Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013099.1 Kokia drynarioides strain JFW-HI SEQ_128117, 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: 97053
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:5432 original size:17 final size:17
Alignment explanation
Indices: 5408--5473 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 17
5398 ATATATATGG
**
5408 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* *
5425 AGATGCAACGACAATAA
1 AAATGCAATGACAATAA
*
5442 AAATGCAATGACATTAA
1 AAATGCAATGACAATAA
* * *
5459 TAATGTAAGGACAAT
1 AAATGCAATGACAAT
5474 TATACTACAG
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:5974 original size:14 final size:14
Alignment explanation
Indices: 5955--5994 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
5945 TCTCTTTCCT
5955 TCTTCTTTTCTTGG
1 TCTTCTTTTCTTGG
*
5969 TCTTCTTCTCTTGG
1 TCTTCTTTTCTTGG
*
5983 CCTTCTTGTTCT
1 TCTTCTT-TTCT
5995 GCTTCTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 19 0.86
15 3 0.14
ACGTcount: A:0.00, C:0.28, G:0.12, T:0.60
Consensus pattern (14 bp):
TCTTCTTTTCTTGG
Found at i:12444 original size:28 final size:28
Alignment explanation
Indices: 12413--12468 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
12403 CAGGTAACAG
*
12413 GCATGACCTTTGGGTCAACAGGGAGTAA
1 GCATGACCTTTGGATCAACAGGGAGTAA
12441 GCATGACCTTTGGATCAACAGGGAGTAA
1 GCATGACCTTTGGATCAACAGGGAGTAA
12469 ATCAGATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.21
Consensus pattern (28 bp):
GCATGACCTTTGGATCAACAGGGAGTAA
Found at i:21187 original size:22 final size:21
Alignment explanation
Indices: 21132--21186 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
21122 AAATATCATT
21132 TTTAATTTTTTTATTTTAATA
1 TTTAATTTTTTTATTTTAATA
* *
21153 TTCTACTATTTTTATTTTAA-A
1 TT-TAATTTTTTTATTTTAATA
21174 GTTTAATTTTTTT
1 -TTTAATTTTTTT
21187 TTATATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTAATTTTTTTATTTTAATA
Found at i:22301 original size:19 final size:18
Alignment explanation
Indices: 22277--22315 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
22267 AAAAAAACAT
*
22277 AAAGTAAATTCAATATAAA
1 AAAGTAAATTAAAT-TAAA
22296 AAAGTAAATTAAATTAAA
1 AAAGTAAATTAAATTAAA
22314 AA
1 AA
22316 TGAACTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAGTAAATTAAATTAAA
Found at i:22744 original size:8 final size:8
Alignment explanation
Indices: 22731--22759 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
22721 CAATAAATAA
22731 AAATTATT
1 AAATTATT
22739 AAATTATT
1 AAATTATT
22747 AAA-TATT
1 AAATTATT
22754 AAATTA
1 AAATTA
22760 AAATAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
AAATTATT
Found at i:24266 original size:19 final size:20
Alignment explanation
Indices: 24238--24279 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
24228 AAATTTAAGA
24238 ATATTAATTATA-AAAAAAT
1 ATATTAATTATATAAAAAAT
* *
24257 ATATTTATTATATTAAAAAT
1 ATATTAATTATATAAAAAAT
24277 ATA
1 ATA
24280 AATAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATTAATTATATAAAAAAT
Found at i:25619 original size:23 final size:23
Alignment explanation
Indices: 25574--25631 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
25564 AAAATATGAC
* **
25574 AATG-TTTAAAATTTTTATTAAA
1 AATGTTTTAAAATTTATAAAAAA
25596 AATGTTTTAAAATTTATAAAAAA
1 AATGTTTTAAAATTTATAAAAAA
**
25619 AAAATTTTAAAAT
1 AATGTTTTAAAAT
25632 AAACAAATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 4 0.13
23 26 0.87
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (23 bp):
AATGTTTTAAAATTTATAAAAAA
Found at i:32253 original size:20 final size:20
Alignment explanation
Indices: 32228--32273 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
32218 CACCACGATT
32228 GTGCAAAAAGAGGCACCAAA
1 GTGCAAAAAGAGGCACCAAA
* *
32248 GTGCAAATAGAGGCACCGAA
1 GTGCAAAAAGAGGCACCAAA
32268 GTGCAA
1 GTGCAA
32274 TCCCGTACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.20, G:0.28, T:0.09
Consensus pattern (20 bp):
GTGCAAAAAGAGGCACCAAA
Found at i:33771 original size:3 final size:3
Alignment explanation
Indices: 33763--33832 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
33753 ACATGCATCT
33763 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
33811 TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
33833 CGTTAGCGAG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:34574 original size:127 final size:127
Alignment explanation
Indices: 34384--34695 Score: 401
Period size: 127 Copynumber: 2.5 Consensus size: 127
34374 CAACGTTTTA
* * * * * * * **
34384 AGTCATAGTTGGAATCTTCTAAGTTGTGAGTACATAAAGGGAGCAGACTAGTTGAGGTATGGTTG
1 AGTCGTAGTTGGAATCTGCTAAGCTGTGAGTACATAGAGGGTGCAAACAAGTTGTCGTATGGTTG
*
34449 AGGATCCACAACCCCTCGTAGATAAAAACTGTCAGAGGAAATCATGAATGCTCCGTTCCTAT
66 AGGATCCACAACCCCTCGCAGATAAAAACTGTCAGAGGAAATCATGAATGCTCCGTTCCTAT
* *
34511 AGTCGTAGTTGGAATCTGCTAAACTGTGAGTACATAGAGGGTGCAAACAAGCTGTCGTATGGTTG
1 AGTCGTAGTTGGAATCTGCTAAGCTGTGAGTACATAGAGGGTGCAAACAAGTTGTCGTATGGTTG
* ** * ** * *
34576 ATGATCCACAACCCCTCGCAGATAAAAGTTGTCAGAGGCAATTGTGGATGCTCCGTTCGTAT
66 AGGATCCACAACCCCTCGCAGATAAAAACTGTCAGAGGAAATCATGAATGCTCCGTTCCTAT
* * *
34638 AGTCGCAGTTGAAATCTGCTAAGCTATGAGTACATAGAGGGTG-AAGACAAGTTGTCGT
1 AGTCGTAGTTGGAATCTGCTAAGCTGTGAGTACATAGAGGGTGCAA-ACAAGTTGTCGT
34696 TTCGTTCATA
Statistics
Matches: 159, Mismatches: 25, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
126 2 0.01
127 157 0.99
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (127 bp):
AGTCGTAGTTGGAATCTGCTAAGCTGTGAGTACATAGAGGGTGCAAACAAGTTGTCGTATGGTTG
AGGATCCACAACCCCTCGCAGATAAAAACTGTCAGAGGAAATCATGAATGCTCCGTTCCTAT
Found at i:35942 original size:2 final size:2
Alignment explanation
Indices: 35935--35961 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35925 GGAAATTAGG
35935 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
35962 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35966 original size:2 final size:2
Alignment explanation
Indices: 35961--35996 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
35951 ATATATATAT
35961 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35997 TTTATAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36548 original size:37 final size:35
Alignment explanation
Indices: 36467--36548 Score: 80
Period size: 37 Copynumber: 2.3 Consensus size: 35
36457 AACTTACGTA
**
36467 TTAA-TTA-TTAACTTTATACTTTTAATGTATTAT
1 TTAATTTATTTAACTTTATACTTTTAATAAATTAT
*
36500 TTAATTTATTTAACTTTTATAATTTTTAATAAATT-T
1 TTAATTTATTTAAC-TTTAT-ACTTTTAATAAATTAT
*
36536 TTATTTTAATTTA
1 TTAATTT-ATTTA
36549 TAATAATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
33 4 0.10
34 3 0.08
35 5 0.12
36 12 0.30
37 16 0.40
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (35 bp):
TTAATTTATTTAACTTTATACTTTTAATAAATTAT
Found at i:37505 original size:30 final size:29
Alignment explanation
Indices: 37464--37538 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
37454 AAATTTTAAA
* *
37464 TTAATAATAATAAAATTGTACTATAATTCT
1 TTAAAAATAATAAAATT-TAATATAATTCT
* *
37494 TTAAAAATAATAATAATTTAATTTAATTTT
1 TTAAAAATAATAA-AATTTAATATAATTCT
*
37524 TTAAAAATTATAAAA
1 TTAAAAATAATAAAA
37539 ATATAAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.05
30 33 0.85
31 4 0.10
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (29 bp):
TTAAAAATAATAAAATTTAATATAATTCT
Found at i:37548 original size:15 final size:17
Alignment explanation
Indices: 37527--37567 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
37517 TAATTTTTTA
37527 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
37543 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
37559 AAAATTATA
1 AAAATTATA
37568 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:38020 original size:19 final size:19
Alignment explanation
Indices: 37996--38037 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
37986 CATTGGACTT
*
37996 TTACTTTTTTGGCTCATAA
1 TTACTTTGTTGGCTCATAA
38015 TTACTTTGTTGGCTCATAA
1 TTACTTTGTTGGCTCATAA
38034 TTAC
1 TTAC
38038 AATTCTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (19 bp):
TTACTTTGTTGGCTCATAA
Found at i:46184 original size:21 final size:21
Alignment explanation
Indices: 46160--46201 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
46150 CAAATAATGA
**
46160 CAAAAAGTATTTATACCTTTT
1 CAAAAAGTATCAATACCTTTT
46181 CAAAAAGTATCAATACCTTTT
1 CAAAAAGTATCAATACCTTTT
46202 ATCAGGTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (21 bp):
CAAAAAGTATCAATACCTTTT
Found at i:50063 original size:26 final size:26
Alignment explanation
Indices: 50027--50080 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
50017 GATCCGGACT
50027 ATGTGGCATGAAAGAAGAGCTCTAAA
1 ATGTGGCATGAAAGAAGAGCTCTAAA
50053 ATGTGGCATGAAAGAAGAGCTCTAAA
1 ATGTGGCATGAAAGAAGAGCTCTAAA
50079 AT
1 AT
50081 CCCAAAGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.26, T:0.20
Consensus pattern (26 bp):
ATGTGGCATGAAAGAAGAGCTCTAAA
Found at i:51413 original size:69 final size:66
Alignment explanation
Indices: 51317--51456 Score: 181
Period size: 69 Copynumber: 2.1 Consensus size: 66
51307 AATAAATAAA
* * *
51317 AAATTATATGTTTTTTGACGGAATTAACCGAATTAAAACTAAATATAAATTGTATCATTAATTAT
1 AAATTATATGTTTTTTAACCGAATTAACCAAATTAAAACTAAATATAAATTGTATCATTAATTAT
51382 T
66 T
* ** * *
51383 AAATTGATAATGTTTATTTAACCGAATTAACTAAATTAAAACTACGTATAATTTGTATTATTAAT
1 AAATT-AT-ATGTTT-TTTAACCGAATTAACCAAATTAAAACTAAATATAAATTGTATCATTAAT
51448 TATT
63 TATT
51452 AAATT
1 AAATT
51457 TGGTTAATTC
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
66 5 0.08
67 2 0.03
68 6 0.10
69 50 0.79
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (66 bp):
AAATTATATGTTTTTTAACCGAATTAACCAAATTAAAACTAAATATAAATTGTATCATTAATTAT
T
Found at i:52400 original size:19 final size:19
Alignment explanation
Indices: 52358--52404 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
52348 TATTTTATAA
*
52358 AATTATAACA-AAAAATTTG
1 AATTATAA-ATAAAAAATTG
*
52377 CATTATAAATAAAAAATTG
1 AATTATAAATAAAAAATTG
52396 AATTA-AAAT
1 AATTATAAAT
52405 TTTAGTGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (19 bp):
AATTATAAATAAAAAATTG
Found at i:56245 original size:383 final size:383
Alignment explanation
Indices: 55538--56269 Score: 1349
Period size: 383 Copynumber: 1.9 Consensus size: 383
55528 TATAATTTTG
* *
55538 AAAAAAAAATATTGTCATGTTGCAAATTTTCTCGACATTAAGGGGAGACAAATTAGTTAAATAAT
1 AAAAAAAAAAATTATCATGTTGCAAATTTTCTCGACATTAAGGGGAGACAAATTAGTTAAATAAT
55603 TATGTCATCATTTTTTCTTTTGTGATCCTCACTAATATTATGTGCACAAAGTTTGAAGGATAAAA
66 TATGTCATCATTTTTTCTTTTGTGATCCTCACTAATATTATGTGCACAAAGTTTGAAGGATAAAA
*
55668 ATTATTTGCTAGATATGTTTAGTGATGACATTTAGAGATTCTATATACCAGTTGATACATATACT
131 ATTATTTGATAGATATGTTTAGTGATGACATTTAGAGATTCTATATACCAGTTGATACATATACT
*
55733 AGCTAAAATGCTCCAAATAATTATGTCCCAGAAGAATAATATGATAAAAAATAAGTCTTGAGCAT
196 AGCTAAAATACTCCAAATAATTATGTCCCAGAAGAATAATATGATAAAAAATAAGTCTTGAGCAT
55798 GCTAGAAGCATGACAAGCTAGTCGACTCCATAAAACAAAAAATCATTGAAAGAAAGGAGAAAGAA
261 GCTAGAAGCATGACAAGCTAGTCGACTCCATAAAACAAAAAATCATTGAAAGAAAGGAGAAAGAA
55863 ATGAAGATGATCACATAGTAAAAGCGGAGACAAATTAGTTATGTTGACTCCATAAAAC
326 ATGAAGATGATCACATAGTAAAAGCGGAGACAAATTAGTTATGTTGACTCCATAAAAC
*
55921 AAAAAAAAAAATTATCATGTTGCAAATTTTCTTGACATTAAGGGGAGACAAATTAGTTAAATAAT
1 AAAAAAAAAAATTATCATGTTGCAAATTTTCTCGACATTAAGGGGAGACAAATTAGTTAAATAAT
55986 TATGTCATCATTTTTTCTTTTGTGATCCTCACTAATATTATGTGCACAAAGTTTGAAGGATAAAA
66 TATGTCATCATTTTTTCTTTTGTGATCCTCACTAATATTATGTGCACAAAGTTTGAAGGATAAAA
*
56051 ATTATTTGATAGATATGTTTAGTGATGACATTTAGAGATT-TCATATACTAGTTGATACATATAC
131 ATTATTTGATAGATATGTTTAGTGATGACATTTAGAGATTCT-ATATACCAGTTGATACATATAC
* * *
56115 TAGCTAAAATACTCCAAATAATTATGTCCCGGAAGGATAATGTGATAAAAAATAAGTCTTGAGCA
195 TAGCTAAAATACTCCAAATAATTATGTCCCAGAAGAATAATATGATAAAAAATAAGTCTTGAGCA
*
56180 TGCTAGAAGCATGACAAGCTAGTTGACTCCATAAAACAAAAAATCATTGAAAGAAAGGAGAAAGA
260 TGCTAGAAGCATGACAAGCTAGTCGACTCCATAAAACAAAAAATCATTGAAAGAAAGGAGAAAGA
*
56245 AATGAAGATGGTCACATAGTAAAAG
325 AATGAAGATGATCACATAGTAAAAG
56270 GAGGCGGGTA
Statistics
Matches: 337, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
382 1 0.00
383 336 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (383 bp):
AAAAAAAAAAATTATCATGTTGCAAATTTTCTCGACATTAAGGGGAGACAAATTAGTTAAATAAT
TATGTCATCATTTTTTCTTTTGTGATCCTCACTAATATTATGTGCACAAAGTTTGAAGGATAAAA
ATTATTTGATAGATATGTTTAGTGATGACATTTAGAGATTCTATATACCAGTTGATACATATACT
AGCTAAAATACTCCAAATAATTATGTCCCAGAAGAATAATATGATAAAAAATAAGTCTTGAGCAT
GCTAGAAGCATGACAAGCTAGTCGACTCCATAAAACAAAAAATCATTGAAAGAAAGGAGAAAGAA
ATGAAGATGATCACATAGTAAAAGCGGAGACAAATTAGTTATGTTGACTCCATAAAAC
Found at i:58008 original size:17 final size:17
Alignment explanation
Indices: 57988--58029 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
57978 CTCCCTTGAC
*
57988 CTTTAACCTTTCATCTT
1 CTTTAACCTTTCATATT
58005 CTTTAACCTTTCATATT
1 CTTTAACCTTTCATATT
58022 CTTGTAAC
1 CTT-TAAC
58030 TACTTTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.50
Consensus pattern (17 bp):
CTTTAACCTTTCATATT
Found at i:58013 original size:24 final size:24
Alignment explanation
Indices: 57968--58015 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
57958 ATGGATATTC
*
57968 AACCTTTCATCTCCCTTGACCTTT
1 AACCTTTCATCTCCCTTAACCTTT
* *
57992 AACCTTTCATCTTCTTTAACCTTT
1 AACCTTTCATCTCCCTTAACCTTT
58016 CATATTCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.02, T:0.46
Consensus pattern (24 bp):
AACCTTTCATCTCCCTTAACCTTT
Found at i:58687 original size:21 final size:21
Alignment explanation
Indices: 58663--58702 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
58653 TTTTATATTG
* *
58663 TTTCGCTATTGTTTTTAATGT
1 TTTCACTATCGTTTTTAATGT
*
58684 TTTCACTGTCGTTTTTAAT
1 TTTCACTATCGTTTTTAAT
58703 ATTATTTGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.12, G:0.12, T:0.60
Consensus pattern (21 bp):
TTTCACTATCGTTTTTAATGT
Found at i:71810 original size:79 final size:78
Alignment explanation
Indices: 71674--71906 Score: 360
Period size: 79 Copynumber: 2.9 Consensus size: 78
71664 ATTGGTTCCA
* *
71674 TGAATTGGCCTTTAAGTGCCCAAAACACTGATCAGCATTTGAAGAGTTTCCCCTTGGTCTTTTGA
1 TGAATTGGCCTTTAAGTGTCCAAAAC-C-GATCAGCATTTGAAGAGTTTCCCTTTGGTCTTTTGA
71739 AGAGTCACCTTGTCT
64 AGAGTCACCTTGTCT
*
71754 TGAATTGGCCTTTAAGTGTACCAAAACCGATCAGCATTTCAAGAGTTTCCCTTTGGTCTTTTGAA
1 TGAATTGGCCTTTAAGTGT-CCAAAACCGATCAGCATTTGAAGAGTTTCCCTTTGGTCTTTTGAA
71819 GAGTCACCTTGTCT
65 GAGTCACCTTGTCT
* * *
71833 TGAATTGGCCTTTAAGTGCTCCAAAATCAATCAGCATTTGAAGAGTCTT-CCTTTGATCTTTTGA
1 TGAATTGGCCTTTAAGTG-TCCAAAACCGATCAGCATTTGAAGAGT-TTCCCTTTGGTCTTTTGA
71897 AGAGTCACCT
64 AGAGTCACCT
71907 GATCAAGCAT
Statistics
Matches: 143, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
79 114 0.80
80 22 0.15
81 7 0.05
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (78 bp):
TGAATTGGCCTTTAAGTGTCCAAAACCGATCAGCATTTGAAGAGTTTCCCTTTGGTCTTTTGAAG
AGTCACCTTGTCT
Found at i:72250 original size:51 final size:50
Alignment explanation
Indices: 72121--72365 Score: 273
Period size: 51 Copynumber: 4.9 Consensus size: 50
72111 GCATAACTTG
* * * **
72121 ATTTAATGATGTAAACTTTAACTAACATGGGAGTTATATAATGC--GT-AAC
1 ATTT-ATGATGCAAAC-TTAACTAACATGAGAGTTACATAATGCATGTCATT
* ** *
72170 A-TAATGATGCACTCTTATCTAACATGAGAGTTACATAATGCATGTCATT
1 ATTTATGATGCAAACTTAACTAACATGAGAGTTACATAATGCATGTCATT
72219 ATTTATGATGCAAACTTAACTAATCATGAGAGTTACATAATGCATGTCATT
1 ATTTATGATGCAAACTTAACTAA-CATGAGAGTTACATAATGCATGTCATT
** *
72270 ATTTATGAAACAAACTTAACTATTCATGAGAGTTACATAATGCATGTCATT
1 ATTTATGATGCAAACTTAACTA-ACATGAGAGTTACATAATGCATGTCATT
* * * * *
72321 ATTTAAGATGCATACTTAACTAACTTGAAAGTTACATAGTGCATG
1 ATTTATGATGCAAACTTAACTAACATGAGAGTTACATAATGCATG
72366 ACTTTATTAA
Statistics
Matches: 166, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
46 24 0.14
47 8 0.05
48 3 0.02
49 3 0.02
50 36 0.22
51 92 0.55
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (50 bp):
ATTTATGATGCAAACTTAACTAACATGAGAGTTACATAATGCATGTCATT
Found at i:76059 original size:78 final size:79
Alignment explanation
Indices: 75926--76155 Score: 311
Period size: 79 Copynumber: 2.9 Consensus size: 79
75916 ATTGGTACCA
* *
75926 TGAATTGGCCTTTAAGTGCCCCAAAAACCGATCAGCATTTGAAGAGTTTCTCCTTGGTCTTTTGA
1 TGAATTGGCCTTTAAGTGCACC-AAAACCGATCAGCATTTGAAGAGTTTCCCCTTGGTCTTTTGA
*
75991 AGAGTCAC-TTGTCT
65 AGAGTCACATTATCT
* *
76005 TGAATTGGCCTTTAAGTGCACCAAAACCGATTAACATTTGAAGAGTTTCCCCTTGGTCTTTTGAA
1 TGAATTGGCCTTTAAGTGCACCAAAACCGATCAGCATTTGAAGAGTTTCCCCTTGGTCTTTTGAA
76070 GAGTCACATTATCT
66 GAGTCACATTATCT
* * * * * * * *
76084 TAAATTGCCCTGTAAGTGCTCCAAAATCGACCAGCATTTGAAGAATCTT-CCCTTGATCTTTTGA
1 TGAATTGGCCTTTAAGTGCACCAAAACCGATCAGCATTTGAAGAGT-TTCCCCTTGGTCTTTTGA
76148 AGAGTCAC
65 AGAGTCAC
76156 CTGATCAAGC
Statistics
Matches: 134, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
78 47 0.35
79 85 0.63
80 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (79 bp):
TGAATTGGCCTTTAAGTGCACCAAAACCGATCAGCATTTGAAGAGTTTCCCCTTGGTCTTTTGAA
GAGTCACATTATCT
Found at i:76487 original size:101 final size:101
Alignment explanation
Indices: 76369--76596 Score: 332
Period size: 101 Copynumber: 2.3 Consensus size: 101
76359 GATGCCAACT
* * *
76369 TTAACTAACATGGGAGTTATATAATGCATAACATAATTTATGATGCAATCTTAACTAA-CATTAG
1 TTAACTAACATGGGAGTTACATAATGCATAACATAATTTATGATGCAAACTTAACTAATCATAAG
*
76433 AGTTACATAATGCATGTTATTATTTATGATACAAAC
66 AGTTACATAATGCATGTCATTATTTATGATACAAAC
* *
76469 TTAACTAATCATGGGAGTTACATAATGCATATCATTATTTATGATGCAAACTTAACTAATCATAA
1 TTAACTAA-CATGGGAGTTACATAATGCATAACATAATTTATGATGCAAACTTAACTAATCATAA
* *
76534 GAGTTACATAATGCATGTCATTATTTATGATGCATAC
65 GAGTTACATAATGCATGTCATTATTTATGATACAAAC
* * **
76571 TCAACTAACTTGAAAGTTACATAATG
1 TTAACTAACATGGGAGTTACATAATG
76597 TATGACTTTA
Statistics
Matches: 114, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
100 8 0.07
101 61 0.54
102 45 0.39
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (101 bp):
TTAACTAACATGGGAGTTACATAATGCATAACATAATTTATGATGCAAACTTAACTAATCATAAG
AGTTACATAATGCATGTCATTATTTATGATACAAAC
Found at i:76506 original size:51 final size:50
Alignment explanation
Indices: 76352--76596 Score: 301
Period size: 51 Copynumber: 4.8 Consensus size: 50
76342 GCATGACTTG
* * * * *
76352 ATTTAATGATGCCAACTTTAACTAACATGGGAGTTATATAATGCATAACATA
1 ATTT-ATGATGCAAAC-TTAACTAACATGAGAGTTACATAATGCATATCATT
* * * *
76404 ATTTATGATGCAATCTTAACTAACATTAGAGTTACATAATGCATGTTATT
1 ATTTATGATGCAAACTTAACTAACATGAGAGTTACATAATGCATATCATT
* *
76454 ATTTATGATACAAACTTAACTAATCATGGGAGTTACATAATGCATATCATT
1 ATTTATGATGCAAACTTAACTAA-CATGAGAGTTACATAATGCATATCATT
* *
76505 ATTTATGATGCAAACTTAACTAATCATAAGAGTTACATAATGCATGTCATT
1 ATTTATGATGCAAACTTAACTAA-CATGAGAGTTACATAATGCATATCATT
* * * *
76556 ATTTATGATGCATACTCAACTAACTTGAAAGTTACATAATG
1 ATTTATGATGCAAACTTAACTAACATGAGAGTTACATAATG
76597 TATGACTTTA
Statistics
Matches: 168, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
50 64 0.38
51 100 0.60
52 4 0.02
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (50 bp):
ATTTATGATGCAAACTTAACTAACATGAGAGTTACATAATGCATATCATT
Found at i:86603 original size:30 final size:30
Alignment explanation
Indices: 86569--86630 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
86559 ACTTATTTTA
* *
86569 TTGTTAATTTTATTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTACTATTTTAGAGACAT
86599 TTGTTAATTTTATTACTATTTTAGAGACAT
1 TTGTTAATTTTATTACTATTTTAGAGACAT
86629 TT
1 TT
86631 ATTTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTATTACTATTTTAGAGACAT
Found at i:90251 original size:16 final size:15
Alignment explanation
Indices: 90216--90254 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
90206 GCAGCGACCA
90216 AAAAG-AAGGGGGAG
1 AAAAGAAAGGGGGAG
*
90230 AAAAGAAAGGGAGGAT
1 AAAAGAAAGGG-GGAG
90246 AAAAGAAAG
1 AAAAGAAAG
90255 AGAAGAGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 5 0.23
16 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.03
Consensus pattern (15 bp):
AAAAGAAAGGGGGAG
Found at i:90252 original size:21 final size:22
Alignment explanation
Indices: 90228--90276 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
90218 AAGAAGGGGG
* *
90228 AGAAAAGA-AAGGGAGGATAAA
1 AGAAAAGAGAAGAGAGGAAAAA
90249 AG-AAAGAGAAGAGAGGAAAAA
1 AGAAAAGAGAAGAGAGGAAAAA
90270 AGAAAAG
1 AGAAAAG
90277 GGGATGCGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.21
21 15 0.62
22 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (22 bp):
AGAAAAGAGAAGAGAGGAAAAA
Found at i:92520 original size:30 final size:30
Alignment explanation
Indices: 92486--92647 Score: 115
Period size: 30 Copynumber: 5.6 Consensus size: 30
92476 ATTTTATTTA
* *
92486 AAAATTACATTTTGACCCTTAAACTTTTCT
1 AAAATCACATTTTAACCCTTAAACTTTTCT
** * *
92516 AAAATTGCATTTTAACCCTCAAACTTTACT
1 AAAATCACATTTTAACCCTTAAACTTTTCT
* *
92546 AAAA-CACATTTTAACCCCTAAA-TTTTCCC
1 AAAATCACATTTTAACCCTTAAACTTTT-CT
* *
92575 AAAATCACATTTTGATCC-TAAAC--TTC-
1 AAAATCACATTTTAACCCTTAAACTTTTCT
** * *
92601 CCAATCACA-TTTAGACTC-TAAACTTTCCT
1 AAAATCACATTTTA-ACCCTTAAACTTTTCT
*
92630 TAAATCACATTTTAACCC
1 AAAATCACATTTTAACCC
92648 CAAATTCTTT
Statistics
Matches: 103, Mismatches: 21, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
25 3 0.03
26 14 0.14
27 1 0.01
28 7 0.07
29 33 0.32
30 45 0.44
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATCACATTTTAACCCTTAAACTTTTCT
Found at i:92578 original size:29 final size:28
Alignment explanation
Indices: 92523--92647 Score: 103
Period size: 29 Copynumber: 4.4 Consensus size: 28
92513 TCTAAAATTG
* *
92523 CATTTTAACCCTCAAACTTTACTAAAACA
1 CATTTTAACCCT-AAACTTTCCCAAAACA
*
92552 CATTTTAACCCCTAAATTTTCCCAAAATCA
1 CATTTTAA-CCCTAAACTTTCCCAAAA-CA
* * *
92582 CATTTTGATCCTAAAC-TTCCC-AATCA
1 CATTTTAACCCTAAACTTTCCCAAAACA
* * *
92608 CA-TTTAGACTCTAAACTTTCCTTAAATCA
1 CATTTTA-ACCCTAAACTTTCC-CAAAACA
92637 CATTTTAACCC
1 CATTTTAACCC
92648 CAAATTCTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
25 3 0.04
26 11 0.14
27 6 0.08
28 5 0.06
29 35 0.45
30 17 0.22
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (28 bp):
CATTTTAACCCTAAACTTTCCCAAAACA
Found at i:93492 original size:24 final size:25
Alignment explanation
Indices: 93458--93504 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
93448 TCCCATATTC
* *
93458 CAATTTTAAAAATAA-TTTTCGAAA
1 CAATTTAAAAAAAAACTTTTCGAAA
93482 CAATTTAAAAAAAAACTTTTCGA
1 CAATTTAAAAAAAAACTTTTCGA
93505 CAATTACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.34
Consensus pattern (25 bp):
CAATTTAAAAAAAAACTTTTCGAAA
Found at i:95078 original size:41 final size:41
Alignment explanation
Indices: 95030--95127 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
95020 AAACAGTAGT
* * * *
95030 GGCGTTTATGAGAAAACGCCGTTAAAGGTCAGAACATTAGC
1 GGCGTTTATGAGAAAACGCCGCTAAAAGTAAGAACATTAAC
* * *
95071 GGTGTTTATAAGAAAACGCCGCTAAAAGTAAGAGCATTAAC
1 GGCGTTTATGAGAAAACGCCGCTAAAAGTAAGAACATTAAC
95112 GGCGTTTATGAGAAAA
1 GGCGTTTATGAGAAAA
95128 ATACCGCTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (41 bp):
GGCGTTTATGAGAAAACGCCGCTAAAAGTAAGAACATTAAC
Done.