Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008709.1 Hibiscus syriacus cultivar Beakdansim tig00111758_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: 3030657
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 15
Found at i:1924979 original size:23 final size:23
Alignment explanation
Indices: 1924953--1925024 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
1924943 GGTTCTACGA
*
1924953 GGTCTTTCGGGGCAATTCTATGT
1 GGTCTTTCGGGACAATTCTATGT
* * *
1924976 GGTCCTTCGGGACAAATTCTACGC
1 GGTCTTTCGGGAC-AATTCTATGT
*
1925000 GGTCCTTT-GGGACAAATCTATGT
1 GGT-CTTTCGGGACAATTCTATGT
1925023 GG
1 GG
1925025 CACTTCGGTG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
23 20 0.51
24 16 0.41
25 3 0.08
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (23 bp):
GGTCTTTCGGGACAATTCTATGT
Found at i:1925003 original size:24 final size:24
Alignment explanation
Indices: 1924945--1925016 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
1924935 AAGTCGAGGG
* *
1924945 TTCTACGAGGTCTTTCGGGGC-AA
1 TTCTACGAGGTCCTTCGGGACAAA
* *
1924968 TTCTATGTGGTCCTTCGGGACAAA
1 TTCTACGAGGTCCTTCGGGACAAA
* *
1924992 TTCTACGCGGTCCTTTGGGACAAA
1 TTCTACGAGGTCCTTCGGGACAAA
1925016 T
1 T
1925017 CTATGTGGCA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 17 0.41
24 24 0.59
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.32
Consensus pattern (24 bp):
TTCTACGAGGTCCTTCGGGACAAA
Found at i:1936093 original size:60 final size:58
Alignment explanation
Indices: 1936029--1936202 Score: 179
Period size: 60 Copynumber: 2.9 Consensus size: 58
1936019 AGTATAATTC
* *
1936029 TCATTTTAAATTAGTACCTAAATTTTTAAATATTCCAATTTTATCCCGAAACTATGA-CT
1 TCATTCTAAATTAGT-CCTAAATTTTTAAATATTCCAATTTCATCCC-AAACTATGACCT
* * * * ***
1936088 ATCATTCTAAATTAATCCTCAAACTTTTGAACATTTTGATTTCATCACCAAACTATGACCT
1 -TCATTCTAAATTAGTCCT-AAATTTTTAAATATTCCAATTTCATC-CCAAACTATGACCT
* * *
1936149 TCATTCTAAATTGGTTCCCAAATTTTTTAATATTCCAATTTCATCCCAAACTAT
1 TCATTCTAAATTAG-TCCTAAATTTTTAAATATTCCAATTTCATCCCAAACTAT
1936203 ACATATGTAA
Statistics
Matches: 92, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
59 12 0.13
60 73 0.79
61 7 0.08
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.41
Consensus pattern (58 bp):
TCATTCTAAATTAGTCCTAAATTTTTAAATATTCCAATTTCATCCCAAACTATGACCT
Found at i:1936422 original size:60 final size:60
Alignment explanation
Indices: 1936323--1936483 Score: 198
Period size: 60 Copynumber: 2.7 Consensus size: 60
1936313 AGATGAATTT
** * * **
1936323 GGGATGAAATTGGAATATTCAAAAGTGT-GGGTACCAATTTAGAAAGAGGGTCATAGTTTA
1 GGGATGAAATTAAAATATTCAAAAGTTTAAGG-ACCAATTTAGAAAGAGAATCATAGTTTA
* * * * * *
1936383 GGGATGAGATTAGAATGTTCAAAATTTTAAGGACTAATTTAGAATGAGAATCATAGTTTA
1 GGGATGAAATTAAAATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAATCATAGTTTA
1936443 GGGATGAAATTAAAATATTCAAAAGTTTAAGGACCAATTTA
1 GGGATGAAATTAAAATATTCAAAAGTTTAAGGACCAATTTA
1936484 AAATAAAAGT
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 83 0.98
61 2 0.02
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.30
Consensus pattern (60 bp):
GGGATGAAATTAAAATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAATCATAGTTTA
Found at i:1950193 original size:21 final size:21
Alignment explanation
Indices: 1950167--1950224 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
1950157 AAATTTTTGC
1950167 CTTATGGTATCGATACTCATT
1 CTTATGGTATCGATACTCATT
1950188 CTTATGGTATCGATACTCATT
1 CTTATGGTATCGATACTCATT
1950209 CTTATGGTATCGATAC
1 CTTATGGTATCGATAC
1950225 CCTCACTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (21 bp):
CTTATGGTATCGATACTCATT
Found at i:1956171 original size:21 final size:21
Alignment explanation
Indices: 1956145--1956191 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1956135 CGATTCCCCC
1956145 CCCCCCAAGAGGGTACCGATT
1 CCCCCCAAGAGGGTACCGATT
*
1956166 CCCCCCAAGAGGGTATCGATT
1 CCCCCCAAGAGGGTACCGATT
1956187 CCCCC
1 CCCCC
1956192 TGAATGGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.43, G:0.21, T:0.15
Consensus pattern (21 bp):
CCCCCCAAGAGGGTACCGATT
Found at i:1958395 original size:21 final size:21
Alignment explanation
Indices: 1958348--1958390 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1958338 TTCAAAGATC
1958348 ATTGATGATCATCAAAAGAAA
1 ATTGATGATCATCAAAAGAAA
*
1958369 ATTGATGATC-TTAAAA-AAA
1 ATTGATGATCATCAAAAGAAA
1958388 ATT
1 ATT
1958391 TTGATAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 5 0.24
21 10 0.48
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (21 bp):
ATTGATGATCATCAAAAGAAA
Found at i:1962060 original size:21 final size:20
Alignment explanation
Indices: 1962035--1962098 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 20
1962025 TTGGTGCAGA
1962035 GGGAATCGATACCCCCTTGAG
1 GGGAATCGATACCCCC-TGAG
* * **
1962056 GGGAACCGATTCCCCCCACAG
1 GGGAATCGA-TACCCCCTGAG
1962077 GGGAATCGATACCCCCTGAG
1 GGGAATCGATACCCCCTGAG
1962097 GG
1 GG
1962099 TTATAGATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
20 10 0.29
21 18 0.53
22 6 0.18
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.14
Consensus pattern (20 bp):
GGGAATCGATACCCCCTGAG
Found at i:1966189 original size:4 final size:4
Alignment explanation
Indices: 1966182--1966258 Score: 65
Period size: 4 Copynumber: 20.0 Consensus size: 4
1966172 CATTCATTTT
* *
1966182 TTTC TTTC TTTC TTTC TTTC TTT- TTTC -TT- TTTC TTTT TTTT TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* *
1966227 TTTT TTTC TTT- TTAT- TTTC TCTC ATTTC TTTC
1 TTTC TTTC TTTC TT-TC TTTC TTTC -TTTC TTTC
1966259 CCTTATCTCA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
3 10 0.16
4 48 0.79
5 3 0.05
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:1972513 original size:9 final size:10
Alignment explanation
Indices: 1972501--1972541 Score: 59
Period size: 9 Copynumber: 4.2 Consensus size: 10
1972491 ACTTCATTCA
1972501 TTTC-ATTTT
1 TTTCAATTTT
1972510 TTTCAATTTTT
1 TTTCAA-TTTT
1972521 TTTCAATTTT
1 TTTCAATTTT
1972531 TTTC-ATTTT
1 TTTCAATTTT
1972540 TT
1 TT
1972542 AGTAGGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 11 0.37
10 9 0.30
11 10 0.33
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTCAATTTT
Found at i:1972522 original size:11 final size:11
Alignment explanation
Indices: 1972506--1972541 Score: 58
Period size: 10 Copynumber: 3.5 Consensus size: 11
1972496 ATTCATTTCA
1972506 TTTTTTTCAAT
1 TTTTTTTCAAT
1972517 TTTTTTTCAA-
1 TTTTTTTCAAT
1972527 TTTTTTTC-AT
1 TTTTTTTCAAT
1972537 TTTTT
1 TTTTT
1972542 AGTAGGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 1 0.04
10 13 0.54
11 10 0.42
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTCAAT
Found at i:1975773 original size:12 final size:12
Alignment explanation
Indices: 1975752--1975801 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
1975742 ACCTGAAAAG
*
1975752 ACAAGAAAAATA
1 ACAAGTAAAATA
1975764 ACAAGTAAAACTA
1 ACAAGTAAAA-TA
1975777 TACAA--AAAATGA
1 -ACAAGTAAAAT-A
1975789 ACAAGTAAAATA
1 ACAAGTAAAATA
1975801 A
1 A
1975802 AAATGCTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
11 5 0.16
12 16 0.50
13 7 0.22
14 4 0.12
ACGTcount: A:0.68, C:0.10, G:0.08, T:0.14
Consensus pattern (12 bp):
ACAAGTAAAATA
Found at i:1979797 original size:22 final size:21
Alignment explanation
Indices: 1979753--1979799 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1979743 AAGAAAGATA
1979753 GAAAATTATCTTAATGGGTAT
1 GAAAATTATCTTAATGGGTAT
*
1979774 GAAAATTATGTT-ATGATGGTAT
1 GAAAATTATCTTAATG--GGTAT
1979796 GAAA
1 GAAA
1979800 TGTGATATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 3 0.13
21 11 0.48
22 9 0.39
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.36
Consensus pattern (21 bp):
GAAAATTATCTTAATGGGTAT
Found at i:1980521 original size:25 final size:26
Alignment explanation
Indices: 1980480--1980528 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
1980470 AAACAACTCC
1980480 ATTATATTGAAAATTATATCATATGA
1 ATTATATTGAAAATTATATCATATGA
* *
1980506 ATTATA-TGAAATTTATATTATAT
1 ATTATATTGAAAATTATATCATAT
1980529 AAACAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (26 bp):
ATTATATTGAAAATTATATCATATGA
Found at i:1983081 original size:2 final size:2
Alignment explanation
Indices: 1983076--1983263 Score: 120
Period size: 2 Copynumber: 92.0 Consensus size: 2
1983066 CTTATATAAG
* *
1983076 TA TA TA CTA TA GA TA TA TA CT- TA TA TA TG TA TA TA -A TA TA TA
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1983118 TA -A GTA TA TA TA TA AA CTA TA AA GTA GA -A GTA GA -A GTA TA TA
1 TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA -TA TA TA
* * * ** *
1983160 AA CTA TA TA GTA TA TA TA GTA TA TA AA TA TA AA GCG TA TA AA T-
1 TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA
1983203 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1983244 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
1983264 AGTATAATAT
Statistics
Matches: 147, Mismatches: 21, Indels: 36
0.72 0.10 0.18
Matches are distributed among these distances:
1 7 0.05
2 127 0.86
3 13 0.09
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (2 bp):
TA
Found at i:1983096 original size:29 final size:29
Alignment explanation
Indices: 1983052--1983115 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
1983042 TTATGCATAC
1983052 AATATA-AGTATATACTTATATAAGTATAT
1 AATATAGA-TATATACTTATATAAGTATAT
* *
1983081 ACTATAGATATATACTTATATATGTATAT
1 AATATAGATATATACTTATATAAGTATAT
1983110 AATATA
1 AATATA
1983116 TATAAGTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 30 0.97
30 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (29 bp):
AATATAGATATATACTTATATAAGTATAT
Found at i:1983276 original size:11 final size:12
Alignment explanation
Indices: 1983068--1983279 Score: 84
Period size: 12 Copynumber: 17.9 Consensus size: 12
1983058 AGTATATACT
1983068 TATATAAGTATA
1 TATATAAGTATA
1983080 TACTAT-AG-ATA
1 TA-TATAAGTATA
*
1983091 TATACTTA-TATA
1 TATA-TAAGTATA
*
1983103 TGTAT-A-TAATA
1 TATATAAGT-ATA
1983114 TATATAAGTATA
1 TATATAAGTATA
*
1983126 TATATAA--A-C
1 TATATAAGTATA
*
1983135 TATA-AAGTAGA
1 TATATAAGTATA
*
1983146 -AGTAGAAGTATA
1 TA-TATAAGTATA
1983158 TAAACTATATAGTATA
1 T--A-TATA-AGTATA
1983174 TATAGT-A-TATA
1 TATA-TAAGTATA
*
1983185 AATATAAAGCGTATA
1 TATAT-AA--GTATA
*
1983200 AATTATAA-TATA
1 TA-TATAAGTATA
1983212 TATAT-A-TATA
1 TATATAAGTATA
1983222 TATATATA-TATA
1 TATATA-AGTATA
1983234 TATATATA-TATA
1 TATATA-AGTATA
1983246 TATATATA-TATA
1 TATATA-AGTATA
1983258 TATATAAGTATA
1 TATATAAGTATA
1983270 -ATATAAGTAT
1 TATATAAGTAT
1983280 GTAAACTATA
Statistics
Matches: 165, Mismatches: 9, Indels: 53
0.73 0.04 0.23
Matches are distributed among these distances:
8 2 0.01
9 4 0.02
10 18 0.11
11 37 0.22
12 74 0.45
13 6 0.04
14 2 0.01
15 12 0.07
16 10 0.06
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (12 bp):
TATATAAGTATA
Found at i:1983417 original size:15 final size:15
Alignment explanation
Indices: 1983393--1983422 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1983383 TGTATGATCA
1983393 ATGATACATGTATGT
1 ATGATACATGTATGT
*
1983408 ATGATGCATGTATGT
1 ATGATACATGTATGT
1983423 GTGTATATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (15 bp):
ATGATACATGTATGT
Found at i:1989820 original size:16 final size:16
Alignment explanation
Indices: 1989801--1989853 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
1989791 TGTAACTTAT
1989801 AAGTCATGTAAATATC
1 AAGTCATGTAAATATC
* *
1989817 AAGTCATATAAATGTC
1 AAGTCATGTAAATATC
** * *
1989833 ATCTCATGTCAATAAC
1 AAGTCATGTAAATATC
1989849 AAGTC
1 AAGTC
1989854 GGATTATTTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (16 bp):
AAGTCATGTAAATATC
Found at i:1993969 original size:2 final size:2
Alignment explanation
Indices: 1993945--1993990 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
1993935 TCTTTTTTAT
*
1993945 TA TA T- TA TA T- TA TT TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1993984 TA TA TA T
1 TA TA TA T
1993991 TAATATAGCG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:1993996 original size:12 final size:11
Alignment explanation
Indices: 1993942--1993997 Score: 62
Period size: 12 Copynumber: 5.0 Consensus size: 11
1993932 CTTTCTTTTT
1993942 TATTATAT-TA
1 TATTATATATA
*
1993952 TATTATTTATTA
1 TATTATATA-TA
1993964 TATATATATATA
1 TAT-TATATATA
1993976 TATATATATATA
1 TAT-TATATATA
1993988 TATTA-ATATA
1 TATTATATATA
1993998 GCGTAATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
10 12 0.29
11 2 0.05
12 22 0.54
13 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TATTATATATA
Found at i:1994234 original size:39 final size:39
Alignment explanation
Indices: 1994102--1994436 Score: 398
Period size: 39 Copynumber: 8.6 Consensus size: 39
1994092 GTTTTTAAAA
* * * *
1994102 TATATATATTATATAGCTTTGAAAATGATTTTTGAAAA-T
1 TATATATAATATATAGTTTTTAAAA-CATTTTTGAAAACT
*
1994141 GTATATATATTATATAGTTTTTAAAACA-TTTTGAAAA--
1 -TATATATAATATATAGTTTTTAAAACATTTTTGAAAACT
* * *
1994178 TGTATATAATATATAGTTTTTAAATCATTTTTGAAAATT
1 TATATATAATATATAGTTTTTAAAACATTTTTGAAAACT
**
1994217 TATATATAATATATAGTTTTTAAAACATTTTTGAAAAAA
1 TATATATAATATATAGTTTTTAAAACATTTTTGAAAACT
*** *
1994256 TATATATAATATATAGTTTTTTTAAAA-AAAATTAAAAACT
1 TATATATAATATATAG--TTTTTAAAACATTTTTGAAAACT
*
1994296 TATATATATTATATAGTTTTTAAAACATTTTTGAAAACT
1 TATATATAATATATAGTTTTTAAAACATTTTTGAAAACT
*
1994335 TATATATAATATATAGTTTTTAAAATATTTTTGAAAA--
1 TATATATAATATATAGTTTTTAAAACATTTTTGAAAACT
* *
1994372 TATATATATTATATAGTTTTTTTAAAACA-TTTTGAAAACA
1 TATATATAATATATAG--TTTTTAAAACATTTTTGAAAACT
1994412 TATATATAATATATAGTTTTTAAAA
1 TATATATAATATATAGTTTTTAAAA
1994437 AAACATTTTG
Statistics
Matches: 259, Mismatches: 26, Indels: 22
0.84 0.08 0.07
Matches are distributed among these distances:
36 24 0.09
37 24 0.09
38 36 0.14
39 106 0.41
40 60 0.23
41 9 0.03
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (39 bp):
TATATATAATATATAGTTTTTAAAACATTTTTGAAAACT
Found at i:1994300 original size:116 final size:117
Alignment explanation
Indices: 1994004--1994436 Score: 464
Period size: 116 Copynumber: 3.7 Consensus size: 117
1993994 TATAGCGTAA
* * *
1994004 TTTTTAAAAATATTTTTG-AAAAATATA-ATA-TATATAATTTTTTAGAAAACAGTTTTTGAAAA
1 TTTTT-AAAACATTTTTGAAAAAATATATATATTATATAGTTTTTT-TAAAACA--TTTTGAAAA
* * * * *
1994066 C-ATA-A-AGTATA-A-TGTTTAAAAAATCGGTTTTTAAAA--TATATATATTATATAG
62 CTATATATAATATATAGTTTTTAAAACAT---TTTTGAAAACTTATATATAATATATAG
* * * ** *
1994118 CTTTGAAAATGATTTTTGAAAATGTATATATATTATATAG--TTTTTAAAACATTTTGAAAA-TG
1 TTTTTAAAA-CATTTTTGAAAAAATATATATATTATATAGTTTTTTTAAAACATTTTGAAAACTA
* *
1994180 TATATAATATATAGTTTTTAAATCATTTTTGAAAATTTATATATAATATATAG
65 TATATAATATATAGTTTTTAAAACATTTTTGAAAACTTATATATAATATATAG
* * ** *
1994233 TTTTTAAAACATTTTTGAAAAAATATATATAATATATAGTTTTTTTAAAAAAAATTAAAAACTTA
1 TTTTTAAAACATTTTTGAAAAAATATATATATTATATAGTTTTTTTAAAACATTTTGAAAAC-TA
*
1994298 TATATATTATATAGTTTTTAAAACATTTTTGAAAACTTATATATAATATATAG
65 TATATAATATATAGTTTTTAAAACATTTTTGAAAACTTATATATAATATATAG
*
1994351 TTTTTAAAATATTTTTG--AAAATATATATATTATATAGTTTTTTTAAAACATTTTGAAAACATA
1 TTTTTAAAACATTTTTGAAAAAATATATATATTATATAGTTTTTTTAAAACATTTTGAAAAC-TA
1994414 TATATAATATATAGTTTTTAAAA
65 TATATAATATATAGTTTTTAAAA
1994437 AAACATTTTG
Statistics
Matches: 268, Mismatches: 36, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
112 11 0.04
113 13 0.05
114 47 0.18
115 34 0.13
116 90 0.34
117 6 0.02
118 67 0.25
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (117 bp):
TTTTTAAAACATTTTTGAAAAAATATATATATTATATAGTTTTTTTAAAACATTTTGAAAACTAT
ATATAATATATAGTTTTTAAAACATTTTTGAAAACTTATATATAATATATAG
Found at i:1994498 original size:7 final size:7
Alignment explanation
Indices: 1994488--1994524 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
1994478 ATATATAATA
1994488 TATTATT
1 TATTATT
1994495 TATTA-T
1 TATTATT
1994501 TATTA-T
1 TATTATT
1994507 TATTATT
1 TATTATT
1994514 TATTATT
1 TATTATT
1994521 TATT
1 TATT
1994525 TTTGTTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TATTATT
Found at i:1994507 original size:16 final size:16
Alignment explanation
Indices: 1994488--1994520 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1994478 ATATATAATA
1994488 TATTATT-TATTATTAT
1 TATTATTAT-TTATTAT
1994504 TATTATTATTTATTAT
1 TATTATTATTTATTAT
1994520 T
1 T
1994521 TATTTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTATTATTTATTAT
Found at i:1995730 original size:8 final size:8
Alignment explanation
Indices: 1995713--1995769 Score: 53
Period size: 9 Copynumber: 6.9 Consensus size: 8
1995703 TATTTATATC
*
1995713 TATTTATT
1 TATTTTTT
1995721 TATTTTTT
1 TATTTTTT
*
1995729 TATTATTAT
1 TATT-TTTT
*
1995738 T-TTTTTA
1 TATTTTTT
1995745 TATTTTTTT
1 TA-TTTTTT
1995754 TATATTTTT
1 TAT-TTTTT
1995763 TATTTTT
1 TATTTTT
1995770 CTTTTAACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
7 3 0.08
8 18 0.45
9 19 0.47
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (8 bp):
TATTTTTT
Found at i:1995737 original size:14 final size:14
Alignment explanation
Indices: 1995720--1995769 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1995710 ATCTATTTAT
1995720 TTATTTTTTTATTA
1 TTATTTTTTTATTA
1995734 TTATTTTTTTA-TA
1 TTATTTTTTTATTA
*
1995747 TT-TTTTTTATATTTT
1 TTATTTTTT-TA-TTA
1995762 TTATTTTT
1 TTATTTTT
1995770 CTTTTAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 6 0.19
13 6 0.19
14 11 0.35
15 3 0.10
16 5 0.16
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (14 bp):
TTATTTTTTTATTA
Found at i:1995738 original size:22 final size:22
Alignment explanation
Indices: 1995684--1995769 Score: 92
Period size: 22 Copynumber: 4.0 Consensus size: 22
1995674 TTCACTATTA
*
1995684 TTATTATTA-TTATTAATTTTAT
1 TTATTATTATTTATTTATTTT-T
1995706 TTA-TATCTATTTATTTATTTTT
1 TTATTAT-TATTTATTTATTTTT
*
1995728 TTATTATTATTTTTTTATATTTT
1 TTATTATTATTTATTTAT-TTTT
1995751 TT-TTA-TATTT-TTTATTTTT
1 TTATTATTATTTATTTATTTTT
1995770 CTTTTAACTT
Statistics
Matches: 58, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.07
20 5 0.09
21 8 0.14
22 22 0.38
23 19 0.33
ACGTcount: A:0.23, C:0.01, G:0.00, T:0.76
Consensus pattern (22 bp):
TTATTATTATTTATTTATTTTT
Found at i:1995751 original size:11 final size:11
Alignment explanation
Indices: 1995699--1995763 Score: 62
Period size: 11 Copynumber: 5.6 Consensus size: 11
1995689 ATTATTATTA
*
1995699 ATTTTATTTAT
1 ATTTTTTTTAT
1995710 ATCTATTTATTTAT
1 AT-T-TTT-TTTAT
1995724 -TTTTTTATTAT
1 ATTTTTT-TTAT
1995735 -TATTTTTTTAT
1 AT-TTTTTTTAT
1995746 ATTTTTTTTAT
1 ATTTTTTTTAT
1995757 ATTTTTT
1 ATTTTTT
1995764 ATTTTTCTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
10 1 0.02
11 30 0.64
12 8 0.17
13 3 0.06
14 5 0.11
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.77
Consensus pattern (11 bp):
ATTTTTTTTAT
Found at i:1995774 original size:11 final size:10
Alignment explanation
Indices: 1995719--1995775 Score: 62
Period size: 11 Copynumber: 5.4 Consensus size: 10
1995709 TATCTATTTA
1995719 TTTATTTTTT
1 TTTATTTTTT
1995729 TATTATTATTTT
1 T-TTATT-TTTT
1995741 TTTATATTTTT
1 TTTAT-TTTTT
*
1995752 TTTA-TATTT
1 TTTATTTTTT
1995761 TTTATTTTTCT
1 TTTATTTTT-T
1995772 TTTA
1 TTTA
1995776 ACTTATTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
9 8 0.20
10 4 0.10
11 22 0.55
12 6 0.15
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:1995774 original size:22 final size:22
Alignment explanation
Indices: 1995681--1995775 Score: 70
Period size: 25 Copynumber: 4.1 Consensus size: 22
1995671 ATTTTCACTA
* *
1995681 TTATTATTATTATTATTAATTTTAT
1 TTATTA-TATT-TT-TTATTTTTTT
*
1995706 TTATATCTATTTATTTATTTTTTT
1 TTAT-TATATTT-TTTATTTTTTT
*
1995730 ATTATTAT-TTTTTTA-TATTTT
1 -TTATTATATTTTTTATTTTTTT
1995751 TT-TTATATTTTTTATTTTTCTT
1 TTATTATATTTTTTATTTTT-TT
1995773 TTA
1 TTA
1995776 ACTTATTCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
19 4 0.07
20 9 0.16
21 8 0.14
22 8 0.14
23 3 0.05
24 11 0.19
25 13 0.23
26 1 0.02
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (22 bp):
TTATTATATTTTTTATTTTTTT
Found at i:1995782 original size:47 final size:47
Alignment explanation
Indices: 1995683--1995802 Score: 131
Period size: 47 Copynumber: 2.6 Consensus size: 47
1995673 TTTCACTATT
* * *
1995683 ATTATTATTATTATTA-ATTTTATTTATATCTATTTATTTATTTTTTT
1 ATTATTATT-TTTTTATATTTTTTTTATATCTATTTATTTATTTTTTA
*
1995730 ATTATTATTTTTTTATATTTTTTTTATAT-TTTTTATTT-TTCTTTTA
1 ATTATTATTTTTTTATATTTTTTTTATATCTATTTATTTATT-TTTTA
*
1995776 ACTTATTCTTTTTTT-TACTTTTTTTTA
1 A-TTATTATTTTTTTATA-TTTTTTTTA
1995803 CTTTTCCCTC
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
45 2 0.03
46 20 0.31
47 42 0.66
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (47 bp):
ATTATTATTTTTTTATATTTTTTTTATATCTATTTATTTATTTTTTA
Found at i:1995799 original size:9 final size:10
Alignment explanation
Indices: 1995783--1995807 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1995773 TTAACTTATT
1995783 CTTTTTTTTA
1 CTTTTTTTTA
1995793 CTTTTTTTTA
1 CTTTTTTTTA
1995803 CTTTT
1 CTTTT
1995808 CCCTCTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (10 bp):
CTTTTTTTTA
Found at i:1995868 original size:14 final size:13
Alignment explanation
Indices: 1995848--1995902 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 13
1995838 TCCTTTTGAC
1995848 TTTT-TTTATTTA
1 TTTTATTTATTTA
*
1995860 TTTTATTTTATTTCC
1 TTTTA-TTTATTT-A
*
1995875 TTTGATTTA-TTA
1 TTTTATTTATTTA
1995887 TTTTA-TTATTTA
1 TTTTATTTATTTA
1995899 TTTT
1 TTTT
1995903 TTCCTAACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
11 3 0.09
12 15 0.43
13 2 0.06
14 11 0.31
15 4 0.11
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:1999887 original size:85 final size:85
Alignment explanation
Indices: 1999723--2000645 Score: 1001
Period size: 85 Copynumber: 10.8 Consensus size: 85
1999713 CATTTTTTAT
* *
1999723 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAATACCTTCGAGTTCGATTACA
1 ATTTACAGCATAGATCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACA
1999788 CTCAGCTCAAAGGCATATCCA
65 CTCAGCTCAAAGGCATATCCA
*** * * *
1999809 ATTCGTAGCATAGATCAAGGCGAAAAGGGCTATCTGTCGACAAAGACCTTCGAGTTCGATTACAC
1 ATTTACAGCATAGATCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACAC
1999874 TCAGCTCAAAGGCATAT-CA
66 TCAGCTCAAAGGCATATCCA
** * *
1999893 ATTTACAATATA-ACTCAAGGCGATAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACA
1 ATTTACAGCATAGA-TCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACA
* * *
1999957 CTCAGGTCAAAGGCACATCAA
65 CTCAGCTCAAAGGCATATCCA
* * * * *
1999978 ATTTACAGCATAGCTCAAGGCGAGAAAGGTTATATATTAACAAAAGACCTTCGAGTTCGATTACA
1 ATTTACAGCATAGATCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACA
* *
2000043 CTCAGCTCACATGCATAT-CA
65 CTCAGCTCAAAGGCATATCCA
* *
2000063 ATTTACAGCATA-ACTCAAGGCGAGAAGGGTTATCTGACAACCAAGACCTTCGAGTTCGATTACA
1 ATTTACAGCATAGA-TCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACA
* *
2000127 CTCAGCTCAAAGGCACATCAA
65 CTCAGCTCAAAGGCATATCCA
** * *
2000148 ATTTACAGCATATCTCAAGGCGAGAAGGGTTATCTGT-TACAAAAGACCTTCGAGTTCGATTGCA
1 ATTTACAGCATAGATCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACA
2000212 CTCAGCTCAAAGGCATAT-CA
65 CTCAGCTCAAAGGCATATCCA
* * * *
2000232 ATTTATAGCATA-ACTCAAGGCGAGAAGGGATATCTGTCAACTAATACCTTCGAGTTCGATTACA
1 ATTTACAGCATAGA-TCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACA
* *
2000296 CTCAGCTCAAAGACACA-CCAA
65 CTCAGCTCAAAGGCATATCC-A
* * * *
2000317 ATTTAAAGCATAGCTCAAGACGAGAAGGGTTATCTATCATTA-AAAGACCTTCGAGTTCGATTAC
1 ATTTACAGCATAGATCAAGGCGAGAAGGGTTATCTGTCA--ACAAAGACCTTCGAGTTCGATTAC
*
2000381 ACTCAGCTCAAAGGCATATCAA
64 ACTCAGCTCAAAGGCATATCCA
* * * *
2000403 ATTTGCAGCATA-ACTCAATGG-GAGAAGGGTTATCTGTTAACCAAGACCCTCGAGTTCGATTAC
1 ATTTACAGCATAGA-TCAA-GGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTAC
* ** * **
2000466 ACTCAACTCCGAGGCACATTAA
64 ACTCAGCTCAAAGGCATATCCA
* * *
2000488 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTTTCATTA-AAAGACCTTCGAGTTCGATTAC
1 ATTTACAGCATAGATCAAGGCGAGAAGGGTTATCTGTCA--ACAAAGACCTTCGAGTTCGATTAC
* *
2000552 ACTCAGCT-AAAGGGCATGTCAA
64 ACTCAGCTCAAA-GGCATATCCA
* *** * * ** * * *
2000574 ATTTACAGTATTTCTTAAGTCGAGAAAAGTTATCTGTCAACAAA-AACTGACGAGTTCGATTCCA
1 ATTTACAGCATAGATCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCT-TCGAGTTCGATTACA
*
2000638 TTCAGCTC
65 CTCAGCTC
2000646 GATGACACAT
Statistics
Matches: 700, Mismatches: 110, Indels: 54
0.81 0.13 0.06
Matches are distributed among these distances:
83 1 0.00
84 187 0.27
85 307 0.44
86 201 0.29
87 4 0.01
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (85 bp):
ATTTACAGCATAGATCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACAC
TCAGCTCAAAGGCATATCCA
Found at i:2000178 original size:255 final size:254
Alignment explanation
Indices: 1999723--2000563 Score: 1117
Period size: 255 Copynumber: 3.3 Consensus size: 254
1999713 CATTTTTTAT
*
1999723 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAATACCTTCGAGTTCGATTACA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACA
*** * * * *
1999788 CTCAGCTCAAAGGCATATCCAATTCGTAGCATAGA-TCAAGGCGAAAAGGGCTATCTGTCGACAA
66 CTCAGCTCAAA-GCATAT-CAATTTAAAGCATA-ACTCAAGGCGAGAAGGGTTATCTGACAACAA
**
1999852 AGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATC-AATTTACAATATAACTCAAGGCGA
128 AGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGCGA
* *
1999916 TAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGGTCAAAGGCACATCAA
193 GAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAA
* * * *
1999978 ATTTACAGCATAGCTCAAGGCGAGAAAGGTTATATATTAACAAAAGACCTTCGAGTTCGATTACA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACA
* * *
2000043 CTCAGCTCACATGCATATCAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGACAACCAAG
66 CTCAGCTCA-AAGCATATCAATTTAAAGCATAACTCAAGGCGAGAAGGGTTATCTGACAACAAAG
* *
2000108 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATATCTCAAGGCGAGA
130 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGCGAGA
* *
2000173 AGGGTTATCTGTTACAA--AAGACCTTCGAGTTCGATTGCACTCAGCTCAAAGGCATATC-A
195 AGGGTTATCTG-T-CAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAA
* * * * *
2000232 ATTTATAGCATAACTCAAGGCGAGAAGGGATATCTGTCAAC-TAATACCTTCGAGTTCGATTACA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACA
* * * *
2000296 CTCAGCTCAAAGACACACCAAATTTAAAGCATAGCTCAAGACGAGAAGGGTTATCT-ATCATTA-
66 CTCAGCTCAAAG-CATATC-AATTTAAAGCATAACTCAAGGCGAGAAGGGTTATCTGA-CA--AC
*
2000359 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTGCAGCATAACTCAATGG
126 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAA-GG
* * * ** *
2000424 -GAGAAGGGTTATCTGTTAACCAAGACCCTCGAGTTCGATTACACTCAACTCCGAGGCACATTAA
190 CGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAA
* * **
2000488 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTTTCATTAAAAGACCTTCGAGTTCGATTACA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACA
2000553 CTCAGCT-AAAG
66 CTCAGCTCAAAG
2000564 GGCATGTCAA
Statistics
Matches: 514, Mismatches: 57, Indels: 29
0.86 0.09 0.05
Matches are distributed among these distances:
252 2 0.00
253 38 0.07
254 145 0.28
255 253 0.49
256 45 0.09
257 31 0.06
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (254 bp):
ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACA
CTCAGCTCAAAGCATATCAATTTAAAGCATAACTCAAGGCGAGAAGGGTTATCTGACAACAAAGA
CCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGCGAGAA
GGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAA
Found at i:2000389 original size:339 final size:340
Alignment explanation
Indices: 1999723--2000580 Score: 1231
Period size: 339 Copynumber: 2.5 Consensus size: 340
1999713 CATTTTTTAT
* * *
1999723 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAATACCTTCGAGTTCGATTACA
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAC-CAAGACCTTCGAGTTCGATTACA
* * *** * * *
1999788 CTCAGCTCAAAGGCATATCCAATTCGTAGCATAGATCAAGGCGAAAAGGGCTATCTGTCGAC-AA
65 CTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGT-TACAAA
* *
1999852 AGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAATTTACAATATAACTCAAGGCGAT
129 AGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAATTTACAACATAACTCAAGGCGAG
* * * *
1999917 AAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGGTCAAAGGCACATCAAATTT
194 AAGGGATATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACACCAAATTT
* * *
1999982 ACAGCATAGCTCAAGGCGAGAAAGGTTATATATTAACAAAAGACCTTCGAGTTCGATTACACTCA
259 AAAGCATAGCTCAAGACGAGAAAGGTTATATATCAACAAAAGACCTTCGAGTTCGATTACACTCA
* *
2000047 GCTCACATGCATATC-A
324 GCTCAAAGGCATATCAA
*
2000063 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGACAACCAAGACCTTCGAGTTCGATTACAC
1 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACAC
* *
2000128 TCAGCTCAAAGGCACATCAAATTTACAGCATATCTCAAGGCGAGAAGGGTTATCTGTTACAAAAG
66 TCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTTACAAAAG
* * *
2000193 ACCTTCGAGTTCGATTGCACTCAGCTCAAAGGCATATCAATTTATAGCATAACTCAAGGCGAGAA
131 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAATTTACAACATAACTCAAGGCGAGAA
* *
2000258 GGGATATCTGTCAACTAATACCTTCGAGTTCGATTACACTCAGCTCAAAGACACACCAAATTTAA
196 GGGATATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACACCAAATTTAA
* * **
2000323 AGCATAGCTCAAGACGAGAAGGGTTATCTATCATTAAAAGACCTTCGAGTTCGATTACACTCAGC
261 AGCATAGCTCAAGACGAGAAAGGTTATATATCAACAAAAGACCTTCGAGTTCGATTACACTCAGC
2000388 TCAAAGGCATATCAA
326 TCAAAGGCATATCAA
* * *
2000403 ATTTGCAGCATAACTCAATGG-GAGAAGGGTTATCTGTTAACCAAGACCCTCGAGTTCGATTACA
1 ATTTACAGCATAACTCAA-GGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACA
* ** * *
2000467 CTCAACTCCGAGGCACATTAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCT-TTCATTAA
65 CTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTT-A-CAA
*
2000531 AAGACCTTCGAGTTCGATTACACTCAGCT-AAAGGGCATGTCAAATTTACA
128 AAGACCTTCGAGTTCGATTACACTCAGCTCAAA-GGCATATC-AATTTACA
2000581 GTATTTCTTA
Statistics
Matches: 463, Mismatches: 48, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
338 2 0.00
339 264 0.57
340 151 0.33
341 39 0.08
342 7 0.02
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (340 bp):
ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACAC
TCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTTACAAAAG
ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAATTTACAACATAACTCAAGGCGAGAA
GGGATATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACACACCAAATTTAA
AGCATAGCTCAAGACGAGAAAGGTTATATATCAACAAAAGACCTTCGAGTTCGATTACACTCAGC
TCAAAGGCATATCAA
Found at i:2001416 original size:39 final size:38
Alignment explanation
Indices: 2001314--2001680 Score: 462
Period size: 39 Copynumber: 9.4 Consensus size: 38
2001304 TGAAAATGAT
2001314 TTTTTGAAAATGTATATATAATATATAGTTTTTAAAACA
1 TTTTTGAAAAT-TATATATAATATATAGTTTTTAAAACA
* *
2001353 -TTTT-AAAAATATATATAATATATAGTTTTTAAATCA
1 TTTTTGAAAATTATATATAATATATAGTTTTTAAAACA
2001389 TTTTT-AAACACTTATATATAATATATAGTTTTTAAAACA
1 TTTTTGAAA-A-TTATATATAATATATAGTTTTTAAAACA
*
2001428 TTTTTGAATATATATATATATATAATATAGTTTTTAAAACA
1 TTTTTGAAAAT-TATATATA-AT-ATATAGTTTTTAAAACA
*
2001469 TTTTTGAAAACTTATATATATTATATAGTTTTTAAAACA
1 TTTTTGAAAA-TTATATATAATATATAGTTTTTAAAACA
*
2001508 TTTTTGAAAACTTATATATATTATATAG-TTTTAAAACA
1 TTTTTGAAAA-TTATATATAATATATAGTTTTTAAAACA
*
2001546 TTTTTGAAAACTTATTTATAATATATAGTTTTTAAAACA
1 TTTTTGAAAA-TTATATATAATATATAGTTTTTAAAACA
*
2001585 TTTTTGAAAA-TATATATATTATATAGTTTTTTTAAAACA
1 TTTTTGAAAATTATATATAATATATAG--TTTTTAAAACA
2001624 -TTTTGTAAACA-TATATATAATATATAGTTTTTTAAAAAAACA
1 TTTTTG-AAA-ATTATATATAATATATAG-TTTTT---AAAACA
2001666 -TTTTGAAAATTATAT
1 TTTTTGAAAATTATAT
2001681 GGTTTTTTAA
Statistics
Matches: 299, Mismatches: 12, Indels: 32
0.87 0.03 0.09
Matches are distributed among these distances:
36 26 0.09
37 25 0.08
38 47 0.16
39 125 0.42
40 22 0.07
41 42 0.14
42 12 0.04
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (38 bp):
TTTTTGAAAATTATATATAATATATAGTTTTTAAAACA
Found at i:2001576 original size:77 final size:77
Alignment explanation
Indices: 2001314--2001680 Score: 498
Period size: 77 Copynumber: 4.7 Consensus size: 77
2001304 TGAAAATGAT
* *
2001314 TTTTTGAAAA-TGTATATATAATATATAGTTTTTAAAACA-TTTT-AAAAATATATATAATATAT
1 TTTTTGAAAACT-TATATATAATATATAGTTTTTAAAACATTTTTGAAAATTATATATATTATAT
*
2001376 AGTTTTTAAATCA
65 AGTTTTTAAAACA
*
2001389 TTTTT-AAACACTTATATATAATATATAGTTTTTAAAACATTTTTGAATATATATATATATATAA
1 TTTTTGAAA-ACTTATATATAATATATAGTTTTTAAAACATTTTTGAA-A-AT-TATATATATTA
2001453 TATAGTTTTTAAAACA
62 TATAGTTTTTAAAACA
*
2001469 TTTTTGAAAACTTATATATATTATATAGTTTTTAAAACATTTTTGAAAACTTATATATATTATAT
1 TTTTTGAAAACTTATATATAATATATAGTTTTTAAAACATTTTTGAAAA-TTATATATATTATAT
2001534 AG-TTTTAAAACA
65 AGTTTTTAAAACA
*
2001546 TTTTTGAAAACTTATTTATAATATATAGTTTTTAAAACATTTTTGAAAA-TATATATATTATATA
1 TTTTTGAAAACTTATATATAATATATAGTTTTTAAAACATTTTTGAAAATTATATATATTATATA
2001610 GTTTTTTTAAAACA
66 G--TTTTTAAAACA
* *
2001624 -TTTTGTAAACATATATATAATATATAGTTTTTTAAAAAAACA-TTTTGAAAATTATAT
1 TTTTTGAAAACTTATATATAATATATAG-TTTTT---AAAACATTTTTGAAAATTATAT
2001681 GGTTTTTTAA
Statistics
Matches: 264, Mismatches: 11, Indels: 28
0.87 0.04 0.09
Matches are distributed among these distances:
74 3 0.01
75 49 0.19
76 5 0.02
77 83 0.31
78 32 0.12
79 3 0.01
80 75 0.28
81 14 0.05
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (77 bp):
TTTTTGAAAACTTATATATAATATATAGTTTTTAAAACATTTTTGAAAATTATATATATTATATA
GTTTTTAAAACA
Found at i:2002920 original size:6 final size:6
Alignment explanation
Indices: 2002909--2002998 Score: 58
Period size: 6 Copynumber: 14.5 Consensus size: 6
2002899 TCTCTATTTA
* *
2002909 TTTATT TTTATT TTTA-T TATATT TTTATAT TTTATAT TTT-TA TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTAT-T TTTAT-T TTTATT TTTATT
* * * * *
2002957 TTTCTT TTGACTT ATTCTT TTTTTT CTTATATT TTTATT TTT
1 TTTATT TTTA-TT TTTATT TTTATT -TT-TATT TTTATT TTT
2002999 TCCCTCTCTT
Statistics
Matches: 65, Mismatches: 13, Indels: 12
0.72 0.14 0.13
Matches are distributed among these distances:
5 7 0.11
6 37 0.57
7 18 0.28
8 3 0.05
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:2002943 original size:15 final size:16
Alignment explanation
Indices: 2002906--2002956 Score: 63
Period size: 15 Copynumber: 3.3 Consensus size: 16
2002896 TTATCTCTAT
*
2002906 TTATT-TATTTTTATTT
1 TTATTATATTTTTA-TA
2002922 TTATTATATTTTTATA
1 TTATTATATTTTTATA
2002938 TT-TTATATTTTTAT-
1 TTATTATATTTTTATA
2002952 TTATT
1 TTATT
2002957 TTTCTTTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
14 2 0.06
15 14 0.44
16 8 0.25
17 8 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTATATTTTTATA
Found at i:2002950 original size:56 final size:57
Alignment explanation
Indices: 2002872--2002999 Score: 145
Period size: 58 Copynumber: 2.2 Consensus size: 57
2002862 TTATTTTCAC
* *
2002872 TATTATTATTTTTTAAAATTTTATTTA-TCTCTATTT-ATTTATT-TTTATTTTTATTA
1 TATTTTTATTTTTTAAAATTTTATTTATTCTCT-TTTGACTTATTCTTT-TTTTTATTA
* * * * *
2002928 TATTTTTATATTTTATATTTTTATTTATTTTTCTTTTGACTTATTCTTTTTTTTCTTA
1 TATTTTTATTTTTTAAAATTTTATTTA-TTCTCTTTTGACTTATTCTTTTTTTTATTA
2002986 TATTTTTATTTTTT
1 TATTTTTATTTTTT
2003000 CCCTCTCTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
56 23 0.38
57 3 0.05
58 31 0.52
59 3 0.05
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.73
Consensus pattern (57 bp):
TATTTTTATTTTTTAAAATTTTATTTATTCTCTTTTGACTTATTCTTTTTTTTATTA
Found at i:2002958 original size:17 final size:17
Alignment explanation
Indices: 2002911--2002958 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
2002901 TCTATTTATT
2002911 TATTTTTATTT-TTATTA
1 TATTTTTATTTATT-TTA
2002928 TATTTTTA--TATTTTA
1 TATTTTTATTTATTTTA
2002943 TATTTTTATTTATTTT
1 TATTTTTATTTATTTT
2002959 TCTTTTGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 12 0.43
16 2 0.07
17 14 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TATTTTTATTTATTTTA
Found at i:2002972 original size:26 final size:27
Alignment explanation
Indices: 2002916--2002972 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
2002906 TTATTTATTT
*
2002916 TTATTTTTATTATATTTTTATATTTTA
1 TTATTTTTATTATATTTTTATATTTGA
*
2002943 -TATTTTTATT-TATTTTTCT-TTTGA
1 TTATTTTTATTATATTTTTATATTTGA
2002967 CTTATT
1 -TTATT
2002973 CTTTTTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 8 0.31
26 14 0.54
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (27 bp):
TTATTTTTATTATATTTTTATATTTGA
Found at i:2004067 original size:118 final size:118
Alignment explanation
Indices: 2003859--2004102 Score: 488
Period size: 118 Copynumber: 2.1 Consensus size: 118
2003849 ATTACTTTCT
2003859 ACCAATATATATGTTTTATATTAGAGGGAAACGTACTGTTGTCTGTTGGGATTTATTCTTTTGAT
1 ACCAATATATATGTTTTATATTAGAGGGAAACGTACTGTTGTCTGTTGGGATTTATTCTTTTGAT
2003924 AAAGCGAACAATTTACACGCTATACAGCATCCCAAGCACGTGTCTCGTAGAGG
66 AAAGCGAACAATTTACACGCTATACAGCATCCCAAGCACGTGTCTCGTAGAGG
2003977 ACCAATATATATGTTTTATATTAGAGGGAAACGTACTGTTGTCTGTTGGGATTTATTCTTTTGAT
1 ACCAATATATATGTTTTATATTAGAGGGAAACGTACTGTTGTCTGTTGGGATTTATTCTTTTGAT
2004042 AAAGCGAACAATTTACACGCTATACAGCATCCCAAGCACGTGTCTCGTAGAGG
66 AAAGCGAACAATTTACACGCTATACAGCATCCCAAGCACGTGTCTCGTAGAGG
2004095 ACCAATAT
1 ACCAATAT
2004103 CGATGCTTAA
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 126 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (118 bp):
ACCAATATATATGTTTTATATTAGAGGGAAACGTACTGTTGTCTGTTGGGATTTATTCTTTTGAT
AAAGCGAACAATTTACACGCTATACAGCATCCCAAGCACGTGTCTCGTAGAGG
Found at i:2006415 original size:14 final size:15
Alignment explanation
Indices: 2006390--2006420 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2006380 ACAACCTCAC
2006390 AACCTCTAAACCATA
1 AACCTCTAAACCATA
2006405 AACCT-TAAACCATA
1 AACCTCTAAACCATA
2006419 AA
1 AA
2006421 TAATAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (15 bp):
AACCTCTAAACCATA
Found at i:2007049 original size:3 final size:3
Alignment explanation
Indices: 2007041--2007086 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2007031 AAGGACTAAT
2007041 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2007087 ATTTTCAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2011918 original size:15 final size:15
Alignment explanation
Indices: 2011900--2011950 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
2011890 TTCTTTTAAT
2011900 TTTTATATTTAAAGA
1 TTTTATATTTAAAGA
** **
2011915 TTTTATA-AGAATTA
1 TTTTATATTTAAAGA
*
2011929 TTATATATTTAAAGA
1 TTTTATATTTAAAGA
2011944 TTTTATA
1 TTTTATA
2011951 AGTCACAATA
Statistics
Matches: 25, Mismatches: 10, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTTATATTTAAAGA
Found at i:2011962 original size:29 final size:29
Alignment explanation
Indices: 2011903--2011965 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
2011893 TTTTAATTTT
* *
2011903 TATATTTAAAGATTTTATAAGAATTATTA
1 TATATTTAAAGATTTTATAAGAATCAATA
*
2011932 TATATTTAAAGATTTTATAAGTCA-CAATA
1 TATATTTAAAGATTTTATAAG-AATCAATA
2011961 TATAT
1 TATAT
2011966 ATATATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (29 bp):
TATATTTAAAGATTTTATAAGAATCAATA
Found at i:2011965 original size:2 final size:2
Alignment explanation
Indices: 2011958--2012009 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
2011948 ATAAGTCACA
2011958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2011999 AT AT AT AT AT A
1 AT AT AT AT AT A
2012010 AGTCCATGCA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2013036 original size:22 final size:22
Alignment explanation
Indices: 2013008--2013052 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2012998 CCAGACATAG
2013008 ACCTGTGATCACTAGCATCACC
1 ACCTGTGATCACTAGCATCACC
2013030 ACCTGTGATCACTAGCATCACC
1 ACCTGTGATCACTAGCATCACC
2013052 A
1 A
2013053 GCCCAGTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.36, G:0.13, T:0.22
Consensus pattern (22 bp):
ACCTGTGATCACTAGCATCACC
Found at i:2017363 original size:166 final size:167
Alignment explanation
Indices: 2017178--2017489 Score: 382
Period size: 166 Copynumber: 1.9 Consensus size: 167
2017168 GTTTTAAGGA
*
2017178 TAATGATTTAGCGGCG-TTTTTATATAAACGCCGCAAAATAATAGAACTTTAACGGCGTTGTT-A
1 TAATGATTTAGCGGCGTTTTTTA-ATAAACGCCGCAAAATAATAGAACTTTAACAGCGTTGTTCA
* ** * * * *
2017241 TTAAAACGCCGCTATAAAGTG-TTACTTTAGTGTCGTTTTTAAACAAAAACGCC-GTAAAATATT
65 -GAAAACGCCGCTATAAAG-GCTTAAGTTAGTGGCGTTTTGAAACAAAAACGCCACT-AAACATT
*
2017304 TGGACATTAGTGGCGTTTTTATACAAATGCAGCAATAAATT
127 TGGACAGTAGTGGCGTTTTTATACAAATGCAGCAATAAATT
* * * * * *
2017345 TAAT-ATTTAGTGGCGTTTTTTAATCAACGCCGCAATATAATATAACTTTAGCAGCGTTTTTCAG
1 TAATGATTTAGCGGCGTTTTTTAATAAACGCCGCAAAATAATAGAACTTTAACAGCGTTGTTCAG
* * * *
2017409 AAAATGCCGCTATAGAGGCTTAAGTTAGTGGCGTTTTGAAACACAAACGCCACTCAACATTTGGA
66 AAAACGCCGCTATAAAGGCTTAAGTTAGTGGCGTTTTGAAACAAAAACGCCACTAAACATTTGGA
2017474 CAGTAGTGGCGTTTTT
131 CAGTAGTGGCGTTTTT
2017490 TAAGTAAACG
Statistics
Matches: 122, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
165 1 0.01
166 109 0.89
167 12 0.10
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (167 bp):
TAATGATTTAGCGGCGTTTTTTAATAAACGCCGCAAAATAATAGAACTTTAACAGCGTTGTTCAG
AAAACGCCGCTATAAAGGCTTAAGTTAGTGGCGTTTTGAAACAAAAACGCCACTAAACATTTGGA
CAGTAGTGGCGTTTTTATACAAATGCAGCAATAAATT
Found at i:2021863 original size:43 final size:42
Alignment explanation
Indices: 2021816--2021949 Score: 117
Period size: 43 Copynumber: 3.1 Consensus size: 42
2021806 TTTATTGTGA
*
2021816 CGTTTGTGATAAAAACGCCGCTAAATATTGACACCAATTGCGG
1 CGTTTGT-ATAAAAACGCCGCTAAATATCGACACCAATTGCGG
* ** *
2021859 CGTTTTTA-AGACAAACGCCGCTAAATATCGGTACCTATTGCGG
1 CGTTTGTATA-A-AAACGCCGCTAAATATCGACACCAATTGCGG
* * * ** * *
2021902 CATTTGTTTAACAAACGCCGCTACATATCGTTACCTATTGTGG
1 CGTTTGTATAA-AAACGCCGCTAAATATCGACACCAATTGCGG
2021945 CGTTT
1 CGTTT
2021950 TTGGTTAACA
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.01
42 2 0.03
43 72 0.95
44 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (42 bp):
CGTTTGTATAAAAACGCCGCTAAATATCGACACCAATTGCGG
Found at i:2022008 original size:12 final size:14
Alignment explanation
Indices: 2021972--2022008 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2021962 CGCCGCGAAC
2021972 TTTAGCGGCGCTAT
1 TTTAGCGGCGCTAT
2021986 TTTCAGCGGCGC-AT
1 TTT-AGCGGCGCTAT
2022000 TTT-GCGGCG
1 TTTAGCGGCG
2022009 TTTTTCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
14 8 0.36
15 8 0.36
ACGTcount: A:0.11, C:0.24, G:0.32, T:0.32
Consensus pattern (14 bp):
TTTAGCGGCGCTAT
Found at i:2027657 original size:20 final size:20
Alignment explanation
Indices: 2027632--2027677 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2027622 TCTGGCAATG
* *
2027632 AACCGGCTGAAAA-TCGGTAA
1 AACCGGCTAAAAACT-GGCAA
2027652 AACCGGCTAAAAACTGGCAA
1 AACCGGCTAAAAACTGGCAA
2027672 AACCGG
1 AACCGG
2027678 TTTGAACCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (20 bp):
AACCGGCTAAAAACTGGCAA
Found at i:2028340 original size:24 final size:24
Alignment explanation
Indices: 2028276--2028330 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
2028266 TATGTTGTAA
2028276 TTGATTTGAATCATTTTGTTTCAC
1 TTGATTTGAATCATTTTGTTTCAC
2028300 TTGATTTGAATCATTTTGTTTCAC
1 TTGATTTGAATCATTTTGTTTCAC
2028324 TTGATTT
1 TTGATTT
2028331 TATGGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.20, C:0.11, G:0.13, T:0.56
Consensus pattern (24 bp):
TTGATTTGAATCATTTTGTTTCAC
Found at i:2031288 original size:16 final size:17
Alignment explanation
Indices: 2031255--2031287 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2031245 CTACCCCCAT
2031255 AGGTATCGATACCCCCC
1 AGGTATCGATACCCCCC
2031272 AGGTATCGATACCCCC
1 AGGTATCGATACCCCC
2031288 ATGCAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.39, G:0.18, T:0.18
Consensus pattern (17 bp):
AGGTATCGATACCCCCC
Found at i:2036866 original size:21 final size:22
Alignment explanation
Indices: 2036820--2036899 Score: 76
Period size: 21 Copynumber: 3.6 Consensus size: 22
2036810 CCCTAAGACT
2036820 GGTATCGATACCCCCTTGAATA
1 GGTATCGATACCCCCTTGAATA
2036842 -GTATCGATA-CCCC-TGCAATA
1 GGTATCGATACCCCCTTG-AATA
* * * *
2036862 GGTATGGATAACCATCTTTGAATG
1 GGTATCGAT-ACC-CCCTTGAATA
2036886 GGTATCGATACCCC
1 GGTATCGATACCCC
2036900 TGATGGTACG
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
19 2 0.04
20 8 0.17
21 16 0.35
22 2 0.04
23 4 0.09
24 12 0.26
25 2 0.04
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (22 bp):
GGTATCGATACCCCCTTGAATA
Found at i:2039616 original size:21 final size:21
Alignment explanation
Indices: 2039592--2039639 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2039582 GCAGGTACTA
*
2039592 ATACCCTATGAAGGGGTATCG
1 ATACCCTATGAAGGGGTACCG
2039613 ATACCCTATGAAGGGGTACCG
1 ATACCCTATGAAGGGGTACCG
2039634 ATACCC
1 ATACCC
2039640 CTCACGCTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (21 bp):
ATACCCTATGAAGGGGTACCG
Found at i:2051633 original size:14 final size:13
Alignment explanation
Indices: 2051609--2051642 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2051599 AAGGCTATAG
*
2051609 TTTTCTTTTCTTT
1 TTTTTTTTTCTTT
2051622 TTCTTTTTTTCTTT
1 TT-TTTTTTTCTTT
2051636 TTTTTTT
1 TTTTTTT
2051643 ATAAATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Found at i:2052215 original size:16 final size:16
Alignment explanation
Indices: 2052190--2052220 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2052180 TATATTATAG
*
2052190 TTTTTGAAAACATATT
1 TTTTTAAAAACATATT
2052206 TTTTTAAAAACATAT
1 TTTTTAAAAACATAT
2052221 AATATATGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (16 bp):
TTTTTAAAAACATATT
Found at i:2052266 original size:39 final size:38
Alignment explanation
Indices: 2052102--2052265 Score: 149
Period size: 38 Copynumber: 4.3 Consensus size: 38
2052092 TTTTTGAAAG
*
2052102 TATATAGTATACGTTTTGAAAACTTATTTTTAAAAACGTA
1 TATATA-TATAGGTTTTGAAAAC-TATTTTTAAAAACGTA
* * * * *
2052142 TA-ATATATAGTTTTTGAAATCGTGTTTTTGAAAACATA
1 TATATATATAGGTTTTGAAAAC-TATTTTTAAAAACGTA
* *
2052180 TATAT-TATAGTTTTTGAAAACATATTTTTTTAAAAACATA
1 TATATATATAGGTTTTGAAAAC-TA--TTTTTAAAAACGTA
*
2052220 TA-ATATAT-GGTTTTGAAAAC-ATTTTTAGAAACGTA
1 TATATATATAGGTTTTGAAAACTATTTTTAAAAACGTA
2052255 TATACTATATA
1 TATA-TATATA
2052266 TAATCTTTGA
Statistics
Matches: 103, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
35 14 0.14
36 1 0.01
37 6 0.06
38 44 0.43
39 18 0.17
40 20 0.19
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (38 bp):
TATATATATAGGTTTTGAAAACTATTTTTAAAAACGTA
Found at i:2052343 original size:9 final size:8
Alignment explanation
Indices: 2052331--2052402 Score: 58
Period size: 8 Copynumber: 8.8 Consensus size: 8
2052321 CTTTAATATA
2052331 TATTTTTT
1 TATTTTTT
*
2052339 ATATTTCTT
1 -TATTTTTT
*
2052348 T-TTATTT
1 TATTTTTT
2052355 TATTTTTT
1 TATTTTTT
2052363 TATTTTTT
1 TATTTTTT
*
2052371 TATTTCATT
1 TATTT-TTT
*
2052380 TA-TTTAT
1 TATTTTTT
2052387 TATTTATTT
1 TATTT-TTT
2052396 TCATTTT
1 T-ATTTT
2052403 GATTTAGGTC
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
7 8 0.16
8 23 0.46
9 15 0.30
10 4 0.08
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (8 bp):
TATTTTTT
Found at i:2052372 original size:21 final size:21
Alignment explanation
Indices: 2052331--2052402 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
2052321 CTTTAATATA
2052331 TATTTTTTATATTTCTTTTTATTT
1 TATTTTTT-TA-TT-TTTTTATTT
2052355 TATTTTTTTATTTTTTTATTT
1 TATTTTTTTATTTTTTTATTT
* * *
2052376 CATTTATTTA-TTATTTATTT
1 TATTTTTTTATTTTTTTATTT
2052396 TCATTTT
1 T-ATTTT
2052403 GATTTAGGTC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
20 9 0.21
21 21 0.50
22 2 0.05
23 2 0.05
24 8 0.19
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (21 bp):
TATTTTTTTATTTTTTTATTT
Found at i:2052386 original size:4 final size:4
Alignment explanation
Indices: 2052348--2052395 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
2052338 TATATTTCTT
* *
2052348 TTTA TTTTA TTTT TTTA TTTT TTTA TTTCA TTTA TTTA -TTA TTTA TTT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTT
2052396 TCATTTTGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
3 3 0.08
4 26 0.70
5 8 0.22
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:2053657 original size:17 final size:18
Alignment explanation
Indices: 2053635--2053672 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2053625 TTTTTGTTAA
*
2053635 TTTCTTAATTTAAC-TTT
1 TTTCTTAATCTAACGTTT
*
2053652 TTTCTTCATCTAACGTTT
1 TTTCTTAATCTAACGTTT
2053670 TTT
1 TTT
2053673 ACTTTTTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.18, C:0.16, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTCTTAATCTAACGTTT
Found at i:2057303 original size:2 final size:2
Alignment explanation
Indices: 2057296--2057330 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2057286 TTTTGGTGAT
2057296 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2057331 TATGAATTAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2064306 original size:7 final size:7
Alignment explanation
Indices: 2064294--2064319 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2064284 ATTAGCTGAA
2064294 AATATTT
1 AATATTT
2064301 AATATTT
1 AATATTT
2064308 AATATTT
1 AATATTT
2064315 AATAT
1 AATAT
2064320 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AATATTT
Found at i:2066854 original size:13 final size:13
Alignment explanation
Indices: 2066836--2066860 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2066826 AGCTACGTTT
2066836 GTTTCTCTCTCTA
1 GTTTCTCTCTCTA
2066849 GTTTCTCTCTCT
1 GTTTCTCTCTCT
2066861 CTTTTTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.32, G:0.08, T:0.56
Consensus pattern (13 bp):
GTTTCTCTCTCTA
Found at i:2067896 original size:3 final size:3
Alignment explanation
Indices: 2067882--2067935 Score: 51
Period size: 3 Copynumber: 18.0 Consensus size: 3
2067872 CCATTCGTTT
*
2067882 TTA TTA TT- TTA TTA TTAA TTA TTA TTA TTTA TTA ATA TTAA TT- TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA -TTA TTA TTA TT-A TTA TTA
2067928 TTA -TA TTA
1 TTA TTA TTA
2067936 CAGGCCATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
2 6 0.14
3 28 0.65
4 9 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2067905 original size:10 final size:9
Alignment explanation
Indices: 2067882--2067935 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 9
2067872 CCATTCGTTT
2067882 TTATTATT-
1 TTATTATTA
2067890 TTATTATTAA
1 TTATTATT-A
2067900 TTATTATTA
1 TTATTATTA
*
2067909 TTTATTAATA
1 -TTATTATTA
2067919 TTAATT-TTA
1 TT-ATTATTA
2067928 TTA-TATTA
1 TTATTATTA
2067936 CAGGCCATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 1 0.03
8 12 0.31
9 7 0.18
10 19 0.49
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTATTATTA
Found at i:2068695 original size:21 final size:21
Alignment explanation
Indices: 2068669--2068708 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2068659 TGGTAAAATA
*
2068669 TATTTA-AATAAATAAATATTG
1 TATTTATAA-AAACAAATATTG
2068690 TATTTATAAAAACAAATAT
1 TATTTATAAAAACAAATAT
2068709 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (21 bp):
TATTTATAAAAACAAATATTG
Found at i:2069797 original size:17 final size:18
Alignment explanation
Indices: 2069775--2069809 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2069765 ATTTCTTTCA
2069775 ATTATTTTT-TATCCTTT
1 ATTATTTTTATATCCTTT
2069792 ATTATTTTTATATCCTTT
1 ATTATTTTTATATCCTTT
2069810 TTAGATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTATTTTTATATCCTTT
Found at i:2071325 original size:35 final size:34
Alignment explanation
Indices: 2071286--2071355 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 34
2071276 CGTTCACATA
*
2071286 TTTACATTTGTATTTGCATTTTGCATTTTTGCATT
1 TTTACATTTGTATTTACATTTT-CATTTTTGCATT
*
2071321 TTTACGTTTGTATTTACATTTTCATTTTTGCATT
1 TTTACATTTGTATTTACATTTTCATTTTTGCATT
2071355 T
1 T
2071356 GCATCTTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 13 0.39
35 20 0.61
ACGTcount: A:0.17, C:0.11, G:0.10, T:0.61
Consensus pattern (34 bp):
TTTACATTTGTATTTACATTTTCATTTTTGCATT
Found at i:2077562 original size:22 final size:22
Alignment explanation
Indices: 2077538--2077635 Score: 155
Period size: 22 Copynumber: 4.5 Consensus size: 22
2077528 GAAATATTTC
*
2077538 TTCAAAGATGATAGATTCTCTC
1 TTCAAAGATGATAGATTCTCTT
*
2077560 TTCAAAGATGAAAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2077582 TTCAAAGATGAT-GTATTCTCTT
1 TTCAAAGATGATAG-ATTCTCTT
2077604 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2077626 TTCAAA-ATGA
1 TTCAAAGATGA
2077636 AACTTTATTG
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
21 5 0.07
22 65 0.92
23 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:2079147 original size:3 final size:3
Alignment explanation
Indices: 2079133--2079205 Score: 87
Period size: 3 Copynumber: 24.0 Consensus size: 3
2079123 CTATTCGTTT
* *
2079133 TTA TTA TT- TTA TTA TTA TTAA TAA TTA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
2079178 TTTA TTA TTA TTA TTA TTAA TT- TTA TTA
1 -TTA TTA TTA TTA TTA TT-A TTA TTA TTA
2079206 AATTACATGT
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
2 4 0.07
3 49 0.80
4 8 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2079169 original size:22 final size:22
Alignment explanation
Indices: 2079141--2079198 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
2079131 TTTTATTATT
2079141 TTATTATTATTAATAATTAATA
1 TTATTATTATTAATAATTAATA
* * *
2079163 TTATTATTATTATTATTTATTA
1 TTATTATTATTAATAATTAATA
2079185 TTATTATTATTAAT
1 TTATTATTATTAAT
2079199 TTTATTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATTATTATTAATAATTAATA
Found at i:2079203 original size:25 final size:25
Alignment explanation
Indices: 2079134--2079206 Score: 96
Period size: 25 Copynumber: 3.0 Consensus size: 25
2079124 TATTCGTTTT
*
2079134 TATTATT-TTATTATTATTAATAAT
1 TATTATTATTATTATTATTATTAAT
* *
2079158 TAATATTATTATTATTATTATTTAT
1 TATTATTATTATTATTATTATTAAT
2079183 TATTATTATTATTAATT-TTATTAA
1 TATTATTATTATT-ATTATTATTAA
2079207 ATTACATGTC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
24 6 0.14
25 33 0.79
26 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TATTATTATTATTATTATTATTAAT
Found at i:2080478 original size:2 final size:2
Alignment explanation
Indices: 2080471--2080504 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2080461 TTTTAATTTG
2080471 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2080505 TCTTTTTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2080943 original size:21 final size:21
Alignment explanation
Indices: 2080919--2080958 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2080909 TTAAAAAAAA
*
2080919 TATTTA-AATAAATAAATATTG
1 TATTTATAA-AAACAAATATTG
2080940 TATTTATAAAAACAAATAT
1 TATTTATAAAAACAAATAT
2080959 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (21 bp):
TATTTATAAAAACAAATATTG
Found at i:2081185 original size:2 final size:2
Alignment explanation
Indices: 2081178--2081208 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2081168 ATGTATACAA
2081178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2081209 CTTTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2083549 original size:81 final size:82
Alignment explanation
Indices: 2083387--2083609 Score: 210
Period size: 81 Copynumber: 2.8 Consensus size: 82
2083377 TACGATCTGG
* * * * *
2083387 AATGTTAATATTTTTATTAATAAAATGAGTTACGCCCAAGAATGTCATTGTTCATTAAGAAATAG
1 AATGTTAATACTTTTATTAATAAAATGAGTTACACCCAAGAATATCATTGTTCACTAAGAAATAA
*** * *
2083452 GTTGTTATTTGTAATGT
66 GTTACAATATGAAATGT
* *
2083469 AATGTTAATACTTTT-TTAATAAAAT-ATGTTGCACCCAAGAATATCATTTTTCACTAAGAAATA
1 AATGTTAATACTTTTATTAATAAAATGA-GTTACACCCAAGAATATCATTGTTCACTAAGAAATA
2083532 AGTTACAATATG--A---
65 AGTTACAATATGAAATGT
* * * * * *
2083545 AATGTTAATATTTTTATTAATAAAATG-GATTTCGCTCAAGGATATCATAGTTCACTAAGAAATA
1 AATGTTAATACTTTTATTAATAAAATGAG-TTACACCCAAGAATATCATTGTTCACTAAGAAATA
2083609 A
65 A
2083610 ATTGTGGTCT
Statistics
Matches: 119, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
76 15 0.13
77 40 0.34
79 1 0.01
80 1 0.01
81 48 0.40
82 14 0.12
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (82 bp):
AATGTTAATACTTTTATTAATAAAATGAGTTACACCCAAGAATATCATTGTTCACTAAGAAATAA
GTTACAATATGAAATGT
Found at i:2083599 original size:77 final size:76
Alignment explanation
Indices: 2083363--2083647 Score: 263
Period size: 77 Copynumber: 3.7 Consensus size: 76
2083353 TTTACGATTT
* * *
2083363 ACTAAGAAATATGTTACGATCTGGAATGTTAATATTTTTATTAATAAAATGAGTTACGCCCAAGA
1 ACTAAGAAATAAGTTACGATATGGAATGTTAATATTTTTATTAATAAAATGA-TTTCGCCCAAGA
*
2083428 ATGTCATTGTTC
65 ATATCATTGTTC
* * * * * *
2083440 ATTAAGAAATAGGTTGTTATTTG-TAATGTAATGTTAATACTTTT-TTAATAAAAT-ATGTTGCA
1 ACTAAGAAATA---AGTTA--CGAT-ATGGAATGTTAATATTTTTATTAATAAAATGAT-TT-CG
*
2083502 CCCAAGAATATCATTTTTC
58 CCCAAGAATATCATTGTTC
* * * *
2083521 ACTAAGAAATAAGTTACAATATGAAATGTTAATATTTTTATTAATAAAATGGATTTCGCTCAAGG
1 ACTAAGAAATAAGTTACGATATGGAATGTTAATATTTTTATTAATAAAAT-GATTTCGCCCAAGA
*
2083586 ATATCATAGTTC
65 ATATCATTGTTC
* ** * *
2083598 ACTAAGAAATAAATTGTGGTCTGGAATGTTAATA-TTTTATTAATAAAATG
1 ACTAAGAAATAAGTTACGATATGGAATGTTAATATTTTTATTAATAAAATG
2083648 GATTGCCCAC
Statistics
Matches: 169, Mismatches: 27, Indels: 26
0.76 0.12 0.12
Matches are distributed among these distances:
75 1 0.01
76 32 0.19
77 64 0.38
78 6 0.04
79 3 0.02
80 7 0.04
81 39 0.23
82 17 0.10
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (76 bp):
ACTAAGAAATAAGTTACGATATGGAATGTTAATATTTTTATTAATAAAATGATTTCGCCCAAGAA
TATCATTGTTC
Found at i:2084654 original size:134 final size:136
Alignment explanation
Indices: 2084494--2084745 Score: 350
Period size: 135 Copynumber: 1.9 Consensus size: 136
2084484 AAAAAAATTG
* * * * * *
2084494 AATAGAACATGATATATTGAACTTTCAAATTTAAAAGTATCGATATTTTTAGAAAAGAATCGATA
1 AATAGAAAATGATATATTGAAATTTCAAATTTAAAAGTATCAATACTTTTAGAAAAGAATCAACA
* *
2084559 TTTTGC-AGC-TTCTCATTTGT-CATGTTTTTCTTTAAATTCAAAAGTATCGATACTGTCAAATT
66 CTTTACGA-CATTCTCATTT-TCCATGTTTTTCTTTAAATTCAAAAGTATCGATACTGTCAAATT
2084621 TTAAAAAA
129 TTAAAAAA
* * *
2084629 AATAGAAAATGATAT-TTTAAATTTCAAATTTAAAAGTATCAATACTTTTATAAAAGTATCAACA
1 AATAGAAAATGATATATTGAAATTTCAAATTTAAAAGTATCAATACTTTTAGAAAAGAATCAACA
*
2084693 CTTTACGACATTCTCATTTTCCATGTTTTTCTTTAAATTCGAAAGTATCGATA
66 CTTTACGACATTCTCATTTTCCATGTTTTTCTTTAAATTCAAAAGTATCGATA
2084746 TTTTTGAAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
134 47 0.46
135 55 0.54
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.40
Consensus pattern (136 bp):
AATAGAAAATGATATATTGAAATTTCAAATTTAAAAGTATCAATACTTTTAGAAAAGAATCAACA
CTTTACGACATTCTCATTTTCCATGTTTTTCTTTAAATTCAAAAGTATCGATACTGTCAAATTTT
AAAAAA
Found at i:2084684 original size:20 final size:20
Alignment explanation
Indices: 2084659--2084696 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2084649 ATTTCAAATT
*
2084659 TAAAAGTATCAATACTTTTA
1 TAAAAGTATCAACACTTTTA
2084679 TAAAAGTATCAACACTTT
1 TAAAAGTATCAACACTTT
2084697 ACGACATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (20 bp):
TAAAAGTATCAACACTTTTA
Found at i:2084953 original size:68 final size:68
Alignment explanation
Indices: 2084844--2085210 Score: 284
Period size: 77 Copynumber: 5.0 Consensus size: 68
2084834 AATATTTTTT
* * *
2084844 GACGCAACTCATTTTATTAATAAAAATATTAACATTGCATATCACAACCTATGTATTAGTGAACC
1 GACGCAACCCATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTATTAGTGAACC
2084909 ATG
66 ATG
* *
2084912 GACGCAACCCATTTTATTAATAAAAATACTAACATTCCATATCGCAACCTATTTATTAGTGAACA
1 GACGCAACCCATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTATTAGTGAAC-
2084977 ATGACATTATTG
65 ----C---A-TG
* * ** *
2084989 GACGCAACCCATTTTATTAATAAAAATATTAACATTCTAGATCGTAACCTATTTATTAGTGAACA
1 GACGCAACCCATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTATTAGTGAACC
2085054 ATG
66 ATG
* * * * * *
2085057 ATATTCTTAGGTGCAACCTATTTTATTAATAAAAATATTAAAATTCCATATCACAACTTGTTTCT
1 -GA--C------GCAACCCATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTAT
2085122 TAGTGAACCATG
57 TAGTGAACCATG
* * * ** * *
2085134 ACATTCTTGGAATCAATCCATTTTATTAATAAAAATATTAACATTCCAGATCACAATTTGTTTCT
1 -GA--C---G---CAACCCATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTAT
2085199 TAGTGAACCATG
57 TAGTGAACCATG
2085211 ACATGTTTAG
Statistics
Matches: 248, Mismatches: 30, Indels: 33
0.80 0.10 0.11
Matches are distributed among these distances:
68 61 0.25
69 2 0.01
71 1 0.00
73 1 0.00
74 1 0.00
76 1 0.00
77 181 0.73
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (68 bp):
GACGCAACCCATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTATTAGTGAACC
ATG
Found at i:2084969 original size:39 final size:38
Alignment explanation
Indices: 2084914--2085113 Score: 99
Period size: 40 Copynumber: 5.2 Consensus size: 38
2084904 GAACCATGGA
2084914 CGCAACCCATTTTATTAATAAAAATACTAACATTCCATAT
1 CGCAACCCATTTTATTAATAAAAATA-TAACATT-CATAT
* * * * *
2084954 CGCAACCTA-TTTATTAGTGAACA-ATGACATT-AT-T
1 CGCAACCCATTTTATTAATAAAAATATAACATTCATAT
*
2084988 GGACGCAACCCATTTTATTAATAAAAATATTAACATTCTAGAT
1 ---CGCAACCCATTTTATTAATAAAAATA-TAACATTC-ATAT
* * * * * * * *
2085031 CGTAACCTA-TTTATTAGTGAACA-ATGATATTCTTAGGT
1 CGCAACCCATTTTATTAATAAAAATATAACATTCATA--T
* *
2085069 -GCAACCTATTTTATTAATAAAAATATTAAAATTCCATAT
1 CGCAACCCATTTTATTAATAAAAATA-TAACATT-CATAT
*
2085108 CACAAC
1 CGCAAC
2085114 TTGTTTCTTA
Statistics
Matches: 116, Mismatches: 28, Indels: 32
0.66 0.16 0.18
Matches are distributed among these distances:
34 1 0.01
35 2 0.02
36 1 0.01
37 27 0.23
38 25 0.22
39 25 0.22
40 30 0.26
41 3 0.03
42 1 0.01
43 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.34
Consensus pattern (38 bp):
CGCAACCCATTTTATTAATAAAAATATAACATTCATAT
Found at i:2084995 original size:37 final size:37
Alignment explanation
Indices: 2084954--2085084 Score: 97
Period size: 37 Copynumber: 3.5 Consensus size: 37
2084944 CATTCCATAT
2084954 CGCAACCTA-TTTATTAGTGAACAATGACATTATTGGA
1 CGCAACCTATTTTATTAGTGAACAATGACATT-TTGGA
* * * * * * *
2084991 CGCAACCCATTTTATTAATAAAAATATTAACATTCTAGA
1 CGCAACCTATTTTATTAGTGAACA-A-TGACATTTTGGA
* *
2085030 TCGTAACCTA-TTTATTAGTGAACAATGATATTCTTAGG-
1 -CGCAACCTATTTTATTAGTGAACAATGACATT-TT-GGA
*
2085068 TGCAACCTATTTTATTA
1 CGCAACCTATTTTATTA
2085085 ATAAAAATAT
Statistics
Matches: 69, Mismatches: 18, Indels: 13
0.69 0.18 0.13
Matches are distributed among these distances:
37 20 0.29
38 20 0.29
39 16 0.23
40 13 0.19
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (37 bp):
CGCAACCTATTTTATTAGTGAACAATGACATTTTGGA
Found at i:2085038 original size:77 final size:77
Alignment explanation
Indices: 2084910--2085214 Score: 378
Period size: 77 Copynumber: 4.0 Consensus size: 77
2084900 TAGTGAACCA
* *
2084910 TGGACGCAACCCATTTTATTAATAAAAATACTAACATTCCATATCGCAACCTATTTATTAGTGAA
1 TGGACGCAACCCATTTTATTAATAAAAATATTAACATTCCAGATCGCAACCTATTTATTAGTGAA
*
2084975 CAATGACATTAT
66 CAATGACATTCT
* *
2084987 TGGACGCAACCCATTTTATTAATAAAAATATTAACATTCTAGATCGTAACCTATTTATTAGTGAA
1 TGGACGCAACCCATTTTATTAATAAAAATATTAACATTCCAGATCGCAACCTATTTATTAGTGAA
*
2085052 CAATGATATTCT
66 CAATGACATTCT
* * * * * * * *
2085064 TAGG-TGCAACCTATTTTATTAATAAAAATATTAAAATTCCATATCACAACTTGTTTCTTAGTGA
1 T-GGACGCAACCCATTTTATTAATAAAAATATTAACATTCCAGATCGCAACCTATTTATTAGTGA
*
2085128 ACCATGACATTCT
65 ACAATGACATTCT
** * * ** * *
2085141 TGGAATCAATCCATTTTATTAATAAAAATATTAACATTCCAGATCACAATTTGTTTCTTAGTGAA
1 TGGACGCAACCCATTTTATTAATAAAAATATTAACATTCCAGATCGCAACCTATTTATTAGTGAA
*
2085206 CCATGACAT
66 CAATGACAT
2085215 GTTTAGGTTT
Statistics
Matches: 201, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
76 2 0.01
77 197 0.98
78 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.36
Consensus pattern (77 bp):
TGGACGCAACCCATTTTATTAATAAAAATATTAACATTCCAGATCGCAACCTATTTATTAGTGAA
CAATGACATTCT
Found at i:2085206 original size:154 final size:154
Alignment explanation
Indices: 2084847--2085189 Score: 434
Period size: 154 Copynumber: 2.3 Consensus size: 154
2084837 ATTTTTTGAC
* * * * *
2084847 GCAACTCATTTTATTAATAAAAATATTAACATTGCATATCACAACCTATGTATTAGTGAACCATG
1 GCAACCCATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTATTAGTGAACAATG
* * *
2084912 -GA--C------GCAACCCATTTTATTAATAAAAATACTAACATTCCATATCGCAACCTATTTAT
66 ATATTCTTAGGTGCAACCCATTTTATTAATAAAAATACTAAAATTCCATATCACAACCTATTTAT
*
2084968 TAGTGAACAATGACATTATTGGAC
131 TAGTGAACAATGACATTATTGGAA
* **
2084992 GCAACCCATTTTATTAATAAAAATATTAACATTCTAGATCGTAACCTATTTATTAGTGAACAATG
1 GCAACCCATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTATTAGTGAACAATG
* * * * *
2085057 ATATTCTTAGGTGCAACCTATTTTATTAATAAAAATATTAAAATTCCATATCACAACTTGTTTCT
66 ATATTCTTAGGTGCAACCCATTTTATTAATAAAAATACTAAAATTCCATATCACAACCTATTTAT
* *
2085122 TAGTGAACCATGACATTCTTGGAA
131 TAGTGAACAATGACATTATTGGAA
* *
2085146 TCAATCCATTTTATTAATAAAAATATTAACATTCCAGATCACAA
1 GCAACCCATTTTATTAATAAAAATATTAACATTCCAGATCACAA
2085190 TTTGTTTCTT
Statistics
Matches: 165, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
145 57 0.35
146 1 0.01
148 1 0.01
154 106 0.64
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (154 bp):
GCAACCCATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTATTAGTGAACAATG
ATATTCTTAGGTGCAACCCATTTTATTAATAAAAATACTAAAATTCCATATCACAACCTATTTAT
TAGTGAACAATGACATTATTGGAA
Found at i:2085377 original size:19 final size:20
Alignment explanation
Indices: 2085353--2085391 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
2085343 ATTAATAATA
2085353 TTTATTGTTTATAAC-TTTT
1 TTTATTGTTTATAACATTTT
2085372 TTTATTGTTTATAACATTTT
1 TTTATTGTTTATAACATTTT
2085392 AGGTGTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTATTGTTTATAACATTTT
Found at i:2094146 original size:18 final size:18
Alignment explanation
Indices: 2094123--2094165 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2094113 CTTTAGATTA
*
2094123 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
* *
2094141 TTTATTTATTTCTTATCT
1 TTTATTTAATTATTATCT
2094159 TTTATTT
1 TTTATTT
2094166 TAGAAACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:2094230 original size:22 final size:22
Alignment explanation
Indices: 2094212--2094255 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2094202 TACTATTATT
* *
2094212 TATTATTTTATCTTTTATTTTA
1 TATTATTATACCTTTTATTTTA
*
2094234 TTTTATTATACCTTTTATTTTA
1 TATTATTATACCTTTTATTTTA
2094256 CCTTTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTATTATACCTTTTATTTTA
Found at i:2094266 original size:17 final size:17
Alignment explanation
Indices: 2094207--2094283 Score: 54
Period size: 17 Copynumber: 4.4 Consensus size: 17
2094197 TTTATTACTA
*
2094207 TTATTTATTATTTTATCT
1 TTATTT-TTATTTTACCT
2094225 TT-TATTTTATTTTA--T
1 TTAT-TTTTATTTTACCT
*
2094240 TATACCTTTTATTTTACCT
1 T-TA-TTTTTATTTTACCT
2094259 TTATTTTTATCTTT-CCT
1 TTATTTTTAT-TTTACCT
2094276 TGTATTTT
1 T-TATTTT
2094284 CTTTAAAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
15 2 0.04
16 1 0.02
17 29 0.59
18 15 0.31
19 2 0.04
ACGTcount: A:0.18, C:0.10, G:0.01, T:0.70
Consensus pattern (17 bp):
TTATTTTTATTTTACCT
Found at i:2094267 original size:12 final size:12
Alignment explanation
Indices: 2094214--2094265 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
2094204 CTATTATTTA
*
2094214 TTATTTTATCTT
1 TTATTTTACCTT
2094226 TTATTTTA--TT
1 TTATTTTACCTT
*
2094236 TTATTATACCTT
1 TTATTTTACCTT
2094248 TTATTTTACC-T
1 TTATTTTACCTT
2094259 TTATTTT
1 TTATTTT
2094266 TATCTTTCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
10 9 0.25
11 8 0.22
12 19 0.53
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTTTACCTT
Found at i:2094272 original size:12 final size:12
Alignment explanation
Indices: 2094214--2094272 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
2094204 CTATTATTTA
2094214 TTATTTTATCTT
1 TTATTTTATCTT
2094226 TTATTTTA--TT
1 TTATTTTATCTT
* *
2094236 TTATTATACCTT
1 TTATTTTATCTT
*
2094248 TTATTTTA-CCT
1 TTATTTTATCTT
2094259 TTATTTTTATCTT
1 TTA-TTTTATCTT
2094272 T
1 T
2094273 CCTTGTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 9 0.23
11 5 0.13
12 22 0.56
13 3 0.08
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTTTATCTT
Found at i:2094364 original size:16 final size:16
Alignment explanation
Indices: 2094305--2094411 Score: 58
Period size: 16 Copynumber: 6.2 Consensus size: 16
2094295 AACAGTTCTT
2094305 TTTTTAATTTTATTTT-
1 TTTTT-ATTTTATTTTA
*
2094321 GTTTTATCTTTATTTTCCCA
1 TTTTTAT-TTTATTTT---A
2094341 CTTCTTTATTTTATTTTA
1 -TT-TTTATTTTATTTTA
*
2094359 TTTTTATTATTATTTTC
1 TTTTTATT-TTATTTTA
***
2094376 TGTTTTAACAT-TTTTA
1 T-TTTTATTTTATTTTA
2094392 TATTTTATTTT-TTTTA
1 T-TTTTATTTTATTTTA
2094408 TTTT
1 TTTT
2094412 ATGAAATTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
15 5 0.07
16 35 0.49
17 11 0.15
18 6 0.08
21 9 0.13
22 5 0.07
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTTATTTTATTTTA
Found at i:2094480 original size:16 final size:15
Alignment explanation
Indices: 2094442--2094478 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
2094432 CATTTATTTT
*
2094442 ATTTTTTATTTTAAC
1 ATTTTTTATATTAAC
2094457 ATTTTTTATATTAAC
1 ATTTTTTATATTAAC
2094472 ATTTTTT
1 ATTTTTT
2094479 TAAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTTTATATTAAC
Found at i:2094542 original size:34 final size:34
Alignment explanation
Indices: 2094474--2094539 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
2094464 ATATTAACAT
*
2094474 TTTTTTAAAATTTAATATTTCCTTCTTTGATTTA
1 TTTTTTAAAATTTAATATTTACTTCTTTGATTTA
* * *
2094508 TTTTTTAAAA-TTAATTTTTATTTCTTTTATTT
1 TTTTTTAAAATTTAATATTTACTTCTTTGATTT
2094540 TATAATCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.67
Consensus pattern (34 bp):
TTTTTTAAAATTTAATATTTACTTCTTTGATTTA
Found at i:2095693 original size:21 final size:22
Alignment explanation
Indices: 2095618--2095694 Score: 90
Period size: 21 Copynumber: 3.6 Consensus size: 22
2095608 TGATGCATGG
* *
2095618 GGTATCGATACAATTAT-GAACA
1 GGTATCGATACCA-TATGGAAGA
2095640 -GTATCGATACCATATGGAAGA
1 GGTATCGATACCATATGGAAGA
2095661 GGTATCGATACCTATATGG-AG-
1 GGTATCGATACC-ATATGGAAGA
2095682 GGTATCGATACCA
1 GGTATCGATACCA
2095695 GGGAACATCG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
20 4 0.08
21 27 0.54
22 13 0.26
23 6 0.12
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (22 bp):
GGTATCGATACCATATGGAAGA
Found at i:2096159 original size:18 final size:19
Alignment explanation
Indices: 2096119--2096161 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
2096109 ATGATATGTA
**
2096119 TTATATGTTATGTGATATG
1 TTATATGTTATGACATATG
2096138 -TATATGTTAT-ACATATG
1 TTATATGTTATGACATATG
2096155 TTATATG
1 TTATATG
2096162 ATGATGATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.51
Consensus pattern (19 bp):
TTATATGTTATGACATATG
Found at i:2096527 original size:23 final size:24
Alignment explanation
Indices: 2096496--2096541 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2096486 TGTTATATGT
* *
2096496 GGTCCTTCGGGA-CATTTCTACGC
1 GGTCATTCGGGATAATTTCTACGC
2096519 GGTCATTCGGGATAATTTCTACG
1 GGTCATTCGGGATAATTTCTACG
2096542 TGCCCCTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (24 bp):
GGTCATTCGGGATAATTTCTACGC
Found at i:2099646 original size:22 final size:22
Alignment explanation
Indices: 2099615--2099669 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
2099605 TGTATAAATA
2099615 GTATCGATACCATATG-GAAGAG
1 GTATCGATACCATATGTGAAG-G
* *
2099637 GTATCAATACC-TATGTGGAGG
1 GTATCGATACCATATGTGAAGG
2099658 GTATCGATACCA
1 GTATCGATACCA
2099670 GGGAACATCG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (22 bp):
GTATCGATACCATATGTGAAGG
Found at i:2100549 original size:23 final size:24
Alignment explanation
Indices: 2100523--2100569 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
2100513 TGTGTTATAT
*
2100523 GTGGTCTTTCGGGAT-ATTTCTAC
1 GTGGTCCTTCGGGATAATTTCTAC
2100546 GTGGTCCTTCGGGATAATTTCTAC
1 GTGGTCCTTCGGGATAATTTCTAC
2100570 TTTCCCCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.15, C:0.19, G:0.26, T:0.40
Consensus pattern (24 bp):
GTGGTCCTTCGGGATAATTTCTAC
Found at i:2100828 original size:12 final size:12
Alignment explanation
Indices: 2100811--2100842 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2100801 TATGGTTGCT
2100811 AATAATGATAAG
1 AATAATGATAAG
*
2100823 AATAATAATAAG
1 AATAATGATAAG
2100835 AATAATGA
1 AATAATGA
2100843 AATGATATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (12 bp):
AATAATGATAAG
Found at i:2105053 original size:86 final size:86
Alignment explanation
Indices: 2104847--2105041 Score: 311
Period size: 86 Copynumber: 2.3 Consensus size: 86
2104837 AAGAACATCT
* *
2104847 CACATGACTTTCCCGTGAAGAGG-GTCATCCAAATATCATCTCACCTGGTTCAAATCCGCGAAGG
1 CACATGACTTTCCCGTGAAGAGGAGTCATCCAAAGATCATCTCACCTGGTTCAAACCCGCGAAGG
*
2104911 GGAACCACCTGAAGAATATAC
66 GGAACCACCTAAAGAATATAC
* * *
2104932 CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCATCTGGTTCAGACCCGCGAAGG
1 CACATGACTTTCCCGTGAAGAGGAGTCATCCAAAGATCATCTCACCTGGTTCAAACCCGCGAAGG
2104997 GGAACCACCTAAAGAATATAC
66 GGAACCACCTAAAGAATATAC
* *
2105018 CACTTGGCTTTCCCGTGAAGAGGA
1 CACATGACTTTCCCGTGAAGAGGA
2105042 ATCAACTAAA
Statistics
Matches: 100, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
85 22 0.22
86 78 0.78
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (86 bp):
CACATGACTTTCCCGTGAAGAGGAGTCATCCAAAGATCATCTCACCTGGTTCAAACCCGCGAAGG
GGAACCACCTAAAGAATATAC
Found at i:2105849 original size:200 final size:200
Alignment explanation
Indices: 2105472--2105982 Score: 727
Period size: 200 Copynumber: 2.5 Consensus size: 200
2105462 CCAGCAAATC
* * * *
2105472 TACAATATAGCTCAAGGCGAGAAGAGCTATTTGT-AACAAAACTTTCAAGTTCGATTCCATTCAC
1 TACAACATAGCTCAAGGCGAGAAGGGCTATATGTCAACAAAACTTTTAAGTTCGATTCCATTCAC
* * * * *
2105536 CTCGAATGCATATTAATCGCATGGTAGCATCGAGGAACTACTTTCCGGTTAAAGTTTAAACCGAG
66 CTCGAAGGCATATCAACCGCATGGTAGCATCGAAGAACTATTTTCCGGTTAAAGTTTAAACCGAG
*
2105601 GTCTTTAAGTCGAGAAGAAGACATAGGTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAACC
131 ATCTTTAAGTCGAGAAGAAGACATAGGTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAACC
*
2105666 GAGTG
196 GAATG
*
2105671 TACAACATAGCTCAAGGCGAGAAGGGCTATATGTCAACAAAACTTTTAAGTTCGATTCCATTCAG
1 TACAACATAGCTCAAGGCGAGAAGGGCTATATGTCAACAAAACTTTTAAGTTCGATTCCATTCAC
* * * *
2105736 CTCAAAGGCATATCAACCGCATGGTAGCAACGAAGAACTATTTTCCTGTTGAAGTTTAAACCGAG
66 CTCGAAGGCATATCAACCGCATGGTAGCATCGAAGAACTATTTTCCGGTTAAAGTTTAAACCGAG
* *
2105801 ATCTTTAAGTCGAGAAGAAGACATAGGTTGGCTGCGATTTAGCAACAAGGAACTATCTCCTAGCC
131 ATCTTTAAGTCGAGAAGAAGACATAGGTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAACC
*
2105866 GAATT
196 GAATG
* * * * * * *
2105871 TACAACATAGTTCAAGGAGAGAAGGGTTATCTGTCAACAAAAACCTTTGAGTTCGATTTCATTCA
1 TACAACATAGCTCAAGGCGAGAAGGGCTATATGTCAAC-AAAACTTTTAAGTTCGATTCCATTCA
* ** *
2105936 CCTCGAGGGCATATCAACCATATGGTAGCATCGATGAACTACTTTTC
65 CCTCGAAGGCATATCAACCGCATGGTAGCATCGAAGAACTA-TTTTC
2105983 GATTGAATTT
Statistics
Matches: 276, Mismatches: 33, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
199 31 0.11
200 183 0.66
201 57 0.21
202 5 0.02
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (200 bp):
TACAACATAGCTCAAGGCGAGAAGGGCTATATGTCAACAAAACTTTTAAGTTCGATTCCATTCAC
CTCGAAGGCATATCAACCGCATGGTAGCATCGAAGAACTATTTTCCGGTTAAAGTTTAAACCGAG
ATCTTTAAGTCGAGAAGAAGACATAGGTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAACC
GAATG
Found at i:2107001 original size:12 final size:12
Alignment explanation
Indices: 2106967--2107027 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
2106957 AAAAACCTCT
2106967 TTTA-TATTTATA
1 TTTATTATTT-TA
2106979 TTTATTA--TTA
1 TTTATTATTTTA
2106989 TTTATTATTTTA
1 TTTATTATTTTA
2107001 TCTT-TTATTTTA
1 T-TTATTATTTTA
*
2107013 -TTATACATTTTA
1 TTTAT-TATTTTA
2107025 TTT
1 TTT
2107028 TAACTTTATT
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
10 11 0.27
11 2 0.05
12 22 0.54
13 6 0.15
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:2107013 original size:17 final size:17
Alignment explanation
Indices: 2106964--2107029 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 17
2106954 TTTAAAAACC
2106964 TCTTTTATATTTATATTTA
1 TCTTTTAT-TTTAT-TTTA
*
2106983 T-TATTATTTATTATTTTA
1 TCTTTTA-TT-TTATTTTA
*
2107001 TCTTTTATTTTATTATA
1 TCTTTTATTTTATTTTA
2107018 -CATTTTATTTTA
1 TC-TTTTATTTTA
2107030 ACTTTATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
16 1 0.03
17 17 0.43
18 12 0.30
19 10 0.25
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (17 bp):
TCTTTTATTTTATTTTA
Found at i:2107100 original size:16 final size:16
Alignment explanation
Indices: 2107079--2107109 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2107069 AACATTTCTT
2107079 TTTTATCTTTATTTTG
1 TTTTATCTTTATTTTG
2107095 TTTTATCTTTATTTT
1 TTTTATCTTTATTTT
2107110 CCCACTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATCTTTATTTTG
Found at i:2107226 original size:51 final size:50
Alignment explanation
Indices: 2107162--2107275 Score: 126
Period size: 51 Copynumber: 2.2 Consensus size: 50
2107152 CTTTTATCAT
* * * *
2107162 TTTTATATTTTATTTT-TTTTCTTTTCTGAAATTTAATATTTTCTTCATTT-A
1 TTTTATTTTTTATTTTAATTT-TTTTAT-AAATTTAATATTTCCTTC-TTTGA
2107213 TTTTATTTTTTATTTTAACATTTTTTTATAAATTTAATATTTCCTTCTTTGA
1 TTTTATTTTTTATTTT-A-ATTTTTTTATAAATTTAATATTTCCTTCTTTGA
2107265 -TTTATTTTTTA
1 TTTTATTTTTTA
2107276 AAATTTAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
51 29 0.53
52 18 0.33
53 5 0.09
54 3 0.05
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (50 bp):
TTTTATTTTTTATTTTAATTTTTTTATAAATTTAATATTTCCTTCTTTGA
Found at i:2111864 original size:30 final size:30
Alignment explanation
Indices: 2111799--2111856 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
2111789 CTTGCATTCG
2111799 CCCGCCTTGCATCTGTCCACCCCACATCCT
1 CCCGCCTTGCATCTGTCCACCCCACATCCT
* *
2111829 CCCGCCTTGCATCTGTTCGCCCCACATC
1 CCCGCCTTGCATCTGTCCACCCCACATC
2111857 AGTCCGCCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.12, C:0.52, G:0.12, T:0.24
Consensus pattern (30 bp):
CCCGCCTTGCATCTGTCCACCCCACATCCT
Found at i:2113208 original size:25 final size:22
Alignment explanation
Indices: 2113172--2113221 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 22
2113162 TTGTCACATC
2113172 ATATTTTCTAAAAGTATATTAAAAA
1 ATATTTTCTAAAA--A-ATTAAAAA
2113197 ATATGTTT-TAAAAAATTAAAAA
1 ATAT-TTTCTAAAAAATTAAAAA
2113219 ATA
1 ATA
2113222 AAACAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 11 0.46
23 1 0.04
25 9 0.38
26 3 0.12
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (22 bp):
ATATTTTCTAAAAAATTAAAAA
Found at i:2118834 original size:2 final size:2
Alignment explanation
Indices: 2118829--2118857 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2118819 TCTCTCTCTC
2118829 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2118858 CTGTGAGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2120774 original size:41 final size:41
Alignment explanation
Indices: 2120729--2120809 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
2120719 CTATCGCAAA
*
2120729 TTCGCGTTGCGATAAT-TGAAAATCG-CGTTGCGATTTTCCAT
1 TTCGCATTGCGATAATCT-AAAAT-GTCGTTGCGATTTTCCAT
* *
2120770 TTCGCATTGCGATAGTCTACAATGTCGTTGCGATTTTCCA
1 TTCGCATTGCGATAATCTAAAATGTCGTTGCGATTTTCCA
2120810 AATTCGTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 1 0.03
41 33 0.94
42 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (41 bp):
TTCGCATTGCGATAATCTAAAATGTCGTTGCGATTTTCCAT
Found at i:2120818 original size:19 final size:19
Alignment explanation
Indices: 2120754--2120822 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
2120744 TTGAAAATCG
*
2120754 CGTTGCGATTTTCC-ATTT
1 CGTTGCGATTTTCCAAATT
** *
2120772 CGCATTGCGATAGTCTACAATGT
1 CG--TTGCGATTTTCCA-AAT-T
2120795 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
2120814 CGTTGCGAT
1 CGTTGCGAT
2120823 AGTCTACAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
18 2 0.05
19 10 0.26
20 12 0.31
21 10 0.26
22 2 0.05
23 3 0.08
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:2120842 original size:22 final size:22
Alignment explanation
Indices: 2120776--2120866 Score: 82
Period size: 22 Copynumber: 4.3 Consensus size: 22
2120766 CCATTTCGCA
*
2120776 TTGCGATAGTCTACA-ATGTCG
1 TTGCGATAGTCTACAGTTGTCG
* * **
2120797 TTGCGAT--TTTCCAAAT-TCG
1 TTGCGATAGTCTACAGTTGTCG
*
2120816 TTGCGATAGTCTACAGTTGTTG
1 TTGCGATAGTCTACAGTTGTCG
*
2120838 TTGCGAAAGTCTACAGTTGTCG
1 TTGCGATAGTCTACAGTTGTCG
*
2120860 TTACGAT
1 TTGCGAT
2120867 TTTCCAAATT
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
19 14 0.25
20 2 0.04
21 12 0.22
22 27 0.49
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (22 bp):
TTGCGATAGTCTACAGTTGTCG
Found at i:2120843 original size:41 final size:40
Alignment explanation
Indices: 2120754--2120830 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
2120744 TTGAAAATCG
*
2120754 CGTTGCGATTTTCCATTTCGCATTGCGATAGTCTACAATGT
1 CGTTGCGATTTTCCAATTCG-ATTGCGATAGTCTACAATGT
2120795 CGTTGCGATTTTCCAAATTCG-TTGCGATAGTCTACA
1 CGTTGCGATTTTCC-AATTCGATTGCGATAGTCTACA
2120831 GTTGTTGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
40 15 0.44
41 14 0.41
42 5 0.15
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTTCCAATTCGATTGCGATAGTCTACAATGT
Found at i:2120974 original size:6 final size:6
Alignment explanation
Indices: 2120965--2121009 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
2120955 AGACACGTAT
* *
2120965 TACCAT TACCA- TACCAT TACCA- TACCAG TACCAG TACCAG TACCA
1 TACCAG TACCAG TACCAG TACCAG TACCAG TACCAG TACCAG TACCA
2121010 CGACCACGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.36, C:0.36, G:0.07, T:0.22
Consensus pattern (6 bp):
TACCAG
Found at i:2120981 original size:11 final size:11
Alignment explanation
Indices: 2120965--2121009 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
2120955 AGACACGTAT
*
2120965 TACCATTACCA
1 TACCAGTACCA
*
2120976 TACCATTACCA
1 TACCAGTACCA
2120987 TACCAGTACCA
1 TACCAGTACCA
2120998 GTACCAGTACCA
1 -TACCAGTACCA
2121010 CGACCACGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.36, C:0.36, G:0.07, T:0.22
Consensus pattern (11 bp):
TACCAGTACCA
Done.