Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011059.1 Kokia drynarioides strain JFW-HI SEQ_126030, 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: 143208
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 98 characters in sequence are not A, C, G, or T
Found at i:1629 original size:36 final size:36
Alignment explanation
Indices: 1534--1613 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
1524 AAGAATGTTG
* * *
1534 AATGTCCAGCTATTTCATCATCTCTGATGGCTCTTA
1 AATGTCTAGCAATTTCATCATCTCTGATGGCCCTTA
* * *
1570 AATGTCTAGCAATCTCATCATCTCTGTTGGCCCTTG
1 AATGTCTAGCAATTTCATCATCTCTGATGGCCCTTA
1606 AATGTCTA
1 AATGTCTA
1614 CTTGTTTCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (36 bp):
AATGTCTAGCAATTTCATCATCTCTGATGGCCCTTA
Found at i:4192 original size:18 final size:18
Alignment explanation
Indices: 4146--4199 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
4136 ACTTTAATTT
*
4146 TAATTATTATTTTTTCAA
1 TAATAATTATTTTTTCAA
* *
4164 TATATATTTATTTTTTCGA
1 TA-ATAATTATTTTTTCAA
*
4183 TAATAATTATTTCTTCA
1 TAATAATTATTTTTTCA
4200 CATTTTCACA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.59
Consensus pattern (18 bp):
TAATAATTATTTTTTCAA
Found at i:11405 original size:2 final size:2
Alignment explanation
Indices: 11398--11438 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
11388 AACACATAGT
*
11398 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
11439 GAAGTGTATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:24509 original size:21 final size:22
Alignment explanation
Indices: 24485--24526 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
24475 AAAGATTTTA
*
24485 ATAAATAAAAAT-TTATAAATT
1 ATAAATAAAAATAATATAAATT
*
24506 ATAAATTAAAATAATATAAAT
1 ATAAATAAAAATAATATAAAT
24527 AAAATGGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAAATAAAAATAATATAAATT
Found at i:26311 original size:47 final size:48
Alignment explanation
Indices: 26260--26361 Score: 108
Period size: 45 Copynumber: 2.2 Consensus size: 48
26250 CTATTTTAAG
*
26260 ATTTTTTAAAT-AATTTTTTGAG-TATTGA-GATTTTTTAGGCTTTTATT
1 ATTTTTTAAATGAATTTTTTGAGATATTAATGATTTTTTA-G-TTTTATT
* *
26307 A-TTTTT--ATGAATTTTTTGAGATTTTAATGATTTTTTAGTTTTGTT
1 ATTTTTTAAATGAATTTTTTGAGATATTAATGATTTTTTAGTTTTATT
*
26352 ATATTTTAAA
1 ATTTTTTAAA
26362 AAAAATATGT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
44 2 0.04
45 18 0.40
46 14 0.31
47 10 0.22
48 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.12, T:0.61
Consensus pattern (48 bp):
ATTTTTTAAATGAATTTTTTGAGATATTAATGATTTTTTAGTTTTATT
Found at i:30042 original size:23 final size:23
Alignment explanation
Indices: 29921--30043 Score: 113
Period size: 23 Copynumber: 5.3 Consensus size: 23
29911 TAGCGCGCTA
*
29921 TCTGTTTAGCAC-GTCTCGTGCTC
1 TCTGTTTAGCACTGTGT-GTGCTC
*
29944 TCTGTTATTAGCACTGTGTATGCTC
1 TCTG-T-TTAGCACTGTGTGTGCTC
** * * *
29969 TCTGAGTAGCACTTTGTGTGTTA
1 TCTGTTTAGCACTGTGTGTGCTC
* * * *
29992 TCTGATTAGTACTTTGTGTACTC
1 TCTGTTTAGCACTGTGTGTGCTC
30015 TCTGTTTAGCACTGTGTGTGCTC
1 TCTGTTTAGCACTGTGTGTGCTC
30038 TCTGTT
1 TCTGTT
30044 GCCTAGCACT
Statistics
Matches: 80, Mismatches: 17, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
23 60 0.75
24 1 0.01
25 16 0.20
26 3 0.04
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (23 bp):
TCTGTTTAGCACTGTGTGTGCTC
Found at i:30082 original size:69 final size:69
Alignment explanation
Indices: 29941--30090 Score: 162
Period size: 69 Copynumber: 2.1 Consensus size: 69
29931 ACGTCTCGTG
* *
29941 CTCTCTGTTATTAGCACTGTGTATGCTCTCTGAGTAGCACTTTGTGTGTTATCTGATTAGTACTT
1 CTCTCTG-T-TTAGCACTGTGTATGCTCTCTGAGTAGCACTTTATGTGCTATCTGATTAGTACTT
30006 TGTGTA
64 TGTGTA
* * * * *
30012 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTGCCTAGCAC-TTATGTGCTCTTTG-TTAGTATT
1 CTCTCTGTTTAGCACTGTGTATGCTCTCTG-AG--TAGCACTTTATGTGCTATCTGATTAGTACT
30075 TTG-GTA
63 TTGTGTA
*
30081 CTCTTTGTTT
1 CTCTCTGTTT
30091 GTTTCGTATA
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
69 33 0.49
70 12 0.18
71 17 0.25
72 6 0.09
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (69 bp):
CTCTCTGTTTAGCACTGTGTATGCTCTCTGAGTAGCACTTTATGTGCTATCTGATTAGTACTTTG
TGTA
Found at i:33098 original size:24 final size:26
Alignment explanation
Indices: 33049--33099 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
33039 CCTGCCAAGG
*
33049 TCTCTCTTCCTTTTTCTTTTTCTATT
1 TCTCTCTTCCTTTTTCTTTATCTATT
33075 TCTCT-TTCCTTTTAT-TTTAT-TATT
1 TCTCTCTTCCTTTT-TCTTTATCTATT
33099 T
1 T
33100 TCAGTTGTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 5 0.22
25 12 0.52
26 6 0.26
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.71
Consensus pattern (26 bp):
TCTCTCTTCCTTTTTCTTTATCTATT
Found at i:34439 original size:26 final size:26
Alignment explanation
Indices: 34399--34452 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
34389 GATTTGTGAG
*
34399 TTAGATTCTTTGTATGCCGTGTTACA
1 TTAGATTCTTGGTATGCCGTGTTACA
34425 TTAGATTCTTGGTATGCCGTGTTACA
1 TTAGATTCTTGGTATGCCGTGTTACA
34451 TT
1 TT
34453 TTATTTTCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (26 bp):
TTAGATTCTTGGTATGCCGTGTTACA
Found at i:39936 original size:15 final size:15
Alignment explanation
Indices: 39918--39974 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
39908 TTGCCACCTT
*
39918 CACCACCTCCGCCCC
1 CACCACCTCCTCCCC
* *
39933 CACCTCCATCATCCCC
1 CACCACC-TCCTCCCC
*
39949 TTCACCACCTCCTCCTC
1 --CACCACCTCCTCCCC
39966 CACCACCTC
1 CACCACCTC
39975 TACCAACACA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
15 15 0.45
16 6 0.18
17 6 0.18
18 6 0.18
ACGTcount: A:0.16, C:0.65, G:0.02, T:0.18
Consensus pattern (15 bp):
CACCACCTCCTCCCC
Found at i:39936 original size:33 final size:32
Alignment explanation
Indices: 39890--39974 Score: 82
Period size: 33 Copynumber: 2.6 Consensus size: 32
39880 CCCAGATTCT
*
39890 CCTCCACCACCACCACCT-TTGCCACCTTCACCA
1 CCTCCACCACCACCACCTCAT-CC-CCTTCACCA
* * *
39923 CCTCCGCCCCCACCTCCATCATCCCCTTCACCA
1 CCTCCACCACCACCACC-TCATCCCCTTCACCA
* *
39956 CCTCCTCCTCCACCACCTC
1 CCTCCACCACCACCACCTC
39975 TACCAACACA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
32 2 0.05
33 37 0.86
34 3 0.07
35 1 0.02
ACGTcount: A:0.16, C:0.62, G:0.02, T:0.19
Consensus pattern (32 bp):
CCTCCACCACCACCACCTCATCCCCTTCACCA
Found at i:48549 original size:19 final size:19
Alignment explanation
Indices: 48511--48549 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
48501 ATAATATATA
* *
48511 TATATATATATAGCTGGAT
1 TATAGATATATAGCTAGAT
*
48530 TATAGATATATTGCTAGAT
1 TATAGATATATAGCTAGAT
48549 T
1 T
48550 TATTGCAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (19 bp):
TATAGATATATAGCTAGAT
Found at i:57057 original size:22 final size:22
Alignment explanation
Indices: 57032--57078 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
57022 ATTAATCATA
* *
57032 TCTGCATTGTCGCATGCTTTTC
1 TCTGCATAGTCGCACGCTTTTC
*
57054 TCTGCATAGTTGCACGCTTTTC
1 TCTGCATAGTCGCACGCTTTTC
57076 TCT
1 TCT
57079 ATTTTCTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.11, C:0.28, G:0.17, T:0.45
Consensus pattern (22 bp):
TCTGCATAGTCGCACGCTTTTC
Found at i:64938 original size:29 final size:30
Alignment explanation
Indices: 64905--64961 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
64895 TAATTTAATG
*
64905 TGTAATATTATATAT-AAATTTTGATTTTA
1 TGTAATATTATACATGAAATTTTGATTTTA
*
64934 TGTAATTTTATACATGAAATTTTGATTT
1 TGTAATATTATACATGAAATTTTGATTT
64962 CATTTAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (30 bp):
TGTAATATTATACATGAAATTTTGATTTTA
Found at i:88546 original size:18 final size:17
Alignment explanation
Indices: 88520--88553 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
88510 TTTTTTTCTC
88520 TCTTTTCCTTGTCCTTG
1 TCTTTTCCTTGTCCTTG
88537 TCTTTGTCCTTGTCCTT
1 TCTTT-TCCTTGTCCTT
88554 CTTCTCCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.00, C:0.29, G:0.12, T:0.59
Consensus pattern (17 bp):
TCTTTTCCTTGTCCTTG
Found at i:92856 original size:32 final size:33
Alignment explanation
Indices: 92820--92901 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 33
92810 TTGAAATACT
*
92820 TTTTAAATTTTTATAACAAT-TTTTATATAT-TA
1 TTTTAAATTTTTATAA-AATGTTATATATATATA
* *
92852 TTTT-AATTTTT-TTAAATGTTATATTTATATA
1 TTTTAAATTTTTATAAAATGTTATATATATATA
* *
92883 TTTTAAAATTTTATTAAAT
1 TTTTAAATTTTTATAAAAT
92902 AAATACTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 3 0.07
30 10 0.24
31 13 0.31
32 10 0.24
33 6 0.14
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (33 bp):
TTTTAAATTTTTATAAAATGTTATATATATATA
Found at i:92873 original size:21 final size:22
Alignment explanation
Indices: 92838--92897 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
92828 TTTTATAACA
*
92838 ATTTTTATATATTATTTTA-AT
1 ATTTTTAAATATTATTTTATAT
* *
92859 TTTTTTAAATGTTATATTTATAT
1 ATTTTTAAATATTAT-TTTATAT
* *
92882 ATTTTAAAATTTTATT
1 ATTTTTAAATATTATT
92898 AAATAAATAC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 12 0.39
22 5 0.16
23 14 0.45
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTTTTAAATATTATTTTATAT
Found at i:101569 original size:4 final size:4
Alignment explanation
Indices: 101560--101612 Score: 54
Period size: 4 Copynumber: 13.2 Consensus size: 4
101550 AAATAAACGG
* * * *
101560 GAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA G-AA GAAG GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA
101608 GAAA G
1 GAAA G
101613 GAAATGTGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 3 0.07
4 34 0.83
5 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:101592 original size:17 final size:15
Alignment explanation
Indices: 101560--101612 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
101550 AAATAAACGG
*
101560 GAAAGAAAGAAAGAAA
1 GAAAG-AAGAAGGAAA
*
101576 GGAAGAAGGAGAGGAAA
1 GAAAGAA-GA-AGGAAA
101593 GAAAGAAGAAGGAAA
1 GAAAGAAGAAGGAAA
101608 GAAAG
1 GAAAG
101613 GAAATGTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 13 0.41
16 8 0.25
17 11 0.34
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (15 bp):
GAAAGAAGAAGGAAA
Found at i:101616 original size:20 final size:20
Alignment explanation
Indices: 101564--101612 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
101554 AAACGGGAAA
101564 GAAAGAAAGAAAGGAAGAAG
1 GAAAGAAAGAAAGGAAGAAG
*
101584 GAGAGGAAAGAAA-GAAGAAG
1 GA-AAGAAAGAAAGGAAGAAG
101604 GAAAGAAAG
1 GAAAGAAAG
101613 GAAATGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 6 0.23
20 11 0.42
21 9 0.35
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (20 bp):
GAAAGAAAGAAAGGAAGAAG
Found at i:101727 original size:33 final size:33
Alignment explanation
Indices: 101688--101785 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 33
101678 AATTTTATTT
101688 AATTTTTAACAGATTTATTGAAGATGGATAATC
1 AATTTTTAACAGATTTATTGAAGATGGATAATC
** * *
101721 AATTTTT-----ATTTATT-AA-AT-TTTATTT
1 AATTTTTAACAGATTTATTGAAGATGGATAATC
101746 AATTTTTAACAGATTTATTGAAGATGGATAATC
1 AATTTTTAACAGATTTATTGAAGATGGATAATC
101779 AATTTTT
1 AATTTTT
101786 TGTATGCATT
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
25 10 0.20
26 2 0.04
27 2 0.04
28 7 0.14
30 7 0.14
31 2 0.04
32 2 0.04
33 17 0.35
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (33 bp):
AATTTTTAACAGATTTATTGAAGATGGATAATC
Found at i:101785 original size:58 final size:58
Alignment explanation
Indices: 101666--101785 Score: 240
Period size: 58 Copynumber: 2.1 Consensus size: 58
101656 TAAAATCATA
101666 TTTTATTTATTAAATTTTATTTAATTTTTAACAGATTTATTGAAGATGGATAATCAAT
1 TTTTATTTATTAAATTTTATTTAATTTTTAACAGATTTATTGAAGATGGATAATCAAT
101724 TTTTATTTATTAAATTTTATTTAATTTTTAACAGATTTATTGAAGATGGATAATCAAT
1 TTTTATTTATTAAATTTTATTTAATTTTTAACAGATTTATTGAAGATGGATAATCAAT
101782 TTTT
1 TTTT
101786 TGTATGCATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.53
Consensus pattern (58 bp):
TTTTATTTATTAAATTTTATTTAATTTTTAACAGATTTATTGAAGATGGATAATCAAT
Found at i:105248 original size:45 final size:45
Alignment explanation
Indices: 105124--105257 Score: 180
Period size: 45 Copynumber: 3.0 Consensus size: 45
105114 GGGAGGAATA
* * * **
105124 GAGTATCGCGATGGCTCGTCAAACTCAA-CCTGATATCCTTCCCTT
1 GAGTATTGCGGTGGCTCGTCAAACT-AAGGCTGATATCCTTGGCTT
*
105169 GAGTATTGCGGTGGCTCGTCAAATTAAGGCTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTAAGGCTGATATCCTTGGCTT
* *
105214 GAGTATTGCGGTGGCTCGTCAAACTGAGGTTGATATCCTTGGCT
1 GAGTATTGCGGTGGCTCGTCAAACTAAGGCTGATATCCTTGGCT
105258 CGATGAGCTA
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
44 2 0.03
45 77 0.97
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.31
Consensus pattern (45 bp):
GAGTATTGCGGTGGCTCGTCAAACTAAGGCTGATATCCTTGGCTT
Found at i:107197 original size:16 final size:16
Alignment explanation
Indices: 107176--107222 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
107166 TGATGGGGAT
107176 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
107192 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
107207 A-TATTTTGATAATTA
1 ATTATTTTGATAATTA
107222 A
1 A
107223 GTAGTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
14 9 0.35
15 6 0.23
16 11 0.42
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:107510 original size:20 final size:21
Alignment explanation
Indices: 107485--107527 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
107475 TACTTATTAC
*
107485 TACTAATAA-CAAAATAAAAT
1 TACTAACAAGCAAAATAAAAT
*
107505 TACTAACAAGCAAAATTAAAT
1 TACTAACAAGCAAAATAAAAT
107526 TA
1 TA
107528 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACAAGCAAAATAAAAT
Found at i:115701 original size:56 final size:56
Alignment explanation
Indices: 115641--115752 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
115631 TATTTTCATA
115641 GAATGTTTTAATATTTTATTCTTTTAGAATTATTAATACAAAAGAAAACTAAAATT
1 GAATGTTTTAATATTTTATTCTTTTAGAATTATTAATACAAAAGAAAACTAAAATT
115697 GAATGTTTTAATATTTTATTCTTTTAGAATTATTAATACAAAAGAAAACTAAAATT
1 GAATGTTTTAATATTTTATTCTTTTAGAATTATTAATACAAAAGAAAACTAAAATT
115753 ATCATTATCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (56 bp):
GAATGTTTTAATATTTTATTCTTTTAGAATTATTAATACAAAAGAAAACTAAAATT
Found at i:122403 original size:12 final size:12
Alignment explanation
Indices: 122371--122413 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
122361 TTAATACAAA
* *
122371 ATTTTAAATTCG
1 ATTTAAAATTTG
122383 ATTTGAAAATTTG
1 ATTT-AAAATTTG
*
122396 ATTTAAAATTTT
1 ATTTAAAATTTG
122408 ATTTAA
1 ATTTAA
122414 GTTTAATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (12 bp):
ATTTAAAATTTG
Found at i:129520 original size:20 final size:19
Alignment explanation
Indices: 129495--129532 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
129485 TTATTCTTCA
129495 GCTTTTTTTTTTTTTTTTT
1 GCTTTTTTTTTTTTTTTTT
129514 NGCTTTTTTTTTTTTTTTT
1 -GCTTTTTTTTTTTTTTTT
129533 ACATTATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.05, G:0.05, T:0.87
Consensus pattern (19 bp):
GCTTTTTTTTTTTTTTTTT
Found at i:136968 original size:24 final size:22
Alignment explanation
Indices: 136897--136968 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
136887 TTATTTTATT
136897 TTAAATTTATTATGGTTTGATCTC
1 TTAAATTTATTATGG-TTGAT-TC
* *
136921 TT-AATCTATT-TGTGTTTATT-
1 TTAAATTTATTATG-GTTGATTC
136941 TTAAATTTATTATGGTATGATGTC
1 TTAAATTTATTATGGT-TGAT-TC
136965 TTAA
1 TTAA
136969 TAAAGTATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
20 2 0.05
21 10 0.26
22 11 0.29
23 9 0.24
24 6 0.16
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.56
Consensus pattern (22 bp):
TTAAATTTATTATGGTTGATTC
Found at i:138277 original size:6 final size:6
Alignment explanation
Indices: 138266--138307 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
138256 TAAGACTTGT
138266 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
138308 ATGTGGAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:138687 original size:31 final size:30
Alignment explanation
Indices: 138649--138756 Score: 87
Period size: 31 Copynumber: 3.6 Consensus size: 30
138639 TTAATATAAC
* *
138649 ATTTGGTATCTTAACTTAACATTTTTTCCTA
1 ATTTGGTACCTAAACTT-ACATTTTTTCCTA
*
138680 ATTTGGTACCTAAAC--ACTTTTTTGATCC-A
1 ATTTGGTACCTAAACTTACATTTTT--TCCTA
** * *
138709 ATTTGGTATATGAACTTGACACTTTTTCCTA
1 ATTTGGTACCTAAACTT-ACATTTTTTCCTA
*
138740 ATTCGGTACCTAAACTT
1 ATTTGGTACCTAAACTT
138757 TTTTGGACCC
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
28 7 0.12
29 13 0.22
30 6 0.10
31 27 0.46
32 6 0.10
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (30 bp):
ATTTGGTACCTAAACTTACATTTTTTCCTA
Found at i:138742 original size:60 final size:61
Alignment explanation
Indices: 138649--138835 Score: 211
Period size: 60 Copynumber: 3.1 Consensus size: 61
138639 TTAATATAAC
* *
138649 ATTTGGTATCTTAACTTAACATTTTTTCCTAATTTGGTACCTAAACACTTTTTT-GATCCA
1 ATTTGGTATCTGAACTTGACATTTTTTCCTAATTTGGTACCTAAACACTTTTTTAGATCCA
* * * * *
138709 ATTTGGTATATGAACTTGACACTTTTTCCTAATTCGGTACCT-AA-ACTTTTTTGGACCCA
1 ATTTGGTATCTGAACTTGACATTTTTTCCTAATTTGGTACCTAAACACTTTTTTAGATCCA
* * * * * * * *
138768 ATTTGATACCTGAACTTGACATTTTTTCTTATTTTGGTATCTAAGC-TTTTTTTAGATTCA
1 ATTTGGTATCTGAACTTGACATTTTTTCCTAATTTGGTACCTAAACACTTTTTTAGATCCA
138828 ATTTGGTA
1 ATTTGGTA
138836 CCTAAATTTA
Statistics
Matches: 104, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
58 8 0.08
59 41 0.39
60 55 0.53
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.47
Consensus pattern (61 bp):
ATTTGGTATCTGAACTTGACATTTTTTCCTAATTTGGTACCTAAACACTTTTTTAGATCCA
Found at i:138787 original size:59 final size:58
Alignment explanation
Indices: 138661--138819 Score: 192
Period size: 59 Copynumber: 2.7 Consensus size: 58
138651 TTGGTATCTT
* * * *
138661 AACTTAACATTTTTTCCTAATTTGGTACCTAAACACTTTTTTGATCCAATTTGGTATATG
1 AACTTGACATTTTTTCCTAATTTGGTACCT-AA-ACTTTTTTGACCCAATTTGATACATG
* * *
138721 AACTTGACACTTTTTCCTAATTCGGTACCTAAACTTTTTTGGACCCAATTTGATACCTG
1 AACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTT-GACCCAATTTGATACATG
* * * *
138780 AACTTGACATTTTTTCTTATTTTGGTATCTAAGCTTTTTT
1 AACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTT
138820 TAGATTCAAT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
58 8 0.09
59 50 0.59
60 27 0.32
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.46
Consensus pattern (58 bp):
AACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTGACCCAATTTGATACATG
Found at i:139148 original size:80 final size:78
Alignment explanation
Indices: 138997--139155 Score: 203
Period size: 80 Copynumber: 2.0 Consensus size: 78
138987 ATTAGATACC
* * *
138997 AAATTAGGAAAAAGAGTCAAGTTCAAGTATCAAATTAGACCCCAAAAAATTTAAGTATCAACTTA
1 AAATTAGGAAAAAGAGTCAAGTTCAAGTATCAAATTAGACCCAAAAAAATTTAAGTACCAA-AT-
*
139062 TAAAAAAAAGTGTCA
64 TAGAAAAAAGTGTCA
* * * *
139077 AAATTAGGAAAAAGTGTCAAGTTTAATTATCAAATTAGA-CCAAAAAATATTTAGGTACCAAATT
1 AAATTAGGAAAAAGAGTCAAGTTCAAGTATCAAATTAGACCCAAAAAA-ATTTAAGTACCAAATT
*
139141 AGGAAAAAGTGTCA
65 AGAAAAAAGTGTCA
139155 A
1 A
139156 GTTCAGGTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
78 14 0.20
79 8 0.12
80 47 0.68
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (78 bp):
AAATTAGGAAAAAGAGTCAAGTTCAAGTATCAAATTAGACCCAAAAAAATTTAAGTACCAAATTA
GAAAAAAGTGTCA
Found at i:139236 original size:3 final size:3
Alignment explanation
Indices: 139228--139254 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
139218 AATATGTTGC
139228 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
139255 TCAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:141162 original size:24 final size:22
Alignment explanation
Indices: 141091--141162 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
141081 TTAATTTATT
141091 TTAAATTTATTATGGTTTGATCTC
1 TTAAATTTATTATGG-TTGAT-TC
* *
141115 TT-AATCTATT-TGTGTTTATT-
1 TTAAATTTATTATG-GTTGATTC
141135 TTAAATTTATTATGGTATGATGTC
1 TTAAATTTATTATGGT-TGAT-TC
141159 TTAA
1 TTAA
141163 TAAAGTATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
20 2 0.05
21 10 0.26
22 11 0.29
23 9 0.24
24 6 0.16
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.56
Consensus pattern (22 bp):
TTAAATTTATTATGGTTGATTC
Found at i:143181 original size:909 final size:899
Alignment explanation
Indices: 141424--143208 Score: 3480
Period size: 909 Copynumber: 2.0 Consensus size: 899
141414 TATTATGGTG
141424 TGATGTCTTAATAAAGTATGAAATTAGAGAAATAAAGTGGCATGAATGACCAAAGAATAAAGTGT
1 TGATGTCTTAATAAAGTATGAAATTAGAGAAATAAAGTGGCATGAATGACCAAAGAATAAAGTGT
141489 CATTATATTACTAGGGAAAAGTAATATTGTGTCGATTTGGGTTTTATAAATAAAAGAATCTTCAC
66 CATTATATTACTAGGGAAAAGTAATATTGTGTCGATTTGGGTTTTATAAATAAAAGAATCTTCAC
141554 TATAATCTACAACTCTGTGCAAAAAATAAAGGTATAATACCATAAATAACCCCTATACTTTTCAA
131 TATAATCTACAACTCTGTGCAAAAAATAAAGGTATAATACCATAAATAACCCCTATACTTTTCAA
141619 AATGGTCCTTGTGTCAATTTTTTTGTTAAAATTTTTATTCTTTTCAAGTTTCCATTGATTTCTAA
196 AATGGTCCTTGTGTCAATTTTTTTGTTAAAATTTTTATTCTTTTCAAGTTTCCATTGATTTCTAA
141684 ATCAAATGCATCATCTATGGTCTTTAATCTGGACCTGGGATCGCCATAAACAATCATCGGAATTA
261 ATCAAATGCATCATCTATGGTCTTTAATCTGGACCTGGGATCGCCATAAACAATCATCGGAATTA
141749 ATTCTATAACCTCTTCTCTCATTGCCAGTTGTTCATCCTTTCAAACTTGAAGCAATGTTTGGTTG
326 ATTCTATAACCTCTTCTCTCATTGCCAGTTGTTCATCCTTTCAAACTTGAAGCAATGTTTGGTTG
141814 ATTTTTACTTTTCCAACTCTTAAATCCTTTGATGAATTGAACACTTGAAAATATCATCTTTTTCA
391 ATTTTTACTTTTCCAACTCTTAAATCCTTTGATGAATTGAACACTTGAAAATATCATCTTTTTCA
141879 TTAAGTTAGCCGTCCATGGCCTTTTCTTCCATATCCAATTTTTGCTTTTATTCCAAATAGGTCCT
456 TTAAGTTAGCCGTCCATGGCCTTTTCTTCCATATCCAATTTTTGCTTTTATTCCAAATAGGTCCT
141944 TCCATCATTTTTAAGCTTTCCAAACTCCAAAACCTTCCATTTTCTTTGGAACTTCTGAAAGAAAG
521 TCCATCATTTTTAAGCTTTCCAAACTCCAAAACCTTCCATTTTCTTTGGAACTTCTGAAAGAAAG
142009 TCATAAAAGAGAGTTAGTAGACACCTTAAACTTCTTATAGAATTAATTTTGAGGTGTGAGAGAGA
586 TCATAAAAGAGAGTTAGTAGACACCTTAAACTTCTTATAGAATTAATTTTGAGGTGTGAGAGAGA
142074 TAAAGGACTAAATCGAGAAAATTTGAATTCAAGGGTTAAGGTAAGAAATGGTTAAATCCTCATGA
651 TAAAGGACTAAATCGAGAAAATTTGAATTCAAGGGTTAAGGTAAGAAATGGTTAAATCCTCATGA
142139 TATACATGTATTTTACTGTTATTTAGCATGGAAATCATTGAATTATAGCATATAGCTTACATGTG
716 TATACATGTATTTTACTGTTATTTAGCATGGAAATCATTGAATTATAGCATATAGCTTACATGTG
142204 TTTGTGTGAAAATGAAGAGAAAGAGAAGAGAGGCAAGGATCAAATTGAAGACAAAGGAAAAGAAT
781 TTTGTGTGAAAATGAAGAGAAAGAGAAGAGAGGCAAGGATCAAATTGAAGACAAAGGAAAAGAAT
142269 AGAACAATGGGTAAAAGAGAAGGAAATCAGCCTTTTTGTTGTAAGTACTACAAT
846 AGAACAATGGGTAAAAGAGAAGGAAATCAGCCTTTTTGTTGTAAGTACTACAAT
142323 NNNNNNNNNNTGATGTCTTAATAAAGTATGAAATTAGAGAAATAAAGTGGCATGAATGACCAAAG
1 ----------TGATGTCTTAATAAAGTATGAAATTAGAGAAATAAAGTGGCATGAATGACCAAAG
142388 AATAAAGTGTCATTATATTACTAGGGAAAAGTAATATTGTGTCGATTTGGGTTTTATAAATAAAA
56 AATAAAGTGTCATTATATTACTAGGGAAAAGTAATATTGTGTCGATTTGGGTTTTATAAATAAAA
142453 GAATCTTCACTATAATCTACAACTCTGTGCAAAAAATAAAGGTATAATACCATAAATAACCCCTA
121 GAATCTTCACTATAATCTACAACTCTGTGCAAAAAATAAAGGTATAATACCATAAATAACCCCTA
142518 TACTTTTCAAAATGGTCCTTGTGTCAATTTTTTTGTTAAAATTTTTATTCTTTTCAAGTTTCCAT
186 TACTTTTCAAAATGGTCCTTGTGTCAATTTTTTTGTTAAAATTTTTATTCTTTTCAAGTTTCCAT
142583 TGATTTCTAAATCAAATGCATCATCTATGGTCTTTAATCTGGACCTGGGATCGCCATAAACAATC
251 TGATTTCTAAATCAAATGCATCATCTATGGTCTTTAATCTGGACCTGGGATCGCCATAAACAATC
142648 ATCGGAATTAATTCTATAACCTCTTCTCTCATTGCCAGTTGTTCATCCTTTCAAACTTGAAGCAA
316 ATCGGAATTAATTCTATAACCTCTTCTCTCATTGCCAGTTGTTCATCCTTTCAAACTTGAAGCAA
142713 TGTTTGGTTGATTTTTACTTTTCCAACTCTTAAATCCTTTGATGAATTGAACACTTGAAAATATC
381 TGTTTGGTTGATTTTTACTTTTCCAACTCTTAAATCCTTTGATGAATTGAACACTTGAAAATATC
142778 ATCTTTTTCATTAAGTTAGCCGTCCATGGCCTTTTCTTCCATATCCAATTTTTGCTTTTATTCCA
446 ATCTTTTTCATTAAGTTAGCCGTCCATGGCCTTTTCTTCCATATCCAATTTTTGCTTTTATTCCA
142843 AATAGGTCCTTCCATCATTTTTAAGCTTTCCAAACTCCAAAACCTTCCATTTTCTTTGGAACTTC
511 AATAGGTCCTTCCATCATTTTTAAGCTTTCCAAACTCCAAAACCTTCCATTTTCTTTGGAACTTC
142908 TGAAAGAAAGTCATAAAAGAGAGTTAGTAGACACCTTAAACTTCTTATAGAATTAATTTTGAGGT
576 TGAAAGAAAGTCATAAAAGAGAGTTAGTAGACACCTTAAACTTCTTATAGAATTAATTTTGAGGT
142973 GTGAGAGAGATAAAGGACTAAATCGAGAAAATTTGAATTCAAGGGTTAAGGTAAGAAATGGTTAA
641 GTGAGAGAGATAAAGGACTAAATCGAGAAAATTTGAATTCAAGGGTTAAGGTAAGAAATGGTTAA
143038 ATCCTCATGATATACATGTATTTTACTGTTATTTAGCATGGAAATCATTGAATTATAGCATATAG
706 ATCCTCATGATATACATGTATTTTACTGTTATTTAGCATGGAAATCATTGAATTATAGCATATAG
143103 CTTACATGTGTTTGTGTGAAAATGAAGAGAAAGAGAAGAGAGGCAAGGATCAAATTGAAGACAAA
771 CTTACATGTGTTTGTGTGAAAATGAAGAGAAAGAGAAGAGAGGCAAGGATCAAATTGAAGACAAA
143168 GGAAAAGAATAGAACAATGGGTAAAAGAGAAGGAAATCAGC
836 GGAAAAGAATAGAACAATGGGTAAAAGAGAAGGAAATCAGC
Statistics
Matches: 876, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
909 876 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (899 bp):
TGATGTCTTAATAAAGTATGAAATTAGAGAAATAAAGTGGCATGAATGACCAAAGAATAAAGTGT
CATTATATTACTAGGGAAAAGTAATATTGTGTCGATTTGGGTTTTATAAATAAAAGAATCTTCAC
TATAATCTACAACTCTGTGCAAAAAATAAAGGTATAATACCATAAATAACCCCTATACTTTTCAA
AATGGTCCTTGTGTCAATTTTTTTGTTAAAATTTTTATTCTTTTCAAGTTTCCATTGATTTCTAA
ATCAAATGCATCATCTATGGTCTTTAATCTGGACCTGGGATCGCCATAAACAATCATCGGAATTA
ATTCTATAACCTCTTCTCTCATTGCCAGTTGTTCATCCTTTCAAACTTGAAGCAATGTTTGGTTG
ATTTTTACTTTTCCAACTCTTAAATCCTTTGATGAATTGAACACTTGAAAATATCATCTTTTTCA
TTAAGTTAGCCGTCCATGGCCTTTTCTTCCATATCCAATTTTTGCTTTTATTCCAAATAGGTCCT
TCCATCATTTTTAAGCTTTCCAAACTCCAAAACCTTCCATTTTCTTTGGAACTTCTGAAAGAAAG
TCATAAAAGAGAGTTAGTAGACACCTTAAACTTCTTATAGAATTAATTTTGAGGTGTGAGAGAGA
TAAAGGACTAAATCGAGAAAATTTGAATTCAAGGGTTAAGGTAAGAAATGGTTAAATCCTCATGA
TATACATGTATTTTACTGTTATTTAGCATGGAAATCATTGAATTATAGCATATAGCTTACATGTG
TTTGTGTGAAAATGAAGAGAAAGAGAAGAGAGGCAAGGATCAAATTGAAGACAAAGGAAAAGAAT
AGAACAATGGGTAAAAGAGAAGGAAATCAGCCTTTTTGTTGTAAGTACTACAAT
Done.