Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold498
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: 1804022
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
File 13 of 17
Found at i:1270114 original size:15 final size:15
Alignment explanation
Indices: 1270094--1270143 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
1270084 AAATATTTTA
1270094 AAATTTATATAATAT
1 AAATTTATATAATAT
* *
1270109 AAATTTTTAAAATATT
1 AAATTTATATAATA-T
*
1270125 TAATTTATATAAATAT
1 AAATTTATAT-AATAT
1270141 AAA
1 AAA
1270144 ATATTTTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 12 0.44
16 11 0.41
17 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATTTATATAATAT
Found at i:1272108 original size:29 final size:26
Alignment explanation
Indices: 1272045--1272108 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 26
1272035 AAATTCAATG
1272045 TAAATTTTAATTTTTTTTATATTAAAA
1 TAAA-TTTAATTTTTTTTATATTAAAA
1272072 TAAA-TTAATTTACTTTTTATATTAGTAAA
1 TAAATTTAATTT--TTTTTATATTA--AAA
1272101 -AAATTTAA
1 TAAATTTAA
1272109 AATTTTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
25 7 0.22
27 15 0.47
28 3 0.09
29 7 0.22
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (26 bp):
TAAATTTAATTTTTTTTATATTAAAA
Found at i:1272210 original size:18 final size:20
Alignment explanation
Indices: 1272175--1272214 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
1272165 TCAATTTAAG
*
1272175 AAATTATTTTATTGAAATTA
1 AAATTATTTTAATGAAATTA
1272195 AAATT-TTTTAAT-AAATTA
1 AAATTATTTTAATGAAATTA
1272213 AA
1 AA
1272215 TAAATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 6 0.32
20 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
AAATTATTTTAATGAAATTA
Found at i:1272222 original size:19 final size:19
Alignment explanation
Indices: 1272200--1272246 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
1272190 AATTAAAATT
* *
1272200 TTTTAATAAATTAAATAAA
1 TTTTAATAAATAAAAAAAA
*
1272219 TTTT-ATTAATAAAAAAAA
1 TTTTAATAAATAAAAAAAA
1272237 TTATTAATAA
1 TT-TTAATAA
1272247 TGATAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 13 0.59
19 6 0.27
20 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTAATAAATAAAAAAAA
Found at i:1272237 original size:22 final size:21
Alignment explanation
Indices: 1272195--1272237 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1272185 ATTGAAATTA
**
1272195 AAATTTTTTAATAAATTAAAT
1 AAATTTTTTAATAAAAAAAAT
1272216 AAATTTTATTAATAAAAAAAAT
1 AAATTTT-TTAATAAAAAAAAT
1272238 TATTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTTTTTAATAAAAAAAAT
Found at i:1273667 original size:38 final size:38
Alignment explanation
Indices: 1273625--1273736 Score: 116
Period size: 38 Copynumber: 3.1 Consensus size: 38
1273615 TAAAATTCTC
1273625 TAATCG-TAAATCACCA-TCTAATTTTAAATTAAATTTTT
1 TAATCGAT-AATCACCAGT-TAATTTTAAATTAAATTTTT
* *
1273663 TAATCGATAATTATCAGTTAATTTTAAATTAAATTTTT
1 TAATCGATAATCACCAGTTAATTTTAAATTAAATTTTT
*
1273701 TAA-CCAT-A--A--A-TTAATTTTAAATTAAATTTTT
1 TAATCGATAATCACCAGTTAATTTTAAATTAAATTTTT
1273732 TAATC
1 TAATC
1273737 ATCGATTAAT
Statistics
Matches: 68, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
31 24 0.35
32 2 0.03
34 1 0.01
36 1 0.01
37 3 0.04
38 35 0.51
39 2 0.03
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (38 bp):
TAATCGATAATCACCAGTTAATTTTAAATTAAATTTTT
Found at i:1273756 original size:30 final size:31
Alignment explanation
Indices: 1273680--1273759 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
1273670 TAATTATCAG
*
1273680 TTAATTTTAAATTAAATTTTTTAACCATAAA
1 TTAATTTCAAATTAAATTTTTTAACCATAAA
* * **
1273711 TTAATTTTAAATTAAATTTTTTAATCATCGA
1 TTAATTTCAAATTAAATTTTTTAACCATAAA
*
1273742 TTAA-TTCAATTTAAATTT
1 TTAATTTCAAATTAAATTT
1273760 AATTTGGCTC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 12 0.27
31 32 0.73
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.51
Consensus pattern (31 bp):
TTAATTTCAAATTAAATTTTTTAACCATAAA
Found at i:1274208 original size:7 final size:7
Alignment explanation
Indices: 1274196--1274225 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1274186 AATTCTATTC
1274196 AAAATTT
1 AAAATTT
1274203 AAAATTT
1 AAAATTT
1274210 AAAATTT
1 AAAATTT
1274217 AAAATTT
1 AAAATTT
1274224 AA
1 AA
1274226 TTTAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAAATTT
Found at i:1274343 original size:13 final size:13
Alignment explanation
Indices: 1274325--1274358 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
1274315 ATAAAAAATT
1274325 AATTTAATTTTTA
1 AATTTAATTTTTA
1274338 AATTTAA-TTTTA
1 AATTTAATTTTTA
1274350 AATTTAATT
1 AATTTAATT
1274359 ATTTGTACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AATTTAATTTTTA
Found at i:1275133 original size:21 final size:22
Alignment explanation
Indices: 1275101--1275150 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
1275091 TTTATTTATA
*
1275101 TTATA-ATCTTATTTA-AATATT
1 TTATATATCTTATATATAA-ATT
1275122 TTATATAT-TTATATATAAATT
1 TTATATATCTTATATATAAATT
*
1275143 TAATATAT
1 TTATATAT
1275151 ACATAGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATATATCTTATATATAAATT
Found at i:1275439 original size:16 final size:16
Alignment explanation
Indices: 1275396--1275449 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1275386 GAAAATCGAT
1275396 TAATTTAAACTTAAAAA
1 TAATTTAAACTT-AAAA
* **
1275413 TGATTCGAACTTAAAA
1 TAATTTAAACTTAAAA
* *
1275429 TAATTTAAACTCAAAT
1 TAATTTAAACTTAAAA
1275445 TAATT
1 TAATT
1275450 AAAATAATTA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 20 0.69
17 9 0.31
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (16 bp):
TAATTTAAACTTAAAA
Found at i:1275460 original size:13 final size:14
Alignment explanation
Indices: 1275442--1275486 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 14
1275432 TTTAAACTCA
1275442 AATTAA-TTAAAAT
1 AATTAATTTAAAAT
1275455 AATTAATTTAAAAT
1 AATTAATTTAAAAT
*
1275469 AACTCGAATTTAAAAT
1 AA-T-TAATTTAAAAT
1275485 AA
1 AA
1275487 ATAAATTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 6 0.21
14 9 0.32
15 1 0.04
16 12 0.43
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (14 bp):
AATTAATTTAAAAT
Found at i:1275589 original size:16 final size:15
Alignment explanation
Indices: 1275570--1275648 Score: 52
Period size: 16 Copynumber: 5.0 Consensus size: 15
1275560 ATGAATTCAT
1275570 AATAATTTAAAATCAA
1 AATAATTTAAAAT-AA
*
1275586 AATAATTAAAAAATAA
1 AATAATT-TAAAATAA
* *
1275602 AATAACTTAAACTTAAA
1 AATAATTTAAA-AT-AA
* **
1275619 AATAATCTGAAAATTT
1 AATAAT-TTAAAATAA
1275635 AA-AATTTAAAATAA
1 AATAATTTAAAATAA
1275649 CTAAACTCAA
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
14 6 0.13
15 6 0.13
16 18 0.38
17 13 0.28
18 4 0.09
ACGTcount: A:0.63, C:0.05, G:0.01, T:0.30
Consensus pattern (15 bp):
AATAATTTAAAATAA
Found at i:1275611 original size:17 final size:17
Alignment explanation
Indices: 1275578--1275612 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1275568 ATAATAATTT
1275578 AAAATCAAAATAATTAA
1 AAAATCAAAATAATTAA
1275595 AAAAT-AAAATAACTTAA
1 AAAATCAAAATAA-TTAA
1275612 A
1 A
1275613 CTTAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAATCAAAATAATTAA
Found at i:1275892 original size:32 final size:32
Alignment explanation
Indices: 1275852--1275933 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 32
1275842 TGTTATTATT
*
1275852 ATAAATTTAATGAATATTAAATAAAATTACTCG
1 ATAAATTTAATAAATATTAAATAAAATTACT-G
*
1275885 -TAAATTTAATAAATATTAAATATAATTACTG
1 ATAAATTTAATAAATATTAAATAAAATTACTG
*
1275916 ATAAATTTAATAATTATT
1 ATAAATTTAATAAATATT
1275934 TAAAATATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.02
32 44 0.98
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (32 bp):
ATAAATTTAATAAATATTAAATAAAATTACTG
Found at i:1276826 original size:2 final size:2
Alignment explanation
Indices: 1276808--1276841 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1276798 CAGATGGTTT
* *
1276808 TA TA TA TT TA TA CA 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 TA
1276842 GTTTTGAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1277981 original size:50 final size:50
Alignment explanation
Indices: 1277823--1277982 Score: 196
Period size: 50 Copynumber: 3.2 Consensus size: 50
1277813 AGTTGCTTAG
* * *
1277823 AGTCAACAATTACGGTCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAAT
1 AGTCAATAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * * * * *
1277873 AGTCAACAATTAC-GACTACCTCTCTTGATTATCAAAAGTTAGTGAAGAAT
1 AGTCAATAATTACGGTC-ACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* *
1277923 AGTCAATAATTACGGTCGCCTCTCTCGATTGTTAAAGGTTGGTGAAGAAT
1 AGTCAATAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
*
1277973 AGTTAATAAT
1 AGTCAATAAT
1277983 GGCAATACCT
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 88 0.96
51 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (50 bp):
AGTCAATAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:1282367 original size:50 final size:50
Alignment explanation
Indices: 1282308--1282467 Score: 266
Period size: 50 Copynumber: 3.2 Consensus size: 50
1282298 AGTTGTTTAG
* **
1282308 AGTCAACAATTACGGCCACCTCTCTTTATTATCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCAATTATCAAAGGTTGGTGAAGAAT
*
1282358 AGTCAACAATTACGACCACCTCTCTCAATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCAATTATCAAAGGTTGGTGAAGAAT
* *
1282408 AGTCAACAATTACGACCACCTCTCTCGATTTTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCAATTATCAAAGGTTGGTGAAGAAT
1282458 AGTCAACAAT
1 AGTCAACAAT
1282468 GGCAATACCT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 104 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (50 bp):
AGTCAACAATTACGACCACCTCTCTCAATTATCAAAGGTTGGTGAAGAAT
Found at i:1288695 original size:2 final size:2
Alignment explanation
Indices: 1288688--1288728 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1288678 TAAAAGTAAG
* * *
1288688 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1288729 GTCTTATAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1294377 original size:2 final size:2
Alignment explanation
Indices: 1294372--1294413 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1294362 TACGTGTGTG
1294372 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
1294414 ATTTTAACTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1295106 original size:10 final size:10
Alignment explanation
Indices: 1295078--1295276 Score: 79
Period size: 9 Copynumber: 19.9 Consensus size: 10
1295068 TTTTAAAATC
*
1295078 TAAATATT-G
1 TAAATATTAT
1295087 TAAATATTAT
1 TAAATATTAT
1295097 TAAATGTTATTAT
1 TAAA---TATTAT
*
1295110 TAATATTTTAT
1 TAA-ATATTAT
*
1295121 GTAATATATCAT
1 -TAA-ATATTAT
1295133 TAAATATTA-
1 TAAATATTAT
1295142 TAAATATAAATAT
1 TAAATAT---TAT
*
1295155 TAAA-ATAATT
1 TAAATATTA-T
1295165 TAATATATTAT
1 TAA-ATATTAT
* *
1295176 GAAGTGTTATTAT
1 TAA---ATATTAT
1295189 TAAAATATT-T
1 T-AAATATTAT
1295199 TAATATATTA-
1 TAA-ATATTAT
1295209 TAAATATTAT
1 TAAATATTAT
*
1295219 T--ATTTTAT
1 TAAATATTAT
1295227 T-AA-A-TA-
1 TAAATATTAT
1295233 TAAATATTAT
1 TAAATATTAT
1295243 TAAAT-TTA-
1 TAAATATTAT
1295251 T--ATATTAT
1 TAAATATTAT
1295259 TAAATATTAT
1 TAAATATTAT
1295269 T-AATATTA
1 TAAATATTA
1295277 AGTATATTAT
Statistics
Matches: 148, Mismatches: 14, Indels: 56
0.68 0.06 0.26
Matches are distributed among these distances:
6 3 0.02
7 7 0.05
8 10 0.07
9 37 0.25
10 37 0.25
11 16 0.11
12 16 0.11
13 19 0.13
14 3 0.02
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.50
Consensus pattern (10 bp):
TAAATATTAT
Found at i:1295169 original size:43 final size:43
Alignment explanation
Indices: 1295122--1295316 Score: 138
Period size: 43 Copynumber: 4.6 Consensus size: 43
1295112 ATATTTTATG
* *
1295122 TAATATATCATTAAATATTATAAATATAAATATTAAAATAATT
1 TAATATATTATTAAATATTATAAATATAAATATTATAATAATT
* * * * * *
1295165 TAATATATTATGAAGTGTTATTATTA-AAATATTTTAATATATT
1 TAATATATTATTAAATATTATAAATATAAATATTATAATA-ATT
* *
1295208 ATAA-ATATTATT--ATTTTATTAAATATAAATATTATTA-AATT
1 -TAATATATTATTAAATATTA-TAAATATAAATATTATAATAATT
* *
1295249 T-ATATATTATTAAATATTATTAATATTAAGTATATTATCAATCA-T
1 TAATATATTATTAAATATTATAAATA-TAA--ATATTAT-AATAATT
* *
1295294 TATTATATT-TTTAATATTA-AAAT
1 TAATATATTATTAAATATTATAAAT
1295317 TTTTAAACAT
Statistics
Matches: 117, Mismatches: 22, Indels: 25
0.71 0.13 0.15
Matches are distributed among these distances:
39 1 0.01
40 9 0.08
41 12 0.10
42 24 0.21
43 39 0.33
44 13 0.11
45 12 0.10
46 7 0.06
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (43 bp):
TAATATATTATTAAATATTATAAATATAAATATTATAATAATT
Found at i:1295175 original size:79 final size:81
Alignment explanation
Indices: 1295090--1295270 Score: 201
Period size: 83 Copynumber: 2.2 Consensus size: 81
1295080 AATATTGTAA
* *
1295090 ATATTATTAAATGTTATTATT-AATATTTT-ATGTA-ATATATCATTA-AATATTA-TAAATATA
1 ATATTATTAAATGTTATTATTAAATATTTTAATATATATAAAT-ATTATAATATTATTAAATATA
1295150 AATATTAAAATAATTTAAT
65 AATATTAAAA-AATTT-AT
* * * *
1295169 ATATTATGAAGTGTTATTATTAAAATATTTTAATATATTATAAATATTATTATTTTATTAAATAT
1 ATATTATTAAATGTTATTATT-AAATATTTTAATATA-TATAAATATTATAATATTATTAAATAT
**
1295234 AAATATTATTAAATTTAT
64 AAATATTAAAAAATTTAT
*
1295252 ATATTATTAAATATTATTA
1 ATATTATTAAATGTTATTA
1295271 ATATTAAGTA
Statistics
Matches: 84, Mismatches: 11, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
79 19 0.23
81 8 0.10
82 4 0.05
83 22 0.26
84 15 0.18
85 16 0.19
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (81 bp):
ATATTATTAAATGTTATTATTAAATATTTTAATATATATAAATATTATAATATTATTAAATATAA
ATATTAAAAAATTTAT
Found at i:1295195 original size:34 final size:33
Alignment explanation
Indices: 1295132--1295222 Score: 121
Period size: 34 Copynumber: 2.8 Consensus size: 33
1295122 TAATATATCA
* *
1295132 TTAA-ATATTATAAATATAAATATTAAAATAAT
1 TTAATATATTATAAATATTATTATTAAAATAAT
* * *
1295164 TTAATATATTATGAAGTGTTATTATTAAAATATT
1 TTAATATATTAT-AAATATTATTATTAAAATAAT
1295198 TTAATATATTATAAATATTATTATT
1 TTAATATATTATAAATATTATTATT
1295223 TTATTAAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
32 4 0.08
33 18 0.36
34 28 0.56
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (33 bp):
TTAATATATTATAAATATTATTATTAAAATAAT
Found at i:1295223 original size:25 final size:25
Alignment explanation
Indices: 1295194--1295299 Score: 108
Period size: 24 Copynumber: 4.1 Consensus size: 25
1295184 ATTATTAAAA
1295194 TATTTTAATATATTATAAATATTAT
1 TATTTTAATATATTATAAATATTAT
* *
1295219 TATTTTATTA-AATATAAATATTAT
1 TATTTTAATATATTATAAATATTAT
*
1295243 TAAATTT-ATATATTATTAAATATTAT
1 T-ATTTTAATATATTA-TAAATATTAT
* *
1295269 TAATATTAAGTATATTATCAATCATTAT
1 T-ATTTTAA-TATATTATAAAT-ATTAT
1295297 TAT
1 TAT
1295300 ATTTTTAATA
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
24 16 0.24
25 16 0.24
26 15 0.22
27 7 0.10
28 13 0.19
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (25 bp):
TATTTTAATATATTATAAATATTAT
Found at i:1295263 original size:32 final size:33
Alignment explanation
Indices: 1295203--1295265 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
1295193 ATATTTTAAT
*
1295203 ATATTATAAATATTATTATTTTATTAAATATAA
1 ATATTATAAATATTATTATATTATTAAATATAA
1295236 ATATTATTAAAT-TTA-TATATTATTAAATAT
1 ATATTA-TAAATATTATTATATTATTAAATAT
1295266 TATTAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.50
33 9 0.32
34 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
ATATTATAAATATTATTATATTATTAAATATAA
Found at i:1295275 original size:16 final size:16
Alignment explanation
Indices: 1295209--1295314 Score: 70
Period size: 16 Copynumber: 6.2 Consensus size: 16
1295199 TAATATATTA
*
1295209 TAAATATTATTATTTTAT
1 TAAATATTATTA--ATAT
* * *
1295227 TAAATATAAATATTAT
1 TAAATATTATTAATAT
*
1295243 TAAAT-TTATATATTAT
1 TAAATATTAT-TAATAT
1295259 TAAATATTATTAATAT
1 TAAATATTATTAATAT
*
1295275 TAAGTATATTATCAATCAT
1 TAA--ATATTATTAAT-AT
* *
1295294 TATTATATTTTTAATAT
1 TA-AATATTATTAATAT
1295311 TAAA
1 TAAA
1295315 ATTTTTAAAC
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
15 2 0.03
16 29 0.40
17 8 0.11
18 29 0.40
19 4 0.06
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (16 bp):
TAAATATTATTAATAT
Found at i:1295285 original size:18 final size:18
Alignment explanation
Indices: 1295262--1295313 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
1295252 ATATTATTAA
1295262 ATATTATTAATATTAAGT
1 ATATTATTAATATTAAGT
* *
1295280 ATATTATCAATCATT-ATT
1 ATATTATTAAT-ATTAAGT
*
1295298 ATATTTTTAATATTAA
1 ATATTATTAATATTAA
1295314 AATTTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 3 0.11
18 22 0.79
19 3 0.11
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (18 bp):
ATATTATTAATATTAAGT
Found at i:1295297 original size:111 final size:112
Alignment explanation
Indices: 1295079--1295299 Score: 240
Period size: 111 Copynumber: 2.0 Consensus size: 112
1295069 TTTAAAATCT
* ** *
1295079 AAATATTGTAAATATTATTAAATGTTATTATTAATATTTTATGTAATATATCATTAAATATTATA
1 AAATATTGTAAATATTATTAAATATTATTATTAATATTAAATATAATATATCATTAAATATTATA
* *
1295144 AATATAAATATTAAAATAATTTAATATATTATGAAGTGTTATTATTA
66 AATATAAATATTAAAATAATTTAATATATTATCAAGTATTATTATTA
* * *
1295191 AAATATTTTAATATATTA-TAAATATTATTATT-TTATTAAATATAA-ATATTATTAAAT-TTAT
1 AAATATTGTAA-ATATTATTAAATATTATTATTAATATTAAATATAATATATCATTAAATATTAT
* *
1295252 ATATTATTAAATATT--ATTAATATTAAGTATATTATCAA-TCATTATTAT
65 A-AATA-TAAATATTAAAATAAT-TTAA-TATATTATCAAGT-ATTATTAT
1295300 ATTTTTAATA
Statistics
Matches: 92, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
109 10 0.11
110 19 0.21
111 34 0.37
112 23 0.25
113 6 0.07
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (112 bp):
AAATATTGTAAATATTATTAAATATTATTATTAATATTAAATATAATATATCATTAAATATTATA
AATATAAATATTAAAATAATTTAATATATTATCAAGTATTATTATTA
Found at i:1295337 original size:33 final size:35
Alignment explanation
Indices: 1295254--1295337 Score: 91
Period size: 33 Copynumber: 2.4 Consensus size: 35
1295244 AAATTTATAT
*
1295254 ATTATTAAATATTATTAATATTAAGTATATTATCAATC
1 ATTATTAAAT-TT-TTAATATTAAG-ATATTATCAAAC
* * *
1295292 ATTATTATATTTTTAATATTAA-A-ATTTTTAAAC
1 ATTATTAAATTTTTAATATTAAGATATTATCAAAC
1295325 ATTATTAAATTTT
1 ATTATTAAATTTT
1295338 AATTATTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
33 19 0.46
34 1 0.02
36 10 0.24
37 2 0.05
38 9 0.22
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (35 bp):
ATTATTAAATTTTTAATATTAAGATATTATCAAAC
Found at i:1295769 original size:19 final size:18
Alignment explanation
Indices: 1295736--1295772 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1295726 ATTTTTATTA
1295736 ATATTTTAATATATTTAT
1 ATATTTTAATATATTTAT
*
1295754 ATATTTATATTATATTTAT
1 ATATTT-TAATATATTTAT
1295773 GTTATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTTTAATATATTTAT
Found at i:1295788 original size:22 final size:20
Alignment explanation
Indices: 1295721--1295812 Score: 75
Period size: 20 Copynumber: 4.5 Consensus size: 20
1295711 AATACTAAAG
*
1295721 ATATCATTTTTATTAATATTT
1 ATATTATTTTTATT-ATATTT
* *
1295742 -TAATATATTTA-TATATTT
1 ATATTATTTTTATTATATTT
*
1295760 ATATTATATTTATGTTATATTT
1 ATATTAT-TTT-TATTATATTT
1295782 AGT-TTATTTTTATTATATTT
1 A-TATTATTTTTATTATATTT
1295802 -TAATTATTTTT
1 AT-ATTATTTTT
1295813 TAAGCTTGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
18 7 0.12
19 6 0.11
20 27 0.47
21 4 0.07
22 12 0.21
23 1 0.02
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (20 bp):
ATATTATTTTTATTATATTT
Found at i:1295802 original size:11 final size:11
Alignment explanation
Indices: 1295726--1295814 Score: 59
Period size: 11 Copynumber: 8.6 Consensus size: 11
1295716 TAAAGATATC
1295726 ATTTTTATTA-
1 ATTTTTATTAT
1295736 ATATTTTA--AT
1 AT-TTTTATTAT
*
1295746 ATATTTA-TAT
1 ATTTTTATTAT
*
1295756 ATTTATATTAT
1 ATTTTTATTAT
* *
1295767 ATTTATGTTAT
1 ATTTTTATTAT
1295778 A--TTTAGTT-T
1 ATTTTTA-TTAT
1295787 ATTTTTATTAT
1 ATTTTTATTAT
*
1295798 ATTTTAATTAT
1 ATTTTTATTAT
1295809 -TTTTTA
1 ATTTTTA
1295815 AGCTTGTGTT
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
9 9 0.14
10 20 0.32
11 34 0.54
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.66
Consensus pattern (11 bp):
ATTTTTATTAT
Found at i:1296030 original size:20 final size:20
Alignment explanation
Indices: 1296005--1296051 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1295995 CATAATTTTT
*
1296005 ATTTATTTAAAATATTATAA
1 ATTTATATAAAATATTATAA
* * *
1296025 ATTTATATAAATTTTTATAT
1 ATTTATATAAAATATTATAA
1296045 ATTTATA
1 ATTTATA
1296052 CTTCATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTATATAAAATATTATAA
Found at i:1308973 original size:22 final size:22
Alignment explanation
Indices: 1308923--1308973 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1308913 AAATTGAGAA
* *
1308923 ATGTATAAATTAATTATGATTC
1 ATGTATAAATTAATTAAGATAC
*
1308945 ATATATAAGATTAATTAAG-TAC
1 ATGTATAA-ATTAATTAAGATAC
1308967 ATGTATA
1 ATGTATA
1308974 GGTTACTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (22 bp):
ATGTATAAATTAATTAAGATAC
Found at i:1313458 original size:18 final size:18
Alignment explanation
Indices: 1313421--1313459 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1313411 ATTAATTTTA
*
1313421 AATTTTTATGTATTAGAT
1 AATTTTTATGTATTAAAT
1313439 AATTTTTAT-TATATAAAT
1 AATTTTTATGTAT-TAAAT
1313457 AAT
1 AAT
1313460 ACATATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
AATTTTTATGTATTAAAT
Found at i:1313538 original size:48 final size:48
Alignment explanation
Indices: 1313486--1313581 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
1313476 AGCATAAACA
*
1313486 TTAAAAGATATATTAAGTTATTTAAATTTTAGAATTTAATAAAAAATT
1 TTAAAAAATATATTAAGTTATTTAAATTTTAGAATTTAATAAAAAATT
1313534 TTAAAAAATATATTAAGTTATTTAAATTTTAGAATTTAATAAAAAATT
1 TTAAAAAATATATTAAGTTATTTAAATTTTAGAATTTAATAAAAAATT
1313582 AAATTATTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (48 bp):
TTAAAAAATATATTAAGTTATTTAAATTTTAGAATTTAATAAAAAATT
Found at i:1313845 original size:18 final size:18
Alignment explanation
Indices: 1313814--1313878 Score: 51
Period size: 20 Copynumber: 3.4 Consensus size: 18
1313804 TATTTAAGGT
1313814 ATATATTTATATAAATTTTA
1 ATATA-TTA-ATAAATTTTA
1313834 ATATATTAAT-AATTCTTA
1 ATATATTAATAAATT-TTA
* * *
1313852 TTATATAAATTAATATTTTT
1 ATATATTAA-TAA-ATTTTA
1313872 ATATATT
1 ATATATT
1313879 CATGTTTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
17 4 0.11
18 12 0.33
19 4 0.11
20 13 0.36
21 3 0.08
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATATTAATAAATTTTA
Found at i:1313902 original size:16 final size:17
Alignment explanation
Indices: 1313852--1313905 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 17
1313842 ATAATTCTTA
* *
1313852 TTATATAAATTAATATT
1 TTATATATATTCATATT
*
1313869 TT-TATATATTCATGTT
1 TTATATATATTCATATT
*
1313885 TTATTTATATT-ATATT
1 TTATATATATTCATATT
1313901 TTATA
1 TTATA
1313906 AAATATCATG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 21 0.70
17 9 0.30
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (17 bp):
TTATATATATTCATATT
Found at i:1317811 original size:19 final size:19
Alignment explanation
Indices: 1317779--1317824 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1317769 ATTATTTTAG
* *
1317779 ATATGATAATATAATTATAA
1 ATATAATAAAATAATTA-AA
1317799 AT-TAATAAAATAATTAAA
1 ATATAATAAAATAATTAAA
1317817 ATATAATA
1 ATATAATA
1317825 TGATATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.17
19 17 0.74
20 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
ATATAATAAAATAATTAAA
Found at i:1318019 original size:53 final size:53
Alignment explanation
Indices: 1317961--1318112 Score: 286
Period size: 53 Copynumber: 2.9 Consensus size: 53
1317951 AAAATTATTT
* *
1317961 AAGTATCATTGTATTTTTTTATATCGATAAGATCTTTTGAGAAGTTTCTTGTC
1 AAGTATCATTGTATTTTTTTATATCGATAAGATCTTTCGAGAAGTTTCTTATC
1318014 AAGTATCATTGTATTTTTTTATATCGATAAGATCTTTCGAGAAGTTTCTTATC
1 AAGTATCATTGTATTTTTTTATATCGATAAGATCTTTCGAGAAGTTTCTTATC
1318067 AAGTATCATTGTATTTTTTTATATCGATAAGATCTTTCGAGAAGTT
1 AAGTATCATTGTATTTTTTTATATCGATAAGATCTTTCGAGAAGTT
1318113 CCACCGTGCT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 97 1.00
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.47
Consensus pattern (53 bp):
AAGTATCATTGTATTTTTTTATATCGATAAGATCTTTCGAGAAGTTTCTTATC
Found at i:1318991 original size:3 final size:3
Alignment explanation
Indices: 1318985--1319032 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
1318975 ATAAGTATAG
* *
1318985 ATT ATT AGT GTT 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 ATT ATT ATT
1319033 TAATATCATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1320182 original size:4 final size:4
Alignment explanation
Indices: 1320173--1320204 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
1320163 AGATTCCACG
1320173 TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA
1320205 CAAATGCTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:1325825 original size:53 final size:53
Alignment explanation
Indices: 1325723--1325826 Score: 122
Period size: 53 Copynumber: 1.9 Consensus size: 53
1325713 TGATTTTCAC
* ***
1325723 TAATATATAAAAAAATTTTAAAAATTTGAGCATAACTTGTATCGTATATATGCA
1 TAATATATAAAAAAACTTTAAAAATTTGA-CATAACTTGTATAACATATATGCA
*
1325777 TAATATA-AAAAAAACTTTAAAAATTTGA-ATATATTTGTATTAACATATAT
1 TAATATATAAAAAAACTTTAAAAATTTGACATA-ACTTGTA-TAACATATAT
1325827 CCGTATTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
51 3 0.07
52 6 0.14
53 27 0.63
54 7 0.16
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.38
Consensus pattern (53 bp):
TAATATATAAAAAAACTTTAAAAATTTGACATAACTTGTATAACATATATGCA
Found at i:1327197 original size:2 final size:2
Alignment explanation
Indices: 1327190--1327214 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1327180 CTCATGTTTC
1327190 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 A
1327215 ACTTTCTACT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1328207 original size:20 final size:20
Alignment explanation
Indices: 1328182--1328230 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1328172 GAATCAAATT
*
1328182 TATTAATTAAAAAATTTAAA
1 TATTAAATAAAAAATTTAAA
* * *
1328202 TATTAAATAAATATTTTTAA
1 TATTAAATAAAAAATTTAAA
1328222 TATTAAATA
1 TATTAAATA
1328231 TTATAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTAAATAAAAAATTTAAA
Found at i:1328272 original size:19 final size:18
Alignment explanation
Indices: 1328230--1328273 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1328220 AATATTAAAT
*
1328230 ATTATAAATAATTAATAA
1 ATTATATATAATTAATAA
* *
1328248 AATATATATATTTAGATAA
1 ATTATATATAATTA-ATAA
1328267 ATTATAT
1 ATTATAT
1328274 GATCTGCAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTATATATAATTAATAA
Found at i:1333499 original size:28 final size:27
Alignment explanation
Indices: 1333451--1333527 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 27
1333441 TAAAATTTTT
* *
1333451 ATAAATAAA-AAATATTTTAAATAT-GA
1 ATAAATAAATAAAT-TATTAAATATAAA
*
1333477 GTATAATAAATAAATTATATAAATATAAA
1 ATA-AATAAATAAATTAT-TAAATATAAA
*
1333506 ATAAATACATAAATTATTAAAT
1 ATAAATAAATAAATTATTAAAT
1333528 CTACTCAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
26 2 0.05
27 13 0.31
28 24 0.57
29 3 0.07
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (27 bp):
ATAAATAAATAAATTATTAAATATAAA
Found at i:1333527 original size:20 final size:20
Alignment explanation
Indices: 1333483--1333527 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1333473 ATGAGTATAA
*
1333483 TAAATAAATTATATAAATAT
1 TAAATAAATTACATAAATAT
*
1333503 AAAATAAA-TACATAAATTAT
1 TAAATAAATTACATAAA-TAT
1333523 TAAAT
1 TAAAT
1333528 CTACTCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAATAAATTACATAAATAT
Found at i:1333916 original size:19 final size:19
Alignment explanation
Indices: 1333894--1333932 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1333884 TATATTTATT
*
1333894 TAAAT-TTAATTATAATATA
1 TAAATATTAA-TATAAAATA
1333913 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
1333932 T
1 T
1333933 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAATATTAATATAAAATA
Found at i:1334702 original size:18 final size:18
Alignment explanation
Indices: 1334659--1334720 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
1334649 TAATATTTTT
1334659 TATTAAAT-AATTTAAAA
1 TATTAAATAAATTTAAAA
*
1334676 -AAT-AA-AAATTTAAAA
1 TATTAAATAAATTTAAAA
1334691 TATTAAATAAATCTT--AA
1 TATTAAATAAAT-TTAAAA
1334708 TACTTAAATAAAT
1 TA-TTAAATAAAT
1334721 AAACACCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
15 11 0.30
16 4 0.11
17 6 0.16
18 14 0.38
19 2 0.05
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
TATTAAATAAATTTAAAA
Found at i:1338102 original size:17 final size:18
Alignment explanation
Indices: 1338056--1338108 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 18
1338046 AGTTTGCTAA
*
1338056 AAAAAAAGAAAGCAACTT
1 AAAAAAAGAAATCAACTT
*
1338074 AAAAGCAAAGAATTCAACTT
1 AAAA--AAAGAAATCAACTT
1338094 -AAAAAAGAAATCAAC
1 AAAAAAAGAAATCAAC
1338109 ATAGCTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 11 0.37
18 4 0.13
19 3 0.10
20 12 0.40
ACGTcount: A:0.64, C:0.13, G:0.09, T:0.13
Consensus pattern (18 bp):
AAAAAAAGAAATCAACTT
Found at i:1338631 original size:4 final size:4
Alignment explanation
Indices: 1338622--1338689 Score: 68
Period size: 4 Copynumber: 16.5 Consensus size: 4
1338612 ATTTAAAAAT
*
1338622 ATAA ATAA ATAA ATAA ATAA ATAA ATAA TATAA ATATA A-AA ATAT ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA -ATAA ATA-A ATAA ATAA ATAA
*
1338671 A-AA TATAT ATAA TATAA AT
1 ATAA -ATAA ATAA -ATAA AT
1338690 TATTAAATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
3 4 0.07
4 39 0.72
5 11 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (4 bp):
ATAA
Found at i:1338718 original size:33 final size:32
Alignment explanation
Indices: 1338628--1338726 Score: 85
Period size: 33 Copynumber: 3.0 Consensus size: 32
1338618 AAATATAAAT
* *
1338628 AAATAAATAAATAA-ATAAATAATATAAATATAA
1 AAATATATAAA-AATATAAA-AATATAAATATTA
*
1338661 AAATATATAAAAATATATATAATATAAATTATTA
1 AAATATATAAAAATATA-AAAATATAAA-TATTA
* *
1338695 AATTAT-TAAAATTTATAAAAATATAAAATATT
1 AAATATATAAAA-ATATAAAAATAT-AAATATT
1338727 TTAAAAATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
32 2 0.04
33 36 0.65
34 17 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (32 bp):
AAATATATAAAAATATAAAAATATAAATATTA
Found at i:1338719 original size:8 final size:8
Alignment explanation
Indices: 1338615--1338722 Score: 51
Period size: 8 Copynumber: 12.6 Consensus size: 8
1338605 ACGCTACATT
1338615 TAAAAATA
1 TAAAAATA
1338623 TAAATAA-A
1 TAAA-AATA
1338631 TAAATAA-A
1 TAAA-AATA
1338639 TAAATAAATAA
1 T-AA-AAAT-A
*
1338650 TATAAATA
1 TAAAAATA
1338658 TAAAAATATA
1 T-AAAA-ATA
1338668 TAAAAATA
1 TAAAAATA
*
1338676 TATATAATA
1 TA-AAAATA
*
1338685 T-AAATTA
1 TAAAAATA
* *
1338692 TTAAATTA
1 TAAAAATA
*
1338700 TTAAAATTTA
1 -TAAAA-ATA
1338710 TAAAAATA
1 TAAAAATA
1338718 TAAAA
1 TAAAA
1338723 TATTTTAAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
7 5 0.06
8 34 0.41
9 32 0.39
10 9 0.11
11 2 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
TAAAAATA
Found at i:1338835 original size:90 final size:81
Alignment explanation
Indices: 1338653--1338886 Score: 191
Period size: 90 Copynumber: 2.8 Consensus size: 81
1338643 TAAATAATAT
* *
1338653 AAATATAAAAATA-TATAAAAATATAT--ATAATATAAATTATTAAATTATTAAAATTT-ATAA-
1 AAATATAAAAATATTA-AAAAATATATAAATAAAATATATTATTAAATTATTAAAATTTAATAAT
1338713 AAATATAAAATATTTTA
65 AAATATAAAATATTTTA
1338730 AAA-ATAAATTTAATATGTAAAAAATATATAAATAAAATATATTATTAAATTATT-AAATTTAAT
1 AAATATAAA---AATAT-TAAAAAATATATAAATAAAATATATTATTAAATTATTAAAATTTAAT
1338793 AATAAATAATAAATTTATAATTTTA
62 AATAAAT-ATAAA---AT-ATTTTA
* * * *
1338818 AATACGTTATAAAAATATCATAAAAATA-ATTAAATATAATATA--ATAAAAATATTAAAATTTT
1 AA-A---TATAAAAATATTA-AAAAATATA-TAAATAAAATATATTATTAAATTATTAAAA-TTT
1338880 AATAATA
59 AATAATA
1338887 TAAATTATTA
Statistics
Matches: 128, Mismatches: 6, Indels: 33
0.77 0.04 0.20
Matches are distributed among these distances:
76 5 0.04
77 3 0.02
79 4 0.03
80 10 0.08
81 8 0.06
82 25 0.20
83 4 0.03
84 5 0.04
87 2 0.02
88 17 0.13
89 6 0.05
90 34 0.27
93 5 0.04
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (81 bp):
AAATATAAAAATATTAAAAAATATATAAATAAAATATATTATTAAATTATTAAAATTTAATAATA
AATATAAAATATTTTA
Found at i:1338986 original size:25 final size:23
Alignment explanation
Indices: 1338943--1338990 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1338933 AATCTACTCA
*
1338943 TTTAAAAAACTTTTAAATTAAAT
1 TTTAAAAAAATTTTAAATTAAAT
1338966 TTTAAAAAAATTTTATCAATTAAAT
1 TTTAAAAAAATTTTA--AATTAAAT
1338991 CAAACAGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.64
25 8 0.36
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTAAAAAAATTTTAAATTAAAT
Found at i:1339118 original size:13 final size:14
Alignment explanation
Indices: 1339077--1339124 Score: 64
Period size: 13 Copynumber: 3.5 Consensus size: 14
1339067 TCATAAATAA
1339077 AATTATATCA-TAT
1 AATTATATCATTAT
1339090 AATTATATCATATAT
1 AATTATATCAT-TAT
1339105 AATTATAT-ATTAT
1 AATTATATCATTAT
*
1339118 AAATATA
1 AATTATA
1339125 ATAAATGCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 19 0.59
14 2 0.06
15 11 0.34
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (14 bp):
AATTATATCATTAT
Found at i:1341651 original size:3 final size:3
Alignment explanation
Indices: 1341643--1341670 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1341633 ATTTTGTCCA
1341643 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1341671 TAATTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1341700 original size:12 final size:12
Alignment explanation
Indices: 1341670--1341708 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1341660 TTATTATTAT
1341670 TTAAT-TAAAAA
1 TTAATATAAAAA
*
1341681 TT-ATATAAATA
1 TTAATATAAAAA
1341692 TTAATATAAAAA
1 TTAATATAAAAA
1341704 TTAAT
1 TTAAT
1341709 TTTTAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 2 0.08
11 9 0.38
12 13 0.54
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TTAATATAAAAA
Found at i:1341747 original size:27 final size:27
Alignment explanation
Indices: 1341692--1341745 Score: 85
Period size: 25 Copynumber: 2.1 Consensus size: 27
1341682 TATATAAATA
1341692 TTAATATAAAAATTAATTTTTAATATT
1 TTAATATAAAAATTAATTTTTAATATT
*
1341719 TTAATAT-AAAA-TATTTTTTAATATT
1 TTAATATAAAAATTAATTTTTAATATT
1341744 TT
1 TT
1341746 TTTCAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 15 0.58
26 4 0.15
27 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTAATATAAAAATTAATTTTTAATATT
Found at i:1341988 original size:10 final size:10
Alignment explanation
Indices: 1341973--1342006 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
1341963 TTAAATTATT
1341973 ATTTAAAAAA
1 ATTTAAAAAA
1341983 ATTT-AAAAA
1 ATTTAAAAAA
1341992 ATTTAAAAAA
1 ATTTAAAAAA
1342002 TATTT
1 -ATTT
1342007 TTATATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 9 0.41
11 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATTTAAAAAA
Found at i:1344013 original size:21 final size:20
Alignment explanation
Indices: 1343987--1344031 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 20
1343977 TAGATTCGGT
1343987 ATAATTATATAATAT-TAAAAA
1 ATAATTA-A-AATATATAAAAA
1344008 ATAATTAAAATATAATAAAAA
1 ATAATTAAAATAT-ATAAAAA
1344029 ATA
1 ATA
1344032 TGATATGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.23
20 1 0.05
21 16 0.73
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATTAAAATATATAAAAA
Found at i:1344085 original size:58 final size:57
Alignment explanation
Indices: 1344023--1344156 Score: 141
Period size: 60 Copynumber: 2.3 Consensus size: 57
1344013 TAAAATATAA
1344023 TAAAA-AATATGATATGACATGAA-AAAAATA-T-AAATATTATATAAATATAAGATTATTT
1 TAAAATAATATGATATGA-AT-AATAAAAATATTAAAAT-TTATATAAATATAA-A-TATTT
* **
1344081 TAAAATATATATAATATGAATAATAAATGTATTAAAATTTATATAAATATAAATATTT
1 TAAAATA-ATATGATATGAATAATAAAAATATTAAAATTTATATAAATATAAATATTT
1344139 TAAATATAATTATGATAT
1 TAAA-ATAA-TATGATAT
1344157 AACAAAATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
58 17 0.26
59 19 0.29
60 25 0.38
61 4 0.06
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (57 bp):
TAAAATAATATGATATGAATAATAAAAATATTAAAATTTATATAAATATAAATATTT
Found at i:1348792 original size:114 final size:114
Alignment explanation
Indices: 1348592--1348805 Score: 331
Period size: 114 Copynumber: 1.9 Consensus size: 114
1348582 TATCAAGATG
*
1348592 AATTTTTCTGATTGTATAATATGAAATTGTGCTTTTAATCGAATTATTTGTGCAAAAATTCTTGC
1 AATTTTTCTAATTGTATAATATGAAATTGTGCTTTTAATCGAATTATTTGTGCAAAAATTCTTGC
*
1348657 ACATACAACATTTCTTATAGATAACAGACAAACATGTGACCAAAAAATA
66 ACATACAACATTTCTTATAGATAACAAACAAACATGTGACCAAAAAATA
* * *
1348706 AATTTTTTTAATTGTATAATCTGAAATTGTGTTTTTAATCGAATTATTTGTGCGAAAAA-TCTTG
1 AATTTTTCTAATTGTATAATATGAAATTGTGCTTTTAATCGAATTATTTGTGC-AAAAATTCTTG
* * * *
1348770 CACATGCAGCATTTCTTGTAGATAACAAATAAACAT
65 CACATACAACATTTCTTATAGATAACAAACAAACAT
1348806 AGAACCAATG
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
114 85 0.94
115 5 0.06
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Consensus pattern (114 bp):
AATTTTTCTAATTGTATAATATGAAATTGTGCTTTTAATCGAATTATTTGTGCAAAAATTCTTGC
ACATACAACATTTCTTATAGATAACAAACAAACATGTGACCAAAAAATA
Found at i:1352815 original size:2 final size:2
Alignment explanation
Indices: 1352808--1352849 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1352798 CTTAAATTTG
1352808 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
1352850 GATTAGAGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1353160 original size:18 final size:18
Alignment explanation
Indices: 1353139--1353174 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1353129 ACTATATATT
1353139 ATTT-ATATAATAAAAATA
1 ATTTAATAT-ATAAAAATA
1353157 ATTTAATATATAAAAATA
1 ATTTAATATATAAAAATA
1353175 TAAAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTTAATATATAAAAATA
Found at i:1353166 original size:21 final size:21
Alignment explanation
Indices: 1353142--1353189 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1353132 ATATATTATT
*
1353142 TATATAATAAAAAT-AATTTAA
1 TATATAA-AAAAATAAAATTAA
*
1353163 TATATAAAAATATAAAATTAA
1 TATATAAAAAAATAAAATTAA
1353184 TATATA
1 TATATA
1353190 TTATATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TATATAAAAAAATAAAATTAA
Found at i:1353206 original size:26 final size:26
Alignment explanation
Indices: 1353131--1353206 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
1353121 ATTATAATAC
* * *
1353131 TATATATTATTTATATAATAAAAATAA
1 TATATATTATATAAAT-ATAAAATTAA
* *
1353158 TTTA-ATATATAAAAATATAAAATTAA
1 TATATAT-TATATAAATATAAAATTAA
1353184 TATATATTATATAAATATAAAAT
1 TATATATTATATAAATATAAAAT
1353207 AAATCAAGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
26 29 0.73
27 11 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
TATATATTATATAAATATAAAATTAA
Found at i:1353280 original size:17 final size:17
Alignment explanation
Indices: 1353249--1353306 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 17
1353239 AGCTCAATTC
*
1353249 ATTTTTAAATAAATTTAT
1 ATTTTTATAT-AATTTAT
1353267 ATTTTTATATAATTT-T
1 ATTTTTATATAATTTAT
*
1353283 ATTTTT-TA-AATATAAT
1 ATTTTTATATAAT-TTAT
1353299 ATTTTTAT
1 ATTTTTAT
1353307 TTAAATACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
14 3 0.09
15 3 0.09
16 14 0.40
17 6 0.17
18 9 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTTATATAATTTAT
Found at i:1353287 original size:16 final size:18
Alignment explanation
Indices: 1353249--1353294 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1353239 AGCTCAATTC
1353249 ATTTTTAAATAAATTTAT
1 ATTTTTAAATAAATTTAT
* *
1353267 ATTTTTATATAATTTTAT
1 ATTTTTAAATAAATTTAT
1353285 -TTTTTAAATA
1 ATTTTTAAATA
1353295 TAATATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTAAATAAATTTAT
Found at i:1353297 original size:19 final size:19
Alignment explanation
Indices: 1353250--1353313 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
1353240 GCTCAATTCA
1353250 TTTTTAAATA-AA-TTTAT
1 TTTTTAAATATAATTTTAT
1353267 ATTTTT--ATATAATTTTAT
1 -TTTTTAAATATAATTTTAT
1353285 TTTTTAAATATAATATTT-T
1 TTTTTAAATATAAT-TTTAT
*
1353304 TATTTAAATA
1 TTTTTAAATA
1353314 CTTTTATATC
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
16 3 0.08
17 7 0.17
18 10 0.25
19 17 0.43
20 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTAAATATAATTTTAT
Found at i:1356992 original size:22 final size:22
Alignment explanation
Indices: 1356953--1356997 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1356943 TTAATTTAGT
* * * *
1356953 TTTGATTTATTTTTTTATTAAA
1 TTTGATTCAATTTCTTATCAAA
1356975 TTTGATTCAATTTCTTATCAAA
1 TTTGATTCAATTTCTTATCAAA
1356997 T
1 T
1356998 AATAACAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (22 bp):
TTTGATTCAATTTCTTATCAAA
Found at i:1365996 original size:2 final size:2
Alignment explanation
Indices: 1365989--1366034 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1365979 CCGGAGGAGG
*
1365989 GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1366031 -A GA G
1 GA GA G
1366035 CCGGACTGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1366521 original size:21 final size:20
Alignment explanation
Indices: 1366480--1366557 Score: 60
Period size: 21 Copynumber: 4.0 Consensus size: 20
1366470 CAATGATATA
1366480 ATTAAA-ATA-AATTTAATT
1 ATTAAATATATAATTTAATT
1366498 ATTAAAGTATATAATTATAA-T
1 ATTAAA-TATATAATT-TAATT
* *
1366519 ATTAAATATAATAA-ATATTT
1 ATTAAATAT-ATAATTTAATT
*
1366539 A-AAAATATAT-ATTTAATT
1 ATTAAATATATAATTTAATT
1366557 A
1 A
1366558 AATAATTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
17 1 0.02
18 13 0.27
19 8 0.17
20 8 0.17
21 15 0.31
22 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (20 bp):
ATTAAATATATAATTTAATT
Found at i:1369368 original size:21 final size:22
Alignment explanation
Indices: 1369326--1369369 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
1369316 ATGTGATATT
*
1369326 AAATATAATATTTACTTAATAA
1 AAATATAATATTTACGTAATAA
1369348 AAATAT-ATATTTGACGT-ATAA
1 AAATATAATATTT-ACGTAATAA
1369369 A
1 A
1369370 TACGATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (22 bp):
AAATATAATATTTACGTAATAA
Found at i:1370206 original size:14 final size:13
Alignment explanation
Indices: 1370187--1370232 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
1370177 AATTTTTTTA
1370187 TATATTTTAAATAT
1 TATATTTT-AATAT
*
1370201 TATATTTTTATAAT
1 TATATTTTAAT-AT
1370215 TATATTTTAATAT
1 TATATTTTAATAT
1370228 T-TATT
1 TATATT
1370233 AAAAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 4 0.14
13 5 0.17
14 20 0.69
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATATTTTAATAT
Found at i:1370732 original size:30 final size:29
Alignment explanation
Indices: 1370691--1370747 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
1370681 TATATTAATT
* *
1370691 TTTTTAAAAATTTTATATATTTAAATTTTC
1 TTTTAAAAAATTATATAT-TTTAAATTTTC
*
1370721 TTTTAAAAAATTATATATTTTATATTT
1 TTTTAAAAAATTATATATTTTAAATTT
1370748 ATATCTAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTAAAAAATTATATATTTTAAATTTTC
Found at i:1372348 original size:27 final size:27
Alignment explanation
Indices: 1372318--1372390 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
1372308 CCACAATTTG
1372318 TGTTTGTCAAAAATGGTGGTTCCTTTA
1 TGTTTGTCAAAAATGGTGGTTCCTTTA
* * *
1372345 TGTTTGTCAAAACTGGTAGTTCCTTTG
1 TGTTTGTCAAAAATGGTGGTTCCTTTA
* *
1372372 TGTTTATCAAAATTGGTGG
1 TGTTTGTCAAAAATGGTGG
1372391 CTAATTTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.22, C:0.11, G:0.23, T:0.44
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTCCTTTA
Found at i:1376830 original size:27 final size:27
Alignment explanation
Indices: 1376752--1376830 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
1376742 CAAAAGCCAC
* * *
1376752 CCTTTGTGTTTGTAAAAAATGATAGTT
1 CCTTTGTGTTTGTCAAAAATGGTGGTT
* *
1376779 CCTTTATGTTTGTCAAAAATAGTGGTT
1 CCTTTGTGTTTGTCAAAAATGGTGGTT
* *
1376806 CCTTTGTTTTTGTCAAAATTGGTGG
1 CCTTTGTGTTTGTCAAAAATGGTGG
1376831 CTAATTTTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (27 bp):
CCTTTGTGTTTGTCAAAAATGGTGGTT
Found at i:1377251 original size:2 final size:2
Alignment explanation
Indices: 1377244--1377272 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1377234 TCTTTGCTTT
1377244 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
1377273 GGTATTTTTG
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:1377818 original size:30 final size:28
Alignment explanation
Indices: 1377764--1377836 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 28
1377754 CCCATTTTCG
1377764 ACTAATTGATCAAACTATCATTGTTTATACA
1 ACTAATT-ATCAAACTATCATTGTTT-TA-A
*
1377795 ACTAATTATCAAAGCT-TCGTTGTTTTAA
1 ACTAATTATCAAA-CTATCATTGTTTTAA
*
1377823 AATAATTTATCAAA
1 ACTAA-TTATCAAA
1377837 ATATTATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 5 0.13
29 10 0.26
30 14 0.37
31 9 0.24
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (28 bp):
ACTAATTATCAAACTATCATTGTTTTAA
Found at i:1378391 original size:29 final size:29
Alignment explanation
Indices: 1378356--1378441 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 29
1378346 TATGGATGCA
1378356 AAAATAAAAATATTTTAATAATTTATTTT
1 AAAATAAAAATATTTTAATAATTTATTTT
*
1378385 AAAATAATAATATTTTAATAA-TTAGTTTT
1 AAAATAAAAATATTTTAATAATTTA-TTTT
* *
1378414 ATAAGTAAAAATAATTTAATCAATTTAT
1 A-AAATAAAAATATTTTAAT-AATTTAT
1378442 CAATTTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.06
29 25 0.51
30 15 0.31
31 3 0.06
32 3 0.06
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (29 bp):
AAAATAAAAATATTTTAATAATTTATTTT
Found at i:1378392 original size:15 final size:16
Alignment explanation
Indices: 1378356--1378402 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1378346 TATGGATGCA
*
1378356 AAAATAAAAATATTTT
1 AAAATAATAATATTTT
*
1378372 --AATAAT-TTATTTT
1 AAAATAATAATATTTT
1378385 AAAATAATAATATTTT
1 AAAATAATAATATTTT
1378401 AA
1 AA
1378403 TAATTAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 6 0.24
14 5 0.20
15 6 0.24
16 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAATAATAATATTTT
Found at i:1378406 original size:14 final size:14
Alignment explanation
Indices: 1378358--1378406 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1378348 TGGATGCAAA
*
1378358 AATAAAAATATTTT
1 AATAATAATATTTT
*
1378372 AATAAT-TTATTTT
1 AATAATAATATTTT
1378385 AAAATAATAATATTTT
1 --AATAATAATATTTT
1378401 AATAAT
1 AATAAT
1378407 TAGTTTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 6 0.21
14 11 0.38
15 6 0.21
16 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAATAATATTTT
Found at i:1379782 original size:2 final size:2
Alignment explanation
Indices: 1379775--1379800 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1379765 CTCACTAACT
1379775 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
1379801 CCCCTCTAAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1386949 original size:3 final size:3
Alignment explanation
Indices: 1386941--1386973 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1386931 AGAGAAAAGA
1386941 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1386974 TTAAATGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1387017 original size:7 final size:7
Alignment explanation
Indices: 1387001--1387036 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
1386991 AGAAAGGAAG
1387001 AATT-AA
1 AATTAAA
1387007 AATTAAA
1 AATTAAA
1387014 AATTAAA
1 AATTAAA
1387021 AATTAAA
1 AATTAAA
1387028 AATTAAA
1 AATTAAA
1387035 AA
1 AA
1387037 AAAGATGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.14
7 25 0.86
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATTAAA
Found at i:1388699 original size:21 final size:22
Alignment explanation
Indices: 1388660--1388702 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1388650 ACGAATATTG
* *
1388660 AAATTTAGTACATATTTAATTA
1 AAATTTAATACATACTTAATTA
1388682 AAATTTAAT-CATACTTAATTA
1 AAATTTAATACATACTTAATTA
1388703 TATTATTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (22 bp):
AAATTTAATACATACTTAATTA
Found at i:1392389 original size:21 final size:21
Alignment explanation
Indices: 1392364--1392409 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1392354 TTTATCTTTG
1392364 ATTTAAAACTT-AATTATTTAT
1 ATTT-AAACTTGAATTATTTAT
**
1392385 ATTTAAGTTTGAATTATTTAT
1 ATTTAAACTTGAATTATTTAT
1392406 ATTT
1 ATTT
1392410 GAGTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (21 bp):
ATTTAAACTTGAATTATTTAT
Found at i:1392414 original size:21 final size:21
Alignment explanation
Indices: 1392375--1392421 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1392365 TTTAAAACTT
*
1392375 AATTATTTATATTTAAGTTTG
1 AATTATTTATATTTAAGTTTA
*
1392396 AATTATTTATATTTGAGTTTA
1 AATTATTTATATTTAAGTTTA
1392417 AATTA
1 AATTA
1392422 AAATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (21 bp):
AATTATTTATATTTAAGTTTA
Found at i:1392857 original size:19 final size:18
Alignment explanation
Indices: 1392833--1392889 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
1392823 TTATGAAATT
1392833 TTTAATAAAAATCATATTA
1 TTTAATAAAAAT-ATATTA
*
1392852 TTTAATTAAATATATATTA
1 TTTAA-TAAAAATATATTA
* * *
1392871 TTTATTAAATATTTATTA
1 TTTAATAAAAATATATTA
1392889 T
1 T
1392890 ATTCCATACT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 13 0.38
19 15 0.44
20 6 0.18
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAATAAAAATATATTA
Found at i:1392877 original size:18 final size:19
Alignment explanation
Indices: 1392833--1392889 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
1392823 TTATGAAATT
*
1392833 TTTAA-TAAAAATCATATTA
1 TTTAATTAAATAT-ATATTA
1392852 TTTAATTAAATATATATTA
1 TTTAATTAAATATATATTA
*
1392871 TTT-ATTAAATATTTATTA
1 TTTAATTAAATATATATTA
1392889 T
1 T
1392890 ATTCCATACT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
18 15 0.43
19 14 0.40
20 6 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAATTAAATATATATTA
Found at i:1393327 original size:19 final size:19
Alignment explanation
Indices: 1393305--1393341 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1393295 TTAAAATTTA
*
1393305 AATTATTTTTAATTTAATT
1 AATTATTTATAATTTAATT
*
1393324 AATTATTTATGATTTAAT
1 AATTATTTATAATTTAAT
1393342 ATATTTTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
AATTATTTATAATTTAATT
Found at i:1393440 original size:25 final size:26
Alignment explanation
Indices: 1393398--1393467 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 26
1393388 TTTTACTTGT
*
1393398 AATATAATAATATCTTAAAAAGTT-A-A
1 AATAT-AT-ATATTTTAAAAAGTTGATA
*
1393424 AATTATATATATTTT-AAAATTTGATA
1 AA-TATATATATTTTAAAAAGTTGATA
*
1393450 AATATTTATATTTTAAAA
1 AATATATATATTTTAAAA
1393468 TAATTTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
24 6 0.16
25 18 0.49
26 10 0.27
27 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (26 bp):
AATATATATATTTTAAAAAGTTGATA
Found at i:1393541 original size:30 final size:29
Alignment explanation
Indices: 1393483--1393551 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
1393473 TTTATTAATA
*
1393483 TATAAAAAATTAAATTTGAAAATAAAAAT
1 TATAAAAATTTAAATTTGAAAATAAAAAT
* *
1393512 TAATAAAAATTTAAATTT-AAATTTTAAAAT
1 T-ATAAAAATTTAAATTTGAAA-ATAAAAAT
1393542 TATCAAAAAT
1 TAT-AAAAAT
1393552 AATTTTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 6 0.18
30 28 0.82
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (29 bp):
TATAAAAATTTAAATTTGAAAATAAAAAT
Found at i:1393898 original size:17 final size:19
Alignment explanation
Indices: 1393865--1393917 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 19
1393855 TATAAGGCGA
1393865 AAATATATATATATATAAT
1 AAATATATATATATATAAT
*
1393884 AAATATATA-AT-TATATT
1 AAATATATATATATATAAT
* *
1393901 AAATTTATTTA-ATATAA
1 AAATATATATATATATAA
1393918 ATTATTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 12 0.43
18 7 0.25
19 9 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATATATATATATATAAT
Found at i:1393931 original size:31 final size:34
Alignment explanation
Indices: 1393872--1393964 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 34
1393862 CGAAAATATA
*
1393872 TATATATATAATAAA-TATATAATTATATT-AAATT
1 TATATAAAT-ATAAATTAT-TAATTATATTAAAATT
*
1393906 TAT-TTAATATAAATTATTAA-TATATTAAAATT
1 TATATAAATATAAATTATTAATTATATTAAAATT
*
1393938 TATATAAATATATAATTTTTAAATTAT
1 TATATAAATATA-AATTATT-AATTAT
1393965 GTTATATAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
31 6 0.12
32 16 0.33
33 13 0.27
34 9 0.18
35 2 0.04
36 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
TATATAAATATAAATTATTAATTATATTAAAATT
Found at i:1393948 original size:18 final size:16
Alignment explanation
Indices: 1393896--1393961 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 16
1393886 ATATATAATT
*
1393896 ATATTAAATTTATTTA
1 ATATTAAATTTATTAA
1393912 ATA-TAAA-TTATTAA
1 ATATTAAATTTATTAA
1393926 TATATTAAAATTTATATAA
1 -ATATT-AAATTTAT-TAA
1393945 ATA-TATAATTT-TTAA
1 ATATTA-AATTTATTAA
1393960 AT
1 AT
1393962 TATGTTATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
14 6 0.14
15 12 0.28
16 6 0.14
17 9 0.21
18 7 0.16
19 3 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTAAATTTATTAA
Found at i:1394281 original size:12 final size:11
Alignment explanation
Indices: 1394260--1394294 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
1394250 ATTAAATTTG
1394260 TATTATAAATAT
1 TATTA-AAATAT
1394272 TATTTAAAATAT
1 TA-TTAAAATAT
1394284 TATTAAAATAT
1 TATTAAAATAT
1394295 AAGTATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.41
12 10 0.45
13 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TATTAAAATAT
Found at i:1399171 original size:14 final size:14
Alignment explanation
Indices: 1399140--1399182 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1399130 TAATTTCTTA
*
1399140 ATAATT-TTTTATAA
1 ATAATTATTTTA-AT
1399154 ATAATTATTTTAAT
1 ATAATTATTTTAAT
*
1399168 ATAATTAATTTAAT
1 ATAATTATTTTAAT
1399182 A
1 A
1399183 ATTATATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATAATTATTTTAAT
Found at i:1400348 original size:16 final size:17
Alignment explanation
Indices: 1400323--1400354 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1400313 ATTATAATAA
1400323 TAAAATTATATATTTAG
1 TAAAATTATATATTTAG
1400340 TAAAA-TATATATTTA
1 TAAAATTATATATTTA
1400355 AAATTAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TAAAATTATATATTTAG
Found at i:1400488 original size:14 final size:14
Alignment explanation
Indices: 1400444--1400502 Score: 52
Period size: 18 Copynumber: 4.1 Consensus size: 14
1400434 TATTTTTATA
1400444 TATTTTAATAATATT
1 TATTTTAAT-ATATT
1400459 TAAGATTTTAATATATAT
1 T---ATTTTAATATAT-T
1400477 TATTTT-ATATATT
1 TATTTTAATATATT
1400490 TA-TTTAAT-TATT
1 TATTTTAATATATT
1400502 T
1 T
1400503 TAATTAATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
12 8 0.21
13 5 0.13
14 6 0.15
15 6 0.15
17 4 0.10
18 10 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (14 bp):
TATTTTAATATATT
Found at i:1400501 original size:12 final size:13
Alignment explanation
Indices: 1400465--1400502 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1400455 TATTTAAGAT
1400465 TTTAATATATATTA
1 TTTAATATAT-TTA
*
1400479 TTTTATATATTTA
1 TTTAATATATTTA
1400492 TTTAAT-TATTT
1 TTTAATATATTT
1400503 TAATTAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 5 0.23
13 8 0.36
14 9 0.41
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTAATATATTTA
Found at i:1402224 original size:13 final size:13
Alignment explanation
Indices: 1402206--1402231 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1402196 CAATTTTTTG
1402206 TGTATCGATACAT
1 TGTATCGATACAT
1402219 TGTATCGATACAT
1 TGTATCGATACAT
1402232 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1402856 original size:2 final size:2
Alignment explanation
Indices: 1402802--1402839 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1402792 TTTAGAATTA
*
1402802 AT AT CT AT AT -T 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 AT AT A
1402840 AGATCGATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1403758 original size:35 final size:33
Alignment explanation
Indices: 1403696--1403765 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
1403686 TTGAATACAT
*
1403696 AATTATTATTTAATAAAATTAAATTATAAATTA
1 AATTATTATTTAATAAAATTAAATTATAAAATA
*
1403729 AATTTTTA-TTAATAATAATTATAATTTATAAAATA
1 AATTATTATTTAATAA-AATTA-AA-TTATAAAATA
1403764 AA
1 AA
1403766 AATAAAAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 7 0.22
33 12 0.38
34 2 0.06
35 11 0.34
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
AATTATTATTTAATAAAATTAAATTATAAAATA
Found at i:1403939 original size:16 final size:18
Alignment explanation
Indices: 1403907--1403939 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1403897 CAATTTTATT
1403907 ATTTTATTTAGTTAATTA
1 ATTTTATTTAGTTAATTA
1403925 ATTTT-TTTA-TTAATT
1 ATTTTATTTAGTTAATT
1403940 TCTTTCATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
ATTTTATTTAGTTAATTA
Found at i:1404279 original size:2 final size:2
Alignment explanation
Indices: 1404272--1404298 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1404262 ATGAATACGA
1404272 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 A
1404299 AATGAAATCT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1404540 original size:14 final size:14
Alignment explanation
Indices: 1404492--1404534 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1404482 TATTTAATTT
*
1404492 ATTAAAATAAAATAAA
1 ATTATAATAAAAT--A
*
1404508 ATTGTAATAAAATA
1 ATTATAATAAAATA
1404522 ATTATAATAAAAT
1 ATTATAATAAAAT
1404535 GGTTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.54
16 11 0.46
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
ATTATAATAAAATA
Found at i:1406095 original size:21 final size:21
Alignment explanation
Indices: 1406069--1406125 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
1406059 AAATATAGAT
1406069 TTGGATGAAATG-ATGCATTGG
1 TTGGATGAAA-GAATGCATTGG
**
1406090 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAGAATGCATTGG
*
1406111 TTGGATGAAAAAATG
1 TTGGATGAAAGAATG
1406126 TAACTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGGATGAAAGAATGCATTGG
Found at i:1406133 original size:21 final size:21
Alignment explanation
Indices: 1406090--1406133 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1406080 GATGCATTGG
* **
1406090 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAAAATGCAACTT
*
1406111 TTGGATGAAAAAATGTAACTT
1 TTGGATGAAAAAATGCAACTT
1406132 TT
1 TT
1406134 AATAACTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (21 bp):
TTGGATGAAAAAATGCAACTT
Found at i:1411129 original size:21 final size:21
Alignment explanation
Indices: 1411104--1411157 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1411094 ATAGATTTGA
1411104 ATGAAATG-ATGCATTGGTTGG
1 ATGAAA-GAATGCATTGGTTGG
**
1411125 ATGAAAGAATGCATTTTTTGG
1 ATGAAAGAATGCATTGGTTGG
1411146 ATGAAA-AATGCA
1 ATGAAAGAATGCA
1411158 ACTTTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 7 0.23
21 23 0.77
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (21 bp):
ATGAAAGAATGCATTGGTTGG
Found at i:1411163 original size:20 final size:21
Alignment explanation
Indices: 1411121--1411163 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1411111 GATGCATTGG
**
1411121 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAGAATGCAACTT
1411142 TTGGATGAAA-AATGCAACTT
1 TTGGATGAAAGAATGCAACTT
1411162 TT
1 TT
1411164 AATAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (21 bp):
TTGGATGAAAGAATGCAACTT
Found at i:1411163 original size:21 final size:21
Alignment explanation
Indices: 1411121--1411163 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1411111 GATGCATTGG
*
1411121 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAGAATGCACTTT
1411142 TTGGATGAAA-AATGCAACTTT
1 TTGGATGAAAGAATGC-ACTTT
1411163 T
1 T
1411164 AATAACCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (21 bp):
TTGGATGAAAGAATGCACTTT
Found at i:1417215 original size:29 final size:29
Alignment explanation
Indices: 1417174--1417247 Score: 114
Period size: 28 Copynumber: 2.5 Consensus size: 29
1417164 AGGTAAAAAG
*
1417174 ATATTTAATTTTTTAAGTTTTTAAAAAATAT
1 ATATTT-ATTTTTTAA-TATTTAAAAAATAT
1417205 ATATTTATTTTTTAATATTTAAAAAATAT
1 ATATTTATTTTTTAATATTTAAAAAATAT
1417234 -TATTTATTTTTTAA
1 ATATTTATTTTTTAA
1417248 AGATTTGATT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 14 0.33
29 13 0.31
30 9 0.21
31 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (29 bp):
ATATTTATTTTTTAATATTTAAAAAATAT
Found at i:1417253 original size:29 final size:28
Alignment explanation
Indices: 1417175--1417271 Score: 106
Period size: 29 Copynumber: 3.2 Consensus size: 28
1417165 GGTAAAAAGA
*
1417175 TATTTAATTTTTTAAGTTTTTAAAAAATAT
1 TATTT-ATTTTTTAAG-ATTTAAAAAATAT
*
1417205 ATATTTATTTTTTAATATTTAAAAAATAT
1 -TATTTATTTTTTAAGATTTAAAAAATAT
1417234 TATTTATTTTTTAAAGATTTGATTAAAAATA-
1 TATTTATTTTTT-AAGATTT-A--AAAAATAT
1417265 TATTTAT
1 TATTTAT
1417272 CATTTAAATT
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
28 12 0.20
29 18 0.31
30 10 0.17
31 12 0.20
32 7 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (28 bp):
TATTTATTTTTTAAGATTTAAAAAATAT
Found at i:1417548 original size:20 final size:22
Alignment explanation
Indices: 1417525--1417568 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1417515 AAATGATTTT
*
1417525 ATTAA-AA-TATTTTTATTTAA
1 ATTAATAATTATTATTATTTAA
1417545 ATTAATTAATTATTATTATTTAA
1 ATTAA-TAATTATTATTATTTAA
1417568 A
1 A
1417569 AATTTATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
22 2 0.10
23 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTAATAATTATTATTATTTAA
Found at i:1420851 original size:19 final size:20
Alignment explanation
Indices: 1420819--1420857 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1420809 TAAAATTATG
1420819 TAAAATTAATTTTTT-ATTA
1 TAAAATTAATTTTTTCATTA
1420838 TAAAATT-ATCTTTTTCATTA
1 TAAAATTAAT-TTTTTCATTA
1420858 ATTAATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 12 0.67
20 4 0.22
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TAAAATTAATTTTTTCATTA
Found at i:1421966 original size:22 final size:22
Alignment explanation
Indices: 1421923--1421966 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1421913 TTGTGGTTGC
* **
1421923 TGTTGTTGTTGCTATTTTCGAT
1 TGTTGCTGTTGCTATTGCCGAT
*
1421945 TGTTGCTGTTGCTGTTGCCGAT
1 TGTTGCTGTTGCTATTGCCGAT
1421967 CTACTTCTGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.14, G:0.27, T:0.52
Consensus pattern (22 bp):
TGTTGCTGTTGCTATTGCCGAT
Done.