Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, 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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 17 of 64
Found at i:2280343 original size:62 final size:62
Alignment explanation
Indices: 2280263--2280427 Score: 190
Period size: 62 Copynumber: 2.6 Consensus size: 62
2280253 TTTTTTTAGA
* * *
2280263 GATTATTCTAGATTTTTTTGCCAGAAAATGCCTTAAATAATCCCCTA-ATAAAAATTGAAGGG
1 GATTATTCAAGATGTTTTTGCCAGAAAATGCCTTAAATAATCCCCTACA-AAAAATTAAAGGG
* * * *
2280325 GATTATTCAAGATGTTTTTAGCCA-AAAATGCATTGAATAATCCCTTACAAAAAATTAAATGG
1 GATTATTCAAGATGTTTTT-GCCAGAAAATGCCTTAAATAATCCCCTACAAAAAATTAAAGGG
** * *
2280387 GATTATTCAAGGCGTTTTTGGCTGAAAAATGCCTTAAATAA
1 GATTATTCAAGATGTTTTTGCCAG-AAAATGCCTTAAATAA
2280428 CATTTTTTAT
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
61 2 0.02
62 65 0.76
63 19 0.22
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (62 bp):
GATTATTCAAGATGTTTTTGCCAGAAAATGCCTTAAATAATCCCCTACAAAAAATTAAAGGG
Found at i:2292495 original size:20 final size:19
Alignment explanation
Indices: 2292466--2292503 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2292456 TCCGAGATTT
2292466 TCATTATTTATATTTTTTAA
1 TCATTATTTAT-TTTTTTAA
*
2292486 TCATTTTTTATTTTTTTA
1 TCATTATTTATTTTTTTA
2292504 TTTTTTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (19 bp):
TCATTATTTATTTTTTTAA
Found at i:2292508 original size:15 final size:15
Alignment explanation
Indices: 2292488--2292519 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2292478 TTTTTTAATC
*
2292488 ATTTTTTATTTTTTT
1 ATTTTTTATGTTTTT
2292503 ATTTTTTATGTTTTT
1 ATTTTTTATGTTTTT
2292518 AT
1 AT
2292520 ACACATGTTT
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:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (15 bp):
ATTTTTTATGTTTTT
Found at i:2292644 original size:20 final size:20
Alignment explanation
Indices: 2292590--2292644 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
2292580 ACACTTATTC
*
2292590 TAATTATTTAAAAATAAAAA
1 TAATAATTTAAAAATAAAAA
* *
2292610 T-ATGAA-CTAATAAATAAAAT
1 TAAT-AATTTAA-AAATAAAAA
2292630 TAATAATTTAAAAAT
1 TAATAATTTAAAAAT
2292645 TAGAGAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
19 5 0.19
20 17 0.63
21 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
TAATAATTTAAAAATAAAAA
Found at i:2294271 original size:7 final size:7
Alignment explanation
Indices: 2294250--2294290 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
2294240 TTAATTCCAT
2294250 AAAAT-A
1 AAAATGA
2294256 AAAAT-A
1 AAAATGA
*
2294262 AAAAAG-
1 AAAATGA
2294268 AAAATGA
1 AAAATGA
2294275 AAAATGA
1 AAAATGA
2294282 AAAATGA
1 AAAATGA
2294289 AA
1 AA
2294291 TTGGGCTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
6 15 0.48
7 16 0.52
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (7 bp):
AAAATGA
Found at i:2294271 original size:13 final size:14
Alignment explanation
Indices: 2294250--2294290 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
2294240 TTAATTCCAT
*
2294250 AAAATAAAAAT-AA
1 AAAAGAAAAATGAA
2294263 AAAAG-AAAATGAA
1 AAAAGAAAAATGAA
*
2294276 AAATGAAAAATGAA
1 AAAAGAAAAATGAA
2294290 A
1 A
2294291 TTGGGCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.21
13 10 0.42
14 9 0.38
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (14 bp):
AAAAGAAAAATGAA
Found at i:2294291 original size:19 final size:18
Alignment explanation
Indices: 2294250--2294290 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
2294240 TTAATTCCAT
2294250 AAAATAAAAATAAAAAAG
1 AAAATAAAAATAAAAAAG
*
2294268 AAAATGAAAAATGAAAAATG
1 AAAAT-AAAAAT-AAAAAAG
2294288 AAA
1 AAA
2294291 TTGGGCTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 6 0.30
20 9 0.45
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (18 bp):
AAAATAAAAATAAAAAAG
Found at i:2294702 original size:8 final size:8
Alignment explanation
Indices: 2294691--2294778 Score: 53
Period size: 8 Copynumber: 11.4 Consensus size: 8
2294681 TTTGATTTTA
2294691 TTGTTGTT
1 TTGTTGTT
2294699 TTGTTGTT
1 TTGTTGTT
2294707 TTGTTGCTT
1 TTGTTG-TT
* *
2294716 TTATGGTT
1 TTGTTGTT
*
2294724 TT-TATGGT
1 TTGT-TGTT
2294732 TT-TT-TT
1 TTGTTGTT
2294738 TTGTTG-T
1 TTGTTGTT
*
2294745 TT-TTCTT
1 TTGTTGTT
*
2294752 TTG-GGATT
1 TTGTTG-TT
*
2294760 TTTTTGTT
1 TTGTTGTT
2294768 TTGTTGTT
1 TTGTTGTT
2294776 TTG
1 TTG
2294779 CTTTTGCTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 16
0.69 0.12 0.18
Matches are distributed among these distances:
6 5 0.08
7 10 0.16
8 39 0.64
9 7 0.11
ACGTcount: A:0.03, C:0.02, G:0.22, T:0.73
Consensus pattern (8 bp):
TTGTTGTT
Found at i:2294789 original size:20 final size:18
Alignment explanation
Indices: 2294761--2294817 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 18
2294751 TTTGGGATTT
2294761 TTTTGTTTTGTTGTTTTGC
1 TTTTGTTTTGTT-TTTTGC
*
2294780 TTTTGCTTTTGTTTTTTTGT
1 TTTTG-TTTTG-TTTTTTGC
2294800 TTTTGTCTTTGTTTTTTG
1 TTTTGT-TTTGTTTTTTG
2294818 GAAAAATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 13 0.38
20 19 0.56
21 2 0.06
ACGTcount: A:0.00, C:0.05, G:0.18, T:0.77
Consensus pattern (18 bp):
TTTTGTTTTGTTTTTTGC
Found at i:2295271 original size:207 final size:207
Alignment explanation
Indices: 2294915--2295296 Score: 545
Period size: 207 Copynumber: 1.8 Consensus size: 207
2294905 AGATCATGCC
* ** *
2294915 CAGAGGTTTTACAAATCTCAACATTTGTAAAAGCTCCTCTAATCAAAGGCATTGAAACTTTAAAA
1 CAGAGGTCTTACAAATCTCAACATTTACAAAAGCTACTCTAATCAAAGGCATTGAAACTTTAAAA
* * * * * **
2294980 ATTAAAAATATTTTGTCCAAAGGACTTATAGATTATATCTGGAGGTCTTACAAATGTTGACATCT
66 ATTAAAAATATTTTGTCCAAAGGACTCAGAAATTATATCTGGAGATCTTACAAATCTCAACATCT
2295045 ATGAAAACTCCTCTAATAAGAGGCATT-AGAACTTTAAAGATTTAAAATGTTTACTTTGAACTCT
131 ATGAAAACTCCTCTAATAAGAGGCATTGA-AACTTTAAAGATTTAAAATGTTTACTTTGAACTCT
2295109 TAGAGATTATTTT
195 TAGAGATTATTTT
*
2295122 CAGAGGTCTTACAAATCTCAACATTTACAAAAGCTACTCTAATCAGAA-GTATTGAAACTTTAAA
1 CAGAGGTCTTACAAATCTCAACATTTACAAAAGCTACTCTAATCA-AAGGCATTGAAACTTTAAA
* * *
2295186 ATTTTAAAATATTTTG-CCAAGAGGACTCAGAAATTATATTTGGAGATCTTACAAATCTCAACAT
65 AATTAAAAATATTTTGTCCAA-AGGACTCAGAAATTATATCTGGAGATCTTACAAATCTCAACAT
* ** *
2295250 TTATGAATGCTCCTTTAATAAGAGGCATTGAAACTTTAAAGATTTAA
129 CTATGAAAACTCCTCTAATAAGAGGCATTGAAACTTTAAAGATTTAA
2295297 CCTAGTGGTC
Statistics
Matches: 153, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
206 4 0.03
207 146 0.95
208 3 0.02
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (207 bp):
CAGAGGTCTTACAAATCTCAACATTTACAAAAGCTACTCTAATCAAAGGCATTGAAACTTTAAAA
ATTAAAAATATTTTGTCCAAAGGACTCAGAAATTATATCTGGAGATCTTACAAATCTCAACATCT
ATGAAAACTCCTCTAATAAGAGGCATTGAAACTTTAAAGATTTAAAATGTTTACTTTGAACTCTT
AGAGATTATTTT
Found at i:2295296 original size:104 final size:104
Alignment explanation
Indices: 2294917--2295296 Score: 382
Period size: 104 Copynumber: 3.7 Consensus size: 104
2294907 ATCATGCCCA
* * *
2294917 GAGGTTTTACAAATCTCAACATTTGTAAAAGCTCCTCTAATCAA-AGGCATTGAAACTTTAAAAA
1 GAGGTCTTACAAATCTCAACATTTATAAAAGCTCCTCTAAT-AAGAGGCATTGAAACTTTAAAGA
* * * *
2294981 TTAAAAATATTTTGTCCAA-AGGACTTATAGATTATATCTG
65 TTTAAAATATTTTG-CCAAGAGGACTCAGAGATTATATTTG
* ** *
2295021 GAGGTCTTACAAATGTTGACATCTATGAAAA-CTCCTCTAATAAGAGGCATT-AGAACTTTAAAG
1 GAGGTCTTACAAATCTCAACATTTAT-AAAAGCTCCTCTAATAAGAGGCATTGA-AACTTTAAAG
* * *** *
2295084 ATTTAAAAT-GTTTACTTTGA--ACTCTTAGAGATTAT-TTTCA
64 ATTTAAAATATTTTGCCAAGAGGACTC--AGAGATTATATTT-G
* * * * *
2295124 GAGGTCTTACAAATCTCAACATTTACAAAAGCTACTCTAATCAGAAGTATTGAAACTTTAAA-AT
1 GAGGTCTTACAAATCTCAACATTTATAAAAGCTCCTCTAATAAGAGGCATTGAAACTTTAAAGA-
*
2295188 TTTAAAATATTTTGCCAAGAGGACTCAGAAATTATATTTG
65 TTTAAAATATTTTGCCAAGAGGACTCAGAGATTATATTTG
* * * *
2295228 GAGATCTTACAAATCTCAACATTTATGAATGCTCCTTTAATAAGAGGCATTGAAACTTTAAAGAT
1 GAGGTCTTACAAATCTCAACATTTATAAAAGCTCCTCTAATAAGAGGCATTGAAACTTTAAAGAT
2295293 TTAA
66 TTAA
2295297 CCTAGTGGTC
Statistics
Matches: 219, Mismatches: 42, Indels: 30
0.75 0.14 0.10
Matches are distributed among these distances:
101 3 0.01
102 8 0.04
103 69 0.32
104 127 0.58
105 8 0.04
106 4 0.02
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (104 bp):
GAGGTCTTACAAATCTCAACATTTATAAAAGCTCCTCTAATAAGAGGCATTGAAACTTTAAAGAT
TTAAAATATTTTGCCAAGAGGACTCAGAGATTATATTTG
Found at i:2295369 original size:73 final size:73
Alignment explanation
Indices: 2295232--2295366 Score: 200
Period size: 73 Copynumber: 1.9 Consensus size: 73
2295222 TATTTGGAGA
* * * *
2295232 TCTTACAAATCTCAACATTTATGAATGCTCCTTTAATAAGAGGCATTGAAACTTTAAAGATTTAA
1 TCTTACAAATCTCAACATCTATAAAAGCTCCTCTAATAAGAGGCATTGAAACTTTAAAGATTTAA
2295297 CCTAGTGG
66 CCTAGTGG
* * *
2295305 TCTTATAAATCTCGACATCTATAAAAGCTCCTCTAATCAGAGGCATTGAAACTTTAAA-ATTT
1 TCTTACAAATCTCAACATCTATAAAAGCTCCTCTAATAAGAGGCATTGAAACTTTAAAGATTT
2295367 TAAAATGTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
72 4 0.07
73 51 0.93
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (73 bp):
TCTTACAAATCTCAACATCTATAAAAGCTCCTCTAATAAGAGGCATTGAAACTTTAAAGATTTAA
CCTAGTGG
Found at i:2295535 original size:41 final size:41
Alignment explanation
Indices: 2295452--2295553 Score: 106
Period size: 41 Copynumber: 2.5 Consensus size: 41
2295442 CCCAGCGGTC
2295452 TTAGAAATCATTTAGAAATTTAAGATTTTGCCTAGAAATCT
1 TTAGAAATCATTTAGAAATTTAAGATTTTGCCTAGAAATCT
* *
2295493 TTAGAATTCATTT-GAAGATTTGAA-ATTTTGCTCTA-AAGTCT
1 TTAGAAATCATTTAGAA-ATTT-AAGATTTTGC-CTAGAAATCT
*
2295534 TT-GAAAATCTTTTA-AAATTT
1 TTAG-AAATCATTTAGAAATTT
2295554 TGAGCTTTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
40 8 0.15
41 39 0.75
42 5 0.10
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (41 bp):
TTAGAAATCATTTAGAAATTTAAGATTTTGCCTAGAAATCT
Found at i:2295739 original size:21 final size:23
Alignment explanation
Indices: 2295710--2295765 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
2295700 TTGAATTCTA
*
2295710 TTCACTTCAAAA-TTTTCACT-T
1 TTCATTTCAAAAGTTTTCACTGT
2295731 TTCATTTCAAAAGTTTTTCACTGT
1 TTCATTTCAAAAG-TTTTCACTGT
*
2295755 TT-GTTTCAAAA
1 TTCATTTCAAAA
2295766 AATCTTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 11 0.37
23 16 0.53
24 3 0.10
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48
Consensus pattern (23 bp):
TTCATTTCAAAAGTTTTCACTGT
Found at i:2296024 original size:25 final size:25
Alignment explanation
Indices: 2295996--2296044 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2295986 GCGAACATGC
** *
2295996 AAATATCTTTTTCTGATGCAAATGT
1 AAATATCTTTCCCTAATGCAAATGT
*
2296021 AAATGTCTTTCCCTAATGCAAATG
1 AAATATCTTTCCCTAATGCAAATG
2296045 ATCCATGCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (25 bp):
AAATATCTTTCCCTAATGCAAATGT
Found at i:2296521 original size:20 final size:20
Alignment explanation
Indices: 2296480--2296521 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2296470 CCTTTTCAAC
*
2296480 AACATTAATCCTGCATTAAA
1 AACATTAATCCTGCAATAAA
*
2296500 AACATTAATCCTTCAATGAAA
1 AACATTAATCCTGCAAT-AAA
2296521 A
1 A
2296522 GTATTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.48, C:0.19, G:0.05, T:0.29
Consensus pattern (20 bp):
AACATTAATCCTGCAATAAA
Found at i:2297671 original size:18 final size:17
Alignment explanation
Indices: 2297648--2297691 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2297638 TTGTTCTTCC
* *
2297648 CCTTTTTTCTCATTT-T
1 CCTTTTTTTTCCTTTCT
2297664 CCTTTTTTTTCCTTTCCT
1 CCTTTTTTTTCCTTT-CT
2297682 CCTTTTTTTT
1 CCTTTTTTTT
2297692 TACTCTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 13 0.54
18 11 0.46
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.70
Consensus pattern (17 bp):
CCTTTTTTTTCCTTTCT
Found at i:2297739 original size:19 final size:19
Alignment explanation
Indices: 2297666--2297741 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 19
2297656 CTCATTTTCC
* *
2297666 TTTTTTTTCCTTTCCTCCTT
1 TTTTTTTTCCTTT-TTCTTT
* *
2297686 TTTTTTTACTCTATTTCTTT
1 TTTTTTTTC-CTTTTTCTTT
2297706 TTCATTTTTT-C--TTTCTTT
1 TT--TTTTTTCCTTTTTCTTT
2297724 TTTTTTTTCCTTTTTCTT
1 TTTTTTTTCCTTTTTCTT
2297742 GTTCTCTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
16 6 0.13
17 1 0.02
18 9 0.20
19 6 0.13
20 15 0.33
21 3 0.07
22 5 0.11
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTTTTCCTTTTTCTTT
Found at i:2297750 original size:31 final size:31
Alignment explanation
Indices: 2297702--2297760 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2297692 TACTCTATTT
* *
2297702 CTTTTTCATTTTTTCTTTCTTTTTTTTTTTC
1 CTTTTTCATTTTCTCTTTATTTTTTTTTTTC
2297733 CTTTTTC-TTGTTCTCTTTATTTTTTTTT
1 CTTTTTCATT-TTCTCTTTATTTTTTTTT
2297761 ATTTTTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (31 bp):
CTTTTTCATTTTCTCTTTATTTTTTTTTTTC
Found at i:2297765 original size:28 final size:28
Alignment explanation
Indices: 2297719--2297793 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
2297709 ATTTTTTCTT
**
2297719 TCTTTTTTTTTTTCCTTTTT-CTTGTTC
1 TCTTTTTTTTTTTTATTTTTACTTGTTC
* *
2297746 TCTTTATTTTTTTTTATTTTTACTTTTTT
1 TCTTT-TTTTTTTTTATTTTTACTTGTTC
* *
2297775 TCATTTTTTTTCTTATTTT
1 TCTTTTTTTTTTTTATTTT
2297794 CTCCTTCTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 5 0.12
28 26 0.65
29 9 0.22
ACGTcount: A:0.07, C:0.12, G:0.01, T:0.80
Consensus pattern (28 bp):
TCTTTTTTTTTTTTATTTTTACTTGTTC
Found at i:2297780 original size:16 final size:16
Alignment explanation
Indices: 2297748--2297782 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2297738 TCTTGTTCTC
* *
2297748 TTTATTTTTTTTTATT
1 TTTACTTTTTTTCATT
2297764 TTTACTTTTTTTCATT
1 TTTACTTTTTTTCATT
2297780 TTT
1 TTT
2297783 TTTCTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTACTTTTTTTCATT
Found at i:2297804 original size:28 final size:29
Alignment explanation
Indices: 2297752--2297819 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 29
2297742 GTTCTCTTTA
* *
2297752 TTTTTTT-TTATTTTTACTTTTTTTCA-T
1 TTTTTTTCTTATTTTTACCTTCTTTCACT
2297779 TTTTTTTCTTATTTTCT-CCTTCTTTCACCT
1 TTTTTTTCTTATTTT-TACCTTCTTTCA-CT
2297809 TTATTTTTCTT
1 TT-TTTTTCTT
2297820 TTCCTTCAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 7 0.21
28 15 0.44
29 1 0.03
30 3 0.09
31 8 0.24
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (29 bp):
TTTTTTTCTTATTTTTACCTTCTTTCACT
Found at i:2298277 original size:5 final size:5
Alignment explanation
Indices: 2298263--2298347 Score: 59
Period size: 5 Copynumber: 16.8 Consensus size: 5
2298253 ATCAAATATT
* *
2298263 TTTTC TTTTTC TTTTC -TTTC TTTTC ATTATTC TCTTC -TTGC TTTTC
1 TTTTC -TTTTC TTTTC TTTTC TTTTC -TT-TTC TTTTC TTTTC TTTTC
* * * *
2298309 TTTT- TTCTC TTTTT TTATTT TTTTC TTTTC TTTCC TTTT
1 TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTT
2298348 TTCCTTTTTC
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
4 9 0.14
5 38 0.60
6 13 0.21
7 3 0.05
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:2298284 original size:9 final size:9
Alignment explanation
Indices: 2298270--2298346 Score: 52
Period size: 9 Copynumber: 8.3 Consensus size: 9
2298260 ATTTTTTCTT
2298270 TTTCTTTTC
1 TTTCTTTTC
2298279 TTTCTTTTC
1 TTTCTTTTC
*
2298288 ATTATTCTCTTC
1 --T-TTCTTTTC
*
2298300 TTGCTTTTC
1 TTTCTTTTC
2298309 TTT-TTTCTC
1 TTTCTTT-TC
*
2298318 TTT-TTTTA
1 TTTCTTTTC
2298326 TTT-TTTTC
1 TTTCTTTTC
*
2298334 TTTTCTTTCC
1 -TTTCTTTTC
2298344 TTT
1 TTT
2298347 TTTCCTTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
8 11 0.20
9 31 0.56
10 5 0.09
11 1 0.02
12 7 0.13
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.75
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:2298316 original size:21 final size:20
Alignment explanation
Indices: 2298263--2298319 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
2298253 ATCAAATATT
* *
2298263 TTTTCTTTTTCTTTTCTTTC
1 TTTTCTTTTTCTCTTCTTGC
*
2298283 TTTTCATTATTCTCTTCTTGC
1 TTTTC-TTTTTCTCTTCTTGC
2298304 TTTTCTTTTTTCTCTT
1 TTTTC-TTTTTCTCTT
2298320 TTTTTATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 5 0.16
21 26 0.84
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTCTTTTTCTCTTCTTGC
Found at i:2298330 original size:18 final size:18
Alignment explanation
Indices: 2298309--2298361 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
2298299 CTTGCTTTTC
2298309 TTTTTTCTCTTTTTTTAT
1 TTTTTTCTCTTTTTTTAT
* **
2298327 TTTTTTCT-TTTCTTTCC
1 TTTTTTCTCTTTTTTTAT
*
2298344 TTTTTTC-CTTTTTCTAT
1 TTTTTTCTCTTTTTTTAT
2298361 T
1 T
2298362 CAGGTCCCCT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTCTCTTTTTTTAT
Found at i:2298335 original size:34 final size:35
Alignment explanation
Indices: 2298269--2298362 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 35
2298259 TATTTTTTCT
*
2298269 TTTTCTTTTCTT-TCTTTTCATTATTCTCTTC-TTGC
1 TTTTCTTTT-TTCTCTTTT-TTTATTCTCTTCTTTGC
* * *
2298304 TTTTCTTTTTTCTCTTTTTTTATTTTTTTCTTTTC
1 TTTTCTTTTTTCTCTTTTTTTATTCTCTTCTTTGC
* *
2298339 TTTCCTTTTTTC-CTTTTTCTATTC
1 TTTTCTTTTTTCTCTTTTTTTATTC
2298363 AGGTCCCCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
34 21 0.42
35 29 0.58
ACGTcount: A:0.04, C:0.20, G:0.01, T:0.74
Consensus pattern (35 bp):
TTTTCTTTTTTCTCTTTTTTTATTCTCTTCTTTGC
Found at i:2298355 original size:25 final size:25
Alignment explanation
Indices: 2298304--2298356 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
2298294 CTCTTCTTGC
* *
2298304 TTTTCTTTTTTCTCTTTTTTTATTT
1 TTTTCTTTTTTCTCCTTTTTTACTT
*
2298329 TTTTCTTTTCTT-TCCTTTTTTCCTT
1 TTTTCTTTT-TTCTCCTTTTTTACTT
2298354 TTT
1 TTT
2298357 CTATTCAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTTCTTTTTTCTCCTTTTTTACTT
Found at i:2303194 original size:7 final size:7
Alignment explanation
Indices: 2303173--2303208 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
2303163 AGGATAAAAA
2303173 TTATTAT
1 TTATTAT
2303180 TTATTTAT
1 TTA-TTAT
2303188 TTATTAT
1 TTATTAT
2303195 TTATTA-
1 TTATTAT
2303201 TTATTAT
1 TTATTAT
2303208 T
1 T
2303209 ATTTAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.22
7 14 0.52
8 7 0.26
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATTAT
Found at i:2303439 original size:7 final size:8
Alignment explanation
Indices: 2303397--2303467 Score: 52
Period size: 9 Copynumber: 8.4 Consensus size: 8
2303387 ATTATTTAGC
*
2303397 AAAAGTAA
1 AAAAATAA
*
2303405 ATAAATAA
1 AAAAATAA
*
2303413 AAAAATGCA
1 AAAAAT-AA
*
2303422 TAAAATAA
1 AAAAATAA
2303430 AAAAATAAA
1 AAAAAT-AA
*
2303439 AAAAACTAG
1 AAAAA-TAA
*
2303448 AAACATAA
1 AAAAATAA
2303456 AATAAATAA
1 AA-AAATAA
2303465 AAA
1 AAA
2303468 TAAAAAAGAT
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
8 22 0.46
9 25 0.52
10 1 0.02
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (8 bp):
AAAAATAA
Found at i:2303443 original size:17 final size:17
Alignment explanation
Indices: 2303407--2303467 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
2303397 AAAAGTAAAT
** *
2303407 AAATAAAAAAATGCATA
1 AAATAAAAAAATAAAAA
2303424 AAATAAAAAAATAAAAA
1 AAATAAAAAAATAAAAA
* * *
2303441 AAACTAGAAACATAAAAT
1 AAA-TAAAAAAATAAAAA
2303459 AAATAAAAA
1 AAATAAAAA
2303468 TAAAAAAGAT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 22 0.61
18 14 0.39
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (17 bp):
AAATAAAAAAATAAAAA
Found at i:2304493 original size:46 final size:46
Alignment explanation
Indices: 2304440--2304577 Score: 170
Period size: 46 Copynumber: 3.0 Consensus size: 46
2304430 GCATGTGAAT
* * * * *
2304440 TAATTGCATAAATCAAACACTGAATTTTCCTACAAAATCTTCAATG
1 TAATTGCATGAATCAAGCACTAAAATTTACTACAAAATCTTCAATG
* * * *
2304486 TAATTGCATGAATCAAGCACTAAAAATTACTGCAAAATCTTTAACG
1 TAATTGCATGAATCAAGCACTAAAATTTACTACAAAATCTTCAATG
* *
2304532 TAATTGCATGAAT-AAGCACCAAAATTTACTTCAAAATCTTCAATG
1 TAATTGCATGAATCAAGCACTAAAATTTACTACAAAATCTTCAATG
2304577 T
1 T
2304578 TTTTTTCAAT
Statistics
Matches: 78, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
45 28 0.36
46 50 0.64
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (46 bp):
TAATTGCATGAATCAAGCACTAAAATTTACTACAAAATCTTCAATG
Found at i:2304567 original size:45 final size:46
Alignment explanation
Indices: 2304472--2304574 Score: 154
Period size: 45 Copynumber: 2.3 Consensus size: 46
2304462 AATTTTCCTA
* *
2304472 CAAAATCTTCAATGTAATTGCATGAATCAAGCACTAAAAATTACTG
1 CAAAATCTTCAACGTAATTGCATGAATCAAGCACCAAAAATTACTG
* * *
2304518 CAAAATCTTTAACGTAATTGCATGAAT-AAGCACCAAAATTTACTT
1 CAAAATCTTCAACGTAATTGCATGAATCAAGCACCAAAAATTACTG
2304563 CAAAATCTTCAA
1 CAAAATCTTCAA
2304575 TGTTTTTTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 26 0.51
46 25 0.49
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (46 bp):
CAAAATCTTCAACGTAATTGCATGAATCAAGCACCAAAAATTACTG
Found at i:2305388 original size:51 final size:51
Alignment explanation
Indices: 2305333--2305445 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 51
2305323 ACAAGAAAGA
**
2305333 AAGATTTGCAAAAATCCAAGTTTTGTAAAGGTTATAGATTCAAAAAGATGC
1 AAGATTTGCAAAAATCCAAGTTTCATAAAGGTTATAGATTCAAAAAGATGC
* * * * * * ** *
2305384 AAGATTCGTAAGACTCCAAGTTTCATAAATGTTCTAGATTCGTAAAGATGT
1 AAGATTTGCAAAAATCCAAGTTTCATAAAGGTTATAGATTCAAAAAGATGC
2305435 AAGATTTGCAA
1 AAGATTTGCAA
2305446 GGATTTTTAG
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.31
Consensus pattern (51 bp):
AAGATTTGCAAAAATCCAAGTTTCATAAAGGTTATAGATTCAAAAAGATGC
Found at i:2306135 original size:33 final size:32
Alignment explanation
Indices: 2306094--2306182 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 32
2306084 TCAAGATCGG
2306094 ATGACTAGGATGAAATCATGAGTCAAAAATAA
1 ATGACTAGGATGAAATCATGAGTCAAAAATAA
* *
2306126 AGTGACTAGGATCG-AGT--TGAGGTAAAAAATAA
1 A-TGACTAGGAT-GAAATCATGA-GTCAAAAATAA
* *
2306158 ATGATTAGGATGAAACCATGAGTCA
1 ATGACTAGGATGAAATCATGAGTCA
2306183 TAAGAAATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
30 1 0.02
31 13 0.29
32 15 0.33
33 15 0.33
34 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.24, T:0.22
Consensus pattern (32 bp):
ATGACTAGGATGAAATCATGAGTCAAAAATAA
Found at i:2306230 original size:120 final size:121
Alignment explanation
Indices: 2306064--2306330 Score: 335
Period size: 120 Copynumber: 2.2 Consensus size: 121
2306054 ACTATAGGTC
* ** *
2306064 AAAAAATGATCTA-ACTTGAGTCAAGATCGGATGACTAGGATGAAATCATGAGTCAAAAATAAAG
1 AAAAAATGATCTAGACTTGAGCCAAGATCGGATGACTAGGACAAAATCACGAGTCAAAAATAAAG
* * * * **
2306128 TGACTAGGATCGAGTTGAGG-TAAAAAATAAATGATTAGGATGAAACCATGAGTCAT
66 TGACCAAGATCGAGTTAAGGAT-AAAAATAAATGATCAGGACAAAACCATGAGTCAT
* * * *
2306184 AAGAAATGATCTAGA-TTGTGCCAAGATCGGGTGACTAGGACAAAATCGCGAGTCAAAAATAAAG
1 AAAAAATGATCTAGACTTGAGCCAAGATCGGATGACTAGGACAAAATCACGAGTCAAAAATAAAG
* * *
2306248 TGACCAAGATCGAGTTAAGGATGAAAATAAATGATCGGGACAAAACCTTGAGTCAT
66 TGACCAAGATCGAGTTAAGGATAAAAATAAATGATCAGGACAAAACCATGAGTCAT
*
2306304 AAAAAATGATCTAGAC-TAAGCCAAGAT
1 AAAAAATGATCTAGACTTGAGCCAAGAT
2306331 TGAGTGAGTG
Statistics
Matches: 124, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
120 122 0.98
121 2 0.02
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.21
Consensus pattern (121 bp):
AAAAAATGATCTAGACTTGAGCCAAGATCGGATGACTAGGACAAAATCACGAGTCAAAAATAAAG
TGACCAAGATCGAGTTAAGGATAAAAATAAATGATCAGGACAAAACCATGAGTCAT
Found at i:2311439 original size:44 final size:44
Alignment explanation
Indices: 2311364--2311449 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
2311354 ATTATTTAGC
* * *
2311364 AAAAGTAAATAAATAATAAAATACATGAAATATATAAATAAAAAT
1 AAAAGTAAATAAAAAATAAAATACATAAAATAAATAAA-AAAAAT
*
2311409 AAAA-TAAATAAAAAACTCAAA-ACATAAAATAAATAAAAAAA
1 AAAAGTAAATAAAAAA-TAAAATACATAAAATAAATAAAAAAA
2311450 GATACCTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 4 0.11
44 24 0.67
45 8 0.22
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (44 bp):
AAAAGTAAATAAAAAATAAAATACATAAAATAAATAAAAAAAAT
Found at i:2312507 original size:45 final size:46
Alignment explanation
Indices: 2312438--2312526 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 46
2312428 ATCTTTAACA
*
2312438 TAATTGCATGAATCAAGCACCAAAATTTATTGCAAATTCTTCAATG
1 TAATTGCATGAATCAAGCACCAAAATTTACTGCAAATTCTTCAATG
*
2312484 TAATTGCATGACT-AAGCACCAAAATTTACTGCAAATTCTTCAA
1 TAATTGCATGAATCAAGCACCAAAATTTACTGCAAATTCTTCAA
2312527 CATTTTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 29 0.71
46 12 0.29
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.31
Consensus pattern (46 bp):
TAATTGCATGAATCAAGCACCAAAATTTACTGCAAATTCTTCAATG
Found at i:2315211 original size:18 final size:17
Alignment explanation
Indices: 2315188--2315233 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2315178 TTGATAAAAA
*
2315188 TTTTATTTTTTTATTTAT
1 TTTTATTTTTATATTT-T
*
2315206 TTTTATTTTGATATTTT
1 TTTTATTTTTATATTTT
*
2315223 TATTATTTTTA
1 TTTTATTTTTA
2315234 AATATTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTATTTTTATATTTT
Found at i:2317230 original size:18 final size:17
Alignment explanation
Indices: 2317200--2317233 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2317190 TTAATTATGG
2317200 AAAATAAAAATAAAAAC
1 AAAATAAAAATAAAAAC
*
2317217 AAAATTAAAGATAAAAA
1 AAAA-TAAAAATAAAAA
2317234 TGAAATTGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAATAAAAATAAAAAC
Found at i:2323800 original size:63 final size:63
Alignment explanation
Indices: 2323710--2323876 Score: 171
Period size: 63 Copynumber: 2.6 Consensus size: 63
2323700 TTTTTTTAGA
* * *
2323710 GATTATTCTAGAT-TTTTTTGCCAAAAAAATGCCTTAAATAATCC-CCTA-ATAAAAATTGAA-G
1 GATTATTCAAGATGTTTTTAGCC--AAAAATGCCTTAAATAATCCTCCTACA-AAAAATTAAATG
2323771 G
63 G
* * **
2323772 GAATTATTCAAGATGTTTTTAGCCAAAAATGCATTGAATAATCCTTTTACAAAAAATTAAATGG
1 G-ATTATTCAAGATGTTTTTAGCCAAAAATGCCTTAAATAATCCTCCTACAAAAAATTAAATGG
* * *
2323836 GATTATTCAAGGTGTTTTTGGCTGAAAAATGCCTTAAATAA
1 GATTATTCAAGATGTTTTTAGC-CAAAAATGCCTTAAATAA
2323877 CATTTTTTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
62 19 0.22
63 41 0.47
64 27 0.31
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (63 bp):
GATTATTCAAGATGTTTTTAGCCAAAAATGCCTTAAATAATCCTCCTACAAAAAATTAAATGG
Found at i:2331305 original size:42 final size:42
Alignment explanation
Indices: 2331259--2331345 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
2331249 TTTGGAGAAG
* * * *
2331259 AAACATCTTAAATAATGATCATTTAATGCATTTCTTCAACCC
1 AAACACCTTAAACAATCATCATTTAAGGCATTTCTTCAACCC
*
2331301 AAACACCTTGAACAATCATCATTTAAGGCATTTCTTCAACCC
1 AAACACCTTAAACAATCATCATTTAAGGCATTTCTTCAACCC
2331343 AAA
1 AAA
2331346 ATTTATTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (42 bp):
AAACACCTTAAACAATCATCATTTAAGGCATTTCTTCAACCC
Found at i:2331403 original size:40 final size:39
Alignment explanation
Indices: 2331359--2331462 Score: 93
Period size: 40 Copynumber: 2.6 Consensus size: 39
2331349 TATTTGAATG
**
2331359 ATGATTTATTGAAGGCCTTTTTTGGAGAAAAACAACTTAA
1 ATGATTTATTGAAGGCCTTTTTTAAAG-AAAACAACTTAA
* * *
2331399 ATGATCATCATTGAAGG-CATTTTTAAAGAAAACACCTTAA
1 ATGAT--TTATTGAAGGCCTTTTTTAAAGAAAACAACTTAA
* *
2331439 ATGATTAATATTTAAGGCATTTTT
1 ATGATT--TATTGAAGGCCTTTTT
2331463 AAAAAGGAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
38 1 0.02
40 28 0.56
41 12 0.24
42 9 0.18
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (39 bp):
ATGATTTATTGAAGGCCTTTTTTAAAGAAAACAACTTAA
Found at i:2331463 original size:40 final size:40
Alignment explanation
Indices: 2331387--2331465 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
2331377 TTTTTGGAGA
*
2331387 AAAACAACTTAAATGATCATCATTGAAGGCATTTTTAAAG
1 AAAACAACTTAAATGATAATCATTGAAGGCATTTTTAAAG
* *
2331427 AAAACACCTTAAATGATTAAT-ATTTAAGGCATTTTTAAA
1 AAAACAACTTAAATGA-TAATCATTGAAGGCATTTTTAAA
2331466 AAGGAAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 32 0.91
41 3 0.09
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (40 bp):
AAAACAACTTAAATGATAATCATTGAAGGCATTTTTAAAG
Found at i:2331574 original size:212 final size:207
Alignment explanation
Indices: 2331055--2331746 Score: 819
Period size: 211 Copynumber: 3.4 Consensus size: 207
2331045 AGAATAGTTT
* *
2331055 TTAAATAATGATCATTTAAGGCGTTTCTTCAA-CTCAAACACCTTGAATGATCATCATTTAAGGT
1 TTAAATAATGATCATTTAAGGCATTTCTTCAACCT-AAACACCTTGAATGATCATCATTTAAGGC
* * * * *
2331119 GTTTTTTCAACCCAAATTTTATTTGAATGATGATTTATTGAAGACATTTTTTAGAGAAAAATGCC
65 ATTTCTTCAACCCAAAATTTATTTGAATGATGATTTATTGAAGGC-TTTTTT-GAGAAAAATACC
* * * *
2331184 TTAAATGATCATCATTAAAGACATTTATAAAGAAAATGCCTTAAATGATCAACATTTAAGGCATT
128 TTAAATGATCATCATTGAAGGCATTTTTAAAGAAAA-ACCTTAAATGAT-AACATTTAAGGCATT
2331249 TTTGGAGAAGAAACAT--C
191 TTT-GAGAAGAAA-ATGCC
* * **
2331266 TTAAATAATGATCATTTAATGCATTTCTTCAACCCAAACACCTTGAACAATCATCATTTAAGGCA
1 TTAAATAATGATCATTTAAGGCATTTCTTCAACCTAAACACCTTGAATGATCATCATTTAAGGCA
* *
2331331 TTTCTTCAACCCAAAATTTATTTGAATGATGATTTATTGAAGGCCTTTTTTGGAGAAAAACAACT
66 TTTCTTCAACCCAAAATTTATTTGAATGATGATTTATTGAAGG-CTTTTTT-GAGAAAAATACCT
*
2331396 TAAATGATCATCATTGAAGGCATTTTTAAAGAAAACACCTTAAATGATTAATATTTAAGGCATTT
129 TAAATGATCATCATTGAAGGCATTTTTAAAGAAAA-ACCTTAAATGA-TAACATTTAAGGCATTT
* *
2331461 TTAAAAAGGAAAATGCC
192 TTGAGAA-GAAAATGCC
* ** *
2331478 ATAAATAATGATCATTTAAGGCATTTCTTCAACCTAAATGCCTTGAATGATCATCATTTAAGGCG
1 TTAAATAATGATCATTTAAGGCATTTCTTCAACCTAAACACCTTGAATGATCATCATTTAAGGCA
*
2331543 TTTCTTCAACCCAAAATTTATTTGAATGATGA-TTATTGAAGG-TGTTTTTCAGAAAAATTACCT
66 TTTCTTCAACCCAAAATTTATTTGAATGATGATTTATTGAAGGCT-TTTTTGAGAAAAA-TACCT
**
2331606 TAAATGATCATCATTGAAGGTGTTTTTAAAG-AAAA-C------G----CATTTAAGGCATTTTT
129 TAAATGATCATCATTGAAGGCATTTTTAAAGAAAAACCTTAAATGATAACATTTAAGGCA--TTT
*
2331659 TTGAGAAG-AAACGCC
192 TTGAGAAGAAAATGCC
** **
2331674 TTAAATAATGATCATTTAAGGTGTTTCTTCAACCTAAATGCCTT-AATGATCATCATTTAAGGCA
1 TTAAATAATGATCATTTAAGGCATTTCTTCAACCTAAACACCTTGAATGATCATCATTTAAGGCA
2331738 TTTCTTCAA
66 TTTCTTCAA
2331747 TTTGAATGAT
Statistics
Matches: 428, Mismatches: 43, Indels: 36
0.84 0.08 0.07
Matches are distributed among these distances:
195 28 0.07
196 57 0.13
197 1 0.00
198 8 0.02
201 1 0.00
207 1 0.00
208 1 0.00
209 11 0.03
210 42 0.10
211 185 0.43
212 93 0.22
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (207 bp):
TTAAATAATGATCATTTAAGGCATTTCTTCAACCTAAACACCTTGAATGATCATCATTTAAGGCA
TTTCTTCAACCCAAAATTTATTTGAATGATGATTTATTGAAGGCTTTTTTGAGAAAAATACCTTA
AATGATCATCATTGAAGGCATTTTTAAAGAAAAACCTTAAATGATAACATTTAAGGCATTTTTGA
GAAGAAAATGCC
Found at i:2341498 original size:42 final size:42
Alignment explanation
Indices: 2341447--2341542 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
2341437 GCTAGCTTGC
* * *
2341447 AAAAGAGAAAAAAAAGAAAAAAAGTTGT-AAAAATGAAAATAA
1 AAAAAAGAAAAAAAAGAAAAAAAGTGGTGAAAAA-GAAAAGAA
* * *
2341489 AAAAAAGAAAAAAAAGCAATAAAGTGGTGAAAAAGCAAAGAA
1 AAAAAAGAAAAAAAAGAAAAAAAGTGGTGAAAAAGAAAAGAA
*
2341531 AAGAAAGAAAAA
1 AAAAAAGAAAAA
2341543 TTAGCAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
42 41 0.89
43 5 0.11
ACGTcount: A:0.73, C:0.02, G:0.17, T:0.08
Consensus pattern (42 bp):
AAAAAAGAAAAAAAAGAAAAAAAGTGGTGAAAAAGAAAAGAA
Found at i:2343014 original size:19 final size:20
Alignment explanation
Indices: 2342992--2343035 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2342982 CAAATATACT
2342992 AATTTCTTGTTG-ATATGCA
1 AATTTCTTGTTGAATATGCA
* * *
2343011 AATTTGTTTTTGAATATGCT
1 AATTTCTTGTTGAATATGCA
2343031 AATTT
1 AATTT
2343036 TGACCTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.52
Consensus pattern (20 bp):
AATTTCTTGTTGAATATGCA
Found at i:2346031 original size:23 final size:24
Alignment explanation
Indices: 2345983--2346031 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
2345973 ACTCTAAAGT
* **
2345983 AAGAATTAAAAGATTTTAAAGTAA
1 AAGAATTAAAAGATTGTAAACAAA
2346007 AAGAATT-AAAGATTGTAAACAAA
1 AAGAATTAAAAGATTGTAAACAAA
2346030 AA
1 AA
2346032 ATCCTTGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.61, C:0.02, G:0.12, T:0.24
Consensus pattern (24 bp):
AAGAATTAAAAGATTGTAAACAAA
Found at i:2346355 original size:18 final size:17
Alignment explanation
Indices: 2346315--2346366 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2346305 CCAATAACTT
2346315 AACTAAAAGAAATAAAG
1 AACTAAAAGAAATAAAG
*
2346332 AACTAAAAGAAACT-TAG
1 AACTAAAAGAAA-TAAAG
2346349 AAACTAAAAGAAA-AAAG
1 -AACTAAAAGAAATAAAG
2346366 A
1 A
2346367 GAAATGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 1 0.03
17 16 0.53
18 13 0.43
ACGTcount: A:0.69, C:0.08, G:0.12, T:0.12
Consensus pattern (17 bp):
AACTAAAAGAAATAAAG
Found at i:2351749 original size:39 final size:42
Alignment explanation
Indices: 2351702--2351780 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
2351692 TATTGTTTTT
*
2351702 TATATATAT-TTTCTTAT-TT-TTA-TCTTATGTATTATTAAA
1 TATATATATCTTTCTTATATTATTATTATTAT-TATTATTAAA
*
2351741 TATATATATCTTTTTTATATTATTATTATTATTATTATTA
1 TATATATATCTTTCTTATATTATTATTATTATTATTATTA
2351781 TTATTATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 9 0.26
40 7 0.21
41 2 0.06
42 11 0.32
43 5 0.15
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (42 bp):
TATATATATCTTTCTTATATTATTATTATTATTATTATTAAA
Found at i:2351766 original size:3 final size:3
Alignment explanation
Indices: 2351758--2351791 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2351748 ATCTTTTTTA
2351758 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2351792 CTTGTAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2352108 original size:17 final size:17
Alignment explanation
Indices: 2352086--2352120 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2352076 CAAAGGAAAC
2352086 ACACAGAAAAAAAATAG
1 ACACAGAAAAAAAATAG
* *
2352103 ACACAGAGAAGAAATAG
1 ACACAGAAAAAAAATAG
2352120 A
1 A
2352121 AGTTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.11, G:0.17, T:0.06
Consensus pattern (17 bp):
ACACAGAAAAAAAATAG
Found at i:2352232 original size:4 final size:4
Alignment explanation
Indices: 2352225--2352253 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2352215 TTTTTTTTTG
2352225 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
2352254 ATTATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:2352305 original size:6 final size:6
Alignment explanation
Indices: 2352294--2352382 Score: 82
Period size: 6 Copynumber: 15.5 Consensus size: 6
2352284 TTTAATATTC
* *
2352294 TTTTAT TTTTAT CTTTA- TTTTAT TTTTAT TTTTA- TTTTA- CTTT-T
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* *
2352338 TTTTAT TTTTAT TTTCAC TTTTA- TTTTAT GTTATTA- TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT -TT-TTAT TTTTAT TTT
2352383 CTTTAAATAA
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
5 23 0.33
6 41 0.59
7 2 0.03
8 3 0.04
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:2352314 original size:17 final size:16
Alignment explanation
Indices: 2352294--2352382 Score: 99
Period size: 17 Copynumber: 5.2 Consensus size: 16
2352284 TTTAATATTC
2352294 TTTTATTTTTATCTTTA
1 TTTTATTTTTAT-TTTA
2352311 TTTTATTTTTATTTTTA
1 TTTTATTTTTA-TTTTA
*
2352328 TTTTACTTTT-TTTTA
1 TTTTATTTTTATTTTA
*
2352343 TTTTTATTTTCACTTTTA
1 -TTTTATTTTTA-TTTTA
2352361 TTTTATGTTATTATTTTA
1 TTTTAT-TT-TTATTTTA
2352379 TTTT
1 TTTT
2352383 CTTTAAATAA
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
15 5 0.08
16 8 0.13
17 30 0.48
18 17 0.27
19 2 0.03
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.78
Consensus pattern (16 bp):
TTTTATTTTTATTTTA
Found at i:2352343 original size:27 final size:29
Alignment explanation
Indices: 2352294--2352382 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 29
2352284 TTTAATATTC
2352294 TTTTATTTTTATCTTTATTTTATTTTTAT
1 TTTTATTTTTATCTTTATTTTATTTTTAT
*
2352323 TTTTA-TTTTA-CTTTTTTTTATTTTTAT
1 TTTTATTTTTATCTTTATTTTATTTTTAT
* * *
2352350 TTTCACTTTTAT-TTTATGTTATTATTTTAT
1 TTTTATTTTTATCTTTATTTTA-T-TTTTAT
2352380 TTT
1 TTT
2352383 CTTTAAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
27 20 0.38
28 17 0.33
29 6 0.12
30 9 0.17
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.78
Consensus pattern (29 bp):
TTTTATTTTTATCTTTATTTTATTTTTAT
Found at i:2352464 original size:59 final size:57
Alignment explanation
Indices: 2352401--2352675 Score: 300
Period size: 61 Copynumber: 4.7 Consensus size: 57
2352391 AAAATCCAAA
* *
2352401 AAAAAATATTTTTGGGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAATTTTC
* * *
2352458 ATAAAAAGTTTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 A-AAAAA---TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAATTTTC
* ** * * *
2352519 AAAAAAGGTTTTTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTTC
1 AAAAAA---TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAA-TTTTC
* * * *
2352580 TAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTC
1 -AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAATTTTC
* * *
2352638 CAAAAATA-TTTTGGGAAAAAATTGAAAGTATCAATTTT
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
2352676 TCCTGCACAA
Statistics
Matches: 195, Mismatches: 17, Indels: 13
0.87 0.08 0.06
Matches are distributed among these distances:
56 27 0.14
57 8 0.04
58 9 0.05
59 43 0.22
60 48 0.25
61 54 0.28
62 6 0.03
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.38
Consensus pattern (57 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAATTTTC
Found at i:2352553 original size:60 final size:58
Alignment explanation
Indices: 2352417--2352675 Score: 290
Period size: 60 Copynumber: 4.4 Consensus size: 58
2352407 TATTTTTGGG
* * *
2352417 GAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATTTTCATAAAAAGTTTTTTTTTGAG
1 GAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAATTTTCA-AAAAA--TTTTTTTTGAA
*
2352478 GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGTTTTTTTTGAA
1 GAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAATTTTCAAAAAA--TTTTTTTTGAA
* * * * *
2352538 GAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTTCTAAAAAA-TATTTTTGGA
1 GAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAA-TTTTC-AAAAAATTTTTTTTGAA
* * * * * **
2352597 GAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTCCAAAAATATTTTGGGAA
1 GAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAATTTTCAAAAAATTTTTTTTGAA
2352655 -AAAA-TTGAAAGTATCAATTTT
1 GAAAAGTTGAAAGTATCAATTTT
2352676 TCCTGCACAA
Statistics
Matches: 178, Mismatches: 17, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
56 17 0.10
57 9 0.05
58 9 0.05
59 43 0.24
60 48 0.27
61 46 0.26
62 6 0.03
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.38
Consensus pattern (58 bp):
GAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAATTTTCAAAAAATTTTTTTTGAA
Found at i:2355698 original size:20 final size:19
Alignment explanation
Indices: 2355673--2355722 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
2355663 TGGTTGAAGG
* *
2355673 TTTTTTTTGTCATTTTAGGA
1 TTTTTTTTGTAATGTTA-GA
2355693 TTTTTTTTAGTAATGTTAGA
1 TTTTTTTT-GTAATGTTAGA
2355713 TTTCTTTTTG
1 TTT-TTTTTG
2355723 CAATATGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.16, C:0.04, G:0.14, T:0.66
Consensus pattern (19 bp):
TTTTTTTTGTAATGTTAGA
Found at i:2355699 original size:21 final size:20
Alignment explanation
Indices: 2355673--2355722 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
2355663 TGGTTGAAGG
* *
2355673 TTTTTTTTGTCATTTTAGGAT
1 TTTTTTTTGTAATGTTA-GAT
*
2355694 TTTTTTTAGTAATGTTAGAT
1 TTTTTTTTGTAATGTTAGAT
*
2355714 TTCTTTTTG
1 TTTTTTTTG
2355723 CAATATGACT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.16, C:0.04, G:0.14, T:0.66
Consensus pattern (20 bp):
TTTTTTTTGTAATGTTAGAT
Found at i:2356595 original size:23 final size:23
Alignment explanation
Indices: 2356581--2356654 Score: 78
Period size: 24 Copynumber: 3.2 Consensus size: 23
2356571 TGAAAAATGG
2356581 AAAAAAAAAAAGATGAAAAAAAA
1 AAAAAAAAAAAGATGAAAAAAAA
*
2356604 AAAAAAAAAAAGAAAGAAAAAAAA
1 AAAAAAAAAAAG-ATGAAAAAAAA
* * * **
2356628 GAAGAAAAAATGA-GAAAATGAA
1 AAAAAAAAAAAGATGAAAAAAAA
2356650 AAAAA
1 AAAAA
2356655 GATATTCAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 10 0.24
23 13 0.31
24 19 0.45
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (23 bp):
AAAAAAAAAAAGATGAAAAAAAA
Found at i:2356599 original size:12 final size:12
Alignment explanation
Indices: 2356584--2356637 Score: 74
Period size: 12 Copynumber: 4.5 Consensus size: 12
2356574 AAAATGGAAA
*
2356584 AAAAAAAAGATG
1 AAAAAAAAGAAG
*
2356596 AAAAAAAA-AAA
1 AAAAAAAAGAAG
2356607 AAAAAAAAGAAAG
1 AAAAAAAAG-AAG
2356620 AAAAAAAAGAAG
1 AAAAAAAAGAAG
2356632 AAAAAA
1 AAAAAA
2356638 TGAGAAAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
11 9 0.24
12 17 0.46
13 11 0.30
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (12 bp):
AAAAAAAAGAAG
Found at i:2356599 original size:13 final size:12
Alignment explanation
Indices: 2356583--2356645 Score: 62
Period size: 12 Copynumber: 5.3 Consensus size: 12
2356573 AAAAATGGAA
2356583 AAAAAAAAAGATG
1 AAAAAAAAAGA-G
2356596 AAAAAAAAA-A-
1 AAAAAAAAAGAG
2356606 AAAAAAAAAGA-
1 AAAAAAAAAGAG
2356617 AAGAAAAAAA-AG
1 AA-AAAAAAAGAG
*
2356629 AAGAAAAAATGAG
1 AA-AAAAAAAGAG
2356642 AAAA
1 AAAA
2356646 TGAAAAAAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
10 9 0.20
11 4 0.09
12 19 0.42
13 13 0.29
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (12 bp):
AAAAAAAAAGAG
Found at i:2356606 original size:20 final size:20
Alignment explanation
Indices: 2356581--2356637 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 20
2356571 TGAAAAATGG
* *
2356581 AAAAAAAAAAAGATGAAAAA
1 AAAAAAAAAAAAAAGAAAAA
2356601 AAAAAAAAAAAAAAGAAAGAA
1 AAAAAAAAAAAAAAGAAA-AA
2356622 AAAAAAGAAGAAAAAA
1 AAAAAA-AA-AAAAAA
2356638 TGAGAAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 16 0.50
21 8 0.25
22 2 0.06
23 6 0.19
ACGTcount: A:0.88, C:0.00, G:0.11, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAAAAAAGAAAAA
Found at i:2356654 original size:1 final size:1
Alignment explanation
Indices: 2356581--2356637 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
2356571 TGAAAAATGG
* ** * * * *
2356581 AAAAAAAAAAAGATGAAAAAAAAAAAAAAAAAAAGAAAGAAAAAAAAGAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2356638 TGAGAAAATG
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.88, C:0.00, G:0.11, T:0.02
Consensus pattern (1 bp):
A
Found at i:2364222 original size:23 final size:24
Alignment explanation
Indices: 2364174--2364222 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
2364164 ACTCTAAAGT
* **
2364174 AAGAATTAAAAGATTTTAAAGTAA
1 AAGAATTAAAAGATTGTAAACAAA
2364198 AAGAATT-AAAGATTGTAAACAAA
1 AAGAATTAAAAGATTGTAAACAAA
2364221 AA
1 AA
2364223 ATCCTTGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.61, C:0.02, G:0.12, T:0.24
Consensus pattern (24 bp):
AAGAATTAAAAGATTGTAAACAAA
Found at i:2364547 original size:18 final size:17
Alignment explanation
Indices: 2364505--2364556 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2364495 CCAATAACTT
2364505 AACTAAAAGAAATAAAG
1 AACTAAAAGAAATAAAG
*
2364522 AACTAAAAGAAACT-TAG
1 AACTAAAAGAAA-TAAAG
2364539 AAGCTAAAAGAAA-AAAG
1 AA-CTAAAAGAAATAAAG
2364556 A
1 A
2364557 GAAATGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 19 0.63
18 11 0.37
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.12
Consensus pattern (17 bp):
AACTAAAAGAAATAAAG
Found at i:2369881 original size:6 final size:6
Alignment explanation
Indices: 2369853--2370001 Score: 52
Period size: 6 Copynumber: 23.7 Consensus size: 6
2369843 GTAAGTCTAT
* * *
2369853 TTTTTT TTTTGTA TTTTACA TTTTTA -TTTAA TTTTTA TTTTTA TTTATTA
1 TTTTTA TTTT-TA TTTT-TA TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA
* * *
2369903 TTATTG TTTTTA TATATATT- TCTTTTA TTTTTA -TCTTA TGTATTTA
1 TTTTTA TTTTTA T-T-T-TTA T-TTTTA TTTTTA TTTTTA T-T-TTTA
** * * * * * * *
2369949 TTAATA TATATA TCTTTTA TTATTA TTATTA TTATTA TTATTA TTATTA
1 TTTTTA TTTTTA T-TTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
2369998 TTTT
1 TTTT
2370002 GTTAATATTT
Statistics
Matches: 111, Mismatches: 21, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
5 8 0.07
6 70 0.63
7 24 0.22
8 7 0.06
9 2 0.02
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (6 bp):
TTTTTA
Found at i:2369933 original size:21 final size:19
Alignment explanation
Indices: 2369872--2370001 Score: 78
Period size: 19 Copynumber: 6.9 Consensus size: 19
2369862 TGTATTTTAC
2369872 ATTTTTATTTA--ATTTTT
1 ATTTTTATTTATTATTTTT
*
2369889 ATTTTTATTTATTATTATT
1 ATTTTTATTTATTATTTTT
*
2369908 GTTTTTATATATATT-TCTTTT
1 ATTTTTAT-T-TATTAT-TTTT
2369929 ATTTTTATCTTATGTA--TTT
1 ATTTTTAT-TTAT-TATTTTT
** *
2369948 ATTAATATATA-TATCTTTT
1 ATTTTTATTTATTAT-TTTT
* *
2369967 ATTATTA-TTATTATTATT
1 ATTTTTATTTATTATTTTT
*
2369985 ATTATTA-TTATTATTTT
1 ATTTTTATTTATTATTTT
2370002 GTTAATATTT
Statistics
Matches: 90, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
16 2 0.02
17 11 0.12
18 23 0.26
19 33 0.37
20 5 0.06
21 16 0.18
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
ATTTTTATTTATTATTTTT
Found at i:2369973 original size:3 final size:3
Alignment explanation
Indices: 2369965--2369999 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2369955 TATATATCTT
2369965 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2370000 TTGTTAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2370078 original size:12 final size:12
Alignment explanation
Indices: 2370040--2370079 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
2370030 TTATACGTTA
2370040 TAATTTATCTGT
1 TAATTTATCTGT
2370052 T-ATTTAAT-T-T
1 TAATTT-ATCTGT
2370062 TAATTTATCTGT
1 TAATTTATCTGT
2370074 TAATTT
1 TAATTT
2370080 TTTATTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 4 0.17
11 10 0.42
12 10 0.42
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (12 bp):
TAATTTATCTGT
Found at i:2370078 original size:18 final size:19
Alignment explanation
Indices: 2370040--2370091 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2370030 TTATACGTTA
*
2370040 TAATTTATCTGTTATTTAATTT
1 TAATTTATCTGTTA---ATTTT
2370062 TAATTTATCTGTTAATTTT
1 TAATTTATCTGTTAATTTT
*
2370081 TTATTTATCTG
1 TAATTTATCTG
2370092 ATTTATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.50
22 14 0.50
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.63
Consensus pattern (19 bp):
TAATTTATCTGTTAATTTT
Found at i:2370086 original size:19 final size:21
Alignment explanation
Indices: 2370040--2370091 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
2370030 TTATACGTTA
*
2370040 TAATTTATCTGTTATTTAATTT
1 TAATTTATCTGTTAATT-ATTT
2370062 TAATTTATCTGTTAATT-TTT
1 TAATTTATCTGTTAATTATTT
2370082 T-ATTTATCTG
1 TAATTTATCTG
2370092 ATTTATTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 9 0.31
20 4 0.14
22 16 0.55
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.63
Consensus pattern (21 bp):
TAATTTATCTGTTAATTATTT
Found at i:2370100 original size:19 final size:19
Alignment explanation
Indices: 2370008--2370100 Score: 62
Period size: 22 Copynumber: 4.5 Consensus size: 19
2369998 TTTTGTTAAT
*
2370008 ATTTATATTTATATTTATCAG
1 ATTTAT-TTTA-ATTTATCTG
*
2370029 ATTATACGTTATAATTTATCTG
1 ATT-TA--TTTTAATTTATCTG
2370051 TTATTTAATTTTAATTTATCTG
1 --ATTT-ATTTTAATTTATCTG
* *
2370073 -TTAATTTTTTATTTATCTG
1 ATTTA-TTTTAATTTATCTG
2370092 ATTTATTTT
1 ATTTATTTT
2370101 CATTAATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
18 1 0.02
19 19 0.33
20 3 0.05
21 3 0.05
22 23 0.40
23 4 0.07
24 5 0.09
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.61
Consensus pattern (19 bp):
ATTTATTTTAATTTATCTG
Found at i:2370433 original size:3 final size:3
Alignment explanation
Indices: 2370427--2370468 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2370417 TTTTTGTTAT
2370427 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2370469 GTAGTAGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2370505 original size:6 final size:6
Alignment explanation
Indices: 2370494--2370560 Score: 54
Period size: 6 Copynumber: 11.7 Consensus size: 6
2370484 TGTTTAATAT
* * *
2370494 TTTTTA TTTTTA TTTTTA -TTTTA CTTTT- TTTTT- TTTTCA CTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
2370539 -TTTTA TGTTATTA -TTTTA TTTT
1 TTTTTA T-TT-TTA TTTTTA TTTT
2370561 CTTTAAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
5 21 0.41
6 25 0.49
7 2 0.04
8 3 0.06
ACGTcount: A:0.15, C:0.04, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:2370516 original size:27 final size:27
Alignment explanation
Indices: 2370493--2370543 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
2370483 TTGTTTAATA
* *
2370493 TTTTTTATTTTT-ATTTTTATTTTACT
1 TTTTTTATTTTTCACTTTTATTTTAAT
*
2370519 TTTTTTTTTTTTCACTTTTATTTTA
1 TTTTTTATTTTTCACTTTTATTTTA
2370544 TGTTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTTTTATTTTTCACTTTTATTTTAAT
Found at i:2370735 original size:57 final size:57
Alignment explanation
Indices: 2370588--2370790 Score: 243
Period size: 60 Copynumber: 3.5 Consensus size: 57
2370578 AAAAAAAATA
*
2370588 TTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGTTTT
1 TTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC-AAAAAAG-TGT
2370648 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAG-GT
1 TTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGTGT
** * * *
2370705 TTTTGTGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTTC--AAAACT-A
1 TTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTTCAAAAAAGTGT
* *
2370761 TTTTGGGAAAAAATTGAAAATATCAATTTT
1 TTTTGGG-AAAAGTTGAAAGTATCAATTTT
2370791 TCCTGCACAA
Statistics
Matches: 130, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
55 2 0.02
56 29 0.22
57 40 0.31
58 5 0.04
59 7 0.05
60 45 0.35
61 2 0.02
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.37
Consensus pattern (57 bp):
TTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGTGT
Found at i:2373844 original size:22 final size:22
Alignment explanation
Indices: 2373801--2373851 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2373791 TGGTTGAAGG
* *
2373801 TTTTTTTTGTCATTTTAGGATT
1 TTTTTTTTGTAATGTTAGGATT
2373823 TTTTTTTTAGTAATGTTA-GATT
1 TTTTTTTT-GTAATGTTAGGATT
*
2373845 TCTTTTT
1 TTTTTTT
2373852 GCAATATGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.16, C:0.04, G:0.12, T:0.69
Consensus pattern (22 bp):
TTTTTTTTGTAATGTTAGGATT
Found at i:2374755 original size:24 final size:21
Alignment explanation
Indices: 2374723--2374766 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2374713 AAAATGGAAA
2374723 AAAAAAAGATGAAGGAAAAAAAAT
1 AAAAAAAGA--AA-GAAAAAAAAT
2374747 AAAAAAAGAAAGAAAAAAAA
1 AAAAAAAGAAAGAAAAAAAA
2374767 GAAGAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
24 9 0.45
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (21 bp):
AAAAAAAGAAAGAAAAAAAAT
Found at i:2374771 original size:12 final size:13
Alignment explanation
Indices: 2374747--2374779 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2374737 GAAAAAAAAT
2374747 AAAAAAAGAAAGA
1 AAAAAAAGAAAGA
2374760 AAAAAAAG-AAGA
1 AAAAAAAGAAAGA
2374772 AGAAAAAA
1 A-AAAAAA
2374780 TGAGAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAGA
Found at i:2374785 original size:16 final size:14
Alignment explanation
Indices: 2374747--2374796 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
2374737 GAAAAAAAAT
2374747 AAAAAAAG-AAAGA
1 AAAAAAAGAAAAGA
2374760 AAAAAAAGAAGAAGA
1 AAAAAAAGAA-AAGA
*
2374775 AAAAATGAGAAAATGA
1 AAAAA-AAGAAAA-GA
2374791 AAAAAA
1 AAAAAA
2374797 GATATTCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 8 0.26
14 1 0.03
15 11 0.35
16 11 0.35
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (14 bp):
AAAAAAAGAAAAGA
Found at i:2376027 original size:22 final size:22
Alignment explanation
Indices: 2376002--2376060 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
2375992 GAATATTTTG
*
2376002 ATGAGAATTTTTGAGAACTC-AA
1 ATGAGAATCTTTGAG-ACTCAAA
**
2376024 ATGAGAATCTTTGAGTTTCAAA
1 ATGAGAATCTTTGAGACTCAAA
2376046 ATGAGAATCTTTGAG
1 ATGAGAATCTTTGAG
2376061 GAGTGAAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 2 0.06
22 31 0.94
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.34
Consensus pattern (22 bp):
ATGAGAATCTTTGAGACTCAAA
Found at i:2376291 original size:43 final size:42
Alignment explanation
Indices: 2376243--2376324 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 42
2376233 GCCTTTGAAC
*
2376243 TCAAATGAAAAGCTTTAAATTTTTGGATGTGAATTTCCAAAAT
1 TCAAATGAAAAGCTTTAAATTTTTGGATATGAA-TTCCAAAAT
* *
2376286 TCAAATGAAAAGCTTTAGATTTTTGGCTATGAATTCCAA
1 TCAAATGAAAAGCTTTAAATTTTTGGATATGAATTCCAA
2376325 GTTTGCCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 6 0.17
43 30 0.83
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (42 bp):
TCAAATGAAAAGCTTTAAATTTTTGGATATGAATTCCAAAAT
Found at i:2376740 original size:42 final size:41
Alignment explanation
Indices: 2376599--2376975 Score: 407
Period size: 42 Copynumber: 9.0 Consensus size: 41
2376589 ATGATTGTCA
* ** * *
2376599 AGGAGTAATTTACATTTCAAAGTCGTGTTGCCTCTATTTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
2376640 AGGAGCAATTTATTTTCCAAAGTTTCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAG--TCGTGGTGCCTCTGTTTAG
*
2376681 AGGAGCAATTTATTTTTTCAAAGTCGTGGTTGCCTCTCTTTAG
1 AGGAGCAATTTA-TTTTTCAAAGTCGTGG-TGCCTCTGTTTAG
2376724 AGGAGCAATTTATTTTTCAAAGTCGTGGTTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGG-TGCCTCTGTTTAG
* * *
2376766 AGGAACAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
*
2376808 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * * * **
2376849 AGGAGCAATGTACTTTTCAAAAGTTGAGGTGCCTCTAATTAG
1 AGGAGCAATTTATTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
* * * * **
2376891 AGGAGCCATTTATTTTTCCAAAGTCATTGAGCCTCTAATTAG
1 AGGAGCAATTTATTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
* * * * *
2376933 AGGAGCCATTTATTTTTTCAAAGTTGTTGAGCCTCTGCTTAG
1 AGGAGCAATTTA-TTTTTCAAAGTCGTGGTGCCTCTGTTTAG
2376975 A
1 A
2376976 AGAGTTTTGA
Statistics
Matches: 296, Mismatches: 30, Indels: 19
0.86 0.09 0.06
Matches are distributed among these distances:
40 4 0.01
41 82 0.28
42 166 0.56
43 44 0.15
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (41 bp):
AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:2377242 original size:25 final size:24
Alignment explanation
Indices: 2377214--2377280 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
2377204 TTATTTCTTT
*
2377214 TATTTTATATCTTATGTATTATTAA
1 TATTTTATATCTTAT-TACTATTAA
* *
2377239 TATTCTATATCCTTATTACTATTAT
1 TATTTTATAT-CTTATTACTATTAA
* *
2377264 TATTTTCTGTCTTATTA
1 TATTTTATATCTTATTA
2377281 TATGTATATT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
24 7 0.20
25 23 0.66
26 5 0.14
ACGTcount: A:0.27, C:0.10, G:0.03, T:0.60
Consensus pattern (24 bp):
TATTTTATATCTTATTACTATTAA
Found at i:2377348 original size:19 final size:20
Alignment explanation
Indices: 2377324--2377370 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
2377314 TATTTGTTAT
2377324 TTAATTTTTAAATTATCT-A
1 TTAATTTTTAAATTATCTGA
* *
2377343 TTAATTTTTGATTTATCTGA
1 TTAATTTTTAAATTATCTGA
*
2377363 TTTATTTT
1 TTAATTTT
2377371 CATTAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (20 bp):
TTAATTTTTAAATTATCTGA
Found at i:2377756 original size:6 final size:6
Alignment explanation
Indices: 2377745--2377832 Score: 67
Period size: 6 Copynumber: 14.5 Consensus size: 6
2377735 TTTAATATTC
* *
2377745 TTTTAT TTTTA- TCTTA- TTTTAT TTTTAT TTTTAT TTTACTTT TCTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT--TAT T-TTTAT
* *
2377794 TTTTAT TTTCAC TTTTA- TTTTA- TTTTATT ATTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T -TTTTAT TTT
2377833 CTTTAAATAA
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
5 18 0.26
6 36 0.53
7 4 0.06
8 8 0.12
9 2 0.03
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:2377767 original size:5 final size:5
Alignment explanation
Indices: 2377745--2377832 Score: 74
Period size: 5 Copynumber: 16.8 Consensus size: 5
2377735 TTTAATATTC
* *
2377745 TTTTA TTTTTA TCTTA TTTTA TTTTTA TTTTTA TTTTA CTTTT- CTTTA
1 TTTTA -TTTTA TTTTA TTTTA -TTTTA -TTTTA TTTTA -TTTTA TTTTA
2377793 TTTTTA TTTTCA CTTTTA TTTTA TTTTA --TTA TTTTA TTTT
1 -TTTTA TTTT-A -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
2377833 CTTTAAATAA
Statistics
Matches: 70, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
3 3 0.04
4 3 0.04
5 34 0.49
6 26 0.37
7 4 0.06
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:2377772 original size:22 final size:22
Alignment explanation
Indices: 2377745--2377832 Score: 99
Period size: 22 Copynumber: 3.9 Consensus size: 22
2377735 TTTAATATTC
*
2377745 TTTTATTTTTATCTTATTTTAT
1 TTTTATTTTTATTTTATTTTAT
*
2377767 TTTTATTTTTATTTTACTTT-T
1 TTTTATTTTTATTTTATTTTAT
*
2377788 CTTTATTTTTATTTTCACTTTTA-
1 TTTTATTTTTATTTT-A-TTTTAT
2377811 TTTTATTTTATTATTTTATTTT
1 TTTTA-TTT-TTATTTTATTTT
2377833 CTTTAAATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
21 15 0.27
22 19 0.34
23 11 0.20
24 4 0.07
25 7 0.12
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTATTTTTATTTTATTTTAT
Found at i:2377837 original size:17 final size:16
Alignment explanation
Indices: 2377740--2377837 Score: 55
Period size: 16 Copynumber: 6.1 Consensus size: 16
2377730 ATTTGTTTAA
* *
2377740 TATTCTTTTATTTTTA
1 TATTATTTTATTTTTT
*
2377756 TCTTATTTTATTTTTAT
1 TATTATTTTATTTTT-T
*
2377773 TTTTATTTTACTTTTCTT
1 TATTATTTTA-TTTT-TT
*
2377791 TA-T-TTTTATTTTCACT
1 TATTATTTTATTTT--TT
2377807 T-TTATTTTA---TTT
1 TATTATTTTATTTTTT
2377819 TATTATTTTATTTTCTT
1 TATTATTTTATTTT-TT
2377836 TA
1 TA
2377838 AATAAAATCC
Statistics
Matches: 63, Mismatches: 8, Indels: 21
0.68 0.09 0.23
Matches are distributed among these distances:
12 2 0.03
13 8 0.13
14 1 0.02
15 4 0.06
16 22 0.35
17 19 0.30
18 6 0.10
19 1 0.02
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTATTTTATTTTTT
Found at i:2377933 original size:61 final size:59
Alignment explanation
Indices: 2377859--2378126 Score: 368
Period size: 61 Copynumber: 4.5 Consensus size: 59
2377849 AAAAAATATA
* *
2377859 TTTTTGGA-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAACTTTTCAAAAAAGGTTT
1 TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGG--T
2377919 TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGTT
1 TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGG-T
** *
2377979 TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTTCTAAAAAA--T
1 TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTTC-AAAAAAGGT
* *
2378038 ATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCGTTAAAAATAAATTTTCAAAAAAGG-
1 TTTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGT
*
2378096 -TTTTTGAAGAAAAGTTGAAAGTATCAATTTT
1 TTTTTTGAGGAAAAGTTGAAAGTATCAATTTT
2378127 TCCTGCACAA
Statistics
Matches: 190, Mismatches: 11, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
57 34 0.18
58 8 0.04
59 38 0.20
60 51 0.27
61 53 0.28
62 6 0.03
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (59 bp):
TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGT
Found at i:2382276 original size:18 final size:18
Alignment explanation
Indices: 2382253--2382291 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2382243 ATGCCAAAAT
2382253 GAAGCCATTTATTTATAG
1 GAAGCCATTTATTTATAG
2382271 GAAGCCATTTATTTATAG
1 GAAGCCATTTATTTATAG
2382289 GAA
1 GAA
2382292 TCCTTCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (18 bp):
GAAGCCATTTATTTATAG
Found at i:2386109 original size:146 final size:139
Alignment explanation
Indices: 2385940--2386283 Score: 354
Period size: 146 Copynumber: 2.4 Consensus size: 139
2385930 AAAAAAAAAC
* *
2385940 AAAAAAAAAGC-AAGAAAGAAAGACATGCACCTTAGAGATGAGAATCTGGGCAAAAAGTGAATAA
1 AAAAAAAGAGCAAAGAAAGAAAGACATGTACCTTAGAGATGAGAATCTGGGCAAAAAGTGAATAA
* * ** * *
2386004 AGTTTCAATTATAATTAAAAAAAAAAAGAAAATAGAATTTAGCAAAGTAGAATGCTCCAGTTGAA
66 AGTTTCAATTAGAATT-AAAAAAAAAA-AAAAT----TTAAG-AAAGTAGAATGCTAAAATGGAA
2386069 GTT-AAATGTTTCCAAT
124 -TTCAAATGTTTCCAAT
* * * * *
2386085 AAAAAAAGAGCAAAGAAAGAAAGACATGTACCTTGGAGATGAGAGTTTAAGACAAAAAGTGAATA
1 AAAAAAAGAGCAAAGAAAGAAAGACATGTACCTTAGAGATGAGAATCT-GGGCAAAAAGTGAATA
* * * ** * *
2386150 ATGTTTTAGTTAGAATTCCAAAAAAAAAAAATTTAAGAAAGTGGAATGCTAAAATGGAATTCAGA
65 AAGTTTCAATTAGAATTAAAAAAAAAAAAAATTTAAGAAAGTAGAATGCTAAAATGGAATTCAAA
2386215 TGTTTCCAAT
130 TGTTTCCAAT
* * *
2386225 AAAAGAAAGAGCAAAGAAAGAAAGACATGTACC-TCGAAGATGAG-CTCAGGGCAAAAAGT
1 AAAA-AAAGAGCAAAGAAAGAAAGACATGTACCTTAG-AGATGAGAATCTGGGCAAAAAGT
2386284 AAATGAAGCA
Statistics
Matches: 168, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
139 11 0.07
140 36 0.21
141 39 0.23
145 15 0.09
146 40 0.24
147 27 0.16
ACGTcount: A:0.50, C:0.10, G:0.19, T:0.21
Consensus pattern (139 bp):
AAAAAAAGAGCAAAGAAAGAAAGACATGTACCTTAGAGATGAGAATCTGGGCAAAAAGTGAATAA
AGTTTCAATTAGAATTAAAAAAAAAAAAAATTTAAGAAAGTAGAATGCTAAAATGGAATTCAAAT
GTTTCCAAT
Found at i:2387385 original size:60 final size:60
Alignment explanation
Indices: 2387242--2387394 Score: 173
Period size: 59 Copynumber: 2.5 Consensus size: 60
2387232 TCTTTTAAGA
* **
2387242 AAAAAAAATAAAAGACATTCGCATTTGCATCATTTGCAAAAGACATTTGACCTGCATGCTGC
1 AAAAAAAA-AAAAGACATTCACATTTGCATCATAAG-AAAAGACATTTGACCTGCATGCTGC
* * * * * * * *
2387304 AAAAAAACAAAAGAAAATCACATTTGCATTATAAG-AAAGTCATTTGATCTGTATGTTGC
1 AAAAAAAAAAAAGACATTCACATTTGCATCATAAGAAAAGACATTTGACCTGCATGCTGC
2387363 AAAAAAGAAAAAAGACATTCACATTTGCATCA
1 AAAAAA-AAAAAAGACATTCACATTTGCATCA
2387395 CATGCGTTTA
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
59 26 0.35
60 21 0.28
61 21 0.28
62 7 0.09
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (60 bp):
AAAAAAAAAAAAGACATTCACATTTGCATCATAAGAAAAGACATTTGACCTGCATGCTGC
Found at i:2387550 original size:26 final size:26
Alignment explanation
Indices: 2387513--2387584 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
2387503 TCCTGAGAAT
*
2387513 GACATTTGCATTTGCATCATAACCAA
1 GACATTTGCATTTGCATCATAACAAA
* * *
2387539 GACATTTACATTTGTATCATAAGAAA
1 GACATTTGCATTTGCATCATAACAAA
* *
2387565 GGCATTTGCATTTTCATCAT
1 GACATTTGCATTTGCATCAT
2387585 TGCATCTGTA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (26 bp):
GACATTTGCATTTGCATCATAACAAA
Found at i:2387911 original size:23 final size:23
Alignment explanation
Indices: 2387875--2387918 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2387865 ACCTCAATCA
2387875 AGATTAGCTAGCATTGTAAGCTC
1 AGATTAGCTAGCATTGTAAGCTC
* * *
2387898 AGATTAGTTGGCATTTTAAGC
1 AGATTAGCTAGCATTGTAAGC
2387919 CCAACCTAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (23 bp):
AGATTAGCTAGCATTGTAAGCTC
Found at i:2388249 original size:23 final size:22
Alignment explanation
Indices: 2388186--2388258 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
2388176 TTGAGATTTG
2388186 TAAGACCTCCAGGCATAATCTC
1 TAAGACCTCCAGGCATAATCTC
*
2388208 TAAAACCTCCAGGCATAATCTC
1 TAAGACCTCCAGGCATAATCTC
***
2388230 TAAGACCTTTTGGGCATAATCTC
1 TAAGACC-TCCAGGCATAATCTC
2388253 TAAGAC
1 TAAGAC
2388259 ATTTAGACAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 27 0.60
23 18 0.40
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (22 bp):
TAAGACCTCCAGGCATAATCTC
Found at i:2388386 original size:22 final size:22
Alignment explanation
Indices: 2388335--2388386 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
2388325 TTAAGATTTG
* * *
2388335 TAAAATCTCTAAGCATAATCTC
1 TAAAACCTCTAAGCATAATATA
* *
2388357 TAAGACCTCTAGGCATAATATA
1 TAAAACCTCTAAGCATAATATA
2388379 TAAAACCT
1 TAAAACCT
2388387 TTGAGCAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (22 bp):
TAAAACCTCTAAGCATAATATA
Found at i:2388387 original size:149 final size:149
Alignment explanation
Indices: 2388118--2388388 Score: 380
Period size: 149 Copynumber: 1.8 Consensus size: 149
2388108 ACTTTCGGGT
* * * * *
2388118 AAAACATTTTAAATTTTCAAAGTTTCAATGCCTCCACTACGAGGAGCATTCAAAGATTTTGAGAT
1 AAAACATTTTAAAATTTCAAAGTTTCAATGCCTCCACTACAAGGAGCAATAAAAGATTTTAAGAT
* * * * *
2388183 TTGTAAGACCTCCAGGCATAATCTCTAAAACCTCCAGGCATAATCTCTAAGACCTTTTGGGCATA
66 TTGTAAAACCTCCAAGCATAATCTCTAAAACCTCCAGGCATAATATATAAAACCTTTTGGGCATA
2388248 ATCTCTAAGACATTTAGAC
131 ATCTCTAAGACATTTAGAC
** * *
2388267 AAAACATTTTAAAATTTCAAAGTTTCAATGCCTCTGCTATAAGGAGTAATAAAAGATTTTAAGAT
1 AAAACATTTTAAAATTTCAAAGTTTCAATGCCTCCACTACAAGGAGCAATAAAAGATTTTAAGAT
* * * *
2388332 TTGTAAAATCTCTAAGCATAATCTCTAAGACCTCTAGGCATAATATATAAAACCTTT
66 TTGTAAAACCTCCAAGCATAATCTCTAAAACCTCCAGGCATAATATATAAAACCTTT
2388389 GAGCAAAACA
Statistics
Matches: 104, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
149 104 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (149 bp):
AAAACATTTTAAAATTTCAAAGTTTCAATGCCTCCACTACAAGGAGCAATAAAAGATTTTAAGAT
TTGTAAAACCTCCAAGCATAATCTCTAAAACCTCCAGGCATAATATATAAAACCTTTTGGGCATA
ATCTCTAAGACATTTAGAC
Found at i:2388568 original size:124 final size:126
Alignment explanation
Indices: 2388220--2388590 Score: 391
Period size: 126 Copynumber: 2.9 Consensus size: 126
2388210 AAACCTCCAG
* *
2388220 GCATAATCTCTAAGACCTTTTGGGCATAATCTCTAAGACATTTAGA-CAAAACATTTTAAAATTT
1 GCATAATCTCTAAGACC-TTT-GGCATAATCTATAAGAC--TTAGAGCAAAACATTTTAAATTTT
* * * * * *
2388284 CAAAGTTTCAATGCCTCTGCTATAAGGAGTAATAAAAGATTTTAAGATTTGTAA-A-ATCTCTAA
62 CAAAGTTTCAATGCCTTTGATATAAGGAGTATTCAAAGATTTTGAGATTTGTAAGACATCTCGAA
* * * * *
2388347 GCATAATCTCTAAGACCTCTAGGCATAATATATAAAACCTTTGAGCAAAACATTTAAAATTTTTC
1 GCATAATCTCTAAGACCT-TTGGCATAATCTATAAGA-CTTAGAGCAAAACATTTTAAA-TTTTC
*
2388412 -AAGTTTCAACT-CCTTT-ACTATGAGGAGTATTCAAAGATTTTGAGATTTGTAAGACATCT-GA
63 AAAGTTTCAA-TGCCTTTGA-TATAAGGAGTATTCAAAGATTTTGAGATTTGTAAGACATCTCGA
2388473 A
126 A
* * * *
2388474 -CATAATCTCTAAGA-CTTTGGCATAACCTGTAAGACTTCCGAGCAAAATATTTTAAATTTTCAA
1 GCATAATCTCTAAGACCTTTGGCATAATCTATAAGACTT-AGAGCAAAACATTTTAAATTTTCAA
* * * *
2388537 AGTTTCAATGCCTTTGATACAAGAAGCATTCAATGATTTTGAGATTTGTAAGAC
65 AGTTTCAATGCCTTTGATATAAGGAGTATTCAAAGATTTTGAGATTTGTAAGAC
2388591 TTCCAGGTGT
Statistics
Matches: 205, Mismatches: 27, Indels: 27
0.79 0.10 0.10
Matches are distributed among these distances:
123 9 0.04
124 74 0.36
125 7 0.03
126 84 0.41
127 27 0.13
128 4 0.02
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (126 bp):
GCATAATCTCTAAGACCTTTGGCATAATCTATAAGACTTAGAGCAAAACATTTTAAATTTTCAAA
GTTTCAATGCCTTTGATATAAGGAGTATTCAAAGATTTTGAGATTTGTAAGACATCTCGAA
Found at i:2398000 original size:149 final size:140
Alignment explanation
Indices: 2397713--2398010 Score: 355
Period size: 149 Copynumber: 2.1 Consensus size: 140
2397703 AAGCAAAAAA
* *
2397713 AAAAAAAAGCAAAGATAGAAAGACATGCACCTCGAATATGAGAATCTAGGCAAAAAGTGAATAAA
1 AAAAAAAAGCAAAGATAGAAAGACATGCACCTCGAATATGAGAATCGAGACAAAAAGTGAATAAA
* *** *
2397778 GCTTTAGTTATAATTCCAAAAAAAAAAAGAATTTGGGAAAGTAGAATGCTAAAGTTGAAGTTAAA
66 GCTTTAGTTAGAATTCCAAAAAAAAAAAGAATTCAAGAAAGTAGAATGCTAAAGTGGAAGTTAAA
2397843 TGTTTCCAAT
131 TGTTTCCAAT
* * * * *
2397853 AAAAAAATGTAAAGATAGAAAGACATGTACTTC-AGATATGAGAGTCCGAGACAAAAAGTGAATA
1 AAAAAAAAGCAAAGATAGAAAGACATGCACCTCGA-ATATGAGAAT-CGAGACAAAAAGTGAATA
* *
2397917 ATGCTTTAGTTAGAATTCCAAAAAAAAAAAAGAAGAAAGAATTCAAGAAAGTGGAATGCTAAAGT
64 AAGCTTTAGTTAGAATTCC------AAAAAA-AA-AAAGAATTCAAGAAAGTAGAATGCTAAAGT
*
2397982 GGAAGTTAGATGTTTCCAAT
121 GGAAGTTAAATGTTTCCAAT
*
2398002 AAAAGAAAG
1 AAAAAAAAG
2398011 AACAAAAAAA
Statistics
Matches: 131, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
139 1 0.01
140 38 0.29
141 33 0.25
147 6 0.05
148 2 0.02
149 51 0.39
ACGTcount: A:0.50, C:0.09, G:0.19, T:0.22
Consensus pattern (140 bp):
AAAAAAAAGCAAAGATAGAAAGACATGCACCTCGAATATGAGAATCGAGACAAAAAGTGAATAAA
GCTTTAGTTAGAATTCCAAAAAAAAAAAGAATTCAAGAAAGTAGAATGCTAAAGTGGAAGTTAAA
TGTTTCCAAT
Found at i:2398092 original size:149 final size:149
Alignment explanation
Indices: 2397814--2398092 Score: 350
Period size: 149 Copynumber: 1.9 Consensus size: 149
2397804 AAGAATTTGG
* * * *
2397814 GAAAGTAGAATGCTAAAGTTGAAGTTAAATGTTTCCAATAAAAAAATGTAAAGATAGAAAGACAT
1 GAAAGTAGAATGCTAAAGTGGAAGTTAAATGTTTCCAATAAAAAAATGCAAAAAAAGAAAGACAT
* * * * * * *
2397879 GTACTTCAGATATGAGAGTCCGAGACAAAAAGTGAATAATGCTTTAGTTAGAATTCCAAAAAAAA
66 GTACTTCAGAGATGAGACTCCGAGACAAAAAGTAAATAAAGCATAAGTTAGAATCCCAAAAAAAA
2397944 AAAAGAAGAAAGAATTCAA
131 AAAAGAAGAAAGAATTCAA
* * *
2397963 GAAAGTGGAATGCTAAAGTGGAAGTTAGATGTTTCCAATAAAAGAAA-GAACAAAAAAAGGAAGA
1 GAAAGTAGAATGCTAAAGTGGAAGTTAAATGTTTCCAATAAAA-AAATG--CAAAAAAAGAAAGA
** *
2398027 CATGTAC-TCAGAGATGAG-CT-CGAGGTAAAAAGTAAATAAAGCATAAGTTAGAATCCCAAATA
63 CATGTACTTCAGAGATGAGACTCCGAGACAAAAAGTAAATAAAGCATAAGTTAGAATCCCAAAAA
2398089 AAAA
128 AAAA
2398093 GGAAGATAAA
Statistics
Matches: 110, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
148 38 0.35
149 42 0.38
150 13 0.12
151 17 0.15
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.21
Consensus pattern (149 bp):
GAAAGTAGAATGCTAAAGTGGAAGTTAAATGTTTCCAATAAAAAAATGCAAAAAAAGAAAGACAT
GTACTTCAGAGATGAGACTCCGAGACAAAAAGTAAATAAAGCATAAGTTAGAATCCCAAAAAAAA
AAAAGAAGAAAGAATTCAA
Found at i:2399657 original size:23 final size:23
Alignment explanation
Indices: 2399624--2399690 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
2399614 AGATAAGACC
*
2399624 TAAGCCAAGATTAGCTAGCACTG
1 TAAGCCTAGATTAGCTAGCACTG
* * *
2399647 TAAG-CTCAGATTAACTAGCATTT
1 TAAGCCT-AGATTAGCTAGCACTG
*
2399670 TAAGCCTAGATTAGCTGGCAC
1 TAAGCCTAGATTAGCTAGCAC
2399691 CCAAATCAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
22 1 0.03
23 32 0.91
24 2 0.06
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (23 bp):
TAAGCCTAGATTAGCTAGCACTG
Found at i:2399944 original size:22 final size:22
Alignment explanation
Indices: 2399918--2399981 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
2399908 TAATACCTTC
*
2399918 AAGCATAATCTCTAAAACCTC-
1 AAGCATAATCTCTAAGACCTCT
2399939 ATAGCATAATCTCTAAGACCTCT
1 A-AGCATAATCTCTAAGACCTCT
*
2399962 AAGCATAATCTGTAAGACCT
1 AAGCATAATCTCTAAGACCT
2399982 TTAGGACAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
21 1 0.03
22 37 0.95
23 1 0.03
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (22 bp):
AAGCATAATCTCTAAGACCTCT
Found at i:2400095 original size:149 final size:147
Alignment explanation
Indices: 2399825--2400109 Score: 324
Period size: 149 Copynumber: 1.9 Consensus size: 147
2399815 TTCAAAGATT
* * * *
2399825 TGTAAGACCTTCAGGTAAAACATTTTAAATTTTCAAAGTTGCAATGCCTTCACTAGAGGAACATT
1 TGTAAGACCTTCAGGCAAAACATTTTAAAATTTCAAAGTTGCAATGCCTTCACTAAAGGAACAAT
* * * * *
2399890 CAAAGACTTTGAGATTTATAATACCTTCAAGCATAATCTCTAAAACCTCATAGCATAATCTCTAA
66 AAAAGACTTTAAGATTTATAAAACCTTCAAGCATAATCTCTAAAACCTCATAGCATAATATATAA
2399955 GACCTCTAAGCATAATC
131 GACCTCTAAGCATAATC
* * **
2399972 TGTAAGACCTTTAGGACAAAACATTTTAAAATTTCAAAGTTTCAATGCC-TCTACTACAAGGAGT
1 TGTAAGACCTTCAGG-CAAAACATTTTAAAATTTCAAAGTTGCAATGCCTTC-ACTA-AAGGAAC
* * * * * * *
2400036 AATAAAAGATTTTAAGATTTGTAAAACC-TCTGAGCATAATCTTTGAGACCT-TTAGGCATAATA
63 AATAAAAGACTTTAAGATTTATAAAACCTTC-AAGCATAATCTCTAAAACCTCATA-GCATAATA
2400099 TATAAGACCTC
126 TATAAGACCTC
2400110 CATGCAATTT
Statistics
Matches: 113, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
147 16 0.14
148 38 0.34
149 59 0.52
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (147 bp):
TGTAAGACCTTCAGGCAAAACATTTTAAAATTTCAAAGTTGCAATGCCTTCACTAAAGGAACAAT
AAAAGACTTTAAGATTTATAAAACCTTCAAGCATAATCTCTAAAACCTCATAGCATAATATATAA
GACCTCTAAGCATAATC
Found at i:2401619 original size:12 final size:12
Alignment explanation
Indices: 2401602--2401633 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2401592 CAATCTCGAT
2401602 AAACCCTAGAAC
1 AAACCCTAGAAC
2401614 AAACCCTAGAAC
1 AAACCCTAGAAC
*
2401626 CAACCCTA
1 AAACCCTA
2401634 AGCCACAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.38, G:0.06, T:0.09
Consensus pattern (12 bp):
AAACCCTAGAAC
Found at i:2402103 original size:14 final size:14
Alignment explanation
Indices: 2402075--2402130 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
2402065 GAAGAGAGGG
**
2402075 AGAAAAAAACTAGA
1 AGAAAAAAAAAAGA
2402089 AGAAAAAAAAAAG-
1 AGAAAAAAAAAAGA
*
2402102 A-AAAATAAAAAGA
1 AGAAAAAAAAAAGA
* *
2402115 AGAAGAAGAAAAGA
1 AGAAAAAAAAAAGA
2402129 AG
1 AG
2402131 CTGTGACAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
12 10 0.29
13 2 0.06
14 22 0.65
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AGAAAAAAAAAAGA
Found at i:2404436 original size:11 final size:10
Alignment explanation
Indices: 2404401--2404439 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
2404391 ACCTTCTTTC
2404401 AAAAACAAAA
1 AAAAACAAAA
2404411 AAAAA-AAAA
1 AAAAACAAAA
2404420 AAAAACAAAA
1 AAAAACAAAA
2404430 AGAAAACAAA
1 A-AAAACAAA
2404440 TTAACAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.33
10 10 0.37
11 8 0.30
ACGTcount: A:0.90, C:0.08, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:2406050 original size:2 final size:2
Alignment explanation
Indices: 2406043--2406067 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2406033 TGATTTCATT
2406043 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2406068 TTGAAGTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2408069 original size:22 final size:21
Alignment explanation
Indices: 2408041--2408118 Score: 61
Period size: 22 Copynumber: 3.6 Consensus size: 21
2408031 AAAAGCCATA
2408041 AGCCCAGATTAGTTGGTACATT
1 AGCCCAGATTAGTTGG-ACATT
* * *
2408063 AGCCCAGTTTAGCTAG-CATAT
1 AGCCCAGATTAGTTGGACAT-T
*
2408084 CAGCCCAGATTAATTGG-CATGT
1 -AGCCCAGATTAGTTGGACAT-T
2408106 AAGCCCAGATTAG
1 -AGCCCAGATTAG
2408119 CTGAAAAAGT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 3 0.07
21 1 0.02
22 40 0.91
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (21 bp):
AGCCCAGATTAGTTGGACATT
Found at i:2408389 original size:32 final size:32
Alignment explanation
Indices: 2408351--2408537 Score: 108
Period size: 32 Copynumber: 5.8 Consensus size: 32
2408341 CTAATGAGGT
*
2408351 TTTAAGCCCAGTTTAGTTGGCACTAAAAGAAA
1 TTTAAGCCCAGTTTAGCTGGCACTAAAAGAAA
* * * * *
2408383 TTTAAGCTCACTTTAACTGGCAATCAAAGAAAA
1 TTTAAGCCCAGTTTAGCTGGCACTAAAAG-AAA
* ** * ** ** *
2408416 CTTAAGCTTAGTCTAGCTAACACCCAATGAAA
1 TTTAAGCCCAGTTTAGCTGGCACTAAAAGAAA
* * * *
2408448 TTTAAGCCCATTTTAGTTGGTACT-AAGGAAAA
1 TTTAAGCCCAGTTTAGCTGGCACTAAAAG-AAA
* * * *
2408480 TATAAGCCCAGTCTAGCTAGCACTCGTAAAA-AAT
1 TTTAAGCCCAGTTTAGCTGGCA--C-TAAAAGAAA
2408514 TTTAAGCCCAGTTTAGCTGGCACT
1 TTTAAGCCCAGTTTAGCTGGCACT
2408538 TGTGGAAAAA
Statistics
Matches: 111, Mismatches: 38, Indels: 13
0.69 0.23 0.08
Matches are distributed among these distances:
31 4 0.04
32 60 0.54
33 22 0.20
34 22 0.20
35 1 0.01
36 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (32 bp):
TTTAAGCCCAGTTTAGCTGGCACTAAAAGAAA
Found at i:2408907 original size:15 final size:14
Alignment explanation
Indices: 2408870--2408908 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2408860 GTCATAAATT
2408870 AAAAAAAAA-AAAC
1 AAAAAAAAAGAAAC
*
2408883 ACAAAAAAAGGAAAC
1 A-AAAAAAAAGAAAC
2408898 AAAAAAAAAGA
1 AAAAAAAAAGA
2408909 GGAAGTATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 1 0.05
14 16 0.73
15 5 0.23
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAAAC
Found at i:2411594 original size:37 final size:36
Alignment explanation
Indices: 2411553--2411625 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
2411543 ATAAATAAAA
** * *
2411553 TAATAAAAGATTAATAAATATATAATAATAAAATTTT
1 TAATAAAAGAGAAATAAATAAAT-ATAAAAAAATTTT
*
2411590 TAATAAAAGAGAAATATATAAATATAAAAAAATTTT
1 TAATAAAAGAGAAATAAATAAATATAAAAAAATTTT
2411626 ATTTTTTAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
36 12 0.39
37 19 0.61
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (36 bp):
TAATAAAAGAGAAATAAATAAATATAAAAAAATTTT
Found at i:2411750 original size:24 final size:24
Alignment explanation
Indices: 2411723--2411804 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 24
2411713 AAATCTTATG
*
2411723 TGAAACCTAACCAGAAG-CCTTAAA
1 TGAAACCTAA-CACAAGACCTTAAA
*
2411747 TGAAACCCTAATACAAGACCTTAAA
1 TGAAA-CCTAACACAAGACCTTAAA
**
2411772 TGAAACCCTAA-AGTGAGACCTTAAAA
1 TGAAA-CCTAACA-CAAGACCTT-AAA
2411798 TGAAACC
1 TGAAACC
2411805 CTAAAGTGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
24 10 0.20
25 32 0.64
26 8 0.16
ACGTcount: A:0.46, C:0.23, G:0.12, T:0.18
Consensus pattern (24 bp):
TGAAACCTAACACAAGACCTTAAA
Found at i:2411805 original size:26 final size:25
Alignment explanation
Indices: 2411740--2411834 Score: 111
Period size: 25 Copynumber: 3.8 Consensus size: 25
2411730 TAACCAGAAG
**
2411740 CCTTAAATGAAACCCTAATA-CAAGA
1 CCTTAAATGAAACCCTAA-AGTGAGA
2411765 CCTTAAATGAAACCCTAAAGTGAGA
1 CCTTAAATGAAACCCTAAAGTGAGA
*
2411790 CCTTAAAATGAAACCCTAAAGTGAAA
1 CCTT-AAATGAAACCCTAAAGTGAGA
* * *
2411816 CCCTAAGTAAAACCCTAAA
1 CCTTAAATGAAACCCTAAA
2411835 CCCTACATAA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
24 1 0.02
25 38 0.61
26 23 0.37
ACGTcount: A:0.47, C:0.23, G:0.11, T:0.19
Consensus pattern (25 bp):
CCTTAAATGAAACCCTAAAGTGAGA
Found at i:2411809 original size:13 final size:13
Alignment explanation
Indices: 2411768--2411834 Score: 84
Period size: 13 Copynumber: 5.3 Consensus size: 13
2411758 TACAAGACCT
2411768 TAAA-TGAAACCC
1 TAAAGTGAAACCC
* *
2411780 TAAAGTGAGACCT
1 TAAAGTGAAACCC
*
2411793 TAAAATGAAACCC
1 TAAAGTGAAACCC
2411806 TAAAGTGAAACCC
1 TAAAGTGAAACCC
*
2411819 T-AAGTAAAACCC
1 TAAAGTGAAACCC
2411831 TAAA
1 TAAA
2411835 CCCTACATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
12 15 0.33
13 31 0.67
ACGTcount: A:0.49, C:0.21, G:0.12, T:0.18
Consensus pattern (13 bp):
TAAAGTGAAACCC
Found at i:2411828 original size:12 final size:12
Alignment explanation
Indices: 2411800--2411833 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2411790 CCTTAAAATG
*
2411800 AAACCCTAAAGTG
1 AAACCCT-AAGTA
2411813 AAACCCTAAGTA
1 AAACCCTAAGTA
2411825 AAACCCTAA
1 AAACCCTAA
2411834 ACCCTACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.50, C:0.26, G:0.09, T:0.15
Consensus pattern (12 bp):
AAACCCTAAGTA
Found at i:2413254 original size:26 final size:27
Alignment explanation
Indices: 2413222--2413277 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
2413212 GAATTGTAAG
*
2413222 AACAAAATTTAAATCGCTTGAAACA-A
1 AACAAAATTTAAATCGCATGAAACATA
*
2413248 AACAAAATTTAAATTGCATGAAACATA
1 AACAAAATTTAAATCGCATGAAACATA
2413275 AAC
1 AAC
2413278 TGAAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.23
Consensus pattern (27 bp):
AACAAAATTTAAATCGCATGAAACATA
Found at i:2420845 original size:65 final size:64
Alignment explanation
Indices: 2420761--2420993 Score: 215
Period size: 65 Copynumber: 3.6 Consensus size: 64
2420751 AAAAACAAAG
*
2420761 AATTTTTTAAAATTAATTCATAAAATCTTAGCAATATATTAAAGGATTTTATAAGTTTGAAAAT
1 AATTTTTTAAAATTAATTCATAAAATCTTAGCAACATATTAAAGGATTTTATAAGTTTGAAAAT
* ** * * *
2420825 AATTTTTTAAAAATTAATTCACAAAATCCAATCAACATATTAAAAGG-TTTTATAAATTTTAAAA
1 AATTTTTT-AAAATTAATTCATAAAATCTTAGCAACATATT-AAAGGATTTTATAAGTTTGAAAA
2420889 TT
64 -T
* * ** *
2420891 AA-TTTTTAAAATATAATTTATAAAAT-TTTGCCAACATATTAAAAAATTTTAT-TGATTTGAAA
1 AATTTTTTAAAAT-TAATTCATAAAATCTTAG-CAACATATTAAAGGATTTTATAAG-TTTGAAA
2420953 ATT
63 A-T
* * * *
2420956 ACTTTTTGAAGACTAATTCATAAAATCTT-GTCAACATA
1 AATTTTTTAAAATTAATTCATAAAATCTTAG-CAACATA
2420994 GTGAAAAATT
Statistics
Matches: 136, Mismatches: 24, Indels: 17
0.77 0.14 0.10
Matches are distributed among these distances:
64 16 0.12
65 103 0.76
66 17 0.12
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (64 bp):
AATTTTTTAAAATTAATTCATAAAATCTTAGCAACATATTAAAGGATTTTATAAGTTTGAAAAT
Done.