Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009278.1 Corchorus capsularis cultivar CVL-1 contig09299, 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: 60331
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Found at i:99 original size:30 final size:31
Alignment explanation
Indices: 65--131 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
55 AAGAAGGGGC
65 AATCAGCAATTAAGTTCAATAAGAAA-AAGT
1 AATCAGCAATTAAGTTCAATAAGAAAGAAGT
** *
95 AATCAGTGATTAAGTTCAATAAGAAAGATGT
1 AATCAGCAATTAAGTTCAATAAGAAAGAAGT
126 AATCAG
1 AATCAG
132 TAAAAGGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 24 0.73
31 9 0.27
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.25
Consensus pattern (31 bp):
AATCAGCAATTAAGTTCAATAAGAAAGAAGT
Found at i:131 original size:31 final size:30
Alignment explanation
Indices: 73--132 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
63 GCAATCAGCA
73 ATTAAGTTCAATAAGAAAAAGTAATCAGTG
1 ATTAAGTTCAATAAGAAAAAGTAATCAGTG
*
103 ATTAAGTTCAATAAGAAAGATGTAATCAGT
1 ATTAAGTTCAATAAGAAA-AAGTAATCAGT
133 AAAAGGTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (30 bp):
ATTAAGTTCAATAAGAAAAAGTAATCAGTG
Found at i:294 original size:107 final size:109
Alignment explanation
Indices: 169--373 Score: 351
Period size: 107 Copynumber: 1.9 Consensus size: 109
159 AGTAAAGTGA
*
169 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAA-A-ATTAATTAGAGTC
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC
*
232 AAGGTAATAGAAAGCAGTAAATCAATAATTAAGTGAAAAGAAAT
66 AAAGTAATAGAAAGCAGTAAATCAATAATTAAGTGAAAAGAAAT
276 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC
* * *
341 AAAGTAATAGTAATCAGTAAATCGATAATTAAG
66 AAAGTAATAGAAAGCAGTAAATCAATAATTAAG
374 AGTTAAAATG
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
107 49 0.54
108 1 0.01
109 41 0.45
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (109 bp):
TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTC
AAAGTAATAGAAAGCAGTAAATCAATAATTAAGTGAAAAGAAAT
Found at i:308 original size:54 final size:53
Alignment explanation
Indices: 169--373 Score: 254
Period size: 54 Copynumber: 3.8 Consensus size: 53
159 AGTAAAGTGA
*
169 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAA-AAAT
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAGAAAT
* * *
221 TAATTAGAGTCAAG-GTAATAGAAAGCAGTAAATCAATAATTAAGTGAAAAGAAAT
1 TAA-T-CAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGT-AAAAGAAAT
* *
276 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGT-AAAAGAAAT
* * *
330 TAATCAGAGTCAA-AGTAATAGTAATCAGTAAATCGATAATTAAG
1 TAATC--AGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAG
374 AGTTAAAATG
Statistics
Matches: 132, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
52 3 0.02
53 36 0.27
54 53 0.40
55 35 0.27
56 5 0.04
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (53 bp):
TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAGAAAT
Found at i:648 original size:22 final size:21
Alignment explanation
Indices: 559--851 Score: 168
Period size: 22 Copynumber: 13.6 Consensus size: 21
549 AATAGCAGGC
559 AATCAGTAAAAAGTAAAAAGGT
1 AATCAGTAAAAAGT-AAAAGGT
* * **
581 -ACCTG-AAAGGGTAAAAAGAGT
1 AATCAGTAAAAAGT-AAAAG-GT
*
602 AATCAGTAAAAGAGTAAAATAGT
1 AATCAGTAAAA-AGTAAAA-GGT
*
625 AATCAGCAAAAAGTAAGAAGGT
1 AATCAGTAAAAAGTAA-AAGGT
* *
647 AATCA--ACAAGAGTAAAATAGT
1 AATCAGTA-AAAAGTAAAA-GGT
* *
668 AGTCAGTAGAAAGTAAATA-GT
1 AATCAGTAAAAAGTAAA-AGGT
* *
689 AATCAGT-AAGAGTAAAAAAAGT
1 AATCAGTAAAAAGT--AAAAGGT
* * *
711 AATAAGTAAGAAGTAAAAGGA
1 AATCAGTAAAAAGTAAAAGGT
*
732 AATCAGT-AAGAGTAAAAAGGT
1 AATCAGTAAAAAGT-AAAAGGT
* * *
753 GATCAGTAAAGAGTAAAAAGCT
1 AATCAGTAAAAAGT-AAAAGGT
* * *
775 AATCAGCAAGAAGTAAAAAGAT
1 AATCAGTAAAAAGT-AAAAGGT
* *
797 AATCAGTAAAACGCAAAAGGT
1 AATCAGTAAAAAGTAAAAGGT
* *
818 AATTAGTAAAAACTAAAAGAGT
1 AATCAGTAAAAAGTAAAAG-GT
840 AATCAGTAAAAA
1 AATCAGTAAAAA
852 AGGACCAGAA
Statistics
Matches: 208, Mismatches: 45, Indels: 36
0.72 0.16 0.12
Matches are distributed among these distances:
20 22 0.11
21 71 0.34
22 86 0.41
23 27 0.13
24 2 0.01
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.18
Consensus pattern (21 bp):
AATCAGTAAAAAGTAAAAGGT
Found at i:660 original size:43 final size:42
Alignment explanation
Indices: 611--950 Score: 247
Period size: 43 Copynumber: 7.7 Consensus size: 42
601 TAATCAGTAA
*
611 AAGAGTAAAATAGTAATCAGCAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAAC
* * **
654 AAGAGTAAAATAGTAGTCAGTAGAAAGTAAATA-GTAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA-AGGTAATCAAC
* * * * **
696 AAGAGTAAAAAAAGTAATAAGTAAGAAGTAAAAGGAAATCAGT
1 AAGAGT-AAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAAC
* * * *
739 AAGAGTAAAA-AGGTGATCAGTAAAGAGTAAAAAGCTAATCAGC
1 AAGAGTAAAATA-GTAATCAGTAAAAAGT-AAAAGGTAATCAAC
* * *
782 AAGAAGTAAAA-AGATAATCAGTAAAACGCAAAAGGTAATTAGTA-
1 AAG-AGTAAAATAG-TAATCAGTAAAAAGTAAAAGGTAATCA--AC
* * * * * *
826 AAAACTAAAAGAGTAATCAGTAAAAAAGGACCAGAAAATAGTAATCAGTAA
1 AAGAGTAAAATAGTAATCAGT-AAAAA-G----TAAAA-GGTAATCA--AC
*
877 AAGAGTAAAATGGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAAC
*
920 AAGAGTAAAATAGTAATCAGTACAAAGTAAA
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA
951 GAATAATCAG
Statistics
Matches: 238, Mismatches: 40, Indels: 39
0.75 0.13 0.12
Matches are distributed among these distances:
41 1 0.00
42 32 0.13
43 130 0.55
44 27 0.11
45 10 0.04
46 2 0.01
49 5 0.02
50 14 0.06
51 17 0.07
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.18
Consensus pattern (42 bp):
AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAAC
Found at i:687 original size:21 final size:20
Alignment explanation
Indices: 599--984 Score: 143
Period size: 22 Copynumber: 17.6 Consensus size: 20
589 GGGTAAAAAG
599 AGTAATCAGTAAAAGAGTAAAAT
1 AGTAATCAGT-AAA-AGT-AAAT
*
622 AGTAATCAGCAAAAAGTAAGA-
1 AGTAATCAG-TAAAAGTAA-AT
** *
643 AGGTAATCAACAAGAGTAAAAT
1 A-GTAATCAGTAAAAGT-AAAT
*
665 AGTAGTCAGTAGAAAGTAAAT
1 AGTAATCAGTA-AAAGTAAAT
* *
686 AGTAATCAGTAAGAGTAAAAAA
1 AGTAATCAGTAAAAGT--AAAT
*
708 AGTAATAAGTAAGAAGTAAA-
1 AGTAATCAGTAA-AAGTAAAT
* * *
728 AGGAAATCAGTAAGAGTAAAA
1 A-GTAATCAGTAAAAGTAAAT
* *
749 AGGTGATCAGTAAAGAGTAAAA
1 A-GTAATCAGTAAA-AGTAAAT
* *
771 AGCTAATCAGCAAGAAGTAAAA
1 AG-TAATCAGTAA-AAGTAAAT
*
793 AGATAATCAGTAAAACGCAAA-
1 AG-TAATCAGTAAAA-GTAAAT
* * *
814 AGGTAATTAGTAAAAACTAAAAG
1 A-GTAATCAGT-AAAAGT-AAAT
*
837 AGTAATCAGTAAAAAAGGACCAGAAAAT
1 AGTAATCAGT----AA--A--AGTAAAT
865 AGTAATCAGTAAAAGAGTAAAAT
1 AGTAATCAGT-AAA-AGT-AAAT
*
888 GGTAATCAGTAAAAAGTAAGA-
1 AGTAATCAGT-AAAAGTAA-AT
** *
909 AGGTAATCAACAAGAGTAAAAT
1 A-GTAATCAGTAAAAGT-AAAT
*
931 AGTAATCAGTACAAAGTAAAG
1 AGTAATCAGTA-AAAGTAAAT
*
952 AATAATCAGTGAAATAGT-AAT
1 AGTAATCAGT-AAA-AGTAAAT
*
973 GGTAATCAGTAA
1 AGTAATCAGTAA
985 TTCAGTAAAA
Statistics
Matches: 283, Mismatches: 46, Indels: 71
0.71 0.12 0.18
Matches are distributed among these distances:
20 13 0.05
21 104 0.37
22 110 0.39
23 35 0.12
25 6 0.02
27 1 0.00
28 13 0.05
29 1 0.00
ACGTcount: A:0.55, C:0.07, G:0.19, T:0.19
Consensus pattern (20 bp):
AGTAATCAGTAAAAGTAAAT
Found at i:849 original size:15 final size:15
Alignment explanation
Indices: 831--884 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
821 TAGTAAAAAC
831 TAAAAGAGTAATCAG
1 TAAAAGAGTAATCAG
* * *
846 TAAAAAAG-GACCAG
1 TAAAAGAGTAATCAG
*
860 -AAAATAGTAATCAG
1 TAAAAGAGTAATCAG
874 TAAAAGAGTAA
1 TAAAAGAGTAA
885 AATGGTAATC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 6 0.20
14 8 0.27
15 16 0.53
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (15 bp):
TAAAAGAGTAATCAG
Found at i:913 original size:22 final size:21
Alignment explanation
Indices: 866--984 Score: 93
Period size: 21 Copynumber: 5.5 Consensus size: 21
856 CCAGAAAATA
866 GTAATCAGTAAAAGAGTAAAATG
1 GTAATCAGTAAAA-AGTAAAA-G
889 GTAATCAGTAAAAAGTAAGAAG
1 GTAATCAGTAAAAAGTAA-AAG
* *
911 GTAATCA--ACAAGAGTAAAATA
1 GTAATCAGTA-AAAAGTAAAA-G
*
932 GTAATCAGTACAAAGT-AAAG
1 GTAATCAGTAAAAAGTAAAAG
* * *
952 AATAATCAGTGAAATAGT-AATG
1 -GTAATCAGT-AAAAAGTAAAAG
974 GTAATCAGTAA
1 GTAATCAGTAA
985 TTCAGTAAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
20 5 0.06
21 33 0.42
22 25 0.32
23 16 0.20
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (21 bp):
GTAATCAGTAAAAAGTAAAAG
Found at i:936 original size:116 final size:114
Alignment explanation
Indices: 754--961 Score: 247
Period size: 116 Copynumber: 1.8 Consensus size: 114
744 TAAAAAGGTG
* ** *
754 ATCAGTAAAGAGTAAAAAGCTAATCAGCAAGAAGTAAAAAGATAATCAGTAAAACGCAAAAGGTA
1 ATCAGTAAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAGATAATCAACAAAACGCAAAAAGTA
* *
819 ATTAGTAAAAACTAAAAGAGTAATCAGTAAAAAAGGACCAGAAAATAGTA
66 ATCAGTAAAAACT-AAAGAATAATCAGTAAAAAAGGACCAGAAAATAGTA
* * * * * * *
869 ATCAGTAAAAGAGTAAAATGGTAATCAGTAAAAAGTAAGAAGGTAATCAACAAGA-GTAAAATAG
1 ATCAGT-AAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAGATAATCAACAAAACGCAAAA-AG
* *
933 TAATCAGTACAAAGTAAAGAATAATCAGT
64 TAATCAGTAAAAACTAAAGAATAATCAGT
962 GAAATAGTAA
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
115 24 0.32
116 52 0.68
ACGTcount: A:0.55, C:0.09, G:0.18, T:0.18
Consensus pattern (114 bp):
ATCAGTAAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAGATAATCAACAAAACGCAAAAAGTA
ATCAGTAAAAACTAAAGAATAATCAGTAAAAAAGGACCAGAAAATAGTA
Found at i:3698 original size:16 final size:16
Alignment explanation
Indices: 3674--3713 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3664 TTCTGCATTG
*
3674 AATTCTGAATTCTGAA
1 AATTGTGAATTCTGAA
*
3690 AATTGTGAATTCTGTA
1 AATTGTGAATTCTGAA
*
3706 ATTTGTGA
1 AATTGTGA
3714 TTTGCGAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (16 bp):
AATTGTGAATTCTGAA
Found at i:3786 original size:28 final size:28
Alignment explanation
Indices: 3745--3798 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
3735 TGTGAGTTGT
3745 GACTATGCAAGTATATATACTGAAATAA
1 GACTATGCAAGTATATATACTGAAATAA
* *
3773 GACTATGTATGTATATATACTGAAAT
1 GACTATGCAAGTATATATACTGAAAT
3799 CTGTACAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (28 bp):
GACTATGCAAGTATATATACTGAAATAA
Found at i:3881 original size:12 final size:12
Alignment explanation
Indices: 3864--3889 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3854 ATTATTCTGA
3864 TTGGAAACAGAT
1 TTGGAAACAGAT
3876 TTGGAAACAGAT
1 TTGGAAACAGAT
3888 TT
1 TT
3890 TGATGATGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (12 bp):
TTGGAAACAGAT
Found at i:8003 original size:46 final size:47
Alignment explanation
Indices: 7918--8010 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 47
7908 TTTCTAGTTG
7918 CAACTGAAAAATTAACCAAAAAACAAAATCCCAAACGAAAATCTGTAA
1 CAACTGAAAAATTAACCAAAAAACAAAATCCCAAACG-AAATCTGTAA
7966 CAACTGAAAAATTAA-CAAAAAA-AAAATCCCAAACGAAATCTGTAA
1 CAACTGAAAAATTAACCAAAAAACAAAATCCCAAACGAAATCTGTAA
8011 ACTTGCACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
45 10 0.22
46 13 0.29
47 7 0.16
48 15 0.33
ACGTcount: A:0.59, C:0.19, G:0.06, T:0.15
Consensus pattern (47 bp):
CAACTGAAAAATTAACCAAAAAACAAAATCCCAAACGAAATCTGTAA
Found at i:13205 original size:16 final size:16
Alignment explanation
Indices: 13171--13244 Score: 89
Period size: 16 Copynumber: 4.7 Consensus size: 16
13161 GGCAATTGGG
*
13171 CGGGTTCGGGTA-CTT
1 CGGGTTCGGGTATTTT
*
13186 CGGGTTCGGGCATTTT
1 CGGGTTCGGGTATTTT
*
13202 CGGGTTCGGGT-TCTGT
1 CGGGTTCGGGTAT-TTT
13218 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
13234 CGGGTTTGGGT
1 CGGGTTCGGGT
13245 TCGGGTTCGG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
15 12 0.24
16 37 0.74
17 1 0.02
ACGTcount: A:0.04, C:0.16, G:0.42, T:0.38
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:13209 original size:6 final size:6
Alignment explanation
Indices: 13200--13292 Score: 50
Period size: 6 Copynumber: 15.5 Consensus size: 6
13190 TTCGGGCATT
* *
13200 TTCGGG TTCGGG TTC-TG -TCGGG TTCGGG TATTTTCGGG TTTGGG TTCGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG ----TTCGGG TTCGGG TTCGGG
* * * * **
13250 TTCGGA CTC-GG ATCGGG TTCGGA CCCGGG -TCGGG TTCGGG TTC
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTC
13293 ACTTTCGATA
Statistics
Matches: 65, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
4 2 0.03
5 9 0.14
6 48 0.74
10 6 0.09
ACGTcount: A:0.04, C:0.19, G:0.43, T:0.33
Consensus pattern (6 bp):
TTCGGG
Found at i:13226 original size:32 final size:31
Alignment explanation
Indices: 13171--13246 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 31
13161 GGCAATTGGG
*
13171 CGGGTTCGGGTACTTCGGGTTCGGGCATTTT
1 CGGGTTCGGGTTCTTCGGGTTCGGGCATTTT
*
13202 CGGGTTCGGGTTCTGTCGGGTTCGGGTATTTT
1 CGGGTTCGGGTTCT-TCGGGTTCGGGCATTTT
*
13234 CGGGTTTGGGTTC
1 CGGGTTCGGGTTC
13247 GGGTTCGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 13 0.32
32 28 0.68
ACGTcount: A:0.04, C:0.17, G:0.41, T:0.38
Consensus pattern (31 bp):
CGGGTTCGGGTTCTTCGGGTTCGGGCATTTT
Found at i:13267 original size:17 final size:17
Alignment explanation
Indices: 13245--13288 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
13235 GGGTTTGGGT
*
13245 TCGGGTTCGGACTCGGA
1 TCGGGTTCGGACCCGGA
*
13262 TCGGGTTCGGACCCGGG
1 TCGGGTTCGGACCCGGA
13279 TCGGGTTCGG
1 TCGGGTTCGG
13289 GTTCACTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.07, C:0.25, G:0.45, T:0.23
Consensus pattern (17 bp):
TCGGGTTCGGACCCGGA
Found at i:15536 original size:19 final size:19
Alignment explanation
Indices: 15512--15555 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
15502 GCTTTTCGTT
15512 TGGGTCAGGGTGGTTTGAG
1 TGGGTCAGGGTGGTTTGAG
15531 TGGGTCAGGGTGGTTTGAG
1 TGGGTCAGGGTGGTTTGAG
15550 TGGGTC
1 TGGGTC
15556 TCGGCAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.09, C:0.07, G:0.52, T:0.32
Consensus pattern (19 bp):
TGGGTCAGGGTGGTTTGAG
Found at i:23807 original size:8 final size:8
Alignment explanation
Indices: 23794--23827 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
23784 CACCTTCTTG
23794 AAAAATTC
1 AAAAATTC
23802 AAAAATTC
1 AAAAATTC
*
23810 AGAAACTTC
1 A-AAAATTC
23819 AAAAATTC
1 AAAAATTC
23827 A
1 A
23828 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:23921 original size:15 final size:15
Alignment explanation
Indices: 23901--23930 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23891 GTTATATTGA
*
23901 AAAATATAAAAAAAT
1 AAAATAAAAAAAAAT
23916 AAAATAAAAAAAAAT
1 AAAATAAAAAAAAAT
23931 TTCGACCAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAATAAAAAAAAAT
Found at i:25516 original size:33 final size:32
Alignment explanation
Indices: 25419--25523 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 32
25409 TTGCAAAGAA
*
25419 TGTTTTAGATGTTGTTTGCAATGATACTAAACC
1 TGTTTTAG-TGTTGTTTGCAATGATACTAAATC
* * * *
25452 TAATTTGAGTGTTCTTTGCAATGAAACTAAATC
1 T-GTTTTAGTGTTGTTTGCAATGATACTAAATC
**
25485 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
1 TGTTTT-AGTGTTGTTTGCAATGATACTAAATC
*
25518 TTTTTT
1 TGTTTT
25524 GGATGCTAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
32 3 0.05
33 50 0.86
34 5 0.09
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.47
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGCAATGATACTAAATC
Found at i:30105 original size:12 final size:12
Alignment explanation
Indices: 30090--30120 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
30080 AAACTCAAAA
30090 GAAGAAAATGAT
1 GAAGAAAATGAT
*
30102 GAAGAAGATGAT
1 GAAGAAAATGAT
30114 GAAGAAA
1 GAAGAAA
30121 TGGAATAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.29, T:0.13
Consensus pattern (12 bp):
GAAGAAAATGAT
Found at i:31325 original size:11 final size:10
Alignment explanation
Indices: 31294--31336 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
31284 TTCTTGCTTC
31294 CAATGA-CTT
1 CAATGATCTT
*
31303 CAATGCTCTT
1 CAATGATCTT
31313 CAATTGATCTT
1 CAA-TGATCTT
*
31324 CAATGGTCTT
1 CAATGATCTT
31334 CAA
1 CAA
31337 GCCTTCAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 5 0.17
10 15 0.52
11 9 0.31
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (10 bp):
CAATGATCTT
Found at i:34082 original size:24 final size:25
Alignment explanation
Indices: 34039--34096 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 25
34029 CTTTTTATAT
34039 TAGCTTTAGACTTTACTAATAGTGC
1 TAGCTTTAGACTTTACTAATAGTGC
*
34064 TAGCTTTAG-CTTTAGTAATAGTGC
1 TAGCTTTAGACTTTACTAATAGTGC
34088 TAGCTTTAG
1 TAGCTTTAG
34097 TTAACTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (25 bp):
TAGCTTTAGACTTTACTAATAGTGC
Found at i:36213 original size:2 final size:2
Alignment explanation
Indices: 36206--36239 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
36196 AACCACATGG
36206 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36240 GTAATTTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36941 original size:78 final size:70
Alignment explanation
Indices: 36859--37013 Score: 231
Period size: 70 Copynumber: 2.2 Consensus size: 70
36849 CAATTAAAAT
* * * * * *
36859 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
36924 AGTTG
66 AGTTG
*
36929 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
36994 AGTTG
66 AGTTG
36999 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
37014 ACCTAAACAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
70 75 0.97
71 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (70 bp):
AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTG
Found at i:37217 original size:62 final size:62
Alignment explanation
Indices: 37120--37249 Score: 206
Period size: 62 Copynumber: 2.1 Consensus size: 62
37110 AGATAAAATG
* * * * *
37120 GTAAAATATAATAGTTATAAGGATATTAAATTTAATTATATAAAAATTGAGTTTTTAGTTGA
1 GTAAAATAAAATAATTATAAAGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGA
*
37182 GTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGA
1 GTAAAATAAAATAATTATAAAGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGA
37244 GTAAAA
1 GTAAAA
37250 CTATAAAAAC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (62 bp):
GTAAAATAAAATAATTATAAAGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGA
Found at i:37298 original size:244 final size:246
Alignment explanation
Indices: 36857--37357 Score: 882
Period size: 244 Copynumber: 2.0 Consensus size: 246
36847 TTCAATTAAA
*
36857 ATAG-TAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTT
1 ATAGATAAAATGGTAAAATATAATAGTTATAAGGATATTAAATTTAATTATATAAAAATTGAGTT
36921 TTTAGTTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATA
66 TTTAGTT-AG----A-AGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATA
36986 GAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATACATTTAACAAA
125 GAGTTTTTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATACATTTAACAAA
** *
37051 TAAGGGTATAATAGGTGATTCAAAAGTTTTACACCTGAACGTACTTTTTAATATAGT
190 TAAGGGTATAATAGACGATTCAAAAGTTTTACACCTGAACATACTTTTTAATATAGT
37108 ATAGATAAAATGGTAAAATATAATAGTTATAAGGATATTAAATTTAATTATATAAAAATTGAGTT
1 ATAGATAAAATGGTAAAATATAATAGTTATAAGGATATTAAATTTAATTATATAAAAATTGAGTT
37173 TTTAGTT-G-AGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTT
66 TTTAGTTAGAAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTT
*
37236 TTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATACATTTGACAAATAAGGG
131 TTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATACATTTAACAAATAAGGG
37301 TATAATAGACGATTCAAAAGTTTTACACCTGAACATACTTTTTAATATAGT
196 TATAATAGACGATTCAAAAGTTTTACACCTGAACATACTTTTTAATATAGT
37352 ATAGAT
1 ATAGAT
37358 TTATGACATG
Statistics
Matches: 244, Mismatches: 5, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
244 173 0.71
250 1 0.00
251 4 0.02
252 66 0.27
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.35
Consensus pattern (246 bp):
ATAGATAAAATGGTAAAATATAATAGTTATAAGGATATTAAATTTAATTATATAAAAATTGAGTT
TTTAGTTAGAAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTT
TTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATACATTTAACAAATAAGGG
TATAATAGACGATTCAAAAGTTTTACACCTGAACATACTTTTTAATATAGT
Found at i:37990 original size:2 final size:2
Alignment explanation
Indices: 37983--38010 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
37973 AAACATAACG
37983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38011 TTAATTCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46368 original size:16 final size:16
Alignment explanation
Indices: 46347--46396 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
46337 GTTTTCGGGT
46347 TCGGGTTAAATTTGGG
1 TCGGGTTAAATTTGGG
* *
46363 TCGGGTT-GATTCGGG
1 TCGGGTTAAATTTGGG
46378 TTCGGGTTAAATTTGGG
1 -TCGGGTTAAATTTGGG
46395 TC
1 TC
46397 AGATTGATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 6 0.21
16 16 0.57
17 6 0.21
ACGTcount: A:0.14, C:0.10, G:0.38, T:0.38
Consensus pattern (16 bp):
TCGGGTTAAATTTGGG
Found at i:46377 original size:32 final size:32
Alignment explanation
Indices: 46340--46447 Score: 162
Period size: 32 Copynumber: 3.4 Consensus size: 32
46330 TCAAGCCGTT
*
46340 TTCGGGTTCGGGTTAAATTTGGGTCGGGTTGA
1 TTCGGGTTCGGGTTAAATTTGGGTCAGGTTGA
*
46372 TTCGGGTTCGGGTTAAATTTGGGTCAGATTGA
1 TTCGGGTTCGGGTTAAATTTGGGTCAGGTTGA
* * * *
46404 TTCAGGTTCGGGTCAATTTTGGGTCAGGTTAA
1 TTCGGGTTCGGGTTAAATTTGGGTCAGGTTGA
46436 TTCGGGTTCGGG
1 TTCGGGTTCGGG
46448 CTCGGGTTGG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 68 1.00
ACGTcount: A:0.15, C:0.11, G:0.37, T:0.37
Consensus pattern (32 bp):
TTCGGGTTCGGGTTAAATTTGGGTCAGGTTGA
Found at i:46623 original size:20 final size:20
Alignment explanation
Indices: 46590--46628 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
46580 CATAGATGAA
*
46590 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
46610 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
46629 GAATTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:46665 original size:16 final size:15
Alignment explanation
Indices: 46646--46735 Score: 72
Period size: 16 Copynumber: 5.7 Consensus size: 15
46636 GGTTTTTTTA
*
46646 GGTTCGGGTTTTATCG
1 GGTTCGGATTTT-TCG
*
46662 GGTTTCAGATTTTTCG
1 GG-TTCGGATTTTTCG
*
46678 GGTTCTGATTTTTTCG
1 GGTTCGGA-TTTTTCG
* *
46694 GGTTTGAGCTTTTTCG
1 GGTTCG-GATTTTTCG
* *
46710 GGTTCGGGTTTTTTTG
1 GGTTC-GGATTTTTCG
46726 GGTTCGGATT
1 GGTTCGGATT
46736 CGGGCGGGTT
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
15 9 0.15
16 41 0.68
17 10 0.17
ACGTcount: A:0.07, C:0.11, G:0.32, T:0.50
Consensus pattern (15 bp):
GGTTCGGATTTTTCG
Found at i:46722 original size:32 final size:32
Alignment explanation
Indices: 46646--46729 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
46636 GGTTTTTTTA
*
46646 GGTTCGGGTTTTATCGGGTTTCAGATTTTTCG
1 GGTTCGGGTTTTTTCGGGTTTCAGATTTTTCG
* * * *
46678 GGTTCTGATTTTTTCGGGTTTGAGCTTTTTCG
1 GGTTCGGGTTTTTTCGGGTTTCAGATTTTTCG
*
46710 GGTTCGGGTTTTTTTGGGTT
1 GGTTCGGGTTTTTTCGGGTT
46730 CGGATTCGGG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.06, C:0.11, G:0.32, T:0.51
Consensus pattern (32 bp):
GGTTCGGGTTTTTTCGGGTTTCAGATTTTTCG
Found at i:47215 original size:2 final size:2
Alignment explanation
Indices: 47208--47279 Score: 63
Period size: 2 Copynumber: 36.0 Consensus size: 2
47198 TTCTTCTTTT
* * * *
47208 TG TG TG TG TG TG TG TG TG CG TG TG TG AG CG TG TG TG TG CG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
** * **
47250 TG TG CA TG CG CA TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
47280 AAGTTTTAAT
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.04, C:0.08, G:0.47, T:0.40
Consensus pattern (2 bp):
TG
Found at i:52562 original size:18 final size:19
Alignment explanation
Indices: 52527--52562 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
52517 AACTTTTTAT
*
52527 AATGTATAAATTTTACAAA
1 AATGTATAAATGTTACAAA
52546 AATGTAT-AATGTTACAA
1 AATGTATAAATGTTACAA
52563 TAAAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (19 bp):
AATGTATAAATGTTACAAA
Done.