Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 37
Found at i:4510911 original size:34 final size:33
Alignment explanation
Indices: 4510868--4510933 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
4510858 TATAAGATTA
* * *
4510868 TGTTTGTGGTCTTAATTTTTAAAACTTTTCATTG
1 TGTTTGTGGTCCTAACTTTCAAAA-TTTTCATTG
4510902 TGTTTGTGGTCCTAACTTTCAAAATTTTCATT
1 TGTTTGTGGTCCTAACTTTCAAAATTTTCATT
4510934 CTATTTAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 8 0.28
34 21 0.72
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.53
Consensus pattern (33 bp):
TGTTTGTGGTCCTAACTTTCAAAATTTTCATTG
Found at i:4511734 original size:6 final size:6
Alignment explanation
Indices: 4511666--4511736 Score: 72
Period size: 6 Copynumber: 11.8 Consensus size: 6
4511656 TTTCAATGTA
* * * * *
4511666 AATTTG GATTTG GATTTG AATTTT AATTTG TAA-TTG AAGTTG AAATTG
1 AATTTG AATTTG AATTTG AATTTG AATTTG -AATTTG AATTTG AATTTG
*
4511714 AAATTG AATTTG AATTTG AATTT
1 AATTTG AATTTG AATTTG AATTT
4511737 TATTTTTAGC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
5 2 0.04
6 53 0.93
7 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (6 bp):
AATTTG
Found at i:4512418 original size:20 final size:20
Alignment explanation
Indices: 4512371--4512461 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
4512361 ATATGTTTCT
*
4512371 ATTCTAATGTAAGGTAATGT
1 ATTCTAATGTAAGGTAATGC
*
4512391 ACTCTAATGTAAGGTAATGC
1 ATTCTAATGTAAGGTAATGC
* ** *
4512411 ATTATAATGTTCCTGATAATGC
1 ATTCTAATG-T-AAGGTAATGC
*
4512433 -TTCTAATGTAAGGTAATGT
1 ATTCTAATGTAAGGTAATGC
*
4512452 ATTGTAATGT
1 ATTCTAATGT
4512462 CATGTAATTA
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
19 6 0.11
20 34 0.62
21 8 0.15
22 7 0.13
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCTAATGTAAGGTAATGC
Found at i:4512616 original size:19 final size:18
Alignment explanation
Indices: 4512569--4512618 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
4512559 CCATAAAGAC
*
4512569 AAATTAAAAATA-AAATA
1 AAATTAAAAACATAAATA
*
4512586 AAATAAACAAACATAAATA
1 AAATTAA-AAACATAAATA
4512605 AATATTAAAAACAT
1 AA-ATTAAAAACAT
4512619 TACATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 6 0.22
18 4 0.15
19 13 0.48
20 4 0.15
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATTAAAAACATAAATA
Found at i:4512642 original size:14 final size:13
Alignment explanation
Indices: 4512610--4512648 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
4512600 AAATAAATAT
* *
4512610 TAAAAACATTACA
1 TAAAAATATTAAA
4512623 TAAAAATATTAAA
1 TAAAAATATTAAA
4512636 TACAAAATATTAA
1 TA-AAAATATTAA
4512649 TGTTCAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAAAATATTAAA
Found at i:4514903 original size:15 final size:14
Alignment explanation
Indices: 4514883--4515012 Score: 62
Period size: 15 Copynumber: 9.4 Consensus size: 14
4514873 ATTATCACAA
4514883 ATAATTAATAAAATT
1 ATAATTAATAAAA-T
4514898 ATAATTATATAAAA-
1 ATAATTA-ATAAAAT
*
4514912 ATAATATAATATAAT
1 ATAAT-TAATAAAAT
*
4514927 ATAA-TAA-AATATT
1 ATAATTAATAA-AAT
*
4514940 ATCATTAATAAAA-
1 ATAATTAATAAAAT
* *
4514953 AT--TTAAATATATT
1 ATAATT-AATAAAAT
*
4514966 CTAA-TAATTTAAAAT
1 ATAATTAA--TAAAAT
*
4514981 ATAA-T-ATAATAT
1 ATAATTAATAAAAT
4514993 ACTAATTAATAAAAT
1 A-TAATTAATAAAAT
4515008 ATAAT
1 ATAAT
4515013 ATTTTTTAAT
Statistics
Matches: 87, Mismatches: 13, Indels: 31
0.66 0.10 0.24
Matches are distributed among these distances:
11 2 0.02
12 12 0.14
13 16 0.18
14 21 0.24
15 30 0.34
16 6 0.07
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAATTAATAAAAT
Found at i:4514990 original size:20 final size:19
Alignment explanation
Indices: 4514947--4514991 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
4514937 ATTATCATTA
* *
4514947 ATAAAAATTTAAATATATT
1 ATAATAATTTAAATATAAT
*
4514966 CTAATAATTTAAAATATAAT
1 ATAATAATTT-AAATATAAT
4514986 ATAATA
1 ATAATA
4514992 TACTAATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAATAATTTAAATATAAT
Found at i:4526325 original size:5 final size:5
Alignment explanation
Indices: 4526317--4526342 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4526307 CCACTACTAA
4526317 TACCT TACCT TACCT TACCT TACCT T
1 TACCT TACCT TACCT TACCT TACCT T
4526343 CTATTGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.38, G:0.00, T:0.42
Consensus pattern (5 bp):
TACCT
Found at i:4533677 original size:26 final size:26
Alignment explanation
Indices: 4533629--4533678 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
4533619 AGGTTGAGAC
* *
4533629 TCAAATTTTAAAATATATTATATTTT
1 TCAAATTTTAAAATAAATAATATTTT
4533655 TCAAATTTT-AAATAAATCAATATT
1 TCAAATTTTAAAATAAAT-AATATT
4533679 GATTCAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (26 bp):
TCAAATTTTAAAATAAATAATATTTT
Found at i:4537981 original size:30 final size:29
Alignment explanation
Indices: 4537942--4538000 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
4537932 GAGAATTTAC
* *
4537942 ATGAACTACGTGATTAAATGTATATGTGA
1 ATGAACTACGAGATTAAATGAATATGTGA
* *
4537971 ATGAAGCTACGAGTTTATATGAATATGTGA
1 ATGAA-CTACGAGATTAAATGAATATGTGA
4538001 TATGTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGAACTACGAGATTAAATGAATATGTGA
Found at i:4538090 original size:27 final size:27
Alignment explanation
Indices: 4538059--4538116 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
4538049 ATGTGTCATG
4538059 AGAGCTAGGGATATAGTTGACATGCCA
1 AGAGCTAGGGATATAGTTGACATGCCA
*
4538086 AGAGCTAGGGATATAGTTGGCATGCCA
1 AGAGCTAGGGATATAGTTGACATGCCA
4538113 AGAG
1 AGAG
4538117 TCGAGAGTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.33, T:0.21
Consensus pattern (27 bp):
AGAGCTAGGGATATAGTTGACATGCCA
Found at i:4538292 original size:23 final size:23
Alignment explanation
Indices: 4538258--4538325 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
4538248 CATCTTATAT
*
4538258 GGCACTTTGGTGCATTTCTACGC
1 GGCACTTAGGTGCATTTCTACGC
* *
4538281 GGCACTTAGGTGCAATTCTACGT
1 GGCACTTAGGTGCATTTCTACGC
* * *
4538304 GGCACTTCGATGCATTTATACG
1 GGCACTTAGGTGCATTTCTACG
4538326 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (23 bp):
GGCACTTAGGTGCATTTCTACGC
Found at i:4540631 original size:152 final size:152
Alignment explanation
Indices: 4540355--4540659 Score: 556
Period size: 152 Copynumber: 2.0 Consensus size: 152
4540345 GTCGAGTTAG
*
4540355 ACTCAAGTTTAGGAGGGAAAAATACTCGACTTGACCTGAGAAAATAATATAATTATACATTATAT
1 ACTCAAGTTTAGGAGGGAAAAATACTCAACTTGACCTGAGAAAATAATATAATTATACATTATAT
* *
4540420 ATTTAGAGATAAGTACAATAATACTTCTCTATTTATATACTTTTTCAATTAGATCCATATTTTAT
66 ATTTAGAGATAAATACAATAACACTTCTCTATTTATATACTTTTTCAATTAGATCCATATTTTAT
4540485 CAAATAAAATTAATATATATAT
131 CAAATAAAATTAATATATATAT
** *
4540507 ACTCAAGTTTAGGAGGGAAAAATACTCAACTTGAGTTGAGAAAATAATATAGTTATACATTATAT
1 ACTCAAGTTTAGGAGGGAAAAATACTCAACTTGACCTGAGAAAATAATATAATTATACATTATAT
4540572 ATTTAGAGATAAATACAATAACACTTCTCTATTTATATACTTTTTCAATTAGATCCATATTTTAT
66 ATTTAGAGATAAATACAATAACACTTCTCTATTTATATACTTTTTCAATTAGATCCATATTTTAT
4540637 CAAATAAAATTAATATATATAT
131 CAAATAAAATTAATATATATAT
4540659 A
1 A
4540660 TATATATGTG
Statistics
Matches: 147, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 147 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (152 bp):
ACTCAAGTTTAGGAGGGAAAAATACTCAACTTGACCTGAGAAAATAATATAATTATACATTATAT
ATTTAGAGATAAATACAATAACACTTCTCTATTTATATACTTTTTCAATTAGATCCATATTTTAT
CAAATAAAATTAATATATATAT
Found at i:4555533 original size:16 final size:16
Alignment explanation
Indices: 4555514--4555547 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4555504 CAATATACGA
4555514 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
4555530 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
4555546 AT
1 AT
4555548 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:4555621 original size:16 final size:18
Alignment explanation
Indices: 4555589--4555622 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
4555579 TATTAATGTA
4555589 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
4555607 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
4555623 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:4556295 original size:130 final size:130
Alignment explanation
Indices: 4556091--4556338 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
4556081 AATTTTCTTC
* * *
4556091 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTAGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
4556156 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
4556221 TAATTAGGTAGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCATAT
1 TAATTAGGTAGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
4556286 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
4556339 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTAGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:4556781 original size:35 final size:35
Alignment explanation
Indices: 4556735--4556810 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
4556725 AATTAAATTT
*
4556735 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTATTTTGGAAATTAGGGTTTAGAATGA
*
4556770 AATTGAATTATTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTATTTTGGAAATTAGGGTTTAGAATGA
4556805 AATTGA
1 AATTGA
4556811 TGACTGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.41
Consensus pattern (35 bp):
AATTGAATTATTTTGGAAATTAGGGTTTAGAATGA
Found at i:4566115 original size:26 final size:27
Alignment explanation
Indices: 4566071--4566133 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
4566061 GTTTAAAACA
* *
4566071 TTTTTTGAAAATATGTATATTATATAG
1 TTTTTTGAAAATATATATAATATATAG
4566098 TTTTTTGAAAAT-TATATAATATATAG
1 TTTTTTGAAAATATATATAATATATAG
4566124 -TTTTTGAAAA
1 TTTTTTGAAAA
4566134 CGTTTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 10 0.29
26 12 0.35
27 12 0.35
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.51
Consensus pattern (27 bp):
TTTTTTGAAAATATATATAATATATAG
Found at i:4566140 original size:37 final size:36
Alignment explanation
Indices: 4566099--4566226 Score: 127
Period size: 37 Copynumber: 3.4 Consensus size: 36
4566089 ATTATATAGT
4566099 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACG
1 TTTTTGAAAATTATATAATATATA-TTTTTGAAAACG
*
4566136 TTTTT-AAAATATATATAATATATACTTTTGAAAACG
1 TTTTTGAAAAT-TATATAATATATATTTTTGAAAACG
* * *
4566172 -TTATGAAAACATTTATATAATATATAATTTTTAAAAAACC
1 TTTTTG-AAA-A-TTATATAATATAT-ATTTTT-GAAAACG
*
4566212 ATTTTGAAAA-TATAT
1 TTTTTGAAAATTATAT
4566227 TTTTTGAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
35 3 0.04
36 16 0.21
37 26 0.34
38 13 0.17
39 7 0.09
40 8 0.10
41 4 0.05
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (36 bp):
TTTTTGAAAATTATATAATATATATTTTTGAAAACG
Found at i:4566140 original size:65 final size:61
Alignment explanation
Indices: 4566034--4566291 Score: 163
Period size: 63 Copynumber: 4.0 Consensus size: 61
4566024 TTGCAAATTG
* * *
4566034 TTTTTGAAAATACATATATAATATATAGTTTAAAACATTTTTTGAAAATATGTATATTATATAGT
1 TTTTTGAAAAT--ATATATAATATATAGTTTAAAACA-TTTTT-AAAATATATATAATATATACT
*
4566099 TTTTTGAAAAT-TATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATAC-
1 TTTTTGAAAATATATATAATATATAG--TTT-AAAACATTTTTAAAATATATATAATATATACT
* * * * * * * * *
4566161 -TTTTGAAAACGT-TATGAAAACATTTA-TATAATATATAATTTTTAAAAAACCATTTTGAAAAT
1 TTTTTGAAAA--TATAT-ATAATATATAGTTTAA-A-A-CATTTTTAAAATA-TA-TAT-AATAT
4566223 ATA-T
57 ATACT
*
4566227 TTTTTGAAAAT-TATATAATATATAGTTTTTGAAAAC-GTTTTAAAATATATATAATATATACT
1 TTTTTGAAAATATATATAATATATAG--TTT-AAAACATTTTTAAAATATATATAATATATACT
4566289 TTT
1 TTT
4566292 GAAAACGTTA
Statistics
Matches: 150, Mismatches: 24, Indels: 41
0.70 0.11 0.19
Matches are distributed among these distances:
60 2 0.01
61 19 0.13
62 21 0.14
63 32 0.21
64 32 0.21
65 22 0.15
66 8 0.05
67 12 0.08
68 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (61 bp):
TTTTTGAAAATATATATAATATATAGTTTAAAACATTTTTAAAATATATATAATATATACT
Found at i:4566207 original size:27 final size:27
Alignment explanation
Indices: 4566177--4566277 Score: 75
Period size: 27 Copynumber: 3.7 Consensus size: 27
4566167 AAACGTTATG
4566177 AAAACATTTATATAATATATAATTTTTAA
1 AAAACATTT-TATAATATATAATTTTT-A
*
4566206 AAAACCATTTTGA-AA-ATAT-ATTTTTT
1 AAAA-CATTTT-ATAATATATAATTTTTA
* * * *
4566232 GAAA-ATTATATAATATATAGTTTTTG
1 AAAACATTTTATAATATATAATTTTTA
* *
4566258 AAAACGTTTTAAAATATATA
1 AAAACATTTTATAATATATA
4566278 TAATATATAC
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
23 1 0.02
24 6 0.11
25 4 0.07
26 11 0.19
27 18 0.32
28 4 0.07
29 7 0.12
30 6 0.11
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.44
Consensus pattern (27 bp):
AAAACATTTTATAATATATAATTTTTA
Found at i:4566233 original size:15 final size:16
Alignment explanation
Indices: 4566213--4566242 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4566203 TAAAAAACCA
4566213 TTTTGAAAA-TATATT
1 TTTTGAAAATTATATT
4566228 TTTTGAAAATTATAT
1 TTTTGAAAATTATAT
4566243 AATATATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTTGAAAATTATATT
Found at i:4566274 original size:25 final size:23
Alignment explanation
Indices: 4566212--4566275 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 23
4566202 TTAAAAAACC
*
4566212 ATTTTGAAAATATATTTTTTGAAA
1 ATTTT-AAAATATAGTTTTTGAAA
*
4566236 ATTATATAATATATAGTTTTTGAAA
1 ATT-T-TAAAATATAGTTTTTGAAA
4566261 ACGTTTTAAAATATA
1 A--TTTTAAAATATA
4566276 TATAATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
24 3 0.09
25 26 0.79
26 2 0.06
27 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (23 bp):
ATTTTAAAATATAGTTTTTGAAA
Found at i:4566282 original size:36 final size:37
Alignment explanation
Indices: 4566228--4566416 Score: 206
Period size: 39 Copynumber: 5.1 Consensus size: 37
4566218 AAAATATATT
4566228 TTTTGAAAAT-TATATAATATATAGTTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACG
*
4566264 TTTT-AAAATATATATAATATATA-CTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACG
* * * * *
4566299 TTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
1 TTTTG-AAA-ATATATATAATATATAGTTTTTGAAAA-CG
* *
4566339 TTTTGAAAATATATATAATATATAGTTTTTTTAAAAACA
1 TTTTGAAAATATATATAATATATAG--TTTTTGAAAACG
* * *
4566378 TTTTAAAAATTTATATATTATAT-GTTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACG
4566414 TTT
1 TTT
4566417 ATATATATAT
Statistics
Matches: 131, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
35 19 0.15
36 30 0.23
37 3 0.02
38 31 0.24
39 33 0.25
40 15 0.11
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACG
Found at i:4566301 original size:127 final size:127
Alignment explanation
Indices: 4566092--4566352 Score: 497
Period size: 127 Copynumber: 2.0 Consensus size: 127
4566082 TATGTATATT
4566092 ATATAGTTTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATAT
1 ATATA-TTTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATAT
4566157 ATACTTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAAACCATTTTGAAA
65 ATACTTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTT-AAAAACCATTTTGAAA
4566221 ATATATTTTTTGAAAATTATATAATATATAGTTTTTGAAAACG-TTTTAAAATATATATAATATA
1 ATATATTTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATA
4566285 TACTTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAA
66 TACTTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAA
4566347 ATATAT
1 ATATAT
4566353 ATAATATATA
Statistics
Matches: 132, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
126 22 0.17
127 67 0.51
128 38 0.29
129 5 0.04
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (127 bp):
ATATATTTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATA
TACTTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAA
Found at i:4567634 original size:19 final size:19
Alignment explanation
Indices: 4567610--4567662 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
4567600 ACCTTTAAAA
4567610 TAATTTTTTTTCATTTATT
1 TAATTTTTTTTCATTTATT
* *
4567629 TAATTTTTCTTCATTTTTT
1 TAATTTTTTTTCATTTATT
*
4567648 TTATTTTTTTT-ATTT
1 TAATTTTTTTTCATTT
4567663 GTTTTTCTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 4 0.13
19 26 0.87
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (19 bp):
TAATTTTTTTTCATTTATT
Found at i:4567667 original size:19 final size:18
Alignment explanation
Indices: 4567612--4567668 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
4567602 CTTTAAAATA
* *
4567612 ATTTTTTTTCATTTATTTA
1 ATTTTTTTT-ATTTTTTTT
*
4567631 ATTTTTCTTCATTTTTTTT
1 ATTTTT-TTTATTTTTTTT
4567650 ATTTTTTTTATTTGTTTTT
1 ATTTTTTTTATTT-TTTTT
4567669 CTATCTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.19
19 24 0.75
20 2 0.06
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (18 bp):
ATTTTTTTTATTTTTTTT
Found at i:4567668 original size:10 final size:9
Alignment explanation
Indices: 4567612--4567668 Score: 60
Period size: 9 Copynumber: 6.0 Consensus size: 9
4567602 CTTTAAAATA
4567612 ATTTTTTTT
1 ATTTTTTTT
* *
4567621 CATTTATTTA
1 -ATTTTTTTT
*
4567631 ATTTTTCTTC
1 ATTTTT-TTT
4567641 ATTTTTTTT
1 ATTTTTTTT
4567650 ATTTTTTTT
1 ATTTTTTTT
4567659 ATTTGTTTTT
1 ATTT-TTTTT
4567669 CTATCTAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
9 20 0.50
10 20 0.50
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:4568738 original size:17 final size:17
Alignment explanation
Indices: 4568718--4568750 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4568708 CTCACTAACC
*
4568718 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
4568735 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
4568751 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:4569401 original size:19 final size:19
Alignment explanation
Indices: 4569367--4569411 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
4569357 ATTTAGACGT
4569367 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
4569385 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
4569404 TTTGCATT
1 TTTGCATT
4569412 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:4572986 original size:84 final size:81
Alignment explanation
Indices: 4572796--4573637 Score: 771
Period size: 84 Copynumber: 10.2 Consensus size: 81
4572786 ACCTGCCACC
* * ** * * *
4572796 AAGACCTTTGAGTTCGACTACGCTCAGCTCCTAGGCACATCATTTATAGAATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCTAG
*
4572861 AAGGGCTATCTG-CCA
66 AAGGGTTATCTGACCA
* * * * * * * * * *
4572876 AAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCGTAACTCAAGGCTA
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCATATCATTTGCAGCATAACTTAAGTCTA
*
4572941 GAAGGGTTATCTGTTAGCA
65 GAAGGGTTATCTG--ACCA
* * * * *
4572960 AAGACCTTTGAGTTCGACTACGCTCAGCTCCTAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCTAG
*
4573025 AAGGGCTATCTG-CCA
66 AAGGGTTATCTGACCA
* * * * ** * * * * *
4573040 AAGACCCTTAAGTTCGATTACACTCAGCTTTAAGGGCATAACATTTACAACATAACTCAAGGCTA
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCATATCATTTGCAGCATAACTTAAGTCTA
*
4573105 GAAGGGTTATCTGTTAGCA
65 GAAGGGTTATCTG--ACCA
* * * *
4573124 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCTAG
*
4573189 AAGGGCTATCTG-CCA
66 AAGGGTTATCTGACCA
**** * * *** * *
4573204 AAGACCCCCAAGTTCGATTACACTCAGCTTCGGGGGCACATCATTTGCAGCATAACTTAAGTCGA
1 AAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGCATAACTTAAGTCTA
4573269 GAAGGGTTATCT-ACCAACAA
65 GAAGGGTTATCTGA-C--C-A
* ** *
4573289 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAATACAACTTAAGTCTAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCTAG
*
4573354 AAGGGTTATCTGCCAACAA
66 AAGGGTTATCTG---ACCA
* ** *
4573373 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAATACAACTTAAGTCTAG
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCTAG
* *
4573438 AAGGGTTGTCTGCCAACAA
66 AAGGGTTATCTG---ACCA
* * *
4573457 AAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCATATCATTTACAGCATAACTCAAGGCTA
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCATATCATTTGCAGCATAACTTAAGTCTA
4573521 GAAGGGTTATCTGTGACCAA
65 GAAGGGTTATC--TGACC-A
* * * *
4573541 AAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT-TGA
1 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCT-A
* *
4573605 GAAGGGCTATCTG-CTA
65 GAAGGGTTATCTGACCA
*
4573621 AAGACCTTCGAGTTCGA
1 AAGACCTTTGAGTTCGA
4573638 TTATATTCAA
Statistics
Matches: 624, Mismatches: 114, Indels: 48
0.79 0.15 0.06
Matches are distributed among these distances:
80 97 0.16
81 111 0.18
82 3 0.00
83 74 0.12
84 308 0.49
85 27 0.04
86 2 0.00
87 1 0.00
88 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (81 bp):
AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCTAG
AAGGGTTATCTGACCA
Found at i:4573038 original size:164 final size:165
Alignment explanation
Indices: 4572768--4573533 Score: 918
Period size: 164 Copynumber: 4.6 Consensus size: 165
4572758 TGCAGCTTAG
* * * * *
4572768 CTCAAGGCCAGAAGGGCTACCTGCC-AC-CAAGACCTTTGAGTTCGACTACGCTCAGCTCCTAGG
1 CTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
**
4572831 CACATCATTTATAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTA
66 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTA
* *
4572896 CACTCAGCTTCAAGGGCATAACATTTACAGCGTAA
131 CACTCAGCTTCAAGGGCATAACATTTACAACATAA
** * *
4572931 CTCAAGGCTAGAAGGGTTATCTGTTAGC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCTAGG
1 CTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
4572995 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTA
66 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTA
*
4573060 CACTCAGCTTTAAGGGCATAACATTTACAACATAA
131 CACTCAGCTTCAAGGGCATAACATTTACAACATAA
** *
4573095 CTCAAGGCTAGAAGGGTTATCTGTTAGC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
* **
4573159 CACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTA
66 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTA
** * * * *
4573224 CACTCAGCTTCGGGGGCACATCATTTGCAGCATAA
131 CACTCAGCTTCAAGGGCATAACATTTACAACATAA
* * * * *
4573259 CTTAAGTCGAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
* * * * * *
4573324 CATATCATTTGCA-ATACAACTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGA-CCTTCGAGTT
66 CACATCATTTGCAGA-ATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCTT-AAGTT
* * * * * * *
4573387 CGACTACGCTCAGCTCCAA-GGCATATCATTTGCAATACAA
125 CGATTACACTCAGCTTCAAGGGCATAACATTTACAACATAA
* * *
4573427 CTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACG
1 CTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-G
* * * * * * * *
4573491 GCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
65 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG
4573534 TGACCAAAAG
Statistics
Matches: 535, Mismatches: 58, Indels: 15
0.88 0.10 0.02
Matches are distributed among these distances:
163 20 0.04
164 305 0.57
165 70 0.13
166 1 0.00
167 3 0.01
168 113 0.21
169 23 0.04
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (165 bp):
CTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTA
CACTCAGCTTCAAGGGCATAACATTTACAACATAA
Found at i:4574339 original size:26 final size:27
Alignment explanation
Indices: 4574295--4574357 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
4574285 GTTTAAAACA
* *
4574295 TTTTTTGAAAATATGTATATTATATAG
1 TTTTTTGAAAATATATATAATATATAG
4574322 TTTTTTGAAAAT-TATATAATATATAG
1 TTTTTTGAAAATATATATAATATATAG
4574348 -TTTTTGAAAA
1 TTTTTTGAAAA
4574358 CGTTTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 10 0.29
26 12 0.35
27 12 0.35
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.51
Consensus pattern (27 bp):
TTTTTTGAAAATATATATAATATATAG
Found at i:4574364 original size:37 final size:36
Alignment explanation
Indices: 4574323--4574450 Score: 127
Period size: 37 Copynumber: 3.4 Consensus size: 36
4574313 ATTATATAGT
4574323 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACG
1 TTTTTGAAAATTATATAATATATA-TTTTTGAAAACG
*
4574360 TTTTT-AAAATATATATAATATATACTTTTGAAAACG
1 TTTTTGAAAAT-TATATAATATATATTTTTGAAAACG
* * *
4574396 -TTATGAAAACATTTATATAATATATAATTTTTAAAAAACC
1 TTTTTG-AAA-A-TTATATAATATAT-ATTTTT-GAAAACG
*
4574436 ATTTTGAAAA-TATAT
1 TTTTTGAAAATTATAT
4574451 TTTTTGAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
35 3 0.04
36 16 0.21
37 26 0.34
38 13 0.17
39 7 0.09
40 8 0.10
41 4 0.05
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (36 bp):
TTTTTGAAAATTATATAATATATATTTTTGAAAACG
Found at i:4574364 original size:65 final size:61
Alignment explanation
Indices: 4574258--4574515 Score: 163
Period size: 63 Copynumber: 4.0 Consensus size: 61
4574248 TTGCAAATTG
* * *
4574258 TTTTTGAAAATACATATATAATATATAGTTTAAAACATTTTTTGAAAATATGTATATTATATAGT
1 TTTTTGAAAAT--ATATATAATATATAGTTTAAAACA-TTTTT-AAAATATATATAATATATACT
*
4574323 TTTTTGAAAAT-TATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATAC-
1 TTTTTGAAAATATATATAATATATAG--TTT-AAAACATTTTTAAAATATATATAATATATACT
* * * * * * * * *
4574385 -TTTTGAAAACGT-TATGAAAACATTTA-TATAATATATAATTTTTAAAAAACCATTTTGAAAAT
1 TTTTTGAAAA--TATAT-ATAATATATAGTTTAA-A-A-CATTTTTAAAATA-TA-TAT-AATAT
4574447 ATA-T
57 ATACT
*
4574451 TTTTTGAAAAT-TATATAATATATAGTTTTTGAAAAC-GTTTTAAAATATATATAATATATACT
1 TTTTTGAAAATATATATAATATATAG--TTT-AAAACATTTTTAAAATATATATAATATATACT
4574513 TTT
1 TTT
4574516 GAAAACGTTA
Statistics
Matches: 150, Mismatches: 24, Indels: 41
0.70 0.11 0.19
Matches are distributed among these distances:
60 2 0.01
61 19 0.13
62 21 0.14
63 32 0.21
64 32 0.21
65 22 0.15
66 8 0.05
67 12 0.08
68 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (61 bp):
TTTTTGAAAATATATATAATATATAGTTTAAAACATTTTTAAAATATATATAATATATACT
Found at i:4574431 original size:27 final size:27
Alignment explanation
Indices: 4574401--4574501 Score: 75
Period size: 27 Copynumber: 3.7 Consensus size: 27
4574391 AAACGTTATG
4574401 AAAACATTTATATAATATATAATTTTTAA
1 AAAACATTT-TATAATATATAATTTTT-A
*
4574430 AAAACCATTTTGA-AA-ATAT-ATTTTTT
1 AAAA-CATTTT-ATAATATATAATTTTTA
* * * *
4574456 GAAA-ATTATATAATATATAGTTTTTG
1 AAAACATTTTATAATATATAATTTTTA
* *
4574482 AAAACGTTTTAAAATATATA
1 AAAACATTTTATAATATATA
4574502 TAATATATAC
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
23 1 0.02
24 6 0.11
25 4 0.07
26 11 0.19
27 18 0.32
28 4 0.07
29 7 0.12
30 6 0.11
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.44
Consensus pattern (27 bp):
AAAACATTTTATAATATATAATTTTTA
Found at i:4574457 original size:15 final size:16
Alignment explanation
Indices: 4574437--4574466 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4574427 TAAAAAACCA
4574437 TTTTGAAAA-TATATT
1 TTTTGAAAATTATATT
4574452 TTTTGAAAATTATAT
1 TTTTGAAAATTATAT
4574467 AATATATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTTGAAAATTATATT
Found at i:4574498 original size:25 final size:23
Alignment explanation
Indices: 4574436--4574499 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 23
4574426 TTAAAAAACC
*
4574436 ATTTTGAAAATATATTTTTTGAAA
1 ATTTT-AAAATATAGTTTTTGAAA
*
4574460 ATTATATAATATATAGTTTTTGAAA
1 ATT-T-TAAAATATAGTTTTTGAAA
4574485 ACGTTTTAAAATATA
1 A--TTTTAAAATATA
4574500 TATAATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
24 3 0.09
25 26 0.79
26 2 0.06
27 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (23 bp):
ATTTTAAAATATAGTTTTTGAAA
Found at i:4574506 original size:36 final size:37
Alignment explanation
Indices: 4574452--4574640 Score: 206
Period size: 39 Copynumber: 5.1 Consensus size: 37
4574442 AAAATATATT
4574452 TTTTGAAAAT-TATATAATATATAGTTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACG
*
4574488 TTTT-AAAATATATATAATATATA-CTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACG
* * * * *
4574523 TTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
1 TTTTG-AAA-ATATATATAATATATAGTTTTTGAAAA-CG
* *
4574563 TTTTGAAAATATATATAATATATAGTTTTTTTAAAAACA
1 TTTTGAAAATATATATAATATATAG--TTTTTGAAAACG
* * *
4574602 TTTTAAAAATTTATATATTATAT-GTTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACG
4574638 TTT
1 TTT
4574641 ATATATATAT
Statistics
Matches: 131, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
35 19 0.15
36 30 0.23
37 3 0.02
38 31 0.24
39 33 0.25
40 15 0.11
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACG
Found at i:4574525 original size:127 final size:127
Alignment explanation
Indices: 4574316--4574576 Score: 497
Period size: 127 Copynumber: 2.0 Consensus size: 127
4574306 TATGTATATT
4574316 ATATAGTTTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATAT
1 ATATA-TTTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATAT
4574381 ATACTTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAAACCATTTTGAAA
65 ATACTTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTT-AAAAACCATTTTGAAA
4574445 ATATATTTTTTGAAAATTATATAATATATAGTTTTTGAAAACG-TTTTAAAATATATATAATATA
1 ATATATTTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATA
4574509 TACTTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAA
66 TACTTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAA
4574571 ATATAT
1 ATATAT
4574577 ATAATATATA
Statistics
Matches: 132, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
126 22 0.17
127 67 0.51
128 38 0.29
129 5 0.04
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (127 bp):
ATATATTTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATA
TACTTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAA
Found at i:4575857 original size:20 final size:20
Alignment explanation
Indices: 4575834--4575889 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
4575824 ACCTTTAAAA
4575834 TAATTTTTTTTTCATTTATT
1 TAATTTTTTTTTCATTTATT
*
4575854 TAA-TTTTTCTTCATTT-TT
1 TAATTTTTTTTTCATTTATT
*
4575872 T--TTTATTTTT-ATTTATT
1 TAATTTTTTTTTCATTTATT
4575889 T
1 T
4575890 GTTTTTCTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 4 0.13
17 9 0.29
18 3 0.10
19 12 0.39
20 3 0.10
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (20 bp):
TAATTTTTTTTTCATTTATT
Found at i:4575871 original size:10 final size:10
Alignment explanation
Indices: 4575838--4575896 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
4575828 TTAAAATAAT
4575838 TTTTTTTTCA
1 TTTTTTTTCA
* *
4575848 -TTTATTTAA
1 TTTTTTTTCA
*
4575857 TTTTTCTTCA
1 TTTTTTTTCA
*
4575867 TTTTTTTTTA
1 TTTTTTTTCA
4575877 TTTTTATTT-A
1 TTTTT-TTTCA
4575887 TTTGTTTTTC
1 TTT-TTTTTC
4575897 TATCTAATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
9 7 0.18
10 26 0.68
11 5 0.13
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.78
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:4579586 original size:16 final size:17
Alignment explanation
Indices: 4579565--4579616 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
4579555 TTTCTAATTT
4579565 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
4579581 AATTACTCATAA-TTT--
1 AATTACTC-TAACTTTCA
*
4579596 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
4579613 AATT
1 AATT
4579617 TTATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 10 0.34
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:4580694 original size:44 final size:44
Alignment explanation
Indices: 4580532--4580756 Score: 160
Period size: 45 Copynumber: 5.1 Consensus size: 44
4580522 TCTATCCTTA
* * * *
4580532 TTTTTATAATCAT-ACTTTTTATCTTTAAAATTGAGATTTCTAATAT
1 TTTTTA-AATC-TCACTTTTTACCTTTATAATTGAGACTCCTAAT-T
* * * *
4580578 TTTTTAAATCTCATTTTTTA-TTTATATAATTGAG-GTCTTTAATT
1 TTTTTAAATCTCACTTTTTACCTT-TATAATTGAGACTC-CTAATT
* ** *
4580622 TTTTTCAATCAT-GTTTTCTTACTTTTATAATTGAGACTCCTAATT
1 TTTTTAAATC-TCACTTT-TTACCTTTATAATTGAGACTCCTAATT
*
4580667 TTTTT-AATCTCAACTTTTTACCTTTATAATTAAGAC-CCTTAATT
1 TTTTTAAATCTC-ACTTTTTACCTTTATAATTGAGACTCC-TAATT
* * *
4580711 TTTTTAATTCTC-CTTTCTACATTTATAATTGAGAC-CTCTAATT
1 TTTTTAAATCTCACTTTTTACCTTTATAATTGAGACTC-CTAATT
4580754 TTT
1 TTT
4580757 AAAATTTCAT
Statistics
Matches: 149, Mismatches: 18, Indels: 27
0.77 0.09 0.14
Matches are distributed among these distances:
43 32 0.21
44 50 0.34
45 56 0.38
46 11 0.07
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (44 bp):
TTTTTAAATCTCACTTTTTACCTTTATAATTGAGACTCCTAATT
Found at i:4580736 original size:43 final size:43
Alignment explanation
Indices: 4580636--4580756 Score: 140
Period size: 43 Copynumber: 2.8 Consensus size: 43
4580626 TCAATCATGT
*
4580636 TTTCTTACTTTTATAATTGAGACTCC-TAATTTTTTTAATCTCAAC
1 TTTC-TACATTTATAATTGAGAC-CCTTAATTTTTTTAATCTC-AC
* * *
4580681 TTTTTACCTTTATAATTAAGACCCTTAATTTTTTTAATTCTC-C
1 TTTCTACATTTATAATTGAGACCCTTAATTTTTTTAA-TCTCAC
4580724 TTTCTACATTTATAATTGAGA-CCTCTAATTTTT
1 TTTCTACATTTATAATTGAGACCCT-TAATTTTT
4580757 AAAATTTCAT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
42 3 0.04
43 29 0.43
44 28 0.42
45 7 0.10
ACGTcount: A:0.26, C:0.17, G:0.04, T:0.52
Consensus pattern (43 bp):
TTTCTACATTTATAATTGAGACCCTTAATTTTTTTAATCTCAC
Found at i:4581011 original size:23 final size:22
Alignment explanation
Indices: 4580960--4581012 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
4580950 TTGCACATTT
* *
4580960 CAATATTAATTTTCTATTATAA
1 CAATAATAATTTTATATTATAA
*
4580982 CAGTAATAATTTTATAGTTATAA
1 CAATAATAATTTTATA-TTATAA
*
4581005 TAATAATA
1 CAATAATA
4581013 GTAGTGATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (22 bp):
CAATAATAATTTTATATTATAA
Found at i:4581022 original size:18 final size:18
Alignment explanation
Indices: 4580996--4581030 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4580986 AATAATTTTA
* *
4580996 TAGTTATAATAATAATAG
1 TAGTGATAACAATAATAG
4581014 TAGTGATAACAATAATA
1 TAGTGATAACAATAATA
4581031 ATGATAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.34
Consensus pattern (18 bp):
TAGTGATAACAATAATAG
Found at i:4581711 original size:20 final size:20
Alignment explanation
Indices: 4581671--4581714 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
4581661 TATTCCATGG
*
4581671 TAATTTTTTATTCTCCCTGA
1 TAATTTTTTATTCTCACTGA
*
4581691 TAATTTTTTATTCTCAGTGA
1 TAATTTTTTATTCTCACTGA
4581711 TAAT
1 TAAT
4581715 CTTATATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.55
Consensus pattern (20 bp):
TAATTTTTTATTCTCACTGA
Found at i:4581725 original size:18 final size:18
Alignment explanation
Indices: 4581704--4581738 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4581694 TTTTTTATTC
4581704 TCAGTGATAATCTTATAT
1 TCAGTGATAATCTTATAT
*
4581722 TCAGTGGTAATCTTATA
1 TCAGTGATAATCTTATA
4581739 AGTGAATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (18 bp):
TCAGTGATAATCTTATAT
Found at i:4585419 original size:5 final size:5
Alignment explanation
Indices: 4585409--4585592 Score: 258
Period size: 5 Copynumber: 37.4 Consensus size: 5
4585399 AAAACGAATC
4585409 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
4585459 ATAAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT A-ATAT AATAAT
1 AT-AAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT -ATAAT
4585510 ATAAT AT-A- ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
*
4585556 ATAAT AT-AT A-ATAT AATAAT ATAAT ATAAC ATAAT AT
1 ATAAT ATAAT ATA-AT -ATAAT ATAAT ATAAT ATAAT AT
4585593 CTTTTTCAAA
Statistics
Matches: 164, Mismatches: 2, Indels: 26
0.85 0.01 0.14
Matches are distributed among these distances:
3 4 0.02
4 10 0.06
5 137 0.84
6 11 0.07
7 2 0.01
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:4585515 original size:66 final size:67
Alignment explanation
Indices: 4585410--4585584 Score: 200
Period size: 66 Copynumber: 2.5 Consensus size: 67
4585400 AAACGAATCA
4585410 TAATATAATATAATATAATAT-A-ATATAATATAATATAATATAATATAATATAAATATAATATA
1 TAATATAATATAATATAATATAATATATAATAT-A-ATAATATAATATAA-AT-AATATAATAT-
4585473 ATATAATA
61 A-ATAATA
4585481 TAATATAATATAATATATAATATAATAATATAATATAATAATATAATAT-AATAATAT-A-AT-A
1 TAATATAATAT-A-ATATAATATAAT-ATATAATATAATAATATAATATAAATAATATAATATAA
4585542 TAATA
63 TAATA
4585547 TAATATAATATAATATATAATATAATAATATAATATAA
1 TAATATAATAT-A-ATATAATATAAT-ATATAATATAA
4585585 CATAATATCT
Statistics
Matches: 99, Mismatches: 0, Indels: 15
0.87 0.00 0.13
Matches are distributed among these distances:
66 44 0.44
69 2 0.02
70 1 0.01
71 16 0.16
72 3 0.03
73 10 0.10
74 13 0.13
75 1 0.01
76 9 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (67 bp):
TAATATAATATAATATAATATAATATATAATATAATAATATAATATAAATAATATAATATAATAA
TA
Found at i:4589600 original size:35 final size:35
Alignment explanation
Indices: 4589554--4589665 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
4589544 AAAATATTCC
* * *
4589554 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
4589589 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
** * * *
4589624 TCAATTAAATTTTAAACCCTAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
4589659 TCAATTT
1 TCAATTT
4589666 AAGGTTTAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
Found at i:4592358 original size:18 final size:18
Alignment explanation
Indices: 4592335--4592371 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4592325 AAGGTTATAC
4592335 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
4592353 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
4592371 A
1 A
4592372 TATATAGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:4593324 original size:19 final size:19
Alignment explanation
Indices: 4593300--4593348 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
4593290 CTGCTCACGG
4593300 TACTGTTCATACCATATTT
1 TACTGTTCATACCATATTT
4593319 TACTGTTCATACCATATTT
1 TACTGTTCATACCATATTT
*
4593338 TACTATTCATA
1 TACTGTTCATA
4593349 AAAACTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (19 bp):
TACTGTTCATACCATATTT
Found at i:4595162 original size:35 final size:35
Alignment explanation
Indices: 4595123--4595198 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
4595113 AAAACAATCA
*
4595123 TCAATTTCATTCTAAACCCCAATTTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
4595158 TCAATTTCATTTTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
4595193 TCAATT
1 TCAATT
4595199 AAATTTAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:4595738 original size:135 final size:130
Alignment explanation
Indices: 4595596--4595848 Score: 389
Period size: 135 Copynumber: 1.9 Consensus size: 130
4595586 TATTTATATA
* * **
4595596 ATCAATTTGGTCTTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
4595661 TTAGCACATGATCATGTCATGACACGTGTCATTGGTGACACATGTCACTACCTAATTATTTATAT
66 TTAACACATGATCATG--AT-ACA--TGTCATTGGTGACACATGTCACCACCTAATTATTTATAT
4595726 ATGCT
126 ATGCT
4595731 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
4595796 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGATACATGTCATTGGTGACACATGTCACCACCTAATTA
4595849 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
130 30 0.27
132 2 0.02
133 2 0.02
135 76 0.69
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGATACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:4596332 original size:16 final size:18
Alignment explanation
Indices: 4596311--4596344 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
4596301 ATTTCTTATT
4596311 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
4596327 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
4596345 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:4596401 original size:30 final size:30
Alignment explanation
Indices: 4596344--4596401 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
4596334 TAAATGATTC
* **
4596344 ATACATTAATATATGAATATATTTTTATTT
1 ATACATTAATATATAAATATACATTTATTT
4596374 ATACATCTAA-ATATAAATATACATTTAT
1 ATACAT-TAATATATAAATATACATTTAT
4596402 ATAAATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (30 bp):
ATACATTAATATATAAATATACATTTATTT
Found at i:4616651 original size:19 final size:19
Alignment explanation
Indices: 4616627--4616695 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
4616617 ATGACCAACA
* * *
4616627 AATTCGTAACGCGATCTCG
1 AATTCGCAACGCGAACTCC
*
4616646 AATTCGCAACACGAACTCC
1 AATTCGCAACGCGAACTCC
**
4616665 AATTTCGCAACGCGAATCTAT
1 AA-TTCGCAACGCGAA-CTCC
4616686 AATTCGCAAC
1 AATTCGCAAC
4616696 ACAGAAGTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 17 0.41
20 20 0.49
21 4 0.10
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.23
Consensus pattern (19 bp):
AATTCGCAACGCGAACTCC
Found at i:4616709 original size:20 final size:18
Alignment explanation
Indices: 4616646--4616710 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 18
4616636 CGCGATCTCG
4616646 AATTCGCAACACGAACTCCA
1 AATTCGCAACACGAA-T-CA
* *
4616666 ATTTCGCAACGCGAATCTA
1 AATTCGCAACACGAATC-A
4616685 TAATTCGCAACACAGAAGTCA
1 -AATTCGCAACAC-GAA-TCA
4616706 AATTC
1 AATTC
4616711 ACAAAGCGCG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.03
19 2 0.05
20 28 0.76
21 4 0.11
22 2 0.05
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (18 bp):
AATTCGCAACACGAATCA
Found at i:4617286 original size:19 final size:20
Alignment explanation
Indices: 4617264--4617315 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
4617254 ATCGCAACGA
4617264 GATTTT-AGTTTCGCGTTGC
1 GATTTTAAGTTTCGCGTTGC
* * *
4617283 GATTTTCATTTTCGCGTTGT
1 GATTTTAAGTTTCGCGTTGC
*
4617303 AATTTTAAGTTTC
1 GATTTTAAGTTTC
4617316 AGAAACTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.15, C:0.13, G:0.19, T:0.52
Consensus pattern (20 bp):
GATTTTAAGTTTCGCGTTGC
Found at i:4619136 original size:62 final size:61
Alignment explanation
Indices: 4619029--4619149 Score: 145
Period size: 62 Copynumber: 2.0 Consensus size: 61
4619019 AGGTCGGTAC
* * * *
4619029 TTTACGTGAAGTCAATGGTGCATGGCGTGATGAGGTACGGTCTTTACGTGGTGAAGTAGAGT
1 TTTACGCGAAGACAATGGTGCATGACGTGATGAGGTAC-GTCTTTACGTGATGAAGTAGAGT
* * *
4619091 TTTACGCGAAGACAATGGTGCATTACGTGGTGAGGTATC-TACTTTACGTGATGAGGTAG
1 TTTACGCGAAGACAATGGTGCATGACGTGATGAGGTA-CGT-CTTTACGTGATGAAGTAG
4619150 CCGCTCTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
61 1 0.02
62 48 0.96
63 1 0.02
ACGTcount: A:0.24, C:0.12, G:0.33, T:0.31
Consensus pattern (61 bp):
TTTACGCGAAGACAATGGTGCATGACGTGATGAGGTACGTCTTTACGTGATGAAGTAGAGT
Found at i:4619495 original size:21 final size:21
Alignment explanation
Indices: 4619444--4619604 Score: 114
Period size: 21 Copynumber: 7.7 Consensus size: 21
4619434 GATTCACCTG
* **
4619444 TCATCGTTCAAGAGGCGTCTC
1 TCATCCTTCAAGAGGCCCCTC
* *
4619465 -CTATCGTTCAAGAGGCCCCTA
1 TC-ATCCTTCAAGAGGCCCCTC
*
4619486 TCATCCTTCAAGATGCCCCTC
1 TCATCCTTCAAGAGGCCCCTC
* * *
4619507 CCA-CCGTTCAAGAGGCCCATG
1 TCATCC-TTCAAGAGGCCCCTC
* *
4619528 TCATCGTTCAAGAGGTCCCTC
1 TCATCCTTCAAGAGGCCCCTC
* *
4619549 CCA-CCGTTCAAGAGGCCCCTG
1 TCATCC-TTCAAGAGGCCCCTC
* *
4619570 TCATCGTTCAAGAGGTCCCTC
1 TCATCCTTCAAGAGGCCCCTC
*
4619591 CCA-CCATTCAAGAG
1 TCATCC-TTCAAGAG
4619605 CCCGATTCAC
Statistics
Matches: 108, Mismatches: 25, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
20 5 0.05
21 100 0.93
22 3 0.03
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCCTTCAAGAGGCCCCTC
Found at i:4619496 original size:42 final size:41
Alignment explanation
Indices: 4619440--4619604 Score: 222
Period size: 42 Copynumber: 3.9 Consensus size: 41
4619430 GCTCGATTCA
* * *
4619440 CCTGTCATCGTTCAAGAGGCGTCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGC-CCTCCCACCGTTCAAGAGGCC
* * *
4619482 CCTATCATCCTTCAAGATGCCCCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGA-GGCCCTCCCACCGTTCAAGAGGCC
*
4619524 CATGTCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGG-CCCTCCCACCGTTCAAGAGGCC
*
4619566 CCTGTCATCGTTCAAGAGGTCCCTCCCACCATTCAAGAG
1 CCTGTCATCGTTCAAGAGG-CCCTCCCACCGTTCAAGAG
4619605 CCCGATTCAC
Statistics
Matches: 109, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
41 1 0.01
42 106 0.97
43 2 0.02
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.23
Consensus pattern (41 bp):
CCTGTCATCGTTCAAGAGGCCCTCCCACCGTTCAAGAGGCC
Found at i:4621041 original size:78 final size:78
Alignment explanation
Indices: 4620949--4621099 Score: 257
Period size: 78 Copynumber: 1.9 Consensus size: 78
4620939 AATTTATTTG
*
4620949 TAAAAGTTGATTTGTTTAATTGATGAGGAAATAATAATTATTTTTTGCTTGTTTAATTGATTTGT
1 TAAAAGTTGATTTGTTTAATTGATGAGGAAATAATAATTAATTTTTGCTTGTTTAATTGATTTGT
4621014 AAAAGTTGCTTTA
66 AAAAGTTGCTTTA
* * **
4621027 TAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTAATTTTTGCTTGTTTAATTGATTTGT
1 TAAAAGTTGATTTGTTTAATTGATGAGGAAATAATAATTAATTTTTGCTTGTTTAATTGATTTGT
4621092 AAAAGTTG
66 AAAAGTTG
4621100 ATTTGTTGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 68 1.00
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.50
Consensus pattern (78 bp):
TAAAAGTTGATTTGTTTAATTGATGAGGAAATAATAATTAATTTTTGCTTGTTTAATTGATTTGT
AAAAGTTGCTTTA
Found at i:4621093 original size:37 final size:37
Alignment explanation
Indices: 4620960--4621094 Score: 110
Period size: 37 Copynumber: 3.5 Consensus size: 37
4620950 AAAAGTTGAT
* * ** *
4620960 TTGTTTAATTGATGAGGAAATAATAATTATTTTTTGC
1 TTGTTTAATTGATGTGTAAATAATTCTTAATTTTTGC
* * *** *
4620997 TTGTTTAATTGATTTGTAAA-AGTTGCTTTATAAAAGTTGAT
1 TTGTTTAATTGATGTGTAAATAATT-C--T-TAATTTTTG-C
4621038 TTGTTTAATTGATGTGTAAATAATTCTTAATTTTTGC
1 TTGTTTAATTGATGTGTAAATAATTCTTAATTTTTGC
*
4621075 TTGTTTAATTGATTTGTAAA
1 TTGTTTAATTGATGTGTAAA
4621095 AGTTGATTTG
Statistics
Matches: 74, Mismatches: 18, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
36 2 0.03
37 36 0.49
38 6 0.08
39 2 0.03
40 5 0.07
41 20 0.27
42 3 0.04
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (37 bp):
TTGTTTAATTGATGTGTAAATAATTCTTAATTTTTGC
Found at i:4621257 original size:29 final size:29
Alignment explanation
Indices: 4621223--4621280 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
4621213 ATTCGCGTTT
*
4621223 CGAATTTGACTTTCACAACAATCGCAACA
1 CGAATTTGAATTTCACAACAATCGCAACA
* *
4621252 CGAATTTGAATTTCGCAATAATCGCAACA
1 CGAATTTGAATTTCACAACAATCGCAACA
4621281 AAAAATCGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (29 bp):
CGAATTTGAATTTCACAACAATCGCAACA
Found at i:4621535 original size:12 final size:12
Alignment explanation
Indices: 4621520--4621560 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
4621510 AAGCCGGTTG
*
4621520 TGATTGGGATTT
1 TGATTGCGATTT
**
4621532 TGATTTTGATTT
1 TGATTGCGATTT
4621544 TGATTGCGATTT
1 TGATTGCGATTT
4621556 TGATT
1 TGATT
4621561 TCCTTTTGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.17, C:0.02, G:0.24, T:0.56
Consensus pattern (12 bp):
TGATTGCGATTT
Found at i:4621536 original size:6 final size:6
Alignment explanation
Indices: 4621527--4621561 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
4621517 TTGTGATTGG
**
4621527 GATTTT GATTTT GATTTT GATTGC GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
4621562 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:4624638 original size:14 final size:14
Alignment explanation
Indices: 4624605--4624638 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4624595 AGAAATCATT
4624605 AAAAAATTATATAA
1 AAAAAATTATATAA
* *
4624619 ATAAAATTATGTAA
1 AAAAAATTATATAA
4624633 AAAAAA
1 AAAAAA
4624639 AATTAGAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAAAATTATATAA
Found at i:4624824 original size:20 final size:20
Alignment explanation
Indices: 4624780--4624868 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
4624770 CAAAACATTT
*
4624780 GTGTTGCGAAACTAAAA--C
1 GTGTTGCGAAATTAAAATTC
*
4624798 CTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
*
4624818 GTGTTGCG-AATTAAGAAATC
1 GTGTTGCGAAATTAA-AATTC
* * *
4624838 GAGTTAC-AAATTTGAAATTC
1 GTGTTGCGAAA-TTAAAATTC
4624858 AGTGTTGCGAA
1 -GTGTTGCGAA
4624869 CGTTTCGAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
18 15 0.28
19 6 0.11
20 23 0.43
21 8 0.15
22 2 0.04
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:4630477 original size:175 final size:175
Alignment explanation
Indices: 4630186--4630540 Score: 701
Period size: 175 Copynumber: 2.0 Consensus size: 175
4630176 TTAATATTTA
4630186 ATAATCTAAATGGTGGTTCAGTAAACATACGTTCATGTACGATGTATATCTATGTGCATGTTTTT
1 ATAATCTAAATGGTGGTTCAGTAAACATACGTTCATGTACGATGTATATCTATGTGCATGTTTTT
4630251 CGCTATATATATATGTGGGATGCTGTATCGAATATTTCCTTTCTTTATACAAAACATTTACATGA
66 CGCTATATATATATGTGGGATGCTGTATCGAATATTTCCTTTCTTTATACAAAACATTTACATGA
4630316 GATCTGAAAACAAAAGTGACTAGTATAACTGTATTTGATAACTTT
131 GATCTGAAAACAAAAGTGACTAGTATAACTGTATTTGATAACTTT
4630361 ATAATCTAAATGGTGGTTCAGTAAACATACGTTCATGTACGATGTATATCTATGTGCATGTTTTT
1 ATAATCTAAATGGTGGTTCAGTAAACATACGTTCATGTACGATGTATATCTATGTGCATGTTTTT
*
4630426 CGGTATATATATATGTGGGATGCTGTATCGAATATTTCCTTTCTTTATACAAAACATTTACATGA
66 CGCTATATATATATGTGGGATGCTGTATCGAATATTTCCTTTCTTTATACAAAACATTTACATGA
4630491 GATCTGAAAACAAAAGTGACTAGTATAACTGTATTTGATAACTTT
131 GATCTGAAAACAAAAGTGACTAGTATAACTGTATTTGATAACTTT
4630536 ATAAT
1 ATAAT
4630541 GCATCATAAT
Statistics
Matches: 179, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 179 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (175 bp):
ATAATCTAAATGGTGGTTCAGTAAACATACGTTCATGTACGATGTATATCTATGTGCATGTTTTT
CGCTATATATATATGTGGGATGCTGTATCGAATATTTCCTTTCTTTATACAAAACATTTACATGA
GATCTGAAAACAAAAGTGACTAGTATAACTGTATTTGATAACTTT
Found at i:4634560 original size:15 final size:16
Alignment explanation
Indices: 4634540--4634580 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4634530 GTTTACTTCA
*
4634540 GAATGATT-AAGCGTT
1 GAATGATTCAAACGTT
*
4634555 GAATGATTCAAATGTT
1 GAATGATTCAAACGTT
4634571 GAATGATTCA
1 GAATGATTCA
4634581 GAGGCTCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (16 bp):
GAATGATTCAAACGTT
Found at i:4638422 original size:12 final size:12
Alignment explanation
Indices: 4638399--4638423 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4638389 AATGAATTGA
4638399 TAAACGAGTTTG
1 TAAACGAGTTTG
4638411 TAAACGAGTTTG
1 TAAACGAGTTTG
4638423 T
1 T
4638424 TCATGAACAT
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:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (12 bp):
TAAACGAGTTTG
Found at i:4642808 original size:14 final size:14
Alignment explanation
Indices: 4642782--4642820 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
4642772 GGTCAAAGAA
*
4642782 AGTCAATGGTCAAC
1 AGTCAACGGTCAAC
*
4642796 AGTTAACGGTCAAC
1 AGTCAACGGTCAAC
*
4642810 GGTCAACGGTC
1 AGTCAACGGTC
4642821 CGATCGGGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.21
Consensus pattern (14 bp):
AGTCAACGGTCAAC
Found at i:4642888 original size:19 final size:19
Alignment explanation
Indices: 4642864--4642938 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
4642854 GTCGGGTCAG
*
4642864 ACCGGTCAAACCGGTTCGA
1 ACCGGTCAAACCGGTTCAA
*
4642883 ACCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTCAA
*
4642902 ACCGGTCAGAACCGGTTGAAA
1 ACCGGTCA-AACCGGTT-CAA
* *
4642923 ACCGATTAAACCGGTT
1 ACCGGTCAAACCGGTT
4642939 TCCAGCAGCC
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
18 2 0.04
19 19 0.41
20 17 0.37
21 8 0.17
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAA
Found at i:4642906 original size:29 final size:31
Alignment explanation
Indices: 4642864--4642938 Score: 111
Period size: 29 Copynumber: 2.5 Consensus size: 31
4642854 GTCGGGTCAG
4642864 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
4642893 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
* *
4642923 ACCGATTAAACCGGTT
1 ACCGGTCAAACCGGTT
4642939 TCCAGCAGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.59
30 14 0.34
31 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:4650134 original size:5 final size:5
Alignment explanation
Indices: 4650120--4650177 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
4650110 AACGGTCAAC
* * *
4650120 GGTCG AGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC--G GGTCG
4650169 GGTCG GGTC
1 GGTCG GGTC
4650178 AACGGTCAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 35 0.81
7 8 0.19
ACGTcount: A:0.09, C:0.22, G:0.50, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:4650145 original size:34 final size:34
Alignment explanation
Indices: 4650106--4650195 Score: 105
Period size: 34 Copynumber: 2.7 Consensus size: 34
4650096 AACGATTAAC
*
4650106 GGTCAACGGTCAACGGTCGAGTC-GGGTCGGGTCG
1 GGTCAACGGTC-ACGGTCGAGTCACGGTCGGGTCG
* *
4650140 GGTCAACGGTC-GGGTCGGGTCAACGGTCGGGTCG
1 GGTCAACGGTCACGGTCGAGTC-ACGGTCGGGTCG
*
4650174 GGTCAACGGTCA-GGTCGGGTCA
1 GGTCAACGGTCACGGTCGAGTCA
4650196 GATCGGTCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
32 8 0.16
33 1 0.02
34 41 0.82
ACGTcount: A:0.14, C:0.23, G:0.44, T:0.18
Consensus pattern (34 bp):
GGTCAACGGTCACGGTCGAGTCACGGTCGGGTCG
Found at i:4650150 original size:17 final size:17
Alignment explanation
Indices: 4650130--4650195 Score: 123
Period size: 17 Copynumber: 3.9 Consensus size: 17
4650120 GGTCGAGTCG
4650130 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
4650147 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
4650164 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
*
4650181 GGTCAGGTCGGGTCA
1 GGTCGGGTCGGGTCA
4650196 GATCGGTCAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:4650174 original size:22 final size:22
Alignment explanation
Indices: 4650113--4650177 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
4650103 AACGGTCAAC
*
4650113 GGTCAACGGTCGAGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
* *
4650135 GGTC--GGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
4650157 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
4650178 AACGGTCAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 4 0.12
22 26 0.76
24 4 0.12
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:4650215 original size:19 final size:19
Alignment explanation
Indices: 4650193--4650231 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
4650183 TCAGGTCGGG
*
4650193 TCAGATCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
4650212 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
4650231 T
1 T
4650232 GAAACCGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.21
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:4650219 original size:10 final size:10
Alignment explanation
Indices: 4650202--4650241 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
4650192 GTCAGATCGG
4650202 TCAAACCGGT
1 TCAAACCGGT
*
4650212 TCAGACCGG-
1 TCAAACCGGT
4650221 TCAAACCGGT
1 TCAAACCGGT
*
4650231 TGAAACCGGT
1 TCAAACCGGT
4650241 T
1 T
4650242 TCCAGCAGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:4650238 original size:19 final size:19
Alignment explanation
Indices: 4650199--4650240 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
4650189 CGGGTCAGAT
*
4650199 CGGTCAAACCGGTTCAGAC
1 CGGTCAAACCGGTTCAAAC
*
4650218 CGGTCAAACCGGTTGAAAC
1 CGGTCAAACCGGTTCAAAC
4650237 CGGT
1 CGGT
4650241 TTCCAGCAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.17
Consensus pattern (19 bp):
CGGTCAAACCGGTTCAAAC
Found at i:4660563 original size:45 final size:45
Alignment explanation
Indices: 4660504--4660598 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
4660494 TATGAAATTA
4660504 ATAATTTTAAAAGATAACAAGTCAACGTGCAATTCCTTCGTTAAT
1 ATAATTTTAAAAGATAACAAGTCAACGTGCAATTCCTTCGTTAAT
* * * *
4660549 ATAATTTTAAAAGATAACACGTCGATGTGCAATTCCTTGGTTAAT
1 ATAATTTTAAAAGATAACAAGTCAACGTGCAATTCCTTCGTTAAT
4660594 ATAAT
1 ATAAT
4660599 ATTTTCCTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.35
Consensus pattern (45 bp):
ATAATTTTAAAAGATAACAAGTCAACGTGCAATTCCTTCGTTAAT
Found at i:4667515 original size:19 final size:20
Alignment explanation
Indices: 4667473--4667515 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4667463 GAAATGTTCA
* *
4667473 TCTAAAGTACACTAATTTTT
1 TCTAAAGTACACTAAGTCTT
4667493 TCTAAAGTACACT-AGTCTT
1 TCTAAAGTACACTAAGTCTT
4667512 TCTA
1 TCTA
4667516 TCATGTCTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.42
Consensus pattern (20 bp):
TCTAAAGTACACTAAGTCTT
Found at i:4681595 original size:22 final size:22
Alignment explanation
Indices: 4681567--4681620 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
4681557 ATACGCTACT
4681567 GAAAATGTTATCTTTTTCTATC
1 GAAAATGTTATCTTTTTCTATC
4681589 GAAAATGTTATCTTTTTCTATC
1 GAAAATGTTATCTTTTTCTATC
4681611 GAAAATGTTA
1 GAAAATGTTA
4681621 ATATGAAGCG
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:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (22 bp):
GAAAATGTTATCTTTTTCTATC
Found at i:4688406 original size:12 final size:13
Alignment explanation
Indices: 4688374--4688403 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4688364 TAATTTAAAT
4688374 TAAAATAAAATTA
1 TAAAATAAAATTA
*
4688387 TAAAATAAAATTT
1 TAAAATAAAATTA
4688400 TAAA
1 TAAA
4688404 TAACTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAATAAAATTA
Found at i:4692015 original size:23 final size:23
Alignment explanation
Indices: 4691976--4692035 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
4691966 ATCAAGTAAA
* *
4691976 ATAATAAATTAGATAGCGTTTAT
1 ATAATAAAATAGGTAGCGTTTAT
**
4691999 ATAATGTAATAGGTAGCGTTTAT
1 ATAATAAAATAGGTAGCGTTTAT
4692022 ATAATAAAATAGGT
1 ATAATAAAATAGGT
4692036 TAATTACTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.37
Consensus pattern (23 bp):
ATAATAAAATAGGTAGCGTTTAT
Found at i:4692098 original size:23 final size:23
Alignment explanation
Indices: 4692072--4692122 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
4692062 GATAACATAT
* **
4692072 TAGGTAGCGTTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
4692095 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
4692118 TAGGT
1 TAGGT
4692123 TAATTACTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:4692109 original size:87 final size:87
Alignment explanation
Indices: 4691954--4692197 Score: 380
Period size: 87 Copynumber: 2.8 Consensus size: 87
4691944 ATATCATTTA
* * * * *
4691954 ACTGGAAATATTATCAAGTAAAATAATAAATTAGATAGCGTTTATATAATGTAATAGGTAGCGTT
1 ACTGGAAATATTATCAAGCAAAATAACATATTAGGTAGCGTTTATATAATGTAATAGGTAGCGCT
4692019 TATATAATAAAATAGGTTAATT
66 TATATAATAAAATAGGTTAATT
* **
4692041 ACTGAAAATATTATCAAGCATGATAACATATTAGGTAGCGTTTATATAATGTAATAGGTAGCGCT
1 ACTGGAAATATTATCAAGCAAAATAACATATTAGGTAGCGTTTATATAATGTAATAGGTAGCGCT
4692106 TATATAATAAAATAGGTTAATT
66 TATATAATAAAATAGGTTAATT
* * * *
4692128 ACTGGAAATATTATTAAACACAATAACATATTAGGTAGCGTTTATATAATGTAATAGATAGCGCT
1 ACTGGAAATATTATCAAGCAAAATAACATATTAGGTAGCGTTTATATAATGTAATAGGTAGCGCT
4692193 TATAT
66 TATAT
4692198 TGATATATTC
Statistics
Matches: 143, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 143 1.00
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (87 bp):
ACTGGAAATATTATCAAGCAAAATAACATATTAGGTAGCGTTTATATAATGTAATAGGTAGCGCT
TATATAATAAAATAGGTTAATT
Found at i:4692542 original size:198 final size:198
Alignment explanation
Indices: 4692210--4692878 Score: 848
Period size: 198 Copynumber: 3.4 Consensus size: 198
4692200 ATATATTCTA
* * * *
4692210 TCATAAAATCAGTATATTTATACCG-GTAATATTGCAAATTTATCTATTATATTATAATTATCGG
1 TCATAAAATCAGTATATTTATACCGAGT-ACATTGTAAATTTACCTATTACATTATAATTATCGG
** * * *
4692274 TTTTAATGTTTTTGGGATCGAAACAATTT--TAAATATATCGACACTTTATGAGTGCACCTCGTT
65 TTTCGATG-TTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGAGTGCACCTCGTT
* * * **
4692337 GGACATTCATTCTGGAAAAAAATATCGACACAAACTTAAAACGTGTCGATACATTATGTAGATAT
128 AGACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCT
4692402 ATTTTC
193 ATTTTC
* ** * * *
4692408 TTATAAAATTGGTATATTTCTACCGAGTACATTGTAAATTTACCTAATACATTGTAATTATCGGT
1 TCATAAAATCAGTATATTTATACCGAGTACATTGTAAATTTACCTATTACATTATAATTATCGGT
* *
4692473 TTCGAT-TTTATGGGATCGATACTTTTAATAAATGTATCGACATTTTATGTGTGCACCTCGTTAG
66 TTCGATGTTT-TGGGATCGATACTTTTAATAAATGTATCGACACTTTATGAGTGCACCTCGTTAG
*
4692537 ACATTCATTATGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTAT
130 ACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTAT
4692602 TTTC
195 TTTC
* * * *
4692606 TCATAAAA-CTAATAGATTTCTACCGAGTACATTGTAAATTTACCTATTACATTGTAATTATCGG
1 TCATAAAATC-AGTATATTTATACCGAGTACATTGTAAATTTACCTATTACATTATAATTATCGG
* *
4692670 TTTCGATGCTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTT
65 TTTCGATG-TTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGAGTGCACCTCGTTA
* * *** *
4692735 GACATTCATTCTAGACAAAATGTATCGACAC-TTTTTAAATTTGTGTCGATACATTATGTAGACC
129 GACATTCATTCTGGA-AAAAAGTATCGACACAAACTTAAA-ATGTGTCGATACATTATGTAGACC
*
4692799 TATTCTC
192 TATTTTC
* * * *
4692806 TCATAAAATCGGTATATTTATA-CTAGTTACATTGTAAATTTATCTATTATATTATAATTATCGG
1 TCATAAAATCAGTATATTTATACCGAG-TACATTGTAAATTTACCTATTACATTATAATTATCGG
4692870 TTTCGATGT
65 TTTCGATGT
4692879 AACATATGTG
Statistics
Matches: 412, Mismatches: 48, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
196 6 0.01
197 11 0.03
198 216 0.52
199 74 0.18
200 104 0.25
201 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (198 bp):
TCATAAAATCAGTATATTTATACCGAGTACATTGTAAATTTACCTATTACATTATAATTATCGGT
TTCGATGTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGAGTGCACCTCGTTAGA
CATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTATT
TTC
Found at i:4693020 original size:31 final size:30
Alignment explanation
Indices: 4692979--4693072 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
4692969 TTATAATAAA
*
4692979 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAA-TAATAATAATTTT-TTAT
*
4693009 TAATAAAATATAATAATCATAATTTTTTAT
1 TAATAAAATATAATAATAATAATTTTTTAT
* * *
4693039 TTATAAAAT-T-ATAGAT-ATAATATTTTAA
1 TAATAAAATATAATA-ATAATAATTTTTTAT
4693067 TAATAA
1 TAATAA
4693073 TATTGACATA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
28 18 0.33
29 5 0.09
30 24 0.44
31 8 0.15
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TAATAAAATATAATAATAATAATTTTTTAT
Found at i:4693072 original size:14 final size:14
Alignment explanation
Indices: 4692990--4693076 Score: 52
Period size: 14 Copynumber: 6.2 Consensus size: 14
4692980 AATAAATATA
**
4692990 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
4693005 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
** *
4693018 ATAATAATCATAAT
1 ATTTTAATAATAAT
* * * *
4693032 TTTTTATTTATAAA
1 ATTTTAATAATAAT
*
4693046 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
4693060 ATTTTAATAATAAT
1 ATTTTAATAATAAT
4693074 ATT
1 ATT
4693077 GACATAAATA
Statistics
Matches: 53, Mismatches: 16, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
13 10 0.19
14 38 0.72
15 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:4693072 original size:28 final size:28
Alignment explanation
Indices: 4693004--4693072 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
4692994 ATAATAATTT
*
4693004 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
4693031 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
4693059 TATTTTAATAATAA
1 TATTTTAATAATAA
4693073 TATTGACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:4693123 original size:22 final size:24
Alignment explanation
Indices: 4693098--4693151 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
4693088 TATTAAATCA
*
4693098 ATTATTCTAATATT-TTAA-AAAT
1 ATTATTATAATATTGTTAATAAAT
*
4693120 ATTATTATTATATTGTTAATAAAT
1 ATTATTATAATATTGTTAATAAAT
*
4693144 AATATTAT
1 ATTATTAT
4693152 TTTATTGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 12 0.44
23 4 0.15
24 11 0.41
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTATTATAATATTGTTAATAAAT
Found at i:4693149 original size:24 final size:23
Alignment explanation
Indices: 4693107--4693159 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
4693097 AATTATTCTA
*
4693107 ATATT-TTAAAAATATTATTATT
1 ATATTGTTAAAAATAATATTATT
4693129 ATATTGTTAATAAATAATATTATT
1 ATATTGTTAA-AAATAATATTATT
*
4693153 TTATTGT
1 ATATTGT
4693160 ATTTGATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 5 0.19
23 4 0.15
24 18 0.67
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
ATATTGTTAAAAATAATATTATT
Found at i:4693779 original size:31 final size:30
Alignment explanation
Indices: 4693742--4693832 Score: 82
Period size: 30 Copynumber: 3.1 Consensus size: 30
4693732 TAAAAAATAA
*
4693742 AAAATATAATTTATAATAATTTTATT-TTAAT
1 AAAATATAA-TAATAATAATTTT-TTATTAAT
* *
4693773 AAAATATAATAATCATAATTTTTTATTTAT
1 AAAATATAATAATAATAATTTTTTATTAAT
* *
4693803 AAAAT-T-ATAGAT-ATAATATTTTAATAAT
1 AAAATATAATA-ATAATAATTTTTTATTAAT
4693831 AA
1 AA
4693833 TATTTACATA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
28 18 0.35
29 5 0.10
30 20 0.38
31 9 0.17
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (30 bp):
AAAATATAATAATAATAATTTTTTATTAAT
Found at i:4693832 original size:14 final size:14
Alignment explanation
Indices: 4693750--4693851 Score: 57
Period size: 14 Copynumber: 7.2 Consensus size: 14
4693740 AAAAAATATA
**
4693750 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
4693765 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
** *
4693778 ATAATAATCATAAT
1 ATTTTAATAATAAT
* * * *
4693792 TTTTTATTTATAAA
1 ATTTTAATAATAAT
*
4693806 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
4693820 ATTTTAATAATAAT
1 ATTTTAATAATAAT
4693834 A-TTTACATAAATAAT
1 ATTTTA-AT-AATAAT
4693849 ATT
1 ATT
4693852 AAATAAATTA
Statistics
Matches: 65, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
13 14 0.22
14 38 0.58
15 12 0.18
16 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:4693832 original size:28 final size:28
Alignment explanation
Indices: 4693764--4693832 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
4693754 ATAATAATTT
*
4693764 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
4693791 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
4693819 TATTTTAATAATAA
1 TATTTTAATAATAA
4693833 TATTTACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:4693857 original size:14 final size:15
Alignment explanation
Indices: 4693815--4693859 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
4693805 AATTATAGAT
*
4693815 ATAATATTTTAAT-A
1 ATAATATTTAAATAA
*
4693829 ATAATATTTACATAA
1 ATAATATTTAAATAA
4693844 ATAATA-TTAAATAA
1 ATAATATTTAAATAA
4693858 AT
1 AT
4693860 TATTCTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATATTTAAATAA
Found at i:4693919 original size:24 final size:24
Alignment explanation
Indices: 4693868--4693919 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
4693858 ATTATTCTAA
4693868 TATT-TTAAAAATAATAATATTAT
1 TATTGTTAAAAATAATAATATTAT
*
4693891 T-TTGTTAATAAATAATAGTATT-T
1 TATTGTTAA-AAATAATAATATTAT
4693914 TATTGT
1 TATTGT
4693920 ATTTGATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 7 0.28
24 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (24 bp):
TATTGTTAAAAATAATAATATTAT
Found at i:4694221 original size:23 final size:23
Alignment explanation
Indices: 4694173--4694222 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
4694163 ACATATTTTA
*
4694173 TTATATAAGCGATACATATTACG
1 TTATATAAGCGATACATAATACG
* * *
4694196 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGATACATAATACG
4694219 TTAT
1 TTAT
4694223 TGTGCTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (23 bp):
TTATATAAGCGATACATAATACG
Found at i:4694288 original size:87 final size:87
Alignment explanation
Indices: 4694157--4694380 Score: 340
Period size: 87 Copynumber: 2.6 Consensus size: 87
4694147 ACAAATTAAA
* * *
4694157 TAATTAACATATTTTATTATATAAGCGATACATATTACGTTATATAAGCGCTACCTAATATGTTA
1 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTA
* *
4694222 TTGTGCTTAATAATGTTTCCAG
66 TTGTGCTTAATAATATTTACAG
* * * * *
4694244 TAATTAACCTAATTTATTATATAAGCGCTGCCTATTACATTATATAAGCGGTACTTAATATGTTA
1 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTA
* *
4694309 TTGTGTTTAATAATATTTATAG
66 TTGTGCTTAATAATATTTACAG
4694331 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAGCG
1 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAGCG
4694381 TCACCTATTA
Statistics
Matches: 122, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 122 1.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (87 bp):
TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTA
TTGTGCTTAATAATATTTACAG
Found at i:4694373 original size:110 final size:110
Alignment explanation
Indices: 4694259--4694508 Score: 412
Period size: 110 Copynumber: 2.3 Consensus size: 110
4694249 AACCTAATTT
* * *
4694259 ATTATATAAGCGCTGCCTATTACATTATATAAGCGGTACTTAATATGTTATTGTGTTTAATAATA
1 ATTATATAAGCGCTACCTATTACATTATATAAGCAGTACCTAATATGTTATTGTGTTTAATAATA
4694324 TTTATAGTAATTAACATATTTTATTATATAAGCGCTACCTATTAC
66 TTTATAGTAATTAACATATTTTATTATATAAGCGCTACCTATTAC
*
4694369 ATTATATAAGCG-TCACCTATTACATTATATAAGCAGTACCTAATATGTTATTGTGTTTGATAAT
1 ATTATATAAGCGCT-ACCTATTACATTATATAAGCAGTACCTAATATGTTATTGTGTTTAATAAT
* * *
4694433 GTTTCTAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTAC
65 ATTTATAGTAATTAACATATTTTATTATATAAGCGCTACCTATTAC
*
4694479 ATTATATAAGCGCTACCTATTACATCATAT
1 ATTATATAAGCGCTACCTATTACATTATAT
4694509 TTTTACTTGT
Statistics
Matches: 130, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
109 1 0.01
110 128 0.98
111 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (110 bp):
ATTATATAAGCGCTACCTATTACATTATATAAGCAGTACCTAATATGTTATTGTGTTTAATAATA
TTTATAGTAATTAACATATTTTATTATATAAGCGCTACCTATTAC
Found at i:4694419 original size:23 final size:22
Alignment explanation
Indices: 4694346--4694410 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 22
4694336 AACATATTTT
4694346 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCG-TACCTATTAC
4694369 ATTATATAAGCGTCACCTATTAC
1 ATTATATAAGCGT-ACCTATTAC
4694392 ATTATATAAGCAGTACCTA
1 ATTATATAAGC-GTACCTA
4694411 ATATGTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
22 1 0.03
23 37 0.93
24 2 0.05
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (22 bp):
ATTATATAAGCGTACCTATTAC
Found at i:4694482 original size:23 final size:23
Alignment explanation
Indices: 4694447--4694508 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
4694437 CTAGTAATTA
**
4694447 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
4694470 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
4694493 ACCTATTACATCATAT
1 ACCTATTACATTATAT
4694509 TTTTACTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:4702667 original size:30 final size:30
Alignment explanation
Indices: 4702616--4702995 Score: 168
Period size: 30 Copynumber: 12.8 Consensus size: 30
4702606 ACAATTTATG
** *
4702616 TATTTTAACTTTAAAAAATATATTTTATTTT
1 TATTTTAAC-TTATTAAATATATTTTATTCT
*
4702647 TATTTTAACTTATTAAATATATTTTATTAT
1 TATTTTAACTTATTAAATATATTTTATTCT
* ** * **
4702677 CAAATTAAATTAAAAAATATATTTTATTCT
1 TATTTTAACTTATTAAATATATTTTATTCT
* * *
4702707 TATTTT-A-GTATAAAATATTTTTTTATTCT
1 TATTTTAACTTATTAAATA-TATTTTATTCT
* * **
4702736 T-GTCTAACTTAAAAAATATATTTTA-TCT
1 TATTTTAACTTATTAAATATATTTTATTCT
* * *
4702764 CATCTTAACTT-TTAAAAATATAATTTTATTAT
1 TATTTTAACTTATT--AAATAT-ATTTTATTCT
* * * *
4702796 CATTTTAAATT-TTAAAAATGTATTGTATTCT
1 TATTTTAACTTATT--AAATATATTTTATTCT
* * *
4702827 TACTTTAAATTATTAAATATGTTTTATT-T
1 TATTTTAACTTATTAAATATATTTTATTCT
* *
4702856 ATATATTAAC--A-TAAA-AGTATTTTAATCT
1 -TATTTTAACTTATTAAATA-TATTTTATTCT
* * *
4702884 TATTTTAGCTTA-AACAATATACTTTATTCT
1 TATTTTAACTTATTA-AATATATTTTATTCT
* *
4702914 TGTCTTAACTTA--AAATGTATATTTTATTCT
1 TATTTTAACTTATTAAA--TATATTTTATTCT
*
4702944 TATTTTAAC-T-TTAAA-AT-TTATATT-T
1 TATTTTAACTTATTAAATATATTTTATTCT
*
4702969 TATTTTAATCTTCATTTAAAAATATTT
1 TATTTTAA-CTT-A-TTAAATATATTT
4702996 AACATATATT
Statistics
Matches: 266, Mismatches: 56, Indels: 53
0.71 0.15 0.14
Matches are distributed among these distances:
25 9 0.03
26 8 0.03
27 21 0.08
28 17 0.06
29 30 0.11
30 122 0.46
31 35 0.13
32 24 0.09
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (30 bp):
TATTTTAACTTATTAAATATATTTTATTCT
Found at i:4702697 original size:60 final size:60
Alignment explanation
Indices: 4702626--4702972 Score: 243
Period size: 60 Copynumber: 5.8 Consensus size: 60
4702616 TATTTTAACT
* *
4702626 TTAAAAAATATATTTTATTTTTATTTTAACTTATTAAATATATTTTATTATCAAATTAAA
1 TTAAAAAATATATTTTATTCTTATTTTAACTTATTAAATATATTTTATTATCATATTAAA
* * * * *
4702686 TTAAAAAATATATTTTATTCTTATTTT-A-GTA-TAAA-ATATTTTTTTATTCTTGTCTAAC
1 TTAAAAAATATATTTTATTCTTATTTTAACTTATTAAATATATTTTATTA-TCATAT-TAAA
* * *
4702744 TTAAAAAATATATTTTA-TCTCATCTTAACTT-TTAAAAATATAATTTTATTATCATTTTAAA
1 TTAAAAAATATATTTTATTCTTATTTTAACTTATT--AAATAT-ATTTTATTATCATATTAAA
* * * * * *
4702805 TTTTAAAAATGTATTGTATTCTTACTTTAAATTATTAAATATGTTTTATTTAT-ATATTAACA
1 -TTAAAAAATATATTTTATTCTTATTTTAACTTATTAAATATATTTTA-TTATCATATTAA-A
* * * * * * ** * *
4702867 -T--AAAA-GTATTTTAATCTTATTTTAGCTTA-AACAATATACTTTATTCTTGTCTTAAC
1 TTAAAAAATATATTTTATTCTTATTTTAACTTATTA-AATATATTTTATTATCATATTAAA
** *
4702923 TTAAAATGTATATTTTATTCTTATTTTAACTT-TAAAATTTATATTTTATT
1 TTAAAAAATATATTTTATTCTTATTTTAACTTATTAAA--TATATTTTATT
4702973 TTAATCTTCA
Statistics
Matches: 223, Mismatches: 41, Indels: 45
0.72 0.13 0.15
Matches are distributed among these distances:
56 14 0.06
57 48 0.22
58 27 0.12
59 7 0.03
60 49 0.22
61 27 0.12
62 31 0.14
63 18 0.08
64 2 0.01
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (60 bp):
TTAAAAAATATATTTTATTCTTATTTTAACTTATTAAATATATTTTATTATCATATTAAA
Found at i:4702755 original size:58 final size:60
Alignment explanation
Indices: 4702620--4702952 Score: 193
Period size: 57 Copynumber: 5.6 Consensus size: 60
4702610 TTTATGTATT
* *
4702620 TTAACTTTAAAAAATATATTTTATTTTTATTTTAACTTATTAAATATATTTTATTATCAAA
1 TTAAC-TTAAAAAATATATTTTATTCTTATTTTAACGTATTAAATATATTTTATTATCAAA
* * ***
4702681 TTAAATTAAAAAATATATTTTATTCTTATTTT-A-GTA-TAAA-ATATTTTTTTATTCTTG
1 TTAACTTAAAAAATATATTTTATTCTTATTTTAACGTATTAAATATATTTTATTA-TCAAA
* * * **
4702738 TCTAACTTAAAAAATATATTTTA-TCTCATCTTAAC-TTTTAAAAATATAATTTTATTATCATT
1 T-TAACTTAAAAAATATATTTTATTCTTATTTTAACGTATT--AAATAT-ATTTTATTATCAAA
* * * * * ** * *
4702800 TTAAATTTTAAAAATGTATTGTATTCTTACTTTAAATTATTAAATATGTTTTATTTAT-ATA
1 TT-AACTTAAAAAATATATTTTATTCTTATTTTAACGTATTAAATATATTTTA-TTATCAAA
* * * * * * * * ****
4702861 TTAAC--ATAAAA-GTATTTTAATCTTATTTTAGCTTA-AACAATATACTTTATTCTTGTC
1 TTAACTTAAAAAATATATTTTATTCTTATTTTAACGTATTA-AATATATTTTATTATCAAA
**
4702918 TTAACTTAAAATGTATATTTTATTCTTATTTTAAC
1 TTAACTTAAAAAATATATTTTATTCTTATTTTAAC
4702953 TTTAAAATTT
Statistics
Matches: 209, Mismatches: 45, Indels: 37
0.72 0.15 0.13
Matches are distributed among these distances:
56 14 0.07
57 48 0.23
58 28 0.13
59 5 0.02
60 46 0.22
61 17 0.08
62 32 0.15
63 16 0.08
64 3 0.01
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (60 bp):
TTAACTTAAAAAATATATTTTATTCTTATTTTAACGTATTAAATATATTTTATTATCAAA
Found at i:4702954 original size:180 final size:178
Alignment explanation
Indices: 4702617--4702972 Score: 411
Period size: 180 Copynumber: 2.0 Consensus size: 178
4702607 CAATTTATGT
* * * * *
4702617 ATTTTAACTTTAAAAAATATATTTTATTTTTATTTTAACTTATTAAATATATTTTATTATCAAAT
1 ATTTTAAATTTAAAAAATATATTGTATTCTTACTTTAAATTATTAAATATATTTTATTATCAAAT
* **
4702682 TAAATTAAAAAATATATTTTATTCTTATTTTAGTATAAAATATTTTTTTATTCTTGTCTAACTTA
66 TAAATT-AAAAATATATTTTAATCTTATTTTAGTATAAAATATTACTTTATTCTTGTCTAACTTA
4702747 AAAAATATATTTTATCTCATCTTAACTTTTAAAA-ATATAATTTTATTATC
130 AAAAATATATTTTATCTCATCTTAAC-TTTAAAATATAT-ATTTTATTATC
* * * *
4702797 ATTTTAAATTTTAAAAATGTATTGTATTCTTACTTTAAATTATTAAATATGTTTTATTTAT-ATA
1 ATTTTAAATTTAAAAAATATATTGTATTCTTACTTTAAATTATTAAATATATTTTA-TTATCAAA
*
4702861 TTAACA-T-AAAA-GTATTTTAATCTTATTTTAGCT-TAAACA-ATATACTTTATTCTTGTCTTA
65 TTAA-ATTAAAAATATATTTTAATCTTATTTTAG-TATAAA-ATAT-TACTTTATTCTTGTC-TA
** * * *
4702921 ACTTAAAATGTATATTTTATTCTTATTTTAACTTTAAAATTTATATTTTATT
125 ACTTAAAAAATATATTTTA-TCTCATCTTAACTTTAAAATATATATTTTATT
4702973 TTAATCTTCA
Statistics
Matches: 150, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
177 24 0.16
178 19 0.13
179 34 0.23
180 68 0.45
181 5 0.03
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (178 bp):
ATTTTAAATTTAAAAAATATATTGTATTCTTACTTTAAATTATTAAATATATTTTATTATCAAAT
TAAATTAAAAATATATTTTAATCTTATTTTAGTATAAAATATTACTTTATTCTTGTCTAACTTAA
AAAATATATTTTATCTCATCTTAACTTTAAAATATATATTTTATTATC
Found at i:4703132 original size:29 final size:29
Alignment explanation
Indices: 4703071--4703222 Score: 114
Period size: 30 Copynumber: 5.1 Consensus size: 29
4703061 ATATATTTGG
*
4703071 AATATA-TTTAAA-TTAAGA-CAAAATAA
1 AATATATTTTAAATTTAAGATAAAAATAA
* *
4703097 AATATATTTTTAAAATTTAAGATAAGAACAA
1 AATATA-TTTT-AAATTTAAGATAAAAATAA
* * * *
4703128 AATATATTTTTCAGTTAAAAATAAAAATAA
1 AATATA-TTTTAAATTTAAGATAAAAATAA
* *
4703158 AATATATTTTAAAGTTAAGATAATAATAA
1 AATATATTTTAAATTTAAGATAAAAATAA
* *
4703187 AATAAATACTTTTAAA-TTAAAATTAATAATAA
1 AAT--ATA-TTTTAAATTTAAGA-TAAAAATAA
4703219 AATA
1 AATA
4703223 ATTAAAAAAT
Statistics
Matches: 101, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
26 6 0.06
28 3 0.03
29 23 0.23
30 26 0.26
31 24 0.24
32 19 0.19
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.36
Consensus pattern (29 bp):
AATATATTTTAAATTTAAGATAAAAATAA
Found at i:4703162 original size:61 final size:60
Alignment explanation
Indices: 4703090--4703222 Score: 160
Period size: 61 Copynumber: 2.2 Consensus size: 60
4703080 AAATTAAGAC
* * * *
4703090 AAAATAAAATATATTTTTAAAATTTAAGATAAGAACAAAAT-ATATTTTTCAGTTAAAAATA
1 AAAATAAAATATA-TTTT-AAAGTTAAGATAAGAACAAAATAATACTTTTAAATTAAAAATA
* * *
4703151 AAAATAAAATATATTTTAAAGTTAAGATAATAATAAAATAAATACTTTTAAATTAAAATTA
1 AAAATAAAATATATTTTAAAGTTAAGATAAGAACAAAAT-AATACTTTTAAATTAAAAATA
*
4703212 ATAATAAAATA
1 AAAATAAAATA
4703223 ATTAAAAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 19 0.31
60 4 0.06
61 39 0.63
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (60 bp):
AAAATAAAATATATTTTAAAGTTAAGATAAGAACAAAATAATACTTTTAAATTAAAAATA
Found at i:4706677 original size:58 final size:59
Alignment explanation
Indices: 4706615--4706900 Score: 271
Period size: 58 Copynumber: 4.8 Consensus size: 59
4706605 TGGGCCATTG
* * * *
4706615 CTTTGTTGAGTCACTAATTATTAAAAGTTAC-AAATGATCCTCTGACTATATA-G-CTTTA
1 CTTTGTTGAGTCTCCAACTATTAAAAGTTACAAAATGATCCTC-GACTATA-AGGACGTTA
* * * * *
4706673 CTTTGTTGAGTCTCCAACTATTAAAAATTACAAAATTATCTTTTGACTATAAGG-CATTA
1 CTTTGTTGAGTCTCCAACTATTAAAAGTTACAAAATGATC-CTCGACTATAAGGACGTTA
* * * *
4706732 TTTTGTTAAGTCTTCCGACTATTAAAAGTTACAAAATGATCATACGACTAT-AGGACGTTA
1 CTTTGTTGAGTC-TCCAACTATTAAAAGTTACAAAATGATCCT-CGACTATAAGGACGTTA
* * * *
4706792 CTTTGTTGAGTC-CCGACTATTAAAAGTTACAAAATAATCCTCCGATTAT-AGGAAGTTA
1 CTTTGTTGAGTCTCCAACTATTAAAAGTTACAAAATGATCCT-CGACTATAAGGACGTTA
* * *
4706850 CTTTGTTGAGTCCCCCAATTATTAAAAGTTACGAAATGATCACTCGACTAT
1 CTTTGTTGAGT-CTCCAACTATTAAAAGTTACAAAATGATC-CTCGACTAT
4706901 TCATATGTTT
Statistics
Matches: 191, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
58 80 0.42
59 34 0.18
60 75 0.39
61 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (59 bp):
CTTTGTTGAGTCTCCAACTATTAAAAGTTACAAAATGATCCTCGACTATAAGGACGTTA
Found at i:4706855 original size:118 final size:117
Alignment explanation
Indices: 4706633--4706900 Score: 299
Period size: 118 Copynumber: 2.3 Consensus size: 117
4706623 AGTCACTAAT
* * *
4706633 TATTAAAAGTTACAAATGATCCTCTGACTATATAGCTTTACTTTGTTGAGTCTCCAACTATTAAA
1 TATTAAAAGTTACAAATGATCATC-GACTATAGAGCGTTACTTTGTTGAGTCTCCAACTATTAAA
* * ** * * ** *
4706698 AATTACAAAATTATCTTTTGACTATAAGGCATTATTTTGTTAAGTCTTCCGAC
65 AATTACAAAATAATCCTCCGACTATAAGGAATTACTTTGTTAAGTCCCCCAAC
*
4706751 TATTAAAAGTTACAAAATGATCATACGACTATAG-GACGTTACTTTGTTGAGTC-CCGACTATTA
1 TATTAAAAGTTAC-AAATGATCAT-CGACTATAGAG-CGTTACTTTGTTGAGTCTCCAACTATTA
* * * *
4706814 AAAGTTACAAAATAATCCTCCGATTAT-AGGAAGTTACTTTGTTGAGTCCCCCAAT
63 AAAATTACAAAATAATCCTCCGACTATAAGGAA-TTACTTTGTTAAGTCCCCCAAC
4706869 TATTAAAAGTTACGAAATGATCACTCGACTAT
1 TATTAAAAGTTAC-AAATGATCA-TCGACTAT
4706901 TCATATGTTT
Statistics
Matches: 127, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
117 4 0.03
118 89 0.70
119 33 0.26
120 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (117 bp):
TATTAAAAGTTACAAATGATCATCGACTATAGAGCGTTACTTTGTTGAGTCTCCAACTATTAAAA
ATTACAAAATAATCCTCCGACTATAAGGAATTACTTTGTTAAGTCCCCCAAC
Found at i:4712645 original size:18 final size:19
Alignment explanation
Indices: 4712622--4712658 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
4712612 ACAGTAATCC
4712622 TATTCTC-TGGTAATCTTT
1 TATTCTCATGGTAATCTTT
4712640 TATTCTCAGTGGTAATCTT
1 TATTCTCA-TGGTAATCTT
4712659 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (19 bp):
TATTCTCATGGTAATCTTT
Found at i:4716049 original size:35 final size:35
Alignment explanation
Indices: 4716010--4716151 Score: 214
Period size: 35 Copynumber: 4.0 Consensus size: 35
4716000 TGAGTAAGAA
4716010 GAACGAAAGAAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGAAAGCATCGGCACTTTCGATTCAAGT
*
4716045 GAACGAAAGGAAA-CATCGGCACTTTCGATTCAAGAA
1 GAACGAAA-GAAAGCATCGGCACTTTCGATTCAAG-T
*
4716081 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGAAAGCATCGGCACTTTCGATTCAAGT
* **
4716116 GAACGAAAGGAAGCATCAACACTTTCGATTCAAGT
1 GAACGAAAGAAAGCATCGGCACTTTCGATTCAAGT
4716151 G
1 G
4716152 TTCATCTTTT
Statistics
Matches: 99, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
35 66 0.67
36 33 0.33
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (35 bp):
GAACGAAAGAAAGCATCGGCACTTTCGATTCAAGT
Found at i:4716121 original size:71 final size:71
Alignment explanation
Indices: 4716005--4716149 Score: 254
Period size: 71 Copynumber: 2.0 Consensus size: 71
4715995 GAAGGTGAGT
**
4716005 AAGAAGAACGAAAGAAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAACATCGGCACTTT
1 AAGAAGAACGAAAGAAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAACATCAACACTTT
4716070 CGATTC
66 CGATTC
* *
4716076 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAGCATCAACACTTT
1 AAGAAGAACGAAAGAAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAACATCAACACTTT
4716141 CGATTC
66 CGATTC
4716147 AAG
1 AAG
4716150 TGTTCATCTT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (71 bp):
AAGAAGAACGAAAGAAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAACATCAACACTTT
CGATTC
Found at i:4716393 original size:19 final size:19
Alignment explanation
Indices: 4716369--4716407 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
4716359 TAGGTTCTAG
4716369 AAGGCTGTTAGCAACAGTT
1 AAGGCTGTTAGCAACAGTT
4716388 AAGGCTGTTAGCAACAGTT
1 AAGGCTGTTAGCAACAGTT
4716407 A
1 A
4716408 CTATGGGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (19 bp):
AAGGCTGTTAGCAACAGTT
Found at i:4718936 original size:6 final size:6
Alignment explanation
Indices: 4718925--4718950 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4718915 ATTTAATCTC
4718925 TGATAA TGATAA TGATAA TGATAA TG
1 TGATAA TGATAA TGATAA TGATAA TG
4718951 TTAAGCACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (6 bp):
TGATAA
Done.