Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007867.1 Hibiscus syriacus cultivar Beakdansim tig00110239_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: 3477501
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 18
Found at i:1220050 original size:15 final size:16
Alignment explanation
Indices: 1220022--1220051 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1220012 CTAAGGCCAT
1220022 TTTCTTATTTCTCTCC
1 TTTCTTATTTCTCTCC
1220038 TTTCTTA-TTCTCTC
1 TTTCTTATTTCTCTC
1220052 TTAGACGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTCTTATTTCTCTCC
Found at i:1221063 original size:135 final size:132
Alignment explanation
Indices: 1220905--1221256 Score: 378
Period size: 135 Copynumber: 2.6 Consensus size: 132
1220895 AGTCGAACAA
* * * *
1220905 AAGGTTGAATAAGTTCTTCTCATTATGCACTTCTTCTTCTTCTTCAGATGAGTTATTCTC-TTCA
1 AAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TCTCCAGATGAGTT-TTCTCATT-A
* * * * * *
1220969 TGAACTTCTTCTGGAAATGCTGATCCTTAAAAGAGG-T-GTTGATTCAACTTCATATGTGATGAA
63 TGAACTTCTTCTGGAAAT-ATGAT-CTCAAAAGAGGTTCGTTCATTCAACTCCATAAGTGATAAA
*
1221032 TTAAGAT
126 TCAAGAT
* *
1221039 AAGGGTCGAACAAGTTCTTTTCATTATGAACTTATTCTTCCTCTCCAGATGAGTTCTTCTCATTA
1 AA-GGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTCTCCAGATGAGTT-TTCTCATTA
* ** * *
1221104 TGAACTTCTTCTAG-AATATGATCTCAAGTGGGGTTCTTCTTTCATTCAACTCCATAAGTGATAA
63 TGAACTTCTTCTGGAAATATGATCTCAAAAGAGG---TTCGTTCATTCAACTCCATAAGTGATAA
1221168 ATCAAGAT
125 ATCAAGAT
1221176 AAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCCAGATGAG--TTCTCATTATGA
1 AAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTCTCCAGATGAGTTTTCTCATTATGA
*
1221238 ACTTTTTCTGGAAA-ATGAT
66 ACTTCTTCTGGAAATATGAT
1221257 GATGATGATC
Statistics
Matches: 186, Mismatches: 23, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
131 26 0.14
132 9 0.05
133 4 0.02
134 16 0.09
135 64 0.34
136 38 0.20
137 29 0.16
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (132 bp):
AAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTCTCCAGATGAGTTTTCTCATTATGA
ACTTCTTCTGGAAATATGATCTCAAAAGAGGTTCGTTCATTCAACTCCATAAGTGATAAATCAAG
AT
Found at i:1221319 original size:118 final size:117
Alignment explanation
Indices: 1221167--1221470 Score: 371
Period size: 118 Copynumber: 2.6 Consensus size: 117
1221157 ATAAGTGATA
* *
1221167 AATCAAG-ATAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTC-CAGATGAGTTCT
1 AATCAAGAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTCAGATGAGTTCT
** * * ** *
1221230 CATTATGAACTTTTTCTGGAAAATGATGATGATGATCTATCTCCTTCTGTGATTG
66 CATTATGAACTCCTTCTAG-AAAT--TGATGATGATATATCTCCTTCTGCAATAG
* *
1221285 AATTAAGCAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTC
1 AATCAAGAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTC-TCAGATGAG---
* *
1221349 TTCTCATTATGAACTCCTTCTAGAAATTGATGTTGATATATCTCTTTCTGCAATAG
62 TTCTCATTATGAACTCCTTCTAGAAATTGATGATGATATATCTCCTTCTGCAATAG
* * *
1221405 AGTCGAGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTC
1 AATCAAGAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTC-TCAGATGAGTTC
1221470 T
65 T
1221471 TCTTATTACA
Statistics
Matches: 162, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
118 48 0.30
119 3 0.02
120 39 0.24
121 48 0.30
122 4 0.02
123 20 0.12
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (117 bp):
AATCAAGAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTCAGATGAGTTCT
CATTATGAACTCCTTCTAGAAATTGATGATGATATATCTCCTTCTGCAATAG
Found at i:1221447 original size:121 final size:117
Alignment explanation
Indices: 1221168--1221596 Score: 400
Period size: 111 Copynumber: 3.7 Consensus size: 117
1221158 TAAGTGATAA
* * *
1221168 ATCAAG-ATAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTC--CAGATGAG---T
1 ATCAAGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCT
** * *
1221227 TCTCATTATGAACTTTTTCTGGAAAATGATGATGATGATCTATCTCCTTCTGTGATTG
66 TCTCATTATGAACTCCTTCT-G-AAAT--TGATGTTGATCTATCTCCTTC--TGAATG
* * *
1221285 AATTAAGCAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTC
1 -ATCAAGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTC
* *
1221349 TTCTCATTATGAACTCCTTCTAGAAATTGATGTTGATATATCTCTTTCTGCAATAG
65 TTCTCATTATGAACTCCTTCT-GAAATTGATGTTGATCTATCTCCTTCTG-AAT-G
*
1221405 AGTCGAGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTC
1 A-TCAAGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTC
* ** * * * * *** **
1221470 TTCTTATTACAAAC-ACTTATGGAA---ATGTTGATCCATCAAGTGATGAAT-
65 TTCTCATTATGAACTCCTTCTGAAATTGATGTTGATCTATCTCCTTCTGAATG
* * *
1221518 -TCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTC-TCCTTTTTCAGATGAGTTC
1 ATCAAGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTC
1221581 TTCTCATTATGAACTC
65 TTCTCATTATGAACTC
1221597 TACCTGGCAA
Statistics
Matches: 264, Mismatches: 35, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
110 3 0.01
111 66 0.25
115 3 0.01
116 14 0.05
118 45 0.17
119 9 0.03
120 38 0.14
121 62 0.23
122 4 0.02
123 20 0.08
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Consensus pattern (117 bp):
ATCAAGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCT
TCTCATTATGAACTCCTTCTGAAATTGATGTTGATCTATCTCCTTCTGAATG
Found at i:1222070 original size:22 final size:22
Alignment explanation
Indices: 1222045--1222124 Score: 124
Period size: 22 Copynumber: 3.6 Consensus size: 22
1222035 AATAAAGCTT
* **
1222045 TCATCTTTGAAAAGAGGATCTA
1 TCATCTTTGAAGAGAAAATCTA
1222067 TCATCTTTGAAGAGAAAATCTA
1 TCATCTTTGAAGAGAAAATCTA
1222089 TCATCTTTGAAGAGAAAATCTA
1 TCATCTTTGAAGAGAAAATCTA
*
1222111 TCATCATTGAAGAG
1 TCATCTTTGAAGAG
1222125 TGTAGATATA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (22 bp):
TCATCTTTGAAGAGAAAATCTA
Found at i:1228510 original size:42 final size:42
Alignment explanation
Indices: 1228436--1228519 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
1228426 TAGTTTTTTT
* * * *
1228436 CATTTGCTCTTTTGAATCATCTTGAAATTTTTTTGCTTGATC
1 CATTTGCTCATTTGAATAATCTGGAAATTTTTTTACTTGATC
1228478 CATTTGCTCATTTGAATAATTCTGGAAA-TTTTTTACTTGATC
1 CATTTGCTCATTTGAATAA-TCTGGAAATTTTTTTACTTGATC
1228520 AAACATCTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 30 0.81
43 7 0.19
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (42 bp):
CATTTGCTCATTTGAATAATCTGGAAATTTTTTTACTTGATC
Found at i:1230410 original size:12 final size:12
Alignment explanation
Indices: 1230386--1230448 Score: 58
Period size: 12 Copynumber: 5.3 Consensus size: 12
1230376 TTAATACTTG
1230386 AAAATAA-AATA
1 AAAATAATAATA
*
1230397 AAAATATTAATA
1 AAAATAATAATA
1230409 AAAATAATATATA
1 AAAATAATA-ATA
* * *
1230422 TAAAT-ATTATG
1 AAAATAATAATA
*
1230433 AAAATAATAAGA
1 AAAATAATAATA
1230445 AAAA
1 AAAA
1230449 ATTTTGAAAG
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
11 12 0.30
12 21 0.52
13 7 0.17
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:1230436 original size:25 final size:23
Alignment explanation
Indices: 1230386--1230448 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
1230376 TTAATACTTG
1230386 AAAATAA-AATAAAAATATTAAT
1 AAAATAATAATAAAAATATTAAT
*
1230408 AAAAATAATATATATAAATATT-AT
1 -AAAATAATA-ATAAAAATATTAAT
*
1230432 GAAAATAATAAGAAAAA
1 -AAAATAATAATAAAAA
1230449 ATTTTGAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 12 0.35
24 12 0.35
25 10 0.29
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (23 bp):
AAAATAATAATAAAAATATTAAT
Found at i:1231223 original size:16 final size:17
Alignment explanation
Indices: 1231202--1231241 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
1231192 AAAATATGAT
1231202 TAATTTTATC-TAAAAG
1 TAATTTTATCATAAAAG
*
1231218 TAA-TTTA-CATAAAAT
1 TAATTTTATCATAAAAG
1231233 TAATTTTAT
1 TAATTTTAT
1231242 AAATAGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
14 1 0.05
15 12 0.60
16 7 0.35
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (17 bp):
TAATTTTATCATAAAAG
Found at i:1231306 original size:3 final size:3
Alignment explanation
Indices: 1231298--1231323 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1231288 TATATGACTA
1231298 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1231324 AACATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1231351 original size:25 final size:28
Alignment explanation
Indices: 1231313--1231366 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 28
1231303 TAATAATAAT
1231313 AATAATAATAAAAC-AT-A-TAAAATTA
1 AATAATAATAAAACAATGACTAAAATTA
1231338 AATAATAACT-AAACAATGACTAAAATTA
1 AATAATAA-TAAAACAATGACTAAAATTA
1231366 A
1 A
1231367 TAACATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 12 0.48
26 3 0.12
27 1 0.04
28 9 0.36
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (28 bp):
AATAATAATAAAACAATGACTAAAATTA
Found at i:1231614 original size:26 final size:26
Alignment explanation
Indices: 1231564--1231614 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1231554 AGTCTATTAA
*
1231564 AATAAAAATAAAAAAAATCACAATTG
1 AATAAAAATAAAAAAAATCAAAATTG
* * *
1231590 AATAATAATAAATAAAATTAAAATT
1 AATAAAAATAAAAAAAATCAAAATT
1231615 ACATGTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (26 bp):
AATAAAAATAAAAAAAATCAAAATTG
Found at i:1232861 original size:48 final size:48
Alignment explanation
Indices: 1232779--1232877 Score: 153
Period size: 48 Copynumber: 2.1 Consensus size: 48
1232769 GCATGAAGAA
*
1232779 GTTGATGATGCAAGAGTCTCCCATGGAGTCGAGGTGGTCAATAATGAG
1 GTTGATGATGCAAGAGTCTCCCATGAAGTCGAGGTGGTCAATAATGAG
* * * *
1232827 GTTGATGATGCAAGAGTCTCTCATGAAGTTGAGGTGGTTACTAATGAG
1 GTTGATGATGCAAGAGTCTCCCATGAAGTCGAGGTGGTCAATAATGAG
1232875 GTT
1 GTT
1232878 CAACATAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.26, C:0.12, G:0.32, T:0.29
Consensus pattern (48 bp):
GTTGATGATGCAAGAGTCTCCCATGAAGTCGAGGTGGTCAATAATGAG
Found at i:1244912 original size:31 final size:31
Alignment explanation
Indices: 1244801--1244912 Score: 129
Period size: 31 Copynumber: 3.6 Consensus size: 31
1244791 TTATATTTTA
*
1244801 CGGAACATATGGACAGAATTACCTATG-TCTTT
1 CGGAACATATGGACAG-TTTACCTATGTTC-TT
* *
1244833 C-GAGACATATGGACAGTATACCTATGTTCTA
1 CGGA-ACATATGGACAGTTTACCTATGTTCTT
* *
1244864 AGGAACATATGGACAGTTTACCTAGGTTCTT
1 CGGAACATATGGACAGTTTACCTATGTTCTT
*
1244895 CGGAACCTATGGACAGTT
1 CGGAACATATGGACAGTT
1244913 GCCGAGGATC
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
31 51 0.75
32 17 0.25
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (31 bp):
CGGAACATATGGACAGTTTACCTATGTTCTT
Found at i:1255812 original size:20 final size:20
Alignment explanation
Indices: 1255787--1255831 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1255777 TATCTGGAAA
* *
1255787 AAAAATCTGGTCTGGGGTTT
1 AAAAATCCGGCCTGGGGTTT
1255807 AAAAATCCGGCCTGGGGTTT
1 AAAAATCCGGCCTGGGGTTT
1255827 AAAAA
1 AAAAA
1255832 ATTGGATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGCCTGGGGTTT
Found at i:1261304 original size:24 final size:24
Alignment explanation
Indices: 1261272--1261340 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
1261262 AGCTTGTGAA
1261272 TCACTTGGAGAGAGAATCAATTCC
1 TCACTTGGAGAGAGAATCAATTCC
1261296 TCACTTGGAGAGAGAATCAATTCC
1 TCACTTGGAGAGAGAATCAATTCC
* *
1261320 TCACCTGGAGAGATAATCAAT
1 TCACTTGGAGAGAGAATCAAT
1261341 CACCTTCAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (24 bp):
TCACTTGGAGAGAGAATCAATTCC
Found at i:1264361 original size:20 final size:20
Alignment explanation
Indices: 1264309--1264362 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1264299 AACTTAATAT
*
1264309 TATTATTTTTAAAATATTAAAA
1 TATTATTTTT--ATTATTAAAA
*
1264331 TATT-TAATTTATTATTAAAA
1 TATTAT-TTTTATTATTAAAA
1264351 TATTATTTTTAT
1 TATTATTTTTAT
1264363 AATTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 18 0.67
21 2 0.07
22 7 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTTTTATTATTAAAA
Found at i:1264402 original size:31 final size:29
Alignment explanation
Indices: 1264338--1264419 Score: 85
Period size: 33 Copynumber: 2.7 Consensus size: 29
1264328 AAATATTTAA
* * *
1264338 TTTATT-ATTAAAATATTATTTTTATAAT
1 TTTATTAATAAAAATATTATATTGATAAT
1264366 TTTATTAATAAAAATATTAATATTGATATAT
1 TTTATTAATAAAAATATT-ATATTGATA-AT
*
1264397 TTTATTGAAATAAAAATTTTATA
1 TTTATT--AATAAAAATATTATA
1264420 AATTATATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 6 0.13
29 10 0.22
30 7 0.16
31 8 0.18
32 3 0.07
33 11 0.24
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TTTATTAATAAAAATATTATATTGATAAT
Found at i:1264510 original size:23 final size:23
Alignment explanation
Indices: 1264461--1264511 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1264451 GTGTTATATT
**
1264461 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
1264484 ATATTTTAAATATTTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
1264507 ATATT
1 ATATT
1264512 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:1264567 original size:19 final size:19
Alignment explanation
Indices: 1264494--1264567 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
1264484 ATATTTTAAA
1264494 TATTT-TTATTAA-AATAT
1 TATTTATTATTAATAATAT
*
1264511 TATTAGATTATTATATTAATAT
1 TATT-TATTATTA-A-TAATAT
** *
1264533 TAAATA-TATAAATAATAT
1 TATTTATTATTAATAATAT
1264551 TATTTATTATTAATAAT
1 TATTTATTATTAATAAT
1264568 TTAATAATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
17 4 0.09
18 10 0.23
19 16 0.37
20 5 0.12
21 1 0.02
22 7 0.16
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (19 bp):
TATTTATTATTAATAATAT
Found at i:1264674 original size:23 final size:23
Alignment explanation
Indices: 1264644--1264694 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
1264634 TTAAAATAAA
1264644 AATATAATTGATTATATTATTAT
1 AATATAATTGATTATATTATTAT
*
1264667 AATATAATTGATTATTTTATTAT
1 AATATAATTGATTATATTATTAT
1264690 AATAT
1 AATAT
1264695 TAAAAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
AATATAATTGATTATATTATTAT
Found at i:1264712 original size:22 final size:23
Alignment explanation
Indices: 1264684--1264730 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
1264674 TTGATTATTT
1264684 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
*
1264706 TATTATATTATTAAAAATATTAA
1 TATTATAATATTAAAAATATTAA
1264729 TA
1 TA
1264731 AATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:1264729 original size:23 final size:24
Alignment explanation
Indices: 1264685--1264762 Score: 90
Period size: 23 Copynumber: 3.3 Consensus size: 24
1264675 TGATTATTTT
*
1264685 ATTATAATATTAAAAATA-TAAT-
1 ATTATATTATTAAAAATATTAATA
1264707 ATTATATTATTAAAAATATTAATA
1 ATTATATTATTAAAAATATTAATA
* * *
1264731 AATATATT-TTAAATATTTTAATA
1 ATTATATTATTAAAAATATTAATA
1264754 ATTAATATT
1 ATT-ATATT
1264763 TTTGATTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 17 0.35
23 19 0.40
24 12 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTATATTATTAAAAATATTAATA
Found at i:1264738 original size:21 final size:22
Alignment explanation
Indices: 1264691--1264747 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1264681 TTTTATTATA
*
1264691 ATATTAAAAATA-TAATATTAT
1 ATATTAAAAATATTAATATAAT
1264712 ATTATTAAAAATATTAATA-AAT
1 A-TATTAAAAATATTAATATAAT
**
1264734 ATATTTTAAATATT
1 ATATTAAAAATATT
1264748 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 12 0.39
22 14 0.45
23 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATTAAAAATATTAATATAAT
Found at i:1267559 original size:23 final size:23
Alignment explanation
Indices: 1267533--1267615 Score: 80
Period size: 23 Copynumber: 3.5 Consensus size: 23
1267523 TATTTATTTA
1267533 TTTAAATAAAAATTATTTAAAAT
1 TTTAAATAAAAATTATTTAAAAT
* *
1267556 TTTATATATAAATTATTTAAATAT
1 TTTAAATAAAAATTATTTAAA-AT
*
1267580 TTTAAA-AATTAAA-TATTTAAAAA
1 TTTAAATAA--AAATTATTTAAAAT
*
1267603 ATTAAATATAAAA
1 TTTAAATA-AAAA
1267616 AATTAAAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
23 29 0.59
24 16 0.33
25 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAAATAAAAATTATTTAAAAT
Found at i:1267591 original size:16 final size:16
Alignment explanation
Indices: 1267572--1267622 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
1267562 TATAAATTAT
*
1267572 TTAAATATTTTAAAAA
1 TTAAATATTTAAAAAA
1267588 TTAAATATTTAAAAAA
1 TTAAATATTTAAAAAA
1267604 TTAAATA--TAAAAAA
1 TTAAATATTTAAAAAA
1267618 TTAAA
1 TTAAA
1267623 AATAAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
14 12 0.35
16 22 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAATATTTAAAAAA
Found at i:1267614 original size:14 final size:14
Alignment explanation
Indices: 1267583--1267629 Score: 67
Period size: 14 Copynumber: 3.2 Consensus size: 14
1267573 TAAATATTTT
1267583 AAAAATTAAATATTTA
1 AAAAATTAAATA--TA
1267599 AAAAATTAAATATA
1 AAAAATTAAATATA
*
1267613 AAAAATTAAAAATA
1 AAAAATTAAATATA
1267627 AAA
1 AAA
1267630 TTTAAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 18 0.60
16 12 0.40
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAATTAAATATA
Found at i:1267623 original size:21 final size:21
Alignment explanation
Indices: 1267599--1267645 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1267589 TAAATATTTA
*
1267599 AAAAATTAAATATAAAAAATT
1 AAAAATAAAATATAAAAAATT
* **
1267620 AAAAATAAAATTTAAATTATT
1 AAAAATAAAATATAAAAAATT
1267641 AAAAA
1 AAAAA
1267646 AATATATTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAATAAAATATAAAAAATT
Found at i:1267645 original size:16 final size:15
Alignment explanation
Indices: 1267572--1267646 Score: 75
Period size: 16 Copynumber: 5.0 Consensus size: 15
1267562 TATAAATTAT
*
1267572 TTAAATATTTTAAAAA
1 TTAAATA-TTAAAAAA
1267588 TTAAATATTTAAAAAA
1 TTAAATA-TTAAAAAA
1267604 TTAAATA-TAAAAAA
1 TTAAATATTAAAAAA
* *
1267618 TTAAA-AAT-AAAAT
1 TTAAATATTAAAAAA
1267631 TTAAATTATTAAAAAA
1 TTAAA-TATTAAAAAA
1267647 ATATATTGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
13 10 0.20
14 13 0.25
15 2 0.04
16 26 0.51
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAAATATTAAAAAA
Found at i:1270259 original size:23 final size:23
Alignment explanation
Indices: 1270223--1270311 Score: 92
Period size: 23 Copynumber: 4.0 Consensus size: 23
1270213 GAGTCGAGGG
*
1270223 TTCTACGCGGTCCTTTGGGATAA
1 TTCTACGCGGTCCTTTGGGACAA
* * *
1270246 TTCTACGTGTTCCTTTGGGACAT
1 TTCTACGCGGTCCTTTGGGACAA
*
1270269 TTCTACGCGGTCCTTCGGGAC-A
1 TTCTACGCGGTCCTTTGGGACAA
* * *
1270291 -TCTATGTGGTCTTTTGGGACA
1 TTCTACGCGGTCCTTTGGGACA
1270312 TTTTATGTGG
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
21 16 0.30
23 37 0.70
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (23 bp):
TTCTACGCGGTCCTTTGGGACAA
Found at i:1270275 original size:46 final size:44
Alignment explanation
Indices: 1270223--1270314 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 44
1270213 GAGTCGAGGG
* *
1270223 TTCTACGCGGTCCTTTGGGATAATTCTACGTGTTCCTTTGGGACAT
1 TTCTACGCGGTCCTTCGGGA-AA-TCTACGTGGTCCTTTGGGACAT
* * *
1270269 TTCTACGCGGTCCTTCGGGACATCTATGTGGTCTTTTGGGACAT
1 TTCTACGCGGTCCTTCGGGAAATCTACGTGGTCCTTTGGGACAT
1270313 TT
1 TT
1270315 TATGTGGCAC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
44 21 0.51
45 1 0.02
46 19 0.46
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.39
Consensus pattern (44 bp):
TTCTACGCGGTCCTTCGGGAAATCTACGTGGTCCTTTGGGACAT
Found at i:1270321 original size:22 final size:22
Alignment explanation
Indices: 1270231--1270321 Score: 76
Period size: 23 Copynumber: 4.1 Consensus size: 22
1270221 GGTTCTACGC
* * *
1270231 GGTCCTTTGGGATAATTCTACGT
1 GGTCCTTTGGGA-CATTTTATGT
* * *
1270254 GTTCCTTTGGGACATTTCTACGC
1 GGTCCTTTGGGACATTT-TATGT
* *
1270277 GGTCCTTCGGGACA-TCTATGT
1 GGTCCTTTGGGACATTTTATGT
*
1270298 GGTCTTTTGGGACATTTTATGT
1 GGTCCTTTGGGACATTTTATGT
1270320 GG
1 GG
1270322 CACTTTGTTG
Statistics
Matches: 54, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
21 15 0.28
22 12 0.22
23 27 0.50
ACGTcount: A:0.14, C:0.19, G:0.27, T:0.40
Consensus pattern (22 bp):
GGTCCTTTGGGACATTTTATGT
Found at i:1280998 original size:31 final size:29
Alignment explanation
Indices: 1280963--1281029 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
1280953 AAATATATAA
* *
1280963 TTCAAAAATTACAATTTAGGTCCCTAAACTT
1 TTCAAAAATTACAATTTAGCT-ACTAAAC-T
** *
1280994 TTCAAAGTTTATAATTTAGCTACTAAACT
1 TTCAAAAATTACAATTTAGCTACTAAACT
1281023 TTCAAAA
1 TTCAAAA
1281030 CTTATATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 7 0.23
30 6 0.20
31 17 0.57
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37
Consensus pattern (29 bp):
TTCAAAAATTACAATTTAGCTACTAAACT
Found at i:1281034 original size:29 final size:31
Alignment explanation
Indices: 1280963--1281047 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 31
1280953 AAATATATAA
* * *
1280963 TTCAAAAATTACAATTTAGGTCCCTAAACTT
1 TTCAAAAATTATAATTTAGCTCACTAAACTT
**
1280994 TTCAAAGTTTATAATTTAGCT-ACTAAAC-T
1 TTCAAAAATTATAATTTAGCTCACTAAACTT
* *
1281023 TTCAAAACTTATATTTTAG-TCACTA
1 TTCAAAAATTATAATTTAGCTCACTA
1281048 GTCAGTATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
28 1 0.02
29 21 0.47
30 6 0.13
31 17 0.38
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (31 bp):
TTCAAAAATTATAATTTAGCTCACTAAACTT
Found at i:1281273 original size:19 final size:20
Alignment explanation
Indices: 1281217--1281257 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1281207 ATATACATGT
1281217 AATATATATACATATTATAA
1 AATATATATACATATTATAA
1281237 AATATATATACATATTATAA
1 AATATATATACATATTATAA
1281257 A
1 A
1281258 CACTTATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
AATATATATACATATTATAA
Found at i:1282029 original size:24 final size:24
Alignment explanation
Indices: 1282002--1282053 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
1281992 TAACTCGTAT
*
1282002 AAATTGCACCGAAGTGCCGTGTAG
1 AAATTGCACCGAAGTGCCGTATAG
1282026 AAATTGCACCGAAGTGCCGTATAG
1 AAATTGCACCGAAGTGCCGTATAG
1282050 AAAT
1 AAAT
1282054 GTTACAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (24 bp):
AAATTGCACCGAAGTGCCGTATAG
Found at i:1282107 original size:23 final size:23
Alignment explanation
Indices: 1282046--1282131 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
1282036 GAAGTGCCGT
* *
1282046 ATAGAAATGTTACAAAGGACCAC
1 ATAGAAATGTCACGAAGGACCAC
* * *
1282069 ATAGTATTATCACGAAGGACCAC
1 ATAGAAATGTCACGAAGGACCAC
* *
1282092 ATAGAAATGTCCCGAAGGACCGC
1 ATAGAAATGTCACGAAGGACCAC
* *
1282115 GTAGAAATGTCCCGAAG
1 ATAGAAATGTCACGAAG
1282132 AACCGCGTAG
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.17
Consensus pattern (23 bp):
ATAGAAATGTCACGAAGGACCAC
Found at i:1282136 original size:23 final size:23
Alignment explanation
Indices: 1282093--1282141 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
1282083 AAGGACCACA
*
1282093 TAGAAATGTCCCGAAGGACCGCG
1 TAGAAATGTCCCGAAGAACCGCG
1282116 TAGAAATGTCCCGAAGAACCGCG
1 TAGAAATGTCCCGAAGAACCGCG
1282139 TAG
1 TAG
1282142 TACCCTCGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.29, T:0.14
Consensus pattern (23 bp):
TAGAAATGTCCCGAAGAACCGCG
Found at i:1282280 original size:44 final size:44
Alignment explanation
Indices: 1282227--1282318 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
1282217 TTTATTATAT
* * *
1282227 CTTATATCACATAG-ACAAATAATCACGTAGGTCATGTCACATGG
1 CTTATATCACAT-GTACAAATAATCACGTAGATCATATCACATAG
* *
1282271 CTTATATCACATGTTCATATAATCACGTAGATCATATCACATAG
1 CTTATATCACATGTACAAATAATCACGTAGATCATATCACATAG
1282315 CTTA
1 CTTA
1282319 ATCTTGTCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.32
Consensus pattern (44 bp):
CTTATATCACATGTACAAATAATCACGTAGATCATATCACATAG
Found at i:1288888 original size:24 final size:24
Alignment explanation
Indices: 1288861--1288917 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
1288851 CACCAAAGCT
*
1288861 CGTATAAATTACACCGAAGTGCCA
1 CGTAGAAATTACACCGAAGTGCCA
** *
1288885 CGTAGAAATTGTACCGAAGTGCCT
1 CGTAGAAATTACACCGAAGTGCCA
*
1288909 CATAGAAAT
1 CGTAGAAAT
1288918 GTCTCGAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
CGTAGAAATTACACCGAAGTGCCA
Found at i:1288935 original size:23 final size:23
Alignment explanation
Indices: 1288874--1288996 Score: 83
Period size: 23 Copynumber: 5.3 Consensus size: 23
1288864 ATAAATTACA
* *
1288874 CCGAAGTG-CCACGTAGAAATTGTA
1 CCGAA-TGACCACATAGAAA-TGTC
*
1288898 CCGAAGTG-CCTCATAGAAATGTC
1 CCGAA-TGACCACATAGAAATGTC
* *
1288921 TCGAATGACCACATA-ATATTGTC
1 CCGAATGACCACATAGA-AATGTC
* * * *
1288944 CCGAAGGACCGCGTGGAAATG-C
1 CCGAATGACCACATAGAAATGTC
*
1288966 TCCGAATGACCACATAGAATTGTC
1 -CCGAATGACCACATAGAAATGTC
1288990 CCGAATG
1 CCGAATG
1288997 GCCGCGTAGA
Statistics
Matches: 77, Mismatches: 17, Indels: 11
0.73 0.16 0.10
Matches are distributed among these distances:
22 4 0.05
23 54 0.70
24 19 0.25
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (23 bp):
CCGAATGACCACATAGAAATGTC
Found at i:1288963 original size:46 final size:46
Alignment explanation
Indices: 1288911--1289009 Score: 141
Period size: 46 Copynumber: 2.2 Consensus size: 46
1288901 AAGTGCCTCA
1288911 TAGAAATG-TCTCGAATGACCACATA-ATATTGTCCCGAA-GGACCGCG
1 TAGAAATGCTC-CGAATGACCACATAGA-ATTGTCCCGAATGG-CCGCG
*
1288957 TGGAAATGCTCCGAATGACCACATAGAATTGTCCCGAATGGCCGCG
1 TAGAAATGCTCCGAATGACCACATAGAATTGTCCCGAATGGCCGCG
1289003 TAGAAAT
1 TAGAAAT
1289010 CTCGACTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
46 43 0.90
47 5 0.10
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.21
Consensus pattern (46 bp):
TAGAAATGCTCCGAATGACCACATAGAATTGTCCCGAATGGCCGCG
Found at i:1289006 original size:23 final size:23
Alignment explanation
Indices: 1288938--1289007 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
1288928 ACCACATAAT
*
1288938 ATTGTCCCGAA-GGACCGCGTGGA
1 ATTGTCCCGAATGG-CCGCGTAGA
* * * *
1288961 AATG-CTCCGAATGACCACATAGA
1 ATTGTC-CCGAATGGCCGCGTAGA
1288984 ATTGTCCCGAATGGCCGCGTAGA
1 ATTGTCCCGAATGGCCGCGTAGA
1289007 A
1 A
1289008 ATCTCGACTC
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
22 1 0.03
23 32 0.91
24 2 0.06
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.19
Consensus pattern (23 bp):
ATTGTCCCGAATGGCCGCGTAGA
Found at i:1289144 original size:44 final size:44
Alignment explanation
Indices: 1289091--1289182 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
1289081 TTTATTATAT
** * *
1289091 CTTATATCACATATACAAATAATCACGTAGGTCATGTCACATGG
1 CTTATATCACATATACAAATAATCACGTAAATCATATCACATAG
* ** *
1289135 CTTATATCACATGTTTATATAATCACGTAAATCATATCACATAG
1 CTTATATCACATATACAAATAATCACGTAAATCATATCACATAG
1289179 CTTA
1 CTTA
1289183 ATCTTATCCT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.34
Consensus pattern (44 bp):
CTTATATCACATATACAAATAATCACGTAAATCATATCACATAG
Found at i:1291349 original size:21 final size:21
Alignment explanation
Indices: 1291323--1291382 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1291313 GTGAACTGCC
1291323 ATATTAATGA-TGTGGATCATT
1 ATATTAAT-ATTGTGGATCATT
*
1291344 ATATTAGTATTGTGGATCATT
1 ATATTAATATTGTGGATCATT
* * *
1291365 ATGTTAGTACTGTGGATC
1 ATATTAATATTGTGGATC
1291383 GTCATGTTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 34 0.97
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (21 bp):
ATATTAATATTGTGGATCATT
Found at i:1291389 original size:21 final size:21
Alignment explanation
Indices: 1291333--1291398 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1291323 ATATTAATGA
* *
1291333 TGTGGATCATTATATTAGTAT
1 TGTGGATCATTATGTTAGTAC
1291354 TGTGGATCATTATGTTAGTAC
1 TGTGGATCATTATGTTAGTAC
* *
1291375 TGTGGATCGTCATGTTAGTAC
1 TGTGGATCATTATGTTAGTAC
1291396 TGT
1 TGT
1291399 AAAATATCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.23, C:0.09, G:0.24, T:0.44
Consensus pattern (21 bp):
TGTGGATCATTATGTTAGTAC
Found at i:1292119 original size:20 final size:20
Alignment explanation
Indices: 1292094--1292140 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1292084 AAAAGAAATT
*
1292094 TCGAGATTAGCAATCCTCCA
1 TCGAGAATAGCAATCCTCCA
1292114 TCGAGAATAGCAATCCTCCA
1 TCGAGAATAGCAATCCTCCA
1292134 TCGAGAA
1 TCGAGAA
1292141 AGCTATCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (20 bp):
TCGAGAATAGCAATCCTCCA
Found at i:1292299 original size:19 final size:20
Alignment explanation
Indices: 1292257--1292300 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1292247 AATTGTTTCT
*
1292257 TAAAAAAAGCATTGAATCAT
1 TAAAAAAAGCATTGAATCAG
* *
1292277 TAAAAAAAG-ATTTAATTAG
1 TAAAAAAAGCATTGAATCAG
1292296 TAAAA
1 TAAAA
1292301 TAAACTAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.27
Consensus pattern (20 bp):
TAAAAAAAGCATTGAATCAG
Found at i:1294244 original size:3 final size:3
Alignment explanation
Indices: 1294238--1294286 Score: 71
Period size: 3 Copynumber: 15.3 Consensus size: 3
1294228 TTAAAAAAAT
1294238 TAA TAA TAA TAA TAA TAA TAA GTAA TTAA TAA TAA TAA TAA TAA GTAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA -TAA TAA TAA TAA TAA TAA -TAA
1294286 T
1 T
1294287 TAAAAGTAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
3 34 0.79
4 9 0.21
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1294271 original size:23 final size:23
Alignment explanation
Indices: 1294241--1294289 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1294231 AAAAAATTAA
1294241 TAATAATAATAATAATAAGTAAT
1 TAATAATAATAATAATAAGTAAT
1294264 TAATAATAATAATAATAAGTAAT
1 TAATAATAATAATAATAAGTAAT
1294287 TAA
1 TAA
1294290 AAGTAGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
TAATAATAATAATAATAAGTAAT
Found at i:1294821 original size:138 final size:138
Alignment explanation
Indices: 1294474--1294888 Score: 523
Period size: 138 Copynumber: 3.0 Consensus size: 138
1294464 TTAGGTAAAT
* * * * * *
1294474 TTGGAGATAACACGATTCCTACGTGATGAGGAAATCTGGTTATCTAAGGTTGACACTACTCCTAC
1 TTGGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACACAACTCCTAC
* * *
1294539 ATGATGAGGAGATATGGTC-AGTGGATGACACTA-CTCCTACGTGATGAGGATGTCTGGCCATCT
66 GTGATGAGGAGATATGGTCGA-TGGATGACAC-AGTTCCTACGTGATGAGGACGTCTGGCCATCT
1294602 TTAGGGATAA
129 TTAGGGATAA
* * *
1294612 -TGGAGATAATACGGTTCTTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACACAACTCCTAT
1 TTGGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACACAACTCCTAC
* * * * * *
1294676 GTAATGAGGTGATTTGTTCGATGGATGACACGGTTCCTACGTGATGAGGACGTCTGGTCATCTTT
66 GTGATGAGGAGATATGGTCGATGGATGACACAGTTCCTACGTGATGAGGACGTCTGGCCATCTTT
1294741 AGGGATAA
131 AGGGATAA
* * * * * **
1294749 TTGGAGACAACACGGTTCCTACGCGATAACGAAGTCTGACTATCTAAAGATGACGA-GGCTCCTA
1 TTGGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGAC-ACAACTCCTA
* * *
1294813 CGTGATGAGGAGATCTGGTCGGTGGATGACACAGTTCCTACGTAATGAGGACGTCTGGCCATCTT
65 CGTGATGAGGAGATATGGTCGATGGATGACACAGTTCCTACGTGATGAGGACGTCTGGCCATCTT
1294878 TAGGGATAA
130 TAGGGATAA
1294887 TT
1 TT
1294889 TGTTTAAAGA
Statistics
Matches: 237, Mismatches: 36, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
137 116 0.49
138 120 0.51
139 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (138 bp):
TTGGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACACAACTCCTAC
GTGATGAGGAGATATGGTCGATGGATGACACAGTTCCTACGTGATGAGGACGTCTGGCCATCTTT
AGGGATAA
Found at i:1295004 original size:67 final size:67
Alignment explanation
Indices: 1294917--1295148 Score: 329
Period size: 67 Copynumber: 3.5 Consensus size: 67
1294907 GTCAAAAGAG
* * * *
1294917 AAAACTTGTTTCAAGGGAAACAATCGCAAAGGTTTTATGTTTCAAGAAAAACTGTCTCAAGAGAG
1 AAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTTATGTTTCAAGAGAAACTATCTCAAGAGAG
1294982 AC
66 AC
** *
1294984 AAAACTTGTTTTGAGAGAAACAATCTCTAAGGTTTTATGTTTCAAGAGAAACTATCTCAAGAGAG
1 AAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTTATGTTTCAAGAGAAACTATCTCAAGAGAG
1295049 AC
66 AC
* * * * * *
1295051 AAAATTTGTTTCAAGAGAAACAATCTTAAAAGTTATATGTTTCAAGAGAAACAATCTCAAAAGAG
1 AAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTTATGTTTCAAGAGAAACTATCTCAAGAGAG
*
1295116 AT
66 AC
*
1295118 AAAATTTGTTTCAAGAGAAACAATCTCAAAG
1 AAAACTTGTTTCAAGAGAAACAATCTCAAAG
1295149 TTTATCAATT
Statistics
Matches: 146, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 146 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (67 bp):
AAAACTTGTTTCAAGAGAAACAATCTCAAAGGTTTTATGTTTCAAGAGAAACTATCTCAAGAGAG
AC
Found at i:1295032 original size:31 final size:31
Alignment explanation
Indices: 1294997--1295108 Score: 93
Period size: 31 Copynumber: 3.5 Consensus size: 31
1294987 ACTTGTTTTG
1294997 AGAGAAACAATCTCTAAGGTTTTATGTTTCA
1 AGAGAAACAATCTCTAAGGTTTTATGTTTCA
* * **
1295028 AGAGAAACTATCTCAAGAGAGACAAAATT-TGTTTCA
1 AGAGAAACAATCTCTA-AG-G----TTTTATGTTTCA
* *
1295064 AGAGAAACAATCT-TAAAAGTTATATGTTTCA
1 AGAGAAACAATCTCT-AAGGTTTTATGTTTCA
1295095 AGAGAAACAATCTC
1 AGAGAAACAATCTC
1295109 AAAAGAGATA
Statistics
Matches: 62, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
30 1 0.02
31 34 0.55
32 2 0.03
33 1 0.02
34 1 0.02
35 1 0.02
36 20 0.32
37 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (31 bp):
AGAGAAACAATCTCTAAGGTTTTATGTTTCA
Found at i:1295068 original size:36 final size:34
Alignment explanation
Indices: 1295021--1295148 Score: 154
Period size: 36 Copynumber: 3.7 Consensus size: 34
1295011 TAAGGTTTTA
*
1295021 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACAATCTCAA-AGAGA-AAAATT
* ** *
1295057 TGTTTCAAGAGAAACAATCTTAAA-AG--TTATA
1 TGTTTCAAGAGAAACAATCTCAAAGAGAAAAATT
1295088 TGTTTCAAGAGAAACAATCTCAAAAGAGATAAAATT
1 TGTTTCAAGAGAAACAATCTC-AAAGAGA-AAAATT
1295124 TGTTTCAAGAGAAACAATCTCAAAG
1 TGTTTCAAGAGAAACAATCTCAAAG
1295149 TTTATCAATT
Statistics
Matches: 78, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
31 22 0.28
32 3 0.04
33 2 0.03
34 2 0.03
35 5 0.06
36 44 0.56
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (34 bp):
TGTTTCAAGAGAAACAATCTCAAAGAGAAAAATT
Found at i:1295113 original size:31 final size:33
Alignment explanation
Indices: 1294923--1295148 Score: 149
Period size: 36 Copynumber: 6.8 Consensus size: 33
1294913 AGAGAAAACT
* * **
1294923 TGTTTCAAGGGAAACAATCGCAAAG-G-TTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGAGATAATA
* ** * *
1294954 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGAGAAACAATCTCAA-AGAGATAATA
** * **
1294988 CTTGTTTTGAGAGAAACAATCTCTAAG-G-TTTTA
1 --TGTTTCAAGAGAAACAATCTCAAAGAGATAATA
* * *
1295021 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACAATCTCAA-AGAG--ATAATA
* *
1295057 TGTTTCAAGAGAAACAATCTTAAA-AG-TTATA
1 TGTTTCAAGAGAAACAATCTCAAAGAGATAATA
*
1295088 TGTTTCAAGAGAAACAATCTCAAAAGAGATAAAATT
1 TGTTTCAAGAGAAACAATCTC-AAAGAGAT--AATA
1295124 TGTTTCAAGAGAAACAATCTCAAAG
1 TGTTTCAAGAGAAACAATCTCAAAG
1295149 TTTATCAATT
Statistics
Matches: 145, Mismatches: 35, Indels: 26
0.70 0.17 0.13
Matches are distributed among these distances:
31 59 0.41
32 7 0.05
33 5 0.03
34 5 0.03
35 7 0.05
36 62 0.43
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAATCTCAAAGAGATAATA
Found at i:1295517 original size:36 final size:36
Alignment explanation
Indices: 1295476--1295615 Score: 113
Period size: 37 Copynumber: 3.8 Consensus size: 36
1295466 AAACTCTCTG
*
1295476 AAGCGAGACGAAATTTGTTTCGAGAG-GAATTATCTC
1 AAGCGAGAC-AAATTTGTTTCGAGAGAAAATTATCTC
** *
1295512 AAGCGAGACAAAATTTGTTTTTAGAGAAAATTGTCTC
1 AAGCGAGAC-AAATTTGTTTCGAGAGAAAATTATCTC
* * * *
1295549 AAGAGAGACAAACTTTGTTTTTGAGA-AAAATTGTCTT
1 AAGCGAGACAAA-TTTG-TTTCGAGAGAAAATTATCTC
* * *
1295586 TAGTGAGACGACACTTTGTTTCGAGAGAAA
1 AAGCGAGAC-A-AATTTGTTTCGAGAGAAA
1295616 CAATCTCAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
36 26 0.30
37 44 0.51
38 15 0.17
39 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (36 bp):
AAGCGAGACAAATTTGTTTCGAGAGAAAATTATCTC
Found at i:1295557 original size:37 final size:37
Alignment explanation
Indices: 1295480--1295584 Score: 124
Period size: 37 Copynumber: 2.9 Consensus size: 37
1295470 TCTCTGAAGC
* ** * * *
1295480 GAGACGAAATTTGTTTCGAGAG-GAATTATCTCAAGC
1 GAGACAAAATTTGTTTTTAGAGAAAATTGTCTCAAGA
1295516 GAGACAAAATTTGTTTTTAGAGAAAATTGTCTCAAGA
1 GAGACAAAATTTGTTTTTAGAGAAAATTGTCTCAAGA
*
1295553 GAGACAAACTTTGTTTTT-GAGAAAAATTGTCT
1 GAGACAAAATTTGTTTTTAGAG-AAAATTGTCT
1295585 TTAGTGAGAC
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 22 0.37
37 38 0.63
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.32
Consensus pattern (37 bp):
GAGACAAAATTTGTTTTTAGAGAAAATTGTCTCAAGA
Found at i:1301664 original size:5 final size:6
Alignment explanation
Indices: 1301647--1301671 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1301637 TACATACATG
1301647 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
1301672 GAAACTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:1303381 original size:7 final size:7
Alignment explanation
Indices: 1303359--1303432 Score: 87
Period size: 7 Copynumber: 10.7 Consensus size: 7
1303349 ATGGTTAAAA
1303359 TTAAATC
1 TTAAATC
*
1303366 -TAAACC
1 TTAAATC
1303372 TTAAATC
1 TTAAATC
1303379 TTAAATC
1 TTAAATC
*
1303386 TTAAACC
1 TTAAATC
1303393 TTAAATC
1 TTAAATC
1303400 TTAAATC
1 TTAAATC
*
1303407 TTAAACC
1 TTAAATC
* *
1303414 CTAACTC
1 TTAAATC
*
1303421 TTAAACC
1 TTAAATC
1303428 TTAAA
1 TTAAA
1303433 CATTAACCCT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
6 5 0.09
7 50 0.91
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (7 bp):
TTAAATC
Found at i:1303388 original size:14 final size:14
Alignment explanation
Indices: 1303359--1303462 Score: 97
Period size: 14 Copynumber: 7.4 Consensus size: 14
1303349 ATGGTTAAAA
1303359 TTAAATC-TAAACC
1 TTAAATCTTAAACC
*
1303372 TTAAATCTTAAATC
1 TTAAATCTTAAACC
* *
1303386 TTAAACCTTAAATC
1 TTAAATCTTAAACC
1303400 TTAAATCTTAAACC
1 TTAAATCTTAAACC
* *
1303414 CTAACTCTTAAACC
1 TTAAATCTTAAACC
1303428 TTAAA-CATT-AACC
1 TTAAATC-TTAAACC
*
1303441 CTAAATCATATTAAACC
1 TTAAATC---TTAAACC
1303458 TTAAA
1 TTAAA
1303463 CATTAACCCC
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
13 16 0.21
14 48 0.64
16 3 0.04
17 8 0.11
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (14 bp):
TTAAATCTTAAACC
Found at i:1303439 original size:21 final size:21
Alignment explanation
Indices: 1303359--1303438 Score: 117
Period size: 21 Copynumber: 3.9 Consensus size: 21
1303349 ATGGTTAAAA
1303359 TTAAATC-TAAACCTTAAATC
1 TTAAATCTTAAACCTTAAATC
1303379 TTAAATCTTAAACCTTAAATC
1 TTAAATCTTAAACCTTAAATC
* *
1303400 TTAAATCTTAAACCCTAACTC
1 TTAAATCTTAAACCTTAAATC
* *
1303421 TTAAACCTTAAACATTAA
1 TTAAATCTTAAACCTTAA
1303439 CCCTAAATCA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 7 0.13
21 47 0.87
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (21 bp):
TTAAATCTTAAACCTTAAATC
Found at i:1303457 original size:30 final size:31
Alignment explanation
Indices: 1303421--1303494 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
1303411 ACCCTAACTC
1303421 TTAAACCTTAAACATTAA-CCCTAAATCATA
1 TTAAACCTTAAACATTAACCCCTAAATCATA
1303451 TTAAACCTTAAACATTAACCCCTAAATCATA
1 TTAAACCTTAAACATTAACCCCTAAATCATA
* *
1303482 CTAAACCCTAAAC
1 TTAAACCTTAAAC
1303495 TCAAAATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 18 0.44
31 23 0.56
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (31 bp):
TTAAACCTTAAACATTAACCCCTAAATCATA
Found at i:1311615 original size:26 final size:25
Alignment explanation
Indices: 1311555--1311616 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
1311545 TTTTTGTTTC
1311555 TTAA-TTTTTTATTACTTAATTGTT
1 TTAATTTTTTTATTACTTAATTGTT
* * * *
1311579 TGAATTGTTTTTATTATTTAGTTCTTT
1 TTAATT-TTTTTATTACTTAATT-GTT
1311606 TTAATTTTTTT
1 TTAATTTTTTT
1311617 GTTGTACCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
24 3 0.10
25 1 0.03
26 19 0.63
27 7 0.23
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.69
Consensus pattern (25 bp):
TTAATTTTTTTATTACTTAATTGTT
Found at i:1313984 original size:32 final size:32
Alignment explanation
Indices: 1313943--1314003 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
1313933 TTTCTGATTT
*
1313943 AGGTTGCTTTCGGTTCGAATTAATTTTGGATC
1 AGGTTGCTTTCAGTTCGAATTAATTTTGGATC
* *
1313975 AGGTTGCTTTCAGTTTGGATTAATTTTGG
1 AGGTTGCTTTCAGTTCGAATTAATTTTGG
1314004 TTTGAATTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.18, C:0.10, G:0.26, T:0.46
Consensus pattern (32 bp):
AGGTTGCTTTCAGTTCGAATTAATTTTGGATC
Found at i:1322444 original size:20 final size:21
Alignment explanation
Indices: 1322419--1322511 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1322409 TTTTCCCAAT
*
1322419 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1322439 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1322460 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1322480 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1322501 TCGCAATGCGA
1 TCGCAATGCGA
1322512 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1322525 original size:20 final size:20
Alignment explanation
Indices: 1322500--1322594 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1322490 AATTGGGAAA
*
1322500 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1322520 ATCGCAATGCGATAATAAAA
1 ATCGCAACGCGATACTGACT
* *
1322540 ACTCGCAACGAGATACTTACT
1 A-TCGCAACGCGATACTGACT
*
1322561 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1322581 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1322595 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 48 0.79
21 13 0.21
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1322526 original size:41 final size:41
Alignment explanation
Indices: 1322419--1322511 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1322409 TTTTCCCAAT
1322419 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1322460 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1322501 TCGCAATGCGA
1 TCGCAATGCGA
1322512 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1322546 original size:41 final size:40
Alignment explanation
Indices: 1322497--1322574 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
1322487 GCGAATTGGG
* * *
1322497 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATA
* *
1322537 AAAACTCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAA-TCGCAACGAGATACTGACTATCGCAACGCGATA
1322575 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
40 4 0.12
41 28 0.88
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (40 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATA
Found at i:1322810 original size:22 final size:22
Alignment explanation
Indices: 1322782--1322825 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1322772 CACTCTCTCA
1322782 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1322804 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1322826 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1323114 original size:20 final size:20
Alignment explanation
Indices: 1323089--1323126 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1323079 CGATTCTCTC
1323089 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1323109 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1323127 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1324466 original size:18 final size:18
Alignment explanation
Indices: 1324445--1324489 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1324435 TCCACTTCGG
*
1324445 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1324463 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1324481 GAGCCATCA
1 GAGCCATCA
1324490 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1325024 original size:19 final size:20
Alignment explanation
Indices: 1324970--1325025 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1324960 ATAGTTACTT
* *
1324970 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1324990 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
1325010 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
1325026 AAATTGCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1325048 original size:14 final size:14
Alignment explanation
Indices: 1325025--1325082 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1325015 ATGCGAAATG
*
1325025 AAAATTGCAACGAC
1 AAAATCGCAACGAC
*
1325039 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1325055 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1325071 AAAATCGCAACG
1 AAAATCGCAACG
1325083 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1325072 original size:32 final size:33
Alignment explanation
Indices: 1325009--1325099 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1324999 GGAAATGGCT
*
1325009 ATCGCAATGCGAAATGAAAATTGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1325042 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1325074 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1325100 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1325135 original size:14 final size:14
Alignment explanation
Indices: 1325116--1325173 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1325106 TTGTGTTTCG
1325116 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1325130 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1325146 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1325162 CGTTGCGATTTT
1 CGTTGCGATTTT
1325174 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1325150 original size:32 final size:33
Alignment explanation
Indices: 1325111--1325189 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1325101 GCGATTTGTG
1325111 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1325143 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1325176 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1325190 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1325188 original size:19 final size:19
Alignment explanation
Indices: 1325130--1325247 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
1325120 GCGATTTTGT
1325130 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1325148 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
1325162 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
1325181 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
1325201 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1325220 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1325240 TGTTGCGA
1 CGTTGCGA
1325248 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1326012 original size:24 final size:24
Alignment explanation
Indices: 1325985--1326038 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1325975 GTATTCGAAA
* *
1325985 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1326009 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1326033 TTTGAT
1 TTTGAT
1326039 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1326230 original size:12 final size:12
Alignment explanation
Indices: 1326213--1326237 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1326203 ATATAATCCT
1326213 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1326225 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1326237 G
1 G
1326238 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1328566 original size:33 final size:33
Alignment explanation
Indices: 1328529--1328655 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
1328519 GGAAATTACT
*
1328529 ATCGCAATGTGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
1328562 ATCGCAATGCCAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1328594 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1328628 ATCACAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1328656 CGAATTTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
32 1 0.01
33 79 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1328620 original size:19 final size:19
Alignment explanation
Indices: 1328529--1328659 Score: 67
Period size: 19 Copynumber: 7.7 Consensus size: 19
1328519 GGAAATTACT
*
1328529 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1328548 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1328562 ATCGCAATGCCAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1328581 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1328595 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1328614 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
1328628 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1328647 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1328660 TTTAATTTCG
Statistics
Matches: 79, Mismatches: 18, Indels: 30
0.62 0.14 0.24
Matches are distributed among these distances:
14 26 0.33
15 3 0.04
16 5 0.06
17 4 0.05
18 3 0.04
19 38 0.48
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1328636 original size:66 final size:66
Alignment explanation
Indices: 1328530--1328662 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
1328520 GAAATTACTA
* * *
1328530 TCGCAATGTGAAATGAAAATCGCAACGAGAGAATCGCAATGCCAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCCAAATGAAAATCGCAACGCGAAT
1328595 T
66 T
* *
1328596 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCCAAATGAAAATCGCAACGCGAAT
1328661 T
66 T
1328662 T
1 T
1328663 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCCAAATGAAAATCGCAACGCGAAT
T
Found at i:1328677 original size:19 final size:20
Alignment explanation
Indices: 1328655--1328697 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1328645 AAATCGCAAC
1328655 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1328674 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1328694 GCGA
1 GCGA
1328698 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1328682 original size:14 final size:14
Alignment explanation
Indices: 1328683--1328716 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1328673 TGCGATTTTC
1328683 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
1328697 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
1328711 ATTTTC
1 ATTTTC
1328717 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1328857 original size:14 final size:14
Alignment explanation
Indices: 1328838--1328874 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1328828 CATCAATTAA
1328838 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1328852 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1328866 ACAAATCAA
1 ACAAATCAA
1328875 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1330315 original size:42 final size:42
Alignment explanation
Indices: 1330269--1330352 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1330259 CGATGACAGT
* * *
1330269 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
1330311 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
1330353 TGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1332434 original size:33 final size:33
Alignment explanation
Indices: 1332377--1332475 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
1332367 ACGAGATAAT
*
1332377 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
1332411 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
1332444 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
1332476 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1332469 original size:19 final size:19
Alignment explanation
Indices: 1332352--1332536 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
1332342 TCTTTTGGTT
*
1332352 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1332371 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1332391 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1332409 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1332425 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1332443 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1332458 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1332478 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1332497 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1332516 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1332535 GA
1 GA
1332537 TTTTGGTTTC
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 62 0.45
20 45 0.33
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1332490 original size:39 final size:38
Alignment explanation
Indices: 1332447--1332536 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
1332437 GCGACCAGAC
1332447 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
1332486 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
1332524 AATCGCAATGCGA
1 AATCGCAACGCGA
1332537 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:1332565 original size:19 final size:19
Alignment explanation
Indices: 1332532--1332598 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1332522 AAAATCGCAA
**
1332532 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
1332551 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
1332570 TGCGATAGTTATTTTCGCGT
1 TGCGATTTTTA-TTTCGCGT
1332590 TGCGATTTT
1 TGCGATTTT
1332599 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 26 0.63
20 15 0.37
ACGTcount: A:0.10, C:0.15, G:0.25, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1333183 original size:21 final size:19
Alignment explanation
Indices: 1333159--1333287 Score: 71
Period size: 20 Copynumber: 6.3 Consensus size: 19
1333149 AAGTATCTCG
1333159 TTGCGATTTTTTATTATCGCA
1 TTGCGATTTTTTA-T-TCGCA
** *
1333180 TTGCGA-TAGTAAGTATCGCA
1 TTGCGATTTTTTA-T-TCGCA
* *
1333200 TTGCGATTTTCTCAATTCGCG
1 TTGCGATTTT-T-TATTCGCA
*
1333221 TTGCGATTTACTTATTCGCA
1 TTGCGATTT-TTTATTCGCA
** *
1333241 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTT--TTATTCGCA
*
1333262 TTGCGATTTACTTATTCGCA
1 TTGCGATTT-TTTATTCGCA
1333282 TTGCGA
1 TTGCGA
1333288 ATTTGGAAAA
Statistics
Matches: 83, Mismatches: 18, Indels: 15
0.72 0.16 0.13
Matches are distributed among these distances:
20 43 0.52
21 36 0.43
22 2 0.02
23 2 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42
Consensus pattern (19 bp):
TTGCGATTTTTTATTCGCA
Found at i:1333206 original size:20 final size:20
Alignment explanation
Indices: 1333113--1333206 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1333103 CGCTATGTAA
* *
1333113 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
1333133 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* ** * *
1333153 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTAAGT
*
1333174 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
1333194 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1333207 TTTCTCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:1333225 original size:41 final size:41
Alignment explanation
Indices: 1333134--1333268 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
1333124 AAAGTCAGTA
* * * * *
1333134 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
*
1333174 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* ** *
1333216 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCTCAAT
1333257 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1333269 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 74 0.91
42 3 0.04
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
Found at i:1333239 original size:20 final size:20
Alignment explanation
Indices: 1333195--1333287 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
1333185 ATAGTAAGTA
*
1333195 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
1333216 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
1333236 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTAAT
* *
1333257 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
1333277 TCGCATTGCGA
1 TCGCATTGCGA
1333288 ATTTGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:1333269 original size:41 final size:41
Alignment explanation
Indices: 1333195--1333287 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1333185 ATAGTAAGTA
*
1333195 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1333236 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1333277 TCGCATTGCGA
1 TCGCATTGCGA
1333288 ATTTGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1338274 original size:65 final size:65
Alignment explanation
Indices: 1338187--1338347 Score: 277
Period size: 65 Copynumber: 2.5 Consensus size: 65
1338177 TACACTAAGA
*
1338187 GTGCATCGATGCATCAAGTGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
*
1338252 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATTCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
* * *
1338317 GTGTATCAATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
1338348 CAATTTAATT
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 91 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
Found at i:1344390 original size:39 final size:39
Alignment explanation
Indices: 1344336--1344411 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
1344326 ATGAGATTTG
* * * *
1344336 TCTTGTTTAGCAGGAGCTGTTCTTGTCCGACTACGAGAA
1 TCTTGTTCAGCAGGAGCTATCCTAGTCCGACTACGAGAA
* *
1344375 TCTTGTTCAGGAGGAGCTATCCTAGTCCGACTCCGAG
1 TCTTGTTCAGCAGGAGCTATCCTAGTCCGACTACGAG
1344412 TTAAAGGGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (39 bp):
TCTTGTTCAGCAGGAGCTATCCTAGTCCGACTACGAGAA
Found at i:1345533 original size:2 final size:2
Alignment explanation
Indices: 1345526--1345556 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1345516 ATCTAGAACA
1345526 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
1345557 CACGCAACAT
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:1345798 original size:12 final size:12
Alignment explanation
Indices: 1345783--1345816 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1345773 GAAACACATT
1345783 GATAAAAATATC
1 GATAAAAATATC
1345795 GATAAAAATATC
1 GATAAAAATATC
*
1345807 AATAAAAATA
1 GATAAAAATA
1345817 CAACTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (12 bp):
GATAAAAATATC
Found at i:1353553 original size:12 final size:12
Alignment explanation
Indices: 1353536--1353563 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1353526 TTCACACCAC
1353536 TGTTATGTCCAT
1 TGTTATGTCCAT
1353548 TGTTATGTCCAT
1 TGTTATGTCCAT
1353560 TGTT
1 TGTT
1353564 CATCCAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.54
Consensus pattern (12 bp):
TGTTATGTCCAT
Found at i:1359845 original size:3 final size:3
Alignment explanation
Indices: 1359839--1359869 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1359829 TTCTTCTTCT
1359839 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1359870 ATTTTTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:1363975 original size:13 final size:13
Alignment explanation
Indices: 1363957--1363984 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1363947 CATCACTTTG
1363957 AATTCATTTTTCA
1 AATTCATTTTTCA
1363970 AATTCATTTTTCA
1 AATTCATTTTTCA
1363983 AA
1 AA
1363985 CTAAATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTCATTTTTCA
Found at i:1369867 original size:21 final size:21
Alignment explanation
Indices: 1369843--1369899 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
1369833 GGGCTTGATA
*
1369843 GTATCGATACTATTGTTCATG
1 GTATCGATACTACTGTTCATG
*
1369864 GTATTGATAAC-ACTGTTCATG
1 GTATCGAT-ACTACTGTTCATG
1369885 GTATCGATACTACTG
1 GTATCGATACTACTG
1369900 CAGCAGTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (21 bp):
GTATCGATACTACTGTTCATG
Found at i:1369990 original size:23 final size:23
Alignment explanation
Indices: 1369961--1370015 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 23
1369951 ACTGTTTATG
*
1369961 GTATCGATACTACTGTTCACACA
1 GTATCGATACTACTATTCACACA
*
1369984 GTATCGAT--T-CTATTCATACA
1 GTATCGATACTACTATTCACACA
*
1370004 ATATCGATACTA
1 GTATCGATACTA
1370016 TTCATACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 16 0.62
21 1 0.04
22 1 0.04
23 8 0.31
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (23 bp):
GTATCGATACTACTATTCACACA
Found at i:1370008 original size:20 final size:20
Alignment explanation
Indices: 1369971--1370035 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
1369961 GTATCGATAC
* * *
1369971 TACTGTTCACACAGTATCGA
1 TACTATTCATACAATATCGA
*
1369991 TTCTATTCATACAATATCGA
1 TACTATTCATACAATATCGA
1370011 TACTATTCATACAATAT-G-
1 TACTATTCATACAATATCGA
1370029 TACTATT
1 TACTATT
1370036 TATAAAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
18 7 0.17
19 1 0.03
20 32 0.80
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (20 bp):
TACTATTCATACAATATCGA
Found at i:1372064 original size:14 final size:15
Alignment explanation
Indices: 1372045--1372085 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
1372035 AGAGAAAGCT
1372045 AGAAAAAGGAAAACA
1 AGAAAAAGGAAAACA
*
1372060 A-AAAAA-GAAAATA
1 AGAAAAAGGAAAACA
1372073 AGAAAAAGGAAAA
1 AGAAAAAGGAAAA
1372086 ATTGAGAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 7 0.30
14 10 0.43
15 6 0.26
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (15 bp):
AGAAAAAGGAAAACA
Found at i:1375556 original size:13 final size:13
Alignment explanation
Indices: 1375538--1375564 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1375528 AACAAAGTTT
1375538 AACACCAAGTAAG
1 AACACCAAGTAAG
1375551 AACACCAAGTAAG
1 AACACCAAGTAAG
1375564 A
1 A
1375565 CAGTCATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.22, G:0.15, T:0.07
Consensus pattern (13 bp):
AACACCAAGTAAG
Found at i:1377138 original size:190 final size:193
Alignment explanation
Indices: 1376815--1377196 Score: 743
Period size: 190 Copynumber: 2.0 Consensus size: 193
1376805 CCCAAGCTAG
1376815 TTGAGCAGAGTCATCATGTAACTACTTTCATTCACTCATATGCCTTGGAAACTCTTAATTTCTTA
1 TTGAGCAGAGTCATCATGTAACTACTTTCATTCACTCATATGCCTTGGAAACTCTTAATTTCTTA
1376880 TGGAGTTTTTCCTATTTATGCCCTTGCATAGAGGAGCGCCCCTTTCTATTTTGCAAGTTTTAAAC
66 TGGAGTTTTTCCTATTTATGCCCTTGCATAGAGGAGCGCCCCTTTCTATTTTGCAAGTTTTAAAC
1376945 ACTAGGGATCTTTAC-TTACCCTTAAAA-A-TTTTGAAGTCTAGGCAAATAGAAAGTTCTTTC
131 ACTAGGGATCTTTACTTTACCCTTAAAATATTTTTGAAGTCTAGGCAAATAGAAAGTTCTTTC
1377005 TTGAGCAGAGTCATCATGTAACTACTTTCATTCACTCATATGCCTTGGAAACTCTTAATTTCTTA
1 TTGAGCAGAGTCATCATGTAACTACTTTCATTCACTCATATGCCTTGGAAACTCTTAATTTCTTA
1377070 TGGAGTTTTTCCTATTTATGCCCTTGCATAGAGGAGCGCCCCTTTCTATTTTGCAAGTTTTAAAC
66 TGGAGTTTTTCCTATTTATGCCCTTGCATAGAGGAGCGCCCCTTTCTATTTTGCAAGTTTTAAAC
1377135 ACTAGGGATCTTTACTTTACCCTTAAAATATTTTTGAAGTCTAGGCAAATAGAAAGTTCTTT
131 ACTAGGGATCTTTACTTTACCCTTAAAATATTTTTGAAGTCTAGGCAAATAGAAAGTTCTTT
1377197 TCTAAAAATT
Statistics
Matches: 189, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
190 145 0.77
191 12 0.06
192 1 0.01
193 31 0.16
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (193 bp):
TTGAGCAGAGTCATCATGTAACTACTTTCATTCACTCATATGCCTTGGAAACTCTTAATTTCTTA
TGGAGTTTTTCCTATTTATGCCCTTGCATAGAGGAGCGCCCCTTTCTATTTTGCAAGTTTTAAAC
ACTAGGGATCTTTACTTTACCCTTAAAATATTTTTGAAGTCTAGGCAAATAGAAAGTTCTTTC
Found at i:1383885 original size:21 final size:21
Alignment explanation
Indices: 1383851--1383909 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
1383841 CATCAAGGTA
* *
1383851 TTTGTGGAGGCCATAAAATCT
1 TTTGTAGAGACCATAAAATCT
1383872 TTTGTAGAGACCATAAAATCT
1 TTTGTAGAGACCATAAAATCT
*
1383893 TTTGTCGAGACCATAAA
1 TTTGTAGAGACCATAAA
1383910 TTCCTACAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (21 bp):
TTTGTAGAGACCATAAAATCT
Found at i:1384748 original size:50 final size:50
Alignment explanation
Indices: 1384673--1384772 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
1384663 TGGGCGGATT
1384673 GTATCGGAGTAGAAAACTCTTGCATAAATCTGCCCATGACTCCATTGAGC
1 GTATCGGAGTAGAAAACTCTTGCATAAATCTGCCCATGACTCCATTGAGC
1384723 GTATCGGAGTAGAAAACTCTTGCATAAATCTGCCCATGACTCCATTGAGC
1 GTATCGGAGTAGAAAACTCTTGCATAAATCTGCCCATGACTCCATTGAGC
1384773 CGGAATGAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (50 bp):
GTATCGGAGTAGAAAACTCTTGCATAAATCTGCCCATGACTCCATTGAGC
Found at i:1390909 original size:41 final size:42
Alignment explanation
Indices: 1390797--1390910 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 42
1390787 CCAAAATTTG
* *
1390797 TAAGTCCTTCGGGACATCAATAAGTCTTTCGAGCATGACGAT
1 TAAGTCCTTCGGGACATCTATAAGTCTTTCGAGCAGGACGAT
* * * * *
1390839 TAAATCTTTCGGGTCATCTGTAAGTCTTTCGAGCAGGATGA-
1 TAAGTCCTTCGGGACATCTATAAGTCTTTCGAGCAGGACGAT
* *
1390880 TAAGTCCTTCGGGCCATCTATAAGGCTTTCG
1 TAAGTCCTTCGGGACATCTATAAGTCTTTCG
1390911 GGTAAGATGT
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
41 26 0.43
42 34 0.57
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (42 bp):
TAAGTCCTTCGGGACATCTATAAGTCTTTCGAGCAGGACGAT
Found at i:1391138 original size:257 final size:257
Alignment explanation
Indices: 1390676--1391885 Score: 1662
Period size: 257 Copynumber: 4.7 Consensus size: 257
1390666 TTTTTATAAG
* * *
1390676 TTGAAAAATGGGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTAA
1 TTGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGA
*
1390741 AAAGTAAGAAAGCGATTTACAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTTGTAAGTCCTT
66 AAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTTGTAAGTCCTT
* * * * *
1390806 CGGGACATCAATAAGTCTTTCGAGCATGACGATTAAATCTTTCGGGTCATCTGTAAGTCTTTCGA
131 CGGGCCATCAGTATGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGA
* * *
1390871 GCAGGATGATAAGTCCTTCGGGCCATCTATAAGGCTTTCGGGTAAGATGTTTTCTCATGAAT
196 GCAGGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGTAAGATGTTTTCACATGAAT
* ** * *
1390933 TTGAAAAATGAGAAAGCGATTTAGAAAGTTTCTCATTTAATGTTTTCAGAAAATAAAAATTTTGA
1 TTGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGA
* *
1390998 AAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAGTAAGTCCTT
66 AAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTTGTAAGTCCTT
* * * * *
1391063 CGGGCCATCAGTATGTCCTTAGAGAATGATGCTTAAATCCTTCGGGTCATATGTAAGTCTTTCGA
131 CGGGCCATCAGTATGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGA
* * * * * *
1391128 GCAAGATGATAAGTCATTCGAGCCAT-TCGTAAGACCTTCGGGTAGGATGTTTTCACATAAAT
196 GCAGGATGATAAGTCCTTCGGGCCATCT-ATAAGACCTTCGGGTAAGATGTTTTCACATGAAT
* *
1391190 TTGAAATAA-GAGAAAACGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATTTTTG
1 TTGAAA-AATGAGAAAACGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTG
**
1391254 AAAAGTAAGAAAAAGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTTGTAAGTCCA
65 AAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTTGTAAGTCC-
* * * * *
1391319 TT-AGGCCATCAGTATATCTTTCGAGCATGATGATTAAATCTTTCAGGTCATCTGTAAGTCTTTA
129 TTCGGGCCATCAGTATGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTC
* * ** *
1391383 GAGTAGGATGATAAGTCCTTCAGGCCATCCGTAAGACCTTCGGATAAGATGTTTTCACGA-GAAT
194 GAGCAGGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGTAAGATGTTTTCAC-ATGAAT
* * * * *
1391447 TTGAAAAATGAGAAAACGATTTCCATAGTTTCTCATTTAGTATTTTCAGATAATGAAATTTTTTA
1 TTGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGA
* * *
1391512 TAAGTAAGAAAGCAATTTCCAAAGTTTCTTA-CCAGTAAACTATTTCCAAAATTTGTAAGTCTTT
66 AAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTTGTAAGTCCTT
* * * * *
1391576 CAGGCC-TCAGT-TAATCTTTCGAGCATGATGATTTAATCCTTTGAGTCATCTGTAAGTCTTTCG
131 CGGGCCATCAGTAT-GTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCG
* * * * * **
1391639 AGCATGATAATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTCCACATGTTT
195 AGCAGGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGTAAGATGTTTTCACATGAAT
*
1391702 TTCG-AAAATGAGAAAACGGTTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTG
1 TT-GAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTG
* *
1391766 AAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCTT
65 AAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTTGTAAGTCCT
* * * * *
1391831 TCGGGCTATCAGTAAGTCTTTCCAGCATGATGATTAAATCATTCGGGTTATCTGT
130 TCGGGCCATCAGTATGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGT
1391886 CGATCTTACT
Statistics
Matches: 837, Mismatches: 103, Indels: 26
0.87 0.11 0.03
Matches are distributed among these distances:
254 2 0.00
255 186 0.22
256 75 0.09
257 569 0.68
258 5 0.01
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (257 bp):
TTGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGA
AAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTTGTAAGTCCTT
CGGGCCATCAGTATGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGA
GCAGGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGTAAGATGTTTTCACATGAAT
Found at i:1391417 original size:41 final size:42
Alignment explanation
Indices: 1391311--1391417 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 42
1391301 CCAAAATTTG
* *
1391311 TAAGTCCATT-AGGCCATCAGTATA-TCTTTCGAGCATGATGAT
1 TAAGTCC-TTCAGGCCATCAGTA-AGTCTTTAGAGCAGGATGAT
* * * * *
1391353 TAAATCTTTCAGGTCATCTGTAAGTCTTTAGAGTAGGATGA-
1 TAAGTCCTTCAGGCCATCAGTAAGTCTTTAGAGCAGGATGAT
*
1391394 TAAGTCCTTCAGGCCATCCGTAAG
1 TAAGTCCTTCAGGCCATCAGTAAG
1391418 ACCTTCGGAT
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
41 23 0.44
42 29 0.56
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (42 bp):
TAAGTCCTTCAGGCCATCAGTAAGTCTTTAGAGCAGGATGAT
Found at i:1395464 original size:20 final size:20
Alignment explanation
Indices: 1395415--1395475 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 20
1395405 ATACCGGGAG
* *
1395415 GGGTATCGGTACCATAGTAG
1 GGGTATCGATACCATAGTAA
*
1395435 GGTAGTATCGATACCATGGTAA
1 GG--GTATCGATACCATAGTAA
1395457 GGGTATCGATACCA-AGTAA
1 GGGTATCGATACCATAGTAA
1395476 CATCGAACCT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 4 0.11
20 14 0.40
22 17 0.49
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.25
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:1398381 original size:59 final size:57
Alignment explanation
Indices: 1398282--1398409 Score: 148
Period size: 59 Copynumber: 2.2 Consensus size: 57
1398272 ATGGAACTAA
* * * * *
1398282 GTGTGCAAAATGTTAAGAAATTTATTCTAAGTGTACGAATTTTTGTATTGGGCACTTT
1 GTGTGCAAAATATTAAGAAATTCATACTAAGTATACGAATTTTAGTA-TGGGCACTTT
* * * *
1398340 GTGTGCTAAAATATTAAGAAATTCATACTACGTATATGAATTTTAGTATGGGCAGTAT
1 GTGTGC-AAAATATTAAGAAATTCATACTAAGTATACGAATTTTAGTATGGGCACTTT
*
1398398 ATGTGCAAAATA
1 GTGTGCAAAATA
1398410 AGAAATTAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
57 6 0.10
58 19 0.32
59 34 0.58
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.38
Consensus pattern (57 bp):
GTGTGCAAAATATTAAGAAATTCATACTAAGTATACGAATTTTAGTATGGGCACTTT
Found at i:1398840 original size:81 final size:81
Alignment explanation
Indices: 1398691--1399331 Score: 868
Period size: 81 Copynumber: 8.0 Consensus size: 81
1398681 GTGCCTTTGA
* * *
1398691 GGCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCAT
1 GGCCTAACTGTGAAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1398756 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * ** **
1398772 GGCCTAATTGTGAAATTGGTAGAAAGGTGCCAATTATGCCAGTTAGATGAACAATTAAATATTGT
1 GGCCTAACTGTGAAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1398837 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * *
1398853 GGCCTCACTGTGAAATTGGTAGAAATGTACAAATTATG-CAGTTAGATGAACGG-TAAATAGCGT
1 GGCCTAACTGTGAAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1398916 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * * ** *
1398932 GGCCTAACTTTGAAATTGGTAGAAATGTACTAATTATGCCAGTTAGATGAACGATTAAATTTCAT
1 GGCCTAACTGTGAAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1398997 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
*
1399013 GGCCTAACTGTGAAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACTGTTAAATACCGT
1 GGCCTAACTGTGAAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
*
1399078 TTAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * *
1399094 GGCCTAACTATGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAATGATTAAATACCGT
1 GGCCTAACTGTGAAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
*
1399159 TGAGTAAATGAATAAT
66 TGAGTAAAAGAATAAT
* * * *
1399175 GGCATAATTGTGCAA-T--T-G---GGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCAT
1 GGCCTAACTGTGAAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1399233 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * * * *
1399249 GGTCTAACTGTGCAATTGGTAGAAATGTACCAATTATGCCAATTAGATGAATGGTTAAATACCAT
1 GGCCTAACTGTGAAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
* *
1399314 TAAGTAAAAGAACAAT
66 TGAGTAAAAGAATAAT
1399330 GG
1 GG
1399332 ATTAGTTGTG
Statistics
Matches: 495, Mismatches: 56, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
74 64 0.13
75 1 0.00
77 2 0.00
78 2 0.00
79 59 0.12
80 28 0.06
81 339 0.68
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (81 bp):
GGCCTAACTGTGAAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
TGAGTAAAAGAATAAT
Found at i:1399114 original size:241 final size:242
Alignment explanation
Indices: 1398691--1399331 Score: 897
Period size: 241 Copynumber: 2.7 Consensus size: 242
1398681 GTGCCTTTGA
* *
1398691 GGCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCAT
1 GGCCTAACTTTGCAATTGGTAGAAA-GTACCAATTATGCCAGTTAGATGAACGGTTAAATACCAT
* *
1398756 TGAGTAAAAGAATAATGGCCTAATTGTGAAATTGGTAGAAAGGTGCCAATTATGCCAGTTAGATG
65 TGAGTAAAAGAATAATGGCCTAACTGTGAAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATG
** ** * * * *
1398821 AACAATTAAATATTGTTGAGTAAAAGAATAATGGCCTCACTGTGAAATTGGTAGAAATGTACAAA
130 AACTGTTAAATACCGTTAAGTAAAAGAATAATGGCCTAACTATGAAATTGGTAGAAAGGTACAAA
*
1398886 TTATG-CAGTTAGATGAACG-GTAAATAGCGTTGAGTAAAAGAATAAT
195 TTATGCCAGTTAGATGAACGAGTAAATACCGTTGAGTAAAAGAATAAT
* * * **
1398932 GGCCTAACTTTGAAATTGGTAGAAATGTACTAATTATGCCAGTTAGATGAACGATTAAATTTCAT
1 GGCCTAACTTTGCAATTGGTAGAAA-GTACCAATTATGCCAGTTAGATGAACGGTTAAATACCAT
1398997 TGAGTAAAAGAATAATGGCCTAACTGTGAAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATG
65 TGAGTAAAAGAATAATGGCCTAACTGTGAAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATG
* * *
1399062 AACTGTTAAATACCGTTTAGTAAAAGAATAATGGCCTAACTATGCAATTGGTAGAAAGGTACCAA
130 AACTGTTAAATACCGTTAAGTAAAAGAATAATGGCCTAACTATGAAATTGGTAGAAAGGTACAAA
* * *
1399127 TTATGCCAGTTAGATGAATGATTAAATACCGTTGAGTAAATGAATAAT
195 TTATGCCAGTTAGATGAACGAGTAAATACCGTTGAGTAAAAGAATAAT
*
1399175 GGCATAA-TTGTGCAATT-G--G---GTACCAATTATGCCAGTTAGATGAACGGTTAAATACCAT
1 GGCCTAACTT-TGCAATTGGTAGAAAGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCAT
* * * *
1399233 TGAGTAAAAGAATAATGGTCTAACTGTGCAATTGGTAGAAATGTACCAATTATGCCAATTAGATG
65 TGAGTAAAAGAATAATGGCCTAACTGTGAAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATG
* *
1399298 AA-TGGTTAAATACCATTAAGTAAAAGAACAATGG
130 AACT-GTTAAATACCGTTAAGTAAAAGAATAATGG
1399332 ATTAGTTGTG
Statistics
Matches: 359, Mismatches: 37, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
235 1 0.00
236 125 0.35
240 1 0.00
241 180 0.50
242 16 0.04
243 36 0.10
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (242 bp):
GGCCTAACTTTGCAATTGGTAGAAAGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCATT
GAGTAAAAGAATAATGGCCTAACTGTGAAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGA
ACTGTTAAATACCGTTAAGTAAAAGAATAATGGCCTAACTATGAAATTGGTAGAAAGGTACAAAT
TATGCCAGTTAGATGAACGAGTAAATACCGTTGAGTAAAAGAATAAT
Found at i:1400513 original size:25 final size:25
Alignment explanation
Indices: 1400475--1400530 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
1400465 AACTAACACC
* *
1400475 TTTTGCATTTGCATTTGGCATCTATA
1 TTTT-CATTCGCATTTGACATCTATA
1400501 TTTTCATTCGCATTTGACATCTATA
1 TTTTCATTCGCATTTGACATCTATA
1400526 TTTTC
1 TTTTC
1400531 TTTTGTACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.20, C:0.18, G:0.11, T:0.52
Consensus pattern (25 bp):
TTTTCATTCGCATTTGACATCTATA
Found at i:1402771 original size:2 final size:2
Alignment explanation
Indices: 1402760--1402801 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1402750 AAAAGGTGAT
1402760 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1402800 TA
1 TA
1402802 AATAATAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1404564 original size:20 final size:20
Alignment explanation
Indices: 1404491--1404565 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 20
1404481 TTCCAAAATT
*
1404491 TGTAAGTCCTTCGGGTCATC
1 TGTAAGTCTTTCGGGTCATC
* *
1404511 AGTAAGTCTTTCGAG-CATGAC
1 TGTAAGTCTTTCGGGTCAT--C
*
1404532 -GATTAAATCTTTCGGGTCATC
1 TG--TAAGTCTTTCGGGTCATC
1404553 TGTAAGTCTTTCG
1 TGTAAGTCTTTCG
1404566 AGCAGGATGA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 3 0.07
20 23 0.53
21 2 0.05
22 12 0.28
23 3 0.07
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (20 bp):
TGTAAGTCTTTCGGGTCATC
Done.