Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014723.1 Kokia drynarioides strain JFW-HI SEQ_129762, 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: 144286
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 77 characters in sequence are not A, C, G, or T
Found at i:1080 original size:25 final size:23
Alignment explanation
Indices: 1036--1085 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1026 ACACTAGCGC
1036 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
1059 GCTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
1082 GCTC
1 GCTC
1086 AGTACTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.10, C:0.24, G:0.24, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:1119 original size:23 final size:23
Alignment explanation
Indices: 1089--1178 Score: 87
Period size: 23 Copynumber: 3.9 Consensus size: 23
1079 TGTGCTCAGT
1089 ACTTTGTGTACTCTCTGTTTAGC
1 ACTTTGTGTACTCTCTGTTTAGC
*
1112 ACTTTGTGTGCTCTCTGTTGTCCAGC
1 ACTTTGTGTACTCTCTGTT-T--AGC
* *
1138 ACTTATGTG--CTCTCTGTTCAGT
1 ACTT-TGTGTACTCTCTGTTTAGC
*
1160 ACTTCG-GTACTCTCTGTTT
1 ACTTTGTGTACTCTCTGTTT
1179 GTTCCATTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 15 0.27
23 18 0.32
24 1 0.02
25 9 0.16
26 7 0.12
27 4 0.07
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (23 bp):
ACTTTGTGTACTCTCTGTTTAGC
Found at i:1162 original size:62 final size:61
Alignment explanation
Indices: 1037--1162 Score: 141
Period size: 62 Copynumber: 2.0 Consensus size: 61
1027 CACTAGCGCG
* **
1037 CTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTTTGTGTGCTCAGTACTTTGTGTA
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTTTATGTGCTCA-TACTTTCAGTA
* *
1099 CTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGTCCAGCAC-TTATGTGCTC-T-CTGTTCAGTA
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGTT-T--AGCACTTTATGTGCTCATACT-TTCAGTA
1161 CT
1 CT
1163 TCGGTACTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
61 2 0.04
62 38 0.69
63 1 0.02
64 9 0.16
65 5 0.09
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.44
Consensus pattern (61 bp):
CTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTTTATGTGCTCATACTTTCAGTA
Found at i:2704 original size:166 final size:166
Alignment explanation
Indices: 2430--2766 Score: 665
Period size: 166 Copynumber: 2.0 Consensus size: 166
2420 ATATTCTAAC
2430 TCTTAACTCGACACTATTACTGTTCCAACTCCGGTTCAAAAACGCGAATGTTACAATATTCATAC
1 TCTTAACTCGACACTATTACTGTTCCAACTCCGGTTCAAAAACGCGAATGTTACAATATTCATAC
2495 TCAATAATGATAATCATATTACATTTCATAAATATATTCAATTATCATAATTACTCACTTGTAAA
66 TCAATAATGATAATCATATTACATTTCATAAATATATTCAATTATCATAATTACTCACTTGTAAA
2560 TGTGACATTCATGTCTTAATTCTATTTAAACGTAAT
131 TGTGACATTCATGTCTTAATTCTATTTAAACGTAAT
*
2596 TCTTAACTCGACACTATTACTGTTCCAACTCCGGTTGAAAAACGCGAATGTTACAATATTCATAC
1 TCTTAACTCGACACTATTACTGTTCCAACTCCGGTTCAAAAACGCGAATGTTACAATATTCATAC
2661 TCAATAATGATAATCATATTACATTTCATAAATATATTCAATTATCATAATTACTCACTTGTAAA
66 TCAATAATGATAATCATATTACATTTCATAAATATATTCAATTATCATAATTACTCACTTGTAAA
2726 TGTGACATTCATGTCTTAATTCTATTTAAACGTAAT
131 TGTGACATTCATGTCTTAATTCTATTTAAACGTAAT
2762 TCTTA
1 TCTTA
2767 CAATAATTTA
Statistics
Matches: 170, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 170 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (166 bp):
TCTTAACTCGACACTATTACTGTTCCAACTCCGGTTCAAAAACGCGAATGTTACAATATTCATAC
TCAATAATGATAATCATATTACATTTCATAAATATATTCAATTATCATAATTACTCACTTGTAAA
TGTGACATTCATGTCTTAATTCTATTTAAACGTAAT
Found at i:3415 original size:18 final size:18
Alignment explanation
Indices: 3373--3418 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
3363 ACAAAAGTAG
3373 ATAAAAACTAGAAAAAAA
1 ATAAAAACTAGAAAAAAA
* *
3391 ATCAAAA-TATAAAAGAAA
1 ATAAAAACTAGAAAA-AAA
3409 ATAAAAACTA
1 ATAAAAACTA
3419 AATATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 6 0.26
18 15 0.65
19 2 0.09
ACGTcount: A:0.74, C:0.07, G:0.04, T:0.15
Consensus pattern (18 bp):
ATAAAAACTAGAAAAAAA
Found at i:3421 original size:23 final size:22
Alignment explanation
Indices: 3382--3427 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
3372 GATAAAAACT
*
3382 AGAAAAAAAATCAAAATATAAA
1 AGAAAAAAAAACAAAATATAAA
*
3404 AGAAAATAAAAACTAAATATAAA
1 AGAAAA-AAAAACAAAATATAAA
3427 A
1 A
3428 AATTAAGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (22 bp):
AGAAAAAAAAACAAAATATAAA
Found at i:3873 original size:4 final size:4
Alignment explanation
Indices: 3864--3904 Score: 55
Period size: 4 Copynumber: 9.8 Consensus size: 4
3854 TTTCTTCCTT
*
3864 TTTC TTTC TTTC TTTC TTCCC TTTC TTTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TT-TC TTTC -TTTC TTTC TTTC TTT
3905 TATTTTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 26 0.79
5 7 0.21
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:3877 original size:18 final size:18
Alignment explanation
Indices: 3854--3915 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 18
3844 GATGGAAAAT
*
3854 TTTCTTCCTTTTTCTTTC
1 TTTCTTTCTTTTTCTTTC
3872 TTTCTTTCTTCCCTTTCTTTTC
1 TTTCTTTCTT---TTTC-TTTC
*
3894 TTTCTTTCTTTTATTTTTC
1 TTTCTTTCTTTT-TCTTTC
3913 TTT
1 TTT
3916 TCAGCTTCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 9 0.24
19 9 0.24
20 1 0.03
21 4 0.11
22 14 0.38
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTCTTTCTTTTTCTTTC
Found at i:3889 original size:13 final size:12
Alignment explanation
Indices: 3854--3904 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
3844 GATGGAAAAT
3854 TTTCTTCC-TT-
1 TTTCTTCCTTTC
*
3864 TTTCTTTCTTTC
1 TTTCTTCCTTTC
3876 TTTCTTCCCTTTC
1 TTTCTT-CCTTTC
*
3889 TTTTCTTTCTTTC
1 -TTTCTTCCTTTC
3902 TTT
1 TTT
3905 TATTTTTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 7 0.21
11 2 0.06
12 9 0.26
13 10 0.29
14 6 0.18
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTCTTCCTTTC
Found at i:30277 original size:26 final size:26
Alignment explanation
Indices: 30241--30292 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
30231 GATGGGGGTA
30241 CAGAGTTTAAATTGACTTTTTATTTT
1 CAGAGTTTAAATTGACTTTTTATTTT
30267 CAGAGTTTAAATTGACTTTTTATTTT
1 CAGAGTTTAAATTGACTTTTTATTTT
30293 TACTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.54
Consensus pattern (26 bp):
CAGAGTTTAAATTGACTTTTTATTTT
Found at i:35781 original size:21 final size:22
Alignment explanation
Indices: 35757--35801 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
35747 AGAAGAAGTT
35757 TTTTTTTAAAT-T-TTTTTATAA
1 TTTTTTT-AATGTCTTTTTATAA
35778 -TTTTTTAATGTCTTTTTATAA
1 TTTTTTTAATGTCTTTTTATAA
35799 TTT
1 TTT
35802 CAGAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.14
20 7 0.33
21 9 0.43
22 2 0.10
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTTTTAATGTCTTTTTATAA
Found at i:36161 original size:77 final size:77
Alignment explanation
Indices: 36025--36183 Score: 300
Period size: 77 Copynumber: 2.1 Consensus size: 77
36015 TTCAAAAGTT
*
36025 GCAAAACTGAGATCGGAGAGACACTAAAAGTTTCCAAAAGACTATTAGAAAGCAAATTAGTCTTC
1 GCAACACTGAGATCGGAGAGACACTAAAAGTTTCCAAAAGACTATTAGAAAGCAAATTAGTCTTC
36090 GTCATATGATCA
66 GTCATATGATCA
*
36102 GCAACACTGAGATCGGAGAGACACTAAAAGTTTCCAAAAGACTATTAGAAAGCAGATTAGTCTTC
1 GCAACACTGAGATCGGAGAGACACTAAAAGTTTCCAAAAGACTATTAGAAAGCAAATTAGTCTTC
36167 GTCATATGATCA
66 GTCATATGATCA
36179 GCAAC
1 GCAAC
36184 TTTATTTAAA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
77 80 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (77 bp):
GCAACACTGAGATCGGAGAGACACTAAAAGTTTCCAAAAGACTATTAGAAAGCAAATTAGTCTTC
GTCATATGATCA
Found at i:41448 original size:19 final size:20
Alignment explanation
Indices: 41406--41449 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
41396 CATTTCATAT
41406 ATAAA-AATCATATTTAAGA
1 ATAAATAATCATATTTAAGA
*
41425 A-AAATAATTATATTTAA-A
1 ATAAATAATCATATTTAAGA
41443 ATAAATA
1 ATAAATA
41450 TTTAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
ATAAATAATCATATTTAAGA
Found at i:41724 original size:20 final size:20
Alignment explanation
Indices: 41672--41724 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
41662 CTCCAGTGAG
* *
41672 ACTTCTATCGGTAGAACTCC
1 ACTTCTATCGATAGAACTAC
*
41692 ACTTCTA-CTGATATAACTAC
1 ACTTCTATC-GATAGAACTAC
*
41712 AGTTCTATCGATA
1 ACTTCTATCGATA
41725 CCTTGAAGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (20 bp):
ACTTCTATCGATAGAACTAC
Found at i:43069 original size:27 final size:27
Alignment explanation
Indices: 43037--43092 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
43027 CTCATGAAAG
43037 AATGAATAGAGTCAAAGAATCAAAGCT
1 AATGAATAGAGTCAAAGAATCAAAGCT
*
43064 AATGAATATAGTCAAAGAATCAAAGCT
1 AATGAATAGAGTCAAAGAATCAAAGCT
43091 AA
1 AA
43093 GTATTCTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.54, C:0.11, G:0.16, T:0.20
Consensus pattern (27 bp):
AATGAATAGAGTCAAAGAATCAAAGCT
Found at i:44302 original size:25 final size:23
Alignment explanation
Indices: 44274--44319 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
44264 GTTGGATCCA
44274 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
44299 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
44320 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:44406 original size:13 final size:13
Alignment explanation
Indices: 44385--44418 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
44375 ACAATATAAC
44385 AATAATAATCCTA
1 AATAATAATCCTA
*
44398 AATATTAATCCTA
1 AATAATAATCCTA
*
44411 AAAAATAA
1 AATAATAA
44419 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:45381 original size:20 final size:20
Alignment explanation
Indices: 45347--45420 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 20
45337 ATTTTTGTCT
45347 TTTTCTTATTCTTTTTTCTGAA
1 TTTT-TTATTCTTTTTTC-GAA
45369 TTTTCTT-TT-TTTTTTCG-A
1 TTTT-TTATTCTTTTTTCGAA
*
45387 TTTTTTCA-T-TTTTTTCGAC
1 TTTTTT-ATTCTTTTTTCGAA
45406 TTTTTT-TTCTTTTTT
1 TTTTTTATTCTTTTTT
45421 TTAAATAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
17 2 0.04
18 15 0.33
19 13 0.28
20 7 0.15
21 2 0.04
22 7 0.15
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.76
Consensus pattern (20 bp):
TTTTTTATTCTTTTTTCGAA
Found at i:45421 original size:20 final size:19
Alignment explanation
Indices: 45358--45421 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
45348 TTTCTTATTC
*
45358 TTTTTTCTGAATTTTCTTT-T
1 TTTTTTC-G-ATTTTTTTTCT
45378 TTTTTTCGA--TTTTTTCAT
1 TTTTTTCGATTTTTTTTC-T
45396 TTTTTTCGACTTTTTTTTCT
1 TTTTTTCGA-TTTTTTTTCT
45416 TTTTTT
1 TTTTTT
45422 TAAATAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
16 5 0.13
18 11 0.29
19 1 0.03
20 14 0.37
21 7 0.18
ACGTcount: A:0.08, C:0.11, G:0.05, T:0.77
Consensus pattern (19 bp):
TTTTTTCGATTTTTTTTCT
Found at i:46358 original size:5 final size:6
Alignment explanation
Indices: 46344--46403 Score: 70
Period size: 6 Copynumber: 10.3 Consensus size: 6
46334 TTGTATAATT
* * *
46344 AAAATA AAAATA AAAAT- AAAAT- AAAATA AAACTA AAAATG AAAATG
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
46390 AAAATG AAAATA AA
1 AAAATA AAAATA AA
46404 TATACTAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
5 10 0.20
6 39 0.80
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:49906 original size:113 final size:113
Alignment explanation
Indices: 49708--49929 Score: 408
Period size: 113 Copynumber: 2.0 Consensus size: 113
49698 TAGAAATCCC
*
49708 TAAATTATGCTGATACCTCTATTCAAGCATAAAAGCAACTGACTCTAGGTTGATTAATTGAAATT
1 TAAATTATGCTAATACCTCTATTCAAGCATAAAAGCAACTGACTCTAGGTTGATTAATTGAAATT
*
49773 TCTTTCTAATTAAAACCCCTATTGTCACATTAATTCGATCTATGGATT
66 TCTTTCTAATTAAAACCCCTATTATCACATTAATTCGATCTATGGATT
49821 TAAATTATGCTAATACCTCTATTCAAGCATAAAAGCAACTGACTCTAGGTTGATTAATTGAAATT
1 TAAATTATGCTAATACCTCTATTCAAGCATAAAAGCAACTGACTCTAGGTTGATTAATTGAAATT
* *
49886 TTTTTCTAATTAAAACCCCTATTATCGCATTAATTCGATCTATG
66 TCTTTCTAATTAAAACCCCTATTATCACATTAATTCGATCTATG
49930 AATTCTCCTA
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 105 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (113 bp):
TAAATTATGCTAATACCTCTATTCAAGCATAAAAGCAACTGACTCTAGGTTGATTAATTGAAATT
TCTTTCTAATTAAAACCCCTATTATCACATTAATTCGATCTATGGATT
Found at i:50086 original size:15 final size:15
Alignment explanation
Indices: 50066--50104 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
50056 GCACATCAAA
*
50066 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
50081 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
50095 CAAGAATTAA
1 CAAGAATTAA
50105 GCACACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:50512 original size:25 final size:23
Alignment explanation
Indices: 50484--50529 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
50474 GTTGGATCCA
50484 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
50509 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
50530 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:55394 original size:50 final size:50
Alignment explanation
Indices: 55319--55428 Score: 220
Period size: 50 Copynumber: 2.2 Consensus size: 50
55309 AAAGTTGAGA
55319 TTTAATGTCTTGCATTTCTGAAATGAATATGGGCCCATTAATCCACCATG
1 TTTAATGTCTTGCATTTCTGAAATGAATATGGGCCCATTAATCCACCATG
55369 TTTAATGTCTTGCATTTCTGAAATGAATATGGGCCCATTAATCCACCATG
1 TTTAATGTCTTGCATTTCTGAAATGAATATGGGCCCATTAATCCACCATG
55419 TTTAATGTCT
1 TTTAATGTCT
55429 CGATATTATA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (50 bp):
TTTAATGTCTTGCATTTCTGAAATGAATATGGGCCCATTAATCCACCATG
Found at i:57647 original size:42 final size:42
Alignment explanation
Indices: 57598--57680 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
57588 CAAATATTTT
*
57598 TAAACCCAAATATAATTTTATTCTTTAAA-AACACTCATAAAC
1 TAAACCCAAATATAATTTTATTC-CTAAATAACACTCATAAAC
57640 TAAACCCAAATATAATTTTATTCCTAAATAACACTCATAAA
1 TAAACCCAAATATAATTTTATTCCTAAATAACACTCATAAA
57681 AAAACTCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 4 0.10
42 35 0.90
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (42 bp):
TAAACCCAAATATAATTTTATTCCTAAATAACACTCATAAAC
Found at i:65468 original size:5 final size:5
Alignment explanation
Indices: 65458--65484 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
65448 AAATTTTATG
65458 TTTTC TTTTC TTTTC TTTTC TTTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT
65485 CTTCATGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:76196 original size:13 final size:11
Alignment explanation
Indices: 76164--76206 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
76154 TCATTTTCTA
*
76164 AATAAAATAAT
1 AATAAAATATT
76175 AAT-AAATATTT
1 AATAAAATA-TT
76186 AAGTAAAATATT
1 AA-TAAAATATT
76198 AATAAAATA
1 AATAAAATA
76207 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 5 0.18
13 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AATAAAATATT
Found at i:82891 original size:29 final size:28
Alignment explanation
Indices: 82839--82893 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
82829 AAACTTATAA
* *
82839 AAATATTTTTTTTTTGTTTAAAGATGTT
1 AAATATTTTTTTTATCTTTAAAGATGTT
*
82867 AAATATTTTTTTTATCTTCTGAAGATG
1 AAATATTTTTTTTATCTT-TAAAGATG
82894 AATCATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56
Consensus pattern (28 bp):
AAATATTTTTTTTATCTTTAAAGATGTT
Found at i:82904 original size:83 final size:82
Alignment explanation
Indices: 82803--82960 Score: 280
Period size: 83 Copynumber: 1.9 Consensus size: 82
82793 GATTATTTTT
** *
82803 TGAAGATGAATCATAAAATGGATATAAAACTTATAAAAATATTTTTTTTTTGTTTAAAGATGTTA
1 TGAAGATGAATCATAAAATGGATATAAAACGAATAAAAATA-TTTTTTTTTGTTTAAAGATGCTA
82868 AATATTTTTTTTATCTTC
65 AATATTTTTTTTATCTTC
82886 TGAAGATGAATCATAAAATGGATATAAAACGAATAAAAATATTTTTTTTTGTTTAAAGATGCTAA
1 TGAAGATGAATCATAAAATGGATATAAAACGAATAAAAATATTTTTTTTTGTTTAAAGATGCTAA
82951 ATATTTTTTT
66 ATATTTTTTT
82961 GTTTCTCAAG
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
82 33 0.46
83 39 0.54
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (82 bp):
TGAAGATGAATCATAAAATGGATATAAAACGAATAAAAATATTTTTTTTTGTTTAAAGATGCTAA
ATATTTTTTTTATCTTC
Found at i:86782 original size:19 final size:20
Alignment explanation
Indices: 86746--86787 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
86736 AAATATTTAA
86746 TATTTTATTTAAAATAATAT
1 TATTTTATTTAAAATAATAT
*
86766 TATTTTA-TTAAAGTAATAT
1 TATTTTATTTAAAATAATAT
86785 TAT
1 TAT
86788 ATTAAAGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TATTTTATTTAAAATAATAT
Found at i:86785 original size:16 final size:16
Alignment explanation
Indices: 86743--86795 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
86733 AATAAATATT
*
86743 TAATATTTTATTTAAAA
1 TAATATTTTA-TTAAAG
86760 TAATATTATTTTATTAAAG
1 T-A-A-TATTTTATTAAAG
*
86779 TAATATTATATTAAAG
1 TAATATTTTATTAAAG
86795 T
1 T
86796 GTAAAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 13 0.42
17 2 0.06
18 2 0.06
19 7 0.23
20 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (16 bp):
TAATATTTTATTAAAG
Found at i:88746 original size:28 final size:29
Alignment explanation
Indices: 88692--88747 Score: 87
Period size: 28 Copynumber: 1.9 Consensus size: 29
88682 AACATTAGAG
*
88692 ATTTTGGGAGATTTCATATTAGGGATTTTA
1 ATTTTGGGAGA-TTAATATTAGGGATTTTA
88722 ATTTTGGGAGA-TAATATTAGGGATTT
1 ATTTTGGGAGATTAATATTAGGGATTT
88748 AGGATTAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 14 0.56
30 11 0.44
ACGTcount: A:0.29, C:0.02, G:0.25, T:0.45
Consensus pattern (29 bp):
ATTTTGGGAGATTAATATTAGGGATTTTA
Found at i:89571 original size:5 final size:5
Alignment explanation
Indices: 89556--89585 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
89546 TTTCATTACT
89556 TTTTCC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TTTT
89586 GTTCTTTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:99218 original size:31 final size:31
Alignment explanation
Indices: 99181--99242 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
99171 TTGGTTACTG
*
99181 AACTATTCAAAAGTTTTCATTTAAGTCACTA
1 AACTATTCAAAAGTTTTCATCTAAGTCACTA
* *
99212 AACTATTGAAAAGTTTTTATCTAAGTCACTA
1 AACTATTCAAAAGTTTTCATCTAAGTCACTA
99243 GGTTTTTAAT
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:0.39, C:0.15, G:0.08, T:0.39
Consensus pattern (31 bp):
AACTATTCAAAAGTTTTCATCTAAGTCACTA
Found at i:103645 original size:40 final size:40
Alignment explanation
Indices: 103601--103691 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 40
103591 AATAATGAAA
* * **
103601 TAAAGCAATAGCAGCATTTTTTCATAAATGCCGCAAAAGG
1 TAAAGCAATAGCAGCATTTTCTCACAAACACCGCAAAAGG
* **
103641 TAAAGCAATAGCTGTGTTTTCTCACAAACACCGCAAAAGG
1 TAAAGCAATAGCAGCATTTTCTCACAAACACCGCAAAAGG
103681 TAAAGCAATAG
1 TAAAGCAATAG
103692 TGACGTTTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.23
Consensus pattern (40 bp):
TAAAGCAATAGCAGCATTTTCTCACAAACACCGCAAAAGG
Found at i:103762 original size:83 final size:83
Alignment explanation
Indices: 103675--103866 Score: 219
Period size: 83 Copynumber: 2.3 Consensus size: 83
103665 CAAACACCGC
* * * ** *
103675 AAAAGGTAAAGCAATAGTGACGTTTATGGGAAAAGCGTCGTAAAAGGTAAAGAGCAATAGTGGCG
1 AAAAGGTAAAGCAATAGCGACGTTTATGAG-AAA-CGCCACAAAAGGTAAAGAGCAATAGCGGCG
*
103740 CTTATGGGAAAA-TGC-CGT
64 CTTATGGGAAAATTGCTAGT
* *
103758 AAAAGGTAAAGAGCAATAGCGACGTTTATGAGAAACGCCACAAAAGGTAAGGAGCATTAGCGGCG
1 AAAAGGT-AA-AGCAATAGCGACGTTTATGAGAAACGCCACAAAAGGTAAAGAGCAATAGCGGCG
*
103823 TTTATGGGAAAATTGCTAGT
64 CTTATGGGAAAATTGCTAGT
* *
103843 -AAAGGTTAAGCAATAGCGGCGTTT
1 AAAAGGTAAAGCAATAGCGACGTTT
103867 TCCCATAAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
82 15 0.16
83 43 0.46
84 14 0.15
85 21 0.23
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (83 bp):
AAAAGGTAAAGCAATAGCGACGTTTATGAGAAACGCCACAAAAGGTAAAGAGCAATAGCGGCGCT
TATGGGAAAATTGCTAGT
Found at i:103772 original size:42 final size:42
Alignment explanation
Indices: 103675--103835 Score: 177
Period size: 41 Copynumber: 3.9 Consensus size: 42
103665 CAAACACCGC
*
103675 AAAAGGT-AA-AGCAATAGTGACGTTTATGGGAAAA-GCGTCGT
1 AAAAGGTAAAGAGCAATAGCGACGTTTATGGGAAAATGC--CGT
* * *
103716 AAAAGGTAAAGAGCAATAGTGGCGCTTATGGGAAAATGCCGT
1 AAAAGGTAAAGAGCAATAGCGACGTTTATGGGAAAATGCCGT
* * **
103758 AAAAGGTAAAGAGCAATAGCGACGTTTATGAG-AAACGCCAC
1 AAAAGGTAAAGAGCAATAGCGACGTTTATGGGAAAATGCCGT
* * *
103799 AAAAGGTAAGGAGCATTAGCGGCGTTTATGGGAAAAT
1 AAAAGGTAAAGAGCAATAGCGACGTTTATGGGAAAAT
103836 TGCTAGTAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
41 41 0.40
42 36 0.35
43 23 0.23
44 2 0.02
ACGTcount: A:0.40, C:0.12, G:0.29, T:0.19
Consensus pattern (42 bp):
AAAAGGTAAAGAGCAATAGCGACGTTTATGGGAAAATGCCGT
Found at i:103860 original size:41 final size:42
Alignment explanation
Indices: 103675--103866 Score: 173
Period size: 41 Copynumber: 4.6 Consensus size: 42
103665 CAAACACCGC
* * *
103675 AAAAGGTAA-AGCAATAGTGACGTTTATGGGAAAA-GCGTCGT
1 AAAAGGTAAGAGCAATAGCGGCGTTTATGGGAAAATGC-TAGT
* * *
103716 AAAAGGTAAAGAGCAATAGTGGCGCTTATGGGAAAATGC-CGT
1 AAAAGGT-AAGAGCAATAGCGGCGTTTATGGGAAAATGCTAGT
* * * * *
103758 AAAAGGTAAAGAGCAATAGCGACGTTTATGAG-AAACGCCA-C
1 AAAAGGT-AAGAGCAATAGCGGCGTTTATGGGAAAATGCTAGT
*
103799 AAAAGGTAAGGAGCATTAGCGGCGTTTATGGGAAAATTGCTAGT
1 AAAAGGTAA-GAGCAATAGCGGCGTTTATGGGAAAA-TGCTAGT
*
103843 -AAAGGTTA-AGCAATAGCGGCGTTT
1 AAAAGGTAAGAGCAATAGCGGCGTTT
103867 TCCCATAAAT
Statistics
Matches: 126, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
40 2 0.02
41 53 0.42
42 36 0.29
43 33 0.26
44 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (42 bp):
AAAAGGTAAGAGCAATAGCGGCGTTTATGGGAAAATGCTAGT
Found at i:119815 original size:32 final size:32
Alignment explanation
Indices: 119779--119843 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
119769 TCATTTACCC
119779 ATTTTAATACTAAAACTAATAAAAACAACATA
1 ATTTTAATACTAAAACTAATAAAAACAACATA
119811 ATTTTAATACTAAAACTAATAAAAACAACATA
1 ATTTTAATACTAAAACTAATAAAAACAACATA
119843 A
1 A
119844 ATATGCATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (32 bp):
ATTTTAATACTAAAACTAATAAAAACAACATA
Found at i:121532 original size:23 final size:22
Alignment explanation
Indices: 121500--121580 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 22
121490 ACACTAGCGC
*
121500 GCTCTTTGTTTAGCACGTCTCGT
1 GCTCTCTGTTTAGCACGTCT-GT
*
121523 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCAC-GTCTGT
* * * *
121548 GCTCTTTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCAC-GTCTGT
121571 GCTCTCTGTT
1 GCTCTCTGTT
121581 GCCCAGCACT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
23 28 0.58
24 1 0.02
25 16 0.33
26 3 0.06
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46
Consensus pattern (22 bp):
GCTCTCTGTTTAGCACGTCTGT
Found at i:121549 original size:25 final size:25
Alignment explanation
Indices: 121521--121580 Score: 88
Period size: 23 Copynumber: 2.5 Consensus size: 25
121511 AGCACGTCTC
121521 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
* *
121546 GTGCTCT-T-TGATTAGCACTTTGT
1 GTGCTCTCTGTTATTAGCACTGTGT
121569 GTGCTCTCTGTT
1 GTGCTCTCTGTT
121581 GCCCAGCACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 20 0.67
24 2 0.07
25 8 0.27
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (25 bp):
GTGCTCTCTGTTATTAGCACTGTGT
Found at i:128574 original size:23 final size:23
Alignment explanation
Indices: 128543--128620 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
128533 AGTACGTCCC
128543 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTG--ATTAGCACTGTGT
* ** * *
128568 GTGCTCTCTGATTAACGTTTTTT
1 GTGCTCTCTGATTAGCACTGTGT
128591 GTGCTCTCTGATTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTGTGT
128614 GTGCTCT
1 GTGCTCT
128621 TTGTTGCCCA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 33 0.77
25 10 0.23
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.45
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTGTGT
Found at i:132405 original size:113 final size:113
Alignment explanation
Indices: 132207--132433 Score: 427
Period size: 113 Copynumber: 2.0 Consensus size: 113
132197 AAGTATGACG
* * *
132207 AAATGCAGCTACAGCTTCAAAATATGATGAAAATGTTTCAGCATAATCAATCACAGAATCCGCTA
1 AAATGCAGCTACAGCTTCAAAATATGATGAAAATCTTTCAGCAGAATCAAACACAGAATCCGCTA
132272 TCTTAGACTTTTGTTTTTTCTTATTATGAGAATAATATACACAATATT
66 TCTTAGACTTTTGTTTTTTCTTATTATGAGAATAATATACACAATATT
132320 AAATGCAGCTACAGCTTCAAAATATGATGAAAATCTTTCAGCAGAATCAAACACAGAATCCGCTA
1 AAATGCAGCTACAGCTTCAAAATATGATGAAAATCTTTCAGCAGAATCAAACACAGAATCCGCTA
132385 TCTTAGACTTTTGTTTTTTCTTATTATGAGAATAATATACACAATATT
66 TCTTAGACTTTTGTTTTTTCTTATTATGAGAATAATATACACAATATT
132433 A
1 A
132434 CTTTTGAATA
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 111 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (113 bp):
AAATGCAGCTACAGCTTCAAAATATGATGAAAATCTTTCAGCAGAATCAAACACAGAATCCGCTA
TCTTAGACTTTTGTTTTTTCTTATTATGAGAATAATATACACAATATT
Found at i:132526 original size:15 final size:15
Alignment explanation
Indices: 132506--132538 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
132496 ATTTGAAATT
132506 ATTGGTTAGATTTGA
1 ATTGGTTAGATTTGA
*
132521 ATTGGTTGGATTTGA
1 ATTGGTTAGATTTGA
132536 ATT
1 ATT
132539 TATAGGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (15 bp):
ATTGGTTAGATTTGA
Found at i:135181 original size:26 final size:28
Alignment explanation
Indices: 135120--135186 Score: 75
Period size: 30 Copynumber: 2.4 Consensus size: 28
135110 ATGAACGAAG
* *
135120 AATTAAATAAAATCACAATAATTTAGAA
1 AATTAAATAAAATCACAATAAATGAGAA
*
135148 AGAGTTAAATAAAATC-C-ATAAATGATAA
1 A-A-TTAAATAAAATCACAATAAATGAGAA
135176 AATTAAATAAA
1 AATTAAATAAA
135187 CATATCATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 9 0.26
27 1 0.03
28 10 0.29
29 2 0.06
30 12 0.35
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (28 bp):
AATTAAATAAAATCACAATAAATGAGAA
Found at i:136804 original size:31 final size:31
Alignment explanation
Indices: 136768--136834 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
136758 GTTATACTTT
*
136768 CATATACA-TAATTAAATCAATATTAAAATTTA
1 CATATA-AGTAATTAAATCAA-ATCAAAATTTA
*
136800 -ATATAAGTAATTAAATGAAATCAAAATTTA
1 CATATAAGTAATTAAATCAAATCAAAATTTA
136830 CATAT
1 CATAT
136835 CAATGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 11 0.35
31 20 0.65
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (31 bp):
CATATAAGTAATTAAATCAAATCAAAATTTA
Found at i:140270 original size:31 final size:33
Alignment explanation
Indices: 140198--140290 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 33
140188 ATTTAATTAA
* *
140198 TTTTTTAAAATTTAAAAATATT-AAAA--AA-T
1 TTTTTTAGAATTTAAAAATTTTAAAAATTAATT
* * * *
140227 TATTTTATAATTT-TAATTTTTAAAAA-TAATT
1 TTTTTTAGAATTTAAAAATTTTAAAAATTAATT
140258 TTTTTTAGAATTTAAAAATTTTAAAAATTAATT
1 TTTTTTAGAATTTAAAAATTTTAAAAATTAATT
140291 AAAGGCTTAC
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
28 5 0.10
29 15 0.30
30 2 0.04
31 12 0.24
32 11 0.22
33 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (33 bp):
TTTTTTAGAATTTAAAAATTTTAAAAATTAATT
Found at i:140733 original size:16 final size:16
Alignment explanation
Indices: 140707--140739 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
140697 ACAATCATTT
140707 ATATTTC-AAAATAAA
1 ATATTTCAAAAATAAA
140722 ATATTCTCAAAAATAAA
1 ATATT-TCAAAAATAAA
140739 A
1 A
140740 ATCACTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 2 0.12
17 9 0.56
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (16 bp):
ATATTTCAAAAATAAA
Done.