Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008283.1 Hibiscus syriacus cultivar Beakdansim tig00110945_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: 2862730
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 14
Found at i:1708911 original size:2 final size:2
Alignment explanation
Indices: 1708904--1708950 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1708894 GGAGGAGTTT
1708904 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1708946 TC TC T
1 TC TC T
1708951 GATCGATGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1709522 original size:8 final size:9
Alignment explanation
Indices: 1709501--1709535 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1709491 TTTCATTTGG
1709501 TTTTTTATA
1 TTTTTTATA
1709510 TTTTTTATA
1 TTTTTTATA
*
1709519 TTTTTTTTA
1 TTTTTTATA
*
1709528 TTATTTAT
1 TTTTTTAT
1709536 TATTATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTATA
Found at i:1709524 original size:18 final size:18
Alignment explanation
Indices: 1709501--1709554 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
1709491 TTTCATTTGG
*
1709501 TTTTTTATATTTTTTATA
1 TTTTTTATATTATTTATA
*
1709519 TTTTTTTTATTATTTATTA
1 TTTTTTATATTATTTA-TA
1709538 TTATTATTATTATTATT
1 TT-TT-TTA-TATTATT
1709555 ATTTATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 14 0.48
19 4 0.14
20 2 0.07
21 2 0.07
22 7 0.24
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTATATTATTTATA
Found at i:1709531 original size:3 final size:3
Alignment explanation
Indices: 1709525--1709565 Score: 64
Period size: 3 Copynumber: 13.0 Consensus size: 3
1709515 TATATTTTTT
1709525 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
1709566 ATTACAAGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1709532 original size:12 final size:12
Alignment explanation
Indices: 1709501--1709558 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
1709491 TTTCATTTGG
*
1709501 TTTT-TTATATT
1 TTTTATTATTTT
1709512 TTTTA-TATTTT
1 TTTTATTATTTT
1709523 TTTTATTATTTAT
1 TTTTATTATTT-T
* *
1709536 TATTATTATTAT
1 TTTTATTATTTT
*
1709548 TATTATTATTT
1 TTTTATTATTT
1709559 ATTATTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
11 14 0.35
12 16 0.40
13 10 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTATTTT
Found at i:1711012 original size:22 final size:22
Alignment explanation
Indices: 1710979--1711021 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1710969 TTATTATATT
* *
1710979 AAAAATTATTTTTATTTTTTAA
1 AAAAATTATTTTAATTATTTAA
1711001 AAAAATGT-TTTTAATTATTTA
1 AAAAAT-TATTTTAATTATTTA
1711022 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
AAAAATTATTTTAATTATTTAA
Found at i:1711659 original size:26 final size:27
Alignment explanation
Indices: 1711607--1711664 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
1711597 TAATTCTTTC
*
1711607 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
1711635 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
1711661 TTTT
1 TTTT
1711665 ATTTTCAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:1717770 original size:114 final size:114
Alignment explanation
Indices: 1717567--1717792 Score: 362
Period size: 114 Copynumber: 2.0 Consensus size: 114
1717557 AAGTGCCATG
* * * *
1717567 TGCTCATAGTAGAAATAATAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATGTGATC
1 TGCTCATAGTAGAAATAAAAAGACCCAATAGCATATTCTGGAAGTATTCTTTGAGTTATCTGATC
* * *
1717632 TGGTTTGGTATAAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
66 TGGTTCGGTAGAAACCCCAAAACCAATCATTAGAATTGAAAGATGAATT
1717681 TGCTCATAGTAGAAATAAAAAGACCCAATAGCATATTCTGGAAGTATTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAAAAGACCCAATAGCATATTCTGGAAGTATTCTTTGAGTTATCTGATC
* * *
1717746 TGGTTCGGTAGGAACCCTAGAACCAATCATTAGAATTGAAAGATGAA
66 TGGTTCGGTAGAAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
1717793 CTGCATGATC
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAAAAGACCCAATAGCATATTCTGGAAGTATTCTTTGAGTTATCTGATC
TGGTTCGGTAGAAACCCCAAAACCAATCATTAGAATTGAAAGATGAATT
Found at i:1720351 original size:22 final size:22
Alignment explanation
Indices: 1720323--1720365 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1720313 TACACTCTTC
*
1720323 AAAGATGATAGATTCCCTTTTT
1 AAAGATGACAGATTCCCTTTTT
*
1720345 AAAGATGACAGATTCTCTTTT
1 AAAGATGACAGATTCCCTTTT
1720366 ATCCAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (22 bp):
AAAGATGACAGATTCCCTTTTT
Found at i:1721087 original size:113 final size:111
Alignment explanation
Indices: 1720751--1721087 Score: 455
Period size: 113 Copynumber: 3.0 Consensus size: 111
1720741 TCCATCACAT
* * *
1720751 GATGGATCAGCTTTTCTAGAAAAAGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAGAAG
1 GATGGATCAGCTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* * *
1720816 TTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT-TATCATTC
65 TTCATAATGAGAAGAACTTGTTCAA-CTTTTG-CTGAATTCTATCACTC
* * * *
1720864 GATGGATCAGCATTGCCAGGGCAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAG
1 GATGGATCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
*
1720929 TTTATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTC-ATCACTC
65 TTCATAATGAGAAGAACTTGTTCAAC-TTTTGCT-GAATTCTATCACTC
* *
1720977 GATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAG
1 GATGGATCAGCTTTTCCAGAGA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1721042 TTCATAATGAGAAGAACTTGTTCAATCTTTTGCATG-ATTCTATCAC
65 TTCATAATGAGAAGAACTTGTTCAA-CTTTTGC-TGAATTCTATCAC
1721088 AGAAAGAGAT
Statistics
Matches: 198, Mismatches: 18, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
112 7 0.04
113 189 0.95
114 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (111 bp):
GATGGATCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAACTTTTGCTGAATTCTATCACTC
Found at i:1721350 original size:3 final size:3
Alignment explanation
Indices: 1721342--1721406 Score: 103
Period size: 3 Copynumber: 21.0 Consensus size: 3
1721332 TTTTTTATAT
1721342 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
*
1721388 ATA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
1721407 ATTACAAGCC
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 52 0.90
4 6 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1721379 original size:28 final size:28
Alignment explanation
Indices: 1721339--1721406 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
1721329 TGGTTTTTTA
*
1721339 TATTTATTATTATTATTATTATTATTAT
1 TATTTATTATTATTATTATTAATATTAT
1721367 TATTTATTATTATTATTATTAATATTAT
1 TATTTATTATTATTATTATTAATATTAT
1721395 TATTTATTATTA
1 TATTTATTATTA
1721407 ATTACAAGCC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
TATTTATTATTATTATTATTAATATTAT
Found at i:1722690 original size:14 final size:15
Alignment explanation
Indices: 1722652--1722706 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
1722642 AAATAAGGGC
*
1722652 TATAAATTTTAATAT
1 TATATATTTTAATAT
* *
1722667 TTTATATTTTAATCT
1 TATATATTTTAATAT
*
1722682 TAT-TATTTTAATTT
1 TATATATTTTAATAT
*
1722696 TATATGTTTTA
1 TATATATTTTA
1722707 GTCACCAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 13 0.39
15 20 0.61
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (15 bp):
TATATATTTTAATAT
Found at i:1722836 original size:17 final size:16
Alignment explanation
Indices: 1722804--1722849 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
1722794 ATATGTTTAA
*
1722804 ATTATTATTTT-CATT
1 ATTATTATTTTAAATT
1722819 ATTATTATATTTAAATT
1 ATTATTAT-TTTAAATT
*
1722836 ATTTTTATTTTAAA
1 ATTATTATTTTAAA
1722850 AAAAATGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 8 0.30
16 9 0.33
17 10 0.37
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTATTATTTTAAATT
Found at i:1731653 original size:92 final size:92
Alignment explanation
Indices: 1731496--1731681 Score: 345
Period size: 92 Copynumber: 2.0 Consensus size: 92
1731486 AAAATTCGAT
* * *
1731496 AATTTTGGAGCTTTGAATGAGAAATTGATCTAAACGTTGTTGAGGAAAGTGTGGAACCAAAATCT
1 AATTTTAGAGCTTTGAATGAGAAATTGATCTAAACATTGTTGAAGAAAGTGTGGAACCAAAATCT
1731561 GTTTTGGAATTAAAAGTATAAATATTA
66 GTTTTGGAATTAAAAGTATAAATATTA
1731588 AATTTTAGAGCTTTGAATGAGAAATTGATCTAAACATTGTTGAAGAAAGTGTGGAACCAAAATCT
1 AATTTTAGAGCTTTGAATGAGAAATTGATCTAAACATTGTTGAAGAAAGTGTGGAACCAAAATCT
1731653 GTTTTGGAATTAAAAGTATAAATATTA
66 GTTTTGGAATTAAAAGTATAAATATTA
1731680 AA
1 AA
1731682 AGGTTTCTTT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.33
Consensus pattern (92 bp):
AATTTTAGAGCTTTGAATGAGAAATTGATCTAAACATTGTTGAAGAAAGTGTGGAACCAAAATCT
GTTTTGGAATTAAAAGTATAAATATTA
Found at i:1732631 original size:14 final size:14
Alignment explanation
Indices: 1732609--1732647 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1732599 ATACACAAAT
1732609 GCATGGTGATTAAC
1 GCATGGTGATTAAC
* * *
1732623 GCATTGTGACTAGC
1 GCATGGTGATTAAC
1732637 GCATGGTGATT
1 GCATGGTGATT
1732648 TGCCTTTTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (14 bp):
GCATGGTGATTAAC
Found at i:1733092 original size:45 final size:45
Alignment explanation
Indices: 1733041--1733188 Score: 190
Period size: 45 Copynumber: 3.3 Consensus size: 45
1733031 TAATTCAAGG
1733041 CTTTTGATTATTGGGTTGTC-AAAAGTAAAATCAAAGGATCAGTTC
1 CTTTTGATTATTGGGTTG-CAAAAAGTAAAATCAAAGGATCAGTTC
* * *
1733086 CTTTTGATTATTGTGTTGCAAAAACTAAAATCAAAGGATTAGTTC
1 CTTTTGATTATTGGGTTGCAAAAAGTAAAATCAAAGGATCAGTTC
* * * * * *
1733131 GTTTCGATTATTGGATTGCGAAAATTAAAATCAAAGGATTAGTTC
1 CTTTTGATTATTGGGTTGCAAAAAGTAAAATCAAAGGATCAGTTC
*
1733176 CTTGTGATTATTG
1 CTTTTGATTATTG
1733189 TGTCGGTAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
44 1 0.01
45 89 0.99
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (45 bp):
CTTTTGATTATTGGGTTGCAAAAAGTAAAATCAAAGGATCAGTTC
Found at i:1733469 original size:54 final size:53
Alignment explanation
Indices: 1733344--1733469 Score: 166
Period size: 54 Copynumber: 2.3 Consensus size: 53
1733334 AATCTTGCGT
*
1733344 TGATTCTAACTTTGTAAAGGAAATAAATTCAATTATTTCCTTGAGAATCTTAAA
1 TGATTCTAACTTTGT-AAGGAAATAAATTCAATTATTTACTTGAGAATCTTAAA
* * *
1733398 TGATTCTAACTTTGTAAGGAAAATAAA-TC-GTTGAATTTATTTGAGAATCTTGAA
1 TGATTCTAACTTTGTAAGG-AAATAAATTCAATT--ATTTACTTGAGAATCTTAAA
1733452 TGATTCTAACTTTGTAAG
1 TGATTCTAACTTTGTAAG
1733470 ATTATAACTT
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
52 2 0.03
53 6 0.09
54 57 0.88
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.40
Consensus pattern (53 bp):
TGATTCTAACTTTGTAAGGAAATAAATTCAATTATTTACTTGAGAATCTTAAA
Found at i:1733477 original size:16 final size:16
Alignment explanation
Indices: 1733453--1733485 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1733443 AATCTTGAAT
*
1733453 GATTCTAACTTTGTAA
1 GATTATAACTTTGTAA
1733469 GATTATAACTTTGTAA
1 GATTATAACTTTGTAA
1733485 G
1 G
1733486 GTATTTTCTT
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:0.33, C:0.09, G:0.15, T:0.42
Consensus pattern (16 bp):
GATTATAACTTTGTAA
Found at i:1733774 original size:39 final size:39
Alignment explanation
Indices: 1733711--1733798 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 39
1733701 TTTGTATAAC
*
1733711 AATTTATTTTCCTACTTTATGAAAGGAAATAAATC-GTTG
1 AATTTATTTTCCTACTTTACGAAAGGAAATAAATCAG-TG
* *
1733750 AGTTTATTTTCCT-CTTTTACGAAAGGAAATAAGTCAGTG
1 AATTTATTTTCCTAC-TTTACGAAAGGAAATAAATCAGTG
1733789 AATTTATTTT
1 AATTTATTTT
1733799 TTGTGAAACT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 1 0.02
39 41 0.95
40 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (39 bp):
AATTTATTTTCCTACTTTACGAAAGGAAATAAATCAGTG
Found at i:1733952 original size:97 final size:96
Alignment explanation
Indices: 1733732--1733991 Score: 255
Period size: 97 Copynumber: 2.7 Consensus size: 96
1733722 CTACTTTATG
* * * *
1733732 AAAGGAAATAAATCGTT-GAGTTTATTTTCCTCTTTT-ACGAAAGGAAATAAGTCAGTGAATTTA
1 AAAGGAAATAAATCGTTAGA-TTTATTTTCCTATTTTGA-AAAAGGAAATAAATCAGTAAATTTA
* ** *
1733795 TTTTTTGTGAAACTTATATGATTCTGATTTGGA
64 TTTTCTGAAAAACTTAAATGATTCTGATTTGGA
* * * * *
1733828 AAAAGAAATAAATCG-TAGGATTTATTTTCTTTTTTTGAAAAAAGAAATAAATCGGTAAATTTAT
1 AAAGGAAATAAATCGTTA-GATTTATTTTCCTATTTTGAAAAAGGAAATAAATCAGTAAATTTAT
* *
1733892 TTTCCT-AAAAATCTTAAATGATTCTTATATT-TA
65 TTT-CTGAAAAA-CTTAAATGATTCTGAT-TTGGA
* *
1733925 AAAGGAAATAAATCGTTAGATTTATTTTCCTATTGTGTAAAAGGAAATAAATCA-TAGAATTT-T
1 AAAGGAAATAAATCGTTAGATTTATTTTCCTATTTTGAAAAAGGAAATAAATCAGTA-AATTTAT
1733988 TTTC
65 TTTC
1733992 CCTAGGAGAG
Statistics
Matches: 135, Mismatches: 21, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
95 2 0.01
96 61 0.45
97 68 0.50
98 4 0.03
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (96 bp):
AAAGGAAATAAATCGTTAGATTTATTTTCCTATTTTGAAAAAGGAAATAAATCAGTAAATTTATT
TTCTGAAAAACTTAAATGATTCTGATTTGGA
Found at i:1735976 original size:39 final size:39
Alignment explanation
Indices: 1735915--1736063 Score: 187
Period size: 39 Copynumber: 3.9 Consensus size: 39
1735905 ATGATTCTGA
*
1735915 TTTGTAAAAGG-AA-AAATCATTGGATTTAGTTTCCTAT
1 TTTGTAAAAGGAAATAAATCATTGGATTTATTTTCCTAT
* *
1735952 TTAT-TAAAAGGAAATAAATCATTGGATTTATTTTCTTGT
1 TT-TGTAAAAGGAAATAAATCATTGGATTTATTTTCCTAT
* * * *
1735991 TTTGTAAAAGGAAATAAATCGTTAGATTTATTTTGCGAT
1 TTTGTAAAAGGAAATAAATCATTGGATTTATTTTCCTAT
* *
1736030 TTTGTAAAACGAAATAAATCATTGGATTTTTTTT
1 TTTGTAAAAGGAAATAAATCATTGGATTTATTTT
1736064 GAGAATCTTG
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
37 9 0.09
38 4 0.04
39 82 0.86
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.44
Consensus pattern (39 bp):
TTTGTAAAAGGAAATAAATCATTGGATTTATTTTCCTAT
Found at i:1736167 original size:94 final size:95
Alignment explanation
Indices: 1735984--1736157 Score: 239
Period size: 94 Copynumber: 1.8 Consensus size: 95
1735974 TGGATTTATT
*
1735984 TTCTTGTTTTGTAAAAGGAAATAAATCGTTAGATTTATTTTGCGATTTTGTAAAACGAAATAAAT
1 TTCTTGTTTTGTAAAAGGAAATAAATCGTTAGATTTATTTTGCGATTTTGTAAAAAGAAATAAAT
* ***
1736049 CATTGGATTTTTTTTGAGAATCTTGTATGA
66 CAGTGGATTGAATTTGAGAATCTTGTATGA
*
1736079 TTCTTG-TTTGTAAAATGAAATAAATCGTTAGATTTATTTT-C-ATGATTT-TAAAAAGAAAATA
1 TTCTTGTTTTGTAAAAGGAAATAAATCGTTAGATTTATTTTGCGAT--TTTGTAAAAAG-AAATA
1736140 AATCAGTGGATTGAATTT
63 AATCAGTGGATTGAATTT
1736158 ATTTTTCTTG
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
92 2 0.03
93 7 0.10
94 55 0.79
95 6 0.09
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.43
Consensus pattern (95 bp):
TTCTTGTTTTGTAAAAGGAAATAAATCGTTAGATTTATTTTGCGATTTTGTAAAAAGAAATAAAT
CAGTGGATTGAATTTGAGAATCTTGTATGA
Found at i:1739199 original size:20 final size:20
Alignment explanation
Indices: 1739171--1739209 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1739161 AATTTGATCC
1739171 TTATATTATTATT-TTTATTA
1 TTATATTA-TATTATTTATTA
*
1739191 TTATTTTATATTATTTATT
1 TTATATTATATTATTTATT
1739210 TTGTTACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATATTATATTATTTATTA
Found at i:1739204 original size:10 final size:11
Alignment explanation
Indices: 1739174--1739206 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
1739164 TTGATCCTTA
1739174 TATTATTATTTT
1 TATTATTA-TTT
1739186 TATTATTATTT
1 TATTATTATTT
1739197 TA-TATTATTT
1 TATTATTATTT
1739207 ATTTTGTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
11 5 0.24
12 8 0.38
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTATTATTT
Found at i:1739241 original size:21 final size:21
Alignment explanation
Indices: 1739197--1739246 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1739187 ATTATTATTT
* *
1739197 TATATTATTTATTTTGTTACA
1 TATATTATATATTTTGTTAAA
1739218 TATATGTATATATTTT-TTAAA
1 TATAT-TATATATTTTGTTAAA
*
1739239 TATTTTAT
1 TATATTAT
1739247 TTATATACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 13 0.52
22 9 0.36
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (21 bp):
TATATTATATATTTTGTTAAA
Found at i:1743523 original size:93 final size:93
Alignment explanation
Indices: 1743364--1743546 Score: 357
Period size: 93 Copynumber: 2.0 Consensus size: 93
1743354 AAGAACTCAG
1743364 AAAGAATAGAGCAAATGCCTCAGAGCTATATTACTCTCTCACAAAGAGAAGAATGGAATGGGTGA
1 AAAGAATAGAGCAAATGCCTCAGAGCTATATTACTCTCTCACAAAGAGAAGAATGGAATGGGTGA
1743429 TCACAAATGAGGAGGAGAGCTCTCTCTC
66 TCACAAATGAGGAGGAGAGCTCTCTCTC
1743457 AAAGAATAGAGCAAATGCCTCAGAGCTATATTACTCTCTCACAAAGAGAAGAATGGAATGGGTGA
1 AAAGAATAGAGCAAATGCCTCAGAGCTATATTACTCTCTCACAAAGAGAAGAATGGAATGGGTGA
*
1743522 TCACAAATGAGGATGAGAGCTCTCT
66 TCACAAATGAGGAGGAGAGCTCTCT
1743547 ATTTATAGTA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (93 bp):
AAAGAATAGAGCAAATGCCTCAGAGCTATATTACTCTCTCACAAAGAGAAGAATGGAATGGGTGA
TCACAAATGAGGAGGAGAGCTCTCTCTC
Found at i:1744299 original size:8 final size:8
Alignment explanation
Indices: 1744272--1744302 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1744262 TATTTTTTCC
1744272 TTTTTATT
1 TTTTTATT
1744280 TTTCTTATT
1 TTT-TTATT
1744289 TTTTTATT
1 TTTTTATT
1744297 TTTTTA
1 TTTTTA
1744303 AATAGTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTATT
Found at i:1744423 original size:22 final size:19
Alignment explanation
Indices: 1744378--1744465 Score: 63
Period size: 21 Copynumber: 4.5 Consensus size: 19
1744368 CTCTCTCTAT
* *
1744378 TTTATTTATACTTTTATATTC
1 TTTATTTTTA-TTTTAT-TCC
*
1744399 TTTATTTTTACTTTTTTTAGCC
1 TTTATTTTTA-TTTTATT--CC
*
1744421 TTTATATTTATTTTATTCC
1 TTTATTTTTATTTTATTCC
* *
1744440 TTTATTTAT-TTTTATT-T
1 TTTATTTTTATTTTATTCC
1744457 TTTATTTTT
1 TTTATTTTT
1744466 GTTCTCATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
17 8 0.14
18 7 0.12
19 9 0.16
20 1 0.02
21 21 0.38
22 10 0.18
ACGTcount: A:0.18, C:0.08, G:0.01, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTTATTCC
Found at i:1744533 original size:6 final size:6
Alignment explanation
Indices: 1744522--1744546 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1744512 ACATTATTAT
1744522 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
1744547 GTCATTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:1745406 original size:15 final size:14
Alignment explanation
Indices: 1745386--1745423 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
1745376 TGTTGGTTTC
*
1745386 TATTTTTCTTTCATT
1 TATTTTTCTTT-ACT
1745401 TATTTTTCTTTACT
1 TATTTTTCTTTACT
1745415 T-TTTTTCTT
1 TATTTTTCTT
1745424 ATTTTTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.36
14 3 0.14
15 11 0.50
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTTCTTTACT
Found at i:1749712 original size:100 final size:99
Alignment explanation
Indices: 1749590--1749797 Score: 285
Period size: 100 Copynumber: 2.1 Consensus size: 99
1749580 CCAAATTATA
** *
1749590 ATTATATATATATATACAATAAAGCTTGATTTGTCCCTCTAGA-GCAATTGGTTAAATGCTCCGA
1 ATTATATATATATATACAATAAAGCTTGAGCTGTCCCTCT-GATGCAATTGGTTAAACGC-CCGA
* *
1749654 CTTTATGGATAATATTCAGCTAGCCTGATAAAGGTG
64 CTTTATGGATAAGATTCAGCTAACCTGATAAAGGTG
* * *
1749690 ATTATAT-TATACTATACGATAAAGCTTGAGCTGTCCCTCTGATGCAATTGGTTAAACGCCTGGC
1 ATTATATATATA-TATACAATAAAGCTTGAGCTGTCCCTCTGATGCAATTGGTTAAACGCCCGAC
1749754 TTTATGGATAAGATTCAGCTAACCTGATAAAGGTG
65 TTTATGGATAAGATTCAGCTAACCTGATAAAGGTG
* *
1749789 TTTACATAT
1 ATTATATAT
1749798 TGAGTTGTCT
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
99 47 0.49
100 48 0.51
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (99 bp):
ATTATATATATATATACAATAAAGCTTGAGCTGTCCCTCTGATGCAATTGGTTAAACGCCCGACT
TTATGGATAAGATTCAGCTAACCTGATAAAGGTG
Found at i:1751123 original size:84 final size:85
Alignment explanation
Indices: 1750978--1751762 Score: 709
Period size: 84 Copynumber: 9.4 Consensus size: 85
1750968 GAAACTATTG
** * * ** * * *
1750978 GCAGCATAACTCAAGGCGAGAAGGGTTATTTTTCAAC-AAAGACCTTTGAGTTCAACAACGCTCA
1 GCAGCATAGTTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
1751042 GCTTC-AAGGCACATCATTT
66 GCTTCAAAGGCACATCATTT
** * * * *
1751061 ATAGCATAGTTCAATGCTAGAAGGGTTATTTGCGACCAAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAGTTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
* * *
1751126 GCTCCGAGGGCACATCATTT
66 GCTTCAAAGGCACATCATTT
* * ** * * ** *
1751146 ACAGCACAACTCAAGGATATAAGGGTTATCTGTTAAC-AAAGACCTTCGAGTTCGACTACACTCA
1 GCAGCATAGTTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
* *
1751210 GC-TCTAAGGCATATCATTT
66 GCTTCAAAGGCACATCATTT
** * * * *
1751229 GCAGCATAACTCAGGGCTAGAAGGGTTATTTGCCAACAAAATACCTTCGAGTTTGACTACGCTCA
1 GCAGCATAGTTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
*
1751294 GC-TCTAAGGCACATCATTT
66 GCTTCAAAGGCACATCATTT
* * * * * * *
1751313 GCAGCATAGTTGAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCAAGTTCGACTACGCCCA
1 GCAGCATAGTTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
* *
1751378 GC-TCCAAGGCACATCGTTT
66 GCTTCAAAGGCACATCATTT
** * * * *
1751397 ATAGCATAACTT-AATGCTAGAAGGGTTATCTGTCC-AC-AAAGACCTTCGAGTTCGATTACACT
1 GCAGCAT-AGTTCAAGGCTAGAAGGGTTATCTG-CCAACAAAAGACCTTCGAGTTCGACTACGCT
*
1751459 CAG-TTCAAAGGTACATCATTT
64 CAGCTTCAAAGGCACATCATTT
* * * * * *
1751480 GCAGCATAGCTT-AAGTCGAGTAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACCACGCTC
1 GCAGCATAG-TTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTC
*
1751544 AGC-TCCAAGGCACATCATTT
65 AGCTTCAAAGGCACATCATTT
* * * * * *
1751564 GCAACATAGCTT-AAGGCAAGAATGGCTATTTTCCAACAAAAGACCTTCGAGTTCGACTACGCTC
1 GCAGCATAG-TTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTC
* * *
1751628 AGC-TCCAAGACACGTCATTT
65 AGCTTCAAAGGCACATCATTT
* ** * * * * *
1751648 ACAGCATAACTCAAGGTTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCTATTACACTCA
1 GCAGCATAGTTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
*
1751713 GC-TCAAAGGCATATCATTT
66 GCTTCAAAGGCACATCATTT
* * *
1751732 GCAGCATAGCTCAAGGCGAGAAGGGCTATCT
1 GCAGCATAGTTCAAGGCTAGAAGGGTTATCT
1751763 ATCAGCAAGA
Statistics
Matches: 572, Mismatches: 119, Indels: 21
0.80 0.17 0.03
Matches are distributed among these distances:
82 3 0.01
83 132 0.23
84 393 0.69
85 44 0.08
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (85 bp):
GCAGCATAGTTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
GCTTCAAAGGCACATCATTT
Found at i:1751277 original size:168 final size:167
Alignment explanation
Indices: 1750979--1751756 Score: 831
Period size: 168 Copynumber: 4.6 Consensus size: 167
1750969 AAACTATTGG
* * ** * * *
1750979 CAGCATAACTCAAGGCGAGAAGGGTTATTTTTCAACAAAGACCTTTGAGTTCAACAACGCTCAGC
1 CAGCATAACTCAAGGAGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGC
* ** * * * *
1751044 TTCAAGGCACATCATTTATAGCATAGTTCAATGCTAGAAGGGTTATTTGCGACCAAAAGACCTTC
66 TCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATTTGCCAACAAAAGACCTTC
*
1751109 GAGTTCGACTACGCTCAGCTCCGAGGGCACATCATTTA
131 GAGTTCGACTACGCTCAGCTCC-AAGGCACATCATTTA
* * * ** *
1751147 CAGCACAACTCAAGGATATAAGGGTTATCTGTTAACAAAGACCTTCGAGTTCGACTACACTCAGC
1 CAGCATAACTCAAGGAGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGC
* * * * *
1751212 TCTAAGGCATATCATTTGCAGCATAACTCAGGGCTAGAAGGGTTATTTGCCAACAAAATACCTTC
66 TCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATTTGCCAACAAAAGACCTTC
* * *
1751277 GAGTTTGACTACGCTCAGCTCTAAGGCACATCATTTG
131 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
** * ** * * *
1751314 CAGCATAGTTGAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCAAGTTCGACTACGCCCAG
1 CAGCATAACTCAAGGAGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAG
* ** * * * *
1751379 CTCCAAGGCACATCGTTTATAGCATAACTTAATGCTAGAAGGGTTATCTGTCC-AC-AAAGACCT
65 CTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATTTG-CCAACAAAAGACCT
* * * * * *
1751442 TCGAGTTCGATTACACTCAGTTCAAAGGTACATCATTTG
129 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* * ** * * *
1751481 CAGCATAGCTTAAGTCGAGTAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACCACGCTCAG
1 CAGCATAACTCAAGGAGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAG
* * * * * *
1751546 CTCCAAGGCACATCATTTGCAACATAGCTTAAGGCAAGAATGGCTATTTTCCAACAAAAGACCTT
65 CTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATTTGCCAACAAAAGACCTT
* *
1751611 CGAGTTCGACTACGCTCAGCTCCAAGACACGTCATTTA
130 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
** * * * *
1751649 CAGCATAACTCAAGGTTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCTATTACACTCAG
1 CAGCATAACTCAAGGAGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTACGCTCAG
* * *
1751714 CTCAAAGGCATATCATTTGCAGCATAGCTCAAGGCGAGAAGGG
65 CTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGG
1751757 CTATCTATCA
Statistics
Matches: 505, Mismatches: 100, Indels: 10
0.82 0.16 0.02
Matches are distributed among these distances:
166 2 0.00
167 178 0.35
168 323 0.64
169 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (167 bp):
CAGCATAACTCAAGGAGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGC
TCCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATTTGCCAACAAAAGACCTTC
GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
Found at i:1751447 original size:251 final size:249
Alignment explanation
Indices: 1750978--1751756 Score: 963
Period size: 251 Copynumber: 3.1 Consensus size: 249
1750968 GAAACTATTG
** * *
1750978 GCAGCATAACTCAAGGCGAGAAGGGTTATTTTTCAACAAAGACCTTTGAGTTCAACAACGCTCAG
1 GCAGCATAACTCAAGGCGAGAAGGGTTATTTGCCAACAAAGACCTTCGAGTTCGACAACGCTCAG
** * * *
1751043 CT-TCAAGGCACATCATTTATAGCATAGTTCAA-TGCTAGAAGGGTTATTTG-CGACCAAAAGAC
66 CTCT-AAGGCACATCATTTGCAGCATAGTT-AAGT-CAAGAAGGGCTATTTGCCAACC-AAAGAC
* * *
1751105 CTTCGAGTTCGACTACGCTCAGCTCCGAGGGCACATCATTTACAGCACAACTCAAGGATATAAGG
127 CTTCGAGTTCGACTACGCTCAGCTCC-AAGGCACATCATTTACAGCATAACTCAAGGATAGAAGG
** * *
1751170 GTTATCTGTTAACAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCATATCATTT
191 GTTATCTGTCCACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCATTT
* * * * *
1751229 GCAGCATAACTCAGGGCTAGAAGGGTTATTTGCCAACAAAATACCTTCGAGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCGAGAAGGGTTATTTGCCAAC-AAAGACCTTCGAGTTCGACAACGCTCA
* *
1751294 GCTCTAAGGCACATCATTTGCAGCATAGTTGAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCT
65 GCTCTAAGGCACATCATTTGCAGCATAGTT-AAGTCAAGAAGGGCTATTTGCCAACCAAAGACCT
* * * * * * *
1751359 TCAAGTTCGACTACGCCCAGCTCCAAGGCACATCGTTTATAGCATAACTTAATGCTAGAAGGGTT
129 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGATAGAAGGGTT
* * *
1751424 ATCTGTCCACAAAGACCTTCGAGTTCGATTACACTCAGTTCAAAGGTACATCATTT
194 ATCTGTCCACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCATTT
* * * * * * *
1751480 GCAGCATAGCTTAAGTCGAGTAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACCACGCTCA
1 GCAGCATAACTCAAGGCGAGAAGGGTTATTTGCCAA-CAAAGACCTTCGAGTTCGACAACGCTCA
* * * * * *
1751545 GCTCCAAGGCACATCATTTGCAACATAGCTTAAGGCAAGAATGGCTATTTTCCAACAAAAGACCT
65 GCTCTAAGGCACATCATTTGCAGCATAG-TTAAGTCAAGAAGGGCTATTTGCCAACCAAAGACCT
* * *
1751610 TCGAGTTCGACTACGCTCAGCTCCAAGACACGTCATTTACAGCATAACTCAAGGTTAGAAGGGTT
129 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGATAGAAGGGTT
* *
1751675 ATCTG-CCAACAAAAGACCTTTGAGTTCTATTACACTCAGCTCAAAGGCATATCATTT
194 ATCTGTCC-AC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCATTT
*
1751732 GCAGCATAGCTCAAGGCGAGAAGGG
1 GCAGCATAACTCAAGGCGAGAAGGG
1751757 CTATCTATCA
Statistics
Matches: 451, Mismatches: 69, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
250 2 0.00
251 284 0.63
252 159 0.35
253 6 0.01
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (249 bp):
GCAGCATAACTCAAGGCGAGAAGGGTTATTTGCCAACAAAGACCTTCGAGTTCGACAACGCTCAG
CTCTAAGGCACATCATTTGCAGCATAGTTAAGTCAAGAAGGGCTATTTGCCAACCAAAGACCTTC
GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGATAGAAGGGTTAT
CTGTCCACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCATTT
Found at i:1752365 original size:19 final size:19
Alignment explanation
Indices: 1752321--1752371 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
1752311 TAGATTGGTT
*
1752321 TATTATATTATTAATAAACA
1 TATTATACTA-TAATAAACA
* *
1752341 TGTTATA-TATACATAAATA
1 TATTATACTATA-ATAAACA
1752360 TATTATACTATA
1 TATTATACTATA
1752372 GATTATAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 10 0.38
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (19 bp):
TATTATACTATAATAAACA
Found at i:1753290 original size:21 final size:21
Alignment explanation
Indices: 1753264--1753314 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1753254 TGGAGCGACC
* *
1753264 CACGACCTGACCCGCAACACG
1 CACGACCCGACCCACAACACG
1753285 CACGACCCGACCCACAACACG
1 CACGACCCGACCCACAACACG
*
1753306 CATGACCCG
1 CACGACCCG
1753315 TGTGTTTCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.49, G:0.18, T:0.04
Consensus pattern (21 bp):
CACGACCCGACCCACAACACG
Found at i:1753477 original size:12 final size:13
Alignment explanation
Indices: 1753457--1753491 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
1753447 AATTTGATCC
1753457 TTATATTATTATT
1 TTATATTATTATT
1753470 TT-TATTATTATT
1 TTATATTATTATT
1753482 TTATATTATT
1 TTATATTATT
1753492 TACTTTGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATATTATTATT
Found at i:1753490 original size:10 final size:11
Alignment explanation
Indices: 1753460--1753492 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
1753450 TTGATCCTTA
1753460 TATTATTATTTT
1 TATTATTA-TTT
1753472 TATTATTATTT
1 TATTATTATTT
1753483 TA-TATTATTT
1 TATTATTATTT
1753493 ACTTTGTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
11 5 0.24
12 8 0.38
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTATTATTT
Found at i:1753552 original size:45 final size:47
Alignment explanation
Indices: 1753469--1753579 Score: 108
Period size: 45 Copynumber: 2.4 Consensus size: 47
1753459 ATATTATTAT
* * *
1753469 TTTTATTATTATTTTATATTATTTACTTTGTTACATATACGTATATA
1 TTTTATTATTATTTTATATTATATACTTTATTACATATACATATATA
*
1753516 TTTT-TTA-TATTTTAT-TTATATACCTATTATTA-ATATATATATATA
1 TTTTATTATTATTTTATATTATATA-CT-TTATTACATATACATATATA
*
1753561 -TATATTAATTATTTT-TATT
1 TTTTATT-ATTATTTTATATT
1753580 TGATTATTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
44 8 0.15
45 23 0.43
46 10 0.19
47 12 0.23
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (47 bp):
TTTTATTATTATTTTATATTATATACTTTATTACATATACATATATA
Found at i:1753669 original size:2 final size:2
Alignment explanation
Indices: 1753664--1753706 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1753654 TTATTATTAT
1753664 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
1753706 T
1 T
1753707 TATTTTTATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1753751 original size:19 final size:18
Alignment explanation
Indices: 1753704--1753753 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
1753694 TATATATATA
*
1753704 TATTATTTTTATCTTTTTT
1 TATTATTTTTCT-TTTTTT
*
1753723 TACTA-TTTTCTTTTTTT
1 TATTATTTTTCTTTTTTT
1753740 TATTATTATTTCTT
1 TATTATT-TTTCTT
1753754 CTCCTAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 10 0.38
18 6 0.23
19 10 0.38
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTATTTTTCTTTTTTT
Found at i:1753954 original size:13 final size:14
Alignment explanation
Indices: 1753936--1753968 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1753926 ACTTTATTTA
1753936 TTATTTTTC-CTTT
1 TTATTTTTCTCTTT
1753949 TTATTTTTCTCTTT
1 TTATTTTTCTCTTT
1753963 TT-TTTT
1 TTATTTT
1753969 GATTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (14 bp):
TTATTTTTCTCTTT
Found at i:1754050 original size:19 final size:20
Alignment explanation
Indices: 1754012--1754056 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1754002 TCTACTATTA
*
1754012 TTTTCTTTCTTTTTACTTTT
1 TTTTCTCTCTTTTTACTTTT
1754032 TTTTCTCTCTTTTTA-TTTT
1 TTTTCTCTCTTTTTACTTTT
*
1754051 ATTTCT
1 TTTTCT
1754057 ATTTTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTCTCTCTTTTTACTTTT
Found at i:1754093 original size:22 final size:19
Alignment explanation
Indices: 1754048--1754116 Score: 57
Period size: 21 Copynumber: 3.4 Consensus size: 19
1754038 CTCTTTTTAT
* *
1754048 TTTATTTCTATTTTTATATTC
1 TTTATTTTTA-TTTTAT-TCC
*
1754069 TTTATTTTTACTTTTTTTAGCC
1 TTTATTTTTA-TTTTATT--CC
*
1754091 TTTATATTTATTTTATTCC
1 TTTATTTTTATTTTATTCC
1754110 TTTATTT
1 TTTATTT
1754117 ATTTTAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
19 8 0.21
20 1 0.03
21 20 0.51
22 10 0.26
ACGTcount: A:0.17, C:0.10, G:0.01, T:0.71
Consensus pattern (19 bp):
TTTATTTTTATTTTATTCC
Found at i:1754118 original size:54 final size:52
Alignment explanation
Indices: 1754009--1754118 Score: 125
Period size: 52 Copynumber: 2.1 Consensus size: 52
1753999 TATTCTACTA
* * * *
1754009 TTATTTTCTTTCTTTTTACTTTTTTTTCTCTCTTTTTATTTTATTTCTATTT
1 TTATATTCTTTATTTTTACTTTTTTTGCTCTCTTTTTATTTTATTCCTATTT
*
1754061 TTATATTCTTTATTTTTACTTTTTTTAGC-CTTTATATTTATTTTATTCCT-TTAT
1 TTATATTCTTTATTTTTACTTTTTTT-GCTCTCT-T-TTTATTTTATTCCTATT-T
1754115 TTAT
1 TTAT
1754119 TTTAATTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
52 27 0.55
53 4 0.08
54 18 0.37
ACGTcount: A:0.15, C:0.12, G:0.01, T:0.73
Consensus pattern (52 bp):
TTATATTCTTTATTTTTACTTTTTTTGCTCTCTTTTTATTTTATTCCTATTT
Found at i:1754237 original size:17 final size:17
Alignment explanation
Indices: 1754196--1754237 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1754186 ATTATTATTT
*
1754196 TTTTATTTTTATTTTTA
1 TTTTATTTTTATCTTTA
* *
1754213 TGTCATTTTTATCTTTA
1 TTTTATTTTTATCTTTA
1754230 TTTTATTT
1 TTTTATTT
1754238 GCTTCCCTAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTATTTTTATCTTTA
Found at i:1755632 original size:21 final size:21
Alignment explanation
Indices: 1755607--1755647 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1755597 ATAATAAATA
*
1755607 TAATAACGAAAAAAAATAATT
1 TAATAAAGAAAAAAAATAATT
* *
1755628 TAATAAAGTAAAATAATAAT
1 TAATAAAGAAAAAAAATAAT
1755648 ATTGTAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (21 bp):
TAATAAAGAAAAAAAATAATT
Found at i:1756405 original size:37 final size:36
Alignment explanation
Indices: 1756355--1756492 Score: 172
Period size: 37 Copynumber: 3.8 Consensus size: 36
1756345 GTGCTTGTGG
* * * * *
1756355 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
* *
1756392 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
1756429 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
1756463 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1756493 GGACGAAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:1756466 original size:34 final size:35
Alignment explanation
Indices: 1756389--1756489 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
1756379 TTAGTAGAAC
1756389 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
1756427 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
1756460 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1756490 GTAGGACGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:1757339 original size:105 final size:105
Alignment explanation
Indices: 1757036--1757693 Score: 931
Period size: 105 Copynumber: 6.3 Consensus size: 105
1757026 CATTGTTTCA
* * *
1757036 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACTGGGATA-TTGTTTGTTGACA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGA-AGTTG-TTGTTGACA
* * * * *
1757099 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
63 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
1757142 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
1757202 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1757242 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
* *
1757307 AGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1757347 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTATTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
1757412 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1757452 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA---GTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1757514 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1757554 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
* * * *
1757619 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1757660 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
1757694 CGCGGATGGC
Statistics
Matches: 508, Mismatches: 30, Indels: 25
0.90 0.05 0.04
Matches are distributed among these distances:
100 84 0.17
101 2 0.00
102 105 0.21
104 6 0.01
105 201 0.40
106 85 0.17
107 3 0.01
109 22 0.04
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1757606 original size:207 final size:208
Alignment explanation
Indices: 1757035--1757693 Score: 936
Period size: 207 Copynumber: 3.2 Consensus size: 208
1757025 GCATTGTTTC
* *
1757035 AAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGATATTGTTTGTTGACAA
1 AAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGA-A-TG-TTGTTGACAA
* * * * *
1757100 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
63 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
**
1757165 GTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
128 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
*
1757225 GAACTTGCATTGTCTG
193 GAACTTGCGTTGTCTG
* * * *
1757241 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 AAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAA--TGTTGTTGACAAG
* *
1757306 CAGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* * *
1757371 TTGAAATTGGCTCTGAGATTGGGAAGTTGTTATTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
129 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
1757436 AACTTGCGTTGTCTG
194 AACTTGCGTTGTCTG
* * *
1757451 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-GTTGTTGACAAGCA
1 AAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAATGTTGTTGACAAGCA
1757515 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
* * *
1757580 GAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGA
131 GAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
*
1757645 ACTTGTGTTGTCTCG
195 ACTTGCGTTGTCT-G
*
1757660 -AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AAGT-CCA--ATATCCTCCGTCGTGAAGTTGAAAT
1757694 CGCGGATGGC
Statistics
Matches: 408, Mismatches: 34, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
205 83 0.20
206 47 0.12
207 104 0.25
208 50 0.12
209 6 0.01
210 96 0.24
211 22 0.05
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (208 bp):
AAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAATGTTGTTGACAAGCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
CTTGCGTTGTCTG
Found at i:1758659 original size:35 final size:34
Alignment explanation
Indices: 1758366--1758659 Score: 188
Period size: 36 Copynumber: 8.4 Consensus size: 34
1758356 GAAGATTTTG
* * *
1758366 TGTTTCAAGAGCAACTGTCTCAAGATAGACGAAAAT
1 TGTTTCAAGA-AAACTGTCTCAAGAGAGAC-AAATT
*
1758402 TGATTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGA-AAACTGTCTCAAGAGAGAC-AAA-TT
* * * *
1758439 AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGA-AAACTGTCTCAAGAGAGAC-AAATT
* * *
1758475 TGTTTCAAAGAAAACATAT-TC---A-A-A-TATTT
1 TGTTTC-AAGAAAAC-TGTCTCAAGAGAGACAAATT
* * *
1758504 TGTTTCAAGGGAAACTGTCTCAAGATATACGAAATT
1 TGTTTCAA-GAAAACTGTCTCAAGAGAGAC-AAATT
1758540 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGA-AAACTGTCTCAAGAGAGAC-AAATT
* * *
1758576 TATTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
1 TGTTTCAA-GAAAACTGTCTCAAGAGAGACAAATT
* * * * *
1758611 TCTTTTAGTGAAAACGGTCTCAAGCGAGACAAATCT
1 TGTTTCA-AGAAAACTGTCTCAAGAGAGACAAAT-T
*
1758647 TGTTTTAAGAAAA
1 TGTTTCAAGAAAA
1758660 ACAATCATGA
Statistics
Matches: 204, Mismatches: 38, Indels: 33
0.74 0.14 0.12
Matches are distributed among these distances:
28 4 0.02
29 16 0.08
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 36 0.18
36 108 0.53
37 35 0.17
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (34 bp):
TGTTTCAAGAAAACTGTCTCAAGAGAGACAAATT
Found at i:1759116 original size:18 final size:18
Alignment explanation
Indices: 1759089--1759124 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1759079 TGATGAATCC
* *
1759089 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
1759107 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1759125 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:1760179 original size:23 final size:25
Alignment explanation
Indices: 1760153--1760209 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
1760143 TTTTTGTCCA
1760153 TTTTTCTTTTTGAT-TT-TTGCTCT
1 TTTTTCTTTTTGATCTTGTTGCTCT
* * *
1760176 TTTTTCCTTTTGTTCTTGTTTCTCT
1 TTTTTCTTTTTGATCTTGTTGCTCT
1760201 TTTTTCTTT
1 TTTTTCTTT
1760210 GTTTTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 12 0.43
24 2 0.07
25 14 0.50
ACGTcount: A:0.02, C:0.16, G:0.07, T:0.75
Consensus pattern (25 bp):
TTTTTCTTTTTGATCTTGTTGCTCT
Found at i:1760207 original size:16 final size:16
Alignment explanation
Indices: 1760167--1760213 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1760157 TCTTTTTGAT
* *
1760167 TTTTGCTCTTTTTTCC
1 TTTTGTTCTTGTTTCC
1760183 TTTTGTTCTTGTTTCTC
1 TTTTGTTCTTGTTTC-C
1760200 TTTT-TTCTTTGTTT
1 TTTTGTTC-TTGTTT
1760214 TTTTTTTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (16 bp):
TTTTGTTCTTGTTTCC
Found at i:1760250 original size:16 final size:16
Alignment explanation
Indices: 1760202--1760251 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
1760192 TGTTTCTCTT
1760202 TTTTCTTTGTTTT-TT-
1 TTTTCTTT-TTTTGTTC
1760217 TTTTAC-TTTTTTGCTTC
1 TTTT-CTTTTTTTG-TTC
1760234 TTTTCTTTTTTTGTTC
1 TTTTCTTTTTTTGTTC
1760250 TT
1 TT
1760252 GATTGGATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
14 4 0.13
15 6 0.20
16 9 0.30
17 11 0.37
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.80
Consensus pattern (16 bp):
TTTTCTTTTTTTGTTC
Found at i:1765026 original size:15 final size:15
Alignment explanation
Indices: 1764998--1765036 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1764988 ATAAACAAAA
1764998 AAATATTATGATATAAT
1 AAATA-TAT-ATATAAT
*
1765015 ATATATATATATAAT
1 AAATATATATATAAT
1765030 AAATATA
1 AAATATA
1765037 ATAACGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 3 0.15
17 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AAATATATATATAAT
Found at i:1765061 original size:21 final size:24
Alignment explanation
Indices: 1765025--1765084 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
1765015 ATATATATAT
* *
1765025 ATAATAAATATAATAACG-AAAA-A
1 ATAAT-AATGTAATAAAGTAAAATA
*
1765048 A-AATAATTTAATAAAGTAAAATA
1 ATAATAATGTAATAAAGTAAAATA
1765071 ATAATAATGTAATA
1 ATAATAATGTAATA
1765085 TAATATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 10 0.32
22 7 0.23
23 3 0.10
24 11 0.35
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (24 bp):
ATAATAATGTAATAAAGTAAAATA
Found at i:1765077 original size:16 final size:16
Alignment explanation
Indices: 1765056--1765093 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1765046 AAAAATAATT
1765056 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
1765072 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
1765088 T-ATAAA
1 TAATAAA
1765094 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:1765833 original size:37 final size:36
Alignment explanation
Indices: 1765783--1765920 Score: 172
Period size: 37 Copynumber: 3.8 Consensus size: 36
1765773 GTGCTTGTGG
* * * * *
1765783 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
* *
1765820 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
1765857 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
1765891 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1765921 GGACGAAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:1765894 original size:34 final size:35
Alignment explanation
Indices: 1765817--1765917 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
1765807 TTAGTAGAAC
1765817 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
1765855 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
1765888 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1765918 GTAGGACGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:1766635 original size:3 final size:3
Alignment explanation
Indices: 1766627--1766658 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1766617 GTCTGGTCTT
1766627 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1766659 TACATTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1772833 original size:36 final size:37
Alignment explanation
Indices: 1772694--1772848 Score: 213
Period size: 37 Copynumber: 4.2 Consensus size: 37
1772684 GCCTTTGGGT
*
1772694 CAGTTTTCTCTAAAAACAAATTTTGTCTCACTTGAGA
1 CAGTTTTCTCTAAAAACAAATTTCGTCTCACTTGAGA
*
1772731 CAGTTTTCTCTAAAAACAAACTTCGTCTCACTTGAGA
1 CAGTTTTCTCTAAAAACAAATTTCGTCTCACTTGAGA
* * *
1772768 CAGTTTTTTCTAAAAACAAATTTTGTCTCGCTTGAGA
1 CAGTTTTCTCTAAAAACAAATTTCGTCTCACTTGAGA
* * * *
1772805 CA-ATTTCTCTGAAAACAAATTTCATCTCGCTTGAGA
1 CAGTTTTCTCTAAAAACAAATTTCGTCTCACTTGAGA
*
1772841 CATTTTTC
1 CAGTTTTC
1772849 CTTTGAGATG
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
36 31 0.30
37 74 0.70
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (37 bp):
CAGTTTTCTCTAAAAACAAATTTCGTCTCACTTGAGA
Found at i:1773223 original size:21 final size:21
Alignment explanation
Indices: 1773199--1773263 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
1773189 TGAGATTTTT
1773199 TCCCTTTAAACAAGTTTTGTC
1 TCCCTTTAAACAAGTTTTGTC
*
1773220 TCCCTTTAAACAAGTTTTGCC
1 TCCCTTTAAACAAGTTTTGTC
*
1773241 TCCCTTGAAACAAGTTTTGTC
1 TCCCTTTAAACAAGTTTTGTC
1773262 TC
1 TC
1773264 ATTTGAGACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (21 bp):
TCCCTTTAAACAAGTTTTGTC
Found at i:1773269 original size:21 final size:21
Alignment explanation
Indices: 1773201--1773277 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
1773191 AGATTTTTTC
1773201 CCTTT-AAACAAGTTTTGTCT
1 CCTTTGAAACAAGTTTTGTCT
*
1773221 CCCTTT-AAACAAGTTTTGCCT
1 -CCTTTGAAACAAGTTTTGTCT
*
1773242 CCCTTGAAACAAGTTTTGTCT
1 CCTTTGAAACAAGTTTTGTCT
* *
1773263 CATTTGAGAC-AGTTT
1 CCTTTGAAACAAGTTT
1773278 CCCTTGAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
20 9 0.18
21 40 0.82
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (21 bp):
CCTTTGAAACAAGTTTTGTCT
Found at i:1773813 original size:34 final size:33
Alignment explanation
Indices: 1773752--1773822 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 33
1773742 ACCTTACAAC
*
1773752 TCCCTAGTTTTTCACGGGTTAAACTAGAACATT
1 TCCCTAGTTTTACACGGGTTAAACTAGAACATT
* *
1773785 TCCCTAGCTTTTACACGGGCTT-AGCTAGAACCTT
1 TCCCTAG-TTTTACACGGG-TTAAACTAGAACATT
1773819 TCCC
1 TCCC
1773823 CTTTACAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 7 0.21
34 24 0.73
35 2 0.06
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (33 bp):
TCCCTAGTTTTACACGGGTTAAACTAGAACATT
Found at i:1774268 original size:34 final size:34
Alignment explanation
Indices: 1774229--1774296 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
1774219 TTCGAAATGG
*
1774229 AGTGCATGGATGCACT-CAGGGTGCATCGATGCAC
1 AGTGCATGGATACACTGCA-GGTGCATCGATGCAC
*
1774263 AGTGCATGGATACACTGCAGGTGCATGGATGCAC
1 AGTGCATGGATACACTGCAGGTGCATCGATGCAC
1774297 TACAGGGTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.21
Consensus pattern (34 bp):
AGTGCATGGATACACTGCAGGTGCATCGATGCAC
Found at i:1774300 original size:24 final size:20
Alignment explanation
Indices: 1774230--1774317 Score: 100
Period size: 19 Copynumber: 4.8 Consensus size: 20
1774220 TCGAAATGGA
1774230 GTGCATGGATGCACT-CAGG
1 GTGCATGGATGCACTACAGG
*
1774249 GTGCATCGATG--C-ACA--
1 GTGCATGGATGCACTACAGG
* *
1774264 GTGCATGGATACACTGCA-G
1 GTGCATGGATGCACTACAGG
1774283 GTGCATGGATGCACTACAGG
1 GTGCATGGATGCACTACAGG
1774303 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1774318 TTGACACCCT
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
15 9 0.16
17 4 0.07
18 2 0.04
19 26 0.46
20 16 0.28
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTACAGG
Found at i:1774563 original size:21 final size:21
Alignment explanation
Indices: 1774539--1774578 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1774529 ATGTTTAATG
1774539 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
1774560 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
1774579 CCAATTCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:1777792 original size:19 final size:19
Alignment explanation
Indices: 1777730--1777817 Score: 87
Period size: 19 Copynumber: 4.8 Consensus size: 19
1777720 TTGAAATGGA
1777730 GTGCATGGATGCACTCAGG
1 GTGCATGGATGCACTCAGG
* *
1777749 GTGAATCGATGCA--CA--
1 GTGCATGGATGCACTCAGG
*
1777764 GTGTATGGATGCACTGCA-G
1 GTGCATGGATGCACT-CAGG
*
1777783 GTGCATGGATGTACTACAGG
1 GTGCATGGATGCACT-CAGG
1777803 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1777818 TTGACACCCT
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
15 11 0.20
17 2 0.04
18 2 0.04
19 26 0.46
20 15 0.27
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (19 bp):
GTGCATGGATGCACTCAGG
Found at i:1782604 original size:41 final size:41
Alignment explanation
Indices: 1782559--1782642 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
1782549 ATAATCCCAT
1782559 GACCTGGTCCGAATATAACATTAGTAACATTGATGTTAGAA
1 GACCTGGTCCGAATATAACATTAGTAACATTGATGTTAGAA
1782600 GACCTGGTCCGAATATAACATTAGTAACATTGATGTTAGAA
1 GACCTGGTCCGAATATAACATTAGTAACATTGATGTTAGAA
1782641 GA
1 GA
1782643 GCCGGGCTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (41 bp):
GACCTGGTCCGAATATAACATTAGTAACATTGATGTTAGAA
Found at i:1790537 original size:21 final size:21
Alignment explanation
Indices: 1790505--1790552 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1790495 GAATAAACAA
*
1790505 ATAT-TATTTATTATATATAT
1 ATATATATATATTATATATAT
*
1790525 ATATATATATATTATATTTAT
1 ATATATATATATTATATATAT
*
1790546 TTATATA
1 ATATATA
1790553 AATAATAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATATATATATTATATATAT
Found at i:1790581 original size:16 final size:15
Alignment explanation
Indices: 1790553--1790587 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1790543 TATTTATATA
*
1790553 AATAATAAGAATAAT
1 AATAAAAAGAATAAT
1790568 AATAAAAAGTAATAAT
1 AATAAAAAG-AATAAT
1790584 AATA
1 AATA
1790588 GAATAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (15 bp):
AATAAAAAGAATAAT
Found at i:1790615 original size:12 final size:12
Alignment explanation
Indices: 1790553--1790617 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
1790543 TATTTATATA
1790553 AATAA-TAAGAAT
1 AATAATTAA-AAT
*
1790565 AATAATAAAAAGT
1 AATAATTAAAA-T
*
1790578 AATAATAATAGAAT
1 AATAAT--TAAAAT
1790592 AAT-ATTACAAAT
1 AATAATTA-AAAT
1790604 AATAATTAAAAT
1 AATAATTAAAAT
1790616 AA
1 AA
1790618 AAGGAATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
11 2 0.05
12 19 0.44
13 15 0.35
14 4 0.09
15 3 0.07
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (12 bp):
AATAATTAAAAT
Found at i:1790672 original size:29 final size:29
Alignment explanation
Indices: 1790600--1790672 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
1790590 ATAATATTAC
1790600 AAATAATAATTAAAATAAAAGGAATTAAAA
1 AAATAATAATTAAAATAAAA-GAATTAAAA
* * *
1790630 ATATAGT-ATTAAAATATAA-AATATAAAA
1 AAATAATAATTAAAATAAAAGAAT-TAAAA
*
1790658 AAATAATAATCAAAA
1 AAATAATAATTAAAA
1790673 ATGAAATTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
27 3 0.09
28 10 0.29
29 17 0.49
30 5 0.14
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.26
Consensus pattern (29 bp):
AAATAATAATTAAAATAAAAGAATTAAAA
Found at i:1791966 original size:3 final size:3
Alignment explanation
Indices: 1791960--1792019 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
1791950 ATTATTTATT
* *
1791960 TAA TAA TAA T-A TAA T-A TAA TAA T-A TTA CAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
*
1792003 -AA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1792020 ATAAAACAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
2 8 0.17
3 37 0.77
4 3 0.06
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1792007 original size:18 final size:17
Alignment explanation
Indices: 1791960--1792020 Score: 70
Period size: 18 Copynumber: 3.6 Consensus size: 17
1791950 ATTATTTATT
* *
1791960 TAATAATAATATAAT-A
1 TAATAATAAAACAATAA
**
1791976 TAATAATATTACAATAA
1 TAATAATAAAACAATAA
1791993 TAATAAATAAAACAATAA
1 TAAT-AATAAAACAATAA
1792011 TAATAATAAA
1 TAATAATAAA
1792021 TAAAACAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
16 13 0.33
17 11 0.28
18 15 0.38
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATAATAAAACAATAA
Found at i:1792017 original size:21 final size:22
Alignment explanation
Indices: 1791988--1792037 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 22
1791978 ATAATATTAC
1791988 AATAATAATAAATAAAAC-AAT
1 AATAATAATAAATAAAACAAAT
1792009 AATAATAATAAATAAAACAAAT
1 AATAATAATAAATAAAACAAAT
1792031 AA-AATAA
1 AATAATAA
1792038 AAAACTAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (22 bp):
AATAATAATAAATAAAACAAAT
Found at i:1792037 original size:24 final size:23
Alignment explanation
Indices: 1791961--1792033 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 23
1791951 TTATTTATTT
* *
1791961 AATAATAATATAATATAATAATATTA
1 AATAATAATA-AATAAAACAA-A-TA
1791987 CAATAATAATAAATAAAAC-AAT-
1 -AATAATAATAAATAAAACAAATA
1792009 AATAATAATAAATAAAACAAATA
1 AATAATAATAAATAAAACAAATA
1792032 AA
1 AA
1792034 ATAAAAAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
21 18 0.43
22 3 0.07
23 3 0.07
24 1 0.02
25 1 0.02
26 6 0.14
27 10 0.24
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
AATAATAATAAATAAAACAAATA
Found at i:1793095 original size:113 final size:113
Alignment explanation
Indices: 1792368--1793095 Score: 1048
Period size: 113 Copynumber: 6.4 Consensus size: 113
1792358 ATTGAGCAAT
* *
1792368 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCAAGT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGCTGATCCATCAAGT
* * *
1792433 GATGAATTCGAGCAAAAAGTTGAACAAGTTTTTCTCATTATGAACTTA
66 GATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* * *
1792481 TTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGTAATGATGATCCATCGAA
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-CTCTGGAAATGCTGATCCATC-AA
* * *
1792545 -TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
64 GTGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* * * *
1792594 TTCTTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTATCTCTGGAAAAGCTGATCCATCGAGT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGCTGATCCATCAAGT
* * *
1792659 GATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
66 GATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* * *
1792707 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTAGAAATGCTGATCCATCAAGT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGCTGATCCATCAAGT
* * * * *
1792772 AATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATAAACTTC
66 GATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* * * *
1792820 TTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTATCTCTGGAAAAGCTAATCCATCAAGT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGCTGATCCATCAAGT
* * *
1792885 GATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
66 GATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* * * *
1792933 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAATGCTAATCCATCAAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGCTGATCCATCAAGT
* * *
1792998 GATGAATTCAAGCAAAAAGTTGAACAAGTTCTTTTCATTATGAACTTC
66 GATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
1793046 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-CTCTGGAAAT
1793096 ATTTTAAGAA
Statistics
Matches: 554, Mismatches: 56, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
112 2 0.00
113 548 0.99
114 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGCTGATCCATCAAGT
GATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
Found at i:1793233 original size:76 final size:76
Alignment explanation
Indices: 1793107--1793288 Score: 303
Period size: 76 Copynumber: 2.4 Consensus size: 76
1793097 TTTTAAGAAA
* * *
1793107 AAACATTC-TGCACTGTAGGGCTTACAGCTGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 AAACA-TCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
1793171 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
1793183 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1793248 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1793259 AAACATCATGCATTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
1793289 TGAGAAATAG
Statistics
Matches: 100, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
75 2 0.02
76 98 0.98
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:1793988 original size:22 final size:22
Alignment explanation
Indices: 1793963--1794017 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1793953 TATAAAGCTT
1793963 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1793985 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1794007 TCATCTTTGAA
1 TCATCTTTGAA
1794018 GAGTGTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1794512 original size:54 final size:54
Alignment explanation
Indices: 1794383--1794540 Score: 198
Period size: 54 Copynumber: 3.0 Consensus size: 54
1794373 AGAATAACTG
* * * *
1794383 GTTCGTAAAACATTTGACAACACATGCATCATCTTATGTGGTTTCTGCTC--A-
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAAAT
* * * *
1794434 GAT-GTAAAACACTTGATAACACATTCATCCTTTTCTATGGTTTCTGCTCAAAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAAAT
* *
1794487 GTTCGTAAAGCATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAAAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAAAT
1794541 TTCTCAATCA
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
50 39 0.44
51 2 0.02
52 1 0.01
53 2 0.02
54 45 0.51
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAAAT
Found at i:1798850 original size:17 final size:16
Alignment explanation
Indices: 1798830--1798936 Score: 79
Period size: 17 Copynumber: 6.2 Consensus size: 16
1798820 ATTTCTCCCC
1798830 TTTTTCTTTTTCCCTTTT
1 TTTTTCTTTTT-CC-TTT
* *
1798848 TTTTTCCTTTTTTCTCAT
1 TTTTT-CTTTTTCCT-TT
*
1798866 TTTTCCTTTTTCATCTTT
1 TTTTTCTTTTTC--CTTT
*
1798884 TTTTTCTTTTTTTCTTT
1 TTTTTC-TTTTTCCTTT
* *
1798901 TTTCTCATTTTTCTTTT
1 TTTTTC-TTTTTCCTTT
*
1798918 TTTTTCTTTTTTCTTT
1 TTTTTCTTTTTCCTTT
1798934 TTT
1 TTT
1798937 CTTTCTTTGC
Statistics
Matches: 70, Mismatches: 14, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
16 11 0.16
17 29 0.41
18 17 0.24
19 13 0.19
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTCTTTTTCCTTT
Found at i:1798858 original size:9 final size:8
Alignment explanation
Indices: 1798846--1798940 Score: 79
Period size: 8 Copynumber: 11.4 Consensus size: 8
1798836 TTTTTCCCTT
1798846 TTTTTTTCC
1 TTTTTTT-C
1798855 TTTTTTCTC
1 TTTTTT-TC
* *
1798864 ATTTTTCC
1 TTTTTTTC
*
1798872 TTTTTCATC
1 TTTTT-TTC
1798881 TTTTTTTTC
1 -TTTTTTTC
1798890 TTTTTTTC
1 TTTTTTTC
1798898 TTTTTTCTC
1 TTTTTT-TC
1798907 ATTTTTCTT-
1 -TTTTT-TTC
1798916 TTTTTTTC
1 TTTTTTTC
1798924 -TTTTTTC
1 TTTTTTTC
1798931 -TTTTTTC
1 TTTTTTTC
1798938 TTT
1 TTT
1798941 CTTTGCTGGA
Statistics
Matches: 72, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
7 16 0.22
8 26 0.36
9 17 0.24
10 12 0.17
11 1 0.01
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1798858 original size:10 final size:9
Alignment explanation
Indices: 1798845--1798944 Score: 73
Period size: 9 Copynumber: 11.3 Consensus size: 9
1798835 CTTTTTCCCT
1798845 TTTTTTTTC
1 TTTTTTTTC
*
1798854 -CTTTTTTC
1 TTTTTTTTC
* *
1798862 TCATTTTTCC
1 T-TTTTTTTC
**
1798872 TTTTTCATC
1 TTTTTTTTC
1798881 TTTTTTTTC
1 TTTTTTTTC
1798890 -TTTTTTTC
1 TTTTTTTTC
*
1798898 TTTTTTCTC
1 TTTTTTTTC
* *
1798907 ATTTTTCT-
1 TTTTTTTTC
1798915 TTTTTTTTC
1 TTTTTTTTC
1798924 TTTTTTCTT-
1 TTTTTT-TTC
*
1798933 TTTTCTTTC
1 TTTTTTTTC
1798942 TTT
1 TTT
1798945 GCTGGATTTT
Statistics
Matches: 71, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
8 23 0.32
9 39 0.55
10 9 0.13
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1798902 original size:33 final size:33
Alignment explanation
Indices: 1798843--1798938 Score: 124
Period size: 36 Copynumber: 2.8 Consensus size: 33
1798833 TTCTTTTTCC
1798843 CTTTTTTTTTCCTTTTTTCTCATTTTTC-C-TTTTT
1 CTTTTTTTTT-CTTTTTTCT--TTTTTCTCATTTTT
1798877 CATCTTTTTTTTCTTTTTTTCTTTTTTCTCATTTTT
1 C-T-TTTTTTTTC-TTTTTTCTTTTTTCTCATTTTT
1798913 CTTTTTTTTTCTTTTTTCTTTTTTCT
1 CTTTTTTTTTCTTTTTTCTTTTTTCT
1798939 TTCTTTGCTG
Statistics
Matches: 57, Mismatches: 0, Indels: 11
0.84 0.00 0.16
Matches are distributed among these distances:
33 15 0.26
34 16 0.28
35 4 0.07
36 22 0.39
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (33 bp):
CTTTTTTTTTCTTTTTTCTTTTTTCTCATTTTT
Found at i:1798908 original size:43 final size:44
Alignment explanation
Indices: 1798846--1798965 Score: 142
Period size: 43 Copynumber: 2.8 Consensus size: 44
1798836 TTTTTCCCTT
1798846 TTTTTTTCCTTTTTTCTCATTTTTCCTTTTTCATCTT-TTTTTTC
1 TTTTTTT-CTTTTTTCTCATTTTTCCTTTTTCATCTTCTTTTTTC
*
1798890 TTTTTTTCTTTTTTCTCATTTTT-CTTTTT--TTTTCTTTTTTC
1 TTTTTTTCTTTTTTCTCATTTTTCCTTTTTCATCTTCTTTTTTC
* *
1798931 -TTTTTTCTTTCTTTGCTGGATTTTTCTTTTTTCAT
1 TTTTTTTCTTT-TTT-CT-CATTTTTCCTTTTTCAT
1798966 TATTTGTTGG
Statistics
Matches: 66, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
40 13 0.20
41 10 0.15
42 8 0.12
43 22 0.33
44 12 0.18
46 1 0.02
ACGTcount: A:0.04, C:0.17, G:0.03, T:0.77
Consensus pattern (44 bp):
TTTTTTTCTTTTTTCTCATTTTTCCTTTTTCATCTTCTTTTTTC
Found at i:1798920 original size:24 final size:22
Alignment explanation
Indices: 1798848--1798940 Score: 62
Period size: 26 Copynumber: 3.8 Consensus size: 22
1798838 TTTCCCTTTT
* *
1798848 TTTTTCCTTTTTTCTCATTTTTCC
1 TTTTTTCTTTTTT-TC-TTTTTTC
1798872 TTTTTCATCTTTTTTTTCTTTTTTTC
1 TTTTT--TC-TTTTTTTC-TTTTTTC
*
1798898 TTTTTTCTCATTTTTCTTTTTTTTTC
1 -TTTTT-TC-TTTTT-TTCTTTTTTC
1798924 TTTTTTC-TTTTTTCTTT
1 TTTTTTCTTTTTTTCTTT
1798941 CTTTGCTGGA
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
21 5 0.09
22 4 0.07
24 7 0.12
25 5 0.09
26 23 0.40
27 13 0.23
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTTCTTTTTTTCTTTTTTC
Found at i:1798954 original size:26 final size:26
Alignment explanation
Indices: 1798925--1798977 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1798915 TTTTTTTTCT
* *
1798925 TTTTTCTTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCATTATTTGCTGGA
*
1798951 TTTTTCTTTTTTCATTATTTGTTGGA
1 TTTTTCTTTTTTCATTATTTGCTGGA
1798977 T
1 T
1798978 GAGTATAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.08, C:0.11, G:0.11, T:0.70
Consensus pattern (26 bp):
TTTTTCTTTTTTCATTATTTGCTGGA
Found at i:1798955 original size:33 final size:32
Alignment explanation
Indices: 1798884--1798963 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 32
1798874 TTTCATCTTT
***
1798884 TTTTTCTTTTTTTCTTTTTTCTCATTTTTCTTTT
1 TTTTTC-TTTTTTCTTTTTTCT-ATTTTTCTGGA
1798918 TTTTTCTTTTTTCTTTTTTCT-TTCTTTGCTGGA
1 TTTTTCTTTTTTCTTTTTTCTATT-TTT-CTGGA
1798951 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
1798964 ATTATTTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
31 2 0.05
32 3 0.07
33 30 0.73
34 6 0.15
ACGTcount: A:0.03, C:0.15, G:0.04, T:0.79
Consensus pattern (32 bp):
TTTTTCTTTTTTCTTTTTTCTATTTTTCTGGA
Found at i:1801802 original size:12 final size:12
Alignment explanation
Indices: 1801767--1801814 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
1801757 GAAATATGAA
*
1801767 AAATGTAAATAC
1 AAATGTAAATGC
*
1801779 AAACGTAAAAATGC
1 AAATGT--AAATGC
1801793 AAATGTAAATGC
1 AAATGTAAATGC
1801805 AAATGTAAAT
1 AAATGTAAAT
1801815 ATATGAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 21 0.68
14 10 0.32
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.23
Consensus pattern (12 bp):
AAATGTAAATGC
Found at i:1801823 original size:26 final size:25
Alignment explanation
Indices: 1801767--1801826 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
1801757 GAAATATGAA
1801767 AAATGTAAATACAAACGTAAAAATG
1 AAATGTAAATACAAACGTAAAAATG
* *
1801792 CAAATGTAAATGCAAATGTAAATATATG
1 -AAATGTAAATACAAACGTAAA-A-ATG
1801820 -AATGTAA
1 AAATGTAA
1801827 TAATAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 26 0.87
27 1 0.03
28 3 0.10
ACGTcount: A:0.55, C:0.07, G:0.13, T:0.25
Consensus pattern (25 bp):
AAATGTAAATACAAACGTAAAAATG
Found at i:1803436 original size:28 final size:26
Alignment explanation
Indices: 1803381--1803438 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
1803371 AAACATTAAT
*
1803381 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
1803407 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
1803435 AAAA
1 AAAA
1803439 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:1804051 original size:20 final size:20
Alignment explanation
Indices: 1804026--1804077 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
1804016 TTTCTTCGAT
1804026 ATTAAAAAAATAAATAAATA
1 ATTAAAAAAATAAATAAATA
* * * *
1804046 ATTAAAACAATTAATATATG
1 ATTAAAAAAATAAATAAATA
*
1804066 ATTTAAAAAATA
1 ATTAAAAAAATA
1804078 GGATATTTAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
ATTAAAAAAATAAATAAATA
Found at i:1804257 original size:18 final size:16
Alignment explanation
Indices: 1804226--1804260 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1804216 GAATAAACAA
1804226 ATATTATTTATTATAT
1 ATATTATTTATTATAT
1804242 ATATATATTTATT-TAT
1 ATAT-TATTTATTATAT
1804258 ATA
1 ATA
1804261 AATAATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTATTTATTATAT
Found at i:1804277 original size:16 final size:14
Alignment explanation
Indices: 1804261--1804303 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
1804251 TATTTATATA
1804261 AATAATAAGAATAAT
1 AATAATAA-AATAAT
*
1804276 AATAA-AAAGTAAT
1 AATAATAAAATAAT
1804289 AATAATAAAATAAT
1 AATAATAAAATAAT
1804303 A
1 A
1804304 TTGCAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 10 0.40
14 10 0.40
15 5 0.20
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (14 bp):
AATAATAAAATAAT
Found at i:1804317 original size:3 final size:3
Alignment explanation
Indices: 1804261--1804303 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
1804251 TATTTATATA
* *
1804261 AAT AAT AAG AAT AAT AAT AAA AAGT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT A
1804304 TTGCAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:1804323 original size:12 final size:12
Alignment explanation
Indices: 1804261--1804325 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
1804251 TATTTATATA
1804261 AATAA-TAAGAAT
1 AATAATTAA-AAT
*
1804273 AATAATAAAAAGT
1 AATAATTAAAA-T
1804286 AATAATAATAAAAT
1 AATAAT--TAAAAT
*
1804300 AAT-ATTGCAAAT
1 AATAATT-AAAAT
1804312 AATAATTAAAAT
1 AATAATTAAAAT
1804324 AA
1 AA
1804326 AAGGAATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
11 1 0.02
12 20 0.47
13 14 0.33
14 4 0.09
15 4 0.09
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (12 bp):
AATAATTAAAAT
Found at i:1804380 original size:29 final size:29
Alignment explanation
Indices: 1804308--1804380 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
1804298 ATAATATTGC
1804308 AAATAATAATTAAAATAAAAGGAATTAAAA
1 AAATAATAATTAAAATAAAA-GAATTAAAA
* * *
1804338 ATATAGT-ATTAAAATATAA-AATATAAAA
1 AAATAATAATTAAAATAAAAGAAT-TAAAA
*
1804366 AAATAATAATCAAAA
1 AAATAATAATTAAAA
1804381 ATGAAATTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
27 3 0.09
28 10 0.29
29 17 0.49
30 5 0.14
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.26
Consensus pattern (29 bp):
AAATAATAATTAAAATAAAAGAATTAAAA
Found at i:1805678 original size:3 final size:3
Alignment explanation
Indices: 1805672--1805731 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
1805662 ATTATTTATT
*
1805672 TAA TAA TAA T-A TAA T-A TAA TAA TAT TAA -AA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
*
1805715 -AA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1805732 ATAAAACAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
2 8 0.16
3 38 0.78
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1805703 original size:11 final size:11
Alignment explanation
Indices: 1805672--1805732 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
1805662 ATTATTTATT
1805672 TAATAATAAT-A
1 TAATAA-AATAA
*
1805683 TAATATAATAA
1 TAATAAAATAA
*
1805694 TATTAAAATAA
1 TAATAAAATAA
1805705 TAAT-AAATAA
1 TAATAAAATAA
*
1805715 -AACAATAATAA
1 TAATAA-AATAA
1805726 TAATAAA
1 TAATAAA
1805733 TAAAACAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 2 0.05
10 10 0.25
11 24 0.60
12 4 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:1805749 original size:21 final size:21
Alignment explanation
Indices: 1805700--1805740 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1805690 ATAATATTAA
1805700 AATAATAATAAATAAAACAAT
1 AATAATAATAAATAAAACAAT
1805721 AATAATAATAAATAAAACAA
1 AATAATAATAAATAAAACAA
1805741 ATGAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (21 bp):
AATAATAATAAATAAAACAAT
Found at i:1820884 original size:17 final size:16
Alignment explanation
Indices: 1820857--1820892 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1820847 ACGAATCACT
*
1820857 ATTTTTGATATCTAAA
1 ATTTTTGATATATAAA
1820873 ATTTTGTGATATATAAA
1 ATTTT-TGATATATAAA
1820890 ATT
1 ATT
1820893 ATACACCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (16 bp):
ATTTTTGATATATAAA
Found at i:1824585 original size:27 final size:27
Alignment explanation
Indices: 1824540--1824608 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
1824530 GAAGATAAAA
** *
1824540 TATTTTATTGTATTATATTAAATTAA-
1 TATTTTATTAAATTTTATTAAATTAAC
*
1824566 TAATTTTATTAAATTTTATTATATTAAC
1 T-ATTTTATTAAATTTTATTAAATTAAC
*
1824594 T-TTTTATTAATTTTT
1 TATTTTATTAAATTTT
1824609 TAGTTATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 14 0.39
27 21 0.58
28 1 0.03
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (27 bp):
TATTTTATTAAATTTTATTAAATTAAC
Found at i:1830981 original size:21 final size:22
Alignment explanation
Indices: 1830951--1831055 Score: 122
Period size: 23 Copynumber: 4.7 Consensus size: 22
1830941 AGAACCCCCA
* *
1830951 GGGGGTATCGATTCCCCTTC-G
1 GGGGGAATCGGTTCCCCTTCAG
1830972 GGGGGAATCGGTTCCCCTTCAGG
1 GGGGGAATCGGTTCCCCTTCA-G
*
1830995 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTC-AG
*
1831018 GGGGGAATTGGTTCCCCTTCAG
1 GGGGGAATCGGTTCCCCTTCAG
* * *
1831040 GAGGGTATCGATTCCC
1 GGGGGAATCGGTTCCC
1831056 TCTGCACCAA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
21 18 0.25
22 13 0.18
23 40 0.56
24 1 0.01
ACGTcount: A:0.15, C:0.26, G:0.34, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCCTTCAG
Found at i:1838120 original size:29 final size:29
Alignment explanation
Indices: 1838047--1838114 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
1838037 GGCCCTCAAT
* *
1838047 TTTTTTGTATTTATAATTAAGGTCCCTAA
1 TTTTTTATATTTATAATTAAGGCCCCTAA
1838076 TTTTTTATATTTATAATT-AGGCCCCTAA
1 TTTTTTATATTTATAATTAAGGCCCCTAA
1838104 -TTTTTATATTT
1 TTTTTTATATTT
1838115 TCATAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 11 0.30
28 9 0.24
29 17 0.46
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.56
Consensus pattern (29 bp):
TTTTTTATATTTATAATTAAGGCCCCTAA
Found at i:1838315 original size:118 final size:116
Alignment explanation
Indices: 1838072--1838305 Score: 346
Period size: 118 Copynumber: 2.0 Consensus size: 116
1838062 ATTAAGGTCC
* **
1838072 CTAATTTTTTATATTTATAATTAGGCCCCTAATTTTTATATTTTCATAAAATTTTAGTTTTTGAC
1 CTAATTTTTTATATTTATAATTAGGCCCCTAATTCTTATAAGTTCATAAAATTTTAGTTTTTGAC
* * *
1838137 CCCCTTGTTTCATTTCTCTTATTAATTCATCTAATTTTGAATTAGATTTAA
66 CCCCTTGTTTCATTTATCTTATTAATTCATCTAATTTTAAATTAAATTTAA
1838188 CTAATTTTTTATATTTATAATTAGGCCCCCTAATTCTTATAAGTTCATAAAATGTTTAGTTTTTG
1 CTAATTTTTTATATTTATAATTAGG-CCCCTAATTCTTATAAGTTCATAAAAT-TTTAGTTTTTG
* *
1838253 ACCCTCTT-TTTCCATTTATCTTATTTATTCAT-TCAATTTTAAATTAAATTTAA
64 ACCCCCTTGTTT-CATTTATCTTATTAATTCATCT-AATTTTAAATTAAATTTAA
1838306 TCATATTTTT
Statistics
Matches: 106, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
116 25 0.24
117 28 0.26
118 53 0.50
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.52
Consensus pattern (116 bp):
CTAATTTTTTATATTTATAATTAGGCCCCTAATTCTTATAAGTTCATAAAATTTTAGTTTTTGAC
CCCCTTGTTTCATTTATCTTATTAATTCATCTAATTTTAAATTAAATTTAA
Found at i:1851655 original size:20 final size:21
Alignment explanation
Indices: 1851630--1851670 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
1851620 ACTTTGTATA
1851630 ATAGTATCGATACCAT-AGGC
1 ATAGTATCGATACCATCAGGC
1851650 ATAGTATCGATACCATCAGGC
1 ATAGTATCGATACCATCAGGC
1851671 CACAACGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (21 bp):
ATAGTATCGATACCATCAGGC
Found at i:1851788 original size:19 final size:21
Alignment explanation
Indices: 1851751--1851790 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
1851741 TGCAGATATT
1851751 TCATCCCCAAATGGCTAGAAA
1 TCATCCCCAAATGGCTAGAAA
1851772 TCATCCCC-AAT-GCTAGAAA
1 TCATCCCCAAATGGCTAGAAA
1851791 CAACTACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 3 0.16
21 8 0.42
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.20
Consensus pattern (21 bp):
TCATCCCCAAATGGCTAGAAA
Found at i:1852571 original size:19 final size:20
Alignment explanation
Indices: 1852525--1852575 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1852515 AAATTATTTG
* *
1852525 TGAGTATCGATATTGACCCT
1 TGAGTATCGATATTGAACCA
*
1852545 TCAGTATCGATA-TGAACCA
1 TGAGTATCGATATTGAACCA
1852564 TGAGTATCGATA
1 TGAGTATCGATA
1852576 CCCACCACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (20 bp):
TGAGTATCGATATTGAACCA
Found at i:1853837 original size:21 final size:19
Alignment explanation
Indices: 1853799--1853844 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1853789 AATTAATCCT
1853799 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
1853819 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
1853840 A-TAAT
1 ACTAAT
1853845 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:1855023 original size:19 final size:19
Alignment explanation
Indices: 1855001--1855039 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1854991 AAATCTACTT
1855001 CTCACGTTCTCATCTGCTC
1 CTCACGTTCTCATCTGCTC
1855020 CTCACGTTCTCATCTGCTC
1 CTCACGTTCTCATCTGCTC
1855039 C
1 C
1855040 ATTGGCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.44, G:0.10, T:0.36
Consensus pattern (19 bp):
CTCACGTTCTCATCTGCTC
Found at i:1856541 original size:19 final size:19
Alignment explanation
Indices: 1856512--1856557 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
1856502 GACTAGGAGC
*
1856512 TGTTG-TTGGGGCTGGTGG
1 TGTTGATTGGGGCTGGTGA
1856530 TGTTGATTGGGGCTGGTGA
1 TGTTGATTGGGGCTGGTGA
1856549 TGTTGATTG
1 TGTTGATTG
1856558 AACTGGGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.07, C:0.04, G:0.48, T:0.41
Consensus pattern (19 bp):
TGTTGATTGGGGCTGGTGA
Found at i:1856765 original size:24 final size:24
Alignment explanation
Indices: 1856738--1856794 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1856728 GGGTTACCAA
* *
1856738 TGGTGGCACATCAGTGGGCACACC-
1 TGGTGGAACATCAATGGGCAC-CCT
*
1856762 TGGTAGAACATCAATGGGCACCCT
1 TGGTGGAACATCAATGGGCACCCT
1856786 TGGTGGAAC
1 TGGTGGAAC
1856795 GTCTGGAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.25, C:0.25, G:0.32, T:0.19
Consensus pattern (24 bp):
TGGTGGAACATCAATGGGCACCCT
Found at i:1864278 original size:21 final size:19
Alignment explanation
Indices: 1864240--1864285 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1864230 AATTATTCCT
1864240 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
1864260 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
1864281 A-TAAT
1 ACTAAT
1864286 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:1871286 original size:122 final size:123
Alignment explanation
Indices: 1871069--1871313 Score: 483
Period size: 122 Copynumber: 2.0 Consensus size: 123
1871059 GTGATGTATG
1871069 TATCAGTACTGTTCTTCTAGTACTCATACTCAGGCCCGAAAATGCCCTTCTTTTACCCCAGAATA
1 TATCAGTACTGTTCTTCTAGTACTCATACTCAGGCCCGAAAATGCCCTTCTTTTACCCCAGAATA
1871134 TCCTATTGAGGTTCTCAATTGTTATTAGAGTGTTATGTCTGATAAA-GGGCTCATAAA
66 TCCTATTGAGGTTCTCAATTGTTATTAGAGTGTTATGTCTGATAAAGGGGCTCATAAA
1871191 TATCAGTACTGTTCTTCTAGTACTCATACTCAGGCCCGAAAATGCCCTTCTTTTACCCCAGAATA
1 TATCAGTACTGTTCTTCTAGTACTCATACTCAGGCCCGAAAATGCCCTTCTTTTACCCCAGAATA
1871256 TCCTATTGAGGTTCTCAATTGTTATTAGAGTGTTATGTCTGATAAAGGGGCTCATAAA
66 TCCTATTGAGGTTCTCAATTGTTATTAGAGTGTTATGTCTGATAAAGGGGCTCATAAA
1871314 GAGTCCATAA
Statistics
Matches: 122, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
122 111 0.91
123 11 0.09
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (123 bp):
TATCAGTACTGTTCTTCTAGTACTCATACTCAGGCCCGAAAATGCCCTTCTTTTACCCCAGAATA
TCCTATTGAGGTTCTCAATTGTTATTAGAGTGTTATGTCTGATAAAGGGGCTCATAAA
Found at i:1871476 original size:49 final size:49
Alignment explanation
Indices: 1871404--1871505 Score: 195
Period size: 49 Copynumber: 2.1 Consensus size: 49
1871394 ACCTAATGAT
*
1871404 CTACATGTGATAAAGTTGAGTTAGAAGTGCGTTACCTTGTGATTCTAAG
1 CTACATGTGATAAAGTTGAGTTAGAAGTGAGTTACCTTGTGATTCTAAG
1871453 CTACATGTGATAAAGTTGAGTTAGAAGTGAGTTACCTTGTGATTCTAAG
1 CTACATGTGATAAAGTTGAGTTAGAAGTGAGTTACCTTGTGATTCTAAG
1871502 CTAC
1 CTAC
1871506 TGAAAGTGTC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (49 bp):
CTACATGTGATAAAGTTGAGTTAGAAGTGAGTTACCTTGTGATTCTAAG
Found at i:1872162 original size:23 final size:23
Alignment explanation
Indices: 1872115--1872164 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1872105 AATAACATAT
* **
1872115 TAGGTAGCGCTTATACAATGTAA
1 TAGGTAGCACTTATACAATAAAA
*
1872138 TAGGTAGCACTTATATAATAAAA
1 TAGGTAGCACTTATACAATAAAA
1872161 TAGG
1 TAGG
1872165 CATTTAACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (23 bp):
TAGGTAGCACTTATACAATAAAA
Done.