Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000002.1 Hibiscus syriacus cultivar Beakdansim tig00000003_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: 2131600
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:505860 original size:19 final size:20
Alignment explanation
Indices: 505819--505868 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
505809 GAAACCCCTT
*
505819 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
505839 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
505858 TGAAGATACAT
1 TGAAAATACAT
505869 TCTCTTGGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:506058 original size:25 final size:25
Alignment explanation
Indices: 506030--506084 Score: 89
Period size: 22 Copynumber: 2.3 Consensus size: 25
506020 AGTGCACATG
506030 CTTGAATGATGCACATGGCAGCCTA
1 CTTGAATGATGCACATGGCAGCCTA
506055 CTTG-A--ATGCACATGGCAGCCTA
1 CTTGAATGATGCACATGGCAGCCTA
506077 CTTGAATG
1 CTTGAATG
506085 CACATGGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 21 0.78
23 1 0.04
24 1 0.04
25 4 0.15
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (25 bp):
CTTGAATGATGCACATGGCAGCCTA
Found at i:506066 original size:22 final size:22
Alignment explanation
Indices: 506038--506091 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
506028 TGCTTGAATG
506038 ATGCACATGGCAGCCTACTTGA
1 ATGCACATGGCAGCCTACTTGA
506060 ATGCACATGGCAGCCTACTTGA
1 ATGCACATGGCAGCCTACTTGA
506082 ATGCACATGG
1 ATGCACATGG
506092 GTCTTCTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (22 bp):
ATGCACATGGCAGCCTACTTGA
Found at i:506809 original size:30 final size:32
Alignment explanation
Indices: 506770--506834 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 32
506760 ACATGCTGCC
**
506770 ATGATATCTAAATGATATGCAAACATAATA-A
1 ATGATATCTAAAACATATGCAAACATAATATA
*
506801 ATGA-ATCTAAAACATATGTAAACATAATATA
1 ATGATATCTAAAACATATGCAAACATAATATA
506832 ATG
1 ATG
506835 CTAAGTAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.29
Consensus pattern (32 bp):
ATGATATCTAAAACATATGCAAACATAATATA
Found at i:509368 original size:27 final size:28
Alignment explanation
Indices: 509315--509378 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
509305 TTTTTGAATT
* **
509315 TTTCTTTTTCTTTTCTTTTCTTCTTTTC
1 TTTCTTTTTCTCTTCTTTTAATCTTTTC
509343 -TTCTTTTTCTCTTCTTTTGAAT-TTTTC
1 TTTCTTTTTCTCTTCTTTT-AATCTTTTC
509370 TTTCTTTTT
1 TTTCTTTTT
509379 GCACTCCCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 22 0.71
28 9 0.29
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.77
Consensus pattern (28 bp):
TTTCTTTTTCTCTTCTTTTAATCTTTTC
Found at i:509373 original size:22 final size:20
Alignment explanation
Indices: 509316--509374 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 20
509306 TTTTGAATTT
509316 TTCTTTT-TCTTTTCTTT-TC
1 TTCTTTTAT-TTTTCTTTCTC
* *
509335 TTCTTTTCTTCTT-TTTCTC
1 TTCTTTTATTTTTCTTTCTC
509354 TTCTTTTGAATTTTTCTTTCT
1 TTCTTTT--ATTTTTCTTTCT
509375 TTTTGCACTC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 3 0.09
19 19 0.59
20 1 0.03
21 4 0.12
22 5 0.16
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (20 bp):
TTCTTTTATTTTTCTTTCTC
Found at i:509673 original size:19 final size:20
Alignment explanation
Indices: 509645--509684 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
509635 GGATAATAAT
509645 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
509665 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
509684 A
1 A
509685 GGATGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:510139 original size:19 final size:20
Alignment explanation
Indices: 510098--510148 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
510088 GAAACCCCTT
*
510098 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
510118 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
510137 TGAAGATACATG
1 TGAAAATACATG
510149 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:511079 original size:30 final size:31
Alignment explanation
Indices: 511040--511099 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
511030 ACATGCTGCC
**
511040 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
511071 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
511100 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:512097 original size:15 final size:15
Alignment explanation
Indices: 512077--512112 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
512067 ATTATTAGCT
512077 TTATAATATATGTTA
1 TTATAATATATGTTA
*
512092 TTATAATATATTTTA
1 TTATAATATATGTTA
*
512107 TGATAA
1 TTATAA
512113 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TTATAATATATGTTA
Found at i:519431 original size:16 final size:16
Alignment explanation
Indices: 519410--519473 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
519400 CTTTTTGAAT
519410 TTTTCTTTTTCTTTTC
1 TTTTCTTTTTCTTTTC
519426 TTTTC---TTCTTTTC
1 TTTTCTTTTTCTTTTC
*
519439 TGATT-TTTTTCTTCTT-
1 T-TTTCTTTTTCTT-TTC
*
519455 TTGTCTTTTTC-TTTC
1 TTTTCTTTTTCTTTTC
519470 TTTT
1 TTTT
519474 TGCACTCCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 15
0.66 0.07 0.27
Matches are distributed among these distances:
13 9 0.24
14 4 0.11
15 5 0.14
16 17 0.46
17 2 0.05
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTC
Found at i:519434 original size:13 final size:12
Alignment explanation
Indices: 519410--519468 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 12
519400 CTTTTTGAAT
519410 TTTTC-TTTTTC
1 TTTTCTTTTTTC
519421 TTTTCTTTTCTTC
1 TTTTCTTTT-TTC
519434 TTTTCTGATTTTT-
1 TTTTCT--TTTTTC
*
519447 TTCTTCTTTTGTC
1 TT-TTCTTTTTTC
519460 TTTTTCTTT
1 -TTTTCTTT
519469 CTTTTTGCAC
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
11 5 0.12
12 7 0.17
13 17 0.43
14 8 0.20
15 3 0.08
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:519434 original size:19 final size:19
Alignment explanation
Indices: 519412--519468 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
519402 TTTTGAATTT
519412 TTCTTTTTCTTTTCTTTTC
1 TTCTTTTTCTTTTCTTTTC
519431 TTC-TTTTCTGATTT-TTTTC
1 TTCTTTTTCT--TTTCTTTTC
519450 TTCTTTTGTCTTTTTCTTT
1 TTCTTTT-TC-TTTTCTTT
519469 CTTTTTGCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
20 9 0.28
21 5 0.16
22 1 0.03
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (19 bp):
TTCTTTTTCTTTTCTTTTC
Found at i:519467 original size:32 final size:32
Alignment explanation
Indices: 519397--519468 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
519387 CTTGGATTGC
*
519397 TTTCTTTTTGAATTTTTCTTTTTCTTTTCTTT
1 TTTCTTTTTGAATTTTTCTTCTTCTTTTCTTT
*
519429 TCTTCTTTTCTG-ATTTTT-TTCTTCTTTTGTCTT
1 T-TTCTTTT-TGAATTTTTCTTCTTCTTTTCT-TT
519462 TTTCTTT
1 TTTCTTT
519469 CTTTTTGCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
32 17 0.49
33 16 0.46
34 2 0.06
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.76
Consensus pattern (32 bp):
TTTCTTTTTGAATTTTTCTTCTTCTTTTCTTT
Found at i:519769 original size:19 final size:20
Alignment explanation
Indices: 519741--519780 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
519731 GGATAATAAT
519741 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
519761 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
519780 A
1 A
519781 GGATGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:520235 original size:19 final size:20
Alignment explanation
Indices: 520196--520244 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
520186 AACCCCTTTA
* *
520196 AAAATACTTGATTTTTGATG
1 AAAATACATGATTTTTAATG
520216 AAAATACATGA-TTTTAATG
1 AAAATACATGATTTTTAATG
*
520235 AAGATACATG
1 AAAATACATG
520245 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
AAAATACATGATTTTTAATG
Found at i:521180 original size:30 final size:31
Alignment explanation
Indices: 521141--521200 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
521131 ACATGCTGCC
**
521141 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
521172 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
521201 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:523746 original size:27 final size:27
Alignment explanation
Indices: 523684--523746 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
523674 TTTTTGAATT
*
523684 TTTCTTTTTCTTTTCTTTTATTCTTTTC
1 TTTC-TTTTCTCTTCTTTTATTCTTTTC
*
523712 TGAT-TTTTCTCTTCTTTTA-TCTTTTTC
1 T-TTCTTTTCTCTTCTTTTATTC-TTTTC
523739 TTTCTTTT
1 TTTCTTTT
523747 TGCACTCCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
26 3 0.10
27 24 0.83
28 1 0.03
29 1 0.03
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (27 bp):
TTTCTTTTCTCTTCTTTTATTCTTTTC
Found at i:524042 original size:19 final size:20
Alignment explanation
Indices: 524014--524053 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
524004 GGATAATAAT
524014 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
524034 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
524053 A
1 A
524054 GGATGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:524508 original size:19 final size:20
Alignment explanation
Indices: 524469--524517 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
524459 AACCCCTTTA
* *
524469 AAAATACTTGATTTTTGATG
1 AAAATACATGATTTTTAATG
524489 AAAATACATGA-TTTTAATG
1 AAAATACATGATTTTTAATG
*
524508 AAGATACATG
1 AAAATACATG
524518 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
AAAATACATGATTTTTAATG
Found at i:525448 original size:30 final size:31
Alignment explanation
Indices: 525409--525468 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
525399 ACATGCTGCC
*
525409 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAAGATATGCAAACATAATAA
*
525440 ATGA-ATCTAAAAGATATGTAAACATAATA
1 ATGATATCTAAAAGATATGCAAACATAATA
525469 TAAAGCTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAAGATATGCAAACATAATAA
Found at i:532921 original size:19 final size:18
Alignment explanation
Indices: 532886--532933 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
532876 CTTGGCTTTG
532886 CTTTCTTTTTGAA-TTTT
1 CTTTCTTTTTGAATTTTT
**
532903 CTTCTTCTTTTTGTCTTTTT
1 C-T-TTCTTTTTGAATTTTT
532923 CTTTCTTTTTG
1 CTTTCTTTTTG
532934 CACTCCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.04
18 10 0.38
19 10 0.38
20 5 0.19
ACGTcount: A:0.04, C:0.17, G:0.06, T:0.73
Consensus pattern (18 bp):
CTTTCTTTTTGAATTTTT
Found at i:535207 original size:19 final size:19
Alignment explanation
Indices: 535158--535207 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
535148 TGAATTTTTC
535158 CTTTTCT-TTTCTTT-TCTT
1 CTTTTCTCTTT-TTTCTCTT
**
535176 CTTTTCTGATTTTTCTCTT
1 CTTTTCTCTTTTTTCTCTT
*
535195 CTTTTGTCTTTTT
1 CTTTTCTCTTTTT
535208 CTTTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.02, C:0.20, G:0.04, T:0.74
Consensus pattern (19 bp):
CTTTTCTCTTTTTTCTCTT
Found at i:535210 original size:32 final size:32
Alignment explanation
Indices: 535140--535213 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
535130 CTTGGATTGC
*
535140 TTTCTTTTTGAATTTTTCCTTTTCTTTTCTTT
1 TTTCTTTTTGAATTTTTCCTCTTCTTTTCTTT
*
535172 TCTTCTTTTCTG-ATTTTT-CTCTTCTTTTGTCTT
1 T-TTCTTTT-TGAATTTTTCCTCTTCTTTTCT-TT
535205 TTTCTTTTT
1 TTTCTTTTT
535214 TTTTGCACTC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
31 1 0.03
32 18 0.49
33 16 0.43
34 2 0.05
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.74
Consensus pattern (32 bp):
TTTCTTTTTGAATTTTTCCTCTTCTTTTCTTT
Found at i:535512 original size:19 final size:20
Alignment explanation
Indices: 535484--535523 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
535474 GGATAATAAT
535484 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
535504 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
535523 A
1 A
535524 GGATGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:535969 original size:19 final size:20
Alignment explanation
Indices: 535928--535978 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
535918 GAAACCCCTT
*
535928 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
535948 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
535967 TGAAGATACATG
1 TGAAAATACATG
535979 CTCTTGGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:538577 original size:13 final size:13
Alignment explanation
Indices: 538556--538593 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
538546 GAGAAAAATC
538556 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
*
538569 AGAAGAAAAGAAA
1 AGAAAAAAAGAAA
*
538582 AGAAAAAGAGAA
1 AGAAAAAAAGAA
538594 GTTCAAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:542857 original size:301 final size:301
Alignment explanation
Indices: 542315--542891 Score: 1136
Period size: 301 Copynumber: 1.9 Consensus size: 301
542305 AATGTAAGTG
542315 CAACTTTTAATATTTCAGATCTTTCTCCATTTGATGACAATGACGATTTGAGGGCAAATCGCTCA
1 CAACTTTTAATATTTCAGATCTTTCTCCATTTGATGACAATGACGATTTGAGGGCAAATCGCTCA
542380 AAAGAAGGGGAGGATGATGTGATCACAACTACACAAATGGATCCTGAAGTTATGCCCAAAGGACC
66 AAAGAAGGGGAGGATGATGTGATCACAACTACACAAATGGATCCTGAAGTTATGCCCAAAGGACC
542445 TATCACTCGTGCAAAGGTAAAACAATTCAGGGAAGTACTTTCTCATAAGTGCATTAATGTTTTTA
131 TATCACTCGTGCAAAGGTAAAACAATTCAGGGAAGTACTTTCTCATAAGTGCATTAATGTTTTTA
542510 AATCTTTTAATGAGAAAGAACCATTAGATAATAGGTTGTTTAATATGTTACATATTGAATATTAA
196 AATCTTTTAATGAGAAAGAACCATTAGATAATAGGTTGTTTAATATGTTACATATTGAATATTAA
542575 ATAACCTATAGTCATAAGTGCCTTAATGTTTTTATATTATA
261 ATAACCTATAGTCATAAGTGCCTTAATGTTTTTATATTATA
*
542616 CAACTTTTAATATTTTAGATCTTTCTCCATTTGATGACAATGACGATTTGAGGGCAAATCGCTCA
1 CAACTTTTAATATTTCAGATCTTTCTCCATTTGATGACAATGACGATTTGAGGGCAAATCGCTCA
542681 AAAGAAGGGGAGGATGATGTGATCACAACTACACAAATGGATCCTGAAGTTATGCCCAAAGGACC
66 AAAGAAGGGGAGGATGATGTGATCACAACTACACAAATGGATCCTGAAGTTATGCCCAAAGGACC
*
542746 TATCACTCGTGCAAAGGTAAAACAATTCAGGGAAGTACTTTCTCATAAGTGCCTTAATGTTTTTA
131 TATCACTCGTGCAAAGGTAAAACAATTCAGGGAAGTACTTTCTCATAAGTGCATTAATGTTTTTA
542811 AATCTTTTAATGAGAAAGAACCATTAGATAATAGGTTGTTTAATATGTTACATATTGAATATTAA
196 AATCTTTTAATGAGAAAGAACCATTAGATAATAGGTTGTTTAATATGTTACATATTGAATATTAA
542876 ATAACCTATAGTCATA
261 ATAACCTATAGTCATA
542892 TTTTTATATT
Statistics
Matches: 274, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
301 274 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (301 bp):
CAACTTTTAATATTTCAGATCTTTCTCCATTTGATGACAATGACGATTTGAGGGCAAATCGCTCA
AAAGAAGGGGAGGATGATGTGATCACAACTACACAAATGGATCCTGAAGTTATGCCCAAAGGACC
TATCACTCGTGCAAAGGTAAAACAATTCAGGGAAGTACTTTCTCATAAGTGCATTAATGTTTTTA
AATCTTTTAATGAGAAAGAACCATTAGATAATAGGTTGTTTAATATGTTACATATTGAATATTAA
ATAACCTATAGTCATAAGTGCCTTAATGTTTTTATATTATA
Found at i:550616 original size:36 final size:36
Alignment explanation
Indices: 550543--550647 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
550533 ATTTATAAGT
* * *
550543 TGGTGATAATATAGGCGTGAT-ATAGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
550578 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
550614 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
550648 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:553239 original size:19 final size:20
Alignment explanation
Indices: 553198--553248 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
553188 GAAACCCCTT
*
553198 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
*
553218 TGAAAATACATTA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
553237 TGAAGATACATG
1 TGAAAATACATG
553249 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:554201 original size:30 final size:31
Alignment explanation
Indices: 554162--554221 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
554152 ACATGCTGCC
**
554162 ATGATATCTAAATGATATGTAAACATAATAA
1 ATGATATCTAAAACATATGTAAACATAATAA
554193 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGTAAACATAATA
554222 TAAAGCTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.30
Consensus pattern (31 bp):
ATGATATCTAAAACATATGTAAACATAATAA
Found at i:556612 original size:30 final size:32
Alignment explanation
Indices: 556573--556635 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
556563 ACATGCTTCC
**
556573 ATGATATCTAAATGATATGTAAACAT-AATAA
1 ATGATATCTAAAACATATGTAAACATAAATAA
556604 ATGA-ATCTAAAACATATGTAAACATAAATAA
1 ATGATATCTAAAACATATGTAAACATAAATAA
556635 A
1 A
556636 GCTAAGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.29
Consensus pattern (32 bp):
ATGATATCTAAAACATATGTAAACATAAATAA
Found at i:559150 original size:19 final size:19
Alignment explanation
Indices: 559114--559151 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
559104 CAAAAAAAGT
*
559114 AACAAGAAAGAAGAAAAAA
1 AACAAGAAAGAAAAAAAAA
559133 AACAA-AAAGAAAAGAAAAA
1 AACAAGAAAGAAAA-AAAAA
559152 GACTTCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (19 bp):
AACAAGAAAGAAAAAAAAA
Found at i:559360 original size:16 final size:15
Alignment explanation
Indices: 559334--559385 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
559324 GAGTTGTAAG
559334 TTATC-TTCATTTTT
1 TTATCTTTCATTTTT
*
559348 TTATCATTTCATTTCT
1 TTATC-TTTCATTTTT
559364 TTATTCTTTCATCTTTT
1 TTA-TCTTTCAT-TTTT
559381 CTTAT
1 -TTAT
559386 TTCATTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 5 0.16
16 17 0.55
17 6 0.19
18 3 0.10
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATCTTTCATTTTT
Found at i:565696 original size:20 final size:21
Alignment explanation
Indices: 565655--565699 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
565645 TTATATTATG
*
565655 TTTATTTATGTTTTACGTTCA
1 TTTATTTATGTTTTACATTCA
565676 TTTA-TTATGTTTT-CATATCA
1 TTTATTTATGTTTTACAT-TCA
565696 TTTA
1 TTTA
565700 CATGTCATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 16 0.73
21 4 0.18
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.62
Consensus pattern (21 bp):
TTTATTTATGTTTTACATTCA
Found at i:566647 original size:19 final size:20
Alignment explanation
Indices: 566618--566658 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
566608 CCATTCAGCC
*
566618 AAGTGCATGTATTTTTATTA
1 AAGTGCATGTATTTTCATTA
566638 AAGT-CATGTATTTTCATTA
1 AAGTGCATGTATTTTCATTA
566657 AA
1 AA
566659 AATCAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.46
Consensus pattern (20 bp):
AAGTGCATGTATTTTCATTA
Found at i:569406 original size:17 final size:17
Alignment explanation
Indices: 569384--569455 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
569374 AATTAAGAGT
569384 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
569401 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
* *
569418 TATTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* * *
569435 TAACTTTATTCAATGAAC
1 T-AGTTTAATAAATGAAC
569453 TAG
1 TAG
569456 GACTTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 31 0.69
18 14 0.31
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.39
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:569462 original size:20 final size:19
Alignment explanation
Indices: 569428--569476 Score: 82
Period size: 20 Copynumber: 2.6 Consensus size: 19
569418 TATTTTAATT
569428 AATGAACTA-ACTTTATTC
1 AATGAACTAGACTTTATTC
569446 AATGAACTAGGACTTTATTC
1 AATGAACTA-GACTTTATTC
569466 AATGAACTAGA
1 AATGAACTAGA
569477 TGCATGAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.31
19 2 0.07
20 18 0.62
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (19 bp):
AATGAACTAGACTTTATTC
Found at i:573270 original size:12 final size:11
Alignment explanation
Indices: 573249--573290 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
573239 TGCTGGAAAG
573249 AAGATAAAAAAT
1 AAGAT-AAAAAT
*
573261 AAGATTAAAAT
1 AAGATAAAAAT
573272 AAGATAAAGAA-
1 AAGATAAA-AAT
573283 AAGATAAA
1 AAGATAAA
573291 GGAATTGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 20 0.74
12 7 0.26
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (11 bp):
AAGATAAAAAT
Found at i:577036 original size:12 final size:12
Alignment explanation
Indices: 577019--577048 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
577009 GGATTTTTTA
*
577019 TTTTTTTTGCCT
1 TTTTTTTTACCT
577031 TTTTTTTTACCT
1 TTTTTTTTACCT
577043 TTTTTT
1 TTTTTT
577049 GTTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTTTTTACCT
Found at i:577425 original size:11 final size:12
Alignment explanation
Indices: 577395--577441 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
577385 TTTGTGCTGG
577395 AAACAAGATAAA
1 AAACAAGATAAA
* *
577407 AAATAAGAT-TA
1 AAACAAGATAAA
577418 AAACAAGATAAA
1 AAACAAGATAAA
*
577430 GAA-AAGATAAA
1 AAACAAGATAAA
577441 A
1 A
577442 GAATTACAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:577425 original size:23 final size:21
Alignment explanation
Indices: 577395--577441 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
577385 TTTGTGCTGG
577395 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGA-TA
*
577418 AAACAAGATAAAGAAAAGATA
1 AAACAAGATAAAAAAAAGATA
577439 AAA
1 AAA
577442 GAATTACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 4 0.17
23 14 0.61
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (21 bp):
AAACAAGATAAAAAAAAGATA
Found at i:588442 original size:21 final size:21
Alignment explanation
Indices: 588418--588457 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
588408 CTCATTTTCA
588418 CTCTCAAT-TCTCTTTTCAATG
1 CTCTCAATGTCT-TTTTCAATG
588439 CTCTCAATGTCTTTTTCAA
1 CTCTCAATGTCTTTTTCAA
588458 CACTCGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.20, C:0.28, G:0.05, T:0.47
Consensus pattern (21 bp):
CTCTCAATGTCTTTTTCAATG
Found at i:589331 original size:5 final size:5
Alignment explanation
Indices: 589313--589366 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
589303 CCCTCTTTAA
* *
589313 ATTTT CTTTT -TTTT ATTTT ATTTT ATTTT -TCTTT CTTTTT ATTTT -TTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT-TTT -ATTTT ATTTT ATTTT
589362 ATTTT
1 ATTTT
589367 TTTACTAAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
4 9 0.21
5 29 0.69
6 3 0.07
7 1 0.02
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (5 bp):
ATTTT
Found at i:589343 original size:25 final size:25
Alignment explanation
Indices: 589314--589367 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
589304 CCTCTTTAAA
589314 TTTTCTTT-TTTTTATTTTATTTTAT
1 TTTTCTTTCTTTTTATTTT-TTTTAT
589339 TTTTCTTTCTTTTTATTTTTTTTAT
1 TTTTCTTTCTTTTTATTTTTTTTAT
589364 TTTT
1 TTTT
589368 TTACTAAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 18 0.64
26 10 0.36
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (25 bp):
TTTTCTTTCTTTTTATTTTTTTTAT
Found at i:589367 original size:10 final size:10
Alignment explanation
Indices: 589313--589369 Score: 55
Period size: 9 Copynumber: 5.8 Consensus size: 10
589303 CCCTCTTTAA
*
589313 ATTTTCTTTT
1 ATTTTTTTTT
*
589323 -TTTTATTTT
1 ATTTTTTTTT
589332 ATTTTATTTTT
1 ATTTT-TTTTT
* *
589343 CTTTCTTTTT
1 ATTTTTTTTT
589353 A-TTTTTTTT
1 ATTTTTTTTT
589362 ATTTTTTT
1 ATTTTTTT
589370 ACTAAGCCGA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 16 0.42
10 15 0.39
11 7 0.18
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:590967 original size:18 final size:18
Alignment explanation
Indices: 590910--590990 Score: 71
Period size: 17 Copynumber: 4.5 Consensus size: 18
590900 TAGTTAAATA
*
590910 AATGAACT-ACTTTGA-TG
1 AATGAACTAACTTT-ATTC
*
590927 AATGAACT-ATTTTAATT-
1 AATGAACTAACTTT-ATTC
*
590944 AATGAACTAACTTTTTTC
1 AATGAACTAACTTTATTC
590962 AATGAACTAGAACTTTATTC
1 AATGAACT--AACTTTATTC
590982 AATGAACTA
1 AATGAACTA
590991 GATGCATGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
17 23 0.43
18 14 0.26
20 17 0.31
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (18 bp):
AATGAACTAACTTTATTC
Found at i:590975 original size:20 final size:20
Alignment explanation
Indices: 590944--590992 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
590934 TATTTTAATT
*
590944 AATGAACT--AACTTTTTTC
1 AATGAACTAGAACTTTATTC
590962 AATGAACTAGAACTTTATTC
1 AATGAACTAGAACTTTATTC
590982 AATGAACTAGA
1 AATGAACTAGA
590993 TGCATGAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 8 0.29
20 20 0.71
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (20 bp):
AATGAACTAGAACTTTATTC
Found at i:595099 original size:2 final size:2
Alignment explanation
Indices: 595092--595132 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
595082 TGGTAGCGGA
595092 AT 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 AT A
595133 AGTTGGTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:600354 original size:16 final size:15
Alignment explanation
Indices: 600321--600372 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
600311 GTAAGTTATC
600321 TTCATTTTTTATCAT
1 TTCATTTTTTATCAT
600336 TTCATTTCTTTATTC-T
1 TTCATTT-TTTA-TCAT
* * *
600352 TTCATCTTTTCTTAT
1 TTCATTTTTTATCAT
600367 TTCATT
1 TTCATT
600373 ACCATATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 11 0.37
17 2 0.07
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCATTTTTTATCAT
Found at i:603074 original size:19 final size:20
Alignment explanation
Indices: 603033--603083 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
603023 GAAACCCCTT
*
603033 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
603053 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
603072 TGAAGATACATG
1 TGAAAATACATG
603084 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:607258 original size:19 final size:20
Alignment explanation
Indices: 607217--607267 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
607207 GAAACCCCTT
*
607217 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
607237 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
607256 TGAAGATACATG
1 TGAAAATACATG
607268 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:608836 original size:19 final size:20
Alignment explanation
Indices: 608812--608862 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
608802 CGGCCAAGAG
* *
608812 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
608831 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
608851 CATGTATTTTCA
1 CATGTATTTTCA
608863 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:622431 original size:19 final size:20
Alignment explanation
Indices: 622407--622457 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
622397 CGGCCAAGAG
* *
622407 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
622426 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
622446 CATGTATTTTCA
1 CATGTATTTTCA
622458 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:626820 original size:19 final size:20
Alignment explanation
Indices: 626779--626829 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
626769 GAAACCCCTT
*
626779 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
626799 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
626818 TGAAGATACATG
1 TGAAAATACATG
626830 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:635329 original size:32 final size:33
Alignment explanation
Indices: 635268--635334 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
635258 ACTAAATTAA
* *
635268 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAATAGAAAATGGATAG
635300 AAGAAAGGAAATGA-TAAGAA-AGAAAATGGATAG
1 AAGAAA-GAAATGATTAA-AATAGAAAATGGATAG
635333 AA
1 AA
635335 ATGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.60, C:0.00, G:0.25, T:0.15
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATAGAAAATGGATAG
Found at i:641871 original size:13 final size:13
Alignment explanation
Indices: 641849--641878 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
641839 ACTAAACACC
641849 TTTC-ACATACCT
1 TTTCAACATACCT
641861 TTTCAACATACCT
1 TTTCAACATACCT
641874 TTTCA
1 TTTCA
641879 TCTTTGGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:647817 original size:25 final size:25
Alignment explanation
Indices: 647765--647816 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
647755 ATCAACAAAT
* *
647765 AAATTGAAGCACTCCAAAAAGAAGA
1 AAATTAAAGAACTCCAAAAAGAAGA
647790 AAATTAAAGAACT-CAAAAAGAAGA
1 AAATTAAAGAACTCCAAAAAGAAGA
647814 AAA
1 AAA
647817 AAAGAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.63, C:0.12, G:0.13, T:0.12
Consensus pattern (25 bp):
AAATTAAAGAACTCCAAAAAGAAGA
Found at i:647824 original size:25 final size:26
Alignment explanation
Indices: 647770--647825 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
647760 CAAATAAATT
* **
647770 GAAGCACTCCAAAAAGAAGAAAATTA
1 GAAGAACTCCAAAAAGAAGAAAAAAA
647796 -AAGAACT-CAAAAAGAAGAAAAAAA
1 GAAGAACTCCAAAAAGAAGAAAAAAA
647820 GAAGAA
1 GAAGAA
647826 AAGTAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.66, C:0.11, G:0.16, T:0.07
Consensus pattern (26 bp):
GAAGAACTCCAAAAAGAAGAAAAAAA
Found at i:652522 original size:35 final size:35
Alignment explanation
Indices: 652468--652547 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
652458 GATACTATTT
*
652468 TCATCACCATATTCCATCACCATTGCATGCCTATA
1 TCATCACCATATTCCATCACCATTGCACGCCTATA
* * *
652503 TCATCACCATCTTCTATCACCATTTCACGCCTATA
1 TCATCACCATATTCCATCACCATTGCACGCCTATA
652538 TCATCACCAT
1 TCATCACCAT
652548 TCCCTTACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.33
Consensus pattern (35 bp):
TCATCACCATATTCCATCACCATTGCACGCCTATA
Found at i:653886 original size:8 final size:8
Alignment explanation
Indices: 653873--653910 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
653863 GTTATGAACC
653873 ATATATTT
1 ATATATTT
653881 ATATATTT
1 ATATATTT
653889 ATAT-TTAT
1 ATATATT-T
653897 ATATATTT
1 ATATATTT
653905 -TATATT
1 ATATATT
653911 ACTTAGCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 8 0.29
8 18 0.64
9 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
ATATATTT
Found at i:653893 original size:14 final size:14
Alignment explanation
Indices: 653874--653900 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
653864 TTATGAACCA
653874 TATATTTATATATT
1 TATATTTATATATT
653888 TATATTTATATAT
1 TATATTTATATAT
653901 ATTTTATATT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATATTTATATATT
Found at i:654993 original size:13 final size:11
Alignment explanation
Indices: 654952--655036 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
654942 ACAATTTGTC
654952 CATCACCATTAT
1 CATCACCA-TAT
*
654964 CA-CGCCTATAT
1 CATCACC-ATAT
654975 CATCACCATAGT
1 CATCACCATA-T
654987 CCATCACCATTAT
1 -CATCACCA-TAT
*
655000 CA-CGCCTATAT
1 CATCACC-ATAT
655011 CATCACCATATT
1 CATCACCATA-T
655023 CCATCACCATAT
1 -CATCACCATAT
655035 CA
1 CA
655037 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:654996 original size:36 final size:36
Alignment explanation
Indices: 654949--655053 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
654939 GATACAATTT
654949 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
654985 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
655021 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
655054 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:655219 original size:15 final size:15
Alignment explanation
Indices: 655195--655230 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
655185 TTTGATAACT
*
655195 ATTCTATCCATTTCA
1 ATTCTTTCCATTTCA
655210 ATTCTTTCCATTTCA
1 ATTCTTTCCATTTCA
*
655225 TTTCTT
1 ATTCTT
655231 AATTACTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTCTTTCCATTTCA
Found at i:659523 original size:36 final size:36
Alignment explanation
Indices: 659476--659580 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
659466 GATACAATAT
659476 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
659512 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
659548 TTACATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
659581 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:664892 original size:12 final size:12
Alignment explanation
Indices: 664875--664900 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
664865 CAAAAATAAG
664875 AAGTGCAAAGTC
1 AAGTGCAAAGTC
664887 AAGTGCAAAGTC
1 AAGTGCAAAGTC
664899 AA
1 AA
664901 AGAAAGCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.15
Consensus pattern (12 bp):
AAGTGCAAAGTC
Found at i:673664 original size:23 final size:23
Alignment explanation
Indices: 673619--673664 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
673609 GTATAATATA
**
673619 TATAAATATGAAAATAATTATCT
1 TATAAATATGAAAATAAGCATCT
673642 TATAACATATG-AAATAAGCATCT
1 TATAA-ATATGAAAATAAGCATCT
673665 ATAGGTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.35
Consensus pattern (23 bp):
TATAAATATGAAAATAAGCATCT
Found at i:675474 original size:33 final size:33
Alignment explanation
Indices: 675431--675497 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
675421 AAGCAAGCAA
* * *
675431 TACATAATGGTTTCACAAATCGATATTCTTTCT
1 TACATAATGGTTCCACAAACCAATATTCTTTCT
*
675464 TACATGATGGTTCCACAAACCAATATTCTTTCT
1 TACATAATGGTTCCACAAACCAATATTCTTTCT
675497 T
1 T
675498 CCTCGATAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (33 bp):
TACATAATGGTTCCACAAACCAATATTCTTTCT
Found at i:677672 original size:22 final size:23
Alignment explanation
Indices: 677644--677710 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
677634 AAATCCAGCA
* *
677644 AAGAAA-TCAAAGCCCTCAAAAG
1 AAGAAATTAAAAGCACTCAAAAG
* *
677666 AAGAAATTGAAAGCACTAAAAAG
1 AAGAAATTAAAAGCACTCAAAAG
*
677689 AATAAATTAAAAGCACTCAAAA
1 AAGAAATTAAAAGCACTCAAAA
677711 AGAATAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
22 6 0.16
23 32 0.84
ACGTcount: A:0.60, C:0.15, G:0.12, T:0.13
Consensus pattern (23 bp):
AAGAAATTAAAAGCACTCAAAAG
Found at i:677715 original size:24 final size:24
Alignment explanation
Indices: 677652--677718 Score: 93
Period size: 23 Copynumber: 2.9 Consensus size: 24
677642 CAAAGAAATC
* * *
677652 AAAGCCCTC-AAAAGAAGAAATTG
1 AAAGCACTCAAAAAGAATAAATTA
677675 AAAGCACT-AAAAAGAATAAATTA
1 AAAGCACTCAAAAAGAATAAATTA
677698 AAAGCACTCAAAAAGAATAAA
1 AAAGCACTCAAAAAGAATAAA
677719 AAGAAAAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
23 27 0.69
24 12 0.31
ACGTcount: A:0.61, C:0.13, G:0.12, T:0.13
Consensus pattern (24 bp):
AAAGCACTCAAAAAGAATAAATTA
Found at i:677727 original size:14 final size:14
Alignment explanation
Indices: 677708--677740 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
677698 AAAGCACTCA
677708 AAAAGAATAA-AAAG
1 AAAAGAA-AAGAAAG
677722 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
677736 AAAAG
1 AAAAG
677741 TTGAAGCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:681490 original size:23 final size:24
Alignment explanation
Indices: 681464--681510 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
681454 GGATAATTCA
*
681464 ATGGTTACGGAATGGTGAT-GAAT
1 ATGGTAACGGAATGGTGATAGAAT
* *
681487 ATGGTAATGGGATGGTGATAGAAT
1 ATGGTAACGGAATGGTGATAGAAT
681511 TTACGTGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.32, C:0.02, G:0.36, T:0.30
Consensus pattern (24 bp):
ATGGTAACGGAATGGTGATAGAAT
Found at i:684886 original size:15 final size:15
Alignment explanation
Indices: 684866--684917 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
684856 TGATAAGTAA
684866 ATGAAATAAGAAAAT
1 ATGAAATAAGAAAAT
* *
684881 ATGAAAGAA-ATAACAA
1 ATGAAATAAGA-AA-AT
684897 ATGAAATAAGAAAAT
1 ATGAAATAAGAAAAT
684912 ATGAAA
1 ATGAAA
684918 GAAATAACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 17 0.57
16 11 0.37
17 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.13, T:0.17
Consensus pattern (15 bp):
ATGAAATAAGAAAAT
Found at i:684892 original size:19 final size:19
Alignment explanation
Indices: 684868--684924 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
684858 ATAAGTAAAT
684868 GAAATAAGAAAATATGAAA
1 GAAATAAGAAAATATGAAA
*
684887 GAAAT-A-ACAA-AT----
1 GAAATAAGAAAATATGAAA
684899 GAAATAAGAAAATATGAAA
1 GAAATAAGAAAATATGAAA
684918 GAAATAA
1 GAAATAA
684925 CAAATGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 14
0.64 0.04 0.31
Matches are distributed among these distances:
12 5 0.17
13 1 0.03
14 3 0.10
15 2 0.07
16 2 0.07
17 3 0.10
18 1 0.03
19 12 0.41
ACGTcount: A:0.68, C:0.02, G:0.14, T:0.16
Consensus pattern (19 bp):
GAAATAAGAAAATATGAAA
Found at i:684900 original size:31 final size:31
Alignment explanation
Indices: 684864--684936 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
684854 AATGATAAGT
684864 AAATGAAATAAGAAAATATGAAAGAAATAAC
1 AAATGAAATAAGAAAATATGAAAGAAATAAC
684895 AAATGAAATAAGAAAATATGAAAGAAATAAC
1 AAATGAAATAAGAAAATATGAAAGAAATAAC
684926 AAATGAAATAA
1 AAATGAAATAA
684937 TAAGAATAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.68, C:0.03, G:0.12, T:0.16
Consensus pattern (31 bp):
AAATGAAATAAGAAAATATGAAAGAAATAAC
Found at i:684902 original size:16 final size:16
Alignment explanation
Indices: 684881--684933 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
684871 ATAAGAAAAT
684881 ATGAAAGAAATAACAA
1 ATGAAAGAAATAACAA
* *
684897 ATGAAATAAGA-AA-AT
1 ATGAAAGAA-ATAACAA
684912 ATGAAAGAAATAACAA
1 ATGAAAGAAATAACAA
684928 ATGAAA
1 ATGAAA
684934 TAATAAGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 11 0.37
16 17 0.57
17 1 0.03
ACGTcount: A:0.68, C:0.04, G:0.13, T:0.15
Consensus pattern (16 bp):
ATGAAAGAAATAACAA
Found at i:685166 original size:13 final size:13
Alignment explanation
Indices: 685148--685177 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
685138 GATGTAGGAG
685148 TCTTTTTTTTTCT
1 TCTTTTTTTTTCT
685161 TCTTTTTTTTTCT
1 TCTTTTTTTTTCT
685174 TCTT
1 TCTT
685178 GTTGCAGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TCTTTTTTTTTCT
Found at i:685564 original size:23 final size:24
Alignment explanation
Indices: 685538--685584 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
685528 GGATAATTCA
*
685538 ATGGTTACGGAATGGTGAT-GAAT
1 ATGGTAACGGAATGGTGATAGAAT
* *
685561 ATGGTAATGGGATGGTGATAGAAT
1 ATGGTAACGGAATGGTGATAGAAT
685585 TTACGTGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.32, C:0.02, G:0.36, T:0.30
Consensus pattern (24 bp):
ATGGTAACGGAATGGTGATAGAAT
Found at i:686718 original size:14 final size:14
Alignment explanation
Indices: 686699--686734 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
686689 GCTGTCCTGG
686699 AGTTGTCCTAGTTA
1 AGTTGTCCTAGTTA
686713 AGTTGTCCTAGTTA
1 AGTTGTCCTAGTTA
686727 AGGTTGTC
1 A-GTTGTC
686735 TTACAAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.42
Consensus pattern (14 bp):
AGTTGTCCTAGTTA
Found at i:695870 original size:23 final size:24
Alignment explanation
Indices: 695844--695897 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
695834 AAATCCAGCA
695844 AAGAAAATCAAAGCACT-CAAAAG
1 AAGAAAATCAAAGCACTACAAAAG
* * *
695867 AAGAAATTGAAAGCACTAGAAAAG
1 AAGAAAATCAAAGCACTACAAAAG
695891 AAGAAAA
1 AAGAAAA
695898 AGAAAAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATCAAAGCACTACAAAAG
Found at i:699410 original size:90 final size:91
Alignment explanation
Indices: 699254--699435 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 91
699244 CCTAGAACAC
*
699254 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTACATGAGGATCATTTAGGCGACAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTACATGAGGATCATTTAGGCGACAAGATG
*
699319 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
** * * * * * *
699345 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTACATGTGGTTTATTTAGGCGCCAATATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTACATGAGGATCATTTAGGCGACAAGATG
699409 AAGAGCTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
699435 C
1 C
699436 ATCATTTCCC
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 62 0.77
91 19 0.23
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTACATGAGGATCATTTAGGCGACAAGATG
AAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:703348 original size:26 final size:27
Alignment explanation
Indices: 703304--703375 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 27
703294 AGTGCTTCAA
*** * *
703304 CTTCTTTCTTTTCTTTGCTTTGCTTTT
1 CTTCTTTCTTTTGAGTGCTTGGATTTT
*
703331 CTTCTTT-TTTTTAGTGC-TGGATTTT
1 CTTCTTTCTTTTGAGTGCTTGGATTTT
*
703356 TTTCTTTCTTTTGAGTGCTT
1 CTTCTTTCTTTTGAGTGCTT
703376 CACTTTGTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
25 12 0.33
26 16 0.44
27 8 0.22
ACGTcount: A:0.04, C:0.17, G:0.12, T:0.67
Consensus pattern (27 bp):
CTTCTTTCTTTTGAGTGCTTGGATTTT
Found at i:705935 original size:5 final size:5
Alignment explanation
Indices: 705921--705978 Score: 66
Period size: 5 Copynumber: 11.8 Consensus size: 5
705911 CTTTTTGAAT
* **
705921 TTTTC TTTTTC TTTTC TTTTC TTTTC TTTTC TTTT- TTCTC TGAT- TTTTC
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
705970 TTTTC TTTT
1 TTTTC TTTT
705979 GTCTTTTTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
4 5 0.11
5 35 0.78
6 5 0.11
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:705993 original size:10 final size:9
Alignment explanation
Indices: 705926--705996 Score: 61
Period size: 10 Copynumber: 7.2 Consensus size: 9
705916 TGAATTTTTC
705926 TTTTTCTTT
1 TTTTTCTTT
705935 TCTTTTCTTT
1 T-TTTTCTTT
705945 TCTTTTCTTT
1 T-TTTTCTTT
* **
705955 TTTCTCTGA
1 TTTTTCTTT
705964 TTTTTCTTTT
1 TTTTTC-TTT
705974 CTTTTGTCTTT
1 -TTTT-TCTTT
705985 TTCTTTCTTT
1 TT-TTTCTTT
705995 TT
1 TT
705997 GCACTCCAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
9 11 0.22
10 29 0.57
11 9 0.18
12 2 0.04
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.79
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:706733 original size:19 final size:21
Alignment explanation
Indices: 706690--706741 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
706680 GAAACCCCTT
706690 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
706711 TGAAAATACATTA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
706730 TGAACATACATG
1 TGAAAATACATG
706742 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:711693 original size:11 final size:11
Alignment explanation
Indices: 711679--711734 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
711669 TCTTTTTGAA
711679 TTCTTTTTCTT
1 TTCTTTTTCTT
711690 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
711703 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
711716 TGTCTTTTTC-T
1 T-TCTTTTTCTT
711727 TTCTTTTT
1 TTCTTTTT
711735 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:711703 original size:19 final size:18
Alignment explanation
Indices: 711679--711734 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
711669 TCTTTTTGAA
711679 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
711697 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
711716 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
711734 T
1 T
711735 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:714688 original size:35 final size:36
Alignment explanation
Indices: 714641--714708 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
714631 ATTTAGAAGT
714641 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
714676 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
714709 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:718198 original size:19 final size:20
Alignment explanation
Indices: 718159--718201 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
718149 TTGCTTTACT
*
718159 TTTTCTTTTGCTTTTGATTC
1 TTTTCTTTTGCTTTTCATTC
*
718179 TTTTCTTTT-CTTTTCTTTC
1 TTTTCTTTTGCTTTTCATTC
718198 TTTT
1 TTTT
718202 GCACTCCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTGCTTTTCATTC
Found at i:722713 original size:15 final size:14
Alignment explanation
Indices: 722693--722740 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 14
722683 TACTTTGATA
722693 TCATTTCTTTCCATT
1 TCATTTCTTT-CATT
*
722708 TCATTTCTTATTAATT
1 TCATTTC-T-TTCATT
722724 TCCATTTCTTTCATT
1 T-CATTTCTTTCATT
722739 TC
1 TC
722741 TTATTTCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 1 0.04
15 13 0.46
16 6 0.21
17 8 0.29
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (14 bp):
TCATTTCTTTCATT
Found at i:722754 original size:33 final size:32
Alignment explanation
Indices: 722694--722755 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
722684 ACTTTGATAT
**
722694 CATTTCTTTCCATTTCATTTCTTATTAATTTC
1 CATTTCTTTCCATTTCATTTCCAATTAATTTC
722726 CATTTCTTT-CATTTCTTATTTCCAATTAAT
1 CATTTCTTTCCATTTC--ATTTCCAATTAAT
722756 CATTTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 6 0.23
32 9 0.35
33 11 0.42
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (32 bp):
CATTTCTTTCCATTTCATTTCCAATTAATTTC
Found at i:723261 original size:21 final size:22
Alignment explanation
Indices: 723237--723285 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
723227 GTTGTGTCTT
*
723237 TATT-GCAGGAGTTTGATGACC
1 TATTCGCAAGAGTTTGATGACC
*
723258 TATTTCCGGAAGAGTTTGATGACC
1 TA-TT-CGCAAGAGTTTGATGACC
723282 TATT
1 TATT
723286 TCCGGAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 2 0.09
22 2 0.09
23 2 0.09
24 17 0.74
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (22 bp):
TATTCGCAAGAGTTTGATGACC
Found at i:723272 original size:24 final size:24
Alignment explanation
Indices: 723245--723294 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
723235 TTTATTGCAG
723245 GAGTTTGATGACCTATTTCCGGAA
1 GAGTTTGATGACCTATTTCCGGAA
723269 GAGTTTGATGACCTATTTCCGGAA
1 GAGTTTGATGACCTATTTCCGGAA
723293 GA
1 GA
723295 AATTGATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (24 bp):
GAGTTTGATGACCTATTTCCGGAA
Found at i:723300 original size:24 final size:24
Alignment explanation
Indices: 723249--723302 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
723239 TTGCAGGAGT
**
723249 TTGATGACCTATTTCCGGAAGAGT
1 TTGATGACCTATTTCCGGAAGAAA
723273 TTGATGACCTATTTCCGGAAGAAA
1 TTGATGACCTATTTCCGGAAGAAA
723297 TTGATG
1 TTGATG
723303 TGATCTTGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (24 bp):
TTGATGACCTATTTCCGGAAGAAA
Found at i:724840 original size:35 final size:35
Alignment explanation
Indices: 724729--724841 Score: 111
Period size: 35 Copynumber: 3.2 Consensus size: 35
724719 TAAGATACTA
*
724729 CCTATAAT-ATCACAATCTTCCATCACCATTTTCACG
1 CCTAT-ATCATCACAATATTCCATCACCA-TTTCACG
* * * *
724765 CCTAAAACATCACAATCTTCCATCACCATTGCACG
1 CCTATATCATCACAATATTCCATCACCATTTCACG
* * * * *
724800 GCTATATCATTACCATATTCTATCACCATTTAACG
1 CCTATATCATCACAATATTCCATCACCATTTCACG
724835 CCTATAT
1 CCTATAT
724842 AACCACCAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
35 39 0.62
36 24 0.38
ACGTcount: A:0.32, C:0.32, G:0.04, T:0.32
Consensus pattern (35 bp):
CCTATATCATCACAATATTCCATCACCATTTCACG
Found at i:725245 original size:6 final size:6
Alignment explanation
Indices: 725209--725247 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
725199 GTGTTGCAAC
* *
725209 AAAAAG TAAAAG AAATAAG AAAAAC AAAAAG AAAAAG AA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AA
725248 GTGACAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:725283 original size:14 final size:13
Alignment explanation
Indices: 725266--725295 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
725256 TTTGGAGTGC
725266 AAAAGAAAGAAAAA
1 AAAAG-AAGAAAAA
725280 AAAAGAAGAAAAA
1 AAAAGAAGAAAAA
725293 AAA
1 AAA
725296 TTCAACGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAAAAA
Found at i:728390 original size:36 final size:36
Alignment explanation
Indices: 728286--728390 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 36
728276 ATTTATAAGT
* * *
728286 TGGTGATAATATTGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* *
728321 TGGTGGTGATATAGGCATGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
728357 TGGTGATGATATAGGCGTGATAATAGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
728391 AGATTGTATC
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
35 17 0.28
36 44 0.72
ACGTcount: A:0.29, C:0.05, G:0.35, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:732432 original size:22 final size:20
Alignment explanation
Indices: 732389--732433 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
732379 TATATGAGTC
* *
732389 TTTTTCTTTTCTTTTTGTTT
1 TTTTTCTTTTCTTGTTGCTT
732409 TTTTTCTTCTTTCTTGTTGCTT
1 TTTTTC-T-TTTCTTGTTGCTT
732431 TTT
1 TTT
732434 GTTGTAGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 1 0.05
22 14 0.67
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTTTCTTTTCTTGTTGCTT
Found at i:734142 original size:25 final size:22
Alignment explanation
Indices: 734084--734156 Score: 83
Period size: 28 Copynumber: 3.0 Consensus size: 22
734074 ATGTATCATA
734084 ATATAGGCGTGATATGGTGATG
1 ATATAGGCGTGATATGGTGATG
734106 ATATAGGCGGCGATGGACTATGGTGATG
1 ATATA---GGCG-T-GA-TATGGTGATG
734134 ATATAGGCGTGATAATGGTGATG
1 ATATAGGCGTGAT-ATGGTGATG
734157 GACAGATTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
22 6 0.14
23 11 0.25
24 1 0.02
25 8 0.18
26 1 0.02
27 2 0.05
28 15 0.34
ACGTcount: A:0.27, C:0.07, G:0.37, T:0.29
Consensus pattern (22 bp):
ATATAGGCGTGATATGGTGATG
Found at i:736435 original size:35 final size:35
Alignment explanation
Indices: 736323--736434 Score: 170
Period size: 35 Copynumber: 3.2 Consensus size: 35
736313 TAAGATACTA
736323 CCTATAACATTACCATCTTCCATCACCATTTTCACG
1 CCTATAACATTACCATCTTCCATCACCA-TTTCACG
* **
736359 CCTATAACATCACCATCTTCCATCACCATTGGACG
1 CCTATAACATTACCATCTTCCATCACCATTTCACG
* *
736394 CCTATATCATTACCATCTTCTATCACCATTTCACG
1 CCTATAACATTACCATCTTCCATCACCATTTCACG
736429 CCTATA
1 CCTATA
736435 TAACCACCAA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 41 0.60
36 27 0.40
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.32
Consensus pattern (35 bp):
CCTATAACATTACCATCTTCCATCACCATTTCACG
Found at i:736668 original size:6 final size:6
Alignment explanation
Indices: 736600--736664 Score: 103
Period size: 6 Copynumber: 10.8 Consensus size: 6
736590 ATTTAAATTC
*
736600 TTTCCA TTTCCA TTTTCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA
* *
736648 TTTCCT TTTCCT TTTCC
1 TTTCCA TTTCCA TTTCC
736665 TTTTTATTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.12, C:0.32, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTCCA
Found at i:746431 original size:30 final size:31
Alignment explanation
Indices: 746397--746456 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
746387 CTTAGCTTTA
**
746397 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
746427 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
746457 GGAAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:747361 original size:19 final size:21
Alignment explanation
Indices: 747337--747388 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
747327 CGTCCAAGAG
*
747337 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
747356 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
747377 CATGTATTTTCA
1 CATGTATTTTCA
747389 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:751568 original size:19 final size:21
Alignment explanation
Indices: 751544--751595 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
751534 CGGCCAAGAG
*
751544 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
*
751563 CATGTATTTTTATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
751584 CATGTATTTTCA
1 CATGTATTTTCA
751596 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 6 0.21
21 12 0.43
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:756585 original size:15 final size:16
Alignment explanation
Indices: 756552--756591 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
756542 CTTTATTATC
756552 TTATTTCATCTTTCAT
1 TTATTTCATCTTTCAT
**
756568 TTATTT-ATCTTTTGT
1 TTATTTCATCTTTCAT
756583 TTATTTCAT
1 TTATTTCAT
756592 TCTAATCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.17, C:0.12, G:0.03, T:0.68
Consensus pattern (16 bp):
TTATTTCATCTTTCAT
Found at i:761329 original size:22 final size:25
Alignment explanation
Indices: 761301--761354 Score: 78
Period size: 22 Copynumber: 2.3 Consensus size: 25
761291 AAATTCCAGC
761301 AAAGAAATCG-AAGCACTC-AAAAG
1 AAAGAAATCGAAAGCACTCAAAAAG
*
761324 -AAGAAATTGAAAGCACTCAAAAAG
1 AAAGAAATCGAAAGCACTCAAAAAG
761348 AAAGAAA
1 AAAGAAA
761355 AGAAAAGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 8 0.30
23 8 0.30
24 5 0.19
25 6 0.22
ACGTcount: A:0.61, C:0.13, G:0.17, T:0.09
Consensus pattern (25 bp):
AAAGAAATCGAAAGCACTCAAAAAG
Found at i:761361 original size:25 final size:23
Alignment explanation
Indices: 761302--761359 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
761292 AATTCCAGCA
*
761302 AAGAAATCG-AAGCACTCAAAAG
1 AAGAAATAGAAAGCACTCAAAAG
*
761324 AAGAAATTGAAAGCACTCAAAAAG
1 AAGAAATAGAAAGCACTC-AAAAG
761348 AAAGAAA-AGAAA
1 -AAGAAATAGAAA
761360 AGATAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 8 0.26
23 8 0.26
24 9 0.29
25 6 0.19
ACGTcount: A:0.62, C:0.12, G:0.17, T:0.09
Consensus pattern (23 bp):
AAGAAATAGAAAGCACTCAAAAG
Found at i:764829 original size:586 final size:585
Alignment explanation
Indices: 763659--764790 Score: 1996
Period size: 586 Copynumber: 1.9 Consensus size: 585
763649 AGGGAGTTCT
*
763659 TGATGCGATCATGCCAAGGAACAAACTTCTTCAACACATGATCACTTCATGGATGTTCTGCCATG
1 TGATGCGATCATGCCAAGGAACAAACTTCTTCAACACATGATCACTTAATGGATGTTCTGCCATG
763724 TTGATTCTAAGGGAGTCTTACCTTATTTTATTATTTATTTACTCATTTATGCATTACATGTCACA
66 TTGATTCTAAGGGAGTCTTACCTTATTTTATTATTTATTTACTCATTTATGCATTACATGTCACA
*
763789 TGAATATGTTTATCTTATTCTTAATTTTTGCTTGAATATTATATGCTGTCATTTATATGTATAAT
131 TGAATATGTTTATATTATTCTTAATTTTTGCTTGAATATTATATGCTGTCATTTATATGTATAAT
*
763854 ATATGATATTCACGCATGACTTATTAATTCACATCTTTATATAACTCATTCAATGCATATGCTTT
196 ATATGATATTCACGCATGACTTATTAATTCACATCTTTATATAACTCATTCAATGCATATGCATT
763919 CATAGTTAGCTCATTTGAATTATTAACATAGGTGGAAGCATGCATTCATAATTATCATAGCTCAA
261 CATAGTTAGCTCATTTGAATTATTAACATAGGTGGAAGCATGCATTCATAATTATCATAGCTCAA
763984 TTCCTATCTAATTATTTGTTTACACACTTTGTCTAGGTTCATTGGATGCTAAGAAGACTAAAGGC
326 TTCCTATCTAATTATTTGTTTACACACTTTGTCTAGGTTCATTGGATGCTAAGAAGACTAAAGGC
* *
764049 AATTGAAGAGTTGGTTGGACAGTTCACGTCAGTCAGATTGATCTACATTTTTGAACATGTTCCAA
391 AATTGAAGAGTTGGTTGGACAGTTCACGTCAGTCAGATTGATCTACATATTTGAACATGTTACAA
* *
764114 GCATCTTTGGGTGATGAAGTCTCTTAACATTTAATCCCCTATCTCTTATCTTTCCAACGCAGTTT
456 ACATCTTTGGGTGATGAAGTCTCTTAACATTTAATCCCCTATCTCGTATCTTTCCAACGCAGTTT
* * * * *
764179 AAATCATATCAATCCGATATTGGGAGATCAAGATATGCCCAGATTAATTAAGACACTGCAGGCTG
521 AAATCACATCAATACAATATCGGGAGATCAAGATATGCCCAGATTAATGAAGACACTGCAGGCTG
* * *
764244 TGATGCGATCATGCCAAGGACCAAACTTCTTCAACACATGATCACTTAATGGACT-TTTTGCCTT
1 TGATGCGATCATGCCAAGGAACAAACTTCTTCAACACATGATCACTTAATGGA-TGTTCTGCCAT
764308 GTTGATTCTAAGGGAGTCTTACCTTATTTTATTATTTATTTACTCATTTATGCATTACATGTCAC
65 GTTGATTCTAAGGGAGTCTTACCTTATTTTATTATTTATTTACTCATTTATGCATTACATGTCAC
* * *
764373 GTGAATATGTTTATATTATTCTTAATTTTTTTCTTGAATATTATATGCTGTCATTTATATGTGTA
130 ATGAATATGTTTATATTATTCTTAA-TTTTTGCTTGAATATTATATGCTGTCATTTATATGTATA
* *
764438 ATATTTGATATTCATGCATGACTTATTAATTCACATCTTTATATAACTCATTCAATGCATATGCA
194 ATATATGATATTCACGCATGACTTATTAATTCACATCTTTATATAACTCATTCAATGCATATGCA
*
764503 TTCATAGTTAGCTCATTTGCATTATTAACATAGGTGGAAGCATGCATTCATAATTATCATAGCTC
259 TTCATAGTTAGCTCATTTGAATTATTAACATAGGTGGAAGCATGCATTCATAATTATCATAGCTC
* *
764568 AATTCCTATCTAATTATTTGTTTACATACTTTGTCTAGTTTCATTGGATGCTAAGAAGACTAAAG
324 AATTCCTATCTAATTATTTGTTTACACACTTTGTCTAGGTTCATTGGATGCTAAGAAGACTAAAG
*
764633 GCAATTGAAGAGTTGGTTGGACAGTTCACGTTAGTCAGATTGATCTACATATTTGAACATGTTAC
389 GCAATTGAAGAGTTGGTTGGACAGTTCACGTCAGTCAGATTGATCTACATATTTGAACATGTTAC
* *
764698 AAACATCTTTGGGTGATTAAGTCTCTTAACATTTAATCCCCTATCTCGTATCTTTCCAACGCATT
454 AAACATCTTTGGGTGATGAAGTCTCTTAACATTTAATCCCCTATCTCGTATCTTTCCAACGCAGT
*
764763 TTGAATCACATCAATACAATATCGGGAG
519 TTAAATCACATCAATACAATATCGGGAG
764791 CTTGAGATAT
Statistics
Matches: 519, Mismatches: 26, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
585 146 0.28
586 373 0.72
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (585 bp):
TGATGCGATCATGCCAAGGAACAAACTTCTTCAACACATGATCACTTAATGGATGTTCTGCCATG
TTGATTCTAAGGGAGTCTTACCTTATTTTATTATTTATTTACTCATTTATGCATTACATGTCACA
TGAATATGTTTATATTATTCTTAATTTTTGCTTGAATATTATATGCTGTCATTTATATGTATAAT
ATATGATATTCACGCATGACTTATTAATTCACATCTTTATATAACTCATTCAATGCATATGCATT
CATAGTTAGCTCATTTGAATTATTAACATAGGTGGAAGCATGCATTCATAATTATCATAGCTCAA
TTCCTATCTAATTATTTGTTTACACACTTTGTCTAGGTTCATTGGATGCTAAGAAGACTAAAGGC
AATTGAAGAGTTGGTTGGACAGTTCACGTCAGTCAGATTGATCTACATATTTGAACATGTTACAA
ACATCTTTGGGTGATGAAGTCTCTTAACATTTAATCCCCTATCTCGTATCTTTCCAACGCAGTTT
AAATCACATCAATACAATATCGGGAGATCAAGATATGCCCAGATTAATGAAGACACTGCAGGCTG
Found at i:770543 original size:90 final size:91
Alignment explanation
Indices: 770424--770596 Score: 267
Period size: 90 Copynumber: 1.9 Consensus size: 91
770414 CCCATGTGCC
* * *
770424 TTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGAACAGACCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTCT
770489 CTCCCTATTCGGCCAAGCCATATGTT
66 CTCCCTATTCGGCCAAGCCATATGTT
* * * *
770515 TTGCATATGAACA-ACCCCATGTGTCTTGCATGTGGTTTATTTAGGCGCCAAGATGAAGAGCTCT
1 TTGCATATGAACAGACCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTCT
*
770579 CTCTCTATTCGGCCAAGC
66 CTCCCTATTCGGCCAAGC
770597 ATCATTTCCC
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 62 0.84
91 12 0.16
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (91 bp):
TTGCATATGAACAGACCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTCT
CTCCCTATTCGGCCAAGCCATATGTT
Found at i:771418 original size:23 final size:21
Alignment explanation
Indices: 771360--771419 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 21
771350 AAAAATCAGC
*
771360 AAAGAAAACA-AAAGCACTAA
1 AAAGAAAAAAGAAAGCACTAA
*
771380 AAAGAAGAAATTGAAAGCACTTGAA
1 AAAGAA-AAA-AGAAAGCAC-T-AA
771405 AAAGAAAAAAGAAAG
1 AAAGAAAAAAGAAAG
771420 AAAGAAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 6 0.19
21 2 0.06
23 12 0.38
24 4 0.12
25 8 0.25
ACGTcount: A:0.67, C:0.08, G:0.17, T:0.08
Consensus pattern (21 bp):
AAAGAAAAAAGAAAGCACTAA
Found at i:774929 original size:90 final size:91
Alignment explanation
Indices: 774775--774956 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 91
774765 CCTAGAACAC
* *
774775 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTACATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTACATGAGGATCATTTAGGCACCAAGATG
*
774840 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
** * * * * *
774866 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTACATGAGGATCATTTAGGCACCAAGATG
774930 AAGAGCTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
774956 C
1 C
774957 ATCATTTCCC
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 62 0.77
91 19 0.23
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTACATGAGGATCATTTAGGCACCAAGATG
AAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:783946 original size:19 final size:20
Alignment explanation
Indices: 783922--783972 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
783912 CGGCCAAGAG
* *
783922 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
783941 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
783961 CATGTATTTTCA
1 CATGTATTTTCA
783973 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:785914 original size:16 final size:16
Alignment explanation
Indices: 785883--785929 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
785873 TGGTAATGAA
785883 ATAAGAAAAGATGAAA-G
1 ATAA-AAAA-ATGAAATG
*
785900 AATAAAGAAATGAAATG
1 -ATAAAAAAATGAAATG
785917 ATAAAAAAATGAA
1 ATAAAAAAATGAA
785930 GATAACTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 18 0.69
17 4 0.15
18 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (16 bp):
ATAAAAAAATGAAATG
Found at i:794352 original size:13 final size:12
Alignment explanation
Indices: 794333--794418 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
794323 ATATAGGCGT
794333 GATATGGTGATG
1 GATATGGTGATG
794345 GAATATGGTGAT-
1 G-ATATGGTGATG
*
794357 GATATAGGCG-T-
1 GATAT-GGTGATG
794368 GATAATGGTGATG
1 GAT-ATGGTGATG
794381 GACTATGGTGAT-
1 GA-TATGGTGATG
*
794393 GATATAGGCG-T-
1 GATAT-GGTGATG
794404 GATAATGGTGATG
1 GAT-ATGGTGATG
794417 GA
1 GA
794419 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:794388 original size:36 final size:36
Alignment explanation
Indices: 794315--794419 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
794305 ATTTAGAAGT
* *
794315 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
794350 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
794386 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
794420 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:796151 original size:19 final size:20
Alignment explanation
Indices: 796127--796177 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
796117 CGGCCAAGAG
* *
796127 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
796146 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
796166 CATGTATTTTCA
1 CATGTATTTTCA
796178 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:800294 original size:19 final size:20
Alignment explanation
Indices: 800270--800320 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
800260 CGGCCAAGAG
* *
800270 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
800289 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
800309 CATGTATTTTCA
1 CATGTATTTTCA
800321 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:837563 original size:36 final size:36
Alignment explanation
Indices: 837511--837623 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
837501 GATACTATTT
*
837511 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
837547 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
837583 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
837618 ACATCA
1 TCATCA
837624 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Done.