Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 23 of 226
Found at i:10493871 original size:115 final size:115
Alignment explanation
Indices: 10493660--10493899 Score: 410
Period size: 115 Copynumber: 2.1 Consensus size: 115
10493650 AAATATTTCT
10493660 GGCGTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTTACAGTTAAAG
1 GGCGTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTTACAGTTAAAG
** *
10493725 GAAATTTGTGGCGTTTCTTCGTAAAACGCCGGTAATATATCACTTTTAGC
66 GAAATTTGTGGCGTTTCTTCACAAAACGCCGGTAATATATCACCTTTAGC
*
10493775 GGCGTTTTTCAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTTACAGTTAAAG
1 GGCGTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTTACAGTTAAAG
*
10493840 GAAATTT-TCGGCGTTTCTTCACAAAATGCCGGTAATATATCACCTTTAGC
66 GAAATTTGT-GGCGTTTCTTCACAAAACGCCGGTAATATATCACCTTTAGC
10493890 GGCGCTTTTT
1 GGCG-TTTTT
10493900 TTGAAGCGCC
Statistics
Matches: 118, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
114 1 0.01
115 112 0.95
116 5 0.04
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (115 bp):
GGCGTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTTACAGTTAAAG
GAAATTTGTGGCGTTTCTTCACAAAACGCCGGTAATATATCACCTTTAGC
Found at i:10494394 original size:14 final size:13
Alignment explanation
Indices: 10494377--10494428 Score: 68
Period size: 14 Copynumber: 3.8 Consensus size: 13
10494367 CCTAAACCCC
*
10494377 AAACCTAAAACTCT
1 AAACCT-AAACTGT
10494391 AAACTCTAAACTGT
1 AAAC-CTAAACTGT
10494405 AAACCCTAAACTGT
1 AAA-CCTAAACTGT
10494419 AAACCTAAAC
1 AAACCTAAAC
10494429 CATATTTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
13 7 0.20
14 25 0.71
15 3 0.09
ACGTcount: A:0.48, C:0.27, G:0.04, T:0.21
Consensus pattern (13 bp):
AAACCTAAACTGT
Found at i:10494401 original size:7 final size:7
Alignment explanation
Indices: 10494384--10494428 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
10494374 CCCAAACCTA
10494384 AAACTCT
1 AAACTCT
10494391 AAACTCT
1 AAACTCT
*
10494398 AAACTGT
1 AAACTCT
*
10494405 AAACCCT
1 AAACTCT
*
10494412 AAACTGT
1 AAACTCT
10494419 AAAC-CT
1 AAACTCT
10494425 AAAC
1 AAAC
10494429 CATATTTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.47, C:0.27, G:0.04, T:0.22
Consensus pattern (7 bp):
AAACTCT
Found at i:10494401 original size:21 final size:21
Alignment explanation
Indices: 10494367--10494427 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
10494357 AATCATAAAT
* *
10494367 CCTAAACCCCAAACCTAAAAC
1 CCTAAACTCTAAACCTAAAAC
* *
10494388 TCTAAACTCTAAA-CTGTAAAC
1 CCTAAACTCTAAACCT-AAAAC
*
10494409 CCTAAACTGTAAACCTAAA
1 CCTAAACTCTAAACCTAAA
10494428 CCATATTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.46, C:0.31, G:0.03, T:0.20
Consensus pattern (21 bp):
CCTAAACTCTAAACCTAAAAC
Found at i:10494794 original size:23 final size:21
Alignment explanation
Indices: 10494767--10494822 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
10494757 ACCCTAACCG
* *
10494767 TAACCCCTAAATCCCTTAACCCC
1 TAACCCCTAAA--CCATAACACC
*
10494790 TAACCCCTAAAGCATAACACC
1 TAACCCCTAAACCATAACACC
10494811 TAACCCCTAAAC
1 TAACCCCTAAAC
10494823 TTTAAATCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.62
23 11 0.38
ACGTcount: A:0.38, C:0.43, G:0.02, T:0.18
Consensus pattern (21 bp):
TAACCCCTAAACCATAACACC
Found at i:10495318 original size:75 final size:77
Alignment explanation
Indices: 10495181--10495324 Score: 202
Period size: 75 Copynumber: 1.9 Consensus size: 77
10495171 CCGCTAAAGT
* * * *
10495181 AAGCATTAGCGGCGCTTTACTAGAAAACGCTGCTAACGCCACTGAAAGTTAAGAAAACGGTGCCG
1 AAGCAATAGCGGCGCTTCACTAGAAAACGCCGCTAACGCCACTGAAAGATAAGAAAACGGTGCCG
10495246 TTGGGCACCCCC
66 TTGGGCACCCCC
* * **
10495258 AAGCAATAGCGGCGCTTCACTA-AAAACGCCGCTAAGGCCTC-GAAAGATCTGAAAACGGTGCCG
1 AAGCAATAGCGGCGCTTCACTAGAAAACGCCGCTAACGCCACTGAAAGATAAGAAAACGGTGCCG
10495321 TTGG
66 TTGG
10495325 ACATATGTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
75 23 0.39
76 16 0.27
77 20 0.34
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (77 bp):
AAGCAATAGCGGCGCTTCACTAGAAAACGCCGCTAACGCCACTGAAAGATAAGAAAACGGTGCCG
TTGGGCACCCCC
Found at i:10495530 original size:72 final size:70
Alignment explanation
Indices: 10495428--10495620 Score: 190
Period size: 72 Copynumber: 2.7 Consensus size: 70
10495418 TGAGAAAATG
*
10495428 ACACCATTTGGCTTAGGTTTTTTAGCGGCGCTTCCCCAAAAACGCCGCTAAAT-CCCAAAAACTA
1 ACACCGTTTGGCTTAGG--TTTTAGCGGCGCTTCCCCAAAAACGCCGCTAAATCCCCAAAAAC-A
10495492 CGGAAACA
63 CGGAAACA
* **** * *
10495500 ACACCGTTTGGCTTAGGATTATTAGTGGCGCTTGATTAAAAACGTCGCTAAATCCCCAGAAACAC
1 ACACCGTTTGGCTTAGG-TT-TTAGCGGCGCTTCCCCAAAAACGCCGCTAAATCCCCAAAAACAC
*
10495565 GGAAACG
64 GGAAACA
*** * * * *
10495572 ATGTCGTTGGGCTTTGGTTTTTGCGGCGCTTCCCGAAAAACGCCGCTAA
1 ACACCGTTTGGCTTAGGTTTTAGCGGCGCTTCCCCAAAAACGCCGCTAA
10495621 TTCTTATTTT
Statistics
Matches: 97, Mismatches: 22, Indels: 6
0.78 0.18 0.05
Matches are distributed among these distances:
70 23 0.24
71 4 0.04
72 62 0.64
73 8 0.08
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (70 bp):
ACACCGTTTGGCTTAGGTTTTAGCGGCGCTTCCCCAAAAACGCCGCTAAATCCCCAAAAACACGG
AAACA
Found at i:10507387 original size:21 final size:22
Alignment explanation
Indices: 10507351--10507400 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
10507341 TGAAAATTAC
*
10507351 TACATAATTGTTAAAACTTATA
1 TACAAAATTGTTAAAACTTATA
*
10507373 TACAAAATT-TTAAAATTTATA
1 TACAAAATTGTTAAAACTTATA
*
10507394 TAAAAAA
1 TACAAAA
10507401 CATAAATTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (22 bp):
TACAAAATTGTTAAAACTTATA
Found at i:10513328 original size:8 final size:8
Alignment explanation
Indices: 10513315--10513343 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
10513305 CACTAGAGAC
10513315 CAGTGTTA
1 CAGTGTTA
10513323 CAGTGTTA
1 CAGTGTTA
10513331 CAGTGTTA
1 CAGTGTTA
10513339 CAGTG
1 CAGTG
10513344 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:10516171 original size:5 final size:5
Alignment explanation
Indices: 10516148--10516216 Score: 108
Period size: 5 Copynumber: 14.4 Consensus size: 5
10516138 TTTTTATGTT
10516148 TTATA -TATA TTAT- TT-TA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
*
10516195 TTATA TTATA TTGTA TTATA TT
1 TTATA TTATA TTATA TTATA TT
10516217 CTATAAGTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
3 1 0.02
4 8 0.14
5 50 0.85
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:10516243 original size:17 final size:17
Alignment explanation
Indices: 10516221--10516256 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
10516211 TATATTCTAT
10516221 AAGTAAAAATAAAA-ATA
1 AAGT-AAAATAAAATATA
10516238 AAGTAAAATAAAATATA
1 AAGTAAAATAAAATATA
10516255 AA
1 AA
10516257 AAAAAGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (17 bp):
AAGTAAAATAAAATATA
Found at i:10530409 original size:6 final size:6
Alignment explanation
Indices: 10530389--10530437 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
10530379 CTGTCGCTTC
* * *
10530389 CACTGT CACTG- --CTGT CACTGT CACTAT CACTAT CACTGC CACTGT
1 CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT
10530434 CACT
1 CACT
10530438 AGCACTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 3 0.08
6 33 0.92
ACGTcount: A:0.20, C:0.37, G:0.12, T:0.31
Consensus pattern (6 bp):
CACTGT
Found at i:10530426 original size:18 final size:18
Alignment explanation
Indices: 10530403--10530443 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
10530393 GTCACTGCTG
*
10530403 TCACTGTCACTATCACTA
1 TCACTGCCACTATCACTA
*
10530421 TCACTGCCACTGTCACTA
1 TCACTGCCACTATCACTA
*
10530439 GCACT
1 TCACT
10530444 ATTTGCTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.37, G:0.10, T:0.29
Consensus pattern (18 bp):
TCACTGCCACTATCACTA
Found at i:10537223 original size:20 final size:19
Alignment explanation
Indices: 10537198--10537247 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
10537188 AATTAAGTTT
*
10537198 ATTTAAAATAAAAATATTAA
1 ATTTAAAATAAAAATA-GAA
*
10537218 ATTTAAATTCAAAAATAGAA
1 ATTTAAAAT-AAAAATAGAA
*
10537238 ATTTATAATA
1 ATTTAAAATA
10537248 TTAACTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 17 0.68
21 7 0.28
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
ATTTAAAATAAAAATAGAA
Found at i:10537438 original size:15 final size:14
Alignment explanation
Indices: 10537386--10537448 Score: 65
Period size: 14 Copynumber: 4.4 Consensus size: 14
10537376 ATATTAGTTA
* *
10537386 AAAATGTATAATAT
1 AAAATATATAATTT
*
10537400 ATAATATATAATTT
1 AAAATATATAATTT
10537414 AAAA-ACTATAATTCT
1 AAAATA-TATAATT-T
10537429 AAAATATATAATTT
1 AAAATATATAATTT
*
10537443 TAAATA
1 AAAATA
10537449 GTTAAAACAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
13 1 0.02
14 27 0.66
15 12 0.29
16 1 0.02
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (14 bp):
AAAATATATAATTT
Found at i:10537613 original size:19 final size:19
Alignment explanation
Indices: 10537579--10537642 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
10537569 AATTAATTTT
10537579 TATTTTTA-AACTTTTTTAAC
1 TATTTTTACAA-TTTTTT-AC
10537599 TATTTTTACAATTTTTTA-
1 TATTTTTACAATTTTTTAC
*
10537617 TAGTTTTTACATTTTTTTAC
1 TA-TTTTTACAATTTTTTAC
10537637 -ATTTTT
1 TATTTTT
10537643 GTAATAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
18 7 0.17
19 17 0.43
20 14 0.35
21 2 0.05
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.66
Consensus pattern (19 bp):
TATTTTTACAATTTTTTAC
Found at i:10537633 original size:10 final size:10
Alignment explanation
Indices: 10537601--10537642 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
10537591 TTTTTAACTA
*
10537601 TTTTTACAAT
1 TTTTTACATT
* *
10537611 TTTTTATA-G
1 TTTTTACATT
10537620 TTTTTACATT
1 TTTTTACATT
10537630 TTTTTACATT
1 TTTTTACATT
10537640 TTT
1 TTT
10537643 GTAATAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.26
10 20 0.74
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.69
Consensus pattern (10 bp):
TTTTTACATT
Found at i:10538583 original size:13 final size:13
Alignment explanation
Indices: 10538543--10538602 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 13
10538533 TAAACTAAAT
* *
10538543 TTTTCAAAAATAT
1 TTTTCAAAAACAC
* *
10538556 TTTTTAAAAATAC
1 TTTTCAAAAACAC
* *
10538569 TTTTCCACAACAC
1 TTTTCAAAAACAC
*
10538582 TTTTTAAAAACAC
1 TTTTCAAAAACAC
10538595 TTTTCAAA
1 TTTTCAAA
10538603 TGTATTACTA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (13 bp):
TTTTCAAAAACAC
Found at i:10538947 original size:40 final size:40
Alignment explanation
Indices: 10538889--10538969 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
10538879 TATAAATCAT
*
10538889 TAACACTATTATTAATATAACATCATTTCACATTAACATA
1 TAACACAATTATTAATATAACATCATTTCACATTAACATA
* * *
10538929 TAACACAATTATTGATATAACGTCATTTTACATTAACATA
1 TAACACAATTATTAATATAACATCATTTCACATTAACATA
10538969 T
1 T
10538970 TGCGTACATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.38
Consensus pattern (40 bp):
TAACACAATTATTAATATAACATCATTTCACATTAACATA
Found at i:10541175 original size:11 final size:11
Alignment explanation
Indices: 10541159--10541197 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
10541149 TTTATTGTTA
10541159 TTTGCTACTAT
1 TTTGCTACTAT
*
10541170 TTTGCTATTAT
1 TTTGCTACTAT
* *
10541181 ATTGTTACTAT
1 TTTGCTACTAT
10541192 TTTGCT
1 TTTGCT
10541198 GTTATTATTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (11 bp):
TTTGCTACTAT
Found at i:10541192 original size:22 final size:21
Alignment explanation
Indices: 10541156--10541203 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
10541146 TGTTTTATTG
10541156 TTATTTGCTACTATTTTGCTA
1 TTATTTGCTACTATTTTGCTA
* *
10541177 TTATATTGTTACTATTTTGCTG
1 TTAT-TTGCTACTATTTTGCTA
10541199 TTATT
1 TTATT
10541204 ATTTGGATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.19, C:0.10, G:0.10, T:0.60
Consensus pattern (21 bp):
TTATTTGCTACTATTTTGCTA
Found at i:10547055 original size:83 final size:82
Alignment explanation
Indices: 10546956--10547116 Score: 286
Period size: 83 Copynumber: 2.0 Consensus size: 82
10546946 ACTAAACCCC
*
10546956 AATCTATTTTTTTAAAATTTATAATTAATTTACTCAAATAATCCTAAACCCTAATTTATTTGATT
1 AATCTATTTTTTTAAAATTTATAATTAATTTACTCAAATAACCCTAAACCCTAATTTATTTGATT
10547021 TTTTCCTTAAAAATACT
66 TTTTCCTTAAAAATACT
*
10547038 AATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTGAT
1 AATCT-ATTTTTTTAAAATTTATAATTAATTTACTCAAATAACCCTAAACCCTAATTTATTTGAT
*
10547103 TTTTTTCTTAAAAA
65 TTTTTCCTTAAAAA
10547117 CCATAAACAC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
82 5 0.07
83 70 0.93
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.47
Consensus pattern (82 bp):
AATCTATTTTTTTAAAATTTATAATTAATTTACTCAAATAACCCTAAACCCTAATTTATTTGATT
TTTTCCTTAAAAATACT
Found at i:10550150 original size:3 final size:3
Alignment explanation
Indices: 10550142--10550166 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10550132 CATATTATCT
10550142 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
10550167 AGGAAACTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:10550674 original size:6 final size:6
Alignment explanation
Indices: 10550663--10550688 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
10550653 CTCACTGGTT
10550663 GGGAAA GGGAAA GGGAAA GGGAAA GG
1 GGGAAA GGGAAA GGGAAA GGGAAA GG
10550689 AGCTTTTGTC
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:0.54, T:0.00
Consensus pattern (6 bp):
GGGAAA
Found at i:10551872 original size:35 final size:35
Alignment explanation
Indices: 10551833--10551899 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
10551823 GTTCAAATAA
10551833 AAATATGGCATGTGACTGATTCAAATAGAGAAAAC
1 AAATATGGCATGTGACTGATTCAAATAGAGAAAAC
* *
10551868 AAATATGGCTTGTGATTGATTCAAATAGAGAA
1 AAATATGGCATGTGACTGATTCAAATAGAGAA
10551900 CGTCATAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (35 bp):
AAATATGGCATGTGACTGATTCAAATAGAGAAAAC
Found at i:10562317 original size:23 final size:23
Alignment explanation
Indices: 10562291--10562365 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
10562281 ATAAGTGCCA
10562291 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
10562314 CACTGA-ATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
10562336 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
10562359 CACTGAT
1 CACTGAT
10562366 CAATAACACT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
22 22 0.44
23 28 0.56
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:10568473 original size:17 final size:17
Alignment explanation
Indices: 10568449--10568482 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
10568439 GTATTTAATA
10568449 AATTACAC-AAATTTAT
1 AATTACACTAAATTTAT
10568465 AATTAACACTAAATTTAT
1 AATT-ACACTAAATTTAT
10568483 TCCAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTACACTAAATTTAT
Found at i:10570463 original size:2 final size:2
Alignment explanation
Indices: 10570456--10570484 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10570446 GGGCCCAAAT
10570456 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
10570485 TTTTATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:10575825 original size:16 final size:16
Alignment explanation
Indices: 10575788--10575818 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10575778 GTTGGGTTAG
10575788 GGTTTTATGGATTTTA
1 GGTTTTATGGATTTTA
*
10575804 GGTTTTATGGGTTTT
1 GGTTTTATGGATTTT
10575819 GAGTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.29, T:0.58
Consensus pattern (16 bp):
GGTTTTATGGATTTTA
Found at i:10575839 original size:11 final size:10
Alignment explanation
Indices: 10575825--10575880 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
10575815 TTTTGAGTTT
10575825 TTTTTATTATA
1 TTTTT-TTATA
10575836 TTTTTTT-TAA
1 TTTTTTTAT-A
* *
10575846 GTTTTGTATA
1 TTTTTTTATA
*
10575856 TTTTTTTATT
1 TTTTTTTATA
10575866 TTTTATTTATA
1 TTTT-TTTATA
10575877 TTTT
1 TTTT
10575881 CTTGAGATGT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 1 0.03
10 20 0.56
11 15 0.42
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.77
Consensus pattern (10 bp):
TTTTTTTATA
Found at i:10575935 original size:15 final size:15
Alignment explanation
Indices: 10575915--10575947 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
10575905 TTTAATTTGA
10575915 TATTTACAACC-ATCG
1 TATTTAC-ACCAATCG
10575930 TATTTACACCAATCG
1 TATTTACACCAATCG
10575945 TAT
1 TAT
10575948 ATTTGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.36
Consensus pattern (15 bp):
TATTTACACCAATCG
Found at i:10578451 original size:37 final size:38
Alignment explanation
Indices: 10578392--10578471 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 38
10578382 TGTCAATTTA
* *
10578392 TTACTTCGGATTTATTCGATGAGGCACTGGGTGCCAAC
1 TTACTTCGGATTTAATCGATGAGACACTGGGTGCCAAC
* * *
10578430 TTACTTCTG-TTTAATCGATGAGACACTGGGTGTCAAT
1 TTACTTCGGATTTAATCGATGAGACACTGGGTGCCAAC
10578467 TTACT
1 TTACT
10578472 ACTTTGAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 29 0.78
38 8 0.22
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (38 bp):
TTACTTCGGATTTAATCGATGAGACACTGGGTGCCAAC
Found at i:10580369 original size:29 final size:28
Alignment explanation
Indices: 10580299--10580359 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
10580289 AATTTTAATA
10580299 AAAAAAAAGAGAGAGTTGAAAGAAAAAT
1 AAAAAAAAGAGAGAGTTGAAAGAAAAAT
10580327 AAAAAAAAGAGAGAGTTGAAAGAAAAAT
1 AAAAAAAAGAGAGAGTTGAAAGAAAAAT
10580355 AAAAA
1 AAAAA
10580360 TTAAGTGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (28 bp):
AAAAAAAAGAGAGAGTTGAAAGAAAAAT
Found at i:10595244 original size:155 final size:152
Alignment explanation
Indices: 10595055--10595448 Score: 623
Period size: 153 Copynumber: 2.6 Consensus size: 152
10595045 TCTTGGTTTA
*
10595055 TAAAAATATACTATTTTTTA-TTTTTTTATTTTACATTATTTTATTACATTATATTTGAAATGTA
1 TAAAAATATACTATTTTTTATTTTTTTTATTTTACATTATTTTAGTACATTATATTTGAAATGTA
*
10595119 TTAATTTATTGTGTTTTTTAAATAAATTTTTTTAAAAAAACTCTTATTTCGGCCCTATGTTCGTA
66 TTAATTTAGTGTGTTTTTTAAATAAA--TTTTTAAAAAAACTCTTATTTCGGCCCTATGTTCGTA
*
10595184 TTTTTTTCCTGAATTTTATTACTTT
129 -TTTTTTCCCGAATTTTATTACTTT
*
10595209 TAAAAATATACTATTTTCTATTTTTTTTATTTTACATTATTTTAGTACATTATATTTGAAATGTA
1 TAAAAATATACTATTTTTTATTTTTTTTATTTTACATTATTTTAGTACATTATATTTGAAATGTA
* ** *
10595274 TTAATTTAGTGTGTGTTTTAAATAAATTTTTAAAAAAACTCTTATTTCGGGTCTTTGTTCGTATT
66 TTAATTTAGTGTGTTTTTTAAATAAATTTTTAAAAAAACTCTTATTTCGGCCCTATGTTCGTATT
*
10595339 TTTTCCCGGATTTTATTACTTT
131 TTTTCCCGAATTTTATTACTTT
*
10595361 TAAAAA-ATA-TATTATTTTATTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
1 TAAAAATATACTATT-TTTTATT-TTTT-TTATTTTACATTATTTTAGTACATTATATTTGAAAT
10595424 GTATTAATTTAGTGTGTTTTTTAAA
63 GTATTAATTTAGTGTGTTTTTTAAA
10595449 AGTAATAAAA
Statistics
Matches: 224, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
150 4 0.02
151 9 0.04
152 32 0.14
153 93 0.42
154 19 0.08
155 67 0.30
ACGTcount: A:0.30, C:0.07, G:0.08, T:0.55
Consensus pattern (152 bp):
TAAAAATATACTATTTTTTATTTTTTTTATTTTACATTATTTTAGTACATTATATTTGAAATGTA
TTAATTTAGTGTGTTTTTTAAATAAATTTTTAAAAAAACTCTTATTTCGGCCCTATGTTCGTATT
TTTTCCCGAATTTTATTACTTT
Found at i:10595383 original size:8 final size:8
Alignment explanation
Indices: 10595370--10595405 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
10595360 TTAAAAAATA
10595370 TATTATTT
1 TATTATTT
10595378 TATTATTT
1 TATTATTT
10595386 TATTATTT
1 TATTATTT
10595394 TACATTATTT
1 T--ATTATTT
10595404 TA
1 TA
10595406 GTACATTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 18 0.69
10 8 0.31
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (8 bp):
TATTATTT
Found at i:10595801 original size:19 final size:18
Alignment explanation
Indices: 10595764--10595802 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
10595754 TAAAAAGTTA
*
10595764 TATTATTTTGGAATTTTT
1 TATTATTTTGGAATATTT
*
10595782 TATTATTTTTGTAATATTT
1 TATTA-TTTTGGAATATTT
10595801 TA
1 TA
10595803 GTAAAATACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TATTATTTTGGAATATTT
Found at i:10597147 original size:17 final size:17
Alignment explanation
Indices: 10597121--10597160 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
10597111 CTAAAATATA
*
10597121 AAATTATTTTTAATTTT
1 AAATTATTTTAAATTTT
* *
10597138 TAATTTTTTTAAATTTT
1 AAATTATTTTAAATTTT
10597155 AAATTA
1 AAATTA
10597161 ATAAAAATAA
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AAATTATTTTAAATTTT
Found at i:10597148 original size:16 final size:17
Alignment explanation
Indices: 10597122--10597156 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
10597112 TAAAATATAA
*
10597122 AATTATTTTTAATTTTT
1 AATTATTTTTAAATTTT
10597139 AATT-TTTTTAAATTTT
1 AATTATTTTTAAATTTT
10597155 AA
1 AA
10597157 ATTAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
AATTATTTTTAAATTTT
Found at i:10598766 original size:22 final size:24
Alignment explanation
Indices: 10598733--10598779 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
10598723 TATAAAAATA
10598733 TTATTAATTTT-ACAATATATTTT
1 TTATTAATTTTAACAATATATTTT
*
10598756 TTATT-ATTTTAATAATATATTTT
1 TTATTAATTTTAACAATATATTTT
10598779 T
1 T
10598780 ACATATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
TTATTAATTTTAACAATATATTTT
Found at i:10598786 original size:23 final size:24
Alignment explanation
Indices: 10598746--10598794 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
10598736 TTAATTTTAC
*
10598746 AATATATTTTTTATTATTTTA-AT
1 AATATATTTTTTAATATTTTATAT
10598769 AATATA-TTTTTACATATTTTATAT
1 AATATATTTTTTA-ATATTTTATAT
10598793 AA
1 AA
10598795 AAAATAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 13 0.57
24 4 0.17
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
AATATATTTTTTAATATTTTATAT
Found at i:10598989 original size:15 final size:17
Alignment explanation
Indices: 10598957--10598989 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
10598947 AAAGGTTCAC
10598957 TTCATTTTAATATATTT
1 TTCATTTTAATATATTT
10598974 TTCA-TTTAAT-TATTT
1 TTCATTTTAATATATTT
10598989 T
1 T
10598990 CACCCACATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (17 bp):
TTCATTTTAATATATTT
Found at i:10599437 original size:20 final size:20
Alignment explanation
Indices: 10599414--10599457 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
10599404 CCAGGTTCAC
10599414 GGTTTAGAATTCGGGTTTAA
1 GGTTTAGAATTCGGGTTTAA
* * * *
10599434 GGTTTGGACTTTGTGTTTAA
1 GGTTTAGAATTCGGGTTTAA
10599454 GGTT
1 GGTT
10599458 CAATATTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.32, T:0.45
Consensus pattern (20 bp):
GGTTTAGAATTCGGGTTTAA
Found at i:10607247 original size:23 final size:23
Alignment explanation
Indices: 10607227--10607294 Score: 118
Period size: 23 Copynumber: 3.0 Consensus size: 23
10607217 TTAAATTTTG
*
10607227 AATTATTTAATGATAATATTTAA
1 AATTATTTAGTGATAATATTTAA
*
10607250 AATTATTTAGCGATAATATTTAA
1 AATTATTTAGTGATAATATTTAA
10607273 AATTATTTAGTGATAATATTTA
1 AATTATTTAGTGATAATATTTA
10607295 GTGATAATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.47
Consensus pattern (23 bp):
AATTATTTAGTGATAATATTTAA
Found at i:10607248 original size:13 final size:13
Alignment explanation
Indices: 10607230--10607308 Score: 62
Period size: 13 Copynumber: 6.5 Consensus size: 13
10607220 AATTTTGAAT
10607230 TATTTAATGATAA
1 TATTTAATGATAA
*
10607243 TATTTAA--A-AT
1 TATTTAATGATAA
**
10607253 TATTTAGCGATAA
1 TATTTAATGATAA
*
10607266 TATTTAA--A-AT
1 TATTTAATGATAA
*
10607276 TATTTAGTGATAA
1 TATTTAATGATAA
*
10607289 TATTTAGTGATAA
1 TATTTAATGATAA
10607302 TATTTAA
1 TATTTAA
10607309 AAAACAATCT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
10 14 0.27
11 2 0.04
12 2 0.04
13 34 0.65
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.47
Consensus pattern (13 bp):
TATTTAATGATAA
Found at i:10610874 original size:18 final size:18
Alignment explanation
Indices: 10610851--10610886 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
10610841 TCCGTAAATA
10610851 TTTATAAAAATATTTATG
1 TTTATAAAAATATTTATG
10610869 TTTATAAAAATATTTATG
1 TTTATAAAAATATTTATG
10610887 GCTCAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TTTATAAAAATATTTATG
Found at i:10627269 original size:7 final size:7
Alignment explanation
Indices: 10627257--10627281 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
10627247 CCAATCCTTT
10627257 TATAATA
1 TATAATA
10627264 TATAATA
1 TATAATA
10627271 TATAATA
1 TATAATA
10627278 TATA
1 TATA
10627282 CAAAAACCCT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATAATA
Found at i:10628440 original size:38 final size:38
Alignment explanation
Indices: 10628398--10628474 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
10628388 GAAGAAGACC
10628398 CCTTTCCCATCGTTATGAGGGTATTTATAGGGGAGGCT
1 CCTTTCCCATCGTTATGAGGGTATTTATAGGGGAGGCT
10628436 CCTTTCCCATCGTTATGAGGGTATTTATAGGGGAGGCT
1 CCTTTCCCATCGTTATGAGGGTATTTATAGGGGAGGCT
10628474 C
1 C
10628475 TCTTGTCTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.34
Consensus pattern (38 bp):
CCTTTCCCATCGTTATGAGGGTATTTATAGGGGAGGCT
Found at i:10628655 original size:18 final size:18
Alignment explanation
Indices: 10628615--10628655 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
10628605 AGTGATCTCT
* *
10628615 AAAAGAATGTTTACATTT
1 AAAAGAATGTTTACACTA
*
10628633 GAAAGAATGTTTACACTA
1 AAAAGAATGTTTACACTA
10628651 AAAAG
1 AAAAG
10628656 CGGGTGGCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (18 bp):
AAAAGAATGTTTACACTA
Found at i:10636849 original size:29 final size:30
Alignment explanation
Indices: 10636815--10636909 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
10636805 TGTATATGAT
*
10636815 ACATG-AACTTTAATTTGGTGT-AATTATAC
1 ACATGAAACTTTAATTTGGT-TCAAATATAC
* *
10636844 ACATGAAACTTTGATTGTGGTTCAAATATAT
1 ACATGAAACTTTAATT-TGGTTCAAATATAC
* *
10636875 AAATGAAACTTTAATTTTGATTC-AATCATAC
1 ACATGAAACTTTAA-TTTGGTTCAAAT-ATAC
10636906 ACAT
1 ACAT
10636910 TTAATGAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
29 5 0.09
30 13 0.25
31 33 0.62
32 2 0.04
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (30 bp):
ACATGAAACTTTAATTTGGTTCAAATATAC
Found at i:10650399 original size:24 final size:24
Alignment explanation
Indices: 10650357--10650405 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
10650347 ACAGTAATCC
* *
10650357 TTTATTTTATCTTATCTTATTTTA
1 TTTACTTTATCTTATCTTAATTTA
10650381 TTTACTTTATCTT-TGCTTAATTTA
1 TTTACTTTATCTTAT-CTTAATTTA
10650405 T
1 T
10650406 AGGATTTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.20, C:0.10, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTACTTTATCTTATCTTAATTTA
Found at i:10655214 original size:58 final size:58
Alignment explanation
Indices: 10655144--10655257 Score: 194
Period size: 58 Copynumber: 2.0 Consensus size: 58
10655134 TTTCAAGGTT
*
10655144 AGCCAGTTTCCGTCCATC-AACAGGGTTTCATTGTATTCAATTTAGTAGTGTGATTGTC
1 AGCCAGTTTCCGTCCATCGAA-AGGGTTTCATTGTATTCAATTTAATAGTGTGATTGTC
*
10655202 AGCCAGTTTCCGTCCATCGAAAGGGTTTCTTTGTATTCAATTTAATAGTGTGATTG
1 AGCCAGTTTCCGTCCATCGAAAGGGTTTCATTGTATTCAATTTAATAGTGTGATTG
10655258 AATATCAGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
58 51 0.96
59 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.39
Consensus pattern (58 bp):
AGCCAGTTTCCGTCCATCGAAAGGGTTTCATTGTATTCAATTTAATAGTGTGATTGTC
Found at i:10665266 original size:15 final size:15
Alignment explanation
Indices: 10665248--10665281 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
10665238 GAAAAAAAAA
10665248 AAAGAAAAGAAAAGC
1 AAAGAAAAGAAAAGC
* *
10665263 AAAGTAAAGCAAAGC
1 AAAGAAAAGAAAAGC
10665278 AAAG
1 AAAG
10665282 GCAAATTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.09, G:0.21, T:0.03
Consensus pattern (15 bp):
AAAGAAAAGAAAAGC
Found at i:10665626 original size:3 final size:3
Alignment explanation
Indices: 10665618--10665647 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
10665608 ACCCATTTTC
10665618 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
10665648 TGAGAGATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:10671123 original size:45 final size:44
Alignment explanation
Indices: 10671057--10671256 Score: 276
Period size: 45 Copynumber: 4.4 Consensus size: 44
10671047 AGTATACAGT
* * *
10671057 AATCAGTAACGGTAGCAGTAACAGTATTCAACACACAAAGTGCTG
1 AATC-GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCG
* *
10671102 AATCTGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCG
1 AATC-GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCG
10671147 AATCGATAACAGTAACAGTAACAGTATT-AGACACACAAAGTGCCG
1 AATCG-TAACAGTAACAGTAACAGTATTCA-ACACACAAAGTGCCG
* *
10671192 AGTCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 AATC-GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCG
10671237 AATCAGTAACAGTAACAGTA
1 AATC-GTAACAGTAACAGTA
10671257 GTCGGCACAT
Statistics
Matches: 139, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
44 1 0.01
45 137 0.99
46 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (44 bp):
AATCGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCG
Found at i:10671162 original size:39 final size:42
Alignment explanation
Indices: 10671072--10671278 Score: 206
Period size: 45 Copynumber: 4.8 Consensus size: 42
10671062 GTAACGGTAG
* * *
10671072 CAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAACAGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATC-G-GA-AGTAA
* *
10671117 CGGTAACAGTATTCGACACACAAAGTGCCGAATCGATAACAGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATCG--GA-AGTAA
* *
10671162 CAGTAACAGTATTAGACACACAAAGTGCCGAGTCGGTAACAGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATCGG--A-AGTAA
10671207 CAGTAACAGTATTCGACACACAAAGTGCCGAATC---AGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATCGGAAGTAA
* * * *
10671246 CAGTAACAGTAGTCGGCACA-TAAGTGCCTAATC
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATC
10671279 AGTAAGCCGG
Statistics
Matches: 146, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
38 11 0.08
39 23 0.16
44 1 0.01
45 111 0.76
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (42 bp):
CAGTAACAGTATTCGACACACAAAGTGCCGAATCGGAAGTAA
Found at i:10671201 original size:90 final size:90
Alignment explanation
Indices: 10671057--10671256 Score: 314
Period size: 90 Copynumber: 2.2 Consensus size: 90
10671047 AGTATACAGT
* * * * *
10671057 AATCAGTAACGGTAGCAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAACAGTAACGGTA
1 AATCAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGGTAACAGTAACAGTA
10671122 ACAGTATTCGACACACAAAGTGCCG
66 ACAGTATTCGACACACAAAGTGCCG
*
10671147 AATC-GATAACAGTAACAGTAACAGTATT-AGACACACAAAGTGCCGAGTCGGTAACAGTAACAG
1 AATCAG-TAACAGTAACAGTAACAGTATTCA-ACACACAAAGTGCCGAATCGGTAACAGTAACAG
10671210 TAACAGTATTCGACACACAAAGTGCCG
64 TAACAGTATTCGACACACAAAGTGCCG
10671237 AATCAGTAACAGTAACAGTA
1 AATCAGTAACAGTAACAGTA
10671257 GTCGGCACAT
Statistics
Matches: 101, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
89 2 0.02
90 98 0.97
91 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (90 bp):
AATCAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGGTAACAGTAACAGTA
ACAGTATTCGACACACAAAGTGCCG
Found at i:10674275 original size:5 final size:5
Alignment explanation
Indices: 10674265--10674290 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
10674255 TGAGCATTCG
10674265 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
10674291 AATTTTCGAG
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:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:10675426 original size:9 final size:9
Alignment explanation
Indices: 10675409--10675439 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
10675399 TCGAGTTGAT
10675409 TCGAATAAC
1 TCGAATAAC
*
10675418 TCGATTAAC
1 TCGAATAAC
10675427 TCGAATAAC
1 TCGAATAAC
10675436 TCGA
1 TCGA
10675440 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:10676069 original size:22 final size:23
Alignment explanation
Indices: 10676040--10676114 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 23
10676030 TTTAAATTGA
10676040 TTAT-ATAATTTATTAAAAT-AT
1 TTATAATAATTTATTAAAATAAT
**
10676061 TTATAATAAAATATTAGAAGATACAT
1 TTATAATAATTTATTA-AA-ATA-AT
*
10676087 TT-TAATAATTTATTAAATTAAT
1 TTATAATAATTTATTAAAATAAT
10676109 TTATAA
1 TTATAA
10676115 ATTCACATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
21 4 0.09
22 13 0.30
23 7 0.16
24 4 0.09
25 11 0.26
26 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (23 bp):
TTATAATAATTTATTAAAATAAT
Found at i:10676302 original size:21 final size:21
Alignment explanation
Indices: 10676269--10676321 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
10676259 CATTGTTTCT
* * *
10676269 AATCTTACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
10676290 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
10676311 AATCTCACCGC
1 AATCTCACCGC
10676322 CACCACTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.34, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:10677982 original size:2 final size:2
Alignment explanation
Indices: 10677975--10678027 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
10677965 CTTTTCTGTT
*
10677975 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
10678017 AA TC TA TA TA T
1 TA TA TA TA TA T
10678028 TGTTCTGGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:10688918 original size:20 final size:19
Alignment explanation
Indices: 10688884--10688937 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
10688874 AACAACAGAG
*
10688884 TAATCTAATTATTTATGATTT
1 TAATC-AATTTTTTAT-ATTT
*
10688905 TAATCAATTTTTTATTTTT
1 TAATCAATTTTTTATATTT
* *
10688924 TTATTAATTTTTTA
1 TAATCAATTTTTTA
10688938 GAAAAGTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 15 0.52
20 9 0.31
21 5 0.17
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
TAATCAATTTTTTATATTT
Found at i:10691634 original size:2 final size:2
Alignment explanation
Indices: 10691621--10691684 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
10691611 CTCATCCACA
* *
10691621 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
10691663 TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC
10691685 CCACTCTTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.52
Consensus pattern (2 bp):
TC
Found at i:10699671 original size:15 final size:16
Alignment explanation
Indices: 10699651--10699685 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
10699641 GAGAAGTACT
10699651 TATTTAAT-TATTTTA
1 TATTTAATATATTTTA
*
10699666 TATTTAATATATTTTT
1 TATTTAATATATTTTA
10699682 TATT
1 TATT
10699686 CAAGTAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTAATATATTTTA
Found at i:10708675 original size:26 final size:26
Alignment explanation
Indices: 10708645--10708695 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
10708635 TTCAAAGAAT
*
10708645 TTTGATCTCTGTTGAAAAATAATTCA
1 TTTGATATCTGTTGAAAAATAATTCA
*
10708671 TTTGATATCTGTTGACAAATAATTC
1 TTTGATATCTGTTGAAAAATAATTC
10708696 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (26 bp):
TTTGATATCTGTTGAAAAATAATTCA
Found at i:10712839 original size:42 final size:42
Alignment explanation
Indices: 10712766--10712854 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
10712756 ACAACAATTC
* * *
10712766 CAACAACAACAGCAGCAACGTATGTTACAGCAGCAGCAACAA
1 CAACAACAACAGCAGCAACGCAAGTTACAGCAGAAGCAACAA
* * * *
10712808 CAACAACAACAGCAGCAGCAGCAAG-TGCAGCAGAATCAGCAA
1 CAACAACAACAGCAGCAAC-GCAAGTTACAGCAGAAGCAACAA
10712850 CAACA
1 CAACA
10712855 GTCACTAGCT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 36 0.92
43 3 0.08
ACGTcount: A:0.46, C:0.29, G:0.18, T:0.07
Consensus pattern (42 bp):
CAACAACAACAGCAGCAACGCAAGTTACAGCAGAAGCAACAA
Found at i:10725189 original size:14 final size:15
Alignment explanation
Indices: 10725167--10725195 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
10725157 GTTAGGTCCC
10725167 CCATGTTGCGTCTCA
1 CCATGTTGCGTCTCA
10725182 CCAT-TTGCGTCTCA
1 CCATGTTGCGTCTCA
10725196 AAAGGTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.34, G:0.17, T:0.34
Consensus pattern (15 bp):
CCATGTTGCGTCTCA
Found at i:10725941 original size:14 final size:14
Alignment explanation
Indices: 10725900--10725943 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
10725890 TTTTCAAATT
* *
10725900 TCGAGTTAATCGAA
1 TCGAGTTATTCGAG
10725914 TCGAGTTATTCGAG
1 TCGAGTTATTCGAG
10725928 TCGAGTTATTCGAG
1 TCGAGTTATTCGAG
10725942 TC
1 TC
10725944 AACTCGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (14 bp):
TCGAGTTATTCGAG
Found at i:10726167 original size:19 final size:20
Alignment explanation
Indices: 10726132--10726174 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
10726122 TCAAATTTTG
*
10726132 AAAATATTTGTTAAAATTC-
1 AAAATATTTGATAAAATTCT
10726151 AAAATATTT-ATAGAAATTCT
1 AAAATATTTGATA-AAATTCT
10726171 AAAA
1 AAAA
10726175 AAATTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 15 0.71
20 4 0.19
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (20 bp):
AAAATATTTGATAAAATTCT
Found at i:10726181 original size:20 final size:19
Alignment explanation
Indices: 10726145--10726193 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 19
10726135 ATATTTGTTA
* *
10726145 AAATTCAAAATATTTATAG
1 AAATTCAAAAAAATTATAG
10726164 AAATTCTAAAAAAATTAT--
1 AAATTC-AAAAAAATTATAG
10726182 AAATT-AAAAAAA
1 AAATTCAAAAAAA
10726194 CTAAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 7 0.26
18 5 0.19
19 6 0.22
20 9 0.33
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
AAATTCAAAAAAATTATAG
Found at i:10728029 original size:20 final size:21
Alignment explanation
Indices: 10728001--10728046 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
10727991 TTCAAACTAA
10728001 AAAAATTTAAATAATAAAAT-
1 AAAAATTTAAATAATAAAATG
* *
10728021 AAAAGTTTAAATATTAAAATG
1 AAAAATTTAAATAATAAAATG
10728042 AAAAA
1 AAAAA
10728047 AAATAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAAATTTAAATAATAAAATG
Found at i:10736924 original size:2 final size:2
Alignment explanation
Indices: 10736917--10736941 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10736907 GATAACTAGT
10736917 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
10736942 TATTTTAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10737220 original size:21 final size:20
Alignment explanation
Indices: 10737191--10737239 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 20
10737181 TCTCTAAAAT
10737191 TTTGATAAA-TATTTATATTTA
1 TTTG-TAAAGTATTT-TATTTA
10737212 TCTTGTAAATGTATTTTATTTA
1 T-TTGTAAA-GTATTTTATTTA
10737234 TTTGTA
1 TTTGTA
10737240 GAGGCAACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 10 0.40
22 10 0.40
23 5 0.20
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTGTAAAGTATTTTATTTA
Found at i:10744432 original size:2 final size:2
Alignment explanation
Indices: 10744427--10744464 Score: 51
Period size: 2 Copynumber: 18.5 Consensus size: 2
10744417 TTTGCATGGT
10744427 TA TA TA TA TA TA TA TA TA TA TA TGA TA TA -A TGA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA T-A TA TA T
10744465 TACTAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 1 0.03
2 28 0.85
3 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:10747330 original size:34 final size:34
Alignment explanation
Indices: 10747292--10747361 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
10747282 TAAAATACTA
* *
10747292 ATTTTA-TAAATTTTCTATAATTTTCACAATTTTT
1 ATTTTATTAAATTTTCTATAAATTT-AAAATTTTT
* *
10747326 ATTTTATTATATTTTTTATAAATTTAAAATTTTT
1 ATTTTATTAAATTTTCTATAAATTTAAAATTTTT
10747360 AT
1 AT
10747362 AATTTTTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 16 0.52
35 15 0.48
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.61
Consensus pattern (34 bp):
ATTTTATTAAATTTTCTATAAATTTAAAATTTTT
Found at i:10747454 original size:31 final size:31
Alignment explanation
Indices: 10747419--10747478 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
10747409 TGTTAAAAAT
10747419 TCTTATAAAATAA-TTAAAAACTCAATTAAGA
1 TCTTATAAAATAATTTAAAAA-TCAATTAAGA
10747450 TCTTATAAAATAATTTAAAAATCAATTAA
1 TCTTATAAAATAATTTAAAAATCAATTAA
10747479 ACAGTCACGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (31 bp):
TCTTATAAAATAATTTAAAAATCAATTAAGA
Found at i:10756438 original size:50 final size:50
Alignment explanation
Indices: 10756379--10756480 Score: 179
Period size: 50 Copynumber: 2.0 Consensus size: 50
10756369 TTTGCCAGCT
10756379 CAACATTAGCATCTACAAAAACAATTTAAAAA-ATCCACATGTATCCAGTC
1 CAACATTAGCATCTACAAAAACAA-TTAAAAATATCCACATGTATCCAGTC
*
10756429 CAACATTAGCATCTGCAAAAACAATTAAAAATATCCACATGTATCCAGTC
1 CAACATTAGCATCTACAAAAACAATTAAAAATATCCACATGTATCCAGTC
10756479 CA
1 CA
10756481 CCTTGTTGAG
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 7 0.14
50 43 0.86
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.24
Consensus pattern (50 bp):
CAACATTAGCATCTACAAAAACAATTAAAAATATCCACATGTATCCAGTC
Found at i:10760975 original size:137 final size:139
Alignment explanation
Indices: 10760755--10761023 Score: 436
Period size: 137 Copynumber: 1.9 Consensus size: 139
10760745 AAAACAGCTA
* *
10760755 AAAATTGAAATCAATTATGGAATGCGTTACATTCAAAATAACAATAAACAAAATATGGATATAAC
1 AAAATTGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAAC
* * * *
10760820 ACTAGCTACAAAAGTAATTTACCAATATCATGTGGTAACAAGTTCACCTGAAAGTG-AGATATGA
66 ACTAACTACAAAAGTAATTTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCA-ATATGA
10760884 AAGTTATGCC
130 AAGTTATGCC
* *
10760894 AAAA-TGAAATCATTTATGGCATGAGTTACATTCAAAATAACAAT-AACAAAAGATGGATATAAC
1 AAAATTGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAAC
10760957 ACTAACTACAAAAGTAATTTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAA
66 ACTAACTACAAAAGTAATTTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAA
10761022 AG
131 AG
10761024 ACATGCCATT
Statistics
Matches: 121, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
137 79 0.65
138 38 0.31
139 4 0.03
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (139 bp):
AAAATTGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAAC
ACTAACTACAAAAGTAATTTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAA
AGTTATGCC
Found at i:10776962 original size:8 final size:8
Alignment explanation
Indices: 10776949--10776977 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
10776939 ACTATTCTTC
10776949 TTTTTTCT
1 TTTTTTCT
10776957 TTTTTTCT
1 TTTTTTCT
10776965 TTTTTT-T
1 TTTTTTCT
10776972 TTTTTT
1 TTTTTT
10776978 GGTTTTGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (8 bp):
TTTTTTCT
Found at i:10776977 original size:15 final size:15
Alignment explanation
Indices: 10776946--10776976 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
10776936 AAAACTATTC
10776946 TTCTTTTTTCTTTTT
1 TTCTTTTTTCTTTTT
10776961 TTCTTTTTT-TTTTT
1 TTCTTTTTTCTTTTT
10776975 TT
1 TT
10776977 TGGTTTTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTCTTTTTTCTTTTT
Found at i:10778638 original size:15 final size:16
Alignment explanation
Indices: 10778608--10778638 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10778598 AGTAAAAGTT
10778608 AATTTAATTATTGATA
1 AATTTAATTATTGATA
10778624 AATTTAATT-TTGATA
1 AATTTAATTATTGATA
10778639 CTCAAATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
AATTTAATTATTGATA
Found at i:10782554 original size:17 final size:18
Alignment explanation
Indices: 10782519--10782562 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
10782509 ATTTAAAATT
10782519 TATTTAAAAATACAAAAA
1 TATTTAAAAATACAAAAA
*
10782537 TATTTCAAAATA-AAAAA
1 TATTTAAAAATACAAAAA
10782554 TATTATAAA
1 TATT-TAAA
10782563 GTTAAAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
TATTTAAAAATACAAAAA
Found at i:10782587 original size:19 final size:19
Alignment explanation
Indices: 10782546--10782589 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
10782536 ATATTTCAAA
* * *
10782546 ATAAAAAATATTATAAAGT
1 ATAAAAAACAATATAAAAT
10782565 -TAAAAAACAATATAAAAT
1 ATAAAAAACAATATAAAAT
10782583 ATAAAAA
1 ATAAAAA
10782590 TTTACTGCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (19 bp):
ATAAAAAACAATATAAAAT
Found at i:10782797 original size:25 final size:26
Alignment explanation
Indices: 10782747--10782798 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
10782737 GTAAACTTTG
* *
10782747 ATTTATAAAGTTTTAAAAATATTAAA
1 ATTTATAAAGTTTAAAAAATAGTAAA
*
10782773 ATTTCTAAA-TTTAAAAAATAGTAAA
1 ATTTATAAAGTTTAAAAAATAGTAAA
10782798 A
1 A
10782799 ATTAGTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (26 bp):
ATTTATAAAGTTTAAAAAATAGTAAA
Found at i:10782799 original size:26 final size:26
Alignment explanation
Indices: 10782747--10782801 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
10782737 GTAAACTTTG
* *
10782747 ATTTATAAAGTTTTAAAAATATTAAA
1 ATTTATAAAGTTTAAAAAATATAAAA
*
10782773 ATTTCTAAA-TTTAAAAAATAGTAAAA
1 ATTTATAAAGTTTAAAAAATA-TAAAA
10782799 ATT
1 ATT
10782802 AGTTTTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (26 bp):
ATTTATAAAGTTTAAAAAATATAAAA
Found at i:10783440 original size:15 final size:14
Alignment explanation
Indices: 10783411--10783443 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10783401 AGCTTTTTTT
10783411 TCTTTTTCTTCCTC
1 TCTTTTTCTTCCTC
*
10783425 TCTTTTTCTT-ATC
1 TCTTTTTCTTCCTC
10783438 TCTTTT
1 TCTTTT
10783444 ATTTCATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (14 bp):
TCTTTTTCTTCCTC
Found at i:10792765 original size:16 final size:17
Alignment explanation
Indices: 10792734--10792767 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
10792724 AAAATTAATG
*
10792734 ATTAAATTTAATAAAAA
1 ATTAAATTTAACAAAAA
10792751 ATTAAA-TTAACAAAAA
1 ATTAAATTTAACAAAAA
10792767 A
1 A
10792768 AATTATAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTAAATTTAACAAAAA
Found at i:10800729 original size:20 final size:20
Alignment explanation
Indices: 10800685--10800729 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
10800675 GAAACGAAAC
10800685 AGAAA-GAAAGAAAGAAAAG
1 AGAAAGGAAAGAAAGAAAAG
* * *
10800704 AAAAAGGAAAGAAAGGAAGG
1 AGAAAGGAAAGAAAGAAAAG
10800724 AGAAAG
1 AGAAAG
10800730 CCACGACCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
AGAAAGGAAAGAAAGAAAAG
Found at i:10801723 original size:40 final size:37
Alignment explanation
Indices: 10801631--10801728 Score: 99
Period size: 40 Copynumber: 2.6 Consensus size: 37
10801621 TAGATTAATT
**
10801631 CGATGAGGCACTGGGTGCCAATTTACTTCGGTTTAGC
1 CGATGAGGCACTGGGTGCCAATTTACTTCGAATTAGC
* * * *
10801668 CGATGA-GAAGTTGGGTGTCAATTTATTACTTCGAATTATC
1 CGATGAGGCA-CTGGGTGCCAA--T-TTACTTCGAATTAGC
10801708 CGATGAGGCACTGGGTGCCAA
1 CGATGAGGCACTGGGTGCCAA
10801729 ACTGGTGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
36 2 0.04
37 15 0.32
39 1 0.02
40 27 0.57
41 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (37 bp):
CGATGAGGCACTGGGTGCCAATTTACTTCGAATTAGC
Found at i:10805386 original size:17 final size:19
Alignment explanation
Indices: 10805341--10805386 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
10805331 CAATTTCATA
10805341 AATTTTAAATAAATCACAAT
1 AATTTT-AATAAATCACAAT
10805361 ATTATTTTAA-AAATCA-AAT
1 A--ATTTTAATAAATCACAAT
10805380 AATTTTA
1 AATTTTA
10805387 TAATATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 6 0.25
19 4 0.17
20 7 0.29
21 2 0.08
22 5 0.21
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTTTAATAAATCACAAT
Found at i:10816184 original size:21 final size:20
Alignment explanation
Indices: 10816146--10816184 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
10816136 CCCTCGGTTA
* *
10816146 TTTTTTTTCCATTGTTTTTC
1 TTTTTTTTCCACTATTTTTC
10816166 TTTTTCTTTCCACTATTTT
1 TTTTT-TTTCCACTATTTT
10816185 ACTTGCTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTTTTTTCCACTATTTTTC
Found at i:10829035 original size:35 final size:35
Alignment explanation
Indices: 10828993--10829064 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
10828983 ATGCTATTTC
10828993 ATCAATTTAGATTTCATTTATTTTTTAAAAAATCA
1 ATCAATTTAGATTTCATTTATTTTTTAAAAAATCA
10829028 ATCAATTTAGATTTCATTTATTTTTTAAAAAATCA
1 ATCAATTTAGATTTCATTTATTTTTTAAAAAATCA
10829063 AT
1 AT
10829065 GATTAACTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (35 bp):
ATCAATTTAGATTTCATTTATTTTTTAAAAAATCA
Found at i:10840617 original size:52 final size:52
Alignment explanation
Indices: 10840546--10840659 Score: 158
Period size: 52 Copynumber: 2.2 Consensus size: 52
10840536 ATCAAGTGAC
** *
10840546 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGTGG
1 AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGTGACAAAGT-G
* *
10840598 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTG
1 AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGTGACAAAGTG
10840650 ATAAGTGATA
1 A-AAGTGATA
10840660 GCTTCGGCTA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
52 43 0.78
53 12 0.22
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (52 bp):
AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGTGACAAAGTG
Found at i:10840702 original size:46 final size:46
Alignment explanation
Indices: 10840598--10840702 Score: 174
Period size: 46 Copynumber: 2.3 Consensus size: 46
10840588 TGACAAGTGG
* **
10840598 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAAAC
*
10840644 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTTATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAAAC
10840690 AAAGTGATAAGTG
1 AAAGTGATAAGTG
10840703 GCTACACTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAAAC
Found at i:10840712 original size:37 final size:37
Alignment explanation
Indices: 10840665--10840811 Score: 226
Period size: 37 Copynumber: 4.0 Consensus size: 37
10840655 TGATAGCTTC
* *
10840665 GGCTATACTTATCTTATCAAGAAACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
*
10840702 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
*
10840739 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
**
10840776 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
10840811 G
1 G
10840812 ATCATGCGTA
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 87 0.85
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
Found at i:10845354 original size:15 final size:15
Alignment explanation
Indices: 10845334--10845363 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10845324 AGCATAGCAG
10845334 TGTGGATATATTTTT
1 TGTGGATATATTTTT
10845349 TGTGGATATATTTTT
1 TGTGGATATATTTTT
10845364 GTTTATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (15 bp):
TGTGGATATATTTTT
Found at i:10846857 original size:22 final size:22
Alignment explanation
Indices: 10846829--10846870 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
10846819 TTTATTGTTC
10846829 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
10846851 AAACATGAGAGCTTAGTACG
1 AAACATGAGAGCTTAGTACG
10846871 GGTCAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.21
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:10848628 original size:13 final size:13
Alignment explanation
Indices: 10848589--10848641 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
10848579 AGTTTAGCAA
10848589 TACTTTTGAAAAG
1 TACTTTTGAAAAG
* ** *
10848602 TGCCGTGGAAAAG
1 TACTTTTGAAAAG
*
10848615 TACTTTTGAGAAG
1 TACTTTTGAAAAG
*
10848628 TGCTTTTGAAAAG
1 TACTTTTGAAAAG
10848641 T
1 T
10848642 TTGGTGTCAA
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:10848638 original size:26 final size:26
Alignment explanation
Indices: 10848589--10848693 Score: 79
Period size: 26 Copynumber: 4.0 Consensus size: 26
10848579 AGTTTAGCAA
** *
10848589 TACTTTTGAAAAGTGCCGTGGAAAAG
1 TACTTTTGAAAAGTGCTTTTGAAAAG
*
10848615 TACTTTTGAGAAGTGCTTTTGAAAAG
1 TACTTTTGAAAAGTGCTTTTGAAAAG
* *
10848641 T--TTGGTGTCAAAAAGTGCTTTTGAAAAA
1 TACTT--T-T-GAAAAGTGCTTTTGAAAAG
* * *
10848669 TGCTTTTGATAAGTGTTTTTGAAAA
1 TACTTTTGAAAAGTGCTTTTGAAAA
10848694 ATTTGAGTGT
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
24 2 0.03
26 39 0.62
27 2 0.03
28 18 0.29
30 2 0.03
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (26 bp):
TACTTTTGAAAAGTGCTTTTGAAAAG
Found at i:10848672 original size:13 final size:13
Alignment explanation
Indices: 10848650--10848695 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
10848640 GTTTGGTGTC
10848650 AAAAAGTGCTTTTG
1 AAAAA-TGCTTTTG
10848664 AAAAATGCTTTTG
1 AAAAATGCTTTTG
* * *
10848677 ATAAGTGTTTTTG
1 AAAAATGCTTTTG
10848690 AAAAAT
1 AAAAAT
10848696 TTGAGTGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 22 0.81
14 5 0.19
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (13 bp):
AAAAATGCTTTTG
Found at i:10853281 original size:21 final size:21
Alignment explanation
Indices: 10853238--10853282 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
10853228 TAGTTACATA
*
10853238 TTTAAATATAAATATATGATT
1 TTTAAATATAAATATAAGATT
*
10853259 TTTAAATATGAAATA-AAGTTT
1 TTTAAATAT-AAATATAAGATT
10853280 TTT
1 TTT
10853283 TTAAGAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (21 bp):
TTTAAATATAAATATAAGATT
Found at i:10870838 original size:17 final size:16
Alignment explanation
Indices: 10870818--10870879 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 16
10870808 TATACTTAAA
*
10870818 AAAAATTTAATATGTT
1 AAAAATTTAATATATT
*
10870834 CAAAATTTTAATATATTT
1 -AAAAATTTAATATA-TT
*
10870852 AAATATATTAAGTATATT
1 AAAAAT-TTAA-TATATT
10870870 AAAAATTTAA
1 AAAAATTTAA
10870880 AATTTTAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
17 20 0.54
18 13 0.35
19 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (16 bp):
AAAAATTTAATATATT
Found at i:10870936 original size:17 final size:17
Alignment explanation
Indices: 10870910--10870980 Score: 63
Period size: 17 Copynumber: 4.0 Consensus size: 17
10870900 CAACATTTTC
*
10870910 TTTAACATATTTAAAAT
1 TTTAATATATTTAAAAT
*
10870927 TTTAATATATTTAAAAAAA
1 TTTAATATATTT--AAAAT
*
10870946 TTTAACT-TTTTTAAAAT
1 TTTAA-TATATTTAAAAT
*
10870963 TTTAAATATATTAAAAAT
1 TTT-AATATATTTAAAAT
10870981 ATTTTTTCTC
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
17 19 0.44
18 10 0.23
19 13 0.30
20 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAATATATTTAAAAT
Found at i:10870939 original size:9 final size:9
Alignment explanation
Indices: 10870910--10870984 Score: 55
Period size: 9 Copynumber: 8.3 Consensus size: 9
10870900 CAACATTTTC
*
10870910 TTTAACATA
1 TTTAAAATA
10870919 TTTAAAAT-
1 TTTAAAATA
*
10870927 TTTAATATA
1 TTTAAAATA
*
10870936 TTTAAAAAAA
1 TTT-AAAATA
** *
10870946 TTTAACTTT
1 TTTAAAATA
10870955 TTTAAAAT-
1 TTTAAAATA
10870963 TTTAAATATA
1 TTTAAA-ATA
*
10870973 TTAAAAATA
1 TTTAAAATA
10870982 TTT
1 TTT
10870985 TTTCTCTTTA
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
8 13 0.26
9 25 0.50
10 12 0.24
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (9 bp):
TTTAAAATA
Found at i:10870950 original size:36 final size:36
Alignment explanation
Indices: 10870910--10870984 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
10870900 CAACATTTTC
10870910 TTTAACATATTTAAAATTTT-AATATATTTAAAAAAA
1 TTTAACATATTTAAAATTTTAAATATA-TTAAAAAAA
* * *
10870946 TTTAACTTTTTTAAAATTTTAAATATATTAAAAATA
1 TTTAACATATTTAAAATTTTAAATATATTAAAAAAA
10870982 TTT
1 TTT
10870985 TTTCTCTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
36 29 0.83
37 6 0.17
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (36 bp):
TTTAACATATTTAAAATTTTAAATATATTAAAAAAA
Found at i:10871016 original size:9 final size:9
Alignment explanation
Indices: 10870997--10871077 Score: 60
Period size: 9 Copynumber: 8.8 Consensus size: 9
10870987 TCTCTTTACC
10870997 TATTAAAATA
1 TATT-AAATA
10871007 TATTAAATA
1 TATTAAATA
10871016 TATTAAA-A
1 TATTAAATA
*
10871024 T-TTCAATA
1 TATTAAATA
10871032 TATTTAAAAAATA
1 TA-TT---AAATA
*
10871045 TATTGAATA
1 TATTAAATA
10871054 TATTAAA-A
1 TATTAAATA
* *
10871062 TTTTTAATA
1 TATTAAATA
10871071 TATTAAA
1 TATTAAA
10871078 ATTTTAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
7 4 0.07
8 10 0.18
9 28 0.50
10 6 0.11
12 2 0.04
13 6 0.11
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (9 bp):
TATTAAATA
Found at i:10871054 original size:38 final size:38
Alignment explanation
Indices: 10871001--10871078 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
10870991 TTTACCTATT
10871001 AAAATATATTAAATATATTAAAA-TTTCAATATATTTAA
1 AAAATATATTAAATATATTAAAATTTTCAATATA-TTAA
* *
10871039 AAAATATATTGAATATATTAAAATTTTTAATATATTAA
1 AAAATATATTAAATATATTAAAATTTTCAATATATTAA
10871077 AA
1 AA
10871079 TTTTAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 28 0.76
39 9 0.24
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (38 bp):
AAAATATATTAAATATATTAAAATTTTCAATATATTAA
Found at i:10871072 original size:17 final size:17
Alignment explanation
Indices: 10870997--10871085 Score: 81
Period size: 17 Copynumber: 4.9 Consensus size: 17
10870987 TCTCTTTACC
10870997 TATTAAAATATATTAAATA
1 TATTAAAAT-T-TTAAATA
*
10871016 TATTAAAA-TTTCAATA
1 TATTAAAATTTTAAATA
*
10871032 TATTTAAAAAATATATTGAATA
1 TA-TT--AAAAT-T-TTAAATA
*
10871054 TATTAAAATTTTTAATA
1 TATTAAAATTTTAAATA
10871071 TATTAAAATTTTAAA
1 TATTAAAATTTTAAA
10871086 ATTGGTTATA
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
16 8 0.13
17 23 0.38
18 1 0.02
19 17 0.28
21 3 0.05
22 8 0.13
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
TATTAAAATTTTAAATA
Found at i:10871150 original size:63 final size:62
Alignment explanation
Indices: 10871050--10871190 Score: 173
Period size: 63 Copynumber: 2.3 Consensus size: 62
10871040 AAATATATTG
* * * *
10871050 AATATATTAAAATTTTT---AATATATTAAAATTTTAAAATTGGTTATAATT-AACATTTTTT
1 AATATATTTAAATTTTTAAAAATATATCAAAATATTAAAATTAGTTATAATTAAAC-TTTTTT
** *
10871109 AATATATTTATTTTTTTAAAAATATATCAAATATATTAAAATTAGTTATACTTAAACTTTTTT
1 AATATATTTAAATTTTTAAAAATATATCAAA-ATATTAAAATTAGTTATAATTAAACTTTTTT
10871172 AATATATTTAAATTTTTAA
1 AATATATTTAAATTTTTAA
10871191 TATATTTAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 14 0.21
62 10 0.15
63 41 0.60
64 3 0.04
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (62 bp):
AATATATTTAAATTTTTAAAAATATATCAAAATATTAAAATTAGTTATAATTAAACTTTTTT
Found at i:10871189 original size:17 final size:17
Alignment explanation
Indices: 10871167--10871200 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
10871157 TACTTAAACT
10871167 TTTTTAATATATTTAAA
1 TTTTTAATATATTTAAA
10871184 TTTTTAATATATTTAAA
1 TTTTTAATATATTTAAA
10871201 AAAATTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTAATATATTTAAA
Found at i:10871225 original size:27 final size:28
Alignment explanation
Indices: 10871184--10871236 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
10871174 TATATTTAAA
*
10871184 TTTTTAATATATTTAAAAAAATTAAGTT
1 TTTTTAAAATATTTAAAAAAATTAAGTT
* *
10871212 TTTTTAAAAT-TTTAAATATATTAAG
1 TTTTTAAAATATTTAAAAAAATTAAG
10871237 AAAATCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (28 bp):
TTTTTAAAATATTTAAAAAAATTAAGTT
Found at i:10872763 original size:34 final size:33
Alignment explanation
Indices: 10872714--10872779 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
10872704 AATCAGAACA
10872714 TTTAAGAAAACATAAATAATAAAAAATAAAAAAT
1 TTTAAGAAAACATAAA-AATAAAAAATAAAAAAT
*
10872748 TTTAAGAATAA-ATAAAAATAATAAATAAAAAA
1 TTTAAGAA-AACATAAAAATAAAAAATAAAAAA
10872780 CGAAAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 15 0.50
34 13 0.43
35 2 0.07
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (33 bp):
TTTAAGAAAACATAAAAATAAAAAATAAAAAAT
Found at i:10872770 original size:13 final size:13
Alignment explanation
Indices: 10872754--10872778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10872744 AAATTTTAAG
10872754 AATAAATAAAAAT
1 AATAAATAAAAAT
10872767 AATAAATAAAAA
1 AATAAATAAAAA
10872779 ACGAAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AATAAATAAAAAT
Found at i:10874611 original size:23 final size:24
Alignment explanation
Indices: 10874571--10874616 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
10874561 GGTATGTGCT
10874571 ATTAATTAACTATATATT-TTCCA
1 ATTAATTAACTATATATTGTTCCA
10874594 ATTAATTAACTAGT-TATTGTTCC
1 ATTAATTAACTA-TATATTGTTCC
10874617 TTTTTTCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.35, C:0.13, G:0.04, T:0.48
Consensus pattern (24 bp):
ATTAATTAACTATATATTGTTCCA
Found at i:10875610 original size:17 final size:17
Alignment explanation
Indices: 10875575--10875613 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
10875565 TTTTTTGGAG
*
10875575 TTTTATATTCTAATATA
1 TTTTATATTCAAATATA
* *
10875592 TTTTATATTGAAATTTA
1 TTTTATATTCAAATATA
10875609 TTTTA
1 TTTTA
10875614 AATATATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTATATTCAAATATA
Found at i:10875633 original size:23 final size:23
Alignment explanation
Indices: 10875603--10875696 Score: 78
Period size: 22 Copynumber: 4.3 Consensus size: 23
10875593 TTTATATTGA
10875603 AATT-TAT-TTTAAATATATAA-
1 AATTATATATTTAAATATATAAT
*
10875623 AATTATATATTTAAATTTATAAT
1 AATTATATATTTAAATATATAAT
* * *
10875646 GATTATAT-TTT-AAT-TCTTAT
1 AATTATATATTTAAATATATAAT
10875666 AGATTATATATTTAAAT-TA-AAT
1 A-ATTATATATTTAAATATATAAT
10875688 AATTGATAT
1 AATT-ATAT
10875697 TAATTACTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
20 8 0.13
21 16 0.27
22 25 0.42
23 11 0.18
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (23 bp):
AATTATATATTTAAATATATAAT
Found at i:10876485 original size:3 final size:3
Alignment explanation
Indices: 10876479--10876506 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
10876469 ATCGCTATCT
10876479 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
10876507 TTCCATCTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:10876513 original size:12 final size:12
Alignment explanation
Indices: 10876504--10876530 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
10876494 TCATCATCAT
10876504 CATTTCCATCTC
1 CATTTCCATCTC
10876516 CATTTCCATCTC
1 CATTTCCATCTC
10876528 CAT
1 CAT
10876531 CTTGATCTTC
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:0.41, G:0.00, T:0.41
Consensus pattern (12 bp):
CATTTCCATCTC
Found at i:10899048 original size:24 final size:24
Alignment explanation
Indices: 10899021--10899068 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
10899011 CATTAGTACA
10899021 TGCCAAAATTACAAAAAGAAACGT
1 TGCCAAAATTACAAAAAGAAACGT
*
10899045 TGCCAAAATTACAGAAAGAAACGT
1 TGCCAAAATTACAAAAAGAAACGT
10899069 CACCAACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.17
Consensus pattern (24 bp):
TGCCAAAATTACAAAAAGAAACGT
Found at i:10899074 original size:24 final size:24
Alignment explanation
Indices: 10899023--10899074 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
10899013 TTAGTACATG
**
10899023 CCAAAATTACAAAAAGAAACGTTG
1 CCAAAATTACAAAAAGAAACGTCA
*
10899047 CCAAAATTACAGAAAGAAACGTCA
1 CCAAAATTACAAAAAGAAACGTCA
10899071 CCAA
1 CCAA
10899075 CATTGAGTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.21, G:0.12, T:0.13
Consensus pattern (24 bp):
CCAAAATTACAAAAAGAAACGTCA
Done.