Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011845.1 Corchorus capsularis cultivar CVL-1 contig11866, whole genome shotgun sequence
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: 64897
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1048 original size:21 final size:21
Alignment explanation
Indices: 1024--1194 Score: 151
Period size: 22 Copynumber: 8.3 Consensus size: 21
1014 TCTTTGAATC
*
1024 ACTGATCACCTTTTACTCTTT
1 ACTGATTACCTTTTACTCTTT
*
1045 ACTGATTACTATTTTACTC-TT
1 ACTGATTAC-CTTTTACTCTTT
*
1066 ACTGATTACTATTTTACTC-TT
1 ACTGATTAC-CTTTTACTCTTT
*
1087 ACTGATTACCTTTTA--C-TG
1 ACTGATTACCTTTTACTCTTT
*
1105 A-TTATTA--TTTTACTCTTT
1 ACTGATTACCTTTTACTCTTT
*
1123 ACTGATTACCTTCTTACTTTTT
1 ACTGATTACCTT-TTACTCTTT
* **
1145 ACTGATAAATATTTTACTCTTT
1 ACTGAT-TACCTTTTACTCTTT
*
1167 ACTGATTACCATTTTGCTCTTT
1 ACTGATTACC-TTTTACTCTTT
1189 ACTGAT
1 ACTGAT
1195 CTCTCTTTAC
Statistics
Matches: 124, Mismatches: 16, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
15 5 0.04
17 6 0.05
18 5 0.04
19 5 0.04
20 5 0.04
21 43 0.35
22 52 0.42
23 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.51
Consensus pattern (21 bp):
ACTGATTACCTTTTACTCTTT
Found at i:1089 original size:35 final size:35
Alignment explanation
Indices: 1061--1140 Score: 124
Period size: 35 Copynumber: 2.2 Consensus size: 35
1051 TACTATTTTA
1061 CTCTTACTGATTACTATTTTACTCTTACTGATTAC
1 CTCTTACTGATTACTATTTTACTCTTACTGATTAC
* *
1096 CTTTTACTGATTATTATTTTACTCTTTACTGATTAC
1 CTCTTACTGATTACTATTTTACTC-TTACTGATTAC
1132 CTTCTTACT
1 C-TCTTACT
1141 TTTTACTGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 12 0.30
37 6 0.15
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (35 bp):
CTCTTACTGATTACTATTTTACTCTTACTGATTAC
Found at i:1290 original size:15 final size:15
Alignment explanation
Indices: 1234--1291 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
1224 ACTGATTACT
1234 CTTTACTTTTTACCA
1 CTTTACTTTTTACCA
*
1249 TTTTACTTTTTACCGA
1 CTTTACTTTTTACC-A
1265 TCTCTCTTTACTTTTTACCA
1 -----CTTTACTTTTTACCA
1285 CTTTACT
1 CTTTACT
1292 GATTACTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
15 20 0.57
16 1 0.03
20 1 0.03
21 13 0.37
ACGTcount: A:0.17, C:0.26, G:0.02, T:0.55
Consensus pattern (15 bp):
CTTTACTTTTTACCA
Found at i:1290 original size:36 final size:36
Alignment explanation
Indices: 1161--1291 Score: 169
Period size: 36 Copynumber: 3.7 Consensus size: 36
1151 AAATATTTTA
** * *
1161 CTCTTTACTGATTACCATTTTGCTCTTTACTGATCT
1 CTCTTTACTTTTTACCATTTTACTTTTTACTGATCT
1197 CTCTTTACTTTTTACCATTCTT-C-TTTTACTGAT-T
1 CTCTTTACTTTTTACCATT-TTACTTTTTACTGATCT
*
1231 ACTCTTTACTTTTTACCATTTTACTTTTTACCGATCT
1 -CTCTTTACTTTTTACCATTTTACTTTTTACTGATCT
*
1268 CTCTTTACTTTTTACCACTTTACT
1 CTCTTTACTTTTTACCATTTTACT
1292 GATTACTATT
Statistics
Matches: 85, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
34 3 0.04
35 29 0.34
36 50 0.59
37 3 0.04
ACGTcount: A:0.17, C:0.25, G:0.04, T:0.54
Consensus pattern (36 bp):
CTCTTTACTTTTTACCATTTTACTTTTTACTGATCT
Found at i:1323 original size:25 final size:26
Alignment explanation
Indices: 1293--1354 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
1283 CACTTTACTG
*
1293 ATTACTATTTGCTCTC-TTGAATTTA
1 ATTACTATTTGCACTCTTTGAATTTA
*
1318 ATTACTATTTTCACTCTTTGAATTTA
1 ATTACTATTTGCACTCTTTGAATTTA
* *
1344 ATCACCATTTG
1 ATTACTATTTG
1355 TCATTTTACT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (26 bp):
ATTACTATTTGCACTCTTTGAATTTA
Found at i:1393 original size:33 final size:33
Alignment explanation
Indices: 1319--1401 Score: 116
Period size: 32 Copynumber: 2.5 Consensus size: 33
1309 TTGAATTTAA
*
1319 TTACTATTTTCACTCTTTGAATTTAATCACCATT
1 TTACCATTTT-ACTCTTTGAATTTAATCACCATT
*
1353 TGT--CATTTTACTCTTTGAATTTAATTACCATT
1 T-TACCATTTTACTCTTTGAATTTAATCACCATT
1385 TTACCATTTTACTCTTT
1 TTACCATTTTACTCTTT
1402 ACCGATTACT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 1 0.02
32 23 0.52
33 18 0.41
34 1 0.02
35 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.04, T:0.53
Consensus pattern (33 bp):
TTACCATTTTACTCTTTGAATTTAATCACCATT
Found at i:1554 original size:41 final size:41
Alignment explanation
Indices: 1437--1536 Score: 150
Period size: 40 Copynumber: 2.4 Consensus size: 41
1427 TTTTTATTCT
*
1437 TTACTGATTTACTGATTACTTCTTTTACTTTTACTC-TTAA
1 TTACTGATTTACTGATTACTTCTTTTACTTTAACTCTTTAA
*
1477 TTAC-CATTTTACTGATTACTTCTTTTACTTTAACTCTTTAA
1 TTACTGA-TTTACTGATTACTTCTTTTACTTTAACTCTTTAA
1518 TTACTGATTTCACTGATTA
1 TTACTGATTT-ACTGATTA
1537 ATCTCTTACC
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
39 1 0.02
40 32 0.60
41 11 0.21
42 9 0.17
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (41 bp):
TTACTGATTTACTGATTACTTCTTTTACTTTAACTCTTTAA
Found at i:7530 original size:19 final size:21
Alignment explanation
Indices: 7494--7535 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
7484 TTTCTTCTAT
7494 TTTAATTACTTGCAA-TTTAG
1 TTTAATTACTTGCAATTTTAG
*
7514 TTTAATTA-TTTCAATTTTAG
1 TTTAATTACTTGCAATTTTAG
7534 TT
1 TT
7536 CATAGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAATTACTTGCAATTTTAG
Found at i:9478 original size:107 final size:105
Alignment explanation
Indices: 9225--9484 Score: 341
Period size: 102 Copynumber: 2.5 Consensus size: 105
9215 AATTTTTCTA
* ** * * *
9225 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGTCTCAACTTAGTG-AATTAATTATATATTTTA
1 ACCCTTAAAATAAAAATAAAAATTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
* * * *
9288 TTTCTTAAACCCTATAACAATATTATTAGTTATGGAGTTT
66 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
* * *
9328 ACCCTTAAAAT--AAA-AAAAATTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAAATTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
*
9390 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT
9432 ACCCTTAAAATAAAAATAAAAATTTAATTTGGGGCTAAACTTAGTGAAATTAA
1 ACCCTTAAAATAAAAATAAAAATTTAATTTGGGGCTAAACTTAGTGAAATTAA
9485 GGCTAAACTT
Statistics
Matches: 135, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
100 10 0.07
101 15 0.11
102 35 0.26
103 11 0.08
104 26 0.19
106 3 0.02
107 35 0.26
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAAATTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:10648 original size:19 final size:21
Alignment explanation
Indices: 10607--10653 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
10597 TTTTGGTTCG
10607 AAATTTTACCTTTTTTAT-TT
1 AAATTTTACCTTTTTTATCTT
*
10627 TAATTTT-CCTTATTTT-TCTT
1 AAATTTTACCTT-TTTTATCTT
10647 AAATTTT
1 AAATTTT
10654 TAAAAAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (21 bp):
AAATTTTACCTTTTTTATCTT
Found at i:13194 original size:9 final size:9
Alignment explanation
Indices: 13180--13211 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
13170 TTACTACTGG
13180 TTACTCCTT
1 TTACTCCTT
13189 TTACTCCTT
1 TTACTCCTT
*
13198 TTACTTCTT
1 TTACTCCTT
13207 TTACT
1 TTACT
13212 GCTAACCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.59
Consensus pattern (9 bp):
TTACTCCTT
Found at i:13264 original size:32 final size:32
Alignment explanation
Indices: 13226--13297 Score: 110
Period size: 32 Copynumber: 2.2 Consensus size: 32
13216 ACCCTTTTAC
13226 TTTTACTCCGCTT-TACTGATTACTTCTTCTTA
1 TTTTACTCC-CTTCTACTGATTACTTCTTCTTA
* *
13258 TTTTACTCCCTTCTACTGATTGCTTCTTCTTC
1 TTTTACTCCCTTCTACTGATTACTTCTTCTTA
13290 TTTTACTC
1 TTTTACTC
13298 TTGATTACCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 3 0.08
32 34 0.92
ACGTcount: A:0.12, C:0.28, G:0.06, T:0.54
Consensus pattern (32 bp):
TTTTACTCCCTTCTACTGATTACTTCTTCTTA
Found at i:13346 original size:16 final size:16
Alignment explanation
Indices: 13327--13393 Score: 53
Period size: 16 Copynumber: 4.7 Consensus size: 16
13317 TTACTTCTTT
13327 TTACTTTTACTCTTAA
1 TTACTTTTACTCTTAA
*
13343 TTACTATTT-CTC-TGA
1 TTACT-TTTACTCTTAA
13358 TTAC--TT-CT-TT--
1 TTACTTTTACTCTTAA
13368 -TACTTTTACTCTTAA
1 TTACTTTTACTCTTAA
13383 TTACTTTTACT
1 TTACTTTTACT
13394 AATTACTTCT
Statistics
Matches: 41, Mismatches: 1, Indels: 18
0.68 0.02 0.30
Matches are distributed among these distances:
9 3 0.07
11 2 0.05
12 7 0.17
13 2 0.05
15 6 0.15
16 18 0.44
17 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.01, T:0.58
Consensus pattern (16 bp):
TTACTTTTACTCTTAA
Found at i:13438 original size:23 final size:22
Alignment explanation
Indices: 13411--13453 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
13401 TCTCTTACTT
*
13411 TTACTTTTTTTAGCTTTTACTGA
1 TTACTTCTTTTA-CTTTTACTGA
13434 TTACTTCTTTTACTTTTACT
1 TTACTTCTTTTACTTTTACT
13454 CTTTTTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.16, C:0.16, G:0.05, T:0.63
Consensus pattern (22 bp):
TTACTTCTTTTACTTTTACTGA
Found at i:13495 original size:38 final size:38
Alignment explanation
Indices: 13271--13506 Score: 244
Period size: 38 Copynumber: 6.1 Consensus size: 38
13261 TACTCCCTTC
* * * *
13271 TACTGATTGCTTCTTCTT-CTTTTACTCTTGATTACCAATT
1 TACTGATTACTTCTT-TTACTTTTACTCTT-TTTAGC-TTT
* *
13311 TACTGCTTACTTCTTTTTACTTTTACTCTTAATTA-CTATT
1 TACTGATTACTTC-TTTTACTTTTACTCTT-TTTAGCT-TT
* *
13351 TCTCTGATTACTTCTTTTACTTTTACTCTTAATTA-CTTT
1 T-ACTGATTACTTCTTTTACTTTTACTCTT-TTTAGCTTT
* * *
13390 TACTAATTACTTCTCTTACTTTTACTTTTTTTAGCTTT
1 TACTGATTACTTCTTTTACTTTTACTCTTTTTAGCTTT
*
13428 TACTGATTACTTCTTTTACTTTTACTCTTTTTAGTTTT
1 TACTGATTACTTCTTTTACTTTTACTCTTTTTAGCTTT
* * *
13466 TACTGATTACTTCTCTTACTCTTACTCTTTTTAGCCTT
1 TACTGATTACTTCTTTTACTTTTACTCTTTTTAGCTTT
13504 TAC
1 TAC
13507 CTTTTTTACT
Statistics
Matches: 172, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
37 3 0.02
38 99 0.58
39 3 0.02
40 40 0.23
41 27 0.16
ACGTcount: A:0.18, C:0.21, G:0.04, T:0.57
Consensus pattern (38 bp):
TACTGATTACTTCTTTTACTTTTACTCTTTTTAGCTTT
Found at i:13602 original size:32 final size:31
Alignment explanation
Indices: 13563--13668 Score: 133
Period size: 32 Copynumber: 3.3 Consensus size: 31
13553 TTTACTGATA
* * *
13563 ACTTTTACTTCCTTCTGTTGATTACTTTTTTT
1 ACTTTTACTT-CTTCTGCTGAATACTTCTTTT
*
13595 ACTTTTACTT-TACTCTGCTAAATACTTCTTTT
1 ACTTTTACTTCT--TCTGCTGAATACTTCTTTT
13627 ACTTTTACTTCTTCCTGCTGAATACTTCTTTT
1 ACTTTTACTTCTT-CTGCTGAATACTTCTTTT
13659 ACTTTTACTT
1 ACTTTTACTT
13669 TTACTTCATT
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
30 1 0.02
31 1 0.02
32 62 0.95
33 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.05, T:0.57
Consensus pattern (31 bp):
ACTTTTACTTCTTCTGCTGAATACTTCTTTT
Found at i:13684 original size:38 final size:37
Alignment explanation
Indices: 13591--13696 Score: 123
Period size: 32 Copynumber: 2.9 Consensus size: 37
13581 TGATTACTTT
* *
13591 TTTTACTTTTACTTTACTCTGCTAAATACTTCTTTTAC
1 TTTTACTTTTACTTCA-TCTGCTGAATACTTCTTTTAC
13629 TTTTAC--TT-CTTC--CTGCTGAATACTTCTTTTAC
1 TTTTACTTTTACTTCATCTGCTGAATACTTCTTTTAC
* *
13661 TTTTACTTTTACTTCATTCTGCTGATTAATTCTTTT
1 TTTTACTTTTACTTCA-TCTGCTGAATACTTCTTTT
13697 GTTTTTTAGT
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
32 25 0.43
34 2 0.03
35 7 0.12
36 2 0.03
38 22 0.38
ACGTcount: A:0.18, C:0.21, G:0.05, T:0.57
Consensus pattern (37 bp):
TTTTACTTTTACTTCATCTGCTGAATACTTCTTTTAC
Found at i:13745 original size:19 final size:20
Alignment explanation
Indices: 13708--13745 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13698 TTTTTTAGTT
*
13708 TAATTACTCTTGCATTAAAC
1 TAATTACTCTTGAATTAAAC
13728 TAATTACTC-TGAATTAAA
1 TAATTACTCTTGAATTAAA
13746 ATATCTGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (20 bp):
TAATTACTCTTGAATTAAAC
Found at i:13798 original size:55 final size:54
Alignment explanation
Indices: 13728--13832 Score: 149
Period size: 55 Copynumber: 1.9 Consensus size: 54
13718 TGCATTAAAC
* * *
13728 TAATTACTCTGAATTAAAAT-ATCTGCTGATTACTCTTTCTTTTATTTCTTTAGCT
1 TAATTACTCTAAATTAAAATAATCTGCT-ATTACCCCTTCTTTTA-TTCTTTAGCT
*
13783 TAATTACTCTAAATTAAACTAATCTGCTATTACCCCTTCTTTTATTCTTT
1 TAATTACTCTAAATTAAAATAATCTGCTATTACCCCTTCTTTTATTCTTT
13833 TTACTCTGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
54 6 0.13
55 32 0.71
56 7 0.16
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.50
Consensus pattern (54 bp):
TAATTACTCTAAATTAAAATAATCTGCTATTACCCCTTCTTTTATTCTTTAGCT
Found at i:13907 original size:86 final size:86
Alignment explanation
Indices: 13753--13919 Score: 214
Period size: 86 Copynumber: 1.9 Consensus size: 86
13743 AAAATATCTG
* * *
13753 CTGATTACTCTTTCTTTTATTTCTTTAGCTTAATTACTCTAAATTAAACTAATCTGCTATTACCC
1 CTGATTACCCTTTCTTTTATTTCTTTAGCTTAATTACTCGAAATTAAACTAATCTACTATTACCC
13818 CTTCTTTTA-TTCTTTTTACT
66 CTTCTTTTACTTCTTTTTACT
* * * *
13838 CTGATTACCCTTTCTTTTATTCTTTTTGGCTTAATTACT-GAGAATTAAACT-ATCTACTGTTTG
1 CTGATTACCCTTTCTTTTATT-TCTTTAGCTTAATTACTCGA-AATTAAACTAATCTACT-ATTA
*
13901 CTCCTTCTTTTACTTCTTT
63 CCCCTTCTTTTACTTCTTT
13920 AGTTTAATTA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
85 27 0.39
86 37 0.53
87 6 0.09
ACGTcount: A:0.20, C:0.21, G:0.06, T:0.53
Consensus pattern (86 bp):
CTGATTACCCTTTCTTTTATTTCTTTAGCTTAATTACTCGAAATTAAACTAATCTACTATTACCC
CTTCTTTTACTTCTTTTTACT
Found at i:13948 original size:43 final size:44
Alignment explanation
Indices: 13886--13975 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 44
13876 TGAGAATTAA
* * *
13886 ACTATCTACTGTTTGCTCCTTCTTTTACT-TCTT-TAGTTTAATT
1 ACTATCTACTGATTACTCCTTATTTTACTCT-TTCTAGTTTAATT
*
13929 ACTATCTATTGATTACTCCTTATTTTACTCTTTCTAGTTTAATT
1 ACTATCTACTGATTACTCCTTATTTTACTCTTTCTAGTTTAATT
13973 ACT
1 ACT
13976 CTGAATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
43 27 0.66
44 14 0.34
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.54
Consensus pattern (44 bp):
ACTATCTACTGATTACTCCTTATTTTACTCTTTCTAGTTTAATT
Found at i:13955 original size:99 final size:97
Alignment explanation
Indices: 13839--14016 Score: 241
Period size: 99 Copynumber: 1.8 Consensus size: 97
13829 CTTTTTACTC
* * * * * *
13839 TGATTACCCTTTCTTTTATTCTTTTTGGCTTAATTACTGAGAATTAAACTATCTACTGTTTGCTC
1 TGATTACCCTTTATTTTACTCTTTCTAGCTTAATTACTCAGAATTAAACTATCTACTGTAT-CTC
*
13904 CTTCTTTTACTTCTTTAGTTTAATTACTATCTAT
65 CTCCTTTTAC-TCTTTAGTTTAATTACTATCTAT
* *
13938 TGATTACTCC-TTATTTTACTCTTTCTAGTTTAATTACTCTGAATTAAACTATCTACTGTATCTC
1 TGATTAC-CCTTTATTTTACTCTTTCTAGCTTAATTACTCAGAATTAAACTATCTACTGTATCTC
14002 CTCCTTTTACTCTTT
65 CTCCTTTTACTCTTT
14017 CTAGTTCAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
97 5 0.07
98 12 0.17
99 50 0.72
100 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.52
Consensus pattern (97 bp):
TGATTACCCTTTATTTTACTCTTTCTAGCTTAATTACTCAGAATTAAACTATCTACTGTATCTCC
TCCTTTTACTCTTTAGTTTAATTACTATCTAT
Found at i:14081 original size:33 final size:33
Alignment explanation
Indices: 14044--14128 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
14034 AATTTAACCA
*
14044 ATTTACTGATTACTCTTTTTAATTTTGCTACCT
1 ATTTACTGATTACTCTTTTTAATTTTACTACCT
* * *
14077 ATTTACTGATTACTCATTTTACTTTTACTCCCT
1 ATTTACTGATTACTCTTTTTAATTTTACTACCT
14110 -TTTACTGATTACTTCTTTT
1 ATTTACTGATTAC-TCTTTT
14129 ACTCTTACTC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 12 0.26
33 34 0.74
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.55
Consensus pattern (33 bp):
ATTTACTGATTACTCTTTTTAATTTTACTACCT
Found at i:14099 original size:16 final size:14
Alignment explanation
Indices: 14078--14145 Score: 64
Period size: 16 Copynumber: 4.4 Consensus size: 14
14068 TTGCTACCTA
14078 TTTACTGATTACTCAT
1 TTTACT-ATTACTC-T
*
14094 TTTACTTTTACTCCCT
1 TTTACTATTACT--CT
14110 TTTACTGATTACTTCT
1 TTTACT-ATTAC-TCT
*
14126 TTTACTCTTACTCT
1 TTTACTATTACTCT
14140 TTTACT
1 TTTACT
14146 TTCACTGATT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 9 0.20
15 9 0.20
16 21 0.47
17 5 0.11
18 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.03, T:0.56
Consensus pattern (14 bp):
TTTACTATTACTCT
Found at i:14119 original size:32 final size:30
Alignment explanation
Indices: 14045--14145 Score: 114
Period size: 33 Copynumber: 3.2 Consensus size: 30
14035 ATTTAACCAA
* *
14045 TTTACTGATTACTCTTTTTAATTTTGCTACCT
1 TTTACTGATTACTC-TTTTACTTTTACT-CCT
14077 ATTTACTGATTACTCATTTTACTTTTACTCCCT
1 -TTTACTGATTACTC-TTTTACTTTTACT-CCT
*
14110 TTTACTGATTACTTCTTTTACTCTTACT-CT
1 TTTACTGATTAC-TCTTTTACTTTTACTCCT
14140 TTTACT
1 TTTACT
14146 TTCACTGATT
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
30 8 0.13
32 24 0.39
33 30 0.48
ACGTcount: A:0.19, C:0.22, G:0.04, T:0.55
Consensus pattern (30 bp):
TTTACTGATTACTCTTTTACTTTTACTCCT
Found at i:14160 original size:36 final size:38
Alignment explanation
Indices: 14108--14184 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 38
14098 CTTTTACTCC
* * *
14108 CTTTTACTGATTACTTCTTTTACT-CTTAC-TCTTTTA
1 CTTTCACTGATTACTTCTTCTACTGATTACTTCTTTTA
14144 CTTTCACTGATTACTTCTTCTACTGATTACTTCTTTTA
1 CTTTCACTGATTACTTCTTCTACTGATTACTTCTTTTA
14182 CTT
1 CTT
14185 CTACTCTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 22 0.61
37 4 0.11
38 10 0.28
ACGTcount: A:0.17, C:0.23, G:0.04, T:0.56
Consensus pattern (38 bp):
CTTTCACTGATTACTTCTTCTACTGATTACTTCTTTTA
Found at i:14170 original size:16 final size:16
Alignment explanation
Indices: 14149--14183 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
14139 TTTTACTTTC
14149 ACTGATTACTTCTTCT
1 ACTGATTACTTCTTCT
*
14165 ACTGATTACTTCTTTT
1 ACTGATTACTTCTTCT
14181 ACT
1 ACT
14184 TCTACTCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.23, G:0.06, T:0.51
Consensus pattern (16 bp):
ACTGATTACTTCTTCT
Found at i:14311 original size:53 final size:51
Alignment explanation
Indices: 14212--14354 Score: 159
Period size: 53 Copynumber: 2.8 Consensus size: 51
14202 TCCTCTGATG
* *
14212 ACTTCTTTTACTTCTTTAACTTAATTACTCTGATTTAAACTTACTACTA-ATCT
1 ACTTCTTTTACTTC-TTAGCTTAATTACTCTGAATTAAACTTACTAC-AGAT-T
* * *
14265 CCATTCTTTTACTTCTTAGCTTAATTGCTCTGAATTAGA-TTGACTACAGATT
1 AC-TTCTTTTACTTCTTAGCTTAATTACTCTGAATTAAACTT-ACTACAGATT
*
14317 ACTTC-TTT-CTTCTTAGCTTAATTACTCAGAATTAAACT
1 ACTTCTTTTACTTCTTAGCTTAATTACTCTGAATTAAACT
14355 AACCTCTGAT
Statistics
Matches: 77, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
49 25 0.32
50 4 0.05
51 3 0.04
52 5 0.06
53 28 0.36
54 12 0.16
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.46
Consensus pattern (51 bp):
ACTTCTTTTACTTCTTAGCTTAATTACTCTGAATTAAACTTACTACAGATT
Found at i:17588 original size:22 final size:22
Alignment explanation
Indices: 17536--17597 Score: 108
Period size: 21 Copynumber: 2.9 Consensus size: 22
17526 ACTATATGAA
17536 CCTGTGCAAAATGCAAATATGG
1 CCTGTGCAAAATGCAAATATGG
*
17558 TC-GTGCAAAATGCAAATATGG
1 CCTGTGCAAAATGCAAATATGG
17579 CCTGTGCAAAATGCAAATA
1 CCTGTGCAAAATGCAAATA
17598 CTGAATGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 20 0.54
22 17 0.46
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (22 bp):
CCTGTGCAAAATGCAAATATGG
Found at i:19257 original size:13 final size:14
Alignment explanation
Indices: 19233--19285 Score: 65
Period size: 13 Copynumber: 3.9 Consensus size: 14
19223 ATTTTTAATT
19233 AAAATATATATTTA
1 AAAATATATATTTA
*
19247 CAAAT-TATATTTA
1 AAAATATATATTTA
* *
19260 TATATA-ATATTTA
1 AAAATATATATTTA
19273 AAAATATATATTT
1 AAAATATATATTT
19286 TTGGACCGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 22 0.69
14 10 0.31
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
AAAATATATATTTA
Found at i:20422 original size:63 final size:63
Alignment explanation
Indices: 20323--20445 Score: 210
Period size: 63 Copynumber: 2.0 Consensus size: 63
20313 CGTGTATTAG
* *
20323 TACACAACTTTATTTCAGTTTGATTTGGGCTCGAATTAGTTTGATTTGTAAATGTTTGGATAT
1 TACACAACTTTATTTCAGTTTGATTTGGGCCCGAATTAGTTTAATTTGTAAATGTTTGGATAT
* *
20386 TACACAACTTTATTTCAGTTTGATTTGTGCCCGAATTGGTTTAATTTGTAAATGTTTGGA
1 TACACAACTTTATTTCAGTTTGATTTGGGCCCGAATTAGTTTAATTTGTAAATGTTTGGA
20446 CTCGATTCTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.46
Consensus pattern (63 bp):
TACACAACTTTATTTCAGTTTGATTTGGGCCCGAATTAGTTTAATTTGTAAATGTTTGGATAT
Found at i:21275 original size:22 final size:22
Alignment explanation
Indices: 21197--21276 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
21187 GTCTCTGTGT
*
21197 GGTTATCAAAATTTCATAATGA
1 GGTTATCAAAATTTCATAAGGA
* * ** *
21219 GATTATCAAACTTTTGTAAGAA
1 GGTTATCAAAATTTCATAAGGA
* *
21241 GGTTATTATAATTTCATAAGGA
1 GGTTATCAAAATTTCATAAGGA
*
21263 GGTTATGAAAATTT
1 GGTTATCAAAATTT
21277 TATAGTGTAA
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGGA
Found at i:21350 original size:22 final size:22
Alignment explanation
Indices: 21322--21378 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
21312 GGTAGATTAT
21322 CAAGATTTCATAGTGTGGTTAC
1 CAAGATTTCATAGTGTGGTTAC
* **
21344 CAAGATTTCAGAGTGTGGTTTT
1 CAAGATTTCATAGTGTGGTTAC
*
21366 CAAAATTTCATAG
1 CAAGATTTCATAG
21379 AAAGGTTATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (22 bp):
CAAGATTTCATAGTGTGGTTAC
Found at i:21396 original size:44 final size:44
Alignment explanation
Indices: 21318--21422 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 44
21308 CAAAGGTAGA
* *** * ***
21318 TTATCAAGATTTCATAGTGTGGTTACCAAGATTTCAGAGTGTGG
1 TTATCAAAATTTCATAGAAAGGTTACCAAAATTTCAGAGAAAGG
* * *
21362 TTTTCAAAATTTCATAGAAAGGTTATCAAAATTTCATAGAAAGG
1 TTATCAAAATTTCATAGAAAGGTTACCAAAATTTCAGAGAAAGG
21406 TTATCAAAATTTCATAG
1 TTATCAAAATTTCATAG
21423 GATCAAGTTA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCATAGAAAGGTTACCAAAATTTCAGAGAAAGG
Found at i:21438 original size:24 final size:22
Alignment explanation
Indices: 21360--21453 Score: 127
Period size: 22 Copynumber: 4.2 Consensus size: 22
21350 TTCAGAGTGT
*
21360 GGTTTTCAAAATTTCATAGAAA
1 GGTTATCAAAATTTCATAGAAA
21382 GGTTATCAAAATTTCATAGAAA
1 GGTTATCAAAATTTCATAGAAA
21404 GGTTATCAAAATTTCATAGGATCAA
1 GGTTATCAAAATTTCATA-GA--AA
* *
21429 -GTTATTAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATAGAAA
21450 GGTT
1 GGTT
21454 TGATAGTGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 8
0.86 0.04 0.11
Matches are distributed among these distances:
21 2 0.03
22 42 0.65
23 3 0.05
24 16 0.25
25 2 0.03
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGAAA
Found at i:21443 original size:46 final size:44
Alignment explanation
Indices: 21360--21612 Score: 131
Period size: 44 Copynumber: 5.9 Consensus size: 44
21350 TTCAGAGTGT
*
21360 GGTTTTCAAAATTTCATAGAAAGGTTATCAAAATTTCATAGAAA
1 GGTTATCAAAATTTCATAGAAAGGTTATCAAAATTTCATAGAAA
* *
21404 GGTTATCAAAATTTCATAGGATCAA-GTTATTAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATA-GA--AAGGTTATCAAAATTTCATAGAAA
* * ***
21450 GGTT-T---GA--T-AGT-G-AA-GTTATCAGAATTTCATAGTGT
1 GGTTATCAAAATTTCA-TAGAAAGGTTATCAAAATTTCATAGAAA
* * *
21485 GGTTATCAAAATTTCATA-AGGAGGTTATTAAAATTTCATAG--T
1 GGTTATCAAAATTTCATAGA-AAGGTTATCAAAATTTCATAGAAA
* * * * *
21527 GGTTACCGAAATTTCATAGGAATGTTATAAAAATTTCATA-AGAA
1 GGTTATCAAAATTTCATAGAAAGGTTATCAAAATTTCATAGA-AA
* * * ** * *
21571 GGTTATTAAATTTTTAATAGGGAGGTTATCAAAGTTTTATAG
1 GGTTATCAAA-ATTTCATAGAAAGGTTATCAAAATTTCATAG
21613 TATGGATATC
Statistics
Matches: 158, Mismatches: 30, Indels: 40
0.69 0.13 0.18
Matches are distributed among these distances:
35 22 0.14
36 1 0.01
38 1 0.01
39 2 0.01
40 2 0.01
41 2 0.01
42 36 0.23
43 1 0.01
44 40 0.25
45 26 0.16
46 23 0.15
47 2 0.01
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGAAAGGTTATCAAAATTTCATAGAAA
Found at i:21489 original size:22 final size:22
Alignment explanation
Indices: 21456--21613 Score: 110
Period size: 22 Copynumber: 7.2 Consensus size: 22
21446 GGAAGGTTTG
* *
21456 ATAGTGAAGTTATCAGAATTTC
1 ATAGTGAGGTTATCAAAATTTC
*
21478 ATAGTGTGGTTATCAAAATTTC
1 ATAGTGAGGTTATCAAAATTTC
*
21500 ATAAG-GAGGTTATTAAAATTTC
1 AT-AGTGAGGTTATCAAAATTTC
* *
21522 ATAGT--GGTTACCGAAATTTC
1 ATAGTGAGGTTATCAAAATTTC
* *
21542 ATAG-GAATGTTATAAAAATTTC
1 ATAGTG-AGGTTATCAAAATTTC
* * * *
21564 ATAAG-AAGGTTATTAAATTTTTA
1 AT-AGTGAGGTTATCAAA-ATTTC
* * *
21587 ATAGGGAGGTTATCAAAGTTTT
1 ATAGTGAGGTTATCAAAATTTC
21609 ATAGT
1 ATAGT
21614 ATGGATATCA
Statistics
Matches: 106, Mismatches: 22, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
20 16 0.15
21 2 0.02
22 69 0.65
23 19 0.18
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.38
Consensus pattern (22 bp):
ATAGTGAGGTTATCAAAATTTC
Found at i:21494 original size:125 final size:121
Alignment explanation
Indices: 21348--21574 Score: 312
Period size: 125 Copynumber: 1.8 Consensus size: 121
21338 GGTTACCAAG
* *
21348 ATTTCAGAGTGTGGTTTTCAAAATTTCAT-AGAAAGGTTATCAAAATTTCATAGAAAGGTTATCA
1 ATTTCAGAGTGTGGTTATCAAAATTTCATAAG-AAGGTTATCAAAATTTCATAG--AGGTTACCA
* *
21412 AAATTTCATAGGATCAAGTTATTAAAATTTCATAGGAAGGTTTGATAGTGAAGTTATCAGA
63 AAATTTCATAGGA--AAGTTATAAAAATTTCATAAGAAGGTTTGATAGTGAAGTTATCAGA
* * * * *
21473 ATTTCATAGTGTGGTTATCAAAATTTCATAAGGAGGTTATTAAAATTTCATAGTGGTTACCGAAA
1 ATTTCAGAGTGTGGTTATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGAGGTTACCAAAA
*
21538 TTTCATAGGAATGTTATAAAAATTTCATAAGAAGGTT
66 TTTCATAGGAAAGTTATAAAAATTTCATAAGAAGGTT
21575 ATTAAATTTT
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
121 24 0.26
123 19 0.21
125 46 0.51
126 2 0.02
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (121 bp):
ATTTCAGAGTGTGGTTATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGAGGTTACCAAAA
TTTCATAGGAAAGTTATAAAAATTTCATAAGAAGGTTTGATAGTGAAGTTATCAGA
Found at i:21542 original size:42 final size:43
Alignment explanation
Indices: 21472--21566 Score: 122
Period size: 42 Copynumber: 2.2 Consensus size: 43
21462 AAGTTATCAG
* *
21472 AATTTCATAGTGTGGTTATCAAAATTTCATAAGG-AGGTTATTAA
1 AATTTCATAG-GTGGTTACCAAAATTTCAT-AGGAAGGTTATAAA
* *
21516 AATTTCATA-GTGGTTACCGAAATTTCATAGGAATGTTATAAA
1 AATTTCATAGGTGGTTACCAAAATTTCATAGGAAGGTTATAAA
21558 AATTTCATA
1 AATTTCATA
21567 AGAAGGTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
41 3 0.07
42 34 0.74
44 9 0.20
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (43 bp):
AATTTCATAGGTGGTTACCAAAATTTCATAGGAAGGTTATAAA
Found at i:22064 original size:22 final size:22
Alignment explanation
Indices: 22039--22094 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
22029 AATAGTGTAA
* *
22039 TTATCATAATTTCATAGGGAGG
1 TTATCAAAATTTCATAAGGAGG
* * *
22061 TTATCACAATTTCATAATGTGG
1 TTATCAAAATTTCATAAGGAGG
22083 TTATCAAAATTT
1 TTATCAAAATTT
22095 TATGTAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGAGG
Found at i:22742 original size:93 final size:93
Alignment explanation
Indices: 22562--22748 Score: 268
Period size: 93 Copynumber: 2.0 Consensus size: 93
22552 AATTGTTTAA
* * *
22562 ACTTTTATAATTTTAGTCAACTAAAAACTTTATTTTTATTTAATTAAATCTAATATCCTTATAAT
1 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
** *
22627 TAATTTATTTTGACCATTTTACTATTTT
66 TAATTTATTTTGACCAAATTACTAATTT
* * *
22655 ACTTTTATAGTTTTACTCAACTACAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
*
22720 TATTTTAGTTTTG-CCAAATTACTAATTT
66 TAATTTA-TTTTGACCAAATTACTAATTT
22748 A
1 A
22749 ATTAAAAAGC
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
93 78 0.94
94 5 0.06
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.50
Consensus pattern (93 bp):
ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
TAATTTATTTTGACCAAATTACTAATTT
Found at i:24381 original size:2 final size:2
Alignment explanation
Indices: 24370--24401 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
24360 CGCTAGGTTT
24370 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24402 TCAAAATCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26598 original size:21 final size:23
Alignment explanation
Indices: 26567--26612 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
26557 TCGTTTTGGT
*
26567 TTTTATATTTT-TGTTTGTTTCG
1 TTTTATATTTTGTGTTTGTTACG
*
26589 TTTT-TATTTTGTTTTTGTTACG
1 TTTTATATTTTGTGTTTGTTACG
26611 TT
1 TT
26613 ATCAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.09, C:0.04, G:0.13, T:0.74
Consensus pattern (23 bp):
TTTTATATTTTGTGTTTGTTACG
Found at i:33816 original size:19 final size:20
Alignment explanation
Indices: 33779--33819 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
33769 CATCACATTC
*
33779 ACATTAGAATAATGTAGTGT
1 ACATTAGAATAATGGAGTGT
33799 ACATTAGAA-AATGGAGTGT
1 ACATTAGAATAATGGAGTGT
33818 AC
1 AC
33820 CTTTTCGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.29
Consensus pattern (20 bp):
ACATTAGAATAATGGAGTGT
Found at i:42823 original size:30 final size:30
Alignment explanation
Indices: 42789--42910 Score: 163
Period size: 30 Copynumber: 4.1 Consensus size: 30
42779 AAATTCTTCT
* *
42789 TCGGGATCCTCATCCGGGTCAAAATCTTTC
1 TCGGGATCCTCATCCGGGTCAAAATCCTCC
* *
42819 TCGGGATCCTCGTCCGGGTAAAAATCCTCC
1 TCGGGATCCTCATCCGGGTCAAAATCCTCC
42849 TCGGGATCCTCATCCGGGTCAAAATCCTCC
1 TCGGGATCCTCATCCGGGTCAAAATCCTCC
* * ** *
42879 TCGAGATCTTCATCAAGGTCAAAATCATCC
1 TCGGGATCCTCATCCGGGTCAAAATCCTCC
42909 TC
1 TC
42911 AGAATCCGAA
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 81 1.00
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (30 bp):
TCGGGATCCTCATCCGGGTCAAAATCCTCC
Found at i:45731 original size:11 final size:11
Alignment explanation
Indices: 45714--45743 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
45704 GAAAAAGACA
45714 GCTCTCTCACC
1 GCTCTCTCACC
*
45725 TCTCTCTCACC
1 GCTCTCTCACC
45736 GCTCTCTC
1 GCTCTCTC
45744 TCTAAAGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.53, G:0.07, T:0.33
Consensus pattern (11 bp):
GCTCTCTCACC
Found at i:50568 original size:36 final size:36
Alignment explanation
Indices: 50434--50871 Score: 300
Period size: 36 Copynumber: 12.1 Consensus size: 36
50424 GAAGATGACT
* * *
50434 ACCCTCGATCACTCTCG-ACTGAACTGAAGAAAGACC
1 ACCCTCGATCATTC-CGAACTAAACTGAAGAACGACC
* * * ** *
50470 ACCCTTGGTCATTCCGGCAC-AAACTTTAGAAAGACC
1 ACCCTCGATCATTCC-GAACTAAACTGAAGAACGACC
* * * ** * *
50506 ACCCTGGGTCA-ACTTAAATAAACTGAAAAACGACC
1 ACCCTCGATCATTCCGAACTAAACTGAAGAACGACC
* * *
50541 ACCCTCGATCATTCGGAACTAAACTGAAAAACAACC
1 ACCCTCGATCATTCCGAACTAAACTGAAGAACGACC
* * *
50577 ACACACGATCATTCCG-ACATAAACTGAAGAAAGACC
1 ACCCTCGATCATTCCGAAC-TAAACTGAAGAACGACC
* * * *
50613 ACCCTGGGTCAATT-TGAAATAAACTGAAGAACGACC
1 ACCCTCGATC-ATTCCGAACTAAACTGAAGAACGACC
* *
50649 ACCCTCGATCATTCCGAATTGAAATAAACTGAAGAATGACC
1 ACCCTCGATCATTCC-----GAACTAAACTGAAGAACGACC
** * * *
50690 ACCCTAAATCATTCTGAACTGAACTGAAGAACAACC
1 ACCCTCGATCATTCCGAACTAAACTGAAGAACGACC
*
50726 ACCCTCGATCATTCCG-ACTTAAACTGAAGAACAACC
1 ACCCTCGATCATTCCGAAC-TAAACTGAAGAACGACC
* *
50762 ACCCTCGATCATTCCG-ACTCAAACTGAAGAAAGACA
1 ACCCTCGATCATTCCGAACT-AAACTGAAGAACGACC
* * * * *
50798 ACCCTGGGTCAATT--GAAATAAACTGAGGAACGACG
1 ACCCTCGATC-ATTCCGAACTAAACTGAAGAACGACC
* * * *
50833 ACCCTCGATCATTCCGAACTGAACTTAAGAGCAACC
1 ACCCTCGATCATTCCGAACTAAACTGAAGAACGACC
50869 ACC
1 ACC
50872 ATGGGTCATT
Statistics
Matches: 314, Mismatches: 69, Indels: 38
0.75 0.16 0.09
Matches are distributed among these distances:
34 4 0.01
35 53 0.17
36 216 0.69
37 9 0.03
41 32 0.10
ACGTcount: A:0.38, C:0.29, G:0.15, T:0.18
Consensus pattern (36 bp):
ACCCTCGATCATTCCGAACTAAACTGAAGAACGACC
Found at i:50791 original size:149 final size:143
Alignment explanation
Indices: 50455--50871 Score: 412
Period size: 149 Copynumber: 2.9 Consensus size: 143
50445 CTCTCGACTG
* * ** * ** * *
50455 AACTGAAGAAAGACCACCCTTGGTC-ATTCCGGCACAAACTTTAGAAAGACCACCCTGGGTCAAC
1 AACTGAAGAAAGACCACCCTCGATCAATT-CGAAATAAACTGAAGAAAGACAACCCTGAGTCAA-
* * * * *
50519 TT-AAATAAACTGAAAAACGACCACCCTCGATCATTCGGAACTAAACTGAAAAACAACCACACAC
64 TTGAAATAAACTGAAGAACGACCACCCTCGATCATTCCGAACTGAACTGAAGAACAACCACCCAC
50583 GATCATTCCGACATA
129 GATCATTCCGACATA
* * * * * *
50598 AACTGAAGAAAGACCACCCTGGGTCAATTTGAAATAAACTGAAGAACGACCACCCTCGATCATTC
1 AACTGAAGAAAGACCACCCTCGATCAATTCGAAATAAACTGAAGAAAGACAACCCT-G---AGT-
* ** *
50663 CGAATTGAAATAAACTGAAGAATGACCACCCTAAATCATTCTGAACTGAACTGAAGAACAACCAC
61 C-AATTGAAATAAACTGAAGAACGACCACCCTCGATCATTCCGAACTGAACTGAAGAACAACCAC
* *
50728 CCTCGATCATTCCGACTTA
125 CCACGATCATTCCGACATA
* *
50747 AACTGAAGAACA-ACCACCCTCGATC-ATTCCG-ACTCAAACTGAAGAAAGACAACCCTGGGTCA
1 AACTGAAGAA-AGACCACCCTCGATCAATT-CGAAAT-AAACTGAAGAAAGACAACCCTGAGTCA
* * * *
50809 ATTGAAATAAACTGAGGAACGACGACCCTCGATCATTCCGAACTGAACTTAAGAGCAACCACC
63 ATTGAAATAAACTGAAGAACGACCACCCTCGATCATTCCGAACTGAACTGAAGAACAACCACC
50872 ATGGGTCATT
Statistics
Matches: 227, Mismatches: 36, Indels: 22
0.80 0.13 0.08
Matches are distributed among these distances:
143 100 0.44
144 5 0.02
145 1 0.00
147 1 0.00
148 9 0.04
149 110 0.48
150 1 0.00
ACGTcount: A:0.39, C:0.28, G:0.15, T:0.18
Consensus pattern (143 bp):
AACTGAAGAAAGACCACCCTCGATCAATTCGAAATAAACTGAAGAAAGACAACCCTGAGTCAATT
GAAATAAACTGAAGAACGACCACCCTCGATCATTCCGAACTGAACTGAAGAACAACCACCCACGA
TCATTCCGACATA
Found at i:50881 original size:143 final size:143
Alignment explanation
Indices: 50438--50873 Score: 461
Period size: 143 Copynumber: 3.0 Consensus size: 143
50428 ATGACTACCC
* * * * * **
50438 TCGATCACTCTCGAC-TGAACTGAAGAAAGACCACCCTTGGTCATTCCGGCACAAACTTTAGAAA
1 TCGATCATTC-CGACATAAACTGAAGAAAGACCACCCTCGGTCATTCCGACTCAAACTGAAGAAA
* * *
50502 GACCACCCTGGGTCAACTT-AAATAAACTGAAAAACGACCACCCTCGATCATTCGGAACTAAACT
65 GACCACCCTGGGTCAA-TTGAAATAAACTGAAGAACGACCACCCTCGATCATTCCGAACTGAACT
*
50566 GAAAAACAACCACACA
129 GAAGAACAACCAC-CA
* * *
50582 -CGATCATTCCGACATAAACTGAAGAAAGACCACCCTGGGTCAATT-TGAAAT-AAACTGAAGAA
1 TCGATCATTCCGACATAAACTGAAGAAAGACCACCCTCGGTC-ATTCCG-ACTCAAACTGAAGAA
* ** * ** *
50644 CGACCACCCTCGATCATTCCGAATTGAAATAAACTGAAGAATGACCACCCTAAATCATTCTGAAC
64 AGACCACCCT-G---GGT-C-AATTGAAATAAACTGAAGAACGACCACCCTCGATCATTCCGAAC
*
50709 TGAACTGAAGAACAACCACCC
123 TGAACTGAAGAACAACCACCA
* *
50730 TCGATCATTCCGACTTAAACTGAAGAACA-ACCACCCTCGATCATTCCGACTCAAACTGAAGAAA
1 TCGATCATTCCGACATAAACTGAAGAA-AGACCACCCTCGGTCATTCCGACTCAAACTGAAGAAA
* * * *
50794 GACAACCCTGGGTCAATTGAAATAAACTGAGGAACGACGACCCTCGATCATTCCGAACTGAACTT
65 GACCACCCTGGGTCAATTGAAATAAACTGAAGAACGACCACCCTCGATCATTCCGAACTGAACTG
*
50859 AAGAGCAACCACCA
130 AAGAACAACCACCA
50873 T
1 T
50874 GGGTCATTGT
Statistics
Matches: 240, Mismatches: 38, Indels: 29
0.78 0.12 0.09
Matches are distributed among these distances:
142 4 0.02
143 109 0.45
144 5 0.02
145 1 0.00
147 1 0.00
148 10 0.04
149 109 0.45
150 1 0.00
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.19
Consensus pattern (143 bp):
TCGATCATTCCGACATAAACTGAAGAAAGACCACCCTCGGTCATTCCGACTCAAACTGAAGAAAG
ACCACCCTGGGTCAATTGAAATAAACTGAAGAACGACCACCCTCGATCATTCCGAACTGAACTGA
AGAACAACCACCA
Found at i:50953 original size:24 final size:24
Alignment explanation
Indices: 50879--50956 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
50869 ACCATGGGTC
* * *
50879 ATTGTAACATTAAAT-AGTTGAAA
1 ATTGAAACATTGAATAATTTGAAA
* *
50902 GATTGAAGCATTGAATAATTTGGAA
1 -ATTGAAACATTGAATAATTTGAAA
*
50927 ATTGAAACATTGAATGA-TTGAAGA
1 ATTGAAACATTGAATAATTTGAA-A
50951 ATTGAA
1 ATTGAA
50957 GAAAGACCAC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
23 4 0.09
24 34 0.77
25 6 0.14
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (24 bp):
ATTGAAACATTGAATAATTTGAAA
Found at i:51314 original size:140 final size:140
Alignment explanation
Indices: 51129--51409 Score: 499
Period size: 140 Copynumber: 2.0 Consensus size: 140
51119 TGGATCAATT
*
51129 AACTTAAGATGGACCACCCTAGATCTGTTGAAATTCACTGTAGAGAGATTGCCCTGGATCTATTA
1 AACTTAAGATGGACCACCCTAGATCTGTTGAAATTCACTGTAGAGAGATCGCCCTGGATCTATTA
*
51194 ACTGAAGAAAGATCGCCATGGATCAATAAATAAACTGAAGAAAAATCGTCCTAGATCAATTTAAA
66 ACTGAAGAAAGATCGCCATGGATCAATAAATAAACTGAAGAAAAATCGCCCTAGATCAATTTAAA
51259 TTCACTAAAG
131 TTCACTAAAG
* *
51269 AACTTAAGATGGACCGCCCTAGGTCTGTTGAAATTCACTGTAGAGAGATCGCCCTGGATCTATTA
1 AACTTAAGATGGACCACCCTAGATCTGTTGAAATTCACTGTAGAGAGATCGCCCTGGATCTATTA
* *
51334 ATTGAAGAAAGATCGCCCTGGATCAATAAATAAACTGAAGAAAAATCGCCCTAGATCAATTTAAA
66 ACTGAAGAAAGATCGCCATGGATCAATAAATAAACTGAAGAAAAATCGCCCTAGATCAATTTAAA
*
51399 TTCCCTAAAG
131 TTCACTAAAG
51409 A
1 A
51410 GAGATCGGCC
Statistics
Matches: 134, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 134 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (140 bp):
AACTTAAGATGGACCACCCTAGATCTGTTGAAATTCACTGTAGAGAGATCGCCCTGGATCTATTA
ACTGAAGAAAGATCGCCATGGATCAATAAATAAACTGAAGAAAAATCGCCCTAGATCAATTTAAA
TTCACTAAAG
Found at i:52146 original size:49 final size:49
Alignment explanation
Indices: 52093--52218 Score: 234
Period size: 49 Copynumber: 2.6 Consensus size: 49
52083 TCCTATCCTG
*
52093 TTTCAAAAATTAATTATCATATAATAATCAATAATCCATAAATTATAAA
1 TTTCAAAAATTAATTATCATATAATAATCAATAATCCAGAAATTATAAA
*
52142 TTTCAAAAATTAATTATCATATAATAATCAATAATTCAGAAATTATAAA
1 TTTCAAAAATTAATTATCATATAATAATCAATAATCCAGAAATTATAAA
52191 TTTCAAAAATTAATTATCATATAATAAT
1 TTTCAAAAATTAATTATCATATAATAAT
52219 TAATTATCAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 75 1.00
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.38
Consensus pattern (49 bp):
TTTCAAAAATTAATTATCATATAATAATCAATAATCCAGAAATTATAAA
Found at i:52221 original size:18 final size:17
Alignment explanation
Indices: 52100--52236 Score: 83
Period size: 18 Copynumber: 8.2 Consensus size: 17
52090 CTGTTTCAAA
52100 AATTAATTATCATATAAT
1 AATTAATTATCATA-AAT
* *
52118 AATCAATAATCCATAAAT
1 AATTAATTAT-CATAAAT
* *
52136 TATAAATT-TC--AAA-
1 AATTAATTATCATAAAT
52149 AATTAATTATCATATAAT
1 AATTAATTATCATA-AAT
* * *
52167 AATCAATAATTCAGAAAT
1 AATTAATTA-TCATAAAT
* *
52185 TATAAATT-TC--AAA-
1 AATTAATTATCATAAAT
52198 AATTAATTATCATATAAT
1 AATTAATTATCATA-AAT
52216 AATTAATTATCATATAAT
1 AATTAATTATCATA-AAT
52234 AAT
1 AAT
52237 CAATAATCCA
Statistics
Matches: 92, Mismatches: 15, Indels: 24
0.70 0.11 0.18
Matches are distributed among these distances:
13 12 0.13
14 10 0.11
16 5 0.05
17 5 0.05
18 52 0.57
19 8 0.09
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.39
Consensus pattern (17 bp):
AATTAATTATCATAAAT
Found at i:53493 original size:19 final size:19
Alignment explanation
Indices: 53469--53520 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 19
53459 ATGTGAATTT
53469 TACTTATCAGTAATAATAA
1 TACTTATCAGTAATAATAA
53488 TACTTATC---AATAATAA
1 TACTTATCAGTAATAATAA
53504 TACTTATCAGTAATAAT
1 TACTTATCAGTAATAAT
53521 TTTACTTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 16 0.53
19 14 0.47
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (19 bp):
TACTTATCAGTAATAATAA
Found at i:53526 original size:19 final size:19
Alignment explanation
Indices: 53464--53527 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
53454 TTTTAATGTG
53464 AATTTTACTTATCAGTAAT
1 AATTTTACTTATCAGTAAT
** *
53483 AATAATACTTATCAATAAT
1 AATTTTACTTATCAGTAAT
53502 AA---TACTTATCAGTAAT
1 AATTTTACTTATCAGTAAT
53518 AATTTTACTT
1 AATTTTACTT
53528 GTCTTTCACA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
16 15 0.39
19 23 0.61
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (19 bp):
AATTTTACTTATCAGTAAT
Found at i:53972 original size:18 final size:19
Alignment explanation
Indices: 53949--53985 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
53939 CCCATCGCCC
53949 ATTTGTTA-TGTTATAATA
1 ATTTGTTATTGTTATAATA
*
53967 ATTTGTTATTTTTATAATA
1 ATTTGTTATTGTTATAATA
53986 TTCAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (19 bp):
ATTTGTTATTGTTATAATA
Found at i:55277 original size:22 final size:21
Alignment explanation
Indices: 55242--55293 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
55232 TCCGTTGACG
* *
55242 AAATAAT-TAAATAAAAGGAT
1 AAATAATAAAAATAAAACGAT
*
55262 AATTAAATAAAAATAAAACGAT
1 AAAT-AATAAAAATAAAACGAT
55284 AAATAATAAA
1 AAATAATAAA
55294 GATTCTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 9 0.35
22 14 0.54
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (21 bp):
AAATAATAAAAATAAAACGAT
Found at i:57327 original size:12 final size:11
Alignment explanation
Indices: 57305--57339 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
57295 GCTTTATCTC
57305 TTTTC-TTCTT
1 TTTTCTTTCTT
57315 TTTCTCTTTCTT
1 TTT-TCTTTCTT
57327 TTTTCTTTCTT
1 TTTTCTTTCTT
57338 TT
1 TT
57340 CTTTTTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.13
11 12 0.52
12 8 0.35
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:57337 original size:15 final size:15
Alignment explanation
Indices: 57301--57346 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
57291 TAGAGCTTTA
57301 TCTCTTTTCTTCTTTT
1 TCTCTTTTCTT-TTTT
57317 TCTC-TTTCTTTTTT
1 TCTCTTTTCTTTTTT
*
57331 CTTTCTTTTCTTTTTT
1 -TCTCTTTTCTTTTTT
57347 GATTGCTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 4 0.15
15 9 0.33
16 14 0.52
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TCTCTTTTCTTTTTT
Found at i:57899 original size:22 final size:22
Alignment explanation
Indices: 57871--57915 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
57861 ATGGGTATCC
57871 TTTCCCCATTTTCAACAAGTTA
1 TTTCCCCATTTTCAACAAGTTA
57893 TTTCCCCATTTTCAACAAGTTA
1 TTTCCCCATTTTCAACAAGTTA
57915 T
1 T
57916 GCTTCTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.04, T:0.42
Consensus pattern (22 bp):
TTTCCCCATTTTCAACAAGTTA
Found at i:60354 original size:13 final size:14
Alignment explanation
Indices: 60332--60363 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
60322 AAAAATATGC
60332 AAAT-ATTAAGC-T
1 AAATAATTAAGCAT
60344 AAATAATTAAGCAT
1 AAATAATTAAGCAT
60358 AAATAA
1 AAATAA
60364 ACAAAAATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.22
13 7 0.39
14 7 0.39
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (14 bp):
AAATAATTAAGCAT
Found at i:60977 original size:19 final size:19
Alignment explanation
Indices: 60955--61013 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
60945 TTTAACTACA
60955 CTGACTTTACTTAATTACC
1 CTGACTTTACTTAATTACC
* * * * *
60974 CTGAATTAAGTT-ACTA-A
1 CTGACTTTACTTAATTACC
60991 CTGACTTTACTTAATTACC
1 CTGACTTTACTTAATTACC
61010 CTGA
1 CTGA
61014 ATTAAGCTAC
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
17 9 0.32
18 6 0.21
19 13 0.46
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (19 bp):
CTGACTTTACTTAATTACC
Found at i:61001 original size:36 final size:36
Alignment explanation
Indices: 60949--61098 Score: 180
Period size: 35 Copynumber: 4.2 Consensus size: 36
60939 GATTCATTTA
*
60949 ACTACACTGACTTTACTTAATTACCCTGAATTAAGTT
1 ACTA-ACTGACTTTACTTAATTACCCTAAATTAAGTT
* *
60986 ACTAACTGACTTTACTTAATTACCCTGAATTAAGCT
1 ACTAACTGACTTTACTTAATTACCCTAAATTAAGTT
* * * *
61022 ACTTATTGAC-CTACTTGATTACCCTAAATTAAGTT
1 ACTAACTGACTTTACTTAATTACCCTAAATTAAGTT
* *
61057 GATTAA-TGA-TTTACTTAATTAACCTAAATTAAGTT
1 -ACTAACTGACTTTACTTAATTACCCTAAATTAAGTT
61092 ACTAACT
1 ACTAACT
61099 AGCTTTAGCT
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
34 4 0.04
35 47 0.48
36 42 0.43
37 4 0.04
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.39
Consensus pattern (36 bp):
ACTAACTGACTTTACTTAATTACCCTAAATTAAGTT
Found at i:61999 original size:16 final size:16
Alignment explanation
Indices: 61978--62011 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
61968 CGAACCCTCT
61978 TTTTCTTTT-TCTCTTC
1 TTTTCTTTTCT-TCTTC
61994 TTTTCTTTTCTTCTTC
1 TTTTCTTTTCTTCTTC
62010 TT
1 TT
62012 CCTCCTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTCTTTTCTTCTTC
Found at i:64535 original size:71 final size:71
Alignment explanation
Indices: 64460--64885 Score: 344
Period size: 71 Copynumber: 5.9 Consensus size: 71
64450 CTCCCGACTG
***
64460 AACTGAAGAAAGACCACCCTTGGTCATTCCGACAC-AAACTGAAGAAAAACCACCCTGGGTCAAC
1 AACTGAAGAAAGACCACCCTCAATCATTCCGA-ACTAAACTGAAGAAAAACCACCCTGGGTCAAC
64524 TGAAATA
65 TGAAATA
* * * * *
64531 AACTGAAGAACGACCACCCTCGATCATTCCGAACTAAACTGAA-AAACAACCACCCTCGATCATT
1 AACTGAAGAAAGACCACCCTCAATCATTCCGAACTAAACTGAAGAAA-AACCACCCTGGGTCA-A
* *
64595 CCGACATA
64 CTGAAATA
* * * ** **
64603 AACTGAAGAAAGACCACCCT-AGGTCAATT-TGAAATAAACTGAAGAACGACCACCCTCGATCAT
1 AACTGAAGAAAGACCACCCTCA-ATC-ATTCCGAACTAAACTGAAGAAAAACCACCCT-G---GG
*
64666 TCCGAATTGAAATA
60 T-C-AACTGAAATA
* * * * * * *
64680 AACTGAAGAATGACCACCCTCAATCATTCTGAACTGAACTGAAGAACAACCACCCCTCGATCATT
1 AACTGAAGAAAGACCACCCTCAATCATTCCGAACTAAACTGAAGAAAAACCA-CCCTGGGTCA-A
* *
64745 CCG-ACTCA
64 CTGAAAT-A
*
64753 AACTGAAGAACA-ACCACCCTCAATCATTCCG-ACTCAAACTGAAGAAAGACCACCCTGGGTCAA
1 AACTGAAGAA-AGACCACCCTCAATCATTCCGAACT-AAACTGAAGAAAAACCACCCTGGGTCAA
*
64816 TTGAAATA
64 CTGAAATA
* * * * **
64824 AACTGAGGAACGACCACCCTCAATCATTCCGAACTGAACTTAAGAGCAACCACCCTGGGTCA
1 AACTGAAGAAAGACCACCCTCAATCATTCCGAACTAAACTGAAGAAAAACCACCCTGGGTCA
64886 TTAAAGCATT
Statistics
Matches: 281, Mismatches: 52, Indels: 44
0.75 0.14 0.12
Matches are distributed among these distances:
70 5 0.02
71 102 0.36
72 66 0.23
73 50 0.18
74 1 0.00
76 4 0.01
77 47 0.17
78 6 0.02
ACGTcount: A:0.39, C:0.29, G:0.15, T:0.17
Consensus pattern (71 bp):
AACTGAAGAAAGACCACCCTCAATCATTCCGAACTAAACTGAAGAAAAACCACCCTGGGTCAACT
GAAATA
Found at i:64583 original size:107 final size:108
Alignment explanation
Indices: 64439--64808 Score: 383
Period size: 107 Copynumber: 3.4 Consensus size: 108
64429 GAAGATGACT
* * * * *
64439 ACCCTCGATCACTCCCG-ACTGAACTGAAGAAAGACCACCCTTGGTCATTCCGACACAAACTGAA
1 ACCCTCGATCA-TTCCGAACTAAACTGAAGAAAAACCACCCTCGATCATTCCGACACAAACTGAA
*
64503 GAAAAACCACCCTGGGTCAA-CTGAAATAAACTGAAGAACGACC
65 GAAAAACCACCCTAGGTCAATCTGAAATAAACTGAAGAACGACC
*
64546 ACCCTCGATCATTCCGAACTAAACTGAA-AAACAACCACCCTCGATCATTCCGACATAAACTGAA
1 ACCCTCGATCATTCCGAACTAAACTGAAGAAA-AACCACCCTCGATCATTCCGACACAAACTGAA
* *
64610 GAAAGACCACCCTAGGTCAATTTGAAATAAACTGAAGAACGACC
65 GAAAAACCACCCTAGGTCAATCTGAAATAAACTGAAGAACGACC
* ** * * *
64654 ACCCTCGATCATTCCGAATTGAAATAAACTGAAGAATGACCACCCTCAATCATTCTGA-ACTGAA
1 ACCCTCGATCATTCC-----GAACTAAACTGAAGAAAAACCACCCTCGATCATTCCGACAC-AAA
* * * * * * *
64718 CTGAAGAACAACCACCCCTCGATCATTCCG-ACTCAAACTGAAGAACAACC
60 CTGAAGAAAAACCA-CCCTAGGTCAATCTGAAAT-AAACTGAAGAACGACC
* *
64768 ACCCTCAATCATTCCG-ACTCAAACTGAAGAAAGACCACCCT
1 ACCCTCGATCATTCCGAACT-AAACTGAAGAAAAACCACCCT
64809 GGGTCAATTG
Statistics
Matches: 222, Mismatches: 28, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
106 7 0.03
107 67 0.30
108 39 0.18
109 21 0.09
112 1 0.00
113 46 0.21
114 41 0.18
ACGTcount: A:0.38, C:0.31, G:0.14, T:0.17
Consensus pattern (108 bp):
ACCCTCGATCATTCCGAACTAAACTGAAGAAAAACCACCCTCGATCATTCCGACACAAACTGAAG
AAAAACCACCCTAGGTCAATCTGAAATAAACTGAAGAACGACC
Found at i:64715 original size:108 final size:104
Alignment explanation
Indices: 64495--64784 Score: 276
Period size: 113 Copynumber: 2.7 Consensus size: 104
64485 ATTCCGACAC
*
64495 AAACTGAAGAAAAACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATTC
1 AAACTGAAGAAAAACCACCCTAGGTCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATTC
* *
64560 CGAACTAAACTGAAAAACAACCACCCTCGATCATTCCGACAT
66 CGAAATAAACTGAAAAACAACCACCCTCAATCATT-C--CAT
* *
64602 AAACTGAAGAAAGACCACCCTAGGTCAATTTGAAATAAACTGAAGAACGACCACCCTCGATCATT
1 AAACTGAAGAAAAACCACCCTAGGTCAA-CTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* ** *
64667 CCGAATTGAAATAAACTGAAGAATGACCACCCTCAATCATTCTGAACT
65 CC-----GAAATAAACTGAAAAACAACCACCCTCAATCATTC--CA-T
* * * * * * * * *
64715 GAACTGAAGAACAACCACCCCTCGATCATTCCG-ACTCAAACTGAAGAACAACCACCCTCAATCA
1 AAACTGAAGAAAAACCA-CCCTAGGTCA-ACTGAAAT-AAACTGAAGAACGACCACCCTCGATCA
64779 TTCCGA
63 TTCCGA
64785 CTCAAACTGA
Statistics
Matches: 151, Mismatches: 22, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
107 26 0.17
108 37 0.25
109 2 0.01
112 2 0.01
113 46 0.30
114 38 0.25
ACGTcount: A:0.40, C:0.29, G:0.13, T:0.18
Consensus pattern (104 bp):
AAACTGAAGAAAAACCACCCTAGGTCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATTC
CGAAATAAACTGAAAAACAACCACCCTCAATCATTCCAT
Found at i:64887 original size:36 final size:36
Alignment explanation
Indices: 64439--64879 Score: 357
Period size: 36 Copynumber: 12.1 Consensus size: 36
64429 GAAGATGACT
* *
64439 ACCCTCGATCACTCCCG-ACTGAACTGAAGAA-AGACC
1 ACCCTCGATCA-TTCCGAACTAAACTGAAGAACA-ACC
* * *
64475 ACCCTTGGTCATTCCGACAC-AAACTGAAGAAAAACC
1 ACCCTCGATCATTCCGA-ACTAAACTGAAGAACAACC
* * * * * *
64511 ACCCTGGGTCA-ACTGAAATAAACTGAAGAACGACC
1 ACCCTCGATCATTCCGAACTAAACTGAAGAACAACC
*
64546 ACCCTCGATCATTCCGAACTAAACTGAAAAACAACC
1 ACCCTCGATCATTCCGAACTAAACTGAAGAACAACC
64582 ACCCTCGATCATTCCG-ACATAAACTGAAGAA-AGACC
1 ACCCTCGATCATTCCGAAC-TAAACTGAAGAACA-ACC
* * * * *
64618 ACCCTAGGTCAATT-TGAAATAAACTGAAGAACGACC
1 ACCCTCGATC-ATTCCGAACTAAACTGAAGAACAACC
* **
64654 ACCCTCGATCATTCCGAATTGAAATAAACTGAAGAATGACC
1 ACCCTCGATCATTCC-----GAACTAAACTGAAGAACAACC
* * *
64695 ACCCTCAATCATTCTGAACTGAACTGAAGAACAACC
1 ACCCTCGATCATTCCGAACTAAACTGAAGAACAACC
64731 ACCCCTCGATCATTCCG-ACTCAAACTGAAGAACAACC
1 A-CCCTCGATCATTCCGAACT-AAACTGAAGAACAACC
*
64768 ACCCTCAATCATTCCG-ACTCAAACTGAAGAA-AGACC
1 ACCCTCGATCATTCCGAACT-AAACTGAAGAACA-ACC
* * * * *
64804 ACCCTGGGTCAATT--GAAATAAACTGAGGAACGACC
1 ACCCTCGATC-ATTCCGAACTAAACTGAAGAACAACC
* * * *
64839 ACCCTCAATCATTCCGAACTGAACTTAAGAGCAACC
1 ACCCTCGATCATTCCGAACTAAACTGAAGAACAACC
64875 ACCCT
1 ACCCT
64880 GGGTCATTAA
Statistics
Matches: 329, Mismatches: 52, Indels: 48
0.77 0.12 0.11
Matches are distributed among these distances:
34 4 0.01
35 58 0.18
36 195 0.59
37 39 0.12
41 33 0.10
ACGTcount: A:0.38, C:0.30, G:0.14, T:0.17
Consensus pattern (36 bp):
ACCCTCGATCATTCCGAACTAAACTGAAGAACAACC
Done.