Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1602
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: 73913
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2293 original size:16 final size:16
Alignment explanation
Indices: 2266--2305 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
2256 CGCGCTGTTT
2266 GTTTCA-CCTTATAAA
1 GTTTCAGCCTTATAAA
2281 GTTTCAGCCTTATAAA
1 GTTTCAGCCTTATAAA
*
2297 GTTGCAGCC
1 GTTTCAGCC
2306 AAACTTGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (16 bp):
GTTTCAGCCTTATAAA
Found at i:2768 original size:15 final size:16
Alignment explanation
Indices: 2733--2857 Score: 69
Period size: 15 Copynumber: 8.4 Consensus size: 16
2723 TAAATATTAA
*
2733 TATATTTATATTAATAT
1 TATATATATATTAAT-T
2750 T-TATATATTATTAATT
1 TATATATA-TATTAATT
*
2766 TATAT-TATATAAATT
1 TATATATATATTAATT
*
2781 T-TA-ATATATTTATT
1 TATATATATATTAATT
2795 TA-AT-TATATTATATT
1 TATATATATATTA-ATT
*
2810 T-TA-AT-TATTTTATT
1 TATATATATA-TTAATT
2824 TATAT-TATATT--TT
1 TATATATATATTAATT
* *
2837 TATATAT-TATAAAAT
1 TATATATATATTAATT
2852 TATATA
1 TATATA
2858 GCCGTAACAT
Statistics
Matches: 85, Mismatches: 8, Indels: 32
0.68 0.06 0.26
Matches are distributed among these distances:
13 10 0.12
14 25 0.29
15 28 0.33
16 11 0.13
17 11 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATATATATATTAATT
Found at i:2830 original size:14 final size:15
Alignment explanation
Indices: 2726--2847 Score: 93
Period size: 14 Copynumber: 8.5 Consensus size: 15
2716 TAGACATTAA
*
2726 ATATTA-ATATATTT
1 ATATTATATTTATTT
2740 ATATTA-A--TATTT
1 ATATTATATTTATTT
*
2752 ATA-TATTATTAATTT
1 ATATTA-TATTTATTT
**
2767 ATATTATATAAATTT
1 ATATTATATTTATTT
*
2782 -TAATATATTTATTT
1 ATATTATATTTATTT
2796 A-ATTATATTATATTT
1 ATATTATATT-TATTT
2811 -TAATTAT-TTTATTT
1 AT-ATTATATTTATTT
2825 ATATTATATTT-TTAT
1 ATATTATATTTATT-T
2840 ATATTATA
1 ATATTATA
2848 AAATTATATA
Statistics
Matches: 90, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
11 2 0.02
12 8 0.09
13 1 0.01
14 37 0.41
15 35 0.39
16 7 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATATTATATTTATTT
Found at i:2853 original size:53 final size:53
Alignment explanation
Indices: 2723--2856 Score: 141
Period size: 53 Copynumber: 2.5 Consensus size: 53
2713 TTTTAGACAT
* *
2723 TAAATATTAATATATTTATATTAA-TAT-TTATATATTATTAATTTATATTATA
1 TAAATTTTAATATATTTATA-AAATTATATTATATATTATTAATTTATATTATA
** * *
2775 TAAATTTTAATATATTTATTTAATTATATTATATTTTAATTATTTTAT-TTATA
1 TAAATTTTAATATATTTATAAAATTATATTATATATT-ATTAATTTATATTATA
* *
2828 TTATATTTTTATATA-TTATAAAATTATAT
1 -TAAATTTTAATATATTTATAAAATTATAT
2857 AGCCGTAACA
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
51 3 0.04
52 21 0.30
53 25 0.36
54 21 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (53 bp):
TAAATTTTAATATATTTATAAAATTATATTATATATTATTAATTTATATTATA
Found at i:3665 original size:13 final size:13
Alignment explanation
Indices: 3633--3658 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3623 CTCTTAAGCA
3633 TCTCTTTTGTATC
1 TCTCTTTTGTATC
3646 TCTCTTTTGTATC
1 TCTCTTTTGTATC
3659 CATCTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.08, T:0.62
Consensus pattern (13 bp):
TCTCTTTTGTATC
Found at i:7712 original size:27 final size:26
Alignment explanation
Indices: 7676--7766 Score: 105
Period size: 27 Copynumber: 3.5 Consensus size: 26
7666 AAACCACCCA
*
7676 TTGTTTGTCAAAAATTGTGGTTACTT
1 TTGTTTGTCAAAAATGGTGGTTACTT
*
7702 TGTGTTTGTCAAAAATGGTGGTTTCTTT
1 T-TGTTTGTCAAAAATGGTGGTTAC-TT
* * *
7730 TTATTTGTCAAAAATGGTGG-CA-TG
1 TTGTTTGTCAAAAATGGTGGTTACTT
7754 TTGTTTGTCAAAA
1 TTGTTTGTCAAAA
7767 TTTGTGGCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
24 13 0.23
26 1 0.02
27 39 0.70
28 3 0.05
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (26 bp):
TTGTTTGTCAAAAATGGTGGTTACTT
Found at i:8275 original size:23 final size:23
Alignment explanation
Indices: 8249--8313 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 23
8239 TTGATGATTG
8249 ATTGAGTTTATAGATTTTATTTT
1 ATTGAGTTTATAGATTTTATTTT
* *
8272 ATTGAG-TT-T-GA--TGA-TTG
1 ATTGAGTTTATAGATTTTATTTT
8289 ATTGAGTTTATAGATTTTATTTT
1 ATTGAGTTTATAGATTTTATTTT
8312 AT
1 AT
8314 GTTAAAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
17 8 0.25
18 4 0.12
19 1 0.03
20 4 0.12
21 1 0.03
22 4 0.12
23 10 0.31
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (23 bp):
ATTGAGTTTATAGATTTTATTTT
Found at i:8282 original size:40 final size:40
Alignment explanation
Indices: 8222--8313 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 40
8212 AATCTTTGAT
* *
8222 ATTTCATTTTAGTGAGTTTGATGATTGATTGAGTTTATAG
1 ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG
8262 ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG
1 ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG
8302 ATTTTATTTTAT
1 ATTTTATTTTAT
8314 GTTAAAAGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.25, C:0.01, G:0.18, T:0.55
Consensus pattern (40 bp):
ATTTTATTTTATTGAGTTTGATGATTGATTGAGTTTATAG
Found at i:8304 original size:17 final size:17
Alignment explanation
Indices: 8234--8297 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
8224 TTCATTTTAG
8234 TGAGTTTGATGATTGAT
1 TGAGTTTGATGATTGAT
* *
8251 TGAGTTTATAGATTTTATTTTAT
1 TGAG-TT-T-GA--TGA-TTGAT
8274 TGAGTTTGATGATTGAT
1 TGAGTTTGATGATTGAT
8291 TGAGTTT
1 TGAGTTT
8298 ATAGATTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
17 15 0.41
18 4 0.11
19 1 0.03
20 4 0.11
21 1 0.03
22 4 0.11
23 8 0.22
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (17 bp):
TGAGTTTGATGATTGAT
Found at i:8404 original size:21 final size:20
Alignment explanation
Indices: 8364--8404 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
8354 GATTTTAATG
**
8364 ATTTATTTAATTTTTGTTAT
1 ATTTATTTAATTTTCATTAT
8384 ATTTATGTTAATTTTCATTAT
1 ATTTAT-TTAATTTTCATTAT
8405 GATGATTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (20 bp):
ATTTATTTAATTTTCATTAT
Found at i:9955 original size:155 final size:155
Alignment explanation
Indices: 9790--10286 Score: 417
Period size: 154 Copynumber: 3.2 Consensus size: 155
9780 CATCGAATCG
* *
9790 CTTCTATGCCAAAGGTATAGT-TTTAGGGTAGGTTTACCTTTTTCTTATTATTTTTACG-CTCTT
1 CTTCTATGCCAAAGGTATA-TATTTAGGATAGGTTTATCTTTTTCTTATTATTTTTACGTCT-TT
* *
9853 TAGGGTTACCAAGATACTTTCACATCG-AAG-ATATACCTTAA-AGGCATTTTCGTAACTTTTCT
64 TAAGATTACCAAGATACTTTCACATCGAAAGTAT-TACC-TAAGA-GCATTTTCGTAACTTTTCT
* * * * *
9915 AAAATCGAGTGCTAGATAGTTACCAGGTCA
126 AAAACCAAGTCCTAGATAGTCACCAGATCA
* * * * * * *
9945 TTTCTATGCCAATGGTGTATATTTATGATAGGTTTGTCTTTTTCTTATCA-TTTTGCGTCTTTTA
1 CTTCTATGCCAAAGGTATATATTTAGGATAGGTTTATCTTTTTCTTATTATTTTTACGTCTTTTA
* ** * * *
10009 AGATTATCGGGATACTTTCACGTCGAAAGTATTACCTAAGAGCATTTTCTTAATTTTTCTAAAAC
66 AGATTACCAAGATACTTTCACATCGAAAGTATTACCTAAGAGCATTTTCGTAACTTTTCTAAAAC
* *
10074 CAAGTCCTAGATAGTCACTAGATCG
131 CAAGTCCTAGATAGTCACCAGATCA
* * * *
10099 CTTCTGTGCCAAAAGTATATATTTAGAATAGGTTTATCTTTTTATTTATTATTTTATA--TCTTT
1 CTTCTATGCCAAAGGTATATATTTAGGATAGGTTTATCTTTTT-CTTATTATTTT-TACGTCTTT
* * * * * * * **
10162 TAAGATTATCGAGATATTTTTACGTCGAAGGTA-TACCCCAAG-GCATTTT-GTTAA-TTCACTA
64 TAAGATTACCAAGATACTTTCACATCGAAAGTATTA-CCTAAGAGCATTTTCG-TAACTTTTCTA
* * * *
10223 GAACCAAATCCTAAATAGTCAGCA-AGTCA
127 AAACCAAGTCCTAGATAGTCACCAGA-TCA
* *
10252 CTTTTATGCCAAAGGTATGTATTTAGGAATAGGTT
1 CTTCTATGCCAAAGGTATATATTTAGG-ATAGGTT
10287 CGTCATTTTA
Statistics
Matches: 276, Mismatches: 54, Indels: 25
0.78 0.15 0.07
Matches are distributed among these distances:
152 1 0.00
153 48 0.17
154 127 0.46
155 94 0.34
156 5 0.02
157 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (155 bp):
CTTCTATGCCAAAGGTATATATTTAGGATAGGTTTATCTTTTTCTTATTATTTTTACGTCTTTTA
AGATTACCAAGATACTTTCACATCGAAAGTATTACCTAAGAGCATTTTCGTAACTTTTCTAAAAC
CAAGTCCTAGATAGTCACCAGATCA
Found at i:12379 original size:16 final size:16
Alignment explanation
Indices: 12358--12392 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
12348 TCGGTAGATG
12358 AATCGCCCATCTAATT
1 AATCGCCCATCTAATT
12374 AATCGCCCATCTAATT
1 AATCGCCCATCTAATT
12390 AAT
1 AAT
12393 TTTCGATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (16 bp):
AATCGCCCATCTAATT
Found at i:12797 original size:13 final size:13
Alignment explanation
Indices: 12779--12804 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12769 CATTATTCCA
12779 TATATCGATACAT
1 TATATCGATACAT
12792 TATATCGATACAT
1 TATATCGATACAT
12805 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
TATATCGATACAT
Found at i:15226 original size:51 final size:52
Alignment explanation
Indices: 15169--15284 Score: 139
Period size: 51 Copynumber: 2.2 Consensus size: 52
15159 CAATTCTCCG
** * * *
15169 CAATCGGGGATATTCCATC-TCTGATTTTATTTTC-AAAACACTAA-TTTTCTA
1 CAATCGGGGATACCCCAACTTC-GATTTTATTTCCAAAAACACCAATTTTTC-A
*
15220 TAATCGGGGATACCCCAACTTCGATTTTATTTCCAAAAACACCAATTTTTCA
1 CAATCGGGGATACCCCAACTTCGATTTTATTTCCAAAAACACCAATTTTTCA
15272 CAATCGGGGATAC
1 CAATCGGGGATAC
15285 TACAACCCCG
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
51 26 0.47
52 24 0.44
53 5 0.09
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (52 bp):
CAATCGGGGATACCCCAACTTCGATTTTATTTCCAAAAACACCAATTTTTCA
Found at i:15343 original size:28 final size:27
Alignment explanation
Indices: 15274--15349 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
15264 ATTTTTCACA
*
15274 ATCGGGGATACTACAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
15301 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
15327 TTCGAAGGGATACTCCAACCCCG
1 ATCG--GGGATACTCCAACCCCG
15350 GCTTCATTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.11
27 22 0.50
28 17 0.39
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:15492 original size:52 final size:51
Alignment explanation
Indices: 15170--15712 Score: 195
Period size: 52 Copynumber: 10.4 Consensus size: 51
15160 AATTCTCCGC
* * * * * * *
15170 AATCGGGGATATTCCATCTCTGATTTTATTTTCAAAACACTAA-TTTTCTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTC-AA
* ** *
15221 AATCGGGGATACCCCAACTTCGATTTTATTTCCAAAAACACCAATTTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTTCAA
* * * ** * * *** *
15273 AATCGGGGATACTACAACCCCG--TTAATCATCGGGGATACTCCAACCCCGTT-AT
1 AATCGGGGATACTCCAACCCCGATTTTAT-TTC--CAAAACACCAA--TTTTTCAA
** ** * * *** *
15326 TTTCGAAGGGATACTCCAACCCCGGCTTCATTTCCAAAATATTGATTTCTCAA
1 AATCG--GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCAA
* * * **
15379 AATCGGTGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTC-AA
* * * *
15431 AATCAGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTTCAA
* * * * * * * **
15483 AATCGGGGATATTCTAACCCCG--TTAATCATCGAGGATACTCCAACCCCGTTATTTCCG
1 AATCGGGGATACTCCAACCCCGATTTTAT-TTCCA--AAACACCAA-----TT-TTTCAA
** * * *** *
15541 AA---GGGATACTCCAACCCCGGCTTCATTTCCAAAATATTGATTTCTCAA
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCAA
* * * * **
15589 AATCGGGGATACTCTAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTC-AA
* * * *
15641 AATCAGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAA-TTTTTCAA
*
15694 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
15713 TCGTTATTTC
Statistics
Matches: 347, Mismatches: 114, Indels: 60
0.67 0.22 0.12
Matches are distributed among these distances:
48 5 0.01
49 2 0.01
50 9 0.03
51 98 0.28
52 115 0.33
53 53 0.15
54 13 0.04
55 31 0.09
56 5 0.01
57 10 0.03
58 6 0.02
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (51 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCAA
Found at i:15822 original size:212 final size:210
Alignment explanation
Indices: 15170--15822 Score: 1011
Period size: 210 Copynumber: 3.1 Consensus size: 210
15160 AATTCTCCGC
* * * * * * * *
15170 AATCGGGGATATTCCATCTCTGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGATACC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACT
* * *
15234 CCAACTTCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTACAACCCCGTTAA
66 CCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTAA
* *
15299 TCATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGCTTCATTTCCAAA
131 TCATCGAGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGGCTTCATTTCCAAA
15364 ATATTGATTTCTCAA
196 ATATTGATTTCTCAA
*
15379 AATCGGTGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACT
* *
15444 CCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATATTCTAACCCCGTTAA
66 CCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTAA
15509 TCATCGAGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGGCTTCATTTCCAAA
131 TCATCGAGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGGCTTCATTTCCAAA
15574 ATATTGATTTCTCAA
196 ATATTGATTTCTCAA
* *
15589 AATCGGGGATACTCTAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACT
* *
15654 CCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTTCACAATCGAGGATACTCCAACCTCGTTA
66 CCAGCTCCGATTTTATTTCCAAAAACACCAA-TTTTTCACAATCGGGGATACTCCAACCCCGTTA
* * ** * * * *
15719 TTTCATCGAGGATACTCCCACCCCGTTACCTCCGAGGGGATACTCTAACCCCGGCTTTATTCCCA
130 -ATCATCGAGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGGCTTCATTTCCA
*
15784 AAATATTGATTTCTCAT
194 AAATATTGATTTCTCAA
*
15801 AATTGGGGATACTCCAACCCCG
1 AATCGGGGATACTCCAACCCCG
15823 TTATTTCCGA
Statistics
Matches: 407, Mismatches: 34, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
209 41 0.10
210 245 0.60
211 29 0.07
212 92 0.23
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (210 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACT
CCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTAA
TCATCGAGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGGCTTCATTTCCAAA
ATATTGATTTCTCAA
Found at i:21085 original size:21 final size:20
Alignment explanation
Indices: 21059--21097 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
21049 GTTGGGACCT
21059 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
21080 TGTATCGATACATTTAGA
1 TGTATCGATACATTTAGA
21098 CAAAAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:23428 original size:20 final size:22
Alignment explanation
Indices: 23403--23452 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
23393 ACCCAGAATA
*
23403 TATCGATACA-ATGAGAA-ATG
1 TATCGATACATATGAAAACATG
* *
23423 TATCGATTCATTTGAAAACATG
1 TATCGATACATATGAAAACATG
23445 TATCGATA
1 TATCGATA
23453 TATTTAGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 9 0.38
21 5 0.21
22 10 0.42
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (22 bp):
TATCGATACATATGAAAACATG
Found at i:26143 original size:21 final size:21
Alignment explanation
Indices: 26117--26156 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
26107 TTTGCTTCCT
26117 CTTGAATCTGTGAGATTGTTA
1 CTTGAATCTGTGAGATTGTTA
26138 CTTGAATCTGTGAGATTGT
1 CTTGAATCTGTGAGATTGT
26157 AAGTGCCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (21 bp):
CTTGAATCTGTGAGATTGTTA
Found at i:26457 original size:16 final size:16
Alignment explanation
Indices: 26436--26473 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
26426 TAATAAAAAT
26436 ATATTTACA-TATTTAA
1 ATATTTA-ATTATTTAA
26452 ATATTTAATTATTTAA
1 ATATTTAATTATTTAA
*
26468 TTATTT
1 ATATTT
26474 TTCAATAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTTAATTATTTAA
Found at i:28035 original size:14 final size:15
Alignment explanation
Indices: 28005--28036 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
27995 GGGTTGAACA
28005 TTAGATACAATTTTT
1 TTAGATACAATTTTT
28020 TTAGATACAATTTTT
1 TTAGATACAATTTTT
28035 TT
1 TT
28037 CAATTTGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (15 bp):
TTAGATACAATTTTT
Found at i:28727 original size:2 final size:2
Alignment explanation
Indices: 28720--28760 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
28710 ATTGAATTGG
*
28720 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT 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
28761 AAAGAGAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30041 original size:2 final size:2
Alignment explanation
Indices: 30036--30068 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30026 AGAGAAGTCA
30036 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30069 AAAGAGAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48312 original size:24 final size:25
Alignment explanation
Indices: 48266--48350 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 25
48256 TAATTTTTAT
48266 ATTATATTATATTATTTTTATTTAAAT-
1 ATTAT-TTA-ATT-TTTTTATTTAAATA
48293 ATT-TTTAATTTTTTTAATTTAAATA
1 ATTATTTAATTTTTTT-ATTTAAATA
*
48318 ATTATTTAAATTGTTATTTTTATTAAATA
1 ATTATTT-AATT-TT-TTTAT-TTAAATA
48347 ATTA
1 ATTA
48351 ATTTTTTTCA
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
23 5 0.10
24 11 0.22
25 6 0.12
26 4 0.08
27 7 0.14
28 3 0.06
29 14 0.28
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (25 bp):
ATTATTTAATTTTTTTATTTAAATA
Found at i:48607 original size:27 final size:27
Alignment explanation
Indices: 48584--48753 Score: 97
Period size: 25 Copynumber: 6.2 Consensus size: 27
48574 TTTTTATGTA
48584 TTATGATT-ATATTTAAAATATTATATAT
1 TTAT-ATTAATATTT-AAATATTATATAT
*
48612 TTATATTAATATTTATATATTAT-TAAT
1 TTATATTAATATTTAAATATTATAT-AT
*
48639 TTATATTTTATAAATTTTAATATATTTATATAT
1 TTATA--TTA-ATA-TTTAA-ATA-TTATATAT
* *
48672 TTATA-TCATATTT--ATATTATTTAT
1 TTATATTAATATTTAAATATTATATAT
*
48696 ATTATATT-ATATTTTAATTATT-TATA-
1 -TTATATTAATA-TTTAAATATTATATAT
** * *
48722 TTATATT-ATATTTGTATATTATAAAA
1 TTATATTAATATTTAAATATTATATAT
48748 TTATAT
1 TTATAT
48754 CGTAGTCAAC
Statistics
Matches: 114, Mismatches: 12, Indels: 34
0.71 0.08 0.21
Matches are distributed among these distances:
24 14 0.12
25 24 0.21
26 11 0.10
27 21 0.18
28 17 0.15
29 5 0.04
30 3 0.03
31 4 0.04
32 3 0.03
33 11 0.10
34 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (27 bp):
TTATATTAATATTTAAATATTATATAT
Found at i:48663 original size:68 final size:65
Alignment explanation
Indices: 48551--48711 Score: 159
Period size: 68 Copynumber: 2.4 Consensus size: 65
48541 GTAAAATTTA
* ** * *
48551 AATATTTATATTTTATT-TTTATATTTTTATGTATTATGATTATATTTAAAATATTATATATTTA
1 AATATTTATATATTATTATTTATA-TTTTATAAATTATGAATATATTT-AAATATT-TATA-TCA
48615 TATT
62 TATT
* *
48619 AATATTTATATATTATTAATTTATATTTTATAAATT-TTAATATATTTATATATTTATATCATAT
1 AATATTTATATATTATT-ATTTATATTTTATAAATTATGAATATATTTAAATATTTATATCATAT
48683 T
65 T
* *
48684 TATA-TTATTTA-TATTATATTATATTTTA
1 AATATTTATATATTATTAT-TTATATTTTA
48712 ATTATTTATA
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
62 2 0.02
63 14 0.17
64 6 0.07
65 9 0.11
66 4 0.05
67 6 0.07
68 25 0.31
69 9 0.11
70 6 0.07
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (65 bp):
AATATTTATATATTATTATTTATATTTTATAAATTATGAATATATTTAAATATTTATATCATATT
Found at i:48684 original size:11 final size:10
Alignment explanation
Indices: 48605--48732 Score: 89
Period size: 9 Copynumber: 13.3 Consensus size: 10
48595 TTTAAAATAT
48605 TATATATTTA
1 TATATATTTA
48615 TATTAATATTTA
1 TA-T-ATATTTA
*
48627 TATATTATTAA
1 TATA-TATTTA
*
48638 TTTATATTT-
1 TATATATTTA
*
48647 TATAAATTT-
1 TATATATTTA
48656 TA-ATATATT-
1 TATATAT-TTA
48665 TATATATTTA
1 TATATATTTA
48675 TATCATATTTA
1 TAT-ATATTTA
48686 TAT-TATTTA
1 TATATATTTA
*
48695 TAT-TATAT-
1 TATATATTTA
48703 TATAT-TTTA
1 TATATATTTA
48712 -AT-TATTTA
1 TATATATTTA
48720 TAT-TATATTA
1 TATATAT-TTA
48730 TAT
1 TAT
48733 TTGTATATTA
Statistics
Matches: 98, Mismatches: 8, Indels: 24
0.75 0.06 0.18
Matches are distributed among these distances:
7 1 0.01
8 14 0.14
9 34 0.35
10 20 0.20
11 20 0.20
12 9 0.09
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (10 bp):
TATATATTTA
Found at i:48720 original size:20 final size:20
Alignment explanation
Indices: 48609--48728 Score: 79
Period size: 20 Copynumber: 5.8 Consensus size: 20
48599 AAATATTATA
48609 TATTTATATTAATATTTATATAT
1 TATTTATATT-ATATTT-TA-AT
*
48632 TATTAAT-TTATATTTT-AT
1 TATTTATATTATATTTTAAT
* *
48650 AAATTT-TAATATA-TTT-AT
1 -TATTTATATTATATTTTAAT
*
48668 ATATTTATATCATATTTATATTATT
1 -TATTTATATTATATTT-TA--A-T
48693 TATATTATATTATATTTTAAT
1 TAT-TTATATTATATTTTAAT
48714 TATTTATATTATATT
1 TATTTATATTATATT
48729 ATATTTGTAT
Statistics
Matches: 79, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
18 13 0.16
19 12 0.15
20 15 0.19
21 11 0.14
22 3 0.04
23 6 0.08
24 6 0.08
25 13 0.16
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTATATTATATTTTAAT
Found at i:49806 original size:23 final size:24
Alignment explanation
Indices: 49780--49826 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
49770 AGATTTTTCC
49780 TTATGAATTTTATT-TAAAATATT
1 TTATGAATTTTATTATAAAATATT
* *
49803 TTATTAATTTTTTTATAAAATATT
1 TTATGAATTTTATTATAAAATATT
49827 CTATCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TTATGAATTTTATTATAAAATATT
Found at i:50274 original size:14 final size:14
Alignment explanation
Indices: 50257--50310 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
50247 ACGGGAAGAG
50257 AAAAAAAGGAAAAA
1 AAAAAAAGGAAAAA
*
50271 AAAAAAAAGAAAGAA
1 AAAAAAAGGAAA-AA
50286 AAAAAGAGAGAGAAAAA
1 AAAAA-A-AG-GAAAAA
50303 AGAAAAAA
1 A-AAAAAA
50311 ATTACGTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 11 0.33
15 7 0.21
16 2 0.06
17 5 0.15
18 8 0.24
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAAGGAAAAA
Found at i:50370 original size:19 final size:17
Alignment explanation
Indices: 50332--50376 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
50322 GTATTATTTT
50332 TTTAT-TATTTAAAATA
1 TTTATATATTTAAAATA
50348 -TTATATATTTATATAATA
1 TTTATATATTTA-A-AATA
50366 TTTATATATTT
1 TTTATATATTT
50377 TATGTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.16
16 6 0.24
17 1 0.04
18 4 0.16
19 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATATATTTAAAATA
Found at i:52068 original size:17 final size:18
Alignment explanation
Indices: 52027--52071 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
52017 AATTTAAATA
*
52027 AATAAATATTTATTTATTT
1 AATAAA-ATTTAATTATTT
52046 AATAAAATTTAATT-TTT
1 AATAAAATTTAATTATTT
*
52063 ATTAAAATT
1 AATAAAATT
52072 AGATAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 11 0.46
18 7 0.29
19 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATAAAATTTAATTATTT
Found at i:52267 original size:28 final size:29
Alignment explanation
Indices: 52209--52263 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
52199 TTTAATGCAT
*
52209 AATTATTATTTAATAAAAATTATAAATTA
1 AATTATTATTTAATAAAAACTATAAATTA
* *
52238 AATTTTTA-TTAATAATAACTA-AAATT
1 AATTATTATTTAATAAAAACTATAAATT
52264 TAAAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.22
28 11 0.48
29 7 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (29 bp):
AATTATTATTTAATAAAAACTATAAATTA
Found at i:56398 original size:48 final size:48
Alignment explanation
Indices: 56334--56643 Score: 416
Period size: 48 Copynumber: 6.6 Consensus size: 48
56324 TGAGAGGAGT
** * *
56334 GACAATGTGCCAATTCAAGGCCAACGACATCGAGCTAAGGGAAAAATG
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATG
* *
56382 GACAATGTGGTGATTCAAGGCCAGCGACATTAAGCTAAGGG-AAAATG
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATG
*
56429 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA-TGAAAAAGTG
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAA-TG
*
56477 GACAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGGG-AAAATG
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATG
* * *
56524 TACAATGTGCTGATTCAAGGCCAGCGACATTTAGCTAATGGAAAAATG
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATG
* * *
56572 GATAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA--TAAAAGT-
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATG
* * *
56617 GCCAATATGCTGATTCAATGCCAGCGA
1 GACAATGTGCTGATTCAAGGCCAGCGA
56644 TATCGAATTT
Statistics
Matches: 234, Mismatches: 24, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
45 23 0.10
46 6 0.03
47 85 0.36
48 119 0.51
49 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (48 bp):
GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATG
Found at i:56464 original size:95 final size:94
Alignment explanation
Indices: 56334--56643 Score: 428
Period size: 95 Copynumber: 3.3 Consensus size: 94
56324 TGAGAGGAGT
** * * *
56334 GACAATGTGCCAATTCAAGGCCAACGACATCGAGCTAAGGGAAAAATGGACAATGTGGTGATTCA
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA-GGAAAAATGGACAATGTGCTGATTCA
*
56399 AGGCCAGCGACATTAAGCTAAGGGAAAATG
65 AGGCCAGCGACATTGAGCTAAGGGAAAATG
*
56429 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATGAAAAAGTGGACAATGTGCTGATTCA
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGAAAAA-TGGACAATGTGCTGATTCA
*
56494 AGGCCAACGACATTGAGCTAAGGGAAAATG
65 AGGCCAGCGACATTGAGCTAAGGGAAAATG
* * *
56524 TACAATGTGCTGATTCAAGGCCAGCGACATTTAGCTAATGGAAAAATGGATAATGTGCTGATTCA
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA-GGAAAAATGGACAATGTGCTGATTCA
*
56589 AGGCCAGCGACATTGAGCTAA--TAAAA-G
65 AGGCCAGCGACATTGAGCTAAGGGAAAATG
* * *
56616 TGCCAATATGCTGATTCAATGCCAGCGA
1 -GACAATGTGCTGATTCAAGGCCAGCGA
56644 TATCGAATTT
Statistics
Matches: 194, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
92 1 0.01
93 27 0.14
94 6 0.03
95 154 0.79
96 6 0.03
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (94 bp):
GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGAAAAATGGACAATGTGCTGATTCAA
GGCCAGCGACATTGAGCTAAGGGAAAATG
Found at i:56592 original size:143 final size:140
Alignment explanation
Indices: 56331--56649 Score: 478
Period size: 143 Copynumber: 2.3 Consensus size: 140
56321 AGATGAGAGG
** *
56331 AGTGACAATGTGCCAATTCAAGGCCAACGACATCGAGCTAAGGGAAAAATGGACAATGTGGTGAT
1 AGTGACAATGTGCTGATTCAAGGCCAACGACATCGAGCTAAGGGAAAAATGGACAATGTGCTGAT
*
56396 TCAAGGCCAGCGACATTAAGCTAAGGGAAAATGGACAATGTGCTGATTCAAGGCCAGCGACATTG
66 TCAAGGCCAGCGACATTAAGCTAAGGAAAAATGGACAATGTGCTGATTCAAGGCCAGCGACATTG
56461 AGCTAATGAAAA
131 AGCTAAT--AAA
* *
56473 AGTGGACAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGGG-AAAATGTACAATGTGCTGA
1 AGT-GACAATGTGCTGATTCAAGGCCAACGACATCGAGCTAAGGGAAAAATGGACAATGTGCTGA
* *
56537 TTCAAGGCCAGCGACATTTAGCTAATGGAAAAATGGATAATGTGCTGATTCAAGGCCAGCGACAT
65 TTCAAGGCCAGCGACATTAAGCTAA-GGAAAAATGGACAATGTGCTGATTCAAGGCCAGCGACAT
56602 TGAGCTAATAAA
129 TGAGCTAATAAA
* * * * *
56614 AGTGCCAATATGCTGATTCAATGCCAGCGATATCGA
1 AGTGACAATGTGCTGATTCAAGGCCAACGACATCGA
56650 ATTTTAAGAT
Statistics
Matches: 161, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
140 27 0.17
141 6 0.04
142 44 0.27
143 84 0.52
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (140 bp):
AGTGACAATGTGCTGATTCAAGGCCAACGACATCGAGCTAAGGGAAAAATGGACAATGTGCTGAT
TCAAGGCCAGCGACATTAAGCTAAGGAAAAATGGACAATGTGCTGATTCAAGGCCAGCGACATTG
AGCTAATAAA
Found at i:56771 original size:28 final size:28
Alignment explanation
Indices: 56714--57722 Score: 296
Period size: 32 Copynumber: 33.1 Consensus size: 28
56704 GCTTTTAAAA
* *
56714 AAAAGGTGCCACTAACTTCTGTGGGCTTTG
1 AAAAGATGCCACTGAC-T-TGTGGGCTTTG
* *
56744 AAGAGATGCCACT-ACCTTGTGGGTTTTG
1 AAAAGATGCCACTGA-CTTGTGGGCTTTG
*
56772 AAAAGATGCCACTAACTTGTGGGCTTT-
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* *
56799 AGAAGGATGCCACTGACTTGTCGGCTTTG
1 A-AAAGATGCCACTGACTTGTGGGCTTTG
* * *
56828 AAAAGTTGCCACTGACTCGTCGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* *
56856 AAAAGTTGCCACTGACTTGTGGGCTTGG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* *
56884 AAAAGATGCCACCGACTTGTGTGGGTTTTG
1 AAAAGATGCCACTGAC-T-TGTGGGCTTTG
* * ** *
56914 AAATGGGTTGCCACCAACTTGTGTGGGCTATG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
* ** *
56946 AAATGAGTTGCCACCAACTTGTGTGGGCATTG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
* * *
56978 AAAGGATACCACTGACTTGTGGGCTTTA
1 AAAAGATGCCACTGACTTGTGGGCTTTG
*
57006 AAAAGATGCCACCGACTTGTGTGGGCTTTG
1 AAAAGATGCCACTGAC-T-TGTGGGCTTTG
** * * ** *
57036 ACATGGGCTACCACCAACTTGTGTGGGCTATG
1 A-A-AAGATGCCACTGAC-T-TGTGGGCTTTG
* ** *
57068 AAATGAGTTGCCACCAACTTGTGTGGGCATTG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
*
57100 -AAAGGTCGCCACTGACTTGTGGGCTTTG
1 AAAAGAT-GCCACTGACTTGTGGGCTTTG
* * *
57128 AAAGGGTGCCACTGTCTTGTGGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* *
57156 AAAAGATGTCACCGACTTGTATGGGCTTTG
1 AAAAGATGCCACTGACTTG--TGGGCTTTG
* * * **
57186 AAATGGGTTGTCACCAACTTGTGTGGGCTTTG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
* **
57218 AAATGAGTTGCCACCAACTTGTGTGGACTTTG
1 AAA--AGATGCCACTGACTTGTG-GG-CTTTG
* ** *
57250 AAATGAGTTGCCACCAACTTGTGTAGGCTTTC
1 AAA--AGATGCCACTGACTTGTG--GGCTTTG
* * ** *
57282 AAATGGGTTGCCACCAACTTGTGTGGGCTTTC
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
* * ** *
57314 AAATAGGTTGTCACCAAATTGTGTGGGCTTTG
1 AAA-A-GATGCCA-CTGACT-TGTGGGCTTTG
* ** *
57346 AAATAGGTTGCCACCAACTTATGTGGGCTTTC
1 AAA-A-GATGCCACTGAC-T-TGTGGGCTTTG
* *
57378 AAATGAGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
* * *
57410 AAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
*
57438 AAAAGATGCCACCGACTTGTGTGGGCTTTG
1 AAAAGATGCCACTGAC-T-TGTGGGCTTTG
* * **
57468 AAATGGGTTGCCACCAACTTGTGTGGACTTTG
1 AAA--AGATGCCACTGACTTGTG-GG-CTTTG
* * *
57500 AAATGAGTTGCAACCGACTTGTATGGGCTTTG
1 AAA--AGATGCCACTGACTTG--TGGGCTTTG
* * **
57532 AAATGGGTTGCCACCAACTTGTGTGGGCTTTG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
* * ** *
57564 AAATATGTTACCACCAACTTGTGTGGGCTTTC
1 AAA-A-GATGCCACTGAC-T-TGTGGGCTTTG
* *
57596 AAATGAGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
* * *
57628 AAAGGGTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGATGCCACTGAC-T-TGTGGGCTTTG
* * **
57658 AAAGGGTGCCACCCACTTGTGTAGGCTTTG
1 AAAAGATGCCACTGACTTGTG--GGCTTTG
* * *
57688 AAATGGGTTGCCACTAACTTGTGTGGGCTTTG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
57720 AAA
1 AAA
57723 TGAGTTGCCA
Statistics
Matches: 816, Mismatches: 114, Indels: 96
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.00
28 212 0.26
29 19 0.02
30 143 0.18
31 13 0.02
32 401 0.49
33 13 0.02
34 14 0.02
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (28 bp):
AAAAGATGCCACTGACTTGTGGGCTTTG
Found at i:56810 original size:56 final size:55
Alignment explanation
Indices: 56714--57188 Score: 279
Period size: 56 Copynumber: 8.1 Consensus size: 55
56704 GCTTTTAAAA
* *
56714 AAAAGGTGCCACTAACTTCTGTGGGCTTTGAAGAGATGCCACT-ACCTTGTGGGTTTTG
1 AAAAGATGCCACTAAC-T-TGTGGGCTTTGAAG-GATGCCACTGA-CTTGTGGGCTTTG
*
56772 AAAAGATGCCACTAACTTGTGGGCTTTAGAAGGATGCCACTGACTTGTCGGCTTTG
1 AAAAGATGCCACTAACTTGTGGGCTTT-GAAGGATGCCACTGACTTGTGGGCTTTG
* * * * * * *
56828 AAAAGTTGCCACTGACTCGTCGGCTTTGAAAAGTTGCCACTGACTTGTGGGCTTGG
1 AAAAGATGCCACTAACTTGTGGGCTTTG-AAGGATGCCACTGACTTGTGGGCTTTG
** * * ** *
56884 AAAAGATGCCACCGACTTGTGTGGGTTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTATG
1 AAAAGATGCCACTAAC-T-TGTGGGCTTTG-AA--GGATGCCACTGAC-T-TGTGGGCTTTG
* * * * *
56946 AAATGAGTTGCCACCAACTTGTGTGGGCATTGAAAGGATACCACTGACTTGTGGGCTTTA
1 AAA--AGATGCCACTAAC-T-TGTGGGCTTTG-AAGGATGCCACTGACTTGTGGGCTTTG
** * * ** *
57006 AAAAGATGCCACCGACTTGTGTGGGCTTTGACATGGGCTACCACCAACTTGTGTGGGCTATG
1 AAAAGATGCCACTAAC-T-TGTGGGCTTTGA-A--GGATGCCACTGAC-T-TGTGGGCTTTG
* * *
57068 AAATGAGTTGCCACCAACTTGTGTGGGCATTGAAAGG-TCGCCACTGACTTGTGGGCTTTG
1 AAA--AGATGCCACTAAC-T-TGTGGGCTTTG-AAGGAT-GCCACTGACTTGTGGGCTTTG
* * ** * * *
57128 AAAGGGTGCCACTGTCTTGTGGGCTTTGAAAAGATGTCACCGACTTGTATGGGCTTTG
1 AAAAGATGCCACTAACTTGTGGGCTTTG-AAGGATGCCACTGACTTG--TGGGCTTTG
57186 AAA
1 AAA
57189 TGGGTTGTCA
Statistics
Matches: 339, Mismatches: 55, Indels: 46
0.77 0.12 0.10
Matches are distributed among these distances:
55 1 0.00
56 114 0.34
57 10 0.03
58 71 0.21
60 45 0.13
61 5 0.01
62 41 0.12
64 51 0.15
65 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (55 bp):
AAAAGATGCCACTAACTTGTGGGCTTTGAAGGATGCCACTGACTTGTGGGCTTTG
Found at i:56856 original size:84 final size:84
Alignment explanation
Indices: 56737--56903 Score: 212
Period size: 84 Copynumber: 2.0 Consensus size: 84
56727 AACTTCTGTG
* * * *
56737 GGCTTTGAAGAGATGCCACTACCTTGTGGGTTTTGAAAAGATGCCACTAACTTGTGGGCTTTAG-
1 GGCTTTGAAAAGATGCCACTACCTCGTCGGCTTTGAAAAGATGCCACTAACTTGTGGGC-TTAGA
* *
56801 AAGGATGCCACTGACTTGTC
65 AAAGATGCCACCGACTTGTC
* * * *
56821 GGCTTTGAAAAGTTGCCACTGA-CTCGTCGGCTTTGAAAAGTTGCCACTGACTTGTGGGCTTGGA
1 GGCTTTGAAAAGATGCCACT-ACCTCGTCGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTAGA
56885 AAAGATGCCACCGACTTGT
65 AAAGATGCCACCGACTTGT
56904 GTGGGTTTTG
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
83 3 0.04
84 67 0.94
85 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (84 bp):
GGCTTTGAAAAGATGCCACTACCTCGTCGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTAGAA
AAGATGCCACCGACTTGTC
Found at i:56934 original size:32 final size:32
Alignment explanation
Indices: 56890--57734 Score: 923
Period size: 32 Copynumber: 27.2 Consensus size: 32
56880 TTGGAAAAGA
* *
56890 TGCCACCGACTTGTGTGGGTTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
56922 TGCCACCAACTTGTGTGGGCTATGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
56954 TGCCACCAACTTGTGTGGGCATTGAAA--GGA
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* ** ** *
56984 TACCACTGAC-T-TGTGGGCTTT-AAA-AAGA
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
57012 TGCCACCGACTTGTGTGGGCTTTGACATGGGC
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
57044 TACCACCAACTTGTGTGGGCTATGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
57076 TGCCACCAACTTGTGTGGGCATTGAAA--GGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* **
57106 CGCCACTGAC-T-TGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*** * *
57134 TGCCACTGTC-T-TGTGGGCTTTGAAA--AGA
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
57162 TGTCACCGACTTGTATGGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
57194 TGTCACCAACTTGTGTGGGCTTTGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
57226 TGCCACCAACTTGTGTGGACTTTGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
57258 TGCCACCAACTTGTGTAGGCTTTCAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
57290 TGCCACCAACTTGTGTGGGCTTTCAAATAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
57322 TGTCACCAAATTGTGTGGGCTTTGAAATAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
57354 TGCCACCAACTTATGTGGGCTTTCAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
57386 TGCCACCGACTTGTGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
57416 TGCCACTAAC-T-TGTGGGCTTTGAAA--AGA
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
57444 TGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
57476 TGCCACCAACTTGTGTGGACTTTGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
57508 TGCAACCGACTTGTATGGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
**
57540 TGCCACCAACTTGTGTGGGCTTTGAAATATGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
57572 TACCACCAACTTGTGTGGGCTTTCAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
57604 TGCCACCGACTTGTGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
57634 TGCCACCGACTTGTGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
57664 TGCCACCCACTTGTGTAGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
57696 TGCCACTAACTTGTGTGGGCTTTGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
57728 TGCCACC
1 TGCCACC
57735 GATGAATAAA
Statistics
Matches: 694, Mismatches: 101, Indels: 36
0.84 0.12 0.04
Matches are distributed among these distances:
27 5 0.01
28 84 0.12
29 8 0.01
30 117 0.17
31 9 0.01
32 471 0.68
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
Found at i:68534 original size:2 final size:2
Alignment explanation
Indices: 68527--68564 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
68517 TTTATGTAAT
*
68527 TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
68565 CACCTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:70942 original size:18 final size:17
Alignment explanation
Indices: 70915--70948 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
70905 TTAAAAAGTT
70915 AAAAAATAATAATTTTA
1 AAAAAATAATAATTTTA
*
70932 AAAATAATAATTATTTT
1 AAAA-AATAATAATTTT
70949 TAATATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAAAATAATAATTTTA
Found at i:72189 original size:12 final size:11
Alignment explanation
Indices: 72136--72192 Score: 53
Period size: 12 Copynumber: 4.9 Consensus size: 11
72126 TTTTTAATAA
*
72136 TTAATAATATAT
1 TTAAT-ATAAAT
*
72148 TTAAATTTAAAT
1 TT-AATATAAAT
72160 TTAATTATAAAT
1 TTAA-TATAAAT
72172 TT-ATATAAAT
1 TTAATATAAAT
72182 ATTAATATAAA
1 -TTAATATAAA
72193 AATAAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 23 0.61
13 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTAATATAAAT
Found at i:73480 original size:22 final size:22
Alignment explanation
Indices: 73450--73494 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
73440 TAAAATATTT
*
73450 AAATTTAAAT-TTAATTATAAAA
1 AAATATAAATATTAA-TATAAAA
73472 AAATATAAATATTAATATAAAA
1 AAATATAAATATTAATATAAAA
73494 A
1 A
73495 TAAATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATATAAATATTAATATAAAA
Done.