Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008709.1 Hibiscus syriacus cultivar Beakdansim tig00111758_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: 3030657
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 15
Found at i:1337137 original size:41 final size:40
Alignment explanation
Indices: 1337013--1337147 Score: 170
Period size: 41 Copynumber: 3.4 Consensus size: 40
1337003 TGTTTTTTTA
1337013 AATATATATAT-TATATTCAAAAATGTTTT-AAAACTATAT
1 AATATATATATATATATTC-AAAATGTTTTCAAAACTATAT
* * * * *
1337052 -AT-TATATAAATGTTTTAAAAATGATTTCAAAACTATAT
1 AATATATATATATATATTCAAAATGTTTTCAAAACTATAT
*
1337090 ATTATATATATATATATTCAAAATGTTTTCAAAAACTATAT
1 AATATATATATATATATTCAAAATGTTTTC-AAAACTATAT
1337131 AATATATATATATATAT
1 AATATATATATATATAT
1337148 ATATATATAT
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
37 15 0.19
38 16 0.20
39 1 0.01
40 21 0.27
41 26 0.33
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (40 bp):
AATATATATATATATATTCAAAATGTTTTCAAAACTATAT
Found at i:1337165 original size:52 final size:50
Alignment explanation
Indices: 1337059--1337191 Score: 162
Period size: 52 Copynumber: 2.6 Consensus size: 50
1337049 TATATTATAT
* * *
1337059 AAATGTTTT-AAAAATGATTTCAAAACTATATATTATATATATATATATTCA
1 AAATGTTTTCAAAAATCATAT-AATA-TATATATTATATATATATATATTCA
*
1337110 AAATGTTTTCAAAAA-CTATATAATATATATATATATATATATATATATTTTA
1 AAATGTTTTCAAAAATC-ATATAATATATATAT-TATATATATATATA-TTCA
*
1337162 AAATGTTTTCAAAAATCATATATTATATAT
1 AAATGTTTTCAAAAATCATATAATATATAT
1337192 GTTTCCAATA
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
50 7 0.10
51 26 0.36
52 38 0.53
53 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (50 bp):
AAATGTTTTCAAAAATCATATAATATATATATTATATATATATATATTCA
Found at i:1337229 original size:39 final size:36
Alignment explanation
Indices: 1337161--1337266 Score: 101
Period size: 37 Copynumber: 2.9 Consensus size: 36
1337151 TATATATTTT
* * * *
1337161 AAAATGTTTTCAAAAATCATATATTATATATGTTTCCA
1 AAAACGTTTTCAAAAAT--TATATAAAATATATTTCCA
1337199 ATAAA-GTTTTCCAAAAATTATATAAAATATATTTCCA
1 A-AAACGTTTT-CAAAAATTATATAAAATATATTTCCA
*
1337236 AAAACCGTTTTC-AAAATTATAT-ATATATATT
1 AAAA-CGTTTTCAAAAATTATATAAAATATATT
1337267 GTATGTATTT
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
35 8 0.13
36 13 0.22
37 18 0.30
38 11 0.18
39 10 0.17
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (36 bp):
AAAACGTTTTCAAAAATTATATAAAATATATTTCCA
Found at i:1337234 original size:37 final size:35
Alignment explanation
Indices: 1337145--1337266 Score: 117
Period size: 36 Copynumber: 3.4 Consensus size: 35
1337135 TATATATATA
* *
1337145 TATATATATATATTT--TAAAATGTTTTCAAAAAT
1 TATATATATATATTTCCAAAAACGTTTTCAAAAAT
*
1337178 CATATATTATATATGTTTCCAATAAA-GTTTTCCAAAAAT
1 --TATA-TATATATATTTCCAA-AAACGTTTT-CAAAAAT
*
1337217 TATATAAAATATATTTCCAAAAACCGTTTTC-AAAAT
1 TATAT-ATATATATTTCCAAAAA-CGTTTTCAAAAAT
1337253 TATATATATATATT
1 TATATATATATATT
1337267 GTATGTATTT
Statistics
Matches: 74, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
35 12 0.16
36 24 0.32
37 17 0.23
38 11 0.15
39 10 0.14
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.43
Consensus pattern (35 bp):
TATATATATATATTTCCAAAAACGTTTTCAAAAAT
Found at i:1338469 original size:102 final size:102
Alignment explanation
Indices: 1338289--1338640 Score: 526
Period size: 102 Copynumber: 3.5 Consensus size: 102
1338279 TGTGCAAAGG
* * **
1338289 ATGGTAAATGTTCTTCAATAGGGAATGATGGCGGAGCTGTATTTCGGGTTATCGCGGATGGAGGA
1 ATGGTAAATGTTCTTCAATAGGGAATGGTGGCGGAGCTGTATTTTGGGTTCGCGCGGATGGAGGA
* **
1338354 GATGGT-GCTAACACCACTGGAAAACTTGGAGCCAAGG
66 GATGGTGGC-AACACCACTGGAATACTTGGAGCCAACA
* * * *
1338391 TTGGTAAATTTTCTTCAATAGGAAATGGTGGCGGAGCTGTATTTTGGGTTCGCGCGGATTGAGGA
1 ATGGTAAATGTTCTTCAATAGGGAATGGTGGCGGAGCTGTATTTTGGGTTCGCGCGGATGGAGGA
*
1338456 GATGGTGGCAACACCACTGGAATACTAGGAGCCAACA
66 GATGGTGGCAACACCACTGGAATACTTGGAGCCAACA
* * * *
1338493 ATGGTAAATGTTCTTCAATAGGGAATGGTGGTGGAGCTGTATTTTGGGCTCGCACTGATGGAGGA
1 ATGGTAAATGTTCTTCAATAGGGAATGGTGGCGGAGCTGTATTTTGGGTTCGCGCGGATGGAGGA
*
1338558 GATGGTGGCAACACCACTGGAATTCTTGGAGCCAACA
66 GATGGTGGCAACACCACTGGAATACTTGGAGCCAACA
*
1338595 ATGGTAAATTTTCTTCAATAGGGAATGGTGGCGGAGCTGTATTTTG
1 ATGGTAAATGTTCTTCAATAGGGAATGGTGGCGGAGCTGTATTTTG
1338641 AGGCGTCGGT
Statistics
Matches: 225, Mismatches: 24, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
102 223 0.99
103 2 0.01
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.27
Consensus pattern (102 bp):
ATGGTAAATGTTCTTCAATAGGGAATGGTGGCGGAGCTGTATTTTGGGTTCGCGCGGATGGAGGA
GATGGTGGCAACACCACTGGAATACTTGGAGCCAACA
Found at i:1344291 original size:29 final size:29
Alignment explanation
Indices: 1344249--1344314 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
1344239 AGGATGAGTT
*
1344249 GGGTCGGATGTATACTCTGAAATCGGGCC
1 GGGTCGGATGTATACTCTAAAATCGGGCC
*
1344278 GGGTCGGATGTATACTCTAAAATCGGGTC
1 GGGTCGGATGTATACTCTAAAATCGGGCC
1344307 GGGTCGGA
1 GGGTCGGA
1344315 GTCAGATGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.24
Consensus pattern (29 bp):
GGGTCGGATGTATACTCTAAAATCGGGCC
Found at i:1344389 original size:33 final size:32
Alignment explanation
Indices: 1344316--1344376 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
1344306 CGGGTCGGAG
* *
1344316 TCAGATGGATGATATAAAATTTTTTAGTCCAA
1 TCAGGTGGAGGATATAAAATTTTTTAGTCCAA
*
1344348 TCGGGTGGAGGATATAAAATTTTTTAGTC
1 TCAGGTGGAGGATATAAAATTTTTTAGTC
1344377 GAGTTCAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (32 bp):
TCAGGTGGAGGATATAAAATTTTTTAGTCCAA
Found at i:1349416 original size:15 final size:15
Alignment explanation
Indices: 1349396--1349448 Score: 97
Period size: 15 Copynumber: 3.5 Consensus size: 15
1349386 AAAGAGGGGC
1349396 CCTTCTTCTGCTTAG
1 CCTTCTTCTGCTTAG
*
1349411 CCTTCTTCTACTTAG
1 CCTTCTTCTGCTTAG
1349426 CCTTCTTCTGCTTAG
1 CCTTCTTCTGCTTAG
1349441 CCTTCTTC
1 CCTTCTTC
1349449 CACGATTGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.08, C:0.36, G:0.09, T:0.47
Consensus pattern (15 bp):
CCTTCTTCTGCTTAG
Found at i:1356063 original size:24 final size:24
Alignment explanation
Indices: 1356036--1356081 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1356026 ATTTTTCTAC
* *
1356036 TTTCATAGCATATTTTTTCTCTGT
1 TTTCATAACACATTTTTTCTCTGT
*
1356060 TTTCATAACACGTTTTTTCTCT
1 TTTCATAACACATTTTTTCTCT
1356082 ACCTTTTGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.07, T:0.57
Consensus pattern (24 bp):
TTTCATAACACATTTTTTCTCTGT
Found at i:1359687 original size:28 final size:28
Alignment explanation
Indices: 1359655--1359710 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1359645 CTGTTGGAAA
1359655 GGTTTTGTTCCCAACATCTACTGTTCTC
1 GGTTTTGTTCCCAACATCTACTGTTCTC
1359683 GGTTTTGTTCCCAACATCTACTGTTCTC
1 GGTTTTGTTCCCAACATCTACTGTTCTC
1359711 TTATCTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (28 bp):
GGTTTTGTTCCCAACATCTACTGTTCTC
Found at i:1364720 original size:21 final size:21
Alignment explanation
Indices: 1364690--1364737 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1364680 GCAGGGGTAC
* *
1364690 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
1364711 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
1364732 ATGCCA
1 ATGCCA
1364738 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:1364784 original size:63 final size:63
Alignment explanation
Indices: 1364711--1364847 Score: 145
Period size: 63 Copynumber: 2.2 Consensus size: 63
1364701 TCCACTTCAT
* * * * *
1364711 ATGCCAAGCCCACCAGTTTATATGCC-ATCTCCG-CAGGGTTACATTCCGAGCCCG-CAGGGTTA
1 ATGCCTAGCCCACCAGGTTACATGCCTAGC-CCGCCA-GGTTACATGCCGAGCCCGCCA-GGTTA
1364773 C
63 C
* * * *
1364774 ATTCCTAGCCCGCCAGGTTACATGCCTAGCCCGCCAGGTTACATGCCTAGTCCGCCAGGTTAC
1 ATGCCTAGCCCACCAGGTTACATGCCTAGCCCGCCAGGTTACATGCCGAGCCCGCCAGGTTAC
1364837 ATGCCTAGCCC
1 ATGCCTAGCCC
1364848 GTAGGGTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
63 55 0.90
64 6 0.10
ACGTcount: A:0.20, C:0.36, G:0.22, T:0.22
Consensus pattern (63 bp):
ATGCCTAGCCCACCAGGTTACATGCCTAGCCCGCCAGGTTACATGCCGAGCCCGCCAGGTTAC
Found at i:1364855 original size:21 final size:21
Alignment explanation
Indices: 1364747--1364848 Score: 152
Period size: 21 Copynumber: 4.9 Consensus size: 21
1364737 ATCTCCGCAG
* *
1364747 GGTTACATTCCGAGCCCG-CA
1 GGTTACATGCCTAGCCCGCCA
*
1364767 GGGTTACATTCCTAGCCCGCCA
1 -GGTTACATGCCTAGCCCGCCA
1364789 GGTTACATGCCTAGCCCGCCA
1 GGTTACATGCCTAGCCCGCCA
*
1364810 GGTTACATGCCTAGTCCGCCA
1 GGTTACATGCCTAGCCCGCCA
1364831 GGTTACATGCCTAGCCCG
1 GGTTACATGCCTAGCCCG
1364849 TAGGGTTTTA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
21 74 0.97
22 2 0.03
ACGTcount: A:0.19, C:0.35, G:0.25, T:0.22
Consensus pattern (21 bp):
GGTTACATGCCTAGCCCGCCA
Found at i:1365437 original size:33 final size:34
Alignment explanation
Indices: 1365378--1365474 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
1365368 AAATGTTTTT
*
1365378 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
1365412 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
1365445 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
1365475 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:1365481 original size:34 final size:33
Alignment explanation
Indices: 1365376--1365481 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
1365366 ATAAATGTTT
*
1365376 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
1365410 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
1365442 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
1365477 TTAAA
1 TTAAA
1365482 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:1366084 original size:126 final size:126
Alignment explanation
Indices: 1365859--1366462 Score: 1165
Period size: 126 Copynumber: 4.8 Consensus size: 126
1365849 TTTAAGTTAT
*
1365859 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1365924 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
1365985 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1366050 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
1366111 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
1366176 GCGCCCCCGGGAACGCACCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
1366237 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAAAGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1366302 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
1366363 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGAC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1366428 GCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
1366463 CCGATTATAG
Statistics
Matches: 472, Mismatches: 6, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
125 32 0.07
126 440 0.93
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (126 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:1366543 original size:8 final size:8
Alignment explanation
Indices: 1366530--1366570 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1366520 TCACAATCTT
1366530 TCAAATTC
1 TCAAATTC
1366538 TCAAATTC
1 TCAAATTC
* *
1366546 CCAAACTC
1 TCAAATTC
1366554 T-AAATTC
1 TCAAATTC
1366561 TCAAATTC
1 TCAAATTC
1366569 TC
1 TC
1366571 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:1369585 original size:13 final size:13
Alignment explanation
Indices: 1369567--1369606 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
1369557 TACATAAATA
1369567 TATTTAATATAAT
1 TATTTAATATAAT
1369580 TATTTAATATAA-
1 TATTTAATATAAT
*
1369592 TATTTAATATTAT
1 TATTTAATATAAT
1369605 TA
1 TA
1369607 GTTATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTAATATAAT
Found at i:1373439 original size:20 final size:20
Alignment explanation
Indices: 1373414--1373457 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
1373404 TATTTTTCTC
1373414 TTTAGGGTTAAAGTTTAGGG
1 TTTAGGGTTAAAGTTTAGGG
1373434 TTTAGGGTTAAAGTTTAGGG
1 TTTAGGGTTAAAGTTTAGGG
1373454 TTTA
1 TTTA
1373458 AAATTAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.43
Consensus pattern (20 bp):
TTTAGGGTTAAAGTTTAGGG
Found at i:1373464 original size:20 final size:20
Alignment explanation
Indices: 1373421--1373464 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1373411 CTCTTTAGGG
***
1373421 TTAAAGTTTAGGGTTTAGGG
1 TTAAAGTTTAGGGTTTAAAA
1373441 TTAAAGTTTAGGGTTTAAAA
1 TTAAAGTTTAGGGTTTAAAA
1373461 TTAA
1 TTAA
1373465 TGGTTTATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (20 bp):
TTAAAGTTTAGGGTTTAAAA
Found at i:1378309 original size:13 final size:14
Alignment explanation
Indices: 1378291--1378320 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1378281 TACTTTGCAT
1378291 TTTATTTTTC-ATG
1 TTTATTTTTCTATG
1378304 TTTATTTTTCTATG
1 TTTATTTTTCTATG
1378318 TTT
1 TTT
1378321 TTACATTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.73
Consensus pattern (14 bp):
TTTATTTTTCTATG
Found at i:1385437 original size:55 final size:57
Alignment explanation
Indices: 1385360--1385468 Score: 141
Period size: 55 Copynumber: 1.9 Consensus size: 57
1385350 AGTACTTCGC
* * * *
1385360 TTAGGATGAAAACCCGAGAGGGCATCCTAAGTCG-AAAAAG-AAAAAGAAAAAATGT
1 TTAGGATGAAAAACCGAAAGGGCACCCTAAATCGTAAAAAGAAAAAAGAAAAAATGT
* * *
1385415 TTAGGGTGAAAAACCGAAAGGGCGCCCTAAATTGTAAAAAGAAAAAAGAAAAAA
1 TTAGGATGAAAAACCGAAAGGGCACCCTAAATCGTAAAAAGAAAAAAGAAAAAA
1385469 GAAAAGAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
55 27 0.60
56 6 0.13
57 12 0.27
ACGTcount: A:0.51, C:0.12, G:0.23, T:0.14
Consensus pattern (57 bp):
TTAGGATGAAAAACCGAAAGGGCACCCTAAATCGTAAAAAGAAAAAAGAAAAAATGT
Found at i:1385460 original size:7 final size:7
Alignment explanation
Indices: 1385450--1385510 Score: 76
Period size: 7 Copynumber: 9.3 Consensus size: 7
1385440 CCTAAATTGT
1385450 AAAAAGA
1 AAAAAGA
1385457 AAAAAGA
1 AAAAAGA
1385464 AAAAAG-
1 AAAAAGA
1385470 -AAAAGA
1 AAAAAGA
1385476 AAAAAGA
1 AAAAAGA
*
1385483 GAAAAG-
1 AAAAAGA
1385489 AAAAAG-
1 AAAAAGA
*
1385495 AGAAAGA
1 AAAAAGA
1385502 AAAAAGA
1 AAAAAGA
1385509 AA
1 AA
1385511 TAAGGTGGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
5 5 0.11
6 10 0.21
7 32 0.68
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:1385475 original size:19 final size:19
Alignment explanation
Indices: 1385451--1385510 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
1385441 CTAAATTGTA
1385451 AAAAGAAAAAAGAAAAAAG
1 AAAAGAAAAAAGAAAAAAG
*
1385470 AAAAGAAAAAAGAGAAAAG
1 AAAAGAAAAAAGAAAAAAG
*
1385489 AAAA-AGAGAAAGAAAAAAG
1 AAAAGA-AAAAAGAAAAAAG
1385508 AAA
1 AAA
1385511 TAAGGTGGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 1 0.03
19 36 0.97
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAGAAAAAAG
Found at i:1385487 original size:26 final size:26
Alignment explanation
Indices: 1385450--1385510 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
1385440 CCTAAATTGT
1385450 AAAAAGAAAAAAGAAAAA-AGAAAAGA
1 AAAAAGAAAAAAGAAAAAGAG-AAAGA
*
1385476 AAAAAGAGAAAAGAAAAAGAGAAAGA
1 AAAAAGAAAAAAGAAAAAGAGAAAGA
1385502 AAAAAGAAA
1 AAAAAGAAA
1385511 TAAGGTGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 30 0.94
27 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (26 bp):
AAAAAGAAAAAAGAAAAAGAGAAAGA
Found at i:1391137 original size:2 final size:2
Alignment explanation
Indices: 1391130--1391168 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1391120 GCGAAGTGAC
* *
1391130 AG AG AG AG AG AG AG AG AG AG AG GG GG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1391169 TTAATAACGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1392403 original size:21 final size:21
Alignment explanation
Indices: 1392379--1392432 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
1392369 GCGAATATGT
*
1392379 AATTCGCATTGCGATTTTCCA
1 AATTCGCGTTGCGATTTTCCA
*
1392400 AATTCGCGTTGTGATTTTCCA
1 AATTCGCGTTGCGATTTTCCA
1392421 AATTCGCGTTGC
1 AATTCGCGTTGC
1392433 AAATCTGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (21 bp):
AATTCGCGTTGCGATTTTCCA
Found at i:1392488 original size:20 final size:20
Alignment explanation
Indices: 1392456--1392522 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
1392446 TTTTTCAAAT
* * *
1392456 TCGCAATGCGAATCTATAAA
1 TCGCAACGCGAATTTGTAAA
*
1392476 TCACAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
1392496 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
1392516 TCGCAAC
1 TCGCAAC
1392523 ACATAAGTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:1392539 original size:20 final size:20
Alignment explanation
Indices: 1392516--1392621 Score: 83
Period size: 20 Copynumber: 5.3 Consensus size: 20
1392506 AATTTGTAAA
1392516 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
1392536 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
* * **
1392556 TCGTAACTCGAATTTGT-AAA-
1 TCGCAACAC--ATAAGTCAAAT
* *
1392576 TCGAAACACAAAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
1392596 TCGCAACACAAAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
1392616 TTGCAA
1 TCGCAA
1392622 TGCGAAATTT
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
18 3 0.04
19 3 0.04
20 54 0.78
21 7 0.10
22 2 0.03
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.22
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:1392543 original size:60 final size:60
Alignment explanation
Indices: 1392496--1392664 Score: 205
Period size: 60 Copynumber: 2.8 Consensus size: 60
1392486 AATTTGTAAA
* *
1392496 TCGCAACGCGAATTTGTAAATCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACGCGAATTTGTAAATCGAAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
* * * * *
1392556 TCGTAACTCGAATTTGTAAATCGAAACACAAAAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAATTTGTAAATCGAAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
* * * * *
1392616 TTGCAATGCGAAATTT-TAAATTCGTAACGCAATAGTCAAATTCGCAACG
1 TCGCAACGCG-AATTTGTAAA-TCGAAACACAAAAGTCAAATTCGCAACG
1392665 TGAAACACAA
Statistics
Matches: 92, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
60 63 0.68
61 29 0.32
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (60 bp):
TCGCAACGCGAATTTGTAAATCGAAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
Found at i:1392658 original size:20 final size:20
Alignment explanation
Indices: 1392528--1392664 Score: 91
Period size: 20 Copynumber: 6.8 Consensus size: 20
1392518 GCAACACATA
*
1392528 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCAAT
* *
1392548 AGTCAAATTCGTAACTCGAATT
1 AGTCAAATTCGCAACGC-AA-T
* * * *
1392570 TGT-AAA-TCGAAACACAAA
1 AGTCAAATTCGCAACGCAAT
* *
1392588 AGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCAAT
* *
1392608 AGTCAAATTTGCAATGCGAA-
1 AGTCAAATTCGCAACGC-AAT
* * *
1392628 ATTTTAAATTCGTAACGCAAT
1 A-GTCAAATTCGCAACGCAAT
1392649 AGTCAAATTCGCAACG
1 AGTCAAATTCGCAACG
1392665 TGAAACACAA
Statistics
Matches: 90, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
18 2 0.02
19 5 0.06
20 62 0.69
21 18 0.20
22 3 0.03
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCAAT
Found at i:1392822 original size:22 final size:22
Alignment explanation
Indices: 1392779--1392826 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1392769 CTACGGCAAC
* **
1392779 ATCCGTCCCCATCTTTGACGAA
1 ATCCATCCCCATCTCCGACGAA
*
1392801 ATCCATCCCCATCTCCGGCGAA
1 ATCCATCCCCATCTCCGACGAA
1392823 ATCC
1 ATCC
1392827 GTCTATCTCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.42, G:0.12, T:0.23
Consensus pattern (22 bp):
ATCCATCCCCATCTCCGACGAA
Found at i:1393194 original size:20 final size:20
Alignment explanation
Indices: 1393171--1393231 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
1393161 AAACTTAAAT
1393171 TCGCAACACGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
*
1393191 TCGCAACAC------CAAAA
1 TCGCAACACGAAAATGAAAA
*
1393205 TCGCAACGCGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
1393225 TCGCAAC
1 TCGCAAC
1393232 GCGATTTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
14 12 0.38
20 20 0.62
ACGTcount: A:0.49, C:0.26, G:0.15, T:0.10
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:1393218 original size:14 final size:14
Alignment explanation
Indices: 1393186--1393219 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1393176 ACACGAAAAT
1393186 GAAAATCGCAACAC
1 GAAAATCGCAACAC
* *
1393200 CAAAATCGCAACGC
1 GAAAATCGCAACAC
1393214 GAAAAT
1 GAAAAT
1393220 GAAAATCGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.26, G:0.15, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACAC
Found at i:1393817 original size:22 final size:22
Alignment explanation
Indices: 1393792--1393842 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1393782 ATGTTGACAC
* *
1393792 ATCCGTCCCTATCTCTGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
1393814 ATCCATCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
1393836 ATCCGTC
1 ATCCGTC
1393843 TATCTCCATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.41, G:0.14, T:0.24
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1394231 original size:14 final size:14
Alignment explanation
Indices: 1394199--1394232 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1394189 ACACGAAAAT
1394199 GAAAATCGCAACAC
1 GAAAATCGCAACAC
* *
1394213 CAAAATCGCAACGC
1 GAAAATCGCAACAC
1394227 GAAAAT
1 GAAAAT
1394233 GAAAATCGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.26, G:0.15, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACAC
Found at i:1396414 original size:42 final size:42
Alignment explanation
Indices: 1396363--1396485 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 42
1396353 GCCCGATACA
* * *
1396363 CCTATCATCATTCAAGAGGCGCCTCCTATCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
* * *
1396405 CCTCTCATCA-TCGAATAAGCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCATTC-AAGAGGCCCCTCCCACCGTTCAAGAGGCC
* * * *
1396447 CCTATCATCGTTCAAGAGGTCCCGCCCGCCGTTCAAGAG
1 CCTATCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAG
1396486 CCAGATTCAT
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
41 2 0.03
42 62 0.94
43 2 0.03
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (42 bp):
CCTATCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
Found at i:1396447 original size:21 final size:21
Alignment explanation
Indices: 1396368--1396485 Score: 94
Period size: 21 Copynumber: 5.6 Consensus size: 21
1396358 ATACACCTAT
* *
1396368 CATCATTCAAGAGGCGCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* *
1396389 TATCGTTCAAGAGGCCCCTCT
1 CATCGTTCAAGAGGCCCCTCC
* * *
1396410 CATC-ATCGAATAAGCCCCTCC
1 CATCGTTC-AAGAGGCCCCTCC
* **
1396431 CACCGTTCAAGAGGCCCCTAT
1 CATCGTTCAAGAGGCCCCTCC
* *
1396452 CATCGTTCAAGAGGTCCCGCC
1 CATCGTTCAAGAGGCCCCTCC
**
1396473 CGCCGTTCAAGAG
1 CATCGTTCAAGAG
1396486 CCAGATTCAT
Statistics
Matches: 73, Mismatches: 22, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
20 2 0.03
21 69 0.95
22 2 0.03
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.20
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:1397969 original size:66 final size:65
Alignment explanation
Indices: 1397813--1397988 Score: 239
Period size: 66 Copynumber: 2.6 Consensus size: 65
1397803 TGGGGTACAC
* *
1397813 TTTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAATTGATTTGTTTAATTGATGAGGAATTAA
1 TTTTTTTGCTTGTTTAATTG-ATTTGT--A---AAAGTTGATTTGTTTAATTGATGAGGAAATAA
1397877 GAATTA
60 GAATTA
* *
1397883 -TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATT
1397947 A
65 A
1397948 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1397989 GTTTTAAATT
Statistics
Matches: 99, Mismatches: 4, Indels: 10
0.88 0.04 0.09
Matches are distributed among these distances:
64 16 0.16
65 18 0.18
66 40 0.40
67 1 0.01
68 4 0.04
69 20 0.20
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.53
Consensus pattern (65 bp):
TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
Found at i:1398129 original size:20 final size:20
Alignment explanation
Indices: 1398081--1398129 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1398071 CGTAAAATAA
*
1398081 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGAAAGTCAAATTC
***
1398101 GCAACGCGAAAGTCAAATTC
1 GCGTTGCGAAAGTCAAATTC
1398121 GCGTTGCGA
1 GCGTTGCGA
1398130 TTTTCGGTTT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (20 bp):
GCGTTGCGAAAGTCAAATTC
Found at i:1399154 original size:18 final size:18
Alignment explanation
Indices: 1399131--1399167 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1399121 CAAAATTTAT
1399131 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1399149 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1399167 A
1 A
1399168 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1399587 original size:25 final size:25
Alignment explanation
Indices: 1399553--1399602 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1399543 TATTATTTTC
*
1399553 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1399578 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1399603 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:1400057 original size:18 final size:18
Alignment explanation
Indices: 1400034--1400069 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1400024 AAGTCGGTTG
*
1400034 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1400052 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1400070 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1402365 original size:24 final size:24
Alignment explanation
Indices: 1402331--1402384 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1402321 CCATCACATC
1402331 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
1402355 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
1402379 ATCAAA
1 ATCAAA
1402385 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1403161 original size:14 final size:15
Alignment explanation
Indices: 1403125--1403162 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1403115 GAAATCATTG
1403125 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1403140 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1403155 AAAAATTA
1 AAAAATTA
1403163 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1403342 original size:19 final size:20
Alignment explanation
Indices: 1403315--1403387 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 20
1403305 AACTAAAACC
*
1403315 TGTTGCGAAATT-AAATTCG
1 TGTTACGAAATTGAAATTCG
*
1403334 TGTTACGAATTTGAAATTC-
1 TGTTACGAAATTGAAATTCG
* * *
1403353 AGTTGCGAATTTGAAATTCTG
1 TGTTACGAAATTGAAATTC-G
* *
1403374 CGTTGCGAAATTGA
1 TGTTACGAAATTGA
1403388 CTATCGCGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 27 0.60
20 6 0.13
21 12 0.27
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (20 bp):
TGTTACGAAATTGAAATTCG
Found at i:1403352 original size:20 final size:19
Alignment explanation
Indices: 1403335--1403371 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1403325 TTAAATTCGT
1403335 GTTACGAATTTGAAATTCA
1 GTTACGAATTTGAAATTCA
*
1403354 GTTGCGAATTTGAAATTC
1 GTTACGAATTTGAAATTC
1403372 TGCGTTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (19 bp):
GTTACGAATTTGAAATTCA
Found at i:1403444 original size:20 final size:20
Alignment explanation
Indices: 1403419--1403481 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
1403409 TTCTCTATTA
*
1403419 CGATTTACAAATTCGCGTTG
1 CGATTTACAGATTCGCGTTG
1403439 CGATTTACAGATTCGCGTTG
1 CGATTTACAGATTCGCGTTG
*
1403459 CGATTTACAGATTAGCGTTG
1 CGATTTACAGATTCGCGTTG
1403479 CGA
1 CGA
1403482 ATTTGGAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (20 bp):
CGATTTACAGATTCGCGTTG
Found at i:1403518 original size:20 final size:20
Alignment explanation
Indices: 1403473--1403522 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1403463 TTACAGATTA
*
1403473 GCGTTGCGAATTTGGAAACT
1 GCGTTGCGAAATTGGAAACT
* *
1403493 GGGTTGCGAAATTGG-AATT
1 GCGTTGCGAAATTGGAAACT
1403512 CGCGTTGCGAA
1 -GCGTTGCGAA
1403523 TTTAACTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.24, C:0.14, G:0.34, T:0.28
Consensus pattern (20 bp):
GCGTTGCGAAATTGGAAACT
Found at i:1403533 original size:20 final size:20
Alignment explanation
Indices: 1403510--1403565 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
1403500 GAAATTGGAA
*
1403510 TTCGCGTTGCGAATTTAACT
1 TTCGCGTTGCAAATTTAACT
1403530 TTCGCGTTGCAAATTTAACT
1 TTCGCGTTGCAAATTTAACT
1403550 TTCGCGTTGCAAATTT
1 TTCGCGTTGCAAATTT
1403566 GTTGGCTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (20 bp):
TTCGCGTTGCAAATTTAACT
Found at i:1410034 original size:23 final size:26
Alignment explanation
Indices: 1409966--1410055 Score: 84
Period size: 27 Copynumber: 3.5 Consensus size: 26
1409956 TTATTACAAA
1409966 TATTA-AATATATT-AAATAATATTATT
1 TATTATAA-ATATTAAAATAAT-TTATT
* *
1409992 TATCATAAA-ACTTAATATAA-TTATT
1 TATTATAAATA-TTAAAATAATTTATT
1410017 T-TTA-AAATATTAAAATAATTTATT
1 TATTATAAATATTAAAATAATTTATT
1410041 TATTATTAAATATTA
1 TATTA-TAAATATTA
1410056 TTTTTATAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
23 11 0.21
24 9 0.17
25 10 0.19
26 7 0.13
27 15 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
TATTATAAATATTAAAATAATTTATT
Found at i:1410042 original size:22 final size:22
Alignment explanation
Indices: 1409968--1410042 Score: 53
Period size: 23 Copynumber: 3.1 Consensus size: 22
1409958 ATTACAAATA
1409968 TTAAATATATT-AAATAATATTAT
1 TTAAA-ATATTAAAATAAT-TTAT
* * *
1409991 TTATCATAAAACTTAATATAATTATTT
1 TTA--A-AATA-TTAAAATAATT-TAT
1410018 TTAAAATATTAAAATAATTTAT
1 TTAAAATATTAAAATAATTTAT
1410040 TTA
1 TTA
1410043 TTATTAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
22 5 0.12
23 13 0.32
24 3 0.08
25 4 0.10
26 4 0.10
27 11 0.28
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAAAATATTAAAATAATTTAT
Found at i:1410068 original size:50 final size:50
Alignment explanation
Indices: 1409948--1410069 Score: 115
Period size: 50 Copynumber: 2.4 Consensus size: 50
1409938 CAAGTTTTTA
* * *
1409948 AAAATTATTTATTACAAATATTAAATATATTAAATAATATTATTTATCA-T
1 AAAATTATTT-TTATAATTTTTAAATATATTAAATAATATTATTTATCATT
* * * * *
1409998 AAAACTTAATATAATTATTTTTAAA-ATATTAAAATAAT-TTATTTATTATT
1 AAAA-TTATTTTTATAATTTTTAAATATATT-AAATAATATTATTTATCATT
1410048 AAATATTATTTTTATAATTTTT
1 AAA-ATTATTTTTATAATTTTT
1410070 TTAATAAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
49 14 0.25
50 37 0.66
51 5 0.09
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
AAAATTATTTTTATAATTTTTAAATATATTAAATAATATTATTTATCATT
Found at i:1410174 original size:91 final size:86
Alignment explanation
Indices: 1410020--1410189 Score: 200
Period size: 89 Copynumber: 1.9 Consensus size: 86
1410010 AATTATTTTT
* * * * *
1410020 AAAATATTAAAATAATTTATTTATTATTAAATATTATTTTTATAATTTTTTTAATAAAAATATTA
1 AAAATATTAAAATAAATTATTTATTATTAAATAATAATGTTATAATTTATTT-ATAAAAATATT-
*
1410085 ATATTGGTATATTTTATTGAAATA
64 A-ATTAGTATATTTTATTGAAATA
1410109 AAAATATTATAAATTAAATTATTTATTTATTAAAGTAATAATGTTAT-ATTATATTT-TAAAAAT
1 AAAATATTA-AAA-TAAATTATTTA-TTATTAAA-TAATAATGTTATAATT-TATTTATAAAAAT
1410172 ATTAATTAGTATATTTTA
61 ATTAATTAGTATATTTTA
1410190 AATATCTTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
89 22 0.31
90 4 0.06
91 20 0.29
92 11 0.16
93 13 0.19
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (86 bp):
AAAATATTAAAATAAATTATTTATTATTAAATAATAATGTTATAATTTATTTATAAAAATATTAA
TTAGTATATTTTATTGAAATA
Found at i:1410410 original size:22 final size:23
Alignment explanation
Indices: 1410382--1410428 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1410372 TTGATTATTT
1410382 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
1410404 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
1410427 TA
1 TA
1410429 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:1410433 original size:22 final size:22
Alignment explanation
Indices: 1410390--1410433 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1410380 TTTATTATAA
*
1410390 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
1410412 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
1410434 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:1410673 original size:42 final size:42
Alignment explanation
Indices: 1410626--1410717 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
1410616 CCCGAAATCT
* *
1410626 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTGTTCCGAAAAATGTTTTCC
* *
1410668 CGTGTTTGTTTCACGTAATTTGTGTTCCGAAAAATGTTTTCT
1 CGTGTTTGTTTCACGTAATTCGTGTTCCGAAAAATGTTTTCC
*
1410710 AGTGTTTG
1 CGTGTTTG
1410718 GTTGGAGGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTGTTCCGAAAAATGTTTTCC
Found at i:1410956 original size:23 final size:22
Alignment explanation
Indices: 1410918--1410978 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
1410908 TCAAAAACTA
* *
1410918 ATTATTAAAATATTTACAATAT
1 ATTATTAATATTTTTACAATAT
*
1410940 ATTTATTAATATTTTTAATAATAT
1 A-TTATTAATATTTTT-ACAATAT
*
1410964 AATATT-ATATTTTTA
1 ATTATTAATATTTTTA
1410979 ATATTATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 9 0.27
23 16 0.48
24 7 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTATTAATATTTTTACAATAT
Found at i:1410959 original size:21 final size:22
Alignment explanation
Indices: 1410926--1410989 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
1410916 TAATTATTAA
** *
1410926 AATATTTACAATATAT-TTATT
1 AATATTTTTAATATATAATATT
1410947 AATATTTTTAATAATATAATATT
1 AATATTTTTAAT-ATATAATATT
1410970 -ATATTTTTAATATTATAATA
1 AATATTTTTAATA-TATAATA
1410990 AAATAATCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 11 0.30
22 22 0.59
23 4 0.11
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATTTTTAATATATAATATT
Found at i:1410973 original size:22 final size:23
Alignment explanation
Indices: 1410943--1410989 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
1410933 ACAATATATT
1410943 TATTAATATTTTTAATAATATAA
1 TATTAATATTTTTAATAATATAA
*
1410966 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTTTAATAATATAA
1410988 TA
1 TA
1410990 AAATAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTTTAATAATATAA
Found at i:1411027 original size:23 final size:23
Alignment explanation
Indices: 1410979--1411027 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1410969 TATATTTTTA
*
1410979 ATATTATAATAAAATAATCAATT
1 ATATTATAATAAAATAATCAAAT
*
1411002 ATATTATAATAATATAAT-ATAAT
1 ATATTATAATAAAATAATCA-AAT
1411025 ATA
1 ATA
1411028 AGATATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATTATAATAAAATAATCAAAT
Found at i:1411197 original size:23 final size:23
Alignment explanation
Indices: 1411171--1411215 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1411161 AATAATATTT
1411171 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
** * *
1411194 TAATTGATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1411216 ATATAACACT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1411541 original size:15 final size:14
Alignment explanation
Indices: 1411507--1411560 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
1411497 CCAGAAATGT
*
1411507 AATTCATTTTCCAG
1 AATTCAATTTCCAG
*
1411521 AATTCAAATTCCAG
1 AATTCAATTTCCAG
*
1411535 TAATTCATTTTCCAG
1 -AATTCAATTTCCAG
1411550 AATTCAATTTC
1 AATTCAATTTC
1411561 TAAAAAACCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:1423464 original size:2 final size:2
Alignment explanation
Indices: 1423457--1423487 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1423447 TACCGAATGA
1423457 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 A
1423488 CTTGAATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1425393 original size:18 final size:18
Alignment explanation
Indices: 1425372--1425407 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1425362 TAATTAAAAA
1425372 TATTCATATAATTTTTCT
1 TATTCATATAATTTTTCT
1425390 TATTCATATAATTTTTCT
1 TATTCATATAATTTTTCT
1425408 AACCCAAAAC
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:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTCATATAATTTTTCT
Found at i:1428001 original size:17 final size:18
Alignment explanation
Indices: 1427981--1428018 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1427971 ATTTATAAGG
1427981 TATATTTTATT-ATATTT
1 TATATTTTATTAATATTT
*
1427998 TATATTTTGTTAATATTT
1 TATATTTTATTAATATTT
1428016 TAT
1 TAT
1428019 TTAATTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TATATTTTATTAATATTT
Found at i:1428022 original size:12 final size:12
Alignment explanation
Indices: 1427988--1428065 Score: 52
Period size: 12 Copynumber: 6.5 Consensus size: 12
1427978 AGGTATATTT
* *
1427988 TATTATATTTTA
1 TATTTTATTTAA
*
1428000 TATTTT-GTTAA
1 TATTTTATTTAA
1428011 TATTTTATTTAA
1 TATTTTATTTAA
* *
1428023 TTATTGTA-TTATT
1 -TATTTTATTTA-A
* *
1428036 TATTTTTTTTAG
1 TATTTTATTTAA
1428048 TATTTTATTTAA
1 TATTTTATTTAA
*
1428060 TGTTTT
1 TATTTT
1428066 TTATTTTTTT
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
11 9 0.18
12 32 0.64
13 9 0.18
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (12 bp):
TATTTTATTTAA
Found at i:1437470 original size:14 final size:14
Alignment explanation
Indices: 1437439--1437476 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1437429 AGGGATGTTC
*
1437439 GAAAGAAAAAGAGA
1 GAAAGAAAAAGACA
1437453 GAAA-AAAAAGACA
1 GAAAGAAAAAGACA
1437466 TGAAAGAAAAA
1 -GAAAGAAAAA
1437477 AATGGAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 8 0.38
14 8 0.38
15 5 0.24
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.03
Consensus pattern (14 bp):
GAAAGAAAAAGACA
Found at i:1438797 original size:20 final size:20
Alignment explanation
Indices: 1438772--1438866 Score: 89
Period size: 20 Copynumber: 5.0 Consensus size: 20
1438762 AACCAAATTG
1438772 CCCAGGGGG-AACAGATTCCC
1 CCCAGGGGGTAAC-GATTCCC
*
1438792 CCCAGGGGGTATCGATTCCC
1 CCCAGGGGGTAACGATTCCC
*
1438812 CCCAGGGGGTATCGATT--C
1 CCCAGGGGGTAACGATTCCC
1438830 CCC---GGG-AACAGATTCCC
1 CCCAGGGGGTAAC-GATTCCC
*
1438847 CCCA-GGGGTATCGATTCCC
1 CCCAGGGGGTAACGATTCCC
1438866 C
1 C
1438867 GGGTATAGAT
Statistics
Matches: 65, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
14 2 0.03
15 7 0.11
17 4 0.06
18 4 0.06
19 11 0.17
20 35 0.54
21 2 0.03
ACGTcount: A:0.19, C:0.36, G:0.28, T:0.17
Consensus pattern (20 bp):
CCCAGGGGGTAACGATTCCC
Found at i:1438855 original size:34 final size:35
Alignment explanation
Indices: 1438805--1438882 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 35
1438795 AGGGGGTATC
1438805 GATTCCCCCCAGGGGGTATCGATTCCCCGGGAACA
1 GATTCCCCCCAGGGGGTATCGATTCCCCGGGAACA
* *
1438840 GATTCCCCCCA-GGGGTATCGATTCCCCGGGTATA
1 GATTCCCCCCAGGGGGTATCGATTCCCCGGGAACA
1438874 GATTCCCCC
1 GATTCCCCC
1438883 TGCATGGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 30 0.73
35 11 0.27
ACGTcount: A:0.18, C:0.36, G:0.26, T:0.21
Consensus pattern (35 bp):
GATTCCCCCCAGGGGGTATCGATTCCCCGGGAACA
Found at i:1438872 original size:15 final size:15
Alignment explanation
Indices: 1438818--1438881 Score: 58
Period size: 15 Copynumber: 4.0 Consensus size: 15
1438808 TCCCCCCAGG
1438818 GGGTATCGATTCCCC
1 GGGTATCGATTCCCC
*
1438833 GGG-AACAGATTCCCCCC
1 GGGTATC-GATT--CCCC
1438850 AGGGGTATCGATTCCCC
1 --GGGTATCGATTCCCC
*
1438867 GGGTATAGATTCCCC
1 GGGTATCGATTCCCC
1438882 CTGCATGGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 2 0.05
15 21 0.52
17 8 0.20
19 7 0.17
20 2 0.05
ACGTcount: A:0.19, C:0.33, G:0.27, T:0.22
Consensus pattern (15 bp):
GGGTATCGATTCCCC
Found at i:1439018 original size:21 final size:21
Alignment explanation
Indices: 1438994--1439035 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1438984 ATTTGAATAT
*
1438994 TATGAAGGGATATCGATTCCC
1 TATGAAGGGATACCGATTCCC
*
1439015 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGATACCGATTCCC
1439036 CTCATTCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAAGGGATACCGATTCCC
Found at i:1441690 original size:21 final size:21
Alignment explanation
Indices: 1441664--1441705 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1441654 ATTTGAATAT
*
1441664 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1441685 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1441706 CCCATTCCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1443714 original size:3 final size:3
Alignment explanation
Indices: 1443689--1443737 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
1443679 TATCTGCTCC
* * * * *
1443689 TGA TGA CGA TGA CGA TCA TGA TGA TGG TGA TGA TGA TGA TAA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1443737 T
1 T
1443738 AGTGAGGAGT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.06, G:0.31, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:1447561 original size:18 final size:16
Alignment explanation
Indices: 1447538--1447571 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
1447528 CCAAATAATT
1447538 ATATATAATTATAAAAAA
1 ATATAT-ATTA-AAAAAA
1447556 ATATATATTAAAAAAA
1 ATATATATTAAAAAAA
1447572 TTACCTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATATATATTAAAAAAA
Found at i:1448118 original size:22 final size:22
Alignment explanation
Indices: 1448090--1448133 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1448080 TCTAACGAGT
1448090 CTAAAAGAACCCATAACTTAAG
1 CTAAAAGAACCCATAACTTAAG
1448112 CTAAAAGAACCCATAACTTAAG
1 CTAAAAGAACCCATAACTTAAG
1448134 GAAATACGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.09, T:0.18
Consensus pattern (22 bp):
CTAAAAGAACCCATAACTTAAG
Found at i:1456229 original size:13 final size:13
Alignment explanation
Indices: 1456211--1456236 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1456201 ATTTGATAAA
1456211 GAAATAATTTTTT
1 GAAATAATTTTTT
1456224 GAAATAATTTTTT
1 GAAATAATTTTTT
1456237 ATTAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
GAAATAATTTTTT
Found at i:1456687 original size:14 final size:16
Alignment explanation
Indices: 1456656--1456695 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1456646 TAGGTTAAAG
1456656 TATAATTTTATTTATA
1 TATAATTTTATTTATA
1456672 TATAATTTCT-TTTATA
1 TATAATTT-TATTTATA
*
1456688 TATTATTT
1 TATAATTT
1456696 ACAAATACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TATAATTTTATTTATA
Found at i:1459783 original size:14 final size:14
Alignment explanation
Indices: 1459764--1459793 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1459754 TTGATCTTTT
1459764 AAGTTTTATTAAGA
1 AAGTTTTATTAAGA
*
1459778 AAGTTTTATTGAGA
1 AAGTTTTATTAAGA
1459792 AA
1 AA
1459794 CTCAATGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (14 bp):
AAGTTTTATTAAGA
Found at i:1460229 original size:33 final size:33
Alignment explanation
Indices: 1460143--1460231 Score: 160
Period size: 33 Copynumber: 2.7 Consensus size: 33
1460133 TAATATTAAA
* *
1460143 TCATTAAACTATTATCAAAGGTGATACTGATAT
1 TCATTAAACTATTACCAAAGTTGATACTGATAT
1460176 TCATTAAACTATTACCAAAGTTGATACTGATAT
1 TCATTAAACTATTACCAAAGTTGATACTGATAT
1460209 TCATTAAACTATTACCAAAGTTG
1 TCATTAAACTATTACCAAAGTTG
1460232 GTGGCTAACT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (33 bp):
TCATTAAACTATTACCAAAGTTGATACTGATAT
Found at i:1460427 original size:16 final size:16
Alignment explanation
Indices: 1460406--1460584 Score: 99
Period size: 16 Copynumber: 10.8 Consensus size: 16
1460396 TAAAGTCTGT
*
1460406 TTACTTTCGGTTTGGG
1 TTACTTTCGGTTCGGG
* *
1460422 TTACTTTCGGTTCAGA
1 TTACTTTCGGTTCGGG
* * **
1460438 TTAATTTCTGTTTAGG
1 TTACTTTCGGTTCGGG
*
1460454 TTGCTTTCGGTTCGGG
1 TTACTTTCGGTTCGGG
*
1460470 TTTAAATTT-GGTTCGGG
1 -TT-ACTTTCGGTTCGGG
**
1460487 TTACTTTCGGTTCGAT
1 TTACTTTCGGTTCGGG
* **
1460503 TTAGTTTTAGTTCGGG
1 TTACTTTCGGTTCGGG
* * *
1460519 TTGCTTTTGGTTCGAG
1 TTACTTTCGGTTCGGG
* *
1460535 TTAATTTCAGTTTCAGTTCGGA
1 TT-A---C--TTTCGGTTCGGG
*
1460557 TTAATTTCGGTTCGGG
1 TTACTTTCGGTTCGGG
1460573 TTACTTTCGGTT
1 TTACTTTCGGTT
1460585 TCGCTAAATT
Statistics
Matches: 119, Mismatches: 35, Indels: 18
0.69 0.20 0.10
Matches are distributed among these distances:
15 4 0.03
16 90 0.76
17 10 0.08
18 3 0.03
20 1 0.01
21 1 0.01
22 10 0.08
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.49
Consensus pattern (16 bp):
TTACTTTCGGTTCGGG
Found at i:1460569 original size:38 final size:38
Alignment explanation
Indices: 1460501--1460586 Score: 93
Period size: 38 Copynumber: 2.3 Consensus size: 38
1460491 TTTCGGTTCG
* * ** *
1460501 ATTT-AGTTTTAGTTCGGGTTGCTTTTGGTTCGAGTTA
1 ATTTCAGTTTCAGTTCGGATTAATTTCGGTTCGAGTTA
*
1460538 ATTTCAGTTTCAGTTCGGATTAATTTCGGTTCGGGTTA
1 ATTTCAGTTTCAGTTCGGATTAATTTCGGTTCGAGTTA
* *
1460576 CTTTCGGTTTC
1 ATTTCAGTTTC
1460587 GCTAAATTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
37 4 0.10
38 36 0.90
ACGTcount: A:0.14, C:0.13, G:0.24, T:0.49
Consensus pattern (38 bp):
ATTTCAGTTTCAGTTCGGATTAATTTCGGTTCGAGTTA
Found at i:1463864 original size:22 final size:22
Alignment explanation
Indices: 1463828--1463870 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1463818 CTGTTAATAT
** *
1463828 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTACATGATATAATTC
1463850 CAGGAGTTACATGATATAATT
1 CAGGAGTTACATGATATAATT
1463871 TCGAGAGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (22 bp):
CAGGAGTTACATGATATAATTC
Found at i:1464791 original size:65 final size:64
Alignment explanation
Indices: 1464671--1464877 Score: 226
Period size: 65 Copynumber: 3.2 Consensus size: 64
1464661 TTTCAAAGTG
* * ** *
1464671 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AATATCGAATGCATT
1 ATGCATCGATGCACCAA-CCATGCATCGATGCACTC-T-GACTATTTTGAAACATCGAATGCATT
1464734 TC
63 TC
* * *
1464736 ATGCATCGATGCA-CATACTATGCATGGATGCACT-TAGAGT-TTTATGAAAACATCGAATGCAT
1 ATGCATCGATGCACCA-ACCATGCATCGATGCACTCT-GACTATTT-TG-AAACATCGAATGCAT
*
1464798 TTG
62 TTC
*
1464801 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTGACTATTTTGAAACATCGAATGCATTTC
1 ATGCATCGATGCACCAACCATGCATCGATGCACTCTGACTATTTTGAAACATCGAATGCATTTC
1464865 ATGCATCGATGCA
1 ATGCATCGATGCA
1464878 ATCTTAGTGC
Statistics
Matches: 120, Mismatches: 14, Indels: 17
0.79 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 46 0.38
65 61 0.51
66 6 0.05
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCACCAACCATGCATCGATGCACTCTGACTATTTTGAAACATCGAATGCATTTC
Found at i:1465102 original size:23 final size:24
Alignment explanation
Indices: 1465058--1465103 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1465048 AAATAAGTTC
1465058 AAACATCCAACAACCATCAAATTT
1 AAACATCCAACAACCATCAAATTT
1465082 AAACATCCAGA-AA-CATCAAATT
1 AAACATCCA-ACAACCATCAAATT
1465104 CAATCCAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.43
24 11 0.52
25 1 0.05
ACGTcount: A:0.52, C:0.26, G:0.02, T:0.20
Consensus pattern (24 bp):
AAACATCCAACAACCATCAAATTT
Found at i:1467056 original size:23 final size:22
Alignment explanation
Indices: 1467026--1467105 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
1467016 GCATGACCTT
1467026 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
1467048 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
1467070 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
1467092 ATGCATCAATGCAC
1 GTGCATCGATGCAC
1467106 TGTTAGGTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 15 0.33
22 15 0.33
23 16 0.35
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1467080 original size:44 final size:42
Alignment explanation
Indices: 1467030--1467124 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 42
1467020 GACCTTGTGC
* **
1467030 ATCGATGCACATTCAAGGCGTGCATCGGTGCACCT-TCATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCAATGCA-CTGTCA-GGTGT
*
1467074 ATCGATGCACATTCAAGGATGCATCAATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCAATGCACTGTCAGGTGT
1467116 ATCGATGCA
1 ATCGATGCA
1467125 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 16 0.35
43 12 0.26
44 18 0.39
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCAATGCACTGTCAGGTGT
Found at i:1467082 original size:21 final size:20
Alignment explanation
Indices: 1467026--1467124 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 20
1467016 GCATGACCTT
1467026 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTC-A-G
* *
1467048 CGTGCATCGGTGCACCTTCATG
1 -GTGCATCGATGCACATTCA-G
*
1467070 GTGTATCGATGCACATTCAAG
1 GTGCATCGATGCACATTC-AG
* *
1467091 GATGCATCAATGCAC-TGTTAG
1 G-TGCATCGATGCACAT-TCAG
*
1467112 GTGTATCGATGCA
1 GTGCATCGATGCA
1467125 TTAAGCACAA
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
20 10 0.16
21 21 0.34
22 15 0.24
23 16 0.26
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (20 bp):
GTGCATCGATGCACATTCAG
Found at i:1471607 original size:17 final size:17
Alignment explanation
Indices: 1471585--1471634 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1471575 AAATTCTTCT
1471585 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
1471602 AACA-T--T-GATACTCA
1 AACATTCATAGAAAC-CA
1471616 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
1471633 AA
1 AA
1471635 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:1474259 original size:18 final size:19
Alignment explanation
Indices: 1474213--1474261 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
1474203 TTGGACCCTT
1474213 AGTGCATCGATGCACTAAA
1 AGTGCATCGATGCACTAAA
1474232 AGTGCATCGATGCA-TAAA
1 AGTGCATCGATGCACTAAA
1474250 A-TGCATTCGATG
1 AGTGCA-TCGATG
1474262 TTTCAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.14
18 11 0.38
19 14 0.48
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCACTAAA
Found at i:1474366 original size:65 final size:64
Alignment explanation
Indices: 1474213--1474389 Score: 191
Period size: 65 Copynumber: 2.8 Consensus size: 64
1474203 TTGGACCCTT
*
1474213 AGTGCATCGATGCACTA-AAAGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCA-TAGTAAGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCAG
* * * *
1474277 AGTGCATCGATGCATGGCT-GGTGCATCGATGCATCAAATGTATTCGATGTTTTCATAAA-A-CT
1 AGTGCATCGATGCATAG-TAAGTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATAGC-
*
1474339 CTG
62 CAG
* * * *
1474342 AGTGCATCGATGCATAGTATGTGCATCGATGCCTGAAAGGCATTCGAT
1 AGTGCATCGATGCATAGTAAGTGCATCGATGCATAAAATGCATTCGAT
1474390 ATTCAATTTA
Statistics
Matches: 95, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
63 1 0.01
64 43 0.45
65 48 0.51
66 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (64 bp):
AGTGCATCGATGCATAGTAAGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCAG
Found at i:1475817 original size:20 final size:19
Alignment explanation
Indices: 1475794--1475833 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
1475784 TGTCGAACCT
1475794 TTGGTATCGATACCCACTTA
1 TTGGTATCGATACCC-CTTA
1475814 TTGGTATCGATACCCCTTA
1 TTGGTATCGATACCCCTTA
1475833 T
1 T
1475834 CTGACGTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (19 bp):
TTGGTATCGATACCCCTTA
Found at i:1479604 original size:17 final size:17
Alignment explanation
Indices: 1479561--1479596 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1479551 TTTTTTGTTT
1479561 GGAATGCTTTTATTGAG
1 GGAATGCTTTTATTGAG
1479578 GGAATGCTTTTATTGAG
1 GGAATGCTTTTATTGAG
1479595 GG
1 GG
1479597 GGTGCTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.06, G:0.33, T:0.39
Consensus pattern (17 bp):
GGAATGCTTTTATTGAG
Found at i:1482365 original size:15 final size:15
Alignment explanation
Indices: 1482347--1482392 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1482337 ATACGTCAAA
1482347 ATGTTCTATGTGAAT
1 ATGTTCTATGTGAAT
* *
1482362 ATGTGCTAAGTGAAT
1 ATGTTCTATGTGAAT
* *
1482377 ATGTTATATGGGAAT
1 ATGTTCTATGTGAAT
1482392 A
1 A
1482393 AATGATAAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (15 bp):
ATGTTCTATGTGAAT
Found at i:1482585 original size:23 final size:23
Alignment explanation
Indices: 1482551--1482652 Score: 71
Period size: 23 Copynumber: 4.3 Consensus size: 23
1482541 GAGTCGAGGG
*
1482551 TTCTACGCGGTCCTTCGGGATAA
1 TTCTACGTGGTCCTTCGGGATAA
* * *
1482574 TTCTACGTGGTCATTCGAGAAAAA
1 TTCTACGTGGTCCTTCG-GGATAA
** * *
1482598 TTCTACACGGTCCTTAGGGACAA
1 TTCTACGTGGTCCTTCGGGATAA
* * *
1482621 ATCTATGTGGTACTTCGGTGCAT-A
1 TTCTACGTGGTCCTTCGG-G-ATAA
1482645 TTCTACGT
1 TTCTACGT
1482653 AACACTTTGT
Statistics
Matches: 57, Mismatches: 19, Indels: 5
0.70 0.23 0.06
Matches are distributed among these distances:
23 31 0.54
24 25 0.44
25 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGATAA
Found at i:1482622 original size:24 final size:23
Alignment explanation
Indices: 1482551--1482622 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
1482541 GAGTCGAGGG
*
1482551 TTCTACGCGGTCCTTCGGGATAA
1 TTCTACGCGGTCCTTCGGGAAAA
* * *
1482574 TTCTACGTGGTCATTCGAGAAAAA
1 TTCTACGCGGTCCTTCG-GGAAAA
* *
1482598 TTCTACACGGTCCTTAGGGACAAA
1 TTCTACGCGGTCCTTCGGGA-AAA
1482622 T
1 T
1482623 CTATGTGGTA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
23 17 0.45
24 21 0.55
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGAAAA
Found at i:1487490 original size:22 final size:22
Alignment explanation
Indices: 1487463--1487512 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
1487453 ACTGAAGTAG
1487463 GTATCGGTATCATAGAAGATAA
1 GTATCGGTATCATAGAAGATAA
1487485 GTATCGGTATCATAGAAGATAA
1 GTATCGGTATCATAGAAGATAA
1487507 GTATCG
1 GTATCG
1487513 ATATTGTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (22 bp):
GTATCGGTATCATAGAAGATAA
Found at i:1488121 original size:32 final size:32
Alignment explanation
Indices: 1488079--1488152 Score: 139
Period size: 32 Copynumber: 2.3 Consensus size: 32
1488069 TTAAGTAAAT
*
1488079 ATATTCTATGGGAATAAATGATAAGTTGAGAA
1 ATATTATATGGGAATAAATGATAAGTTGAGAA
1488111 ATATTATATGGGAATAAATGATAAGTTGAGAA
1 ATATTATATGGGAATAAATGATAAGTTGAGAA
1488143 ATATTATATG
1 ATATTATATG
1488153 AAATGCAATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.45, C:0.01, G:0.20, T:0.34
Consensus pattern (32 bp):
ATATTATATGGGAATAAATGATAAGTTGAGAA
Found at i:1488335 original size:24 final size:23
Alignment explanation
Indices: 1488302--1488388 Score: 81
Period size: 24 Copynumber: 3.7 Consensus size: 23
1488292 CGGTTCTTCA
1488302 GGAC-AATTCTACGTGGTCATTCG
1 GGACAAATTCTACGTGGT-ATTCG
* *
1488325 GGACAAATTCTACGAGGTGTTTCG
1 GGACAAATTCTACGTGGT-ATTCG
*
1488349 GGACAAA-TCTATGTGGTACTTCG
1 GGACAAATTCTACGTGGTA-TTCG
*
1488372 GTG-CATATTCTACGTGG
1 G-GACAAATTCTACGTGG
1488389 CACTTTAGAG
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
23 20 0.38
24 32 0.62
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (23 bp):
GGACAAATTCTACGTGGTATTCG
Found at i:1488371 original size:23 final size:22
Alignment explanation
Indices: 1488296--1488372 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 22
1488286 TCAACGCGGT
* *
1488296 TCTTCAGGACAATTCTACGTGG
1 TCTTCGGGACAAATCTACGTGG
*
1488318 TCATTCGGGACAAATTCTACGAGG
1 TC-TTCGGGACAAA-TCTACGTGG
* *
1488342 TGTTTCGGGACAAATCTATGTGG
1 T-CTTCGGGACAAATCTACGTGG
1488365 TACTTCGG
1 T-CTTCGG
1488373 TGCATATTCT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
22 2 0.05
23 22 0.50
24 20 0.45
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.31
Consensus pattern (22 bp):
TCTTCGGGACAAATCTACGTGG
Found at i:1488427 original size:33 final size:33
Alignment explanation
Indices: 1488385--1488453 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1488375 CATATTCTAC
1488385 GTGGCACTTTAGAGCAAATTCTATATGGTAGTG
1 GTGGCACTTTAGAGCAAATTCTATATGGTAGTG
* * *
1488418 GTGGCACTTTGGTGTAAATTCTATATGGTAGTG
1 GTGGCACTTTAGAGCAAATTCTATATGGTAGTG
1488451 GTG
1 GTG
1488454 ACTGCAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.36
Consensus pattern (33 bp):
GTGGCACTTTAGAGCAAATTCTATATGGTAGTG
Found at i:1500460 original size:16 final size:17
Alignment explanation
Indices: 1500422--1500466 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
1500412 ATTTTGTTAG
1500422 TAATTTATTTAACTATT
1 TAATTTATTTAACTATT
*
1500439 TAATTTTTTTAA-TATT
1 TAATTTATTTAACTATT
* *
1500455 TTATTTAATTAA
1 TAATTTATTTAA
1500467 TTTTTTTTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATTTATTTAACTATT
Found at i:1500467 original size:16 final size:16
Alignment explanation
Indices: 1500424--1500471 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1500414 TTTGTTAGTA
*
1500424 ATTTATTTAACTATTTA
1 ATTTATTTAA-TATTTT
*
1500441 ATTTTTTTAATATTTT
1 ATTTATTTAATATTTT
*
1500457 ATTTAATTAAT-TTTT
1 ATTTATTTAATATTTT
1500472 TTTGCATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 4 0.15
16 14 0.52
17 9 0.33
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTATTTAATATTTT
Found at i:1506828 original size:97 final size:97
Alignment explanation
Indices: 1506654--1506830 Score: 302
Period size: 97 Copynumber: 1.8 Consensus size: 97
1506644 ATTAATTATT
* *
1506654 AAAATATCACCTCTTTATATAAAATATTCTTTCTAATATTAATTTTAAAAAATATAAAATAAATA
1 AAAATATCACATCTTTATATAAAATATTCTTTCTAATATTAATTTAAAAAAATATAAAATAAATA
*
1506719 TTAAATTCTAATGAAAAAGAATGTAAAGCTAA
66 TTAAAGTCTAATGAAAAAGAATGTAAAGCTAA
*
1506751 AAAATATCACATCTTTATTTAAAATATTCTTTCTAATATTAATTTAAAAAAATATAAAATAAATA
1 AAAATATCACATCTTTATATAAAATATTCTTTCTAATATTAATTTAAAAAAATATAAAATAAATA
1506816 TTAATAGT-TAATGAA
66 TTAA-AGTCTAATGAA
1506831 TAATAATTCA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
97 73 0.97
98 2 0.03
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.38
Consensus pattern (97 bp):
AAAATATCACATCTTTATATAAAATATTCTTTCTAATATTAATTTAAAAAAATATAAAATAAATA
TTAAAGTCTAATGAAAAAGAATGTAAAGCTAA
Found at i:1507869 original size:20 final size:21
Alignment explanation
Indices: 1507831--1507875 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
1507821 CTGTCTTTCT
*
1507831 TTTAATAATAATTTTTTAATA
1 TTTAATAATAATTTATTAATA
1507852 TTTAATAAT-ATTTATTAATA
1 TTTAATAATAATTTATTAATA
1507872 TTTA
1 TTTA
1507876 TTAACTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTAATAATAATTTATTAATA
Found at i:1507885 original size:10 final size:10
Alignment explanation
Indices: 1507831--1507879 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
1507821 CTGTCTTTCT
*
1507831 TTTAATAATAA
1 TTTATTAAT-A
*
1507842 TTTTTTAATA
1 TTTATTAATA
*
1507852 TTTAATAATA
1 TTTATTAATA
1507862 TTTATTAATA
1 TTTATTAATA
1507872 TTTATTAA
1 TTTATTAA
1507880 CTTTTAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
10 26 0.79
11 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TTTATTAATA
Found at i:1507885 original size:20 final size:19
Alignment explanation
Indices: 1507836--1507885 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
1507826 TTTCTTTTAA
1507836 TAATAATTTT-TTAATATT
1 TAATAATTTTATTAATATT
1507854 TAATAATATTTATTAATATT
1 TAATAAT-TTTATTAATATT
*
1507874 TATTAACTTTTA
1 TAATAA-TTTTA
1507886 AAATTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 7 0.25
19 3 0.11
20 17 0.61
21 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TAATAATTTTATTAATATT
Found at i:1507967 original size:33 final size:32
Alignment explanation
Indices: 1507883--1507982 Score: 96
Period size: 33 Copynumber: 3.1 Consensus size: 32
1507873 TTATTAACTT
1507883 TTAAAA-TTAATTTTTTAAAAATATTAA-AAAAA
1 TTAAAATTTAATTTTTTAAAAATA--AATAAAAA
** * * *
1507915 TTATTATTCACTTTTTTAAAAATAAATAAATA
1 TTAAAATTTAATTTTTTAAAAATAAATAAAAA
* *
1507947 TTAAAATTTAATTTTATTAAAAATGAATAAACA
1 TTAAAATTTAATTTT-TTAAAAATAAATAAAAA
1507980 TTA
1 TTA
1507983 TTAACTGTTA
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
31 2 0.04
32 19 0.35
33 33 0.61
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (32 bp):
TTAAAATTTAATTTTTTAAAAATAAATAAAAA
Found at i:1508502 original size:11 final size:11
Alignment explanation
Indices: 1508488--1508527 Score: 57
Period size: 10 Copynumber: 3.8 Consensus size: 11
1508478 TTTATATTAT
1508488 ATTTTTATTG-
1 ATTTTTATTGC
*
1508498 AATTTTATT-C
1 ATTTTTATTGC
1508508 ATTTTTATTGC
1 ATTTTTATTGC
1508519 ATTTTTATT
1 ATTTTTATT
1508528 TATTTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (11 bp):
ATTTTTATTGC
Found at i:1508511 original size:20 final size:21
Alignment explanation
Indices: 1508488--1508538 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1508478 TTTATATTAT
1508488 ATTTTTATTG-AATTTTATTC
1 ATTTTTATTGCAATTTTATTC
* *
1508508 ATTTTTATTGCATTTTTATTT
1 ATTTTTATTGCAATTTTATTC
1508529 ATTTTATATT
1 ATTTT-TATT
1508539 TTTTATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 10 0.37
21 13 0.48
22 4 0.15
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (21 bp):
ATTTTTATTGCAATTTTATTC
Found at i:1508538 original size:11 final size:10
Alignment explanation
Indices: 1508482--1508539 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
1508472 TTTAGCTTTA
1508482 TATTATATTTT
1 TATT-TATTTT
* *
1508493 TATTGAATTT
1 TATTTATTTT
*
1508503 TATTCATTTT
1 TATTTATTTT
*
1508513 TATTGCATTTT
1 TATT-TATTTT
1508524 TATTTATTTT
1 TATTTATTTT
1508534 ATATTT
1 -TATTT
1508540 TTTATAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
10 21 0.52
11 19 0.47
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (10 bp):
TATTTATTTT
Found at i:1509345 original size:29 final size:29
Alignment explanation
Indices: 1509320--1509391 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
1509310 ATGGGTGTTA
1509320 GATCGGGAAATATAGTCTGACGGGTGCCT
1 GATCGGGAAATATAGTCTGACGGGTGCCT
1509349 GATCGGGAAATATAGTCTGACGGGTGCCT
1 GATCGGGAAATATAGTCTGACGGGTGCCT
1509378 GATCGGGAAATATA
1 GATCGGGAAATATA
1509392 CTGTTCAACG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.24
Consensus pattern (29 bp):
GATCGGGAAATATAGTCTGACGGGTGCCT
Found at i:1512987 original size:75 final size:75
Alignment explanation
Indices: 1512864--1513013 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 75
1512854 GTATCATTTC
*
1512864 AGAACAGATCAGACAGGCTATATTAGCTTTAATATTCAAGTCCAGAAACATGTAGTAAATCCTTG
1 AGAACAGATCAGACAGGCTATATTAGCTTTAATATTCAAGTCCAGAAACATGTAGTAAATCCATG
1512929 TTATTAGCTT
66 TTATTAGCTT
*
1512939 AGAACAGATCAGACAGGCTTTATTAGCTTTAATATTCAAGTCCAGAAACATGTAGTAAATCCATG
1 AGAACAGATCAGACAGGCTATATTAGCTTTAATATTCAAGTCCAGAAACATGTAGTAAATCCATG
1513004 TTATTAGCTT
66 TTATTAGCTT
1513014 TAATATTGAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (75 bp):
AGAACAGATCAGACAGGCTATATTAGCTTTAATATTCAAGTCCAGAAACATGTAGTAAATCCATG
TTATTAGCTT
Found at i:1515799 original size:23 final size:24
Alignment explanation
Indices: 1515773--1515827 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
1515763 TAACATGTTA
1515773 TCTGTCTTTA-TGACATATTTATT-
1 TCTGTCTTTAGTGACATATTT-TTC
1515796 TCTG-CTTTAGTGACATATTTTTC
1 TCTGTCTTTAGTGACATATTTTTC
1515819 TCTGTCTTT
1 TCTGTCTTT
1515828 TGGTAGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.24
23 18 0.62
24 4 0.14
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.56
Consensus pattern (24 bp):
TCTGTCTTTAGTGACATATTTTTC
Found at i:1520524 original size:22 final size:20
Alignment explanation
Indices: 1520499--1520543 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
1520489 ACCGAAGTGG
*
1520499 GTATCGGTACCATAGAAGAGAA
1 GTATCAGTACCATAG--GAGAA
*
1520521 GTATCAGTACTATAGGAGAA
1 GTATCAGTACCATAGGAGAA
1520541 GTA
1 GTA
1520544 CCGATACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
22 13 0.62
ACGTcount: A:0.40, C:0.11, G:0.27, T:0.22
Consensus pattern (20 bp):
GTATCAGTACCATAGGAGAA
Found at i:1521144 original size:24 final size:24
Alignment explanation
Indices: 1521089--1521181 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
1521079 GAGTCGAGGG
**
1521089 TTCTACGCAGTCCTTCGGGAC-AA
1 TTCTACGTGGTCCTTCGGGACAAA
*
1521112 -TCTATGTGGTCCTTCGGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
** *
1521135 TTCTACGTGGTTATTCGGGATAAA
1 TTCTACGTGGTCCTTCGGGACAAA
*
1521159 TTCTACGTGG-CACTTCGGTACAA
1 TTCTACGTGGTC-CTTCGGGACAA
1521182 TTTATATGAG
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
22 17 0.30
23 2 0.04
24 37 0.66
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGACAAA
Found at i:1523294 original size:12 final size:12
Alignment explanation
Indices: 1523275--1523313 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1523265 GATGAGGAAG
1523275 AGGAAGAAGAGA
1 AGGAAGAAGAGA
* *
1523287 ATGAAGAAGCGA
1 AGGAAGAAGAGA
1523299 AGGAAGAAGAGA
1 AGGAAGAAGAGA
1523311 AGG
1 AGG
1523314 TAGTAGTGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.54, C:0.03, G:0.41, T:0.03
Consensus pattern (12 bp):
AGGAAGAAGAGA
Found at i:1527392 original size:65 final size:64
Alignment explanation
Indices: 1527281--1527401 Score: 172
Period size: 65 Copynumber: 1.9 Consensus size: 64
1527271 CATTTTGTGC
* * *
1527281 ACCGATGCACAGCCATGCATCGATGCACTCCTGATTTTATTAAAACATCGAATGTATTTTATAT
1 ACCGATGCACAGCCATGAATCGATGCACTCCTGATCTTATTAAAACATCAAATGTATTTTATAT
* *
1527345 ACCGATGCACAGACCATGAATCGATGCACTCCTAGCTCTT-TTGAAACATCAAATGTA
1 ACCGATGCACAG-CCATGAATCGATGCACTCCT-GATCTTATTAAAACATCAAATGTA
1527402 ATTAGTGTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
64 12 0.24
65 34 0.68
66 4 0.08
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (64 bp):
ACCGATGCACAGCCATGAATCGATGCACTCCTGATCTTATTAAAACATCAAATGTATTTTATAT
Found at i:1527413 original size:65 final size:64
Alignment explanation
Indices: 1527281--1527419 Score: 165
Period size: 65 Copynumber: 2.2 Consensus size: 64
1527271 CATTTTGTGC
* * * *
1527281 ACCGATGCACAGCCATGCATCGATGCACTCCTGATTTTATTAAAACATCGAATGTATTTTATAT
1 ACCGATGCACAGCCATGAATCGATGCACTCCTGATCTTATTAAAACATCAAATGTATATTATAT
* *
1527345 ACCGATGCACAGACCATGAATCGATGCACTCCTAGCTCTT-TTGAAACATCAAATGTA-ATTAGT
1 ACCGATGCACAG-CCATGAATCGATGCACTCCT-GATCTTATTAAAACATCAAATGTATATTA-T
*
1527408 GT
63 AT
*
1527410 ACCGCTGCAC
1 ACCGATGCAC
1527420 CCCAAGTGTA
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
64 15 0.23
65 45 0.70
66 4 0.06
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (64 bp):
ACCGATGCACAGCCATGAATCGATGCACTCCTGATCTTATTAAAACATCAAATGTATATTATAT
Found at i:1529609 original size:28 final size:29
Alignment explanation
Indices: 1529548--1529617 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
1529538 TTTTGACCTT
*
1529548 AAATTTTTTAATGTTTATGCATAGAACTC
1 AAATTTTTTAATGTTTATGCATAAAACTC
1529577 AAATTTTTTAATGTTTATGCATAAAACTC
1 AAATTTTTTAATGTTTATGCATAAAACTC
1529606 -AATTTTTTAATG
1 AAATTTTTTAATG
1529618 CATAAAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 12 0.30
29 28 0.70
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (29 bp):
AAATTTTTTAATGTTTATGCATAAAACTC
Done.