Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009623.1 Corchorus capsularis cultivar CVL-1 contig09644, 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: 129115
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:7515 original size:21 final size:20
Alignment explanation
Indices: 7489--7551 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 20
7479 AAAAAATAAG
*
7489 GCTTATAAGATTACTAAAAAT
1 GCTTATAAG-TTACTAAAAAA
**
7510 GCTTATGAAGTTTGTAAAAAA
1 GCTTAT-AAGTTACTAAAAAA
7531 GCTTATATAGCTTACTTAAAA
1 GCTTATA-AG-TTAC-TAAAA
7552 CCTTATTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
20 1 0.03
21 22 0.67
22 5 0.15
23 5 0.15
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.35
Consensus pattern (20 bp):
GCTTATAAGTTACTAAAAAA
Found at i:23201 original size:22 final size:22
Alignment explanation
Indices: 23094--23534 Score: 165
Period size: 22 Copynumber: 19.8 Consensus size: 22
23084 TTTTTGATGA
*
23094 CTTATGAAATTTTGATAACATT
1 CTTATGAAATTTTGATAACCTT
* * *
23116 CTTATGAAATTTTAATAACGATG
1 CTTATGAAATTTTGATAAC-CTT
* * *
23139 C-TATGGAATTTCGAGAATCCTT
1 CTTATGAAATTTTGATAA-CCTT
**
23161 -TTAT-AAATTTTTTTTAACCTT
1 CTTATGAAA-TTTTGATAACCTT
**
23182 CTTATGAAATTTTGATAACCAA
1 CTTATGAAATTTTGATAACCTT
* * * *
23204 CACTATGAGATGTTGATAACCTC
1 C-TTATGAAATTTTGATAACCTT
* * * *
23227 CATATGATATATTGATAA-TTAT
1 CTTATGAAATTTTGATAACCT-T
* * * *
23249 CACGTTATGAAAATTTAAAAACCTC
1 --C-TTATGAAATTTTGATAACCTT
*
23274 CATATG-AATTGTT-AGTAA--TT
1 CTTATGAAATT-TTGA-TAACCTT
* * *
23294 ACACTCTGAAATTTTGATAATCAC-A
1 -C-TTATGAAATTTTGATAA-C-CTT
* *
23319 C-TATGAGATTGTGATAACC-T
1 CTTATGAAATTTTGATAACCTT
* *
23339 CGCTATTAAATTTTGATAAACCTT
1 C-TTATGAAATTTTGAT-AACCTT
* * *
23363 CCTATAAAATTTTGATAAACCTC
1 CTTATGAAATTTTGAT-AACCTT
* * *
23386 CCTATAAAATTTTGATAACCTC
1 CTTATGAAATTTTGATAACCTT
*
23408 CTTTATGAAATCTTGATAACC-T
1 C-TTATGAAATTTTGATAACCTT
* *
23430 CATTATGAAATTTTGTTAATCTT
1 C-TTATGAAATTTTGATAACCTT
* *
23453 CCTATGAAATTTTGATAACCCT
1 CTTATGAAATTTTGATAACCTT
* *
23475 CTTATGAAA-TTTGA-AAACTAAA
1 CTTATGAAATTTTGATAACCT--T
* *
23497 C-GATGAAATTTTGATAACTTT
1 CTTATGAAATTTTGATAACCTT
*
23518 CATATGAAATTTTGATA
1 CTTATGAAATTTTGATA
23535 TCATCCCTGA
Statistics
Matches: 314, Mismatches: 72, Indels: 66
0.69 0.16 0.15
Matches are distributed among these distances:
20 6 0.02
21 25 0.08
22 176 0.56
23 91 0.29
24 4 0.01
25 11 0.04
26 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.39
Consensus pattern (22 bp):
CTTATGAAATTTTGATAACCTT
Found at i:23210 original size:23 final size:23
Alignment explanation
Indices: 23175--23534 Score: 189
Period size: 22 Copynumber: 16.1 Consensus size: 23
23165 AAATTTTTTT
*
23175 TAACCTTC-TTATGAAATTTTGA
1 TAACCTTCACTATGAAATTTTGA
** * *
23197 TAACCAACACTATGAGATGTTGA
1 TAACCTTCACTATGAAATTTTGA
* * *
23220 TAACCTCCA-TATGATATATTGA
1 TAACCTTCACTATGAAATTTTGA
* * *
23242 TAA-TTATCACGTTATGAAAATTTAA
1 TAACCT-TCAC--TATGAAATTTTGA
* *
23267 AAACCTCCA-TATG-AATTGTT-A
1 TAACCTTCACTATGAAATT-TTGA
*
23288 GTAA--TTACACTCTGAAATTTTGA
1 -TAACCTT-CACTATGAAATTTTGA
* * * *
23311 TAATC-ACACTATGAGATTGTGA
1 TAACCTTCACTATGAAATTTTGA
* *
23333 TAACC-TCGCTATTAAATTTTGA
1 TAACCTTCACTATGAAATTTTGA
*
23355 TAAACCTTC-CTATAAAATTTTGA
1 T-AACCTTCACTATGAAATTTTGA
* *
23378 TAAACC-TCCCTATAAAATTTTGA
1 T-AACCTTCACTATGAAATTTTGA
* ** *
23401 TAACCTCCTTTATGAAATCTTGA
1 TAACCTTCACTATGAAATTTTGA
* *
23424 TAACC-TCATTATGAAATTTTGT
1 TAACCTTCACTATGAAATTTTGA
*
23446 TAATCTTC-CTATGAAATTTTGA
1 TAACCTTCACTATGAAATTTTGA
* *
23468 TAACCCTC-TTATGAAA-TTTGA
1 TAACCTTCACTATGAAATTTTGA
* ** *
23489 -AAACTAAACGATGAAATTTTGA
1 TAACCTTCACTATGAAATTTTGA
*
23511 TAACTTTCA-TATGAAATTTTGA
1 TAACCTTCACTATGAAATTTTGA
23533 TA
1 TA
23535 TCATCCCTGA
Statistics
Matches: 257, Mismatches: 59, Indels: 44
0.71 0.16 0.12
Matches are distributed among these distances:
20 4 0.02
21 18 0.07
22 135 0.53
23 84 0.33
24 2 0.01
25 13 0.05
26 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (23 bp):
TAACCTTCACTATGAAATTTTGA
Found at i:23397 original size:46 final size:44
Alignment explanation
Indices: 23302--23472 Score: 166
Period size: 45 Copynumber: 3.8 Consensus size: 44
23292 TTACACTCTG
* * * * * *
23302 AAATTTTGATAATC-ACACTATGAGATTGTGATAACCTCGCTATT
1 AAATTTTGATAACCTTC-CTATGAAATTTTGATAACCTCACTATA
* *
23346 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACCTTCCTATGAAATTTTGAT-AACCTCACTATA
* * *
23392 AAATTTTGATAACC-TCCTTTATGAAATCTTGATAACCTCATTATG
1 AAATTTTGATAACCTTCC--TATGAAATTTTGATAACCTCACTATA
* *
23437 AAATTTTGTTAATCTTCCTATGAAATTTTGATAACC
1 AAATTTTGATAACCTTCCTATGAAATTTTGATAACC
23473 CTCTTATGAA
Statistics
Matches: 106, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
44 30 0.28
45 40 0.38
46 36 0.34
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (44 bp):
AAATTTTGATAACCTTCCTATGAAATTTTGATAACCTCACTATA
Found at i:23441 original size:45 final size:42
Alignment explanation
Indices: 23096--23553 Score: 183
Period size: 44 Copynumber: 10.3 Consensus size: 42
23086 TTTGATGACT
* * * * *
23096 TATGAAATTTTGATAACATTCTTATGAAATTTTAATAACGATGC
1 TATGAAATTTTGATAAC-CTCCTATGAAATTTTGATAAC-CTCC
* * * ** ** *
23140 TATGGAATTTCGAGAATCCTTTTAT-AAATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAA-CCTCCTATGAAA-TTTTGATAACC-TCC
* * *
23184 TATGAAATTTTGATAACCAACACTATGAGATGTTGATAACCTCC
1 TATGAAATTTTGATAACC-TC-CTATGAAATTTTGATAACCTCC
* * ** * * *
23228 ATATGATATATTGATAATTATCACGTTATGAAAATTTAAAAACCTCC
1 -TATGAAATTTTGATAA-CCTC-C--TATGAAATTTTGATAACCTCC
* * * *
23275 ATATG-AATTGTT-AGTAA-TTACACTCTGAAATTTTGATAATCACAC
1 -TATGAAATT-TTGA-TAACCT-C-CTATGAAATTTTGATAACCTC-C
* * *
23320 TATGAGATTGTGATAACCTCGCTATTAAATTTTGATAAACCTTCC
1 TATGAAATTTTGATAACCTC-CTATGAAATTTTGAT-AACC-TCC
* *
23365 TATAAAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCC
1 TATGAAATTTTGAT-AACCT-CCTATGAAATTTTGATAACCTCC
* * * *
23409 TTTATGAAATCTTGATAACCTCATTATGAAATTTTGTTAATCTTCC
1 --TATGAAATTTTGATAACCTC-CTATGAAATTTTGATAA-CCTCC
* * *
23455 TATGAAATTTTGATAACCCTCTTATGAAA-TTTGA-AAACTAAAC
1 TATGAAATTTTGATAA-CCTCCTATGAAATTTTGATAACCT--CC
* * * * *
23498 GATGAAATTTTGATAACTTTCATATGAAATTTTGATATCATCC
1 TATGAAATTTTGATAAC-CTCCTATGAAATTTTGATAACCTCC
*
23541 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
23554 TACTCCATAA
Statistics
Matches: 312, Mismatches: 71, Indels: 64
0.70 0.16 0.14
Matches are distributed among these distances:
41 1 0.00
42 15 0.05
43 35 0.11
44 110 0.35
45 80 0.26
46 44 0.14
47 27 0.09
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (42 bp):
TATGAAATTTTGATAACCTCCTATGAAATTTTGATAACCTCC
Found at i:23727 original size:22 final size:21
Alignment explanation
Indices: 23675--23755 Score: 60
Period size: 22 Copynumber: 3.8 Consensus size: 21
23665 TTTGACCTCT
*
23675 TTATGAAATTTTGATAATCTC
1 TTATGAAATTTTGATAATCGC
* * *
23696 TTAATAAAATTTTGTTGATCGC
1 TT-ATGAAATTTTGATAATCGC
*
23718 TCTATGAAA--TTGATAATCAC
1 T-TATGAAATTTTGATAATCGC
23738 ATTAT-ATAATTTTGATAA
1 -TTATGA-AATTTTGATAA
23756 CCTCGCTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
19 1 0.02
20 13 0.28
21 3 0.07
22 28 0.61
23 1 0.02
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (21 bp):
TTATGAAATTTTGATAATCGC
Found at i:23866 original size:44 final size:44
Alignment explanation
Indices: 23768--23867 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 44
23758 TCGCTTTAAG
* * *
23768 ATTTTAATAACAACACTATGAAAATTTGATAACCTTTCTATAAA
1 ATTTTAATAACCACACTATGAAAATTTAATAACCTTCCTATAAA
* * * *
23812 ATTGTGATAACCACACTAT-TAAATTTCAATAACCTTCCTATGAA
1 ATTTTAATAACCACACTATGAAAATTT-AATAACCTTCCTATAAA
23856 ATTTTAATAACC
1 ATTTTAATAACC
23868 TGATCGTATG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
43 6 0.13
44 40 0.87
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (44 bp):
ATTTTAATAACCACACTATGAAAATTTAATAACCTTCCTATAAA
Found at i:23881 original size:24 final size:22
Alignment explanation
Indices: 23783--23884 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 22
23773 AATAACAACA
* * *
23783 CTATGAAAATTTGATAACCTTT
1 CTATGAAATTTTAATAACCTTC
* * * *
23805 CTATAAAATTGTGATAACC-AC
1 CTATGAAATTTTAATAACCTTC
* *
23826 ACTATTAAATTTCAATAACCTTC
1 -CTATGAAATTTTAATAACCTTC
23849 CTATGAAATTTTAATAACCTGATC
1 CTATGAAATTTTAATAACCT--TC
*
23873 GTATGAAATTTT
1 CTATGAAATTTT
23885 GGTAACCTCC
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
22 49 0.78
23 1 0.02
24 13 0.21
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (22 bp):
CTATGAAATTTTAATAACCTTC
Found at i:24435 original size:13 final size:13
Alignment explanation
Indices: 24397--24435 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
24387 GTCTAAATTG
24397 AAATTTT-ATAAT
1 AAATTTTAATAAT
*
24409 TAATTTTAAATAAT
1 AAATTTT-AATAAT
24423 AAATTTTAATAAT
1 AAATTTTAATAAT
24436 GTCAATTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 6 0.26
13 6 0.26
14 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AAATTTTAATAAT
Found at i:27907 original size:16 final size:16
Alignment explanation
Indices: 27883--27931 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
27873 AAATTTGTTG
*
27883 TTTTACTTTGTTAATA
1 TTTTTCTTTGTTAATA
*
27899 TTTTTCTTTTATTAATA
1 TTTTTC-TTTGTTAATA
27916 TTTTAT-TTTGTTAATA
1 TTTT-TCTTTGTTAATA
27932 ATTTCTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 14 0.50
17 13 0.46
18 1 0.04
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (16 bp):
TTTTTCTTTGTTAATA
Found at i:27940 original size:16 final size:16
Alignment explanation
Indices: 27889--27940 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
27879 GTTGTTTTAC
27889 TTTGTTAATATTTTTCT
1 TTTGTTAATA-TTTTCT
* *
27906 TTTATTAATATTTTAT
1 TTTGTTAATATTTTCT
*
27922 TTTGTTAATAATTTCT
1 TTTGTTAATATTTTCT
27938 TTT
1 TTT
27941 CTTACTTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 21 0.70
17 9 0.30
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (16 bp):
TTTGTTAATATTTTCT
Found at i:28728 original size:44 final size:44
Alignment explanation
Indices: 28663--28749 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
28653 ATACTAATAC
*
28663 TATTTTTCTTTGGTCTTGTTTGACATTACGTTTGGAGATAAAAT
1 TATTTTTCTTTGGTCTAGTTTGACATTACGTTTGGAGATAAAAT
* *
28707 TATTTTTCTTTGGTCTAGTTTGGCATTGCGTTTGGAGATAAAA
1 TATTTTTCTTTGGTCTAGTTTGACATTACGTTTGGAGATAAAA
28750 AAGTTGTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.22, C:0.09, G:0.21, T:0.48
Consensus pattern (44 bp):
TATTTTTCTTTGGTCTAGTTTGACATTACGTTTGGAGATAAAAT
Found at i:37351 original size:30 final size:30
Alignment explanation
Indices: 37315--37375 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
37305 CCTTGTCCAA
37315 ACCTTTTCCCTAGTGAAACCCCACATGTCG
1 ACCTTTTCCCTAGTGAAACCCCACATGTCG
37345 ACCTTTTCCCTAGTGAAACCCCACATGTCG
1 ACCTTTTCCCTAGTGAAACCCCACATGTCG
37375 A
1 A
37376 TTTGCTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.36, G:0.13, T:0.26
Consensus pattern (30 bp):
ACCTTTTCCCTAGTGAAACCCCACATGTCG
Found at i:49756 original size:23 final size:23
Alignment explanation
Indices: 49726--49772 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
49716 GGGGTGATTC
*
49726 GTTTGTATCTTTTATTTTTCAAT
1 GTTTGTATCTTTTATTTGTCAAT
49749 GTTTGTATCTTTTATTTGTCAAT
1 GTTTGTATCTTTTATTTGTCAAT
49772 G
1 G
49773 CATGTGCGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.09, G:0.13, T:0.62
Consensus pattern (23 bp):
GTTTGTATCTTTTATTTGTCAAT
Found at i:58435 original size:20 final size:21
Alignment explanation
Indices: 58398--58444 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
58388 AAAGTTCCTT
*
58398 ATTTTATGATAGTATTATAAC
1 ATTTTATGATACTATTATAAC
*
58419 ATTTT-TGATACTCTTATAAC
1 ATTTTATGATACTATTATAAC
*
58439 CTTTTA
1 ATTTTA
58445 AAAATACTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (21 bp):
ATTTTATGATACTATTATAAC
Found at i:59223 original size:22 final size:22
Alignment explanation
Indices: 59178--59223 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
59168 AACTTACTTA
* **
59178 AATACCTATGATGTGTAAGGTT
1 AATACCTATGATGTCTAAAATT
*
59200 AATACGTATGATGTCTAAAATT
1 AATACCTATGATGTCTAAAATT
59222 AA
1 AA
59224 ATTAAAAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (22 bp):
AATACCTATGATGTCTAAAATT
Found at i:59586 original size:12 final size:12
Alignment explanation
Indices: 59569--59599 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
59559 CCAAACATGA
59569 TGAACTTTTTGT
1 TGAACTTTTTGT
59581 TGAACTTTTTGT
1 TGAACTTTTTGT
59593 TGAACTT
1 TGAACTT
59600 ACCAGTCCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (12 bp):
TGAACTTTTTGT
Found at i:74589 original size:2 final size:2
Alignment explanation
Indices: 74573--74616 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
74563 CAGCTGTACC
*
74573 AT AT AGT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
74615 AT
1 AT
74617 TTCCATCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:106464 original size:348 final size:348
Alignment explanation
Indices: 105413--107532 Score: 2865
Period size: 348 Copynumber: 6.0 Consensus size: 348
105403 CTTGAATCTG
* * * * *
105413 GGCCAAGTGCTTCTTTCCCCACAGGTGACAGTTTAAGTCCTCTGAACGAGTGCAGCTTACGTTAC
1 GGCCAAGTGCTTCTTTCCCGAAAGGTGACAGTTCAAGTCCTCCGAACGAGTGCAGCTTATGTTAC
* *
105478 AGATGGTGCACTGAAATTGAGGATTCTGATCCCCAGCATGTTTCTTCCCAATCTGCTGCTGGTCT
66 AGATGGTGCACTGAAATTGAGGATTCTTATCCCCAGCATGTTTCGTCCCAATCTGCTGCTGGTCT
* *
105543 TGTACATTTTCCTTGTCCTCATGTTTTAGTTGATTTCCTGCCATATTGTTTGGTAACAACTTGTT
131 TGTACATTTTCCTTG------TGTTTTAGTTGATTTCCTGCCATATTGTTTGCTAAAAACTTGTT
* * * *
105608 TGGTTCCTCATTTGGCAGGTCATGTTTGGTTCCATTGCTTACCCCAGTTGTAAGATCCACTGCTT
190 TGGTTCCTCATTGGGCAGGTCAGGTTTGTTTCCATTGCTTATCCCAGTTGTAAGATCCACTGCTT
* *
105673 TGCTGGATATATGTGTACCGTTGCTGGTTGCACATTTCTCAGCATCATATTTGGAAACATCAGAG
255 TGCTGGATATATGTGTACCATTGCTGGTTGCACATTTCTCAGCATCATTTTTGGAAACATCAGAG
* *
105738 TTTTTAGCCACTGAAGCGGCTGAGACTTT
320 TTCTTAGCCACTGAAGCAGCTGAGACTTT
* * * *
105767 GGCCAAGTGCTTCTTTCCTGAAAGGTGACAATTCAAGTCCTCCGAATGACTGCAGCTTATGTTAC
1 GGCCAAGTGCTTCTTTCCCGAAAGGTGACAGTTCAAGTCCTCCGAACGAGTGCAGCTTATGTTAC
* * *
105832 AGATGGTGCACTGAAATTGGGGATTCTCATCCCTAGCATGTTTCGTCCCAATCTGCTGCTGGTCT
66 AGATGGTGCACTGAAATTGAGGATTCTTATCCCCAGCATGTTTCGTCCCAATCTGCTGCTGGTCT
* * * * * *
105897 GGTACATTTTCCTTGTGTTGTACTTGTAGCCAATATCCTGTCATATTGTTTGCTAGAAACTTGTT
131 TGTACATTTTCCTTGTGTT-T--TAGTTG---ATTTCCTGCCATATTGTTTGCTAAAAACTTGTT
* * **
105962 TGTTTCCTCATTGGGTAGGTTGGGTTTGTTTCCATTGCTTATCCCAGTTGTAAGATCCACTGCTT
190 TGGTTCCTCATTGGGCAGGTCAGGTTTGTTTCCATTGCTTATCCCAGTTGTAAGATCCACTGCTT
* * * * *
106027 TGCTGGATATATGTGTACCATTGCTTGATGCACATTTTTCAGCATTATTTTTGGAAACATCAGTG
255 TGCTGGATATATGTGTACCATTGCTGGTTGCACATTTCTCAGCATCATTTTTGGAAACATCAGAG
106092 TTCTTAGCCACTGAAGCAGCTGAGACTTT
320 TTCTTAGCCACTGAAGCAGCTGAGACTTT
* * * * *
106121 GGCCAAATGCTTCTTTCCCGAGAGGTGACAGTTCAAGTTCTCCAAACCAGTGCAGCTTATGTTAC
1 GGCCAAGTGCTTCTTTCCCGAAAGGTGACAGTTCAAGTCCTCCGAACGAGTGCAGCTTATGTTAC
* * * *
106186 AGATGATGCACTGAAATTGAGGATTATTATCCCCAGCATGTATCTTCCCAATCTGCTGCTGGTCT
66 AGATGGTGCACTGAAATTGAGGATTCTTATCCCCAGCATGTTTCGTCCCAATCTGCTGCTGGTCT
* *
106251 TGTACATTTTCCTTGTGTTTTAGTTGATTTCCTGCCATATTGTTTGCTAAAAACCTGTTTTGTTC
131 TGTACATTTTCCTTGTGTTTTAGTTGATTTCCTGCCATATTGTTTGCTAAAAACTTGTTTGGTTC
*
106316 CTCATTGGGCAGGTCAGGTTTGTTTCCATTGCTTATCCCAGTTGTAAGATCCACTGCTTTGGTGG
196 CTCATTGGGCAGGTCAGGTTTGTTTCCATTGCTTATCCCAGTTGTAAGATCCACTGCTTTGCTGG
** * *
106381 ATATATGTGTACTGTTGCTGGTTGCACATTTCTCAGCATCATTTTTGGTAACATCAGACTTCTTA
261 ATATATGTGTACCATTGCTGGTTGCACATTTCTCAGCATCATTTTTGGAAACATCAGAGTTCTTA
**
106446 GCCACTGAAGTGGCTGAGACTTT
326 GCCACTGAAGCAGCTGAGACTTT
* *
106469 GGCCAAAGCGGCTGAGACTTTGGCCTTGTGCTTCTTTCCAGAATGGTGACAGTTCAAGTCCTCTG
1 GGCC-AA---G-T--G-C-TT---C---T--TTC---CC-GAAAGGTGACAGTTCAAGTCCTCCG
** * *
106534 AACGAGCACAGCTTATGTTACAGATGGTGCACTGAAATTGGGGATTCTTATCCCCAGCATGTTTA
45 AACGAGTGCAGCTTATGTTACAGATGGTGCACTGAAATTGAGGATTCTTATCCCCAGCATGTTTC
* * ** ***
106599 GTCCCAATCTGCTGCTGGTCTTGTACATTTTCCTTGTGATGTAGCCGATTTCCTGTTGTATTGTT
110 GTCCCAATCTGCTGCTGGTCTTGTACATTTTCCTTGTGTTTTAGTTGATTTCCTGCCATATTGTT
* * * * * *
106664 TGCCAGAAACTTGTTTGGTTCCTCATTGGGCAGGTCAGCTTCGTTTCCATCGCTTATTCCAGTTG
175 TGCTAAAAACTTGTTTGGTTCCTCATTGGGCAGGTCAGGTTTGTTTCCATTGCTTATCCCAGTTG
* * *
106729 GAAGATCCACTACTTCGCTGGATATATGTGTACCATTGCTGGTTGCACATTTCTCAGCATCATTT
240 TAAGATCCACTGCTTTGCTGGATATATGTGTACCATTGCTGGTTGCACATTTCTCAGCATCATTT
*
106794 TTGGAAACATCAGAGTTCTTAGCCACTGATGCAGCTGAGACTTT
305 TTGGAAACATCAGAGTTCTTAGCCACTGAAGCAGCTGAGACTTT
* * *
106838 GGCCAAGTGCTTCTTTCCCGAAAGGTGACAGTTCATGTCCTCCAAACGAGTGCAGCTTATGTGAC
1 GGCCAAGTGCTTCTTTCCCGAAAGGTGACAGTTCAAGTCCTCCGAACGAGTGCAGCTTATGTTAC
* * * * *
106903 AGATGGTGCACCGAAATTGAGGGTTATTATCCCCAGCATGTATCTTCCCAATCTGCTGCTGGTCT
66 AGATGGTGCACTGAAATTGAGGATTCTTATCCCCAGCATGTTTCGTCCCAATCTGCTGCTGGTCT
*
106968 TGTACATTTTCCTTGTGTTTTAGTTGATTTCCTGCCATATTGTTTGCTAAAAACCTGTTTGGTTC
131 TGTACATTTTCCTTGTGTTTTAGTTGATTTCCTGCCATATTGTTTGCTAAAAACTTGTTTGGTTC
* *
107033 CTCATTGGGCAGGTCGGGTTTGTTTCCGTTGCTTATCCCAGTTGTAAGATCCACTGCTTTGCTGG
196 CTCATTGGGCAGGTCAGGTTTGTTTCCATTGCTTATCCCAGTTGTAAGATCCACTGCTTTGCT-G
* * *
107098 GA-ATGTGTGTACCATTGCTGGCTGCACATTTCTCGGCATCATTTTTGGAAACATCAGAGTTCTT
260 GATATATGTGTACCATTGCTGGTTGCACATTTCTCAGCATCATTTTTGGAAACATCAGAGTTCTT
**
107162 AGCCACTGAAGTGGCTGAGACTTT
325 AGCCACTGAAGCAGCTGAGACTTT
** * * * **
107186 GGCCTTGTGCTTCTTTCCAGAACGGTGACAGTTCAAGTCCTCTGAACGAGCACAGCTTATGTTAC
1 GGCCAAGTGCTTCTTTCCCGAAAGGTGACAGTTCAAGTCCTCCGAACGAGTGCAGCTTATGTTAC
* *
107251 AGATGGTGCACTGAAATTGGGGATTCTTATCCCCAGCATGTTTAGTCCCAATCTGCTGCTGGTCT
66 AGATGGTGCACTGAAATTGAGGATTCTTATCCCCAGCATGTTTCGTCCCAATCTGCTGCTGGTCT
* ** * * * *
107316 TGTACATTTTCCTTGTGTTGTAGCCGATTTCCTGTCGTATTGTTTGCCAGAAACTTGTTTGGTTC
131 TGTACATTTTCCTTGTGTTTTAGTTGATTTCCTGCCATATTGTTTGCTAAAAACTTGTTTGGTTC
* * * * * *
107381 CTCATTGGGCAGGTCAGCTTTGTTTCCATCGCTTATTCCAGTTGGAAGATCCACTACTTCGCTGG
196 CTCATTGGGCAGGTCAGGTTTGTTTCCATTGCTTATCCCAGTTGTAAGATCCACTGCTTTGCTGG
107446 ATATATGTGTACCATTGCTGGTTGCACATTTCTCAGCATCATTTTTGGAAACATCAGAGTTCTTA
261 ATATATGTGTACCATTGCTGGTTGCACATTTCTCAGCATCATTTTTGGAAACATCAGAGTTCTTA
107511 GCCACTGAAGCAGCTGAGACTT
326 GCCACTGAAGCAGCTGAGACTT
107533 GGACCTTGAA
Statistics
Matches: 1541, Mismatches: 196, Indels: 64
0.86 0.11 0.04
Matches are distributed among these distances:
347 3 0.00
348 770 0.50
349 8 0.01
351 8 0.01
352 3 0.00
353 2 0.00
354 434 0.28
355 1 0.00
356 1 0.00
357 3 0.00
360 3 0.00
361 1 0.00
362 1 0.00
363 1 0.00
364 1 0.00
365 4 0.00
368 4 0.00
369 293 0.19
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (348 bp):
GGCCAAGTGCTTCTTTCCCGAAAGGTGACAGTTCAAGTCCTCCGAACGAGTGCAGCTTATGTTAC
AGATGGTGCACTGAAATTGAGGATTCTTATCCCCAGCATGTTTCGTCCCAATCTGCTGCTGGTCT
TGTACATTTTCCTTGTGTTTTAGTTGATTTCCTGCCATATTGTTTGCTAAAAACTTGTTTGGTTC
CTCATTGGGCAGGTCAGGTTTGTTTCCATTGCTTATCCCAGTTGTAAGATCCACTGCTTTGCTGG
ATATATGTGTACCATTGCTGGTTGCACATTTCTCAGCATCATTTTTGGAAACATCAGAGTTCTTA
GCCACTGAAGCAGCTGAGACTTT
Found at i:106866 original size:717 final size:700
Alignment explanation
Indices: 105413--107532 Score: 3137
Period size: 717 Copynumber: 3.0 Consensus size: 700
105403 CTTGAATCTG
* * * * ** * * *
105413 GGCCAAGTGCTTCTTTCCCCACAGGTGACAGTTTAAGTCCTCTGAACGAGTGCAGCTTACGTTAC
1 GGCCAAATGCTTCTTTCCCGAAAGGTGACAGTTCAAGTCCTCCAAACCAGTGCAGCTTATGTGAC
* * * * *
105478 AGATGGTGCACTGAAATTGAGGATTCTGATCCCCAGCATGTTTCTTCCCAATCTGCTGCTGGTCT
66 AGATGATGCACCGAAATTGAGGATTATTATCCCCAGCATGTATCTTCCCAATCTGCTGCTGGTCT
* * *
105543 TGTACATTTTCCTTGTCCTCATGTTTTAGTTGATTTCCTGCCATATTGTTTGGTAACAACTTGTT
131 TGTACATTTTCCTTG------TGTTTTAGTTGATTTCCTGCCATATTGTTTGCTAAAAACCTGTT
* * * *
105608 TGGTTCCTCATTTGGCAGGTCATGTTTGGTTCCATTGCTTACCCCAGTTGTAAGATCCACTGCTT
190 TGGTTCCTCATTGGGCAGGTCAGGTTTGTTTCCATTGCTTATCCCAGTTGTAAGATCCACTGCTT
* * *
105673 TGCT-GGATATATGTGTACCGTTGCTGGTTGCACATTTCTCAGCATCATATTTGGAAACATCAGA
255 TGCTGGGA-ATATGTGTACCATTGCTGGCTGCACATTTCTCAGCATCATTTTTGGAAACATCAGA
* * ** * *
105737 GTTTTTAGCCACT---G-AAGCGGCTGAGACTTTGGCCAAGTGCTTCTTTCCTGAAAGGTGACAA
319 CTTCTTAGCCACTGAAGTAAGCGGCTGAGACTTTGGCCTTGTGCTTCTTTCCAGAAAGGTGACAG
* * * *
105798 TTCAAGTCCTCCGAATGA-CTGCAGCTTATGTTACAGATGGTGCACTGAAATTGGGGATTCTCAT
384 TTCAAGTCCTCTGAACGAGC-ACAGCTTATGTTACAGATGGTGCACTGAAATTGGGGATTCTTAT
* * *
105862 CCCTAGCATGTTTCGTCCCAATCTGCTGCTGGTCTGGTACATTTTCCTTGTGTTGTACTTGTAGC
448 CCCCAGCATGTTTAGTCCCAATCTGCTGCTGGTCTTGTACATTTTCC-T-TG-TG-A--TGTAGC
* * * * * * ** *
105927 CAATATCCTGTCATATTGTTTGCTAGAAACTTGTTTGTTTCCTCATTGGGTAGGTTGGGTTTGTT
507 CGATTTCCTGTCGTATTGTTTGCCAGAAACTTGTTTGGTTCCTCATTGGGCAGGTCAGCTTTGTT
* * * * * * *
105992 TCCATTGCTTATCCCAGTTGTAAGATCCACTGCTTTGCTGGATATATGTGTACCATTGCTTGATG
572 TCCATCGCTTATTCCAGTTGGAAGATCCACTACTTCGCTGGATATATGTGTACCATTGCTGGTTG
* * *
106057 CACATTTTTCAGCATTATTTTTGGAAACATCAGTGTTCTTAGCCACTGAAGCAGCTGAGACTTT
637 CACATTTCTCAGCATCATTTTTGGAAACATCAGAGTTCTTAGCCACTGAAGCAGCTGAGACTTT
* * *
106121 GGCCAAATGCTTCTTTCCCGAGAGGTGACAGTTCAAGTTCTCCAAACCAGTGCAGCTTATGTTAC
1 GGCCAAATGCTTCTTTCCCGAAAGGTGACAGTTCAAGTCCTCCAAACCAGTGCAGCTTATGTGAC
*
106186 AGATGATGCACTGAAATTGAGGATTATTATCCCCAGCATGTATCTTCCCAATCTGCTGCTGGTCT
66 AGATGATGCACCGAAATTGAGGATTATTATCCCCAGCATGTATCTTCCCAATCTGCTGCTGGTCT
*
106251 TGTACATTTTCCTTGTGTTTTAGTTGATTTCCTGCCATATTGTTTGCTAAAAACCTGTTTTGTTC
131 TGTACATTTTCCTTGTGTTTTAGTTGATTTCCTGCCATATTGTTTGCTAAAAACCTGTTTGGTTC
*
106316 CTCATTGGGCAGGTCAGGTTTGTTTCCATTGCTTATCCCAGTTGTAAGATCCACTGCTTTGGT-G
196 CTCATTGGGCAGGTCAGGTTTGTTTCCATTGCTTATCCCAGTTGTAAGATCCACTGCTTTGCTGG
** * *
106380 GATATATGTGTACTGTTGCTGGTTGCACATTTCTCAGCATCATTTTTGGTAACATCAGACTTCTT
261 GA-ATATGTGTACCATTGCTGGCTGCACATTTCTCAGCATCATTTTTGGAAACATCAGACTTCTT
106445 AGCCACTGAAGTGGCTGAGACTTTGGCCAAAGCGGCTGAGACTTTGGCCTTGTGCTTCTTTCCAG
325 AGCCACTG-A-------AG----T-----AAGCGGCTGAGACTTTGGCCTTGTGCTTCTTTCCAG
*
106510 AATGGTGACAGTTCAAGTCCTCTGAACGAGCACAGCTTATGTTACAGATGGTGCACTGAAATTGG
373 AAAGGTGACAGTTCAAGTCCTCTGAACGAGCACAGCTTATGTTACAGATGGTGCACTGAAATTGG
106575 GGATTCTTATCCCCAGCATGTTTAGTCCCAATCTGCTGCTGGTCTTGTACATTTTCCTTGTGATG
438 GGATTCTTATCCCCAGCATGTTTAGTCCCAATCTGCTGCTGGTCTTGTACATTTTCCTTGTGATG
*
106640 TAGCCGATTTCCTGTTGTATTGTTTGCCAGAAACTTGTTTGGTTCCTCATTGGGCAGGTCAGCTT
503 TAGCCGATTTCCTGTCGTATTGTTTGCCAGAAACTTGTTTGGTTCCTCATTGGGCAGGTCAGCTT
*
106705 CGTTTCCATCGCTTATTCCAGTTGGAAGATCCACTACTTCGCTGGATATATGTGTACCATTGCTG
568 TGTTTCCATCGCTTATTCCAGTTGGAAGATCCACTACTTCGCTGGATATATGTGTACCATTGCTG
*
106770 GTTGCACATTTCTCAGCATCATTTTTGGAAACATCAGAGTTCTTAGCCACTGATGCAGCTGAGAC
633 GTTGCACATTTCTCAGCATCATTTTTGGAAACATCAGAGTTCTTAGCCACTGAAGCAGCTGAGAC
106835 TTT
698 TTT
* * *
106838 GGCCAAGTGCTTCTTTCCCGAAAGGTGACAGTTCATGTCCTCCAAACGAGTGCAGCTTATGTGAC
1 GGCCAAATGCTTCTTTCCCGAAAGGTGACAGTTCAAGTCCTCCAAACCAGTGCAGCTTATGTGAC
* *
106903 AGATGGTGCACCGAAATTGAGGGTTATTATCCCCAGCATGTATCTTCCCAATCTGCTGCTGGTCT
66 AGATGATGCACCGAAATTGAGGATTATTATCCCCAGCATGTATCTTCCCAATCTGCTGCTGGTCT
106968 TGTACATTTTCCTTGTGTTTTAGTTGATTTCCTGCCATATTGTTTGCTAAAAACCTGTTTGGTTC
131 TGTACATTTTCCTTGTGTTTTAGTTGATTTCCTGCCATATTGTTTGCTAAAAACCTGTTTGGTTC
* *
107033 CTCATTGGGCAGGTCGGGTTTGTTTCCGTTGCTTATCCCAGTTGTAAGATCCACTGCTTTGCTGG
196 CTCATTGGGCAGGTCAGGTTTGTTTCCATTGCTTATCCCAGTTGTAAGATCCACTGCTTTGCTGG
* * *
107098 GAATGTGTGTACCATTGCTGGCTGCACATTTCTCGGCATCATTTTTGGAAACATCAGAGTTCTTA
261 GAATATGTGTACCATTGCTGGCTGCACATTTCTCAGCATCATTTTTGGAAACATCAGACTTCTTA
*
107163 GCCACTGAAGT----GGCTGAGACTTTGGCCTTGTGCTTCTTTCCAGAACGGTGACAGTTCAAGT
326 GCCACTGAAGTAAGCGGCTGAGACTTTGGCCTTGTGCTTCTTTCCAGAAAGGTGACAGTTCAAGT
107224 CCTCTGAACGAGCACAGCTTATGTTACAGATGGTGCACTGAAATTGGGGATTCTTATCCCCAGCA
391 CCTCTGAACGAGCACAGCTTATGTTACAGATGGTGCACTGAAATTGGGGATTCTTATCCCCAGCA
*
107289 TGTTTAGTCCCAATCTGCTGCTGGTCTTGTACATTTTCCTTGTGTTGTAGCCGATTTCCTGTCGT
456 TGTTTAGTCCCAATCTGCTGCTGGTCTTGTACATTTTCCTTGTGATGTAGCCGATTTCCTGTCGT
107354 ATTGTTTGCCAGAAACTTGTTTGGTTCCTCATTGGGCAGGTCAGCTTTGTTTCCATCGCTTATTC
521 ATTGTTTGCCAGAAACTTGTTTGGTTCCTCATTGGGCAGGTCAGCTTTGTTTCCATCGCTTATTC
107419 CAGTTGGAAGATCCACTACTTCGCTGGATATATGTGTACCATTGCTGGTTGCACATTTCTCAGCA
586 CAGTTGGAAGATCCACTACTTCGCTGGATATATGTGTACCATTGCTGGTTGCACATTTCTCAGCA
107484 TCATTTTTGGAAACATCAGAGTTCTTAGCCACTGAAGCAGCTGAGACTT
651 TCATTTTTGGAAACATCAGAGTTCTTAGCCACTGAAGCAGCTGAGACTT
107533 GGACCTTGAA
Statistics
Matches: 1303, Mismatches: 86, Indels: 58
0.90 0.06 0.04
Matches are distributed among these distances:
696 354 0.27
702 172 0.13
705 1 0.00
708 132 0.10
709 2 0.00
713 1 0.00
716 1 0.00
717 486 0.37
718 3 0.00
719 1 0.00
720 2 0.00
721 2 0.00
722 1 0.00
723 144 0.11
724 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (700 bp):
GGCCAAATGCTTCTTTCCCGAAAGGTGACAGTTCAAGTCCTCCAAACCAGTGCAGCTTATGTGAC
AGATGATGCACCGAAATTGAGGATTATTATCCCCAGCATGTATCTTCCCAATCTGCTGCTGGTCT
TGTACATTTTCCTTGTGTTTTAGTTGATTTCCTGCCATATTGTTTGCTAAAAACCTGTTTGGTTC
CTCATTGGGCAGGTCAGGTTTGTTTCCATTGCTTATCCCAGTTGTAAGATCCACTGCTTTGCTGG
GAATATGTGTACCATTGCTGGCTGCACATTTCTCAGCATCATTTTTGGAAACATCAGACTTCTTA
GCCACTGAAGTAAGCGGCTGAGACTTTGGCCTTGTGCTTCTTTCCAGAAAGGTGACAGTTCAAGT
CCTCTGAACGAGCACAGCTTATGTTACAGATGGTGCACTGAAATTGGGGATTCTTATCCCCAGCA
TGTTTAGTCCCAATCTGCTGCTGGTCTTGTACATTTTCCTTGTGATGTAGCCGATTTCCTGTCGT
ATTGTTTGCCAGAAACTTGTTTGGTTCCTCATTGGGCAGGTCAGCTTTGTTTCCATCGCTTATTC
CAGTTGGAAGATCCACTACTTCGCTGGATATATGTGTACCATTGCTGGTTGCACATTTCTCAGCA
TCATTTTTGGAAACATCAGAGTTCTTAGCCACTGAAGCAGCTGAGACTTT
Found at i:109397 original size:14 final size:14
Alignment explanation
Indices: 109378--109406 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
109368 CAAAAATTAT
109378 GCATATTAAAAATG
1 GCATATTAAAAATG
109392 GCATATTAAAAATG
1 GCATATTAAAAATG
109406 G
1 G
109407 AAATTAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (14 bp):
GCATATTAAAAATG
Found at i:118953 original size:6 final size:6
Alignment explanation
Indices: 118942--118969 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
118932 CTTGAAGGGC
118942 TTTCTT TTTCTT TTTCTT TTTCTT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTC
118970 AAAGCTAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:120341 original size:2 final size:2
Alignment explanation
Indices: 120334--120359 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
120324 ATACTGTTTG
120334 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
120360 CTGTTTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:122996 original size:23 final size:23
Alignment explanation
Indices: 122970--123046 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 23
122960 AATATTAGGG
122970 ATTTAAATTGATTTTAGAGACTT
1 ATTTAAATTGATTTTAGAGACTT
* *
122993 ATTTGAGTTGATTTT-GCA-ACATT
1 ATTTAAATTGATTTTAG-AGAC-TT
123016 AGGGATTTAAATTGATTTTAGAGACTT
1 ----ATTTAAATTGATTTTAGAGACTT
123043 ATTT
1 ATTT
123047 GAGCTGATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 16
0.68 0.06 0.26
Matches are distributed among these distances:
22 3 0.07
23 20 0.48
27 16 0.38
28 3 0.07
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (23 bp):
ATTTAAATTGATTTTAGAGACTT
Found at i:123017 original size:50 final size:50
Alignment explanation
Indices: 122963--123075 Score: 208
Period size: 50 Copynumber: 2.3 Consensus size: 50
122953 ACTTGAAAAT
*
122963 ATTAGGGATTTAAATTGATTTTAGAGACTTATTTGAGTTGATTTTGCAAC
1 ATTAGGGATTTAAATTGATTTTAGAGACTTATTTGAGCTGATTTTGCAAC
123013 ATTAGGGATTTAAATTGATTTTAGAGACTTATTTGAGCTGATTTTGCAAC
1 ATTAGGGATTTAAATTGATTTTAGAGACTTATTTGAGCTGATTTTGCAAC
*
123063 ATTAGGGACTTAA
1 ATTAGGGATTTAA
123076 TTAACCAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (50 bp):
ATTAGGGATTTAAATTGATTTTAGAGACTTATTTGAGCTGATTTTGCAAC
Found at i:123807 original size:2 final size:2
Alignment explanation
Indices: 123757--123788 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
123747 AAGTGATGAC
123757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
123789 TTCAAATGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:125409 original size:67 final size:66
Alignment explanation
Indices: 125296--125422 Score: 159
Period size: 67 Copynumber: 1.9 Consensus size: 66
125286 TAACCTTCTT
* * *
125296 ATGAAATTTTGTTAACCACCTTGAGGAATTTTGAAAACCTCAATATGAAATTTTGATAACTTCCC
1 ATGAAATTTTGATAACCACCTTGAGGAATGTTGAAAACCTCAATATGAAATATTGATAACTTCCC
125361 A
66 A
* * *
125362 ATGAAATTTTGATAACCAACACTATGA-G-ATGTTGATAACCTCCATATGATATATTGATAAC
1 ATGAAATTTTGATAACC-AC-CT-TGAGGAATGTTGAAAACCTCAATATGAAATATTGATAAC
125423 CACGTTATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
66 16 0.31
67 30 0.58
68 3 0.06
69 3 0.06
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.34
Consensus pattern (66 bp):
ATGAAATTTTGATAACCACCTTGAGGAATGTTGAAAACCTCAATATGAAATATTGATAACTTCCC
A
Found at i:125493 original size:24 final size:22
Alignment explanation
Indices: 125208--125721 Score: 219
Period size: 22 Copynumber: 23.6 Consensus size: 22
125198 ATGATCCCAT
125208 TATGAAATTTTGATAACCTTC-C
1 TATGAAATTTTGATAACC-TCAC
* **
125230 TATGAAATTTTAATAATGAT-AC
1 TATGAAATTTTGATAA-CCTCAC
* * * ***
125252 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTCAC
* ** *
125274 TAT-AATTTTTTTTAACCTTC-T
1 TATGAAATTTTGATAACC-TCAC
* *
125295 TATGAAATTTTGTTAACCAC-C
1 TATGAAATTTTGATAACCTCAC
* *
125316 T-TGAGGAATTTTGAAAACCTCAA
1 TATGA--AATTTTGATAACCTCAC
* *
125339 TATGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCTCAC
* *
125361 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
* *
125384 TATGAGATGTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * * **
125405 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTCAC
* * *
125428 TATGAAAATTTAAAAACCT-AC
1 TATGAAATTTTGATAACCTCAC
* *
125449 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTCAC
*
125472 TCTGAAATTTTGATAACCTCAC
1 TATGAAATTTTGATAACCTCAC
*
125494 TATGAAATTTTGATAAATCTTC-C
1 TATGAAATTTTGAT-AA-CCTCAC
* * *
125517 TATAAAATTTTGATAAACATCCC
1 TATGAAATTTTGAT-AACCTCAC
* * *
125540 TATAAAATTTTGATAACTTTC-T
1 TATGAAATTTTGATAAC-CTCAC
* *
125562 TATGAAATCTTGATAA-CT-GC
1 TATGAAATTTTGATAACCTCAC
*
125582 ----AAATTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCAC
* * *
125600 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCAC
* * *
125622 TATGAAATTTTAATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCAC
*
125644 TATGAAATTTTGATAACCCTC-T
1 TATGAAATTTTGATAA-CCTCAC
* *
125666 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CAC
*
125688 TATGAAATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCAC
*
125709 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
125722 TACTCCATAA
Statistics
Matches: 366, Mismatches: 91, Indels: 72
0.69 0.17 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
20 18 0.05
21 24 0.07
22 239 0.65
23 66 0.18
24 6 0.02
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:125524 original size:23 final size:22
Alignment explanation
Indices: 125476--125577 Score: 100
Period size: 23 Copynumber: 4.5 Consensus size: 22
125466 TCACACTCTG
* *
125476 AAATTTTGAT-AACCTCACTATG
1 AAATTTTGATAAACTTC-CTATA
125498 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAA-CTTCCTATA
*
125521 AAATTTTGATAAACATCCCTATA
1 AAATTTTGATAAAC-TTCCTATA
* *
125544 AAATTTTGAT-AACTTTCTTATG
1 AAATTTTGATAAAC-TTCCTATA
*
125566 AAATCTTGATAA
1 AAATTTTGATAA
125578 CTGCAAATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
22 28 0.41
23 37 0.54
24 3 0.04
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAAACTTCCTATA
Found at i:125531 original size:45 final size:44
Alignment explanation
Indices: 125476--125578 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 44
125466 TCACACTCTG
* *
125476 AAATTTTGATAACCTCACTATGAAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAACATCACTATAAAATTTTGATAAAT-TTCCTATA
* * * *
125521 AAATTTTGATAAACATCCCTATAAAATTTTGATAACTTTCTTATG
1 AAATTTTGAT-AACATCACTATAAAATTTTGATAAATTTCCTATA
*
125566 AAATCTTGATAAC
1 AAATTTTGATAAC
125579 TGCAAATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.06
45 25 0.50
46 22 0.44
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.40
Consensus pattern (44 bp):
AAATTTTGATAACATCACTATAAAATTTTGATAAATTTCCTATA
Found at i:125966 original size:88 final size:88
Alignment explanation
Indices: 125803--125969 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 88
125793 AAAAATACCA
* * * **
125803 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
125868 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* *
125891 CTATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACA
1 CTATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
*
125954 ACACTATGAAATTTTG
64 ACACTATAAAATTTTG
125970 ATAATCTTCC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 4 0.06
88 61 0.91
89 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (88 bp):
CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:126182 original size:22 final size:22
Alignment explanation
Indices: 126135--126182 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
126125 ATTTTTATAA
*
126135 TTAACCTCCCATGAAATATTAG
1 TTAACCTCCAATGAAATATTAG
*
126157 -TAACCTCCTAATGAAAT-TTTG
1 TTAACCTCC-AATGAAATATTAG
126178 TTAAC
1 TTAAC
126183 TACACTATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.35
Consensus pattern (22 bp):
TTAACCTCCAATGAAATATTAG
Found at i:126225 original size:22 final size:21
Alignment explanation
Indices: 125828--126443 Score: 170
Period size: 22 Copynumber: 27.8 Consensus size: 21
125818 AATCACATTT
* *
125828 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTC-CTA
*
125850 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTC-CTA
* * * *
125872 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTC-CTA
* * * *
125894 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTC-CTA
* *
125916 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTC-CTA
**
125938 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTC-CTA
* *
125960 TGAAATTTTGATAATCTTCCAA
1 TGAAATTTTGATAA-CCTCCTA
**
125982 T-AAATTTTGATAATATGATCTCTA
1 TGAAATTTTGAT-A-A-CCTC-CTA
*
126006 TGAAATTTCGATAATCACT-CTA
1 TGAAATTTTGATAA-C-CTCCTA
* *
126028 TGAGA-TTTGATAACCTTCTA
1 TGAAATTTTGATAACCTCCTA
* *
126048 TCAAATTTTGGT-A-CTCCTCA
1 TGAAATTTTGATAACCTCCT-A
* *
126068 TGAAATCGAGACTTTTATAACCTAATTCATA
1 TGAAAT------TTTGATAACC----TCCTA
*
126099 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTC-CTA
* * *
126121 TAAAATTTTTATAATTAACCTCCCA
1 TGAAA--TTT-TGA-TAACCTCCTA
*
126146 TGAAATATT-AGTAACCTCCTAA
1 TGAAATTTTGA-TAACCTCCT-A
*
126168 TGAAATTTTGTTAA-CTACACTA
1 TGAAATTTTGATAACCT-C-CTA
126190 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTC-CTA
* *
126212 TGACATTTTGATAA--TCACTT
1 TGAAATTTTGATAACCTC-CTA
** *
126232 TGATAACCTTTCT-ATAAAAT--TG
1 TGA-AA--TTT-TGATAACCTCCTA
*
126254 TGATAA---T--TAACCACACTA
1 TGA-AATTTTGATAACCTC-CTA
** *
126272 TGAAATTTCAATAACCAACCTA
1 TGAAATTTTGATAACC-TCCTA
* *
126294 AGAAATTTTAATAACCTCCATA
1 TGAAATTTTGATAACCTCC-TA
* *
126316 TGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACCTC-CTA
*
126338 TGTGAAATTTTGATAACTTCCATA
1 --TGAAATTTTGATAACCTCC-TA
* *
126362 TGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACCTC-CTA
*
126384 TGGAATTTTGATAACCTCCTCA
1 TGAAATTTTGATAACCTCCT-A
* * *
126406 TGAAATTATAATAACCATCTTA
1 TGAAATTTTGATAACC-TCCTA
*
126428 TGAAATTTTAATAACC
1 TGAAATTTTGATAACC
126444 ACATAGAGAT
Statistics
Matches: 447, Mismatches: 91, Indels: 112
0.69 0.14 0.17
Matches are distributed among these distances:
15 3 0.01
16 1 0.00
17 2 0.00
18 4 0.01
19 6 0.01
20 21 0.05
21 41 0.09
22 263 0.59
23 31 0.07
24 26 0.06
25 27 0.06
26 10 0.02
27 1 0.00
28 1 0.00
31 7 0.02
32 3 0.01
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.38
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCCTA
Found at i:126360 original size:46 final size:45
Alignment explanation
Indices: 126295--126412 Score: 186
Period size: 46 Copynumber: 2.6 Consensus size: 45
126285 ACCAACCTAA
*
126295 GAAATTTTAATAACCTCCATATGAAATTTTGGTAACCACACTATG
1 GAAATTTTGATAACCTCCATATGAAATTTTGGTAACCACACTATG
*
126340 TGAAATTTTGATAACTTCCATATGAAATTTTGGTAACCACACTATG
1 -GAAATTTTGATAACCTCCATATGAAATTTTGGTAACCACACTATG
126386 G-AATTTTGATAACCTCC-TCATGAAATT
1 GAAATTTTGATAACCTCCAT-ATGAAATT
126413 ATAATAACCA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
43 1 0.01
44 23 0.34
45 1 0.01
46 43 0.63
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (45 bp):
GAAATTTTGATAACCTCCATATGAAATTTTGGTAACCACACTATG
Found at i:127649 original size:100 final size:100
Alignment explanation
Indices: 127476--127675 Score: 382
Period size: 100 Copynumber: 2.0 Consensus size: 100
127466 TCAGATACTA
*
127476 AAGATGATGTGGGGCATCCCTATTGGTCATGTTGGATCCTAATTAATGATGATAATATAACTTTA
1 AAGATGATGTGGGGCATCCCTATTGGTCATGTTGGATCCTAATTAATGAGGATAATATAACTTTA
127541 TATTATTTTAATAGTAAAATAATTAAACTATTATT
66 TATTATTTTAATAGTAAAATAATTAAACTATTATT
127576 AAGATGATGTGGGGCATCCCTATTGGTCATGTTGGATCCTAATTAATGAGGATAATATAACTTTA
1 AAGATGATGTGGGGCATCCCTATTGGTCATGTTGGATCCTAATTAATGAGGATAATATAACTTTA
*
127641 TATTATTTTAATAGTAAAGTAATTAAACTATTATT
66 TATTATTTTAATAGTAAAATAATTAAACTATTATT
127676 TAATAATGGT
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (100 bp):
AAGATGATGTGGGGCATCCCTATTGGTCATGTTGGATCCTAATTAATGAGGATAATATAACTTTA
TATTATTTTAATAGTAAAATAATTAAACTATTATT
Found at i:127725 original size:31 final size:31
Alignment explanation
Indices: 127690--127755 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
127680 AATGGTAATG
*
127690 ACAATTTAGAAATATGTTTTAAAAA-AAAGGT
1 ACAA-TTAGAAATATATTTTAAAAATAAAGGT
* *
127721 ACAATTGGAAATATATTTTAAAAATAAGGGT
1 ACAATTAGAAATATATTTTAAAAATAAAGGT
127752 ACAA
1 ACAA
127756 CTGGAAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.30
Consensus pattern (31 bp):
ACAATTAGAAATATATTTTAAAAATAAAGGT
Found at i:127733 original size:30 final size:31
Alignment explanation
Indices: 127698--127762 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
127688 TGACAATTTA
* *
127698 GAAATATGTTTTAAAAA-AAAGGTACAATTG
1 GAAATATATTTTAAAAATAAAGGTACAACTG
*
127728 GAAATATATTTTAAAAATAAGGGTACAACTG
1 GAAATATATTTTAAAAATAAAGGTACAACTG
127759 GAAA
1 GAAA
127763 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.28
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAAGGTACAACTG
Found at i:128772 original size:2 final size:2
Alignment explanation
Indices: 128765--128791 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
128755 CTTATTAAAT
128765 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
128792 TTGATGTTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.