Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008245.1 Hibiscus syriacus cultivar Beakdansim tig00110895_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: 6601124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 33
Found at i:1189857 original size:24 final size:26
Alignment explanation
Indices: 1189816--1189863 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
1189806 TTTTGACATC
*
1189816 TTTTATATTGTAATAAAT-TAATATT
1 TTTTATATTGTAAAAAATCTAATATT
*
1189841 TTTTA-ATTTTAAAAAATCTAATA
1 TTTTATATTGTAAAAAATCTAATA
1189864 AAATATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTTATATTGTAAAAAATCTAATATT
Found at i:1190418 original size:3 final size:3
Alignment explanation
Indices: 1190410--1190471 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
1190400 TATGTAATAT
1190410 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1190458 GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GA
1190472 GTGATGAGCT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1191350 original size:2 final size:2
Alignment explanation
Indices: 1191345--1191379 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1191335 GATATATTCA
1191345 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1191380 TTTTAAGGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1202614 original size:5 final size:5
Alignment explanation
Indices: 1202606--1202631 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1202596 ATTAATTTAA
1202606 AATAT AATAT AATAT AATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT A
1202632 TTATTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:1216920 original size:9 final size:9
Alignment explanation
Indices: 1216906--1216937 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1216896 CTTTGCTTCA
*
1216906 TCTTCGTCT
1 TCTTCGTTT
1216915 TCTTCGTTT
1 TCTTCGTTT
1216924 TCTTCGTTT
1 TCTTCGTTT
1216933 TCTTC
1 TCTTC
1216938 TCCCCTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.28, G:0.09, T:0.62
Consensus pattern (9 bp):
TCTTCGTTT
Found at i:1221127 original size:6 final size:6
Alignment explanation
Indices: 1221116--1221161 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
1221106 TATTAGGTTC
* *
1221116 TGGACT TGGACT TGGACT TGGACT TGAACT TGAACT TGGACT TGGA
1 TGGACT TGGACT TGGACT TGGACT TGGACT TGGACT TGGACT TGGA
1221162 TTTTAATAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (6 bp):
TGGACT
Found at i:1227467 original size:563 final size:563
Alignment explanation
Indices: 1226357--1227481 Score: 2009
Period size: 563 Copynumber: 2.0 Consensus size: 563
1226347 TTACACAATT
*
1226357 CCATGAATGTTGAGTTTAACTTTCAACACTCCCCTCAAACTCGACTTTCCATTCTAAGCTTTTCT
1 CCATGAATGCTGAGTTTAACTTTCAACACTCCCCTCAAACTCGACTTTCCATTCTAAGCTTTTCT
* *
1226422 AAGTTTGTCATCTCCAATCGATTCTTCATTTGTTATGGGATCACTCTTTGCAAAGAGACTAAATA
66 AAGTTTGTCATCTCCAATCAATTCTTCATTTGTTATGAGATCACTCTTTGCAAAGAGACTAAATA
*
1226487 GTAAAACATTATTTAATTCATAATCGTTGTACCTTTCTGGTATTCTTCTCTCTCTTGTGGATCTT
131 ATAAAACATTATTTAATTCATAATCGTTGTACCTTTCTGGTATTCTTCTCTCTCTTGTGGATCTT
* *
1226552 CGAACTTTTGTGGGAGGTGCTTCAGAATCTTCTATTATGTTGCTAGCAATGTTGATGCTGCTTGA
196 CGAACTTCTGTGGGAGGTGCTTCAGAATCTTCTATTATGTTACTAGCAATGTTGATGCTGCTTGA
1226617 AGACGATGGTACATTTTGCTGAGGACCTTGATCATCAGCTTGTTCATCTTGATTGATAAGATCGT
261 AGACGATGGTACATTTTGCTGAGGACCTTGATCATCAGCTTGTTCATCTTGATTGATAAGATCGT
1226682 CATCTTTATCTTCATTAAAAAATAGTCCTTCAACTTTCTTTTCCTCTTTGCTCCATCTCCAATAT
326 CATCTTTATCTTCATTAAAAAATAGTCCTTCAACTTTCTTTTCCTCTTTGCTCCATCTCCAATAT
* *
1226747 TCTGCTTCATCAAACTCGACATCTCTTGAAATTATTACTTTCTTGGTAATAGGATTATATAATCT
391 TCTGCTTCATCAAACTCGACATCTCTTAAAATTATTACTTTCTTGGTAAAAGGATTATATAATCT
* * *
1226812 GTAAGCTTTTCTTCTTTCATCATAGCCAATGAAAATATATTTTTCTCCTCTGTTATCAAGCTTCT
456 GTAAGCTTTTCTTCTTTCATCATAGCCAATGAAAATACATTTTTCTCCTCTATCATCAAGCTTCT
* *
1226877 TTCTGGTATGTTCATAAACGAGGGCATATGCGATGCA-CCAAG
521 TTCTGGTATATTCAGAAACGAGGGCATATGCGATGCATCCAAG
1226919 CCATGAATGCTGAGTTTAACTTTCAACACTCCCCCTCAAACTCGACTTTCCATTCTAAGCTTTTC
1 CCATGAATGCTGAGTTTAACTTTCAACACT-CCCCTCAAACTCGACTTTCCATTCTAAGCTTTTC
* *
1226984 TAAGTTTTTCATCTCCAATCAATTCTTCATTTGTTATGAGATCACTCTTTGCAAAGAGACTGAAT
65 TAAGTTTGTCATCTCCAATCAATTCTTCATTTGTTATGAGATCACTCTTTGCAAAGAGACTAAAT
*
1227049 AATGAAACATTATTTAATTCATAATCGTTGTACCTTTCTGGTATTCTTCTCTCTCTTGTGGATCT
130 AATAAAACATTATTTAATTCATAATCGTTGTACCTTTCTGGTATTCTTCTCTCTCTTGTGGATCT
* * *
1227114 TCGAACTTCTGTGGGAGGTGCTTCAGAATCTTTTATTATGTTACTAGCAATGTTGCTGCTTCTTG
195 TCGAACTTCTGTGGGAGGTGCTTCAGAATCTTCTATTATGTTACTAGCAATGTTGATGCTGCTTG
* * *
1227179 ACGATGATGGTACATTTTGTTGAGGACCTTGATCATCAGCTTGTTCATCTTGATTGATAAGATCG
260 AAGACGATGGTACATTTTGCTGAGGACCTTGATCATCAGCTTGTTCATCTTGATTGATAAGATCG
1227244 TCATCTTTATCTTCATTAAAAAATAGTCCTTCAACTTTCTTTTCCTCTTTGCTCCATCTCCAATA
325 TCATCTTTATCTTCATTAAAAAATAGTCCTTCAACTTTCTTTTCCTCTTTGCTCCATCTCCAATA
*
1227309 TTCTGCTTCATTAAACTCGACATCTCTTAAAATTATTACTTTCTTGGTAAAAGGATTATATAATC
390 TTCTGCTTCATCAAACTCGACATCTCTTAAAATTATTACTTTCTTGGTAAAAGGATTATATAATC
1227374 TGTAAGCTTTTCTTCTTTCATCATAGCCAATGAAAATACATTTTTCTCCTCTATCATCAAGCTTC
455 TGTAAGCTTTTCTTCTTTCATCATAGCCAATGAAAATACATTTTTCTCCTCTATCATCAAGCTTC
* *
1227439 TTTCTGGTCTATTCAGAAACGTGGGCATATGCGATGCATCCAA
520 TTTCTGGTATATTCAGAAACGAGGGCATATGCGATGCATCCAA
1227482 CAGGTGTCCA
Statistics
Matches: 536, Mismatches: 25, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
562 29 0.05
563 503 0.94
564 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (563 bp):
CCATGAATGCTGAGTTTAACTTTCAACACTCCCCTCAAACTCGACTTTCCATTCTAAGCTTTTCT
AAGTTTGTCATCTCCAATCAATTCTTCATTTGTTATGAGATCACTCTTTGCAAAGAGACTAAATA
ATAAAACATTATTTAATTCATAATCGTTGTACCTTTCTGGTATTCTTCTCTCTCTTGTGGATCTT
CGAACTTCTGTGGGAGGTGCTTCAGAATCTTCTATTATGTTACTAGCAATGTTGATGCTGCTTGA
AGACGATGGTACATTTTGCTGAGGACCTTGATCATCAGCTTGTTCATCTTGATTGATAAGATCGT
CATCTTTATCTTCATTAAAAAATAGTCCTTCAACTTTCTTTTCCTCTTTGCTCCATCTCCAATAT
TCTGCTTCATCAAACTCGACATCTCTTAAAATTATTACTTTCTTGGTAAAAGGATTATATAATCT
GTAAGCTTTTCTTCTTTCATCATAGCCAATGAAAATACATTTTTCTCCTCTATCATCAAGCTTCT
TTCTGGTATATTCAGAAACGAGGGCATATGCGATGCATCCAAG
Found at i:1229703 original size:16 final size:16
Alignment explanation
Indices: 1229682--1229715 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1229672 AGTCATGGAC
* *
1229682 ATAATTATGTGTGGTT
1 ATAATTATATGTGATT
1229698 ATAATTATATGTGATT
1 ATAATTATATGTGATT
1229714 AT
1 AT
1229716 CTGTATTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (16 bp):
ATAATTATATGTGATT
Found at i:1230988 original size:103 final size:103
Alignment explanation
Indices: 1230804--1231124 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
1230794 GTCGAGGGTC
1230804 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1230869 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1230907 TATGGGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1230972 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
1231010 TATGTGGTCATTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
1231075 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1231113 TATGTGGTCCTT
1 TATGTGGTCCTT
1231125 ATGGACATTA
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1231174 original size:23 final size:23
Alignment explanation
Indices: 1231143--1231208 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
1231133 TATTATATGG
1231143 CACTACGGTGCAATTCTACGCGA
1 CACTACGGTGCAATTCTACGCGA
* * *
1231166 CACTCCGGTGCAATTCTACGTGG
1 CACTACGGTGCAATTCTACGCGA
* *
1231189 CACTTCGGTGCAATTATACG
1 CACTACGGTGCAATTCTACG
1231209 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (23 bp):
CACTACGGTGCAATTCTACGCGA
Found at i:1231429 original size:16 final size:16
Alignment explanation
Indices: 1231378--1231430 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1231368 GCTATGTGAT
1231378 ATATGTATATGATGTGTG
1 ATATG-ATAT-ATGTGTG
* * **
1231396 ATATGATGTGTGCATG
1 ATATGATATATGTGTG
1231412 ATATGATATATGTGTG
1 ATATGATATATGTGTG
1231428 ATA
1 ATA
1231431 GGGGTTATGG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (16 bp):
ATATGATATATGTGTG
Found at i:1234834 original size:23 final size:24
Alignment explanation
Indices: 1234807--1234857 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1234797 TGTTCGTGTT
1234807 TGTTCATTTA-ATG-TCTACGAACG
1 TGTTCATTTATATGTTC-ACGAACG
*
1234830 TGTTCGTTTATATGTTCACGAACG
1 TGTTCATTTATATGTTCACGAACG
1234854 TGTT
1 TGTT
1234858 AATGAACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 9 0.36
24 14 0.56
25 2 0.08
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43
Consensus pattern (24 bp):
TGTTCATTTATATGTTCACGAACG
Found at i:1234909 original size:70 final size:70
Alignment explanation
Indices: 1234824--1235005 Score: 301
Period size: 70 Copynumber: 2.6 Consensus size: 70
1234814 TTAATGTCTA
* * * *
1234824 CGAACGTGTTCGTTTATATGTTCACGAACGTGTTAATGAACATGTTTGTTTAGCGTTTGTTTCAT
1 CGAACGTGTTCGTTTATATGTTCACGAACGTGTTCATGAACATGTTTGTTTAGAGTTTATTTAAT
1234889 GTTCG
66 GTTCG
* *
1234894 CGAAAGTGTTCGTTTATATGTTCACTAACGTGTTCATGAACATGTTTGTTTAGAGTTTATTTAAT
1 CGAACGTGTTCGTTTATATGTTCACGAACGTGTTCATGAACATGTTTGTTTAGAGTTTATTTAAT
1234959 GTTCG
66 GTTCG
*
1234964 CGAACGTGTTCGTTTATATGTTCAAGAACGTGTTCATGAACA
1 CGAACGTGTTCGTTTATATGTTCACGAACGTGTTCATGAACA
1235006 AACTAAAGAA
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 103 1.00
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (70 bp):
CGAACGTGTTCGTTTATATGTTCACGAACGTGTTCATGAACATGTTTGTTTAGAGTTTATTTAAT
GTTCG
Found at i:1234979 original size:34 final size:34
Alignment explanation
Indices: 1234861--1234979 Score: 89
Period size: 34 Copynumber: 3.4 Consensus size: 34
1234851 ACGTGTTAAT
* * * *
1234861 GAACATGTTTGTTTAGCGTTTGTTTCATGTTCGC
1 GAACATGTTCGTTTAGAGTTTATTTAATGTTCGC
* * * **
1234895 GAA-AGTGTTCGTTTATATGTTCA-CTAACGTGTTCAT
1 GAACA-TGTTCGTTTAGA-GTTTATTTAA--TGTTCGC
*
1234931 GAACATGTTTGTTTAGAGTTTATTTAATGTTCGC
1 GAACATGTTCGTTTAGAGTTTATTTAATGTTCGC
*
1234965 GAACGTGTTCGTTTA
1 GAACATGTTCGTTTA
1234980 TATGTTCAAG
Statistics
Matches: 62, Mismatches: 17, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
33 1 0.02
34 32 0.52
35 7 0.11
36 21 0.34
37 1 0.02
ACGTcount: A:0.21, C:0.13, G:0.22, T:0.45
Consensus pattern (34 bp):
GAACATGTTCGTTTAGAGTTTATTTAATGTTCGC
Found at i:1234986 original size:24 final size:23
Alignment explanation
Indices: 1234953--1234998 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1234943 TTAGAGTTTA
**
1234953 TTTAATGTTCGCGAACGTGTTCG
1 TTTAATGTTCAAGAACGTGTTCG
1234976 TTTATATGTTCAAGAACGTGTTC
1 TTTA-ATGTTCAAGAACGTGTTC
1234999 ATGAACAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (23 bp):
TTTAATGTTCAAGAACGTGTTCG
Found at i:1236084 original size:23 final size:23
Alignment explanation
Indices: 1236058--1236102 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1236048 TAAGAGTGTT
1236058 GTTGCTAGTTAGTTAAAGAAGTG
1 GTTGCTAGTTAGTTAAAGAAGTG
1236081 GTTGCTAGTTAGTTAAAGAAGT
1 GTTGCTAGTTAGTTAAAGAAGT
1236103 TGTTAGCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (23 bp):
GTTGCTAGTTAGTTAAAGAAGTG
Found at i:1239275 original size:27 final size:27
Alignment explanation
Indices: 1239237--1239288 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1239227 ATACACTCTA
**
1239237 CACCACCTGGGAGTGTTGCTGAAGAAT
1 CACCACCTGGGAGTGGGGCTGAAGAAT
1239264 CACCACCTGGGAGTGGGGCTGAAGA
1 CACCACCTGGGAGTGGGGCTGAAGA
1239289 TACTGGTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.35, T:0.17
Consensus pattern (27 bp):
CACCACCTGGGAGTGGGGCTGAAGAAT
Found at i:1240941 original size:23 final size:23
Alignment explanation
Indices: 1240915--1240964 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1240905 TTAAGAGTGT
1240915 TGTTGCTAGTTAGTTAAAGAAGC
1 TGTTGCTAGTTAGTTAAAGAAGC
*
1240938 TGTTGCTAGTTAGTTAAAGAAGT
1 TGTTGCTAGTTAGTTAAAGAAGC
1240961 TGTT
1 TGTT
1240965 AGCTGGCGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.28, C:0.06, G:0.26, T:0.40
Consensus pattern (23 bp):
TGTTGCTAGTTAGTTAAAGAAGC
Found at i:1241879 original size:40 final size:41
Alignment explanation
Indices: 1241798--1241899 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 41
1241788 TTCTCAGTTG
** *
1241798 AACTGAAAATGTTATAAAAAAATGTAAACTTTTTTATTGTC
1 AACTGAAAATGTTATAAAAAAATGTAAACTTTTCGAATGTC
* *
1241839 AACTGAAAATGTTAT-ACAGAATGT-AACATTTTCGAATGTC
1 AACTGAAAATGTTATAAAAAAATGTAAAC-TTTTCGAATGTC
** *
1241879 AACCAAAAATATTATAAAAAA
1 AACTGAAAATGTTATAAAAAA
1241900 TATTTTTAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
39 3 0.06
40 28 0.57
41 18 0.37
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (41 bp):
AACTGAAAATGTTATAAAAAAATGTAAACTTTTCGAATGTC
Found at i:1249133 original size:20 final size:20
Alignment explanation
Indices: 1249110--1249165 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1249100 ATTCGCGTTG
*
1249110 CATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTC
1249130 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
*
1249150 CAGTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1249166 AGTCTACAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:1249313 original size:5 final size:5
Alignment explanation
Indices: 1249291--1249340 Score: 64
Period size: 5 Copynumber: 9.6 Consensus size: 5
1249281 CGTATTACCA
* *
1249291 CGACC ACGACC ACGACC CGACC CGACC CGACC CGATC CGACC CGATC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGA
1249341 GACGAGAAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
5 30 0.73
6 11 0.27
ACGTcount: A:0.24, C:0.52, G:0.20, T:0.04
Consensus pattern (5 bp):
CGACC
Found at i:1249852 original size:6 final size:6
Alignment explanation
Indices: 1249836--1249867 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1249826 GTCCGTCTCG
1249836 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1249868 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:1250030 original size:22 final size:22
Alignment explanation
Indices: 1249980--1250031 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1249970 AATTTGGAAA
1249980 ATCGCAA-AGACAACTGTAGACT
1 ATCGCAACA-ACAACTGTAGACT
*
1250002 GTCGCAACAACAACTGTAGACT
1 ATCGCAACAACAACTGTAGACT
*
1250024 ATTGCAAC
1 ATCGCAAC
1250032 GCGAAATGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCGCAACAACAACTGTAGACT
Found at i:1255249 original size:21 final size:20
Alignment explanation
Indices: 1255211--1255250 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1255201 GGAATTTTGG
1255211 CTTTGAAATGGTTCGAAATA
1 CTTTGAAATGGTTCGAAATA
* *
1255231 CTTTGTAAATTGTTTGAAAT
1 CTTTG-AAATGGTTCGAAAT
1255251 TATTTTAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (20 bp):
CTTTGAAATGGTTCGAAATA
Found at i:1257732 original size:23 final size:22
Alignment explanation
Indices: 1257702--1257762 Score: 88
Period size: 23 Copynumber: 2.8 Consensus size: 22
1257692 CAATTCCCCT
*
1257702 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTC-A
1257725 AGGGGGAATCGATTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
*
1257747 A-GGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
1257763 TCTGCCCTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.39
22 2 0.06
23 20 0.56
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:1263317 original size:28 final size:28
Alignment explanation
Indices: 1263277--1263332 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1263267 ATGACTGAAT
1263277 CCTCAAGACATTCATATACGCTTCGTTG
1 CCTCAAGACATTCATATACGCTTCGTTG
1263305 CCTCAAGACATTCATATACGCTTCGTTG
1 CCTCAAGACATTCATATACGCTTCGTTG
1263333 ATATGCTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (28 bp):
CCTCAAGACATTCATATACGCTTCGTTG
Found at i:1265299 original size:21 final size:21
Alignment explanation
Indices: 1265273--1265440 Score: 149
Period size: 21 Copynumber: 7.9 Consensus size: 21
1265263 CATATAAAAT
* *
1265273 TGTCCCTAAGGACCTCATATA
1 TGTCCCGAAGGACCACATATA
1265294 TGTCCCGAAGGACCACATATA
1 TGTCCCGAAGGACCACATATA
1265315 TGTCCCGAAGGACCACATATAA
1 TGTCCCGAAGGACCACATAT-A
* *
1265337 T-TCTCCTTAAGGACCACACATA
1 TGTC-CC-GAAGGACCACATATA
* * ** * *
1265359 TATTCTAAAGGACCAAATATG
1 TGTCCCGAAGGACCACATATA
* *
1265380 TGTCCCGAAGAACTACATATA
1 TGTCCCGAAGGACCACATATA
* * * **
1265401 CGTTCCAAAGGATTACATATA
1 TGTCCCGAAGGACCACATATA
1265422 TGTCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
1265441 AAACCCTCGA
Statistics
Matches: 115, Mismatches: 28, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
21 95 0.83
22 7 0.06
23 13 0.11
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATATA
Found at i:1266204 original size:20 final size:20
Alignment explanation
Indices: 1266175--1266273 Score: 180
Period size: 20 Copynumber: 5.0 Consensus size: 20
1266165 GGTATCAGTG
1266175 CCCTTCAGGTATCGATACTA
1 CCCTTCAGGTATCGATACTA
* *
1266195 CCCTTAAGGTATCGATACCA
1 CCCTTCAGGTATCGATACTA
1266215 CCCTTCAGGTATCGATACTA
1 CCCTTCAGGTATCGATACTA
1266235 CCCTTCAGGTATCGATACTA
1 CCCTTCAGGTATCGATACTA
1266255 CCCTTCAGGTATCGATACT
1 CCCTTCAGGTATCGATACT
1266274 CTTTGAATAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 75 1.00
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.29
Consensus pattern (20 bp):
CCCTTCAGGTATCGATACTA
Found at i:1268678 original size:11 final size:12
Alignment explanation
Indices: 1268662--1268698 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1268652 TGAATCGTGA
1268662 AGGAAAAA-ATG
1 AGGAAAAAGATG
1268673 AGGAAAAAGAT-
1 AGGAAAAAGATG
1268684 AGGAATAAAGATG
1 AGGAA-AAAGATG
1268697 AG
1 AG
1268699 AGAAGGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 13 0.57
12 8 0.35
13 2 0.09
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (12 bp):
AGGAAAAAGATG
Found at i:1269785 original size:3 final size:3
Alignment explanation
Indices: 1269707--1269766 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
1269697 AAAATATGCT
*
1269707 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1269755 TAA TAA TAA TAA
1 TAA TAA TAA TAA
1269767 ATCCTTCAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1271580 original size:20 final size:20
Alignment explanation
Indices: 1271555--1271593 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1271545 TAAATTAAAT
*
1271555 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
1271575 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
1271594 TATTCTATTA
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:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:1271672 original size:54 final size:52
Alignment explanation
Indices: 1271554--1271704 Score: 250
Period size: 54 Copynumber: 2.9 Consensus size: 52
1271544 CTAAATTAAA
*
1271554 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
* *
1271606 TATTATATAGGATCATTTTTAATTAGATAGAATTAGTTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG--TTTTTATTCTATTAGT
1271660 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
1271705 GTTGCTAATT
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
51 10 0.11
52 33 0.36
54 49 0.53
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:1271686 original size:20 final size:20
Alignment explanation
Indices: 1271661--1271700 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1271651 TCTATTAGTT
*
1271661 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
1271681 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
1271701 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:1276344 original size:20 final size:20
Alignment explanation
Indices: 1276306--1276344 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1276296 TCTATTAGTT
* *
1276306 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
*
1276326 ATTAGATAGAATTAGTTTT
1 ATTAGATAGAATCAGTTTT
1276345 TTATTCTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:1276358 original size:53 final size:52
Alignment explanation
Indices: 1276279--1276378 Score: 182
Period size: 53 Copynumber: 1.9 Consensus size: 52
1276269 ATCAGTTTTA
1276279 ATAGAATCAGTTTTTATTCTATTAGTTATTAGATAGGATCATTTTTAATTAG
1 ATAGAATCAGTTTTTATTCTATTAGTTATTAGATAGGATCATTTTTAATTAG
*
1276331 ATAGAATTAGTTTTTTATTCTATTAGTTATTAGATAGGATCATTTTTA
1 ATAGAATCAG-TTTTTATTCTATTAGTTATTAGATAGGATCATTTTTA
1276379 TTCTGTTGCT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 9 0.20
53 37 0.80
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (52 bp):
ATAGAATCAGTTTTTATTCTATTAGTTATTAGATAGGATCATTTTTAATTAG
Found at i:1278813 original size:171 final size:172
Alignment explanation
Indices: 1278561--1278898 Score: 669
Period size: 171 Copynumber: 2.0 Consensus size: 172
1278551 TTTGTATTAG
1278561 CAGAATGAGCTTATTGATTGCTTTAGAATAATGGTGTTTGCACGACGTGCTGCTTTTTCTTTTTT
1 CAGAATGAGCTTATTGATTGCTTTAGAATAATGGTGTTTGCACGACGTGCTGCTTTTTCTTTTTT
1278626 TATTGTTGACACTTAGACTGATGATAATCTTAGTAGTTTTAGTGATCGTGATGCAAGCATTTATA
66 TATTGTTGACACTTAGACTGATGATAATCTTAGTAGTTTTAGTGATCGTGATGCAAGCATTTATA
1278691 CAAATTGATCTTGTAAATGTATATTTCCTTTGATGATGTCTC
131 CAAATTGATCTTGTAAATGTATATTTCCTTTGATGATGTCTC
1278733 CAGAATGAGCTTATTGATTGCTTTAGAATAATGGTG-TTGCACGACGTGCTGCTTTTTCTTTTTT
1 CAGAATGAGCTTATTGATTGCTTTAGAATAATGGTGTTTGCACGACGTGCTGCTTTTTCTTTTTT
1278797 TATTGTTGACACTTAGACTGATGATAATCTTAGTAGTTTTAGTGATCGTGATGCAAGCATTTATA
66 TATTGTTGACACTTAGACTGATGATAATCTTAGTAGTTTTAGTGATCGTGATGCAAGCATTTATA
1278862 CAAATTGATCTTGTAAATGTATATTTCCTTTGATGAT
131 CAAATTGATCTTGTAAATGTATATTTCCTTTGATGAT
1278899 ATTGTCTCCT
Statistics
Matches: 166, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
171 130 0.78
172 36 0.22
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.43
Consensus pattern (172 bp):
CAGAATGAGCTTATTGATTGCTTTAGAATAATGGTGTTTGCACGACGTGCTGCTTTTTCTTTTTT
TATTGTTGACACTTAGACTGATGATAATCTTAGTAGTTTTAGTGATCGTGATGCAAGCATTTATA
CAAATTGATCTTGTAAATGTATATTTCCTTTGATGATGTCTC
Found at i:1279558 original size:44 final size:44
Alignment explanation
Indices: 1279495--1279581 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
1279485 ACTGTAAGTA
*
1279495 GTGTTTAAGTTAAACTCTAAACCCTAACATAAATAAAAAACTAC
1 GTGTTTAACTTAAACTCTAAACCCTAACATAAATAAAAAACTAC
* * **
1279539 GTGTTTAACTTAAACTCTAAATCCTAACTTATCTAAAAAACTA
1 GTGTTTAACTTAAACTCTAAACCCTAACATAAATAAAAAACTA
1279582 TCTCCTAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.31
Consensus pattern (44 bp):
GTGTTTAACTTAAACTCTAAACCCTAACATAAATAAAAAACTAC
Found at i:1279747 original size:23 final size:23
Alignment explanation
Indices: 1279711--1279866 Score: 150
Period size: 23 Copynumber: 6.5 Consensus size: 23
1279701 AAATTAAAAA
* ***
1279711 AAAACCCTGTTTACCAGAATCGG
1 AAAACTCTGTTTACCAGTGCCGG
* * *
1279734 AAAACTCTGCTTACCAGTGTCGA
1 AAAACTCTGTTTACCAGTGCCGG
*
1279757 AAAACTTTGTTTACCAGTGCCGG
1 AAAACTCTGTTTACCAGTGCCGG
*
1279780 AAAACTTTGTTTACCAGTGCCGG
1 AAAACTCTGTTTACCAGTGCCGG
* *
1279803 AAAACTCTGTTTACTAGAGCCGGAACCG
1 AAAACTCTGTTTACCAGTGCC-G----G
*
1279831 AAAAACTCTGTTTACCAGAGCCGG
1 -AAAACTCTGTTTACCAGTGCCGG
1279855 AAAACTCTGTTT
1 AAAACTCTGTTT
1279867 CTACATGGTA
Statistics
Matches: 114, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
23 90 0.79
24 2 0.02
28 2 0.02
29 20 0.18
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (23 bp):
AAAACTCTGTTTACCAGTGCCGG
Found at i:1281560 original size:20 final size:20
Alignment explanation
Indices: 1281532--1281570 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1281522 CAATCTTTTT
*
1281532 TCGATTAGCAAATTATCTAC
1 TCGAATAGCAAATTATCTAC
1281552 TCGAATAGCAAATTATCTA
1 TCGAATAGCAAATTATCTA
1281571 TTGATTTGGG
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:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (20 bp):
TCGAATAGCAAATTATCTAC
Found at i:1282282 original size:20 final size:21
Alignment explanation
Indices: 1282257--1282311 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1282247 TTGGTAATTA
1282257 GCGTTGCGAATTT-GAAAATC
1 GCGTTGCGAATTTGGAAAATC
**
1282277 GCGTTGCGCTTTTGGAAAATC
1 GCGTTGCGAATTTGGAAAATC
*
1282298 GCGTTGTG-ATTTGG
1 GCGTTGCGAATTTGG
1282312 GAACATGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.20, C:0.15, G:0.31, T:0.35
Consensus pattern (21 bp):
GCGTTGCGAATTTGGAAAATC
Found at i:1282296 original size:21 final size:20
Alignment explanation
Indices: 1282257--1282303 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
1282247 TTGGTAATTA
1282257 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
**
1282277 GCGTTGCGCTTTTGGAAAATC
1 GCGTTGCGAATTT-GAAAATC
1282298 GCGTTG
1 GCGTTG
1282304 TGATTTGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:1282314 original size:21 final size:21
Alignment explanation
Indices: 1282257--1282314 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1282247 TTGGTAATTA
1282257 GCGTTGCGAATTT--GAAAATC
1 GCGTTGCG-ATTTGGGAAAATC
* *
1282277 GCGTTGCGCTTTTGGAAAATC
1 GCGTTGCGATTTGGGAAAATC
*
1282298 GCGTTGTGATTTGGGAA
1 GCGTTGCGATTTGGGAA
1282315 CATGTGTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.09
20 8 0.25
21 21 0.66
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (21 bp):
GCGTTGCGATTTGGGAAAATC
Found at i:1283444 original size:336 final size:338
Alignment explanation
Indices: 1282831--1283506 Score: 1212
Period size: 336 Copynumber: 2.0 Consensus size: 338
1282821 TTCCTGTGTC
* *
1282831 GACACTTCACAACAAAATGGGGTCGTCGAACGTAAAAACCGTCATCTTCTTGAGGTAACTCGAAC
1 GACACTTCACAACAAAATAGGGTCGCCGAACGTAAAAACCGTCATCTTCTTGAGGTAACTCGAAC
*
1282896 ACTCATTTTTTCTTCTAATGTTCCAAAATACCTTTGGGGTGAGGCTCTCTTGACAACTATTTTTC
66 ACTCATTTTTTCTTCTAATGTTCCAAAATACCTTTGGGGTGAGGCTCTCTTAACAACTATTTTTC
* * *
1282961 TAATCAATTGTTTGCCTAGTAAGATTCTTGCCTTTAAGTGTCCACGGGATATCATTTCCATTAAA
131 TAATCAATCGTTTGACTAGTAAGATTCTTGCCTTTAAGTGTCCACGGGATATCATTTCCACTAAA
*
1283026 TTCCCTCACTTCAAACCTTTTACCTCTTCTGTTCGTCTTCGTGTCTTTGGTTGTACTGCCTTTGT
196 TTCCCTCACTTCAAACCTTTTACCTCTTCTGTTCCTCTTCGTGTCTTTGGTTGTACTGCCTTTGT
*
1283091 CCGTGACCACAATCCTCATAAATCTAAACTTAATCCTCGGGCAATTC-G-GTGTCTTTGTAGGTT
261 CCATGACCACAATCCTCATAAATCTAAACTTAATCCTCGGGCAATTCGGTGTGTCTTTGTAGGTT
*
1283154 ATTCATCCCGTCA
326 ATTCATCCCATCA
* *
1283167 GACACTTCACAACAAAATAGGGTCGCCGAATGTAAAAACCGTCATCTTCTTGAGGTAACTCGAGC
1 GACACTTCACAACAAAATAGGGTCGCCGAACGTAAAAACCGTCATCTTCTTGAGGTAACTCGAAC
1283232 ACTCATTTTTTCTTCTAATGTTCCAAAATACCTTTGGGGTGAGGCTCTCTTAACAACTATTTTTC
66 ACTCATTTTTTCTTCTAATGTTCCAAAATACCTTTGGGGTGAGGCTCTCTTAACAACTATTTTTC
* *
1283297 TAATCAATCGTTTGACTAGTAAGATTCTTGCCTTTAAGTGTCCATGGGATATCCTTTCCACTAAA
131 TAATCAATCGTTTGACTAGTAAGATTCTTGCCTTTAAGTGTCCACGGGATATCATTTCCACTAAA
1283362 TTCCCTCACTTCAAACCTTTTACCTCTTCTGTTCCTCTTCGTGTCTTTGGTTGTACTGCCTTTGT
196 TTCCCTCACTTCAAACCTTTTACCTCTTCTGTTCCTCTTCGTGTCTTTGGTTGTACTGCCTTTGT
*
1283427 CCATGACCACAATCCTCATAAATCTAAATTTAATCCTCGGGCAATTCGGTGTGTCTTTGTAGGTT
261 CCATGACCACAATCCTCATAAATCTAAACTTAATCCTCGGGCAATTCGGTGTGTCTTTGTAGGTT
1283492 ATTCATCCCATCA
326 ATTCATCCCATCA
1283505 GA
1 GA
1283507 AAGGTTATCG
Statistics
Matches: 324, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
336 294 0.91
337 1 0.00
338 29 0.09
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (338 bp):
GACACTTCACAACAAAATAGGGTCGCCGAACGTAAAAACCGTCATCTTCTTGAGGTAACTCGAAC
ACTCATTTTTTCTTCTAATGTTCCAAAATACCTTTGGGGTGAGGCTCTCTTAACAACTATTTTTC
TAATCAATCGTTTGACTAGTAAGATTCTTGCCTTTAAGTGTCCACGGGATATCATTTCCACTAAA
TTCCCTCACTTCAAACCTTTTACCTCTTCTGTTCCTCTTCGTGTCTTTGGTTGTACTGCCTTTGT
CCATGACCACAATCCTCATAAATCTAAACTTAATCCTCGGGCAATTCGGTGTGTCTTTGTAGGTT
ATTCATCCCATCA
Found at i:1285770 original size:23 final size:23
Alignment explanation
Indices: 1285738--1285795 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
1285728 TCAGAATTAA
*
1285738 AAAACCCTGTTTACCCA-AACCGG
1 AAAACTCTGTTTA-CCAGAACCGG
**
1285761 AAAACTCTGTTTACCAGAGTCGG
1 AAAACTCTGTTTACCAGAACCGG
1285784 AAAACTCTGTTT
1 AAAACTCTGTTT
1285796 CTACAGAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 3 0.10
23 28 0.90
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (23 bp):
AAAACTCTGTTTACCAGAACCGG
Found at i:1287754 original size:22 final size:22
Alignment explanation
Indices: 1287705--1287753 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1287695 ATAAATTATT
**
1287705 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
1287727 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
1287750 TAAA
1 TAAA
1287754 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1287798 original size:80 final size:80
Alignment explanation
Indices: 1287708--1287857 Score: 264
Period size: 80 Copynumber: 1.9 Consensus size: 80
1287698 AATTATTTAA
* *
1287708 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1287773 CCATACAACTACAAT
66 CCATACAACTACAAT
* *
1287788 AATAAATCAATTCATGTTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1287853 CCATA
66 CCATA
1287858 TTTTAAAATA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.33
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:1287845 original size:134 final size:132
Alignment explanation
Indices: 1287694--1288154 Score: 533
Period size: 134 Copynumber: 3.4 Consensus size: 132
1287684 CAACTACAAT
*
1287694 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
1287759 TAAAATAAATCAATCCATACAACTACAAT-AATAAATCAATTCATGTTTTAAAATAAATCAATCC
66 TAAAATAAATCAATCCATACAA-TA-AATAAATAAATCAATTCAT-TTTTAAAATAAATCAATCC
1287823 ATACA
128 ATACA
**
1287828 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATGGATACTAATAAATTATT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
* *** **
1287893 TAAAATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATC
66 TAAAATAAATCAATCCATACAAT-AAATAAAT-AA---AT-C-AATTCATT-TTTAAAATAAATC
1287958 AATCCATACA
123 AATCCATACA
* *
1287968 ACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
1288027 TAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA-TCTATATTTTAAAATAAAT
66 TAAAATAAATCAATCCATAC-AAT-AA--A--T-AAATAAATCAATTC-AT-TTTTAAAATAAAT
** *
1288091 CAATGGATACT
122 CAATCCATACA
* * *
1288102 AATAAATTAGTTAAAATAAATCAATCCATATTTTAAAACAAATCAATTCATAC
1 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1288155 AACTACAATA
Statistics
Matches: 279, Mismatches: 25, Indels: 40
0.81 0.07 0.12
Matches are distributed among these distances:
133 4 0.01
134 180 0.65
135 8 0.03
136 4 0.01
137 1 0.00
138 4 0.01
139 5 0.02
140 73 0.26
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.34
Consensus pattern (132 bp):
AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
TAAAATAAATCAATCCATACAATAAATAAATAAATCAATTCATTTTTAAAATAAATCAATCCATA
CA
Found at i:1287846 original size:32 final size:32
Alignment explanation
Indices: 1287805--1288278 Score: 269
Period size: 32 Copynumber: 16.4 Consensus size: 32
1287795 CAATTCATGT
*
1287805 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1287837 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
**
1287859 TTTAAAATAAATCAATGGATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1287891 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1287913 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1287945 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
1287975 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1287993 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1288025 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1288057 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
**
1288079 TTTAAAATAAATCAATGGATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* * * *
1288111 GTTAAAATAAATCAATCCATATTTTAAAACAAATCAA
1 TTTAAAATAAATCAATCCATA--CT--AATAAAT-TA
* ** **
1288148 TTCATACAACTACAAT-AATAAAT-C-AATCCA-TA
1 TT--TA-AAATA-AATCAATCCATACTAATAAATTA
1288180 TTTTAAAATAAATCAATCCATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
1288213 TTTAAAATAAATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1288235 TTTAAAATAAATAAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1288267 TTTAAAATAAAT
1 TTTAAAATAAAT
1288279 TATTTTAAAA
Statistics
Matches: 348, Mismatches: 24, Indels: 140
0.68 0.05 0.27
Matches are distributed among these distances:
20 1 0.00
22 71 0.20
23 7 0.02
24 6 0.02
25 2 0.01
26 29 0.08
27 8 0.02
28 15 0.04
29 4 0.01
30 14 0.04
31 12 0.03
32 149 0.43
33 4 0.01
34 4 0.01
36 6 0.02
37 2 0.01
39 2 0.01
40 9 0.03
41 3 0.01
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:1287852 original size:54 final size:54
Alignment explanation
Indices: 1287788--1288278 Score: 547
Period size: 54 Copynumber: 9.1 Consensus size: 54
1287778 CAACTACAAT
* *
1287788 AATAAATCAATTCATGTTTTAAAATAAATCAATCCATACAAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* **
1287842 AATAAATCAATCCATATTTTAAAATAAATCAATGGATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
1287896 AATAAATCAA-TCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATTC-ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * ** ** * ** *
1287950 AATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-TTTTAAAATAAAT-C
1 AATAAATCAATTCAT---ATTTTAA-AATAAATCAATCCATACTAATAAATTATTTAA
** **
1288006 AATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAAT-C-AATTCATAT-TTTAAAATAAATCAATCCATACTAATAAATTATTTAA
** *
1288062 AATAAATCAA-TCTATATTTTAAAATAAATCAATGGATACTAATAAATTAGTTAA
1 AATAAATCAATTC-ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * * *
1288116 AATAAATCAATCCATATTTTAAAACAAATCAATTCATAC-AACTACA--A--T--
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAA-TAAATTATTTAA
*
1288164 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
1288218 AATAAATCAATTCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1288272 AATAAAT
1 AATAAAT
1288279 TATTTTAAAA
Statistics
Matches: 366, Mismatches: 49, Indels: 44
0.80 0.11 0.10
Matches are distributed among these distances:
48 40 0.11
49 2 0.01
50 2 0.01
52 2 0.01
53 3 0.01
54 259 0.71
55 15 0.04
56 10 0.03
57 13 0.04
58 20 0.05
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (54 bp):
AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:1287917 original size:22 final size:22
Alignment explanation
Indices: 1287891--1287933 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1287881 TAATAAATTA
1287891 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCTATAT
1287913 TTTAAAATAAATCAATCTATA
1 TTTAAAATAAATCAATCTATA
1287934 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCTATAT
Found at i:1287942 original size:22 final size:22
Alignment explanation
Indices: 1287893--1287941 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1287883 ATAAATTATT
**
1287893 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCTATATAA
1287915 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCTATA-TAA
1287938 TAAA
1 TAAA
1287942 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATAAATCAATCTATATAA
Found at i:1288010 original size:188 final size:188
Alignment explanation
Indices: 1287693--1288278 Score: 801
Period size: 188 Copynumber: 3.1 Consensus size: 188
1287683 ACAACTACAA
1287693 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
* *
1287758 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATTCATGTTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
* * **
1287823 ATACAAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATGGATAC
131 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATAAATAAATAC
*
1287881 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
1287946 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
** * **
1288011 ATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C
131 ATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-AAATAAATAC
** ** * * * * * *
1288070 -AATCTA-TATTTTAAAATAAATCAATGGATA--CT--AATAAATTAGT-TAAAATAAATCAATC
1 TAATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACT-AATAAAT-
* *
1288128 CATATTTTAAAACAAATCAATTCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAAT
63 --TA-TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAAT
* **
1288193 CAATCCATACTAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATAAATCCATAC
125 CAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATAAATAAATAC
1288257 TAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
1288279 TATTTTAAAA
Statistics
Matches: 353, Mismatches: 34, Indels: 22
0.86 0.08 0.05
Matches are distributed among these distances:
183 4 0.01
184 15 0.04
186 7 0.02
187 13 0.04
188 298 0.84
189 11 0.03
190 5 0.01
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (188 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATAAATAAATAC
Found at i:1288022 original size:22 final size:23
Alignment explanation
Indices: 1287947--1288021 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
1287937 ATAAATTATT
1287947 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
1287969 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
1287995 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
1288018 TAAA
1 TAAA
1288022 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:1288144 original size:22 final size:22
Alignment explanation
Indices: 1288112--1288201 Score: 99
Period size: 22 Copynumber: 3.9 Consensus size: 22
1288102 AATAAATTAG
1288112 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
* * *
1288134 TTAAAACAAATCAATTCATACAACT
1 TTAAAATAAATCAATCCAT---ATT
**
1288159 ACAATAATAAATCAATCCATATT
1 TTAA-AATAAATCAATCCATATT
1288182 TTAAAATAAATCAATCCATA
1 TTAAAATAAATCAATCCATA
1288202 CTAATAAATT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
22 33 0.61
23 4 0.07
25 4 0.07
26 13 0.24
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (22 bp):
TTAAAATAAATCAATCCATATT
Found at i:1288207 original size:18 final size:19
Alignment explanation
Indices: 1288163--1288210 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
1288153 ACAACTACAA
*
1288163 TAATAAATCAATCCATATTT
1 TAATAAATCAATCCATA-TC
1288183 TAAAATAAATCAATCCATA-C
1 T--AATAAATCAATCCATATC
1288203 TAATAAAT
1 TAATAAAT
1288211 TATTTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 7 0.28
20 2 0.08
22 16 0.64
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAATCAATCCATATC
Found at i:1288239 original size:22 final size:22
Alignment explanation
Indices: 1288213--1288313 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
1288203 TAATAAATTA
* *
1288213 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATAAATCCATAT
1288235 TTTAAAATAAATAAATCCATACT
1 TTTAAAATAAATAAATCCATA-T
** * ** **
1288258 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-AAATCCA-TAT
*
1288282 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATAAATCCATAT
*
1288304 TTTATAATAA
1 TTTAAAATAA
1288314 TTTATTTTAA
Statistics
Matches: 58, Mismatches: 18, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
22 31 0.53
23 12 0.21
24 13 0.22
25 2 0.03
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATAAATCCATAT
Found at i:1288287 original size:15 final size:15
Alignment explanation
Indices: 1288258--1288420 Score: 211
Period size: 15 Copynumber: 10.5 Consensus size: 15
1288248 AATCCATACT
1288258 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
1288272 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1288287 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
1288309 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
1288324 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
1288339 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1288354 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1288369 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1288384 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1288399 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1288414 AATAAAT
1 AATAAAT
1288421 AACCTTATTA
Statistics
Matches: 133, Mismatches: 8, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
14 9 0.07
15 107 0.80
17 1 0.01
18 2 0.02
19 3 0.02
20 1 0.01
22 10 0.08
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1290267 original size:3 final size:3
Alignment explanation
Indices: 1290211--1290251 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
1290201 GTTTATTTAT
* *
1290211 TTA TTA TTA TTA TT- TTA CTA TTA TTT TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1290252 AATAAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1291830 original size:23 final size:21
Alignment explanation
Indices: 1291789--1291845 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
1291779 AATATTATAT
1291789 TATATTTTT-AT-TTTATTTAA
1 TATATTTTTAATATTTATTT-A
1291809 TCATATTTTTAATATTTATTTA
1 T-ATATTTTTAATATTTATTTA
*
1291831 TTTATTTTTAATATT
1 TATATTTTTAATATT
1291846 AAAGAAAGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 1 0.03
21 21 0.64
22 4 0.12
23 7 0.21
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TATATTTTTAATATTTATTTA
Found at i:1291836 original size:21 final size:21
Alignment explanation
Indices: 1291781--1291845 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
1291771 ATAAATAAAA
1291781 TATTATATTATATTTTT-AT-TT
1 TATT-TATT-TATTTTTAATATT
*
1291802 TATTTAATCATATTTTTAATATT
1 TATTT-AT-TTATTTTTAATATT
1291825 TATTTATTTATTTTTAATATT
1 TATTTATTTATTTTTAATATT
1291846 AAAGAAAGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 1 0.03
21 26 0.68
22 4 0.11
23 7 0.18
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTATTTATTTTTAATATT
Found at i:1292871 original size:16 final size:16
Alignment explanation
Indices: 1292850--1292881 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1292840 TAAGTTCTGA
1292850 ATTTTGTTTTTTATTT
1 ATTTTGTTTTTTATTT
1292866 ATTTTGTTTTTTATTT
1 ATTTTGTTTTTTATTT
1292882 GCATGCGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (16 bp):
ATTTTGTTTTTTATTT
Found at i:1293977 original size:32 final size:31
Alignment explanation
Indices: 1293933--1294000 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1293923 GGCTTTAGAG
*
1293933 AAGTTAGAAGTGAAGGT-TATCCCCTATATGTA
1 AAGTTAGAAGTGAA-ATCTAT-CCCTATATGTA
*
1293965 AAGTTAGGAGTGAAATCTATCCCTATATGTA
1 AAGTTAGAAGTGAAATCTATCCCTATATGTA
1293996 AAGTT
1 AAGTT
1294001 TTGTTTGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 17 0.52
32 16 0.48
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (31 bp):
AAGTTAGAAGTGAAATCTATCCCTATATGTA
Found at i:1294149 original size:27 final size:26
Alignment explanation
Indices: 1294103--1294153 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
1294093 TTGCATCTTT
*
1294103 ACATCTTTGCATTTTCATTTTACATCC
1 ACATATTTGCATTTTCA-TTTACATCC
1294130 ACATATTTGCATTTGT-ATTTACAT
1 ACATATTTGCATTT-TCATTTACAT
1294154 TTTCATCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 14 0.64
28 1 0.05
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.49
Consensus pattern (26 bp):
ACATATTTGCATTTTCATTTACATCC
Found at i:1299249 original size:54 final size:54
Alignment explanation
Indices: 1299157--1299262 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 54
1299147 GATGATTGAG
* * *
1299157 AAATCTGGGCAGAAGCCATAAGAAAGAATGGATATGTTGTCAAATGTTTTACGA
1 AAATCTGGGCAGAAGCCACAAGAAAGAATGAATATGTTGCCAAATGTTTTACGA
* * *
1299211 AAATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGCCAAATGTTTTAC
1 AAATCTGGGCAGAAGCCACAAGAAAGAATGAATATGTTGCCAAATGTTTTAC
1299263 AAACCAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (54 bp):
AAATCTGGGCAGAAGCCACAAGAAAGAATGAATATGTTGCCAAATGTTTTACGA
Found at i:1299661 original size:22 final size:22
Alignment explanation
Indices: 1299631--1299740 Score: 150
Period size: 22 Copynumber: 5.0 Consensus size: 22
1299621 TCTACATCTA
* * *
1299631 CATTATTCAAAAATGATATATT
1 CATTCTTCAAAGATGATAGATT
1299653 CATTCTTCAAAGATGATAGATT
1 CATTCTTCAAAGATGATAGATT
*
1299675 CACTCTTCAAAGATGATAGATT
1 CATTCTTCAAAGATGATAGATT
*
1299697 CACTCTTCAAAGATGATAGATT
1 CATTCTTCAAAGATGATAGATT
*
1299719 C-TCTCTTCAAAGATGAAAGATT
1 CAT-TCTTCAAAGATGATAGATT
1299741 TATTGGATTT
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
22 81 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (22 bp):
CATTCTTCAAAGATGATAGATT
Found at i:1300381 original size:128 final size:121
Alignment explanation
Indices: 1300082--1300362 Score: 373
Period size: 127 Copynumber: 2.2 Consensus size: 121
1300072 TTTTCAGAGG
1300082 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGACTCTATCACAGAAGAAGATAGATCAA
1 AGTTCATAATGAGAAGAACTTGTTC-ACCTTTTGCTTGACTCTATCACAGAAGAAGATAGATCAA
* ** * * * *
1300147 CATCAACATTTCCAGAGGAGTTCATAATCAGAAGAACTCATCTGAAGATGAAGAATA
65 CACCAACATTTCCAGAAAAGTTCATAATCAGAAAAACTCATCTGAAGAGGAAAAAGA
* * *
1300204 AGTTCATAATGAAAAGAAAAGAACTTGTTCAGTCTTTTGCTCGACTCTATCACAGAAGGAGATAG
1 AGTTCATAATG---AG--AAGAACTTGTTCA-CCTTTTGCTTGACTCTATCACAGAAGAAGATAG
* *
1300269 ATCAACACCAATATTTCCAGAAAAAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAAAAGA
60 ATCAACACCAACATTTCCAG-AAAAGTTCATAATCAGAAAAACTCATCTGAAGAGGAAAAAGA
1300332 AGTTCATAATGAGAAGAACTTGTTCGACCTT
1 AGTTCATAATGAGAAGAACTTGTTC-ACCTT
1300363 AGCTTGATTG
Statistics
Matches: 138, Mismatches: 13, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
122 11 0.08
123 15 0.11
124 1 0.01
125 4 0.03
126 1 0.01
127 60 0.43
128 46 0.33
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (121 bp):
AGTTCATAATGAGAAGAACTTGTTCACCTTTTGCTTGACTCTATCACAGAAGAAGATAGATCAAC
ACCAACATTTCCAGAAAAGTTCATAATCAGAAAAACTCATCTGAAGAGGAAAAAGA
Found at i:1300611 original size:137 final size:139
Alignment explanation
Indices: 1300281--1300635 Score: 468
Period size: 139 Copynumber: 2.6 Consensus size: 139
1300271 CAACACCAAT
** * *
1300281 ATTTCCAGAAAAAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAAAAGAAGTTCATAATGAGA
1 ATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
* * * * *
1300346 AGAACTTGTTCGACCTTAGCTTGATTGATCATCTATGGAGTTGAATAAAAGAAGAACCTCACTTG
66 AGAACTTGTTCAACCTTAGCTTAATTCATCATCTATGAAGTTGAATAAAAGAAGAACATCACTTG
*
1300411 AGGATCAAT
131 AGGATCAAC
* * * *
1300420 ATTTTCAG-AGGAAGTTCATAATGAGAAGAACTCATCTAAAAAGGAAGAAAAAGTTCATAATGAG
1 ATTTCCAGAAGG-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAG
* * * * *
1300484 AAGAACTTGTTCAACCTT-GCCTTAATTCATCATTTATGAAGTTGAATCAATG-A-CACATC-TT
65 AAGAACTTGTTCAACCTTAG-CTTAATTCATCATCTATGAAGTTGAATAAAAGAAGAACATCACT
1300545 TCGAGGATCAAC
129 T-GAGGATCAAC
*
1300557 ATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGACGAGGAAGAAGAAGTTCATAATGAGA
1 ATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
1300622 AGAACTTGTTCAAC
66 AGAACTTGTTCAAC
1300636 TTTTTGCTAG
Statistics
Matches: 188, Mismatches: 24, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
136 2 0.01
137 83 0.44
138 6 0.03
139 97 0.52
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (139 bp):
ATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTAGCTTAATTCATCATCTATGAAGTTGAATAAAAGAAGAACATCACTTG
AGGATCAAC
Found at i:1300865 original size:3 final size:3
Alignment explanation
Indices: 1300857--1300903 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
1300847 GTTTATTTAT
*
1300857 TTA TTA TTA TTA TT- TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1300904 AATAAATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1307822 original size:21 final size:21
Alignment explanation
Indices: 1307745--1307912 Score: 219
Period size: 21 Copynumber: 8.0 Consensus size: 21
1307735 AGTCGAGGGT
* * *
1307745 TCTATATGGTCATTCGGGAAA
1 TCTATGTGGTCCTTCGGGACA
* ** * *
1307766 TATATGTAATCCTTTGGAACA
1 TCTATGTGGTCCTTCGGGACA
* * *
1307787 TATATGTGGTACTTCGGTACA
1 TCTATGTGGTCCTTCGGGACA
* *
1307808 CCTATTTGGTCCTTCGGGACA
1 TCTATGTGGTCCTTCGGGACA
1307829 TCTATGTGGTCCTTCGGGACA
1 TCTATGTGGTCCTTCGGGACA
1307850 TCTATGTGGTCCTTCGGGACA
1 TCTATGTGGTCCTTCGGGACA
1307871 TCTATGTGGTCCTTCGGGACA
1 TCTATGTGGTCCTTCGGGACA
1307892 TCTATGTGGTCCTTCGGGACA
1 TCTATGTGGTCCTTCGGGACA
1307913 AATTCTATGT
Statistics
Matches: 127, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 127 1.00
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.35
Consensus pattern (21 bp):
TCTATGTGGTCCTTCGGGACA
Found at i:1313136 original size:54 final size:54
Alignment explanation
Indices: 1313074--1313179 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 54
1313064 GATGATTGAG
* * *
1313074 AAATCTGGGCAAAAGCCATAAGAAA-GAATGGATATGTTGTCAAATGTTTTACGA
1 AAATCTGGGCAAAAGCCACAAGAAATG-ATGAATATGTTGCCAAATGTTTTACGA
* * *
1313128 AAATCTGGGCAGAAGCCACATGAAATGATGAATGTGTTGCCAAATGTTTTAC
1 AAATCTGGGCAAAAGCCACAAGAAATGATGAATATGTTGCCAAATGTTTTAC
1313180 AAACCAGTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 44 0.98
55 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (54 bp):
AAATCTGGGCAAAAGCCACAAGAAATGATGAATATGTTGCCAAATGTTTTACGA
Found at i:1313575 original size:22 final size:22
Alignment explanation
Indices: 1313547--1313634 Score: 97
Period size: 22 Copynumber: 4.0 Consensus size: 22
1313537 TCTACATCTA
* *
1313547 CATTCTTCAAAAATGATATATT
1 CATTCTTCAAAGATGATAGATT
*
1313569 CATTCTTCAAAGATAATAGATT
1 CATTCTTCAAAGATGATAGATT
** *
1313591 CACGCTTCAAATATGATAGATT
1 CATTCTTCAAAGATGATAGATT
*
1313613 C-TCTCTTCAAAGATGAAAGATT
1 CAT-TCTTCAAAGATGATAGATT
1313635 TATTGGATTT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (22 bp):
CATTCTTCAAAGATGATAGATT
Found at i:1313620 original size:44 final size:44
Alignment explanation
Indices: 1313551--1313634 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
1313541 CATCTACATT
*
1313551 CTTCAAAAATGATATATTCATTCTTCAAAGAT-AATAGATTCACG
1 CTTCAAAAATGATAGATTCATTCTTCAAAGATGAA-AGATTCACG
*
1313595 CTTCAAATATGATAGATTC-TCTCTTCAAAGATGAAAGATT
1 CTTCAAAAATGATAGATTCAT-TCTTCAAAGATGAAAGATT
1313635 TATTGGATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
43 1 0.03
44 33 0.92
45 2 0.06
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (44 bp):
CTTCAAAAATGATAGATTCATTCTTCAAAGATGAAAGATTCACG
Found at i:1314231 original size:122 final size:122
Alignment explanation
Indices: 1314014--1314340 Score: 546
Period size: 122 Copynumber: 2.7 Consensus size: 122
1314004 GATGGATCAG
*
1314014 CATTTCTAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
1 CATTTCCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
* * **
1314079 AGAACTTATTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCAGCATTAA
66 AGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGCACCAA
* *
1314136 CATTTCCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGATGAAGAATAAGTTCATAATGAGA
1 CATTTCCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
1314201 AGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGCACCAA
66 AGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGCACCAA
* **
1314258 TATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAG
1 CATTTCCAG-AGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAG
*
1314323 AAGAACTTGTTCGACCTT
65 AAGAACTTGTTCAACCTT
1314341 AGCTTGATTC
Statistics
Matches: 191, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
122 123 0.64
123 68 0.36
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (122 bp):
CATTTCCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGCACCAA
Found at i:1314435 original size:139 final size:137
Alignment explanation
Indices: 1314255--1314613 Score: 488
Period size: 139 Copynumber: 2.6 Consensus size: 137
1314245 AGATCAGCAC
**
1314255 CAATATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
1 CAATATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* * * * * *
1314320 GAGAAGAACTTGTTCGACCTTAGCTTGATTCATCATCTATGGAGTTGAATGAAAGAATAACCTCA
66 GAGAAGAACTTGTTCAACCTTACCTTAATTCATCATATATGAAGTTGAATCAAAG-A-AACCTC-
1314385 CTT-AAGGAT
128 CTTCAAGGAT
* * * *
1314394 CAATATTTTCAGAGGAAGTTCATAATGAGAAGAACCCATCTGAAAAGGAAGAAAAAGTTCATAAT
1 CAATATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* * * *
1314459 GAGAATAACTTGTTCAACCTTACCTTAATTCATCATATATGAAGTTGAATCAATGACACCTCTTT
66 GAGAAGAACTTGTTCAACCTTACCTTAATTCATCATATATGAAGTTGAATCAAAGAAACCTCCTT
*
1314524 CGAGGAT
131 CAAGGAT
** *
1314531 CAGCATTTCCAGAAGG-AGTTCATAATGAGAAGAACTCATCTGACGAGGAAGAAGAAGTTCATAA
1 CAATATTTCCAG-AGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1314595 TGAGAAGAACTTGTTCAAC
65 TGAGAAGAACTTGTTCAAC
1314614 TTTTTGCTAG
Statistics
Matches: 193, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
136 2 0.01
137 81 0.42
138 4 0.02
139 106 0.55
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (137 bp):
CAATATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTACCTTAATTCATCATATATGAAGTTGAATCAAAGAAACCTCCTT
CAAGGAT
Found at i:1315856 original size:14 final size:15
Alignment explanation
Indices: 1315824--1315863 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1315814 ATATTCTTAT
1315824 TTTATGATATTTCAA
1 TTTATGATATTTCAA
1315839 TTTATGACTA-TT-AA
1 TTTATGA-TATTTCAA
1315853 TTTAT-ATATTT
1 TTTATGATATTT
1315864 TACATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.09
13 3 0.13
14 7 0.30
15 9 0.39
16 2 0.09
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (15 bp):
TTTATGATATTTCAA
Found at i:1315873 original size:21 final size:20
Alignment explanation
Indices: 1315849--1315892 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1315839 TTTATGACTA
1315849 TTAAT-TTATATATTTTACATT
1 TTAATCTTA-ATATTTTA-ATT
*
1315870 TTAATCTTACTATTTTAATT
1 TTAATCTTAATATTTTAATT
1315890 TTA
1 TTA
1315893 TTTGTTTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 12 0.57
22 3 0.14
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAATCTTAATATTTTAATT
Found at i:1315992 original size:23 final size:23
Alignment explanation
Indices: 1315948--1315992 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1315938 GTTCTAATAT
*
1315948 TTTTATATAATATTTAATTATTA
1 TTTTATATAATATTGAATTATTA
*
1315971 TTTTATTTAATA-TGAATATATT
1 TTTTATATAATATTGAAT-TATT
1315993 TAATTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTATATAATATTGAATTATTA
Found at i:1323161 original size:53 final size:53
Alignment explanation
Indices: 1323070--1323277 Score: 296
Period size: 53 Copynumber: 3.9 Consensus size: 53
1323060 TCTTCGAATG
* * *
1323070 ACGGG-TCTGCTCCCTCTTG-TTCAGGGAGTAGAATTTGAATAATCTTCTGCTT
1 ACGGGTTC-GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTT
* * *
1323122 ACGGTTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTTGAACAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTT
* * *
1323175 ACGGGTTCGCTCCCTCTTGCTTTAGGGAGTAAAACTCGAACAATCTTTTG-TCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCT-T
1323228 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1323278 GTGTGATTCT
Statistics
Matches: 140, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
52 15 0.11
53 125 0.89
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (53 bp):
ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTT
Found at i:1323763 original size:42 final size:43
Alignment explanation
Indices: 1323713--1323795 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 43
1323703 GGACTTATGG
1323713 ATGACCCGAAGGA-TTTAATCATCATGCTCGAAAGACTTACAA
1 ATGACCCGAAGGATTTTAATCATCATGCTCGAAAGACTTACAA
*
1323755 ATGACCCGAAGGATTTTCATCATCATGCTCGAAAGACTTAC
1 ATGACCCGAAGGATTTTAATCATCATGCTCGAAAGACTTAC
1323796 TGATGAATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 13 0.33
43 26 0.67
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGACCCGAAGGATTTTAATCATCATGCTCGAAAGACTTACAA
Found at i:1323871 original size:80 final size:80
Alignment explanation
Indices: 1323751--1323960 Score: 339
Period size: 80 Copynumber: 2.6 Consensus size: 80
1323741 CGAAAGACTT
* *
1323751 ACAAATGACCCGAAGGATTTTCATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACTAC
1 ACAAATTACCCGAAGGA-TTTAATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACTAC
*
1323816 TCTTCGGTGAAGGCTC
65 TCTTCGGAGAAGGCTC
*
1323832 ACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACTACT
1 ACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACTACT
* *
1323897 CTTTGGAGAAGGCTT
66 CTTCGGAGAAGGCTC
* *
1323912 ACAAATTACCCGAAGAACTTAATCATCATGCTCGAAAGACTTACTGATG
1 ACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
1323961 GCCCGAAGGA
Statistics
Matches: 121, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
80 105 0.87
81 16 0.13
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (80 bp):
ACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACTACT
CTTCGGAGAAGGCTC
Found at i:1323968 original size:42 final size:42
Alignment explanation
Indices: 1323920--1324002 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
1323910 TTACAAATTA
1323920 CCCGAAGAACTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGAACTTAATCATCATGCTCGAAAGACTTACTGATGG
* *
1323962 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATG
1 CCCGAAGAACTTAATCATCATGCTCGAAAGACTTACTGATG
1324003 ACACTTACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (42 bp):
CCCGAAGAACTTAATCATCATGCTCGAAAGACTTACTGATGG
Found at i:1323994 original size:22 final size:21
Alignment explanation
Indices: 1323928--1323996 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
1323918 TACCCGAAGA
1323928 ACTTAATCATCATGCTCGAAAG
1 ACTT-ATCATCATGCTCGAAAG
* * *
1323950 ACTTA-C-TGATGGCCCGAAGG
1 ACTTATCATCAT-GCTCGAAAG
1323970 ACTTCATCATCATGCTCGAAAG
1 ACTT-ATCATCATGCTCGAAAG
1323992 ACTTA
1 ACTTA
1323997 CTGATGACAC
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.08
20 12 0.32
21 3 0.08
22 16 0.43
23 3 0.08
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (21 bp):
ACTTATCATCATGCTCGAAAG
Found at i:1324273 original size:41 final size:41
Alignment explanation
Indices: 1324218--1324324 Score: 133
Period size: 42 Copynumber: 2.6 Consensus size: 41
1324208 CCCGAAGGTT
* * * *
1324218 TTACGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGC
1 TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
* * *
1324259 TTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAC
1 TTACAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGAC
*
1324301 TTACTGATGGCCCGAAGGACTTAT
1 TTACAGATGGCCCGAAGGACTTAT
1324325 AAATTGTGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 20 0.37
42 34 0.63
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.25
Consensus pattern (41 bp):
TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
Found at i:1324298 original size:214 final size:214
Alignment explanation
Indices: 1324040--1324441 Score: 678
Period size: 214 Copynumber: 1.9 Consensus size: 214
1324030 CTCTTCCGTG
* * *
1324040 AAGGCTTACAAATTACCCTAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAATG
1 AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* *
1324105 ACTTAAAAATTGTGAAATTTTGAAAATCGCATTATTTGTTTTCAAAAATTTCATCTTCTCAAAAC
66 ACTTAAAAATTGTGAAATTTTGAAAATCGCATTATTCGTTTTCAAAAATTCCATCTTCTCAAAAC
* *
1324170 ATCGTTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAG
131 ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTACGGATGGCCCGAAG
1324235 GACTTATCATCTTGCTCTA
196 GACTTATCATCTTGCTCTA
*
1324254 AAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* * *
1324319 ACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAAC
66 ACTTAAAAATTGTGAAATTTTGAAAATCGCATTATTCGTTTTCAAAAATTCCATCTTCTCAAAAC
* * *
1324384 ATTATTTTTTATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTATGGATGG
131 ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTACGGATGG
1324442 TTTGCTTCAC
Statistics
Matches: 174, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
214 174 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (214 bp):
AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
ACTTAAAAATTGTGAAATTTTGAAAATCGCATTATTCGTTTTCAAAAATTCCATCTTCTCAAAAC
ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTACGGATGGCCCGAAG
GACTTATCATCTTGCTCTA
Found at i:1337047 original size:32 final size:32
Alignment explanation
Indices: 1336979--1337052 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
1336969 TGGGGGTCTG
* *
1336979 AGAGCCTACCCAAGGGAGTATCTTAAAGCCTA
1 AGAGCCTACCCAAGGAAGTACCTTAAAGCCTA
*** *
1337011 AGAGCCTACCCAAGGAAGTACCTTGGGGCCTT
1 AGAGCCTACCCAAGGAAGTACCTTAAAGCCTA
1337043 AGAGCCTACC
1 AGAGCCTACC
1337053 TAAGAAAATG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.18
Consensus pattern (32 bp):
AGAGCCTACCCAAGGAAGTACCTTAAAGCCTA
Found at i:1337067 original size:32 final size:32
Alignment explanation
Indices: 1337006--1337067 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
1336996 GTATCTTAAA
* *
1337006 GCCTAAGAGCCTACCCAAGGAAGTACCTTGGG
1 GCCTAAGAGCCTACCCAAGAAAATACCTTGGG
* * *
1337038 GCCTTAGAGCCTACCTAAGAAAATGCCTTG
1 GCCTAAGAGCCTACCCAAGAAAATACCTTG
1337068 AGCCCTCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.19
Consensus pattern (32 bp):
GCCTAAGAGCCTACCCAAGAAAATACCTTGGG
Found at i:1340334 original size:20 final size:20
Alignment explanation
Indices: 1340306--1340375 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
1340296 TTGGGTAAGT
*
1340306 AGTACCGATATTGTTCTTAC
1 AGTACCGATATTGTTCATAC
* * * *
1340326 AGTATCGATACTATATGA-AC
1 AGTACCGATATTGT-TCATAC
* *
1340346 AGTATCGATATTGTTCATAT
1 AGTACCGATATTGTTCATAC
1340366 AGTACCGATA
1 AGTACCGATA
1340376 CCAAAGGTAA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 2 0.05
20 35 0.92
21 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (20 bp):
AGTACCGATATTGTTCATAC
Found at i:1342354 original size:16 final size:16
Alignment explanation
Indices: 1342335--1342366 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1342325 GTTTATACAA
*
1342335 TTAATCACTGCACTTG
1 TTAATCACTGAACTTG
1342351 TTAATCACTGAACTTG
1 TTAATCACTGAACTTG
1342367 GAATTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (16 bp):
TTAATCACTGAACTTG
Found at i:1345119 original size:32 final size:32
Alignment explanation
Indices: 1345078--1345163 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 32
1345068 ATATCTTGGA
* *
1345078 GCCTGAGAGCCTACCCAAGGGAGTACCTTAAG
1 GCCTAAGAGCCTACCCAAGGAAGTACCTTAAG
* * **
1345110 GCCTAAGAGCCTACCCAAGAAAGTACGTTGGG
1 GCCTAAGAGCCTACCCAAGGAAGTACCTTAAG
*
1345142 GCCTTAGAGCCTACCCAAGGAA
1 GCCTAAGAGCCTACCCAAGGAA
1345164 ATGCCCTGGG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (32 bp):
GCCTAAGAGCCTACCCAAGGAAGTACCTTAAG
Found at i:1345174 original size:32 final size:33
Alignment explanation
Indices: 1345078--1345193 Score: 105
Period size: 32 Copynumber: 3.6 Consensus size: 33
1345068 ATATCTTGGA
* * * **
1345078 GCCTGAGAGCCTACCCAAGG-GAGTACCTTAAG
1 GCCTAAGAGCCTACCCAAGGAAAGTACCCTGGG
**
1345110 GCCTAAGAGCCTACCCAA-GAAAGTACGTTGGG
1 GCCTAAGAGCCTACCCAAGGAAAGTACCCTGGG
* *
1345142 GCCTTAGAGCCTACCCAAGGAAA-TGCCCTGGG
1 GCCTAAGAGCCTACCCAAGGAAAGTACCCTGGG
*
1345174 GCCTCAA-AGCTTACCCAAGG
1 GCCT-AAGAGCCTACCCAAGG
1345194 TCACCTTTTG
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
31 1 0.01
32 64 0.91
33 5 0.07
ACGTcount: A:0.28, C:0.29, G:0.27, T:0.16
Consensus pattern (33 bp):
GCCTAAGAGCCTACCCAAGGAAAGTACCCTGGG
Found at i:1345177 original size:64 final size:64
Alignment explanation
Indices: 1345073--1345192 Score: 143
Period size: 64 Copynumber: 1.9 Consensus size: 64
1345063 AAGGAATATC
* * *
1345073 TTGGAGCCTGAGAGCCTACCCAAGGGAGTACCTTAAGGCCT-AAGAGCCTACCCAAGAAAGTACG
1 TTGGAGCCTGAGAGCCTACCCAAGGAAATACCCTAAGGCCTCAA-AGCCTACCCAAGAAAGTACG
* * * ** *
1345137 TTGGGGCCTTAGAGCCTACCCAAGGAAATGCCCTGGGGCCTCAAAGCTTACCCAAG
1 TTGGAGCCTGAGAGCCTACCCAAGGAAATACCCTAAGGCCTCAAAGCCTACCCAAG
1345193 GTCACCTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
64 44 0.96
65 2 0.04
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (64 bp):
TTGGAGCCTGAGAGCCTACCCAAGGAAATACCCTAAGGCCTCAAAGCCTACCCAAGAAAGTACG
Found at i:1348283 original size:8 final size:9
Alignment explanation
Indices: 1348268--1348315 Score: 66
Period size: 8 Copynumber: 5.6 Consensus size: 9
1348258 TTGAAACAAT
1348268 TATAATATA
1 TATAATATA
1348277 T-TAATATA
1 TATAATATA
1348285 TATAA-ACTA
1 TATAATA-TA
1348294 TATAATA-A
1 TATAATATA
1348302 TATAATATA
1 TATAATATA
1348311 TATAA
1 TATAA
1348316 ATTATATAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 17 0.49
9 17 0.49
10 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (9 bp):
TATAATATA
Found at i:1348298 original size:26 final size:26
Alignment explanation
Indices: 1348268--1348323 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
1348258 TTGAAACAAT
1348268 TATAAT-ATATTAATATATATAAACTA
1 TATAATAATA-TAATATATATAAACTA
*
1348294 TATAATAATATAATATATATAAATTA
1 TATAATAATATAATATATATAAACTA
1348320 TATA
1 TATA
1348324 GTTTCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 25 0.89
27 3 0.11
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATAATATAATATATATAAACTA
Found at i:1348304 original size:17 final size:18
Alignment explanation
Indices: 1348268--1348315 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
1348258 TTGAAACAAT
1348268 TATAATATAT-TAATATA
1 TATAATATATATAATATA
1348285 TATAA-ACTATATAATA-A
1 TATAATA-TATATAATATA
1348302 TATAATATATATAA
1 TATAATATATATAA
1348316 ATTATATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 21 0.75
18 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
TATAATATATATAATATA
Found at i:1348365 original size:22 final size:23
Alignment explanation
Indices: 1348335--1348389 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
1348325 TTTCTTTTTA
1348335 TATACTATATATAAATTAAATA-T
1 TATA-TATATATAAATTAAATAGT
*
1348358 TATATATATATAAATTATATAGT
1 TATATATATATAAATTAAATAGT
1348381 T-TATATATA
1 TATATATATA
1348390 GTTTATATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 24 0.80
23 6 0.20
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TATATATATATAAATTAAATAGT
Found at i:1348387 original size:11 final size:11
Alignment explanation
Indices: 1348373--1348398 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1348363 ATATATAAAT
1348373 TATATAGTTTA
1 TATATAGTTTA
1348384 TATATAGTTTA
1 TATATAGTTTA
1348395 TATA
1 TATA
1348399 CTACTATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:1349198 original size:22 final size:23
Alignment explanation
Indices: 1349150--1349203 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
1349140 AACCGTTTTG
1349150 ACCTG-AACTAACATCGATCCGA
1 ACCTGAAACTAACATCGATCCGA
*
1349172 A-CTGAAATTAAC-TCGATCCGA
1 ACCTGAAACTAACATCGATCCGA
1349193 ACCTG-AACTAA
1 ACCTGAAACTAA
1349204 AACTGATGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.39, C:0.28, G:0.13, T:0.20
Consensus pattern (23 bp):
ACCTGAAACTAACATCGATCCGA
Found at i:1352156 original size:611 final size:613
Alignment explanation
Indices: 1351157--1352386 Score: 1720
Period size: 612 Copynumber: 2.0 Consensus size: 613
1351147 GTACTTGAAT
*
1351157 AAACTAACTACGACTATCGATGCTAGAACAAATCAAATTAAGTTTTGGAAAAGCCCGACTCAGAT
1 AAACTAACTACGACTATCGATGCTAGAACAAATCAAATTAAGTTTTGGAAAAGACCGACTCAGAT
** **
1351222 TATATTGTCTCGCTGAGGATCAAATTTGATTTCAGTTTCCCTTAGTGGATCGCCGCTAAGTGTGT
66 TATATTGTCTCGCTGAGGATCAAATCCGATTTCAGTTTCCCTTAACGGATCGCCGCTAAGTGTGT
* * * *
1351287 TCACAGGAAGTCGAATATGCCATAAGCCGATCCTTCCCCCCAACTATAAAACATAATAACATCTA
131 TCACAAGAAGTCGAATATGCCACAAGCCGATCCTTCCCCCCAACTATAAAACAGAACAACATCTA
* ** *
1351352 GATCAACGTTGACTTTTTGATATGAAAGTGTTTTGATTTTAAAGGATAGGATGATTGTCAATCCT
196 GACCAACGTCAACTTTTTGATATGAAAGCGTTTTGATTTTAAAGGATAGGATGATTGTCAATCCT
* * * * * * *
1351417 AGTTTGCAGAAAACTAAAAATGTGACCCGAAGGATGTTTAGTGCTTTTTAATTCTCACATTTGGA
261 AATTTGCAGAAAACTAAAAATGTAACCCAAAGGATGTTAAGTGCTTTTCAATTCTCACAGTTAGA
* * * *
1351482 ATTGAGTCATCACTACCTCTCGGCTAAATGGAAAATTAGCTAAGCATGATATAAATTATACTTAG
326 ATTGAGTCATCACTACCTCTCGGCTAAATAGAAAATTAACTAAGCATGATAGAAATCATACTTAG
* ** * *
1351547 CATGTTTTATAAAAAATTATAAAACTTAAGTAAAGTAAAAACAGG-AATGAAATAGAATG-AAAC
391 CATGTCTTATAAAAAACGATAAAACTTAAGTAAAGTAAAAAC-GGAAATGAAATAAAAAGAAAAC
* * * * * *
1351610 TTCTATAAAA-TAGAAATAAAATAACCAATATAAATTTAATATATCCAAGTCA-GACACCTAAGG
455 TTCTATAAAATTA-AAATAAAATAACAAAGATAAATTCAAGATATCCAAGACATG-CACCTAAAG
* * *
1351673 AGGGTATTTATAGGTTTTAAAATCCCTAAAATAGCAAAGAAATTCAAATGCAAAATAATCCTAAA
518 AGGGTATTTACAGGTTTCAAAATCCCTAAAATAACAAAGAAATTCAAATGCAAAATAATCCTAAA
1351738 GATAATTCCAAGTGTTTTGAATTCAAACTTA
583 GATAATTCCAAGTGTTTTGAATTCAAACTTA
* * *
1351769 AAACTAACTACGACTATCG-TCGCTAGAGCAAATCAAATTAAGTTTTGGAAAAGACCGGCAT-GG
1 AAACTAACTACGACTATCGAT-GCTAGAACAAATCAAATTAAGTTTTGGAAAAGACCGAC-TCAG
* * * * * *
1351832 ATTATGTTGTCTCGTTGAGGATCGAATCCGATTTTAGTTTCCCTTAACGGATTGTCGCTAAGTGT
64 ATTATATTGTCTCGCTGAGGATCAAATCCGATTTCAGTTTCCCTTAACGGATCGCCGCTAAGTGT
* * ** * * * * * *
1351897 GTTCACAAGAAGTTGAATATGCCACATG-TTATCTTTCCTCCTAATTGTAAATCAGAACAACATC
129 GTTCACAAGAAGTCGAATATGCCACAAGCCGATCCTTCCCCCCAACTATAAAACAGAACAACATC
1351961 TAGACCAACGTCAACTTTTTGATATGAAAGCGTTTTGATTTTAAAGGATAGG-TCGATTGTCAAT
194 TAGACCAACGTCAACTTTTTGATATGAAAGCGTTTTGATTTTAAAGGATAGGAT-GATTGTCAAT
* * *
1352025 CCTAATTTTCAGAAAACTGAATATGTAACCCAAAGGATGTTAAGTGCTTTTCAATTCTCACAGTT
258 CCTAATTTGCAGAAAACTAAAAATGTAACCCAAAGGATGTTAAGTGCTTTTCAATTCTCACAGTT
* *
1352090 AGAATTGAGTCATCGCTACCTCTTGGCTAAATAGAAAATTAACTAAGCATGATAGAAATCATACT
323 AGAATTGAGTCATCACTACCTCTCGGCTAAATAGAAAATTAACTAAGCATGATAGAAATCATACT
* *
1352155 TAGCATGTCTTATAAAAAGCGATAAACCTTAAGTAAAGTAAAAACGGAAATGAAATAAAAAGAAA
388 TAGCATGTCTTATAAAAAACGATAAAACTTAAGTAAAGTAAAAACGGAAATGAAATAAAAAGAAA
* * * *
1352220 ACTTTTATAAAATTAAAATAAAATAACAAAGATAAATTCACGATATCCATGACATGCCCCTAAAG
453 ACTTCTATAAAATTAAAATAAAATAACAAAGATAAATTCAAGATATCCAAGACATGCACCTAAAG
* *
1352285 AGGGTATTTACAGGTTTCCAAATCCCTAAAATAACAAAGAAATTCAAATGCAAAATAATCTTAAA
518 AGGGTATTTACAGGTTTCAAAATCCCTAAAATAACAAAGAAATTCAAATGCAAAATAATCCTAAA
1352350 GATAATTCCAAGTGTTTTGAATTCAAACTTA
583 GATAATTCCAAGTGTTTTGAATTCAAACTTA
1352381 AAACTA
1 AAACTA
1352387 GATTTCCTAA
Statistics
Matches: 541, Mismatches: 70, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
610 3 0.01
611 251 0.46
612 283 0.52
613 4 0.01
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (613 bp):
AAACTAACTACGACTATCGATGCTAGAACAAATCAAATTAAGTTTTGGAAAAGACCGACTCAGAT
TATATTGTCTCGCTGAGGATCAAATCCGATTTCAGTTTCCCTTAACGGATCGCCGCTAAGTGTGT
TCACAAGAAGTCGAATATGCCACAAGCCGATCCTTCCCCCCAACTATAAAACAGAACAACATCTA
GACCAACGTCAACTTTTTGATATGAAAGCGTTTTGATTTTAAAGGATAGGATGATTGTCAATCCT
AATTTGCAGAAAACTAAAAATGTAACCCAAAGGATGTTAAGTGCTTTTCAATTCTCACAGTTAGA
ATTGAGTCATCACTACCTCTCGGCTAAATAGAAAATTAACTAAGCATGATAGAAATCATACTTAG
CATGTCTTATAAAAAACGATAAAACTTAAGTAAAGTAAAAACGGAAATGAAATAAAAAGAAAACT
TCTATAAAATTAAAATAAAATAACAAAGATAAATTCAAGATATCCAAGACATGCACCTAAAGAGG
GTATTTACAGGTTTCAAAATCCCTAAAATAACAAAGAAATTCAAATGCAAAATAATCCTAAAGAT
AATTCCAAGTGTTTTGAATTCAAACTTA
Found at i:1355441 original size:22 final size:21
Alignment explanation
Indices: 1355414--1355454 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1355404 ATGTGAACAA
1355414 AATAATGATAAACAATAATAAT
1 AATAATGATAAAC-ATAATAAT
**
1355436 AATAATTTTAAACATAATA
1 AATAATGATAAACATAATA
1355455 TTACTATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (21 bp):
AATAATGATAAACATAATAAT
Found at i:1359834 original size:155 final size:156
Alignment explanation
Indices: 1359552--1359862 Score: 615
Period size: 155 Copynumber: 2.0 Consensus size: 156
1359542 TGCGAGAAGT
1359552 AATGTAATTCGTATTTTGTTGTAATTGGGAATTTTTTTTATTTGTTATTTGTTTCAGTAGCTAGG
1 AATGTAATTCGTATTTTGTTGTAATTGGGAATTTTTTTTATTTGTTATTTGTTTCAGTAGCTAGG
1359617 GATTTGGGGACTAGGGTTTTAGCCGAGCATGGAATCTGATAAAGGCAAGCTATTCGTGGGAGGGA
66 GATTTGGGGACTAGGGTTTTAGCCGAGCATGGAATCTGATAAAGGCAAGCTATTCGTGGGAGGGA
1359682 TATCTCGGGAGAC-ACTGAAGCTACC
131 TATCTCGGGAGACAACTGAAGCTACC
1359707 AATGTAATTCGTATTTTGTTGTAATTGGGAATTTTTTTTATTTGTTATTTGTTTCAGTAGCTAGG
1 AATGTAATTCGTATTTTGTTGTAATTGGGAATTTTTTTTATTTGTTATTTGTTTCAGTAGCTAGG
1359772 GATTTGGGGACTAGGGTTTTAGCCGAGCATGGAATCTGATAAAGGCAAGCTATTCGTGGGAGGGA
66 GATTTGGGGACTAGGGTTTTAGCCGAGCATGGAATCTGATAAAGGCAAGCTATTCGTGGGAGGGA
1359837 TATCTCGGGAGACAACTGAAGCTACC
131 TATCTCGGGAGACAACTGAAGCTACC
1359863 CTCAATGATC
Statistics
Matches: 155, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
155 143 0.92
156 12 0.08
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.36
Consensus pattern (156 bp):
AATGTAATTCGTATTTTGTTGTAATTGGGAATTTTTTTTATTTGTTATTTGTTTCAGTAGCTAGG
GATTTGGGGACTAGGGTTTTAGCCGAGCATGGAATCTGATAAAGGCAAGCTATTCGTGGGAGGGA
TATCTCGGGAGACAACTGAAGCTACC
Found at i:1361462 original size:18 final size:18
Alignment explanation
Indices: 1361439--1361480 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1361429 TTCTAGATTT
1361439 TGCTGAAAAGGTCCATTA
1 TGCTGAAAAGGTCCATTA
1361457 TGCTGAAAAGGTCCATTA
1 TGCTGAAAAGGTCCATTA
*
1361475 TTCTGA
1 TGCTGA
1361481 GAAGTTGCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (18 bp):
TGCTGAAAAGGTCCATTA
Found at i:1362453 original size:22 final size:24
Alignment explanation
Indices: 1362422--1362498 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 24
1362412 CGAAACCACA
1362422 ATATATTTTCAAAAATATA-ATAT
1 ATATATTTTCAAAAATATATATAT
1362445 AT-TATTTTC-AAAATAATATATAAT
1 ATATATTTTCAAAAAT-ATATAT-AT
* *
1362469 ATATACTTTCAAAATTATATATAT
1 ATATATTTTCAAAAATATATATAT
1362493 ATATAT
1 ATATAT
1362499 ATATATGCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
21 5 0.11
22 10 0.22
23 4 0.09
24 11 0.24
25 12 0.26
26 4 0.09
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATATTTTCAAAAATATATATAT
Found at i:1362490 original size:18 final size:18
Alignment explanation
Indices: 1362467--1362542 Score: 52
Period size: 18 Copynumber: 4.4 Consensus size: 18
1362457 ATAATATATA
1362467 ATATATACTTTCAAAATT
1 ATATATACTTTCAAAATT
* *
1362485 ATATATA-TAT--ATA-T
1 ATATATACTTTCAAAATT
* *
1362499 ATATATGCTTTCAAAACT
1 ATATATACTTTCAAAATT
* * *
1362517 ATACATATTTTCAAATTT
1 ATATATACTTTCAAAATT
1362535 ATAATATA
1 AT-ATATA
1362543 TGTAATATTG
Statistics
Matches: 42, Mismatches: 11, Indels: 9
0.68 0.18 0.15
Matches are distributed among these distances:
14 7 0.17
15 4 0.10
17 4 0.10
18 23 0.55
19 4 0.10
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (18 bp):
ATATATACTTTCAAAATT
Found at i:1362510 original size:32 final size:31
Alignment explanation
Indices: 1362460--1362524 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 31
1362450 TTTCAAAATA
* *
1362460 ATATATAATATATACTTTCAAAATTATATAT
1 ATATATAATATATACTTTCAAAACTATACAT
*
1362491 ATATATATATATATGCTTTCAAAACTATACAT
1 ATATATA-ATATATACTTTCAAAACTATACAT
1362523 AT
1 AT
1362525 TTTCAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 7 0.23
32 23 0.77
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (31 bp):
ATATATAATATATACTTTCAAAACTATACAT
Found at i:1362762 original size:31 final size:30
Alignment explanation
Indices: 1362727--1362798 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 30
1362717 ATTAATATAT
*
1362727 AATTAAAAAAATTTGAAAGTTAAAGCGATTA
1 AATTAAAAAAATTTGAAAGTTAAA-CAATTA
* ** *
1362758 AATTAGGAGTAATTTGAAAGTTAAATAATTA
1 AATTA-AAAAAATTTGAAAGTTAAACAATTA
1362789 AATTAAAAAA
1 AATTAAAAAA
1362799 TAAACTTTAG
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
30 2 0.06
31 14 0.44
32 16 0.50
ACGTcount: A:0.56, C:0.01, G:0.12, T:0.31
Consensus pattern (30 bp):
AATTAAAAAAATTTGAAAGTTAAACAATTA
Found at i:1363857 original size:21 final size:21
Alignment explanation
Indices: 1363823--1363895 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
1363813 ATACTGACTA
* *
1363823 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
1363844 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
** *
1363864 TCGCGTTGTGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
1363885 TCGCAATGCGA
1 TCGCAATGCGA
1363896 ATACGTAAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:1363965 original size:41 final size:41
Alignment explanation
Indices: 1363885--1363978 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
1363875 TTTTCATAAT
* *
1363885 TCGCAATGCGAA-TACGTAAATCACAACGCGATTAAGTAAA
1 TCGCAATGCGAATTACGAAAATCACAACGCGAATAAGTAAA
* * * *
1363925 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCACAACGCGAATAAGTAAA
1363966 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1363979 CTTACTATCG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 12 0.26
41 35 0.74
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCACAACGCGAATAAGTAAA
Found at i:1363977 original size:20 final size:20
Alignment explanation
Indices: 1363885--1363996 Score: 127
Period size: 20 Copynumber: 5.5 Consensus size: 20
1363875 TTTTCATAAT
1363885 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * * *
1363905 TCACAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1363925 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
1363946 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1363966 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
1363986 TCGCAATGCGA
1 TCGCAATGCGA
1363997 TTTACATAGC
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 56 0.73
21 18 0.23
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1364262 original size:27 final size:27
Alignment explanation
Indices: 1364205--1364257 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1364195 CATCGCCGGC
* *
1364205 GAAATCCCTCACAACCATTCACAGTCA
1 GAAATCCCTCACAACCATTCAAAATCA
*
1364232 GAAATCCCTCACAATCATTCAGAAAT
1 GAAATCCCTCACAACCATTCA-AAAT
1364258 GGAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.21
Consensus pattern (27 bp):
GAAATCCCTCACAACCATTCAAAATCA
Found at i:1364612 original size:14 final size:14
Alignment explanation
Indices: 1364593--1364648 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
1364583 TTTCATTTCG
1364593 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1364607 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1364626 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1364640 CGTTGCGAT
1 CGTTGCGAT
1364649 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1364618 original size:33 final size:33
Alignment explanation
Indices: 1364576--1364672 Score: 167
Period size: 33 Copynumber: 2.9 Consensus size: 33
1364566 GAAAATCGCA
1364576 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1364609 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
1364642 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
1364673 ATTATCTCGT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 46 0.75
34 15 0.25
ACGTcount: A:0.10, C:0.25, G:0.22, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1364674 original size:20 final size:19
Alignment explanation
Indices: 1364571--1364697 Score: 103
Period size: 20 Copynumber: 7.1 Consensus size: 19
1364561 GAAATGAAAA
* *
1364571 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
1364590 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
*
1364606 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
1364623 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
1364639 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
1364656 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTCTCATT
* *
1364676 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTCTCATT
1364696 TC
1 TC
1364698 AACTAAAAGA
Statistics
Matches: 86, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 23 0.27
16 2 0.02
17 2 0.02
19 28 0.33
20 30 0.35
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTCTCATT
Found at i:1368243 original size:14 final size:14
Alignment explanation
Indices: 1368224--1368259 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1368214 ATTGTTTAAT
1368224 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1368238 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1368252 TGATTTGT
1 TGATTTGT
1368260 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:1368390 original size:19 final size:18
Alignment explanation
Indices: 1368366--1368457 Score: 76
Period size: 19 Copynumber: 5.4 Consensus size: 18
1368356 AAAAAGTACT
1368366 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
1368385 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
1368399 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
1368418 ATCGCAA-CGAAA-G--A
1 ATCGCAAGCGAAATGAAA
1368432 ATCGCAACGCGAAACT-AAA
1 ATCGCAA-GCGAAA-TGAAA
1368451 ATCGCAA
1 ATCGCAA
1368458 CGTGAAACTA
Statistics
Matches: 60, Mismatches: 2, Indels: 22
0.71 0.02 0.26
Matches are distributed among these distances:
14 18 0.30
15 1 0.02
16 8 0.13
17 7 0.12
18 1 0.02
19 25 0.42
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:1368403 original size:14 final size:14
Alignment explanation
Indices: 1368384--1368440 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1368374 GCGAAATGAA
1368384 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1368398 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1368417 AATCGCAACGAAAG
1 AATCGCAACGAGAG
1368431 AATCGCAACG
1 AATCGCAACG
1368441 CGAAACTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1368411 original size:33 final size:33
Alignment explanation
Indices: 1368366--1368459 Score: 154
Period size: 33 Copynumber: 2.8 Consensus size: 33
1368356 AAAAAGTACT
* *
1368366 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAGA
1368399 ATCGCAACGCGAAATGAAAATCGCAACGAAAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAGA
1368432 ATCGCAACGCGAAACT-AAAATCGCAACG
1 ATCGCAACGCGAAA-TGAAAATCGCAACG
1368460 TGAAACTAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
33 57 0.98
34 1 0.02
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAAAGA
Found at i:1368458 original size:19 final size:18
Alignment explanation
Indices: 1368398--1368474 Score: 72
Period size: 19 Copynumber: 4.3 Consensus size: 18
1368388 GCAACGAGAG
1368398 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAAT-AA
*
1368417 AATCGCAA--CG-AA-AG
1 AATCGCAACGCGAAATAA
1368431 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAA-TAA
*
1368450 AATCGCAACGTGAAACTAA
1 AATCGCAACGCGAAA-TAA
*
1368469 ATTCGC
1 AATCGC
1368475 GTTGCGATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
14 9 0.18
16 4 0.08
17 4 0.08
19 32 0.65
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.13
Consensus pattern (18 bp):
AATCGCAACGCGAAATAA
Found at i:1368492 original size:19 final size:19
Alignment explanation
Indices: 1368470--1368606 Score: 114
Period size: 19 Copynumber: 7.7 Consensus size: 19
1368460 TGAAACTAAA
1368470 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1368489 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1368504 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
1368522 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1368541 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1368556 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1368574 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1368593 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1368607 AGACATTAAG
Statistics
Matches: 92, Mismatches: 15, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
14 17 0.18
16 6 0.07
17 6 0.07
19 53 0.58
20 10 0.11
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1368532 original size:52 final size:52
Alignment explanation
Indices: 1368470--1368586 Score: 216
Period size: 52 Copynumber: 2.2 Consensus size: 52
1368460 TGAAACTAAA
1368470 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
*
1368522 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
*
1368574 TTCGCATTGCGAT
1 TTCGCGTTGCGAT
1368587 AGTAATTTCC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (52 bp):
TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
Found at i:1368595 original size:52 final size:52
Alignment explanation
Indices: 1368487--1368606 Score: 177
Period size: 52 Copynumber: 2.3 Consensus size: 52
1368477 TGCGATTTTC
* ** *
1368487 ATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATAGTA
*
1368539 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATAGTA
1 ATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATAGTA
*
1368591 ATTTCCGCGTTGCGAT
1 ATTT-CGCATTGCGAT
1368607 AGACATTAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
52 51 0.84
53 10 0.16
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.42
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATAGTA
Done.