Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014000.1 Kokia drynarioides strain JFW-HI SEQ_129031, 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: 23283
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Found at i:2124 original size:3 final size:3
Alignment explanation
Indices: 2116--2167 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
2106 AATGGGTTTT
2116 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2164 TAA T
1 TAA T
2168 TATTATTATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2172 original size:3 final size:3
Alignment explanation
Indices: 2166--2202 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
2156 AATAATAATA
2166 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2203 CAGCAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:2927 original size:15 final size:15
Alignment explanation
Indices: 2907--2949 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2897 TTGGGAATGA
*
2907 TGGGAAGGATGGCTT
1 TGGGAAAGATGGCTT
*
2922 TGGGAATGATGG-TT
1 TGGGAAAGATGGCTT
2936 TAGGGAAAGATGGC
1 T-GGGAAAGATGGC
2950 AATGGTGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 21 0.88
ACGTcount: A:0.26, C:0.05, G:0.44, T:0.26
Consensus pattern (15 bp):
TGGGAAAGATGGCTT
Found at i:3007 original size:93 final size:93
Alignment explanation
Indices: 2896--3131 Score: 409
Period size: 93 Copynumber: 2.5 Consensus size: 93
2886 CGCCACAGGC
*
2896 TTTGGGAATGATGGGAAGGATGGCTTTGGGAATGATGGTTTAGGGAAAGATGGCAATGGTGGGAA
1 TTTGGCAATGATGGGAAGGATGGCTTTGGGAATGATGGTTTAGGGAAAGATGGCAATGGTGGGAA
* *
2961 TGTTTTTTTAAGCAAACTTGTGGATGGA
66 TGTTTTTGTAAGCAAACTTGTGGACGGA
2989 TTTGGCAATGATGGGAAGGATGGCTTTGGGAATGATGGTTTAGGGAAAGATGGCAATGGTGGGAA
1 TTTGGCAATGATGGGAAGGATGGCTTTGGGAATGATGGTTTAGGGAAAGATGGCAATGGTGGGAA
*
3054 TGTTTTTGTAAGCAAACTTGTGGACGGG
66 TGTTTTTGTAAGCAAACTTGTGGACGGA
* * *
3082 TTTGGCAATGATGGTATGGATGGCTTTGGGAATGAGGGTTTAGGGAAAGA
1 TTTGGCAATGATGGGAAGGATGGCTTTGGGAATGATGGTTTAGGGAAAGA
3132 GGGCTTTGGG
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 136 1.00
ACGTcount: A:0.26, C:0.05, G:0.39, T:0.30
Consensus pattern (93 bp):
TTTGGCAATGATGGGAAGGATGGCTTTGGGAATGATGGTTTAGGGAAAGATGGCAATGGTGGGAA
TGTTTTTGTAAGCAAACTTGTGGACGGA
Found at i:3018 original size:15 final size:15
Alignment explanation
Indices: 3000--3042 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2990 TTGGCAATGA
*
3000 TGGGAAGGATGGCTT
1 TGGGAAAGATGGCTT
*
3015 TGGGAATGATGG-TT
1 TGGGAAAGATGGCTT
3029 TAGGGAAAGATGGC
1 T-GGGAAAGATGGC
3043 AATGGTGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 21 0.88
ACGTcount: A:0.26, C:0.05, G:0.44, T:0.26
Consensus pattern (15 bp):
TGGGAAAGATGGCTT
Found at i:3112 original size:108 final size:107
Alignment explanation
Indices: 3016--3304 Score: 328
Period size: 123 Copynumber: 2.5 Consensus size: 107
3006 GGATGGCTTT
*
3016 GGGAATGATGG-TTTAGGGAAAGATGGCAATGGTGGGAATGTTTTTGTAAGCAAACTTGTGGACG
1 GGGAAAGATGGCTTT-GGGAAAGATGGCAATGGTGGGAATGTTTTT-TAAGCAAACTTGTGGACG
3080 GGTTTGGCAATGATGGTATGGATGGCTTTGGGAATGAGGGTTTA
64 GGTTTGGCAATGATGGTATGGATGGCTTTGGGAATGAGGGTTTA
* * * *
3124 GGGAAAGAGGGCTTTGGGAATGAGGGTTTAGGGAAAGAGGGCAATGGTGGGAATGTTTTTTTAAG
1 GGGAAAGATGGCTTTGGGAA--A--G---ATGG-CA-A-TG----G-TGGGAATG-TTTTTTAAG
*
3189 CAAACTTGTGGATGGGTTTGGCAATGATGGTATGGATGGCTTTGGGAATGAGGGTTTA
50 CAAACTTGTGGACGGGTTTGGCAATGATGGTATGGATGGCTTTGGGAATGAGGGTTTA
* *
3247 GGGAAAGATGGCTTTGGGAATGATGGCAATGGTGGGAGTGGTTTTTTAAGCAAACTTG
1 GGGAAAGATGGCTTTGGGAAAGATGGCAATGGTGGGAAT-GTTTTTTAAGCAAACTTG
3305 GCGTTTGAGG
Statistics
Matches: 151, Mismatches: 12, Indels: 36
0.76 0.06 0.18
Matches are distributed among these distances:
108 37 0.25
109 5 0.03
110 1 0.01
112 1 0.01
113 1 0.01
114 1 0.01
115 4 0.03
116 4 0.03
117 1 0.01
118 1 0.01
119 1 0.01
122 1 0.01
123 88 0.58
124 5 0.03
ACGTcount: A:0.25, C:0.06, G:0.39, T:0.30
Consensus pattern (107 bp):
GGGAAAGATGGCTTTGGGAAAGATGGCAATGGTGGGAATGTTTTTTAAGCAAACTTGTGGACGGG
TTTGGCAATGATGGTATGGATGGCTTTGGGAATGAGGGTTTA
Found at i:3133 original size:15 final size:15
Alignment explanation
Indices: 3109--3164 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
3099 GGATGGCTTT
*
3109 GGGAATGAGGGTTTA
1 GGGAAAGAGGGTTTA
3124 GGGAAAGAGGGCTTT-
1 GGGAAAGAGGG-TTTA
*
3139 GGGAATGAGGGTTTA
1 GGGAAAGAGGGTTTA
3154 GGGAAAGAGGG
1 GGGAAAGAGGG
3165 CAATGGTGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 3 0.08
15 30 0.83
16 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.50, T:0.20
Consensus pattern (15 bp):
GGGAAAGAGGGTTTA
Found at i:3139 original size:30 final size:30
Alignment explanation
Indices: 3103--3165 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
3093 TGGTATGGAT
3103 GGCTTTGGGAATGAGGGTTTAGGGAAAGAG
1 GGCTTTGGGAATGAGGGTTTAGGGAAAGAG
3133 GGCTTTGGGAATGAGGGTTTAGGGAAAGAG
1 GGCTTTGGGAATGAGGGTTTAGGGAAAGAG
3163 GGC
1 GGC
3166 AATGGTGGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.05, G:0.48, T:0.22
Consensus pattern (30 bp):
GGCTTTGGGAATGAGGGTTTAGGGAAAGAG
Found at i:3152 original size:123 final size:123
Alignment explanation
Indices: 3001--3269 Score: 484
Period size: 123 Copynumber: 2.2 Consensus size: 123
2991 TGGCAATGAT
* * *
3001 GGGAAGGATGGCTTTGGGAATGATGGTTTAGGGAAAGATGGCAATGGTGGGAATGTTTTTGTAAG
1 GGGAAAGATGGCTTTGGGAATGAGGGTTTAGGGAAAGAGGGCAATGGTGGGAATGTTTTTGTAAG
3066 CAAACTTGTGGACGGGTTTGGCAATGATGGTATGGATGGCTTTGGGAATGAGGGTTTA
66 CAAACTTGTGGACGGGTTTGGCAATGATGGTATGGATGGCTTTGGGAATGAGGGTTTA
* *
3124 GGGAAAGAGGGCTTTGGGAATGAGGGTTTAGGGAAAGAGGGCAATGGTGGGAATGTTTTTTTAAG
1 GGGAAAGATGGCTTTGGGAATGAGGGTTTAGGGAAAGAGGGCAATGGTGGGAATGTTTTTGTAAG
*
3189 CAAACTTGTGGATGGGTTTGGCAATGATGGTATGGATGGCTTTGGGAATGAGGGTTTA
66 CAAACTTGTGGACGGGTTTGGCAATGATGGTATGGATGGCTTTGGGAATGAGGGTTTA
3247 GGGAAAGATGGCTTTGGGAATGA
1 GGGAAAGATGGCTTTGGGAATGA
3270 TGGCAATGGT
Statistics
Matches: 139, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
123 139 1.00
ACGTcount: A:0.25, C:0.05, G:0.41, T:0.29
Consensus pattern (123 bp):
GGGAAAGATGGCTTTGGGAATGAGGGTTTAGGGAAAGAGGGCAATGGTGGGAATGTTTTTGTAAG
CAAACTTGTGGACGGGTTTGGCAATGATGGTATGGATGGCTTTGGGAATGAGGGTTTA
Found at i:3265 original size:15 final size:15
Alignment explanation
Indices: 3223--3273 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
3213 TGATGGTATG
3223 GATGGCTTTGGGAAT
1 GATGGCTTTGGGAAT
* *
3238 GA-GGGTTTAGGGAAA
1 GATGGCTTT-GGGAAT
3253 GATGGCTTTGGGAAT
1 GATGGCTTTGGGAAT
3268 GATGGC
1 GATGGC
3274 AATGGTGGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 5 0.17
15 20 0.67
16 5 0.17
ACGTcount: A:0.24, C:0.06, G:0.43, T:0.27
Consensus pattern (15 bp):
GATGGCTTTGGGAAT
Found at i:3660 original size:23 final size:23
Alignment explanation
Indices: 3634--3685 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
3624 TTTTCAGAAA
*
3634 ACTAAAATAAAATATTATTAATT
1 ACTAAAATAAAATATTATAAATT
* *
3657 ACTAAATTAAAATTTTATAAATT
1 ACTAAAATAAAATATTATAAATT
3680 A-TAAAA
1 ACTAAAA
3686 GACTTAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
ACTAAAATAAAATATTATAAATT
Found at i:4604 original size:26 final size:26
Alignment explanation
Indices: 4567--4624 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
4557 ACTTTTAAAT
* *
4567 AAAT-AATTAATAAAATCGATCGGTC
1 AAATCAATTAATAAAATCAATCGATC
* *
4592 AAATCAATTAATAGAATCAATTGATC
1 AAATCAATTAATAAAATCAATCGATC
4618 AAATCAA
1 AAATCAA
4625 CCACTACAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.28
Consensus pattern (26 bp):
AAATCAATTAATAAAATCAATCGATC
Found at i:5505 original size:10 final size:9
Alignment explanation
Indices: 5480--5706 Score: 90
Period size: 9 Copynumber: 24.2 Consensus size: 9
5470 CGATAAAAAA
*
5480 ATAAAAATCA
1 ATAAAAAT-T
*
5490 ATAAAAGTT
1 ATAAAAATT
5499 ATAAAAATT
1 ATAAAAATT
**
5508 ATTAAATTTT
1 A-TAAAAATT
5518 AATAAAAA-T
1 -ATAAAAATT
*
5527 AT-AAAATA
1 ATAAAAATT
*
5535 ATTAAAATT
1 ATAAAAATT
5544 -TATAAAATT
1 ATA-AAAATT
*
5553 AGAAAAAATT
1 A-TAAAAATT
5563 ATAAAAATT
1 ATAAAAATT
* **
5572 GTAAATTTTT
1 ATAAA-AATT
**
5582 ATAAAAAAAAC
1 AT--AAAAATT
5593 ATAACAAATT
1 ATAA-AAATT
5603 AT-AAAATAT
1 ATAAAAAT-T
*
5612 ATAGAAA-T
1 ATAAAAATT
*
5620 ATAAAAAAT
1 ATAAAAATT
5629 AT-AAAATT
1 ATAAAAATT
* *
5637 TTATAAAGTCGT
1 ATA-AAAAT--T
*
5649 AAAAAAATT
1 ATAAAAATT
*
5658 ATAAAAAAT
1 ATAAAAATT
*
5667 ATAAAGAAAT
1 ATAAA-AATT
5677 AT-AAAATT
1 ATAAAAATT
5685 AGTAAAAAATT
1 A-T-AAAAATT
5696 ATAAAAATT
1 ATAAAAATT
5705 AT
1 AT
5707 TGTATCAAAA
Statistics
Matches: 162, Mismatches: 33, Indels: 45
0.68 0.14 0.19
Matches are distributed among these distances:
7 4 0.02
8 26 0.16
9 66 0.41
10 46 0.28
11 15 0.09
12 5 0.03
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:5567 original size:27 final size:28
Alignment explanation
Indices: 5501--5568 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 28
5491 TAAAAGTTAT
* *
5501 AAAAATTATTAAATTTTAATAAAAATATA
1 AAAAATTA-TAAAATTTAATAAAAATAGA
*
5530 AAATAA-T-TAAAATTT-ATAAAATTAGA
1 AAA-AATTATAAAATTTAATAAAAATAGA
5556 AAAAATTATAAAA
1 AAAAATTATAAAA
5569 ATTGTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
25 2 0.06
26 13 0.39
27 12 0.36
29 4 0.12
30 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (28 bp):
AAAAATTATAAAATTTAATAAAAATAGA
Found at i:5622 original size:17 final size:16
Alignment explanation
Indices: 5602--5635 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5592 CATAACAAAT
*
5602 TATAAAATATATAGAAA
1 TATAAAAAATATA-AAA
5619 TATAAAAAATATAAAA
1 TATAAAAAATATAAAA
5635 T
1 T
5636 TTTATAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
TATAAAAAATATAAAA
Found at i:5641 original size:19 final size:18
Alignment explanation
Indices: 5526--5671 Score: 57
Period size: 19 Copynumber: 7.8 Consensus size: 18
5516 TTAATAAAAA
5526 TATAAAATAAT-TAAAATT
1 TATAAAA-AATATAAAATT
* * *
5544 TAT-AAAATTAGAAAAAAT
1 TATAAAAAATA-TAAAATT
* * *
5562 TATAAAAATTGTAAATTTT
1 TATAAAAAATATAAA-ATT
* *
5581 TATAAAAAAAACATAACAAAT
1 TAT--AAAAAATATAA-AATT
*
5602 TATAAAATATATAGAAA--
1 TATAAAAAATATA-AAATT
5619 TATAAAAAATATAAAATTT
1 TATAAAAAATATAAAA-TT
*** * *
5638 TATAAAGTCGTAAAAAAAT
1 TATAAA-AAATATAAAATT
5657 TATAAAAAATATAAA
1 TATAAAAAATATAAA
5672 GAAATATAAA
Statistics
Matches: 92, Mismatches: 24, Indels: 24
0.66 0.17 0.17
Matches are distributed among these distances:
16 5 0.05
17 15 0.16
18 19 0.21
19 33 0.36
20 7 0.08
21 12 0.13
22 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (18 bp):
TATAAAAAATATAAAATT
Found at i:5679 original size:19 final size:19
Alignment explanation
Indices: 5605--5682 Score: 61
Period size: 19 Copynumber: 4.1 Consensus size: 19
5595 AACAAATTAT
*
5605 AAAATATATAGAAATATAA
1 AAAATATAAAGAAATATAA
* * *
5624 AAAATAT-AA-AATTTTAT
1 AAAATATAAAGAAATATAA
* * *
5641 AAAGTCGTAAAAAAATTATAA
1 AAAAT-ATAAAGAAA-TATAA
5662 AAAATATAAAGAAATATAA
1 AAAATATAAAGAAATATAA
5681 AA
1 AA
5683 TTAGTAAAAA
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
17 9 0.21
18 2 0.05
19 16 0.37
20 9 0.21
21 7 0.16
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAATATAAAGAAATATAA
Found at i:5680 original size:38 final size:38
Alignment explanation
Indices: 5619--5702 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 38
5609 TATATAGAAA
** *
5619 TATAAAAAATATAAAATTTTAT-AAAGTCGTAAAAAAAT
1 TATAAAAAATATAAAATAATATAAAAGTAGT-AAAAAAT
*
5657 TATAAAAAATATAAAGA-AATATAAAATTAGTAAAAAAT
1 TATAAAAAATATAAA-ATAATATAAAAGTAGTAAAAAAT
5695 TATAAAAA
1 TATAAAAA
5703 TTATTGTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
38 33 0.82
39 7 0.17
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (38 bp):
TATAAAAAATATAAAATAATATAAAAGTAGTAAAAAAT
Found at i:8033 original size:10 final size:9
Alignment explanation
Indices: 8020--8111 Score: 62
Period size: 9 Copynumber: 9.8 Consensus size: 9
8010 CAAAAAAACC
*
8020 TTTTCATAA
1 TTTTTATAA
*
8029 TTTTTATGA
1 TTTTTATAA
8038 TTTTTATAAA
1 TTTTTAT-AA
*
8048 ATTTTATAA
1 TTTTTATAA
*
8057 TTTTTACGT-T
1 TTTTTA--TAA
8067 TTTTTATAA
1 TTTTTATAA
8076 TTTTTA-ATA
1 TTTTTATA-A
8085 TTTTTATTAAA
1 TTTTTA-T-AA
* *
8096 ATTTAATAA
1 TTTTTATAA
8105 TTTTTAT
1 TTTTTAT
8112 CTTCTACTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
8 2 0.03
9 41 0.64
10 14 0.22
11 6 0.09
12 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:8061 original size:28 final size:27
Alignment explanation
Indices: 8020--8088 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
8010 CAAAAAAACC
*
8020 TTTTCATAATTTTTATGATTTTTATAAAA
1 TTTT-ATAATTTTTACG-TTTTTATAAAA
* *
8049 TTTTATAATTTTTACGTTTTTTTATAA
1 TTTTATAATTTTTACGTTTTTATAAAA
8076 TTTT-TAATATTTT
1 TTTTATAAT-TTTT
8089 TATTAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 4 0.11
27 17 0.47
28 11 0.31
29 4 0.11
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (27 bp):
TTTTATAATTTTTACGTTTTTATAAAA
Found at i:8088 original size:19 final size:18
Alignment explanation
Indices: 8028--8111 Score: 69
Period size: 19 Copynumber: 4.4 Consensus size: 18
8018 CCTTTTCATA
* *
8028 ATTTTTATGATTTTTATAA
1 ATTTTTATAATTTTTA-AT
* *
8047 AATTTTATAATTTTTACGT
1 ATTTTTATAATTTTTA-AT
*
8066 TTTTTTATAATTTTTAAT
1 ATTTTTATAATTTTTAAT
**
8084 ATTTTTATTAAAATTTAAT
1 ATTTTTA-TAATTTTTAAT
8103 AATTTTTAT
1 -ATTTTTAT
8112 CTTCTACTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
18 7 0.13
19 38 0.73
20 7 0.13
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTTTTATAATTTTTAAT
Found at i:9239 original size:15 final size:15
Alignment explanation
Indices: 9219--9249 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
9209 TATTCTGCTT
9219 ATATTAATATAGTTA
1 ATATTAATATAGTTA
9234 ATATTAATATAGTTA
1 ATATTAATATAGTTA
9249 A
1 A
9250 GATACTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATATTAATATAGTTA
Found at i:18044 original size:2 final size:2
Alignment explanation
Indices: 18039--18080 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
18029 TATACAAATC
18039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18080 A
1 A
18081 GCAATATGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.