Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020279.1 Corchorus olitorius cultivar O-4 contig20312, 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: 160609
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1331 original size:28 final size:23
Alignment explanation
Indices: 1275--1320 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1265 GTAAACTATA
1275 TAGTTATATAAAACCATGAGGTT
1 TAGTTATATAAAACCATGAGGTT
1298 TAGTTATATAAAACCATGAGGTT
1 TAGTTATATAAAACCATGAGGTT
1321 GCGTTTGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (23 bp):
TAGTTATATAAAACCATGAGGTT
Found at i:1600 original size:24 final size:24
Alignment explanation
Indices: 1573--1621 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
1563 GCTGACTTTT
1573 TCTTTTTC-ATGAAAAAACAGGGTA
1 TCTTTTTCTA-GAAAAAACAGGGTA
1597 TCTTTTTCTAGAAAAAACAGGGTA
1 TCTTTTTCTAGAAAAAACAGGGTA
1621 T
1 T
1622 GCAAGTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (24 bp):
TCTTTTTCTAGAAAAAACAGGGTA
Found at i:2029 original size:7 final size:7
Alignment explanation
Indices: 1993--2028 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
1983 AAATTTAGTA
1993 ATTGATT
1 ATTGATT
2000 ATTGATT
1 ATTGATT
2007 ATTGATT
1 ATTGATT
2014 ATTGATT
1 ATTGATT
*
2021 AGTGATT
1 ATTGATT
2028 A
1 A
2029 GGAGGGACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.53
Consensus pattern (7 bp):
ATTGATT
Found at i:2551 original size:21 final size:23
Alignment explanation
Indices: 2520--2645 Score: 132
Period size: 24 Copynumber: 5.4 Consensus size: 23
2510 GTCCCTGGAA
*
2520 CTGGCGGCGGCAT-CCAGCTTCCTC
1 CTGGCGGC-GC-TGCCAGCTTCCCC
*
2544 CTGGCGGCGCTGGCCAGCTTCCTC
1 CTGGCGGCGCT-GCCAGCTTCCCC
2568 CTGGCGGCGCTGGCCAGCTTCCCC
1 CTGGCGGCGCT-GCCAGCTTCCCC
*
2592 CCGGCGGCG-T-CCAGCTTCCCC
1 CTGGCGGCGCTGCCAGCTTCCCC
* * *
2613 CTGGTGGTGCTGGTCAGCTTCCCC
1 CTGGCGGCGCT-GCCAGCTTCCCC
2637 CTGGCGGCG
1 CTGGCGGCG
2646 GTATGCTTCC
Statistics
Matches: 89, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
21 17 0.19
22 2 0.02
23 3 0.03
24 67 0.75
ACGTcount: A:0.05, C:0.42, G:0.33, T:0.20
Consensus pattern (23 bp):
CTGGCGGCGCTGCCAGCTTCCCC
Found at i:2552 original size:24 final size:23
Alignment explanation
Indices: 2520--2664 Score: 101
Period size: 24 Copynumber: 6.3 Consensus size: 23
2510 GTCCCTGGAA
2520 CTGGCGGCGGCATCCAGCTTCCTC
1 CTGGCGGCGGC-TCCAGCTTCCTC
2544 CTGGCGGC-GCTGGCCAGCTTCCTC
1 CTGGCGGCGGCT--CCAGCTTCCTC
*
2568 CTGGCGGC-GCTGGCCAGCTTCCCC
1 CTGGCGGCGGCT--CCAGCTTCCTC
* *
2592 CCGGCGGC-G-TCCAGCTTCCCC
1 CTGGCGGCGGCTCCAGCTTCCTC
* *
2613 CTGGTGGTGCTGG-T-CAGCTTCCCC
1 CTGG-CG-GC-GGCTCCAGCTTCCTC
2637 CTGGCGGCGG-T--ATGCTTCCTC
1 CTGGCGGCGGCTCCA-GCTTCCTC
2658 CTGGCGG
1 CTGGCGG
2665 TGGCATGCTG
Statistics
Matches: 108, Mismatches: 6, Indels: 17
0.82 0.05 0.13
Matches are distributed among these distances:
20 1 0.01
21 31 0.29
22 4 0.04
23 6 0.06
24 64 0.59
25 2 0.02
ACGTcount: A:0.05, C:0.41, G:0.33, T:0.21
Consensus pattern (23 bp):
CTGGCGGCGGCTCCAGCTTCCTC
Found at i:2606 original size:45 final size:45
Alignment explanation
Indices: 2533--2664 Score: 151
Period size: 45 Copynumber: 2.9 Consensus size: 45
2523 GCGGCGGCAT
*
2533 CCAGCTTCCTCCTGGCGGCGCTGGCCAGCTTCCTCCTGGCGGCGCTGG
1 CCAGCTTCCCCCTGGCGGCG-T--CCAGCTTCCTCCTGGCGGCGCTGG
* * * *
2581 CCAGCTTCCCCCCGGCGGCGTCCAGCTTCCCCCTGGTGGTGCTGG
1 CCAGCTTCCCCCTGGCGGCGTCCAGCTTCCTCCTGGCGGCGCTGG
*
2626 TCAGCTTCCCCCTGGCGGCGGT--ATGCTTCCTCCTGGCGG
1 CCAGCTTCCCCCTGGCGGC-GTCCA-GCTTCCTCCTGGCGG
2665 TGGCATGCTG
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
44 1 0.01
45 51 0.70
46 2 0.03
47 1 0.01
48 18 0.25
ACGTcount: A:0.05, C:0.42, G:0.32, T:0.22
Consensus pattern (45 bp):
CCAGCTTCCCCCTGGCGGCGTCCAGCTTCCTCCTGGCGGCGCTGG
Found at i:2655 original size:21 final size:21
Alignment explanation
Indices: 2584--2673 Score: 67
Period size: 21 Copynumber: 4.1 Consensus size: 21
2574 GCGCTGGCCA
* *
2584 GCTTCCCCCCGGCGGCGTCCA-
1 GCTTCCCCCTGGCGGCG-GCAT
*
2605 GCTTCCCCCTGGTGGTGCTGGTCA-
1 GCTTCCCCCTGG-CG-GC-GG-CAT
*
2629 GCTTCCCCCTGGCGGCGGTAT
1 GCTTCCCCCTGGCGGCGGCAT
* *
2650 GCTTCCTCCTGGCGGTGGCAT
1 GCTTCCCCCTGGCGGCGGCAT
2671 GCT
1 GCT
2674 GCTTCCCCCT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
20 1 0.02
21 34 0.61
22 3 0.05
23 3 0.05
24 15 0.27
ACGTcount: A:0.04, C:0.39, G:0.32, T:0.24
Consensus pattern (21 bp):
GCTTCCCCCTGGCGGCGGCAT
Found at i:20650 original size:17 final size:16
Alignment explanation
Indices: 20604--20646 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
20594 CTATATTACT
20604 AGTGATCTAAGATCACC
1 AGTGATC-AAGATCACC
20621 AGTGATGCAAGATCACC
1 AGTGAT-CAAGATCACC
*
20638 GGTGATCAA
1 AGTGATCAA
20647 AGATTACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (16 bp):
AGTGATCAAGATCACC
Found at i:22907 original size:15 final size:16
Alignment explanation
Indices: 22880--22911 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
22870 TTCTTTCTGG
22880 TTTGTTGGGTGGGTTA
1 TTTGTTGGGTGGGTTA
22896 TTTGTT-GGTGGGTTA
1 TTTGTTGGGTGGGTTA
22911 T
1 T
22912 GAAAAATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.06, C:0.00, G:0.41, T:0.53
Consensus pattern (16 bp):
TTTGTTGGGTGGGTTA
Found at i:29087 original size:55 final size:55
Alignment explanation
Indices: 29023--29134 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
29013 TTACATTTAC
*
29023 TTTGAATTTGGAAGATAGGCAAGCCAATAATAATGGTTGATGTAACAACTAAATT
1 TTTGAATTTGGAAGAGAGGCAAGCCAATAATAATGGTTGATGTAACAACTAAATT
29078 TTTGAATTTGGAAGAGAGGCAAGCCAATAATAATGGTTGATGTAACAACTAAATT
1 TTTGAATTTGGAAGAGAGGCAAGCCAATAATAATGGTTGATGTAACAACTAAATT
29133 TT
1 TT
29135 GGGAAATTCT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (55 bp):
TTTGAATTTGGAAGAGAGGCAAGCCAATAATAATGGTTGATGTAACAACTAAATT
Found at i:29869 original size:19 final size:20
Alignment explanation
Indices: 29845--29891 Score: 87
Period size: 19 Copynumber: 2.4 Consensus size: 20
29835 ACTAATACTC
29845 TATATAAATTAATAATAA-T
1 TATATAAATTAATAATAATT
29864 TATATAAATTAATAATAATT
1 TATATAAATTAATAATAATT
29884 TATATAAA
1 TATATAAA
29892 AAATCAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TATATAAATTAATAATAATT
Found at i:47132 original size:29 final size:30
Alignment explanation
Indices: 47074--47135 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
47064 ATTAAGAAAG
*
47074 AACCCAATTTGAGTGACAAGAAAAGTAAAA
1 AACCCAATTTGAGTAACAAGAAAAGTAAAA
* *
47104 AACCCATTTTGAGTAACAAGCAAA-TAAAA
1 AACCCAATTTGAGTAACAAGAAAAGTAAAA
47133 AAC
1 AAC
47136 TCAGCTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.53, C:0.16, G:0.13, T:0.18
Consensus pattern (30 bp):
AACCCAATTTGAGTAACAAGAAAAGTAAAA
Found at i:63426 original size:22 final size:22
Alignment explanation
Indices: 63401--63449 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
63391 TGTCAACCTT
*
63401 AATCATTCAAAACAACATCTAA
1 AATCATACAAAACAACATCTAA
**
63423 AATCA-ACCCAACAACATCTAA
1 AATCATACAAAACAACATCTAA
63444 AATCAT
1 AATCAT
63450 GGAGGGGCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (22 bp):
AATCATACAAAACAACATCTAA
Found at i:63973 original size:16 final size:15
Alignment explanation
Indices: 63938--63981 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
63928 ATTAATAGGT
*
63938 TTAATTATT-ATTAAA
1 TTAATTATTAATT-CA
63953 TTAATTAGTTAATTCA
1 TTAATTA-TTAATTCA
63969 TTAATTATTAATT
1 TTAATTATTAATT
63982 AATCAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 13 0.50
16 10 0.38
17 3 0.12
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
TTAATTATTAATTCA
Found at i:71620 original size:24 final size:24
Alignment explanation
Indices: 71579--71653 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
71569 AGGCATTACC
* *
71579 CTGAGTTTTAGGCTTGCTCTGTTT
1 CTGAGGTTTAGGCATGCTCTGTTT
*
71603 CTGGGGTTTAGGCATGCTCTGTTT
1 CTGAGGTTTAGGCATGCTCTGTTT
*
71627 CTGAGTTTTAGGCATGCTCTGTTT
1 CTGAGGTTTAGGCATGCTCTGTTT
71651 CTG
1 CTG
71654 TTAATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.45
Consensus pattern (24 bp):
CTGAGGTTTAGGCATGCTCTGTTT
Found at i:76450 original size:38 final size:38
Alignment explanation
Indices: 76404--76536 Score: 182
Period size: 38 Copynumber: 3.6 Consensus size: 38
76394 GTCAGTAGGT
76404 AACTTAATTCAGGGTAATTAAGCAAGTCAGTAATAAGC
1 AACTTAATTCAGGGTAATTAAGCAAGTCAGTAATAAGC
*
76442 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATAAGC
1 AACTTAATTCAGGGTAATTAAGCAAGTCAGTAATAAGC
* * * * *
76480 AACTTAATTCAGGGCAATTAAGCGAGCCTGT-A-AA-T
1 AACTTAATTCAGGGTAATTAAGCAAGTCAGTAATAAGC
*
76515 AACTTAATTCCGGGTAATTAAG
1 AACTTAATTCAGGGTAATTAAG
76537 TAAATAACTT
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
35 20 0.23
36 2 0.02
37 1 0.01
38 63 0.73
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (38 bp):
AACTTAATTCAGGGTAATTAAGCAAGTCAGTAATAAGC
Found at i:76595 original size:27 final size:27
Alignment explanation
Indices: 76509--76593 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
76499 AAGCGAGCCT
*
76509 GTAAATAACTTAATTCCGGGTAATTAA
1 GTAAATAACTTAATTCAGGGTAATTAA
76536 GTAAATAACTTAATTCAGGGTAATTAA
1 GTAAATAACTTAATTCAGGGTAATTAA
* * *
76563 GTAAGTAACTTAATTCAGGGTAGTTGA
1 GTAAATAACTTAATTCAGGGTAATTAA
76590 GTAA
1 GTAA
76594 GTCAGTCACC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (27 bp):
GTAAATAACTTAATTCAGGGTAATTAA
Found at i:77014 original size:34 final size:33
Alignment explanation
Indices: 76971--77135 Score: 133
Period size: 37 Copynumber: 4.8 Consensus size: 33
76961 CAGTCTCAAG
*
76971 TTTAGTTTTCCAATTGGACAAGTTCCCACCAGGT
1 TTTAGTTTTCAAATTGGA-AAGTTCCCACCAGGT
77005 TTTAGTTTTCAAATTAGGAAAGTT----CCAGGT
1 TTTAGTTTTCAAATT-GGAAAGTTCCCACCAGGT
* * *
77035 TTTAGTTTTCAAATCGGAAAAGTTCCCAACATGTT
1 TTTAGTTTTCAAATTGG-AAAGTTCCCACCA-GGT
* *
77070 TTTAAGTTTTCAAATTGGGAAGGTTCCCATTCA-GT
1 TTT-AGTTTTCAAATT-GGAAAGTTCCCA-CCAGGT
*
77105 TTTCAAAGTTTTTAAATTGGGAAAGTTCCCA
1 TTT---AGTTTTCAAATT-GGAAAGTTCCCA
77136 TCAAAAGCAC
Statistics
Matches: 109, Mismatches: 10, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
29 2 0.02
30 26 0.24
34 21 0.19
35 12 0.11
36 20 0.18
37 28 0.26
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (33 bp):
TTTAGTTTTCAAATTGGAAAGTTCCCACCAGGT
Found at i:77039 original size:64 final size:66
Alignment explanation
Indices: 76971--77096 Score: 175
Period size: 64 Copynumber: 1.9 Consensus size: 66
76961 CAGTCTCAAG
* * * *
76971 TTTAGTTTTCCAATTGGACAAGTTCCCACCA-GGTTTT-AGTTTTCAAATTAGGAAAGTTCCAGG
1 TTTAGTTTTCAAATCGGAAAAGTTCCCAACATGGTTTTAAGTTTTCAAATTAGGAAAGTTCCAGG
77034 T
66 T
* * *
77035 TTTAGTTTTCAAATCGGAAAAGTTCCCAACATGTTTTTAAGTTTTCAAATTGGGAAGGTTCC
1 TTTAGTTTTCAAATCGGAAAAGTTCCCAACATGGTTTTAAGTTTTCAAATTAGGAAAGTTCC
77097 CATTCAGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
64 27 0.51
65 5 0.09
66 21 0.40
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (66 bp):
TTTAGTTTTCAAATCGGAAAAGTTCCCAACATGGTTTTAAGTTTTCAAATTAGGAAAGTTCCAGG
T
Found at i:77078 original size:36 final size:36
Alignment explanation
Indices: 76974--77136 Score: 130
Period size: 36 Copynumber: 4.7 Consensus size: 36
76964 TCTCAAGTTT
* * *
76974 AGTTTTCCAATT-GGACAAGTTCCCA-CCAGGTTTT-
1 AGTTTTCAAATTGGGA-AAGTTCCCATACAGTTTTTA
* *
77008 AGTTTTCAAATTAGGAAAGTT--C---CAGGTTTT-
1 AGTTTTCAAATTGGGAAAGTTCCCATACAGTTTTTA
* *
77038 AGTTTTCAAATCGGAAAAGTTCCCA-ACATGTTTTTA
1 AGTTTTCAAATTGGGAAAGTTCCCATACA-GTTTTTA
* * *
77074 AGTTTTCAAATTGGGAAGGTTCCCATTCAGTTTTCAA
1 AGTTTTCAAATTGGGAAAGTTCCCATACAGTTTT-TA
*
77111 AGTTTTTAAATTGGGAAAGTTCCCAT
1 AGTTTTCAAATTGGGAAAGTTCCCAT
77137 CAAAAGCACT
Statistics
Matches: 108, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
30 26 0.24
32 2 0.02
34 18 0.17
35 8 0.07
36 27 0.25
37 27 0.25
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (36 bp):
AGTTTTCAAATTGGGAAAGTTCCCATACAGTTTTTA
Found at i:77106 original size:64 final size:62
Alignment explanation
Indices: 76969--77111 Score: 153
Period size: 64 Copynumber: 2.2 Consensus size: 62
76959 TCCAGTCTCA
* * * * *
76969 AGTTTAGTTTTCCAATTGGACAAGTTCCCACCAGGTTTTAGTTTTCAAATTAGGAAAGTTCC
1 AGTTCAGTTTTCAAATCGGAAAAGTTCCCAACAGGTTTTAGTTTTCAAATTAGGAAAGTTCC
* * * *
77031 AGGTTTTAGTTTTCAAATCGGAAAAGTTCCCAACATGTTTTTAAGTTTTCAAATTGGGAAGGTTC
1 A-G-TTCAGTTTTCAAATCGGAAAAGTTCCCAACA-GGTTTT-AGTTTTCAAATTAGGAAAGTT-
77096 CC
61 CC
77098 A-TTCAGTTTTCAAA
1 AGTTCAGTTTTCAAA
77112 GTTTTTAAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 39 0.57
65 5 0.07
66 19 0.28
67 3 0.04
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (62 bp):
AGTTCAGTTTTCAAATCGGAAAAGTTCCCAACAGGTTTTAGTTTTCAAATTAGGAAAGTTCC
Found at i:80191 original size:12 final size:12
Alignment explanation
Indices: 80174--80257 Score: 78
Period size: 12 Copynumber: 7.0 Consensus size: 12
80164 TCAGCAACAT
*
80174 CTCTTTCTTTAA
1 CTCTTTCTTCAA
80186 CTCTTTCTTCAA
1 CTCTTTCTTCAA
* *
80198 CCCTTTCTTGAA
1 CTCTTTCTTCAA
*
80210 CTTTTTCTTCAA
1 CTCTTTCTTCAA
* * *
80222 TTTTTTCTTGAA
1 CTCTTTCTTCAA
*
80234 CTCTTTTTTCAA
1 CTCTTTCTTCAA
* *
80246 CCCTTTTTTCAA
1 CTCTTTCTTCAA
80258 TTGGATCTGG
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.17, C:0.26, G:0.02, T:0.55
Consensus pattern (12 bp):
CTCTTTCTTCAA
Found at i:80203 original size:24 final size:24
Alignment explanation
Indices: 80176--80251 Score: 98
Period size: 24 Copynumber: 3.2 Consensus size: 24
80166 AGCAACATCT
*
80176 CTTTCTTTAACTCTTTCTTCAACC
1 CTTTCTTGAACTCTTTCTTCAACC
* **
80200 CTTTCTTGAACTTTTTCTTCAATT
1 CTTTCTTGAACTCTTTCTTCAACC
* *
80224 TTTTCTTGAACTCTTTTTTCAACC
1 CTTTCTTGAACTCTTTCTTCAACC
80248 CTTT
1 CTTT
80252 TTTCAATTGG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.16, C:0.26, G:0.03, T:0.55
Consensus pattern (24 bp):
CTTTCTTGAACTCTTTCTTCAACC
Found at i:80439 original size:24 final size:24
Alignment explanation
Indices: 80408--80453 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
80398 ACTACTTTTT
80408 CAACATTTTCATT-TACATTTTCCA
1 CAACATTTTC-TTCTACATTTTCCA
80432 CAACATTTTCTTCTACATTTTC
1 CAACATTTTCTTCTACATTTTC
80454 AACCAGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (24 bp):
CAACATTTTCTTCTACATTTTCCA
Found at i:80463 original size:24 final size:24
Alignment explanation
Indices: 80408--80466 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
80398 ACTACTTTTT
*
80408 CAACATTTTCATTTACATTTTCCA
1 CAACATTTTCATTTACATTTTCAA
80432 CAACATTTTC-TTCTACATTTTCAA
1 CAACATTTTCATT-TACATTTTCAA
* *
80456 CCAGATTTTCA
1 CAACATTTTCA
80467 GCTAAATCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.07
24 28 0.93
ACGTcount: A:0.29, C:0.25, G:0.02, T:0.44
Consensus pattern (24 bp):
CAACATTTTCATTTACATTTTCAA
Found at i:80699 original size:13 final size:13
Alignment explanation
Indices: 80681--80709 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
80671 GTAGATTCAA
80681 CATTATAAACTTT
1 CATTATAAACTTT
80694 CATTATAAACTTT
1 CATTATAAACTTT
80707 CAT
1 CAT
80710 AAGTCCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (13 bp):
CATTATAAACTTT
Found at i:82578 original size:33 final size:33
Alignment explanation
Indices: 82469--82585 Score: 112
Period size: 33 Copynumber: 3.6 Consensus size: 33
82459 AAAAAAATTG
* * * * * *
82469 GACCGG-TCGTGACCGACCCGTGGTCAAGTCGT
1 GACCGGATCGCGACCGGCCCATGGGCTAGTCGC
* * *
82501 GACCGAATCGCGACCTGCCCGTGGGCTAGTCGC
1 GACCGGATCGCGACCGGCCCATGGGCTAGTCGC
*
82534 GACCGGATCGCGA-CGGCCCATGGGCTATTCGC
1 GACCGGATCGCGACCGGCCCATGGGCTAGTCGC
*
82566 GATCCGGGTCGCGACCGGCC
1 GA-CCGGATCGCGACCGGCC
82586 ATATTTTGGA
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 23 0.33
33 42 0.60
34 5 0.07
ACGTcount: A:0.15, C:0.35, G:0.35, T:0.15
Consensus pattern (33 bp):
GACCGGATCGCGACCGGCCCATGGGCTAGTCGC
Found at i:84532 original size:22 final size:22
Alignment explanation
Indices: 84508--84590 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 22
84498 ATATGGAAAG
*
84508 GTTATCAAAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGTGTA
* *
84530 GTTACCAAAATTTCATA-TGAAA
1 GTTATCAAAATTTCATAGTG-TA
* *
84552 ATTATCAAAACTTCATAGTGTA
1 GTTATCAAAATTTCATAGTGTA
*
84574 GTTATGAAAATTTCATA
1 GTTATCAAAATTTCATA
84591 CAAAGGTTAC
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 2 0.04
22 45 0.92
23 2 0.04
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGTA
Found at i:84599 original size:22 final size:21
Alignment explanation
Indices: 84504--84722 Score: 86
Period size: 22 Copynumber: 10.0 Consensus size: 21
84494 AATTATATGG
84504 AAAGGTTATCAAAATTTCATA
1 AAAGGTTATCAAAATTTCATA
*** *
84525 GTGTGGTTACCAAAATTTCATA
1 -AAAGGTTATCAAAATTTCATA
* *
84547 TGAAA-ATTATCAAAACTTCAT-
1 --AAAGGTTATCAAAATTTCATA
** *
84568 AGTGTAGTTATGAAAATTTCATA
1 AAAG--GTTATCAAAATTTCATA
* * *
84591 CAAAGGTTACCGAATTTTCATAA
1 -AAAGGTTATCAAAATTTCAT-A
* * *
84614 AAAGATTATTAAAATTTCCTA
1 AAAGGTTATCAAAATTTCATA
** * *
84635 GGGAGGTTAACAAAATTTTATA
1 -AAAGGTTATCAAAATTTCATA
*
84657 CGAAA-GTTATCAAAATTTTATA
1 --AAAGGTTATCAAAATTTCATA
**
84679 ATTTGGTTATCAAAATTTCATA
1 A-AAGGTTATCAAAATTTCATA
*
84701 AGAAGGTTAAT-AAAATGTCATA
1 A-AAGGTT-ATCAAAATTTCATA
84723 GGGAGGGAAT
Statistics
Matches: 141, Mismatches: 44, Indels: 24
0.67 0.21 0.11
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 1 0.01
22 130 0.92
23 6 0.04
24 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (21 bp):
AAAGGTTATCAAAATTTCATA
Found at i:84911 original size:23 final size:23
Alignment explanation
Indices: 84870--84913 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
84860 GGAGGATATC
* * *
84870 AAATTTTTATGGTGTGGTTACTA
1 AAATTTTCATAGTGCGGTTACTA
84893 AAATTTTCATAGTGCGGTTAC
1 AAATTTTCATAGTGCGGTTAC
84914 CAATTATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.43
Consensus pattern (23 bp):
AAATTTTCATAGTGCGGTTACTA
Found at i:84997 original size:22 final size:23
Alignment explanation
Indices: 84854--85065 Score: 99
Period size: 22 Copynumber: 9.7 Consensus size: 23
84844 AGTTTCATTC
* *
84854 TCATAGGGAGGATATC-AAATTT
1 TCATAGTGAGGTTATCGAAATTT
* * * *
84876 TTATGGTGTGGTTA-CTAAAATTT
1 TCATAGTGAGGTTATC-GAAATTT
* * *
84899 TCATAGTGCGGTTA-C-CAATTA
1 TCATAGTGAGGTTATCGAAATTT
* * *
84920 T-ATAGTGTGATTATCAAAATTT
1 TCATAGTGAGGTTATCGAAATTT
* * *
84942 T-ATAGGGAGATTATC-AAAATT
1 TCATAGTGAGGTTATCGAAATTT
* * * *
84963 CCACATTAAGGTTATCGAAA-TT
1 TCATAGTGAGGTTATCGAAATTT
* *
84985 TCATAGTGTGGTTAT-TAAATTT
1 TCATAGTGAGGTTATCGAAATTT
*
85007 TCATAG-GAGGTTATTGAAA-TT
1 TCATAGTGAGGTTATCGAAATTT
*
85028 TCATAATGAGGTTATC-AAATTT
1 TCATAGTGAGGTTATCGAAATTT
*
85050 TCACAGT-ATGGTTATC
1 TCATAGTGA-GGTTATC
85066 AGTATTTCTA
Statistics
Matches: 144, Mismatches: 35, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
20 10 0.07
21 33 0.23
22 80 0.56
23 21 0.15
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (23 bp):
TCATAGTGAGGTTATCGAAATTT
Found at i:85019 original size:43 final size:43
Alignment explanation
Indices: 84971--85052 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
84961 TTCCACATTA
* * *
84971 AGGTTATCGAAATTTCATAGTGTGGTTATTAAATTTTCATAGG
1 AGGTTATCGAAATTTCATAATGAGGTTATCAAATTTTCATAGG
*
85014 AGGTTATTGAAATTTCATAATGAGGTTATCAAATTTTCA
1 AGGTTATCGAAATTTCATAATGAGGTTATCAAATTTTCA
85053 CAGTATGGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.41
Consensus pattern (43 bp):
AGGTTATCGAAATTTCATAATGAGGTTATCAAATTTTCATAGG
Found at i:92391 original size:31 final size:31
Alignment explanation
Indices: 92353--92414 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
92343 GAGTTTTGTA
**
92353 AAACTTTTGAATCACCTATTATACCCTTATT
1 AAACTTTTGAATCACCTAACATACCCTTATT
*
92384 AAACTTTTGAATCGCCTAACATACCCTTATT
1 AAACTTTTGAATCACCTAACATACCCTTATT
92415 TTTTCGAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (31 bp):
AAACTTTTGAATCACCTAACATACCCTTATT
Found at i:93295 original size:16 final size:16
Alignment explanation
Indices: 93271--93304 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
93261 TTGGCCTCAT
93271 GTCACTCGGGTTTTGG
1 GTCACTCGGGTTTTGG
*
93287 GTCATTCGGGTTTTGG
1 GTCACTCGGGTTTTGG
93303 GT
1 GT
93305 TTTTTTGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.15, G:0.38, T:0.41
Consensus pattern (16 bp):
GTCACTCGGGTTTTGG
Found at i:99117 original size:17 final size:17
Alignment explanation
Indices: 99097--99129 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
99087 TATTTATTGA
99097 ATAATTATAATTATTTT
1 ATAATTATAATTATTTT
*
99114 ATAATTATTATTATTT
1 ATAATTATAATTATTT
99130 CAGTAAATAA
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATTATAATTATTTT
Found at i:129476 original size:22 final size:22
Alignment explanation
Indices: 129451--129528 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 22
129441 TTCATGGGAA
*
129451 GTTATCAAAATTTCATTTTGTG
1 GTTATCAAAATTTCATATTGTG
* **
129473 GTTATCAAGATTTCATATAAT-
1 GTTATCAAAATTTCATATTGTG
* * *
129494 GCTGTCAAAATTTCATAGTGTG
1 GTTATCAAAATTTCATATTGTG
129516 GTTATCAAAATTT
1 GTTATCAAAATTT
129529 TATTAGGAGA
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
21 15 0.35
22 28 0.65
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (22 bp):
GTTATCAAAATTTCATATTGTG
Found at i:129546 original size:43 final size:43
Alignment explanation
Indices: 129456--129572 Score: 121
Period size: 43 Copynumber: 2.7 Consensus size: 43
129446 GGGAAGTTAT
** * * *
129456 CAAAATTTCATTTTGTGGTTATCAAGATTTCATATAATGCTGT
1 CAAAATTTCATAGTGTGGTTATCAAAATTTCATATAATGATGC
*
129499 CAAAATTTCATAGTGTGGTTATCAAAATTTTAT-TAGGA-GATGC
1 CAAAATTTCATAGTGTGGTTATCAAAATTTCATATA--ATGATGC
* **
129542 CAAAATTTCATGGTGTGGTTATTGAAATTTC
1 CAAAATTTCATAGTGTGGTTATCAAAATTTC
129573 GGTTATCAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 2 0.03
43 59 0.95
44 1 0.02
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (43 bp):
CAAAATTTCATAGTGTGGTTATCAAAATTTCATATAATGATGC
Found at i:129966 original size:22 final size:22
Alignment explanation
Indices: 129941--130159 Score: 115
Period size: 22 Copynumber: 9.8 Consensus size: 22
129931 TCATTGTGTT
129941 GTTATCAAAATTTCATAGGGAA
1 GTTATCAAAATTTCATAGGGAA
** *
129963 GTTATCAAAAAATCATATGGAA
1 GTTATCAAAATTTCATAGGGAA
* **
129985 GTTATCAAAATTCCATAAAGACA
1 GTTATCAAAATTTCATAGGGA-A
*
130008 GGTTA-CTAAAATTTTATA-GGAA
1 -GTTATC-AAAATTTCATAGGGAA
** *
130030 GGTTATCAAAATTTCATAATGTA
1 -GTTATCAAAATTTCATAGGGAA
** **
130053 GTTAGT-AAAATTTCATAAAGCG
1 GTTA-TCAAAATTTCATAGGGAA
* **
130075 GTTGTCAAAATTTTTTAGGG-A
1 GTTATCAAAATTTCATAGGGAA
* * *
130096 GATTA-CAAAAATTTCATTGTGAG
1 G-TTATC-AAAATTTCATAGGGAA
* *
130119 GTTATCAAAATTTCATAAGAGAGG
1 GTTATCAAAATTTCAT-AGGGA-A
*
130143 GTTATCACAATTTCATA
1 GTTATCAAAATTTCATA
130160 ATGTAAGTGT
Statistics
Matches: 152, Mismatches: 32, Indels: 25
0.73 0.15 0.12
Matches are distributed among these distances:
21 3 0.02
22 106 0.70
23 14 0.09
24 29 0.19
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGGAA
Found at i:130129 original size:66 final size:67
Alignment explanation
Indices: 129947--130136 Score: 178
Period size: 66 Copynumber: 2.8 Consensus size: 67
129937 TGTTGTTATC
* ** * *
129947 AAAATTTCATAGGGAAG-TTATCAAAAAATCATATGGAAGTTATCAAAATTCCATAAAGACAGGT
1 AAAATTTTATA-GGAAGATTATCAAAATTTCATAT-GTAGTTATCAAAATTTCATAAAGACAGGT
130011 TACT
64 TACT
*
130015 AAAATTTTATAGGAAGGTTATCAAAATTTCATAATGTAGTTAGT-AAAATTTCATAAAG-C-GGT
1 AAAATTTTATAGGAAGATTATCAAAATTTCAT-ATGTAGTTA-TCAAAATTTCATAAAGACAGGT
*
130077 T-GT
64 TACT
* *
130080 CAAAATTTTTTAGGGAGATTA-CAAAAATTTCAT-TGTGAGGTTATCAAAATTTCATAA
1 -AAAATTTTATAGGAAGATTATC-AAAATTTCATATGT-A-GTTATCAAAATTTCATAA
130137 GAGAGGGTTA
Statistics
Matches: 105, Mismatches: 9, Indels: 18
0.80 0.07 0.14
Matches are distributed among these distances:
64 3 0.03
65 4 0.04
66 47 0.45
67 6 0.06
68 42 0.40
69 3 0.03
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (67 bp):
AAAATTTTATAGGAAGATTATCAAAATTTCATATGTAGTTATCAAAATTTCATAAAGACAGGTTA
CT
Found at i:136255 original size:23 final size:23
Alignment explanation
Indices: 136222--136269 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
136212 ATTAACTAAT
136222 AGAAACCGTTTGGTTTATTTGAG
1 AGAAACCGTTTGGTTTATTTGAG
*
136245 AGAAACTGTTTGGTTTATTTGAG
1 AGAAACCGTTTGGTTTATTTGAG
136268 AG
1 AG
136270 GTTTGTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.06, G:0.27, T:0.40
Consensus pattern (23 bp):
AGAAACCGTTTGGTTTATTTGAG
Found at i:136500 original size:17 final size:17
Alignment explanation
Indices: 136478--136517 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
136468 GAATTTCCTT
136478 TCTTCAATCTGGGTTTC
1 TCTTCAATCTGGGTTTC
136495 TCTTCAATCTGGGTTTC
1 TCTTCAATCTGGGTTTC
136512 TCTTCA
1 TCTTCA
136518 CTATTGTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.12, C:0.25, G:0.15, T:0.47
Consensus pattern (17 bp):
TCTTCAATCTGGGTTTC
Found at i:138009 original size:178 final size:178
Alignment explanation
Indices: 137703--138032 Score: 502
Period size: 178 Copynumber: 1.9 Consensus size: 178
137693 CCGGTTATCC
* *
137703 GATTAAGATGATTTAAGTGTCTATTAAAAGATTATTCCATGATCTACAACTTTCATTAAGGACTC
1 GATTAAGATGATTCAAGTGTCTATTAAAAGATTATTCCATGATCTACAACTTTCATGAAGGACTC
* * * *
137768 GAAAAATAAATTTAATGTTTTAAGTATAAAAAATGCTTCTAAAAAATTTGTTGTTTTGGTTAACG
66 GAAAAATAAATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAAAATTAGTTGTTTCGGTTAACG
*
137833 GGAATAGACGGTCCACTTAATATTATATAACTTTTGCTCCAAATGTCT
131 GAAATAGACGGTCCACTTAATATTATATAACTTTTGCTCCAAATGTCT
* * * *
137881 GATTGAGATGATTCAAGTGTCTCTTCAAAAG-TTGTTTCATGATCTACAACTTTCATGAAGGACT
1 GATTAAGATGATTCAAGTGTCTATT-AAAAGATTATTCCATGATCTACAACTTTCATGAAGGACT
* *
137945 CGAAAACTAAATTTAATG-TTCAAGGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAA
65 CGAAAAATAAATTTAATGTTTCAA-GTATAAAAAATGCTTCCAAAAAATTAGTTGTTTCGGTTAA
*
138009 CGGAAATAGACGGTCTACTTAATA
129 CGGAAATAGACGGTCCACTTAATA
138033 CTACATAATT
Statistics
Matches: 136, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
177 4 0.03
178 127 0.93
179 5 0.04
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (178 bp):
GATTAAGATGATTCAAGTGTCTATTAAAAGATTATTCCATGATCTACAACTTTCATGAAGGACTC
GAAAAATAAATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAAAATTAGTTGTTTCGGTTAACG
GAAATAGACGGTCCACTTAATATTATATAACTTTTGCTCCAAATGTCT
Found at i:141974 original size:30 final size:30
Alignment explanation
Indices: 141914--141974 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
141904 CAGCAATATC
*
141914 ATGACGCCTAACAACTTGATGAGGAAATTG
1 ATGACGCCTAACAACTTGACGAGGAAATTG
141944 ATGACGCCTAACAACTTGACGA-GAAGATTG
1 ATGACGCCTAACAACTTGACGAGGAA-ATTG
141974 A
1 A
141975 AAGCAGGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (30 bp):
ATGACGCCTAACAACTTGACGAGGAAATTG
Found at i:143475 original size:14 final size:14
Alignment explanation
Indices: 143456--143482 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
143446 TGGCATTTGA
143456 CAACTTTGAGTGTC
1 CAACTTTGAGTGTC
143470 CAACTTTGAGTGT
1 CAACTTTGAGTGT
143483 TATTTCTGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (14 bp):
CAACTTTGAGTGTC
Found at i:144044 original size:14 final size:14
Alignment explanation
Indices: 144025--144051 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
144015 AATCAAAAAC
144025 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
144039 AAAAAAAAAACAA
1 AAAAAAAAAACAA
144052 GACAAGCGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAA
Found at i:144046 original size:12 final size:11
Alignment explanation
Indices: 144019--144045 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
144009 AACATTAATC
144019 AAAAACAAAAA
1 AAAAACAAAAA
144030 AAAAACAAAAA
1 AAAAACAAAAA
144041 AAAAA
1 AAAAA
144046 AAACAAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:151886 original size:42 final size:42
Alignment explanation
Indices: 151835--151927 Score: 127
Period size: 45 Copynumber: 2.2 Consensus size: 42
151825 AGTGTATTAC
*
151835 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAA-AAAG
151876 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAAAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAAAAAG
*
151920 CTAGTATT
1 CTAATATT
151928 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
44 11 0.24
45 25 0.54
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (42 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAAAAAG
Found at i:154586 original size:68 final size:70
Alignment explanation
Indices: 154459--154604 Score: 253
Period size: 69 Copynumber: 2.1 Consensus size: 70
154449 TAATTAAAAT
154459 AGTAAAATGGTAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAG-TTTT
1 AGTAAAATGGTAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
154523 AGTTG
66 AGTTG
*
154528 AGTAAAATGGTAAAATAAAAT-GATTATAA-GATATTAGATTTAATTAAATAAAATTAGAGTTTT
1 AGTAAAATGGTAAAATAAAATAG-TTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTT
154591 TAGTTG
65 TAGTTG
154597 AGTAAAAT
1 AGTAAAAT
154605 AATAAACGTT
Statistics
Matches: 74, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
68 30 0.41
69 44 0.59
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (70 bp):
AGTAAAATGGTAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTG
Found at i:155274 original size:30 final size:31
Alignment explanation
Indices: 155240--155298 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
155230 CATTTTTTCC
*
155240 TTTGTGATAATTCGG-AGCCGTTTTGTCCCT
1 TTTGTGATAATTCGGTAGCCATTTTGTCCCT
* *
155270 TTTGTGATAGTTCGGTGGCCATTTTGTCC
1 TTTGTGATAATTCGGTAGCCATTTTGTCC
155299 ATTAAACTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (31 bp):
TTTGTGATAATTCGGTAGCCATTTTGTCCCT
Found at i:155497 original size:25 final size:25
Alignment explanation
Indices: 155444--155489 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
155434 TTTGTTGAAT
155444 TAAA-TATTTAAAATATAAATTAAA
1 TAAATTATTTAAAATATAAATTAAA
*
155468 TAAATTATTTAAAA-ATTAATTA
1 TAAATTATTTAAAATATAAATTA
155490 TGAAAAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
TAAATTATTTAAAATATAAATTAAA
Found at i:158351 original size:23 final size:21
Alignment explanation
Indices: 158298--158337 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
158288 TATATATATA
*
158298 TATATATTAAATAAATAATTT
1 TATATTTTAAATAAATAATTT
158319 TATATTTTAAA-AAATAATT
1 TATATTTTAAATAAATAATT
158338 CTTTTATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATATTTTAAATAAATAATTT
Found at i:159305 original size:17 final size:17
Alignment explanation
Indices: 159283--159325 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
159273 GAGAGGTACT
159283 ATCCGCCACTGCTTCGA
1 ATCCGCCACTGCTTCGA
159300 ATCCGCCACTGCTTCGA
1 ATCCGCCACTGCTTCGA
159317 ATCCGCCAC
1 ATCCGCCAC
159326 GGATAGTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.19, C:0.44, G:0.16, T:0.21
Consensus pattern (17 bp):
ATCCGCCACTGCTTCGA
Found at i:160531 original size:31 final size:30
Alignment explanation
Indices: 160493--160595 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 30
160483 TAGCCTAATC
160493 GCTCAAATAAGGGCCTAACGTTTGCCAAAAT
1 GCTCAAATAAGGGCCTAACGTTT-CCAAAAT
* * * **
160524 GCTCAAATAAGGGCTTGATC-TTT-TAATTT
1 GCTCAAATAAGGGCCT-AACGTTTCCAAAAT
*
160553 GGC-CAAATAAGGGCCTAACGTTATCGAAAAT
1 -GCTCAAATAAGGGCCTAACGTT-TCCAAAAT
160584 GCTCAAATAAGG
1 GCTCAAATAAGG
160596 ACTCGATCTT
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 2 0.04
29 17 0.30
30 5 0.09
31 30 0.54
32 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (30 bp):
GCTCAAATAAGGGCCTAACGTTTCCAAAAT
Found at i:160589 original size:60 final size:60
Alignment explanation
Indices: 160496--160609 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 60
160486 CCTAATCGCT
* *
160496 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCTTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGACTCGATCTTTTAATTTGGC
*
160556 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGACTCGATCTTTTAA
1 CAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGACTCGATCTTTTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
60 49 0.98
61 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGACTCGATCTTTTAATTTGGC
Done.