Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008185.1 Hibiscus syriacus cultivar Beakdansim tig00110788_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3563405
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 16
Found at i:1886880 original size:9 final size:9
Alignment explanation
Indices: 1886868--1886968 Score: 58
Period size: 9 Copynumber: 10.3 Consensus size: 9
1886858 GGTCGGGTCG
*
1886868 GGTCAGACC
1 GGTCAAACC
1886877 GGTCAAACC
1 GGTCAAACC
*
1886886 GGTTCAGACC
1 GG-TCAAACC
*
1886896 GATCAAACC
1 GGTCAAACC
1886905 GGTCAAAACC
1 GGTC-AAACC
*
1886915 AGTCATAACC
1 GGTCA-AACC
*
1886925 GGTTGAAAACC
1 GG-T-CAAACC
**
1886936 GGTCATAAGT
1 GGTCA-AACC
*
1886946 GGTTGAAAACC
1 GG-T-CAAACC
1886957 GGTCAAACC
1 GGTCAAACC
1886966 GGT
1 GGT
1886969 TTCCAGCCCT
Statistics
Matches: 69, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
9 29 0.42
10 26 0.38
11 12 0.17
12 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1886892 original size:19 final size:19
Alignment explanation
Indices: 1886870--1886907 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1886860 TCGGGTCGGG
*
1886870 TCAGACCGGTCAAACCGGT
1 TCAGACCGATCAAACCGGT
1886889 TCAGACCGATCAAACCGGT
1 TCAGACCGATCAAACCGGT
1886908 CAAAACCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.16
Consensus pattern (19 bp):
TCAGACCGATCAAACCGGT
Found at i:1886913 original size:10 final size:10
Alignment explanation
Indices: 1886874--1886968 Score: 54
Period size: 10 Copynumber: 9.6 Consensus size: 10
1886864 GTCGGGTCAG
1886874 ACCGGTC-AA
1 ACCGGTCAAA
*
1886883 ACCGGTTC-AG
1 ACCGG-TCAAA
*
1886893 ACCGATC-AA
1 ACCGGTCAAA
1886902 ACCGGTCAAA
1 ACCGGTCAAA
* *
1886912 ACCAGTCATA
1 ACCGGTCAAA
*
1886922 ACCGGTTGAAA
1 ACCGG-TCAAA
*
1886933 ACCGGTCATA
1 ACCGGTCAAA
** *
1886943 AGTGGTTGAAA
1 ACCGG-TCAAA
1886954 ACCGGTC-AA
1 ACCGGTCAAA
1886963 ACCGGT
1 ACCGGT
1886969 TTCCAGCCCT
Statistics
Matches: 64, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
9 22 0.34
10 28 0.44
11 14 0.22
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:1886935 original size:21 final size:21
Alignment explanation
Indices: 1886874--1886969 Score: 94
Period size: 21 Copynumber: 4.8 Consensus size: 21
1886864 GTCGGGTCAG
* *
1886874 ACCGGTCA-AACCGGTT-CAG
1 ACCGGTCATAACCGGTTGAAA
* *
1886893 ACCGATCA-AACCGG-TCAAA
1 ACCGGTCATAACCGGTTGAAA
*
1886912 ACCAGTCATAACCGGTTGAAA
1 ACCGGTCATAACCGGTTGAAA
**
1886933 ACCGGTCATAAGTGGTTGAAA
1 ACCGGTCATAACCGGTTGAAA
1886954 ACCGGTCA-AACCGGTT
1 ACCGGTCATAACCGGTT
1886970 TCCAGCCCTC
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
18 1 0.02
19 20 0.32
20 12 0.19
21 30 0.48
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (21 bp):
ACCGGTCATAACCGGTTGAAA
Found at i:1892255 original size:14 final size:15
Alignment explanation
Indices: 1892238--1892304 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 15
1892228 TAATGACCTA
1892238 AAAATAA-TAATAAT
1 AAAATAATTAATAAT
1892252 AAAATTAAATTAAT-AT
1 AAAA-T-AATTAATAAT
**
1892268 TTAATAATTAATAATT
1 AAAATAATTAATAA-T
*
1892284 ATAATAATTAA-AAT
1 AAAATAATTAATAAT
1892298 AAAATAA
1 AAAATAA
1892305 AACAATAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 18 0.41
15 5 0.11
16 17 0.39
17 4 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATAATTAATAAT
Found at i:1892290 original size:16 final size:14
Alignment explanation
Indices: 1892259--1892294 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
1892249 AATAAAATTA
1892259 AATTAATATTTAAT
1 AATTAATATTTAAT
1892273 AATTAATAATTATAAT
1 AATTAAT-ATT-TAAT
1892289 AATTAA
1 AATTAA
1892295 AATAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTAATATTTAAT
Found at i:1892545 original size:53 final size:53
Alignment explanation
Indices: 1892465--1892688 Score: 297
Period size: 53 Copynumber: 4.2 Consensus size: 53
1892455 CCTCTTCTTT
* * * * * *
1892465 GAACAATCTTCGA-CTAGCGGGTTCGCTCCCTCTTACTTTAGGGAATATAATTC
1 GAACAATCTTCTACCTA-CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* * *
1892518 GAACAACCTTCTACCTACGGGTTCGCTCCCTCTTGCTTTAGGGGGTAGAACTC
1 GAACAATCTTCTACCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* * *
1892571 GAACAATCTTCTACTTATGGGTTTGCTCCCTCTTGCTTCAGGGAGTAGAACTC
1 GAACAATCTTCTACCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* * *
1892624 GAACAATCTTCTGCCTATGGGTTTGCTCCCTCTTGCTTCAGGGAGTAGAACTC
1 GAACAATCTTCTACCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
1892677 GAACAATCTTCT
1 GAACAATCTTCT
1892689 GGTGTGATTC
Statistics
Matches: 155, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
53 152 0.98
54 3 0.02
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (53 bp):
GAACAATCTTCTACCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
Found at i:1893152 original size:42 final size:42
Alignment explanation
Indices: 1893106--1893244 Score: 233
Period size: 42 Copynumber: 3.3 Consensus size: 42
1893096 AAACTCACAA
* * *
1893106 ATGACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTG
1 ATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTATTG
1893148 ATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTATTG
1 ATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTATTG
* *
1893190 ATGGCCCGAAGGATTTCATCATCATGCTCAAAAGACTTATTG
1 ATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTATTG
1893232 ATGACCCGAAGGA
1 ATGACCCGAAGGA
1893245 CTTATAAATT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (42 bp):
ATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTATTG
Found at i:1893248 original size:20 final size:19
Alignment explanation
Indices: 1893129--1893249 Score: 53
Period size: 20 Copynumber: 5.9 Consensus size: 19
1893119 TTTAATCATC
* *
1893129 ATGCTCGAAAGACTTACTG
1 ATGCCCGAAAGACTTATTG
* * *
1893148 ATGACCCGAAGGATTTCATCATC
1 ATG-CCCGAAAGACTT-AT--TG
*
1893171 ATGCTCGAAAGACTTATTG
1 ATGCCCGAAAGACTTATTG
* * *
1893190 ATGGCCCGAAGGATTTCATCATC
1 AT-GCCCGAAAGACTT-AT--TG
* *
1893213 ATGCTCAAAAGACTTATTG
1 ATGCCCGAAAGACTTATTG
*
1893232 ATGACCCGAAGGACTTAT
1 ATG-CCCGAAAGACTTAT
1893250 AAATTGTGAA
Statistics
Matches: 72, Mismatches: 21, Indels: 17
0.65 0.19 0.15
Matches are distributed among these distances:
19 10 0.14
20 30 0.42
21 7 0.10
22 18 0.25
23 7 0.10
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (19 bp):
ATGCCCGAAAGACTTATTG
Found at i:1893413 original size:41 final size:41
Alignment explanation
Indices: 1893358--1893464 Score: 133
Period size: 42 Copynumber: 2.6 Consensus size: 41
1893348 CCCAAAGGTT
* * *
1893358 TTACAGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGC
1 TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
* * *
1893399 TTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAC
1 TTACAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGAC
* *
1893441 TTACTGATGGCCCGAATGACTTAT
1 TTACAGATGGCCCGAAGGACTTAT
1893465 AAATTATGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 21 0.39
42 33 0.61
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.26
Consensus pattern (41 bp):
TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
Found at i:1901956 original size:2 final size:2
Alignment explanation
Indices: 1901949--1901985 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1901939 ATGTAATGAA
1901949 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
1901986 AACCTTTACA
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:1902124 original size:21 final size:21
Alignment explanation
Indices: 1902098--1902158 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 21
1902088 TGAATTTAAC
*
1902098 ACACATAATATAATATAT-CAT
1 ACACAT-ATATAATATATGAAT
*
1902119 ACACATTATACTAAAATATGAAT
1 ACACA-TATA-TAATATATGAAT
1902142 ACA-AGTATATAATATAT
1 ACACA-TATATAATATAT
1902159 AAACTTATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 15 0.45
22 13 0.39
23 5 0.15
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.33
Consensus pattern (21 bp):
ACACATATATAATATATGAAT
Found at i:1903941 original size:3 final size:3
Alignment explanation
Indices: 1903933--1904001 Score: 54
Period size: 3 Copynumber: 23.0 Consensus size: 3
1903923 TATAATGACC
* **
1903933 TAA TAA TAA TAA TAA TAA -AA T-T TAA TTAA TATA TAA TTTT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TA-A TAA -TAA TAA TAA
*
1903979 TTA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
1904002 AACAATAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
2 5 0.10
3 40 0.77
4 7 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:1903983 original size:16 final size:16
Alignment explanation
Indices: 1903939--1903986 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1903929 GACCTAATAA
* *
1903939 TAATAATAATAAAATT
1 TAATAATTATAATATT
*
1903955 TAATTAATATATAATTTT
1 TAA-TAAT-TATAATATT
1903973 TAATAATTATAATA
1 TAATAATTATAATA
1903987 ATAATAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 9 0.35
17 8 0.31
18 9 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAATAATTATAATATT
Found at i:1910166 original size:22 final size:22
Alignment explanation
Indices: 1910140--1910187 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
1910130 AGAAAATGTC
1910140 TTTTAATATATATTAAAGAATT
1 TTTTAATATATATTAAAGAATT
*
1910162 TTTTAATATATTTTAAAGAATT
1 TTTTAATATATATTAAAGAATT
1910184 TTTT
1 TTTT
1910188 TATTATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTTAATATATATTAAAGAATT
Found at i:1910170 original size:20 final size:20
Alignment explanation
Indices: 1910147--1910197 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
1910137 GTCTTTTAAT
1910147 ATATATTAAAGAATTTTTTA
1 ATATATTAAAGAATTTTTTA
*
1910167 ATATATTTTAAAGAATTTTTTT
1 ATATA--TTAAAGAATTTTTTA
1910189 AT-TATTAAA
1 ATATATTAAA
1910198 AAAAGTTGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.18
20 5 0.18
21 2 0.07
22 16 0.57
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
ATATATTAAAGAATTTTTTA
Found at i:1921422 original size:15 final size:15
Alignment explanation
Indices: 1921402--1921435 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1921392 GGTCAACTCC
1921402 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1921417 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1921432 GGTC
1 GGTC
1921436 GGGTCAACCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1921435 original size:8 final size:7
Alignment explanation
Indices: 1921401--1921432 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1921391 TGGTCAACTC
1921401 CGGTCAA
1 CGGTCAA
1921408 CGGTCAA
1 CGGTCAA
1921415 CGGGTCAA
1 C-GGTCAA
1921423 CGGTCAA
1 CGGTCAA
1921430 CGG
1 CGG
1921433 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:1921467 original size:18 final size:18
Alignment explanation
Indices: 1921444--1921489 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1921434 TCGGGTCAAC
*
1921444 CGGGTCGGGTAAATGGGT
1 CGGGTCGGGTAAACGGGT
*
1921462 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
1921480 CGGGTCGGGT
1 CGGGTCGGGT
1921490 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.11, C:0.17, G:0.52, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:1921485 original size:13 final size:13
Alignment explanation
Indices: 1921409--1921467 Score: 64
Period size: 13 Copynumber: 4.3 Consensus size: 13
1921399 TCCGGTCAAC
*
1921409 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1921424 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1921437 GGTCAACCGGGTCG
1 GGTCAA-CGGGTCG
* *
1921451 GGTAAATGGGTCG
1 GGTCAACGGGTCG
1921464 GGTC
1 GGTC
1921468 GGGTCAACGG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
13 15 0.38
14 12 0.31
15 12 0.31
ACGTcount: A:0.19, C:0.22, G:0.42, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1923601 original size:23 final size:24
Alignment explanation
Indices: 1923575--1923681 Score: 110
Period size: 24 Copynumber: 4.5 Consensus size: 24
1923565 AAACGGAGAT
*
1923575 ATCAGAAATCA-AACATAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
1923598 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
1923622 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAGAACAGAATTCAG
** *
1923646 ATCAGATGTCA-AACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAG
1923669 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1923682 TAAAATATTC
Statistics
Matches: 64, Mismatches: 18, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
23 29 0.45
24 35 0.55
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:1926654 original size:20 final size:19
Alignment explanation
Indices: 1926611--1926652 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1926601 ATAGTGCATT
1926611 AAAACAGATTAAATGTGAA
1 AAAACAGATTAAATGTGAA
1926630 AAAACAGATTAAATGTGAA
1 AAAACAGATTAAATGTGAA
1926649 AAAA
1 AAAA
1926653 ACTTTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.62, C:0.05, G:0.14, T:0.19
Consensus pattern (19 bp):
AAAACAGATTAAATGTGAA
Found at i:1926662 original size:2 final size:2
Alignment explanation
Indices: 1926657--1926691 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1926647 AAAAAAACTT
1926657 TA TA TA TA TA 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 TA TA TA TA TA T
1926692 GTATGTGTGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1926829 original size:12 final size:12
Alignment explanation
Indices: 1926812--1926853 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1926802 AGGTCTGCAG
1926812 TCTGCAGACCAC
1 TCTGCAGACCAC
1926824 TCTGCAGACCAC
1 TCTGCAGACCAC
*
1926836 ATCTACAGA-CA-
1 -TCTGCAGACCAC
1926847 TCTGCAG
1 TCTGCAG
1926854 CAGAAGAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 6 0.22
12 14 0.52
13 7 0.26
ACGTcount: A:0.29, C:0.36, G:0.17, T:0.19
Consensus pattern (12 bp):
TCTGCAGACCAC
Found at i:1927082 original size:22 final size:22
Alignment explanation
Indices: 1927054--1927616 Score: 826
Period size: 22 Copynumber: 25.6 Consensus size: 22
1927044 ATAATAATTT
*
1927054 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*
1927076 TTTTAAAATAAATCAATCCATG
1 TTTTAAAATAAATCAATCCATA
* *
1927098 TTTTAAAATAAATTAATCTATA
1 TTTTAAAATAAATCAATCCATA
***
1927120 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
1927142 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*** *
1927164 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
1927186 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1927208 TTTTAAAATAAATCAATACATA
1 TTTTAAAATAAATCAATCCATA
1927230 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1927252 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1927274 TTTTAAAACAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1927296 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
1927318 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
1927340 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
1927362 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
1927384 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1927406 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *
1927428 TTTTAAAATAAATCAATTCGTA
1 TTTTAAAATAAATCAATCCATA
** *
1927450 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATCCATA
1927472 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1927494 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1927516 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
1927538 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
1927560 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
1927582 TTTTAAAATAAATCAATATATA
1 TTTTAAAATAAATCAATCCATA
1927604 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1927617 TTTAAAATAG
Statistics
Matches: 488, Mismatches: 47, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
21 12 0.02
22 464 0.95
23 12 0.02
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:1927633 original size:11 final size:12
Alignment explanation
Indices: 1927581--1927630 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
1927571 ATCAATCCAT
1927581 ATTTTAAAATAA
1 ATTTTAAAATAA
* * *
1927593 A--TCAATATAT
1 ATTTTAAAATAA
1927603 ATTTTAAAATAA
1 ATTTTAAAATAA
*
1927615 ATTTTAAAATAG
1 ATTTTAAAATAA
1927627 ATTT
1 ATTT
1927631 AAATGATTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
10 7 0.24
12 22 0.76
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:1936192 original size:76 final size:75
Alignment explanation
Indices: 1936065--1936242 Score: 221
Period size: 76 Copynumber: 2.3 Consensus size: 75
1936055 TAATAGAGAG
* ** * * *
1936065 GATTTATCTCACTTGAGATTATTTTTCTTAAAACAAAATTTGACTCACTTGAGATAATTTTTACT
1 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAAATTAGACTCACTTGAGACAATTTTTACT
1936130 CGAAACAAGAA
66 CGAAACAAG-A
* * * *
1936141 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTAGTCTCGCTTGAGACGATTTTTACT
1 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAAATTAGACTCACTTGAGACAATTTTTACT
*
1936206 CGAAAGAAGA
66 CGAAACAAGA
* *
1936216 CATTTCATTTTACTCAAGATTGTTTTT
1 GATTT-ATTTCACTCAAGATTGTTTTT
1936243 AAAGAAGATT
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
75 5 0.06
76 83 0.94
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (75 bp):
GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAAATTAGACTCACTTGAGACAATTTTTACT
CGAAACAAGA
Found at i:1936267 original size:73 final size:75
Alignment explanation
Indices: 1936087--1936267 Score: 217
Period size: 76 Copynumber: 2.4 Consensus size: 75
1936077 TTGAGATTAT
* * * * *
1936087 TTTTCTTAAAACAAAATTTGACTCACTTGAGATAATTTTTACTCGAAACAAGAAGATTTATTTCA
1 TTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCGAAACAAGAACATTTATTTCA
1936152 CTCAAGATTG
66 CTCAAGATTG
* * *
1936162 TTTTTCTTAAAACAAGATTAGTCTCGCTTGAGACGATTTTTACTCGAAAGAAG-ACATTTCATTT
1 -TTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCGAAACAAGAACATTT-ATTT
*
1936226 TACTCAAGATTG
64 CACTCAAGATTG
*
1936238 -TTT-TT-AAAGAAGATTTTGTCTCGCTTGAGA
1 TTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGA
1936268 TAGTTTCCCT
Statistics
Matches: 92, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
72 7 0.08
73 17 0.18
74 3 0.03
75 5 0.05
76 60 0.65
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (75 bp):
TTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCGAAACAAGAACATTTATTTCA
CTCAAGATTG
Found at i:1936299 original size:39 final size:37
Alignment explanation
Indices: 1936250--1936838 Score: 557
Period size: 39 Copynumber: 16.0 Consensus size: 37
1936240 TTTAAAGAAG
*
1936250 ATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA-AA
*
1936288 GATTTTATCTCGCTTGAGGTAGTTTCCCTTGAAACAGAA
1 -ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA-AA
* * *
1936327 GATTTTATCTCGCTTGAGGTAATTTCCCTCGAAACAAAA
1 -ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-AAA
*
1936366 TATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAAAA
1 -ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-AAA
*
1936405 GATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAAA
1 -ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
* * *
1936443 AGTTTTTATCTCGCTTGAGATAATTTCCATCGAAACAAAA
1 A--TTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-AAA
* * * *
1936483 TATTTTACCTCACTTAAGATAGTTTCCCTCGAAACAAAA
1 -ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-AAA
1936522 GATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-AA
1 -ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
* * *
1936559 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
* **
1936595 A-TTT-TCTCTCTTGAGACGGTTTCCCTTGAAAC-AA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
* ** * *
1936629 ATTTTGTCTCTTTTGATACAGTTTCCCTTGAAAC-AA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
* * *
1936665 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
* * *
1936701 ATTTTATCTCTCTTGAGACAGTTTCCTTTGAAAC-AA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
* * *
1936737 ATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA-AA
*
1936775 A----A-CT---TTGAGA-ACGTTTCCCTTGAAAC-GA
1 ATTTTATCTCGCTTGAGATA-GTTTCCCTTGAAACAAA
* * * *
1936803 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
1936839 GTTTTTGAGA
Statistics
Matches: 488, Mismatches: 42, Indels: 42
0.85 0.07 0.07
Matches are distributed among these distances:
28 2 0.00
29 1 0.00
30 19 0.04
33 4 0.01
34 30 0.06
35 6 0.01
36 177 0.36
37 4 0.01
38 6 0.01
39 234 0.48
40 4 0.01
41 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (37 bp):
ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
Found at i:1936819 original size:66 final size:68
Alignment explanation
Indices: 1936503--1936838 Score: 297
Period size: 72 Copynumber: 4.8 Consensus size: 68
1936493 CACTTAAGAT
* * * * * * *
1936503 AGTTTCCCTCGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCT
1 AGTTTCCCTTGAAAC--AA-ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAA---T-ACA
1936568 CTCTTGAGAC
59 CTCTTGAGAC
* * * * * *
1936578 AGTTTCCCTTGAAACAAA-TTT-TCTCTCTTGAGACGGTTTCCCTTGAAACAAATTTTGTCTCTT
1 AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAA---T-ACACTC
*
1936641 TTGATAC
62 TTGAGAC
* * *
1936648 AGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTC
1 AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAA---TA-CACTC
1936713 TTGAGAC
62 TTGAGAC
* *
1936720 AGTTTCCTTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAA-A-ACT-TTG
1 AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AATACACTCTTG
1936782 AGA-
65 AGAC
*
1936785 ACGTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
1 A-GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
1936839 GTTTTTGAGA
Statistics
Matches: 238, Mismatches: 18, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
65 2 0.01
66 54 0.23
67 2 0.01
69 1 0.00
70 62 0.26
71 6 0.03
72 93 0.39
73 4 0.02
75 14 0.06
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (68 bp):
AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATACACTCTTGA
GAC
Found at i:1936942 original size:124 final size:124
Alignment explanation
Indices: 1936757--1937021 Score: 318
Period size: 124 Copynumber: 2.1 Consensus size: 124
1936747 CCTTGAGATA
* *
1936757 GTTTCTCTTGAAACACAAAACTTTGAGAACGTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGAC
1 GTTTCCCTTGAAACACAAAACTTTGAGAACGTTTCCCTTGAAACGAATTTTATCTCCCTTGAGAC
* * ***
1936822 AGTTTCTCTTGAAACA-AGTTTTTGAGACAGTTTCTCTTGAAATATAAACTTTTAAAAT
66 AATTTATCTTGAAACACAACCTTTGAGACAGTTTCTCTTGAAATATAAACTTTTAAAAT
* ** * *
1936880 GTTTCCCTTGAGACACAAAATCTTTGAGATTGTTTCCCTTGAAAC-ATGTTTTATCTCTCTTGAG
1 GTTTCCCTTGAAACACAAAA-CTTTGAGAACGTTTCCCTTGAAACGA-ATTTTATCTCCCTTGAG
* * * * * *
1936944 ACAATTTATCTTGAAACACCAACCTTTGAGACAGTTTCTCTTGAAACACCAACCTTTGAGATT
64 ACAATTTATCTTGAAACA-CAACCTTTGAGACAGTTTCTCTTGAAATA-TAAACTTTTAAAAT
1937007 GTTTCCCTTGAAACA
1 GTTTCCCTTGAAACA
1937022 ATAAATTTTA
Statistics
Matches: 118, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
123 19 0.16
124 52 0.44
126 24 0.20
127 23 0.19
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (124 bp):
GTTTCCCTTGAAACACAAAACTTTGAGAACGTTTCCCTTGAAACGAATTTTATCTCCCTTGAGAC
AATTTATCTTGAAACACAACCTTTGAGACAGTTTCTCTTGAAATATAAACTTTTAAAAT
Found at i:1937011 original size:30 final size:30
Alignment explanation
Indices: 1936939--1937021 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
1936929 TTTATCTCTC
* *
1936939 TTGAGACAATTTATCTTGAAACACCAACCT
1 TTGAGACAGTTTCTCTTGAAACACCAACCT
1936969 TTGAGACAGTTTCTCTTGAAACACCAACCT
1 TTGAGACAGTTTCTCTTGAAACACCAACCT
** *
1936999 TTGAGATTGTTTCCCTTGAAACA
1 TTGAGACAGTTTCTCTTGAAACA
1937022 ATAAATTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (30 bp):
TTGAGACAGTTTCTCTTGAAACACCAACCT
Found at i:1937478 original size:91 final size:90
Alignment explanation
Indices: 1937323--1937760 Score: 621
Period size: 91 Copynumber: 4.8 Consensus size: 90
1937313 AAACCGATCA
* * ** *
1937323 AGAGTTCTTAATAAGAAGAACTCATCCAACGAGACAGAAAAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAA-GAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
1937388 CAACCTTGGTTCAAGATTTCCAGTGG
65 CAACCTTGGTTCAAGATTTCCAGTGG
*
1937414 AGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAAAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAA-GAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
1937479 CAACCTTGGTTCAAGATTTCCAGTGG
65 CAACCTTGGTTCAAGATTTCCAGTGG
* *
1937505 AGAGTTCATAATGAGAAGAACT-ATCTATAGAGGGAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCA-AGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
1937569 CAACCTGGGTTCAAGATTTCCAGTGG
65 CAACCTTGGTTCAAGATTTCCAGTGG
* * *
1937595 AGAGTTCATAATGAGAAGAACTCATCCATAAAGGAAGAAGAAGTTCATAATCAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCA-AGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
** *
1937660 CAACCTTGCATCAACATTTCCAGCAT-G
65 CAACCTTGGTTCAAGATTTCCAG--TGG
* * *
1937687 -GAGTTCATAATGAAAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAATAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCC-AAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
1937751 CAACTTTGGT
65 CAACCTTGGT
1937761 GATTCCATCA
Statistics
Matches: 314, Mismatches: 28, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
90 84 0.27
91 227 0.72
92 2 0.01
93 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (90 bp):
AGAGTTCATAATGAGAAGAACTCATCCAAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTGGTTCAAGATTTCCAGTGG
Found at i:1937667 original size:181 final size:182
Alignment explanation
Indices: 1937323--1937754 Score: 624
Period size: 181 Copynumber: 2.4 Consensus size: 182
1937313 AAACCGATCA
* * ** *
1937323 AGAGTTCTTAATAAGAAGAACTCATCCA-ACGAGACAGAAAAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCCATA-GAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
* * *
1937387 TCAACCTTGGTTCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGA
65 TCAACCTGGGTTCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGA
* ** *
1937452 AGAAGTTCATAATGAAAAGAACTTGTTCAACCTTGGTTCAAGATTTCCAG-TGG
130 AGAAGTTCATAATCAAAAGAACTTGTTCAACCTTGCATCAACATTTCCAGAT-G
* *
1937505 AGAGTTCATAATGAGAAGAACT-ATCTATAGAGGGAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCATAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
1937569 CAACCTGGGTTCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCATA-AAGGAAGA
66 CAACCTGGGTTCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCA-ACAAGGAAGA
*
1937633 AGAAGTTCATAATCAGAAGAACTTGTTCAACCTTGCATCAACATTTCCAGCATG
130 AGAAGTTCATAATCAAAAGAACTTGTTCAACCTTGCATCAACATTTCCAG-ATG
* *
1937687 -GAGTTCATAATGAAAAGAACTCATCCGAT-GAGGGAGAAGAAGTTCATAATGAGAATAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCC-ATAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
1937750 TCAAC
65 TCAAC
1937755 TTTGGTGATT
Statistics
Matches: 225, Mismatches: 19, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
181 159 0.71
182 63 0.28
183 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.25
Consensus pattern (182 bp):
AGAGTTCATAATGAGAAGAACTCATCCATAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTGGGTTCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAA
GAAGTTCATAATCAAAAGAACTTGTTCAACCTTGCATCAACATTTCCAGATG
Found at i:1937978 original size:132 final size:129
Alignment explanation
Indices: 1937799--1938070 Score: 334
Period size: 132 Copynumber: 2.1 Consensus size: 129
1937789 ATTTTTTATT
* ** *
1937799 TTCGCTCAAATCCATTGCAGAATGAGTTGGATCAACGACAACTTTTAGCTCAATTCTATCACAGA
1 TTCGCTCAAATACATCACAGAAAGAGTTGGATCAACGACAACTTTTAGCTCAATTCTATCACAG-
*
1937864 AGGAGGTAGGTAGATCAGCACC-AGCATCTCGTTCGA-TTCCATCACAAGATGAGATGGATC-AC
65 A--AGG-AGGTAGATCAACACCGA-CATCTCGTT-GATTTCCATCACAAGATGAGATGGATCAAC
1937926 ATTTG
125 ATTTG
* * * * *
1937931 TTCGCTCAAATACATCATAGAAAGAGTTGGATTATCGTCAACTTTTAGCTCGATTCTATCACAGA
1 TTCGCTCAAATACATCACAGAAAGAGTTGGATCAACGACAACTTTTAGCTCAATTCTATCACAGA
* * * *
1937996 AGGAGGTAGATCAACATCGACATCTCGTTTATTTTCATCACAAGATGAGGTGGATCAACATTTG
66 AGGAGGTAGATCAACACCGACATCTCGTTGATTTCCATCACAAGATGAGATGGATCAACATTTG
*
1938060 TTAGCTCAAAT
1 TTCGCTCAAAT
1938071 CTATGACATA
Statistics
Matches: 122, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
127 1 0.01
128 44 0.36
129 21 0.17
131 1 0.01
132 55 0.45
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (129 bp):
TTCGCTCAAATACATCACAGAAAGAGTTGGATCAACGACAACTTTTAGCTCAATTCTATCACAGA
AGGAGGTAGATCAACACCGACATCTCGTTGATTTCCATCACAAGATGAGATGGATCAACATTTG
Found at i:1938100 original size:132 final size:131
Alignment explanation
Indices: 1937822--1938070 Score: 328
Period size: 128 Copynumber: 1.9 Consensus size: 131
1937812 ATTGCAGAAT
* * *
1937822 GAGTTGGATCAACGACAACTTTTAGCTCAATTCTATCACAGAAGGAGGTAGGTAGATCAGCACCA
1 GAGTTGGATCATCGTCAACTTTTAGCTCAATTCTATCACAGAA-GAGGTAGGTAGATCAACACCA
* *
1937887 GCATCTCGTTCGATTCCATCACAAGATGAGATGGATCACATTTGTTCGCTCAAATACATCATAGA
65 GCATCTCGTTCGATTCCATCACAAGATGAGATGGATCACATTTGTTAGCTCAAATACATCATACA
1937952 AA
130 AA
* * *
1937954 GAGTTGGATTATCGTCAACTTTTAGCTCGATTCTATCACAG-A-AGG-AGGTAGATCAACATC-G
1 GAGTTGGATCATCGTCAACTTTTAGCTCAATTCTATCACAGAAGAGGTAGGTAGATCAACACCAG
* * *
1938015 ACATCTCGTT-TATTTTCATCACAAGATGAGGTGGATCAACATTTGTTAGCTCAAAT
66 -CATCTCGTTCGA-TTCCATCACAAGATGAGATGGATC-ACATTTGTTAGCTCAAAT
1938071 CTATGACATA
Statistics
Matches: 104, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
127 2 0.02
128 44 0.42
129 20 0.19
131 1 0.01
132 37 0.36
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (131 bp):
GAGTTGGATCATCGTCAACTTTTAGCTCAATTCTATCACAGAAGAGGTAGGTAGATCAACACCAG
CATCTCGTTCGATTCCATCACAAGATGAGATGGATCACATTTGTTAGCTCAAATACATCATACAA
A
Found at i:1945248 original size:62 final size:61
Alignment explanation
Indices: 1945158--1945414 Score: 246
Period size: 61 Copynumber: 4.3 Consensus size: 61
1945148 CATCTTTGTA
**
1945158 ACAATTAATTTATTCTAAAATGGATATTTACTCCACTAATCCTCTCTTTTTCTTCTTTCTG
1 ACAATTAATTTACCCTAAAATGGATATTTACTCCACTAATCCTCTCTTTTTCTTCTTTCTG
** ** * *
1945219 ACAATTAATTTACCCTTAAAATGGATATTTACTAGACTGGTCCTTTCTTTTTCTTCTTTTTG
1 ACAATTAATTTACCC-TAAAATGGATATTTACTCCACTAATCCTCTCTTTTTCTTCTTTCTG
* * ** *
1945281 ACAAATAATTTACCCTAAAACGGATATTTACTCCACTGGT-C-CTC----ACTTC--T-TG
1 ACAATTAATTTACCCTAAAATGGATATTTACTCCACTAATCCTCTCTTTTTCTTCTTTCTG
* * * * * *
1945333 ACAATTAATTCACCCTAAAATGGAAATTTACTCGGATTAA-CCTCTATTTTTCTTCTTTCTA
1 ACAATTAATTTACCCTAAAATGGATATTTACTC-CACTAATCCTCTCTTTTTCTTCTTTCTG
*
1945394 ACAATCAATTTACCCTAAAAT
1 ACAATTAATTTACCCTAAAAT
1945415 AGTGGAATTG
Statistics
Matches: 158, Mismatches: 27, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
52 31 0.20
53 4 0.03
54 2 0.01
55 4 0.03
58 4 0.03
59 2 0.01
60 2 0.01
61 55 0.35
62 54 0.34
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.42
Consensus pattern (61 bp):
ACAATTAATTTACCCTAAAATGGATATTTACTCCACTAATCCTCTCTTTTTCTTCTTTCTG
Found at i:1948925 original size:2 final size:2
Alignment explanation
Indices: 1948918--1948983 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1948908 TAAACCTTCT
1948918 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1948960 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
1948984 ATTAAACAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1949824 original size:22 final size:22
Alignment explanation
Indices: 1949805--1949846 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1949795 GTCGTAAATT
*
1949805 TATA-TAAC-TTTTAAGTTAAA
1 TATAGTAACATTTTAAATTAAA
1949825 TATAGTAACATTTTAAATTAAA
1 TATAGTAACATTTTAAATTAAA
1949847 AATCATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
22 11 0.58
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (22 bp):
TATAGTAACATTTTAAATTAAA
Found at i:1954283 original size:75 final size:76
Alignment explanation
Indices: 1954075--1954282 Score: 249
Period size: 75 Copynumber: 2.7 Consensus size: 76
1954065 CAAAGCCAAA
* * * * **
1954075 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGA-TCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
1954140 TTTGGCTCCGAG
65 TTTGGCTCCGAG
* * *
1954152 ATTTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCTAAACATT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
1954216 TTTGTTCCGAG
66 TTGGCTCCGAG
* * * *
1954227 AATTCCAGTATGCTCGGAGGGAACTGATCCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGAT-CCCCCCCATAGGAGGAACCGATTCCCCC
1954283 TGTTCAACGG
Statistics
Matches: 112, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
75 65 0.58
76 18 0.16
77 29 0.26
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:1960076 original size:20 final size:20
Alignment explanation
Indices: 1960051--1960090 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1960041 TTTTGCTGCA
1960051 GAGGGAATCGATCCCCCCTT
1 GAGGGAATCGATCCCCCCTT
*
1960071 GAGGGAATCGATTCCCCCTT
1 GAGGGAATCGATCCCCCCTT
1960091 TGAAGGGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.23
Consensus pattern (20 bp):
GAGGGAATCGATCCCCCCTT
Found at i:1960088 original size:21 final size:22
Alignment explanation
Indices: 1960053--1960134 Score: 89
Period size: 21 Copynumber: 3.8 Consensus size: 22
1960043 TTGCTGCAGA
1960053 GGGAATCGA-TCCCCCCTTGA-
1 GGGAATCGATTCCCCCCTTGAG
*
1960073 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCGATTCCCCCCTTG-AG
* **
1960096 GGGAACCGATTCCCCCC-ACAG
1 GGGAATCGATTCCCCCCTTGAG
*
1960117 GGGAATCGATACCCCCCT
1 GGGAATCGATTCCCCCCT
1960135 GGGGTTCTGC
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
20 9 0.18
21 26 0.51
22 1 0.02
23 15 0.29
ACGTcount: A:0.22, C:0.35, G:0.24, T:0.18
Consensus pattern (22 bp):
GGGAATCGATTCCCCCCTTGAG
Found at i:1962891 original size:74 final size:76
Alignment explanation
Indices: 1962709--1962914 Score: 256
Period size: 75 Copynumber: 2.7 Consensus size: 76
1962699 CAAAGCCAAA
* * * * **
1962709 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
1962773 TTTGGCTCCGAG
65 TTTGGCTCCGAG
* *
1962785 ATTTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACATT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
1962849 TTTGTTCCGAG
66 TTGGCTCCGAG
* * * *
1962860 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
1962915 TGTTCAACGG
Statistics
Matches: 113, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
74 21 0.19
75 61 0.54
76 31 0.27
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:1971684 original size:23 final size:21
Alignment explanation
Indices: 1971658--1971707 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1971648 GAAACCATAC
1971658 CATAAAAACATAGAAAAATATAT
1 CATAAAAACA-A-AAAAATATAT
* *
1971681 CATAAAGACAAAAAAATATGT
1 CATAAAAACAAAAAAATATAT
1971702 CATAAA
1 CATAAA
1971708 GGTAGTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 15 0.60
22 1 0.04
23 9 0.36
ACGTcount: A:0.64, C:0.10, G:0.06, T:0.20
Consensus pattern (21 bp):
CATAAAAACAAAAAAATATAT
Found at i:1971900 original size:8 final size:8
Alignment explanation
Indices: 1971887--1971915 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1971877 GATTAAGTAT
1971887 ATATTTTG
1 ATATTTTG
1971895 ATATTTTG
1 ATATTTTG
1971903 ATATTTTG
1 ATATTTTG
1971911 A-ATTT
1 ATATTT
1971916 AGTTTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 4 0.19
8 17 0.81
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (8 bp):
ATATTTTG
Found at i:1972741 original size:14 final size:16
Alignment explanation
Indices: 1972711--1972743 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1972701 GTTTTATCCA
1972711 TATTTATTTGTTAATT
1 TATTTATTTGTTAATT
1972727 TATTT-TTTG-TAATT
1 TATTTATTTGTTAATT
1972741 TAT
1 TAT
1972744 ATGTAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (16 bp):
TATTTATTTGTTAATT
Found at i:1983855 original size:23 final size:23
Alignment explanation
Indices: 1983800--1983876 Score: 61
Period size: 23 Copynumber: 3.4 Consensus size: 23
1983790 AAAAGATAAG
*
1983800 ATAAAGAAAACAAAGATAAAATA
1 ATAAAGAAAACAAAGATAAAAAA
* * *
1983823 GT-AAGTAAAATAAATATAAAAAA
1 ATAAAG-AAAACAAAGATAAAAAA
*
1983846 ATAAAGAAAA-AGAAGA-AATAAA
1 ATAAAGAAAACA-AAGATAAAAAA
*
1983868 ATATAGAAA
1 ATAAAGAAA
1983877 TAAAACAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
22 17 0.40
23 23 0.53
24 3 0.07
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.16
Consensus pattern (23 bp):
ATAAAGAAAACAAAGATAAAAAA
Found at i:1983875 original size:22 final size:22
Alignment explanation
Indices: 1983830--1983893 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
1983820 ATAGTAAGTA
*
1983830 AAATAAATATAAA-AAAATAAAG
1 AAATAAA-ACAAATAAAATAAAG
* *
1983852 AAA-AAGAAGAAATAAAATATAG
1 AAATAA-AACAAATAAAATAAAG
1983874 AAATAAAACAAAT-AAATAAA
1 AAATAAAACAAATAAAATAAA
1983894 ATAATAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
21 12 0.34
22 21 0.60
23 2 0.06
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.16
Consensus pattern (22 bp):
AAATAAAACAAATAAAATAAAG
Found at i:1983970 original size:29 final size:28
Alignment explanation
Indices: 1983883--1983957 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
1983873 GAAATAAAAC
* *
1983883 AAATAAATA-AAATAATAATAAAAAAGTAA
1 AAATAAATATATAT-ATAA-AAAAAAATAA
* *
1983912 AAATATATATATATATAAAAAAAAAAAA
1 AAATAAATATATATATAAAAAAAAATAA
1983940 AAAGTAAATATATATATA
1 AAA-TAAATATATATATA
1983958 TAAATTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 11 0.28
29 25 0.64
30 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (28 bp):
AAATAAATATATATATAAAAAAAAATAA
Found at i:1985293 original size:105 final size:104
Alignment explanation
Indices: 1984985--1985538 Score: 796
Period size: 105 Copynumber: 5.3 Consensus size: 104
1984975 GCATTGTTCC
* * * ** * *
1984985 GAGTCTAATATCCTCCGTCT-TGAAGTTGAAATTGGCTCTAAAACCGAGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGT-TGTGAAGTTGAAATTGGCTCT-GAATTGAGAAGTT-GTTGTTGACA
* * * * *
1985049 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
63 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1985091 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAA-TGA-AA-TT-TTGTTGACAAGC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAGAAGTTGTTGTTGACAAGC
1985152 AGCGGTCCCTTCGTCGT-AGAGTTGAACTTGCGTTGTCTG
66 AGCGGTCCCTTCGTCGTGA-AGTTGAACTTGCGTTGTCTG
*
1985191 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATTGAGAAGTTGTTGTTGACAAG
* *
1985256 CAACGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1985296 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATTGAGAAGTTGTTGTTGACAAG
1985361 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1985401 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTAAGAAGTTATTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA-TTGAGAAGTTGTTGTTGACAAG
1985466 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1985506 GAGTCTAATATTCTTCGTTGTGAAGTTGAAATT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1985539 TATTCTCGAG
Statistics
Matches: 414, Mismatches: 25, Indels: 19
0.90 0.05 0.04
Matches are distributed among these distances:
99 1 0.00
100 83 0.20
101 1 0.00
102 4 0.01
103 4 0.01
104 5 0.01
105 282 0.68
106 34 0.08
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (104 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1985704 original size:36 final size:36
Alignment explanation
Indices: 1985657--1985732 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
1985647 TGTTTGGAGA
* * *
1985657 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
* *
1985693 GAAACTATCTCAAGCGAGATAAAATTCATTTCAATG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
1985729 GAAA
1 GAAA
1985733 TGTTTTCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:1985853 original size:105 final size:104
Alignment explanation
Indices: 1985632--1985903 Score: 442
Period size: 105 Copynumber: 2.6 Consensus size: 104
1985622 TTCGTTAAAT
* ** *
1985632 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* * * *
1985694 AAACTATCTCAAGCGAGATAAAATTCATTTCAATGGAAA
66 AAACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAA
1985733 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1985798 AAACTATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAG-AAAAAAATCATTTCAAGGGAAA
1985838 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1985903 A
66 A
1985904 GGGAAATGTT
Statistics
Matches: 159, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
101 46 0.29
103 3 0.02
104 25 0.16
105 85 0.53
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.31
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAA
Found at i:1985984 original size:58 final size:58
Alignment explanation
Indices: 1985858--1985984 Score: 136
Period size: 58 Copynumber: 2.2 Consensus size: 58
1985848 GTTTATGTTT
* * *
1985858 CAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAGGGAAATGTTTTCAA
1 CAAGA-AAAATGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGA--GAAATGATCTCAA
* *
1985919 -AAG-AAAATGTCTCAAGGGAGACGAAATTTTCTGTTTCGAGGGA-AACT-ATCTCAA
1 CAAGAAAAATGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAGAAATGATCTCAA
1985973 GCAAGATAAAAT
1 -CAAGA-AAAAT
1985985 CTTCTTAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
54 5 0.09
55 3 0.05
56 3 0.05
58 43 0.75
60 3 0.05
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (58 bp):
CAAGAAAAATGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAGAAATGATCTCAA
Found at i:1986094 original size:36 final size:36
Alignment explanation
Indices: 1986049--1986163 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 36
1986039 GGTCTCAAGC
*
1986049 GAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGT
1 GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
* * ** * **
1986085 GAAATAAATCTTCTTTCGAGAAAAACAGTCTCAAGT
1 GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
* *
1986121 GAGACAAAGT-ATGTTTTAAGAAAAACAAAT-TTGAGT
1 GAGATAAA-TCTTGTTTTAAGAAAAAC-AATCTTGAGT
1986157 GAGATAA
1 GAGATAA
1986164 TCATCTGCAT
Statistics
Matches: 59, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
36 56 0.95
37 3 0.05
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.28
Consensus pattern (36 bp):
GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
Found at i:1986125 original size:72 final size:75
Alignment explanation
Indices: 1986002--1986163 Score: 217
Period size: 72 Copynumber: 2.2 Consensus size: 75
1985992 AAAAAATAGC
* * *
1986002 CTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAA-TCTTGTTTT
1 CTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAGT-ATGTTTT
1986066 AAGAAAAAC-AAT
63 AAGAAAAACAAAT
*
1986078 CTTGAGTGAAATAAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAAG
1 CTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAGTATGTTTTAAG
1986141 AAAAACAAAT
66 AAAAACAAAT
*
1986151 -TTGAGTGAGATAA
1 CTTGAGTGAAATAA
1986164 TCATCTGCAT
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
72 48 0.61
73 15 0.19
75 4 0.05
76 12 0.15
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (75 bp):
CTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAGTATGTTTTAAG
AAAAACAAAT
Found at i:1987691 original size:180 final size:180
Alignment explanation
Indices: 1987294--1987827 Score: 876
Period size: 180 Copynumber: 2.9 Consensus size: 180
1987284 ACCAGGTTTA
* *
1987294 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAACAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* **
1987359 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAG-C-GGGCTTTCGAGT
*
1987423 TTCCTTTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
128 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCA-CTTTAGAGGGACAAATC
* * * *
1987477 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAACAGTTGAGCAAACATCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1987542 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTCTATTCATAAAG-GGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAA--TCTATTCATAAAGCGGGCTTTCGAGTT
1987606 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTC-CTTTAGAGGGACAAATC
129 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCACTTTAGAGGGACAAATC
1987657 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1987722 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAG-C-GGGCTTTCGAGTT
1987787 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
129 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCA-CTTTA
1987828 CGGATTTAAT
Statistics
Matches: 329, Mismatches: 14, Indels: 16
0.92 0.04 0.04
Matches are distributed among these distances:
178 13 0.04
180 114 0.35
181 47 0.14
182 46 0.14
183 95 0.29
184 1 0.00
185 13 0.04
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (180 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCGGGCTTTCGAGTTTC
CTCTATAACCAATTGCCTTAGTGGAATAGCTCACTTTAGAGGGACAAATC
Found at i:1991635 original size:15 final size:15
Alignment explanation
Indices: 1991583--1991627 Score: 90
Period size: 15 Copynumber: 3.0 Consensus size: 15
1991573 AAAACCATGT
1991583 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1991598 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1991613 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1991628 GAAATAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:1991722 original size:32 final size:31
Alignment explanation
Indices: 1991650--1991753 Score: 88
Period size: 32 Copynumber: 3.3 Consensus size: 31
1991640 TTAATTAAAT
* *
1991650 TAAAATAAAGAGAAAACAAATTAAATAAAAGA
1 TAAAATAAAGA-AAAAAAAATAAAATAAAAGA
* *
1991682 TAAGATAAAGAAAACAAAAATAAAATAGTAAG-
1 TAAAATAAAGAAAA-AAAAATAAAATA-AAAGA
* *
1991714 TAAAATAAATATAAAAAAATAAAGA-AAAAGA
1 TAAAATAAAGAAAAAAAAATAAA-ATAAAAGA
1991745 -AGAAATAAA
1 TA-AAATAAA
1991754 TATAGAAATA
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
30 4 0.07
31 20 0.34
32 32 0.54
33 3 0.05
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (31 bp):
TAAAATAAAGAAAAAAAAATAAAATAAAAGA
Found at i:1991754 original size:21 final size:21
Alignment explanation
Indices: 1991716--1991778 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1991706 ATAGTAAGTA
* *
1991716 AAATAAATATAAAAAAATAAAG
1 AAATAAA-ACAAATAAATAAAG
* *
1991738 AAA-AAGAAGAAATAAATATAG
1 AAATAA-AACAAATAAATAAAG
1991759 AAATAAAACAAATAAATAAA
1 AAATAAAACAAATAAATAAA
1991779 ATAATAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 28 0.82
22 6 0.18
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (21 bp):
AAATAAAACAAATAAATAAAG
Found at i:1991775 original size:25 final size:24
Alignment explanation
Indices: 1991715--1991806 Score: 71
Period size: 25 Copynumber: 3.7 Consensus size: 24
1991705 AATAGTAAGT
* * *
1991715 AAAATAAATATAAAAAAATAAAGAAA
1 AAAATAAATA-AATATAAT-AATAAA
*
1991741 AAGAAGAAATAAATATAGA-AATAAA
1 AA-AATAAATAAATATA-ATAATAAA
1991766 ACAAATAAATAAA-ATAATAATAAA
1 A-AAATAAATAAATATAATAATAAA
*
1991790 AAAATAAAAATAATATA
1 AAAATAAATA-AATATA
1991807 TATATATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
23 9 0.17
24 12 0.22
25 18 0.33
26 7 0.13
27 8 0.15
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (24 bp):
AAAATAAATAAATATAATAATAAA
Found at i:1991807 original size:2 final size:2
Alignment explanation
Indices: 1991802--1991826 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1991792 AATAAAAATA
1991802 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 A
1991827 ATAAAAAATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1992346 original size:37 final size:37
Alignment explanation
Indices: 1992255--1992356 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 37
1992245 GTGCTTGTGG
* * * * *
1992255 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
* *
1992292 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
* * *
1992329 ATCCTATTTTTAAGAGTTTGAATTCTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAG
1992357 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
Found at i:1995402 original size:23 final size:22
Alignment explanation
Indices: 1995350--1995403 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
1995340 AAGCGTTATG
** *
1995350 AAAGTAGAAGAAAACGTGTCATG
1 AAAGTAG-AGAAAACGTACCATA
*
1995373 AATGTAGAGAAAATCGTACCATA
1 AAAGTAGAGAAAA-CGTACCATA
1995396 AAAGTAGA
1 AAAGTAGA
1995404 ATTATCAGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.50, C:0.09, G:0.22, T:0.19
Consensus pattern (22 bp):
AAAGTAGAGAAAACGTACCATA
Found at i:2005078 original size:16 final size:16
Alignment explanation
Indices: 2005057--2005093 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
2005047 GATGTATGTA
2005057 TCCATTGAACTTTGTC
1 TCCATTGAACTTTGTC
2005073 TCCATTGAACTTTGTC
1 TCCATTGAACTTTGTC
2005089 TCCAT
1 TCCAT
2005094 ATTCATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.19, C:0.27, G:0.11, T:0.43
Consensus pattern (16 bp):
TCCATTGAACTTTGTC
Found at i:2007616 original size:2 final size:2
Alignment explanation
Indices: 2007609--2007638 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2007599 AAACATTGTA
*
2007609 AG AG AG AG AG AA 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
2007639 TAGGGGTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2012031 original size:21 final size:19
Alignment explanation
Indices: 2011995--2012046 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
2011985 ATATACGTTT
*
2011995 TATGAACAATAAAATA-CAA
1 TATGAACAGTAAAATATC-A
*
2012014 TATGAACAGTGAACAATATCG
1 TATGAACAGT-AA-AATATCA
2012035 TATGAACAGTAA
1 TATGAACAGTAA
2012047 TAAACAGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 9 0.32
20 4 0.14
21 14 0.50
22 1 0.04
ACGTcount: A:0.52, C:0.12, G:0.13, T:0.23
Consensus pattern (19 bp):
TATGAACAGTAAAATATCA
Found at i:2012064 original size:22 final size:22
Alignment explanation
Indices: 2012036--2012079 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2012026 ACAATATCGT
*
2012036 ATGAACAGTAATAAACAGTACC
1 ATGAACAATAATAAACAGTACC
*
2012058 ATGAACAATAATGAACAGTACC
1 ATGAACAATAATAAACAGTACC
2012080 CAAATGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (22 bp):
ATGAACAATAATAAACAGTACC
Found at i:2012146 original size:21 final size:21
Alignment explanation
Indices: 2012113--2012173 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
2012103 GTCAGAGAGG
*
2012113 AACCGATTCCCCTGCTACAGGA
1 AACCGA-TACCCTGCTACAGGA
2012135 AACCGATACCCTGCTACAGGA
1 AACCGATACCCTGCTACAGGA
2012156 AACCGATACCCTGCTACA
1 AACCGATACCCTGCTACA
2012174 ATACTGCTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 32 0.84
22 6 0.16
ACGTcount: A:0.31, C:0.36, G:0.16, T:0.16
Consensus pattern (21 bp):
AACCGATACCCTGCTACAGGA
Found at i:2013931 original size:19 final size:19
Alignment explanation
Indices: 2013903--2013940 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2013893 TTTTTCCATT
2013903 AGGGGAAATC-GATACCCCC
1 AGGGGAAATCTG-TACCCCC
*
2013922 AGGGGGAATCTGTACCCCC
1 AGGGGAAATCTGTACCCCC
2013941 TGCGTAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.26, C:0.32, G:0.29, T:0.13
Consensus pattern (19 bp):
AGGGGAAATCTGTACCCCC
Found at i:2014811 original size:26 final size:25
Alignment explanation
Indices: 2014775--2014831 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 25
2014765 TAAAAATTGT
2014775 TGTCACGACGAACGTCACCCTAGGTG
1 TGTCACGACGAACGTCACCCTA-GTG
2014801 TGTCACGACGAACGTCACCCTAGTG
1 TGTCACGACGAACGTCACCCTAGTG
*
2014826 CGTCAC
1 TGTCAC
2014832 TAAATGTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 8 0.27
26 22 0.73
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.19
Consensus pattern (25 bp):
TGTCACGACGAACGTCACCCTAGTG
Found at i:2015122 original size:29 final size:29
Alignment explanation
Indices: 2015090--2015188 Score: 96
Period size: 29 Copynumber: 3.4 Consensus size: 29
2015080 AAACAGTTAC
*
2015090 ATTAAAATAAATGTCTAAACCTTTTATAA
1 ATTAAAATAAATGTCTAAACTTTTTATAA
* * *
2015119 ATTATAATAAAAGTCTAAAGTTTTTATAAA
1 ATTAAAATAAATGTCTAAACTTTTTAT-AA
2015149 ATATAAAA-AAATG--TAAACATTTTTATAA
1 AT-TAAAATAAATGTCTAAAC-TTTTTATAA
* *
2015177 ATGATAATAAAT
1 ATTAAAATAAAT
2015189 AACAAATTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
27 3 0.05
28 12 0.21
29 30 0.53
30 8 0.14
31 4 0.07
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (29 bp):
ATTAAAATAAATGTCTAAACTTTTTATAA
Found at i:2015362 original size:29 final size:30
Alignment explanation
Indices: 2015287--2015362 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
2015277 GCCAAACTCC
* *
2015287 TTACAAATTACAAT-AATGCAATATACTTT
1 TTACAAATTACAATAAAAGCAACATACTTT
*
2015316 TTACAAATTATAATAAAAG-AACATACTTT
1 TTACAAATTACAATAAAAGCAACATACTTT
*
2015345 TTACAATTTACAATAAAA
1 TTACAAATTACAATAAAA
2015363 ACCCAAAGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 38 0.93
30 3 0.07
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.36
Consensus pattern (30 bp):
TTACAAATTACAATAAAAGCAACATACTTT
Found at i:2017398 original size:16 final size:16
Alignment explanation
Indices: 2017377--2017419 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
2017367 AAAAGTTTCT
2017377 TGCAAATTTTTTTGGA
1 TGCAAATTTTTTTGGA
2017393 TGCAAATTTTTTTGGA
1 TGCAAATTTTTTTGGA
*
2017409 GGCAAATTTTT
1 TGCAAATTTTT
2017420 GCTCCAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.49
Consensus pattern (16 bp):
TGCAAATTTTTTTGGA
Found at i:2021401 original size:3 final size:3
Alignment explanation
Indices: 2021393--2021418 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2021383 AGAAATTTTA
2021393 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2021419 ATTGGTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2023537 original size:12 final size:12
Alignment explanation
Indices: 2023520--2023556 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2023510 ATTTATAAGA
2023520 GAGGAGAGATGC
1 GAGGAGAGATGC
*
2023532 GA-G-GAGATGT
1 GAGGAGAGATGC
2023542 GAGGAGAGATGC
1 GAGGAGAGATGC
2023554 GAG
1 GAG
2023557 AACGGAAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.38
11 2 0.10
12 11 0.52
ACGTcount: A:0.32, C:0.05, G:0.51, T:0.11
Consensus pattern (12 bp):
GAGGAGAGATGC
Found at i:2025101 original size:59 final size:60
Alignment explanation
Indices: 2025036--2025196 Score: 186
Period size: 58 Copynumber: 2.7 Consensus size: 60
2025026 AATTGAAATA
* * *
2025036 TTCAAAAGTTTGAGGACTAATTTAGAAA-GAGGATCATACTTT-AGGATAAAATTAGAGTG
1 TTCAAAAGTTTAAGGACTAATTTA-AAATGAGGATCATACTTTGAGGATAAAATTAGAATC
* * * *
2025095 TTCAAAAGTTTAAAGACTAATTTAAAATGA-G-TCATAGTTTGGGGATCAAATTAGAATC
1 TTCAAAAGTTTAAGGACTAATTTAAAATGAGGATCATACTTTGAGGATAAAATTAGAATC
* * * *
2025153 TTTAAAAGTTTAAGGACCAATTTAAAATGAGGATTATAGTTTGA
1 TTCAAAAGTTTAAGGACTAATTTAAAATGAGGATCATACTTTGA
2025197 AGACATATAA
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
57 8 0.09
58 44 0.51
59 25 0.29
60 9 0.10
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (60 bp):
TTCAAAAGTTTAAGGACTAATTTAAAATGAGGATCATACTTTGAGGATAAAATTAGAATC
Found at i:2025164 original size:58 final size:59
Alignment explanation
Indices: 2025015--2025183 Score: 184
Period size: 58 Copynumber: 2.9 Consensus size: 59
2025005 TTTGGATAAA
* *
2025015 TTTGGGGATGAAATT-GAAATATTCAAAAGTTTGAGGACTAATTTAGAAA-GAGGATCATAC
1 TTTGGGGATAAAATTAG-AATATTCAAAAGTTTAAGGACTAATTTA-AAATGA-GATCATAC
* * * * *
2025075 TTT-AGGATAAAATTAGAGTGTTCAAAAGTTTAAAGACTAATTTAAAATGAG-TCATAG
1 TTTGGGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGATCATAC
* * * *
2025132 TTTGGGGATCAAATTAGAATCTTTAAAAGTTTAAGGACCAATTTAAAATGAG
1 TTTGGGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAG
2025184 GATTATAGTT
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
57 8 0.09
58 45 0.49
59 35 0.38
60 4 0.04
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (59 bp):
TTTGGGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGATCATAC
Found at i:2026114 original size:17 final size:17
Alignment explanation
Indices: 2026092--2026141 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2026082 AAATTCTTCT
2026092 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
2026109 AACA-T--T-GATACTCA
1 AACATTCATAGAAAC-CA
2026123 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
2026140 AA
1 AA
2026142 ACATGAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 1 0.04
16 1 0.04
17 9 0.35
18 4 0.15
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (17 bp):
AACATTCATAGAAACCA
Found at i:2026461 original size:14 final size:13
Alignment explanation
Indices: 2026442--2026474 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2026432 TTTTTAACAT
2026442 ATATATATAATATA
1 ATATATAT-ATATA
2026456 ATATATATATATA
1 ATATATATATATA
2026469 A-ATATA
1 ATATATA
2026475 GATGGATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 6 0.32
14 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATATATATATA
Found at i:2026461 original size:16 final size:14
Alignment explanation
Indices: 2026440--2026474 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
2026430 TTTTTTTAAC
2026440 ATATATATATAATATA
1 ATATATATAT-ATA-A
2026456 ATATATATATATAA
1 ATATATATATATAA
2026470 ATATA
1 ATATA
2026475 GATGGATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 3 0.16
16 10 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATATATATATAA
Found at i:2034042 original size:21 final size:21
Alignment explanation
Indices: 2034018--2034057 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2034008 TTCCTACACA
2034018 ACTTATCTAATAT-CCTTTTAT
1 ACTTAT-TAATATACCTTTTAT
*
2034039 ACTTATTTATATACCTTTT
1 ACTTATTAATATACCTTTT
2034058 TCCATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (21 bp):
ACTTATTAATATACCTTTTAT
Found at i:2034071 original size:21 final size:21
Alignment explanation
Indices: 2034025--2034071 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
2034015 ACAACTTATC
*
2034025 TAATATCCTTTTATACTTATT
1 TAATATCCTTTTATACATATT
*
2034046 T-ATATACCTTTT-TCCATATT
1 TAATAT-CCTTTTATACATATT
2034066 TAATAT
1 TAATAT
2034072 GCTGTATGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATATCCTTTTATACATATT
Found at i:2034477 original size:21 final size:21
Alignment explanation
Indices: 2034448--2034488 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2034438 GGCACTGTAT
*
2034448 ATTTGTCCCGAAGGACCACTG
1 ATTTATCCCGAAGGACCACTG
2034469 ATTTATCCCGAAGGACCACT
1 ATTTATCCCGAAGGACCACT
2034489 CCTTAAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (21 bp):
ATTTATCCCGAAGGACCACTG
Found at i:2035257 original size:14 final size:14
Alignment explanation
Indices: 2035238--2035266 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2035228 CTACACCATG
2035238 TATCGATGCATCCC
1 TATCGATGCATCCC
2035252 TATCGATGCATCCC
1 TATCGATGCATCCC
2035266 T
1 T
2035267 TGAAGGGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.31
Consensus pattern (14 bp):
TATCGATGCATCCC
Found at i:2039337 original size:21 final size:21
Alignment explanation
Indices: 2039311--2039350 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2039301 TTCTTACACA
2039311 ACTTATCTAATAT-CCTTTTAT
1 ACTTAT-TAATATACCTTTTAT
*
2039332 ACTTATTTATATACCTTTT
1 ACTTATTAATATACCTTTT
2039351 TCCTCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (21 bp):
ACTTATTAATATACCTTTTAT
Found at i:2039777 original size:18 final size:18
Alignment explanation
Indices: 2039745--2039797 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
2039735 ACTGTATATT
* *
2039745 TGTCCCAAAGGACCACTA
1 TGTCCCGAAGAACCACTA
*
2039763 TGTCCTGAAGAACCACTA
1 TGTCCCGAAGAACCACTA
*
2039781 TGTCCCGAAGGACCACT
1 TGTCCCGAAGAACCACT
2039798 CCTTAAGAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGAACCACTA
Found at i:2041988 original size:25 final size:25
Alignment explanation
Indices: 2041954--2042045 Score: 175
Period size: 25 Copynumber: 3.7 Consensus size: 25
2041944 ACTTGCTTAG
2041954 TTTGAGCATTTAATTAGAAATGTTC
1 TTTGAGCATTTAATTAGAAATGTTC
2041979 TTTGAGCATTTAATTAGAAATGTTC
1 TTTGAGCATTTAATTAGAAATGTTC
2042004 TTTGAGCATTTAATTAGAAATGTTC
1 TTTGAGCATTTAATTAGAAATGTTC
*
2042029 TTTGAGCTTTTAATTAG
1 TTTGAGCATTTAATTAG
2042046 TTAACTTGGT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
25 66 1.00
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (25 bp):
TTTGAGCATTTAATTAGAAATGTTC
Found at i:2045260 original size:29 final size:31
Alignment explanation
Indices: 2045200--2045269 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
2045190 CACCTCATGC
* *
2045200 CATCCAATTATTAGTAAGATTACAAATAAGT
1 CATCCAATTATTAGAAAGATCACAAATAAGT
*
2045231 CATCCAATT-TTAGAAAG-TCACAAATGAGT
1 CATCCAATTATTAGAAAGATCACAAATAAGT
*
2045260 CACCCAATTA
1 CATCCAATTA
2045270 ATCAGACAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.53
30 7 0.21
31 9 0.26
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (31 bp):
CATCCAATTATTAGAAAGATCACAAATAAGT
Found at i:2049655 original size:22 final size:21
Alignment explanation
Indices: 2049627--2049668 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2049617 TTTTATAATG
*
2049627 TTTATATCTTAGATTTTTTTAA
1 TTTATATCTTA-ATATTTTTAA
*
2049649 TTTATATTTTAATATTTTTA
1 TTTATATCTTAATATTTTTA
2049669 TCATTTCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTATATCTTAATATTTTTAA
Found at i:2065765 original size:14 final size:15
Alignment explanation
Indices: 2065684--2065771 Score: 88
Period size: 15 Copynumber: 5.5 Consensus size: 15
2065674 TAATAAGGTT
2065684 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
2065699 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
2065714 AATTATTATAAAATATAGA
1 ATTTATT-TTAAA-AT--A
2065733 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
2065751 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
2065765 ATTTATT
1 ATTTATT
2065772 AGTATGAATT
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
14 12 0.19
15 30 0.48
16 4 0.06
17 2 0.03
18 1 0.02
19 1 0.02
20 2 0.03
21 4 0.06
22 6 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:2065788 original size:18 final size:18
Alignment explanation
Indices: 2065765--2065843 Score: 58
Period size: 18 Copynumber: 4.4 Consensus size: 18
2065755 ATTTTAAATA
2065765 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
2065783 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AGTATGAATTG
* *
2065805 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
2065819 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
2065837 ATTTATT
1 ATTTATT
2065844 TTAAAATATA
Statistics
Matches: 46, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
14 9 0.20
15 1 0.02
16 2 0.04
17 1 0.02
18 15 0.33
20 4 0.09
22 14 0.30
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.53
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:2065790 original size:22 final size:22
Alignment explanation
Indices: 2065774--2065816 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2065764 AATTTATTAG
2065774 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
2065796 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
2065817 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:2065790 original size:32 final size:32
Alignment explanation
Indices: 2065751--2065848 Score: 126
Period size: 32 Copynumber: 3.4 Consensus size: 32
2065741 TTTTAAAATA
2065751 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
2065783 ATTTATTTT-AA-AA--TA-T-G---G-ATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
2065805 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
2065837 ATTTATTTTAAA
1 ATTTATTTTAAA
2065849 ATATAGATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
22 13 0.23
23 3 0.05
24 2 0.04
26 3 0.05
27 2 0.04
28 3 0.05
30 2 0.04
31 3 0.05
32 25 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTG
Found at i:2065816 original size:54 final size:54
Alignment explanation
Indices: 2065751--2066328 Score: 246
Period size: 54 Copynumber: 10.4 Consensus size: 54
2065741 TTTTAAAATA
2065751 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
*
2065805 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
* * **
2065859 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATTTA-TTAGTATGAATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * ** *
2065908 TATGGA-TTGATTTATTTTA-AAGTATGGATTGATTTATTTT-AAATAATTTATTA
1 -ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAAT-ATGGATTG
* ** * * * * * ** *
2065961 ATATAGATTGATTTATTT-TAAAATAT-AGATTGATTTATTATTATAGTTGTATAGATTG
1 ATTTATTTTAAATAATTTAT-TAGTATGA-ATTGATTTATT-TTA-A--AATATGGATTG
*
2066019 ATTTATTTTAAATAATTTGTTAGTATGAATTGATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT-AA-AA--TA-T-G----GATTG
** * *
2066083 ATTTATTTTAAATAATTTATTTTTATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
* * * *
2066137 ATTTATTATT--GTAGTTGTA-T-GGATTG-ATTGATTTATTTT-AAATA---ATTT
1 ATTTATT-TTAAATAATT-TATTAGTA-TGAATTGATTTATTTTAAAATATGGATTG
* * ** * * *
2066185 ATTAATATCGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTAGTATGGA
1 ATTTATTTTAAATAATTTA--TT--AGTATGAATTGATTTA-TTT---TAA---A--A-TATGGA
2066250 TTG
52 TTG
* * *
2066253 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
2066307 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
2066329 TTGTAATTGT
Statistics
Matches: 400, Mismatches: 68, Indels: 112
0.69 0.12 0.19
Matches are distributed among these distances:
47 5 0.01
48 36 0.09
49 6 0.01
50 5 0.01
51 7 0.02
52 19 0.05
53 16 0.04
54 157 0.39
55 11 0.03
56 1 0.00
57 5 0.01
58 37 0.09
59 6 0.01
60 5 0.01
62 3 0.01
63 5 0.01
64 56 0.14
65 2 0.00
66 2 0.00
68 16 0.04
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
Found at i:2065887 original size:80 final size:80
Alignment explanation
Indices: 2065796--2065945 Score: 273
Period size: 80 Copynumber: 1.9 Consensus size: 80
2065786 TATTTTAAAA
2065796 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
2065861 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
* * *
2065876 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAGTATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
2065941 TTATT
66 TTATT
2065946 TTAAATAATT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
TTATTATTGTAGTTG
Found at i:2065895 original size:134 final size:134
Alignment explanation
Indices: 2065751--2066264 Score: 746
Period size: 134 Copynumber: 3.7 Consensus size: 134
2065741 TTTTAAAATA
2065751 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
2065816 ATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTGTATGG
66 ATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTGTATGG
2065881 ATTG
131 ATTG
* *
2065885 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAGTATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
* * *
2065950 ATAATTTATTAATAT-AGATTGATTTATTTTAAAATATAGATTGATTTATTATTATAGTTGTATA
66 ATAATTTATTAGTATGA-ATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTGTATG
2066014 GATTG
130 GATTG
*
2066019 ATTTATTTTAAATAATTTGTTAGTATGAATTGATTTATTTTAAATAATTTATTAGTATAGATTGA
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT-AA-AA--TA-T-G----GATTGA
** *
2066084 TTTATTTTAAATAATTTATTTTTATGGATTGATTTATTTTAAAATAT-GAATTGATTTATTATTG
56 TTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAG-ATTGATTTATTATTG
2066148 TAGTTGTATGGATTGATTG
120 TAGTTGTAT-G---GATTG
* *
2066167 ATTTATTTTAAATAATTTATTAATATCG-ATTGATTTATTTTAAAATATGAATTGATTTATTTTA
1 ATTTATTTTAAATAATTTATTAGTAT-GAATTGATTTATTTTAAAATATGGATTGATTTATTTTA
*
2066231 AATAATTTATTAGTATGGATTGATTTATTTTAAA
65 AATAATTTATTAGTATGAATTGATTTATTTTAAA
2066265 TAATTTATTT
Statistics
Matches: 344, Mismatches: 18, Indels: 32
0.87 0.05 0.08
Matches are distributed among these distances:
133 1 0.00
134 166 0.48
135 2 0.01
136 1 0.00
138 48 0.14
139 1 0.00
140 1 0.00
142 1 0.00
143 2 0.01
144 74 0.22
146 2 0.01
147 2 0.01
148 42 0.12
149 1 0.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (134 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
ATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTGTATGG
ATTG
Found at i:2065916 original size:32 final size:32
Alignment explanation
Indices: 2065875--2065982 Score: 128
Period size: 32 Copynumber: 3.7 Consensus size: 32
2065865 TATTGTAGTT
2065875 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2065907 GTATGGATTGATTTA-TTT---T-A---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2065929 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
2065961 ATATAGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
2065983 ATATAGATTG
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
22 16 0.25
23 3 0.05
24 1 0.02
26 1 0.02
27 2 0.03
28 1 0.02
30 1 0.02
31 3 0.05
32 36 0.56
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:2065922 original size:18 final size:19
Alignment explanation
Indices: 2065899--2065945 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 19
2065889 ATTTTAAATA
2065899 ATTTATT-AGTATGGATTG
1 ATTTATTAAGTATGGATTG
2065917 ATTTATTTTAAAGTATGGATTG
1 ATTTA--TT-AAGTATGGATTG
2065939 ATTTATT
1 ATTTATT
2065946 TTAAATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.20
20 4 0.16
22 16 0.64
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (19 bp):
ATTTATTAAGTATGGATTG
Found at i:2065931 original size:22 final size:22
Alignment explanation
Indices: 2065906--2065950 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2065896 ATAATTTATT
2065906 AGTATGGATTGATTTATTTTAA
1 AGTATGGATTGATTTATTTTAA
2065928 AGTATGGATTGATTTATTTTAA
1 AGTATGGATTGATTTATTTTAA
2065950 A
1 A
2065951 TAATTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (22 bp):
AGTATGGATTGATTTATTTTAA
Found at i:2065976 original size:18 final size:18
Alignment explanation
Indices: 2065953--2066006 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 18
2065943 ATTTTAAATA
2065953 ATTTATTAATATAGATTG
1 ATTTATTAATATAGATTG
2065971 ATTTATTTTAAAATATAGATTG
1 ATTTA--TT--AATATAGATTG
*
2065993 ATTTATTATTATAG
1 ATTTATTAATATAG
2066007 TTGTATAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 11 0.35
20 4 0.13
22 16 0.52
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATAGATTG
Found at i:2065985 original size:22 final size:22
Alignment explanation
Indices: 2065960--2066030 Score: 88
Period size: 22 Copynumber: 3.0 Consensus size: 22
2065950 ATAATTTATT
2065960 AATATAGATTGATTTATTTTAA
1 AATATAGATTGATTTATTTTAA
2065982 AATATAGATTGATTTATTATTATA
1 AATATAGATTGATTTATT-TTA-A
**
2066006 GTTGTATAGATTGATTTATTTTAA
1 --AATATAGATTGATTTATTTTAA
2066030 A
1 A
2066031 TAATTTGTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
22 18 0.43
23 3 0.07
24 2 0.05
25 3 0.07
26 16 0.38
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (22 bp):
AATATAGATTGATTTATTTTAA
Found at i:2066051 original size:32 final size:32
Alignment explanation
Indices: 2066015--2066296 Score: 180
Period size: 32 Copynumber: 8.5 Consensus size: 32
2066005 AGTTGTATAG
*
2066015 ATTGATTTATTTTAAATAATTTGTTAGTATGA
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
2066047 ATTGATTTATTTTAAATAATTTATTAGTAT-A
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
** *
2066078 GATTGATTTATTTTAAATAATTTATTTTTATGG
1 -ATTGATTTATTTTAAATAATTTATTAGTATGA
* *
2066111 ATTGATTTATTTTAAAATATGAATTGATT--TAT-T
1 ATTGATTTATTTT--AA-AT-AATTTATTAGTATGA
* * * * *
2066144 ATTGTAGTTGTATGGATTGATTGATTTATTTTA-AAT-A
1 ATTG-A-TT-TAT--TTTAAATAATTTA--TTAGTATGA
* * * ** * * *
2066181 ATTTATTAATATCGATTGATTTATTTTAAAATATGA
1 ATTGATTTATTTTAAATAATTTA--TT--AGTATGA
*
2066217 ATTGATTTATTTTAAATAATTTATTAGTATGG
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
* *
2066249 ATTGATTTATTTTAAATAATTTATTTGTATGG
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
2066281 ATTGATTTATTTTAAA
1 ATTGATTTATTTTAAA
2066297 ATATAGATTG
Statistics
Matches: 205, Mismatches: 27, Indels: 36
0.76 0.10 0.13
Matches are distributed among these distances:
31 1 0.00
32 138 0.67
33 4 0.02
34 15 0.07
35 9 0.04
36 31 0.15
37 5 0.02
38 2 0.01
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (32 bp):
ATTGATTTATTTTAAATAATTTATTAGTATGA
Found at i:2066068 original size:14 final size:14
Alignment explanation
Indices: 2066019--2066105 Score: 57
Period size: 14 Copynumber: 5.6 Consensus size: 14
2066009 GTATAGATTG
2066019 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* * *
2066033 ATTTGTTAGTATGAATTG
1 ATTTATT--T-T-AAATA
2066051 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
2066065 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
2066083 ATTTATTTTAAATA
1 ATTTATTTTAAATA
2066097 ATTTATTTT
1 ATTTATTTT
2066106 TATGGATTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
14 27 0.49
15 3 0.05
16 4 0.07
17 3 0.05
18 18 0.33
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:2066253 original size:116 final size:111
Alignment explanation
Indices: 2065881--2066259 Score: 365
Period size: 116 Copynumber: 3.4 Consensus size: 111
2065871 AGTTGTATGG
**
2065881 ATTGATTTATT-TTAAATAATTTATTAGTATGGATTGATTTA-T-TTT-AAAGTATG-GATTGAT
1 ATTGATTTATTATT-AATAATTTATTAGTATGGATTGATTTATTATTTGTTAGTATGAGATTGAT
2065941 TTATTTTAAATAATTTATTAATATAGATTGATTTATTTTAAAATATA
65 TTATTTTAAATAATTTATTAATATAGATTGATTTATTTTAAAATATA
* * * *
2065988 GATTGATTTATTATT-ATAGTTGTA-TAG-ATTGATTTATTTTAAATAATTTGTTAGTATGA-AT
1 -ATTGATTTATTATTAATAATT-TATTAGTATGGATTGA-TTT--ATTATTTGTTAGTATGAGAT
*
2066049 TGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT--AA-ATA
61 TGATTTATTTTAAATAATTTATTAATATAGATTGATTTATTTTAAAATATA
* * * * * *
2066097 ATTTATTT-TTATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTT-GTATGGA
1 ATTGATTTATTAT-TAATAATTTA--TT--AGTATGGATTGATTTATTATT-T-GTTAGTAT-GA
*
2066160 TTGATTGATTTATTTTAAATAATTTATTAATATCGATTGATTTATTTTAAAATATGA
58 --GATTGATTTATTTTAAATAATTTATTAATATAGATTGATTTATTTTAAAATAT-A
2066217 ATTGATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATT
1 ATTGATTTATTATT-AATAATTTATTAGTATGGATTGATTTATT
2066260 TTAAATAATT
Statistics
Matches: 217, Mismatches: 25, Indels: 50
0.74 0.09 0.17
Matches are distributed among these distances:
106 7 0.03
107 15 0.07
108 22 0.10
109 9 0.04
110 2 0.01
111 9 0.04
112 55 0.25
113 9 0.04
114 6 0.03
116 59 0.27
118 4 0.02
119 2 0.01
120 16 0.07
121 2 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (111 bp):
ATTGATTTATTATTAATAATTTATTAGTATGGATTGATTTATTATTTGTTAGTATGAGATTGATT
TATTTTAAATAATTTATTAATATAGATTGATTTATTTTAAAATATA
Found at i:2066288 original size:18 final size:18
Alignment explanation
Indices: 2066235--2066292 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
2066225 ATTTTAAATA
*
2066235 ATTTATTAGTATGGATTG
1 ATTTATTTGTATGGATTG
* *
2066253 ATTTATTT-TA---AATA
1 ATTTATTTGTATGGATTG
2066267 ATTTATTTGTATGGATTG
1 ATTTATTTGTATGGATTG
2066285 ATTTATTT
1 ATTTATTT
2066293 TAAAATATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
14 10 0.32
15 2 0.06
17 2 0.06
18 17 0.55
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (18 bp):
ATTTATTTGTATGGATTG
Found at i:2066399 original size:30 final size:31
Alignment explanation
Indices: 2066343--2066400 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2066333 AATTGTATGG
* * *
2066343 ATTATTTAAATTTTAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
2066374 ATTATTTAAATCTCA-TATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
2066401 CTTTTAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:2071344 original size:31 final size:31
Alignment explanation
Indices: 2071308--2071368 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
2071298 ATTAGTAATC
2071308 AACATATTATTTCTTTTCTATTTTAATCACT
1 AACATATTATTTCTTTTCTATTTTAATCACT
*
2071339 AACATATTATTTCTTTTCTATTTTGATCAC
1 AACATATTATTTCTTTTCTATTTTAATCAC
2071369 CAATTTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.28, C:0.16, G:0.02, T:0.54
Consensus pattern (31 bp):
AACATATTATTTCTTTTCTATTTTAATCACT
Found at i:2071917 original size:25 final size:23
Alignment explanation
Indices: 2071868--2071917 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 23
2071858 TTATTCTAAA
* *
2071868 AAATAAATGTATAATTTTATTTT
1 AAATAAATGTATAATTTAATATT
*
2071891 AAATAAATATTATAAATTTAATATT
1 AAATAAAT-GTAT-AATTTAATATT
2071916 AA
1 AA
2071918 TTTTATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 8 0.36
24 3 0.14
25 11 0.50
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATAAATGTATAATTTAATATT
Found at i:2074499 original size:30 final size:30
Alignment explanation
Indices: 2074454--2074513 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2074444 ATCAGATATA
2074454 TTAACGTCACATAGCATACAAGACAAAAAC
1 TTAACGTCACATAGCATACAAGACAAAAAC
* *
2074484 TTAATGTCCCATAGCATACAAGACAAAAAC
1 TTAACGTCACATAGCATACAAGACAAAAAC
2074514 CCGAGTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.48, C:0.23, G:0.10, T:0.18
Consensus pattern (30 bp):
TTAACGTCACATAGCATACAAGACAAAAAC
Found at i:2077133 original size:2 final size:2
Alignment explanation
Indices: 2077126--2077161 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2077116 TCAGAGATAC
2077126 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2077162 GAATGTTACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2078153 original size:14 final size:14
Alignment explanation
Indices: 2078134--2078165 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2078124 AGCTATAATA
2078134 TATTATCATAAATT
1 TATTATCATAAATT
*
2078148 TATTATCATAACTT
1 TATTATCATAAATT
2078162 TATT
1 TATT
2078166 TTAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATCATAAATT
Found at i:2079067 original size:10 final size:10
Alignment explanation
Indices: 2079052--2079129 Score: 75
Period size: 10 Copynumber: 7.1 Consensus size: 10
2079042 CATTTAAATG
2079052 ATAAACGAAC
1 ATAAACGAAC
2079062 ATAAACGAAC
1 ATAAACGAAC
*
2079072 ACAAACGAAC
1 ATAAACGAAC
2079082 AAACGTAAACGAAC
1 --A--TAAACGAAC
*
2079096 ATAATAAATGAAC
1 ---ATAAACGAAC
2079109 ATAAACGAAC
1 ATAAACGAAC
2079119 ATAAACGAAC
1 ATAAACGAAC
2079129 A
1 A
2079130 AAAAAAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
10 39 0.67
12 1 0.02
13 8 0.14
14 8 0.14
15 2 0.03
ACGTcount: A:0.60, C:0.19, G:0.10, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:2079389 original size:10 final size:10
Alignment explanation
Indices: 2079374--2079421 Score: 60
Period size: 10 Copynumber: 4.4 Consensus size: 10
2079364 CACCATGTTC
2079374 GAACATAAAT
1 GAACATAAAT
2079384 GAACATAAAT
1 GAACATAAAT
2079394 GAACGAACATAAAT
1 ----GAACATAAAT
2079408 GAACATAAAT
1 GAACATAAAT
2079418 GAAC
1 GAAC
2079422 GAACATATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 24 0.71
14 10 0.29
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.17
Consensus pattern (10 bp):
GAACATAAAT
Found at i:2079402 original size:24 final size:24
Alignment explanation
Indices: 2079373--2079437 Score: 112
Period size: 24 Copynumber: 2.6 Consensus size: 24
2079363 GCACCATGTT
2079373 CGAACATAAATGAACATAAATGAA
1 CGAACATAAATGAACATAAATGAA
2079397 CGAACATAAATGAACATAAATGAA
1 CGAACATAAATGAACATAAATGAA
2079421 CGAACATATAATTGAAC
1 CGAACATA-AA-TGAAC
2079438 GTTCACGAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
24 32 0.82
25 2 0.05
26 5 0.13
ACGTcount: A:0.55, C:0.14, G:0.12, T:0.18
Consensus pattern (24 bp):
CGAACATAAATGAACATAAATGAA
Found at i:2079436 original size:16 final size:14
Alignment explanation
Indices: 2079384--2079438 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
2079374 GAACATAAAT
2079384 GAACATAAATGAAC
1 GAACATAAATGAAC
2079398 GAACATAAAT----
1 GAACATAAATGAAC
2079408 GAACATAAATGAAC
1 GAACATAAATGAAC
2079422 GAACATATAATTGAAC
1 GAACATA-AA-TGAAC
2079438 G
1 G
2079439 TTCACGAACG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
10 10 0.29
14 17 0.49
15 2 0.06
16 6 0.17
ACGTcount: A:0.55, C:0.13, G:0.15, T:0.18
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:2082048 original size:21 final size:21
Alignment explanation
Indices: 2082022--2082073 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
2082012 TGCATAGACC
2082022 TGTGCAAAGTACTTCAGAGAA
1 TGTGCAAAGTACTTCAGAGAA
2082043 TGTGCAAAGTACTTCAGAGAA
1 TGTGCAAAGTACTTCAGAGAA
* *
2082064 TCTACAAAGT
1 TGTGCAAAGT
2082074 GCTTTAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.25
Consensus pattern (21 bp):
TGTGCAAAGTACTTCAGAGAA
Found at i:2084569 original size:19 final size:19
Alignment explanation
Indices: 2084521--2084570 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
2084511 AGCAATCAAT
** *
2084521 TTAAAATAATTTTTCTATA
1 TTAAAATAATTTTTAAACA
*
2084540 TGAAAACTAATTTTTAAACA
1 TTAAAA-TAATTTTTAAACA
2084560 TTAAAATAATT
1 TTAAAATAATT
2084571 AAAATAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (19 bp):
TTAAAATAATTTTTAAACA
Found at i:2085326 original size:2 final size:2
Alignment explanation
Indices: 2085315--2085346 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2085305 TTGTAAGTTC
2085315 TA TA -A TA 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 TA TA TA TA T
2085347 GTTCATTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2087399 original size:24 final size:24
Alignment explanation
Indices: 2087372--2087447 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 24
2087362 CGTTAATTTA
*
2087372 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
* **
2087396 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
* *** *
2087420 CGTTTATGTTTGTTCGATTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
2087444 CGTT
1 CGTT
2087448 TATGTTCATT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.11, C:0.13, G:0.25, T:0.51
Consensus pattern (24 bp):
CGTTCATGAACGTTCGGTTATGTT
Found at i:2087408 original size:10 final size:10
Alignment explanation
Indices: 2087383--2087454 Score: 54
Period size: 10 Copynumber: 6.4 Consensus size: 10
2087373 GTTCGTGAAC
*
2087383 GTTCGGTTAT
1 GTTCGTTTAT
2087393 GTTCGTTTAT
1 GTTCGTTTAT
2087403 GTTCGTTCGGTTAT
1 GTTCG-T---TTAT
2087417 GTTCGTTTATGTTT
1 GTTCGTTTA----T
*
2087431 GTTCGATTAT
1 GTTCGTTTAT
2087441 GTTCGTTTAT
1 GTTCGTTTAT
2087451 GTTC
1 GTTC
2087455 ATTCATTTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
10 31 0.61
11 1 0.02
13 1 0.02
14 18 0.35
ACGTcount: A:0.10, C:0.11, G:0.24, T:0.56
Consensus pattern (10 bp):
GTTCGTTTAT
Done.