Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 41 of 356
Found at i:13475294 original size:14 final size:14
Alignment explanation
Indices: 13475256--13475296 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
13475246 TGAAAGATAT
13475256 TAATACTTTTAAATA
1 TAATA-TTTTAAATA
13475271 TAA-ATATTTAAATA
1 TAATAT-TTTAAATA
13475285 TAATATTTTAAA
1 TAATATTTTAAA
13475297 ATTTGAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.04
14 18 0.75
15 5 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (14 bp):
TAATATTTTAAATA
Found at i:13488547 original size:16 final size:16
Alignment explanation
Indices: 13488526--13488577 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
13488516 TTTGGTTCGC
13488526 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
13488542 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
13488558 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
13488574 TGTA
1 TGTA
13488578 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:13488624 original size:45 final size:44
Alignment explanation
Indices: 13488558--13488652 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
13488548 GGATTAGAGG
*
13488558 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* * ***
13488603 TGTAATGGAATAGAGGCGTAATAGTAGTCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
13488647 TGTAAT
1 TGTAAT
13488653 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 21 0.48
45 23 0.52
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:13488833 original size:18 final size:17
Alignment explanation
Indices: 13488812--13488846 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13488802 TTATTATTAA
*
13488812 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
13488830 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
13488847 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:13492466 original size:19 final size:19
Alignment explanation
Indices: 13492442--13492520 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
13492432 TGTAAAATAA
13492442 AAAAAATA-AAAAAATACTT
1 AAAAAATACAAAAAATA-TT
*
13492461 AAAAAA-ACACAAAATATT
1 AAAAAATACAAAAAATATT
** *
13492479 AAAAAATATTAAAAATATA
1 AAAAAATACAAAAAATATT
*
13492498 AAAAAAT-CATAAAA-ATT
1 AAAAAATACAAAAAATATT
13492515 AAAAAA
1 AAAAAA
13492521 CCCCAAAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
17 8 0.16
18 13 0.27
19 28 0.57
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (19 bp):
AAAAAATACAAAAAATATT
Found at i:13492480 original size:18 final size:18
Alignment explanation
Indices: 13492441--13492520 Score: 76
Period size: 18 Copynumber: 4.3 Consensus size: 18
13492431 ATGTAAAATA
*
13492441 AAAAAAATAAAAAAATACTT
1 AAAAAAAT-CAAAAATA-TT
13492461 AAAAAAA-CACAAAATATT
1 AAAAAAATCA-AAAATATT
*
13492479 AAAAAATATTAAAAATA-T
1 AAAAAA-ATCAAAAATATT
13492497 AAAAAAATCATAAAA-ATT
1 AAAAAAATCA-AAAATATT
13492515 AAAAAA
1 AAAAAA
13492521 CCCCAAAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
17 4 0.08
18 27 0.52
19 13 0.25
20 8 0.15
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAAAATCAAAAATATT
Found at i:13492484 original size:10 final size:10
Alignment explanation
Indices: 13492439--13492520 Score: 59
Period size: 9 Copynumber: 8.7 Consensus size: 10
13492429 ATATGTAAAA
*
13492439 TAAAAAAAAT
1 TAAAAAATAT
*
13492449 AAAAAAATACT
1 TAAAAAATA-T
13492460 TAAAAAA-A-
1 TAAAAAATAT
* *
13492468 CACAAAATAT
1 TAAAAAATAT
13492478 TAAAAAATAT
1 TAAAAAATAT
13492488 T-AAAAATA-
1 TAAAAAATAT
13492496 TAAAAAA-AT
1 TAAAAAATAT
* *
13492505 CATAAAA-AT
1 TAAAAAATAT
13492514 TAAAAAA
1 TAAAAAA
13492521 CCCCAAAAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
8 7 0.12
9 25 0.45
10 17 0.30
11 7 0.12
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:13502799 original size:13 final size:13
Alignment explanation
Indices: 13502781--13502806 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13502771 TTACCATTAG
13502781 AAAAAAAAACAAA
1 AAAAAAAAACAAA
13502794 AAAAAAAAACAAA
1 AAAAAAAAACAAA
13502807 TTACACTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACAAA
Found at i:13508254 original size:2 final size:2
Alignment explanation
Indices: 13508247--13508276 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13508237 TTAACTGAGG
13508247 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
13508277 AGTACATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13512639 original size:32 final size:31
Alignment explanation
Indices: 13512581--13512655 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
13512571 TTTAAAATAT
* * *
13512581 TATAAATTGATTACTTGAATTTAATAACACA
1 TATAAATTAATTAATTGAATTCAATAACACA
* *
13512612 TGATAAATTAATTAATTTAATTCAATAACTCA
1 T-ATAAATTAATTAATTGAATTCAATAACACA
*
13512644 TATTAATTAATT
1 TATAAATTAATT
13512656 GAACTTGTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 11 0.30
32 26 0.70
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (31 bp):
TATAAATTAATTAATTGAATTCAATAACACA
Found at i:13514341 original size:20 final size:20
Alignment explanation
Indices: 13514316--13514359 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
13514306 GGGGGACCTT
13514316 TAAGAATGATGAGGTTAGAG
1 TAAGAATGATGAGGTTAGAG
13514336 TAAGAATGATGAGGTTAGAG
1 TAAGAATGATGAGGTTAGAG
13514356 TAAG
1 TAAG
13514360 TGAGGGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.34, T:0.25
Consensus pattern (20 bp):
TAAGAATGATGAGGTTAGAG
Found at i:13515220 original size:13 final size:13
Alignment explanation
Indices: 13515210--13515246 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
13515200 TTCCAAAGCT
13515210 CTTTTCAAAAGTA
1 CTTTTCAAAAGTA
*
13515223 CTTCTCAAAAGTA
1 CTTTTCAAAAGTA
*
13515236 TTTTTCAAAAG
1 CTTTTCAAAAG
13515247 CAATGAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (13 bp):
CTTTTCAAAAGTA
Found at i:13517256 original size:17 final size:16
Alignment explanation
Indices: 13517234--13517293 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 16
13517224 ATAATGATTC
*
13517234 TTTAATTTTATATATTT
1 TTTAATTTT-TATAATT
13517251 TTTAATTTTTATAATT
1 TTTAATTTTTATAATT
* *
13517267 TATAATTTTTACTTATT
1 TTTAATTTTTA-TAATT
13517284 TTT-ATTTTTA
1 TTTAATTTTTA
13517294 ACGATTATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 23 0.61
17 15 0.39
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTAATTTTTATAATT
Found at i:13517260 original size:9 final size:9
Alignment explanation
Indices: 13517239--13517288 Score: 52
Period size: 10 Copynumber: 5.7 Consensus size: 9
13517229 GATTCTTTAA
13517239 TTTTATATAT
1 TTTTATA-AT
13517249 TTTT-TAAT
1 TTTTATAAT
13517257 TTTTATAA-
1 TTTTATAAT
13517265 -TTTATAAT
1 TTTTATAAT
*
13517273 TTTTACTTAT
1 TTTTA-TAAT
13517283 TTTTAT
1 TTTTAT
13517289 TTTTAACGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
7 7 0.20
8 6 0.17
9 10 0.29
10 12 0.34
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTATAAT
Found at i:13518127 original size:33 final size:31
Alignment explanation
Indices: 13518087--13518154 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 31
13518077 TGCATTCGTA
13518087 TTTTTATTTCAT-TTGTTTCAAGCTTTATTGTAT
1 TTTTTATTTCATATTGTTTCAAG-TTT-TT-TAT
*
13518120 TTTTTATTTTATATTGTTTCAAGTTTTTTAT
1 TTTTTATTTCATATTGTTTCAAGTTTTTTAT
13518151 TTTT
1 TTTT
13518155 AATTAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
31 7 0.21
32 2 0.06
33 14 0.42
34 10 0.30
ACGTcount: A:0.18, C:0.06, G:0.07, T:0.69
Consensus pattern (31 bp):
TTTTTATTTCATATTGTTTCAAGTTTTTTAT
Found at i:13518542 original size:45 final size:45
Alignment explanation
Indices: 13518476--13518561 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
13518466 AAATTTGAAA
* **
13518476 TATTTTTATATATGAAATATTTCAATTAATTATTTCAAATATCAT
1 TATTTTTATACATGAAATATTTCAAACAATTATTTCAAATATCAT
* *
13518521 TATTTTTATACGTGAAGTATTTCAAACAATTATTTCAAATA
1 TATTTTTATACATGAAATATTTCAAACAATTATTTCAAATA
13518562 CATATACAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.48
Consensus pattern (45 bp):
TATTTTTATACATGAAATATTTCAAACAATTATTTCAAATATCAT
Found at i:13518752 original size:49 final size:49
Alignment explanation
Indices: 13518690--13518783 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
13518680 TTGATTTTAT
* *
13518690 AAATAAAAGATTTATTAATTAAAAAGATGAATTACA-AATAAAAAATTAA
1 AAATAAAAGATTTATTAACTAAAAAAATGAATTA-AGAATAAAAAATTAA
* * *
13518739 AAATAATATATTTATTAACTAAAAAAATTAATTAAGAATAAAAAA
1 AAATAAAAGATTTATTAACTAAAAAAATGAATTAAGAATAAAAAA
13518784 AGTTTGAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 1 0.03
49 38 0.97
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (49 bp):
AAATAAAAGATTTATTAACTAAAAAAATGAATTAAGAATAAAAAATTAA
Found at i:13519876 original size:23 final size:23
Alignment explanation
Indices: 13519806--13519865 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
13519796 CATCAATTTA
*
13519806 ATGATTTTTTATATTAGATAAAT
1 ATGATTTTTTATGTTAGATAAAT
13519829 ATGATTTTTTATGTTAGATAAAT
1 ATGATTTTTTATGTTAGATAAAT
13519852 ATGATTTTTTATGT
1 ATGATTTTTTATGT
13519866 ATGTAATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (23 bp):
ATGATTTTTTATGTTAGATAAAT
Found at i:13527650 original size:10 final size:10
Alignment explanation
Indices: 13527631--13527662 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
13527621 AATATGAAAA
13527631 ATAA-AAATT
1 ATAACAAATT
13527640 ATAACAAATT
1 ATAACAAATT
13527650 ATAACAAATT
1 ATAACAAATT
13527660 ATA
1 ATA
13527663 GAATTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAACAAATT
Found at i:13527696 original size:10 final size:9
Alignment explanation
Indices: 13527631--13527696 Score: 53
Period size: 10 Copynumber: 6.8 Consensus size: 9
13527621 AATATGAAAA
13527631 ATAAAAATT
1 ATAAAAATT
13527640 ATAACAAATT
1 ATAA-AAATT
13527650 ATAACAAATT
1 ATAA-AAATT
*
13527660 AT-AGAATT
1 ATAAAAATT
*
13527668 ATTTAAAATT
1 A-TAAAAATT
13527678 ATTTAAAAATT
1 A--TAAAAATT
13527689 ATTAAAAA
1 A-TAAAAA
13527697 CAATGTTCAT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
8 5 0.10
9 6 0.12
10 30 0.60
11 9 0.18
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (9 bp):
ATAAAAATT
Found at i:13534946 original size:12 final size:12
Alignment explanation
Indices: 13534929--13534953 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13534919 GTTCTTGTTG
13534929 TTTTATTATTTC
1 TTTTATTATTTC
13534941 TTTTATTATTTC
1 TTTTATTATTTC
13534953 T
1 T
13534954 AATATCTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTATTTC
Found at i:13538758 original size:46 final size:46
Alignment explanation
Indices: 13538696--13539010 Score: 450
Period size: 46 Copynumber: 6.8 Consensus size: 46
13538686 TTTGATATGA
* * * * *
13538696 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTCTTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATGT
* *
13538742 TCCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATGT
* **
13538788 TGCCATAGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATGT
**
13538834 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATGT
* *
13538880 TGCCATGGTATTTTTCAACCATGGTCTTATTCATTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATGT
** *
13538926 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATGT
* **
13538972 TTCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
13539011 TTCAGAAAGC
Statistics
Matches: 246, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 246 1.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATGT
Found at i:13541684 original size:19 final size:19
Alignment explanation
Indices: 13541660--13541706 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
13541650 AATGCCTCCT
*
13541660 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
13541679 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
13541698 TATGCATTA
1 TTTGCATTA
13541707 AATTTCACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:13543375 original size:14 final size:15
Alignment explanation
Indices: 13543356--13543384 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13543346 GTTTCCATTT
13543356 TCTTTCT-TCTTCCC
1 TCTTTCTCTCTTCCC
13543370 TCTTTCTCTCTTCCC
1 TCTTTCTCTCTTCCC
13543385 CTACAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTTTCTCTCTTCCC
Found at i:13543928 original size:40 final size:40
Alignment explanation
Indices: 13543880--13544017 Score: 186
Period size: 40 Copynumber: 3.5 Consensus size: 40
13543870 CTTTTCAGGT
* *
13543880 CAAATCCTATCCACCTTAAGTTACCGTAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
* * *
13543920 TAAATCCTATTCACTTTAAATTACCATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
* * **
13543960 CAAATCCTATCCACTTTGAGGTATTATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
*
13544000 CGAATCCTATCCACTTTA
1 CAAATCCTATCCACTTTA
13544018 TATTCTCGAG
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 84 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.30
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
Found at i:13548577 original size:46 final size:47
Alignment explanation
Indices: 13548507--13548734 Score: 313
Period size: 46 Copynumber: 5.0 Consensus size: 47
13548497 TTCGACATGA
* * ** * *
13548507 TGCCATGGTATCTTTCAACTATGGTTTTACTAGTTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTACATTTCATATCAGGT
* * * *
13548553 TGCCATGGTATCTTTCAACCATGGTCTTA-TTCATTTCATGTTACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTACATTTCATATCAGGT
*
13548599 TGCCATGGTATCTTTCAACCATAGTCTTA-TACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTACATTTCATATCAGGT
13548645 TGCCATGGTATCTTTCAACCATGGTCTTAC-ACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTACATTTCATATCAGGT
*
13548691 TGCCATGGTATCTTTCAACCATGGTCTTAC-ACATTTCATTTCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACTACATTTCATATCAG
13548735 AGAGCACACT
Statistics
Matches: 166, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
45 5 0.03
46 161 0.97
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTACATTTCATATCAGGT
Found at i:13554521 original size:43 final size:43
Alignment explanation
Indices: 13554447--13554581 Score: 135
Period size: 43 Copynumber: 3.1 Consensus size: 43
13554437 GAAAGAAATA
* * * *
13554447 CCGCTAAAGACCATGACCTTTAGCGGTGCTTTCCCCACAAACG
1 CCGCTAAAAACCATGACCTTTAACGGCGCTTTTCCCACAAACG
* * * **
13554490 CCGCTAAAAACCATGACCTTTAACGACGCTTTTTCTACAAATA
1 CCGCTAAAAACCATGACCTTTAACGGCGCTTTTCCCACAAACG
* ** * *
13554533 CTGCTAAAAATAATGACTTTTAACGGCGCTTTTCTCACAAACG
1 CCGCTAAAAACCATGACCTTTAACGGCGCTTTTCCCACAAACG
*
13554576 CTGCTA
1 CCGCTA
13554582 TAGAACAAGA
Statistics
Matches: 73, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (43 bp):
CCGCTAAAAACCATGACCTTTAACGGCGCTTTTCCCACAAACG
Found at i:13558021 original size:23 final size:23
Alignment explanation
Indices: 13557995--13558041 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
13557985 CAGAGAAAGA
13557995 AAAGAAACAACTACCTGAAAATT
1 AAAGAAACAACTACCTGAAAATT
*
13558018 AAAGAAACAACTTCCTGAAAATT
1 AAAGAAACAACTACCTGAAAATT
13558041 A
1 A
13558042 TATCAACCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.55, C:0.17, G:0.09, T:0.19
Consensus pattern (23 bp):
AAAGAAACAACTACCTGAAAATT
Found at i:13558647 original size:19 final size:19
Alignment explanation
Indices: 13558620--13558664 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
13558610 CTAATCTCTA
*
13558620 TTTTATATTTTATTTTTAT
1 TTTTATATTTCATTTTTAT
*
13558639 TTTTGTATTTCATTTTTAT
1 TTTTATATTTCATTTTTAT
13558658 TTGTTAT
1 TT-TTAT
13558665 CAATATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTTATATTTCATTTTTAT
Found at i:13558971 original size:7 final size:7
Alignment explanation
Indices: 13558959--13559099 Score: 54
Period size: 7 Copynumber: 19.7 Consensus size: 7
13558949 ACTAATTAAT
13558959 CTAAACC
1 CTAAACC
13558966 CTAAACC
1 CTAAACC
*
13558973 CTTAATCC
1 C-TAAACC
* *
13558981 ATAAACT
1 CTAAACC
13558988 CTAAACC
1 CTAAACC
*
13558995 CTAAAATC
1 CT-AAACC
*
13559003 CTAAAAC
1 CTAAACC
* *
13559010 ATAAACA
1 CTAAACC
* *
13559017 ATTAACC
1 CTAAACC
13559024 CTAAACCC
1 CTAAA-CC
13559032 CT-AACC
1 CTAAACC
*
13559038 CTTAACCC
1 C-TAAACC
13559046 CT-AACC
1 CTAAACC
*
13559052 ACTAAACT
1 -CTAAACC
*
13559060 TTAAACC
1 CTAAACC
*
13559067 C-CAACC
1 CTAAACC
13559073 CTTAAACC
1 C-TAAACC
* *
13559081 ATAATCC
1 CTAAACC
*
13559088 ATAAACC
1 CTAAACC
*
13559095 TTAAA
1 CTAAA
13559100 ATAGTAACTC
Statistics
Matches: 98, Mismatches: 27, Indels: 18
0.69 0.19 0.13
Matches are distributed among these distances:
6 11 0.11
7 61 0.62
8 26 0.27
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:13559007 original size:22 final size:21
Alignment explanation
Indices: 13558959--13559007 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
13558949 ACTAATTAAT
*
13558959 CTAAACCCTAAACCCTTAATC
1 CTAAACCCTAAACCCTAAATC
*
13558980 CATAAACTCTAAACCCTAAAATC
1 C-TAAACCCTAAACCCT-AAATC
13559003 CTAAA
1 CTAAA
13559008 ACATAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.75
23 5 0.21
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (21 bp):
CTAAACCCTAAACCCTAAATC
Found at i:13559034 original size:29 final size:29
Alignment explanation
Indices: 13558960--13559035 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
13558950 CTAATTAATC
* ** **
13558960 TAAACCCTAAACCCTTAATCCATAAACTC
1 TAAACCCTAAACCCCTAAAACATAAACAA
**
13558989 TAAACCCTAAAATCCTAAAACATAAACAA
1 TAAACCCTAAACCCCTAAAACATAAACAA
*
13559018 TTAACCCTAAACCCCTAA
1 TAAACCCTAAACCCCTAA
13559036 CCCTTAACCC
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (29 bp):
TAAACCCTAAACCCCTAAAACATAAACAA
Found at i:13559036 original size:14 final size:14
Alignment explanation
Indices: 13559019--13559058 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
13559009 CATAAACAAT
13559019 TAACCCTAAACCCC
1 TAACCCTAAACCCC
*
13559033 TAACCCTTAACCCC
1 TAACCCTAAACCCC
13559047 TAACCACTAAAC
1 TAACC-CTAAAC
13559059 TTTAAACCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.38, C:0.45, G:0.00, T:0.17
Consensus pattern (14 bp):
TAACCCTAAACCCC
Found at i:13559147 original size:14 final size:14
Alignment explanation
Indices: 13559111--13559156 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
13559101 TAGTAACTCA
*
13559111 TAAATCTTAAACCC
1 TAAATCATAAACCC
* * *
13559125 TTAACCATATACCC
1 TAAATCATAAACCC
13559139 TAAATCATAAACCC
1 TAAATCATAAACCC
13559153 TAAA
1 TAAA
13559157 CTATAATGAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAATCATAAACCC
Found at i:13559383 original size:15 final size:14
Alignment explanation
Indices: 13559360--13559394 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
13559350 AAACCACCCT
*
13559360 TAAACCATAATCCC
1 TAAACCATAATCCA
13559374 TAAACTCATAATCCA
1 TAAAC-CATAATCCA
13559389 TAAACC
1 TAAACC
13559395 TTAAAATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCATAATCCA
Found at i:13561017 original size:33 final size:33
Alignment explanation
Indices: 13560975--13561041 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
13560965 GCAACTGAGA
13560975 ATGATAAAAGAACGCTGAGAAGATTAGCTGGTG
1 ATGATAAAAGAACGCTGAGAAGATTAGCTGGTG
*
13561008 ATGATAAAAGGACGCTGAGAAGATTAGCTGGTG
1 ATGATAAAAGAACGCTGAGAAGATTAGCTGGTG
13561041 A
1 A
13561042 CTATGTCCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.09, G:0.31, T:0.21
Consensus pattern (33 bp):
ATGATAAAAGAACGCTGAGAAGATTAGCTGGTG
Found at i:13563135 original size:44 final size:44
Alignment explanation
Indices: 13563094--13564340 Score: 654
Period size: 44 Copynumber: 27.4 Consensus size: 44
13563084 TGTTATCTTT
** *
13563094 CTGAAGTTGCAGTGGAGCAGATTGAAGCCATTAATCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATATAAATCTTATCTCC
* ** * * * *
13563138 CTAAAGTCACAGTAGAGCAGATTGAAAATAGCAAATCTTATCTCT
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATA-TAAATCTTATCTCC
* * * * *
13563183 CTGAAGTTGCAGTAGAGTAGATTAAAGCTATAAACCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATATAAATCTTATCTCC
* * * * *
13563227 CTAAAGTTGCAGTAGAGCAGGTTGAAG-TCACAAATCTTATCTTC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGAT-ATAAATCTTATCTCC
** * *
13563271 CTGAAGTTGCAGTGGAGCAGACCGAAGATAGAAAATCTTATCTCT
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATA-TAAATCTTATCTCC
* * * * * *
13563316 CTGAAGTTGTAGTAGAGCAGATTAAAGCTATAAACCTTATCTAC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATATAAATCTTATCTCC
* * * * * * * *
13563360 TTAAAGTTACAGTGGGGCAGGTTGAAGTTACAAGTCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATATAAATCTTATCTCC
* * * * * *
13563404 CTGAAGTTGCAGTGGGGCAGACTAAAGATAGTGAATCTTATTTCT
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATA-TAAATCTTATCTCC
* * * ** * * * *
13563449 CTGAAATGGCAGTGAAATATATTAAAGCTACAAATTAGAAATCTTATCTCT
1 CTGAAGTTGCAGTGGAGCAGATT---G--A-AGA-TATAAATCTTATCTCC
* * * * * *
13563500 CTGAAGTTGTAGTGGAGTAGATTGAAGTTACAGATTTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATATAAATCTTATCTCC
* * * *
13563544 TTGAAGTTGCAGTGGAGAATATTGAAGATAGCAAATCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATA-TAAATCTTATCTCC
* * * * *
13563589 CTGAAGCTGCAGTGGAGCAGATTGAAGTTATAGATCTTACCTCT
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATATAAATCTTATCTCC
* * * * * * *
13563633 CTGAAGTTGCAGTAGAACAAATTGAAGTTACAGATCTTATCTCA
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATATAAATCTTATCTCC
* ** * *
13563677 TTGAAGTTGCAGTGGAATAGATCGAAGATAGGAAATCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATA-TAAATCTTATCTCC
* * * * * *
13563722 ATGAAGTTGCAGTGGAACAAATTGAA-ACTACAAGTCTAATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGA-TATAAATCTTATCTCC
* * ** *
13563766 CTGAAGTTGCAGTAGAGCAGACTGAAGATAGCGAATCTTATTTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATA-TAAATCTTATCTCC
* * * * * * *
13563811 TTTAAGTTGCAGTAGAACAGATTAAAGCTACAAATTACAAGTCTCATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAG----ATA-TA-AA-TCTTATCTCC
* * * * * *
13563862 TTAAAGTTGTAGTGGAGCAGACTGAAGATAACAAATCTTATTTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGAT-ATAAATCTTATCTCC
* * * *
13563907 CTGAAGTTGCAGTGGAACAGATTAAAGCTACAAATTACAAGTCTCATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAG----ATA-TA-AA-TCTTATCTCC
* * * * * *
13563958 CTGAAGTTGCTGTGGAGCAAACTAAAGATAAAGAATCTTATTTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATATA-AATCTTATCTCC
* * **
13564003 CTGAAGTTGCAGTAGAACAGATT-AATGATACAAATTTCAAATCGGATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAA-GAT----A--T-AAATCTTATCTCC
* * * *
13564054 CTGAAGTTACAGTGGAGAAGATTGAAG-TCATTACTCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGAT-ATAAATCTTATCTCC
* ** *
13564098 CTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATATAAATCTTATCTCC
* * * *** *
13564142 TTTAAGTTGCAGTGGAGAAGATTGAAGATGCGAATCTTATTTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATATAAATCTTATCTCC
* * ** *
13564186 CTAAAATTGCAGTGGAATAGATTAAAGATACGAGTTACAAATCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATT---GA-A-GA--TATAAATCTTATCTCC
** * *
13564237 CTGAAGTTGCAGTGGAGCAGATT-ATAGATGCAAGTCTAATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGA-AGATATAAATCTTATCTCC
* * * * * *
13564281 TTGAAGTTACAGTGGAGTAGATCGAAG-TACTAATTCCTATC-CC
1 CTGAAGTTGCAGTGGAGCAGATTGAAGATA-TAAATCTTATCTCC
*
13564324 ACTGAAGATGCAGTGGA
1 -CTGAAGTTGCAGTGGA
13564341 TTGGAATGAG
Statistics
Matches: 908, Mismatches: 244, Indels: 102
0.72 0.19 0.08
Matches are distributed among these distances:
43 4 0.00
44 453 0.50
45 260 0.29
46 8 0.01
47 10 0.01
48 4 0.00
49 7 0.01
50 6 0.01
51 151 0.17
52 5 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGCAGATTGAAGATATAAATCTTATCTCC
Found at i:13563289 original size:133 final size:133
Alignment explanation
Indices: 13563094--13564302 Score: 673
Period size: 133 Copynumber: 8.8 Consensus size: 133
13563084 TGTTATCTTT
* ** ** * * ** *
13563094 CTGAAGTTGCAGTGGAGCAGATTGAAGCCATTAATCTTATCTCCCTAAAGTCACAGTAGAGCAGA
1 CTGAAGTTGCAGTAGAGCAGATTGAAGTTACAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA
* * *
13563159 TTGAAAATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTAAAGCTATAAACCTTATC
66 TTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAATCTTATC
13563224 TCC
131 TCC
* * *
13563227 CTAAAGTTGCAGTAGAGCAGGTTGAAGTCACAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA
1 CTGAAGTTGCAGTAGAGCAGATTGAAGTTACAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA
** * * *
13563292 CCGAAGATAGAAAATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATTAAAGCTATAAACCTTATC
66 TTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAATCTTATC
*
13563357 TAC
131 TCC
* * * * * * * * *
13563360 TTAAAGTTACAGTGGGGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGGGCAGA
1 CTGAAGTTGCAGTAGAGCAGATTGAAGTTACAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA
* * ** * * * ** *
13563425 CTAAAGATAGTGAATCTTATTTCTCTGAAATGGCAGT-GAAATATATTAAAGCTACAAATTAGAA
66 TTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAG-AGCAGATTAAAGCT----A-T--AA
*
13563489 ATCTTATCTCT
123 ATCTTATCTCC
* * * * * * *
13563500 CTGAAGTTGTAGTGGAGTAGATTGAAGTTACAGATTTTATC-TCCTTGAAGTTGCAGTGGAGAAT
1 CTGAAGTTGCAGTAGAGCAGATTGAAGTTACAAATCTTATCTTCC-TGAAGTTGCAGTGGAGCAG
* * * * * * *
13563564 ATTGAAGATAGCAAATCTTATCTCCCTGAAGCTGCAGTGGAGCAGATTGAAGTTATAGATCTTAC
65 ATTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAATCTTAT
*
13563629 CTCT
130 CTCC
* * * * **
13563633 CTGAAGTTGCAGTAGAACAAATTGAAGTTACAGATCTTATC-TCATTGAAGTTGCAGTGGAATAG
1 CTGAAGTTGCAGTAGAGCAGATTGAAGTTACAAATCTTATCTTC-CTGAAGTTGCAGTGGAGCAG
* * * * * * * *
13563697 ATCGAAGATAGGAAATCTTATCTC-CATGAAGTTGCAGTGGAACAAATTGAAA-CTACAAGTCTA
65 ATTGAAGATAGCAAATCTTATCTCTC-TGAAGTTGCAGTAGAGCAGATT-AAAGCTATAAATCTT
13563760 ATCTCC
128 ATCTCC
* * * * * *
13563766 CTGAAGTTGCAGTAGAGCAGACTGAAGATAGCGAATCTTAT-TTCCTTTAAGTTGCAGTAGAACA
1 CTGAAGTTGCAGTAGAGCAGATTGAAGTTA-CAAATCTTATCTTCC-TGAAGTTGCAGTGGAGCA
* * * * * * * *
13563830 GATTAAAGCTA-CAAATTACAAGTCTCATCTC-CTTAAAGTTGTAGTGGAGCAGACTGAAGATAA
64 GATTGAAGATAGCAAA-T-C---T-T-ATCTCTC-TGAAGTTGCAGTAGAGCAGATTAAAGCT-A
* *
13563893 CAAATCTTATTTCC
120 TAAATCTTATCTCC
* * * * * *
13563907 CTGAAGTTGCAGTGGAACAGATTAAAGCTACAAATTACAAGTCTCATCTCCCTGAAGTTGCTGTG
1 CTGAAGTTGCAGTAGAGCAGATTGAAGTTACAAA-T-C---T-T-ATCTTCCTGAAGTTGCAGTG
* * * * * * * *
13563972 GAGCAAACTAAAGATA-AAGAATCTTATTTCCCTGAAGTTGCAGTAGAACAGATTAATGATACAA
59 GAGCAGATTGAAGATAGCA-AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAA--A-GC--
* **
13564036 ATTTCAAATCGGATCTCC
118 -TAT-AAATCTTATCTCC
* * * * ** * *
13564054 CTGAAGTTACAGTGGAGAAGATTGAAGTCATTACTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 CTGAAGTTGCAGTAGAGCAGATTGAAGTTACAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA
* ** * * * * * ***
13564119 TTAAAGCCA-CAAATCTTATCTC-CTTTAAGTTGCAGTGGAGAAGATTGAAGATGCGAATCTTAT
66 TTGAAGATAGCAAATCTTATCTCTC-TGAAGTTGCAGTAGAGCAGATTAAAGCTATAAATCTTAT
*
13564182 TTCC
130 CTCC
* * * ** *
13564186 CTAAAATTGCAGTGGAATAGATTAAAGATACGAGTTACAAATCTTATCTCCCTGAAGTTGCAGTG
1 CTGAAGTTGCAGTAGAGCAGATT---G--A--AGTTACAAATCTTATCTTCCTGAAGTTGCAGTG
* * * * *
13564251 GAGCAGATT-ATAGAT-GCAAGTCTAATCTC-CTTGAAGTTACAGTGGAGTAGAT
59 GAGCAGATTGA-AGATAGCAAATCTTATCTCTC-TGAAGTTGCAGTAGAGCAGAT
13564303 CGAAGTACTA
Statistics
Matches: 832, Mismatches: 192, Indels: 98
0.74 0.17 0.09
Matches are distributed among these distances:
132 29 0.03
133 357 0.43
134 36 0.04
135 3 0.00
136 1 0.00
137 3 0.00
138 4 0.00
139 105 0.13
140 154 0.19
141 62 0.07
142 4 0.00
143 2 0.00
145 2 0.00
146 3 0.00
147 62 0.07
148 5 0.01
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (133 bp):
CTGAAGTTGCAGTAGAGCAGATTGAAGTTACAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA
TTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAATCTTATC
TCC
Found at i:13563311 original size:89 final size:89
Alignment explanation
Indices: 13563086--13564307 Score: 462
Period size: 89 Copynumber: 13.4 Consensus size: 89
13563076 ATGGCGAATG
* * * **
13563086 TTATCTTTCTGAAGTTGCAGTGGAGCAGATTGAAGCCATTAATCTTATCTCCCTAAAGTCACAGT
1 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATAAATCTTATCTCCCTAAAGTTGCAGT
13563151 AGAGCAGATTGAAAATAGCAAATC
66 AGAGCAGATTGAAAATAGCAAATC
* * * *
13563175 TTATC-TCTCTGAAGTTGCAGTAGAGTAGATTAAAGCTATAAACCTTATCTCCCTAAAGTTGCAG
1 TTATCTTC-CTGAAGTTGCAGTGGAGCAGATTGAAGCTATAAATCTTATCTCCCTAAAGTTGCAG
* *
13563239 TAGAGCAGGTTG-AAGTCA-CAAATC
65 TAGAGCAGATTGAAAAT-AGCAAATC
** * * * * *
13563263 TTATCTTCCTGAAGTTGCAGTGGAGCAGACCGAAGATAGAAAATCTTATCTCTCTGAAGTTGTAG
1 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA-TAAATCTTATCTCCCTAAAGTTGCAG
* * *
13563328 TAGAGCAGATT-AAAGCTA-TAAACC
65 TAGAGCAGATTGAAA-ATAGCAAATC
* * * * * * * * * *
13563352 TTATCTACTTAAAGTTACAGTGGGGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGT
1 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATAAATCTTATCTCCCTAAAGTTGCAGT
* * * **
13563417 GGGGCAGACT-AAAGATAGTGAATC
66 AGAGCAGATTGAAA-ATAGCAAATC
* * * ** * * * *
13563441 TTAT-TTCTCTGAAATGGCAGTGAAATATATTAAAGCTACAAATTAGAAATCTTATCTCTCTGAA
1 TTATCTTC-CTGAAGTTGCAGTGGAGCAGATTGAAGCT----A-T--AAATCTTATCTCCCTAAA
* * * ** * *
13563505 GTTGTAGTGGAGTAGATTGAAGTTA-CAGATT
58 GTTGCAGTAGAGCAGATTGAAAATAGCAAATC
* * * * * *
13563536 TTATC-TCCTTGAAGTTGCAGTGGAGAATATTGAAGATAGCAAATCTTATCTCCCTGAAGCTGCA
1 TTATCTTCC-TGAAGTTGCAGTGGAGCAGATTGAAGCTA-TAAATCTTATCTCCCTAAAGTTGCA
* ** * *
13563600 GTGGAGCAGATTGAAGTTA-TAGATC
64 GTAGAGCAGATTGAAAATAGCAAATC
* * * * * * * ** *
13563625 TTA-CCTCTCTGAAGTTGCAGTAGAACAAATTGAAGTTACAGATCTTATCTCATTGAAGTTGCAG
1 TTATCTTC-CTGAAGTTGCAGTGGAGCAGATTGAAGCTATAAATCTTATCTCCCTAAAGTTGCAG
* ** * * *
13563689 TGGAATAGATCGAAGATAGGAAATC
65 TAGAGCAGATTGAAAATAGCAAATC
* * * * * * *
13563714 TTATC-TCCATGAAGTTGCAGTGGAACAAATTGAAACTACAAGTCTAATCTCCCTGAAGTTGCAG
1 TTATCTTCC-TGAAGTTGCAGTGGAGCAGATTGAAGCTATAAATCTTATCTCCCTAAAGTTGCAG
* * *
13563778 TAGAGCAGACTGAAGATAGCGAATC
65 TAGAGCAGATTGAAAATAGCAAATC
* * * * * *
13563803 TTAT-TTCCTTTAAGTTGCAGTAGAACAGATTAAAGCTACAAATTACAAGTCTCATCTCCTTAAA
1 TTATCTTCC-TGAAGTTGCAGTGGAGCAGATTGAAGCT----A-TA-AA-TCTTATCTCCCTAAA
* * * * *
13563867 GTTGTAGTGGAGCAGACTGAAGATAACAAATC
58 GTTGCAGTAGAGCAGATTGAAAATAGCAAATC
* * * *
13563899 TTAT-TTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAATTACAAGTCTCATCTCCCTGAA
1 TTATCTT-CCTGAAGTTGCAGTGGAGCAGATTGAAGCT----A-TA-AA-TCTTATCTCCCTAAA
* * * * *
13563963 GTTGCTGTGGAGCAAACT-AAAGATA-AAGAATC
58 GTTGCAGTAGAGCAGATTGAAA-ATAGCA-AATC
* * * ** *
13563995 TTAT-TTCCCTGAAGTTGCAGTAGAACAGATT-AATGATACAAATTTCAAATCGGATCTCCCTGA
1 TTATCTT-CCTGAAGTTGCAGTGGAGCAGATTGAA-G---C---TAT-AAATCTTATCTCCCTAA
* * * * *
13564058 AGTTACAGTGGAGAAGATTG-AAGT--CATTACTC
57 AGTTGCAGTAGAGCAGATTGAAAATAGCA--AATC
* * * * * *
13564090 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCTTATCTCCTTTAAGTTGCAGT
1 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATAAATCTTATCTCCCTAAAGTTGCAGT
* * * *
13564155 GGAGAAGATTGAAGAT-GCGAATC
66 AGAGCAGATTGAAAATAGCAAATC
* * ** * * *
13564178 TTAT-TTCCCTAAAATTGCAGTGGAATAGATTAAAGATACGAGTTACAAATCTTATCTCCCTGAA
1 TTATCTT-CCTGAAGTTGCAGTGGAGCAGATT---G--A--AGCTATAAATCTTATCTCCCTAAA
* * *
13564242 GTTGCAGTGGAGCAGATT-ATAGAT-GCAAGTC
58 GTTGCAGTAGAGCAGATTGA-AAATAGCAAATC
* * * *
13564273 TAATC-TCCTTGAAGTTACAGTGGAGTAGATCGAAG
1 TTATCTTCC-TGAAGTTGCAGTGGAGCAGATTGAAG
13564308 TACTAATTCC
Statistics
Matches: 886, Mismatches: 188, Indels: 119
0.74 0.16 0.10
Matches are distributed among these distances:
87 1 0.00
88 176 0.20
89 336 0.38
90 5 0.01
91 1 0.00
92 2 0.00
93 3 0.00
94 6 0.01
95 133 0.15
96 213 0.24
97 7 0.01
98 1 0.00
99 1 0.00
102 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (89 bp):
TTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATAAATCTTATCTCCCTAAAGTTGCAGT
AGAGCAGATTGAAAATAGCAAATC
Found at i:13563707 original size:273 final size:273
Alignment explanation
Indices: 13563218--13563717 Score: 596
Period size: 273 Copynumber: 1.8 Consensus size: 273
13563208 AGCTATAAAC
*
13563218 CTTATCTCCCTAAAGTTGCAGTAGAGCAGGTTGAAGTCACAAATCTTATCTTCCTGAAGTTGCAG
1 CTTATCTCCCTAAAGTTGCAGTAGAGCAGATTGAAGTCACAAATCTTATCTTCCTGAAGTTGCAG
* * * *
13563283 TGGAGCAGACCGAAGATAGAAAATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATTAAAGCTATA
66 TGGAGAAGACCGAAGATAGAAAATCTTATCTCCCTGAAGCTGCAGTAGAGCAGATTAAAGCTATA
* * ** ** *
13563348 AACCTTATCTACTTAAAGTTACAGTGGGGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTG
131 AACCTTACCTACTTAAAGTTACAGTAGAACAAATTGAAGTTACAAGTCTTATCTCACTGAAGTTG
**
13563413 CAGTGGGGCAGACTAAAGATAGTG-AATCTTATTTCTCTGAAATGGCAGTGAAATATATTAAAGC
196 CAGTGGAACAGACTAAAGATAG-GAAATCTTATTTCTCTGAAATGGCAGTGAAATATATTAAAGC
13563477 TACAAATTAGAAAT
260 TACAAATTAGAAAT
* * * * * * * *
13563491 CTTATCTCTCTGAAGTTGTAGTGGAGTAGATTGAAGTTACAGATTTTATC-TCCTTGAAGTTGCA
1 CTTATCTCCCTAAAGTTGCAGTAGAGCAGATTGAAGTCACAAATCTTATCTTCC-TGAAGTTGCA
* ** * * * *
13563555 GTGGAGAATATTGAAGATAGCAAATCTTATCTCCCTGAAGCTGCAGTGGAGCAGATTGAAGTTAT
65 GTGGAGAAGACCGAAGATAGAAAATCTTATCTCCCTGAAGCTGCAGTAGAGCAGATTAAAGCTAT
* * * * *
13563620 AGATCTTACCT-CTCTGAAGTTGCAGTAGAACAAATTGAAGTTAC-AGATCTTATCTCATTGAAG
130 AAACCTTACCTACT-TAAAGTTACAGTAGAACAAATTGAAGTTACAAG-TCTTATCTCACTGAAG
* *
13563683 TTGCAGTGGAATAGA-TCGAAGATAGGAAATCTTAT
193 TTGCAGTGGAACAGACT-AAAGATAGGAAATCTTAT
13563718 CTCCATGAAG
Statistics
Matches: 186, Mismatches: 36, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
272 9 0.05
273 177 0.95
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (273 bp):
CTTATCTCCCTAAAGTTGCAGTAGAGCAGATTGAAGTCACAAATCTTATCTTCCTGAAGTTGCAG
TGGAGAAGACCGAAGATAGAAAATCTTATCTCCCTGAAGCTGCAGTAGAGCAGATTAAAGCTATA
AACCTTACCTACTTAAAGTTACAGTAGAACAAATTGAAGTTACAAGTCTTATCTCACTGAAGTTG
CAGTGGAACAGACTAAAGATAGGAAATCTTATTTCTCTGAAATGGCAGTGAAATATATTAAAGCT
ACAAATTAGAAAT
Found at i:13563914 original size:96 final size:96
Alignment explanation
Indices: 13563387--13564257 Score: 615
Period size: 96 Copynumber: 9.4 Consensus size: 96
13563377 CAGGTTGAAG
* * * *** *
13563387 TTACAAGTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTAAAGATAGTGAATCTTATTTCTCTG
1 TTACAAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAATCTTATTTCCCTG
* * * * *
13563452 AAATGGCAGTGAAATATATTAAAGCTACAAA
66 AAGTTGCAGTGGAACAGATTAAAGCTACAAA
* * * * * * * * * * * *
13563483 TTAGAAATCTTATCTCTCTGAAGTTGTAGTGGAGTAGATTGAAG-TTACAGATTTTATCTCCTTG
1 TTACAAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAATCTTATTTCCCTG
* * *
13563547 AAGTTGCAGTGGAGA-ATATTGAAGATAGCAAA
66 AAGTTGCAGTGGA-ACAGATTAAAGCTA-CAAA
* * * * * ** *
13563579 -T-C---T-T-ATCTCCCTGAAGCTGCAGTGGAGCAGATTGAAG-TTATAGATCTTACCTCTCTG
1 TTACAAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAATCTTATTTCCCTG
* * * * *
13563636 AAGTTGCAGTAGAACAAATTGAAGTTACAGA
66 AAGTTGCAGTGGAACAGATTAAAGCTACAAA
** ** ** * *
13563667 -T-C---T-T-ATCTCATTGAAGTTGCAGTGGAATAGA-TCGAAGATAGGAAATCTTATCTCCAT
1 TTACAAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGATAACAAATCTTATTTCCCT
*
13563724 GAAGTTGCAGTGGAACAAATT---G----AAA
65 GAAGTTGCAGTGGAACAGATTAAAGCTACAAA
* * * * * * *
13563749 CTACAAGTCTAATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATAGCGAATCTTATTTCCTTT
1 TTACAAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAATCTTATTTCCCTG
*
13563814 AAGTTGCAGTAGAACAGATTAAAGCTACAAA
66 AAGTTGCAGTGGAACAGATTAAAGCTACAAA
* * *
13563845 TTACAAGTCTCATCTCCTTAAAGTTGTAGTGGAGCAGACTGAAGATAACAAATCTTATTTCCCTG
1 TTACAAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAATCTTATTTCCCTG
13563910 AAGTTGCAGTGGAACAGATTAAAGCTACAAA
66 AAGTTGCAGTGGAACAGATTAAAGCTACAAA
* * *
13563941 TTACAAGTCTCATCTCCCTGAAGTTGCTGTGGAGCAAACTAAAGATAA-AGAATCTTATTTCCCT
1 TTACAAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACA-AATCTTATTTCCCT
* * *
13564005 GAAGTTGCAGTAGAACAGATTAATGATACAAA
65 GAAGTTGCAGTGGAACAGATTAAAGCTACAAA
* * ** * * * * ** * *
13564037 TTTCAAATCGGATCTCCCTGAAGTTACAGTGGAGAAGATTGAAG-TCATTACTCTTATCTCCCTG
1 TTACAAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAATCTTATTTCCCTG
* *
13564101 AAGTTGCAGTGGAGCAGATTAAAGCCACAAA
66 AAGTTGCAGTGGAACAGATTAAAGCTACAAA
* * * * * * *
13564132 -T-C---T-T-ATCTCCTTTAAGTTGCAGTGGAGAAGATTGAAGAT-GCGAATCTTATTTCCCTA
1 TTACAAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAATCTTATTTCCCTG
* * * * *
13564189 AAATTGCAGTGGAATAGATTAAAGATACGAG
66 AAGTTGCAGTGGAACAGATTAAAGCTACAAA
* *
13564220 TTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 TTACAAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGA
13564258 TTATAGATGC
Statistics
Matches: 624, Mismatches: 121, Indels: 61
0.77 0.15 0.08
Matches are distributed among these distances:
82 2 0.00
83 1 0.00
84 1 0.00
86 1 0.00
87 2 0.00
88 101 0.16
89 160 0.26
90 4 0.01
91 1 0.00
92 1 0.00
93 2 0.00
94 2 0.00
95 98 0.16
96 248 0.40
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (96 bp):
TTACAAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAATCTTATTTCCCTG
AAGTTGCAGTGGAACAGATTAAAGCTACAAA
Found at i:13563984 original size:51 final size:51
Alignment explanation
Indices: 13563814--13563984 Score: 151
Period size: 51 Copynumber: 3.5 Consensus size: 51
13563804 TATTTCCTTT
* * * * * *
13563814 AAGTTGCAGTAGAACAGATTAAAGCTACAAATTACAAGTCTCATCTCCTTA
1 AAGTTGCTGTGGAGCAGACTAAAGCTACAAATTACAAGTCTCATCTCCCTG
* * *
13563865 AAGTTG-TAGTGGAGCAGACTGAAGATAACAAA-T-C---T-T-ATTTCCCTG
1 AAGTTGCT-GTGGAGCAGACTAAAGCT-ACAAATTACAAGTCTCATCTCCCTG
* * *
13563910 AAGTTGCAGTGGAACAGATTAAAGCTACAAATTACAAGTCTCATCTCCCTG
1 AAGTTGCTGTGGAGCAGACTAAAGCTACAAATTACAAGTCTCATCTCCCTG
*
13563961 AAGTTGCTGTGGAGCAAACTAAAG
1 AAGTTGCTGTGGAGCAGACTAAAG
13563985 ATAAAGAATC
Statistics
Matches: 91, Mismatches: 19, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
44 5 0.05
45 27 0.30
46 2 0.02
47 1 0.01
49 1 0.01
50 2 0.02
51 48 0.53
52 5 0.05
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (51 bp):
AAGTTGCTGTGGAGCAGACTAAAGCTACAAATTACAAGTCTCATCTCCCTG
Found at i:13564338 original size:183 final size:182
Alignment explanation
Indices: 13563760--13564340 Score: 454
Period size: 183 Copynumber: 3.1 Consensus size: 182
13563750 TACAAGTCTA
* * * * * * *
13563760 ATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGATAGCGAATCTTATTTCCTTTAAGTTGCAGTA
1 ATCTCCCTGAAGATGCAGTGGAGAAGATTGAAGAT-GCGAATCTTATTTCCCTAAAATTGCAGTA
* * ** * * ** * *
13563825 GAACAGATTAAAGCTACAAATTACAAGTCTCATCTCCTTAAAGTTGTAGTGGAGCAGACTGAAGA
65 GAACAGATTAAAGATACAAATTACAAATCGGATCTCCCTGAAGTTACAGTGGAGAAGATTGAAG-
* * * * * * *
13563890 TAACA-AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAATTACAAGTCT
129 T--CATACTCTAATCTCCCTGAAGTTACAGTGGAGCAGATCAAAGCCACAAA-T-C----CT
* * * * ** * *
13563951 CATCTCCCTGAAGTTGCTGTGGAGCAA-ACTAAAGATAAAGAATCTTATTTCCCTGAAGTTGCAG
1 -ATCTCCCTGAAGATGCAGTGGAG-AAGATTGAAGAT-GCGAATCTTATTTCCCTAAAATTGCAG
* *
13564015 TAGAACAGATTAATGATACAAATTTCAAATCGGATCTCCCTGAAGTTACAGTGGAGAAGATTGAA
63 TAGAACAGATTAAAGATACAAATTACAAATCGGATCTCCCTGAAGTTACAGTGGAGAAGATTGAA
* * * *
13564080 GTCATTACTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCTT
128 GTCA-TACTCTAATCTCCCTGAAGTTACAGTGGAGCAGATCAAAGCCACAAATCCT
* * * *
13564136 ATCTCCTTTAAGTTGCAGTGGAGAAGATTGAAGATGCGAATCTTATTTCCCTAAAATTGCAGTGG
1 ATCTCCCTGAAGATGCAGTGGAGAAGATTGAAGATGCGAATCTTATTTCCCTAAAATTGCAGTAG
* * * ** * *
13564201 AATAGATTAAAGATACGAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-ATAGA
66 AACAGATTAAAGATACAAATTACAAATCGGATCTCCCTGAAGTTACAGTGGAGAAGATTGA-AG-
* * * * * *
13564265 TGCA-AGTCTAATCTCCTTGAAGTTACAGTGGAGTAGATCGAAG-TACTAATTCCT
129 T-CATACTCTAATCTCCCTGAAGTTACAGTGGAGCAGATCAAAGCCAC-AAATCCT
13564319 ATC-CCACTGAAGATGCAGTGGA
1 ATCTCC-CTGAAGATGCAGTGGA
13564341 TTGGAATGAG
Statistics
Matches: 323, Mismatches: 57, Indels: 27
0.79 0.14 0.07
Matches are distributed among these distances:
182 5 0.02
183 132 0.41
184 28 0.09
185 3 0.01
189 3 0.01
190 1 0.00
191 43 0.13
192 107 0.33
193 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (182 bp):
ATCTCCCTGAAGATGCAGTGGAGAAGATTGAAGATGCGAATCTTATTTCCCTAAAATTGCAGTAG
AACAGATTAAAGATACAAATTACAAATCGGATCTCCCTGAAGTTACAGTGGAGAAGATTGAAGTC
ATACTCTAATCTCCCTGAAGTTACAGTGGAGCAGATCAAAGCCACAAATCCT
Found at i:13566633 original size:26 final size:26
Alignment explanation
Indices: 13566604--13566685 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
13566594 TGATACAAAT
*
13566604 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGATAAATGTTCCA
*
13566630 TGATAATGGGTTAGATAAATGTTTCA
1 TGATAATGGGTTAGATAAATGTTCCA
*
13566656 TGATAATGGGCTAGATAAATGTTCCA
1 TGATAATGGGTTAGATAAATGTTCCA
13566682 TGAT
1 TGAT
13566686 GGGAATTTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGATAAATGTTCCA
Found at i:13578212 original size:26 final size:26
Alignment explanation
Indices: 13578183--13578290 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
13578173 TGATACAAAT
*
13578183 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGATAAATGTTCCA
*
13578209 TGATAATGGGTTAGATAAATGTTTCA
1 TGATAATGGGTTAGATAAATGTTCCA
*
13578235 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGATAAATGTTCCA
13578261 TGATAATGGGTTAGATAAATGTTCCA
1 TGATAATGGGTTAGATAAATGTTCCA
13578287 TGAT
1 TGAT
13578291 GGGAATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGATAAATGTTCCA
Found at i:13586741 original size:14 final size:14
Alignment explanation
Indices: 13586708--13586742 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
13586698 CCCTTGTTTG
13586708 TGTTTTCTTGATAA
1 TGTTTTCTTGATAA
* *
13586722 TCTTTTCTTGATAT
1 TGTTTTCTTGATAA
13586736 TGTTTTC
1 TGTTTTC
13586743 CAATTTTATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.14, C:0.11, G:0.11, T:0.63
Consensus pattern (14 bp):
TGTTTTCTTGATAA
Found at i:13586831 original size:2 final size:2
Alignment explanation
Indices: 13586824--13586855 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13586814 AAGATTTTAC
13586824 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
13586856 TAAACAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:13588812 original size:31 final size:29
Alignment explanation
Indices: 13588745--13588813 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
13588735 ATGATAACGT
* ** *
13588745 AAATGATTAAAATGTAACATTTCAAATAT
1 AAATGACTAAAATGTAACAAGTCAAATAA
*
13588774 AAGTGACTAAAATGTAATCTAAGTCAAATAA
1 AAATGACTAAAATGTAA-C-AAGTCAAATAA
13588805 AAATGACTA
1 AAATGACTA
13588814 TTTTTATAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 15 0.47
30 1 0.03
31 16 0.50
ACGTcount: A:0.52, C:0.09, G:0.10, T:0.29
Consensus pattern (29 bp):
AAATGACTAAAATGTAACAAGTCAAATAA
Found at i:13592514 original size:40 final size:37
Alignment explanation
Indices: 13592440--13592574 Score: 143
Period size: 35 Copynumber: 3.7 Consensus size: 37
13592430 CATGGCAAAG
* *
13592440 TGTGAAATGTAGGTATGGTA--TCATCCATATTGAGT
1 TGTGAAATGTAGGTATGATATTTCATCCATACTGAGT
13592475 TGTGAAATGTAGGTATGATATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGATATT-TC--ATCCATACTGAGT
** * *
13592515 TAAGAAATGTAGGTATGACATTTC--CCATACCGAGT
1 TGTGAAATGTAGGTATGATATTTCATCCATACTGAGT
* *
13592550 TGTAAAATGTAGGTATGGTATTTCA
1 TGTGAAATGTAGGTATGATATTTCA
13592575 ATGAGGAAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
35 48 0.58
38 2 0.02
39 2 0.02
40 31 0.37
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (37 bp):
TGTGAAATGTAGGTATGATATTTCATCCATACTGAGT
Found at i:13597298 original size:3 final size:3
Alignment explanation
Indices: 13597284--13597328 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
13597274 TTCTTAGATT
* *
13597284 TTA TTAA TTA TTA TTG TTA ATA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13597329 TGATTTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:13598358 original size:27 final size:26
Alignment explanation
Indices: 13598307--13598400 Score: 91
Period size: 27 Copynumber: 3.4 Consensus size: 26
13598297 ATGCCTTATT
13598307 GGTGTGTTTGGGAGGATATGA-TATACC
1 GGTGTGTTT-GGAGGATAT-ATTATACC
* *
13598334 GGTGTGTTTGGAAGGCTATATTATACT
1 GGTGTGTTTGG-AGGATATATTATACC
*
13598361 GGTGTGTTATGGAGGATTTATATTATTCC
1 GGTGTGTT-TGGAGGA--TATATTATACC
13598390 GGGTGTGTTTG
1 -GGTGTGTTTG
13598401 TGTTGGATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
26 3 0.05
27 31 0.55
28 3 0.05
29 11 0.20
30 8 0.14
ACGTcount: A:0.19, C:0.06, G:0.34, T:0.40
Consensus pattern (26 bp):
GGTGTGTTTGGAGGATATATTATACC
Found at i:13605409 original size:42 final size:42
Alignment explanation
Indices: 13605358--13605687 Score: 380
Period size: 42 Copynumber: 7.9 Consensus size: 42
13605348 GTTTACAAAC
* *
13605358 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
13605400 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
13605442 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTGTAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG-AA
* * *
13605484 AAAAATGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
13605526 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-AGG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA-A
* * * ****
13605568 GAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
** * * * ***
13605610 CTAATCGCCGCTAAAGAACATGTTCTTTAGTGGC-ATT-TTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
* * *
13605650 ACAAACGCCGCAAAAGAACATGTTCTTTAGTGGCGCTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT
13605688 TTATACAAAA
Statistics
Matches: 254, Mismatches: 29, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
40 33 0.13
41 8 0.03
42 210 0.83
43 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
Found at i:13605624 original size:126 final size:127
Alignment explanation
Indices: 13605358--13605687 Score: 429
Period size: 126 Copynumber: 2.6 Consensus size: 127
13605348 GTTTACAAAC
* *
13605358 AAAAA-CGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATG
1 AAAAATCGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATG
13605422 TTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAA
66 TTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAA
*
13605484 AAAAAT-GCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATG
1 AAAAATCGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATG
** * **
13605548 TTCTTTAGCGGCGCTTA-AGGGAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT-TTT
66 TTCTTTAGCGGCGCTTAGA-AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAA
*** * * * *** * *
13605609 TCTAATCGCCGCTAAAGAACATGTTCTTTAGTGGC-ATT-TTTACAAACGCCGCAAAAGAACATG
1 AAAAATCGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATG
*
13605672 TTCTTTAGTGGCGCTT
66 TTCTTTAGCGGCGCTT
13605688 TTATACAAAA
Statistics
Matches: 180, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
124 35 0.19
125 7 0.04
126 138 0.77
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (127 bp):
AAAAATCGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATG
TTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAA
Found at i:13605779 original size:14 final size:14
Alignment explanation
Indices: 13605756--13605789 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
13605746 GCCCTCCTGT
*
13605756 AGCAAAATTTCAAA
1 AGCAACATTTCAAA
13605770 AGCAACATTTCAAA
1 AGCAACATTTCAAA
13605784 AGCAAC
1 AGCAAC
13605790 CAATAGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.53, C:0.21, G:0.09, T:0.18
Consensus pattern (14 bp):
AGCAACATTTCAAA
Found at i:13606082 original size:21 final size:21
Alignment explanation
Indices: 13606014--13606084 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
13606004 TTTTGCTCTG
* *
13606014 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
13606035 CTCCGCTTCCCTCGCTGCAGT
1 CTCTGCTTCCCTCGCTGCAGC
* * *
13606056 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTGCAGC
13606077 CTCTGCTT
1 CTCTGCTT
13606085 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.45, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:13608580 original size:19 final size:19
Alignment explanation
Indices: 13608556--13608597 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
13608546 GGACTACGTT
*
13608556 GGGGAACTGTTAGGGATTA
1 GGGGAAATGTTAGGGATTA
* *
13608575 GGGGAAATTTTAGGGATTT
1 GGGGAAATGTTAGGGATTA
13608594 GGGG
1 GGGG
13608598 GAGATGTCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.45, T:0.29
Consensus pattern (19 bp):
GGGGAAATGTTAGGGATTA
Found at i:13609258 original size:230 final size:231
Alignment explanation
Indices: 13608927--13609435 Score: 772
Period size: 230 Copynumber: 2.2 Consensus size: 231
13608917 TAATGCAAAT
*** * **
13608927 TTGCGGCG-TTTA-ATAAAAGCGCCACTAAAACCAACTAAGTAAACGGCGTTGTTTTCCGTAACA
1 TTGCGGCGTTTTATATAAAA-CGCCACTAAATGTAA-TAAGAAAACGGCGTCATTTTCCGTAACA
* * *
13608990 CCATTTCGATTTTGCGGCGTTTATATATAAGCGCCACTAAATATAAGGTCAAACGCAGTCGTTTA
64 CCATTTCGAGTTTGCGACGTTTATATATAAACGCCACTAAATATAAGGTCAAACGCAGTCGTTTA
* *
13609055 AAGCAAACTCCTGTAATCTTTAAAATATATTTGCGGCGTTTTGGGTGTAACGCCACAAATATC-C
129 AAGCAAACTCCTGTAATCTTTAAAATATATTTGCGGCGTTTTGGGTGTAACGCCACAAATAACAA
* * * *
13609119 TTGAAAACGATGCCGTTTCTGTAACAAAGAAAACATAC
194 TGGAAAACGACGCCGTTCCCGTAACAAAGAAAACATAC
* *
13609157 TTGCGGCGTTTTATCTAAAACGCCACTAAATGTAATAAGAAAACGGCGTCATTTTTCGTAACACC
1 TTGCGGCGTTTTATATAAAACGCCACTAAATGTAATAAGAAAACGGCGTCATTTTCCGTAACACC
* *
13609222 ATTTCGAGTTTGCGACGTTTATATATAAATGCCACTAAATATAAGGTCAAACGCAGTCGTTTAAC
66 ATTTCGAGTTTGCGACGTTTATATATAAACGCCACTAAATATAAGGTCAAACGCAGTCGTTTAAA
* *
13609287 GCAAACTCGTGTAATCTTTAAAATATATTTGCGGCGTTTTGGGTGTAACGCCACTAATAACAATG
131 GCAAACTCCTGTAATCTTTAAAATATATTTGCGGCGTTTTGGGTGTAACGCCACAAATAACAATG
*
13609352 GAAAACGACGCCGTTCCCGTAACAAAGAAAACATAG
196 GAAAACGACGCCGTTCCCGTAACAAAGAAAACATAC
*
13609388 TTGCGGCGTTTTGTATAAAACGCCACTAAATGTAATAAGAAAACGGCG
1 TTGCGGCGTTTTATATAAAACGCCACTAAATGTAATAAGAAAACGGCG
13609436 CCGTTTTCTT
Statistics
Matches: 252, Mismatches: 24, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
230 152 0.60
231 95 0.38
232 5 0.02
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (231 bp):
TTGCGGCGTTTTATATAAAACGCCACTAAATGTAATAAGAAAACGGCGTCATTTTCCGTAACACC
ATTTCGAGTTTGCGACGTTTATATATAAACGCCACTAAATATAAGGTCAAACGCAGTCGTTTAAA
GCAAACTCCTGTAATCTTTAAAATATATTTGCGGCGTTTTGGGTGTAACGCCACAAATAACAATG
GAAAACGACGCCGTTCCCGTAACAAAGAAAACATAC
Found at i:13609865 original size:7 final size:7
Alignment explanation
Indices: 13609853--13609930 Score: 66
Period size: 7 Copynumber: 11.1 Consensus size: 7
13609843 CCTTAAATTT
13609853 CCAAACC
1 CCAAACC
13609860 CCAAACC
1 CCAAACC
*
13609867 CCAAACA
1 CCAAACC
** *
13609874 TTAAACT
1 CCAAACC
* *
13609881 CTAAACT
1 CCAAACC
* *
13609888 CAAAAAC
1 CCAAACC
*
13609895 CCAAATC
1 CCAAACC
13609902 CCAAACC
1 CCAAACC
13609909 CCAAACC
1 CCAAACC
13609916 CCAAACC
1 CCAAACC
*
13609923 ACAAACC
1 CCAAACC
13609930 C
1 C
13609931 TTACATCCGA
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 58 1.00
ACGTcount: A:0.47, C:0.45, G:0.00, T:0.08
Consensus pattern (7 bp):
CCAAACC
Found at i:13610250 original size:15 final size:16
Alignment explanation
Indices: 13610222--13610252 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
13610212 CCCTAACACG
13610222 ACCCCTATAACCCTAA
1 ACCCCTATAACCCTAA
13610238 ACCCCTA-AACCCTAA
1 ACCCCTATAACCCTAA
13610253 GTCTTAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.39, C:0.45, G:0.00, T:0.16
Consensus pattern (16 bp):
ACCCCTATAACCCTAA
Found at i:13610541 original size:18 final size:21
Alignment explanation
Indices: 13610518--13610566 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 21
13610508 ATTAATCACG
13610518 ATATTAATTTG-GTG-TTT-T
1 ATATTAATTTGTGTGATTTAT
* *
13610536 ATATTACTTTGTTTGATTTAT
1 ATATTAATTTGTGTGATTTAT
13610557 ATATTAATTT
1 ATATTAATTT
13610567 AGTCGAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 10 0.40
19 2 0.08
20 3 0.12
21 10 0.40
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (21 bp):
ATATTAATTTGTGTGATTTAT
Found at i:13611208 original size:40 final size:38
Alignment explanation
Indices: 13611114--13611212 Score: 101
Period size: 39 Copynumber: 2.5 Consensus size: 38
13611104 CGTCGTTGGC
* * *
13611114 CTTATTTTTTTGCGGCGCTTTTTGTGAATCGCCGCTATTG
1 CTTA-TTTTTAGCGGCG-TTTTCGTGAATCGCCGCTAATG
* *
13611154 CTTATTATTAGCGGCGTTTTCGTTAATGCGCCGCTAATG
1 CTTATTTTTAGCGGCGTTTTCGTGAAT-CGCCGCTAATG
13611193 -TTCAATTTTTAGCGGCGTTT
1 CTT--ATTTTTAGCGGCGTTT
13611213 GTTGTCCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
38 11 0.22
39 20 0.40
40 19 0.38
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.44
Consensus pattern (38 bp):
CTTATTTTTAGCGGCGTTTTCGTGAATCGCCGCTAATG
Found at i:13613056 original size:21 final size:21
Alignment explanation
Indices: 13613032--13613082 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
13613022 TTAAACATAT
13613032 ATATAAATATAAAATAATTA-A
1 ATATAAATAT-AAATAATTATA
*
13613053 ATATAAATATTAATAATTATA
1 ATATAAATATAAATAATTATA
*
13613074 TTATAAATA
1 ATATAAATA
13613083 AATAAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATAAATATAAATAATTATA
Found at i:13614325 original size:26 final size:26
Alignment explanation
Indices: 13614289--13614341 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
13614279 AGGTACGATG
13614289 TTTACTTAATTCCAATTTCAACATTT
1 TTTACTTAATTCCAATTTCAACATTT
13614315 TTTACTTAATTCCAATTTCAACATTT
1 TTTACTTAATTCCAATTTCAACATTT
13614341 T
1 T
13614342 GCATTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTACTTAATTCCAATTTCAACATTT
Found at i:13616608 original size:30 final size:30
Alignment explanation
Indices: 13616572--13616629 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
13616562 CTTAAAAAAA
** *
13616572 TACAAAATGGTTATTAAATTATTTAAAAGT
1 TACAAAATAATTATTAAATTATTCAAAAGT
13616602 TACAAAATAATTATTAAATTATTCAAAA
1 TACAAAATAATTATTAAATTATTCAAAA
13616630 AATTTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (30 bp):
TACAAAATAATTATTAAATTATTCAAAAGT
Found at i:13622529 original size:18 final size:18
Alignment explanation
Indices: 13622494--13622545 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
13622484 TTTTGAAAAG
13622494 ATTTATATAAAAATATTAA
1 ATTTATATAAAAA-ATTAA
* *
13622513 ATTTAAATAAAAAATTAT
1 ATTTATATAAAAAATTAA
*
13622531 ATTTATTTAAAAAAT
1 ATTTATATAAAAAAT
13622546 GGTCGAGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 17 0.59
19 12 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTATATAAAAAATTAA
Found at i:13622767 original size:21 final size:19
Alignment explanation
Indices: 13622730--13622768 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
13622720 AGAAATTTAA
13622730 TAAAAAATATTAATAATAG
1 TAAAAAATATTAATAATAG
*
13622749 TAAAAATTATATAATTAATA
1 TAAAAAATAT-TAA-TAATA
13622769 AGCAACTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
TAAAAAATATTAATAATAG
Found at i:13623745 original size:31 final size:30
Alignment explanation
Indices: 13623721--13623780 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
13623711 TTTATATTTT
13623721 ATGCATCATTATATTAAACTATTTAAATATA
1 ATGCATCATTATATTAAA-TATTTAAATATA
**
13623752 ATTTATCATTATATTAAATATTTAAATAT
1 ATGCATCATTATATTAAATATTTAAATAT
13623781 CATTTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (30 bp):
ATGCATCATTATATTAAATATTTAAATATA
Found at i:13623776 original size:30 final size:30
Alignment explanation
Indices: 13623725--13623803 Score: 115
Period size: 30 Copynumber: 2.6 Consensus size: 30
13623715 TATTTTATGC
13623725 ATCATTATATTAAACTATTTAAATATAATTT
1 ATCATTATATTAAA-TATTTAAATATAATTT
*
13623756 ATCATTATATTAAATATTTAAATATCATTT
1 ATCATTATATTAAATATTTAAATATAATTT
* *
13623786 ATTATTGTATTAAA-ATTT
1 ATCATTATATTAAATATTT
13623804 TTAAAATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 4 0.09
30 27 0.60
31 14 0.31
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (30 bp):
ATCATTATATTAAATATTTAAATATAATTT
Found at i:13636970 original size:11 final size:10
Alignment explanation
Indices: 13636955--13637030 Score: 55
Period size: 11 Copynumber: 7.2 Consensus size: 10
13636945 ATAAAGGATG
13636955 AATAAAAGAA
1 AATAAAAGAA
*
13636965 AGATAAAATTAA
1 A-ATAAAA-GAA
*
13636977 AATAAAATAAA
1 AATAAAA-GAA
*
13636988 GAATAAAATAA
1 -AATAAAAGAA
*
13636999 AAGAAAAGAA
1 AATAAAAGAA
13637009 AAGTAAAAGAA
1 AA-TAAAAGAA
*
13637020 AA-CAAAGAA
1 AATAAAAGAA
13637029 AA
1 AA
13637031 GAAGAGGAGG
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
9 8 0.15
10 11 0.20
11 26 0.47
12 10 0.18
ACGTcount: A:0.76, C:0.01, G:0.11, T:0.12
Consensus pattern (10 bp):
AATAAAAGAA
Found at i:13636980 original size:22 final size:22
Alignment explanation
Indices: 13636955--13637009 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
13636945 ATAAAGGATG
13636955 AATAAAAGAAAG-ATAAAATTAA
1 AATAAAAGAAAGAATAAAA-TAA
*
13636977 AATAAAATAAAGAATAAAATAA
1 AATAAAAGAAAGAATAAAATAA
*
13636999 AAGAAAAGAAA
1 AATAAAAGAAA
13637010 AGTAAAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 23 0.79
23 6 0.21
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (22 bp):
AATAAAAGAAAGAATAAAATAA
Found at i:13636984 original size:5 final size:5
Alignment explanation
Indices: 13636955--13637021 Score: 53
Period size: 5 Copynumber: 12.4 Consensus size: 5
13636945 ATAAAGGATG
* *
13636955 AATAA AAGAA AGATAA AATTAA AATAA AATAAA GAATAA AATAA AAGAA
1 AATAA AATAA A-ATAA AA-TAA AATAA AAT-AA -AATAA AATAA AATAA
* *
13637004 AAGAA AAGTAA AAGAA AA
1 AATAA AA-TAA AATAA AA
13637022 CAAAGAAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
5 32 0.62
6 17 0.33
7 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.13
Consensus pattern (5 bp):
AATAA
Found at i:13636994 original size:12 final size:12
Alignment explanation
Indices: 13636954--13636999 Score: 60
Period size: 11 Copynumber: 4.0 Consensus size: 12
13636944 AATAAAGGAT
*
13636954 GAATAAAAGAAA
1 GAATAAAATAAA
*
13636966 G-ATAAAATTAA
1 GAATAAAATAAA
13636977 -AATAAAATAAA
1 GAATAAAATAAA
13636988 GAATAAAATAAA
1 GAATAAAATAAA
13637000 AGAAAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 17 0.59
12 12 0.41
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (12 bp):
GAATAAAATAAA
Found at i:13636994 original size:17 final size:17
Alignment explanation
Indices: 13636954--13637000 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
13636944 AATAAAGGAT
*
13636954 GAATAAAAGAAAGATAAA
1 GAATAAAATAAA-ATAAA
*
13636972 -ATTAAAATAAAATAAA
1 GAATAAAATAAAATAAA
13636988 GAATAAAATAAAA
1 GAATAAAATAAAA
13637001 GAAAAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (17 bp):
GAATAAAATAAAATAAA
Found at i:13637017 original size:16 final size:15
Alignment explanation
Indices: 13636992--13637033 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
13636982 AATAAAGAAT
13636992 AAAA-TAAAAGAAAA
1 AAAAGTAAAAGAAAA
13637006 GAAAAGTAAAAGAAAA
1 -AAAAGTAAAAGAAAA
*
13637022 CAAAG-AAAAGAA
1 AAAAGTAAAAGAA
13637034 GAGGAGGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 7 0.28
15 8 0.32
16 10 0.40
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (15 bp):
AAAAGTAAAAGAAAA
Found at i:13637031 original size:5 final size:5
Alignment explanation
Indices: 13636992--13637033 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
13636982 AATAAAGAAT
* *
13636992 AAAAT AAAAG AAAAG AAAAG TAAAAG AAAA- CAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AA
13637034 GAGGAGGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 3 0.09
5 24 0.75
6 5 0.16
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (5 bp):
AAAAG
Found at i:13646692 original size:16 final size:16
Alignment explanation
Indices: 13646673--13646703 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13646663 ATTTAAGTAA
*
13646673 ATATTATTTTATTATT
1 ATATTATTGTATTATT
13646689 ATATTATTGTATTAT
1 ATATTATTGTATTAT
13646704 ATTAATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
ATATTATTGTATTATT
Found at i:13647832 original size:18 final size:18
Alignment explanation
Indices: 13647809--13647866 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
13647799 TAGATAAATG
13647809 TACTGAATGACTGATTGT
1 TACTGAATGACTGATTGT
*
13647827 TACTGAATGATTGATTGT
1 TACTGAATGACTGATTGT
* * *
13647845 TTCTGAATGACTAATTAT
1 TACTGAATGACTGATTGT
13647863 TACT
1 TACT
13647867 AAATAACAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.43
Consensus pattern (18 bp):
TACTGAATGACTGATTGT
Found at i:13647895 original size:31 final size:31
Alignment explanation
Indices: 13647858--13647924 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
13647848 TGAATGACTA
13647858 ATTATTACTAAATAACAATAAACAATTGATT
1 ATTATTACTAAATAACAATAAACAATTGATT
13647889 ATTATTACTAAATAACAATAAACAATTGATT
1 ATTATTACTAAATAACAATAAACAATTGATT
13647920 ATTAT
1 ATTAT
13647925 CGAAAAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (31 bp):
ATTATTACTAAATAACAATAAACAATTGATT
Found at i:13647933 original size:31 final size:31
Alignment explanation
Indices: 13647858--13647933 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
13647848 TGAATGACTA
* *
13647858 ATTATTACTAAATAACAATAAACAATTGATT
1 ATTATGACAAAATAACAATAAACAATTGATT
* *
13647889 ATTATTACTAAATAACAATAAACAATTGATT
1 ATTATGACAAAATAACAATAAACAATTGATT
13647920 ATTATCGA-AAAATA
1 ATTAT-GACAAAATA
13647934 TTGACTGATA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 41 0.98
32 1 0.02
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (31 bp):
ATTATGACAAAATAACAATAAACAATTGATT
Found at i:13650002 original size:12 final size:12
Alignment explanation
Indices: 13649985--13650009 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13649975 AAGGTAATGC
13649985 ACACGATATGGT
1 ACACGATATGGT
13649997 ACACGATATGGT
1 ACACGATATGGT
13650009 A
1 A
13650010 ACAAGTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (12 bp):
ACACGATATGGT
Found at i:13657546 original size:33 final size:33
Alignment explanation
Indices: 13657504--13657569 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
13657494 AGTGTGGGGG
13657504 TATTTGATAAACCGTAAATTATACATATTTTTA
1 TATTTGATAAACCGTAAATTATACATATTTTTA
13657537 TATTTGATAAACCGTAAATTATACATATTTTTA
1 TATTTGATAAACCGTAAATTATACATATTTTTA
13657570 CCCCATGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (33 bp):
TATTTGATAAACCGTAAATTATACATATTTTTA
Found at i:13660867 original size:23 final size:22
Alignment explanation
Indices: 13660836--13660878 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
13660826 AAAATCCATA
* *
13660836 CCAAATCATGCCAAATCATAAG
1 CCAAATCATACCAAAACATAAG
13660858 CCAAAGTCATACCAAAACATA
1 CCAAA-TCATACCAAAACATA
13660879 TGTTTCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.49, C:0.28, G:0.07, T:0.16
Consensus pattern (22 bp):
CCAAATCATACCAAAACATAAG
Found at i:13661651 original size:42 final size:43
Alignment explanation
Indices: 13661541--13661705 Score: 135
Period size: 43 Copynumber: 3.8 Consensus size: 43
13661531 AAGTTGTACA
* * *
13661541 ATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACACGAAATCAAATATCG
* *
13661584 ATGCCACTGTCTCAGAAAAT-GTCTTACACGAAATCAAATAT-G
1 ATGCCACTGTCCCAG-ACATGGTCTTACACGAAATCAAATATCG
* * *
13661626 ATGCTGA-TGTCCCAGACATGGTCTTACACATAAATCTCAA-ATCG
1 ATGC-CACTGTCCCAGACATGGTCTTACAC-GAAATC-AAATATCG
* **
13661670 ATGCCAAC-GTCCTAGATGTGGTCTTACACGAAATCA
1 ATGCC-ACTGTCCCAGACATGGTCTTACACGAAATCA
13661706 CAATCAGAAT
Statistics
Matches: 97, Mismatches: 16, Indels: 19
0.73 0.12 0.14
Matches are distributed among these distances:
41 3 0.03
42 23 0.24
43 43 0.44
44 28 0.29
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACATGGTCTTACACGAAATCAAATATCG
Found at i:13669915 original size:4 final size:4
Alignment explanation
Indices: 13669908--13669988 Score: 72
Period size: 4 Copynumber: 19.8 Consensus size: 4
13669898 GTTAAAAAAA
* *** * *
13669908 AAAG AAAG AAAG AAAG AAAG AAAG ATAG AAAG AGTT ACAG AGAG CAAACG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAA-G
**
13669958 TGAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
13669989 TAGAAAAGGG
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
4 57 0.93
5 3 0.05
6 1 0.02
ACGTcount: A:0.65, C:0.04, G:0.26, T:0.05
Consensus pattern (4 bp):
AAAG
Found at i:13678395 original size:10 final size:10
Alignment explanation
Indices: 13678376--13678435 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
13678366 TGAAATTCTA
13678376 AAAGATAAAT
1 AAAGATAAAT
13678386 ACAA-ATAAAT
1 A-AAGATAAAT
*
13678396 AAAGATAGAT
1 AAAGATAAAT
13678406 AAAGATAAAT
1 AAAGATAAAT
13678416 AAAGATAAAT
1 AAAGATAAAT
13678426 GAAA-ATAAAT
1 -AAAGATAAAT
13678436 CTTAAAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.68, C:0.02, G:0.10, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:13682373 original size:10 final size:10
Alignment explanation
Indices: 13682353--13682404 Score: 59
Period size: 10 Copynumber: 4.8 Consensus size: 10
13682343 TTCATGCTTA
13682353 AAATCCATACC
1 AAAT-CATACC
13682364 AAATCATACC
1 AAATCATACC
13682374 AAATCATAAGCC
1 AAATCAT-A-CC
13682386 AAAGTCATACC
1 AAA-TCATACC
*
13682397 AAAACATA
1 AAATCATA
13682405 TGTTTCATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
10 17 0.46
11 10 0.27
12 6 0.16
13 4 0.11
ACGTcount: A:0.52, C:0.27, G:0.04, T:0.17
Consensus pattern (10 bp):
AAATCATACC
Found at i:13682394 original size:23 final size:22
Alignment explanation
Indices: 13682362--13682404 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
13682352 AAAATCCATA
*
13682362 CCAAATCATACCAAATCATAAG
1 CCAAATCATACCAAAACATAAG
13682384 CCAAAGTCATACCAAAACATA
1 CCAAA-TCATACCAAAACATA
13682405 TGTTTCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.51, C:0.28, G:0.05, T:0.16
Consensus pattern (22 bp):
CCAAATCATACCAAAACATAAG
Found at i:13683148 original size:43 final size:42
Alignment explanation
Indices: 13683087--13683180 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
13683077 TCCCAGGCAT
* *
13683087 GGTCTTACATGTAATCAAATATCGATG-TCACTGTCGTAGACAG
1 GGTCTTACATGAAATCAAATA-CGATGCTCA-TGTCCTAGACAG
* * *
13683130 GGTCTTACATGAAATCAAATACGCTGCTGATGTCCTAGACAT
1 GGTCTTACATGAAATCAAATACGATGCTCATGTCCTAGACAG
13683172 GGTCTTACA
1 GGTCTTACA
13683181 CGTAAATCTC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
42 23 0.51
43 22 0.49
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (42 bp):
GGTCTTACATGAAATCAAATACGATGCTCATGTCCTAGACAG
Found at i:13683188 original size:43 final size:43
Alignment explanation
Indices: 13683074--13683224 Score: 132
Period size: 43 Copynumber: 3.5 Consensus size: 43
13683064 TACAATACCA
* *
13683074 ATGTCCCAGGCATGGTCTTACATGT-AATCAAATATCGATGTC
1 ATGTCCTAGACATGGTCTTACATGTAAATCAAATATCGATGTC
* * * *
13683116 ACTGTCGTAGACAGGGTCTTACATG-AAATCAAATA-CGCTGCTG
1 A-TGTCCTAGACATGGTCTTACATGTAAATCAAATATCGATG-TC
* * *
13683159 ATGTCCTAGACATGGTCTTACACGTAAATCTCAA-ATCGATGCC
1 ATGTCCTAGACATGGTCTTACATGTAAATC-AAATATCGATGTC
*
13683202 AACGTTCC-AGACATGGTCTTACA
1 -ATG-TCCTAGACATGGTCTTACA
13683225 CAAAATCACA
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
42 25 0.29
43 36 0.41
44 23 0.26
45 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (43 bp):
ATGTCCTAGACATGGTCTTACATGTAAATCAAATATCGATGTC
Found at i:13683326 original size:28 final size:28
Alignment explanation
Indices: 13683286--13683342 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
13683276 CTATGGTTCG
*
13683286 TACGGGGCTTTCAACAGTCGTTACATTA
1 TACGGGGCTTTCAAAAGTCGTTACATTA
13683314 TACGGGGCTTTCAAAAGTCGTTACATTA
1 TACGGGGCTTTCAAAAGTCGTTACATTA
13683342 T
1 T
13683343 CGAAACTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (28 bp):
TACGGGGCTTTCAAAAGTCGTTACATTA
Found at i:13685373 original size:16 final size:16
Alignment explanation
Indices: 13685341--13685400 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
13685331 TTTACTGGTC
13685341 ATAATTATTAAATTAAT
1 ATAA-TATTAAATTAAT
13685358 ATAATATTAGAA-TAAT
1 ATAATATTA-AATTAAT
*
13685374 ATAATA-AACAATTAAT
1 ATAATATTA-AATTAAT
*
13685390 A-AAAATTAAAT
1 ATAATATTAAAT
13685401 AAAAGAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
15 9 0.25
16 21 0.58
17 6 0.17
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (16 bp):
ATAATATTAAATTAAT
Found at i:13686499 original size:18 final size:18
Alignment explanation
Indices: 13686474--13686534 Score: 104
Period size: 18 Copynumber: 3.4 Consensus size: 18
13686464 AGATAAATGC
13686474 ACTGAATGACTGATTGTT
1 ACTGAATGACTGATTGTT
* *
13686492 ATTGAATGATTGATTGTT
1 ACTGAATGACTGATTGTT
13686510 ACTGAATGACTGATTGTT
1 ACTGAATGACTGATTGTT
13686528 ACTGAAT
1 ACTGAAT
13686535 AACAATGAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (18 bp):
ACTGAATGACTGATTGTT
Found at i:13688813 original size:21 final size:21
Alignment explanation
Indices: 13688789--13688832 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
13688779 TATTGATTTA
* *
13688789 TTGCAGATCAAGTCAAGTTAC
1 TTGCAGAACAAGTCAAGTCAC
13688810 TTGCAGAACAAGTCAAGTCAC
1 TTGCAGAACAAGTCAAGTCAC
13688831 TT
1 TT
13688833 TCTATAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (21 bp):
TTGCAGAACAAGTCAAGTCAC
Found at i:13690985 original size:12 final size:12
Alignment explanation
Indices: 13690970--13691000 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
13690960 AACCACACGC
13690970 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
13690982 CCGTGTGCTAGG
1 CCGTGTGCCAGG
13690994 CCGTGTG
1 CCGTGTG
13691001 AAAACTAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.29, G:0.42, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:13697365 original size:50 final size:50
Alignment explanation
Indices: 13697306--13697407 Score: 152
Period size: 50 Copynumber: 2.0 Consensus size: 50
13697296 TAATATTAAA
*
13697306 AATCAAATATAGATGAACCGAGTCGAACCTAAATTTACCT-TTCTTAAATT
1 AATCAAATATAGATGAACCGAGTCGAACCCAAATTTA-CTATTCTTAAATT
* * *
13697356 AATCAAATATAGATGAATCGGGTCGAACCCAAATTTACTATTTTTAAATT
1 AATCAAATATAGATGAACCGAGTCGAACCCAAATTTACTATTCTTAAATT
13697406 AA
1 AA
13697408 ATTGAGTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
49 2 0.04
50 45 0.96
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (50 bp):
AATCAAATATAGATGAACCGAGTCGAACCCAAATTTACTATTCTTAAATT
Found at i:13698078 original size:17 final size:17
Alignment explanation
Indices: 13698056--13698089 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
13698046 CCTGATCTCA
13698056 CCATCAAGGTAAATACC
1 CCATCAAGGTAAATACC
13698073 CCATCAAGGTAAATACC
1 CCATCAAGGTAAATACC
13698090 GTCTTCTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.29, G:0.12, T:0.18
Consensus pattern (17 bp):
CCATCAAGGTAAATACC
Found at i:13712164 original size:15 final size:15
Alignment explanation
Indices: 13712144--13712172 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13712134 TAATATTGCA
13712144 AATATAAAAAAATAT
1 AATATAAAAAAATAT
13712159 AATATAAAAAAATA
1 AATATAAAAAAATA
13712173 AAAAAAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AATATAAAAAAATAT
Found at i:13712781 original size:12 final size:12
Alignment explanation
Indices: 13712719--13712784 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
13712709 ATTTTCGTTT
13712719 TTATATATTGTTA
1 TTAT-TATTGTTA
* **
13712732 TTATTTTTCCTA
1 TTATTATTGTTA
* **
13712744 ATATTATTAATA
1 TTATTATTGTTA
13712756 TTATTATT-TCTA
1 TTATTATTGT-TA
13712768 TTATTATTGTTA
1 TTATTATTGTTA
13712780 TTATT
1 TTATT
13712785 GACATCCTGA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
12 37 0.88
13 5 0.12
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.64
Consensus pattern (12 bp):
TTATTATTGTTA
Found at i:13712865 original size:15 final size:15
Alignment explanation
Indices: 13712837--13712916 Score: 51
Period size: 15 Copynumber: 5.5 Consensus size: 15
13712827 TATTATTAGT
* *
13712837 TATTACTATTTGTAG
1 TATTATTATATGTAG
*
13712852 TATTATTATATGTAA
1 TATTATTATATGTAG
* * **
13712867 TATTAGTATAGGTTT
1 TATTATTATATGTAG
13712882 TATTA-TATATGTAAG
1 TATTATTATATGT-AG
13712897 TA-TATGTATATG-A-
1 TATTAT-TATATGTAG
13712910 TATTATT
1 TATTATT
13712917 TTGATTACTT
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
13 3 0.06
14 12 0.24
15 30 0.59
16 6 0.12
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (15 bp):
TATTATTATATGTAG
Found at i:13717574 original size:33 final size:33
Alignment explanation
Indices: 13717536--13717605 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
13717526 AAGTAATTTG
13717536 AGCTTGTATTTTGGACTGTTTTGTTTTATTTAA
1 AGCTTGTATTTTGGACTGTTTTGTTTTATTTAA
13717569 AGCTTGTATTTTGGACTGTTTTGTTTTATTTAA
1 AGCTTGTATTTTGGACTGTTTTGTTTTATTTAA
13717602 AGCT
1 AGCT
13717606 CGGGTAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.56
Consensus pattern (33 bp):
AGCTTGTATTTTGGACTGTTTTGTTTTATTTAA
Found at i:13721363 original size:12 final size:12
Alignment explanation
Indices: 13721346--13721393 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
13721336 TGGGAGTAAA
13721346 GTTTTATATTTG
1 GTTTTATATTTG
*
13721358 GTTTTATATGTTAAA
1 GTTTTATAT-TT--G
13721373 GTTTTATATTTG
1 GTTTTATATTTG
*
13721385 GTTTCATAT
1 GTTTTATAT
13721394 GTTAATGACA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 17 0.57
13 2 0.07
14 2 0.07
15 9 0.30
ACGTcount: A:0.23, C:0.02, G:0.15, T:0.60
Consensus pattern (12 bp):
GTTTTATATTTG
Found at i:13721376 original size:27 final size:27
Alignment explanation
Indices: 13721342--13721398 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
13721332 TTAGTGGGAG
*
13721342 TAAAGTTTTATATTTGGTTTTATATGT
1 TAAAGTTTTATATTTGGTTTCATATGT
13721369 TAAAGTTTTATATTTGGTTTCATATGT
1 TAAAGTTTTATATTTGGTTTCATATGT
13721396 TAA
1 TAA
13721399 TGACATACTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (27 bp):
TAAAGTTTTATATTTGGTTTCATATGT
Found at i:13721378 original size:15 final size:14
Alignment explanation
Indices: 13721342--13721383 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
13721332 TTAGTGGGAG
13721342 TAAAGTTTTATATT
1 TAAAGTTTTATATT
*
13721356 T--GGTTTTATATGT
1 TAAAGTTTTATAT-T
13721369 TAAAGTTTTATATT
1 TAAAGTTTTATATT
13721383 T
1 T
13721384 GGTTTCATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
12 9 0.39
13 2 0.09
14 3 0.13
15 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.60
Consensus pattern (14 bp):
TAAAGTTTTATATT
Found at i:13730578 original size:23 final size:24
Alignment explanation
Indices: 13730529--13730578 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
13730519 TTAACTATTT
* **
13730529 ATTTTTTATTTTTCAATTTAACTA
1 ATTTTATATTTTTCAATTTAAAAA
13730553 ATTTTATATTTTT-AATTTAAAAA
1 ATTTTATATTTTTCAATTTAAAAA
13730576 ATT
1 ATT
13730579 ATAAAATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTTATATTTTTCAATTTAAAAA
Found at i:13731174 original size:14 final size:14
Alignment explanation
Indices: 13731155--13731193 Score: 50
Period size: 12 Copynumber: 3.1 Consensus size: 14
13731145 GTGTCCGCCC
13731155 ATATTAATTTTTTA
1 ATATTAATTTTTTA
13731169 ATATT-A-TTTTT-
1 ATATTAATTTTTTA
13731180 ATA-TAATTTTTTA
1 ATATTAATTTTTTA
13731193 A
1 A
13731194 AAAATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
10 1 0.05
11 4 0.18
12 10 0.45
13 2 0.09
14 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATATTAATTTTTTA
Found at i:13731841 original size:16 final size:16
Alignment explanation
Indices: 13731822--13731867 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 16
13731812 AAAGAAATTT
13731822 ATAATTAAATTTAATA
1 ATAATTAAATTTAATA
13731838 ATAATTAAAATATTTAATA
1 ATAATT--AA-ATTTAATA
13731857 ATAAATTAAAT
1 AT-AATTAAAT
13731868 AGATTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.23
17 2 0.08
18 4 0.15
19 10 0.38
20 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAATTAAATTTAATA
Found at i:13731876 original size:22 final size:19
Alignment explanation
Indices: 13731830--13731873 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
13731820 TTATAATTAA
*
13731830 ATTTAATAATAATTAAAAT
1 ATTTAATAATAATTAAAAG
13731849 ATTTAATAATAAATTAAATAG
1 ATTTAATAAT-AATTAAA-AG
13731870 ATTT
1 ATTT
13731874 TAAATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
20 7 0.32
21 5 0.23
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTTAATAATAATTAAAAG
Found at i:13735327 original size:21 final size:21
Alignment explanation
Indices: 13735301--13735356 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
13735291 CACCATTGTT
* *
13735301 TCTAATCTCACTGCTACATTA
1 TCTAATCTCACCGCTACAGTA
13735322 TCTAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
* *
13735343 ACTAATCTTACCGC
1 TCTAATCTCACCGC
13735357 CACCGCTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.32, G:0.07, T:0.32
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAGTA
Found at i:13736062 original size:15 final size:14
Alignment explanation
Indices: 13736044--13736095 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
13736034 ATTATATTAT
*
13736044 AATATAAAACAAAGA
1 AATA-AAAAAAAAGA
13736059 AATAAAAGAAAAAGA
1 AATAAAA-AAAAAGA
*
13736074 AATAGAAAAGAAAGA
1 AATA-AAAAAAAAGA
*
13736089 AAGAAAA
1 AATAAAA
13736096 CGAAACAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 6 0.19
15 23 0.72
16 3 0.09
ACGTcount: A:0.77, C:0.02, G:0.13, T:0.08
Consensus pattern (14 bp):
AATAAAAAAAAAGA
Found at i:13736448 original size:18 final size:19
Alignment explanation
Indices: 13736419--13736454 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
13736409 TGTGAAAATT
*
13736419 TGAAATTTAGGGATTTAAG
1 TGAAATTTAGGGAGTTAAG
13736438 TGAAA-TTAGGGAGTTAA
1 TGAAATTTAGGGAGTTAA
13736455 ATTTAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (19 bp):
TGAAATTTAGGGAGTTAAG
Found at i:13739764 original size:38 final size:38
Alignment explanation
Indices: 13739713--13739785 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
13739703 AACTGTTTTT
13739713 TTTTCTTTGGGTTTATCCTTTTAATATGTAATTGTCGG
1 TTTTCTTTGGGTTTATCCTTTTAATATGTAATTGTCGG
13739751 TTTTCTTTGGGTTTATCCTTTTAATATGTAATTGT
1 TTTTCTTTGGGTTTATCCTTTTAATATGTAATTGT
13739786 GTTTTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.16, C:0.10, G:0.16, T:0.58
Consensus pattern (38 bp):
TTTTCTTTGGGTTTATCCTTTTAATATGTAATTGTCGG
Found at i:13742371 original size:18 final size:19
Alignment explanation
Indices: 13742335--13742373 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13742325 AATACTTTTT
* *
13742335 AAAAGTATTTTTAGGTTAA
1 AAAAATATTTTTAGATTAA
13742354 AAAAATATTTTTA-ATTAA
1 AAAAATATTTTTAGATTAA
13742372 AA
1 AA
13742374 GTTAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (19 bp):
AAAAATATTTTTAGATTAA
Found at i:13745539 original size:21 final size:22
Alignment explanation
Indices: 13745499--13745545 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
13745489 CTCTGCTCAA
*
13745499 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
*
13745520 ACTCCACCTGCTGTGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
13745542 ACTC
1 ACTC
13745546 ACTCCTTCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.23
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:13752176 original size:2 final size:2
Alignment explanation
Indices: 13752169--13752204 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
13752159 GCTTTCACTA
* *
13752169 CT CT CT CT CT CT CT CT CT CT CT CA CT CT CT CA CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
13752205 GATGTTTGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.06, C:0.50, G:0.00, T:0.44
Consensus pattern (2 bp):
CT
Found at i:13759930 original size:12 final size:12
Alignment explanation
Indices: 13759913--13759960 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
13759903 TATCAATTCG
13759913 ATTAAATAAATC
1 ATTAAATAAATC
*
13759925 ATTAAA-AAA-A
1 ATTAAATAAATC
*
13759935 ACTAAATAAATC
1 ATTAAATAAATC
*
13759947 ATTAAAAAAATC
1 ATTAAATAAATC
13759959 AT
1 AT
13759961 GTTCAACCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
10 5 0.17
11 6 0.21
12 18 0.62
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (12 bp):
ATTAAATAAATC
Found at i:13759943 original size:22 final size:22
Alignment explanation
Indices: 13759915--13759956 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
13759905 TCAATTCGAT
13759915 TAAATAAATCATTAAAAAAAAC
1 TAAATAAATCATTAAAAAAAAC
13759937 TAAATAAATCATTAAAAAAA
1 TAAATAAATCATTAAAAAAA
13759957 TCATGTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAATAAATCATTAAAAAAAAC
Found at i:13760737 original size:31 final size:32
Alignment explanation
Indices: 13760696--13760761 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 32
13760686 TTTAAATTAA
*
13760696 TTAATTAGATA-AATATTATTTTATTAATATT
1 TTAATGAGATATAATATTATTTTATTAATATT
* *
13760727 TTAATGAGATATTTATTATTATTTTATTATTATT
1 TTAATGAGATA--TAATATTATTTTATTAATATT
13760761 T
1 T
13760762 ATTTAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 10 0.34
34 19 0.66
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (32 bp):
TTAATGAGATATAATATTATTTTATTAATATT
Found at i:13762914 original size:21 final size:21
Alignment explanation
Indices: 13762890--13762961 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
13762880 CTCTCTGAAA
13762890 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* *
13762911 TGAAA-G-ATACCATGACAACATGAT
1 TGAAATGTGTA--A-GAC--CATGGT
13762935 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
13762957 TGAAA
1 TGAAA
13762962 CCATGGTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 11 0.28
22 8 0.21
24 8 0.21
25 6 0.15
26 1 0.03
27 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:13762966 original size:12 final size:12
Alignment explanation
Indices: 13762949--13762973 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13762939 AATGTGTAAG
13762949 ACCATGGTTGAA
1 ACCATGGTTGAA
13762961 ACCATGGTTGAA
1 ACCATGGTTGAA
13762973 A
1 A
13762974 GATACCATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (12 bp):
ACCATGGTTGAA
Found at i:13762997 original size:58 final size:58
Alignment explanation
Indices: 13762903--13763019 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
13762893 AATGTGTAAG
*
13762903 ACCATGGTTGAAAGATACCATGACAACATGATATGAAATGTGTAAGACCATGGTTGAA
1 ACCATGGTTGAAAGATACCATGACAACATGACATGAAATGTGTAAGACCATGGTTGAA
* *
13762961 ACCATGGTTGAAAGATACCATGGCAACGTGACATGAAATGTGTAAGACCATGGTTGAA
1 ACCATGGTTGAAAGATACCATGACAACATGACATGAAATGTGTAAGACCATGGTTGAA
13763019 A
1 A
13763020 GATACCATAG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (58 bp):
ACCATGGTTGAAAGATACCATGACAACATGACATGAAATGTGTAAGACCATGGTTGAA
Done.