Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 8 of 106
Found at i:1197036 original size:23 final size:22
Alignment explanation
Indices: 1197010--1197073 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 22
1197000 TTGTTCCAAT
1197010 TGATTCTGTAAGACCTCCAGGCA
1 TGATTCTGTAAGACCTCC-GGCA
*
1197033 TGATTCTGTAAGACCTCCGACA
1 TGATTCTGTAAGACCTCCGGCA
* *
1197055 TGATT-TTTAAGACTTCCGG
1 TGATTCTGTAAGACCTCCGG
1197074 GCATAATTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.30
22 8 0.22
23 18 0.49
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.31
Consensus pattern (22 bp):
TGATTCTGTAAGACCTCCGGCA
Found at i:1197172 original size:22 final size:22
Alignment explanation
Indices: 1197145--1197186 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1197135 CTCAATCAAT
* *
1197145 TTTGTAAGATCTTCGGGCATGA
1 TTTGTAAGACCTCCGGGCATGA
1197167 TTTGTAAGACCTCCGGGCAT
1 TTTGTAAGACCTCCGGGCAT
1197187 AAAATTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (22 bp):
TTTGTAAGACCTCCGGGCATGA
Found at i:1197380 original size:49 final size:49
Alignment explanation
Indices: 1197244--1197449 Score: 274
Period size: 48 Copynumber: 4.3 Consensus size: 49
1197234 TGCGACGTCA
* * *
1197244 AGCTTTTCCAAGATGAAAATTTTAAAGTTGTGGAGTCTCTGTTGAGAGG
1 AGCTTTTCCAAGATGAAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGG
* * *
1197293 AGCTTTTTCAAGA-AAAAATTTTAAAGTTGTTGAGCCTCTGCTAAGAGG
1 AGCTTTTCCAAGATGAAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGG
* * *
1197341 AGCTTTTCCAAGATGAGAATTTTAAAGTTGTAGAGCCTCTGTTGAGAGG
1 AGCTTTTCCAAGATGAAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGG
* * * *
1197390 AGCTTTTTC-AGATG-AGATTTTAAAATTATTGAGCCTCTGCTGAGAGG
1 AGCTTTTCCAAGATGAAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGG
1197437 AGCTTTTCCAAGA
1 AGCTTTTCCAAGA
1197450 AAAAAATGAT
Statistics
Matches: 135, Mismatches: 20, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
47 35 0.26
48 50 0.37
49 50 0.37
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.34
Consensus pattern (49 bp):
AGCTTTTCCAAGATGAAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGG
Found at i:1197566 original size:3 final size:3
Alignment explanation
Indices: 1197558--1197598 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
1197548 AGGTCTACTT
* *
1197558 TAA TAA TAA TAT TAA TAA TAA TAA TAA TATA TAA AAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA T
1197599 TATTAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1197624 original size:8 final size:8
Alignment explanation
Indices: 1197606--1197646 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
1197596 AATTATTAAT
1197606 TATATAAAA
1 TATA-AAAA
1197615 TATAAAAA
1 TATAAAAA
1197623 TATAAAAA
1 TATAAAAA
*
1197631 AATAAAAA
1 TATAAAAA
*
1197639 GATAAAAA
1 TATAAAAA
1197647 AAGACACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 26 0.87
9 4 0.13
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (8 bp):
TATAAAAA
Found at i:1197634 original size:18 final size:17
Alignment explanation
Indices: 1197611--1197648 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1197601 TTAATTATAT
1197611 AAAATATAAAA-ATATAAA
1 AAAATA-AAAAGATA-AAA
1197629 AAAATAAAAAGATAAAA
1 AAAATAAAAAGATAAAA
1197646 AAA
1 AAA
1197649 GACACAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAATAAAAAGATAAAA
Found at i:1197763 original size:34 final size:34
Alignment explanation
Indices: 1197702--1197772 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
1197692 GTGGCTGGCA
*
1197702 CCCGACCAGCCACCCTACAACCATATCTACCAGC
1 CCCGACCAGCCACCCTACAACCATATCTACCACC
* * *
1197736 CCCGACCAGCCA-TCTACCAGCCTTATCTACCACC
1 CCCGACCAGCCACCCTA-CAACCATATCTACCACC
1197770 CCC
1 CCC
1197773 ACACTCACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 3 0.09
34 29 0.91
ACGTcount: A:0.25, C:0.52, G:0.08, T:0.14
Consensus pattern (34 bp):
CCCGACCAGCCACCCTACAACCATATCTACCACC
Found at i:1197940 original size:21 final size:20
Alignment explanation
Indices: 1197914--1197959 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 20
1197904 AAATACCCAA
1197914 AAACAGAAACGCAAAAAACAG
1 AAACAGAAACGCAAAAAA-AG
1197935 AAACAGAAACGCAAAAAAAG
1 AAACAGAAACGCAAAAAAAG
1197955 AAACA
1 AAACA
1197960 TAGAAACAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.70, C:0.17, G:0.13, T:0.00
Consensus pattern (20 bp):
AAACAGAAACGCAAAAAAAG
Found at i:1197970 original size:14 final size:14
Alignment explanation
Indices: 1197931--1197973 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1197921 AACGCAAAAA
1197931 ACAGAAACAGAAAC
1 ACAGAAACAGAAAC
* * *
1197945 GCAAAAAAAGAAAC
1 ACAGAAACAGAAAC
*
1197959 ATAGAAACAGAAAC
1 ACAGAAACAGAAAC
1197973 A
1 A
1197974 AAAAAAAAGT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.67, C:0.16, G:0.14, T:0.02
Consensus pattern (14 bp):
ACAGAAACAGAAAC
Found at i:1204686 original size:9 final size:10
Alignment explanation
Indices: 1204674--1204717 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
1204664 TTGTTTCTTT
1204674 TGTATT-TTA
1 TGTATTATTA
1204683 TGTATT-TTA
1 TGTATTATTA
1204692 T-TATTTATTA
1 TGTA-TTATTA
1204702 T-TATTATTA
1 TGTATTATTA
1204711 TGTATTA
1 TGTATTA
1204718 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 2 0.06
9 19 0.59
10 11 0.34
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (10 bp):
TGTATTATTA
Found at i:1204698 original size:16 final size:15
Alignment explanation
Indices: 1204679--1204743 Score: 67
Period size: 16 Copynumber: 4.1 Consensus size: 15
1204669 TCTTTTGTAT
1204679 TTTATGTATTTTATTA
1 TTTAT-TATTTTATTA
1204695 TTTATTATTATTATTA
1 TTTATTATT-TTATTA
* * *
1204711 TGTATTAATATATATA
1 TTTATTATTTTAT-TA
*
1204727 TTTATTTTTTTATTA
1 TTTATTATTTTATTA
1204742 TT
1 TT
1204744 AGATTAGATT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
15 11 0.28
16 29 0.73
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTATTATTTTATTA
Found at i:1204785 original size:8 final size:8
Alignment explanation
Indices: 1204685--1204792 Score: 52
Period size: 8 Copynumber: 13.8 Consensus size: 8
1204675 GTATTTTATG
*
1204685 TATTTTAT
1 TATTATAT
1204693 TATT-TAT
1 TATTATAT
1204700 TATTATTAT
1 TATTA-TAT
*
1204709 TA-TGTAT
1 TATTATAT
*
1204716 TAATATAT
1 TATTATAT
1204724 ATATT-TAT
1 -TATTATAT
* *
1204732 TTTTTTAT
1 TATTATAT
*
1204740 TATTAGAT
1 TATTATAT
1204748 TAGATT-TA-
1 T--ATTATAT
1204756 TATGTATA-
1 TAT-TATAT
1204764 TAGTTATA-
1 TA-TTATAT
1204772 TA-TATAT
1 TATTATAT
1204779 TATTATAT
1 TATTATAT
1204787 TATTAT
1 TATTAT
1204793 TTTTTTTCTC
Statistics
Matches: 80, Mismatches: 8, Indels: 24
0.71 0.07 0.21
Matches are distributed among these distances:
6 6 0.08
7 18 0.22
8 43 0.54
9 10 0.12
10 3 0.04
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (8 bp):
TATTATAT
Found at i:1205237 original size:25 final size:25
Alignment explanation
Indices: 1205208--1205261 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1205198 CTGGGAGTGA
*
1205208 GAAAAAATTTT-TAGAAATTTTTGG
1 GAAAAAATTTTCTAGAAATTTCTGG
* *
1205232 CGAAAAATTTTTCTGGAAATTTCTGG
1 -GAAAAAATTTTCTAGAAATTTCTGG
1205258 GAAA
1 GAAA
1205262 TTTCCAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.37
Consensus pattern (25 bp):
GAAAAAATTTTCTAGAAATTTCTGG
Found at i:1205830 original size:6 final size:6
Alignment explanation
Indices: 1205809--1205893 Score: 50
Period size: 6 Copynumber: 13.7 Consensus size: 6
1205799 TCTAATATTC
* * *
1205809 TTTTTA TCTTTA -TTTTA TTTTTTA TTTCT- GTTTTA CTTTTCT- TTATTTA
1 TTTTTA TTTTTA TTTTTA -TTTTTA TTTTTA TTTTTA -TTTT-TA TT-TTTA
* *
1205858 TTTTTA TTTTTA TTTATC TTTTTA TTATTCTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TT-TT-TA TTTT
1205894 CTTTAAATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
5 7 0.12
6 32 0.53
7 16 0.27
8 5 0.08
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:1205873 original size:16 final size:15
Alignment explanation
Indices: 1205845--1205893 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1205835 TCTGTTTTAC
*
1205845 TTTTCTTTATTTATT
1 TTTTTTTTATTTATT
*
1205860 TTTATTTTTATTTATC
1 TTT-TTTTTATTTATT
*
1205876 TTTTTATTATTCTATT
1 TTTTTTTTATT-TATT
1205892 TT
1 TT
1205894 CTTTAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTTTATTTATT
Found at i:1206002 original size:58 final size:59
Alignment explanation
Indices: 1205910--1206088 Score: 261
Period size: 58 Copynumber: 3.0 Consensus size: 59
1205900 ATAAAAATGA
*
1205910 AAATTTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1 AAATTTT-AAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* * *
1205970 AAATTTT-TAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCTTTAAAAAT
1 AAATTTTAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* * *
1206028 AAATTTTCAAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAGAAAT
1 AAATTTT--AAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1206089 TGCTAATGTA
Statistics
Matches: 106, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
58 54 0.51
60 7 0.07
61 45 0.42
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.36
Consensus pattern (59 bp):
AAATTTTAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
Found at i:1220491 original size:19 final size:21
Alignment explanation
Indices: 1220467--1220505 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
1220457 TAAAAATTAT
1220467 TTTTTAATTA-AT-TATTTAA
1 TTTTTAATTATATATATTTAA
*
1220486 TTTTTATTTATATATATTTA
1 TTTTTAATTATATATATTTA
1220506 TATAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTTAATTATATATATTTAA
Found at i:1220519 original size:30 final size:31
Alignment explanation
Indices: 1220485--1220556 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
1220475 TAATTATTTA
* *
1220485 ATTTTTATTTATATATATTTATATAATA-AT
1 ATTTTTATTTATATATATTTAAAAAATATAT
** *
1220515 ATTTTTAAATATTTATATTTAAAAAATATAT
1 ATTTTTATTTATATATATTTAAAAAATATAT
1220546 ATTTTATATTT
1 ATTTT-TATTT
1220557 TTAAAAAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
30 23 0.70
31 7 0.21
32 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
ATTTTTATTTATATATATTTAAAAAATATAT
Found at i:1220551 original size:22 final size:22
Alignment explanation
Indices: 1220526--1220574 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1220516 TTTTTAAATA
1220526 TTTATA-TTTAAAAAATATATAT
1 TTTATATTTTAAAAAA-ATATAT
*
1220548 TTTATATTTTTAAAAAATATAT
1 TTTATATTTTAAAAAAATATAT
1220570 TTTAT
1 TTTAT
1220575 TAATTTCGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTATATTTTAAAAAAATATAT
Found at i:1221365 original size:15 final size:14
Alignment explanation
Indices: 1221346--1221391 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
1221336 TAATCATAAT
1221346 TTAATATAAATTAA
1 TTAATATAAATTAA
1221360 TATAATCAT-AATTAA
1 T-TAAT-ATAAATTAA
1221375 TTAATA-AAATATAA
1 TTAATATAAAT-TAA
1221389 TTA
1 TTA
1221392 TTAATTAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 4 0.14
14 11 0.39
15 11 0.39
16 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAATATAAATTAA
Found at i:1221371 original size:21 final size:20
Alignment explanation
Indices: 1221331--1221399 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
1221321 ACTTTTTTAT
*
1221331 TAAATTAATCATAATTTAATA
1 TAAATTAAT-ATAATATAATA
1221352 TAAATTAATATAATCATAAT-
1 TAAATTAATATAAT-ATAATA
*
1221372 T-AATTAATAAAATATAATTA
1 TAAATTAATATAATATAA-TA
*
1221392 TTAATTAA
1 TAAATTAA
1221400 CTCATTTCTC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.10
19 12 0.29
20 7 0.17
21 19 0.45
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATTAATATAATATAATA
Found at i:1221378 original size:19 final size:18
Alignment explanation
Indices: 1221354--1221396 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
1221344 ATTTAATATA
*
1221354 AATTAATATAATCATAATT
1 AATTAATAAAAT-ATAATT
1221373 AATTAATAAAATATAATT
1 AATTAATAAAATATAATT
1221391 -ATTAAT
1 AATTAAT
1221397 TAACTCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 6 0.26
19 11 0.48
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTAATAAAATATAATT
Found at i:1221797 original size:9 final size:9
Alignment explanation
Indices: 1221783--1221827 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
1221773 AAGCTTTAGA
1221783 TTTTTCTTT
1 TTTTTCTTT
*
1221792 TTTTTCTGT
1 TTTTTCTTT
* *
1221801 TTTCTCTCT
1 TTTTTCTTT
*
1221810 TTTTTCTTC
1 TTTTTCTTT
1221819 TTTTTCTTT
1 TTTTTCTTT
1221828 CCCTCCTCAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:1221812 original size:20 final size:20
Alignment explanation
Indices: 1221787--1221825 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1221777 TTTAGATTTT
1221787 TCTTTTTT-TTCTGTTTTCTC
1 TCTTTTTTCTTCT-TTTTCTC
1221807 TCTTTTTTCTTCTTTTTCT
1 TCTTTTTTCTTCTTTTTCT
1221826 TTCCCTCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.77
Consensus pattern (20 bp):
TCTTTTTTCTTCTTTTTCTC
Found at i:1221814 original size:11 final size:10
Alignment explanation
Indices: 1221786--1221823 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 10
1221776 CTTTAGATTT
1221786 TTCTTTTTT-
1 TTCTTTTTTC
*
1221795 TTCTGTTTTC
1 TTCTTTTTTC
1221805 TCTCTTTTTTC
1 T-TCTTTTTTC
1221816 TTCTTTTT
1 TTCTTTTT
1221824 CTTTCCCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.32
10 8 0.32
11 9 0.36
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:1222224 original size:17 final size:17
Alignment explanation
Indices: 1222204--1222244 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1222194 TTTTACTCTC
**
1222204 TTTTGTTTTTTTTTTTT
1 TTTTGTTTTTTTTGCTT
1222221 TTTTGTTTTTTTTGCTT
1 TTTTGTTTTTTTTGCTT
1222238 TTTTGTT
1 TTTTGTT
1222245 GGTTTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (17 bp):
TTTTGTTTTTTTTGCTT
Found at i:1222234 original size:9 final size:9
Alignment explanation
Indices: 1222204--1222255 Score: 61
Period size: 9 Copynumber: 5.4 Consensus size: 9
1222194 TTTTACTCTC
1222204 TTTTGTTTT
1 TTTTGTTTT
1222213 TTTT-TTTT
1 TTTTGTTTT
1222221 TTTTGTTTT
1 TTTTGTTTT
1222230 TTTTGCTTTT
1 TTTTG-TTTT
1222240 TTGTTGGTTTT
1 TT-TT-GTTTT
1222251 CTTTT
1 -TTTT
1222256 AGGATGATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.21
9 13 0.34
10 6 0.16
11 8 0.21
12 3 0.08
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.85
Consensus pattern (9 bp):
TTTTGTTTT
Found at i:1222722 original size:2 final size:2
Alignment explanation
Indices: 1222715--1222754 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1222705 AAACAATTGG
* *
1222715 AT AT AT AT AT AT GT AC 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
1222755 GCGATGAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1223829 original size:14 final size:15
Alignment explanation
Indices: 1223810--1223840 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1223800 CCTCTAAAGA
1223810 TTGAAA-AAAAAAAT
1 TTGAAAGAAAAAAAT
1223824 TTGAAAGAAAAAAAT
1 TTGAAAGAAAAAAAT
1223839 TT
1 TT
1223841 TCTTTGGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (15 bp):
TTGAAAGAAAAAAAT
Found at i:1237859 original size:82 final size:80
Alignment explanation
Indices: 1237751--1237921 Score: 238
Period size: 82 Copynumber: 2.1 Consensus size: 80
1237741 TTTACTCATA
1237751 TTAA-AAAAATCATTGTATTGTAGGAAACAAATACTT-ATTCCGTCACAAATTATTTAAATCTTA
1 TTAAGAAAAATCATTGTATTGTAGGAAACAAATA-TTCATTCCGTCACAAATTATTTAAATCTTA
1237814 TTGATTTTCACAAAAT
65 TTGATTTTCACAAAAT
* * * * *
1237830 TTAAGAAAAATTATTGTATATTGTAGGAAACAAATATTCATTCCGTCATAAATTGTTTAAGTTTT
1 TTAAGAAAAATCATTG--TATTGTAGGAAACAAATATTCATTCCGTCACAAATTATTTAAATCTT
* *
1237895 GTTGATTTTCATAAAAT
64 ATTGATTTTCACAAAAT
1237912 TTAAGAAAAA
1 TTAAGAAAAA
1237922 AATTTGATTT
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
79 4 0.05
80 10 0.12
81 2 0.02
82 65 0.80
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (80 bp):
TTAAGAAAAATCATTGTATTGTAGGAAACAAATATTCATTCCGTCACAAATTATTTAAATCTTAT
TGATTTTCACAAAAT
Found at i:1246429 original size:32 final size:32
Alignment explanation
Indices: 1246360--1246457 Score: 103
Period size: 32 Copynumber: 3.1 Consensus size: 32
1246350 AACAAAAAAA
* * * *
1246360 AAAACCTCAAAACCTTGAAAATCC-AAAACTAC
1 AAAACCTTAAAACCTTCAAAACCCTAAAA-TTC
1246392 AAAACCTTAAAACCTTCAAAACCCTAAAATTC
1 AAAACCTTAAAACCTTCAAAACCCTAAAATTC
* * *
1246424 GAAACCTTAAAA--TCCAAAACCTTAAAATTC
1 AAAACCTTAAAACCTTCAAAACCCTAAAATTC
1246454 AAAA
1 AAAA
1246458 TCCAAAAGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
30 19 0.33
32 34 0.60
33 4 0.07
ACGTcount: A:0.53, C:0.26, G:0.02, T:0.19
Consensus pattern (32 bp):
AAAACCTTAAAACCTTCAAAACCCTAAAATTC
Found at i:1246434 original size:15 final size:15
Alignment explanation
Indices: 1246391--1246457 Score: 89
Period size: 15 Copynumber: 4.3 Consensus size: 15
1246381 TCCAAAACTA
1246391 CAAAACCTTAAAACCTT
1 CAAAACCTTAAAA--TT
*
1246408 CAAAACCCTAAAATT
1 CAAAACCTTAAAATT
* *
1246423 CGAAACCTTAAAATC
1 CAAAACCTTAAAATT
1246438 CAAAACCTTAAAATT
1 CAAAACCTTAAAATT
1246453 CAAAA
1 CAAAA
1246458 TCCAAAAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
15 32 0.73
17 12 0.27
ACGTcount: A:0.52, C:0.25, G:0.01, T:0.21
Consensus pattern (15 bp):
CAAAACCTTAAAATT
Found at i:1248113 original size:30 final size:30
Alignment explanation
Indices: 1248048--1248135 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
1248038 CAAAACCTTT
*
1248048 AAAATCC-AAAACTACAAAACCCTAAAACCTTC
1 AAAATCCTAAAACT-CAAAACCTTAAAA--TTC
* *
1248080 AAAA-CCTTAAAATTCGAAACCTTAAAATTC
1 AAAATCC-TAAAACTCAAAACCTTAAAATTC
*
1248110 AAAATCCTAAACCTCAAAACCTTAAA
1 AAAATCCTAAAACTCAAAACCTTAAA
1248136 CCCTAAAACT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
30 23 0.49
31 4 0.09
32 15 0.32
33 5 0.11
ACGTcount: A:0.52, C:0.26, G:0.01, T:0.20
Consensus pattern (30 bp):
AAAATCCTAAAACTCAAAACCTTAAAATTC
Found at i:1248137 original size:15 final size:15
Alignment explanation
Indices: 1248062--1248137 Score: 64
Period size: 15 Copynumber: 4.9 Consensus size: 15
1248052 TCCAAAACTA
*
1248062 CAAAACCCTAAAACCTT
1 CAAAA-CCTTAAACC-T
**
1248079 CAAAACCTTAAAATT
1 CAAAACCTTAAACCT
* **
1248094 CGAAACCTTAAAATT
1 CAAAACCTTAAACCT
1248109 CAAAATCC-TAAACCT
1 CAAAA-CCTTAAACCT
1248124 CAAAACCTTAAACC
1 CAAAACCTTAAACC
1248138 CTAAAACTCC
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
14 2 0.04
15 35 0.70
16 8 0.16
17 5 0.10
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.21
Consensus pattern (15 bp):
CAAAACCTTAAACCT
Found at i:1255625 original size:6 final size:6
Alignment explanation
Indices: 1255614--1255660 Score: 76
Period size: 6 Copynumber: 7.7 Consensus size: 6
1255604 AGATGGCCCA
*
1255614 TTTTAT TTTTAT TTTTAT TTTTAT TTTTATT TTTTAT TATTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT TTTT
1255661 TAGGTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 32 0.84
7 6 0.16
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:1255661 original size:13 final size:13
Alignment explanation
Indices: 1255614--1255662 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
1255604 AGATGGCCCA
1255614 TTTTA-TTTTTAT
1 TTTTATTTTTTAT
1255626 TTTTA-TTTTTAT
1 TTTTATTTTTTAT
1255638 TTTTATTTTTTAT
1 TTTTATTTTTTAT
*
1255651 TATTATTTTTTA
1 TTTTATTTTTTA
1255663 GGTTTTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
12 17 0.49
13 18 0.51
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:1255687 original size:19 final size:19
Alignment explanation
Indices: 1255613--1255687 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 19
1255603 AAGATGGCCC
1255613 ATTTT-ATTTTTA-TTTTT
1 ATTTTAATTTTTATTTTTT
*
1255630 ATTTTTATTTTTATTTTTT
1 ATTTTAATTTTTATTTTTT
*
1255649 ATTATTATTTTTTAGGTTTTTT
1 ATT-TTAATTTTTA--TTTTTT
* *
1255671 ATTCTAAATTTTATTTT
1 ATTTTAATTTTTATTTT
1255688 AATTATTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
17 5 0.10
18 7 0.15
19 12 0.25
20 8 0.17
21 7 0.15
22 9 0.19
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.76
Consensus pattern (19 bp):
ATTTTAATTTTTATTTTTT
Found at i:1256518 original size:7 final size:7
Alignment explanation
Indices: 1256506--1256560 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
1256496 TTCCTTAATT
1256506 TTTTTTA
1 TTTTTTA
1256513 TTTTTTA
1 TTTTTTA
1256520 TTTTTTA
1 TTTTTTA
*
1256527 ATTTTTA
1 TTTTTTA
**
1256534 -ACTTTA
1 TTTTTTA
1256540 TTTTATT-
1 TTTT-TTA
1256547 TTATTTTA
1 TT-TTTTA
1256555 TTTTTT
1 TTTTTT
1256561 TAGTGATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
6 4 0.10
7 29 0.74
8 6 0.15
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTA
Found at i:1256750 original size:62 final size:60
Alignment explanation
Indices: 1256574--1256942 Score: 307
Period size: 61 Copynumber: 6.2 Consensus size: 60
1256564 TGATTTTCCT
* * * * * *
1256574 AAAATAAAATTTTCAAAAAAAATTATTATTGAGGAAAAGTTGAAAGTATCAA----CCTTG
1 AAAATAAAAATTTAAAAAAAAAATATT-TTAAGGGAAAGTTGAAAGTATCAATTTTTCTTG
*** ** *
1256631 AAAATAATTTTTTTTTAAAAAAAATACTTTTAAGGGAAAGTTGAAAGTATTAA-TTTTCTTG
1 AAAATAA-AAATTTAAAAAAAAAATA-TTTTAAGGGAAAGTTGAAAGTATCAATTTTTCTTG
* *
1256692 AAAATAAAAAAGGTTT-AAAAAAAAATATTTTTAGGGAAAGTTAAAAGTATCAATTTTTCTTG
1 AAAAT-AAAAA--TTTAAAAAAAAAATATTTTAAGGGAAAGTTGAAAGTATCAATTTTTCTTG
* *
1256754 AAAATAAAAAGGTTT--TAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTT-
1 AAAATAAAAA--TTTAAAAAAAAAATATTTTAAGGG-AAAGTTGAAAGTATCAATTTTTCTTG
* * ** *
1256814 AAAATTAAAATTTCAAAAAAAAA-A-TTCGAGGAAAAGTTGAAAGTATCAATTTTTCTTG
1 AAAATAAAAATTTAAAAAAAAAATATTTTAAGGGAAAGTTGAAAGTATCAATTTTTCTTG
* * *
1256872 -AAATTAAAATTTCAAAAAAACAAAATATTTTAAGGAAAAGTTGAAAAGTATCAA--TTTCTTT
1 AAAATAAAAATTT--AAAAAA-AAAATATTTTAAGGGAAAGTTG-AAAGTATCAATTTTTCTTG
1256933 AAAATAAAAA
1 AAAATAAAAA
1256943 CTTTTAAATG
Statistics
Matches: 264, Mismatches: 28, Indels: 35
0.81 0.09 0.11
Matches are distributed among these distances:
57 44 0.17
58 42 0.16
59 8 0.03
60 38 0.14
61 73 0.28
62 46 0.17
63 13 0.05
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (60 bp):
AAAATAAAAATTTAAAAAAAAAATATTTTAAGGGAAAGTTGAAAGTATCAATTTTTCTTG
Found at i:1260968 original size:35 final size:34
Alignment explanation
Indices: 1260924--1261007 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 34
1260914 TCAATCCTGG
* * * *
1260924 TCATCTTTATTCTCTGACCAGCGATTCAGTCTCGG
1 TCATTTTTATTCT-TGACCAGCAATTCAATCTCGA
* **
1260959 TTATTTTTATTCGTTGACTTGCAATTCAATCTCGA
1 TCATTTTTATTC-TTGACCAGCAATTCAATCTCGA
1260994 TCATTTTTATTCTT
1 TCATTTTTATTCTT
1261008 CAACTTACAG
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
34 2 0.05
35 37 0.93
36 1 0.03
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (34 bp):
TCATTTTTATTCTTGACCAGCAATTCAATCTCGA
Found at i:1261022 original size:35 final size:35
Alignment explanation
Indices: 1260961--1261035 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
1260951 AGTCTCGGTT
* * *
1260961 ATTTTTATTCGTTGACTTGCAATTCAATCTCGATC
1 ATTTTTATTCGTTAACTTACAATTCAATCTCAATC
*
1260996 ATTTTTATTC-TTCAACTTACAGTTCAATCTCAATC
1 ATTTTTATTCGTT-AACTTACAATTCAATCTCAATC
1261031 ATTTT
1 ATTTT
1261036 CATTTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 2 0.06
35 33 0.94
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.48
Consensus pattern (35 bp):
ATTTTTATTCGTTAACTTACAATTCAATCTCAATC
Found at i:1268024 original size:26 final size:26
Alignment explanation
Indices: 1267996--1268102 Score: 81
Period size: 27 Copynumber: 3.8 Consensus size: 26
1267986 TTAATGCATT
1267996 AAATAAAAATTTTTAAAATTTTTTATA
1 AAATAAAAA-TTTTAAAATTTTTTATA
* * *
1268023 AAATCAAAATTTTATAATTTTTAATGTGAAA
1 AAATAAAAATTTTA-AAATTTT--T-T-ATA
*
1268054 AAATAAAAAATTTTAAAATTAATTT-TA
1 AAAT-AAAAATTTTAAAATT-TTTTATA
*
1268081 AAATATAAAATGTTAAAATTTT
1 AAATA-AAAATTTTAAAATTTT
1268103 GAATGTTAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
26 7 0.11
27 32 0.51
29 2 0.03
30 2 0.03
31 10 0.16
32 10 0.16
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (26 bp):
AAATAAAAATTTTAAAATTTTTTATA
Found at i:1268101 original size:59 final size:58
Alignment explanation
Indices: 1267996--1268119 Score: 155
Period size: 59 Copynumber: 2.1 Consensus size: 58
1267986 TTAATGCATT
* * * *
1267996 AAATAAAAATTTTTAAAATTTTTTATAAAATCAAAATTTTATAATTTTTAATGTGAAA
1 AAATAAAAAATTTTAAAATTTTTTATAAAATCAAAATGTTAAAATTTTGAATGTGAAA
*
1268054 AAATAAAAAATTTTAAAATTAATTTTA-AAATAT-AAAATGTTAAAATTTTGAATGTTAAA
1 AAATAAAAAATTTTAAAATT--TTTTATAAA-ATCAAAATGTTAAAATTTTGAATGTGAAA
1268113 AAA-AAAA
1 AAATAAAA
1268120 GATGACATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
58 23 0.40
59 28 0.48
60 7 0.12
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.40
Consensus pattern (58 bp):
AAATAAAAAATTTTAAAATTTTTTATAAAATCAAAATGTTAAAATTTTGAATGTGAAA
Found at i:1270071 original size:23 final size:24
Alignment explanation
Indices: 1270020--1270083 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
1270010 AAAATTATTT
*
1270020 TAAAAAATTTAAAAA-TTACATAA
1 TAAAAATTTTAAAAATTTACATAA
* *
1270043 TTAAAATTTTAAAAATTTATAT-A
1 TAAAAATTTTAAAAATTTACATAA
1270066 TAAAAATTTAATAAAAAT
1 TAAAAATTT--TAAAAAT
1270084 ATAATAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 22 0.65
24 5 0.15
25 7 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAAAATTTTAAAAATTTACATAA
Found at i:1270090 original size:22 final size:22
Alignment explanation
Indices: 1270022--1270091 Score: 56
Period size: 22 Copynumber: 3.1 Consensus size: 22
1270012 AATTATTTTA
* *
1270022 AAAAATTTAA-AAATTACATAAT
1 AAAAATTTAATAAA-AATATAAT
*
1270044 TAAAATTT--TAAAAATTTATATAT
1 AAAAATTTAATAAAAA--TATA-AT
1270067 AAAAATTTAATAAAAATATAAT
1 AAAAATTTAATAAAAATATAAT
1270089 AAA
1 AAA
1270092 TTATATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
20 1 0.03
21 3 0.08
22 15 0.39
23 13 0.34
25 6 0.16
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAATTTAATAAAAATATAAT
Found at i:1277540 original size:2 final size:2
Alignment explanation
Indices: 1277535--1277578 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1277525 TTTTTAGGGC
* * *
1277535 AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT GT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1277577 AT
1 AT
1277579 TTTGTTAGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1285030 original size:17 final size:17
Alignment explanation
Indices: 1285008--1285040 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1284998 TGATAGAATA
*
1285008 GAATAAGATAATATTAT
1 GAATAAAATAATATTAT
1285025 GAATAAAATAATATTA
1 GAATAAAATAATATTA
1285041 AATAATATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (17 bp):
GAATAAAATAATATTAT
Found at i:1286540 original size:23 final size:22
Alignment explanation
Indices: 1286484--1286531 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1286474 TTTATTTGAT
* *
1286484 AAAA-AATTAATTGATCAACAA
1 AAAATAATTTATTAATCAACAA
*
1286505 AAAATAATTTATTAATCAATAA
1 AAAATAATTTATTAATCAACAA
1286527 AAAAT
1 AAAAT
1286532 GAGATTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATAATTTATTAATCAACAA
Found at i:1286657 original size:18 final size:18
Alignment explanation
Indices: 1286646--1286743 Score: 65
Period size: 18 Copynumber: 5.2 Consensus size: 18
1286636 AATTTTACTT
1286646 ATAAATAAAATTATATTA
1 ATAAATAAAATTATATTA
*
1286664 ATAAAT-AAATAATATTA
1 ATAAATAAAATTATATTA
*
1286681 TATGAATAAATAATATACTATTA
1 -ATAAAT-AA-AAT-TA-TATTA
*
1286704 ATAAATAATATTA-ATTTA
1 ATAAATAAAATTATA-TTA
* * *
1286722 TTTAATAAATATTATAATA
1 ATAAATAAA-ATTATATTA
1286741 ATA
1 ATA
1286744 TTATTAATAA
Statistics
Matches: 60, Mismatches: 11, Indels: 17
0.68 0.12 0.19
Matches are distributed among these distances:
17 11 0.18
18 20 0.33
19 9 0.15
20 4 0.07
21 5 0.08
22 6 0.10
23 5 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (18 bp):
ATAAATAAAATTATATTA
Found at i:1286671 original size:22 final size:22
Alignment explanation
Indices: 1286646--1286757 Score: 85
Period size: 22 Copynumber: 5.2 Consensus size: 22
1286636 AATTTTACTT
1286646 ATAAATAAAATTATATTAATAA
1 ATAAATAAAATTATATTAATAA
* *
1286668 ATAAATAATATTATATGAATAA
1 ATAAATAAAATTATATTAATAA
1286690 AT-AAT---A-TACTATTAATAA
1 ATAAATAAAATTA-TATTAATAA
* *
1286708 ATAATATTAATTTAT-TTAATAA
1 ATAA-ATAAAATTATATTAATAA
*
1286730 ATATTATAATAA-TATTATTAATAA
1 ATA-AATAA-AATTA-TATTAATAA
1286754 ATAA
1 ATAA
1286758 TATACTATTA
Statistics
Matches: 71, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
17 2 0.03
18 11 0.15
19 1 0.01
20 2 0.03
21 3 0.04
22 37 0.52
23 3 0.04
24 12 0.17
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (22 bp):
ATAAATAAAATTATATTAATAA
Found at i:1286693 original size:40 final size:39
Alignment explanation
Indices: 1286646--1286760 Score: 110
Period size: 40 Copynumber: 2.8 Consensus size: 39
1286636 AATTTTACTT
1286646 ATAAATAAAATTATATTAATAAATAAATAATATTATATGA
1 ATAAATAAAATTATATTAATAAATAAATAATATTAT-TGA
* *
1286686 ATAAATAATA-TACTATTAATAAATAATATTAAT-TTATTTA
1 ATAAATAAAATTA-TATTAATAAATAA-A-TAATATTATTGA
* *
1286726 ATAAATATTATAATAATATT-ATTAATAAATAATAT
1 ATAAATA--A-AATTATATTAATAAATAAATAATAT
1286761 ACTATTAATA
Statistics
Matches: 62, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
39 2 0.03
40 35 0.56
41 7 0.11
42 12 0.19
43 5 0.08
44 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (39 bp):
ATAAATAAAATTATATTAATAAATAAATAATATTATTGA
Found at i:1286738 original size:27 final size:26
Alignment explanation
Indices: 1286703--1286816 Score: 92
Period size: 27 Copynumber: 4.4 Consensus size: 26
1286693 ATATACTATT
1286703 AATAA-ATAATATTAATTTATTTAATA
1 AATAATATAATATTAATTTA-TTAATA
* *
1286729 AATATTATAATAAT-A-TTATTAATA
1 AATAATATAATATTAATTTATTAATA
* * * *
1286753 AATAATATACTATTAATATAATATATT
1 AATAATATAATATTAATTTATTA-ATA
* *
1286780 AATAA-ATATTATTATAATATATTAATA
1 AATAATATAATA-T-TAATTTATTAATA
1286807 AATAATATAA
1 AATAATATAA
1286817 AGAATAATAA
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
24 17 0.25
25 4 0.06
26 14 0.20
27 22 0.32
28 12 0.17
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (26 bp):
AATAATATAATATTAATTTATTAATA
Found at i:1286760 original size:64 final size:55
Alignment explanation
Indices: 1286709--1286815 Score: 171
Period size: 55 Copynumber: 1.9 Consensus size: 55
1286699 TATTAATAAA
*
1286709 TAATATTAATTTATTTAATAAATATTATAATAATATTATTAATAAATAATATACTAT
1 TAATA-TAATATA-TTAATAAATATTATAATAATATTATTAATAAATAATATACTAT
*
1286766 TAATATAATATATTAATAAATATTATTATAATA-TATTAATAAATAATATA
1 TAATATAATATATTAATAAATATTATAATAATATTATTAATAAATAATATA
1286816 AAGAATAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
54 17 0.35
55 20 0.42
56 6 0.12
57 5 0.10
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (55 bp):
TAATATAATATATTAATAAATATTATAATAATATTATTAATAAATAATATACTAT
Found at i:1286768 original size:18 final size:17
Alignment explanation
Indices: 1286667--1286815 Score: 107
Period size: 18 Copynumber: 8.8 Consensus size: 17
1286657 TATATTAATA
*
1286667 AATAAATAATATTATATG
1 AATAAATAATA-TATATT
1286685 AATAAATAATATACTATT
1 AATAAATAATATA-TATT
1286703 AATAAATAATAT-TAATT
1 AATAAATAATATAT-ATT
** *
1286720 --TATTTAATAAATATT
1 AATAAATAATATATATT
1286735 -AT-AATAATAT-TATT
1 AATAAATAATATATATT
1286749 AATAAATAATATACTATT
1 AATAAATAATATA-TATT
*
1286767 AAT--ATAATATATTAATA
1 AATAAATAATATA-T-ATT
* *
1286784 AATATTATTATAATATATT
1 AATA-AATAAT-ATATATT
1286803 AATAAATAATATA
1 AATAAATAATATA
1286816 AAGAATAATA
Statistics
Matches: 105, Mismatches: 13, Indels: 27
0.72 0.09 0.19
Matches are distributed among these distances:
14 4 0.04
15 17 0.16
16 20 0.19
17 13 0.12
18 37 0.35
19 6 0.06
20 5 0.05
21 3 0.03
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (17 bp):
AATAAATAATATATATT
Found at i:1286806 original size:47 final size:41
Alignment explanation
Indices: 1286711--1286806 Score: 97
Period size: 42 Copynumber: 2.2 Consensus size: 41
1286701 TTAATAAATA
*
1286711 ATATTAATTTATTTAATAAATATTATAATAATATTATTAAT
1 ATATTAATATATTTAATAAATATTATAATAATATTATTAAT
*
1286752 A-AATAATATACTATTAATATAATA-TATTAATAAATATTATTATAAT
1 ATATTAATATA-T-TTAATA-AATATTA-TAAT-AATATTA-T-TAAT
1286798 ATATTAATA
1 ATATTAATA
1286807 AATAATATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
40 7 0.16
41 2 0.05
42 8 0.18
43 8 0.18
44 7 0.16
45 1 0.02
46 5 0.11
47 6 0.14
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (41 bp):
ATATTAATATATTTAATAAATATTATAATAATATTATTAAT
Found at i:1286886 original size:13 final size:13
Alignment explanation
Indices: 1286870--1286899 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1286860 AATATTTTAA
*
1286870 TATTAAATATTAT
1 TATTAAATATAAT
1286883 TATTAAATATAAT
1 TATTAAATATAAT
1286896 TATT
1 TATT
1286900 TTTAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATTAAATATAAT
Found at i:1286888 original size:19 final size:18
Alignment explanation
Indices: 1286843--1286928 Score: 67
Period size: 19 Copynumber: 4.9 Consensus size: 18
1286833 TTATTTTAAG
* *
1286843 TATTTTTATATTAACATAA
1 TATTTTAATATTAA-ATAT
1286862 TATTTTAATATTAAATAT
1 TATTTTAATATTAAATAT
*
1286880 TATTATTAA-A-TATA-AT
1 TATT-TTAATATTAAATAT
1286896 TATTTTTAATATT-AATA-
1 TA-TTTTAATATTAAATAT
*
1286913 -ATTTTAATAATAAATA
1 TATTTTAATATTAAATA
1286929 ATTTCAATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
15 9 0.16
16 13 0.23
17 7 0.12
18 10 0.18
19 17 0.30
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTTTAATATTAAATAT
Found at i:1286928 original size:16 final size:16
Alignment explanation
Indices: 1286863--1286959 Score: 57
Period size: 15 Copynumber: 6.3 Consensus size: 16
1286853 TTAACATAAT
*
1286863 ATTTTAATATTAAATA
1 ATTTTAATAATAAATA
*
1286879 TTATTATTAA-ATATAATTA
1 --ATT-TTAATA-ATAAATA
* *
1286898 TTTTTAAT-ATTAATA
1 ATTTTAATAATAAATA
1286913 ATTTTAATAATAAATA
1 ATTTTAATAATAAATA
*
1286929 A-TTT--CAAT--AT-
1 ATTTTAATAATAAATA
1286939 ATTTTAATAATAAATA
1 ATTTTAATAATAAATA
1286955 ATTTT
1 ATTTT
1286960 TTATATTTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 22
0.66 0.10 0.24
Matches are distributed among these distances:
10 1 0.02
11 5 0.08
13 6 0.10
15 17 0.28
16 16 0.27
17 2 0.03
18 4 0.07
19 9 0.15
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTAATAATAAATA
Found at i:1286930 original size:35 final size:35
Alignment explanation
Indices: 1286864--1286931 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
1286854 TAACATAATA
* *
1286864 TTTTAATATTAAATATTATTATTAAATATAATTAT
1 TTTTAATATTAAATATTATTAATAAAAATAATTAT
1286899 TTTTAATATT-AATAATT-TTAATAATAAATAATT
1 TTTTAATATTAAAT-ATTATTAATAA-AAATAATT
1286932 TCAATATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 9 0.31
35 20 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (35 bp):
TTTTAATATTAAATATTATTAATAAAAATAATTAT
Found at i:1286946 original size:26 final size:25
Alignment explanation
Indices: 1286902--1286972 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 25
1286892 TAATTATTTT
1286902 TAATATTAATA-ATTTTAATAATAAA
1 TAAT-TTAATATATTTTAATAATAAA
1286927 TAATTTCAATATATTTTAATAATAAA
1 TAATTT-AATATATTTTAATAATAAA
**
1286953 TAATTTTTTATATTTTAATA
1 TAATTTAATATATTTTAATA
1286973 GTTATATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.05
25 20 0.48
26 20 0.48
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (25 bp):
TAATTTAATATATTTTAATAATAAA
Found at i:1286970 original size:25 final size:26
Alignment explanation
Indices: 1286909--1286972 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
1286899 TTTTAATATT
1286909 AATA-ATTTTAATAATAAATAATTTC
1 AATATATTTTAATAATAAATAATTTC
1286934 AATATATTTTAATAATAAATAATTT-
1 AATATATTTTAATAATAAATAATTTC
**
1286959 TTTATATTTTAATA
1 AATATATTTTAATA
1286973 GTTATATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 16 0.44
26 20 0.56
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:1288267 original size:72 final size:72
Alignment explanation
Indices: 1288186--1288323 Score: 188
Period size: 72 Copynumber: 1.9 Consensus size: 72
1288176 AAATTTTTTT
* *
1288186 AAAAAGAATCAAACCTAGAAAAACCCCTTAATGAGACA-TTCTTAAAAAGAATCAAACAAAAAAA
1 AAAAAGAATCAAACCTAGAAAAACCCCTTAATGAGAAATTTC-CAAAAAGAATCAAACAAAAAAA
1288250 AAAACCCC
65 AAAACCCC
* * ** **
1288258 AAAAAGAATCGAACCTAGAAAAAGCCCTTGTTGAGAAATTTCCAAAAAGAATCAAACCCAAAAAA
1 AAAAAGAATCAAACCTAGAAAAACCCCTTAATGAGAAATTTCCAAAAAGAATCAAACAAAAAAAA
1288323 A
66 A
1288324 TCCTTGTTGA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 54 0.95
73 3 0.05
ACGTcount: A:0.57, C:0.20, G:0.09, T:0.14
Consensus pattern (72 bp):
AAAAAGAATCAAACCTAGAAAAACCCCTTAATGAGAAATTTCCAAAAAGAATCAAACAAAAAAAA
AAACCCC
Found at i:1295879 original size:21 final size:22
Alignment explanation
Indices: 1295855--1295897 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1295845 TATTAAATGT
*
1295855 TATAATTATTT-TTTTAATTTA
1 TATAATTATTTATTTCAATTTA
1295876 TATAATTATTTATTTCAATTTA
1 TATAATTATTTATTTCAATTTA
1295898 AGAAAGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TATAATTATTTATTTCAATTTA
Found at i:1296130 original size:74 final size:75
Alignment explanation
Indices: 1296073--1296233 Score: 261
Period size: 74 Copynumber: 2.2 Consensus size: 75
1296063 ATTTTTGTCT
* *
1296073 AGTTAACATAAATTTTGATAAAGTTCAACTTGACAAATATTAT-ATTTTTTAACATAAAAACATC
1 AGTTAACATAAATTTTGACAAAGTCCAACTTGACAAATATTATGATTTTTTAACATAAAAACATC
1296137 AACTTTATCA
66 AACTTTATCA
*
1296147 AGTTAACATAAATTTTGACAAAGTCCAACTTGACAAATATTATGTTTTTTTAACATAAAAACATC
1 AGTTAACATAAATTTTGACAAAGTCCAACTTGACAAATATTATGATTTTTTAACATAAAAACATC
* * *
1296212 AGCTATGTCA
66 AACTTTATCA
1296222 AGTTAACATAAA
1 AGTTAACATAAA
1296234 ACTTGATGAT
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
74 41 0.51
75 39 0.49
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.35
Consensus pattern (75 bp):
AGTTAACATAAATTTTGACAAAGTCCAACTTGACAAATATTATGATTTTTTAACATAAAAACATC
AACTTTATCA
Found at i:1296448 original size:163 final size:163
Alignment explanation
Indices: 1296105--1296473 Score: 399
Period size: 163 Copynumber: 2.3 Consensus size: 163
1296095 GTTCAACTTG
* * *
1296105 ACAAATATTATATTTTTTAACATAAAAACATCAACTTTATCAAGTTAACATAAATTTTGACAAAG
1 ACAAAGATTATATTTTTTAACATAAAAATATCATCTTTATCAAGTTAACATAAATTTTGACAAAG
* *
1296170 TCCAACTTGACAAATATTATGTTTTTTTAACATAAAAACATCAGCTATGTCAAGTTAACATAAAA
66 TCCAACTTGACAAAGATTATGTTATTTTAACATAAAAACATCAGCTATGTCAAGTTAACATAAAA
* ** *
1296235 CTTGATGATTAAAATTTTAAATATGATAAAATC
131 CTTAAAAATTAAAATTTTAAATATGATAAAATA
* * * * * * *
1296268 ATAAAGACTACATTTTTTAACATAAAAGTGTTATCTTTATCAAGTTAACATAAATTTTGATAAAG
1 ACAAAGATTATATTTTTTAACATAAAAATATCATCTTTATCAAGTTAACATAAATTTTGACAAAG
** * * * * *
1296333 TTTAATTTGACAAAGA-T-TG-TATTTTAACATAAAAACATCATCTTTTTTAAGTTAACATAAAA
66 TCCAACTTGACAAAGATTATGTTATTTTAACATAAAAACATCAGCTATGTCAAGTTAACATAAAA
* * **
1296395 TTTAACAAAGTT-TAATTTTAAATTTAATG-TAATTTA
131 CTTAA-AAA-TTAAAATTTTAAA--T-ATGATAAAATA
*
1296431 ACAAAGATTGTATTTTTTAACA-AAAAATATCATCTTTATCAAG
1 ACAAAGATTATATTTTTTAACATAAAAATATCATCTTTATCAAG
1296474 CTAAAATAGA
Statistics
Matches: 167, Mismatches: 34, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
160 41 0.25
161 12 0.07
162 21 0.13
163 90 0.54
164 3 0.02
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.38
Consensus pattern (163 bp):
ACAAAGATTATATTTTTTAACATAAAAATATCATCTTTATCAAGTTAACATAAATTTTGACAAAG
TCCAACTTGACAAAGATTATGTTATTTTAACATAAAAACATCAGCTATGTCAAGTTAACATAAAA
CTTAAAAATTAAAATTTTAAATATGATAAAATA
Found at i:1296779 original size:181 final size:184
Alignment explanation
Indices: 1296425--1296782 Score: 596
Period size: 184 Copynumber: 2.0 Consensus size: 184
1296415 AATTTAATGT
* *
1296425 AATTTAACAAAGATTGTATTTTTTAACAAAAAATATCATCTTTATCAAGCTAAAATAGACAAATA
1 AATTTAACAAAAATTGTATTTTTTAACAAAAAATATCATCTTTATCAAGCTAAAATAAACAAATA
* *
1296490 TTGCATTTAGCTTGCTGAAAATATCATTTTTTGTCAAGTTATATTTCATAATTTGTACAAAACGT
66 TTGCATTTAGCTTGATGAAAATATCATTTTTTGTCAAGTTATATTTCATAATTTGTACAAAACAT
1296555 CCACTTTGTTAAGTTTAACAATATATTTTGTCCCTACATGCATTAACTTGATGA
131 CCACTTTGTTAAGTTTAACAATATATTTTGTCCCTACATGCATTAACTTGATGA
* * * * *
1296609 AATTTGACAAAAATTGTATTTTTTAACGAAAAATGTTATCTTTATCAAGCTAAATTAAACAAATA
1 AATTTAACAAAAATTGTATTTTTTAACAAAAAATATCATCTTTATCAAGCTAAAATAAACAAATA
1296674 TTGCATTTAGCTTGATG-AAATATCA-TTTTTGTCAAGTTATATTTCAT-ATTTGTACAAAACAT
66 TTGCATTTAGCTTGATGAAAATATCATTTTTTGTCAAGTTATATTTCATAATTTGTACAAAACAT
**
1296736 CCGTTTTGTTAAGTTTAACAATATATTTTGTCCCTACATGCATTAAC
131 CCACTTTGTTAAGTTTAACAATATATTTTGTCCCTACATGCATTAAC
1296783 AACTAACTTC
Statistics
Matches: 163, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
181 59 0.36
182 22 0.13
183 8 0.05
184 74 0.45
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (184 bp):
AATTTAACAAAAATTGTATTTTTTAACAAAAAATATCATCTTTATCAAGCTAAAATAAACAAATA
TTGCATTTAGCTTGATGAAAATATCATTTTTTGTCAAGTTATATTTCATAATTTGTACAAAACAT
CCACTTTGTTAAGTTTAACAATATATTTTGTCCCTACATGCATTAACTTGATGA
Found at i:1300229 original size:15 final size:16
Alignment explanation
Indices: 1300199--1300232 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1300189 TCTTTTTAAA
1300199 ATTATAATTATTTTAT
1 ATTATAATTATTTTAT
1300215 ATTATAATT-TTTTAT
1 ATTATAATTATTTTAT
1300230 ATT
1 ATT
1300233 TTCAAATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTATAATTATTTTAT
Found at i:1302433 original size:99 final size:99
Alignment explanation
Indices: 1302324--1302510 Score: 295
Period size: 100 Copynumber: 1.9 Consensus size: 99
1302314 AATAAAAATA
* *
1302324 AAATTTATAAAA-TGAACATTATAAATATTTATATACATAATTTGTTCTAATATGCATGTAACAC
1 AAATTTATAAAACTGAACATTATAAATATTTAAATACATAATTTGTTCCAATATGCATGTAACAC
*
1302388 AAAGTTTTAATCTTATAACATTCATAAACAAATTT
66 AAAG-TTTAATCTAATAACATTCATAAACAAATTT
* * * *
1302423 AAATTTATAAAACTGAATATTATAAATATTTAAATACATAATTTGTTCCAGTATGTATGTAACAG
1 AAATTTATAAAACTGAACATTATAAATATTTAAATACATAATTTGTTCCAATATGCATGTAACAC
1302488 AAAGTTTAATCTAATAACATTCA
66 AAAGTTTAATCTAATAACATTCA
1302511 AATTGTTTCA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
99 30 0.38
100 50 0.62
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (99 bp):
AAATTTATAAAACTGAACATTATAAATATTTAAATACATAATTTGTTCCAATATGCATGTAACAC
AAAGTTTAATCTAATAACATTCATAAACAAATTT
Found at i:1307168 original size:21 final size:21
Alignment explanation
Indices: 1307143--1307209 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 21
1307133 CAAATTCCCA
1307143 AAAAGTCTAGAAGCAATGTAC
1 AAAAGTCTAGAAGCAATGTAC
* * *
1307164 AAAAG---AGTATCAAAT-TCCC
1 AAAAGTCTAGAAGC-AATGT-AC
1307183 AAAAGTCTAGAAGCAATGTATC
1 AAAAGTCTAGAAGCAATGTA-C
1307205 AAAAG
1 AAAAG
1307210 AGTCTAAGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
18 5 0.15
19 9 0.27
21 8 0.24
22 11 0.33
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.19
Consensus pattern (21 bp):
AAAAGTCTAGAAGCAATGTAC
Found at i:1307197 original size:40 final size:42
Alignment explanation
Indices: 1307131--1307212 Score: 150
Period size: 40 Copynumber: 2.0 Consensus size: 42
1307121 TAATACAAAA
1307131 ATCAAATTCCCAAAAAGTCTAGAAGCAATGTA-CAAAAGAGT
1 ATCAAATTCCCAAAAAGTCTAGAAGCAATGTATCAAAAGAGT
1307172 ATCAAATTCCC-AAAAGTCTAGAAGCAATGTATCAAAAGAGT
1 ATCAAATTCCCAAAAAGTCTAGAAGCAATGTATCAAAAGAGT
1307213 CTAAGTGTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 20 0.50
41 20 0.50
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (42 bp):
ATCAAATTCCCAAAAAGTCTAGAAGCAATGTATCAAAAGAGT
Found at i:1316053 original size:13 final size:13
Alignment explanation
Indices: 1316035--1316059 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1316025 CAAATTGGTG
1316035 AAAAAGTAAAAAA
1 AAAAAGTAAAAAA
1316048 AAAAAGTAAAAA
1 AAAAAGTAAAAA
1316060 TTTTTAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (13 bp):
AAAAAGTAAAAAA
Found at i:1327732 original size:161 final size:161
Alignment explanation
Indices: 1327398--1328898 Score: 1436
Period size: 161 Copynumber: 9.4 Consensus size: 161
1327388 CATCACCTAT
* * * *
1327398 ATGATATTAAACTTTTTCAAATGATTGAATTTGGTTTTCACAGTTGATATATGTGAAAAAGTTAT
1 ATGATATTAAACTTGTCCAAATGATTGAACTTGGTTTTCACAGTTGATATGTGTGAAAAAGTTAT
* * * * *
1327463 TGTTTACCTTTGTTTAGGACTTTTTGTGACGTTAAAAGGC-AAAATGTAAATTTGCTATTATTGT
66 CGTTTACATTTGTTTAGGACTTTTTATGCCGTTAAAAGGCAAAAATGCAAATTTGCTATTATTGT
* *
1327527 TCTATTTTAACAGCTTGGATAGCTTTAATAC
131 TCTATTTTAACAGTTTGGATAGCTTCAATAC
* * * *
1327558 ATGATATTAAACTTGTCCGAATAATTGAACTTGGTTTTCACAGTTGATATGTGTGAAAAAGCTAA
1 ATGATATTAAACTTGTCCAAATGATTGAACTTGGTTTTCACAGTTGATATGTGTGAAAAAGTTAT
* * ** * *
1327623 CGTTTACATTTGTTTAAGATTTTTTATGCTATTAAAAGGTAAAAATGGAAATTTGCTATTATTGT
66 CGTTTACATTTGTTTAGGACTTTTTATGCCGTTAAAAGGCAAAAATGCAAATTTGCTATTATTGT
* **
1327688 TCTGTTTTAACAAATTGGATAGCTTCAATAC
131 TCTATTTTAACAGTTTGGATAGCTTCAATAC
* * * ** ** * *
1327719 ATGATAATAAACTTGTTCAAATGATTAAACTTGG-TTTCTATGGTTGATAAATATGAAAAAGTTG
1 ATGATATTAAACTTGTCCAAATGATTGAACTTGGTTTTC-ACAGTTGATATGTGTGAAAAAGTTA
* ** * * * * * *
1327783 TCATTTATGTCTATTTAGGACTTTTTTAT--CGTTAAAAGGTAAAAATGCAAAATTGCCATTGTT
65 TCGTTTACATTTGTTTAGGAC-TTTTTATGCCGTTAAAAGGCAAAAATGCAAATTTGCTATTATT
* *
1327846 ATTCTATTTTAACAGTTTGGATAGCTTCCATAC
129 GTTCTATTTTAACAGTTTGGATAGCTTCAATAC
* * * * *
1327879 ATGATATTAAACTTTTTCAAATGATTGAACTTGGTTTTCACAGTTGATATGTATGAAAACGTTGT
1 ATGATATTAAACTTGTCCAAATGATTGAACTTGGTTTTCACAGTTGATATGTGTGAAAAAGTTAT
* * * * *
1327944 -GTTTACCTTTGTTTATGACTTTTTGTGCCGTTAAAAGGC-AAAATGTAAATTGGCTATTATTGT
66 CGTTTACATTTGTTTAGGACTTTTTATGCCGTTAAAAGGCAAAAATGCAAATTTGCTATTATTGT
* ** *
1328007 TCTATTTTAATAGTTCAGATAGCTTTAATAC
131 TCTATTTTAACAGTTTGGATAGCTTCAATAC
* * * * * * * * * *
1328038 ATGATATTAAATTTATCCAAATAATTAAACTTGGTTTCCATAGTTGATATGTTTGGAAAAGCTAA
1 ATGATATTAAACTTGTCCAAATGATTGAACTTGGTTTTCACAGTTGATATGTGTGAAAAAGTTAT
** ** * *
1328103 CGTTTATGTTTGTTTAGGACTTTTTATGCTATT-AAA---AAAAATACAAATTCGCTATTATTGT
66 CGTTTACATTTGTTTAGGACTTTTTATGCCGTTAAAAGGCAAAAATGCAAATTTGCTATTATTGT
* *
1328164 TCTATTTTAACAATTTGTATAGCTTCAATAC
131 TCTATTTTAACAGTTTGGATAGCTTCAATAC
** * * * * * ** * **
1328195 ATGATAACAAATTTGTCCAAATAATTGAACTCGATTTTTATGGTTGATATGTGTAAAAAAAATAT
1 ATGATATTAAACTTGTCCAAATGATTGAACTTGGTTTTCACAGTTGATATGTGTGAAAAAGTTAT
* * * * * * * * *
1328260 TGTTTACATCTATTTAGGACTTTTTGTACCGTTAATAA-GCAAAAATACAAAATTACTGTTATTG
66 CGTTTACATTTGTTTAGGACTTTTTATGCCGTTAA-AAGGCAAAAATGCAAATTTGCTATTATTG
* *
1328324 TTCTAGTTTAATAGTTTGGATAGCTTCAATAC
130 TTCTATTTTAACAGTTTGGATAGCTTCAATAC
*** * * * * * *
1328356 ATGATATTAAACTTGTTTGAATAATTAAACTTGGTTTTCACAATTGATATGTGTAAAAAAGCTAA
1 ATGATATTAAACTTGTCCAAATGATTGAACTTGGTTTTCACAGTTGATATGTGTGAAAAAGTTAT
** ** *
1328421 CGTTTACATCTT-TTTAGGACTTTTTATGTTGTTAAAAGGCAAAAATATAAATTTGCTATTGTTG
66 CGTTTACAT-TTGTTTAGGACTTTTTATGCCGTTAAAAGGCAAAAATGCAAATTTGCTATTATTG
*
1328485 TTCTATTTTAACAGTTTAGATAGCTTCAATAC
130 TTCTATTTTAACAGTTTGGATAGCTTCAATAC
** ** *
1328517 ATGATAAAAAACTTGTCTGAATGATTGAAATTGG-TTTCTA-AGATTGATATGTGTGAAAAAGTT
1 ATGATATTAAACTTGTCCAAATGATTGAACTTGGTTTTC-ACAG-TTGATATGTGTGAAAAAGTT
* * * * * * *
1328580 ATCGTTTACATTTATTTAAGATTTTTTTTTTGCCATTAAAAAGCAAAAATGCAAATTTACTATTA
64 ATCGTTTACATTTGTTTAGGA--CTTTTTATGCCGTTAAAAGGCAAAAATGCAAATTTGCTATTA
* * * *
1328645 TTATTCTATTTTAATAGTTTGGATAGCTTTAATAA
127 TTGTTCTATTTTAACAGTTTGGATAGCTTCAATAC
* * *** * *
1328680 ATGATATTAAATTTTTTTGAATGATTGAACTTGGTTTTCACAGTTGATATATGT-AAAAAGTTGT
1 ATGATATTAAACTTGTCCAAATGATTGAACTTGGTTTTCACAGTTGATATGTGTGAAAAAGTTAT
* * * * * * *
1328744 TGTTTATC-TCTGTTTAGGACTTTTTATGCCATTAAAAGGCAAAAATACAAATTAGCTGTTATTA
66 CGTTTA-CATTTGTTTAGGACTTTTTATGCCGTTAAAAGGCAAAAATGCAAATTTGCTATTATTG
* * *
1328808 TTTTGTTTTAATAGTTTGGATAGCTTCAATAC
130 TTCTATTTTAACAGTTTGGATAGCTTCAATAC
* *
1328840 ATGATATTAAACTTATCCAAATGATTGAATTTGG-TTTC-CATGATTGATATGTGTGAAAA
1 ATGATATTAAACTTGTCCAAATGATTGAACTTGGTTTTCACA-G-TTGATATGTGTGAAAA
1328899 GGTAAAATGT
Statistics
Matches: 1090, Mismatches: 226, Indels: 49
0.80 0.17 0.04
Matches are distributed among these distances:
157 120 0.11
158 9 0.01
159 119 0.11
160 349 0.32
161 355 0.33
162 30 0.03
163 102 0.09
164 6 0.01
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (161 bp):
ATGATATTAAACTTGTCCAAATGATTGAACTTGGTTTTCACAGTTGATATGTGTGAAAAAGTTAT
CGTTTACATTTGTTTAGGACTTTTTATGCCGTTAAAAGGCAAAAATGCAAATTTGCTATTATTGT
TCTATTTTAACAGTTTGGATAGCTTCAATAC
Found at i:1332214 original size:20 final size:20
Alignment explanation
Indices: 1332191--1332229 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1332181 TGTTATATAC
*
1332191 ACCAATCATTATTTATAAAT
1 ACCAATCATTACTTATAAAT
1332211 ACCAATCATTACTTATAAA
1 ACCAATCATTACTTATAAA
1332230 CCCTTAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (20 bp):
ACCAATCATTACTTATAAAT
Found at i:1332730 original size:24 final size:25
Alignment explanation
Indices: 1332703--1332764 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
1332693 ATATGCTTGC
1332703 ATATATAAATATATATATTAATAA-
1 ATATATAAATATATATATTAATAAG
* *
1332727 ATATAATAAA-ATATGTCTTAATAAG
1 ATAT-ATAAATATATATATTAATAAG
*
1332752 ATAAATATAATAT
1 ATATATA-AATAT
1332765 CGATTGACCT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 19 0.61
25 10 0.32
26 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (25 bp):
ATATATAAATATATATATTAATAAG
Found at i:1332791 original size:31 final size:31
Alignment explanation
Indices: 1332753--1332852 Score: 82
Period size: 31 Copynumber: 3.2 Consensus size: 31
1332743 CTTAATAAGA
1332753 TAAATATAATATCGATTGACCTTTTCAAAAT
1 TAAATATAATATCGATTGACCTTTTCAAAAT
** * * *
1332784 TAAATAT-ATAATAAAATATG-TCTTAAT-AAGA-
1 TAAATATAAT-AT-CGAT-TGACCTT-TTCAAAAT
*
1332815 TAAATATAATATCGATTGACCCTTTCAAAAT
1 TAAATATAATATCGATTGACCTTTTCAAAAT
1332846 TAAATAT
1 TAAATAT
1332853 CTAAATCTGC
Statistics
Matches: 50, Mismatches: 11, Indels: 16
0.65 0.14 0.21
Matches are distributed among these distances:
29 3 0.06
30 9 0.18
31 25 0.50
32 10 0.20
33 3 0.06
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (31 bp):
TAAATATAATATCGATTGACCTTTTCAAAAT
Found at i:1332796 original size:62 final size:62
Alignment explanation
Indices: 1332727--1332852 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
1332717 ATATTAATAA
*
1332727 ATATAATAAAATATGTCTTAATAAGATAAATATAATATCGATTGACCTTTTCAAAATTAAAT
1 ATATAATAAAATATGTCTTAATAAGATAAATATAATATCGATTGACCCTTTCAAAATTAAAT
1332789 ATATAATAAAATATGTCTTAATAAGATAAATATAATATCGATTGACCCTTTCAAAATTAAAT
1 ATATAATAAAATATGTCTTAATAAGATAAATATAATATCGATTGACCCTTTCAAAATTAAAT
1332851 AT
1 AT
1332853 CTAAATCTGC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (62 bp):
ATATAATAAAATATGTCTTAATAAGATAAATATAATATCGATTGACCCTTTCAAAATTAAAT
Found at i:1338973 original size:14 final size:14
Alignment explanation
Indices: 1338954--1338981 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1338944 CCCTTTTTCC
1338954 AAACTCATTCTCTT
1 AAACTCATTCTCTT
1338968 AAACTCATTCTCTT
1 AAACTCATTCTCTT
1338982 CTAAAGAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (14 bp):
AAACTCATTCTCTT
Found at i:1339120 original size:28 final size:27
Alignment explanation
Indices: 1339068--1339127 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
1339058 ATTATAGTAA
*
1339068 AATATTTAAATTTTAAAATTTTTAATTT
1 AATATTTAAATTATAAAATTTTTAA-TT
*
1339096 AATATTTAAATTAT-GAATTTATTAATT
1 AATATTTAAATTATAAAATTT-TTAATT
1339123 AATAT
1 AATAT
1339128 CATAATTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 12 0.41
28 17 0.59
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
AATATTTAAATTATAAAATTTTTAATT
Found at i:1343621 original size:22 final size:22
Alignment explanation
Indices: 1343595--1343638 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1343585 TGTATATTTA
*
1343595 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
1343617 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
1343639 GACAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:1347692 original size:22 final size:22
Alignment explanation
Indices: 1347667--1347710 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1347657 TGTATATTTA
1347667 TATTTGCAT-CTCTAGAATTAAG
1 TATTTGCATCCT-TAGAATTAAG
*
1347689 TATTTGTATCCTTAGAATTAAG
1 TATTTGCATCCTTAGAATTAAG
1347711 GAAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGCATCCTTAGAATTAAG
Found at i:1351037 original size:23 final size:25
Alignment explanation
Indices: 1351006--1351055 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
1350996 TATATATTAA
1351006 AAAATTATTTAAT-TT-T-AAATTT
1 AAAATTATTTAATATTATAAAATTT
1351028 AAAATATATTTAATATTATAAAATTT
1 AAAAT-TATTTAATATTATAAAATTT
1351054 AA
1 AA
1351056 CATTTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.21
23 8 0.33
24 2 0.08
25 1 0.04
26 8 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AAAATTATTTAATATTATAAAATTT
Found at i:1357079 original size:26 final size:26
Alignment explanation
Indices: 1357026--1357085 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
1357016 AATTTTGATA
* *
1357026 AATTATAATAAGAAAGATATTCTCAT
1 AATTATAATAAGAAAGATATTATAAT
*
1357052 AATTATAATTAG-AAGAGTATTATAAT
1 AATTATAATAAGAAAGA-TATTATAAT
*
1357078 AAGTATAA
1 AATTATAA
1357086 CCAATCATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.35
Consensus pattern (26 bp):
AATTATAATAAGAAAGATATTATAAT
Found at i:1362669 original size:21 final size:21
Alignment explanation
Indices: 1362645--1362684 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1362635 CCCATTCTGC
1362645 TCACCACTTT-TTAAACCCATT
1 TCACCA-TTTCTTAAACCCATT
1362666 TCACCATTTCTTAAACCCA
1 TCACCATTTCTTAAACCCA
1362685 CTTCCTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (21 bp):
TCACCATTTCTTAAACCCATT
Found at i:1362673 original size:33 final size:33
Alignment explanation
Indices: 1362605--1362673 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
1362595 AATTTTTCAT
* *
1362605 ATTCTACTTACCACTTTATAAACCAACTTCCCC
1 ATTCTACTCACCACTTTATAAACCAACTTCACC
* * * *
1362638 ATTCTGCTCACCACTTTTTAAACCCATTTCACC
1 ATTCTACTCACCACTTTATAAACCAACTTCACC
1362671 ATT
1 ATT
1362674 TCTTAAACCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.28, C:0.35, G:0.01, T:0.36
Consensus pattern (33 bp):
ATTCTACTCACCACTTTATAAACCAACTTCACC
Found at i:1365971 original size:25 final size:27
Alignment explanation
Indices: 1365928--1365985 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 27
1365918 TGAGTATTAT
1365928 AATA-ATTTTGGTCAATTATAATAAAA
1 AATATATTTTGGTCAATTATAATAAAA
*
1365954 AATATATTTT-GT-AATTATGATAAAA
1 AATATATTTTGGTCAATTATAATAAAA
1365979 AATATAT
1 AATATAT
1365986 ATTATAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 19 0.63
26 6 0.20
27 5 0.17
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (27 bp):
AATATATTTTGGTCAATTATAATAAAA
Found at i:1366204 original size:26 final size:26
Alignment explanation
Indices: 1366174--1366223 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1366164 GACCAGTTAC
* * *
1366174 AATAAGAAACATATTTTTATAATTAT
1 AATAAAAAACATATTATAATAATTAT
*
1366200 AATAAAAAAGATATTATAATAATT
1 AATAAAAAACATATTATAATAATT
1366224 TAAATTAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (26 bp):
AATAAAAAACATATTATAATAATTAT
Found at i:1366971 original size:21 final size:21
Alignment explanation
Indices: 1366920--1366987 Score: 102
Period size: 21 Copynumber: 3.2 Consensus size: 21
1366910 TAATTTTATA
*
1366920 TTTATA-TTAAAAATTAATAT
1 TTTATATTTAAAAAATAATAT
1366940 TTTATATTTTAAAAAATAATAT
1 TTTATA-TTTAAAAAATAATAT
*
1366962 TTTATATTTAAAAAGTAATAT
1 TTTATATTTAAAAAATAATAT
1366983 TTTAT
1 TTTAT
1366988 TAATTTCGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 6 0.14
21 19 0.43
22 19 0.43
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (21 bp):
TTTATATTTAAAAAATAATAT
Found at i:1370578 original size:22 final size:22
Alignment explanation
Indices: 1370525--1370579 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
1370515 GCCATGCAAG
* *
1370525 TTGAAATTCAAATATTCACAAT
1 TTGAAATTCAAAAAATCACAAT
*
1370547 TTG-AATTCAAAAAATCATAAT
1 TTGAAATTCAAAAAATCACAAT
1370568 TTGAAATTCAAA
1 TTGAAATTCAAA
1370580 GATTAGCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (22 bp):
TTGAAATTCAAAAAATCACAAT
Found at i:1370590 original size:22 final size:21
Alignment explanation
Indices: 1370525--1370590 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
1370515 GCCATGCAAG
*
1370525 TTGAAATTCAAATATTCACAAT
1 TTGAAATTCAAAAATT-ACAAT
* *
1370547 TTG-AATTCAAAAAATCATAAT
1 TTGAAATTC-AAAAATTACAAT
*
1370568 TTGAAATTCAAAGATTAGCAAT
1 TTGAAATTCAAAAATTA-CAAT
1370590 T
1 T
1370591 CAAATATGCA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.35
Consensus pattern (21 bp):
TTGAAATTCAAAAATTACAAT
Found at i:1370633 original size:17 final size:17
Alignment explanation
Indices: 1370613--1370657 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
1370603 AGGTTCAAAG
* *
1370613 ATTCACAAAACTTTCAT
1 ATTCACAAAAATTTCAA
1370630 ATTCACAAAAATTTCAA
1 ATTCACAAAAATTTCAA
1370647 ATTCACAAAAA
1 ATTCACAAAAA
1370658 CACAAATTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTCACAAAAATTTCAA
Found at i:1370685 original size:17 final size:17
Alignment explanation
Indices: 1370663--1370808 Score: 75
Period size: 17 Copynumber: 8.6 Consensus size: 17
1370653 AAAAACACAA
*
1370663 ATTCGTAAGAATTGGAG
1 ATTCGTAAGAATTGAAG
* *
1370680 ATTCGTAAAAATTAAAG
1 ATTCGTAAGAATTGAAG
* *
1370697 ATTCATAA-AATTTGCAG
1 ATTCGTAAGAA-TTGAAG
* * *
1370714 CTTTGTAAGAATTTTTAA-
1 ATTCGTAAGAA--TTGAAG
1370732 ATTCGTAAGAATTGAAG
1 ATTCGTAAGAATTGAAG
* **
1370749 GTTCACAA-AGATTGAAG
1 ATTCGTAAGA-ATTGAAG
* *
1370766 ATTCGTAAGAACT-CAG
1 ATTCGTAAGAATTGAAG
* *
1370782 ATCCGTAAGAATAGAAG
1 ATTCGTAAGAATTGAAG
* *
1370799 GTTCGCAAGA
1 ATTCGTAAGA
1370809 TTTTTAGATT
Statistics
Matches: 93, Mismatches: 29, Indels: 14
0.68 0.21 0.10
Matches are distributed among these distances:
16 19 0.20
17 58 0.62
18 12 0.13
19 4 0.04
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.29
Consensus pattern (17 bp):
ATTCGTAAGAATTGAAG
Found at i:1371148 original size:46 final size:45
Alignment explanation
Indices: 1371098--1371222 Score: 112
Period size: 46 Copynumber: 2.8 Consensus size: 45
1371088 CTTGTAGGGA
* * *
1371098 TTCACAACCAAAATTTCAAATATTCTTATTCAAAAAATTTTAATGT
1 TTCACATCCAAAATTTCAAA-ATTCTCATTCAAAAAATTTTAAGGT
** * *
1371144 TTCACATTTAATATTTCAAAAGTTCTCATT-TAAAAATTTTAAGGT
1 TTCACATCCAAAATTTCAAAA-TTCTCATTCAAAAAATTTTAAGGT
* * *
1371189 TT--TATCCAAAATTTCAAAGATTCTGATACAAAAA
1 TTCACATCCAAAATTTCAAA-ATTCTCATTCAAAAA
1371223 CTTTGGGGAT
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
43 18 0.29
44 5 0.08
45 16 0.26
46 23 0.37
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (45 bp):
TTCACATCCAAAATTTCAAAATTCTCATTCAAAAAATTTTAAGGT
Found at i:1372701 original size:9 final size:9
Alignment explanation
Indices: 1372674--1372746 Score: 70
Period size: 9 Copynumber: 8.8 Consensus size: 9
1372664 TTGAATCTTC
1372674 TTTTTTTC-
1 TTTTTTTCA
1372682 TTTTTTT--
1 TTTTTTTCA
1372689 TTTTTTTCA
1 TTTTTTTCA
*
1372698 TTTTTGTACA
1 TTTTT-TTCA
1372708 --TTTTTCA
1 TTTTTTTCA
1372715 TTTTTTTCA
1 TTTTTTTCA
*
1372724 CTTTTTTCA
1 TTTTTTTCA
1372733 --TTTTTCA
1 TTTTTTTCA
1372740 TTTTTTT
1 TTTTTTT
1372747 ACTTCATCAG
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
7 17 0.31
8 10 0.18
9 25 0.45
10 3 0.05
ACGTcount: A:0.10, C:0.11, G:0.01, T:0.78
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:1372711 original size:18 final size:18
Alignment explanation
Indices: 1372690--1372737 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
1372680 TCTTTTTTTT
1372690 TTTTTTCATTTTTGTACA-
1 TTTTTTCATTTTT-TACAC
*
1372708 -TTTTTCATTTTTTTCAC
1 TTTTTTCATTTTTTACAC
1372725 TTTTTTCATTTTT
1 TTTTTTCATTTTT
1372738 CATTTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 3 0.11
17 12 0.44
18 12 0.44
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTTTCATTTTTTACAC
Found at i:1372711 original size:25 final size:25
Alignment explanation
Indices: 1372675--1372750 Score: 95
Period size: 25 Copynumber: 3.1 Consensus size: 25
1372665 TGAATCTTCT
**
1372675 TTTTTTC-TTTTTTTTTTTTTTCA-
1 TTTTTTCATTTTTCATTTTTTTCAC
1372698 TTTTTGTACATTTTTCATTTTTTTCAC
1 TTTTT-T-CATTTTTCATTTTTTTCAC
1372725 TTTTTTCATTTTTCATTTTTTT-AC
1 TTTTTTCATTTTTCATTTTTTTCAC
1372749 TT
1 TT
1372751 CATCAGTTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.11
24 5 0.11
25 17 0.36
26 15 0.32
27 5 0.11
ACGTcount: A:0.11, C:0.12, G:0.01, T:0.76
Consensus pattern (25 bp):
TTTTTTCATTTTTCATTTTTTTCAC
Found at i:1376805 original size:19 final size:20
Alignment explanation
Indices: 1376782--1376828 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1376772 ATTTAGAAAT
*
1376782 ATATTTTTTAAA-AAAATTT
1 ATATTTTTTAAAGAAAATTA
*
1376801 TTA-TTTTTAAAGAAAATTA
1 ATATTTTTTAAAGAAAATTA
1376820 ATATTTTTT
1 ATATTTTTT
1376829 TCTTAAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 8 0.35
19 10 0.43
20 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
ATATTTTTTAAAGAAAATTA
Found at i:1379760 original size:229 final size:228
Alignment explanation
Indices: 1378949--1379842 Score: 775
Period size: 228 Copynumber: 3.9 Consensus size: 228
1378939 AAGGCGGAGG
* * * * * * * * * * * **
1378949 ACAAGGTGAAGGGTAGACTCCTTCTGGATGTTGTAATCCGCAAGAGTACGCCCGTCCTCCAATTG
1 ACAAGATGAAGAGTCGATTCCTTTTGGATATTGTAATCAGCCAGGGTACGGCCGTCCTCGAGCTG
* * * ** * * * * * * * * *
1379014 CTTCCCAGCGAAAATGAGCCTCTGCTGATCGGGAGGAATCCCCTCCTTATCTTGAATTTTCGCCT
66 CTTCCCGGCGAAGATCAAACGCTGCTGATCCGGAGGGATGCCTTCCTTGTCTTGGATCTTGGCCT
* * * * * * * * * * * *
1379079 TCACATTATCGATCGTATCAGAACTCTCCACCTCAAGTGTAATCGTTTTTCCGGTCAGCGTCTTC
131 TGACATTGTCGATTGTGTCTGAGCTCTCCACCTCAAGGGTAATGGTTTTGCCGGTCAGGGTTTTG
* *
1379144 ACGAAA-ATCTGCATCCCCCCACGGAGCCTCAGC
196 AC-AAAGATCTGCATGCCCCCACGGAGCCGCAGC
* * * * * * * * * * *
1379177 ACAAGGTGAAGGGTAGACTCCTTCTGGATGTTGTAATCCGCCAGGGTCCTGCCATCCTCCAGCTG
1 ACAAGATGAAGAGTCGATTCCTTTTGGATATTGTAATCAGCCAGGGTACGGCCGTCCTCGAGCTG
* ** * * * * *
1379242 CTTCCCGGCGAAGATCAACCTTTGCTGATCCGGAGGGATCCCTTCCTTATCCTGGATTTTCGCCT
66 CTTCCCGGCGAAGATCAAACGCTGCTGATCCGGAGGGATGCCTTCCTTGTCTTGGATCTTGGCCT
* * * * * * * * *
1379307 TGACGTTGTCAATTGTATCTGAGCTCTCTACCTCCAGGGTAATTGTTTTACCGGTCAAGGTTTTA
131 TGACATTGTCGATTGTGTCTGAGCTCTCCACCTCAAGGGTAATGGTTTTGCCGGTCAGGGTTTTG
* * *
1379372 ACAAAAATCTGCATGCCCCCGCGTAGCCGCAGC
196 ACAAAGATCTGCATGCCCCCACGGAGCCGCAGC
* *
1379405 ACAAGATGAAGAGTCGATTCCTTTTGGATATTGTAATCCGCCAGGGTACGGCCGTCCTCTAGCTG
1 ACAAGATGAAGAGTCGATTCCTTTTGGATATTGTAATCAGCCAGGGTACGGCCGTCCTCGAGCTG
* * * *
1379470 CTTGCCGGCAAAGATCAATCGCTGCTGGTCCGGAGGGATGCCTTCCTTGTCTTGGATCTTGGCCT
66 CTTCCCGGCGAAGATCAAACGCTGCTGATCCGGAGGGATGCCTTCCTTGTCTTGGATCTTGGCCT
* * * * * * * *
1379535 TGACATTGTCGATCGTGTCAGAGCTTTCGACTTCAAGAGTAATGGTCTTGCCGGTTAGGGTTTTG
131 TGACATTGTCGATTGTGTCTGAGCTCTCCACCTCAAGGGTAATGGTTTTGCCGGTCAGGGTTTTG
* * * * *
1379600 ACGAAGATCTGCATGCCGCCACGGAGGCGGAGG
196 ACAAAGATCTGCATGCCCCCACGGAGCCGCAGC
* * * * * * *
1379633 ACAAGATGGAGAGTGGATTCCTTTTGGATGTT-TATAGTCAGCGAGGGTGCGGCCGTCTTCGAGT
1 ACAAGATGAAGAGTCGATTCCTTTTGGATATTGTA-A-TCAGCCAGGGTACGGCCGTCCTCGAGC
* * *
1379697 TGCTTCCCGGCGAAGATCAAACGCTGTTGATCAGGAGGAATGCCTTCCTTGTCTTGGATCTTGGC
64 TGCTTCCCGGCGAAGATCAAACGCTGCTGATCCGGAGGGATGCCTTCCTTGTCTTGGATCTTGGC
* * * * * * *
1379762 CTTTACATTATCGATTGTGTCTGAGCTCTCCACCTCGAGGGTGATGGTTTTGCCAGTGAGGGTCT
129 CTTGACATTGTCGATTGTGTCTGAGCTCTCCACCTCAAGGGTAATGGTTTTGCCGGTCAGGGTTT
1379827 TGACAAAGATCTGCAT
194 TGACAAAGATCTGCAT
1379843 ATTCAACGAG
Statistics
Matches: 549, Mismatches: 114, Indels: 5
0.82 0.17 0.01
Matches are distributed among these distances:
227 5 0.01
228 399 0.73
229 145 0.26
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (228 bp):
ACAAGATGAAGAGTCGATTCCTTTTGGATATTGTAATCAGCCAGGGTACGGCCGTCCTCGAGCTG
CTTCCCGGCGAAGATCAAACGCTGCTGATCCGGAGGGATGCCTTCCTTGTCTTGGATCTTGGCCT
TGACATTGTCGATTGTGTCTGAGCTCTCCACCTCAAGGGTAATGGTTTTGCCGGTCAGGGTTTTG
ACAAAGATCTGCATGCCCCCACGGAGCCGCAGC
Found at i:1380856 original size:31 final size:30
Alignment explanation
Indices: 1380796--1380868 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
1380786 TCTTATAAAT
1380796 TTTGAAATTTAATCTATATATTCATACGAAA
1 TTTGAAATTTAATCTATATATTCA-ACGAAA
* *
1380827 TTTGAAATTTAATCTTTGTACTTGC-ACGAAA
1 TTTGAAATTTAATCTATATA-TT-CAACGAAA
*
1380858 TTTAAAATTTA
1 TTTGAAATTTA
1380869 GTCCTTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 34 0.92
32 2 0.05
33 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (30 bp):
TTTGAAATTTAATCTATATATTCAACGAAA
Found at i:1382597 original size:31 final size:31
Alignment explanation
Indices: 1382556--1382642 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
1382546 CTTTTGTATT
*
1382556 AAAGGAACTAAATTTCAAATTTCATACGAGTA
1 AAAGG-ACTAAATTTCAAATTTCATACAAGTA
* *
1382588 AAAGGACTAAATTTCAAATTTCGTGCAAGTA
1 AAAGGACTAAATTTCAAATTTCATACAAGTA
* * *
1382619 TAGGGATTAAA-TTCAAATTTCATA
1 AAAGGACTAAATTTCAAATTTCATA
1382643 AAAATATAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 11 0.23
31 31 0.66
32 5 0.11
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (31 bp):
AAAGGACTAAATTTCAAATTTCATACAAGTA
Found at i:1382730 original size:20 final size:20
Alignment explanation
Indices: 1382717--1382755 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1382707 AAGTCAATGC
1382717 CACATCATTGAAGTCAACAA
1 CACATCATTGAAGTCAACAA
1382737 CACATCATTGAAGTCAACA
1 CACATCATTGAAGTCAACA
1382756 CCCATATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.26, G:0.10, T:0.21
Consensus pattern (20 bp):
CACATCATTGAAGTCAACAA
Found at i:1383366 original size:21 final size:22
Alignment explanation
Indices: 1383342--1383391 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1383332 TCATCTCTTT
1383342 TCTTTCTT-TCTATCTT-TTCTA
1 TCTTT-TTCTCTATCTTCTTCTA
*
1383363 TCTTTTTCTTTATCTTCTTCTA
1 TCTTTTTCTCTATCTTCTTCTA
*
1383385 TTTTTTT
1 TCTTTTT
1383392 GTTTTCGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 12 0.48
22 11 0.44
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (22 bp):
TCTTTTTCTCTATCTTCTTCTA
Found at i:1383510 original size:28 final size:29
Alignment explanation
Indices: 1383457--1383513 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
1383447 TGACTATCAC
*
1383457 CTTTCTTCTTTTCTTCATTCTCCCTTTTT
1 CTTTCTTCTTTTCTTCATCCTCCCTTTTT
*
1383486 CTTTC-TCTTTTCTTC-TCCTTTCCTTTTT
1 CTTTCTTCTTTTCTTCATCC-TCCCTTTTT
1383514 TGCTAGCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 18 0.72
29 5 0.20
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.67
Consensus pattern (29 bp):
CTTTCTTCTTTTCTTCATCCTCCCTTTTT
Found at i:1384345 original size:16 final size:17
Alignment explanation
Indices: 1384312--1384349 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1384302 TCCTTTTGTA
* *
1384312 TTTTTTCATTTTTCTTT
1 TTTTTTCATGTTTATTT
1384329 TTTTTTC-TGTTTATTT
1 TTTTTTCATGTTTATTT
1384345 TTTTT
1 TTTTT
1384350 ACTTGCACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.05, C:0.08, G:0.03, T:0.84
Consensus pattern (17 bp):
TTTTTTCATGTTTATTT
Found at i:1384703 original size:22 final size:22
Alignment explanation
Indices: 1384676--1384734 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
1384666 TCATTGCCCA
*
1384676 CCTTTTTT-TTTTTCATTTC-TC
1 CCTTTTTTCTTTTT-TTTTCTTC
1384697 CCTTTTTTCTTTATTTTTTCTTC
1 CCTTTTTTCTTT-TTTTTTCTTC
*
1384720 TCTTTTTTCTTTTTT
1 CCTTTTTTCTTTTTT
1384735 GCAATTGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 8 0.24
22 10 0.30
23 15 0.45
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.76
Consensus pattern (22 bp):
CCTTTTTTCTTTTTTTTTCTTC
Found at i:1384725 original size:12 final size:11
Alignment explanation
Indices: 1384698--1384731 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1384688 TCATTTCTCC
1384698 CTTTTTTCTTT
1 CTTTTTTCTTT
*
1384709 ATTTTTTCTTCT
1 CTTTTTTCTT-T
1384721 CTTTTTTCTTT
1 CTTTTTTCTTT
1384732 TTTGCAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (11 bp):
CTTTTTTCTTT
Found at i:1385097 original size:63 final size:63
Alignment explanation
Indices: 1384998--1385124 Score: 227
Period size: 63 Copynumber: 2.0 Consensus size: 63
1384988 AGCAAATTTG
*
1384998 TGAACTAACCATTACAAAGATTACATACGGTATTACTTTCATCTTTTAATGAACAAAATTCTT
1 TGAACTAACCATTACAAAGATTACATACGGTATTACTTTCATCTTTCAATGAACAAAATTCTT
* *
1385061 TGAACTAACCATTACAAAGATTACATATGGTATTACTTTTATCTTTCAATGAACAAAATTCTT
1 TGAACTAACCATTACAAAGATTACATACGGTATTACTTTCATCTTTCAATGAACAAAATTCTT
1385124 T
1 T
1385125 AGCAAATTCA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (63 bp):
TGAACTAACCATTACAAAGATTACATACGGTATTACTTTCATCTTTCAATGAACAAAATTCTT
Found at i:1385143 original size:4 final size:4
Alignment explanation
Indices: 1385134--1385161 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1385124 TAGCAAATTC
1385134 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1385162 TTAACTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:1387777 original size:21 final size:22
Alignment explanation
Indices: 1387753--1387795 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1387743 GCCAGAATAA
1387753 AATTCTAAAGTCT-TAAACATC
1 AATTCTAAAGTCTATAAACATC
* *
1387774 AATTGTAATGTCTCATAAACAT
1 AATTCTAAAGTCT-ATAAACAT
1387796 TATTTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (22 bp):
AATTCTAAAGTCTATAAACATC
Found at i:1392055 original size:8 final size:8
Alignment explanation
Indices: 1392042--1392066 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1392032 ACTTGGTCTC
1392042 TCTCTCTT
1 TCTCTCTT
1392050 TCTCTCTT
1 TCTCTCTT
1392058 TCTCTCTT
1 TCTCTCTT
1392066 T
1 T
1392067 ATATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (8 bp):
TCTCTCTT
Found at i:1392877 original size:15 final size:15
Alignment explanation
Indices: 1392853--1392883 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1392843 AAAGAAAACC
*
1392853 AATAATTAAATAATA
1 AATAACTAAATAATA
1392868 AATAACTAAATAATA
1 AATAACTAAATAATA
1392883 A
1 A
1392884 TAATAAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAACTAAATAATA
Found at i:1394330 original size:27 final size:26
Alignment explanation
Indices: 1394300--1394354 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
1394290 CAAATATAAA
*
1394300 ATAAAATTATTCTATTTTATTTTAATT
1 ATAAAATTATTCTATTTTATATT-ATT
* *
1394327 ATAATATTATTTTATTTTATATTATT
1 ATAAAATTATTCTATTTTATATTATT
1394353 AT
1 AT
1394355 GATCTTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
ATAAAATTATTCTATTTTATATTATT
Found at i:1394352 original size:18 final size:17
Alignment explanation
Indices: 1394312--1394354 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1394302 AAAATTATTC
1394312 TATT-TTATTTTAATTA
1 TATTATTATTTTAATTA
* *
1394328 TAATATTATTTTATTTTA
1 TATTATTATTTTA-ATTA
1394346 TATTATTAT
1 TATTATTAT
1394355 GATCTTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 8 0.36
18 11 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTATTATTTTAATTA
Found at i:1395503 original size:228 final size:227
Alignment explanation
Indices: 1395053--1395615 Score: 565
Period size: 228 Copynumber: 2.5 Consensus size: 227
1395043 CCTTTTCAAG
* * * * * * *
1395053 ATGCAGATTTTCGTTAAAACTCTCACCGGAAAAACCATCACCCTGGAGGTGGAGAGCTCCGACAC
1 ATGCAGATTTTCGTCAAAACCCTGA-CGGGAAAACCATCACTCTGGAGGTGGAAAGCTCAGACAC
* * * * * * * * * *
1395118 CATCGACAATGTCAAGGCCAAGATCCAAGACAAGGAAGGCATCCCTCCCGATCAACAGCGCTTGA
65 CATCGATAACGTCAAGGCCAAGATTCAAGACTAGGAGGGGATCCCTCCAGACCAACAACGCTTCA
* * * * * * *
1395183 TCTTTGCCGGGAAGCAACTCGAAGACGGCCGAACTCTCGCTGACTATAACATCCAAAAGGAATCT
130 TCTTCGCCGGCAAACAACTCGAAGACGGCCGAACCCTCGCGGACTACAACATCCAAAAGGAATCG
* * * *
1395248 ACTCTACACTTGGTCCTCCGTCTTCGTGGCGGT
195 ACCCTACACTTGGTCCTCAGGCTTCGTGGAGGT
* * * *
1395281 ATGCAAATTTTCGTCAAAACCCTGACTGGGAAAACCATTACTCTGGAGGTCGAAAGCTCTGACAC
1 ATGCAGATTTTCGTCAAAACCCTGAC-GGGAAAACCATCACTCTGGAGGTGGAAAGCTCAGACAC
* * * *
1395346 CATCGATAACGTCAAAGCTAAGATTCAGGACTAGGAGGGGATCCCTCCAGACCAGCAACGGC-TC
65 CATCGATAACGTCAAGGCCAAGATTCAAGACTAGGAGGGGATCCCTCCAGACCAACAAC-GCTTC
* * * * * *
1395410 ATCTTCGCCGGCAAACAACTCGAAGATGGTCGCACCCTTGCGGACTACAATATCCAAAAGGAGTC
129 ATCTTCGCCGGCAAACAACTCGAAGACGGCCGAACCCTCGCGGACTACAACATCCAAAAGGAATC
* * *
1395475 GACCCTTCACCTT-GTTCTTAGGCTTCGTGGAGGT
194 GACCCTACA-CTTGGTCCTCAGGCTTCGTGGAGGT
* * * * * *
1395509 ATGCAGATTTTTGTGAAGACCCTGACCGGAAAGACAATCACTCTGGAGGTGGAAAGCTCAGATAC
1 ATGCAGATTTTCGTCAAAACCCTGACGGGAAA-ACCATCACTCTGGAGGTGGAAAGCTCAGACAC
* * *
1395574 AATCGATAACGTGAAGGCGAAGATTCAAGA-TAAGGAGGGGAT
65 CATCGATAACGTCAAGGCCAAGATTCAAGACT-AGGAGGGGAT
1395616 TCCGCCTGAT
Statistics
Matches: 271, Mismatches: 59, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
227 7 0.03
228 259 0.96
229 5 0.02
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.21
Consensus pattern (227 bp):
ATGCAGATTTTCGTCAAAACCCTGACGGGAAAACCATCACTCTGGAGGTGGAAAGCTCAGACACC
ATCGATAACGTCAAGGCCAAGATTCAAGACTAGGAGGGGATCCCTCCAGACCAACAACGCTTCAT
CTTCGCCGGCAAACAACTCGAAGACGGCCGAACCCTCGCGGACTACAACATCCAAAAGGAATCGA
CCCTACACTTGGTCCTCAGGCTTCGTGGAGGT
Found at i:1395784 original size:22 final size:23
Alignment explanation
Indices: 1395756--1395809 Score: 101
Period size: 22 Copynumber: 2.4 Consensus size: 23
1395746 TGGGTGTTTG
1395756 ACTTTTTCTGGTGTTGTC-TTTA
1 ACTTTTTCTGGTGTTGTCTTTTA
1395778 ACTTTTTCTGGTGTTGTCTTTTA
1 ACTTTTTCTGGTGTTGTCTTTTA
1395801 ACTTTTTCT
1 ACTTTTTCT
1395810 AATGTTTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.09, C:0.15, G:0.15, T:0.61
Consensus pattern (23 bp):
ACTTTTTCTGGTGTTGTCTTTTA
Found at i:1395833 original size:41 final size:41
Alignment explanation
Indices: 1395784--1395921 Score: 188
Period size: 41 Copynumber: 3.4 Consensus size: 41
1395774 TTTAACTTTT
* * * *
1395784 TCTGGTGTTGTCTTTTAACTTTTTCTAATGTTTGTCATCTC
1 TCTGGTGTTGTCTTTTAACTTTTTCTAGTGTTTTTCTTCTA
* *
1395825 TCTGGTGTTGTCTTTTAACTTTTTCTAGCGTTTTTCTTTTA
1 TCTGGTGTTGTCTTTTAACTTTTTCTAGTGTTTTTCTTCTA
*
1395866 TCTGGTGTTGTCTTTTAGA-TTTTTCTAGTGTTTTTCTTCTT
1 TCTGGTGTTGTCTTTTA-ACTTTTTCTAGTGTTTTTCTTCTA
*
1395907 TCTGGTGTTTTCTTT
1 TCTGGTGTTGTCTTT
1395922 GCCTTATAGT
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 85 0.99
42 1 0.01
ACGTcount: A:0.09, C:0.14, G:0.16, T:0.61
Consensus pattern (41 bp):
TCTGGTGTTGTCTTTTAACTTTTTCTAGTGTTTTTCTTCTA
Found at i:1403031 original size:21 final size:21
Alignment explanation
Indices: 1403007--1403077 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
1402997 TAGGCATAAT
1403007 GGATTGATTGGTTTTGATAGA
1 GGATTGATTGGTTTTGATAGA
* *
1403028 GGATTGATCT-GATGT-ATCAGA
1 GGATTGAT-TGGTTTTGAT-AGA
*
1403049 GGATCGATTGGTTTTGATA-A
1 GGATTGATTGGTTTTGATAGA
1403069 GGGATTGAT
1 -GGATTGAT
1403078 CTGATGCATC
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
20 4 0.10
21 32 0.82
22 3 0.08
ACGTcount: A:0.25, C:0.04, G:0.32, T:0.38
Consensus pattern (21 bp):
GGATTGATTGGTTTTGATAGA
Found at i:1403074 original size:42 final size:42
Alignment explanation
Indices: 1403007--1403099 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
1402997 TAGGCATAAT
* * *
1403007 GGATTGATTGGTTTTGATAGAGGATTGATCTGATGTATCAGA
1 GGATCGATTGGTTTTGATAGAGGATTGATCTGATGCATCAAA
1403049 GGATCGATTGGTTTTGATA-AGGGATTGATCTGATGCATCAAA
1 GGATCGATTGGTTTTGATAGA-GGATTGATCTGATGCATCAAA
1403091 GGATCGATT
1 GGATCGATT
1403100 AATTCTTGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 1 0.02
42 46 0.98
ACGTcount: A:0.27, C:0.08, G:0.30, T:0.35
Consensus pattern (42 bp):
GGATCGATTGGTTTTGATAGAGGATTGATCTGATGCATCAAA
Found at i:1404510 original size:7 final size:7
Alignment explanation
Indices: 1404498--1404535 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
1404488 ATATTGAAAT
1404498 TAATTAA
1 TAATTAA
1404505 TAATT-A
1 TAATTAA
1404511 T-ATATAA
1 TAAT-TAA
1404518 TAATTAA
1 TAATTAA
1404525 TAATTAA
1 TAATTAA
1404532 TAAT
1 TAAT
1404536 AAAAAAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 2 0.07
6 3 0.11
7 21 0.75
8 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TAATTAA
Found at i:1405580 original size:13 final size:14
Alignment explanation
Indices: 1405550--1405593 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
1405540 TAATTTTTTG
1405550 AATTTTTATATATT-
1 AATTTTTAT-TATTA
1405564 -ATTTTTATT-TTA
1 AATTTTTATTATTA
1405576 AA-TTTTATTATTA
1 AATTTTTATTATTA
1405589 AATTT
1 AATTT
1405594 ATGCATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 2 0.08
12 8 0.31
13 14 0.54
14 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
AATTTTTATTATTA
Found at i:1406041 original size:13 final size:13
Alignment explanation
Indices: 1406023--1406047 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1406013 CTTTAAAATC
1406023 AAAATCCTAAACT
1 AAAATCCTAAACT
1406036 AAAATCCTAAAC
1 AAAATCCTAAAC
1406048 CTTAAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATCCTAAACT
Done.