Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008905.1 Hibiscus syriacus cultivar Beakdansim tig00112191_pilon, 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: 61633
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:430 original size:195 final size:194
Alignment explanation
Indices: 1--444 Score: 729
Period size: 194 Copynumber: 2.3 Consensus size: 194
*
1 CTAAATAATGTATCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAAA
1 CTAAATAATGTATCGACAATTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAAA
66 GGGTGCAACAATAAAGTGTCGATCTATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAA
66 GGGTGCAACAATAAAGTGTCGATCTATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAA
131 GTATAATGTAATAGGTAATTTCAATCTAACCGGTACAAGTATACGGTTTTATGAGAGAATAGGT
131 GTATAATGTAATAGGTAATTTCAATCTAACCGGTACAAGTATACGGTTTTATGAGAGAATAGGT
* * * * *
195 CTAAATAATGTATCGAC-ACTTTGTAGTTTGTGTTGATATTTTTGGTCTATAATGAATGGCAAAC
1 CTAAATAATGTATCGACAATTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAA-
*
259 AGGGTGCAACAATAAAGTGTCG-TCCATATATAAAAAGTGTCGAT-CGATAAACATCGAAACCCA
65 AGGGTGCAACAATAAAGTGTCGAT-C-TATATAAAAAGTGTCGATCCCATAAACATCGAAACCCA
322 TAAGTATAATGTAATAGGTAATTTTCAATCTAA-CGGTACAAGTATATCGGTTTTATGAGAGAAT
128 TAAGTATAATGTAATAGGTAA-TTTCAATCTAACCGGTACAAGTATA-CGGTTTTATGAGAGAAT
386 AGGT
191 AGGT
*
390 CTAAATCATGTATCGACAATTTTTTAG-TTGTGTCGATATTTTT-GTCCAGAATGAA
1 CTAAATAATGTATCGACAATTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
445 ATATTAATGC
Statistics
Matches: 231, Mismatches: 13, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
193 41 0.18
194 102 0.44
195 81 0.35
196 7 0.03
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (194 bp):
CTAAATAATGTATCGACAATTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAAA
GGGTGCAACAATAAAGTGTCGATCTATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAA
GTATAATGTAATAGGTAATTTCAATCTAACCGGTACAAGTATACGGTTTTATGAGAGAATAGGT
Found at i:581 original size:19 final size:21
Alignment explanation
Indices: 557--625 Score: 79
Period size: 23 Copynumber: 3.2 Consensus size: 21
547 ATACTTTACA
557 ATATAAGC-A-CTATTACATT
1 ATATAAGCTACCTATTACATT
576 ATATAAACGCTACCTATTACATT
1 ATAT-AA-GCTACCTATTACATT
*
599 ATATAAGCGCTACCTATTACATC
1 ATATAA--GCTACCTATTACATT
622 ATAT
1 ATAT
626 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
19 4 0.09
20 2 0.05
21 2 0.05
22 3 0.07
23 33 0.75
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (21 bp):
ATATAAGCTACCTATTACATT
Found at i:596 original size:23 final size:23
Alignment explanation
Indices: 566--625 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
556 AATATAAGCA
566 CTATTACATTATATAAACGCTAC
1 CTATTACATTATATAAACGCTAC
*
589 CTATTACATTATATAAGCGCTAC
1 CTATTACATTATATAAACGCTAC
*
612 CTATTACATCATAT
1 CTATTACATTATAT
626 TTTTACCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.37
Consensus pattern (23 bp):
CTATTACATTATATAAACGCTAC
Found at i:704 original size:22 final size:22
Alignment explanation
Indices: 643--703 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
633 TATTATATTG
643 AAAGTGTCCATACTTTTTATAA
1 AAAGTGTCCATACTTTTTATAA
* * *
665 AAAGTATCTATCCTTTTTAT-A
1 AAAGTGTCCATACTTTTTATAA
686 AAAGTGTCCATACTTTTT
1 AAAGTGTCCATACTTTTT
704 TCACTGTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (22 bp):
AAAGTGTCCATACTTTTTATAA
Found at i:1102 original size:22 final size:23
Alignment explanation
Indices: 1069--1139 Score: 101
Period size: 22 Copynumber: 3.2 Consensus size: 23
1059 AATAGGTAAA
*
1069 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
1092 AT-TAATGTAATAGGTAGCG-TT
1 ATATAATGTAATAGGTAGCGCTT
* *
1113 ATATAATGTTATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1136 ATAT
1 ATAT
1140 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 4 0.09
22 31 0.72
23 8 0.19
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1587 original size:23 final size:23
Alignment explanation
Indices: 1541--1612 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1531 ATAAGTAAAA
* *
1541 ATATGATGTAATA-GTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
*
1563 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1586 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1609 ATAT
1 ATAT
1613 GTAAAGTATC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 12 0.27
23 32 0.73
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1912 original size:471 final size:473
Alignment explanation
Indices: 665--2924 Score: 3266
Period size: 471 Copynumber: 4.8 Consensus size: 473
655 CTTTTTATAA
* *
665 AAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGAAAAACATTAATTTAAGG
1 AAAGTATCTATCCTTTTTATAAAAGTGTCAATACTTTTTTCACTGTGGAAAACATTAATTTAAGG
730 TTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCG-CTAATGA-TTATTTTTT
66 TTATC-TTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTT
793 ACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATACATTTATTATTATCT
129 ACGTTAC-G-ATATA-TATTATTAAATTAAAAACAATAAACATATAT-TACA-TTATTATTATCT
*
858 TTGGTTAATATTGTTAATTTAAATACTAAATAATA-TTTATAAAATATCAAAACAATCAAATAAT
189 TTGGTTAATATTGTTAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-AT
* * *
922 TTTTTGTGTAAATGAAATTATTAAATT-A-ATTGTATGTGGAAAACATGAAACACTGTTAAAAAA
253 TTTTTATGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAA
* *
985 ATTGAAACATAAATTACATAACTTTAAAAAAAAATATCGATCCTTTTTATAAAAAGTATGAACAC
318 ATTGAAACATAAATTACATAACTTT-AAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACAC
1050 TTTCAATATAATAGGTAAAATATGATGTAATAGGTAGCGCTTAT-TAATGTAATAGGTAGCGTTA
382 TTTCAATAT-ATAGGTAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTA
*
1114 TATAATGTTATAGGTAGTGCTTATATTGT
446 TATAATGTAATA-GTAGTGCTTATATTGT
1143 AAAGTATCTATCCTTTTTTATAAAAGTGTTC-ATACTTTTTTCACTGTGGAAAACATTAATTTAA
1 AAAGTATCTATCC-TTTTTATAAAAGTG-TCAATACTTTTTTCACTGTGGAAAACATTAATTTAA
*
1207 GGTTATCTTTTAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTT
64 GGTTATCTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTT
*
1272 ACGTTACG--GTATATTATTAAATTAAAAAACAAT-AACATATATATACATATTTATTATTATC-
129 ACGTTACGATATATATTATTAAATT-AAAAACAATAAACATATAT-TAC--A-TTATTATTATCT
1333 TTGGTTAATATTGTTAATTTAAATTCTAAATAATATTTTAT-AAATAT-AAAACAATCAAATATT
189 TTGGTTAATATTGTTAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATATT
1396 TTTTATGTAAATGAAATTATTAAATT-A-ATTGTAGGTGGAAAACATGAAACACTATTAAAAAAA
254 TTTTATGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAA
1459 TTGAAACATAAATTACATAACTTT-AAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTT
319 TTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTT
* *
1523 TCAATATAATAAGTAAAAATATGATGTAATA-GTAGCACTTATATAATGTAATAGGTAGCGTTTA
384 TCAATAT-ATAGGT-AAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCG-TTA
1587 TATAATGTAATAGGTAGTGCTTATA-TGT
446 TATAATGTAATA-GTAGTGCTTATATTGT
1615 AAAGTATCTATCCTTTTTATAAAAGTGTCAATAC-TTTTTCACTGTGGAAAACATTAATTTAAAG
1 AAAGTATCTATCCTTTTTATAAAAGTGTCAATACTTTTTTCACTGTGGAAAACATTAATTT-AAG
* *
1679 G-TATATTTGAGTGAGTTTTAAGATATTAATTTAATAATTATAGGCGTCTAATGATTTATTTTTA
65 GTTATCTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTA
*
1743 CGTTACGATATATATTATTAAATTAAAAACAATAAACATATATTTCA-TATTATTATCTTTGGTT
130 CGTTACGATATATATTATTAAATTAAAAACAATAAACATATATTACATTATTATTATCTTTGGTT
*
1807 AATATTGTTAAATT-AATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATATTTTTTAT
195 AATATTGTTAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATATTTTTTAT
*
1871 GTAAATGAAATTATTAAATTAATATTGTAGATGGAAAACATGAAACACTATTAAAAAAATTGAAA
260 GTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAA
* *
1936 TAAAAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAAT
325 -CATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAAT
2001 ATATAGGTAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTACGCG-TATATAA--
389 ATATAGGTAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTA-GCGTTATATAATG
2063 -AATAGTA--GCTTAT-TTGT
453 TAATAGTAGTGCTTATATTGT
* *
2080 AAAG--T-TATCCTTTTTATAAAAGTGTCCATACTTTTTTTACTGTGGAAAACATTAATTTAAGG
1 AAAGTATCTATCCTTTTTATAAAAGTGTCAATACTTTTTTCACTGTGGAAAACATTAATTTAAGG
2142 TTATCTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGA-TTATTTTTTA
66 TTATCTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTTA
*
2206 CGTTACGGTATATATTATTATTAAATTAAAAAC-ATAAACATATATTACATATTTATTATTATAT
130 CGTTAC-G-ATATA-TATTATTAAATTAAAAACAATAAACATATATTAC--A-TTATTATTATCT
2270 TTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA
189 TTGGTTAATATTGTT-AATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-A
2335 TTTTTTATGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAA
252 TTTTTTATGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAA
* * * * *
2400 ACTTGAAAC--AAATTACATAACTTTAAAAAAA-TATCGATTCTTTTTATAAAAAGGATCGATAC
317 AATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACAC
*
2462 TTTACAATATATAGGTAAAA-AT-ATG----A--T---G--TA-AT-A-G--ATA-G-CGC-TTA
382 TTT-CAATATATAGGTAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTA
*
2506 TAT--TGT-A-A--AGCGCTTATATTGT
446 TATAATGTAATAGTAGTGCTTATATTGT
* * * *
2528 AAAGTATCTATCCTTTTTATAGAAGTATCAATACTTATTTCACTGTAGAAAACATTAATTTAAGG
1 AAAGTATCTATCCTTTTTATAAAAGTGTCAATACTTTTTTCACTGTGGAAAACATTAATTTAAGG
* **** *
2593 TTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATATTTATCTAATGATTTGTTTTTT
66 TTATC-TTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTT-ATTTTT
* * *
2658 ATGTTACGGTATATATCATTAAATTAAAAACAATAAACATATATTACATATTATTATTATCTTTG
129 ACGTTACGATATATATTATTAAATTAAAAACAATAAACATATATTAC--ATTATTATTATCTTTG
*
2723 GTTAATATTGTTAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATATTTTT
192 GTTAATATTGTTAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATATTTTT
2788 T-TGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAT
257 TATGT--AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
*
2851 TGAAATATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAAGTATGGACACTT
320 TGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTAT-AAAAAGTATGGACACTT
*
2916 TCAACATAT
384 TCAATATAT
2925 TATAATGTAA
Statistics
Matches: 1660, Mismatches: 62, Indels: 147
0.89 0.03 0.08
Matches are distributed among these distances:
445 1 0.00
447 10 0.01
448 34 0.02
449 96 0.06
450 67 0.04
451 103 0.06
452 60 0.04
453 14 0.01
454 1 0.00
455 2 0.00
456 2 0.00
458 1 0.00
461 1 0.00
462 32 0.02
463 90 0.05
464 1 0.00
465 32 0.02
466 18 0.01
467 37 0.02
468 61 0.04
469 106 0.06
470 100 0.06
471 199 0.12
472 190 0.11
473 164 0.10
474 38 0.02
475 51 0.03
476 18 0.01
478 54 0.03
479 72 0.04
480 5 0.00
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (473 bp):
AAAGTATCTATCCTTTTTATAAAAGTGTCAATACTTTTTTCACTGTGGAAAACATTAATTTAAGG
TTATCTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTAC
GTTACGATATATATTATTAAATTAAAAACAATAAACATATATTACATTATTATTATCTTTGGTTA
ATATTGTTAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATATTTTTTATG
TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAAC
ATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATAT
ATAGGTAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTATATAATGTAA
TAGTAGTGCTTATATTGT
Found at i:2062 original size:22 final size:23
Alignment explanation
Indices: 2012--2062 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
2002 TATAGGTAAA
* *
2012 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCGT
2035 ATATAATGTAATAGGTA-CGCGT
1 ATATAATGTAATAGGTAGCGCGT
2057 ATATAA
1 ATATAA
2063 AATAGTAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCGT
Found at i:2414 original size:19 final size:20
Alignment explanation
Indices: 2377--2414 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2367 TTGTAGGTGG
*
2377 AAAACATGAAACACTATTAA
1 AAAACATGAAACACAATTAA
*
2397 AAAACTTGAAACA-AATTA
1 AAAACATGAAACACAATTA
2415 CATAACTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.61, C:0.13, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAACATGAAACACAATTAA
Found at i:2519 original size:16 final size:16
Alignment explanation
Indices: 2498--2531 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2488 TGTAATAGAT
2498 AGCGCTTATATTGTAA
1 AGCGCTTATATTGTAA
2514 AGCGCTTATATTGTAA
1 AGCGCTTATATTGTAA
2530 AG
1 AG
2532 TATCTATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (16 bp):
AGCGCTTATATTGTAA
Found at i:8688 original size:62 final size:62
Alignment explanation
Indices: 8586--8707 Score: 140
Period size: 62 Copynumber: 2.0 Consensus size: 62
8576 AGAATATTTT
* *
8586 AATTATTATAAAATGATCATTAAACTTCTCAAACAATTACAAAATA-ATCATTAAAATTTATTA
1 AATTATTATAAAATGAACATTAAACTTATCAAACAATTACAAAA-AGATCATT-AAATTTATTA
* * *** *
8649 AATTATTAT-AAATGAACATTCAACTTATGAAATTGTTACAAAAAGATCCTTAAATTTAT
1 AATTATTATAAAATGAACATTAAACTTATCAAACAATTACAAAAAGATCATTAAATTTAT
8708 CAAAATTTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
61 9 0.18
62 32 0.64
63 9 0.18
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (62 bp):
AATTATTATAAAATGAACATTAAACTTATCAAACAATTACAAAAAGATCATTAAATTTATTA
Found at i:10204 original size:7 final size:7
Alignment explanation
Indices: 10194--10218 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
10184 ATTTATTAAT
10194 TATAAAA
1 TATAAAA
10201 TATAAAA
1 TATAAAA
10208 TATAAAA
1 TATAAAA
10215 TATA
1 TATA
10219 TATGATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
TATAAAA
Found at i:12748 original size:26 final size:26
Alignment explanation
Indices: 12700--12749 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
12690 CGTAGATCTT
*
12700 ATGAGGAATAATCTTCTAGAATTTTA
1 ATGAGGAATAAACTTCTAGAATTTTA
*
12726 ATGAGGAAGTAAACTTTTA-AATTT
1 ATGAGGAA-TAAACTTCTAGAATTT
12750 CAAGAAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (26 bp):
ATGAGGAATAAACTTCTAGAATTTTA
Found at i:13626 original size:2 final size:2
Alignment explanation
Indices: 13619--13687 Score: 85
Period size: 2 Copynumber: 37.0 Consensus size: 2
13609 CGTTTGGAGT
*
13619 TA TA TA TA TA TA TA TA TA TA TA T- TA T- TT TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
13658 TA TA TA TA TA TA TA TA TG TA TA -A TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13688 GTTTGTGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
1 5 0.08
2 54 0.92
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13794 original size:38 final size:37
Alignment explanation
Indices: 13671--13942 Score: 197
Period size: 36 Copynumber: 7.4 Consensus size: 37
13661 ATATATATAT
* * * *
13671 ATATGTATAATAATATAGTTTGTGAAAATGTTTTTGATA
1 ATATATATAAT-ATATAGTTTTTGAAAATATTTTT-AAA
* * *
13710 A-A-ATATAATATATACTTTTCAGAAAATGATTTTCGAAA
1 ATATATATAATATATAGTTTT-TGAAAAT-ATTTT-TAAA
* *
13748 ATTTATATATTATATAGTTTTTGAAAATATTTTT--A
1 ATATATATAATATATAGTTTTTGAAAATATTTTTAAA
*
13783 A-A-ATATAATATATAG-TTTTGAAAATATTTTAAAAA
1 ATATATATAATATATAGTTTTTGAAAATATTTT-TAAA
* * * * *
13818 CATTTATATATTGTATAGTTTTT-AAAACATTTTAAAA
1 -ATATATATAATATATAGTTTTTGAAAATATTTTTAAA
*
13855 ACT-TATATAATATATAGTTTTT-AAAACATTTTTAAA
1 A-TATATATAATATATAGTTTTTGAAAATATTTTTAAA
* ** *
13891 AAATATATAATATATAGTTTTAAAAAATA-TTTTGAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTTAAA
* *
13927 ATGTATATATTATATA
1 ATATATATAATATATA
13943 AATTATATTT
Statistics
Matches: 189, Mismatches: 29, Indels: 33
0.75 0.12 0.13
Matches are distributed among these distances:
32 15 0.08
33 12 0.06
35 3 0.02
36 78 0.41
37 22 0.12
38 33 0.17
39 11 0.06
40 15 0.08
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTGAAAATATTTTTAAA
Found at i:13971 original size:18 final size:19
Alignment explanation
Indices: 13950--13987 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
13940 ATAAATTATA
13950 TTTAGTATATTA-TTATTT
1 TTTAGTATATTATTTATTT
* *
13968 TTTATTATTTTATTTATTT
1 TTTAGTATATTATTTATTT
13987 T
1 T
13988 ATTCATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (19 bp):
TTTAGTATATTATTTATTT
Found at i:13995 original size:18 final size:17
Alignment explanation
Indices: 13967--14026 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 17
13957 TATTATTATT
13967 TTTTATTATTTTATTTA
1 TTTTATTATTTTATTTA
13984 TTTTATTCATTTTATTTA
1 TTTTATT-ATTTTATTTA
*
14002 TTTTAATTTATTTCATTT-
1 TTTT-A-TTATTTTATTTA
14020 TTTTATT
1 TTTTATT
14027 TACAGGCCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
16 2 0.05
17 8 0.21
18 18 0.46
19 9 0.23
20 2 0.05
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTATTATTTTATTTA
Found at i:14024 original size:27 final size:26
Alignment explanation
Indices: 13965--14028 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 26
13955 TATATTATTA
*
13965 TTTTTTA-TTATTTTATTTATTTTAT
1 TTTTTTATTTATTTTATTTATTTCAT
*
13990 TCATTTTATTTATTTTAATTTATTTCAT
1 T-TTTTTATTTATTTT-ATTTATTTCAT
14018 TTTTTTATTTA
1 TTTTTTATTTA
14029 CAGGCCCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 1 0.03
26 5 0.15
27 16 0.48
28 11 0.33
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTTTATTTATTTTATTTATTTCAT
Found at i:18927 original size:84 final size:83
Alignment explanation
Indices: 18636--20264 Score: 1516
Period size: 84 Copynumber: 19.7 Consensus size: 83
18626 TTAAAGACAA
* * * * * *
18636 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAGACTTTCGAGTTCGACTACG
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
* *
18701 CTCAGCTCAAAGGCATAT
66 CTCAGCTCCAAGGCACAT
* * * * * *
18719 CATTTTCAACATAGTTTAAGTCGTGAAGGGCTATCTGCCAACCAAAGACCTTC-AGGTTCGATTA
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGA-GTTCGACTA
* * *
18783 CACTCAGCTTCGAAGGCATAT
64 CGCTCAGC-TCCAAGGCACAT
* *
18804 CATTTGCAGTAT-GACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
1 CATTTGCAGCATAG-CTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTA
*
18868 CGCTCAACTCCAAGGCACAT
64 CGCTCAGCTCCAAGGCACAT
* * * * * * * *
18888 AATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAATACATTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
18953 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * *
18972 CATTTGCAACATAGCTAAAGTCGAGAAGGGTTATCTG-C--CAAAGACCCTT-GAGTTCGATTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGA-CCTTCGAGTTCGACTAC
* * *
19033 ACTCAGCTTCGAGGGCACAT
65 GCTCAGC-TCCAAGGCACAT
** * ** * * *
19053 CATTTATAGCATAACACAAAG-CTAGAAGGGTTATC--CATAACCAAAAGACCTTCTAGTTCGAC
1 CATTTGCAGCATAGC-TTAAGTCGAGAAGGGTTATCTGC-CAA-C-AAAGACCTTCGAGTTCGAC
* *
19115 TACGCTCAACTCCAAGGCATAT
62 TACGCTCAGCTCCAAGGCACAT
* * * *
19137 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTAT
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
* *
19202 GCTCAGTTCCAAGACACAT
65 GCTCAGCTCCAAGGCACAT
* * * *
19221 TATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA-CATG-C--CAAAGACCCTCGAGTTCGATTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATC-TGCCAACAAAGACCTTCGAGTTCGACTAC
* * * *
19282 ACTCAGCTTCGAGGGTACAT
65 GCTCAGC-TCCAAGGCACAT
* * ** * *
19302 CA--T-----A-A-CTCAACG-CTAGAAGGGTTATCTGTGACCAAAAGAGCTTCGAGTTCGACTA
1 CATTTGCAGCATAGCTTAA-GTCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTA
*
19357 CGCTCAGCTCCAAGGCATAT
64 CGCTCAGCTCCAAGGCACAT
* * * * *
19377 CATTTACAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTAT
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
19442 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* *
19461 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATTTG-C--CAAAGACCTTTGAGTTCGACTACG
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
* *
19523 GTCAGCTCCAAGACACAT
66 CTCAGCTCCAAGGCACAT
** * * * * * *
19541 CATTTGCAGCATAGCTTAAGTTAAGAAGGGCTATATG-C--CAAAGACCCTCGAGTTTGATTACA
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
* *
19603 CTCAGCTTCGAGGGGCACAT
66 CTCAGC-TCCA-AGGCACAT
* * *
19623 CATTTGCAGCATAACTTAAGTCGAGAAGAGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
19688 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * * *
19707 CATTTGCAGTATAACTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCTCAAGTTCGATTACA
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
* *
19769 CTCAGCTTCAAGGGAACAT
66 CTCAGCTCCAA-GGCACAT
* *
19788 CATTTGCA-TATAGCTTAAGTCGAGAAGGGTTATCTG-C--CAAAGATCCTT-GAGTTCGATTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGA-CCTTCGAGTTCGACTAC
* * *
19848 ACTCAGCTTCGAGGGCACAT
65 GCTCAGC-TCCAAGGCACAT
* * * * *
19868 CATTTGCAGCACAACTTAAGTCTAGTAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
* *
19933 GTTCAGCTACAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
*
19952 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
* *
20017 GCTCAGCTCCAAGGTATAT
65 GCTCAGCTCCAAGGCACAT
* * * * * *
20036 CATTTGCAGCATAACTTAAGTCTATAATGGTTGTCTGCCAACAAAAGACCTTCGAGGTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
20101 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * *
20120 CATTTGTAGCATAGCTTAAGTCGAGAATGGCTATCTGCCAACCGAAGACCTTCGAGTTAGATTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
** * *
20185 ATTCAGCT-CAGAGGCAAACC
65 GCTCAGCTCCA-AGGCACA-T
* * * *
20205 CAAATTTACAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCGAAGACCTTCGAGTT
1 C--ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTT
20265 AGATTGCATT
Statistics
Matches: 1273, Mismatches: 212, Indels: 118
0.79 0.13 0.07
Matches are distributed among these distances:
72 16 0.01
73 3 0.00
74 1 0.00
75 11 0.01
76 25 0.02
77 1 0.00
79 1 0.00
80 234 0.18
81 91 0.07
82 43 0.03
83 46 0.04
84 601 0.47
85 120 0.09
86 27 0.02
87 53 0.04
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (83 bp):
CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACAT
Found at i:19086 original size:249 final size:249
Alignment explanation
Indices: 18636--20247 Score: 1713
Period size: 249 Copynumber: 6.5 Consensus size: 249
18626 TTAAAGACAA
* * * * *
18636 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAA-CAAAGACTTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * * * *
18700 GCTCAGCTCAAAGGCATATCATTTTCAACATAGTTTAAGTCGTGAAGGGCTATCTGCCAACCAAA
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAA
* * * * *
18765 GA-CCTTCAGGTTCGATTACACTCAGCTTCGAAGGCATATCATTTGCAGTATGACTTAAGTCAAG
127 GACCCTTGA-GTTCGATTACACTCAGCTTCGAAGGCACATCATTTGCAGCATAACTTAAGTCTAG
*
18829 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACAT
191 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * * * * * * * *
18888 AATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAATACATTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * *
18953 GCTCAGCTCCAAGGCACATCATTTGCAACATAGCTAAAGTCGAGAAGGGTTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* ** **
19018 CTTGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTATAGCATAACACAAAG-CTAGAAGG
131 CTTGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTGCAGCATAAC-TTAAGTCTAGAAGG
* * * *
19082 GTTATC--CATAACCAAAAGACCTTCTAGTTCGACTACGCTCAACTCCAAGGCATAT
195 GTTATCTGC-CAA-CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * *
19137 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * *
19202 GCTCAGTTCCAAGACACATTATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA-CATGCCAAAGAC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC-TGCCAAAGAC
* * * *
19266 CCTCGAGTTCGATTACACTCAGCTTCG-AGG---GT-A----CATCATAACTCAACG-CTAGAAG
130 CCTTGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTGCAGCATAACTTAA-GTCTAGAAG
** * * *
19321 GGTTATCTGTGACCAAAAGAGCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
194 GGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * *
19377 CATTTACAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* *
19442 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATTTGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * ** * * *
19507 TTTGAGTTCGACTACGGTCAGC-TCCAAGACACATCATTTGCAGCATAGCTTAAGT-TAAGAAGG
131 CTTGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTGCAGCATAACTTAAGTCT-AGAAGG
* * * * * * * *
19570 GCTATATG-C--C-AAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGGCACAT
195 GTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCA-AGGCACAT
* *
19623 CATTTGCAGCATAACTTAAGTCGAGAAGAGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* *
19688 GCTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
** * * * *
19753 CTCAAGTTCGATTACACTCAGCTTC-AAGGGAACATCATTTGCA-TATAGCTTAAGTCGAGAAGG
131 CTTGAGTTCGATTACACTCAGCTTCGAA-GGCACATCATTTGCAGCATAACTTAAGTCTAGAAGG
* * * *
19816 GTTATCTG-C--C-AAAGATCCTT-GAGTTCGATTACACTCAGCTTCGAGGGCACAT
195 GTTATCTGCCAACAAAAGA-CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACAT
* * * * *
19868 CATTTGCAGCACAACTTAAGTCTAGTAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* *
19933 GTTCAGCTACAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAA
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAA
* * * * * *
19998 GA-CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGTATATCATTTGCAGCATAACTTAAGTCTAT
127 GACCCTT-GAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTGCAGCATAACTTAAGTCTAG
* * *
20061 AATGGTTGTCTGCCAACAAAAGACCTTCGAGGTCGACTACGCTCAGCTCCAAGGCACAT
191 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * * * * *
20120 CATTTGTAGCATAGCTTAAGTCGAGAATGGCTATCTGCCAACCGAAGACCTTCGAGTTAGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
** * * * *
20185 ATTCAGCT-CAGAGGCAAACCCAAATTTACAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
66 GCTCAGCTCCA-AGGCACA-TC--ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
20248 CCGAAGACCT
Statistics
Matches: 1161, Mismatches: 156, Indels: 87
0.83 0.11 0.06
Matches are distributed among these distances:
239 4 0.00
240 204 0.18
241 1 0.00
243 1 0.00
244 26 0.02
245 123 0.11
246 197 0.17
247 21 0.02
248 45 0.04
249 283 0.24
250 9 0.01
251 6 0.01
252 116 0.10
253 91 0.08
255 34 0.03
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (249 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
CTTGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGG
TTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
Found at i:20885 original size:2 final size:2
Alignment explanation
Indices: 20878--20964 Score: 121
Period size: 2 Copynumber: 46.0 Consensus size: 2
20868 TATTTTGTTT
* *
20878 TA TA TA TA TA TA TA TA T- TA T- TT TG T- TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20916 T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20957 TA TA TA TA
1 TA TA TA TA
20965 GTAATATAGT
Statistics
Matches: 79, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
1 5 0.06
2 74 0.94
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (2 bp):
TA
Found at i:21027 original size:22 final size:23
Alignment explanation
Indices: 20987--21029 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
20977 GTGAAAATGT
20987 TTTTGACAAAATATTATATATAG
1 TTTTGACAAAATATTATATATAG
21010 TTTTGA-AAACAT-TTATATAT
1 TTTTGACAAA-ATATTATATAT
21030 TGTATAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (23 bp):
TTTTGACAAAATATTATATATAG
Found at i:21062 original size:27 final size:27
Alignment explanation
Indices: 21005--21062 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
20995 AAATATTATA
* * *
21005 TATAGTTTTGAAAACATTTATATATTG
1 TATAGTTTTGAAAACATTTAAAAACTG
*
21032 TATAGTTTTTAAAACATTTTAAAAACT-
1 TATAGTTTTGAAAACA-TTTAAAAACTG
21059 TATA
1 TATA
21063 TAGTATATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (27 bp):
TATAGTTTTGAAAACATTTAAAAACTG
Found at i:21132 original size:30 final size:31
Alignment explanation
Indices: 21060--21170 Score: 89
Period size: 32 Copynumber: 3.3 Consensus size: 31
21050 TTAAAAACTT
**
21060 ATATAGTATATAGTTTTTAAAACATTTTTAAA
1 ATATA-TATATAGTTTAAAAAACATTTTTAAA
21092 ATATAATATATAGTTTAAAAAACATTTTTTTAAAA
1 ATAT-ATATATAGTTTAAAAAACA--TTTTT-AAA
* * *
21127 TTATATAATATATAATTTTAAAAA-ATATTTTGAA
1 --ATAT-ATATATAGTTTAAAAAACAT-TTTTAAA
21161 ATATATATAT
1 ATATATATAT
21171 TATATAAATT
Statistics
Matches: 67, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
31 6 0.09
32 24 0.36
33 1 0.01
34 8 0.12
35 7 0.10
36 1 0.01
37 20 0.30
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (31 bp):
ATATATATATAGTTTAAAAAACATTTTTAAA
Found at i:21133 original size:37 final size:35
Alignment explanation
Indices: 21022--21176 Score: 129
Period size: 36 Copynumber: 4.4 Consensus size: 35
21012 TTGAAAACAT
* * ** *
21022 TTATATATTGTATAGTTTTTAAAACATTTTAAAAA
1 TTATATAATATATAGTTTAAAAAACATTTTTAAAA
* **
21057 CTTATATAGTATATAGTTTTTAAAACATTTTT-AAA
1 -TTATATAATATATAGTTTAAAAAACATTTTTAAAA
21092 --ATATAATATATAGTTTAAAAAACATTTTTTTAAAA
1 TTATATAATATATAGTTTAAAAAACA--TTTTTAAAA
* * *
21127 TTATATAATATATAATTTTAAAAA-ATATTTTGAAA
1 TTATATAATATATAGTTTAAAAAACAT-TTTTAAAA
*
21162 TATATATATTATATA
1 T-TATATAATATATA
21177 AATTACATTT
Statistics
Matches: 102, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
32 21 0.21
34 6 0.06
35 14 0.14
36 41 0.40
37 20 0.20
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (35 bp):
TTATATAATATATAGTTTAAAAAACATTTTTAAAA
Found at i:21213 original size:17 final size:17
Alignment explanation
Indices: 21193--21254 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
21183 ATTTAGTATA
21193 TTATTATTTTTTATTAT
1 TTATTATTTTTTATTAT
* *
21210 TTATTA-TTTTAATCAT
1 TTATTATTTTTTATTAT
21226 TTATTTATTTTAATT-TTAT
1 TTA-TTATTTT--TTATTAT
21245 TTATT-TTTTT
1 TTATTATTTTT
21255 ATTTACAGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
15 1 0.03
16 11 0.30
17 13 0.35
18 5 0.14
19 6 0.16
20 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATTATTTTTTATTAT
Found at i:21250 original size:23 final size:24
Alignment explanation
Indices: 21196--21259 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
21186 TAGTATATTA
*
21196 TTATTT-TTTA-TTATTTATTATT
1 TTATTTATTTATTTATTTATAATT
* *
21218 TTAATCATTTATTTATTT-TAATT
1 TTATTTATTTATTTATTTATAATT
*
21241 TTATTTATTTTTTTATTTA
1 TTATTTATTTATTTATTTA
21260 CAGGCCCAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 4 0.12
23 23 0.70
24 6 0.18
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (24 bp):
TTATTTATTTATTTATTTATAATT
Found at i:21258 original size:17 final size:17
Alignment explanation
Indices: 21193--21256 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 17
21183 ATTTAGTATA
21193 TTATTATTTTT-TATTAT
1 TTATT-TTTTTATATTAT
* *
21210 TTATTATTTTA-ATCAT
1 TTATTTTTTTATATTAT
*
21226 TTATTTATTTTAATTTTAT
1 TTATTT-TTTT-ATATTAT
21245 TTATTTTTTTAT
1 TTATTTTTTTAT
21257 TTACAGGCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 13 0.34
17 11 0.29
18 5 0.13
19 9 0.24
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTTTTTTATATTAT
Found at i:22080 original size:20 final size:20
Alignment explanation
Indices: 22055--22147 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
22045 TTTTCCCAAT
22055 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
22075 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
22095 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
22116 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
22137 TCGCAATGCGA
1 TCGCAATGCGA
22148 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:22097 original size:41 final size:41
Alignment explanation
Indices: 22052--22147 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
22042 CGATTTTCCC
22052 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
22093 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
22134 AAATCGCAATGCGA
1 AATTCGCAATGCGA
22148 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:22101 original size:21 final size:20
Alignment explanation
Indices: 22055--22147 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
22045 TTTTCCCAAT
*
22055 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
22075 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
22095 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
22116 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
22137 TCGCAATGCGA
1 TCGCAATGCGA
22148 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:22160 original size:41 final size:41
Alignment explanation
Indices: 22074--22208 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
22064 GAATAAGTAA
* * *
22074 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
22115 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
22156 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
22197 TTCGCAACGCGA
1 ATCGCAACGCGA
22209 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:22161 original size:20 final size:20
Alignment explanation
Indices: 22136--22230 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
22126 AATTGGGAAA
*
22136 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
22156 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
22177 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
22197 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
22217 TTCGCAACGCGATA
1 ATCGCAACGCGATA
22231 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:22445 original size:22 final size:22
Alignment explanation
Indices: 22417--22460 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
22407 CACTCTCTCA
*
22417 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
*
22439 CCCATCTCCGGCAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
22461 TATCTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:22749 original size:20 final size:20
Alignment explanation
Indices: 22724--22761 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22714 CGATTCTCTC
22724 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
22744 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
22762 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:24090 original size:18 final size:18
Alignment explanation
Indices: 24064--24108 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
24054 CTCCACTTTG
*
24064 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
24082 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
24100 GAGCCATCA
1 GAGCCATCA
24109 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:24633 original size:19 final size:20
Alignment explanation
Indices: 24590--24645 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
24580 CTCAACACGA
24590 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
24610 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
24629 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
24646 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:24653 original size:14 final size:14
Alignment explanation
Indices: 24634--24691 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
24624 ATGCGAAATG
24634 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
24648 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
24664 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
24680 AAAATCACAACG
1 AAAATCGCAACG
24692 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:24676 original size:32 final size:33
Alignment explanation
Indices: 24618--24708 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
24608 GGAAATGGCT
*
24618 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
24651 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
24683 ATCACAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
24709 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:24713 original size:19 final size:18
Alignment explanation
Indices: 24618--24713 Score: 66
Period size: 19 Copynumber: 5.6 Consensus size: 18
24608 GGAAATGGCT
24618 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
24637 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
24651 ATCGCAACGCGAAATG-AA
1 ATCGCAA-GCGAAATGAAA
*
24669 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
*
24683 ATCACAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
24702 ATCGCAATGCGA
1 ATCGCAA-GCGA
24714 TTTGTGTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 22
0.67 0.08 0.25
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 6 0.10
17 2 0.03
18 11 0.19
19 20 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:24759 original size:32 final size:32
Alignment explanation
Indices: 24720--24830 Score: 204
Period size: 32 Copynumber: 3.4 Consensus size: 32
24710 GCGATTTGTG
24720 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
24752 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
24784 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
*
24817 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
24831 AGCCATTTCC
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 59 0.77
33 18 0.23
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:24829 original size:19 final size:18
Alignment explanation
Indices: 24720--24871 Score: 121
Period size: 14 Copynumber: 8.9 Consensus size: 18
24710 GCGATTTGTG
24720 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
24736 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
24752 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
24768 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
24784 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
24800 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
* **
24817 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGAT-TTCA
*
24836 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGAT-TTCA
24856 TTTCGCGTTGCGATTT
1 TTTCGCGTTGCGATTT
24872 TAAGTTTCGT
Statistics
Matches: 109, Mismatches: 12, Indels: 28
0.73 0.08 0.19
Matches are distributed among these distances:
14 30 0.28
15 3 0.03
16 10 0.09
17 2 0.02
18 24 0.22
19 23 0.21
20 17 0.16
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.44
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:24849 original size:20 final size:19
Alignment explanation
Indices: 24815--24869 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
24805 TTGCGATTTT
*
24815 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
24834 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
24854 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
24870 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:26734 original size:14 final size:14
Alignment explanation
Indices: 26715--26750 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
26705 ATTGTTTAAT
26715 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
26729 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
26743 TGATTTGT
1 TGATTTGT
26751 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:27316 original size:14 final size:14
Alignment explanation
Indices: 27297--27332 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
27287 ATTGTTTAAT
27297 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
27311 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
27325 TGATTTGT
1 TGATTTGT
27333 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:27905 original size:14 final size:14
Alignment explanation
Indices: 27886--27921 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
27876 ATTCTTTAAT
27886 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
27900 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
27914 TGATTTGT
1 TGATTTGT
27922 TTAATTGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:28486 original size:14 final size:14
Alignment explanation
Indices: 28467--28502 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
28457 ATTGTTTAAT
28467 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
28481 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
28495 TGATTTGT
1 TGATTTGT
28503 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:29071 original size:14 final size:14
Alignment explanation
Indices: 29052--29087 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
29042 ATTGTTTAAT
29052 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
29066 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
29080 TGATTTGT
1 TGATTTGT
29088 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:29160 original size:584 final size:588
Alignment explanation
Indices: 26471--29461 Score: 5670
Period size: 585 Copynumber: 5.1 Consensus size: 588
26461 TGGTAAGTCA
*
26471 AATGCAAGTCTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
*
26536 TCAATAATTTGTTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
26601 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTAC-GGGTCACAAAGTTGTTGATTCT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
26665 TGATTCAATAATTGATGAAGAAAT-AG-A--ATTATTA-TTTTTGATTGTTTAATTGATTTGTAA
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
*
26725 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATATTTTGTGTTG-AATGTAATAG
261 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
26789 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
326 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
26854 CTATCGCAACGAGAAAATCGCAATGCGATTTTCATTTCGCATTGCGA-TTTCTCGTTGCGATAAC
391 CTATCGCAACGAGAAAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAAC
26918 CATTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAA
456 CATTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAA
26983 TGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACA
521 TGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACA
27048 CAT
586 CAT
27051 AATGCAAGTTTTGTTAAC--ATATA-TCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
27113 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC-TGTTTGAGCAAATGTTTGGTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
27177 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
27242 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
*
27307 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAT
261 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
27372 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
326 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
* *
27437 CTATCGCAACGAGAAAATCGCAATGCAATTTTCATTTCGCATTGCGATTTTCTCATTGCGATAAC
391 CTATCGCAACGAGAAAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAAC
27502 CATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCA
456 CA-TTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCA
27567 ATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATAC
520 ATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATAC
27632 ACAT
585 ACAT
27636 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
*
27701 TCAATAATTTTCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
27766 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
*
27831 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTCTTTAATTGATTTGTAA
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
27896 AAGATGATTTGTAAATGTTGATTTGTTTAATTG-TGTGTACATAATTTGTGTTGAAATGTAATAG
261 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
27960 TTGATTTGTTGA-TTTCAATCTGCTTTATGTTGAAGGC-AAACAGACTATCGCAACGCGAAATGG
326 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
28023 CTATCGCAACGAGAAAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAAC
391 CTATCGCAACGAGAAAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAAC
28088 CATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCA
456 CA-TTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCA
28153 ATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATAC
520 ATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATAC
28218 ACAT
585 ACAT
28222 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATG-TTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
28286 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
28351 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCAC-AAGTTGTTGATTCT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
*
28415 TGATTCAATAATTGATAAAGAAATAAG-A--ATTATTATTTTTTGATTGTTTAATTGATTTGTAA
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
28477 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
261 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
28542 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
326 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
28607 CTATCGCAACGAGAAAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAAC
391 CTATCGCAACGAGAAAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAAC
28672 CATTTCGCATTGCGATAGTC-AATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGC-A
456 CATTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAA
28735 TGTTCAAACTCAAGTTACT-ATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACA
521 TGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACA
28799 CAT
586 CAT
28802 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
* * * *
28867 TCAATAATTTACTGTTTGTAGGTTTTAGATATGTTGGAAGTCTTGTTTGAGAAAATGTTTGGTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
28932 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
28997 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
29062 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAA-TTGTGTTGAAATGTAATAG
261 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
29126 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
326 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
29191 CTATCGCAACGAGAAAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAAC
391 CTATCGCAACGAGAAAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAAC
29256 CATTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAA
456 CATTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAA
29321 TGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACA
521 TGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACA
29386 CAT
586 CAT
*
29389 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATATTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
29454 TCAATAAT
66 TCAATAAT
29462 AATTGTTAAA
Statistics
Matches: 2367, Mismatches: 20, Indels: 41
0.97 0.01 0.02
Matches are distributed among these distances:
576 64 0.03
577 126 0.05
578 7 0.00
579 1 0.00
580 110 0.05
581 223 0.09
582 204 0.09
583 165 0.07
584 320 0.14
585 403 0.17
586 288 0.12
587 150 0.06
588 122 0.05
589 184 0.08
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (588 bp):
AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
CTATCGCAACGAGAAAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAAC
CATTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAACTGAACAGATCATAGCAA
TGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACA
CAT
Found at i:30386 original size:24 final size:24
Alignment explanation
Indices: 30330--30388 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
30320 AGTCAGTATT
* *
30330 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
30354 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
30378 CGAATTTTGAT
1 CGAAATTTGAT
30389 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:30580 original size:12 final size:12
Alignment explanation
Indices: 30563--30587 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30553 ATATAATCCT
30563 GAAGAAGAAAAA
1 GAAGAAGAAAAA
30575 GAAGAAGAAAAA
1 GAAGAAGAAAAA
30587 G
1 G
30588 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:30596 original size:15 final size:15
Alignment explanation
Indices: 30578--30615 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
30568 AGAAAAAGAA
30578 GAAGAAAAAGTCCCC
1 GAAGAAAAAGTCCCC
30593 GAAGAAAAAGTCCCC
1 GAAGAAAAAGTCCCC
30608 GAAGAAAA
1 GAAGAAAA
30616 GAAAATGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.53, C:0.21, G:0.21, T:0.05
Consensus pattern (15 bp):
GAAGAAAAAGTCCCC
Found at i:32910 original size:19 final size:19
Alignment explanation
Indices: 32888--32985 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
32878 GGAAATTACT
32888 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
32907 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
32921 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
32940 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
32954 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
32973 ATCGCAACGCGAA
1 ATCGCAATGCGAA
32986 TTTAATTTCA
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:32930 original size:33 final size:33
Alignment explanation
Indices: 32888--32981 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
32878 GGAAATTACT
32888 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
32921 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
32954 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
32982 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:33003 original size:19 final size:20
Alignment explanation
Indices: 32981--33023 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
32971 AAATCGCAAC
32981 GCGAATTT-AATTTCACGTT
1 GCGAATTTCAATTTCACGTT
* * *
33000 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCACGTT
33020 GCGA
1 GCGA
33024 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCACGTT
Found at i:33183 original size:14 final size:14
Alignment explanation
Indices: 33164--33200 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
33154 CATCAATTAA
33164 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
33178 ACAAATCACCTTTT
1 ACAAATCAACTTTT
33192 ACAAATCAA
1 ACAAATCAA
33201 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:34600 original size:21 final size:21
Alignment explanation
Indices: 34571--34651 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
34561 GAATGGTGGG
*
34571 AGGGACCTCTTCAACGATGAT
1 AGGGGCCTCTTCAACGATGAT
* * * **
34592 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTCAACGATGAT
* * *
34613 AGGGGACTC-TCGAGGAATGAT
1 AGGGGCCTCTTCAACG-ATGAT
34634 AGGGGCCTCTTCAACGAT
1 AGGGGCCTCTTCAACGAT
34652 AGGAGTGGAC
Statistics
Matches: 41, Mismatches: 17, Indels: 4
0.66 0.27 0.06
Matches are distributed among these distances:
20 3 0.07
21 34 0.83
22 4 0.10
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.22
Consensus pattern (21 bp):
AGGGGCCTCTTCAACGATGAT
Found at i:34633 original size:42 final size:41
Alignment explanation
Indices: 34556--34678 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 41
34546 GTGAATCGGG
* * * *
34556 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGATAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
34598 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
34640 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
34679 CGAGTCGGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 4 0.06
42 59 0.86
43 6 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:35365 original size:21 final size:21
Alignment explanation
Indices: 35341--35415 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
35331 GTGACGGGAT
35341 AGGTGATGGCTCTCGTTGTAG
1 AGGTGATGGCTCTCGTTGTAG
* ** *
35362 AGGTGTATAG-TCGGGTTG-ATC
1 AGGTG-ATGGCTCTCGTTGTA-G
*
35383 AGGTGATGGCTCT-G-GGT-G
1 AGGTGATGGCTCTCGTTGTAG
35401 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
35416 AAGTGGAGGA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
18 13 0.32
19 2 0.05
20 5 0.12
21 18 0.44
22 3 0.07
ACGTcount: A:0.15, C:0.13, G:0.41, T:0.31
Consensus pattern (21 bp):
AGGTGATGGCTCTCGTTGTAG
Found at i:36793 original size:19 final size:19
Alignment explanation
Indices: 36675--36860 Score: 158
Period size: 19 Copynumber: 10.1 Consensus size: 19
36665 GTCTTTGGTT
*
36675 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
36694 GATAATGAAGAATCGCAACGC
1 GA-AATGAA-AATCGCAACGC
**
36715 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
36733 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
36749 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
36767 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
36782 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
* *
36802 GAAATTAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
*
36821 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
*
36840 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
36859 GA
1 GA
36861 TTTTGGTTTC
Statistics
Matches: 137, Mismatches: 16, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 61 0.45
20 30 0.22
21 15 0.11
22 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:36819 original size:39 final size:38
Alignment explanation
Indices: 36675--36860 Score: 158
Period size: 33 Copynumber: 5.1 Consensus size: 38
36665 GTCTTTGGTT
*
36675 GAAATGAAAATCGCAACGAGATAATGAAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAA-AATCGCAACGC
** *
36715 GGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** * *
36749 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
* *
36782 GAAATGAAAATCGCAACCGCGAAATTAAAATCACAACGC
1 GAAATGAAAATCGCAA-CGCGAAATGAAAATCGCAACGC
* *
36821 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
36859 GA
1 GA
36861 TTTTGGTTTC
Statistics
Matches: 122, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
33 42 0.34
34 13 0.11
35 3 0.02
36 1 0.01
38 21 0.17
39 28 0.23
41 14 0.11
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:36889 original size:19 final size:19
Alignment explanation
Indices: 36856--36926 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
36846 AAAATCGCAA
**
36856 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
36875 TGCGATTTTTATTTCGCGT
1 TGCGATTTTCATTTCGCGT
**
36894 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
*
36914 TGCGATTCTCATT
1 TGCGATTTTCATT
36927 CTCGAAACTA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 28 0.64
20 16 0.36
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:37468 original size:20 final size:20
Alignment explanation
Indices: 37443--37494 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
37433 CGCTAAGTAA
*
37443 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
37463 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
37483 ATCTCGTTGCGA
1 ATCGCGTTGCGA
37495 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:37532 original size:20 final size:20
Alignment explanation
Indices: 37443--37536 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
37433 CGCTAAGTAA
*
37443 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
37463 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
37483 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
**
37504 ATCGAATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
37524 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
37537 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 46 0.79
21 12 0.21
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:37555 original size:41 final size:41
Alignment explanation
Indices: 37525--37620 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
37515 ATAGTCAGTA
* * *
37525 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
37566 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
37607 TCGCATTGCGAATT
1 TCGCATTGCGAATT
37621 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:37569 original size:20 final size:20
Alignment explanation
Indices: 37525--37617 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
37515 ATAGTCAGTA
* **
37525 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
37546 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
37566 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
37587 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
37607 TCGCATTGCGA
1 TCGCATTGCGA
37618 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:45051 original size:37 final size:37
Alignment explanation
Indices: 44978--45051 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
44968 GTTGAAAAAT
* *
44978 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
45015 ATTTATATAATTTTTTTTATAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
45052 TGGTTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 13 0.41
38 19 0.59
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:50631 original size:47 final size:47
Alignment explanation
Indices: 50560--50658 Score: 117
Period size: 47 Copynumber: 2.1 Consensus size: 47
50550 GTTGAGTTCT
* * *
50560 TTTAAAAAAATAGTGAGTTCGTATGCGCTAAAATGTAACCGAATCAA
1 TTTAAAAAAATAGTAAATTCGTATGCGCTAAAAAGTAACCGAATCAA
* * * * **
50607 TTTAAAAAAATCGTAAATTTGTATGCGTTAAAAAGTAATCTTATCAA
1 TTTAAAAAAATAGTAAATTCGTATGCGCTAAAAAGTAACCGAATCAA
50654 TTTAA
1 TTTAA
50659 GAGTCTTAGT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (47 bp):
TTTAAAAAAATAGTAAATTCGTATGCGCTAAAAAGTAACCGAATCAA
Found at i:51619 original size:3 final size:3
Alignment explanation
Indices: 51611--51654 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
51601 CGGGCTTAAA
* *
51611 TAT TAT TAT TAAT TAT TAT TAT TAT GAT TAT TAA TAT TAT TAT T
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
51655 GCTTTTGCAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:53268 original size:21 final size:23
Alignment explanation
Indices: 53221--53275 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
53211 TGTGTCGTAG
53221 TATATAT-TGTTGTTGTGAATATA
1 TATATATATG-TGTTGTGAATATA
*
53244 TATATATATGTG-TGTGCATAT-
1 TATATATATGTGTTGTGAATATA
*
53265 TATATTTATGT
1 TATATATATGT
53276 ATTGACTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 10 0.34
22 8 0.28
23 9 0.31
24 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (23 bp):
TATATATATGTGTTGTGAATATA
Found at i:53720 original size:20 final size:21
Alignment explanation
Indices: 53695--53733 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53685 CAAATTTCAA
*
53695 GATTTT-TTATCAAGTTAAAG
1 GATTTTCTTAACAAGTTAAAG
53715 GATTTTCTTAACAAGTTAA
1 GATTTTCTTAACAAGTTAA
53734 TTCGAAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.44
Consensus pattern (21 bp):
GATTTTCTTAACAAGTTAAAG
Found at i:57583 original size:31 final size:30
Alignment explanation
Indices: 57545--57613 Score: 111
Period size: 31 Copynumber: 2.3 Consensus size: 30
57535 GTTTACTTCA
*
57545 AAATGATTAAGCGCTAAATAATTCAAATGTT
1 AAATGATTAAGCGCTAAATAATTC-AATATT
*
57576 AAATGATTAAGCGCTAAATGATTCAATATT
1 AAATGATTAAGCGCTAAATAATTCAATATT
57606 AAATGATT
1 AAATGATT
57614 CAGAGACTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 13 0.36
31 23 0.64
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (30 bp):
AAATGATTAAGCGCTAAATAATTCAATATT
Found at i:57595 original size:15 final size:15
Alignment explanation
Indices: 57545--57598 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
57535 GTTTACTTCA
57545 AAATGATTAAGCGCT
1 AAATGATTAAGCGCT
* ** *
57560 AAATAATTCAAATGTT
1 AAATGATT-AAGCGCT
57576 AAATGATTAAGCGCT
1 AAATGATTAAGCGCT
57591 AAATGATT
1 AAATGATT
57599 CAATATTAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
15 19 0.63
16 11 0.37
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.31
Consensus pattern (15 bp):
AAATGATTAAGCGCT
Found at i:58232 original size:16 final size:17
Alignment explanation
Indices: 58211--58250 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
58201 TTGAAAATCA
58211 AATATT-GTTTTTCAAC
1 AATATTGGTTTTTCAAC
58227 AATATTTGGTTTTTCAAC
1 AATA-TTGGTTTTTCAAC
58245 AATATT
1 AATATT
58251 TGGCAACCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.18
17 4 0.18
18 14 0.64
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (17 bp):
AATATTGGTTTTTCAAC
Found at i:58240 original size:18 final size:18
Alignment explanation
Indices: 58217--58253 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
58207 ATCAAATATT
58217 GTTTTTCAACAATATTTG
1 GTTTTTCAACAATATTTG
58235 GTTTTTCAACAATATTTG
1 GTTTTTCAACAATATTTG
58253 G
1 G
58254 CAACCATCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.49
Consensus pattern (18 bp):
GTTTTTCAACAATATTTG
Done.