Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2999.1
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: 170946
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.30
Warning! 9967 characters in sequence are not A, C, G, or T
Found at i:481 original size:26 final size:26
Alignment explanation
Indices: 420--525 Score: 137
Period size: 26 Copynumber: 4.2 Consensus size: 26
410 GGCCTAGCTT
*
420 CTTTT-AAT-AACTGGGGCAAAAGCC
1 CTTTTCAATAAACTGGGGCATAAGCC
*
444 C-TTTCGATAAACTGGGGCATAAGCC
1 CTTTTCAATAAACTGGGGCATAAGCC
*
469 CTTTTCAATAAACTAGGGCATAAGCC
1 CTTTTCAATAAACTGGGGCATAAGCC
** *
495 CTTTTCGGTAAACTGGGGCATAAACC
1 CTTTTCAATAAACTGGGGCATAAGCC
521 CTTTT
1 CTTTT
526 GCACTTACTC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
23 3 0.04
24 3 0.04
25 16 0.23
26 49 0.69
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (26 bp):
CTTTTCAATAAACTGGGGCATAAGCC
Found at i:600 original size:20 final size:20
Alignment explanation
Indices: 575--689 Score: 155
Period size: 20 Copynumber: 5.8 Consensus size: 20
565 TTATGAATAC
*
575 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
595 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
615 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* * * *
635 ATCATGTACATTTTATACCT
1 ATCATGTGCATATCATACAT
655 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
675 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
690 TCCCACATAT
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.09
20 76 0.89
21 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:606 original size:11 final size:11
Alignment explanation
Indices: 575--630 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
565 TTATGAATAC
575 ATCATGTGCAT
1 ATCATGTGCAT
* *
586 TTCA--TACAT
1 ATCATGTGCAT
595 ATCATGTGCAT
1 ATCATGTGCAT
*
606 ATCA--TACAT
1 ATCATGTGCAT
615 ATCATGTGCAT
1 ATCATGTGCAT
626 ATCAT
1 ATCAT
631 ACATATCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:615 original size:9 final size:9
Alignment explanation
Indices: 587--639 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
577 CATGTGCATT
587 TCATACATA
1 TCATACATA
*
596 TCATGTGCATA
1 TCA--TACATA
607 TCATACATA
1 TCATACATA
*
616 TCATGTGCATA
1 TCA--TACATA
627 TCATACATA
1 TCATACATA
636 TCAT
1 TCAT
640 GTACATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
9 20 0.56
11 16 0.44
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.36
Consensus pattern (9 bp):
TCATACATA
Found at i:7538 original size:18 final size:18
Alignment explanation
Indices: 7512--7546 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7502 TCGTAACGTT
*
7512 GTGTTGTTTGGAAAACAA
1 GTGTCGTTTGGAAAACAA
*
7530 GTGTCGTTTTGAAAACA
1 GTGTCGTTTGGAAAACA
7547 CGTCCCAGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (18 bp):
GTGTCGTTTGGAAAACAA
Found at i:8147 original size:25 final size:26
Alignment explanation
Indices: 8116--8202 Score: 140
Period size: 26 Copynumber: 3.4 Consensus size: 26
8106 AACTGGGAAA
8116 AAGCCC-TTTCGGTAAACTGGGGCAT
1 AAGCCCTTTTCGGTAAACTGGGGCAT
** *
8141 AAGCCCTTTTCAATAAACTAGGGCAT
1 AAGCCCTTTTCGGTAAACTGGGGCAT
8167 AAGCCCTTTTCGGTAAACTGGGGCAT
1 AAGCCCTTTTCGGTAAACTGGGGCAT
8193 AAGCCCTTTT
1 AAGCCCTTTT
8203 GCACTTCCTC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
25 6 0.11
26 49 0.89
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (26 bp):
AAGCCCTTTTCGGTAAACTGGGGCAT
Found at i:8277 original size:20 final size:20
Alignment explanation
Indices: 8252--8326 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
8242 TTATGAATAC
8252 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* * *
8272 ATCATGTGCATTTTATACCT
1 ATCATGTGCATATCATACAT
*
8292 ATCATGTGAATATCATATCA-
1 ATCATGTGCATATCATA-CAT
8312 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
8327 TCCCACGTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 8 0.17
20 38 0.81
21 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:10200 original size:207 final size:207
Alignment explanation
Indices: 9746--10434 Score: 1071
Period size: 207 Copynumber: 3.3 Consensus size: 207
9736 GTTACAATAT
* * *
9746 TCTGTCCTCCGTCAAATATGGAGACGCTAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCA
1 TCTGCCCTCCGTCGAATATGGAGACGCCAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCA
* * * * * * * * *
9811 AATCATCTTAGACTTGCTTCAGCATAAGCATGCGAGAA-CCAAGTCAACTATGTCTTCGATTTGC
66 AATCATCTTAGACTTGCTTCAACGTAAACACGTGA-AAGCCAAATCAGCTATGTCTTTGATTTGT
* * * *
9875 TCCTTGTAAG--CAAGGATGCCAAATCATCTTAGATCTTGCTTTAGTACAAACATCTGAAGGCCA
130 TCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTTGCTTCAGTATAAACATCTGAAGGCCA
9938 GATCTGCTATGTG
195 GATCTGCTATGTG
* *
9951 TCTGCCCTCCGTCGAATATGGAGACGCCAAACTTCAATTTGTTCTCTGACAATACAGAGATGCAA
1 TCTGCCCTCCGTCGAATATGGAGACGCCAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCA
*
10016 AATCATCTTAGACTTGCTTCAATGTAAACACGTGAAAGCCAAATCAGCTATGTCTTTGATTTGTT
66 AATCATCTTAGACTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTATGTCTTTGATTTGTT
* * *
10081 CCTTGTAAGCACAAGGATGCCAAACCATATTGGATCTTGCTTCAGTATAAACATCTAAAGGCAAG
131 CCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTTGCTTCAGTATAAACATCTGAAGGCCAG
10146 ATCTGCTATGTG
196 ATCTGCTATGTG
*
10158 TCTGCCCTCCGTCGAATATGGAGACGCCAAAATTTC-ATTTGTTCTCTGACAATACAGAGATGCC
1 TCTGCCCTCCGTCGAATATGGAGACGCC-AAACTTCGATTTGTTCTCTGACAATACAGAGATGCC
* * *
10222 AAATCACCTTAGACTTGCTTCAACGTAAACTCGTGAAAGCCAAATTAGCTATGTCTTTGATTTGT
65 AAATCATCTTAGACTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTATGTCTTTGATTTGT
10287 TCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTTGCTTCAGTATAAACATCTGAAGGCCA
130 TCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTTGCTTCAGTATAAACATCTGAAGGCCA
*
10352 GATCTGCTATGCG
195 GATCTGCTATGTG
* *
10365 TCTGCCCTCCGTCGAATATGGAGACGCCAAACCTCGATTTGTTCTCTGACAATACAGAGATACCA
1 TCTGCCCTCCGTCGAATATGGAGACGCCAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCA
10430 AATCA
66 AATCA
10435 GCTATGTCTT
Statistics
Matches: 444, Mismatches: 35, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
204 2 0.00
205 121 0.27
206 5 0.01
207 310 0.70
208 6 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (207 bp):
TCTGCCCTCCGTCGAATATGGAGACGCCAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCA
AATCATCTTAGACTTGCTTCAACGTAAACACGTGAAAGCCAAATCAGCTATGTCTTTGATTTGTT
CCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTTGCTTCAGTATAAACATCTGAAGGCCAG
ATCTGCTATGTG
Found at i:10463 original size:83 final size:86
Alignment explanation
Indices: 10364--10524 Score: 229
Period size: 90 Copynumber: 1.9 Consensus size: 86
10354 TCTGCTATGC
*
10364 GTCTGCCCTCCGTCGAATATGGAGACGCCAAA-C-C-TCGATTTGTTCTCTGACAATACAGAGAT
1 GTCTGCCCTCCGTCGAATATGGAGACGCCAAATCTCTTCGATTTGTTCTCTGACAATACAGAGAC
10426 ACCAAATCAGCTATGTCTTCG
66 ACCAAATCAGCTATGTCTTCG
* *
10447 GTCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTGTTCTCTGACAATACAG
1 GTCTGCCCTCCGTCGAATATGGAGACGCCAAATC----TCTTCGATTTGTTCTCTGACAATACAG
*
10512 AGACGCCAAATCA
62 AGACACCAAATCA
10525 TCTTGGATCT
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
83 30 0.45
84 1 0.01
89 1 0.01
90 35 0.52
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (86 bp):
GTCTGCCCTCCGTCGAATATGGAGACGCCAAATCTCTTCGATTTGTTCTCTGACAATACAGAGAC
ACCAAATCAGCTATGTCTTCG
Found at i:23802 original size:15 final size:15
Alignment explanation
Indices: 23782--23841 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
23772 TAATATAATT
23782 AATGATATATATAAA
1 AATGATATATATAAA
*
23797 AATGATATAT-TCTAA
1 AATGATATATAT-AAA
* *
23812 AATCATATAATATATA
1 AATGATAT-ATATAAA
*
23828 AATAATATATATAA
1 AATGATATATATAA
23842 CGAATATATG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
14 1 0.03
15 24 0.67
16 10 0.28
17 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (15 bp):
AATGATATATATAAA
Found at i:28151 original size:27 final size:26
Alignment explanation
Indices: 28103--28162 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
28093 GCGAGGCTGC
*
28103 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
28130 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
28156 CAGATAT
1 CAGATAT
28163 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:28223 original size:71 final size:67
Alignment explanation
Indices: 28130--28271 Score: 178
Period size: 67 Copynumber: 2.1 Consensus size: 67
28120 TCACCAGATA
* * * *
28130 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAA-GCCACCAGATTGCAGCG
1 CAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTCGC-AAGGCCACCAGATTGCAGCG
*
28194 AGGCTGC
61 AGGCTAC
*
28201 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTCGCAAGGCCACCAGATTGCAGCGAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTCGCAAGGCCACCAGATTGCAGCGAGGCT
28266 AC
66 AC
28268 CAGA
1 CAGA
28272 ACGCTTCCTC
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
66 2 0.03
67 37 0.58
71 25 0.39
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTCGCAAGGCCACCAGATTGCAGCGAGGCT
AC
Found at i:28934 original size:27 final size:27
Alignment explanation
Indices: 28904--28967 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
28894 GGGGAAAAAT
*
28904 GGTAATTTTACCCCACAAGGGTATTTC
1 GGTAATTCTACCCCACAAGGGTATTTC
* *
28931 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCCACAAGGGTATTTC
**
28958 AATAATTCTA
1 GGTAATTCTA
28968 ACTTATCCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCCACAAGGGTATTTC
Found at i:34187 original size:27 final size:26
Alignment explanation
Indices: 34139--34198 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
34129 GCGAGGCTGC
*
34139 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
34166 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
34192 CAGATAT
1 CAGATAT
34199 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:34969 original size:27 final size:27
Alignment explanation
Indices: 34939--35029 Score: 128
Period size: 27 Copynumber: 3.4 Consensus size: 27
34929 AGGGAAAAAT
* * *
34939 GGTAATTTTACCCCACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
34966 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
**
34993 AATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
35020 GGTAATTCTA
1 GGTAATTCTA
35030 TAACTTATCC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:37496 original size:29 final size:28
Alignment explanation
Indices: 37428--37497 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 28
37418 TACCTGTATC
* *
37428 TGGCCCATTAAGCCCAATCATATTCATA
1 TGGCCCATTAGGCCCAATCACATTCATA
* * *
37456 TGGCCTACTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCC-AATCACATTCATA
*
37485 TGGCCCGTTAGGC
1 TGGCCCATTAGGC
37498 TTAGTCACAT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 12 0.36
29 21 0.64
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAATCACATTCATA
Found at i:40554 original size:24 final size:24
Alignment explanation
Indices: 40504--40557 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
40494 AATCGAATTT
*
40504 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTAGTCACACTC
40528 GCACACATAGTGCCATAGT-ACAC-C
1 GCACACATAGTG-C-TAGTCACACTC
40552 GCACAC
1 GCACAC
40558 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 5 0.19
26 3 0.11
ACGTcount: A:0.30, C:0.37, G:0.17, T:0.17
Consensus pattern (24 bp):
GCACACATAGTGCTAGTCACACTC
Found at i:43139 original size:74 final size:74
Alignment explanation
Indices: 43010--43161 Score: 232
Period size: 74 Copynumber: 2.1 Consensus size: 74
43000 CTGAATCCCC
* *
43010 TATTCTGAATTTAAAAATTCACCATAAATTGTAAAAAAATAATTAGAAGTCATGTTTTATATGTA
1 TATTCTAAATTTAAAAATTCACCATAAATTGTAAAAAAATAATTAGAAGTCATGTTCTATATGTA
43075 TAGATTCCT
66 TAGATTCCT
* * * *
43084 TATTCTAAATTTAAAAATTCACCATAAATTGTACAAAAATAATTATAAGTTATGTTCTATATTTA
1 TATTCTAAATTTAAAAATTCACCATAAATTGTAAAAAAATAATTAGAAGTCATGTTCTATATGTA
* *
43149 TATATTTCT
66 TAGATTCCT
43158 TATT
1 TATT
43162 GAGTCTAGTT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (74 bp):
TATTCTAAATTTAAAAATTCACCATAAATTGTAAAAAAATAATTAGAAGTCATGTTCTATATGTA
TAGATTCCT
Found at i:47501 original size:29 final size:29
Alignment explanation
Indices: 47438--47544 Score: 85
Period size: 29 Copynumber: 3.8 Consensus size: 29
47428 TTCACAGACC
* * * *
47438 TGTATCTGGCCCATTAAGACC-AATCATA
1 TGTATATGGCCCATTAGGCCCAAATCACA
*
47466 T-TCATATGGCCCATTAGGCCCAAATCACC
1 TGT-ATATGGCCCATTAGGCCCAAATCACA
* * *
47495 TGTATATTGCCCATTCGGCCAAAATCACA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* * *
47524 TTTATATAG-CCGTTAGGCCCA
1 TGTATATGGCCCATTAGGCCCA
47545 GTCACATTTA
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
27 1 0.02
28 25 0.40
29 35 0.56
30 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (29 bp):
TGTATATGGCCCATTAGGCCCAAATCACA
Found at i:47542 original size:28 final size:28
Alignment explanation
Indices: 47446--47556 Score: 82
Period size: 29 Copynumber: 3.9 Consensus size: 28
47436 CCTGTATCTG
* * * *
47446 GCCCATTAAGACC-AATCATATTCATATG
1 GCCCATT-AGGCCAAATCACATTTATATA
* * *
47474 GCCCATTAGGCCCAAATCACCTGTATATT
1 GCCCATTAGG-CCAAATCACATTTATATA
*
47503 GCCCATTCGGCCAAAATCACATTTATATA
1 GCCCATTAGGCC-AAATCACATTTATATA
* * *
47532 G-CCGTTAGGCCCAGTCACATTTATA
1 GCCCATTAGGCCAAATCACATTTATA
47557 ATCATGCTCA
Statistics
Matches: 66, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
27 14 0.21
28 19 0.29
29 33 0.50
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (28 bp):
GCCCATTAGGCCAAATCACATTTATATA
Found at i:51919 original size:28 final size:27
Alignment explanation
Indices: 51887--51995 Score: 119
Period size: 28 Copynumber: 3.9 Consensus size: 27
51877 TACCTGTATC
* *
51887 TGGCCCATTAAGCCCAATCATATTCATA
1 TGGCCCATTAGGCCCAATCACATT-ATA
**
51915 TGGCCCATTAGGCCCAAATCACCGTATA
1 TGGCCCATTAGGCCC-AATCACATTATA
*
51943 TGGCCCATTAGGCCTGAATCACATTTATA
1 TGGCCCATTAGGCC-CAATCACA-TTATA
* *
51972 TGGCCCGTTAGGCCCAGTCACATT
1 TGGCCCATTAGGCCCAATCACATT
51996 TATAATCATC
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
27 2 0.03
28 43 0.63
29 23 0.34
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (27 bp):
TGGCCCATTAGGCCCAATCACATTATA
Found at i:56115 original size:23 final size:23
Alignment explanation
Indices: 56078--56121 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
56068 GATCCTTTCA
56078 CCCTTAAAATATTTTCACTATTAG
1 CCCTTAAAATATTTTCA-TATTAG
*
56102 CCCTTCAAA-ATTTTCATATT
1 CCCTTAAAATATTTTCATATT
56122 TACACTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 7 0.37
24 8 0.42
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.43
Consensus pattern (23 bp):
CCCTTAAAATATTTTCATATTAG
Found at i:64483 original size:215 final size:214
Alignment explanation
Indices: 64105--64536 Score: 686
Period size: 215 Copynumber: 2.0 Consensus size: 214
64095 TCAAGTCAGC
64105 CACAGACTATTTTTGAAAGTATCGCCTTGGAAGAAAGTTCTTCGATTTGGTCAAAAAAGAAAGCT
1 CACAGACTATTTTTGAAAGTATCGCCTTGGAAGAAAGTTCTTCGATTTGGTCAAAAAAGAAAGCT
* *
64170 TAGTCAACAATTTATCAGGCAGTACGAGACCATTGAGAGGATTAGGCCAATAGCCTACTAATTAA
66 TAATCAACAATTTATCAGGCAGTAAGAGACCATTGAGAGGATTAGGCCAATAGCCTACTAATTAA
*
64235 ATTTGTTGTTAGAGTTAGAAAAGATTCATAATGTCTTCCATGTATCGATTTTACAATGGTATTGA
131 ATTTGTTGTTAGAGTTAGAAAAGATTCATAATGTCTTCCA-GTATCAATTTTACAATGGTATTGA
64300 TCAGATCCATCACACAATTT
195 TCAGATCCATCACACAATTT
* ***
64320 CACAGAGTATTTTTGAAAGTATCGCCTTGGAAGAAAGTTCCTT-GATTTGGTTGGAAAAGAAAGC
1 CACAGACTATTTTTGAAAGTATCGCCTTGGAAGAAAGTT-CTTCGATTTGGTCAAAAAAGAAAGC
* * * * * *
64384 TTAATCAGCAGTTTATCAGGCAGTAAGAGACCATTGAGAGGATTAGGCCAATATCTTATTGATTA
65 TTAATCAACAATTTATCAGGCAGTAAGAGACCATTGAGAGGATTAGGCCAATAGCCTACTAATTA
*
64449 ACTTTGTTGTTAGAGTTAGAAAAGATTCATAATGTCTTCCAGTATCAATTTTACAATGGTATTGA
130 AATTTGTTGTTAGAGTTAGAAAAGATTCATAATGTCTTCCAGTATCAATTTTACAATGGTATTGA
* * *
64514 TCAGATCCTTCATACGATTT
195 TCAGATCCATCACACAATTT
64534 CAC
1 CAC
64537 CTGTTGATGT
Statistics
Matches: 199, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
214 43 0.22
215 153 0.77
216 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (214 bp):
CACAGACTATTTTTGAAAGTATCGCCTTGGAAGAAAGTTCTTCGATTTGGTCAAAAAAGAAAGCT
TAATCAACAATTTATCAGGCAGTAAGAGACCATTGAGAGGATTAGGCCAATAGCCTACTAATTAA
ATTTGTTGTTAGAGTTAGAAAAGATTCATAATGTCTTCCAGTATCAATTTTACAATGGTATTGAT
CAGATCCATCACACAATTT
Found at i:66320 original size:24 final size:25
Alignment explanation
Indices: 66293--66344 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
66283 ATGTATGAAT
66293 TATAAAATATAT-AAAATATGTACA
1 TATAAAATATATAAAAATATGTACA
* * *
66317 TAT-ATATATGTAAAAATATGTATA
1 TATAAAATATATAAAAATATGTACA
66341 TATA
1 TATA
66345 TATTTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (25 bp):
TATAAAATATATAAAAATATGTACA
Found at i:66354 original size:24 final size:24
Alignment explanation
Indices: 66299--66354 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
66289 GAATTATAAA
66299 ATATAT-AAAATATGTACATATAT
1 ATATATAAAAATATGTACATATAT
* *
66322 ATATGTAAAAATATGTATATATAT
1 ATATATAAAAATATGTACATATAT
*
66346 ATTTATAAA
1 ATATATAAA
66355 GGTTAGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (24 bp):
ATATATAAAAATATGTACATATAT
Found at i:68484 original size:44 final size:43
Alignment explanation
Indices: 68435--68850 Score: 225
Period size: 44 Copynumber: 9.6 Consensus size: 43
68425 ATCTACTCTG
* * * *
68435 CTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTTT-CTTCAATCTGCTCCA
* * ** * * *
68479 CTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCCTTTCTTCAATCTGCTCCA
* **
68522 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATC-CTTTCTTCAATCTGCTCCA
* ** *
68566 CTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTCCGGTCTACTCCA
1 CTGTAACCTCAGGGAGATAAGATCCT----TTCTTCAATCTGCTCCA
* * *
68612 CTGTAACCTCAGGGAGATAAGA--CTTGCATATTCAACCTGCCCCA
1 CTGTAACCTCAGGGAGATAAGATCCTT---TCTTCAATCTGCTCCA
* * * * * * **
68656 CTGTAACTTCGGGGAGATAAG--GCTTTATGT-GACCTGCTCTG
1 CTGTAACCTCAGGGAGATAAGATCCTTTCT-TCAATCTGCTCCA
* * * * *
68697 CTGTAACTTCAGAGAGATAGGATCCTTTATTTTAATCTGCTCC-
1 CTGTAACCTCAGGGAGATAAGATCCTTT-CTTCAATCTGCTCCA
* * * * * ** * * * *
68740 TTATAACTTCAAGGAGATAGGATAGTGTCCTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCCTTTCTTCAATCTGCTCCA
* * ** *
68783 CTGTAATCTCAAGGAGATAAGATCTCTGGCGTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATC-CTTTCTTCAATCTGCTCCA
68827 CTGTAACCTCAGGGAGATAAGATC
1 CTGTAACCTCAGGGAGATAAGATC
68851 TGAAATATTC
Statistics
Matches: 285, Mismatches: 71, Indels: 32
0.73 0.18 0.08
Matches are distributed among these distances:
41 29 0.10
42 13 0.05
43 74 0.26
44 134 0.47
45 2 0.01
46 33 0.12
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (43 bp):
CTGTAACCTCAGGGAGATAAGATCCTTTCTTCAATCTGCTCCA
Found at i:68646 original size:90 final size:87
Alignment explanation
Indices: 68423--68849 Score: 306
Period size: 87 Copynumber: 4.9 Consensus size: 87
68413 AGACTTGATG
* * * * *
68423 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATCCTT-TATTTTAATCCGCTCCACTGTAACT
1 CGATCTACTCCGCTGTAACCTCAGGGAGATAAGAT-CTTGCATTTCAATCTGCTCCACTGTAACT
* * *
68487 TCAGGGAGATAGGATAGTGTCTT
65 TCAGGGAGATAAGATAATGTCTC
* *
68510 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGC--TTCAATCTGCTCCACTGTAAC
1 CGATCTACTCCGCTGTAACCTCAGGGAGATAAGATCT-T-GCATTTCAATCTGCTCCACTGTAAC
*
68573 CTCAGGGAGATAAGATCTGAAAT-TCTC
64 TTCAGGGAGATAAGA--T--AATGTCTC
* * * *
68600 CGGTCTACTCCACTGTAACCTCAGGGAGATAAGA-CTTGCATATTCAACCTGCCCCACTGTAACT
1 CGATCTACTCCGCTGTAACCTCAGGGAGATAAGATCTTGCAT-TTCAATCTGCTCCACTGTAACT
* * *
68664 TCGGGGAGATAAGGCTTTATG--T-
65 TCAGGGAGATAA-G-ATAATGTCTC
* * * * * * * * * *
68686 -GACCTGCTCTGCTGTAACTTCAGAGAGATAGGATCCTT-TATTTTAATCTGCTCC-TTATAACT
1 CGATCTACTCCGCTGTAACCTCAGGGAGATAAGAT-CTTGCATTTCAATCTGCTCCACTGTAACT
* * *
68748 TCAAGGAGATAGGATAGTGTC-C
65 TCAGGGAGATAAGATAATGTCTC
* * * *
68770 TCGATCTGCTCCGCTGTAATCTCAAGGAGATAAGATCTCTGGC--GTCAATCTGCTCCACTGTAA
1 -CGATCTACTCCGCTGTAACCTCAGGGAGATAAGATCT-T-GCATTTCAATCTGCTCCACTGTAA
*
68833 CCTCAGGGAGATAAGAT
63 CTTCAGGGAGATAAGAT
68850 CTGAAATATT
Statistics
Matches: 260, Mismatches: 56, Indels: 48
0.71 0.15 0.13
Matches are distributed among these distances:
82 3 0.01
83 1 0.00
84 15 0.06
85 37 0.14
86 43 0.17
87 88 0.34
88 3 0.01
89 3 0.01
90 64 0.25
91 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (87 bp):
CGATCTACTCCGCTGTAACCTCAGGGAGATAAGATCTTGCATTTCAATCTGCTCCACTGTAACTT
CAGGGAGATAAGATAATGTCTC
Found at i:70141 original size:7 final size:7
Alignment explanation
Indices: 70089--70141 Score: 65
Period size: 7 Copynumber: 7.9 Consensus size: 7
70079 TAGCTTCTCA
70089 ATTTTTC
1 ATTTTTC
*
70096 AATTTTC
1 ATTTTTC
70103 A-TTTTC
1 ATTTTTC
*
70109 TTTTTTC
1 ATTTTTC
70116 ATTTTTC
1 ATTTTTC
*
70123 A-TTCTC
1 ATTTTTC
70129 ATTTTTC
1 ATTTTTC
70136 ATTTTT
1 ATTTTT
70142 TTCAGAGTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
6 10 0.26
7 29 0.74
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTTTTC
Found at i:70141 original size:20 final size:20
Alignment explanation
Indices: 70083--70141 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
70073 TCCCCTTAGC
*
70083 TTCTCAATTTTTCAATTTTCA
1 TTCTC-ATTTTTCATTTTTCA
* *
70104 TTTTCTTTTTTCATTTTTCA
1 TTCTCATTTTTCATTTTTCA
70124 TTCTCATTTTTCATTTTT
1 TTCTCATTTTTCATTTTT
70142 TTCAGAGTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
20 29 0.88
21 4 0.12
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCTCATTTTTCATTTTTCA
Found at i:71084 original size:6 final size:6
Alignment explanation
Indices: 71075--71103 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
71065 TCTCAGTTTC
71075 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
71104 TTCCTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (6 bp):
ATTTTG
Found at i:77659 original size:10 final size:9
Alignment explanation
Indices: 77641--77679 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
77631 TCGTAGATAA
*
77641 AAAAGAAAT
1 AAAATAAAT
77650 AAAATAAAAT
1 AAAAT-AAAT
77660 AAAATAAAT
1 AAAATAAAT
77669 AAAA-AAAT
1 AAAATAAAT
77677 AAA
1 AAA
77680 TAGAATAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 7 0.25
9 12 0.43
10 9 0.32
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (9 bp):
AAAATAAAT
Found at i:77673 original size:15 final size:15
Alignment explanation
Indices: 77637--77674 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
77627 ATTTTCGTAG
77637 ATAAAAAAGAAATAAA
1 ATAAAAAAGAAAT-AA
*
77653 ATAAAATA-AAATAA
1 ATAAAAAAGAAATAA
77667 ATAAAAAA
1 ATAAAAAA
77675 ATAAATAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 9 0.45
15 4 0.20
16 7 0.35
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (15 bp):
ATAAAAAAGAAATAA
Found at i:83013 original size:40 final size:40
Alignment explanation
Indices: 82919--83063 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
82909 TACTCGAATG
*
82919 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
82960 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
83000 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
83040 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
83064 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:87480 original size:41 final size:41
Alignment explanation
Indices: 87423--87503 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
87413 GCCAATGTAT
* *
87423 ATATATAGCAGAAGCTATCTC-AATCTCACACAGTAAGTGCA
1 ATATATAACAGAAGCTATCTCGAAT-TCACACACTAAGTGCA
* *
87464 ATATATAACCGAAGCTATCTCGAATTCGCACACTAAGTGC
1 ATATATAACAGAAGCTATCTCGAATTCACACACTAAGTGC
87504 TCATAATTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 32 0.91
42 3 0.09
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (41 bp):
ATATATAACAGAAGCTATCTCGAATTCACACACTAAGTGCA
Found at i:93422 original size:13 final size:15
Alignment explanation
Indices: 93395--93426 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
93385 TTTGTTATAT
93395 TTTTATGGTATATGA
1 TTTTATGGTATATGA
93410 TTTTATGG-A-ATGA
1 TTTTATGGTATATGA
93423 TTTT
1 TTTT
93427 CTTAAAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (15 bp):
TTTTATGGTATATGA
Found at i:101666 original size:146 final size:145
Alignment explanation
Indices: 101465--101754 Score: 544
Period size: 146 Copynumber: 2.0 Consensus size: 145
101455 ATTCATATTT
*
101465 TAGAAAGTGTGATATAGAGGTATACCTATTAGATTTGTTCTAGTTGAATGATGTTGTTATGAGTT
1 TAGAAAGTGTGATACAGAGGTATACCTATTAGATTTGTTCTAGTTGAATGATGTTGTTATGAGTT
*
101530 AAAGCTGCTTCGATTGATAAAATTATCACGTTGATGGAAGTTTGAAAGGTCTGTTGCATGTTAAC
66 AAAGCTGCTCCGATTGAT-AAATTATCACGTTGATGGAAGTTTGAAAGGTCTGTTGCATGTTAAC
101595 AAAGTTGAAAACAGTC
130 AAAGTTGAAAACAGTC
101611 TAGAAAGTGTGATACAGAGGTATACCTATTAGATTTGTTCTAGTTGAATGATGTTGTTATGAGTT
1 TAGAAAGTGTGATACAGAGGTATACCTATTAGATTTGTTCTAGTTGAATGATGTTGTTATGAGTT
*
101676 AAAGCTGCTCCGATTGATAAATTATCACGTTGATGGAAGTTTGAAAGGTCTGTTGCATGTTAGCA
66 AAAGCTGCTCCGATTGATAAATTATCACGTTGATGGAAGTTTGAAAGGTCTGTTGCATGTTAACA
101741 AAGTTGAAAACAGT
131 AAGTTGAAAACAGT
101755 TGAAGGTGTT
Statistics
Matches: 141, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
145 60 0.43
146 81 0.57
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (145 bp):
TAGAAAGTGTGATACAGAGGTATACCTATTAGATTTGTTCTAGTTGAATGATGTTGTTATGAGTT
AAAGCTGCTCCGATTGATAAATTATCACGTTGATGGAAGTTTGAAAGGTCTGTTGCATGTTAACA
AAGTTGAAAACAGTC
Found at i:101908 original size:51 final size:51
Alignment explanation
Indices: 101848--101948 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
101838 CGAACAGATT
101848 GGAATGTGTTTTAATACAAGAATGTGAAGTGATAGTTTATGCTTTCAGGTA
1 GGAATGTGTTTTAATACAAGAATGTGAAGTGATAGTTTATGCTTTCAGGTA
* *
101899 GGAATGTGTTTTAATACAATAATGTGAAGTGATAGTTTATGCTTTTAGGT
1 GGAATGTGTTTTAATACAAGAATGTGAAGTGATAGTTTATGCTTTCAGGT
101949 TAAAGTCTCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.31, C:0.05, G:0.25, T:0.40
Consensus pattern (51 bp):
GGAATGTGTTTTAATACAAGAATGTGAAGTGATAGTTTATGCTTTCAGGTA
Found at i:103726 original size:40 final size:40
Alignment explanation
Indices: 103628--103890 Score: 309
Period size: 40 Copynumber: 6.6 Consensus size: 40
103618 TCCTCGTTCA
* * * ** *
103628 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
103667 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
103707 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
103747 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
103787 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
103827 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
103867 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
103891 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:109876 original size:17 final size:18
Alignment explanation
Indices: 109854--109888 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
109844 TTACATTGAA
109854 GTGTTTT-AGTGAAAACC
1 GTGTTTTCAGTGAAAACC
*
109871 GTGTTTTCATTGAAAACC
1 GTGTTTTCAGTGAAAACC
109889 CTTCTTAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (18 bp):
GTGTTTTCAGTGAAAACC
Found at i:110973 original size:29 final size:29
Alignment explanation
Indices: 110931--111017 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
110921 TATTAAGACC
* *
110931 AATCATATTCATATGGCCCATTAGGCCCA
1 AATCACATTTATATGGCCCATTAGGCCCA
* * *
110960 AATCAC-TTGTATATGGTCAATTCA-GCCAA
1 AATCACATT-TATATGGCCCATT-AGGCCCA
*
110989 AATCACATTTATATGGCCCGTTAGGCCCA
1 AATCACATTTATATGGCCCATTAGGCCCA
111018 GTCACTTTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (29 bp):
AATCACATTTATATGGCCCATTAGGCCCA
Found at i:112483 original size:16 final size:16
Alignment explanation
Indices: 112462--112493 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
112452 AAGTTCAGGA
112462 TTTCGAGATTTTTGGG
1 TTTCGAGATTTTTGGG
112478 TTTCGAGATTTTTGGG
1 TTTCGAGATTTTTGGG
112494 GCGTTACAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.31, T:0.50
Consensus pattern (16 bp):
TTTCGAGATTTTTGGG
Found at i:115144 original size:23 final size:23
Alignment explanation
Indices: 115107--115150 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
115097 GATCCTTTCA
115107 CCCTTAAAATATTTTCACTATTAG
1 CCCTTAAAATATTTTCA-TATTAG
*
115131 CCCTTCAAA-ATTTTCATATT
1 CCCTTAAAATATTTTCATATT
115151 TACACTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 7 0.37
24 8 0.42
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.43
Consensus pattern (23 bp):
CCCTTAAAATATTTTCATATTAG
Found at i:124082 original size:27 final size:27
Alignment explanation
Indices: 124051--124228 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
124041 TAAATTGTAC
124051 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
124078 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
124104 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
124132 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
124160 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
124187 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
124214 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
124229 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:124165 original size:82 final size:81
Alignment explanation
Indices: 124052--124207 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
124042 AAATTGTACA
* *
124052 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
124116 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
124133 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
124198 TGCGAGTTGA
65 TGCGAATTGA
124208 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:124219 original size:82 final size:81
Alignment explanation
Indices: 124048--124228 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
124038 GATTAAATTG
* *
124048 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
124113 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
124129 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
124193 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
124211 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
124229 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:127086 original size:215 final size:214
Alignment explanation
Indices: 126715--127146 Score: 650
Period size: 215 Copynumber: 2.0 Consensus size: 214
126705 TCAAGTCAAC
* *
126715 CACAGAGTATTTTTGAAAGTATCGCCTTGGAAGAAAGTTATTCGATTTGGTCGAAAAATAGAGCT
1 CACAGAGTATTTTTGAAAGTATCGCCTTGGAAGAAAGTTATTCGATTTGGTCGAAAAAGAAAGCT
* *
126780 TAGTCAACAATTTATCAGGCAGTACGAGACCATTGAGAGGATTAGGCCAATAGCCTACTAATTAA
66 TAATCAACAATTTATCAGGCAGTAAGAGACCATTGAGAGGATTAGGCCAATAGCCTACTAATTAA
* *
126845 CTTTGCTGTTAGAGTTAGAAAAGATTCATAATGTCTTCCATGTATCGATTTTACAATGGTATTGA
131 CTTTGCTGTTAGAGTTAGAAAAGATTCATAATGTCTTCCA-ATATCAATTTTACAATGGTATTGA
126910 TCAGATCCATCACACAATTT
195 TCAGATCCATCACACAATTT
* * * *
126930 CACAGAGTATTTTTGAAAGTATCGCCTTGGAAGAAAGTTCCTT-GATTTTGTTGGAAAAGAAAGC
1 CACAGAGTATTTTTGAAAGTATCGCCTTGGAAGAAAGTT-ATTCGATTTGGTCGAAAAAGAAAGC
* * * * * *
126994 TTAATCAGCAGTTTATCAGGCAGTAAGAGACCATTGAGAGGATTAGGCCAATATCTTATTGATTA
65 TTAATCAACAATTTATCAGGCAGTAAGAGACCATTGAGAGGATTAGGCCAATAGCCTACTAATTA
* *
127059 ACTTTGTTGTTAGAGTTAGCAAAGATTCATAATGTCTTCCAATATCAATTTTACAATGGTATTGA
130 ACTTTGCTGTTAGAGTTAGAAAAGATTCATAATGTCTTCCAATATCAATTTTACAATGGTATTGA
* * *
127124 TCAGATCCTTCATACGATTT
195 TCAGATCCATCACACAATTT
127144 CAC
1 CAC
127147 CTGTTGATGT
Statistics
Matches: 195, Mismatches: 21, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
214 42 0.22
215 151 0.77
216 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (214 bp):
CACAGAGTATTTTTGAAAGTATCGCCTTGGAAGAAAGTTATTCGATTTGGTCGAAAAAGAAAGCT
TAATCAACAATTTATCAGGCAGTAAGAGACCATTGAGAGGATTAGGCCAATAGCCTACTAATTAA
CTTTGCTGTTAGAGTTAGAAAAGATTCATAATGTCTTCCAATATCAATTTTACAATGGTATTGAT
CAGATCCATCACACAATTT
Found at i:133878 original size:41 final size:41
Alignment explanation
Indices: 133821--133901 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
133811 GCCAATGTAT
* *
133821 ATATATAGCAGAAGCTATCTC-AATCTCACACAGTAAGTGCA
1 ATATATAACAGAAGCTATCTCGAAT-TCACACACTAAGTGCA
* *
133862 ATATATAACCGAAGCTATCTCGAATTCGCACACTAAGTGC
1 ATATATAACAGAAGCTATCTCGAATTCACACACTAAGTGC
133902 CCATAATTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 32 0.91
42 3 0.09
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (41 bp):
ATATATAACAGAAGCTATCTCGAATTCACACACTAAGTGCA
Found at i:141373 original size:79 final size:81
Alignment explanation
Indices: 141237--141421 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
141227 TTGAATGATG
*
141237 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
141301 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
141316 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
141378 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
141396 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
141422 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:141435 original size:40 final size:40
Alignment explanation
Indices: 141238--141421 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
141228 TGAATGATGT
* * * *
141238 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
141278 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
141318 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
141356 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
141397 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
141422 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:141443 original size:79 final size:79
Alignment explanation
Indices: 141290--141454 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
141280 GGACTAAGAT
* **
141290 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
141355 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
141369 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
141432 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
141448 CCGAAGG
1 CCGAAGG
141455 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:149349 original size:79 final size:81
Alignment explanation
Indices: 149213--149397 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
149203 TTGAATGATG
*
149213 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
149277 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
149292 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
149354 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
149372 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
149398 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:149411 original size:40 final size:40
Alignment explanation
Indices: 149214--149397 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
149204 TGAATGATGT
* * * *
149214 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
149254 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
149294 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
149332 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
149373 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
149398 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:149419 original size:79 final size:79
Alignment explanation
Indices: 149266--149430 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
149256 GGACTAAGAT
* **
149266 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
149331 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
149345 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
149408 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
149424 CCGAAGG
1 CCGAAGG
149431 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:151455 original size:13 final size:15
Alignment explanation
Indices: 151415--151459 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
151405 GAAAAAAATT
151415 ATTTT-TGGTATAT-
1 ATTTTATGGTATATG
151428 -TTTTATGGTATATG
1 ATTTTATGGTATATG
151442 ATTTTATGG-A-ATG
1 ATTTTATGGTATATG
151455 ATTTT
1 ATTTT
151460 GTTAAAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.14
13 16 0.55
14 1 0.03
15 8 0.28
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (15 bp):
ATTTTATGGTATATG
Found at i:152602 original size:42 final size:42
Alignment explanation
Indices: 152555--152652 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
152545 ACTGAGTGTA
* * * * *
152555 CGTGTAAGAACATATCTGGGATATGGGATCGATATGAGATTT
1 CGTGTAAGACCATATCTGGGATATAGCATCAATAAGAGATTT
152597 CGTGTAAGACCATATCTGGGATATAGCATCAATAAGAGATTT
1 CGTGTAAGACCATATCTGGGATATAGCATCAATAAGAGATTT
*
152639 CATGTAAGACCATA
1 CGTGTAAGACCATA
152653 ACTGAGTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (42 bp):
CGTGTAAGACCATATCTGGGATATAGCATCAATAAGAGATTT
Found at i:152697 original size:40 final size:40
Alignment explanation
Indices: 152647--152727 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
152637 TTCATGTAAG
*
152647 ACCATAACTGAGTTATTGGCATCTATACGAGATTACGTGT
1 ACCATAACTGAGTTATTGGCATCTATACGAGATAACGTGT
152687 ACCATAACTGAGTTATTGGCATCTATACGAGATAACGTGT
1 ACCATAACTGAGTTATTGGCATCTATACGAGATAACGTGT
152727 A
1 A
152728 AGAACATTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (40 bp):
ACCATAACTGAGTTATTGGCATCTATACGAGATAACGTGT
Found at i:157978 original size:85 final size:85
Alignment explanation
Indices: 157832--158010 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
157822 GGCCGGCCAT
*
157832 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
157897 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
157917 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
157982 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
158002 GAGCATGGG
1 GAGCATGGG
158011 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.39, C:0.08, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:161600 original size:42 final size:42
Alignment explanation
Indices: 161527--161632 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
161517 TTAGGGTTAC
* *
161527 AGAG-ATTACGTGTAAGGCCATATATGGGATATGGCATCGATA
1 AGAGAATT-CGTGTAAGACCATATATGCGATATGGCATCGATA
* *
161569 TGAGAATTCGTGTAAGACCATATCTGCGATATGGCATCGATA
1 AGAGAATTCGTGTAAGACCATATATGCGATATGGCATCGATA
* *
161611 AGAGATTTCATGTAAGACCATA
1 AGAGAATTCGTGTAAGACCATA
161633 GCTGGCATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 53 0.95
43 3 0.05
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (42 bp):
AGAGAATTCGTGTAAGACCATATATGCGATATGGCATCGATA
Found at i:161667 original size:43 final size:41
Alignment explanation
Indices: 161554--161675 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 41
161544 CCATATATGG
* * *
161554 GATATGGCATCGATATGAGAATTCGTGTAAGACCATATCTGC
1 GATATCGCATCGATATGAG-ATTCATGTAAGACCATAGCTGC
* *
161596 GATATGGCATCGATAAGAGATTTCATGTAAGACCATAGCTG-
1 GATATCGCATCGATATGAGA-TTCATGTAAGACCATAGCTGC
* * *
161637 GCATATTCGTATTGATATGAGATTACATGTAAGGCCATA
1 G-ATA-TCGCATCGATATGAGATT-CATGTAAGACCATA
161676 TCTGATATAT
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
41 2 0.03
42 41 0.60
43 25 0.37
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (41 bp):
GATATCGCATCGATATGAGATTCATGTAAGACCATAGCTGC
Found at i:170813 original size:90 final size:90
Alignment explanation
Indices: 170660--170839 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
170650 CACGAGGGGT
170660 TCACATGTAACACCCCGAACCCGAGACCGACACCGGAGTCGAACACGAGGTGTTAACAGACTTTA
1 TCACATGTAACACCCCGAACCCGAGACCGACACCGGAGTCGAACACGAGGTGTTAACAGACTTTA
170725 AACCCTTTATAAAAATATTTCTCAG
66 AACCCTTTATAAAAATATTTCTCAG
*
170750 TCACATGTCACACCCCGAACCCGAGACCGACACCGGAGTCGAACACGAGGTGTTAACAGACTTTA
1 TCACATGTAACACCCCGAACCCGAGACCGACACCGGAGTCGAACACGAGGTGTTAACAGACTTTA
170815 AACCCTTTATAAAAATATTTCTCAG
66 AACCCTTTATAAAAATATTTCTCAG
170840 ACACTGCTAA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (90 bp):
TCACATGTAACACCCCGAACCCGAGACCGACACCGGAGTCGAACACGAGGTGTTAACAGACTTTA
AACCCTTTATAAAAATATTTCTCAG
Done.