Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold117
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: 3231771
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 68836 characters in sequence are not A, C, G, or T
File 8 of 18
Found at i:1206672 original size:12 final size:13
Alignment explanation
Indices: 1206650--1206681 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
1206640 GTAATTTGGC
1206650 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
1206663 AAAA-AAAAAAAG
1 AAAAGAAAAAAAG
1206675 AAAAGAA
1 AAAAGAA
1206682 GGGGGACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:1207378 original size:2 final size:2
Alignment explanation
Indices: 1207373--1207401 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1207363 TGTGTGTGTG
1207373 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 T
1207402 TGATTGTTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1210419 original size:2 final size:2
Alignment explanation
Indices: 1210412--1210437 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1210402 AACATATTAG
1210412 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1210438 GACTATTTAT
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):
TA
Found at i:1211134 original size:2 final size:2
Alignment explanation
Indices: 1211129--1211166 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1211119 TAATATACAG
1211129 AT AT AT AT AT AT 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
1211167 GCTGGCTAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1211257 original size:6 final size:6
Alignment explanation
Indices: 1211249--1211302 Score: 99
Period size: 6 Copynumber: 9.0 Consensus size: 6
1211239 CCTAAATAAC
*
1211249 CCAAAC CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT
1 CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT
1211297 CCAAAT
1 CCAAAT
1211303 TTAAGAAGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (6 bp):
CCAAAT
Found at i:1211997 original size:20 final size:17
Alignment explanation
Indices: 1211974--1212015 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
1211964 AATTACTAAT
1211974 TAATAAAATTTATATAAATA
1 TAATAAAA--TAT-TAAATA
1211994 TAAT-AAATATTAAATA
1 TAATAAAATATTAAATA
1212010 TAATAA
1 TAATAA
1212016 TAAATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.48
17 4 0.19
19 3 0.14
20 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAAAATATTAAATA
Found at i:1212015 original size:19 final size:21
Alignment explanation
Indices: 1211993--1212032 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
1211983 TTATATAAAT
1211993 ATAATAAA-TATT-AAATATA
1 ATAATAAATTATTAAAATATA
1212012 ATAATAAATTATTAAAATATA
1 ATAATAAATTATTAAAATATA
1212033 TGAATATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 4 0.21
21 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATAAATTATTAAAATATA
Found at i:1212026 original size:20 final size:20
Alignment explanation
Indices: 1211954--1212032 Score: 66
Period size: 17 Copynumber: 4.2 Consensus size: 20
1211944 TTTAAATTTT
*
1211954 ATATAAT-ATAAATTACT-A
1 ATATAATAATAAATTATTAA
*
1211972 AT-TAATAA-AATTTA-TATA
1 ATATAATAATAAATTATTA-A
1211990 A-AT-ATAATAAA-TATTAA
1 ATATAATAATAAATTATTAA
1212007 ATATAATAATAAATTATTAAA
1 ATATAATAATAAATTATT-AA
1212028 ATATA
1 ATATA
1212033 TGAATATAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
16 1 0.02
17 17 0.35
18 12 0.24
19 8 0.16
20 4 0.08
21 7 0.14
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATAATAATAAATTATTAA
Found at i:1212038 original size:21 final size:18
Alignment explanation
Indices: 1211991--1212044 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 18
1211981 ATTTATATAA
1211991 ATATAATAAATATTAAAT
1 ATATAATAAATATTAAAT
1212009 ATAATAATAAATTATTAAAAT
1 AT-ATAATAAA-TATT-AAAT
1212030 ATATGAATATAATAT
1 ATAT-AATA-AATAT
1212045 AGTTACATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.06
19 8 0.26
20 6 0.19
21 13 0.42
22 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
ATATAATAAATATTAAAT
Found at i:1212074 original size:16 final size:16
Alignment explanation
Indices: 1212053--1212084 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1212043 ATAGTTACAT
1212053 AAATTATGAAGTAAGA
1 AAATTATGAAGTAAGA
1212069 AAATTATGAAGTAAGA
1 AAATTATGAAGTAAGA
1212085 TGAGAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (16 bp):
AAATTATGAAGTAAGA
Found at i:1217962 original size:3 final size:3
Alignment explanation
Indices: 1217954--1217985 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1217944 AACCAAATTA
1217954 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1217986 ACGGACACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1218919 original size:31 final size:31
Alignment explanation
Indices: 1218857--1218924 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
1218847 CCATCGGCCA
**
1218857 CCCATTCAATACCAAATAACGTGACTCAGGT
1 CCCATTCAATACCAAATAACGTGACAAAGGT
*
1218888 CCCATTCATTACCAAATAACGTGACAAAGGT
1 CCCATTCAATACCAAATAACGTGACAAAGGT
*
1218919 CTCATT
1 CCCATT
1218925 TATGGTGTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.25
Consensus pattern (31 bp):
CCCATTCAATACCAAATAACGTGACAAAGGT
Found at i:1221932 original size:22 final size:22
Alignment explanation
Indices: 1221920--1222003 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 22
1221910 TTTTAGATTC
1221920 AAATTTTAAATTTATTAAATAT
1 AAATTTTAAATTTATTAAATAT
** * *
1221942 AAATTTTAAA-AAAATAAATTT
1 AAATTTTAAATTTATTAAATAT
*
1221963 ATAATTATATAAATTAATTAAAT-T
1 A-AATT-T-TAAATTTATTAAATAT
*
1221987 AAATTTTATATTTATTA
1 AAATTTTAAATTTATTA
1222004 TATTTTAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
21 17 0.34
22 15 0.30
23 5 0.10
24 6 0.12
25 7 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATTTTAAATTTATTAAATAT
Found at i:1221944 original size:15 final size:15
Alignment explanation
Indices: 1221926--1221992 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
1221916 ATTCAAATTT
1221926 TAAATTTATTAAATA
1 TAAATTTATTAAATA
* *
1221941 TAAATTT-TAAAAAAA
1 TAAATTTAT-TAAATA
1221956 TAAATTTA-TAATTATA
1 TAAATTTATTAA--ATA
*
1221972 TAAATTAATTAAAT-
1 TAAATTTATTAAATA
1221986 TAAATTT
1 TAAATTT
1221993 TATATTTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
14 9 0.22
15 20 0.49
16 9 0.22
17 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAATTTATTAAATA
Found at i:1227090 original size:2 final size:2
Alignment explanation
Indices: 1227083--1227109 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1227073 GAAGATTGTG
1227083 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
1227110 GTTGATCACA
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:1227364 original size:34 final size:34
Alignment explanation
Indices: 1227300--1227482 Score: 260
Period size: 34 Copynumber: 5.4 Consensus size: 34
1227290 AATGAGGTCC
* *
1227300 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
1227333 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1227367 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
1227401 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1227435 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1227469 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1227483 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 11 0.08
34 121 0.92
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1231961 original size:34 final size:34
Alignment explanation
Indices: 1231895--1232079 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
1231885 AAGTGGGAGA
* *
1231895 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1231928 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1231962 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1231996 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1232030 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1232064 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1232080 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1236170 original size:6 final size:6
Alignment explanation
Indices: 1236159--1236193 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1236149 CTAAACCCCT
* *
1236159 AACCTG AACCTG AACCTG AACCTT AACCCG AACCT
1 AACCTG AACCTG AACCTG AACCTG AACCTG AACCT
1236194 AAATTTAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.34, C:0.37, G:0.11, T:0.17
Consensus pattern (6 bp):
AACCTG
Found at i:1236749 original size:16 final size:16
Alignment explanation
Indices: 1236727--1236765 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
1236717 CATAATATAA
1236727 AAATATAAT-TAAAAT
1 AAATATAATATAAAAT
1236742 ATAATATAATATAAAAT
1 A-AATATAATATAAAAT
1236759 AAATATA
1 AAATATA
1236766 TAAATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.05
16 14 0.64
17 7 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATAATATAAAAT
Found at i:1236770 original size:29 final size:27
Alignment explanation
Indices: 1236718--1236814 Score: 74
Period size: 29 Copynumber: 3.4 Consensus size: 27
1236708 TTACATTAGC
1236718 ATAATATAAAAATATAATTAAAATATAAT
1 ATAATAT-AAAATA-AATTAAAATATAAT
**
1236747 ATAATATAAAATAAATATATAAATATTTT
1 ATAATATAAAATAAAT-TA-AAATATAAT
* *
1236776 AAAATATATAATAAAAATTAATAAT-TAAT
1 ATAATATA-AA-ATAAATTAA-AATATAAT
1236805 AT-ATA-AAAAT
1 ATAATATAAAAT
1236815 TTATATAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
25 1 0.02
26 2 0.04
27 4 0.07
28 11 0.20
29 25 0.45
30 7 0.13
31 5 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
ATAATATAAAATAAATTAAAATATAAT
Found at i:1236778 original size:22 final size:22
Alignment explanation
Indices: 1236736--1236856 Score: 89
Period size: 22 Copynumber: 5.7 Consensus size: 22
1236726 AAAATATAAT
*
1236736 TAAA-ATATAATATAATATAAAA
1 TAAATATATAA-ATAATTTAAAA
*
1236758 TAAATATATAAATATTTTAAAA
1 TAAATATATAAATAATTTAAAA
*
1236780 TATATA-ATAAA-AA-TTAATAA
1 TAAATATATAAATAATTTAA-AA
* *
1236800 TTAATATATAAA-AATTT-ATA
1 TAAATATATAAATAATTTAAAA
*
1236820 TAAATATA-AAATATTTTAAACA
1 TAAATATATAAATAATTTAAA-A
1236842 T-AAT-TATAAGATAAT
1 TAAATATATAA-ATAAT
1236857 AAAATACATA
Statistics
Matches: 79, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
19 7 0.09
20 21 0.27
21 19 0.24
22 26 0.33
23 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (22 bp):
TAAATATATAAATAATTTAAAA
Found at i:1236782 original size:34 final size:33
Alignment explanation
Indices: 1236744--1236833 Score: 85
Period size: 34 Copynumber: 2.7 Consensus size: 33
1236734 ATTAAAATAT
* *
1236744 AATATAATATAAAATAAATATATAAATATTTTAA
1 AATAT-ATATAAAATAAATATATAAATATATAAA
* *
1236778 AATATATAATAAAAATTAATA-ATTAATATATAAA
1 AATATAT-AT-AAAATAAATATATAAATATATAAA
*
1236812 AATTTATATAAATATAAA-ATAT
1 AATATATATAAA-ATAAATATAT
1236834 TTTAAACATA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
32 4 0.09
33 10 0.22
34 23 0.50
35 9 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (33 bp):
AATATATATAAAATAAATATATAAATATATAAA
Found at i:1236810 original size:21 final size:21
Alignment explanation
Indices: 1236721--1236830 Score: 67
Period size: 21 Copynumber: 5.4 Consensus size: 21
1236711 CATTAGCATA
*
1236721 ATATAAAAA-T-ATAATTAAA
1 ATATAAAAATTAATAATTAAT
*
1236740 ATATAATATAATATAA-AATAAAT
1 ATATAA-A-AAT-TAATAATTAAT
*
1236763 ATATAAATATTTTAA-AA-T-AT
1 ATATAAA-A-ATTAATAATTAAT
1236783 ATAATAAAAATTAATAATTAAT
1 AT-ATAAAAATTAATAATTAAT
*
1236805 ATATAAAAATTTAT-A-TAA-
1 ATATAAAAATTAATAATTAAT
1236823 ATATAAAA
1 ATATAAAA
1236831 TATTTTAAAC
Statistics
Matches: 75, Mismatches: 6, Indels: 21
0.74 0.06 0.21
Matches are distributed among these distances:
18 8 0.11
19 13 0.17
20 9 0.12
21 19 0.25
22 12 0.16
23 13 0.17
24 1 0.01
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATAAAAATTAATAATTAAT
Found at i:1236827 original size:42 final size:41
Alignment explanation
Indices: 1236721--1236828 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 41
1236711 CATTAGCATA
* *
1236721 ATATAAAAATATA-ATTAAAATATAATATAATATAAAATAAAT
1 ATATAAAAATTTATA-T-AAATATAATAAAATATAAAATAAAT
* * *
1236763 ATATAAATATTT-TAAAATATATAATAAAA-ATTAATAATTAAT
1 ATATAAAAATTTATATAA-ATATAATAAAATA-TAA-AATAAAT
1236805 ATATAAAAATTTATATAAATATAA
1 ATATAAAAATTTATATAAATATAA
1236829 AATATTTTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
40 3 0.06
41 13 0.24
42 34 0.63
43 4 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (41 bp):
ATATAAAAATTTATATAAATATAATAAAATATAAAATAAAT
Found at i:1236837 original size:20 final size:21
Alignment explanation
Indices: 1236760--1236837 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 21
1236750 ATATAAAATA
1236760 AATATAT-AAATATTTTA-A-
1 AATATATAAAATATTTTATAT
* * *
1236778 AATATATAATAAAAATTAATAATT
1 AATATATAA-AATATTTTAT-A-T
1236802 AATATATAAAA-A-TTTATAT
1 AATATATAAAATATTTTATAT
1236821 AA-ATATAAAATATTTTA
1 AATATATAAAATATTTTA
1236838 AACATAATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
18 15 0.31
19 5 0.10
20 11 0.23
21 4 0.08
22 2 0.04
23 2 0.04
24 9 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATATATAAAATATTTTATAT
Found at i:1244060 original size:20 final size:23
Alignment explanation
Indices: 1244018--1244062 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 23
1244008 TTTTAAAAAA
*
1244018 ATAATAAATTATAAATATTTTTT
1 ATAATAAATTATAAATATCTTTT
1244041 ATAA-AAATT-TAAA-ATCTTTT
1 ATAATAAATTATAAATATCTTTT
1244061 AT
1 AT
1244063 TTTAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 4 0.19
22 5 0.24
23 4 0.19
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAATAAATTATAAATATCTTTT
Found at i:1246566 original size:14 final size:16
Alignment explanation
Indices: 1246547--1246579 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1246537 ATAATTTTTT
1246547 TTTAAAATA-TAA-AA
1 TTTAAAATACTAATAA
1246561 TTTAAAATACTAATAA
1 TTTAAAATACTAATAA
1246577 TTT
1 TTT
1246580 TTTGAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 3 0.18
16 5 0.29
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAAATACTAATAA
Found at i:1247924 original size:12 final size:12
Alignment explanation
Indices: 1247909--1247938 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1247899 AATTTATATG
1247909 TAAATGTAAATA
1 TAAATGTAAATA
1247921 TAAATGTAAATA
1 TAAATGTAAATA
1247933 TAAATG
1 TAAATG
1247939 CAGATGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (12 bp):
TAAATGTAAATA
Found at i:1249227 original size:23 final size:23
Alignment explanation
Indices: 1249201--1249250 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1249191 AAGTGTGTAG
* * *
1249201 CATAATATAAACATTTTTGTCAC
1 CATAAAATAAACATTTTCGTCAA
1249224 CATAAAATAAACATTTTCGTCAA
1 CATAAAATAAACATTTTCGTCAA
1249247 CATA
1 CATA
1249251 CACTGCAAAT
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:0.44, C:0.18, G:0.04, T:0.34
Consensus pattern (23 bp):
CATAAAATAAACATTTTCGTCAA
Found at i:1253235 original size:13 final size:13
Alignment explanation
Indices: 1253217--1253257 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
1253207 GAAAAGGAGA
1253217 ATATTGACTCACC
1 ATATTGACTCACC
*
1253230 ATATTGACGCACC
1 ATATTGACTCACC
1253243 ATATTGACTCACC
1 ATATTGACTCACC
1253256 AT
1 AT
1253258 TTCTCCAGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.32, C:0.29, G:0.10, T:0.29
Consensus pattern (13 bp):
ATATTGACTCACC
Found at i:1256569 original size:19 final size:20
Alignment explanation
Indices: 1256534--1256575 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1256524 AAAAAAGCAT
**
1256534 AAAAAAAAGAATTTGAA-AA
1 AAAAAAAAGAAACTGAACAA
1256553 AAAAAAAAGAAACTGAACAA
1 AAAAAAAAGAAACTGAACAA
1256573 AAA
1 AAA
1256576 TAACGAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.76, C:0.05, G:0.10, T:0.10
Consensus pattern (20 bp):
AAAAAAAAGAAACTGAACAA
Found at i:1260168 original size:2 final size:2
Alignment explanation
Indices: 1260161--1260199 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1260151 TAGATTCGAA
1260161 AG AG AG AG 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 AG AG AG AG A
1260200 CCAAAACAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1261714 original size:129 final size:129
Alignment explanation
Indices: 1261484--1261742 Score: 491
Period size: 129 Copynumber: 2.0 Consensus size: 129
1261474 GCAGATCAAG
1261484 CTGCTTCACCTCCGCCAAATTATCCATATCTTGCAAAGTGACAACAAGATTTTAGAGAACCCCTT
1 CTGCTTCACCTCCGCCAAATTATCCATATCTTGCAAAGTGACAACAAGATTTTAGAGAACCCCTT
*
1261549 GTTTTTACTTACTGCTAGCTACATTCAGCCAGTCAACCATTTAGGAAGTATGAATATCCTGCAA
66 GTTTTTACTTACTGCTAACTACATTCAGCCAGTCAACCATTTAGGAAGTATGAATATCCTGCAA
* *
1261613 CTGCTTCACCTCCGCTAAATTATCCATATCTTGCAAAGTGACATCAAGATTTTAGAGAACCCCTT
1 CTGCTTCACCTCCGCCAAATTATCCATATCTTGCAAAGTGACAACAAGATTTTAGAGAACCCCTT
1261678 GTTTTTACTTACTGCTAACTACATTCAGCCAGTCAACCATTTAGGAAGTATGAATATCCTGCAA
66 GTTTTTACTTACTGCTAACTACATTCAGCCAGTCAACCATTTAGGAAGTATGAATATCCTGCAA
1261742 C
1 C
1261743 CAAACATATT
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 127 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (129 bp):
CTGCTTCACCTCCGCCAAATTATCCATATCTTGCAAAGTGACAACAAGATTTTAGAGAACCCCTT
GTTTTTACTTACTGCTAACTACATTCAGCCAGTCAACCATTTAGGAAGTATGAATATCCTGCAA
Found at i:1261772 original size:129 final size:128
Alignment explanation
Indices: 1261507--1261774 Score: 385
Period size: 129 Copynumber: 2.1 Consensus size: 128
1261497 GCCAAATTAT
*
1261507 CCATATCTTGCAAAGTGACAACAAGATTTTAGAGAACCCCTTGTTTTTACTTACTGCTAGCTACA
1 CCATATCTTGCAAAGTGACAACAAGATTTTAGAGAACCCCTTGTTTTTACTTACTGCTAACTACA
** * ** * *
1261572 TTCAGCCAGTCAACCATTTAGGAAGTATGAATATCCTGCAACTGCTTCACCTCCGCTAAATTAT
66 TTCAGCCAGTCAACCATTTAGGAAGTATGAATATCCTGCAAC-GCAACACATCCGAGAAACTAG
*
1261636 CCATATCTTGCAAAGTGACATCAAGATTTTAGAGAACCCCTTGTTTTTACTTACTGCTAACTACA
1 CCATATCTTGCAAAGTGACAACAAGATTTTAGAGAACCCCTTGTTTTTACTTACTGCTAACTACA
* ** *
1261701 TTCAGCCAGTCAACCATTTAGGAAGTATGAATATCCTGCAAC-CAAACATATTTGAGACACTAG
66 TTCAGCCAGTCAACCATTTAGGAAGTATGAATATCCTGCAACGC-AACACATCCGAGAAACTAG
1261764 CCACTATCTTG
1 CCA-TATCTTG
1261775 TAGGAAACAG
Statistics
Matches: 124, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
127 1 0.01
128 11 0.09
129 112 0.90
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (128 bp):
CCATATCTTGCAAAGTGACAACAAGATTTTAGAGAACCCCTTGTTTTTACTTACTGCTAACTACA
TTCAGCCAGTCAACCATTTAGGAAGTATGAATATCCTGCAACGCAACACATCCGAGAAACTAG
Found at i:1261888 original size:100 final size:102
Alignment explanation
Indices: 1261730--1261929 Score: 280
Period size: 100 Copynumber: 2.0 Consensus size: 102
1261720 AGGAAGTATG
* ** * *
1261730 AATATCCTGCAACCAAACATATTTGAGACACTAGCCACTATCTTGTAGGAAACAGAATAACCTAA
1 AATATCCTGCAACCAAACA-ATTTGAGACACTAACCACTATCTTACAGCAAAAAGAATAACCTAA
*
1261795 GATACCAATAGA-TAATTTTAACCAAAATAT-CTGAAGA
65 GACACCAATAGACT-ATTTTAACCAAAATATACTGAAGA
* * *
1261832 AATATCCTGCAACCAAAC-ATTTGAGACACTAATCATTATCTTACAGCAAAAAGAATAAGCTAAG
1 AATATCCTGCAACCAAACAATTTGAGACACTAACCACTATCTTACAGCAAAAAGAATAACCTAAG
1261896 ACACCAATAGACTATTTTAACCAAAATATACTGA
66 ACACCAATAGACTATTTTAACCAAAATATACTGA
1261930 CCGACTCTTG
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
100 64 0.74
101 5 0.06
102 18 0.21
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.24
Consensus pattern (102 bp):
AATATCCTGCAACCAAACAATTTGAGACACTAACCACTATCTTACAGCAAAAAGAATAACCTAAG
ACACCAATAGACTATTTTAACCAAAATATACTGAAGA
Found at i:1272110 original size:20 final size:21
Alignment explanation
Indices: 1272087--1272130 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1272077 AAAAAAGCAT
*
1272087 AAAAAAAGAAATTGAA-AAAA
1 AAAAAAAGAAACTGAACAAAA
**
1272107 AAAAACCGAAACTGAACAAAA
1 AAAAAAAGAAACTGAACAAAA
1272128 AAA
1 AAA
1272131 CTGAAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.75, C:0.09, G:0.09, T:0.07
Consensus pattern (21 bp):
AAAAAAAGAAACTGAACAAAA
Found at i:1274298 original size:20 final size:21
Alignment explanation
Indices: 1274275--1274318 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1274265 AAAAAAGCAT
*
1274275 AAAAAAAGAAATTGAA-AAAA
1 AAAAAAAGAAACTGAACAAAA
**
1274295 AAAAACTGAAACTGAACAAAA
1 AAAAAAAGAAACTGAACAAAA
1274316 AAA
1 AAA
1274319 CTGAAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.75, C:0.07, G:0.09, T:0.09
Consensus pattern (21 bp):
AAAAAAAGAAACTGAACAAAA
Found at i:1275551 original size:3 final size:3
Alignment explanation
Indices: 1275545--1275588 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
1275535 ATCATTTTTT
* *
1275545 TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA CAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1275589 CATATGCTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1279564 original size:3 final size:3
Alignment explanation
Indices: 1279551--1279579 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1279541 TAGGCAAATC
1279551 ATA ATA A-A ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1279580 TATAGTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1283190 original size:55 final size:55
Alignment explanation
Indices: 1283111--1283251 Score: 255
Period size: 55 Copynumber: 2.6 Consensus size: 55
1283101 CAAAACAAAG
* *
1283111 GAAAAACCCAAGAGGCAAAGAAGAAGATTTGAAAGGAAAAAAAACAGAGGAGGAA
1 GAAAAACCCAAGAGGCAAAGAAGAAGATTGGAAAGGAAAAAAAACAAAGGAGGAA
1283166 GAAAAACCCAAGAGGCAAAGAAGAAGATTGGAAAGGAAAAAAAACAAAGGAGGAA
1 GAAAAACCCAAGAGGCAAAGAAGAAGATTGGAAAGGAAAAAAAACAAAGGAGGAA
*
1283221 GAAAAACCCAGGAGGCAAAGAAGAAGATTGG
1 GAAAAACCCAAGAGGCAAAGAAGAAGATTGG
1283252 TTTTGTAGGG
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 83 1.00
ACGTcount: A:0.57, C:0.10, G:0.28, T:0.05
Consensus pattern (55 bp):
GAAAAACCCAAGAGGCAAAGAAGAAGATTGGAAAGGAAAAAAAACAAAGGAGGAA
Found at i:1283339 original size:2 final size:2
Alignment explanation
Indices: 1283301--1283325 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1283291 ACGTAAAAAC
1283301 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 A
1283326 CGTTGGAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1283678 original size:55 final size:51
Alignment explanation
Indices: 1283580--1283694 Score: 126
Period size: 55 Copynumber: 2.2 Consensus size: 51
1283570 ATTTGAGCAT
* *
1283580 TAATTTTTTTTATGTAAATATATAAATTTTAAATTCATTATATT-TTTTAA
1 TAATTTTTTTTATGTAAATATATAAATTTTAAATTCAATATATTATTTAAA
*
1283630 TAATTTTATTTTATGATAAA-ATATTAAAATATTTATAATTTAATATATTATTTAAA
1 TAATTTT-TTTTATG-TAAATATA-T-AAAT-TTTA-AATTCAATATATTATTTAAA
*
1283686 TAAATTTTT
1 TAATTTTTT
1283695 ATATTCAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
50 7 0.13
51 10 0.19
52 5 0.09
53 4 0.07
54 4 0.07
55 13 0.24
56 11 0.20
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.56
Consensus pattern (51 bp):
TAATTTTTTTTATGTAAATATATAAATTTTAAATTCAATATATTATTTAAA
Found at i:1284151 original size:23 final size:22
Alignment explanation
Indices: 1284117--1284162 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
1284107 AAGTTATCAA
1284117 TTTATTAAATTA-TAATATATAT
1 TTTATTAAATTATTAATA-ATAT
*
1284139 TTTATTTATATTATTAATAATAT
1 TTTA-TTAAATTATTAATAATAT
1284162 T
1 T
1284163 ATATATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 12 0.57
24 5 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTATTAAATTATTAATAATAT
Found at i:1284335 original size:17 final size:17
Alignment explanation
Indices: 1284292--1284333 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1284282 ATTTTCCTTC
1284292 TAATAATTTATCTAAAT
1 TAATAATTTATCTAAAT
* *
1284309 AAATAATTTAT-TAATT
1 TAATAATTTATCTAAAT
1284325 TAATAATTT
1 TAATAATTT
1284334 TAAATACGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATAATTTATCTAAAT
Found at i:1284695 original size:24 final size:23
Alignment explanation
Indices: 1284659--1284703 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
1284649 CTTATTAAAT
1284659 AAAAATAAAAAAATAAAATTTATA
1 AAAAATAAAAAAA-AAAATTTATA
** *
1284683 AAAAATATTAAAAAAATTTTA
1 AAAAATAAAAAAAAAAATTTA
1284704 AGTCTATTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAATAAAAAAAAAAATTTATA
Found at i:1285952 original size:19 final size:19
Alignment explanation
Indices: 1285928--1285973 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
1285918 GAAATTAATG
*
1285928 AAAAATGAATGAAA-ATAAA
1 AAAAATGAA-AAAAGATAAA
1285947 AAAAAT-AAAAAATGATAAA
1 AAAAATGAAAAAA-GATAAA
1285966 AAAAATGA
1 AAAAATGA
1285974 TTTTATAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 3 0.13
18 2 0.09
19 17 0.74
20 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (19 bp):
AAAAATGAAAAAAGATAAA
Found at i:1287343 original size:33 final size:33
Alignment explanation
Indices: 1287297--1287361 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
1287287 TTTGAGAAGC
*
1287297 CAGCTCAGTATTAACGTTCACTTAAAGATCTTA
1 CAGCTCAGCATTAACGTTCACTTAAAGATCTTA
1287330 CAGCTCAGCATTAACGTTCACTTAAAGATCTT
1 CAGCTCAGCATTAACGTTCACTTAAAGATCTT
1287362 TGACTGAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (33 bp):
CAGCTCAGCATTAACGTTCACTTAAAGATCTTA
Found at i:1288641 original size:30 final size:30
Alignment explanation
Indices: 1288607--1288714 Score: 91
Period size: 30 Copynumber: 3.7 Consensus size: 30
1288597 TATTTTTATA
1288607 AAAAATTTATTTAGATATAAATCAAAAGTT
1 AAAAATTTATTTAGATATAAATCAAAAGTT
* * * *
1288637 AAAAATATATTTTGATAAAAATTAAAAGTT
1 AAAAATTTATTTAGATATAAATCAAAAGTT
* *
1288667 --AAATTT-TGTTA-AAATAAATTGAAAA-TT
1 AAAAATTTAT-TTAGATATAAA-TCAAAAGTT
* *
1288694 AAGAATTTATTTAAATATAAA
1 AAAAATTTATTTAGATATAAA
1288715 AAAATATAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
27 8 0.13
28 12 0.20
29 8 0.13
30 33 0.54
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (30 bp):
AAAAATTTATTTAGATATAAATCAAAAGTT
Found at i:1289799 original size:22 final size:22
Alignment explanation
Indices: 1289765--1289806 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1289755 ATTTTTATTT
* *
1289765 TTTTATTATTAATATCTATATA
1 TTTTATGAATAATATCTATATA
*
1289787 TTTTATGAATAATATTTATA
1 TTTTATGAATAATATCTATA
1289807 CTACATACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTATGAATAATATCTATATA
Found at i:1293136 original size:22 final size:22
Alignment explanation
Indices: 1293111--1293190 Score: 58
Period size: 22 Copynumber: 3.6 Consensus size: 22
1293101 ATTTTATTTC
1293111 TTTATTATTAATATCTATATAT
1 TTTATTATTAATATCTATATAT
* * * *
1293133 TTTATGAATAATATTTATACTAC
1 TTTATTATTAATATCTATA-TAT
* *
1293156 ATAATT-TTAATA-CATATATAT
1 TTTATTATTAATATC-TATATAT
1293177 TTT-TATATTAATAT
1 TTTAT-TATTAATAT
1293191 TATTATCTTT
Statistics
Matches: 41, Mismatches: 12, Indels: 9
0.66 0.19 0.15
Matches are distributed among these distances:
20 1 0.02
21 4 0.10
22 31 0.76
23 5 0.12
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (22 bp):
TTTATTATTAATATCTATATAT
Found at i:1293531 original size:21 final size:21
Alignment explanation
Indices: 1293505--1293544 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1293495 ATTTTATTAT
1293505 TTTATAATAATAAAAAATTTA
1 TTTATAATAATAAAAAATTTA
* *
1293526 TTTATATTAATATAAAATT
1 TTTATAATAATAAAAAATT
1293545 AAATTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTATAATAATAAAAAATTTA
Found at i:1295777 original size:2 final size:2
Alignment explanation
Indices: 1295770--1295812 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1295760 AAAGGAAGGA
1295770 AT AT AT AT AT AT AT AT 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
1295812 A
1 A
1295813 AAATAATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1297916 original size:19 final size:19
Alignment explanation
Indices: 1297892--1297930 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1297882 GAATCGAGTC
1297892 TGGAACTACAATTGAAAGT
1 TGGAACTACAATTGAAAGT
1297911 TGGAACTACAATTGAAAGT
1 TGGAACTACAATTGAAAGT
1297930 T
1 T
1297931 TTGAAGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (19 bp):
TGGAACTACAATTGAAAGT
Found at i:1299151 original size:2 final size:2
Alignment explanation
Indices: 1299144--1299170 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1299134 ATGCATACGT
1299144 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1299171 TAAAAAGCCA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1304203 original size:32 final size:33
Alignment explanation
Indices: 1304136--1304204 Score: 79
Period size: 32 Copynumber: 2.1 Consensus size: 33
1304126 ACAAAGAGTG
* ***
1304136 AAAAGCATGAAAACAAATAAATGAAAAACCTAA
1 AAAAGCATGAAAACAAAGAAATGAAAAAAAAAA
1304169 AAAAGCAT-AAAA-AAAGAAATTGAAAAAAAAAA
1 AAAAGCATGAAAACAAAGAAA-TGAAAAAAAAAA
1304201 AAAA
1 AAAA
1304205 AGGAAGCTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 6 0.19
32 17 0.55
33 8 0.26
ACGTcount: A:0.74, C:0.07, G:0.09, T:0.10
Consensus pattern (33 bp):
AAAAGCATGAAAACAAAGAAATGAAAAAAAAAA
Found at i:1305617 original size:2 final size:2
Alignment explanation
Indices: 1305610--1305658 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
1305600 CAACTCAGAA
* * *
1305610 AT AT AT AT AT TT AT GT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1305652 AT AT AT A
1 AT AT AT A
1305659 AAAGAAAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1309009 original size:2 final size:2
Alignment explanation
Indices: 1309002--1309078 Score: 118
Period size: 2 Copynumber: 38.5 Consensus size: 2
1308992 ATGCATACGT
* * * *
1309002 AC AC AC AC AC GC AC AC AC GC GC AC AC AC AC AC AC AC AT AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1309044 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1309079 AAACCAACAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.47, C:0.48, G:0.04, T:0.01
Consensus pattern (2 bp):
AC
Found at i:1319526 original size:2 final size:2
Alignment explanation
Indices: 1319519--1319553 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1319509 ACAAAAAGAA
1319519 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1319554 GCAAAGCAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1329588 original size:22 final size:22
Alignment explanation
Indices: 1329544--1329589 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1329534 AAACAACAAC
* *
1329544 AACAAAGAGTGAAAAACATGAA
1 AACAAAGAATGAAAAACACGAA
1329566 AACAAATGAATGAAAAAC-CGAA
1 AACAAA-GAATGAAAAACACGAA
1329588 AA
1 AA
1329590 AAGCATAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.65, C:0.11, G:0.15, T:0.09
Consensus pattern (22 bp):
AACAAAGAATGAAAAACACGAA
Found at i:1329619 original size:18 final size:19
Alignment explanation
Indices: 1329598--1329644 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1329588 AAAAGCATAG
*
1329598 AAAACGAAATTGAA-AAAA
1 AAAACGAAACTGAACAAAA
*
1329616 AAAATGAAACTGAACAAAA
1 AAAACGAAACTGAACAAAA
1329635 AAAACTGAAA
1 AAAAC-GAAA
1329645 GAAAATGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 12 0.50
19 8 0.33
20 4 0.17
ACGTcount: A:0.70, C:0.09, G:0.11, T:0.11
Consensus pattern (19 bp):
AAAACGAAACTGAACAAAA
Found at i:1331248 original size:2 final size:2
Alignment explanation
Indices: 1331241--1331274 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1331231 TATAGACAGC
1331241 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1331275 CAATAAGACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1335118 original size:2 final size:2
Alignment explanation
Indices: 1335111--1335137 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1335101 TCATGACCAC
1335111 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 A
1335138 TACACCTACA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1343920 original size:3 final size:3
Alignment explanation
Indices: 1343914--1343946 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1343904 CATCATCATC
*
1343914 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1343947 TTTAGTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1347816 original size:55 final size:56
Alignment explanation
Indices: 1347737--1347878 Score: 232
Period size: 55 Copynumber: 2.6 Consensus size: 56
1347727 CAAAACAAAG
* *
1347737 GAAAAACCCAAGAGGCAAAGAAGAAGATTTGAAAGGAAAAAAAA-CAGAGGAGGAA
1 GAAAAACCCAAGAGGCAAAGAAGAAGATTGGAAAGGAAAAAAAACCAAAGGAGGAA
1347792 GAAAAACCCAAGAGGCAAAGAAGAAGATTGGAAAGGAAAAAAAACCAAAGGAGGAA
1 GAAAAACCCAAGAGGCAAAGAAGAAGATTGGAAAGGAAAAAAAACCAAAGGAGGAA
* * *
1347848 GACAAACCCAGGAGGCAACGAAGAAGATTGG
1 GAAAAACCCAAGAGGCAAAGAAGAAGATTGG
1347879 TTTTGTAGGG
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
55 43 0.53
56 38 0.47
ACGTcount: A:0.55, C:0.12, G:0.28, T:0.05
Consensus pattern (56 bp):
GAAAAACCCAAGAGGCAAAGAAGAAGATTGGAAAGGAAAAAAAACCAAAGGAGGAA
Found at i:1349145 original size:28 final size:27
Alignment explanation
Indices: 1349114--1349189 Score: 64
Period size: 29 Copynumber: 2.6 Consensus size: 27
1349104 TAAAATAGTT
1349114 AATTGATATTTTTTAAAAATAAATTAAA
1 AATTGA-ATTTTTTAAAAATAAATTAAA
* *
1349142 AATTAAGAGTTTATTT-AACATAAATTAAA
1 AATT--GAATTT-TTTAAAAATAAATTAAA
*
1349171 ATTATTGACTTTTTTAAAA
1 A--ATTGAATTTTTTAAAA
1349190 CAATAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
28 7 0.18
29 23 0.61
30 5 0.13
31 3 0.08
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (27 bp):
AATTGAATTTTTTAAAAATAAATTAAA
Found at i:1349411 original size:128 final size:128
Alignment explanation
Indices: 1349264--1349521 Score: 516
Period size: 128 Copynumber: 2.0 Consensus size: 128
1349254 CATTTCAAAT
1349264 AAAACTTTTAAAAATTCAAAATATAATCTCTTGTTAAATAAAAATAAAAAAGTAAAATTTATAAA
1 AAAACTTTTAAAAATTCAAAATATAATCTCTTGTTAAATAAAAATAAAAAAGTAAAATTTATAAA
1349329 AAATATTAAAAAAAATTAACTCTTTTGAATTCAATTATTATCAATTAAAACATAATTTTTCAA
66 AAATATTAAAAAAAATTAACTCTTTTGAATTCAATTATTATCAATTAAAACATAATTTTTCAA
1349392 AAAACTTTTAAAAATTCAAAATATAATCTCTTGTTAAATAAAAATAAAAAAGTAAAATTTATAAA
1 AAAACTTTTAAAAATTCAAAATATAATCTCTTGTTAAATAAAAATAAAAAAGTAAAATTTATAAA
1349457 AAATATTAAAAAAAATTAACTCTTTTGAATTCAATTATTATCAATTAAAACATAATTTTTCAA
66 AAATATTAAAAAAAATTAACTCTTTTGAATTCAATTATTATCAATTAAAACATAATTTTTCAA
1349520 AA
1 AA
1349522 TTTCCTCAAG
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 130 1.00
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.36
Consensus pattern (128 bp):
AAAACTTTTAAAAATTCAAAATATAATCTCTTGTTAAATAAAAATAAAAAAGTAAAATTTATAAA
AAATATTAAAAAAAATTAACTCTTTTGAATTCAATTATTATCAATTAAAACATAATTTTTCAA
Found at i:1349726 original size:18 final size:19
Alignment explanation
Indices: 1349700--1349735 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1349690 TTTAATACAT
1349700 ATATATATTTTTTATATTA
1 ATATATATTTTTTATATTA
1349719 ATAT-TATTTTTTATATT
1 ATATATATTTTTTATATT
1349736 TTTTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATATATATTTTTTATATTA
Found at i:1350714 original size:9 final size:9
Alignment explanation
Indices: 1350702--1350735 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1350692 TTATAACGAG
1350702 ATAAAAAAA
1 ATAAAAAAA
*
1350711 ATAATAAAA
1 ATAAAAAAA
1350720 AT-AAAAAA
1 ATAAAAAAA
1350728 ATAAAAAA
1 ATAAAAAA
1350736 TTGAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:1351132 original size:50 final size:51
Alignment explanation
Indices: 1351077--1351181 Score: 194
Period size: 50 Copynumber: 2.1 Consensus size: 51
1351067 CAAAACACAT
*
1351077 AAAACAATAAAATCTCTTTCATGCCTGGATAAAGTTAGTGCTG-AAAAAAA
1 AAAACAATAAAATCTCTTTCATGCCTGGATAAAGTCAGTGCTGCAAAAAAA
1351127 AAAACAATAAAATCTCTTTCATGCCTGGATAAAGTCAGTGCTGCAAAAAAA
1 AAAACAATAAAATCTCTTTCATGCCTGGATAAAGTCAGTGCTGCAAAAAAA
1351178 AAAA
1 AAAA
1351182 TAAAAGATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 42 0.79
51 11 0.21
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (51 bp):
AAAACAATAAAATCTCTTTCATGCCTGGATAAAGTCAGTGCTGCAAAAAAA
Found at i:1354720 original size:2 final size:2
Alignment explanation
Indices: 1354713--1354741 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1354703 ATGCATACGT
1354713 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1354742 TAAAATGCCA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1357640 original size:2 final size:2
Alignment explanation
Indices: 1357633--1357692 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
1357623 ACAAAAAGAA
*
1357633 AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT A- 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
1357674 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1357693 GCAAACCAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1362002 original size:17 final size:17
Alignment explanation
Indices: 1361980--1362016 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1361970 TCCAACTCTT
1361980 TATTTTATTA-ATATTTA
1 TATTTT-TTATATATTTA
1361997 TATTTTTTATATATTTA
1 TATTTTTTATATATTTA
1362014 TAT
1 TAT
1362017 ATAATTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTTTTTATATATTTA
Found at i:1362739 original size:5 final size:5
Alignment explanation
Indices: 1362729--1362760 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1362719 AGATGCAAAT
1362729 TTTTG TTTTG TTTTG TTTTG TTTT- TTTT- TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1362761 CTCAGCCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (5 bp):
TTTTG
Found at i:1364480 original size:9 final size:9
Alignment explanation
Indices: 1364450--1364507 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
1364440 TTCTGAGAAG
*
1364450 GGCAACGGT
1 GGCAATGGT
* *
1364459 GGCATTGGA
1 GGCAATGGT
1364468 GGCAATGGT
1 GGCAATGGT
** *
1364477 GGCAGCGGA
1 GGCAATGGT
1364486 GGCAATGGT
1 GGCAATGGT
1364495 GGCAATGGT
1 GGCAATGGT
1364504 GGCA
1 GGCA
1364508 GCCTGAAAGG
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.22, C:0.16, G:0.47, T:0.16
Consensus pattern (9 bp):
GGCAATGGT
Found at i:1364489 original size:27 final size:27
Alignment explanation
Indices: 1364450--1364509 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
1364440 TTCTGAGAAG
* * *
1364450 GGCAACGGTGGCATTGGAGGCAATGGT
1 GGCAGCGGAGGCAATGGAGGCAATGGT
*
1364477 GGCAGCGGAGGCAATGGTGGCAATGGT
1 GGCAGCGGAGGCAATGGAGGCAATGGT
1364504 GGCAGC
1 GGCAGC
1364510 CTGAAAGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.22, C:0.17, G:0.47, T:0.15
Consensus pattern (27 bp):
GGCAGCGGAGGCAATGGAGGCAATGGT
Found at i:1364507 original size:18 final size:18
Alignment explanation
Indices: 1364450--1364507 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
1364440 TTCTGAGAAG
* *
1364450 GGCAACGGTGGCATTGGA
1 GGCAATGGTGGCAATGGA
**
1364468 GGCAATGGTGGCAGCGGA
1 GGCAATGGTGGCAATGGA
*
1364486 GGCAATGGTGGCAATGGT
1 GGCAATGGTGGCAATGGA
1364504 GGCA
1 GGCA
1364508 GCCTGAAAGG
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:0.22, C:0.16, G:0.47, T:0.16
Consensus pattern (18 bp):
GGCAATGGTGGCAATGGA
Found at i:1365932 original size:13 final size:13
Alignment explanation
Indices: 1365914--1365943 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1365904 TTTAAATATT
1365914 TATTAAATATAAA
1 TATTAAATATAAA
1365927 TATTAAATATAAA
1 TATTAAATATAAA
1365940 TATT
1 TATT
1365944 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TATTAAATATAAA
Found at i:1366558 original size:24 final size:25
Alignment explanation
Indices: 1366518--1366567 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
1366508 AAATAGATCC
1366518 TTTTTCAAGGATCATGACATTTTTT
1 TTTTTCAAGGATCATGACATTTTTT
*
1366543 TTTTTTAAGGAT-ATGACATTTTTT
1 TTTTTCAAGGATCATGACATTTTTT
1366567 T
1 T
1366568 CTTAAACCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.56
Consensus pattern (25 bp):
TTTTTCAAGGATCATGACATTTTTT
Found at i:1366638 original size:21 final size:21
Alignment explanation
Indices: 1366608--1366650 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1366598 ATCCATTTTT
* *
1366608 AAAGACCAATCTACTTTTAAA
1 AAAGACCAATCCACCTTTAAA
*
1366629 AAAGATCAATCCACCTTTAAA
1 AAAGACCAATCCACCTTTAAA
1366650 A
1 A
1366651 GATCACTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAGACCAATCCACCTTTAAA
Found at i:1371791 original size:2 final size:2
Alignment explanation
Indices: 1371784--1371815 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1371774 AAGTTAGATG
1371784 AT AT AT 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
1371816 TATTGACACA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1372045 original size:17 final size:17
Alignment explanation
Indices: 1372014--1372046 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1372004 TTAAATTACT
1372014 TAATATATTATTTATAG
1 TAATATATTATTTATAG
1372031 TAATA-ATTATATTATA
1 TAATATATTAT-TTATA
1372047 TAAAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TAATATATTATTTATAG
Found at i:1372825 original size:24 final size:25
Alignment explanation
Indices: 1372780--1372829 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
1372770 CAAAAATATT
1372780 ATTTAATTAATAAAATTAATTTTTA
1 ATTTAATTAATAAAATTAATTTTTA
*
1372805 ATTTAATT-TTAAAA-TATATTTTTA
1 ATTTAATTAATAAAATTA-ATTTTTA
1372829 A
1 A
1372830 AAAAATTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 13 0.57
25 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTTAATTAATAAAATTAATTTTTA
Found at i:1373946 original size:21 final size:20
Alignment explanation
Indices: 1373913--1373951 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1373903 TTCATATTAA
1373913 ATTAAAAAATTAT-TAAAAC
1 ATTAAAAAATTATATAAAAC
1373932 ATTAATAAAATTTATATAAA
1 ATTAA-AAAA-TTATATAAA
1373952 TAATAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 4 0.24
21 4 0.24
22 4 0.24
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTAAAAAATTATATAAAAC
Found at i:1374706 original size:6 final size:6
Alignment explanation
Indices: 1374695--1374719 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1374685 TTAAAAGAAA
1374695 ACCCAG ACCCAG ACCCAG ACCCAG A
1 ACCCAG ACCCAG ACCCAG ACCCAG A
1374720 GACCATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCCAG
Found at i:1374737 original size:14 final size:14
Alignment explanation
Indices: 1374720--1374747 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1374710 CAGACCCAGA
1374720 GACCATTAAAACAG
1 GACCATTAAAACAG
1374734 GACCATTAAAACAG
1 GACCATTAAAACAG
1374748 CAACAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (14 bp):
GACCATTAAAACAG
Found at i:1376048 original size:14 final size:15
Alignment explanation
Indices: 1376029--1376062 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1376019 AAAATTTTAA
*
1376029 TATATTTTATA-ATT
1 TATATTATATATATT
1376043 TATATTATATATATT
1 TATATTATATATATT
1376058 TATAT
1 TATAT
1376063 AATAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATTATATATATT
Found at i:1376284 original size:6 final size:6
Alignment explanation
Indices: 1376233--1376287 Score: 76
Period size: 6 Copynumber: 9.3 Consensus size: 6
1376223 CAGCAATCTC
* * *
1376233 CCCCCT CCCCTC CCCCCT CCCC-T CCCCTT CCCCTT CCCCTT CCCCTT
1 CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT
1376280 CCCCTT CC
1 CCCCTT CC
1376288 TCCCAAGTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
5 5 0.11
6 39 0.89
ACGTcount: A:0.00, C:0.75, G:0.00, T:0.25
Consensus pattern (6 bp):
CCCCTT
Found at i:1376284 original size:18 final size:17
Alignment explanation
Indices: 1376234--1376287 Score: 81
Period size: 17 Copynumber: 3.1 Consensus size: 17
1376224 AGCAATCTCC
* *
1376234 CCCCTCCCCTCCCCCCT
1 CCCCTCCCCTTCCCCTT
1376251 CCCCTCCCCTTCCCCTT
1 CCCCTCCCCTTCCCCTT
1376268 CCCCTTCCCCTTCCCCTT
1 CCCC-TCCCCTTCCCCTT
1376286 CC
1 CC
1376288 TCCCAAGTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
17 19 0.56
18 15 0.44
ACGTcount: A:0.00, C:0.74, G:0.00, T:0.26
Consensus pattern (17 bp):
CCCCTCCCCTTCCCCTT
Found at i:1377512 original size:24 final size:23
Alignment explanation
Indices: 1377472--1377532 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 23
1377462 ATTGAATGGT
* * *
1377472 AATATAA-ATTTTAATAATTTTA
1 AATATAATATATTAATAAATATA
1377494 AATATAATATGATTAATAAATATA
1 AATATAATAT-ATTAATAAATATA
1377518 AATATAATATATTAA
1 AATATAATATATTAA
1377533 ATATTACATG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.21
23 7 0.21
24 20 0.59
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AATATAATATATTAATAAATATA
Found at i:1378220 original size:16 final size:16
Alignment explanation
Indices: 1378178--1378221 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
1378168 TTATAATGTT
1378178 ATATATATT-TAAAT-
1 ATATATATTATAAATA
*
1378192 ATATA-AATA-AAATA
1 ATATATATTATAAATA
1378206 ATATATATTATAAATA
1 ATATATATTATAAATA
1378222 GAAAATGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 6 0.25
14 10 0.42
15 3 0.12
16 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATATTATAAATA
Found at i:1378552 original size:2 final size:2
Alignment explanation
Indices: 1378547--1378592 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1378537 ATAAGCGCGC
1378547 AT AT AT AT AT AT AT AT 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
1378589 AT AT
1 AT AT
1378593 GACCCCTCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1379473 original size:33 final size:34
Alignment explanation
Indices: 1379436--1379507 Score: 110
Period size: 36 Copynumber: 2.1 Consensus size: 34
1379426 GGGGAGGGCA
1379436 TGGCTTCTT-GGGGAATGGAGGAATCTCTGGAAG
1 TGGCTTCTTGGGGGAATGGAGGAATCTCTGGAAG
*
1379469 TGGCTTCTTAGGGGGGAATGGAGGAATCTTTGGAAG
1 TGGCTTCTT--GGGGGAATGGAGGAATCTCTGGAAG
1379505 TGG
1 TGG
1379508 AGGAAGTGGC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
33 9 0.26
36 26 0.74
ACGTcount: A:0.21, C:0.10, G:0.42, T:0.28
Consensus pattern (34 bp):
TGGCTTCTTGGGGGAATGGAGGAATCTCTGGAAG
Found at i:1379600 original size:33 final size:33
Alignment explanation
Indices: 1379551--1379630 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
1379541 TTTTGGCTTG
* * * *
1379551 TAGATGGGAACAGGTGGCGGAAGTGGCTTCTTA
1 TAGACGGGAACTGGTGGAGGAAGTGGCTTATTA
* * *
1379584 TAGACTGGAACTGGTGGAGGCAGTGGTTTATTA
1 TAGACGGGAACTGGTGGAGGAAGTGGCTTATTA
*
1379617 TATACGGGAACTGG
1 TAGACGGGAACTGG
1379631 AGGGGGTTTG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.25, C:0.11, G:0.38, T:0.26
Consensus pattern (33 bp):
TAGACGGGAACTGGTGGAGGAAGTGGCTTATTA
Found at i:1379653 original size:57 final size:57
Alignment explanation
Indices: 1379581--1379820 Score: 345
Period size: 57 Copynumber: 4.2 Consensus size: 57
1379571 AAGTGGCTTC
* * * * *
1379581 TTATAGACTGGAACTGGTGGAGGCAGTGGTTTATTATATACGGGAACTGGAGGGGGT
1 TTATAGACTGGAACTGGTGGAGGAAGTGGTTTCTTGTATACAGGAACTGGAGGAGGT
* * * * * *
1379638 TTGTAGACTGGAACTGGAGGAGGGAGTGGTTTGTTGTATACTGGCACTGGAGGAGGT
1 TTATAGACTGGAACTGGTGGAGGAAGTGGTTTCTTGTATACAGGAACTGGAGGAGGT
1379695 TTATAGACTGGAACTGGTGGAGGAAGTGGTTTCTTGTATACAGGAACTGGAGGAGGT
1 TTATAGACTGGAACTGGTGGAGGAAGTGGTTTCTTGTATACAGGAACTGGAGGAGGT
* * *
1379752 TTATAGATTGGAACTGGCGGAGGAAGTGGCTTCTTGTATACAGGAACTGGAGGAGGT
1 TTATAGACTGGAACTGGTGGAGGAAGTGGTTTCTTGTATACAGGAACTGGAGGAGGT
*
1379809 TTATATACTGGA
1 TTATAGACTGGA
1379821 GGCTTGTAGA
Statistics
Matches: 164, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 164 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.28
Consensus pattern (57 bp):
TTATAGACTGGAACTGGTGGAGGAAGTGGTTTCTTGTATACAGGAACTGGAGGAGGT
Found at i:1379741 original size:33 final size:33
Alignment explanation
Indices: 1379701--1379915 Score: 142
Period size: 33 Copynumber: 6.5 Consensus size: 33
1379691 AGGTTTATAG
*
1379701 ACTGGAACTGGTGGAGGAAGTGGTTTCTTGTAT
1 ACTGGAACTGGCGGAGGAAGTGGTTTCTTGTAT
* * *
1379734 ACAGGAACT---GGAGG-A--GGTTTATAG-AT
1 ACTGGAACTGGCGGAGGAAGTGGTTTCTTGTAT
*
1379760 --TGGAACTGGCGGAGGAAGTGGCTTCTTGTAT
1 ACTGGAACTGGCGGAGGAAGTGGTTTCTTGTAT
* * * *** *
1379791 ACAGGAACTGGAGGAGGTTTATATACTGGAGGCTTGTAG
1 ACTGGAACTGGCGGAGG-----A-AGTGGTTTCTTGTAT
* *
1379830 ACTGGAACTGGCGGAGGAAGTGGCTTATTGTAT
1 ACTGGAACTGGCGGAGGAAGTGGTTTCTTGTAT
*
1379863 ACCGGAACTGGCGGAGGAAGTGGTGGTTTCTTGTAT
1 ACTGGAACTGGCGGAGGAA---GTGGTTTCTTGTAT
*
1379899 ACTGGAACTGGAGGAGG
1 ACTGGAACTGGCGGAGG
1379916 TTTATAGACC
Statistics
Matches: 137, Mismatches: 27, Indels: 33
0.70 0.14 0.17
Matches are distributed among these distances:
24 6 0.04
26 2 0.01
27 12 0.09
28 1 0.01
29 1 0.01
30 11 0.08
31 2 0.01
33 48 0.35
34 1 0.01
36 27 0.20
38 1 0.01
39 25 0.18
ACGTcount: A:0.25, C:0.11, G:0.38, T:0.27
Consensus pattern (33 bp):
ACTGGAACTGGCGGAGGAAGTGGTTTCTTGTAT
Found at i:1379838 original size:72 final size:72
Alignment explanation
Indices: 1379746--1379879 Score: 214
Period size: 72 Copynumber: 1.9 Consensus size: 72
1379736 AGGAACTGGA
* * *
1379746 GGAGGTTTATAGATTGGAACTGGCGGAGGAAGTGGCTTCTTGTATACAGGAACTGGAGGAGGTTT
1 GGAGGCTTATAGACTGGAACTGGCGGAGGAAGTGGCTTATTGTATACAGGAACTGGAGGAGGTTT
1379811 ATATACT
66 ATATACT
* * *
1379818 GGAGGCTTGTAGACTGGAACTGGCGGAGGAAGTGGCTTATTGTATACCGGAACTGGCGGAGG
1 GGAGGCTTATAGACTGGAACTGGCGGAGGAAGTGGCTTATTGTATACAGGAACTGGAGGAGG
1379880 AAGTGGTGGT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.25, C:0.12, G:0.38, T:0.25
Consensus pattern (72 bp):
GGAGGCTTATAGACTGGAACTGGCGGAGGAAGTGGCTTATTGTATACAGGAACTGGAGGAGGTTT
ATATACT
Found at i:1379906 original size:36 final size:33
Alignment explanation
Indices: 1379760--1379987 Score: 132
Period size: 33 Copynumber: 6.5 Consensus size: 33
1379750 GTTTATAGAT
1379760 TGGAACTGGCGGAGGAAGTGGCTTCTTGTATAC
1 TGGAACTGGCGGAGGAAGTGGCTTCTTGTATAC
* * * *** *
1379793 AGGAACTGGAGGAGGTTTATATACTGGAGGCTTGTAGAC
1 TGGAACTGGCGGAGG-----A-AGTGGCTTCTTGTATAC
*
1379832 TGGAACTGGCGGAGGAAGTGGCTTATTGTATAC
1 TGGAACTGGCGGAGGAAGTGGCTTCTTGTATAC
* *
1379865 CGGAACTGGCGGAGGAAGTGGTGGTTTCTTGTATAC
1 TGGAACTGGCGGAGGAA---GTGGCTTCTTGTATAC
* * *** * *
1379901 TGGAACTGGAGGAGGTTTATAGACCGGAGGCTTGTAAAT
1 TGGAACTGGCGGAGG---A-AG--TGGCTTCTTGTATAC
* * *
1379940 TGGAACAGGTGGAGGGAGTGGCTTCTTGTATAC
1 TGGAACTGGCGGAGGAAGTGGCTTCTTGTATAC
*
1379973 TGGAACTGGAGGAGG
1 TGGAACTGGCGGAGG
1379988 TTTGTAGATT
Statistics
Matches: 143, Mismatches: 37, Indels: 30
0.68 0.18 0.14
Matches are distributed among these distances:
33 62 0.43
34 1 0.01
35 2 0.01
36 27 0.19
37 1 0.01
38 1 0.01
39 48 0.34
40 1 0.01
ACGTcount: A:0.24, C:0.12, G:0.38, T:0.26
Consensus pattern (33 bp):
TGGAACTGGCGGAGGAAGTGGCTTCTTGTATAC
Found at i:1379906 original size:108 final size:105
Alignment explanation
Indices: 1379761--1379987 Score: 319
Period size: 108 Copynumber: 2.1 Consensus size: 105
1379751 TTTATAGATT
* *
1379761 GGAACTGGCGGAGGAAGTGGCTTCTTGTATACAGGAACTGGAGGAGGTTTATATACTGGAGGCTT
1 GGAACTGGCGGAGGAAGTGGCTTCTTGTATACAGGAACTGGAGGAGGTTTATAGACCGGAGGCTT
* *
1379826 GTAGACTGGAACTGGCGGAGGAAGTGGCTTATTGTATACC
66 GTAAACTGGAACAGGCGGAGGAAGTGGCTTATTGTATACC
* *
1379866 GGAACTGGCGGAGGAAGTGGTGGTTTCTTGTATACTGGAACTGGAGGAGGTTTATAGACCGGAGG
1 GGAACTGGCGGAGGAA---GTGGCTTCTTGTATACAGGAACTGGAGGAGGTTTATAGACCGGAGG
* * * * *
1379931 CTTGTAAATTGGAACAGGTGGAGGGAGTGGCTTCTTGTATACT
63 CTTGTAAACTGGAACAGGCGGAGGAAGTGGCTTATTGTATACC
*
1379974 GGAACTGGAGGAGG
1 GGAACTGGCGGAGG
1379988 TTTGTAGATT
Statistics
Matches: 107, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
105 16 0.15
108 91 0.85
ACGTcount: A:0.24, C:0.12, G:0.38, T:0.26
Consensus pattern (105 bp):
GGAACTGGCGGAGGAAGTGGCTTCTTGTATACAGGAACTGGAGGAGGTTTATAGACCGGAGGCTT
GTAAACTGGAACAGGCGGAGGAAGTGGCTTATTGTATACC
Found at i:1379968 original size:33 final size:32
Alignment explanation
Indices: 1379931--1380085 Score: 99
Period size: 33 Copynumber: 5.2 Consensus size: 32
1379921 AGACCGGAGG
1379931 CTTGTAAATTGGAACAGGTGGAGGGAGTGGCTT
1 CTTGTAAATTGGAAC-GGTGGAGGGAGTGGCTT
* *
1379964 CTTGTATACTGGAAC--TGGA-GGA--GG--T
1 CTTGTAAATTGGAACGGTGGAGGGAGTGGCTT
*
1379989 -TTGTAGATTGGAACTGGTGGAGGGAGTGGCTT
1 CTTGTAAATTGGAAC-GGTGGAGGGAGTGGCTT
** *
1380021 CTTGTAAACCGGAAC--CGGA-GGA--GG--T
1 CTTGTAAATTGGAACGGTGGAGGGAGTGGCTT
* *
1380046 -TTATAGATTGGAACCGGTGGAGGGAGTGGCTT
1 CTTGTAAATTGGAA-CGGTGGAGGGAGTGGCTT
1380078 CTTGTAAA
1 CTTGTAAA
1380086 CCGGAACCGG
Statistics
Matches: 89, Mismatches: 15, Indels: 36
0.64 0.11 0.26
Matches are distributed among these distances:
24 21 0.24
25 3 0.03
27 11 0.12
28 6 0.07
29 6 0.07
30 11 0.12
32 2 0.02
33 29 0.33
ACGTcount: A:0.24, C:0.11, G:0.38, T:0.27
Consensus pattern (32 bp):
CTTGTAAATTGGAACGGTGGAGGGAGTGGCTT
Found at i:1379992 original size:24 final size:24
Alignment explanation
Indices: 1379965--1380011 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1379955 GAGTGGCTTC
*
1379965 TTGTATACTGGAACTGGAGGAGGT
1 TTGTAGACTGGAACTGGAGGAGGT
* *
1379989 TTGTAGATTGGAACTGGTGGAGG
1 TTGTAGACTGGAACTGGAGGAGG
1380012 GAGTGGCTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.06, G:0.40, T:0.30
Consensus pattern (24 bp):
TTGTAGACTGGAACTGGAGGAGGT
Found at i:1380014 original size:57 final size:57
Alignment explanation
Indices: 1379926--1380098 Score: 274
Period size: 57 Copynumber: 3.0 Consensus size: 57
1379916 TTTATAGACC
* * * * *
1379926 GGAGGCTTGTAAATTGGAACAGGTGGAGGGAGTGGCTTCTTGTATACTGGAACTGGA
1 GGAGGTTTGTAGATTGGAACAGGTGGAGGGAGTGGCTTCTTGTAAACCGGAACCGGA
*
1379983 GGAGGTTTGTAGATTGGAACTGGTGGAGGGAGTGGCTTCTTGTAAACCGGAACCGGA
1 GGAGGTTTGTAGATTGGAACAGGTGGAGGGAGTGGCTTCTTGTAAACCGGAACCGGA
* *
1380040 GGAGGTTTATAGATTGGAACCGGTGGAGGGAGTGGCTTCTTGTAAACCGGAACCGGA
1 GGAGGTTTGTAGATTGGAACAGGTGGAGGGAGTGGCTTCTTGTAAACCGGAACCGGA
1380097 GG
1 GG
1380099 GGGAAGTGGT
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 108 1.00
ACGTcount: A:0.24, C:0.12, G:0.40, T:0.24
Consensus pattern (57 bp):
GGAGGTTTGTAGATTGGAACAGGTGGAGGGAGTGGCTTCTTGTAAACCGGAACCGGA
Found at i:1380107 original size:33 final size:33
Alignment explanation
Indices: 1380055--1380134 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
1380045 TTTATAGATT
*
1380055 GGAACCGGTGGAGGGAGTGGCTTCTT-GTAAACC
1 GGAACCGGAGGAGGGAGTGG-TTCTTCGTAAACC
* *
1380088 GGAACCGGAGG-GGGAAGTGGTTTTTCGTATACC
1 GGAACCGGAGGAGGG-AGTGGTTCTTCGTAAACC
*
1380121 GGAACTGGAGGAGG
1 GGAACCGGAGGAGG
1380135 TTTATAGACT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 7 0.17
33 31 0.77
34 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.42, T:0.20
Consensus pattern (33 bp):
GGAACCGGAGGAGGGAGTGGTTCTTCGTAAACC
Found at i:1380149 original size:57 final size:57
Alignment explanation
Indices: 1380079--1380353 Score: 388
Period size: 57 Copynumber: 4.8 Consensus size: 57
1380069 GAGTGGCTTC
* * * * *
1380079 TTGTAAACCGGAACCGGAGGGGGAAGTGGTTTTTCGTATACCGGAACTGGAGGAGGT
1 TTGTAGACTGGAACAGGAGGGGGATGTGGTTTTTCGTATACAGGAACTGGAGGAGGT
* * *
1380136 TTATAGACTGGAACGGGAGGGGGAAGTGGTTTTTCGTATACAGGAACTGGAGGAGGT
1 TTGTAGACTGGAACAGGAGGGGGATGTGGTTTTTCGTATACAGGAACTGGAGGAGGT
* * *
1380193 TTGTAGACTGGAACGGGAGGGGGATGTGGCTTTTCGTACACAGGAACTGGAGGAGGT
1 TTGTAGACTGGAACAGGAGGGGGATGTGGTTTTTCGTATACAGGAACTGGAGGAGGT
* * *
1380250 TTGTCGACTGGAACAGGCGGAGGATGTGGTTTTTCGTATACAGGAACTGGAGGAGGT
1 TTGTAGACTGGAACAGGAGGGGGATGTGGTTTTTCGTATACAGGAACTGGAGGAGGT
* * * *
1380307 TTGTAGACTGGAACAGGTGGAGGATGTGGTTTTTCGTACACCGGAAC
1 TTGTAGACTGGAACAGGAGGGGGATGTGGTTTTTCGTATACAGGAAC
1380354 CGGTGGCGGA
Statistics
Matches: 199, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 199 1.00
ACGTcount: A:0.24, C:0.12, G:0.39, T:0.25
Consensus pattern (57 bp):
TTGTAGACTGGAACAGGAGGGGGATGTGGTTTTTCGTATACAGGAACTGGAGGAGGT
Found at i:1380194 original size:27 final size:27
Alignment explanation
Indices: 1380163--1380308 Score: 72
Period size: 27 Copynumber: 5.2 Consensus size: 27
1380153 AGGGGGAAGT
1380163 GGTTTTTCGTATACAGGAACTGGAGGA
1 GGTTTTTCGTATACAGGAACTGGAGGA
* * *
1380190 GG--TTT-GTAGACTGGAACGGGAGGGGGA
1 GGTTTTTCGTATACAGGAACTGGA---GGA
* *
1380217 TGTGGCTTTTCGTACACAGGAACTGGAGGA
1 ---GGTTTTTCGTATACAGGAACTGGAGGA
*
1380247 GGTTTGTCG-ACTGGAACAGG--C-GGAGGA
1 GGTTTTTCGTA-T---ACAGGAACTGGAGGA
1380274 TGTGGTTTTTCGTATACAGGAACTGGAGGA
1 ---GGTTTTTCGTATACAGGAACTGGAGGA
1380304 GGTTT
1 GGTTT
1380309 GTAGACTGGA
Statistics
Matches: 89, Mismatches: 10, Indels: 40
0.64 0.07 0.29
Matches are distributed among these distances:
24 13 0.15
25 3 0.03
26 1 0.01
27 28 0.31
28 1 0.01
29 1 0.01
30 25 0.28
31 1 0.01
32 3 0.03
33 13 0.15
ACGTcount: A:0.23, C:0.12, G:0.39, T:0.27
Consensus pattern (27 bp):
GGTTTTTCGTATACAGGAACTGGAGGA
Found at i:1380239 original size:147 final size:147
Alignment explanation
Indices: 1379967--1380245 Score: 350
Period size: 147 Copynumber: 1.9 Consensus size: 147
1379957 GTGGCTTCTT
* * * * * *
1379967 GTATACTGGAACTGGAGGAGGTTTGTAGATTGGAACTGGTGGAGGGAGTGGCTTCTTGTAAACCG
1 GTATACCGGAACTGGAGGAGGTTTATAGACTGGAACGGGAGGAGGGAGTGGCTTCTTGTAAACAG
* * *
1380032 GAACCGGAGGAGGTTTATAGATTGGAACCGGTGGAGGGAGTGGCTTCTTGTAAACCGGAACCGGA
66 GAACCGGAGGAGGTTTATAGACTGGAACCGGAGGAGGGAGTGGCTTCTTGTAAACAGGAACCGGA
1380097 GGGGGAAGTGGTTTTTC
131 GGGGGAAGTGGTTTTTC
* *
1380114 GTATACCGGAACTGGAGGAGGTTTATAGACTGGAACGGGAGG-GGGAAGTGG-TTTTTCGTATAC
1 GTATACCGGAACTGGAGGAGGTTTATAGACTGGAACGGGAGGAGGG-AGTGGCTTCTT-GTAAAC
* * * *
1380177 AGGAACTGGAGGAGGTTTGTAGACTGGAACGGGAGG-GGGATGTGGCTT-TTCGTACACAGGAAC
64 AGGAACCGGAGGAGGTTTATAGACTGGAACCGGAGGAGGGA-GTGGCTTCTT-GTAAACAGGAAC
*
1380240 TGGAGG
127 CGGAGG
1380246 AGGTTTGTCG
Statistics
Matches: 112, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
146 13 0.12
147 99 0.88
ACGTcount: A:0.24, C:0.12, G:0.40, T:0.24
Consensus pattern (147 bp):
GTATACCGGAACTGGAGGAGGTTTATAGACTGGAACGGGAGGAGGGAGTGGCTTCTTGTAAACAG
GAACCGGAGGAGGTTTATAGACTGGAACCGGAGGAGGGAGTGGCTTCTTGTAAACAGGAACCGGA
GGGGGAAGTGGTTTTTC
Found at i:1380281 original size:30 final size:30
Alignment explanation
Indices: 1380247--1380338 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
1380237 AACTGGAGGA
1380247 GGTTTGTCGACTGGAACAGGCGGAGGATGT
1 GGTTTGTCGACTGGAACAGGCGGAGGATGT
*
1380277 GGTTTTTCG--T--ATACAGGAACTGGAGGA---
1 GGTTTGTCGACTGGA-ACAGG--C-GGAGGATGT
* *
1380304 GGTTTGTAGACTGGAACAGGTGGAGGATGT
1 GGTTTGTCGACTGGAACAGGCGGAGGATGT
1380334 GGTTT
1 GGTTT
1380339 TTCGTACACC
Statistics
Matches: 47, Mismatches: 4, Indels: 22
0.64 0.05 0.30
Matches are distributed among these distances:
26 1 0.02
27 18 0.38
28 1 0.02
29 2 0.04
30 24 0.51
31 1 0.02
ACGTcount: A:0.22, C:0.10, G:0.40, T:0.28
Consensus pattern (30 bp):
GGTTTGTCGACTGGAACAGGCGGAGGATGT
Found at i:1380327 original size:27 final size:27
Alignment explanation
Indices: 1380240--1380330 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 27
1380230 ACACAGGAAC
*
1380240 TGGAGGAGGTTTGTCGACTGGAACAGG
1 TGGAGGAGGTTTGTAGACTGGAACAGG
* * *
1380267 CGGAGGATGTGGTTTTTCGTATACAGGAAC---
1 TGGAGGA---GG--TTT-GTAGACTGGAACAGG
1380297 TGGAGGAGGTTTGTAGACTGGAACAGG
1 TGGAGGAGGTTTGTAGACTGGAACAGG
1380324 TGGAGGA
1 TGGAGGA
1380331 TGTGGTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 18
0.66 0.10 0.25
Matches are distributed among these distances:
24 10 0.21
25 3 0.06
27 15 0.31
30 8 0.17
32 3 0.06
33 9 0.19
ACGTcount: A:0.24, C:0.10, G:0.42, T:0.24
Consensus pattern (27 bp):
TGGAGGAGGTTTGTAGACTGGAACAGG
Found at i:1381771 original size:2 final size:2
Alignment explanation
Indices: 1381759--1381791 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1381749 ATAATCTTTT
*
1381759 TA TA TA AA 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 T
1381792 TGGTTGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1383734 original size:15 final size:15
Alignment explanation
Indices: 1383698--1383747 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1383688 ATTTTATTTA
*
1383698 AATATAAT-TATAA-
1 AATATAATAAATAAT
*
1383711 AATAT-ATAAATATT
1 AATATAATAAATAAT
1383725 AATATAATAAATAAT
1 AATATAATAAATAAT
*
1383740 AAAATAAT
1 AATATAAT
1383748 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 2 0.07
13 8 0.27
14 5 0.17
15 15 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AATATAATAAATAAT
Found at i:1388034 original size:2 final size:2
Alignment explanation
Indices: 1388027--1388056 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1388017 ATTCAAATAC
1388027 AT AT 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
1388057 TTTCCTTGGA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1405870 original size:21 final size:22
Alignment explanation
Indices: 1405832--1405873 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1405822 TTTTTTTGTC
**
1405832 TTTTAAAATTCAAGGATTTTTT
1 TTTTAAAAAACAAGGATTTTTT
1405854 TTTTAAAAAACAA-GATTTTT
1 TTTTAAAAAACAAGGATTTTT
1405874 AATATCGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (22 bp):
TTTTAAAAAACAAGGATTTTTT
Found at i:1414453 original size:10 final size:10
Alignment explanation
Indices: 1414440--1414491 Score: 56
Period size: 9 Copynumber: 5.3 Consensus size: 10
1414430 ATTTATATTA
1414440 ATTTTTAAAT
1 ATTTTTAAAT
*
1414450 A-TTTAAAAT
1 ATTTTTAAAT
1414459 ATTTTTAAAT
1 ATTTTTAAAT
1414469 AATTTTTTAAAT
1 -A-TTTTTAAAT
1414481 -TTTTT-AAT
1 ATTTTTAAAT
1414489 ATT
1 ATT
1414492 ATGTTAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
8 3 0.08
9 15 0.42
10 8 0.22
11 1 0.03
12 9 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTTTAAAT
Found at i:1414453 original size:20 final size:20
Alignment explanation
Indices: 1414430--1414504 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 20
1414420 ATTTAATTTA
1414430 ATTTATATTAATTTTTAAAT
1 ATTTATATTAATTTTTAAAT
* *
1414450 ATTTAAAAT-ATTTTTAAAT
1 ATTTATATTAATTTTTAAAT
*
1414469 AATTT-T-TTAAATTTTTTAAT
1 -ATTTATATT-AATTTTTAAAT
* *
1414489 A-TTATGTTAAATTTTA
1 ATTTATATTAATTTTTA
1414505 TCAAATAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
18 3 0.07
19 18 0.42
20 22 0.51
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (20 bp):
ATTTATATTAATTTTTAAAT
Found at i:1421509 original size:20 final size:22
Alignment explanation
Indices: 1421484--1421529 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
1421474 TTCGATAATT
*
1421484 TTTATTT-TAAATAAAAAAT-A
1 TTTATTTAAAAATAAAAAATAA
1421504 TTTATTTAAAAATAAAAAATAA
1 TTTATTTAAAAATAAAAAATAA
1421526 TTTA
1 TTTA
1421530 AATAAAACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
21 11 0.48
22 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTATTTAAAAATAAAAAATAA
Found at i:1421536 original size:21 final size:21
Alignment explanation
Indices: 1421492--1421536 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1421482 TTTTTATTTT
**
1421492 AAATAAAAAATATTTATTTAA
1 AAATAAAAAATATTTAAATAA
1421513 AAATAAAAAATAATTTAAATAA
1 AAATAAAAAAT-ATTTAAATAA
1421535 AA
1 AA
1421537 CCTAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAAAAAATATTTAAATAA
Found at i:1422872 original size:101 final size:102
Alignment explanation
Indices: 1422686--1422889 Score: 374
Period size: 101 Copynumber: 2.0 Consensus size: 102
1422676 AGTTTTTTTG
1422686 GGGGGTATTAATGATCTTGCAATGATATCGTATCTACCAAAAATGAAGGGTTTCTTCTTGATGCA
1 GGGGGTATTAATGATCTTGCAATGATATCGTATCTACCAAAAATGAAGGGTTTCTTCTTGATGCA
*
1422751 AAGGGAAGCCCTTCTTTGTTTGCCTCACCAGTTTGAT
66 AAGGGAAGCCATTCTTTGTTTGCCTCACCAGTTTGAT
* *
1422788 GGGGTTATTAATGATCTTTCAATGATATCGTATCTACCAAAAATGAAGGG-TTCTTCTTGATGCA
1 GGGGGTATTAATGATCTTGCAATGATATCGTATCTACCAAAAATGAAGGGTTTCTTCTTGATGCA
1422852 AAGGGAAGCCATTCTTTGTTTGCCTCACCAGTTTGAT
66 AAGGGAAGCCATTCTTTGTTTGCCTCACCAGTTTGAT
1422889 G
1 G
1422890 AATTTTATGA
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
101 51 0.52
102 48 0.48
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (102 bp):
GGGGGTATTAATGATCTTGCAATGATATCGTATCTACCAAAAATGAAGGGTTTCTTCTTGATGCA
AAGGGAAGCCATTCTTTGTTTGCCTCACCAGTTTGAT
Found at i:1423133 original size:2 final size:2
Alignment explanation
Indices: 1423126--1423154 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1423116 GCAAAATGAC
1423126 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1423155 GTGACTGTCC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1423877 original size:26 final size:26
Alignment explanation
Indices: 1423840--1423889 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1423830 TATTTTCACA
1423840 GGTTCATCGTTAAATTATTATTTCAG
1 GGTTCATCGTTAAATTATTATTTCAG
*
1423866 GGTTCATTGTTAAATTATTATTTC
1 GGTTCATCGTTAAATTATTATTTC
1423890 CTCTATTGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (26 bp):
GGTTCATCGTTAAATTATTATTTCAG
Found at i:1433891 original size:13 final size:13
Alignment explanation
Indices: 1433873--1433897 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1433863 CTAAATAAAA
1433873 AAATTATAATTTT
1 AAATTATAATTTT
1433886 AAATTATAATTT
1 AAATTATAATTT
1433898 AATTCGATCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAATTATAATTTT
Found at i:1434123 original size:2 final size:2
Alignment explanation
Indices: 1434116--1434150 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1434106 TAGCAACGAC
1434116 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1434151 ATTGCAACGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.