Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019118.1 Corchorus olitorius cultivar O-4 contig19151, 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: 81209
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2707 original size:20 final size:20
Alignment explanation
Indices: 2675--2732 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 20
2665 TAAATAATTT
2675 TATGAAA-TTTGATAATCAA
1 TATGAAATTTTGATAATCAA
*
2694 TATGAAATTTTGATAACCTCCA
1 TATGAAATTTTGATAA--TCAA
* *
2716 TTTAAAATTTTGATAAT
1 TATGAAATTTTGATAAT
2733 TACACAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 7 0.21
20 9 0.27
22 17 0.52
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (20 bp):
TATGAAATTTTGATAATCAA
Found at i:2897 original size:22 final size:22
Alignment explanation
Indices: 2765--3523 Score: 216
Period size: 22 Copynumber: 35.1 Consensus size: 22
2755 GATACTATAC
* * *
2765 AATTTCGAGAACCTCCATATGA
1 AATTTTGATAACCTCCCTATGA
* *
2787 AATTTT-ATTAACTTTCCTAT-A
1 AATTTTGA-TAACCTCCCTATGA
* * *
2808 GGATTTTG-TTACACTCCCTATAAA
1 -AATTTTGATAAC-CTCCCTAT-GA
* * *
2832 AATTTTAATAACC-ACCTAATAA
1 AATTTTGATAACCTCCCT-ATGA
*
2854 AATTTTGATAACCACCCTATGA
1 AATTTTGATAACCTCCCTATGA
*
2876 AATTTTGATAACCTCCCAATGA
1 AATTTTGATAACCTCCCTATGA
* * * * ** *
2898 AATGTTGTTAAGGGCACATTACGA
1 AATTTTGATAA--CCTCCCTATGA
* * *
2922 AATTTTGATAACCTTCCGATAA
1 AATTTTGATAACCTCCCTATGA
* * *
2944 AATATTGATAACCAT-ACGATGA
1 AATTTTGATAACC-TCCCTATGA
* * *
2966 AATTGTGAT-ACCTCACTATAA
1 AATTTTGATAACCTCCCTATGA
*
2987 AAGTTTT-ATAAACCTCCCTATAA
1 AA-TTTTGAT-AACCTCCCTATGA
* *
3010 AATTTTGATAACCTCCATTTGA
1 AATTTTGATAACCTCCCTATGA
*
3032 AATTTTGATAACCT--C-ATAA
1 AATTTTGATAACCTCCCTATGA
* * *
3051 AAATTTGA-AA-ATCACTTCATGA
1 AATTTTGATAACCTC-CCT-ATGA
*
3073 AATTTTGATAACCAT-CTTATGA
1 AATTTTGATAACC-TCCCTATGA
* *
3095 AATTTTGATAACATCCGTAT-A
1 AATTTTGATAACCTCCCTATGA
* * * * *
3116 AATTTTTTATAAGCTTCTTATAA
1 AA-TTTTGATAACCTCCCTATGA
* *
3139 AATTTTGTTAACCT-CCTACGA
1 AATTTTGATAACCTCCCTATGA
*** * *
3160 AATTTTGATAAGAACACTATTA
1 AATTTTGATAACCTCCCTATGA
*
3182 AATTTTGATAA-C-CCCAATGA
1 AATTTTGATAACCTCCCTATGA
* ** *
3202 AATTTTGATAA-TTAACTACATAA
1 AATTTTGATAACCTCCCT--ATGA
** * *
3225 AATTACGATAACTTACCTATGA
1 AATTTTGATAACCTCCCTATGA
* * * * * *
3247 AAATCTGTTGATCTCCCTATAA
1 AATTTTGATAACCTCCCTATGA
* * * *
3269 AATTTTGAGAACCACACTATCA
1 AATTTTGATAACCTCCCTATGA
* *
3291 AATTTT-ATTAATCTCACTAT-A
1 AATTTTGA-TAACCTCCCTATGA
* **
3312 AATTTTGATAAACTCATTATGAAA
1 AATTTTGATAACCTCCCTATG--A
* *
3336 AATTTT-ATTAATCTCACTAT-A
1 AATTTTGA-TAACCTCCCTATGA
* **
3357 AATTTTGATAAACTCATTATGA
1 AATTTTGATAACCTCCCTATGA
* * * * *
3379 AATTTTAATTACCACACAATGA
1 AATTTTGATAACCTCCCTATGA
* *
3401 AAATTTGATAA-CTCCCTCTG-
1 AATTTTGATAACCTCCCTATGA
* ** *
3421 AA-----AT-ACCACATTATAA
1 AATTTTGATAACCTCCCTATGA
* *
3437 AATTTTGATAACCACACTATGA
1 AATTTTGATAACCTCCCTATGA
* * * *
3459 AATTTTGATAATCTCGCTCTAA
1 AATTTTGATAACCTCCCTATGA
*
3481 AATTTCGATAACCTCCC-ATGA
1 AATTTTGATAACCTCCCTATGA
*
3502 AATTTTGGTAACCT--CTATGA
1 AATTTTGATAACCTCCCTATGA
3522 AA
1 AA
3524 ATGTGATTAT
Statistics
Matches: 538, Mismatches: 149, Indels: 102
0.68 0.19 0.13
Matches are distributed among these distances:
14 1 0.00
15 6 0.01
16 2 0.00
17 1 0.00
18 2 0.00
19 10 0.02
20 25 0.05
21 92 0.17
22 310 0.58
23 48 0.09
24 40 0.07
25 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (22 bp):
AATTTTGATAACCTCCCTATGA
Found at i:3116 original size:107 final size:106
Alignment explanation
Indices: 3005--3212 Score: 226
Period size: 107 Copynumber: 1.9 Consensus size: 106
2995 TAAACCTCCC
* *
3005 TATAAAATTTTGATAACCTCCATT-TGAAATTTTGATAACCTCATA-AAAATTTGA-AA-ATCAC
1 TATAAAATTTTGATAACCTCC-TTATAAAATTTTGATAACCTCATACAAAATTTGATAAGAACAC
**
3066 TTCATGAAATTTTGATAACCATCTTATGAAATTTTGATAACATCCG
65 -T-ATGAAATTTTGATAACC--CCAATGAAATTTTGATAACATCCG
* * * * * * *
3112 TATAAATTTTTTATAAGCTTCTTATAAAATTTTGTTAACCTCCTACGAAATTTTGATAAGAACAC
1 TATAAAATTTTGATAACCTCCTTATAAAATTTTGATAACCTCATAC-AAAATTTGATAAGAACAC
*
3177 TATTAAATTTTGATAACCCCAATGAAATTTTGATAA
65 TATGAAATTTTGATAACCCCAATGAAATTTTGATAA
3213 TTAACTACAT
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
106 2 0.02
107 51 0.61
109 24 0.29
110 3 0.04
111 4 0.05
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (106 bp):
TATAAAATTTTGATAACCTCCTTATAAAATTTTGATAACCTCATACAAAATTTGATAAGAACACT
ATGAAATTTTGATAACCCCAATGAAATTTTGATAACATCCG
Found at i:3316 original size:21 final size:21
Alignment explanation
Indices: 3263--3385 Score: 88
Period size: 21 Copynumber: 5.6 Consensus size: 21
3253 GTTGATCTCC
* * *
3263 CTATAAAATTTTGAGAACCACA
1 CTATAAAATTTT-ATAAACTCA
* *
3285 CTATCAAATTTTATTAATCTCA
1 CTATAAAATTTTA-TAAACTCA
3307 CTAT-AAATTTTGATAAACTCA
1 CTATAAAATTTT-ATAAACTCA
* *
3328 TTATGAAAAATTTTATTAATCTCA
1 CTAT--AAAATTTTA-TAAACTCA
3352 CTAT-AAATTTTGATAAACTCA
1 CTATAAAATTTT-ATAAACTCA
* *
3373 TTATGAAATTTTA
1 CTATAAAATTTTA
3386 ATTACCACAC
Statistics
Matches: 83, Mismatches: 10, Indels: 17
0.75 0.09 0.15
Matches are distributed among these distances:
21 36 0.43
22 29 0.35
23 1 0.01
24 17 0.20
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (21 bp):
CTATAAAATTTTATAAACTCA
Found at i:3338 original size:24 final size:24
Alignment explanation
Indices: 3311--3380 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
3301 ATCTCACTAT
3311 AAATTTTGATAAACTCATTATGAA
1 AAATTTTGATAAACTCATTATGAA
* *
3335 AAATTTT-ATTAATCTCACTAT---
1 AAATTTTGA-TAAACTCATTATGAA
3356 AAATTTTGATAAACTCATTATGAA
1 AAATTTTGATAAACTCATTATGAA
3380 A
1 A
3381 TTTTAATTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
21 17 0.46
22 1 0.03
23 1 0.03
24 18 0.49
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (24 bp):
AAATTTTGATAAACTCATTATGAA
Found at i:3346 original size:45 final size:45
Alignment explanation
Indices: 3290--3380 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
3280 CCACACTATC
3290 AAATTTTATTAATCTCACTATAAATTTTGATAAACTCATTATGAA
1 AAATTTTATTAATCTCACTATAAATTTTGATAAACTCATTATGAA
3335 AAATTTTATTAATCTCACTATAAATTTTGATAAACTCATTATGAA
1 AAATTTTATTAATCTCACTATAAATTTTGATAAACTCATTATGAA
3380 A
1 A
3381 TTTTAATTAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (45 bp):
AAATTTTATTAATCTCACTATAAATTTTGATAAACTCATTATGAA
Found at i:3405 original size:45 final size:44
Alignment explanation
Indices: 3290--3411 Score: 140
Period size: 45 Copynumber: 2.8 Consensus size: 44
3280 CCACACTATC
* * *
3290 AAATTTTATTAATCTCACTATAAATTTTGATAAACTCATTATGAA
1 AAATTTTATTAACCACACAATAAATTTTGATAAACTCATTATG-A
* * *
3335 AAATTTTATTAATCTCACTATAAATTTTGATAAACTCATTATG-
1 AAATTTTATTAACCACACAATAAATTTTGATAAACTCATTATGA
*
3378 AAATTTTAATT-ACCACACAATGAAAATTTGATAA
1 AAATTTT-ATTAACCACACAAT-AAATTTTGATAA
3412 CTCCCTCTGA
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
43 14 0.20
44 14 0.20
45 43 0.61
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.40
Consensus pattern (44 bp):
AAATTTTATTAACCACACAATAAATTTTGATAAACTCATTATGA
Found at i:3466 original size:58 final size:59
Alignment explanation
Indices: 3371--3483 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 59
3361 TTGATAAACT
* * *
3371 CATTATGAAATTTTAATTACCACACAATGAAAATTTGATAA-CTCCCTCTGAAATACCA
1 CATTATAAAATTTTAATAACCACACAATGAAAATTTGATAATCTCCCTCTAAAATACCA
* * * *
3429 CATTATAAAATTTTGATAACCACACTATGAAATTTTGATAATCTCGCTCTAAAAT
1 CATTATAAAATTTTAATAACCACACAATGAAAATTTGATAATCTCCCTCTAAAAT
3484 TTCGATAACC
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
58 36 0.77
59 11 0.23
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.34
Consensus pattern (59 bp):
CATTATAAAATTTTAATAACCACACAATGAAAATTTGATAATCTCCCTCTAAAATACCA
Found at i:3525 original size:21 final size:22
Alignment explanation
Indices: 3479--3525 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
3469 ATCTCGCTCT
3479 AAAATTTCGATAACCTCCCATG
1 AAAATTTCGATAACCTCCCATG
* * *
3501 -AAATTTTGGTAACCT-CTATG
1 AAAATTTCGATAACCTCCCATG
3521 AAAAT
1 AAAAT
3526 GTGATTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (22 bp):
AAAATTTCGATAACCTCCCATG
Found at i:3778 original size:22 final size:22
Alignment explanation
Indices: 3635--3782 Score: 70
Period size: 22 Copynumber: 6.8 Consensus size: 22
3625 GATTATCTTT
* *
3635 TTATGAAATTTTGATAACATCC
1 TTATGAAATTTCGATAACCTCC
* * * *
3657 ATATAAAATTTCGATAATCGCC
1 TTATGAAATTTCGATAACCTCC
* * ***
3679 CTATGAAATTTTGATAA-CGAG
1 TTATGAAATTTCGATAACCTCC
*
3700 TGTATGAAATTATAG-TAACCTCC
1 T-TATGAAATT-TCGATAACCTCC
* * * ** *
3723 CTGTAAAATTTTTATAAACTTCC
1 TTATGAAATTTCGAT-AACCTCC
*
3746 -CATG-AATTTCGATAACCTCC
1 TTATGAAATTTCGATAACCTCC
3766 TTATGAAATTTCGATAA
1 TTATGAAATTTCGATAA
3783 TATCCCATGA
Statistics
Matches: 90, Mismatches: 29, Indels: 14
0.68 0.22 0.11
Matches are distributed among these distances:
20 6 0.07
21 13 0.14
22 62 0.69
23 9 0.10
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (22 bp):
TTATGAAATTTCGATAACCTCC
Found at i:3792 original size:21 final size:21
Alignment explanation
Indices: 3743--3796 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
3733 TTTATAAACT
*
3743 TCCCATG-AATTTCGATAACC
1 TCCCATGAAATTTCGATAACA
* *
3763 TCCTTATGAAATTTCGATAATA
1 TCC-CATGAAATTTCGATAACA
3785 TCCCATGAAATT
1 TCCCATGAAATT
3797 GTGATAAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 3 0.11
21 11 0.39
22 14 0.50
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.35
Consensus pattern (21 bp):
TCCCATGAAATTTCGATAACA
Found at i:3847 original size:22 final size:22
Alignment explanation
Indices: 3818--3873 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
3808 ACTATACTCG
3818 CTATAAAATTTTGAAAACCACA
1 CTATAAAATTTTGAAAACCACA
* * *
3840 TTATAAAATATTGAGAACCACA
1 CTATAAAATTTTGAAAACCACA
*
3862 CTATAAACTTTT
1 CTATAAAATTTT
3874 AGTTACCACA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.32
Consensus pattern (22 bp):
CTATAAAATTTTGAAAACCACA
Found at i:6171 original size:10 final size:11
Alignment explanation
Indices: 6139--6173 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
6129 GGTGCTTGGA
6139 TTTTTCTAATT
1 TTTTTCTAATT
*
6150 TTTTTTTAATT
1 TTTTTCTAATT
6161 TTTTTCT-ATT
1 TTTTTCTAATT
6171 TTT
1 TTT
6174 GATTTGTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTCTAATT
Found at i:7152 original size:17 final size:16
Alignment explanation
Indices: 7099--7153 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 16
7089 ATAAGTCTTC
7099 AAAAT-TTTTTATAAAA
1 AAAATATTTTT-TAAAA
*
7115 AAAATTATTGTTTTGAAA
1 AAAA-TATT-TTTTAAAA
7133 AAAATATTTTTTAAATA
1 AAAATATTTTTTAAA-A
7150 AAAA
1 AAAA
7154 AGGCAAAGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 10 0.30
17 10 0.30
18 10 0.30
19 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
AAAATATTTTTTAAAA
Found at i:8210 original size:41 final size:41
Alignment explanation
Indices: 8153--8230 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
8143 ATGACTTTCT
* *
8153 TTTCTTAACTAAATTTTCTTAAAAACACTTATAAAATTCCA
1 TTTCTTAACTAAATTTTCTTAAAAAAACTCATAAAATTCCA
*
8194 TTTCTTAACTGAATTTTCTTAAAAAAACTCATAAAAT
1 TTTCTTAACTAAATTTTCTTAAAAAAACTCATAAAAT
8231 AAAACAGCCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.42, C:0.15, G:0.01, T:0.41
Consensus pattern (41 bp):
TTTCTTAACTAAATTTTCTTAAAAAAACTCATAAAATTCCA
Found at i:12117 original size:18 final size:17
Alignment explanation
Indices: 12094--12127 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12084 TTGTTTTCTC
12094 GTTTGATCCAATGTTAAA
1 GTTTGATCCAAT-TTAAA
*
12112 GTTTGATTCAATTTAA
1 GTTTGATCCAATTTAA
12128 TAATGTTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (17 bp):
GTTTGATCCAATTTAAA
Found at i:13016 original size:99 final size:99
Alignment explanation
Indices: 12847--13043 Score: 292
Period size: 99 Copynumber: 2.0 Consensus size: 99
12837 AAGAGTCTTG
* *
12847 ATAATTACCATAATTATCTCTAACATATAAAGATAATATGGTTAATAAATATAATCACCATAATT
1 ATAATCACCATAATTATCTCTAACATATAAAGATAATATGGTTAATAAATATAATCACCAGAATT
*
12912 ATCTCT-A-ATATATGGATAATATGGTTAATAAT
66 ATCTCTAATATATATGAATAATATGGTTAATAAT
**
12944 ATAATCACCATAATTATCTCTATTATA-AATATGGATAATATGGTTAATAAATATAATCACCAGA
1 ATAATCACCATAATTATCTCTAACATATAA-A--GATAATATGGTTAATAAATATAATCACCAGA
*
13008 GTTATCTCTAATATATATGAATAATATGGTTAATAA
63 ATTATCTCTAATATATATGAATAATATGGTTAATAA
13044 AGGTAATTGG
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
96 2 0.02
97 25 0.28
99 38 0.43
100 1 0.01
101 23 0.26
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (99 bp):
ATAATCACCATAATTATCTCTAACATATAAAGATAATATGGTTAATAAATATAATCACCAGAATT
ATCTCTAATATATATGAATAATATGGTTAATAAT
Found at i:13044 original size:50 final size:50
Alignment explanation
Indices: 12847--13044 Score: 269
Period size: 50 Copynumber: 4.0 Consensus size: 50
12837 AAGAGTCTTG
* * *
12847 ATAATTACCATAATTATCTCTAACATATA-AAGATAATATGGTTAATAAAT
1 ATAATCACCATAATTATCTCTAATATATATGA-ATAATATGGTTAATAAAT
*
12897 ATAATCACCATAATTATCTCT-A-ATATATGGATAATATGGTTAAT-AAT
1 ATAATCACCATAATTATCTCTAATATATATGAATAATATGGTTAATAAAT
* *
12944 ATAATCACCATAATTATCTCTATTATAAATATGGATAATATGGTTAATAAAT
1 ATAATCACCATAATTATCTCTA--ATATATATGAATAATATGGTTAATAAAT
* *
12996 ATAATCACCAGAGTTATCTCTAATATATATGAATAATATGGTTAATAAA
1 ATAATCACCATAATTATCTCTAATATATATGAATAATATGGTTAATAAA
13045 GGTAATTGGT
Statistics
Matches: 134, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
47 24 0.18
48 19 0.14
49 1 0.01
50 46 0.34
51 21 0.16
52 23 0.17
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (50 bp):
ATAATCACCATAATTATCTCTAATATATATGAATAATATGGTTAATAAAT
Found at i:14050 original size:18 final size:18
Alignment explanation
Indices: 14027--14088 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
14017 GATAAGATAA
14027 GCACGGAGCTTAGTTGTT
1 GCACGGAGCTTAGTTGTT
* *
14045 GCACGGAGC-AAGTTGAAATAA
1 GCACGGAGCTTAGTTG---T-T
14066 GCACGGAGCTTAGTTGTT
1 GCACGGAGCTTAGTTGTT
14084 GCACG
1 GCACG
14089 AAGAAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 5 0.14
18 14 0.40
19 1 0.03
20 1 0.03
21 9 0.26
22 5 0.14
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (18 bp):
GCACGGAGCTTAGTTGTT
Found at i:17672 original size:35 final size:35
Alignment explanation
Indices: 17632--17706 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
17622 AGTTCGTTTA
*
17632 TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGGCTCGTTTATTATTCATTTAAG
*
17667 TGTTCACGAACATGCTCGTTTATTATTCATTTAAG
1 TGTTCACGAACAGGCTCGTTTATTATTCATTTAAG
17702 TGTTC
1 TGTTC
17707 GTTTATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (35 bp):
TGTTCACGAACAGGCTCGTTTATTATTCATTTAAG
Found at i:17769 original size:16 final size:16
Alignment explanation
Indices: 17748--17779 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17738 TATAATTATT
17748 TATATATTAATAATAA
1 TATATATTAATAATAA
*
17764 TATATATTATTAATAA
1 TATATATTAATAATAA
17780 AAATAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:17774 original size:19 final size:19
Alignment explanation
Indices: 17732--17784 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
17722 GAACGTTCGT
* *
17732 TTATTATATAATTATTTATA
1 TTATTA-ATAATAATATATA
17752 -TATTAATAATAATATATA
1 TTATTAATAATAATATATA
*
17770 TTATTAATAAAAATA
1 TTATTAATAATAATA
17785 ATAATATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATTAATAATAATATATA
Found at i:17786 original size:25 final size:27
Alignment explanation
Indices: 17756--17805 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
17746 TTTATATATT
17756 AATAATAATA-TATATTAT-TAATAAA
1 AATAATAATATTATATTATCTAATAAA
*
17781 AATAATAATATTCTATTATCTAATA
1 AATAATAATATTATATTATCTAATA
17806 TATTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 7 0.32
27 5 0.23
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (27 bp):
AATAATAATATTATATTATCTAATAAA
Found at i:17851 original size:17 final size:16
Alignment explanation
Indices: 17829--17865 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
17819 ATTTAATTAT
17829 TATATATAATATATATA
1 TATATATAAT-TATATA
17846 TATATATAATTATATA
1 TATATATAATTATATA
17862 -ATAT
1 TATAT
17866 TTTGTTCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 6 0.30
17 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TATATATAATTATATA
Found at i:17934 original size:18 final size:18
Alignment explanation
Indices: 17907--17941 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17897 AATTATTACA
17907 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
17925 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
17942 CAATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:28528 original size:15 final size:16
Alignment explanation
Indices: 28503--28532 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28493 AATAATTATT
28503 TTTAGATTATAATATA
1 TTTAGATTATAATATA
28519 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
28533 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:33306 original size:332 final size:329
Alignment explanation
Indices: 28998--33672 Score: 4079
Period size: 333 Copynumber: 14.2 Consensus size: 329
28988 AATAAGAAAT
* * * * *
28998 GCGTAAAAAGCCCTCCAATCTTTTCGGCGTTGAATTTTATA-TTTTTATGAGTATTTTAG-TAAA
1 GCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCT-AA
* * * *
29061 AAATTGA-GAAGAAATCTTTCGTGTCAATTTTTACAAAATTTTA-CTCGAAATTGTGTACTAACA
65 AAATTGAGGAA-AAATATTTCGAGTCAATTTTTGCAAAATTTTAGC-CGAAATCGTGTACT----
* * * * ** ** * *
29124 AACCATCACGGTTTTCGGCTAAAATCGCATTCTAGGAACCGGCTCAATATTGCATGATTTTTGGC
124 AA-CATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGC
* * * *
29189 TCCAAGACTACTTGAATTATCTATATTCATCTAATCAAATCTCAGCCACATTAGATTTAAGGGTT
188 GCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT-GATTTAAGGATT
* * *
29254 TGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAATAGGAAA
252 TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAA
29319 AACGATATTAGAAA
317 AACGATATTA-AAA
* *
29333 -CGTCAAAAG-CCTTTCAATCTTTTTGGCGTTGAATTATATATTTTTTTATGAGTATTTTAGCCA
1 GCGTGAAAAGTCC-TTCAATCTTTTTGGCGTTGAATTATATA-TTTTTTATGAGTATTTTAGCTA
** * * * *
29396 AAAATTGAGGAAATGTCTTTCAAGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAATCA
64 AAAATTGAGGAAAAATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA-CA
* ** ** * *
29461 TCACAGTTTTTGGCTAAAAATGCGATTTAGGACCCCGGCTCAGTTATGCCTGATTTTTGGCGCCA
128 TCACAGTTTTTGGCTAAAAACGCG-TTCCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCA
* * * *
29526 AGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTCTT
192 AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT-GATTTAAGGATTTGTT
* * * * *
29591 TTTACAAGCATCTAAATCTTGTTTCGATTTAATTAAAAATTAATTGAG-AAAAATATGAAAAATG
256 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACG
*
29655 ATACTAAAA
321 ATATTAAAA
* * * * * * * *
29664 GCTTGAAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTTTGTGAGTATTTAATCCA
1 GCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAA-T-TATATATTTTTTATGAGTATTTTAGCTA
* * * * * * *
29729 AAAATTGAGGAAAAATTTTTCGGGTCATTTTTTACAGAACTTTAGCC-AAA------A-T--C-G
64 AAAATTGAGGAAAAATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACAT
* * * * *
29783 CACGGTTTTTGGCTAAAATCGCGTTTCGGGGCTCCGACTCAGTTTTGCAAGATTTTTGGCG-CAG
129 CACAGTTTTTGGCTAAAAACGCGTTCCGGGGC-CCGGCTCAGTTTTGCATGATTTTTGGCGCCA-
* * * *
29847 AAACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTACATTTAAGGA-TT-TT
192 AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT-GATTTAAGGATTTGTT
* * *
29910 TTTACTACCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATG-AAAAGG
256 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACG
29973 AGTATTAAAA
321 A-TATTAAAA
* ** * * * ** *
29983 GCGCGAAAAACCCTTCAAACTTTTTTGC---G---TATATATTTTAT-TGAGTATCATGGCTAAA
1 GCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAA
* * * *
30041 AATTGAGGAAATATCTTTC-AGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTAATAATCAT
66 AATTGAGGAAAAATATTTCGA-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA-CAT
* * * * * * *
30105 CACGGTTTTTGGCTAAAAACGCGTTACGGGGCCGGGTTCAGTTTTGAATGATTTTTGGTGCCGAG
129 CACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAG
* **
30170 ACTCCTTGAAATATCTATATTCATCTAACCAAA--T---CC-C--------AACCA-TTGTTTTT
194 ACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGATTTAAGGATTTGTTTTT
* * *
30220 ACGAGCATCTGAATCATGTTTC-ATTTTAATTAAAAATTAATTCAGAAAAAAATAAGAAAAAC-A
259 ACGAGCATCTGAATCTTGTTTCGA-TTTAATTAGAAATTAATTCAG-AAAAAATATGAAAAACGA
*
30283 GTATTAGAA
322 -TATTAAAA
* * * * * *
30292 GCATGAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTATAAGTATTGTGGCTAAA
1 GCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAA
* * ** *
30357 AATTGAGGAAAAATATTTTGGGTCAATTTTTGCAAAATACTAGCCGAAATCGTG---TAACATTA
66 AATTGAGGAAAAATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACATCA
* * * * * * *
30419 CGGTTTTTTTTTGGCTTAAAA-GTGTTCTAGGGCCCCGGGTCAGTTTTGTATGATTTTTGGCGCC
131 CAG----TTTTTGGCTAAAAACGCGTTC-CGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCC
* ** * *
30483 ATA-AAT-GATGCAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGAATTAAGGAATT
191 A-AGACTCCTTG-AAATATCTATATTCATCTAATCAAATCTCAGCCACATT-GATTTAAGGATTT
* *
30546 -TTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAGTATGAAA
253 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAA-TATGAAA
* *
30610 AAAGAT-TTAGAA
317 AACGATATTAAAA
* ** * * *
30622 GCGTAAAAAACCCTTCAATATTTTTGGCGATGAATTATATATATTTTTTATGAGTATTTTAGCCA
1 GCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAA-T-TATATATTTTTTATGAGTATTTTAGCTA
* * * * *
30687 AAATTTGAGGAAATATTTTTTTCGA-TCAATTTTTGCAAAATGTTAGCCGAAATCGTGTAATAAA
64 AAAATTGAGGAAA-A-ATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT-AA
* * *
30751 TCATCACAGTTTTTGGCTAAAAACGCATTCCAGGGCCACATG-TCAGTTTTGCATGATTTTTGGC
126 -CATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCC-C-GGCTCAGTTTTGCATGATTTTTGGC
* * * * * * * *
30815 GCTAAAAATCCTTGAGATATCCATATTAATCTAATCAAATCTCATCCACATTGCATTTAATGATT
188 GCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTG-ATTTAAGGATT
* ** * *
30880 TGTTTTTACGAGTATCTCTATCTTGTTTCGATTTAATTACAAATTAATTCAAAAAAAATATGAAA
252 TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAA
*
30945 AACGATATGAACAA
317 AACGATATTAA-AA
* * * * *
30959 -CATGAAAAGTCCTCCAATCTTTTTGGCGTTAAATTATATATATTTAATGAGTATTTTAGAC-AA
1 GCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAG-CTAA
* * *
31022 AAATTAAGAAAAAAT-TTTCTG-GTCAATTTTTTGCAAAATTTTAGCCGAAATCGTGCACTAACC
65 AAATTGAGGAAAAATATTTC-GAGTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA-C
* * * * ** * *
31085 ATCACTGCTTTTTTTGCTAAAAATGCGTTTCGGGGCCCCAACTCAGTTTCGCATGATTTTTGCCG
127 ATCACAG--TTTTTGGCTAAAAACGCGTTCCGGGG-CCCGGCTCAGTTTTGCATGATTTTTGGCG
* * * *
31150 TCAAGACTCCTTGAAATATCTATATTTATCTAATCAAATCTCAGCTACATTGCATTTAAGGATGT
189 CCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTG-ATTTAAGGATTT
* * *
31215 GTTTTTACTAGCATCTGAATCTTGTTTTGATTTAATTTGAAATTAATTCAG-AAAAATATGAAAA
253 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAA
*
31279 ACGATACTAAAA
318 ACGATATTAAAA
* * * * *
31291 GCGTGAAAAGTTCTGCAATCTTTTTGGCATTGAAATATATATATTTTATGAGTATTTTAGAC-AA
1 GCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAG-CTAA
* * *
31355 AAATTGAGGAAAAATAATTCTGA-TAAATTTTTGCAAAATATTAGCCGAAATCGTGTACGTTAGT
65 AAATTGAGGAAAAATATTTC-GAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TA--
* * * * *
31419 CGAAATTAC-GTTTTTTTTTTTTGCTAAAAACGCGTTCTGGGGTCCCGG-TACAGTGTTGCATGA
125 --ACATCACAG------TTTTTGGCTAAAAACGCGTTCCGGGG-CCCGGCT-CAGTTTTGCATGA
* * * *
31482 TTTTTGGCGCTAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCGGCCACAATGGATT
180 TTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCAC-ATTGATT
* *** * * * * *
31547 TAAGGATTT-CTAAAACAAGAATCTGAATCATGTTTCGATTTAATCAGAAATTAATT-TGAAAAA
244 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAA
* *
31610 TAATAGGAAAAACGATATTAGAA
308 -AATATGAAAAACGATATTAAAA
* * * * * * * *
31633 GCATGAAAAGCCCTTCAATCTTATTGGCGTTGAATTATATAATTTTAATGAGTATTATGGCTAAT
1 GCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAA
* *
31698 AATTGAGG--AAATA-----A--C---TTTGGCTAAAA---T---CG--TTC--G-A-TAATCAT
66 AATTGAGGAAAAATATTTCGAGTCAATTTTTGC-AAAATTTTAGCCGAAATCGTGTACTAA-CAT
* * * * ** * *
31739 CACGGTTTTTGGCTAAAATCGCGTTTCGGGACCCTGATTCAGTTTTGCAAGATTTTTGGCGACAA
129 CACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCC-GGCTCAGTTTTGCATGATTTTTGGCGCCAA
* * * * * * * *
31804 GACTCTTTGAGATATCCATATTCATCTAATTAAATATCAGCAACATTGGATTTAAGAATTTCTTT
193 GACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT-GATTTAAGGATTTGTTT
* * * *
31869 TTATGAGCATTTGAATCTTATTTCGATTTAATTAGAAATTAATTCA-AAAAAATAAT-AAAAATG
257 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAT-ATGAAAAACG
31932 ATATTAAAA
321 ATATTAAAA
* * * * *
31941 GCTTG-AAAGTTCTCCAATCTTTTTGGCATTAAATTATATATATATATATATTATGAGTATTTTA
1 GCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAA-T-TATATAT-T-T-T-TTATGAGTATTTTA
* * *
32005 G-TCAAAAATTGTCGGAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC
60 GCT-AAAAATTG-AGGAAAAATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC
* * * * *
32069 TAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGAGGCCTCGGCTTAGTTTTGCATTATTTTT-
123 TAA-CATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCC-CGGCTCAGTTTTGCATGATTTTTG
* ** * * * *
32133 GCACTGAGACTTCTTGAAATATCTTTATTCATCTAATCAAGTCTCAGCCACATTGAATCTAAGGA
186 GCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTG-ATTTAAGGA
* *
32198 TTTGTTTTTACGAGCCTCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCCG-AAAAATATGA
250 TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGA
32262 AAAACGATATTAAAA
315 AAAACGATATTAAAA
* * * * * * * *
32277 GTGTG-AAAGTCCTCCAGTCTTTTTGGTGTTGAATTATATATATGTTATGAGTGTTGTGT-CCT-
1 GCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATT-T-TAGCTA
* * * * * *
32339 AAAATTGA-GACAAAATATTTCGGGTTAATTTTTGCAAAAGTTTAGCCAAAATAGT-T--TACCA
64 AAAATTGAGGA-AAAATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACA
* ** *
32400 TCACAGTTTTTTTTGCTAAAAACGCGTTCCGAAGCTCCGAG-TCAGTTTTGCATGATTTTTGGTG
128 TCACAG--TTTTTGGCTAAAAACGCGTTCCGGGGC-CCG-GCTCAGTTTTGCATGATTTTTGGCG
* * * * * *
32464 GCAAAACTCCTTGAAACATCTATATTTATCTAACCAAATCTTAGCCACACTTGATTTAAGGATTT
189 CCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACA-TTGATTTAAGGATTT
* * * * *
32529 GTTTTTA-GAGCATTTGAATCATGTTTCAATTTAATTAGAAATTAATT-TGAAAAAATA-GGAAA
253 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAA
* *
32591 ACTTATATTAGAA
318 AC-GATATTAAAA
* * * * *
32604 GCGTGAGAA-T-C-TCACTCTTTTTGGCGTTGAATTATATATTTTTAATGAGTATTGTGGCTAAA
1 GCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAA
*
32666 AATTGA-GAAAAGTATTTC-ATGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC---CATC
66 AATTGAGGAAAAATATTTCGA-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACATC
** * *
32726 ATTGTTTTTGGCTAAAAACGCGTTCCGGGGTCCTGGGTCAGTTTTGCATGATTTTTGGCGCCAAG
130 ACAGTTTTTGGCTAAAAACGCGTTCCGGGG-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAG
* *
32791 ACTCCTTAAAATATATCTATATTCATCTAACCAAATCTCAGCCACATTGTATTTAAGGATTTGTT
194 ACTCCTT-GAA-ATATCTATATTCATCTAATCAAATCTCAGCCACATTG-ATTTAAGGATTTGTT
*** * * * * ** * *
32856 TTTACGAATTTCTAAATCTTATTTTGATTTAATCAGAAATTAATTTGGAAATAAAATAGGGAAAA
256 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AA-AAAATATGAAAAA
32921 CGATATTAAAA
319 CGATATTAAAA
* * * * * *
32932 GCGTGAAAAATGCTTTC-ATTTTTTTTGCGTTGAATTATATATTTTTTATGAGTATTTTCGCTAG
1 GCGTGAAAAGT-CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTAA
* * * *
32996 AAATCGAGGAAAAATATTTCGAGTCAATTTTTGGAAAATTTTAGCTGAAATCTTGTACTAACAAT
65 AAATTGAGGAAAAATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC-AT
* * * * * *
33061 CACAATTTTCGGCTAAAAATGCGTTCCGGGGTCTGGCTCAGTTTTGCATGATTTTTGGTGCCAAG
129 CACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAG
* * * * *
33126 GCTCCTTGAAATATCTATATTCATTTAACCAAATCTTAGCCACATTAGATTTAAGGATTTATTTT
194 ACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT-GATTTAAGGATTTGTTTT
* * * *
33191 TACGAGCATCTGAATCTTGGTTCGATTTAATTAGAAATTAATTCGGAAAGAAATAGGAAAAACAA
258 TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAA-AAATATGAAAAACGA
*
33256 TATTAGAA
322 TATTAAAA
* * *** * * * *
33264 GCGTTAAAAGCCCTTCAATCTTTTTGATATCGAATCATATATTTTTCATGAGTATTTTAGCCAAA
1 GCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAA
* * * * *
33329 AACTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATC
66 AATTGAGGAAAAATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA-CATC
* * * *
33394 ACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCACGGCTCTGTTTTGCATGATTTTTGGCGCCGAG
130 ACAGTTTTTGGCTAAAAACGCGTTCCGGGGCC-CGGCTCAGTTTTGCATGATTTTTGGCGCCAAG
* * *
33459 ACTCCTTGAAATATCTTTATTCATCTAATAAAATCTCAGTCACATTGGATTTAAGGATTT-TTTT
194 ACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT-GATTTAAGGATTTGTTTT
* * * * * *
33523 TATGCGCATCTAAATCTTGTATCAATTTAATTAGATATTAATTCAGAAAAAA-ATGAAAAACGAT
258 TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGAT
33587 ATTAAAA
323 ATTAAAA
* * * * * *
33594 GCTTGAAAAGTCCTCCAATATTTTTGACGTTTAATTATATATATTTTATGAGTACTTTT-G-TCA
1 GCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTA-TTTTAGCT-A
33657 AAAATTGAGGAAAAAT
64 AAAATTGAGGAAAAAT
33673 CTTTTAGGTC
Statistics
Matches: 3530, Mismatches: 607, Indels: 411
0.78 0.13 0.09
Matches are distributed among these distances:
306 6 0.00
307 66 0.02
308 27 0.01
309 144 0.04
310 89 0.03
311 15 0.00
312 10 0.00
313 23 0.01
314 6 0.00
315 19 0.01
316 135 0.04
317 4 0.00
318 8 0.00
319 82 0.02
320 11 0.00
321 154 0.04
322 90 0.03
323 10 0.00
324 95 0.03
325 90 0.03
326 17 0.00
327 101 0.03
328 88 0.02
329 50 0.01
330 136 0.04
331 129 0.04
332 368 0.10
333 545 0.15
334 256 0.07
335 136 0.04
336 319 0.09
337 62 0.02
338 11 0.00
339 2 0.00
340 43 0.01
341 103 0.03
342 80 0.02
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (329 bp):
GCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAA
AATTGAGGAAAAATATTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACATCA
CAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGAC
TCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGATTTAAGGATTTGTTTTTAC
GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATT
AAAA
Found at i:37037 original size:18 final size:17
Alignment explanation
Indices: 37016--37050 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
37006 TTGTTTTGTC
37016 GTTTGATACAATGTTAAT
1 GTTTGATACAAT-TTAAT
*
37034 GTTTGATTCAATTTAAT
1 GTTTGATACAATTTAAT
37051 AATGTTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (17 bp):
GTTTGATACAATTTAAT
Found at i:38476 original size:12 final size:12
Alignment explanation
Indices: 38459--38490 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
38449 GTGAACATCA
38459 AACGAACATGTT
1 AACGAACATGTT
38471 AACGAACATGTT
1 AACGAACATGTT
38483 AACGAACA
1 AACGAACA
38491 ATAATTGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.19
Consensus pattern (12 bp):
AACGAACATGTT
Found at i:38540 original size:18 final size:18
Alignment explanation
Indices: 38517--38551 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
38507 ACATAAACTG
38517 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
38535 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
38552 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:38697 original size:16 final size:16
Alignment explanation
Indices: 38676--38707 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38666 TTTATAATTT
38676 TTATTAATAATATATA
1 TTATTAATAATATATA
*
38692 TTATTATTAATATATA
1 TTATTAATAATATATA
38708 AATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTAATAATATATA
Found at i:38700 original size:19 final size:19
Alignment explanation
Indices: 38676--38723 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
38666 TTTATAATTT
* *
38676 TTATTAATAATATATATTA
1 TTATTAATAATATAAATAA
38695 TTATTAAT-ATATAAATAA
1 TTATTAATAATATAAATAA
38713 TTATATAATAA
1 TTAT-TAATAA
38724 ACGAACGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 12 0.48
19 12 0.48
20 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTATTAATAATATAAATAA
Found at i:38796 original size:35 final size:35
Alignment explanation
Indices: 38749--38827 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
38739 TTATATAAAA
*
38749 GAACACTAAAATGAACAATAAACGAGCCTGTTCGT
1 GAACACTAAAATGAACAATAAACGAGCATGTTCGT
*
38784 GAACACTTAAATGAACAATAAACGAGCATGTTCGT
1 GAACACTAAAATGAACAATAAACGAGCATGTTCGT
38819 GAACA-TAAA
1 GAACACTAAA
38828 CGAACTAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 3 0.07
35 38 0.93
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.20
Consensus pattern (35 bp):
GAACACTAAAATGAACAATAAACGAGCATGTTCGT
Found at i:59201 original size:127 final size:125
Alignment explanation
Indices: 58855--59229 Score: 633
Period size: 128 Copynumber: 2.9 Consensus size: 125
58845 CCACCTGCAA
*
58855 AAAAGTGATATTTCGAAAATTTATTAAGTAAAATCAAGTAATTAATATAATTTATCTCAATTACA
1 AAAAGTGATATTTCGAAAATTTATTAAGTAATATCAAGTAATTAATATAATTTATCTCAATTACA
* *
58920 ATTTTAGTGACTAATATTATCATTAAAAAAGTAAAAATCCTCTACTATTTTAGATTCCTGTAG
66 ATTTCAGTGACTAATA-TA--ATTAAAAAAGTCAAAATCCTCTACTATTTTAGATTCCTGTAG
*
58983 AAAAGTGATATTTCGAAATTTTATTAAGTAATATCAAGTAATTAATATAATTTATCTCAATTACA
1 AAAAGTGATATTTCGAAAATTTATTAAGTAATATCAAGTAATTAATATAATTTATCTCAATTACA
59048 ATTTCAGTGACTAATATAATTAAAAAAGTCAAAATCCTCTACTATTTTAGATTCCTGTAG
66 ATTTCAGTGACTAATATAATTAAAAAAGTCAAAATCCTCTACTATTTTAGATTCCTGTAG
*
59108 AAAAGTATGATATTTCGAAAATTTATTAAGTAATATCAAGTAATTAATATAATTATATCTCACTT
1 AAAAG--TGATATTTCGAAAATTTATTAAGTAATATCAAGTAATTAATATAATT-TATCTCAATT
*
59173 ACAATTTCAATGACTAATATAATTAAAAAAGTCAAAAATCCTCTACTATTTTAGATT
63 ACAATTTCAGTGACTAATATAATTAAAAAAGTC-AAAATCCTCTACTATTTTAGATT
59230 GGTTACCGAG
Statistics
Matches: 236, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
125 46 0.19
127 48 0.20
128 119 0.50
129 23 0.10
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (125 bp):
AAAAGTGATATTTCGAAAATTTATTAAGTAATATCAAGTAATTAATATAATTTATCTCAATTACA
ATTTCAGTGACTAATATAATTAAAAAAGTCAAAATCCTCTACTATTTTAGATTCCTGTAG
Found at i:61534 original size:13 final size:13
Alignment explanation
Indices: 61516--61543 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
61506 TGTCGTCTTT
61516 ATACCGTCTTCAA
1 ATACCGTCTTCAA
61529 ATACCGTCTTCAA
1 ATACCGTCTTCAA
61542 AT
1 AT
61544 TCATCTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (13 bp):
ATACCGTCTTCAA
Found at i:63521 original size:2 final size:2
Alignment explanation
Indices: 63514--63542 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
63504 GTCCTTATGA
63514 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
63543 ATTGTTTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:70652 original size:2 final size:2
Alignment explanation
Indices: 70645--70679 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
70635 CTCGTACTTT
70645 TA TA TA TA GTA 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
70680 ATAATCAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:76211 original size:21 final size:22
Alignment explanation
Indices: 76164--76212 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
76154 ACAGACCTAT
76164 TTGCAGATATTACAGGCTTTGC
1 TTGCAGATATTACAGGCTTTGC
*
76186 -AGCAGA-AGTTACAGGC-TTGC
1 TTGCAGATA-TTACAGGCTTTGC
76206 TTGCAGA
1 TTGCAGA
76213 GATTGAGGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (22 bp):
TTGCAGATATTACAGGCTTTGC
Found at i:76318 original size:30 final size:30
Alignment explanation
Indices: 76282--76344 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
76272 GTTTAGATGC
76282 TCCACTCAATGTAGGGCGTCCAGTGGGTGT
1 TCCACTCAATGTAGGGCGTCCAGTGGGTGT
*
76312 TCCACTCAATGTAGGGCGTCCAGTTGGTGT
1 TCCACTCAATGTAGGGCGTCCAGTGGGTGT
76342 TCC
1 TCC
76345 GGGTCTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.29
Consensus pattern (30 bp):
TCCACTCAATGTAGGGCGTCCAGTGGGTGT
Found at i:80947 original size:2 final size:2
Alignment explanation
Indices: 80942--80998 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
80932 TTTTCAGCTG
80942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
80983 AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT
80999 TAAAAGTAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.