcount: A:0.16, C:0.19, G:0.35, T:0.29
Consensus pattern (48 bp):
CGGCGGTTGCATAAACAGCGTCTGCGTTTCTTTCGGAGGCGGAGGCGC
Found at i:1434606 original size:96 final size:96
Alignment explanation
Indices: 1434442--1434666 Score: 326
Period size: 96 Copynumber: 2.3 Consensus size: 96
1434432 GGGCGGCGTT
* * * *
1434442 TGCATAAACAGCGTTTGCGTTTCTTTCGGAGGTGGAGGTGCCGGCGGTTGCATAAATAGCGTCTG
1 TGCATAAACAGAGTTTGCGTTTCTTTCGGAGGCGGAGGCGCCGGCGGTTGCATAAACAGCGTCTG
* *
1434507 CGTTTCTTTATGATGCGGAGGCGCCGGTGGC
66 CGTTTCTTTAGGAGGCGGAGGCGCCGGTGGC
* * *
1434538 TGCATAAACAGAGGTTGCGTTTCTTTCGGAGGCGGATGCGTCGGCGGTTGCATAAACAGCGTCTG
1 TGCATAAACAGAGTTTGCGTTTCTTTCGGAGGCGGAGGCGCCGGCGGTTGCATAAACAGCGTCTG
* *
1434603 CGTTTCTTTAGGAGGCGGAGGCGCTGGTGGT
66 CGTTTCTTTAGGAGGCGGAGGCGCCGGTGGC
*
1434634 TGCATTAAA-AGAGTTTGCGTCTCTTTCGGAGGC
1 TGCA-TAAACAGAGTTTGCGTTTCTTTCGGAGGC
1434667 TGTTGCATGA
Statistics
Matches: 115, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
96 111 0.97
97 4 0.03
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (96 bp):
TGCATAAACAGAGTTTGCGTTTCTTTCGGAGGCGGAGGCGCCGGCGGTTGCATAAACAGCGTCTG
CGTTTCTTTAGGAGGCGGAGGCGCCGGTGGC
Found at i:1442455 original size:59 final size:60
Alignment explanation
Indices: 1442310--1442455 Score: 201
Period size: 60 Copynumber: 2.5 Consensus size: 60
1442300 ATAATCGGGT
*
1442310 AAAG-TACATAAATAGTCCATCGACTATAGGGTGATGCTTTGTTGAGTCACTCGACTATTA
1 AAAGTTACA-AAATAGTTCATCGACTATAGGGTGATGCTTTGTTGAGTCACTCGACTATTA
* * *
1442370 AAAGTTACAAAATGGTT-ATTCAACTATAGGGTGTTGCTTTGTTGAGTCA-TCGACTATTA
1 AAAGTTACAAAATAGTTCA-TCGACTATAGGGTGATGCTTTGTTGAGTCACTCGACTATTA
1442429 AAAGTTACAAAATAGTTGCAT-GACTAT
1 AAAGTTACAAAATAGTT-CATCGACTAT
1442456 TTAGCATGTT
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
59 32 0.42
60 39 0.51
61 5 0.07
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (60 bp):
AAAGTTACAAAATAGTTCATCGACTATAGGGTGATGCTTTGTTGAGTCACTCGACTATTA
Found at i:1449191 original size:2 final size:2
Alignment explanation
Indices: 1449186--1449228 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1449176 TTTTTTCTTT
1449186 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
1449228 T
1 T
1449229 TGTAGGAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1459488 original size:3 final size:3
Alignment explanation
Indices: 1459480--1459504 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1459470 TTTATGTTAT
1459480 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1459505 GGGTAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1463547 original size:20 final size:20
Alignment explanation
Indices: 1463441--1463546 Score: 97
Period size: 20 Copynumber: 5.2 Consensus size: 20
1463431 CAGTGTCGTT
*
1463441 GCGATACTGACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* *
1463461 GCGATACTTACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* *
1463481 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TATCGCAAC
* * *
1463502 GAGATACTGACTTTCTCAAC
1 GCGATACTGACTATCGCAAC
* *
1463522 GTGATTCTGACTATCGCAAC
1 GCGATACTGACTATCGCAAC
1463542 GCGAT
1 GCGAT
1463547 TTACATAGCG
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
19 2 0.03
20 52 0.75
21 13 0.19
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:1464094 original size:19 final size:19
Alignment explanation
Indices: 1464056--1464122 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1464046 TTCGAGAATG
1464056 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1464076 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* **
1464095 AAAAACGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1464114 AAAATCGCA
1 AAAATCGCA
1464123 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 28 0.72
20 11 0.28
ACGTcount: A:0.49, C:0.25, G:0.16, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1464140 original size:19 final size:19
Alignment explanation
Indices: 1464118--1464262 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
1464108 GAAACCAAAA
*
1464118 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1464137 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1464156 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
1464170 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1464189 TCGCGTTGCGA---T--TT
1 TCGCGTTGCGATTTTCATT
**
1464203 TC-CGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1464221 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1464241 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1464261 TC
1 TC
1464263 AACCAAAAGA
Statistics
Matches: 103, Mismatches: 10, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
13 8 0.08
14 13 0.13
16 4 0.04
17 3 0.03
18 3 0.03
19 41 0.40
20 30 0.29
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1464188 original size:33 final size:32
Alignment explanation
Indices: 1464151--1464237 Score: 138
Period size: 33 Copynumber: 2.7 Consensus size: 32
1464141 GTTGCGATTT
1464151 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTC-CGTCGCGATAG
* *
1464184 TCATTTCGCGTTGCGATTTTCCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCCGTCGCGATAG
1464216 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1464238 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 16 0.32
33 34 0.68
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.39
Consensus pattern (32 bp):
TCATTTCGCGTTGCGATTCTCCGTCGCGATAG
Found at i:1464239 original size:20 final size:20
Alignment explanation
Indices: 1464205--1464262 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1464195 TGCGATTTTC
**
1464205 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
1464225 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1464245 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1464263 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1465173 original size:64 final size:61
Alignment explanation
Indices: 1465060--1465216 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 61
1465050 TTGTTTAAGG
* * * *
1465060 TGCATCGATGCACATGCAGTGCATCGATGCATGAATTTAAATAGAAAACATCGAATATGATTT
1 TGCATCGATGCATA-GGAGTGCATCGATGCATCAATTTAAATAGAAAACATCGAATAGGA-TT
* *
1465123 ATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATA-CAAACATCGAATAGGATT
1 -TGCATCGATGCAT-AGGAGTGCATCGATGCAT--CAATTTAAATAGAAAACATCGAATAGGATT
*
1465186 TGCATTGATGCAT-GGTAGTGCATCGATGCAT
1 TGCATCGATGCATAGG-AGTGCATCGATGCAT
1465217 ACCTTCATTA
Statistics
Matches: 82, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
60 2 0.02
61 15 0.18
62 12 0.15
63 2 0.02
64 42 0.51
65 8 0.10
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (61 bp):
TGCATCGATGCATAGGAGTGCATCGATGCATCAATTTAAATAGAAAACATCGAATAGGATT
Found at i:1465726 original size:18 final size:18
Alignment explanation
Indices: 1465703--1465737 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1465693 CTAGGAGATT
1465703 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1465721 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1465738 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1466071 original size:2 final size:2
Alignment explanation
Indices: 1466064--1466091 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1466054 GAACATGTGA
1466064 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
1466092 GTCTAAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1466902 original size:146 final size:145
Alignment explanation
Indices: 1466637--1466944 Score: 519
Period size: 146 Copynumber: 2.1 Consensus size: 145
1466627 GAGTCGAGGG
* * **
1466637 TCTACGCGGTCCTTTGGGATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAT
1 TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATAT
1466702 GATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATG
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATG
1466767 GCACTACGGTGCAAT
131 GCACTACGGTGCAAT
* *
1466782 TTTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATAC
1 TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATA-
*
1466847 TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATAT
65 TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATAT
*
1466912 GGCACTACGGTGTAAT
130 GGCACTACGGTGCAAT
1466928 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1466945 TGCAATTATA
Statistics
Matches: 152, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
145 59 0.39
146 93 0.61
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (145 bp):
TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATAT
GATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATG
GCACTACGGTGCAAT
Found at i:1466945 original size:23 final size:23
Alignment explanation
Indices: 1466912--1466956 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1466902 ATTATTATAT
* *
1466912 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
1466935 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
1466957 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1469080 original size:51 final size:52
Alignment explanation
Indices: 1468984--1469086 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 52
1468974 GATGAGTCAG
1468984 GGAGTTACGTGATGAGGTCAATGGCCTTGCGTGAGGAGATCGATACTCTACT
1 GGAGTTACGTGATGAGGTCAATGGCCTTGCGTGAGGAGATCGATACTCTACT
1469036 GGAGTTACGTGATGAGGTCAAT-GCCTTGCGTGAGGAGATCGATACTCTACT
1 GGAGTTACGTGATGAGGTCAATGGCCTTGCGTGAGGAGATCGATACTCTACT
1469087 CGATAACGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 29 0.57
52 22 0.43
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.27
Consensus pattern (52 bp):
GGAGTTACGTGATGAGGTCAATGGCCTTGCGTGAGGAGATCGATACTCTACT
Found at i:1469721 original size:21 final size:21
Alignment explanation
Indices: 1469697--1469763 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1469687 TCATTCCTCG
1469697 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1469718 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1469739 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1469760 AGAG
1 AGAG
1469764 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1469721 original size:42 final size:42
Alignment explanation
Indices: 1469645--1469763 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1469635 GACTCGCCTG
* * * * * * *
1469645 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1469687 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1469729 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1469764 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1471120 original size:14 final size:14
Alignment explanation
Indices: 1471101--1471136 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1471091 ATTGTTTAAT
1471101 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1471115 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1471129 TGATTTGT
1 TGATTTGT
1471137 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1471280 original size:14 final size:14
Alignment explanation
Indices: 1471261--1471298 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1471251 GCGAAATGAA
1471261 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1471275 AATCGCAACGAGAT
1 AATCGCAACGAGAG
1471289 AATCGCAACG
1 AATCGCAACG
1471299 CGAAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1471355 original size:33 final size:32
Alignment explanation
Indices: 1471313--1471439 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
1471303 ATTAAATTCG
*
1471313 CGTTGCGATTTTCACTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
1471346 CGTTGCGATTTTCATTTCGTATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1471379 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1471412 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1471440 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1471372 original size:19 final size:18
Alignment explanation
Indices: 1471315--1471439 Score: 67
Period size: 19 Copynumber: 7.4 Consensus size: 18
1471305 TAAATTCGCG
*
1471315 TTGCGATTTTCACTTCGCA
1 TTGCGATTTTCATTTCG-A
**
1471334 TTGCGA--TTC-CCTCG-
1 TTGCGATTTTCATTTCGA
1471348 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCG-A
** *
1471367 TTGCGAAATT-A--GCG-
1 TTGCGATTTTCATTTCGA
1471381 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCG-A
*
1471400 TTGCGA--TTC-TCTCG-
1 TTGCGATTTTCATTTCGA
1471414 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCG-A
1471433 TTGCGAT
1 TTGCGAT
1471440 AGTAATTTCC
Statistics
Matches: 80, Mismatches: 11, Indels: 30
0.66 0.09 0.25
Matches are distributed among these distances:
14 20 0.25
15 1 0.01
16 16 0.20
17 15 0.19
18 1 0.01
19 27 0.34
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.43
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGA
Found at i:1471376 original size:66 final size:66
Alignment explanation
Indices: 1471306--1471438 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
1471296 ACGCGAAATT
* *
1471306 AAATTCGCGTTGCGATTTTCACTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGTATTGC
1 AAATTAGCGTTGCGATTTTCACTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1471371 G
66 G
* *
1471372 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCACTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1471437 G
66 G
1471438 A
1 A
1471439 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCACTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1473623 original size:12 final size:12
Alignment explanation
Indices: 1473606--1473630 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1473596 TCTTCGGGGA
1473606 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1473618 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1473630 C
1 C
1473631 GGATTATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1473833 original size:23 final size:24
Alignment explanation
Indices: 1473800--1473852 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
1473790 CTGAAACATC
*
1473800 ATCAAAATCCGAGTA-TGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1473823 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1473847 ATCAAA
1 ATCAAA
1473853 TTTTGAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1474611 original size:20 final size:20
Alignment explanation
Indices: 1474586--1474636 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1474576 TGTATTATCT
1474586 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
1474606 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
1474626 CGTTGCGAAAG
1 CGTTGCGAAAG
1474637 GCAATCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.20
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:1474907 original size:19 final size:20
Alignment explanation
Indices: 1474849--1474918 Score: 133
Period size: 20 Copynumber: 3.5 Consensus size: 20
1474839 ATTCATTTGA
1474849 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1474869 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1474889 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
1474908 CTATCGCAACG
1 CTATCGCAACG
1474919 ACAAAATTGC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 17 0.34
20 33 0.66
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1474988 original size:20 final size:20
Alignment explanation
Indices: 1474963--1475001 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1474953 CGATTCTCTC
1474963 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
1474983 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
1475002 CCTTCAACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:1475103 original size:14 final size:14
Alignment explanation
Indices: 1475084--1475120 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1475074 CATCAATTAA
1475084 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1475098 ACAAATCATCTTTT
1 ACAAATCAACATTT
1475112 ACAAATCAA
1 ACAAATCAA
1475121 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1477009 original size:20 final size:20
Alignment explanation
Indices: 1476986--1477039 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1476976 GAAACTTAAA
1476986 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
1477006 ATCGCAACAC-AGAAATGGCT
1 ATCGCAACGCGA-AAATGACT
*
1477026 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
1477040 TAAAAATCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1477061 original size:14 final size:14
Alignment explanation
Indices: 1477042--1477099 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1477032 ATGCGAAATA
1477042 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1477056 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1477072 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1477088 AAAATCGCAACG
1 AAAATCGCAACG
1477100 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1477084 original size:32 final size:33
Alignment explanation
Indices: 1477026--1477115 Score: 137
Period size: 32 Copynumber: 2.8 Consensus size: 33
1477016 AGAAATGGCT
1477026 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
*
1477059 ATCGCAATGCGAAAT-GAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
* * *
1477091 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAATGCGAAATAAAAATCGCA
1477116 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.56
33 23 0.44
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATAAAAATCGCAACGACAAA
Found at i:1477133 original size:19 final size:18
Alignment explanation
Indices: 1477111--1477173 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
1477101 GAAACACAAA
1477111 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
1477130 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
1477146 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
1477162 TCGCATTGCGAT
1 TCGCATTGCGAT
1477174 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.24
16 8 0.22
18 10 0.27
19 10 0.27
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:1477209 original size:20 final size:20
Alignment explanation
Indices: 1477158--1477201 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1477148 GTTGCGATTT
*
1477158 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
1477177 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
1477197 CATTT
1 CATTT
1477202 TCGTGTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:1477726 original size:18 final size:18
Alignment explanation
Indices: 1477700--1477744 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1477690 GTCGATCAGA
**
1477700 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCAAGG
*
1477718 TGATAGCTCTGGGCAAGG
1 TGATGGCTCTGGGCAAGG
1477736 TGATGGCTC
1 TGATGGCTC
1477745 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCAAGG
Found at i:1479112 original size:20 final size:20
Alignment explanation
Indices: 1479064--1479122 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1479054 AATAGTTTCT
** *
1479064 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1479084 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
1479104 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
1479123 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1479683 original size:20 final size:20
Alignment explanation
Indices: 1479577--1479711 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
1479567 CGCTTTGAAA
*
1479577 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
1479598 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
1479618 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1479638 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
1479659 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
1479679 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1479699 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1479712 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1479683 original size:61 final size:61
Alignment explanation
Indices: 1479577--1479714 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
1479567 CGCTTTGAAA
* * * *
1479577 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
1479638 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
1479699 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
1479715 CCCAATTCAC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1479730 original size:61 final size:61
Alignment explanation
Indices: 1479577--1479732 Score: 143
Period size: 61 Copynumber: 2.6 Consensus size: 61
1479567 CGCTTTGAAA
* ** * * * * *
1479577 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCACGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * * *
1479638 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCACGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
1479699 ATCGCATTGCGATTTTCCCAAT-TCACGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCACGTTGCGAT
1479733 TTACTTATTC
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
61 76 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCACGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1479822 original size:21 final size:21
Alignment explanation
Indices: 1479782--1479822 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1479772 ACTGTAGACC
**
1479782 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1479803 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1479823 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1483850 original size:20 final size:20
Alignment explanation
Indices: 1483806--1483865 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
1483796 CGAATGCAAA
* *
1483806 CAGTGTACCGATACACCTATG
1 CAGTGTATCGATACACC-CTG
1483827 -AGTGTATCGATACACCCTG
1 CAGTGTATCGATACACCCTG
* *
1483846 CAGTGTATCCATAAACCCTG
1 CAGTGTATCGATACACCCTG
1483866 TCTGCAACGG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.06
20 32 0.94
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (20 bp):
CAGTGTATCGATACACCCTG
Found at i:1484124 original size:12 final size:12
Alignment explanation
Indices: 1484107--1484136 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1484097 AGAAGTTTTT
1484107 CATTCTTATTTA
1 CATTCTTATTTA
*
1484119 CATTCTTATTTT
1 CATTCTTATTTA
1484131 CATTCT
1 CATTCT
1484137 CTCTTGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (12 bp):
CATTCTTATTTA
Found at i:1486114 original size:81 final size:83
Alignment explanation
Indices: 1486002--1486179 Score: 236
Period size: 81 Copynumber: 2.2 Consensus size: 83
1485992 TGGACCCTTA
1486002 GTGCATCGGTGCACTAAGAGTGCAACGATGCATAAAATGCATTCGATGTTTCAAAAT-AGCCAAA
1 GTGCATCGGTGCACT-AGAGTGCAACGATGCATAAAATGCATTCGATG-TTCAAAATAAGCCAAA
*
1486066 GTGCATCGATGCATGG-TTT
64 GTGCATCGATGCATGGATTG
* * * ** * **
1486085 GTGCATCGATGCACT-GAGTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATCCATGGT
1 GTGCATCGGTGCACTAGAGTGCAACGATGCATAAAATGCATTCGATGTTCAAAATAAGCCAAAGT
1486149 GCATCGATGCATGGATTG
66 GCATCGATGCATGGATTG
1486167 GTGCATCGGTGCA
1 GTGCATCGGTGCA
1486180 TCACCCTGAA
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
80 6 0.07
81 49 0.59
82 14 0.17
83 14 0.17
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (83 bp):
GTGCATCGGTGCACTAGAGTGCAACGATGCATAAAATGCATTCGATGTTCAAAATAAGCCAAAGT
GCATCGATGCATGGATTG
Found at i:1486123 original size:17 final size:17
Alignment explanation
Indices: 1486086--1486130 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1486076 GCATGGTTTG
*
1486086 TGCATCGATGCACTGAG
1 TGCATCGATGCACTGAA
1486103 TGCATCGATGCA-TGAAA
1 TGCATCGATGCACTG-AA
1486120 TGCATTCGATG
1 TGCA-TCGATG
1486131 TTCAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 2 0.08
17 17 0.68
18 6 0.24
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (17 bp):
TGCATCGATGCACTGAA
Found at i:1492437 original size:23 final size:22
Alignment explanation
Indices: 1492409--1492488 Score: 81
Period size: 21 Copynumber: 3.6 Consensus size: 22
1492399 GCATGGCCTT
*
1492409 GTGCATTGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
1492431 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
1492453 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
1492475 ATGCATTGATGCAC
1 GTGCATCGATGCAC
1492489 TGTTAGGTGT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
21 15 0.33
22 15 0.33
23 15 0.33
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.28
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1503484 original size:30 final size:31
Alignment explanation
Indices: 1503416--1503484 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 31
1503406 AAATTATATA
* *
1503416 TTTGGTAAAGTTTGGTGACCAAAGTATAAAC
1 TTTGGAAAAGTTTGGTGACCAAAATATAAAC
* *
1503447 TTT-GAAAAGTTTAGG-GACCAAAATGT-AAT
1 TTTGGAAAAGTTT-GGTGACCAAAATATAAAC
1503476 TTTGGAAAA
1 TTTGGAAAA
1503485 ATTACAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
29 5 0.16
30 22 0.69
31 5 0.16
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (31 bp):
TTTGGAAAAGTTTGGTGACCAAAATATAAAC
Found at i:1503907 original size:38 final size:38
Alignment explanation
Indices: 1503856--1503928 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
1503846 CAAAGTGTTC
1503856 TTGTTGAAAACATTTTGATATTTCGATATAACAAAAGA
1 TTGTTGAAAACATTTTGATATTTCGATATAACAAAAGA
1503894 TTGTTGAAAACATTTTGATATTTCGATATAACAAA
1 TTGTTGAAAACATTTTGATATTTCGATATAACAAA
1503929 TTAAGATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.38
Consensus pattern (38 bp):
TTGTTGAAAACATTTTGATATTTCGATATAACAAAAGA
Found at i:1504252 original size:75 final size:75
Alignment explanation
Indices: 1504144--1504329 Score: 304
Period size: 75 Copynumber: 2.5 Consensus size: 75
1504134 TTGTCCAGAT
*
1504144 GGAACCGATTCCCCCCCAAGGGGGTACCAATTCCCCCCGAATGGTTTGGCTCCGAGAAATTCCAG
1 GGAACCGATT-CCCCCCAAGGGGGTACCGATTCCCCCCGAATGGTTTGGCTCCGAGAAATTCCAG
1504209 TATGCTCGAAG
65 TATGCTCGAAG
* * *
1504220 GGAACCGATTCCCCCCAAGGGGGTACCGATTCCCCCTGAATGGTTTGGCTCTGAGAAATTCTAGT
1 GGAACCGATTCCCCCCAAGGGGGTACCGATTCCCCCCGAATGGTTTGGCTCCGAGAAATTCCAGT
1504285 ATGCTCGAAG
66 ATGCTCGAAG
*
1504295 GGAACCGATTCCCCCC-A-GGGGTATCGATTCCCCCC
1 GGAACCGATTCCCCCCAAGGGGGTACCGATTCCCCCC
1504330 ACTGTTCAAC
Statistics
Matches: 104, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
73 16 0.15
74 1 0.01
75 77 0.74
76 10 0.10
ACGTcount: A:0.22, C:0.32, G:0.25, T:0.21
Consensus pattern (75 bp):
GGAACCGATTCCCCCCAAGGGGGTACCGATTCCCCCCGAATGGTTTGGCTCCGAGAAATTCCAGT
ATGCTCGAAG
Found at i:1511578 original size:13 final size:14
Alignment explanation
Indices: 1511560--1511589 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1511550 TAAGGGGGAG
1511560 TAATTTCAAAA-CT
1 TAATTTCAAAATCT
1511573 TAATTTCAAAATCT
1 TAATTTCAAAATCT
1511587 TAA
1 TAA
1511590 AATTACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATTTCAAAATCT
Found at i:1511669 original size:38 final size:37
Alignment explanation
Indices: 1511627--1511699 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 37
1511617 AAAGGGGGAG
1511627 ATTGTTGAAAACATTTTGATATTTCGATATAACAAAAA
1 ATTGTTGAAAACATTTTGAT-TTTCGATATAACAAAAA
*
1511665 ATTGTTGAAAACATTTTGATTTTTGATATAACAAA
1 ATTGTTGAAAACATTTTGATTTTCGATATAACAAA
1511700 TTAAGATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 14 0.41
38 20 0.59
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (37 bp):
ATTGTTGAAAACATTTTGATTTTCGATATAACAAAAA
Found at i:1511933 original size:21 final size:21
Alignment explanation
Indices: 1511909--1511948 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1511899 CAGATTGTCC
1511909 AGAGGGAAACGATTCCCCCCA
1 AGAGGGAAACGATTCCCCCCA
* *
1511930 AGAGGGTATCGATTCCCCC
1 AGAGGGAAACGATTCCCCC
1511949 TGAATGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.33, G:0.25, T:0.15
Consensus pattern (21 bp):
AGAGGGAAACGATTCCCCCCA
Found at i:1512017 original size:19 final size:19
Alignment explanation
Indices: 1511993--1512042 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
1511983 CGAAGGGAAC
1511993 CGATTCCCCCCAGGGGTAT
1 CGATTCCCCCCAGGGGTAT
1512012 CGATTCCCCCCAGGGGTAT
1 CGATTCCCCCCAGGGGTAT
1512031 CGATTCCCCCCA
1 CGATTCCCCCCA
1512043 CTGTTCAACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.16, C:0.42, G:0.22, T:0.20
Consensus pattern (19 bp):
CGATTCCCCCCAGGGGTAT
Found at i:1514421 original size:22 final size:22
Alignment explanation
Indices: 1514393--1514472 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
1514383 TTTTCGAAAG
*
1514393 TACTGTAGCAGATACTGCATCT
1 TACTGTAGCAGTTACTGCATCT
* * *
1514415 TACTGTAGCAGTTAATGTAGCT
1 TACTGTAGCAGTTACTGCATCT
1514437 TACTGTAGCAGTTACTGCAGT-T
1 TACTGTAGCAGTTACTGCA-TCT
*
1514459 TATTGTAGCAGTTA
1 TACTGTAGCAGTTA
1514473 TTGTAGCAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (22 bp):
TACTGTAGCAGTTACTGCATCT
Found at i:1514435 original size:12 final size:12
Alignment explanation
Indices: 1514418--1514482 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
1514408 TGCATCTTAC
1514418 TGTAGCAGTTAA
1 TGTAGCAGTTAA
*
1514430 TGTAGC--TTAC
1 TGTAGCAGTTAA
1514440 TGTAGCAGTT-A
1 TGTAGCAGTTAA
* *
1514451 -CT-GCAGTTTAT
1 TGTAGCAG-TTAA
*
1514462 TGTAGCAGTTAT
1 TGTAGCAGTTAA
1514474 TGTAGCAGT
1 TGTAGCAGT
1514483 GAACAGTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
9 4 0.10
10 12 0.29
12 22 0.52
13 4 0.10
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (12 bp):
TGTAGCAGTTAA
Found at i:1514466 original size:44 final size:44
Alignment explanation
Indices: 1514393--1514479 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
1514383 TTTTCGAAAG
1514393 TACTGTAGCAGATACTGCATCTTACTGTAGCAGTTAATGTAGCT
1 TACTGTAGCAGATACTGCATCTTACTGTAGCAGTTAATGTAGCT
* * *
1514437 TACTGTAGCAGTTACTGCAGT-TTATTGTAGCAGTTATTGTAGC
1 TACTGTAGCAGATACTGCA-TCTTACTGTAGCAGTTAATGTAGC
1514480 AGTGAACAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 38 0.97
45 1 0.03
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (44 bp):
TACTGTAGCAGATACTGCATCTTACTGTAGCAGTTAATGTAGCT
Found at i:1514471 original size:13 final size:13
Alignment explanation
Indices: 1514453--1514482 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1514443 AGCAGTTACT
1514453 GCAGTTTATTGTA
1 GCAGTTTATTGTA
1514466 GCAG-TTATTGTA
1 GCAGTTTATTGTA
1514478 GCAGT
1 GCAGT
1514483 GAACAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (13 bp):
GCAGTTTATTGTA
Found at i:1520026 original size:2 final size:2
Alignment explanation
Indices: 1520013--1520052 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1520003 TGCACCTTTC
* *
1520013 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1520053 CCACACATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1520381 original size:30 final size:30
Alignment explanation
Indices: 1520322--1520417 Score: 158
Period size: 30 Copynumber: 3.2 Consensus size: 30
1520312 CCCGAAGGAC
* *
1520322 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1520351 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1520381 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1520411 CTATCCA
1 CTATCCA
1520418 TATGTTCCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 19 0.31
30 43 0.69
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1520498 original size:32 final size:32
Alignment explanation
Indices: 1520409--1520504 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
1520399 GATCCTCGGT
* *
1520409 AACTATCCATATGTTCCTTAGAACATAGGT-A
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
* *
1520440 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGTAA
1520472 AACTGTCCATATGTTCCGTAGAACATAGGTAA
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
1520504 A
1 A
1520505 CCCTCGACTC
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
30 4 0.07
31 20 0.37
32 26 0.48
33 4 0.07
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (32 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTAA
Found at i:1524229 original size:2 final size:2
Alignment explanation
Indices: 1524216--1524253 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1524206 TGCACCTTTC
* *
1524216 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1524254 CCACACATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1524590 original size:30 final size:30
Alignment explanation
Indices: 1524527--1524619 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
1524517 GAAGGACCTA
* * *
1524527 TCCAGAGGTCACAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
1524556 TCCAGAGGTCATAAAGATCCTCGGTAATTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1524586 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1524616 TCCA
1 TCCA
1524620 TATGTTCCTT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 16 0.28
30 42 0.72
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1524648 original size:31 final size:30
Alignment explanation
Indices: 1524608--1524705 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 30
1524598 AAAGATCCTC
*
1524608 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* * *
1524638 GGTATACTGTCTATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
*
1524669 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
1524701 GGTAA
1 GGTAA
1524706 ACCCTCGACT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
30 6 0.11
31 24 0.44
32 24 0.44
33 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:1525623 original size:21 final size:21
Alignment explanation
Indices: 1525599--1525643 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1525589 CTATGTTCGT
* * *
1525599 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1525620 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1525641 TTG
1 TTG
1525644 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1526759 original size:23 final size:23
Alignment explanation
Indices: 1526715--1526760 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1526705 TAGTGGTTGG
* *
1526715 TTTAATGGATGTTTAAATTTTAT
1 TTTAATGGATATTTAAAGTTTAT
1526738 TTTAATGGTATATTT-AAGTTTAT
1 TTTAATGG-ATATTTAAAGTTTAT
1526761 CTTGGTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (23 bp):
TTTAATGGATATTTAAAGTTTAT
Found at i:1528382 original size:4 final size:4
Alignment explanation
Indices: 1528373--1528432 Score: 57
Period size: 4 Copynumber: 14.5 Consensus size: 4
1528363 TATTTTTAAG
* * * * *
1528373 ATTT ATTT ATTT ATTT ATTT ATTT ACTG ATTT AAGATT GTCT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT -A-TTT ATTT ATTT ATTT
1528423 ATTT ATTT AT
1 ATTT ATTT AT
1528433 CTTTTGAATT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
4 41 0.93
5 1 0.02
6 2 0.05
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (4 bp):
ATTT
Found at i:1528422 original size:38 final size:38
Alignment explanation
Indices: 1528376--1528460 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 38
1528366 TTTTAAGATT
*
1528376 TATTTATTTATTTATTTAT-TTACTGATTTAAGATTGTC
1 TATTTATTTATTTATTTATCTT-CTGAATTAAGATTGTC
* * *
1528414 TATTTATTTATTTATTTATCTTTTGAATTAAGGTTGTG
1 TATTTATTTATTTATTTATCTTCTGAATTAAGATTGTC
1528452 TATTTATTT
1 TATTTATTT
1528461 TTAAACACTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 40 0.95
39 2 0.05
ACGTcount: A:0.25, C:0.04, G:0.09, T:0.62
Consensus pattern (38 bp):
TATTTATTTATTTATTTATCTTCTGAATTAAGATTGTC
Found at i:1528633 original size:19 final size:19
Alignment explanation
Indices: 1528591--1528634 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1528581 TCAATTCATA
1528591 TAATTATTAATATATTTTT
1 TAATTATTAATATATTTTT
*
1528610 AAATTATTAATA-ATTTCTT
1 TAATTATTAATATATTT-TT
1528629 TAATTA
1 TAATTA
1528635 AAATGATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATTATTAATATATTTTT
Found at i:1533440 original size:31 final size:32
Alignment explanation
Indices: 1533352--1533476 Score: 116
Period size: 31 Copynumber: 4.0 Consensus size: 32
1533342 CAATAATCTT
* * *
1533352 TCAAA-TATTATTAAATGGTTA-TCAAACTT-
1 TCAAATTATTATAAAATGGTCATTTAAACTTA
* * * *
1533381 TCTAAATAATTCTAAAATGTTCATTTAAATTTA
1 TC-AAATTATTATAAAATGGTCATTTAAACTTA
1533414 TCAAATTATTATAAAATGGT-ATTTAAACTTA
1 TCAAATTATTATAAAATGGTCATTTAAACTTA
* * *
1533445 TCAAAATATTATAAAATGATC-TTTAATCTTA
1 TCAAATTATTATAAAATGGTCATTTAAACTTA
1533476 T
1 T
1533477 TGAAATTTAT
Statistics
Matches: 77, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
29 2 0.03
30 3 0.04
31 49 0.64
32 21 0.27
33 2 0.03
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (32 bp):
TCAAATTATTATAAAATGGTCATTTAAACTTA
Found at i:1533442 original size:63 final size:61
Alignment explanation
Indices: 1533352--1533470 Score: 143
Period size: 63 Copynumber: 1.9 Consensus size: 61
1533342 CAATAATCTT
* * * *
1533352 TCAAATATTATTAAATGGTTATCAAACTT-TCTAAATAATTCTAAAATGTTCATTTAAATTTA
1 TCAAATATTATAAAATGGTTATCAAACTTATCAAAAT-ATTATAAAATGATC-TTTAAATTTA
*
1533414 TCAAATTATTATAAAATGG-TATTTAAACTTATCAAAATATTATAAAATGATCTTTAA
1 TCAAA-TATTATAAAATGGTTA-TCAAACTTATCAAAATATTATAAAATGATCTTTAA
1533471 TCTTATTGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
62 12 0.24
63 31 0.63
64 6 0.12
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (61 bp):
TCAAATATTATAAAATGGTTATCAAACTTATCAAAATATTATAAAATGATCTTTAAATTTA
Found at i:1533483 original size:63 final size:64
Alignment explanation
Indices: 1533357--1533488 Score: 139
Period size: 63 Copynumber: 2.1 Consensus size: 64
1533347 ATCTTTCAAA
* * * *
1533357 TATTATTAAATGGTTATCAAACTTTCTAAATAATTCTAAAATGTTCATTTAAATTTATCAAA-T
1 TATTATAAAATGGTTATCAAACTTTCAAAATAATTATAAAATGATCATTTAAATTTATCAAATT
* *
1533420 TATTATAAAATGG-TATTTAAACTTATCAAAAT-ATTATAAAATGATC-TTT-AATCTTATTGAA
1 TATTATAAAATGGTTA-TCAAACTT-TCAAAATAATTATAAAATGATCATTTAAAT-TTA-TCAA
1533481 ATT
62 ATT
1533484 TATTA
1 TATTA
1533489 CTACCTTAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
61 3 0.05
62 8 0.14
63 35 0.60
64 12 0.21
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (64 bp):
TATTATAAAATGGTTATCAAACTTTCAAAATAATTATAAAATGATCATTTAAATTTATCAAATT
Found at i:1553372 original size:14 final size:13
Alignment explanation
Indices: 1553350--1553385 Score: 63
Period size: 14 Copynumber: 2.7 Consensus size: 13
1553340 AAATATTTGT
1553350 AAAATTAAACATA
1 AAAATTAAACATA
1553363 AAATATTAAACATA
1 AAA-ATTAAACATA
1553377 AAAATTAAA
1 AAAATTAAA
1553386 TTAATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (13 bp):
AAAATTAAACATA
Found at i:1554065 original size:6 final size:6
Alignment explanation
Indices: 1554054--1554079 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1554044 AGACACGTAT
1554054 GACCAC GACCAC GACCAC GACCAC GA
1 GACCAC GACCAC GACCAC GACCAC GA
1554080 GACGAGACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.46, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:1554762 original size:40 final size:42
Alignment explanation
Indices: 1554681--1554858 Score: 274
Period size: 40 Copynumber: 4.3 Consensus size: 42
1554671 CGTTGCGATT
1554681 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
1554723 TTGGACTATCGTAACGAATTTGG-A-AAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
1554763 TTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
1554805 TTGGACTATCGCAACGAATTT-GAA-AAATCGTAACTCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
1554845 TTCGACAATCGCAA
1 TTGGACTATCGCAA
1554859 TGCGAATATG
Statistics
Matches: 126, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
40 63 0.50
41 5 0.04
42 58 0.46
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:1554821 original size:82 final size:82
Alignment explanation
Indices: 1554684--1554858 Score: 305
Period size: 82 Copynumber: 2.1 Consensus size: 82
1554674 TGCGATTTTG
* *
1554684 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGTAACGAATTTGGAAA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAAAA
1554749 ATCGCAACGCGAACTTC
66 ATCGCAACGCGAACTTC
1554766 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAAAA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAAAA
* *
1554831 ATCGTAACTCGAACTTC
66 ATCGCAACGCGAACTTC
*
1554848 GACAATCGCAA
1 GACTATCGCAA
1554859 TGCGAATATG
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 88 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (82 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAAAA
ATCGCAACGCGAACTTC
Found at i:1554864 original size:21 final size:19
Alignment explanation
Indices: 1554681--1554858 Score: 95
Period size: 21 Copynumber: 8.7 Consensus size: 19
1554671 CGTTGCGATT
* *
1554681 TTGGACTATCGCAACGAAT
1 TTGGACAATCGCAACGAAC
*
1554700 TTGGAATAAATCGCAACGCGAAC
1 TTGG-A-CAATCGCAA--CGAAC
* * *
1554723 TTGGACTATCGTAACGAAT
1 TTGGACAATCGCAACGAAC
*
1554742 TTGGAAAATCGCAACGCGAAC
1 TTGGACAATCGCAA--CGAAC
* * *
1554763 TTCGACTATCGCAACGAAT
1 TTGGACAATCGCAACGAAC
*
1554782 TTGGAATAAATCGCAACGCGAAC
1 TTGG-A-CAATCGCAA--CGAAC
* *
1554805 TTGGACTATCGCAACGAAT
1 TTGGACAATCGCAACGAAC
* * *
1554824 TTGAAAAATCGTAACTCGAAC
1 TTGGACAATCGCAA--CGAAC
*
1554845 TTCGACAATCGCAA
1 TTGGACAATCGCAA
1554859 TGCGAATATG
Statistics
Matches: 116, Mismatches: 31, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
19 40 0.34
20 2 0.02
21 56 0.48
22 2 0.02
23 16 0.14
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (19 bp):
TTGGACAATCGCAACGAAC
Found at i:1554902 original size:21 final size:21
Alignment explanation
Indices: 1554873--1554925 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1554863 AATATGTAAA
*
1554873 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
1554894 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
1554915 TCGTGTTGCGA
1 TCGCGTTGCGA
1554926 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:1557616 original size:11 final size:11
Alignment explanation
Indices: 1557600--1557628 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1557590 GCATCAGGTA
1557600 CATACTCGGAC
1 CATACTCGGAC
1557611 CATACTCGGAC
1 CATACTCGGAC
1557622 CATACTC
1 CATACTC
1557629 ATCCGCCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.38, G:0.14, T:0.21
Consensus pattern (11 bp):
CATACTCGGAC
Found at i:1566838 original size:19 final size:19
Alignment explanation
Indices: 1566814--1566854 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1566804 ACCGGTTGAA
1566814 AACTGGTAAAA-TCGGGGTG
1 AACTGGTAAAACT-GGGGTG
1566833 AACTGGTAAAACTGGGGTG
1 AACTGGTAAAACTGGGGTG
1566852 AAC
1 AAC
1566855 CGGTTGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (19 bp):
AACTGGTAAAACTGGGGTG
Found at i:1567171 original size:24 final size:25
Alignment explanation
Indices: 1567125--1567171 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
1567115 AAACTCAAAA
*
1567125 AAAATTAGAAGTTCGATTGAAGCCT
1 AAAATTAGAAGTTCAATTGAAGCCT
* *
1567150 AAAATTTG-AGTTCAATTTAAGC
1 AAAATTAGAAGTTCAATTGAAGC
1567172 GAAAGAATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (25 bp):
AAAATTAGAAGTTCAATTGAAGCCT
Found at i:1574189 original size:2 final size:2
Alignment explanation
Indices: 1574184--1574216 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1574174 AAAAGGGAGT
1574184 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1574217 TCTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1580802 original size:24 final size:24
Alignment explanation
Indices: 1580766--1580827 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
1580756 TATTGGGTTA
* *
1580766 AACATAAATGAACGCACATAAACG
1 AACATAACTGAACGAACATAAACG
*
1580790 AACATAACCGAACGAACATAAACG
1 AACATAACTGAACGAACATAAACG
*
1580814 AATATAACTGAACG
1 AACATAACTGAACG
1580828 TTCACGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.53, C:0.21, G:0.13, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGAACATAAACG
Found at i:1580803 original size:14 final size:14
Alignment explanation
Indices: 1580786--1580815 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1580776 AACGCACATA
*
1580786 AACGAACATAACCG
1 AACGAACATAAACG
1580800 AACGAACATAAACG
1 AACGAACATAAACG
1580814 AA
1 AA
1580816 TATAACTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.23, G:0.13, T:0.07
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:1583701 original size:31 final size:31
Alignment explanation
Indices: 1583582--1583702 Score: 84
Period size: 31 Copynumber: 3.7 Consensus size: 31
1583572 TATTAGATTG
*
1583582 TAAAATAAAAATAAATATAAAAAGAGAAAAATATA
1 TAAAAT-AAAATAAA-AT-AAAAGAGTAAAATA-A
* **
1583617 TAAATAATAATAATAAAATAAAATAGATACCA-AA
1 T-AA-AATAA-AATAAAATAAAAGAG-TAAAATAA
* * *
1583651 GAAAATAAAAGT-TAGTAAAAGAGTAAAATAA
1 TAAAATAAAA-TAAAATAAAAGAGTAAAATAA
1583682 TAAAATAAAATAAAATAAAAG
1 TAAAATAAAATAAAATAAAAG
1583703 GACCAAAATG
Statistics
Matches: 66, Mismatches: 13, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
30 4 0.06
31 28 0.42
32 6 0.09
33 2 0.03
34 1 0.02
35 8 0.12
36 8 0.12
37 9 0.14
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (31 bp):
TAAAATAAAATAAAATAAAAGAGTAAAATAA
Found at i:1585832 original size:33 final size:33
Alignment explanation
Indices: 1585790--1585856 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1585780 TACCCTTAAT
*
1585790 ATTTTTGTCAGCAACTACCAAATCAATATGCCA
1 ATTTTTGTCAGCAACTACCAAACCAATATGCCA
1585823 ATTTTTGTCAGCAACTACCAAACCAATATGCCA
1 ATTTTTGTCAGCAACTACCAAACCAATATGCCA
1585856 A
1 A
1585857 ATTCCAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.25, G:0.09, T:0.28
Consensus pattern (33 bp):
ATTTTTGTCAGCAACTACCAAACCAATATGCCA
Found at i:1594918 original size:31 final size:32
Alignment explanation
Indices: 1594882--1594945 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
1594872 TCACCCAACC
* * *
1594882 AATTAATATAATAGCTTAATTGGTA-TAATTT
1 AATTAATAGAAGAGCATAATTGGTATTAATTT
*
1594913 AATTAATAGAAGAGCATATTTGGTATTAATTT
1 AATTAATAGAAGAGCATAATTGGTATTAATTT
1594945 A
1 A
1594946 TGAATTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (32 bp):
AATTAATAGAAGAGCATAATTGGTATTAATTT
Found at i:1598376 original size:100 final size:101
Alignment explanation
Indices: 1598255--1598461 Score: 287
Period size: 100 Copynumber: 2.0 Consensus size: 101
1598245 TTGACGCAGT
*
1598255 TGAAGAAAAAATTAGGCAATTTGATCCAAGAGGGCAAAATGTGCA-TAGTGTTCTCAAACCAGAT
1 TGAAGAAAAAA-TAGGCAATTTGATCCAAGAGGGCAAAATGTGCAGT-GTGTTCTCAAAACAGAT
1598319 GAAGACGAGCT-TGTAGATGTAC-TACAAGTACTGATGC
64 GAAGACG-GCTGTGTAGATGTACATACAAGTACTGATGC
* *
1598356 TGAAGAGAAAAA-AGGCAATTTGATCCAAGAGGGCAACATGTGCAGTGTGTTCTCAAAACGGATG
1 TGAAGA-AAAAATAGGCAATTTGATCCAAGAGGGCAAAATGTGCAGTGTGTTCTCAAAACAGATG
* * * *
1598420 AAGATGGGTGTGTAGCTGTACATATAAGTACTGATGC
65 AAGACGGCTGTGTAGATGTACATACAAGTACTGATGC
1598457 TGAAG
1 TGAAG
1598462 CCAAGTTGGA
Statistics
Matches: 95, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
99 2 0.02
100 62 0.65
101 26 0.27
102 5 0.05
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.24
Consensus pattern (101 bp):
TGAAGAAAAAATAGGCAATTTGATCCAAGAGGGCAAAATGTGCAGTGTGTTCTCAAAACAGATGA
AGACGGCTGTGTAGATGTACATACAAGTACTGATGC
Found at i:1599323 original size:154 final size:150
Alignment explanation
Indices: 1599006--1599384 Score: 440
Period size: 154 Copynumber: 2.5 Consensus size: 150
1598996 GGGAGGATTT
* ** * * * * *
1599006 AATACTGCTGAGACTAAGGGTGATGCCTCAGTAGCCTTTCACAAGCATTGCAAGAAAAGGTTTCA
1 AATACTGCCGAGACTAAACGTAATGCCTCAGAAGCCTTGCACAGGCATTGCAAGAAAAGGTTTTA
* * * * *
1599071 GATGTTTATTCTGTCTATGGTTTGGTTTCTGGTAAATTAATATTTCTATTTATCCATCATTTTGT
66 GACGTTTCTTCTGTCTATGGTCTGGTTTCTGGTAAATTAACATATCTATTTATCCATCATTTTGT
*
1599136 AGAGGGATTTGCTCGATTCA
131 AGAGGGATATGCTCGATTCA
* * * *
1599156 AATACTGCTGAGACTACACTTAATGCCTCAGAAGCCCTTGCA-AGGCATTGGAAGAAAAGGTTTT
1 AATACTGCCGAGACTAAACGTAATGCCTCAGAAG-CCTTGCACAGGCATTGCAAGAAAAGGTTTT
* * *
1599220 AGACGTTTCTTTTGTCTGTGGTCTGGTTTTCTGGTAATTTATACATATCTATTTATATCCAT-AT
65 AGACGTTTCTTCTGTCTATGGTCTGG-TTTCTGGTAAATTA-ACATATCTA-TT-TATCCATCA-
* *
1599284 TTTTGTAGAGGG-TCATGCTGGATTTA
125 TTTTGTAGAGGGAT-ATGCTCGATTCA
* * *
1599310 AATACTGCCGAGACTAAAGGTGATGCCTCAGAAGCCTTGCACAGGCATTACAAGAAAAGGTTTTA
1 AATACTGCCGAGACTAAACGTAATGCCTCAGAAGCCTTGCACAGGCATTGCAAGAAAAGGTTTTA
1599375 GACGTTTCTT
66 GACGTTTCTT
1599385 ATCCATAATC
Statistics
Matches: 193, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
150 68 0.35
151 19 0.10
152 7 0.04
153 11 0.06
154 88 0.46
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (150 bp):
AATACTGCCGAGACTAAACGTAATGCCTCAGAAGCCTTGCACAGGCATTGCAAGAAAAGGTTTTA
GACGTTTCTTCTGTCTATGGTCTGGTTTCTGGTAAATTAACATATCTATTTATCCATCATTTTGT
AGAGGGATATGCTCGATTCA
Found at i:1600309 original size:18 final size:18
Alignment explanation
Indices: 1600286--1600322 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1600276 GTGGAGTGAT
1600286 ATCTATTCTACAAGTTTA
1 ATCTATTCTACAAGTTTA
1600304 ATCTATTCTACAAGTTTA
1 ATCTATTCTACAAGTTTA
1600322 A
1 A
1600323 CATATACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.43
Consensus pattern (18 bp):
ATCTATTCTACAAGTTTA
Found at i:1602504 original size:7 final size:7
Alignment explanation
Indices: 1602492--1602520 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1602482 ATTTTTTTCA
1602492 TTAAAAT
1 TTAAAAT
1602499 TTAAAA-
1 TTAAAAT
1602505 TTAAAAT
1 TTAAAAT
1602512 TTAAAAT
1 TTAAAAT
1602519 TT
1 TT
1602521 TATTTGTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TTAAAAT
Found at i:1602509 original size:13 final size:13
Alignment explanation
Indices: 1602491--1602519 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1602481 GATTTTTTTC
1602491 ATTAAAATTTAAA
1 ATTAAAATTTAAA
1602504 ATTAAAATTTAAA
1 ATTAAAATTTAAA
1602517 ATT
1 ATT
1602520 TTATTTGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTAAAATTTAAA
Found at i:1607548 original size:2 final size:2
Alignment explanation
Indices: 1607541--1607569 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1607531 ATTCTTTATC
1607541 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1607570 TAATACGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1611248 original size:14 final size:14
Alignment explanation
Indices: 1611229--1611269 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1611219 TAGGCAATAT
*
1611229 TGGAATATGCATTC
1 TGGAATATACATTC
1611243 TGGAATATACATTC
1 TGGAATATACATTC
*
1611257 CGGAATATACATT
1 TGGAATATACATT
1611270 TGCATTCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (14 bp):
TGGAATATACATTC
Found at i:1612971 original size:35 final size:35
Alignment explanation
Indices: 1612918--1613031 Score: 167
Period size: 35 Copynumber: 3.3 Consensus size: 35
1612908 TCGTCTATAG
* *
1612918 TAGAAC-GAAGGGAGGCATCGCACTTTCGATTCAAG
1 TAGAACGGAA-GGAAGCATCGCACTTTCGATTCAAC
* * *
1612953 AAGAACGGAAGGAAGCATCGCACGTTCGATTCAAT
1 TAGAACGGAAGGAAGCATCGCACTTTCGATTCAAC
1612988 TAGAACGGAAGGAAGCATCGCACTTTCGATTCAAC
1 TAGAACGGAAGGAAGCATCGCACTTTCGATTCAAC
1613023 TAGAACGGA
1 TAGAACGGA
1613032 TGATTTACTA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
35 68 0.96
36 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.18
Consensus pattern (35 bp):
TAGAACGGAAGGAAGCATCGCACTTTCGATTCAAC
Found at i:1613153 original size:14 final size:14
Alignment explanation
Indices: 1613134--1613174 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1613124 GGGAGAATAT
*
1613134 TGGAATATGCATTA
1 TGGAATATACATTA
*
1613148 TGGAATATACATTC
1 TGGAATATACATTA
*
1613162 CGGAATATACATT
1 TGGAATATACATT
1613175 TGCATTCTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (14 bp):
TGGAATATACATTA
Found at i:1615347 original size:12 final size:12
Alignment explanation
Indices: 1615332--1615374 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1615322 TAATAAAGAA
1615332 AAAAATATAAAT
1 AAAAATATAAAT
*
1615344 AAAAAAATAAAT
1 AAAAATATAAAT
*
1615356 AATAAATAAAAACT
1 AA-AAATATAAA-T
1615370 AAAAA
1 AAAAA
1615375 AGGAATACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 13 0.50
13 10 0.38
14 3 0.12
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (12 bp):
AAAAATATAAAT
Found at i:1615362 original size:19 final size:18
Alignment explanation
Indices: 1615315--1615367 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
1615305 GATAATTAGG
1615315 ATAAATAT-AATAAAGAAA
1 ATAAATATAAATAAA-AAA
1615333 A-AAATATAAATAAAAAA
1 ATAAATATAAATAAAAAA
1615350 ATAAATAATAAATAAAAA
1 ATAAAT-ATAAATAAAAA
1615368 CTAAAAAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.31
18 11 0.34
19 11 0.34
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (18 bp):
ATAAATATAAATAAAAAA
Found at i:1616607 original size:10 final size:10
Alignment explanation
Indices: 1616595--1616652 Score: 57
Period size: 10 Copynumber: 6.0 Consensus size: 10
1616585 AAATAATAAT
*
1616595 AAATGAAATT
1 AAATGAAATA
*
1616605 AAAT-TAATA
1 AAATGAAATA
* *
1616614 AAATGAATTG
1 AAATGAAATA
1616624 AAATGAAATA
1 AAATGAAATA
*
1616634 AAATAAAATA
1 AAATGAAATA
1616644 AAAT-AAATA
1 AAATGAAATA
1616653 TTAATAATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
9 12 0.31
10 27 0.69
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (10 bp):
AAATGAAATA
Found at i:1616619 original size:19 final size:19
Alignment explanation
Indices: 1616595--1616652 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
1616585 AAATAATAAT
*
1616595 AAATGAAATTAAATTAATA
1 AAATGAAATTAAATAAATA
1616614 AAATG-AATTGAAATGAAATA
1 AAATGAAATT-AAAT-AAATA
* *
1616634 AAATAAAATAAAATAAATA
1 AAATGAAATTAAATAAATA
1616653 TTAATAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.12
19 14 0.42
20 12 0.36
21 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (19 bp):
AAATGAAATTAAATAAATA
Found at i:1616822 original size:34 final size:32
Alignment explanation
Indices: 1616748--1616918 Score: 116
Period size: 34 Copynumber: 5.0 Consensus size: 32
1616738 TCAAAACTAT
1616748 ATATTATATAGTTTTCAAAAATGATTTTAAAA
1 ATATTATATAGTTTTCAAAAATGATTTTAAAA
* *
1616780 ATATTATATAAGTTTTCCAAAATGTTTTGTTAAAACTA
1 ATATTATAT-AGTTTTCAAAAATG-ATT-TT-AAA--A
* *
1616818 TATATTATATAAATTTTCCAAAAATGTTTTTAAAA
1 -ATATTATAT-AGTTTT-CAAAAATGATTTTAAAA
*
1616853 ATATATATTATA-TTTTC-AAAATGATTTCAAAA
1 ATAT-TA-TATAGTTTTCAAAAATGATTTTAAAA
* *
1616885 CTATATACTACATAATTTTC-AAAATG-TTTTAAAA
1 --ATAT--TATATAGTTTTCAAAAATGATTTTAAAA
1616919 CTTATATATT
Statistics
Matches: 116, Mismatches: 9, Indels: 26
0.77 0.06 0.17
Matches are distributed among these distances:
32 22 0.19
33 14 0.12
34 24 0.21
35 19 0.16
36 6 0.05
37 3 0.03
38 3 0.03
39 18 0.16
40 7 0.06
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (32 bp):
ATATTATATAGTTTTCAAAAATGATTTTAAAA
Found at i:1616849 original size:73 final size:67
Alignment explanation
Indices: 1616736--1616928 Score: 221
Period size: 73 Copynumber: 2.8 Consensus size: 67
1616726 CTAAAAACAT
*
1616736 TTTCAAAACTATATATTATATAGTTTTCAAAAATGATTTTAAAAATAT-TA-TATAAGTTTTCCA
1 TTTCAAAACTATATATTATATAATTTTCAAAAATG-TTTTAAAAATATATATTAT-A-TTTT-CA
*
1616799 AAATGTT
62 AAATG-A
*
1616806 TTGTTAAAACTATATATTATATAAATTTTCCAAAAATGTTTTTAAAAATATATATTATATTTTCA
1 TT-TCAAAACTATATATTATAT-AATTTT-CAAAAATG-TTTTAAAAATATATATTATATTTTCA
1616871 AAATGA
62 AAATGA
* * *
1616877 TTTCAAAACTATATACTACATAATTTTC-AAAATGTTTTAAAACTTATATATT
1 TTTCAAAACTATATATTATATAATTTTCAAAAATGTTTTAAAA-ATATATATT
1616929 GTATATAAGT
Statistics
Matches: 109, Mismatches: 8, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
66 8 0.07
67 14 0.13
68 1 0.01
69 6 0.06
70 18 0.17
71 20 0.18
72 12 0.11
73 24 0.22
74 3 0.03
75 3 0.03
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (67 bp):
TTTCAAAACTATATATTATATAATTTTCAAAAATGTTTTAAAAATATATATTATATTTTCAAAAT
GA
Found at i:1616860 original size:40 final size:39
Alignment explanation
Indices: 1616780--1616865 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 39
1616770 GATTTTAAAA
* * *
1616780 ATATTATATAAGTTTTCCAAAATGTTTTGTTAAAACTAT
1 ATATTATATAAATTTTCCAAAATGTTTTGTAAAAAATAT
1616819 ATATTATATAAATTTTCCAAAAATGTTTT-T-AAAAATAT
1 ATATTATATAAATTTTCC-AAAATGTTTTGTAAAAAATAT
1616857 ATATTATAT
1 ATATTATAT
1616866 TTTCAAAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
38 16 0.36
39 18 0.41
40 10 0.23
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.47
Consensus pattern (39 bp):
ATATTATATAAATTTTCCAAAATGTTTTGTAAAAAATAT
Found at i:1616919 original size:34 final size:34
Alignment explanation
Indices: 1616735--1616946 Score: 175
Period size: 32 Copynumber: 5.9 Consensus size: 34
1616725 TCTAAAAACA
* *
1616735 TTTTCAAAACTATATATTATATAGTTTTCAAAAATG
1 TTTTTAAAACTATATA-TATATAATTTTC-AAAATG
*
1616771 ATTTTAAAA--ATAT-TATATAAGTTTTCCAAAATG
1 TTTTTAAAACTATATATATATAA-TTTT-CAAAATG
1616804 TTTTGTTAAAACTATATATTATATAAATTTTCCAAAAATG
1 -TTT-TTAAAACTATATA-TATAT-AATTTT-C-AAAATG
*
1616844 TTTTTAAAAATATATAT-TAT-ATTTTCAAAATG
1 TTTTTAAAACTATATATATATAATTTTCAAAATG
* * *
1616876 ATTTCAAAACTATATACTACATAATTTTCAAAATG
1 TTTTTAAAACTATATA-TATATAATTTTCAAAATG
1616911 -TTTTAAAACTTATATATTGTATATAAGTTTTCAAAA
1 TTTTTAAAAC-TATATA---TATATAA-TTTTCAAAA
1616947 ACGTTTTAAA
Statistics
Matches: 147, Mismatches: 12, Indels: 32
0.77 0.06 0.17
Matches are distributed among these distances:
32 25 0.17
33 12 0.08
34 22 0.15
35 24 0.16
36 10 0.07
37 11 0.07
38 21 0.14
39 14 0.10
40 8 0.05
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (34 bp):
TTTTTAAAACTATATATATATAATTTTCAAAATG
Found at i:1616960 original size:107 final size:105
Alignment explanation
Indices: 1616740--1616983 Score: 239
Period size: 107 Copynumber: 2.2 Consensus size: 105
1616730 AAACATTTTC
* * *
1616740 AAAACTATATATTATATAGTTTTCAAAAATGATTTTAAAAATATTATATAAGTTTTCCAAAATGT
1 AAAAATATATA-T-TATA-TTTTC-AAAATGATTTCAAAAATATTACATAAGTTTTCCAAAATG-
* *
1616805 TTTGTTAAAACTATATATTATATAAATTTTCCAAAAATGTTTT-T
61 TTTGTTAAAACTATATATTATATAAATTTTCCAAAAACGTTTTAA
1616849 AAAAATATATATTATATTTTCAAAATGATTTCAAAACTATATACTACATAA-TTTT-CAAAATG-
1 AAAAATATATATTATATTTTCAAAATGATTTCAAAA--ATAT--TACATAAGTTTTCCAAAATGT
*
1616911 TT-TTAAAACTTATATATTGTATATAAGTTTT-CAAAAACGTTTTAAA
62 TTGTTAAAAC-TATATA-T-TATATAAATTTTCCAAAAACGTTTT-AA
* *
1616957 AAAAACTATATAATACATATTTCAAAA
1 AAAAA-TATATATTATAT-TTTCAAAA
1616984 ATATATTTTT
Statistics
Matches: 116, Mismatches: 8, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
104 7 0.06
105 22 0.19
106 17 0.15
107 26 0.22
108 10 0.09
109 26 0.22
110 8 0.07
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.42
Consensus pattern (105 bp):
AAAAATATATATTATATTTTCAAAATGATTTCAAAAATATTACATAAGTTTTCCAAAATGTTTGT
TAAAACTATATATTATATAAATTTTCCAAAAACGTTTTAA
Found at i:1619773 original size:35 final size:35
Alignment explanation
Indices: 1619727--1619797 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
1619717 TAAAAAAGAA
1619727 AGAAAGAATGCACTACTATTGAAAATTTGCCACCT
1 AGAAAGAATGCACTACTATTGAAAATTTGCCACCT
1619762 AGAAAGAATGCACTACTATTGAAAATTTGCCACCT
1 AGAAAGAATGCACTACTATTGAAAATTTGCCACCT
1619797 A
1 A
1619798 TAGATGTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (35 bp):
AGAAAGAATGCACTACTATTGAAAATTTGCCACCT
Found at i:1622519 original size:20 final size:19
Alignment explanation
Indices: 1622494--1622547 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
1622484 GCGAAATAAA
1622494 AATCGCAATGCGATCTCCAG
1 AATCGCAATGCGATC-CCAG
*
1622514 AATCGCAAAT-CAGTTCCCAG
1 AATCGC-AATGC-GATCCCAG
1622534 AATCGCAATGCGAT
1 AATCGCAATGCGAT
1622548 AGTACAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 5 0.17
20 18 0.62
21 6 0.21
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (19 bp):
AATCGCAATGCGATCCCAG
Found at i:1622601 original size:20 final size:20
Alignment explanation
Indices: 1622576--1622788 Score: 133
Period size: 20 Copynumber: 10.5 Consensus size: 20
1622566 GATTTTCCAT
**
1622576 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGAA
* * *
1622596 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATCCGAA
* * * *
1622616 TATCGCAATGAGTATCCGTAA
1 AATCGCAACGCGAATCCG-AA
* * *
1622637 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
*
1622657 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCG-AA
* * *
1622678 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
*
1622698 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCG-AA
* * *
1622719 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGAA
* * *
1622739 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGAA
* * *
1622759 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
1622779 AATCGCAACG
1 AATCGCAACG
1622789 ATTACCTAAA
Statistics
Matches: 148, Mismatches: 38, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
20 101 0.68
21 47 0.32
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGAA
Found at i:1622662 original size:41 final size:41
Alignment explanation
Indices: 1622632--1622789 Score: 264
Period size: 41 Copynumber: 3.9 Consensus size: 41
1622622 AATGAGTATC
*
1622632 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
*
1622673 CGTAAAATCGTAACGCGTATCCGTAAATCGCAACGACAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
* *
1622714 CGTAAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
*
1622755 CGT-AAATCGCAATGCGTATCCGTAAATCGCAACGA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGA
1622790 TTACCTAAAT
Statistics
Matches: 110, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
40 30 0.27
41 80 0.73
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
Found at i:1623492 original size:20 final size:20
Alignment explanation
Indices: 1623467--1623542 Score: 92
Period size: 20 Copynumber: 4.1 Consensus size: 20
1623457 TCGTAATTCG
1623467 AAATGAAAATCGCAATGCGA
1 AAATGAAAATCGCAATGCGA
1623487 AAATGAAAATCGCAA--CG-
1 AAATGAAAATCGCAATGCGA
*
1623504 -AGTG--AATCGCAATGCGA
1 AAATGAAAATCGCAATGCGA
*
1623521 AAATGAAAATCGCAACGCGA
1 AAATGAAAATCGCAATGCGA
1623541 AA
1 AA
1623543 TTACGTTGCA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
14 8 0.17
16 5 0.11
18 5 0.11
20 29 0.62
ACGTcount: A:0.49, C:0.17, G:0.21, T:0.13
Consensus pattern (20 bp):
AAATGAAAATCGCAATGCGA
Found at i:1623583 original size:33 final size:33
Alignment explanation
Indices: 1623557--1623706 Score: 246
Period size: 33 Copynumber: 4.5 Consensus size: 33
1623547 GTTGCAATTT
1623557 TCATTTCGCATTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCATTGCGATTCTCTCGTTGCGATAG
*
1623590 TCATTTCGCATTGCGATTCTCTCGTTGAGATAG
1 TCATTTCGCATTGCGATTCTCTCGTTGCGATAG
**
1623623 TCATTTCGCATTGCGATTCTCTCGTTGCGATTT
1 TCATTTCGCATTGCGATTCTCTCGTTGCGATAG
*
1623656 TTATTTCGCATTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCATTGCGATTCTCTCGTTGCGATAG
*
1623689 TCATTTCCGCGTTGCGAT
1 TCATTT-CGCATTGCGAT
1623707 AGCCTGTTTT
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 97 0.91
34 10 0.09
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (33 bp):
TCATTTCGCATTGCGATTCTCTCGTTGCGATAG
Found at i:1623586 original size:14 final size:14
Alignment explanation
Indices: 1623567--1623686 Score: 60
Period size: 14 Copynumber: 7.5 Consensus size: 14
1623557 TCATTTCGCA
1623567 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1623581 TTGCGATAGTCATTTCG
1 TTGCGAT--TC-TCTCG
1623598 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
* *
1623614 TTGAGATAGTCATTTCG
1 TTGCGAT--TC-TCTCG
1623631 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
* *
1623647 TTGCGATTTTTATTTCG
1 TTGCGA---TTCTCTCG
1623664 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1623680 TTGCGAT
1 TTGCGAT
1623687 AGTCATTTCC
Statistics
Matches: 81, Mismatches: 10, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
14 26 0.32
16 18 0.22
17 18 0.22
19 19 0.23
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.42
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1623827 original size:14 final size:14
Alignment explanation
Indices: 1623808--1623844 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1623798 CATCAATTAA
1623808 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1623822 ACAAATCATCTTTT
1 ACAAATCAACATTT
1623836 ACAAATCAA
1 ACAAATCAA
1623845 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1625293 original size:42 final size:42
Alignment explanation
Indices: 1625214--1625295 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
1625204 CCTCTTCAAC
* *
1625214 GATGACAGTGGCCTCTTGAACAGTAGGAGATGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACAGTAGGAGAGGACTCTTGAGG
* * *
1625256 GATGATAGGGGCCTCTTGAAC-GATAGGGGAGGCCTCTTGA
1 GATGACAGGGGCCTCTTGAACAG-TAGGAGAGGACTCTTGA
1625296 ACGATTACAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.03
42 33 0.97
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACAGTAGGAGAGGACTCTTGAGG
Found at i:1625786 original size:94 final size:94
Alignment explanation
Indices: 1625625--1625945 Score: 563
Period size: 94 Copynumber: 3.4 Consensus size: 94
1625615 CAATGACAAT
1625625 ACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACA
1 ACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACA
1625690 AATATTAACTTCACAGTGTTAAAGAATAC
66 AATATTAACTTCACAGTGTTAAAGAATAC
1625719 ACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACA
1 ACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACA
1625784 AATATTAACTTCACAGTGTTAAAGAATAC
66 AATATTAACTTCACAGTGTTAAAGAATAC
*
1625813 ACAGTTTAGCAGAATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAATGAC
1 ACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAA-GAC
* *
1625877 AAATACTAACTTCACAGTGTTAAAGAATAA
65 AAATATTAACTTCACAGTGTTAAAGAATAC
* * * *
1625907 ACAGTTTAGCAGTATTGACAGCAACCAAATAAATTTACT
1 ACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1625946 AAGCAATCTA
Statistics
Matches: 219, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
93 22 0.10
94 197 0.90
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (94 bp):
ACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACA
AATATTAACTTCACAGTGTTAAAGAATAC
Found at i:1627694 original size:20 final size:19
Alignment explanation
Indices: 1627645--1627699 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1627635 TTAAATGAAA
*
1627645 ATCGCAACGAGAGAATGACT
1 ATCGCAACGCGA-AATGACT
1627665 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
1627685 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
1627700 AAAAATCGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 5 0.15
20 26 0.79
21 2 0.06
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Done.