Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 6 of 24
Found at i:1162481 original size:14 final size:14
Alignment explanation
Indices: 1162448--1162474 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1162438 TTATAAAAAT
1162448 ATATTTTATTTTTA
1 ATATTTTATTTTTA
1162462 ATATTTTATTTTT
1 ATATTTTATTTTT
1162475 TGTATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
ATATTTTATTTTTA
Found at i:1166235 original size:3 final size:3
Alignment explanation
Indices: 1166227--1166269 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1166217 TGATTTTGAT
1166227 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1166270 CAATTTTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1167473 original size:2 final size:2
Alignment explanation
Indices: 1167466--1167497 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1167456 CTATTTTTAG
1167466 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
1167498 GTGACCGCCA
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:1174309 original size:2 final size:2
Alignment explanation
Indices: 1174302--1174329 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1174292 TGAAATATTT
1174302 TA 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 TA
1174330 AATTAGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1175344 original size:2 final size:2
Alignment explanation
Indices: 1175332--1175371 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1175322 TGGGGAATTG
* * *
1175332 CT CT CT GT CT CT CT GT CT CT AT 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 CT CT CT CT
1175372 GAAAGCTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.42, G:0.05, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1176892 original size:2 final size:2
Alignment explanation
Indices: 1176885--1176922 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1176875 ATTCTCTTTT
**
1176885 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1176923 GTATTATAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1176923 original size:10 final size:10
Alignment explanation
Indices: 1176885--1176933 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
1176875 ATTCTCTTTT
*
1176885 TATATATATA
1 TATATATAGA
*
1176895 TATATATATA
1 TATATATAGA
*
1176905 TATATATAGG
1 TATATATAGA
1176915 TATATATAG-
1 TATATATAGA
1176924 TAT-TATAGA
1 TATATATAGA
1176933 T
1 T
1176934 GTACACTGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
8 5 0.14
9 4 0.11
10 27 0.75
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (10 bp):
TATATATAGA
Found at i:1178382 original size:65 final size:65
Alignment explanation
Indices: 1178278--1178411 Score: 250
Period size: 65 Copynumber: 2.1 Consensus size: 65
1178268 CACTCTCTTC
* *
1178278 GCAAGTTAAAATGATATAGACTGGTGAAAATACATACCTCATGAAATATAGCAGACACCAAGAAG
1 GCAAGTTAAAACGATATAGACTGGTGAAAATACATACCTCATGAAATACAGCAGACACCAAGAAG
1178343 GCAAGTTAAAACGATATAGACTGGTGAAAATACATACCTCATGAAATACAGCAGACACCAAGAAG
1 GCAAGTTAAAACGATATAGACTGGTGAAAATACATACCTCATGAAATACAGCAGACACCAAGAAG
1178408 GCAA
1 GCAA
1178412 TAAGAATGGC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.18
Consensus pattern (65 bp):
GCAAGTTAAAACGATATAGACTGGTGAAAATACATACCTCATGAAATACAGCAGACACCAAGAAG
Found at i:1183339 original size:2 final size:2
Alignment explanation
Indices: 1183332--1183367 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1183322 AGCAGAACAA
1183332 AG 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 AG
1183368 TTCTGGAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1183924 original size:12 final size:12
Alignment explanation
Indices: 1183907--1183947 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
1183897 AGGTCAAAAT
*
1183907 TTTATTTTATTA
1 TTTATTATATTA
1183919 TTTATTATATTA
1 TTTATTATATTA
1183931 -TT-TTATATT-
1 TTTATTATATTA
1183940 TTTATTAT
1 TTTATTAT
1183948 TAATTAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 9 0.35
11 6 0.23
12 11 0.42
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTATATTA
Found at i:1183933 original size:25 final size:24
Alignment explanation
Indices: 1183904--1183958 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 24
1183894 AGTAGGTCAA
1183904 AATTTTAT-TTTATTATTTATTATATT
1 AATTTTATATTT-TTA-TTATTA-ATT
1183930 -ATTTTATATTTTTATTATTAATT
1 AATTTTATATTTTTATTATTAATT
1183953 AATTTT
1 AATTTT
1183959 GTGAATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 3 0.11
24 11 0.41
25 10 0.37
26 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
AATTTTATATTTTTATTATTAATT
Found at i:1185833 original size:8 final size:8
Alignment explanation
Indices: 1185822--1185923 Score: 62
Period size: 8 Copynumber: 11.5 Consensus size: 8
1185812 AAATTTAATA
1185822 ATTTATAT
1 ATTTATAT
1185830 ATTTATAT
1 ATTTATAT
1185838 CATAATTATAT
1 -AT--TTATAT
1185849 ATTTTATTAT
1 A-TTTA-TAT
1185859 ATTATAATTAT
1 ATT-T-A-TAT
*
1185870 ATTTAAAAT
1 ATTT-ATAT
1185879 ATTTATAT
1 ATTTATAT
*
1185887 -TTATATAA
1 ATT-TATAT
* *
1185895 ATTTAAAA
1 ATTTATAT
1185903 ATTTATAT
1 ATTTATAT
1185911 ATTTATATT
1 ATTTATA-T
1185920 ATTT
1 ATTT
1185924 TATTTTAATT
Statistics
Matches: 78, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
7 2 0.03
8 32 0.41
9 20 0.26
10 9 0.12
11 15 0.19
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (8 bp):
ATTTATAT
Found at i:1185874 original size:20 final size:21
Alignment explanation
Indices: 1185819--1185874 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
1185809 ATTAAATTTA
*
1185819 ATAATT-TATATATTTATATC
1 ATAATTATATTTATTTATATC
* *
1185839 ATAATTATATATTTTATTATATT
1 ATAATTATAT-TTAT-TTATATC
1185862 ATAATTATATTTA
1 ATAATTATATTTA
1185875 AAATATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.21
21 3 0.10
22 4 0.14
23 16 0.55
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATAATTATATTTATTTATATC
Found at i:1185903 original size:26 final size:25
Alignment explanation
Indices: 1185807--1185918 Score: 95
Period size: 28 Copynumber: 4.2 Consensus size: 25
1185797 TTTATTAATA
1185807 TTAT-TAAATTTAATAATTTATATAT
1 TTATATAAATTTAA-AATTTATATAT
* *
1185832 TTATATCATAATTATATATTTTAT-TAT
1 TTATAT-A-AATT-TAAAATTTATATAT
*
1185859 ATTATAATTATATTTAAAATATT-TATAT
1 -TTAT-A-TAAATTTAAAAT-TTATATAT
1185887 TTATATAAATTTAAAAATTTATATAT
1 TTATATAAATTT-AAAATTTATATAT
1185913 TTATAT
1 TTATAT
1185919 TATTTTATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
25 12 0.17
26 18 0.26
27 13 0.19
28 22 0.31
29 4 0.06
30 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (25 bp):
TTATATAAATTTAAAATTTATATAT
Found at i:1185925 original size:26 final size:26
Alignment explanation
Indices: 1185808--1185925 Score: 98
Period size: 26 Copynumber: 4.4 Consensus size: 26
1185798 TTATTAATAT
* *
1185808 TATTAAATTTAATAATTTATATATTTA
1 TATTATATTTAAAAATTT-TATATTTA
* * * *
1185835 TATCATAATTATATATTTTATTATATTA
1 TATTATATTTAAAAATTTTA-TAT-TTA
1185863 TAATTATATTT-AAAATATTTATATTTA
1 T-ATTATATTTAAAAAT-TTTATATTTA
*
1185890 TA-TAAATTTAAAAATTTATATATTTA
1 TATTATATTTAAAAATTT-TATATTTA
1185916 TATTAT-TTTA
1 TATTATATTTA
1185926 TTTTAATTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
25 8 0.11
26 22 0.31
27 21 0.29
28 10 0.14
29 11 0.15
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (26 bp):
TATTATATTTAAAAATTTTATATTTA
Found at i:1186178 original size:2 final size:2
Alignment explanation
Indices: 1186171--1186202 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1186161 ATTATTTATT
*
1186171 TA TA TA TA AA 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 TA TA TA
1186203 CTTTTGCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1186702 original size:22 final size:22
Alignment explanation
Indices: 1186657--1186702 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1186647 TTAAAATTTT
* *
1186657 TAATTATTTTTTAAAATAATAA
1 TAATAATTTTTTAAAATAAAAA
1186679 TAATAATTTTTTATAAA-AAAAA
1 TAATAATTTTTTA-AAATAAAAA
1186701 TA
1 TA
1186703 TAAATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATAATTTTTTAAAATAAAAA
Found at i:1192672 original size:2 final size:2
Alignment explanation
Indices: 1192665--1192708 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1192655 GGATTCCCCA
1192665 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1192707 TC
1 TC
1192709 ACAACTATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1193401 original size:17 final size:16
Alignment explanation
Indices: 1193381--1193437 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
1193371 GATTTAAAAT
1193381 TTAAATAATATTTATTA
1 TTAAATAATATTT-TTA
* *
1193398 TTAATTTAATTTTTTTA
1 TTAA-ATAATATTTTTA
* *
1193415 TTATATAAAATTTTTAA
1 TTAAATAATATTTTT-A
1193432 TTAAAT
1 TTAAAT
1193438 TCTTTTAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
16 8 0.26
17 16 0.52
18 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAAATAATATTTTTA
Found at i:1193742 original size:24 final size:21
Alignment explanation
Indices: 1193710--1193789 Score: 65
Period size: 24 Copynumber: 3.6 Consensus size: 21
1193700 ACATAATATA
*
1193710 AAAAAATTAATTAAAATATGGTAT
1 AAAATATTAATTAAAAT-T--TAT
*
1193734 AAAATATTAATAAAAATTAATAT
1 AAAATATTAATTAAAATT--TAT
1193757 ATAAATATT--TTAAAATTTAT
1 A-AAATATTAATTAAAATTTAT
*
1193777 ATAATATTAATTA
1 AAAATATTAATTA
1193790 TTAATATGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
19 6 0.13
20 4 0.09
21 3 0.06
22 7 0.15
23 5 0.11
24 22 0.47
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
AAAATATTAATTAAAATTTAT
Found at i:1193862 original size:19 final size:19
Alignment explanation
Indices: 1193838--1193886 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1193828 AATAGAATGG
1193838 TAATATATTA-AAATAATAT
1 TAATATATTATAAAT-ATAT
*
1193857 TAATATAATATAAATATAT
1 TAATATATTATAAATATAT
*
1193876 GAAT-TATTATA
1 TAATATATTATA
1193887 TCTAAACGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 6 0.23
19 16 0.62
20 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TAATATATTATAAATATAT
Found at i:1194128 original size:17 final size:17
Alignment explanation
Indices: 1194106--1194138 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1194096 TTTTATATAT
1194106 TTTTAAAATAACAAAAA
1 TTTTAAAATAACAAAAA
*
1194123 TTTTAAAATAATAAAA
1 TTTTAAAATAACAAAA
1194139 TTATTTGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
TTTTAAAATAACAAAAA
Found at i:1205454 original size:27 final size:27
Alignment explanation
Indices: 1205373--1205455 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
1205363 TTTGACAAAC
* *
1205373 AATAAGCCATAATTTTTAACAAACAAAA
1 AATAA-CCATCATTTTTAACAAACACAA
* * * * *
1205401 AAGAACTA-CTATTTTTTATAAATACAA
1 AATAACCATC-ATTTTTAACAAACACAA
*
1205428 AATAACCATCATTTTTGACAAACACAA
1 AATAACCATCATTTTTAACAAACACAA
1205455 A
1 A
1205456 GGGTGTTTTT
Statistics
Matches: 41, Mismatches: 12, Indels: 5
0.71 0.21 0.09
Matches are distributed among these distances:
27 36 0.88
28 5 0.12
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.29
Consensus pattern (27 bp):
AATAACCATCATTTTTAACAAACACAA
Found at i:1207374 original size:21 final size:22
Alignment explanation
Indices: 1207336--1207381 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1207326 ATTTGTTGAA
* **
1207336 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTACGGAGTACT
1207357 ACTCCACCTGCTACGGAGTACT
1 ACTCCACCTGCTACGGAGTACT
1207379 ACT
1 ACT
1207382 TGTCTGAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTACGGAGTACT
Found at i:1208520 original size:13 final size:13
Alignment explanation
Indices: 1208502--1208528 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1208492 GACATCATTC
1208502 AGAACTCTAGTTG
1 AGAACTCTAGTTG
1208515 AGAACTCTAGTTG
1 AGAACTCTAGTTG
1208528 A
1 A
1208529 TCCATCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (13 bp):
AGAACTCTAGTTG
Found at i:1210002 original size:28 final size:27
Alignment explanation
Indices: 1209984--1210044 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
1209974 TGATAAACAA
*
1209984 AAAAAAACTTATTATTTTTAATAAATAT
1 AAAAAAAC-TACTATTTTTAATAAATAT
*
1210012 AAAATAACTACTATTTTTAATAAATAT
1 AAAAAAACTACTATTTTTAATAAATAT
1210039 AAAAAA
1 AAAAAA
1210045 TAATTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 23 0.77
28 7 0.23
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (27 bp):
AAAAAAACTACTATTTTTAATAAATAT
Found at i:1210653 original size:13 final size:13
Alignment explanation
Indices: 1210635--1210696 Score: 53
Period size: 13 Copynumber: 4.9 Consensus size: 13
1210625 TTATATATTT
1210635 TTATATATTATAA
1 TTATATATTATAA
1210648 TTATATATT-TAA
1 TTATATATTATAA
1210660 TT-TAT-TTA-AA
1 TTATATATTATAA
*
1210670 TTTAATATATTAATTA
1 -TT-ATATATT-ATAA
1210686 TT-TATATTATA
1 TTATATATTATA
1210697 TAAATTATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 15
0.70 0.04 0.26
Matches are distributed among these distances:
10 4 0.10
11 5 0.12
12 7 0.17
13 18 0.45
14 2 0.05
15 3 0.08
16 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTATATATTATAA
Found at i:1210688 original size:31 final size:32
Alignment explanation
Indices: 1210653--1210712 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1210643 TATAATTATA
*
1210653 TATTTA-ATTTATTTAAATT-TAATATATTAAT
1 TATTTATA-TTATATAAATTATAATATATTAAT
1210684 TATTTATATTATATAAATTATAATATATT
1 TATTTATATTATATAAATTATAATATATT
1210713 TATATTAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TATTTATATTATATAAATTATAATATATTAAT
Found at i:1210703 original size:22 final size:22
Alignment explanation
Indices: 1210642--1210719 Score: 61
Period size: 22 Copynumber: 3.4 Consensus size: 22
1210632 TTTTTATATA
*
1210642 TTATAATTATAT-ATTTAATTTAT
1 TTAT-ATTATATAAATTAA-TTAT
* *
1210665 TTAAATT-TAATATATTAATTAT
1 TTATATTAT-ATAAATTAATTAT
1210687 TTATATTATATAAATTATAATATAT
1 TTATATTATATAAA-T-TAAT-TAT
1210712 TTATATTA
1 TTATATTA
1210720 GATTTACTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
21 1 0.02
22 19 0.43
23 9 0.20
24 4 0.09
25 11 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATATTATATAAATTAATTAT
Found at i:1210779 original size:23 final size:23
Alignment explanation
Indices: 1210749--1210817 Score: 81
Period size: 21 Copynumber: 3.1 Consensus size: 23
1210739 GTAATTTATT
*
1210749 TAAT-TAAAATATAATATGATAA
1 TAATATAAAATATAATATAATAA
*
1210771 TAATATAAAATATAAAATAATAA
1 TAATATAAAATATAATATAATAA
* *
1210794 -AA-ATATAATATAATATAAAAA
1 TAATATAAAATATAATATAATAA
1210815 TAA
1 TAA
1210818 AACGAAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 16 0.40
22 8 0.20
23 16 0.40
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (23 bp):
TAATATAAAATATAATATAATAA
Found at i:1210796 original size:16 final size:17
Alignment explanation
Indices: 1210769--1210819 Score: 79
Period size: 16 Copynumber: 3.1 Consensus size: 17
1210759 ATAATATGAT
1210769 AATAATATAAAATATAA
1 AATAATATAAAATATAA
1210786 AATAATA-AAAATATAA
1 AATAATATAAAATATAA
*
1210802 TATAATATAAAA-ATAA
1 AATAATATAAAATATAA
1210818 AA
1 AA
1210820 CGAAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 20 0.65
17 11 0.35
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAATATAAAATATAA
Found at i:1210819 original size:23 final size:22
Alignment explanation
Indices: 1210753--1210819 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
1210743 TTTATTTAAT
* *
1210753 TAAAATATAATATGATAATAATA
1 TAAAATATAATAT-AAAATAAAA
* *
1210776 TAAAATATAAAATAATA-AAAA
1 TAAAATATAATATAAAATAAAA
*
1210797 TATAATATAATATAAAAATAAAA
1 TAAAATATAATAT-AAAATAAAA
1210820 CGAAATTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
21 14 0.40
22 5 0.14
23 16 0.46
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (22 bp):
TAAAATATAATATAAAATAAAA
Found at i:1213261 original size:20 final size:20
Alignment explanation
Indices: 1213222--1213260 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1213212 AATATAAAAT
*
1213222 TTTATATTTATTACATTATA
1 TTTATATTTATTAAATTATA
1213242 TTTATA-TTATTAAA-TATA
1 TTTATATTTATTAAATTATA
1213260 T
1 T
1213261 AATATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATATTTATTAAATTATA
Found at i:1226212 original size:6 final size:6
Alignment explanation
Indices: 1226201--1226256 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
1226191 TCATTGATGC
* * * * *
1226201 ATGTGT ATGTGT ATGTGT AT-T-T ATGTAT GTATGT ACGTTT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1226247 ATGTGT ATGT
1 ATGTGT ATGT
1226257 AAATTTTCCC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
4 3 0.08
5 2 0.05
6 34 0.87
ACGTcount: A:0.20, C:0.02, G:0.27, T:0.52
Consensus pattern (6 bp):
ATGTGT
Found at i:1231117 original size:2 final size:2
Alignment explanation
Indices: 1231110--1231153 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1231100 CATAGGAAAA
1231110 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
1231152 AT
1 AT
1231154 TTGCCTTGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1231697 original size:16 final size:16
Alignment explanation
Indices: 1231676--1231707 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1231666 AAAAAAGATT
*
1231676 AAAAAAAGGAAAAAAA
1 AAAAAAAAGAAAAAAA
1231692 AAAAAAAAGAAAAAAA
1 AAAAAAAAGAAAAAAA
1231708 CCATCAGCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAA
Found at i:1233208 original size:18 final size:18
Alignment explanation
Indices: 1233174--1233212 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1233164 TATATTGGGC
*
1233174 TCTTTCTTTTTTATTTTT
1 TCTTTCTTTTCTATTTTT
1233192 TCTTTCTTTTACT-TTTTT
1 TCTTTCTTTT-CTATTTTT
1233210 TCT
1 TCT
1233213 AAAATGTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (18 bp):
TCTTTCTTTTCTATTTTT
Found at i:1235268 original size:27 final size:27
Alignment explanation
Indices: 1235220--1235274 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
1235210 ATTTTATTTT
*
1235220 TAAAAATATTTTATAATTAAAATTAAA
1 TAAAAATATTTTATAATTAAAAATAAA
1235247 TAAAAATATTTTA-AATTAAAAAATAAA
1 TAAAAATATTTTATAATT-AAAAATAAA
1235274 T
1 T
1235275 TCAAGTCAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
TAAAAATATTTTATAATTAAAAATAAA
Found at i:1238251 original size:17 final size:18
Alignment explanation
Indices: 1238229--1238280 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1238219 TAAAATATAA
*
1238229 AAATAA-TTATATTTTTT
1 AAATAATTTATAATTTTT
*
1238246 AAATAATTTTTAATTTTT
1 AAATAATTTATAATTTTT
*
1238264 AAATTAAATTA-AATTTT
1 AAA-TAATTTATAATTTT
1238281 ATTCATGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 6 0.21
18 18 0.62
19 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATAATTTATAATTTTT
Found at i:1242043 original size:4 final size:4
Alignment explanation
Indices: 1242027--1242062 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
1242017 TTCTTCTAAC
*
1242027 TGTT TGAT TGTT TGTT TGTT TGTT TGTT TGTT TGTT
1 TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT
1242063 CGGTAGTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.25, T:0.72
Consensus pattern (4 bp):
TGTT
Found at i:1242437 original size:18 final size:20
Alignment explanation
Indices: 1242391--1242439 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
1242381 AATATAAATT
1242391 TATTATTTAAATACTTACAG
1 TATTATTTAAATACTTACAG
* *
1242411 TA-AATTTAAATATTTA-A-
1 TATTATTTAAATACTTACAG
1242428 TATTATTTAAAT
1 TATTATTTAAAT
1242440 TAAAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 2 0.08
18 9 0.36
19 12 0.48
20 2 0.08
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (20 bp):
TATTATTTAAATACTTACAG
Found at i:1242574 original size:13 final size:13
Alignment explanation
Indices: 1242556--1242582 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1242546 ATATGAATAA
1242556 AATAAATTTAGAT
1 AATAAATTTAGAT
1242569 AATAAATTTAGAT
1 AATAAATTTAGAT
1242582 A
1 A
1242583 TTCGATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
AATAAATTTAGAT
Found at i:1243951 original size:24 final size:26
Alignment explanation
Indices: 1243887--1243969 Score: 73
Period size: 26 Copynumber: 3.1 Consensus size: 26
1243877 TTATAATATA
*
1243887 AAAAATAATATAAATATGATAA-ATATAT
1 AAAAA-AATAT-AATAT-ATAATATATTT
* *
1243915 ATAAAAAT-TTATATATTAATATATTT
1 AAAAAAATATAATATA-TAATATATTT
1243941 AAAAAAATATAAATATATAATAT-TTT
1 AAAAAAATAT-AATATATAATATATTT
1243967 AAA
1 AAA
1243970 TATATTTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
24 1 0.02
25 7 0.15
26 19 0.41
27 10 0.22
28 9 0.20
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (26 bp):
AAAAAAATATAATATATAATATATTT
Found at i:1243974 original size:24 final size:25
Alignment explanation
Indices: 1243893--1243974 Score: 78
Period size: 24 Copynumber: 3.2 Consensus size: 25
1243883 TATAAAAAAT
*
1243893 AATATAAATATGATAAATATATATAAA
1 AATATAAATAT-AT-AATATATTTAAA
* *
1243920 AATTTATATAT-TAATATATTTAAAAA
1 AATATAAATATATAATATATTT--AAA
1243946 AATATAAATATATAATAT-TTTAAA
1 AATATAAATATATAATATATTTAAA
*
1243970 TATAT
1 AATAT
1243975 TTATAAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
24 15 0.33
25 1 0.02
26 15 0.33
27 15 0.33
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (25 bp):
AATATAAATATATAATATATTTAAA
Found at i:1244856 original size:21 final size:21
Alignment explanation
Indices: 1244814--1244860 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1244804 GTATTATTCA
* * * *
1244814 TTTCCCTTTTTTGTTTTTAAT
1 TTTCTCTTTTTTCTTGTCAAT
1244835 TTTCTCTTTTTTCTTGTCAAT
1 TTTCTCTTTTTTCTTGTCAAT
1244856 TTTCT
1 TTTCT
1244861 TTATTTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.17, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTCTCTTTTTTCTTGTCAAT
Found at i:1251088 original size:33 final size:33
Alignment explanation
Indices: 1251045--1251130 Score: 84
Period size: 32 Copynumber: 2.6 Consensus size: 33
1251035 ACTTATAAAA
* *
1251045 ATAATATAAATATTTTAATATATCAAAATTCAT
1 ATAAAATAAATATTTTAAAATATCAAAATTCAT
* * * *
1251078 ATAAAATAAAT-TATTAAAATTTTAAAATTTAT
1 ATAAAATAAATATTTTAAAATATCAAAATTCAT
*
1251110 ATAAATATTTAATATTTTAAA
1 ATAAA-A-TAAATATTTTAAA
1251131 CTTATAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
32 21 0.50
33 11 0.26
34 4 0.10
35 6 0.14
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (33 bp):
ATAAAATAAATATTTTAAAATATCAAAATTCAT
Found at i:1251150 original size:27 final size:28
Alignment explanation
Indices: 1251077--1251152 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 28
1251067 TCAAAATTCA
1251077 TATAAAATAAATTATTAAA-ATTTTAAAAT
1 TATAAAA-AAA-TATTAAATATTTTAAAAT
* * * *
1251106 T-TATATAAATATTTAATATTTTAAACT
1 TATAAAAAAATATTAAATATTTTAAAAT
1251133 TATAAAAAAATA-TAAATATT
1 TATAAAAAAATATTAAATATT
1251153 ATATAAATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
26 6 0.16
27 20 0.53
28 11 0.29
29 1 0.03
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (28 bp):
TATAAAAAAATATTAAATATTTTAAAAT
Found at i:1251944 original size:3 final size:3
Alignment explanation
Indices: 1251936--1251961 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1251926 GGAGTATTCT
1251936 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1251962 CATATTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1255882 original size:34 final size:34
Alignment explanation
Indices: 1255823--1255887 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
1255813 ACCAATAGCC
*
1255823 ATTTTTTTGAAAGTTGAATATTTAAATATTTAAT
1 ATTTTTTTGAAAGTTGAATATTTAAAAATTTAAT
*
1255857 ATTTTTTT-AAACGGTTTAATA-TTAAAAATTT
1 ATTTTTTTGAAA--GTTGAATATTTAAAAATTT
1255888 GAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 3 0.11
34 17 0.63
35 7 0.26
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (34 bp):
ATTTTTTTGAAAGTTGAATATTTAAAAATTTAAT
Found at i:1256185 original size:22 final size:23
Alignment explanation
Indices: 1256159--1256201 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1256149 GTTTCTTAAT
**
1256159 ATGATAT-ATTTTTTTAATTGAG
1 ATGATATGATTTACTTAATTGAG
1256181 ATGATATGATTTACTTAATTG
1 ATGATATGATTTACTTAATTG
1256202 TTTATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (23 bp):
ATGATATGATTTACTTAATTGAG
Found at i:1256334 original size:21 final size:21
Alignment explanation
Indices: 1256310--1256350 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1256300 ATTTTTAATT
1256310 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
1256331 TAAATATTAATATAAAATAT
1 TAAATATTAATATAAAATAT
1256351 TTTTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:1257112 original size:20 final size:21
Alignment explanation
Indices: 1257087--1257129 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1257077 AGATTGAGTG
*
1257087 ATTTGAATTGTT-TTAATTTA
1 ATTTGAATTATTATTAATTTA
*
1257107 ATTTGAATTATTATTTATTTA
1 ATTTGAATTATTATTAATTTA
1257128 AT
1 AT
1257130 AAAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
ATTTGAATTATTATTAATTTA
Found at i:1257151 original size:22 final size:22
Alignment explanation
Indices: 1257116--1257202 Score: 62
Period size: 22 Copynumber: 4.1 Consensus size: 22
1257106 AATTTGAATT
1257116 ATTATTT--ATTTAATAAAAAA
1 ATTATTTAAATTTAATAAAAAA
*
1257136 ATTATTTAAATTTAATTATAAAA
1 ATTATTTAAATTTAA-TAAAAAA
* * *
1257159 A-TATATAAATATTTAT-AAAAT
1 ATTATTTAAAT-TTAATAAAAAA
1257180 ATT-TTTAAA--TAATAAAATAA
1 ATTATTTAAATTTAATAAAA-AA
1257200 ATT
1 ATT
1257203 TACAAATAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
18 3 0.06
19 3 0.06
20 11 0.21
21 9 0.17
22 16 0.31
23 10 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTATTTAAATTTAATAAAAAA
Found at i:1257204 original size:18 final size:17
Alignment explanation
Indices: 1257173--1257224 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
1257163 ATAAATATTT
**
1257173 ATAAAATATTTTTAAATA
1 ATAAAATAAATTTAAA-A
*
1257191 ATAAAATAAATTTACAA
1 ATAAAATAAATTTAAAA
1257208 ATAAAATAAAATTTAAA
1 ATAAAAT-AAATTTAAA
1257225 CTTAAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 8 0.28
18 21 0.72
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAAATAAATTTAAAA
Found at i:1257230 original size:18 final size:18
Alignment explanation
Indices: 1257190--1257235 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
1257180 ATTTTTAAAT
1257190 AATAAAAT-AAATTTACA
1 AATAAAATAAAATTTACA
1257207 AATAAAATAAAATTTA-A
1 AATAAAATAAAATTTACA
* *
1257224 ACTTAAATAAAA
1 AATAAAATAAAA
1257236 AATTTGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (18 bp):
AATAAAATAAAATTTACA
Found at i:1281161 original size:19 final size:19
Alignment explanation
Indices: 1281137--1281185 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1281127 ATTATGACAC
* *
1281137 ATAAAAATATAAAAATAAA
1 ATAAAAATACAAAAAAAAA
1281156 ATAAAAATACAAAAAAAAA
1 ATAAAAATACAAAAAAAAA
*
1281175 ATAAAACTACA
1 ATAAAAATACA
1281186 CGGTTGCCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (19 bp):
ATAAAAATACAAAAAAAAA
Found at i:1285579 original size:5 final size:5
Alignment explanation
Indices: 1285569--1285595 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1285559 GGATGGGAGT
1285569 GGTGG GGTGG GGTGG GGTGG GGTGG GG
1 GGTGG GGTGG GGTGG GGTGG GGTGG GG
1285596 GGGAGTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.81, T:0.19
Consensus pattern (5 bp):
GGTGG
Found at i:1286017 original size:18 final size:18
Alignment explanation
Indices: 1285994--1286028 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1285984 CAAAAACAGT
*
1285994 AGCAACCACTTTACCAAG
1 AGCAACAACTTTACCAAG
*
1286012 AGCAACAACTTTCCCAA
1 AGCAACAACTTTACCAA
1286029 CCTCTGCAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.34, G:0.09, T:0.17
Consensus pattern (18 bp):
AGCAACAACTTTACCAAG
Found at i:1286570 original size:12 final size:11
Alignment explanation
Indices: 1286553--1286639 Score: 51
Period size: 11 Copynumber: 8.2 Consensus size: 11
1286543 ATGTATTTAA
1286553 AATTTTTATATT
1 AATTTTTAT-TT
1286565 AATTTTTATTT
1 AATTTTTATTT
**
1286576 AATTTAAATTT
1 AATTTTTATTT
*
1286587 AA---ATA-TT
1 AATTTTTATTT
1286594 AA-TTTTATTT
1 AATTTTTATTT
**
1286604 -ATTAATATTTT
1 AATTTTTA-TTT
*
1286615 AATTATTATTT
1 AATTTTTATTT
1286626 AATTTTATATTT
1 AATTTT-TATTT
1286638 AA
1 AA
1286640 CAGCAAAGAT
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
7 4 0.07
8 2 0.03
9 3 0.05
10 5 0.08
11 24 0.40
12 22 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
AATTTTTATTT
Found at i:1286585 original size:29 final size:29
Alignment explanation
Indices: 1286547--1286604 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1286537 TAATGGATGT
**
1286547 ATTTAAAATTTTTATATTAATTTTTATTTA
1 ATTTAAAATTTAAATATTAA-TTTTATTTA
1286577 ATTT-AAATTTAAATATTAATTTTATTTA
1 ATTTAAAATTTAAATATTAATTTTATTTA
1286605 TTAATATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 9 0.35
29 13 0.50
30 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
ATTTAAAATTTAAATATTAATTTTATTTA
Found at i:1286965 original size:32 final size:32
Alignment explanation
Indices: 1286919--1287014 Score: 85
Period size: 37 Copynumber: 2.9 Consensus size: 32
1286909 AAAATATATT
1286919 TTATAATTT-AATTTAATTATT-TT-ATTT-AA
1 TTAT-ATTTAAATTTAATTATTCTTAATTTAAA
1286948 TCTATATTATAATATTTAATTCGATATCTTAATTTAAA
1 T-TATATT-TAA-ATTTAATT--AT-TCTTAATTTAAA
*
1286986 TTATATTTAAATTTAATTATT-ATAATTTA
1 TTATATTTAAATTTAATTATTCTTAATTTA
1287015 TATAATAATA
Statistics
Matches: 56, Mismatches: 1, Indels: 18
0.75 0.01 0.24
Matches are distributed among these distances:
29 4 0.07
30 4 0.07
31 8 0.14
32 9 0.16
33 2 0.04
34 2 0.04
35 9 0.16
36 5 0.09
37 10 0.18
38 3 0.05
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (32 bp):
TTATATTTAAATTTAATTATTCTTAATTTAAA
Found at i:1287539 original size:17 final size:17
Alignment explanation
Indices: 1287489--1287530 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
1287479 AAAATTTATT
1287489 AAATTTATAACTTTTAA
1 AAATTTATAACTTTTAA
* *
1287506 AATTTTATAATTTTTAA
1 AAATTTATAACTTTTAA
1287523 AAATTTAT
1 AAATTTAT
1287531 TAATATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
AAATTTATAACTTTTAA
Found at i:1287983 original size:35 final size:37
Alignment explanation
Indices: 1287935--1288004 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
1287925 AATAATTTAA
1287935 TAAAGATCAAATTA-ATTTAAATTTAAAAAATTTATT
1 TAAAGATCAAATTATATTTAAATTTAAAAAATTTATT
* * * *
1287971 TAAAGCTC-AATTATATTTTATTTTAAAATATTTA
1 TAAAGATCAAATTATATTTAAATTTAAAAAATTTA
1288005 ATTATTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 5 0.17
36 24 0.83
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (37 bp):
TAAAGATCAAATTATATTTAAATTTAAAAAATTTATT
Found at i:1298964 original size:12 final size:11
Alignment explanation
Indices: 1298936--1298970 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
1298926 CATATTGAAC
1298936 AAAAAAAGAA-
1 AAAAAAAGAAG
1298946 AAAAAAAGAAG
1 AAAAAAAGAAG
1298957 AAAGAAAAGAAG
1 AAA-AAAAGAAG
1298969 AA
1 AA
1298971 GGGTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.43
11 3 0.13
12 10 0.43
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:1299453 original size:16 final size:15
Alignment explanation
Indices: 1299406--1299448 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 15
1299396 TTTAATTTTT
1299406 TTATTTAAATTTAAA
1 TTATTTAAATTTAAA
*
1299421 TTAAATTAAATTTAAA
1 TT-ATTTAAATTTAAA
1299437 TTATTT-AATTTA
1 TTATTTAAATTTA
1299449 TAAATAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATTTAAATTTAAA
Found at i:1300026 original size:15 final size:14
Alignment explanation
Indices: 1300007--1300040 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1299997 AAAAAAATTA
*
1300007 AATATATTTATATT
1 AATATATATATATT
1300021 ATATATATATATATT
1 A-ATATATATATATT
1300036 AATAT
1 AATAT
1300041 TTAAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATATATATATATT
Found at i:1301031 original size:37 final size:36
Alignment explanation
Indices: 1300960--1301032 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
1300950 TAATATTAAA
*
1300960 AAATTTAAAAATATTTTTATATTAATATTTATAATT
1 AAATTTAAAAATATTTTTATATTAATATTAATAATT
*
1300996 AAATTTAAATATAATTTTTATTATTTAA-A-TAATAATT
1 AAATTTAAAAAT-ATTTTTA-TA-TTAATATTAATAATT
1301033 TAAACTGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 11 0.34
37 14 0.44
38 3 0.09
39 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
AAATTTAAAAATATTTTTATATTAATATTAATAATT
Found at i:1310409 original size:31 final size:31
Alignment explanation
Indices: 1310374--1310436 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1310364 TATTTAATAC
* *
1310374 ATTAACTTATTGAATTAAAAAATAATCATTT
1 ATTAAATTATTGAATTAAAAAATAATAATTT
* *
1310405 ATTAAATTATTTATTTAAAAAATAATAATTT
1 ATTAAATTATTGAATTAAAAAATAATAATTT
1310436 A
1 A
1310437 AATTGATATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (31 bp):
ATTAAATTATTGAATTAAAAAATAATAATTT
Found at i:1312853 original size:21 final size:20
Alignment explanation
Indices: 1312799--1312853 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
1312789 TTTAAAATAT
1312799 TTATATATTAATATTATATTA
1 TTATAT-TTAATATTATATTA
*
1312820 TT-T-TTT-ATGTTATATTTA
1 TTATATTTAATATTATA-TTA
1312838 TTATATTTAATATTAT
1 TTATATTTAATATTAT
1312854 CAAGATCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 7 0.25
18 7 0.25
19 2 0.07
20 4 0.14
21 8 0.29
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTATATTTAATATTATATTA
Found at i:1314366 original size:17 final size:17
Alignment explanation
Indices: 1314334--1314367 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1314324 TACTTAAAAC
1314334 TTATTGTTTATTTTATT
1 TTATTGTTTATTTTATT
1314351 TTATT-TTTATTATTATT
1 TTATTGTTTATT-TTATT
1314368 ATTGTTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTATTGTTTATTTTATT
Found at i:1315606 original size:32 final size:35
Alignment explanation
Indices: 1315552--1315636 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 35
1315542 TTTAAAAATT
* *
1315552 TATAATTTATTTTATT-ATTATAATTTTAAA-TAAA
1 TATAATTTAATTTATTAAATATAA-TTTAAATTAAA
*
1315586 -A-AATTTTA-TTATTAAATATAATTTAAATTAAA
1 TATAATTTAATTTATTAAATATAATTTAAATTAAA
1315618 TATAATTTAATTTATTAAA
1 TATAATTTAATTTATTAAA
1315637 AAATAGTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
31 11 0.26
32 15 0.36
33 2 0.05
34 6 0.14
35 8 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (35 bp):
TATAATTTAATTTATTAAATATAATTTAAATTAAA
Found at i:1315615 original size:16 final size:16
Alignment explanation
Indices: 1315596--1315627 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1315586 AAATTTTATT
1315596 ATTAAATATAATTTAA
1 ATTAAATATAATTTAA
1315612 ATTAAATATAATTTAA
1 ATTAAATATAATTTAA
1315628 TTTATTAAAA
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:0.00, T:0.44
Consensus pattern (16 bp):
ATTAAATATAATTTAA
Found at i:1315694 original size:22 final size:22
Alignment explanation
Indices: 1315671--1315711 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1315661 AATAAATAAT
1315671 TTTTAT-TATATAATTTTATCA
1 TTTTATATATATAATTTTATCA
*
1315692 TTTTATATATATTATTTTAT
1 TTTTATATATATAATTTTAT
1315712 TTCTATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTATATATATAATTTTATCA
Found at i:1316445 original size:18 final size:18
Alignment explanation
Indices: 1316424--1316465 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1316414 AAATATATAT
* *
1316424 TAAATACTAATACAAATA
1 TAAATACTAAAAAAAATA
*
1316442 TAAATACTAAAAAAAATC
1 TAAATACTAAAAAAAATA
1316460 TAAATA
1 TAAATA
1316466 ATTTAACGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAATACTAAAAAAAATA
Found at i:1316849 original size:3 final size:3
Alignment explanation
Indices: 1316841--1316882 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1316831 TTTATCTTAG
1316841 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1316883 CAATTTATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1317273 original size:17 final size:17
Alignment explanation
Indices: 1317253--1317292 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1317243 CTGAAATTTA
*
1317253 AAAATTTTATT-AATAAT
1 AAAATTTT-TTAAAAAAT
1317270 AAAATTTTTTAAAAAAT
1 AAAATTTTTTAAAAAAT
1317287 AAAATT
1 AAAATT
1317293 AATTTCATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATTTTTTAAAAAAT
Found at i:1317997 original size:20 final size:21
Alignment explanation
Indices: 1317952--1317994 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1317942 ATAAGTGTTT
1317952 TTAA-ATA-TTTTAAAATTAA
1 TTAATATATTTTTAAAATTAA
1317971 TTAATATATTTTTAATAA-TAA
1 TTAATATATTTTTAA-AATTAA
1317992 TTA
1 TTA
1317995 TATTGTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.19
20 3 0.14
21 12 0.57
22 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAATATATTTTTAAAATTAA
Found at i:1318239 original size:22 final size:24
Alignment explanation
Indices: 1318197--1318255 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 24
1318187 AAGAACTTAT
1318197 TTTA-TTATAATAAAAATATAAAA
1 TTTATTTATAATAAAAATATAAAA
1318220 TTTATTTA-AATAAAAA-ATAAAA
1 TTTATTTATAATAAAAATATAAAA
*
1318242 TATATTGTATAATA
1 TTTATT-TATAATA
1318256 TTTTAACCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 11 0.34
23 14 0.44
24 7 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
TTTATTTATAATAAAAATATAAAA
Found at i:1318255 original size:24 final size:24
Alignment explanation
Indices: 1318201--1318255 Score: 78
Period size: 22 Copynumber: 2.3 Consensus size: 24
1318191 ACTTATTTTA
*
1318201 TTATAATAAAAATATAAAATTTAT
1 TTATAATAAAAATATAAAATATAT
1318225 TTA-AATAAAAA-ATAAAATATAT
1 TTATAATAAAAATATAAAATATAT
1318247 TGTATAATA
1 T-TATAATA
1318256 TTTTAACCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 11 0.39
23 10 0.36
24 7 0.25
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TTATAATAAAAATATAAAATATAT
Found at i:1326006 original size:15 final size:17
Alignment explanation
Indices: 1325986--1326026 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
1325976 ATTTTAATAA
1325986 ATATTTATT-ATTT-TT
1 ATATTTATTAATTTATT
1326001 ATATTTATTAAATTTATT
1 ATATTTATT-AATTTATT
1326019 ATATTTAT
1 ATATTTAT
1326027 ATCATATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.39
17 4 0.17
18 10 0.43
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTTATTAATTTATT
Found at i:1328982 original size:2 final size:2
Alignment explanation
Indices: 1328971--1329006 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
1328961 GTTTTATAAC
1328971 TA TA -A TA TA TA TCA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
1329007 CCATATGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1329613 original size:23 final size:23
Alignment explanation
Indices: 1329586--1329629 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1329576 GAGTTTGAAC
1329586 TGTAAAAATT-AATATTTAATAGG
1 TGTAAAAATTAAATA-TTAATAGG
*
1329609 TGTAAAATTTAAATATTAATA
1 TGTAAAAATTAAATATTAATA
1329630 TTTATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (23 bp):
TGTAAAAATTAAATATTAATAGG
Found at i:1337431 original size:105 final size:105
Alignment explanation
Indices: 1337247--1337442 Score: 270
Period size: 105 Copynumber: 1.9 Consensus size: 105
1337237 TGCAGTCTAC
* *
1337247 ACCTTTAAAACTCACGTGTTTGTCACTGTCATTGCTCTCTTCGGATGCTTTCCTTCCCTAGCGTC
1 ACCTTTAAAACTCACATGTTTGTCACTGTCATTGCTCTCTTCGGATGCTTTCCCTCCCTAGCGTC
*
1337312 TAATTGCCAACTGCTACATTATTTTACCAAATGCGTCTGT
66 TAATTGCCAACTGCTACATCATTTTACCAAATGCGTCTGT
* * *
1337352 ACCTTTAAAACTCACATGTTTGTCACTGTCGA-TG-TCCTCTTCTGATGCTTTCCCTGCCTAGCT
1 ACCTTTAAAACTCACATGTTTGTCACTGTC-ATTGCT-CTCTTCGGATGCTTTCCCTCCCTAGCG
* ***
1337415 TCTGATTGCTGGCTGCTACATCATTTTA
64 TCTAATTGCCAACTGCTACATCATTTTA
1337443 ACATGCTTCC
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
104 1 0.01
105 77 0.97
106 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.39
Consensus pattern (105 bp):
ACCTTTAAAACTCACATGTTTGTCACTGTCATTGCTCTCTTCGGATGCTTTCCCTCCCTAGCGTC
TAATTGCCAACTGCTACATCATTTTACCAAATGCGTCTGT
Found at i:1339596 original size:18 final size:18
Alignment explanation
Indices: 1339548--1339598 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 18
1339538 TTTATAATAA
1339548 AATTTAAATAAAAA-TAT
1 AATTTAAATAAAAATTAT
* *
1339565 --TTTTATTAATAAATTAT
1 AATTTAAATAA-AAATTAT
1339582 AATTTAAATAAAAATTA
1 AATTTAAATAAAAATTA
1339599 AATCAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
15 7 0.27
16 3 0.12
17 3 0.12
18 6 0.23
19 7 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTTAAATAAAAATTAT
Found at i:1339600 original size:45 final size:49
Alignment explanation
Indices: 1339482--1339601 Score: 119
Period size: 50 Copynumber: 2.5 Consensus size: 49
1339472 AAATTAAAAT
* *
1339482 TTTAT-TTTATTATTAAAAGTT-AATAAAAAATATTTTTATATTAATATTAA
1 TTTATATTTA-TAATAAAAATTAAAT-AAAAATATTTTTATATTAATA-TAA
* *
1339532 TTTATTTTTATAATAAAATTTAAATAAAAATA-TTTT-TATTAATA-AA
1 TTTATATTTATAATAAAAATTAAATAAAAATATTTTTATATTAATATAA
1339578 -TTATAATTTA-AATAAAAATTAAAT
1 TTTAT-ATTTATAATAAAAATTAAAT
1339602 CAATTTAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
45 17 0.27
46 6 0.10
48 8 0.13
49 4 0.06
50 21 0.33
51 7 0.11
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (49 bp):
TTTATATTTATAATAAAAATTAAATAAAAATATTTTTATATTAATATAA
Found at i:1341386 original size:6 final size:6
Alignment explanation
Indices: 1341377--1341413 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1341367 ACTGGAAAGG
1341377 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G
1341414 GTGGTACTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:1341923 original size:16 final size:16
Alignment explanation
Indices: 1341904--1341934 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1341894 TATTTGATTT
1341904 ATTAAAATTAAATAGA
1 ATTAAAATTAAATAGA
*
1341920 ATTATAATTAAATAG
1 ATTAAAATTAAATAG
1341935 TTTATTCATT
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:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
ATTAAAATTAAATAGA
Found at i:1342530 original size:42 final size:40
Alignment explanation
Indices: 1342484--1342575 Score: 100
Period size: 39 Copynumber: 2.3 Consensus size: 40
1342474 TTTAATTTTT
* **
1342484 TTAATTTAAATTTCAAATAAATTATTTATTAATTTAAATTAA
1 TTAATTTAAATTTC-AATAAATTATTTAATAA-TTAAAAAAA
**
1342526 TTAATTT-AA-TTCAATTTATTATTTAATAATTAAAAAAA
1 TTAATTTAAATTTCAATAAATTATTTAATAATTAAAAAAA
1342564 TT-ATTTAAATTT
1 TTAATTTAAATTT
1342576 AATTATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
37 4 0.09
38 11 0.26
39 16 0.37
40 3 0.07
41 2 0.05
42 7 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (40 bp):
TTAATTTAAATTTCAATAAATTATTTAATAATTAAAAAAA
Found at i:1342575 original size:33 final size:32
Alignment explanation
Indices: 1342553--1342620 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 32
1342543 ATTATTTAAT
1342553 AATTA-AAAAAATTATTTAAATTTAATTATAAA
1 AATTATAAAAAATT-TTTAAATTTAATTATAAA
*
1342585 AATTATAAAAAATTTTTATTTATATTAATTATAAA
1 AATTATAAAAAATTTTTA--AAT-TTAATTATAAA
1342620 A
1 A
1342621 CATAAATTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 9 0.29
33 8 0.26
34 2 0.06
35 12 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
AATTATAAAAAATTTTTAAATTTAATTATAAA
Found at i:1343543 original size:27 final size:27
Alignment explanation
Indices: 1343513--1343648 Score: 71
Period size: 27 Copynumber: 5.0 Consensus size: 27
1343503 ATAATATGTA
1343513 AAAAAAATTAAAATATGATAAAAATAT
1 AAAAAAATTAAAATATGATAAAAATAT
* * *
1343540 AAAAATATTTTAAAA-ATTAT-ATAATAT
1 AAAAA-A-ATTAAAATATGATAAAAATAT
** * * *
1343567 AAAATATCTTAAAATTTTATATAAATAT
1 AAAA-AAATTAAAATATGATAAAAATAT
* * * * *
1343595 -AAAATATTTAAATATAATTATAATAT
1 AAAAAAATTAAAATATGATAAAAATAT
* *
1343621 AATAAAATATATAAATATGATATAAATA
1 AAAAAAAT-TA-AAATATGATAAAAATA
1343649 AATAATTATT
Statistics
Matches: 79, Mismatches: 22, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
26 22 0.28
27 27 0.34
28 12 0.15
29 18 0.23
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (27 bp):
AAAAAAATTAAAATATGATAAAAATAT
Found at i:1343578 original size:26 final size:25
Alignment explanation
Indices: 1343535--1343622 Score: 95
Period size: 26 Copynumber: 3.3 Consensus size: 25
1343525 ATATGATAAA
1343535 AATATAAAAATATTTTAAAAATTATAT
1 AATAT-AAAATA-TTTAAAAATTATAT
*
1343562 AATATAAAATATCTTAAAATTTTATAT
1 AATATAAAATAT-TTAAAA-ATTATAT
* *
1343589 AAATATAAAATATTTAAATATAATTAT
1 -AATATAAAATATTTAAAAATTA-TAT
1343616 AATATAA
1 AATATAA
1343623 TAAAATATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
25 1 0.02
26 21 0.40
27 19 0.36
28 12 0.23
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATAAAATATTTAAAAATTATAT
Found at i:1343599 original size:28 final size:27
Alignment explanation
Indices: 1343520--1343648 Score: 122
Period size: 28 Copynumber: 4.7 Consensus size: 27
1343510 GTAAAAAAAA
* *
1343520 TTAAAATATGATAAAAATATAAAAATATT
1 TTAAAATATTATATAAATAT-AAAATA-T
1343549 TTAAAA-ATTATAT-AATATAAAATAT
1 TTAAAATATTATATAAATATAAAATAT
*
1343574 CTTAAAATTTTATATAAATATAAAATAT
1 -TTAAAATATTATATAAATATAAAATAT
*
1343602 TTAAATATAATTATA-ATATAATAAAATAT
1 TTAAA-AT-ATTATATAAAT-ATAAAATAT
* *
1343631 AT-AAATATGATATAAATA
1 TTAAAATATTATATAAATA
1343649 AATAATTATT
Statistics
Matches: 85, Mismatches: 8, Indels: 17
0.77 0.07 0.15
Matches are distributed among these distances:
25 1 0.01
26 18 0.21
27 21 0.25
28 24 0.28
29 21 0.25
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (27 bp):
TTAAAATATTATATAAATATAAAATAT
Found at i:1343632 original size:23 final size:24
Alignment explanation
Indices: 1343606--1343650 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1343596 AAATATTTAA
*
1343606 ATATAATTATAATAT-AATAAAAT
1 ATATAAATATAATATAAATAAAAT
*
1343629 ATATAAATATGATATAAATAAA
1 ATATAAATATAATATAAATAAA
1343651 TAATTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
ATATAAATATAATATAAATAAAAT
Found at i:1343646 original size:55 final size:53
Alignment explanation
Indices: 1343516--1343648 Score: 139
Period size: 55 Copynumber: 2.5 Consensus size: 53
1343506 ATATGTAAAA
* *
1343516 AAAAT-TA-AAATATGATAAAAATATAAAAATATTTTAAAAATTATATAATAT
1 AAAATATATAAATATGATATAAATATAAAAATATTTAAAAAATTATATAATAT
* * *
1343567 AAAATATCTTAAAATTTTATATAAATAT-AAAATATTTAAATATAATTATA-ATATAAT
1 AAAATAT-AT-AAATATGATATAAATATAAAAATATTTAAA-A-AATTATATA-AT-AT
1343624 AAAATATATAAATATGATATAAATA
1 AAAATATATAAATATGATATAAATA
1343649 AATAATTATT
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
51 5 0.08
52 1 0.02
54 11 0.17
55 30 0.45
56 10 0.15
57 9 0.14
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.38
Consensus pattern (53 bp):
AAAATATATAAATATGATATAAATATAAAAATATTTAAAAAATTATATAATAT
Found at i:1343652 original size:23 final size:23
Alignment explanation
Indices: 1343584--1343650 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 23
1343574 CTTAAAATTT
* **
1343584 TATATAAATATAAAAT-ATTTAA
1 TATATAAATATAATATAATAAAA
*
1343606 -ATATAATTATAATATAATAAAA
1 TATATAAATATAATATAATAAAA
*
1343628 TATATAAATATGATATAAATAAA
1 TATATAAATATAATAT-AATAAA
1343651 TAATTATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 13 0.36
22 4 0.11
23 13 0.36
24 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (23 bp):
TATATAAATATAATATAATAAAA
Found at i:1344251 original size:11 final size:11
Alignment explanation
Indices: 1344237--1344271 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1344227 TAAAAATATT
*
1344237 TATATTTAATA
1 TATATTAAATA
1344248 TATATTAAATA
1 TATATTAAATA
1344259 TATATTCAAATA
1 TATATT-AAATA
1344271 T
1 T
1344272 TAATATAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (11 bp):
TATATTAAATA
Found at i:1344501 original size:19 final size:21
Alignment explanation
Indices: 1344453--1344510 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
1344443 AATAAATTTT
1344453 ATATAAAT-TTA-ATTATAAAAA
1 ATATAAATATTACA-TAT-AAAA
1344474 ATATAAATATTAC-TATAAAA
1 ATATAAATATTACATATAAAA
1344494 ATAT-AATATTACATATA
1 ATATAAATATTACATATA
1344511 TTTTAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
19 8 0.24
20 12 0.35
21 11 0.32
22 3 0.09
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAAATATTACATATAAAA
Found at i:1346959 original size:21 final size:25
Alignment explanation
Indices: 1346909--1346960 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 25
1346899 AATTACCACG
1346909 TTTAATTATTAATATTCAAATAACT
1 TTTAATTATTAATATTCAAATAACT
*
1346934 TTTAATT-TT-ATA-TCAAATTA-T
1 TTTAATTATTAATATTCAAATAACT
1346955 TTTAAT
1 TTTAAT
1346961 ATAAATTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 7 0.27
22 7 0.27
23 3 0.12
24 2 0.08
25 7 0.27
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTAATTATTAATATTCAAATAACT
Found at i:1347502 original size:11 final size:11
Alignment explanation
Indices: 1347474--1347509 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1347464 AATTTTTATA
*
1347474 TATTTATATAT
1 TATTTATAAAT
1347485 TATTTTATAAAT
1 TA-TTTATAAAT
1347497 TATTTATAAAT
1 TATTTATAAAT
1347508 TA
1 TA
1347510 AGTATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTTATAAAT
Found at i:1347910 original size:21 final size:20
Alignment explanation
Indices: 1347885--1347942 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
1347875 ATTATTTTAC
1347885 ATATAATTATAGTATATAAAA
1 ATATAATTATA-TATATAAAA
* *
1347906 ATATAA-TATAAATATATAA
1 ATATAATTATATATATAAAA
*
1347925 ATTTAATTA-ATATATAAA
1 ATATAATTATATATATAAA
1347943 TTAAAATCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 19 0.61
20 6 0.19
21 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
ATATAATTATATATATAAAA
Found at i:1348218 original size:17 final size:18
Alignment explanation
Indices: 1348196--1348239 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1348186 TATATAATAT
*
1348196 TTATATTTAA-GATTTTA
1 TTATATTTAATAATTTTA
*
1348213 TTATATTTAATAATTTTG
1 TTATATTTAATAATTTTA
1348231 TTATATTTA
1 TTATATTTA
1348240 TATTTGTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
TTATATTTAATAATTTTA
Found at i:1349495 original size:7 final size:6
Alignment explanation
Indices: 1349476--1349512 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
1349466 TGAGTTTAGA
*
1349476 TAAAAT TAAATT TAAAATT TAAATT TAAATT TAAATT
1 TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT
1349513 ATTATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:1349555 original size:12 final size:12
Alignment explanation
Indices: 1349476--1349567 Score: 53
Period size: 12 Copynumber: 7.5 Consensus size: 12
1349466 TGAGTTTAGA
*
1349476 TAAAATTAAATT
1 TAAAATTTAATT
1349488 TAAAATTTAAATT
1 TAAAATTT-AATT
*
1349501 T-AAATTTAAAT
1 TAAAATTTAATT
* * *
1349512 TATTATTTTAATA
1 TA-AAATTTAATT
* *
1349525 AAAATATTTTTATT
1 TAAA-A-TTTAATT
1349539 T-AAATTTAATT
1 TAAAATTTAATT
* *
1349550 TAAAATATAATA
1 TAAAATTTAATT
1349562 TAAAAT
1 TAAAAT
1349568 AATATTTATA
Statistics
Matches: 59, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
11 11 0.19
12 29 0.49
13 14 0.24
14 5 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAAATTTAATT
Found at i:1349797 original size:19 final size:19
Alignment explanation
Indices: 1349760--1349797 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1349750 TTAAGTTAAT
*
1349760 TTAAATTATTAATTATTTA
1 TTAAATTATTAAATATTTA
1349779 TTAAATTATTTAAAT-TTTA
1 TTAAATTA-TTAAATATTTA
1349798 ATATAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTAAATTATTAAATATTTA
Found at i:1352768 original size:3 final size:3
Alignment explanation
Indices: 1352760--1352798 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1352750 GACCTTTACC
1352760 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1352799 TTTACTTTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1361380 original size:12 final size:12
Alignment explanation
Indices: 1361363--1361392 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1361353 TTCTTACTGC
1361363 TTGGCTGGCTGG
1 TTGGCTGGCTGG
1361375 TTGGCTGGCTGG
1 TTGGCTGGCTGG
*
1361387 CTGGCT
1 TTGGCT
1361393 CCTTTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.20, G:0.47, T:0.33
Consensus pattern (12 bp):
TTGGCTGGCTGG
Found at i:1365065 original size:3 final size:3
Alignment explanation
Indices: 1365057--1365082 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1365047 CAACAAACAT
1365057 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
1365083 GAGAGAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1365617 original size:6 final size:6
Alignment explanation
Indices: 1365600--1365633 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1365590 TGCTACGAAC
*
1365600 TCTTTT TTTTTT TC-TTT TCTTTT TCTTTT TCTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTT
1365634 CTGTTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TCTTTT
Found at i:1365622 original size:17 final size:17
Alignment explanation
Indices: 1365600--1365633 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1365590 TGCTACGAAC
*
1365600 TCTTTTTTTTTTTCTTT
1 TCTTTTTCTTTTTCTTT
1365617 TCTTTTTCTTTTTCTTT
1 TCTTTTTCTTTTTCTTT
1365634 CTGTTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TCTTTTTCTTTTTCTTT
Found at i:1365634 original size:21 final size:21
Alignment explanation
Indices: 1365604--1365643 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1365594 ACGAACTCTT
* *
1365604 TTTTTTTTTCTTTTCTTTTTC
1 TTTTTCTTTCTGTTCTTTTTC
1365625 TTTTTCTTTCTGTTCTTTT
1 TTTTTCTTTCTGTTCTTTT
1365644 ACCTTAGACC
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:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (21 bp):
TTTTTCTTTCTGTTCTTTTTC
Found at i:1366196 original size:17 final size:18
Alignment explanation
Indices: 1366176--1366209 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1366166 CATTAAATAC
1366176 AAAAATTTTAA-AAAAAT
1 AAAAATTTTAATAAAAAT
1366193 AAAAATTTTAATAAAAA
1 AAAAATTTTAATAAAAA
1366210 AGAATTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATTTTAATAAAAAT
Found at i:1367781 original size:7 final size:7
Alignment explanation
Indices: 1367759--1367793 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
1367749 TGCAAATGCT
1367759 AATTTAAA
1 AATTT-AA
*
1367767 AATATAA
1 AATTTAA
1367774 AATTTAA
1 AATTTAA
1367781 AATTTAA
1 AATTTAA
1367788 AATTTA
1 AATTTA
1367794 TTAAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AATTTAA
Found at i:1368611 original size:20 final size:21
Alignment explanation
Indices: 1368561--1368622 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
1368551 AATATTTTTG
1368561 ATATAAATATTTTTAAT-T-TT
1 ATATAAAT-TTTTTAATATATT
* *
1368581 ATTTAATTTTTTTAATATATT
1 ATATAAATTTTTTAATATATT
**
1368602 -TATAAATTTTAAAATATATT
1 ATATAAATTTTTTAATATATT
1368622 A
1 A
1368623 AATATGGATA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
19 8 0.24
20 23 0.70
21 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATAAATTTTTTAATATATT
Found at i:1372571 original size:26 final size:26
Alignment explanation
Indices: 1372529--1372580 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1372519 TTAATATGTT
1372529 TAAATAATTTTATTAATT-TAATATAA
1 TAAATAATTTTATTAATTAT-ATATAA
1372555 TAAATAAGTTTTA-TAATTATATATAA
1 TAAATAA-TTTTATTAATTATATATAA
1372581 AATTATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TAAATAATTTTATTAATTATATATAA
Found at i:1372626 original size:18 final size:18
Alignment explanation
Indices: 1372570--1372630 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
1372560 AAGTTTTATA
*
1372570 ATTATATATAAAATTATTT
1 ATTA-ATATTAAATTATTT
*
1372589 AAT-ATATTATAATT-TTT
1 ATTAATATTA-AATTATTT
*
1372606 ATTAATTTTAAATTATTT
1 ATTAATATTAAATTATTT
1372624 ATTAATA
1 ATTAATA
1372631 AAATCATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 14 0.41
18 18 0.53
19 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTAATATTAAATTATTT
Found at i:1375662 original size:61 final size:61
Alignment explanation
Indices: 1375564--1375697 Score: 142
Period size: 61 Copynumber: 2.2 Consensus size: 61
1375554 AAGGTCAAGG
* * * *
1375564 CCTTTGGGAAAGAGTAGTGTAATGTGTTAAGCCTTTGGAAAGATGAAATAATCTATATGGA
1 CCTTTGGGAAAGAGTAGCGTAATGTCTTAAGCCTTTGGAAAGACGAAATAATCAATATGGA
* * * ** * * *
1375625 CCTTTGGGAAGGTGTAGCGTAATGTCTTGAGTTTTTGGGAAGGCGAGATAATCAATATGGA
1 CCTTTGGGAAAGAGTAGCGTAATGTCTTAAGCCTTTGGAAAGACGAAATAATCAATATGGA
* *
1375686 TCTTTTGGAAAG
1 CCTTTGGGAAAG
1375698 TCAAGCCTTC
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.30, C:0.09, G:0.29, T:0.32
Consensus pattern (61 bp):
CCTTTGGGAAAGAGTAGCGTAATGTCTTAAGCCTTTGGAAAGACGAAATAATCAATATGGA
Found at i:1375861 original size:40 final size:38
Alignment explanation
Indices: 1375807--1375901 Score: 118
Period size: 39 Copynumber: 2.4 Consensus size: 38
1375797 ATAATAGTCT
* *
1375807 CAAGCCTTTGTCATCGACAAGATAATAATTTTGAATTCG
1 CAAGCCTTTGTCATCAACAAGATAATAA-TTTAAATTCG
** *
1375846 CAAGCCTTTTGTCATCAATGAGATAATAATTTAAATTCT
1 CAAGCC-TTTGTCATCAACAAGATAATAATTTAAATTCG
*
1375885 CAAGTCTTTGTCATCAA
1 CAAGCCTTTGTCATCAA
1375902 TGAAAAAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
38 11 0.22
39 19 0.39
40 19 0.39
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36
Consensus pattern (38 bp):
CAAGCCTTTGTCATCAACAAGATAATAATTTAAATTCG
Found at i:1375883 original size:39 final size:38
Alignment explanation
Indices: 1375807--1375915 Score: 128
Period size: 38 Copynumber: 2.8 Consensus size: 38
1375797 ATAATAGTCT
* ** *
1375807 CAAGCCTTTGTCATCGACAAGATAATAATTTTGAATTCG
1 CAAGCCTTTGTCATCAATGAGATAATAA-TTTAAATTCG
*
1375846 CAAGCCTTTTGTCATCAATGAGATAATAATTTAAATTCT
1 CAAGCC-TTTGTCATCAATGAGATAATAATTTAAATTCG
* * *
1375885 CAAGTCTTTGTCATCAATGAAAAAATAATTT
1 CAAGCCTTTGTCATCAATGAGATAATAATTT
1375916 TTAAATTTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
38 23 0.38
39 19 0.31
40 19 0.31
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (38 bp):
CAAGCCTTTGTCATCAATGAGATAATAATTTAAATTCG
Found at i:1375902 original size:38 final size:38
Alignment explanation
Indices: 1375804--1375934 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 38
1375794 GGCATAATAG
* ** *
1375804 TCTCAAGCCTTTGTCATCGACAAGATAATAATTTTGAAT
1 TCTCAAGCCTTTGTCATCAATGAGATAATAA-TTTAAAT
*
1375843 TCGCAAGCCTTTTGTCATCAATGAGATAATAATTTAAAT
1 TCTCAAGCC-TTTGTCATCAATGAGATAATAATTTAAAT
* * *
1375882 TCTCAAGTCTTTGTCATCAATGAAAAAATAATTTTTAAAT
1 TCTCAAGCCTTTGTCATCAATGAGATAATAA--TTTAAAT
* *
1375922 TTTCAGGCCTTTG
1 TCTCAAGCCTTTG
1375935 CTGTAAACGA
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
38 20 0.26
39 21 0.27
40 36 0.47
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (38 bp):
TCTCAAGCCTTTGTCATCAATGAGATAATAATTTAAAT
Found at i:1376391 original size:77 final size:77
Alignment explanation
Indices: 1376137--1376398 Score: 289
Period size: 78 Copynumber: 3.4 Consensus size: 77
1376127 GAGATATTAG
* * * * *
1376137 GATGATTCTTGACAA-CGTGTTGGCTACATAATGCTTTAGAAACCTTTTTGGCTAGATGATCCTT
1 GATGATTCTTGAAAAGCCTTTTGGCTAGATAATGCCTTAGAAACCTTTTTGGCTAGATGATCCTT
1376201 GCATCT-ATGTTGA
66 G-AT-TAATGTTGA
** * *
1376214 GATTCTTCTT-AAAGAGCCTTTTGGCTAGATGATGTCTTAGAAACCTTTTTGGCTAGATGATCCT
1 GATGATTCTTGAAA-AGCCTTTTGGCTAGATAATGCCTTAGAAACCTTTTTGGCTAGATGATCCT
* *
1376278 TGAATATATATTGA
65 TGATTA-ATGTTGA
* * * ** *
1376292 GATGATTCTTAAAAAACCTTTTGGCTAGATAATGCCTTAGAAACATTTTTGTTTAGA-AATCCTT
1 GATGATTCTTGAAAAGCCTTTTGGCTAGATAATGCCTTAGAAACCTTTTTGGCTAGATGATCCTT
1376356 GATTAGATGTTGA
66 GATTA-ATGTTGA
*
1376369 GATGATTCTTGAAAAGCCTTTTGTCTAGAT
1 GATGATTCTTGAAAAGCCTTTTGGCTAGAT
1376399 GATCCTTGAA
Statistics
Matches: 154, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
76 3 0.02
77 53 0.34
78 95 0.62
79 3 0.02
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (77 bp):
GATGATTCTTGAAAAGCCTTTTGGCTAGATAATGCCTTAGAAACCTTTTTGGCTAGATGATCCTT
GATTAATGTTGA
Done.