Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015099.1 Corchorus olitorius cultivar O-4 contig15132, 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: 64892
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Found at i:461 original size:74 final size:72
Alignment explanation
Indices: 333--474 Score: 196
Period size: 74 Copynumber: 1.9 Consensus size: 72
323 TGGCCTTATA
* * *
333 TGAGCAAAGGAATGATGAGTTTTAATCAAAATTTTCGAAATCAGTTTTAATCAAAACTATGATTT
1 TGAGCAAAGGAATGACGAGTTTTAATCAAAATTTTCAAAATCAGTTTTAATCAAAACAATGATTT
398 CGAGCTG
66 CGAGCTG
* **
405 TGAGCAAAGGAATGACG-GTTTTAATCAAAAGATGTTTTAAAATCAGTTTTGGTCAAAACAATGA
1 TGAGCAAAGGAATGACGAGTTTTAATC-AAA-AT-TTTCAAAATCAGTTTTAATCAAAACAATGA
469 TTTCGA
63 TTTCGA
475 AGTGACTGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
71 9 0.15
72 19 0.31
73 2 0.03
74 31 0.51
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (72 bp):
TGAGCAAAGGAATGACGAGTTTTAATCAAAATTTTCAAAATCAGTTTTAATCAAAACAATGATTT
CGAGCTG
Found at i:2132 original size:50 final size:50
Alignment explanation
Indices: 1934--2121 Score: 245
Period size: 50 Copynumber: 3.7 Consensus size: 50
1924 GAAGATTTAC
1934 AATAAGATTGCATTCCATTTGTGAG-CCTAAGATCAAAATTCGCTTTTCAA
1 AATAAGATTGCATTCCATTTGTGAGTCC-AAGATCAAAATTCGCTTTTCAA
* * * * *
1984 AGTAAAATTGCTTTTGCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAA
1 AATAAGATTGC-ATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
* *
2035 AACGAA-ATTGCATTCCATTTATGAGTCCAAGATCAAAATTCGCTTTTCAA
1 AA-TAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
* * *
2085 AATAAGATTGCACTCCATTTGTGAGACCAAGACCAAA
1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAA
2122 GGTCGATTTT
Statistics
Matches: 118, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
49 2 0.02
50 73 0.62
51 40 0.34
52 3 0.03
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (50 bp):
AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
Found at i:3011 original size:50 final size:50
Alignment explanation
Indices: 2775--2995 Score: 388
Period size: 50 Copynumber: 4.4 Consensus size: 50
2765 CATCCGAATT
*
2775 CATAAGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAA
1 CATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAA
*
2825 CATAGGCTATTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAA
1 CATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAA
* * *
2875 TATAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTATCAA
1 CATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAA
*
2925 CATAGGCTTTTCCACAAGCCAAATTCGTTTCCATACGAGTCAATTATCAA
1 CATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAA
2975 CATAGGCTTTTCCACAAGCCA
1 CATAGGCTTTTCCACAAGCCA
2996 CATCCATTTC
Statistics
Matches: 161, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 161 1.00
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29
Consensus pattern (50 bp):
CATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAA
Found at i:3099 original size:50 final size:50
Alignment explanation
Indices: 3023--3253 Score: 356
Period size: 50 Copynumber: 4.6 Consensus size: 50
3013 TGCATTACCT
*
3023 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACAGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
3073 TTTTAAGATTGAATTGGTAGATAGTTCAAAGGATAAGCGGAAGACGATCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
3123 TTTTAAGATTGAATTGGTAGACAGTTTAAAGGATAAGCGAAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
3173 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGTAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* * * *
3223 TTTTGATATT-AGATTGGAAGACAATTCAAAG
1 TTTTAAGATTGA-ATTGGTAGACAGTTCAAAG
3254 AAGTTGATCG
Statistics
Matches: 166, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
49 1 0.01
50 165 0.99
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:3685 original size:28 final size:29
Alignment explanation
Indices: 3611--3686 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 29
3601 CATTTACACG
*
3611 TCCAGGGGCATTTTGGTCACCTTCGCATG
1 TCCAGGGGCATTTTGGTCACCTTCGCATA
* * * *
3640 TCCAAGGGCATTTTGGTCA-TTTTGTATA
1 TCCAGGGGCATTTTGGTCACCTTCGCATA
*
3668 TTCAGGGGCATTTTGGTCA
1 TCCAGGGGCATTTTGGTCA
3687 ATTCTTATCT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 22 0.55
29 18 0.45
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (29 bp):
TCCAGGGGCATTTTGGTCACCTTCGCATA
Found at i:19563 original size:18 final size:18
Alignment explanation
Indices: 19540--19590 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
19530 CTAGCCCTAA
19540 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAACTAG
19558 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAACTAG
19576 AACTAGAAGAGAAAA
1 AACTAGAAGA-AAAA
19591 AGAAGAAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 28 0.88
19 4 0.12
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.10
Consensus pattern (18 bp):
AACTAGAAGAAAAACTAG
Found at i:20225 original size:19 final size:18
Alignment explanation
Indices: 20192--20227 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20182 TGGAAATAAT
20192 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
20210 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
20228 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:20680 original size:15 final size:15
Alignment explanation
Indices: 20660--20697 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
20650 TCATCATTCT
20660 TAAGTAGCCATAATC
1 TAAGTAGCCATAATC
20675 TAAGTAGCCATAATC
1 TAAGTAGCCATAATC
*
20690 AAAGTAGC
1 TAAGTAGC
20698 TTTAATCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (15 bp):
TAAGTAGCCATAATC
Found at i:27566 original size:24 final size:24
Alignment explanation
Indices: 27534--27580 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
27524 CATTCCGTTG
27534 AAATTCTTCCTTGTCCTTCAACTA
1 AAATTCTTCCTTGTCCTTCAACTA
*
27558 AAATTCTTCCTTGTCCTTTAACT
1 AAATTCTTCCTTGTCCTTCAACT
27581 TCAACAGTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.04, T:0.45
Consensus pattern (24 bp):
AAATTCTTCCTTGTCCTTCAACTA
Found at i:32741 original size:27 final size:28
Alignment explanation
Indices: 32697--32751 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
32687 ATTAGGTTGG
*
32697 TTTTGGACTTGCACTTGGACATTTTAGC
1 TTTTGGACTTACACTTGGACATTTTAGC
* *
32725 TTTT-GACTTACATTTGGACCTTTTAGC
1 TTTTGGACTTACACTTGGACATTTTAGC
32752 CTTGAATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (28 bp):
TTTTGGACTTACACTTGGACATTTTAGC
Found at i:33452 original size:289 final size:289
Alignment explanation
Indices: 32933--33514 Score: 1110
Period size: 289 Copynumber: 2.0 Consensus size: 289
32923 TAATTTTTAC
32933 AATAAAAACAACCATAATTCCAATGCTCCTCATTTCTTTGGTTTGTCCTTCGAAATCTTAGTGTT
1 AATAAAAACAACCATAATTCCAATGCTCCTCATTTCTTTGGTTTGTCCTTCGAAATCTTAGTGTT
32998 TCTTCAGAATAGTATCAATGATTAAATGGCTTGCTATGAGTGCCTTTGGCCAAGCTCATTGACTT
66 TCTTCAGAATAGTATCAATGATTAAATGGCTTGCTATGAGTGCCTTTGGCCAAGCTCATTGACTT
33063 CTTGCTTATAAGCATAACGAAGCTCAAATTCGCCATGGAAAGTGGGCCCGATTAATGGTACTGCA
131 CTTGCTTATAAGCATAACGAAGCTCAAATTCGCCATGGAAAGTGGGCCCGATTAATGGTACTGCA
*
33128 GAAAGCCCGGGAGCTCGCGGATCAATAAAACAAAAATAAACAGAAGCGGATTCGAAGTAATTAAA
196 GAAAGCCCGGGAGCTCGCGGATCAATAAAACAAAAATAAACAGAAGCAGATTCGAAGTAATTAAA
33193 TAGAAAGTAAGGGAAGCTGAAATCAGAGG
261 TAGAAAGTAAGGGAAGCTGAAATCAGAGG
*
33222 AATAAAAACAACCATAATTCCAATGCTCCTCATTTCTTTGGTTTGTCCTTCGAAATTTTAGTGTT
1 AATAAAAACAACCATAATTCCAATGCTCCTCATTTCTTTGGTTTGTCCTTCGAAATCTTAGTGTT
*
33287 TCTTCAGAATAGTATCAATGATTAAATGGCTTGCTATGAGTGCCTTTGGCCAAGCTCCTTGACTT
66 TCTTCAGAATAGTATCAATGATTAAATGGCTTGCTATGAGTGCCTTTGGCCAAGCTCATTGACTT
* *
33352 CTTGCTTATAAGCATAACGGAGCTCAAATTCGCCATGGAAAGTGGGCCCGATTAGTGGTACTGCA
131 CTTGCTTATAAGCATAACGAAGCTCAAATTCGCCATGGAAAGTGGGCCCGATTAATGGTACTGCA
33417 GAAAGCCCGGGAGCTCGCGGATCAATAAAACAAAAATAAACAGAAGCAGATTCGAAGTAATTAAA
196 GAAAGCCCGGGAGCTCGCGGATCAATAAAACAAAAATAAACAGAAGCAGATTCGAAGTAATTAAA
*
33482 TAGAAAGTAAGGGAAGCTGAAATCAGGGG
261 TAGAAAGTAAGGGAAGCTGAAATCAGAGG
33511 AATA
1 AATA
33515 GAATGCAGGG
Statistics
Matches: 287, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
289 287 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (289 bp):
AATAAAAACAACCATAATTCCAATGCTCCTCATTTCTTTGGTTTGTCCTTCGAAATCTTAGTGTT
TCTTCAGAATAGTATCAATGATTAAATGGCTTGCTATGAGTGCCTTTGGCCAAGCTCATTGACTT
CTTGCTTATAAGCATAACGAAGCTCAAATTCGCCATGGAAAGTGGGCCCGATTAATGGTACTGCA
GAAAGCCCGGGAGCTCGCGGATCAATAAAACAAAAATAAACAGAAGCAGATTCGAAGTAATTAAA
TAGAAAGTAAGGGAAGCTGAAATCAGAGG
Found at i:33554 original size:23 final size:23
Alignment explanation
Indices: 33528--33574 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
33518 TGCAGGGCAT
33528 GTCAAGTACAAACA-AGCAGTAAA
1 GTCAA-TACAAACAGAGCAGTAAA
* *
33551 GTCAATGCAAATAGAGCAGTAAA
1 GTCAATACAAACAGAGCAGTAAA
33574 G
1 G
33575 ATTAAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.49, C:0.15, G:0.21, T:0.15
Consensus pattern (23 bp):
GTCAATACAAACAGAGCAGTAAA
Found at i:36456 original size:22 final size:22
Alignment explanation
Indices: 36431--36523 Score: 118
Period size: 22 Copynumber: 4.2 Consensus size: 22
36421 AATTAAGCTA
*
36431 AGAAGTAGAGGAAAGAGTAATC
1 AGAAGTAAAGGAAAGAGTAATC
36453 AGAAGTAAAAGGAAA-AGTAATC
1 AGAAGT-AAAGGAAAGAGTAATC
*
36475 AGAAGT-AGGAGAAAGAGTAATC
1 AGAAGTAAAG-GAAAGAGTAATC
* *
36497 AGAAGTAAAAGAAAGAGTAATT
1 AGAAGTAAAGGAAAGAGTAATC
36519 AGAAG
1 AGAAG
36524 AGTAATTAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
20 2 0.03
21 4 0.06
22 48 0.77
23 8 0.13
ACGTcount: A:0.55, C:0.03, G:0.28, T:0.14
Consensus pattern (22 bp):
AGAAGTAAAGGAAAGAGTAATC
Found at i:36494 original size:44 final size:44
Alignment explanation
Indices: 36431--36523 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 44
36421 AATTAAGCTA
36431 AGAAGTAGAGGAAAGAGTAATCAGAAGTAAAAGGAAA-AGTAATC
1 AGAAGTAGAGGAAAGAGTAATCAGAAGTAAAA-GAAAGAGTAATC
*
36475 AGAAGTAG-GAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATT
1 AGAAGTAGAG-GAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATC
36519 AGAAG
1 AGAAG
36524 AGTAATTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
43 5 0.11
44 41 0.89
ACGTcount: A:0.55, C:0.03, G:0.28, T:0.14
Consensus pattern (44 bp):
AGAAGTAGAGGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATC
Found at i:36584 original size:57 final size:56
Alignment explanation
Indices: 36522--36719 Score: 297
Period size: 57 Copynumber: 3.5 Consensus size: 56
36512 AGTAATTAGA
36522 AGAGTAATTAAACTAAAAGGAGTCAAAGAAAGAGCAATTGGAAGATTAGTTTAATTC
1 AGAGTAATTAAACTAAAAGGAGT-AAAGAAAGAGCAATTGGAAGATTAGTTTAATTC
* *
36579 AGAGTAATTAAACTAAAAGGAGTATACGGAAGAGCAATTGGAAGATTAGTTTAATTC
1 AGAGTAATTAAACTAAAAGGAGTA-AAGAAAGAGCAATTGGAAGATTAGTTTAATTC
* * *
36636 AGAGTAATTAAACTAAAAAGAGTAAAGGAAAGAGTAATTGGAATATTAGTTTAATTC
1 AGAGTAATTAAACTAAAAGGAGTAAA-GAAAGAGCAATTGGAAGATTAGTTTAATTC
* *
36693 AAAGTAATTAAACTAAAAAGAAGTAAA
1 AGAGTAATTAAACT-AAAAGGAGTAAA
36720 AGGAAGAGTA
Statistics
Matches: 128, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
56 2 0.02
57 116 0.91
58 10 0.08
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.25
Consensus pattern (56 bp):
AGAGTAATTAAACTAAAAGGAGTAAAGAAAGAGCAATTGGAAGATTAGTTTAATTC
Found at i:36738 original size:22 final size:22
Alignment explanation
Indices: 36711--36775 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
36701 TAAACTAAAA
*
36711 AGAAGTAAAAGGAAGAGTAATC
1 AGAAGTAAAAGAAAGAGTAATC
* *
36733 AGAAGTAGAAGAAAAAGTAATC
1 AGAAGTAAAAGAAAGAGTAATC
36755 AGAAGTAAAAGAAAGAGTAAT
1 AGAAGTAAAAGAAAGAGTAAT
36776 ATTAGAGTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.58, C:0.03, G:0.25, T:0.14
Consensus pattern (22 bp):
AGAAGTAAAAGAAAGAGTAATC
Found at i:36883 original size:22 final size:22
Alignment explanation
Indices: 36852--36919 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
36842 TTAAACTAAA
36852 AAGAGTAAAAGAAAAAGTAATC
1 AAGAGTAAAAGAAAAAGTAATC
* *
36874 AAGAGCAAAAGAAGAAGTAATC
1 AAGAGTAAAAGAAAAAGTAATC
* *
36896 -AGAAGTAAAGGAAAGAGTAATC
1 AAG-AGTAAAAGAAAAAGTAATC
36918 AA
1 AA
36920 AAGATTAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
21 2 0.05
22 35 0.92
23 1 0.03
ACGTcount: A:0.60, C:0.06, G:0.22, T:0.12
Consensus pattern (22 bp):
AAGAGTAAAAGAAAAAGTAATC
Found at i:37006 original size:22 final size:22
Alignment explanation
Indices: 36957--37128 Score: 161
Period size: 22 Copynumber: 7.9 Consensus size: 22
36947 AGCTAAAAAA
*
36957 AAGTAAAAGGAAA-AGTAATCGG
1 AAGTAAAA-GAAAGAGTAATCAG
** * *
36979 GCGTAGAAGGAAGAGTAATCAG
1 AAGTAAAAGAAAGAGTAATCAG
* ** * **
37001 AAGTAGAAGGGAGTGTAAAAAG
1 AAGTAAAAGAAAGAGTAATCAG
*
37023 -AGTAAAAGAAAAAGTAATCCAG
1 AAGTAAAAGAAAGAGTAAT-CAG
*
37045 -AGTAAAAGAAAAAGTAATCAG
1 AAGTAAAAGAAAGAGTAATCAG
**
37066 AAGTAACGGAAAGAGTAATCAG
1 AAGTAAAAGAAAGAGTAATCAG
*
37088 GAGTAAAAGAAAGAGTAATCAG
1 AAGTAAAAGAAAGAGTAATCAG
37110 AAGTAAAAGAAAGAGTAAT
1 AAGTAAAAGAAAGAGTAAT
37129 ATTAGAATAA
Statistics
Matches: 122, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
21 18 0.15
22 104 0.85
ACGTcount: A:0.54, C:0.05, G:0.27, T:0.14
Consensus pattern (22 bp):
AAGTAAAAGAAAGAGTAATCAG
Found at i:40618 original size:22 final size:22
Alignment explanation
Indices: 40576--40619 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
40566 TATTCATATG
*
40576 AAATTATGATAATCTCCCTATT
1 AAATTATGATAATCTCACTATT
40598 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCT-CACTATT
40620 TTTGATGACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (22 bp):
AAATTATGATAATCTCACTATT
Found at i:40644 original size:22 final size:22
Alignment explanation
Indices: 40619--41193 Score: 217
Period size: 22 Copynumber: 26.3 Consensus size: 22
40609 ATTACACTAT
*
40619 TTTTGATGACCTCCTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * *
40641 TTTTGTTAACTTTCTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * * *
40663 TTTTAATAAACGATAC-TATAAAA
1 TTTTGAT-AAC-CTCCTTATGAAA
* * **
40686 TTTCGAGAACCTTTTTAT-AAA
1 TTTTGATAACCTCCTTATGAAA
** ** *
40707 TTTTTTTTAAGTTTCTTATGAAA
1 -TTTTGATAACCTCCTTATGAAA
* * * * *
40730 TTTTGTTAATCTCCCTAAGGAA
1 TTTTGATAACCTCCTTATGAAA
40752 TTTTGA-AGACCTCAC-TATGAAA
1 TTTTGATA-ACCTC-CTTATGAAA
* **
40774 TTTTGATAACTTCCCAATGAAA
1 TTTTGATAACCTCCTTATGAAA
* *
40796 TTTTGATAACCAACAC-TATGAGA
1 TTTTGATAACC-TC-CTTATGAAA
* * *
40819 TGTTGATAACCTCCATATGATA
1 TTTTGATAACCTCCTTATGAAA
* * *
40841 TATTGATAACCACGTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * * *
40863 ATTTAAAAACCTCCATATG-AA
1 TTTTGATAACCTCCTTATGAAA
* *
40884 TTGTT-AGTAA-TTACAC-TCTGAAA
1 TT-TTGA-TAACCT-C-CTTATGAAA
* * *
40907 TTTTGATAATCACAC-TATAAAA
1 TTTTGATAACCTC-CTTATGAAA
*
40929 TTGTGATAACCTCGC-TATGAAA
1 TTTTGATAACCTC-CTTATGAAA
*
40951 CTTTGATAAACCTTCCTGTA--AAA
1 TTTTGAT-AACC-TCCT-TATGAAA
* * *
40974 TTTTGATAAACATCCCTATAAAA
1 TTTTGAT-AACCTCCTTATGAAA
40997 TTTTGATAACCTCCTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * *
41019 TCTTGATGA----C-TA-CAAA
1 TTTTGATAACCTCCTTATGAAA
**
41035 TTTTGATAACCTCCTTATGATT
1 TTTTGATAACCTCCTTATGAAA
*
41057 TTTTGATAACCTCATTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * * *
41079 TTTTGTTAATCTCCCTAAGAAA
1 TTTTGATAACCTCCTTATGAAA
* * *
41101 TTTTGATGTACATAC-TATGAAA
1 TTTTGAT-AACCTCCTTATGAAA
* *
41123 TTTTGA-AAACTAAAC-TATGAAA
1 TTTTGATAACCT--CCTTATGAAA
* *
41145 TTTTGATAACCTTCATATGAAA
1 TTTTGATAACCTCCTTATGAAA
*
41167 TTTTGATATCCTCC-T-TGAAA
1 TTTTGATAACCTCCTTATGAAA
41187 TTTTGAT
1 TTTTGAT
41194 TACTCCATAA
Statistics
Matches: 413, Mismatches: 104, Indels: 74
0.70 0.18 0.13
Matches are distributed among these distances:
16 10 0.02
17 2 0.00
18 1 0.00
20 15 0.04
21 18 0.04
22 285 0.69
23 75 0.18
24 5 0.01
25 2 0.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TTTTGATAACCTCCTTATGAAA
Found at i:40825 original size:45 final size:45
Alignment explanation
Indices: 40764--40883 Score: 120
Period size: 45 Copynumber: 2.7 Consensus size: 45
40754 TTGAAGACCT
* * *
40764 CACTATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAA
1 CACTATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAA
* *
40809 CACTATGAGATGTTGATAACCTCCATATGATATATTGATAACC-A
1 CACTATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAA
** * *
40853 CGTTATGAAAAT-TTAAAAACCTCCATATGAA
1 CACTATG-AAATGTTGATAACCTCCATATGAA
40884 TTGTTAGTAA
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
44 25 0.40
45 37 0.60
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (45 bp):
CACTATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAA
Found at i:40978 original size:23 final size:23
Alignment explanation
Indices: 40904--41005 Score: 100
Period size: 23 Copynumber: 4.5 Consensus size: 23
40894 TTACACTCTG
* *
40904 AAATTTTGATAATCA-CACTATA
1 AAATTTTGATAAACATCCCTATA
* * * *
40926 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACATCCCTATA
* * * *
40948 AAACTTTGATAAACCTTCCTGTA
1 AAATTTTGATAAACATCCCTATA
40971 AAATTTTGATAAACATCCCTATA
1 AAATTTTGATAAACATCCCTATA
40994 AAATTTTGATAA
1 AAATTTTGATAA
41006 CCTCCTTATG
Statistics
Matches: 63, Mismatches: 15, Indels: 3
0.78 0.19 0.04
Matches are distributed among these distances:
21 2 0.03
22 22 0.35
23 39 0.62
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (23 bp):
AAATTTTGATAAACATCCCTATA
Found at i:41324 original size:22 final size:22
Alignment explanation
Indices: 41299--41657 Score: 165
Period size: 22 Copynumber: 16.3 Consensus size: 22
41289 AATCACATTT
* *
41299 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
41321 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * * *
41343 TAAAATTATGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
41365 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* ** *
41387 TGTAATTTTGATAACCTAGCTT
1 TGAAATTTTGATAACCTCTCTA
* *
41409 TGAAATTTTGATAACAAT-ACTA
1 TGAAATTTTGATAAC-CTCTCTA
**
41431 TGAAATTTTGATAATAT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
41453 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTCTA
* * *
41477 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
41499 TGAGA-TTTGATAACCTTCTATA
1 TGAAATTTTGATAACC-TCTCTA
* *
41521 TCAAATTTTGGT-A-CTC-CATA
1 TGAAATTTTGATAACCTCTC-TA
41541 TGAAA--TTG--AACCTTTTACTTCATA
1 TGAAATTTTGATAACC---T-C-TC-TA
* *
41565 TGAAA-TTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
41586 TGAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCTCTA
* *
41608 TGAAA-TATCAGTAACCTC-CTTA
1 TGAAATTTTGA-TAACCTCTC-TA
* * *
41630 TGAAATTTT-TTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
41651 TGAAATT
1 TGAAATT
41658 CTTATAAAAT
Statistics
Matches: 258, Mismatches: 51, Indels: 57
0.70 0.14 0.16
Matches are distributed among these distances:
17 1 0.00
18 4 0.02
20 8 0.03
21 50 0.19
22 151 0.59
23 10 0.04
24 15 0.06
25 15 0.06
27 4 0.02
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:41325 original size:44 final size:44
Alignment explanation
Indices: 41274--41467 Score: 157
Period size: 44 Copynumber: 4.4 Consensus size: 44
41264 AAAAATACCA
* *
41274 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCT
* * * * * *
41318 TTATGAAATTTTGATAACCTC-TCTAT-AAAATTATGTTGACCCCT
1 CTATGAAATTTTGATAATCACAT-TATGAAAATT-TGATAACCTCT
* * **
41362 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTAG
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCT
* * **
41406 CTTTGAAATTTTGATAA-CA-ATACTATGAAATTTTGATAATAT-T
1 CTATGAAATTTTGATAATCACAT--TATGAAAATTTGATAACCTCT
41449 CCTAT-AAATTTTGATAATC
1 -CTATGAAATTTTGATAATC
41468 CGATCTCTAT
Statistics
Matches: 118, Mismatches: 24, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
42 2 0.02
43 21 0.18
44 90 0.76
45 5 0.04
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCT
Found at i:41437 original size:88 final size:88
Alignment explanation
Indices: 41274--41437 Score: 217
Period size: 88 Copynumber: 1.9 Consensus size: 88
41264 AAAAATACCA
* * *
41274 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTTTATGAAATTTTGATAACATC
*
41339 TCTATAAAATTATGTTGACCCCT
66 ACTATAAAATTATGTTGACCCCT
* *
41362 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTAGC-TT-TGAAATTTTGATAACA
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCT--CTTTATGAAATTTTGATAAC-
*
41425 AT-ACTATGAAATT
63 ATCACTATAAAATT
41438 TTGATAATAT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
88 62 0.94
89 3 0.05
90 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.41
Consensus pattern (88 bp):
CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTTTATGAAATTTTGATAACATC
ACTATAAAATTATGTTGACCCCT
Found at i:41740 original size:22 final size:22
Alignment explanation
Indices: 41697--41836 Score: 106
Period size: 22 Copynumber: 6.3 Consensus size: 22
41687 TGATAATCTC
*** *
41697 TTTGATAACCTTTATATAAAAT
1 TTTGATAACCTACCTATGAAAT
*
41719 TGTGATAACC-ACACTATGAAAT
1 TTTGATAACCTAC-CTATGAAAT
** * *
41741 TTCAATAACCTTCCTAAGAAAT
1 TTTGATAACCTACCTATGAAAT
*
41763 TTTAATAACCTGATCCTATGAAAT
1 TTTGATAACCT-A-CCTATGAAAT
*
41787 TTTGGTAACC-ACACTATGAAAT
1 TTTGATAACCTAC-CTATGAAAT
* *
41809 TTTGATAACCTTCCCATGAAA-
1 TTTGATAACCTACCTATGAAAT
41830 TTTGATA
1 TTTGATA
41837 TATGAAATTT
Statistics
Matches: 94, Mismatches: 18, Indels: 13
0.75 0.14 0.10
Matches are distributed among these distances:
21 8 0.09
22 67 0.71
23 2 0.02
24 17 0.18
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (22 bp):
TTTGATAACCTACCTATGAAAT
Found at i:41796 original size:46 final size:44
Alignment explanation
Indices: 41732--41832 Score: 105
Period size: 46 Copynumber: 2.2 Consensus size: 44
41722 GATAACCACA
*
41732 CTATGAAATTTCAATAACCTTC-CTAAGAAATTTTAATAACCTGATC
1 CTATGAAATTTCAATAACC-ACACTAAGAAATTTTAATAACCT--TC
*** * *
41778 CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTC
1 CTATGAAATTTCAATAACCACACTAAGAAATTTTAATAACCTTC
*
41822 CCATGAAATTT
1 CTATGAAATTT
41833 GATATATGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
44 12 0.26
45 1 0.02
46 34 0.72
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.36
Consensus pattern (44 bp):
CTATGAAATTTCAATAACCACACTAAGAAATTTTAATAACCTTC
Found at i:41868 original size:36 final size:37
Alignment explanation
Indices: 41801--41873 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 37
41791 GTAACCACAC
*
41801 TATGAAATTTTGATAACCTTCCCATGAAA-TTTGATA
1 TATGAAATTTTGATAACCTACCCATGAAATTTTGATA
* * *
41837 TATGAAATTTTGGTAA-CTACACTATGGAATTTTGATA
1 TATGAAATTTTGATAACCTAC-CCATGAAATTTTGATA
41874 ATCACACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 3 0.10
36 21 0.68
37 7 0.23
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.40
Consensus pattern (37 bp):
TATGAAATTTTGATAACCTACCCATGAAATTTTGATA
Found at i:42074 original size:19 final size:20
Alignment explanation
Indices: 42043--42080 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
42033 ATTGACATTT
42043 AAAAAATTGAAATT-AAAAG
1 AAAAAATTGAAATTCAAAAG
42062 AAAAATATT-AAATTCAAAA
1 AAAAA-ATTGAAATTCAAAA
42081 AATAATAGTA
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:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (20 bp):
AAAAAATTGAAATTCAAAAG
Found at i:42350 original size:165 final size:167
Alignment explanation
Indices: 42094--42428 Score: 463
Period size: 165 Copynumber: 2.0 Consensus size: 167
42084 AATAGTAAAG
*
42094 GAAATTTGCATGTTCATCAACGAAAATCAATTTGACAAACTTATAGTTCGGTCTAAATTGAAATT
1 GAAATTTGCATGTTCATCAACGAAAATCAATTTGACAAACTTATAATTCGGTCTAAATTGAAATT
42159 TTCAAATAATAAAATTATAGTAAATTTTAATAATGACAATTTAGAAATATATTTG-AA-AAAAGG
66 TTCAAATAATAAAATTATAGTAAATTTTAATAATGACAATTTAGAAATATATTTGAAATAAAAGG
* *
42222 GTACAATCGGAAAACATAAAGT-TTCCCGTTATTCGTA
131 GTACAATCGAAAAACATAAAGTCTT-CCATTATTCGTA
42259 GAAATTTGCATGTTCATCAATC-AAAATCAATTT-ACAAACTTATAATTCGGTCTAAATTGAAAT
1 GAAATTTGCATGTTCATCAA-CGAAAATCAATTTGACAAACTTATAATTCGGTCTAAATTGAAAT
* *
42322 TTT-ATAATTAATTTTTAAA-T-TA-TAAATTTTAATAATGTCAATTTAGAAATATATTTGAAAA
65 TTTCA-AA-TAA---TAAAATTATAGTAAATTTTAATAATGACAATTTAGAAATATATTTG--AA
*
42383 ATTAAAAGGGTACAATCGAAAAATATAAAGTCTTCCATTATTCGTA
123 A-TAAAAGGGTACAATCGAAAAACATAAAGTCTTCCATTATTCGTA
42429 CTTTTATATG
Statistics
Matches: 152, Mismatches: 6, Indels: 19
0.86 0.03 0.11
Matches are distributed among these distances:
163 1 0.01
164 34 0.22
165 68 0.45
166 3 0.02
167 1 0.01
168 6 0.04
170 37 0.24
171 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (167 bp):
GAAATTTGCATGTTCATCAACGAAAATCAATTTGACAAACTTATAATTCGGTCTAAATTGAAATT
TTCAAATAATAAAATTATAGTAAATTTTAATAATGACAATTTAGAAATATATTTGAAATAAAAGG
GTACAATCGAAAAACATAAAGTCTTCCATTATTCGTA
Found at i:45966 original size:18 final size:18
Alignment explanation
Indices: 45943--45993 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
45933 TGAAATTATT
45943 TAATTATTAAATAAATAA
1 TAATTATTAAATAAATAA
* ** *
45961 TAATTAATATTTGAATAA
1 TAATTATTAAATAAATAA
*
45979 TTATTATTAAA-AAAT
1 TAATTATTAAATAAAT
45994 CCACATGTGC
Statistics
Matches: 24, Mismatches: 9, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TAATTATTAAATAAATAA
Found at i:54591 original size:12 final size:12
Alignment explanation
Indices: 54574--54601 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
54564 GTACGTTTAT
54574 ACGACACGAAAC
1 ACGACACGAAAC
54586 ACGACACGAAAC
1 ACGACACGAAAC
54598 ACGA
1 ACGA
54602 ATTGCCAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.32, G:0.18, T:0.00
Consensus pattern (12 bp):
ACGACACGAAAC
Found at i:61253 original size:24 final size:24
Alignment explanation
Indices: 61204--61255 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
61194 TTGGAGATTC
*
61204 GAAGTTCGTGTTTAAAGACTTATT
1 GAAGTTCGTGTTTAAAGACATATT
61228 GAAGTTCGTGTTTAAAGACA-ATTT
1 GAAGTTCGTGTTTAAAGACATA-TT
61252 GAAG
1 GAAG
61256 ATTTGAAGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.37
Consensus pattern (24 bp):
GAAGTTCGTGTTTAAAGACATATT
Done.