Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011086.1 Kokia drynarioides strain JFW-HI SEQ_126059, 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: 108862
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1013 original size:18 final size:18
Alignment explanation
Indices: 992--1026 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
982 AACCTATAAT
*
992 TTTATGTGAACTTATGTA
1 TTTATGCGAACTTATGTA
*
1010 TTTATGCGAAGTTATGT
1 TTTATGCGAACTTATGT
1027 TATTGTGCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.20, T:0.49
Consensus pattern (18 bp):
TTTATGCGAACTTATGTA
Found at i:3414 original size:55 final size:55
Alignment explanation
Indices: 3330--3440 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
3320 TGGCTGTTAA
3330 CCACAAGGTCGGAGGTTCAAGCCCTCCTTCTAGCGTTTTTCTTTTGGTTTAATTT
1 CCACAAGGTCGGAGGTTCAAGCCCTCCTTCTAGCGTTTTTCTTTTGGTTTAATTT
3385 CCACAAGGTCGGAGGTTCAAGCCCTCCTTCTAGCGTTTTTCTTTTGGTTTAATTT
1 CCACAAGGTCGGAGGTTCAAGCCCTCCTTCTAGCGTTTTTCTTTTGGTTTAATTT
3440 C
1 C
3441 ATCTTTGGTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (55 bp):
CCACAAGGTCGGAGGTTCAAGCCCTCCTTCTAGCGTTTTTCTTTTGGTTTAATTT
Found at i:4230 original size:19 final size:20
Alignment explanation
Indices: 4193--4231 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
4183 TTAATTTAAA
4193 GATAAAATTTACAAAATTCT
1 GATAAAATTTACAAAATTCT
4213 GATAAAATTTAC-AAATTCT
1 GATAAAATTTACAAAATTCT
4232 TTATTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (20 bp):
GATAAAATTTACAAAATTCT
Found at i:7263 original size:34 final size:33
Alignment explanation
Indices: 7191--7268 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 33
7181 GGTAATAGGC
* * * *
7191 ATGACCTTGGGTCAATAGGGAGCAAATGAGCATT
1 ATGACCTTGGGTCAACAGGGAGAAAACGAG-ATA
7225 ATGACCTTGGTGTCAACAGGGAGTAAAACGAG-TA
1 ATGACCTTGG-GTCAACAGGGAG-AAAACGAGATA
7259 ATGACCTTGG
1 ATGACCTTGG
7269 AAGTTCATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
34 21 0.55
35 11 0.29
36 6 0.16
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.23
Consensus pattern (33 bp):
ATGACCTTGGGTCAACAGGGAGAAAACGAGATA
Found at i:10291 original size:9 final size:9
Alignment explanation
Indices: 10277--10304 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
10267 GGCACCGACC
10277 GAATTGAAA
1 GAATTGAAA
10286 GAATTGAAA
1 GAATTGAAA
10295 GAATTGAAA
1 GAATTGAAA
10304 G
1 G
10305 CTCAGCTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.25, T:0.21
Consensus pattern (9 bp):
GAATTGAAA
Found at i:18071 original size:6 final size:6
Alignment explanation
Indices: 18060--18093 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
18050 AATCATTCAC
*
18060 AAATAT AAATAT AAATAT AAGTAT ATAATAT AAA
1 AAATAT AAATAT AAATAT AAATAT A-AATAT AAA
18094 GTCTATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:18095 original size:14 final size:14
Alignment explanation
Indices: 18061--18106 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
18051 ATCATTCACA
18061 AATATAAA-TATA-
1 AATATAAAGTATAT
18073 AATAT-AAGTATAT
1 AATATAAAGTATAT
*
18086 AATATAAAGTCTAT
1 AATATAAAGTATAT
18100 AAT-TAAA
1 AATATAAA
18107 ATAAATTAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 2 0.07
12 9 0.30
13 9 0.30
14 10 0.33
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (14 bp):
AATATAAAGTATAT
Found at i:19294 original size:7 final size:7
Alignment explanation
Indices: 19282--19353 Score: 72
Period size: 7 Copynumber: 10.3 Consensus size: 7
19272 CTCAGAAAAG
19282 TCAACGA
1 TCAACGA
*
19289 TCAACGG
1 TCAACGA
* *
19296 TTAACGG
1 TCAACGA
* *
19303 TCAATGG
1 TCAACGA
19310 TCAACGA
1 TCAACGA
*
19317 TCAACTA
1 TCAACGA
19324 TCAACGA
1 TCAACGA
*
19331 TCAACGG
1 TCAACGA
*
19338 TCAACGG
1 TCAACGA
19345 TCAACGA
1 TCAACGA
19352 TC
1 TC
19354 GGTCAATGCT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 55 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (7 bp):
TCAACGA
Found at i:19306 original size:14 final size:14
Alignment explanation
Indices: 19281--19350 Score: 86
Period size: 14 Copynumber: 5.0 Consensus size: 14
19271 TCTCAGAAAA
19281 GTCAACGATCAACG
1 GTCAACGATCAACG
* * *
19295 GTTAACGGTCAATG
1 GTCAACGATCAACG
*
19309 GTCAACGATCAACT
1 GTCAACGATCAACG
*
19323 ATCAACGATCAACG
1 GTCAACGATCAACG
*
19337 GTCAACGGTCAACG
1 GTCAACGATCAACG
19351 ATCGGTCAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 45 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (14 bp):
GTCAACGATCAACG
Found at i:19313 original size:21 final size:21
Alignment explanation
Indices: 19281--19353 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
19271 TCTCAGAAAA
*
19281 GTCAACGATCAACGGTTAACG
1 GTCAACGATCAACGGTCAACG
* * * *
19302 GTCAATGGTCAACGATCAACT
1 GTCAACGATCAACGGTCAACG
*
19323 ATCAACGATCAACGGTCAACG
1 GTCAACGATCAACGGTCAACG
19344 GTCAACGATC
1 GTCAACGATC
19354 GGTCAATGCT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (21 bp):
GTCAACGATCAACGGTCAACG
Found at i:20977 original size:48 final size:48
Alignment explanation
Indices: 20903--20995 Score: 177
Period size: 48 Copynumber: 1.9 Consensus size: 48
20893 TAATTTAGCT
*
20903 CTTTTATTTTGTGTAATTTACGTGCATGTTAATTTTCATAATGATGCA
1 CTTTTATTTTGTGTAATTTACATGCATGTTAATTTTCATAATGATGCA
20951 CTTTTATTTTGTGTAATTTACATGCATGTTAATTTTCATAATGAT
1 CTTTTATTTTGTGTAATTTACATGCATGTTAATTTTCATAATGAT
20996 AAGTTTGGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.52
Consensus pattern (48 bp):
CTTTTATTTTGTGTAATTTACATGCATGTTAATTTTCATAATGATGCA
Found at i:20985 original size:26 final size:26
Alignment explanation
Indices: 20908--20986 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
20898 TAGCTCTTTT
*
20908 ATTTTGTGTAATTTACGTGCATGTTA
1 ATTTTGTGTAATTTACATGCATGTTA
** * *
20934 ATTTT-CATAA--T-GATGCACT-TTT
1 ATTTTGTGTAATTTACATGCA-TGTTA
20956 ATTTTGTGTAATTTACATGCATGTTA
1 ATTTTGTGTAATTTACATGCATGTTA
20982 ATTTT
1 ATTTT
20987 CATAATGATA
Statistics
Matches: 38, Mismatches: 9, Indels: 12
0.64 0.15 0.20
Matches are distributed among these distances:
22 11 0.29
23 5 0.13
25 5 0.13
26 17 0.45
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (26 bp):
ATTTTGTGTAATTTACATGCATGTTA
Found at i:23530 original size:22 final size:22
Alignment explanation
Indices: 23491--23539 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
23481 TAGTCATATA
* *
23491 ATAAATTATTAGTATAATTAAT
1 ATAATTTATTAGTATAATAAAT
* *
23513 ATAATTTATTATTTTAATAAAT
1 ATAATTTATTAGTATAATAAAT
23535 -TAATT
1 ATAATT
23540 AAATTTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATAATTTATTAGTATAATAAAT
Found at i:23544 original size:26 final size:28
Alignment explanation
Indices: 23506--23561 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 28
23496 TTATTAGTAT
23506 AATTAATATAATTT-A-TTATTTTAATA
1 AATTAATATAATTTAATTTATTTTAATA
23532 AATTAAT-TAAATTTAAATTTATTTTAATA
1 AATTAATAT-AATTT-AATTTATTTTAATA
23561 A
1 A
23562 TAAATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 1 0.04
26 12 0.46
28 1 0.04
29 12 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
AATTAATATAATTTAATTTATTTTAATA
Found at i:23577 original size:15 final size:14
Alignment explanation
Indices: 23552--23591 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
23542 ATTTAAATTT
23552 ATTTT-AATAATAA
1 ATTTTAAATAATAA
23565 ATTTTAAAATAAT-A
1 ATTTT-AAATAATAA
23579 ATTTTAAATAATA
1 ATTTTAAATAATA
23592 TTCTTCATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 12 0.50
14 6 0.25
15 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAAATAATAA
Found at i:23644 original size:15 final size:15
Alignment explanation
Indices: 23624--23680 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
23614 ACTCAATATT
*
23624 AATATTTTAACAATA
1 AATATTTTAAAAATA
23639 AATATTTATTAAAATTATA
1 AATA-TT-TTAAAA--ATA
* *
23658 AATATATTAATAATA
1 AATATTTTAAAAATA
23673 AATATTTT
1 AATATTTT
23681 GTAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 14 0.41
16 2 0.06
17 10 0.29
18 1 0.03
19 7 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAAAAATA
Found at i:52634 original size:22 final size:22
Alignment explanation
Indices: 52609--52650 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
52599 AATAATTTTT
52609 ATTTGGAATT-TTGAATTAAAGG
1 ATTT-GAATTATTGAATTAAAGG
*
52631 ATTTTAATTATTGAATTAAA
1 ATTTGAATTATTGAATTAAA
52651 ATTTTGTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.45
Consensus pattern (22 bp):
ATTTGAATTATTGAATTAAAGG
Found at i:53998 original size:27 final size:27
Alignment explanation
Indices: 53954--54060 Score: 126
Period size: 27 Copynumber: 3.9 Consensus size: 27
53944 ACTGAAGGCT
* *
53954 TGAGGATTATTCTTATTCTGGCTCGAA
1 TGAGCATTATTCTGATTCTGGCTCGAA
*
53981 TGAGCATTAATCTGATTCTGGCTCGAGA
1 TGAGCATTATTCTGATTCTGGCTCGA-A
* *
54009 -GAGCGTTATTTTGATTCTGGCTCGAA
1 TGAGCATTATTCTGATTCTGGCTCGAA
**
54035 CAAGCATTATTCTGATTCTAGGCTCG
1 TGAGCATTATTCTGATTCT-GGCTCG
54061 TAAGAGCTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.01
27 60 0.88
28 7 0.10
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (27 bp):
TGAGCATTATTCTGATTCTGGCTCGAA
Found at i:54082 original size:24 final size:24
Alignment explanation
Indices: 54049--54155 Score: 142
Period size: 24 Copynumber: 4.5 Consensus size: 24
54039 CATTATTCTG
* * *
54049 ATTCTAGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCATAGGAGCTAACC
54073 ATTCTGGGCTCATAGGAGCTAACC
1 ATTCTGGGCTCATAGGAGCTAACC
*
54097 GTTCTGGGCTCATAGGAGCTAACC
1 ATTCTGGGCTCATAGGAGCTAACC
* * * *
54121 GTTTTGGACTCCTAGGAGCTAACC
1 ATTCTGGGCTCATAGGAGCTAACC
54145 ATTCTGGGCTC
1 ATTCTGGGCTC
54156 GTATTGGTTA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (24 bp):
ATTCTGGGCTCATAGGAGCTAACC
Found at i:58584 original size:36 final size:36
Alignment explanation
Indices: 58508--58584 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
58498 ATATAAACAG
* * **
58508 TCACATGGCATGAAGAACATACCCGCATATTTTCTA
1 TCACATGGCATGAAGAACATACCCACAAATTCACTA
* *
58544 TCACATGGCATGAATAACATACCCACAAATTCACTT
1 TCACATGGCATGAAGAACATACCCACAAATTCACTA
58580 TCACA
1 TCACA
58585 ACAATCATCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.36, C:0.27, G:0.10, T:0.26
Consensus pattern (36 bp):
TCACATGGCATGAAGAACATACCCACAAATTCACTA
Found at i:60621 original size:30 final size:30
Alignment explanation
Indices: 60585--60642 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
60575 GGAACACGAC
60585 CGTGTGGCTTACAT-GACCTAGGCACACAGT
1 CGTGTGGCTTAC-TCGACCTAGGCACACAGT
*
60615 CGTGTGGCTTACTCGTCCTAGGCACACA
1 CGTGTGGCTTACTCGACCTAGGCACACA
60643 ACCATGTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.24
Consensus pattern (30 bp):
CGTGTGGCTTACTCGACCTAGGCACACAGT
Found at i:60780 original size:22 final size:22
Alignment explanation
Indices: 60735--60776 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
60725 TTAAATATAG
*
60735 AACATTAATCCAAGTCATTTAT
1 AACATTAATCCAAGTCATTAAT
*
60757 AACATTAA-CCAATTCATTAA
1 AACATTAATCCAAGTCATTAA
60777 ATAAATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.33
Consensus pattern (22 bp):
AACATTAATCCAAGTCATTAAT
Found at i:64397 original size:21 final size:21
Alignment explanation
Indices: 64373--64428 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
64363 TATTTTATAT
* *
64373 ATTTTATATTTTAGTTAATAA
1 ATTTTATATTTTAGTCAAAAA
*
64394 ATTTATTTATTTTAGTCAAAAA
1 ATTT-TATATTTTAGTCAAAAA
* *
64416 AATTTCTATTTTA
1 ATTTTATATTTTA
64429 TTTTAATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (21 bp):
ATTTTATATTTTAGTCAAAAA
Found at i:68886 original size:314 final size:315
Alignment explanation
Indices: 68271--68892 Score: 1005
Period size: 314 Copynumber: 2.0 Consensus size: 315
68261 TACCGCAATT
* * * *
68271 ATTGTTGTTGTTTTGTATATCATTTTACTGGCTGAAGATCGGATCATCATCATCTCTTAAACTCA
1 ATTGTTGTTGTTTTGTAGATCATTTTACTAGCTGAAGATCGAATCATCATCATCTCCTAAACTCA
** *
68336 CACTATCACGGAGTTTGTCGGTAGATTTTGCATCACTTGGTCTTATGGCATGTACTAGTATGATA
66 CACTATCACGGAGTTTGTCGGTAGATTTCACATCACTTGGTCTTATGGCATGTACTAGGATGATA
68401 TTAAATTTGATGTTGAACTAAAGATGTTGAAATCTTATCATTTTGATTATGAAGATGCATGAAGT
131 TTAAATTTGATGTTGAACTAAAGATGTTGAAATCTTATCATTTTGATTATGAAGATGCATGAAGT
* *
68466 ACAACTTAGTTGTTTAAGCTTATGATGCTTGTAAAGACTTAAAAGTTATGTATGTAGTGTGATGC
196 ACAACTTAGTTGTTTAAGCTTATGATGCTTGTAAAGACATAAAAGTTATGTATGTAGTGTGATGA
**
68531 CTTAATACATAACTTGTGTTGACATGTTTTACTTATGTCTTGGCATAACATAGTG
261 CTTAATACATAACTTGTGTTGACATGTTAAACTTATGTCTTGGCATAACATAGTG
* * * *
68586 ATTGTTGTTGTTTTGTAGATCGTTTTGCTAGCTGAAGATCGAATCATCGTCATCTCCTGAACTCA
1 ATTGTTGTTGTTTTGTAGATCATTTTACTAGCTGAAGATCGAATCATCATCATCTCCTAAACTCA
* *
68651 CACTATCACGGAGTTTGTCGGTAGA-TTCACATCACTTGGTCTTATGGTATGTACTAGGATGATC
66 CACTATCACGGAGTTTGTCGGTAGATTTCACATCACTTGGTCTTATGGCATGTACTAGGATGATA
* * *
68715 TTAACTTTGATGTTGAACTAAAGATGTTGAAATCTTGTCATTTTGATTGTGAAGATGCATGAAGT
131 TTAAATTTGATGTTGAACTAAAGATGTTGAAATCTTATCATTTTGATTATGAAGATGCATGAAGT
*
68780 ACAACTTAGTTGTTT-AGCTTATGATGCTTGTAAAGACATAGAAGTTATGTATGTAGTGTGATGA
196 ACAACTTAGTTGTTTAAGCTTATGATGCTTGTAAAGACATAAAAGTTATGTATGTAGTGTGATGA
* * *
68844 CTTAATGCATAACTTGTGTTTGATATGTTAAACTTGTGTCTTGGCATAA
261 CTTAATACATAACTTGTG-TTGACATGTTAAACTTATGTCTTGGCATAA
68893 TTTTTGAGAT
Statistics
Matches: 282, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
313 63 0.22
314 137 0.49
315 82 0.29
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.39
Consensus pattern (315 bp):
ATTGTTGTTGTTTTGTAGATCATTTTACTAGCTGAAGATCGAATCATCATCATCTCCTAAACTCA
CACTATCACGGAGTTTGTCGGTAGATTTCACATCACTTGGTCTTATGGCATGTACTAGGATGATA
TTAAATTTGATGTTGAACTAAAGATGTTGAAATCTTATCATTTTGATTATGAAGATGCATGAAGT
ACAACTTAGTTGTTTAAGCTTATGATGCTTGTAAAGACATAAAAGTTATGTATGTAGTGTGATGA
CTTAATACATAACTTGTGTTGACATGTTAAACTTATGTCTTGGCATAACATAGTG
Found at i:80884 original size:13 final size:12
Alignment explanation
Indices: 80859--80883 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
80849 GCCTGTTCAT
80859 ATTATTTTTAAA
1 ATTATTTTTAAA
80871 ATTATTTTTAAA
1 ATTATTTTTAAA
80883 A
1 A
80884 AATATTTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTATTTTTAAA
Found at i:81334 original size:23 final size:24
Alignment explanation
Indices: 81301--81345 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
81291 ATAAACTTAA
81301 AATAGAATAAATTAAAT-TATTTT
1 AATAGAATAAATTAAATATATTTT
*
81324 AATAGATTAAATTAAATATATT
1 AATAGAATAAATTAAATATATT
81346 CCATTTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
AATAGAATAAATTAAATATATTTT
Found at i:83075 original size:15 final size:15
Alignment explanation
Indices: 83052--83082 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
83042 ACGTGTTATC
83052 TGATGATCAAGAATA
1 TGATGATCAAGAATA
*
83067 TGATTATCAAGAATA
1 TGATGATCAAGAATA
83082 T
1 T
83083 TTATTATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.32
Consensus pattern (15 bp):
TGATGATCAAGAATA
Found at i:85636 original size:21 final size:20
Alignment explanation
Indices: 85603--85656 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
85593 TTGAATTAAA
*
85603 AAAAACTTCAAAAAT-TATTTT
1 AAAAA-TTCAAAAATATA-TAT
85624 AAAAATTCTAAAAATATATAT
1 AAAAATTC-AAAAATATATAT
85645 AAAAATTTCAAA
1 AAAAA-TTCAAA
85657 TGTGTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 3 0.10
21 21 0.72
22 5 0.17
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTCAAAAATATATAT
Found at i:86162 original size:22 final size:22
Alignment explanation
Indices: 86137--86197 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
86127 CTTTGAAATT
*
86137 AGTGCCTTGATTTTTCTCCTAC
1 AGTGTCTTGATTTTTCTCCTAC
86159 AGTGTCTTGATTTTTCTCCTAC
1 AGTGTCTTGATTTTTCTCCTAC
86181 AGTGTCTTGATTTTTCT
1 AGTGTCTTGATTTTTCT
86198 TCCGACATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.13, C:0.21, G:0.15, T:0.51
Consensus pattern (22 bp):
AGTGTCTTGATTTTTCTCCTAC
Found at i:86967 original size:17 final size:17
Alignment explanation
Indices: 86945--86979 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
86935 ATTTTTCTCC
86945 TAAAATATTTG-TAAAAA
1 TAAAATA-TTGATAAAAA
86962 TAAAATATTGATAAAAA
1 TAAAATATTGATAAAAA
86979 T
1 T
86980 GTTCAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
TAAAATATTGATAAAAA
Found at i:93173 original size:22 final size:22
Alignment explanation
Indices: 93148--93189 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
93138 GAAGAATGCC
93148 AGAAGAAAAATCAAGGCACTGT
1 AGAAGAAAAATCAAGGCACTGT
93170 AGAAGAAAAATCAAGGCACT
1 AGAAGAAAAATCAAGGCACT
93190 AATTTCAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.14, G:0.21, T:0.12
Consensus pattern (22 bp):
AGAAGAAAAATCAAGGCACTGT
Found at i:96615 original size:22 final size:22
Alignment explanation
Indices: 96590--96631 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
96580 GAAGAATGCC
96590 AGAAGAAAAATCAAGGCACTGT
1 AGAAGAAAAATCAAGGCACTGT
96612 AGAAGAAAAATCAAGGCACT
1 AGAAGAAAAATCAAGGCACT
96632 AATTTCATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.14, G:0.21, T:0.12
Consensus pattern (22 bp):
AGAAGAAAAATCAAGGCACTGT
Found at i:102187 original size:17 final size:18
Alignment explanation
Indices: 102157--102190 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
102147 AATTTCTATT
102157 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
102175 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
102191 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:102738 original size:42 final size:42
Alignment explanation
Indices: 102659--102740 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
102649 CTTTATTCTT
* *
102659 TTATATCATATATATATATTAATTAGTAATAACATTAATAAA
1 TTATATCATATATATATATTAAATAATAATAACATTAATAAA
*
102701 TTATAT-ATATATATTTACTTAAATAATAAGTAA-ATTAATA
1 TTATATCATATATATATA-TTAAATAATAA-TAACATTAATA
102741 TTTATTTTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 10 0.29
42 22 0.63
43 3 0.09
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (42 bp):
TTATATCATATATATATATTAAATAATAATAACATTAATAAA
Done.