Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1088
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: 88335
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:32 original size:19 final size:19
Alignment explanation
Indices: 8--55 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1 CCATCTT
8 TTTATATATAATTA-ATAGA
1 TTTATATATAATTATATA-A
* *
27 TTTATATTTTATTATATAA
1 TTTATATATAATTATATAA
*
46 TATATATATA
1 TTTATATATA
56 TAATAGTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TTTATATATAATTATATAA
Found at i:782 original size:20 final size:22
Alignment explanation
Indices: 748--791 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
738 GATATATACA
748 AATTATTATAAATT-AAAAATT
1 AATTATTATAAATTAAAAAATT
*
769 AATTA-TATATATTAAAAAATT
1 AATTATTATAAATTAAAAAATT
790 AA
1 AA
792 CTGTACATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTATTATAAATTAAAAAATT
Found at i:2509 original size:17 final size:16
Alignment explanation
Indices: 2487--2529 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2477 TATATTTTAA
2487 AAATTAATAAAAATATT
1 AAATT-ATAAAAATATT
*
2504 AAATTATTAAAA-ATT
1 AAATTATAAAAATATT
2519 AAATT-TAAAAA
1 AAATTATAAAAA
2530 ATATATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.21
15 8 0.33
16 6 0.25
17 5 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTATAAAAATATT
Found at i:2513 original size:27 final size:27
Alignment explanation
Indices: 2449--2520 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 27
2439 TATTATAACA
*
2449 TAAA-TATTAAAATATATAATAAATTATT
1 TAAATTATTAAAA-AT-TAATAAAATATT
*
2477 TATATT-TTAAAAATTAATAAAA-ATAT
1 TAAATTATTAAAAATTAATAAAATAT-T
2503 TAAATTATTAAAAATTAA
1 TAAATTATTAAAAATTAA
2521 ATTTAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
25 2 0.05
26 13 0.34
27 13 0.34
28 9 0.24
29 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAATTATTAAAAATTAATAAAATATT
Found at i:2521 original size:15 final size:14
Alignment explanation
Indices: 2480--2545 Score: 50
Period size: 15 Copynumber: 4.8 Consensus size: 14
2470 AATTATTTAT
2480 ATTTTAAAAATT-A
1 ATTTTAAAAATTAA
*
2493 A--TAAAAATATTAA
1 ATTTTAAAA-ATTAA
2506 ATTATTAAAAATTAA
1 ATT-TTAAAAATTAA
*
2521 A-TTTAAAAAATATA
1 ATTTTAAAAATTA-A
*
2535 TTTTTAAAAAT
1 ATTTTAAAAAT
2546 AACAAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
11 5 0.12
12 3 0.07
13 12 0.29
14 2 0.05
15 14 0.34
16 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTTTAAAAATTAA
Found at i:2542 original size:28 final size:27
Alignment explanation
Indices: 2476--2553 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
2466 AATAAATTAT
2476 TTATA-TTTTAAAAATTAATAAAAATA
1 TTATATTTTTAAAAATTAATAAAAATA
* *
2502 TTAAATTATTAAAAATTAAATTTAAAAA-A
1 TTATATTTTTAAAAATT-AA--TAAAAATA
*
2531 -TATATTTTTAAAAA-TAACAAAAA
1 TTATATTTTTAAAAATTAATAAAAA
2554 AATGCAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
24 5 0.12
26 6 0.14
27 11 0.26
28 14 0.33
29 1 0.02
30 6 0.14
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (27 bp):
TTATATTTTTAAAAATTAATAAAAATA
Found at i:3497 original size:20 final size:21
Alignment explanation
Indices: 3464--3505 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
3454 TCTGAGAATT
3464 TTATTCAGATGTATCGATACA
1 TTATTCAGATGTATCGATACA
3485 TTATTCA-ATGTATCGATACA
1 TTATTCAGATGTATCGATACA
3505 T
1 T
3506 GCAGGTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (21 bp):
TTATTCAGATGTATCGATACA
Found at i:8192 original size:105 final size:106
Alignment explanation
Indices: 8025--8220 Score: 322
Period size: 105 Copynumber: 1.9 Consensus size: 106
8015 GTTAAAGTTA
* *
8025 AGATATTCATAAAACTCTTCTGCAAATTCACAAGCAATTTTAATGAGTACTATGCGACTATATTA
1 AGATATTCATAAAACTCTTCTGCAAATTCACAAGCAATTTTAATGAGTACCATACGACTATATTA
*
8090 AATTAATTTATCTAAAATGTAAAAGTTGCAACTGAAGATTG
66 AATTAATTTATCTAAAATATAAAAGTTGCAACTGAAGATTG
* *
8131 AGATATTCAT-ATACTCTTTTGCAAATTCACAAGCAATTTTAATGAGTACCATACGACTATATTA
1 AGATATTCATAAAACTCTTCTGCAAATTCACAAGCAATTTTAATGAGTACCATACGACTATATTA
* *
8195 ACTTAATTTATCTGAAATATAAAAGT
66 AATTAATTTATCTAAAATATAAAAGT
8221 GGGTTAGTTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
105 73 0.88
106 10 0.12
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (106 bp):
AGATATTCATAAAACTCTTCTGCAAATTCACAAGCAATTTTAATGAGTACCATACGACTATATTA
AATTAATTTATCTAAAATATAAAAGTTGCAACTGAAGATTG
Found at i:8680 original size:6 final size:6
Alignment explanation
Indices: 8669--8693 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
8659 CCATCATTTG
8669 TCTTGT TCTTGT TCTTGT TCTTGT T
1 TCTTGT TCTTGT TCTTGT TCTTGT T
8694 TGCCTCCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (6 bp):
TCTTGT
Found at i:9939 original size:2 final size:2
Alignment explanation
Indices: 9932--9966 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9922 ACGTCAAATT
9932 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9967 GTATGTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9971 original size:4 final size:4
Alignment explanation
Indices: 9964--9988 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
9954 TATATATATA
9964 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
9989 GTTCATTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:10198 original size:2 final size:2
Alignment explanation
Indices: 10186--10222 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
10176 ATTCCTTATT
* *
10186 TA TA TA AA TA TA TA TA AA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10223 TGTGTACGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:10222 original size:10 final size:10
Alignment explanation
Indices: 10186--10221 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
10176 ATTCCTTATT
10186 TATATAAATA
1 TATATAAATA
10196 TATATAAATA
1 TATATAAATA
*
10206 TATATATATA
1 TATATAAATA
10216 TATATA
1 TATATA
10222 TTGTGTACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TATATAAATA
Found at i:10765 original size:2 final size:2
Alignment explanation
Indices: 10758--10782 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10748 TTGTTTCAAT
10758 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
10783 CTTTTGTGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14523 original size:157 final size:153
Alignment explanation
Indices: 13862--14819 Score: 612
Period size: 157 Copynumber: 6.1 Consensus size: 153
13852 CTATGTGATG
* * * * * * * *
13862 AACCTATCCTAAATACCCACCTT-TAGCATAAAAGCAGACCCGATGATAACCTAGGGCTCGATTC
1 AACCTATCCTAAATACCCACCTTCGA-CA-AAAAACAAACTCGATGACAACCTAGGACTTGGTTC
* * * * * * * * *
13926 TGAAAAATTATAAAAAT-GCTCCTAAAGGATACCTTCAACGTGAAAGTATCCTGGTACACCTAAA
64 TAAAAAATTATGAAAATACCT-CTAAGGGATACCTTCGACGTAAAAGTA-CCCGATACCCCTAAA
* * *
13990 GGACTTAAAAGGGACTAGAAATGGTGATA
127 GGACTTAAAAAGGATTATAAATGG-G-TA
* * * ** * * * * * *
14019 AACCTATTCTAAATGCCCACCTTC-AGCATCAAAGTAGACTCGGTGATAACCTAAGACTCGGTTT
1 AACCTATCCTAAATACCCACCTTCGA-CA-AAAAACAAACTCGATGACAACCTAGGACTTGGTTC
* * * *
14083 TAAAAAAATTATGAAAATACC-CTTAAAGGATACCTTCGACGTGAAAGTATCCTAGTAACCCCTA
64 T-AAAAAATTATGAAAATACCTC-TAAGGGATACCTTCGACGTAAAAGTACCCGA-T-ACCCCTA
** * *
14147 AAAAACCTAAAAAGGATTTATAGATGGGGTA
125 AAGGACTTAAAAAGGA-TTATAAAT-GGGTA
* * * * *
14178 AACCTATCCTAAATACCCACCTTTGGCCTAAAAGCAAACTCGATGACAACCTAAGACTTGGTTCT
1 AACCTATCCTAAATACCCACC-TTCGACAAAAAACAAACTCGATGACAACCTAGGACTTGGTTCT
* * *
14243 -AAGAATTTTGAAAATA-CTCCTAAGGGATACCTTCGACATAAAAGTACCCTGATACCCCTAAAT
65 AAAAAATTATGAAAATACCT-CTAAGGGATACCTTCGACGTAAAAGTACCC-GATACCCCTAAA-
* * *
14306 GG-CTTAAAAAGGATTCATATA-GAGATG
127 GGACTTAAAAAGGATT-ATAAATG-GGTA
* * * * * * **
14333 AACCTATCCTAAACATCTACCTTC-AGCATAAAAACGAACTCGTTGACGACCTAGGACTTGACTC
1 AACCTATCCTAAATACCCACCTTCGA-CA-AAAAACAAACTCGATGACAACCTAGGACTTGGTTC
* * * * * * *
14397 TGAAAAAATTATGAAAATACCTTTAGGGGATACCTTTGATGTGAAAGTATCCCGGTACCCTTAAA
64 T-AAAAAATTATGAAAATACCTCTAAGGGATACCTTCGACGTAAAAGTA-CCCGATACCCCTAAA
*
14462 GGACTTAAAAAAGGATTATAAAATGGGTG
127 GGACTT-AAAAAGGATTAT-AAATGGGTA
* * * *
14491 AACCTATCCTAAATACTCACCTTCGACAAAAAAAAAACCCGATAACAACCTAGGACTTGGTTCTA
1 AACCTATCCTAAATACCCACCTTCGACAAAAAACAAACTCGATGACAACCTAGGACTTGGTTCTA
* * ** * * * * * *
14556 GAAAATTAAGAAAATGTCTCTAGGGGATACCTTTGATGTAAAAGTACTCGATATCCCTAATGGAC
66 AAAAATTATGAAAATACCTCTAAGGGATACCTTCGACGTAAAAGTACCCGATACCCCTAAAGGA-
* *
14621 CTTAAAAAGGACTATAAAGGGAGTA
130 CTTAAAAAGGATTATAAATGG-GTA
* * * * * * *
14646 AACCTATCCTAAATACCCACTTTCGACATGAAAACTAACTTGGTGACAACCTAAGAGTTGGTTCT
1 AACCTATCCTAAATACCCACCTTCGACA-AAAAACAAACTCGATGACAACCTAGGACTTGGTTCT
* ** * * * * *
14711 -TAAAATTACAAAAATGCCTCTATGGGTATA-CTTC--CGATATAAAGTATCCTGGTAACCCTAA
65 AAAAAATTATGAAAATACCTCTAAGGG-ATACCTTCGACG-TA-AAAGTA-CCCGATACCCCTAA
* * *
14772 ATGACTTAAAAATGA-TAAAAATAGGGTA
126 AGGACTTAAAAAGGATTATAAAT-GGGTA
14800 AACCTATCCTAAATACCCAC
1 AACCTATCCTAAATACCCAC
14820 ATTTGGCATG
Statistics
Matches: 637, Mismatches: 129, Indels: 73
0.76 0.15 0.09
Matches are distributed among these distances:
153 1 0.00
154 39 0.06
155 145 0.23
156 112 0.18
157 174 0.27
158 84 0.13
159 71 0.11
160 9 0.01
161 2 0.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.25
Consensus pattern (153 bp):
AACCTATCCTAAATACCCACCTTCGACAAAAAACAAACTCGATGACAACCTAGGACTTGGTTCTA
AAAAATTATGAAAATACCTCTAAGGGATACCTTCGACGTAAAAGTACCCGATACCCCTAAAGGAC
TTAAAAAGGATTATAAATGGGTA
Found at i:14726 original size:155 final size:149
Alignment explanation
Indices: 14173--14868 Score: 437
Period size: 155 Copynumber: 4.5 Consensus size: 149
14163 TTTATAGATG
* * * *
14173 GGGTAAACCTATCCTAAATACCCACCTTT-GGCCT-AAAAGCAAACTCGATGACAACCTAAGACT
1 GGGTAAACCTATCCTAAATACCCA-CTTTCGACATGAAAA-C-AACCCGGTGACAACCTAAGACT
** * * * ** * *
14236 TGGTTC-TAAGAATTTTGAAAAT-ACTCCTAAGGGATACCTTCGACATAAAAGTACCCTGATACC
63 TGGTTCTTAA-AATTAAGAAAATGCCT-CTAGGGGATACCTTTGATGT-AAAGTACTC-GGTA-C
*
14299 CCTAAATGG-CTTAAAAAGGAT-TCATATA
123 CCT-AATGGACTTAAAAAGGATAT-A-AAA
* * * * * * * * * * *
14327 GAGATGAACCTATCCTAAACATCTACCTTC-AGCATAAAAACGAACTCGTTGACGACCTAGGACT
1 G-GGTAAACCTATCCTAAATACCCACTTTCGA-CATGAAAAC-AACCCGGTGACAACCTAAGACT
** * * * * *
14391 TGACTCTGAAAAAATTATGAAAATACCTTTAGGGGATACCTTTGATGTGAAAGTATCCCGGTACC
63 TGGTTCT--TAAAATTAAGAAAATGCCTCTAGGGGATACCTTTGATGT-AAAGTA-CTCGGTACC
*
14456 CTTAAAGGACTTAAAAAAGGATTATAAAA
124 C-TAATGGACTT-AAAAAGGA-TATAAAA
* * * ** * * * *
14485 TGGGTGAACCTATCCTAAATACTCACCTTCGACAAAAAAAAAACCCGATAACAACCTAGGACTTG
1 -GGGTAAACCTATCCTAAATACCCACTTTCGACATGAAAACAACCCGGTGACAACCTAAGACTTG
* * *
14550 GTTCTAGAAAATTAAGAAAATGTCTCTAGGGGATACCTTTGATGTAAAAGTACTCGATATCCCTA
65 GTTCT-TAAAATTAAGAAAATGCCTCTAGGGGATACCTTTGATGT-AAAGTACTCGGTA-CCCTA
*
14615 ATGGACCTTAAAAAGGACTATAAAG
127 ATGGA-CTTAAAAAGGA-TATAAAA
** *
14640 GGAGTAAACCTATCCTAAATACCCACTTTCGACATGAAAACTAACTTGGTGACAACCTAAGAGTT
1 GG-GTAAACCTATCCTAAATACCCACTTTCGACATGAAAAC-AACCCGGTGACAACCTAAGACTT
* * *
14705 GGTTCTTAAAATTACA-AAAATGCCTCTATGGGTATA-CTTCCGATATAAAGTA-TCCTGGTAAC
64 GGTTCTTAAAATTA-AGAAAATGCCTCTA-GGGGATACCTT-TGATGTAAAGTACT-C-GGT-AC
* *
14767 CCTAAAT-GACTTAAAAATGATAAAAATA
123 CCT-AATGGACTTAAAAAGGATATAAA-A
* *
14795 GGGTAAACCTATCCTAAATACCCACATTT-GGCATGAAAGCAGACCCGGTGACAACCTAAGACTT
1 GGGTAAACCTATCCTAAATACCCAC-TTTCGACATGAAAACA-ACCCGGTGACAACCTAAGACTT
*
14859 AGTT-TTAAAA
64 GGTTCTTAAAA
14869 ACTTACGAAA
Statistics
Matches: 435, Mismatches: 77, Indels: 61
0.76 0.13 0.11
Matches are distributed among these distances:
153 7 0.02
154 66 0.15
155 144 0.33
156 100 0.23
157 66 0.15
158 47 0.11
159 4 0.01
160 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.25
Consensus pattern (149 bp):
GGGTAAACCTATCCTAAATACCCACTTTCGACATGAAAACAACCCGGTGACAACCTAAGACTTGG
TTCTTAAAATTAAGAAAATGCCTCTAGGGGATACCTTTGATGTAAAGTACTCGGTACCCTAATGG
ACTTAAAAAGGATATAAAA
Found at i:14845 original size:154 final size:156
Alignment explanation
Indices: 13966--14938 Score: 385
Period size: 156 Copynumber: 6.2 Consensus size: 156
13956 ACCTTCAACG
** * *
13966 TGAAAGTATCCTGGT-ACACCTAAAGGACTTAAAAGGGACTAGAAAT-GGTGATAAACCTATTCT
1 TGAAAGTATCCTGGTAAC-CCTAAAGGACTTAAAAATGA-TAAAAATAGG-G-TAAACCTATCCT
* * * * * * ** *
14029 AAATGCCCACCTTC-AGCAT-CAAAGTAGACTCGGTGATAACCTAAGACTCGGTTTTAAAAAAAT
62 AAATACCCACTTTCGA-CATGAAAACTA-ACCCGGTGACAACCTAAGACTTAGTTTT-AAAAACT
* * * *
14092 TATGAAAATA-CCCT-TAAAGGATACCTT-CGACG
124 TACGAAAATATCCCTAT-GAGTATA-CTTCCGACA
* ** * * * * *
14124 TGAAAGTATCCTAGTAACCCCTAAAAAACCTAAAAAGGATTTATAGATGGGGTAAACCTATCCTA
1 TGAAAGTATCCTGGTAA-CCCTAAAGGACTTAAAAATGA--TAAAAATAGGGTAAACCTATCCTA
* * * * * * * * *
14189 AATACCCACCTTT-GGCCT-AAAAGCAAACTCGATGACAACCTAAGACTTGGTTCTAAGAA-TTT
63 AATACCCA-CTTTCGACATGAAAA-CTAACCCGGTGACAACCTAAGACTTAGTTTTAAAAACTTA
* * *
14251 TGAAAATA-CTCCTAAG-GGATACCTT-CGACA
126 CGAAAATATC-CCTATGAGTATA-CTTCCGACA
* * * * * ** * * *
14281 TAAAAGTACCCTGATACCCCTAAATGG-CTTAAAAAGGATTCATATAGAGATGAACCTATCCTAA
1 TGAAAGTATCCTGGTAACCCTAAA-GGACTTAAAAATGATAAAAATAG-GGTAAACCTATCCTAA
* * * * * * * * * * * * * * *
14345 ACATCTACCTTC-AGCATAAAAACGAACTCGTTGACGACCTAGGACTTGACTCTGAAAAAATTAT
64 ATACCCACTTTCGA-CATGAAAACTAACCCGGTGACAACCTAAGACTT-AGTTTTAAAAACTTAC
* * * * **
14409 GAAAATA--CCTTTAGGGGATACCTT-TGATG
127 GAAAATATCCCTAT-GAGTATA-CTTCCGACA
* * *
14438 TGAAAGTATCCCGGT-ACCCTTAAAGGACTTAAAAAAGGATTATAAAAT-GGGTGAACCTATCCT
1 TGAAAGTATCCTGGTAACCC-TAAAGGACTT-AAAAATGA-TA-AAAATAGGGTAAACCTATCCT
* * * ** * * * * *
14501 AAATACTCACCTTCGACA-AAAAAAAAACCCGATAACAACCTAGGACTTGGTTCTAGAAAA-TTA
62 AAATACCCACTTTCGACATGAAAACTAACCCGGTGACAACCTAAGACTTAGTTTTA-AAAACTTA
* * * * * * **
14564 AGAAAATGTCTCTA-GGGGATACCTT-TGATG
126 CGAAAATATCCCTATGAGTATA-CTTCCGACA
* * * * * * *
14594 TAAAAGTA--CTCGATATCCCTAATGGACCTTAAAAAGGACTATAAA-GGGAGTAAACCTATCCT
1 TGAAAGTATCCT-GGTAACCCTAAAGGA-CTTAAAAATGA-TAAAAATAGG-GTAAACCTATCCT
** * *
14656 AAATACCCACTTTCGACATGAAAACTAACTTGGTGACAACCTAAGAGTTGGTTCTT-AAAA-TTA
62 AAATACCCACTTTCGACATGAAAACTAACCCGGTGACAACCTAAGACTTAGTT-TTAAAAACTTA
* *
14719 C-AAAA-ATGCCTCTATGGGTATACTTCCGATA
126 CGAAAATAT-CC-CTATGAGTATACTTCCGACA
*
14750 T-AAAGTATCCTGGTAACCCTAAATGACTTAAAAATGATAAAAATAGGGTAAACCTATCCTAAAT
1 TGAAAGTATCCTGGTAACCCTAAAGGACTTAAAAATGATAAAAATAGGGTAAACCTATCCTAAAT
* *
14814 ACCCACATTT-GGCATGAAAGC-AGACCCGGTGACAACCTAAGACTTAGTTTTAAAAACTTACGA
66 ACCCAC-TTTCGACATGAAAACTA-ACCCGGTGACAACCTAAGACTTAGTTTTAAAAACTTACGA
* * *
14877 AAATATCCCTATGAGTATACTTTCGGCG
129 AAATATCCCTATGAGTATACTTCCGACA
* *
14905 TGAAAGTATCTTGGTAACCTTAAAGGACTTAAAA
1 TGAAAGTATCCTGGTAACCCTAAAGGACTTAAAA
14939 TAATGCTACA
Statistics
Matches: 631, Mismatches: 136, Indels: 98
0.73 0.16 0.11
Matches are distributed among these distances:
153 4 0.01
154 82 0.13
155 144 0.23
156 153 0.24
157 108 0.17
158 56 0.09
159 68 0.11
160 14 0.02
161 2 0.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (156 bp):
TGAAAGTATCCTGGTAACCCTAAAGGACTTAAAAATGATAAAAATAGGGTAAACCTATCCTAAAT
ACCCACTTTCGACATGAAAACTAACCCGGTGACAACCTAAGACTTAGTTTTAAAAACTTACGAAA
ATATCCCTATGAGTATACTTCCGACA
Found at i:16087 original size:19 final size:21
Alignment explanation
Indices: 16041--16094 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
16031 TTTCAACAAT
16041 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAACAGTAA
* *
16062 ATGTATCGATACATA-AGT-A
1 TTGTATCGATACAAACAGTAA
16081 TTGTATCGATACAA
1 TTGTATCGATACAA
16095 TGTATCACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (21 bp):
TTGTATCGATACAAACAGTAA
Found at i:20963 original size:19 final size:18
Alignment explanation
Indices: 20912--21001 Score: 75
Period size: 19 Copynumber: 5.1 Consensus size: 18
20902 TTGAATTCCA
20912 ATAA-TTTGTATCGATAC
1 ATAAGTTTGTATCGATAC
* *
20929 ATTCAGTAAATGTATCGATAC
1 A-TAAGT--TTGTATCGATAC
20950 ATAAGTGTTGTATCGATAC
1 ATAAGT-TTGTATCGATAC
20969 --AA---TGTATCGATAC
1 ATAAGTTTGTATCGATAC
20982 ATAAGTTTTGTATCGATAC
1 ATAAG-TTTGTATCGATAC
21001 A
1 A
21002 ATGTATCGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
13 11 0.19
15 2 0.03
17 3 0.05
18 2 0.03
19 24 0.41
20 4 0.07
21 12 0.21
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
ATAAGTTTGTATCGATAC
Found at i:20976 original size:13 final size:13
Alignment explanation
Indices: 20958--20982 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20948 ACATAAGTGT
20958 TGTATCGATACAA
1 TGTATCGATACAA
20971 TGTATCGATACA
1 TGTATCGATACA
20983 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:20978 original size:32 final size:32
Alignment explanation
Indices: 20937--21009 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
20927 ACATTCAGTA
20937 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
20969 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
21001 AATGTATCG
1 AATGTATCG
21010 CTAGGAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:21071 original size:13 final size:13
Alignment explanation
Indices: 21053--21078 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21043 CATTTTTCTG
21053 TGTATCGATACAT
1 TGTATCGATACAT
21066 TGTATCGATACAT
1 TGTATCGATACAT
21079 CTATTCTTTG
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:21096 original size:34 final size:33
Alignment explanation
Indices: 21033--21099 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
21023 GCCAAGGAAA
*
21033 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
*
21066 TGTATCGATACATCTATTCTTTGTATCGATACAT
1 TGTATCGATACAT-TATTCTGTGTATCGATACAT
21100 CTAGGAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:23495 original size:51 final size:52
Alignment explanation
Indices: 23438--23560 Score: 171
Period size: 51 Copynumber: 2.4 Consensus size: 52
23428 CAATTCTCCG
* *
23438 CAATCGGGGATA-TCCCAACTCCGATTTTATTTTC-AAAACACTAA-TTTTCTA
1 CAATCGGGGATACT-CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-A
*
23489 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTTTTCA
23542 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
23561 CCCGTTAATC
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
51 30 0.47
52 1 0.02
53 28 0.44
54 5 0.08
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (52 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCA
Found at i:23552 original size:53 final size:51
Alignment explanation
Indices: 23438--23560 Score: 169
Period size: 53 Copynumber: 2.4 Consensus size: 51
23428 CAATTCTCCG
* *
23438 CAATCGGGGATA-TCCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTA
1 CAATCGGGGATACT-CCAACTCCGATTTTATTTCCAAAACACCAATTTTCTA
*
23489 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTT-TCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAACACCAATTTTCT-A
23542 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
23561 CCCGTTAATC
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
51 30 0.47
52 2 0.03
53 32 0.50
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (51 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTA
Found at i:23574 original size:27 final size:28
Alignment explanation
Indices: 23544--23618 Score: 109
Period size: 27 Copynumber: 2.7 Consensus size: 28
23534 ATTTTTCACA
23544 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
23571 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
23599 -TGAGGGGATACTCCAACCCC
1 AT-CGGGGATACTCCAACCCC
23619 TGCTTTATTC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:23723 original size:79 final size:79
Alignment explanation
Indices: 23571--23745 Score: 210
Period size: 79 Copynumber: 2.2 Consensus size: 79
23561 CCCGTTAATC
* ** * *
23571 ATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCTGCTTTATTCTTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAAAGGATACTCCAACCCCTGCTTTATTCTCAAAAC
**
23636 ATTGATTTCTCATA
66 ATCAATTTCTCATA
* * * *
23650 ATCGGGGATATTCCAACCCCGTTATTTCCGAAAGGATACTCTAATCCC-GGTTTCATT-TCCAAA
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAAAGGATACTCCAACCCCTGCTTT-ATTCT-CAAA
*
23713 ACATCAATTTCTCTTA
64 ACATCAATTTCTCATA
23729 ATCGGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
23746 TCCGATTTTA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
78 5 0.06
79 76 0.94
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAAAGGATACTCCAACCCCTGCTTTATTCTCAAAAC
ATCAATTTCTCATA
Found at i:23759 original size:51 final size:51
Alignment explanation
Indices: 23704--23847 Score: 168
Period size: 51 Copynumber: 2.8 Consensus size: 51
23694 TCCCGGTTTC
* *
23704 ATTTCCAAAACATCAA-TTTCTCTTAATCGGGGATACTCCAACTCCGATTTT
1 ATTTCCAAAACACCAATTTTC-CATAATCGGGGATACTCCAACTCCGATTTT
* * *
23755 ATTTCTAAAACACCCATTTTCCATAATCGGGGATACTCCAACTTCGATTTT
1 ATTTCCAAAACACCAATTTTCCATAATCGGGGATACTCCAACTCCGATTTT
* * *
23806 ATTTCCAAAGCACCGACTTTTCACA-AA-CGGGGATATTCCAAC
1 ATTTCCAAAACACC-AATTTTC-CATAATCGGGGATACTCCAAC
23848 CCCGTTATTT
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
51 67 0.84
52 11 0.14
53 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (51 bp):
ATTTCCAAAACACCAATTTTCCATAATCGGGGATACTCCAACTCCGATTTT
Found at i:23943 original size:27 final size:27
Alignment explanation
Indices: 23905--23957 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
23895 CATCAATTTT
23905 TCATCGGAGATACTCCAACCCCGTTAA
1 TCATCGGAGATACTCCAACCCCGTTAA
* * *
23932 TCATCGGGGATACTCCCACCTCGTTA
1 TCATCGGAGATACTCCAACCCCGTTA
23958 TTTTCAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.25
Consensus pattern (27 bp):
TCATCGGAGATACTCCAACCCCGTTAA
Found at i:24036 original size:76 final size:76
Alignment explanation
Indices: 23938--24122 Score: 212
Period size: 79 Copynumber: 2.4 Consensus size: 76
23928 TTAATCATCG
* * * * *
23938 GGGATACTCCCACCTCGTTATTTTCAAGGG-GCT-AAACCCCTGGCTTTATTCCTAAAATATTGA
1 GGGATACTCCAACCCCGTTATTTTCAAGGGAACTCAAACCCC-AGCTTTATTCCTAAAATATTAA
24001 TTTCTCATAATC
65 TTTCTCATAATC
* * *
24013 GAGGATACTCCAACCCCGTTATTTTCGAGGGAATACTCTAACCCCAGCTTTATTTCTAAAATATT
1 G-GGATACTCCAACCCCGTTATTTTCAAGGG-A-ACTCAAACCCCAGCTTTATTCCTAAAATATT
24078 AATTTCTCATAATC
63 AATTTCTCATAATC
24092 GGGAATACTCCAACCCCAGTTTTATTTTCAA
1 GGG-ATACTCCAACCCC-G--TTATTTTCAA
24123 ATCATCGATT
Statistics
Matches: 92, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
75 1 0.01
76 26 0.28
78 2 0.02
79 47 0.51
80 7 0.08
82 9 0.10
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (76 bp):
GGGATACTCCAACCCCGTTATTTTCAAGGGAACTCAAACCCCAGCTTTATTCCTAAAATATTAAT
TTCTCATAATC
Found at i:24117 original size:51 final size:51
Alignment explanation
Indices: 24041--24159 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
24031 TTATTTTCGA
* * *
24041 GGGAATACTCTAACCCCAGCTTTATTTCTAAAAT-ATTAATTTCTCATAATC
1 GGGAATACTCCAACCCCAGCTTTATTT-TAAAATCATCAATTTCTCACAATC
* * * *
24092 GGGAATACTCCAACCCCAGTTTTATTTTCAAATCATCGATTTTTCACAATC
1 GGGAATACTCCAACCCCAGCTTTATTTTAAAATCATCAATTTCTCACAATC
*
24143 GGGGATACTCCAACCCC
1 GGGAATACTCCAACCCC
24160 GTTATTTTCA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
50 5 0.08
51 54 0.92
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
GGGAATACTCCAACCCCAGCTTTATTTTAAAATCATCAATTTCTCACAATC
Found at i:36436 original size:52 final size:52
Alignment explanation
Indices: 36366--36486 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
36356 GAAAATTTGT
36366 CTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGCAAATTTAC
1 CTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGCAAATTTAC
* *
36418 CTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGCAAATTTGC
1 CTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGCAAATTTAC
36470 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
36487 AAGATTAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGCAAATTTAC
Found at i:36496 original size:52 final size:52
Alignment explanation
Indices: 36358--36506 Score: 194
Period size: 52 Copynumber: 2.9 Consensus size: 52
36348 CGAAATATGA
* *
36358 AAATTTGTCTGCATGTATCGATACATTTCA-TAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACA-ATCATTAGTGTATCGATACATCTAGGC
* **
36410 AAATTTACCTGCATGTATCGATAC-ATTTTATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACAATCAT-TAGTGTATCGATACATCTAGGC
** *
36462 AAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCAATACA
1 AAATTTGCCTGCATGTATCGATACAATCATTAGTGTATCGATACA
36507 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
50 1 0.01
52 81 0.96
53 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACAATCATTAGTGTATCGATACATCTAGGC
Found at i:36586 original size:19 final size:18
Alignment explanation
Indices: 36562--36659 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
36552 TAGCTTACAT
36562 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
36581 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
36594 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
36613 TGTATCGATAC--A-TTA
1 TGTATCGATACAAACTTA
36628 T-T-TCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
36646 TGTATCGATACAAA
1 TGTATCGATACAAA
36660 TCATTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 18 0.27
14 2 0.03
15 4 0.06
16 4 0.06
18 5 0.08
19 24 0.36
20 9 0.14
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:36598 original size:32 final size:32
Alignment explanation
Indices: 36557--36657 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
36547 GGCAGTAGCT
*
36557 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
36589 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
* *
36621 TACATTATTTCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
36654 TACA
1 TACA
36658 AATCATTGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 50 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:36599 original size:13 final size:13
Alignment explanation
Indices: 36581--36605 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36571 ACAAAACTTA
36581 TGTATCGATACAT
1 TGTATCGATACAT
36594 TGTATCGATACA
1 TGTATCGATACA
36606 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:36884 original size:18 final size:18
Alignment explanation
Indices: 36861--36896 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
36851 CTAGGCCGAA
36861 ATATGTCGAATCCTCCAC
1 ATATGTCGAATCCTCCAC
*
36879 ATATGTCGAATCTTCCAC
1 ATATGTCGAATCCTCCAC
36897 CTACTAGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.31
Consensus pattern (18 bp):
ATATGTCGAATCCTCCAC
Found at i:38024 original size:7 final size:7
Alignment explanation
Indices: 38012--38045 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
38002 CCTCTGCAAA
38012 AAAAAAC
1 AAAAAAC
*
38019 AAAAAAA
1 AAAAAAC
38026 AAACAAAC
1 AAA-AAAC
38034 AAAAAAC
1 AAAAAAC
38041 AAAAA
1 AAAAA
38046 GGGTCCGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:38025 original size:11 final size:11
Alignment explanation
Indices: 38009--38045 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
37999 CATCCTCTGC
38009 AAAAAAAAACA
1 AAAAAAAAACA
38020 AAAAAAAAACA
1 AAAAAAAAACA
*
38031 AACAAAAAACA
1 AAAAAAAAACA
38042 AAAA
1 AAAA
38046 GGGTCCGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:38033 original size:15 final size:14
Alignment explanation
Indices: 38009--38045 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
37999 CATCCTCTGC
38009 AAAAAAAAACAAAA
1 AAAAAAAAACAAAA
38023 AAAAAACAAACAAAA
1 AAAAAA-AAACAAAA
38038 AACAAAAA
1 AA-AAAAA
38046 GGGTCCGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 11 0.52
16 4 0.19
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAACAAAA
Found at i:39127 original size:37 final size:37
Alignment explanation
Indices: 39077--39180 Score: 190
Period size: 37 Copynumber: 2.8 Consensus size: 37
39067 CATGCATTTG
*
39077 TAACATTTGATTTTGCATGATGCATTTGTGACATTCA
1 TAACATTTCATTTTGCATGATGCATTTGTGACATTCA
*
39114 TAACATTTCATTTTGCATGATGCATTTATGACATTCA
1 TAACATTTCATTTTGCATGATGCATTTGTGACATTCA
39151 TAACATTTCATTTTGCATGATGCATTTGTG
1 TAACATTTCATTTTGCATGATGCATTTGTG
39181 CTTCAGCTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.44
Consensus pattern (37 bp):
TAACATTTCATTTTGCATGATGCATTTGTGACATTCA
Found at i:39587 original size:29 final size:29
Alignment explanation
Indices: 39546--39870 Score: 360
Period size: 28 Copynumber: 11.3 Consensus size: 29
39536 CTCACCTTCC
*
39546 AAAGCCCACAAGTCAATGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
*
39575 AAAGCCCATAAGTCAGTGGCA-CATTTTC-
1 AAAGCCCACAAGTCAGTGGCATC-TTTTCA
* *
39603 AAAGCCCACAAGTCAGTGGCAACCTTT-A
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
*
39631 GAAGCCCACAAGTCAGTGGCATCTTTTCAA
1 AAAGCCCACAAGTCAGTGGCATCTTTTC-A
* *
39661 AAAGCCCACAAGTCAGTGGCACTTTTTTCG
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCA
*
39691 ACAGCCCACAAGTCAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
* *
39720 AAAGCCCACAAGTC-GTTGCATCTTCTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
* * *
39748 AAA-CCCACAAGTCAATGGCAAC-CTTCAA
1 AAAGCCCACAAGTCAGTGGCATCTTTTC-A
*
39776 AAAGCCCACAAGTTAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
* * * * * *
39805 AAAACCCATAAGTTAGTGGTACCTTCTC-
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
* *
39833 AAAGCCCACAAGTCAGTGGCAACCTTT-A
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
39861 AAAGCCCACA
1 AAAGCCCACA
39871 CAAGTTGGTG
Statistics
Matches: 248, Mismatches: 37, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
27 12 0.05
28 102 0.41
29 84 0.34
30 44 0.18
31 6 0.02
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTCA
Found at i:39946 original size:43 final size:43
Alignment explanation
Indices: 39892--39973 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
39882 CATCTTCTTC
* *
39892 TAAGTCAAATATCGCTGGTCC-TGAATCAGCATATTGGCACCTT
1 TAAGTCAAATATCACTGG-CCTTAAATCAGCATATTGGCACCTT
* *
39935 TAAGTCCAATATCATTGGCCTTAAATCAGCATATTGGCA
1 TAAGTCAAATATCACTGGCCTTAAATCAGCATATTGGCA
39974 TTTTTAACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 2 0.06
43 32 0.94
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (43 bp):
TAAGTCAAATATCACTGGCCTTAAATCAGCATATTGGCACCTT
Found at i:44277 original size:19 final size:18
Alignment explanation
Indices: 44253--44295 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
44243 AATTGTTCCC
44253 TTTCATG-TTTTGATATCAT
1 TTTCATGATTTT--TATCAT
*
44272 TTTCATGATTTTTATGAT
1 TTTCATGATTTTTATCAT
44290 TTTCAT
1 TTTCAT
44296 AAACTTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 7 0.32
20 4 0.18
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.60
Consensus pattern (18 bp):
TTTCATGATTTTTATCAT
Found at i:46162 original size:8 final size:8
Alignment explanation
Indices: 46149--46197 Score: 89
Period size: 8 Copynumber: 6.0 Consensus size: 8
46139 TTAATTTTGA
46149 TTTTGATT
1 TTTTGATT
46157 TTTTGATTT
1 TTTTGA-TT
46166 TTTTGATT
1 TTTTGATT
46174 TTTTGATT
1 TTTTGATT
46182 TTTTGATT
1 TTTTGATT
46190 TTTTGATT
1 TTTTGATT
46198 ACTATATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
8 32 0.80
9 8 0.20
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (8 bp):
TTTTGATT
Found at i:46344 original size:34 final size:34
Alignment explanation
Indices: 46306--46375 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
46296 GAACGATATA
46306 ATTTACTCTTGTCTGAGAAAAATAGATTTTCGGC
1 ATTTACTCTTGTCTGAGAAAAATAGATTTTCGGC
46340 ATTTACTCTTGTCTGAGAAAAATAGATTTTCGGC
1 ATTTACTCTTGTCTGAGAAAAATAGATTTTCGGC
46374 AT
1 AT
46376 GTGCCCACCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (34 bp):
ATTTACTCTTGTCTGAGAAAAATAGATTTTCGGC
Found at i:46950 original size:19 final size:21
Alignment explanation
Indices: 46903--46954 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
46893 TTCAATAATT
*
46903 TGTATCGATACATTCAGTAAA
1 TGTATCGATACATTAAGTAAA
*
46924 TCTATCGATACA-TAAGT-AA
1 TGTATCGATACATTAAGTAAA
46943 TGTATCGATACA
1 TGTATCGATACA
46955 GTGTATCGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 13 0.46
20 4 0.14
21 11 0.39
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATTAAGTAAA
Found at i:47034 original size:21 final size:21
Alignment explanation
Indices: 46989--47053 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
46979 AAGGAAATGT
* *
46989 ATCGATACATT-TATAGAATAT
1 ATCGATACATTGTATCG-ATAC
47010 ATCGATACATTGTATCGATAC
1 ATCGATACATTGTATCGATAC
**
47031 ATCGAT-TTTTGTATCGATAC
1 ATCGATACATTGTATCGATAC
47051 ATC
1 ATC
47054 TAGGAAGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
20 15 0.38
21 20 0.51
22 4 0.10
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (21 bp):
ATCGATACATTGTATCGATAC
Found at i:47179 original size:38 final size:38
Alignment explanation
Indices: 47128--47203 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
47118 CTACTTCGAG
47128 CTATTTTTCTGCTTTTCCATTGTTCATTCAAAACATGT
1 CTATTTTTCTGCTTTTCCATTGTTCATTCAAAACATGT
47166 CTATTTTTCTGCTTTTCCATTGTTCATTCAAAACATGT
1 CTATTTTTCTGCTTTTCCATTGTTCATTCAAAACATGT
47204 TTTTAACACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.21, G:0.08, T:0.50
Consensus pattern (38 bp):
CTATTTTTCTGCTTTTCCATTGTTCATTCAAAACATGT
Found at i:49617 original size:73 final size:75
Alignment explanation
Indices: 49446--49710 Score: 300
Period size: 75 Copynumber: 3.5 Consensus size: 75
49436 TAATCAGGAT
*
49446 TACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTTATCGAGGATACTCCAACCCCGTTAT
1 TACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCGAGGATACTCCAACCCCGTTAT
49511 TTTGAGGGGA
66 TTTGAGGGGA
* * * *
49521 TACTCCAACCTCGGTTTTGTTTCTAAAACATCAATTTTTCATCG-GGATACTCTAACCTCGTTAT
1 TACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCGAGGATACTCCAACCCCGTTAT
*
49585 TTT-TGGGGA
66 TTTGAGGGGA
* * ** * * *
49594 TATTCCAACCCCGGTTTTATTTCTAAAATATTGATTTTTCATAATTGGGGATACTCCAACCCCAT
1 TACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTC---ATCGAGGATACTCCAACCCCGT
* *
49659 TATTTTCACAGGGA
63 TATTTTGA-GGGGA
* * * * *
49673 TACTCCAATCCCGATTTTATTTTTGAAACATCTATTTT
1 TACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTT
49711 CTATAATGGG
Statistics
Matches: 158, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
73 39 0.25
74 21 0.13
75 41 0.26
76 3 0.02
77 20 0.13
79 34 0.22
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (75 bp):
TACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCGAGGATACTCCAACCCCGTTAT
TTTGAGGGGA
Found at i:55676 original size:52 final size:50
Alignment explanation
Indices: 55591--55720 Score: 172
Period size: 52 Copynumber: 2.6 Consensus size: 50
55581 TACCTACATA
* * * * *
55591 TATCGATACATTGAAGAATGTATCAATATATTTGATTCAAAAACCCAGAATG
1 TATCGATACAATAAAGAATGTATCGATAGATTTGAGTC-AAAA-CCAGAATG
*
55643 TATCGATACAATAAAGAATGTATCGATAGATTTGAGTCAAAATCAGAATG
1 TATCGATACAATAAAGAATGTATCGATAGATTTGAGTCAAAACCAGAATG
55693 TATCGATACAATGAAA-AATGTATCGATA
1 TATCGATACAAT-AAAGAATGTATCGATA
55721 CATGTTTATT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
50 31 0.44
51 7 0.10
52 33 0.46
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (50 bp):
TATCGATACAATAAAGAATGTATCGATAGATTTGAGTCAAAACCAGAATG
Found at i:55713 original size:50 final size:52
Alignment explanation
Indices: 55591--55720 Score: 176
Period size: 50 Copynumber: 2.5 Consensus size: 52
55581 TACCTACATA
* * * * *
55591 TATCGATACATTGAAGAATGTATCAATATATTTGATTCAAAAACCCAGAATG
1 TATCGATACAATGAAAAATGTATCGATAGATTTGAGTCAAAAACCCAGAATG
*
55643 TATCGATACAAT-AAAGAATGTATCGATAGATTTGAGTC-AAAA-TCAGAATG
1 TATCGATACAATGAAA-AATGTATCGATAGATTTGAGTCAAAAACCCAGAATG
55693 TATCGATACAATGAAAAATGTATCGATA
1 TATCGATACAATGAAAAATGTATCGATA
55721 CATGTTTATT
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
50 31 0.44
51 9 0.13
52 30 0.43
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (52 bp):
TATCGATACAATGAAAAATGTATCGATAGATTTGAGTCAAAAACCCAGAATG
Found at i:55793 original size:20 final size:21
Alignment explanation
Indices: 55770--55813 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
55760 CTGTATCAAG
55770 ACATTCACTTA-TGTATTGAT
1 ACATTCACTTATTGTATTGAT
55790 ACATTCACTTATTGTATTGAT
1 ACATTCACTTATTGTATTGAT
55811 ACA
1 ACA
55814 AATTATTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (21 bp):
ACATTCACTTATTGTATTGAT
Found at i:57748 original size:18 final size:19
Alignment explanation
Indices: 57711--57754 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
57701 TTATAATTAA
*
57711 ATTTAAATAAAAATATATT
1 ATTTTAATAAAAATATATT
*
57730 ATTTTAATATAAA-ATATT
1 ATTTTAATAAAAATATATT
57748 ATTTTAA
1 ATTTTAA
57755 ATTAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTTAATAAAAATATATT
Found at i:58415 original size:18 final size:20
Alignment explanation
Indices: 58392--58431 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
58382 TTCAGTTATC
58392 TATTTAA-A-TTTAAAAATT
1 TATTTAATATTTTAAAAATT
*
58410 TATTTAATATTTTAAAGATT
1 TATTTAATATTTTAAAAATT
58430 TA
1 TA
58432 AGTAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 1 0.05
20 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTTAATATTTTAAAAATT
Found at i:58459 original size:13 final size:14
Alignment explanation
Indices: 58443--58479 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
58433 GTAAAATTAT
58443 TAAATTTAAA-AAA
1 TAAATTTAAATAAA
58456 TAAATTTAAATAAA
1 TAAATTTAAATAAA
*
58470 -AAAATTAAAT
1 TAAATTTAAAT
58480 TCATTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 19 0.86
14 3 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATTTAAATAAA
Found at i:58473 original size:18 final size:18
Alignment explanation
Indices: 58450--58496 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
58440 TATTAAATTT
58450 AAAAAATAAATTTAAATA
1 AAAAAATAAATTTAAATA
* *
58468 AAAAAATTAAA-TTCATTA
1 AAAAAA-TAAATTTAAATA
58486 AAAAAATAAAT
1 AAAAAATAAAT
58497 AAAATCTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAAATAAATTTAAATA
Found at i:58592 original size:24 final size:23
Alignment explanation
Indices: 58536--58596 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
58526 TACTTAACGT
* *
58536 ATTTTTAATTATATAATATATTA
1 ATTTTTATTTATACAATATATTA
58559 ATTTTATATTTATACACAT-TATATA
1 ATTTT-TATTTATACA-ATATAT-TA
58584 ATTTTTATTTATA
1 ATTTTTATTTATA
58597 TAAAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 5 0.15
24 19 0.58
25 9 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTTTTATTTATACAATATATTA
Found at i:58723 original size:15 final size:15
Alignment explanation
Indices: 58705--58754 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
58695 AAAATTAAAT
58705 TAAAAATTATTTTTA
1 TAAAAATTATTTTTA
*
58720 TAAAAATTA----AA
1 TAAAAATTATTTTTA
*
58731 TTAAAATTATTTTTA
1 TAAAAATTATTTTTA
58746 TAAAAATTA
1 TAAAAATTA
58755 AATTAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
11 9 0.33
15 18 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAAAAATTATTTTTA
Found at i:58724 original size:27 final size:27
Alignment explanation
Indices: 58689--58764 Score: 136
Period size: 26 Copynumber: 2.8 Consensus size: 27
58679 TTTTATTAAA
58689 TTATCAAAAATTAAATTAAAAATTATTT
1 TTAT-AAAAATTAAATTAAAAATTATTT
58717 TTATAAAAATTAAATT-AAAATTATTT
1 TTATAAAAATTAAATTAAAAATTATTT
58743 TTATAAAAATTAAATTAAAAAT
1 TTATAAAAATTAAATTAAAAAT
58765 AATAATATGA
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
26 26 0.55
27 17 0.36
28 4 0.09
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (27 bp):
TTATAAAAATTAAATTAAAAATTATTT
Found at i:59317 original size:23 final size:23
Alignment explanation
Indices: 59265--59318 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
59255 AAATAATTAT
*
59265 AAATATTAAGATTTTAATTTTAA
1 AAATATTAAGATATTAATTTTAA
** *
59288 ATTTATTAA-ATATTATTTTTTAA
1 AAATATTAAGATATTA-ATTTTAA
59311 AAATATTA
1 AAATATTA
59319 CATAATTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
AAATATTAAGATATTAATTTTAA
Found at i:63525 original size:13 final size:14
Alignment explanation
Indices: 63500--63531 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
63490 ATAGTTGGCT
63500 TTGACTATTGATTG
1 TTGACTATTGATTG
63514 TTGACT-TTGATTG
1 TTGACTATTGATTG
63527 TTGAC
1 TTGAC
63532 CATTTACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.19, C:0.09, G:0.22, T:0.50
Consensus pattern (14 bp):
TTGACTATTGATTG
Found at i:63530 original size:20 final size:20
Alignment explanation
Indices: 63486--63523 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
63476 CTCGATTTCG
*
63486 ATTGATAGTTGGCTTTGACT
1 ATTGATAGTTGACTTTGACT
*
63506 ATTGATTGTTGACTTTGA
1 ATTGATAGTTGACTTTGA
63524 TTGTTGACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.08, G:0.24, T:0.47
Consensus pattern (20 bp):
ATTGATAGTTGACTTTGACT
Found at i:69835 original size:49 final size:49
Alignment explanation
Indices: 69665--70327 Score: 332
Period size: 49 Copynumber: 14.2 Consensus size: 49
69655 TCGAAGATGC
* * ** * * *
69665 GAAGAATGACAATGTGCTGATTCAAGGCCAGTGACATTAGATTTAAAGAA
1 GAAG-ATGCCAATATGCTGATTCAAGGCCAACGATATTGGATTTAAAGAT
* ** ** **
69715 G-A-ATGCCAATGTGCTGAGACAAGGCCAACGATATTGGGCTTAGGGAT
1 GAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGATTTAAAGAT
*
69762 GTTAAAGATGCCAATATGCTGATTCAAGGCCAACGATATCGGATTTAAAGAT
1 G---AAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGATTTAAAGAT
* * ** *
69814 GAAGATGCTAATGTGCTGATTCAAGGCCAGTGACATTGG-TCTTAAAGAT
1 GAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGAT-TTAAAGAT
* * * * *
69863 GACGGTGCCAATATGCTGATTCAAGGCCAACAATATCGGACTTAAAGAT
1 GAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGATTTAAAGAT
* * *
69912 GAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG-------GCT
1 GAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGATTTAAAGAT
* ** * *
69954 --TG-TGCCAATATGCTGATTCAAGGCCAGTGACATTAG-TCTTAAAG--
1 GAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGAT-TTAAAGAT
* *
69998 GCAAGATGCCAATATG-TCGATTCAAAGCCAACGATATTGG-------GCT
1 G-AAGATGCCAATATGCT-GATTCAAGGCCAACGATATTGGATTTAAAGAT
* * * ***
70041 ---TATGCCAATGTACTGATTCAAGGCCAGTAATATTGG-TCTTAAAGAT
1 GAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGAT-TTAAAGAT
* * * ** * *
70087 GCCAG-TGCCAATATGCTGATTCAAGGTCAGCGATACCGAACTTAAAGAT
1 G-AAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGATTTAAAGAT
* * ** * *
70136 GAAGATGCCAATGTGCTGATTCAAGGTCGGCGACATTGGACTT-AA-A-
1 GAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGATTTAAAGAT
* * *
70182 G--G-TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
1 GAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGATTTAAAGAT
** *** * *
70228 GAAGATGCCAATGCGCTGATTCAAGGCTGGCGACATTGGACTT-AA-A-
1 GAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGATTTAAAGAT
* * *
70274 G--G-TGCCAATATGCTAATTCAAGGCCAACGATATTGGACTT--AGAA
1 GAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGATTTAAAGAT
70318 GAAGATGCCA
1 GAAGATGCCA
70328 CCAACTTGTG
Statistics
Matches: 477, Mismatches: 90, Indels: 95
0.72 0.14 0.14
Matches are distributed among these distances:
39 58 0.12
40 2 0.00
41 1 0.00
42 3 0.01
43 67 0.14
44 5 0.01
45 1 0.00
46 7 0.01
47 43 0.09
48 35 0.07
49 215 0.45
50 1 0.00
51 1 0.00
52 38 0.08
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
GAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGATTTAAAGAT
Found at i:69836 original size:148 final size:146
Alignment explanation
Indices: 69675--69947 Score: 370
Period size: 148 Copynumber: 1.8 Consensus size: 146
69665 GAAGAATGAC
*
69675 AATGTGCTGATTCAAGGCCAGTGACATTAGAT-TTAAAGAAGA-ATGCCAATGTGCTGAGACAAG
1 AATGTGCTGATTCAAGGCCAGTGACATT-GATCTTAAAGAAGACATGCCAATATGCTGAGACAAG
* * * **
69738 GCCAACGATATTGGGCTTAGGGATGTTAAAGATGCCAATATGCTGATTCAAGGCCAACGATATCG
65 GCCAACAATATCGGACTTAAAGATG---AAGATGCCAATATGCTGATTCAAGGCCAACGATATCG
69803 GATTTAAAGATGAAGATGCT
127 GATTTAAAGATGAAGATGCT
* * * **
69823 AATGTGCTGATTCAAGGCCAGTGACATTGGTCTTAAAGATGACGGTGCCAATATGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGTGACATTGATCTTAAAGAAGAC-ATGCCAATATGCTGAGACAAG
* *
69888 GCCAACAATATCGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATAT
65 GCCAACAATATCGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAACGATAT
69948 TGGGCTTGTG
Statistics
Matches: 109, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
147 35 0.32
148 37 0.34
150 37 0.34
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (146 bp):
AATGTGCTGATTCAAGGCCAGTGACATTGATCTTAAAGAAGACATGCCAATATGCTGAGACAAGG
CCAACAATATCGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAACGATATCGGATT
TAAAGATGAAGATGCT
Found at i:70047 original size:87 final size:87
Alignment explanation
Indices: 69868--70110 Score: 303
Period size: 87 Copynumber: 2.8 Consensus size: 87
69858 AAGATGACGG
** * *
69868 TGCCAATATGCTGATTCAAGGCCAACAATATCGGACTTAAAGATG-AAGGTGCCAATATGCTGAT
1 TGCCAATATGCTGATTCAAGGCCAGTAATATTGGTCTTAAAGA-GCAA-GTGCCAATATGCTGAT
* * *
69932 TCAAGGCCAGCGATATTGGGCTTG
64 TCAAAGCCAACGATATTGGGCTTA
* * *
69956 TGCCAATATGCTGATTCAAGGCCAGTGACATTAGTCTTAAAG-GCAAGATGCCAATATG-TCGAT
1 TGCCAATATGCTGATTCAAGGCCAGTAATATTGGTCTTAAAGAGCAAG-TGCCAATATGCT-GAT
70019 TCAAAGCCAACGATATTGGGCTTA
64 TCAAAGCCAACGATATTGGGCTTA
* * *
70043 TGCCAATGTACTGATTCAAGGCCAGTAATATTGGTCTTAAAGATGCCAGTGCCAATATGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGTAATATTGGTCTTAAAGA-GCAAGTGCCAATATGCTGATT
70108 CAA
65 CAA
70111 GGTCAGCGAT
Statistics
Matches: 133, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
86 3 0.02
87 73 0.55
88 52 0.39
89 5 0.04
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (87 bp):
TGCCAATATGCTGATTCAAGGCCAGTAATATTGGTCTTAAAGAGCAAGTGCCAATATGCTGATTC
AAAGCCAACGATATTGGGCTTA
Found at i:70227 original size:92 final size:92
Alignment explanation
Indices: 70091--70327 Score: 363
Period size: 92 Copynumber: 2.6 Consensus size: 92
70081 AAAGATGCCA
* ** * *
70091 GTGCCAATATGCTGATTCAAGGTCAGCGATACCGAACTTAAAGATGAAGATGCCAATGTGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGCGCTGAT
70156 TCAAGG-TCGGCGACATTGGACTTAAAG
66 TCAAGGCT-GGCGACATTGGACTTAAAG
*
70183 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGATGCCAATGCGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGCGCTGAT
70248 TCAAGGCTGGCGACATTGGACTTAAAG
66 TCAAGGCTGGCGACATTGGACTTAAAG
* * *
70275 GTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTT--AGAAGAAGATGCCA
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCA
70328 CCAACTTGTG
Statistics
Matches: 134, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
90 13 0.10
92 120 0.90
93 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (92 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGCGCTGAT
TCAAGGCTGGCGACATTGGACTTAAAG
Found at i:70368 original size:29 final size:29
Alignment explanation
Indices: 70336--70641 Score: 326
Period size: 29 Copynumber: 10.7 Consensus size: 29
70326 CACCAACTTG
*
70336 TGTGGGCTTTTG-AAGGTTGCCACTTGACT
1 TGTGGGCTTTTGAAAGGGTGCCAC-TGACT
* *
70365 TGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGGTGCCACTGACT
* * *
70394 TATGGG-TTTTGAAAAGGGTACCATTGACT
1 TGTGGGCTTTTG-AAAGGGTGCCACTGACT
*
70423 TATGGGC-TTTGAAAGGGGTGCCA-TCGACT
1 TGTGGGCTTTTGAAA-GGGTGCCACT-GACT
*
70452 TGTGGGC-TTTGAAAGGGGTGCCACCGACT
1 TGTGGGCTTTTGAAA-GGGTGCCACTGACT
*
70481 TGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGGTGCCACTGACT
* * * * *
70509 TGTGGGCTTTGGAAAAGATGCCACTAAGT
1 TGTGGGCTTTTGAAAGGGTGCCACTGACT
70538 TGTGGGC-TTTGAAAGGGGTGCCACTGACT
1 TGTGGGCTTTTGAAA-GGGTGCCACTGACT
*
70567 TGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGGTGCCACTGACT
* *
70595 TGTGGGC-TTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGGTGCCACTGACT
*
70623 TGTGGACTTTTG-AAGGGTG
1 TGTGGGCTTTTGAAAGGGTG
70642 AGGAATGTCT
Statistics
Matches: 237, Mismatches: 28, Indels: 25
0.82 0.10 0.09
Matches are distributed among these distances:
27 4 0.02
28 83 0.35
29 133 0.56
30 17 0.07
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAGGGTGCCACTGACT
Found at i:70636 original size:86 final size:85
Alignment explanation
Indices: 70336--70632 Score: 359
Period size: 86 Copynumber: 3.4 Consensus size: 85
70326 CACCAACTTG
* * * * *
70336 TGTGGGCTTTTG-AAGGTTGCCACTTGACTTGTGGGCTTTTGAAA-AGATGCCACTGACTTATGG
1 TGTGGGC-TTTGAAAAGATGCCAC-TGACTTGTGGGC-TTTGAAAGGGGTGCCACTGACTTGTGG
* * *
70399 G-TTTTGAAAAGGGTACCATTGACT
63 GCTTTTG--AAGGTTGCCACTGACT
* * * *
70423 TATGGGCTTTGAAAGGGGTGCCA-TCGACTTGTGGGCTTTGAAAGGGGTGCCACCGACTTGTGGG
1 TGTGGGCTTTGAAA-AGATGCCACT-GACTTGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGG
70487 CTTTTGAAGGTTGCCACTGACT
64 CTTTTGAAGGTTGCCACTGACT
* *
70509 TGTGGGCTTTGGAAAAGATGCCACTAAGTTGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGC
1 TGTGGGCTTT-GAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGC
70574 TTTTGAAGGTTGCCACTGACT
65 TTTTGAAGGTTGCCACTGACT
*
70595 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGACTTT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTT
70633 TGAAGGGTGA
Statistics
Matches: 185, Mismatches: 18, Indels: 16
0.84 0.08 0.07
Matches are distributed among these distances:
85 25 0.14
86 108 0.58
87 40 0.22
88 12 0.06
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (85 bp):
TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCT
TTTGAAGGTTGCCACTGACT
Found at i:72093 original size:19 final size:18
Alignment explanation
Indices: 72069--72135 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
72059 ATCCGGACCC
72069 TTTTTGTTATTGTTGTTTT
1 TTTTTGTT-TTGTTGTTTT
*
72088 TTTTTGTTTTATTTGTTTT
1 TTTTTGTTTT-GTTGTTTT
* * *
72107 GTTTTGTTTTTTTGTTGT
1 TTTTTGTTTTGTTGTTTT
72125 TTTTT-TTTTGT
1 TTTTTGTTTTGT
72136 GCGGAGGATG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
17 5 0.12
18 13 0.31
19 24 0.57
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (18 bp):
TTTTTGTTTTGTTGTTTT
Found at i:72096 original size:10 final size:10
Alignment explanation
Indices: 72081--72132 Score: 70
Period size: 10 Copynumber: 5.2 Consensus size: 10
72071 TTTGTTATTG
72081 TTGTTTTTTT
1 TTGTTTTTTT
*
72091 TTG-TTTTAT
1 TTGTTTTTTT
*
72100 TTGTTTTGTT
1 TTGTTTTTTT
72110 TTGTTTTTTT
1 TTGTTTTTTT
72120 GTTGTTTTTTT
1 -TTGTTTTTTT
72131 TT
1 TT
72133 TGTGCGGAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 8 0.22
10 18 0.50
11 10 0.28
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85
Consensus pattern (10 bp):
TTGTTTTTTT
Found at i:72097 original size:5 final size:5
Alignment explanation
Indices: 72081--72131 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
72071 TTTGTTATTG
* * *
72081 TTGTT TTTTT TTGTT TT-AT TTGTT TTGTT TTGTT TTTTT GTTGTT TT-TT
1 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT -TTGTT TTGTT
72130 TT
1 TT
72132 TTGTGCGGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
4 7 0.18
5 27 0.71
6 4 0.11
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.84
Consensus pattern (5 bp):
TTGTT
Found at i:72097 original size:9 final size:9
Alignment explanation
Indices: 72069--72131 Score: 63
Period size: 9 Copynumber: 6.6 Consensus size: 9
72059 ATCCGGACCC
*
72069 TTTTTGTTA
1 TTTTTGTTT
*
72078 TTGTTGTTTT
1 TTTTTG-TTT
72088 TTTTTGTTT
1 TTTTTGTTT
*
72097 TATTTGTTT
1 TTTTTGTTT
72106 TGTTTTGTTTT
1 T-TTTTG-TTT
72117 TTTGTTGTTT
1 TTT-TTGTTT
72127 TTTTT
1 TTTTT
72132 TTGTGCGGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
9 19 0.42
10 19 0.42
11 7 0.16
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.83
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:72106 original size:14 final size:13
Alignment explanation
Indices: 72078--72132 Score: 69
Period size: 13 Copynumber: 4.2 Consensus size: 13
72068 CTTTTTGTTA
72078 TTGTTGTTTTTTT
1 TTGTTGTTTTTTT
72091 TTGTT-TTATTTGTT
1 TTGTTGTT-TTT-TT
72105 TTGTT-TTGTTTTT
1 TTGTTGTT-TTTTT
72118 TTGTTGTTTTTTT
1 TTGTTGTTTTTTT
72131 TT
1 TT
72133 TGTGCGGAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
12 2 0.05
13 22 0.58
14 14 0.37
ACGTcount: A:0.02, C:0.00, G:0.15, T:0.84
Consensus pattern (13 bp):
TTGTTGTTTTTTT
Found at i:72116 original size:27 final size:27
Alignment explanation
Indices: 72069--72135 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 27
72059 ATCCGGACCC
72069 TTTTTGTTATTGTTGTTTTTTTTTGTT-
1 TTTTTGTT-TTGTTGTTTTTTTTTGTTG
72096 TTATTTGTTTTGTT-TTGTTTTTTTGTTG
1 TT-TTTGTTTTGTTGTT-TTTTTTTGTTG
*
72124 TTTTTTTTTTGT
1 TTTTTGTTTTGT
72136 GCGGAGGATG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
26 2 0.06
27 26 0.72
28 8 0.22
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (27 bp):
TTTTTGTTTTGTTGTTTTTTTTTGTTG
Found at i:72133 original size:14 final size:13
Alignment explanation
Indices: 72078--72135 Score: 71
Period size: 14 Copynumber: 4.3 Consensus size: 13
72068 CTTTTTGTTA
*
72078 TTGTTGTTTTTTT
1 TTGTTTTTTTTTT
*
72091 TTGTTTTATTTGTT
1 TTGTTTT-TTTTTT
*
72105 TTGTTTTGTTTTT
1 TTGTTTTTTTTTT
72118 TTGTTGTTTTTTTT
1 TTGTT-TTTTTTTT
72132 TTGT
1 TTGT
72136 GCGGAGGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
13 15 0.39
14 23 0.61
ACGTcount: A:0.02, C:0.00, G:0.16, T:0.83
Consensus pattern (13 bp):
TTGTTTTTTTTTT
Found at i:88102 original size:51 final size:51
Alignment explanation
Indices: 87962--88109 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
87952 CGAAATATGA
87962 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* * *
88014 AAATTTGCCTGCATATATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
88066 -AATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
88110 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
50 2 0.02
51 36 0.42
52 46 0.53
53 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:88116 original size:13 final size:13
Alignment explanation
Indices: 88098--88122 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88088 CAAAGATCAG
88098 TGTATCGATACAA
1 TGTATCGATACAA
88111 TGTATCGATACA
1 TGTATCGATACA
88123 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Done.