Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008512.1 Hibiscus syriacus cultivar Beakdansim tig00111372_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: 1759229
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1450222 original size:20 final size:20
Alignment explanation
Indices: 1450193--1450243 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1450183 TTTTCCAGAT
*
1450193 ATTTTTCAGAAATGTAATTC
1 ATTTTCCAGAAATGTAATTC
1450213 ATTTTCCAGAAATGTAATTC
1 ATTTTCCAGAAATGTAATTC
1450233 ATTTTCCAGAA
1 ATTTTCCAGAA
1450244 TTCAAATTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (20 bp):
ATTTTCCAGAAATGTAATTC
Found at i:1450251 original size:20 final size:20
Alignment explanation
Indices: 1450193--1450252 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1450183 TTTTCCAGAT
* **
1450193 ATTTTTCAGAAATGTAATTC
1 ATTTTCCAGAAATCAAATTC
**
1450213 ATTTTCCAGAAATGTAATTC
1 ATTTTCCAGAAATCAAATTC
*
1450233 ATTTTCCAGAATTCAAATTC
1 ATTTTCCAGAAATCAAATTC
1450253 CAGTAATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (20 bp):
ATTTTCCAGAAATCAAATTC
Found at i:1450262 original size:15 final size:15
Alignment explanation
Indices: 1450226--1450292 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
1450216 TTCCAGAAAT
**
1450226 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
1450241 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
** *
1450255 GTAATTCATTTTTCA
1 GTAATTCAAATTCCA
*
1450270 GTAATTCAAATTTCA
1 GTAATTCAAATTCCA
1450285 GTAATTCA
1 GTAATTCA
1450293 TTTTCCGAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
14 12 0.27
15 32 0.73
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.42
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:1450276 original size:30 final size:29
Alignment explanation
Indices: 1450226--1450298 Score: 119
Period size: 30 Copynumber: 2.5 Consensus size: 29
1450216 TTCCAGAAAT
1450226 GTAATTCATTTTCCAGAATTCAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
* *
1450255 GTAATTCATTTTTCAGTAATTCAAATTTCA
1 GTAATTCATTTTCCAG-AATTCAAATTCCA
1450285 GTAATTCATTTTCC
1 GTAATTCATTTTCC
1450299 GAAAAACCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.44
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTCCA
Found at i:1453268 original size:149 final size:149
Alignment explanation
Indices: 1453091--1453459 Score: 562
Period size: 149 Copynumber: 2.5 Consensus size: 149
1453081 CCACTGACTC
* *
1453091 TTGTCTGTCCACCTTCAGAATCCAATTGCTTCTTATCCTTCTTAGACTCATCCGACTCACTTTCT
1 TTGTCTGTCCA-CTTCAGAATCCAATTGCTTCTTATCCTTCTTAGACTCATCCGACTTACTCTCT
*
1453156 TCAGTTTCTGGTGTGTTTAAGTTGCCAGTACCACCATCTTTAGCCCCACTAGCATCCTTGGGTAA
65 TCAGTTTCTGGTGTGTTTAAGTTGCCAGTACCACCATCTTTAGCCCCACTAGCATCCTTGGGAAA
* *
1453221 ATTCTCACCGCTGTTGTTG-
130 ATTCTCACCACTATTGTTGT
* * *
1453240 TTGTCTGTCCACTTTCAGAATCCAATTGCTTCCTATCCTTCTTAAACTCA-CCTGAATTACTCTC
1 TTGTCTGTCCAC-TTCAGAATCCAATTGCTTCTTATCCTTCTTAGACTCATCC-GACTTACTCTC
* *
1453304 TTCAGTTTCTGGTGTGTTTAAGTTTCCAGTACCGCCATCTTTAGCCCCACTAGCATCCTTGGGAA
64 TTCAGTTTCTGGTGTGTTTAAGTTGCCAGTACCACCATCTTTAGCCCCACTAGCATCCTTGGGAA
1453369 AATTCTCACCACTATTGTTGT
129 AATTCTCACCACTATTGTTGT
* * * *
1453390 TTGTCCGTTCAACTTCAGAATCCAATTGCTTCTTATCCTTCTCAGACTCATCCAACTTACTCTCT
1 TTGTCTG-TCCACTTCAGAATCCAATTGCTTCTTATCCTTCTTAGACTCATCCGACTTACTCTCT
1453455 TCAGT
65 TCAGT
1453460 ATTCCCATTG
Statistics
Matches: 198, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
148 3 0.02
149 134 0.68
150 55 0.28
151 6 0.03
ACGTcount: A:0.20, C:0.29, G:0.13, T:0.38
Consensus pattern (149 bp):
TTGTCTGTCCACTTCAGAATCCAATTGCTTCTTATCCTTCTTAGACTCATCCGACTTACTCTCTT
CAGTTTCTGGTGTGTTTAAGTTGCCAGTACCACCATCTTTAGCCCCACTAGCATCCTTGGGAAAA
TTCTCACCACTATTGTTGT
Found at i:1459403 original size:21 final size:21
Alignment explanation
Indices: 1459377--1459418 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1459367 AAAAAAAACG
*
1459377 GATCCGGATATTT-GGATATCC
1 GATCC-GAAATTTCGGATATCC
1459398 GATCCGAAATTTCGGATATCC
1 GATCCGAAATTTCGGATATCC
1459419 AATTTTTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (21 bp):
GATCCGAAATTTCGGATATCC
Found at i:1463632 original size:20 final size:20
Alignment explanation
Indices: 1463591--1463638 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1463581 AATGATTTTC
***
1463591 TTTTG-AAAGCAAAATTGGA
1 TTTTGAAAAGCAAAATAAAA
1463610 TTTTGAAAAGCAAAATAAAA
1 TTTTGAAAAGCAAAATAAAA
1463630 TTTTGAAAA
1 TTTTGAAAA
1463639 ATGATTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAGCAAAATAAAA
Found at i:1466701 original size:2 final size:2
Alignment explanation
Indices: 1466694--1466743 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1466684 TTTATACTCG
1466694 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1466736 AT AT AT AT
1 AT AT AT AT
1466744 CTCAACGTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1469347 original size:22 final size:21
Alignment explanation
Indices: 1469322--1469372 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
1469312 ACCCTCATCA
*
1469322 TTATTTTTCATATATTTATTTT
1 TTATTTTTCATAT-TTTATTTG
* *
1469344 TTATTTTGCTTATTTTATTTG
1 TTATTTTTCATATTTTATTTG
1469365 TT-TTTTTC
1 TTATTTTTC
1469373 TTTTCTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 5 0.20
21 9 0.36
22 11 0.44
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.75
Consensus pattern (21 bp):
TTATTTTTCATATTTTATTTG
Found at i:1469388 original size:14 final size:13
Alignment explanation
Indices: 1469365--1469395 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
1469355 ATTTTATTTG
1469365 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
1469378 TTTTATTTCTTTTC
1 TTTT-TTTCTTTTC
1469392 TTTT
1 TTTT
1469396 CTTATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:1469438 original size:17 final size:17
Alignment explanation
Indices: 1469397--1469438 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
1469387 TTTTCTTTTC
1469397 TTATTTTATTTTATATA
1 TTATTTTATTTTATATA
1469414 TTAGTTTTA-TTTATATA
1 TTA-TTTTATTTTATATA
1469431 TTTATTTT
1 -TTATTTT
1469439 CATTGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATTTTATTTTATATA
Found at i:1469539 original size:9 final size:9
Alignment explanation
Indices: 1469524--1469697 Score: 66
Period size: 9 Copynumber: 19.6 Consensus size: 9
1469514 GCTCGTTATC
1469524 TTTATTTTGA
1 TTTATTTT-A
1469534 -TTATTTTA
1 TTTATTTTA
1469542 TTTATTTT-
1 TTTATTTTA
*
1469550 TCTTAATTT-
1 T-TTATTTTA
*
1469559 TTTA-TTTC
1 TTTATTTTA
*
1469567 TTT-TGTT-
1 TTTATTTTA
* *
1469574 TTTATGTTC
1 TTTATTTTA
1469583 TTTATTTTA
1 TTTATTTTA
1469592 TTTTATTTT-
1 -TTTATTTTA
1469601 TTTATCTTTA
1 TTTAT-TTTA
1469611 TTT-TATTT-
1 TTTAT-TTTA
*
1469619 TTTATGTCT-
1 TTTAT-TTTA
1469628 TTT-TTTTA
1 TTTATTTTA
*
1469636 TCTTATTTTCC
1 T-TTATTTT-A
*
1469647 TTT-TTTTC
1 TTTATTTTA
1469655 TTTATTTTTA
1 TTTA-TTTTA
**
1469665 TTTCCTTTA
1 TTTATTTTA
*
1469674 TTTTATTTTT
1 -TTTATTTTA
*
1469684 TTTAGTTTA
1 TTTATTTTA
1469693 TTTAT
1 TTTAT
1469698 CTTCATTGCC
Statistics
Matches: 129, Mismatches: 18, Indels: 35
0.71 0.10 0.19
Matches are distributed among these distances:
7 8 0.06
8 28 0.22
9 62 0.48
10 30 0.23
11 1 0.01
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1469544 original size:5 final size:5
Alignment explanation
Indices: 1469534--1469695 Score: 58
Period size: 5 Copynumber: 33.2 Consensus size: 5
1469524 TTTATTTTGA
* * * * *
1469534 TTATT TTA-T TTATT TT-TCT TAATT TTTTAT TTCTT TTGTTT TTATG
1 TTATT TTATT TTATT TTAT-T TTATT TTAT-T TTATT TT-ATT TTATT
* *
1469580 TTCTT T-ATT TTATT TTA-T TT-TT TTATCT TTATT TTATT TT-TT ATGTCTT
1 TTATT TTATT TTATT TTATT TTATT TTAT-T TTATT TTATT TTATT -T-TATT
* ** * **
1469629 TT-TT TTATC TTATT TTCCT TT-TT TT-CT TTATT TT-TAT TTCCT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTAT-T TTATT TTATT
*
1469676 TTATT TT-TT TTAGT TTATT T
1 TTATT TTATT TTATT TTATT T
1469696 ATCTTCATTG
Statistics
Matches: 118, Mismatches: 22, Indels: 34
0.68 0.13 0.20
Matches are distributed among these distances:
4 31 0.26
5 69 0.58
6 16 0.14
7 2 0.02
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:1469588 original size:59 final size:58
Alignment explanation
Indices: 1469522--1469634 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 58
1469512 CTGCTCGTTA
*
1469522 TCTTTATTTTGA-TTATTTTATTTAT-TTT-TCTTAATTTTTTATTTCTTTTGTTTTTATGT
1 TCTTTATTTT-ATTTATTTT-TTTATCTTTAT-TTAATTTTTTATGTCTTTT-TTTTTATGT
*
1469581 TCTTTATTTTATTTTATTTTTTTATCTTTATTTTATTTTTTATGTCTTTTTTTT
1 TCTTTATTTTA-TTTATTTTTTTATCTTTATTTAATTTTTTATGTCTTTTTTTT
1469635 ATCTTATTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
58 1 0.02
59 19 0.40
60 27 0.56
61 1 0.02
ACGTcount: A:0.14, C:0.05, G:0.04, T:0.77
Consensus pattern (58 bp):
TCTTTATTTTATTTATTTTTTTATCTTTATTTAATTTTTTATGTCTTTTTTTTTATGT
Found at i:1469610 original size:6 final size:5
Alignment explanation
Indices: 1469583--1469695 Score: 62
Period size: 5 Copynumber: 23.4 Consensus size: 5
1469573 TTTTATGTTC
*
1469583 TTTAT TTTAT TTTA- TTT-T TTTAT CTTTAT TTTAT TTT-T TATGTCT
1 TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT TTTAT TTTAT T-T-TAT
* ** * **
1469628 TTT-T TTTAT CTTAT TTTCC TTT-T TTT-C TTTAT TTT-T ATTTCC TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT TTTAT
*
1469675 TTTAT TTT-T TTTAG TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TT
1469696 ATCTTCATTG
Statistics
Matches: 85, Mismatches: 12, Indels: 22
0.71 0.10 0.18
Matches are distributed among these distances:
4 23 0.27
5 53 0.62
6 7 0.08
7 2 0.02
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:1469632 original size:18 final size:19
Alignment explanation
Indices: 1469573--1469685 Score: 86
Period size: 19 Copynumber: 5.6 Consensus size: 19
1469563 TTTCTTTTGT
*
1469573 TTTTATGTTCTTTAT-TTTA
1 TTTTAT-TTTTTTATCTTTA
1469592 TTTTATTTTTTTATCTTTA
1 TTTTATTTTTTTATCTTTA
* *
1469611 TTTTATTTTTTATGTCTTTT
1 TTTTATTTTTT-TATCTTTA
* * *
1469631 TTTTATCTTATTTTCCTTTTTT
1 TTTTAT-TT-TTTT-ATCTTTA
1469653 TCTTTATTTTTATT-TCCTTTA
1 T-TTTATTTTT-TTAT-CTTTA
1469674 TTTTATTTTTTT
1 TTTTATTTTTTT
1469686 TAGTTTATTT
Statistics
Matches: 79, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
18 7 0.09
19 23 0.29
20 22 0.28
21 9 0.11
22 13 0.16
23 5 0.06
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTATTTTTTTATCTTTA
Found at i:1469632 original size:31 final size:29
Alignment explanation
Indices: 1469583--1469700 Score: 105
Period size: 29 Copynumber: 3.9 Consensus size: 29
1469573 TTTTATGTTC
*
1469583 TTTATTTTATTTT-ATTTTTTTATCTTTAT
1 TTTATTTT-TTTTCTTTTTTTTATCTTTAT
1469612 TTTATTTTTTATGTCTTTTTTTTATC-TTAT
1 TTTATTTTTT-T-TCTTTTTTTTATCTTTAT
**
1469642 TTTCCTTTTTTTCTTTATTTTTATTTCCTTTAT
1 TTTATTTTTTTTCTTT-TTTTTA--T-CTTTAT
** *
1469675 TTTATTTTTTTTAGTTTATTTATCTT
1 TTTATTTTTTTTCTTTTTTTTATCTT
1469701 CATTGCCTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
28 7 0.10
29 19 0.26
30 14 0.19
31 11 0.15
32 6 0.08
33 16 0.22
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.77
Consensus pattern (29 bp):
TTTATTTTTTTTCTTTTTTTTATCTTTAT
Found at i:1469653 original size:23 final size:24
Alignment explanation
Indices: 1469627--1469687 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
1469617 TTTTTATGTC
1469627 TTTTTTTTATCTTAT-TTTCCTTT-
1 TTTTTTTTAT-TTATATTTCCTTTA
* *
1469650 TTTTCTTTATTTTTATTTCCTTTA
1 TTTTTTTTATTTATATTTCCTTTA
*
1469674 TTTTATTTTTTTTA
1 TTTT-TTTTATTTA
1469688 GTTTATTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 3 0.10
23 17 0.57
24 4 0.13
25 6 0.20
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTTTTTATTTATATTTCCTTTA
Found at i:1469682 original size:19 final size:19
Alignment explanation
Indices: 1469588--1469685 Score: 72
Period size: 20 Copynumber: 4.8 Consensus size: 19
1469578 TGTTCTTTAT
*
1469588 TTTATTTTATTTTTTTATC
1 TTTATTTTATTTTTTTACC
**
1469607 TTTATTTTATTTTTTATGTC
1 TTTATTTTATTTTTT-TACC
*
1469627 TTTTTTTTATCTTATTTT-CC
1 TTTATTTTAT-TT-TTTTACC
* *
1469647 TTTTTTTCTTTATTTTTATTTCC
1 --TTTAT-TTTATTTTT-TTACC
1469670 TTTATTTTATTTTTTT
1 TTTATTTTATTTTTTT
1469686 TAGTTTATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
19 17 0.25
20 22 0.33
21 9 0.13
22 12 0.18
23 7 0.10
ACGTcount: A:0.12, C:0.08, G:0.01, T:0.79
Consensus pattern (19 bp):
TTTATTTTATTTTTTTACC
Found at i:1469687 original size:14 final size:14
Alignment explanation
Indices: 1469519--1469695 Score: 82
Period size: 14 Copynumber: 12.8 Consensus size: 14
1469509 ATTCTGCTCG
**
1469519 TTATCTTTATTTTGA
1 TTAT-TTTATTTTTT
*
1469534 TTATTTTATTTATT
1 TTATTTTATTTTTT
* *
1469548 TT-TCTTA-ATTTT
1 TTATTTTATTTTTT
1469560 TTATTTCT-TTTGTTT
1 TTATTT-TATTT-TTT
* * *
1469575 TTATGTTCTTTATT
1 TTATTTTATTTTTT
1469589 TTATTTTA-TTTTT
1 TTATTTTATTTTTT
*
1469602 TTATCTTTA-TTTTA
1 TTAT-TTTATTTTTT
* *
1469616 TT-TTTTATGTCTT
1 TTATTTTATTTTTT
*
1469629 TT-TTTTATCTTATT
1 TTATTTTAT-TTTTT
** *
1469643 TTCCTTT-TTTTCT
1 TTATTTTATTTTTT
**
1469656 TTATTTTTATTTCCT
1 TTA-TTTTATTTTTT
1469671 TTATTTTATTTTTT
1 TTATTTTATTTTTT
*
1469685 TTAGTTTATTT
1 TTATTTTATTT
1469696 ATCTTCATTG
Statistics
Matches: 123, Mismatches: 28, Indels: 23
0.71 0.16 0.13
Matches are distributed among these distances:
12 9 0.07
13 30 0.24
14 58 0.47
15 26 0.21
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (14 bp):
TTATTTTATTTTTT
Found at i:1472744 original size:2 final size:2
Alignment explanation
Indices: 1472737--1472763 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1472727 CCCTCCTTAC
1472737 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1472764 GCATTGATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1473184 original size:3 final size:3
Alignment explanation
Indices: 1473176--1473232 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
1473166 CTGAGTTTTA
* * * * *
1473176 ATT ATT ATT ATT ATT ACT ACT ACT ATT AGT ATT ATT ATT -TT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1473223 AGT ATT ATT A
1 ATT ATT ATT A
1473233 CTACATTTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:1473601 original size:35 final size:35
Alignment explanation
Indices: 1473555--1473630 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
1473545 CACTGCCATT
* *
1473555 TCAATCTACAGTGATCGGGAATCACCGTTCACCAG
1 TCAATCTACAGTGATCGGGAATCACCATCCACCAG
1473590 TCAATCTACAGTGATCGGGAATCACCATCCACCAG
1 TCAATCTACAGTGATCGGGAATCACCATCCACCAG
1473625 TCAATC
1 TCAATC
1473631 ACCAAGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.22
Consensus pattern (35 bp):
TCAATCTACAGTGATCGGGAATCACCATCCACCAG
Found at i:1476389 original size:21 final size:21
Alignment explanation
Indices: 1476365--1476413 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1476355 TCAATTTCTT
*
1476365 GAAAACAAATTATTTTGGGTA
1 GAAAACAAATCATTTTGGGTA
1476386 GAAAACAAATCATTTTGGGTA
1 GAAAACAAATCATTTTGGGTA
1476407 GAAAACA
1 GAAAACA
1476414 TGTCTGGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (21 bp):
GAAAACAAATCATTTTGGGTA
Found at i:1480861 original size:37 final size:35
Alignment explanation
Indices: 1480778--1480924 Score: 100
Period size: 36 Copynumber: 4.1 Consensus size: 35
1480768 GTCGCCTTTA
* * * * *
1480778 AGATTGTTTCTCTCGAAAGAAATTTTGTCTCGCTTG
1 AGATAGTTTCTCTTGAAACAAA-ATTGTCTCACTTG
*
1480814 GGATAGTTTCTCTTGAAACAAAATTGATCTCACTTG
1 AGATAGTTTCTCTTGAAACAAAATTG-TCTCACTTG
* * * * *
1480850 AGATTGTTT-TCTTAAAAACAAATTTTATCTCGCTTG
1 AGATAGTTTCTCTT-GAAACAAA-ATTGTCTCACTTG
* * *
1480886 AGACAGTTTTTCTT-AAAAACAAATTCGTCTCACTTG
1 AGATAGTTTCTCTTGAAACA-AAATT-GTCTCACTTG
1480922 AGA
1 AGA
1480925 CAGTCTTCCT
Statistics
Matches: 87, Mismatches: 18, Indels: 12
0.74 0.15 0.10
Matches are distributed among these distances:
35 13 0.15
36 68 0.78
37 6 0.07
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (35 bp):
AGATAGTTTCTCTTGAAACAAAATTGTCTCACTTG
Found at i:1480880 original size:36 final size:36
Alignment explanation
Indices: 1480797--1480924 Score: 125
Period size: 36 Copynumber: 3.6 Consensus size: 36
1480787 CTCTCGAAAG
* * * *
1480797 AAATTTTGTCTCGCTTGGGATAGTTTCTCTT-GAAAC
1 AAATTTTATCTCACTTGAGATAGTTT-TCTTAAAAAC
* * *
1480833 AAAATTGATCTCACTTGAGATTGTTTTCTTAAAAAC
1 AAATTTTATCTCACTTGAGATAGTTTTCTTAAAAAC
* *
1480869 AAATTTTATCTCGCTTGAGACAGTTTTTCTTAAAAAC
1 AAATTTTATCTCACTTGAGATAG-TTTTCTTAAAAAC
**
1480906 AAA-TTCGTCTCACTTGAGA
1 AAATTTTATCTCACTTGAGA
1480925 CAGTCTTCCT
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
35 4 0.05
36 55 0.73
37 16 0.21
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (36 bp):
AAATTTTATCTCACTTGAGATAGTTTTCTTAAAAAC
Found at i:1480925 original size:36 final size:36
Alignment explanation
Indices: 1480841--1480997 Score: 132
Period size: 36 Copynumber: 4.5 Consensus size: 36
1480831 ACAAAATTGA
** **
1480841 TCTCACTTGAGATTG-TTTTCTTAAAAACAAATTTTA
1 TCTCACTTGAGACAGTTTTTCTTAAAAACAAA-TTCG
*
1480877 TCTCGCTTGAGACAGTTTTTCTTAAAAACAAATTCG
1 TCTCACTTGAGACAGTTTTTCTTAAAAACAAATTCG
* * *
1480913 TCTCACTTGAGACAGTCTTCCTTAAGACACAAA----
1 TCTCACTTGAGACAGTTTTTCTTAA-AAACAAATTCG
* **
1480946 ---CATTTGAGATTGTTTTTCTTAAAAACAAATTCCG
1 TCTCACTTGAGACAGTTTTTCTTAAAAACAAATT-CG
1480980 TCTCACTTGAGACAGTTT
1 TCTCACTTGAGACAGTTT
1480998 CACCTAGAAA
Statistics
Matches: 93, Mismatches: 18, Indels: 19
0.72 0.14 0.15
Matches are distributed among these distances:
29 6 0.06
30 17 0.18
36 36 0.39
37 34 0.37
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (36 bp):
TCTCACTTGAGACAGTTTTTCTTAAAAACAAATTCG
Found at i:1481025 original size:67 final size:66
Alignment explanation
Indices: 1480891--1481027 Score: 181
Period size: 67 Copynumber: 2.1 Consensus size: 66
1480881 GCTTGAGACA
* * *
1480891 GTTTTTCTTAAAAACAAATTCGTCTCACTTGAGACAGTCTTCCTTAAGACACAAACATTTGAGAT
1 GTTTTTCTTAAAAACAAATTCGTCTCACTTGAGACAGTCTTCCCTAAAACACAAACATTTGAAAT
1480956 T
66 T
*
1480957 GTTTTTCTTAAAAACAAATTCCGTCTCACTTGAGACAGT-TTCACCTAGAAATAC-AA-ATTCTG
1 GTTTTTCTTAAAAACAAATT-CGTCTCACTTGAGACAGTCTTC-CCTA-AAACACAAACATT-TG
1481019 AAATT
62 AAATT
1481024 GTTT
1 GTTT
1481028 CACTTGAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
66 26 0.41
67 33 0.52
68 4 0.06
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.36
Consensus pattern (66 bp):
GTTTTTCTTAAAAACAAATTCGTCTCACTTGAGACAGTCTTCCCTAAAACACAAACATTTGAAAT
T
Found at i:1481043 original size:67 final size:66
Alignment explanation
Indices: 1480897--1481043 Score: 167
Period size: 67 Copynumber: 2.2 Consensus size: 66
1480887 GACAGTTTTT
* * * *
1480897 CTTAAAAACAAATTCGTCTCACTTGAGACAGTCTTCCTTAAGACACAAACATTTGAGATTGTTTT
1 CTTAAAAACAAATTCGTCTCACTTGAGACAGTCTTCCCTAAAACACAAACATTTGAAATTGTTTC
*
1480962 T
66 A
*
1480963 CTTAAAAACAAATTCCGTCTCACTTGAGACAGT-TTCACCTAGAAATAC-AA-ATTCTGAAATTG
1 CTTAAAAACAAATT-CGTCTCACTTGAGACAGTCTTC-CCTA-AAACACAAACATT-TGAAATTG
1481025 TTTCA
62 TTTCA
1481030 CTTGAAAAA-AAATT
1 CTT-AAAAACAAATT
1481044 GATAAACCTT
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
66 20 0.29
67 41 0.59
68 9 0.13
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (66 bp):
CTTAAAAACAAATTCGTCTCACTTGAGACAGTCTTCCCTAAAACACAAACATTTGAAATTGTTTC
A
Found at i:1481119 original size:66 final size:66
Alignment explanation
Indices: 1481045--1481501 Score: 675
Period size: 66 Copynumber: 6.9 Consensus size: 66
1481035 AAAAAAATTG
* * *
1481045 ATAAACCTTTGAGATTATTTCTCTTGAAACAAATTTTGTCTCGCTTTAGAAAATTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAA
1481110 C
66 C
* * *
1481111 ATAAACCTTTGATATT-TTTATCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTG-AA
*
1481175 AA
65 AC
* *
1481177 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCACGCTTAAGACAATTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAA
1481242 C
66 C
*
1481243 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTTGCTTGAGACAATTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAA
1481308 C
66 C
* * *
1481309 ATAAACCTTTAAGATTGTTTATCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCCCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAA
1481374 C
66 C
* * * * **
1481375 ATAAACCTTTGAGATTATTTATCTCGAAACAAATTTTGTCT-GTCTTGAGGCCGTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCG-CTTGAGACAATTTCTCTTGAA
1481439 AC
65 AC
* * * *
1481441 ATAAACCTTTGAGATTGTTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACTATCTCTCTT
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTT
1481502 AAGACCGTTT
Statistics
Matches: 352, Mismatches: 35, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
65 42 0.12
66 269 0.76
67 41 0.12
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (66 bp):
ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAA
C
Found at i:1481588 original size:37 final size:36
Alignment explanation
Indices: 1481538--1481608 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
1481528 ATTTGAGATT
* **
1481538 GTTTCACTCGAAACAAAGTTTCGTCTCACTTGAGACA
1 GTTTCACTCGAAACAAA-ATTAATCTCACTTGAGACA
* *
1481575 GTTTCTCTTGAAACAAAATTAATCTCACTTGAGA
1 GTTTCACTCGAAACAAAATTAATCTCACTTGAGA
1481609 TTGTTGTCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 14 0.48
37 15 0.52
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (36 bp):
GTTTCACTCGAAACAAAATTAATCTCACTTGAGACA
Found at i:1482014 original size:3 final size:3
Alignment explanation
Indices: 1482006--1482080 Score: 71
Period size: 3 Copynumber: 25.3 Consensus size: 3
1481996 CCGGGTTTTA
* * * * * *
1482006 ATT ATT ATT ATT AAT ATT ATC ATT ATT ATT ATT ACT ACT ACT ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
1482054 ATT ATT ATT -TT ATT AAT AGT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1482081 CTACATTTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
2 2 0.03
3 58 0.97
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:1485271 original size:16 final size:17
Alignment explanation
Indices: 1485252--1485298 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 17
1485242 AATTAGGAAA
1485252 AAATATTATTATTT-TT
1 AAATATTATTATTTGTT
1485268 AAATATTAGTATAATTTGTT
1 AAATATTA-T-T-ATTTGTT
*
1485288 CAATATTATTA
1 AAATATTATTA
1485299 ACATTGATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 8 0.31
17 2 0.08
18 2 0.08
19 5 0.19
20 9 0.35
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (17 bp):
AAATATTATTATTTGTT
Found at i:1485414 original size:27 final size:27
Alignment explanation
Indices: 1485378--1485438 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
1485368 AAATAAAAAA
* *
1485378 TAAAATAAAATATATT-GATTAT-TTAT
1 TAAAATAAAA-ACATTACATTATATTAT
1485404 TAAAATAAAAACATTACATTATATTAT
1 TAAAATAAAAACATTACATTATATTAT
1485431 TAAAATAA
1 TAAAATAA
1485439 TATCCTAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 4 0.13
26 15 0.48
27 12 0.39
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAAATAAAAACATTACATTATATTAT
Found at i:1500281 original size:19 final size:17
Alignment explanation
Indices: 1500246--1500284 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1500236 ATTTGATTTC
1500246 TCTGTGTTTCTCTTCTT
1 TCTGTGTTTCTCTTCTT
*
1500263 TCTGTGTATTTTCTATCTT
1 TCTGTGT-TTCTCT-TCTT
1500282 TCT
1 TCT
1500285 TTGTCTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.05, C:0.21, G:0.10, T:0.64
Consensus pattern (17 bp):
TCTGTGTTTCTCTTCTT
Found at i:1500711 original size:3 final size:3
Alignment explanation
Indices: 1500705--1500782 Score: 111
Period size: 3 Copynumber: 26.0 Consensus size: 3
1500695 TATATGTATT
* * *
1500705 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1500753 TAA TAA TAA TAA TTA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1500783 ATAAATTTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1500801 original size:14 final size:14
Alignment explanation
Indices: 1500782--1500816 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1500772 TATAATAATA
1500782 AATAAATTTATGTG
1 AATAAATTTATGTG
1500796 AATAAATTTATGTG
1 AATAAATTTATGTG
1500810 AATAAAT
1 AATAAAT
1500817 GGTTTTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (14 bp):
AATAAATTTATGTG
Found at i:1502320 original size:19 final size:17
Alignment explanation
Indices: 1502285--1502323 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1502275 ATTTGATTTC
1502285 TCTGTGTTTCTCTTCTT
1 TCTGTGTTTCTCTTCTT
*
1502302 TCTGTGTATTTTCTGTCTT
1 TCTGTGT-TTCTCT-TCTT
1502321 TCT
1 TCT
1502324 TTGTCTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.03, C:0.21, G:0.13, T:0.64
Consensus pattern (17 bp):
TCTGTGTTTCTCTTCTT
Found at i:1502749 original size:3 final size:3
Alignment explanation
Indices: 1502743--1502805 Score: 90
Period size: 3 Copynumber: 21.0 Consensus size: 3
1502733 TATATGTATT
* * *
1502743 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA TTA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1502791 TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA
1502806 ATAAATTAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1504027 original size:3 final size:3
Alignment explanation
Indices: 1504014--1504048 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1504004 ACCTAACCCC
* *
1504014 ATT AGT ATT ATT ATT ATT ATT ATT ATC ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1504049 CGTGTTCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1505372 original size:60 final size:60
Alignment explanation
Indices: 1505287--1505467 Score: 274
Period size: 66 Copynumber: 2.9 Consensus size: 60
1505277 TTTCTCCCCC
*
1505287 AAAAGTTGTAGTAGACCCAAACTTTAACACAACTTTTCTTCTTCCCCCCCCCCCCCCA-A
1 AAAAGTTGTAGTAGACCAAAACTTTAACACAACTTTTCTTCTTCCCCCCCCCCCCCCACA
1505346 ACAAAGTTGTAGTAGACCAAAACTTTAACACAACTTTTCTTCTTCCCACCCCACGCCACCCCACC
1 A-AAAGTTGTAGTAGACCAAAACTTTAACACAACTTTTCTTCTTCCC-CCCC-C-CC-CCCCA-C
1505411 TA
60 -A
1505413 AAAAGTTGTAGTAGACCAAAACTTTAACACAACTTTTCTTCTCTCCCCCCCCCCC
1 AAAAGTTGTAGTAGACCAAAACTTTAACACAACTTTTCTTCT-TCCCCCCCCCCC
1505468 ACCCCACCCC
Statistics
Matches: 112, Mismatches: 1, Indels: 14
0.88 0.01 0.11
Matches are distributed among these distances:
59 1 0.01
60 44 0.39
61 4 0.04
62 1 0.01
63 3 0.03
64 7 0.06
65 1 0.01
66 45 0.40
67 6 0.05
ACGTcount: A:0.30, C:0.38, G:0.07, T:0.25
Consensus pattern (60 bp):
AAAAGTTGTAGTAGACCAAAACTTTAACACAACTTTTCTTCTTCCCCCCCCCCCCCCACA
Found at i:1505425 original size:66 final size:63
Alignment explanation
Indices: 1505287--1505508 Score: 290
Period size: 60 Copynumber: 3.4 Consensus size: 63
1505277 TTTCTCCCCC
*
1505287 AAAAGTTGTAGTAGACCCAAACTTTAACACAACTTTTCTTCTTCCCCCCC-CCC-CCCCA--A
1 AAAAGTTGTAGTAGACCAAAACTTTAACACAACTTTTCTTCTTCCCCCCCACCCACCCCACCA
1505346 ACAAAGTTGTAGTAGACCAAAACTTTAACACAACTTTTCTTCTTCCCACCCCACGCCACCCCACC
1 A-AAAGTTGTAGTAGACCAAAACTTTAACACAACTTTTCTTCTTCCC-CCCCAC-CCACCCCACC
1505411 TA
63 -A
1505413 AAAAGTTGTAGTAGACCAAAACTTTAACACAACTTTTCTTCTCTCCCCCCCCCCCACCCCACCCC
1 AAAAGTTGTAGTAGACCAAAACTTTAACACAACTTTTCTTCT-T----CCCCCCCA-CCCACCCC
*
1505478 ACCC
60 ACCA
* *
1505482 AAAAGTTGTAGTAGACCCATACTTTAA
1 AAAAGTTGTAGTAGACCAAAACTTTAA
1505509 GAACCCATTG
Statistics
Matches: 145, Mismatches: 4, Indels: 18
0.87 0.02 0.11
Matches are distributed among these distances:
59 1 0.01
60 44 0.30
61 4 0.03
62 1 0.01
63 2 0.01
64 5 0.03
66 41 0.28
67 3 0.02
69 25 0.17
70 15 0.10
71 4 0.03
ACGTcount: A:0.31, C:0.37, G:0.08, T:0.24
Consensus pattern (63 bp):
AAAAGTTGTAGTAGACCAAAACTTTAACACAACTTTTCTTCTTCCCCCCCACCCACCCCACCA
Found at i:1510931 original size:20 final size:20
Alignment explanation
Indices: 1510885--1510933 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1510875 TTAGTTTTTT
*
1510885 TAATAATTTTTAAAAGAAAA
1 TAATATTTTTTAAAAGAAAA
**
1510905 TCGTATTTTTTAAAA-AATAA
1 TAATATTTTTTAAAAGAA-AA
1510925 TAATATTTT
1 TAATATTTT
1510934 AAAATTTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (20 bp):
TAATATTTTTTAAAAGAAAA
Found at i:1511340 original size:20 final size:23
Alignment explanation
Indices: 1511312--1511368 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
1511302 TTAAAGTCAT
*
1511312 TTATCATCAATCGATGTTCACCA
1 TTATCATCAATCAATGTTCACCA
1511335 TTATCATCAATCAATGTTCACCA
1 TTATCATCAATCAATGTTCACCA
1511358 TTATCATCAAT
1 TTATCATCAAT
1511369 TACTATCGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (23 bp):
TTATCATCAATCAATGTTCACCA
Found at i:1511590 original size:31 final size:31
Alignment explanation
Indices: 1511489--1511596 Score: 82
Period size: 31 Copynumber: 3.5 Consensus size: 31
1511479 TACATCAAAT
* *
1511489 GTCCTTAAAC-TATGAGCTTCATTTTAAATTA
1 GTCCTTAAACTTATGATC-TCATTCTAAATTA
* * * *
1511520 GTTCTTAAACTTTTGA-AT-ATTCTAATTTTA
1 GTCCTTAAACTTATGATCTCATTCTAA-ATTA
*
1511550 -TCCTGAAAC-TATGATTCTCATTCTAAATTA
1 GTCCTTAAACTTATGA-TCTCATTCTAAATTA
*
1511580 GTCCTTAAACTTTTGAT
1 GTCCTTAAACTTATGAT
1511597 TCTTCCAATT
Statistics
Matches: 58, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
28 4 0.07
29 13 0.22
30 8 0.14
31 25 0.43
32 8 0.14
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.45
Consensus pattern (31 bp):
GTCCTTAAACTTATGATCTCATTCTAAATTA
Found at i:1511607 original size:60 final size:60
Alignment explanation
Indices: 1511490--1511612 Score: 158
Period size: 60 Copynumber: 2.0 Consensus size: 60
1511480 ACATCAAATG
* * * * *
1511490 TCCTTAAACTATGAGCTTCATTTTAAATTAGTTCTTAAACTTTTGAATATTCTAATTTTA
1 TCCTGAAACTATGAGCTTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCA
* * *
1511550 TCCTGAAACTATGA-TTCTCATTCTAAATTAGTCCTTAAACTTTTGATTCTTCCAATTTCA
1 TCCTGAAACTATGAGCT-TCATTCTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCA
1511610 TCC
1 TCC
1511613 CCAAATTCAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
59 1 0.02
60 53 0.98
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.46
Consensus pattern (60 bp):
TCCTGAAACTATGAGCTTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCA
Found at i:1511862 original size:59 final size:60
Alignment explanation
Indices: 1511752--1511912 Score: 182
Period size: 59 Copynumber: 2.7 Consensus size: 60
1511742 GTTTAAGTTA
* ** * * * **
1511752 AAATTGAAATATTAAAAAAGTTTGGGGATTACTTTAGAATGAAAGTAATAGTTTGGGGATG
1 AAATTGAAATATT-CAAAAGTTTAAGAACTAATTTAGAATGAAAGTAATAGTTTAAGGATG
* * *
1511813 AAATTGAAATGTTCAAAAGTTTGAGAACTAA-TTAGAATGACAA-TCATAGTTTAAGGATG
1 AAATTGAAATATTCAAAAGTTTAAGAACTAATTTAGAATGA-AAGTAATAGTTTAAGGATG
*
1511872 AAATTGAAATATTTAAAAGTTTAAGAACTAATTTAGAATGA
1 AAATTGAAATATTCAAAAGTTTAAGAACTAATTTAGAATGA
1511913 GGATCATAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
59 50 0.58
60 24 0.28
61 12 0.14
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (60 bp):
AAATTGAAATATTCAAAAGTTTAAGAACTAATTTAGAATGAAAGTAATAGTTTAAGGATG
Found at i:1519248 original size:14 final size:14
Alignment explanation
Indices: 1519229--1519275 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
1519219 TTGGTCGACT
1519229 CGGCTCGGTTCAGA
1 CGGCTCGGTTCAGA
1519243 CGGCTCGG-TCA-A
1 CGGCTCGGTTCAGA
1519255 ---CTCGGTTCAGA
1 CGGCTCGGTTCAGA
1519266 CGGCTCGGTT
1 CGGCTCGGTT
1519276 GGCTCGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
9 5 0.18
10 3 0.11
11 1 0.04
12 1 0.04
13 3 0.11
14 15 0.54
ACGTcount: A:0.13, C:0.30, G:0.34, T:0.23
Consensus pattern (14 bp):
CGGCTCGGTTCAGA
Found at i:1519281 original size:23 final size:23
Alignment explanation
Indices: 1519228--1519289 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
1519218 ATTGGTCGAC
1519228 TCGGCTCGGTTCAGACGGCTCGG
1 TCGGCTCGGTTCAGACGGCTCGG
**
1519251 TCAACTCGGTTCAGACGGCTCGG
1 TCGGCTCGGTTCAGACGGCTCGG
* *
1519274 TTGGCTCGGTTTAGAC
1 TCGGCTCGGTTCAGAC
1519290 TGGTCCAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.13, C:0.27, G:0.34, T:0.26
Consensus pattern (23 bp):
TCGGCTCGGTTCAGACGGCTCGG
Found at i:1522429 original size:26 final size:26
Alignment explanation
Indices: 1522392--1522482 Score: 82
Period size: 26 Copynumber: 3.6 Consensus size: 26
1522382 ACGATCGTTT
*
1522392 TTTTTTA-AAAAAATTTATATATTTA
1 TTTTTTATTAAAAATTTATATATTTA
1522417 TTTTTTATTAAAAATTTAT-T-TTT-
1 TTTTTTATTAAAAATTTATATATTTA
* * ** *
1522440 GTTTTTCTTATGATTTTATATATTTA
1 TTTTTTATTAAAAATTTATATATTTA
*
1522466 TTTTTTAATATAAAATT
1 TTTTTTATTA-AAAATT
1522483 ATGTAATTGT
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
23 14 0.29
24 4 0.08
25 11 0.22
26 17 0.35
27 3 0.06
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTTTATTAAAAATTTATATATTTA
Found at i:1522484 original size:26 final size:25
Alignment explanation
Indices: 1522392--1522484 Score: 75
Period size: 25 Copynumber: 3.7 Consensus size: 25
1522382 ACGATCGTTT
1522392 TTTTTTAA-AAAAATTTATATATTTA
1 TTTTTTAATAAAAA-TTATATATTTA
* * *
1522417 TTTTTTATTAAAAATT-TATTTTTG
1 TTTTTTAATAAAAATTATATATTTA
* * **
1522441 TTTTTCTTAT-GATTTTATATATTTA
1 TTTTT-TAATAAAAATTATATATTTA
1522466 TTTTTTAATATAAAATTAT
1 TTTTTTAATA-AAAATTAT
1522485 GTAATTGTCA
Statistics
Matches: 49, Mismatches: 14, Indels: 9
0.68 0.19 0.12
Matches are distributed among these distances:
24 17 0.35
25 22 0.45
26 10 0.20
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTTTTAATAAAAATTATATATTTA
Found at i:1528137 original size:2 final size:2
Alignment explanation
Indices: 1528130--1528167 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
1528120 AGATGACCAA
1528130 AT AT AT AT AT ACT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
1528168 CTTAGACATC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 32 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1532090 original size:19 final size:19
Alignment explanation
Indices: 1532068--1532110 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1532058 TTTTATAGCA
*
1532068 TTTTTTTG-TTTTTTTAATT
1 TTTTTTTGATTGTTTT-ATT
*
1532087 TTTTATTGATTGTTTTATT
1 TTTTTTTGATTGTTTTATT
1532106 TTTTT
1 TTTTT
1532111 CGTTTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.81
Consensus pattern (19 bp):
TTTTTTTGATTGTTTTATT
Found at i:1532121 original size:13 final size:14
Alignment explanation
Indices: 1532098--1532124 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1532088 TTTATTGATT
1532098 GTTTTATTTTTTTC
1 GTTTTATTTTTTTC
1532112 GTTTTATTTTTTT
1 GTTTTATTTTTTT
1532125 AGAGTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.07, T:0.81
Consensus pattern (14 bp):
GTTTTATTTTTTTC
Found at i:1533514 original size:2 final size:2
Alignment explanation
Indices: 1533507--1533535 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1533497 TGATTTAGCA
1533507 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 A
1533536 ACACAAATGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1538777 original size:11 final size:11
Alignment explanation
Indices: 1538741--1538771 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1538731 GAAACAGCAA
1538741 TTTTACACAGG
1 TTTTACACAGG
1538752 TTTTACACAGG
1 TTTTACACAGG
1538763 TTTTACACA
1 TTTTACACA
1538772 TTTTTTCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (11 bp):
TTTTACACAGG
Found at i:1547127 original size:4 final size:4
Alignment explanation
Indices: 1547120--1547146 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1547110 TTTAATTATA
1547120 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1547147 ATAATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:1547133 original size:8 final size:8
Alignment explanation
Indices: 1547084--1547146 Score: 56
Period size: 8 Copynumber: 7.8 Consensus size: 8
1547074 TTTAACCCTT
1547084 TTTATTTA
1 TTTATTTA
*
1547092 TATGTATATA
1 T-T-TATTTA
* *
1547102 TATATATA
1 TTTATTTA
*
1547110 TTTAATTA
1 TTTATTTA
*
1547118 -TAATTTA
1 TTTATTTA
1547125 TTTATTTA
1 TTTATTTA
1547133 TTTATTTA
1 TTTATTTA
1547141 TTTATT
1 TTTATT
1547147 ATAATTTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
7 5 0.11
8 32 0.73
9 1 0.02
10 6 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (8 bp):
TTTATTTA
Found at i:1547360 original size:7 final size:7
Alignment explanation
Indices: 1547348--1547405 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
1547338 ATTATATGTA
1547348 TATTTAT
1 TATTTAT
1547355 TATTTATT
1 TATTTA-T
1547363 TATTTAT
1 TATTTAT
1547370 TA-TTAT
1 TATTTAT
* *
1547376 T-GTTAC
1 TATTTAT
*
1547382 TATTTAG
1 TATTTAT
1547389 TATTT-T
1 TATTTAT
1547395 TATTATAT
1 TATT-TAT
1547403 TAT
1 TAT
1547406 ACATACATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
6 13 0.31
7 18 0.43
8 11 0.26
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (7 bp):
TATTTAT
Found at i:1547421 original size:19 final size:19
Alignment explanation
Indices: 1547397--1547441 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
1547387 AGTATTTTTA
1547397 TTATATTATACATACATTT
1 TTATATTATACATACATTT
* *
1547416 TTATATTTATATATATATTT
1 TTATA-TTATACATACATTT
1547436 TT-TATT
1 TTATATT
1547442 TTATTTATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 7 0.30
20 14 0.61
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATATTATACATACATTT
Found at i:1547450 original size:22 final size:21
Alignment explanation
Indices: 1547391--1547471 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 21
1547381 CTATTTAGTA
* * *
1547391 TTTTTATTATATTATACATACA
1 TTTTTATTTTATTATATATA-T
1547413 TTTTTATATTTA-TATATATAT
1 TTTTTAT-TTTATTATATATAT
1547434 TTTTTATTTTATT-TATACTAT
1 TTTTTATTTTATTATATA-TAT
1547455 TTATTTATTTTCATTAT
1 TT-TTTATTTT-ATTAT
1547472 GTTTTTAGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
20 8 0.16
21 13 0.26
22 22 0.44
23 6 0.12
24 1 0.02
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTATTTTATTATATATAT
Found at i:1548772 original size:19 final size:19
Alignment explanation
Indices: 1548748--1548784 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1548738 ACCTTACTAA
1548748 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
1548767 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
1548785 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:1552178 original size:11 final size:10
Alignment explanation
Indices: 1552164--1552220 Score: 64
Period size: 11 Copynumber: 5.5 Consensus size: 10
1552154 AAAGGGTAAA
1552164 AAAAAAGAAG
1 AAAAAAGAAG
1552174 CAAAAAAGAAG
1 -AAAAAAGAAG
1552185 AAAACAA-AAG
1 AAAA-AAGAAG
1552195 AAAAAAGAAAG
1 AAAAAAG-AAG
1552206 AACAAAA-AAG
1 AA-AAAAGAAG
1552216 AAAAA
1 AAAAA
1552221 GAAAAAGGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
9 5 0.12
10 16 0.38
11 17 0.40
12 4 0.10
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:1552178 original size:14 final size:15
Alignment explanation
Indices: 1552161--1552218 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
1552151 CAAAAAGGGT
1552161 AAAAAAAAAG-AAGC
1 AAAAAAAAAGAAAGC
* *
1552175 AAAAAAGAAGAAAAC
1 AAAAAAAAAGAAAGC
1552190 AAAAGAAAAAAGAAAG-
1 -AAA-AAAAAAGAAAGC
*
1552206 AACAAAAAAGAAA
1 AAAAAAAAAGAAA
1552219 AAGAAAAAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
14 19 0.53
15 5 0.14
16 3 0.08
17 9 0.25
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAAGC
Found at i:1552199 original size:21 final size:21
Alignment explanation
Indices: 1552166--1552224 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 21
1552156 AGGGTAAAAA
1552166 AAAAGAAGCAAAAAAG-AAGAA-
1 AAAA-AAG-AAAAAAGAAAGAAC
1552187 AACAAAAGAAAAAAGAAAGAAC
1 AA-AAAAGAAAAAAGAAAGAAC
1552209 AAAAAAG-AAAAAGAAA
1 AAAAAAGAAAAAAGAAA
1552225 AAGGGACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 16 0.46
21 15 0.43
22 4 0.11
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAAAAAGAAAGAAC
Found at i:1552859 original size:22 final size:22
Alignment explanation
Indices: 1552831--1552885 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1552821 GCTACCCCAT
*
1552831 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAACATCAAATGC
1552853 CAAACCTTTGAACATCAAATGC
1 CAAACCTTTGAACATCAAATGC
1552875 CAAACCTTTGA
1 CAAACCTTTGA
1552886 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAACATCAAATGC
Found at i:1553961 original size:106 final size:106
Alignment explanation
Indices: 1553832--1554661 Score: 1381
Period size: 106 Copynumber: 7.8 Consensus size: 106
1553822 ATATCGTGCC
* * *
1553832 ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1553897 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1553938 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
1554003 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1554044 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1554109 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1554150 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
1554215 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1554256 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
1554321 AATTTCAAAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1554362 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
1554427 AATTTCAGAGCCAATTTTAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1554468 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
1554533 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1554574 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1554639 AATTTCAGAGCCAATTTCAACTT
66 AATTTCAGAGCCAATTTCAACTT
1554662 AATAATGATG
Statistics
Matches: 672, Mismatches: 52, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 672 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1554114 original size:212 final size:212
Alignment explanation
Indices: 1553832--1554661 Score: 1525
Period size: 212 Copynumber: 3.9 Consensus size: 212
1553822 ATATCGTGCC
* *
1553832 ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1553897 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
1553962 TCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
1554027 ACATCGAAGGATATTGG
196 ACATCGAAGGATATTGG
* * *
1554044 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1554109 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
*
1554174 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
1554239 ACATCGAAGGATATTGG
196 ACATCGAAGGATATTGG
1554256 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1554321 AATTTCAAAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCGAGACAACACAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
* *
1554386 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTTAACTTC
131 TCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
1554451 ACATCGAAGGATATTGG
196 ACATCGAAGGATATTGG
* *
1554468 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1554533 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
*
1554598 TCACAACGAAGGGACGGCTAGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTT
131 TCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTT
1554662 AATAATGATG
Statistics
Matches: 597, Mismatches: 21, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
212 597 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (212 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
TCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
ACATCGAAGGATATTGG
Found at i:1555275 original size:85 final size:83
Alignment explanation
Indices: 1554944--1555279 Score: 326
Period size: 80 Copynumber: 4.0 Consensus size: 83
1554934 TATTTGTCAA
* * *
1554944 CAAAGACCTTCGAGTTCGATTACACTCAACTCCAAGGCACATCATTTACAACATAGCTCAAGGCT
1 CAAAGACCTTCGAGTTCGATTACACTCAACTCCAAGGCAAATCATTTACAACATAACTCAAGACT
* *
1555009 AGAAGGGCTATCTGTCAG
66 AGAAGGGCTATCTGCCAT
* * * * * *
1555027 CAAAGACCTTCGAGTTCG---ACACTCAGCTCCAAGGCACATCATTTGCAATATAACTCAAGGCA
1 CAAAGACCTTCGAGTTCGATTACACTCAACTCCAAGGCAAATCATTTACAACATAACTCAAGACT
* * *
1555089 AGAAGGGCTATTTTCCAA
66 AGAAGGGCTATCTGCCAT
* * * * **
1555107 CAAAAGACCTTCGAGTTCGACTACGCTTAACTCCAAGG-AATATCATTTGCAGTATAACTCAA-A
1 C-AAAGACCTTCGAGTTCGATTACACTCAACTCCAAGGCAA-ATCATTTACAACATAACTCAAGA
*
1555170 GCTAGAAAGG-TGATCTGCCAT
64 -CTAGAAGGGCT-ATCTGCCAT
* * *
1555191 CAAAGACCTTCGAGATCAATTACATTCAACT-CAGAGGCAAATCAAATTTACAACATAACTCAAG
1 CAAAGACCTTCGAGTTCGATTACACTCAACTCCA-AGGCAAATC--ATTTACAACATAACTCAAG
* *
1555255 ACGAGAAGGGTTATCTGCCAT
63 ACTAGAAGGGCTATCTGCCAT
1555276 CAAA
1 CAAA
1555280 ATTGTCGAGT
Statistics
Matches: 209, Mismatches: 31, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
80 54 0.26
81 17 0.08
82 2 0.01
83 50 0.24
84 49 0.23
85 35 0.17
86 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (83 bp):
CAAAGACCTTCGAGTTCGATTACACTCAACTCCAAGGCAAATCATTTACAACATAACTCAAGACT
AGAAGGGCTATCTGCCAT
Found at i:1556572 original size:18 final size:18
Alignment explanation
Indices: 1556536--1556586 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
1556526 TTGTACATAC
*
1556536 ATTTTTATATTTT-TATAT
1 ATTTTT-TATTTTATTTAT
1556554 ATTTTTTATTTTATTTAT
1 ATTTTTTATTTTATTTAT
* *
1556572 ACTATTTA-TTTATTT
1 ATTTTTTATTTTATTT
1556587 TCATTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 13 0.45
18 16 0.55
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTTATTTAT
Found at i:1556587 original size:28 final size:28
Alignment explanation
Indices: 1556539--1556597 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1556529 TACATACATT
* *
1556539 TTTATATTTTTATATATTTTTTATTTTA
1 TTTATATATTTATATATTTTTCATTTTA
*
1556567 TTTATACTATTTATTTA-TTTTCATTTTA
1 TTTATA-TATTTATATATTTTTCATTTTA
1556595 TTT
1 TTT
1556598 TTAGTTTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (28 bp):
TTTATATATTTATATATTTTTCATTTTA
Found at i:1556700 original size:5 final size:5
Alignment explanation
Indices: 1556690--1556718 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1556680 TTTTTCTTCA
1556690 TTTAT TTTAT TTTAT TTTAT TTT-T TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
1556719 ATTTGTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTAT
Found at i:1556802 original size:18 final size:19
Alignment explanation
Indices: 1556781--1556822 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1556771 TTTGGTTTAC
*
1556781 TCTTTAATT-TTGTTACTT
1 TCTTTAATTATTATTACTT
* *
1556799 TCTTTTATTATTATTATTT
1 TCTTTAATTATTATTACTT
1556818 TCTTT
1 TCTTT
1556823 TAACATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (19 bp):
TCTTTAATTATTATTACTT
Found at i:1556835 original size:18 final size:19
Alignment explanation
Indices: 1556797--1556836 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1556787 ATTTTGTTAC
**
1556797 TTTCTTTTATTATTATTAT
1 TTTCTTTTAACATTATTAT
1556816 TTTCTTTTAACATT-TTAT
1 TTTCTTTTAACATTATTAT
1556834 TTT
1 TTT
1556837 AATTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTCTTTTAACATTATTAT
Found at i:1559405 original size:22 final size:23
Alignment explanation
Indices: 1559377--1559422 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1559367 TGATAGACAC
*
1559377 ATCATCACCTAAGCGA-TGTATT
1 ATCATCACCAAAGCGATTGTATT
*
1559399 ATCATCACCAAAGTGATTGTATT
1 ATCATCACCAAAGCGATTGTATT
1559422 A
1 A
1559423 CATGTGTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (23 bp):
ATCATCACCAAAGCGATTGTATT
Found at i:1562342 original size:31 final size:31
Alignment explanation
Indices: 1562269--1562327 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1562259 CAGTTACGCC
* ** *
1562269 AGGGATCATATTACAAACGGACTAAATGGTG
1 AGGGACCATATTGTAAACGGACTAAATAGTG
1562300 AGGGACCATATTGTAAACGGACTAAATA
1 AGGGACCATATTGTAAACGGACTAAATA
1562328 TTGGGGGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.22
Consensus pattern (31 bp):
AGGGACCATATTGTAAACGGACTAAATAGTG
Found at i:1563346 original size:31 final size:31
Alignment explanation
Indices: 1563306--1563372 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1563296 TGTAATATAA
*
1563306 TCCCCCAACATTTAGTCCGCTTGCAATATGG
1 TCCCTCAACATTTAGTCCGCTTGCAATATGG
* * *
1563337 TCCCTCAACATTTAGTCTGTTTGTAATATGG
1 TCCCTCAACATTTAGTCCGCTTGCAATATGG
1563368 TCCCT
1 TCCCT
1563373 GAAGTAACTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (31 bp):
TCCCTCAACATTTAGTCCGCTTGCAATATGG
Found at i:1565317 original size:2 final size:2
Alignment explanation
Indices: 1565310--1565348 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1565300 TCTTATGTTC
1565310 AT AT AT AT 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 AT AT AT AT A
1565349 ATGATTCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1568330 original size:20 final size:20
Alignment explanation
Indices: 1568294--1568331 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1568284 CCTGACTGGT
* *
1568294 TTGGAAGACTTGTAAATCGA
1 TTGGAAGACCTGAAAATCGA
1568314 TTGGAAGACCTGAAAATC
1 TTGGAAGACCTGAAAATC
1568332 AGTTCCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (20 bp):
TTGGAAGACCTGAAAATCGA
Found at i:1569935 original size:36 final size:36
Alignment explanation
Indices: 1569895--1570033 Score: 242
Period size: 36 Copynumber: 3.9 Consensus size: 36
1569885 ACAGTGCTGG
1569895 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
1569931 ACATTGATACATGAATGTACCAAAGATGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
1569967 ACATTGATACACGAATGTATCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
1570003 ACATTGATACACGAATGTATCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
1570034 ATGGATAAAT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 98 1.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:1577380 original size:45 final size:46
Alignment explanation
Indices: 1577331--1577442 Score: 129
Period size: 48 Copynumber: 2.4 Consensus size: 46
1577321 TATAAAATCT
* * * *
1577331 CTTACCATTTATCCCATAAGTTTGTAAGCTTA-TTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTTACCAAAACA
*
1577376 CTTACCATTTAAAATTCCATAAGCTCGTAAGCTTATTTTTACCAATACA
1 CTTACCATTT---ATTCCATAAGCTCGTAAGCTTATTTTTACCAAAACA
*
1577425 CTTGCCA-TTATTCCATAA
1 CTTACCATTTATTCCATAA
1577443 CCATATACCA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
45 19 0.33
48 21 0.37
49 17 0.30
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.38
Consensus pattern (46 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTTACCAAAACA
Found at i:1577466 original size:13 final size:14
Alignment explanation
Indices: 1577445--1577477 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1577435 TTCCATAACC
1577445 ATATACCATAAAAA
1 ATATACCATAAAAA
*
1577459 ATAT-CCATAAACA
1 ATATACCATAAAAA
1577472 ATATAC
1 ATATAC
1577478 AATAGACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (14 bp):
ATATACCATAAAAA
Found at i:1577578 original size:33 final size:33
Alignment explanation
Indices: 1577541--1577607 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
1577531 ACCGTAGTGC
*
1577541 TAATCCGTATGACACATAAGATCATGTCCACCA
1 TAATCCGTATGAAACATAAGATCATGTCCACCA
* *
1577574 TAATCCGTATGAAACATAAGTTCGTGTCCACCA
1 TAATCCGTATGAAACATAAGATCATGTCCACCA
1577607 T
1 T
1577608 CTGTACTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.27
Consensus pattern (33 bp):
TAATCCGTATGAAACATAAGATCATGTCCACCA
Found at i:1585047 original size:45 final size:46
Alignment explanation
Indices: 1584993--1585104 Score: 138
Period size: 48 Copynumber: 2.4 Consensus size: 46
1584983 TATAAAATCT
* * * *
1584993 CTTATCATTTATCCCATAAGCTTGTAAGCTTA-TTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTTACCAAAACA
*
1585038 CTTACCATTTAAAATTCCATAAGCTCGTAAGCTTATTTTTACCAATACA
1 CTTACCATTT---ATTCCATAAGCTCGTAAGCTTATTTTTACCAAAACA
1585087 CTTACCA-TTATTCCATAA
1 CTTACCATTTATTCCATAA
1585105 CCATATACCA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
45 18 0.31
48 22 0.38
49 18 0.31
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.38
Consensus pattern (46 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTTACCAAAACA
Found at i:1585240 original size:33 final size:33
Alignment explanation
Indices: 1585203--1585269 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1585193 ACCGTAGTGC
1585203 TAATCCGTATAACACATAAGGTCGTGTCCACCA
1 TAATCCGTATAACACATAAGGTCGTGTCCACCA
*
1585236 TAATCCGTATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATAACACATAAGGTCGTGTCCACCA
1585269 T
1 T
1585270 CTGTACTAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (33 bp):
TAATCCGTATAACACATAAGGTCGTGTCCACCA
Found at i:1588663 original size:36 final size:36
Alignment explanation
Indices: 1588623--1588761 Score: 233
Period size: 36 Copynumber: 3.9 Consensus size: 36
1588613 ACGGTATTGG
1588623 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
1588659 ACATTGATACACGAATGTACCAAAGTTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
1588695 ACATTGATACATGAATGTATCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
**
1588731 ACATTGATACACGAATGTATTAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
1588762 ATGGATAAAT
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 97 1.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:1589487 original size:9 final size:9
Alignment explanation
Indices: 1589473--1589497 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1589463 TCAATACCTC
1589473 AACATTTCA
1 AACATTTCA
1589482 AACATTTCA
1 AACATTTCA
1589491 AACATTT
1 AACATTT
1589498 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (9 bp):
AACATTTCA
Found at i:1593986 original size:7 final size:7
Alignment explanation
Indices: 1593974--1594002 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1593964 TTTACTACCT
1593974 CTTTATG
1 CTTTATG
1593981 CTTTATG
1 CTTTATG
1593988 CTTTATG
1 CTTTATG
1593995 CTTTATG
1 CTTTATG
1594002 C
1 C
1594003 AACATGTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
CTTTATG
Found at i:1595633 original size:11 final size:11
Alignment explanation
Indices: 1595619--1595643 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1595609 TGACTCAGAA
1595619 GATGATCCATG
1 GATGATCCATG
1595630 GATGATCCATG
1 GATGATCCATG
1595641 GAT
1 GAT
1595644 AAGAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (11 bp):
GATGATCCATG
Found at i:1596100 original size:24 final size:24
Alignment explanation
Indices: 1596018--1596100 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
1596008 AAATATTTTA
* * *
1596018 TCTGATTTCCGACTTGAATTCTGT
1 TCTGATATCTGACCTGAATTCTGT
1596042 TCTGATA-CATGACCTGAATTCTGT
1 TCTGATATC-TGACCTGAATTCTGT
* *
1596066 TCTGATTTCTGATCC-GGATTCTGT
1 TCTGATATCTGA-CCTGAATTCTGT
1596090 TCTGATATCTG
1 TCTGATATCTG
1596101 TTTTGATTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.02
24 46 0.92
25 3 0.06
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (24 bp):
TCTGATATCTGACCTGAATTCTGT
Found at i:1596994 original size:2 final size:2
Alignment explanation
Indices: 1596987--1597029 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
1596977 ATGTTACATG
1596987 TA TA TA TA -A GTA 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
1597029 T
1 T
1597030 TTATCATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1597808 original size:14 final size:13
Alignment explanation
Indices: 1597784--1597823 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
1597774 AATTTACTAA
1597784 TTATAATTAAGAT
1 TTATAATTAAGAT
1597797 TTATAATATAAGGA-
1 TTATAAT-TAA-GAT
1597811 TTATAATTAAGAT
1 TTATAATTAAGAT
1597824 AGAAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.08
13 10 0.42
14 10 0.42
15 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (13 bp):
TTATAATTAAGAT
Found at i:1607594 original size:24 final size:24
Alignment explanation
Indices: 1607549--1607613 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 24
1607539 TACTAAATAG
* * *
1607549 AATTTTAATGTATTTTATTATTAA
1 AATTTTAATATATATTAATATTAA
* *
1607573 AATTTTAATATCTATTAATATTAG
1 AATTTTAATATATATTAATATTAA
*
1607597 AGTTTTATATGATATAT
1 AATTTTA-AT-ATATAT
1607614 GCTCCTTATA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
24 25 0.78
25 2 0.06
26 5 0.16
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (24 bp):
AATTTTAATATATATTAATATTAA
Found at i:1608872 original size:2 final size:2
Alignment explanation
Indices: 1608865--1608908 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1608855 TTTTAAATAA
1608865 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1608907 AT
1 AT
1608909 TCAACGTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1610846 original size:29 final size:29
Alignment explanation
Indices: 1610803--1610906 Score: 136
Period size: 29 Copynumber: 3.6 Consensus size: 29
1610793 ACCGTTAACC
1610803 GGGTGGTATTTTGGTAATTATTTTGAAAA
1 GGGTGGTATTTTGGTAATTATTTTGAAAA
* * *
1610832 TGGTGGTATTATGGTAATTATCTTGAAAA
1 GGGTGGTATTTTGGTAATTATTTTGAAAA
* * *
1610861 GGGTGCTATTTTTGTAATTATTTTTAAAA
1 GGGTGGTATTTTGGTAATTATTTTGAAAA
* *
1610890 GGGTGATATTTTCGTAA
1 GGGTGGTATTTTGGTAA
1610907 AATGGTTGAT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.28, C:0.03, G:0.24, T:0.45
Consensus pattern (29 bp):
GGGTGGTATTTTGGTAATTATTTTGAAAA
Found at i:1618008 original size:29 final size:29
Alignment explanation
Indices: 1617953--1618008 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
1617943 CGTTGACCGG
* **
1617953 GTGGTATTTTGATAATTATTTTAAAAATA
1 GTGGTATTCTGATAATTACCTTAAAAATA
* *
1617982 GTGGTATTCTGGTAATTACCTTGAAAA
1 GTGGTATTCTGATAATTACCTTAAAAA
1618009 GGGTGTTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (29 bp):
GTGGTATTCTGATAATTACCTTAAAAATA
Found at i:1618018 original size:29 final size:29
Alignment explanation
Indices: 1617986--1618054 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
1617976 AAAATAGTGG
* * *
1617986 TATTCTGGTAATTACCTTGAAAAGGGTGT
1 TATTCTCGTAATTAACTTGAAAAGGGTGC
* * *
1618015 TATTTTCGTAATTAATTTTAAAAGGGTGC
1 TATTCTCGTAATTAACTTGAAAAGGGTGC
*
1618044 TATTTTCGTAA
1 TATTCTCGTAA
1618055 AATGGTTGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (29 bp):
TATTCTCGTAATTAACTTGAAAAGGGTGC
Found at i:1618789 original size:24 final size:24
Alignment explanation
Indices: 1618754--1618826 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
1618744 ATTTTTGACG
*
1618754 GGATTTTGATATGATACTTGACCT
1 GGATTTTAATATGATACTTGACCT
* * *
1618778 GGATTTTTATATGATACATGACAT
1 GGATTTTAATATGATACTTGACCT
* * *
1618802 GGATTCTAATCTGCTACTTGACCT
1 GGATTTTAATATGATACTTGACCT
1618826 G
1 G
1618827 AATTATGTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (24 bp):
GGATTTTAATATGATACTTGACCT
Found at i:1618850 original size:2 final size:2
Alignment explanation
Indices: 1618843--1618877 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1618833 GTTTTAAATT
1618843 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
1618878 CCGTTATGAG
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:1620338 original size:471 final size:471
Alignment explanation
Indices: 1619456--1620549 Score: 2035
Period size: 471 Copynumber: 2.3 Consensus size: 471
1619446 GGGGGTTACA
* *
1619456 GAAAATGACGAGTTTAGAACATACTAAATAGTCGAGTAAGCATTGTGTAACTTTTAATAGCAAAG
1 GAAAATGACGAGTTTAGAACATACTAAATAGTCGGGTAAGCATTTTGTAACTTTTAATAGCAAAG
1619521 AGACTCAACAAAACAACACTCTATAGTTAGAAGATCATTTTGTAACTTTTAATAGTCAAGAGACT
66 AGACTCAACAAAACAACACTCTATAGTTAGAAGATCATTTTGTAACTTTTAATAGTCAAGAGACT
* *
1619586 CAATAAAGCATCACACTATAATGGTAAAGTACACAAATTGTCCCTTACTATATGGTCATGCTTCT
131 CAATAAAGCATCACACTATAGTGGTAAAGTACACAAATAGTCCCTTACTATATGGTCATGCTTCT
*
1619651 TTTAGTCCTCCAACTATTAAAAGTTACAAAATGATTCTCCAATTATTGGGTGTTGCTTTGTTGAA
196 TTTAGTCCTCCAACTATTAAAAGTTACAAAATGATTCTCCAATTATTGGGTATTGCTTTGTTGAA
1619716 TCCCCTGACTATTCAAAGTTACAAAATGGTCACCCCAATTATTTAGTATGTTCCAAACTCATCCT
261 TCCCCTGACTATTCAAAGTTACAAAATGGTCACCCCAATTATTTAGTATGTTCCAAACTCATCCT
*
1619781 TTATCATTAAAATTTTGACAATAGTATGAGTTGGATGTTAACCTGTTGACTGAGATATGATAATT
326 TTATCATTAAAATTTTGACAATAGTATGAGTTGGATGTTAACCCGTTGACTGAGATATGATAATT
1619846 TTTTTAGATTATGAGATTATATTTTATCATATCTCAGTCAGTATGTTAACATCCAACTCAGATTG
391 TTTTTAGATTATGAGATTATATTTTATCATATCTCAGTCAGTATGTTAACATCCAACTCAGATTG
1619911 CCATCACTTTTTAATG
456 CCATCACTTTTTAATG
*
1619927 GAAAATGATGAGTTTAGAACATACTAAATAGTCGGGTAAGCATTTTGTAACTTTTAATAGCAAAG
1 GAAAATGACGAGTTTAGAACATACTAAATAGTCGGGTAAGCATTTTGTAACTTTTAATAGCAAAG
*
1619992 AGACTCAACAAAACAACACTCTATAGTTAGAAGATCATTTTGTAACTTTTAATAGTTAAGAGACT
66 AGACTCAACAAAACAACACTCTATAGTTAGAAGATCATTTTGTAACTTTTAATAGTCAAGAGACT
1620057 CAATAAAGCATCACACTATAGTGGTAAAGTACACAAATAGTCCCTTACTATATGGTCATGCTTCT
131 CAATAAAGCATCACACTATAGTGGTAAAGTACACAAATAGTCCCTTACTATATGGTCATGCTTCT
*
1620122 TTTAGTCCTCCAACTATTAAAAGTTACAAAATGATTCTCCGATTATTGGGTATTGCTTTGTTGAA
196 TTTAGTCCTCCAACTATTAAAAGTTACAAAATGATTCTCCAATTATTGGGTATTGCTTTGTTGAA
*
1620187 TCCCCTGACTATTCAAAGTTACAAAATGGTCACCCCAATTATTTAGTATGTTCCAAACTCGTCCT
261 TCCCCTGACTATTCAAAGTTACAAAATGGTCACCCCAATTATTTAGTATGTTCCAAACTCATCCT
* *
1620252 TTTTCATTAAAATTTTGACAATAGTATGAGTTGGATGTTAACCCGTTTACTGAGATATGATAATT
326 TTATCATTAAAATTTTGACAATAGTATGAGTTGGATGTTAACCCGTTGACTGAGATATGATAATT
* *
1620317 TTTTTAGATTATGAGATTATATTTTATTATATCTCAGTCAGTATGTTAACATCCAGCTCAGATTG
391 TTTTTAGATTATGAGATTATATTTTATCATATCTCAGTCAGTATGTTAACATCCAACTCAGATTG
*
1620382 CCATCATTTTTTAATG
456 CCATCACTTTTTAATG
*
1620398 GAAAATGACGAGTTTAGAACATACTAAATAGTCGGGTAAGCATTTTGTAACTTTTAATAGCAGAG
1 GAAAATGACGAGTTTAGAACATACTAAATAGTCGGGTAAGCATTTTGTAACTTTTAATAGCAAAG
*
1620463 GGACTCAACAAAACAACACTCTATAGTTAGAAGATCATTTTGTAACTTTTAATAGTCAAGAGACT
66 AGACTCAACAAAACAACACTCTATAGTTAGAAGATCATTTTGTAACTTTTAATAGTCAAGAGACT
1620528 CAATAAAGCATCACACTATAGT
131 CAATAAAGCATCACACTATAGT
1620550 CGGGGGACTA
Statistics
Matches: 604, Mismatches: 19, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
471 604 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (471 bp):
GAAAATGACGAGTTTAGAACATACTAAATAGTCGGGTAAGCATTTTGTAACTTTTAATAGCAAAG
AGACTCAACAAAACAACACTCTATAGTTAGAAGATCATTTTGTAACTTTTAATAGTCAAGAGACT
CAATAAAGCATCACACTATAGTGGTAAAGTACACAAATAGTCCCTTACTATATGGTCATGCTTCT
TTTAGTCCTCCAACTATTAAAAGTTACAAAATGATTCTCCAATTATTGGGTATTGCTTTGTTGAA
TCCCCTGACTATTCAAAGTTACAAAATGGTCACCCCAATTATTTAGTATGTTCCAAACTCATCCT
TTATCATTAAAATTTTGACAATAGTATGAGTTGGATGTTAACCCGTTGACTGAGATATGATAATT
TTTTTAGATTATGAGATTATATTTTATCATATCTCAGTCAGTATGTTAACATCCAACTCAGATTG
CCATCACTTTTTAATG
Found at i:1624587 original size:20 final size:20
Alignment explanation
Indices: 1624540--1624589 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1624530 CACGGAATGT
*
1624540 AAGATTATCAGTAGGAATAA
1 AAGATTACCAGTAGGAATAA
1624560 AA-AGTTACCAGT-GGTAATAA
1 AAGA-TTACCAGTAGG-AATAA
1624580 AAGATTACCA
1 AAGATTACCA
1624590 ATAAATAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.12
20 22 0.85
21 1 0.04
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (20 bp):
AAGATTACCAGTAGGAATAA
Found at i:1625436 original size:36 final size:38
Alignment explanation
Indices: 1625387--1625463 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 38
1625377 ATAGTATTAC
*
1625387 AAATTGTAAAATATTTATAT-GTTTTCTTTAAAAAATT
1 AAATTGTAAAATATTTATATAATTTTCTTTAAAAAATT
* * *
1625424 AAATT-TATAATATTTATATAATTTTTTTTACAAAATT
1 AAATTGTAAAATATTTATATAATTTTCTTTAAAAAATT
1625461 AAA
1 AAA
1625464 AATATAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (38 bp):
AAATTGTAAAATATTTATATAATTTTCTTTAAAAAATT
Found at i:1627566 original size:21 final size:21
Alignment explanation
Indices: 1627542--1627597 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1627532 TTGCTCCTCT
*
1627542 TGCTCATCTTGTTCTTCATGC
1 TGCTCATCTTGTTCCTCATGC
*
1627563 TGCTCCTCTTGTTCCTCATG-
1 TGCTCATCTTGTTCCTCATGC
*
1627583 T-C-CATCATGTTCCTC
1 TGCTCATCTTGTTCCTC
1627598 TTCTTTTCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 11 0.35
19 1 0.03
20 1 0.03
21 18 0.58
ACGTcount: A:0.09, C:0.34, G:0.12, T:0.45
Consensus pattern (21 bp):
TGCTCATCTTGTTCCTCATGC
Found at i:1627591 original size:30 final size:30
Alignment explanation
Indices: 1627528--1627608 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
1627518 AAGCCTTCTC
* * * * *
1627528 CATGTTGCTCCTCTTGCTCATCTTGTTCTT
1 CATGTTGCTCCTCTTGTTCCTCATGTCCAT
*
1627558 CATGCTGCTCCTCTTGTTCCTCATGTCCAT
1 CATGTTGCTCCTCTTGTTCCTCATGTCCAT
* *
1627588 CATGTTCCTCTTCTT-TTCCTC
1 CATGTTGCTCCTCTTGTTCCTC
1627609 CCTCTTCTCC
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 6 0.14
30 36 0.86
ACGTcount: A:0.07, C:0.35, G:0.11, T:0.47
Consensus pattern (30 bp):
CATGTTGCTCCTCTTGTTCCTCATGTCCAT
Found at i:1627633 original size:18 final size:18
Alignment explanation
Indices: 1627610--1627659 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
1627600 CTTTTCCTCC
1627610 CTCTTCTCCCTCTCCCAT
1 CTCTTCTCCCTCTCCCAT
* *
1627628 CTCTTCTCCCTCACTCAT
1 CTCTTCTCCCTCTCCCAT
* *
1627646 CTCTACTTCCTCTC
1 CTCTTCTCCCTCTC
1627660 TTTTATCTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.08, C:0.52, G:0.00, T:0.40
Consensus pattern (18 bp):
CTCTTCTCCCTCTCCCAT
Found at i:1627883 original size:48 final size:48
Alignment explanation
Indices: 1627831--1627928 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 48
1627821 TTCCCCACAA
** *
1627831 CAGCCTCCTTTTTAACACCATCCTTATTCATCAAATTATCCTGCCCAC
1 CAGCCTCCTTTCCAACACCATCCTCATTCATCAAATTATCCTGCCCAC
*
1627879 CAGCCTCCTTTCCGACACCATCCTCATTCATCAAATTATCCTGCCCAC
1 CAGCCTCCTTTCCAACACCATCCTCATTCATCAAATTATCCTGCCCAC
1627927 CA
1 CA
1627929 AGACTCAACT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.24, C:0.41, G:0.05, T:0.30
Consensus pattern (48 bp):
CAGCCTCCTTTCCAACACCATCCTCATTCATCAAATTATCCTGCCCAC
Found at i:1628141 original size:48 final size:48
Alignment explanation
Indices: 1628089--1628186 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 48
1628079 TCCCCCACAA
** * *
1628089 CAGCCTCCTTTTTAACTCCATCCTTATTCATCAAATTATCCTGCCCAC
1 CAGCCTCCTTTCCAACACCATCCTCATTCATCAAATTATCCTGCCCAC
*
1628137 CAGCCTCCTTTCCGACACCATCCTCATTCATCAAATTATCCTGCCCAC
1 CAGCCTCCTTTCCAACACCATCCTCATTCATCAAATTATCCTGCCCAC
1628185 CA
1 CA
1628187 AGACTCAACT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.23, C:0.41, G:0.05, T:0.31
Consensus pattern (48 bp):
CAGCCTCCTTTCCAACACCATCCTCATTCATCAAATTATCCTGCCCAC
Found at i:1628209 original size:258 final size:258
Alignment explanation
Indices: 1627752--1628266 Score: 994
Period size: 258 Copynumber: 2.0 Consensus size: 258
1627742 ATGGCTGTCT
1627752 CCATCCAAATCCCACTGCACCAGTCGAGGTTCATCCTCCTTACTTTCCTCACAATCCATACCATC
1 CCATCCAAATCCCACTGCACCAGTCGAGGTTCATCCTCCTTACTTTCCTCACAATCCATACCATC
*
1627817 CTCATTCCCCACAACAGCCTCCTTTTTAACACCATCCTTATTCATCAAATTATCCTGCCCACCAG
66 CTCATCCCCCACAACAGCCTCCTTTTTAACACCATCCTTATTCATCAAATTATCCTGCCCACCAG
1627882 CCTCCTTTCCGACACCATCCTCATTCATCAAATTATCCTGCCCACCAAGACTCAACTCAATATTA
131 CCTCCTTTCCGACACCATCCTCATTCATCAAATTATCCTGCCCACCAAGACTCAACTCAATATTA
*
1627947 TGTTCGTCCAACTGTGATCCCTCGTGAGATTCATTAACCAAATCAGAAGACAACTTGAAATCA
196 TGTTCCTCCAACTGTGATCCCTCGTGAGATTCATTAACCAAATCAGAAGACAACTTGAAATCA
*
1628010 CCATCCAAATGCCACTGCACCAGTCGAGGTTCATCCTCCTTACTTTCCTCACAATCCATACCATC
1 CCATCCAAATCCCACTGCACCAGTCGAGGTTCATCCTCCTTACTTTCCTCACAATCCATACCATC
*
1628075 CTCATCCCCCACAACAGCCTCCTTTTTAACTCCATCCTTATTCATCAAATTATCCTGCCCACCAG
66 CTCATCCCCCACAACAGCCTCCTTTTTAACACCATCCTTATTCATCAAATTATCCTGCCCACCAG
1628140 CCTCCTTTCCGACACCATCCTCATTCATCAAATTATCCTGCCCACCAAGACTCAACTCAATATTA
131 CCTCCTTTCCGACACCATCCTCATTCATCAAATTATCCTGCCCACCAAGACTCAACTCAATATTA
1628205 TGTTCCTCCAACTGTGATCCCTCGTGAGATTCATTAACCAAATCAGAAGACAACTTGAAATC
196 TGTTCCTCCAACTGTGATCCCTCGTGAGATTCATTAACCAAATCAGAAGACAACTTGAAATC
1628267 CCCAGGAACA
Statistics
Matches: 253, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
258 253 1.00
ACGTcount: A:0.28, C:0.36, G:0.08, T:0.28
Consensus pattern (258 bp):
CCATCCAAATCCCACTGCACCAGTCGAGGTTCATCCTCCTTACTTTCCTCACAATCCATACCATC
CTCATCCCCCACAACAGCCTCCTTTTTAACACCATCCTTATTCATCAAATTATCCTGCCCACCAG
CCTCCTTTCCGACACCATCCTCATTCATCAAATTATCCTGCCCACCAAGACTCAACTCAATATTA
TGTTCCTCCAACTGTGATCCCTCGTGAGATTCATTAACCAAATCAGAAGACAACTTGAAATCA
Found at i:1634301 original size:30 final size:30
Alignment explanation
Indices: 1634245--1634311 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1634235 GTTGTTGCCA
** *
1634245 TTGTTGTTGTCCTCTTTGTTGTTAATGTTG
1 TTGTTGTTGTCCTCTTTGTTAATAATGATG
1634275 TTGTTGTTGTCCTCTTTGTTAATAATGATG
1 TTGTTGTTGTCCTCTTTGTTAATAATGATG
*
1634305 CTGTTGT
1 TTGTTGT
1634312 CGTTGTTGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.10, C:0.10, G:0.22, T:0.57
Consensus pattern (30 bp):
TTGTTGTTGTCCTCTTTGTTAATAATGATG
Found at i:1634349 original size:39 final size:39
Alignment explanation
Indices: 1634306--1634525 Score: 153
Period size: 39 Copynumber: 5.3 Consensus size: 39
1634296 ATAATGATGC
1634306 TGTTGTCGTTGTTGTTGCCTTCGTTGCCATCCTGGGTAG
1 TGTTGTCGTTGTTGTTGCCTTCGTTGCCATCCTGGGTAG
1634345 TGTTGAT-GTTGTTGTTGCCTTCGTTGCCATCCTTGGTGAAGTTGATG
1 TGTTG-TCGTTGTTGTTGCCTTCGTTGCCATCC-T-G-G--G-T-A-G
* * *
1634392 TTTTTGTTGTTGTTGTTGCCTTCGTTGCCATCCTTGGTGGTGTTG
1 -TGTTGTCGTTGTTGTTGCCTTCGTTGCCATCC----TGG-GTAG
* *
1634437 ATGTTGTTC-TTGTTGTTCCCTTCGTTGCCATCCTTGGT-G
1 -TGTTG-TCGTTGTTGTTGCCTTCGTTGCCATCCTGGGTAG
* * * * *
1634476 -G-TGTTGATATTGTTGCCTTCGTTGCCATCCTTGGTCG
1 TGTTGTCGTTGTTGTTGCCTTCGTTGCCATCCTGGGTAG
*
1634513 TGTTGACGTTGTT
1 TGTTGTCGTTGTT
1634526 AGTGGTGGTG
Statistics
Matches: 145, Mismatches: 17, Indels: 38
0.73 0.09 0.19
Matches are distributed among these distances:
35 1 0.01
36 28 0.19
37 2 0.01
38 1 0.01
39 37 0.26
40 4 0.03
41 3 0.02
42 1 0.01
44 1 0.01
45 29 0.20
46 2 0.01
47 3 0.02
48 30 0.21
49 1 0.01
50 1 0.01
51 1 0.01
ACGTcount: A:0.06, C:0.18, G:0.28, T:0.47
Consensus pattern (39 bp):
TGTTGTCGTTGTTGTTGCCTTCGTTGCCATCCTGGGTAG
Found at i:1634355 original size:36 final size:36
Alignment explanation
Indices: 1634315--1634525 Score: 143
Period size: 36 Copynumber: 5.2 Consensus size: 36
1634305 CTGTTGTCGT
*
1634315 TGTTGTTGCCTTCGTTGCCATCCTGGGTAGTGTTGA
1 TGTTGTTGCCTTCGTTGCCATCCTTGGTAGTGTTGA
*
1634351 TGTTGTTGTTGCCTTCGTTGCCATCCTTGGTGAAGTTGATGTTTTTGTTGT
1 ---TGTTGTTGCCTTCGTTGCCATCC-T--TG--G-T-A-G----TGTTGA
*
1634402 TGTTGTTGCCTTCGTTGCCATCCTTGGTGGTGTTGA
1 TGTTGTTGCCTTCGTTGCCATCCTTGGTAGTGTTGA
*
1634438 TGTTGTTCTTGTTGTTCCCTTCGTTGCCATCCTTGGTGGTGTTGA
1 ---TG---TTGTTG---CCTTCGTTGCCATCCTTGGTAGTGTTGA
* *
1634483 TATTGTTGCCTTCGTTGCCATCCTTGGTCGTGTTGA
1 TGTTGTTGCCTTCGTTGCCATCCTTGGTAGTGTTGA
*
1634519 CGTTGTT
1 TGTTGTT
1634526 AGTGGTGGTG
Statistics
Matches: 143, Mismatches: 8, Indels: 45
0.73 0.04 0.23
Matches are distributed among these distances:
36 37 0.26
39 31 0.22
40 2 0.01
42 9 0.06
43 1 0.01
44 1 0.01
45 31 0.22
46 1 0.01
47 2 0.01
48 23 0.16
51 5 0.03
ACGTcount: A:0.07, C:0.18, G:0.28, T:0.47
Consensus pattern (36 bp):
TGTTGTTGCCTTCGTTGCCATCCTTGGTAGTGTTGA
Found at i:1634355 original size:45 final size:45
Alignment explanation
Indices: 1634306--1634488 Score: 218
Period size: 45 Copynumber: 4.1 Consensus size: 45
1634296 ATAATGATGC
* *
1634306 TGTTGTCGTTGTTGTTGCCTTCGTTGCCATCCTGGGTAGTGTTGA
1 TGTTGTCGTTGTTGTTGCCTTCGTTGCCATCCTTGGTGGTGTTGA
**
1634351 -----T-GTTGTTGTTGCCTTCGTTGCCATCCTTGGTGAAGTTGA
1 TGTTGTCGTTGTTGTTGCCTTCGTTGCCATCCTTGGTGGTGTTGA
*
1634390 TGTTTTTGTTGTTGTTGTTGCCTTCGTTGCCATCCTTGGTGGTGTTGA
1 TG---TTGTCGTTGTTGTTGCCTTCGTTGCCATCCTTGGTGGTGTTGA
*
1634438 TGTTGTTC-TTGTTGTTCCCTTCGTTGCCATCCTTGGTGGTGTTGA
1 TGTTG-TCGTTGTTGTTGCCTTCGTTGCCATCCTTGGTGGTGTTGA
*
1634483 TATTGT
1 TGTTGT
1634489 TGCCTTCGTT
Statistics
Matches: 119, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
39 34 0.29
40 1 0.01
44 1 0.01
45 43 0.36
46 1 0.01
47 1 0.01
48 38 0.32
ACGTcount: A:0.07, C:0.17, G:0.28, T:0.48
Consensus pattern (45 bp):
TGTTGTCGTTGTTGTTGCCTTCGTTGCCATCCTTGGTGGTGTTGA
Found at i:1634358 original size:48 final size:48
Alignment explanation
Indices: 1634300--1634490 Score: 201
Period size: 48 Copynumber: 4.2 Consensus size: 48
1634290 TTGTTAATAA
* *
1634300 TGATGCTGTTGTCGTTGTTGTTGCCTTCGTTGCCATCCTGGGTAGTGT
1 TGATGTTGTTGTCGTTGTTGTTGCCTTCGTTGCCATCCTTGGTAGTGT
*
1634348 TGA--------T-GTTGTTGTTGCCTTCGTTGCCATCCTTGGTGA-AGT
1 TGATGTTGTTGTCGTTGTTGTTGCCTTCGTTGCCATCCTTGGT-AGTGT
* * *
1634387 TGATGTTTTTGTTGTTGTTGTTGCCTTCGTTGCCATCCTTGGTGGTGT
1 TGATGTTGTTGTCGTTGTTGTTGCCTTCGTTGCCATCCTTGGTAGTGT
* *
1634435 TGATGTTG-T-TC-TTGTTGTTCCCTTCGTTGCCATCCTTGGTGGTGT
1 TGATGTTGTTGTCGTTGTTGTTGCCTTCGTTGCCATCCTTGGTAGTGT
*
1634480 TGATATTGTTG
1 TGATGTTGTTG
1634491 CCTTCGTTGC
Statistics
Matches: 122, Mismatches: 8, Indels: 27
0.78 0.05 0.17
Matches are distributed among these distances:
39 34 0.28
40 2 0.02
45 40 0.33
46 2 0.02
47 2 0.02
48 42 0.34
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.48
Consensus pattern (48 bp):
TGATGTTGTTGTCGTTGTTGTTGCCTTCGTTGCCATCCTTGGTAGTGT
Found at i:1635552 original size:20 final size:20
Alignment explanation
Indices: 1635527--1635569 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1635517 TTGGTCAAAT
* *
1635527 TAATTTTTTTATGTTTAATG
1 TAATTTTTATAGGTTTAATG
1635547 TAATTTTTATAGGTTTAATG
1 TAATTTTTATAGGTTTAATG
1635567 TAA
1 TAA
1635570 AAAAGTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (20 bp):
TAATTTTTATAGGTTTAATG
Found at i:1641933 original size:24 final size:24
Alignment explanation
Indices: 1641906--1641993 Score: 70
Period size: 24 Copynumber: 3.7 Consensus size: 24
1641896 GATATGAGAA
*
1641906 ATCAAAACAGAATTCAGAACATAT
1 ATCAGAACAGAATTCAGAACATAT
* * * * *
1641930 ATCATAATAGAATCCA-AATCAGAA
1 ATCAGAACAGAATTCAGAA-CATAT
* ** *
1641954 ATCAGAACAAAATTCAGGTCATGT
1 ATCAGAACAGAATTCAGAACATAT
1641978 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
1641994 AGTCGGAAAT
Statistics
Matches: 47, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
23 2 0.04
24 45 0.96
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGAACATAT
Found at i:1641968 original size:48 final size:48
Alignment explanation
Indices: 1641902--1642007 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 48
1641892 CGGAGATATG
* * * *
1641902 AGAAATCAAAACAGAATTCAGAACATATATCATAATAGAATCCAAATC
1 AGAAATCAGAACAAAATTCAGAACATATATCAGAACAGAATCCAAATC
** * * *
1641950 AGAAATCAGAACAAAATTCAGGTCATGTATCAGAACAGAATTCAAGTC
1 AGAAATCAGAACAAAATTCAGAACATATATCAGAACAGAATCCAAATC
*
1641998 GGAAATCAGA
1 AGAAATCAGA
1642008 TAAAATATTT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (48 bp):
AGAAATCAGAACAAAATTCAGAACATATATCAGAACAGAATCCAAATC
Found at i:1642005 original size:24 final size:25
Alignment explanation
Indices: 1641951--1642007 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
1641941 ATCCAAATCA
* *
1641951 GAAATCAGAACAAAATTCAGGTCAT
1 GAAATCAGAACAAAATTCAAGTCAG
* *
1641976 G-TATCAGAACAGAATTCAAGTC-G
1 GAAATCAGAACAAAATTCAAGTCAG
1641999 GAAATCAGA
1 GAAATCAGA
1642008 TAAAATATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 1 0.04
24 24 0.92
25 1 0.04
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.19
Consensus pattern (25 bp):
GAAATCAGAACAAAATTCAAGTCAG
Found at i:1646760 original size:17 final size:17
Alignment explanation
Indices: 1646740--1646772 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1646730 CAGAACATAT
1646740 ATCAGAACAGAATTCAA
1 ATCAGAACAGAATTCAA
1646757 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
1646773 GGCCATGTAT
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:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (17 bp):
ATCAGAACAGAATTCAA
Found at i:1646771 original size:41 final size:41
Alignment explanation
Indices: 1646714--1646804 Score: 137
Period size: 41 Copynumber: 2.2 Consensus size: 41
1646704 GAGATATCAT
*
1646714 AAATCAAAACAGAATTCAGAACATATATCAGAACAGAATTC
1 AAATCAGAACAGAATTCAGAACATATATCAGAACAGAATTC
** *
1646755 AAATCAGAACAGAATTCAGGCCATGTATCAGAACAGAATTC
1 AAATCAGAACAGAATTCAGAACATATATCAGAACAGAATTC
*
1646796 AAGTCAGAA
1 AAATCAGAA
1646805 ATCAGATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (41 bp):
AAATCAGAACAGAATTCAGAACATATATCAGAACAGAATTC
Found at i:1646804 original size:17 final size:17
Alignment explanation
Indices: 1646741--1646804 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
1646731 AGAACATATA
*
1646741 TCAGAACAGAATTCAAA
1 TCAGAACAGAATTCAAG
1646758 TCAGAACAGAATTCAGGCCATG
1 TCAGAACAGAATTCA----A-G
1646780 TATCAGAACAGAATTCAAG
1 --TCAGAACAGAATTCAAG
1646799 TCAGAA
1 TCAGAA
1646805 ATCAGATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
17 21 0.54
19 1 0.03
20 1 0.03
21 1 0.03
24 15 0.38
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (17 bp):
TCAGAACAGAATTCAAG
Done.