Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013415.1 Kokia drynarioides strain JFW-HI SEQ_128440, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 126813
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:170 original size:31 final size:31
Alignment explanation
Indices: 129--248 Score: 84
Period size: 31 Copynumber: 4.0 Consensus size: 31
119 AAAAAAGATT
*
129 AGGTATCAAATTAGAAAAAAGAGTCAAGTTC
1 AGGTACCAAATTAGAAAAAAGAGTCAAGTTC
* **** * * *
160 AGGTACCAAATT-G-GACCCTA-TAAAATTT
1 AGGTACCAAATTAGAAAAAAGAGTCAAGTTC
* * * *
188 AAGTACCAACTTAAAAAAAAGTGTCAAGTTC
1 AGGTACCAAATTAGAAAAAAGAGTCAAGTTC
* *
219 AGGTACCAAATTAGGAAAAAGTGTCAAGTT
1 AGGTACCAAATTAGAAAAAAGAGTCAAGTT
249 TGAATACCAA
Statistics
Matches: 61, Mismatches: 25, Indels: 6
0.66 0.27 0.07
Matches are distributed among these distances:
28 15 0.25
29 2 0.03
30 2 0.03
31 42 0.69
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.24
Consensus pattern (31 bp):
AGGTACCAAATTAGAAAAAAGAGTCAAGTTC
Found at i:238 original size:90 final size:90
Alignment explanation
Indices: 129--319 Score: 228
Period size: 90 Copynumber: 2.1 Consensus size: 90
119 AAAAAAGATT
* * *
129 AGGTATCAAATTAGAAAAAAGAGTCAAGTTCAG-GTACCAAATTGGACCCTATAAAAT-TT-AAG
1 AGGTATCAAATTAGAAAAAAGAGTCAAGTT-AGAATACCAAATTGGA--CAAAAAAATATTCAAG
* *
191 TACCAACTTAA-AAAAAAGTGTCAAGTTC
63 TACCAAATTAAGAAAAAA-TGTCAAATTC
* * * *
219 AGGTACCAAATTAGGAAAAAGTGTCAAGTTTGAATACCAAATTGGACAAAAAAATATTCAAGTAC
1 AGGTATCAAATTAGAAAAAAGAGTCAAGTTAGAATACCAAATTGGACAAAAAAATATTCAAGTAC
284 CAAATTAAGAAAAAATGTCAAATTC
66 CAAATTAAGAAAAAATGTCAAATTC
*
309 AAGTATCAAAT
1 AGGTATCAAAT
320 ATTGTACTAA
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
88 7 0.08
89 3 0.03
90 70 0.81
91 6 0.07
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (90 bp):
AGGTATCAAATTAGAAAAAAGAGTCAAGTTAGAATACCAAATTGGACAAAAAAATATTCAAGTAC
CAAATTAAGAAAAAATGTCAAATTC
Found at i:312 original size:31 final size:31
Alignment explanation
Indices: 182--319 Score: 101
Period size: 31 Copynumber: 4.5 Consensus size: 31
172 GGACCCTATA
* *
182 AAATTTAAGTACCAACTTAA-AAAAAAGTGTC
1 AAATTCAAGTACCAAATTAAGAAAAAA-TGTC
* * * *
213 AAGTTCAGGTACCAAATTAGGAAAAAGTGTC
1 AAATTCAAGTACCAAATTAAGAAAAAATGTC
* * *
244 AAGTTTGAA-TACCAAATT-GGACAAAAA----
1 AA-ATTCAAGTACCAAATTAAGA-AAAAATGTC
271 AATATTCAAGTACCAAATTAAGAAAAAATGTC
1 AA-ATTCAAGTACCAAATTAAGAAAAAATGTC
*
303 AAATTCAAGTATCAAAT
1 AAATTCAAGTACCAAAT
320 ATTGTACTAA
Statistics
Matches: 83, Mismatches: 15, Indels: 18
0.72 0.13 0.16
Matches are distributed among these distances:
27 6 0.07
28 14 0.17
29 2 0.02
30 3 0.04
31 48 0.58
32 10 0.12
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (31 bp):
AAATTCAAGTACCAAATTAAGAAAAAATGTC
Found at i:4738 original size:22 final size:22
Alignment explanation
Indices: 4688--4738 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
4678 ACAATAAAAT
*
4688 AGCAATATAGTGGCAAAACGAC
1 AGCAAAATAGTGGCAAAACGAC
4710 A-CAAAAATAGTGGCAAAAC-AGC
1 AGC-AAAATAGTGGCAAAACGA-C
4732 AGCAAAA
1 AGCAAAA
4739 ACAGTGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.08
22 22 0.88
23 1 0.04
ACGTcount: A:0.53, C:0.18, G:0.20, T:0.10
Consensus pattern (22 bp):
AGCAAAATAGTGGCAAAACGAC
Found at i:7789 original size:20 final size:20
Alignment explanation
Indices: 7753--7790 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
7743 TTCAGGGGTG
*
7753 TAAAATATATAGAAAATTCT
1 TAAAATATATACAAAATTCT
7773 TAAAAT-TATACATAAATT
1 TAAAATATATACA-AAATT
7791 TTGATTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
TAAAATATATACAAAATTCT
Found at i:8407 original size:22 final size:23
Alignment explanation
Indices: 8360--8406 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
8350 TGATGTATAT
8360 AAATATAAAATTTTAATAATTTA
1 AAATATAAAATTTTAATAATTTA
*
8383 AAAT-TAATATTTTAAT-ATTTA
1 AAATATAAAATTTTAATAATTTA
8404 AAA
1 AAA
8407 AGGTGAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.35
22 11 0.48
23 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATATAAAATTTTAATAATTTA
Found at i:16288 original size:27 final size:27
Alignment explanation
Indices: 16236--16289 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
16226 AACTAGTAAA
* *
16236 ATTTATGATTTTTCGTTTTTCTTGTTT
1 ATTTATGATTTTTCATTTTACTTGTTT
*
16263 ATTTATTATTTTT-ATTTTACTGTGTTT
1 ATTTATGATTTTTCATTTTACT-TGTTT
16290 TATTAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.70
Consensus pattern (27 bp):
ATTTATGATTTTTCATTTTACTTGTTT
Found at i:23320 original size:16 final size:16
Alignment explanation
Indices: 23291--23324 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23281 ATATTCTTAC
*
23291 TAAAATATTATAATAT
1 TAAAAAATTATAATAT
*
23307 TAAAAAATTTTAATAT
1 TAAAAAATTATAATAT
23323 TA
1 TA
23325 TTTAAATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAAAATTATAATAT
Found at i:31474 original size:20 final size:20
Alignment explanation
Indices: 31449--31492 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
31439 TCAAGCCTTG
31449 TTAACTAAATTATATATTAT
1 TTAACTAAATTATATATTAT
31469 TTAACTAAATTATATATTAT
1 TTAACTAAATTATATATTAT
31489 TTAA
1 TTAA
31493 ATTGAACTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAACTAAATTATATATTAT
Found at i:31486 original size:81 final size:81
Alignment explanation
Indices: 31388--31553 Score: 323
Period size: 81 Copynumber: 2.0 Consensus size: 81
31378 GCAAGCCTTG
*
31388 TTAACTAAATTATATATTATTTAAATTGAATTCGCTTCCACCATATTCCATTCAAGCCTTGTTAA
1 TTAACTAAATTATATATTATTTAAATTGAACTCGCTTCCACCATATTCCATTCAAGCCTTGTTAA
31453 CTAAATTATATATTAT
66 CTAAATTATATATTAT
31469 TTAACTAAATTATATATTATTTAAATTGAACTCGCTTCCACCATATTCCATTCAAGCCTTGTTAA
1 TTAACTAAATTATATATTATTTAAATTGAACTCGCTTCCACCATATTCCATTCAAGCCTTGTTAA
31534 CTAAATTATATATTAT
66 CTAAATTATATATTAT
31550 TTAA
1 TTAA
31554 ATTTAATTAA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (81 bp):
TTAACTAAATTATATATTATTTAAATTGAACTCGCTTCCACCATATTCCATTCAAGCCTTGTTAA
CTAAATTATATATTAT
Found at i:39113 original size:15 final size:15
Alignment explanation
Indices: 39093--39126 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
39083 AAACGATGTT
*
39093 AATAAATAATAAATA
1 AATAAACAATAAATA
39108 AATAAACAATAAATA
1 AATAAACAATAAATA
39123 AATA
1 AATA
39127 TATGCACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAAACAATAAATA
Found at i:43474 original size:21 final size:20
Alignment explanation
Indices: 43448--43492 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
43438 TATATGAAAT
* *
43448 GTCACATTAATGTCGTTAACA
1 GTCACATCAACGTCG-TAACA
*
43469 GTCACATCAACGTTGTAACA
1 GTCACATCAACGTCGTAACA
43489 GTCA
1 GTCA
43493 ATATTAGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (20 bp):
GTCACATCAACGTCGTAACA
Found at i:48826 original size:115 final size:115
Alignment explanation
Indices: 48700--48929 Score: 460
Period size: 115 Copynumber: 2.0 Consensus size: 115
48690 GAAAGCAGTT
48700 TTAGATCTTAATAAATGATTTTTTGTTAGAGCTTACATGTTTTCTTTGCATTTTGTGTATTATTT
1 TTAGATCTTAATAAATGATTTTTTGTTAGAGCTTACATGTTTTCTTTGCATTTTGTGTATTATTT
48765 GATAATAAAAAGAACAATTCTTTTAGGATTAAAAATGTTTAGGGTTACTA
66 GATAATAAAAAGAACAATTCTTTTAGGATTAAAAATGTTTAGGGTTACTA
48815 TTAGATCTTAATAAATGATTTTTTGTTAGAGCTTACATGTTTTCTTTGCATTTTGTGTATTATTT
1 TTAGATCTTAATAAATGATTTTTTGTTAGAGCTTACATGTTTTCTTTGCATTTTGTGTATTATTT
48880 GATAATAAAAAGAACAATTCTTTTAGGATTAAAAATGTTTAGGGTTACTA
66 GATAATAAAAAGAACAATTCTTTTAGGATTAAAAATGTTTAGGGTTACTA
48930 AACAACCTGG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 115 1.00
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (115 bp):
TTAGATCTTAATAAATGATTTTTTGTTAGAGCTTACATGTTTTCTTTGCATTTTGTGTATTATTT
GATAATAAAAAGAACAATTCTTTTAGGATTAAAAATGTTTAGGGTTACTA
Found at i:51974 original size:27 final size:27
Alignment explanation
Indices: 51933--52000 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
51923 ATATTTGGAG
*
51933 ATATT-TTTCATTAAT-TAATTAATTAA
1 ATATTATTTTATTAATAT-ATTAATTAA
* *
51959 ATATTATTTTATTAATATTTTACTTAA
1 ATATTATTTTATTAATATATTAATTAA
51986 ATATTTATTATTATT
1 ATA-TTATT-TTATT
52001 TTATTTAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 5 0.14
27 19 0.54
28 6 0.17
29 5 0.14
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (27 bp):
ATATTATTTTATTAATATATTAATTAA
Found at i:51990 original size:13 final size:11
Alignment explanation
Indices: 51963--52005 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
51953 AATTAAATAT
51963 TATTTTATTAA
1 TATTTTATTAA
51974 TATTTTACTTAA
1 TATTTTA-TTAA
*
51986 -ATATTTATTAT
1 TAT-TTTATTAA
51997 TATTTTATT
1 TATTTTATT
52006 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:54508 original size:24 final size:24
Alignment explanation
Indices: 54474--54541 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
54464 ACTTTGACTT
*
54474 AAACAACTAAACAGAGTTTAATTG
1 AAACAACTAAACAGAGTTTAATTA
*
54498 AAACAAATAAACAGAGTTTAATTA
1 AAACAACTAAACAGAGTTTAATTA
54522 AAACAACTAAACAGAGTTTA
1 AAACAACTAAACAGAGTTTA
54542 TCTGAAAGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.24
Consensus pattern (24 bp):
AAACAACTAAACAGAGTTTAATTA
Found at i:56516 original size:24 final size:24
Alignment explanation
Indices: 56489--56539 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
56479 AATTTGACTC
* *
56489 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
56513 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
56537 AAA
1 AAA
56540 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:60382 original size:16 final size:16
Alignment explanation
Indices: 60363--60393 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60353 TACATGCGAA
60363 AAATAATAAAATAAAT
1 AAATAATAAAATAAAT
*
60379 AAATAATAAATTAAA
1 AAATAATAAAATAAA
60394 ATTTTAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAATAAAATAAAT
Found at i:65834 original size:6 final size:6
Alignment explanation
Indices: 65823--65858 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
65813 AATGCTCTTC
65823 CCATCA CCATCA CCATCA CCATCA CCATCA CCATCA
1 CCATCA CCATCA CCATCA CCATCA CCATCA CCATCA
65859 TCATGACCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (6 bp):
CCATCA
Found at i:68014 original size:15 final size:15
Alignment explanation
Indices: 67960--68016 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
67950 TTTATACTAC
*
67960 AAAACATTTATTATT
1 AAAATATTTATTATT
* *
67975 AATATATTTATAAATGT
1 AAAATATTTAT-TAT-T
67992 AAAAAATATTTATTATT
1 --AAAATATTTATTATT
68009 AAAATATT
1 AAAATATT
68017 AATATTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.30
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:69712 original size:25 final size:23
Alignment explanation
Indices: 69673--69718 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
69663 TTATGTGTCG
*
69673 GTTAATTAGTTGAGTTGAATTTA
1 GTTAATTAGTTGAGTTAAATTTA
69696 GTTAATTAAAGTTGAGTTAAATT
1 GTTAATT--AGTTGAGTTAAATT
69719 ATTTACTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
25 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.46
Consensus pattern (23 bp):
GTTAATTAGTTGAGTTAAATTTA
Found at i:75317 original size:42 final size:42
Alignment explanation
Indices: 75258--75341 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
75248 TTTAGTCCCT
75258 ACAAAATAAAAGGATCACAAATAGCCCAAATTAATAGAATCA
1 ACAAAATAAAAGGATCACAAATAGCCCAAATTAATAGAATCA
75300 ACAAAATAAAAGGATCACAAATAGCCCAAATTAATAGAATCA
1 ACAAAATAAAAGGATCACAAATAGCCCAAATTAATAGAATCA
75342 TACTCACAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.57, C:0.17, G:0.10, T:0.17
Consensus pattern (42 bp):
ACAAAATAAAAGGATCACAAATAGCCCAAATTAATAGAATCA
Found at i:76923 original size:27 final size:27
Alignment explanation
Indices: 76883--76937 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
76873 AGTGTTTGTT
*
76883 GCTGCTGCAAAATGTTCCCAAAAACAG
1 GCTGCTACAAAATGTTCCCAAAAACAG
* *
76910 GCTGCTACAGAATGTTTCCAAAAACAG
1 GCTGCTACAAAATGTTCCCAAAAACAG
76937 G
1 G
76938 TTGCATGCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (27 bp):
GCTGCTACAAAATGTTCCCAAAAACAG
Found at i:80537 original size:68 final size:67
Alignment explanation
Indices: 80428--80562 Score: 184
Period size: 68 Copynumber: 2.0 Consensus size: 67
80418 TGGGGGAGAA
* * *
80428 TATTTAGCTTACGGGCTTTGCACTATGTGCATCTTGCGTGTTATCAGTTTGTAATAGCTCTTATG
1 TATTTAGCCTACGGGCTTTGCACTATGTGCATCTTGCGTGTTATCAG-TTGGAATAACTCTTATG
80493 AGC
65 AGC
* *
80496 TATTTAGCCTATGGGCTTTGCA-TCATGTGCAT-TTGGTGTGTTATCAGTTGGAATAACTCTTAT
1 TATTTAGCCTACGGGCTTTGCACT-ATGTGCATCTT-GCGTGTTATCAGTTGGAATAACTCTTAT
80559 GAGC
64 GAGC
80563 AATCTGGTGT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
67 21 0.35
68 39 0.65
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (67 bp):
TATTTAGCCTACGGGCTTTGCACTATGTGCATCTTGCGTGTTATCAGTTGGAATAACTCTTATGA
GC
Found at i:80580 original size:38 final size:37
Alignment explanation
Indices: 80529--80601 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 37
80519 CATGTGCATT
80529 TGGTGTGTTATCAGTTGGAATAACTCTTATGAGCAATC
1 TGGTGTGTTATCAGTTGGAA-AACTCTTATGAGCAATC
* *
80567 TGGTGTGTTATCAGTTGTAAAGCTCTTATGAGCAA
1 TGGTGTGTTATCAGTTGGAAAACTCTTATGAGCAA
80602 ATTGTCATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (37 bp):
TGGTGTGTTATCAGTTGGAAAACTCTTATGAGCAATC
Found at i:85185 original size:40 final size:39
Alignment explanation
Indices: 85127--85223 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 39
85117 GAAAACGTCA
*
85127 CAAAAGGTAAAGTC-ATAGC-AACGTTTTTCTATAAAAGCCG
1 CAAAAGGTAAAG-CAATAGCGAAC-TTTTTC-ATAAAAGACG
* * *
85167 CAAAAAGTAAAGCAATAGCGGCACTTTTTCATAAACGACG
1 CAAAAGGTAAAGCAATAGC-GAACTTTTTCATAAAAGACG
85207 CAAAAGGTAAAGCAATA
1 CAAAAGGTAAAGCAATA
85224 ACAGCATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
39 1 0.02
40 40 0.82
41 6 0.12
42 2 0.04
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.21
Consensus pattern (39 bp):
CAAAAGGTAAAGCAATAGCGAACTTTTTCATAAAAGACG
Found at i:85293 original size:41 final size:41
Alignment explanation
Indices: 85240--85552 Score: 337
Period size: 41 Copynumber: 7.7 Consensus size: 41
85230 TTTATAGAAA
* * * * *
85240 AAACGCCACTAAAGGTCAGATCATTAGCGACGCCTCCACAT
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCACAT
* * ***
85281 AAATGCCGCTAAAGGTCGGAGCA-TAGCGGCG-TTT-ATGGG
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCA-CAT
* * *
85320 AAAGCGCCGCTAAAGGTCAAAGCACTA-CTGGCGCTTTTACAT
1 AAA-CGCCGCTAAAGGTCAGAGCATTAGC-GGCGCTTTCACAT
*
85362 AAACGCCGCTAAAGGTTAGAGCATTAGCGGCGCTTTCACAT
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCACAT
* **
85403 AAACGCCGCTAAAGGTCAAATTATTAGCGGCGCTTTCACAT
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCACAT
*
85444 AAACGCTGCTAAAGGTCAGAGCATTAGCGGCGCTTTCACAT
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCACAT
** ** * *
85485 AAACGTAGCTAAAGGTCAGAGCATTAGCGATGCTTCCAAAT
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCACAT
* *
85526 AAACACCGTTAAAGGTCAGAGCATTAG
1 AAACGCCGCTAAAGGTCAGAGCATTAG
85553 TGGCACTTAT
Statistics
Matches: 227, Mismatches: 38, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
38 1 0.00
39 4 0.02
40 25 0.11
41 189 0.83
42 7 0.03
43 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (41 bp):
AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTCACAT
Found at i:85580 original size:123 final size:123
Alignment explanation
Indices: 85240--85587 Score: 373
Period size: 123 Copynumber: 2.8 Consensus size: 123
85230 TTTATAGAAA
* * * *
85240 AAACGCCA-CTAAAGGTCAGATCATTAGCGACGCCTCCACATAAATGCCGCTAAAGGTCGGAGCA
1 AAACG-CAGCTAAAGGTCAGAGCATTAGCGACGCTTCCACATAAACGCCGCTAAAGGTCAGAGCA
* * * * *
85304 -TAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAAAGCACTACTGGCGCTTTTACAT
65 TTAGCGGCGCTTATGGAAAAGCGCTGCTAAAGGTCAGAGCACTACTGGCGCTTTCACAT
* * * * * **
85362 AAACGCCGCTAAAGGTTAGAGCATTAGCGGCGCTTTCACATAAACGCCGCTAAAGGTCAAATTAT
1 AAACGCAGCTAAAGGTCAGAGCATTAGCGACGCTTCCACATAAACGCCGCTAAAGGTCAGAGCAT
* * *
85427 TAGCGGCGCTT-T-CACATAAACGCTGCTAAAGGTCAGAGCATTAGC-GGCGCTTTCACAT
66 TAGCGGCGCTTATGGA-A-AAGCGCTGCTAAAGGTCAGAGCACTA-CTGGCGCTTTCACAT
* * * * *
85485 AAACGTAGCTAAAGGTCAGAGCATTAGCGATGCTTCCAAATAAACACCGTTAAAGGTCAGAGCAT
1 AAACGCAGCTAAAGGTCAGAGCATTAGCGACGCTTCCACATAAACGCCGCTAAAGGTCAGAGCAT
* * * *
85550 TAGTGGCACTTATGGAAAAGCACTGTTAAAGGTCAGAG
66 TAGCGGCGCTTATGGAAAAGCGCTGCTAAAGGTCAGAG
85588 TAATAACGGC
Statistics
Matches: 182, Mismatches: 37, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
121 1 0.01
122 53 0.29
123 124 0.68
124 3 0.02
125 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (123 bp):
AAACGCAGCTAAAGGTCAGAGCATTAGCGACGCTTCCACATAAACGCCGCTAAAGGTCAGAGCAT
TAGCGGCGCTTATGGAAAAGCGCTGCTAAAGGTCAGAGCACTACTGGCGCTTTCACAT
Found at i:86393 original size:25 final size:25
Alignment explanation
Indices: 86358--86405 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
86348 GGATGTATCT
86358 TATAGAAAGGTGCTAATTAATTTCC
1 TATAGAAAGGTGCTAATTAATTTCC
* *
86383 TATAGAGAGGTGTTAATTAATTT
1 TATAGAAAGGTGCTAATTAATTT
86406 GTGAAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (25 bp):
TATAGAAAGGTGCTAATTAATTTCC
Found at i:89864 original size:42 final size:43
Alignment explanation
Indices: 89693--89876 Score: 192
Period size: 43 Copynumber: 4.3 Consensus size: 43
89683 ATCTATTAAT
* * * * *
89693 TTTAGCGGCATTTGTGGGATAAA-CACCGTTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGA-AAAGCGCCGCTAAAGATCACGTTC
*
89736 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGATCACGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCACGTTC
* * * * *
89779 TTTAGCGGTGTTTGTGGGGAAAGTGCCGCTAATGACCACGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCACGTTC
* * * * *
89822 TTTAGTGGCGTTAGT-GAAAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCACGTTC
*
89864 TATAGCGGCGTTT
1 TTTAGCGGCGTTT
89877 TTCATCATAA
Statistics
Matches: 115, Mismatches: 25, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
42 32 0.28
43 83 0.72
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCACGTTC
Found at i:91897 original size:24 final size:26
Alignment explanation
Indices: 91850--91900 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
91840 TTTTTGTATT
* *
91850 TATTTATGTTTAATAATTATAATTAA
1 TATTTATGTTTAATAAATAAAATTAA
91876 TATTTAT-TTT-ATAAATAAAATTAA
1 TATTTATGTTTAATAAATAAAATTAA
91900 T
1 T
91901 TATATTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 13 0.57
25 3 0.13
26 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
TATTTATGTTTAATAAATAAAATTAA
Found at i:105065 original size:13 final size:13
Alignment explanation
Indices: 105047--105071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
105037 AAATTGTATA
105047 TTTTATACATATC
1 TTTTATACATATC
105060 TTTTATACATAT
1 TTTTATACATAT
105072 ATATTGTTTT
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:0.12, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTATACATATC
Found at i:105083 original size:18 final size:18
Alignment explanation
Indices: 105060--105097 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
105050 TATACATATC
*
105060 TTTTATACATATATATTG
1 TTTTATACATATATAATG
*
105078 TTTTATATATATATAATG
1 TTTTATACATATATAATG
105096 TT
1 TT
105098 ATTTCCACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (18 bp):
TTTTATACATATATAATG
Found at i:105253 original size:2 final size:2
Alignment explanation
Indices: 105246--105280 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
105236 TCAAAATTTC
*
105246 AT AT AT AT AT AC 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 AT A
105281 CTGTTATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:105290 original size:125 final size:125
Alignment explanation
Indices: 105141--105372 Score: 455
Period size: 125 Copynumber: 1.9 Consensus size: 125
105131 TTATATTTAC
105141 ATATATATATATATACTGTTATACAATTCTTTTTATATAAACCATTTATATATATGTTTCCGACT
1 ATATATATATATATACTGTTATACAATTCTTTTTATATAAACCATTTATATATATGTTTCCGACT
105206 TATTTTTTCATAACATCACTTACTCCTATTTCAAAATTTCATATATATATACATATATAT
66 TATTTTTTCATAACATCACTTACTCCTATTTCAAAATTTCATATATATATACATATATAT
*
105266 ATATATATATATATACTGTTATACAATTCTTTTTATATAAACCATTTATATATATGTTTCTGACT
1 ATATATATATATATACTGTTATACAATTCTTTTTATATAAACCATTTATATATATGTTTCCGACT
105331 TATTTTTTCATAACATCACTTACTCCTATTTCAAAATTTCAT
66 TATTTTTTCATAACATCACTTACTCCTATTTCAAAATTTCAT
105373 CTGCTACTAT
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 106 1.00
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.48
Consensus pattern (125 bp):
ATATATATATATATACTGTTATACAATTCTTTTTATATAAACCATTTATATATATGTTTCCGACT
TATTTTTTCATAACATCACTTACTCCTATTTCAAAATTTCATATATATATACATATATAT
Found at i:106622 original size:22 final size:22
Alignment explanation
Indices: 106592--106635 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
106582 ATTAGGAAAT
*
106592 CATG-TTTTTGGTTTGAGTTATA
1 CATGCTTTTTGGTTGGA-TTATA
106614 CATGCTTTTTGGTTGGATTATA
1 CATGCTTTTTGGTTGGATTATA
106636 TTTTGAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.18, C:0.07, G:0.23, T:0.52
Consensus pattern (22 bp):
CATGCTTTTTGGTTGGATTATA
Found at i:107514 original size:71 final size:71
Alignment explanation
Indices: 107349--107500 Score: 250
Period size: 71 Copynumber: 2.1 Consensus size: 71
107339 AGAGGACAAA
* *
107349 CTACGGATACAACCAAGACTTCTATCGGTAGAACAAACTCCAAAGAGCAAATAAGTTGTGGCCTG
1 CTACCGATACAACCAAGACTTCTATCGGTAGAACAAACTCCAAAGAGCAAAGAAGTTGTGGCCTG
107414 GGACTT
66 GGACTT
* * *
107420 CTACCGATACAACCAAGACTTCTATTGGTAGAACAAACTCTAGAGAGCAAAGAAGTTGTGGCCTG
1 CTACCGATACAACCAAGACTTCTATCGGTAGAACAAACTCCAAAGAGCAAAGAAGTTGTGGCCTG
107485 GGACTT
66 GGACTT
*
107491 CTATCGATAC
1 CTACCGATAC
107501 TTGGAAGGCT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 75 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (71 bp):
CTACCGATACAACCAAGACTTCTATCGGTAGAACAAACTCCAAAGAGCAAAGAAGTTGTGGCCTG
GGACTT
Found at i:111376 original size:41 final size:41
Alignment explanation
Indices: 111262--111498 Score: 149
Period size: 41 Copynumber: 5.8 Consensus size: 41
111252 TATGGGAATC
* * * * * * **
111262 ACGCCGCTATTGCTTAACCTTTAGCGACATTTTTCCCATAA
1 ACGCCGCTAATGCTTTACCTTTTGCGGCGTTTATGACATAA
* * * *
111303 ACGCTGCTAATGCTTTTACATTTTGTGACGTTTATGAC-TAA
1 ACGCCGCTAATGC-TTTACCTTTTGCGGCGTTTATGACATAA
* * **
111344 ACGCCGCTAATGCTCTTACTTTTTGCGGCGTTTCTCCCATAA
1 ACGCCGCTAATGCT-TTACCTTTTGCGGCGTTTATGACATAA
* * * * * *
111386 ACGTCACTATTGTTTTACCTTTTGCGGCGTTTCT-CCTATAA
1 ACGCCGCTAATGCTTTACCTTTTGCGGCGTTTATGAC-ATAA
** * * *
111427 ACGTTGCTATTACTTTACCTTTTGCGGCGTTTATGA-AAAA
1 ACGCCGCTAATGCTTTACCTTTTGCGGCGTTTATGACATAA
* *
111467 ACGCCAC-AATTGCTTTACTTTTTGCGGCGTTT
1 ACGCCGCTAA-TGCTTTACCTTTTGCGGCGTTT
111499 TCGTTCCAAA
Statistics
Matches: 155, Mismatches: 35, Indels: 13
0.76 0.17 0.06
Matches are distributed among these distances:
39 1 0.01
40 30 0.19
41 95 0.61
42 29 0.19
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (41 bp):
ACGCCGCTAATGCTTTACCTTTTGCGGCGTTTATGACATAA
Found at i:115776 original size:96 final size:96
Alignment explanation
Indices: 115597--115829 Score: 272
Period size: 96 Copynumber: 2.4 Consensus size: 96
115587 GCTGTTGTCG
* * * * * * *
115597 AAGAAGGAAAAGAAGATCACTTGATCAGCAAGTAAAAGAAACATAAGATGGAAGACGAAAGTTGT
1 AAGAAGGAAAACAAGATTACTTGATCGGCAAGAAAAAGAAACAGAAGATGGAAGACCAAAGTTGC
**
115662 CATGAAATTTGAAACCTAAGTT-TCATTGATA
66 CATGAAAAATGAAACCTAAGTTCT-ATTGATA
* *
115693 AAGAAGGAAAACAATATTACTTGATCGGCAAGAAAAAGAAACGGAAGATGGAAGACCAAAGTTGC
1 AAGAAGGAAAACAAGATTACTTGATCGGCAAGAAAAAGAAACAGAAGATGGAAGACCAAAGTTGC
* * *
115758 CAT-AAAAATGAAACCCTAAGTTCTGTTGGTG
66 CATGAAAAATGAAA-CCTAAGTTCTATTGATA
* * * *
115789 AAGGAGGAAAACAAGATTACTTGGTCGGCAAGCAAATGAAA
1 AAGAAGGAAAACAAGATTACTTGATCGGCAAGAAAAAGAAA
115830 TAAAAAGACA
Statistics
Matches: 116, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
95 8 0.07
96 107 0.92
97 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.23, T:0.19
Consensus pattern (96 bp):
AAGAAGGAAAACAAGATTACTTGATCGGCAAGAAAAAGAAACAGAAGATGGAAGACCAAAGTTGC
CATGAAAAATGAAACCTAAGTTCTATTGATA
Found at i:116285 original size:324 final size:323
Alignment explanation
Indices: 115692--116810 Score: 1420
Period size: 324 Copynumber: 3.5 Consensus size: 323
115682 TTTCATTGAT
* * * *
115692 AAAGAAGGAAAACAATATTACTTGATCGGCAAGAAAAAGAAACGGAAGATGGAAGACCAAAGTTG
1 AAAGAAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAACAGAAGATGGAAGACCAAAGTTG
* * * * **
115757 CCATAAAAATGAAACCCTAAG-TTCTGTTGGTGAAGGAGGAAAACAAGATTACTTGGTCGGCAAG
66 CCATGAAATTGGAACCCTAAGTTTC-GTTAGTGAAGGAGGAAAACAAGATTACTTGGTCAACAAG
* * ** ** * *
115821 CAAATGAAATAAAAAGACAAGCGGTGATGGAAAGAAGAAGTAGAAGACAAATAACATTAATAATC
130 CAAAAGAAA-CAAAAGATGAGCGACGATAGAAAGAAGAAGTAGAAGACAAAAAACATTAATAATC
* * * * *
115886 AGATAAATAGATAAGATGTGCCATAACTCAGAAGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCA
194 AGAGAAAGAGAAAAGATGTGCCATAACTTAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCA
* * *
115951 TGGAGAAGGAGAACAAAATGATGATTGAGAAATAGGGTCTCAAATCCTATCATGAAGTTGTTGTG
259 TGGAGAAGGAGAACAAAATGATGATTGAAAAAAAGGGTCTCAAATCCTATCATGAAGTTGTTGTC
* * * * **
116016 GAAGAAGGAAAAGAAGATTACTTGATCGACAAGCATAAGAAATAGAAGATGGAAGATGAAAGTTG
1 AAAGAAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAACAGAAGATGGAAGACCAAAGTTG
**
116081 CCATGAAATTGGAACCCTAAGTTTTTTTAGTGAAGGAGGAAAACAAGATTACTTGGTCAACAAGC
66 CCATGAAATTGGAACCCTAAGTTTCGTTAGTGAAGGAGGAAAACAAGATTACTTGGTCAACAAGC
*
116146 AAAAGAAACAAAAGATGAGCGACGATAGAAAAAAAGAAGTAGAAGACAAAAAACATTAATAATCA
131 AAAAGAAACAAAAGATGAGCGACGATAG-AAAGAAGAAGTAGAAGACAAAAAACATTAATAATCA
* *
116211 GAGAAAGAGAAAAGATGTGCCATAACTTAGATGGAATTGCCCAAGTTTGTAACTCGTCTAGTCAT
195 GAGAAAGAGAAAAGATGTGCCATAACTTAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCAT
* * * * * *
116276 GGTGAAGGAGAACAAAATGATAATT-AACAAAAAGGGTC-CTAAATCTTGTAATGAAGTTGTTAT
260 GGAGAAGGAGAACAAAATGATGATTGAA-AAAAAGGGTCTC-AAATCCTATCATGAAGTTGTTGT
116339 C
323 C
* * * * * * * *
116340 AAAGAAAGAAAACAATATTACTTGATTGGCAAGTAAAAGAAATAGAAGATGAAAGACGAAAGTTG
1 AAAGAAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAACAGAAGATGGAAGACCAAAGTTG
*
116405 CCATGAAATTGGAACCCTAAGTTTCGTTAGTGAAGGAGGAAAACAAAATTACTTGGTCAACAAGC
66 CCATGAAATTGGAACCCTAAGTTTCGTTAGTGAAGGAGGAAAACAAGATTACTTGGTCAACAAGC
* * * * * *
116470 GAAAGAAACAAAA-AGGCAAGCGACGATAGAAAGAAGAAGCAAAAGACAAACAACATTAATAATT
131 AAAAGAAACAAAAGATG--AGCGACGATAGAAAGAAGAAGTAGAAGACAAAAAACATTAATAATC
* * * *
116534 AGAGAAAGAGACAATATGTGCCATAACTTATATGGTATTACCCAAGTTTGTAGCTCGTCTAGTCA
194 AGAGAAAGAGAAAAGATGTGCCATAACTTAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCA
*
116599 TGGAGAAGGAGAACAAAATGATGATTGAAAAAGAA-GGTCTCAAATCCTATCATGAAGCTGTTGT
259 TGGAGAAGGAGAACAAAATGATGATTGAAAAA-AAGGGTCTCAAATCCTATCATGAAGTTGTTGT
*
116663 T
323 C
* * * * *
116664 AAAGAAGGAAAAGAAGATTACTTTATCAACAAGCAAAAGAAACAGAATATGGAAGATCAAAGTTG
1 AAAGAAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAACAGAAGATGGAAGACCAAAGTTG
* * * ** * **
116729 CCATGAAATTGGAAACTTAAGTTTCGTTGGTGAAAAAGGAAAACAAGATTACTTGATCGGCAAGC
66 CCATGAAATTGGAACCCTAAGTTTCGTTAGTGAAGGAGGAAAACAAGATTACTTGGTCAACAAGC
**
116794 AAAAGAAATGAAAGATG
131 AAAAGAAACAAAAGATG
116811 GAAGACGAAA
Statistics
Matches: 682, Mismatches: 103, Indels: 19
0.85 0.13 0.02
Matches are distributed among these distances:
323 18 0.03
324 644 0.94
325 20 0.03
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (323 bp):
AAAGAAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAACAGAAGATGGAAGACCAAAGTTG
CCATGAAATTGGAACCCTAAGTTTCGTTAGTGAAGGAGGAAAACAAGATTACTTGGTCAACAAGC
AAAAGAAACAAAAGATGAGCGACGATAGAAAGAAGAAGTAGAAGACAAAAAACATTAATAATCAG
AGAAAGAGAAAAGATGTGCCATAACTTAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCATG
GAGAAGGAGAACAAAATGATGATTGAAAAAAAGGGTCTCAAATCCTATCATGAAGTTGTTGTC
Found at i:116832 original size:96 final size:96
Alignment explanation
Indices: 116668--116899 Score: 270
Period size: 96 Copynumber: 2.4 Consensus size: 96
116658 GTTGTTAAAG
* * * *
116668 AAGGAAAAGAAGATTACTTTATCAACAAGCAAAAGAAACAGAATATGGAAGATCAAAGTTGCCAT
1 AAGGAAAACAAGATTACTTGATCAGCAAGCAAAAGAAACAGAAGATGGAAGATCAAAGTTGCCAT
* * * * *
116733 GAAATTGGAAACTTAAGTTTCGTTGGTGAAA
66 GAAATTAGAAACCTAAGTTCCATTGATGAAA
* * *
116764 AAGGAAAACAAGATTACTTGATCGGCAAGCAAAAGAAA-TGAAAGATGGAAGA-CGAAAGTTGCT
1 AAGGAAAACAAGATTACTTGATCAGCAAGCAAAAGAAACAG-AAGATGGAAGATC-AAAGTTGCC
* *
116827 ATGAAATTAGAACCCTAAGTTCCATTGATGAAG
64 ATGAAATTAGAAACCTAAGTTCCATTGATGAAA
* * * *
116860 GAGAAAAACAAGATTACTTGGTCAGCAAGAAAAAGAAACA
1 AAGGAAAACAAGATTACTTGATCAGCAAGCAAAAGAAACA
116900 AAAAGGCAAG
Statistics
Matches: 113, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
95 2 0.02
96 111 0.98
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.20
Consensus pattern (96 bp):
AAGGAAAACAAGATTACTTGATCAGCAAGCAAAAGAAACAGAAGATGGAAGATCAAAGTTGCCAT
GAAATTAGAAACCTAAGTTCCATTGATGAAA
Found at i:117138 original size:420 final size:419
Alignment explanation
Indices: 116347--118746 Score: 3121
Period size: 420 Copynumber: 5.7 Consensus size: 419
116337 ATCAAAGAAA
* * * *
116347 GAAAACAATATTACTTGATTGGCAAGTAAAAGAAAT-AGAAGATGAAAGACGAAAGTTGCCATGA
1 GAAAACAAGATTACTTGATCGGCAAGCAAAAGAAATGA-AAGATGGAAGACGAAAGTTGCCATGA
* * * * * *
116411 AATTGGAACCCTAAGTTTCGTTAGTGAAGGAGGAAAACAAAATTACTTGGTCAACAAGCGAAAGA
65 AATTGGAACCCTAAGTTCCGTTGGTGAAGAAGGAAAACAAGATTACTTGGTCGACAAGCAAAAGA
* * * * * *
116476 AACAAAAAGGCAAGCGACGATAGAAAGAAGAAGCAAAAGACAAACAACATTAATAATTAGAGAAA
130 AACAAAAAGACAAGCAACAATAGAAAGAAGAAGCAGAAGACAAACAAAATTAATAATCAGAGAAA
* * * * *
116541 GAGACAATATGTGCCATAACTTATATGGTATTACCCAAGTTTGTAGCTCGTCTAGTCATGGAGAA
195 GAGAAAAGATGTGCCATAACTCAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCATGGAGAA
* * **
116606 GGAGAACAAAATGATGATTGAAAAAGAAGGTCTCAAATCCTATCATGAAGCTGTTGTTAAAGAAG
260 GGAGAACAAAATGATGATTGAGAAAGAGGGTCTCAAATCCTATCATGAAGCTGTTGTCGAAGAAG
* * *
116671 GAAAAGAAGATTACTTTATCAACAAGCAAAAGAAACAGAATATGGAAGATCAAAGTTGCCATGAA
325 GAAAAGAAGATTACTTGATCGACAAGCAAAAGAAACAGAAGATGGAAGA-CAAAGTTGCCATGAA
* *
116736 ATTGGAAACTTAAGTTTCGTTGGTGAAAAAG
389 ATTGGAACCCTAAGTTTCGTTGGTGAAAAAG
*
116767 GAAAACAAGATTACTTGATCGGCAAGCAAAAGAAATGAAAGATGGAAGACGAAAGTTGCTATGAA
1 GAAAACAAGATTACTTGATCGGCAAGCAAAAGAAATGAAAGATGGAAGACGAAAGTTGCCATGAA
* * * * * *
116832 ATTAGAACCCTAAGTTCCATTGATGAAGGAGAAAAACAAGATTACTTGGTC-AGCAAGAAAAAGA
66 ATTGGAACCCTAAGTTCCGTTGGTGAAGAAGGAAAACAAGATTACTTGGTCGA-CAAGCAAAAGA
* * * * *
116896 AACAAAAAGGCAAGCAACGATAGAAAGAAGAAGTAGAAGACAAACAACATTAATAATCAGATAAA
130 AACAAAAAGACAAGCAACAATAGAAAGAAGAAGCAGAAGACAAACAAAATTAATAATCAGAGAAA
* * * *
116961 GAGACAAGATGTGTCATAACTCAGATGGTACTGCCCAAGTTTGTAGCTCGTCTAGTCATAGAGAA
195 GAGAAAAGATGTGCCATAACTCAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCATGGAGAA
* * *
117026 GGAGAACAAAATGATGATAGAGAAAGAGGGTCTCAAATCCTATCATGAAGTTGTTGTTGAAGAAG
260 GGAGAACAAAATGATGATTGAGAAAGAGGGTCTCAAATCCTATCATGAAGCTGTTGTCGAAGAAG
* *
117091 GAAAAGAAGATTACTTGATCGACAAGCAAAAGAAATAGAACATGGAAGACGAAAGTTGCCATGAA
325 GAAAAGAAGATTACTTGATCGACAAGCAAAAGAAACAGAAGATGGAAGAC-AAAGTTGCCATGAA
* *
117156 ATTGGAACCCTAAGTTTCATTGGTGAATAAG
389 ATTGGAACCCTAAGTTTCGTTGGTGAAAAAG
* * *
117187 GAAAACAAGATTACTTGATCGGCAAG-AAAAAAAATGGAAGGTGGAAGACGAAAGTTGCCATGAA
1 GAAAACAAGATTACTTGATCGGCAAGCAAAAGAAATGAAAGATGGAAGACGAAAGTTGCCATGAA
*
117251 ATTGGAACCCTAAGTTCCGTTGGTGTAGAAGGAAAACAAGATTACTTGGTCGACAAGCAAAAGAA
66 ATTGGAACCCTAAGTTCCGTTGGTGAAGAAGGAAAACAAGATTACTTGGTCGACAAGCAAAAGAA
* ** * * * * *
117316 ATAAAAAGATTAGCAAAAATAAAAAACAAGAAACTA-AAGACAAAGAAAATTAATAATCAGAGAA
131 ACAAAAAGACAAGCAACAAT-AGAAAGAAGAAGC-AGAAGACAAACAAAATTAATAATCAGAGAA
* * *
117380 AAATAAAAGATGTGCCATAACTCAGATGGTATTGTCCAAGTTTGTAGCTCGTCTAGTCATGGAGA
194 AGAGAAAAGATGTGCCATAACTCAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCATGGAGA
* * * * * *
117445 ATGAGAACAAAATGATGATTAAGAAAAAGGGTCTCAAATCCTGTTATGAAACTGTTGTCGAAGAA
259 AGGAGAACAAAATGATGATTGAGAAAGAGGGTCTCAAATCCTATCATGAAGCTGTTGTCGAAGAA
* *
117510 GGAAAAGAAGATTACTTGATCGACAAGTAAAAGAAACAGAAGATGGAAGATCAAAGTTACCATGA
324 GGAAAAGAAGATTACTTGATCGACAAGCAAAAGAAACAGAAGATGGAAGA-CAAAGTTGCCATGA
* * *
117575 AATTGGAAACCTAAGGTTCGTTGGTGAATAAG
388 AATTGGAACCCTAAGTTTCGTTGGTGAAAAAG
** * * ** *
117607 GAAAACAAGATTACTTGATCGATAAGCAAAAGAAACGGAAGATAAAAGACGAAAGTTACCATGAA
1 GAAAACAAGATTACTTGATCGGCAAGCAAAAGAAATGAAAGATGGAAGACGAAAGTTGCCATGAA
* * *
117672 ATTGGAACCCTAAGTTTCGTTGGTGAATAAGGAAAACAAGATTACTTGGTTGACAAGCAAAAGAA
66 ATTGGAACCCTAAGTTCCGTTGGTGAAGAAGGAAAACAAGATTACTTGGTCGACAAGCAAAAGAA
**** *
117737 ACAAAAAGACAAGCGGTGATAGAAAGAAGAAGC-GAAAGACAAACAAAATTAATAATCATAGAAA
131 ACAAAAAGACAAGCAACAATAGAAAGAAGAAGCAG-AAGACAAACAAAATTAATAATCAGAGAAA
* * *
117801 GAGAAAAGATGTGCCATAACTCAAATGGTATTGCCCAAGTTTGTAGCTCGTATAATCATGGAGAA
195 GAGAAAAGATGTGCCATAACTCAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCATGGAGAA
* *
117866 GGAGAACAAAATGATGATTGAGAAAGAGGGTCTCAAATCCTTTCATGAAGGTGTTGTCGAAGAAG
260 GGAGAACAAAATGATGATTGAGAAAGAGGGTCTCAAATCCTATCATGAAGCTGTTGTCGAAGAAG
*
117931 GAAAAGAAGATTACTTGATCGACAAGCAAAAGAAACAAAAGATGGAAGACCAAAGTTGCCATGAA
325 GAAAAGAAGATTACTTGATCGACAAGCAAAAGAAACAGAAGATGGAAGA-CAAAGTTGCCATGAA
*
117996 ATTGGAACCCTAAG-TTCGCTGGT-AAAGAAG
389 ATTGGAACCCTAAGTTTCGTTGGTGAAA-AAG
* * * * *
118026 GAAAACAAGATTACTTGATCGACAAGAAAAAGAAACGGAAGATGGAAGATGAAAGTTGCCATGAA
1 GAAAACAAGATTACTTGATCGGCAAGCAAAAGAAATGAAAGATGGAAGACGAAAGTTGCCATGAA
* *
118091 ATTGGAACCCTAGGTTCCGTTGGTGTAGAAGGAAAACAAGATTACTTGGTCGACAAGCAAAAGAA
66 ATTGGAACCCTAAGTTCCGTTGGTGAAGAAGGAAAACAAGATTACTTGGTCGACAAGCAAAAGAA
* * * * * * *
118156 ACAAAAAGATGAA-CGACAATAGATACAAGAAACAGAAGACAAAGAAAATTAATAATTAGAGAAA
131 ACAAAAAGA-CAAGCAACAATAGAAAGAAGAAGCAGAAGACAAACAAAATTAATAATCAGAGAAA
* * * * *
118220 AATAAAAGATGTGCCATAACTCAGATGGTATTGTCCAAGTTCGTAGCTCATCTAGTCATGGAGAA
195 GAGAAAAGATGTGCCATAACTCAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCATGGAGAA
* * * *
118285 GGAGAACAAAATGATGATTGAGAAAGAGGGTCTCAAATCTTGTCATGAAGCTATTGTGGAAGAAG
260 GGAGAACAAAATGATGATTGAGAAAGAGGGTCTCAAATCCTATCATGAAGCTGTTGTCGAAGAAG
* * * * * *
118350 GAAAAAAAGATTACTAGATCGGCAAGCAAAAGATATAGAAGATTGAAGACGAAAGTTGCCATGAA
325 GAAAAGAAGATTACTTGATCGACAAGCAAAAGAAACAGAAGATGGAAGAC-AAAGTTGCCATGAA
118415 ATTGGAACCCTAAGTTTCGTTGGT-AAAGAAG
389 ATTGGAACCCTAAGTTTCGTTGGTGAAA-AAG
* * * *
118446 GAAAACAATATTACTTGATCAGCAAGCAAAAGAAA-CAGAAGATGGAAGATGAAAGTTGCCATGA
1 GAAAACAAGATTACTTGATCGGCAAGCAAAAGAAATGA-AAGATGGAAGACGAAAGTTGCCATGA
* * * * * *
118510 AATTGGAACCTTAAGCTCCGTTGGT--AG-AGGAAAACAAGA-TATTTGATCGGCAAGTAAAAGA
65 AATTGGAACCCTAAGTTCCGTTGGTGAAGAAGGAAAACAAGATTACTTGGTCGACAAGCAAAAGA
* ** * * *
118571 AATAAAAAGACAAGCAGTAATAGAAAGAAGAAGAAGAAGACAGAC--AA--CAT--TCAGAGAAA
130 AACAAAAAGACAAGCAACAATAGAAAGAAGAAGCAGAAGACAAACAAAATTAATAATCAGAGAAA
* * * * * * * *
118630 GAGACAAGATGTGCCATAATTTAGATGGTATTGCCCAAGTTTATAGCTTGTCTAATCATGAAAAA
195 GAGAAAAGATGTGCCATAACTCAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCATGGAGAA
* * *
118695 GGAGAACAAAATGATGATTGAGAAATAAGGTCTCAAATCCTATTATGAAGCT
260 GGAGAACAAAATGATGATTGAGAAAGAGGGTCTCAAATCCTATCATGAAGCT
118747 TACTTGAAGT
Statistics
Matches: 1747, Mismatches: 216, Indels: 44
0.87 0.11 0.02
Matches are distributed among these distances:
410 107 0.06
412 2 0.00
414 2 0.00
415 2 0.00
416 49 0.03
417 12 0.01
418 5 0.00
419 472 0.27
420 987 0.56
421 109 0.06
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.20
Consensus pattern (419 bp):
GAAAACAAGATTACTTGATCGGCAAGCAAAAGAAATGAAAGATGGAAGACGAAAGTTGCCATGAA
ATTGGAACCCTAAGTTCCGTTGGTGAAGAAGGAAAACAAGATTACTTGGTCGACAAGCAAAAGAA
ACAAAAAGACAAGCAACAATAGAAAGAAGAAGCAGAAGACAAACAAAATTAATAATCAGAGAAAG
AGAAAAGATGTGCCATAACTCAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCATGGAGAAG
GAGAACAAAATGATGATTGAGAAAGAGGGTCTCAAATCCTATCATGAAGCTGTTGTCGAAGAAGG
AAAAGAAGATTACTTGATCGACAAGCAAAAGAAACAGAAGATGGAAGACAAAGTTGCCATGAAAT
TGGAACCCTAAGTTTCGTTGGTGAAAAAG
Found at i:117252 original size:95 final size:96
Alignment explanation
Indices: 117083--117318 Score: 366
Period size: 95 Copynumber: 2.5 Consensus size: 96
117073 AAGTTGTTGT
*
117083 TGAAGAAGGAAAAGAAGATTACTTGATCGACAAGCAAAAGAAATAGAACATGGAAGACGAAAGTT
1 TGAAGAAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAATAGAACATGGAAGACGAAAGTT
*
117148 GCCATGAAATTGGAACCCTAAGTTTCATTGG
66 GCCATGAAATTGGAACCCTAAGTTCCATTGG
* * * * **
117179 TGAATAAGGAAAACAAGATTACTTGATCGGCAAG-AAAAAAAATGGAAGGTGGAAGACGAAAGTT
1 TGAAGAAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAATAGAACATGGAAGACGAAAGTT
*
117243 GCCATGAAATTGGAACCCTAAGTTCCGTTGG
66 GCCATGAAATTGGAACCCTAAGTTCCATTGG
* *
117274 TGTAGAAGGAAAACAAGATTACTTGGTCGACAAGCAAAAGAAATA
1 TGAAGAAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAATA
117319 AAAAGATTAG
Statistics
Matches: 124, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
95 85 0.69
96 39 0.31
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (96 bp):
TGAAGAAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAATAGAACATGGAAGACGAAAGTT
GCCATGAAATTGGAACCCTAAGTTCCATTGG
Found at i:117672 original size:96 final size:96
Alignment explanation
Indices: 117508--117739 Score: 358
Period size: 96 Copynumber: 2.4 Consensus size: 96
117498 GTTGTCGAAG
* * **
117508 AAGGAAAAGAAGATTACTTGATCGACAAGTAAAAGAAACAGAAGATGGAAGATCAAAGTTACCAT
1 AAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAACAGAAGATAAAAGATCAAAGTTACCAT
117573 GAAATTGGAAACCTAAGGTTCGTTGGTGAAT
66 GAAATTGGAAACCTAAGGTTCGTTGGTGAAT
* *
117604 AAGGAAAACAAGATTACTTGATCGATAAGCAAAAGAAACGGAAGATAAAAGA-CGAAAGTTACCA
1 AAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAACAGAAGATAAAAGATC-AAAGTTACCA
* *
117668 TGAAATTGGAACCCTAAGTTTCGTTGGTGAAT
65 TGAAATTGGAAACCTAAGGTTCGTTGGTGAAT
* *
117700 AAGGAAAACAAGATTACTTGGTTGACAAGCAAAAGAAACA
1 AAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAACA
117740 AAAAGACAAG
Statistics
Matches: 123, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
95 1 0.01
96 122 0.99
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (96 bp):
AAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAACAGAAGATAAAAGATCAAAGTTACCAT
GAAATTGGAAACCTAAGGTTCGTTGGTGAAT
Found at i:118088 original size:95 final size:96
Alignment explanation
Indices: 117925--118166 Score: 369
Period size: 95 Copynumber: 2.5 Consensus size: 96
117915 GGTGTTGTCG
*
117925 AAGAAGGAAAAGAAGATTACTTGATCGACAAGCAAAAGAAACAAAAGATGGAAGACCAAAGTTGC
1 AAGAAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAACAAAAGATGGAAGACCAAAGTTGC
117990 CATGAAATTGGAACCCTAAGTT-CGCTGGTA
66 CATGAAATTGGAACCCTAAGTTCCGCTGGTA
* ** **
118020 AAGAAGGAAAACAAGATTACTTGATCGACAAGAAAAAGAAACGGAAGATGGAAGATGAAAGTTGC
1 AAGAAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAACAAAAGATGGAAGACCAAAGTTGC
* * *
118085 CATGAAATTGGAACCCTAGGTTCCGTTGGTG
66 CATGAAATTGGAACCCTAAGTTCCGCTGGTA
* *
118116 TAGAAGGAAAACAAGATTACTTGGTCGACAAGCAAAAGAAACAAAAAGATG
1 AAGAAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAAC-AAAAGATG
118167 AACGACAATA
Statistics
Matches: 131, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
95 80 0.61
96 45 0.34
97 6 0.05
ACGTcount: A:0.45, C:0.13, G:0.24, T:0.17
Consensus pattern (96 bp):
AAGAAGGAAAACAAGATTACTTGATCGACAAGCAAAAGAAACAAAAGATGGAAGACCAAAGTTGC
CATGAAATTGGAACCCTAAGTTCCGCTGGTA
Found at i:118508 original size:96 final size:95
Alignment explanation
Indices: 118344--118572 Score: 311
Period size: 96 Copynumber: 2.4 Consensus size: 95
118334 GCTATTGTGG
* * * * *
118344 AAGAAGGAAAAAAAGATTACTAGATCGGCAAGCAAAAGATATAGAAGATTGAAGACGAAAGTTGC
1 AAGAAGGAAAACAAGATTACTTGATCGGCAAGCAAAAGAAACAGAAGATGGAAGACGAAAGTTGC
* *
118409 CATGAAATTGGAACCCTAAGTTTCGTTGGT
66 CATGAAATTGGAACCCTAAGCTCCGTTGGT
* * *
118439 AAAGAAGGAAAACAATATTACTTGATCAGCAAGCAAAAGAAACAGAAGATGGAAGATGAAAGTTG
1 -AAGAAGGAAAACAAGATTACTTGATCGGCAAGCAAAAGAAACAGAAGATGGAAGACGAAAGTTG
*
118504 CCATGAAATTGGAACCTTAAGCTCCGTTGGT
65 CCATGAAATTGGAACCCTAAGCTCCGTTGGT
* *
118535 -AG-AGGAAAACAAGA-TATTTGATCGGCAAGTAAAAGAAA
1 AAGAAGGAAAACAAGATTACTTGATCGGCAAGCAAAAGAAA
118573 TAAAAAGACA
Statistics
Matches: 118, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
92 21 0.18
93 11 0.09
94 2 0.02
96 84 0.71
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.20
Consensus pattern (95 bp):
AAGAAGGAAAACAAGATTACTTGATCGGCAAGCAAAAGAAACAGAAGATGGAAGACGAAAGTTGC
CATGAAATTGGAACCCTAAGCTCCGTTGGT
Found at i:121995 original size:19 final size:18
Alignment explanation
Indices: 121961--122026 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 18
121951 AGAAATAGCA
121961 GAAAAT-TTTTCTCAACT
1 GAAAATATTTTCTCAACT
121978 GAAAATATTTTCTGCAACAGT
1 GAAAATATTTTCT-CAAC--T
* *
121999 CAAAAAATTTTCCTCAACT
1 GAAAATATTTT-CTCAACT
122018 GAAAATATT
1 GAAAATATT
122027 ATTTTACATT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
17 6 0.15
18 6 0.15
19 12 0.30
21 14 0.35
22 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.35
Consensus pattern (18 bp):
GAAAATATTTTCTCAACT
Done.