Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 62
Found at i:1353687 original size:27 final size:27
Alignment explanation
Indices: 1353622--1353681 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 27
1353612 AAAAATTTAC
*
1353622 AGGACTAAAATAACAAAAACAGAAAGTTAA
1 AGGACT-AAAT-A-AAAAACAGAAAGTAAA
1353652 AGGACTAAATAAAAAACAGAAAGTAAA
1 AGGACTAAATAAAAAACAGAAAGTAAA
1353679 AGG
1 AGG
1353682 GTTAAACCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 18 0.62
28 1 0.03
29 4 0.14
30 6 0.21
ACGTcount: A:0.63, C:0.08, G:0.17, T:0.12
Consensus pattern (27 bp):
AGGACTAAATAAAAAACAGAAAGTAAA
Found at i:1364529 original size:25 final size:24
Alignment explanation
Indices: 1364501--1364548 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1364491 CAGAATTTGA
*
1364501 GGATAGAAGTGCCAAAGAAAATAAT
1 GGATAAAAG-GCCAAAGAAAATAAT
* *
1364526 GGATAAAAGGCCCAGGAAAATAA
1 GGATAAAAGGCCAAAGAAAATAA
1364549 CCAATATAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.52, C:0.10, G:0.25, T:0.12
Consensus pattern (24 bp):
GGATAAAAGGCCAAAGAAAATAAT
Found at i:1369823 original size:20 final size:20
Alignment explanation
Indices: 1369800--1369838 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1369790 CAAATCTATT
1369800 GACACATACTAAAATAGAAC
1 GACACATACTAAAATAGAAC
* *
1369820 GACACGTATTAAAATAGAA
1 GACACATACTAAAATAGAA
1369839 ACAAAATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.15, G:0.13, T:0.18
Consensus pattern (20 bp):
GACACATACTAAAATAGAAC
Found at i:1374055 original size:6 final size:6
Alignment explanation
Indices: 1373784--1374053 Score: 345
Period size: 6 Copynumber: 45.8 Consensus size: 6
1373774 AAGTTCAAGA
* * * * * * * *
1373784 AGAAGA AGAAGA AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * *
1373832 AGGAGG AGAAGGG AGGAGG AGAAGG AGGAGA AGAAGG AGGAGG AGAAGG
1 AGAAGG AGAA-GG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* *
1373881 AGGAGA AGAAGG AG-A-- AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1373926 AG-A-- AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1373971 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
*
1374019 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGA AGAAG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAG
1374054 AAAGGCTTTT
Statistics
Matches: 241, Mismatches: 16, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
3 4 0.02
4 2 0.01
5 2 0.01
6 228 0.95
7 5 0.02
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:1377645 original size:21 final size:21
Alignment explanation
Indices: 1377619--1377693 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
1377609 GTTTCCAGAT
* *
1377619 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
1377640 TCGCAATGCGAACTTGGACCA
1 TCGCAATGCGAACTTGGACTA
*
1377661 TCGCAATGCAAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1377682 TCGCAATGCGAA
1 TCGCAATGCGAA
1377694 TATGTAAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:1377837 original size:6 final size:6
Alignment explanation
Indices: 1377798--1377836 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1377788 GACACGTATT
*
1377798 ACCACG ACCACG ACCACG ACCACG ACCACG ACCCCG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1377837 CGAGACGGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.31, C:0.54, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1378340 original size:6 final size:6
Alignment explanation
Indices: 1378324--1378355 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1378314 GTCCATCTCG
1378324 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1378356 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:1378523 original size:21 final size:21
Alignment explanation
Indices: 1378499--1378548 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1378489 CCAAGTTCGC
* *
1378499 AAGTTCGCATTGTGATAGTCG
1 AAGTTCGCATCGCGATAGTCG
*
1378520 AAGTTCGCGTCGCGATAGTCG
1 AAGTTCGCATCGCGATAGTCG
1378541 AAGTTCGC
1 AAGTTCGC
1378549 GTTGCGAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (21 bp):
AAGTTCGCATCGCGATAGTCG
Found at i:1378549 original size:21 final size:21
Alignment explanation
Indices: 1378512--1378555 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1378502 TTCGCATTGT
1378512 GATAGTCGAAGTTCGCGTCGC
1 GATAGTCGAAGTTCGCGTCGC
*
1378533 GATAGTCGAAGTTCGCGTTGC
1 GATAGTCGAAGTTCGCGTCGC
1378554 GA
1 GA
1378556 ATCGATTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.25
Consensus pattern (21 bp):
GATAGTCGAAGTTCGCGTCGC
Found at i:1378990 original size:25 final size:26
Alignment explanation
Indices: 1378937--1378991 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
1378927 AAAAGCTAAA
* *
1378937 TTTATATTAAATTGAAAATGATTTTT
1 TTTATAGTAAATTGAAAATGATTTGT
1378963 TTTATAGTAAATT-AAAATG-TTATGT
1 TTTATAGTAAATTGAAAATGATT-TGT
1378988 TTTA
1 TTTA
1378992 ATTATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 2 0.08
25 12 0.46
26 12 0.46
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (26 bp):
TTTATAGTAAATTGAAAATGATTTGT
Found at i:1379402 original size:15 final size:16
Alignment explanation
Indices: 1379382--1379414 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1379372 TATATTTTTA
*
1379382 TATTAATTAA-TAATT
1 TATTAATCAATTAATT
1379397 TATTAATCAATTAATT
1 TATTAATCAATTAATT
1379413 TA
1 TA
1379415 AATCAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTAATCAATTAATT
Found at i:1385472 original size:3 final size:3
Alignment explanation
Indices: 1385464--1385489 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1385454 TTTGATTGAC
1385464 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1385490 ATAAAACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1387597 original size:23 final size:22
Alignment explanation
Indices: 1387554--1387598 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1387544 TTTGTTCGAG
***
1387554 ATTCTATTTAATTTTTTTATAA
1 ATTCTATTTAATTTAAATATAA
1387576 ATTCTATTTAAATTTAAATATAA
1 ATTCTATTT-AATTTAAATATAA
1387599 TTATTTATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTCTATTTAATTTAAATATAA
Found at i:1388429 original size:3 final size:3
Alignment explanation
Indices: 1388421--1388479 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
1388411 AAATTTAAAT
** *
1388421 TTA TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA ATA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
1388470 TTA TTTA TTA
1 TTA -TTA TTA
1388480 AATATTACAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 42 0.88
4 6 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1388449 original size:18 final size:18
Alignment explanation
Indices: 1388426--1388486 Score: 86
Period size: 18 Copynumber: 3.2 Consensus size: 18
1388416 TAAATTTATT
1388426 ATTATTATTATTATTAAA
1 ATTATTATTATTATTAAA
*
1388444 ATTATTATTATTATTAAT
1 ATTATTATTATTATTAAA
1388462 ATTATTTATTATTTATTAAA
1 ATTA-TTATTA-TTATTAAA
1388482 TATTA
1 -ATTA
1388487 CAAAGCCCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 21 0.55
19 6 0.16
20 7 0.18
21 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTATTATTATTATTAAA
Found at i:1389697 original size:19 final size:20
Alignment explanation
Indices: 1389673--1389718 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1389663 TCTTTCATAA
1389673 TATTTTGAAT-TATTATATT
1 TATTTTGAATATATTATATT
* *
1389692 TATTTTTAATATTTTATATT
1 TATTTTGAATATATTATATT
1389712 TAGTTTT
1 TA-TTTT
1389719 ATAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 10 0.43
21 4 0.17
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (20 bp):
TATTTTGAATATATTATATT
Found at i:1389708 original size:20 final size:20
Alignment explanation
Indices: 1389680--1389736 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1389670 TAATATTTTG
1389680 AATTATTATATTTATTTTTA-
1 AATT-TTATATTTATTTTTAT
*
1389700 ATATTTTATATTTAGTTTTAT
1 A-ATTTTATATTTATTTTTAT
*
1389721 AATTTTA-ATTTCTTTT
1 AATTTTATATTTATTTT
1389737 ATTTTGATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 7 0.22
20 21 0.66
21 4 0.12
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
AATTTTATATTTATTTTTAT
Found at i:1390551 original size:20 final size:20
Alignment explanation
Indices: 1390518--1390555 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1390508 AAATTTTTTA
* *
1390518 TATATCTTAGTATTTCATAG
1 TATATATTAATATTTCATAG
1390538 TATATATTAATATTTCAT
1 TATATATTAATATTTCAT
1390556 TTTATTTGCA
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:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (20 bp):
TATATATTAATATTTCATAG
Found at i:1393978 original size:36 final size:36
Alignment explanation
Indices: 1393894--1393991 Score: 121
Period size: 36 Copynumber: 2.7 Consensus size: 36
1393884 TTACATTCTT
* *
1393894 ATTCTTACTTTTTACATCTTTGCATTTCCATCTTGT
1 ATTCTTACTTTTTACATCTTTGCATTACCATCTTGC
1393930 ATTCTTACTTTTTACATCTTTGCATTACACAGT-TTGC
1 ATTCTTACTTTTTACATCTTTGCATTAC-CA-TCTTGC
*
1393967 ATTCTTA-TTTTTGCAT-TTATGCATT
1 ATTCTTACTTTTTACATCTT-TGCATT
1393992 TTCGCATTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
35 2 0.04
36 41 0.73
37 12 0.21
38 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.54
Consensus pattern (36 bp):
ATTCTTACTTTTTACATCTTTGCATTACCATCTTGC
Found at i:1397588 original size:188 final size:188
Alignment explanation
Indices: 1397271--1397637 Score: 734
Period size: 188 Copynumber: 2.0 Consensus size: 188
1397261 CACCGGCAAC
1397271 AAGGTCGAATTTGACAAATCTACTCATTAATTGCTCTAACCGATCATCATTCAGTTCTTGCACAT
1 AAGGTCGAATTTGACAAATCTACTCATTAATTGCTCTAACCGATCATCATTCAGTTCTTGCACAT
1397336 CTGTTTTCAAAAGTATACCAAGACAGTAGAAGGTAACCTCTGCATCACTGATTTCAGAGAAAAGA
66 CTGTTTTCAAAAGTATACCAAGACAGTAGAAGGTAACCTCTGCATCACTGATTTCAGAGAAAAGA
1397401 GACAAGACATTGATATCACCGGGGAACATGTCTCTAGCATATCCTCCTCGGTATGGTT
131 GACAAGACATTGATATCACCGGGGAACATGTCTCTAGCATATCCTCCTCGGTATGGTT
1397459 AAGGTCGAATTTGACAAATCTACTCATTAATTGCTCTAACCGATCATCATTCAGTTCTTGCACAT
1 AAGGTCGAATTTGACAAATCTACTCATTAATTGCTCTAACCGATCATCATTCAGTTCTTGCACAT
1397524 CTGTTTTCAAAAGTATACCAAGACAGTAGAAGGTAACCTCTGCATCACTGATTTCAGAGAAAAGA
66 CTGTTTTCAAAAGTATACCAAGACAGTAGAAGGTAACCTCTGCATCACTGATTTCAGAGAAAAGA
1397589 GACAAGACATTGATATCACCGGGGAACATGTCTCTAGCATATCCTCCTC
131 GACAAGACATTGATATCACCGGGGAACATGTCTCTAGCATATCCTCCTC
1397638 CTCGTGTATG
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
188 179 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (188 bp):
AAGGTCGAATTTGACAAATCTACTCATTAATTGCTCTAACCGATCATCATTCAGTTCTTGCACAT
CTGTTTTCAAAAGTATACCAAGACAGTAGAAGGTAACCTCTGCATCACTGATTTCAGAGAAAAGA
GACAAGACATTGATATCACCGGGGAACATGTCTCTAGCATATCCTCCTCGGTATGGTT
Found at i:1398405 original size:31 final size:31
Alignment explanation
Indices: 1398364--1398426 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1398354 GCACATATAA
*
1398364 AATCTATCAACTCTGTAATTGAAGAATTCAG
1 AATCTATCAACTCTGCAATTGAAGAATTCAG
* **
1398395 AATCTGTCAACTCTGCAATTGATTAATTCAG
1 AATCTATCAACTCTGCAATTGAAGAATTCAG
1398426 A
1 A
1398427 CCACATCTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (31 bp):
AATCTATCAACTCTGCAATTGAAGAATTCAG
Found at i:1400371 original size:50 final size:50
Alignment explanation
Indices: 1400296--1400445 Score: 255
Period size: 50 Copynumber: 3.0 Consensus size: 50
1400286 TGATTGAGAA
1400296 ATTTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC
1 ATTTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC
1400346 ATTTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC
1 ATTTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC
* * * * *
1400396 ATCTAAGCAGAAACCACAGAAAATGATGCATGTGTTGTCAAATGTTTTAC
1 ATTTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC
1400446 GAACTAGTTA
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 95 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (50 bp):
ATTTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC
Found at i:1400840 original size:22 final size:22
Alignment explanation
Indices: 1400814--1400890 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
1400804 CATCTACCTC
1400814 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1400836 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
1400858 TTTAAAGATGATAGATTCCCTT
1 TTCAAAGATGATAGATTCTCTT
*
1400880 TTCACAGATGA
1 TTCAAAGATGA
1400891 AAGCTTTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1401691 original size:76 final size:76
Alignment explanation
Indices: 1401565--1402714 Score: 1951
Period size: 76 Copynumber: 15.4 Consensus size: 76
1401555 CTATTTCCTA
* *
1401565 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTCTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1401630 AGCCTTAGGGT
66 AGCCTTAGGGT
1401641 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1401706 AGCCTTAGGGT
66 AGCCTTAGGGT
1401717 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1401782 AGCCTTAGAGT
66 AGCCTTAGGGT
1401793 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1401858 AACCTTAGGCT
66 AGCCTTAGGGT
*
1401869 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1401934 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1401945 CATCTGTAAGTCCTACAGTACATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1402009 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1402020 CATCTGT-AGTCCTACAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1402084 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1402095 CATCTGTAAGTCCTACAGTGTATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1402160 AGCCTTAGGGT
66 AGCCTTAGGGT
* * * *
1402171 TATCTGTAAGTCCTACAATGTATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1402236 AACCTTGGGGT
66 AGCCTTAGGGT
*
1402247 CATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1402311 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1402322 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1402386 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1402397 CATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1402460 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1402471 CATCTGTAAGTCATGCAGTGCATGATGTTTCC-AAAAGCCTTC-GGAGC-TTTTGATG-TTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1402532 AGCCTTA-GGT
66 AGCCTTAGGGT
*
1402542 CATCTGTAAGTCCTGCA--GCATGAT-TTTCCAAAAAGCCTTCGGGAGC-TTTTGATG-TTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1402602 AGCCTTAGGGT
66 AGCCTTAGGGT
1402613 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1402678 A-CCTTCGGGT
66 AGCCTTAGGGT
* *
1402688 CATCTGT-A-CCCTTCAGTGCATGATGTT
1 CATCTGTAAGTCCTACAGTGCATGATGTT
1402715 CAAATATTTC
Statistics
Matches: 1030, Mismatches: 33, Indels: 25
0.95 0.03 0.02
Matches are distributed among these distances:
68 5 0.00
69 17 0.02
70 26 0.03
71 38 0.04
72 13 0.01
73 37 0.04
74 145 0.14
75 219 0.21
76 530 0.51
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1402156 original size:302 final size:304
Alignment explanation
Indices: 1401565--1402714 Score: 1969
Period size: 302 Copynumber: 3.8 Consensus size: 304
1401555 CTATTTCCTA
*
1401565 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTCTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1401630 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
1401695 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
*
1401760 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGAGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
* *
1401825 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTAGGCT
261 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
1401869 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1401934 AGCCTTAGGGTCATCTGTAAGTCCTACAGTACATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
1401998 GATGTTTTCAAAGCCTTAGGGTCATCTGT-AGTCCTACAGTGCATGATGTTTCCAAAAAGCATTC
131 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
*
1402062 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGTATGATGTTTCC
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
1402127 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
261 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
* * * * *
1402171 TATCTGTAAGTCCTACAATGTATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * *
1402236 AACCTTGGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
1402300 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
*
1402365 GGGAGC-TTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCC
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
1402429 -AAAAGCCTTCGGGAGC-TTTTGATGTTTTCAAAGCCTTAGGGT
261 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
*
1402471 CATCTGTAAGTCATGCAGTGCATGATGTTTCC-AAAAGCCTTC-GGAGC-TTTTGATG-TTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1402532 AGCCTTA-GGTCATCTGTAAGTCCTGCA--GCATGAT-TTTCCAAAAAGCCTTCGGGAGC-TTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
1402592 GATG-TTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
* * *
1402656 GGGAGCTTTTTGATGTTTTCAAA-CCTTCGGGTCATCTGT-A-CCCTTCAGTGCATGATGTT
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTT
1402715 CAAATATTTC
Statistics
Matches: 810, Mismatches: 32, Indels: 23
0.94 0.04 0.03
Matches are distributed among these distances:
289 17 0.02
290 1 0.00
291 80 0.10
292 29 0.04
293 23 0.03
295 20 0.02
296 11 0.01
297 8 0.01
298 4 0.00
299 10 0.01
300 53 0.07
301 32 0.04
302 327 0.40
303 72 0.09
304 123 0.15
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (304 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
Found at i:1402855 original size:3 final size:3
Alignment explanation
Indices: 1402847--1402909 Score: 58
Period size: 3 Copynumber: 21.0 Consensus size: 3
1402837 AAATTTAAAT
** * *
1402847 TTA TTA TTA TTA AAA TTA -AA TTA TTA TTA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1402894 -TA TTTA TTA TTTA TTA
1 TTA -TTA TTA -TTA TTA
1402910 AATATTACAA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
2 3 0.06
3 41 0.84
4 5 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1402872 original size:20 final size:21
Alignment explanation
Indices: 1402835--1402878 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
1402825 ATTTTTCATT
*
1402835 TTAAATTTAAATTTATTATTA
1 TTAAAATTAAATTTATTATTA
1402856 TTAAAATTAAA-TTATTATTA
1 TTAAAATTAAATTTATTATTA
1402876 TTA
1 TTA
1402879 TTATTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAAAATTAAATTTATTATTA
Found at i:1407732 original size:60 final size:60
Alignment explanation
Indices: 1407623--1407738 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
1407613 GTCGGAGATC
** * ****
1407623 ATTTTATAACTTTTAATTTTTGGAAGGCTCAACAAAACAACGTTTTATAGTTAGAATACT
1 ATTTTATAACTTTTAATAGTTGGAAGACTCAACAAAACAACACACTATAGTTAGAATACT
*
1407683 ATTTTGTAACTTTTAATAGTT-GAATGACTCAACAAAACAACACACTATAGTTAGAA
1 ATTTTATAACTTTTAATAGTTGGAA-GACTCAACAAAACAACACACTATAGTTAGAA
1407739 GATCATTTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 3 0.06
60 44 0.94
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTTGGAAGACTCAACAAAACAACACACTATAGTTAGAATACT
Found at i:1408058 original size:12 final size:12
Alignment explanation
Indices: 1408041--1408065 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1408031 AAACTTGAAC
1408041 TGAATTAAGAGG
1 TGAATTAAGAGG
1408053 TGAATTAAGAGG
1 TGAATTAAGAGG
1408065 T
1 T
1408066 AGATTTAAAA
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:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (12 bp):
TGAATTAAGAGG
Found at i:1408465 original size:3 final size:3
Alignment explanation
Indices: 1408457--1408482 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1408447 TGAAAAACTT
1408457 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
1408483 CTCGGTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1416819 original size:46 final size:46
Alignment explanation
Indices: 1416763--1416896 Score: 250
Period size: 46 Copynumber: 2.9 Consensus size: 46
1416753 CAAAAAGGAA
* *
1416763 AGAACTCCAAATAAGTTTCTAAAAGACATTGCAGATAGTTATGGGG
1 AGAACCCCAAATGAGTTTCTAAAAGACATTGCAGATAGTTATGGGG
1416809 AGAACCCCAAATGAGTTTCTAAAAGACATTGCAGATAGTTATGGGG
1 AGAACCCCAAATGAGTTTCTAAAAGACATTGCAGATAGTTATGGGG
1416855 AGAACCCCAAATGAGTTTCTAAAAGACATTGCAGATAGTTAT
1 AGAACCCCAAATGAGTTTCTAAAAGACATTGCAGATAGTTAT
1416897 TTAAGATACA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (46 bp):
AGAACCCCAAATGAGTTTCTAAAAGACATTGCAGATAGTTATGGGG
Found at i:1423687 original size:37 final size:36
Alignment explanation
Indices: 1423643--1423759 Score: 157
Period size: 35 Copynumber: 3.2 Consensus size: 36
1423633 TGGCAATCAA
*
1423643 CTTTGAAAATTTAGTTTTTAAAGTTTGGTAAATTTTT
1 CTTTGAAAA-TTAGTTTTTAAAGTTTGGTAAATGTTT
*
1423680 CTTTGAAAATGA-TTTTTAAAGTTTGGTAAATGTTT
1 CTTTGAAAATTAGTTTTTAAAGTTTGGTAAATGTTT
* *
1423715 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAATTAGTTTTT-AAAGTTTGGTAAATGTTT
*
1423752 -GTTGAAAA
1 CTTTGAAAA
1423760 ATGATAATGG
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
35 32 0.44
36 14 0.19
37 26 0.36
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (36 bp):
CTTTGAAAATTAGTTTTTAAAGTTTGGTAAATGTTT
Found at i:1427811 original size:36 final size:37
Alignment explanation
Indices: 1427697--1427816 Score: 165
Period size: 35 Copynumber: 3.3 Consensus size: 37
1427687 TGGCAACCAA
* *
1427697 CTTTGAAAAATTGGTTTCCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
1427734 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* * *
1427769 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATATTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
1427806 -GTTGAAAAATA
1 CTTTGAAAAATA
1427817 ATAATAGGAT
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 29 0.38
36 20 0.26
37 27 0.36
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1451026 original size:2 final size:2
Alignment explanation
Indices: 1451021--1451057 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1451011 TATATATTAC
1451021 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1451058 TACCTCATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1454576 original size:16 final size:16
Alignment explanation
Indices: 1454555--1454587 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1454545 TACTATTCAT
*
1454555 GTGAATAGTGAATTTC
1 GTGAATAGTGAAATTC
1454571 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
1454587 G
1 G
1454588 GTCAGCGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:1477557 original size:59 final size:60
Alignment explanation
Indices: 1477435--1477566 Score: 153
Period size: 59 Copynumber: 2.2 Consensus size: 60
1477425 CTGAGGTGAC
**
1477435 GAAAGGCGCATCCCCAGGGATGCGATTTACCTGGTTTTACGCTGAGTTAGATGTCACGTGT
1 GAAAGGCGCATCCCCAGGGATGCGATTTACCT-GTTTTACGCTGAGTTAGATACCACGTGT
* ** *
1477496 GAAAGGCGCATCCCC-GGGATGCGCTTTACCT-TTATTTTGCTGA-TTCAGTTACCACGTGT
1 GAAAGGCGCATCCCCAGGGATGCGATTTACCTGTT-TTACGCTGAGTT-AGATACCACGTGT
*
1477555 GAAAGACGCATC
1 GAAAGGCGCATC
1477567 TCCGAAAGAC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
58 4 0.06
59 28 0.45
60 15 0.24
61 15 0.24
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (60 bp):
GAAAGGCGCATCCCCAGGGATGCGATTTACCTGTTTTACGCTGAGTTAGATACCACGTGT
Found at i:1477901 original size:19 final size:20
Alignment explanation
Indices: 1477870--1477907 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1477860 TTTAAATTTA
1477870 TTAATTAATTATTTTTTGTG
1 TTAATTAATTATTTTTTGTG
1477890 TTAATT-ATTATTTTTTGT
1 TTAATTAATTATTTTTTGT
1477908 CTACAGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (20 bp):
TTAATTAATTATTTTTTGTG
Found at i:1478033 original size:24 final size:25
Alignment explanation
Indices: 1477983--1478040 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
1477973 AGCGATATGG
*
1477983 TAATATTT-TTTTTATAATTAATGT
1 TAATATTTATTGTTATAATTAATGT
**
1478007 TAATATTTATTGTTATGTTTAAT-T
1 TAATATTTATTGTTATAATTAATGT
1478031 TAA-ATTTATT
1 TAATATTTATT
1478041 ATGAATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.23
24 12 0.40
25 11 0.37
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (25 bp):
TAATATTTATTGTTATAATTAATGT
Found at i:1479698 original size:21 final size:20
Alignment explanation
Indices: 1479666--1479735 Score: 104
Period size: 21 Copynumber: 3.4 Consensus size: 20
1479656 TATGTCATCT
1479666 CCGCACGGTTACATTCCTAGC
1 CCGCA-GGTTACATTCCTAGC
1479687 CCGCAGGATTACATTCCTAGC
1 CCGCAGG-TTACATTCCTAGC
*
1479708 CCGCCAGGTTACATGCCTAGC
1 CCG-CAGGTTACATTCCTAGC
1479729 CCGCAGG
1 CCGCAGG
1479736 GTTTTATACC
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
20 6 0.13
21 36 0.78
22 4 0.09
ACGTcount: A:0.20, C:0.37, G:0.23, T:0.20
Consensus pattern (20 bp):
CCGCAGGTTACATTCCTAGC
Found at i:1480291 original size:34 final size:34
Alignment explanation
Indices: 1480248--1480314 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
1480238 ATAAATGTTT
*
1480248 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
1 TTAAAATACAAATAATAGTATTCAAAATTTAAAA
* *
1480282 TTAAAATACAAATAATATTATTCGAAATTTAAA
1 TTAAAATACAAATAATAGTATTCAAAATTTAAA
1480315 TTATTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (34 bp):
TTAAAATACAAATAATAGTATTCAAAATTTAAAA
Found at i:1494034 original size:32 final size:32
Alignment explanation
Indices: 1493966--1494067 Score: 79
Period size: 32 Copynumber: 3.3 Consensus size: 32
1493956 TTAAATAGTT
* * * * *
1493966 ATTATATTTTATATTAATATAAT-TATATAAA
1 ATTATTTTTTTTATTAAAATAATATTTATATA
1493997 TATTATTTTTTTTATTAAAATAATATTTATATA
1 -ATTATTTTTTTTATTAAAATAATATTTATATA
* * * *
1494030 ATTA--TTATTTATTTAAAT-TTATTAAT-TA
1 ATTATTTTTTTTATTAAAATAATATTTATATA
1494058 ATTATTTTTT
1 ATTATTTTTT
1494068 GTGTTAATTA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
28 6 0.11
29 6 0.11
30 15 0.26
32 24 0.42
33 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
ATTATTTTTTTTATTAAAATAATATTTATATA
Found at i:1494076 original size:28 final size:27
Alignment explanation
Indices: 1494028--1494080 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
1494018 AATATTTATA
1494028 TAATTATTATTTATTTAAATTTATTAAT
1 TAATTATTATTTATTTAAA-TTATTAAT
* *
1494056 TAATTATTTTTTGTGTT-AATTATTA
1 TAATTATTATTTAT-TTAAATTATTA
1494081 TTTTTTGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 6 0.27
28 14 0.64
29 2 0.09
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (27 bp):
TAATTATTATTTATTTAAATTATTAAT
Found at i:1494082 original size:19 final size:20
Alignment explanation
Indices: 1494051--1494088 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1494041 TTTAAATTTA
1494051 TTAATTAATTATTTTTTGTG
1 TTAATTAATTATTTTTTGTG
1494071 TTAATT-ATTATTTTTTGT
1 TTAATTAATTATTTTTTGT
1494089 CTACAGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (20 bp):
TTAATTAATTATTTTTTGTG
Found at i:1495880 original size:21 final size:21
Alignment explanation
Indices: 1495850--1495922 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
1495840 TATGTCATCT
*
1495850 CCGCACGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
1495871 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
1495892 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
1495913 CCGCAGGGTT
1 CCGCAGGGTT
1495923 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.36, G:0.25, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:1496479 original size:34 final size:34
Alignment explanation
Indices: 1496433--1496499 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
1496423 ATAAATGTTT
*
1496433 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
1 TTAAAATACAAATAATAGTATTCAAAATTTAAAA
* * *
1496467 TTAAAATGCAAATAATATTATTCGAAATTTAAA
1 TTAAAATACAAATAATAGTATTCAAAATTTAAA
1496500 TTATTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (34 bp):
TTAAAATACAAATAATAGTATTCAAAATTTAAAA
Found at i:1505809 original size:17 final size:17
Alignment explanation
Indices: 1505784--1505829 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
1505774 AAAAAATGTT
1505784 GAAAAAAAAATAGCAGTTC
1 GAAAAAAAAA-A-CAGTTC
*
1505803 GAAAAAAAAAACTGTTC
1 GAAAAAAAAAACAGTTC
1505820 GAAAAAAAAA
1 GAAAAAAAAA
1505830 GACATGAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 15 0.58
18 1 0.04
19 10 0.38
ACGTcount: A:0.65, C:0.09, G:0.13, T:0.13
Consensus pattern (17 bp):
GAAAAAAAAAACAGTTC
Found at i:1510223 original size:20 final size:21
Alignment explanation
Indices: 1510169--1510223 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 21
1510159 ATTATATTTT
* *
1510169 ATATTAATATAATT-ATATAA
1 ATATTTATATAATTAAAATAA
* * *
1510189 ATATTTTTTTTATTAAAAT-A
1 ATATTTATATAATTAAAATAA
1510209 ATATTTATATAATTA
1 ATATTTATATAATTA
1510224 TTATTTATTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATTTATATAATTAAAATAA
Found at i:1510270 original size:17 final size:18
Alignment explanation
Indices: 1510241--1510276 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
1510231 TTTAAATTTA
1510241 TTAATTAATTATTTTTTG
1 TTAATTAATTATTTTTTG
1510259 TTAATT-ATTATTTTTTG
1 TTAATTAATTATTTTTTG
1510276 T
1 T
1510277 CTACAGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTAATTAATTATTTTTTG
Found at i:1510402 original size:24 final size:25
Alignment explanation
Indices: 1510352--1510409 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
1510342 AACGATATGG
*
1510352 TAATATTT-TTTTTATAATTAATGT
1 TAATATTTATTGTTATAATTAATGT
**
1510376 TAATATTTATTGTTATGTTTAAT-T
1 TAATATTTATTGTTATAATTAATGT
1510400 TAA-ATTTATT
1 TAATATTTATT
1510410 ATGAATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.23
24 12 0.40
25 11 0.37
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (25 bp):
TAATATTTATTGTTATAATTAATGT
Found at i:1512067 original size:21 final size:21
Alignment explanation
Indices: 1512037--1512109 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
1512027 TATGTCATCT
*
1512037 CCGCACGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
1512058 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
1512079 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
1512100 CCGCAGGGTT
1 CCGCAGGGTT
1512110 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.36, G:0.25, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:1512662 original size:34 final size:34
Alignment explanation
Indices: 1512619--1512725 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
1512609 ATAAATGTTT
1512619 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
* * * *
1512653 TTAAAATACAAATAATATTATTCGAAATTTAAAT
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
* *
1512687 TTAAAATATAAATTATAGTATTCAAAATTTAACA
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
1512721 TTAAA
1 TTAAA
1512726 TTCAAGTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCAAAATTTAAAA
Found at i:1513039 original size:2 final size:2
Alignment explanation
Indices: 1513032--1513056 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1513022 AACTTAAATT
1513032 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1513057 TTATCCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1513386 original size:127 final size:127
Alignment explanation
Indices: 1513160--1513535 Score: 639
Period size: 127 Copynumber: 3.0 Consensus size: 127
1513150 TTTAAAGTCT
* *
1513160 CCTAAGGAATAATATGTATTGACATGAATAG-TTCTCGGGGAACATAAGTGACATAATAGGGTAA
1 CCTAAGGAATAATAGGTATTGACATGAATAGTTTCT-GGGGGACATAAGTGACATAATAGGGTAA
*
1513224 TGATATCATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGGTCC
65 TGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGGTCC
1513287 CCTAAGGAATAATAGGTATTGACATGAATAGTTTCTGGGGGACATAAGTGACATAATAGGGTAAT
1 CCTAAGGAATAATAGGTATTGACATGAATAGTTTCTGGGGGACATAAGTGACATAATAGGGTAAT
* *
1513352 GATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCAGGGAACGCGCCTTCACAGTCC
66 GATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGGTCC
* * * *
1513414 CCTAAGGAATAATAGGTATTGACATAAATAGTTCCCGGGGGACATAAGTGACATAATAGGGCAAT
1 CCTAAGGAATAATAGGTATTGACATGAATAGTTTCTGGGGGACATAAGTGACATAATAGGGTAAT
*
1513479 AATAACATATTCTCTGACAAAATAATGGAAGGCGC-CCCCCGGGAACGCGCCTTCACG
66 GATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
1513536 TGAATAGTAC
Statistics
Matches: 236, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
126 20 0.08
127 212 0.90
128 4 0.02
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (127 bp):
CCTAAGGAATAATAGGTATTGACATGAATAGTTTCTGGGGGACATAAGTGACATAATAGGGTAAT
GATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGGTCC
Found at i:1522072 original size:19 final size:17
Alignment explanation
Indices: 1522035--1522073 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1522025 CTTAGTTTTT
*
1522035 TTTATTAAATTTGTCTA
1 TTTATTAAATTTATCTA
1522052 TTTATTAAATTAGTATCTA
1 TTTATTAAATT--TATCTA
1522071 TTT
1 TTT
1522074 TTTGGCCCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
19 8 0.42
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (17 bp):
TTTATTAAATTTATCTA
Found at i:1530342 original size:37 final size:37
Alignment explanation
Indices: 1530270--1530342 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
1530260 TTATATTTTT
*
1530270 ATTTTTGTAAAAAAATTATATAAATATTATGAATTTA
1 ATTTTTGTAAAAAAATTATATAAATATTATCAATTTA
*
1530307 ATTTTT-TAAAGAAAA-TATATAAATATTTTACAATTT
1 ATTTTTGTAAA-AAAATTATATAAATATTAT-CAATTT
1530343 GTAATATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 17 0.53
37 15 0.47
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
ATTTTTGTAAAAAAATTATATAAATATTATCAATTTA
Found at i:1531172 original size:53 final size:54
Alignment explanation
Indices: 1531092--1531210 Score: 206
Period size: 53 Copynumber: 2.2 Consensus size: 54
1531082 TTACAAAGGG
*
1531092 ATGTACCGATACTCTCTTGAATGCATCGATACACACCAACATC-AATGTATTTT
1 ATGTACCGATACTCTCTTGAATGCATCGATACACACCAACATCGAATGCATTTT
1531145 ATGTACCGATA-TACTCTTGAATGCATCGATACACACCAACATCGAATGCATTTT
1 ATGTACCGATACT-CTCTTGAATGCATCGATACACACCAACATCGAATGCATTTT
1531199 ATGTACCGATAC
1 ATGTACCGATAC
1531211 ACAGCTGATG
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
52 1 0.02
53 41 0.66
54 20 0.32
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (54 bp):
ATGTACCGATACTCTCTTGAATGCATCGATACACACCAACATCGAATGCATTTT
Found at i:1531222 original size:53 final size:53
Alignment explanation
Indices: 1531092--1531231 Score: 194
Period size: 53 Copynumber: 2.6 Consensus size: 53
1531082 TTACAAAGGG
* * *
1531092 ATGTACCGATACTCTCTTGAATGCATCGATACACACCAACATCAATGTATTTT
1 ATGTACCGATACACGCTTGAATGCATCGATACACACCAACATCAATGCATTTT
* *
1531145 ATGTACCGATATACTCTTGAATGCATCGATACACACCAACATCGAATGCATTTT
1 ATGTACCGATACACGCTTGAATGCATCGATACACACCAACATC-AATGCATTTT
*
1531199 ATGTACCGATACACAGC-TG-ATGCATCAATACAC
1 ATGTACCGATACAC-GCTTGAATGCATCGATACAC
1531232 TCCTGGCTCC
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
53 54 0.68
54 24 0.30
55 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.29
Consensus pattern (53 bp):
ATGTACCGATACACGCTTGAATGCATCGATACACACCAACATCAATGCATTTT
Found at i:1543206 original size:18 final size:19
Alignment explanation
Indices: 1543179--1543215 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1543169 ATATACAAAA
*
1543179 AGTAAGTTAAT-TATAGTT
1 AGTAAATTAATATATAGTT
1543197 AGTAAATTAATATATAGTT
1 AGTAAATTAATATATAGTT
1543216 GATTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (19 bp):
AGTAAATTAATATATAGTT
Found at i:1544153 original size:53 final size:47
Alignment explanation
Indices: 1544090--1544212 Score: 169
Period size: 45 Copynumber: 2.5 Consensus size: 47
1544080 ATAAAAATCA
*
1544090 TAAATTATTTATTAATATATTTTAAAAAATTTACTAACTTACTTTCTATATAT
1 TAAATAATTTATTAATATATTTT--AAAA--T--TAACTTACTTTCTATATAT
1544143 TAAATAATTTATTAATATATTTT--AATTAACTTACTTTCTATATAT
1 TAAATAATTTATTAATATATTTTAAAATTAACTTACTTTCTATATAT
1544188 TAAATAATTTATTAATATATTTTAA
1 TAAATAATTTATTAATATATTTTAA
1544213 TCAACTATAT
Statistics
Matches: 67, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
45 42 0.63
47 1 0.01
49 2 0.03
53 22 0.33
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (47 bp):
TAAATAATTTATTAATATATTTTAAAATTAACTTACTTTCTATATAT
Found at i:1544167 original size:22 final size:22
Alignment explanation
Indices: 1544136--1544287 Score: 99
Period size: 22 Copynumber: 6.5 Consensus size: 22
1544126 ACTTACTTTC
1544136 TATATATTAAATAATTTATTAA
1 TATATATTAAATAATTTATTAA
* * * **
1544158 TATATTTTAATTAACTTACTTTC
1 TATATATTAAATAATTTA-TTAA
1544181 TATATATTAAATAATTTATTAA
1 TATATATTAAATAATTTATTAA
*
1544203 TATAT-TTTAATCAACTATATATTAA
1 TATATATTAAAT-AA-T-T-TATTAA
* * * **
1544228 TTTACTAACTATAATTAACTTACTTTC
1 TATA-T-A-T-TAAATAATTTA-TTAA
1544255 TATATATTAAATAATTTATTAA
1 TATATATTAAATAATTTATTAA
*
1544277 TATATTTTAAA
1 TATATATTAAA
1544288 GAACTTTTTA
Statistics
Matches: 96, Mismatches: 23, Indels: 22
0.68 0.16 0.16
Matches are distributed among these distances:
21 5 0.05
22 36 0.38
23 27 0.28
24 2 0.02
25 10 0.10
26 4 0.04
27 6 0.06
29 3 0.03
30 3 0.03
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATATTAAATAATTTATTAA
Found at i:1544174 original size:45 final size:45
Alignment explanation
Indices: 1544124--1544218 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
1544114 AAAAATTTAC
1544124 TAACTTACTTTCTATATATTAAATAATTTATTAATATATTTTAAT
1 TAACTTACTTTCTATATATTAAATAATTTATTAATATATTTTAAT
1544169 TAACTTACTTTCTATATATTAAATAATTTATTAATATATTTTAAT
1 TAACTTACTTTCTATATATTAAATAATTTATTAATATATTTTAAT
*
1544214 CAACT
1 TAACT
1544219 ATATATTAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (45 bp):
TAACTTACTTTCTATATATTAAATAATTTATTAATATATTTTAAT
Found at i:1544226 original size:37 final size:36
Alignment explanation
Indices: 1544180--1544286 Score: 99
Period size: 37 Copynumber: 2.9 Consensus size: 36
1544170 AACTTACTTT
1544180 CTATATATTAAATAATTTATTAATATATTTTAATCAA
1 CTATATATTAAATAATTTATTAATATATTTTAAT-AA
* * * * ** * **
1544217 CTATATATTAATTTACTAACTATAAT-TAACTTACTTT
1 CTATATATTAAATAATTTA-T-TAATATATTTTAATAA
1544254 CTATATATTAAATAATTTATTAATATATTTTAA
1 CTATATATTAAATAATTTATTAATATATTTTAA
1544287 AGAACTTTTT
Statistics
Matches: 51, Mismatches: 16, Indels: 7
0.69 0.22 0.09
Matches are distributed among these distances:
35 4 0.08
36 6 0.12
37 30 0.59
38 7 0.14
39 4 0.08
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (36 bp):
CTATATATTAAATAATTTATTAATATATTTTAATAA
Found at i:1544250 original size:18 final size:19
Alignment explanation
Indices: 1544215--1544264 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
1544205 TATTTTAATC
*
1544215 AACTATATATTAATTTACT
1 AACTATATATTAACTTACT
1544234 AACTATA-ATTAACTTACT
1 AACTATATATTAACTTACT
**
1544252 TTCTATATATTAA
1 AACTATATATTAA
1544265 ATAATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (19 bp):
AACTATATATTAACTTACT
Found at i:1547579 original size:2 final size:2
Alignment explanation
Indices: 1547572--1547602 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1547562 GACAATTTTA
1547572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1547603 CACACACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1549326 original size:35 final size:35
Alignment explanation
Indices: 1549249--1549365 Score: 175
Period size: 35 Copynumber: 3.3 Consensus size: 35
1549239 TTACCCATTC
* *
1549249 CTATTTTC-AACAAACATCTACCAAACTTTGAAGAA
1 CTATTTTCAAAGAAACATTTACCAAACTTTGAA-AA
1549284 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAA
1 CTA-TTTTCAAAGAAACATTTACCAAACTTTGAAAA
1549319 CTATTTTCAAAGAAACATTTACCAAACTTTGAAAA
1 CTATTTTCAAAGAAACATTTACCAAACTTTGAAAA
*
1549354 CCATTTTCAAAG
1 CTATTTTCAAAG
1549366 TTGGTTGCCA
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
34 1 0.01
35 52 0.68
36 23 0.30
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.31
Consensus pattern (35 bp):
CTATTTTCAAAGAAACATTTACCAAACTTTGAAAA
Found at i:1553073 original size:21 final size:21
Alignment explanation
Indices: 1553049--1553109 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1553039 TTCAAAGAAA
1553049 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
* *
1553070 CATTT-TCGAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
1553084 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
1553105 CATTT
1 CATTT
1553110 TCAAAGTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 5 0.17
15 6 0.21
16 1 0.03
19 1 0.03
20 6 0.21
21 10 0.34
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:1553083 original size:35 final size:35
Alignment explanation
Indices: 1553011--1553115 Score: 167
Period size: 35 Copynumber: 3.0 Consensus size: 35
1553001 AACATCTACC
**
1553011 AAAC-TTTACCAAACTTTGAAAAATATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAG
*
1553046 AAACATTTACCAAACTTTGAAAACCATTTTCGAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1553081 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1553116 TTGGTTGCCA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
35 46 0.71
36 19 0.29
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (35 bp):
AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
Found at i:1554723 original size:2 final size:2
Alignment explanation
Indices: 1554716--1554746 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1554706 AGAAATTGTA
1554716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1554747 ATTGTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1557432 original size:30 final size:30
Alignment explanation
Indices: 1557396--1557462 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1557386 AGTGAATCGG
*
1557396 CGATTCAAACTGGTTTTACCGGTTTTCAGC
1 CGATTCAAACCGGTTTTACCGGTTTTCAGC
**
1557426 CGATTCACCCCGGTTTTACCGGTTTTCAGC
1 CGATTCAAACCGGTTTTACCGGTTTTCAGC
*
1557456 CGGTTCA
1 CGATTCA
1557463 TTACCAGACC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.16, C:0.28, G:0.21, T:0.34
Consensus pattern (30 bp):
CGATTCAAACCGGTTTTACCGGTTTTCAGC
Found at i:1561221 original size:16 final size:17
Alignment explanation
Indices: 1561200--1561235 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1561190 CCGAGATGTC
1561200 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
1561216 ACATTGACTTTTACAAA
1 ACATTGACTTTTACAAA
1561233 ACA
1 ACA
1561236 ATTAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:1561988 original size:20 final size:21
Alignment explanation
Indices: 1561963--1562043 Score: 89
Period size: 20 Copynumber: 4.0 Consensus size: 21
1561953 GGCACATAGA
1561963 ATTTGTCCCGAAGGA-CACAT
1 ATTTGTCCCGAAGGACCACAT
* *
1561983 ATTTGTCCCGGATGACCACAT
1 ATTTGTCCCGAAGGACCACAT
* *
1562004 ATTTGT--CGGAGGACCATAT
1 ATTTGTCCCGAAGGACCACAT
*
1562023 A-TTATCCCGAAGGACCACAT
1 ATTTGTCCCGAAGGACCACAT
1562043 A
1 A
1562044 AAATCCTCGA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
18 3 0.06
19 12 0.24
20 25 0.49
21 11 0.22
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (21 bp):
ATTTGTCCCGAAGGACCACAT
Found at i:1562601 original size:18 final size:19
Alignment explanation
Indices: 1562575--1562616 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1562565 TCAATATTAC
*
1562575 ATGTTAGTATAT-TAACTT
1 ATGTCAGTATATCTAACTT
* *
1562593 ATGTCAGTATTTCTAGCTT
1 ATGTCAGTATATCTAACTT
1562612 ATGTC
1 ATGTC
1562617 CAATTATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (19 bp):
ATGTCAGTATATCTAACTT
Found at i:1564564 original size:79 final size:80
Alignment explanation
Indices: 1564379--1564763 Score: 465
Period size: 79 Copynumber: 4.8 Consensus size: 80
1564369 GCAATTAGTC
* * * * * * * * *
1564379 TTCATCCAACTTGCATTATTGGCATCTTTCTGTCAAATGCACCA-TTGGGCATTTAGTCTTTTTA
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA-CAGTAGGCCA-TTAATC-TTTTA
*
1564443 CCCAAAGGTATTTAACCT
63 CTCAAAGGTATTTAACCT
* * * * * ** *
1564461 TTCATCTAACTGACATAATTGACACCTTTATGCCAAAGGCATAGTTAGACTTTTAGTC-TTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAG-TAGGCCATTAATCTTTTACT
*
1564525 CAAAGGTATTTAATC-
65 CAAAGGTATTTAACCT
*
1564540 TTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGCACAGTAGGCCATTAATCTTTTACTC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGTAGGCCATTAATCTTTTACTC
1564605 AAAGGTA-TTAACCT
66 AAAGGTATTTAACCT
*
1564619 TTCATCTAACTGGCATAATTGACACATTTCTGCC-AATGCACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAG-TAGGCCATTAATCTTTTACT
1564683 CAAAGGTATTTAACCT
65 CAAAGGTATTTAACCT
* * *
1564699 TTCATCTAACAGGCATAATTGACACCTTTCTGCCAAATGCAAAGCTAGGTCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAG-TAGGCCATTAATCTTTTACT
1564764 TTAGAAAATT
Statistics
Matches: 263, Mismatches: 33, Indels: 15
0.85 0.11 0.05
Matches are distributed among these distances:
78 23 0.09
79 113 0.43
80 58 0.22
81 29 0.11
82 38 0.14
83 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (80 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGTAGGCCATTAATCTTTTACTC
AAAGGTATTTAACCT
Found at i:1566085 original size:17 final size:18
Alignment explanation
Indices: 1566063--1566097 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1566053 ACTGAATATT
1566063 TGTCCCGAA-GACCACTA
1 TGTCCCGAAGGACCACTA
1566080 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1566098 ATAAATCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1566790 original size:35 final size:36
Alignment explanation
Indices: 1566751--1566822 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 36
1566741 CGTTCAAAGA
*
1566751 TGGTATCGATACCATTCTT-AAGGTATCGGTACCCT
1 TGGTATCGATACCATTCTTCAAGGTATCAGTACCCT
**
1566786 TGGTATCGATACTGTTCTTCAAGGTATCAGTACCCT
1 TGGTATCGATACCATTCTTCAAGGTATCAGTACCCT
1566822 T
1 T
1566823 TGAATTCCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 17 0.52
36 16 0.48
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (36 bp):
TGGTATCGATACCATTCTTCAAGGTATCAGTACCCT
Found at i:1577526 original size:105 final size:105
Alignment explanation
Indices: 1577338--1577537 Score: 258
Period size: 105 Copynumber: 1.9 Consensus size: 105
1577328 GAGTTGAGGG
* * * *
1577338 TCTACGCGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCCTTTGCGACACAT
1 TCTACGCGGACCTTCGGGACATATAGATATCCTATGGAACATCTATGAAGTCCTTTGAGACACAT
* * *
1577403 ATTTGGTCCTTAGCATATGTATATGATTCTTAAGGAATTT
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTT
* * * * * *
1577443 TCTACGCGGACCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGT-CTTGTGAGACACA
1 TCTACGCGGACCTTCGGGACATATAGATATCCTATGGAACATCTATGAAGTCCTT-TGAGACACA
*
1577507 TACTTGATCCCTAGTATATGTATATGATTCT
65 TACTTGATCCCTAGCATATGTATATGATTCT
1577538 CAATGAATGA
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
104 3 0.04
105 77 0.96
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (105 bp):
TCTACGCGGACCTTCGGGACATATAGATATCCTATGGAACATCTATGAAGTCCTTTGAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTT
Found at i:1577602 original size:23 final size:23
Alignment explanation
Indices: 1577576--1577643 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1577566 ATTATTATAT
*
1577576 GGCACTACGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTACGC
* *
1577599 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
1577622 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
1577644 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1577695 original size:16 final size:17
Alignment explanation
Indices: 1577674--1577706 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1577664 TGCACAACCT
1577674 CTATAG-ACTCACATAC
1 CTATAGTACTCACATAC
*
1577690 CTATAGTTCTCACATAC
1 CTATAGTACTCACATAC
1577707 GTCCATGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (17 bp):
CTATAGTACTCACATAC
Found at i:1583006 original size:22 final size:23
Alignment explanation
Indices: 1582955--1583014 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1582945 ATATGGACTA
*
1582955 CGGTACAATTCTACGCGGCACTC
1 CGGTGCAATTCTACGCGGCACTC
*
1582978 CGGTGCAATTCTACGTGGCACT-
1 CGGTGCAATTCTACGCGGCACTC
*
1583000 CGGTGCAATTATACG
1 CGGTGCAATTCTACG
1583015 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTC
Found at i:1583066 original size:16 final size:17
Alignment explanation
Indices: 1583045--1583077 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1583035 TGCACAACCT
1583045 CTATAG-ACTCACATAC
1 CTATAGTACTCACATAC
*
1583061 CTATAGTTCTCACATAC
1 CTATAGTACTCACATAC
1583078 GTCCATGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (17 bp):
CTATAGTACTCACATAC
Found at i:1592580 original size:2 final size:2
Alignment explanation
Indices: 1592573--1592599 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1592563 CAGCTTCTGT
1592573 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1592600 CCGAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1614840 original size:3 final size:3
Alignment explanation
Indices: 1614832--1614879 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1614822 CGATAAAATC
1614832 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1614880 CAACAACAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1617802 original size:83 final size:83
Alignment explanation
Indices: 1617674--1617993 Score: 424
Period size: 83 Copynumber: 3.8 Consensus size: 83
1617664 ATGAATTGAA
* * *
1617674 TGTAATCGAGCGCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
1 TGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
* *
1617739 ATGTGTCTTAGAGCTGAG
66 ATGTGCCTTGGAGCTGAG
* * * * * * *
1617757 TGTAATCGAACTCGAATGTATTTGTTGATAGATAACCCTTATAGCCTTGAATCATGCTGCAAATT
1 TGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
* *
1617822 ATATACCTTGGAGCTGAG
66 ATGTGCCTTGGAGCTGAG
* * *
1617840 TGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
1 TGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
1617905 GATGTGCCTTGGAGCTGAG
65 GATGTGCCTTGGAGCTGAG
* *
1617924 CGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTTCTAGCCTTGAGTTATGCTGCA
1 TGTAATCGAACTCGAAGGTCTTT-GTTGACAGATAA-CC--CTTCTAGCCTTGAGTTATGCTGCA
1617989 AATGA
62 AATGA
1617994 ACACGATATC
Statistics
Matches: 203, Mismatches: 29, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
83 89 0.44
84 83 0.41
85 2 0.01
87 29 0.14
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (83 bp):
TGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
ATGTGCCTTGGAGCTGAG
Found at i:1619000 original size:26 final size:26
Alignment explanation
Indices: 1618964--1619025 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
1618954 AAAGGAAACA
1618964 ATAGCTCTTTTAATGCTTTCAGAGTT
1 ATAGCTCTTTTAATGCTTTCAGAGTT
*
1618990 ATAGCTCTTTTAATGCTTTTAGAGTT
1 ATAGCTCTTTTAATGCTTTCAGAGTT
*
1619016 ATATCTCTTT
1 ATAGCTCTTT
1619026 GACAAATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.50
Consensus pattern (26 bp):
ATAGCTCTTTTAATGCTTTCAGAGTT
Found at i:1619504 original size:83 final size:83
Alignment explanation
Indices: 1619395--1619608 Score: 394
Period size: 83 Copynumber: 2.6 Consensus size: 83
1619385 AGCTAGCTGA
* * *
1619395 ATCCATAAAGAC-GGGCGTTTAACCAATTACTCTAGAGGGACAGCTCAATATATAAACACCTTTA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATATAAACACCTTTA
1619459 TCAGGTTAACTGAATATC
66 TCAGGTTAACTGAATATC
1619477 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATATAAACACCTTTA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATATAAACACCTTTA
1619542 TCAGGTTAACTGAATATC
66 TCAGGTTAACTGAATATC
1619560 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
1619609 GCTTTATTGT
Statistics
Matches: 128, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
82 11 0.09
83 117 0.91
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (83 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATATAAACACCTTTA
TCAGGTTAACTGAATATC
Found at i:1619697 original size:95 final size:96
Alignment explanation
Indices: 1619525--1619722 Score: 281
Period size: 95 Copynumber: 2.1 Consensus size: 96
1619515 GGACAACTCA
** * * * * *
1619525 ATATATAAACACCTTTATCAGGTTAACTGAATATCATCCATAAAGTCGGGGCGTTTAACCAATTG
1 ATATATAGTCACCTATATCAGGCTAACTGAATATCATCCATAAAGCCGAGGAGTTTAACCAATTG
1619590 CTCTAGAGGGACAACTCAAGCTTTATTGTAT
66 CTCTAGAGGGACAACTCAAGCTTTATTGTAT
* * *
1619621 AT-TATAGTCACCTATATCAGGCTAGCTGAATCTTATCCATAAAGCCGAGGAGTTTAACCAATTG
1 ATATATAGTCACCTATATCAGGCTAACTGAATATCATCCATAAAGCCGAGGAGTTTAACCAATTG
**
1619685 CTCTAGAGGGACAGTTCAAGCTTTATTGTAT
66 CTCTAGAGGGACAACTCAAGCTTTATTGTAT
1619716 ATATATA
1 ATATATA
1619723 ATATTATAAT
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 83 0.93
96 6 0.07
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (96 bp):
ATATATAGTCACCTATATCAGGCTAACTGAATATCATCCATAAAGCCGAGGAGTTTAACCAATTG
CTCTAGAGGGACAACTCAAGCTTTATTGTAT
Found at i:1622194 original size:13 final size:13
Alignment explanation
Indices: 1622178--1622207 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1622168 CTTAATTGCG
1622178 AAAATTTAAATTT
1 AAAATTTAAATTT
1622191 AAAATTTAAATTT
1 AAAATTTAAATTT
1622204 AAAA
1 AAAA
1622208 ATTCGATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATTTAAATTT
Found at i:1622358 original size:15 final size:15
Alignment explanation
Indices: 1622335--1622381 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1622325 GAAAAAATAT
*
1622335 TAAATAAATTAAGAA
1 TAAAAAAATTAAGAA
1622350 TAAAAAAATTAAGAA
1 TAAAAAAATTAAGAA
1622365 TAAAAAAA-TAA-AA
1 TAAAAAAATTAAGAA
1622378 TAAA
1 TAAA
1622382 GGAAAAGACT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 6 0.19
14 3 0.10
15 22 0.71
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (15 bp):
TAAAAAAATTAAGAA
Found at i:1627522 original size:36 final size:37
Alignment explanation
Indices: 1627439--1627522 Score: 111
Period size: 35 Copynumber: 2.3 Consensus size: 37
1627429 TTAAACTTTT
* *
1627439 TTTTATATTTTTAATTTTGTAAAAAAATTATATAAATA
1 TTTTATA-ATTTAATTTTGTAAAAAAAATATATAAATA
1627477 --TTATGAATTTAATTTT-TAAAAAAAATATATAAATA
1 TTTTAT-AATTTAATTTTGTAAAAAAAATATATAAATA
1627512 TTTTATAATTT
1 TTTTATAATTT
1627523 GTAATATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
35 18 0.44
36 18 0.44
37 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (37 bp):
TTTTATAATTTAATTTTGTAAAAAAAATATATAAATA
Found at i:1627976 original size:21 final size:21
Alignment explanation
Indices: 1627951--1627994 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1627941 AATTAAAATT
1627951 ATTTTAA-TATTTTTATTTGAA
1 ATTTTAACT-TTTTTATTTGAA
1627972 ATTTTAACTTTTTTATTTGAA
1 ATTTTAACTTTTTTATTTGAA
1627993 AT
1 AT
1627995 AATAAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (21 bp):
ATTTTAACTTTTTTATTTGAA
Found at i:1636860 original size:16 final size:16
Alignment explanation
Indices: 1636804--1636860 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
1636794 GAGTAGCTCG
1636804 AAAATA-TAATATATT-
1 AAAATATTAAT-TATTA
*
1636819 AAGATATT-ATT-TTA
1 AAAATATTAATTATTA
* *
1636833 AAAAAATAAATTATTA
1 AAAATATTAATTATTA
1636849 AAAATATTAATT
1 AAAATATTAATT
1636861 TTGATGTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
13 2 0.06
14 6 0.19
15 10 0.31
16 14 0.44
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAAATATTAATTATTA
Found at i:1636862 original size:31 final size:31
Alignment explanation
Indices: 1636804--1636862 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
1636794 GAGTAGCTCG
*
1636804 AAAATATAATATATTAAGATATTATTTTAAA
1 AAAATATAATATATTAAAATATTATTTTAAA
1636835 AAAATA-AAT-TATTAAAAATATTAATTTT
1 AAAATATAATATATT-AAAATATT-ATTTT
1636863 GATGTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 4 0.16
30 10 0.40
31 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (31 bp):
AAAATATAATATATTAAAATATTATTTTAAA
Found at i:1638163 original size:2 final size:2
Alignment explanation
Indices: 1638151--1638190 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1638141 TTCAATATCA
*
1638151 AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1638191 GGGTTAAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1664711 original size:2 final size:2
Alignment explanation
Indices: 1664704--1664728 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1664694 TCCTAAAGGC
1664704 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1664729 TCATGTATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1668315 original size:15 final size:14
Alignment explanation
Indices: 1668293--1668321 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1668283 ATATATTTAT
1668293 TTTATTTTTTTAAA
1 TTTATTTTTTTAAA
1668307 TTTATTTTTTTAAA
1 TTTATTTTTTTAAA
1668321 T
1 T
1668322 AAGCGTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTATTTTTTTAAA
Found at i:1672176 original size:13 final size:14
Alignment explanation
Indices: 1672148--1672179 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
1672138 GTGCAAGATT
1672148 ACCCGACCCGGTTG
1 ACCCGACCCGGTTG
1672162 ACCCGACCC-GTTG
1 ACCCGACCCGGTTG
1672175 ACCCG
1 ACCCG
1672180 TCGTGTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.16, C:0.47, G:0.25, T:0.12
Consensus pattern (14 bp):
ACCCGACCCGGTTG
Found at i:1674378 original size:31 final size:31
Alignment explanation
Indices: 1674289--1674416 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 31
1674279 AGAGTCGAGG
1674289 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* *
1674320 GTTTTACCTATG-TCTTTC-GAGATATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
1674352 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
1674383 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
1674414 GTT
1 GTT
1674417 ATCGAGGATC
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 53 0.66
32 27 0.34
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:1674449 original size:30 final size:30
Alignment explanation
Indices: 1674408--1674474 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1674398 TCGGGACCTA
* *
1674408 TGGACAGTTATCGAGGATCTTTATGACATC
1 TGGATAGTTATCGAGGATCTTTATAACATC
* *
1674438 TGGATAGTTATCGATGATCTTTATAACCTC
1 TGGATAGTTATCGAGGATCTTTATAACATC
1674468 TGGATAG
1 TGGATAG
1674475 GTCCTTCGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (30 bp):
TGGATAGTTATCGAGGATCTTTATAACATC
Found at i:1677927 original size:21 final size:21
Alignment explanation
Indices: 1677901--1677946 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1677891 GATTTCTGGG
* *
1677901 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1677922 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1677943 CAAG
1 CAAG
1677947 CGAATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1678017 original size:23 final size:22
Alignment explanation
Indices: 1677973--1678017 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1677963 AATGTCATGG
*
1677973 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1677995 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1678018 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1679361 original size:32 final size:32
Alignment explanation
Indices: 1679320--1679416 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 32
1679310 GAGTCTAGGG
*
1679320 TTTACCTATGTTCTACGGAATATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
1679352 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
1679383 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
1679415 TT
1 TT
1679417 ACTAGGTTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
31 26 0.48
32 28 0.52
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:1679406 original size:31 final size:31
Alignment explanation
Indices: 1679322--1679414 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 31
1679312 GTCTAGGGTT
* * *
1679322 TACCTATGTTCTACGGAATATATGGACAGTTT
1 TACCTATGTTCTAAGGAACATATGGACAG-TA
***
1679354 TACCTATG-TCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTAAGGA-ACATATGGACAGTA
1679385 TACCTATGTTCTAAGGAACATATGGACAGT
1 TACCTATGTTCTAAGGAACATATGGACAGT
1679415 TTACTAGGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
31 27 0.53
32 24 0.47
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGTA
Found at i:1679465 original size:30 final size:30
Alignment explanation
Indices: 1679431--1679495 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
1679421 GGTTCTTCGG
1679431 GACCTATGAACAGTTACCGAGGATCTTTAT
1 GACCTATGAACAGTTACCGAGGATCTTTAT
* * *
1679461 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTATGAACAGTTACCGAGGATCTTTAT
1679491 GACCT
1 GACCT
1679496 CTGGATAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (30 bp):
GACCTATGAACAGTTACCGAGGATCTTTAT
Found at i:1679496 original size:30 final size:30
Alignment explanation
Indices: 1679442--1679503 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1679432 ACCTATGAAC
1679442 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
1679472 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
1679502 AG
1 AG
1679504 GTCATTCGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (30 bp):
AGTTACCGAGGATCTTTATGACCTCTGGAT
Found at i:1684808 original size:29 final size:29
Alignment explanation
Indices: 1684765--1684847 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
1684755 CTCACCTAAC
*
1684765 TAAATTGATGTAAGCAATGATATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
1684795 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
1684824 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1684848 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.34
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1688230 original size:15 final size:15
Alignment explanation
Indices: 1688210--1688239 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1688200 CTTTCTCATA
1688210 GTTATTGTTGGAATT
1 GTTATTGTTGGAATT
*
1688225 GTTATTGTTGTAATT
1 GTTATTGTTGGAATT
1688240 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
GTTATTGTTGGAATT
Found at i:1695443 original size:77 final size:78
Alignment explanation
Indices: 1695351--1695528 Score: 277
Period size: 77 Copynumber: 2.3 Consensus size: 78
1695341 TGACCTGCTG
* * *
1695351 ATGGTATACAGATCGATAATAGTATAAAACTTGAAAGATTATCGACGAAGCAGTCGACTCTTTAG
1 ATGGTATACAGATCGATAATAGTATAAAAATTGAAAGATTATCAACCAAGCAGTCGACTCTTTAG
*
1695416 CCCACAT-ACAAA
66 CCCACATAAAAAA
* * *
1695428 ATGGTATACAGATCGATAATAGTATAAAAATTGTAAGATTATCAACCAAGCAGTTGGCTCTTTAG
1 ATGGTATACAGATCGATAATAGTATAAAAATTGAAAGATTATCAACCAAGCAGTCGACTCTTTAG
1695493 CCCACATAAAAAA
66 CCCACATAAAAAA
*
1695506 ATGGTATACAGATCTATAATAGT
1 ATGGTATACAGATCGATAATAGT
1695529 TTTTTAAAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
77 66 0.72
78 26 0.28
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (78 bp):
ATGGTATACAGATCGATAATAGTATAAAAATTGAAAGATTATCAACCAAGCAGTCGACTCTTTAG
CCCACATAAAAAA
Found at i:1705775 original size:39 final size:39
Alignment explanation
Indices: 1705721--1705801 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
1705711 GATAATTAAG
1705721 TAGATTTTTTTGTTGTAATTTTAAGGGTTAAAGATGACT
1 TAGATTTTTTTGTTGTAATTTTAAGGGTTAAAGATGACT
1705760 TAGATTTTTTTGTTGTAATTTTAAGGGTTAAAGATGACT
1 TAGATTTTTTTGTTGTAATTTTAAGGGTTAAAGATGACT
1705799 TAG
1 TAG
1705802 TAATTAGGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.48
Consensus pattern (39 bp):
TAGATTTTTTTGTTGTAATTTTAAGGGTTAAAGATGACT
Found at i:1707803 original size:65 final size:63
Alignment explanation
Indices: 1707708--1707849 Score: 162
Period size: 65 Copynumber: 2.2 Consensus size: 63
1707698 CACATTGAAT
* *
1707708 GTGCATCGATGCACTCTTTAAAGAAGAAACATCAAATGCAATTAGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCAAAGGCAATTAGTGCATCGATGCAT-AGGTA
* * * * * *
1707771 GTGCATTGATGCATCCCTTTAAA-AATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGT
1 GTGCATCGATGCA-CCCTTTAAAGAA-G-AAACATCAAAGGCAATTAGTGCATCGATGCATAGGT
1707835 A
63 A
1707836 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1707850 AGGATAAAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
63 14 0.21
64 12 0.18
65 40 0.61
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCAAAGGCAATTAGTGCATCGATGCATAGGTA
Found at i:1707869 original size:24 final size:20
Alignment explanation
Indices: 1707837--1707893 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 20
1707827 GCATGGGTAG
1707837 TGCATCGATGCACAGGATAAAGAA
1 TGCATCGATGCAC-GG-T--AGAA
*
1707861 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCACGGTAGAA
1707881 TGCATCGATGCAC
1 TGCATCGATGCAC
1707894 TTCATGGGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 1 0.03
24 13 0.41
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (20 bp):
TGCATCGATGCACGGTAGAA
Found at i:1707882 original size:20 final size:20
Alignment explanation
Indices: 1707857--1707894 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1707847 CACAGGATAA
1707857 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
1707877 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
1707895 TCATGGGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:1708688 original size:18 final size:18
Alignment explanation
Indices: 1708665--1708736 Score: 101
Period size: 18 Copynumber: 4.0 Consensus size: 18
1708655 GAGGGTCTAC
1708665 GTGGT-CTTTCGGGACATA
1 GTGGTCCTTT-GGGACATA
1708683 GTGGTCCTTTGGGACATA
1 GTGGTCCTTTGGGACATA
1708701 GTGGTCCTTTGGGACATA
1 GTGGTCCTTTGGGACATA
* * *
1708719 CTGGTCATTCGGGACATA
1 GTGGTCCTTTGGGACATA
1708737 TGTGTTCTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
18 46 0.92
19 4 0.08
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (18 bp):
GTGGTCCTTTGGGACATA
Found at i:1711814 original size:65 final size:63
Alignment explanation
Indices: 1711708--1711849 Score: 162
Period size: 65 Copynumber: 2.2 Consensus size: 63
1711698 CACATTAAAT
* * * *
1711708 GTGCATCGATGCACTCTTTAAAGAAGAAACGTTGAATGTAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGTAATTGGTGCATCGATGCAT-AGGTA
* * *
1711771 GTGCATCGATGCATCCCTTTAAA-AATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGT
1 GTGCATCGATGCA-CCCTTTAAAGAA-G-AAACATCGAAGGTAATTGGTGCATCGATGCATAGGT
1711835 A
63 A
*
1711836 GTGCATTGATGCAC
1 GTGCATCGATGCAC
1711850 ATATTAAAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
63 15 0.22
64 12 0.18
65 40 0.60
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGTAATTGGTGCATCGATGCATAGGTA
Found at i:1711882 original size:20 final size:20
Alignment explanation
Indices: 1711857--1711894 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1711847 CACATATTAA
1711857 AGAATGCATCGATGCACTGC
1 AGAATGCATCGATGCACTGC
*
1711877 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
1711895 TCAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGC
Found at i:1712690 original size:18 final size:18
Alignment explanation
Indices: 1712667--1712718 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
1712657 GGGTCTACGC
*
1712667 GGTCCTTCGGAACATAGT
1 GGTCCTTCGGGACATAGT
*
1712685 GGTCCTTTGGGACATAGT
1 GGTCCTTCGGGACATAGT
1712703 GGTCCTTCGGGACATA
1 GGTCCTTCGGGACATA
1712719 TGTGTTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:1713346 original size:16 final size:16
Alignment explanation
Indices: 1713325--1713361 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1713315 TTAAAAGATT
1713325 TGAATTGTATAAGCTC
1 TGAATTGTATAAGCTC
1713341 TGAATTGTATAAGCTC
1 TGAATTGTATAAGCTC
1713357 TGAAT
1 TGAAT
1713362 AGTTCTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (16 bp):
TGAATTGTATAAGCTC
Found at i:1713601 original size:6 final size:6
Alignment explanation
Indices: 1713590--1713635 Score: 56
Period size: 6 Copynumber: 7.2 Consensus size: 6
1713580 CTTAACATCC
*
1713590 CATTGT CATTGT CAGATATCT CATTGT CATTGT CATTGT CATTGT C
1 CATTGT CATTGT C--AT-TGT CATTGT CATTGT CATTGT CATTGT C
1713636 TCAAATTCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 28 0.80
7 2 0.06
8 2 0.06
9 3 0.09
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (6 bp):
CATTGT
Found at i:1731188 original size:22 final size:22
Alignment explanation
Indices: 1731163--1731376 Score: 347
Period size: 22 Copynumber: 9.7 Consensus size: 22
1731153 CTCATGATTC
* *
1731163 AATCCACTAATATTGAGTGTTA
1 AATCCACTAGTATTAAGTGTTA
1731185 AATCCACTAGTATTAAGTGTTA
1 AATCCACTAGTATTAAGTGTTA
**
1731207 AATCCACTAGTATTAAGCATTA
1 AATCCACTAGTATTAAGTGTTA
*
1731229 AATCCACTAGTATTAAGTATTA
1 AATCCACTAGTATTAAGTGTTA
*
1731251 AATCCATTAGTATTAAGTGTTA
1 AATCCACTAGTATTAAGTGTTA
*
1731273 AATCCACTAGTATTAAGTATTA
1 AATCCACTAGTATTAAGTGTTA
*
1731295 AATCCACTAGTATTAAGTATTA
1 AATCCACTAGTATTAAGTGTTA
1731317 AATCCACTAGTATTAAGTGTTA
1 AATCCACTAGTATTAAGTGTTA
*
1731339 AATCTACTAGTATTAAGTGTTA
1 AATCCACTAGTATTAAGTGTTA
1731361 AATCCACTAGTATTAA
1 AATCCACTAGTATTAA
1731377 ATATTAATTC
Statistics
Matches: 180, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 180 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (22 bp):
AATCCACTAGTATTAAGTGTTA
Found at i:1735669 original size:66 final size:66
Alignment explanation
Indices: 1735563--1735695 Score: 232
Period size: 66 Copynumber: 2.0 Consensus size: 66
1735553 CTCATGATTC
*
1735563 AATCCACTACTATTGAGTGTTAAATCCACTAGTATTAAGTGTTAAATCCACTATTATT-AAGTAT
1 AATCCACTACTATTAAGTGTTAAATCCACTAGTATTAAGTGTTAAATCCACTATTATTGAA-TAT
1735627 TA
65 TA
*
1735629 AATCCACTAGTATTAAGTGTTAAATCCACTAGTATTAAGTGTTAAATCCACTATTATTGAATATT
1 AATCCACTACTATTAAGTGTTAAATCCACTAGTATTAAGTGTTAAATCCACTATTATTGAATATT
1735694 A
66 A
1735695 A
1 A
1735696 TTCTATGTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 62 0.97
67 2 0.03
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (66 bp):
AATCCACTACTATTAAGTGTTAAATCCACTAGTATTAAGTGTTAAATCCACTATTATTGAATATT
A
Found at i:1735695 original size:22 final size:22
Alignment explanation
Indices: 1735563--1735686 Score: 203
Period size: 22 Copynumber: 5.6 Consensus size: 22
1735553 CTCATGATTC
* *
1735563 AATCCACTACTATTGAGTGTTA
1 AATCCACTAGTATTAAGTGTTA
1735585 AATCCACTAGTATTAAGTGTTA
1 AATCCACTAGTATTAAGTGTTA
* *
1735607 AATCCACTATTATTAAGTATTA
1 AATCCACTAGTATTAAGTGTTA
1735629 AATCCACTAGTATTAAGTGTTA
1 AATCCACTAGTATTAAGTGTTA
1735651 AATCCACTAGTATTAAGTGTTA
1 AATCCACTAGTATTAAGTGTTA
*
1735673 AATCCACTATTATT
1 AATCCACTAGTATT
1735687 GAATATTAAT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 95 1.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
AATCCACTAGTATTAAGTGTTA
Done.