Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010658.1 Kokia drynarioides strain JFW-HI SEQ_125601, 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: 85195
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:533 original size:29 final size:29
Alignment explanation
Indices: 501--1043 Score: 322
Period size: 29 Copynumber: 18.5 Consensus size: 29
491 TGCACGGGAG
* * *
501 CAAAATGGTAGTTTTGGAAGGTTTGAAGT
1 CAAAATGGTATTTTTGGAAGGTTCGAGGT
530 CAAAAATGAG-ATTTTTGGAA-GTTCGAGGGT
1 C-AAAATG-GTATTTTTGGAAGGTTCGA-GGT
560 -AAAATGGTAATTTTTGGAAGGTTCGAGGT
1 CAAAATGGT-ATTTTTGGAAGGTTCGAGGT
* * * *
589 CAAAAATAGG-ATTTTTAGAAGTTTTGGGGGT
1 C-AAAAT-GGTATTTTTGGAAG-GTTCGAGGT
* *
620 -AAAATGGTAATTTTTAGAAGGTTCGGGGT
1 CAAAATGGT-ATTTTTGGAAGGTTCGAGGT
* * *
649 CAAAAATGGGATTTATT-TAA-GTTCGGGGGT
1 C-AAAATGGTATTT-TTGGAAGGTTC-GAGGT
* * *
679 -AAAATAGTAATTTTTAGAAGGTTCGGGGT
1 CAAAATGGT-ATTTTTGGAAGGTTCGAGGT
*
708 CAAAAATTGG-ATTTTTTGAA-GTTCGAGGGT
1 C-AAAA-TGGTATTTTTGGAAGGTTCGA-GGT
* *
738 --AAATGGTAATTTTTAGAAGGTTCGAGTT
1 CAAAATGGT-ATTTTTGGAAGGTTCGAGGT
* *
766 CACAAATGGGATTTTTGGAA-GTTCGGGGGT
1 CA-AAATGGTATTTTTGGAAGGTTC-GAGGT
* *
796 -AAAATGGTAATTTTTTGAAGGTTCGAGAT
1 CAAAATGGT-ATTTTTGGAAGGTTCGAGGT
* *
825 CAAAAATGGGATTTTTGGAA-GTTCGGGGGT
1 C-AAAATGGTATTTTTGGAAGGTTC-GAGGT
* * *
855 -AAATTGGTAATTTTTGAAAGGTTCGGGGT
1 CAAAATGGT-ATTTTTGGAAGGTTCGAGGT
* * * *
884 CAAAATGGGATTTTTGGAAGTTTGGGGGT
1 CAAAATGGTATTTTTGGAAGGTTCGAGGT
* *
913 -AAAATGGTAATTTTTGAAAGGTTCGGGGT
1 CAAAATGGT-ATTTTTGGAAGGTTCGAGGT
*
942 CAAAAATGGGATTTTTGGAA-GTTCGAGGGT
1 C-AAAATGGTATTTTTGGAAGGTTCGA-GGT
* *
972 -AAAATGGTAATTTTAGGAATGTTC-AGGAT
1 CAAAATGGT-ATTTTTGGAAGGTTCGAGG-T
*
1001 CAAAAAT-GAATTTTTGGAA-GTTCGAGGGT
1 C-AAAATGGTATTTTTGGAAGGTTCGA-GGT
*
1030 -AAAATGGTAATTTT
1 CAAAATGGTATTTTT
1044 CGGACAGTTT
Statistics
Matches: 412, Mismatches: 52, Indels: 101
0.73 0.09 0.18
Matches are distributed among these distances:
26 3 0.01
27 9 0.02
28 65 0.16
29 153 0.37
30 128 0.31
31 50 0.12
32 4 0.01
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (29 bp):
CAAAATGGTATTTTTGGAAGGTTCGAGGT
Found at i:592 original size:59 final size:59
Alignment explanation
Indices: 502--1043 Score: 718
Period size: 59 Copynumber: 9.2 Consensus size: 59
492 GCACGGGAGC
* * * * *
502 AAAATGGT-AGTTTTGGAAGGTTTGAAGTCAAAAATGAGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
560 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATAGGATTTTTAGAAGTTTTGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGGT
* * *
620 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTATT-TAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTT-TTGGAAGTTCGGGGGT
* * * * * *
679 AAAATAGTAATTTTTAGAAGGTTCGGGGTCAAAAATTGGATTTTTTGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
738 -AAATGGTAATTTTTAGAAGGTTCGAGTTCACAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
796 AAAATGGTAATTTTTTGAAGGTTCGAGATCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * *
855 AAATTGGTAATTTTTGAAAGGTTCGGGGTC-AAAATGGGATTTTTGGAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
913 AAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * *
972 AAAATGGTAATTTTAGGAATGTTC-AGGATCAAAAAT-GAATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGAGG-TCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1030 AAAATGGTAATTTT
1 AAAATGGTAATTTT
1044 CGGACAGTTT
Statistics
Matches: 436, Mismatches: 41, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
58 154 0.35
59 230 0.53
60 50 0.11
61 2 0.00
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:799 original size:117 final size:117
Alignment explanation
Indices: 502--1043 Score: 704
Period size: 117 Copynumber: 4.6 Consensus size: 117
492 GCACGGGAGC
* * * * * *
502 AAAATGGT-AGTTTTGGAAGGTTTGAAGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATG
1 AAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATG
* * * *
566 GTAATTTTTGGAAGGTTCGAGGTCAAAAATAGGATTTTTAGAAGTTTTGGGGGT
66 GTAATTTTT-GAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAG-TTCGAGGGT
* *
620 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTATT-TAAGTTCGGGGGTAAAAT
1 AAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTT-TTGGAAGTTCGGGGGTAAAAT
* * * *
684 AGTAATTTTTAGAAGGTTCGGGGTCAAAAATTGGATTTTTTGAAGTTCGAGGGT
65 GGTAATTTTT-GAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* *
738 -AAATGGTAATTTTTAGAAGGTTCGAGTTCACAAATGGGATTTTTGGAAGTTCGGGGGTAAAATG
1 AAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATG
* *
802 GTAATTTTTTGAAGGTTCGAGATCAAAAATGGGATTTTTGGAAGTTCGGGGGT
66 GTAA-TTTTTGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
855 AAATTGGTAATTTTT-GAAAGGTTCGGGGTC-AAAATGGGATTTTTGGAAGTTTGGGGGTAAAAT
1 AAAATGGTAATTTTTAG-AAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAT
*
918 GGTAATTTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
65 GGTAATTTTTG-AAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
972 AAAATGGTAA-TTTTAGGAATGTTC-AGGATCAAAAAT-GAATTTTTGGAAGTTCGAGGGTAAAA
1 AAAATGGTAATTTTTA-GAAGGTTCGAGG-TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAA
1034 TGGTAATTTT
64 TGGTAATTTT
1044 CGGACAGTTT
Statistics
Matches: 374, Mismatches: 39, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
116 14 0.04
117 224 0.60
118 50 0.13
119 84 0.22
120 2 0.01
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (117 bp):
AAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATG
GTAATTTTTGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
Found at i:2091 original size:19 final size:19
Alignment explanation
Indices: 2064--2100 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2054 TTTTCGTTTT
*
2064 ATTATTATTATTATTATTC
1 ATTAATATTATTATTATTC
2083 ATTAATATTATTATTATT
1 ATTAATATTATTATTATT
2101 AAAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTAATATTATTATTATTC
Found at i:2116 original size:21 final size:20
Alignment explanation
Indices: 2086--2124 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2076 ATTATTCATT
*
2086 AATATTATTATTATTAAAAA
1 AATATTATTATTAATAAAAA
2106 AATATTTATTATTAATAAA
1 AATA-TTATTATTAATAAA
2125 TATTATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATTATTATTAATAAAAA
Found at i:2119 original size:3 final size:3
Alignment explanation
Indices: 2062--2101 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
2052 ACTTTTCGTT
*
2062 TTA TTA TTA TTA TTA TTA TTCA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
2102 AAAAAATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2935 original size:12 final size:11
Alignment explanation
Indices: 2918--2958 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
2908 ATAGTAATTT
2918 TAAATTTGAAAA
1 TAAATTT-AAAA
2930 TAAATTTAAAA
1 TAAATTTAAAA
2941 T---TTTAAAA
1 TAAATTTAAAA
2949 TAAATTTAAA
1 TAAATTTAAA
2959 GAGAGTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.31
11 11 0.42
12 7 0.27
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:2939 original size:18 final size:17
Alignment explanation
Indices: 2898--2958 Score: 68
Period size: 19 Copynumber: 3.4 Consensus size: 17
2888 TTTTAGCGTT
* *
2898 ATTTAAATTTATAGTAA
1 ATTTAAATTTAAAATAA
*
2915 TTTTAAATTTGAAAATAA
1 ATTTAAATTT-AAAATAA
2933 ATTTAAAATTTTAAAATAA
1 ATTT-AAA-TTTAAAATAA
2952 ATTTAAA
1 ATTTAAA
2959 GAGAGTTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 9 0.24
18 11 0.30
19 14 0.38
20 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:2941 original size:19 final size:19
Alignment explanation
Indices: 2913--2958 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2903 AATTTATAGT
*
2913 AATTTTAAATTTGAAAATA
1 AATTTAAAATTTGAAAATA
*
2932 AATTTAAAATTTTAAAATA
1 AATTTAAAATTTGAAAATA
2951 AATTTAAA
1 AATTTAAA
2959 GAGAGTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTTAAAATTTGAAAATA
Found at i:20529 original size:15 final size:16
Alignment explanation
Indices: 20509--20544 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
20499 ACCTTATAAC
20509 TATTTTTT-AAGTTAA
1 TATTTTTTAAAGTTAA
*
20524 TATTTTTTAAATTTAA
1 TATTTTTTAAAGTTAA
20540 TATTT
1 TATTT
20545 AAAATAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TATTTTTTAAAGTTAA
Found at i:21152 original size:26 final size:26
Alignment explanation
Indices: 21123--21180 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
21113 TGAAATGATT
21123 ATATAAAAAATTTTAATAAATA-AAAA
1 ATATAAAAAA-TTTAATAAATATAAAA
* *
21149 ATAT-ATAAATTTATTAAATATTAAAA
1 ATATAAAAAATTTAATAAATA-TAAAA
21175 ATATAA
1 ATATAA
21181 TATATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 10 0.37
25 4 0.15
26 12 0.44
27 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATAAAAAATTTAATAAATATAAAA
Found at i:21173 original size:27 final size:27
Alignment explanation
Indices: 21143--21204 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
21133 TTTTAATAAA
21143 TAAAAAATAT-ATAAATTTATTAAATAT
1 TAAAAAATATAATAAATTTATTAAAT-T
* *
21170 T-AAAAATATAATATATTTTTTAAATT
1 TAAAAAATATAATAAATTTATTAAATT
21196 TAAAAAATA
1 TAAAAAATA
21205 ATATGTGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAAAAATATAATAAATTTATTAAATT
Found at i:21198 original size:26 final size:27
Alignment explanation
Indices: 21145--21208 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 27
21135 TTAATAAATA
*
21145 AAAAATAT-ATAAATTTATTAAATATT
1 AAAAATATAATATATTTATTAAATATT
*
21171 AAAAATATAATATATTTTTTAAAT-TT
1 AAAAATATAATATATTTATTAAATATT
21197 AAAAA-ATAATAT
1 AAAAATATAATAT
21209 GTGTGAACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 7 0.20
26 15 0.43
27 13 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AAAAATATAATATATTTATTAAATATT
Found at i:22554 original size:22 final size:22
Alignment explanation
Indices: 22510--22597 Score: 63
Period size: 24 Copynumber: 3.8 Consensus size: 22
22500 TTTCTTTAAA
*
22510 AATATTTATATTATTTT-TAATTT
1 AATATTTA-ATAATTTTAT-ATTT
22533 AATATTTAATAATTTTATATTTTT
1 AATATTTAATAATTTTATA--TTT
* *
22557 AATTTATTAA-AATTTTATATAT
1 AATAT-TTAATAATTTTATATTT
*
22579 AATCATTTTAATATTTTTA
1 AAT-A-TTTAATAATTTTA
22598 ATGATTACAT
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
22 13 0.25
23 13 0.25
24 23 0.43
25 4 0.08
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (22 bp):
AATATTTAATAATTTTATATTT
Found at i:22570 original size:24 final size:24
Alignment explanation
Indices: 22530--22576 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
22520 TTATTTTTAA
22530 TTTAATATTTAATAATTTTATATT
1 TTTAATATTTAATAATTTTATATT
*
22554 TTTAATTTATTAA-AATTTTATAT
1 TTTAATAT-TTAATAATTTTATAT
22577 ATAATCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTAATATTTAATAATTTTATATT
Found at i:23407 original size:19 final size:19
Alignment explanation
Indices: 23373--23409 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
23363 ACACACCCCC
23373 AAATTATTATTGAAATTTT
1 AAATTATTATTGAAATTTT
23392 AAATTGATTATT-AAATTT
1 AAATT-ATTATTGAAATTT
23410 CAAAACATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
AAATTATTATTGAAATTTT
Found at i:30113 original size:6 final size:6
Alignment explanation
Indices: 30102--30139 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
30092 TATAAAATTC
*
30102 AATTTA AATTTA AATTTA ATTTTA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA
30140 AAATAAGAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:33247 original size:51 final size:52
Alignment explanation
Indices: 33125--33248 Score: 144
Period size: 51 Copynumber: 2.4 Consensus size: 52
33115 GTATGTAAGT
* * *
33125 TTTGCAGGTTAAATTTGTTAAATCAGAGGATCAAGCTGACAGAATGTGTAAA
1 TTTGAAGGTTAAATTTGTTAAATCAGAGGATCAAACTGACAAAATGTGTAAA
* * * *
33177 TGTTGTAGGCTAAATTTGTTAAGTCA-A-GATCAAATTGACAAAATGTGTAAA
1 T-TTGAAGGTTAAATTTGTTAAATCAGAGGATCAAACTGACAAAATGTGTAAA
*
33228 CTTTGAAGGTTAAAATTGTTA
1 -TTTGAAGGTTAAATTTGTTA
33249 TTGTATCAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
51 37 0.61
52 3 0.05
53 21 0.34
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (52 bp):
TTTGAAGGTTAAATTTGTTAAATCAGAGGATCAAACTGACAAAATGTGTAAA
Found at i:39661 original size:19 final size:19
Alignment explanation
Indices: 39637--39673 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39627 TTCTATCTAT
39637 TCAATTGTTGATTTTTATC
1 TCAATTGTTGATTTTTATC
* *
39656 TCAATTTTTTATTTTTAT
1 TCAATTGTTGATTTTTAT
39674 TAATTTTAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.08, G:0.05, T:0.65
Consensus pattern (19 bp):
TCAATTGTTGATTTTTATC
Found at i:40083 original size:13 final size:12
Alignment explanation
Indices: 40053--40090 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
40043 AGTATGCTTG
40053 ATTGAAAAAAAA
1 ATTGAAAAAAAA
40065 ATTGAAAAAAGAGA
1 ATTGAAAAAA-A-A
40079 A-TGAAAAAAAA
1 ATTGAAAAAAAA
40090 A
1 A
40091 ATATTACTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.08
12 11 0.46
13 9 0.38
14 2 0.08
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (12 bp):
ATTGAAAAAAAA
Found at i:45520 original size:29 final size:28
Alignment explanation
Indices: 45484--45539 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
45474 AAATTAACAA
* *
45484 TTATAAAAACCGTAAAAATATATAAAATT
1 TTATAAAAACCATAAAAA-ATACAAAATT
*
45513 TTATAAAAATCATAAAAAATACAAAAT
1 TTATAAAAACCATAAAAAATACAAAAT
45540 GCATCAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (28 bp):
TTATAAAAACCATAAAAAATACAAAATT
Found at i:45677 original size:18 final size:17
Alignment explanation
Indices: 45646--45686 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
45636 AAATGTGACG
45646 AAAAATGATAAAAAAAT
1 AAAAATGATAAAAAAAT
*
45663 AAAAATTATAGAAAAAAT
1 AAAAATGATA-AAAAAAT
45681 ATAAAA
1 A-AAAA
45687 AGTTTCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 8 0.38
19 4 0.19
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (17 bp):
AAAAATGATAAAAAAAT
Found at i:45720 original size:9 final size:9
Alignment explanation
Indices: 45703--45853 Score: 85
Period size: 9 Copynumber: 16.0 Consensus size: 9
45693 TTTTGGTACG
*
45703 ATAACTTTT
1 ATAATTTTT
45712 ATAATTTTTT
1 ATAA-TTTTT
45722 ATGAA-TTTT
1 AT-AATTTTT
45731 AT-ATTCCTTT
1 ATAATT--TTT
45741 ATAATTTTT
1 ATAATTTTT
45750 ATAATTTTCT
1 ATAATTTT-T
* *
45760 -TACTACTTT
1 ATAAT-TTTT
* *
45769 AGAAAATTTT
1 A-TAATTTTT
45779 ATAATTTTT
1 ATAATTTTT
45788 -TATATATTTT
1 ATA-AT-TTTT
45798 ATAATTTTT
1 ATAATTTTT
*
45807 ATGATTTTT
1 ATAATTTTT
45816 ATAATTTTTT
1 ATAA-TTTTT
*
45826 AATATTTTTT
1 -ATAATTTTT
* *
45836 CTAACTTTT
1 ATAATTTTT
*
45845 ATTATTTTT
1 ATAATTTTT
45854 TGCCATATGT
Statistics
Matches: 109, Mismatches: 18, Indels: 30
0.69 0.11 0.19
Matches are distributed among these distances:
7 1 0.01
8 3 0.03
9 60 0.55
10 34 0.31
11 11 0.10
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:45730 original size:11 final size:10
Alignment explanation
Indices: 45708--45854 Score: 80
Period size: 10 Copynumber: 15.4 Consensus size: 10
45698 GTACGATAAC
45708 TTTTATAATT
1 TTTTATAATT
45718 TTTTATGAA--
1 TTTTAT-AATT
45727 TTTTAT-ATT
1 TTTTATAATT
*
45736 CCTTTATAA-T
1 -TTTTATAATT
45746 TTTTATAATT
1 TTTTATAATT
* * *
45756 TTCT-TACTA
1 TTTTATAATT
* * **
45765 CTTTAGAAAA
1 TTTTATAATT
45775 TTTTATAATT
1 TTTTATAATT
*
45785 TTTTAT-ATA
1 TTTTATAATT
45794 TTTTATAA-T
1 TTTTATAATT
*
45803 TTTTATGA-T
1 TTTTATAATT
45812 TTTTATAATT
1 TTTTATAATT
45822 TTTTA-ATATT
1 TTTTATA-ATT
* *
45832 TTTTCTAA-C
1 TTTTATAATT
*
45841 TTTTATTATT
1 TTTTATAATT
45851 TTTT
1 TTTT
45855 GCCATATGTC
Statistics
Matches: 102, Mismatches: 23, Indels: 24
0.68 0.15 0.16
Matches are distributed among these distances:
7 1 0.01
9 48 0.47
10 49 0.48
11 4 0.04
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:45732 original size:19 final size:19
Alignment explanation
Indices: 45708--45826 Score: 75
Period size: 19 Copynumber: 5.8 Consensus size: 19
45698 GTACGATAAC
45708 TTTTATAATTTTTTATGAA
1 TTTTATAATTTTTTATGAA
*
45727 TTTTAT-ATTCCTTTAT-AA
1 TTTTATAATT-TTTTATGAA
45745 TTTTTATAATTTTCTTACTACTTTAGAAAA
1 -TTTTATAA-TTT-TT--TA---T-G-A-A
45775 TTTTATAATTTTTTAT-ATA
1 TTTTATAATTTTTTATGA-A
*
45794 TTTTATAA-TTTTTATGAT
1 TTTTATAATTTTTTATGAA
45812 TTTTATAATTTTTTA
1 TTTTATAATTTTTTA
45827 ATATTTTTTC
Statistics
Matches: 80, Mismatches: 4, Indels: 32
0.69 0.03 0.28
Matches are distributed among these distances:
18 20 0.25
19 34 0.43
20 1 0.01
21 4 0.05
22 1 0.01
23 2 0.03
25 2 0.03
26 1 0.01
27 2 0.03
28 3 0.04
29 9 0.11
30 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTTATAATTTTTTATGAA
Found at i:45742 original size:29 final size:27
Alignment explanation
Indices: 45709--45814 Score: 95
Period size: 28 Copynumber: 3.7 Consensus size: 27
45699 TACGATAACT
*
45709 TTTATAATTTTTTATGAATTTTATATTCC
1 TTTATAA-TTTTTAT-AATTTTATATTAC
* *
45738 TTTATAATTTTTATAATTTTCTTACTAC
1 TTTATAATTTTTATAATTTT-ATATTAC
* * * *
45766 TTTAGAAAATTTTATAATTTTTTATATAT
1 TTTA-TAATTTTTATAATTTTATAT-TAC
*
45795 TTTATAATTTTTATGATTTT
1 TTTATAATTTTTATAATTTT
45815 TATAATTTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
27 6 0.09
28 31 0.48
29 27 0.42
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (27 bp):
TTTATAATTTTTATAATTTTATATTAC
Found at i:45815 original size:28 final size:27
Alignment explanation
Indices: 45708--45852 Score: 100
Period size: 29 Copynumber: 5.1 Consensus size: 27
45698 GTACGATAAC
45708 TTTTATAATTTTTTATGAA-TTTTATAT-
1 TTTTATAA-TTTTTAT-AATTTTTATATA
45735 TCCTTTATAATTTTTATAATTTTCT-TACTA
1 T--TTTATAATTTTTATAATTTT-TATA-TA
* * *
45765 CTTTAGAAAATTTTATAATTTTTTATATA
1 TTTTA-TAATTTTTATAA-TTTTTATATA
* *
45794 TTTTATAATTTTTATGATTTTTATAATT
1 TTTTATAATTTTTATAATTTTTAT-ATA
* * *
45822 TTTTAATATTTTTTCTAACTTTTAT-TA
1 TTTT-ATAATTTTTATAATTTTTATATA
45849 TTTT
1 TTTT
45853 TTGCCATATG
Statistics
Matches: 94, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
27 15 0.16
28 31 0.33
29 42 0.45
30 6 0.06
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (27 bp):
TTTTATAATTTTTATAATTTTTATATA
Found at i:45832 original size:19 final size:18
Alignment explanation
Indices: 45775--45834 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 18
45765 CTTTAGAAAA
45775 TTTTATAATTTTTTATAT
1 TTTTATAATTTTTTATAT
45793 ATTTTATAA-TTTTTATGAT
1 -TTTTATAATTTTTTAT-AT
45812 TTTTATAATTTTTTAATAT
1 TTTTATAATTTTTT-ATAT
45831 TTTT
1 TTTT
45835 TCTAACTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
18 15 0.39
19 21 0.55
20 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTATAATTTTTTATAT
Found at i:45852 original size:18 final size:18
Alignment explanation
Indices: 45775--45853 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 18
45765 CTTTAGAAAA
45775 TTTTATAATTTTT-TATAT
1 TTTTATAATTTTTAT-TAT
*
45793 ATTTTATAATTTTTATGAT
1 -TTTTATAATTTTTATTAT
*
45812 TTTTATAATTTTTTAATATT
1 TTTTATAA-TTTTTATTA-T
* *
45832 TTTTCTAACTTTTATTAT
1 TTTTATAATTTTTATTAT
45850 TTTT
1 TTTT
45854 TGCCATATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
18 13 0.25
19 29 0.57
20 9 0.18
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.70
Consensus pattern (18 bp):
TTTTATAATTTTTATTAT
Found at i:48169 original size:2 final size:2
Alignment explanation
Indices: 48162--48190 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
48152 TTTATTATCG
48162 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48191 CTACAAACCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48380 original size:26 final size:25
Alignment explanation
Indices: 48324--48372 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
48314 TAAAAGTACA
* *
48324 ATTTTATTATTTTAAAATAGTTTAT
1 ATTTTATTATTTTAAAAGAGTTAAT
48349 ATTTTTATTATTTTAAAAGA-TTAA
1 A-TTTTATTATTTTAAAAGAGTTAA
48373 ATTATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
ATTTTATTATTTTAAAAGAGTTAAT
Found at i:48438 original size:16 final size:16
Alignment explanation
Indices: 48419--48467 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
48409 AATTTTATTG
*
48419 TTATTAAATTAAAATT
1 TTATTAAATTAAAATA
48435 TTA-TAAATTATAAATA
1 TTATTAAATTA-AAATA
*
48451 AT-TTAAATTAAAA-A
1 TTATTAAATTAAAATA
48465 TTA
1 TTA
48468 CTATTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
14 2 0.07
15 10 0.37
16 15 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTATTAAATTAAAATA
Found at i:68519 original size:22 final size:22
Alignment explanation
Indices: 68494--68546 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
68484 ACGTGTTCAA
68494 TTTTTAAATAAATTGATATAA-C
1 TTTTTAAATAAA-TGATATAAGC
** * *
68516 TTTTTTTATTAATGATATAAGT
1 TTTTTAAATAAATGATATAAGC
68538 TTTTTAAAT
1 TTTTTAAAT
68547 TAAAGAAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTTTAAATAAATGATATAAGC
Found at i:68548 original size:22 final size:23
Alignment explanation
Indices: 68494--68549 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
68484 ACGTGTTCAA
*
68494 TTTTTAAATAAATTGATATAACT
1 TTTTTAAATTAATTGATATAACT
* *
68517 TTTTT-TATTAA-TGATATAAGT
1 TTTTTAAATTAATTGATATAACT
68538 TTTTTAAATTAA
1 TTTTTAAATTAA
68550 AGAAAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 14 0.50
22 9 0.32
23 5 0.18
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (23 bp):
TTTTTAAATTAATTGATATAACT
Found at i:69516 original size:11 final size:10
Alignment explanation
Indices: 69487--69516 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
69477 AACATAAAAA
69487 AAAATTAAAG
1 AAAATTAAAG
69497 AAAATTAAAG
1 AAAATTAAAG
69507 AAAATATAAA
1 AAAAT-TAAA
69517 TATACATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (10 bp):
AAAATTAAAG
Found at i:75838 original size:52 final size:52
Alignment explanation
Indices: 75767--75871 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
75757 GAGTTTTGAT
* *
75767 AATTTTATAGCTAAGTTAAAATTTGATTTATGGATGATACTAAGTTAATCAA
1 AATTTTATAACTAAATTAAAATTTGATTTATGGATGATACTAAGTTAATCAA
75819 AATTTTATAACTAAATTAAAATTTGATTTATGGATGATACTAAGTTAATCAA
1 AATTTTATAACTAAATTAAAATTTGATTTATGGATGATACTAAGTTAATCAA
75871 A
1 A
75872 CTCTTAAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (52 bp):
AATTTTATAACTAAATTAAAATTTGATTTATGGATGATACTAAGTTAATCAA
Done.