Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008909.1 Hibiscus syriacus cultivar Beakdansim tig00112206_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: 2327114
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1681481 original size:31 final size:32
Alignment explanation
Indices: 1681414--1681494 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 32
1681404 AAATATTATT
1681414 TATT-TATTTATTAATATTTATAATAATATAA
1 TATTATATTTATTAATATTTATAATAATATAA
*
1681445 TATTATATTT-TTAATA-TTAT-ATAAAATAA
1 TATTATATTTATTAATATTTATAATAATATAA
*
1681474 TCAATTATATTATAATAATAT
1 T--ATTATATT-TATTAATAT
1681495 AAGATATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
29 9 0.21
30 4 0.10
31 18 0.43
32 6 0.14
33 5 0.12
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (32 bp):
TATTATATTTATTAATATTTATAATAATATAA
Found at i:1681530 original size:29 final size:28
Alignment explanation
Indices: 1681428--1681584 Score: 78
Period size: 29 Copynumber: 5.5 Consensus size: 28
1681418 TATTTATTAA
1681428 TATTTATAATAATA-TAATATTATATTTT
1 TATTT-TAATAATATTAATATTATATTTT
* * * *
1681456 TAATATT-AT-ATA--AA-ATAATCAATTA
1 T-ATTTTAATAATATTAATATTAT-ATTTT
* *
1681481 TATTATAATAATATAAGATATTATATTTT
1 TATTTTAATAATATTA-ATATTATATTTT
*
1681510 TATTTTAATAATATCTAATA-TAAAGTTTT
1 TATTTTAATAATAT-TAATATTATA-TTTT
* *
1681539 ATATATTTAATAATGAATAATATTAT-TTATA
1 -TAT-TTTAATAAT-ATTAATATTATATT-TT
*
1681570 TATTTAAATAATATT
1 TATTTTAATAATATT
1681585 TTAATAAAGA
Statistics
Matches: 97, Mismatches: 17, Indels: 30
0.67 0.12 0.21
Matches are distributed among these distances:
24 7 0.07
25 8 0.08
26 6 0.06
27 2 0.02
28 8 0.08
29 35 0.36
30 13 0.13
31 15 0.15
32 3 0.03
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.50
Consensus pattern (28 bp):
TATTTTAATAATATTAATATTATATTTT
Found at i:1681557 original size:28 final size:29
Alignment explanation
Indices: 1681526--1681581 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
1681516 AATAATATCT
1681526 AATATAAAGT-TTTATATATTT-AATAATG
1 AATA-AAAGTATTTATATATTTAAATAATG
* *
1681554 AATAATATTATTTATATATTTAAATAAT
1 AATAAAAGTATTTATATATTTAAATAAT
1681582 ATTTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 3 0.12
28 15 0.62
29 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (29 bp):
AATAAAAGTATTTATATATTTAAATAATG
Found at i:1681561 original size:19 final size:19
Alignment explanation
Indices: 1681539--1681591 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
1681529 ATAAAGTTTT
*
1681539 ATATATTTAATAATGAATA
1 ATATATTTAATAATAAATA
*
1681558 ATATTATTTATATATTTAAATA
1 ATA-TATTTA-ATA-ATAAATA
1681580 ATAT-TTTAATAA
1 ATATATTTAATAA
1681592 AGATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTAATAATAAATA
Found at i:1681612 original size:23 final size:23
Alignment explanation
Indices: 1681586--1681630 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1681576 AATAATATTT
1681586 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1681609 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1681631 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1681957 original size:14 final size:14
Alignment explanation
Indices: 1681923--1681957 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1681913 AAATGTAATT
*
1681923 CATTTTACGGAAAA
1 CATTTTCCGGAAAA
1681937 CATTTTCCGGAAAA
1 CATTTTCCGGAAAA
*
1681951 CGTTTTC
1 CATTTTC
1681958 TAGAAATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.34
Consensus pattern (14 bp):
CATTTTCCGGAAAA
Found at i:1681985 original size:14 final size:15
Alignment explanation
Indices: 1681965--1682049 Score: 75
Period size: 15 Copynumber: 5.8 Consensus size: 15
1681955 TTCTAGAAAT
1681965 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
1681980 -TAATTCAAATTCCA
1 GTAATTCATTTTCCA
* *
1681994 GGAATTTATTTTCCA
1 GTAATTCATTTTCCA
**
1682009 GTAATTCAAATT-CA
1 GTAATTCATTTTCCA
* **
1682023 GTAGTTCAAATTCCA
1 GTAATTCATTTTCCA
1682038 GTAATTCATTTT
1 GTAATTCATTTT
1682050 TCGAAAAACC
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
14 25 0.46
15 29 0.54
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.42
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:1689020 original size:25 final size:25
Alignment explanation
Indices: 1688992--1689068 Score: 77
Period size: 25 Copynumber: 2.9 Consensus size: 25
1688982 ATTATATTAT
1688992 ATATAAT-TAATATAA-AATATATAAA
1 ATATAATAT-ATATAATAATATA-AAA
1689017 ATATAATATATATAATTAATATAAAA
1 ATATAATATATATAA-TAATATAAAA
*
1689043 ATATAAAATATTATATATATATATAA
1 ATATAATATA-TATA-ATA-ATATAA
1689069 TCGGGGTGGG
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
25 13 0.29
26 13 0.29
27 12 0.27
28 7 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATATAATATATATAATAATATAAAA
Found at i:1689064 original size:18 final size:17
Alignment explanation
Indices: 1688978--1689065 Score: 67
Period size: 18 Copynumber: 5.0 Consensus size: 17
1688968 ACCCGACCCG
1688978 AAATATTATATTATATATA
1 AAATA-TATA-TATATATA
*
1688997 ATTAATATA-AAATATATA
1 A--AATATATATATATATA
1689015 AAATATA-ATATATATA
1 AAATATATATATATATA
*
1689031 ATTAATATA-A-AAATATA
1 A--AATATATATATATATA
1689048 AAATATTATATATATATA
1 AAATA-TATATATATATA
1689066 TAATCGGGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
15 4 0.07
16 17 0.29
17 8 0.14
18 21 0.36
19 2 0.03
20 2 0.03
21 4 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATATATATATATA
Found at i:1689906 original size:23 final size:21
Alignment explanation
Indices: 1689875--1689918 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
1689865 TAAATATTAG
1689875 ATGAGATGAGATAAGATAGTAAT
1 ATGAGATGAGATAA-A-AGTAAT
* *
1689898 ATGATATGATATAAAAGTAAT
1 ATGAGATGAGATAAAAGTAAT
1689919 TTTAGTCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (21 bp):
ATGAGATGAGATAAAAGTAAT
Found at i:1694659 original size:14 final size:14
Alignment explanation
Indices: 1694640--1694672 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1694630 CTACTTAATA
1694640 ATATTCATCTCTAT
1 ATATTCATCTCTAT
1694654 ATATTCATCTCTAT
1 ATATTCATCTCTAT
1694668 ATATT
1 ATATT
1694673 TTTAAGTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTCATCTCTAT
Found at i:1694716 original size:61 final size:61
Alignment explanation
Indices: 1694593--1694718 Score: 182
Period size: 61 Copynumber: 2.1 Consensus size: 61
1694583 AATTATAATA
* ** **
1694593 ATATTCATCTCTATATATTTTTAAATAAGTCCCTATTCTACTTAATAATATTCATCTCTAT
1 ATATTCATCTCTATATATTTTTAAATAAGTCCCTATTCTACTTAATAAAATGAAAATCTAT
*
1694654 ATATTCATCTCTATATATTTTTAAGTAAGTCCCTATTCTACTTAATAAAAATGAAAAT-TAT
1 ATATTCATCTCTATATATTTTTAAATAAGTCCCTATTCTACTTAAT-AAAATGAAAATCTAT
1694715 ATAT
1 ATAT
1694719 ATATATTGAG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 52 0.90
62 6 0.10
ACGTcount: A:0.37, C:0.15, G:0.03, T:0.45
Consensus pattern (61 bp):
ATATTCATCTCTATATATTTTTAAATAAGTCCCTATTCTACTTAATAAAATGAAAATCTAT
Found at i:1696456 original size:16 final size:16
Alignment explanation
Indices: 1696435--1696481 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
1696425 TTAGGGTTCT
1696435 TCGAGTGGATGTGTCG
1 TCGAGTGGATGTGTCG
1696451 TCGAGTGGATGTGTCG
1 TCGAGTGGATGTGTCG
* *
1696467 TCGGGTGGTTGTGTC
1 TCGAGTGGATGTGTC
1696482 ATTGATGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.09, C:0.13, G:0.45, T:0.34
Consensus pattern (16 bp):
TCGAGTGGATGTGTCG
Found at i:1697511 original size:60 final size:60
Alignment explanation
Indices: 1697432--1697576 Score: 197
Period size: 60 Copynumber: 2.4 Consensus size: 60
1697422 TTTGCAATTG
*
1697432 AACTGAAATGTTATAAAAGTTTGAGGACTCATCTAAAAT-GAAAGTCATAGTTTAAGGATGA
1 AACTGAAATGTT-TAAAAGTTTGAGGACTAATCTAAAATGGAAA-TCATAGTTTAAGGATGA
* * * *
1697493 AACTAAAATGTTTAAAAGTTTGAGGACTAATTTAAAATGGTAATCATAGTTTAATGATGA
1 AACTGAAATGTTTAAAAGTTTGAGGACTAATCTAAAATGGAAATCATAGTTTAAGGATGA
*
1697553 AATTGAAAT-TTTAAAAGTTT-AGGA
1 AACTGAAATGTTTAAAAGTTTGAGGA
1697577 ATCAATTTAG
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
58 4 0.05
59 11 0.14
60 47 0.62
61 14 0.18
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (60 bp):
AACTGAAATGTTTAAAAGTTTGAGGACTAATCTAAAATGGAAATCATAGTTTAAGGATGA
Found at i:1697597 original size:59 final size:60
Alignment explanation
Indices: 1697432--1697603 Score: 188
Period size: 60 Copynumber: 2.9 Consensus size: 60
1697422 TTTGCAATTG
* * * * *
1697432 AACTGAAATGTTATAAAAGTTTGAGGACTCATCTAAAATGAAAGTCATAGTTTAAGGATGA
1 AACTAAAATGTT-TAAAAGTTTGAGGAATAATTTAAAATGAAAATCATAGTTTAAGGATGA
* ** *
1697493 AACTAAAATGTTTAAAAGTTTGAGGACTAATTTAAAATGGTAATCATAGTTTAATGATGA
1 AACTAAAATGTTTAAAAGTTTGAGGAATAATTTAAAATGAAAATCATAGTTTAAGGATGA
* * *
1697553 AATTGAAAT-TTTAAAAGTTT-AGGAATCAATTT-AGATGAAAAATCATAGTTT
1 AACTAAAATGTTTAAAAGTTTGAGGAAT-AATTTAAAATG-AAAATCATAGTTT
1697604 GAAGACATGT
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
58 9 0.09
59 27 0.28
60 49 0.51
61 11 0.11
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.34
Consensus pattern (60 bp):
AACTAAAATGTTTAAAAGTTTGAGGAATAATTTAAAATGAAAATCATAGTTTAAGGATGA
Found at i:1705184 original size:43 final size:43
Alignment explanation
Indices: 1705123--1705209 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
1705113 TCAATGACCG
* **
1705123 CTGCTCTCAACCTAAACCAAAAAGAATAAACTGACAACGATCA
1 CTGCTCTCAACCCAAACCAAAAAGAATAAACCAACAACGATCA
1705166 CTGCTCTCAACCCAAACCAAAAAGAATAAACCAACAACGATCA
1 CTGCTCTCAACCCAAACCAAAAAGAATAAACCAACAACGATCA
1705209 C
1 C
1705210 GAGCCAAACT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.47, C:0.31, G:0.08, T:0.14
Consensus pattern (43 bp):
CTGCTCTCAACCCAAACCAAAAAGAATAAACCAACAACGATCA
Found at i:1705244 original size:2 final size:2
Alignment explanation
Indices: 1705237--1705263 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1705227 ATCAACAACC
1705237 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 T
1705264 TACAGTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1717069 original size:2 final size:2
Alignment explanation
Indices: 1717062--1717088 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1717052 GACAGACATG
1717062 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 T
1717089 GTGGATAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1719485 original size:23 final size:23
Alignment explanation
Indices: 1719451--1719537 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
1719441 ACATATTATA
1719451 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1719474 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1719497 CGGTC-CTTCGG-GACAAAATTCTACG
1 TGG-CACTACGGTG-C--AATTCTACG
1719522 TGGCACTACGGTGCAA
1 TGGCACTACGGTGCAA
1719538 ATTTATACGA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
22 1 0.02
23 32 0.62
24 2 0.04
25 16 0.31
26 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:1738999 original size:32 final size:31
Alignment explanation
Indices: 1738963--1739039 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
1738953 GGGGGCTGTG
*
1738963 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
1738995 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
1739026 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
1739040 GTCACATTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:1739959 original size:10 final size:10
Alignment explanation
Indices: 1739941--1740009 Score: 72
Period size: 9 Copynumber: 7.1 Consensus size: 10
1739931 TCGGGTCGGG
*
1739941 TCAACCCGGT
1 TCAAACCGGT
*
1739951 TCAGACCGG-
1 TCAAACCGGT
1739960 TCAAACCGGT
1 TCAAACCGGT
*
1739970 TCAGACCGG-
1 TCAAACCGGT
1739979 TCAAACCGGT
1 TCAAACCGGT
*
1739989 TCAAAACTGG-
1 TC-AAACCGGT
1739999 TCAAACCGGT
1 TCAAACCGGT
1740009 T
1 T
1740010 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 22 0.46
10 20 0.42
11 6 0.12
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1739961 original size:19 final size:19
Alignment explanation
Indices: 1739939--1740009 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
1739929 GGTCGGGTCG
*
1739939 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
1739958 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* *
1739977 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
1739997 GGTCAAACCGGTT
1 GGTCAAACCGGTT
1740010 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 32 0.67
20 16 0.33
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:1745816 original size:11 final size:11
Alignment explanation
Indices: 1745790--1745822 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1745780 CATCCTATTT
1745790 ATTTC-TCTTC
1 ATTTCTTCTTC
1745800 ATTTTCTTCTTC
1 A-TTTCTTCTTC
1745812 ATTTCTTCTTC
1 ATTTCTTCTTC
1745823 CTTCGTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 14 0.67
12 6 0.29
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTTCTTCTTC
Found at i:1756039 original size:8 final size:8
Alignment explanation
Indices: 1756016--1756051 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
1756006 TAAATTATCA
1756016 TATATTTT
1 TATATTTT
*
1756024 AAATATTTT
1 -TATATTTT
1756033 TATATTTT
1 TATATTTT
1756041 TATATTTT
1 TATATTTT
1756049 TAT
1 TAT
1756052 TAATAATAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TATATTTT
Found at i:1756045 original size:27 final size:25
Alignment explanation
Indices: 1755995--1756050 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
1755985 TGGAACCGTC
1755995 TTTAAAATTTTTAAATTATCATATAT
1 TTTAAAATTTTTAAATTATCATAT-T
* * *
1756021 TTTAAATATTTTTATATTTTTATATT
1 TTTAAA-ATTTTTAAATTATCATATT
1756047 TTTA
1 TTTA
1756051 TTAATAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTAAAATTTTTAAATTATCATATT
Found at i:1767477 original size:10 final size:10
Alignment explanation
Indices: 1767462--1767499 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
1767452 TACATTATAT
1767462 TTTTATTGAA
1 TTTTATTGAA
1767472 TTTTATTGAA
1 TTTTATTGAA
*
1767482 TTTTATTGCA
1 TTTTATTGAA
1767492 TATTTATT
1 T-TTTATT
1767500 TATTTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 20 0.77
11 6 0.23
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (10 bp):
TTTTATTGAA
Found at i:1767484 original size:21 final size:21
Alignment explanation
Indices: 1767455--1767507 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
1767445 TTAACTTTAC
1767455 ATTATATTTTTATTGAAT-TTT
1 ATTA-ATTTTTATTGAATATTT
*
1767476 ATTGAA-TTTTATTGCATATTT
1 ATT-AATTTTTATTGAATATTT
*
1767497 ATTTATTTTTA
1 ATTAATTTTTA
1767508 AAAAAAAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 11 0.41
21 15 0.56
22 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (21 bp):
ATTAATTTTTATTGAATATTT
Found at i:1767507 original size:10 final size:10
Alignment explanation
Indices: 1767460--1767507 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
1767450 TTTACATTAT
1767460 ATTTTTATTG
1 ATTTTTATTG
*
1767470 AATTTTATTG
1 ATTTTTATTG
*
1767480 AATTTTATTG
1 ATTTTTATTG
* *
1767490 CATATTTATTT
1 -ATTTTTATTG
1767501 ATTTTTA
1 ATTTTTA
1767508 AAAAAAAGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 25 0.78
11 7 0.22
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (10 bp):
ATTTTTATTG
Found at i:1780204 original size:22 final size:21
Alignment explanation
Indices: 1780179--1780251 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 21
1780169 TTATATGAAA
1780179 TGATATATGAATATGCAATACG
1 TGATATATGAATATG-AATACG
* * **
1780201 TGATACATGTGATATGATATGAAA
1 TGATATATG-AATATGA-AT-ACG
1780225 TGATATATGAATATGTAATACG
1 TGATATATGAATATG-AATACG
1780247 TGATA
1 TGATA
1780252 CATGTGATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
22 15 0.38
23 14 0.36
24 10 0.26
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.34
Consensus pattern (21 bp):
TGATATATGAATATGAATACG
Found at i:1780216 original size:23 final size:22
Alignment explanation
Indices: 1780189--1780263 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
1780179 TGATATATGA
1780189 ATATGCAATACGTGATACATGTG
1 ATATG-AATACGTGATACATGTG
** * *
1780212 ATATGATATGAAATGATATATG-A
1 ATATGA-AT-ACGTGATACATGTG
1780235 ATATGTAATACGTGATACATGTG
1 ATATG-AATACGTGATACATGTG
1780258 ATATGA
1 ATATGA
1780264 TATGAAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
22 11 0.28
23 19 0.47
24 10 0.25
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (22 bp):
ATATGAATACGTGATACATGTG
Found at i:1780228 original size:46 final size:46
Alignment explanation
Indices: 1780163--1780271 Score: 195
Period size: 46 Copynumber: 2.4 Consensus size: 46
1780153 AAGATAAGCT
1780163 ATGTGAT-T-ATATGAAATGATATATGAATATGCAATACGTGATAC
1 ATGTGATATGATATGAAATGATATATGAATATGCAATACGTGATAC
*
1780207 ATGTGATATGATATGAAATGATATATGAATATGTAATACGTGATAC
1 ATGTGATATGATATGAAATGATATATGAATATGCAATACGTGATAC
1780253 ATGTGATATGATATGAAAT
1 ATGTGATATGATATGAAAT
1780272 ACATGGTTAC
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
44 7 0.11
45 1 0.02
46 54 0.87
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (46 bp):
ATGTGATATGATATGAAATGATATATGAATATGCAATACGTGATAC
Found at i:1780480 original size:38 final size:38
Alignment explanation
Indices: 1780424--1780513 Score: 144
Period size: 38 Copynumber: 2.4 Consensus size: 38
1780414 TATAAGATAT
* *
1780424 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
1780462 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
1780500 ATGATAGGTACTTC
1 ATGATAGGTCCTTC
1780514 AGGATACGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:1780496 original size:21 final size:21
Alignment explanation
Indices: 1780432--1780500 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
1780422 ATATGATAGG
* *
1780432 TCCTACGGGACACAGATTACA
1 TCCTTCGGGACACAGATGACA
*
1780453 TCCTTCGGGATGACAG--G---
1 TCCTTCGGGA-CACAGATGACA
1780470 TCCTTCGGGACACAGATGACA
1 TCCTTCGGGACACAGATGACA
1780491 TCCTTCGGGA
1 TCCTTCGGGA
1780501 TGATAGGTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 1 0.03
21 19 0.50
22 4 0.11
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.22
Consensus pattern (21 bp):
TCCTTCGGGACACAGATGACA
Found at i:1780706 original size:20 final size:21
Alignment explanation
Indices: 1780667--1780708 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1780657 TGACATGATG
* *
1780667 TATATATATGTCATATTGAAA
1 TATATACATGTCACATTGAAA
1780688 TATATACATG-CACATTGAAA
1 TATATACATGTCACATTGAAA
1780708 T
1 T
1780709 GTTATGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
TATATACATGTCACATTGAAA
Found at i:1780739 original size:34 final size:34
Alignment explanation
Indices: 1780695--1780771 Score: 145
Period size: 34 Copynumber: 2.3 Consensus size: 34
1780685 AAATATATAC
*
1780695 ATGCACATTGAAATGTTATGATTAAATGGTAAGA
1 ATGCATATTGAAATGTTATGATTAAATGGTAAGA
1780729 ATGCATATTGAAATGTTATGATTAAATGGTAAGA
1 ATGCATATTGAAATGTTATGATTAAATGGTAAGA
1780763 ATGCATATT
1 ATGCATATT
1780772 CATGAAATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (34 bp):
ATGCATATTGAAATGTTATGATTAAATGGTAAGA
Found at i:1782540 original size:2 final size:2
Alignment explanation
Indices: 1782533--1782561 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1782523 TCATTGGAAA
1782533 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 A
1782562 ATAATTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1786388 original size:22 final size:21
Alignment explanation
Indices: 1786363--1786435 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 21
1786353 TTGTATGAAA
1786363 TGATATATGAATATGCAATACG
1 TGATATATGAATATG-AATACG
* * **
1786385 TGATACATGTGATATGATATGAAA
1 TGATATATG-AATATGA-AT-ACG
*
1786409 TGACATATGAATATGTAATACG
1 TGATATATGAATATG-AATACG
1786431 TGATA
1 TGATA
1786436 CATGTGATAT
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
22 14 0.38
23 14 0.38
24 9 0.24
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (21 bp):
TGATATATGAATATGAATACG
Found at i:1786400 original size:23 final size:22
Alignment explanation
Indices: 1786373--1786447 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
1786363 TGATATATGA
1786373 ATATGCAATACGTGATACATGTG
1 ATATG-AATACGTGATACATGTG
* ** *
1786396 ATATG-ATATGAAATGACATATG
1 ATATGAATACGTGAT-ACATGTG
1786418 AATATGTAATACGTGATACATGTG
1 -ATATG-AATACGTGATACATGTG
1786442 ATATGA
1 ATATGA
1786448 TATGAAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 6 0.15
22 7 0.17
23 15 0.38
24 6 0.15
25 6 0.15
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (22 bp):
ATATGAATACGTGATACATGTG
Found at i:1786417 original size:46 final size:46
Alignment explanation
Indices: 1786347--1786459 Score: 187
Period size: 46 Copynumber: 2.5 Consensus size: 46
1786337 AAGATAAGCT
*
1786347 ATGTGAT-TG-TATGAAATGATATATGAATATGCAATACGTGATAC
1 ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
*
1786391 ATGTGATATGATATGAAATGACATATGAATATGTAATACGTGATAC
1 ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
1786437 ATGTGATATGATATGAAAT-ACAT
1 ATGTGATATGATATGAAATGACAT
1786460 GGTTACACAT
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
44 7 0.11
45 6 0.09
46 52 0.80
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (46 bp):
ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
Found at i:1786665 original size:38 final size:38
Alignment explanation
Indices: 1786608--1786693 Score: 136
Period size: 38 Copynumber: 2.3 Consensus size: 38
1786598 TATAAGATAT
*
1786608 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTACGGGACACAGATGACATCCTTCGGG
* * *
1786646 ATGACAGGTCCTTCTGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTACGGGACACAGATGACATCCTTCGGG
1786684 ATGATAGGTC
1 ATGATAGGTC
1786694 ATTCGGGATA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (38 bp):
ATGATAGGTCCTACGGGACACAGATGACATCCTTCGGG
Found at i:1786886 original size:20 final size:20
Alignment explanation
Indices: 1786850--1786945 Score: 73
Period size: 20 Copynumber: 5.0 Consensus size: 20
1786840 TGACATGATG
*
1786850 TATATATATGTCATATTGAAA
1 TATATACATG-CATATTGAAA
1786871 TATATACATGCATATTGAAA
1 TATATACATGCATATTGAAA
*
1786891 TGT-T--ATG---ATT-AAA
1 TATATACATGCATATTGAAA
* *
1786904 TGGTA-AGAATGCATATTGAAA
1 T-ATATA-CATGCATATTGAAA
1786925 TATATACATGCATATTGAAA
1 TATATACATGCATATTGAAA
1786945 T
1 T
1786946 GTTATGATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 21
0.71 0.05 0.24
Matches are distributed among these distances:
13 4 0.07
14 5 0.08
17 6 0.10
19 1 0.02
20 31 0.51
21 14 0.23
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.38
Consensus pattern (20 bp):
TATATACATGCATATTGAAA
Found at i:1786920 original size:54 final size:54
Alignment explanation
Indices: 1786861--1786974 Score: 228
Period size: 54 Copynumber: 2.1 Consensus size: 54
1786851 ATATATATGT
1786861 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
1 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
1786915 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
1 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
1786969 CATATT
1 CATATT
1786975 CATGAAATCT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (54 bp):
CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
Found at i:1791489 original size:3 final size:3
Alignment explanation
Indices: 1791481--1791516 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1791471 TGTCTTTCAA
*
1791481 TTC TTC TTC TTC TTC TTC TTC TTC TTC CTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1791517 AAATCAACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:1794719 original size:17 final size:18
Alignment explanation
Indices: 1794684--1794720 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1794674 GGATTAATAA
1794684 ATCTGAAAAGACATATTG
1 ATCTGAAAAGACATATTG
1794702 ATCTGATAAA-AC-TATTG
1 ATCTGA-AAAGACATATTG
1794719 AT
1 AT
1794721 GTGCATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (18 bp):
ATCTGAAAAGACATATTG
Found at i:1797843 original size:40 final size:40
Alignment explanation
Indices: 1797726--1797851 Score: 121
Period size: 40 Copynumber: 3.1 Consensus size: 40
1797716 TGCCAAGGCA
* * ** *
1797726 TGCCAAGAAGCAATAAAATAACTGGAGTTGCCGGTGCGTT
1 TGCCAATAAGCAATAAAATAACTGGAGTGGGTGGTGTGTT
* * * *
1797766 CGCCAATCAGCAA-ACTAATAA-TCGGAGTGTGTGGTGTGTT
1 TGCCAATAAGCAATA-AAATAACT-GGAGTGGGTGGTGTGTT
* *
1797806 TGCCAATAAGCAATAAAATAACTGGAGTGGGTTGTGTGAT
1 TGCCAATAAGCAATAAAATAACTGGAGTGGGTGGTGTGTT
1797846 TGCCAA
1 TGCCAA
1797852 CTGTGCGTTG
Statistics
Matches: 67, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
39 2 0.03
40 63 0.94
41 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (40 bp):
TGCCAATAAGCAATAAAATAACTGGAGTGGGTGGTGTGTT
Found at i:1803290 original size:11 final size:11
Alignment explanation
Indices: 1803274--1803298 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1803264 AAAATATCTC
1803274 AAATTATAATA
1 AAATTATAATA
1803285 AAATTATAATA
1 AAATTATAATA
1803296 AAA
1 AAA
1803299 AATATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTATAATA
Found at i:1805452 original size:6 final size:6
Alignment explanation
Indices: 1805437--1805487 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
1805427 TAGTGTTCAT
*
1805437 CAAGGA CAAGGG CAAGGG CAAGGG CAAGGG CAAGGG CAAGGG CAAGGG
1 CAAGGG CAAGGG CAAGGG CAAGGG CAAGGG CAAGGG CAAGGG CAAGGG
1805485 CAA
1 CAA
1805488 AAGCCTCGAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.37, C:0.18, G:0.45, T:0.00
Consensus pattern (6 bp):
CAAGGG
Found at i:1824688 original size:21 final size:21
Alignment explanation
Indices: 1824652--1824734 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 21
1824642 TTTGGTGCAG
1824652 AGGGAATCGA-TCCCCCCTTT
1 AGGGAATCGATTCCCCCCTTT
1824672 AGGGAATCGATT-CCCCCTTT
1 AGGGAATCGATTCCCCCCTTT
**
1824692 GAAGGTGAATCGATTCCCCCC-AC
1 --AGG-GAATCGATTCCCCCCTTT
*
1824715 AGGGGAATCGATACCCCCCT
1 A-GGGAATCGATTCCCCCCT
1824735 AGGGTTCTGG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
20 18 0.34
21 16 0.30
22 5 0.09
23 9 0.17
24 5 0.09
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.22
Consensus pattern (21 bp):
AGGGAATCGATTCCCCCCTTT
Found at i:1824705 original size:23 final size:20
Alignment explanation
Indices: 1824652--1824711 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
1824642 TTTGGTGCAG
*
1824652 AGGGAATCGATCCCCCCTTT
1 AGGGAATCGATTCCCCCTTT
1824672 AGGGAATCGATTCCCCCTTT
1 AGGGAATCGATTCCCCCTTT
1824692 GAAGGTGAATCGATTCCCCC
1 --AGG-GAATCGATTCCCCC
1824712 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 19 0.53
22 3 0.08
23 14 0.39
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.25
Consensus pattern (20 bp):
AGGGAATCGATTCCCCCTTT
Found at i:1824738 original size:20 final size:21
Alignment explanation
Indices: 1824653--1824738 Score: 79
Period size: 21 Copynumber: 4.1 Consensus size: 21
1824643 TTGGTGCAGA
1824653 GGGAATCGA-TCCCCCCTTTA-
1 GGGAATCGATTCCCCCC-TTAG
*
1824673 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCGATTCCCCCCTT--AG
* **
1824696 GTGAATCGATTCCCCCCACAG
1 GGGAATCGATTCCCCCCTTAG
*
1824717 GGGAATCGATACCCCCC-TAG
1 GGGAATCGATTCCCCCCTTAG
1824737 GG
1 GG
1824739 TTCTGGTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
20 15 0.28
21 23 0.43
22 1 0.02
23 15 0.28
ACGTcount: A:0.22, C:0.33, G:0.24, T:0.21
Consensus pattern (21 bp):
GGGAATCGATTCCCCCCTTAG
Found at i:1832857 original size:35 final size:34
Alignment explanation
Indices: 1832772--1832858 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
1832762 ATTTGGTATT
*
1832772 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
*
1832806 TAAATGATAATC-AAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAA-CAAAATTACAATAA--GA-ATTAAATGG
1832844 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1832859 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 2 0.04
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:1833448 original size:18 final size:18
Alignment explanation
Indices: 1833425--1833460 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1833415 GCGATGGCGA
*
1833425 CATCATATATGGCTGCGG
1 CATCATAAATGGCTGCGG
1833443 CATCATAAATGGCTGCGG
1 CATCATAAATGGCTGCGG
1833461 TGGATGCTGT
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:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (18 bp):
CATCATAAATGGCTGCGG
Found at i:1835174 original size:17 final size:18
Alignment explanation
Indices: 1835131--1835171 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1835121 GAATTATATT
1835131 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
1835148 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
1835166 ATTAAA
1 AGTAAA
1835172 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:1852073 original size:2 final size:2
Alignment explanation
Indices: 1852068--1852102 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1852058 TCTCTCTCTC
1852068 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
1852103 TAATGTGTGA
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:1852191 original size:2 final size:2
Alignment explanation
Indices: 1852180--1852209 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1852170 AGGAATGAAC
1852180 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1852210 AAATATGCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1855154 original size:28 final size:28
Alignment explanation
Indices: 1855122--1855187 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
1855112 AACCGGTGTA
*
1855122 GATTGAACTGGACTACGCAACGATTCCC
1 GATTGAACCGGACTACGCAACGATTCCC
*
1855150 GATTGAACCGGACTAGGCAACGATTCCC
1 GATTGAACCGGACTACGCAACGATTCCC
1855178 GATTGAACCG
1 GATTGAACCG
1855188 ATTGAACCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (28 bp):
GATTGAACCGGACTACGCAACGATTCCC
Found at i:1855675 original size:2 final size:2
Alignment explanation
Indices: 1855663--1855708 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
1855653 AAATGAGAAT
* * *
1855663 TA TA TA AA TA TA TA TA CA TA TA CA 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
1855705 TA TA
1 TA TA
1855709 AAGTCATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1856637 original size:24 final size:22
Alignment explanation
Indices: 1856587--1856652 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 22
1856577 TTAAACTCAT
1856587 AATATTTATATATATTAACGTAAA
1 AATATTT-T-TATATTAACGTAAA
* *
1856611 AATATTTGTTATATTAACTTATTA
1 AATATTT-TTATATTAACGTA-AA
1856635 AATATGTTTTATTATTAA
1 AATAT-TTTTA-TATTAA
1856653 TTTAATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 11 0.31
24 17 0.47
25 8 0.22
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (22 bp):
AATATTTTTATATTAACGTAAA
Found at i:1856863 original size:31 final size:31
Alignment explanation
Indices: 1856827--1856901 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
1856817 TAACCTACGA
* *
1856827 TGACCACATCTTAATTAAATTAAAACGAAAG
1 TGACCATATCTTAATTAAATAAAAACGAAAG
**
1856858 TGACCATATCTTAATTAAATAAAAATTAAAG
1 TGACCATATCTTAATTAAATAAAAACGAAAG
*
1856889 TGATCATATCTTA
1 TGACCATATCTTA
1856902 TTTTTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (31 bp):
TGACCATATCTTAATTAAATAAAAACGAAAG
Found at i:1858126 original size:2 final size:2
Alignment explanation
Indices: 1858119--1858156 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1858109 ATCTTACTTT
1858119 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
1858157 AGTTACATGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1862866 original size:30 final size:30
Alignment explanation
Indices: 1862830--1862887 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
1862820 CCAAAACTTA
*
1862830 AATAAAATTAAAGTTCTATGTAT-ACGTTTG
1 AATAAAATTAAAATTC-ATGTATAACGTTTG
1862860 AATAAAATTAAAATTCATGTATAACGTT
1 AATAAAATTAAAATTCATGTATAACGTT
1862888 ACACATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (30 bp):
AATAAAATTAAAATTCATGTATAACGTTTG
Found at i:1862914 original size:31 final size:31
Alignment explanation
Indices: 1862869--1862934 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1862859 GAATAAAATT
* * *
1862869 AAAATTCATGTATAACGTTACACATTTAATA
1 AAAATGCATATATAACATTACACATTTAATA
* *
1862900 AAAATGCATATATAACATTATATATTTAATA
1 AAAATGCATATATAACATTACACATTTAATA
1862931 AAAA
1 AAAA
1862935 AATACGTACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.35
Consensus pattern (31 bp):
AAAATGCATATATAACATTACACATTTAATA
Found at i:1867169 original size:16 final size:16
Alignment explanation
Indices: 1867148--1867180 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1867138 ATATATTTCA
*
1867148 TTTTATCTTTTATTTT
1 TTTTATCTTCTATTTT
1867164 TTTTATCTTCTATTTT
1 TTTTATCTTCTATTTT
1867180 T
1 T
1867181 ATTTTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTATCTTCTATTTT
Found at i:1867249 original size:33 final size:32
Alignment explanation
Indices: 1867176--1867251 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
1867166 TTATCTTCTA
1867176 TTTTTATTTTTGTATTGTTATTATTATTATCT
1 TTTTTATTTTTGTATTGTTATTATTATTATCT
* *
1867208 TCTTTATTTTATGTATT-TTA-T-TTATATATAT
1 TTTTTATTTT-TGTATTGTTATTATTAT-TATCT
*
1867239 TTTTTATATTTGT
1 TTTTTATTTTTGT
1867252 TTTTGTGCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
30 7 0.18
31 13 0.34
32 12 0.32
33 6 0.16
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (32 bp):
TTTTTATTTTTGTATTGTTATTATTATTATCT
Found at i:1872911 original size:21 final size:21
Alignment explanation
Indices: 1872887--1872928 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1872877 AGTTTATTTT
1872887 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
1872908 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
1872929 AACTTGAAGC
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:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:1872981 original size:33 final size:33
Alignment explanation
Indices: 1872923--1873021 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
1872913 TTTGTTTCAA
*
1872923 TTATCGAACTT-GAAGCTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1872955 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
1872988 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1873021 T
1 T
1873022 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 11 0.18
33 51 0.82
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.44
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1874265 original size:15 final size:17
Alignment explanation
Indices: 1874239--1874270 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1874229 CTATGAGAAA
1874239 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1874255 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1874271 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1875547 original size:13 final size:13
Alignment explanation
Indices: 1875529--1875554 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1875519 ATTGGGAAAA
1875529 AAGCCCAGTTGAT
1 AAGCCCAGTTGAT
1875542 AAGCCCAGTTGAT
1 AAGCCCAGTTGAT
1875555 GTCATTTTAG
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:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
AAGCCCAGTTGAT
Found at i:1878281 original size:14 final size:14
Alignment explanation
Indices: 1878264--1878291 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1878254 ATCATAATAA
1878264 AATTATATAACTAT
1 AATTATATAACTAT
1878278 AATTATATAACTAT
1 AATTATATAACTAT
1878292 TATTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:1878586 original size:11 final size:10
Alignment explanation
Indices: 1878558--1878593 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1878548 AACAAAAATC
1878558 CCGGTTTTTT
1 CCGGTTTTTT
1878568 CCGGTTTTTT
1 CCGGTTTTTT
*
1878578 CCGATTTTTT
1 CCGGTTTTTT
1878588 GCCGGT
1 -CCGGT
1878594 CCGGTTCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 19 0.83
11 4 0.17
ACGTcount: A:0.03, C:0.22, G:0.22, T:0.53
Consensus pattern (10 bp):
CCGGTTTTTT
Found at i:1879303 original size:20 final size:20
Alignment explanation
Indices: 1879275--1879314 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1879265 GAACCGGCAG
*
1879275 AAAACCGGAAAAAACTGGGA
1 AAAACCGGAAAAAACCGGGA
*
1879295 AAAATCGGAAAAAACCGGGA
1 AAAACCGGAAAAAACCGGGA
1879315 TTTTTGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.15, G:0.25, T:0.05
Consensus pattern (20 bp):
AAAACCGGAAAAAACCGGGA
Found at i:1879599 original size:14 final size:14
Alignment explanation
Indices: 1879580--1879607 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1879570 AAGTGAAAGA
1879580 ATAGTTATATAATT
1 ATAGTTATATAATT
1879594 ATAGTTATATAATT
1 ATAGTTATATAATT
1879608 TTGTTATGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:1880277 original size:12 final size:13
Alignment explanation
Indices: 1880260--1880288 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1880250 TTCCAACAAG
1880260 AATCCCCAAA-CC
1 AATCCCCAAAGCC
1880272 AATCCCCAAAGCC
1 AATCCCCAAAGCC
1880285 AATC
1 AATC
1880289 GTCTTTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.41, C:0.45, G:0.03, T:0.10
Consensus pattern (13 bp):
AATCCCCAAAGCC
Found at i:1885158 original size:2 final size:2
Alignment explanation
Indices: 1885153--1885183 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1885143 TACTGTTAAG
1885153 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
1885184 AAGTCTTGAT
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:1890155 original size:39 final size:39
Alignment explanation
Indices: 1890101--1890176 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
1890091 CTGATGGTGT
1890101 GATTTTATCTGGCCCCGCACAACCTCGACCAAAAAGGGC
1 GATTTTATCTGGCCCCGCACAACCTCGACCAAAAAGGGC
1890140 GATTTTATCTGGCCCCGCACAACCTCGACCAAAAAGG
1 GATTTTATCTGGCCCCGCACAACCTCGACCAAAAAGG
1890177 CATGACATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.18
Consensus pattern (39 bp):
GATTTTATCTGGCCCCGCACAACCTCGACCAAAAAGGGC
Found at i:1892265 original size:18 final size:19
Alignment explanation
Indices: 1892244--1892279 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1892234 TTTTCAAAAA
1892244 TTTTATATATTTT-TATTT
1 TTTTATATATTTTATATTT
*
1892262 TTTTTTATATTTTATATT
1 TTTTATATATTTTATATT
1892280 AAAAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATATATTTTATATTT
Found at i:1897390 original size:19 final size:18
Alignment explanation
Indices: 1897366--1897405 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1897356 AAATATATAA
*
1897366 ATAATAAAGATTAAATATG
1 ATAATAAAGATCAAAT-TG
*
1897385 ATAATAATGATCAAATTG
1 ATAATAAAGATCAAATTG
1897403 ATA
1 ATA
1897406 GAATATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (18 bp):
ATAATAAAGATCAAATTG
Found at i:1902131 original size:17 final size:16
Alignment explanation
Indices: 1902092--1902150 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
1902082 TTATTTTATT
*
1902092 ATATTTAA--TATTTT
1 ATATTTAATTTATTTA
*
1902106 ATTTTTAATTTATTTA
1 ATATTTAATTTATTTA
*
1902122 AGTATTTAATTTTTTTA
1 A-TATTTAATTTATTTA
*
1902139 ATATTTTATTTA
1 ATATTTAATTTA
1902151 ATTTTTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 7 0.19
16 15 0.42
17 14 0.39
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
ATATTTAATTTATTTA
Found at i:1902133 original size:24 final size:23
Alignment explanation
Indices: 1902085--1902156 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 23
1902075 TTAAGGTTTA
*
1902085 TTTTATTATATTTAATATTTTAT
1 TTTTATTATATTTAATATTTAAT
1902108 TTTTAATT-TATTTAAGTATTTAAT
1 TTTT-ATTATATTTAA-TATTTAAT
1902132 TTTT-TTAATATTT--TATTTAAT
1 TTTTATT-ATATTTAATATTTAAT
1902153 TTTT
1 TTTT
1902157 TTTACAGATA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
21 12 0.27
22 2 0.05
23 11 0.25
24 19 0.43
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (23 bp):
TTTTATTATATTTAATATTTAAT
Found at i:1903931 original size:34 final size:34
Alignment explanation
Indices: 1903893--1903957 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
1903883 CCCGATGCCG
* * **
1903893 CCGCCGCCACTGTCACCTAGTTTTATGACCCCCA
1 CCGCCACCACCGTCACAGAGTTTTATGACCCCCA
1903927 CCGCCACCACCGTCACAGAGTTTTATGACCC
1 CCGCCACCACCGTCACAGAGTTTTATGACCC
1903958 TTCCTGGAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.20, C:0.43, G:0.15, T:0.22
Consensus pattern (34 bp):
CCGCCACCACCGTCACAGAGTTTTATGACCCCCA
Found at i:1906814 original size:25 final size:25
Alignment explanation
Indices: 1906759--1906815 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
1906749 AATATATGTA
*
1906759 TAAACAATAATCTGCTACAGTACCG
1 TAAACAATAACCTGCTACAGTACCG
* * *
1906784 TGAACAGTAACCTGCTATAGTACCCG
1 TAAACAATAACCTGCTACAGTA-CCG
1906810 -AAACAA
1 TAAACAA
1906816 ACAAAACAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 22 0.88
26 3 0.12
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.21
Consensus pattern (25 bp):
TAAACAATAACCTGCTACAGTACCG
Found at i:1907337 original size:22 final size:22
Alignment explanation
Indices: 1907306--1907377 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
1907296 CTGAGTGGCA
1907306 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
1907329 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
*
1907351 TATG-AGTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
1907372 TATGAA
1 TATGAA
1907378 ACCCTCGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.44
22 22 0.49
23 3 0.07
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:1907362 original size:21 final size:21
Alignment explanation
Indices: 1907314--1907376 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
1907304 CATATGAAAT
* *
1907314 TTGTCCCGAAGGACCTGTGAAT
1 TTGTCCCGAAGGACCTATG-AG
1907336 TTGTCCCGAAGGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
1907357 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
1907377 AACCCTCGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 21 0.54
22 18 0.46
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:1907974 original size:64 final size:63
Alignment explanation
Indices: 1907841--1907997 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
1907831 TAATGAAGGT
* * * ** *
1907841 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
1907905 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
1907967 G
63 G
*
1907968 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
1907998 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:1913769 original size:25 final size:25
Alignment explanation
Indices: 1913714--1913770 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
1913704 AATATATGTA
*
1913714 TAAACAATAATCTGCTACAGTACCG
1 TAAACAATAACCTGCTACAGTACCG
* * *
1913739 TGAACAGTAACCTGCTATAGTACCCG
1 TAAACAATAACCTGCTACAGTA-CCG
1913765 -AAACAA
1 TAAACAA
1913771 ACAAAACAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 22 0.88
26 3 0.12
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.21
Consensus pattern (25 bp):
TAAACAATAACCTGCTACAGTACCG
Found at i:1914292 original size:22 final size:22
Alignment explanation
Indices: 1914261--1914332 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
1914251 CTGAGTGGCA
1914261 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
1914284 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
*
1914306 TATG-AGTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
1914327 TATGAA
1 TATGAA
1914333 ACCCTCGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.44
22 22 0.49
23 3 0.07
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:1914317 original size:21 final size:21
Alignment explanation
Indices: 1914269--1914331 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
1914259 CATATGAAAT
* *
1914269 TTGTCCCGAAGGACCTGTGAAT
1 TTGTCCCGAAGGACCTATG-AG
1914291 TTGTCCCGAAGGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
1914312 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
1914332 AACCCTCGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 21 0.54
22 18 0.46
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:1914929 original size:64 final size:63
Alignment explanation
Indices: 1914796--1914952 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
1914786 TAATGAAGGT
* * * ** *
1914796 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
1914860 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
1914922 G
63 G
*
1914923 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
1914953 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:1919168 original size:2 final size:2
Alignment explanation
Indices: 1919163--1919212 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1919153 AGTTAATAAG
1919163 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
1919205 TA TA TA TA
1 TA TA TA TA
1919213 ATACTTTAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1919337 original size:21 final size:21
Alignment explanation
Indices: 1919297--1919338 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1919287 CTAGTGAATA
1919297 TTTTTTAAACTTTTAAATTTAG
1 TTTTTTAAAC-TTTAAATTTAG
1919319 TTTTTTAAA-TTTAATATTTA
1 TTTTTTAAACTTTAA-ATTTA
1919339 CAAATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 5 0.26
22 9 0.47
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTTTAAACTTTAAATTTAG
Found at i:1919963 original size:32 final size:32
Alignment explanation
Indices: 1919904--1919996 Score: 87
Period size: 32 Copynumber: 2.9 Consensus size: 32
1919894 AACTGTTAAT
* * * *
1919904 GTGACACATAATACATTATCATTTTAAATGAC
1 GTGACATATATTACATTATTATATTAAATGAC
* * *
1919936 GTGACATATATTACATTTTTATATTAAATTAT
1 GTGACATATATTACATTATTATATTAAATGAC
* * * *
1919968 ATGACATATCTCATATTATTATATTAAAT
1 GTGACATATATTACATTATTATATTAAAT
1919997 TATCACATTA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (32 bp):
GTGACATATATTACATTATTATATTAAATGAC
Found at i:1929081 original size:15 final size:15
Alignment explanation
Indices: 1929061--1929133 Score: 64
Period size: 15 Copynumber: 5.1 Consensus size: 15
1929051 ATTATCGTTG
1929061 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1929076 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
* **
1929091 -A--TAT-TATCGAT
1 AATTTTTATATAAAT
1929102 GAATTTTTATATAAAT
1 -AATTTTTATATAAAT
*
1929118 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1929133 A
1 A
1929134 TTTAGAATTT
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
11 4 0.09
12 2 0.05
13 1 0.02
14 1 0.02
15 31 0.70
16 5 0.11
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1929092 original size:42 final size:42
Alignment explanation
Indices: 1929046--1929134 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
1929036 ATAATAAAAT
*
1929046 AATATATTATCGTTGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1929088 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1929130 AATAT
1 AATAT
1929135 TTAGAATTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (42 bp):
AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
Found at i:1935609 original size:29 final size:29
Alignment explanation
Indices: 1935575--1935631 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1935565 TCACCTATAC
1935575 CCAACTATACAATTCCAGATAATCTTGTG
1 CCAACTATACAATTCCAGATAATCTTGTG
* *
1935604 CCAACTCTACAATTCCGGATAATCTTGT
1 CCAACTATACAATTCCAGATAATCTTGT
1935632 AAACGTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (29 bp):
CCAACTATACAATTCCAGATAATCTTGTG
Found at i:1938748 original size:23 final size:23
Alignment explanation
Indices: 1938716--1938780 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
1938706 CCCAAATTCC
1938716 AAAA-CTTAAATCCTTAATCCCT
1 AAAATCTTAAATCCTTAATCCCT
** *
1938738 AAAATCTTAAATATTTGATCCCT
1 AAAATCTTAAATCCTTAATCCCT
*
1938761 -ATATCTTAATATCCCTTAAT
1 AAAATCTTAA-AT-CCTTAAT
1938781 ATAAAAATAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
22 12 0.36
23 17 0.52
24 4 0.12
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAATCTTAAATCCTTAATCCCT
Found at i:1950503 original size:17 final size:16
Alignment explanation
Indices: 1950469--1950503 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1950459 TTACTATTCA
*
1950469 CGTGAATAGTGCATTT
1 CGTGAATAGTGAATTT
1950485 CGTGAATAGTGAAATTT
1 CGTGAATAGTG-AATTT
1950502 CG
1 CG
1950504 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (16 bp):
CGTGAATAGTGAATTT
Found at i:1955949 original size:18 final size:20
Alignment explanation
Indices: 1955914--1955950 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1955904 AAAAAAATAA
*
1955914 AAATATATATTATTAAAAAC
1 AAATATATATTATAAAAAAC
1955934 AAATATAT-TTA-AAAAAA
1 AAATATATATTATAAAAAA
1955951 AATTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 3 0.19
20 8 0.50
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATATATATTATAAAAAAC
Found at i:1959560 original size:12 final size:12
Alignment explanation
Indices: 1959542--1959575 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1959532 AAAATATGAT
1959542 ATGAACAGTATC
1 ATGAACAGTATC
* *
1959554 GTGAACAATATC
1 ATGAACAGTATC
1959566 ATGAACAGTA
1 ATGAACAGTA
1959576 AAAAATTCGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.24
Consensus pattern (12 bp):
ATGAACAGTATC
Found at i:1960030 original size:17 final size:17
Alignment explanation
Indices: 1959997--1960038 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1959987 GGGATTTTGG
1959997 TAAT-AAAATATTAAAA
1 TAATAAAAATATTAAAA
1960013 TAATAAAAATGATT-AAA
1 TAATAAAAAT-ATTAAAA
1960030 TAAGTAAAA
1 TAA-TAAAA
1960039 GCAATTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
18 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (17 bp):
TAATAAAAATATTAAAA
Found at i:1965321 original size:17 final size:18
Alignment explanation
Indices: 1965292--1965329 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1965282 TTTTGGTAAG
1965292 AAAATATTAAAATAA-TA
1 AAAATATTAAAATAAGTA
1965309 AAAATGATT-AAATAAGTA
1 AAAAT-ATTAAAATAAGTA
1965327 AAA
1 AAA
1965330 GCAATTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAATATTAAAATAAGTA
Found at i:1966006 original size:40 final size:37
Alignment explanation
Indices: 1965962--1966073 Score: 146
Period size: 34 Copynumber: 3.1 Consensus size: 37
1965952 CATACACAGG
*
1965962 TATGATTGATATGTATTATGCATGTGCATGCAAAGCCTGC
1 TATGATTGATAAGTATTATG-A--TGCATGCAAAGCCTGC
1966002 TATGATTGATAAGTA-T-T-ATGCATGCAAAGCCTGC
1 TATGATTGATAAGTATTATGATGCATGCAAAGCCTGC
1966036 TATGATTGATAAGTATTATG-T--ATGCAAAGCCTGC
1 TATGATTGATAAGTATTATGATGCATGCAAAGCCTGC
1966070 TATG
1 TATG
1966074 TCTTTACATA
Statistics
Matches: 68, Mismatches: 1, Indels: 12
0.84 0.01 0.15
Matches are distributed among these distances:
34 48 0.71
35 1 0.01
36 3 0.04
38 1 0.01
39 1 0.01
40 14 0.21
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.35
Consensus pattern (37 bp):
TATGATTGATAAGTATTATGATGCATGCAAAGCCTGC
Found at i:1966024 original size:34 final size:34
Alignment explanation
Indices: 1965986--1966073 Score: 167
Period size: 34 Copynumber: 2.6 Consensus size: 34
1965976 ATTATGCATG
1965986 TGCATGCAAAGCCTGCTATGATTGATAAGTATTA
1 TGCATGCAAAGCCTGCTATGATTGATAAGTATTA
1966020 TGCATGCAAAGCCTGCTATGATTGATAAGTATTA
1 TGCATGCAAAGCCTGCTATGATTGATAAGTATTA
*
1966054 TGTATGCAAAGCCTGCTATG
1 TGCATGCAAAGCCTGCTATG
1966074 TCTTTACATA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (34 bp):
TGCATGCAAAGCCTGCTATGATTGATAAGTATTA
Found at i:1968332 original size:11 final size:10
Alignment explanation
Indices: 1968309--1968341 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1968299 TAAGATAGTT
1968309 AAATAAATAA
1 AAATAAATAA
*
1968319 AAATAAATTA
1 AAATAAATAA
1968329 AAA-AAATAA
1 AAATAAATAA
1968338 AAAT
1 AAAT
1968342 TTACATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAATAAATAA
Found at i:1970846 original size:31 final size:33
Alignment explanation
Indices: 1970798--1970871 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 33
1970788 TTTAAATAGT
*
1970798 TATTATATTTTATATT-AAT-ATATTTATGTAAA
1 TATTAT-TTTTATATTAAATAATATTTATATAAA
* *
1970830 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTATATT-AAATAATATTTATATAAA
1970864 TATTATTT
1 TATTATTT
1970872 ATTAAGAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 8 0.22
32 6 0.17
33 3 0.08
34 19 0.53
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (33 bp):
TATTATTTTTATATTAAATAATATTTATATAAA
Found at i:1970868 original size:34 final size:31
Alignment explanation
Indices: 1970788--1970871 Score: 87
Period size: 34 Copynumber: 2.6 Consensus size: 31
1970778 TTAGTATTTT
* *
1970788 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTATATTAATATA
* * *
1970820 TTTATGTAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTATATT--AAT-ATA
1970854 TTTATATAATTATTATTT
1 TTTATATAATTATTATTT
1970872 ATTAAGAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
31 8 0.19
32 12 0.29
33 3 0.07
34 19 0.45
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTATATTAATATA
Found at i:1971039 original size:17 final size:17
Alignment explanation
Indices: 1971017--1971070 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1971007 AATGTTAATA
1971017 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
1971034 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
1971051 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
1971068 TTT
1 TTT
1971071 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:1972663 original size:21 final size:21
Alignment explanation
Indices: 1972652--1972745 Score: 127
Period size: 21 Copynumber: 4.5 Consensus size: 21
1972642 TATGCCATCT
1972652 CCGCAGGGTTATATTCCGAGC
1 CCGCAGGGTTATATTCCGAGC
1972673 CCGCAGGGTTATATTCCGAGC
1 CCGCAGGGTTATATTCCGAGC
* *
1972694 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTATATTCCGAGC
* * *
1972715 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTATATTCCGAGC
1972736 CCGCAGGGTT
1 CCGCAGGGTT
1972746 TTATACCATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 2 0.03
21 64 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTATATTCCGAGC
Found at i:1972685 original size:42 final size:42
Alignment explanation
Indices: 1972628--1972745 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
1972618 TCATATGCCA
* * * *
1972628 AGCCCACCAGTTTATATGCC-ATCTCCGCAGGGTTATATTCCG
1 AGCCCGCCAGGTTATATGCCGAGC-CCGCAGGGTTACATTCCG
* *
1972670 AGCCCG-CAGGGTTATATTCCGAGCCCGCAGGGTTACATTCCT
1 AGCCCGCCA-GGTTATATGCCGAGCCCGCAGGGTTACATTCCG
* *
1972712 AGCCCGCCAGGTTACATGCCTAGCCCGCAGGGTT
1 AGCCCGCCAGGTTATATGCCGAGCCCGCAGGGTT
1972746 TTATACCATA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 2 0.03
42 58 0.91
43 4 0.06
ACGTcount: A:0.19, C:0.32, G:0.25, T:0.24
Consensus pattern (42 bp):
AGCCCGCCAGGTTATATGCCGAGCCCGCAGGGTTACATTCCG
Found at i:1973317 original size:34 final size:34
Alignment explanation
Indices: 1973267--1973364 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 34
1973257 AAATGTTTTT
*
1973267 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
1973301 AAAATAAAAATAATATTATTCGAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
1973335 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
1973365 CATTAAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:1973992 original size:128 final size:128
Alignment explanation
Indices: 1973764--1974266 Score: 925
Period size: 128 Copynumber: 3.9 Consensus size: 128
1973754 TTACCTGATT
*
1973764 TACTGATATATCTAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1973829 TGACAAAATAATGGAAGGCGCGCCCCCAGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
1973892 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATAATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1973957 TGACAAAATAATGGAAGGCGCGCTCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1974020 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
1974085 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTAAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1974148 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1974213 TGACAAAATAATGGAAGGCGCCCCCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACAAAATAATGGAAGGCG--CGCCCCCGGGAACGCGCCTTCATGTGAATAGT
1974267 ACTCCGATTA
Statistics
Matches: 363, Mismatches: 10, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
128 333 0.92
130 30 0.08
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:1974350 original size:8 final size:8
Alignment explanation
Indices: 1974337--1974377 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1974327 TCACAAGCTT
1974337 TCAAATTC
1 TCAAATTC
1974345 TCAAATTC
1 TCAAATTC
* *
1974353 CCAAACTC
1 TCAAATTC
1974361 T-AAATTC
1 TCAAATTC
1974368 TCAAATTC
1 TCAAATTC
1974376 TC
1 TC
1974378 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:1980242 original size:31 final size:31
Alignment explanation
Indices: 1980204--1980278 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
1980194 AGTAAAAAAA
** * *
1980204 AAGTTTTGGTCACTTATTTTATTGTTTTATT
1 AAGTTTTGGTCACTTACGTTATCGATTTATT
*
1980235 AAGTTTTGGTCACTTGCGTTATCGATTTATT
1 AAGTTTTGGTCACTTACGTTATCGATTTATT
1980266 AAGTTTTGGTCAC
1 AAGTTTTGGTCAC
1980279 GTTGAATATC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (31 bp):
AAGTTTTGGTCACTTACGTTATCGATTTATT
Found at i:1986334 original size:10 final size:10
Alignment explanation
Indices: 1986319--1986346 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1986309 GTTTTGATTT
1986319 TTAAGCTTCC
1 TTAAGCTTCC
1986329 TTAAGCTTCC
1 TTAAGCTTCC
1986339 TTAAGCTT
1 TTAAGCTT
1986347 AGTTATTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.43
Consensus pattern (10 bp):
TTAAGCTTCC
Found at i:1991872 original size:31 final size:31
Alignment explanation
Indices: 1991827--1991896 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1991817 ACATAAGTTG
* *
1991827 TGGTC-CTTATGTTATCATTTTATTAAGATT
1 TGGTCACTTACGTTATCATGTTATTAAGATT
* *
1991857 TGGTCACTTACGTTATCGTGTTATTAAGTTT
1 TGGTCACTTACGTTATCATGTTATTAAGATT
*
1991888 TAGTCACTT
1 TGGTCACTT
1991897 GGACGTTGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 5 0.15
31 29 0.85
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (31 bp):
TGGTCACTTACGTTATCATGTTATTAAGATT
Found at i:1992900 original size:18 final size:18
Alignment explanation
Indices: 1992877--1992919 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1992867 GTTTGAGATA
*
1992877 ACCTAAAGAAAATAAAAT
1 ACCTAAAGAAAATAAAAC
1992895 ACCTAAAGAAAATAAAAC
1 ACCTAAAGAAAATAAAAC
1992913 ACCTAAA
1 ACCTAAA
1992920 TATAATCCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.65, C:0.16, G:0.05, T:0.14
Consensus pattern (18 bp):
ACCTAAAGAAAATAAAAC
Found at i:1993791 original size:31 final size:31
Alignment explanation
Indices: 1993756--1993832 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 31
1993746 TTCAACATCC
* *
1993756 AAGTGACCAAAACTTAATAAAACGATAATGT
1 AAGTGACCAAAACTTAATAAAACAATAACGT
*
1993787 AAGTGA-TAAAACTTAATAAAACAATAACGT
1 AAGTGACCAAAACTTAATAAAACAATAACGT
*
1993817 AAGGGACCAAAACTTA
1 AAGTGACCAAAACTTA
1993833 TGTTTTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 26 0.65
31 14 0.35
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACGT
Found at i:2001702 original size:31 final size:31
Alignment explanation
Indices: 2001664--2001738 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
2001654 TCGAAAAATA
*
2001664 TAATATATGATCATATTTATTTTTATTTAAT
1 TAATATATGATCATATTTACTTTTATTTAAT
* *
2001695 TAATATATGATTATTTTTACTTTTATTTAAT
1 TAATATATGATCATATTTACTTTTATTTAAT
* *
2001726 TAAGATGTGATCA
1 TAATATATGATCA
2001739 CTATCGGTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.55
Consensus pattern (31 bp):
TAATATATGATCATATTTACTTTTATTTAAT
Found at i:2010167 original size:26 final size:28
Alignment explanation
Indices: 2010122--2010186 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
2010112 ACTTTTTATG
* *
2010122 TTTAATTGATTTTAAGTTTAAATATGTT
1 TTTAATTAATTTTAAGTTTAAATATCTT
*
2010150 TTTAATTAATTTT-A-TTTAACTATCTT
1 TTTAATTAATTTTAAGTTTAAATATCTT
2010176 TTTAATATAAT
1 TTTAAT-TAAT
2010187 GTCAGTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.48
27 5 0.15
28 12 0.36
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (28 bp):
TTTAATTAATTTTAAGTTTAAATATCTT
Found at i:2015756 original size:14 final size:15
Alignment explanation
Indices: 2015734--2015780 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
2015724 TATAAGGTAA
*
2015734 TTTTGTTATAATT-T
1 TTTTATTATAATTAT
*
2015748 TTTTATTATACTTAT
1 TTTTATTATAATTAT
*
2015763 TGTTTATTATGATTAT
1 T-TTTATTATAATTAT
2015779 TT
1 TT
2015781 GAAAAAATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.41
15 3 0.11
16 13 0.48
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:2018229 original size:3 final size:3
Alignment explanation
Indices: 2018215--2018252 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2018205 ATTATCACCA
* *
2018215 TCG TCA TCG TCG TCG TCA TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
2018253 CTGAGTAGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.05, C:0.34, G:0.26, T:0.34
Consensus pattern (3 bp):
TCG
Done.