Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 14 of 147
Found at i:3069911 original size:3 final size:3
Alignment explanation
Indices: 3069903--3069934 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3069893 AATTAGGTTT
*
3069903 TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3069935 TGTTTCCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3070368 original size:21 final size:22
Alignment explanation
Indices: 3070337--3070379 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3070327 GAACCATCTA
*
3070337 AAAATTTTTTTGGGATTTTTCT
1 AAAATTTTTTTGGAATTTTTCT
3070359 AAAATTTTTTT-GAATTTTTCT
1 AAAATTTTTTTGGAATTTTTCT
3070380 GGGTCTGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (22 bp):
AAAATTTTTTTGGAATTTTTCT
Found at i:3073836 original size:3 final size:3
Alignment explanation
Indices: 3073822--3073859 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
3073812 AATTAGGTTT
*
3073822 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3073860 TGTTTCCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3081564 original size:12 final size:12
Alignment explanation
Indices: 3081536--3081580 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 12
3081526 TTCTCTTTTT
3081536 TTTTGTTTTTGGTA
1 TTTTG-TTTT-GTA
3081550 TTTTGTTTTGTA
1 TTTTGTTTTGTA
3081562 TTTTTGTTTTGTA
1 -TTTTGTTTTGTA
3081575 TTTTGT
1 TTTTGT
3081581 ATTATTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.30
13 16 0.53
14 5 0.17
ACGTcount: A:0.07, C:0.00, G:0.18, T:0.76
Consensus pattern (12 bp):
TTTTGTTTTGTA
Found at i:3081565 original size:20 final size:19
Alignment explanation
Indices: 3081531--3081583 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
3081521 GTCTGTTCTC
3081531 TTTTT-TTTTGT-TTTTGG
1 TTTTTATTTTGTATTTTGG
* *
3081548 TATTTTGTTTTGTATTTTTG
1 T-TTTTATTTTGTATTTTGG
3081568 TTTTGTATTTTGTATT
1 TTTT-TATTTTGTATT
3081584 ATTTTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 1 0.03
18 4 0.13
19 9 0.30
20 16 0.53
ACGTcount: A:0.08, C:0.00, G:0.15, T:0.77
Consensus pattern (19 bp):
TTTTTATTTTGTATTTTGG
Found at i:3081578 original size:7 final size:7
Alignment explanation
Indices: 3081536--3081583 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
3081526 TTCTCTTTTT
3081536 TTTTGT-
1 TTTTGTA
3081542 TTTTGGTA
1 TTTT-GTA
3081550 TTTTG--
1 TTTTGTA
3081555 TTTTGTA
1 TTTTGTA
*
3081562 TTTT-TG
1 TTTTGTA
3081568 TTTTGTA
1 TTTTGTA
3081575 TTTTGTA
1 TTTTGTA
3081582 TT
1 TT
3081584 ATTTTTGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
5 5 0.14
6 9 0.26
7 17 0.49
8 4 0.11
ACGTcount: A:0.08, C:0.00, G:0.17, T:0.75
Consensus pattern (7 bp):
TTTTGTA
Found at i:3081583 original size:32 final size:30
Alignment explanation
Indices: 3081531--3081592 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
3081521 GTCTGTTCTC
*
3081531 TTTTTTTTTGTTTTTGGTATTTTGTTTTGTA
1 TTTTTTTTTGTTTTTGGTATTAT-TTTTGTA
3081562 TTTTTGTTTTGTATTTT-GTATTATTTTTGTA
1 TTTTT-TTTTGT-TTTTGGTATTATTTTTGTA
3081593 ATATTATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 12 0.43
32 12 0.43
33 4 0.14
ACGTcount: A:0.10, C:0.00, G:0.15, T:0.76
Consensus pattern (30 bp):
TTTTTTTTTGTTTTTGGTATTATTTTTGTA
Found at i:3081614 original size:17 final size:17
Alignment explanation
Indices: 3081580--3081626 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
3081570 TTGTATTTTG
* **
3081580 TATTATTTTTGTAATAT
1 TATTATTTTTATTTTAT
3081597 TATTATTTTTATTTTAT
1 TATTATTTTTATTTTAT
3081614 T-TTA-TTTTATTTT
1 TATTATTTTTATTTT
3081627 GGGACAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 9 0.33
16 3 0.11
17 15 0.56
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (17 bp):
TATTATTTTTATTTTAT
Found at i:3082154 original size:73 final size:73
Alignment explanation
Indices: 3081988--3082562 Score: 721
Period size: 73 Copynumber: 7.9 Consensus size: 73
3081978 AGAATAAGAA
* * * * * * * * *
3081988 GATCAGGATTAAACCACGAATCAAATATTAATGATGACTGAGATTGAACCGCAAGTCGAGGGACT
1 GATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTC-AGGAAAT
3082053 TAATGAAAT
65 TAATGAAAT
* *
3082062 GATCGGGATTAAACCACGAGCCAAAGATTAAAGATGACTGGGACTAAACAGCAAGTCAGGAAATT
1 GATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCAGGAAATT
3082127 AATGAAAT
66 AATGAAAT
* * * *
3082135 GATCGGGATTAAATCACGAGTCAAAGATTAAAGATGACTAGGATTAAACCGCAAGTCA-G--A-G
1 GATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCAGGAAATT
3082196 AATGAAAT
66 AATGAAAT
* * **
3082204 GATCGGGATCAAACCACGAGTTAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCAAAAAATT
1 GATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCAGGAAATT
3082269 AATGAAAT
66 AATGAAAT
* * * **
3082277 GATCAGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCATAAGTCAGAGAAA-
1 GATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCAG-GAAAT
3082341 TAATGAAAT
65 TAATGAAAT
* * * *
3082350 GATCGGGATTAAACCACAAGTCAAAGATTAAAGATGACTAGGACTAAACCGTAAGTTAGGAAATT
1 GATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCAGGAAATT
3082415 AATGAAAT
66 AATGAAAT
* * * * *
3082423 AATTGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACTGCAAGTCAGAGAAA-
1 GATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCAG-GAAAT
3082487 TAATGAAAT
65 TAATGAAAT
** * * * *
3082496 GATCGAAATTAAACCACGAGCCAAAAGATTAAAGATGACTGGGACTAAACCGTAAGTTAAGAAAT
1 GATCGGGATTAAACCACGAGTC-AAAGATTAAAGATGACTGGGACTAAACCGCAAGTCAGGAAAT
3082561 TA
65 TA
3082563 TATAAGACTG
Statistics
Matches: 432, Mismatches: 60, Indels: 18
0.85 0.12 0.04
Matches are distributed among these distances:
69 61 0.14
70 1 0.00
72 6 0.01
73 276 0.64
74 88 0.20
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.21
Consensus pattern (73 bp):
GATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTCAGGAAATT
AATGAAAT
Found at i:3082422 original size:146 final size:146
Alignment explanation
Indices: 3081988--3082562 Score: 807
Period size: 146 Copynumber: 4.0 Consensus size: 146
3081978 AGAATAAGAA
* * * * * **
3081988 GATCAGGATTAAACCACGAATCAAATATTAATGATGACTGAGATTGAACCGCAAGTCGAGGGACT
1 GATCAGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTC-AGAGAAA
*
3082053 TAATGAAATGATCGGGATTAAACCACGAGCCAAAGATTAAAGATGACTGGGACTAAACAGCAAGT
65 TAATGAAATGATCGGGATTAAACCACGAGCCAAAGATTAAAGATGACTGGGACTAAACCGCAAGT
*
3082118 CAGGAAATTAATGAAAT
130 CAAGAAATTAATGAAAT
* * * *
3082135 GATCGGGATTAAATCACGAGTCAAAGATTAAAGATGACTAGGATTAAACCGCAAGTCAGAG----
1 GATCAGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAGAAAT
* **
3082196 AATGAAATGATCGGGATCAAACCACGAGTTAAAGATTAAAGATGACTGGGACTAAACCGCAAGTC
66 AATGAAATGATCGGGATTAAACCACGAGCCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTC
*
3082261 AAAAAATTAATGAAAT
131 AAGAAATTAATGAAAT
**
3082277 GATCAGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCATAAGTCAGAGAAAT
1 GATCAGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAGAAAT
* * * * *
3082342 AATGAAATGATCGGGATTAAACCACAAGTCAAAGATTAAAGATGACTAGGACTAAACCGTAAGTT
66 AATGAAATGATCGGGATTAAACCACGAGCCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTC
*
3082407 AGGAAATTAATGAAAT
131 AAGAAATTAATGAAAT
* ** *
3082423 AATTGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACTGCAAGTCAGAGAAAT
1 GATCAGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAGAAAT
** *
3082488 AATGAAATGATCGAAATTAAACCACGAGCCAAAAGATTAAAGATGACTGGGACTAAACCGTAAGT
66 AATGAAATGATCGGGATTAAACCACGAGCC-AAAGATTAAAGATGACTGGGACTAAACCGCAAGT
*
3082553 TAAGAAATTA
130 CAAGAAATTA
3082563 TATAAGACTG
Statistics
Matches: 382, Mismatches: 41, Indels: 10
0.88 0.09 0.02
Matches are distributed among these distances:
142 130 0.34
146 161 0.42
147 91 0.24
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.21
Consensus pattern (146 bp):
GATCAGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAGAAAT
AATGAAATGATCGGGATTAAACCACGAGCCAAAGATTAAAGATGACTGGGACTAAACCGCAAGTC
AAGAAATTAATGAAAT
Found at i:3083611 original size:16 final size:16
Alignment explanation
Indices: 3083590--3083622 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3083580 TCTGAATCAC
3083590 TTCCTTTCTCATTTTT
1 TTCCTTTCTCATTTTT
*
3083606 TTCCTTTTTCATTTTT
1 TTCCTTTCTCATTTTT
3083622 T
1 T
3083623 CCATTTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (16 bp):
TTCCTTTCTCATTTTT
Found at i:3083621 original size:8 final size:9
Alignment explanation
Indices: 3083602--3083657 Score: 84
Period size: 9 Copynumber: 6.7 Consensus size: 9
3083592 CCTTTCTCAT
3083602 TTTTTTCC-
1 TTTTTTCCA
3083610 -TTTTT-CA
1 TTTTTTCCA
3083617 TTTTTTCCA
1 TTTTTTCCA
3083626 TTTTTTCCA
1 TTTTTTCCA
3083635 TTTTTTCCA
1 TTTTTTCCA
3083644 TTTTTT-CA
1 TTTTTTCCA
3083652 TTTTTT
1 TTTTTT
3083658 TATATTTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
6 1 0.02
7 5 0.11
8 13 0.29
9 26 0.58
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTTCCA
Found at i:3083622 original size:9 final size:9
Alignment explanation
Indices: 3083598--3083677 Score: 76
Period size: 9 Copynumber: 9.1 Consensus size: 9
3083588 ACTTCCTTTC
3083598 TCATTTTTT
1 TCATTTTTT
*
3083607 TC--CTTTT
1 TCATTTTTT
3083614 TCATTTTTT
1 TCATTTTTT
*
3083623 CCATTTTTT
1 TCATTTTTT
*
3083632 CCATTTTTT
1 TCATTTTTT
*
3083641 CCA-TTTTT
1 TCATTTTTT
3083649 TCATTTTTT
1 TCATTTTTT
*
3083658 TATATTTTTT
1 T-CATTTTTT
*
3083668 TAATTTTTT
1 TCATTTTTT
3083677 T
1 T
3083678 TCTCTTTTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
7 6 0.10
8 7 0.11
9 40 0.66
10 8 0.13
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (9 bp):
TCATTTTTT
Found at i:3083763 original size:18 final size:18
Alignment explanation
Indices: 3083740--3083774 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3083730 TTGACAATTC
3083740 AATTGGCAGTACAACTTT
1 AATTGGCAGTACAACTTT
3083758 AATTGGCAGTACAACTT
1 AATTGGCAGTACAACTT
3083775 CCATCCCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (18 bp):
AATTGGCAGTACAACTTT
Found at i:3089507 original size:18 final size:19
Alignment explanation
Indices: 3089484--3089523 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
3089474 CTCTTTTTTC
*
3089484 TTTAAAGTTGCTGTCTT-T
1 TTTAAAGTTGCTATCTTCT
3089502 TTTAAAGTTGCTATCTTCT
1 TTTAAAGTTGCTATCTTCT
3089521 TTT
1 TTT
3089524 TAGACCCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.57
Consensus pattern (19 bp):
TTTAAAGTTGCTATCTTCT
Found at i:3095258 original size:20 final size:20
Alignment explanation
Indices: 3095229--3095287 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
3095219 CAGGTCCGGG
*
3095229 CCCGGGTCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
3095249 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
* *
3095269 CCCAGATCATTTGGGCCTG
1 CCCGGATCAATTGGGCCTG
3095288 CCCCAAATGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.22
Consensus pattern (20 bp):
CCCGGATCAATTGGGCCTGA
Found at i:3095600 original size:11 final size:12
Alignment explanation
Indices: 3095579--3095612 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3095569 AATTATCTAG
*
3095579 ATTTTTTTTTTA
1 ATTTTTATTTTA
3095591 A-TTTTATTTTA
1 ATTTTTATTTTA
3095602 ATTTTTATTTT
1 ATTTTTATTTT
3095613 GGAGGGCTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTATTTTA
Found at i:3096001 original size:31 final size:31
Alignment explanation
Indices: 3095930--3096002 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
3095920 AATTTCCAGA
* *
3095930 TTCCGGCGAAAATTCCGGCGACTTTTGAATT
1 TTCCGGCGACAATTCCGGCGACTTTTGAAGT
*
3095961 TTCCGGCGACAATTCCGGTGAAC-TTTGAAGT
1 TTCCGGCGACAATTCCGGCG-ACTTTTGAAGT
3095992 TTCCGGCGACA
1 TTCCGGCGACA
3096003 GACCCAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 36 0.95
32 2 0.05
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.29
Consensus pattern (31 bp):
TTCCGGCGACAATTCCGGCGACTTTTGAAGT
Found at i:3096091 original size:19 final size:19
Alignment explanation
Indices: 3096067--3096108 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3096057 GGCCAATTTT
*
3096067 CGGCGAAATTCCCAGATTC
1 CGGCGAAATTCCCAGAATC
*
3096086 CGGCGAAATTTCCAGAATC
1 CGGCGAAATTCCCAGAATC
3096105 CGGC
1 CGGC
3096109 ACCGGCGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.31, G:0.24, T:0.19
Consensus pattern (19 bp):
CGGCGAAATTCCCAGAATC
Found at i:3096337 original size:5 final size:5
Alignment explanation
Indices: 3096327--3096369 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
3096317 TTTCAGCCCT
*
3096327 CCGAG CCGAG CCGAG CCGAG CCGAG CCGCA- CCAAG CCGAG CCG
1 CCGAG CCGAG CCGAG CCGAG CCGAG CCG-AG CCGAG CCGAG CCG
3096370 CTCCAGGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 1 0.03
5 32 0.94
6 1 0.03
ACGTcount: A:0.21, C:0.44, G:0.35, T:0.00
Consensus pattern (5 bp):
CCGAG
Found at i:3096404 original size:17 final size:17
Alignment explanation
Indices: 3096382--3096447 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
3096372 CCAGGTTTTT
*
3096382 TTTTTTTTTTTTTTGAA
1 TTTTTTTTTTATTTGAA
*
3096399 TTTTTTTTTTATTTGAC
1 TTTTTTTTTTATTTGAA
** * *
3096416 TTTGATTTTGATCTTGAT
1 TTTTTTTTTTAT-TTGAA
3096434 TTTTTTTCTTTATT
1 TTTTTTT-TTTATT
3096448 CTTTAATTAA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
17 24 0.63
18 10 0.26
19 4 0.11
ACGTcount: A:0.12, C:0.05, G:0.08, T:0.76
Consensus pattern (17 bp):
TTTTTTTTTTATTTGAA
Found at i:3096721 original size:159 final size:159
Alignment explanation
Indices: 3096446--3097202 Score: 1366
Period size: 156 Copynumber: 4.8 Consensus size: 159
3096436 TTTTTCTTTA
* * *
3096446 TTCTTTAATTAATCCAACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACTCCT
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCTTGCATACTCCT
3096511 GAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGAT
65 GAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGAT
* * *
3096576 AATTAATTACTTGGCTGATTTTGATTTTTTT
130 AATTAATTAATTGGTTGATCTTGA-TTTTTT
3096607 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
3096672 AGGTGA-GGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
66 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
3096736 ATTAATTAATTGGTTGATCTTGATTTTTT
131 ATTAATTAATTGGTTGATCTTGATTTTTT
*
3096765 TTCTTTAATTAATCCGACGACGGAACCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
3096830 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
66 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
3096895 ATTAATTAATTGGTTGATCTTGA---TTT
131 ATTAATTAATTGGTTGATCTTGATTTTTT
3096921 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
3096986 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
66 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
3097051 ATTAATTAATTGGTTGATCTTGA---TTT
131 ATTAATTAATTGGTTGATCTTGATTTTTT
* *
3097077 TTCTTTAATTAATCCGACAACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCTTG
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
3097142 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
66 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
3097203 AACAACTAAC
Statistics
Matches: 585, Mismatches: 10, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
156 282 0.48
158 76 0.13
159 159 0.27
160 34 0.06
161 34 0.06
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (159 bp):
TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
ATTAATTAATTGGTTGATCTTGATTTTTT
Found at i:3100425 original size:1 final size:1
Alignment explanation
Indices: 3100421--3100445 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3100411 GTAATTTTTG
3100421 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
3100446 CCACAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3100868 original size:16 final size:16
Alignment explanation
Indices: 3100831--3100869 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
3100821 AAAAAGAAAA
3100831 AAAAAAGGAAAAAATG
1 AAAAAAGGAAAAAATG
* *
3100847 AGAAAATGAAAAAATG
1 AAAAAAGGAAAAAATG
3100863 AAAAAAG
1 AAAAAAG
3100870 AGATCCAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (16 bp):
AAAAAAGGAAAAAATG
Found at i:3102170 original size:42 final size:42
Alignment explanation
Indices: 3102060--3102389 Score: 458
Period size: 42 Copynumber: 8.0 Consensus size: 42
3102050 GTCTAGGAGT
*
3102060 ATTTATTTTTCC-AAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
* * *
3102100 ATTTA-TTTTTCAAAGTCGTGGTACCTCTGTTAAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
3102141 ATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
3102183 ATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
3102225 ATTTAC-TTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
3102266 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
3102308 ATTTA-TCTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACT-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* * * **
3102350 ATTTA-TTTTTCAAAGTCGTAGAGCCTCTGTCAAGAGGAGC
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
3102390 TAAAAAAAAA
Statistics
Matches: 266, Mismatches: 18, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
39 9 0.03
40 8 0.03
41 90 0.34
42 159 0.60
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (42 bp):
ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
Found at i:3102173 original size:83 final size:83
Alignment explanation
Indices: 3102060--3102389 Score: 483
Period size: 83 Copynumber: 4.0 Consensus size: 83
3102050 GTCTAGGAGT
*
3102060 ATTTATTTTTCC-AAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGT
1 ATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGT
3102122 ACCTCTGTTAAGAGGAGCA
65 ACCTCTGTTAAGAGGAGCA
* *
3102141 ATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAGTCGTGGT
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTC-AAAGTCGTGGT
* *
3102206 GCCTCTGTTTAGAGGAGCA
65 ACCTCTGTTAAGAGGAGCA
* *
3102225 ATTTAC-TTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTATTTTTCCAAAGTCGTGGT
1 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTT-CAAAGTCGTGGT
*
3102289 ACCTCTGTTTAGAGGAGCA
65 ACCTCTGTTAAGAGGAGCA
*
3102308 ATTTA-TCTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTAG-
1 ATTTACT-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGT
*
3102371 AGCCTCTGTCAAGAGGAGC
65 A-CCTCTGTTAAGAGGAGC
3102390 TAAAAAAAAA
Statistics
Matches: 226, Mismatches: 15, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
81 14 0.06
82 4 0.02
83 130 0.58
84 78 0.35
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (83 bp):
ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTA
CCTCTGTTAAGAGGAGCA
Found at i:3102223 original size:125 final size:125
Alignment explanation
Indices: 3102080--3102389 Score: 507
Period size: 125 Copynumber: 2.5 Consensus size: 125
3102070 CCAAGTTCGT
3102080 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTACCTCTGTTAAGAGGAGCAATTT
1 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTACCTCTGTTAAGAGGAGCAATTT
*
3102145 ACTTTTCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTA-CTTTTCAAAAGTCGTGG
66 ACTTTTCAAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTATC-TTTCAAAAGTCGTGG
* * *
3102205 TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTT
1 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTACCTCTGTTAAGAGGAGCAATTT
* * *
3102270 ATTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTATCTTTCCAAAGTCGTGG
66 ACTTTTCAAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTATCTTTCAAAAGTCGTGG
* *
3102330 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTAG-AGCCTCTGTCAAGAGGAGC
1 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTA-CCTCTGTTAAGAGGAGC
3102390 TAAAAAAAAA
Statistics
Matches: 171, Mismatches: 12, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
124 1 0.01
125 169 0.99
126 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (125 bp):
TGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTACCTCTGTTAAGAGGAGCAATTT
ACTTTTCAAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTATCTTTCAAAAGTCGTGG
Found at i:3102551 original size:20 final size:20
Alignment explanation
Indices: 3102522--3102559 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3102512 CAGGTCCGGG
*
3102522 CCCGGGTCAATTGGGCCTAA
1 CCCGGATCAATTGGGCCTAA
3102542 CCCGGATCAATTGGGCCT
1 CCCGGATCAATTGGGCCT
3102560 GCCCCAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.32, G:0.29, T:0.21
Consensus pattern (20 bp):
CCCGGATCAATTGGGCCTAA
Found at i:3102873 original size:11 final size:12
Alignment explanation
Indices: 3102852--3102885 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3102842 AATTATCTAG
*
3102852 ATTTTTTTTTTA
1 ATTTTTATTTTA
3102864 A-TTTTATTTTA
1 ATTTTTATTTTA
3102875 ATTTTTATTTT
1 ATTTTTATTTT
3102886 GGAGGGCTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTATTTTA
Found at i:3103273 original size:31 final size:31
Alignment explanation
Indices: 3103202--3103274 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
3103192 AATTTCCAGA
* *
3103202 TTCCGGCGAAAATTCCGGCGACTTTTGAATT
1 TTCCGGCGACAATTCCGGCGACTTTTGAAGT
3103233 TTCCGGCGACAATTCCGGCGAAC-TTTGAAGT
1 TTCCGGCGACAATTCCGGCG-ACTTTTGAAGT
3103264 TTCCGGCGACA
1 TTCCGGCGACA
3103275 GACCCAGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 37 0.95
32 2 0.05
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (31 bp):
TTCCGGCGACAATTCCGGCGACTTTTGAAGT
Found at i:3103363 original size:19 final size:19
Alignment explanation
Indices: 3103339--3103380 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3103329 GGCCAATTTT
*
3103339 CGGCGAAATTCCCAGATTC
1 CGGCGAAATTCCCAGAATC
*
3103358 CGGCGAAATTTCCAGAATC
1 CGGCGAAATTCCCAGAATC
3103377 CGGC
1 CGGC
3103381 ACCGACGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.31, G:0.24, T:0.19
Consensus pattern (19 bp):
CGGCGAAATTCCCAGAATC
Found at i:3103611 original size:15 final size:15
Alignment explanation
Indices: 3103593--3103647 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
3103583 CGCGCGTTTC
*
3103593 AGCCCCTCCAAGCCG
1 AGCCGCTCCAAGCCG
** *
3103608 AGCCGAGCCGAGCCG
1 AGCCGCTCCAAGCCG
*
3103623 AGCCGCACCAAGCCG
1 AGCCGCTCCAAGCCG
3103638 AGCCGCTCCA
1 AGCCGCTCCA
3103648 GGTTTTTTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.22, C:0.47, G:0.27, T:0.04
Consensus pattern (15 bp):
AGCCGCTCCAAGCCG
Found at i:3103613 original size:5 final size:5
Alignment explanation
Indices: 3103603--3103642 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
3103593 AGCCCCTCCA
*
3103603 AGCCG AGCCG AGCCG AGCCG AGCCG CA-CCA AGCCG AGCCG
1 AGCCG AGCCG AGCCG AGCCG AGCCG -AGCCG AGCCG AGCCG
3103643 CTCCAGGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 1 0.03
5 29 0.94
6 1 0.03
ACGTcount: A:0.23, C:0.42, G:0.35, T:0.00
Consensus pattern (5 bp):
AGCCG
Found at i:3103675 original size:15 final size:15
Alignment explanation
Indices: 3103657--3103712 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
3103647 AGGTTTTTTT
*
3103657 TTTTTTTTTTTTTGA
1 TTTTTTTTTATTTGA
3103672 TTTTTTTTTATTTGA
1 TTTTTTTTTATTTGA
* *
3103687 CTTTGATTTTGATCTTGA
1 -TTT-TTTTTTAT-TTGA
3103705 TTTTTTTT
1 TTTTTTTT
3103713 CTTTAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
15 14 0.41
16 7 0.21
17 9 0.26
18 4 0.12
ACGTcount: A:0.11, C:0.04, G:0.09, T:0.77
Consensus pattern (15 bp):
TTTTTTTTTATTTGA
Found at i:3103684 original size:10 final size:10
Alignment explanation
Indices: 3103651--3103684 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3103641 CGCTCCAGGT
*
3103651 TTTTTTTTTT
1 TTTTTTTTTA
3103661 TTTTTTTTTGA
1 TTTTTTTTT-A
3103672 TTTTTTTTTA
1 TTTTTTTTTA
3103682 TTT
1 TTT
3103685 GACTTTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.06, C:0.00, G:0.03, T:0.91
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:3103965 original size:160 final size:159
Alignment explanation
Indices: 3103696--3104151 Score: 783
Period size: 156 Copynumber: 2.9 Consensus size: 159
3103686 ACTTTGATTT
* *
3103696 TGATCTTGATTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTT
1 TGATCTTGATTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTT
* *
3103761 TTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAATCAATTG
65 TTCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
*
3103826 AGAATAATTTCCGATAATTAATTACTTGGC
130 AGAATAATTTCCGATAATTAATTAATTGGC
*
3103856 TGATTTTGATTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
1 TGATCTTGA-TTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
3103921 TTCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
65 TTCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
* *
3103986 AGAATAATTTTCGATAATTAATTAATTGGT
130 AGAATAATTTCCGATAATTAATTAATTGGC
*
3104016 TGATCTTGA---TTTTTCTTTAAATAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTT
1 TGATCTTGATTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTT
*
3104078 TCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTTTGCTAAAAGTATTAGAGTCAATTGA
66 TCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGA
3104143 GAATAATTT
131 GAATAATTT
3104152 TCAACAACTA
Statistics
Matches: 284, Mismatches: 11, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
156 125 0.44
160 118 0.42
161 41 0.14
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (159 bp):
TGATCTTGATTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTT
TCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGA
GAATAATTTCCGATAATTAATTAATTGGC
Found at i:3109388 original size:22 final size:21
Alignment explanation
Indices: 3109346--3109408 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
3109336 GTATTTTGTA
3109346 TTTTATATTTATATTTATATTT
1 TTTTAT-TTTATATTTATATTT
* *
3109368 TTTTATTTTATCTTATGTATTT
1 TTTTATTTTATATT-TATATTT
*
3109390 ATTTATTATTACTATTTAT
1 TTTTATT-TTA-TATTTAT
3109409 TAATATATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
21 7 0.21
22 18 0.55
23 5 0.15
24 3 0.09
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTATTTTATATTTATATTT
Found at i:3109407 original size:51 final size:49
Alignment explanation
Indices: 3109328--3109469 Score: 123
Period size: 51 Copynumber: 2.9 Consensus size: 49
3109318 GTAGGTCCAA
* * *
3109328 TTTAT-TTCGTATTT-TGTATT-TTATATTTA-TATTTATATTTTTTTAT
1 TTTATCTTAGTATTTATATATTATTATATTTATTATTTATATTTGTTT-T
* *
3109374 TTTATCTTATGTATTTATTTATTATTACTATTTATTAATATATATTTGTTTT
1 TTTATCTTA-GTATTTATATATTATTA-TATTTATT-ATTTATATTTGTTTT
* *
3109426 TTTATGTTAATATTTATATA-TATTTATTATTTATCTATTTATAT
1 TTTATCTTAGTATTTATATATTA-TTA-TATTTAT-TATTTATAT
3109470 ATTATAATTT
Statistics
Matches: 78, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
46 5 0.06
47 2 0.03
48 6 0.08
49 5 0.06
50 5 0.06
51 32 0.41
52 11 0.14
53 12 0.15
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.67
Consensus pattern (49 bp):
TTTATCTTAGTATTTATATATTATTATATTTATTATTTATATTTGTTTT
Found at i:3109416 original size:57 final size:60
Alignment explanation
Indices: 3109347--3109481 Score: 138
Period size: 57 Copynumber: 2.3 Consensus size: 60
3109337 TATTTTGTAT
* * * * *
3109347 TTTATAT-TTATATTTATATTTTTTTAT-TTTATCTTATGTATTTATTTATTA-TTA-CTA
1 TTTATATAATATATTTATATTTTTTTATGTTAATATT-TATATATATTTATTATTTATCTA
*
3109404 TTTAT-TAATATATATT-TGTTTTTTTATGTTAATATTTATATATATTTATTATTTATCTA
1 TTTATATAATATAT-TTATATTTTTTTATGTTAATATTTATATATATTTATTATTTATCTA
*
3109463 TTTATATATTATAATTTAT
1 TTTATATAATAT-ATTTAT
3109482 CTATTATTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
56 1 0.02
57 33 0.52
58 11 0.17
59 8 0.13
60 7 0.11
61 3 0.05
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (60 bp):
TTTATATAATATATTTATATTTTTTTATGTTAATATTTATATATATTTATTATTTATCTA
Found at i:3109479 original size:22 final size:21
Alignment explanation
Indices: 3109444--3109562 Score: 102
Period size: 22 Copynumber: 5.7 Consensus size: 21
3109434 AATATTTATA
3109444 TATATTTATTATTTATCTATT
1 TATATTTATTATTTATCTATT
*
3109465 TATATATTATAATTTATCTA-T
1 TATAT-TTATTATTTATCTATT
*
3109486 TATTATTT-TTATTTATCTGTT
1 TA-TATTTATTATTTATCTATT
*
3109507 AATATTT-TTATTTATCTGA-T
1 TATATTTATTATTTATCT-ATT
* * *
3109527 TATTTTCTTTTAATTATCTATT
1 TATATT-TATTATTTATCTATT
* *
3109549 AATATTTTTTATTT
1 TATATTTATTATTT
3109563 TTTTTTCTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
20 29 0.36
21 21 0.26
22 30 0.38
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (21 bp):
TATATTTATTATTTATCTATT
Found at i:3109499 original size:20 final size:20
Alignment explanation
Indices: 3109446--3109562 Score: 117
Period size: 20 Copynumber: 5.5 Consensus size: 20
3109436 TATTTATATA
3109446 TATTTATTATTTATCTATTTAT
1 TATTT-TTATTTATCTA-TTAT
* *
3109468 ATATTATAATTTATCTATTAT
1 -TATTTTTATTTATCTATTAT
* *
3109489 TATTTTTATTTATCTGTTAA
1 TATTTTTATTTATCTATTAT
3109509 TATTTTTATTTATCTGATTAT
1 TATTTTTATTTATCT-ATTAT
* * *
3109530 TTTCTTTTAATTATCTATTAA
1 TAT-TTTTATTTATCTATTAT
3109551 TATTTTTTATTT
1 TA-TTTTTATTT
3109563 TTTTTTCTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
20 31 0.40
21 21 0.27
22 22 0.28
23 4 0.05
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (20 bp):
TATTTTTATTTATCTATTAT
Found at i:3109520 original size:4 final size:4
Alignment explanation
Indices: 3109363--3109501 Score: 52
Period size: 4 Copynumber: 32.8 Consensus size: 4
3109353 TTTATATTTA
* *
3109363 TATT TTTT TATTT TATCT TATG TATT TATT TA-T TATT ACTATT TATT
1 TATT TATT TA-TT TAT-T TATT TATT TATT TATT TATT --TATT TATT
* * * *
3109410 AATATA TATT TGTT TTTT TATGT TA-A TATT TATAT ATATT TA-T TATT
1 --TATT TATT TATT TATT TAT-T TATT TATT TAT-T -TATT TATT TATT
* * * *
3109457 TATC TATT TATA TATT ATAATT TATC TA-T TATT ATTTT TATT TAT
1 TATT TATT TATT TATT -T-ATT TATT TATT TATT -TATT TATT TAT
3109502 CTGTTAATAT
Statistics
Matches: 100, Mismatches: 19, Indels: 32
0.66 0.13 0.21
Matches are distributed among these distances:
3 10 0.10
4 59 0.59
5 18 0.18
6 13 0.13
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (4 bp):
TATT
Found at i:3109538 original size:42 final size:40
Alignment explanation
Indices: 3109446--3109562 Score: 135
Period size: 42 Copynumber: 2.8 Consensus size: 40
3109436 TATTTATATA
* *
3109446 TATTTATTATTTATCTATTTATATATTATAATTTATCTATTAT
1 TATTT-TTATTTATCTA-TTA-ATATTTTTATTTATCTATTAT
*
3109489 TATTTTTATTTATCTGTTAATATTTTTATTTATCTGATTAT
1 TATTTTTATTTATCTATTAATATTTTTATTTATCT-ATTAT
* *
3109530 TTTCTTTTAATTATCTATTAATATTTTTTATTT
1 TAT-TTTTATTTATCTATTAATA-TTTTTATTT
3109563 TTTTTTCTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
40 14 0.22
41 10 0.15
42 27 0.42
43 14 0.22
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (40 bp):
TATTTTTATTTATCTATTAATATTTTTATTTATCTATTAT
Found at i:3110347 original size:8 final size:8
Alignment explanation
Indices: 3110326--3110358 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
3110316 CATTCCCAGG
3110326 TTTTTTT-
1 TTTTTTTA
*
3110333 TTCTTTTA
1 TTTTTTTA
3110341 TTTTTTTA
1 TTTTTTTA
3110349 TTTTTTTA
1 TTTTTTTA
3110357 TT
1 TT
3110359 ATTACTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTA
Found at i:3110361 original size:19 final size:17
Alignment explanation
Indices: 3110326--3110358 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3110316 CATTCCCAGG
3110326 TTTTTTTTTCTTTTATT
1 TTTTTTTTTCTTTTATT
*
3110343 TTTTTATTT-TTTTATT
1 TTTTTTTTTCTTTTATT
3110359 ATTACTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTTTTCTTTTATT
Found at i:3110423 original size:6 final size:6
Alignment explanation
Indices: 3110408--3110461 Score: 64
Period size: 5 Copynumber: 9.8 Consensus size: 6
3110398 TGTTTAATAC
*
3110408 TTTTTA -TTTTA TTTTTA -TTTT- TCTTTA TTTTTA TTTTTA -TTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
3110452 -TTTTA TTTTT
1 TTTTTA TTTTT
3110462 TTAAATAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 22 0.52
6 20 0.48
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:3110434 original size:16 final size:16
Alignment explanation
Indices: 3110408--3110461 Score: 74
Period size: 16 Copynumber: 3.3 Consensus size: 16
3110398 TGTTTAATAC
3110408 TTTTTATTTTATTTTTA
1 TTTTTA-TTTATTTTTA
*
3110425 TTTTTCTTTATTTTTA
1 TTTTTATTTATTTTTA
3110441 TTTTTATTT-TATTTTA
1 TTTTTATTTAT-TTTTA
3110457 TTTTT
1 TTTTT
3110462 TTAAATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 1 0.03
16 28 0.82
17 5 0.15
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTATTTATTTTTA
Found at i:3110442 original size:22 final size:22
Alignment explanation
Indices: 3110409--3110461 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
3110399 GTTTAATACT
3110409 TTTTA-TTTTATTTTTATTTT-
1 TTTTATTTTTATTTTTATTTTA
3110429 TCTTTATTTTTATTTTTATTTTA
1 T-TTTATTTTTATTTTTATTTTA
3110452 TTTTATTTTT
1 TTTTATTTTT
3110462 TTAAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 1 0.03
21 4 0.13
22 24 0.80
23 1 0.03
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTATTTTTATTTTTATTTTA
Found at i:3120922 original size:19 final size:18
Alignment explanation
Indices: 3120898--3120957 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 18
3120888 ATTATGCTTG
3120898 AAAAAAA-GAAAAAATGA
1 AAAAAAATGAAAAAATGA
3120915 AATGAAAAATG-AAAAATGA
1 AA--AAAAATGAAAAAATGA
3120934 AAAAAAATGAAAAAAATGA
1 AAAAAAATG-AAAAAATGA
3120953 AAAAA
1 AAAAA
3120958 GAAAAAAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
17 9 0.24
19 28 0.74
20 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (18 bp):
AAAAAAATGAAAAAATGA
Found at i:3120965 original size:19 final size:19
Alignment explanation
Indices: 3120926--3120971 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3120916 ATGAAAAATG
*
3120926 AAAAATGAAAAAAAATGAA
1 AAAAATGAAAAAAAATAAA
*
3120945 AAAAATGAAAAAAGA-AAA
1 AAAAATGAAAAAAAATAAA
*
3120963 AAAAGTGAA
1 AAAAATGAA
3120972 TGAAAAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (19 bp):
AAAAATGAAAAAAAATAAA
Found at i:3122036 original size:41 final size:42
Alignment explanation
Indices: 3121939--3122162 Score: 177
Period size: 47 Copynumber: 5.1 Consensus size: 42
3121929 CAAGGAGCCA
* *
3121939 TTTATTTTCAAAA-TCGTTGAGCTTCTGATTAAAGGAGCTTTG
1 TTTATTTTCAAAAGTCGTAGAGCCTCTGATTAAAGGAGC-TTG
*
3121981 TTTATCTTTC-AAAGTCGTAGAGCCTCTGATTAAAAGAGC-TG
1 TTTAT-TTTCAAAAGTCGTAGAGCCTCTGATTAAAGGAGCTTG
* * * *
3122022 TTTATTTCCAAAAGTCGTTGAGCCTTTGATTAGAGGAGCTTTG
1 TTTATTTTCAAAAGTCGTAGAGCCTCTGATTAAAGGAGC-TTG
* * *
3122065 TTTATTTATTTTCAAAAGTCGTAGAGCCTTTGATTAGA-GAGCTTTA
1 ----TTTATTTTCAAAAGTCGTAGAGCCTCTGATTAAAGGAGC-TTG
* * * *
3122111 TTTATTTATTTCCAAAAGTCATTGAGCCTTTGATTAGAGGAGCTCTG
1 TTTA--T-TTT-CAAAAGTCGTAGAGCCTCTGATTAAAGGAGCT-TG
3122158 TTTAT
1 TTTAT
3122163 AATCGTTGAG
Statistics
Matches: 153, Mismatches: 14, Indels: 27
0.79 0.07 0.14
Matches are distributed among these distances:
40 3 0.02
41 32 0.21
42 12 0.08
43 28 0.18
44 1 0.01
45 4 0.03
46 32 0.21
47 41 0.27
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.41
Consensus pattern (42 bp):
TTTATTTTCAAAAGTCGTAGAGCCTCTGATTAAAGGAGCTTG
Found at i:3122085 original size:47 final size:47
Alignment explanation
Indices: 3121938--3122162 Score: 242
Period size: 46 Copynumber: 5.0 Consensus size: 47
3121928 TCAAGGAGCC
*
3121938 ATTTATTTTCAAAA-TCGTTGAG-CTTCTGATTAAAGGAGCTTTGTTT
1 ATTTATTTTCAAAAGTCGTTGAGCCTT-TGATTAGAGGAGCTTTGTTT
* * * * *
3121984 A--T-CTTTC-AAAGTCGTAGAGCCTCTGATTAAAAGAGC--TG---
1 ATTTATTTTCAAAAGTCGTTGAGCCTTTGATTAGAGGAGCTTTGTTT
*
3122022 -TTTATTTCCAAAAGTCGTTGAGCCTTTGATTAGAGGAGCTTTGTTT
1 ATTTATTTTCAAAAGTCGTTGAGCCTTTGATTAGAGGAGCTTTGTTT
* *
3122068 ATTTATTTTCAAAAGTCGTAGAGCCTTTGATTAGA-GAGCTTTATTT
1 ATTTATTTTCAAAAGTCGTTGAGCCTTTGATTAGAGGAGCTTTGTTT
* * *
3122114 ATTTATTTCCAAAAGTCATTGAGCCTTTGATTAGAGGAGCTCTGTTT
1 ATTTATTTTCAAAAGTCGTTGAGCCTTTGATTAGAGGAGCTTTGTTT
3122161 AT
1 AT
3122163 AATCGTTGAG
Statistics
Matches: 148, Mismatches: 18, Indels: 25
0.77 0.09 0.13
Matches are distributed among these distances:
39 1 0.01
40 3 0.02
41 27 0.18
42 3 0.02
43 25 0.17
44 3 0.02
46 43 0.29
47 43 0.29
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (47 bp):
ATTTATTTTCAAAAGTCGTTGAGCCTTTGATTAGAGGAGCTTTGTTT
Found at i:3122141 original size:93 final size:85
Alignment explanation
Indices: 3121933--3122162 Score: 261
Period size: 93 Copynumber: 2.6 Consensus size: 85
3121923 AATCGTCAAG
* * *
3121933 GAGCCATTTATTTTCAAAA-TCGTTGAG-CTTCTGATTAAAGGAGCTTTGTTTA-TCTTTCAAAG
1 GAGCTATTTATTTCCAAAAGTCGTTGAGCCTT-TGATTAGAGGAGCTTTGTTTATTCTTTCAAAG
3121995 TCGTAGAGCCTCTGATTAAAA
65 TCGTAGAGCCTCTGATTAAAA
* *
3122016 GAGCTGTTTATTTCCAAAAGTCGTTGAGCCTTTGATTAGAGGAGCTTTGTTTATTTATTTTCAAA
1 GAGCTATTTATTTCCAAAAGTCGTTGAGCCTTTGATTAGAGGAGCTTTGTTTA-TT-CTTTC-AA
* *
3122081 AGTCGTAGAGCCTTTGATT-AGA
63 AGTCGTAGAGCCTCTGATTAAAA
* *
3122103 GAGCTTTATTTATTTATTTCCAAAAGTCATTGAGCCTTTGATTAGAGGAGCTCTGTTTAT
1 GAGC------TATTTATTTCCAAAAGTCGTTGAGCCTTTGATTAGAGGAGCTTTGTTTAT
3122163 AATCGTTGAG
Statistics
Matches: 125, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
83 16 0.13
84 28 0.22
85 3 0.02
86 1 0.01
87 10 0.08
88 20 0.16
92 1 0.01
93 46 0.37
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.40
Consensus pattern (85 bp):
GAGCTATTTATTTCCAAAAGTCGTTGAGCCTTTGATTAGAGGAGCTTTGTTTATTCTTTCAAAGT
CGTAGAGCCTCTGATTAAAA
Found at i:3122388 original size:7 final size:6
Alignment explanation
Indices: 3122381--3122554 Score: 67
Period size: 6 Copynumber: 27.8 Consensus size: 6
3122371 TATTTCGTAT
* * *
3122381 TTTATA TTTATA TTTATG TTT-TA -TTATTA TTTTATTA TTTATC TTATGTA
1 TTTATA TTTATA TTTATA TTTATA TTTA-TA -TTTA-TA TTTATA TT-TATA
* * *
3122431 TTTAT- TATT-TA TTTATT TTTACTA -TT-TA TTAATA TTTATTAA TTTATT
1 TTTATA T-TTATA TTTATA TTTA-TA TTTATA TTTATA TTTA-T-A TTTATA
* *
3122479 TTTTTA TTAATA TTTATA --TATA TTTATTA TTTATCTA TTTATA TATTATAA
1 TTTATA TTTATA TTTATA TTTATA TTTA-TA TTTA--TA TTTATA T-TTAT-A
* *
3122530 TTTATC TGTTAATA TTTTTA TTTAT
1 TTTATA T-TT-ATA TTTATA TTTAT
3122555 CTTATTATTT
Statistics
Matches: 126, Mismatches: 21, Indels: 42
0.67 0.11 0.22
Matches are distributed among these distances:
4 8 0.06
5 6 0.05
6 61 0.48
7 29 0.23
8 22 0.17
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:3122420 original size:31 final size:32
Alignment explanation
Indices: 3122378--3122527 Score: 125
Period size: 31 Copynumber: 4.7 Consensus size: 32
3122368 TTTTATTTCG
3122378 TATTTTA-TATTTATATTTATGT-TTTATTAT
1 TATTTTATTATTTATATTTATGTATTTATTAT
*
3122408 TATTTTATTATTTAT-CTTATGTATTTATTAT
1 TATTTTATTATTTATATTTATGTATTTATTAT
*
3122439 T-TATTTATT-TTTACTATTTATTAATATTTATTAATT
1 TAT-TTTATTATTTA-TATTTA-T-GTATTTATT-A-T
* * * *
3122475 TATTTTTTTATTAATATTTATATATAT-TTAT
1 TATTTTATTATTTATATTTATGTATTTATTAT
3122506 TA-TTTATCTATTTATATATTAT
1 TATTTTAT-TATTTATAT-TTAT
3122528 AATTTATCTG
Statistics
Matches: 99, Mismatches: 8, Indels: 24
0.76 0.06 0.18
Matches are distributed among these distances:
30 22 0.22
31 34 0.34
32 8 0.08
33 3 0.03
34 13 0.13
35 2 0.02
36 13 0.13
37 4 0.04
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.67
Consensus pattern (32 bp):
TATTTTATTATTTATATTTATGTATTTATTAT
Found at i:3122436 original size:4 final size:4
Alignment explanation
Indices: 3122391--3122564 Score: 78
Period size: 4 Copynumber: 42.2 Consensus size: 4
3122381 TTTATATTTA
* *
3122391 TATT TATG T-TT TA-T TA-T TATT T-TAT TATT TATCT TATG TATT TA-T
1 TATT TATT TATT TATT TATT TATT TAT-T TATT TAT-T TATT TATT TATT
* *
3122436 TATT TATT TATT T-TT ACTATT TATT AATATT TATT AATT TATT TTTT
1 TATT TATT TATT TATT --TATT TATT --TATT TATT TATT TATT TATT
* *
3122483 TATT AATATT TATAT ATATT TA-T TATT TATC TATT TATA TATT ATAATT
1 TATT --TATT TAT-T -TATT TATT TATT TATT TATT TATT TATT -T-ATT
* * *
3122532 TATC TGTT AATAT T-TT TATT TATCT TA-T TATT T
1 TATT TATT TAT-T TATT TATT TAT-T TATT TATT T
3122565 TCTTTTAATT
Statistics
Matches: 130, Mismatches: 18, Indels: 44
0.68 0.09 0.23
Matches are distributed among these distances:
3 22 0.17
4 78 0.60
5 14 0.11
6 16 0.12
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (4 bp):
TATT
Found at i:3122446 original size:42 final size:42
Alignment explanation
Indices: 3122400--3122534 Score: 114
Period size: 42 Copynumber: 3.4 Consensus size: 42
3122390 ATATTTATGT
3122400 TTTATTATTAT-TTTATTATTTATCTTATGTATTTATTATTTA
1 TTTATTATTATATTTATTATTTATCTTAT-TATTTATTATTTA
* *
3122442 TTTATTTTTACTATTTATTA-ATAT-TTATTAATTTA-T-TTT-
1 TTTATTATTA-TATTTATTATTTATCTTATT-ATTTATTATTTA
*
3122481 TTTATTA--ATATTTA-TATATAT-TTATTATTTATCTATTTA
1 TTTATTATTATATTTATTATTTATCTTATTATTTAT-TATTTA
*
3122520 TATATTA-TA-ATTTAT
1 TTTATTATTATATTTAT
3122535 CTGTTAATAT
Statistics
Matches: 79, Mismatches: 4, Indels: 22
0.75 0.04 0.21
Matches are distributed among these distances:
35 7 0.09
36 15 0.19
37 2 0.03
38 3 0.04
39 17 0.22
40 4 0.05
41 2 0.03
42 18 0.23
43 4 0.05
44 7 0.09
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (42 bp):
TTTATTATTATATTTATTATTTATCTTATTATTTATTATTTA
Found at i:3122466 original size:10 final size:10
Alignment explanation
Indices: 3122436--3122507 Score: 61
Period size: 10 Copynumber: 7.9 Consensus size: 10
3122426 ATGTATTTAT
3122436 TATTTATT--
1 TATTTATTAA
*
3122444 TATTT-TTAC
1 TATTTATTAA
3122453 TATTTATTAA
1 TATTTATTAA
3122463 TATTTATT-A
1 TATTTATTAA
3122472 -ATTTATT--
1 TATTTATTAA
*
3122479 TTTTTATTAA
1 TATTTATTAA
3122489 TATTTA-TATA
1 TATTTATTA-A
3122499 TATTTATTA
1 TATTTATTA
3122508 TTTATCTATT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
7 2 0.04
8 18 0.34
9 8 0.15
10 23 0.43
11 2 0.04
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (10 bp):
TATTTATTAA
Found at i:3122544 original size:22 final size:22
Alignment explanation
Indices: 3122402--3122561 Score: 75
Period size: 22 Copynumber: 7.2 Consensus size: 22
3122392 ATTTATGTTT
* *
3122402 TATTATTATTTTATTATTTATC
1 TATTAATATATTATTATTTATC
*
3122424 TTATGT-ATTTATTATTTATTTAT-
1 -TAT-TAATATATTA-TTATTTATC
* * * *
3122447 TTTTACTAT-TTATTA-ATATT
1 TATTAATATATTATTATTTATC
* *
3122467 TATTAATTTATT-TT-TTTATTAA
1 TATTAATATATTATTATTTA-T-C
3122489 TATTTATATATATTTATTATTTATC
1 TA-TTA-ATATA-TTATTATTTATC
* *
3122514 TATTTATATATTATAATTTATC
1 TATTAATATATTATTATTTATC
*
3122536 TGTTAATAT-TT-TTATTTATC
1 TATTAATATATTATTATTTATC
3122556 TTATTA
1 -TATTA
3122562 TTTTCTTTTA
Statistics
Matches: 103, Mismatches: 20, Indels: 30
0.67 0.13 0.20
Matches are distributed among these distances:
19 3 0.03
20 21 0.20
21 13 0.13
22 24 0.23
23 16 0.16
24 15 0.15
25 4 0.04
26 3 0.03
27 4 0.04
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (22 bp):
TATTAATATATTATTATTTATC
Found at i:3123449 original size:16 final size:15
Alignment explanation
Indices: 3123430--3123460 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
3123420 TTTTTAGTTT
3123430 TTATTTATTATTATTA
1 TTATTTATTA-TATTA
3123446 TTATTTATTATATTA
1 TTATTTATTATATTA
3123461 GAATTGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTTATTATATTA
Found at i:3123486 original size:5 final size:5
Alignment explanation
Indices: 3123476--3123528 Score: 61
Period size: 5 Copynumber: 9.8 Consensus size: 5
3123466 GTTTAATACT
*
3123476 TTTTA TTTTA TTTTTA TTTTCA TTTTTA TTTCA TTTTTA TTTTA TTTTA
1 TTTTA TTTTA -TTTTA TTTT-A -TTTTA TTTTA -TTTTA TTTTA TTTTA
3123525 TTTT
1 TTTT
3123529 CTTTAAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 27 0.64
6 11 0.26
7 4 0.10
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:3123490 original size:6 final size:6
Alignment explanation
Indices: 3123475--3123528 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
3123465 TGTTTAATAC
* *
3123475 TTTTTA -TTTTA TTTTTA TTTTCA TTTTTA -TTTCA TTTTTA -TTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
3123520 -TTTTA TTTT
1 TTTTTA TTTT
3123529 CTTTAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 19 0.46
6 22 0.54
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:3123491 original size:11 final size:11
Alignment explanation
Indices: 3123475--3123528 Score: 83
Period size: 11 Copynumber: 4.9 Consensus size: 11
3123465 TGTTTAATAC
3123475 TTTTTATTTTA
1 TTTTTATTTTA
3123486 TTTTTATTTTCA
1 TTTTTATTTT-A
*
3123498 TTTTTATTTCA
1 TTTTTATTTTA
3123509 TTTTTATTTTA
1 TTTTTATTTTA
3123520 -TTTTATTTT
1 TTTTTATTTT
3123529 CTTTAAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
10 9 0.22
11 21 0.52
12 10 0.25
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:3123670 original size:115 final size:116
Alignment explanation
Indices: 3123545--3123756 Score: 317
Period size: 115 Copynumber: 1.8 Consensus size: 116
3123535 ATAAAATTAA
3123545 AAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTT-GAAAAT-AAGCTTTCT-AAA
1 AAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTT-CTTCGAAAATAAAG-TTTCTAAAA
*
3123607 AATATTTT-TGGAGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATAAACTTTCT
64 AATATTTTGT-GA-AAAAGTTAAAAGTATTAATTTTCCTTGAAAATAAACTTTCT
* * *
3123661 AAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATTAATTTTCTTCGAAATTAAAGTTTCTAAAAAA
1 AAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTCGAAAATAAAGTTTCTAAAAAA
3123725 TATTTTGTGAAAAAGTTAAAAGTATTAATTTT
66 TATTTTGTGAAAAAGTTAAAAGTATTAATTTT
3123757 TCCTGTACAA
Statistics
Matches: 88, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
114 3 0.03
115 63 0.72
116 21 0.24
117 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (116 bp):
AAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTCGAAAATAAAGTTTCTAAAAAA
TATTTTGTGAAAAAGTTAAAAGTATTAATTTTCCTTGAAAATAAACTTTCT
Found at i:3123758 original size:58 final size:57
Alignment explanation
Indices: 3123545--3123756 Score: 297
Period size: 57 Copynumber: 3.7 Consensus size: 57
3123535 ATAAAATTAA
*
3123545 AAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGCTTTCT
1 AAAAA-ATATTTTTGAG-AAAAGTTGAAAGTATTAATTTTCCTTGAAAATAAAG-TTTCT
*
3123604 -AAAAATATTTTTGGAGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATAAACTTTCT
1 AAAAAATATTTTT-GAGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATAAAGTTTCT
*
3123661 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATTAATTTT-CTTCGAAATTAAAGTTTCT
1 AAAAAATATTTTTGA-GAAAAGTTGAAAGTATTAATTTTCCTT-GAAAATAAAGTTTCT
*
3123719 AAAAAATATTTTGTGA-AAAAGTTAAAAGTATTAATTTT
1 AAAAAATATTTT-TGAGAAAAGTTGAAAGTATTAATTTT
3123757 TCCTGTACAA
Statistics
Matches: 142, Mismatches: 5, Indels: 14
0.88 0.03 0.09
Matches are distributed among these distances:
57 70 0.49
58 69 0.49
59 3 0.02
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (57 bp):
AAAAAATATTTTTGAGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATAAAGTTTCT
Found at i:3129628 original size:119 final size:119
Alignment explanation
Indices: 3129414--3129769 Score: 428
Period size: 119 Copynumber: 3.0 Consensus size: 119
3129404 TTTGTCTTGG
* * * *
3129414 TCACTTGATCTTGGTTCAGTCTAAATCATTTCTTATGATTCGTGGTTCTGTCTCGACCATTTATT
1 TCACTTGATCTTGGCTCAGTCCAAATCATTTCTTATGATTCGTGGTTCTGTCCCGATCATTTATT
* * * * *
3129479 CTCAACCTTGACTTGGTC-CGAGTTGCTTTATTTTGACTTATGGTTTCATCTCGA
66 CTTAACCTTGACTCGATCTTG-GTTGTTTTATTTTGACTTATGGTTTCATCTCGA
*
3129533 TCACTTGATCTTGGCTCAGTCCAAATCATTTCTTATGATTCGTGGTTCCGTCCCGATCATTTATT
1 TCACTTGATCTTGGCTCAGTCCAAATCATTTCTTATGATTCGTGGTTCTGTCCCGATCATTTATT
* * * *
3129598 CTTAACCTTGACTCGATCTTGGTTGTTTTATTTTGACTTGTAGTTTCATCTTGG
66 CTTAACCTTGACTCGATCTTGGTTGTTTTATTTTGACTTATGGTTTCATCTCGA
* * * * * * *
3129652 TCACTTGGTCTTGGCTCAGTCCACATAATTTTTTATGATTCGTGGTTCTATCCCAATCATTCATT
1 TCACTTGATCTTGGCTCAGTCCAAATCATTTCTTATGATTCGTGGTTCTGTCCCGATCATTTATT
* * * * ** * *
3129717 TTTTACCTCGACTCGATCTTGATCATTTTA-TTTGACTCATGGTTTAATCTCGA
66 CTTAACCTTGACTCGATCTTGGTTGTTTTATTTTGACTTATGGTTTCATCTCGA
3129770 CCATCTAACC
Statistics
Matches: 202, Mismatches: 34, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
118 17 0.08
119 184 0.91
120 1 0.00
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (119 bp):
TCACTTGATCTTGGCTCAGTCCAAATCATTTCTTATGATTCGTGGTTCTGTCCCGATCATTTATT
CTTAACCTTGACTCGATCTTGGTTGTTTTATTTTGACTTATGGTTTCATCTCGA
Found at i:3129984 original size:3 final size:3
Alignment explanation
Indices: 3129970--3130004 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3129960 AATTAGATTT
*
3129970 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3130005 TGCTCAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3130354 original size:18 final size:20
Alignment explanation
Indices: 3130323--3130359 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3130313 TTTATGATTA
3130323 TGGGAGTGAATTC-AGGTTT
1 TGGGAGTGAATTCAAGGTTT
*
3130342 TGGG-GTGAGTTCAAGGTT
1 TGGGAGTGAATTCAAGGTT
3130360 GTAGAAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.19, C:0.05, G:0.41, T:0.35
Consensus pattern (20 bp):
TGGGAGTGAATTCAAGGTTT
Found at i:3130806 original size:5 final size:5
Alignment explanation
Indices: 3130776--3130822 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
3130766 TTTTTTTAAT
* * *
3130776 TTTTA TTTTA TTTTA -TTT- TTTGA TTTCA TTTGA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
3130823 TAATGCATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 5 0.14
5 31 0.86
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:3136099 original size:12 final size:12
Alignment explanation
Indices: 3136078--3136108 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3136068 TATTTAATGA
*
3136078 TAAAAATTTTAT
1 TAAAATTTTTAT
3136090 TAAAATTTTTAT
1 TAAAATTTTTAT
3136102 TAAAATT
1 TAAAATT
3136109 ACCTATCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATTTTTAT
Found at i:3137872 original size:21 final size:21
Alignment explanation
Indices: 3137842--3137889 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3137832 TCCAGAAAAT
* * *
3137842 GGATCGATCCCCCCACATAAG
1 GGATCAATCCCCCCAAAGAAG
*
3137863 GGATCAATCCCCTCAAAGAAG
1 GGATCAATCCCCCCAAAGAAG
3137884 GGATCA
1 GGATCA
3137890 TTGGGTAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.31, G:0.21, T:0.15
Consensus pattern (21 bp):
GGATCAATCCCCCCAAAGAAG
Found at i:3152880 original size:24 final size:23
Alignment explanation
Indices: 3152853--3152898 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3152843 TTACTGAAAA
*
3152853 TTAAAAAATTAATGATAAATTTAT
1 TTAAAAAA-TAATAATAAATTTAT
*
3152877 TTAAAATATAATAATAAATTTA
1 TTAAAAAATAATAATAAATTTA
3152899 AATCATAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TTAAAAAATAATAATAAATTTAT
Found at i:3155075 original size:2 final size:2
Alignment explanation
Indices: 3155064--3155101 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3155054 AAGAGGTTTA
*
3155064 AT AT -T AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3155102 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3156744 original size:5 final size:5
Alignment explanation
Indices: 3156736--3156789 Score: 56
Period size: 5 Copynumber: 10.6 Consensus size: 5
3156726 GATCACAGGT
* * *
3156736 TTTTA TTTTTA TTTTTA TTTTA TTTT- TTTGA TTTGA TTTGA TTTTA TTTTA
1 TTTTA -TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
3156787 TTT
1 TTT
3156790 CTAATCCATT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
4 3 0.07
5 31 0.69
6 11 0.24
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:3156756 original size:11 final size:11
Alignment explanation
Indices: 3156735--3156819 Score: 52
Period size: 11 Copynumber: 7.9 Consensus size: 11
3156725 CGATCACAGG
3156735 TTTTTATTTTTA
1 TTTTTA-TTTTA
3156747 TTTTTATTTTA
1 TTTTTATTTTA
*
3156758 -TTTT-TTTGA
1 TTTTTATTTTA
* *
3156767 -TTTGATTTGA
1 TTTTTATTTTA
3156777 -TTTTATTTTA
1 TTTTTATTTTA
* * **
3156787 TTTCTAATCCA
1 TTTTTATTTTA
3156798 TTTCTTATTTTA
1 TTT-TTATTTTA
*
3156810 TTATTATTTT
1 TTTTTATTTT
3156820 TTTAATAAAT
Statistics
Matches: 57, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
9 7 0.12
10 17 0.30
11 21 0.37
12 12 0.21
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.73
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:3160495 original size:13 final size:13
Alignment explanation
Indices: 3160477--3160525 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
3160467 AAGTTGTCTA
*
3160477 ATTTTAGTAACTT
1 ATTTTAATAACTT
3160490 ATTTTAATAAATCTT
1 ATTTTAAT-AA-CTT
*
3160505 ATTATAATAACTT
1 ATTTTAATAACTT
*
3160518 TTTTTAAT
1 ATTTTAAT
3160526 CAATAGTCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 16 0.53
14 4 0.13
15 10 0.33
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (13 bp):
ATTTTAATAACTT
Found at i:3168160 original size:17 final size:17
Alignment explanation
Indices: 3168138--3168188 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 17
3168128 AATTTTTTGA
3168138 ATATATTTAAGTTAAAT
1 ATATATTTAAGTTAAAT
*
3168155 ATATATCTAATAATTTAAAT
1 ATATAT-T--TAAGTTAAAT
3168175 ATATATTTAAGTTA
1 ATATATTTAAGTTA
3168189 GACTCATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 12 0.41
18 1 0.03
19 1 0.03
20 15 0.52
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (17 bp):
ATATATTTAAGTTAAAT
Found at i:3174272 original size:10 final size:10
Alignment explanation
Indices: 3174259--3174300 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
3174249 TTTTTTTCAT
*
3174259 TTTTATTTTA
1 TTTTATTTGA
3174269 TTTT-TTTGA
1 TTTTATTTGA
*
3174278 TTTGATTTGA
1 TTTTATTTGA
*
3174288 TTTTATTTTA
1 TTTTATTTGA
3174298 TTT
1 TTT
3174301 CTAACCCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.26
10 20 0.74
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (10 bp):
TTTTATTTGA
Found at i:3174285 original size:19 final size:20
Alignment explanation
Indices: 3174244--3174291 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
3174234 GATCACAGGT
* *
3174244 TTTTTTTTTTTTCATTTTTA
1 TTTTATTTTTTTCATTTTGA
*
3174264 TTTTATTTTTTTGA-TTTGA
1 TTTTATTTTTTTCATTTTGA
*
3174283 TTTGATTTT
1 TTTTATTTT
3174292 ATTTTATTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.12, C:0.02, G:0.06, T:0.79
Consensus pattern (20 bp):
TTTTATTTTTTTCATTTTGA
Found at i:3194060 original size:12 final size:12
Alignment explanation
Indices: 3194011--3194063 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
3194001 AAATTAAAAT
*
3194011 TTTAATGATAAA
1 TTTAATAATAAA
*
3194023 TTTATTTAA-AAA
1 TTTA-ATAATAAA
* *
3194035 TATAATAGTAAA
1 TTTAATAATAAA
3194047 TTTAATAATAAA
1 TTTAATAATAAA
3194059 TTTAA
1 TTTAA
3194064 ATCATAGACG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
11 2 0.06
12 28 0.88
13 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (12 bp):
TTTAATAATAAA
Found at i:3196318 original size:2 final size:2
Alignment explanation
Indices: 3196311--3196347 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3196301 GGTTTAATCT
*
3196311 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3196348 GGATAGGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3197438 original size:21 final size:21
Alignment explanation
Indices: 3197413--3197453 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3197403 TAATATTCAT
* *
3197413 AAATATTAATAATAAAATTTA
1 AAATAATAAAAATAAAATTTA
*
3197434 AAATAATAAAAATAATATTT
1 AAATAATAAAAATAAAATTT
3197454 TTAAAAAATT
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATAATAAAAATAAAATTTA
Found at i:3198655 original size:44 final size:43
Alignment explanation
Indices: 3198519--3198704 Score: 146
Period size: 44 Copynumber: 4.3 Consensus size: 43
3198509 TTTTTTTATT
* * ***
3198519 TTTTAAAAAATTTAGAAA-GCTCTTCTAAACAGAGGCTCAA-TTT
1 TTTT-AAAAATTTA-AAAGGCTCTTCTAAACAAAAGCTCAACAAC
* * * * * *
3198562 TTTTAAAAACTTTAAAAAGGCTCCTCTCAGC-AAAGACTCGATAAA
1 TTTTAAAAA-TTT-AAAAGGCTCTTCTAAACAAAAG-CTCAACAAC
*
3198607 TTTTAAAAATTTAAAAGGACTCTTCTAAACAAAAGCTCAACGAC
1 TTTTAAAAATTTAAAAGG-CTCTTCTAAACAAAAGCTCAACAAC
* * * *
3198651 TTTTAAAAATATAAATGGCTCTTCTAAGCAAATGCTCAACAAC
1 TTTTAAAAATTTAAAAGGCTCTTCTAAACAAAAGCTCAACAAC
3198694 -TTTAAAAATTT
1 TTTTAAAAATTT
3198705 TATTTTGAAA
Statistics
Matches: 114, Mismatches: 22, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
42 15 0.13
43 40 0.35
44 46 0.40
45 13 0.11
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (43 bp):
TTTTAAAAATTTAAAAGGCTCTTCTAAACAAAAGCTCAACAAC
Found at i:3198688 original size:43 final size:44
Alignment explanation
Indices: 3198607--3198702 Score: 133
Period size: 43 Copynumber: 2.2 Consensus size: 44
3198597 ACTCGATAAA
* *
3198607 TTTTAAAAATTTAAAAGGACTCTTCTAAACAAAAGCTCAACGAC
1 TTTTAAAAATATAAAAGGACTCTTCTAAACAAAAGCTCAACAAC
* * *
3198651 TTTTAAAAATATAAATGG-CTCTTCTAAGCAAATGCTCAACAAC
1 TTTTAAAAATATAAAAGGACTCTTCTAAACAAAAGCTCAACAAC
3198694 -TTTAAAAAT
1 TTTTAAAAAT
3198703 TTTATTTTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 9 0.19
43 22 0.47
44 16 0.34
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (44 bp):
TTTTAAAAATATAAAAGGACTCTTCTAAACAAAAGCTCAACAAC
Found at i:3199065 original size:103 final size:102
Alignment explanation
Indices: 3198669--3199165 Score: 457
Period size: 103 Copynumber: 4.9 Consensus size: 102
3198659 ATATAAATGG
* *
3198669 CTCTTCTAAGCAAATG-CTCAACAACTTTAAAAATTTTAT-TTTGAAAAAGCTCCTCTAAGTACA
1 CTCTTCTAAGCAAA-GACTCAACAACTTTAAAAATTTTATCTTAGAAAAAGCTCCTCTAAGTAGA
*
3198732 -GCTTCAACAACTTTAAAAA--TTTCATCTTAGAAAAAA
65 GGC-TCAACAACTTTAAAAATTTTTCATCTTAAAAAAAA
* * * * *
3198768 CT-TCTCTAAGTAAAGACTCAACAACTTTAAAAA-TTCATCTT-GGAAAAGCTCCTCTAAGCAAA
1 CTCT-TCTAAGCAAAGACTCAACAACTTTAAAAATTTTATCTTAGAAAAAGCTCCTCTAAGTAGA
** * * *
3198830 GATTCAACAACTTTTAAAATTTTT-ATCTTGAAAAAAG
65 GGCTCAACAACTTTAAAAATTTTTCATCTTAAAAAAAA
* * * *
3198867 CT-TATCT-AGACAAAGGCTCAATC-ACTTTAAAAAAATCTTCATCTTGAAAAAAAGGCTCATCT
1 CTCT-TCTAAG-CAAAGACTCAA-CAACTTT--AAAAAT-TTTATCTT-AGAAAAA-GCTCCTCT
* *
3198929 -AGACAGAGGCTCAACAACTTTAAAAATTCTTCATCTTTAAAAAAAA
58 AAG-TAGAGGCTCAACAACTTTAAAAATTTTTCATC-TTAAAAAAAA
* * * * * *
3198975 CTCTTCTAAGCAGAGAATCAACAATTTTAAAAATTTTATCTTAGAAAACGCTCCTCTAATTATAG
1 CTCTTCTAAGCAAAGACTCAACAACTTTAAAAATTTTATCTTAGAAAAAGCTCCTCTAAGTAGAG
*
3199040 GCTCAACAACTTAAAAAATTTTTCATCTTAAAAAAAAA
66 GCTCAACAACTTTAAAAATTTTTCATCTT-AAAAAAAA
* *
3199078 CTCATT-TAAGCAGAAG-CTCAACAACTTTAAAAATTTTATTTTAGAAAAAGCTCATCTAAGTAG
1 CTC-TTCTAAGCA-AAGACTCAACAACTTTAAAAATTTTATCTTAGAAAAAGCTCCTCTAAGTAG
* * * *
3199141 AGGCTCGATAATTTTAAGAATTTTT
64 AGGCTCAACAACTTTAAAAATTTTT
3199166 AACTTGAAAA
Statistics
Matches: 323, Mismatches: 50, Indels: 46
0.77 0.12 0.11
Matches are distributed among these distances:
98 41 0.13
99 60 0.19
100 4 0.01
101 5 0.02
102 2 0.01
103 120 0.37
104 10 0.03
105 13 0.04
106 36 0.11
107 4 0.01
108 25 0.08
109 3 0.01
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.32
Consensus pattern (102 bp):
CTCTTCTAAGCAAAGACTCAACAACTTTAAAAATTTTATCTTAGAAAAAGCTCCTCTAAGTAGAG
GCTCAACAACTTTAAAAATTTTTCATCTTAAAAAAAA
Found at i:3199157 original size:50 final size:50
Alignment explanation
Indices: 3198668--3199211 Score: 336
Period size: 50 Copynumber: 10.7 Consensus size: 50
3198658 AATATAAATG
* * *
3198668 GCTCTTCTAAGCAAATGCTCAACAACTTTAAAAATTTTATTTT-GAAAAA
1 GCTCATCTAAGCAGAGGCTCAACAACTTTAAAAATTTTATTTTAGAAAAA
* * * * *
3198717 GCTCCTCTAAGTACA-GCTTCAACAACTTTAAAAATTTCATCTTAGAAAAA
1 GCTCATCTAAGCAGAGGC-TCAACAACTTTAAAAATTTTATTTTAGAAAAA
* * * * * * *
3198767 ACTTC-TCTAAGTAAAGACTCAACAACTTTAAAAA-TTCATCTT-GGAAAA
1 GC-TCATCTAAGCAGAGGCTCAACAACTTTAAAAATTTTATTTTAGAAAAA
* * ** * *
3198815 GCTCCTCTAAGCAAAGATTCAACAACTTTTAAAATTTTTATCTT-GAAAAAA
1 GCTCATCTAAGCAGAGGCTCAACAAC-TTTAAAAATTTTATTTTAG-AAAAA
* * * * *
3198866 GCTTATCT-AGACAAAGGCTCAATC-ACTTTAAAAAAATCTTCATCTTGAAAAAAA
1 GCTCATCTAAG-CAGAGGCTCAA-CAACTTT--AAAAAT-TTTAT-TTTAGAAAAA
*
3198920 GGCTCATCT-AGACAGAGGCTCAACAACTTTAAAAATTCTTCATCTTTAAAAAAA
1 -GCTCATCTAAG-CAGAGGCTCAACAACTTTAAAAATT-TT-AT-TTTAGAAAAA
* * ** * * *
3198974 ACTCTTCTAAGCAGAGAATCAACAATTTTAAAAATTTTATCTTAGAAAAC
1 GCTCATCTAAGCAGAGGCTCAACAACTTTAAAAATTTTATTTTAGAAAAA
* ** * * * *
3199024 GCTCCTCTAATTATAGGCTCAACAACTTAAAAAATTTTTCATCTTAAAAAAAA
1 GCTCATCTAAGCAGAGGCTCAACAACTTTAAAAA-TTTT-AT-TTTAGAAAAA
* * *
3199077 ACTCATTTAAGCAGAAGCTCAACAACTTTAAAAATTTTATTTTAGAAAAA
1 GCTCATCTAAGCAGAGGCTCAACAACTTTAAAAATTTTATTTTAGAAAAA
* * * * * ** *
3199127 GCTCATCTAAGTAGAGGCTCGATAATTTTAAGAATTTTTAACTT-GAAAACG
1 GCTCATCTAAGCAGAGGCTCAACAACTTTAA-AAATTTTATTTTAGAAAA-A
* *
3199178 GCTCATCT-AGATAAAGGCTCAACAACTTTAAAAA
1 GCTCATCTAAG-CAGAGGCTCAACAACTTTAAAAA
3199212 ATCTCATTTT
Statistics
Matches: 394, Mismatches: 75, Indels: 51
0.76 0.14 0.10
Matches are distributed among these distances:
47 2 0.01
48 27 0.07
49 50 0.13
50 118 0.30
51 65 0.16
52 15 0.04
53 71 0.18
54 21 0.05
55 25 0.06
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (50 bp):
GCTCATCTAAGCAGAGGCTCAACAACTTTAAAAATTTTATTTTAGAAAAA
Found at i:3199183 original size:257 final size:252
Alignment explanation
Indices: 3198679--3199211 Score: 558
Period size: 257 Copynumber: 2.1 Consensus size: 252
3198669 CTCTTCTAAG
* * * * **
3198679 CAAATGCTCAACAACTTTAAAAATTTTATTTTGAAAAAGCTCCTCTAAGTACAGCTTCAACAACT
1 CAAAGGCTCAACAACTTTAAAAATTTTATTTTAAAAAAACTCCTCTAAGCACAGAATCAACAACT
* *
3198744 TTAAAAATTTCATCTTAGAAAAAACTTCTCTAAGTAAAGACTCAACAACTTTAAAAATTCATCTT
66 TTAAAAATTTCATCTTAGAAAAAACTCCTCTAAGTAAAGACTCAACAACTTAAAAAATTCATCTT
** * * * * *
3198809 GGAAAAGCTCCTCTAAGCAAAGATTCAACAACTTTTAAAATTTTTATCTTGAAAAAAGCTTATCT
131 AAAAAAACTCATCTAAGCAAAGACTCAACAACTTTTAAAAATTTTATCTTGAAAAAAGCTCATCT
* *
3198874 AGACAAAGGCTCAATCACTTTAAAAAAATCTTCATCTTGAAAAAAAGGCTCATCTAGA
196 AGACAAAGGCTCAATCAATTTAAAAAAATCTTCAACTTG-AAAAAAGGCTCATCTAGA
* * *
3198932 CAGAGGCTCAACAACTTTAAAAATTCTTCATCTTTAAAAAAAACTCTTCTAAGCAGAGAATCAAC
1 CAAAGGCTCAACAACTTTAAAAATT-TT-AT-TTT-AAAAAAACTCCTCTAAGCACAGAATCAAC
* * ** * * *
3198997 AATTTTAAAAATTTTATCTTAGAAAACGCTCCTCTAATTATAGGCTCAACAACTTAAAAAATTTT
62 AACTTTAAAAATTTCATCTTAGAAAAAACTCCTCTAAGTAAAGACTCAACAACTTAAAAAA---T
* *
3199062 TCATCTTAAAAAAAAACTCATTTAAGCAGAAG-CTCAACAAC-TTTAAAAATTTTAT-TTTAGAA
124 TCATCTT--AAAAAAACTCATCTAAGCA-AAGACTCAACAACTTTTAAAAATTTTATCTTGA-AA
* * * * * * * *
3199124 AAAGCTCATCTA-AGTAGAGGCTCGAT-AATTT-TAAGAATTTTTAACTTG-AAAACGGCTCATC
185 AAAGCTCATCTAGA-CAAAGGCTCAATCAATTTAAAAAAATCTTCAACTTGAAAAAAGGCTCATC
3199185 TAGA
249 TAGA
*
3199189 TAAAGGCTCAACAACTTTAAAAA
1 CAAAGGCTCAACAACTTTAAAAA
3199212 ATCTCATTTT
Statistics
Matches: 229, Mismatches: 39, Indels: 20
0.80 0.14 0.07
Matches are distributed among these distances:
253 23 0.10
254 2 0.01
255 2 0.01
256 3 0.01
257 111 0.48
259 12 0.05
260 16 0.07
261 35 0.15
262 22 0.10
263 3 0.01
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.31
Consensus pattern (252 bp):
CAAAGGCTCAACAACTTTAAAAATTTTATTTTAAAAAAACTCCTCTAAGCACAGAATCAACAACT
TTAAAAATTTCATCTTAGAAAAAACTCCTCTAAGTAAAGACTCAACAACTTAAAAAATTCATCTT
AAAAAAACTCATCTAAGCAAAGACTCAACAACTTTTAAAAATTTTATCTTGAAAAAAGCTCATCT
AGACAAAGGCTCAATCAATTTAAAAAAATCTTCAACTTGAAAAAAGGCTCATCTAGA
Found at i:3212470 original size:50 final size:50
Alignment explanation
Indices: 3212351--3212804 Score: 328
Period size: 50 Copynumber: 8.9 Consensus size: 50
3212341 TTCTAAAAGA
* * * *
3212351 AGAATTTTTAAAGTTGTTGAA-CTTCTA-TCAAGAA-GAGCCTTTTCCAAGATA
1 AGAATTTTTAAAGTTGTT-AAGCCTCTACT-AA-AATGAGCCTTTTTC-ATATG
*
3212402 AGAATTTTTAAAGTTGTTAAGCCTCTACTAAAATGAGCGTTTTTCATATG
1 AGAATTTTTAAAGTTGTTAAGCCTCTACTAAAATGAGCCTTTTTCATATG
* * * * *
3212452 AGAATTTTTAAAGTTGTTAAGCTTCTAC-AAAGAGGAACC-TTTTCTAGGATA
1 AGAATTTTTAAAGTTGTTAAGCCTCTACTAAA-ATGAGCCTTTTTC-A-TATG
* * * * * *
3212503 AAAATTTTTAAAGTTGTTGAGCTTTTACTAAGATGAGCCTTTGTCATATG
1 AGAATTTTTAAAGTTGTTAAGCCTCTACTAAAATGAGCCTTTTTCATATG
* * * * * * *
3212553 AGAATTTTTAAAATCGTTAAGCCTTTACCAAGAGGAGCCTTTTTCATATA
1 AGAATTTTTAAAGTTGTTAAGCCTCTACTAAAATGAGCCTTTTTCATATG
* * *
3212603 AGAATTTTTAAAGTTGTTGAGCATCTTAGTTCTACCAAGATGAGCTTTTTTCATATG
1 AGAATTTTTAAAGTTGTTAAGCCTC-TA---CTA--AA-ATGAGCCTTTTTCATATG
* * * *
3212660 AGAATTTTTAAAGTTGTTGAGCCT-TCACCTAAAA-CAGCTTTTTTCATATT
1 AGAATTTTTAAAGTTGTTAAGCCTCT-A-CTAAAATGAGCCTTTTTCATATG
* * * * * *
3212710 AAAATTTTTAAAAGCTGTTAAGCCTCTACTAAGAGGAGTCTTTTTCATTTG
1 AGAATTTTT-AAAGTTGTTAAGCCTCTACTAAAATGAGCCTTTTTCATATG
* * * * * *
3212761 AGAATTTTTAAAGTTATTGAGCTTCTACCAAGATGAGCTTTTTT
1 AGAATTTTTAAAGTTGTTAAGCCTCTACTAAAATGAGCCTTTTT
3212805 TTAGATTTTA
Statistics
Matches: 323, Mismatches: 61, Indels: 39
0.76 0.14 0.09
Matches are distributed among these distances:
49 8 0.02
50 156 0.48
51 103 0.32
52 10 0.03
54 5 0.02
55 1 0.00
56 2 0.01
57 38 0.12
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (50 bp):
AGAATTTTTAAAGTTGTTAAGCCTCTACTAAAATGAGCCTTTTTCATATG
Found at i:3212742 original size:208 final size:202
Alignment explanation
Indices: 3212379--3212772 Score: 458
Period size: 208 Copynumber: 1.9 Consensus size: 202
3212369 GAACTTCTAT
*
3212379 CAAGAAGAGCCTTTTCCAAGATAAGAATTTTTAAAGTTGTTAAGCCTCTACTAAAATGAGCGTTT
1 CAAGAAGAGCCTTTTCCAAGATAAGAATTTTTAAAGTTGTTAAGCATCTACTAAAATGAGCGTTT
*
3212444 TTCATATGAGAATTTTTAAAGTTGTTAAGCTTCTACAAAGAGGAACCTTTTCTAGGATAAAAATT
66 TTCATATGAGAATTTTTAAAGTTGTTAAGCTTCTACAAAGAGCAACCTTTTCTAGGATAAAAATT
* * * * *
3212509 TTTAAAGTTGTTGAGCTTTTACTAAGATGAGCCTTTGTCATATGAGAATTTTTAAAATCGTTAAG
131 TTTAAAGCTGTTAAGCCTCTACTAAGAGGAGCCTTTGTCATATGAGAATTTTTAAAATCGTTAAG
3212574 CCTTTAC
196 CCTTTAC
* * * *
3212581 CAAGAGGAGCCTTTTTC-ATATAAGAATTTTTAAAGTTGTTGAGCATCTTAGTTCTACCAAGATG
1 CAAGAAGAGCCTTTTCCAAGATAAGAATTTTTAAAGTTGTTAAGCATC-TA---CTA--AA-ATG
* * * *
3212645 AGCTTTTTTCATATGAGAATTTTTAAAGTTGTTGAGCCTTC-ACCTAAA-A-C-AGCTTTTTTCA
59 AGCGTTTTTCATATGAGAATTTTTAAAGTTGTTAAG-CTTCTA-C-AAAGAGCAACCTTTTCT-A
* * * * *
3212706 -TATTAAAATTTTTAAAAGCTGTTAAGCCTCTACTAAGAGGAGTCTTTTTCATTTGAGAATTTTT
120 GGATAAAAATTTTT-AAAGCTGTTAAGCCTCTACTAAGAGGAGCCTTTGTCATATGAGAATTTTT
3212770 AAA
184 AAA
3212773 GTTATTGAGC
Statistics
Matches: 160, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
201 27 0.17
202 17 0.11
205 3 0.02
207 20 0.12
208 84 0.52
209 6 0.04
210 3 0.02
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (202 bp):
CAAGAAGAGCCTTTTCCAAGATAAGAATTTTTAAAGTTGTTAAGCATCTACTAAAATGAGCGTTT
TTCATATGAGAATTTTTAAAGTTGTTAAGCTTCTACAAAGAGCAACCTTTTCTAGGATAAAAATT
TTTAAAGCTGTTAAGCCTCTACTAAGAGGAGCCTTTGTCATATGAGAATTTTTAAAATCGTTAAG
CCTTTAC
Found at i:3212804 original size:101 final size:101
Alignment explanation
Indices: 3212351--3212804 Score: 431
Period size: 101 Copynumber: 4.4 Consensus size: 101
3212341 TTCTAAAAGA
* * * *
3212351 AGAATTTTTAAAGTTGTTGAACTTCTATCAAGAAGAGCCTTTTCCA-AGATAAGAATTTTTAAAG
1 AGAATTTTTAAAGTTGTTGAGCTTCTACCAAGAAGAGCCTTTTTCATA-TTAAGAATTTTTAAAG
*
3212415 TTGTTAAGCCTCTACTAAAATGAGCGTTTTTCATATG
65 TTGTTAAGCCTCTACTAAGATGAGCGTTTTTCATATG
* * * * * *
3212452 AGAATTTTTAAAGTTGTTAAGCTTCTACAAAGAGGAACC-TTTTC-TAGGATAAAAATTTTTAAA
1 AGAATTTTTAAAGTTGTTGAGCTTCTACCAAGAAGAGCCTTTTTCATA--TTAAGAATTTTTAAA
* * * * *
3212515 GTTGTTGAGCTTTTACTAAGATGAGCCTTTGTCATATG
64 GTTGTTAAGCCTCTACTAAGATGAGCGTTTTTCATATG
* * * *
3212553 AGAATTTTTAAAATCGTTAAGCCTT-TACCAAGAGGAGCCTTTTTCATA-TAAGAATTTTTAAAG
1 AGAATTTTTAAAGTTGTTGAG-CTTCTACCAAGAAGAGCCTTTTTCATATTAAGAATTTTTAAAG
* * *
3212616 TTGTTGAGCATCTTAGTTCTACCAAGATGAGCTTTTTTCATATG
65 TTGTTAAGC--C-----TCTACTAAGATGAGCGTTTTTCATATG
* *
3212660 AGAATTTTTAAAGTTGTTGAGCCTTC-ACCTAA-AACAGCTTTTTTCATATTAA-AATTTTTAAA
1 AGAATTTTTAAAGTTGTTGAG-CTTCTACC-AAGAAGAGCCTTTTTCATATTAAGAATTTTT-AA
* * *
3212722 AGCTGTTAAGCCTCTACTAAGAGGAGTC-TTTTTCATTTG
63 AGTTGTTAAGCCTCTACTAAGATGAG-CGTTTTTCATATG
* * *
3212761 AGAATTTTTAAAGTTATTGAGCTTCTACCAAGATGAGCTTTTTT
1 AGAATTTTTAAAGTTGTTGAGCTTCTACCAAGAAGAGCCTTTTT
3212805 TTAGATTTTA
Statistics
Matches: 296, Mismatches: 38, Indels: 38
0.80 0.10 0.10
Matches are distributed among these distances:
100 34 0.11
101 166 0.56
102 9 0.03
103 2 0.01
106 1 0.00
107 68 0.23
108 16 0.05
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (101 bp):
AGAATTTTTAAAGTTGTTGAGCTTCTACCAAGAAGAGCCTTTTTCATATTAAGAATTTTTAAAGT
TGTTAAGCCTCTACTAAGATGAGCGTTTTTCATATG
Found at i:3214194 original size:21 final size:21
Alignment explanation
Indices: 3214165--3214205 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3214155 AAATTTTTAA
* *
3214165 AAATATTATTTTTATTATTTT
1 AAATATTATTATTAATATTTT
*
3214186 AAATTTTATTATTAATATTT
1 AAATATTATTATTAATATTT
3214206 ATATAGGTTA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
AAATATTATTATTAATATTTT
Found at i:3215243 original size:17 final size:18
Alignment explanation
Indices: 3215223--3215268 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3215213 ATCTTTTTAA
**
3215223 TAAATTTTAATT-AATTT
1 TAAATTTTAATTAAAAAT
3215240 TAAAATTTT-ATTAAAAAT
1 T-AAATTTTAATTAAAAAT
3215258 TAAATTTTAAT
1 TAAATTTTAAT
3215269 AAGTGATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAAATTTTAATTAAAAAT
Found at i:3217317 original size:23 final size:25
Alignment explanation
Indices: 3217287--3217337 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
3217277 CATTTGCATA
*
3217287 TATTTCTAGTATT-TT-GTTTTTAT
1 TATTTCTAATATTGTTAGTTTTTAT
*
3217310 TATTTCTAATATTGTTATTTTTTAT
1 TATTTCTAATATTGTTAGTTTTTAT
3217335 TAT
1 TAT
3217338 AATTAATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.50
24 2 0.08
25 10 0.42
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.69
Consensus pattern (25 bp):
TATTTCTAATATTGTTAGTTTTTAT
Found at i:3223182 original size:3 final size:3
Alignment explanation
Indices: 3223174--3223263 Score: 128
Period size: 3 Copynumber: 30.3 Consensus size: 3
3223164 TACAGTATAG
3223174 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
3223222 TGT TAT TAT TAT TAC TAT TAT TA- TAT TTT TTT TAT TTT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3223264 TTTTTCTTCT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
2 2 0.03
3 76 0.97
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:3223731 original size:23 final size:23
Alignment explanation
Indices: 3223703--3223751 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3223693 GACTATGAGG
* * *
3223703 TTTTTTGGATTTTTTTAGATTTT
1 TTTTTTGAATTTTTCTAGAATTT
3223726 TTTTTTGAATTTTTCTAGAATTT
1 TTTTTTGAATTTTTCTAGAATTT
3223749 TTT
1 TTT
3223752 GGGTTTGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.71
Consensus pattern (23 bp):
TTTTTTGAATTTTTCTAGAATTT
Found at i:3226184 original size:9 final size:9
Alignment explanation
Indices: 3226170--3226194 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3226160 AATAATATAT
3226170 AAAAATTCA
1 AAAAATTCA
3226179 AAAAATTCA
1 AAAAATTCA
3226188 AAAAATT
1 AAAAATT
3226195 TTTTTTTTAC
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:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAAATTCA
Found at i:3227638 original size:47 final size:48
Alignment explanation
Indices: 3227510--3228082 Score: 547
Period size: 47 Copynumber: 11.9 Consensus size: 48
3227500 AAATTAAAAA
* * * * * * *
3227510 AAAAAAGCTCTTCTTAGCATAGGTTCAATAACTTT-AAAATTTTATTTG
1 AAAAAA-CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTG
* * * *
3227558 AAAAAAGCTCATCTAAGCAAAGGCTCAACAACTTT-AAAATCTCATCTG
1 AAAAAA-CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTG
* *
3227606 AAAAAACTCCTCTCAGCAGAGGCTTAATAACTTTAAAAATCT-ATTTG
1 AAAAAACTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTG
** * *
3227653 AAAAAGTTCCTCTCAACAGAGGTTCAACAACTTT-AAAATCTCATTTTAG
1 AAAAAACTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCA-TTT-G
* * * *
3227702 AAAAAACTCCTCTCAACATAGGCTCAACGACTTT-AAAATCTCATATG
1 AAAAAACTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTG
* * * * *
3227749 GAAAAGCTCCTTTCAGTAGAGGCTCAACAATTTTAAAAAT-TCATTTG
1 AAAAAACTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTG
* * *
3227796 GAAAAATTCCTCTCAACAGAGGCTCAACAACTTTAAAAAT-TCATTTG
1 AAAAAACTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTG
* * *
3227843 AAAAAGCTCCTCGT-AGTAGAGGCTCAACAA-TTTTAAAATCTCATTTTAG
1 AAAAAACTCCTC-TCAGCAGAGGCTCAACAACTTTAAAAATCTCA-TTT-G
* * * *
3227892 AAAAAGCTCCTCTCAGCAGAGGATCAACGACTTT-AAAATCTCATCT-
1 AAAAAACTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTG
* ** *
3227938 AAAAAAGCTCCTCTTAATAGAGGCTCAACAACTTTAAAAATCTTATTTG
1 AAAAAA-CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTG
** * *
3227987 AAAATGGCTCTTCTTAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTG
1 AAAA-AACTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCAT-TTG
* **
3228037 AAAAAGACTCCTATCAATAGAGGCTCAACAACTTTAAAAATCTCAT
1 AAAAA-ACTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCAT
3228083 ATGTTCTCCA
Statistics
Matches: 436, Mismatches: 72, Indels: 32
0.81 0.13 0.06
Matches are distributed among these distances:
46 20 0.05
47 179 0.41
48 80 0.18
49 113 0.26
50 44 0.10
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.29
Consensus pattern (48 bp):
AAAAAACTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTG
Found at i:3227759 original size:143 final size:142
Alignment explanation
Indices: 3227534--3228082 Score: 599
Period size: 143 Copynumber: 3.8 Consensus size: 142
3227524 TAGCATAGGT
* * * * *
3227534 TCAATAACTTT-AAAATTTTATTTGAAAAAAGCTCATCTAAGCAAAGGCTCAACAACTTTAAAAT
1 TCAACAACTTTAAAAATCTCATTTGAAAAAA-CTCCTCTAA-CAGAGGCTCAACAACTTTAAAAT
* * * *
3227598 CTCATCTGAAAAAACTCCTCTCAGCAGAGGCTTAATAACTTTAAAAATCT-ATTTGAAAAAGTTC
64 CTCATTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTGAAAAAGTTC
*
3227662 CTCTCAACAGAGGT
129 CTCTCAACAGAGGC
* *
3227676 TCAACAACTTT-AAAATCTCATTTTAGAAAAAACTCCTCTCAACATAGGCTCAACGACTTTAAAA
1 TCAACAACTTTAAAAATCTCA-TTT-GAAAAAACTCCTCT-AACAGAGGCTCAACAACTTTAAAA
* * * * *
3227740 TCTCATATGGAAAAGCTCCTTTCAGTAGAGGCTCAACAATTTTAAAAAT-TCATTTGGAAAAA-T
63 TCTCATTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTT-GAAAAAGT
3227803 TCCTCTCAACAGAGGC
127 TCCTCTCAACAGAGGC
* ** *
3227819 TCAACAACTTTAAAAAT-TCATTTGAAAAAGCTCCTCGTAGTAGAGGCTCAACAATTTTAAAATC
1 TCAACAACTTTAAAAATCTCATTTGAAAAAACTCCTC-TAACAGAGGCTCAACAACTTTAAAATC
* * * * *
3227883 TCATTTTAGAAAAAGCTCCTCTCAGCAGAGGATCAACGACTTT-AAAATCTCATCTAAAAAAGCT
65 TCA-TTT-GAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTGAAAAAGTT
* *
3227947 CCTCTTAATAGAGGC
128 CCTCTCAACAGAGGC
* ** * *
3227962 TCAACAACTTTAAAAATCTTATTTGAAAATGGCTCTTCTTAGCAGAGGCTCAACAACTTTAAAAA
1 TCAACAACTTTAAAAATCTCATTTGAAAA-AACTCCTC-TAACAGAGGCTCAACAACTTT-AAAA
* **
3228027 TCTCATCTTGAAAAAGACTCCTATCAATAGAGGCTCAACAACTTTAAAAATCTCAT
63 TCTCAT-TTGAAAAAG-CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCAT
3228083 ATGTTCTCCA
Statistics
Matches: 346, Mismatches: 44, Indels: 29
0.83 0.11 0.07
Matches are distributed among these distances:
141 36 0.10
142 34 0.10
143 169 0.49
144 30 0.09
145 33 0.10
146 34 0.10
147 10 0.03
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (142 bp):
TCAACAACTTTAAAAATCTCATTTGAAAAAACTCCTCTAACAGAGGCTCAACAACTTTAAAATCT
CATTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTGAAAAAGTTCCT
CTCAACAGAGGC
Found at i:3227883 original size:190 final size:191
Alignment explanation
Indices: 3227578--3228082 Score: 646
Period size: 190 Copynumber: 2.6 Consensus size: 191
3227568 ATCTAAGCAA
* * * * *
3227578 AGGCTCAACAACTTT-AAAATCTCATCTGAAAAAACTCCTCTCAGCAGAGGCTTAATAACTTTAA
1 AGGCTCAACAACTTTAAAAATCTCATTTGGAAAAATTCCTCTCAGCAGAGGCTCAACAACTTTAA
* * * *
3227642 AAA-TCTATTTGAAAAAGTTCCTCTCAACAGAGGTTCAACAACTTTAAAATCTCATTTTAGAAAA
66 AAATTC-ATTTGAAAAAGCTCCTCTCAATAGAGGCTCAACAATTTTAAAATCTCATTTTAGAAAA
* * ** *
3227706 AACTCCTCTCAACATAGGCTCAACGACTTTAAAATCTCATATGGAAAAGCTCCT-TTCAGTAG
130 AACTCCTCTCAACAGAGGATCAACGACTTTAAAATCTCATATAAAAAAGCTCCTCTT-AATAG
* *
3227768 AGGCTCAACAATTTTAAAAAT-TCATTTGGAAAAATTCCTCTCAACAGAGGCTCAACAACTTTAA
1 AGGCTCAACAACTTTAAAAATCTCATTTGGAAAAATTCCTCTCAGCAGAGGCTCAACAACTTTAA
*
3227832 AAATTCATTTGAAAAAGCTCCTCGT-AGTAGAGGCTCAACAATTTTAAAATCTCATTTTAGAAAA
66 AAATTCATTTGAAAAAGCTCCTC-TCAATAGAGGCTCAACAATTTTAAAATCTCATTTTAGAAAA
* * *
3227896 AGCTCCTCTCAGCAGAGGATCAACGACTTTAAAATCTCATCTAAAAAAGCTCCTCTTAATAG
130 AACTCCTCTCAACAGAGGATCAACGACTTTAAAATCTCATATAAAAAAGCTCCTCTTAATAG
* * *
3227958 AGGCTCAACAACTTTAAAAATCTTATTT-G-AAAATGGCTCTTCTTAGCAGAGGCTCAACAACTT
1 AGGCTCAACAACTTTAAAAATCTCATTTGGAAAAAT---TCCTCTCAGCAGAGGCTCAACAACTT
* *
3228021 TAAAAATCTCATCTTGAAAAAGACTCCTATCAATAGAGGCTCAACAACTTTAAAAATCTCAT
63 TAAAAAT-TCAT-TTGAAAAAG-CTCCTCTCAATAGAGGCTCAACAA-TTTTAAAATCTCAT
3228083 ATGTTCTCCA
Statistics
Matches: 274, Mismatches: 28, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
189 5 0.02
190 177 0.65
191 15 0.05
192 30 0.11
193 4 0.01
194 10 0.04
195 20 0.07
196 13 0.05
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (191 bp):
AGGCTCAACAACTTTAAAAATCTCATTTGGAAAAATTCCTCTCAGCAGAGGCTCAACAACTTTAA
AAATTCATTTGAAAAAGCTCCTCTCAATAGAGGCTCAACAATTTTAAAATCTCATTTTAGAAAAA
ACTCCTCTCAACAGAGGATCAACGACTTTAAAATCTCATATAAAAAAGCTCCTCTTAATAG
Found at i:3239775 original size:116 final size:115
Alignment explanation
Indices: 3239650--3239922 Score: 383
Period size: 116 Copynumber: 2.3 Consensus size: 115
3239640 TTTTGTGCAG
**
3239650 AAAAAATTGATACTTTCAACTTTTCTCAAAAAATATTCTTTTG-AAACTTT-AATTTCGAGGAAA
1 AAAAAATTGATACTTTCAACTTTTCTC-AAAAATATT-TTTTGAAAACTTTGAATTTCGAAAAAA
*
3239713 ATTGATACTTTCA-CATTTTTCC-CAAAAAATTTTTTTAGAAAATTTATTTTTAA
64 ATTGATACTTTCATC--TTTTCCTCAAAAAACTTTTTT-GAAAATTTATTTTTAA
* * *
3239766 AAAAAATTGATACTTTAAACTTTTTCTCAAAAATATTTTTTGAAAATTTTGATTTTCGAAAAAAA
1 AAAAAATTGATACTTTCAAC-TTTTCTCAAAAATATTTTTTGAAAACTTTGAATTTCGAAAAAAA
*
3239831 TTGATACTTTCATCTTTTCCTCAAAAACCTTTTTTGAAAATTTATTTTTAA
65 TTGATACTTTCATCTTTTCCTCAAAAAACTTTTTTGAAAATTTATTTTTAA
*
3239882 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
1 AAAAAATTGATACTTTCAACTTTT-CTCAAAAATATTTTTT
3239923 TTTGGATTTT
Statistics
Matches: 142, Mismatches: 9, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
115 9 0.06
116 90 0.63
117 42 0.30
118 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.44
Consensus pattern (115 bp):
AAAAAATTGATACTTTCAACTTTTCTCAAAAATATTTTTTGAAAACTTTGAATTTCGAAAAAAAT
TGATACTTTCATCTTTTCCTCAAAAAACTTTTTTGAAAATTTATTTTTAA
Found at i:3239833 original size:59 final size:57
Alignment explanation
Indices: 3239650--3239922 Score: 320
Period size: 58 Copynumber: 4.7 Consensus size: 57
3239640 TTTTGTGCAG
* *
3239650 AAAAAATTGATACTTTCAAC-TTTTCTCAAAAAATATTCTTTTGAAACTTTAATTTCGA
1 AAAAAATTGATACTTTCAACTTTTTCTC-AAAAATATT-TTTTGAAAATTTATTTTCGA
** * **
3239708 GGAAAATTGATACTTTC-ACATTTTTCCCAAAAA-ATTTTTTTAGAAAATTTATTTTTAA
1 AAAAAATTGATACTTTCAAC-TTTTTCTCAAAAATA-TTTTTT-GAAAATTTATTTTCGA
*
3239766 AAAAAATTGATACTTTAAACTTTTTCTCAAAAATATTTTTTGAAAATTTTGATTTTCGA
1 AAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAA-TTT-ATTTTCGA
* * ** *
3239825 AAAAAATTGATACTTTCATCTTTTCCTCAAAAACCTTTTTTGAAAATTTATTTT-TA
1 AAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAATTTATTTTCGA
*
3239881 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
1 A-AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTT
3239923 TTTGGATTTT
Statistics
Matches: 184, Mismatches: 22, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
56 2 0.01
57 54 0.29
58 72 0.39
59 56 0.30
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.44
Consensus pattern (57 bp):
AAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAATTTATTTTCGA
Found at i:3239936 original size:59 final size:58
Alignment explanation
Indices: 3239651--3239924 Score: 315
Period size: 59 Copynumber: 4.7 Consensus size: 58
3239641 TTTGTGCAGA
* * * **
3239651 AAAAATTGATACTTTCAACTTTT-CTCAAAAAATATTCTTTTGAAACTTTAATTTCGAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAAAT-TTTTTTTGAAAATTTATTTTTAAG
* * * *
3239709 GAAAATTGATACTTTCACATTTTTCC-CAAAAAATTTTTTTAGAAAATTTATTTTTAAA
1 AAAAATTGATACTTTCA-ACTTTTCCTCAAAAAATTTTTTTTGAAAATTTATTTTTAAG
* * * *
3239767 AAAAATTGATACTTTAAACTTTTTCTC-AAAAATATTTTTTGAAAATTTTGATTTTCGAA-
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAAATTTTTTTTGAAAA-TTT-ATTTT-TAAG
* **
3239826 AAAAATTGATACTTTCATCTTTTCCTC-AAAAACCTTTTTTGAAAATTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAAATTTTTTTTGAAAATTTATTTTTAAG
3239883 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTT
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAA-ATTTTTTTT
3239925 TGGATTTTAT
Statistics
Matches: 182, Mismatches: 25, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
56 2 0.01
57 53 0.29
58 59 0.32
59 65 0.36
60 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (58 bp):
AAAAATTGATACTTTCAACTTTTCCTCAAAAAATTTTTTTTGAAAATTTATTTTTAAG
Found at i:3239949 original size:5 final size:5
Alignment explanation
Indices: 3239941--3240041 Score: 66
Period size: 5 Copynumber: 19.6 Consensus size: 5
3239931 TTATTTACAA
*
3239941 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAGAAAT AAAA- AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -A-AAAT AAAAT AAAAT
* * *
3239986 AAAGA- AAAGT AAAAT AAAAAT AAAAAT AAAAT AAAAAT AAAAG AACAT
1 AAA-AT AAAAT AAAAT -AAAAT -AAAAT AAAAT -AAAAT AAAAT AAAAT
*
3240034 TAAAT AAA
1 AAAAT AAA
3240042 CCTAATCTAA
Statistics
Matches: 76, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
3 3 0.04
4 4 0.05
5 45 0.59
6 19 0.25
7 2 0.03
8 3 0.04
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:3239976 original size:26 final size:22
Alignment explanation
Indices: 3239940--3240027 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 22
3239930 TTTATTTACA
*
3239940 AAAAATAAAATAATAAAACAAAAT
1 AAAAGTAAAATAA-AAAA-AAAAT
*
3239964 AAAAGTGAGAAATAAAAAAAATAAAG
1 AAAAGT-A-AAAT-AAAAAAA-AAAT
3239990 AAAAGTAAAATAAAAATAAAAAT
1 AAAAGTAAAATAAAAA-AAAAAT
3240013 AAAA-TAAAAATAAAA
1 AAAAGT-AAAATAAAA
3240028 GAACATTAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
22 1 0.02
23 21 0.38
24 11 0.20
25 3 0.05
26 17 0.31
27 2 0.04
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.15
Consensus pattern (22 bp):
AAAAGTAAAATAAAAAAAAAAT
Found at i:3239999 original size:32 final size:30
Alignment explanation
Indices: 3239940--3240021 Score: 78
Period size: 32 Copynumber: 2.6 Consensus size: 30
3239930 TTTATTTACA
*
3239940 AAAAAT-AAAATAATAAAACAAAATAAAAGT
1 AAAAATAAAAAAAATAAAACAAAATAAAA-T
* *
3239970 GAGAAATAAAAAAAATAAAGA-AAAGTAAAAT
1 -AAAAATAAAAAAAATAAA-ACAAAATAAAAT
3240001 AAAAATAAAAATAAAATAAAA
1 AAAAAT-AAAA-AAAATAAAA
3240022 ATAAAAGAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
30 5 0.12
31 11 0.26
32 26 0.60
33 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.15
Consensus pattern (30 bp):
AAAAATAAAAAAAATAAAACAAAATAAAAT
Found at i:3240005 original size:6 final size:6
Alignment explanation
Indices: 3239940--3240027 Score: 67
Period size: 6 Copynumber: 14.7 Consensus size: 6
3239930 TTTATTTACA
* * * *
3239940 AAAAAT -AAAAT AATAAA- ACAAAAT AAAAGT GAGAAAT AAAAAA AATAAAG
1 AAAAAT AAAAAT AA-AAAT A-AAAAT AAAAAT -AAAAAT AAAAAT AA-AAAT
*
3239990 AAAAGT -AAAAT AAAAAT AAAAAT -AAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
3240028 GAACATTAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
5 14 0.22
6 37 0.57
7 14 0.22
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:3240005 original size:12 final size:12
Alignment explanation
Indices: 3239940--3240027 Score: 67
Period size: 13 Copynumber: 7.3 Consensus size: 12
3239930 TTTATTTACA
3239940 AAAAAT-AAAAT
1 AAAAATAAAAAT
3239951 AATAAA-ACAAAAT
1 AA-AAATA-AAAAT
* *
3239964 AAAAGTGAGAAAT
1 AAAAAT-AAAAAT
* *
3239977 AAAAAAAATAAAG
1 AAAAATAA-AAAT
*
3239990 AAAAGT-AAAAT
1 AAAAATAAAAAT
3240001 AAAAATAAAAAT
1 AAAAATAAAAAT
3240013 -AAAATAAAAAT
1 AAAAATAAAAAT
3240024 AAAA
1 AAAA
3240028 GAACATTAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
11 21 0.36
12 15 0.25
13 22 0.37
14 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.15
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:3240010 original size:17 final size:17
Alignment explanation
Indices: 3239990--3240028 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
3239980 AAAAATAAAG
3239990 AAAAGTAAAATAAAAAT
1 AAAAGTAAAATAAAAAT
*
3240007 AAAAATAAAATAAAAAT
1 AAAAGTAAAATAAAAAT
3240024 AAAAG
1 AAAAG
3240029 AACATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (17 bp):
AAAAGTAAAATAAAAAT
Found at i:3241026 original size:251 final size:251
Alignment explanation
Indices: 3240580--3241080 Score: 993
Period size: 251 Copynumber: 2.0 Consensus size: 251
3240570 AAAATTTTTT
3240580 AAAAATTTTCAAAAAAAATTTTCGTCAAAAATCTCCAAAAAATCTTTTCGATTCTCACAGCTATT
1 AAAAATTTTCAAAAAAAATTTTCGTCAAAAATCTCCAAAAAATCTTTTCGATTCTCACAGCTATT
3240645 CTAACACTTCTTAACCTTCTATTAGCCTTCAAAAATTTTCTATATGCCTTTTTCTCTCAATCAAT
66 CTAACACTTCTTAACCTTCTATTAGCCTTCAAAAATTTTCTATATGCCTTTTTCTCTCAATCAAT
*
3240710 AGCCTTTGTGCTCACTGTTTTCTCTGTGTTCTTTCTTCTGTTCTAGTACCTATTTATAGAGATTG
131 AGCCTTTGTGCTCACTGTTTTCTCTGTGTTCTTTCTTCTGTTCTAGTACCTATTTATAAAGATTG
3240775 ATCAAAAAAGTGTCTAATCAATCCCTATTCTTTTTTGGATGGAGATTCAATCTTTA
196 ATCAAAAAAGTGTCTAATCAATCCCTATTCTTTTTTGGATGGAGATTCAATCTTTA
3240831 AAAAATTTTCAAAAAAAATTTTCGTCAAAAATCTCCAAAAAATCTTTTCGATTCTCACAGCTATT
1 AAAAATTTTCAAAAAAAATTTTCGTCAAAAATCTCCAAAAAATCTTTTCGATTCTCACAGCTATT
3240896 CTAACACTTCTTAACCTTCTATTAGCCTTCAAAAATTTTCTATATGCCTTTTTCTCTCAATCAAT
66 CTAACACTTCTTAACCTTCTATTAGCCTTCAAAAATTTTCTATATGCCTTTTTCTCTCAATCAAT
3240961 AGCCTTTGTGCTCACTGTTTTCTCTGTGTTCTTTCTTCTGTTCTAGTACCTATTTATAAAGATTG
131 AGCCTTTGTGCTCACTGTTTTCTCTGTGTTCTTTCTTCTGTTCTAGTACCTATTTATAAAGATTG
3241026 ATCAAAAAAGTGTCTAATCAATCCCTATTCTTTTTTGGATGGAGATTCAATCTTT
196 ATCAAAAAAGTGTCTAATCAATCCCTATTCTTTTTTGGATGGAGATTCAATCTTT
3241081 GAATTCAATC
Statistics
Matches: 249, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
251 249 1.00
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (251 bp):
AAAAATTTTCAAAAAAAATTTTCGTCAAAAATCTCCAAAAAATCTTTTCGATTCTCACAGCTATT
CTAACACTTCTTAACCTTCTATTAGCCTTCAAAAATTTTCTATATGCCTTTTTCTCTCAATCAAT
AGCCTTTGTGCTCACTGTTTTCTCTGTGTTCTTTCTTCTGTTCTAGTACCTATTTATAAAGATTG
ATCAAAAAAGTGTCTAATCAATCCCTATTCTTTTTTGGATGGAGATTCAATCTTTA
Found at i:3241179 original size:22 final size:22
Alignment explanation
Indices: 3241149--3241203 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
3241139 TCTCAATCCA
*
3241149 AAAAAAAAAAATCTGATAAACG
1 AAAAAAAAAAATCAGATAAACG
*
3241171 -AGAAAAAAAATCAGATAAACG
1 AAAAAAAAAAATCAGATAAACG
3241192 AAAAAAGAAAAA
1 AAAAAA-AAAAA
3241204 AAATAACAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 19 0.68
22 4 0.14
23 5 0.18
ACGTcount: A:0.73, C:0.07, G:0.11, T:0.09
Consensus pattern (22 bp):
AAAAAAAAAAATCAGATAAACG
Found at i:3241235 original size:21 final size:21
Alignment explanation
Indices: 3241211--3241294 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
3241201 AAAAAATAAC
*
3241211 AGATAATTAAAAATAATAATA
1 AGATAAATAAAAATAATAATA
* * *
3241232 AGATAAACAAAAA-ATATTACA
1 AGATAAATAAAAATA-ATAATA
3241253 AGATAAATAAAAATAATAATA
1 AGATAAATAAAAATAATAATA
* *
3241274 ATAATAAATAAATTATAATAA
1 A-GATAAATAAA-AATAATAA
3241295 CAAATATATA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 1 0.02
21 32 0.64
22 10 0.20
23 7 0.14
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (21 bp):
AGATAAATAAAAATAATAATA
Found at i:3241293 original size:17 final size:16
Alignment explanation
Indices: 3241258--3241305 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
3241248 TTACAAGATA
3241258 AATAAAAAT-AATAAT
1 AATAAAAATAAATAAT
*
3241273 AATAATAAATAAATTAT
1 AATAA-AAATAAATAAT
*
3241290 AATAACAAATATATAA
1 AATAA-AAATAAATAA
3241306 CTAGATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 5 0.19
16 4 0.15
17 18 0.67
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAAAATAAATAAT
Found at i:3241459 original size:18 final size:18
Alignment explanation
Indices: 3241413--3241464 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
3241403 ATAAATACAT
* *
3241413 AAAATGCAAAAGAAAAGA
1 AAAATACAAAATAAAAGA
* * *
3241431 AAAAAATAAAATAAAATA
1 AAAATACAAAATAAAAGA
3241449 AAAATACAAAATAAAA
1 AAAATACAAAATAAAA
3241465 ATTAAATTGG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.12
Consensus pattern (18 bp):
AAAATACAAAATAAAAGA
Found at i:3241694 original size:43 final size:42
Alignment explanation
Indices: 3241658--3241788 Score: 115
Period size: 42 Copynumber: 3.1 Consensus size: 42
3241648 TCCTTTAGGT
**
3241658 AGAGGCTCAATGACTTT-AAGAAACATAAATGGCTCCTCTAATC
1 AGAGGCTCAACAACTTTGAA-AAA-ATAAATGGCTCCTCTAATC
* * *
3241701 AGAGGCTCAACAACTTTGAAAAAATAAATTGCTCCTCAAAAC
1 AGAGGCTCAACAACTTTGAAAAAATAAATGGCTCCTCTAATC
* * * * * * *
3241743 AGAGGCACCACGACTTTG-GAAAGTAAATTGCT-CTCTAAAC
1 AGAGGCTCAACAACTTTGAAAAAATAAATGGCTCCTCTAATC
3241783 AGAGGC
1 AGAGGC
3241789 ACCACGATTT
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
40 13 0.17
41 12 0.16
42 31 0.41
43 18 0.24
44 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (42 bp):
AGAGGCTCAACAACTTTGAAAAAATAAATGGCTCCTCTAATC
Found at i:3241746 original size:42 final size:41
Alignment explanation
Indices: 3241658--3241826 Score: 169
Period size: 40 Copynumber: 4.1 Consensus size: 41
3241648 TCCTTTAGGT
* * * * *
3241658 AGAGGCTCAATGACTTTAAGAAACATAAATGGCTCCTCTAATC
1 AGAGGCACAACGACTTT--GAAAAATAAATTGCTCCTCTAAAC
* * *
3241701 AGAGGCTCAACAACTTTGAAAAAATAAATTGCTCCTCAAAAC
1 AGAGGCACAACGACTTTG-AAAAATAAATTGCTCCTCTAAAC
* * *
3241743 AGAGGCACCACGACTTTGGAAAGTAAATTGCT-CTCTAAAC
1 AGAGGCACAACGACTTTGAAAAATAAATTGCTCCTCTAAAC
* * * *
3241783 AGAGGCACCACGATTTTGAAAAGTAAACTGCTCCTCTAAAC
1 AGAGGCACAACGACTTTGAAAAATAAATTGCTCCTCTAAAC
3241824 AGA
1 AGA
3241827 ATAGAGGCAA
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
40 36 0.33
41 24 0.22
42 34 0.31
43 15 0.14
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AGAGGCACAACGACTTTGAAAAATAAATTGCTCCTCTAAAC
Found at i:3241790 original size:40 final size:41
Alignment explanation
Indices: 3241683--3241863 Score: 184
Period size: 40 Copynumber: 4.3 Consensus size: 41
3241673 TTAAGAAACA
* * * * * *
3241683 TAAATGGCTCCTCTAATCAGAGGCTCAACAACTTTGAAAAAA
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAG
* *
3241725 TAAATTGCTCCTCAAAACAGAGGCACCACGACTTTGGAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAG
*
3241766 TAAATTGCT-CTCTAAACAGAGGCACCACGATTTTGAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAG
* * **
3241806 TAAACTGCTCCTCTAAACAGAATAGAGGCAACAAAACTTTGAAAAG
1 TAAATTGCTCCTCTAAAC-----AGAGGCACCACGACTTTGAAAAG
3241852 TAAATTGCTCCT
1 TAAATTGCTCCT
3241864 TGACAATCAT
Statistics
Matches: 116, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
40 36 0.31
41 20 0.17
42 30 0.26
46 30 0.26
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (41 bp):
TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAG
Found at i:3242215 original size:43 final size:42
Alignment explanation
Indices: 3242158--3242238 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 42
3242148 TTGGCAAACT
*
3242158 TGGAATTCATATCCAAAAA-TCTAAAGCTTTTCATTTGAATTG
1 TGGAATTCACATCCAAAAATTC-AAAGCTTTTCATTTGAATTG
3242200 TGGAGATTCACATCCAAAAATTCAAAGCTTTTCATTTGA
1 TGGA-ATTCACATCCAAAAATTCAAAGCTTTTCATTTGA
3242239 GTTCAAAGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
42 4 0.11
43 30 0.83
44 2 0.06
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (42 bp):
TGGAATTCACATCCAAAAATTCAAAGCTTTTCATTTGAATTG
Found at i:3243578 original size:10 final size:10
Alignment explanation
Indices: 3243563--3243621 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
3243553 TTAAATCTTT
3243563 TTTTTTTTCA
1 TTTTTTTTCA
3243573 --TTTTTTCA
1 TTTTTTTTCA
* *
3243581 TTTTCTCATTCT
1 TTTT-T-TTTCA
*
3243593 TTTTTTTTCT
1 TTTTTTTTCA
3243603 TTTTTTTTCA
1 TTTTTTTTCA
3243613 TCTTTTTTT
1 T-TTTTTTT
3243622 TCTCATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 8 0.20
10 16 0.40
11 9 0.22
12 7 0.17
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:3243601 original size:22 final size:21
Alignment explanation
Indices: 3243573--3243634 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 21
3243563 TTTTTTTTCA
3243573 TTTTTTCATTTTCTCATTCTTT
1 TTTTTTCATTTT-TCATTCTTT
*
3243595 TTTTTTCTTTTTTTTTCA-TCTTT
1 TTTTTTC---ATTTTTCATTCTTT
3243618 TTTTTCTCATTTTTCAT
1 TTTTT-TCATTTTTCAT
3243635 CCATTGTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
21 7 0.21
22 7 0.21
23 10 0.30
24 5 0.15
25 4 0.12
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTTCATTTTTCATTCTTT
Found at i:3243608 original size:24 final size:24
Alignment explanation
Indices: 3243581--3243631 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3243571 CATTTTTTCA
*
3243581 TTTTCTCATTCTTTTTTTT-TCTTT
1 TTTTCTCA-TCTTTTTTTTCTCATT
*
3243605 TTTTTTCATCTTTTTTTTCTCATT
1 TTTTCTCATCTTTTTTTTCTCATT
3243629 TTT
1 TTT
3243632 CATCCATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTCTCATCTTTTTTTTCTCATT
Done.