Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015081.1 Kokia drynarioides strain JFW-HI SEQ_130125, 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: 135913
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 77 characters in sequence are not A, C, G, or T
Found at i:2654 original size:25 final size:24
Alignment explanation
Indices: 2599--2654 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 24
2589 GAAGAGCACA
2599 ATGATTATTTTTATTAAAAAATTT
1 ATGATTATTTTTATTAAAAAATTT
2623 ATCGATT-TTTTTATTAAAAAACTTTT
1 AT-GATTATTTTTATTAAAAAA--TTT
2649 ATGATT
1 ATGATT
2655 GAAAGAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 16 0.55
25 8 0.28
26 5 0.17
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.54
Consensus pattern (24 bp):
ATGATTATTTTTATTAAAAAATTT
Found at i:4466 original size:31 final size:31
Alignment explanation
Indices: 4429--4491 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
4419 TTTCTTTAAA
4429 TATATATGATTAAATAAAAATTAAAATTTCATG
1 TATATAT--TTAAATAAAAATTAAAATTTCATG
* * *
4462 TATATATTTGAATCACAATTAAAATTTCAT
1 TATATATTTAAATAAAAATTAAAATTTCAT
4492 TACAATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 20 0.74
33 7 0.26
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (31 bp):
TATATATTTAAATAAAAATTAAAATTTCATG
Found at i:30804 original size:33 final size:34
Alignment explanation
Indices: 30766--30843 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 34
30756 TTTTTTCCTC
* * * *
30766 TATATTTTTAGTTAAAAAATATTTAATTTATTTA
1 TATATTTTTAATTAAAAAACATTAAATTAATTTA
30800 -ATATTTTTAATTAAAAAACATTAAATTAATTTA
1 TATATTTTTAATTAAAAAACATTAAATTAATTTA
*
30833 TAAATTTTTAA
1 TATATTTTTAA
30844 AATTTGTCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (34 bp):
TATATTTTTAATTAAAAAACATTAAATTAATTTA
Found at i:31648 original size:21 final size:21
Alignment explanation
Indices: 31622--31662 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
31612 TATGAAAAGC
31622 GTCACAAAAAG-ATCTCAAAAT
1 GTCACAAAAAGTAT-TCAAAAT
31643 GTCACAAAAAGTATTCAAAA
1 GTCACAAAAAGTATTCAAAA
31663 AACGTCACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.54, C:0.17, G:0.10, T:0.20
Consensus pattern (21 bp):
GTCACAAAAAGTATTCAAAAT
Found at i:31669 original size:23 final size:23
Alignment explanation
Indices: 31616--31702 Score: 74
Period size: 22 Copynumber: 3.9 Consensus size: 23
31606 TAAAGCTATG
*
31616 AAAAGCGTCACAAAAAG-ATCTC-
1 AAAAACGTCACAAAAAGTAT-TCA
*
31638 -AAAATGTCACAAAAAGTATTCA
1 AAAAACGTCACAAAAAGTATTCA
* **
31660 AAAAACGTCAC-AAAAGGAAACA
1 AAAAACGTCACAAAAAGTATTCA
* *
31682 AAAAAGGTCACCAAAAGTATT
1 AAAAACGTCACAAAAAGTATT
31703 TTTATTTGGT
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
21 16 0.31
22 20 0.39
23 15 0.29
ACGTcount: A:0.55, C:0.17, G:0.13, T:0.15
Consensus pattern (23 bp):
AAAAACGTCACAAAAAGTATTCA
Found at i:43075 original size:45 final size:46
Alignment explanation
Indices: 43010--43104 Score: 156
Period size: 45 Copynumber: 2.1 Consensus size: 46
43000 AAAATGCTTC
* *
43010 AAAAAATTACTTTTGAAGAGAAATTAAAATTGTCAGGTT-TAAAAA
1 AAAAAATCACTTTTGAAGAGAAATTAAAATTGTCAAGTTCTAAAAA
*
43055 AAAAAATCACTTTTGGAGAGAAATTAAAATTGTCAAGTTCTAAAAA
1 AAAAAATCACTTTTGAAGAGAAATTAAAATTGTCAAGTTCTAAAAA
43101 AAAA
1 AAAA
43105 TGTTTTTTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 36 0.78
46 10 0.22
ACGTcount: A:0.53, C:0.06, G:0.13, T:0.28
Consensus pattern (46 bp):
AAAAAATCACTTTTGAAGAGAAATTAAAATTGTCAAGTTCTAAAAA
Found at i:43699 original size:21 final size:21
Alignment explanation
Indices: 43658--43723 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
43648 TTTTGTTTTA
*
43658 AATTAATTAATATAATAATATCT
1 AATTAATT-AT-TTATAATATCT
*
43681 AATTATATTATTT-TAATATTTT
1 AATTA-ATTATTTATAATA-TCT
43703 AATTAATTATTTATAAT-TCT
1 AATTAATTATTTATAATATCT
43723 A
1 A
43724 TTTTTATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 3 0.08
21 12 0.32
22 12 0.32
23 7 0.19
24 3 0.08
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTAATTATTTATAATATCT
Found at i:44779 original size:2 final size:2
Alignment explanation
Indices: 44772--44796 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44762 AAGTGAAATA
44772 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
44797 CACACAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57572 original size:20 final size:21
Alignment explanation
Indices: 57522--57573 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
57512 ATTTTTTATA
57522 CTATTCATAT-TTTAACAATT
1 CTATTCATATATTTAACAATT
* * * *
57542 CAATCCTTATATTTCA-AATT
1 CTATTCATATATTTAACAATT
57562 CTATTCATATAT
1 CTATTCATATAT
57574 CATGGCAGAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (21 bp):
CTATTCATATATTTAACAATT
Found at i:58517 original size:24 final size:24
Alignment explanation
Indices: 58490--58541 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
58480 AATCGTTATG
58490 TCCCACATCATCTTATTCATGGTC
1 TCCCACATCATCTTATTCATGGTC
*
58514 TCCCACATCATCTTCTTCATGGTC
1 TCCCACATCATCTTATTCATGGTC
58538 TCCC
1 TCCC
58542 CCACCATTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.17, C:0.38, G:0.08, T:0.37
Consensus pattern (24 bp):
TCCCACATCATCTTATTCATGGTC
Found at i:61858 original size:2 final size:2
Alignment explanation
Indices: 61845--61879 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
61835 GTCTGTTAAG
61845 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61880 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:61884 original size:2 final size:2
Alignment explanation
Indices: 61879--61907 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
61869 ATATATATAT
61879 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
61908 TTTTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:62484 original size:16 final size:17
Alignment explanation
Indices: 62449--62486 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
62439 ATATACAAAT
*
62449 AAATATTTTACTATTAA
1 AAATACTTTACTATTAA
*
62466 AAATACTTTA-TATTTA
1 AAATACTTTACTATTAA
62482 AAATA
1 AAATA
62487 ATAATAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATACTTTACTATTAA
Found at i:64631 original size:21 final size:21
Alignment explanation
Indices: 64605--64644 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
64595 GACATTATTT
64605 ATTTTTATTA-TTTACTTTTTC
1 ATTTTTATTACTTTA-TTTTTC
*
64626 ATTTTTCTTACTTTATTTT
1 ATTTTTATTACTTTATTTT
64645 CTGTTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (21 bp):
ATTTTTATTACTTTATTTTTC
Found at i:65659 original size:20 final size:20
Alignment explanation
Indices: 65626--65680 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
65616 TAATAAAAAA
*
65626 TAAAA-AATAGAAAAAATCG
1 TAAAATAATATAAAAAATCG
*
65645 TAAAATAATATAAAAAATTG
1 TAAAATAATATAAAAAATCG
**
65665 TAAAATTTTATAAAAA
1 TAAAATAATATAAAAA
65681 TCACAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 5 0.16
20 26 0.84
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAAATAATATAAAAAATCG
Found at i:65688 original size:29 final size:28
Alignment explanation
Indices: 65645--65736 Score: 98
Period size: 29 Copynumber: 3.1 Consensus size: 28
65635 GAAAAAATCG
*
65645 TAAAATAATATAAAAAATTGTAAAATTTTA
1 TAAAAT-ATA-AAAAAATTATAAAATTTTA
*
65675 TAAAA-ATCACAAAAAATTATCAAAA-TATA
1 TAAAATAT-A-AAAAAATTAT-AAAATTTTA
65704 TAGAAATATAAAAAAATTATAAAATTTTA
1 TA-AAATATAAAAAAATTATAAAATTTTA
65733 TAAA
1 TAAA
65737 GTCGTAAGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
28 8 0.15
29 30 0.57
30 13 0.25
31 2 0.04
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (28 bp):
TAAAATATAAAAAAATTATAAAATTTTA
Found at i:66254 original size:90 final size:90
Alignment explanation
Indices: 66155--66454 Score: 440
Period size: 90 Copynumber: 3.3 Consensus size: 90
66145 AAGAGCAAGA
*
66155 GCTTAATTGCTTTTTTGAAAAATTTTGAGGGCCTTTTTTTATGCATTTTGAAAGTTCAAGTACTC
1 GCTTAATTGCTTTTTTGAAAAAGTTTGAGGGCCTTTTTTTATGCATTTTGAAAGTTCAAGTACTC
66220 GATTGAGTGGAAAAAAAAAGTTGGG
66 GATTGAGTGGAAAAAAAAAGTTGGG
* * *
66245 GCTTAATTGCTTTTTTTAAGAAGTTTGAGGGCCTTTTTTTATGCATTTTGAAAGTTCAAGTACCC
1 GCTTAATTGCTTTTTTGAAAAAGTTTGAGGGCCTTTTTTTATGCATTTTGAAAGTTCAAGTACTC
*
66310 GATTGAGTGGGGAAAAAAAAGTTGGG
66 GATTGAGT-GGAAAAAAAAAGTTGGG
* * **
66336 GCTTAATTGCTTTTTTGAAGAAGTTTGAGGGTCTTTTTTTATGCATTTTGAAAGTTCAAGTGTTC
1 GCTTAATTGCTTTTTTGAAAAAGTTTGAGGGCCTTTTTTTATGCATTTTGAAAGTTCAAGTACTC
* * * ***
66401 AATTGAGTGCAAAAAAATAGAAAGG
66 GATTGAGTGGAAAAAAAAAGTTGGG
*
66426 GCTTAATT-ATTTTTTGAAAAAGTTTGAGG
1 GCTTAATTGCTTTTTTGAAAAAGTTTGAGG
66455 ACTTTTTACA
Statistics
Matches: 190, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
89 19 0.10
90 88 0.46
91 83 0.44
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.39
Consensus pattern (90 bp):
GCTTAATTGCTTTTTTGAAAAAGTTTGAGGGCCTTTTTTTATGCATTTTGAAAGTTCAAGTACTC
GATTGAGTGGAAAAAAAAAGTTGGG
Found at i:66609 original size:16 final size:15
Alignment explanation
Indices: 66587--66632 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
66577 AATTATAAAT
66587 TTTTAATTTAAATAA
1 TTTTAATTTAAATAA
66602 TTTATAATTTATAA-AA
1 TTT-TAATTTA-AATAA
*
66618 TTTTAAATT-AATAA
1 TTTTAATTTAAATAA
66632 T
1 T
66633 GGTAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
13 2 0.07
14 3 0.11
15 8 0.30
16 12 0.44
17 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTAATTTAAATAA
Found at i:76629 original size:20 final size:20
Alignment explanation
Indices: 76601--76663 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
76591 TTTAGAAATA
* *
76601 TTTACAAAATACTTTAAAAC
1 TTTATAAAATAATTTAAAAC
76621 TTTATAAAATAATATTTAAAA-
1 TTTATAAAAT-A-ATTTAAAAC
* *
76642 TTTAT-AAATATTTTATAAC
1 TTTATAAAATAATTTAAAAC
76661 TTT
1 TTT
76664 TCGAAAAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 6 0.17
19 4 0.11
20 13 0.36
21 6 0.17
22 7 0.19
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTATAAAATAATTTAAAAC
Found at i:76647 original size:21 final size:23
Alignment explanation
Indices: 76608--76649 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
76598 ATATTTACAA
76608 AATACTTTAAAACTTTATAAAAT
1 AATACTTTAAAACTTTATAAAAT
76631 AATA-TTTAAAA-TTTATAAA
1 AATACTTTAAAACTTTATAAA
76650 TATTTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 7 0.37
23 4 0.21
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (23 bp):
AATACTTTAAAACTTTATAAAAT
Found at i:77251 original size:28 final size:28
Alignment explanation
Indices: 77215--77277 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
77205 GTACTCAAAT
77215 AAATTAATTTTATTT-GTCAAAATAAAA
1 AAATTAATTTTATTTAGTCAAAATAAAA
*
77242 AAATATAATTTTATTTACTTCAAAAT-AAA
1 AAAT-TAATTTTATTTA-GTCAAAATAAAA
77271 AAATTAA
1 AAATTAA
77278 ATTAAATTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 4 0.12
28 14 0.44
29 7 0.22
30 7 0.22
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.40
Consensus pattern (28 bp):
AAATTAATTTTATTTAGTCAAAATAAAA
Found at i:95544 original size:19 final size:19
Alignment explanation
Indices: 95520--95559 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
95510 GCGTTTAGTT
*
95520 TAATTTTTATCTCTCGTTA
1 TAATTTTTATCTCGCGTTA
95539 TAATTTTTATCTCGCGTTA
1 TAATTTTTATCTCGCGTTA
95558 TA
1 TA
95560 GTATTTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.55
Consensus pattern (19 bp):
TAATTTTTATCTCGCGTTA
Found at i:95566 original size:19 final size:19
Alignment explanation
Indices: 95520--95566 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
95510 GCGTTTAGTT
* *
95520 TAATTTTTATCTCTCGTTA
1 TAATATTTATCTCGCGTTA
*
95539 TAATTTTTATCTCGCGTTA
1 TAATATTTATCTCGCGTTA
*
95558 TAGTATTTA
1 TAATATTTA
95567 ATCTTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (19 bp):
TAATATTTATCTCGCGTTA
Found at i:99707 original size:18 final size:18
Alignment explanation
Indices: 99671--99708 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
99661 ATTTTTTATA
*
99671 AAATATATTAAAAATATT
1 AAATATATTAAAAAAATT
99689 AAATAT-TTAAACAAAATT
1 AAATATATTAAA-AAAATT
99707 AA
1 AA
99709 TTTTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATATATTAAAAAAATT
Found at i:101665 original size:12 final size:12
Alignment explanation
Indices: 101648--101677 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
101638 TCTCTCTGTT
101648 AATTGATAAATA
1 AATTGATAAATA
101660 AATTGATAAATA
1 AATTGATAAATA
101672 AATTGA
1 AATTGA
101678 GTGTTGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (12 bp):
AATTGATAAATA
Found at i:114375 original size:158 final size:158
Alignment explanation
Indices: 114102--114399 Score: 479
Period size: 158 Copynumber: 1.9 Consensus size: 158
114092 AAAAAATAAC
* *
114102 GCAGTTAAGAGCACCAGAACTTTGCCTCATCAAATGCGCCTCGCCTGAAAGGGTCGAGGTGCTTT
1 GCAGTTAAGAGCACCAGAACTGTGCCTCATCAAATGCGCCTCACCTGAAAGGGTCGAGGTGCTTT
* * ** *
114167 TGTTGCCTAGCGCTAAGGCGCAAGGGATAGGCGTGCCTAGGTGCAAAACTTGAGAACACCGATAA
66 TGTTGCCTAGCGCTAAGGCGCAAAGCATAAACGTGCCTAGGTGCAAAACTTGAGAACACCAATAA
114232 ATCCAACCATAGCCTTACAAAACACACT
131 ATCCAACCATAGCCTTACAAAACACACT
* * * *
114260 GCAGTTAAGAGCACCAGAAGTGTGCCTGATCAAATGTGCCTCACCTGAAAGGGTTGAGGTGCTTT
1 GCAGTTAAGAGCACCAGAACTGTGCCTCATCAAATGCGCCTCACCTGAAAGGGTCGAGGTGCTTT
* *
114325 TGTTGCCTAGTGCTAAGGCGCAAAGCATAAACGTGCCTAGGTGCAGAACTTGAGAACACCAATAA
66 TGTTGCCTAGCGCTAAGGCGCAAAGCATAAACGTGCCTAGGTGCAAAACTTGAGAACACCAATAA
114390 ATCCAACCAT
131 ATCCAACCAT
114400 GGACAAGGCT
Statistics
Matches: 127, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
158 127 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.21
Consensus pattern (158 bp):
GCAGTTAAGAGCACCAGAACTGTGCCTCATCAAATGCGCCTCACCTGAAAGGGTCGAGGTGCTTT
TGTTGCCTAGCGCTAAGGCGCAAAGCATAAACGTGCCTAGGTGCAAAACTTGAGAACACCAATAA
ATCCAACCATAGCCTTACAAAACACACT
Found at i:126153 original size:13 final size:14
Alignment explanation
Indices: 126135--126176 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
126125 TTTCAAATTT
126135 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
126148 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
126163 ATTTTAAATAATAT
1 ATTTT-AATAATAT
126177 TCTTCACATC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:126161 original size:16 final size:16
Alignment explanation
Indices: 126139--126175 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
126129 AAATTTATTT
126139 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
126156 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
126171 TAATA
1 TAATA
126176 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:126259 original size:15 final size:15
Alignment explanation
Indices: 126214--126261 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 15
126204 TATTAATGTT
126214 TTAATAATAAATATTTA
1 TTAATAATAAATA--TA
*
126231 TTACAATTATAAATATA
1 TT--AATAATAAATATA
126248 TTAATAATAAATAT
1 TTAATAATAAATAT
126262 TTCGTAGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 11 0.41
17 6 0.22
19 10 0.37
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAATAATAAATATA
Found at i:126970 original size:14 final size:14
Alignment explanation
Indices: 126951--126988 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
126941 TAAAATTATG
126951 TTAAAATTTAAAAA
1 TTAAAATTTAAAAA
* *
126965 TTAAAAATTAAATA
1 TTAAAATTTAAAAA
126979 TT-AAATTTAA
1 TTAAAATTTAA
126989 GATCAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAAATTTAAAAA
Found at i:130722 original size:15 final size:15
Alignment explanation
Indices: 130702--130731 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
130692 AAGCCTTACG
*
130702 AGAAATGAATGGAAA
1 AGAAATCAATGGAAA
130717 AGAAATCAATGGAAA
1 AGAAATCAATGGAAA
130732 GCAAGTTGTA
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:0.60, C:0.03, G:0.23, T:0.13
Consensus pattern (15 bp):
AGAAATCAATGGAAA
Found at i:134222 original size:19 final size:20
Alignment explanation
Indices: 134178--134222 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
134168 TAAAAAAAAA
*
134178 AATAA-AAGTTCAAGTAAAC
1 AATAATAAGCTCAAGTAAAC
*
134197 AGT-ATAAGCTCAAGT-AAC
1 AATAATAAGCTCAAGTAAAC
134215 AATAATAA
1 AATAATAA
134223 CACAATAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (20 bp):
AATAATAAGCTCAAGTAAAC
Found at i:134803 original size:59 final size:58
Alignment explanation
Indices: 134737--134857 Score: 170
Period size: 59 Copynumber: 2.1 Consensus size: 58
134727 AAAAAGAGTT
* *
134737 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTGGATTTAAAAATAATTGGAGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGATTTAAAAATAATTAGA-TTTA
* * * * *
134796 GTTTATGAGTGTTTTTTAAGTATGAAATTATATTTGGGTTTAAAAATATTTAGATTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGATTTAAAAATAATTAGATTTA
134854 GTTT
1 GTTT
134858 GTTGATGGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 8 0.15
59 47 0.85
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (58 bp):
GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGATTTAAAAATAATTAGATTTA
Done.