Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012715.1 Corchorus olitorius cultivar O-4 contig12748, 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: 58839
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:6427 original size:58 final size:59
Alignment explanation
Indices: 6363--6944 Score: 851
Period size: 58 Copynumber: 9.9 Consensus size: 59
6353 CAGATTACCT
* *
6363 TATCTTGTTTTAAAATCCTGTTCAAGGGCTCTGTTAGAGAGTTTTCAATTCAAAATATC
1 TATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATC
* * *
6422 T-TCTTGATTTAAAAATCATGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATAT-
1 TATCTTG-TTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATC
* *
6480 TATCTTATTTTAAAATCCTGTTCGAGGGCTCTGTTAGAGAGTTTTCAATTCAAAATATC
1 TATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATC
* * * *
6539 T-TCTTCATTTAAAAATCCTGTTTGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATAT-
1 TATCTT-GTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATC
*
6597 TATCTTGTTTTAAAATCCTGTTCGAGGGCTCTGTTAGAGAGTTTTCAATTCAAAATATC
1 TATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATC
* *
6656 T-TCTTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATAT-
1 TATCTTG-TTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATC
* *
6714 TATCTTGTTTTAAAATCCTGTTCGAGGGCTATGTTAGAGAGTTTTTCAATTCAAAATATC
1 TATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAG-TTTTCAATTCAAAATATC
* *
6774 T-TCTTGATTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATAT-
1 TATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATC
* *
6831 TATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAATTTTCAA-TCTAAA-ATC
1 TATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATC
* *
6888 TTATCTTGTTTTAAAATCCTGTTCGAGGTCTCCGTTAGAGAGTTTTCAATTTAAAAT
1 -TATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
6945 CTTTTTTTGG
Statistics
Matches: 472, Mismatches: 36, Indels: 29
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.00
57 7 0.01
58 248 0.53
59 214 0.45
60 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (59 bp):
TATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATC
Found at i:6550 original size:117 final size:117
Alignment explanation
Indices: 6362--6942 Score: 1001
Period size: 117 Copynumber: 5.0 Consensus size: 117
6352 TCAGATTACC
*
6362 TTATCTTGTTTTAAAATCCTGTTCAAGGGCTCTGTTAGAGAGTTTTCAATTCAAAATATCTTCTT
1 TTATCTTGTTTTAAAATCCTGTTCGAGGGCTCTGTTAGAGAGTTTTCAATTCAAAATATCTTCTT
*
6427 GATTTAAAAATCATGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATA
66 GATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATA
*
6479 TTATCTTATTTTAAAATCCTGTTCGAGGGCTCTGTTAGAGAGTTTTCAATTCAAAATATCTTCTT
1 TTATCTTGTTTTAAAATCCTGTTCGAGGGCTCTGTTAGAGAGTTTTCAATTCAAAATATCTTCTT
* *
6544 CATTTAAAAATCCTGTTTGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATA
66 GATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATA
6596 TTATCTTGTTTTAAAATCCTGTTCGAGGGCTCTGTTAGAGAGTTTTCAATTCAAAATATCTTCTT
1 TTATCTTGTTTTAAAATCCTGTTCGAGGGCTCTGTTAGAGAGTTTTCAATTCAAAATATCTTCTT
6661 GATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATA
66 GATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATA
*
6713 TTATCTTGTTTTAAAATCCTGTTCGAGGGCTATGTTAGAGAGTTTTTCAATTCAAAATATCTTCT
1 TTATCTTGTTTTAAAATCCTGTTCGAGGGCTCTGTTAGAGAG-TTTTCAATTCAAAATATCTTCT
6778 TGATTT-AAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATA
65 TGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATA
* * *
6830 TTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAATTTTCAA-TCTAAA-ATCTTATC
1 TTATCTTGTTTTAAAATCCTGTTCGAGGGCTCTGTTAGAGAGTTTTCAATTCAAAATATC-T-TC
* *
6893 TTG-TTTTAAAATCCTGTTCGAGGTCTCCGTTAGAGAGTTTTCAATT-TAAA
64 TTGATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAA
6943 ATCTTTTTTT
Statistics
Matches: 446, Mismatches: 14, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
114 3 0.01
115 13 0.03
116 50 0.11
117 352 0.79
118 28 0.06
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (117 bp):
TTATCTTGTTTTAAAATCCTGTTCGAGGGCTCTGTTAGAGAGTTTTCAATTCAAAATATCTTCTT
GATTTAAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCTAAATA
Found at i:7241 original size:30 final size:30
Alignment explanation
Indices: 7219--7325 Score: 118
Period size: 28 Copynumber: 3.7 Consensus size: 30
7209 TTGTGAATCC
*
7219 AGAGGCATTTTGGTCATTTTTTGCACATCT
1 AGAGGCATTTTGGTCATTTTTTGTACATCT
*
7249 AGGGGCATTTTGGTCA--TTTTGTACATCT
1 AGAGGCATTTTGGTCATTTTTTGTACATCT
*
7277 A-AGGGCATTTTGGTCA-TTTTTGCACAT-T
1 AGA-GGCATTTTGGTCATTTTTTGTACATCT
7305 CAG-GAGCATTTTGGTCATTTT
1 -AGAG-GCATTTTGGTCATTTT
7326 CGCACGTCCA
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
28 27 0.40
29 22 0.33
30 18 0.27
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (30 bp):
AGAGGCATTTTGGTCATTTTTTGTACATCT
Found at i:7297 original size:58 final size:57
Alignment explanation
Indices: 7215--7470 Score: 300
Period size: 58 Copynumber: 4.4 Consensus size: 57
7205 CCTTTTGTGA
* *
7215 ATCCAGAGGCATTTTGGTCATTTTTTGCAC-ATCTAGGGGCATTTTGGTCATTTTGTAC
1 ATCCAGGGGCATTTTGGTCA-TTTTTGCACAATC-AGGGGCATTTTGGTCATTTTGCAC
* * * *
7273 ATCTAAGGGCATTTTGGTCATTTTTGCACATTCAGGAGCATTTTGGTCATTTTCGCAC
1 ATCCAGGGGCATTTTGGTCATTTTTGCACAATCAGGGGCATTTTGGTCATTTT-GCAC
* * * * * *
7331 GTCCAGGGGCATTTTAGTCATTTCTGCACAATCCGGGGCATTTTGGTCATTTTTACCC
1 ATCCAGGGGCATTTTGGTCATTTTTGCACAATCAGGGGCATTTTGGTCA-TTTTGCAC
* * * *
7389 ATCCATGGGCATTATGGTCATTTTTGCACAATCAAGGGCATTTTAGTCATTTCTGCAC
1 ATCCAGGGGCATTTTGGTCATTTTTGCACAATCAGGGGCATTTTGGTCATTT-TGCAC
7447 AATCC-GGGGCATTTTGGTCATTTT
1 -ATCCAGGGGCATTTTGGTCATTTT
7471 AGTTTTATTT
Statistics
Matches: 165, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
57 31 0.19
58 126 0.76
59 8 0.05
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (57 bp):
ATCCAGGGGCATTTTGGTCATTTTTGCACAATCAGGGGCATTTTGGTCATTTTGCAC
Found at i:7298 original size:29 final size:28
Alignment explanation
Indices: 7222--7470 Score: 266
Period size: 29 Copynumber: 8.6 Consensus size: 28
7212 TGAATCCAGA
7222 GGCATTTTGGTCATTTTTTGCACATCTAGG
1 GGCATTTTGGTCA-TTTTTGCACATC-AGG
* *
7252 GGCATTTTGGTCA-TTTTGTACATCTAAG
1 GGCATTTTGGTCATTTTTGCACATC-AGG
7280 GGCATTTTGGTCATTTTTGCACATTCAGG
1 GGCATTTTGGTCATTTTTGCACA-TCAGG
* * *
7309 AGCATTTTGGTCATTTTCGCACGTCCAGG
1 GGCATTTTGGTCATTTTTGCACAT-CAGG
* * *
7338 GGCATTTTAGTCATTTCTGCACAATCCGG
1 GGCATTTTGGTCATTTTTGCAC-ATCAGG
* * *
7367 GGCATTTTGGTCATTTTTACCCATCCATG
1 GGCATTTTGGTCATTTTTGCACAT-CAGG
* *
7396 GGCATTATGGTCATTTTTGCACAATCAAG
1 GGCATTTTGGTCATTTTTGCAC-ATCAGG
* * *
7425 GGCATTTTAGTCATTTCTGCACAATCCGG
1 GGCATTTTGGTCATTTTTGCAC-ATCAGG
7454 GGCATTTTGGTCATTTT
1 GGCATTTTGGTCATTTT
7471 AGTTTTATTT
Statistics
Matches: 183, Mismatches: 30, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
28 29 0.16
29 136 0.74
30 18 0.10
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (28 bp):
GGCATTTTGGTCATTTTTGCACATCAGG
Found at i:7370 original size:87 final size:87
Alignment explanation
Indices: 7222--7470 Score: 326
Period size: 87 Copynumber: 2.9 Consensus size: 87
7212 TGAATCCAGA
* * * **
7222 GGCATTTTGGTCATTTTTTGCACATCTAGGGGCATTTTGGTCATTT-TGTAC-ATCTAAGGGCAT
1 GGCATTTTGGTCA-TTTTTGCACATCCAGGGGCATTTTAGTCATTTCTGCACAATC-CGGGGCAT
* *
7285 TTTGGTCATTTTTGCACATTCA-G
64 TTTGGTCATTTTTACACATCCATG
* *
7308 GAGCATTTTGGTCATTTTCGCACGTCCAGGGGCATTTTAGTCATTTCTGCACAATCCGGGGCATT
1 G-GCATTTTGGTCATTTTTGCACATCCAGGGGCATTTTAGTCATTTCTGCACAATCCGGGGCATT
*
7373 TTGGTCATTTTTACCCATCCATG
65 TTGGTCATTTTTACACATCCATG
* *
7396 GGCATTATGGTCATTTTTGCACAAT-CAAGGGCATTTTAGTCATTTCTGCACAATCCGGGGCATT
1 GGCATTTTGGTCATTTTTGCAC-ATCCAGGGGCATTTTAGTCATTTCTGCACAATCCGGGGCATT
7460 TTGGTCATTTT
65 TTGGTCATTTT
7471 AGTTTTATTT
Statistics
Matches: 144, Mismatches: 14, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
86 29 0.20
87 109 0.76
88 6 0.04
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (87 bp):
GGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTTAGTCATTTCTGCACAATCCGGGGCATTT
TGGTCATTTTTACACATCCATG
Found at i:11583 original size:21 final size:21
Alignment explanation
Indices: 11539--11584 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
11529 AGCTCGCGCC
**
11539 TGGGTGCTCAGGCCTACGGGT
1 TGGGTGCTCAGGCCTACGACT
* *
11560 TGGGTGCTCAGGCTTGCGACT
1 TGGGTGCTCAGGCCTACGACT
11581 TGGG
1 TGGG
11585 GACCCAGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.09, C:0.22, G:0.43, T:0.26
Consensus pattern (21 bp):
TGGGTGCTCAGGCCTACGACT
Found at i:15641 original size:24 final size:25
Alignment explanation
Indices: 15595--15642 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
15585 TTTTCTGAAT
* * *
15595 TTTCCATTTTTTTTTTCATTTTTCC
1 TTTCCATTCTTTTTTTAACTTTTCC
15620 TTTCC-TTCTTTTTTTAACTTTTC
1 TTTCCATTCTTTTTTTAACTTTTC
15643 TTCAAACTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTCCATTCTTTTTTTAACTTTTCC
Found at i:17166 original size:28 final size:30
Alignment explanation
Indices: 17135--17194 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 30
17125 GAGGGTAATT
17135 GAGAGA-TGATTCAGTGG-AGAG-CCAGAGA
1 GAGAGACTGATTCA-TGGAAGAGTCCAGAGA
*
17163 GAGAGACTGTTTCATGGAAAGAGTCCAGAGA
1 GAGAGACTGATTCATGG-AAGAGTCCAGAGA
17194 G
1 G
17195 GGTTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 9 0.33
29 6 0.22
30 4 0.15
31 8 0.30
ACGTcount: A:0.35, C:0.12, G:0.37, T:0.17
Consensus pattern (30 bp):
GAGAGACTGATTCATGGAAGAGTCCAGAGA
Found at i:19823 original size:190 final size:190
Alignment explanation
Indices: 19500--19879 Score: 751
Period size: 190 Copynumber: 2.0 Consensus size: 190
19490 GCAAAGAGTG
19500 TACGTTCAGGCTCAGAGTTGAATTCCAAGTCCTTAATACCACTACTCCTTGTATTTGGCATACAA
1 TACGTTCAGGCTCAGAGTTGAATTCCAAGTCCTTAATACCACTACTCCTTGTATTTGGCATACAA
*
19565 CTCCTAGAAAAAATTTAAACGAAAAATTCAACAATTAAAAGTAACTAATAAAATAAAAATAAAAA
66 CTCCTAGAAAAAATTTAAACGAAAAATTCAACAATTAAAAGTAACTAAGAAAATAAAAATAAAAA
19630 ATAAAATAACGAAAAAGAAAAAGATAAGAAATTTTTAGGTAGTAATTTGTCTTCAATCTT
131 ATAAAATAACGAAAAAGAAAAAGATAAGAAATTTTTAGGTAGTAATTTGTCTTCAATCTT
19690 TACGTTCAGGCTCAGAGTTGAATTCCAAGTCCTTAATACCACTACTCCTTGTATTTGGCATACAA
1 TACGTTCAGGCTCAGAGTTGAATTCCAAGTCCTTAATACCACTACTCCTTGTATTTGGCATACAA
19755 CTCCTAGAAAAAATTTAAACGAAAAATTCAACAATTAAAAGTAACTAAGAAAATAAAAATAAAAA
66 CTCCTAGAAAAAATTTAAACGAAAAATTCAACAATTAAAAGTAACTAAGAAAATAAAAATAAAAA
19820 ATAAAATAACGAAAAAGAAAAAGATAAGAAATTTTTAGGTAGTAATTTGTCTTCAATCTT
131 ATAAAATAACGAAAAAGAAAAAGATAAGAAATTTTTAGGTAGTAATTTGTCTTCAATCTT
19880 CTTGTTGTTT
Statistics
Matches: 189, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
190 189 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.28
Consensus pattern (190 bp):
TACGTTCAGGCTCAGAGTTGAATTCCAAGTCCTTAATACCACTACTCCTTGTATTTGGCATACAA
CTCCTAGAAAAAATTTAAACGAAAAATTCAACAATTAAAAGTAACTAAGAAAATAAAAATAAAAA
ATAAAATAACGAAAAAGAAAAAGATAAGAAATTTTTAGGTAGTAATTTGTCTTCAATCTT
Found at i:21435 original size:21 final size:21
Alignment explanation
Indices: 21397--21436 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21387 GGCGCCCACA
* *
21397 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGCCTGAACACCCATG
*
21418 TGGTTTGCCTGATCACCCA
1 TGGTTTGCCTGAACACCCA
21437 GGTAGGTAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (21 bp):
TGGTTTGCCTGAACACCCATG
Found at i:27364 original size:36 final size:36
Alignment explanation
Indices: 27317--27390 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
27307 AACGGTACAA
27317 AATCAACACTAATGAGCTAAATGGAGAAAATCAAGC
1 AATCAACACTAATGAGCTAAATGGAGAAAATCAAGC
27353 AATCAACACTAATGAGCTAAATGGAGAAAATCAAGC
1 AATCAACACTAATGAGCTAAATGGAGAAAATCAAGC
27389 AA
1 AA
27391 CGGCAGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.16
Consensus pattern (36 bp):
AATCAACACTAATGAGCTAAATGGAGAAAATCAAGC
Found at i:32049 original size:18 final size:18
Alignment explanation
Indices: 32026--32060 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
32016 GAAAATCAAT
32026 CAATCAACACTAATGAGG
1 CAATCAACACTAATGAGG
32044 CAATCAACACTAATGAG
1 CAATCAACACTAATGAG
32061 TTAAACGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.14, T:0.17
Consensus pattern (18 bp):
CAATCAACACTAATGAGG
Found at i:38963 original size:2 final size:2
Alignment explanation
Indices: 38956--38981 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38946 TTTTCATTTC
38956 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
38982 CGATTTTCAA
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):
AT
Found at i:44070 original size:19 final size:19
Alignment explanation
Indices: 44046--44089 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
44036 AAACAAATCG
44046 TAATTTCATTTTTTCT-TTT
1 TAATTTC-TTTTTTCTATTT
44065 TAATTTCTTTTTTCTATTT
1 TAATTTCTTTTTTCTATTT
*
44084 TCATTT
1 TAATTT
44090 TTTCCATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (19 bp):
TAATTTCTTTTTTCTATTT
Found at i:44232 original size:20 final size:20
Alignment explanation
Indices: 44203--44249 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
44193 GATCATGCAG
**
44203 ATGC-AAATGTGAGATTAAT
1 ATGCAAAATGTGAGAAAAAT
*
44222 ATGCAAAATGTGATAAAAAT
1 ATGCAAAATGTGAGAAAAAT
44242 ATGCAAAA
1 ATGCAAAA
44250 GAACCCAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (20 bp):
ATGCAAAATGTGAGAAAAAT
Found at i:44404 original size:27 final size:26
Alignment explanation
Indices: 44343--44416 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 26
44333 TGAGCAATGG
* * *
44343 AGTAGAAATGACCACAATGCCCCCTGA
1 AGTACAAACGACCAAAATG-CCCCTGA
44370 AGTACAAACGACCAAAATGCCCCTAGA
1 AGTACAAACGACCAAAATGCCCCT-GA
* * *
44397 TGTGCAAACGACTAAAATGC
1 AGTACAAACGACCAAAATGC
44417 TAAATAAGAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
26 5 0.12
27 35 0.88
ACGTcount: A:0.41, C:0.27, G:0.18, T:0.15
Consensus pattern (26 bp):
AGTACAAACGACCAAAATGCCCCTGA
Found at i:45210 original size:69 final size:69
Alignment explanation
Indices: 45137--45608 Score: 782
Period size: 69 Copynumber: 6.8 Consensus size: 69
45127 CTCTTATGTA
* * * * * * * *
45137 TGGATGGACCCAATGTTTAAACTGACTCGCATGGAAACGAGTTTGACTTATGGAAAAGTCTATGT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
45202 GGCT
66 GGCT
* * *
45206 TGGATGAAACCAAGGCTTGTACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATCT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
*
45271 GACT
66 GGCT
*
45275 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAATTTGGCTTGTGGAAAAGCCTATGT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
45340 GGCT
66 GGCT
*
45344 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCTATGT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
45409 GGCT
66 GGCT
* *
45413 TGGATGGAACCAAGGTTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCGATGT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
45478 GGCT
66 GGCT
45482 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
45547 GGCT
66 GGCT
* *
45551 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAATGAGTTTGGCTTGCGGAAAAG
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
45609 TCTAAGCATT
Statistics
Matches: 377, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 377 1.00
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (69 bp):
TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
GGCT
Found at i:46938 original size:12 final size:11
Alignment explanation
Indices: 46922--46990 Score: 53
Period size: 10 Copynumber: 6.8 Consensus size: 11
46912 TCCATTCTCT
*
46922 TTTGATTTAGA
1 TTTGATTTTGA
46933 TTTTGA-TTTGA
1 -TTTGATTTTGA
46944 TTTGATTTTG-
1 TTTGATTTTGA
46954 TTT-ATTTTGA
1 TTTGATTTTGA
*
46964 TTT--TTTTTA
1 TTTGATTTTGA
*
46973 TTT-CTTTTGA
1 TTTGATTTTGA
46983 -TTGATTTT
1 TTTGATTTT
46991 TTTTTTGAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
9 16 0.33
10 20 0.41
11 8 0.16
12 5 0.10
ACGTcount: A:0.16, C:0.01, G:0.13, T:0.70
Consensus pattern (11 bp):
TTTGATTTTGA
Found at i:46940 original size:6 final size:6
Alignment explanation
Indices: 46921--46967 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
46911 ATCCATTCTC
*
46921 TTTTGA TTTAGA TTTTGA -TTTGA -TTTGA TTTTG- -TTT-A TTTTGA
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
46964 TTTT
1 TTTT
46968 TTTTATTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
4 3 0.09
5 13 0.37
6 19 0.54
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (6 bp):
TTTTGA
Found at i:46964 original size:15 final size:15
Alignment explanation
Indices: 46926--46975 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
46916 TTCTCTTTTG
*
46926 ATTTAGATTTTGATTT
1 ATTTTGATTTTG-TTT
46942 GA-TTTGATTTTGTTT
1 -ATTTTGATTTTGTTT
*
46957 ATTTTGATTTTTTTT
1 ATTTTGATTTTGTTT
46972 ATTT
1 ATTT
46976 CTTTTGATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 1 0.03
15 19 0.63
16 9 0.30
17 1 0.03
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (15 bp):
ATTTTGATTTTGTTT
Found at i:46971 original size:19 final size:20
Alignment explanation
Indices: 46939--46990 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
46929 TAGATTTTGA
*
46939 TTTGATTTGATTTTGTTTAT
1 TTTGATTTGATTTTATTTAT
* *
46959 TTTGATTT-TTTTTATTTCT
1 TTTGATTTGATTTTATTTAT
46978 TTTGA-TTGATTTT
1 TTTGATTTGATTTT
46991 TTTTTTGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 2 0.07
19 17 0.63
20 8 0.30
ACGTcount: A:0.13, C:0.02, G:0.12, T:0.73
Consensus pattern (20 bp):
TTTGATTTGATTTTATTTAT
Found at i:47397 original size:14 final size:15
Alignment explanation
Indices: 47378--47415 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
47368 AAGTGCATTT
*
47378 ATTTTCCTTTTTTC-
1 ATTTTCATTTTTTCA
47392 ATTTTCATTTTTTCA
1 ATTTTCATTTTTTCA
47407 ATTTTCATT
1 ATTTTCATT
47416 CATCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTCATTTTTTCA
Found at i:49520 original size:21 final size:22
Alignment explanation
Indices: 49485--49526 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
49475 CTAAGGTTTA
*
49485 ATGGGATGCATGAATGAATGCC
1 ATGGCATGCATGAATGAATGCC
49507 ATGGCATG-ATGAATGAATGC
1 ATGGCATGCATGAATGAATGC
49527 ATGAGGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.24
Consensus pattern (22 bp):
ATGGCATGCATGAATGAATGCC
Found at i:54454 original size:13 final size:13
Alignment explanation
Indices: 54436--54460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54426 AACATACTTA
54436 AAAACACTTTTGG
1 AAAACACTTTTGG
54449 AAAACACTTTTG
1 AAAACACTTTTG
54461 ATTTTTTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (13 bp):
AAAACACTTTTGG
Found at i:56632 original size:21 final size:20
Alignment explanation
Indices: 56608--56648 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
56598 AATGTGAGTT
56608 TCAAAGTTTTTCTCTTGCTTG
1 TCAAAGTTTTTCTCTT-CTTG
*
56629 TCAAAGTTTTTTTCTTCTTG
1 TCAAAGTTTTTCTCTTCTTG
56649 CTTGTGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.56
Consensus pattern (20 bp):
TCAAAGTTTTTCTCTTCTTG
Done.