Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014411.1 Kokia drynarioides strain JFW-HI SEQ_129449, 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: 38504
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:8236 original size:17 final size:18
Alignment explanation
Indices: 8205--8243 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
8195 AATTTAACCT
8205 TAAACTTTACACTTTATG
1 TAAACTTTACACTTTATG
* *
8223 TAAA-TTTACCCTTTATT
1 TAAACTTTACACTTTATG
8240 TAAA
1 TAAA
8244 AAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.46
Consensus pattern (18 bp):
TAAACTTTACACTTTATG
Found at i:8265 original size:24 final size:26
Alignment explanation
Indices: 8236--8293 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 26
8226 ATTTACCCTT
*
8236 TATTTAAAAAATTTAAAACT-AAAAA
1 TATTTAAAAAATTTAAAAATAAAAAA
*
8261 T-TTT-AAAATTTTAAAAATAAAAAA
1 TATTTAAAAAATTTAAAAATAAAAAA
8285 TATTTAAAA
1 TATTTAAAA
8294 CTTTCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 12 0.43
24 9 0.32
25 4 0.14
26 3 0.11
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
TATTTAAAAAATTTAAAAATAAAAAA
Found at i:8908 original size:16 final size:15
Alignment explanation
Indices: 8869--8910 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
8859 TGTAATAAAA
*
8869 TAAAAATTAATTTTT
1 TAAAAATTTATTTTT
*
8884 TAAACATTTATTTTT
1 TAAAAATTTATTTTT
8899 TATAAAATTTAT
1 TA-AAAATTTAT
8911 ATGTACAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAAAATTTATTTTT
Found at i:10699 original size:51 final size:51
Alignment explanation
Indices: 10574--10811 Score: 264
Period size: 51 Copynumber: 4.6 Consensus size: 51
10564 TTTCATTTAA
** ** * *
10574 TACTCACGATGACATATAGTCATCGGACCTCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACCTAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATT
* *
10627 TACTCACGATGACA-CTGAGTCATCGGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACCT-AGTCATCGGACCTTTAATCCATAAAGGATTCATT
* * *
10678 TACTCACGACGACACCTAGTCATCGGACCTTTAATTCGTAAAGGATTCATT
1 TACTCACGATGACACCTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* * *
10729 TACTCACAAT-ATCACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGA-CACCTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
** * *
10780 TACTCATAATGACACTTAGTCATCAGACCTTT
1 TACTCACGATGACACCTAGTCATCGGACCTTT
10812 TCGTTTATAG
Statistics
Matches: 163, Mismatches: 18, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
50 1 0.01
51 122 0.75
52 13 0.08
53 27 0.17
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACCTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:18132 original size:23 final size:23
Alignment explanation
Indices: 18054--18251 Score: 231
Period size: 23 Copynumber: 8.5 Consensus size: 23
18044 TATACGGAAC
* *
18054 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
18076 -AACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
18098 AGGCAACAGAGAGCACACACAGTGCT
1 A---AACAGAGAGCACACAAAGTGCT
18124 AAACAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
18147 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
18170 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
18193 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
18216 AATAACAGAGAGCACGA-GATGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
18241 AAACAGAGAGC
1 AAACAGAGAGC
18252 GCGCTAGTGT
Statistics
Matches: 158, Mismatches: 10, Indels: 15
0.86 0.05 0.08
Matches are distributed among these distances:
21 11 0.07
22 7 0.04
23 98 0.62
24 2 0.01
25 16 0.10
26 24 0.15
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.11
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:21353 original size:15 final size:15
Alignment explanation
Indices: 21335--21363 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21325 TTCTTAGTTT
21335 TTTTTTTTGTTTTTG
1 TTTTTTTTGTTTTTG
21350 TTTTTTTTGTTTTT
1 TTTTTTTTGTTTTT
21364 TATAGGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (15 bp):
TTTTTTTTGTTTTTG
Found at i:21382 original size:29 final size:28
Alignment explanation
Indices: 21350--21447 Score: 72
Period size: 29 Copynumber: 3.3 Consensus size: 28
21340 TTTGTTTTTG
*
21350 TTTTTTTTGTTTTTTATAGGTCAAAAATT
1 TTTTTTTTATTTTTTA-AGGTCAAAAATT
* * **
21379 TTTTTATTAATTTTTAAAGGTCAATTTTTATT
1 TTTTT-TTTATTTTTTAAGGTCAA---AAATT
*
21411 TTTTATTTTA-TTTTTAAGGGTCCAAAATT
1 TTTT-TTTTATTTTTTAA-GGTCAAAAATT
21440 TTTTTTTT
1 TTTTTTTT
21448 TCAACTTTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
28 4 0.08
29 19 0.36
30 8 0.15
31 6 0.11
32 15 0.28
33 1 0.02
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.63
Consensus pattern (28 bp):
TTTTTTTTATTTTTTAAGGTCAAAAATT
Found at i:21445 original size:32 final size:30
Alignment explanation
Indices: 21360--21459 Score: 87
Period size: 32 Copynumber: 3.3 Consensus size: 30
21350 TTTTTTTTGT
* *
21360 TTTTTATAGGTCAAAA-ATTTTTTTATTAA
1 TTTTTAAAGGTCAAAATTTTTTTTTATTAA
** *
21389 TTTTTAAAGGTCAATTTTTATTTTTTATTTTA
1 TTTTTAAAGGTCAAAATTT-TTTTTTA-TTAA
*
21421 TTTTTAAGGGTCCAAAATTTTTTTTT-TTCAA
1 TTTTTAAAGGT-CAAAATTTTTTTTTATT-AA
*
21452 CTTTTAAA
1 TTTTTAAA
21460 AGATTTTAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
29 13 0.24
30 3 0.05
31 14 0.25
32 19 0.35
33 6 0.11
ACGTcount: A:0.29, C:0.06, G:0.07, T:0.58
Consensus pattern (30 bp):
TTTTTAAAGGTCAAAATTTTTTTTTATTAA
Found at i:26896 original size:217 final size:217
Alignment explanation
Indices: 26507--27616 Score: 1446
Period size: 217 Copynumber: 5.0 Consensus size: 217
26497 AACGTTTAAT
* * * * *
26507 ATACTAGAAAAGGATTGAAAGAAATAGTGACATCACGTCATTTGT-ATCTTTTTTTCAATAGTTT
1 ATACTGGAAAAGGATTGAATGAAATAGTGACACCACGTCATTTGTGTTC-CTTTTTCAATAGTTT
* * *
26571 TATG-TCACATCAGTATTTTTATTCTTAATTTCAACATTTTCATTCGGAAAAAATCAAATTAAAA
65 TATGCT-ACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAAATCAAATTAAAA
*
26635 TTAAAATATTGAAATTCAGGATGAAATTATTGATGTGGCATAAAACTATTGGAAAGGGATAATAT
129 TTAAAATCTTGAAATTCAGGATGAAATTATTGATGTGGCATAAAACTATTGGAAAGGGATAATAT
* *
26700 CCCTTTTTCATATAATCTTTTCTC
194 CCCTTTTTCATACAATCCTTTCTC
* * * * *
26724 ATACTGAAAAAGGATTGAATGAAACAGTGATACCACATCATTTGTGTTTCTTTTTCAATAGTTTT
1 ATACTGGAAAAGGATTGAATGAAATAGTGACACCACGTCATTTGTGTTCCTTTTTCAATAGTTTT
* * *
26789 GTGCTACATCATTATTTTTATTCTTAATTTCAACATTTTCATCCTGAAAAAATCAAATTAAAATT
66 ATGCTACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAAATCAAATTAAAATT
* * *
26854 AAAATCTTGAAATTCAGGATAAAATTCTTGATGTGACATAAAACTATTGAAAAGGGTGAAAAGGG
131 AAAATCTTGAAATTCAGGATGAAATTATTGATGTGGCATAAAACTATT-------G-G-AAAGGG
* *
26919 ATAATATCCCTGTTTCATACAATCTTTTCTC
187 ATAATATCCCTTTTTCATACAATCCTTTCTC
* * *
26950 ATACTGGAAAATGATTGAATGAAATAGTGACATCACGTCATTTGTGTCCCTTTTTCAATAGTTTT
1 ATACTGGAAAAGGATTGAATGAAATAGTGACACCACGTCATTTGTGTTCCTTTTTCAATAGTTTT
* *
27015 ATG-TCACATCAGTATTTTCATTCTTAATTTCAATATTTTCATCCTGAAAAAAT-AAAGTGAAAA
66 ATGCT-ACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAAATCAAA-TTAAAA
* *
27078 TTAAAATCTTGAAATTCAGGATGAAATTGTTAATGTGGCATAAAACTATTGGAAAGGGATAATAT
129 TTAAAATCTTGAAATTCAGGATGAAATTATTGATGTGGCATAAAACTATTGGAAAGGGATAATAT
27143 CCCTGTTTT-ATACAATCCTTTCTC
194 CCCT-TTTTCATACAATCCTTTCTC
*
27167 ATACTGGAAAATGATTGAATGAAATAGTGACACCACGTCATTTGTGTCCCTACGTCATTTGTGTT
1 ATACTGGAAAAGGATTGAATGAAATAGTG-----A---CA--------CC-ACGTCATTTGTGTT
* *
27232 CCTTTTTCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCTTGAA
49 CCTTTTTCAATAGTTTTATGCTACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAA
*
27297 AAAATCAAATTAAAATTAAAATCATGAAA-TCTAGGATGAAATTATTGATGTGGCATAAAACTAT
114 AAAATCAAATTAAAATTAAAATCTTGAAATTC-AGGATGAAATTATTGATGTGGCATAAAACTAT
* * *
27361 TGGAAAGAGATAATATTCCTGTTTCATACAATCCTTTCTC
178 TGGAAAGGGATAATATCCCTTTTTCATACAATCCTTTCTC
* *
27401 ATATTGGAAAAGGATTGAATGAAATAGTGACACCACATCATTTGTG-TCCTTTTTTCAATAGTTT
1 ATACTGGAAAAGGATTGAATGAAATAGTGACACCACGTCATTTGTGTTCC-TTTTTCAATAGTTT
* *
27465 TATGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTTATCCTG-AAAAATCAAATTAAAAT
65 TATGCTACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAAATCAAATTAAAAT
* *
27529 TAAAATCTTGAAATTCAGGATGAAATTGTTGATGTGACATAAAACTATTGGAAAGGGATAATAT-
130 TAAAATCTTGAAATTCAGGATGAAATTATTGATGTGGCATAAAACTATTGGAAAGGGATAATATC
*
27593 CTTTATTTCATACAATCCTTTCTC
195 CCTT-TTTCATACAATCCTTTCTC
27617 TTAATATACT
Statistics
Matches: 793, Mismatches: 62, Indels: 77
0.85 0.07 0.08
Matches are distributed among these distances:
215 2 0.00
216 96 0.12
217 288 0.36
218 8 0.01
219 1 0.00
222 1 0.00
224 1 0.00
225 7 0.01
226 192 0.24
229 1 0.00
233 6 0.01
234 187 0.24
235 3 0.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (217 bp):
ATACTGGAAAAGGATTGAATGAAATAGTGACACCACGTCATTTGTGTTCCTTTTTCAATAGTTTT
ATGCTACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAAATCAAATTAAAATT
AAAATCTTGAAATTCAGGATGAAATTATTGATGTGGCATAAAACTATTGGAAAGGGATAATATCC
CTTTTTCATACAATCCTTTCTC
Found at i:27277 original size:234 final size:230
Alignment explanation
Indices: 26761--27616 Score: 1113
Period size: 234 Copynumber: 3.8 Consensus size: 230
26751 TGATACCACA
* * * * *
26761 TCATTTGTGTTTCTTTTTCAATAGTTTTGTGCTACATCATTATTTTTATTCTTAATTTCAACATT
1 TCATTTGTGTTCCTTTTTCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATT
* * *
26826 TTCATCCTGAAAAAATCAAATTAAAATTAAAATCTTGAAATTCAGGATAAAATTCTTGATGTGAC
66 TTCATCCTGAAAAAATCAAATTAAAATTAAAATCTTGAAATTCAGGATGAAATTGTTGATGTGGC
*
26891 ATAAAACTATTGAAAAGGGTGAAAAGGGATAATATCCCTGTTTCATACAATCTTTTCTCATACTG
131 ATAAAACTATT-------G-G-AAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCATACTG
*
26956 GAAAATGATTGAATGAAATAGTG-----ACATC--------ACG
187 GAAAAGGATTGAATGAAATAGTGACACCACATCATTTGTGTACG
* * *
26987 TCATTTGTGTCCCTTTTTCAATAGTTTTATGTCACATCAGTATTTTCATTCTTAATTTCAATATT
1 TCATTTGTGTTCCTTTTTCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATT
* *
27052 TTCATCCTGAAAAAAT-AAAGTGAAAATTAAAATCTTGAAATTCAGGATGAAATTGTTAATGTGG
66 TTCATCCTGAAAAAATCAAA-TTAAAATTAAAATCTTGAAATTCAGGATGAAATTGTTGATGTGG
* *
27116 CATAAAACTATTGGAAAGGGATAATATCCCTGTTTTATACAATCCTTTCTCATACTGGAAAATGA
130 CATAAAACTATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCATACTGGAAAAGGA
*
27181 TTGAATGAAATAGTGACACCACGTCATTTGTGTCCCTACG
195 TTGAATGAAATAGTGACACCACATCATTTGTG----TACG
27221 TCATTTGTGTTCCTTTTTCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATT
1 TCATTTGTGTTCCTTTTTCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATT
* * *
27286 TTCATCTTGAAAAAATCAAATTAAAATTAAAATCATGAAA-TCTAGGATGAAATTATTGATGTGG
66 TTCATCCTGAAAAAATCAAATTAAAATTAAAATCTTGAAATTC-AGGATGAAATTGTTGATGTGG
* * *
27350 CATAAAACTATTGGAAAGAGATAATATTCCTGTTTCATACAATCCTTTCTCATATTGGAAAAGGA
130 CATAAAACTATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCATACTGGAAAAGGA
27415 TTGAATGAAATAGTGACACCACATCATTTGTGT-C-
195 TTGAATGAAATAGTGACACCACATCATTTGTGTACG
27449 -C--------T--TTTTTCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATT
1 TCATTTGTGTTCCTTTTTCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATT
* *
27503 TTTATCCTG-AAAAATCAAATTAAAATTAAAATCTTGAAATTCAGGATGAAATTGTTGATGTGAC
66 TTCATCCTGAAAAAATCAAATTAAAATTAAAATCTTGAAATTCAGGATGAAATTGTTGATGTGGC
** *
27567 ATAAAACTATTGGAAAGGGATAATATCTTTATTTCATACAATCCTTTCTC
131 ATAAAACTATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTC
27617 TTAATATACT
Statistics
Matches: 569, Mismatches: 40, Indels: 52
0.86 0.06 0.08
Matches are distributed among these distances:
216 94 0.17
217 125 0.22
218 1 0.00
219 2 0.00
222 4 0.01
225 3 0.01
226 124 0.22
227 1 0.00
229 1 0.00
230 1 0.00
233 2 0.00
234 208 0.37
235 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (230 bp):
TCATTTGTGTTCCTTTTTCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATT
TTCATCCTGAAAAAATCAAATTAAAATTAAAATCTTGAAATTCAGGATGAAATTGTTGATGTGGC
ATAAAACTATTGGAAAGGGATAATATCCCTGTTTCATACAATCCTTTCTCATACTGGAAAAGGAT
TGAATGAAATAGTGACACCACATCATTTGTGTACG
Found at i:27604 original size:216 final size:217
Alignment explanation
Indices: 27221--27616 Score: 665
Period size: 216 Copynumber: 1.8 Consensus size: 217
27211 TGTCCCTACG
27221 TCATTTGTGTTCCTTTTTCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATT
1 TCATTTGTGTTCCTTTTTCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATT
* *
27286 TTCATCTTGAAAAAATCAAATTAAAATTAAAATCATGAAATCTAGGATGAAATTATTGATGTGGC
66 TTCATCCTGAAAAAATCAAATTAAAATTAAAATCATGAAATCTAGGATGAAATTATTGATGTGAC
*
27351 ATAAAACTATTGGAAAGAGATAATATTCCTGTTTCATACAATCCTTTCTCATATTGGAAAAGGAT
131 ATAAAACTATTGGAAAGAGATAATATTCCTATTTCATACAATCCTTTCTCATATTGGAAAAGGAT
27416 TGAATGAAATAGTGACACCACA
196 TGAATGAAATAGTGACACCACA
27438 TCATTTGTG-TCCTTTTTTCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACAT
1 TCATTTGTGTTCC-TTTTTCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACAT
* * *
27502 TTTTATCCTG-AAAAATCAAATTAAAATTAAAATCTTGAAAT-TCAGGATGAAATTGTTGATGTG
65 TTTCATCCTGAAAAAATCAAATTAAAATTAAAATCATGAAATCT-AGGATGAAATTATTGATGTG
* *
27565 ACATAAAACTATTGGAAAGGGATAATA-TCTTTATTTCATACAATCCTTTCTC
129 ACATAAAACTATTGGAAAGAGATAATATTC-CTATTTCATACAATCCTTTCTC
27617 TTAATATACT
Statistics
Matches: 168, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
215 3 0.02
216 97 0.58
217 68 0.40
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (217 bp):
TCATTTGTGTTCCTTTTTCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATT
TTCATCCTGAAAAAATCAAATTAAAATTAAAATCATGAAATCTAGGATGAAATTATTGATGTGAC
ATAAAACTATTGGAAAGAGATAATATTCCTATTTCATACAATCCTTTCTCATATTGGAAAAGGAT
TGAATGAAATAGTGACACCACA
Found at i:36955 original size:28 final size:28
Alignment explanation
Indices: 36924--37166 Score: 78
Period size: 29 Copynumber: 8.3 Consensus size: 28
36914 AAAATAGGAT
*
36924 TTTTAGCAGCTCGAGGG-TAAAATGGTAA
1 TTTTAGAAGCTC-AGGGATAAAATGGTAA
* *
36952 TTTTGGAAGTTCAGGGATAAAATGGTAA
1 TTTTAGAAGCTCAGGGATAAAATGGTAA
* * * * ***
36980 TTTTTGGAAGGTTCGGGGTAAAAAATGGGGT
1 -TTTTAGAA-GCTCAGGG-ATAAAATGGTAA
* *
37011 TTTTTGAAGTTCGAGGG-TAAAATGGTAA
1 TTTTAGAAGCTC-AGGGATAAAATGGTAA
* * * * * *
37039 CTTTTAAAAGGTTCGGGGTAAAAAATGGGAT
1 -TTTTAGAA-GCTCAGGG-ATAAAATGGTAA
* * * *
37070 TTTTGGAAGTTTAGGGGTAAAATGGTAA
1 TTTTAGAAGCTCAGGGATAAAATGGTAA
* * * * **
37098 TTTTTAGAAGGTTCGAGGTAAAAAATGTTGT
1 -TTTTAGAA-GCTC-AGGGATAAAATGGTAA
* *
37129 TTTTGGAAGTTCGAGGG-TAAAATGGTAA
1 TTTTAGAAGCTC-AGGGATAAAATGGTAA
37157 TTTTTAGAAG
1 -TTTTAGAAG
37167 GTTCGAGGTT
Statistics
Matches: 159, Mismatches: 43, Indels: 25
0.70 0.19 0.11
Matches are distributed among these distances:
27 4 0.03
28 42 0.26
29 50 0.31
30 37 0.23
31 26 0.16
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (28 bp):
TTTTAGAAGCTCAGGGATAAAATGGTAA
Found at i:37022 original size:59 final size:58
Alignment explanation
Indices: 36952--37401 Score: 605
Period size: 59 Copynumber: 7.6 Consensus size: 58
36942 AAAATGGTAA
* *
36952 TTTTGGAAGTTCAGGGATAAAATGGTAATTTTTGGAAGGTTCGGGGTAAAAAATGGGGT
1 TTTTGGAAGTTCAGGG-TAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGGGGT
* * * * *
37011 TTTTTGAAGTTCGAGGGTAAAATGGTAACTTTTAAAAGGTTCGGGGTAAAAAATGGGAT
1 TTTTGGAAGTTC-AGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGGGGT
* **
37070 TTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGTTGT
1 TTTTGGAAGTTCA-GGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGGGGT
*
37129 TTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTTAAAAATGGGGT
1 TTTTGGAAGTTC-AGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGGGGT
* * ***
37188 TTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTAGAAGGTTCG-GGTTTAAAAATGTTAT
1 TTTTGGAAG-TTCAGGGTAAAATGGTAATTTTTAGAAGGTTCGAGG-TAAAAAATGGGGT
* * * *
37247 TTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTTGAGGTCAAAATTGGGGT
1 TTTTGGAAGTTC-AGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGGGGT
* * *
37306 TTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGGGAT
1 TTTTGGAAGTTCA-GGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGGGGT
37365 TTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAA
1 TTTTGGAAGTTC-AGGGTAAAATGGTAATTTTTAGAA
37402 AGTTAGGGTC
Statistics
Matches: 347, Mismatches: 35, Indels: 18
0.87 0.09 0.05
Matches are distributed among these distances:
58 5 0.01
59 332 0.96
60 10 0.03
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.35
Consensus pattern (58 bp):
TTTTGGAAGTTCAGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGGGGT
Found at i:37153 original size:177 final size:176
Alignment explanation
Indices: 36952--37403 Score: 679
Period size: 177 Copynumber: 2.5 Consensus size: 176
36942 AAAATGGTAA
* * *
36952 TTTTGGAAGTTCAGGGATAAAATGGTAATTTTTGGAAGGTTCGGGGTAAAAAATGGGGTTTTTTG
1 TTTTGGAAGTTCAGGG-TAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGGGGTTTTTGG
* *
37017 AAGTTCGAGGGTAAAATGGTAACTTTTAAAAGGTTCGGGGTAAAAAATGGGATTTTTGGAAGTTT
65 AAGTTCGAGGGTAAAATGGTAATTTTTAAAAGGTTCGGGGTAAAAAATGGGATTTTTGGAAGTTC
**
37082 AGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGTTGT
130 AGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGGGGT
*
37129 TTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTTAAAAATGGGGTTTTTGG
1 TTTTGGAAGTTC-AGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGGGGTTTTTGG
* * * * **
37194 AAGTTTGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGTTTAAAAATGTTATTTTTGGAAGTTC
65 AAGTTCGAGGGTAAAATGGTAATTTTTAAAAGGTTCGGGGTAAAAAATGGGATTTTTGGAAGTTC
* * * *
37259 GGGGGTAAAATGGTAATTTTTAGAAGGTTTGAGGTCAAAATTGGGGT
130 AGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGGGGT
* * *
37306 TTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTTTTGG
1 TTTTGGAAGTTCA-GGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGGGGTTTTTGG
37371 AAGTTCGAGGGTAAAATGGTAATTTTTAGAAAG
65 AAGTTCGAGGGTAAAATGGTAATTTTTA-AAAG
37404 TTAGGGTCCT
Statistics
Matches: 249, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
176 1 0.00
177 241 0.97
178 7 0.03
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.35
Consensus pattern (176 bp):
TTTTGGAAGTTCAGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGGGGTTTTTGGA
AGTTCGAGGGTAAAATGGTAATTTTTAAAAGGTTCGGGGTAAAAAATGGGATTTTTGGAAGTTCA
GGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTAAAAAATGGGGT
Done.