Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001006.1 Kokia drynarioides strain JFW-HI SEQ_112213, 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: 105443
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:682 original size:7 final size:7
Alignment explanation
Indices: 670--713 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
660 TCAGAAAAAA
670 GTCAACG
1 GTCAACG
677 GTCAACG
1 GTCAACG
* *
684 ATCAACT
1 GTCAACG
*
691 GTCAA-A
1 GTCAACG
697 GTCAACG
1 GTCAACG
704 GTCAACG
1 GTCAACG
711 GTC
1 GTC
714 GGTCAACGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:718 original size:11 final size:11
Alignment explanation
Indices: 702--775 Score: 60
Period size: 11 Copynumber: 6.7 Consensus size: 11
692 TCAAAGTCAA
702 CGGTCAACGGT
1 CGGTCAACGGT
*
713 CGGTCAACGAT
1 CGGTCAACGGT
*
724 CGATCAACGG-
1 CGGTCAACGGT
*
734 CTGGTCAACAGT
1 C-GGTCAACGGT
* * **
746 AGATCAATAGT
1 CGGTCAACGGT
757 CGGTCAACGGT
1 CGGTCAACGGT
*
768 CGATCAAC
1 CGGTCAAC
776 TGTTTGACTT
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
10 1 0.02
11 47 0.98
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.19
Consensus pattern (11 bp):
CGGTCAACGGT
Found at i:731 original size:22 final size:22
Alignment explanation
Indices: 705--775 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
695 AAGTCAACGG
705 TCAACGGTCGGTCAACGATCGA
1 TCAACGGTCGGTCAACGATCGA
*
727 TCAACGG-CTGGTCAAC-AGTAGA
1 TCAACGGTC-GGTCAACGA-TCGA
** *
749 TCAATAGTCGGTCAACGGTCGA
1 TCAACGGTCGGTCAACGATCGA
771 TCAAC
1 TCAAC
776 TGTTTGACTT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
21 2 0.05
22 36 0.92
23 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (22 bp):
TCAACGGTCGGTCAACGATCGA
Found at i:5318 original size:29 final size:29
Alignment explanation
Indices: 5243--5311 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 29
5233 GCCTTTTATT
*
5243 AATTCATTTTTTACCCCCAAACTCTTTTAA
1 AATTCA-TTTTTACCCCCAAACTCTTATAA
*
5273 AATCCTATTTTTACCCCCAAACT-TTATAA
1 AATTC-ATTTTTACCCCCAAACTCTTATAA
5302 AATTCATTTT
1 AATTCATTTT
5312 CGACCCCTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.14
29 9 0.26
30 20 0.57
31 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (29 bp):
AATTCATTTTTACCCCCAAACTCTTATAA
Found at i:7004 original size:19 final size:17
Alignment explanation
Indices: 6971--7019 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
6961 ATCCATATGT
* *
6971 ATTTTTAATACTTCTTA
1 ATTTTTTATATTTCTTA
*
6988 ATATTTTTATCATTTCTTG
1 AT-TTTTTAT-ATTTCTTA
7007 ATTTTTTATATTT
1 ATTTTTTATATTT
7020 AAAATTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 6 0.22
18 13 0.48
19 8 0.30
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTTTTTATATTTCTTA
Found at i:8701 original size:228 final size:228
Alignment explanation
Indices: 8304--9602 Score: 1370
Period size: 228 Copynumber: 5.7 Consensus size: 228
8294 TAAAGTTCGA
* *
8304 CCATCCTCCAA-CTGCTTCCCAGCAAAGATCAACCTCTGCTGGTCTGGAGGAATCCCCTCCTTGT
1 CCATCCT-CAAGCTGCTTCCCAGCAAAAATCAACCTCTGCTGGTCTGGAGGAATACCCTCCTTGT
* * *
8368 CCTGAATCTTAGCTTTCACATTGTCAATCGTGTCCGAGCTCTCCACCTCCAGGGTGATGGTTTTC
65 CCTGAATCTTCGCTTTCACATTGTCAATCGTGTCCGAGCTCTCCACCTCCAGTGTGATGGTTTTA
* * * *
8433 CCAGTCAAGGTCTTCACGAATATCTGCATCCCTCCTCTAAGGCGCAAAACCAAATGCAGGGTGGA
130 CCAGTCAAGGTCTTAACAAATATCTGCATCCCTCCTCTAAGGCGCAGAACCAAGTGCAGGGTGGA
*
8498 TTCCTTTTGGATGTTATAGTCCGCAAGTGTCCTC
195 CTCCTTTTGGATGTTATAGTCCGCAAGTGTCCTC
* * *
8532 CCATCCTCCAGCTGCTTACCAGCAAAAATCAACCTCTGCTGGTCTGGAGGAATTCCCTCCTTGTC
1 CCATCCTCAAGCTGCTTCCCAGCAAAAATCAACCTCTGCTGGTCTGGAGGAATACCCTCCTTGTC
* * *
8597 CTGAATCTTCGCTTTCACATTGTCAATAGTGTCCGAGCTCTCAACCTCCAGTGTTATGGTTTTAC
66 CTGAATCTTCGCTTTCACATTGTCAATCGTGTCCGAGCTCTCCACCTCCAGTGTGATGGTTTTAC
8662 CAGTCAAGGTCTTAACAAATATCTGCATCCCTCCTCTAAGGCGCAGAACCAAGTGCAGGGTGGAC
131 CAGTCAAGGTCTTAACAAATATCTGCATCCCTCCTCTAAGGCGCAGAACCAAGTGCAGGGTGGAC
8727 TCCTTTTGGATGTTATAGTCCGCAAGTGTCCTC
196 TCCTTTTGGATGTTATAGTCCGCAAGTGTCCTC
* * * *
8760 CCATCCTCAAGCTGCTTTCCGGCAAAAATCAACCTCTGCTGGTCTGGAGGAATTCCCTCCTTATC
1 CCATCCTCAAGCTGCTTCCCAGCAAAAATCAACCTCTGCTGGTCTGGAGGAATACCCTCCTTGTC
* * * *
8825 CTGAATCTTCGCTTTAACATTGTCAATGGTGTCCGAGCTCTCGACCTCCAGTGTTATGGTTTTAC
66 CTGAATCTTCGCTTTCACATTGTCAATCGTGTCCGAGCTCTCCACCTCCAGTGTGATGGTTTTAC
* *
8890 CAGTCAAGGTCTTAACGAATATCTGCATCCCTCCTCGAAGGCGCAGAACCAAGTGCAGGGTGGAC
131 CAGTCAAGGTCTTAACAAATATCTGCATCCCTCCTCTAAGGCGCAGAACCAAGTGCAGGGTGGAC
* *
8955 TCCTTTTGGATGTTATAATCCGCAAGCGTCCTC
196 TCCTTTTGGATGTTATAGTCCGCAAGTGTCCTC
* * * * * *
8988 CCATCCTCGAGCTGCTTTCCGGCAAAAATCAACCTCTGCTGGTCAGGTGGGATACCCTCCTTGTC
1 CCATCCTCAAGCTGCTTCCCAGCAAAAATCAACCTCTGCTGGTCTGGAGGAATACCCTCCTTGTC
* * * * * * * * * * * *
9053 TTGGATCTTGGCCTTCACGTTATCAATTGTGTCTGAGCTCTCCACCTCCAATGTAATAGTTTTTC
66 CTGAATCTTCGCTTTCACATTGTCAATCGTGTCCGAGCTCTCCACCTCCAGTGTGATGGTTTTAC
* * * * * * ** * * * * * *
9118 CAGTCAAAGTTTTCACAAAAACCTGCATTCCC-CCACGCAGTCGGAGCACCAGGTGAAGGGTCGA
131 CAGTCAAGGTCTTAACAAATATCTGCA-TCCCTCCTCTAAGGCGCAGAACCAAGTGCAGGGTGGA
* * * * * **
9182 CTCCTTCTGAATGTTATAGTCTGCAAGGGTTCGG
195 CTCCTTTTGGATGTTATAGTCCGCAAGTGTCCTC
* * * * *
9216 CCATCTTCAAGCTGTTTCCCAGCAAAAATCAACCTCTGCTGGTCTGGTGGGATACCCTCCTTATC
1 CCATCCTCAAGCTGCTTCCCAGCAAAAATCAACCTCTGCTGGTCTGGAGGAATACCCTCCTTGTC
* * * * * * * ** *
9281 CTGAATCTTGGCCTTAACATTATCAATCGTATCAGAACTCTCCACCTCCAAAGTGATGGTTTTTC
66 CTGAATCTTCGCTTTCACATTGTCAATCGTGTCCGAGCTCTCCACCTCCAGTGTGATGGTTTTAC
* * * * * * * * * * * *
9346 CTGTGAGGGTTTTTACAAATATCTGCATCCCACCCCTAAGACGAAGGA-CAAGGTGGAGGGTAGA
131 CAGTCAAGGTCTTAACAAATATCTGCATCCCTCCTCTAAGGCGCAGAACCAA-GTGCAGGGTGGA
* * * * * * **
9410 CT-CTTTCTGGATGTTGTAATCAGCGAGGGTTCGG
195 CTCCTTT-TGGATGTTATAGTCCGCAAGTGTCCTC
* * * * * * *
9444 CCATCTTCAAGTTGTTTACCGGCAAAGAT-AAGCCTCTGTTGGTCTGGAGGAAT-CCCTTCCTTG
1 CCATCCTCAAGCTGCTTCCCAGCAAAAATCAA-CCTCTGCTGGTCTGGAGGAATACCC-TCCTTG
* * * * * * * * * * *
9507 TCTTGGATCTTGGCCTTGACATTATCAATCGTATCAGAGCTTTCCACCTCGAGTGTGATGGTCTT
64 TCCTGAATCTTCGCTTTCACATTGTCAATCGTGTCCGAGCTCTCCACCTCCAGTGTGATGGTTTT
* * * *
9572 GCCAGT-AAGAGTTTTCACAAAGATCTGCATC
129 ACCAGTCAAG-GTCTTAACAAATATCTGCATC
9603 TGCTGTCAAC
Statistics
Matches: 933, Mismatches: 130, Indels: 16
0.86 0.12 0.01
Matches are distributed among these distances:
227 18 0.02
228 911 0.98
229 4 0.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (228 bp):
CCATCCTCAAGCTGCTTCCCAGCAAAAATCAACCTCTGCTGGTCTGGAGGAATACCCTCCTTGTC
CTGAATCTTCGCTTTCACATTGTCAATCGTGTCCGAGCTCTCCACCTCCAGTGTGATGGTTTTAC
CAGTCAAGGTCTTAACAAATATCTGCATCCCTCCTCTAAGGCGCAGAACCAAGTGCAGGGTGGAC
TCCTTTTGGATGTTATAGTCCGCAAGTGTCCTC
Found at i:15227 original size:17 final size:17
Alignment explanation
Indices: 15207--15243 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
15197 TTAAAATTGG
*
15207 ATTGAGAAAATAATTTA
1 ATTGAGAAAATAAATTA
*
15224 ATTGAGAAATTAAATTA
1 ATTGAGAAAATAAATTA
15241 ATT
1 ATT
15244 AATTGATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (17 bp):
ATTGAGAAAATAAATTA
Found at i:15636 original size:19 final size:18
Alignment explanation
Indices: 15594--15636 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
15584 AAAAAATAAT
*
15594 AAAATTTTATTTTATAGA
1 AAAATTCTATTTTATAGA
*
15612 ATAAATTCTATTTTTTGAGA
1 A-AAATTCTATTTTAT-AGA
15632 AAAAT
1 AAAAT
15637 ACATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 16 0.76
20 4 0.19
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (18 bp):
AAAATTCTATTTTATAGA
Found at i:16450 original size:24 final size:24
Alignment explanation
Indices: 16409--16469 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
16399 GACTAATAAG
* * *
16409 AGTTTGACTCAAATAAATAAACAA
1 AGTTTAACTGAAACAAATAAACAA
* * *
16433 AGTTTAATTGAAACAAATAAATAG
1 AGTTTAACTGAAACAAATAAACAA
16457 AGTTTAACTGAAA
1 AGTTTAACTGAAA
16470 GATTACTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.28
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAA
Found at i:18200 original size:17 final size:17
Alignment explanation
Indices: 18178--18219 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
18168 TACTATAATG
18178 GCAAAAGAACGAAGAGT
1 GCAAAAGAACGAAGAGT
18195 GCAAAAGAACGAAGAGT
1 GCAAAAGAACGAAGAGT
*
18212 ACAAAAGA
1 GCAAAAGA
18220 TGGAGATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.57, C:0.12, G:0.26, T:0.05
Consensus pattern (17 bp):
GCAAAAGAACGAAGAGT
Found at i:44331 original size:34 final size:34
Alignment explanation
Indices: 44288--44355 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
44278 GTATCCCTGC
44288 ATCATATCCACTGACATGTTAAACTGAGTATAAA
1 ATCATATCCACTGACATGTTAAACTGAGTATAAA
44322 ATCATATCCACTGACATGTTAAACTGAGTATAAA
1 ATCATATCCACTGACATGTTAAACTGAGTATAAA
44356 CAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (34 bp):
ATCATATCCACTGACATGTTAAACTGAGTATAAA
Found at i:50175 original size:80 final size:75
Alignment explanation
Indices: 49995--50192 Score: 209
Period size: 80 Copynumber: 2.5 Consensus size: 75
49985 ATCGAATATT
* * * **
49995 AACTCGATTAAAAAAATTATAAAATTATTTAAAAATATTTTAATTTTTTCATTTTATGAAATAAA
1 AACTTGATTAAAAAAATTATAAAATTA-TTCAAGATATTTTAATTTTTTCATTTTAAAAAATAAA
* * *
50060 AATCGAATATC
65 AATAGAACACC
* **
50071 AACTTAATTGGAAAAATTATAAAATTATTCAAGAGTATTTTAA-TTTTTCATTTTTAAAAAAATA
1 AACTTGATTAAAAAAATTATAAAATTATTCAAGA-TATTTTAATTTTTTCA-TTTT---AAAA-A
50135 ATAAAAATAGAACACC
60 ATAAAAATAGAACACC
*
50151 AACTTGATTAAAAAAATTACAAAATTATTCAATGATATTTTA
1 AACTTGATTAAAAAAATTATAAAATTATTCAA-GATATTTTA
50193 TCAATAAAAA
Statistics
Matches: 100, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
75 12 0.12
76 35 0.35
79 2 0.02
80 49 0.49
81 2 0.02
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.38
Consensus pattern (75 bp):
AACTTGATTAAAAAAATTATAAAATTATTCAAGATATTTTAATTTTTTCATTTTAAAAAATAAAA
ATAGAACACC
Found at i:67828 original size:21 final size:21
Alignment explanation
Indices: 67786--67833 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
67776 AAATTAACGA
**
67786 TGTTAGTAAAATTTGTTATTG
1 TGTTAGTAAAATTTAATATTG
* *
67807 TGTTAGTGAAATTTAATCTTG
1 TGTTAGTAAAATTTAATATTG
67828 TAGTTA
1 T-GTTA
67834 TTAGTTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.50
Consensus pattern (21 bp):
TGTTAGTAAAATTTAATATTG
Found at i:68574 original size:23 final size:24
Alignment explanation
Indices: 68535--68590 Score: 80
Period size: 22 Copynumber: 2.4 Consensus size: 24
68525 TAAAGTAAAA
*
68535 AAAAAAAAACCCAAAGTTATAATTG
1 AAAAAAAAACCCAAAGTTATAA-GG
68560 AAAAAAAAA-CC-AAGTTATAAGG
1 AAAAAAAAACCCAAAGTTATAAGG
68582 AAAAAAAAA
1 AAAAAAAAA
68591 ACCTCTCTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 10 0.33
23 9 0.30
24 2 0.07
25 9 0.30
ACGTcount: A:0.68, C:0.09, G:0.09, T:0.14
Consensus pattern (24 bp):
AAAAAAAAACCCAAAGTTATAAGG
Found at i:68591 original size:23 final size:25
Alignment explanation
Indices: 68534--68593 Score: 81
Period size: 23 Copynumber: 2.5 Consensus size: 25
68524 TTAAAGTAAA
*
68534 AAAAAAAAAACCCAAAGTTATAATTG
1 AAAAAAAAAA-CCAAAGTTATAATGG
68560 -AAAAAAAAACC-AAGTTATAA-GG
1 AAAAAAAAAACCAAAGTTATAATGG
68582 AAAAAAAAAACC
1 AAAAAAAAAACC
68594 TCTCTCTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 1 0.03
23 20 0.62
24 2 0.06
25 9 0.28
ACGTcount: A:0.67, C:0.12, G:0.08, T:0.13
Consensus pattern (25 bp):
AAAAAAAAAACCAAAGTTATAATGG
Found at i:69473 original size:2 final size:2
Alignment explanation
Indices: 69460--69508 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
69450 TGCATTAATG
69460 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69503 TA TA TA
1 TA TA TA
69509 GATTATGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:69567 original size:23 final size:23
Alignment explanation
Indices: 69551--69613 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 23
69541 ATTAATATAT
*
69551 AAATAATATATTTATTAAAAATA
1 AAATAAAATATTTATTAAAAATA
* *
69574 AAATAAAATATTAATTGAAATGATA
1 AAATAAAATATTTATT-AAA-AATA
*
69599 AAATTAAATATTTAT
1 AAATAAAATATTTAT
69614 AATTTATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 14 0.42
24 3 0.09
25 16 0.48
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (23 bp):
AAATAAAATATTTATTAAAAATA
Found at i:72825 original size:11 final size:10
Alignment explanation
Indices: 72798--72879 Score: 52
Period size: 10 Copynumber: 8.7 Consensus size: 10
72788 ATTTCAAACT
72798 ATAA-TTTTA
1 ATAATTTTTA
72807 ATAATTTTTA
1 ATAATTTTTA
72817 A-ATATTTTT-
1 ATA-ATTTTTA
*
72826 -T-GTTTTTA
1 ATAATTTTTA
*
72834 ATAA-ATTTA
1 ATAATTTTTA
*
72843 AT-ATTTTTT
1 ATAATTTTTA
**
72852 ATAATGCTTA
1 ATAATTTTTA
72862 ATAATTTTTAA
1 ATAATTTTT-A
72873 ATAATTT
1 ATAATTT
72880 ATATTTTTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
7 5 0.09
8 1 0.02
9 17 0.31
10 23 0.43
11 8 0.15
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:72849 original size:18 final size:18
Alignment explanation
Indices: 72828--72887 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 18
72818 ATATTTTTTG
72828 TTTTTAATAAATTTAATA
1 TTTTTAATAAATTTAATA
*
72846 TTTTTTAT-AATGCTTAATAA
1 TTTTTAATAAAT--TTAAT-A
72866 TTTTTAA-ATAATTT-ATA
1 TTTTTAATA-AATTTAATA
72883 TTTTT
1 TTTTT
72888 TTTATGATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
17 9 0.26
18 9 0.26
19 7 0.20
20 7 0.20
21 3 0.09
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTAATAAATTTAATA
Found at i:72852 original size:19 final size:19
Alignment explanation
Indices: 72828--72888 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
72818 ATATTTTTTG
72828 TTTTTAATAAATTTAATAT
1 TTTTTAATAAATTTAATAT
*
72847 TTTTT-AT-AATGCTTAATAA
1 TTTTTAATAAAT--TTAATAT
72866 TTTTTAA-ATAATTT-ATAT
1 TTTTTAATA-AATTTAATAT
72884 TTTTT
1 TTTTT
72889 TTATGATTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
17 3 0.09
18 10 0.29
19 18 0.51
20 1 0.03
21 3 0.09
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTAATAAATTTAATAT
Found at i:72888 original size:18 final size:18
Alignment explanation
Indices: 72811--72888 Score: 54
Period size: 18 Copynumber: 4.3 Consensus size: 18
72801 ATTTTAATAA
72811 TTTTTAAAT-ATTT-T-T
1 TTTTTAAATAATTTATAT
*
72826 TGTTTTTAATAAATTTAATAT
1 T-TTTTAAAT-AATTT-ATAT
** * *
72847 TTTTTATAATGCTTAATAA
1 TTTTTA-AATAATTTATAT
72866 TTTTTAAATAATTTATAT
1 TTTTTAAATAATTTATAT
72884 TTTTT
1 TTTTT
72889 TTATGATTTC
Statistics
Matches: 46, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
15 1 0.02
16 7 0.15
18 17 0.37
19 9 0.20
20 7 0.15
21 5 0.11
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTTAAATAATTTATAT
Found at i:74684 original size:165 final size:165
Alignment explanation
Indices: 74391--74705 Score: 438
Period size: 165 Copynumber: 1.9 Consensus size: 165
74381 GATATTTATT
* *
74391 TTTAGTTTAAAAGATATGAACTTTTGAGTGTTGAAATGTCATAAAAATCTGGTAGCAAATTTCTT
1 TTTAGTTTAAAAGATATGAACTTTTGAATGTTGAAATGTCATAAAAATCTGGCAGCAAATTTCTT
** *
74456 ATAAAGCAGATTTAGCAGTGACTTTGAAAAATCACCAAAAATTACACAAAATAAAATAGGAAATG
66 ATAAAGCAGATTTAGCAGTGACTGAGAAAAATCACCAAAAATTACACAAAATAAAAGAGGAAATG
* * *
74521 GGCCTTGTATCCCTACAACTTTATAGATTTCGATC
131 AGACTTATATCCCTACAACTTTATAGATTTCGATC
* * * *
74556 TTTATTTTAAAAGATATGAATTTTTTAATGTTGAAA-GATCATAAAAATCTGGCAGTAGAA-TTC
1 TTTAGTTTAAAAGATATGAACTTTTGAATGTTGAAATG-TCATAAAAATCTGGCAGCA-AATTTC
* * * *
74619 TTATAAAATCA-ATTTAGCAGTGACTGAGAAAAATTACCAAAAATTGCACAAGATAAAAGAGGAA
64 TTAT-AAAGCAGATTTAGCAGTGACTGAGAAAAATCACCAAAAATTACACAAAATAAAAGAGGAA
74683 ATGAGACTTATATCCCTACAACT
128 ATGAGACTTATATCCCTACAACT
74706 ATACAAAAGT
Statistics
Matches: 131, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
164 1 0.01
165 123 0.94
166 7 0.05
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (165 bp):
TTTAGTTTAAAAGATATGAACTTTTGAATGTTGAAATGTCATAAAAATCTGGCAGCAAATTTCTT
ATAAAGCAGATTTAGCAGTGACTGAGAAAAATCACCAAAAATTACACAAAATAAAAGAGGAAATG
AGACTTATATCCCTACAACTTTATAGATTTCGATC
Found at i:74915 original size:197 final size:197
Alignment explanation
Indices: 74543--74935 Score: 540
Period size: 197 Copynumber: 2.0 Consensus size: 197
74533 CTACAACTTT
* * *
74543 ATAGATTTCGATCTTTATTTTAAAAGATATGAATTTTTTAATGTTGAAAGATCATAAAAATCTGG
1 ATAGATTTCGATCTTTAATTTAAAAGATATGAATTTTTGAATGTTGAAAGATCATAAAAATCTGC
* * * *
74608 CAGTAGAATTCTTATAAAATCAATTTAGCAGTGACTGAGAAAAATTACCAAAAATTGCACAAGAT
66 CAGCAGAATTCTTATAAAATCAATTTAGCAATGACTGAGAAAAATCACCAAAAATTGCAAAAGAT
* *
74673 AAAAGAGGAAATGAGACTTATATCCCTACAACTATACAAAAGTCTAGTTTAGTTTAGAACAAACG
131 AAAAGAGGAAATGAGACTTATATCCCTACAACTATA-AAAAGTCTAATTTAGTTTAAAACAAACG
74738 GAG
195 GAG
74741 ATAGATTTCGAT-TTTAATTTAAAAGATATGAATTTTTGAATGTTGAAAGATCATAAAAATCTGC
1 ATAGATTTCGATCTTTAATTTAAAAGATATGAATTTTTGAATGTTGAAAGATCATAAAAATCTGC
* ** *
74805 CAGCAGAATTCTTATAAAA-CAGATTTAGCAATGGCTTTGAAAAATCACCAAAAATTGGAAAAGA
66 CAGCAGAATTCTTATAAAATCA-ATTTAGCAATGACTGAGAAAAATCACCAAAAATTGCAAAAGA
* * * * ** * *
74869 TAAAATAGGAAATGAGCCTTATATCTCTATAATCGTAT-GGAAGTCTAATTTCGTTTAAAATAAA
130 TAAAAGAGGAAATGAGACTTATATCCCTACAA-C-TATAAAAAGTCTAATTTAGTTTAAAACAAA
74933 CGG
193 CGG
74936 TGCTTGATTT
Statistics
Matches: 171, Mismatches: 21, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
196 2 0.01
197 153 0.89
198 13 0.08
199 3 0.02
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.31
Consensus pattern (197 bp):
ATAGATTTCGATCTTTAATTTAAAAGATATGAATTTTTGAATGTTGAAAGATCATAAAAATCTGC
CAGCAGAATTCTTATAAAATCAATTTAGCAATGACTGAGAAAAATCACCAAAAATTGCAAAAGAT
AAAAGAGGAAATGAGACTTATATCCCTACAACTATAAAAAGTCTAATTTAGTTTAAAACAAACGG
AG
Found at i:82486 original size:6 final size:6
Alignment explanation
Indices: 82472--82590 Score: 76
Period size: 6 Copynumber: 19.8 Consensus size: 6
82462 CAGATTTGGG
* * * * * * * *
82472 GATGAT GATGGT GATGGA GAGGGG GATGAT GATGGT GATGGA GAGGGG
1 GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT
* * * * * * * * *
82520 GATGAT GATGGT GATGGA GAGGGG GATGAT GATTGT GATGGA GAGGGG
1 GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT
*
82568 GATGAT GATGGT GATGGT GATGG
1 GATGGT GATGGT GATGGT GATGG
82591 GCCTAAGCCC
Statistics
Matches: 82, Mismatches: 31, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
6 82 1.00
ACGTcount: A:0.24, C:0.00, G:0.52, T:0.24
Consensus pattern (6 bp):
GATGGT
Found at i:82500 original size:24 final size:24
Alignment explanation
Indices: 82469--82584 Score: 223
Period size: 24 Copynumber: 4.8 Consensus size: 24
82459 GGCCAGATTT
82469 GGGGATGATGATGGTGATGGAGAG
1 GGGGATGATGATGGTGATGGAGAG
82493 GGGGATGATGATGGTGATGGAGAG
1 GGGGATGATGATGGTGATGGAGAG
82517 GGGGATGATGATGGTGATGGAGAG
1 GGGGATGATGATGGTGATGGAGAG
*
82541 GGGGATGATGATTGTGATGGAGAG
1 GGGGATGATGATGGTGATGGAGAG
82565 GGGGATGATGATGGTGATGG
1 GGGGATGATGATGGTGATGG
82585 TGATGGGCCT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 90 1.00
ACGTcount: A:0.24, C:0.00, G:0.53, T:0.22
Consensus pattern (24 bp):
GGGGATGATGATGGTGATGGAGAG
Found at i:92154 original size:104 final size:102
Alignment explanation
Indices: 91963--92157 Score: 266
Period size: 104 Copynumber: 1.9 Consensus size: 102
91953 CATTCAGATA
* * *
91963 TAAGACCATGGTTGCATCATGGCAGTGAATATATATGTAAGACCATAGTTGGGCTATGGCATTAT
1 TAAGACCATGGTTGCACCATGGCAGTGAATATATATGTAAGACCATAGCTGGGCTATGACATTAT
* *
92028 GATTATAATACCATAATTGGGCTATGACATTCTGACG
66 GATAATAAGACCATAATTGGGCTATGACATTCTGACG
* *
92065 TAAGACCGTGGTTGGACCATGGCAGTGTATATATATATGTAAGACCATAGCTGGGCTATGACATT
1 TAAGACCATGGTTGCACCATGGCAGTG-A-ATATATATGTAAGACCATAGCTGGGCTATGACATT
* * *
92130 CT-AGTAATAAGACTATAGTTGGGCTATG
64 ATGA-TAATAAGACCATAATTGGGCTATG
92158 GCATACCGAT
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
102 24 0.30
103 2 0.03
104 54 0.68
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (102 bp):
TAAGACCATGGTTGCACCATGGCAGTGAATATATATGTAAGACCATAGCTGGGCTATGACATTAT
GATAATAAGACCATAATTGGGCTATGACATTCTGACG
Found at i:92207 original size:33 final size:33
Alignment explanation
Indices: 92000--92208 Score: 132
Period size: 33 Copynumber: 6.2 Consensus size: 33
91990 AATATATATG
* * *
92000 TAAGACCATAGTTGGGCTATGGCATTATGATTA
1 TAAGACCATAGTTGGGCTATGGCATTCTAATGA
* * * * *
92033 TAATACCATAATTGGGCTATGACATTCTGACG-
1 TAAGACCATAGTTGGGCTATGGCATTCTAATGA
* * * * * *
92065 TAAGACCGTGGTTGGACCATGGCAGTGTATATATATA
1 TAAGACCATAGTTGGGCTATGGCA-T-TCTA-AT-GA
* * * *
92102 TGTAAGACCATAGCTGGGCTATGACATTCTAGTAA
1 --TAAGACCATAGTTGGGCTATGGCATTCTAATGA
* * **
92137 TAAGACTATAGTTGGGCTATGGCATACCGATGA
1 TAAGACCATAGTTGGGCTATGGCATTCTAATGA
** *
92170 TAAGACCATAGTTGGATTATGGCATTCTAATGT
1 TAAGACCATAGTTGGGCTATGGCATTCTAATGA
92203 TAAGAC
1 TAAGAC
92209 ATAACCGATA
Statistics
Matches: 128, Mismatches: 41, Indels: 14
0.70 0.22 0.08
Matches are distributed among these distances:
32 17 0.13
33 84 0.66
34 2 0.02
35 2 0.02
36 1 0.01
37 3 0.02
38 1 0.01
39 18 0.14
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (33 bp):
TAAGACCATAGTTGGGCTATGGCATTCTAATGA
Found at i:94551 original size:36 final size:35
Alignment explanation
Indices: 94511--94585 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 35
94501 TACATACAAA
* *
94511 AAAAT-TTAAAAAATATATAATATATCAAATACACTT
1 AAAATATTAAAAAATAAATAA-ATATAAAATACA-TT
*
94547 AAAATATTAAAAAATAAATAAATTTAAAATACATT
1 AAAATATTAAAAAATAAATAAATATAAAATACATT
94582 AAAA
1 AAAA
94586 AAATTATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 6 0.17
36 15 0.43
37 14 0.40
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (35 bp):
AAAATATTAAAAAATAAATAAATATAAAATACATT
Found at i:94565 original size:25 final size:26
Alignment explanation
Indices: 94537--94587 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
94527 ATAATATATC
*
94537 AAATACACTTAAAAT-ATTAAAAAAT
1 AAATAAACTTAAAATAATTAAAAAAT
*
94562 AAATAAATTTAAAATACATTAAAAAA
1 AAATAAACTTAAAATA-ATTAAAAAA
94588 ATTATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.59
27 9 0.41
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (26 bp):
AAATAAACTTAAAATAATTAAAAAAT
Found at i:94726 original size:20 final size:21
Alignment explanation
Indices: 94701--94749 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
94691 AAAACGCATA
*
94701 AAAAATAACATCC-AAACAAC
1 AAAAATAACAACCAAAACAAC
94721 AAAAATAACAACCAAAACAAC
1 AAAAATAACAACCAAAACAAC
94742 AACAAATA
1 AA-AAATA
94750 TAACATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 12 0.46
21 9 0.35
22 5 0.19
ACGTcount: A:0.69, C:0.22, G:0.00, T:0.08
Consensus pattern (21 bp):
AAAAATAACAACCAAAACAAC
Found at i:94732 original size:12 final size:12
Alignment explanation
Indices: 94715--94840 Score: 91
Period size: 12 Copynumber: 10.8 Consensus size: 12
94705 ATAACATCCA
94715 AACAACAAAAAT
1 AACAACAAAAAT
* *
94727 AACAACCAAAAC
1 AACAACAAAAAT
*
94739 AACAACAAATAT
1 AACAACAAAAAT
** *
94751 AAC-ATTAAAAC
1 AACAACAAAAAT
**
94762 AACATTAAAAAT
1 AACAACAAAAAT
94774 ---AACAAAAAT
1 AACAACAAAAAT
* *
94783 AGCAACAAAAAC
1 AACAACAAAAAT
94795 AACAACAAAAAT
1 AACAACAAAAAT
* *
94807 AGCAATAAAAAT
1 AACAACAAAAAT
*
94819 AAC-ACGAAAAT
1 AACAACAAAAAT
94830 AACAATCAAAA
1 AACAA-CAAAA
94841 CAATAAAAAA
Statistics
Matches: 85, Mismatches: 23, Indels: 11
0.71 0.19 0.09
Matches are distributed among these distances:
9 7 0.08
11 16 0.19
12 58 0.68
13 4 0.05
ACGTcount: A:0.69, C:0.17, G:0.02, T:0.11
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:94829 original size:56 final size:55
Alignment explanation
Indices: 94701--94834 Score: 153
Period size: 56 Copynumber: 2.4 Consensus size: 55
94691 AAAACGCATA
* * * *
94701 AAAAATAACATCCAAACAACAAAAATAACAACCAAAACAACAACAAATATAACAT
1 AAAAATAACATCAAAATAACAAAAATAACAACAAAAACAACAACAAAAATAACAT
* * * * *
94756 TAAAACAACATTAAAAATAACAAAAATAGCAACAAAAACAACAACAAAAATAGCAAT
1 AAAAATAACA-TCAAAATAACAAAAATAACAACAAAAACAACAACAAAAATAAC-AT
94813 AAAAATAACA-CGAAAATAACAA
1 AAAAATAACATC-AAAATAACAA
94835 TCAAAACAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
55 8 0.12
56 46 0.72
57 10 0.16
ACGTcount: A:0.69, C:0.18, G:0.02, T:0.11
Consensus pattern (55 bp):
AAAAATAACATCAAAATAACAAAAATAACAACAAAAACAACAACAAAAATAACAT
Found at i:94849 original size:68 final size:66
Alignment explanation
Indices: 94714--94872 Score: 158
Period size: 68 Copynumber: 2.4 Consensus size: 66
94704 AATAACATCC
* * * ** * *
94714 AAACAACAAAAATAACAACCAAAACAACAACAAATATAACATTAAAACAACATTAAAAATAACAA
1 AAACAACAAAAACAACAACAAAAACAACAACAAAAATAACACGAAAACAACAATAAAAACAACAA
94779 A
66 A
* * * * * *
94780 AATAGCAACAAAAACAACAACAAAAATAGCAATAAAAATAACACGAAAATAACAATCAAAACAAT
1 AA-A-CAACAAAAACAACAACAAAAACAACAACAAAAATAACACGAAAACAACAATAAAAACAAC
94845 AAA
64 AAA
94848 AAACAACTCAAAAACAACAA-AAAAA
1 AAACAA--CAAAAACAACAACAAAAA
94873 GTAAACCAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
66 5 0.07
67 7 0.09
68 64 0.84
ACGTcount: A:0.70, C:0.18, G:0.02, T:0.10
Consensus pattern (66 bp):
AAACAACAAAAACAACAACAAAAACAACAACAAAAATAACACGAAAACAACAATAAAAACAACAA
A
Found at i:94861 original size:21 final size:19
Alignment explanation
Indices: 94825--94871 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
94815 AAATAACACG
*
94825 AAAATAACAATCAAAACAAT
1 AAAA-AACAATCAAAACAAC
94845 AAAAAACAACTCAAAAACAAC
1 AAAAAACAA-TC-AAAACAAC
94866 AAAAAA
1 AAAAAA
94872 AGTAAACCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 5 0.21
20 6 0.25
21 13 0.54
ACGTcount: A:0.74, C:0.17, G:0.00, T:0.09
Consensus pattern (19 bp):
AAAAAACAATCAAAACAAC
Found at i:95964 original size:23 final size:22
Alignment explanation
Indices: 95938--96097 Score: 160
Period size: 23 Copynumber: 7.0 Consensus size: 22
95928 TTATTGTTCA
95938 GCACTGTGTGTGCTTACT-TTT
1 GCACTGTGTGTGCTTACTGTTT
*
95959 CAGCACTGTGTATGCTTACTGTTT
1 --GCACTGTGTGTGCTTACTGTTT
* *
95983 AGCACTGTGTGTGCTTATTGATTC
1 -GCACTGTGTGTGCTTACTG-TTT
* * * *
96007 GCAATATATGTGCTTACTATATT
1 GCACTGTGTGTGCTTACTGT-TT
*
96030 TCACTGTGTGTGCTTACTGTTTT
1 GCACTGTGTGTGCTTACTG-TTT
* *
96053 GCACTGCGTGTGCCTACTGATTT
1 GCACTGTGTGTGCTTACTG-TTT
96076 GCACTGTGTGTGCTTACTGTTT
1 GCACTGTGTGTGCTTACTGTTT
96098 CCCCAGCACT
Statistics
Matches: 112, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
22 4 0.04
23 102 0.91
24 6 0.05
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.44
Consensus pattern (22 bp):
GCACTGTGTGTGCTTACTGTTT
Found at i:96044 original size:69 final size:69
Alignment explanation
Indices: 95962--96093 Score: 183
Period size: 69 Copynumber: 1.9 Consensus size: 69
95952 TACTTTTCAG
* * *
95962 CACTGTGTATGCTTACTGTTTAGCACTGTGTGTGCTTATTGATTCGCAATATATGTGCTTACTAT
1 CACTGTGTATGCTTACTGTTTAGCACTGCGTGTGCCTACTGATTCGCAATATATGTGCTTACTAT
96027 ATTT
66 ATTT
* * * * * *
96031 CACTGTGTGTGCTTACTGTTTTGCACTGCGTGTGCCTACTGATTTGCACTGTGTGTGCTTACT
1 CACTGTGTATGCTTACTGTTTAGCACTGCGTGTGCCTACTGATTCGCAATATATGTGCTTACT
96094 GTTTCCCCAG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 54 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (69 bp):
CACTGTGTATGCTTACTGTTTAGCACTGCGTGTGCCTACTGATTCGCAATATATGTGCTTACTAT
ATTT
Found at i:104434 original size:5 final size:5
Alignment explanation
Indices: 104417--104455 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
104407 AGGGCATCTT
*
104417 AAAA- AAAAC AAAAG AAAAG AAAAG AAGAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG AAAA
104456 AGGAAGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
4 4 0.12
5 23 0.72
6 5 0.16
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:104447 original size:16 final size:15
Alignment explanation
Indices: 104428--104470 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
104418 AAAAAAACAA
104428 AAGAAAAGAAAAGAAG
1 AAGAAAAGAAAA-AAG
*
104444 AAGAAAAGAAAAAGG
1 AAGAAAAGAAAAAAG
104459 AAGAAAAAGAAA
1 AAG-AAAAGAAA
104471 GTCAAGATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAAAAAAG
Done.