Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 12 of 187
Found at i:4289313 original size:83 final size:83
Alignment explanation
Indices: 4289170--4289329 Score: 214
Period size: 83 Copynumber: 1.9 Consensus size: 83
4289160 AAAGCATGTG
* * * *
4289170 CATAACACAAATACTAAAACGTTTAAAACATTTACATGAAATGATTGAATTTTAATATATTACAA
1 CATAACACAAATACTAAAACGTTTAAAACATTTACATGAAATAATAGAATTTTAAAATATTAAAA
*
4289235 GAAAGGAGAATCCTGTAC
66 GAAAGAAGAATCCTGTAC
* * * * *
4289253 CATAACACAAATAGT-ACACTGTTTAAATCATTTCCATGAAATAATAGGATTTTAAAATATTAAA
1 CATAACACAAATACTAAAAC-GTTTAAAACATTTACATGAAATAATAGAATTTTAAAATATTAAA
4289317 AGAAAGAAGAATC
65 AGAAAGAAGAATC
4289330 TTGCATCCAC
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
82 3 0.05
83 63 0.95
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.29
Consensus pattern (83 bp):
CATAACACAAATACTAAAACGTTTAAAACATTTACATGAAATAATAGAATTTTAAAATATTAAAA
GAAAGAAGAATCCTGTAC
Found at i:4294897 original size:36 final size:36
Alignment explanation
Indices: 4294850--4294926 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
4294840 ATCTACTGGA
* *
4294850 CTACGGCTGCGAATAGGGGTTCGACTTCGACTTGGG
1 CTACGGCTGCGAATAGAGGTTCGACTACGACTTGGG
4294886 CTACGGCTGCGAATAGAGGTTCGACTACGACTTGGG
1 CTACGGCTGCGAATAGAGGTTCGACTACGACTTGGG
4294922 CTACG
1 CTACG
4294927 ACTTGGGCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.19, C:0.23, G:0.34, T:0.23
Consensus pattern (36 bp):
CTACGGCTGCGAATAGAGGTTCGACTACGACTTGGG
Found at i:4294927 original size:12 final size:12
Alignment explanation
Indices: 4294910--4294936 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4294900 AGAGGTTCGA
4294910 CTACGACTTGGG
1 CTACGACTTGGG
4294922 CTACGACTTGGG
1 CTACGACTTGGG
4294934 CTA
1 CTA
4294937 TGACCATAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (12 bp):
CTACGACTTGGG
Found at i:4295660 original size:36 final size:36
Alignment explanation
Indices: 4295613--4295724 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 36
4295603 CTCCTACTTA
4295613 TGCTTCTCCTAGAAGATCTTACAGGACTTCTGCTAG
1 TGCTTCTCCTAGAAGATCTTACAGGACTTCTGCTAG
* ** * *
4295649 TGCTTCTCCT---AGACCTTATGGGGCTTCTGCTAA
1 TGCTTCTCCTAGAAGATCTTACAGGACTTCTGCTAG
* * * * *
4295682 TGCTTCTCCGAGAAGATCTTGCAGGACTTTTACTTG
1 TGCTTCTCCTAGAAGATCTTACAGGACTTCTGCTAG
4295718 TGCTTCT
1 TGCTTCT
4295725 TTTTGAAAGT
Statistics
Matches: 58, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
33 27 0.47
36 31 0.53
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.37
Consensus pattern (36 bp):
TGCTTCTCCTAGAAGATCTTACAGGACTTCTGCTAG
Found at i:4313051 original size:26 final size:25
Alignment explanation
Indices: 4312988--4313069 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
4312978 GTACACCGTA
*
4312988 GCTC-TTGTGAGCGTCCCATTATATG
1 GCTCTTTGTGAGCTTCCCATTA-ATG
*** *
4313013 GCTCTTCACGAGCTTCCCGATTAAAG
1 GCTCTTTGTGAGCTTCCC-ATTAATG
*
4313039 GCTCTTTGTGAGCTTCCTAATTAATG
1 GCTCTTTGTGAGCTTCC-CATTAATG
4313065 GCTCT
1 GCTCT
4313070 CCGGATCTTC
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
25 4 0.09
26 36 0.82
27 4 0.09
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (25 bp):
GCTCTTTGTGAGCTTCCCATTAATG
Found at i:4313859 original size:82 final size:81
Alignment explanation
Indices: 4313714--4313984 Score: 364
Period size: 82 Copynumber: 3.4 Consensus size: 81
4313704 ACGTATGATT
* * *
4313714 ACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGCCACTTG
1 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGCCTCTTG
4313777 ATCAGATAAGTGTAGC
66 ATCAGATAAGTGTAGC
*
4313793 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGGCTCTT
1 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGCCTCTT
*
4313858 GATCAGATAAGTTTAGC
65 GATCAGATAAGTGTAGC
**
4313875 ACTTATCACTTTGTCACTTGATCAGATAA--GT-G-T-A---ACCACTTATCACTTTGTTTCTTG
1 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGCCTCTTG
*
4313932 ATCAGATAAGTGTAACC
66 ATCAGATAAGTGT-AGC
**
4313949 ACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
4313985 CACTTATCAC
Statistics
Matches: 173, Mismatches: 11, Indels: 17
0.86 0.05 0.08
Matches are distributed among these distances:
73 33 0.19
74 29 0.17
76 3 0.02
77 1 0.01
78 1 0.01
79 10 0.06
80 7 0.04
81 20 0.12
82 69 0.40
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (81 bp):
ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGCCTCTTG
ATCAGATAAGTGTAGC
Found at i:4313924 original size:37 final size:37
Alignment explanation
Indices: 4313836--4314011 Score: 273
Period size: 37 Copynumber: 4.8 Consensus size: 37
4313826 AGCTAAAGCT
* *
4313836 ACCACTTATCACTTTGGCTCTTGATCAGATAAGT-TT
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
* *
4313872 AGCACTTATCACTTTGTCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
*
4313909 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
*
4313946 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
* *
4313983 GCCACTTATCACTTTGTCACTTGATCAGA
1 ACCACTTATCACTTTGTCTCTTGATCAGA
4314012 AGTACTCAAA
Statistics
Matches: 129, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
36 31 0.24
37 98 0.76
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (37 bp):
ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
Found at i:4316381 original size:24 final size:24
Alignment explanation
Indices: 4316354--4316415 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
4316344 TGGCTCTTTG
*
4316354 GAGCTACCCGTTATTGGCTCACAT
1 GAGCTTCCCGTTATTGGCTCACAT
* **
4316378 GAGCTTCCTGATTA-TGGCTCTTAT
1 GAGCTTCCCG-TTATTGGCTCACAT
4316402 GAGCTTCCCGTTAT
1 GAGCTTCCCGTTAT
4316416 ACAGCCCAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 3 0.10
24 25 0.81
25 3 0.10
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (24 bp):
GAGCTTCCCGTTATTGGCTCACAT
Found at i:4316432 original size:49 final size:49
Alignment explanation
Indices: 4316330--4316458 Score: 131
Period size: 49 Copynumber: 2.7 Consensus size: 49
4316320 GACTATCCGG
* ** * *
4316330 AGCTTCCTGATTAATGGCTCTT-TGGAGCTACCCGTTATTGGCTCACATG
1 AGCTTCCTGATTAATGGCTCTTAT-GAGCTTCCCGTTATCAGCCCACATA
*
4316379 AGCTTCCTGATT-ATGGCTCTTATGAGCTTCCCGTTATACAGCCCAGATA
1 AGCTTCCTGATTAATGGCTCTTATGAGCTTCCCGTTAT-CAGCCCACATA
* *
4316428 AGCTT-CTCG-TTAATGGCTCTCAGGAGCTTCC
1 AGCTTCCT-GATTAATGGCTCTTATGAGCTTCC
4316459 TGTTTTATGG
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
48 26 0.38
49 42 0.62
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.33
Consensus pattern (49 bp):
AGCTTCCTGATTAATGGCTCTTATGAGCTTCCCGTTATCAGCCCACATA
Found at i:4316828 original size:18 final size:18
Alignment explanation
Indices: 4316805--4316844 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
4316795 AAATCGAAAA
*
4316805 AATTCGGTTAACCGATCG
1 AATTCGGTTAACCGACCG
4316823 AATTCGGTTAACCGACCG
1 AATTCGGTTAACCGACCG
4316841 AATT
1 AATT
4316845 GATTAACGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (18 bp):
AATTCGGTTAACCGACCG
Found at i:4317307 original size:3 final size:3
Alignment explanation
Indices: 4317294--4317369 Score: 107
Period size: 3 Copynumber: 24.7 Consensus size: 3
4317284 GATTTAACTT
* * *
4317294 TTC TCC TTC TTC TTT TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
4317342 TTC TTC TTC TTC TTC TTC AGTTC TTC TT
1 TTC TTC TTC TTC TTC TTC --TTC TTC TT
4317370 TTTTTCTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
3 62 0.95
5 3 0.05
ACGTcount: A:0.01, C:0.30, G:0.01, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:4321331 original size:37 final size:37
Alignment explanation
Indices: 4321290--4321364 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
4321280 TGTTAATTTC
*
4321290 AAGACTTATTTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
*
4321327 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
4321364 A
1 A
4321365 TTCGGGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (37 bp):
AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
Found at i:4321386 original size:18 final size:19
Alignment explanation
Indices: 4321358--4321393 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4321348 ATTATGTAGT
4321358 GATTCAATTCGGGTAATTC
1 GATTCAATTCGGGTAATTC
*
4321377 GATT-AATTCGGTTAATT
1 GATTCAATTCGGGTAATT
4321394 TTTAACCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (19 bp):
GATTCAATTCGGGTAATTC
Found at i:4331299 original size:41 final size:39
Alignment explanation
Indices: 4331253--4331340 Score: 97
Period size: 41 Copynumber: 2.2 Consensus size: 39
4331243 AAACAGGCTT
*
4331253 TTAGCGGCG-TTTGGACAAAAAGCGCCACTAAAAATCGAGCA
1 TTAGCGGCGCTTTGGA-AAAAA-CGCCACTAAAAAT-AAGCA
** * *
4331294 TTAGCGGCGCTTTTTAGAAAACGCCGCTAAAAATAAGCA
1 TTAGCGGCGCTTTGGAAAAAACGCCACTAAAAATAAGCA
4331333 TTAGCGGC
1 TTAGCGGC
4331341 TTTTTTTGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 12 0.29
40 12 0.29
41 13 0.32
42 4 0.10
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (39 bp):
TTAGCGGCGCTTTGGAAAAAACGCCACTAAAAATAAGCA
Found at i:4331337 original size:39 final size:40
Alignment explanation
Indices: 4331270--4331364 Score: 124
Period size: 39 Copynumber: 2.4 Consensus size: 40
4331260 CGTTTGGACA
* *
4331270 AAAAGCGCCACTAAAAATCGAGCATTAGCGGCGCTTTTTAG
1 AAAAGCGCCGCTAAAAATCAAGCATTAGCGGC-CTTTTTAG
* *
4331311 AAAA-CGCCGCTAAAAAT-AAGCATTAGCGGCTTTTTTTG
1 AAAAGCGCCGCTAAAAATCAAGCATTAGCGGCCTTTTTAG
4331349 AAAAGCGCCGC-AAAAA
1 AAAAGCGCCGCTAAAAA
4331365 GCCTAAGCCC
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
38 15 0.31
39 18 0.37
40 12 0.24
41 4 0.08
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (40 bp):
AAAAGCGCCGCTAAAAATCAAGCATTAGCGGCCTTTTTAG
Found at i:4331458 original size:41 final size:41
Alignment explanation
Indices: 4331400--4331641 Score: 313
Period size: 41 Copynumber: 5.9 Consensus size: 41
4331390 TGAGTTTTTG
* *
4331400 GGGCCTTTAGCGGCGTTTTTGAATAAGCGTCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * * *
4331441 TGGCCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTG
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * * *
4331482 GGGCCTTTAGCGGTGTTTTCGAATAAGCGTCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * * *
4331523 GGGCCTTTAGCGGCGTTTTTTAAGAAGTGCCGCTGATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
** *
4331564 GGATCTTTGGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
**
4331605 TAGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
4331642 AATAAAATCT
Statistics
Matches: 170, Mismatches: 31, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 170 1.00
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.31
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:4331535 original size:82 final size:82
Alignment explanation
Indices: 4331398--4331641 Score: 353
Period size: 82 Copynumber: 3.0 Consensus size: 82
4331388 TCTGAGTTTT
*
4331398 TGGGGCCTTTAGCGGCGTTTTTGAATAAGCGTCGCTAATGCTCTGGCCTTTAGCGGCGTTTTTGG
1 TGGGGCCTTTAGCGGCGTTTTTGAATAAGCGTCGCTAATGCTCTGGCCTTTAGCGGCGTTTTTGA
4331463 AGAAGCGCCGCTAATGC
66 AGAAGCGCCGCTAATGC
* * * *
4331480 TGGGGCCTTTAGCGGTGTTTTCGAATAAGCGTCGCTAATGCTCGGGCCTTTAGCGGCGTTTTTTA
1 TGGGGCCTTTAGCGGCGTTTTTGAATAAGCGTCGCTAATGCTCTGGCCTTTAGCGGCGTTTTTGA
* *
4331545 AGAAGTGCCGCTGATGC
66 AGAAGCGCCGCTAATGC
* ** * * * *
4331562 TCGGATCTTTGGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTAGCCTTTAGCGGCGTTTTTGA
1 TGGGGCCTTTAGCGGCGTTTTTGAATAAGCGTCGCTAATGCTCTGGCCTTTAGCGGCGTTTTTGA
*
4331627 AAAAGCGCCGCTAAT
66 AGAAGCGCCGCTAAT
4331642 AATAAAATCT
Statistics
Matches: 141, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 141 1.00
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.31
Consensus pattern (82 bp):
TGGGGCCTTTAGCGGCGTTTTTGAATAAGCGTCGCTAATGCTCTGGCCTTTAGCGGCGTTTTTGA
AGAAGCGCCGCTAATGC
Found at i:4332333 original size:7 final size:7
Alignment explanation
Indices: 4332323--4332353 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
4332313 AGATTATGAA
4332323 ATTAGGG
1 ATTAGGG
4332330 ATTAGGG
1 ATTAGGG
4332337 ATTAGGG
1 ATTAGGG
4332344 ATTAGGG
1 ATTAGGG
4332351 ATT
1 ATT
4332354 CTAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.39, T:0.32
Consensus pattern (7 bp):
ATTAGGG
Found at i:4333685 original size:145 final size:144
Alignment explanation
Indices: 4333411--4333700 Score: 381
Period size: 145 Copynumber: 2.0 Consensus size: 144
4333401 NNNTCTTAGC
* * * *
4333411 ATAGCAAAATAGTGTCGCTTTATTCTAAATAAAATAATTTTTTGCGGCGTTTTTCATAAACGCCG
1 ATAGCAAAACAGCGTCGCTTTATTCCAAATAAAATAATTTTTTACGGCGTTTTTCATAAACGCCG
* * **
4333476 CAAAAGTTAATCAATAGCGACGTTTTTTTTAAAAAACGCCACAAAAAATAATTTTATTTTAAAAA
66 CAAAAGATAAGCAATAGCGACGTTTTTCATAAAAAACGCCACAAAAAATAA-TTTATTTTAAAAA
4333541 ATAGCGCCATTTTAT
130 ATAGCGCCATTTTAT
* * *
4333556 ATAGCAAAACAGCGTCGTTTTATTCCAAATAAAATAATTTTTTACGGCGTTTTTGATAAAAACGT
1 ATAGCAAAACAGCGTCGCTTTATTCCAAATAAAATAATTTTTTACGGCGTTTTTCAT--AAACGC
* *
4333621 CGCAATAGATAAGCAATAGCGACG-TTTTCATATAAAACGCCAC-AAAAA-AA-TTACTTTTAAA
64 CGCAAAAGATAAGCAATAGCGACGTTTTTCATAAAAAACGCCACAAAAAATAATTTA-TTTT-AA
*
4333682 AAAATAGCGCTATTTTAT
127 AAAATAGCGCCATTTTAT
4333700 A
1 A
4333701 AAATTCCCTC
Statistics
Matches: 127, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
142 3 0.02
143 4 0.03
144 22 0.17
145 56 0.44
146 16 0.13
147 26 0.20
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (144 bp):
ATAGCAAAACAGCGTCGCTTTATTCCAAATAAAATAATTTTTTACGGCGTTTTTCATAAACGCCG
CAAAAGATAAGCAATAGCGACGTTTTTCATAAAAAACGCCACAAAAAATAATTTATTTTAAAAAA
TAGCGCCATTTTAT
Found at i:4336282 original size:25 final size:25
Alignment explanation
Indices: 4336228--4336279 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
4336218 TTTATATTGA
4336228 TTTATAATTTGATCATATGTATGGG
1 TTTATAATTTGATCATATGTATGGG
* *
4336253 GTTATAATTTGATCATAT-TATTGG
1 TTTATAATTTGATCATATGTATGGG
4336277 TTT
1 TTT
4336280 TATCAACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.27, C:0.04, G:0.17, T:0.52
Consensus pattern (25 bp):
TTTATAATTTGATCATATGTATGGG
Found at i:4337361 original size:43 final size:43
Alignment explanation
Indices: 4337300--4337390 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 43
4337290 CTTTGAGTTC
* *
4337300 ATTA-CAAGATTTCCTTGATTAA-ATAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGA-AAATGCATTATATCTTTT
* * *
4337342 ATTACCAAGGTTTACTTGATTAAGAAAATGCATTGTATGTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
4337385 ATTACC
1 ATTACC
4337391 TTGCATATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 4 0.10
43 37 0.88
44 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
Found at i:4337793 original size:43 final size:43
Alignment explanation
Indices: 4337677--4337925 Score: 279
Period size: 43 Copynumber: 5.8 Consensus size: 43
4337667 AGGTTATGTT
* * * * * *
4337677 TTTAGTGGCGTTTTTGCGAGAAGCGCTGCTAAAGGT-TTGATC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
4337719 TATAGCGGCGTTTGTGACAAAAAACGTCGCTAAAGGT-TATGGTC
1 TTTAGCGGCGTTTGTGA-GAAAAGCGCCGCTAAAGGTCT-TGGTC
* * * *
4337763 TTTAGCGGCGTTTGTGGGGAAAGTGCCGCTAAAGGTCTTTGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
4337806 TTTAGCAGCGTTTGTGAGAAAAGCGCCACTAATGCTCTTGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
*
4337849 TTTAGCGGCGTTTGTTG-GAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTG-TGAGAAAAGCGCCGCTAAAGGTCTTGGTC
4337892 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAG
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAG
4337926 TTAGCGATGC
Statistics
Matches: 171, Mismatches: 31, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
42 15 0.09
43 134 0.78
44 22 0.13
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:4338333 original size:23 final size:23
Alignment explanation
Indices: 4338268--4338334 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
4338258 TTTCACTATT
*
4338268 TAATTTCCTTTGTT-TTCATATTC
1 TAATTTTCTTTGTTGTTCAT-TTC
* *
4338291 -GA-TTTCTTTG-TGTTAGATTTC
1 TAATTTTCTTTGTTGTT-CATTTC
4338312 TAATTTTCTTTGTTGTTCATTTC
1 TAATTTTCTTTGTTGTTCATTTC
4338335 AAGTCCTAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
20 1 0.03
21 12 0.35
22 4 0.12
23 13 0.38
24 4 0.12
ACGTcount: A:0.15, C:0.13, G:0.10, T:0.61
Consensus pattern (23 bp):
TAATTTTCTTTGTTGTTCATTTC
Found at i:4338827 original size:19 final size:19
Alignment explanation
Indices: 4338785--4338827 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4338775 TCTATTTATT
*
4338785 TTTAATTCATTTTATTCTA
1 TTTAATTCATTTTATACTA
*
4338804 GTTAATT-ATTTTTATACTA
1 TTTAATTCA-TTTTATACTA
4338823 TTTAA
1 TTTAA
4338828 GATTAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTAATTCATTTTATACTA
Found at i:4344264 original size:23 final size:24
Alignment explanation
Indices: 4344194--4344265 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
4344184 AAAATATTTG
*
4344194 AAATTTACAATTTTGA-ATTAATCT
1 AAATTTACAATTTGGATATTAAT-T
** *
4344218 AAATTTATTATTTGGATAGT-ATT
1 AAATTTACAATTTGGATATTAATT
*
4344241 AAATTTA-AATTTGGATTTTAATT
1 AAATTTACAATTTGGATATTAATT
4344264 AA
1 AA
4344266 CTAATTTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
22 9 0.23
23 13 0.33
24 15 0.38
25 2 0.05
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (24 bp):
AAATTTACAATTTGGATATTAATT
Found at i:4344763 original size:2 final size:2
Alignment explanation
Indices: 4344756--4344790 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4344746 ATAGATTATG
4344756 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 A
4344791 AAAAGTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4348678 original size:11 final size:11
Alignment explanation
Indices: 4348658--4348687 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4348648 CTCTCACGGT
4348658 AAAAAA-AAAA
1 AAAAAAGAAAA
4348668 AAAAAAGAAAA
1 AAAAAAGAAAA
4348679 AAAAAAGAA
1 AAAAAAGAA
4348688 GGAATTTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:4357280 original size:31 final size:31
Alignment explanation
Indices: 4357245--4357314 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
4357235 TCGAAAAGTG
*
4357245 TACCCAATTGAGCCAATTGAATCATTATTTC
1 TACCCAATTGAGCCAATTGAATCATGATTTC
*
4357276 TACCCAATTGAGCCATTTGAATCATGATTTC
1 TACCCAATTGAGCCAATTGAATCATGATTTC
4357307 TACCCAAT
1 TACCCAAT
4357315 AAAGTCCCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (31 bp):
TACCCAATTGAGCCAATTGAATCATGATTTC
Found at i:4357547 original size:29 final size:30
Alignment explanation
Indices: 4357515--4357579 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
4357505 TTAAAAATAT
* * *
4357515 AAATTAAAAAATCATTA-AAAAATTATTAG
1 AAATTAAAAAATAATTAGAAAAATTACTAA
* *
4357544 AAATTTATAAATAATTAGAAAAATTACTAA
1 AAATTAAAAAATAATTAGAAAAATTACTAA
4357574 AAATTA
1 AAATTA
4357580 TAGAAAGTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (30 bp):
AAATTAAAAAATAATTAGAAAAATTACTAA
Found at i:4357560 original size:40 final size:40
Alignment explanation
Indices: 4357516--4357595 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
4357506 TAAAAATATA
*
4357516 AATTA-AAAAATCATTAAAAAATTATTAGAAA-TTTATAAAT
1 AATTAGAAAAATCACT-AAAAATTA-TAGAAAGTTTATAAAT
* *
4357556 AATTAGAAAAATTACTAAAAATTATAGAAAGTTTTTAAAT
1 AATTAGAAAAATCACTAAAAATTATAGAAAGTTTATAAAT
4357596 GTTTTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 6 0.17
40 21 0.60
41 8 0.23
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (40 bp):
AATTAGAAAAATCACTAAAAATTATAGAAAGTTTATAAAT
Found at i:4357580 original size:29 final size:29
Alignment explanation
Indices: 4357523--4357581 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
4357513 ATAAATTAAA
* * *
4357523 AAATCATTAAAAAATTATTAGAAATTTAT
1 AAATAATTAAAAAATTACTAGAAAATTAT
4357552 AAATAATTAGAAAAATTACTA-AAAATTAT
1 AAATAATTA-AAAAATTACTAGAAAATTAT
4357581 A
1 A
4357582 GAAAGTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (29 bp):
AAATAATTAAAAAATTACTAGAAAATTAT
Found at i:4358362 original size:17 final size:18
Alignment explanation
Indices: 4358340--4358384 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
4358330 ATTTATAACA
*
4358340 TTTAATTTTTT-TTAATT
1 TTTAATTTTTTATGAATT
4358357 TTTAATATTTTTATGAATT
1 TTTAAT-TTTTTATGAATT
4358376 TTATAATTT
1 TT-TAATTT
4358385 ATATTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.25
18 5 0.21
19 9 0.38
20 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTAATTTTTTATGAATT
Found at i:4358473 original size:31 final size:29
Alignment explanation
Indices: 4358433--4358508 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
4358423 TTTTTTAACT
*
4358433 TAAAGAATCAATTAAGCCCCTCGTAAAATAA
1 TAAA-AATCAATTAAG-CCATCGTAAAATAA
* *
4358464 TAATAAATCAATTAAGTCATTGTAAAATAA
1 TAA-AAATCAATTAAGCCATCGTAAAATAA
4358494 TAAAAAGTCAATTAA
1 TAAAAA-TCAATTAA
4358509 ATCCTCCATG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 3 0.08
30 22 0.55
31 14 0.35
32 1 0.03
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.28
Consensus pattern (29 bp):
TAAAAATCAATTAAGCCATCGTAAAATAA
Found at i:4366129 original size:8 final size:8
Alignment explanation
Indices: 4366116--4366140 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4366106 GCAAGGGTGG
4366116 ACGTGCTA
1 ACGTGCTA
4366124 ACGTGCTA
1 ACGTGCTA
4366132 ACGTGCTA
1 ACGTGCTA
4366140 A
1 A
4366141 GGCAACGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (8 bp):
ACGTGCTA
Found at i:4395646 original size:4 final size:4
Alignment explanation
Indices: 4395637--4395680 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
4395627 GGTCAGTTAA
4395637 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4395681 CATGCATGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:4404991 original size:34 final size:33
Alignment explanation
Indices: 4404947--4405011 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
4404937 CAGTAAAATA
* *
4404947 TTTTCCGTAAAATTATTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATT-TTACTGGAAAATATTTTAC
*
4404981 TTTTCTGTAAAATTTTACTGGAAAATATTTT
1 TTTTCCGTAAAATTTTACTGGAAAATATTTT
4405012 TTGGTGTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 15 0.54
34 13 0.46
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (33 bp):
TTTTCCGTAAAATTTTACTGGAAAATATTTTAC
Found at i:4408556 original size:18 final size:18
Alignment explanation
Indices: 4408533--4408571 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
4408523 TTAGCAAAGA
4408533 TAGCATCATGGTCCATTT
1 TAGCATCATGGTCCATTT
*
4408551 TAGCATCATGGTCCTTTT
1 TAGCATCATGGTCCATTT
4408569 TAG
1 TAG
4408572 GACCTCCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.41
Consensus pattern (18 bp):
TAGCATCATGGTCCATTT
Found at i:4412582 original size:2 final size:2
Alignment explanation
Indices: 4412575--4412618 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4412565 ATAAATATAA
4412575 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4412617 AG
1 AG
4412619 GAACCTAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4414882 original size:63 final size:63
Alignment explanation
Indices: 4414781--4414969 Score: 308
Period size: 63 Copynumber: 3.0 Consensus size: 63
4414771 GCAAACAGCA
* * *
4414781 AATACAGAACCTTCTCGTTTATTTGATGACCTCTTACTGTGCAGATGGTTCCTTTCTCTCTTT
1 AATACAGAACCTTCTGGTTTGTTTGATGACCTCTTACTGTGCATATGGTTCCTTTCTCTCTTT
* *
4414844 ACTACAGAACCTTCTGGTTTGTTTGATGACCTCTTACTGTGCATATGGTTCCTTTCTCTCATT
1 AATACAGAACCTTCTGGTTTGTTTGATGACCTCTTACTGTGCATATGGTTCCTTTCTCTCTTT
*
4414907 AATACAGAACCTTCTGGTTTGTTTGATGACCTCTTACTGTGCATACT-GTTCCTTTGTCTCTTT
1 AATACAGAACCTTCTGGTTTGTTTGATGACCTCTTACTGTGCATA-TGGTTCCTTTCTCTCTTT
4414970 CTATTATTTC
Statistics
Matches: 117, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
63 116 0.99
64 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.43
Consensus pattern (63 bp):
AATACAGAACCTTCTGGTTTGTTTGATGACCTCTTACTGTGCATATGGTTCCTTTCTCTCTTT
Found at i:4420026 original size:17 final size:18
Alignment explanation
Indices: 4419992--4420026 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4419982 TATTAAAAAC
*
4419992 GATTAAAAATCATATTTA
1 GATTAAAAAGCATATTTA
4420010 GATTAAAAAGCAT-TTTA
1 GATTAAAAAGCATATTTA
4420027 ATTTTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (18 bp):
GATTAAAAAGCATATTTA
Found at i:4430906 original size:21 final size:21
Alignment explanation
Indices: 4430880--4430921 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4430870 TTTCCTTAAC
4430880 CAAAATTCATACTCTAAATTT
1 CAAAATTCATACTCTAAATTT
4430901 CAAAATTCATACTCTAAATTT
1 CAAAATTCATACTCTAAATTT
4430922 AACAGATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (21 bp):
CAAAATTCATACTCTAAATTT
Found at i:4436649 original size:6 final size:7
Alignment explanation
Indices: 4436630--4436655 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4436620 ACTCAATATA
4436630 TATTTTT
1 TATTTTT
4436637 TATTTTT
1 TATTTTT
4436644 TATTTTT
1 TATTTTT
4436651 TATTT
1 TATTT
4436656 AAATTTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TATTTTT
Found at i:4441915 original size:18 final size:18
Alignment explanation
Indices: 4441892--4441933 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
4441882 TATTTTGTTA
4441892 AAAATT-AAATATATAATT
1 AAAATTGAAATA-ATAATT
* *
4441910 AAAATTGCAATAATATTT
1 AAAATTGAAATAATAATT
4441928 AAAATT
1 AAAATT
4441934 TTAAAAACGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
AAAATTGAAATAATAATT
Found at i:4442979 original size:27 final size:27
Alignment explanation
Indices: 4442940--4442992 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4442930 CATTTATTTA
* *
4442940 ATACACATCAAAATATAAAAA-TAAAAC
1 ATACAAATAAAAAT-TAAAAATTAAAAC
4442967 ATACAAATAAAAATTAAAAATTAAAA
1 ATACAAATAAAAATTAAAAATTAAAA
4442993 AAGCATGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (27 bp):
ATACAAATAAAAATTAAAAATTAAAAC
Found at i:4443280 original size:25 final size:25
Alignment explanation
Indices: 4443246--4443295 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
4443236 GCTGAGCTTT
*
4443246 TTACAACTCAATGATGATTCAATAC
1 TTACAACTCAATGATGATCCAATAC
* *
4443271 TTACAACTCAGTGGTGATCCAATAC
1 TTACAACTCAATGATGATCCAATAC
4443296 ATTTTAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (25 bp):
TTACAACTCAATGATGATCCAATAC
Found at i:4447104 original size:7 final size:7
Alignment explanation
Indices: 4447094--4447123 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
4447084 AGTTAATAGT
4447094 AGTTAGC
1 AGTTAGC
4447101 AGTTAGC
1 AGTTAGC
4447108 AGTTAGC
1 AGTTAGC
4447115 AGTTAGC
1 AGTTAGC
4447122 AG
1 AG
4447124 ATATTAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (7 bp):
AGTTAGC
Found at i:4447318 original size:39 final size:39
Alignment explanation
Indices: 4447255--4447339 Score: 143
Period size: 39 Copynumber: 2.2 Consensus size: 39
4447245 CAACCAACCC
* * *
4447255 GATGATGAACTCTGACTAGGTACATATGCAGTAGGCACA
1 GATGGTGAACTCTGACTAGATACATATGCAGCAGGCACA
4447294 GATGGTGAACTCTGACTAGATACATATGCAGCAGGCACA
1 GATGGTGAACTCTGACTAGATACATATGCAGCAGGCACA
4447333 GATGGTG
1 GATGGTG
4447340 GCTAAGACAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (39 bp):
GATGGTGAACTCTGACTAGATACATATGCAGCAGGCACA
Found at i:4450143 original size:19 final size:22
Alignment explanation
Indices: 4450101--4450147 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
4450091 TTTCTAAAAA
4450101 TAAATAATTTTTCAAGAACTTT
1 TAAATAATTTTTCAAGAACTTT
*
4450123 TAAATTATTTTT-AA-AAC-TT
1 TAAATAATTTTTCAAGAACTTT
4450142 TAAATA
1 TAAATA
4450148 TGAAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 7 0.30
20 3 0.13
21 2 0.09
22 11 0.48
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (22 bp):
TAAATAATTTTTCAAGAACTTT
Found at i:4453472 original size:29 final size:29
Alignment explanation
Indices: 4453375--4453472 Score: 76
Period size: 29 Copynumber: 3.4 Consensus size: 29
4453365 ATAAAATTAA
* * *
4453375 ATAATTAAATGATTATTTTTTAACTTTTT
1 ATAATTAGATGATTATTTTATAATTTTTT
* ** * **
4453404 ATAATT-GAGTGATCA-AATAAAATTTATAA
1 ATAATTAGA-TGATTATTTTATAATTT-TTT
4453433 ATAATTA-ATGATTATTTTATAATTTTTT
1 ATAATTAGATGATTATTTTATAATTTTTT
4453461 ATAATTAGATGA
1 ATAATTAGATGA
4453473 CAAAATTATC
Statistics
Matches: 49, Mismatches: 15, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
28 19 0.39
29 30 0.61
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (29 bp):
ATAATTAGATGATTATTTTATAATTTTTT
Found at i:4459969 original size:15 final size:14
Alignment explanation
Indices: 4459949--4459978 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
4459939 TTGCATTTTC
4459949 TTTTCTTTCTTTATT
1 TTTTCTTTC-TTATT
4459964 TTTTCTTTCTTATT
1 TTTTCTTTCTTATT
4459978 T
1 T
4459979 GTTTTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTCTTTCTTATT
Found at i:4460455 original size:22 final size:22
Alignment explanation
Indices: 4460427--4460470 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
4460417 AAAAGTAAAG
4460427 AAAGACAACTTCTTTCTTGCAA
1 AAAGACAACTTCTTTCTTGCAA
4460449 AAAGACAACTTCTTTCTTGCAA
1 AAAGACAACTTCTTTCTTGCAA
4460471 CTTTCGTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (22 bp):
AAAGACAACTTCTTTCTTGCAA
Found at i:4479294 original size:25 final size:25
Alignment explanation
Indices: 4479258--4479312 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
4479248 AAGAAAGGAG
**
4479258 AATTATCAAAATTTAATGAATA-AA
1 AATTATCAAAATTTAAAAAATAGAA
4479282 AATTATACAAAATTTAAAAAATAGAA
1 AATTAT-CAAAATTTAAAAAATAGAA
4479308 AATTA
1 AATTA
4479313 AATTAGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 6 0.22
25 14 0.52
26 7 0.26
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (25 bp):
AATTATCAAAATTTAAAAAATAGAA
Found at i:4480388 original size:27 final size:27
Alignment explanation
Indices: 4480350--4480404 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
4480340 CACATGCAAG
4480350 TTTTAGCATTGTTAACTACTAGTACTA
1 TTTTAGCATTGTTAACTACTAGTACTA
*
4480377 TTTTAGCATTGTTAACTCCTAGTACTA
1 TTTTAGCATTGTTAACTACTAGTACTA
4480404 T
1 T
4480405 CTAATTCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45
Consensus pattern (27 bp):
TTTTAGCATTGTTAACTACTAGTACTA
Found at i:4482613 original size:31 final size:31
Alignment explanation
Indices: 4482578--4482671 Score: 113
Period size: 31 Copynumber: 3.1 Consensus size: 31
4482568 TGAATTTAAA
**
4482578 TGTATATGTTTTATACATTGCCGAATTGATT
1 TGTATATGTGATATACATTGCCGAATTGATT
4482609 TG--TATGTAGATATACATTGCCGAATTTGATT
1 TGTATATGT-GATATACATTGCCGAA-TTGATT
* *
4482640 CGTATATG-GATATATATTGCCGAATTGATT
1 TGTATATGTGATATACATTGCCGAATTGATT
4482670 TG
1 TG
4482672 AGCATTGGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
29 5 0.09
30 21 0.39
31 24 0.44
33 4 0.07
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.44
Consensus pattern (31 bp):
TGTATATGTGATATACATTGCCGAATTGATT
Found at i:4482681 original size:31 final size:30
Alignment explanation
Indices: 4482589--4482671 Score: 121
Period size: 31 Copynumber: 2.7 Consensus size: 30
4482579 GTATATGTTT
* *
4482589 TATACATTGCCGAATTGATTTGTATGTAGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
4482619 TATACATTGCCGAATTTGATTCGTATATGGA
1 TATACATTGCCGAA-TTGATTTGTATATGGA
*
4482650 TATATATTGCCGAATTGATTTG
1 TATACATTGCCGAATTGATTTG
4482672 AGCATTGGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 21 0.45
31 26 0.55
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (30 bp):
TATACATTGCCGAATTGATTTGTATATGGA
Found at i:4482966 original size:43 final size:43
Alignment explanation
Indices: 4482788--4482953 Score: 287
Period size: 43 Copynumber: 3.9 Consensus size: 43
4482778 TTCCGAGGTT
4482788 AGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCAATTTG
1 AGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCAATTTG
4482831 AGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCAATTTG
1 AGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCAATTTG
* *
4482874 AGATTTCGTGTAAGACCATAGCTCGGCTATTGGCATCGATTTG
1 AGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCAATTTG
* * *
4482917 AGATTTCGTGTAAGACCATAGTTGGACTATTAGCATC
1 AGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATC
4482954 GATACGAGAT
Statistics
Matches: 117, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 117 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (43 bp):
AGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCAATTTG
Found at i:4488729 original size:22 final size:22
Alignment explanation
Indices: 4488680--4488738 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
4488670 TTTATACATG
4488680 ACTTAATAATTAATTAAGCTTT
1 ACTTAATAATTAATTAAGCTTT
* *
4488702 AATTAATTAATTAATTATG-TTT
1 ACTTAA-TAATTAATTAAGCTTT
*
4488724 TCTTAACTAATTAAT
1 ACTTAA-TAATTAAT
4488739 CATTACTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 20 0.65
23 11 0.35
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (22 bp):
ACTTAATAATTAATTAAGCTTT
Found at i:4493011 original size:19 final size:20
Alignment explanation
Indices: 4492985--4493045 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
4492975 ATATATATAC
4492985 TAAATAAAATAATAATAAAA
1 TAAATAAAATAATAATAAAA
*
4493005 T-AATAAAATAATATTTAAAA
1 TAAATAAAATAATA-ATAAAA
*
4493025 TCAAATTAAAATATTAATAAA
1 T-AAA-TAAAATAATAATAAA
4493046 CTCATATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 12 0.35
20 7 0.21
22 6 0.18
23 9 0.26
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAATAAAATAATAATAAAA
Found at i:4493543 original size:23 final size:23
Alignment explanation
Indices: 4493496--4493546 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
4493486 ACCTACTTTC
* *
4493496 TTACTGTAGTAATTTTTGGTGTA
1 TTACAGTAGTAATTTTCGGTGTA
4493519 TTACAGTAGTAATTTTCGG-GATA
1 TTACAGTAGTAATTTTCGGTG-TA
4493542 TTACA
1 TTACA
4493547 ATAACGCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGTGTA
Found at i:4495701 original size:9 final size:9
Alignment explanation
Indices: 4495681--4495712 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
4495671 AAACGAAACG
4495681 GAAAGAAAAA
1 GAAAG-AAAA
4495691 GAAAGAAAA
1 GAAAGAAAA
4495700 GAAAGAAAA
1 GAAAGAAAA
4495709 GAAA
1 GAAA
4495713 AGGGAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
GAAAGAAAA
Found at i:4514746 original size:92 final size:92
Alignment explanation
Indices: 4514589--4514775 Score: 313
Period size: 92 Copynumber: 2.0 Consensus size: 92
4514579 AATATTAATT
*
4514589 AAAGATGTCATTTTGTACATTGAAATAGCTACAAAGTAATCATTAACCATACAATGATTAACCCA
1 AAAGATGTCATTTTGTACATTGAAATACCTACAAAGTAATCATTAACCATACAATGATTAACCCA
* **
4514654 AACAACAAAGACTTCACCTTTGCCTAA
66 AACAAAAAAGACTTCACCTTCACCTAA
*
4514681 AAAGATGTCATTTTGTACATTGAAATAACCT-CAAAGTAATCATTAACCATACTATGATTAACCC
1 AAAGATGTCATTTTGTACATTGAAAT-ACCTACAAAGTAATCATTAACCATACAATGATTAACCC
4514745 AAACAAAAAAGACTTCACCTTCACCTAA
65 AAACAAAAAAGACTTCACCTTCACCTAA
4514773 AAA
1 AAA
4514776 ATGACAAATT
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 86 0.97
93 3 0.03
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.27
Consensus pattern (92 bp):
AAAGATGTCATTTTGTACATTGAAATACCTACAAAGTAATCATTAACCATACAATGATTAACCCA
AACAAAAAAGACTTCACCTTCACCTAA
Found at i:4515388 original size:14 final size:14
Alignment explanation
Indices: 4515369--4515399 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4515359 GGAATTGTTT
*
4515369 TAATCTAAATTTAC
1 TAATCTAAATTAAC
4515383 TAATCTAAATTAAC
1 TAATCTAAATTAAC
4515397 TAA
1 TAA
4515400 GAACGAGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:4524221 original size:31 final size:29
Alignment explanation
Indices: 4524183--4524256 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
4524173 ACTACCAAAA
* *
4524183 TAGTCACTTTTGTTTGGCACAGGTTACATTT
1 TAGTCACTTATGTTT-G-AAAGGTTACATTT
* *
4524214 TAGTCACTTATGTTTGAAATGTTACGTTT
1 TAGTCACTTATGTTTGAAAGGTTACATTT
4524243 TAGTCACTTATGTT
1 TAGTCACTTATGTT
4524257 ATCACGTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
30 1 0.03
31 14 0.36
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.47
Consensus pattern (29 bp):
TAGTCACTTATGTTTGAAAGGTTACATTT
Found at i:4524278 original size:31 final size:29
Alignment explanation
Indices: 4524208--4524281 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
4524198 GGCACAGGTT
* *
4524208 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
4524237 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
4524268 ACATTTTAGTCACT
1 ACATTTTAGTCACT
4524282 GAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:4536275 original size:46 final size:43
Alignment explanation
Indices: 4536223--4536456 Score: 235
Period size: 46 Copynumber: 5.6 Consensus size: 43
4536213 TTTGAGTACT
4536223 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG---TAGCTACACTTA
**
4536269 TCTGATCAAGAAACAAAGTGATAAGT-G--GT---TACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTAGCTACACTTA
**
4536306 TCTGATCAAGAAACAAAGTGATAA---GT-G--GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTAGCTACACTTA
*
4536343 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG--T-AGCTACACTTA
**
4536389 TCTGATCAAGTGGTAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG--TAGCTACACTTA
4536434 TCTGATCAAG-GAC-AAGTGATAAG
1 TCTGATCAAGTGACAAAGTGATAAG
4536457 AGGTCATATG
Statistics
Matches: 167, Mismatches: 9, Indels: 27
0.82 0.04 0.13
Matches are distributed among these distances:
35 1 0.01
36 1 0.01
37 61 0.37
40 3 0.02
41 1 0.01
43 11 0.07
44 1 0.01
45 22 0.13
46 66 0.40
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (43 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGTAGCTACACTTA
Found at i:4536302 original size:37 final size:37
Alignment explanation
Indices: 4536261--4536371 Score: 186
Period size: 37 Copynumber: 3.0 Consensus size: 37
4536251 TAGTTTTAGC
4536261 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
*
4536298 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGC
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
** *
4536335 TACACTTATCTGATCAAGTGATAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
4536372 AGCTTCAGCT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (37 bp):
TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
Found at i:4540474 original size:33 final size:35
Alignment explanation
Indices: 4540401--4540474 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
4540391 GGAGAAATAA
**
4540401 AACTATTCACAAGTGTTCATATATAAGTAAATTTT
1 AACTATTCACAAGTGTTCATATATAAGTAAATAGT
*
4540436 AACTATTCACAAGTGTTGATATATAAGTAAA-AGT
1 AACTATTCACAAGTGTTCATATATAAGTAAATAGT
4540470 -ACTAT
1 AACTAT
4540475 GGAGCCTATG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 5 0.14
34 1 0.03
35 30 0.83
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (35 bp):
AACTATTCACAAGTGTTCATATATAAGTAAATAGT
Found at i:4552481 original size:22 final size:22
Alignment explanation
Indices: 4552456--4552503 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
4552446 TTTAAATTTA
*
4552456 ACTTAAGTCTT-GAGACAATGTG
1 ACTTAAGT-TTCGAGACAATGTC
**
4552478 ACTTTTGTTTCGAGACAATGTC
1 ACTTAAGTTTCGAGACAATGTC
4552500 ACTT
1 ACTT
4552504 CGAAGCTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.38
Consensus pattern (22 bp):
ACTTAAGTTTCGAGACAATGTC
Found at i:4552901 original size:89 final size:89
Alignment explanation
Indices: 4552750--4552921 Score: 326
Period size: 89 Copynumber: 1.9 Consensus size: 89
4552740 TGGATTCAAA
4552750 TCCTAAATACAGGTTAACCCTGTACAATCATTACATTCTTTAAATGTGTTTAATTAACAAATGTT
1 TCCTAAATACAGGTTAACCCTGTACAATCATTACATTCTTTAAATGTGTTTAATTAACAAATGTT
4552815 TTATTTATCTACGTGTACAATCAT
66 TTATTTATCTACGTGTACAATCAT
*
4552839 TCCTAAATACAGGTTAACCCTGTACAATCATTCCATTCTTTAAATGTGTTTAATTAACAAATGTT
1 TCCTAAATACAGGTTAACCCTGTACAATCATTACATTCTTTAAATGTGTTTAATTAACAAATGTT
*
4552904 TTATTTGTCTACGTGTAC
66 TTATTTATCTACGTGTAC
4552922 GATATGAGAA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 81 1.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (89 bp):
TCCTAAATACAGGTTAACCCTGTACAATCATTACATTCTTTAAATGTGTTTAATTAACAAATGTT
TTATTTATCTACGTGTACAATCAT
Found at i:4556669 original size:94 final size:94
Alignment explanation
Indices: 4556508--4556698 Score: 337
Period size: 94 Copynumber: 2.0 Consensus size: 94
4556498 CGCAATAAAC
**
4556508 CTTGTTACAATTATGATTTTAATGCTTTGTTATTGCATAAATTGTATACACGAGAATACGGTCAT
1 CTTGTTACAATTATGATTTTAATGCTTTGTTATTGCATAAATTGTATACACGAGAATACAATCAT
4556573 GTTTAACGATAAATCAACTATGTTTAGCA
66 GTTTAACGATAAATCAACTATGTTTAGCA
*
4556602 CTTGTTACAATTATGCTTTTAATGCTTTGTTATTGCATAAATTGTATACACGAGAATACAATCAT
1 CTTGTTACAATTATGATTTTAATGCTTTGTTATTGCATAAATTGTATACACGAGAATACAATCAT
**
4556667 GTTTAACGATAAATCGGCTATGTTTAGCA
66 GTTTAACGATAAATCAACTATGTTTAGCA
4556696 CTT
1 CTT
4556699 AGTATGAAAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.40
Consensus pattern (94 bp):
CTTGTTACAATTATGATTTTAATGCTTTGTTATTGCATAAATTGTATACACGAGAATACAATCAT
GTTTAACGATAAATCAACTATGTTTAGCA
Found at i:4556819 original size:41 final size:39
Alignment explanation
Indices: 4556710--4556850 Score: 131
Period size: 41 Copynumber: 3.5 Consensus size: 39
4556700 GTATGAAATT
* * * **
4556710 TGAGATAGCTTCGGCTAATTATGACAGTTAGTGTGCGATT
1 TGAGATAGCTTCGGCT-ATTAAGGCACTTAGTGTGCGAGA
* *
4556750 TG-GAATAGCTTCGGTTATATATATGCACTTAGTGTGCGAGA
1 TGAG-ATAGCTTCGGCTAT-TA-AGGCACTTAGTGTGCGAGA
4556791 CTGAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCGAGA
1 -TGAGATAGCTTCGGCTAT-TAAGGCACTTAGTGTGCGAGA
* *
4556832 TTATAATAGCTTCGGCTAT
1 TGA-GATAGCTTCGGCTAT
4556851 ACGATGGCAA
Statistics
Matches: 83, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
39 3 0.04
40 17 0.20
41 45 0.54
42 17 0.20
43 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.33
Consensus pattern (39 bp):
TGAGATAGCTTCGGCTATTAAGGCACTTAGTGTGCGAGA
Found at i:4557563 original size:24 final size:23
Alignment explanation
Indices: 4557532--4557602 Score: 92
Period size: 22 Copynumber: 3.1 Consensus size: 23
4557522 TTTTTAGATG
4557532 TATAATGCTGTCCATTTTGAGCA
1 TATAATGCTGTCCATTTTGAGCA
* *
4557555 TATTGATGCTGTCCAATTTGATG--
1 TA-TAATGCTGTCCATTTTGA-GCA
4557578 TATAATGCTGTCCATTTTGAGCA
1 TATAATGCTGTCCATTTTGAGCA
4557601 TA
1 TA
4557603 ATTTGATGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 1 0.03
22 16 0.40
23 6 0.15
24 16 0.40
25 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.41
Consensus pattern (23 bp):
TATAATGCTGTCCATTTTGAGCA
Found at i:4557588 original size:22 final size:22
Alignment explanation
Indices: 4557523--4557597 Score: 89
Period size: 22 Copynumber: 3.3 Consensus size: 22
4557513 ATGTGGTTGT
4557523 TTTTAGATGTATAATGCTGTCCA
1 TTTT-GATGTATAATGCTGTCCA
*
4557546 TTTTGA-GCATATTGATGCTGTCCA
1 TTTTGATG--TA-TAATGCTGTCCA
*
4557570 ATTTGATGTATAATGCTGTCCA
1 TTTTGATGTATAATGCTGTCCA
4557592 TTTTGA
1 TTTTGA
4557598 GCATAATTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
21 1 0.02
22 18 0.41
23 8 0.18
24 16 0.36
25 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (22 bp):
TTTTGATGTATAATGCTGTCCA
Found at i:4561589 original size:15 final size:15
Alignment explanation
Indices: 4561552--4561594 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
4561542 CCAATTCGCC
4561552 CTTT-TTCTTT-TCT
1 CTTTCTTCTTTCTCT
*
4561565 CTTTCGTCTTTCTCT
1 CTTTCTTCTTTCTCT
*
4561580 GTTTCTTCTTTCTCT
1 CTTTCTTCTTTCTCT
4561595 TTTGTTTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 4 0.16
14 5 0.20
15 16 0.64
ACGTcount: A:0.00, C:0.28, G:0.05, T:0.67
Consensus pattern (15 bp):
CTTTCTTCTTTCTCT
Found at i:4561798 original size:21 final size:21
Alignment explanation
Indices: 4561774--4561819 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4561764 AAAATCTTAT
*
4561774 AATATA-ATTATTTAATTAATA
1 AATATATATTACTTAA-TAATA
*
4561795 AATATATTTTACTTAATAATA
1 AATATATATTACTTAATAATA
4561816 AATA
1 AATA
4561820 ATAGATATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
AATATATATTACTTAATAATA
Found at i:4561861 original size:29 final size:27
Alignment explanation
Indices: 4561786--4561861 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 27
4561776 TATAATTATT
*
4561786 TAATTAATAAATATATTTTACTTAATAA
1 TAATTAATAAATATA-TTTACTTAAAAA
* *
4561814 TAAATAATAGATATCTATTTACTTAAAAA
1 TAATTAATA-A-ATATATTTACTTAAAAA
4561843 GTAATTAAATAAATATATT
1 -TAATT-AATAAATATATT
4561862 ACAAATGTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 8 0.21
29 18 0.46
30 9 0.23
31 4 0.10
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (27 bp):
TAATTAATAAATATATTTACTTAAAAA
Found at i:4562496 original size:25 final size:25
Alignment explanation
Indices: 4562462--4562520 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
4562452 GAGCTTCGGA
4562462 TAGCCATATATCGGGAAGTTCAAGC
1 TAGCCATATATCGGGAAGTTCAAGC
*
4562487 TAGCCATATATTGGGAAGTTCAAGC
1 TAGCCATATATCGGGAAGTTCAAGC
*
4562512 GAGCCATAT
1 TAGCCATAT
4562521 CAAGACGCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (25 bp):
TAGCCATATATCGGGAAGTTCAAGC
Found at i:4563619 original size:30 final size:30
Alignment explanation
Indices: 4563570--4563629 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
4563560 TTTATTTATC
4563570 ATTTATCATCTTTTATTATTTCACTTTCCA
1 ATTTATCATCTTTTATTATTTCACTTTCCA
* * *
4563600 ATTTCATCAT-TTTTTTTATTTTATTTTCCA
1 ATTT-ATCATCTTTTATTATTTCACTTTCCA
4563630 TGGATGAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.62
Consensus pattern (30 bp):
ATTTATCATCTTTTATTATTTCACTTTCCA
Found at i:4568405 original size:28 final size:28
Alignment explanation
Indices: 4568355--4568418 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
4568345 GACTCACATT
4568355 CCCAAATC-TCAAATTAAAAAAAAAAAC
1 CCCAAATCTTCAAATTAAAAAAAAAAAC
* *
4568382 CCCAAATCTTTAAA-TAATAAAAAAAATC
1 CCCAAATCTTCAAATTAA-AAAAAAAAAC
4568410 CCCAAATCT
1 CCCAAATCT
4568419 CGTCTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 11 0.33
28 22 0.67
ACGTcount: A:0.56, C:0.23, G:0.00, T:0.20
Consensus pattern (28 bp):
CCCAAATCTTCAAATTAAAAAAAAAAAC
Found at i:4577293 original size:19 final size:19
Alignment explanation
Indices: 4577234--4577293 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
4577224 ACATGTGGTA
*
4577234 AAAAAATT-ATAAAAA-AT
1 AAAAAATTAATAAAAAGTT
4577251 -AAAAATTAATAAAAAGTT
1 AAAAAATTAATAAAAAGTT
* * **
4577269 ATAAAATTAATTAAATTTT
1 AAAAAATTAATAAAAAGTT
4577288 AAAAAA
1 AAAAAA
4577294 AAATATTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 7 0.21
17 7 0.21
18 1 0.03
19 19 0.56
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAAATTAATAAAAAGTT
Found at i:4577336 original size:18 final size:19
Alignment explanation
Indices: 4577309--4577351 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
4577299 TTTTAAATTT
4577309 ATTA-AAAATT-AGAAAAA
1 ATTATAAAATTCAGAAAAA
*
4577326 ATTATAAAATTCATAAAAA
1 ATTATAAAATTCAGAAAAA
4577345 ATATATA
1 AT-TATA
4577352 TTTTAACCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 6 0.27
19 8 0.36
20 4 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
ATTATAAAATTCAGAAAAA
Found at i:4577556 original size:10 final size:9
Alignment explanation
Indices: 4577511--4577719 Score: 81
Period size: 9 Copynumber: 21.9 Consensus size: 9
4577501 CTTTGGTAAG
4577511 ATAATTTTT
1 ATAATTTTT
4577520 ATAATTCTTTTT
1 ATAA---TTTTT
* *
4577532 ACAAATTTT
1 ATAATTTTT
4577541 AT-ATTTTT
1 ATAATTTTT
4577549 ATACATTTTT
1 ATA-ATTTTT
4577559 ATAATTTTCT
1 ATAATTTT-T
*
4577569 -TACGACTTTAT
1 ATA--A-TTTTT
*
4577580 AAAATTTTAT
1 ATAATTTT-T
*
4577590 ATTATTTTCT
1 ATAATTTT-T
*
4577600 AT-ATTTCT
1 ATAATTTTT
4577608 AT-ATATTTT
1 ATAAT-TTTT
*
4577617 ATACTTTTT
1 ATAATTTTT
4577626 -TACGATTTTT
1 ATA--ATTTTT
4577636 ATAAATTTTTT
1 AT-AA-TTTTT
*
4577647 CTAATTTTT
1 ATAATTTTT
*
4577656 AGTAAATTTT
1 A-TAATTTTT
*
4577666 AAATATTTTT
1 ATA-ATTTTT
* *
4577676 ATTAAAATTTA
1 A-T-AATTTTT
4577687 ATAATTTTT
1 ATAATTTTT
4577696 ATAATTTTT
1 ATAATTTTT
4577705 AT--TTTTT
1 ATAATTTTT
*
4577712 ATTATTTT
1 ATAATTTT
4577720 GTTACCACAT
Statistics
Matches: 152, Mismatches: 24, Indels: 48
0.68 0.11 0.21
Matches are distributed among these distances:
7 7 0.05
8 14 0.09
9 58 0.38
10 45 0.30
11 14 0.09
12 14 0.09
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:4577588 original size:39 final size:39
Alignment explanation
Indices: 4577514--4577590 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
4577504 TGGTAAGATA
* * *
4577514 ATTTTTATAATTCTTTTTACAAATTTTATATTTTTATAC
1 ATTTTTATAATTCTTCTTACAAATTTTAAAATTTTATAC
* *
4577553 ATTTTTATAATT-TTCTTACGACTTTATAAAATTTTATA
1 ATTTTTATAATTCTTCTTACAAATTT-TAAAATTTTATA
4577591 TTATTTTCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 10 0.31
39 22 0.69
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.58
Consensus pattern (39 bp):
ATTTTTATAATTCTTCTTACAAATTTTAAAATTTTATAC
Found at i:4577673 original size:20 final size:20
Alignment explanation
Indices: 4577630--4577705 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
4577620 CTTTTTTACG
***
4577630 ATTTTTATAAATTTTTTCTA
1 ATTTTTATAAATTTTAAATA
4577650 ATTTTTAGTAAATTTTAAAT-
1 ATTTTTA-TAAATTTTAAATA
*
4577670 ATTTTTATTAAAATTT-AATA
1 ATTTTTA-TAAATTTTAAATA
*
4577690 ATTTTTATAATTTTTA
1 ATTTTTATAAATTTTA
4577706 TTTTTTATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 9 0.20
20 28 0.61
21 9 0.20
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (20 bp):
ATTTTTATAAATTTTAAATA
Found at i:4589639 original size:46 final size:46
Alignment explanation
Indices: 4589571--4589755 Score: 289
Period size: 46 Copynumber: 4.0 Consensus size: 46
4589561 TGGAAAAGTG
*
4589571 TGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
* * * *
4589617 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACTATATTGAGTTG
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
* * *
4589663 TGAAAAGTAGGTATGGTGTTTCCGTGAAGAAAACCATACTGAGTTG
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
*
4589709 TGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGTTA
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
4589755 T
1 T
4589756 AGCAATGTGA
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 129 1.00
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (46 bp):
TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
Found at i:4603965 original size:34 final size:34
Alignment explanation
Indices: 4603927--4604005 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
4603917 AAGGTTATGT
*
4603927 GTTTTTTAAAAAA-TAATTAAATTAGATTTTAG-
1 GTTTTTTAAAAAATTAATTAAATTAGAGTTTAGA
** *
4603959 GGGTTTTAAATAAATTAATTAAATTAGGGTTTAGA
1 GTTTTTTAAA-AAATTAATTAAATTAGAGTTTAGA
4603994 GTTTTTTAAAAA
1 GTTTTTTAAAAA
4604006 TAAGTTTGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
32 8 0.21
33 3 0.08
34 19 0.50
35 8 0.21
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (34 bp):
GTTTTTTAAAAAATTAATTAAATTAGAGTTTAGA
Found at i:4605971 original size:101 final size:101
Alignment explanation
Indices: 4605812--4606023 Score: 264
Period size: 101 Copynumber: 2.1 Consensus size: 101
4605802 ATGGCCCTGG
*** *
4605812 CATGGTCTTACATTTGTAGTGTCATAACCCAGTTATGATATTATCATCAGAATGCCATAGCCCAG
1 CATGGTCTTACATTCAAAGTGTCATAACCCAGTTATGATATTATCATCAAAATGCCATAGCCCAG
* *
4605877 CTATGGTCTTACATATATATACTGT-CATGGTCCAAC
66 CTATGGTCTTACATATAAACACT-TCCATGGTCCAAC
* * * * * * *
4605913 CATGGTCTTACATTCAAAGTGTCATAACCTAGTTATGGTCTTTTCATTAAAATTCCATAGCCTAG
1 CATGGTCTTACATTCAAAGTGTCATAACCCAGTTATGATATTATCATCAAAATGCCATAGCCCAG
* * *
4605978 TTATGGTCTTACATTTAAACACTTCCATGGTCTAAC
66 CTATGGTCTTACATATAAACACTTCCATGGTCCAAC
4606014 CATGGTCTTA
1 CATGGTCTTA
4606024 TCCATCAATT
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
100 1 0.01
101 93 0.99
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (101 bp):
CATGGTCTTACATTCAAAGTGTCATAACCCAGTTATGATATTATCATCAAAATGCCATAGCCCAG
CTATGGTCTTACATATAAACACTTCCATGGTCCAAC
Found at i:4605996 original size:33 final size:33
Alignment explanation
Indices: 4605914--4606005 Score: 98
Period size: 33 Copynumber: 2.7 Consensus size: 33
4605904 TGGTCCAACC
* *
4605914 ATGGTCTTACATTCAAAGTGT-CATAACCTAGTT
1 ATGGTCTTACATTTAAAAT-TCCATAACCTAGTT
* *
4605947 ATGGTCTTTTCA-TTAAAATTCCATAGCCTAGTT
1 ATGGTC-TTACATTTAAAATTCCATAACCTAGTT
4605980 ATGGTCTTACATTTAAACACTTCCAT
1 ATGGTCTTACATTTAAA-A-TTCCAT
4606006 GGTCTAACCA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
32 5 0.10
33 33 0.67
34 5 0.10
35 6 0.12
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (33 bp):
ATGGTCTTACATTTAAAATTCCATAACCTAGTT
Found at i:4610083 original size:58 final size:59
Alignment explanation
Indices: 4609975--4610089 Score: 139
Period size: 58 Copynumber: 2.0 Consensus size: 59
4609965 ATTCAAAAGA
*
4609975 ACTTCTATTTTATTAAATAAAAATATAAAAATAATTTACTATTAAAATA-TTAAAAACT
1 ACTTCTATTTTATTAAATAAAAATATAAAAATAATTTACTATCAAAATATTTAAAAACT
* **
4610033 ACTTTTATTTTATTAAATGAAATAATAT-AAAA-AATTTTGTA-CAAATATATTTAAAAA
1 ACTTCTATTTTATTAAAT-AAA-AATATAAAAATAATTTACTATCAAA-ATATTTAAAAA
4610090 AATCAATGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
57 3 0.06
58 27 0.55
59 14 0.29
60 5 0.10
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (59 bp):
ACTTCTATTTTATTAAATAAAAATATAAAAATAATTTACTATCAAAATATTTAAAAACT
Found at i:4612272 original size:30 final size:30
Alignment explanation
Indices: 4612238--4612302 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
4612228 ATTAATTAAA
4612238 GAGAGCTTTGAGAAATTTA-AGGAGAAATTT
1 GAGAGCTTTGAGAAATTTAGA-GAGAAATTT
4612268 GAGAGCTTTGAGAAATTTAGAGAGAAATTT
1 GAGAGCTTTGAGAAATTTAGAGAGAAATTT
4612298 GAGAG
1 GAGAG
4612303 TTTTTTGCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 33 0.97
31 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.29, T:0.28
Consensus pattern (30 bp):
GAGAGCTTTGAGAAATTTAGAGAGAAATTT
Found at i:4613476 original size:28 final size:28
Alignment explanation
Indices: 4613445--4613500 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
4613435 TTGTTGTTTC
*
4613445 TGATGATGGGTTAAGAGAAGTAAAATGA
1 TGATGATGGGTTAAAAGAAGTAAAATGA
4613473 TGATGATGGGTTAAAAGAAGTAAAATGA
1 TGATGATGGGTTAAAAGAAGTAAAATGA
4613501 AGATTATGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.25
Consensus pattern (28 bp):
TGATGATGGGTTAAAAGAAGTAAAATGA
Found at i:4621578 original size:21 final size:20
Alignment explanation
Indices: 4621553--4621591 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
4621543 ATGCAAAGTG
4621553 TTTTA-TTTATATATTTTTACT
1 TTTTACTTT-TAT-TTTTTACT
4621574 TTTTACTTTTATTTTTTA
1 TTTTACTTTTATTTTTTA
4621592 TTACTTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 8 0.47
22 3 0.18
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTACTTTTATTTTTTACT
Found at i:4624750 original size:20 final size:20
Alignment explanation
Indices: 4624725--4624764 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4624715 AATATTTTCT
*
4624725 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
4624745 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
4624765 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:4624767 original size:34 final size:35
Alignment explanation
Indices: 4624713--4624779 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
4624703 CAAACAGTAG
* *
4624713 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
4624748 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
4624780 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:4624771 original size:14 final size:14
Alignment explanation
Indices: 4624748--4624787 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
4624738 ACAGAAAAGT
*
4624748 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
4624762 AAATCATTTTACGG
1 AAAACATTTTACAG
4624776 AAAACATTTTAC
1 AAAACATTTTAC
4624788 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:4630322 original size:6 final size:7
Alignment explanation
Indices: 4630303--4630327 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4630293 CAAAATTATT
4630303 ATAAAAA
1 ATAAAAA
4630310 ATAAAAA
1 ATAAAAA
4630317 ATAAAAA
1 ATAAAAA
4630324 ATAA
1 ATAA
4630328 CTAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
ATAAAAA
Found at i:4630360 original size:27 final size:28
Alignment explanation
Indices: 4630330--4630391 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
4630320 AAAAATAACT
*
4630330 AAAATATTAT-AACTTTTTTTATTTACC
1 AAAATATTATAAAATTTTTTTATTTACC
4630357 AAAATATTATAAAATTTTTTTATTTACC
1 AAAATATTATAAAATTTTTTTATTTACC
4630385 AAAATAT
1 AAAATAT
4630392 GCCCAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 10 0.30
28 23 0.70
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (28 bp):
AAAATATTATAAAATTTTTTTATTTACC
Found at i:4630830 original size:11 final size:11
Alignment explanation
Indices: 4630811--4630854 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
4630801 AACACCGAAC
*
4630811 TTTTTGGGTAA
1 TTTTCGGGTAA
4630822 TTTTCGGGTAA
1 TTTTCGGGTAA
4630833 --TTCGGGTAA
1 TTTTCGGGTAA
4630842 TTTTCGGGTAA
1 TTTTCGGGTAA
4630853 TT
1 TT
4630855 CGGTTAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 9 0.30
11 21 0.70
ACGTcount: A:0.18, C:0.07, G:0.27, T:0.48
Consensus pattern (11 bp):
TTTTCGGGTAA
Found at i:4630838 original size:9 final size:9
Alignment explanation
Indices: 4630824--4630898 Score: 107
Period size: 9 Copynumber: 8.2 Consensus size: 9
4630814 TTGGGTAATT
4630824 TTCGGGTAA
1 TTCGGGTAA
4630833 TTCGGGTAA
1 TTCGGGTAA
4630842 TTTTCGGGTAA
1 --TTCGGGTAA
*
4630853 TTCGGTTAA
1 TTCGGGTAA
*
4630862 TTCGGTTAA
1 TTCGGGTAA
4630871 TT-GGGTAA
1 TTCGGGTAA
4630879 TTCGGGTAA
1 TTCGGGTAA
4630888 TTCGGGTAA
1 TTCGGGTAA
4630897 TT
1 TT
4630899 TTTAACCAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
8 7 0.11
9 45 0.74
11 9 0.15
ACGTcount: A:0.21, C:0.09, G:0.29, T:0.40
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:4630841 original size:20 final size:20
Alignment explanation
Indices: 4630816--4630900 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
4630806 CGAACTTTTT
4630816 GGGTAATTTTCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
4630836 GGGTAATTTTCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
* *
4630856 GGTTAA--TTCGGTTAATT-
1 GGGTAATTTTCGGGTAATTC
4630873 GGGTAA--TTCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
4630891 GGGTAATTTT
1 GGGTAATTTT
4630901 TAACCAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
17 15 0.26
18 16 0.28
20 27 0.47
ACGTcount: A:0.21, C:0.08, G:0.29, T:0.41
Consensus pattern (20 bp):
GGGTAATTTTCGGGTAATTC
Found at i:4631542 original size:19 final size:19
Alignment explanation
Indices: 4631518--4631613 Score: 115
Period size: 19 Copynumber: 5.2 Consensus size: 19
4631508 TCTAATTAAG
*
4631518 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTCATT
* * *
4631537 TAATAA-ACTGTTATCATT
1 TAATAACTCTATTTTCATT
*
4631555 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTCATT
* *
4631574 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTCATT
4631592 TAATAACTCTATTTTCATT
1 TAATAACTCTATTTTCATT
4631611 TAA
1 TAA
4631614 AATATAAAAT
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
18 29 0.47
19 33 0.53
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.49
Consensus pattern (19 bp):
TAATAACTCTATTTTCATT
Found at i:4631568 original size:37 final size:37
Alignment explanation
Indices: 4631518--4631613 Score: 165
Period size: 37 Copynumber: 2.6 Consensus size: 37
4631508 TCTAATTAAG
*
4631518 TAATAACTCTATTTTAATTTAATAAACTGTTATCATT
1 TAATAACTCTATTTTAATTTAATAAACTATTATCATT
*
4631555 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTATTATCATT
*
4631592 TAATAACTCTATTTTCATTTAA
1 TAATAACTCTATTTTAATTTAA
4631614 AATATAAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.49
Consensus pattern (37 bp):
TAATAACTCTATTTTAATTTAATAAACTATTATCATT
Found at i:4632221 original size:22 final size:22
Alignment explanation
Indices: 4632196--4632237 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
4632186 TAGTCCTTTG
4632196 GCACCATTGGTGCCGCCAATCA
1 GCACCATTGGTGCCGCCAATCA
*
4632218 GCACCTTTGGTGCCGCCAAT
1 GCACCATTGGTGCCGCCAAT
4632238 GTGATTAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.36, G:0.24, T:0.21
Consensus pattern (22 bp):
GCACCATTGGTGCCGCCAATCA
Found at i:4632327 original size:28 final size:28
Alignment explanation
Indices: 4632290--4632360 Score: 117
Period size: 28 Copynumber: 2.6 Consensus size: 28
4632280 TTTTTGTTTT
*
4632290 TTTAT-ATATTTTGGTAAATAAATAAAA
1 TTTATAATATTTTGGTAAATAAAAAAAA
4632317 TTTATAATATTTTGGTAAATAAAAAAAA
1 TTTATAATATTTTGGTAAATAAAAAAAA
*
4632345 GTTATAATATTTTGGT
1 TTTATAATATTTTGGT
4632361 TATTTTTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 5 0.12
28 36 0.88
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (28 bp):
TTTATAATATTTTGGTAAATAAAAAAAA
Found at i:4643644 original size:33 final size:32
Alignment explanation
Indices: 4643576--4643647 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
4643566 ATTTGCATAT
*
4643576 AAAAATTGATAAAATTATTGTTTAGACCCCCA
1 AAAAATTGATAAAATTATTATTTAGACCCCCA
* * *
4643608 AAAATATTGATAAAA-TGTTATTTGGTCCCCCTA
1 AAAA-ATTGATAAAATTATTATTTAGACCCCC-A
4643641 AAAAATT
1 AAAAATT
4643648 ACTTGACTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
32 19 0.56
33 15 0.44
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (32 bp):
AAAAATTGATAAAATTATTATTTAGACCCCCA
Found at i:4644831 original size:30 final size:31
Alignment explanation
Indices: 4644770--4644837 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
4644760 TTAATTAACT
**
4644770 TATTATTTTAGAATATTTTTAAAATTTTTATA
1 TATT-TTTTAGAATATTTTTAAAATAATTATA
*
4644802 TATTTTTTAGAATTTTTTTAAAA-AATTATA
1 TATTTTTTAGAATATTTTTAAAATAATTATA
4644832 T-TTTTT
1 TATTTTT
4644838 AAAATATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 5 0.15
30 6 0.18
31 18 0.55
32 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (31 bp):
TATTTTTTAGAATATTTTTAAAATAATTATA
Found at i:4644884 original size:27 final size:28
Alignment explanation
Indices: 4644844--4644899 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
4644834 TTTTAAAATA
*
4644844 TAAATTTTAGAATTT-TTATAAATATTT
1 TAAATTTTAAAATTTATTATAAATATTT
* *
4644871 TAAATTTTAAAATTTATTTTGAATATTT
1 TAAATTTTAAAATTTATTATAAATATTT
4644899 T
1 T
4644900 TGTAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (28 bp):
TAAATTTTAAAATTTATTATAAATATTT
Found at i:4656595 original size:18 final size:18
Alignment explanation
Indices: 4656564--4656598 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4656554 TGATTTATTG
4656564 TTTTATTTTATTTATTTA
1 TTTTATTTTATTTATTTA
4656582 TTTTAATTTT-TTTATTT
1 TTTT-ATTTTATTTATTT
4656599 GACTTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTATTTTATTTATTTA
Found at i:4656605 original size:14 final size:13
Alignment explanation
Indices: 4656557--4656598 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
4656547 TAATCTTTGA
*
4656557 TTTATTGTTTTAT
1 TTTATTTTTTTAT
*
4656570 TTTATTTATTTAT
1 TTTATTTTTTTAT
4656583 TTTAATTTTTTTAT
1 TTT-ATTTTTTTAT
4656597 TT
1 TT
4656599 GACTTTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTATTTTTTTAT
Found at i:4669519 original size:21 final size:21
Alignment explanation
Indices: 4669493--4669534 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4669483 AAAAAATCTT
4669493 ATATTTGCAATTAATAATTAA
1 ATATTTGCAATTAATAATTAA
* * *
4669514 ATATTTGTAATTTATATTTAA
1 ATATTTGCAATTAATAATTAA
4669535 TTCAATTACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (21 bp):
ATATTTGCAATTAATAATTAA
Found at i:4676615 original size:26 final size:25
Alignment explanation
Indices: 4676586--4676640 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
4676576 TCAAATATAA
* *
4676586 TATTTTTCTTTAAAAGAATAGAAAAT
1 TATTTTTCCTCAAAA-AATAGAAAAT
*
4676612 TA--TTTCCTCATAAAATAGAAAAT
1 TATTTTTCCTCAAAAAATAGAAAAT
4676635 TATTTT
1 TATTTT
4676641 CAAGGTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
23 12 0.50
24 8 0.33
25 2 0.08
26 2 0.08
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (25 bp):
TATTTTTCCTCAAAAAATAGAAAAT
Found at i:4680916 original size:10 final size:11
Alignment explanation
Indices: 4680890--4680915 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4680880 TAAAATTTAA
4680890 AAAAATATTTT
1 AAAAATATTTT
4680901 AAAAATATTTT
1 AAAAATATTTT
4680912 AAAA
1 AAAA
4680916 TTAAAAAAAG
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:4680946 original size:41 final size:39
Alignment explanation
Indices: 4680873--4681003 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 39
4680863 ATTTTAAAAA
* *
4680873 TTAAAATT--AAAATTTAAAAAAATATTTTAAAAATATT
1 TTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAATATT
*
4680910 TTAAAATTAAAAAAAGTTAAAAAAGTATTTTAAAAAAATT
1 TTAAAATTAAAAAAA-TTAAAAAAGTATTTTAAAAATATT
*
4680950 TTAAAATTAAAAAAATTAAAAAAAAGTATTTTAAAAGTATT
1 TTAAAATTAAAAAAATT--AAAAAAGTATTTTAAAAATATT
*
4680991 TTAAAGTTAAAAA
1 TTAAAATTAAAAA
4681004 TAAAAATAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
37 8 0.10
39 6 0.07
40 37 0.45
41 32 0.39
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (39 bp):
TTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAATATT
Found at i:4680964 original size:9 final size:9
Alignment explanation
Indices: 4680912--4680973 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 9
4680902 AAAATATTTT
4680912 AAAATTAAA
1 AAAATTAAA
4680921 AAAAGTTAAA
1 AAAA-TTAAA
4680931 AAAGTATTTTAAA
1 AAA--A--TTAAA
**
4680944 AAAATT-TT
1 AAAATTAAA
4680952 AAAATTAAA
1 AAAATTAAA
4680961 AAAATTAAA
1 AAAATTAAA
4680970 AAAA
1 AAAA
4680974 AGTATTTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
8 6 0.14
9 19 0.44
10 8 0.19
11 1 0.02
12 1 0.02
13 8 0.19
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (9 bp):
AAAATTAAA
Found at i:4680972 original size:17 final size:17
Alignment explanation
Indices: 4680939--4680972 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4680929 AAAAAGTATT
**
4680939 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTAAAAAA
4680956 TTAAAAAAATTAAAAAA
1 TTAAAAAAATTAAAAAA
4680973 AAGTATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TTAAAAAAATTAAAAAA
Found at i:4680985 original size:11 final size:11
Alignment explanation
Indices: 4680971--4680995 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4680961 AAAATTAAAA
4680971 AAAAGTATTTT
1 AAAAGTATTTT
4680982 AAAAGTATTTT
1 AAAAGTATTTT
4680993 AAA
1 AAA
4680996 GTTAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:4687689 original size:32 final size:33
Alignment explanation
Indices: 4687636--4687701 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
4687626 TTTAGAAGTC
* * *
4687636 TAATTTGATTTGATTTTAAATTTAAT-CGAACT
1 TAATTTAATTTAATTTCAAATTTAATCCGAACT
4687668 TAATTTAATTTAATTTCAAATTTAATCCGAACT
1 TAATTTAATTTAATTTCAAATTTAATCCGAACT
4687701 T
1 T
4687702 GATAAAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 23 0.77
33 7 0.23
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (33 bp):
TAATTTAATTTAATTTCAAATTTAATCCGAACT
Found at i:4691603 original size:6 final size:6
Alignment explanation
Indices: 4691585--4691622 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
4691575 CAAGGAGAGA
*
4691585 AGGGAG A-GGAG AGGGAG AGGGAG AGGGAG AGGCAG AGG
1 AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGG
4691623 AGGTGGTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.34, C:0.03, G:0.63, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:4705434 original size:2 final size:2
Alignment explanation
Indices: 4705427--4705463 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4705417 TTTCAGTTCA
4705427 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
4705464 CTAATTAAAG
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:4706130 original size:2 final size:2
Alignment explanation
Indices: 4706123--4706154 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4706113 ATTTTAGTCC
4706123 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
4706155 CTCTTCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.