Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold320
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: 2598547
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 17 of 17
Found at i:2504760 original size:16 final size:16
Alignment explanation
Indices: 2504709--2504762 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
2504699 TTTTTATATT
* *
2504709 TATATAATTTTTAATA
1 TATATAAATTTTAAAA
* *
2504725 TAT-TAATATTTTATAT
1 TATATAA-ATTTTAAAA
2504741 TATATAAATTTTAAAA
1 TATATAAATTTTAAAA
2504757 TATATA
1 TATATA
2504763 TTCGTATCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 24 0.80
17 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATAAATTTTAAAA
Found at i:2508286 original size:22 final size:22
Alignment explanation
Indices: 2508246--2508290 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2508236 AATAAATAAA
*
2508246 ATTATTATTATATTTATACAAT
1 ATTATTATTATATTCATACAAT
2508268 ATTATTATTAT-TATCATACAAT
1 ATTATTATTATAT-TCATACAAT
2508290 A
1 A
2508291 ATATGTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTATTATTATATTCATACAAT
Found at i:2508554 original size:2 final size:2
Alignment explanation
Indices: 2508547--2508578 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2508537 ATGCATACAA
2508547 AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2508579 CATTGAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2516440 original size:31 final size:33
Alignment explanation
Indices: 2516382--2516443 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
2516372 TAAAAAAATT
* *
2516382 AAAAAGTTAAATATTTAAATTTTATTGTTTATA
1 AAAAAATTAAATAATTAAATTTTATTGTTTATA
2516415 AAAAAATTAAA-AATTAAA-TTTATTGTTTA
1 AAAAAATTAAATAATTAAATTTTATTGTTTA
2516444 ATATCGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 11 0.41
32 6 0.22
33 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (33 bp):
AAAAAATTAAATAATTAAATTTTATTGTTTATA
Found at i:2516781 original size:41 final size:39
Alignment explanation
Indices: 2516722--2516807 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 39
2516712 CTGATCCAAT
* *
2516722 AAAAATTAATTATATAATATTTAAT-ACATATTTATAATTTA
1 AAAAATTAATCATATAATA--AAATAACAT-TTTATAATTTA
*
2516763 AAAAATT-ATCATATTAATAAAATAACATTTTATAATTTT
1 AAAAATTAATCATA-TAATAAAATAACATTTTATAATTTA
2516802 AAAAAT
1 AAAAAT
2516808 CTCTAATCAG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
39 19 0.47
40 9 0.22
41 12 0.30
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (39 bp):
AAAAATTAATCATATAATAAAATAACATTTTATAATTTA
Found at i:2518426 original size:95 final size:95
Alignment explanation
Indices: 2518317--2518498 Score: 310
Period size: 95 Copynumber: 1.9 Consensus size: 95
2518307 GAATTTTTTA
* * *
2518317 AGTACCCAGACCAGATGTCCAGATAACAAAGACAGCAATAAATTAGCCCATTGTTGGATAAGTTG
1 AGTACCCAGACCAGACGTCCAGATAACAAAGACAGCAATAAATTAGCCCACTGTTAGATAAGTTG
2518382 AAGGAAATTTGTACGTAGTTCAGATAACAT
66 AAGGAAATTTGTACGTAGTTCAGATAACAT
* * *
2518412 AGTACCCAGACCAGACGTTCAGATAACAAAGACAGCAATAATTTAGCCCACTGTTATATAAGTTG
1 AGTACCCAGACCAGACGTCCAGATAACAAAGACAGCAATAAATTAGCCCACTGTTAGATAAGTTG
2518477 AAGGAAATTTGTACGTAGTTCA
66 AAGGAAATTTGTACGTAGTTCA
2518499 TCATTTTCTT
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 81 1.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (95 bp):
AGTACCCAGACCAGACGTCCAGATAACAAAGACAGCAATAAATTAGCCCACTGTTAGATAAGTTG
AAGGAAATTTGTACGTAGTTCAGATAACAT
Found at i:2524002 original size:31 final size:33
Alignment explanation
Indices: 2523959--2524024 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 33
2523949 AAGGTTTTCT
*
2523959 TTTATTTATTTATTTATTTTTTAAGAAA-AATGTA
1 TTTATTTA-TAATTTATTTTTTAA-AAATAATGTA
2523993 TTTAATTTATAATTTATTTTTTAAAAATAATG
1 TTT-ATTTATAATTTATTTTTTAAAAATAATG
2524025 GGTTTATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 3 0.10
34 21 0.72
35 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (33 bp):
TTTATTTATAATTTATTTTTTAAAAATAATGTA
Found at i:2527239 original size:3 final size:3
Alignment explanation
Indices: 2527231--2527255 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2527221 CCTTTTGTTT
2527231 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
2527256 ATTTTTGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:2528216 original size:18 final size:16
Alignment explanation
Indices: 2528195--2528231 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
2528185 ATTATATAAA
2528195 TAAATTTGAATTAAAATT
1 TAAATTTGAA--AAAATT
2528213 TAAATTTGAAAAAATT
1 TAAATTTGAAAAAATT
2528229 TAA
1 TAA
2528232 TTTCATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
18 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (16 bp):
TAAATTTGAAAAAATT
Found at i:2529334 original size:25 final size:26
Alignment explanation
Indices: 2529277--2529342 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
2529267 GATTTTGAAT
* *
2529277 TTTTTTAATTTTTTTAAAAAATATAC
1 TTTTTTAACTTTTTTAAAAAATATAA
*
2529303 TTATTTAACTTTTTTAAAAAAT-TAA
1 TTTTTTAACTTTTTTAAAAAATATAA
*
2529328 TTTTTTATCTTTTTT
1 TTTTTTAACTTTTTT
2529343 TTCTCCGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
25 15 0.43
26 20 0.57
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTTTAACTTTTTTAAAAAATATAA
Found at i:2531119 original size:22 final size:22
Alignment explanation
Indices: 2531094--2531138 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2531084 ATCATTTAAA
*
2531094 TAATAAAAAATATTTTTAAATT
1 TAATAAAAAATATTATTAAATT
* * *
2531116 TAATGATAAATATTATTATATT
1 TAATAAAAAATATTATTAAATT
2531138 T
1 T
2531139 TTTATTTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TAATAAAAAATATTATTAAATT
Found at i:2531744 original size:26 final size:26
Alignment explanation
Indices: 2531715--2531777 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
2531705 ATTTTATTAA
2531715 AATATAGTAAATAT-TATTTT-TATATT
1 AATATA-TAAATATATATTTTATA-ATT
*
2531741 AATATATATATATATATTTTATAATT
1 AATATATAAATATATATTTTATAATT
*
2531767 AA-ATTTAAATA
1 AATATATAAATA
2531778 AAAAATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 13 0.41
26 17 0.53
27 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
AATATATAAATATATATTTTATAATT
Found at i:2532880 original size:2 final size:2
Alignment explanation
Indices: 2532873--2532898 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2532863 ATTGGTATGC
2532873 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
2532899 TTGGCTAGAA
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:2534101 original size:20 final size:20
Alignment explanation
Indices: 2534073--2534111 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2534063 CAAGCGAGTG
2534073 TATCCATACTTTAACTAAGC
1 TATCCATACTTTAACTAAGC
* *
2534093 TATCGATACTTTGACTAAG
1 TATCCATACTTTAACTAAG
2534112 AAAGATATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (20 bp):
TATCCATACTTTAACTAAGC
Found at i:2534308 original size:20 final size:21
Alignment explanation
Indices: 2534285--2534332 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2534275 TAAATTATCC
*
2534285 TTTTTAGTTTTAATTTGATTT
1 TTTTTAGTTTTAATTTAATTT
*
2534306 TTTTTA-TTTTTATTTAATTT
1 TTTTTAGTTTTAATTTAATTT
*
2534326 TATTTAG
1 TTTTTAG
2534333 GGTCAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (21 bp):
TTTTTAGTTTTAATTTAATTT
Found at i:2534973 original size:24 final size:24
Alignment explanation
Indices: 2534937--2534982 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2534927 GTGATTATTT
2534937 TTGTTTGTAAAAAATGGTGGCTTG
1 TTGTTTGTAAAAAATGGTGGCTTG
* *
2534961 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTAAAAAATGGTGGCT
2534983 AATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.07, G:0.28, T:0.43
Consensus pattern (24 bp):
TTGTTTGTAAAAAATGGTGGCTTG
Found at i:2536229 original size:109 final size:108
Alignment explanation
Indices: 2535726--2536284 Score: 500
Period size: 108 Copynumber: 5.1 Consensus size: 108
2535716 AACGTCTGGA
* ** * * ** * *
2535726 ATAATTCATTTTTACATTAATTACGTAAATTCAAGTATTAAAAGATTGACTTCGAAATAATTCAT
1 ATAATTTATTTTTTGATTAATTACGTAAATTCAGGCACCAAAAGATTGACCTCGAAATAAATCAT
* * *
2535791 CGTTTAAAGTCATAAAGCGACGTACGAACGTCCTTTATATAGA
66 CGTCTAGAGTCATAAAGCGACGTACGAACGTCCTTTATATAGG
* ** *
2535834 ATAATTTATTTTTTTTGCATTAATTACATAAATTTGGGCACCAAAAGATTGACC-CTAAAATAAA
1 ATAATTTA--TTTTTTG-ATTAATTACGTAAATTCAGGCACCAAAAGATTGACCTC-GAAATAAA
* * ** * *
2535898 TCATCGTCTAGAGTCGTAAAACGATATACGAACGTCCTTTACATAAG
62 TCATCGTCTAGAGTCATAAAGCGACGTACGAACGTCCTTTATATAGG
* ** * *
2535945 ATAATTCT-TTTTTTACATTAATTACGTAAATTCAGATA-AAAAAAATTGACCTCGAAATAAATC
1 ATAATT-TATTTTTT-GATTAATTACGTAAATTCAGGCACCAAAAGATTGACCTCGAAATAAATC
* ** * * *
2536008 AACGTCTAGAGTGGTAAAGCGACGAACAAACG-CCTTTTACATAGG
64 ATCGTCTAGAGTCATAAAGCGACGTACGAACGTCC-TTTATATAGG
* ** * * * * **
2536053 ATAATTTGTTTTTACATTAATTATGTAAATTTAGGCACCAAAAGATTGGTCC-CGTAATAGGTCA
1 ATAATTTATTTTTTGATTAATTACGTAAATTCAGGCACCAAAAGATT-GACCTCGAAATAAATCA
**
2536117 TCGTCTAGAGTCATAAAGTAACGTACGAACG-CCTTTTATATAGG
65 TCGTCTAGAGTCATAAAGCGACGTACGAACGTCC-TTTATATAGG
* * *
2536161 ATAATTTATTTTTTGATTTAATTACGTAAATTCAGGCACTAAAAGATTGACCTCGAAATAGATTA
1 ATAATTTATTTTTTGA-TTAATTACGTAAATTCAGGCACCAAAAGATTGACCTCGAAATAAATCA
* ** ** *
2536226 TCGTTTAGAGTCATAAAATGATATACGAACGTCCTTTATATAAG
65 TCGTCTAGAGTCATAAAGCGACGTACGAACGTCCTTTATATAGG
*
2536270 ATAATTCATTTTTTG
1 ATAATTTATTTTTTG
2536285 TGTAAATTAC
Statistics
Matches: 362, Mismatches: 75, Indels: 27
0.78 0.16 0.06
Matches are distributed among these distances:
107 22 0.06
108 140 0.39
109 113 0.31
110 8 0.02
111 78 0.22
112 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (108 bp):
ATAATTTATTTTTTGATTAATTACGTAAATTCAGGCACCAAAAGATTGACCTCGAAATAAATCAT
CGTCTAGAGTCATAAAGCGACGTACGAACGTCCTTTATATAGG
Found at i:2538009 original size:15 final size:16
Alignment explanation
Indices: 2537978--2538013 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2537968 ATATTTATTA
2537978 GATTTATCATAATTTT
1 GATTTATCATAATTTT
*
2537994 GATTTATGAT-ATTTT
1 GATTTATCATAATTTT
2538009 GATTT
1 GATTT
2538014 CTATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.28, C:0.03, G:0.11, T:0.58
Consensus pattern (16 bp):
GATTTATCATAATTTT
Found at i:2540546 original size:51 final size:51
Alignment explanation
Indices: 2540458--2540615 Score: 192
Period size: 51 Copynumber: 3.1 Consensus size: 51
2540448 GTAGGGCAAA
* * * * **
2540458 CTGCAGCACTTGAGCTACCACCATATGAAATTCTTGGCAGCCCCAGGTCAC
1 CTGCAACACTTGAGCTGCCACCAAACGAAGGTCTTGGCAGCCCCAGGTCAC
* * *
2540509 CTGCAACACTTGAGCTATCC-CCAAACGAAGGTGTTGGCAACCCCAGGTCAC
1 CTGCAACACTTGAGCT-GCCACCAAACGAAGGTCTTGGCAGCCCCAGGTCAC
* * *
2540560 CTGCGACACTTGAGCTGCCACCAAATGAAGGTCTTGGCAGCCCCAGGTCAT
1 CTGCAACACTTGAGCTGCCACCAAACGAAGGTCTTGGCAGCCCCAGGTCAC
2540611 CTGCA
1 CTGCA
2540616 GCAGTACCAG
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
50 2 0.02
51 86 0.96
52 2 0.02
ACGTcount: A:0.25, C:0.33, G:0.22, T:0.20
Consensus pattern (51 bp):
CTGCAACACTTGAGCTGCCACCAAACGAAGGTCTTGGCAGCCCCAGGTCAC
Found at i:2541623 original size:15 final size:16
Alignment explanation
Indices: 2541557--2541628 Score: 78
Period size: 16 Copynumber: 4.7 Consensus size: 16
2541547 AACTCGAATC
*
2541557 TAAAATAA-TCAAATT
1 TAAAATAATTTAAATT
2541572 TAAAATAATTTAAATT
1 TAAAATAATTTAAATT
* * *
2541588 TGAAATAATTTGAACT
1 TAAAATAATTTAAATT
*
2541604 TAAAATGA-TTAAATT
1 TAAAATAATTTAAATT
2541619 TAAAA-AATTT
1 TAAAATAATTT
2541629 GAGTGTTAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
14 1 0.02
15 20 0.43
16 25 0.54
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (16 bp):
TAAAATAATTTAAATT
Found at i:2541638 original size:31 final size:32
Alignment explanation
Indices: 2541571--2541630 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
2541561 ATAATCAAAT
*
2541571 TTAAAATAATTTAAATTTGAAATAATTTGAAC
1 TTAAAATAATTTAAATTTGAAAAAATTTGAAC
*
2541603 TTAAAATGA-TTAAATTT-AAAAAATTTGA
1 TTAAAATAATTTAAATTTGAAAAAATTTGA
2541631 GTGTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 10 0.38
31 8 0.31
32 8 0.31
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.40
Consensus pattern (32 bp):
TTAAAATAATTTAAATTTGAAAAAATTTGAAC
Found at i:2542046 original size:56 final size:56
Alignment explanation
Indices: 2541979--2542090 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
2541969 ATAAATGATG
2541979 GTTGGTAGGAGAATTTAATTTGTTGTTAATTATGGCAAGATAATTCACCATTAATC
1 GTTGGTAGGAGAATTTAATTTGTTGTTAATTATGGCAAGATAATTCACCATTAATC
2542035 GTTGGTAGGAGAATTTAATTTGTTGTTAATTATGGCAAGATAATTCACCATTAATC
1 GTTGGTAGGAGAATTTAATTTGTTGTTAATTATGGCAAGATAATTCACCATTAATC
2542091 AATGCTTATT
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:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (56 bp):
GTTGGTAGGAGAATTTAATTTGTTGTTAATTATGGCAAGATAATTCACCATTAATC
Found at i:2543192 original size:4 final size:4
Alignment explanation
Indices: 2543158--2543250 Score: 70
Period size: 4 Copynumber: 22.8 Consensus size: 4
2543148 ATAAACAAAA
*
2543158 CTTT C-TT C-TT CTTT -TTT CTTT -TCTT CCTT CTTT CTTT CTTTT CTTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CT-TT CTTT CTTT CTTT C-TTT C-TTT
*
2543205 CTTTT CTTTT CTTCT CTTT CTCTT -TCT CTTT CTTT CTTT CTTT CTT
1 C-TTT C-TTT CTT-T CTTT CT-TT CTTT CTTT CTTT CTTT CTTT CTT
2543251 CCATTAAAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 16
0.79 0.04 0.16
Matches are distributed among these distances:
3 11 0.14
4 41 0.53
5 25 0.32
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:2543210 original size:35 final size:35
Alignment explanation
Indices: 2543163--2543252 Score: 109
Period size: 35 Copynumber: 2.6 Consensus size: 35
2543153 CAAAACTTTC
*
2543163 TTCTTCTT-TTTTCTTTTCTTCCTTCTTTCTTTCT-T
1 TTCTT-TTCTTTTCTTTTCTTCCTT-TCTCTTTCTCT
2543198 TTCTTTTCTTTTCTTTTCTTCTCTTTCTCTTTCTCT
1 TTCTTTTCTTTTCTTTTCTTC-CTTTCTCTTTCTCT
2543234 TTC-TTTC-TTTC-TTTCTTCC
1 TTCTTTTCTTTTCTTTTCTTCC
2543253 ATTAAAAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
32 1 0.02
33 7 0.14
34 6 0.12
35 30 0.59
36 7 0.14
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (35 bp):
TTCTTTTCTTTTCTTTTCTTCCTTTCTCTTTCTCT
Found at i:2544431 original size:13 final size:14
Alignment explanation
Indices: 2544409--2544440 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2544399 CTCACAAGTA
2544409 AATT-AATTTTTTT
1 AATTAAATTTTTTT
2544422 -ATTAAATTTTTTT
1 AATTAAATTTTTTT
2544435 AATTAA
1 AATTAA
2544441 GACTTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 9 0.53
14 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
AATTAAATTTTTTT
Found at i:2545803 original size:23 final size:23
Alignment explanation
Indices: 2545777--2545833 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 23
2545767 TTTATTTATT
*
2545777 TATTTGATATTTAAAATTTTAAA
1 TATTTGATATTTAAAATATTAAA
* * * *
2545800 TATTAGATGTTTATAATATTACA
1 TATTTGATATTTAAAATATTAAA
2545823 T-TTT-ATATTTA
1 TATTTGATATTTA
2545834 GATATAAACA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 6 0.22
22 2 0.07
23 19 0.70
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (23 bp):
TATTTGATATTTAAAATATTAAA
Found at i:2545827 original size:15 final size:15
Alignment explanation
Indices: 2545792--2545829 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2545782 GATATTTAAA
*
2545792 ATTTTA-AATATTAG
1 ATTTTATAATATTAC
2545806 ATGTTTATAATATTAC
1 AT-TTTATAATATTAC
2545822 ATTTTATA
1 ATTTTATA
2545830 TTTAGATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 10 0.48
16 9 0.43
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (15 bp):
ATTTTATAATATTAC
Found at i:2547708 original size:51 final size:50
Alignment explanation
Indices: 2547644--2547859 Score: 249
Period size: 51 Copynumber: 4.3 Consensus size: 50
2547634 CGCATATGAA
** *
2547644 GGCAGCCCAAGGTCAGTGGCAACACTTGAGCTGCCACCAAATGCAGGTCTT
1 GGCAGCCC-AGGTCAGCAGCAACACTTGAGCTGCCACCAAATGAAGGTCTT
* * * * *
2547695 GGCAGCCTCAGGTCACCTGCAACACTTGAGCTGCCCCCGAAGGAAGGTCTT
1 GGCAGCC-CAGGTCAGCAGCAACACTTGAGCTGCCACCAAATGAAGGTCTT
* *
2547746 GGCAGCCCCAAGTCAGCAGCAACACTTGAGCTGCCCCCAAAT---GGTCTT
1 GGCAG-CCCAGGTCAGCAGCAACACTTGAGCTGCCACCAAATGAAGGTCTT
* * *
2547794 GGCAGCCCCAAGTCAGCAGCAACACTTGAGCTACCACCAAATGAAGGTCCT
1 GGCAG-CCCAGGTCAGCAGCAACACTTGAGCTGCCACCAAATGAAGGTCTT
2547845 GGCAGACCCAGGTCA
1 GGCAG-CCCAGGTCA
2547860 TCTGCAGGAA
Statistics
Matches: 143, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
48 46 0.32
51 94 0.66
52 3 0.02
ACGTcount: A:0.26, C:0.33, G:0.25, T:0.16
Consensus pattern (50 bp):
GGCAGCCCAGGTCAGCAGCAACACTTGAGCTGCCACCAAATGAAGGTCTT
Found at i:2547848 original size:99 final size:99
Alignment explanation
Indices: 2547644--2547859 Score: 263
Period size: 99 Copynumber: 2.1 Consensus size: 99
2547634 CGCATATGAA
** * *
2547644 GGCAGCCCAAGGTCAGTGGCAACACTTGAGCTGCCACCAAATGCAGGTCTTGGCAGCCTCAGGTC
1 GGCAGCCCAA-GTCAGCAGCAACACTTGAGCTGCCACCAAAT--AGGTCTTGGCAGCCCCAAGTC
* * * * *
2547709 ACCTGCAACACTTGAGCTGCCCCCGAAGGAAGGTCTT
63 ACCAGCAACACTTGAGCTACCACCAAAGGAAGGTCCT
* *
2547746 GGCAGCCCCAAGTCAGCAGCAACACTTGAGCTGCCCCCAAAT-GGTCTTGGCAGCCCCAAGTCAG
1 GGCAG-CCCAAGTCAGCAGCAACACTTGAGCTGCCACCAAATAGGTCTTGGCAGCCCCAAGTCAC
*
2547810 CAGCAACACTTGAGCTACCACCAAATGAAGGTCCT
65 CAGCAACACTTGAGCTACCACCAAAGGAAGGTCCT
*
2547845 GGCAGACCCAGGTCA
1 GGCAG-CCCAAGTCA
2547860 TCTGCAGGAA
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
99 61 0.62
102 33 0.33
103 5 0.05
ACGTcount: A:0.26, C:0.33, G:0.25, T:0.16
Consensus pattern (99 bp):
GGCAGCCCAAGTCAGCAGCAACACTTGAGCTGCCACCAAATAGGTCTTGGCAGCCCCAAGTCACC
AGCAACACTTGAGCTACCACCAAAGGAAGGTCCT
Found at i:2549110 original size:2 final size:2
Alignment explanation
Indices: 2549103--2549136 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2549093 TTATTCCATA
2549103 AT 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 AT
2549137 CTTTTGAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2549536 original size:181 final size:179
Alignment explanation
Indices: 2549230--2550069 Score: 826
Period size: 181 Copynumber: 4.7 Consensus size: 179
2549220 GAGCAACGCA
* * * * * * * *
2549230 TTAATCATCATTAATATATATTCT-GAAGTCAAATTTAAT-AGAAGATTTTATTTATCTATTTAA
1 TTAATTATCATTAATATAAATTCTAAAAATCAAATTTAATCA-AAGATCTCATTTGTCTATCTAA
* ** * * * * *
2549293 TTCAAAATAAAAAA-CCCAATCATTCAATCAATCCTCCAAAACAAGTGATTATTATATATCCACA
65 TTCATAATAAAAAATATCAATCATTCAATCAATCTTTCAAAACAAGCGAGTATTATATATCCACG
* * * ** *
2549357 ATGAACGTTATTATTTGCCATGTTTTACAATGGAAAAAACTTACAATGTG
130 ATGAACATTACTATATGCCACATTTTAAAATGGAAAAAACTTACAATGTG
* * *
2549407 TTAATTATCATTAATATAAATTCTAAAAATTAAATTTAATCAAAGATCTCGTTTGTCTATCTAAA
1 TTAATTATCATTAATATAAATTCTAAAAATCAAATTTAATCAAAGATCTCATTTGTCTATCTAAT
* * * *
2549472 TCATAATAAAAAAAAAATCAATCATTCAATTAATCTTTCAAAACAAGTGTGTATTATATATCCAC
66 TCATAAT--AAAAAATATCAATCATTCAATCAATCTTTCAAAACAAGCGAGTATTATATATCCAC
** *
2549537 GATGAACATTACTATATGCCATGTTTTAAAATGGGAAAAACTTACAATGTG
129 GATGAACATTACTATATGCCACATTTTAAAATGGAAAAAACTTACAATGTG
* * * * ** * * *
2549588 TCAGTTTTCATTAATATACATTCTAAAAATCAAATTTAATTGAAGATTTCAATTGTCTATTTAAT
1 TTAATTATCATTAATATAAATTCTAAAAATCAAATTTAATCAAAGATCTCATTTGTCTATCTAAT
* * *
2549653 TCATAATAAAAAATATCAATCATTCAATCAATCTTTCAAAGCAAACAAGTATTATACTA---A-G
66 TCATAATAAAAAATATCAATCATTCAATCAATCTTTCAAAACAAGCGAGTATTATA-TATCCACG
* * * * *
2549714 ATGAATATTACTATATGTCACATTTTAAAATTGG-AAAAATTTAAAAT-TT
130 ATGAACATTACTATATGCCACATTTTAAAA-TGGAAAAAACTTACAATGTG
** * * * * *
2549763 TTAAGTTCCCATT-AT-T-ATTTCTAAAAATCAAATATAATCGAAGATCTCATTTATATAT-TAT
1 TTAA-TTATCATTAATATAAATTCTAAAAATCAAATTTAATCAAAGATCTCATTTGTCTATCTA-
* * * * *
2549824 ATTCATAATAAAAAGTGTCAATCATTCAATCAATCTTTCAAAACAAGCAAGTATTGTATATACAC
64 ATTCATAATAAAAAATATCAATCATTCAATCAATCTTTCAAAACAAGCGAGTATTATATATCCAC
* * * * *
2549889 GACGAACATTACTATATGCCACATTTTATAATAGAAAAAAAATTACAAAGT-
129 GATGAACATTACTATATGCCACATTTTAAAAT-GGAAAAAACTTACAATGTG
* * * *
2549940 TTAGTTATCATTAATATATATTCTAAAAATTAAATTTAATCAAAGATCTCATTTGTTTATCTAAT
1 TTAATTATCATTAATATAAATTCTAAAAATCAAATTTAATCAAAGATCTCATTTGTCTATCTAAT
* * * * *
2550005 TCATAATAAAAAAATATCAATCATTCAATCAATCTTTTAAAAGAAGAGAGTCTTATATATACACG
66 TCATAAT-AAAAAATATCAATCATTCAATCAATCTTTCAAAACAAGCGAGTATTATATATCCACG
2550070 TTTTGAAAAG
Statistics
Matches: 548, Mismatches: 94, Indels: 39
0.80 0.14 0.06
Matches are distributed among these distances:
172 4 0.01
173 87 0.16
174 1 0.00
175 7 0.01
176 78 0.14
177 41 0.07
178 37 0.07
179 87 0.16
180 59 0.11
181 147 0.27
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (179 bp):
TTAATTATCATTAATATAAATTCTAAAAATCAAATTTAATCAAAGATCTCATTTGTCTATCTAAT
TCATAATAAAAAATATCAATCATTCAATCAATCTTTCAAAACAAGCGAGTATTATATATCCACGA
TGAACATTACTATATGCCACATTTTAAAATGGAAAAAACTTACAATGTG
Found at i:2550380 original size:19 final size:19
Alignment explanation
Indices: 2550356--2550399 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2550346 CATTTTTTAA
*
2550356 AAAAAACTATTATT-TACTT
1 AAAAAACTATCATTCT-CTT
*
2550375 AAAAAATTATCATTCTCTT
1 AAAAAACTATCATTCTCTT
2550394 AAAAAA
1 AAAAAA
2550400 ATTATGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAAACTATCATTCTCTT
Found at i:2552086 original size:3 final size:3
Alignment explanation
Indices: 2552078--2552118 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
2552068 TCACTCTTGA
*
2552078 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2552119 GGTAAAATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2552491 original size:2 final size:2
Alignment explanation
Indices: 2552486--2552526 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2552476 ATTGAGAGAA
* *
2552486 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2552527 GATACACATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2554348 original size:5 final size:5
Alignment explanation
Indices: 2554338--2554374 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
2554328 TATTTTATAA
*
2554338 AATTT AATTT AATTT AATTT AATTT ATATTA AATTT A
1 AATTT AATTT AATTT AATTT AATTT A-ATTT AATTT A
2554375 TCGAAGCGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:2557029 original size:31 final size:33
Alignment explanation
Indices: 2556987--2557048 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
2556977 TTATATTATT
2556987 AAAATAGTATTTTA-TAATTAA-ATTTAAATTA
1 AAAATAGTATTTTATTAATTAATATTTAAATTA
* *
2557018 AAAATATTATTTTATTATTTAATATTTAAAT
1 AAAATAGTATTTTATTAATTAATATTTAAAT
2557049 CAAATTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 13 0.48
32 6 0.22
33 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (33 bp):
AAAATAGTATTTTATTAATTAATATTTAAATTA
Found at i:2557080 original size:21 final size:21
Alignment explanation
Indices: 2557033--2557083 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
2557023 ATTATTTTAT
2557033 TATTTAATATTTAAATCAAATTA
1 TATTTAA-ATTTAAA-CAAATTA
2557056 -ATTTAAATTTATAA-AAATTA
1 TATTTAAATTTA-AACAAATTA
2557076 TATTTAAA
1 TATTTAAA
2557084 ATTCAGCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTTAAATTTAAACAAATTA
Found at i:2569815 original size:18 final size:20
Alignment explanation
Indices: 2569792--2569828 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
2569782 ATATTAACAT
2569792 ATTTTTAAT-TT-TAAATAA
1 ATTTTTAATATTCTAAATAA
2569810 ATTTTTAATATTCTAAATA
1 ATTTTTAATATTCTAAATA
2569829 TATATCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTTTAATATTCTAAATAA
Found at i:2570143 original size:20 final size:19
Alignment explanation
Indices: 2570110--2570148 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2570100 TTGATAAATA
* *
2570110 TATAATATTTAAAATATAAT
1 TATAATA-TAAAAAAATAAT
2570130 TATAATATAAAAAAATAAT
1 TATAATATAAAAAAATAAT
2570149 ACCAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TATAATATAAAAAAATAAT
Found at i:2574633 original size:19 final size:18
Alignment explanation
Indices: 2574600--2574645 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
2574590 AATATTAAAT
*
2574600 ATTTAATTTTATTATTTAA
1 ATTT-ATTTTATTATGTAA
2574619 ATTTATTTTATTTATGTAA
1 ATTTATTTTA-TTATGTAA
2574638 ATGTTATT
1 AT-TTATT
2574646 AACTTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 13 0.54
20 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (18 bp):
ATTTATTTTATTATGTAA
Found at i:2574812 original size:24 final size:25
Alignment explanation
Indices: 2574780--2574828 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2574770 TTAAATAACA
*
2574780 TATAAAAAT-AAATAAATTTAAATT
1 TATAAAAATCAAACAAATTTAAATT
*
2574804 TATAAAAATCAAACAATTTTAAATT
1 TATAAAAATCAAACAAATTTAAATT
2574829 AAAATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
TATAAAAATCAAACAAATTTAAATT
Found at i:2578989 original size:2 final size:2
Alignment explanation
Indices: 2578982--2579030 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2578972 ATAACATTAA
2578982 AT AT AT AT AT 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 AT AT AT AT AT
2579024 AT AT AT A
1 AT AT AT A
2579031 AAAAGGGCCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2581538 original size:164 final size:164
Alignment explanation
Indices: 2581267--2581596 Score: 633
Period size: 164 Copynumber: 2.0 Consensus size: 164
2581257 TTAAAAGATT
2581267 AGAAAATATACCAATGAGATAGAAATCTGATTTGTTAGTCTGAACAAGTAATGCAGCTTATTTAA
1 AGAAAATATACCAATGAGATAGAAATCTGATTTGTTAGTCTGAACAAGTAATGCAGCTTATTTAA
*
2581332 CACCTTTATGAGGCTACATACAGACTGAAAAATGTTGAAAAAGTGGATGTTTAAGTTATAGTACG
66 CACCTTTATGAGGCTACATACAGACTGAAAAATATTGAAAAAGTGGATGTTTAAGTTATAGTACG
2581397 GGTAAAGATGGATTGGAGTTGTGTAGTAACAAGA
131 GGTAAAGATGGATTGGAGTTGTGTAGTAACAAGA
*
2581431 AGAAAATATACCAATGAGATAGAAATCTGATTTGTTGGTCTGAACAAGTAATGCAGCTTATTTAA
1 AGAAAATATACCAATGAGATAGAAATCTGATTTGTTAGTCTGAACAAGTAATGCAGCTTATTTAA
*
2581496 CACCTTTATGAGGCTACATACAGACTGAAAAATATTGAAAAAGTGGATGTTTAGGTTATAGTACG
66 CACCTTTATGAGGCTACATACAGACTGAAAAATATTGAAAAAGTGGATGTTTAAGTTATAGTACG
2581561 GGTAAAGATGGATTGGAGTTGTGTAGTAACAAGA
131 GGTAAAGATGGATTGGAGTTGTGTAGTAACAAGA
2581595 AG
1 AG
2581597 GAAGTGTTTG
Statistics
Matches: 163, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
164 163 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (164 bp):
AGAAAATATACCAATGAGATAGAAATCTGATTTGTTAGTCTGAACAAGTAATGCAGCTTATTTAA
CACCTTTATGAGGCTACATACAGACTGAAAAATATTGAAAAAGTGGATGTTTAAGTTATAGTACG
GGTAAAGATGGATTGGAGTTGTGTAGTAACAAGA
Found at i:2582527 original size:20 final size:21
Alignment explanation
Indices: 2582498--2582555 Score: 93
Period size: 20 Copynumber: 2.9 Consensus size: 21
2582488 GTAAAAAGAC
2582498 AGAATGTATCGATACATT-AA
1 AGAATGTATCGATACATTGAA
*
2582518 AGAATATATCGATACATTGAA
1 AGAATGTATCGATACATTGAA
2582539 A-AATGTATCGATACATT
1 AGAATGTATCGATACATT
2582556 TGGGTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 32 0.91
21 3 0.09
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (21 bp):
AGAATGTATCGATACATTGAA
Found at i:2582566 original size:71 final size:71
Alignment explanation
Indices: 2582450--2582605 Score: 224
Period size: 71 Copynumber: 2.2 Consensus size: 71
2582440 TTTTAACTAG
* * * * *
2582450 ATATATTGATATATTGCAAAATGTATCGATATATCTGGGTAAAAAGACAGAATGTATCGATACAT
1 ATATATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATATATCGATACAT
2582515 T-AAAGA
66 TGAAA-A
*
2582521 ATATATCGATACATTGAAAAATGTATCGATACATTTGGGTAAAAAGACAGAATATATCGATACAT
1 ATATATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATATATCGATACAT
2582586 TGAAAA
66 TGAAAA
* *
2582592 ATATACCAATACAT
1 ATATATCGATACAT
2582606 CTGGATAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
71 73 0.96
72 3 0.04
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (71 bp):
ATATATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATATATCGATACAT
TGAAAA
Found at i:2582573 original size:51 final size:51
Alignment explanation
Indices: 2582518--2582616 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
2582508 GATACATTAA
* * * * *
2582518 AGAATATATCGATACATTGAAAAATGTATCGATACATTTGGGTAAAAAGAC
1 AGAATATATCGATACATTGAAAAATATACCAATACATCTGGATAAAAAGAC
2582569 AGAATATATCGATACATTGAAAAATATACCAATACATCTGGATAAAAA
1 AGAATATATCGATACATTGAAAAATATACCAATACATCTGGATAAAAA
2582617 TGTGACTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.26
Consensus pattern (51 bp):
AGAATATATCGATACATTGAAAAATATACCAATACATCTGGATAAAAAGAC
Found at i:2585215 original size:11 final size:11
Alignment explanation
Indices: 2585193--2585238 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
2585183 ATAGTAATTT
*
2585193 TTATATTAATA
1 TTATATTTATA
*
2585204 TTGTATTTATA
1 TTATATTTATA
*
2585215 TTATTTTTATA
1 TTATATTTATA
*
2585226 TTATAATTATA
1 TTATATTTATA
2585237 TT
1 TT
2585239 TAAATATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TTATATTTATA
Found at i:2585218 original size:22 final size:22
Alignment explanation
Indices: 2585193--2585301 Score: 62
Period size: 22 Copynumber: 4.9 Consensus size: 22
2585183 ATAGTAATTT
* *
2585193 TTATATTAATATTGTATTTATA
1 TTATATTAATATTATAATTATA
* *
2585215 TTATTTTTATATTATAATTATA
1 TTATATTAATATTATAATTATA
2585237 TT-TA--AATATTATGAATTTATA
1 TTATATTAATATTAT-AA-TTATA
* * * *
2585258 TATATTTTGACATTAATAACTCATA
1 T-TATATTAATATT-ATAA-TTATA
* *
2585283 TTATAATAATTTTATAATT
1 TTATATTAATATTATAATT
2585302 TTTAGTTGTA
Statistics
Matches: 63, Mismatches: 17, Indels: 14
0.67 0.18 0.15
Matches are distributed among these distances:
19 7 0.11
20 2 0.03
21 7 0.11
22 22 0.35
23 5 0.08
24 7 0.11
25 11 0.17
26 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (22 bp):
TTATATTAATATTATAATTATA
Found at i:2591852 original size:2 final size:2
Alignment explanation
Indices: 2591845--2591876 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2591835 TAGCTTTTGC
2591845 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2591877 TTTATCTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2594300 original size:3 final size:3
Alignment explanation
Indices: 2594292--2594331 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
2594282 TTACGGAAAT
*
2594292 TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2594332 GATATGACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2598169 original size:19 final size:19
Alignment explanation
Indices: 2598130--2598196 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
2598120 TAAAAATAAA
*
2598130 TTAT-TAATATATTAA-AAT
1 TTATATAATATA-TAATATT
2598148 TTATATAATATATAATATT
1 TTATATAATATATAATATT
2598167 TTAATATAAT-TATAATATT
1 TT-ATATAATATATAATATT
2598186 TTA-ATAATATA
1 TTATATAATATA
2598197 ATATATAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
17 5 0.11
18 10 0.23
19 22 0.50
20 7 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATATAATATATAATATT
Done.