Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007816.1 Hibiscus syriacus cultivar Beakdansim tig00110151_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: 3994936
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 14
Found at i:2072341 original size:21 final size:21
Alignment explanation
Indices: 2072290--2072343 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
2072280 ACCGGAACCC
* ** *
2072290 AAGGTATCGATCCTTTTTTTA
1 AAGGGATCGATCCTTTGGTCA
* *
2072311 AGGGGTTCGATCCTTTGGTCA
1 AAGGGATCGATCCTTTGGTCA
2072332 AAGGGATCGATC
1 AAGGGATCGATC
2072344 TTTTTAGCCA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (21 bp):
AAGGGATCGATCCTTTGGTCA
Found at i:2072486 original size:11 final size:11
Alignment explanation
Indices: 2072472--2072497 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2072462 ACTTTGAATT
2072472 ATTTTTGATAA
1 ATTTTTGATAA
2072483 ATTTTTGATAA
1 ATTTTTGATAA
2072494 ATTT
1 ATTT
2072498 GATTAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (11 bp):
ATTTTTGATAA
Found at i:2076493 original size:15 final size:15
Alignment explanation
Indices: 2076473--2076501 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2076463 AGTATATAGT
2076473 TTTTGAAAACATATG
1 TTTTGAAAACATATG
2076488 TTTTGAAAACATAT
1 TTTTGAAAACATAT
2076502 ATAATATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (15 bp):
TTTTGAAAACATATG
Found at i:2076571 original size:38 final size:38
Alignment explanation
Indices: 2076444--2076689 Score: 197
Period size: 37 Copynumber: 6.6 Consensus size: 38
2076434 TATAATAAAT
** * * *
2076444 ATAGTTTTTGAAAATATATAGTATATAGTTTTTGAAAAC
1 ATAG-TTTTGAAAACGTATAATATATAGTTTTTTAAAAA
* *
2076483 ATATGTTTTGAAAACATAT-ATAATATAG--TTTT--GAA
1 ATA-GTTTTGAAAACGTATAAT-ATATAGTTTTTTAAAAA
*
2076518 ATAGTTTTGAGAACGTATAATATATAGTTTTTTAAAAA
1 ATAGTTTTGAAAACGTATAATATATAGTTTTTTAAAAA
*
2076556 ATAGTTTCGAAAACGTATAATATATAG-TTTTTAAAAA
1 ATAGTTTTGAAAACGTATAATATATAGTTTTTTAAAAA
** * **
2076593 ACGGTTTTGAAAACATATGGTATAT-GATTTTTT-AAAA
1 ATAGTTTTGAAAACGTATAATATATAG-TTTTTTAAAAA
* * *
2076630 ATGGGTTTGAAAACGTATAATATATA-TTTTTCAAAAA
1 ATAGTTTTGAAAACGTATAATATATAGTTTTTTAAAAA
** * *
2076667 CGATTTTTG-AAACATATAATATA
1 ATAGTTTTGAAAACGTATAATATA
2076690 ATTTTTGAAA
Statistics
Matches: 168, Mismatches: 28, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
34 19 0.11
35 6 0.04
36 23 0.14
37 64 0.38
38 33 0.20
39 22 0.13
40 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.41
Consensus pattern (38 bp):
ATAGTTTTGAAAACGTATAATATATAGTTTTTTAAAAA
Found at i:2076725 original size:14 final size:15
Alignment explanation
Indices: 2076706--2076754 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
2076696 GAAAATAGAG
*
2076706 TATTATATA-GTTTT
1 TATTATATATGTTTA
2076720 TATTAT-TATGTTTA
1 TATTATATATGTTTA
*
2076734 TATTATATTATATTTA
1 TATTATA-TATGTTTA
2076750 T-TTAT
1 TATTAT
2076755 TTCATTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 2 0.07
14 16 0.53
15 4 0.13
16 8 0.27
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (15 bp):
TATTATATATGTTTA
Found at i:2093037 original size:87 final size:90
Alignment explanation
Indices: 2092914--2093100 Score: 227
Period size: 91 Copynumber: 2.1 Consensus size: 90
2092904 CTTCTTTATC
* * **
2092914 AATTATCTACTGGAAATGTTGGTCCCTCAACTGAGGCGTCGCTAATTTGAAATGTC-G-TCGAGC
1 AATTCTCTACTGGAAATGATGGTCCCTCAACTGAGGCGTCGCTAATTCAAAATGTCGGATCGAGC
* *
2092977 CAAGGTTCAATATGTTATTCTCATG
66 CAACGTTCAATAAGTTATTCTCATG
* * * *
2093002 AATTCTCTACTGGGAATGATGGT-CCTCAAGTGAGGCGTCGCTGATTCAAAATGTCGTGAATTGA
1 AATTCTCTACTGGAAATGATGGTCCCTCAACTGAGGCGTCGCTAATTCAAAATGTCG-G-ATCGA
* *
2093066 GCCAACGTTGAATAAGTTCTTCTCATG
64 GCCAACGTTCAATAAGTTATTCTCATG
2093093 AATTCTCT
1 AATTCTCT
2093101 GTTGGGAACG
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
87 28 0.34
88 20 0.24
89 1 0.01
91 34 0.41
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (90 bp):
AATTCTCTACTGGAAATGATGGTCCCTCAACTGAGGCGTCGCTAATTCAAAATGTCGGATCGAGC
CAACGTTCAATAAGTTATTCTCATG
Found at i:2094916 original size:39 final size:39
Alignment explanation
Indices: 2094759--2095910 Score: 1445
Period size: 39 Copynumber: 29.6 Consensus size: 39
2094749 GTTTTAAGAA
* * * ** *
2094759 AAACAATCTCAAGTGAGAT-AAATCATCAATTTCTAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
2094797 AAACTATCCCAAGCGAGATAAAAATCTTCTGTTTCAAGTG
1 AAACTATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTG
* *
2094837 AAACTATCTCAAGCGAGATAAAAATCTTATGTTTCAAGTG
1 AAACTATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTG
*
2094877 AAACTATCTCAAGCGAGATAAAATCTTGTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
2094916 AAA-TAATCTCAAGCGTGATAAAATCTTTTGTTTCGAGTG
1 AAACT-ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
*
2094955 AAACTATCTCAAGCGAGAGAAAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
2094994 AAACTATCTCAAGCGAGATAAAATCTTTTTTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
2095033 AAACTATCTCAAGCAAGATAAAATCTTCCGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
*
2095072 AAACTATCTCAAGCAAGATAAAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * *
2095111 AAACTATCTCAAGCAAGATAAAATCTTATGTTTCAAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * * *
2095150 AAATTATCTCAAGCGAGATAAAATCATCTGTTTCAAGTA
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
2095189 AAACTATCTAAAGCGAGATAAAATCTTCTGTTTTGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * *
2095228 AAACTATCTCTAGCAAGATAAAATCTTTTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * *
2095267 AAACTATCTCAAGCGAGATAAAATCTTCTATATCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * * * *
2095306 AAACTATCTCAAGCCATATAAAATCTTATATTTCAAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
2095345 AAATTATCTCAAGCGAGA-AAACATCTTATGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAA-ATCTTCTGTTTCGAGTG
* * *
2095384 AAACTATCTCAAGTGAGATAAAATCTTCTGATTCAAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
** ** * *
2095423 AAACTATCTCAATTGAGATAAAATCTTCTGTTTTAATTA
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * * *
2095462 AAACTATCTCAAGCGAGATAAAATCATCTATTTTGAGTT
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * *
2095501 AAACTATCTCAAACGAGGTTAAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* ** *
2095540 AAACTATATCAAGATAGGTAAAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * * *
2095579 AAACTATCTCAGGCAAGATAAAATCTTTTGTTTCAAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
*
2095618 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTA
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
2095657 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTTGAGTT
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * *
2095696 AAACTGTCTCAAGCGAGATAAAATCTTTTGTATCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
2095735 AAACTATCTCAAGCGAGATAAAATCTTATGTTACGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
2095774 AAACTATCTCAAGCGAGTTAAAATCTTCTGTTTTGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* ** **
2095813 AAACTATCTCAAGCGAGAT-AAATC-T-GGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * *
2095849 AAACAATCTCAAGTGAGAT-AAATCTTATGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * *
2095887 AAATTTTCTCAAGCGATATAAAAT
1 AAACTATCTCAAGCGAGATAAAAT
2095911 ATTGTTTTAA
Statistics
Matches: 973, Mismatches: 132, Indels: 17
0.87 0.12 0.02
Matches are distributed among these distances:
36 29 0.03
37 2 0.00
38 45 0.05
39 821 0.84
40 76 0.08
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
Found at i:2095996 original size:76 final size:75
Alignment explanation
Indices: 2095568--2096091 Score: 317
Period size: 78 Copynumber: 6.9 Consensus size: 75
2095558 TAAAATCTTC
* * * * ** * * *
2095568 TGTTTCGAGT-GAAACTATCTCAGGCAAGATAAAATCTTTTGTTTCAAGTGAAACTATCTCAAGC
1 TGTTTCGAGTAAAAACTATCTCAAGCGAGAT-AAATC--TTGTTTTAAGAAAAACAATCTGAAGT
* * *
2095632 GAGATAAAATCTT
63 GAAATGAAATGTT
* ** ** *
2095645 CTGTTTCGAGT-AAAACTATCTCAAGCGAGATAAAATCTTCTGTTTTGAGTTAAACTGTCTCAAG
1 -TGTTTCGAGTAAAAACTATCTCAAGCGAGAT-AAATC-T-TGTTTTAAGAAAAACAATCTGAAG
* * * *
2095709 CGAGATAAAATCTTT
62 TGAAATGAAAT-GTT
* * * * ** * * *
2095724 TGTATCGAGT-GAAACTATCTCAAGCGAGATAAAATCTTATGTTACGAGTGAAACTATCTCAAGC
1 TGTTTCGAGTAAAAACTATCTCAAGCGAGAT-AAATCTTGTTTTA--AGAAAAACAATCTGAAGT
** * *
2095788 GAGTTAAAATCTT
63 GAAATGAAATGTT
* * * *
2095801 CTGTTTTGAGT-GAAACTATCTCAAGCGAGATAAATCTGGTTTTAAGAAAAACAATCTCAAGTGA
1 -TGTTTCGAGTAAAAACTATCTCAAGCGAGATAAATCTTGTTTTAAGAAAAACAATCTGAAGTGA
* *
2095865 GAT-AAATCTT
65 AATGAAATGTT
* * * * * * * *
2095875 ATGTTTCGAGT-GAAATTTTCTCAAGCGATATAAAATATTGTTTTAAGAAAAACCATATGTAGTG
1 -TGTTTCGAGTAAAAACTATCTCAAGCGAGAT-AAATCTTGTTTTAAGAAAAACAATCTGAAGTG
2095939 AAATGAAATGTCT
64 AAATGAAATGT-T
* * * *
2095952 TGTTTCGAGTAAAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGGAAAATAATCTGCAGTGAA
1 TGTTTCGAGTAAAAACTATCTCAAGCGAGATAAATCTTGTTTTAAGAAAAACAATCTGAAGTGAA
2096017 ATGAAATGTTT
66 ATGAAATG-TT
* * * *
2096028 TGTTTCGAGTAAAAA-TCGTCTCAAGCGAGACAAAGT-TTGTTTTAAGGAAAACAATCTCAAGTG
1 TGTTTCGAGTAAAAACT-ATCTCAAGCGAGATAAA-TCTTGTTTTAAGAAAAACAATCTGAAGTG
2096091 A
64 A
2096092 GATAAAATTT
Statistics
Matches: 377, Mismatches: 57, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
74 33 0.09
75 48 0.13
76 109 0.29
77 34 0.09
78 151 0.40
79 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (75 bp):
TGTTTCGAGTAAAAACTATCTCAAGCGAGATAAATCTTGTTTTAAGAAAAACAATCTGAAGTGAA
ATGAAATGTT
Found at i:2096887 original size:28 final size:28
Alignment explanation
Indices: 2096847--2096905 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
2096837 TACAAGGCTT
*
2096847 AGGTTAACTTGGGAAGGTAATGTGTTTC
1 AGGTTAACTTGGGAAGGTAATGTATTTC
* *
2096875 AGGTTAATTTGGGGAGGTAATGTATTTC
1 AGGTTAACTTGGGAAGGTAATGTATTTC
2096903 AGG
1 AGG
2096906 ATGGCTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.05, G:0.34, T:0.36
Consensus pattern (28 bp):
AGGTTAACTTGGGAAGGTAATGTATTTC
Found at i:2097550 original size:7 final size:7
Alignment explanation
Indices: 2097540--2097618 Score: 108
Period size: 7 Copynumber: 11.0 Consensus size: 7
2097530 TTCTTTCTTC
2097540 TTCTTTT
1 TTCTTTT
2097547 TTC-TTT
1 TTCTTTT
2097553 TTCTTTTT
1 TTC-TTTT
2097561 TTCTTTTT
1 TTC-TTTT
2097569 TTCTTTTT
1 TTC-TTTT
2097577 TTCTTTT
1 TTCTTTT
2097584 TTCTTTT
1 TTCTTTT
2097591 TTCTTTT
1 TTCTTTT
2097598 TTCTTTT
1 TTCTTTT
2097605 TT-TCTTT
1 TTCT-TTT
2097612 TTCTTTT
1 TTCTTTT
2097619 CTCCTATCTT
Statistics
Matches: 68, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
6 7 0.10
7 38 0.56
8 23 0.34
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTCTTTT
Found at i:2097554 original size:1 final size:1
Alignment explanation
Indices: 2097543--2097618 Score: 62
Period size: 1 Copynumber: 76.0 Consensus size: 1
2097533 TTTCTTCTTC
* * * * * * * *
2097543 TTTTTTCTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
2097608 CTTTTTCTTTT
1 TTTTTTTTTTT
2097619 CTCCTATCTT
Statistics
Matches: 55, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:2097561 original size:8 final size:8
Alignment explanation
Indices: 2097528--2097613 Score: 112
Period size: 8 Copynumber: 11.2 Consensus size: 8
2097518 ATTTGATATG
2097528 TTTTCTTT
1 TTTTCTTT
2097536 CTTCTTC-TT
1 -TT-TTCTTT
2097545 TTTTC--T
1 TTTTCTTT
2097551 TTTTCTTT
1 TTTTCTTT
2097559 TTTTCTTT
1 TTTTCTTT
2097567 TTTTCTTT
1 TTTTCTTT
2097575 TTTTC-TT
1 TTTTCTTT
2097582 TTTTC-TT
1 TTTTCTTT
2097589 TTTTC-TT
1 TTTTCTTT
2097596 TTTTCTTT
1 TTTTCTTT
2097604 TTTTCTTT
1 TTTTCTTT
2097612 TT
1 TT
2097614 CTTTTCTCCT
Statistics
Matches: 73, Mismatches: 0, Indels: 9
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.08
7 24 0.33
8 36 0.49
9 4 0.05
10 3 0.04
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTCTTT
Found at i:2097562 original size:14 final size:14
Alignment explanation
Indices: 2097528--2097618 Score: 114
Period size: 14 Copynumber: 6.3 Consensus size: 14
2097518 ATTTGATATG
*
2097528 TTTTCTTTCTTCTTC
1 TTTT-TTTCTTTTTC
2097543 -TTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
2097556 TTTTTTTCTTTTTTTC
1 TTTTTTTC--TTTTTC
2097572 TTTTTTTCTTTTT-
1 TTTTTTTCTTTTTC
2097585 TCTTTTTTCTTTTTTC
1 T-TTTTTTC-TTTTTC
2097601 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
2097615 TTTT
1 TTTT
2097619 CTCCTATCTT
Statistics
Matches: 69, Mismatches: 1, Indels: 13
0.83 0.01 0.16
Matches are distributed among these distances:
13 10 0.14
14 32 0.46
15 12 0.17
16 15 0.22
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:2097584 original size:37 final size:38
Alignment explanation
Indices: 2097528--2097616 Score: 146
Period size: 37 Copynumber: 2.3 Consensus size: 38
2097518 ATTTGATATG
2097528 TTTTCTTTCTTCTTCTTTTTTC-TTTTTCTTTTTTTCTTT
1 TTTTCTTT-TTCTTCTTTTTTCTTTTTTC-TTTTTTCTTT
2097567 TTTTCTTTTT-TTCTTTTTTCTTTTTTCTTTTTTCTTT
1 TTTTCTTTTTCTTCTTTTTTCTTTTTTCTTTTTTCTTT
2097604 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
2097617 TTCTCCTATC
Statistics
Matches: 48, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
37 30 0.62
38 10 0.21
39 8 0.17
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (38 bp):
TTTTCTTTTTCTTCTTTTTTCTTTTTTCTTTTTTCTTT
Found at i:2097631 original size:37 final size:34
Alignment explanation
Indices: 2097528--2097646 Score: 130
Period size: 37 Copynumber: 3.2 Consensus size: 34
2097518 ATTTGATATG
*
2097528 TTTTCTTTCTTCTTCTTTTTTCTTTTTCTTTTTTTC
1 TTTT-TTTCTTTTTCTTTTTTCTTTTTC-TTTTTTC
2097564 TTTTTTTCTTTTTTTCTTTTTTCTTTTTTCTTTTTTC
1 TTTTTTTC--TTTTTCTTTTTTC-TTTTTCTTTTTTC
*
2097601 TTTTTTTCTTTTTCTTTTCTCCTATCTTTCTTTTCTATC
1 TTTTTTTCTTTTTCTTTT-TTCT-T-TTTCTTTT-T-TC
2097640 TTTTTTT
1 TTTTTTT
2097647 TATGTTTTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
35 15 0.21
36 7 0.10
37 35 0.48
38 7 0.10
39 9 0.12
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (34 bp):
TTTTTTTCTTTTTCTTTTTTCTTTTTCTTTTTTC
Found at i:2097656 original size:51 final size:48
Alignment explanation
Indices: 2097533--2097657 Score: 124
Period size: 51 Copynumber: 2.5 Consensus size: 48
2097523 ATATGTTTTC
* * * * * *
2097533 TTTCTTCTTCTTTTTTCTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTT
1 TTTCTTCTTTTTTTTTCTTTTTTTTTTTTTCTTTTCTCCTATCTTTC--T
* *
2097583 TTTCTTTTTTCTTTTTTCTTTTTTTCTTTTTCTTTTCTCCTATCTTTCT
1 TTTCTTCTTT-TTTTTTCTTTTTTTTTTTTTCTTTTCTCCTATCTTTCT
*
2097632 TTTCTATCTTTTTTTTATGTTTTTTT
1 TTTCT-TCTTTTTTTT-TCTTTTTTT
2097658 GTGTTATGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
49 11 0.18
50 20 0.32
51 31 0.50
ACGTcount: A:0.02, C:0.16, G:0.01, T:0.81
Consensus pattern (48 bp):
TTTCTTCTTTTTTTTTCTTTTTTTTTTTTTCTTTTCTCCTATCTTTCT
Found at i:2097925 original size:2 final size:2
Alignment explanation
Indices: 2097918--2097965 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2097908 ACAAGGGATA
2097918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2097960 AT AT AT
1 AT AT AT
2097966 TTGAAAGGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2100947 original size:117 final size:117
Alignment explanation
Indices: 2100735--2101026 Score: 374
Period size: 117 Copynumber: 2.5 Consensus size: 117
2100725 AATGGGGTTT
* * *
2100735 TGAGAGTATAGATTTCCATATGGGGCACTAAGTGTGCTAAATGATAAAGAAATCATATTGAAAAT
1 TGAGTGTATAGATTTCCATATGGAGCACTAAGTGTGCTAAAAGATAAAGAAATCATATTGAAAAT
* * *
2100800 ATGGATTTCTAGATAAGGCATTTTATGTGCTAAAAATGGTAA-GGAAACATAC
66 ATGAATTTCCAGATAAGGCATTTTACGTGCT-AAAATGGTAAGGGAAACATAC
* * *
2100852 TGAGTGTATAGATTTCCATATGGAGCACTCAGTGTGCTAAAGGATAATGAAATCATATTGAAAAT
1 TGAGTGTATAGATTTCCATATGGAGCACTAAGTGTGCTAAAAGATAAAGAAATCATATTGAAAAT
** *
2100917 ATGAATTTCCAGA-AAGGGCATTTTACGTGCTAAAATGGTAAGGGATTCATAT
66 ATGAATTTCCAGATAA-GGCATTTTACGTGCTAAAATGGTAAGGGAAACATAC
* * ** *
2100969 TGAGTGTATGGATTTCCAGATAAAGCACTAAAG-GTGCTACAAAGATAAGGAAATCATA
1 TGAGTGTATAGATTTCCATATGGAGCACT-AAGTGTGCTA-AAAGATAAAGAAATCATA
2101027 CTAATGGTAT
Statistics
Matches: 153, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
116 12 0.08
117 123 0.80
118 18 0.12
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (117 bp):
TGAGTGTATAGATTTCCATATGGAGCACTAAGTGTGCTAAAAGATAAAGAAATCATATTGAAAAT
ATGAATTTCCAGATAAGGCATTTTACGTGCTAAAATGGTAAGGGAAACATAC
Found at i:2101026 original size:59 final size:57
Alignment explanation
Indices: 2100759--2101026 Score: 162
Period size: 59 Copynumber: 4.6 Consensus size: 57
2100749 TCCATATGGG
* * * *
2100759 GCACTAAGTGTGCTAAATGATAAAGAAATCATATTGAAAATATGGATTTCTAGATAAG
1 GCACTAAG-GTGCTAAAAGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAAA
* * * * * *** * * **
2100817 GCATTTTATGTGCTAAAAATGGTAAGGAAA-CATACTGAGTGTATAGATTTCCATATGGA
1 GCA-CTAAGGTGCT-AAAA-GATAAGGAAATCATATTGAAAATATGGATTTCCAGATAAA
* * * * *
2100876 GCACTCAGTGTGCTAAAGGATAATGAAATCATATTGAAAATATGAATTTCCAGA-AAGG
1 GCACTAAG-GTGCTAAAAGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAA-A
* * * * * * ***
2100934 GCATTTTACGTGCTAAAATGGTAAGGGATTCATATTGAGTGTATGGATTTCCAGATAAA
1 GCA-CTAAGGTGCTAAAA-GATAAGGAAATCATATTGAAAATATGGATTTCCAGATAAA
2100993 GCACTAAAGGTGCTACAAAGATAAGGAAATCATA
1 GCACT-AAGGTGCTA-AAAGATAAGGAAATCATA
2101027 CTAATGGTAT
Statistics
Matches: 148, Mismatches: 51, Indels: 21
0.67 0.23 0.10
Matches are distributed among these distances:
57 8 0.05
58 43 0.29
59 84 0.57
60 13 0.09
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (57 bp):
GCACTAAGGTGCTAAAAGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAAA
Found at i:2101235 original size:30 final size:30
Alignment explanation
Indices: 2101179--2101237 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2101169 GATTTATTTA
* *
2101179 ATGACCAAATTATAAATTTGGTAAAGTTTG
1 ATGACCAAAGTATAAAATTGGTAAAGTTTG
*
2101209 ATGATCAAAGTATAAACATTGG-AAAGTTT
1 ATGACCAAAGTATAAA-ATTGGTAAAGTTT
2101238 AGGGACCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (30 bp):
ATGACCAAAGTATAAAATTGGTAAAGTTTG
Found at i:2103263 original size:60 final size:58
Alignment explanation
Indices: 2103156--2103284 Score: 186
Period size: 60 Copynumber: 2.2 Consensus size: 58
2103146 CAACAGGCTG
* *
2103156 CATATTCGGGAATACACTAAAGGATACCTAGAAATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGAAAGATGGTGGACACGACCTTATGTGT
** * *
2103214 CATATTCGGGAACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAA-TACACTAAAGGATACCTAG-AAAGATGGTGGACACGACCTTATGTGT
2103274 CATATTCGGGA
1 CATATTCGGGA
2103285 TTGCACTACG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 12 0.19
59 16 0.25
60 35 0.56
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (58 bp):
CATATTCGGGAATACACTAAAGGATACCTAGAAAGATGGTGGACACGACCTTATGTGT
Found at i:2103371 original size:20 final size:20
Alignment explanation
Indices: 2103346--2103388 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2103336 TATATTGGGC
* *
2103346 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
*
2103366 TATTGTGTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
2103386 TAT
1 TAT
2103389 GGAATAATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.02, G:0.23, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:2110895 original size:19 final size:20
Alignment explanation
Indices: 2110862--2110900 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2110852 ATATGGGCTA
* *
2110862 TGTCTATTGTTTAT-GTTAT
1 TGTCTATGGTATATGGTTAT
2110881 TGTCTATGGTATATGGTTAT
1 TGTCTATGGTATATGGTTAT
2110901 GGAATAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.18, C:0.05, G:0.21, T:0.56
Consensus pattern (20 bp):
TGTCTATGGTATATGGTTAT
Found at i:2112226 original size:57 final size:58
Alignment explanation
Indices: 2112122--2112238 Score: 227
Period size: 57 Copynumber: 2.0 Consensus size: 58
2112112 GTATATTACT
2112122 ATTCATGAAAAAGTATTTTTTTTATTTTTGTTATAACAAACATAATTCATCAATATAG
1 ATTCATGAAAAAGTATTTTTTTTATTTTTGTTATAACAAACATAATTCATCAATATAG
2112180 ATTCATGAAAAAGTATTTTTTTTATTTTT-TTATAACAAACATAATTCATCAATATAG
1 ATTCATGAAAAAGTATTTTTTTTATTTTTGTTATAACAAACATAATTCATCAATATAG
2112237 AT
1 AT
2112239 ACTCGTATTT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 30 0.51
58 29 0.49
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (58 bp):
ATTCATGAAAAAGTATTTTTTTTATTTTTGTTATAACAAACATAATTCATCAATATAG
Found at i:2117655 original size:60 final size:59
Alignment explanation
Indices: 2117573--2117798 Score: 226
Period size: 58 Copynumber: 3.8 Consensus size: 59
2117563 GAGCACTAAG
* *
2117573 TGTGCT-AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAAATAAGGCATTTTA
1 TGTGCTAAAATGATAAGGAAATCATACTGAAAATATGGATTTCCAGATAAGGCATTTTA
* *** * * * *
2117631 TGTGCTAAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCATAT-AGAGCA-CTGA
1 TGTGCT-AAAATGATAAGGAAATCATACTGAAAATATGGATTTCCAGATAAG-GCATTTTA
* * *
2117690 GTGTGCT-AAATGATAATGAAATCATACTGAAAAAATGGATTTCCAGATAGGGCATTTTA
1 -TGTGCTAAAATGATAAGGAAATCATACTGAAAATATGGATTTCCAGATAAGGCATTTTA
* * * ***
2117749 TGTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGATAA
1 TGTGCTAAAATGATAAGGAAATCATACTGAAAATATGGATTTCCAGATAA
2117799 AAGCACTAAG
Statistics
Matches: 132, Mismatches: 29, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
58 48 0.36
59 41 0.31
60 43 0.33
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (59 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAAAATATGGATTTCCAGATAAGGCATTTTA
Found at i:2117718 original size:58 final size:58
Alignment explanation
Indices: 2117543--2117834 Score: 212
Period size: 60 Copynumber: 4.9 Consensus size: 58
2117533 TGGGCTTTTA
* * *
2117543 AGTGTATAGATTTCCGTATGGAGCACTAAGTGTGCTAAATGATAAGGAAATCATATTG
1 AGTGTATAGATTTCCATATAGAGCACTAAGTGTGCTAAATGATAAGGAAATCATACTG
*** * * * * *
2117601 AAAATATGGATTTCCAAATA-AGGCATTTTA-TGTGCTAAAAATGGTAAGGAAATCATACTG
1 AGTGTATAGATTTCCATATAGA-GCA-CTAAGTGTGCT--AAATGATAAGGAAATCATACTG
* *
2117661 AGTGTATAGATTTCCATATAGAGCACTGAGTGTGCTAAATGATAATGAAATCATACTG
1 AGTGTATAGATTTCCATATAGAGCACTAAGTGTGCTAAATGATAAGGAAATCATACTG
**** * * * * * * * *
2117719 AAAAAATGGATTTCCAGATAGGGCATTTTA-TGTGCTAAAATGGTAAGGGAATCATATTG
1 AGTGTATAGATTTCCATATAGAGCA-CTAAGTGTGCT-AAATGATAAGGAAATCATACTG
* * * * * *
2117778 AGTGTATGGATTTCCAGATAAAAGCACTAAGGGTGGTACAAAGATAAGGAAATCATA
1 AGTGTATAGATTTCCATAT-AGAGCACTAAGTGTGCTA-AATGATAAGGAAATCATA
2117835 TTAATGGTAT
Statistics
Matches: 177, Mismatches: 46, Indels: 20
0.73 0.19 0.08
Matches are distributed among these distances:
57 1 0.01
58 66 0.37
59 42 0.24
60 67 0.38
61 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.29
Consensus pattern (58 bp):
AGTGTATAGATTTCCATATAGAGCACTAAGTGTGCTAAATGATAAGGAAATCATACTG
Found at i:2117751 original size:118 final size:117
Alignment explanation
Indices: 2117543--2117834 Score: 413
Period size: 118 Copynumber: 2.5 Consensus size: 117
2117533 TGGGCTTTTA
* * * *
2117543 AGTGTATAGATTTCCGTATGGAGCACTAAGTGTGCTAAATGATAAGGAAATCATATTGAAAATAT
1 AGTGTATAGATTTCCATATAGAGCACTAAGTGTGCTAAATGATAAGGAAATCATACTGAAAAAAT
2117608 GGATTTCCAAATAAGGCATTTTATGTGCTAAAAATGGTAAGGAAATCATACTG
66 GGATTTCCAAATAAGGCATTTTATGTGCT-AAAATGGTAAGGAAATCATACTG
* *
2117661 AGTGTATAGATTTCCATATAGAGCACTGAGTGTGCTAAATGATAATGAAATCATACTGAAAAAAT
1 AGTGTATAGATTTCCATATAGAGCACTAAGTGTGCTAAATGATAAGGAAATCATACTGAAAAAAT
* * * *
2117726 GGATTTCCAGATAGGGCATTTTATGTGCTAAAATGGTAAGGGAATCATATTG
66 GGATTTCCAAATAAGGCATTTTATGTGCTAAAATGGTAAGGAAATCATACTG
* * * * * *
2117778 AGTGTATGGATTTCCAGATAAAAGCACTAAGGGTGGTACAAAGATAAGGAAATCATA
1 AGTGTATAGATTTCCATAT-AGAGCACTAAGTGTGCTA-AATGATAAGGAAATCATA
2117835 TTAATGGTAT
Statistics
Matches: 154, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
117 38 0.25
118 100 0.65
119 16 0.10
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.29
Consensus pattern (117 bp):
AGTGTATAGATTTCCATATAGAGCACTAAGTGTGCTAAATGATAAGGAAATCATACTGAAAAAAT
GGATTTCCAAATAAGGCATTTTATGTGCTAAAATGGTAAGGAAATCATACTG
Found at i:2120096 original size:51 final size:51
Alignment explanation
Indices: 2119997--2120097 Score: 116
Period size: 51 Copynumber: 2.0 Consensus size: 51
2119987 AGCAGTTACT
* *
2119997 AAAATGCAAGAAAATAAAAGTTAGTAGTTAAATAAGAAATAAATAGTGACC
1 AAAATGCAAGAAAATAAAAGTTAGTAGCTAAATAAGAAATAAACAGTGACC
* * **
2120048 AAAATGC-A-AAAATTAAAGTAATAGTAGCTAAATCAGAAATTTACAGTGAC
1 AAAATGCAAGAAAATAAAAGT--TAGTAGCTAAATAAGAAATAAACAGTGAC
2120098 TAAATTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
49 10 0.24
50 1 0.02
51 31 0.74
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (51 bp):
AAAATGCAAGAAAATAAAAGTTAGTAGCTAAATAAGAAATAAACAGTGACC
Found at i:2121352 original size:37 final size:37
Alignment explanation
Indices: 2121273--2121438 Score: 164
Period size: 37 Copynumber: 4.5 Consensus size: 37
2121263 TTTTAAATAG
* *
2121273 TTTTGAAAATGTATAATATATAGTTTTTCAAAAAA-TA
1 TTTTGAAAACGTATAATATATAGTTTTT-AAAAAACGA
2121310 GTTTTGAAAACGTATAATATATAGTTTTTAAAAAACGA
1 -TTTTGAAAACGTATAATATATAGTTTTTAAAAAACGA
* * *
2121348 TTTTGAAAAC--AT-ATATAT-GATTTTTTAAAAATGG
1 TTTTGAAAACGTATAATATATAG-TTTTTAAAAAACGA
* * * *
2121382 TGTTGAAAACGTCTAATATATATTTTTTTAAAAACGA
1 TTTTGAAAACGTATAATATATAGTTTTTAAAAAACGA
*
2121419 TTTCTG-AAACATATAATATA
1 TTT-TGAAAACGTATAATATA
2121439 ATTTTTGAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
33 1 0.01
34 26 0.24
35 2 0.02
36 1 0.01
37 48 0.44
38 30 0.28
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.41
Consensus pattern (37 bp):
TTTTGAAAACGTATAATATATAGTTTTTAAAAAACGA
Found at i:2121388 original size:71 final size:72
Alignment explanation
Indices: 2121284--2121484 Score: 217
Period size: 71 Copynumber: 2.7 Consensus size: 72
2121274 TTTGAAAATG
* *
2121284 TATAATATATAGTTTTTCAAAAAATAGTTTTGAAAACGTATAATATATAGTTTTTAAAAAACGAT
1 TATAATATA-A-TTTTT-GAAAAATAGTGTTGAAAACGTATAATATATAGTTTTTAAAAAACGAT
2121349 TT-TGAAAACA
63 TTCTG-AAACA
* * * * * *
2121359 TAT-ATATGATTTTTTAAAAATGGTGTTGAAAACGTCTAATATATATTTTTTTAAAAACGATTTC
1 TATAATATAATTTTTGAAAAATAGTGTTGAAAACGTATAATATATAGTTTTTAAAAAACGATTTC
2121423 TGAAACA
66 TGAAACA
* * ** *
2121430 TATAATATAATTTTTGAAAACATATTTTTGAAAATATAGTATTATATAGTTTTTA
1 TATAATATAATTTTTGAAAA-ATAGTGTTGAAAACGTA-TAATATATAGTTTTTA
2121485 TTATTATGTT
Statistics
Matches: 104, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
71 51 0.49
72 21 0.20
73 12 0.12
74 17 0.16
75 3 0.03
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (72 bp):
TATAATATAATTTTTGAAAAATAGTGTTGAAAACGTATAATATATAGTTTTTAAAAAACGATTTC
TGAAACA
Found at i:2121533 original size:13 final size:13
Alignment explanation
Indices: 2121512--2121543 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
2121502 TATTTAATAT
2121512 ATTTATTTATTTTG
1 ATTT-TTTATTTTG
2121526 ATTTTTTATTTTG
1 ATTTTTTATTTTG
2121539 ATTTT
1 ATTTT
2121544 GATTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (13 bp):
ATTTTTTATTTTG
Found at i:2123442 original size:23 final size:23
Alignment explanation
Indices: 2123409--2123494 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
2123399 AGTCGAGGGT
*
2123409 TCTACGGGGTCCTTCGGGACAAA
1 TCTACGTGGTCCTTCGGGACAAA
* *
2123432 TCTATGTGGTCCTTCGGGACAAT
1 TCTACGTGGTCCTTCGGGACAAA
*
2123455 TTTACGTGGTCCTTCGGGACAAA
1 TCTACGTGGTCCTTCGGGACAAA
* *
2123478 TTCTACATTGTCCTTCG
1 -TCTACGTGGTCCTTCG
2123495 AGAAAATTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 40 0.75
24 13 0.25
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGACAAA
Found at i:2128687 original size:35 final size:40
Alignment explanation
Indices: 2128608--2128705 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 40
2128598 TACATATAGC
* *
2128608 ATATATAATATATAGTGTTGAAAGCATTTTTTTCGAATATAT
1 ATATATAATATATAGTTTTG--AGAATTTTTTTCGAATATAT
2128650 ATATAT-A-ATATAGTTTTGAGAATTTTTTT-GAA-A-AT
1 ATATATAATATATAGTTTTGAGAATTTTTTTCGAATATAT
2128685 ATATATAATATATAGTTTTGA
1 ATATATAATATATAGTTTTGA
2128706 AAATATATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
35 8 0.15
36 2 0.04
37 15 0.29
38 10 0.19
40 10 0.19
41 1 0.02
42 6 0.12
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (40 bp):
ATATATAATATATAGTTTTGAGAATTTTTTTCGAATATAT
Found at i:2128713 original size:27 final size:25
Alignment explanation
Indices: 2128675--2128733 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
2128665 TTGAGAATTT
2128675 TTTTGAAAATATATATAATATATAG
1 TTTTGAAAATATATATAATATATAG
*
2128700 TTTTGAAAATATATATAGTATATAG
1 TTTTGAAAATATATATAATATATAG
2128725 TTTTGAAAA
1 TTTTGAAAA
2128734 CATTTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (25 bp):
TTTTGAAAATATATATAATATATAG
Found at i:2128750 original size:36 final size:38
Alignment explanation
Indices: 2128700--2128774 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
2128690 TAATATATAG
*
2128700 TTTTG-AAAATATATATAGTATATAGTTTTGAAAACAT
1 TTTTGAAAAATATATATAATATATAGTTTTGAAAACAT
2128737 TTTTGAAAAATATATATAATATATAGTTTTGAAAACAT
1 TTTTGAAAAATATATATAATATATAGTTTTGAAAACAT
2128775 ATAATATATG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 5 0.14
38 31 0.86
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (38 bp):
TTTTGAAAAATATATATAATATATAGTTTTGAAAACAT
Found at i:2128780 original size:23 final size:23
Alignment explanation
Indices: 2128750--2128795 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2128740 TGAAAAATAT
2128750 ATATAATATATAGTTTTGAAAAC
1 ATATAATATATAGTTTTGAAAAC
*
2128773 ATATAATATATGGTTTTGAAAAC
1 ATATAATATATAGTTTTGAAAAC
2128796 GTTTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.39
Consensus pattern (23 bp):
ATATAATATATAGTTTTGAAAAC
Found at i:2128783 original size:61 final size:61
Alignment explanation
Indices: 2128648--2128833 Score: 252
Period size: 63 Copynumber: 3.0 Consensus size: 61
2128638 TTTCGAATAT
** *
2128648 ATATATATAATATAGTTTTGAGAATTTTTTTG-AAAATATATATAATATATAGTTTTGAAAAT
1 ATATATAT-ATATAGTTTTGA-AAACTTTTTGAAAAATATATATAATATATAGTTTTGAAAAC
2128710 ATATATAGTATATAGTTTTGAAAACATTTTTGAAAAATATATATAATATATAGTTTTGAAAAC
1 ATATATA-TATATAGTTTTGAAAAC-TTTTTGAAAAATATATATAATATATAGTTTTGAAAAC
* * **
2128773 ATATA-ATATATGGTTTTGAAAACGTTTT-AAAAACGTATATAATATATAGTTTTGAAAAC
1 ATATATATATATAGTTTTGAAAACTTTTTGAAAAATATATATAATATATAGTTTTGAAAAC
2128832 AT
1 AT
2128834 TTTTGAAAAC
Statistics
Matches: 114, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
59 31 0.27
60 4 0.04
61 18 0.16
62 26 0.23
63 35 0.31
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (61 bp):
ATATATATATATAGTTTTGAAAACTTTTTGAAAAATATATATAATATATAGTTTTGAAAAC
Found at i:2128818 original size:36 final size:35
Alignment explanation
Indices: 2128784--2128868 Score: 109
Period size: 35 Copynumber: 2.4 Consensus size: 35
2128774 TATAATATAT
2128784 GGTTTTGAAAACGTTTTAAAAACGTATATAATATAT
1 GGTTTTGAAAACGTTTTAAAAACG-ATATAATATAT
* * *
2128820 AGTTTTGAAAACATTTTTGAAAACG-TATAATATAT
1 GGTTTTGAAAAC-GTTTTAAAAACGATATAATATAT
*
2128855 GATTTTGAAAACGT
1 GGTTTTGAAAACGT
2128869 GTATAGTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
34 1 0.02
35 20 0.48
36 11 0.26
37 10 0.24
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (35 bp):
GGTTTTGAAAACGTTTTAAAAACGATATAATATAT
Found at i:2128861 original size:35 final size:34
Alignment explanation
Indices: 2128762--2128868 Score: 135
Period size: 36 Copynumber: 3.1 Consensus size: 34
2128752 ATAATATATA
* *
2128762 GTTTTGAAAACATATAATATATGGTTTTGAAAAC
1 GTTTTGAAAACGTATAATATATGATTTTGAAAAC
*
2128796 GTTTTAAAAACGTATATAATATAT-AGTTTTGAAAAC
1 GTTTTGAAAACG--TATAATATATGA-TTTTGAAAAC
*
2128832 ATTTTTGAAAACGTATAATATATGATTTTGAAAAC
1 -GTTTTGAAAACGTATAATATATGATTTTGAAAAC
2128867 GT
1 GT
2128869 GTATAGTATA
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
34 11 0.18
35 20 0.32
36 21 0.34
37 10 0.16
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (34 bp):
GTTTTGAAAACGTATAATATATGATTTTGAAAAC
Found at i:2128863 original size:23 final size:24
Alignment explanation
Indices: 2128834--2128891 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
2128824 TTGAAAACAT
2128834 TTTTGAAAAC-GTATAATATAT-G
1 TTTTGAAAACGGTATAATATATAG
*
2128856 ATTTTGAAAACGTGTATAGTATATAG
1 -TTTTGAAAACG-GTATAATATATAG
2128882 TTTTGAAAAC
1 TTTTGAAAAC
2128892 ATTTTTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 10 0.32
25 20 0.65
26 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (24 bp):
TTTTGAAAACGGTATAATATATAG
Found at i:2128895 original size:60 final size:61
Alignment explanation
Indices: 2128797--2128912 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 61
2128787 TTTGAAAACG
2128797 TTTTAAAAACGTATATAATATATAGTTTTGAAAACA-TTTTTGAAAACGTATAATATATGA
1 TTTTAAAAACGTATATAATATATAGTTTTGAAAACATTTTTTGAAAACGTATAATATATGA
* * * **
2128857 TTTTGAAAACGTGTATAGTATATAGTTTTGAAAACATTTTTTTTAAACGTATAATA
1 TTTTAAAAACGTATATAATATATAGTTTTGAAAACATTTTTTGAAAACGTATAATA
2128913 CGTGGTTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 33 0.66
61 17 0.34
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.42
Consensus pattern (61 bp):
TTTTAAAAACGTATATAATATATAGTTTTGAAAACATTTTTTGAAAACGTATAATATATGA
Found at i:2128921 original size:96 final size:96
Alignment explanation
Indices: 2128712--2128896 Score: 225
Period size: 97 Copynumber: 1.9 Consensus size: 96
2128702 TTGAAAATAT
* * *
2128712 ATATAGTATATAGTTTTGAAAACATTTTTGAAAAATATATATAATATATAGTTTTGAAAACATAT
1 ATATAATACATAGTTTTGAAAACATTTTTGAAAAATATATATAATATAGAGTTTTGAAAACATAT
*
2128777 AATATATGGTTTTGAAAACGTTTTAAAAACG
66 AATATATAGTTTTGAAAACGTTTTAAAAACG
* *
2128808 TATATAATATATAGTTTTGAAAACATTTTTGAAAACGTATA-AT-ATAT-GA-TTTTGAAAACGT
1 -ATATAATACATAGTTTTGAAAACATTTTTGAAAA-ATATATATAATATAGAGTTTTGAAAAC--
* * *
2128869 GTATAGTATATAGTTTTGAAAACATTTT
62 ATATAATATATAGTTTTGAAAACGTTTT
2128897 TTTTAAACGT
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
94 10 0.13
95 1 0.01
96 28 0.36
97 35 0.45
98 4 0.05
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (96 bp):
ATATAATACATAGTTTTGAAAACATTTTTGAAAAATATATATAATATAGAGTTTTGAAAACATAT
AATATATAGTTTTGAAAACGTTTTAAAAACG
Found at i:2129013 original size:6 final size:7
Alignment explanation
Indices: 2128949--2129029 Score: 51
Period size: 8 Copynumber: 11.3 Consensus size: 7
2128939 TGAAAACGTA
2128949 ATATATT
1 ATATATT
2128956 ATATTATT
1 ATA-TATT
*
2128964 ATATACAT
1 ATATA-TT
* *
2128972 ACAAATT
1 ATATATT
2128979 ATATAATT
1 ATAT-ATT
*
2128987 ATATTTT
1 ATATATT
*
2128994 AT-TA-C
1 ATATATT
2128999 ATTATATT
1 A-TATATT
2129007 A-ATATT
1 ATATATT
2129013 ATATATAT
1 ATATAT-T
2129021 ATATATT
1 ATATATT
2129028 AT
1 AT
2129030 TTGTTCAGGT
Statistics
Matches: 56, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
5 1 0.02
6 8 0.14
7 21 0.38
8 26 0.46
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (7 bp):
ATATATT
Found at i:2133887 original size:39 final size:38
Alignment explanation
Indices: 2133827--2133940 Score: 137
Period size: 37 Copynumber: 3.0 Consensus size: 38
2133817 TAGTACTGAA
2133827 AGAAATTTGTTTCAAAA-ATATATATACTATATAGTTTTG
1 AGAAATTT-TTTCAAAATATATATATA-TATATAGTTTTG
*
2133866 AGAAATTTTTTGAAAATATATATA-ATATATAGTTTTG
1 AGAAATTTTTTCAAAATATATATATATATATAGTTTTG
* * *
2133903 A-AAACATTTTTCAATATATATAAATA-ATATAGTTTTG
1 AGAAA-TTTTTTCAAAATATATATATATATATAGTTTTG
2133940 A
1 A
2133941 AAACGTATAA
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
36 3 0.04
37 40 0.60
38 9 0.13
39 15 0.22
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (38 bp):
AGAAATTTTTTCAAAATATATATATATATATAGTTTTG
Found at i:2133982 original size:95 final size:95
Alignment explanation
Indices: 2133849--2134039 Score: 271
Period size: 95 Copynumber: 2.0 Consensus size: 95
2133839 CAAAAATATA
* * *
2133849 TATACTATATAGTTTTGAGAAATTTTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTT
1 TATAATATATAGTTTTGAGAAATGTTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTT
* *
2133914 CAATATATATAAATAATAT-AGTTTTGAAAACG
66 CAAAACATAT-AAT-ATATGA-TTTTGAAAACG
*
2133946 TATAATATATGGTTTTGA-AAATGTTTT-AAAACATATATAATATATAGTTTTGAAAACATTTTT
1 TATAATATATAGTTTTGAGAAATGTTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTT
*
2134009 GAAAACATATAATATATGATTTTGAAAACG
66 CAAAACATATAATATATGATTTTGAAAACG
2134039 T
1 T
2134040 TTTAAAAATG
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
93 16 0.19
94 4 0.05
95 42 0.49
96 8 0.09
97 16 0.19
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.42
Consensus pattern (95 bp):
TATAATATATAGTTTTGAGAAATGTTTTGAAAACATATATAATATATAGTTTTGAAAACATTTTT
CAAAACATATAATATATGATTTTGAAAACG
Found at i:2133989 original size:35 final size:36
Alignment explanation
Indices: 2133934--2134103 Score: 172
Period size: 36 Copynumber: 4.8 Consensus size: 36
2133924 AAATAATATA
*
2133934 GTTTTGAAAACGTATAATATATGGTTTTG-AAA-AT
1 GTTTTGAAAACATATAATATATGGTTTTGAAAACAT
*
2133968 GTTTT-AAAACATATATAATATATAGTTTTGAAAACAT
1 GTTTTGAAAAC--ATATAATATATGGTTTTGAAAACAT
*
2134005 -TTTTGAAAACATATAATATATGATTTTGAAAAC--
1 GTTTTGAAAACATATAATATATGGTTTTGAAAACAT
* ** * * *
2134038 GTTTTAAAAATGTGTATAGTATATAGTTCTGAAAACAT
1 GTTTTGAAAA--CATATAATATATGGTTTTGAAAACAT
*
2134076 TTTTTGAAAACATATAATATATGGTTTT
1 GTTTTGAAAACATATAATATATGGTTTT
2134104 ATTTTTTAAA
Statistics
Matches: 108, Mismatches: 18, Indels: 18
0.75 0.12 0.12
Matches are distributed among these distances:
33 5 0.05
34 13 0.12
35 37 0.34
36 38 0.35
37 7 0.06
38 8 0.07
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (36 bp):
GTTTTGAAAACATATAATATATGGTTTTGAAAACAT
Found at i:2133994 original size:58 final size:60
Alignment explanation
Indices: 2133886--2134002 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
2133876 TGAAAATATA
** *
2133886 TATAATATATAGTTTTGAAAACATTTTTCAATATATATAAATAATATAGTTTTGAAAACG
1 TATAATATATAGTTTTGAAAACATTTTAAAACATATATAAATAATATAGTTTTGAAAACG
* **
2133946 TATAATATATGGTTTTGAAAATGTTTTAAAACATATAT-AAT-ATATAGTTTTGAAAAC
1 TATAATATATAGTTTTGAAAACATTTTAAAACATATATAAATAATATAGTTTTGAAAAC
2134003 ATTTTTGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
58 16 0.31
59 3 0.06
60 32 0.63
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42
Consensus pattern (60 bp):
TATAATATATAGTTTTGAAAACATTTTAAAACATATATAAATAATATAGTTTTGAAAACG
Found at i:2134012 original size:70 final size:71
Alignment explanation
Indices: 2133935--2134103 Score: 252
Period size: 70 Copynumber: 2.4 Consensus size: 71
2133925 AATAATATAG
* * *
2133935 TTTTGAAAACGTATAATATATGGTTTTGAAAATGTTTTAAAACA-TATATAATATATAGTTTTGA
1 TTTTGAAAACATATAATATATGGTTTTGAAAACGTTTTAAAA-AGTATATAATATATAGTTCTGA
2133999 AAACA-T
65 AAACATT
* * *
2134005 TTTTGAAAACATATAATATATGATTTTGAAAACGTTTTAAAAATGTGTATAGTATATAGTTCTGA
1 TTTTGAAAACATATAATATATGGTTTTGAAAACGTTTTAAAAA-GTATATAATATATAGTTCTGA
2134070 AAACATT
65 AAACATT
2134077 TTTTGAAAACATATAATATATGGTTTT
1 TTTTGAAAACATATAATATATGGTTTT
2134104 ATTTTTTAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
69 1 0.01
70 39 0.44
71 22 0.25
72 27 0.30
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (71 bp):
TTTTGAAAACATATAATATATGGTTTTGAAAACGTTTTAAAAAGTATATAATATATAGTTCTGAA
AACATT
Found at i:2134214 original size:15 final size:15
Alignment explanation
Indices: 2134191--2134232 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
2134181 ATTTCATTAC
2134191 ATTACTTTATATTAAT
1 ATTA-TTTATATTAAT
*
2134207 ATTATTTATATTTAT
1 ATTATTTATATTAAT
2134222 -TTATTATATAT
1 ATTATT-TATAT
2134233 ATATATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 5 0.21
15 15 0.62
16 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTATTTATATTAAT
Found at i:2134233 original size:2 final size:2
Alignment explanation
Indices: 2134213--2134258 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
2134203 TAATATTATT
* *
2134213 TA TA TT TA TT TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2134254 TA TA T
1 TA TA T
2134259 TTGTTCAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:2139858 original size:131 final size:131
Alignment explanation
Indices: 2139624--2140002 Score: 544
Period size: 131 Copynumber: 2.9 Consensus size: 131
2139614 GAGAGAAAAT
* ** *
2139624 GATAATATGTAATTATTT-ATAACCGAGAATAAATTAACTCTCATGCCTTAAAGCAGTCATTTAT
1 GATAATATCTAATTATTTCA-ATTCGAGAATAAATTACCTCTCATGCCTTAAAGCAGTCATTTAT
* *
2139688 TACTCCAATCGAAGTGAAGAGATATCACTATTTCATCTTAAAATTTAATATTGAGTTGAGTTGAA
65 TACTCCAATCGAAGTGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGAGTTGAGTAGAA
2139753 AC
130 AC
* *
2139755 GATAATATCTAATTATTTCAATTCGAGAATAAATTACCTCTCATGCCTTCAAGCAATCATTTATT
1 GATAATATCTAATTATTTCAATTCGAGAATAAATTACCTCTCATGCCTTAAAGCAGTCATTTATT
* *
2139820 ACTCCAATCGAAGTGAAGAGATGTCACTATTTCATCTTAAAATTCAATATTGATTTGAGTAGAAA
66 ACTCCAATCGAAGTGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGAGTTGAGTAGAAA
*
2139885 T
131 C
* * * **
2139886 GATAATATCTAATTATTTCCATTCGAGAACAAATGACCGGTCATGCCTTAAAGCAGTCATTTATT
1 GATAATATCTAATTATTTCAATTCGAGAATAAATTACCTCTCATGCCTTAAAGCAGTCATTTATT
* * * * * *
2139951 ACTCCTATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAATGAATATTG
66 ACTCCAATCGAAGTGAAGAGATATCACTATTTCATCTTAAAATTCAATATTG
2140003 TTTCAAGGGA
Statistics
Matches: 222, Mismatches: 25, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
131 221 1.00
132 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (131 bp):
GATAATATCTAATTATTTCAATTCGAGAATAAATTACCTCTCATGCCTTAAAGCAGTCATTTATT
ACTCCAATCGAAGTGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGAGTTGAGTAGAAA
C
Found at i:2146956 original size:3 final size:3
Alignment explanation
Indices: 2146948--2146980 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2146938 ATGTAAAATA
2146948 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2146981 TTGGGATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2146971 original size:14 final size:14
Alignment explanation
Indices: 2146952--2146981 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2146942 AAAATAAATA
2146952 ATAATAATAATAAT
1 ATAATAATAATAAT
2146966 ATAATAATAATAAT
1 ATAATAATAATAAT
2146980 AT
1 AT
2146982 TGGGATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:2146971 original size:17 final size:16
Alignment explanation
Indices: 2146944--2146980 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
2146934 TGGGATGTAA
2146944 AATAAATAATAATAAT
1 AATAAATAATAATAAT
2146960 AATAATATAATAATAAT
1 AATAA-ATAATAATAAT
2146977 AATA
1 AATA
2146981 TTGGGATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAAATAATAATAAT
Found at i:2148785 original size:13 final size:12
Alignment explanation
Indices: 2148752--2148814 Score: 69
Period size: 13 Copynumber: 5.2 Consensus size: 12
2148742 CATGTAATAC
*
2148752 TAAATTATATTAA
1 TAAATTAT-TAAA
2148765 TAAGATTATTAAA
1 TAA-ATTATTAAA
2148778 T-AA-TATTAAA
1 TAAATTATTAAA
2148788 TAATATTATTAAA
1 TAA-ATTATTAAA
2148801 T-AATTATTAAA
1 TAAATTATTAAA
2148812 TAA
1 TAA
2148815 TATAATGTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
10 8 0.18
11 12 0.27
12 4 0.09
13 15 0.34
14 5 0.11
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (12 bp):
TAAATTATTAAA
Found at i:2148786 original size:10 final size:11
Alignment explanation
Indices: 2148769--2148815 Score: 69
Period size: 11 Copynumber: 4.2 Consensus size: 11
2148759 TATTAATAAG
2148769 ATTATTAAATA
1 ATTATTAAATA
2148780 A-TATTAAATAA
1 ATTATTAAAT-A
2148791 TATTATTAAATA
1 -ATTATTAAATA
2148803 ATTATTAAATA
1 ATTATTAAATA
2148814 AT
1 AT
2148816 ATAATGTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.24
11 15 0.45
12 2 0.06
13 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATTATTAAATA
Found at i:2150174 original size:137 final size:133
Alignment explanation
Indices: 2149932--2150194 Score: 472
Period size: 137 Copynumber: 1.9 Consensus size: 133
2149922 CTATAAAGGC
* *
2149932 TGATAGGGAAGCGGTGGCGGATTGATGAACGTGCTCTTGAAGAATCAAACCTAGAAAGCTTTAGA
1 TGATAGGGAAGCGGTGGCGGATTGATGAACGTGCTCTTGAAGAATCAAACCTAGAAAGATCTAGA
2149997 CTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATTGTTTAGGACC
66 CTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATTGTTTAGGACC
2150062 AAT
131 AAT
2150065 TGATAGGGAAGCGGTGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGAAAGATC
1 TGATAGGGAAGCGGTGGCGGATTGATGAACG-TGCTC---TTGAAGAATCAAACCTAGAAAGATC
2150130 TAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATTGTTTAG
62 TAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATTGTTTAG
2150195 TGTTTCTTTT
Statistics
Matches: 124, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
133 31 0.25
134 5 0.04
137 88 0.71
ACGTcount: A:0.31, C:0.13, G:0.33, T:0.23
Consensus pattern (133 bp):
TGATAGGGAAGCGGTGGCGGATTGATGAACGTGCTCTTGAAGAATCAAACCTAGAAAGATCTAGA
CTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATTGTTTAGGACC
AAT
Found at i:2150657 original size:15 final size:17
Alignment explanation
Indices: 2150632--2150665 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2150622 TAAAGGTCCT
2150632 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
2150648 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
2150664 AA
1 AA
2150666 CATGTCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:2152261 original size:122 final size:122
Alignment explanation
Indices: 2152044--2152265 Score: 444
Period size: 122 Copynumber: 1.8 Consensus size: 122
2152034 AACTCTTGGC
2152044 GAAACCTTGAATTCGATTGGTTTGGTGTTGTTTTCCTTTTTCCAGTGGTAATCCGTCAGGTGGAT
1 GAAACCTTGAATTCGATTGGTTTGGTGTTGTTTTCCTTTTTCCAGTGGTAATCCGTCAGGTGGAT
2152109 CACCTAACACTTCTCGAAAATCCTGTAACAAAGATTGTATGTTTGATGAGGTATGAT
66 CACCTAACACTTCTCGAAAATCCTGTAACAAAGATTGTATGTTTGATGAGGTATGAT
2152166 GAAACCTTGAATTCGATTGGTTTGGTGTTGTTTTCCTTTTTCCAGTGGTAATCCGTCAGGTGGAT
1 GAAACCTTGAATTCGATTGGTTTGGTGTTGTTTTCCTTTTTCCAGTGGTAATCCGTCAGGTGGAT
2152231 CACCTAACACTTCTCGAAAATCCTGTAACAAAGAT
66 CACCTAACACTTCTCGAAAATCCTGTAACAAAGAT
2152266 GAAAACACAC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 100 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (122 bp):
GAAACCTTGAATTCGATTGGTTTGGTGTTGTTTTCCTTTTTCCAGTGGTAATCCGTCAGGTGGAT
CACCTAACACTTCTCGAAAATCCTGTAACAAAGATTGTATGTTTGATGAGGTATGAT
Found at i:2154271 original size:15 final size:15
Alignment explanation
Indices: 2154253--2154286 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2154243 TTTTTTGAAA
2154253 TTTTGGCTTTTTTGT
1 TTTTGGCTTTTTTGT
**
2154268 TTTTGTTTTTTTTGT
1 TTTTGGCTTTTTTGT
2154283 TTTT
1 TTTT
2154287 TGCCTCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (15 bp):
TTTTGGCTTTTTTGT
Found at i:2154301 original size:30 final size:31
Alignment explanation
Indices: 2154253--2154310 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
2154243 TTTTTTGAAA
* *
2154253 TTTTGGCTTTTTTGTTTTTGTTTTTTTTGTT
1 TTTTGCCTCTTTTGTTTTTGTTTTTTTTGTT
2154284 TTTTGCCTCTTTT-TTTTTGTTTTTTTT
1 TTTTGCCTCTTTTGTTTTTGTTTTTTTT
2154311 TTGAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.81
Consensus pattern (31 bp):
TTTTGCCTCTTTTGTTTTTGTTTTTTTTGTT
Found at i:2154731 original size:137 final size:137
Alignment explanation
Indices: 2154485--2154758 Score: 503
Period size: 137 Copynumber: 2.0 Consensus size: 137
2154475 CAACTCTGAT
*
2154485 ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
1 ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACATTGCTCTTGTTGAAGAATCAAACCTAGA
2154550 AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTAGCGGCAGTCGCTAGGATT
66 AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTAGCGGCAGTCGCTAGGATT
2154615 GTTTAGG
131 GTTTAGG
* *
2154622 ACCAATTGATAGGGAAGCGGTGGCGGATTGATGAACATTGCTCTTGTTGAAGAATCAAACCTATA
1 ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACATTGCTCTTGTTGAAGAATCAAACCTAGA
* *
2154687 AAGCTCTAGACTCGATGAAGAACAAATGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATT
66 AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTAGCGGCAGTCGCTAGGATT
2154752 GTTTAGG
131 GTTTAGG
2154759 GTTTATTTTA
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 132 1.00
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (137 bp):
ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACATTGCTCTTGTTGAAGAATCAAACCTAGA
AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTAGCGGCAGTCGCTAGGATT
GTTTAGG
Found at i:2160526 original size:16 final size:17
Alignment explanation
Indices: 2160505--2160536 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2160495 GTCGGTTTAG
2160505 AATGGTTAGGA-ATAGA
1 AATGGTTAGGATATAGA
2160521 AATGGTTAGGATATAG
1 AATGGTTAGGATATAG
2160537 GGTAGGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (17 bp):
AATGGTTAGGATATAGA
Found at i:2162949 original size:18 final size:18
Alignment explanation
Indices: 2162926--2162972 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
2162916 TACTAAAATG
2162926 GTATCGATACCGAAGTAT
1 GTATCGATACCGAAGTAT
2162944 GTATCGATACCGAAGTAT
1 GTATCGATACCGAAGTAT
2162962 GTATCGATACC
1 GTATCGATACC
2162973 ATAGAAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (18 bp):
GTATCGATACCGAAGTAT
Found at i:2163643 original size:24 final size:24
Alignment explanation
Indices: 2163567--2163670 Score: 115
Period size: 23 Copynumber: 4.4 Consensus size: 24
2163557 GAGTCGAGGG
* *
2163567 TTCTACGCGGTCCTTCGAGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
* *
2163591 -TCTATGTGGTCCTTCGGGA-TAA
1 TTCTACGTGGTCCTTCGGGACAAA
* *
2163613 TTTTACGTGGTCCTTTGGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
2163637 TTCTACGTGGTCCTTCGAGG-CAAA
1 TTCTACGTGGTCCTTCG-GGACAAA
*
2163661 TTCTATGTGG
1 TTCTACGTGG
2163671 CACTTCAATG
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
22 2 0.03
23 32 0.48
24 30 0.45
25 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGACAAA
Found at i:2163676 original size:24 final size:24
Alignment explanation
Indices: 2163575--2163691 Score: 73
Period size: 24 Copynumber: 5.0 Consensus size: 24
2163565 GGTTCTACGC
* *
2163575 GGTCCTTCGAGACAAA-TCTATGT
1 GGTCCTTCAAGGCAAATTCTATGT
* * *
2163598 GGTCCTTC--GGGATAATTTTACGT
1 GGTCCTTCAAGGCA-AATTCTATGT
** *
2163621 GGTCCTT-TGGGACAAATTCTACGT
1 GGTCCTTCAAGG-CAAATTCTATGT
*
2163645 GGTCCTTCGAGGCAAATTCTATGT
1 GGTCCTTCAAGGCAAATTCTATGT
* *
2163669 GG-CACTTCAATGCAAATTATATG
1 GGTC-CTTCAAGGCAAATTCTATG
2163692 AGCAGTGGTG
Statistics
Matches: 75, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
21 2 0.03
22 2 0.03
23 21 0.28
24 47 0.63
25 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (24 bp):
GGTCCTTCAAGGCAAATTCTATGT
Found at i:2168793 original size:2 final size:2
Alignment explanation
Indices: 2168788--2168824 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2168778 TTTTTTTCGA
2168788 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 A
2168825 GTTTTGGTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2179064 original size:9 final size:9
Alignment explanation
Indices: 2179024--2179074 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
2179014 TTTTTTGAAA
*
2179024 TTTTGGTTT
1 TTTTTGTTT
2179033 TTTGTGTGTTT
1 TTT-T-TGTTT
**
2179044 TTTTTGCCT
1 TTTTTGTTT
2179053 TTTTTGTTT
1 TTTTTGTTT
2179062 TTTTTGTTT
1 TTTTTGTTT
2179071 TTTT
1 TTTT
2179075 GTAAAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 26 0.74
10 2 0.06
11 7 0.20
ACGTcount: A:0.00, C:0.04, G:0.16, T:0.80
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:2182320 original size:24 final size:24
Alignment explanation
Indices: 2182293--2182391 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 24
2182283 CACCACTGCT
2182293 CATATAATTTG-CACCGAAGTG-CCA
1 CATATAATTTGTC-CCGAAG-GACCA
2182317 CATATAATTTGTCCCGAAGGACCA
1 CATATAATTTGTCCCGAAGGACCA
* * * **
2182341 CGTATAATTTATCCTGAATTACCA
1 CATATAATTTGTCCCGAAGGACCA
* * *
2182365 CATAGAA-ATATCCCGAAGGACCA
1 CATATAATTTGTCCCGAAGGACCA
2182388 CATA
1 CATA
2182392 GATCTGTCCC
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
23 17 0.27
24 44 0.71
25 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.25
Consensus pattern (24 bp):
CATATAATTTGTCCCGAAGGACCA
Found at i:2182377 original size:23 final size:23
Alignment explanation
Indices: 2182328--2182393 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
2182318 ATATAATTTG
* * *
2182328 TCCCGAAGGACCACGTATAATTTA
1 TCCCGAAGGACCACATAGAA-ATA
* **
2182352 TCCTGAATTACCACATAGAAATA
1 TCCCGAAGGACCACATAGAAATA
2182375 TCCCGAAGGACCACATAGA
1 TCCCGAAGGACCACATAGA
2182394 TCTGTCCCAA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 18 0.55
24 15 0.45
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (23 bp):
TCCCGAAGGACCACATAGAAATA
Found at i:2183094 original size:20 final size:21
Alignment explanation
Indices: 2183069--2183118 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2183059 TTTGATTACG
*
2183069 GTATCGATAC-CTCTACATAA
1 GTATCGATACTCTCTAAATAA
* *
2183089 GTATCGATACTCTTTAAATCA
1 GTATCGATACTCTCTAAATAA
2183110 GTATCGATA
1 GTATCGATA
2183119 TTGATTATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (21 bp):
GTATCGATACTCTCTAAATAA
Found at i:2187121 original size:17 final size:17
Alignment explanation
Indices: 2187099--2187154 Score: 112
Period size: 17 Copynumber: 3.3 Consensus size: 17
2187089 TTAAGGGAAT
2187099 GAATGGGTGAGATTTGG
1 GAATGGGTGAGATTTGG
2187116 GAATGGGTGAGATTTGG
1 GAATGGGTGAGATTTGG
2187133 GAATGGGTGAGATTTGG
1 GAATGGGTGAGATTTGG
2187150 GAATG
1 GAATG
2187155 TTTTCGTGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.25, C:0.00, G:0.46, T:0.29
Consensus pattern (17 bp):
GAATGGGTGAGATTTGG
Found at i:2187376 original size:18 final size:19
Alignment explanation
Indices: 2187349--2187398 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
2187339 GCCAAATTTT
* *
2187349 GTATCCATACTCATGG-GA
1 GTATCGATACTCAGGGAGA
2187367 GTATCGATACAT-AGGGTAGA
1 GTATCGATAC-TCAGGG-AGA
2187387 GTATCGATACTC
1 GTATCGATACTC
2187399 CTCATAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 12 0.46
19 2 0.08
20 12 0.46
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (19 bp):
GTATCGATACTCAGGGAGA
Found at i:2193338 original size:28 final size:29
Alignment explanation
Indices: 2193242--2193347 Score: 110
Period size: 32 Copynumber: 3.6 Consensus size: 29
2193232 TAAAAAATTG
*
2193242 AATAC-TTATGGTAC-TATTTTGACCCAAAA
1 AATACTTTA-GGTACTTATTTTGA-CTAAAA
* *
2193271 AATGCTTTAGGTACGTATTTTGACTAAAA
1 AATACTTTAGGTACTTATTTTGACTAAAA
*
2193300 ATTATAACTTTAGGTACTTATTTTGA-TTAAA
1 A--AT-ACTTTAGGTACTTATTTTGACTAAAA
2193331 AATACTTTAGGTACTTA
1 AATACTTTAGGTACTTA
2193348 AACAAAAAAG
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
28 14 0.21
29 17 0.25
30 11 0.16
31 7 0.10
32 18 0.27
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (29 bp):
AATACTTTAGGTACTTATTTTGACTAAAA
Found at i:2194697 original size:16 final size:16
Alignment explanation
Indices: 2194678--2194726 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2194668 AAAAAATATC
2194678 AAATAATAAAAATAAA
1 AAATAATAAAAATAAA
*
2194694 AAATAGT-AAAAT-AA
1 AAATAATAAAAATAAA
*
2194708 AAATAACATAAAATAAA
1 AAATAATA-AAAATAAA
2194725 AA
1 AA
2194727 TAAGATAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 7 0.26
15 5 0.19
16 11 0.41
17 4 0.15
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (16 bp):
AAATAATAAAAATAAA
Found at i:2194727 original size:16 final size:16
Alignment explanation
Indices: 2194700--2194735 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2194690 TAAAAAATAG
2194700 TAAAATAAAAATAACA
1 TAAAATAAAAATAACA
*
2194716 TAAAATAAAAATAAGA
1 TAAAATAAAAATAACA
2194732 TAAA
1 TAAA
2194736 GAGAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (16 bp):
TAAAATAAAAATAACA
Found at i:2194862 original size:24 final size:24
Alignment explanation
Indices: 2194817--2194862 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
2194807 GGGACTTAAA
* * **
2194817 TAAATTAAATTAAAATTCAAAAGC
1 TAAATCAAAATAAAATAAAAAAGC
2194841 TAAATCAAAATAAAATAAAAAA
1 TAAATCAAAATAAAATAAAAAA
2194863 TAAATAGATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (24 bp):
TAAATCAAAATAAAATAAAAAAGC
Found at i:2195579 original size:2 final size:2
Alignment explanation
Indices: 2195574--2195602 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2195564 CGAGAGATAG
2195574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2195603 CAGAGATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2196447 original size:38 final size:39
Alignment explanation
Indices: 2196396--2196483 Score: 142
Period size: 39 Copynumber: 2.3 Consensus size: 39
2196386 AAGAAAAATA
* *
2196396 ATCTCAAGTGAGAT-AAATATTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATATTCTGTTTCGAGTAAAACT
*
2196434 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTAAAACT
1 ATCTCAAGCGAGATAAAATATTCTGTTTCGAGTAAAACT
2196473 ATCTCAAGCGA
1 ATCTCAAGCGA
2196484 TAAGTTGATC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 13 0.28
39 33 0.72
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (39 bp):
ATCTCAAGCGAGATAAAATATTCTGTTTCGAGTAAAACT
Found at i:2197085 original size:110 final size:108
Alignment explanation
Indices: 2196940--2197362 Score: 519
Period size: 110 Copynumber: 3.8 Consensus size: 108
2196930 TTTCAGTTAT
* *
2196940 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTAAAAAAATTCTTTTGAAATAATCATCAAG
1 CATCAAGAAA-CCCTAAAAATTAGGCTTAGCTTCTTTAAAAAATTC-TTTGAAATCATCATCAAG
* * *
2197005 AAACCCCTCAAAATCAAGCTTTGTTTCTAAAAACCCATTTGAAAA
64 AAACCCCTGAAAATCAAGCTTAGTTTCTAAAAACTCATTTGAAAA
* * * *
2197050 CATCAAGAAACCCATAAAAATCAGGCTTAGTTTCTTTTAAAAATTCATTGAAATCATCATCAAGA
1 CATCAAGAAACCC-TAAAAATTAGGCTTAGCTTCTTTAAAAAATTCTTTGAAATCATCATCAAGA
* * * *
2197115 AACCCCTGAATATCAGGCTTAGTTTCTTAAAAAAATCTTTTGAAAA
65 AACCCCTGAAAATCAAGCTTAGTTTC-T-AAAAACTCATTTGAAAA
* * * *
2197161 CATAAAAAAACACCT-AAAATTAGGCTTAGCTTCCTTGAAAAAATTCTTTAGAAATGATC-TCAA
1 CATCAAGAAAC-CCTAAAAATTAGGCTTAGCTT-CTTTAAAAAATTCTTT-GAAATCATCATCAA
* * *
2197224 GAAAGCCCTGAAAATTAAGCTTAATTTCTAAAAACTCATTTGAAAA
63 GAAACCCCTGAAAATCAAGCTTAGTTTCTAAAAACTCATTTGAAAA
* *
2197270 CATCAAGAAAACTCTAAAAATTAGGCTTAGCTTCTTTTAAGAAATTCTTTGAAAATCATCATCAA
1 CATCAAG-AAACCCTAAAAATTAGGCTTAGCTTC-TTTAAAAAATTCTTTG-AAATCATCATCAA
*
2197335 G-AACCTCTGAAAATCAAGCTTAGTTTCT
63 GAAACCCCTGAAAATCAAGCTTAGTTTCT
2197363 TTAAAAAATT
Statistics
Matches: 264, Mismatches: 38, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
109 66 0.25
110 119 0.45
111 69 0.26
112 10 0.04
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (108 bp):
CATCAAGAAACCCTAAAAATTAGGCTTAGCTTCTTTAAAAAATTCTTTGAAATCATCATCAAGAA
ACCCCTGAAAATCAAGCTTAGTTTCTAAAAACTCATTTGAAAA
Found at i:2197268 original size:220 final size:224
Alignment explanation
Indices: 2196947--2197383 Score: 636
Period size: 220 Copynumber: 2.0 Consensus size: 224
2196937 TATCATCAAG
* *
2196947 AAACCCCTAAAAATTAGGCTTAGCTTCTTAAAAAAATTCTTTTGAAATAATCATCAAGAAACCCC
1 AAACACCTAAAAATTAGGCTTAGCTTCTTAAAAAAATTCTTTAGAAATAATCATCAAGAAACCCC
**
2197012 TCAAAATCAAGCTTTGTTTCTAAAAACCCATTTGAAAACATCAAG-AAACCCATAAAAATCAGGC
66 TCAAAATCAAGCTTAATTTCTAAAAACCCATTTGAAAACATCAAGAAAACCC-TAAAAATCAGGC
* * *
2197076 TTAGTTTCTTTTAA-AAATTCATTG-AAATCATCATCAAGAAACCCCTGAATATCAGGCTTAGTT
130 TTAGCTTCTTTTAAGAAATTCATTGAAAATCATCATCAAG-AACCCCTGAAAATCAAGCTTAGTT
2197139 TC-TTAAAAAA-ATCTTTTGAAAACATAAAA
194 TCTTTAAAAAATATCTTTTGAAAACATAAAA
* * *
2197168 AAACACCT-AAAATTAGGCTTAGCTTCCTTGAAAAAATTCTTTAGAAATGATC-TCAAGAAAGCC
1 AAACACCTAAAAATTAGGCTTAGCTT-CTTAAAAAAATTCTTTAGAAATAATCATCAAGAAACCC
* * * * *
2197231 CTGAAAATTAAGCTTAATTTCTAAAAACTCATTTGAAAACATCAAGAAAACTCTAAAAATTAGGC
65 CTCAAAATCAAGCTTAATTTCTAAAAACCCATTTGAAAACATCAAGAAAACCCTAAAAATCAGGC
* *
2197296 TTAGCTTCTTTTAAGAAATTCTTTGAAAATCATCATCAAGAACCTCTGAAAATCAAGCTTAGTTT
130 TTAGCTTCTTTTAAGAAATTCATTGAAAATCATCATCAAGAACCCCTGAAAATCAAGCTTAGTTT
*
2197361 CTTTAAAAAATTTCTTTTGAAAA
195 CTTTAAAAAATATCTTTTGAAAA
2197384 TATCTTGTAA
Statistics
Matches: 192, Mismatches: 18, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
220 92 0.48
221 67 0.35
222 22 0.11
223 11 0.06
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (224 bp):
AAACACCTAAAAATTAGGCTTAGCTTCTTAAAAAAATTCTTTAGAAATAATCATCAAGAAACCCC
TCAAAATCAAGCTTAATTTCTAAAAACCCATTTGAAAACATCAAGAAAACCCTAAAAATCAGGCT
TAGCTTCTTTTAAGAAATTCATTGAAAATCATCATCAAGAACCCCTGAAAATCAAGCTTAGTTTC
TTTAAAAAATATCTTTTGAAAACATAAAA
Found at i:2202025 original size:15 final size:15
Alignment explanation
Indices: 2202007--2202077 Score: 65
Period size: 16 Copynumber: 4.5 Consensus size: 15
2201997 ATTTAATTTT
*
2202007 AAAAAATAAAATATC
1 AAAAAATAAAATATA
2202022 AAAAAATAAAA-ATA
1 AAAAAATAAAATATA
2202036 AAAAACAGTAAAATA-A
1 AAAAA-A-TAAAATATA
*
2202052 AAACAATATAAAATAAA
1 AAA-AA-ATAAAATATA
2202069 CAAAAAATA
1 -AAAAAATA
2202078 TGAGGACCTA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
14 7 0.15
15 12 0.25
16 19 0.40
17 7 0.15
18 3 0.06
ACGTcount: A:0.77, C:0.06, G:0.01, T:0.15
Consensus pattern (15 bp):
AAAAAATAAAATATA
Found at i:2202047 original size:16 final size:16
Alignment explanation
Indices: 2202022--2202068 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
2202012 ATAAAATATC
2202022 AAAA-AATAAAAATAA
1 AAAACAATAAAAATAA
*
2202037 AAAACAGT-AAAAT-A
1 AAAACAATAAAAATAA
2202051 AAAACAATATAAAATAA
1 AAAACAATA-AAAATAA
2202068 A
1 A
2202069 CAAAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 8 0.31
15 9 0.35
16 7 0.27
17 2 0.08
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (16 bp):
AAAACAATAAAAATAA
Found at i:2204944 original size:22 final size:22
Alignment explanation
Indices: 2204913--2204956 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2204903 TGATGTACTG
2204913 AATCGCGATTTTGAAACGATCC
1 AATCGCGATTTTGAAACGATCC
*
2204935 AATCGTGATTTTGAAACGATCC
1 AATCGCGATTTTGAAACGATCC
2204957 GAACGCGTTC
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:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (22 bp):
AATCGCGATTTTGAAACGATCC
Found at i:2213265 original size:143 final size:144
Alignment explanation
Indices: 2213073--2213359 Score: 558
Period size: 143 Copynumber: 2.0 Consensus size: 144
2213063 ACATGAGGTC
2213073 ATTCATGAAATGTTTAAGAAATTCAGGAAAAGCATATAATTGAACATCAAAGCTAAAAAGTTAGG
1 ATTCATGAAATGTTTAAGAAATTCAGGAAAAGCATATAATTGAACATCAAAGCTAAAAAGTTAGG
*
2213138 AATCTAACATACAATATTTTGTAATGATTGATGGCTAGACAATCCAGAAAACAAAGCAAGAAGTT
66 AATCTAACATACAATATTTTGTAATGATAGATGGCTAGACAATCCAGAAAACAAAGCAAGAAGTT
2213203 TTGGAAGTTCCTTT
131 TTGGAAGTTCCTTT
2213217 ATTCATGAAATG-TTAAGAAATTCAGGAAAAGCATATAATTGAACATCAAAGCTAAAAAGTTAGG
1 ATTCATGAAATGTTTAAGAAATTCAGGAAAAGCATATAATTGAACATCAAAGCTAAAAAGTTAGG
2213281 AATCTAACATACAATATTTTGTAATGATAGATGGCTAGACAATCCAGAAAACAAAGCAAGAAGTT
66 AATCTAACATACAATATTTTGTAATGATAGATGGCTAGACAATCCAGAAAACAAAGCAAGAAGTT
2213346 TTGGAAGTTCCTTT
131 TTGGAAGTTCCTTT
2213360 CTTATTATTG
Statistics
Matches: 142, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
143 130 0.92
144 12 0.08
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.28
Consensus pattern (144 bp):
ATTCATGAAATGTTTAAGAAATTCAGGAAAAGCATATAATTGAACATCAAAGCTAAAAAGTTAGG
AATCTAACATACAATATTTTGTAATGATAGATGGCTAGACAATCCAGAAAACAAAGCAAGAAGTT
TTGGAAGTTCCTTT
Found at i:2221617 original size:8 final size:8
Alignment explanation
Indices: 2221594--2221623 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
2221584 ATTGGAGTGC
2221594 AAAAAGAA
1 AAAAAGAA
2221602 AGAAAAGAA
1 A-AAAAGAA
2221611 AAAAAGAA
1 AAAAAGAA
2221619 AAAAA
1 AAAAA
2221624 AATCAGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:2221623 original size:26 final size:26
Alignment explanation
Indices: 2221601--2221651 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2221591 TGCAAAAAGA
2221601 AAGAAAAGAAAAAAAGAAAAAAAAAT
1 AAGAAAAGAAAAAAAGAAAAAAAAAT
* * *
2221627 CAGAATAGAAGAAAAGAAAAAAAAA
1 AAGAAAAGAAAAAAAGAAAAAAAAA
2221652 GAATTTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (26 bp):
AAGAAAAGAAAAAAAGAAAAAAAAAT
Found at i:2229258 original size:298 final size:299
Alignment explanation
Indices: 2228722--2229321 Score: 1136
Period size: 298 Copynumber: 2.0 Consensus size: 299
2228712 GTGGATAAAG
2228722 AGATCACACCTATTGGAAGCTTAAATCACCAAGAGATATGAGCTAAAGGATCCATACCTATTCGG
1 AGATCACACCTATTGGAAGCTTAAATCACCAAGAGATATGAGCTAAAGGATCCATACCTATTCGG
2228787 CCACATCACATGCCATGCACATGAGAGCCTTTGGCGCCAAACATGAAGAGAACACACCACCATTC
66 CCACATCACATGCCATGCACATGAGAGCCTTTGGCGCCAAACATGAAGAGAACACACCACCATTC
2228852 GCCAAGGGAAGAAAATGGCGCCAAGATGAACAGCATGACCACCATTGGGCCAGGGAGATGTCTCT
131 GCCAAGGGAAGAAAATGGCGCCAAGATGAACAGCATGA-CACCATTGGGCCAGGGAGATGTCTCT
2228917 CCACCCTTTGACCGAATCATTAAGGCCATTCATGAAGAGTTAGCCGAACCATCACAAGCCCAAAT
195 CCACCCTTTGACCGAATCATTAAGGCCATTCATGAAGAGTTAGCCGAACCATCACAAGCCCAAAT
2228982 GACTTAATTTTTCATTTT-AAA-ATTATGTATCTTCATAA
260 GACTTAATTTTTCATTTTAAAACATTATGTATCTTCATAA
2229020 AGATCACACCTATTGGAAGCTTAAATCACCAAGAGATATGAGCTAAAGGATCCATACCTATTCGG
1 AGATCACACCTATTGGAAGCTTAAATCACCAAGAGATATGAGCTAAAGGATCCATACCTATTCGG
2229085 CCACATCACATGCCATGCACATGAGAGCCTTTGGCGCCAAACATGAAGAG-ACACACCACCATTC
66 CCACATCACATGCCATGCACATGAGAGCCTTTGGCGCCAAACATGAAGAGAACACACCACCATTC
2229149 GGCCAAGGGAAGAAAATGGCGCCAAGATGAACAAGCATGA-ACCATTGGGCCAAGGGAGATGTCT
131 -GCCAAGGGAAGAAAATGGCGCCAAGATGAAC-AGCATGACACCATTGGGCC-AGGGAGATGTCT
2229213 CTCCACCCTTTGACCGAATCATTAAGGCCATTCATGAAGAGTTAGCCGAACCATCACAAGCCCAA
193 CTCCACCCTTTGACCGAATCATTAAGGCCATTCATGAAGAGTTAGCCGAACCATCACAAGCCCAA
2229278 ATGACTTAATTTTTCATTTTAAAACATTATGTATCTTCATAA
258 ATGACTTAATTTTTCATTTTAAAACATTATGTATCTTCATAA
2229320 AG
1 AG
2229322 TTATGTATCT
Statistics
Matches: 297, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
297 25 0.08
298 243 0.82
299 10 0.03
300 19 0.06
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (299 bp):
AGATCACACCTATTGGAAGCTTAAATCACCAAGAGATATGAGCTAAAGGATCCATACCTATTCGG
CCACATCACATGCCATGCACATGAGAGCCTTTGGCGCCAAACATGAAGAGAACACACCACCATTC
GCCAAGGGAAGAAAATGGCGCCAAGATGAACAGCATGACACCATTGGGCCAGGGAGATGTCTCTC
CACCCTTTGACCGAATCATTAAGGCCATTCATGAAGAGTTAGCCGAACCATCACAAGCCCAAATG
ACTTAATTTTTCATTTTAAAACATTATGTATCTTCATAA
Found at i:2231684 original size:28 final size:27
Alignment explanation
Indices: 2231623--2231686 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
2231613 GGAACAATCA
2231623 TTGTAATTTTACAACACAAGGGTATTT
1 TTGTAATTTTACAACACAAGGGTATTT
** ** *
2231650 TCATAATTTTACCCTCATAAGGGTATTT
1 TTGTAATTTTA-CAACACAAGGGTATTT
2231678 TTGTAATTT
1 TTGTAATTT
2231687 CTTATCCAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
27 9 0.31
28 20 0.69
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (27 bp):
TTGTAATTTTACAACACAAGGGTATTT
Found at i:2233907 original size:2 final size:2
Alignment explanation
Indices: 2233902--2233940 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
2233892 TTACTCACAC
* *
2233902 AT AT AT AT CGT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2233941 TGAATACACA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 31 0.97
3 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2234755 original size:25 final size:25
Alignment explanation
Indices: 2234721--2234778 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
2234711 TCCATGCCCA
2234721 TAATAATACTTGACAAAGGATCTTT
1 TAATAATACTTGACAAAGGATCTTT
2234746 TAATAATACTTGACAAAGGATCTTT
1 TAATAATACTTGACAAAGGATCTTT
*
2234771 TAAAAATA
1 TAATAATA
2234779 ATCACATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.34
Consensus pattern (25 bp):
TAATAATACTTGACAAAGGATCTTT
Found at i:2236005 original size:40 final size:40
Alignment explanation
Indices: 2235961--2236038 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
2235951 TGAAGATTCC
2235961 AACTTCGAGAAGCTTGCTTTAGTCCATAAATAGACCTTGT
1 AACTTCGAGAAGCTTGCTTTAGTCCATAAATAGACCTTGT
2236001 AACTTCGAGAAGCTTGCTTTAGTCCATAAATAGACCTT
1 AACTTCGAGAAGCTTGCTTTAGTCCATAAATAGACCTT
2236039 TGTAGCTGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (40 bp):
AACTTCGAGAAGCTTGCTTTAGTCCATAAATAGACCTTGT
Found at i:2244297 original size:21 final size:20
Alignment explanation
Indices: 2244273--2244322 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2244263 TTGAAAATTA
**
2244273 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATAACATTTTG
2244293 TTTTTCAAAATAACATTTTG
1 TTTTTCAAAATAACATTTTG
*
2244313 -CTTTCAAAAT
1 TTTTTCAAAAT
2244323 CAAAACATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTTCAAAATAACATTTTG
Found at i:2247394 original size:17 final size:17
Alignment explanation
Indices: 2247360--2247393 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2247350 TTCCCAAGAG
*
2247360 GCATGTAGAATATTTTT
1 GCATGTAGAAGATTTTT
2247377 GCATAGTAGAAGATTTT
1 GCAT-GTAGAAGATTTT
2247394 GAGAGACCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (17 bp):
GCATGTAGAAGATTTTT
Found at i:2248009 original size:20 final size:20
Alignment explanation
Indices: 2247984--2248023 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2247974 TATGGGTTTG
*
2247984 AGTATCGATACTAGATGAAT
1 AGTATCAATACTAGATGAAT
* *
2248004 AGTATCAATCCTGGATGAAT
1 AGTATCAATACTAGATGAAT
2248024 TGGGACGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (20 bp):
AGTATCAATACTAGATGAAT
Found at i:2249330 original size:32 final size:32
Alignment explanation
Indices: 2249266--2249331 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
2249256 AACGATACAT
* * **
2249266 AACAATGTCGGTGTTGCATTCAGATATTGCAC
1 AACAATGTCAGTGTTACATTCAGATAACGCAC
* *
2249298 AACAATGTTAGTGTTACATTTAGATAACGCAC
1 AACAATGTCAGTGTTACATTCAGATAACGCAC
2249330 AA
1 AA
2249332 TAGTGTGAGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (32 bp):
AACAATGTCAGTGTTACATTCAGATAACGCAC
Found at i:2252027 original size:24 final size:24
Alignment explanation
Indices: 2251991--2252049 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
2251981 CAGTCAAAAC
* * *
2251991 TGCCGCATAGAATTTGCACCGAAG
1 TGCCACATTGAATATGCACCGAAG
*
2252015 TGCCACGTTGAATATGCACCGAAG
1 TGCCACATTGAATATGCACCGAAG
2252039 TGCCACATTGA
1 TGCCACATTGA
2252050 TTTATCCCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (24 bp):
TGCCACATTGAATATGCACCGAAG
Found at i:2252080 original size:23 final size:23
Alignment explanation
Indices: 2252051--2252119 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
2252041 CCACATTGAT
* *
2252051 TTATCCCGAAGGATCGCGTATAA
1 TTATCCCGAAGGACCGCGTAGAA
* * * *
2252074 TTGTCCCAAAGGACCACATAGAA
1 TTATCCCGAAGGACCGCGTAGAA
2252097 TTATCCCGAAGGACCGCGTAGAA
1 TTATCCCGAAGGACCGCGTAGAA
2252120 CCCTCAACTC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (23 bp):
TTATCCCGAAGGACCGCGTAGAA
Found at i:2252260 original size:12 final size:12
Alignment explanation
Indices: 2252243--2252271 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2252233 AACAATTACT
2252243 CATAGCATTTCA
1 CATAGCATTTCA
2252255 CATAGCATTTCA
1 CATAGCATTTCA
2252267 CATAG
1 CATAG
2252272 ATAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.31
Consensus pattern (12 bp):
CATAGCATTTCA
Found at i:2257982 original size:24 final size:24
Alignment explanation
Indices: 2257924--2257982 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
2257914 TAGTCAAAAT
* *
2257924 TGCCACGTAGAATTTGCACCAAAG
1 TGCCACATAGAATATGCACCAAAG
* **
2257948 TGCCACGTAGAATATGCACTGAAG
1 TGCCACATAGAATATGCACCAAAG
*
2257972 TGCTACATAGA
1 TGCCACATAGA
2257983 TTTGTCCCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (24 bp):
TGCCACATAGAATATGCACCAAAG
Found at i:2258013 original size:23 final size:24
Alignment explanation
Indices: 2257982--2258026 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
2257972 TGCTACATAG
*
2257982 ATTTGTCCCAAAGGACCTCGTAAA
1 ATTTGTCCCAAAGGACCGCGTAAA
2258006 ATTT-TCCCAAAGGACCGCGTA
1 ATTTGTCCCAAAGGACCGCGTA
2258027 GAACCTTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (24 bp):
ATTTGTCCCAAAGGACCGCGTAAA
Found at i:2259171 original size:12 final size:12
Alignment explanation
Indices: 2259144--2259236 Score: 55
Period size: 12 Copynumber: 7.8 Consensus size: 12
2259134 ATGGAGATAT
* *
2259144 CATAAATCAAAA
1 CATAATTCAGAA
*
2259156 CATAATTCAGAT
1 CATAATTCAGAA
*
2259168 CAT-ATATCATAA
1 CATAAT-TCAGAA
* * *
2259180 CAAAATCCAGAT
1 CATAATTCAGAA
*
2259192 CAGAAATT-AGAA
1 CA-TAATTCAGAA
*
2259204 CATAATTCAGAT
1 CATAATTCAGAA
* *
2259216 CAGAAATCAGAA
1 CATAATTCAGAA
2259228 CATAATTCA
1 CATAATTCA
2259237 AATCGGAAAT
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
11 6 0.10
12 47 0.80
13 6 0.10
ACGTcount: A:0.52, C:0.17, G:0.08, T:0.24
Consensus pattern (12 bp):
CATAATTCAGAA
Found at i:2259176 original size:24 final size:24
Alignment explanation
Indices: 2259142--2259248 Score: 124
Period size: 24 Copynumber: 4.5 Consensus size: 24
2259132 AAATGGAGAT
* *
2259142 ATCATAAATCAAAACATAATTCAG
1 ATCAGAAATCAGAACATAATTCAG
* * * * *
2259166 ATCATATATCATAACAAAATCCAG
1 ATCAGAAATCAGAACATAATTCAG
*
2259190 ATCAGAAATTAGAACATAATTCAG
1 ATCAGAAATCAGAACATAATTCAG
*
2259214 ATCAGAAATCAGAACATAATTCAA
1 ATCAGAAATCAGAACATAATTCAG
*
2259238 ATCGGAAATCA
1 ATCAGAAATCA
2259249 TATAAAACAT
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAGAACATAATTCAG
Found at i:2269780 original size:23 final size:22
Alignment explanation
Indices: 2269703--2269780 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
2269693 CACCAAAGTT
2269703 CCACATAGAATGTCCCGAAGGA
1 CCACATAGAATGTCCCGAAGGA
* **
2269725 CCACGTAGAAATGTCTTGAAGGA
1 CCACATAG-AATGTCCCGAAGGA
* *
2269748 CCA-AGAAGAATTGTCCCAAAGGA
1 CCACA-TAGAA-TGTCCCGAAGGA
2269771 CCACATAGAA
1 CCACATAGAA
2269781 CCCTCGACTC
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
22 9 0.21
23 33 0.77
24 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.22, T:0.15
Consensus pattern (22 bp):
CCACATAGAATGTCCCGAAGGA
Found at i:2275053 original size:12 final size:12
Alignment explanation
Indices: 2275036--2275060 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2275026 GATGCAAATG
2275036 ATAAAAAATGAA
1 ATAAAAAATGAA
2275048 ATAAAAAATGAA
1 ATAAAAAATGAA
2275060 A
1 A
2275061 GGAAACAAGT
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
ATAAAAAATGAA
Found at i:2276776 original size:14 final size:12
Alignment explanation
Indices: 2276771--2276892 Score: 117
Period size: 12 Copynumber: 10.0 Consensus size: 12
2276761 AGATACTAAT
2276771 ATATAGATA-ATA
1 ATATA-ATATATA
2276783 ATAT-ATATATA
1 ATATAATATATA
*
2276794 TATATATTAATATA
1 -ATATAAT-ATATA
2276808 ATATAATACTATA
1 ATATAATA-TATA
2276821 ATAATAATATATA
1 AT-ATAATATATA
2276834 ATATAATATATA
1 ATATAATATATA
2276846 ATAT-ATACTATA
1 ATATAATA-TATA
* *
2276858 ATAT-ATAAAAA
1 ATATAATATATA
*
2276869 ATATACTATATA
1 ATATAATATATA
*
2276881 TTATAATATATA
1 ATATAATATATA
2276893 CTATCCCGGA
Statistics
Matches: 93, Mismatches: 9, Indels: 16
0.79 0.08 0.14
Matches are distributed among these distances:
10 3 0.03
11 12 0.13
12 48 0.52
13 19 0.20
14 11 0.12
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (12 bp):
ATATAATATATA
Found at i:2276788 original size:2 final size:2
Alignment explanation
Indices: 2276769--2276892 Score: 82
Period size: 2 Copynumber: 68.5 Consensus size: 2
2276759 ATAGATACTA
*
2276769 AT AT AT AG AT A- AT A- AT AT AT AT AT AT AT AT AT -T A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2276807 A- AT AT A- AT ACT AT A- AT A- AT A- AT AT AT A- AT AT A- AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2276843 AT A- AT AT AT ACT AT A- AT AT AT A- AA AA AT AT ACT AT AT AT -T
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
2276883 AT A- AT AT AT A
1 AT AT AT AT AT A
2276893 CTATCCCGGA
Statistics
Matches: 100, Mismatches: 3, Indels: 38
0.71 0.02 0.27
Matches are distributed among these distances:
1 16 0.16
2 78 0.78
3 6 0.06
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:2276820 original size:21 final size:20
Alignment explanation
Indices: 2276780--2276896 Score: 90
Period size: 21 Copynumber: 6.0 Consensus size: 20
2276770 TATATAGATA
2276780 ATAATAT-ATATATATA-TAT
1 ATAATATAATATA-ATACTAT
2276799 ATTAATATAATATAATACTAT
1 A-TAATATAATATAATACTAT
2276820 AATAATA-ATATATAATA-TA-
1 -ATAATATA-ATATAATACTAT
2276839 AT-ATATAATAT-ATACTAT
1 ATAATATAATATAATACTAT
* *
2276857 A-ATATATAAAAAATATACTAT
1 ATA-ATATAATATA-ATACTAT
*
2276878 ATATTATAATAT-ATACTAT
1 ATAATATAATATAATACTAT
2276897 CCCGGACAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 26
0.72 0.05 0.23
Matches are distributed among these distances:
16 3 0.04
17 9 0.11
18 4 0.05
19 15 0.19
20 12 0.15
21 35 0.44
22 2 0.03
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATATAATATAATACTAT
Found at i:2276827 original size:19 final size:19
Alignment explanation
Indices: 2276741--2276896 Score: 135
Period size: 19 Copynumber: 8.0 Consensus size: 19
2276731 TAAACCAAAA
*
2276741 AATA-ATAATATATAGTA-
1 AATATATAATATATACTAT
*
2276758 AATAGATACTAATATATA-GAT
1 AAT--ATA-TAATATATACTAT
2276779 AATAATATATATATATA-TAT
1 AAT-ATATA-ATATATACTAT
*
2276799 ATTAATATAATATAATACTAT
1 AAT-ATATAATAT-ATACTAT
*
2276820 AATA-ATAATATATAATAT
1 AATATATAATATATACTAT
2276838 AATATATAATATATACTAT
1 AATATATAATATATACTAT
*
2276857 AATATATAAAAAATATACTAT
1 AATATAT--AATATATACTAT
2276878 -ATATTATAATATATACTAT
1 AATA-TATAATATATACTAT
2276897 CCCGGACAAA
Statistics
Matches: 118, Mismatches: 9, Indels: 22
0.79 0.06 0.15
Matches are distributed among these distances:
17 3 0.03
18 10 0.08
19 45 0.38
20 29 0.25
21 31 0.26
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (19 bp):
AATATATAATATATACTAT
Found at i:2276891 original size:28 final size:29
Alignment explanation
Indices: 2276767--2276892 Score: 120
Period size: 28 Copynumber: 4.3 Consensus size: 29
2276757 AAATAGATAC
2276767 TAATATATAGATAATAATATA-TATATA-TA
1 TAATATATA-ATAA-AATATACTATATATTA
*
2276796 T-ATAT-TAATATAATATAATACTATA-ATAA
1 TAATATATAATA-AA-AT-ATACTATATATTA
* *
2276825 TAATATATAATATAATATATAATATATACTA
1 TAATATATAATA-AA-ATATACTATATATTA
2276856 TAATATATAA-AAAATATACTATATATTA
1 TAATATATAATAAAATATACTATATATTA
2276884 TAATATATA
1 TAATATATA
2276893 CTATCCCGGA
Statistics
Matches: 83, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
26 4 0.05
27 5 0.06
28 30 0.36
29 9 0.11
30 12 0.14
31 23 0.28
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (29 bp):
TAATATATAATAAAATATACTATATATTA
Found at i:2278374 original size:49 final size:49
Alignment explanation
Indices: 2278302--2278400 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
2278292 AGTTAGTTAG
2278302 TTAGAATTGTGTTATTCAGATGATATAGAATTCATCACAATTCTTCATT
1 TTAGAATTGTGTTATTCAGATGATATAGAATTCATCACAATTCTTCATT
* *
2278351 TTAGAATTGTGTTTTTCAGATGATATAGAATTCATCACATTTCTTCATT
1 TTAGAATTGTGTTATTCAGATGATATAGAATTCATCACAATTCTTCATT
2278400 T
1 T
2278401 CCTCTCTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (49 bp):
TTAGAATTGTGTTATTCAGATGATATAGAATTCATCACAATTCTTCATT
Found at i:2292025 original size:40 final size:40
Alignment explanation
Indices: 2291981--2292087 Score: 196
Period size: 40 Copynumber: 2.7 Consensus size: 40
2291971 AGGACACTAA
* *
2291981 GTGTACATGGTGGGCACGACCTTATGTGTAATACACTTTG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
2292021 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
2292061 GTGTATATGGTGGGCACGACCTTATGT
1 GTGTATATGGTGGGCACGACCTTATGT
2292088 CTAACACTAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (40 bp):
GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
Found at i:2295220 original size:21 final size:21
Alignment explanation
Indices: 2295187--2295229 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2295177 TAAAATAGGA
*
2295187 ATAAAAATCAAAATGATAATG
1 ATAAAAATAAAAATGATAATG
*
2295208 ATAATAATAAAAATGATAATG
1 ATAAAAATAAAAATGATAATG
2295229 A
1 A
2295230 AAGGAAATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (21 bp):
ATAAAAATAAAAATGATAATG
Found at i:2297897 original size:31 final size:31
Alignment explanation
Indices: 2297854--2297931 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
2297844 TCAAACGGTC
*
2297854 GGGGACCATATTGCAAACAAACTAAATGTTG
1 GGGGACCGTATTGCAAACAAACTAAATGTTG
* ** *
2297885 GGGGACCGTATTGTAAACGGACTATATGTTG
1 GGGGACCGTATTGCAAACAAACTAAATGTTG
* **
2297916 AGGGATTGTATTGCAA
1 GGGGACCGTATTGCAA
2297932 GTTTTAAAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.27
Consensus pattern (31 bp):
GGGGACCGTATTGCAAACAAACTAAATGTTG
Found at i:2299398 original size:23 final size:21
Alignment explanation
Indices: 2299365--2299407 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
2299355 GGCTTGTAAT
2299365 AATAATAAATG-AAAATAATGG
1 AATAATAAATGTAAAA-AATGG
2299386 AATATATACAATGTAAAAAATG
1 AATA-ATA-AATGTAAAAAATG
2299408 TTGATTACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 8 0.42
24 4 0.21
ACGTcount: A:0.60, C:0.02, G:0.12, T:0.26
Consensus pattern (21 bp):
AATAATAAATGTAAAAAATGG
Found at i:2304640 original size:5 final size:5
Alignment explanation
Indices: 2304618--2304761 Score: 86
Period size: 5 Copynumber: 27.6 Consensus size: 5
2304608 AAACGGAAAA
** *
2304618 ATAAT ATTAAT AATAAT ATAAT ATGTAAT A-AAT A-GCT ATAGT ATAAGT
1 ATAAT A-TAAT -ATAAT ATAAT A--TAAT ATAAT ATAAT ATAAT ATAA-T
2304666 AT-AT ACTAAT ATAAT ATAAT ATAAT ACT-AT AATAAT A-ATAT ATAAT
1 ATAAT A-TAAT ATAAT ATAAT ATAAT A-TAAT -ATAAT ATA-AT ATAAT
*
2304712 ATAAT ATGTAAT ATAAT AT-AT AATAAT ATACT ATAAT AT-AT ATATAT
1 ATAAT A--TAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATA-AT
2304759 ATA
1 ATA
2304762 CCGGACGAAA
Statistics
Matches: 113, Mismatches: 7, Indels: 37
0.72 0.04 0.24
Matches are distributed among these distances:
4 15 0.13
5 61 0.54
6 26 0.23
7 11 0.10
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:2304676 original size:41 final size:38
Alignment explanation
Indices: 2304618--2304756 Score: 157
Period size: 37 Copynumber: 3.7 Consensus size: 38
2304608 AAACGGAAAA
*
2304618 ATAATATTAATA-ATAATATAATATGTAATA-AATAGCT
1 ATAATAATAATATATAATATAATATGTAATATAATA-CT
2304655 ATAGTATAAGT-ATATACTAATATAATA--TAATATAATACT
1 ATA--ATAA-TAATATA-TAATATAATATGTAATATAATACT
2304694 ATAATAATAATATATAATATAATATGTAATATAATA-T
1 ATAATAATAATATATAATATAATATGTAATATAATACT
2304731 ATAATAAT-ATACTATAATATATATAT
1 ATAATAATAATA-TATAATATA-ATAT
2304757 ATATACCGGA
Statistics
Matches: 90, Mismatches: 1, Indels: 21
0.80 0.01 0.19
Matches are distributed among these distances:
36 14 0.16
37 30 0.33
38 14 0.16
39 16 0.18
40 6 0.07
41 10 0.11
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.40
Consensus pattern (38 bp):
ATAATAATAATATATAATATAATATGTAATATAATACT
Found at i:2306097 original size:2 final size:2
Alignment explanation
Indices: 2306090--2306129 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2306080 GTTTTGACAA
2306090 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
2306130 ACAGTAGCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2326207 original size:16 final size:18
Alignment explanation
Indices: 2326188--2326224 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
2326178 AAAATTTAAG
*
2326188 TTTTTCTTT-ATTTT-TA
1 TTTTTATTTCATTTTGTA
2326204 TTTTTATTTCATTTTGTA
1 TTTTTATTTCATTTTGTA
2326222 TTT
1 TTT
2326225 ATTTTTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 5 0.28
18 5 0.28
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTTATTTCATTTTGTA
Found at i:2326530 original size:26 final size:25
Alignment explanation
Indices: 2326499--2326569 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 25
2326489 CCTCTTAAAT
2326499 TTTTAACTTTTTCTTTTCTCTTTC-
1 TTTTAACTTTTTCTTTTCTCTTTCA
*
2326523 -TTT-A-TTAATT-TTTTCTCTTTCA
1 TTTTAACTT-TTTCTTTTCTCTTTCA
*
2326545 TTTTAACTTTTACTTTTTCTCTTTC
1 TTTTAACTTTTTC-TTTTCTCTTTC
2326570 CTTCATTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
21 13 0.35
22 3 0.08
23 6 0.16
24 2 0.05
25 2 0.05
26 11 0.30
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTAACTTTTTCTTTTCTCTTTCA
Done.