Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010166.1 Corchorus capsularis cultivar CVL-1 contig10187, 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: 99634
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:226 original size:20 final size:21
Alignment explanation
Indices: 186--229 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
176 AAAAATTATA
**
186 AAAAGGGGGGCGGTATTTAGC
1 AAAAGGGGGGCGGTAAATAGC
207 AAAA-GGGGGCGGTAAATAGC
1 AAAAGGGGGGCGGTAAATAGC
227 AAA
1 AAA
230 CCCCTTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.39, C:0.09, G:0.39, T:0.14
Consensus pattern (21 bp):
AAAAGGGGGGCGGTAAATAGC
Found at i:2083 original size:44 final size:44
Alignment explanation
Indices: 2051--2141 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 44
2041 TTACAATTTA
2051 ATGAAGAGATTATCAAAATTCCATAGTGTGGTTACCAAAATTTCAT
1 ATGAA-AG-TTATCAAAATTCCATAGTGTGGTTACCAAAATTTCAT
* * * *
2097 ATGGAAGTTATCAAAATTTCATAGTGTAGTTACCAAATTTTCAT
1 ATGAAAGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCAT
2141 A
1 A
2142 GAATCAGATT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 35 0.85
45 2 0.05
46 4 0.10
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (44 bp):
ATGAAAGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCAT
Found at i:2089 original size:22 final size:22
Alignment explanation
Indices: 2064--2142 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
2054 AAGAGATTAT
*
2064 CAAAATTCCATAGTGTGGTTAC
1 CAAAATTTCATAGTGTGGTTAC
*
2086 CAAAATTTCATA-TG-GAAGTTAT
1 CAAAATTTCATAGTGTG--GTTAC
*
2108 CAAAATTTCATAGTGTAGTTAC
1 CAAAATTTCATAGTGTGGTTAC
*
2130 CAAATTTTCATAG
1 CAAAATTTCATAG
2143 AATCAGATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.02
21 2 0.04
22 43 0.90
23 2 0.04
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGTGTGGTTAC
Found at i:2194 original size:22 final size:22
Alignment explanation
Indices: 2060--2196 Score: 67
Period size: 22 Copynumber: 6.1 Consensus size: 22
2050 AATGAAGAGA
* * *
2060 TTATCAAAATTCCATAGTGTGG
1 TTATTAAAATTTCATAGGGTGG
** * **
2082 TTACCAAAATTTCATATGGAAG
1 TTATTAAAATTTCATAGGGTGG
* * *
2104 TTATCAAAATTTCATAGTGTAG
1 TTATTAAAATTTCATAGGGTGG
** * ** *
2126 TTACCAAATTTTCATAGAATCAGA
1 TTATTAAAATTTCATAGGGT--GG
* * *
2150 TTATTAAAATTTCTTATGTTGG
1 TTATTAAAATTTCATAGGGTGG
*
2172 TTATTGAAATTTCATAGGGTGG
1 TTATTAAAATTTCATAGGGTGG
2194 TTA
1 TTA
2197 ATTATCACAA
Statistics
Matches: 85, Mismatches: 28, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
22 72 0.85
24 13 0.15
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.40
Consensus pattern (22 bp):
TTATTAAAATTTCATAGGGTGG
Found at i:2355 original size:22 final size:22
Alignment explanation
Indices: 2308--2359 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
2298 TTACTAATAT
* * *
2308 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGC
2330 TTATCAAAATTTCATA-TGAAGC
1 TTATCAAAATTTCATAGTG-AGC
2352 TTAT-AAAA
1 TTATCAAAA
2360 GTCTCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGC
Found at i:2451 original size:25 final size:22
Alignment explanation
Indices: 2381--2476 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 22
2371 TAAGGAGTAC
* *
2381 CAAAATTTGATA-GAAGGTTAT
1 CAAAATTTCATAGGAAGATTAT
* *
2402 C-AAATTTCAGA-G-TGATTAT
1 CAAAATTTCATAGGAAGATTAT
* * *
2421 CGAAATTTCATGGAGATCATATTAT
1 CAAAATTTCATAG-GA--AGATTAT
2446 CAAAATTT-ATAGGAAGATTAT
1 CAAAATTTCATAGGAAGATTAT
2467 CAAAATTTCA
1 CAAAATTTCA
2477 GAAACAAAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
19 6 0.11
20 17 0.30
21 15 0.26
22 2 0.04
23 2 0.04
24 3 0.05
25 12 0.21
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGATTAT
Found at i:2572 original size:22 final size:22
Alignment explanation
Indices: 2547--2616 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
2537 GAGGGGTCAA
2547 CAAAATTTTATAAAGAGATTAT
1 CAAAATTTTATAAAGAGATTAT
** * *
2569 CAAAATTACATAAAGAGGTAAT
1 CAAAATTTTATAAAGAGATTAT
* *
2591 C-AAATTTTCTAAATGTGATTA-
1 CAAAATTTTATAAA-GAGATTAT
2612 CAAAA
1 CAAAA
2617 ATTTCATAGT
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
21 10 0.28
22 26 0.72
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (22 bp):
CAAAATTTTATAAAGAGATTAT
Found at i:2611 original size:44 final size:44
Alignment explanation
Indices: 2518--2616 Score: 105
Period size: 44 Copynumber: 2.3 Consensus size: 44
2508 TTACATAATA
* * * *
2518 TGATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAG
1 TGATTATCAAAATTACATAAAGAGGTCAACAAAATTTTATAAAG
* *
2562 AGATTATCAAAATTACATAAAGAGGT-AATC-AAATTTTCTAAATG
1 TGATTATCAAAATTACATAAAGAGGTCAA-CAAAATTTTATAAA-G
2606 TGATTA-CAAAA
1 TGATTATCAAAA
2617 ATTTCATAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
43 18 0.39
44 28 0.61
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.31
Consensus pattern (44 bp):
TGATTATCAAAATTACATAAAGAGGTCAACAAAATTTTATAAAG
Found at i:2758 original size:20 final size:20
Alignment explanation
Indices: 2706--2780 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
2696 TTATGGAGTA
*
2706 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCATGGAGGAT
*
2726 ACCAAAATTTCATGGAGGAT
1 ATCAAAATTTCATGGAGGAT
* *
2746 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTC--ATGGAGGAT
2768 ATCAAAATTTCAT
1 ATCAAAATTTCAT
2781 AGTTTAGTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 30 0.62
22 18 0.38
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (20 bp):
ATCAAAATTTCATGGAGGAT
Found at i:2773 original size:22 final size:22
Alignment explanation
Indices: 2728--3153 Score: 161
Period size: 22 Copynumber: 19.6 Consensus size: 22
2718 GGGAGGATAC
* *
2728 CAAAATTTC--ATGGAGGATAT
1 CAAAATTTCATATGAAGGTTAT
2748 CAAAATTTCATATGAAGGTTAT
1 CAAAATTTCATATGAAGGTTAT
** *
2770 CAAAATTTCATAGTTTA-GTTTT
1 CAAAATTTCATA-TGAAGGTTAT
* * *
2792 CAAAATTTTATAAGAGGGTTAT
1 CAAAATTTCATATGAAGGTTAT
* * *
2814 CAAAATTTCATA-GTATGTAGAT
1 CAAAATTTCATATGAAGGT-TAT
2836 CAAAATTTCATAATG-AGGTTAT
1 CAAAATTTCAT-ATGAAGGTTAT
** * *
2858 CAAAAAATCATAGGGAGGTTAT
1 CAAAATTTCATATGAAGGTTAT
*
2880 CAAAA--T--T-TGTA-GTTAT
1 CAAAATTTCATATGAAGGTTAT
* * * *
2896 CAAGATTTAATAAGAAAGTTAT
1 CAAAATTTCATATGAAGGTTAT
* * *
2918 CAAAATTTTATAGGGAGGTTTAT
1 CAAAATTTCATATGAAGG-TTAT
* * *
2941 CAAAATTTTATAGGAAGATTTAT
1 CAAAATTTCATATGAAG-GTTAT
* *
2964 TAAAATTTCATA-GCGAGGTTAT
1 CAAAATTTCATATG-AAGGTTAT
* * *
2986 CACAATTTCATA-GTATGATTAT
1 CAAAATTTCATATG-AAGGTTAT
* * * *
3008 CAAAATTTAAGTGTG-TGATTA-
1 CAAAATTTCA-TATGAAGGTTAT
* *
3029 CTAACAA-TTCATATGGAGGTTTT
1 C-AA-AATTTCATATGAAGGTTAT
* * * *
3052 TAAATTTTCATAACGTA-GTTAT
1 CAAAATTTCAT-ATGAAGGTTAT
* * *
3074 CAATATATCATATGGAGGTTAT
1 CAAAATTTCATATGAAGGTTAT
* * **
3096 CAACATCTCATAGTGTTGGTTAT
1 CAAAATTTCATA-TGAAGGTTAT
3119 CAAAATTTCAT-TGGGAA-GTTAT
1 CAAAATTTCATAT--GAAGGTTAT
3141 CAAAATTTCATAT
1 CAAAATTTCATAT
3154 TGAGGTCTGC
Statistics
Matches: 306, Mismatches: 70, Indels: 57
0.71 0.16 0.13
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 2 0.01
20 11 0.04
21 16 0.05
22 197 0.64
23 67 0.22
24 2 0.01
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (22 bp):
CAAAATTTCATATGAAGGTTAT
Found at i:2861 original size:66 final size:63
Alignment explanation
Indices: 2728--3015 Score: 185
Period size: 66 Copynumber: 4.5 Consensus size: 63
2718 GGGAGGATAC
* * * * * *
2728 CAAAATTTCATGGA-GGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTA-GTTT
1 CAAAATTTCATAGAGGGTTATCAAAATTTCATA-GTA-GTTATCAAAATTTCATA-ATGAGGTTA
2791 T
63 T
* *
2792 CAAAATTTTATAAGAGGGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAATGAGGTTA
1 CAAAATTTCAT-AGAGGGTTATCAAAATTTCATAGTA-GT-TATCAAAATTTCATAATGAGGTTA
2857 T
63 T
** * * * *
2858 CAAAAAATCATAGGGAGGTTATCAAAA-TT--T-GTAGTTATCAAGATTTAATAA-GAAAGTTAT
1 CAAAATTTCATAGAG-GGTTATCAAAATTTCATAGTAGTTATCAAAATTTCATAATG-AGGTTAT
* * * * * **
2918 CAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGATTTATTAAAATTTCATAGCGAGGT
1 CAAAATTTCATA--GAGGGTTATCAAAATTTCATA-GTAG--TTATCAAAATTTCATAATGAGGT
2983 TAT
61 TAT
* * *
2986 CACAATTTCATAGTATGATTATCAAAATTT
1 CAAAATTTCATAG-AGGGTTATCAAAATTT
3016 AAGTGTGTGA
Statistics
Matches: 175, Mismatches: 32, Indels: 31
0.74 0.13 0.13
Matches are distributed among these distances:
59 1 0.01
60 28 0.16
61 12 0.07
62 7 0.04
63 1 0.01
64 11 0.06
65 13 0.07
66 58 0.33
67 14 0.08
68 29 0.17
69 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (63 bp):
CAAAATTTCATAGAGGGTTATCAAAATTTCATAGTAGTTATCAAAATTTCATAATGAGGTTAT
Found at i:2882 original size:44 final size:44
Alignment explanation
Indices: 2728--3205 Score: 233
Period size: 44 Copynumber: 11.0 Consensus size: 44
2718 GGGAGGATAC
*
2728 CAAAATTTCAT--GGAGGATATCAAAATTTCAT-ATGAAGGTTAT
1 CAAAATTTCATAGGGAGGTTATCAAAATTTCATAATG-AGGTTAT
** * *
2770 CAAAATTTCATAGTTTA-GTTTTCAAAATTTTATAA-GAGGGTTAT
1 CAAAATTTCATAG-GGAGGTTATCAAAATTTCATAATGA-GGTTAT
* * *
2814 CAAAATTTCATA-GTATGTAGATCAAAATTTCATAATGAGGTTAT
1 CAAAATTTCATAGGGAGGT-TATCAAAATTTCATAATGAGGTTAT
** *
2858 CAAAAAATCATAGGGAGGTTATCAAAA-TT--T-GT-A-GTTAT
1 CAAAATTTCATAGGGAGGTTATCAAAATTTCATAATGAGGTTAT
* * * * * * **
2896 CAAGATTTAATAAGAAAGTTATCAAAATTTTATAGGGAGGTTTAT
1 CAAAATTTCATAGGGAGGTTATCAAAATTTCATAATGAGG-TTAT
* * * * **
2941 CAAAATTTTATAGGAAGATTTATTAAAATTTCATAGCGAGGTTAT
1 CAAAATTTCATAGGGAG-GTTATCAAAATTTCATAATGAGGTTAT
* * * * *
2986 CACAATTTCATA-GTATGATTATCAAAATTT-A-AGTGTGTGATTA-
1 CAAAATTTCATAGGGA-GGTTATCAAAATTTCATAATGAG-G-TTAT
* * * * *
3029 CTAACAA-TTCATATGGAGGTTTTTAAATTTTCATAACGTA-GTTAT
1 C-AA-AATTTCATAGGGAGGTTATCAAAATTTCATAATG-AGGTTAT
* * * * * * *
3074 CAATATATCATATGGAGGTTATCAACATCTCATAGTGTTGGTTAT
1 CAAAATTTCATAGGGAGGTTATCAAAATTTCATAATG-AGGTTAT
* * * *
3119 CAAAATTTCATTGGGAAGTTATCAAAATTTCATATTGAGGTCT-G
1 CAAAATTTCATAGGGAGGTTATCAAAATTTCATAATGAGGT-TAT
* *
3163 CAAAA-TTCTTTAGGGAGGTTAACAAAATTTCATAA-GATGGTTA
1 CAAAATTTC-ATAGGGAGGTTATCAAAATTTCATAATGA-GGTTA
3206 AAAGAAATTT
Statistics
Matches: 331, Mismatches: 72, Indels: 64
0.71 0.15 0.14
Matches are distributed among these distances:
38 25 0.08
39 3 0.01
40 1 0.00
41 2 0.01
42 18 0.05
43 16 0.05
44 163 0.49
45 82 0.25
46 21 0.06
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (44 bp):
CAAAATTTCATAGGGAGGTTATCAAAATTTCATAATGAGGTTAT
Found at i:2940 original size:23 final size:23
Alignment explanation
Indices: 2914--3196 Score: 110
Period size: 22 Copynumber: 12.7 Consensus size: 23
2904 AATAAGAAAG
*
2914 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * *
2937 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGGAGGT
* *
2960 TTATTAAAATTTCATAGCGAGG-
1 TTATCAAAATTTCATAGGGAGGT
* * * *
2982 TTATCACAATTTCATA-GTATGA
1 TTATCAAAATTTCATAGGGAGGT
* * *
3004 TTATCAAAATTT-A-AGTGTGTGA
1 TTATCAAAATTTCATAGGGAG-GT
*
3026 TTA-CTAACAA-TTCATATGGAGGT
1 TTATC-AA-AATTTCATAGGGAGGT
* * * *
3049 TT-TTAAATTTTCATAACGTA-G-
1 TTATCAAAATTTCAT-AGGGAGGT
* * *
3070 TTATCAATATATCATATGGAGG-
1 TTATCAAAATTTCATAGGGAGGT
* * **
3092 TTATCAACATCTCATAGTGTTGG-
1 TTATCAAAATTTCATAG-GGAGGT
* *
3115 TTATCAAAATTTCATTGGGAAG-
1 TTATCAAAATTTCATAGGGAGGT
**
3137 TTATCAAAATTTCATATTGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * *
3160 CT-GCAAAA-TTCTTTAGGGAGG-
1 TTATCAAAATTTC-ATAGGGAGGT
*
3181 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
3197 AGATGGTTAA
Statistics
Matches: 189, Mismatches: 54, Indels: 35
0.68 0.19 0.13
Matches are distributed among these distances:
20 1 0.01
21 14 0.07
22 103 0.54
23 68 0.36
24 3 0.02
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGGT
Found at i:2997 original size:128 final size:126
Alignment explanation
Indices: 2786--3015 Score: 282
Period size: 128 Copynumber: 1.8 Consensus size: 126
2776 TTCATAGTTT
* * * *
2786 AGTTTTCAAAATTTTATAAGAGGGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAATG
1 AGTTATCAAAATTTTATAAGAGGGTTATCAAAATTTCATAGGAAGTAGATCAAAATTTCATAACG
*
2851 AGGTTATCAAAAAATCATAGGGA-GGTTATCAAAATTTGTAGTTATCAAGATTTAATAAGAA
66 AGGTTATCAAAAAATCATA-GGATGATTATCAAAATTTGTAGTTATCAAGATTTAATAAGAA
* * * ** * *
2912 AGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGATTTATTAAAATTTCATAG
1 AGTTATCAAAATTTTATA-AGAGGGTTATCAAAATTTCATAGGAAG-TAGATCAAAATTTCATAA
* ** *
2977 CGAGGTTATCACAATTTCATAGTATGATTATCAAAATTT
64 CGAGGTTATCAAAAAATCATAGGATGATTATCAAAATTT
3016 AAGTGTGTGA
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
126 17 0.20
127 24 0.28
128 44 0.52
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.37
Consensus pattern (126 bp):
AGTTATCAAAATTTTATAAGAGGGTTATCAAAATTTCATAGGAAGTAGATCAAAATTTCATAACG
AGGTTATCAAAAAATCATAGGATGATTATCAAAATTTGTAGTTATCAAGATTTAATAAGAA
Found at i:3235 original size:44 final size:45
Alignment explanation
Indices: 3185--3285 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 45
3175 GGGAGGTTAA
* *
3185 CAAAATTTCATAAG-ATGGTTAAAAGAAATTT-ATAAAAAGATTCT
1 CAAAATTTCATAAGTATCGTTAAAA-AAATTTCATAAAAAGATTAT
** * **
3229 GGAAATTCCAT-AGTATCGTTATTAAAATTTCATAAAAAGATTAT
1 CAAAATTTCATAAGTATCGTTAAAAAAATTTCATAAAAAGATTAT
3273 CAAAATTTCATAA
1 CAAAATTTCATAA
3286 TGGGATCATA
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
43 8 0.18
44 35 0.80
45 1 0.02
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.34
Consensus pattern (45 bp):
CAAAATTTCATAAGTATCGTTAAAAAAATTTCATAAAAAGATTAT
Found at i:5106 original size:2 final size:2
Alignment explanation
Indices: 5099--5136 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5089 AGTGTTATGA
5099 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
5137 GAATGTCCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5795 original size:232 final size:232
Alignment explanation
Indices: 5369--5823 Score: 705
Period size: 232 Copynumber: 2.0 Consensus size: 232
5359 CAATTATTAC
*
5369 TATAAATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGAAATAATGTGGTGTCT
1 TATAAATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGAAATAATGTGGTGCCT
** * *
5434 CCTTTTGGCCTTTTTTGGTCTCTTCGCACTTTTCGGGTGACTAAAAAGGCTCTCGATGAATTTCA
66 CCTTTTGGCCTTTTTTGGTCTCTTCGCACTTTTCGGGTGACTAAAAAAACCCTAGATGAATTTCA
* *
5499 TCCCTTACTTCTCCTACAACCCTTTTTTTAATTTACTATTTTTATATTTATGTTTAACTGTGTTT
131 TCCCTTACTTCTCCTACAACCCTTTTTTTAATTTACTATATTTATATTTATGATTAACTGTGTTT
5564 TAATTACATATTAATTGTATGTGGATATCAGAATTTT
196 TAATTACATATTAATTGTATGTGGATATCAGAATTTT
* * * *
5601 TATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGGATTAGTGTGG-GCCT
1 TATAAATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGAAATAATGTGGTGCCT
* * *
5665 CCTTTTGGCTTTTTTTGGTCTTTTCGCACTTTTCGGGTGACTAAAAAAACCCTAGATGAATTTCC
66 CCTTTTGGCCTTTTTTGGTCTCTTCGCACTTTTCGGGTGACTAAAAAAACCCTAGATGAATTTCA
* * * ** *
5730 TCCCTTACTTTTCTTGCTGCCCTTTTTTGTAATTTACTATATTTATATTTATGATTAAGTGTGTT
131 TCCCTTACTTCTCCTACAACCCTTTTTT-TAATTTACTATATTTATATTTATGATTAACTGTGTT
*
5795 TTAATTACATATTAATTGTGTGTGGATAT
195 TTAATTACATATTAATTGTATGTGGATAT
5824 TAGGATTTAC
Statistics
Matches: 201, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
231 84 0.42
232 117 0.58
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (232 bp):
TATAAATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGAAATAATGTGGTGCCT
CCTTTTGGCCTTTTTTGGTCTCTTCGCACTTTTCGGGTGACTAAAAAAACCCTAGATGAATTTCA
TCCCTTACTTCTCCTACAACCCTTTTTTTAATTTACTATATTTATATTTATGATTAACTGTGTTT
TAATTACATATTAATTGTATGTGGATATCAGAATTTT
Found at i:10108 original size:12 final size:12
Alignment explanation
Indices: 10091--10115 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10081 TAAATGTCTC
10091 TACGAAGAACAT
1 TACGAAGAACAT
10103 TACGAAGAACAT
1 TACGAAGAACAT
10115 T
1 T
10116 GTGGAGAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (12 bp):
TACGAAGAACAT
Found at i:11947 original size:90 final size:90
Alignment explanation
Indices: 11772--11934 Score: 199
Period size: 90 Copynumber: 1.8 Consensus size: 90
11762 CTTTACGTGC
* * * *
11772 GTTGCACGTGGCACAACATGTGTGAACTAAATTAATTTTTTTAAAATCTTTGAAAATAATAAGAG
1 GTTGCACGTGGCACAACACGTGTGAACGAAATTAATATGTTTAAAATCTTTGAAAATAATAAGAG
* * *
11837 GTGAAAAATATATTTAATTAATTTA
66 ATCAAAAATATATTAAATTAATTTA
* *
11862 GTTGCACGTGGCAGAACGCGTGTGAACGAAA-TAA-ATGTTT-AAATACTTT-AAAATAATAAGA
1 GTTGCACGTGGCACAACACGTGTGAACGAAATTAATATGTTTAAAAT-CTTTGAAAATAATAAGA
*
11923 GATCACAAATAT
65 GATCAAAAATAT
11935 TCAATTAAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
87 25 0.40
88 8 0.13
89 3 0.05
90 27 0.43
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.32
Consensus pattern (90 bp):
GTTGCACGTGGCACAACACGTGTGAACGAAATTAATATGTTTAAAATCTTTGAAAATAATAAGAG
ATCAAAAATATATTAAATTAATTTA
Found at i:23008 original size:228 final size:233
Alignment explanation
Indices: 22743--23187 Score: 654
Period size: 234 Copynumber: 1.9 Consensus size: 233
22733 AAAGAAATAG
*
22743 TTAGTGTTAGTGTTAGAAGTATAATGATTATAAAATTTCAATTAAAAAAATATTGTGTTAT-AT-
1 TTAGTGTTAGTGTTAGAAGTATAATGATTATAAAATTTCAATT-AAAAAATATTGTGCTATAATG
* * *
22806 TGT-ATATTGTCAAATAAAAATTATCAAGAAAATTAAAATGCAAAGTTA-C-CTATTAATATTAG
65 TATAATATTGTCAAATAAAAATAATCAAGAAAATTAAAATGCAAAGTTATCTATATTAATATTAG
* * *
22868 AAACGTAAATCAAAATTATTATTAAAATTAAAATGCAAGTCAGCCAGCCAATGT-ATCTACAATC
130 AAACGTAAATCAAAATTATTATGAAAATTAAAATGCAAATCAGCCAGCCAATGTAACCTACAATC
22932 AAT-CAATTTGTAAGCTATTTGAAATAGTTAGTGTTAGTA
195 -ATGCAATTTGTAAGCTATTTGAAATAGTTAGTGTTAGTA
* *
22971 TTAGTGTTAGATGTTAGAAGTCT-ATGATTATAAAATTTCAATTAAAAAGTATTGTGCTATAATG
1 TTAGTGTTAG-TGTTAGAAGTATAATGATTATAAAATTTCAATTAAAAAATATTGTGCTATAATG
* *
23035 TATAATATTGTCAAATCAAAATAATCAAGAAAATTAAAATGCAAATTTATCTATATATTAATATT
65 TATAATATTGTCAAATAAAAATAATCAAGAAAATTAAAATGCAAAGTTATC--TATATTAATATT
* * *
23100 AGAAACGTAATTCAAAATTATTATGAAAATTAAAATGCAAATCGGCCATCCAATGTACACCTACA
128 AGAAACGTAAATCAAAATTATTATGAAAATTAAAATGCAAATCAGCCAGCCAATGTA-ACCTACA
23165 ATCATGCAATTTGTAAGCTATTT
192 ATCATGCAATTTGTAAGCTATTT
23188 TTTTTGCTGA
Statistics
Matches: 192, Mismatches: 14, Indels: 14
0.87 0.06 0.06
Matches are distributed among these distances:
227 15 0.08
228 32 0.17
229 13 0.07
230 42 0.22
231 1 0.01
234 61 0.32
235 2 0.01
236 26 0.14
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (233 bp):
TTAGTGTTAGTGTTAGAAGTATAATGATTATAAAATTTCAATTAAAAAATATTGTGCTATAATGT
ATAATATTGTCAAATAAAAATAATCAAGAAAATTAAAATGCAAAGTTATCTATATTAATATTAGA
AACGTAAATCAAAATTATTATGAAAATTAAAATGCAAATCAGCCAGCCAATGTAACCTACAATCA
TGCAATTTGTAAGCTATTTGAAATAGTTAGTGTTAGTA
Found at i:24951 original size:31 final size:31
Alignment explanation
Indices: 24914--24975 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
24904 TATGTTAGAA
*
24914 AAATAAGGATATAATAAGTATTTCAAAAGTT
1 AAATAAGGATATAATAAGCATTTCAAAAGTT
* * *
24945 AAATAAGGGTATAATAGGCGTTTCAAAAGTT
1 AAATAAGGATATAATAAGCATTTCAAAAGTT
24976 TTACAAAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.31
Consensus pattern (31 bp):
AAATAAGGATATAATAAGCATTTCAAAAGTT
Found at i:30434 original size:62 final size:63
Alignment explanation
Indices: 30360--30489 Score: 219
Period size: 62 Copynumber: 2.1 Consensus size: 63
30350 TATGTTACAA
* *
30360 ATCAAACAAACTTAAATACA-GATTTGTACAAAAAACCACCTTTTACAAATCGAATAGAATGTT
1 ATCAAACAAACTTAAATACATGATTTGTAC-AAAAACCACCTTGTACAAATCCAATAGAATGTT
30423 ATCAAA-AAACTTAAATACATGATTTGTACAAAAACCACCTTGTACAAATCCAATAGAATGTT
1 ATCAAACAAACTTAAATACATGATTTGTACAAAAACCACCTTGTACAAATCCAATAGAATGTT
30485 ATCAA
1 ATCAA
30490 GAGAATCCTA
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
62 49 0.77
63 15 0.23
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.27
Consensus pattern (63 bp):
ATCAAACAAACTTAAATACATGATTTGTACAAAAACCACCTTGTACAAATCCAATAGAATGTT
Found at i:33084 original size:21 final size:22
Alignment explanation
Indices: 33060--33101 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
33050 CACAACAATA
*
33060 ATTTAGTT-GAAAAATGAATTC
1 ATTTAGTTAAAAAAATGAATTC
33081 ATTTAGTTAAAAAAATGAATT
1 ATTTAGTTAAAAAAATGAATT
33102 GAATGACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (22 bp):
ATTTAGTTAAAAAAATGAATTC
Found at i:34582 original size:22 final size:23
Alignment explanation
Indices: 34544--34586 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
34534 AAAGGTGGTC
34544 TACTAGGAATATTTAATAATTGG
1 TACTAGGAATATTTAATAATTGG
*
34567 TACTATGAA-ATTTAATAATT
1 TACTAGGAATATTTAATAATT
34587 ATTAGCAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (23 bp):
TACTAGGAATATTTAATAATTGG
Found at i:35281 original size:20 final size:19
Alignment explanation
Indices: 35252--35295 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
35242 TTAGATTTAG
35252 TCAG-TTTTTTGAGTTCAGT
1 TCAGTTTTTTTGAG-TCAGT
35271 TCAGTTTTTTTGAGTCAGT
1 TCAGTTTTTTTGAGTCAGT
35290 T-AGTTT
1 TCAGTTT
35296 GAGGTTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 10 0.42
20 9 0.38
ACGTcount: A:0.16, C:0.09, G:0.20, T:0.55
Consensus pattern (19 bp):
TCAGTTTTTTTGAGTCAGT
Found at i:37900 original size:21 final size:20
Alignment explanation
Indices: 37870--37922 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
37860 ACTAGCGCTG
*
37870 GGCGCCCATGTGGTATGCTT
1 GGCGCCCATGTGGTATGCCT
*
37890 GGCGCCCCATGTGGTTTGCCT
1 GGCG-CCCATGTGGTATGCCT
*
37911 CGCGACCCATGT
1 GGCG-CCCATGT
37923 ACTCCAGTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.09, C:0.32, G:0.32, T:0.26
Consensus pattern (20 bp):
GGCGCCCATGTGGTATGCCT
Found at i:41601 original size:21 final size:21
Alignment explanation
Indices: 41577--41619 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
41567 TGGGCGCTGG
*
41577 GGCTGTGCAGC-TGGGTCCCCA
1 GGCT-TGCAGCATGGGGCCCCA
*
41598 GGCTTGCGGCATGGGGCCCCA
1 GGCTTGCAGCATGGGGCCCCA
41619 G
1 G
41620 CTGGGATCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.09, C:0.33, G:0.42, T:0.16
Consensus pattern (21 bp):
GGCTTGCAGCATGGGGCCCCA
Found at i:43381 original size:21 final size:21
Alignment explanation
Indices: 43348--43396 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
43338 AAGAATTGTA
**
43348 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
43368 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
43389 GCATTCCT
1 GC-TTCCT
43397 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:46867 original size:15 final size:17
Alignment explanation
Indices: 46834--46869 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
46824 TAAAGGTGGC
46834 AAAAAGAACCCGACCCG
1 AAAAAGAACCCGACCCG
46851 AAAAA-AACCCG-CCCG
1 AAAAAGAACCCGACCCG
46866 AAAA
1 AAAA
46870 CCCGATACCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
16 6 0.32
17 5 0.26
ACGTcount: A:0.53, C:0.33, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAGAACCCGACCCG
Found at i:46952 original size:16 final size:16
Alignment explanation
Indices: 46933--47060 Score: 77
Period size: 16 Copynumber: 8.0 Consensus size: 16
46923 AACCCGCCTG
46933 AACCTGAACCCGAAAA
1 AACCTGAACCCGAAAA
*
46949 AACCCGAACCCG-AAA
1 AACCTGAACCCGAAAA
* * **
46964 AAGCTCAAACCTTAAAA
1 AACCT-GAACCCGAAAA
**
46981 AACAC-GAACTTGAAAA
1 AAC-CTGAACCCGAAAA
*
46997 AA-CTCAAACCCGAAAA
1 AACCT-GAACCCGAAAA
*
47013 AACCCGAACCCGAAAA
1 AACCTGAACCCGAAAA
*
47029 AA-CTCAAACCCGAAAA
1 AACCT-GAACCCGAAAA
*
47045 AATCC-GAATCCGAAAA
1 AA-CCTGAACCCGAAAA
47061 TTTACGAAAA
Statistics
Matches: 84, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
14 1 0.01
15 7 0.08
16 68 0.81
17 6 0.07
18 2 0.02
ACGTcount: A:0.52, C:0.30, G:0.10, T:0.08
Consensus pattern (16 bp):
AACCTGAACCCGAAAA
Found at i:46981 original size:32 final size:32
Alignment explanation
Indices: 46939--47060 Score: 172
Period size: 32 Copynumber: 3.8 Consensus size: 32
46929 CCTGAACCTG
*
46939 AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
1 AACCCGAAAAAACCCGAACCCGAAAAAACTCA
** * **
46971 AACCTTAAAAAACACGAACTTGAAAAAACTCA
1 AACCCGAAAAAACCCGAACCCGAAAAAACTCA
47003 AACCCGAAAAAACCCGAACCCGAAAAAACTCA
1 AACCCGAAAAAACCCGAACCCGAAAAAACTCA
* *
47035 AACCCGAAAAAATCCGAATCCGAAAA
1 AACCCGAAAAAACCCGAACCCGAAAA
47061 TTTACGAAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 77 1.00
ACGTcount: A:0.53, C:0.30, G:0.10, T:0.07
Consensus pattern (32 bp):
AACCCGAAAAAACCCGAACCCGAAAAAACTCA
Found at i:47278 original size:31 final size:31
Alignment explanation
Indices: 47208--47315 Score: 171
Period size: 32 Copynumber: 3.4 Consensus size: 31
47198 ACCCAAACAG
*
47208 AACCCGAACCCGAATTAACCAGACCCAAAATC
1 AACCCGAACCCGAATTAACCTGACCC-AAATC
*
47240 AACCCGAACCCGAATTAACCTGACCCAAATT
1 AACCCGAACCCGAATTAACCTGACCCAAATC
47271 AACCCGAACCCGAATTAACCTGACCCAAATCC
1 AACCCGAACCCGAATTAACCTGACCCAAAT-C
*
47303 AACCCGAATCCGA
1 AACCCGAACCCGA
47316 CTCAAGTCCG
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 34 0.48
32 37 0.52
ACGTcount: A:0.40, C:0.38, G:0.10, T:0.12
Consensus pattern (31 bp):
AACCCGAACCCGAATTAACCTGACCCAAATC
Found at i:50715 original size:35 final size:35
Alignment explanation
Indices: 50632--50788 Score: 197
Period size: 35 Copynumber: 4.4 Consensus size: 35
50622 CCATTTGATT
* *
50632 ATTTACTTAATTACACCGAATTAAGTTGCTTACTACTG
1 ATTTACTTAATTACACCGAATTAAGTTGATTAC--C-A
* * *
50670 ATTTACTTAATCACACCGAATTAAATTGATTACCG
1 ATTTACTTAATTACACCGAATTAAGTTGATTACCA
* *
50705 ATTTACTTAATTACACCGACTTAAGTTGATTACAA
1 ATTTACTTAATTACACCGAATTAAGTTGATTACCA
* *
50740 AATTACTTAATTACACCGAATTAAGTTGAGTACCA
1 ATTTACTTAATTACACCGAATTAAGTTGATTACCA
*
50775 AATTACTTAATTAC
1 ATTTACTTAATTAC
50789 TTCATTTTCT
Statistics
Matches: 107, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
35 76 0.71
36 1 0.01
38 30 0.28
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (35 bp):
ATTTACTTAATTACACCGAATTAAGTTGATTACCA
Found at i:50738 original size:19 final size:18
Alignment explanation
Indices: 50636--50768 Score: 58
Period size: 19 Copynumber: 7.3 Consensus size: 18
50626 TTGATTATTT
*
50636 ACTTAATTACACCGAATTA
1 ACTTGATTACACCG-ATTA
* * * *
50655 AGTTGCTTACTACTGATTT
1 ACTTGATTAC-ACCGATTA
* *
50674 ACTTAATCACACCGAATTA
1 ACTTGATTACACCG-ATTA
* *
50693 AATTGATT--ACCGATTT
1 ACTTGATTACACCGATTA
*
50709 ACTTAATTACACCGACTTA
1 ACTTGATTACACCGA-TTA
* **
50728 AGTTGATTACA-AAATT-
1 ACTTGATTACACCGATTA
*
50744 ACTTAATTACACCGAATTA
1 ACTTGATTACACCG-ATTA
*
50763 AGTTGA
1 ACTTGA
50769 GTACCAAATT
Statistics
Matches: 78, Mismatches: 28, Indels: 16
0.64 0.23 0.13
Matches are distributed among these distances:
16 18 0.23
17 6 0.08
18 12 0.15
19 39 0.50
20 3 0.04
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (18 bp):
ACTTGATTACACCGATTA
Found at i:57641 original size:12 final size:12
Alignment explanation
Indices: 57624--57656 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
57614 GCAGATTTAG
57624 GAGAACTTGGTT
1 GAGAACTTGGTT
57636 GAGAACTTGGTT
1 GAGAACTTGGTT
57648 GAGAACTTG
1 GAGAACTTG
57657 AATTAGATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.33, T:0.30
Consensus pattern (12 bp):
GAGAACTTGGTT
Found at i:57998 original size:36 final size:36
Alignment explanation
Indices: 57958--58031 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
57948 AAAATATTAT
* * * *
57958 TATTTTTTTTA-TAGAAAAATCGGAAAAAGGAAAAAC
1 TATTTTTTTTAGAAAAAAAAACGGAAAAA-CAAAAAC
57994 TATTTTTTTTAGAAAAAAAAACGGAAAAACAAAAAC
1 TATTTTTTTTAGAAAAAAAAACGGAAAAACAAAAAC
58030 TA
1 TA
58032 ATTCTTGGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 19 0.58
37 14 0.42
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (36 bp):
TATTTTTTTTAGAAAAAAAAACGGAAAAACAAAAAC
Found at i:63483 original size:13 final size:13
Alignment explanation
Indices: 63465--63501 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
63455 GTGTTAATGG
*
63465 AAAAGAAGAAAAT
1 AAAAGAAAAAAAT
63478 AAAAGAAAAAAAAT
1 AAAAG-AAAAAAAT
63492 AAAAGAAAAA
1 AAAAGAAAAA
63502 GATTTAGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (13 bp):
AAAAGAAAAAAAT
Found at i:63492 original size:14 final size:14
Alignment explanation
Indices: 63473--63501 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
63463 GGAAAAGAAG
63473 AAAATAAAAGAAAA
1 AAAATAAAAGAAAA
63487 AAAATAAAAGAAAA
1 AAAATAAAAGAAAA
63501 A
1 A
63502 GATTTAGACT
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:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (14 bp):
AAAATAAAAGAAAA
Found at i:67436 original size:11 final size:11
Alignment explanation
Indices: 67399--67447 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
67389 AACTCTTAAA
67399 TAATTAATAAT
1 TAATTAATAAT
**
67410 TAATTGGTAAT
1 TAATTAATAAT
*
67421 T-ATTAAAAAT
1 TAATTAATAAT
67431 TAATTAATAAT
1 TAATTAATAAT
*
67442 AAATTA
1 TAATTA
67448 CAAAGATTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
10 7 0.23
11 23 0.77
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (11 bp):
TAATTAATAAT
Found at i:67441 original size:21 final size:21
Alignment explanation
Indices: 67401--67441 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
67391 CTCTTAAATA
* **
67401 ATTAATAATTAATTGGTAATT
1 ATTAAAAATTAATTAATAATT
67422 ATTAAAAATTAATTAATAAT
1 ATTAAAAATTAATTAATAAT
67442 AAATTACAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
ATTAAAAATTAATTAATAATT
Found at i:73346 original size:17 final size:18
Alignment explanation
Indices: 73324--73357 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
73314 GTCAAAATTT
*
73324 GAAGAA-AAATGAAAAAA
1 GAAGAATAAAAGAAAAAA
73341 GAAGAATAAAAGAAAAA
1 GAAGAATAAAAGAAAAA
73358 TGAAAAAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (18 bp):
GAAGAATAAAAGAAAAAA
Found at i:77538 original size:33 final size:33
Alignment explanation
Indices: 77484--77570 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
77474 CAATAATTTG
* *
77484 CAACACCAGATTCAACGAAATACAACACAAGATT
1 CAAC-CCAGATTCAACAAAATACAACACAAGATC
* * *
77518 CAACCTAGATTCAACAAAATACAGCACCAGATC
1 CAACCCAGATTCAACAAAATACAACACAAGATC
77551 CAACCCAGATTCAACAAAAT
1 CAACCCAGATTCAACAAAAT
77571 TGCAACAACG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 43 0.91
34 4 0.09
ACGTcount: A:0.48, C:0.29, G:0.08, T:0.15
Consensus pattern (33 bp):
CAACCCAGATTCAACAAAATACAACACAAGATC
Found at i:80121 original size:21 final size:21
Alignment explanation
Indices: 80076--80115 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
80066 ACAGCTCACC
80076 TGGGTGATCAGACAAACCACA
1 TGGGTGATCAGACAAACCACA
*
80097 TGGGTGCTCAGACAAACCA
1 TGGGTGATCAGACAAACCA
80116 TGTGGGCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (21 bp):
TGGGTGATCAGACAAACCACA
Found at i:86111 original size:22 final size:23
Alignment explanation
Indices: 86089--86140 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
86079 ATAAACCAGA
86089 AAAATGAAAAAGAAG-AA-AAAGA
1 AAAAT-AAAAAGAAGAAAGAAAGA
*
86111 AAAA-AAAAGGAAGAAAGAAAGA
1 AAAATAAAAAGAAGAAAGAAAGA
86133 AAAATAAA
1 AAAATAAA
86141 TAAATAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 8 0.31
21 2 0.08
22 13 0.50
23 3 0.12
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (23 bp):
AAAATAAAAAGAAGAAAGAAAGA
Found at i:86115 original size:16 final size:16
Alignment explanation
Indices: 86086--86136 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
86076 GAGATAAACC
*
86086 AGAAAAATG-AAAAAGA
1 AGAAAAA-GAAAAAAAA
86102 AGAAAAAGAAAAAAAA
1 AGAAAAAGAAAAAAAA
86118 AGGAAGAAAGAAAGAAAAA
1 A-GAA-AAAGAAA-AAAAA
86137 TAAATAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 1 0.03
16 14 0.47
17 3 0.10
18 7 0.23
19 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (16 bp):
AGAAAAAGAAAAAAAA
Found at i:87976 original size:19 final size:17
Alignment explanation
Indices: 87954--88027 Score: 62
Period size: 17 Copynumber: 4.2 Consensus size: 17
87944 TTATCATTAT
87954 TATTTCTTATAT-TATA
1 TATTTCTTATATATATA
*
87970 TTATATT-ATATATATATA
1 -TAT-TTCTTATATATATA
*
87988 TATATCTTATATATATA
1 TATTTCTTATATATATA
*
88005 TATTATAATTATTATATATA
1 TATT-T-CTTA-TATATATA
88025 TAT
1 TAT
88028 ACTATATATT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
16 1 0.02
17 24 0.52
18 7 0.15
19 3 0.07
20 11 0.24
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTTCTTATATATATA
Found at i:87978 original size:15 final size:14
Alignment explanation
Indices: 87960--88039 Score: 78
Period size: 13 Copynumber: 5.6 Consensus size: 14
87950 TTATTATTTC
87960 TTATATTATATTATA
1 TTATATTATA-TATA
87975 TTATA-TATATATA
1 TTATATTATATATA
*
87988 TATATCTTATATATA
1 T-TATATTATATATA
88003 -TATATTATA-ATTA
1 TTATATTATATA-TA
88016 TTATA-TATATATA
1 TTATATTATATATA
88029 CTATATATTAT
1 -T-TATATTAT
88040 TTTTGTCCCA
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
12 1 0.02
13 21 0.38
14 13 0.24
15 17 0.31
16 3 0.05
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TTATATTATATATA
Found at i:87983 original size:2 final size:2
Alignment explanation
Indices: 87961--88036 Score: 78
Period size: 2 Copynumber: 41.5 Consensus size: 2
87951 TATTATTTCT
*
87961 TA TA T- TA TA T- TA TA T- TA TA TA TA TA TA TA TA TC T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
87999 TA TA TA TA T- TA TA -A T- TA T- TA TA TA TA TA TA CTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
88037 TATTTTTGTC
Statistics
Matches: 64, Mismatches: 1, Indels: 18
0.77 0.01 0.22
Matches are distributed among these distances:
1 8 0.12
2 54 0.84
3 2 0.03
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:88010 original size:37 final size:34
Alignment explanation
Indices: 87961--88039 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 34
87951 TATTATTTCT
87961 TATATTATATTAT-ATTATATATATATATATATCTTA
1 TATATTATATTATAATTAT-TATATATATATA-C-TA
87997 TATATATATATTATAATTATTATATATATATACTA
1 TATAT-TATATTATAATTATTATATATATATACTA
88032 TATATTAT
1 TATATTAT
88040 TTTTGTCCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
34 3 0.07
35 7 0.17
36 6 0.15
37 20 0.49
38 5 0.12
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (34 bp):
TATATTATATTATAATTATTATATATATATACTA
Found at i:90474 original size:26 final size:24
Alignment explanation
Indices: 90415--90476 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 24
90405 TGATTATGTA
90415 TTATTATTTATTCTATTTATTTTT
1 TTATTATTTATTCTATTTATTTTT
*
90439 TTAGGGTATTTATT-TATTCTATTCTATT
1 TTA--TTATTTATTCTATT-TATT-T-TT
90467 TTATTATTTA
1 TTATTATTTA
90477 ATATATATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
24 3 0.10
25 4 0.13
26 18 0.58
27 1 0.03
28 5 0.16
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (24 bp):
TTATTATTTATTCTATTTATTTTT
Found at i:96980 original size:29 final size:31
Alignment explanation
Indices: 96946--97012 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
96936 ATCAATTTGA
* *
96946 GATATAACGTTTC-AGAAACG-CCAATTCAG
1 GATATAACGTTACTAGAAACGACCAAATCAG
* *
96975 GATATAACGTTACTTGAAACGATCAAATCAG
1 GATATAACGTTACTAGAAACGACCAAATCAG
97006 GATATAA
1 GATATAA
97013 TCTGACGGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 12 0.38
30 6 0.19
31 14 0.44
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (31 bp):
GATATAACGTTACTAGAAACGACCAAATCAG
Found at i:99463 original size:28 final size:25
Alignment explanation
Indices: 99409--99468 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 25
99399 GGAGCCCGAC
*
99409 TCGCGAATCCCTTTCTCTCTCTTCT
1 TCGCGAATCCCTTTCTCTCTCTCCT
99434 TCGCGAATCCCCTTTCTCTCTCACTCCT
1 TCGCGAAT-CCCTTTCTCTCT--CTCCT
99462 TCGCGAA
1 TCGCGAA
99469 CCAGTGAAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 8 0.26
26 12 0.39
28 11 0.35
ACGTcount: A:0.12, C:0.42, G:0.10, T:0.37
Consensus pattern (25 bp):
TCGCGAATCCCTTTCTCTCTCTCCT
Done.