Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023075.1 Corchorus olitorius cultivar O-4 contig23108, 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: 34613
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Found at i:350 original size:33 final size:33
Alignment explanation
Indices: 313--471 Score: 187
Period size: 33 Copynumber: 4.8 Consensus size: 33
303 GCCCAAGGGT
*
313 AGTCGCGACCGGATTGCGACCAT-CCCGTGGGAC
1 AGTCGCGACCGGATCGCGA-CATGCCCGTGGGAC
* * *
346 AGTCGCGACCGGGTCGCGACTTGCCCGTAGG-C
1 AGTCGCGACCGGATCGCGACATGCCCGTGGGAC
* * * *
378 TAGTCACGACCGGATCGCGACTTGGCCGTGGGAT
1 -AGTCGCGACCGGATCGCGACATGCCCGTGGGAC
* * *
412 AGTCGCGACCGAATCGCGACATTCCCGTGGGAT
1 AGTCGCGACCGGATCGCGACATGCCCGTGGGAC
445 AGTCGCGACCGGATCGCGACATGCCCG
1 AGTCGCGACCGGATCGCGACATGCCCG
472 CCGGCTTATC
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
32 3 0.03
33 104 0.97
ACGTcount: A:0.18, C:0.32, G:0.34, T:0.16
Consensus pattern (33 bp):
AGTCGCGACCGGATCGCGACATGCCCGTGGGAC
Found at i:390 original size:66 final size:67
Alignment explanation
Indices: 291--471 Score: 212
Period size: 66 Copynumber: 2.8 Consensus size: 67
281 GAGATCAGGT
* * *
291 CGGGTCGCGAC-TGCCC-AAGGGTAGTCGCGACCGGATTGCGACCAT-CCCGTGGGACAGTCGCG
1 CGGGTCGCGACTTGCCCGTAGGATAGTCGCGACCGGATCGCGACCATGCCCGTGGGACAGTCGCG
353 AC
66 AC
* * * * *
355 CGGGTCGCGACTTGCCCGTAGGCTAGTCACGACCGGATCGCGA-CTTGGCCGTGGGATAGTCGCG
1 CGGGTCGCGACTTGCCCGTAGGATAGTCGCGACCGGATCGCGACCATGCCCGTGGGACAGTCGCG
419 AC
66 AC
** *
421 CGAATCGCGACATT-CCCGTGGGATAGTCGCGACCGGATCGCGA-CATGCCCG
1 CGGGTCGCGAC-TTGCCCGTAGGATAGTCGCGACCGGATCGCGACCATGCCCG
472 CCGGCTTATC
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
64 11 0.11
65 7 0.07
66 79 0.80
67 2 0.02
ACGTcount: A:0.17, C:0.32, G:0.35, T:0.16
Consensus pattern (67 bp):
CGGGTCGCGACTTGCCCGTAGGATAGTCGCGACCGGATCGCGACCATGCCCGTGGGACAGTCGCG
AC
Found at i:484 original size:33 final size:33
Alignment explanation
Indices: 312--494 Score: 183
Period size: 33 Copynumber: 5.5 Consensus size: 33
302 TGCCCAAGGG
* *
312 TAGTCGCGACCGGATTGCGACCAT-CCCGTGGGA
1 TAGTCGCGACCGGATCGCGA-CATGCCCGTGGCA
* * *
345 CAGTCGCGACCGGGTCGCGACTTGCCCGTAGGC-
1 TAGTCGCGACCGGATCGCGACATGCCCGT-GGCA
* * * *
378 TAGTCACGACCGGATCGCGACTTGGCCGTGGGA
1 TAGTCGCGACCGGATCGCGACATGCCCGTGGCA
* * *
411 TAGTCGCGACCGAATCGCGACATTCCCGTGGGA
1 TAGTCGCGACCGGATCGCGACATGCCCGTGGCA
* *
444 TAGTCGCGACCGGATCGCGACATGCCCGCCGGCT
1 TAGTCGCGACCGGATCGCGACATGCCCG-TGGCA
478 TA-TCGCGATCCGGATCG
1 TAGTCGCGA-CCGGATCG
495 TGATTACCCC
Statistics
Matches: 125, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
32 4 0.03
33 107 0.86
34 14 0.11
ACGTcount: A:0.17, C:0.32, G:0.33, T:0.17
Consensus pattern (33 bp):
TAGTCGCGACCGGATCGCGACATGCCCGTGGCA
Found at i:655 original size:21 final size:21
Alignment explanation
Indices: 625--688 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
615 ATTTACCCCG
*
625 TCTGGCGTCGATGGCTCGTTA
1 TCTGGGGTCGATGGCTCGTTA
646 TCTGGGGTCGATGGCTCGTTA
1 TCTGGGGTCGATGGCTCGTTA
*
667 TCTGGGGTCGATGGATCGTTA
1 TCTGGGGTCGATGGCTCGTTA
688 T
1 T
689 TGTCCATATC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.11, C:0.19, G:0.36, T:0.34
Consensus pattern (21 bp):
TCTGGGGTCGATGGCTCGTTA
Found at i:2297 original size:18 final size:18
Alignment explanation
Indices: 2274--2330 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
2264 GGGCTAAAAT
2274 ACAGGACCGAAAGGTCAA
1 ACAGGACCGAAAGGTCAA
2292 ACAGGACCGAAAGGTCAA
1 ACAGGACCGAAAGGTCAA
*
2310 ACAGGACC-AAGAGGTCGA
1 ACAGGACCGAA-AGGTCAA
2328 ACA
1 ACA
2331 AGCAGAAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
17 2 0.05
18 35 0.95
ACGTcount: A:0.44, C:0.23, G:0.28, T:0.05
Consensus pattern (18 bp):
ACAGGACCGAAAGGTCAA
Found at i:2355 original size:65 final size:64
Alignment explanation
Indices: 2274--2430 Score: 208
Period size: 65 Copynumber: 2.4 Consensus size: 64
2264 GGGCTAAAAT
* * *
2274 ACAGGACCGAAAGGTCAAACAGGACCGAAAGGTCAAACAGGACCAAGAGGTCGAACAAGCAGAAA
1 ACAGGACC-AAAGGTCAAACAGGACCAAAAGGTCAAACAGGACCAAGAGATCAAACAAGCAGAAA
* * *
2339 ACAGGACCAAAGGGTCAAACAGGATCAAAAGGTCAAATAGGACCAAGAGATCAAACAGGCAGAAA
1 ACAGGACCAAA-GGTCAAACAGGACCAAAAGGTCAAACAGGACCAAGAGATCAAACAAGCAGAAA
* * *
2404 ATAGGACGAAAGGTCAAAC-GGAGCAAA
1 ACAGGACCAAAGGTCAAACAGGACCAAA
2431 CTTCTTCATC
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
63 7 0.09
64 11 0.13
65 64 0.78
ACGTcount: A:0.48, C:0.19, G:0.27, T:0.06
Consensus pattern (64 bp):
ACAGGACCAAAGGTCAAACAGGACCAAAAGGTCAAACAGGACCAAGAGATCAAACAAGCAGAAA
Found at i:2360 original size:18 final size:18
Alignment explanation
Indices: 2337--2397 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
2327 AACAAGCAGA
2337 AAACAGGACCAAAGGGTC
1 AAACAGGACCAAAGGGTC
* *
2355 AAACAGGATCAAAAGGTC
1 AAACAGGACCAAAGGGTC
* *
2373 AAATAGGACC-AAGAGATC
1 AAACAGGACCAAAG-GGTC
2391 AAACAGG
1 AAACAGG
2398 CAGAAAATAG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
17 2 0.06
18 33 0.94
ACGTcount: A:0.49, C:0.18, G:0.25, T:0.08
Consensus pattern (18 bp):
AAACAGGACCAAAGGGTC
Found at i:2554 original size:13 final size:13
Alignment explanation
Indices: 2538--2569 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2528 AAAGTCAACG
2538 GTCAACCCTCAAA
1 GTCAACCCTCAAA
*
2551 GTCAACGCTCAAA
1 GTCAACCCTCAAA
2564 GTCAAC
1 GTCAAC
2570 TAGATGATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.34, G:0.12, T:0.16
Consensus pattern (13 bp):
GTCAACCCTCAAA
Found at i:2678 original size:42 final size:42
Alignment explanation
Indices: 2609--2736 Score: 159
Period size: 42 Copynumber: 3.0 Consensus size: 42
2599 CGATCAACGG
*
2609 ATGACGTGGCAGGTTGAC-GGGTCAACGGATGACGTGGCAGC
1 ATGACGTGGCAGGTTGACTCGGTCAACGGATGACGTGGCAGC
* * *
2650 ATGATGTGGCAGGTAGACTCGGTCAACGGATGACGTGGCAGG
1 ATGACGTGGCAGGTTGACTCGGTCAACGGATGACGTGGCAGC
* ** *
2692 ATGACGTGGCGGGTTGACTTAGTAAACAGTGATGACGTGGCAGC
1 ATGACGTGGCAGGTTGACTCGGTCAAC-G-GATGACGTGGCAGC
2736 A
1 A
2737 GCGGATTGGC
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 16 0.22
42 42 0.58
43 1 0.01
44 14 0.19
ACGTcount: A:0.24, C:0.17, G:0.39, T:0.20
Consensus pattern (42 bp):
ATGACGTGGCAGGTTGACTCGGTCAACGGATGACGTGGCAGC
Found at i:2709 original size:13 final size:13
Alignment explanation
Indices: 2607--2701 Score: 70
Period size: 13 Copynumber: 6.9 Consensus size: 13
2597 AACGATCAAC
2607 GGATGACGTGGCA
1 GGATGACGTGGCA
*
2620 GGTTGACG-GGTCAA
1 GGATGACGTGG-C-A
2634 CGGATGACGTGGCA
1 -GGATGACGTGGCA
* *
2648 GCATGATGTGGCA
1 GGATGACGTGGCA
2661 GG-TAGAC-TCGGTCAA
1 GGAT-GACGT-GG-C-A
2676 CGGATGACGTGGCA
1 -GGATGACGTGGCA
2690 GGATGACGTGGC
1 GGATGACGTGGC
2702 GGGTTGACTT
Statistics
Matches: 65, Mismatches: 6, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
12 4 0.06
13 36 0.55
14 4 0.06
15 10 0.15
16 9 0.14
17 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.42, T:0.18
Consensus pattern (13 bp):
GGATGACGTGGCA
Found at i:7386 original size:6 final size:6
Alignment explanation
Indices: 7375--7421 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
7365 TAAAGGAGAG
* * * *
7375 TCGTCT TCGTCT TCGTCT TCGACT TCGTCA TCGTCA TCGTCA TCGTC
1 TCGTCT TCGTCT TCGTCT TCGTCT TCGTCT TCGTCT TCGTCT TCGTC
7422 ATCGCCGAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.09, C:0.34, G:0.17, T:0.40
Consensus pattern (6 bp):
TCGTCT
Found at i:7420 original size:18 final size:18
Alignment explanation
Indices: 7375--7425 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
7365 TAAAGGAGAG
* *
7375 TCGTCTTCGTCTTCGTCT
1 TCGTCTTCGTCATCGTCA
*
7393 TCGACTTCGTCATCGTCA
1 TCGTCTTCGTCATCGTCA
*
7411 TCGTCATCGTCATCG
1 TCGTCTTCGTCATCG
7426 CCGAGTGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.10, C:0.33, G:0.18, T:0.39
Consensus pattern (18 bp):
TCGTCTTCGTCATCGTCA
Found at i:9909 original size:3 final size:3
Alignment explanation
Indices: 9901--9986 Score: 165
Period size: 3 Copynumber: 29.0 Consensus size: 3
9891 AAAACAACTA
9901 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9949 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9987 ATGGCTTATT
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 80 0.98
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:10622 original size:21 final size:22
Alignment explanation
Indices: 10548--10624 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
10538 TATTTTTATG
* * *
10548 AAATTTCGATAATCACCCTATT
1 AAATTTTGATAATTACCCTATA
* * *
10570 AAATTTTGATAATTATCATATG
1 AAATTTTGATAATTACCCTATA
10592 AAATTTTGATAATTA-CCTATA
1 AAATTTTGATAATTACCCTATA
*
10613 AAATTGTGATAA
1 AAATTTTGATAA
10625 ACTCCATAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
21 15 0.32
22 32 0.68
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAATTACCCTATA
Found at i:14150 original size:3 final size:3
Alignment explanation
Indices: 14142--14180 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
14132 TATAGTATAG
14142 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
14181 TACTCCATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:14930 original size:21 final size:21
Alignment explanation
Indices: 14906--14947 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
14896 TATCTTAGAT
*
14906 ATAATATATACTA-TTAAATAA
1 ATAATAAATA-TATTTAAATAA
14927 ATAATAAATATATTTAAATAA
1 ATAATAAATATATTTAAATAA
14948 TAAATAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATAAATATATTTAAATAA
Found at i:16236 original size:45 final size:45
Alignment explanation
Indices: 16183--16279 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
16173 AGTGTATTAT
* * *
16183 CTAA-ATTCTAATACTCCATCTCTAGGTAATTCATTAAAATAAAG
1 CTAATATTCTAATACTCAATCTCTAGATAATTCATCAAAATAAAG
* *
16227 CTAATATTCTACTCCTCAATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTAATACTCAATCTCTAGATAATTCATCAAAATAAAG
16272 CTAATATT
1 CTAATATT
16280 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (45 bp):
CTAATATTCTAATACTCAATCTCTAGATAATTCATCAAAATAAAG
Found at i:18005 original size:84 final size:84
Alignment explanation
Indices: 17839--18167 Score: 588
Period size: 84 Copynumber: 3.9 Consensus size: 84
17829 CCAATAACCA
* *
17839 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
17904 AACACAGAGGCATCTATATC
65 AACACAGAGGCATCTATATC
*
17924 AAAGTCCCTAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
17989 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
*
18008 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCTTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
18073 ACACAGA-GCATCTATATC
66 ACACAGAGGCATCTATATC
* *
18091 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
18156 ACACAGAGGCAT
66 ACACAGAGGCAT
18168 TTCTCCTTAT
Statistics
Matches: 235, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
83 80 0.34
84 115 0.49
85 40 0.17
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:18131 original size:167 final size:169
Alignment explanation
Indices: 17839--18167 Score: 590
Period size: 167 Copynumber: 2.0 Consensus size: 169
17829 CCAATAACCA
* *
17839 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
* *
17904 AACACAGAGGCATCTATATCAAAGTCCCTAAACACATATATAACACAGGGGCAACTCTATTACAA
66 AACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTACAA
17969 AGTCCTCAAACACATATATAACACAGAGGCATCTATATC
131 AGTCCTCAAACACATATATAACACAGAGGCATCTATATC
*
18008 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCTTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
*
18072 AACACAGA-GCATCTATATCAAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTACAA
66 AACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTACAA
18136 AGTCCTCAAACACATATATAACACAGAGGCAT
131 AGTCCTCAAACACATATATAACACAGAGGCAT
18168 TTCTCCTTAT
Statistics
Matches: 154, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
167 85 0.55
168 28 0.18
169 41 0.27
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (169 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
AACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTACAA
AGTCCTCAAACACATATATAACACAGAGGCATCTATATC
Found at i:18167 original size:43 final size:42
Alignment explanation
Indices: 17839--18167 Score: 461
Period size: 43 Copynumber: 7.8 Consensus size: 42
17829 CCAATAACCA
* *
17839 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATT-C
*
17882 AAAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-TC
1 -AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTC
* *
17924 AAAGTCC-CTAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCTC-AAACACATATATAACACAGAGGCATCTCTATT-C
*
17967 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-TC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTC
* * *
18008 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATT-C
* *
18051 AAAGTCTTCAAACACATATATAACACAGA-GCATCTATA-TC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTC
*
18091 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
1 AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATT-C
18134 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCTCAAACACATATATAACACAGAGGCAT
18168 TTCTCCTTAT
Statistics
Matches: 254, Mismatches: 22, Indels: 19
0.86 0.07 0.06
Matches are distributed among these distances:
40 29 0.11
41 79 0.31
42 12 0.05
43 97 0.38
44 37 0.15
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (42 bp):
AAAGTCCTCAAACACATATATAACACAGAGGCATCTCTATTC
Found at i:19068 original size:23 final size:23
Alignment explanation
Indices: 19036--19095 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
19026 CGAAAATGAC
19036 AGCAACTCTAAGAGGAATCAACT
1 AGCAACTCTAAGAGGAATCAACT
*
19059 AGCAATTCTAAGAGGAATCAACT
1 AGCAACTCTAAGAGGAATCAACT
*
19082 AACAACTCTAAGAG
1 AGCAACTCTAAGAG
19096 AAGAAGAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (23 bp):
AGCAACTCTAAGAGGAATCAACT
Found at i:30773 original size:41 final size:41
Alignment explanation
Indices: 30672--31001 Score: 400
Period size: 41 Copynumber: 7.8 Consensus size: 41
30662 CCAAAGACCA
* *
30672 AAAGTCCCCAAACACATATATAACACAGGTGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGG-GCATCTATA-TAC
* *
30715 AAAAGTCCTCAAACACATATACAACACAGAGGCATCTATAT-C
1 -AAAGTCCCCAAACACATATATAACACAG-GGCATCTATATAC
* *
30757 AAAGTCCCCAAACACATATATAACACAGGGGAAACTCCAT-TAC
1 AAAGTCCCCAAACACATATATAACACA-GGG-CA-TCTATATAC
*
30800 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATAT-C
1 AAAGTCCCCAAACACATATATAACACAG-GGCATCTATATAC
30841 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTAT-TAC
1 AAAGTCCCCAAACACATATATAACACA-GGGC-A-TCTATATAC
*
30884 AAAGTCCTCAAACACATATATAACACAGGAGCATCTATAT-C
1 AAAGTCCCCAAACACATATATAACACAGG-GCATCTATATAC
*
30925 AAAGTCCCCAAACACATATATAACACAGGAGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGG-GCATCTATA-TAC
*
30968 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAG-GGCAT
31002 TTCTCCTTAT
Statistics
Matches: 255, Mismatches: 15, Indels: 33
0.84 0.05 0.11
Matches are distributed among these distances:
41 104 0.41
42 15 0.06
43 100 0.39
44 35 0.14
45 1 0.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (41 bp):
AAAGTCCCCAAACACATATATAACACAGGGCATCTATATAC
Found at i:30804 original size:43 final size:42
Alignment explanation
Indices: 30672--30995 Score: 381
Period size: 43 Copynumber: 7.7 Consensus size: 42
30662 CCAAAGACCA
* * *
30672 AAAGTCCCCAAACACATATATAACACAGGTGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGG-GGAACTCTATTAC
* * * *
30715 AAAAGTCCTCAAACACATATACAACACAGAGGCA-TCTA-TATC
1 -AAAGTCCCCAAACACATATATAACACAGGGGAACTCTATTA-C
*
30757 AAAGTCCCCAAACACATATATAACACAGGGGAAACTCCATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGG-AACTCTATTAC
* * *
30800 AAAGTCCTCAAACACATATATAACACAGAGGCA-TCTA-TATC
1 AAAGTCCCCAAACACATATATAACACAGGGGAACTCTATTA-C
30841 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGG-AACTCTATTAC
* * *
30884 AAAGTCCTCAAACACATATATAACACAGGAGCA-TCTA-TATC
1 AAAGTCCCCAAACACATATATAACACAGGGGAACTCTATTA-C
* *
30925 AAAGTCCCCAAACACATATATAACACAGGAGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGG-GGAACTCTATTAC
*
30968 AAAGTCCTCAAACACATATATAACACAG
1 AAAGTCCCCAAACACATATATAACACAG
30996 AGGCATTTCT
Statistics
Matches: 240, Mismatches: 28, Indels: 25
0.82 0.10 0.09
Matches are distributed among these distances:
40 4 0.02
41 95 0.40
42 9 0.04
43 100 0.42
44 32 0.13
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (42 bp):
AAAGTCCCCAAACACATATATAACACAGGGGAACTCTATTAC
Found at i:31030 original size:84 final size:84
Alignment explanation
Indices: 30672--31001 Score: 563
Period size: 84 Copynumber: 3.9 Consensus size: 84
30662 CCAAAGACCA
* * * *
30672 AAAGTCCCCAAACACATATATAACACAGGTGCATCTCTATTCCAAAAGTCCTCAAACACATATAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
30737 AACACAGAGGCATCTATATC
65 AACACAGAGGCATCTATATC
* *
30757 AAAGTCCCCAAACACATATATAACACAGGGGAAACTCCATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
30822 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
30841 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
30906 ACACAG-GAGCATCTATATC
66 ACACAGAG-GCATCTATATC
* *
30925 AAAGTCCCCAAACACATATATAACACAGGAGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
30990 ACACAGAGGCAT
66 ACACAGAGGCAT
31002 TTCTCCTTAT
Statistics
Matches: 233, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
83 1 0.00
84 193 0.83
85 39 0.17
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:31123 original size:2 final size:2
Alignment explanation
Indices: 31112--31160 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
31102 CCAAATTCCC
* *
31112 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31153 AT AT AT AT
1 AT AT AT AT
31161 GTGACAAGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:31724 original size:16 final size:16
Alignment explanation
Indices: 31705--31736 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31695 ATGAAATATG
31705 GTGTCGATTTCAACGC
1 GTGTCGATTTCAACGC
31721 GTGTCGATTTCAACGC
1 GTGTCGATTTCAACGC
31737 AAGAAGGTGC
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:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (16 bp):
GTGTCGATTTCAACGC
Found at i:31936 original size:23 final size:23
Alignment explanation
Indices: 31906--31962 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
31896 CGAAAATGGC
31906 AGCAACTCTAAGAGGAATCAACT
1 AGCAACTCTAAGAGGAATCAACT
31929 AGCAACTCTAAGAGGAATCAACT
1 AGCAACTCTAAGAGGAATCAACT
*
31952 AACAACTCTAA
1 AGCAACTCTAA
31963 AAGAAGAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.46, C:0.23, G:0.14, T:0.18
Consensus pattern (23 bp):
AGCAACTCTAAGAGGAATCAACT
Found at i:32743 original size:45 final size:45
Alignment explanation
Indices: 32694--32820 Score: 218
Period size: 45 Copynumber: 2.8 Consensus size: 45
32684 AATTCTACTT
*
32694 CATCTCTAGGTAATTCATAAAAATAAAGCTAATATTATACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
* * *
32739 CATCTCTAGATAATTCATCAAAATAAAGTTAATATTCTACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
32784 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
32821 ATTGTTGCTT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (45 bp):
CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
Found at i:34052 original size:42 final size:43
Alignment explanation
Indices: 34002--34095 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 43
33992 AATGCATTAC
*
34002 CTAA-ATTCTA-CTCCATCTCTAGGTAATAT-ATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAAT-TCATCAAAATAAAG
*
34043 CTAATATTCTACTCCTCCATCTCTAGATAATTCTTCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
34088 CTAATATT
1 CTAATATT
34096 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
44 1 0.02
45 35 0.76
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Done.