Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 16 of 97
Found at i:7638341 original size:17 final size:18
Alignment explanation
Indices: 7638305--7638342 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
7638295 TTGTGTTACA
* *
7638305 TTTTAGTCATTTGTGCAT
1 TTTTAGTCAATTATGCAT
7638323 TTTTAGTCAATTATG-AT
1 TTTTAGTCAATTATGCAT
7638340 TTT
1 TTT
7638343 GCTTTAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.21, C:0.08, G:0.13, T:0.58
Consensus pattern (18 bp):
TTTTAGTCAATTATGCAT
Found at i:7658956 original size:74 final size:74
Alignment explanation
Indices: 7658835--7658983 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
7658825 CTCAGATCTT
7658835 GAACCCCTATAGTGTTCCTCTATAAATGGGCTAGATAACCATGAAGCTGAAGATACGAACTTGTA
1 GAACCCCTATAGTGTTCCTCTATAAATGGGCTAGATAACCATGAAGCTGAAGATACGAACTTGTA
7658900 ACAGGTTTC
66 ACAGGTTTC
7658909 GAACCCCTATAGTGTTCCTCTATAAATGGGCTAGATAACCATGAAGCTGAAGATACGAACTTGTA
1 GAACCCCTATAGTGTTCCTCTATAAATGGGCTAGATAACCATGAAGCTGAAGATACGAACTTGTA
7658974 ACAGGTTTC
66 ACAGGTTTC
7658983 G
1 G
7658984 CCATTGGAGG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (74 bp):
GAACCCCTATAGTGTTCCTCTATAAATGGGCTAGATAACCATGAAGCTGAAGATACGAACTTGTA
ACAGGTTTC
Found at i:7667766 original size:2 final size:2
Alignment explanation
Indices: 7667759--7667816 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
7667749 CAGATAGAGC
* *
7667759 AT AT AT AT AA AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7667801 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
7667817 TCTTGGATTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7677326 original size:15 final size:15
Alignment explanation
Indices: 7677303--7677407 Score: 75
Period size: 15 Copynumber: 7.0 Consensus size: 15
7677293 CTGACGAACC
7677303 TCATCATCTTCATCA
1 TCATCATCTTCATCA
* * *
7677318 TCTTCATCTTCCTCT
1 TCATCATCTTCATCA
* * **
7677333 TCTTCATCCTCCCCA
1 TCATCATCTTCATCA
* **
7677348 TCCTCATCACCATCA
1 TCATCATCTTCATCA
* **
7677363 TCGTCATCCCCATCA
1 TCATCATCTTCATCA
*
7677378 TCATCATCTTCTTCA
1 TCATCATCTTCATCA
*
7677393 TCATCCTCTTCATCA
1 TCATCATCTTCATCA
7677408 CTCCCTCCAT
Statistics
Matches: 71, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 71 1.00
ACGTcount: A:0.19, C:0.42, G:0.01, T:0.38
Consensus pattern (15 bp):
TCATCATCTTCATCA
Found at i:7677393 original size:12 final size:12
Alignment explanation
Indices: 7677378--7677407 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
7677368 ATCCCCATCA
*
7677378 TCATCATCTTCT
1 TCATCATCCTCT
7677390 TCATCATCCTCT
1 TCATCATCCTCT
7677402 TCATCA
1 TCATCA
7677408 CTCCCTCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (12 bp):
TCATCATCCTCT
Found at i:7689258 original size:2 final size:2
Alignment explanation
Indices: 7689251--7689277 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7689241 GTTTTTAAGG
7689251 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
7689278 TTTTTTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7696556 original size:2 final size:2
Alignment explanation
Indices: 7696549--7696591 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
7696539 TATCACCCCT
* *
7696549 TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TG TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
7696591 T
1 T
7696592 TCTTTCTTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.44, G:0.02, T:0.53
Consensus pattern (2 bp):
TC
Found at i:7705730 original size:9 final size:10
Alignment explanation
Indices: 7705659--7705825 Score: 84
Period size: 10 Copynumber: 17.2 Consensus size: 10
7705649 GTTTAAGACT
7705659 TTTTTAAGGA
1 TTTTTAAGGA
* * **
7705669 TGTTTGAGTT
1 TTTTTAAGGA
*
7705679 TTTTTATGGA
1 TTTTTAAGGA
*
7705689 TTTTTAATG-
1 TTTTTAAGGA
7705698 TTTTTATAGGAA
1 TTTTTA-AGG-A
*
7705710 TTTTTGAGGA
1 TTTTTAAGGA
7705720 TTTTTAA-GA
1 TTTTTAAGGA
7705729 ---TTAAGGA
1 TTTTTAAGGA
*
7705736 --ATTAAGG-
1 TTTTTAAGGA
* *
7705743 TTTTTTAGTAGT
1 TTTTTAAG--GA
*
7705755 TTTTTAATGA
1 TTTTTAAGGA
7705765 TTTTTAAGG-
1 TTTTTAAGGA
*
7705774 TTTTCTATGGA
1 TTTT-TAAGGA
*
7705785 TTTTTAAGAA
1 TTTTTAAGGA
7705795 TTTTTAAGG-
1 TTTTTAAGGA
*
7705804 TTTTTAAAGA
1 TTTTTAAGGA
*
7705814 TTTTTAAAGA
1 TTTTTAAGGA
7705824 TT
1 TT
7705826 AAGGTTTTTT
Statistics
Matches: 119, Mismatches: 25, Indels: 26
0.70 0.15 0.15
Matches are distributed among these distances:
6 4 0.03
7 2 0.02
8 6 0.05
9 24 0.20
10 64 0.54
11 8 0.07
12 11 0.09
ACGTcount: A:0.28, C:0.01, G:0.18, T:0.54
Consensus pattern (10 bp):
TTTTTAAGGA
Found at i:7705776 original size:20 final size:20
Alignment explanation
Indices: 7705755--7705901 Score: 74
Period size: 20 Copynumber: 7.3 Consensus size: 20
7705745 TTTTAGTAGT
7705755 TTTTTAATGATTTTTAAGG-
1 TTTTTAATGATTTTTAAGGA
*
7705774 TTTTCT-ATGGATTTTTAAGAA
1 TTTT-TAAT-GATTTTTAAGGA
* *
7705795 TTTTTAA-GGTTTTTAAAGA
1 TTTTTAATGATTTTTAAGGA
* *
7705814 TTTTTAAAGA---TTAAGGTTT
1 TTTTTAATGATTTTTAAGG--A
* * *
7705833 TTTTTTATAGTTTCTTTAAAGA
1 TTTTTAAT-GATT-TTTAAGGA
* *
7705855 TTTTTAA-GTCTTTTTAAGTA
1 TTTTTAATG-ATTTTTAAGGA
* *
7705875 TTTCTAATGATTTTTAAGAA
1 TTTTTAATGATTTTTAAGGA
7705895 TTTTTAA
1 TTTTTAA
7705902 AGATATTTAT
Statistics
Matches: 94, Mismatches: 20, Indels: 27
0.67 0.14 0.19
Matches are distributed among these distances:
17 5 0.05
19 28 0.30
20 42 0.45
21 8 0.09
22 6 0.06
24 5 0.05
ACGTcount: A:0.29, C:0.03, G:0.12, T:0.56
Consensus pattern (20 bp):
TTTTTAATGATTTTTAAGGA
Found at i:7705791 original size:30 final size:28
Alignment explanation
Indices: 7705737--7705825 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 28
7705727 GATTAAGGAA
*
7705737 TTAAGGTTTTTTAGTAGTTTTTTAATGATTT
1 TTAAGG-TTTTTA-TAGATTTTTAA-GATTT
*
7705768 TTAAGGTTTTCTATGGATTTTTAAGAATTT
1 TTAAGGTTTT-TATAGATTTTTAAG-ATTT
*
7705798 TTAAGGTTTTTAAAGATTTTTAAAGATT
1 TTAAGGTTTTTATAGATTTTT-AAGATT
7705826 AAGGTTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
29 13 0.25
30 30 0.59
31 8 0.16
ACGTcount: A:0.28, C:0.01, G:0.16, T:0.55
Consensus pattern (28 bp):
TTAAGGTTTTTATAGATTTTTAAGATTT
Found at i:7705897 original size:10 final size:10
Alignment explanation
Indices: 7705854--7705901 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
7705844 TTCTTTAAAG
7705854 ATTTTTAAGT
1 ATTTTTAAGT
*
7705864 CTTTTTAAGT
1 ATTTTTAAGT
*
7705874 ATTTCTAA-T
1 ATTTTTAAGT
*
7705883 GATTTTTAAGA
1 -ATTTTTAAGT
7705894 ATTTTTAA
1 ATTTTTAA
7705902 AGATATTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 1 0.03
10 30 0.97
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.56
Consensus pattern (10 bp):
ATTTTTAAGT
Found at i:7705910 original size:20 final size:20
Alignment explanation
Indices: 7705867--7705910 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
7705857 TTTAAGTCTT
* * *
7705867 TTTAAGTATTTCTAATGATT
1 TTTAAGAATTTCTAAAGATA
*
7705887 TTTAAGAATTTTTAAAGATA
1 TTTAAGAATTTCTAAAGATA
7705907 TTTA
1 TTTA
7705911 TGTTGACTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.52
Consensus pattern (20 bp):
TTTAAGAATTTCTAAAGATA
Found at i:7706064 original size:1 final size:1
Alignment explanation
Indices: 7706060--7706120 Score: 95
Period size: 1 Copynumber: 61.0 Consensus size: 1
7706050 AAAAAGAAAG
** *
7706060 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAATTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
7706121 ATATTATTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.03, C:0.00, G:0.02, T:0.95
Consensus pattern (1 bp):
T
Found at i:7712789 original size:2 final size:2
Alignment explanation
Indices: 7712782--7712812 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7712772 AAGTTCTCAT
7712782 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7712813 TATCACAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7713363 original size:10 final size:10
Alignment explanation
Indices: 7713331--7713356 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
7713321 TTGTAGAATT
7713331 CCCTCCACAC
1 CCCTCCACAC
7713341 CCCTCCACAC
1 CCCTCCACAC
7713351 CCCTCC
1 CCCTCC
7713357 TCCCCCCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.73, G:0.00, T:0.12
Consensus pattern (10 bp):
CCCTCCACAC
Found at i:7718292 original size:26 final size:23
Alignment explanation
Indices: 7718243--7718316 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 23
7718233 TTTGTAAAAT
7718243 TTAAAATATTAATAGTTTATATATAA
1 TTAAAATATTAATA--TTA-ATATAA
*
7718269 TTGAAACATTATTAATATTAATATGA
1 TT-AAA-A-TATTAATATTAATATAA
7718295 TTAAAATATTAAATATTAATAT
1 TTAAAATATT-AATATTAATAT
7718317 TTAANTCCTC
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
23 4 0.09
24 12 0.28
25 3 0.07
26 9 0.21
27 6 0.14
28 1 0.02
29 8 0.19
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (23 bp):
TTAAAATATTAATATTAATATAA
Found at i:7725275 original size:24 final size:25
Alignment explanation
Indices: 7725228--7725275 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
7725218 TTTTGTTTTT
* *
7725228 TTAAAATATGAATAGAAAGGAAAAG
1 TTAAAAAATGAATAGAAAAGAAAAG
*
7725253 TTAAAAAAT-AATAGAAAATAAAA
1 TTAAAAAATGAATAGAAAAGAAAA
7725276 TACCAATAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (25 bp):
TTAAAAAATGAATAGAAAAGAAAAG
Found at i:7729694 original size:24 final size:25
Alignment explanation
Indices: 7729647--7729694 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
7729637 TTTTGTTTTT
* *
7729647 TTAAAATATGAATAGAAAGGAAAAG
1 TTAAAAAATGAATAGAAAAGAAAAG
*
7729672 TTAAAAAAT-AATAGAAAATAAAA
1 TTAAAAAATGAATAGAAAAGAAAA
7729695 TACCAATAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (25 bp):
TTAAAAAATGAATAGAAAAGAAAAG
Found at i:7730015 original size:31 final size:31
Alignment explanation
Indices: 7729977--7730038 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
7729967 TATCACTTAC
7729977 TATGTTTTTCTTTGATGATTAAAGATTATTG
1 TATGTTTTTCTTTGATGATTAAAGATTATTG
7730008 TATGTTTTTCTTTGATGATTAAAGATTATTG
1 TATGTTTTTCTTTGATGATTAAAGATTATTG
7730039 CAATATTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.03, G:0.16, T:0.55
Consensus pattern (31 bp):
TATGTTTTTCTTTGATGATTAAAGATTATTG
Found at i:7732574 original size:2 final size:2
Alignment explanation
Indices: 7732567--7732597 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
7732557 TATGTTCATA
*
7732567 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7732598 CACTGTAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:7732598 original size:12 final size:12
Alignment explanation
Indices: 7732563--7732599 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
7732553 ATTTTATGTT
7732563 CATA-ATATATA
1 CATATATATATA
*
7732574 TATATATATATA
1 CATATATATATA
7732586 CATATATATATA
1 CATATATATATA
7732598 CA
1 CA
7732600 CTGTAGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 3 0.13
12 20 0.87
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (12 bp):
CATATATATATA
Found at i:7734066 original size:14 final size:14
Alignment explanation
Indices: 7734043--7734099 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
7734033 GTTCAAATTG
7734043 CAAAAAAATAAAAT
1 CAAAAAAATAAAAT
*
7734057 CAAAATAATAAAAT
1 CAAAAAAATAAAAT
* *
7734071 TAAAAGATAAAAAAAT
1 CAAAA-A-AATAAAAT
* *
7734087 CAGAAAAAGAAAA
1 CAAAAAAATAAAA
7734100 AGGAATTAGA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
14 23 0.68
15 1 0.03
16 10 0.29
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.14
Consensus pattern (14 bp):
CAAAAAAATAAAAT
Found at i:7740100 original size:24 final size:24
Alignment explanation
Indices: 7740068--7740114 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
7740058 TTTTTGAAGA
*
7740068 ATATTATA-TTGAAAATATAAAAAT
1 ATATGATATTTGAAAA-ATAAAAAT
7740092 ATATGATATTTTGAAAAATAAAA
1 ATATGATA-TTTGAAAAATAAAA
7740115 GGGATTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 6 0.30
26 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.36
Consensus pattern (24 bp):
ATATGATATTTGAAAAATAAAAAT
Found at i:7740807 original size:43 final size:42
Alignment explanation
Indices: 7740759--7740886 Score: 157
Period size: 43 Copynumber: 3.0 Consensus size: 42
7740749 TATACTTTTT
** * *
7740759 TGTAATAGACTCCATTATTGAGGAGACTTTAACTTAGGTGTTG
1 TGTAATAGACTATATTATTGAGGAGACTTT-ACTTAGGCGTCG
* *
7740802 TGTAATGGACTATATCATTGAGGAGACCTTTACTTAGGCGTCG
1 TGTAATAGACTATATTATTGAGGAGA-CTTTACTTAGGCGTCG
* *
7740845 TGTAATAGACGATATTATTGAGGAGACCTTGACTTAGGCGTC
1 TGTAATAGACTATATTATTGAGGAGA-CTTTACTTAGGCGTC
7740887 AACCATGAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
43 70 0.95
44 4 0.05
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (42 bp):
TGTAATAGACTATATTATTGAGGAGACTTTACTTAGGCGTCG
Found at i:7742530 original size:14 final size:14
Alignment explanation
Indices: 7742507--7742536 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7742497 TTTAAAGAAT
*
7742507 TCTACTAAAGAAAC
1 TCTACCAAAGAAAC
7742521 TCTACCAAAGAAAC
1 TCTACCAAAGAAAC
7742535 TC
1 TC
7742537 CTCACAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.27, G:0.07, T:0.20
Consensus pattern (14 bp):
TCTACCAAAGAAAC
Found at i:7745423 original size:31 final size:31
Alignment explanation
Indices: 7745383--7745446 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
7745373 TCTACTTGTA
*
7745383 AAAACGAGCCCAAATACCTTAAAACCAGAGG
1 AAAACGAGCCCAAAGACCTTAAAACCAGAGG
* * *
7745414 AAAATGAGCCCAAAGAGCTTAAAACCATAGG
1 AAAACGAGCCCAAAGACCTTAAAACCAGAGG
7745445 AA
1 AA
7745447 TAAATCTCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (31 bp):
AAAACGAGCCCAAAGACCTTAAAACCAGAGG
Found at i:7748497 original size:22 final size:22
Alignment explanation
Indices: 7748471--7748518 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
7748461 CTGCCAAAAC
7748471 AGAATAATTTCTCCCTGCAGCG
1 AGAATAATTTCTCCCTGCAGCG
* *
7748493 AGAATGATTTCTCGCTGCAGCG
1 AGAATAATTTCTCCCTGCAGCG
7748515 AGAA
1 AGAA
7748519 GCAAGGCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (22 bp):
AGAATAATTTCTCCCTGCAGCG
Found at i:7748797 original size:40 final size:37
Alignment explanation
Indices: 7748742--7748844 Score: 127
Period size: 38 Copynumber: 2.7 Consensus size: 37
7748732 ACCCGGTTCA
* *
7748742 TGTGCATTCCCCCACATCGTGCACAT-AGCTGGCGTTATCG
1 TGTGCATCCCCCCACATCGTGCACATCAG-T-GC--CATCG
7748782 TGTGCATCCCCCCACATCGTGCACAATCAGTGCCATCG
1 TGTGCATCCCCCCACATCGTGCAC-ATCAGTGCCATCG
*
7748820 TGTACATCCCCCCACATCGTGCACA
1 TGTGCATCCCCCCACATCGTGCACA
7748845 CGGGCACTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
37 1 0.02
38 27 0.47
40 25 0.43
41 3 0.05
42 2 0.03
ACGTcount: A:0.20, C:0.38, G:0.18, T:0.23
Consensus pattern (37 bp):
TGTGCATCCCCCCACATCGTGCACATCAGTGCCATCG
Found at i:7748837 original size:19 final size:19
Alignment explanation
Indices: 7748778--7748840 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
7748768 AGCTGGCGTT
*
7748778 ATCGTGTGCATCCCCCCAC
1 ATCGTGTACATCCCCCCAC
* ****
7748797 ATCGTGCACAATCAGTGC-C
1 ATCGTGTAC-ATCCCCCCAC
7748816 ATCGTGTACATCCCCCCAC
1 ATCGTGTACATCCCCCCAC
7748835 ATCGTG
1 ATCGTG
7748841 CACACGGGCA
Statistics
Matches: 31, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
18 4 0.13
19 23 0.74
20 4 0.13
ACGTcount: A:0.21, C:0.40, G:0.17, T:0.22
Consensus pattern (19 bp):
ATCGTGTACATCCCCCCAC
Found at i:7748979 original size:45 final size:45
Alignment explanation
Indices: 7748904--7749008 Score: 167
Period size: 45 Copynumber: 2.4 Consensus size: 45
7748894 GCATCCCCCA
* *
7748904 CATCATGCAC-ACATACGGTTACAATCATCATACACAATATCAAT
1 CATCATGCACAACACACGGTTACAATAATCATACACAATATCAAT
*
7748948 CATCATGCACAACACACGGTTACAGTAATCATACACAATATCAAT
1 CATCATGCACAACACACGGTTACAATAATCATACACAATATCAAT
*
7748993 TATCATGCACAACACA
1 CATCATGCACAACACA
7749009 TATATATTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
44 10 0.18
45 46 0.82
ACGTcount: A:0.42, C:0.28, G:0.08, T:0.23
Consensus pattern (45 bp):
CATCATGCACAACACACGGTTACAATAATCATACACAATATCAAT
Found at i:7761039 original size:13 final size:13
Alignment explanation
Indices: 7761021--7761045 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7761011 GGAAAATGGG
7761021 ATTTTATAAAATA
1 ATTTTATAAAATA
7761034 ATTTTATAAAAT
1 ATTTTATAAAAT
7761046 TTTTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:7762212 original size:15 final size:14
Alignment explanation
Indices: 7762189--7762231 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
7762179 GATCAAAGAT
7762189 TTTGGTTTTAAAGC
1 TTTGGTTTTAAAGC
*
7762203 TTTGGATTTTAAAGTT
1 TTTGG-TTTTAAAG-C
*
7762219 TTTAGTTTTAAAG
1 TTTGGTTTTAAAG
7762232 TTGTTTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.20
15 16 0.64
16 4 0.16
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.53
Consensus pattern (14 bp):
TTTGGTTTTAAAGC
Found at i:7767691 original size:159 final size:158
Alignment explanation
Indices: 7767402--7767718 Score: 598
Period size: 159 Copynumber: 2.0 Consensus size: 158
7767392 TCTACCACAC
*
7767402 AGACAGTAAGTTTTTAGCACCAACACTGGGTCTATTTTGGGCCACTTGTCATTGTAACCATTATT
1 AGACAGTAAGTTTCTAGCACCAACACTGGGTCTATTTTGGGCCACTTGTCATTGTAACCATTATT
7767467 GTACATTATAACTTAGTAAATTTTTGTATGTATGAATTTATTTTACTTACACATTACAAAAGATT
66 GTACATTATAACTTAGTAAATTTTTGTATGTATGAATTTATTTTACTTACACATTACAAAAGATT
7767532 TCTTACACGTGTTTCTATAAATATTGTT
131 TCTTACACGTGTTTCTATAAATATTGTT
* *
7767560 NAGACAGTAGGTTTCTAGCACCAACACTGGGTGTATTTTGGGCCACTTGTCATTGTAACCATTAT
1 -AGACAGTAAGTTTCTAGCACCAACACTGGGTCTATTTTGGGCCACTTGTCATTGTAACCATTAT
7767625 TGTACATTATAACTTAGTAAATTTTTGTATGTATGAATTTATTTTACTTACACATTACAAAAGAT
65 TGTACATTATAACTTAGTAAATTTTTGTATGTATGAATTTATTTTACTTACACATTACAAAAGAT
7767690 TTCTTACACGTGTTTCTATAAATATTGTT
130 TTCTTACACGTGTTTCTATAAATATTGTT
7767719 TTATATAAAA
Statistics
Matches: 155, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
159 155 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (158 bp):
AGACAGTAAGTTTCTAGCACCAACACTGGGTCTATTTTGGGCCACTTGTCATTGTAACCATTATT
GTACATTATAACTTAGTAAATTTTTGTATGTATGAATTTATTTTACTTACACATTACAAAAGATT
TCTTACACGTGTTTCTATAAATATTGTT
Found at i:7777191 original size:17 final size:17
Alignment explanation
Indices: 7777166--7777198 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
7777156 TTATTTTTAA
7777166 TATAATTTCTTATATTG
1 TATAATTTCTTATATTG
*
7777183 TATATTTTCTTATATT
1 TATAATTTCTTATATT
7777199 AGAAGCTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TATAATTTCTTATATTG
Found at i:7779111 original size:14 final size:15
Alignment explanation
Indices: 7779094--7779132 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
7779084 TAAAGAATAC
*
7779094 AAAAAGAAGATAAA-
1 AAAAAGAAGAGAAAG
*
7779108 AAAAAAAAGAGAAAG
1 AAAAAGAAGAGAAAG
7779123 AAAAAGAAGA
1 AAAAAGAAGA
7779133 ATGGGAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (15 bp):
AAAAAGAAGAGAAAG
Found at i:7781343 original size:29 final size:29
Alignment explanation
Indices: 7781310--7781393 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
7781300 GAGACCAAAG
7781310 TTATATGCTATGTTTAAAAAATATTATTA
1 TTATATGCTATGTTTAAAAAATATTATTA
* *
7781339 TTATATG-TCATATTTAAAAAATATTGTTA
1 TTATATGCT-ATGTTTAAAAAATATTATTA
* * *
7781368 TTACATGCTACGTTCAAAAAAATATT
1 TTATATGCTATGTT-TAAAAAATATT
7781394 GTTACACGCC
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
28 1 0.02
29 34 0.74
30 11 0.24
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (29 bp):
TTATATGCTATGTTTAAAAAATATTATTA
Found at i:7781416 original size:29 final size:27
Alignment explanation
Indices: 7781385--7781438 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
7781375 CTACGTTCAA
* *
7781385 AAAAATATTGTTACACGCCATGCTTAAG
1 AAAAA-ATTGTTACACACCATACTTAAG
7781413 AAAAAATTGTTACACACCATACTTAA
1 AAAAAATTGTTACACACCATACTTAA
7781439 AGTGTTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (27 bp):
AAAAAATTGTTACACACCATACTTAAG
Found at i:7782856 original size:7 final size:7
Alignment explanation
Indices: 7782813--7782863 Score: 52
Period size: 7 Copynumber: 7.0 Consensus size: 7
7782803 TAATATATAT
7782813 AATAAAA
1 AATAAAA
7782820 AATAAATTA
1 AATAAA--A
7782829 AAT--AA
1 AATAAAA
7782834 AATAAAA
1 AATAAAA
7782841 AGATAAAA
1 A-ATAAAA
7782849 AATGAAAA
1 AAT-AAAA
7782857 AATAAAA
1 AATAAAA
7782864 GAAAAGAGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
5 4 0.11
7 16 0.42
8 14 0.37
9 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (7 bp):
AATAAAA
Found at i:7782859 original size:28 final size:28
Alignment explanation
Indices: 7782814--7782868 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
7782804 AATATATATA
*
7782814 ATAAAAAATAAATTAAATAAAATAAAAAG
1 ATAAAAAATAAA-TAAATAAAAGAAAAAG
7782843 ATAAAAAATGAAA-AAATAAAAGAAAA
1 ATAAAAAAT-AAATAAATAAAAGAAAA
7782869 GAGAGAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 12 0.50
29 9 0.38
30 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (28 bp):
ATAAAAAATAAATAAATAAAAGAAAAAG
Found at i:7783688 original size:13 final size:13
Alignment explanation
Indices: 7783670--7783701 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
7783660 CAGGTAGAGA
7783670 GAGAAAATGAAGG
1 GAGAAAATGAAGG
*
7783683 GAGAAAATGAGGG
1 GAGAAAATGAAGG
7783696 GAGAAA
1 GAGAAA
7783702 GAAAAAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.41, T:0.06
Consensus pattern (13 bp):
GAGAAAATGAAGG
Found at i:7784139 original size:5 final size:5
Alignment explanation
Indices: 7784129--7784169 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
7784119 ACATTTGAAC
7784129 AAATA AAATA AAATA AAAT- -AATA ATAATA AAAT- AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA A-AATA AAATA AAATA AAA
7784170 AGAGATGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
3 3 0.09
4 4 0.12
5 20 0.62
6 5 0.16
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAATA
Found at i:7784299 original size:5 final size:5
Alignment explanation
Indices: 7784280--7784317 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
7784270 ATAAATGAAT
*
7784280 AAAT- AAATAA AAATA AAATA GAATA AAATA AAATA AAA
1 AAATA AAAT-A AAATA AAATA AAATA AAATA AAATA AAA
7784318 GAATAAGACC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
4 4 0.13
5 22 0.73
6 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:7784307 original size:15 final size:15
Alignment explanation
Indices: 7784280--7784316 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
7784270 ATAAATGAAT
7784280 AAATAAATAAAAATA
1 AAATAAATAAAAATA
7784295 AAATAGAAT-AAAATA
1 AAATA-AATAAAAATA
7784310 AAATAAA
1 AAATAAA
7784317 AGAATAAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 16 0.76
16 3 0.14
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
AAATAAATAAAAATA
Found at i:7791832 original size:48 final size:48
Alignment explanation
Indices: 7791768--7791862 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
7791758 GTTAGTCTAG
* * ** **
7791768 CTTTGCATTGTTAGAGAAGACTTTGACTTGGCATATCTGTTGATCTCA
1 CTTTGCATTATCAGAGAAGACTTTGACTAAGCATATCCATTGATCTCA
7791816 CTTTGCATTATCAGAGAAGACTTTGACTAAGCATATCCATTGATCTC
1 CTTTGCATTATCAGAGAAGACTTTGACTAAGCATATCCATTGATCTC
7791863 TCTAGAACTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (48 bp):
CTTTGCATTATCAGAGAAGACTTTGACTAAGCATATCCATTGATCTCA
Found at i:7799100 original size:20 final size:20
Alignment explanation
Indices: 7799053--7799100 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
7799043 AACAAAAAAA
* *
7799053 TAAATAAATAAATAAAATAGT
1 TAAA-AAATAAAAAAAAGAGT
**
7799074 TTTAAAATAAAAAAAAGAGT
1 TAAAAAATAAAAAAAAGAGT
7799094 TAAAAAA
1 TAAAAAA
7799101 AACTGCATAG
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (20 bp):
TAAAAAATAAAAAAAAGAGT
Found at i:7799335 original size:16 final size:16
Alignment explanation
Indices: 7799314--7799346 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
7799304 CTTTAAAAAT
7799314 GTTGAAACTCATGAGG
1 GTTGAAACTCATGAGG
7799330 GTTGAAACTCATGAGG
1 GTTGAAACTCATGAGG
7799346 G
1 G
7799347 GTAGGGGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.24
Consensus pattern (16 bp):
GTTGAAACTCATGAGG
Found at i:7799736 original size:21 final size:22
Alignment explanation
Indices: 7799697--7799746 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
7799687 AGGAAAGCCG
*
7799697 AAAAAAGATAGAGAAGGAA-GA
1 AAAAAAGAGAGAGAAGGAAGGA
7799718 AAAAAAGAGAGA-AAGGGAAGGA
1 AAAAAAGAGAGAGAA-GGAAGGA
*
7799740 AGAAAAG
1 AAAAAAG
7799747 TTGAAAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 15 0.60
22 8 0.32
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (22 bp):
AAAAAAGAGAGAGAAGGAAGGA
Found at i:7799774 original size:37 final size:35
Alignment explanation
Indices: 7799717--7799800 Score: 116
Period size: 37 Copynumber: 2.4 Consensus size: 35
7799707 GAGAAGGAAG
**
7799717 AAAA-AAAGAGAGAAAGGGAAGGAAGAAAAGTTGA
1 AAAAGAAAGAGAGAAAGGGAAGGAAGAAAAGCAGA
7799751 AAAAGAAAGAGAGAAAGAAGGAAGGAAGAAAAGCAGA
1 AAAAGAAAGAGAGAAAG--GGAAGGAAGAAAAGCAGA
*
7799788 AAAAGAGAGAGAG
1 AAAAGAAAGAGAG
7799801 TGAAGGAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
34 4 0.09
35 12 0.27
37 28 0.64
ACGTcount: A:0.63, C:0.01, G:0.33, T:0.02
Consensus pattern (35 bp):
AAAAGAAAGAGAGAAAGGGAAGGAAGAAAAGCAGA
Found at i:7799795 original size:31 final size:31
Alignment explanation
Indices: 7799754--7799813 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
7799744 AAGTTGAAAA
*
7799754 AGAAAGAGAGAAAGAAG-GAAGGAAGAAAAGC
1 AGAAAAAGAGAAAG-AGTGAAGGAAGAAAAGC
*
7799785 AGAAAAAGAGAGAGAGTGAAGGAAGAAAA
1 AGAAAAAGAGAAAGAGTGAAGGAAGAAAA
7799814 AAAATAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.62, C:0.02, G:0.35, T:0.02
Consensus pattern (31 bp):
AGAAAAAGAGAAAGAGTGAAGGAAGAAAAGC
Found at i:7802092 original size:19 final size:19
Alignment explanation
Indices: 7802048--7802085 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
7802038 CCATTTGACT
*
7802048 TATTGGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
7802067 TATTAGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
7802086 GTTTAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTAGAGTATGATTTGAG
Found at i:7803326 original size:13 final size:13
Alignment explanation
Indices: 7803308--7803332 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7803298 GGAGAAATTG
7803308 TGATTTTATAAAA
1 TGATTTTATAAAA
7803321 TGATTTTATAAA
1 TGATTTTATAAA
7803333 TTTTTTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:7805347 original size:11 final size:11
Alignment explanation
Indices: 7805331--7805355 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
7805321 CGCACGCGAG
7805331 AAAATAATAAT
1 AAAATAATAAT
7805342 AAAATAATAAT
1 AAAATAATAAT
7805353 AAA
1 AAA
7805356 TTTTATCGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:7805856 original size:118 final size:117
Alignment explanation
Indices: 7805648--7805877 Score: 415
Period size: 118 Copynumber: 2.0 Consensus size: 117
7805638 TATTGTGATA
7805648 ATACCGCGTTGAGGTGCAATTTGTATATTTCGGTGGTACACGCATCGAGAAAGAAAGTTAGATGA
1 ATACCGCGTTGAGGTGCAATTTGTATATTTCGGTGGTACACGCATCGAGAAAGAAAGTTAGATGA
7805713 AAATTGAAATTTTTAGACATATTAAAAGGATCGAATTTAACATATAANGATCT
66 AAATTGAAATTTTTAGACATATTAAAAGGATCGAATTTAACATATAA-GATCT
*
7805766 ATACCGCGTTGAGGTGCAATTTGTATATTTCGGTGGTACACGCATCGAGAAAGGAAGTTAGATGA
1 ATACCGCGTTGAGGTGCAATTTGTATATTTCGGTGGTACACGCATCGAGAAAGAAAGTTAGATGA
* **
7805831 AAATTGGAATTTTTAGATGTATTAAAAGGATCGAATTTAACATATAA
66 AAATTGAAATTTTTAGACATATTAAAAGGATCGAATTTAACATATAA
7805878 AGATTTAAAG
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 108 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (117 bp):
ATACCGCGTTGAGGTGCAATTTGTATATTTCGGTGGTACACGCATCGAGAAAGAAAGTTAGATGA
AAATTGAAATTTTTAGACATATTAAAAGGATCGAATTTAACATATAAGATCT
Found at i:7805935 original size:19 final size:17
Alignment explanation
Indices: 7805911--7805962 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
7805901 ATTAATGAGA
7805911 AAAATAAAATGAATAGAGT
1 AAAATAAAAT-AATAGA-T
*
7805930 AAAATAATAATAATATAT
1 AAAATAA-AATAATAGAT
*
7805948 AAAA-AAAATATTAGA
1 AAAATAAAATAATAGA
7805963 AGACCAACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 7 0.24
17 2 0.07
18 5 0.17
19 12 0.41
20 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (17 bp):
AAAATAAAATAATAGAT
Found at i:7806381 original size:34 final size:34
Alignment explanation
Indices: 7806341--7806418 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
7806331 GAAGAAAAAG
7806341 AGAGCCATTTAAGGGCCGGTTTTGGAGGCTGAAA
1 AGAGCCATTTAAGGGCCGGTTTTGGAGGCTGAAA
**** *
7806375 AGAGCCATTTTTTTGCTGGTTTTGGAGGCTGAAA
1 AGAGCCATTTAAGGGCCGGTTTTGGAGGCTGAAA
*
7806409 AGTGCCATTT
1 AGAGCCATTT
7806419 TTCTGCTGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.23, C:0.14, G:0.31, T:0.32
Consensus pattern (34 bp):
AGAGCCATTTAAGGGCCGGTTTTGGAGGCTGAAA
Found at i:7806419 original size:34 final size:34
Alignment explanation
Indices: 7806358--7806437 Score: 142
Period size: 34 Copynumber: 2.4 Consensus size: 34
7806348 TTTAAGGGCC
*
7806358 GGTTTTGGAGGCTGAAAAGAGCCATTTTTTTGCT
1 GGTTTTGGAGGCTGAAAAGAGCCATTTTTCTGCT
*
7806392 GGTTTTGGAGGCTGAAAAGTGCCATTTTTCTGCT
1 GGTTTTGGAGGCTGAAAAGAGCCATTTTTCTGCT
7806426 GGTTTTGGAGGC
1 GGTTTTGGAGGC
7806438 CAAAAGTTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.17, C:0.12, G:0.33, T:0.38
Consensus pattern (34 bp):
GGTTTTGGAGGCTGAAAAGAGCCATTTTTCTGCT
Found at i:7806759 original size:5 final size:5
Alignment explanation
Indices: 7806749--7806786 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
7806739 GGTGGGAGAG
* *
7806749 AAAGA AAAGA AAAGA AAAGA AAAGA AAGGT AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
7806787 TAACAAGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:7806876 original size:25 final size:24
Alignment explanation
Indices: 7806818--7806878 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 24
7806808 CCCAACAAGC
7806818 AAGAAAAATGGACATGGTCCAATA
1 AAGAAAAATGGACATGGTCCAATA
7806842 AAGGAAAAATGGACATGGTCCAATTA
1 AA-GAAAAATGGACATGGTCCAA-TA
7806868 AA-AAGAAATGG
1 AAGAA-AAATGG
7806879 GAGAAGTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
24 4 0.12
25 26 0.76
26 4 0.12
ACGTcount: A:0.51, C:0.10, G:0.23, T:0.16
Consensus pattern (24 bp):
AAGAAAAATGGACATGGTCCAATA
Found at i:7809500 original size:23 final size:23
Alignment explanation
Indices: 7809470--7809519 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
7809460 ATTTCCCCAT
* *
7809470 AATTCTTTTTACTACAATATTAC
1 AATTCTTTTTAATACAATACTAC
*
7809493 AATTCTTTTTAATAGAATACTAC
1 AATTCTTTTTAATACAATACTAC
7809516 AATT
1 AATT
7809520 ATCCAATCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (23 bp):
AATTCTTTTTAATACAATACTAC
Found at i:7810083 original size:87 final size:87
Alignment explanation
Indices: 7809916--7810075 Score: 311
Period size: 87 Copynumber: 1.8 Consensus size: 87
7809906 AAGTCACGTG
*
7809916 ATAAGTTTATTGTTCTTACATATAAAAAAGAATATTAAAGTGGTGATAAAAAATGCATGCTTTTC
1 ATAAGTTTATTGTTCTTACATATAAAAAAGAATATTAAAGTGGTGATAAAAAATGCATGCCTTTC
7809981 AAAAAAAAAAAATGATGATAAC
66 AAAAAAAAAAAATGATGATAAC
7810003 ATAAGTTTATTGTTCTTACATATAAAAAAGAATATTAAAGTGGTGATAAAAAATGCATGCCTTTC
1 ATAAGTTTATTGTTCTTACATATAAAAAAGAATATTAAAGTGGTGATAAAAAATGCATGCCTTTC
7810068 AAAAAAAA
66 AAAAAAAA
7810076 TTGATGATAA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.31
Consensus pattern (87 bp):
ATAAGTTTATTGTTCTTACATATAAAAAAGAATATTAAAGTGGTGATAAAAAATGCATGCCTTTC
AAAAAAAAAAAATGATGATAAC
Found at i:7811309 original size:5 final size:5
Alignment explanation
Indices: 7811290--7811342 Score: 56
Period size: 5 Copynumber: 10.4 Consensus size: 5
7811280 GACACCTAAA
*
7811290 AAAAT -AAAT -AAAT AAAAT AAAATT ATAAT AAAAT AAAATAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT -AAA-AT AAAAT
7811336 AAAAT AA
1 AAAAT AA
7811343 TTAAAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
4 8 0.19
5 22 0.52
6 10 0.24
7 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (5 bp):
AAAAT
Found at i:7811317 original size:21 final size:21
Alignment explanation
Indices: 7811286--7811354 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
7811276 TGTAGACACC
*
7811286 TAAAAAAATAAATAAATAAAA
1 TAAAAATATAAATAAATAAAA
*
7811307 TAAAATTAT-AATAAAATAAAA
1 TAAAAATATAAAT-AAATAAAA
*
7811328 TATAAAATA-AAATAATTAAAA
1 TA-AAAATATAAATAAATAAAA
*
7811349 AAAAAA
1 TAAAAA
7811355 AGAATGGCTG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
20 7 0.17
21 25 0.62
22 8 0.20
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAAAATATAAATAAATAAAA
Found at i:7811319 original size:16 final size:17
Alignment explanation
Indices: 7811299--7811342 Score: 72
Period size: 16 Copynumber: 2.6 Consensus size: 17
7811289 AAAAATAAAT
7811299 AAATAAAATAAAAT-TA
1 AAATAAAATAAAATATA
*
7811315 TAATAAAATAAAATATA
1 AAATAAAATAAAATATA
7811332 AAATAAAATAA
1 AAATAAAATAA
7811343 TTAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAAATAAAATATA
Found at i:7811350 original size:28 final size:27
Alignment explanation
Indices: 7811288--7811355 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 27
7811278 TAGACACCTA
*
7811288 AAAAAATAAATAAATAAAATAAAATTAT
1 AAAAAATAAA-AAATAAAATAAAATAAT
*
7811316 AATAAAATAAAATATAAAATAAAATAAT
1 AA-AAAATAAAAAATAAAATAAAATAAT
*
7811344 TAAAAA-AAAAAA
1 AAAAAATAAAAAA
7811356 GAATGGCTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 5 0.14
27 4 0.11
28 18 0.51
29 8 0.23
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (27 bp):
AAAAAATAAAAAATAAAATAAAATAAT
Found at i:7811351 original size:12 final size:13
Alignment explanation
Indices: 7811290--7811352 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 13
7811280 GACACCTAAA
7811290 AAAAT-AAATAAAT
1 AAAATAAAAT-AAT
7811303 AAAATAAAATTATAAT
1 AAAAT-AAA--ATAAT
7811319 AAAATAAAAT-AT
1 AAAATAAAATAAT
7811331 AAAATAAAATAATT
1 AAAATAAAATAA-T
7811345 AAAA-AAAA
1 AAAATAAAA
7811353 AAAGAATGGC
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
12 12 0.27
13 12 0.27
14 5 0.11
15 5 0.11
16 8 0.18
17 2 0.05
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:7811351 original size:17 final size:16
Alignment explanation
Indices: 7811290--7811355 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 16
7811280 GACACCTAAA
7811290 AAAATAAATAAATAAAAT
1 AAAAT-AATAAA-AAAAT
* *
7811308 AAAATTATAATAAAAT
1 AAAATAATAAAAAAAT
7811324 AAAAT-AT---AAAAT
1 AAAATAATAAAAAAAT
7811336 AAAATAATTAAAAAAA-
1 AAAATAA-TAAAAAAAT
7811352 AAAA
1 AAAA
7811356 GAATGGCTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
12 10 0.24
13 1 0.02
14 1 0.02
15 2 0.05
16 14 0.34
17 8 0.20
18 5 0.12
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATAATAAAAAAAT
Found at i:7812889 original size:15 final size:16
Alignment explanation
Indices: 7812865--7812902 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
7812855 ATATGGATCT
*
7812865 AAATAGAAAATAA-AA
1 AAATAAAAAATAATAA
7812880 AAATAAAAAATAATAA
1 AAATAAAAAATAATAA
*
7812896 TAATAAA
1 AAATAAA
7812903 CTAAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (16 bp):
AAATAAAAAATAATAA
Found at i:7814935 original size:8 final size:8
Alignment explanation
Indices: 7814865--7814942 Score: 50
Period size: 8 Copynumber: 9.4 Consensus size: 8
7814855 AAATTATTTG
7814865 TAAAAT-T
1 TAAAATAT
7814872 TAAAATAT
1 TAAAATAT
* *
7814880 TAATATTT
1 TAAAATAT
*
7814888 TATATATAAT
1 TA-AAAT-AT
* *
7814898 TTAAACAT
1 TAAAATAT
*
7814906 TATTAATAT
1 TA-AAATAT
*
7814915 TAATATGAT
1 TAAAAT-AT
7814924 TAAAATAT
1 TAAAATAT
7814932 TAAAATAT
1 TAAAATAT
7814940 TAA
1 TAA
7814943 TATTGTAAAC
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
7 6 0.11
8 27 0.50
9 19 0.35
10 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (8 bp):
TAAAATAT
Found at i:7815058 original size:40 final size:39
Alignment explanation
Indices: 7815014--7815107 Score: 91
Period size: 40 Copynumber: 2.3 Consensus size: 39
7815004 TAAATAAAAA
*
7815014 ATAAAAAATATTAAGATTTTAATCATAATAAT-ATTAAATT
1 ATAAAAAATATTAAGA-ATTAA-CATAATAATAATTAAATT
** *
7815054 ATAAATAAAATATTATTAATTAACATATTAATAATTAAATT
1 AT-AA-AAAATATTAAGAATTAACATAATAATAATTAAATT
*
7815095 ATACTAAAATATT
1 ATA-AAAAATATT
7815108 GATATTTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
40 19 0.42
41 16 0.36
42 10 0.22
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (39 bp):
ATAAAAAATATTAAGAATTAACATAATAATAATTAAATT
Found at i:7815128 original size:7 final size:7
Alignment explanation
Indices: 7815116--7815163 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
7815106 TTGATATTTA
7815116 AATTATT
1 AATTATT
7815123 AATTATT
1 AATTATT
7815130 AA-TATT
1 AATTATT
7815136 --TTAATT
1 AATT-ATT
*
7815142 AATTATC
1 AATTATT
7815149 AATTATT
1 AATTATT
7815156 AA-TATT
1 AATTATT
7815162 AA
1 AA
7815164 AAAATTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
5 1 0.03
6 13 0.37
7 19 0.54
8 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (7 bp):
AATTATT
Found at i:7815131 original size:40 final size:41
Alignment explanation
Indices: 7815045--7815131 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 41
7815035 ATCATAATAA
*
7815045 TATTAAATTATAAATAAAATATTATTAATTAACATATTAAT
1 TATTAAATTATAAATAAAATATTATTAATTAAAATATTAAT
* * * *
7815086 AATTAAATTAT-ACTAAAATATTGA-TATTTAAATTATTAAT
1 TATTAAATTATAAATAAAATATT-ATTAATTAAAATATTAAT
7815126 TATTAA
1 TATTAA
7815132 TATTTTAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
40 28 0.72
41 11 0.28
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (41 bp):
TATTAAATTATAAATAAAATATTATTAATTAAAATATTAAT
Found at i:7815562 original size:2 final size:2
Alignment explanation
Indices: 7815555--7815580 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7815545 CACTTTAGGC
7815555 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
7815581 TTAAGGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7816014 original size:16 final size:17
Alignment explanation
Indices: 7815983--7816015 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
7815973 ATATTTATGA
*
7815983 TAAAAATAATTTTAAAT
1 TAAAAATAATTATAAAT
7816000 TAAAAAT-ATTATAAAT
1 TAAAAATAATTATAAAT
7816016 AATTATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAAATAATTATAAAT
Found at i:7821823 original size:21 final size:23
Alignment explanation
Indices: 7821797--7821846 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
7821787 TTCATTGCCT
7821797 AAAATTACATTT-TTTT-ATAA-A
1 AAAATTAC-TTTGTTTTGATAATA
7821818 AAAATTACTTTGTTTTGATAATA
1 AAAATTACTTTGTTTTGATAATA
7821841 AAAATT
1 AAAATT
7821847 TCAAGCTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.12
21 12 0.46
22 4 0.15
23 7 0.27
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (23 bp):
AAAATTACTTTGTTTTGATAATA
Found at i:7824591 original size:24 final size:23
Alignment explanation
Indices: 7824553--7824605 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
7824543 GTTCGTAGGG
*
7824553 ATAAAACTAATATTTTTAATATTT
1 ATAAAACTAAAATTTTTAA-ATTT
*
7824577 ATAAAAGTAAAATTTTTAAATTT
1 ATAAAACTAAAATTTTTAAATTT
*
7824600 TTAAAA
1 ATAAAA
7824606 AATAAAGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAAAACTAAAATTTTTAAATTT
Found at i:7824606 original size:24 final size:24
Alignment explanation
Indices: 7824553--7824611 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
7824543 GTTCGTAGGG
* *
7824553 ATAAAACTAATATTTTTAATATTT
1 ATAAAAATAAAATTTTTAATATTT
*
7824577 ATAAAAGTAAAATTTTTAA-ATTT
1 ATAAAAATAAAATTTTTAATATTT
*
7824600 TTAAAAAATAAA
1 AT-AAAAATAAA
7824612 GACAAAACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 5 0.17
24 25 0.83
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
ATAAAAATAAAATTTTTAATATTT
Found at i:7825880 original size:19 final size:19
Alignment explanation
Indices: 7825856--7825908 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
7825846 ATTCTTCTTA
*
7825856 ATATATATAAAAAAATATT
1 ATATATATAAAAAAATATC
* * *
7825875 ATATATATTAATATATATC
1 ATATATATAAAAAAATATC
7825894 ATATATTATAAAAAA
1 ATATA-TATAAAAAA
7825909 TTAATTTGGT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATATATAAAAAAATATC
Found at i:7830731 original size:13 final size:13
Alignment explanation
Indices: 7830715--7830764 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
7830705 AATCATAAAC
* *
7830715 AAAAAAATGAATT
1 AAAAAAATAAATA
7830728 AAAAAAATAAATA
1 AAAAAAATAAATA
7830741 ATAAAAAATAAA-A
1 A-AAAAAATAAATA
7830754 AATAAAAATAA
1 AA-AAAAATAA
7830765 TATATATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 1 0.03
13 22 0.67
14 10 0.30
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (13 bp):
AAAAAAATAAATA
Found at i:7830745 original size:32 final size:29
Alignment explanation
Indices: 7830704--7830787 Score: 80
Period size: 32 Copynumber: 2.7 Consensus size: 29
7830694 GTAGACACTA
*
7830704 AAATCATAAACAAAAAAATGAATTAAAAA-AAT
1 AAATAATAAA-AAAAAAA--AA-TAAAAATAAT
7830736 AAATAATAAAAAATAAAAAATAAAAATAAT
1 AAATAATAAAAAA-AAAAAATAAAAATAAT
7830766 ATATATAATAAAAAGAAAAAAA
1 A-A-ATAATAAAAA-AAAAAAA
7830788 AACTTGGTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
29 6 0.13
30 6 0.13
31 4 0.09
32 29 0.63
33 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (29 bp):
AAATAATAAAAAAAAAAAATAAAAATAAT
Found at i:7830746 original size:14 final size:14
Alignment explanation
Indices: 7830716--7830761 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
7830706 ATCATAAACA
* *
7830716 AAAAAATGAATTA-
1 AAAAAATAAATAAT
7830729 AAAAAATAAATAAT
1 AAAAAATAAATAAT
*
7830743 AAAAAATAAAAAAT
1 AAAAAATAAATAAT
7830757 AAAAA
1 AAAAA
7830762 TAATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (14 bp):
AAAAAATAAATAAT
Found at i:7830785 original size:25 final size:22
Alignment explanation
Indices: 7830727--7830786 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 22
7830717 AAAAATGAAT
*
7830727 TAAAAAAATAAATAATAAAAAA
1 TAAAAAAAAAAATAATAAAAAA
*
7830749 TAAAAAATAAAAATAATATATATAA
1 TAAAAAA-AAAAATAATA-A-AAAA
7830774 TAAAAAGAAAAAA
1 TAAAAA-AAAAAA
7830787 AAACTTGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 7 0.22
23 9 0.28
24 1 0.03
25 14 0.44
26 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (22 bp):
TAAAAAAAAAAATAATAAAAAA
Found at i:7831445 original size:78 final size:78
Alignment explanation
Indices: 7831316--7831493 Score: 275
Period size: 78 Copynumber: 2.3 Consensus size: 78
7831306 TTGCGTCGGC
* *
7831316 AGGAGAAGAGTGAGAGAGAGGAAGCCCGACAGGCACTGGATCTGGTGCTTGGGTTGCCACCGGTT
1 AGGAGAAGAGTGAGAGAGAGGAAGCCCGACAAGCACTGGATCTGGTGCTTGGGTTACCACCGGTT
*
7831381 AGCGTGGGTAGAG
66 AGCATGGGTAGAG
* * *
7831394 AGGAGAAGAGTGAGAGAGAGGAAGCCCGACAAGCGCTGGATCTGGTGCTTGGGTTATCGCCGGTT
1 AGGAGAAGAGTGAGAGAGAGGAAGCCCGACAAGCACTGGATCTGGTGCTTGGGTTACCACCGGTT
7831459 AGCATGGGTAGAG
66 AGCATGGGTAGAG
*
7831472 AGAGAGAGAGAGAGAGAGAGAG
1 AG-GAGA-AGAGTGAGAGAGAG
7831494 AGANNNNNNN
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
78 74 0.81
79 4 0.04
80 13 0.14
ACGTcount: A:0.28, C:0.14, G:0.43, T:0.15
Consensus pattern (78 bp):
AGGAGAAGAGTGAGAGAGAGGAAGCCCGACAAGCACTGGATCTGGTGCTTGGGTTACCACCGGTT
AGCATGGGTAGAG
Found at i:7831475 original size:2 final size:2
Alignment explanation
Indices: 7831468--7831496 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7831458 TAGCATGGGT
7831468 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
7831497 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7835486 original size:36 final size:38
Alignment explanation
Indices: 7835446--7835534 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 38
7835436 AAAAAAGAGG
7835446 ATAAAATAATAAA-TA-AAAAAAT-AAT-TCAAATATACA
1 ATAAAATAATAAATTATAAAAAATCAATAT-AAATA-ACA
7835482 ATAAAATAATAAATTTATAAAAAATGCAATATAAATAACA
1 ATAAAATAATAAA-TTATAAAAAAT-CAATATAAATAACA
*
7835522 ATTAAATAATAAA
1 ATAAAATAATAAA
7835535 AAATGATAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
36 13 0.28
38 2 0.04
39 7 0.15
40 15 0.33
41 8 0.17
42 1 0.02
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.27
Consensus pattern (38 bp):
ATAAAATAATAAATTATAAAAAATCAATATAAATAACA
Found at i:7843691 original size:30 final size:31
Alignment explanation
Indices: 7843657--7843722 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
7843647 AATTAAGTTT
*
7843657 TTATA-TATTTAGTTTAAGTCAAATAAATTC
1 TTATATTATTTAGTTTAAATCAAATAAATTC
* *
7843687 TTATATTTTTTATTTTAAATCAAATAAATTC
1 TTATATTATTTAGTTTAAATCAAATAAATTC
7843718 TTATA
1 TTATA
7843723 ATTAATAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (31 bp):
TTATATTATTTAGTTTAAATCAAATAAATTC
Found at i:7843710 original size:31 final size:31
Alignment explanation
Indices: 7843664--7843722 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
7843654 TTTTTATATA
*
7843664 TTTAGTTTAAGTCAAATAAATTCTTATATTT
1 TTTAGTTTAAATCAAATAAATTCTTATATTT
*
7843695 TTTATTTTAAATCAAATAAATTCTTATA
1 TTTAGTTTAAATCAAATAAATTCTTATA
7843723 ATTAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (31 bp):
TTTAGTTTAAATCAAATAAATTCTTATATTT
Found at i:7844068 original size:11 final size:11
Alignment explanation
Indices: 7844024--7844073 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 11
7844014 TAAAAAATAA
7844024 AAAT-TTATTT
1 AAATATTATTT
7844034 AAATATT-TTT
1 AAATATTATTT
7844044 AAATA--ATTT
1 AAATATTATTT
*
7844053 AAAATTTTATTT
1 -AAATATTATTT
7844065 AAATATTAT
1 AAATATTAT
7844074 AACTTAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
9 3 0.09
10 16 0.48
11 10 0.30
12 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
AAATATTATTT
Found at i:7858706 original size:39 final size:41
Alignment explanation
Indices: 7858650--7858732 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 41
7858640 AAGATTTCTT
* *
7858650 AAAGAACAAGAATGG-C-CATTCTAAAACTTTCTTAAAGAA
1 AAAGAAAAAGAAAGGCCTCATTCTAAAACTTTCTTAAAGAA
*
7858689 AAAGAAAAAGAAAGGCCATTCATTCTAAGACTTTCTTAAAGAA
1 AAAGAAAAAGAAAGGCC--TCATTCTAAAACTTTCTTAAAGAA
7858732 A
1 A
7858733 CTCCTTTGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 13 0.35
40 1 0.03
43 23 0.62
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.23
Consensus pattern (41 bp):
AAAGAAAAAGAAAGGCCTCATTCTAAAACTTTCTTAAAGAA
Found at i:7864089 original size:5 final size:5
Alignment explanation
Indices: 7864070--7864104 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
7864060 CTCGAGATTT
*
7864070 TTAGA TTAGA GTTAGT TTAGA TTAGA TTAGA TTAG
1 TTAGA TTAGA -TTAGA TTAGA TTAGA TTAGA TTAG
7864105 TTTTTTTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (5 bp):
TTAGA
Found at i:7864090 original size:16 final size:15
Alignment explanation
Indices: 7864069--7864104 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
7864059 GCTCGAGATT
7864069 TTTAGATTAGAGTTAG
1 TTTAGATTAGA-TTAG
7864085 TTTAGATTAGATTAG
1 TTTAGATTAGATTAG
*
7864100 ATTAG
1 TTTAG
7864105 TTTTTTTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (15 bp):
TTTAGATTAGATTAG
Found at i:7866207 original size:13 final size:13
Alignment explanation
Indices: 7866189--7866217 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
7866179 AAGTAAAAAA
7866189 GTGACAGAAGAGC
1 GTGACAGAAGAGC
7866202 GTGACAGAAGAGC
1 GTGACAGAAGAGC
7866215 GTG
1 GTG
7866218 GCAGCAGCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.41, T:0.10
Consensus pattern (13 bp):
GTGACAGAAGAGC
Found at i:7866738 original size:7 final size:7
Alignment explanation
Indices: 7866726--7866796 Score: 74
Period size: 7 Copynumber: 10.0 Consensus size: 7
7866716 TTTCCTTTTC
7866726 TTTTCTT
1 TTTTCTT
7866733 TTTTCTT
1 TTTTCTT
*
7866740 TTTTCTA
1 TTTTCTT
7866747 TTTTCTCT
1 TTTTCT-T
7866755 TTTTCTT
1 TTTTCTT
*
7866762 AATTTC--
1 -TTTTCTT
7866768 TTTTCTT
1 TTTTCTT
*
7866775 TTTTCTA
1 TTTTCTT
7866782 TTTTCTCT
1 TTTTCT-T
7866790 TTTTCTT
1 TTTTCTT
7866797 AATTTCTTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
5 4 0.08
7 33 0.62
8 16 0.30
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTCTT
Found at i:7866775 original size:35 final size:35
Alignment explanation
Indices: 7866733--7866804 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
7866723 TTCTTTTCTT
7866733 TTTTCTTTTTTCTATTTTCTCTTTTTCTTAATTTC
1 TTTTCTTTTTTCTATTTTCTCTTTTTCTTAATTTC
7866768 TTTTCTTTTTTCTATTTTCTCTTTTTCTTAATTTC
1 TTTTCTTTTTTCTATTTTCTCTTTTTCTTAATTTC
7866803 TT
1 TT
7866805 ACTTTCATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (35 bp):
TTTTCTTTTTTCTATTTTCTCTTTTTCTTAATTTC
Found at i:7866778 original size:43 final size:42
Alignment explanation
Indices: 7866722--7866817 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
7866712 CTTCTTTCCT
*
7866722 TTTCTTTTCTTTTTTCTTTTTTCTATTTTCTCTT-TTTCTTAA
1 TTTCTTTTCTTTTTTCTATTTTCTATTTT-TCTTATTTCTTAA
* *
7866764 TTTCTTTTCTTTTTTCTATTTTCTCTTTTTCTTAATTTCTTAC
1 TTTCTTTTCTTTTTTCTATTTTCTATTTTTCTT-ATTTCTTAA
*
7866807 TTTCATTTCTT
1 TTTCTTTTCTT
7866818 CCTTGTCCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
41 4 0.08
42 27 0.56
43 17 0.35
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (42 bp):
TTTCTTTTCTTTTTTCTATTTTCTATTTTTCTTATTTCTTAA
Found at i:7866802 original size:16 final size:16
Alignment explanation
Indices: 7866734--7866803 Score: 65
Period size: 16 Copynumber: 4.3 Consensus size: 16
7866724 TCTTTTCTTT
*
7866734 TTTCT-TTTTTC-TAT
1 TTTCTCTTTTTCTTAA
7866748 TTTCTCTTTTTCTTAA
1 TTTCTCTTTTTCTTAA
*
7866764 TTTCTTTTCTTTTT-TCTAT
1 TTTC---TCTTTTTCT-TAA
7866783 TTTCTCTTTTTCTTAA
1 TTTCTCTTTTTCTTAA
7866799 TTTCT
1 TTTCT
7866804 TACTTTCATT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
14 5 0.11
15 6 0.13
16 20 0.43
17 1 0.02
18 1 0.02
19 13 0.28
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTCTTTTTCTTAA
Found at i:7878108 original size:2 final size:2
Alignment explanation
Indices: 7878101--7878131 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7878091 TCTGTTCTTC
7878101 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
7878132 TGCATTATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7897378 original size:29 final size:30
Alignment explanation
Indices: 7897300--7897379 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
7897290 TATTTTAAAA
7897300 AAATTCAAATAAGTCTTTATATTTTTATTTT
1 AAATT-AAATAAGTCTTTATATTTTTATTTT
** *
7897331 AAGCTAAATAAGTCATTAT-TTTTTATTTT
1 AAATTAAATAAGTCTTTATATTTTTATTTT
**
7897360 AAATTAAATAAACCTTTATA
1 AAATTAAATAAGTCTTTATA
7897380 ATTGATAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 24 0.60
30 13 0.32
31 3 0.08
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (30 bp):
AAATTAAATAAGTCTTTATATTTTTATTTT
Found at i:7897516 original size:23 final size:25
Alignment explanation
Indices: 7897471--7897517 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
7897461 TGTAACATAC
*
7897471 TGATATATTATAATTGTTGATAATG
1 TGATATATTATAATTGATGATAATG
*
7897496 TGATATATTA-ATTTGAT-ATAAT
1 TGATATATTATAATTGATGATAAT
7897518 AACATGATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 5 0.25
25 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (25 bp):
TGATATATTATAATTGATGATAATG
Found at i:7905666 original size:27 final size:23
Alignment explanation
Indices: 7905656--7905752 Score: 74
Period size: 27 Copynumber: 4.0 Consensus size: 23
7905646 ATTAATATTT
*
7905656 ATTTATAATTTAAATATTATTATGATT
1 ATTTATAATTTAAA-A-TATTA--ATA
*
7905683 ATTTAT--TTTTAAATATTAATA
1 ATTTATAATTTAAAATATTAATA
7905704 ATTTATAATTTATTTAAAATATTAATA
1 ATTTAT-A---ATTTAAAATATTAATA
*
7905731 ATTGATAA-TTAAAATATTAATA
1 ATTTATAATTTAAAATATTAATA
7905753 NNNNNNNNNN
Statistics
Matches: 60, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
21 8 0.13
22 14 0.23
23 6 0.10
24 1 0.02
25 5 0.08
26 1 0.02
27 25 0.42
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTTATAATTTAAAATATTAATA
Found at i:7905673 original size:19 final size:19
Alignment explanation
Indices: 7905594--7905730 Score: 70
Period size: 20 Copynumber: 7.0 Consensus size: 19
7905584 TTATTTTTAT
7905594 TTTATTT-TACATATTAA-A
1 TTTATTTATA-ATATTAATA
7905612 TTTTATTTATAAT-TTAATA
1 -TTTATTTATAATATTAATA
*
7905631 TTCATATTTAAAAATATTAATA
1 TT--TATTT-ATAATATTAATA
7905653 TTTATTTATAAT-TTAA-A
1 TTTATTTATAATATTAATA
* * *
7905670 TATTA-TTATGATTATTTATT
1 T-TTATTTAT-AATATTAATA
** *
7905690 TTTAAATATTAATAATTTATAA
1 TTTATTTA-TAAT-ATTAAT-A
*
7905712 TTTATTTAAAATATTAATA
1 TTTATTTATAATATTAATA
7905731 ATTGATAATT
Statistics
Matches: 92, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
17 6 0.07
18 15 0.16
19 21 0.23
20 22 0.24
21 14 0.15
22 14 0.15
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (19 bp):
TTTATTTATAATATTAATA
Found at i:7905733 original size:20 final size:21
Alignment explanation
Indices: 7905708--7905752 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
7905698 TTAATAATTT
*
7905708 ATAATT-TATTTAAAATATTA
1 ATAATTATAATTAAAATATTA
7905728 ATAATTGATAATTAAAATATTA
1 ATAATT-ATAATTAAAATATTA
7905750 ATA
1 ATA
7905753 NNNNNNNNNN
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.27
22 16 0.73
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATAATTATAATTAAAATATTA
Found at i:7910392 original size:53 final size:50
Alignment explanation
Indices: 7910314--7910429 Score: 121
Period size: 53 Copynumber: 2.3 Consensus size: 50
7910304 GATGAGAAAA
*
7910314 TATTTA-AATTTTTTTAAAAGTAATTA-TCT-TTAAATTATCATTATAACTAT
1 TATTTATAATATTTTTAAAAGTAATTATTCTCTTAAATTATCATTAT---TAT
* * *
7910364 TATTTATAATATTTTTAAAATTAAAATTATTTCTCTTTAATTATTATTATTAT
1 TATTTATAATATTTTTAAAAGT--AATTA-TTCTCTTAAATTATCATTATTAT
7910417 TATTTATAATATT
1 TATTTATAATATT
7910430 ATATAATTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
50 6 0.11
51 13 0.23
53 21 0.38
55 3 0.05
56 13 0.23
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (50 bp):
TATTTATAATATTTTTAAAAGTAATTATTCTCTTAAATTATCATTATTAT
Found at i:7915499 original size:17 final size:19
Alignment explanation
Indices: 7915477--7915511 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
7915467 GGAATAAAAT
7915477 AGATAATG-AGTT-TTTAC
1 AGATAATGTAGTTGTTTAC
7915494 AGATAATGTAGTTGTTTA
1 AGATAATGTAGTTGTTTA
7915512 TATTAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (19 bp):
AGATAATGTAGTTGTTTAC
Found at i:7917757 original size:60 final size:59
Alignment explanation
Indices: 7917664--7917837 Score: 233
Period size: 60 Copynumber: 2.9 Consensus size: 59
7917654 TTATAAAAGA
* *
7917664 GGACCTGAAGTCCCAATTCATATTCGGTGACGTGGGTAGTTCCCACGAGTAGGTAAAGGG
1 GGACCTGAAGTCCCAATTTATATT-GGTGACGTGAGTAGTTCCCACGAGTAGGTAAAGGG
* *
7917724 GGACCTGAAG-CCTCAATTTACATTGGGTGACGTGAGCAGTTCCCACGAGTAGGTAAAGGG
1 GGACCTGAAGTCC-CAATTTATATT-GGTGACGTGAGTAGTTCCCACGAGTAGGTAAAGGG
* * * *
7917784 GGACCTGAAGTCCCGATTTATATATGGTGGCGTGAGTAGTTTCCACGAATAGGT
1 GGACCTGAAGTCCCAATTTATAT-TGGTGACGTGAGTAGTTCCCACGAGTAGGT
7917838 GATGATGTCT
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
59 2 0.02
60 95 0.95
61 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (59 bp):
GGACCTGAAGTCCCAATTTATATTGGTGACGTGAGTAGTTCCCACGAGTAGGTAAAGGG
Found at i:7936350 original size:15 final size:15
Alignment explanation
Indices: 7936330--7936378 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
7936320 CCTTTGCCTC
7936330 CTTTCTTCTCTTAAG
1 CTTTCTTCTCTTAAG
* *
7936345 CTTTC-TCTGCCT--C
1 CTTTCTTCT-CTTAAG
7936358 CTTTCTTCTCTTAAG
1 CTTTCTTCTCTTAAG
7936373 CTTTCT
1 CTTTCT
7936379 CTGCCTCCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
13 7 0.27
14 6 0.23
15 13 0.50
ACGTcount: A:0.08, C:0.33, G:0.06, T:0.53
Consensus pattern (15 bp):
CTTTCTTCTCTTAAG
Found at i:7936360 original size:28 final size:28
Alignment explanation
Indices: 7936324--7936392 Score: 138
Period size: 28 Copynumber: 2.5 Consensus size: 28
7936314 TAATTTCCTT
7936324 TGCCTCCTTTCTTCTCTTAAGCTTTCTC
1 TGCCTCCTTTCTTCTCTTAAGCTTTCTC
7936352 TGCCTCCTTTCTTCTCTTAAGCTTTCTC
1 TGCCTCCTTTCTTCTCTTAAGCTTTCTC
7936380 TGCCTCCTTTCTT
1 TGCCTCCTTTCTT
7936393 TTCTAGCTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.06, C:0.36, G:0.07, T:0.51
Consensus pattern (28 bp):
TGCCTCCTTTCTTCTCTTAAGCTTTCTC
Found at i:7940976 original size:2 final size:2
Alignment explanation
Indices: 7940969--7941000 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
7940959 CTGTCTTTAC
*
7940969 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7941001 TTCACGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:7943541 original size:22 final size:22
Alignment explanation
Indices: 7943510--7943557 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
7943500 CAATGAATTA
* *
7943510 TTAGATATTACATTACTGGTTT
1 TTAGACATTACATCACTGGTTT
**
7943532 TTAGACATTATGTCACTGGTTT
1 TTAGACATTACATCACTGGTTT
7943554 TTAG
1 TTAG
7943558 GTTATTGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (22 bp):
TTAGACATTACATCACTGGTTT
Found at i:7943689 original size:22 final size:22
Alignment explanation
Indices: 7943657--7943698 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
7943647 GTAATACCTA
7943657 AGTCACACAATACCTAAAAACT
1 AGTCACACAATACCTAAAAACT
* *
7943679 AGTCACGCAATGCCTAAAAA
1 AGTCACACAATACCTAAAAA
7943699 TCGGTTACGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.26, G:0.10, T:0.17
Consensus pattern (22 bp):
AGTCACACAATACCTAAAAACT
Found at i:7943890 original size:60 final size:60
Alignment explanation
Indices: 7943821--7943948 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
7943811 TACTTGACGA
* * * * * * *
7943821 AAAATGCTC-ATAATACTCAAATGTTTTTTTTTATGTATCAAAAACCACTCTAAAATACTT
1 AAAATGCTCAAT-ACACTCAAAGGTTTTTCTTCATATATCAAAAACCACTCAAAAATACTC
* * * *
7943881 AAAATGCTCAATACACTTAAAGGTTTTTCTTCGTATATCAAAAATCACTCAAAAATGCTC
1 AAAATGCTCAATACACTCAAAGGTTTTTCTTCATATATCAAAAACCACTCAAAAATACTC
7943941 AAAATGCT
1 AAAATGCT
7943949 TAAAGGTTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 54 0.96
61 2 0.04
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (60 bp):
AAAATGCTCAATACACTCAAAGGTTTTTCTTCATATATCAAAAACCACTCAAAAATACTC
Found at i:7955783 original size:337 final size:330
Alignment explanation
Indices: 7955175--7956288 Score: 1030
Period size: 365 Copynumber: 3.2 Consensus size: 330
7955165 ATATATGTAT
* * * * *
7955175 ACTTTTAATATAAATTTATTTAC-TTTCTATTTTGTGTTTTAACATTACAAAAATTATGACTTAT
1 ACTTTAAATATAAATATATTTACACTT-TATTTTGAG--TTAACATTAC-AAAATTATAACTTAT
* * * *
7955239 CAAATTATTATTATAATATGTATACCATTATTTATATAAATTGATAACATATATAATCAAAGAGA
62 -AAA-TATTATTATAATATATATACCTTTGTTTATATAAATT-ATAACATATA-AATTAAAGAGA
* * * * * **
7955304 ACTTCTGAGATTAGAATAGTTTTGAAATCTAACTATTTTTTGTAATTTCATAAAATTAACGACAA
123 AGTTATGAGATTAGAATAG-TTTGAAAT-T-AGTTTTTTTTTTAATTTCATGTAATTAA-GACAA
* * * *
7955369 A-TCTATATAGTTAATTAAATTAATTCTTGAAACTATTATTATTAATTAACTTATAATGTCTTTC
184 ATTCTATA-A-TTAATTAAATTAATTCAT-AAACTATAATTATTAATTAACTTGTAATGTCTTTT
*
7955433 AATATATATACTTTATATATTGTGTTAATTTATAAAAAATATAATTACTATTATATATATACTAA
246 AATATATATACTTTATATATTGAGTTAATTTATAAAAAATATAATTACTATTATATATATA-TAA
7955498 AATACTTTTAATATACATATAC
310 AATACTTTTAATATA-ATATAC
*
7955520 ACTTTAAATATAAACATATTTACACTTTATTTTGAGTTAACATTAC-AAATTATAACTTATAAA-
1 ACTTTAAATATAAATATATTTACACTTTATTTTGAGTTAACATTACAAAATTATAACTTATAAAT
* * * *
7955583 ATTATTATAATATATTTAACTTTGTTTATATAAACTTATAATATATAAACTTAAAGAGAAGTTGT
66 ATTATTATAATATATATACCTTTGTTTATATAAA-TTATAACATATAAA-TTAAAGAGAAGTTAT
*
7955648 GAGATTAGAATAGTTCTGAAATGTAGTTTTTTTTTTAATTTCACGTAATTAAGAACAAATTCGTA
129 GAGATTAGAATAGTT-TGAAAT-TAGTTTTTTTTTTAATTTCATGTAATTAAG-ACAAATTC-TA
* *
7955713 TAATTAATTAAATTAATTCATAAAGCTATAATTATTAATTAACTTGTAATATCTTTTAATATTTA
190 TAATTAATTAAATTAATTCATAAA-CTATAATTATTAATTAACTTGTAATGTCTTTTAATATATA
* * ** *
7955778 TACTTTTTATATATTAAGTTCATTTATAAGGAATATAGTTACTATTATATATATATATATATATA
254 TAC--TTTATATATTGAGTTAATTTATAAAAAATATAATTACTATTATATATATATA-A-A-ATA
*
7955843 -TATATATATATATATATGAGTGTGTGTGTGTGTATGT
314 CT-T-T-TA-ATATA-AT-A-------------TA--C
* * *
7955880 TCTTTAAATATAAATATATTTAC-TTTCTATTTTGTA-TTAACATTACAAAAATTATAACTCATA
1 ACTTTAAATATAAATATATTTACACTT-TATTTTG-AGTTAACATTAC-AAAATTATAACTTATA
*
7955943 AATTATTAATTACAATATATATACCTTTGTTTATATAAAGTTATAACATATAAATCTAAAGAGAA
63 AA-TATT-ATTATAATATATATACCTTTGTTTATATAAA-TTATAACATATAAAT-TAAAGAGAA
* * *
7956008 GTTATGAGATTAGAATAGTTTGAAAACTTAGTTATTTTTTTAATTTCTTGTAATTAAGGATAAAC
124 GTTATGAGATTAGAATAGTTTG-AAA-TTAGTTTTTTTTTTAATTTCATGTAATTAA-GACAAA-
* * * * *
7956073 TTATATAGTTAATTAAATTATTTAATAAAACTATAATTATTAATTGACTTGTAATGTCTTTTAAT
185 TTCTATAATTAATTAAATTAATTCAT-AAACTATAATTATTAATTAACTTGTAATGTCTTTTAAT
* * * * * *
7956138 ATCTATAC-TT-CATATTGGGTTTATTTATAAAAAATATAATTAATATTATATATATATTAAAAC
249 ATATATACTTTATATATTGAGTTAATTTATAAAAAATATAATTACTATTATATATATA-TAAAAT
*
7956201 ACTTTTAGTAT-ATATAC
313 ACTTTTAATATAATATAC
* * * *
7956218 ACTTTAAATATAAATATATTT--ACTTTCTATTTGTGTTAACATTATAAAAATTATAACTAATAA
1 ACTTTAAATATAAATATATTTACACTTTAT-TTTGAGTTAACATTA-CAAAATTATAACTTATAA
7956281 AT-TTATTA
64 ATATTATTA
7956289 ATTATATTTG
Statistics
Matches: 643, Mismatches: 74, Indels: 115
0.77 0.09 0.14
Matches are distributed among these distances:
334 4 0.01
335 2 0.00
336 7 0.01
337 118 0.18
338 95 0.15
339 51 0.08
340 7 0.01
341 17 0.03
342 1 0.00
343 12 0.02
344 7 0.01
345 29 0.05
346 2 0.00
353 1 0.00
354 2 0.00
356 3 0.00
357 2 0.00
358 3 0.00
359 5 0.01
360 40 0.06
361 40 0.06
362 20 0.03
364 6 0.01
365 162 0.25
366 7 0.01
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (330 bp):
ACTTTAAATATAAATATATTTACACTTTATTTTGAGTTAACATTACAAAATTATAACTTATAAAT
ATTATTATAATATATATACCTTTGTTTATATAAATTATAACATATAAATTAAAGAGAAGTTATGA
GATTAGAATAGTTTGAAATTAGTTTTTTTTTTAATTTCATGTAATTAAGACAAATTCTATAATTA
ATTAAATTAATTCATAAACTATAATTATTAATTAACTTGTAATGTCTTTTAATATATATACTTTA
TATATTGAGTTAATTTATAAAAAATATAATTACTATTATATATATATAAAATACTTTTAATATAA
TATAC
Found at i:7955830 original size:2 final size:2
Alignment explanation
Indices: 7955823--7955859 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
7955813 TAGTTACTAT
7955823 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7955860 GAGTGTGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7957973 original size:13 final size:13
Alignment explanation
Indices: 7957952--7958041 Score: 71
Period size: 12 Copynumber: 6.9 Consensus size: 13
7957942 TAAACATTAC
*
7957952 AGAGGAAAAAAAA
1 AGAGAAAAAAAAA
*
7957965 AGAG-AAAAAATA
1 AGAGAAAAAAAAA
*
7957977 AGA-AACAAAAAA
1 AGAGAAAAAAAAA
*
7957989 TGAGAAAAAAAAA
1 AGAGAAAAAAAAA
7958002 CA-AGAAACAAAAAA
1 -AGAGAAA-AAAAAA
*
7958016 AAATGAAAAGAAAAA
1 AGA-GAAAA-AAAAA
7958031 AGA-AAAAAAAA
1 AGAGAAAAAAAA
7958042 TGTGTACGAC
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
12 22 0.35
13 22 0.35
14 8 0.13
15 11 0.17
ACGTcount: A:0.80, C:0.03, G:0.13, T:0.03
Consensus pattern (13 bp):
AGAGAAAAAAAAA
Found at i:7957986 original size:14 final size:13
Alignment explanation
Indices: 7957957--7958042 Score: 79
Period size: 14 Copynumber: 6.6 Consensus size: 13
7957947 ATTACAGAGG
7957957 AAAAAAA-AAG-A
1 AAAAAAATAAGAA
*
7957968 GAAAAAATAAGAA
1 AAAAAAATAAGAA
*
7957981 ACAAAAAATGAGAA
1 A-AAAAAATAAGAA
*
7957995 AAAAAAACAAGAA
1 AAAAAAATAAGAA
*
7958008 ACAAAAAAAAATGAA
1 A-AAAAAATAA-GAA
*
7958023 AAGAAAA-AAGAA
1 AAAAAAATAAGAA
7958035 AAAAAAAT
1 AAAAAAAT
7958043 GTGTACGACT
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
11 6 0.10
12 12 0.20
13 14 0.23
14 25 0.41
15 4 0.07
ACGTcount: A:0.81, C:0.03, G:0.10, T:0.05
Consensus pattern (13 bp):
AAAAAAATAAGAA
Found at i:7957999 original size:27 final size:27
Alignment explanation
Indices: 7957969--7958043 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
7957959 AAAAAAAGAG
*
7957969 AAAAAATAAGAAACAAAAAATGA-GAA
1 AAAAAAAAAGAAACAAAAAATGATGAA
**
7957995 AAAAAAACAAGAAACAAAAAAAAATGAA
1 AAAAAAA-AAGAAACAAAAAATGATGAA
*
7958023 AAGAAAAAAGAAA-AAAAAATG
1 AAAAAAAAAGAAACAAAAAATG
7958044 TGTACGACTC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 12 0.29
27 20 0.49
28 9 0.22
ACGTcount: A:0.80, C:0.04, G:0.11, T:0.05
Consensus pattern (27 bp):
AAAAAAAAAGAAACAAAAAATGATGAA
Found at i:7958212 original size:28 final size:27
Alignment explanation
Indices: 7958168--7958221 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
7958158 CTAAAAAACC
7958168 CAAAAATCCCTAGTAGCAACCAAAAAT
1 CAAAAATCCCTAGTAGCAACCAAAAAT
*
7958195 CAAAAAT-CCTAGTCTAGCAGCCAAAAA
1 CAAAAATCCCTAG--TAGCAACCAAAAA
7958222 CAACCACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
27 7 0.29
28 12 0.50
ACGTcount: A:0.50, C:0.26, G:0.09, T:0.15
Consensus pattern (27 bp):
CAAAAATCCCTAGTAGCAACCAAAAAT
Found at i:7960289 original size:3 final size:3
Alignment explanation
Indices: 7960272--7960318 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
7960262 GAGAACTTAA
7960272 AAT AA- AAT AAAT AAT AAT AAT AAT AAT AAT AAAT AA- AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
7960317 AA
1 AA
7960319 ACTTCACAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.10
3 30 0.75
4 6 0.15
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:7960319 original size:15 final size:15
Alignment explanation
Indices: 7960271--7960319 Score: 73
Period size: 15 Copynumber: 3.2 Consensus size: 15
7960261 GGAGAACTTA
7960271 AAATAAAATAAATAAT
1 AAATAAAAT-AATAAT
7960287 -AATAATAATAATAAT
1 AAATAA-AATAATAAT
7960302 AAATAAAATAATAAT
1 AAATAAAATAATAAT
7960317 AAA
1 AAA
7960320 CTTCACAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 23 0.74
16 8 0.26
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAAAATAATAAT
Found at i:7967152 original size:28 final size:27
Alignment explanation
Indices: 7967116--7967168 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
7967106 ATATCCTGGT
*
7967116 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
7967143 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
7967169 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:7967236 original size:20 final size:20
Alignment explanation
Indices: 7967213--7967258 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
7967203 CTTCTAAACC
*
7967213 TCAAATCATACTTCAATAAG
1 TCAAATCATACTCCAATAAG
*
7967233 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
7967253 TCAAAT
1 TCAAAT
7967259 GGGGCCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Done.