Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010605.1 Kokia drynarioides strain JFW-HI SEQ_125537, 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: 18565
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:343 original size:3 final size:3
Alignment explanation
Indices: 337--387 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
327 ATTATATTAT
* * * * *
337 TAA TAA TAT TTA T-A TAA TAA TAA TAA TAA TAA TAA TGA CAC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
384 TAA T
1 TAA T
388 TTTTAATGAT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1534 original size:31 final size:30
Alignment explanation
Indices: 1462--1570 Score: 155
Period size: 30 Copynumber: 3.6 Consensus size: 30
1452 ATTGTTCAAC
* ** *
1462 AATCCCATTTTTAACCCCAAAACTTCCAAA
1 AATCCCATTTTTTACCCCCGAACTTCTAAA
1492 AATCCCATTTTTTACCCCCGAACTTCTAAA
1 AATCCCATTTTTTACCCCCGAACTTCTAAA
*
1522 AATCCCATTTTTTTACCCTCGAACTTCTAAA
1 AATCCCA-TTTTTTACCCCCGAACTTCTAAA
*
1553 AATCCCATTTTTGACCCC
1 AATCCCATTTTTTACCCC
1571 GAATTTTTCC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
30 42 0.59
31 29 0.41
ACGTcount: A:0.31, C:0.33, G:0.03, T:0.33
Consensus pattern (30 bp):
AATCCCATTTTTTACCCCCGAACTTCTAAA
Found at i:11695 original size:117 final size:117
Alignment explanation
Indices: 11550--11784 Score: 407
Period size: 117 Copynumber: 2.0 Consensus size: 117
11540 TCTCTATCTT
* *
11550 TCTCAGCACATAATCCCCTTTCTCATCTATCTATTTATACTATTTCGACTCTCCATCTGTCTAAA
1 TCTCAACACATAATCCCCTTTCTCATCTATCTATTTATACTATTTCGACTCTCCATCTATCTAAA
*
11615 TGAATCAATTTACTTCGCACCACCATTTCGTTCTATGTTTTTATGTCCTTCC
66 TGAATCAATTTACTTCGCACCACCATTTCGTTCTATGTTTTTATCTCCTTCC
* *
11667 TCTCAACACATAATCCCTTTTCTCATCTATCTATTTATACTATTTCGATTCTCCATCTATCTAAA
1 TCTCAACACATAATCCCCTTTCTCATCTATCTATTTATACTATTTCGACTCTCCATCTATCTAAA
* *
11732 TGAATCAATTTACTTTGCACCACCATTTTGTTCTATGTTTTTATCTCCTTCC
66 TGAATCAATTTACTTCGCACCACCATTTCGTTCTATGTTTTTATCTCCTTCC
11784 T
1 T
11785 TATTACTACT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 111 1.00
ACGTcount: A:0.23, C:0.28, G:0.06, T:0.44
Consensus pattern (117 bp):
TCTCAACACATAATCCCCTTTCTCATCTATCTATTTATACTATTTCGACTCTCCATCTATCTAAA
TGAATCAATTTACTTCGCACCACCATTTCGTTCTATGTTTTTATCTCCTTCC
Found at i:12071 original size:6 final size:6
Alignment explanation
Indices: 12060--12085 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12050 CTTTCTCCCT
12060 TATACA TATACA TATACA TATACA TA
1 TATACA TATACA TATACA TATACA TA
12086 AGGTCACCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
TATACA
Found at i:12664 original size:4 final size:4
Alignment explanation
Indices: 12655--12685 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
12645 TGCATAAAAA
12655 TTCT TTCT TTCT TTCT TTCT TTCT TTACT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT-CT TT
12686 GGGTTTGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:12876 original size:3 final size:3
Alignment explanation
Indices: 12868--12897 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
12858 AATGGTTTGG
*
12868 GAA GAA GAA GAA GAA GAA GAA GGA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
12898 TAGCAGTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:13252 original size:13 final size:13
Alignment explanation
Indices: 13234--13258 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13224 TATTAAGATA
13234 AATTTGATAATTC
1 AATTTGATAATTC
13247 AATTTGATAATT
1 AATTTGATAATT
13259 TGAAAGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
AATTTGATAATTC
Found at i:13567 original size:20 final size:20
Alignment explanation
Indices: 13542--13605 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
13532 AATTATATAA
13542 AACTTTGGGAACTAAATTAT
1 AACTTTGGGAACTAAATTAT
* * *
13562 AACTTT--TATACTATA-TAA
1 AACTTTGGGA-ACTAAATTAT
13580 AACTTTGGGAACTAAATTAT
1 AACTTTGGGAACTAAATTAT
13600 AACTTT
1 AACTTT
13606 TGTTTTATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
18 9 0.26
19 10 0.29
20 15 0.44
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (20 bp):
AACTTTGGGAACTAAATTAT
Found at i:13593 original size:19 final size:19
Alignment explanation
Indices: 13535--13593 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
13525 CACAAAAAAT
13535 TATATAAAACTTTGGGAAC
1 TATATAAAACTTTGGGAAC
* * *
13554 TAAATTATAACTTT--TATAC
1 TATA-TAAAACTTTGGGA-AC
13573 TATATAAAACTTTGGGAAC
1 TATATAAAACTTTGGGAAC
13592 TA
1 TA
13594 AATTATAACT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
18 9 0.30
19 12 0.40
20 9 0.30
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (19 bp):
TATATAAAACTTTGGGAAC
Found at i:13600 original size:22 final size:22
Alignment explanation
Indices: 13537--13601 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
13527 CAAAAAATTA
13537 TATAAAACTTTGGGAACTAAAT
1 TATAAAACTTTGGGAACTAAAT
*
13559 TAT--AACTTT--TATACT--A-
1 TATAAAACTTTGGGA-ACTAAAT
13575 TATAAAACTTTGGGAACTAAAT
1 TATAAAACTTTGGGAACTAAAT
13597 TATAA
1 TATAA
13602 CTTTTGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
16 3 0.09
17 1 0.03
18 7 0.21
19 6 0.18
20 7 0.21
21 1 0.03
22 8 0.24
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (22 bp):
TATAAAACTTTGGGAACTAAAT
Found at i:14648 original size:96 final size:96
Alignment explanation
Indices: 14464--14655 Score: 239
Period size: 96 Copynumber: 2.0 Consensus size: 96
14454 TCTTTACGAA
* *
14464 AAGGATATTTGATTATTTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCG
1 AAGGATATTCGATTATTTCGATTTGAAGAAAGATTGCACCTAGTAAGTTAAGGCGCAATATTTCG
* * *
14529 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 AAACCGAAGATAAAGAAACATTGCCTCGATT
* *
14560 AAGGGTATTCGATTATTTCGATTTGAAGAGAA-ATTGCACCTAGTGAGTTAAGGCGCAA-ATTTT
1 AAGGATATTCGATTATTTCGATTTGAAGA-AAGATTGCACCTAGTAAGTTAAGGCGCAATA-TTT
* *
14623 TGAAACCCGAA-ATGAAAG-AATATTGCCTCGATT
64 CGAAA-CCGAAGAT-AAAGAAACATTGCCTCGATT
14656 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
95 1 0.01
96 73 0.88
97 9 0.11
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATTTCGATTTGAAGAAAGATTGCACCTAGTAAGTTAAGGCGCAATATTTCG
AAACCGAAGATAAAGAAACATTGCCTCGATT
Found at i:14895 original size:30 final size:30
Alignment explanation
Indices: 14861--14923 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
14851 ATCGGTGTTC
* * *
14861 AAAATGAGACTTTTCTGATTCTC-GGTGGCA
1 AAAATGAGAATTTT-GGATTCTCGGGGGGCA
*
14891 AAAATGATAATTTTGGATTCTCGGGGGGCA
1 AAAATGAGAATTTTGGATTCTCGGGGGGCA
14921 AAA
1 AAA
14924 CGATAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (30 bp):
AAAATGAGAATTTTGGATTCTCGGGGGGCA
Found at i:14909 original size:29 final size:29
Alignment explanation
Indices: 14877--14935 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
14867 AGACTTTTCT
* *
14877 GATTCTC-GGTGGCAAAAATGATAATTTTG
1 GATTCTCGGGGGGC-AAAACGATAATTTTG
14906 GATTCTCGGGGGGCAAAACGATAATTTTG
1 GATTCTCGGGGGGCAAAACGATAATTTTG
14935 G
1 G
14936 GAAAATTCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.31
Consensus pattern (29 bp):
GATTCTCGGGGGGCAAAACGATAATTTTG
Found at i:15041 original size:59 final size:57
Alignment explanation
Indices: 14950--15392 Score: 272
Period size: 59 Copynumber: 7.6 Consensus size: 57
14940 ATTCGGTGTT
* * * *
14950 AAAAATGGACCTTTTGGACA-TCCGAGGGTAAAATGGTAATTTTAGGAAGTTTCGGAGTC
1 AAAAATGGA-ATTTTGGA-AGTTCGAGGGTAAAATGGTAATTTTA-GAAGTTTAGGGGTC
* * *
15009 AAAAATGGAATTTTGGGAAGTTCGATGCTAAAAATGG-AATTTTTAGAAGTTTTA-GGGTT
1 AAAAATGGAATTTT-GGAAGTTCGAGGGT-AAAATGGTAA-TTTTAGAAG-TTTAGGGGTC
* * * *
15068 AAAAATGGAATTTTGGAAGTTCTAGGGTCAAAAATGAG-ATTTTTAGAAGTTAAGGGGTA
1 AAAAATGGAATTTTGGAAGTTCGAGGGT--AAAATG-GTAATTTTAGAAGTTTAGGGGTC
* * *
15127 AAAAATGGGATTTTTGGAAGTT-TAGGGGTAAAATGGTAAATTTTAGAAGTTTTGGGGT-
1 AAAAAT-GGAATTTTGGAAGTTCGA-GGGTAAAATGGT-AATTTTAGAAGTTTAGGGGTC
* * ** * * *
15185 TAAAATGAGATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTT
1 AAAAATG-GAATTTTGGAAGTTCGAGGGTAAAATGGTAA-TTTTAGAAGTTTAGGGGTC
** ** **** * * *
15244 AAAAACAGAATTTTTTAAGTTCGAGGGTAAAAACAAAATTTTTGGAAATTTTGGGGTC
1 AAAAATGGAATTTTGGAAGTTCGAGGGTAAAATGGTAA-TTTTAGAAGTTTAGGGGTC
* * * * * * * *
15302 AAAAATGGGATTTTGGGAAGTTCGGGGGAAAAAATAG-AATTTTTGGAAATTTCGGGTTC
1 AAAAATGGAATTTT-GGAAGTTCGAGGG-TAAAATGGTAA-TTTTAGAAGTTTAGGGGTC
* *
15361 GAAAATGGATTTTTGGAAGTTCG-GTGGTAAAA
1 AAAAATGGAATTTTGGAAGTTCGAG-GGTAAAA
15393 ATAGAATTTT
Statistics
Matches: 311, Mismatches: 54, Indels: 40
0.77 0.13 0.10
Matches are distributed among these distances:
57 9 0.03
58 131 0.42
59 132 0.42
60 39 0.13
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (57 bp):
AAAAATGGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTAGAAGTTTAGGGGTC
Found at i:15042 original size:29 final size:26
Alignment explanation
Indices: 14979--15089 Score: 87
Period size: 30 Copynumber: 3.8 Consensus size: 26
14969 ATCCGAGGGT
14979 AAAATGGTAATTTTAGGAAGTTTCGGAGTCA
1 AAAATGG-AATTTT-GGAAG-TTC-GAGT-A
15010 AAAATGGAATTTTGGGAAGTTCGATGCTA
1 AAAATGGAATTTT-GGAAGTTCGA-G-TA
* * *
15039 AAAATGGAATTTTTAGAAGTTTTAGGGTTA
1 AAAATGGAA-TTTTGGAAG--TTCGAG-TA
15069 AAAATGGAATTTTGGAAGTTC
1 AAAATGGAATTTTGGAAGTTC
15090 TAGGGTCAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
27 2 0.03
28 2 0.03
29 26 0.38
30 28 0.41
31 10 0.15
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (26 bp):
AAAATGGAATTTTGGAAGTTCGAGTA
Found at i:15093 original size:29 final size:28
Alignment explanation
Indices: 14979--15416 Score: 188
Period size: 29 Copynumber: 14.9 Consensus size: 28
14969 ATCCGAGGGT
* *
14979 AAAATGGTAATTTTAGGAAGTTTCGGAGTCA
1 AAAATGG-AATTTT-GGAAGTTTAGG-GTTA
* * *
15010 AAAATGGAATTTTGGGAAG-TTCGATGCTA
1 AAAATGGAATTTT-GGAAGTTTAG-GGTTA
*
15039 AAAATGGAATTTTTAGAAGTTTTAGGGTTA
1 AAAATGGAA-TTTTGGAAG-TTTAGGGTTA
*
15069 AAAATGGAATTTTGGAAGTTCTAGGGTCA
1 AAAATGGAATTTTGGAAGTT-TAGGGTTA
* * * *
15098 AAAATGAGATTTTTAGAAGTTAAGGGGTAA
1 AAAATG-GAATTTTGGAAGTTTA-GGGTTA
* *
15128 AAAATGGGATTTTTGGAAGTTTAGGGGT-
1 AAAAT-GGAATTTTGGAAGTTTAGGGTTA
* *
15156 AAAATGGTAAATTTTAGAAGTTTTGGGGTT-
1 AAAATGG--AATTTTGGAAG-TTTAGGGTTA
*
15186 AAAATGAGATTTTTGGAAGTTTAAGGG-T-
1 AAAATG-GAATTTTGGAAGTTT-AGGGTTA
* *
15214 AAAATGGTAATTTTTAGAAGTTTCGAGGTTA
1 AAAATGG-AA-TTTTGGAAGTTTAG-GGTTA
** ** *
15245 AAAACAGAATTTTTTAAGTTCGAGGG-TA
1 AAAATGGAATTTTGGAAGTT-TAGGGTTA
*** * * *
15273 AAAACAAAATTTTTGGAAATTTTGGGGTCA
1 AAAATGGAA-TTTTGG-AAGTTTAGGGTTA
* ** **
15303 AAAATGGGATTTTGGGAAGTTCGGGGGAA
1 AAAATGGAATTTT-GGAAGTTTAGGGTTA
* * * *
15332 AAAATAGAATTTTTGGAAATTTCGGGTTCG
1 AAAATGGAA-TTTTGGAAGTTTAGGGTT-A
* * *
15362 AAAATGGATTTTTGGAAG-TTCGGTGGTA
1 AAAATGGAATTTTGGAAGTTTAGG-GTTA
* *
15390 AAAATAGAATTTTTTGACAGTTTAGGG
1 AAAATGGAA-TTTTGGA-AGTTTAGGG
15417 ACCTCCGGGG
Statistics
Matches: 312, Mismatches: 66, Indels: 59
0.71 0.15 0.14
Matches are distributed among these distances:
27 3 0.01
28 41 0.13
29 141 0.45
30 106 0.34
31 21 0.07
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAGTTTAGGGTTA
Found at i:15382 original size:58 final size:59
Alignment explanation
Indices: 14987--15403 Score: 263
Period size: 58 Copynumber: 7.1 Consensus size: 59
14977 GTAAAATGGT
* * * * ** * *
14987 AATTTTAGGAAGTTTCGGAGTCAAAAATGGAATTTTGGGAAGTTCGATGCTAAAAATGG
1 AATTTTTGGAAATTTCGGGGTCAAAAATGGGATTTTGGGAAGTTCGGGGGTAAAAATAG
* * ** * * **
15046 AATTTTTAGAAGTTTTAGGGTTAAAAATGGAATTTT-GGAAGTTCTAGGGTCAAAAAT-G
1 AATTTTTGGAAATTTCGGGGTCAAAAATGGGATTTTGGGAAGTTCGGGGGT-AAAAATAG
* * ** * * ** *
15104 AGATTTTTAGAAGTTAAGGGGTAAAAAATGGGATTTTTGGAAGTTTAGGGGT-AAAATGG
1 A-ATTTTTGGAAATTTCGGGGTCAAAAATGGGATTTTGGGAAGTTCGGGGGTAAAAATAG
* * * * * * * *** *
15163 TAAATTTTAGAAGTTTTGGGGT-TAAAATGAGATTTTTGGAAGTTTAAGGGT-AAAATGG
1 -AATTTTTGGAAATTTCGGGGTCAAAAATGGGATTTTGGGAAGTTCGGGGGTAAAAATAG
* * * * ** * ** * * *
15221 TAATTTTTAGAAGTTTCGAGGTTAAAAACAGAATTTT-TTAAGTTCGAGGGTAAAAACAA
1 -AATTTTTGGAAATTTCGGGGTCAAAAATGGGATTTTGGGAAGTTCGGGGGTAAAAATAG
* *
15280 AATTTTTGGAAATTTTGGGGTCAAAAATGGGATTTTGGGAAGTTCGGGGGAAAAAATAG
1 AATTTTTGGAAATTTCGGGGTCAAAAATGGGATTTTGGGAAGTTCGGGGGTAAAAATAG
* * * *
15339 AATTTTTGGAAATTTCGGGTTCGAAAAT-GGATTTTTGGAAGTTCGGTGGTAAAAATAG
1 AATTTTTGGAAATTTCGGGGTCAAAAATGGGATTTTGGGAAGTTCGGGGGTAAAAATAG
15397 AATTTTT
1 AATTTTT
15404 TGACAGTTTA
Statistics
Matches: 292, Mismatches: 58, Indels: 17
0.80 0.16 0.05
Matches are distributed among these distances:
58 142 0.49
59 138 0.47
60 12 0.04
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (59 bp):
AATTTTTGGAAATTTCGGGGTCAAAAATGGGATTTTGGGAAGTTCGGGGGTAAAAATAG
Found at i:17189 original size:12 final size:11
Alignment explanation
Indices: 17172--17216 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
17162 ATAGTAATTT
17172 TAAATTTGAAAA
1 TAAATTT-AAAA
*
17184 TAAATTTAAACT
1 TAAATTTAAA-A
*
17196 TAAATTAAAAA
1 TAAATTTAAAA
17207 TAAATTTAAA
1 TAAATTTAAA
17217 TTTTTAAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 12 0.43
12 16 0.57
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:17193 original size:18 final size:18
Alignment explanation
Indices: 17152--17252 Score: 87
Period size: 18 Copynumber: 5.4 Consensus size: 18
17142 TTTTAACTTT
* *
17152 ATTTAAA-TTTATAGTAA
1 ATTTAAATTTTAAAATAA
* *
17169 TTTTAAATTTGAAAATAA
1 ATTTAAATTTTAAAATAA
17187 ATTTAAACTTAAATTAAAAATAA
1 ATTTAAA-TT---TT-AAAATAA
* *
17210 ATTTAAATTTTTAAACAA
1 ATTTAAATTTTAAAATAA
*
17228 ATTTAATTTTTAAAATAA
1 ATTTAAATTTTAAAATAA
17246 ATTTAAA
1 ATTTAAA
17253 GGGAGTTCGA
Statistics
Matches: 66, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
17 6 0.09
18 39 0.59
19 4 0.06
22 3 0.05
23 14 0.21
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
ATTTAAATTTTAAAATAA
Found at i:17209 original size:23 final size:24
Alignment explanation
Indices: 17171--17216 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
17161 TATAGTAATT
*
17171 TTAAATTTGAAAATAAATTTAAAC
1 TTAAATTTAAAAATAAATTTAAAC
17195 TTAAA-TTAAAAATAAATTTAAA
1 TTAAATTTAAAAATAAATTTAAA
17217 TTTTTAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
TTAAATTTAAAAATAAATTTAAAC
Found at i:18197 original size:199 final size:200
Alignment explanation
Indices: 17615--18301 Score: 1092
Period size: 200 Copynumber: 3.4 Consensus size: 200
17605 TTTCAATCCG
* *
17615 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACTTGCTTCTCAGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCA
* *
17680 GGAAGCTGGGTTTTGAAGATTTCGCTTGTTTTGAGCCTCATTTGGGTCTTCATTTCAGCGTCTCA
66 AGAAGCTGGGTTTTGAAGATTTCGCTTGTTTTGAGCCTCATTTGGGTCTTCTTTTCAGCGTCTCA
** *
17745 TCAGGAAGATGATGGCATCGCTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTT-
131 TCAGGAAGATGATCACATCGCTGTTTAAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTG
17809 GATTCA
196 GA-TCA
* *
17815 CTTCTCAGTATCTCATCTGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCGGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCA
* *
17880 AGAAGCAGGGTTTTAAAGATTTCGCTTGTTTTGAGCCTCATTTGGGTCTTCTTTTCAGCGTCTCA
66 AGAAGCTGGGTTTTGAAGATTTCGCTTGTTTTGAGCCTCATTTGGGTCTTCTTTTCAGCGTCTCA
* *
17945 TCAGGAAGATGATCACATCTCTGTTTAAATCCGCTTCTCTGTATCTAATCAGGAAGACGAATTTG
131 TCAGGAAGATGATCACATCGCTGTTTAAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTG
18010 GATCA
196 GATCA
**
18015 CTTCTCAGTATCTCATTTGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCA
* *
18080 AGAAGCTGAG-TTTGAAGATTTCGCTTGTTTTGAGCCTTATTTGGGTCTTCTTTTCAGCGTCTCA
66 AGAAGCTGGGTTTTGAAGATTTCGCTTGTTTTGAGCCTCATTTGGGTCTTCTTTTCAGCGTCTCA
* *
18144 TCAGGAAGATGATCACATCGCTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGGATTTG
131 TCAGGAAGATGATCACATCGCTGTTTAAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTG
*
18209 GTTCA
196 GATCA
* * * * *
18214 CTTCTCCGTATCTCATCAGGAAGCTAACCGTCTATTGCTTCCACTTGCTTCTCAGTATCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCA
* *
18279 GGAAGCTAGGG-TTCGAAGATTTC
66 AGAAGCT-GGGTTTTGAAGATTTC
18302 ACTCACTTTG
Statistics
Matches: 451, Mismatches: 34, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
199 181 0.40
200 268 0.59
201 2 0.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (200 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCA
AGAAGCTGGGTTTTGAAGATTTCGCTTGTTTTGAGCCTCATTTGGGTCTTCTTTTCAGCGTCTCA
TCAGGAAGATGATCACATCGCTGTTTAAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTG
GATCA
Done.