Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009584.1 Corchorus capsularis cultivar CVL-1 contig09605, 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: 77625
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2040 original size:45 final size:45
Alignment explanation
Indices: 1927--2130 Score: 154
Period size: 44 Copynumber: 4.6 Consensus size: 45
1917 TCCAACATAG
* * * * * *
1927 AAATATTGATAATCATATTGTGAAATTTTAATAACCACACTGTG-
1 AAATTTTGATAATCACACTATGAAATTTTGATAACCACACTATGA
* *
1971 AAATTTTGATAATCACACTGTGAAATTTTGATAAGCACACTATGA
1 AAATTTTGATAATCACACTATGAAATTTTGATAACCACACTATGA
* * **
2016 AAATTTTGATAATCTTC-CTATGAAATTTTGGTAATTACACTAT-A
1 AAATTTTGATAATC-ACACTATGAAATTTTGATAACCACACTATGA
* * * *
2060 AAA--TTGGTAACCGCACTATGAAAATTTTGATAACCTC-CTCAT-A
1 AAATTTTGATAATCACACTATG-AAATTTTGATAACCACACT-ATGA
* *
2103 AAATCTTGATAACCACA-TCATGAAATTT
1 AAATTTTGATAATCACACT-ATGAAATTT
2131 CAATAACCTC
Statistics
Matches: 132, Mismatches: 20, Indels: 16
0.79 0.12 0.10
Matches are distributed among these distances:
41 1 0.01
42 14 0.11
43 18 0.14
44 49 0.37
45 49 0.37
46 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (45 bp):
AAATTTTGATAATCACACTATGAAATTTTGATAACCACACTATGA
Found at i:2058 original size:22 final size:22
Alignment explanation
Indices: 1926--2092 Score: 142
Period size: 22 Copynumber: 7.6 Consensus size: 22
1916 CTCCAACATA
* * * *
1926 GAAATATTGATAATCATATTGT
1 GAAATTTTGATAATCACACTAT
* * *
1948 GAAATTTTAATAACCACACTGT
1 GAAATTTTGATAATCACACTAT
*
1970 GAAATTTTGATAATCACACTGT
1 GAAATTTTGATAATCACACTAT
*
1992 GAAATTTTGATAAGCACACTAT
1 GAAATTTTGATAATCACACTAT
*
2014 GAAAATTTTGATAATCTTC-CTAT
1 G-AAATTTTGATAATC-ACACTAT
* *
2037 GAAATTTTGGTAATTACACTAT
1 GAAATTTTGATAATCACACTAT
* * * *
2059 -AAA-ATTGGTAACCGCACTAT
1 GAAATTTTGATAATCACACTAT
2079 GAAAATTTTGATAA
1 G-AAATTTTGATAA
2093 CCTCCTCATA
Statistics
Matches: 119, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
20 13 0.11
21 4 0.03
22 77 0.65
23 24 0.20
24 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (22 bp):
GAAATTTTGATAATCACACTAT
Found at i:2106 original size:22 final size:22
Alignment explanation
Indices: 2080--2141 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
2070 CCGCACTATG
2080 AAAATTTTGATAACCTCCTCAT
1 AAAATTTTGATAACCTCCTCAT
* * *
2102 AAAATCTTGATAACCACATCAT
1 AAAATTTTGATAACCTCCTCAT
* **
2124 GAAATTTCAATAACCTCC
1 AAAATTTTGATAACCTCC
2142 CTATGAGAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (22 bp):
AAAATTTTGATAACCTCCTCAT
Found at i:2184 original size:22 final size:22
Alignment explanation
Indices: 2159--2209 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2149 AATGAAACTA
* * *
2159 TGATATCCCCTCTATATAATTT
1 TGATAACCCCTCCATAAAATTT
*
2181 TGATAACCTCTCCATAAAATTT
1 TGATAACCCCTCCATAAAATTT
*
2203 TCATAAC
1 TGATAAC
2210 TTCTTTATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (22 bp):
TGATAACCCCTCCATAAAATTT
Found at i:2358 original size:22 final size:22
Alignment explanation
Indices: 2283--2493 Score: 109
Period size: 22 Copynumber: 9.8 Consensus size: 22
2273 CCTCCCTATA
*
2283 AAATTTTGTTAACC-T--TATG
1 AAATTTTGATAACCTTCATATG
* * *
2302 AAATTTTGATAAGC-ACACTATA
1 AAATTTTGATAACCTTCA-TATG
**
2324 AAATTTCAATAACCTTCATATG
1 AAATTTTGATAACCTTCATATG
* * * *
2346 AAATTTTGTTAACCTCCCTAAG
1 AAATTTTGATAACCTTCATATG
* *
2368 AAATTTTGTTAACC-TCTTGATG
1 AAATTTTGATAACCTTCAT-ATG
* *
2390 AAATTTTGGTAA-CTTCTGTATG
1 AAATTTTGATAACCTTC-ATATG
2412 AAATTTTGATAA-CTAT-ACTATG
1 AAATTTTGATAACCT-TCA-TATG
** *
2434 AGGTTTTGATAACCTCCATAT-
1 AAATTTTGATAACCTTCATATG
* * * *
2455 AAAATTTGGTAACC-ACACTATT
1 AAATTTTGATAACCTTCA-TATG
2477 AAATTTTGATAACCTTC
1 AAATTTTGATAACCTTC
2494 CTAATGTAAT
Statistics
Matches: 145, Mismatches: 33, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
19 12 0.08
20 2 0.01
21 16 0.11
22 107 0.74
23 8 0.06
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACCTTCATATG
Found at i:2381 original size:44 final size:42
Alignment explanation
Indices: 2273--2496 Score: 157
Period size: 44 Copynumber: 5.2 Consensus size: 42
2263 TGATAATCCC
2273 CCTCCCTATAAAATTTTGTTAACCT-TATGAAATTTTGATAA
1 CCTCCCTATAAAATTTTGTTAACCTCTATGAAATTTTGATAA
* * * *** *
2314 GCACACTATAAAATTTCAATAACCTTCATATGAAATTTTGTTAA
1 CCTCCCTATAAAATTTTGTTAACC-TC-TATGAAATTTTGATAA
*
2358 CCTCCCTA-AGAAATTTTGTTAACCTCTTGATGAAATTTTGGTAA
1 CCTCCCTATA-AAATTTTGTTAACCTC-T-ATGAAATTTTGATAA
* ** * * * **
2402 CTTCTGTATGAAATTTTGATAACTATACTATGAGGTTTTGATAA
1 CCTCCCTATAAAATTTTGTTAAC-CT-CTATGAAATTTTGATAA
* * * *
2446 CCTCCATATAAAA-TTTGGTAACCACACTATTAAATTTTGATAA
1 CCTCCCTATAAAATTTTGTTAA-C-CTCTATGAAATTTTGATAA
*
2489 CCTTCCTA
1 CCTCCCTA
2497 ATGTAATTTC
Statistics
Matches: 137, Mismatches: 37, Indels: 16
0.72 0.19 0.08
Matches are distributed among these distances:
41 18 0.13
42 1 0.01
43 31 0.23
44 84 0.61
45 2 0.01
46 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (42 bp):
CCTCCCTATAAAATTTTGTTAACCTCTATGAAATTTTGATAA
Found at i:4774 original size:111 final size:108
Alignment explanation
Indices: 4568--4789 Score: 322
Period size: 111 Copynumber: 2.0 Consensus size: 108
4558 ATAATGTAAA
* **
4568 AATTAATTAACAATATCCTAATCAATTTTTTTGTTTTCTTTTTTTTTTCGAATATCTCAGTCTTA
1 AATTAATTAACAATATCCTAATCAATTTTTTTGTTTTC--TTTTTTTCCGAATATCTCAACCTTA
* *
4633 TAATTTATAATGTAAAGTCGGATTATTTTGTTTAAGAATTAATAT
64 AAATTTATAATGTAAAGTCGGATTATTTTGTTGAAGAATTAATAT
4678 AATTAATTAACAATATCCTTAAATCAATTTTTTTGTTTTC-TTTTTTCCGAATAT-TCCAACCTT
1 AATTAATTAACAATATCC-T-AATCAATTTTTTTGTTTTCTTTTTTTCCGAATATCT-CAACCTT
4741 AAAATTTATAATGTAAAAAGTCGGATTATTTTGTTGAAGAATTAATAT
63 AAAATTTATAATGT--AAAGTCGGATTATTTTGTTGAAGAATTAATAT
4789 A
1 A
4790 TCCGATTAAT
Statistics
Matches: 102, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
108 1 0.01
109 31 0.30
110 18 0.18
111 33 0.32
112 19 0.19
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (108 bp):
AATTAATTAACAATATCCTAATCAATTTTTTTGTTTTCTTTTTTTCCGAATATCTCAACCTTAAA
ATTTATAATGTAAAGTCGGATTATTTTGTTGAAGAATTAATAT
Found at i:4869 original size:17 final size:17
Alignment explanation
Indices: 4847--4879 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4837 TACTATACAT
*
4847 TAATATGGATGAAATTA
1 TAATATAGATGAAATTA
4864 TAATATAGATGAAATT
1 TAATATAGATGAAATT
4880 TTATACTCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
TAATATAGATGAAATTA
Found at i:8687 original size:17 final size:17
Alignment explanation
Indices: 8665--8699 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
8655 TTCATACAAT
8665 TATATTTCCCTTTATTC
1 TATATTTCCCTTTATTC
8682 TATATTTCCCTTTATTC
1 TATATTTCCCTTTATTC
8699 T
1 T
8700 GAACAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTTCCCTTTATTC
Found at i:9062 original size:2 final size:2
Alignment explanation
Indices: 9055--9086 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9045 GCCAAGGTAG
9055 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9087 TCAGTGGGTT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:12811 original size:22 final size:22
Alignment explanation
Indices: 12786--12832 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
12776 TTATATTCAT
12786 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
12808 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
12830 TAT
1 TAT
12833 AGTATAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:12828 original size:11 final size:11
Alignment explanation
Indices: 12786--12828 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
12776 TTATATTCAT
*
12786 TATTAATTAAC
1 TATTAATTAGC
*
12797 TATTAATTAGA
1 TATTAATTAGC
12808 TATTAATTAGC
1 TATTAATTAGC
12819 TATTAATTAG
1 TATTAATTAG
12829 ATATAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:12974 original size:2 final size:2
Alignment explanation
Indices: 12967--13000 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12957 GACAAAAATA
12967 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13001 TACATGTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14258 original size:29 final size:29
Alignment explanation
Indices: 14224--14287 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
14214 ACGGAGAAAA
14224 AGGGGAAAGAAATATGAAGGTGAAAACAG
1 AGGGGAAAGAAATATGAAGGTGAAAACAG
14253 AGGGGAAAGAAATATGAAGGTGAAAACAG
1 AGGGGAAAGAAATATGAAGGTGAAAACAG
14282 AGGGGA
1 AGGGGA
14288 GTGATGGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.50, C:0.03, G:0.38, T:0.09
Consensus pattern (29 bp):
AGGGGAAAGAAATATGAAGGTGAAAACAG
Found at i:15536 original size:30 final size:29
Alignment explanation
Indices: 15474--15543 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
15464 ACCGAACCGT
****
15474 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
*
15503 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACTATT-AAAAAGGC
15533 CAAATAAGCCC
1 CAAATAAGCCC
15544 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAGGC
Found at i:18690 original size:31 final size:31
Alignment explanation
Indices: 18650--18790 Score: 183
Period size: 31 Copynumber: 4.5 Consensus size: 31
18640 ACGGTGTCCG
18650 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * *
18681 ATGTGGCACGCCACATATACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
18712 ACATGTCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* ** * *
18743 ACGTGGCATGCCACGTGTTTCAAAAAATGGC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
*
18774 ACGTGGCATGCCACGTG
1 ACGTGGCACGCCACGTG
18791 CACAAAAGGA
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 95 1.00
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.17
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:30205 original size:11 final size:11
Alignment explanation
Indices: 30189--30230 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
30179 TAGTACTCAC
*
30189 TTGCACGTGCA
1 TTGCACGTGTA
* *
30200 TTGCACGTATG
1 TTGCACGTGTA
30211 TTGCACGTGTA
1 TTGCACGTGTA
30222 TTGCACGTG
1 TTGCACGTG
30231 ACCGATCATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (11 bp):
TTGCACGTGTA
Found at i:41175 original size:20 final size:21
Alignment explanation
Indices: 41142--41183 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
41132 GTTAAAGTTT
41142 TTTTTATTAATAATGCTAACG
1 TTTTTATTAATAATGCTAACG
* *
41163 TTTTT-TTATTAATGCTTACG
1 TTTTTATTAATAATGCTAACG
41183 T
1 T
41184 GTTCAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55
Consensus pattern (21 bp):
TTTTTATTAATAATGCTAACG
Found at i:42589 original size:22 final size:22
Alignment explanation
Indices: 42561--42635 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 22
42551 CCTGTGAAAC
42561 TTTGATAACCACACTATAAAAT
1 TTTGATAACCACACTATAAAAT
* ** *
42583 TTTGAT-ATCATTCTATGAAAT
1 TTTGATAACCACACTATAAAAT
42604 TTTGATAACCACACTATAAAAT
1 TTTGATAACCACACTATAAAAT
*
42626 TGTGATAACC
1 TTTGATAACC
42636 TCTATATGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
21 17 0.40
22 26 0.60
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (22 bp):
TTTGATAACCACACTATAAAAT
Found at i:42647 original size:22 final size:22
Alignment explanation
Indices: 42555--42648 Score: 77
Period size: 22 Copynumber: 4.3 Consensus size: 22
42545 TTACCTCCTG
42555 TGAAACTT-TGATAACCACACTA
1 TGAAA-TTGTGATAACCACACTA
* * * **
42577 TAAAATTTTGAT-ATCATTCTA
1 TGAAATTGTGATAACCACACTA
*
42598 TGAAATTTTGATAACCACACTA
1 TGAAATTGTGATAACCACACTA
* *
42620 TAAAATTGTGATAACCTCTA-TA
1 TGAAATTGTGATAACCAC-ACTA
42642 TGAAATT
1 TGAAATT
42649 AATTTTGATG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
21 19 0.33
22 37 0.65
23 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (22 bp):
TGAAATTGTGATAACCACACTA
Found at i:42849 original size:22 final size:23
Alignment explanation
Indices: 42824--42878 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 23
42814 GATTACCTTC
*
42824 TATGAAATTTTTG-TAACCCCAT
1 TATGAAATTTTTGATAACCACAT
42846 TATGAAA-TTTTGATAACCACAT
1 TATGAAATTTTTGATAACCACAT
42868 TATGAAATTTT
1 TATGAAATTTT
42879 GCTGGTCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 5 0.17
22 22 0.73
23 3 0.10
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (23 bp):
TATGAAATTTTTGATAACCACAT
Found at i:43482 original size:30 final size:28
Alignment explanation
Indices: 43446--43521 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 28
43436 TATTATACTA
43446 TAATATTAAGCATATATGTTAGTAATTGAC
1 TAATATTAAGCATAT-T-TTAGTAATTGAC
43476 TAATATTAAG-AGTATTTTAGTAATTGAC
1 TAATATTAAGCA-TATTTTAGTAATTGAC
*
43504 T-A-ATTAAGCATATGTTAG
1 TAATATTAAGCATATTTTAG
43522 CCAGGTTGGA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
26 13 0.30
27 2 0.05
28 13 0.30
29 2 0.05
30 13 0.30
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.41
Consensus pattern (28 bp):
TAATATTAAGCATATTTTAGTAATTGAC
Found at i:43501 original size:28 final size:30
Alignment explanation
Indices: 43446--43516 Score: 98
Period size: 28 Copynumber: 2.5 Consensus size: 30
43436 TATTATACTA
43446 TAATATTAAGCATATATGTTAGTAATTGAC
1 TAATATTAAGCATATATGTTAGTAATTGAC
43476 TAATATTAAG-AGTAT-T-TTAGTAATTGAC
1 TAATATTAAGCA-TATATGTTAGTAATTGAC
43504 T-A-ATTAAGCATAT
1 TAATATTAAGCATAT
43517 GTTAGCCAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
26 9 0.23
27 2 0.05
28 13 0.33
29 2 0.05
30 13 0.33
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.41
Consensus pattern (30 bp):
TAATATTAAGCATATATGTTAGTAATTGAC
Found at i:51384 original size:39 final size:39
Alignment explanation
Indices: 51341--51469 Score: 231
Period size: 39 Copynumber: 3.3 Consensus size: 39
51331 TGGACCACCA
51341 TCGTCTTCCTGATCCTCAAGTTGTCCAACATCTTCCTCT
1 TCGTCTTCCTGATCCTCAAGTTGTCCAACATCTTCCTCT
*
51380 TCGTCTTCCTGATCCTCAAGTTGTCCAACGTCTTCCTCT
1 TCGTCTTCCTGATCCTCAAGTTGTCCAACATCTTCCTCT
*
51419 TCGTCTTCCTGATCCTCAAATTGTCCAACATCTTCCTCT
1 TCGTCTTCCTGATCCTCAAGTTGTCCAACATCTTCCTCT
*
51458 TCGTCATCCTGA
1 TCGTCTTCCTGA
51470 CACGACAACA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 86 1.00
ACGTcount: A:0.16, C:0.36, G:0.11, T:0.38
Consensus pattern (39 bp):
TCGTCTTCCTGATCCTCAAGTTGTCCAACATCTTCCTCT
Found at i:56424 original size:19 final size:20
Alignment explanation
Indices: 56397--56434 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
56387 TACTATTATT
56397 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
56417 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
56435 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:56628 original size:22 final size:22
Alignment explanation
Indices: 56600--56750 Score: 164
Period size: 22 Copynumber: 6.9 Consensus size: 22
56590 TGTATCTATG
*
56600 TGGTTATCAAAATTTCATAAG-A
1 TGGTTACCAAAATTTCAT-AGTA
** *
56622 TGGTTATTATAATTTC-TGAG-A
1 TGGTTACCAAAATTTCAT-AGTA
* *
56643 AGGTTATCAAAATTTCATAGTA
1 TGGTTACCAAAATTTCATAGTA
* *
56665 TGCTTACCGAAATTTCATAGTA
1 TGGTTACCAAAATTTCATAGTA
* * *
56687 TGGTTACCGAAATTCCATAGTG
1 TGGTTACCAAAATTTCATAGTA
56709 TGGTTACCAAAATTTCATAGTA
1 TGGTTACCAAAATTTCATAGTA
56731 TGGTTACCAAAATTTCATAG
1 TGGTTACCAAAATTTCATAG
56751 GATCATATTA
Statistics
Matches: 111, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
21 19 0.17
22 92 0.83
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (22 bp):
TGGTTACCAAAATTTCATAGTA
Found at i:56797 original size:22 final size:23
Alignment explanation
Indices: 56739--56797 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
56729 TATGGTTACC
56739 AAAATTTCATAGGATCATATTATT
1 AAAATTTCATAGGAT-ATATTATT
* *
56763 AAAATCTCTTAGG-T-TGATTATT
1 AAAATTTCATAGGATAT-ATTATT
*
56785 GAAATTTCATAGG
1 AAAATTTCATAGG
56798 GTGGTTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 1 0.03
22 16 0.55
23 1 0.03
24 11 0.38
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (23 bp):
AAAATTTCATAGGATATATTATT
Found at i:56963 original size:22 final size:22
Alignment explanation
Indices: 56915--57221 Score: 114
Period size: 22 Copynumber: 13.8 Consensus size: 22
56905 TTTCATGGGG
* **
56915 AGGTTATCAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAGAA
* *
56937 TGGTTATCAAAATTTCATATAA
1 AGGTTATCAAAATTTCATAGAA
* **
56959 AGGTTAT-AAAAGTCTTAATTTCATA
1 AGGTTATCAAAA-T-TTCA-TAGA-A
* *
56984 AGGAGTA-CTAAAATTTGATAGAA
1 AGG-TTATC-AAAATTTCATAGAA
* *
57007 A-GTTATC-AAATCTCATAGAG
1 AGGTTATCAAAATTTCATAGAA
* *
57027 TGATTATCAAAATTTCATAGAGA
1 AGGTTATCAAAATTTCATAGA-A
**
57050 TCAAATTATCAAAATTT-ATAGAA
1 --AGGTTATCAAAATTTCATAGAA
* * **
57073 AGATTATCAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAGAA
** *
57095 TTGTTATCAAAATTT--TAAAA
1 AGGTTATCAAAATTTCATAGAA
*
57115 CGAGGTTATCAAAATTACAT--AA
1 --AGGTTATCAAAATTTCATAGAA
* *
57137 TGTGATTAT-AAGAATTTCATAGAG
1 AG-G-TTATCAA-AATTTCATAGAA
* * * * *
57161 GGGTCAACAAAATTTTATAAAA
1 AGGTTATCAAAATTTCATAGAA
57183 AGGTTATCAAAATTTCATA-AA
1 AGGTTATCAAAATTTCATAGAA
*
57204 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
57222 AAATGTGATT
Statistics
Matches: 211, Mismatches: 49, Indels: 50
0.68 0.16 0.16
Matches are distributed among these distances:
20 13 0.06
21 30 0.14
22 120 0.57
23 9 0.04
24 12 0.06
25 20 0.09
26 3 0.01
27 4 0.02
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGAA
Found at i:57061 original size:25 final size:21
Alignment explanation
Indices: 57029--57092 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 21
57019 TCATAGAGTG
57029 ATTATCAAAATTTCATAGAGATCAA
1 ATTATCAAAATTT-ATAGA-A--AA
*
57054 ATTATCAAAATTTATAGAAAG
1 ATTATCAAAATTTATAGAAAA
57075 ATTATCAAAATTTTATAG
1 ATTATCAAAA-TTTATAG
57093 TGTTGTTATC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 11 0.30
22 7 0.19
23 1 0.03
24 5 0.14
25 13 0.35
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (21 bp):
ATTATCAAAATTTATAGAAAA
Found at i:57079 original size:21 final size:21
Alignment explanation
Indices: 56993--57092 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 21
56983 AAGGAGTACT
56993 AAAATTTGATAGAAAG-TTATC
1 AAAATTT-ATAGAAAGATTATC
* **
57014 -AAATCTCATAGAGTGATTATC
1 AAAAT-TTATAGAAAGATTATC
*
57035 AAAATTTCATAGAGATCAAATTATC
1 AAAATTT-ATAGA-A--AGATTATC
57060 AAAATTTATAGAAAGATTATC
1 AAAATTTATAGAAAGATTATC
57081 AAAATTTTATAG
1 AAAA-TTTATAG
57093 TGTTGTTATC
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
20 10 0.16
21 18 0.29
22 16 0.25
23 1 0.02
24 5 0.08
25 13 0.21
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (21 bp):
AAAATTTATAGAAAGATTATC
Found at i:57159 original size:88 final size:87
Alignment explanation
Indices: 57054--57246 Score: 201
Period size: 88 Copynumber: 2.2 Consensus size: 87
57044 TAGAGATCAA
* * ***** *
57054 ATTATCAAAATTT-ATAGAAAGATTATCAAAATTTTATAGTGTTGTTATCAAAATTTTA-AAACG
1 ATTAT-AAAATTTCATAGAAAGATCAACAAAATTTTATAAAAAGGTTATCAAAATTTCATAAA-G
*
57117 AGGTTATCAAAATTACATAATGTG
64 AGGTTATCAAAATTACAAAATGTG
** *
57141 ATTATAAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAAAGGTTATCAAAATTTCATAAAGA
1 ATTATAA-AATTTCATAGAAAGATCAACAAAATTTTATAAAAAGGTTATCAAAATTTCATAAAGA
* *
57206 GGTTATCAAATTTTCAAAATGTG
65 GGTTATCAAAATTACAAAATGTG
*
57229 ATTACAAAAATTTCATAG
1 ATTA-TAAAATTTCATAG
57247 TGGTATTTCT
Statistics
Matches: 87, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
86 2 0.02
87 10 0.11
88 70 0.80
89 5 0.06
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (87 bp):
ATTATAAAATTTCATAGAAAGATCAACAAAATTTTATAAAAAGGTTATCAAAATTTCATAAAGAG
GTTATCAAAATTACAAAATGTG
Found at i:57221 original size:66 final size:66
Alignment explanation
Indices: 57055--57221 Score: 164
Period size: 66 Copynumber: 2.5 Consensus size: 66
57045 AGAGATCAAA
* ** * * *
57055 TTATCAAAATTT-ATAGAA-AGATTATCAAAATTTT-ATAGTGTTGTTATCAAAATTTTAAAACG
1 TTATCAAAATTTCATA-AAGAGATTATC-AAATTTTCATAGAGGGGTCAACAAAATTTTAAAACA
57117 AGG
64 AGG
* * * *
57120 TTATCAAAATTACATAATGTGATTAT-AAGAATTTCATAGAGGGGTCAACAAAATTTTATAAA-A
1 TTATCAAAATTTCATAAAGAGATTATCAA-ATTTTCATAGAGGGGTCAACAAAATTTTA-AAACA
57183 AGG
64 AGG
*
57186 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
1 TTATCAAAATTTCATAAAGAGATTATCAAATTTTCA
57222 AAATGTGATT
Statistics
Matches: 81, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
64 2 0.02
65 16 0.20
66 58 0.72
67 5 0.06
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.36
Consensus pattern (66 bp):
TTATCAAAATTTCATAAAGAGATTATCAAATTTTCATAGAGGGGTCAACAAAATTTTAAAACAAG
G
Found at i:57239 original size:44 final size:44
Alignment explanation
Indices: 57103--57245 Score: 114
Period size: 44 Copynumber: 3.2 Consensus size: 44
57093 TGTTGTTATC
* * * * *
57103 AAAATTTTA-AAACGAGGTTATCAAAATTACATAATGTGATTATA
1 AAAATTTCATAAA-GAGGTTATCAAATTTTCAAAATGTGATTACA
* * * * * * *
57147 AGAATTTCATAGAGGGGTCAACAAAATTTTATAAAAAG-G-TTATC-
1 AAAATTTCATAAAGAGGTTATC-AAATTTT-CAAAATGTGATTA-CA
57191 AAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTACA
1 AAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTACA
57235 AAAATTTCATA
1 AAAATTTCATA
57246 GTGGTATTTC
Statistics
Matches: 73, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
42 5 0.07
43 9 0.12
44 47 0.64
45 8 0.11
46 4 0.05
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (44 bp):
AAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTACA
Found at i:57356 original size:20 final size:21
Alignment explanation
Indices: 57331--57378 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
57321 TGAAGTAATC
57331 AAAATTTCAAGG-AGGATATA
1 AAAATTTCAAGGTAGGATATA
*
57351 AAAA-TTC-AGGTAGGATATC
1 AAAATTTCAAGGTAGGATATA
57370 AAAATTTCA
1 AAAATTTCA
57379 TATGAAGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.12
19 14 0.58
20 7 0.29
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (21 bp):
AAAATTTCAAGGTAGGATATA
Found at i:57393 original size:22 final size:22
Alignment explanation
Indices: 57366--57794 Score: 169
Period size: 22 Copynumber: 19.6 Consensus size: 22
57356 TCAGGTAGGA
*
57366 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGGAGGT
**
57388 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGGAGGT
* * * *
57410 TTTCAAATTTTCACA-AGAGAGT
1 TATCAAAATTTCATATGGAG-GT
* *
57432 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGGAGGT
* * *
57453 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGGAGGT
*
57476 TAACAAACA-TTCATAAT-GAGGT
1 TATCAAA-ATTTCAT-ATGGAGGT
**
57498 TATCAAAAAATCATATGGAGGT
1 TATCAAAATTTCATATGGAGGT
* *
57520 TATCCAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGGAGGT
* * * *
57536 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGGAGGT
* *
57558 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGGAGG-T
* *
57581 TATCAAAATTTTATA-GGAAGATT
1 TATCAAAATTTCATATGG-AG-GT
*
57604 TATCAAAATTTCATA-GCGATGT
1 TATCAAAATTTCATATG-GAGGT
*
57626 TATCACAATTTCATAGTGTGA--T
1 TATCAAAATTTCATA-TG-GAGGT
*
57648 TATCAAAATTTCAAAGTGTGA--T
1 TATCAAAATTTCATA-TG-GAGGT
57670 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGGAGGT
* * * ** *
57692 TTTTAAATTTTCATAACGTGGT
1 TATCAAAATTTCATATGGAGGT
* * * *
57714 TATCGATATATCAGATGGAGGT
1 TATCAAAATTTCATATGGAGGT
* * **
57736 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGGAGGT
* *
57759 TATCAGAATTTCAT-TGGGAAGT
1 TATCAAAATTTCATAT-GGAGGT
57781 TATCAAAATTTCAT
1 TATCAAAATTTCAT
57795 GTTGAGGTCT
Statistics
Matches: 306, Mismatches: 72, Indels: 58
0.70 0.17 0.13
Matches are distributed among these distances:
16 8 0.03
17 3 0.01
18 2 0.01
20 5 0.02
21 12 0.04
22 212 0.69
23 60 0.20
24 4 0.01
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGGAGGT
Found at i:57686 original size:172 final size:170
Alignment explanation
Indices: 57366--57692 Score: 369
Period size: 172 Copynumber: 1.9 Consensus size: 170
57356 TCAGGTAGGA
* * **
57366 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAATTTTCACAAGAGAG
1 TATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGTGGAGTTTTCAAATTTTCACAAGAGAG
*
57431 TTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAGATTAACAAACATTCATAATGAG
66 TTATCAAAATTTCATAGGATGTAGATCAAAATTTCATAGGGAGATTAACAAACATTCATAATGAG
*
57496 GTTATCAAAAAATCATATGGAGGTTATCCAAATTTGTAGT
131 ATTATCAAAAAATCATATGGAGGTTATCCAAATTTGTAGT
* * * *
57536 TATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAG-GGAGGTTTATCAAAATTTT-ATAGGA
1 TATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGTGGA-GTTT-TC-AAATTTTCACAAG-
* * * * * *
57599 AGATTTATCAAAATTTCATAGCGATGT-TATCACAATTTCATAGTGTGATTATCAAA-ATTTCA-
62 AGAGTTATCAAAATTTCATAG-GATGTAGATCAAAATTTCATAGGGAGATTAACAAACA-TTCAT
* * *
57661 AAGTGTGATTA-CTAACAATTCATATGGAGGTT
125 AA-TGAGATTATC-AAAAAATCATATGGAGGTT
57693 TTTAAATTTT
Statistics
Matches: 130, Mismatches: 19, Indels: 14
0.80 0.12 0.09
Matches are distributed among these distances:
169 1 0.01
170 38 0.29
171 9 0.07
172 78 0.60
173 4 0.03
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (170 bp):
TATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGTGGAGTTTTCAAATTTTCACAAGAGAG
TTATCAAAATTTCATAGGATGTAGATCAAAATTTCATAGGGAGATTAACAAACATTCATAATGAG
ATTATCAAAAAATCATATGGAGGTTATCCAAATTTGTAGT
Found at i:57908 original size:22 final size:22
Alignment explanation
Indices: 57880--57932 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
57870 AAGGTTCTCG
* * *
57880 AAATTTCATAGTATCGTTATTA
1 AAATTTCATAGGAACGTTATCA
*
57902 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAACGTTATCA
57924 AAATTTCAT
1 AAATTTCAT
57933 TATGGGATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (22 bp):
AAATTTCATAGGAACGTTATCA
Found at i:64766 original size:17 final size:18
Alignment explanation
Indices: 64744--64780 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
64734 GACGGCGTGA
64744 TTTTGTCATTTTTT-ATT
1 TTTTGTCATTTTTTAATT
*
64761 TTTTGTCCTTTTTTAATT
1 TTTTGTCATTTTTTAATT
64779 TT
1 TT
64781 AATTAACTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTTGTCATTTTTTAATT
Found at i:71031 original size:2 final size:2
Alignment explanation
Indices: 71024--71056 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
71014 CTTTTAAGTC
71024 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
71057 GTAAAACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:71693 original size:2 final size:2
Alignment explanation
Indices: 71686--71711 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
71676 CAACTTTTTC
71686 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
71712 GTAATAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:74926 original size:21 final size:21
Alignment explanation
Indices: 74902--74967 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
74892 ATGTCTTGCC
74902 AATATATTTTGACTAAAGGAA
1 AATATATTTTGACTAAAGGAA
74923 AATACT-TTTTGACCT-AAGTG--
1 AATA-TATTTTGA-CTAAAG-GAA
**
74943 GTTATATTTTGACTAAAGGAA
1 AATATATTTTGACTAAAGGAA
74964 AATA
1 AATA
74968 CTTTTTGCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
19 4 0.12
20 11 0.32
21 15 0.44
22 4 0.12
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (21 bp):
AATATATTTTGACTAAAGGAA
Found at i:74972 original size:20 final size:20
Alignment explanation
Indices: 74908--74972 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
74898 TGCCAATATA
74908 TTTTGACTAAAGGAAAATAC
1 TTTTGACTAAAGGAAAATAC
***
74928 TTTTTGACCT-AAGTGGTTATA-
1 -TTTTGA-CTAAAG-GAAAATAC
74949 TTTTGACTAAAGGAAAATAC
1 TTTTGACTAAAGGAAAATAC
74969 TTTT
1 TTTT
74973 TGCTATCCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
19 6 0.18
20 13 0.38
21 9 0.26
22 6 0.18
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.40
Consensus pattern (20 bp):
TTTTGACTAAAGGAAAATAC
Found at i:76899 original size:28 final size:29
Alignment explanation
Indices: 76857--76922 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
76847 TTCACTTTTG
*
76857 AAACGTAAGGAATTAATTTGT-AAAAAAA
1 AAACATAAGGAATTAATTTGTCAAAAAAA
* * *
76885 AAACATAAGGGATTATTTTGTCCAAAACAA
1 AAACATAAGGAATTAATTTGT-CAAAAAAA
76915 AAACATAA
1 AAACATAA
76923 ACGATTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 18 0.56
30 14 0.44
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (29 bp):
AAACATAAGGAATTAATTTGTCAAAAAAA
Found at i:76934 original size:30 final size:30
Alignment explanation
Indices: 76878--76934 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
76868 ATTAATTTGT
**
76878 AAAAAAAAAACATAAGGGATTATTTTGTCC
1 AAAAAAAAAACATAAACGATTATTTTGTCC
* *
76908 AAAACAAAAACATAAACGATTTTTTTG
1 AAAAAAAAAACATAAACGATTATTTTG
76935 GGCATTTAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.28
Consensus pattern (30 bp):
AAAAAAAAAACATAAACGATTATTTTGTCC
Found at i:76999 original size:20 final size:19
Alignment explanation
Indices: 76971--77009 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
76961 AATATACAAC
76971 GTAAAAAGTTAAAGAAAAAA
1 GTAAAAAG-TAAAGAAAAAA
* *
76991 GTAATAAGTCAAGAAAAAA
1 GTAAAAAGTAAAGAAAAAA
77010 AATGTAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.67, C:0.03, G:0.15, T:0.15
Consensus pattern (19 bp):
GTAAAAAGTAAAGAAAAAA
Done.