Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 7 of 373
Found at i:2021713 original size:20 final size:20
Alignment explanation
Indices: 2021688--2021728 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2021678 ATAAATGAAT
2021688 AGACTAAAATACCTTAAATA
1 AGACTAAAATACCTTAAATA
2021708 AGACTAAAATACCTTAAATA
1 AGACTAAAATACCTTAAATA
2021728 A
1 A
2021729 TATACTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.24
Consensus pattern (20 bp):
AGACTAAAATACCTTAAATA
Found at i:2022564 original size:21 final size:21
Alignment explanation
Indices: 2022539--2022580 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2022529 GCATTAATTC
2022539 AATA-AAAAAT-TTAAATAAT
1 AATATAAAAATATTAAATAAT
*
2022558 AATATAAATATATTAAATAAT
1 AATATAAAAATATTAAATAAT
2022579 AA
1 AA
2022581 AGGAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 5 0.25
21 11 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATATAAAAATATTAAATAAT
Found at i:2022587 original size:21 final size:21
Alignment explanation
Indices: 2022549--2022588 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2022539 AATAAAAAAT
*
2022549 TTAAATAATAATATAAATATA
1 TTAAATAATAATAGAAATATA
2022570 TTAAATAATAA-AGGAAATA
1 TTAAATAATAATA-GAAATA
2022589 AATAGTGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
TTAAATAATAATAGAAATATA
Found at i:2026607 original size:20 final size:20
Alignment explanation
Indices: 2026568--2026617 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2026558 AATAATAATA
*
2026568 TTTAGATTTTAGTATTTTTT
1 TTTAGATTTTAGTATATTTT
*
2026588 TTTAGATTTTA-TATAATTT
1 TTTAGATTTTAGTATATTTT
* *
2026607 TATAAATTTTA
1 TTTAGATTTTA
2026618 AGTGATAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (20 bp):
TTTAGATTTTAGTATATTTT
Found at i:2027705 original size:5 final size:5
Alignment explanation
Indices: 2027697--2027725 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2027687 TCATAAGAGA
2027697 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
2027726 CGAGAACTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:2036542 original size:30 final size:30
Alignment explanation
Indices: 2036503--2036560 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
2036493 TTTAACAAAT
2036503 AAATATCTTTAAAATAATAACAAAATTAAC
1 AAATATCTTTAAAATAATAACAAAATTAAC
*
2036533 AAATGTCTTTAAAATAATAACAAAATTA
1 AAATATCTTTAAAATAATAACAAAATTA
2036561 TCAATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.31
Consensus pattern (30 bp):
AAATATCTTTAAAATAATAACAAAATTAAC
Found at i:2047608 original size:32 final size:28
Alignment explanation
Indices: 2047554--2047626 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 28
2047544 GAGAAAATTC
* *
2047554 AATATTTAATTTTTGATATTTCAAAATTTA
1 AATATTTAATTTTTAAGATTTCAAAA--TA
*
2047584 TATATATTTAATTTTTAAGCTTTCAAAATA
1 -A-ATATTTAATTTTTAAGATTTCAAAATA
2047614 AATATTTAATTTT
1 AATATTTAATTTT
2047627 AAAATTTACA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 12 0.32
29 1 0.03
30 2 0.05
31 1 0.03
32 22 0.58
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (28 bp):
AATATTTAATTTTTAAGATTTCAAAATA
Found at i:2050001 original size:31 final size:31
Alignment explanation
Indices: 2049926--2050010 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
2049916 AACTCAAAAC
* *
2049926 TCACTAAACTATTCAGGAA-TTTT-AATTTAAA
1 TCACTAAACTATTTA-AAAGTTTTCAA-TTAAA
* * *
2049957 TCATTAAATTATTTGAAAGTTTTCAATTAAA
1 TCACTAAACTATTTAAAAGTTTTCAATTAAA
*
2049988 TTACTAAACTATTTAAAAGTTTT
1 TCACTAAACTATTTAAAAGTTTT
2050011 TATTGAAGTC
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
30 2 0.05
31 39 0.91
32 2 0.05
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (31 bp):
TCACTAAACTATTTAAAAGTTTTCAATTAAA
Found at i:2054743 original size:28 final size:28
Alignment explanation
Indices: 2054687--2054761 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
2054677 GATATTAATA
** * *
2054687 TATTTTTATTTTAAAATAATATTTTTAT
1 TATTTTTATTTTAAAATTTTATATATAT
2054715 TATTTTTATTTTAAAATTTTATATATAT
1 TATTTTTATTTTAAAATTTTATATATAT
*
2054743 T-TTTATT-TGTTAAAATTTT
1 TATTT-TTATTTTAAAATTTT
2054762 CTATGTGTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 14 0.34
28 27 0.66
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (28 bp):
TATTTTTATTTTAAAATTTTATATATAT
Found at i:2055371 original size:23 final size:23
Alignment explanation
Indices: 2055345--2055388 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2055335 ACCAATTATG
2055345 TAATATA-TAAAAACAATATAATA
1 TAATATATTAAAAAC-ATATAATA
*
2055368 TAATATATTATAAACATATAA
1 TAATATATTAAAAACATATAA
2055389 AATAGATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (23 bp):
TAATATATTAAAAACATATAATA
Found at i:2058706 original size:13 final size:13
Alignment explanation
Indices: 2058690--2058714 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2058680 TCTTAAAGTT
2058690 TTTTTTGTTTTTG
1 TTTTTTGTTTTTG
2058703 TTTTTTGTTTTT
1 TTTTTTGTTTTT
2058715 TTTCAAGGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTTGTTTTTG
Found at i:2058937 original size:40 final size:39
Alignment explanation
Indices: 2058893--2059030 Score: 131
Period size: 40 Copynumber: 3.5 Consensus size: 39
2058883 TGGCGTTTGA
2058893 ATAAAAAACGCCGCTAAAAATCAATCATTAGCGGCGCTAT
1 ATAAAAAACGCCGCTAAAAATCAATCATTAGCGGCGCT-T
* *
2058933 ATAAAAAACGCCGCTAAAGATCGAGT-ATTAGCGGCGCTT
1 ATAAAAAACGCCGCTAAAAATC-AATCATTAGCGGCGCTT
* * * * *
2058972 TTCTAAAAACGCCACTAAAAAT-GAGCATTAGCGGCG-TT
1 AT-AAAAAACGCCGCTAAAAATCAATCATTAGCGGCGCTT
*
2059010 TTACAAAAAGCGCCGC-AAAAA
1 ATA-AAAAA-CGCCGCTAAAAA
2059031 CCTAAACCTA
Statistics
Matches: 82, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
38 14 0.17
39 17 0.21
40 49 0.60
41 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.20
Consensus pattern (39 bp):
ATAAAAAACGCCGCTAAAAATCAATCATTAGCGGCGCTT
Found at i:2059265 original size:41 final size:41
Alignment explanation
Indices: 2059070--2059265 Score: 311
Period size: 41 Copynumber: 4.8 Consensus size: 41
2059060 TTTTTAGCGA
* *
2059070 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTAGTC
1 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTC
* * * *
2059111 TTTAGCGGCGTTTTTGATGAAGCGCCACTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTC
* *
2059152 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAAATCTCTGGTC
1 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTC
2059193 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTC
1 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTC
*
2059234 TTTAGGGGCGTTTTTTAAGAAGCGCCGCTAAA
1 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAAA
2059266 AGCATTTTAT
Statistics
Matches: 144, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 144 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.33
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAAAGCTCTGGTC
Found at i:2059855 original size:15 final size:15
Alignment explanation
Indices: 2059835--2059866 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2059825 TATTTTAATG
2059835 TTTAGGGAGTATGGA
1 TTTAGGGAGTATGGA
*
2059850 TTTAGGGATTATGGA
1 TTTAGGGAGTATGGA
2059865 TT
1 TT
2059867 AGCGTTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (15 bp):
TTTAGGGAGTATGGA
Found at i:2060608 original size:21 final size:21
Alignment explanation
Indices: 2060584--2060651 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
2060574 TAAATAAGGT
2060584 TTAGGGGTTAGTAGTTAGGGG
1 TTAGGGGTTAGTAGTTAGGGG
*
2060605 TTAGGGGTTAG-ATGTTAGAGG
1 TTAGGGGTTAGTA-GTTAGGGG
* * * *
2060626 TTAAGAGTTAGTGATTTAGGGT
1 TTAGGGGTTAGT-AGTTAGGGG
2060648 TTAG
1 TTAG
2060652 ATATTCGGGG
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.03
21 27 0.73
22 8 0.22
23 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.40, T:0.37
Consensus pattern (21 bp):
TTAGGGGTTAGTAGTTAGGGG
Found at i:2060812 original size:50 final size:49
Alignment explanation
Indices: 2060732--2060829 Score: 160
Period size: 50 Copynumber: 2.0 Consensus size: 49
2060722 TAATTGTAAA
* * *
2060732 ATAGGGGTTAGGGTTTAGAGTTTTTGTTTTATGATTTAGGGTTTAGGAG
1 ATAGGGGTTAGGGTTTAGAGTTTCTATTTTACGATTTAGGGTTTAGGAG
2060781 ATAGGGGTTAGGGGTTTAGAGTTTCTATTTTACGATTTAGGGTTTAGGA
1 ATAGGGGTTA-GGGTTTAGAGTTTCTATTTTACGATTTAGGGTTTAGGA
2060830 TTAATTGGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 10 0.22
50 35 0.78
ACGTcount: A:0.21, C:0.02, G:0.34, T:0.43
Consensus pattern (49 bp):
ATAGGGGTTAGGGTTTAGAGTTTCTATTTTACGATTTAGGGTTTAGGAG
Found at i:2064429 original size:27 final size:26
Alignment explanation
Indices: 2064399--2064455 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
2064389 AATTTCGAGG
*
2064399 TTTACAATTTT-TAATTTTTATTAATT
1 TTTA-AATTTTCTAACTTTTATTAATT
* *
2064425 ATTTATATTTTCTCACTTTTATTAATT
1 -TTTAAATTTTCTAACTTTTATTAATT
2064452 TTTA
1 TTTA
2064456 TTATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTAAATTTTCTAACTTTTATTAATT
Found at i:2064759 original size:42 final size:42
Alignment explanation
Indices: 2064703--2064845 Score: 198
Period size: 43 Copynumber: 3.4 Consensus size: 42
2064693 TTTGAGATAA
* * *
2064703 AAAGCGTCGCTAAAGATCATAGTCTTTAGCGGCATTTGTGGG
1 AAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCATTTGTGGG
*
2064745 AAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGATTATG-GGA
1 AAAGCGCCGCTAAAGAACATGGTCTTTAGCGGC-ATT-TGTGGG
*
2064788 AAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTGTGGG
1 AAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCATTTGTGGG
*
2064830 AGAAGCGCCGCAAAAG
1 A-AAGCGCCGCTAAAG
2064846 TTAGCGACGT
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
41 2 0.02
42 35 0.39
43 51 0.57
44 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.22
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCATTTGTGGG
Found at i:2064931 original size:22 final size:22
Alignment explanation
Indices: 2064903--2064946 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2064893 TAGTGGCGCT
*
2064903 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
2064925 AAAAAGCGCCGCTAAAAGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
2064947 TTTTGGTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.27, G:0.20, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:2067004 original size:18 final size:18
Alignment explanation
Indices: 2066977--2067069 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
2066967 TACGACCGTT
*
2066977 TACGGTACTATTCACGTA
1 TACGGCACTATTCACGTA
2066995 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
* *
2067013 TACAGTACTATTCACGTA
1 TACGGCACTATTCACGTA
2067031 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
* *
2067049 TACGGGACTGTTCACGTA
1 TACGGCACTATTCACGTA
2067067 TAC
1 TAC
2067070 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:2072619 original size:23 final size:23
Alignment explanation
Indices: 2072589--2072636 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2072579 CTGATGTAAG
2072589 GTGTTTCTTAGTTTTTTGTTCTT
1 GTGTTTCTTAGTTTTTTGTTCTT
2072612 GTGTTTCTTAGTTTTTTGTTCTT
1 GTGTTTCTTAGTTTTTTGTTCTT
2072635 GT
1 GT
2072637 TCCTTTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.04, C:0.08, G:0.19, T:0.69
Consensus pattern (23 bp):
GTGTTTCTTAGTTTTTTGTTCTT
Found at i:2083171 original size:18 final size:18
Alignment explanation
Indices: 2083150--2083184 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2083140 TTTCCTTTCT
* *
2083150 TTTTTGGCTTTGTTTATC
1 TTTTCGGCTCTGTTTATC
2083168 TTTTCGGCTCTGTTTAT
1 TTTTCGGCTCTGTTTAT
2083185 TGCAAAACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.14, G:0.17, T:0.63
Consensus pattern (18 bp):
TTTTCGGCTCTGTTTATC
Found at i:2088645 original size:42 final size:42
Alignment explanation
Indices: 2088578--2088661 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
2088568 TTTCATAGAG
* * *
2088578 GGTGGTGGTGCAGGAGGACTGGCTCTAATTGGGGCAGCAGGT
1 GGTGGTGGTGCAGGAGAACTAGCTCTAATCGGGGCAGCAGGT
* *
2088620 GGTGGTGGTGGAGGAGAACTAGCTCTAATCGGGGCAGGAGGT
1 GGTGGTGGTGCAGGAGAACTAGCTCTAATCGGGGCAGCAGGT
2088662 TCTGGAGGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.19, C:0.13, G:0.48, T:0.20
Consensus pattern (42 bp):
GGTGGTGGTGCAGGAGAACTAGCTCTAATCGGGGCAGCAGGT
Found at i:2095282 original size:15 final size:15
Alignment explanation
Indices: 2095262--2095293 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2095252 CGAAAACGAT
2095262 AATAATAATAATATA
1 AATAATAATAATATA
*
2095277 AATAATAATAGTATA
1 AATAATAATAATATA
2095292 AA
1 AA
2095294 ACGATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AATAATAATAATATA
Found at i:2095535 original size:28 final size:28
Alignment explanation
Indices: 2095483--2095555 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
2095473 TAGATGTATT
*
2095483 AAAATATATACGTAATAATAGAAATAAA
1 AAAATATATACGTAATAATAAAAATAAA
* * *
2095511 AAAATATATATGTAGTATTAAAAATATATA
1 AAAATATATACGTAATAATAAAAATA-A-A
*
2095541 CATAATATATACGTA
1 -AAAATATATACGTA
2095556 CTAGAAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 22 0.61
29 1 0.03
30 1 0.03
31 12 0.33
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.32
Consensus pattern (28 bp):
AAAATATATACGTAATAATAAAAATAAA
Found at i:2095783 original size:25 final size:25
Alignment explanation
Indices: 2095754--2095804 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2095744 ATGAAATATG
*
2095754 TACATAATATAGT-TATAAAAGAATA
1 TACATAATAAAGTGTATAAAA-AATA
*
2095779 TACATAATAAAGTGTATGAAAAATA
1 TACATAATAAAGTGTATAAAAAATA
2095804 T
1 T
2095805 GATATTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.55, C:0.04, G:0.10, T:0.31
Consensus pattern (25 bp):
TACATAATAAAGTGTATAAAAAATA
Found at i:2098270 original size:9 final size:9
Alignment explanation
Indices: 2098256--2098280 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2098246 AGCTACATAG
2098256 GAACAAAAT
1 GAACAAAAT
2098265 GAACAAAAT
1 GAACAAAAT
2098274 GAACAAA
1 GAACAAA
2098281 TCATGCTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.12, G:0.12, T:0.08
Consensus pattern (9 bp):
GAACAAAAT
Found at i:2110105 original size:21 final size:21
Alignment explanation
Indices: 2110079--2110119 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2110069 AGACGAGCAA
* *
2110079 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2110100 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2110120 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2113050 original size:72 final size:72
Alignment explanation
Indices: 2112927--2113219 Score: 376
Period size: 72 Copynumber: 4.1 Consensus size: 72
2112917 ACTTGATCAC
* * *
2112927 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGCTCA-AAGGATCACAATTGAAATCT
1 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAA-GATCAAAAATGAAATCT
2112991 GGTATTGG
65 GGTATTGG
* * *
2112999 ACCACCCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATCACAATTGAAATCTG
1 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATCAAAAATGAAATCTG
*
2113064 GCATTGG
66 GTATTGG
* * ** * * *
2113071 ACCACTCAACTTATTTGATGACAAATTTAGTGAA-TGAAGGTTCACAAGATCAAAAATGGAACCC
1 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGT-AAGGTTCACAAGATCAAAAATGAAATCT
2113135 GGTATTGG
65 GGTATTGG
* * *
2113143 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAATAAGGTTCGCAAGATCAAAAATGGAATAC-
1 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATCAAAAATGAAAT-CT
*
2113207 GGTATTGA
65 GGTATTGG
2113215 ACCAC
1 ACCAC
2113220 CAATGTTATT
Statistics
Matches: 196, Mismatches: 21, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
71 1 0.01
72 191 0.97
73 4 0.02
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (72 bp):
ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATCAAAAATGAAATCTG
GTATTGG
Found at i:2122031 original size:2 final size:2
Alignment explanation
Indices: 2122026--2122060 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2122016 TTTTTTTCTT
*
2122026 TA TA TA TA TA AA 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
2122061 TCCTCCTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2131551 original size:16 final size:17
Alignment explanation
Indices: 2131520--2131552 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2131510 AAGAAAGGTT
*
2131520 ATTTTAAAATTTTTAAA
1 ATTTTAAAATTATTAAA
2131537 ATTTT-AAATTATTAAA
1 ATTTTAAAATTATTAAA
2131553 GGTAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTTAAAATTATTAAA
Found at i:2134027 original size:16 final size:16
Alignment explanation
Indices: 2134006--2134040 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2133996 TCATAAATGG
2134006 CTTGAATATGTCTAGA
1 CTTGAATATGTCTAGA
2134022 CTTGAATATGTCTAGA
1 CTTGAATATGTCTAGA
2134038 CTT
1 CTT
2134041 CAATCATGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (16 bp):
CTTGAATATGTCTAGA
Found at i:2134784 original size:39 final size:39
Alignment explanation
Indices: 2134725--2134864 Score: 226
Period size: 39 Copynumber: 3.6 Consensus size: 39
2134715 ATCGTGATCT
** * *
2134725 GAAGCCCGAAATCTAGCTGAAGCACATAAGTGTTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
2134764 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
* *
2134803 GAAGCCCGGAGACTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
2134842 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
2134865 TCATCAGAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 93 1.00
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:2144213 original size:70 final size:70
Alignment explanation
Indices: 2144080--2144214 Score: 198
Period size: 70 Copynumber: 1.9 Consensus size: 70
2144070 TAGTTTATTA
* * * * * *
2144080 CTAATTAATTTGCTGCTGTGATATTGTAAATTAGTGGCTGTCCAAATTAGGATAAATTTATGGTG
1 CTAATTAATATGCTGCTGTAATACTGTAAATTAGTGGCTGTCCAAATTAGGACAAAATCATGGTG
2144145 CTTAG
66 CTTAG
* *
2144150 CTAATTAATATGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
1 CTAATTAATATGCTGCTGTAATACTGTAAATTAGTGGCTGTCCAAATTAGGACAAAATCATGGTG
2144215 TTATGTGCTA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
70 57 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTAGTGGCTGTCCAAATTAGGACAAAATCATGGTG
CTTAG
Found at i:2145148 original size:42 final size:42
Alignment explanation
Indices: 2145046--2145155 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
2145036 TAGGCTTCGG
* * * **
2145046 GCCTAACAGGCTATAATGCCGATGAGATAATATCGGGTTCGG
1 GCCTAGCAGGCTATAATGCCGGTGAAATAATATCGGGTTCAA
* *
2145088 GCCTAGCAAGCTATAATGCCGGTGAAATGATATCGGGCTTCAA
1 GCCTAGCAGGCTATAATGCCGGTGAAATAATATCGGG-TTCAA
* *
2145131 GCCTAGCAGGCGA-AATGCCAGTGAA
1 GCCTAGCAGGCTATAATGCCGGTGAA
2145156 TGAGTTCAGA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 43 0.75
43 14 0.25
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (42 bp):
GCCTAGCAGGCTATAATGCCGGTGAAATAATATCGGGTTCAA
Found at i:2150193 original size:224 final size:224
Alignment explanation
Indices: 2149814--2150463 Score: 925
Period size: 224 Copynumber: 2.9 Consensus size: 224
2149804 GTAGTGATAC
* * *
2149814 AACACATGAACAAAGATGCTTTG-AATATTGATAACTAAGAAAGGCACATCCATGAGGACTCAAA
1 AACACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTCACA
* * *
2149878 TGAGAC--TGGATGACCAAAATAAATGATATAAAGCTAGAAGAGACATATAAGTTGCGAGCTTCA
66 --AGACTGTGGACGACCAAAACAAATGATATAAAGCTAGAAGAG--A-ATAAGTTGTGAGCTTCA
*
2149941 CTACTATGCCAATATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACT
126 CTACTATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACT
2150006 CAATTGCGAACCATCGAAGATCTCCATATCATTA
191 CAATTGCGAACCATCGAAGATCTCCATATCATTA
* * *
2150040 AACACATGCACAAAGATTCTTTGAAATATTGGTAACTAAAAAAGGCACATGCATGAGGACTCGAC
1 AACACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTC-AC
*
2150105 AAGACTGTGGACGACCAAAACAAATGATACAAAGCTAGAAGAG-ATAAGTTGTGAGCTTCACTAC
65 AAGACTGTGGACGACCAAAACAAATGATATAAAGCTAGAAGAGAATAAGTTGTGAGCTTCACTAC
* * *
2150169 TATGCCAAAATGTAAACCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAAGGATAAGCTCAAT
130 TATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTCAAT
* *
2150234 TGCGAACCATTGAGGATCTCCATATCATTA
195 TGCGAACCATCGAAGATCTCCATATCATTA
* *
2150264 AACACATGCCCAAAGATGCTTTGAAATATTTGATAACTAAGAAAGACACATGCATGAGGACTCAA
1 AACACATGCACAAAGATGCTTTGAAATA-TTGATAACTAAGAAAGGCACATGCATGAGGACTC--
*
2150329 ACAAGACTGTGGAC-AGCCAAAACAAATGATATAAAACTAGAAGAGACATATAAGTTGTGAGCTT
63 ACAAGACTGTGGACGA-CCAAAACAAATGATATAAAGCTAGAAGAG--A-ATAAGTTGTGAGCTT
* * *
2150393 CACTAAC-ATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTTGACAATAATAA
124 CACT-ACTATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAA
*
2150457 ACACAAT
188 ACTCAAT
2150464 CACGAACCTT
Statistics
Matches: 381, Mismatches: 31, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
224 135 0.35
225 32 0.08
226 66 0.17
227 35 0.09
228 35 0.09
230 76 0.20
231 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (224 bp):
AACACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTCACA
AGACTGTGGACGACCAAAACAAATGATATAAAGCTAGAAGAGAATAAGTTGTGAGCTTCACTACT
ATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTCAATT
GCGAACCATCGAAGATCTCCATATCATTA
Found at i:2155135 original size:19 final size:18
Alignment explanation
Indices: 2155090--2155146 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 18
2155080 TTATTATGTG
* *
2155090 TTATAAATTATATAATATA
1 TTATAAA-TATATAAAACA
* *
2155109 TAAAAAATAATATAAAACA
1 TTATAAAT-ATATAAAACA
*
2155128 TTATAAATTTATAAAACA
1 TTATAAATATATAAAACA
2155146 T
1 T
2155147 AATATTGTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 11 0.37
19 19 0.63
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (18 bp):
TTATAAATATATAAAACA
Found at i:2170216 original size:3 final size:3
Alignment explanation
Indices: 2170208--2170235 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2170198 GACTCTCTGT
2170208 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
2170236 TTCTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:2172577 original size:20 final size:20
Alignment explanation
Indices: 2172552--2172591 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2172542 AAATCTTAAG
2172552 TTACAAATAGAAGAAAGCCA
1 TTACAAATAGAAGAAAGCCA
2172572 TTACAAATAGAAGAAAGCCA
1 TTACAAATAGAAGAAAGCCA
2172592 AAAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.15
Consensus pattern (20 bp):
TTACAAATAGAAGAAAGCCA
Found at i:2174123 original size:29 final size:28
Alignment explanation
Indices: 2174081--2174150 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
2174071 AATATTTTAT
* *
2174081 ATTTTTATAAATTTTAAATAATTAAATTAA
1 ATTTTTAT-TATTTTAAA-AATTAAAATAA
* * *
2174111 TTTTTTATTATTTTTAAGATTAAAATAA
1 ATTTTTATTATTTTAAAAATTAAAATAA
*
2174139 AATTTTATTATT
1 ATTTTTATTATT
2174151 ACTAATTTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
28 19 0.58
29 7 0.21
30 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (28 bp):
ATTTTTATTATTTTAAAAATTAAAATAA
Found at i:2174377 original size:29 final size:28
Alignment explanation
Indices: 2174295--2174377 Score: 66
Period size: 29 Copynumber: 2.9 Consensus size: 28
2174285 ATTTAATGAA
2174295 TTAATTT-TAAAATTAT-T-CATGAATT
1 TTAATTTATAAAATTATATACATGAATT
* * *
2174320 TTGATTTAATATGTAATT-TGATATATGAATT
1 TTAATTT-ATA--AAATTAT-ATACATGAATT
2174351 TTAATTTAGTAAAATTATATACATGAA
1 TTAATTTA-TAAAATTATATACATGAA
2174378 ATTAGACTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
25 6 0.14
27 2 0.05
28 1 0.02
29 16 0.37
30 3 0.07
31 15 0.35
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.48
Consensus pattern (28 bp):
TTAATTTATAAAATTATATACATGAATT
Found at i:2177049 original size:21 final size:22
Alignment explanation
Indices: 2177023--2177068 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
2177013 CTTTGCATAA
*
2177023 TTTTTACTTTTTAAA-AAATAT
1 TTTTTAATTTTTAAATAAATAT
*
2177044 TTTTTAATTTTTAAATATATAT
1 TTTTTAATTTTTAAATAAATAT
2177066 TTT
1 TTT
2177069 ATTTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTTAATTTTTAAATAAATAT
Found at i:2177069 original size:20 final size:21
Alignment explanation
Indices: 2177024--2177080 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
2177014 TTTGCATAAT
* *
2177024 TTTTACTTTTTAAAAAATATT
1 TTTTAATTTTTAAAAAATATA
*
2177045 TTTTAATTTTT-AAATATATA
1 TTTTAATTTTTAAAAAATATA
2177065 TTTT-A--TTTAAAAAATA
1 TTTTAATTTTTAAAAAATA
2177081 AAAAAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 3 0.10
18 6 0.19
19 1 0.03
20 11 0.35
21 10 0.32
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTAATTTTTAAAAAATATA
Found at i:2178530 original size:36 final size:36
Alignment explanation
Indices: 2178458--2178539 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
2178448 GTTAATGAAT
* * *
2178458 AATAAATAAATAAAAATATTTTTAATTTTAGGTATA
1 AATAAATAAAGAAAAATATTATTAATTATAGGTATA
*
2178494 AA-ATAATAAAGAATAAATATTATTAATTATA-TTATA
1 AATA-AATAAAGAA-AAATATTATTAATTATAGGTATA
2178530 AATAAATAAA
1 AATAAATAAA
2178540 ATGCAAATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 1 0.03
36 22 0.56
37 16 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (36 bp):
AATAAATAAAGAAAAATATTATTAATTATAGGTATA
Found at i:2179316 original size:9 final size:10
Alignment explanation
Indices: 2179302--2179333 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
2179292 TTAAAAACAT
2179302 AATACA-TAA
1 AATACATTAA
2179311 AATACATTAA
1 AATACATTAA
2179321 AA-ACATTAA
1 AATACATTAA
2179330 AATA
1 AATA
2179334 AATGTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 15 0.71
10 6 0.29
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (10 bp):
AATACATTAA
Found at i:2181390 original size:18 final size:18
Alignment explanation
Indices: 2181359--2181393 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2181349 TTTAAGTTAT
*
2181359 TTATTTAAAAATATAAAA
1 TTATTGAAAAATATAAAA
*
2181377 TTATTGAAAGATATAAA
1 TTATTGAAAAATATAAA
2181394 TACATACCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
TTATTGAAAAATATAAAA
Found at i:2188232 original size:18 final size:19
Alignment explanation
Indices: 2188211--2188248 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2188201 AAATATATAC
2188211 AATAATTAAAT-T-ATAAAA
1 AATAA-TAAATATCATAAAA
2188229 AATAATAAATATCATAAAA
1 AATAATAAATATCATAAAA
2188248 A
1 A
2188249 TTATAAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 6 0.33
19 7 0.39
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
AATAATAAATATCATAAAA
Found at i:2192831 original size:40 final size:40
Alignment explanation
Indices: 2192786--2192867 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
2192776 AGATATGATC
2192786 GAACTCGAAAAACTTAACTATAATAAGAATAATTCAAAAT
1 GAACTCGAAAAACTTAACTATAATAAGAATAATTCAAAAT
*
2192826 GAACTCGAAAAACTTAACTATAATAAGAATAATTTAAAAT
1 GAACTCGAAAAACTTAACTATAATAAGAATAATTCAAAAT
2192866 GA
1 GA
2192868 CTTGAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.26
Consensus pattern (40 bp):
GAACTCGAAAAACTTAACTATAATAAGAATAATTCAAAAT
Found at i:2192877 original size:16 final size:17
Alignment explanation
Indices: 2192856--2192900 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
2192846 TAATAAGAAT
*
2192856 AATTTAAAATGACTT-G
1 AATTTAAAATGAATTCG
*
2192872 AATTTAAAATTAATTCG
1 AATTTAAAATGAATTCG
*
2192889 AACTTAAAATGA
1 AATTTAAAATGA
2192901 TCTAAACTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.36
Consensus pattern (17 bp):
AATTTAAAATGAATTCG
Found at i:2195544 original size:21 final size:21
Alignment explanation
Indices: 2195520--2195560 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2195510 CATCGTCTAT
* *
2195520 TTATGCTTTATATTTATTTGA
1 TTATACTTTATAATTATTTGA
*
2195541 TTATACTTTTTAATTATTTG
1 TTATACTTTATAATTATTTG
2195561 GACATGTACT
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:0.24, C:0.05, G:0.07, T:0.63
Consensus pattern (21 bp):
TTATACTTTATAATTATTTGA
Found at i:2205779 original size:22 final size:22
Alignment explanation
Indices: 2205751--2205806 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
2205741 AAATAATAAA
2205751 AGAAATATATAACAAATAACAT
1 AGAAATATATAACAAATAACAT
**
2205773 AGAAATATATGTATGAAATAACAT
1 AGAAATATA--TAACAAATAACAT
*
2205797 AAAAATATAT
1 AGAAATATAT
2205807 GAATAGCGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 10 0.34
24 19 0.66
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (22 bp):
AGAAATATATAACAAATAACAT
Found at i:2206826 original size:6 final size:7
Alignment explanation
Indices: 2206809--2206833 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2206799 AAAACTCTCT
2206809 TTTTTTG
1 TTTTTTG
2206816 TTTTTTG
1 TTTTTTG
2206823 TTTTTTG
1 TTTTTTG
2206830 TTTT
1 TTTT
2206834 ATTTATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTTTG
Found at i:2208162 original size:13 final size:14
Alignment explanation
Indices: 2208127--2208160 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2208117 AGTTGATGTT
2208127 TGAAAAATAAAAAC
1 TGAAAAATAAAAAC
* *
2208141 TGAAAAATAGAAAT
1 TGAAAAATAAAAAC
2208155 TGAAAA
1 TGAAAA
2208161 TACCTCAGCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.12, T:0.18
Consensus pattern (14 bp):
TGAAAAATAAAAAC
Found at i:2208418 original size:54 final size:54
Alignment explanation
Indices: 2208339--2208627 Score: 505
Period size: 54 Copynumber: 5.4 Consensus size: 54
2208329 GAAAAGTAGA
*
2208339 TTTTGAAAAACAGACATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
2208393 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
2208447 TTTTGAAAAA-A-AAATTAAAAGACTCAACTCACCTCTCGCAATATGAGTTGAT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
2208499 TTTTGAAAAACAGAAATTAAAAGACTCAACTCACCTCTCGCAATATGAGTTGAT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
2208553 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
2208607 TCTTTG--AAACAGACATTAAAA
1 T-TTTGAAAAACAGAAATTAAAA
2208628 TAGAAATTGA
Statistics
Matches: 228, Mismatches: 4, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
52 50 0.22
53 16 0.07
54 158 0.69
55 4 0.02
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.28
Consensus pattern (54 bp):
TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
Found at i:2208539 original size:106 final size:108
Alignment explanation
Indices: 2208339--2208627 Score: 505
Period size: 106 Copynumber: 2.7 Consensus size: 108
2208329 GAAAAGTAGA
*
2208339 TTTTGAAAAACAGACATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
*
2208404 AGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
66 AGAAATTAAAAGACTCAACTCACCTCTCGCAATATGAGTTGAT
*
2208447 TTTTGAAAAA-A-AAATTAAAAGACTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
2208510 AGAAATTAAAAGACTCAACTCACCTCTCGCAATATGAGTTGAT
66 AGAAATTAAAAGACTCAACTCACCTCTCGCAATATGAGTTGAT
2208553 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTG--AAA
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTGAAAAA
*
2208616 CAGACATTAAAA
65 CAGAAATTAAAA
2208628 TAGAAATTGA
Statistics
Matches: 173, Mismatches: 5, Indels: 7
0.94 0.03 0.04
Matches are distributed among these distances:
106 102 0.59
107 16 0.09
108 51 0.29
109 4 0.02
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.28
Consensus pattern (108 bp):
TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
AGAAATTAAAAGACTCAACTCACCTCTCGCAATATGAGTTGAT
Found at i:2208724 original size:86 final size:84
Alignment explanation
Indices: 2208574--2208869 Score: 325
Period size: 86 Copynumber: 3.4 Consensus size: 84
2208564 AGAAATTAAA
*
2208574 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTG-AAACAGACATTAAAATAGAAATTGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTGAAAACAGA-ATTAAAACAG-AATTGA
* * *
2208638 AAATAGTTCAGTGCGTGAGCCA
63 AAATACTTCAGTGCGTGACCCG
* * *
2208660 AGACGCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAACATGAATTAAAACAGAATTTGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACA-GAATTAAAACAGAA-TTGAA
*
2208725 AATACCTC-G-GCATGTGACCCG
64 AATACTTCAGTGC--GTGACCCG
* *
2208746 AGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTGAAAAACAAAAATTAAAAACAGGAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-AAAAC-AGAATT-AAAACA-GAATT
* *
2208811 GAAAATACCTT-AGT--GTGTCCTG
61 GAAAATA-CTTCAGTGCGTGACCCG
2208833 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
2208870 TTGAAAATAA
Statistics
Matches: 180, Mismatches: 17, Indels: 26
0.81 0.08 0.12
Matches are distributed among these distances:
84 2 0.01
85 7 0.04
86 95 0.53
87 45 0.25
88 9 0.05
89 16 0.09
90 6 0.03
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (84 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTAAAACAGAATTGAAAA
TACTTCAGTGCGTGACCCG
Found at i:2220465 original size:22 final size:22
Alignment explanation
Indices: 2220437--2220492 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
2220427 AAATAATAAA
2220437 AGAAATATATAACAAATAACAT
1 AGAAATATATAACAAATAACAT
**
2220459 AGAAATATATGTATGAAATAACAT
1 AGAAATATA--TAACAAATAACAT
*
2220483 AAAAATATAT
1 AGAAATATAT
2220493 GAATAGCGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 10 0.34
24 19 0.66
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (22 bp):
AGAAATATATAACAAATAACAT
Found at i:2221908 original size:15 final size:15
Alignment explanation
Indices: 2221888--2221921 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2221878 GCAGTCGGTA
*
2221888 TGGCAGAGGGGTAAG
1 TGGCAGAAGGGTAAG
2221903 TGGCAGAAGGGTAAG
1 TGGCAGAAGGGTAAG
2221918 TGGC
1 TGGC
2221922 CGATGGGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.09, G:0.50, T:0.15
Consensus pattern (15 bp):
TGGCAGAAGGGTAAG
Found at i:2222885 original size:21 final size:21
Alignment explanation
Indices: 2222861--2222902 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2222851 AAAGAAATTT
* *
2222861 ATTATATTAAATTAAAAATAA
1 ATTAAATTAAACTAAAAATAA
2222882 ATTAAATTAAACTAAAAATAA
1 ATTAAATTAAACTAAAAATAA
2222903 CTGAACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTAAATTAAACTAAAAATAA
Found at i:2223161 original size:33 final size:34
Alignment explanation
Indices: 2223115--2223178 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
2223105 GACCCGACAA
*
2223115 AAGCTTATGTACCAAATT-AGACAAAAAAATAAG
1 AAGCTTATGTACCAAATTAAGAAAAAAAAATAAG
2223148 AAGCTTA-GATACCAAATTAAGAAAAAAAAAT
1 AAGCTTATG-TACCAAATTAAGAAAAAAAAAT
2223179 GTCTTAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 1 0.04
33 16 0.57
34 11 0.39
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (34 bp):
AAGCTTATGTACCAAATTAAGAAAAAAAAATAAG
Found at i:2228066 original size:28 final size:28
Alignment explanation
Indices: 2228034--2228088 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
2228024 GTAACTCGCG
*
2228034 CATTTCTATGCTCGGATGTCATCACGGC
1 CATTTCTATGCTCAGATGTCATCACGGC
2228062 CATTTCTATGCTCAGATGTCATCACGG
1 CATTTCTATGCTCAGATGTCATCACGG
2228089 GCTTCATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (28 bp):
CATTTCTATGCTCAGATGTCATCACGGC
Found at i:2231229 original size:18 final size:17
Alignment explanation
Indices: 2231184--2231231 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
2231174 TTGTTGAGAA
2231184 ATATTTATTTTAATGTTT
1 ATATTT-TTTTAATGTTT
* *
2231202 TTAGTATTTTTAATGTATT
1 ATA-TTTTTTTAATGT-TT
2231221 ATATTTTTTTA
1 ATATTTTTTTA
2231232 TAAAAATTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
ATATTTTTTTAATGTTT
Found at i:2233222 original size:14 final size:14
Alignment explanation
Indices: 2233203--2233229 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2233193 TTTTATTTTA
2233203 TTTTATTTTTTATC
1 TTTTATTTTTTATC
2233217 TTTTATTTTTTAT
1 TTTTATTTTTTAT
2233230 TTAAAAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTATTTTTTATC
Found at i:2234188 original size:20 final size:21
Alignment explanation
Indices: 2234152--2234193 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
2234142 TACACATTGT
2234152 TTATTTTAAACTTATTATATA
1 TTATTTTAAACTTATTATATA
*
2234173 TTATTTT-AAGTTATTATATA
1 TTATTTTAAACTTATTATATA
2234193 T
1 T
2234194 ATTATCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TTATTTTAAACTTATTATATA
Found at i:2234220 original size:25 final size:24
Alignment explanation
Indices: 2234152--2234252 Score: 84
Period size: 25 Copynumber: 4.1 Consensus size: 24
2234142 TACACATTGT
2234152 TTATTTTAAAC-TTAT-TATA-TA
1 TTATTTTAAACTTTATATATATTA
**
2234173 TTATTTTAAGTTATTATATATATTA
1 TTATTTTAAACT-TTATATATATTA
2234198 TCTATTTTAAACTTTATATATA-TA
1 T-TATTTTAAACTTTATATATATTA
*
2234222 TTAGTTAGTCTAAACTGTTATATATGTTA
1 TTA-TT--T-TAAACT-TTATATATATTA
2234251 TT
1 TT
2234253 CTAAAATTCG
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
21 9 0.14
23 6 0.09
24 9 0.14
25 12 0.19
26 10 0.16
27 6 0.09
28 8 0.12
29 4 0.06
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (24 bp):
TTATTTTAAACTTTATATATATTA
Found at i:2234235 original size:27 final size:28
Alignment explanation
Indices: 2234182--2234246 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 28
2234172 ATTATTTTAA
* *
2234182 GTTATTATATATATTATCTATTTTAAACT
1 GTTA-TATATATATTATCTAGTCTAAACT
2234211 -TTATATATATATTAGT-TAGTCTAAACT
1 GTTATATATATATTA-TCTAGTCTAAACT
2234238 GTTATATAT
1 GTTATATAT
2234247 GTTATTCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 20 0.62
28 12 0.38
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (28 bp):
GTTATATATATATTATCTAGTCTAAACT
Found at i:2234431 original size:24 final size:22
Alignment explanation
Indices: 2234374--2234431 Score: 53
Period size: 24 Copynumber: 2.5 Consensus size: 22
2234364 GGTTACTTAG
*
2234374 TAAACTGTTTTATATGTTTTTT
1 TAAACTGTTTCATATGTTTTTT
**
2234396 TAAAAAGGGTTTCATATTGTTTATTT
1 T--AAACTGTTTCATA-TGTTT-TTT
2234422 TAAACTGTTT
1 TAAACTGTTT
2234432 TTTTATTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
22 1 0.04
24 17 0.63
25 5 0.19
26 4 0.15
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.55
Consensus pattern (22 bp):
TAAACTGTTTCATATGTTTTTT
Found at i:2236849 original size:18 final size:18
Alignment explanation
Indices: 2236828--2236862 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2236818 TGACCCACTA
2236828 AACCCAAACCTAATACCT
1 AACCCAAACCTAATACCT
* *
2236846 AACCCTAGCCTAATACC
1 AACCCAAACCTAATACC
2236863 CAAAAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.40, G:0.03, T:0.17
Consensus pattern (18 bp):
AACCCAAACCTAATACCT
Found at i:2237243 original size:21 final size:22
Alignment explanation
Indices: 2237217--2237261 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2237207 TGATATTAAA
2237217 TTATTATTATTTT-CTTTCTAT
1 TTATTATTATTTTCCTTTCTAT
* *
2237238 TTATTATTTTTTTCCTTTTTAT
1 TTATTATTATTTTCCTTTCTAT
2237260 TT
1 TT
2237262 TATTTTCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (22 bp):
TTATTATTATTTTCCTTTCTAT
Found at i:2237969 original size:15 final size:14
Alignment explanation
Indices: 2237943--2237978 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
2237933 TATATTTTTG
2237943 TTATACTTATATATA
1 TTATA-TTATATATA
2237958 TGTATATTATATATA
1 T-TATATTATATATA
2237973 TTATAT
1 TTATAT
2237979 AGTATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 11 0.55
16 4 0.20
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (14 bp):
TTATATTATATATA
Found at i:2238309 original size:17 final size:17
Alignment explanation
Indices: 2238287--2238349 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
2238277 TTAAATATTG
2238287 TATTTTTATTATGTATA
1 TATTTTTATTATGTATA
* * *
2238304 TATTTTTAATACGGATA
1 TATTTTTATTATGTATA
2238321 TATTTTTTATTACTTGTATA
1 TA-TTTTTATTA--TGTATA
2238341 TATATTTTA
1 TAT-TTTTA
2238350 ATATTATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
17 16 0.44
18 8 0.22
19 1 0.03
20 11 0.31
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.60
Consensus pattern (17 bp):
TATTTTTATTATGTATA
Found at i:2238432 original size:24 final size:24
Alignment explanation
Indices: 2238386--2238432 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2238376 CTTTAATACT
* *
2238386 ATATCATTTTTATTTTTATTTTTC
1 ATATCATTCTTATGTTTATTTTTC
2238410 ATATCA-TCTTATGTTTATGTTTT
1 ATATCATTCTTATGTTTAT-TTTT
2238433 TCAAACTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.21, C:0.09, G:0.04, T:0.66
Consensus pattern (24 bp):
ATATCATTCTTATGTTTATTTTTC
Found at i:2238624 original size:3 final size:3
Alignment explanation
Indices: 2238616--2238666 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
2238606 AATTTTACTT
* * * *
2238616 TTA TTA TTA CTA CTA -TA TTA TTA TTA TTA TTA TCA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2238663 TTA T
1 TTA T
2238667 CATATTTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:2238882 original size:3 final size:3
Alignment explanation
Indices: 2238874--2238927 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
2238864 TATCTCTAAC
2238874 TAT TAT TAT TAT T-T TA- TAT ATAT TAT TAT CTA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TAT TAT
*
2238918 TAC TAT TAT T
1 TAT TAT TAT T
2238928 CTTTATTGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 6 0.14
3 33 0.75
4 5 0.11
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2241601 original size:18 final size:18
Alignment explanation
Indices: 2241546--2241603 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
2241536 TCATTGAAAT
* * *
2241546 TTTTTATAATCTATGTAC
1 TTTTTAAAATATATGTAA
* *
2241564 TTTTAAAAATATATAT-A
1 TTTTTAAAATATATGTAA
*
2241581 TTTTTAAAATTTATGTAA
1 TTTTTAAAATATATGTAA
2241599 TTTTT
1 TTTTT
2241604 TTTATTCATA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTTTAAAATATATGTAA
Found at i:2243045 original size:133 final size:132
Alignment explanation
Indices: 2242871--2243435 Score: 593
Period size: 133 Copynumber: 4.3 Consensus size: 132
2242861 CTATGTCAAG
* * *
2242871 TTTAAGCCTTTTGTTCCAATGGGTTCTAAGTTTTTCTTCCTTTTTTGTTGGCTCCTATGTTCTTT
1 TTTAAGTCTTTTGCTCCAATGGGTTCTAAGTTTTTCTTCCTTTTTTGTTGGCTCGTATGTTCTTT
* * * **
2242936 GTTATAATTGTGCTTTGCTGTAATGTTTATCTTCAAGTCTATTGAATTTTTGAGCTTTTGTTGAA
66 GTTATAATTGTACTTTGCCGTAATGTGTAGATTCAAGTCTATT-AATTTTTGAGCTTTTGTTGAA
2243001 AGT
130 AGT
* * * *
2243004 TTTAACTCTTTTGCTCCAGTGGGTTCCAAGTTTTTCTTCCTTTTTTGTTGGTTCGTATGTTCTTT
1 TTTAAGTCTTTTGCTCCAATGGGTTCTAAGTTTTTCTTCCTTTTTTGTTGGCTCGTATGTTCTTT
* * * * *
2243069 GTTATAATTTTACTTTGCCGTAATATGTAGATTCAAGTCTACTAAAATTTTGAGCTTTTTTTGAA
66 GTTATAATTGTACTTTGCCGTAATGTGTAGATTCAAGTCTA-TTAATTTTTGAGCTTTTGTTGAA
2243134 A-T
130 AGT
* * * * * *
2243136 TTCATGTCGTTTGCTCCAATGGGTTCTAAGTTTTTCTTCC-TTTTTGTTGGTTAGTATGTTCTCT
1 TTTAAGTCTTTTGCTCCAATGGGTTCTAAGTTTTTCTTCCTTTTTTGTTGGCTCGTATGTTCTTT
** * * *
2243200 GTCGTAAATATACTTTGCCGTAATGTGTAGATTCAAGTCTATTAAGTTTTTGAGTTTTTTGTTGA
66 GTTATAATTGTACTTTGCCGTAATGTGTAGATTCAAGTCTATTAA-TTTTTGAG-CTTTTGTTGA
2243265 AAG-
129 AAGT
** * * ** *
2243268 TTTAAGTCTTTTGCTTTAATGGGTTCTAACTCTCACTTCCTTTTTTGTTGGCTGGTATGTTCTTT
1 TTTAAGTCTTTTGCTCCAATGGGTTCTAAGTTTTTCTTCCTTTTTTGTTGGCTCGTATGTTC-TT
* * * * * * * *
2243333 GTGTTATAATTGTAATCT-CCTGAAATGGGTAGCTTC-TGTTCTTTTAAATTTTTGAGCTTTTCT
65 -TGTTATAATTGTACTTTGCC-GTAATGTGTAGATTCAAG-TCTATT-AATTTTTGAGCTTTTGT
2243396 TGAAA-T
126 TGAAAGT
* * *
2243402 TTGATGTCTTTTGCTCCTATGGGTTCTAAGTTTT
1 TTTAAGTCTTTTGCTCCAATGGGTTCTAAGTTTT
2243436 CCTTATCATT
Statistics
Matches: 354, Mismatches: 67, Indels: 21
0.80 0.15 0.05
Matches are distributed among these distances:
130 3 0.01
131 65 0.18
132 76 0.21
133 131 0.37
134 41 0.12
135 36 0.10
136 2 0.01
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.51
Consensus pattern (132 bp):
TTTAAGTCTTTTGCTCCAATGGGTTCTAAGTTTTTCTTCCTTTTTTGTTGGCTCGTATGTTCTTT
GTTATAATTGTACTTTGCCGTAATGTGTAGATTCAAGTCTATTAATTTTTGAGCTTTTGTTGAAA
GT
Found at i:2248809 original size:102 final size:106
Alignment explanation
Indices: 2248584--2248823 Score: 267
Period size: 108 Copynumber: 2.3 Consensus size: 106
2248574 AATGTTGGAG
* * *
2248584 CATGATGCTTGGGAGAGTGTGCAGGTGATGCAGATGATTGTTTAGGAGGTTCAGCTACATGTGGT
1 CATGATGCTTGGGAGAGTGTGCTGGTCATGCAGATGATTGTTTAGGAGGTTCAGCTA-ATGAGGT
* *
2248649 GGTGGTGGATATGTAGGAGCCAAAACTGGCCCTGCAACCGGAC
65 GATGGTAGATA-GTAGGAGCCAAAACTGGCCCTGCAACCGGAC
* * * **
2248692 CATGATGCTTTGGAGAGTATGCTGGTCCTGGGGATGATTGTTTAGGAGGTTCAGCT-A-GAGGTG
1 CATGATGCTTGGGAGAGTGTGCTGGTCATGCAGATGATTGTTTAGGAGGTTCAGCTAATGAGGTG
** * *
2248755 ATGG-AGAT-G-ATGGAGCCAAGGCTGGTCCTGCAACATGG-C
66 ATGGTAGATAGTA-GGAGCCAAAACTGGCCCTGCAAC-CGGAC
*
2248794 CATGATGCTTGGGAGAGTGTGCTGGCCATG
1 CATGATGCTTGGGAGAGTGTGCTGGTCATG
2248824 GAGAGGGTCC
Statistics
Matches: 112, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
101 1 0.01
102 48 0.43
103 2 0.02
104 3 0.03
105 8 0.07
106 1 0.01
108 49 0.44
ACGTcount: A:0.22, C:0.15, G:0.37, T:0.26
Consensus pattern (106 bp):
CATGATGCTTGGGAGAGTGTGCTGGTCATGCAGATGATTGTTTAGGAGGTTCAGCTAATGAGGTG
ATGGTAGATAGTAGGAGCCAAAACTGGCCCTGCAACCGGAC
Found at i:2248932 original size:117 final size:121
Alignment explanation
Indices: 2248724--2248941 Score: 286
Period size: 117 Copynumber: 1.8 Consensus size: 121
2248714 TGGTCCTGGG
* * *
2248724 GATGATTGTTTAGGAGGTTCAGCTAGAGGTGATGGAGATGATGGAGCCAAGGCTGGTCCTGCAAC
1 GATGATTGTTTAGGAGGCTCAACTACAGGTGATGGAGATGATGGAGCCAAGGCTGGTCCTGCAAC
* *
2248789 ATGGCCATGATGCTTGGGAGAGTGTGCTGG-CCATGGAGAGGGTCCAGGTAAGACA
66 ATGACCATGATGATTGGGAGAGTGTGCTGGTCCATGGAGAGGGTCCAGGTAAGACA
* * * *
2248844 GATGATTGTTTAGGAGGCTCAACTACA-G-G-TGGTGATGTTGGAGCCATGGTTGG-CCTAGCAA
1 GATGATTGTTTAGGAGGCTCAACTACAGGTGATGGAGATGATGGAGCCAAGGCTGGTCCT-GCAA
*
2248905 C-TGAACCATGATGATTGGGAGATTGTGCTGGTCCATG
65 CATG-ACCATGATGATTGGGAGAGTGTGCTGGTCCATG
2248942 CAACACAGAC
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
116 5 0.06
117 49 0.58
118 6 0.07
119 1 0.01
120 24 0.28
ACGTcount: A:0.23, C:0.15, G:0.36, T:0.25
Consensus pattern (121 bp):
GATGATTGTTTAGGAGGCTCAACTACAGGTGATGGAGATGATGGAGCCAAGGCTGGTCCTGCAAC
ATGACCATGATGATTGGGAGAGTGTGCTGGTCCATGGAGAGGGTCCAGGTAAGACA
Found at i:2249767 original size:24 final size:26
Alignment explanation
Indices: 2249740--2249788 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
2249730 ATTATTTTGA
*
2249740 TTTA-ATATTTAAAAATT-TATATAT
1 TTTATATATTAAAAAATTATATATAT
*
2249764 TTTATTTATTAAAAAATTATATATA
1 TTTATATATTAAAAAATTATATATA
2249789 ATTATCTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 11 0.52
26 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTATATATTAAAAAATTATATATAT
Found at i:2253200 original size:16 final size:16
Alignment explanation
Indices: 2253181--2253215 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2253171 TGAAATATTA
2253181 AATAATTTAT-TTAAAT
1 AATAATTTATATT-AAT
2253197 AATAATTTATATTAAT
1 AATAATTTATATTAAT
2253213 AAT
1 AAT
2253216 TTATATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATAATTTATATTAAT
Found at i:2253212 original size:13 final size:13
Alignment explanation
Indices: 2253196--2253221 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2253186 TTTATTTAAA
2253196 TAATAATTTATAT
1 TAATAATTTATAT
2253209 TAATAATTTATAT
1 TAATAATTTATAT
2253222 GATTAGATAT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAATAATTTATAT
Found at i:2253467 original size:60 final size:60
Alignment explanation
Indices: 2253401--2253521 Score: 215
Period size: 60 Copynumber: 2.0 Consensus size: 60
2253391 CATAAAGTAG
* *
2253401 TTCTTTCTGGTAAAATGACTTACATTTAAAAAAAATTTTTAAGTCATTTTACAAGAAAGA
1 TTCTTTCTGGTAAAATGACTTACATTTAAAAAAAAATTCTAAGTCATTTTACAAGAAAGA
*
2253461 TTCTTTCTGGTAAAATGACTTTCATTTAAAAAAAAATTCTAAGTCATTTTACAAGAAAGA
1 TTCTTTCTGGTAAAATGACTTACATTTAAAAAAAAATTCTAAGTCATTTTACAAGAAAGA
2253521 T
1 T
2253522 GGCTTATTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (60 bp):
TTCTTTCTGGTAAAATGACTTACATTTAAAAAAAAATTCTAAGTCATTTTACAAGAAAGA
Found at i:2263977 original size:4 final size:4
Alignment explanation
Indices: 2263964--2263997 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
2263954 CTCTTTGATC
2263964 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
2263998 GTGATTTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 22 0.79
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2264550 original size:20 final size:22
Alignment explanation
Indices: 2264505--2264558 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
2264495 ATAGTGGAAT
*
2264505 ATTATTAATTTTTTATAATGTAA
1 ATTATTAATTTTATATAA-GTAA
2264528 ATTATTAATTTTATATAA-T-A
1 ATTATTAATTTTATATAAGTAA
*
2264548 ATTATAAATTT
1 ATTATTAATTT
2264559 AATTTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 11 0.38
21 1 0.03
23 17 0.59
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTATTAATTTTATATAAGTAA
Found at i:2264566 original size:20 final size:20
Alignment explanation
Indices: 2264527--2264566 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2264517 TTATAATGTA
* *
2264527 AATTATTAATTTTATATAAT
1 AATTATAAATTTAATATAAT
*
2264547 AATTATAAATTTAATTTAAT
1 AATTATAAATTTAATATAAT
2264567 TTAATTCACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTATAAATTTAATATAAT
Found at i:2273351 original size:16 final size:16
Alignment explanation
Indices: 2273330--2273374 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
2273320 CATATGATAA
2273330 AAAAATTATAAAAAAT
1 AAAAATTATAAAAAAT
2273346 AAAAATTATAAAAAAT
1 AAAAATTATAAAAAAT
2273362 AAAAATTAATAAA
1 AAAAATT-ATAAA
2273375 GTTATAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 23 0.82
17 5 0.18
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATTATAAAAAAT
Found at i:2273356 original size:9 final size:9
Alignment explanation
Indices: 2273330--2273463 Score: 62
Period size: 9 Copynumber: 14.6 Consensus size: 9
2273320 CATATGATAA
2273330 AAAAATTAT
1 AAAAATTAT
2273339 AAAAA--AT
1 AAAAATTAT
2273346 AAAAATTAT
1 AAAAATTAT
2273355 AAAAA--AT
1 AAAAATTAT
2273362 AAAAATTA-
1 AAAAATTAT
*
2273370 ATAAAGTTAT
1 A-AAAATTAT
*
2273380 AAGAATTATT
1 AAAAATTA-T
**
2273390 AAATTTTAAT
1 AAAAATT-AT
* *
2273400 AAAAAATGT
1 AAAAATTAT
*
2273409 AAAAATATTT
1 AAAAAT-TAT
*
2273419 AAAATTTATT
1 AAAAATTA-T
* *
2273429 AAAAGTTAGAA
1 AAAAATT--AT
2273440 AAAAAGTTAT
1 AAAAA-TTAT
*
2273450 AAAAATTGT
1 AAAAATTAT
2273459 AAAAA
1 AAAAA
2273464 AAATATAAAA
Statistics
Matches: 93, Mismatches: 19, Indels: 26
0.67 0.14 0.19
Matches are distributed among these distances:
7 14 0.15
8 1 0.01
9 39 0.42
10 31 0.33
11 5 0.05
12 3 0.03
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:2275981 original size:18 final size:18
Alignment explanation
Indices: 2275958--2275993 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2275948 AACAGTTAAA
2275958 TTCAATTACTAGTATTAT
1 TTCAATTACTAGTATTAT
2275976 TTCAATTACTAGTATTAT
1 TTCAATTACTAGTATTAT
2275994 ACTATGTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (18 bp):
TTCAATTACTAGTATTAT
Found at i:2281189 original size:16 final size:15
Alignment explanation
Indices: 2281168--2281229 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 15
2281158 GATGTGAATA
2281168 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
2281184 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
2281199 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
2281215 AATAATAATAATTAA
1 -ATAA-AAT-ATTAA
2281230 TATTGACAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
15 8 0.20
16 23 0.57
17 5 0.12
18 4 0.10
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:2281191 original size:24 final size:24
Alignment explanation
Indices: 2281164--2281224 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
2281154 TAATGATGTG
*
2281164 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
2281188 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
2281212 AATAATAATAATA
1 AATAATAA-AATA
2281225 ATTAATATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 6 0.19
24 21 0.68
25 4 0.13
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:2281198 original size:8 final size:8
Alignment explanation
Indices: 2281164--2281229 Score: 62
Period size: 8 Copynumber: 8.0 Consensus size: 8
2281154 TAATGATGTG
*
2281164 AATAATAA
1 AATATTAA
2281172 AATATATAA
1 AATAT-TAA
2281181 AATA-TAA
1 AATATTAA
2281188 AATATTAA
1 AATATTAA
*
2281196 AATATCAA
1 AATATTAA
*
2281204 AATATTAG
1 AATATTAA
*
2281212 AATAATAA
1 AATATTAA
2281220 TAATAATTAA
1 -AAT-ATTAA
2281230 TATTGACAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
7 7 0.15
8 26 0.55
9 10 0.21
10 4 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (8 bp):
AATATTAA
Found at i:2281484 original size:25 final size:25
Alignment explanation
Indices: 2281364--2281579 Score: 104
Period size: 25 Copynumber: 9.0 Consensus size: 25
2281354 TAAATACGTG
* *
2281364 ATAATATTAAAAATATGTACATAAT
1 ATAATATTAAAGATATATACATAAT
*
2281389 A-AAGTGTT-AA-A-ATATACATAAT
1 ATAA-TATTAAAGATATATACATAAT
* *
2281411 AT-A-GTT-AAGATATATACATAAG
1 ATAATATTAAAGATATATACATAAT
* * * *
2281433 ATAACATGTAAAAAAAAATATAAATAAT
1 ATAATAT-T--AAAGATATATACATAAT
*
2281461 ATAATATTAAAGATATATACATAAA
1 ATAATATTAAAGATATATACATAAT
* * *
2281486 ATAGTA-TAATATATATATACGTAAT
1 ATAATATTAA-AGATATATACATAAT
* *
2281511 ATAGA-ATTTAA-A-ATATACCTAAT
1 ATA-ATATTAAAGATATATACATAAT
* *
2281534 AT-AT-TAAAAGA-ATATATATAAT
1 ATAATATTAAAGATATATACATAAT
*
2281556 ATAATATT-AAGAAATATA-ATAAT
1 ATAATATTAAAGATATATACATAAT
2281579 A
1 A
2281580 ACAAAAAAGG
Statistics
Matches: 148, Mismatches: 25, Indels: 38
0.70 0.12 0.18
Matches are distributed among these distances:
20 5 0.03
21 5 0.03
22 36 0.24
23 26 0.18
24 15 0.10
25 40 0.27
26 2 0.01
27 1 0.01
28 18 0.12
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (25 bp):
ATAATATTAAAGATATATACATAAT
Found at i:2282133 original size:30 final size:30
Alignment explanation
Indices: 2282107--2282234 Score: 199
Period size: 30 Copynumber: 4.4 Consensus size: 30
2282097 AATGGAGCAA
* *
2282107 GTGTGGCTAGTGGATTTGGTGGTGGAGAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
2282137 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
*
2282167 GAGTGGCTAGTGGAG-T--TGGTGGAAAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
*
2282194 GCGTGGCTAGTGGAGTTGGTGGTGGAAAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
2282224 GTGTGGCTAGT
1 GTGTGGCTAGT
2282235 TGAGAAAAGT
Statistics
Matches: 90, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
27 25 0.28
28 1 0.01
29 1 0.01
30 63 0.70
ACGTcount: A:0.20, C:0.05, G:0.49, T:0.27
Consensus pattern (30 bp):
GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
Found at i:2282212 original size:57 final size:57
Alignment explanation
Indices: 2282126--2282234 Score: 191
Period size: 57 Copynumber: 1.9 Consensus size: 57
2282116 GTGGATTTGG
* *
2282126 TGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
1 TGGTGGAAAAGGCGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
2282183 TGGTGGAAAAGGCGTGGCTAGTGGAGTTGGTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGAAAAGGCGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTAGT
2282235 TGAGAAAAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.21, C:0.05, G:0.50, T:0.25
Consensus pattern (57 bp):
TGGTGGAAAAGGCGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
Found at i:2283018 original size:13 final size:13
Alignment explanation
Indices: 2283002--2283045 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
2282992 TAAATTGAAA
2283002 AAAACAGAAATTG
1 AAAACAGAAATTG
*
2283015 AAAAGCAGAAATTA
1 AAAA-CAGAAATTG
*
2283029 AAAACAGAATTTG
1 AAAACAGAAATTG
2283042 AAAA
1 AAAA
2283046 GACCTCAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.64, C:0.07, G:0.14, T:0.16
Consensus pattern (13 bp):
AAAACAGAAATTG
Found at i:2283018 original size:14 final size:14
Alignment explanation
Indices: 2282982--2283045 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
2282972 GAGTTGATTT
* *
2282982 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
2282996 TTGAAAAAAACAGAAA
1 TTG--AAAAACAGAAA
*
2283012 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
*
2283026 TT-AAAAACAGAAT
1 TTGAAAAACAGAAA
2283039 TTGAAAA
1 TTGAAAA
2283046 GACCTCAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
13 11 0.26
14 19 0.45
16 12 0.29
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:2283151 original size:75 final size:73
Alignment explanation
Indices: 2283028--2283277 Score: 270
Period size: 75 Copynumber: 3.3 Consensus size: 73
2283018 AGCAGAAATT
* ** * *
2283028 AAAAACAGAATTTGAAAAGACCTCAATGTGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAAG-CCTCAGCGTGTGACCCGAGGCTCAACTCA-CTCTCGCAATATGAG
2283093 TTGATTTTTG
64 TTGATTTTTG
*
2283103 AAAAACAGAAATTGAAAACGCCTCAGCGTGTGACCCGAGGTTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAA-GCCTCAGCGTGTGACCCGAGGCTCAACTCA-CTCTCGCAATATGAG
2283168 TTGATTCTTTTG
64 TTGA-T-TTTTG
** ** * **
2283180 AAAAGTAGAAATTGAAAATAG-CTCAGCACGTGAGCAAAGGCTCAACTCACTTCTCGCAATATGA
1 AAAAACAGAAATTG-AAA-AGCCTCAGCGTGTGACCCGAGGCTCAACTCAC-TCTCGCAATATGA
2283244 GTTGATTTTTG
63 GTTGATTTTTG
* *
2283255 AAAAATAGAAATT-AAAAGGCTCA
1 AAAAACAGAAATTGAAAAGCCTCA
2283278 ACTCACCTCT
Statistics
Matches: 152, Mismatches: 16, Indels: 16
0.83 0.09 0.09
Matches are distributed among these distances:
72 2 0.01
73 7 0.05
75 77 0.51
76 4 0.03
77 57 0.38
78 4 0.03
79 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (73 bp):
AAAAACAGAAATTGAAAAGCCTCAGCGTGTGACCCGAGGCTCAACTCACTCTCGCAATATGAGTT
GATTTTTG
Found at i:2283225 original size:77 final size:75
Alignment explanation
Indices: 2283068--2283271 Score: 268
Period size: 77 Copynumber: 2.7 Consensus size: 75
2283058 TGGCCCGAGA
* * * **
2283068 CTCAACTCATCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAACGCCTCAGCGTG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAAAGCCTCAGCACG
**
2283133 TGACCCGAGG
66 TGACCAAAGG
* *
2283143 TTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAATTGAAAATAG-CTCAGC
1 CTCAACTCACCTCTCGCAATATGAGTTGA-T-TTTTGAAAAATAGAAATTGAAAA-AGCCTCAGC
*
2283207 ACGTGAGCAAAGG
63 ACGTGACCAAAGG
*
2283220 CTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATT-AAAA
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAA
2283272 GGCTCAACTC
Statistics
Matches: 113, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
74 4 0.04
75 44 0.39
76 2 0.02
77 62 0.55
78 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (75 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAAAGCCTCAGCACG
TGACCAAAGG
Found at i:2283297 original size:54 final size:54
Alignment explanation
Indices: 2283215--2283325 Score: 177
Period size: 54 Copynumber: 2.1 Consensus size: 54
2283205 GCACGTGAGC
* * *
2283215 AAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTA
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAAATAAAAATTA
* *
2283269 AAAGGCTCAACTCACCTCTCTCAATATGAGTTAATTTTTGAAAAGTAAAAATTA
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAAATAAAAATTA
2283323 AAA
1 AAA
2283326 ATAGAGTTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (54 bp):
AAAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAAATAAAAATTA
Found at i:2283458 original size:76 final size:75
Alignment explanation
Indices: 2283332--2283580 Score: 279
Period size: 76 Copynumber: 3.3 Consensus size: 75
2283322 AAAAATAGAG
* * * *
2283332 TTTGAAAGACAGAATTTGAAAATA-CCTCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAAT
1 TTTGAAAAACAGAAATTGAAAA-AGCCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAAT
*
2283396 ATAAGTTGATAT
65 ATGAGTTGAT-T
* * * *
2283408 TTTGAAAAACAGAAATTGGAAACGCCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCACAATA
1 TTTGAAAAACAGAAATTGAAAAAGCCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATA
2283473 TGAGTTGATTCT
66 TGAGTTGA-T-T
* * * ** * * *
2283485 TTTGAAAAGCAGAAATTGAAAATAG-CTCAGCACGTGAGCAAAGGTTTAACTCACTTCTCGCAAT
1 TTTGAAAAACAGAAATTGAAAA-AGCCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAAT
2283549 ATGAGTTGATT
65 ATGAGTTGATT
2283560 TTTGAAAAACAGAAATT-AAAA
1 TTTGAAAAACAGAAATTGAAAA
2283581 GGCTCAACTC
Statistics
Matches: 147, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
74 4 0.03
75 17 0.12
76 64 0.44
77 61 0.41
78 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (75 bp):
TTTGAAAAACAGAAATTGAAAAAGCCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATA
TGAGTTGATT
Found at i:2283590 original size:309 final size:309
Alignment explanation
Indices: 2283063--2283738 Score: 1228
Period size: 309 Copynumber: 2.2 Consensus size: 309
2283053 ATGTGTGGCC
* * * *
2283063 CGAGACTCAACTCATCTCTCGCAATATGAGTTGAT-TTTTGAAAAACAGAAATTGAAAACGCCTC
1 CGAGGCTCAACTCACCTCTCGCAATATAAGTTGATATTTTGAAAAACAGAAATTGGAAACGCCTC
* * *
2283127 AGCGTGTGACCCGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAAT
66 AGCGTGTGACCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAGCAGAAAT
2283192 TGAAAATAGCTCAGCACGTGAGCAAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAA
131 TGAAAATAGCTCAGCACGTGAGCAAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAA
*
2283257 AAATAGAAATTAAAAGGCTCAACTCACCTCTCTCAATATGAGTTAATTTTTGAAAAGTAAAAATT
196 AAACAGAAATTAAAAGGCTCAACTCACCTCTCTCAATATGAGTTAATTTTTGAAAAGTAAAAATT
*
2283322 AAAAATAGAGTTTGAAAGACAGAATTTGAAAATACCTCGGCATGTGACT
261 AAAAATAGAGTTTGAAAGACAGAATTTGAAAATACCCCGGCATGTGACT
2283371 CGAGGCTCAACTCACCTCTCGCAATATAAGTTGATATTTTGAAAAACAGAAATTGGAAACGCCTC
1 CGAGGCTCAACTCACCTCTCGCAATATAAGTTGATATTTTGAAAAACAGAAATTGGAAACGCCTC
2283436 AGCGTGTGACCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAGCAGAAAT
66 AGCGTGTGACCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAGCAGAAAT
* *
2283501 TGAAAATAGCTCAGCACGTGAGCAAAGGTTTAACTCACTTCTCGCAATATGAGTTGATTTTTGAA
131 TGAAAATAGCTCAGCACGTGAGCAAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAA
*
2283566 AAACAGAAATTAAAAGGCTCAACTCACCTCTCTCAATATGAGTTGATTTTTGAAAAGTAAAAATT
196 AAACAGAAATTAAAAGGCTCAACTCACCTCTCTCAATATGAGTTAATTTTTGAAAAGTAAAAATT
2283631 AAAAATAGAGTTTGAAAGACAGAATTTGAAAATACCCCGGCATGTGACT
261 AAAAATAGAGTTTGAAAGACAGAATTTGAAAATACCCCGGCATGTGACT
*
2283680 CGAGGCTCAACTCACCTCTCGCAATATAAGTTGATATTTTGAAAAGCAGAAATTGGAAA
1 CGAGGCTCAACTCACCTCTCGCAATATAAGTTGATATTTTGAAAAACAGAAATTGGAAA
2283739 AAAAACAGAA
Statistics
Matches: 354, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
308 32 0.09
309 322 0.91
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (309 bp):
CGAGGCTCAACTCACCTCTCGCAATATAAGTTGATATTTTGAAAAACAGAAATTGGAAACGCCTC
AGCGTGTGACCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAGCAGAAAT
TGAAAATAGCTCAGCACGTGAGCAAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAA
AAACAGAAATTAAAAGGCTCAACTCACCTCTCTCAATATGAGTTAATTTTTGAAAAGTAAAAATT
AAAAATAGAGTTTGAAAGACAGAATTTGAAAATACCCCGGCATGTGACT
Found at i:2283630 original size:54 final size:54
Alignment explanation
Indices: 2283532--2283634 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 54
2283522 GCAAAGGTTT
* *
2283532 AACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTC
1 AACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTC
* **
2283586 AACTCACCTCTCTCAATATGAGTTGATTTTTGAAAAGTAAAAATTAAAA
1 AACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAA
2283635 ATAGAGTTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.31
Consensus pattern (54 bp):
AACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTC
Found at i:2283755 original size:17 final size:18
Alignment explanation
Indices: 2283721--2283756 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2283711 TGATATTTTG
*
2283721 AAAAGCAGAAATTGGAAA
1 AAAAACAGAAATTGGAAA
2283739 AAAAACAGAAATT-GAAA
1 AAAAACAGAAATTGGAAA
2283756 A
1 A
2283757 TACCTCAGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.67, C:0.06, G:0.17, T:0.11
Consensus pattern (18 bp):
AAAAACAGAAATTGGAAA
Found at i:2283975 original size:122 final size:122
Alignment explanation
Indices: 2283774--2284142 Score: 578
Period size: 122 Copynumber: 3.0 Consensus size: 122
2283764 GCGTGTCCTG
* * * * * * *
2283774 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATCAAAACAAAAAAATTGAAAATACCTCAGCG
1 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAAC--ATAAACTAAAAATACCTCAGCG
2283839 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAGAATTAAA
63 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAGAATTAAA
*
2283899 AGGCTTAACTCACCTCTCACAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGC
1 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGC
*
2283964 CCCGAAGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAGAATTAAA
66 CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAGAATTAAA
* *
2284021 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATATCTCAGTGTGC
1 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGC
* * *
2284086 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTG-AAAACAAAAATTAAA
66 CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAGAATTAAA
2284142 A
1 A
2284143 ATACCTCAAC
Statistics
Matches: 228, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
121 15 0.07
122 178 0.78
124 9 0.04
125 26 0.11
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.25
Consensus pattern (122 bp):
AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGC
CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAGAATTAAA
Found at i:2284167 original size:71 final size:70
Alignment explanation
Indices: 2284021--2284196 Score: 212
Period size: 71 Copynumber: 2.5 Consensus size: 70
2284011 AAGAATTAAA
* * * * * * **
2284021 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATATCTCAGTGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
2284085 CCCCG
66 CCCCG
*
2284090 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAACAAAAACTAAAAATACCTCAACGT
* **
2284155 GTCTTG
65 GCCCCG
2284161 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
2284197 CCTTGAAAAG
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
69 26 0.28
70 6 0.07
71 60 0.65
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:2292499 original size:12 final size:12
Alignment explanation
Indices: 2292479--2292514 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2292469 TGGGATATGC
*
2292479 AATGTATGAATG
1 AATGCATGAATG
2292491 AATGCATGAATG
1 AATGCATGAATG
2292503 AATGCATGAATG
1 AATGCATGAATG
2292515 TCAAAATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:2294101 original size:19 final size:19
Alignment explanation
Indices: 2294062--2294101 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2294052 AATATATACA
* * *
2294062 ATATGGTATTTACATATAT
1 ATATGGTATATAAATAAAT
2294081 ATATGGTATATAAATAAAT
1 ATATGGTATATAAATAAAT
2294100 AT
1 AT
2294102 TAGATATAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (19 bp):
ATATGGTATATAAATAAAT
Found at i:2294154 original size:13 final size:12
Alignment explanation
Indices: 2294132--2294172 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
2294122 TATAACTATC
2294132 ATAAAAATATAT
1 ATAAAAATATAT
2294144 ATAACAAATATAT
1 ATAA-AAATATAT
*
2294157 ATAAAATACATAT
1 ATAAAA-ATATAT
2294170 ATA
1 ATA
2294173 GTACATATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 6 0.23
13 20 0.77
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAAAATATAT
Found at i:2294485 original size:11 final size:11
Alignment explanation
Indices: 2294451--2294492 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
2294441 AAATCATTTT
2294451 GAAGAGAGAAA
1 GAAGAGAGAAA
* *
2294462 GAA-AAAAAAA
1 GAAGAGAGAAA
*
2294472 GAAGGGAGAAA
1 GAAGAGAGAAA
2294483 GAAGAGAGAA
1 GAAGAGAGAA
2294493 GGGAGGGGGA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAAA
Found at i:2294966 original size:21 final size:21
Alignment explanation
Indices: 2294940--2295002 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 21
2294930 TAGGTTCTGG
2294940 TTTTTTTTGGG-GGTTGTTTTC
1 TTTTTTTTGGGTGGTT-TTTTC
2294961 TTTTTTTTGGGTTAGGTTTTTT-
1 TTTTTTTTGGG-T-GGTTTTTTC
*
2294983 TTTTTTTTTGGTAGGTTTTT
1 TTTTTTTTGGGT-GGTTTTT
2295003 GGGGGAGGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
21 20 0.53
22 10 0.26
23 4 0.11
24 4 0.11
ACGTcount: A:0.03, C:0.02, G:0.24, T:0.71
Consensus pattern (21 bp):
TTTTTTTTGGGTGGTTTTTTC
Found at i:2295845 original size:18 final size:19
Alignment explanation
Indices: 2295816--2295861 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2295806 CTGTGTTATT
2295816 AAATACAAAAAT-ATTTTCA
1 AAATA-AAAAATGATTTTCA
*
2295835 AAATAAAAAATGTTTTTCA
1 AAATAAAAAATGATTTTCA
*
2295854 ATATAAAA
1 AAATAAAA
2295862 CACTTATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (19 bp):
AAATAAAAAATGATTTTCA
Found at i:2296389 original size:13 final size:13
Alignment explanation
Indices: 2296371--2296398 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2296361 AAAAAATTTA
2296371 TTGATATTTTTTG
1 TTGATATTTTTTG
2296384 TTGATATTTTTTG
1 TTGATATTTTTTG
2296397 TT
1 TT
2296399 ATGAAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (13 bp):
TTGATATTTTTTG
Found at i:2300520 original size:20 final size:20
Alignment explanation
Indices: 2300475--2300526 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
2300465 CCCCACCCAA
*
2300475 ATTTCCCCAAATCCCTAACT
1 ATTTCCCCAAATCCCTAAAT
*
2300495 -TTTCCCCTAATCCCTAAAT
1 ATTTCCCCAAATCCCTAAAT
*
2300514 ATTTCCCCGAATC
1 ATTTCCCCAAATC
2300527 AAAATCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.27, C:0.38, G:0.02, T:0.33
Consensus pattern (20 bp):
ATTTCCCCAAATCCCTAAAT
Found at i:2302680 original size:10 final size:10
Alignment explanation
Indices: 2302650--2302679 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2302640 GGTTAGCTAC
2302650 TCTTTTATTT
1 TCTTTTATTT
2302660 TCTTTTATTT
1 TCTTTTATTT
2302670 TCTTTT-TTT
1 TCTTTTATTT
2302679 T
1 T
2302680 TAAATTACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.20
10 16 0.80
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (10 bp):
TCTTTTATTT
Found at i:2313133 original size:71 final size:72
Alignment explanation
Indices: 2312894--2313296 Score: 563
Period size: 72 Copynumber: 5.6 Consensus size: 72
2312884 ATTAAAAGGT
* * * * * *
2312894 TCAACCCACCTCTCGCAATATGAGTTGATTTTTTGAAAGTA-GAATTTGAAAATACCTCGGCGTG
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAA-AACAAAATTGAAATTACCTCAGCGTG
*
2312958 -CCCGAGGC
64 TCCTGAGGC
*
2312966 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTTAGCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA-AAATTGAAATTACCTCAGCGTGT
*
2313031 TCTGAGGC
65 CCTGAGGC
2313039 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAATTGAAA-TACCTCAGCGTGTC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAATTGAAATTACCTCAGCGTGTC
2313102 CTGAGGC
66 CTGAGGC
** *
2313109 TCAACTCCATTTCTCGCAATATGAGTTGA-ATTTG-AAAACAAAATTGAAATTACCTCAGCGTGT
1 TCAACT-CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAATTGAAATTACCTCAGCGTGT
2313172 CCTGAGGC
65 CCTGAGGC
**
2313180 TCAACTCATTTCTCGCAATATGAGTTGATTTTTTG-AAAACAGAAATTGAAATTACCTCAGCGTG
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACA-AAATTGAAATTACCTCAGCGTG
2313244 TCCTGAGGC
64 TCCTGAGGC
2313253 TCAACTCACCTCT-GCAATATGAGTTGA-TTTTGAAAAACAAAATT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAATT
2313297 AAAAGTTCAA
Statistics
Matches: 305, Mismatches: 17, Indels: 20
0.89 0.05 0.06
Matches are distributed among these distances:
70 73 0.24
71 75 0.25
72 81 0.27
73 76 0.25
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (72 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAATTGAAATTACCTCAGCGTGTC
CTGAGGC
Found at i:2313328 original size:51 final size:50
Alignment explanation
Indices: 2313253--2313350 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 50
2313243 GTCCTGAGGC
*
2313253 TCAACTCACCTCTGCAATATGAGTTGA-TTTTGAAAAACAAAATTAAAAGT
1 TCAACCCACCTCTGCAATATGAGTTGATTTTTG-AAAACAAAATTAAAAGT
*
2313303 TCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTAAA
1 TCAACCCACCTCT-GCAATATGAGTTGATTTTTGAAAACAAAATTAAA
2313351 TTGAAAATAC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 12 0.27
51 27 0.61
52 5 0.11
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (50 bp):
TCAACCCACCTCTGCAATATGAGTTGATTTTTGAAAACAAAATTAAAAGT
Found at i:2313424 original size:129 final size:123
Alignment explanation
Indices: 2313190--2313430 Score: 344
Period size: 129 Copynumber: 1.9 Consensus size: 123
2313180 TCAACTCATT
* * *
2313190 TCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTC
1 TCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTC
2313255 AACTCACCTCTGCAATATGAGTTGATTTTGAAAAACAAAATT-AAAAGTTCAACCCACC
66 AACTCACCTCTGCAATATGAGTTGATTTT-AAAAACAAAATTGAAAAGTTCAACCCACC
2313313 TCTCGCAATATGAGTTGA-TTTTTGAAAACAGAATTAAATTGAAAATACCTCAGGCATGTGACCC
1 TCTCGCAATATGAGTTGATTTTTTGAAAACAG----AAATTGAAAATACCTCA-GC--GTGACCC
2313377 GAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTT-AAAACAAAATTGAAAA
59 GAGGCTCAACTCACCTCT-GCAATATGAGTTG-ATTTTAAAAACAAAATTGAAAA
2313431 TACCTCAGCG
Statistics
Matches: 105, Mismatches: 3, Indels: 13
0.87 0.02 0.11
Matches are distributed among these distances:
122 13 0.12
123 18 0.17
126 16 0.15
127 2 0.02
129 34 0.32
130 17 0.16
131 5 0.05
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (123 bp):
TCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTC
AACTCACCTCTGCAATATGAGTTGATTTTAAAAACAAAATTGAAAAGTTCAACCCACC
Found at i:2313483 original size:73 final size:76
Alignment explanation
Indices: 2313303--2313485 Score: 224
Period size: 79 Copynumber: 2.5 Consensus size: 76
2313293 AATTAAAAGT
* * **
2313303 TCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTAAATTGAAAATACCTCAGGC
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAACAAAACAAAATTGAAAATACCTCAGGC
2313368 ATGTGACCCGAGGC
65 A-GTGA-CCGAGGC
2313382 TCAACTCACCTCTCGCAATATGAGTTGAATTTT------AAAACAAAATTGAAAATACCTCA-GC
1 TCAACTCACCTCTCGCAATATGAGTTG-ATTTTGAAAACAAAACAAAATTGAAAATACCTCAGGC
2313440 -GTG-CCGAGGC
65 AGTGACCGAGGC
2313450 TCAACTCACCTCT-GCAATATGAGTTGATTTTGAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAA
2313486 GTAGAAATTA
Statistics
Matches: 94, Mismatches: 4, Indels: 20
0.80 0.03 0.17
Matches are distributed among these distances:
66 5 0.05
67 13 0.14
68 20 0.21
70 3 0.03
72 2 0.02
73 20 0.21
79 30 0.32
80 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Consensus pattern (76 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAACAAAATTGAAAATACCTCAGGCA
GTGACCGAGGC
Found at i:2313510 original size:52 final size:53
Alignment explanation
Indices: 2313450--2313551 Score: 165
Period size: 52 Copynumber: 1.9 Consensus size: 53
2313440 GTGCCGAGGC
2313450 TCAACTCACCTCT-GCAATATGAGTTGA-TTTTGAAAAGTAGAAATT-AAAAGGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA--AGAAATTGAAAAGGT
2313502 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAGAAATTGAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAGAAATTGAAAA
2313552 TACCTCGCGT
Statistics
Matches: 47, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
52 20 0.43
53 18 0.38
54 9 0.19
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (53 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAGAAATTGAAAAGGT
Found at i:2313582 original size:121 final size:122
Alignment explanation
Indices: 2313382--2313617 Score: 390
Period size: 121 Copynumber: 1.9 Consensus size: 122
2313372 GACCCGAGGC
2313382 TCAACTCACCTCTCGCAATATGAGTTGAATTTTAAAACAAAATTGAAAATACCTCAGCGTGCCGA
1 TCAACTCACCTCTCGCAATATGAGTTGAATTTTAAAACAAAATTGAAAATACCTCAGCGTGCCGA
**
2313447 GGCTCAACTCACCTCT-GCAATATGAGTTGA-TTTTGAAAAGTAGAAATTAAAAGGT
66 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGT
*
2313502 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-AGAAATTGAAAATACCTC-GCGTGCC
1 TCAACTCACCTCTCGCAATATGAGTTGAATTTT-AAAACA-AAATTGAAAATACCTCAGCGTG-C
2313565 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT
63 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT
2313618 GAAATACCTC
Statistics
Matches: 108, Mismatches: 3, Indels: 7
0.92 0.03 0.06
Matches are distributed among these distances:
120 38 0.35
121 40 0.37
122 14 0.13
123 16 0.15
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (122 bp):
TCAACTCACCTCTCGCAATATGAGTTGAATTTTAAAACAAAATTGAAAATACCTCAGCGTGCCGA
GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGT
Done.