Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 41 of 144
Found at i:12421712 original size:24 final size:24
Alignment explanation
Indices: 12421685--12421748 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
12421675 CCTATGCTGT
12421685 TATGCGAACCTATGTTATATGAAG
1 TATGCGAACCTATGTTATATGAAG
*
12421709 TATGCGAACCTATGCTATATGAAG
1 TATGCGAACCTATGTTATATGAAG
*
12421733 TATACGAACCTATGTT
1 TATGCGAACCTATGTT
12421749 GTTGAACGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (24 bp):
TATGCGAACCTATGTTATATGAAG
Found at i:12424611 original size:23 final size:22
Alignment explanation
Indices: 12424542--12424616 Score: 64
Period size: 23 Copynumber: 3.4 Consensus size: 22
12424532 CATTTTGCTG
* *
12424542 GTTGTTTTTTGTGCTA-TTTTG
1 GTTGTTTTTGGTGCTATTTTTA
* * *
12424563 GTTG-TTTTGGTGATGTTTTGGA
1 GTTGTTTTTGGTGCTATTTT-TA
*
12424585 GTTGTTTTTGGTGCTATTTTATT
1 GTTGTTTTTGGTGCTATTTT-TA
12424608 GTTGTTTTT
1 GTTGTTTTT
12424617 AATATTATTT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 8 0.20
21 7 0.17
22 4 0.10
23 22 0.54
ACGTcount: A:0.07, C:0.03, G:0.27, T:0.64
Consensus pattern (22 bp):
GTTGTTTTTGGTGCTATTTTTA
Found at i:12427254 original size:24 final size:23
Alignment explanation
Indices: 12427194--12427247 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
12427184 AAACTTTAGA
* *
12427194 AAAGAAAGAAAAAAAAAAAAAAT
1 AAAGAAATAATAAAAAAAAAAAT
* *
12427217 AAATAAATAATAAAAATAAAAAT
1 AAAGAAATAATAAAAAAAAAAAT
12427240 GAAAGAAA
1 -AAAGAAA
12427248 ACATAAATGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.11
Consensus pattern (23 bp):
AAAGAAATAATAAAAAAAAAAAT
Found at i:12438975 original size:21 final size:20
Alignment explanation
Indices: 12438951--12438995 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
12438941 ACTATCAATT
12438951 TATTTAATTTGATCACCCAAC
1 TATTTAATTTG-TCACCCAAC
**
12438972 TATTTTTTTTTGTCACCCAAC
1 TA-TTTAATTTGTCACCCAAC
12438993 TAT
1 TAT
12438996 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 1 0.05
21 13 0.62
22 7 0.33
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.47
Consensus pattern (20 bp):
TATTTAATTTGTCACCCAAC
Found at i:12439000 original size:22 final size:22
Alignment explanation
Indices: 12438958--12439004 Score: 78
Period size: 21 Copynumber: 2.1 Consensus size: 22
12438948 ATTTATTTAA
12438958 TTTGATCACCCAACTATTTTTT
1 TTTGATCACCCAACTATTTTTT
12438980 TTTG-TCACCCAACTATCTTTTT
1 TTTGATCACCCAACTAT-TTTTT
12439002 TTT
1 TTT
12439005 TTTTAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.19, C:0.23, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTGATCACCCAACTATTTTTT
Found at i:12443262 original size:37 final size:36
Alignment explanation
Indices: 12443209--12443280 Score: 99
Period size: 37 Copynumber: 2.0 Consensus size: 36
12443199 ACCTGCACTG
* * *
12443209 AGCCAGAGAGACATTGTCTCAGGAAAAAAAATGACAC
1 AGCCAGAAAGAAATTGTCCCAGG-AAAAAAATGACAC
*
12443246 AGCCAGAAAGAAATTGTCCCAGGCAAAAAATGACA
1 AGCCAGAAAGAAATTGTCCCAGGAAAAAAATGACA
12443281 GACTCCGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 11 0.35
37 20 0.65
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.12
Consensus pattern (36 bp):
AGCCAGAAAGAAATTGTCCCAGGAAAAAAATGACAC
Found at i:12449713 original size:3 final size:3
Alignment explanation
Indices: 12449705--12449742 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
12449695 GTTTGGTTTG
12449705 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
12449743 AAATTATAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:12456573 original size:3 final size:3
Alignment explanation
Indices: 12456567--12456597 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
12456557 TTTTCTTTCT
12456567 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12456598 CCCTTACGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12457146 original size:6 final size:6
Alignment explanation
Indices: 12457135--12457160 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12457125 GGATATGAAA
12457135 AAGATG AAGATG AAGATG AAGATG AA
1 AAGATG AAGATG AAGATG AAGATG AA
12457161 AGTAAAGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.31, T:0.15
Consensus pattern (6 bp):
AAGATG
Found at i:12457570 original size:2 final size:2
Alignment explanation
Indices: 12457563--12457587 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12457553 TTTCTTTTCT
12457563 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
12457588 ATGTATTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12458668 original size:46 final size:46
Alignment explanation
Indices: 12458586--12458679 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 46
12458576 AGCAATAGTG
* * ** *
12458586 TGCCAACTAATCTTACATTTTGTAATATCTCGAGTTAAACATATTT
1 TGCCAACTAATCTTACACTTTCTAATAAATCAAGTTAAACATATTT
* *
12458632 TGCCCACTATTCTTACACTTTCTAATAAATCAAGTTAAACATATTT
1 TGCCAACTAATCTTACACTTTCTAATAAATCAAGTTAAACATATTT
12458678 TG
1 TG
12458680 TTCATATCAC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.40
Consensus pattern (46 bp):
TGCCAACTAATCTTACACTTTCTAATAAATCAAGTTAAACATATTT
Found at i:12460544 original size:16 final size:18
Alignment explanation
Indices: 12460515--12460552 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
12460505 CCTGTGAGTG
*
12460515 TTTTTTATATTTA-TTTA
1 TTTTTTATAGTTATTTTA
12460532 TTTTTTAT-GTTATTTTA
1 TTTTTTATAGTTATTTTA
12460549 TTTT
1 TTTT
12460553 AAAAGAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTTTATAGTTATTTTA
Found at i:12463770 original size:19 final size:19
Alignment explanation
Indices: 12463746--12463782 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12463736 TGTTATTTTA
*
12463746 TTTTAAAAGAGGAAATTAT
1 TTTTAAAAGAGAAAATTAT
*
12463765 TTTTAAAATAGAAAATTA
1 TTTTAAAAGAGAAAATTA
12463783 AAGTTCACGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
TTTTAAAAGAGAAAATTAT
Found at i:12465059 original size:20 final size:20
Alignment explanation
Indices: 12465034--12465071 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12465024 AATATACGTC
12465034 TGTTTGTCAGAAATTTTGTT
1 TGTTTGTCAGAAATTTTGTT
**
12465054 TGTTTGTGTGAAATTTTG
1 TGTTTGTCAGAAATTTTG
12465072 GTTATTGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.03, G:0.24, T:0.55
Consensus pattern (20 bp):
TGTTTGTCAGAAATTTTGTT
Found at i:12470240 original size:21 final size:21
Alignment explanation
Indices: 12470214--12470323 Score: 102
Period size: 21 Copynumber: 5.3 Consensus size: 21
12470204 TGAATACGCC
*
12470214 AACAGAAGCTCGTAAGAGCTT
1 AACAGAAGCTCATAAGAGCTT
*
12470235 AACAGAAGCTC-GAA-AG-TT
1 AACAGAAGCTCATAAGAGCTT
* * *
12470253 GAATAGAAGCTCATAATAGCTA
1 -AACAGAAGCTCATAAGAGCTT
*
12470275 AACAGAAACTCATAAGAG-TT
1 AACAGAAGCTCATAAGAGCTT
* *
12470295 GAACAAAAGCTCATAAGAGCTG
1 -AACAGAAGCTCATAAGAGCTT
12470317 AACAGAA
1 AACAGAA
12470324 AGTAAAACAC
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
18 2 0.03
19 12 0.17
20 5 0.07
21 50 0.70
22 2 0.03
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.17
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTT
Found at i:12470264 original size:40 final size:42
Alignment explanation
Indices: 12470214--12470324 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
12470204 TGAATACGCC
* * *
12470214 AACAGAAGCTCGTAAGAGCTTAACAGAAGCTC-GAA-AGTTG
1 AACAGAAGCTCATAAGAGCTAAACAGAAACTCAGAAGAGTTG
* * *
12470254 AATAGAAGCTCATAATAGCTAAACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTAAACAGAAACTCAGAAGAGTTG
* *
12470296 AACAAAAGCTCATAAGAGCTGAACAGAAA
1 AACAGAAGCTCATAAGAGCTAAACAGAAA
12470325 GTAAAACACA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 27 0.46
41 2 0.03
42 30 0.51
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACAGAAACTCAGAAGAGTTG
Found at i:12470482 original size:17 final size:17
Alignment explanation
Indices: 12470462--12470506 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
12470452 AAATCCAACT
12470462 CAATAGTATAATTCCAA
1 CAATAGTATAATTCCAA
*
12470479 CAATAAT-TCAATTCCAA
1 CAATAGTAT-AATTCCAA
*
12470496 CAATAGAATAA
1 CAATAGTATAA
12470507 ATAATTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 1 0.04
17 21 0.91
18 1 0.04
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (17 bp):
CAATAGTATAATTCCAA
Found at i:12471355 original size:21 final size:21
Alignment explanation
Indices: 12471330--12471398 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
12471320 TTTTACTTTT
* *
12471330 TGTTCAGTTTTTATGAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
* * *
12471351 TGTTCAACTCTTATGAGTTTT
1 TGTTCAGCTCTTATGAGCTTC
*
12471372 TGTTTAGCTCTTATGAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
12471393 TGTTCA
1 TGTTCA
12471399 ACTTTCGAGC
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.16, C:0.16, G:0.17, T:0.51
Consensus pattern (21 bp):
TGTTCAGCTCTTATGAGCTTC
Found at i:12471612 original size:21 final size:20
Alignment explanation
Indices: 12471584--12471625 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
12471574 ATTAATAGAA
12471584 GTTATGAATGACAGGAAATT
1 GTTATGAATGACAGGAAATT
*
12471604 GTTAGTGAATGACAGGGAATT
1 GTTA-TGAATGACAGGAAATT
12471625 G
1 G
12471626 ACATGATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.36, C:0.05, G:0.31, T:0.29
Consensus pattern (20 bp):
GTTATGAATGACAGGAAATT
Found at i:12473748 original size:11 final size:10
Alignment explanation
Indices: 12473708--12473750 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
12473698 TATTACTCAG
12473708 AATAACTAAA
1 AATAACTAAA
12473718 AATTAACTAAA
1 AA-TAACTAAA
* *
12473729 AACAAATAAA
1 AATAACTAAA
12473739 AATAACATAAA
1 AATAAC-TAAA
12473750 A
1 A
12473751 TGTAAATACG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 12 0.44
11 15 0.56
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (10 bp):
AATAACTAAA
Found at i:12474609 original size:26 final size:24
Alignment explanation
Indices: 12474580--12474635 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
12474570 TCTTGACGTT
*
12474580 TTATCTACAAGTCTTTTTCGAATAAA
1 TTATCTACAAGT-ATTTT-GAATAAA
**
12474606 TTATCTTGAAGTATTTTGAATAAA
1 TTATCTACAAGTATTTTGAATAAA
12474630 TTATCT
1 TTATCT
12474636 TCAAAAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 13 0.48
25 4 0.15
26 10 0.37
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (24 bp):
TTATCTACAAGTATTTTGAATAAA
Found at i:12483778 original size:18 final size:17
Alignment explanation
Indices: 12483716--12483779 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 17
12483706 ATCATCAGCC
12483716 ATAATT-TATAAATCATA
1 ATAATTATATAAAT-ATA
12483733 ATTAATATATTATTAAATA-A
1 A-TAAT-TA-TA-TAAATATA
*
12483753 ATATTTATAGTAAATATA
1 ATAATTATA-TAAATATA
12483771 ATAATTATA
1 ATAATTATA
12483780 ATTTTAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
17 9 0.24
18 15 0.39
19 4 0.11
20 2 0.05
21 3 0.08
22 5 0.13
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
ATAATTATATAAATATA
Found at i:12484144 original size:3 final size:3
Alignment explanation
Indices: 12484138--12484174 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
12484128 CTGACATTTC
12484138 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
12484175 TTATACTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:12486622 original size:21 final size:21
Alignment explanation
Indices: 12486592--12486749 Score: 106
Period size: 21 Copynumber: 7.5 Consensus size: 21
12486582 AAGCCCGAAG
*
12486592 GCTGAACAGAAGCTCATGAGA
1 GCTGAACAGAAGCTCATAAGA
* * * *
12486613 GCTAAACAGAAACCCATAAGG
1 GCTGAACAGAAGCTCATAAGA
* *
12486634 GTTGAACAGAAGCTCGTAAGA
1 GCTGAACAGAAGCTCATAAGA
* * *
12486655 GCTGAACAGAAACCCATAAGG
1 GCTGAACAGAAGCTCATAAGA
* * *
12486676 GTTAAATAGAAGCTCGAT-AGA
1 GCTGAACAGAAGCTC-ATAAGA
* *
12486697 GCTGAAC-GTAAACCCATAA-A
1 GCTGAACAG-AAGCTCATAAGA
* * *
12486717 GGTTAAACAGAAGCTCAAAAGA
1 -GCTGAACAGAAGCTCATAAGA
12486739 GCTGAACAGAA
1 GCTGAACAGAA
12486750 AGTAAACGCG
Statistics
Matches: 97, Mismatches: 34, Indels: 12
0.68 0.24 0.08
Matches are distributed among these distances:
20 4 0.04
21 89 0.92
22 4 0.04
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (21 bp):
GCTGAACAGAAGCTCATAAGA
Found at i:12486656 original size:42 final size:42
Alignment explanation
Indices: 12486596--12486750 Score: 215
Period size: 42 Copynumber: 3.7 Consensus size: 42
12486586 CCGAAGGCTG
* * *
12486596 AACAGAAGCTCATGAGAGCTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
*
12486638 AACAGAAGCTCGTAAGAGCTGAACAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
* *
12486680 AATAGAAGCTCGAT-AGAGCTGAAC-GTAAACCCATAAAGGTTA
1 AACAGAAGCTC-ATAAGAGCTGAACAG-AAACCCATAAGGGTTA
*
12486722 AACAGAAGCTCAAAAGAGCTGAACAGAAA
1 AACAGAAGCTCATAAGAGCTGAACAGAAA
12486751 GTAAACGCGA
Statistics
Matches: 100, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
41 2 0.02
42 96 0.96
43 2 0.02
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
Found at i:12489349 original size:66 final size:66
Alignment explanation
Indices: 12489243--12489371 Score: 231
Period size: 66 Copynumber: 2.0 Consensus size: 66
12489233 TTTAATAGAT
*
12489243 AAAATTAAACCATAAAAATGATAAGAAAACCGAGAAAATGAAATCCAAGATGTGACGCTATACGG
1 AAAATTAAACCATAAAAATGATAAGAAAACCGAGAAAATGAAATCCAAGATGTGAAGCTATACGG
12489308 A
66 A
* *
12489309 AAAATTAAACCATAAGAATGATAAGAAAACCGAGATAATGAAATCCAAGATGTGAAGCTATAC
1 AAAATTAAACCATAAAAATGATAAGAAAACCGAGAAAATGAAATCCAAGATGTGAAGCTATAC
12489372 TGAATTTCTG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (66 bp):
AAAATTAAACCATAAAAATGATAAGAAAACCGAGAAAATGAAATCCAAGATGTGAAGCTATACGG
A
Found at i:12491210 original size:21 final size:21
Alignment explanation
Indices: 12491180--12491337 Score: 106
Period size: 21 Copynumber: 7.5 Consensus size: 21
12491170 AAGCCCGAAG
*
12491180 GCTGAACAGAAGCTCATGAGA
1 GCTGAACAGAAGCTCATAAGA
* * * *
12491201 GCTAAACAGAAACCCATAAGG
1 GCTGAACAGAAGCTCATAAGA
* *
12491222 GTTGAACAGAAGCTCGTAAGA
1 GCTGAACAGAAGCTCATAAGA
* * *
12491243 GCTGAACAGAAACCCATAAGG
1 GCTGAACAGAAGCTCATAAGA
* * *
12491264 GTTAAATAGAAGCTCGAT-AGA
1 GCTGAACAGAAGCTC-ATAAGA
* *
12491285 GCTGAAC-GTAAACCCATAA-A
1 GCTGAACAG-AAGCTCATAAGA
* * *
12491305 GGTTAAACAGAAGCTCAAAAGA
1 -GCTGAACAGAAGCTCATAAGA
12491327 GCTGAACAGAA
1 GCTGAACAGAA
12491338 AGTAAACGCG
Statistics
Matches: 97, Mismatches: 34, Indels: 12
0.68 0.24 0.08
Matches are distributed among these distances:
20 4 0.04
21 89 0.92
22 4 0.04
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (21 bp):
GCTGAACAGAAGCTCATAAGA
Found at i:12491244 original size:42 final size:42
Alignment explanation
Indices: 12491184--12491338 Score: 215
Period size: 42 Copynumber: 3.7 Consensus size: 42
12491174 CCGAAGGCTG
* * *
12491184 AACAGAAGCTCATGAGAGCTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
*
12491226 AACAGAAGCTCGTAAGAGCTGAACAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
* *
12491268 AATAGAAGCTCGAT-AGAGCTGAAC-GTAAACCCATAAAGGTTA
1 AACAGAAGCTC-ATAAGAGCTGAACAG-AAACCCATAAGGGTTA
*
12491310 AACAGAAGCTCAAAAGAGCTGAACAGAAA
1 AACAGAAGCTCATAAGAGCTGAACAGAAA
12491339 GTAAACGCGA
Statistics
Matches: 100, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
41 2 0.02
42 96 0.96
43 2 0.02
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
Found at i:12493937 original size:66 final size:66
Alignment explanation
Indices: 12493831--12493959 Score: 231
Period size: 66 Copynumber: 2.0 Consensus size: 66
12493821 TTTAATAGAT
*
12493831 AAAATTAAACCATAAAAATGATAAGAAAACCGAGAAAATGAAATCCAAGATGTGACGCTATACGG
1 AAAATTAAACCATAAAAATGATAAGAAAACCGAGAAAATGAAATCCAAGATGTGAAGCTATACGG
12493896 A
66 A
* *
12493897 AAAATTAAACCATAAGAATGATAAGAAAACCGAGATAATGAAATCCAAGATGTGAAGCTATAC
1 AAAATTAAACCATAAAAATGATAAGAAAACCGAGAAAATGAAATCCAAGATGTGAAGCTATAC
12493960 TGAATTTCTG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (66 bp):
AAAATTAAACCATAAAAATGATAAGAAAACCGAGAAAATGAAATCCAAGATGTGAAGCTATACGG
A
Found at i:12496644 original size:21 final size:21
Alignment explanation
Indices: 12496620--12496689 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
12496610 ATGAGACCTA
12496620 AACAGAAACCCATAAGGGTTG
1 AACAGAAACCCATAAGGGTTG
* * * *
12496641 AACAGAAGCTCATAAGAGCTG
1 AACAGAAACCCATAAGGGTTG
* * *
12496662 AACAAAAACCCATAATGGTTT
1 AACAGAAACCCATAAGGGTTG
12496683 AACAGAA
1 AACAGAA
12496690 GCTCAATAGA
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (21 bp):
AACAGAAACCCATAAGGGTTG
Found at i:12496737 original size:42 final size:42
Alignment explanation
Indices: 12496599--12496749 Score: 180
Period size: 42 Copynumber: 3.6 Consensus size: 42
12496589 CTAAAGGCTG
* * * *
12496599 AACAGAAGCTC-ATGAGACCTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCAAT-AGAGCTGAACAAAAACCCATAAGGGTTA
* *
12496641 AACAGAAGCTC-ATAAGAGCTGAACAAAAACCCATAATGGTTT
1 AACAGAAGCTCAAT-AGAGCTGAACAAAAACCCATAAGGGTTA
**
12496683 AACAGAAGCTCAATAGAGCTGAATGAAAACCCATAAGGGTTA
1 AACAGAAGCTCAATAGAGCTGAACAAAAACCCATAAGGGTTA
* *
12496725 AACAGAAGCTCAAAAGAGCTAAACA
1 AACAGAAGCTCAATAGAGCTGAACA
12496750 TAAAGTAAAC
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 92 0.98
43 2 0.02
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.15
Consensus pattern (42 bp):
AACAGAAGCTCAATAGAGCTGAACAAAAACCCATAAGGGTTA
Found at i:12498778 original size:49 final size:48
Alignment explanation
Indices: 12498633--12498807 Score: 147
Period size: 49 Copynumber: 3.6 Consensus size: 48
12498623 CTCCCAATCA
* * * *
12498633 CATGGAGGGAGGCTTACGAAAGGTAATAAAGTG-GCTCTGCTCCCAAACA
1 CATGG-GGGAAGCTTACGAAAAGTAATAAAGTGAGCT-TGCTCCCAGACG
* * * * ** *
12498682 CATGGGGGAGGCTTACGAAAAGTAATAATA-TAACCCTATTCCTAGACG
1 CATGGGGGAAGCTTACGAAAAGTAATAA-AGTGAGCTTGCTCCCAGACG
*
12498730 CATGGGGTGAAGCTTACAAAAAGTAATAAAGTGAGCTTGCTCCCAGACG
1 CATGGGG-GAAGCTTACGAAAAGTAATAAAGTGAGCTTGCTCCCAGACG
* * * *
12498779 TATAGGGGGAGGCTTATGAAAAGTGATAA
1 CAT-GGGGGAAGCTTACGAAAAGTAATAA
12498808 CTTGATCTTA
Statistics
Matches: 99, Mismatches: 22, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
48 38 0.38
49 57 0.58
50 4 0.04
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (48 bp):
CATGGGGGAAGCTTACGAAAAGTAATAAAGTGAGCTTGCTCCCAGACG
Found at i:12499143 original size:58 final size:58
Alignment explanation
Indices: 12499074--12499183 Score: 159
Period size: 58 Copynumber: 1.9 Consensus size: 58
12499064 TTAAATCACA
* *
12499074 TCAACCAAGTCTACTCAAC-TGGAATTTACATAATGAAAATCGTGTCAAATCATAGCTT
1 TCAACCAAGTCTACTCAACTTGG-ACTTACATAATAAAAATCGTGTCAAATCATAGCTT
* * *
12499132 TCAACCAAGTCTACTCAGCTTGGACTTACGTGATAAAAATCGTGTCAAATCA
1 TCAACCAAGTCTACTCAACTTGGACTTACATAATAAAAATCGTGTCAAATCA
12499184 CTACCATCGG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 43 0.93
59 3 0.07
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (58 bp):
TCAACCAAGTCTACTCAACTTGGACTTACATAATAAAAATCGTGTCAAATCATAGCTT
Found at i:12499198 original size:58 final size:58
Alignment explanation
Indices: 12499072--12499205 Score: 146
Period size: 58 Copynumber: 2.3 Consensus size: 58
12499062 CGTTAAATCA
* *
12499072 CATCAACCAAGTCTACTCAACTGGAATTTACATAATGAAAATCGTGTCAAATCATAGC
1 CATCAACCAAGTCTACTCAACTGGAACTTACATAATAAAAATCGTGTCAAATCATAGC
** * * *
12499130 TTTCAACCAAGTCTACTCAGCTTGG-ACTTACGTGATAAAAATCGTGTCAAATCACTA-C
1 CATCAACCAAGTCTACTCAAC-TGGAACTTACATAATAAAAATCGTGTCAAATCA-TAGC
** *
12499188 CATCGGCCAAGACTACTC
1 CATCAACCAAGTCTACTC
12499206 GACCCGAATT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
58 57 0.92
59 5 0.08
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.26
Consensus pattern (58 bp):
CATCAACCAAGTCTACTCAACTGGAACTTACATAATAAAAATCGTGTCAAATCATAGC
Found at i:12508583 original size:43 final size:43
Alignment explanation
Indices: 12508534--12508618 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
12508524 TCATCGAATA
* *
12508534 AACCAAAGTAAATATACTGACACACATAGTGCATCATCAGACG
1 AACCAAAGCAAATATACTGACACACAAAGTGCATCATCAGACG
** ***
12508577 AACCAAAGCAAATATGTTGGTGCACAAAGTGCATCATCAGAC
1 AACCAAAGCAAATATACTGACACACAAAGTGCATCATCAGAC
12508619 AAAACCGAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.19
Consensus pattern (43 bp):
AACCAAAGCAAATATACTGACACACAAAGTGCATCATCAGACG
Found at i:12512880 original size:9 final size:9
Alignment explanation
Indices: 12512854--12512897 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
12512844 CTTAAAATGG
12512854 AAAATTTTT
1 AAAATTTTT
*
12512863 CAAACTTTTT
1 -AAAATTTTT
12512873 AAAATTTTT
1 AAAATTTTT
12512882 AAAA-TTTT
1 AAAATTTTT
12512890 AAAATTTT
1 AAAATTTT
12512898 AAAGTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
8 8 0.26
9 15 0.48
10 8 0.26
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (9 bp):
AAAATTTTT
Found at i:12512889 original size:8 final size:8
Alignment explanation
Indices: 12512869--12512900 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
12512859 TTTTCAAACT
12512869 TTTTAAAA
1 TTTTAAAA
12512877 TTTTTAAAA
1 -TTTTAAAA
12512886 TTTTAAAA
1 TTTTAAAA
12512894 TTTTAAA
1 TTTTAAA
12512901 GTAAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTTAAAA
Found at i:12515585 original size:41 final size:41
Alignment explanation
Indices: 12515430--12515594 Score: 215
Period size: 41 Copynumber: 4.0 Consensus size: 41
12515420 TTATTGTTTA
* * *
12515430 ATTCCGTTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGACGTATAGCCTG
* * * *
12515471 ATTTAGTTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGACGTATAGCCTG
*
12515512 ATTCAGTTCACCGGCACTTAGCCTGCTGGACGTATAGTCC-G
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGACGTATAG-CCTG
* * *
12515553 ATTCAATTCACCGGCACATAGCCTGCTAGACGTATAGTCTG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGACGTATAGCCTG
12515594 A
1 A
12515595 ACAATTTCAC
Statistics
Matches: 109, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
40 1 0.01
41 106 0.97
42 2 0.02
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (41 bp):
ATTCAGTTCACCGGCACTTAGCCTGCTAGACGTATAGCCTG
Found at i:12522175 original size:17 final size:17
Alignment explanation
Indices: 12522137--12522177 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
12522127 TGAAATTTAA
*
12522137 AATTTAA-TTTTCATAT
1 AATTTAATTTTTAATAT
12522153 --TTTAATTTTTAATAT
1 AATTTAATTTTTAATAT
12522168 AATTTAATTT
1 AATTTAATTT
12522178 GTATAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
14 5 0.24
15 8 0.38
17 8 0.38
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTAATTTTTAATAT
Found at i:12526060 original size:21 final size:21
Alignment explanation
Indices: 12526031--12526185 Score: 64
Period size: 21 Copynumber: 7.4 Consensus size: 21
12526021 TTGTGTTTAC
*
12526031 TTTCCGTTTAGCTCTTACGAG
1 TTTCTGTTTAGCTCTTACGAG
* * *
12526052 CTTT-TGTTTAACTCATATGAG
1 -TTTCTGTTTAGCTCTTACGAG
* * *
12526073 TTTCTGTTTAGCTCTAATGAA
1 TTTCTGTTTAGCTCTTACGAG
* * *
12526094 CTTCTGTTTAAC-CTTTA-TAGG
1 TTTCTGTTTAGCTC-TTACGA-G
* * *
12526115 TTTCCGTTCAGGTCTTACGAG
1 TTTCTGTTTAGCTCTTACGAG
* * * * * *
12526136 CTTCTGTTCAACCCTTATGGG
1 TTTCTGTTTAGCTCTTACGAG
* *
12526157 TTTCTGTTTAGCTCTAATGAG
1 TTTCTGTTTAGCTCTTACGAG
*
12526178 CTTCTGTT
1 TTTCTGTT
12526186 CAGCCTTCTG
Statistics
Matches: 95, Mismatches: 33, Indels: 11
0.68 0.24 0.08
Matches are distributed among these distances:
20 5 0.05
21 85 0.89
22 5 0.05
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.45
Consensus pattern (21 bp):
TTTCTGTTTAGCTCTTACGAG
Found at i:12526172 original size:84 final size:84
Alignment explanation
Indices: 12526031--12526185 Score: 238
Period size: 84 Copynumber: 1.8 Consensus size: 84
12526021 TTGTGTTTAC
* * * *
12526031 TTTCCGTTTAGCTCTTACGAGCTTTTGTTTAACTCATATGAGTTTCTGTTTAGCTCTAATGAACT
1 TTTCCGTTCAGCTCTTACGAGCTTCTGTTCAACCCATATGAGTTTCTGTTTAGCTCTAATGAACT
12526096 TCTGTTTAACCTTTATAGG
66 TCTGTTTAACCTTTATAGG
* * * *
12526115 TTTCCGTTCAGGTCTTACGAGCTTCTGTTCAACCCTTATGGGTTTCTGTTTAGCTCTAATGAGCT
1 TTTCCGTTCAGCTCTTACGAGCTTCTGTTCAACCCATATGAGTTTCTGTTTAGCTCTAATGAACT
12526180 TCTGTT
66 TCTGTT
12526186 CAGCCTTCTG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 63 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.45
Consensus pattern (84 bp):
TTTCCGTTCAGCTCTTACGAGCTTCTGTTCAACCCATATGAGTTTCTGTTTAGCTCTAATGAACT
TCTGTTTAACCTTTATAGG
Found at i:12526186 original size:42 final size:42
Alignment explanation
Indices: 12526031--12526187 Score: 161
Period size: 42 Copynumber: 3.7 Consensus size: 42
12526021 TTGTGTTTAC
* * * * * *
12526031 TTTCCGTTTAGCTCTTACGAGCTTTTGTTTAACTCATATGAG
1 TTTCCGTTTAGCTCTAACGAGCTTCTGTTCAACCCTTATGGG
* * * * * *
12526073 TTTCTGTTTAGCTCTAATGAACTTCTGTTTAACCTTTATAGG
1 TTTCCGTTTAGCTCTAACGAGCTTCTGTTCAACCCTTATGGG
* * *
12526115 TTTCCGTTCAGGTCTTACGAGCTTCTGTTCAACCCTTATGGG
1 TTTCCGTTTAGCTCTAACGAGCTTCTGTTCAACCCTTATGGG
* *
12526157 TTTCTGTTTAGCTCTAATGAGCTTCTGTTCA
1 TTTCCGTTTAGCTCTAACGAGCTTCTGTTCA
12526188 GCCTTCTGGC
Statistics
Matches: 91, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.45
Consensus pattern (42 bp):
TTTCCGTTTAGCTCTAACGAGCTTCTGTTCAACCCTTATGGG
Found at i:12530349 original size:43 final size:43
Alignment explanation
Indices: 12530240--12530353 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 43
12530230 ACGTCGTTAT
*
12530240 AGAACATGA-TCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAA
1 AGAACATGACT-TTTAGCGGCACTTTTCCCACAAACGCCGCTAA
* * * * * * **
12530283 AGAGCATGACCTCTGGTGACACTTTTCTTACAAACGCCGCTAA
1 AGAACATGACTTTTAGCGGCACTTTTCCCACAAACGCCGCTAA
*
12530326 ATAACATGACTTTTAGCGGCACTTTTCC
1 AGAACATGACTTTTAGCGGCACTTTTCC
12530354 AATCAAGTGA
Statistics
Matches: 53, Mismatches: 17, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (43 bp):
AGAACATGACTTTTAGCGGCACTTTTCCCACAAACGCCGCTAA
Found at i:12532130 original size:9 final size:10
Alignment explanation
Indices: 12532097--12532128 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
12532087 CGATAGTAAT
12532097 AAATTAAAAA
1 AAATTAAAAA
12532107 AAATTAAAAA
1 AAATTAAAAA
12532117 AAATTAAAAA
1 AAATTAAAAA
12532127 AA
1 AA
12532129 TTGAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAATTAAAAA
Found at i:12540601 original size:101 final size:101
Alignment explanation
Indices: 12540417--12540668 Score: 283
Period size: 101 Copynumber: 2.5 Consensus size: 101
12540407 ATTTTCTTTG
* * * * * * * * *
12540417 TGCCATAGTCCAACTATGGTCTTACACAT--GCATTGCCATGGCCCAACGATGGTCTTACATTCG
1 TGCCATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGATCTTACATTCA
* * * * *
12540480 TAGTGTCATAACTCAGTTATGGTCTTATCATCAGAA
66 AAGTGCCATAACCCAATTATGGTCTTATCATCAAAA
* * * * *
12540516 TGTCATAGCCTAGCTATGGTCTTACTTATAAATACTGTCATGGTCCAACCATGATCTTACATTCA
1 TGCCATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGATCTTACATTCA
* *
12540581 AAGTGCCATAACCCAATTATGGTCTTTTCATTAAAA
66 AAGTGCCATAACCCAATTATGGTCTTATCATCAAAA
* *
12540617 TGCCATAGCCCAGCTATGGTCTTACATATAAACATTGCCATGGTTCAACCAT
1 TGCCATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCAT
12540669 ACTCTTATCC
Statistics
Matches: 123, Mismatches: 28, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
99 23 0.19
101 100 0.81
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (101 bp):
TGCCATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGATCTTACATTCA
AAGTGCCATAACCCAATTATGGTCTTATCATCAAAA
Found at i:12540635 original size:33 final size:34
Alignment explanation
Indices: 12540575--12540639 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
12540565 CATGATCTTA
* *
12540575 CATTCAAAGTGCCATAACCCAATTATGGTCTTTT
1 CATTCAAAATGCCATAACCCAACTATGGTCTTTT
* *
12540609 CATT-AAAATGCCATAGCCCAGCTATGGTCTT
1 CATTCAAAATGCCATAACCCAACTATGGTCTT
12540640 ACATATAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 23 0.85
34 4 0.15
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (34 bp):
CATTCAAAATGCCATAACCCAACTATGGTCTTTT
Found at i:12561387 original size:41 final size:41
Alignment explanation
Indices: 12561330--12561650 Score: 245
Period size: 41 Copynumber: 7.8 Consensus size: 41
12561320 ATTTTTAAAC
* * *
12561330 CTTTAGCGGCGTTTTTATTTTAGCGCCGCTAATGGTCCGAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCCGAT
* * * **
12561371 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGC
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCCGAT
*
12561412 CTTTAGCGGCGTTTTTCTCTAAGCGCCGCTAATGCT-CGTAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCCG-AT
* * * * * **
12561453 CTTTAGTGGCGTTTTTATCTGAGCGCCACTAATTCTCTGGC
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCCGAT
* * * **
12561494 CTTTAGCGGCGTTTTTTTCTAAGTGTCGCTAATG-TTAGTAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCCG-AT
* ** * * *
12561535 CTTTAGTGGCGTTTTTATCCGAGCGCCACTAATGCTCTG-G
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCCGAT
** * ** *
12561575 CTTTTAGCGGCGTTTTATAGGTAAGCGCCGCGAATGCAT-TTAC
1 C-TTTAGCGGCGTTTT-TATCTAAGCGCCGCTAATGC-TCCGAT
** *
12561618 CTTTAGCGGCGTTTTTGCCGAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAAT
12561651 AGTAACAAAA
Statistics
Matches: 216, Mismatches: 56, Indels: 16
0.75 0.19 0.06
Matches are distributed among these distances:
40 4 0.02
41 178 0.82
42 32 0.15
43 2 0.01
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCCGAT
Found at i:12561466 original size:82 final size:82
Alignment explanation
Indices: 12561329--12561633 Score: 398
Period size: 82 Copynumber: 3.7 Consensus size: 82
12561319 GATTTTTAAA
* * * *
12561329 CCTTTAGCGGCGTTTTTATTTTAGCGCCGCTAATGGTCCG-ATCTTTAGCGGCGTTTTTATCTGA
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCT-CGTATCTTTAGTGGCGTTTTTATCTGA
12561393 GCGCCACTAATGCTCTGG
65 GCGCCACTAATGCTCTGG
*
12561411 CCTTTAGCGGCGTTTTTCTCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
*
12561476 CGCCACTAATTCTCTGG
66 CGCCACTAATGCTCTGG
* * * * * *
12561493 CCTTTAGCGGCGTTTTTTTCTAAGTGTCGCTAATGTTAGTATCTTTAGTGGCGTTTTTATCCGAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
12561558 CGCCACTAATGCTCTGG
66 CGCCACTAATGCTCTGG
* ** * * * *
12561575 CTTTTAGCGGCGTTTTATAGGTAAGCGCCGCGAATGCAT-TTACCTTTAGCGGCGTTTTT
1 CCTTTAGCGGCGTTTT-TATCTAAGCGCCGCTAATGC-TCGTATCTTTAGTGGCGTTTTT
12561634 GCCGAAGCGC
Statistics
Matches: 196, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
81 2 0.01
82 163 0.83
83 30 0.15
84 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (82 bp):
CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
CGCCACTAATGCTCTGG
Found at i:12563574 original size:10 final size:10
Alignment explanation
Indices: 12563559--12563595 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
12563549 TATTTTTACT
12563559 TATATATGGA
1 TATATATGGA
*
12563569 TATATATGAA
1 TATATATGGA
*
12563579 GATATATGGA
1 TATATATGGA
12563589 TATATAT
1 TATATAT
12563596 AGTTATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (10 bp):
TATATATGGA
Found at i:12564272 original size:8 final size:10
Alignment explanation
Indices: 12564250--12564284 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
12564240 TATTTTTACT
12564250 TATATATGGA
1 TATATATGGA
*
12564260 TATATATGAA
1 TATATATGGA
12564270 TATATATGGA
1 TATATATGGA
12564280 TATAT
1 TATAT
12564285 TTATAGTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (10 bp):
TATATATGGA
Found at i:12564395 original size:27 final size:27
Alignment explanation
Indices: 12564354--12564405 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
12564344 AATAAACAAA
* *
12564354 TAAATAAGTTAGTAATTATTTATTTGT
1 TAAATAAATTAGTAATTAATTATTTGT
*
12564381 TAAATAAATTGGTAATTAATTATTT
1 TAAATAAATTAGTAATTAATTATTT
12564406 AAAAGTAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (27 bp):
TAAATAAATTAGTAATTAATTATTTGT
Found at i:12564574 original size:84 final size:84
Alignment explanation
Indices: 12564429--12564594 Score: 278
Period size: 84 Copynumber: 2.0 Consensus size: 84
12564419 AAAGAAAATG
* * * *
12564429 AGAGTTTTAGCGGCGTTTCTATATAAAAATGCCGCAAAAGGTATCCTTTACCGGCGTTTTAGTCA
1 AGAGTTTTAGCGGCGTTTCTATATAAAAACGCCACAAAAGGTATCCTTTACCGGCGATTTAGTAA
12564494 AAAACGCCACAATTATTTA
66 AAAACGCCACAATTATTTA
* *
12564513 AGAGTTTTAGCGGTGTTTCTATATAAAAACGCCACAAAAGGTATCTTTTACCGGCGATTTAGTAA
1 AGAGTTTTAGCGGCGTTTCTATATAAAAACGCCACAAAAGGTATCCTTTACCGGCGATTTAGTAA
12564578 AAAACGCCACAATTATT
66 AAAACGCCACAATTATT
12564595 GCAATATACG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (84 bp):
AGAGTTTTAGCGGCGTTTCTATATAAAAACGCCACAAAAGGTATCCTTTACCGGCGATTTAGTAA
AAAACGCCACAATTATTTA
Found at i:12565699 original size:11 final size:11
Alignment explanation
Indices: 12565683--12565719 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
12565673 TTGACTTTTC
12565683 TAATTTGATTA
1 TAATTTGATTA
12565694 TAATTTGATTA
1 TAATTTGATTA
*
12565705 TAATTTCATTA
1 TAATTTGATTA
12565716 TAAT
1 TAAT
12565720 GTAGTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (11 bp):
TAATTTGATTA
Found at i:12566517 original size:37 final size:37
Alignment explanation
Indices: 12566474--12566546 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
12566464 TTTAATTACT
*
12566474 TCTGTTTTTTCGGTGCTAATGTATTTCTGTCTTTTTG
1 TCTGTTTTTTCGGTACTAATGTATTTCTGTCTTTTTG
*
12566511 TCTGTTTTTTCGGTACTAATGTATTTTTGTCTTTTT
1 TCTGTTTTTTCGGTACTAATGTATTTCTGTCTTTTT
12566547 TTTCCAGGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.10, C:0.12, G:0.16, T:0.62
Consensus pattern (37 bp):
TCTGTTTTTTCGGTACTAATGTATTTCTGTCTTTTTG
Found at i:12574529 original size:30 final size:30
Alignment explanation
Indices: 12574493--12574550 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
12574483 GTTAAGAGAC
*
12574493 CAGATGGCTCAGATGCAAGCGACAACAAGT
1 CAGATGGCTCAAATGCAAGCGACAACAAGT
12574523 CAGATGGCTCAAATGCAAGCGACAACAA
1 CAGATGGCTCAAATGCAAGCGACAACAA
12574551 TTTAGCAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (30 bp):
CAGATGGCTCAAATGCAAGCGACAACAAGT
Found at i:12574670 original size:66 final size:65
Alignment explanation
Indices: 12574563--12574733 Score: 227
Period size: 66 Copynumber: 2.6 Consensus size: 65
12574553 TAGCAAATTA
* * * *
12574563 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
12574627 G
65 G
*
12574628 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
12574693 G
65 G
* * * *
12574694 CAGCAGCTTAAAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
12574734 CGGCAGCGAG
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
65 2 0.02
66 88 0.94
67 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:12574730 original size:21 final size:21
Alignment explanation
Indices: 12574704--12574816 Score: 91
Period size: 21 Copynumber: 5.4 Consensus size: 21
12574694 CAGCAGCTTA
*
12574704 AAGCAGATGCGGCAGCAAGAG
1 AAGCAGAGGCGGCAGCAAGAG
*
12574725 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGGCGGCAGCAAGAG
* * * * *
12574746 AAGTACAGGCTGCAGCGAGGG
1 AAGCAGAGGCGGCAGCAAGAG
*** * *
12574767 AAGCAGAGGCTAAAGCGAGGG
1 AAGCAGAGGCGGCAGCAAGAG
* * *
12574788 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCGGCAGCAAGAG
12574809 AAGCAGAG
1 AAGCAGAG
12574817 CAGCGTCAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 80 1.00
ACGTcount: A:0.35, C:0.18, G:0.43, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Found at i:12574761 original size:42 final size:42
Alignment explanation
Indices: 12574715--12574816 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
12574705 AGCAGATGCG
* * ** *
12574715 GCAGCAAGAGAAGCAGAGGCGGCAGCGAGAGAAGTACAGGCT
1 GCAGCGAGGGAAGCAGAGGCGAAAGCGAGAGAAGCACAGGCT
* * *
12574757 GCAGCGAGGGAAGCAGAGGCTAAAGCGAGGGAAGCAGAGGCT
1 GCAGCGAGGGAAGCAGAGGCGAAAGCGAGAGAAGCACAGGCT
12574799 GCAGCGAGGGAAGCAGAG
1 GCAGCGAGGGAAGCAGAG
12574817 CAGCGTCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.34, C:0.18, G:0.44, T:0.04
Consensus pattern (42 bp):
GCAGCGAGGGAAGCAGAGGCGAAAGCGAGAGAAGCACAGGCT
Found at i:12574982 original size:43 final size:43
Alignment explanation
Indices: 12574935--12575117 Score: 188
Period size: 43 Copynumber: 4.3 Consensus size: 43
12574925 AGGTGTTGGC
* * *
12574935 CTTTAGTGGCGTTTTTGGTAAAAGCGCCGCTAAAGATAAGGTT
1 CTTTAGCGGCGTTTGTGGTAAAAGCGCCCCTAAAGATAAGGTT
* * *
12574978 CTTTAGCGGCATTTGTGGAAAAAGCGCCCCTAAAGATCATGG-T
1 CTTTAGCGGCGTTTGTGGTAAAAGCGCCCCTAAAGAT-AAGGTT
* * ** *
12575021 CTTTCGCAGCGTTTGTGGGGAAAGCGCCCCTAAAGATTAGGTT
1 CTTTAGCGGCGTTTGTGGTAAAAGCGCCCCTAAAGATAAGGTT
* ** * * * *
12575064 CTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTAAAAGCGCCCCTAAAGATAAGGTT
12575107 CTTTAGCGGCG
1 CTTTAGCGGCG
12575118 CTTCTCCCTA
Statistics
Matches: 114, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
42 2 0.02
43 109 0.96
44 3 0.03
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGTAAAAGCGCCCCTAAAGATAAGGTT
Found at i:12575352 original size:31 final size:33
Alignment explanation
Indices: 12575299--12575360 Score: 101
Period size: 31 Copynumber: 1.9 Consensus size: 33
12575289 AGCGGCATCT
*
12575299 TTTGCGGCGCTTATCAAAGCGCCGCTAAAAGTA
1 TTTGCGGCGCTTATAAAAGCGCCGCTAAAAGTA
12575332 TTTGCGGCGC-TA-AAAAGCGCCGCTAAAAG
1 TTTGCGGCGCTTATAAAAGCGCCGCTAAAAG
12575361 CCTGTTTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 16 0.57
32 2 0.07
33 10 0.36
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (33 bp):
TTTGCGGCGCTTATAAAAGCGCCGCTAAAAGTA
Found at i:12581439 original size:6 final size:6
Alignment explanation
Indices: 12581430--12581454 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12581420 TGGCCATGGG
12581430 TCCCCT TCCCCT TCCCCT TCCCCT T
1 TCCCCT TCCCCT TCCCCT TCCCCT T
12581455 GCTAGCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (6 bp):
TCCCCT
Found at i:12582971 original size:29 final size:30
Alignment explanation
Indices: 12582913--12582969 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12582903 ATAACTATAA
12582913 TTTAAATATAAATTATTTATTTTATTTTAT
1 TTTAAATATAAATTATTTATTTTATTTTAT
* *
12582943 TTTATATATAAA-TATTTGTTTATATTT
1 TTTAAATATAAATTATTTATTT-TATTT
12582970 ATGTATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (30 bp):
TTTAAATATAAATTATTTATTTTATTTTAT
Found at i:12583961 original size:20 final size:20
Alignment explanation
Indices: 12583936--12583975 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12583926 CGTAAAATGA
*
12583936 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
12583956 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
12583976 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:12583965 original size:34 final size:35
Alignment explanation
Indices: 12583921--12583987 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
12583911 CAGTAAAATA
*
12583921 TTTTCCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
* *
12583955 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
12583988 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:12584846 original size:26 final size:27
Alignment explanation
Indices: 12584795--12584848 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
12584785 TTTTAAAATA
* * *
12584795 TTTTAAAATACTTTTTTATTTTTTTAT
1 TTTTAAAATAATTTTTTATGTGTTTAT
12584822 TTTTAAAATAATTTTTTA-GTGTTTAT
1 TTTTAAAATAATTTTTTATGTGTTTAT
12584848 T
1 T
12584849 AAAAAAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (27 bp):
TTTTAAAATAATTTTTTATGTGTTTAT
Found at i:12591448 original size:3 final size:3
Alignment explanation
Indices: 12591434--12591478 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
12591424 AGGGTAATTT
*
12591434 CTA CTG CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
12591479 ATAATAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.31, C:0.33, G:0.02, T:0.33
Consensus pattern (3 bp):
CTA
Found at i:12595840 original size:14 final size:15
Alignment explanation
Indices: 12595814--12595842 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12595804 ATTTAACTTC
12595814 TTAAAAATATAAATA
1 TTAAAAATATAAATA
12595829 TTAAAAAT-TAAATA
1 TTAAAAATATAAATA
12595843 AATAATTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAAAATATAAATA
Found at i:12597678 original size:7 final size:7
Alignment explanation
Indices: 12597668--12597698 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
12597658 AAATATTAAA
*
12597668 AAATATT
1 AAATCTT
12597675 AAATCTT
1 AAATCTT
12597682 AAATCTT
1 AAATCTT
12597689 AAATCTT
1 AAATCTT
12597696 AAA
1 AAA
12597699 AAATATTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (7 bp):
AAATCTT
Found at i:12597810 original size:9 final size:8
Alignment explanation
Indices: 12597770--12597811 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
12597760 TTTTTAATAT
12597770 AATTTTTA
1 AATTTTTA
12597778 AATTTTT-
1 AATTTTTA
12597785 AATATTTTA
1 AAT-TTTTA
*
12597794 AATATTTA
1 AATTTTTA
12597802 CAATTTTTA
1 -AATTTTTA
12597811 A
1 A
12597812 TAACCTATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
7 3 0.10
8 16 0.55
9 10 0.34
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (8 bp):
AATTTTTA
Found at i:12609516 original size:139 final size:139
Alignment explanation
Indices: 12609300--12609593 Score: 588
Period size: 139 Copynumber: 2.1 Consensus size: 139
12609290 TATTATTATT
12609300 AATATTATTATATTATGAAATAAAATAAATTAAGACAAGTGTATGGTGATAAGATGGTATAAGTG
1 AATATTATTATATTATGAAATAAAATAAATTAAGACAAGTGTATGGTGATAAGATGGTATAAGTG
12609365 TAATAATATATATATACACTTGAATTATAATTATTTATTTACTTAAAATTTAAGTAAAAGATATT
66 TAATAATATATATATACACTTGAATTATAATTATTTATTTACTTAAAATTTAAGTAAAAGATATT
12609430 TATGAATTA
131 TATGAATTA
12609439 AATATTATTATATTATGAAATAAAATAAATTAAGACAAGTGTATGGTGATAAGATGGTATAAGTG
1 AATATTATTATATTATGAAATAAAATAAATTAAGACAAGTGTATGGTGATAAGATGGTATAAGTG
12609504 TAATAATATATATATACACTTGAATTATAATTATTTATTTACTTAAAATTTAAGTAAAAGATATT
66 TAATAATATATATATACACTTGAATTATAATTATTTATTTACTTAAAATTTAAGTAAAAGATATT
12609569 TATGAATTA
131 TATGAATTA
12609578 AATATTATTATATTAT
1 AATATTATTATATTAT
12609594 TATTATGTAT
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 155 1.00
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (139 bp):
AATATTATTATATTATGAAATAAAATAAATTAAGACAAGTGTATGGTGATAAGATGGTATAAGTG
TAATAATATATATATACACTTGAATTATAATTATTTATTTACTTAAAATTTAAGTAAAAGATATT
TATGAATTA
Found at i:12609588 original size:3 final size:3
Alignment explanation
Indices: 12609580--12609620 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
12609570 ATGAATTAAA
*
12609580 TAT TAT TA- TAT TAT TAT TAT GTAT TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
12609621 ACTAATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:12609600 original size:28 final size:25
Alignment explanation
Indices: 12609568--12609620 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
12609558 TAAAAGATAT
12609568 TTATGAATTAAATATTATTATATTATTA
1 TTATGAATT-AATATTA--ATATTATTA
* *
12609596 TTATGTATTATTATTAATATTATTA
1 TTATGAATTAATATTAATATTATTA
12609621 ACTAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.39
27 6 0.26
28 8 0.35
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
TTATGAATTAATATTAATATTATTA
Found at i:12609616 original size:19 final size:18
Alignment explanation
Indices: 12609583--12609618 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12609573 AATTAAATAT
*
12609583 TATTATATTATTATTATG
1 TATTATATTAATATTATG
12609601 TATTATTATTAATATTAT
1 TATTA-TATTAATATTAT
12609619 TAACTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TATTATATTAATATTATG
Found at i:12610123 original size:16 final size:17
Alignment explanation
Indices: 12610102--12610136 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12610092 TAAATGAGTT
12610102 AATTAGGAT-TAAATTG
1 AATTAGGATATAAATTG
*
12610118 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
12610135 AA
1 AA
12610137 AAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (17 bp):
AATTAGGATATAAATTG
Found at i:12612996 original size:18 final size:18
Alignment explanation
Indices: 12612973--12613008 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
12612963 TCTGGCATTC
12612973 TCACCTTCTCACTGTAGA
1 TCACCTTCTCACTGTAGA
12612991 TCACCTTCTCACTGTAGA
1 TCACCTTCTCACTGTAGA
12613009 ATAAGTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.33
Consensus pattern (18 bp):
TCACCTTCTCACTGTAGA
Found at i:12621941 original size:30 final size:26
Alignment explanation
Indices: 12621900--12621963 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 26
12621890 AGCTAGTGTC
12621900 CTCTTACATGTATGTATCTAAACTCATT
1 CTCTT-CATG-ATGTATCTAAACTCATT
12621928 CTCTTCATGATGTATCTAAACTCATT
1 CTCTTCATGATGTATCTAAACTCATT
12621954 CTCTTCATGA
1 CTCTTCATGA
12621964 GTTAAGTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 27 0.75
27 4 0.11
28 5 0.14
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (26 bp):
CTCTTCATGATGTATCTAAACTCATT
Found at i:12629817 original size:26 final size:24
Alignment explanation
Indices: 12629783--12629833 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
12629773 TAGTGTAATC
*
12629783 TTTGGTCCAATCAAAAAATAATTTTA
1 TTTGATCCAAT-AAAAAAT-ATTTTA
12629809 TTTGATCCAATAAAAAATATTTTA
1 TTTGATCCAATAAAAAATATTTTA
12629833 T
1 T
12629834 CATTTTCTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 7 0.29
25 7 0.29
26 10 0.42
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (24 bp):
TTTGATCCAATAAAAAATATTTTA
Found at i:12631939 original size:17 final size:19
Alignment explanation
Indices: 12631902--12631939 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12631892 AATATTTACG
*
12631902 TAATAATATTTTTTACATA
1 TAATAATATTTCTTACATA
12631921 TAATAATA-TTCTT-CATA
1 TAATAATATTTCTTACATA
12631938 TA
1 TA
12631940 CATATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 4 0.22
19 8 0.44
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATAATATTTCTTACATA
Found at i:12632312 original size:22 final size:22
Alignment explanation
Indices: 12632286--12632327 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12632276 ACAATTATTA
12632286 TTATTACTTTATTTG-TATTTAT
1 TTATTAC-TTATTTGTTATTTAT
*
12632308 TTATTGCTTATTTGTTATTT
1 TTATTACTTATTTGTTATTT
12632328 CTTAGTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.19, C:0.05, G:0.07, T:0.69
Consensus pattern (22 bp):
TTATTACTTATTTGTTATTTAT
Found at i:12637049 original size:10 final size:10
Alignment explanation
Indices: 12637031--12637063 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
12637021 GAAGTATAAT
*
12637031 AAAATATTAA
1 AAAAAATTAA
12637041 AAAAAATT-A
1 AAAAAATTAA
12637050 AAAAAATTAA
1 AAAAAATTAA
12637060 AAAA
1 AAAA
12637064 GGATACATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:12640668 original size:7 final size:7
Alignment explanation
Indices: 12640651--12640682 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
12640641 TTATTTAAAA
12640651 TATAA-T
1 TATAATT
12640657 TATAATT
1 TATAATT
12640664 TATAATT
1 TATAATT
12640671 TATAATT
1 TATAATT
12640678 TATAA
1 TATAA
12640683 AATAATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
TATAATT
Found at i:12642245 original size:13 final size:13
Alignment explanation
Indices: 12642229--12642294 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
12642219 TTTAAATCAA
12642229 ACTTTTCAAAAAT
1 ACTTTTCAAAAAT
* *
12642242 ACTTCTAAAAAAT
1 ACTTTTCAAAAAT
* * *
12642255 ACTTTTCCACAAC
1 ACTTTTCAAAAAT
*
12642268 ACTTTTCAAAAGT
1 ACTTTTCAAAAAT
*
12642281 ATTTTTCAAAAAT
1 ACTTTTCAAAAAT
12642294 A
1 A
12642295 ATGAAGAACT
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAAT
Found at i:12643733 original size:104 final size:104
Alignment explanation
Indices: 12643553--12643819 Score: 446
Period size: 104 Copynumber: 2.6 Consensus size: 104
12643543 TAACCGTTAT
* * *
12643553 TGGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCATCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
12643618 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
*
12643657 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
12643722 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* * **
12643761 TGGTGGATCA-CGCACATAGCACCACTAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
12643820 TTTATATACA
Statistics
Matches: 153, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
104 152 0.99
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.19
Consensus pattern (104 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:12646676 original size:24 final size:24
Alignment explanation
Indices: 12646649--12646700 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
12646639 TTAGTAAGTC
*
12646649 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
12646673 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
12646697 AAAT
1 AAAT
12646701 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:12647500 original size:95 final size:97
Alignment explanation
Indices: 12647373--12647562 Score: 303
Period size: 95 Copynumber: 2.0 Consensus size: 97
12647363 TCATACTTAC
* *
12647373 TTTCTTCTCTAGTTGGATATTTAATTGGACATTGGAAACCCTTATGATCTTGTGAACTACACTAA
1 TTTCTTCTCTAGTTAGATATTTAATTGGACATTGGAAACCCTTATGATCTTGTGAACTACACCAA
* *
12647438 TAACATTTCATAAAAGGTGATAGCTCAATCGT
66 TAACATTGCACAAAAGGTGATAGCTCAATCGT
* *
12647470 TTTC-TCTCTATTTAGAT-TTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTACACCAA
1 TTTCTTCTCTAGTTAGATATTTAATTGGACATTGGAAACCCTTATGATCTTGTGAACTACACCAA
*
12647533 TAACATTGCACAAAATGTGATAGCTCAATC
66 TAACATTGCACAAAAGGTGATAGCTCAATC
12647563 CTATTCCTCC
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 71 0.83
96 11 0.13
97 4 0.05
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (97 bp):
TTTCTTCTCTAGTTAGATATTTAATTGGACATTGGAAACCCTTATGATCTTGTGAACTACACCAA
TAACATTGCACAAAAGGTGATAGCTCAATCGT
Found at i:12649391 original size:24 final size:25
Alignment explanation
Indices: 12649347--12649394 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
12649337 AAACAACTCT
*
12649347 AAAAGAAACTTAAAAGTAATTCTTG
1 AAAAGAAACTCAAAAGTAATTCTTG
12649372 AAAA-AAACTCAAAGAG-AATTCTT
1 AAAAGAAACTCAAA-AGTAATTCTT
12649395 ATCAACTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.25
Consensus pattern (25 bp):
AAAAGAAACTCAAAAGTAATTCTTG
Found at i:12651887 original size:103 final size:104
Alignment explanation
Indices: 12651708--12651972 Score: 417
Period size: 103 Copynumber: 2.6 Consensus size: 104
12651698 AACCGTTATT
* * * *
12651708 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
12651773 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
12651811 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGG
12651875 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
12651915 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
12651973 TTATGTACAA
Statistics
Matches: 149, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
102 1 0.01
103 82 0.55
104 65 0.44
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:12652334 original size:30 final size:29
Alignment explanation
Indices: 12652300--12652364 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
12652290 TAATCCACCA
12652300 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
12652330 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
12652360 CCCAA
1 CCCAA
12652365 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:12652338 original size:31 final size:30
Alignment explanation
Indices: 12652307--12652364 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12652297 CCACCCAACT
12652307 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
12652337 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
12652365 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:12654464 original size:80 final size:81
Alignment explanation
Indices: 12654347--12654504 Score: 300
Period size: 80 Copynumber: 2.0 Consensus size: 81
12654337 ATATATATAT
12654347 ATATACATGTACACAAAAAAAAATACATAAGTTTAAAACAATTAAAATAATATCAAAATTAATTA
1 ATATACATGTACACAAAAAAAAATACATAAGTTTAAAACAATTAAAATAATATCAAAATTAATTA
12654412 AATAAATTAAACAAAA
66 AATAAATTAAACAAAA
*
12654428 ATATACATGTACAC-ACAAAAAATACATAAGTTTAAAACAATTAAAATAATATCAAAATTAATTA
1 ATATACATGTACACAAAAAAAAATACATAAGTTTAAAACAATTAAAATAATATCAAAATTAATTA
12654492 AATAAATTAAACA
66 AATAAATTAAACA
12654505 TGTGTACACA
Statistics
Matches: 76, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
80 62 0.82
81 14 0.18
ACGTcount: A:0.61, C:0.09, G:0.03, T:0.27
Consensus pattern (81 bp):
ATATACATGTACACAAAAAAAAATACATAAGTTTAAAACAATTAAAATAATATCAAAATTAATTA
AATAAATTAAACAAAA
Found at i:12655760 original size:17 final size:17
Alignment explanation
Indices: 12655735--12655781 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
12655725 GGTTTCTGAA
* * *
12655735 TTTGCTTTGGGCTTCTG
1 TTTGGTTTGGGCCTCAG
12655752 TTTGGTTTGGGCCTCAG
1 TTTGGTTTGGGCCTCAG
*
12655769 TTGGGTTTGGGCC
1 TTTGGTTTGGGCC
12655782 ACATAGGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.02, C:0.17, G:0.36, T:0.45
Consensus pattern (17 bp):
TTTGGTTTGGGCCTCAG
Found at i:12661120 original size:30 final size:31
Alignment explanation
Indices: 12661081--12661140 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
12661071 AGAGATGGGA
*
12661081 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
12661112 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
12661141 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:12661530 original size:12 final size:12
Alignment explanation
Indices: 12661513--12661560 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
12661503 ATAAATACCA
12661513 AAAAATTATTTT
1 AAAAATTATTTT
*
12661525 AAAAATTA---A
1 AAAAATTATTTT
*
12661534 AAAAAGTATTTT
1 AAAAATTATTTT
12661546 AAAAA-TATTTT
1 AAAAATTATTTT
12661557 AAAA
1 AAAA
12661561 TTAAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
9 7 0.23
11 10 0.33
12 13 0.43
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (12 bp):
AAAAATTATTTT
Found at i:12661538 original size:21 final size:21
Alignment explanation
Indices: 12661512--12661551 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12661502 AATAAATACC
*
12661512 AAAAAATTATTTTAAAAATTA
1 AAAAAAGTATTTTAAAAATTA
12661533 AAAAAAGTATTTTAAAAAT
1 AAAAAAGTATTTTAAAAAT
12661552 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
AAAAAAGTATTTTAAAAATTA
Found at i:12661566 original size:17 final size:17
Alignment explanation
Indices: 12661544--12661590 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
12661534 AAAAAGTATT
*
12661544 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
*
12661561 TTAAAAAAATTTAAAAA
1 TTAAAAATATTTAAAAA
* *
12661578 ATAAATATATTTA
1 TTAAAAATATTTA
12661591 TTATATCGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:12661916 original size:14 final size:15
Alignment explanation
Indices: 12661892--12661920 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12661882 AATAAATGAA
12661892 AAAATATATTAAATT
1 AAAATATATTAAATT
12661907 AAAA-ATATTAAATT
1 AAAATATATTAAATT
12661921 TTTTTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATATATTAAATT
Found at i:12666915 original size:17 final size:18
Alignment explanation
Indices: 12666895--12666929 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12666885 AGTCTTTCCT
12666895 AACCCT-ACTTAAAAAAA
1 AACCCTAACTTAAAAAAA
12666912 AACCCTAACTTAAAAAAA
1 AACCCTAACTTAAAAAAA
12666930 TGGACACGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.60, C:0.23, G:0.00, T:0.17
Consensus pattern (18 bp):
AACCCTAACTTAAAAAAA
Found at i:12667840 original size:11 final size:11
Alignment explanation
Indices: 12667822--12667864 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
12667812 TTATTTTTTT
12667822 TACTATTTTGC
1 TACTATTTTGC
* *
12667833 TACAATTTTAC
1 TACTATTTTGC
* *
12667844 TATTATGTTGC
1 TACTATTTTGC
12667855 TACTATTTTG
1 TACTATTTTG
12667865 TTGTATAACT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.53
Consensus pattern (11 bp):
TACTATTTTGC
Found at i:12695104 original size:97 final size:97
Alignment explanation
Indices: 12694938--12695132 Score: 354
Period size: 97 Copynumber: 2.0 Consensus size: 97
12694928 TCTATCTTTT
*
12694938 ACCTACCCTTAGCCAAGCTACGTTACAACCTATTTAAAATACCTATTGATTCAAATTTATATGGT
1 ACCTACCCCTAGCCAAGCTACGTTACAACCTATTTAAAATACCTATTGATTCAAATTTATATGGT
12695003 GACTACATTAGTGGAGAGAAATTGCAAAACTC
66 GACTACATTAGTGGAGAGAAATTGCAAAACTC
* * *
12695035 ACCTACCCCTAGCCAAGCTACGTTACAACCTATTTAAAATACTTATTGATTCAAATTTCTATTGT
1 ACCTACCCCTAGCCAAGCTACGTTACAACCTATTTAAAATACCTATTGATTCAAATTTATATGGT
12695100 GACTACATTAGTGGAGAGAAATTGCAAAACTC
66 GACTACATTAGTGGAGAGAAATTGCAAAACTC
12695132 A
1 A
12695133 ACTTATGAAG
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 94 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (97 bp):
ACCTACCCCTAGCCAAGCTACGTTACAACCTATTTAAAATACCTATTGATTCAAATTTATATGGT
GACTACATTAGTGGAGAGAAATTGCAAAACTC
Found at i:12699115 original size:4 final size:4
Alignment explanation
Indices: 12699106--12699133 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
12699096 TAAATGACAC
12699106 TCCA TCCA TCCA TCCA TCCA TCCA TCCA
1 TCCA TCCA TCCA TCCA TCCA TCCA TCCA
12699134 CTACAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.50, G:0.00, T:0.25
Consensus pattern (4 bp):
TCCA
Found at i:12705093 original size:3 final size:3
Alignment explanation
Indices: 12705085--12705116 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12705075 CCCAGAACCA
12705085 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12705117 GTTCAACTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12706866 original size:20 final size:20
Alignment explanation
Indices: 12706829--12706866 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12706819 TTACTTACAA
*
12706829 ATATTTAAAAATTATATTTT
1 ATATTTAAAAAATATATTTT
12706849 ATATATTAAAAAAT-TATT
1 ATAT-TTAAAAAATATATT
12706867 AATGAGTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTTAAAAAATATATTTT
Found at i:12708323 original size:129 final size:129
Alignment explanation
Indices: 12708093--12708326 Score: 414
Period size: 129 Copynumber: 1.8 Consensus size: 129
12708083 TCGATCTCGA
**
12708093 CCCTGCTCGAAATATGGGCCTAAAAATTTATCCAAACCCAAACCCAGCTCGGCCAGGGCCATATT
1 CCCTGCTCGAAATATGGGCCTAAAAATTTATCCAAACCCAAACCCAGCTCGGCCAGACCCATATT
12708158 AAATTTTACAACACCAAAAAAGTATATATTTAATATATATATATTTGTCCAAGCCCGAGCCCCG
66 AAATTTTACAACACCAAAAAAGTATATATTTAATATATATATATTTGTCCAAGCCCGAGCCCCG
* * * *
12708222 CCCTGCTCGAAATATGGGCCTAAAAATTTGTCCAAGCCCAAGCCCAGCTCGGCCCGACCCATATT
1 CCCTGCTCGAAATATGGGCCTAAAAATTTATCCAAACCCAAACCCAGCTCGGCCAGACCCATATT
12708287 AAATTTTACAACACCAAAAAAGTATATATTTAATATATAT
66 AAATTTTACAACACCAAAAAAGTATATATTTAATATATAT
12708327 TTGATTAAAA
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 99 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (129 bp):
CCCTGCTCGAAATATGGGCCTAAAAATTTATCCAAACCCAAACCCAGCTCGGCCAGACCCATATT
AAATTTTACAACACCAAAAAAGTATATATTTAATATATATATATTTGTCCAAGCCCGAGCCCCG
Found at i:12708344 original size:17 final size:17
Alignment explanation
Indices: 12708322--12708354 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12708312 ATATTTAATA
12708322 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
12708339 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
12708355 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:12714990 original size:20 final size:20
Alignment explanation
Indices: 12714958--12714998 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
12714948 TTATATACCA
*
12714958 ATTAAAATTAATA-TTTAGC
1 ATTAAAATAAATACTTTAGC
12714977 ATTATAAATAAATACTTTAGC
1 ATTA-AAATAAATACTTTAGC
12714998 A
1 A
12714999 AAGCATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 8 0.42
21 7 0.37
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (20 bp):
ATTAAAATAAATACTTTAGC
Found at i:12715888 original size:22 final size:23
Alignment explanation
Indices: 12715839--12715892 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
12715829 GACATTTGAC
*
12715839 TTATTATTTATTATTTTGAATTT
1 TTATTATTTATCATTTTGAATTT
* **
12715862 CTATTATTTA-CATTTTGTTTTT
1 TTATTATTTATCATTTTGAATTT
12715884 TTATTATTT
1 TTATTATTT
12715893 TTTGGAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (23 bp):
TTATTATTTATCATTTTGAATTT
Found at i:12716007 original size:14 final size:14
Alignment explanation
Indices: 12715986--12716025 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
12715976 TTGATTGCCA
12715986 GAAAAATGTTTTCC
1 GAAAAATGTTTTCC
* * *
12716000 GTAAAATGATTTCT
1 GAAAAATGTTTTCC
12716014 GAAAAATGTTTT
1 GAAAAATGTTTT
12716026 ACTTTTCTGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (14 bp):
GAAAAATGTTTTCC
Found at i:12716034 original size:20 final size:20
Alignment explanation
Indices: 12716009--12716048 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12715999 CGTAAAATGA
*
12716009 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
12716029 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
12716049 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:12716038 original size:34 final size:35
Alignment explanation
Indices: 12715994--12716060 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
12715984 CAGAAAAATG
*
12715994 TTTTCCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
* *
12716028 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
12716061 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:12727153 original size:5 final size:5
Alignment explanation
Indices: 12727143--12727167 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12727133 GAAACATGGA
12727143 AGCAT AGCAT AGCAT AGCAT AGCAT
1 AGCAT AGCAT AGCAT AGCAT AGCAT
12727168 GCCATCAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (5 bp):
AGCAT
Found at i:12733906 original size:92 final size:92
Alignment explanation
Indices: 12733749--12734025 Score: 509
Period size: 92 Copynumber: 3.0 Consensus size: 92
12733739 GAGCTGCCAG
*
12733749 GAAATAATAGAAAAAAGATGAATCAACAATTAAACCCAAAAAAAAATCTCTAATCAGAGCTCAAT
1 GAAATAATAGAAAAAAGATGAATCAACAATTAAACCCAAAACAAAATCTCTAATCAGAGCTCAAT
12733814 CCTAACAAAGTAAAAAAAGGCGAAGAA
66 CCTAACAAAGTAAAAAAAGGCGAAGAA
12733841 GAAATAATAGAAAAAAGATGAATCAACAATTAAACCCAAAACAAAATCTCTAATCAGAGCTCAAT
1 GAAATAATAGAAAAAAGATGAATCAACAATTAAACCCAAAACAAAATCTCTAATCAGAGCTCAAT
12733906 CCTAACAAAGTAAAAAAAGGCGAAGAA
66 CCTAACAAAGTAAAAAAAGGCGAAGAA
*
12733933 GAAATAATAGAAAAAAGATGAATCAACAATTAAACCCAAAACAAAATCTCTGATCAGAGCTCAAT
1 GAAATAATAGAAAAAAGATGAATCAACAATTAAACCCAAAACAAAATCTCTAATCAGAGCTCAAT
* *
12733998 CCGAACAAAAGTAAATAAAGGCGAAGAA
66 CCTAAC-AAAGTAAAAAAAGGCGAAGAA
12734026 AAGGATTGCT
Statistics
Matches: 180, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
92 160 0.89
93 20 0.11
ACGTcount: A:0.56, C:0.16, G:0.13, T:0.15
Consensus pattern (92 bp):
GAAATAATAGAAAAAAGATGAATCAACAATTAAACCCAAAACAAAATCTCTAATCAGAGCTCAAT
CCTAACAAAGTAAAAAAAGGCGAAGAA
Found at i:12735359 original size:40 final size:40
Alignment explanation
Indices: 12735304--12735382 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
12735294 ATTTGATTGA
* * *
12735304 GATTAAAATTTTAAAATTCGAAAAGTATAAAAATTAAAAT
1 GATTAAAATTTTAAAACTCAAAAAGTATAAAAACTAAAAT
12735344 GATTAAAATTTTAAAACTCAAAAAGTATAAAAACTAAAA
1 GATTAAAATTTTAAAACTCAAAAAGTATAAAAACTAAAA
12735383 ATCACGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.59, C:0.05, G:0.06, T:0.29
Consensus pattern (40 bp):
GATTAAAATTTTAAAACTCAAAAAGTATAAAAACTAAAAT
Found at i:12735621 original size:17 final size:18
Alignment explanation
Indices: 12735599--12735636 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
12735589 AGCAGTGCTT
12735599 GTGTTTAAGAA-AAACTA
1 GTGTTTAAGAAGAAACTA
* *
12735616 GTGTTTATGAAGAGACTA
1 GTGTTTAAGAAGAAACTA
12735634 GTG
1 GTG
12735637 CACGGCCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (18 bp):
GTGTTTAAGAAGAAACTA
Found at i:12740491 original size:22 final size:23
Alignment explanation
Indices: 12740457--12740507 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
12740447 AAGCTAAGCA
*
12740457 TTATTTAAAT-AAATACTCATAT
1 TTATATAAATAAAATACTCATAT
* *
12740479 TTATATAATTAAAATATTCATAT
1 TTATATAAATAAAATACTCATAT
12740502 TT-TATA
1 TTATATA
12740508 CTATAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (23 bp):
TTATATAAATAAAATACTCATAT
Found at i:12740516 original size:24 final size:23
Alignment explanation
Indices: 12740467--12740516 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
12740457 TTATTTAAAT
*
12740467 AAATACTCATATTTATATAATTA
1 AAATACTCATATTTATATAATAA
*
12740490 AAATATTCATATTT-TATACTATAA
1 AAATACTCATATTTATATA--ATAA
12740514 AAA
1 AAA
12740517 ATTTATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 13 0.57
24 6 0.26
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATACTCATATTTATATAATAA
Found at i:12740528 original size:14 final size:14
Alignment explanation
Indices: 12740509--12740536 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12740499 TATTTTATAC
12740509 TATAAAAAATTTAT
1 TATAAAAAATTTAT
12740523 TATAAAAAATTTAT
1 TATAAAAAATTTAT
12740537 AAATTGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TATAAAAAATTTAT
Found at i:12740619 original size:20 final size:22
Alignment explanation
Indices: 12740594--12740638 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
12740584 CAATAATACA
12740594 TTAAGAATACTA-T-TTAAAAT
1 TTAAGAATACTATTGTTAAAAT
* *
12740614 TTAAGATTATTATTGTTAAAAT
1 TTAAGAATACTATTGTTAAAAT
12740636 TTA
1 TTA
12740639 TTATTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 1 0.05
22 10 0.48
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (22 bp):
TTAAGAATACTATTGTTAAAAT
Found at i:12750256 original size:33 final size:33
Alignment explanation
Indices: 12750219--12750288 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
12750209 TTTGATGATT
12750219 ATCGTTAATCACATCAACTTCTTTAATGATCAA
1 ATCGTTAATCACATCAACTTCTTTAATGATCAA
* * * *
12750252 ATCGTTAGTTACATCAATTTTTTTAATGATCAA
1 ATCGTTAATCACATCAACTTCTTTAATGATCAA
12750285 ATCG
1 ATCG
12750289 ATCAATTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (33 bp):
ATCGTTAATCACATCAACTTCTTTAATGATCAA
Found at i:12764799 original size:2 final size:2
Alignment explanation
Indices: 12764794--12764827 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12764784 ATATATATAT
12764794 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12764828 GAGTACTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12766786 original size:20 final size:21
Alignment explanation
Indices: 12766752--12766792 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12766742 ATTTTTAAAA
*
12766752 TTTAAAAATTCAAAAAGTATT
1 TTTAAAAATTCAAAAAATATT
12766773 TTTAAAAATT-AAAAAATATT
1 TTTAAAAATTCAAAAAATATT
12766793 AAAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
TTTAAAAATTCAAAAAATATT
Done.