Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_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: 6287495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 33
Found at i:1566422 original size:15 final size:15
Alignment explanation
Indices: 1566404--1566435 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1566394 ATATCAAGTC
1566404 TACTGCTATCTAGTT
1 TACTGCTATCTAGTT
*
1566419 TACTGTTATCTAGTT
1 TACTGCTATCTAGTT
1566434 TA
1 TA
1566436 TTGGTATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.50
Consensus pattern (15 bp):
TACTGCTATCTAGTT
Found at i:1569061 original size:16 final size:17
Alignment explanation
Indices: 1569028--1569061 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1569018 TATATTATTT
*
1569028 TTTATACTAAATTTTTA
1 TTTATACTAAACTTTTA
1569045 TTTATACT-AACTTTTA
1 TTTATACTAAACTTTTA
1569061 T
1 T
1569062 AATTAATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATACTAAACTTTTA
Found at i:1569343 original size:20 final size:20
Alignment explanation
Indices: 1569318--1569373 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
1569308 AATTGGCCGG
*
1569318 ATAAGCATGTTGTATGTCGA
1 ATAAGCATGTTGTATATCGA
1569338 ATAAGCATGTTGTATATCGA
1 ATAAGCATGTTGTATATCGA
1569358 ATAAGCATGTTGTATA
1 ATAAGCATGTTGTATA
1569374 CATTCAACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (20 bp):
ATAAGCATGTTGTATATCGA
Found at i:1575585 original size:135 final size:135
Alignment explanation
Indices: 1575343--1575612 Score: 540
Period size: 135 Copynumber: 2.0 Consensus size: 135
1575333 GACCTTGGAG
1575343 AGTCAAGTTTTCAAATTGTCGCGACATTACAAGAACGTCAACCAAGTCATCTGTCGAGTGACACT
1 AGTCAAGTTTTCAAATTGTCGCGACATTACAAGAACGTCAACCAAGTCATCTGTCGAGTGACACT
1575408 GAAGTCACTAAAGCTCATGAGAAGGAGCAATATAGTGCACTCACTCTACAGAGTGGCACCCAAAT
66 GAAGTCACTAAAGCTCATGAGAAGGAGCAATATAGTGCACTCACTCTACAGAGTGGCACCCAAAT
1575473 CAATT
131 CAATT
1575478 AGTCAAGTTTTCAAATTGTCGCGACATTACAAGAACGTCAACCAAGTCATCTGTCGAGTGACACT
1 AGTCAAGTTTTCAAATTGTCGCGACATTACAAGAACGTCAACCAAGTCATCTGTCGAGTGACACT
1575543 GAAGTCACTAAAGCTCATGAGAAGGAGCAATATAGTGCACTCACTCTACAGAGTGGCACCCAAAT
66 GAAGTCACTAAAGCTCATGAGAAGGAGCAATATAGTGCACTCACTCTACAGAGTGGCACCCAAAT
1575608 CAATT
131 CAATT
1575613 TACATGACTA
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
135 135 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (135 bp):
AGTCAAGTTTTCAAATTGTCGCGACATTACAAGAACGTCAACCAAGTCATCTGTCGAGTGACACT
GAAGTCACTAAAGCTCATGAGAAGGAGCAATATAGTGCACTCACTCTACAGAGTGGCACCCAAAT
CAATT
Found at i:1576114 original size:47 final size:47
Alignment explanation
Indices: 1576045--1576140 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
1576035 AACAATCCAG
1576045 GTAGTTTTATTATTCCATGCTCTATAGGAGAAAATTATGTGGCTCAA
1 GTAGTTTTATTATTCCATGCTCTATAGGAGAAAATTATGTGGCTCAA
1576092 GTAGTTTTATTATTCCATGCTCTATAGGAGAAAATTATGTGGCTCAA
1 GTAGTTTTATTATTCCATGCTCTATAGGAGAAAATTATGTGGCTCAA
1576139 GT
1 GT
1576141 GTGAACTTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (47 bp):
GTAGTTTTATTATTCCATGCTCTATAGGAGAAAATTATGTGGCTCAA
Found at i:1581982 original size:2 final size:2
Alignment explanation
Indices: 1581975--1582025 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1581965 GTGAGAGCTC
1581975 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1582017 CT CT CT CT C
1 CT CT CT CT C
1582026 CCACAAAAGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1582286 original size:21 final size:20
Alignment explanation
Indices: 1582241--1582287 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
1582231 TTCAGCATTT
*
1582241 ATATTTTGGTATTGTTATTA
1 ATATTTTGGTATTCTTATTA
*
1582261 GTATTTTGTGTATTCTT-TTAA
1 ATATTTTG-GTATTCTTATT-A
1582282 ATATTT
1 ATATTT
1582288 GGCTTTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.23, C:0.02, G:0.13, T:0.62
Consensus pattern (20 bp):
ATATTTTGGTATTCTTATTA
Found at i:1582630 original size:59 final size:59
Alignment explanation
Indices: 1582544--1582705 Score: 193
Period size: 59 Copynumber: 2.7 Consensus size: 59
1582534 CAATTTATTT
* * * *
1582544 TGTAATTACTGTTT-AGCCCTTTTAGTTTCTATTTTATCTATTTTAGTCCTTTAAATGTA
1 TGTAATTACTTTTTAATCCC-TTAAGTTTCTATTTTATCTATTTTAATCCTTTAAATGTA
*
1582603 TGTAATTACTTTTTAATCCCTTAAGTTTCTATTTTATCTATTTTAATCCTTTAAATGTT
1 TGTAATTACTTTTTAATCCCTTAAGTTTCTATTTTATCTATTTTAATCCTTTAAATGTA
* * * * *
1582662 TGT-ATTCACTATTTTATTCCTTTAACTTTCTGTTTTTTCTATTT
1 TGTAATT-ACT-TTTTAATCCCTTAAGTTTCTATTTTATCTATTT
1582706 AGACCCTTTA
Statistics
Matches: 90, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
58 3 0.03
59 55 0.61
60 32 0.36
ACGTcount: A:0.22, C:0.14, G:0.07, T:0.57
Consensus pattern (59 bp):
TGTAATTACTTTTTAATCCCTTAAGTTTCTATTTTATCTATTTTAATCCTTTAAATGTA
Found at i:1582647 original size:30 final size:31
Alignment explanation
Indices: 1582567--1582705 Score: 112
Period size: 30 Copynumber: 4.6 Consensus size: 31
1582557 TAGCCCTTTT
*
1582567 AGTTTCTATTTTATCTATTTTAGTCCTTTAA
1 AGTTTCTATTTTATCTATTTTAATCCTTTAA
* * * *
1582598 ATGTATGTA-ATTA-CT-TTTTAATCCCTT-A
1 A-GTTTCTATTTTATCTATTTTAATCCTTTAA
1582626 AGTTTCTATTTTATCTATTTTAATCCTTTAA
1 AGTTTCTATTTTATCTATTTTAATCCTTTAA
* * *
1582657 ATGTTTGTA-TTCA-CTATTTTATTCCTTT-A
1 A-GTTTCTATTTTATCTATTTTAATCCTTTAA
* * *
1582686 ACTTTCTGTTTTTTCTATTT
1 AGTTTCTATTTTATCTATTT
1582706 AGACCCTTTA
Statistics
Matches: 83, Mismatches: 17, Indels: 17
0.71 0.15 0.15
Matches are distributed among these distances:
27 5 0.06
28 9 0.11
29 16 0.19
30 33 0.40
31 9 0.11
32 11 0.13
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.58
Consensus pattern (31 bp):
AGTTTCTATTTTATCTATTTTAATCCTTTAA
Found at i:1582735 original size:30 final size:30
Alignment explanation
Indices: 1582680--1582736 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1582670 CTATTTTATT
* * *
1582680 CCTTTAACTTTCTGTTTTTTCTATTTAGAC
1 CCTTTAACTTTATATTTTTGCTATTTAGAC
*
1582710 CCTTTAACTTTATATTTTTGGTATTTA
1 CCTTTAACTTTATATTTTTGCTATTTA
1582737 ATACCTTAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.19, C:0.16, G:0.07, T:0.58
Consensus pattern (30 bp):
CCTTTAACTTTATATTTTTGCTATTTAGAC
Found at i:1582941 original size:22 final size:21
Alignment explanation
Indices: 1582916--1582960 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1582906 ATGTATGTAC
* *
1582916 ATGTTGTAAGTGTTATTATTTT
1 ATGTTGTAAATATT-TTATTTT
1582938 ATGTTGTAAATATTTTATTTT
1 ATGTTGTAAATATTTTATTTT
1582959 AT
1 AT
1582961 ATCGTATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (21 bp):
ATGTTGTAAATATTTTATTTT
Found at i:1584885 original size:68 final size:68
Alignment explanation
Indices: 1584775--1584913 Score: 233
Period size: 68 Copynumber: 2.0 Consensus size: 68
1584765 GGTGATACAA
* **
1584775 AGGAGGGAGGTAGTGTTTTGTGTTTAAGATAAAATGTCTTAACTTTAGCCTTAGTCCCTGAAGTC
1 AGGAGGGAGGTAGTGTTTTGTGTTTAAGATAAAATGGCTTAACTACAGCCTTAGTCCCTGAAGTC
1584840 TCT
66 TCT
* *
1584843 AGGAGGGAGGTAGTGTTTTGTGTTTAAGATAAAATGGGTTAACTACAGCCTTAGTCTCTGAAGTC
1 AGGAGGGAGGTAGTGTTTTGTGTTTAAGATAAAATGGCTTAACTACAGCCTTAGTCCCTGAAGTC
1584908 TCT
66 TCT
1584911 AGG
1 AGG
1584914 GTTTCCGAAG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.35
Consensus pattern (68 bp):
AGGAGGGAGGTAGTGTTTTGTGTTTAAGATAAAATGGCTTAACTACAGCCTTAGTCCCTGAAGTC
TCT
Found at i:1587385 original size:31 final size:32
Alignment explanation
Indices: 1587334--1587410 Score: 111
Period size: 31 Copynumber: 2.4 Consensus size: 32
1587324 GTTTATTTTG
* *
1587334 ATTTTATTCTCCCCATTTTTTATAATTAATTAT
1 ATTTTATTCT-TCTATTTTTTATAATTAATTAT
*
1587367 ATTTTA-TCTTCTATTTTTTATGATTAATTAT
1 ATTTTATTCTTCTATTTTTTATAATTAATTAT
1587398 ATTTTATTCTTCT
1 ATTTTATTCTTCT
1587411 TAAATTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 25 0.62
32 9 0.22
33 6 0.15
ACGTcount: A:0.25, C:0.12, G:0.01, T:0.62
Consensus pattern (32 bp):
ATTTTATTCTTCTATTTTTTATAATTAATTAT
Found at i:1587731 original size:21 final size:22
Alignment explanation
Indices: 1587702--1587748 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1587692 ATTCTGACTA
1587702 TCGCATTGCG-TTTTCCCAAAT
1 TCGCATTGCGATTTTCCCAAAT
* *
1587723 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGATTTTCCCAAAT
1587744 TCGCA
1 TCGCA
1587749 ACGCGAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCCAAAT
Found at i:1587815 original size:20 final size:20
Alignment explanation
Indices: 1587740--1587810 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1587730 GCGATTTTCC
*
1587740 TAAATCGCAACGCGAATACG
1 TAAATCGCAACGCGATTACG
**
1587760 TAAATCGCAACGCGAATTTGG
1 TAAATCGCAACGCG-ATTACG
* * *
1587781 AAAATCGCAATGTGATTACG
1 TAAATCGCAACGCGATTACG
1587801 TAAATCGCAA
1 TAAATCGCAA
1587811 TGTGAATCTG
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGATTACG
Found at i:1587837 original size:40 final size:41
Alignment explanation
Indices: 1587741--1587837 Score: 115
Period size: 41 Copynumber: 2.4 Consensus size: 41
1587731 CGATTTTCCT
* * * *
1587741 AAATCGCAACGCGAATACGTAAATCGCAACGCGAATTTGGA
1 AAATCGCAATGTGATTACGTAAATCGCAACGCGAATCTGGA
* *
1587782 AAATCGCAATGTGATTACGTAAATCGCAATGTGAATCT-GA
1 AAATCGCAATGTGATTACGTAAATCGCAACGCGAATCTGGA
**
1587822 CTATCGCAATGTGATT
1 AAATCGCAATGTGATT
1587838 TACATAGCAC
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 16 0.33
41 32 0.67
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Consensus pattern (41 bp):
AAATCGCAATGTGATTACGTAAATCGCAACGCGAATCTGGA
Found at i:1588038 original size:22 final size:22
Alignment explanation
Indices: 1588013--1588074 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
1588003 GGCGACATCC
1588013 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
1588035 GTCCCCA----CGACGATAA-CA
1 GTCCCCATCTCCGACGA-AATCA
* *
1588053 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
1588075 TTCACGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 14 0.44
19 2 0.06
21 2 0.06
22 14 0.44
ACGTcount: A:0.27, C:0.39, G:0.16, T:0.18
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1588431 original size:20 final size:20
Alignment explanation
Indices: 1588406--1588454 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1588396 CAACGAGTGA
1588406 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1588426 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1588446 ATCGCAACG
1 ATCGCAACG
1588455 AGAGAATCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1588537 original size:20 final size:20
Alignment explanation
Indices: 1588467--1588553 Score: 95
Period size: 20 Copynumber: 4.4 Consensus size: 20
1588457 AGAATCACAA
1588467 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
1588486 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
1588506 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
1588526 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
1588546 TGCGATTT
1 TGCGATTT
1588554 AAAGTTTCAG
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 9 0.15
20 50 0.85
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:1588561 original size:20 final size:20
Alignment explanation
Indices: 1588518--1588561 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1588508 CGATAGTCAT
** *
1588518 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
1588538 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
1588558 TTTC
1 TTTC
1588562 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:1590457 original size:20 final size:20
Alignment explanation
Indices: 1590432--1590635 Score: 294
Period size: 20 Copynumber: 10.5 Consensus size: 20
1590422 AAAATAGTTT
1590432 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1590452 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1590472 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
1590488 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1590506 ACTATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1590526 ACTATAGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1590546 ACTATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1590566 ACTATTGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1590586 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
1590606 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
1590626 ACTATCGCAA
1 ACTATCGCAA
1590636 CGAAAGAATC
Statistics
Matches: 165, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
14 7 0.04
16 4 0.02
17 4 0.02
18 4 0.02
20 146 0.88
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1590481 original size:40 final size:40
Alignment explanation
Indices: 1590432--1590673 Score: 294
Period size: 40 Copynumber: 6.4 Consensus size: 40
1590422 AAAATAGTTT
*
1590432 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
*
1590472 ACTATCGCAA--CG-AGA-GA--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
* *
1590506 ACTATCGCAATGTGAAAATGACTATAGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
* *
1590546 ACTATCGCAATGTGAAAATGACTATTGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
**
1590586 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
1590626 ACTATCGCAA--CG-AAA-GA--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
** *
1590659 AAAATCGCATTGCGA
1 ACTATCGCAATGCGA
1590674 TTCTCTCGTT
Statistics
Matches: 178, Mismatches: 15, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
33 10 0.06
34 37 0.21
35 2 0.01
36 5 0.03
37 7 0.04
38 6 0.03
40 111 0.62
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (40 bp):
ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
Found at i:1590583 original size:60 final size:60
Alignment explanation
Indices: 1590432--1590673 Score: 294
Period size: 60 Copynumber: 4.2 Consensus size: 60
1590422 AAAATAGTTT
* *
1590432 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
* *
1590488 A--ATCGCAATGCGAAAATGACTATCGCAATGTGAAAATGACTATAGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
* *
1590546 ACTATCGCAATGTGAAAATGACTATTGCAATGCGAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
**
1590606 ACTATCGCAATGCGAATTTGACTATCGCAA--CG-AAA-GA--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
** *
1590659 AAAATCGCATTGCGA
1 ACTATCGCAATGCGA
1590674 TTCTCTCGTT
Statistics
Matches: 165, Mismatches: 15, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
53 17 0.10
54 55 0.33
56 5 0.03
57 5 0.03
58 4 0.02
60 79 0.48
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (60 bp):
ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
Found at i:1590791 original size:20 final size:20
Alignment explanation
Indices: 1590766--1590814 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1590756 GCGATTCTCT
1590766 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCAAATTCG
**
1590786 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCAAATTCG
*
1590806 CGTTGCGAT
1 CATTGCGAT
1590815 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
CATTGCGATAGTCAAATTCG
Found at i:1591339 original size:18 final size:19
Alignment explanation
Indices: 1591300--1591341 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1591290 CTCACCTGTC
1591300 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
1591321 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
1591339 ATC
1 ATC
1591342 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:1591395 original size:42 final size:42
Alignment explanation
Indices: 1591295--1591405 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
1591285 CCCGACTCAC
* * * * *
1591295 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAAAGGCCA
* **
1591337 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAAAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAAAGGCCA
*
1591379 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
1591406 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.04
42 51 0.93
43 2 0.04
ACGTcount: A:0.22, C:0.38, G:0.18, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAAAGGCCA
Found at i:1592778 original size:14 final size:14
Alignment explanation
Indices: 1592759--1592794 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1592749 ATTGTTTAAT
1592759 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1592773 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1592787 TGATTTGT
1 TGATTTGT
1592795 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1592973 original size:33 final size:33
Alignment explanation
Indices: 1592931--1593009 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
1592921 AACGAGAGAA
* * **
1592931 TCGCATTGCGATTCACTCGTTGTGATTTTCATT
1 TCGCATTGCGATTCACTCATTGCGATAGTCATT
*
1592964 TCGCATTGCGATTCTCTCATTGCGATAGTCATT
1 TCGCATTGCGATTCACTCATTGCGATAGTCATT
*
1592997 TCCGCGTTGCGAT
1 T-CGCATTGCGAT
1593010 AGTCAATTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 29 0.74
34 10 0.26
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.41
Consensus pattern (33 bp):
TCGCATTGCGATTCACTCATTGCGATAGTCATT
Found at i:1593008 original size:20 final size:20
Alignment explanation
Indices: 1592983--1593069 Score: 122
Period size: 20 Copynumber: 4.3 Consensus size: 20
1592973 GATTCTCTCA
1592983 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
* *
1593003 TTGCGATAGTCAATTCCGCA
1 TTGCGATAGTCATTTCCGCG
*
1593023 TTGCGATAGTCATTTCCGTG
1 TTGCGATAGTCATTTCCGCG
*
1593043 TTGCCATAGTCATATT-CGCG
1 TTGCGATAGTCAT-TTCCGCG
1593063 TTGCGAT
1 TTGCGAT
1593070 TTCCGCGTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 56 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:1593036 original size:40 final size:40
Alignment explanation
Indices: 1592981--1593069 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
1592971 GCGATTCTCT
*
1592981 CATTGCGATAGTCATTTCCGCGTTGCGATAGTCA-ATTCCG
1 CATTGCGATAGTCATTTCCGCGTTGCCATAGTCATATT-CG
*
1593021 CATTGCGATAGTCATTTCCGTGTTGCCATAGTCATATTCG
1 CATTGCGATAGTCATTTCCGCGTTGCCATAGTCATATTCG
*
1593061 CGTTGCGAT
1 CATTGCGAT
1593070 TTCCGCGTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 42 0.93
41 3 0.07
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (40 bp):
CATTGCGATAGTCATTTCCGCGTTGCCATAGTCATATTCG
Found at i:1595436 original size:24 final size:24
Alignment explanation
Indices: 1595402--1595455 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1595392 CTGAAAAATC
1595402 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1595426 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1595450 ATCAAA
1 ATCAAA
1595456 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1595469 original size:24 final size:24
Alignment explanation
Indices: 1595402--1595469 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1595392 CTGAAAAATC
* * *
1595402 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1595426 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1595450 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1595470 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1596343 original size:20 final size:20
Alignment explanation
Indices: 1596316--1596459 Score: 197
Period size: 20 Copynumber: 7.3 Consensus size: 20
1596306 CAGAATCTCG
1596316 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
* *
1596336 TTGTGA-TTACGTATTC-AA
1 TTGCGATTTACGTATTCGCA
1596354 TTGCGATTTACGTA-TCGCA
1 TTGCGATTTACGTATTCGCA
1596373 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1596393 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
** *
1596413 TTGCGATTTACCAAATTCGCG
1 TTGCGATTTA-CGTATTCGCA
1596434 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1596454 TTGCGA
1 TTGCGA
1596460 ATTAGGAAAA
Statistics
Matches: 109, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.08
19 30 0.28
20 53 0.49
21 17 0.16
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:1596443 original size:41 final size:40
Alignment explanation
Indices: 1596316--1596459 Score: 179
Period size: 41 Copynumber: 3.6 Consensus size: 40
1596306 CAGAATCTCG
* ** *
1596316 TTGCGATTTACAG-ATTCGCATTGTGA-TTACGTATTC-AA
1 TTGCGATTTAC-GTATTCGCATTGCGATTTACAAATTCGCA
**
1596354 TTGCGATTTACGTA-TCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACAAATTCGCA
*
1596393 TTGCGATTTACGTATTCGCATTGCGATTTACCAAATTCGCG
1 TTGCGATTTACGTATTCGCATTGCGATTTA-CAAATTCGCA
1596434 TTGCGATTTACGTATTCGCATTGCGA
1 TTGCGATTTACGTATTCGCATTGCGA
1596460 ATTAGGAAAA
Statistics
Matches: 96, Mismatches: 5, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
37 11 0.11
38 22 0.23
39 15 0.16
40 15 0.16
41 33 0.34
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (40 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACAAATTCGCA
Found at i:1596445 original size:61 final size:57
Alignment explanation
Indices: 1596309--1596459 Score: 196
Period size: 61 Copynumber: 2.6 Consensus size: 57
1596299 CGATAGTCAG
* * *
1596309 AATCTCGTTGCGATTTACAG-ATTCGCATTGTGATTACGTATTCAATTGCGATTTACG
1 AATCGCGTTGCGATTTAC-GTATTCGCATTGCGATTACGTATTCAATTGCGATTTACA
* * *
1596366 TATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACCA
1 AATCGCGTTGCGATTTACGTATTCGCATTGCGA-TTACGTATTC-AATTGCGATTTA-CA
1596426 AATTCGCGTTGCGATTTACGTATTCGCATTGCGA
1 AA-TCGCGTTGCGATTTACGTATTCGCATTGCGA
1596460 ATTAGGAAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
56 1 0.01
57 27 0.33
58 10 0.12
59 11 0.14
60 2 0.02
61 30 0.37
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (57 bp):
AATCGCGTTGCGATTTACGTATTCGCATTGCGATTACGTATTCAATTGCGATTTACA
Found at i:1596480 original size:21 final size:21
Alignment explanation
Indices: 1596456--1596496 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1596446 TATTCGCATT
1596456 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
1596477 GCGAATTTGGGAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
1596497 TGCAATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1600947 original size:127 final size:127
Alignment explanation
Indices: 1600749--1601101 Score: 598
Period size: 127 Copynumber: 2.8 Consensus size: 127
1600739 GGGGGCCTCA
1600749 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTTATGTCCCCCGGGAAC
1 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTTATGTCCCCCGGGAAC
* *
1600814 TATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGGCGCGTTCCCGGGGGCGCGCC
66 TATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGGCACGTTCCCAGGGGCGCGCC
* * *
1600876 TTCCATTATTTTGTCAGAGAACATGTTATCATTACCCTATTATTTCACTTATGTCCCCCGGGAAC
1 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTTATGTCCCCCGGGAAC
* * *
1600941 TATTCATGTCAATACATATTATTCCTTAGGGGACCGTGAAGGCACGTTCCCAGGGGTGTGCC
66 TATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGGCACGTTCCCAGGGGCGCGCC
* * *
1601003 TTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTATTATGTCACTTATGTCCCCTGAGAAC
1 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTTATGTCCCCCGGGAAC
*
1601068 TATTCATGTCAATACCTATTATTCCTTAGTGGAC
66 TATTCATGTCAATACCTATTATTCCTTAGGGGAC
1601102 TTTAAAACGC
Statistics
Matches: 210, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
127 210 1.00
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (127 bp):
TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTTATGTCCCCCGGGAAC
TATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGGCACGTTCCCAGGGGCGCGCC
Found at i:1601622 original size:34 final size:34
Alignment explanation
Indices: 1601524--1601627 Score: 145
Period size: 34 Copynumber: 3.1 Consensus size: 34
1601514 TTAACTTGAA
* **
1601524 TTTAATGTTAAATTTCGAATACTATAATTCATAT
1 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
* * *
1601558 TTTAAATTTAAATTTCGAATAATATTATTTGTAT
1 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
*
1601592 TTTAATTTTAAATTTCGACTACTATAATTTGTAT
1 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
1601626 TT
1 TT
1601628 GAAAAACATT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.52
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATACTATAATTTGTAT
Found at i:1602210 original size:42 final size:42
Alignment explanation
Indices: 1602151--1602259 Score: 164
Period size: 42 Copynumber: 2.6 Consensus size: 42
1602141 TATGGTATAA
* * * *
1602151 AACCCTACGGGCTAGGCATGTAACCTGGTGGGCTAGGAGTGT
1 AACCCTGCGGGCTAGGCATGTAACCTGGTAGGCTAAGAATGT
*
1602193 AACCCTGTGGGCTAGGCATGTAACCTGGTAGGCTAAGAATGT
1 AACCCTGCGGGCTAGGCATGTAACCTGGTAGGCTAAGAATGT
*
1602235 AACCCTGCGGGCTAGGAATGTAACC
1 AACCCTGCGGGCTAGGCATGTAACC
1602260 CTGCGGAGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.21
Consensus pattern (42 bp):
AACCCTGCGGGCTAGGCATGTAACCTGGTAGGCTAAGAATGT
Found at i:1602260 original size:21 final size:21
Alignment explanation
Indices: 1602151--1602265 Score: 119
Period size: 21 Copynumber: 5.5 Consensus size: 21
1602141 TATGGTATAA
* *
1602151 AACCCTACGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
* *
1602172 AA-CCTGGTGGGCTAGGAGTGT
1 AACCCT-GCGGGCTAGGAATGT
* *
1602193 AACCCTGTGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
1602214 AA-CCTG-GTAGGCTAAGAATGT
1 AACCCTGCG--GGCTAGGAATGT
1602235 AACCCTGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1602256 AACCCTGCGG
1 AACCCTGCGG
1602266 AGATGACATA
Statistics
Matches: 79, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.01
20 7 0.09
21 63 0.80
22 7 0.09
23 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.21
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1602289 original size:42 final size:42
Alignment explanation
Indices: 1602243--1602340 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
1602233 GTAACCCTGC
* * *
1602243 GGGCTAGGAATGTAACCCTGCGGAGATGACATATGAACTGGT
1 GGGCTAGGCATGTAACCCTGAGGAGATGACATATGAACTGGA
* * * * *
1602285 GGGCTTGGCATATACCCCTGAGGAGATGGCATATGAAGTGGA
1 GGGCTAGGCATGTAACCCTGAGGAGATGACATATGAACTGGA
*
1602327 GGGCTGGGCATGTA
1 GGGCTAGGCATGTA
1602341 CCATTGTGGC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.26, C:0.16, G:0.37, T:0.21
Consensus pattern (42 bp):
GGGCTAGGCATGTAACCCTGAGGAGATGACATATGAACTGGA
Found at i:1603147 original size:13 final size:13
Alignment explanation
Indices: 1603131--1603157 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1603121 TTAGTTCGAT
1603131 AATTACCTCAACA
1 AATTACCTCAACA
1603144 AATTACCTCAACA
1 AATTACCTCAACA
1603157 A
1 A
1603158 TAAGGGGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (13 bp):
AATTACCTCAACA
Found at i:1604099 original size:25 final size:24
Alignment explanation
Indices: 1604054--1604101 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
1604044 ATAATTAGCA
1604054 TAAAAAATAATTAATTAATAAATT
1 TAAAAAATAATTAATTAATAAATT
1604078 TAAATAAATAA-TAATTATATAAAT
1 TAAA-AAATAATTAATTA-ATAAAT
1604102 ATTATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAAAAATAATTAATTAATAAATT
Found at i:1604121 original size:30 final size:30
Alignment explanation
Indices: 1604053--1604150 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 30
1604043 AATAATTAGC
* * *
1604053 ATAAAAAATAATTA-ATTAATA-AATTTAA
1 ATAAAAAATAATTATATAAATATTATTTTA
*
1604081 ATAAATAATAATTATATAAATATTATTTTA
1 ATAAAAAATAATTATATAAATATTATTTTA
* * *
1604111 ATAAAAAATAA-TATTTATATAATTATATTA
1 ATAAAAAATAATTATATAAAT-ATTATTTTA
*
1604141 ATATAAAATA
1 ATAAAAAATA
1604151 TAATAACTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
28 13 0.22
29 13 0.22
30 32 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
ATAAAAAATAATTATATAAATATTATTTTA
Found at i:1615144 original size:14 final size:14
Alignment explanation
Indices: 1615125--1615156 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1615115 CTATTAATTG
1615125 TGAAGTTAAACCAA
1 TGAAGTTAAACCAA
*
1615139 TGAAGTTAAATCAA
1 TGAAGTTAAACCAA
1615153 TGAA
1 TGAA
1615157 TAATGCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (14 bp):
TGAAGTTAAACCAA
Found at i:1615392 original size:84 final size:82
Alignment explanation
Indices: 1615291--1615467 Score: 257
Period size: 84 Copynumber: 2.1 Consensus size: 82
1615281 CACGAAATTT
*
1615291 AATGAACAATGTGGGAATTGAAA-GAACAATGCAATGAATTAAGCTGCATTAATTAAATACCATG
1 AATGAACAATGTGGGAATT-AAATGAACAATGCAAAGAATTAAGCTGCATTAATTAAATACCATG
* *
1615355 CATTAACTCAATTTTTTTTA
65 CATTAAAT-AA-ATTTTTTA
* * *
1615375 AATGAACAATGTTGGAATTAAATGAACATTGCAAAGAATTAAGCTGCATTAATTAAATATCATGC
1 AATGAACAATGTGGGAATTAAATGAACAATGCAAAGAATTAAGCTGCATTAATTAAATACCATGC
1615440 ATTAAATAAATTTTTTA
66 ATTAAATAAATTTTTTA
*
1615457 AATGAATAATG
1 AATGAACAATG
1615468 CAATGAATTA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
82 17 0.20
83 5 0.06
84 63 0.74
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.33
Consensus pattern (82 bp):
AATGAACAATGTGGGAATTAAATGAACAATGCAAAGAATTAAGCTGCATTAATTAAATACCATGC
ATTAAATAAATTTTTTA
Found at i:1615470 original size:62 final size:63
Alignment explanation
Indices: 1615392--1615518 Score: 184
Period size: 62 Copynumber: 2.0 Consensus size: 63
1615382 AATGTTGGAA
* * **
1615392 TTAAATGAACATTGCAAAGAATTAAGCTGCATTAATTAAATATCATGCATTAAAT-AAATTTT
1 TTAAATGAACAATGCAAAGAATTAAGCTGCATTAATTAAATACCAAACATTAAATCAAATTTT
* * *
1615454 TTAAATGAATAATGCAATGAATTAAGTTGCATTAATTAAATACCAAACATTAAATCAAATTTT
1 TTAAATGAACAATGCAAAGAATTAAGCTGCATTAATTAAATACCAAACATTAAATCAAATTTT
1615517 TT
1 TT
1615519 TTTAGTTTTG
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
62 48 0.84
63 9 0.16
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (63 bp):
TTAAATGAACAATGCAAAGAATTAAGCTGCATTAATTAAATACCAAACATTAAATCAAATTTT
Found at i:1622688 original size:3 final size:3
Alignment explanation
Indices: 1622674--1622714 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
1622664 CACCCATTTT
*
1622674 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1622715 CAAAAATACA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1626905 original size:20 final size:21
Alignment explanation
Indices: 1626880--1626926 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1626870 AATTCCTTTG
*
1626880 TTGCATTTGCATCTC-GTATT
1 TTGCATTTCCATCTCTGTATT
*
1626900 TTGCA-TTCCATTTCTGTATT
1 TTGCATTTCCATCTCTGTATT
1626920 TTGCATT
1 TTGCATT
1626927 CATATGTGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 7 0.30
20 15 0.65
21 1 0.04
ACGTcount: A:0.15, C:0.19, G:0.13, T:0.53
Consensus pattern (21 bp):
TTGCATTTCCATCTCTGTATT
Found at i:1631595 original size:20 final size:20
Alignment explanation
Indices: 1631530--1631596 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
1631520 ATGAGGTATA
1631530 GTTCATAATGAGAATAACTT
1 GTTCATAATGAGAATAACTT
* * * * ***
1631550 ATCCAACAAGGAAGAATAAGAA
1 GTTC-ATAATG-AGAATAACTT
1631572 GTTCATAATGAGAATAACTT
1 GTTCATAATGAGAATAACTT
1631592 GTTCA
1 GTTCA
1631597 AAACTCGGCA
Statistics
Matches: 31, Mismatches: 14, Indels: 4
0.63 0.29 0.08
Matches are distributed among these distances:
20 14 0.45
21 8 0.26
22 9 0.29
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (20 bp):
GTTCATAATGAGAATAACTT
Found at i:1631728 original size:116 final size:114
Alignment explanation
Indices: 1631529--1632005 Score: 537
Period size: 116 Copynumber: 4.1 Consensus size: 114
1631519 TATGAGGTAT
* * * *
1631529 AGTTCATAATGAGAATAACTTATCCAACAAGGAAGAATAAGAAGTTCATAATGAGAATAACTTGT
1 AGTTCGTAATGA-AA-AACTCATCCAACGAGGAAG---AAGAAGTTCATAATGAGAAGAACTTGT
* *
1631594 TCAAAACTCGGCATATCCGTCACACAAGGAGTTGGATCAACATTTCAGAAGAAG
61 TCAAAACTCGGCACATCCGTCACACAAGGAGATGGATCAACATTTCAGAAGAAG
* *
1631648 AGTTCGTAATAGAAATAACTCATCCAACGAGTAAGAAGAAGTTCATAATGAGAAGAACTTGTTCG
1 AGTTCGTAAT-GAAA-AACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * *
1631713 AAACTCGACACATCCGTCACACAAGGAGATAGATTAACATTTCAGAAGAGG
64 AAACTCGGCACATCCGTCACACAAGGAGATGGATCAACATTTCAGAAGAAG
* * * * *
1631764 AGTTCATAATGTGAAAAACTCATCTAACGGGGAAGAAGAAGTTTATAATGAGAAAAACTTG-TCT
1 AGTTCGTAA--TGAAAAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC-
* * * *
1631828 AAAACTTGGCACATTCGTCACATAAGGAGATGGATCAACATTTCAGAAGAGG
63 AAAACTCGGCACATCCGTCACACAAGGAGATGGATCAACATTTCAGAAGAAG
* * * * *
1631880 GGTTTGTAATGAGAAGAACTCATCGAACGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCG
1 AGTTCGTAATGA-AA-AACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * **
1631945 AAACTCGGCACATCCAT--CACAAGGAGATGGATCAATATTTTTGAAGAAG
64 AAACTCGGCACATCCGTCACACAAGGAGATGGATCAACATTTCAGAAGAAG
* *
1631994 GGTTTGTAATGA
1 AGTTCGTAATGA
1632006 GATTTATAAT
Statistics
Matches: 309, Mismatches: 42, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
114 42 0.14
115 4 0.01
116 226 0.73
117 6 0.02
118 1 0.00
119 28 0.09
120 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.23
Consensus pattern (114 bp):
AGTTCGTAATGAAAAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAA
ACTCGGCACATCCGTCACACAAGGAGATGGATCAACATTTCAGAAGAAG
Found at i:1632062 original size:20 final size:21
Alignment explanation
Indices: 1632031--1632073 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1632021 GAACTCACCC
*
1632031 AATGAGGAAGAAGATATTCAT
1 AATGAGGAAGAACATATTCAT
*
1632052 AATGA-GAAGAACTTATTCAT
1 AATGAGGAAGAACATATTCAT
1632072 AA
1 AA
1632074 CTTGACACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (21 bp):
AATGAGGAAGAACATATTCAT
Found at i:1632496 original size:139 final size:138
Alignment explanation
Indices: 1632234--1632529 Score: 396
Period size: 139 Copynumber: 2.1 Consensus size: 138
1632224 GATTTCAAAA
* *
1632234 GAAGAGTTCATAATAAGAAGAACTCATCTGACGAAGGGTTCATAATGAGAAGAACTCATCCAACA
1 GAAGAGTTCATAATGAGAAGAACTCATCCGACGAAGGGTTCATAATGAGAAGAACTCATCCAACA
* * **
1632299 ATGAAGAAGAAGTTCGTAATGAGAAGAGCTTGTTCAACCTGGAATCGTCCATTGCACAAAGAGGT
66 AGGAAGAAGAAGTTCGTAATGAGAAGAGCTTGTTCAACCTGGAATCATCCATCACACAAAGAGGT
* *
1632364 TGATAAAT
131 GGATAAAC
* * *
1632372 GTATAGTTCATAATGAGAAGAACTCATCCGACGAAGGGGTTCATAATGAGAATAACTCATCCAAC
1 GAAGAGTTCATAATGAGAAGAACTCATCCGACGAA-GGGTTCATAATGAGAAGAACTCATCCAAC
* * * * * *
1632437 GAGGAAGAAGAATTTCGTAATGAGAAGAGCTTGTTCAACTTAGG-ATCATTCGTCACACAATGAG
65 AAGGAAGAAGAAGTTCGTAATGAGAAGAGCTTGTTCAACCT-GGAATCATCCATCACACAAAGAG
*
1632501 GTGGATTAAC
129 GTGGATAAAC
*
1632511 GAAGAGTTCGTAATGAGAA
1 GAAGAGTTCATAATGAGAA
1632530 CTCACAAAAA
Statistics
Matches: 135, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
138 31 0.23
139 102 0.76
140 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (138 bp):
GAAGAGTTCATAATGAGAAGAACTCATCCGACGAAGGGTTCATAATGAGAAGAACTCATCCAACA
AGGAAGAAGAAGTTCGTAATGAGAAGAGCTTGTTCAACCTGGAATCATCCATCACACAAAGAGGT
GGATAAAC
Found at i:1640485 original size:136 final size:135
Alignment explanation
Indices: 1640210--1640465 Score: 302
Period size: 136 Copynumber: 1.9 Consensus size: 135
1640200 GTCCTAGGTG
* ** * * * *
1640210 CATTTCGACATACATTGTATGTATTAGTTATCGTTGGATTTTGTTTAATGCATAACGGTGTATTT
1 CATTTCGACATACATTGTATATAAAAGTTATCGATCGATTTTGTTTAATGCATAACAGTGCATTT
* *
1640275 TCGTATAAGTACTATGTACTTTCGGCACTAAATATGCAATCATGGTATTCATAATGAATTTGTGA
66 TCGTATAAGTACTATGTACTTTCGGCACTAAATATGCAATCATGGAATTAATAATGAATTTGTGA
1640340 ATCAC
131 ATCAC
*
1640345 CATTTCGATATACATATGTATATAAAAGTTATCGATCGA-TTT-TTTAATGCATAACAGTGCATT
1 CATTTCGACATACAT-TGTATATAAAAGTTATCGATCGATTTTGTTTAATGCATAACAGTGCATT
* * * * * * *
1640408 TTCGTATCAGTATTGTGTGTACTTTTGTCACTATATGTGC-ATCCATGGAATTAATAAT
65 TTCGTATAAGTA--CTATGTACTTTCGGCACTAAATATGCAAT-CATGGAATTAATAAT
1640466 AAGTTTTTGA
Statistics
Matches: 100, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
134 30 0.30
135 19 0.19
136 51 0.51
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (135 bp):
CATTTCGACATACATTGTATATAAAAGTTATCGATCGATTTTGTTTAATGCATAACAGTGCATTT
TCGTATAAGTACTATGTACTTTCGGCACTAAATATGCAATCATGGAATTAATAATGAATTTGTGA
ATCAC
Found at i:1648225 original size:23 final size:23
Alignment explanation
Indices: 1648201--1648320 Score: 136
Period size: 23 Copynumber: 5.2 Consensus size: 23
1648191 TATCTAGAAT
* *
1648201 GACCATATAGGATTTTCCCGTAT
1 GACCATATAGGATTTTCCCGAAG
* *
1648224 GACCACATAGGATTGTCCCGAAG
1 GACCATATAGGATTTTCCCGAAG
1648247 GACCATATAGGATTTTCCC-ATAG
1 GACCATATAGGATTTTCCCGA-AG
* * *
1648270 GACCACATGGGATTGTT-CCGAAA
1 GACCATATAGGATT-TTCCCGAAG
*
1648293 GACCATATAGGATTGTCCCGAAG
1 GACCATATAGGATTTTCCCGAAG
1648316 GACCA
1 GACCA
1648321 CATAAAACCC
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
22 2 0.03
23 75 0.94
24 3 0.04
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (23 bp):
GACCATATAGGATTTTCCCGAAG
Found at i:1648253 original size:46 final size:46
Alignment explanation
Indices: 1648201--1648324 Score: 185
Period size: 46 Copynumber: 2.7 Consensus size: 46
1648191 TATCTAGAAT
* *
1648201 GACCATATAGGATTTTCCCGTATGACCACATAGGATTGTCCCGAAG
1 GACCATATAGGATTTTCCCGTAGGACCACATAGGATTGTCCCGAAA
* * *
1648247 GACCATATAGGATTTTCCCATAGGACCACATGGGATTGTTCCGAAA
1 GACCATATAGGATTTTCCCGTAGGACCACATAGGATTGTCCCGAAA
* *
1648293 GACCATATAGGATTGTCCCGAAGGACCACATA
1 GACCATATAGGATTTTCCCGTAGGACCACATA
1648325 AAACCCTCGA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (46 bp):
GACCATATAGGATTTTCCCGTAGGACCACATAGGATTGTCCCGAAA
Found at i:1654589 original size:19 final size:20
Alignment explanation
Indices: 1654567--1654615 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 20
1654557 CACTGAAGTG
*
1654567 CCACATATTTTCC-GAAGGA
1 CCACATATTGTCCTGAAGGA
1654586 CCACATAGGATTGTCCTGAAGGA
1 CCACAT---ATTGTCCTGAAGGA
1654609 CCACATA
1 CCACATA
1654616 AAATTGTCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 6 0.24
20 1 0.04
22 6 0.24
23 12 0.48
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (20 bp):
CCACATATTGTCCTGAAGGA
Found at i:1654610 original size:23 final size:23
Alignment explanation
Indices: 1654578--1654684 Score: 151
Period size: 23 Copynumber: 4.7 Consensus size: 23
1654568 CACATATTTT
1654578 CCGAAGGACCACATAGGATTGTC
1 CCGAAGGACCACATAGGATTGTC
* **
1654601 CTGAAGGACCACATAAAATTGTC
1 CCGAAGGACCACATAGGATTGTC
* * *
1654624 CCAAATGACCGCATAGGATTGTC
1 CCGAAGGACCACATAGGATTGTC
*
1654647 CCAAAGGACCACATAGGATTGTC
1 CCGAAGGACCACATAGGATTGTC
1654670 CCGAAGGACCACATA
1 CCGAAGGACCACATA
1654685 AAACCCTCAA
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (23 bp):
CCGAAGGACCACATAGGATTGTC
Found at i:1655348 original size:20 final size:20
Alignment explanation
Indices: 1655325--1655376 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1655315 TTCATCTTGG
1655325 TATCGATACTTCCACATCAA
1 TATCGATACTTCCACATCAA
*
1655345 TATCGATACTTCCACATCAG
1 TATCGATACTTCCACATCAA
1655365 TATCGATACTTC
1 TATCGATACTTC
1655377 TACTATGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.33
Consensus pattern (20 bp):
TATCGATACTTCCACATCAA
Found at i:1655391 original size:20 final size:21
Alignment explanation
Indices: 1655368--1655415 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
1655358 ACATCAGTAT
1655368 CGATAC-TTCTACTATGGTAC
1 CGATACTTTCTACTATGGTAC
* *
1655388 CGATACTTTTCTTCTATGGTAT
1 CGATAC-TTTCTACTATGGTAC
1655410 CGATAC
1 CGATAC
1655416 CCACTTTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
22 18 0.75
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (21 bp):
CGATACTTTCTACTATGGTAC
Found at i:1655404 original size:22 final size:22
Alignment explanation
Indices: 1655374--1655415 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1655364 GTATCGATAC
1655374 TTCTACTATGGTACCGATACTT
1 TTCTACTATGGTACCGATACTT
* *
1655396 TTCTTCTATGGTATCGATAC
1 TTCTACTATGGTACCGATAC
1655416 CCACTTTGGA
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:0.21, G:0.14, T:0.43
Consensus pattern (22 bp):
TTCTACTATGGTACCGATACTT
Found at i:1657867 original size:3 final size:3
Alignment explanation
Indices: 1657855--1657923 Score: 122
Period size: 3 Copynumber: 23.0 Consensus size: 3
1657845 CCATTTGTTT
1657855 TTA TTA -TA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
1657900 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
1657924 CAAACAGATC
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 59 0.92
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1659598 original size:13 final size:13
Alignment explanation
Indices: 1659580--1659640 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
1659570 TCCATTTTCT
1659580 AATATTTTAAATA
1 AATATTTTAAATA
1659593 AATATTTTAAATTA
1 AATATTTTAAA-TA
1659607 TATATATTTT-AAT-
1 -A-ATATTTTAAATA
* *
1659620 TAT-TTTTAGATA
1 AATATTTTAAATA
1659632 AATATTTTA
1 AATATTTTA
1659641 TTAATATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
10 4 0.10
11 4 0.10
12 2 0.05
13 16 0.41
14 3 0.08
15 3 0.08
16 7 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
AATATTTTAAATA
Found at i:1660293 original size:23 final size:22
Alignment explanation
Indices: 1660262--1660315 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
1660252 TTATATATAC
1660262 TTATTATTTTCA-TAATATTTTA
1 TTATTATTTT-ATTAATATTTTA
*
1660284 TATATTATTTTATTAATGTTTTA
1 T-TATTATTTTATTAATATTTTA
1660307 TT-TTATTTT
1 TTATTATTTT
1660316 TCAAGTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.24
22 3 0.10
23 19 0.66
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTATTATTTTATTAATATTTTA
Found at i:1663591 original size:16 final size:16
Alignment explanation
Indices: 1663570--1663603 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1663560 ATCAATATAT
*
1663570 TTTTTGCATACATTCA
1 TTTTTGCACACATTCA
1663586 TTTTTGCACACATTCA
1 TTTTTGCACACATTCA
1663602 TT
1 TT
1663604 ATTCATTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTTTGCACACATTCA
Found at i:1663669 original size:3 final size:3
Alignment explanation
Indices: 1663655--1663691 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1663645 ACATTCATTA
*
1663655 AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1663692 TCAAAAGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1672709 original size:112 final size:113
Alignment explanation
Indices: 1672507--1672944 Score: 395
Period size: 112 Copynumber: 3.8 Consensus size: 113
1672497 TTTAATACAT
* ** * * * *
1672507 CACTTGATGGATCAACATTACCAG-GTTGAGTCCATAATGAGAAGAACTCGTTTGAAGAATG-AG
1 CACTTGATGGATCAACTTTACCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
*
1672570 AAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTACTCGAATTCAA
65 AAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTACTCGAATTCAA
* * *
1672619 CACTTGATGGATCAACTTTACCAGATAAAGTTCGTAATGAGAAGAACTTATCTGAAG-AGGAAGA
1 CACTTGATGGATCAACTTTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
* *
1672683 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACATGACTC-TATCACAGAA
66 AGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT---T-ACTCGAAT-TC--AA
* * * ** *
1672738 GGAGATAGATCAACATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 -CA-CTTGAT--GGATCAACTTTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * * ** * *
1672803 AAGAAGAAGTTCATAATGAGAAAAACTTGTTTAACCTTTTGTTTGAATTCAT
62 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTACTCGAATTCAA
* * * * * * * *
1672855 TA-TTCAATGGATCAACTTTTCCAGAGAAAGTTCATAATAAGAATAATTTAT-TAAAG-AGGAAG
1 CACTT-GATGGATCAACTTTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
1672917 AAGAAGTTCATAATGAGAAGAACTTGTT
65 AAGAAGTTCATAATGAGAAGAACTTGTT
1672945 TAACCTTTAT
Statistics
Matches: 267, Mismatches: 42, Indels: 35
0.78 0.12 0.10
Matches are distributed among these distances:
111 35 0.13
112 83 0.31
113 42 0.16
114 1 0.00
115 2 0.01
116 4 0.01
117 6 0.02
119 4 0.01
120 4 0.01
121 4 0.01
123 47 0.18
124 35 0.13
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (113 bp):
CACTTGATGGATCAACTTTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTACTCGAATTCAA
Found at i:1672952 original size:235 final size:234
Alignment explanation
Indices: 1672539--1673043 Score: 683
Period size: 236 Copynumber: 2.2 Consensus size: 234
1672529 AGGTTGAGTC
* * * * * *
1672539 CATAATGAGAAGAACTCGTTTGAAGAATGAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTT
1 CATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCT
* * * *
1672604 TTTACTCGAATTCAACACTTGATGGATCAACTTTACCAGATAAAGTTCGTAATGAGAAGAACTTA
66 TTTACTCGAATTCAACACTTAATGGATCAACTTTACCAGAGAAAGTTCATAATAAGAAGAACTTA
*
1672669 TCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACATGACTCTATCAC
131 TCTAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTTACATGACTCTATCAC
*
1672734 AGAAGGAGATAGATCAACATCAACTTTTCCAG-AGAAAGTT
195 AGAAGGAGATAGATCAACATCAACATTTCCAGAAG-AAGTT
*
1672774 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTTTAACC
1 CATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAAAACTTGTTCAACC
** * ** * * *
1672839 TTTTGTTTGAATTCATTA-TTCAATGGATCAACTTTTCCAGAGAAAGTTCATAATAAGAATAATT
65 TTTTACTCGAATTCAACACTT-AATGGATCAACTTTACCAGAGAAAGTTCATAATAAGAAGAACT
* ** *
1672903 TAT-TAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTATTTGATTCTATCA
129 TATCTAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTACATGACTCTATCA
** * * *
1672967 CAGAAGGAGATAGATCAGTATCAGCATTTCCATAAGGAGTT
194 CAGAAGGAGATAGATCAACATCAACATTTCCAGAAGAAGTT
1673008 CATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAA
1 CATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAA
1673044 TTTGTTCAAC
Statistics
Matches: 237, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
233 7 0.03
234 75 0.32
235 72 0.30
236 83 0.35
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (234 bp):
CATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCT
TTTACTCGAATTCAACACTTAATGGATCAACTTTACCAGAGAAAGTTCATAATAAGAAGAACTTA
TCTAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTACATGACTCTATCACA
GAAGGAGATAGATCAACATCAACATTTCCAGAAGAAGTT
Found at i:1673293 original size:3 final size:3
Alignment explanation
Indices: 1673275--1673351 Score: 70
Period size: 3 Copynumber: 26.0 Consensus size: 3
1673265 TTTAATCCAT
* * *
1673275 TTA TTT TTA TTA -TA TTA TTA TTA TT- TTA TTTA TCA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* *
1673319 TT- TTT TTA TTA TTA TTA TTAA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
1673352 CAAACAGATC
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
2 6 0.10
3 48 0.80
4 6 0.10
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1674926 original size:13 final size:16
Alignment explanation
Indices: 1674908--1674949 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 16
1674898 CCATTTTCTG
1674908 ATATTTTAAA-TA-A-
1 ATATTTTAAATTATAT
1674921 ATATTTTAAATTATAT
1 ATATTTTAAATTATAT
1674937 ATATTTT-AATTAT
1 ATATTTTAAATTAT
1674950 TTTTAGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 10 0.38
14 2 0.08
15 7 0.27
16 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATTTTAAATTATAT
Found at i:1677305 original size:2 final size:2
Alignment explanation
Indices: 1677293--1677359 Score: 107
Period size: 2 Copynumber: 33.0 Consensus size: 2
1677283 TATAATCATT
* *
1677293 TA TA AA TA TA TA TA TA TA TCA AA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
1677336 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
1677360 AAAGATTGTA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 59 0.98
3 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1678443 original size:19 final size:18
Alignment explanation
Indices: 1678412--1678465 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 18
1678402 CTTTATTTAT
1678412 TTTTATAAGAATAAAAATA
1 TTTTATAA-AATAAAAATA
1678431 TTTTACTAAAATAAAAATA
1 TTTTA-TAAAATAAAAATA
1678450 TTATTA-AAAATAAAAA
1 TT-TTATAAAATAAAAA
1678466 AATAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 10 0.30
19 17 0.52
20 6 0.18
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (18 bp):
TTTTATAAAATAAAAATA
Found at i:1683674 original size:16 final size:16
Alignment explanation
Indices: 1683636--1683681 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
1683626 GATTTTTAGA
1683636 AAATAAAAATA-AAAT
1 AAATAAAAATATAAAT
1683651 AAATTAAAAATATAAA-
1 AAA-TAAAAATATAAAT
1683667 AACATAAAAAATATA
1 AA-AT-AAAAATATA
1683682 TTTTCAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 3 0.11
16 11 0.41
17 13 0.48
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (16 bp):
AAATAAAAATATAAAT
Found at i:1684341 original size:16 final size:16
Alignment explanation
Indices: 1684320--1684408 Score: 51
Period size: 16 Copynumber: 5.6 Consensus size: 16
1684310 AGCCAAACTG
1684320 AAAGTAACCCGAATCA
1 AAAGTAACCCGAATCA
*
1684336 AAAGTAATCC-AAGTCGA
1 AAAGTAACCCGAA-TC-A
* *
1684353 AAA-CAACCCGAA-CTG
1 AAAGTAACCCGAATC-A
* * *
1684368 AAAGTAA-ACAAACCA
1 AAAGTAACCCGAATCA
* *
1684383 AAAATAACCTGAATCA
1 AAAGTAACCCGAATCA
1684399 AAAGTAACCC
1 AAAGTAACCC
1684409 AAATTCAATT
Statistics
Matches: 51, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
15 15 0.29
16 30 0.59
17 6 0.12
ACGTcount: A:0.53, C:0.24, G:0.11, T:0.12
Consensus pattern (16 bp):
AAAGTAACCCGAATCA
Found at i:1685065 original size:60 final size:60
Alignment explanation
Indices: 1684888--1685067 Score: 220
Period size: 60 Copynumber: 3.0 Consensus size: 60
1684878 TGAATTTGGA
* * * * * **
1684888 GATGAAATTGAAAGATCTAAAAGTTTAGGGACTAATTTAGAATGAGATTCATAGTTTGGG
1 GATGAAATTGAAATATTTAAAAGTTTAAGGACTAATTTACAATGAGAGTCATAGTTTAAG
* * *
1684948 GATGAAATTCAAATGA-TCAAAAGTTTAAGGACTAATTTACAATGAGAGTCATTGTTTAAG
1 GATGAAATTGAAAT-ATTTAAAAGTTTAAGGACTAATTTACAATGAGAGTCATAGTTTAAG
* *
1685008 GATGAAATTGGAATATTTAAAAGTTTAAGGACTAATTTGA-AATAAGAGTCATAGTTTAAG
1 GATGAAATTGAAATATTTAAAAGTTTAAGGACTAATTT-ACAATGAGAGTCATAGTTTAAG
1685068 ACATATGGTA
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
59 1 0.01
60 99 0.97
61 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (60 bp):
GATGAAATTGAAATATTTAAAAGTTTAAGGACTAATTTACAATGAGAGTCATAGTTTAAG
Found at i:1685067 original size:31 final size:30
Alignment explanation
Indices: 1684969--1685067 Score: 78
Period size: 31 Copynumber: 3.3 Consensus size: 30
1684959 AATGATCAAA
1684969 AGTTTAAGGACTAATTT-ACAATGAGAGTCAT
1 AGTTTAAGGACTAATTTGA-AAT-AGAGTCAT
* * * ** * *
1685000 TGTTTAAGGA-TGAAATTGGAATA-TTTAAA
1 AGTTTAAGGACT-AATTTGAAATAGAGTCAT
1685029 AGTTTAAGGACTAATTTGAAATAAGAGTCAT
1 AGTTTAAGGACTAATTTGAAAT-AGAGTCAT
1685060 AGTTTAAG
1 AGTTTAAG
1685068 ACATATGGTA
Statistics
Matches: 49, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
29 19 0.39
30 4 0.08
31 26 0.53
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.34
Consensus pattern (30 bp):
AGTTTAAGGACTAATTTGAAATAGAGTCAT
Found at i:1692038 original size:70 final size:70
Alignment explanation
Indices: 1691925--1692107 Score: 321
Period size: 70 Copynumber: 2.6 Consensus size: 70
1691915 GTAAAAGATG
**
1691925 GTTTCTTAAACAATGAGGTGTTTGCAGTATAGGGAATGTTAGTGTGAAATGACTTGGTCTCGTGG
1 GTTTCTTAAACAATGAGGTGTTTGCAGTAGGGGGAATGTTAGTGTGAAATGACTTGGTCTCGTGG
1691990 AGTCA
66 AGTCA
1691995 GTTTCTTAAACAATGAGGTGTTTGCAGTAGGGGGAATGTTAGTGTGAAATGACTTGGTCTCGTGG
1 GTTTCTTAAACAATGAGGTGTTTGCAGTAGGGGGAATGTTAGTGTGAAATGACTTGGTCTCGTGG
*
1692060 AGTCG
66 AGTCA
**
1692065 GTTTCTTAAACAATGAGGCATTTGCAGTAGGGGGAATGTTAGT
1 GTTTCTTAAACAATGAGGTGTTTGCAGTAGGGGGAATGTTAGT
1692108 ATGCAATGGT
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 108 1.00
ACGTcount: A:0.25, C:0.10, G:0.32, T:0.33
Consensus pattern (70 bp):
GTTTCTTAAACAATGAGGTGTTTGCAGTAGGGGGAATGTTAGTGTGAAATGACTTGGTCTCGTGG
AGTCA
Found at i:1692990 original size:20 final size:21
Alignment explanation
Indices: 1692967--1693013 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1692957 TTTCTTATTT
*
1692967 TTTTAGTT-TTATTAAATTA-A
1 TTTTA-TTATTATAAAATTATA
1692987 TTTTATTATTATAAAATTATA
1 TTTTATTATTATAAAATTATA
1693008 TTTTAT
1 TTTTAT
1693014 AATTTTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 15 0.62
21 7 0.29
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTATTATTATAAAATTATA
Found at i:1694200 original size:73 final size:72
Alignment explanation
Indices: 1694116--1694258 Score: 189
Period size: 73 Copynumber: 2.0 Consensus size: 72
1694106 AGCATAAAAT
* * * *
1694116 AAATAAAACAAATTTATATTCTAAACCACGAAAACAAA-TAATACTCAAATCACCATTTGGGGGT
1 AAATAAAACAAATTTACATACTAAACCACGAAAACAAACT-ATACACAAATCACCATTT-GGAGT
1694180 AAAAACTAA
64 AAAAACTAA
* * * *
1694189 AAATAATACAAATTTACATACTAAACTATGAAAACAAACTATACACAAATTACCATTTGGAGTAA
1 AAATAAAACAAATTTACATACTAAACCACGAAAACAAACTATACACAAATCACCATTTGGAGTAA
1694254 AAACT
66 AAACT
1694259 CTATATTATA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
72 11 0.18
73 49 0.80
74 1 0.02
ACGTcount: A:0.52, C:0.16, G:0.07, T:0.24
Consensus pattern (72 bp):
AAATAAAACAAATTTACATACTAAACCACGAAAACAAACTATACACAAATCACCATTTGGAGTAA
AAACTAA
Found at i:1696863 original size:21 final size:21
Alignment explanation
Indices: 1696837--1696890 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1696827 TTATGTGGAT
1696837 GAGGTATGTCCAATGCATGGG
1 GAGGTATGTCCAATGCATGGG
1696858 GAGGTATGTCCAATGCATGGG
1 GAGGTATGTCCAATGCATGGG
*
1696879 GTGGTATGTCCA
1 GAGGTATGTCCA
1696891 GTGTTTGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.15, G:0.37, T:0.26
Consensus pattern (21 bp):
GAGGTATGTCCAATGCATGGG
Found at i:1699893 original size:125 final size:125
Alignment explanation
Indices: 1699669--1699917 Score: 417
Period size: 125 Copynumber: 2.0 Consensus size: 125
1699659 TGCTTTTGAG
*
1699669 GACTAATCCGAGCACATTAGTGGAGTACGACCCGGAGATTGAAGCTAAAGCTAGGAGACTCCACG
1 GACTAATCCGAGCACATTAGTGGAGTACGACCCGGAGATCGAAGCTAAAGCTAGGAGACTCCACG
*
1699734 CACAGACACTTCGGGAAAGAAGGAGACAACAATCAAATCTAGAAGAAGAATCAAATTCAA
66 CACAGACACTTCGGGAAAAAAGGAGACAACAATCAAATCTAGAAGAAGAATCAAATTCAA
* * *
1699794 GACTAATCTGGGCATATTAGTGGAGTACGACCCGGAGATCGAAGCTAAAGCTAGGAGACTCCACG
1 GACTAATCCGAGCACATTAGTGGAGTACGACCCGGAGATCGAAGCTAAAGCTAGGAGACTCCACG
* * * *
1699859 CAGAGGCACTTCGGGAAAAAATGAGACAATAATCAAATCTAGAAGAAGAATCAAATTCA
66 CACAGACACTTCGGGAAAAAAGGAGACAACAATCAAATCTAGAAGAAGAATCAAATTCA
1699918 GGTAATACAA
Statistics
Matches: 115, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
125 115 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (125 bp):
GACTAATCCGAGCACATTAGTGGAGTACGACCCGGAGATCGAAGCTAAAGCTAGGAGACTCCACG
CACAGACACTTCGGGAAAAAAGGAGACAACAATCAAATCTAGAAGAAGAATCAAATTCAA
Found at i:1703027 original size:159 final size:160
Alignment explanation
Indices: 1702738--1703056 Score: 631
Period size: 159 Copynumber: 2.0 Consensus size: 160
1702728 CCCCAATTCT
1702738 CTCTTCTCTTTCAATTTCCTTTTTCTATAGACCCCGCCATCCCTATCTCTATCACCTTTTAATTT
1 CTCTTCTCTTTCAATTTCCTTTTTCTATAGACCCCGCCATCCCTATCTCTATCACCTTTTAATTT
1702803 TTAAACTCCCCTCTATCCACACAAAAAACAAAAACCCCATTTACTTCCAATTCAGATACCCCACG
66 TTAAACTCCCCTCTATCCACACAAAAAACAAAAACCCCATTTACTTCCAATTCAGATACCCCACG
1702868 GTAT-ACCAAACTTAAACCCATCAACTCTA
131 GTATAACCAAACTTAAACCCATCAACTCTA
1702897 CTCTTCTCTTTCAATTTCCTTTTTCTATAGACCCCGCCATCCCTATCTCTATCACCTTTTAATTT
1 CTCTTCTCTTTCAATTTCCTTTTTCTATAGACCCCGCCATCCCTATCTCTATCACCTTTTAATTT
1702962 TTAAACTCCCCTCTATCCACACAAAAAACAAAAACCCCATTTACTTCCAATTCAGATACCCCACG
66 TTAAACTCCCCTCTATCCACACAAAAAACAAAAACCCCATTTACTTCCAATTCAGATACCCCACG
1703027 GTATAACCAAACTTAAACCCATCAACTCTA
131 GTATAACCAAACTTAAACCCATCAACTCTA
1703057 TAGTTTCCAT
Statistics
Matches: 159, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
159 134 0.84
160 25 0.16
ACGTcount: A:0.30, C:0.34, G:0.03, T:0.32
Consensus pattern (160 bp):
CTCTTCTCTTTCAATTTCCTTTTTCTATAGACCCCGCCATCCCTATCTCTATCACCTTTTAATTT
TTAAACTCCCCTCTATCCACACAAAAAACAAAAACCCCATTTACTTCCAATTCAGATACCCCACG
GTATAACCAAACTTAAACCCATCAACTCTA
Found at i:1705585 original size:18 final size:17
Alignment explanation
Indices: 1705562--1705599 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
1705552 TTATTTTTAC
1705562 TTTAATTACTTTTACTTA
1 TTTAATTACTTTTA-TTA
*
1705580 TTTAATTGCTTTTATTA
1 TTTAATTACTTTTATTA
1705597 TTT
1 TTT
1705600 TTAATATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTAATTACTTTTATTA
Found at i:1706169 original size:3 final size:3
Alignment explanation
Indices: 1706161--1706198 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1706151 ACAAGTTAGT
1706161 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1706199 GAAAATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1707377 original size:34 final size:32
Alignment explanation
Indices: 1707326--1707389 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
1707316 TAAAAAATTT
1707326 AAATTTTATAAGAAAATAAAAAAATAGAATATG
1 AAATTTTATAAGAAAATAAAAAAATA-AATATG
*
1707359 AAATTTTA-AATGAGAAATAAATAAATAAATA
1 AAATTTTATAA-GA-AAATAAAAAAATAAATA
1707390 AAATGATGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 2 0.07
33 14 0.50
34 12 0.43
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (32 bp):
AAATTTTATAAGAAAATAAAAAAATAAATATG
Found at i:1708650 original size:4 final size:4
Alignment explanation
Indices: 1708624--1708683 Score: 68
Period size: 4 Copynumber: 14.2 Consensus size: 4
1708614 TTGGACCTAA
1708624 AAAT AAA- AAAT AAAAT GAAAT AAAT AAAT AAAT AAAT AATAT AATAT
1 AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AA-AT AA-AT
*
1708671 AAAT AACT AAAT A
1 AAAT AAAT AAAT A
1708684 TGATAATAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.06
4 30 0.60
5 17 0.34
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:1708659 original size:22 final size:22
Alignment explanation
Indices: 1708624--1708693 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 22
1708614 TTGGACCTAA
1708624 AAATAAA-AAATAAAATGAAAT
1 AAATAAATAAATAAAATGAAAT
1708645 AAATAAATAAAT-AAAT-AATAT
1 AAATAAATAAATAAAATGAA-AT
*
1708666 AATATAAATAACTAAATATGATAAT
1 AA-ATAAATAAATAAA-ATGA-AAT
1708691 AAA
1 AAA
1708694 AACTATATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
20 2 0.05
21 15 0.37
22 13 0.32
23 2 0.05
24 3 0.07
25 5 0.12
26 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (22 bp):
AAATAAATAAATAAAATGAAAT
Found at i:1708672 original size:26 final size:26
Alignment explanation
Indices: 1708624--1708683 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
1708614 TTGGACCTAA
1708624 AAATAAA-AAATAAAATGAAATAAAT
1 AAATAAATAAATAAAATGAAATAAAT
*
1708649 AAATAAATAAATAATAT-AATATAAAT
1 AAATAAATAAATAAAATGAA-ATAAAT
*
1708675 AACTAAATA
1 AAATAAATA
1708684 TGATAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 9 0.29
26 22 0.71
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (26 bp):
AAATAAATAAATAAAATGAAATAAAT
Found at i:1708753 original size:22 final size:22
Alignment explanation
Indices: 1708720--1708763 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1708710 ATTTTCAAAA
*
1708720 ATATGTTTTCAAAAATTATTTT
1 ATATGTTTTCAAAAATCATTTT
1708742 ATAT-TTTCTCAAAAATCATTTT
1 ATATGTTT-TCAAAAATCATTTT
1708764 TTTTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATGTTTTCAAAAATCATTTT
Found at i:1708792 original size:38 final size:35
Alignment explanation
Indices: 1708707--1709094 Score: 113
Period size: 35 Copynumber: 11.0 Consensus size: 35
1708697 TATATAATAC
*
1708707 TATA-TTTTCAAAAATATGTTTTCAAAAATTATTT
1 TATAGTTTTCAAAAATATGTTTTCAAAAATTATAT
* * **
1708741 TATATTTTCTCAAAAATCATTTTTTTTAAAATATATAT
1 TATAGTTT-TCAAAAAT-ATGTTTTCAAAAAT-TATAT
* *
1708779 TATACGTTTTC-AAAAT-TATTTT-AAAAACTATATAC
1 TATA-GTTTTCAAAAATATGTTTTCAAAAA-T-TATAT
* **
1708814 CATATGTTTTC-AAAA-CCGTTTT-AAAAACTATATAT
1 TATA-GTTTTCAAAAATATGTTTTCAAAAA-T-TATAT
* * *
1708849 TATACG-TTTC-AGAAT-TATTTT-AAAAACTATAT
1 TATA-GTTTTCAAAAATATGTTTTCAAAAATTATAT
* * * *
1708881 TATACATTTTC-AAAAT-TATTTTAAAAAACTATATAC
1 TATA-GTTTTCAAAAATATGTTTTCAAAAA-T-TATAT
**
1708917 TATATGTTTTC-AAAA-CCGTTTT-AAAAACTATATAT
1 TATA-GTTTTCAAAAATATGTTTTCAAAAA-T-TATAT
* *
1708952 TATACGTTTTCAAAACTAT-TTTTAAAAAAATATATAT
1 TATA-GTTTTCAAAAATATGTTTT-CAAAAAT-TATAT
* *
1708989 TATATGTTTT-TAAAAT-TATTTT-AAAAACTATATAAT
1 TATA-GTTTTCAAAAATATGTTTTCAAAAA-T-TAT-AT
**
1709025 ATATA-TTTTCAAAACCA--TTTT-AAAAACTATATAT
1 -TATAGTTTTCAAAAATATGTTTTCAAAAA-T-TATAT
* * *
1709059 TATAAGTTTTTAAAAATAAGTTTCCAAAAATTATAT
1 TAT-AGTTTTCAAAAATATGTTTTCAAAAATTATAT
1709095 ATTATATATT
Statistics
Matches: 284, Mismatches: 42, Indels: 54
0.75 0.11 0.14
Matches are distributed among these distances:
32 10 0.04
33 17 0.06
34 37 0.13
35 103 0.36
36 54 0.19
37 40 0.14
38 20 0.07
39 3 0.01
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (35 bp):
TATAGTTTTCAAAAATATGTTTTCAAAAATTATAT
Found at i:1708823 original size:35 final size:35
Alignment explanation
Indices: 1708763--1709116 Score: 347
Period size: 35 Copynumber: 10.0 Consensus size: 35
1708753 AAAATCATTT
* * *
1708763 TTTTTAAAA-TATATATTATACGTTTTCAAAATTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
** **
1708797 TTTTAAAAACTATATACCATATGTTTTCAAAACCG
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
* * *
1708832 TTTTAAAAACTATATATTATACG-TTTCAGAATTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
** *
1708866 TTTTAAAAAC--TATATTATACATTTTCAAAATTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
* **
1708899 TTTTAAAAAACTATATACTATATGTTTTCAAAACCG
1 TTTT-AAAAACTATATATTATATGTTTTCAAAACTA
*
1708935 TTTTAAAAACTATATATTATACGTTTTCAAAACTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
* * *
1708970 TTTTTAAAAAAATATATATTATATGTTTTTAAAATTA
1 -TTTT-AAAAACTATATATTATATGTTTTCAAAACTA
* * *
1709007 TTTTAAAAACTATATAATATATATTTTCAAAACCA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
* * *
1709042 TTTTAAAAACTATATATTATAAGTTTTTAAAAATAA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACT-A
* * * *
1709078 GTTTCCAAAAATTATATATTATATATTTTTAAAAACTA
1 -TTT-TAAAAACTATATATTATAT-GTTTTCAAAACTA
1709116 T
1 T
1709117 ATTTGAAATT
Statistics
Matches: 261, Mismatches: 48, Indels: 19
0.80 0.15 0.06
Matches are distributed among these distances:
32 10 0.04
33 14 0.05
34 31 0.12
35 119 0.46
36 30 0.11
37 31 0.12
38 17 0.07
39 9 0.03
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (35 bp):
TTTTAAAAACTATATATTATATGTTTTCAAAACTA
Found at i:1708854 original size:70 final size:69
Alignment explanation
Indices: 1708763--1709073 Score: 358
Period size: 72 Copynumber: 4.5 Consensus size: 69
1708753 AAAATCATTT
* * **
1708763 TTTTTAAAA-TATATATTATACGTTTTCAAAATTATTTTAAAAACTATATACCATATGTTTTCAA
1 TTTTAAAAACTATATATTATACGTTTTCAAAATTATTTTAAAAACTATATA-TATACATTTTCAA
*
1708827 AACCG
65 AACCA
*
1708832 TTTTAAAAACTATATATTATACG-TTTCAGAATTATTTTAAAAACTATAT-TATACATTTTCAAA
1 TTTTAAAAACTATATATTATACGTTTTCAAAATTATTTTAAAAACTATATATATACATTTTCAAA
**
1708895 ATTA
66 ACCA
* * *** *
1708899 TTTTAAAAAACTATATACTATATGTTTTCAAAACCGTTTTAAAAACTATATATTATACGTTTTCA
1 TTTT-AAAAACTATATATTATACGTTTTCAAAATTATTTTAAAAACTATATA-TATACATTTTCA
*
1708964 AAACTA
64 AAACCA
* * * *
1708970 TTTTTAAAAAAATATATATTATATGTTTTTAAAATTATTTTAAAAACTATATAATATATATTTTC
1 -TTTT-AAAAACTATATATTATACGTTTTCAAAATTATTTTAAAAACTATAT-ATATACATTTTC
1709035 AAAACCA
63 AAAACCA
* *
1709042 TTTTAAAAACTATATATTATAAGTTTTTAAAA
1 TTTTAAAAACTATATATTATACGTTTTCAAAA
1709074 ATAAGTTTCC
Statistics
Matches: 208, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
67 16 0.08
68 17 0.08
69 55 0.26
70 39 0.19
71 20 0.10
72 60 0.29
73 1 0.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (69 bp):
TTTTAAAAACTATATATTATACGTTTTCAAAATTATTTTAAAAACTATATATATACATTTTCAAA
ACCA
Found at i:1709472 original size:20 final size:20
Alignment explanation
Indices: 1709447--1709520 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
1709437 TTTTCCCAAT
*
1709447 TCGCAATGCCAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1709467 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1709488 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
*
1709508 TCGCAACGCGAAT
1 TCGCAATGCGAAT
1709521 TGGGAAAATC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1709490 original size:21 final size:21
Alignment explanation
Indices: 1709464--1709534 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
1709454 GCCAATAAGT
1709464 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
1709485 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
1709505 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
1709526 AAATCGCAA
1 AAATCGCAA
1709535 TGTGATACTG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.39
21 25 0.61
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.15
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:1709504 original size:41 final size:41
Alignment explanation
Indices: 1709447--1709536 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
1709437 TTTTCCCAAT
1709447 TCGCAATGCCAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCCAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
1709488 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCCAATAAGTAAATCGCAACGCGAATTGGGAAAA
1709529 TCGCAATG
1 TCGCAATG
1709537 TGATACTGAC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (41 bp):
TCGCAATGCCAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1709552 original size:41 final size:41
Alignment explanation
Indices: 1709466--1709601 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
1709456 CAATAAGTAA
* * *
1709466 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGAG-ATACTG-ACT
*
1709507 ATCGCAACGCGAATTGGGAAAATCGCAATGTGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGAGATACTGACT
* * *** * *
1709548 ATCGCAATGCGATAATAAAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGAGATACTGACT
*
1709590 TTCGCAACGCGA
1 ATCGCAACGCGA
1709602 TACTGTCTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
40 4 0.05
41 43 0.54
42 32 0.41
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGAGATACTGACT
Found at i:1709596 original size:20 final size:20
Alignment explanation
Indices: 1709571--1709623 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1709561 AATAAAAAAA
*
1709571 TCGCAACGAGATACT-TACTT
1 TCGCAACGCGATACTGT-CTT
1709591 TCGCAACGCGATACTGTCTT
1 TCGCAACGCGATACTGTCTT
1709611 TCGCAACGCGATA
1 TCGCAACGCGATA
1709624 ATACATAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGTCTT
Found at i:1709839 original size:22 final size:22
Alignment explanation
Indices: 1709811--1709854 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1709801 CACTCTCTCA
1709811 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1709833 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1709855 TATCTAAATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1711496 original size:18 final size:18
Alignment explanation
Indices: 1711475--1711519 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1711465 TCCACTTCGG
*
1711475 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1711493 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1711511 GAGCCATCA
1 GAGCCATCA
1711520 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1712040 original size:19 final size:20
Alignment explanation
Indices: 1711986--1712052 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
1711976 TAGTTTACTT
* *
1711986 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
* *
1712006 TTGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1712026 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1712045 TCGCAACG
1 TCGCAACG
1712053 ACAAAATCGC
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 14 0.38
20 23 0.62
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1712060 original size:14 final size:14
Alignment explanation
Indices: 1712041--1712098 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1712031 ATGCGAAATG
1712041 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1712055 AAAATCGCAATGCGAAAT
1 AAAATCGCAA--CG--AC
*
1712073 AAAATCGCAATGAC
1 AAAATCGCAACGAC
1712087 AAAATCGCAACG
1 AAAATCGCAACG
1712099 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 3 0.08
18 11 0.31
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1712116 original size:33 final size:33
Alignment explanation
Indices: 1712025--1712117 Score: 161
Period size: 32 Copynumber: 2.8 Consensus size: 33
1712015 GGAAATGGCT
*
1712025 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1712058 ATCGCAATGCGAAAT-AAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
*
1712090 ATCGCAACGCGAAATGAAAATCGCAATG
1 ATCGCAATGCGAAATGAAAATCGCAATG
1712118 CGATTTGTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.53
33 27 0.47
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAATGACAAA
Found at i:1712151 original size:14 final size:14
Alignment explanation
Indices: 1712132--1712189 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1712122 TTGTGTTTCG
1712132 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1712146 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1712162 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1712178 CGTTGCGATTTT
1 CGTTGCGATTTT
1712190 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1712166 original size:32 final size:33
Alignment explanation
Indices: 1712127--1712205 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1712117 GCGATTTGTG
1712127 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1712159 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1712192 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1712206 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1712204 original size:19 final size:19
Alignment explanation
Indices: 1712146--1712263 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
1712136 GCGATTTTGT
1712146 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1712164 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
1712178 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
1712197 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
1712217 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1712236 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1712256 TGTTGCGA
1 CGTTGCGA
1712264 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1714279 original size:33 final size:36
Alignment explanation
Indices: 1714234--1714318 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 36
1714224 AAAACAGACT
* ***
1714234 ATCGCAACGCGAAATGGCTATCGCAA-CG-A-GAAA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
1714267 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
1714305 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
1714319 ATCGCAATGC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
33 22 0.51
35 2 0.05
37 1 0.02
38 18 0.42
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:1714285 original size:19 final size:19
Alignment explanation
Indices: 1714263--1714363 Score: 132
Period size: 19 Copynumber: 5.8 Consensus size: 19
1714253 ATCGCAACGA
1714263 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1714282 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1714301 GAAAATCGCAATGC-----
1 GAAAATCGCAATGCGAAAT
1714315 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1714334 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1714348 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1714364 TTTTCATTTC
Statistics
Matches: 74, Mismatches: 0, Indels: 18
0.80 0.00 0.20
Matches are distributed among these distances:
14 25 0.34
15 1 0.01
16 2 0.03
17 2 0.03
19 44 0.59
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1714319 original size:33 final size:33
Alignment explanation
Indices: 1714282--1714363 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
1714272 AATGCGAAAT
* *
1714282 GAAAATCGCAATGCGAAATGAAAATCGCAATGC
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGA
1714315 GAAAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGA
1714348 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1714364 TTTTCATTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAACGA
Found at i:1714319 original size:52 final size:51
Alignment explanation
Indices: 1714234--1714363 Score: 169
Period size: 52 Copynumber: 2.6 Consensus size: 51
1714224 AAAACAGACT
*** * *
1714234 ATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAAATCGCAATGCGAAAATCGCAATGCGAAATGAAA
1714286 ATCGCAATGCGAAATGAAAATCGCAATGCGAAAATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAAATCGCAATGCGAAAATCGCAATGCGAAATGAAA
1714338 ATCGCAA-CG--A-GAAAATCGCAATGCGA
1 ATCGCAAGCGAAATGAAAATCGCAATGCGA
1714364 TTTTCATTTC
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
47 16 0.22
48 1 0.01
50 2 0.03
52 53 0.74
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (51 bp):
ATCGCAAGCGAAATGAAAATCGCAATGCGAAAATCGCAATGCGAAATGAAA
Found at i:1714439 original size:20 final size:20
Alignment explanation
Indices: 1714382--1714439 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
1714372 TCGCATTGCG
* * *
1714382 ATTTTCTCGTTGTGATAACC
1 ATTTTCGCGTTGCGATAGCC
1714402 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
1714422 ATTTTTGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1714440 TCAAATGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1715525 original size:24 final size:24
Alignment explanation
Indices: 1715498--1715551 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1715488 GTATTCGAAA
* *
1715498 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1715522 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1715546 TTTGAT
1 TTTGAT
1715552 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1718367 original size:33 final size:33
Alignment explanation
Indices: 1718310--1718408 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
1718300 ACGAGATAAT
*
1718310 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
1718344 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
1718377 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
1718409 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1718402 original size:19 final size:19
Alignment explanation
Indices: 1718285--1718469 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
1718275 TCTTTTGGTT
*
1718285 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1718304 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1718324 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1718342 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1718358 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1718376 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1718391 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1718411 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1718430 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1718449 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1718468 GA
1 GA
1718470 TTTTGGTTTC
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 62 0.45
20 45 0.33
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1718423 original size:39 final size:38
Alignment explanation
Indices: 1718380--1718469 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
1718370 GCGACCAGAC
1718380 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
1718419 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
1718457 AATCGCAATGCGA
1 AATCGCAACGCGA
1718470 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:1719114 original size:21 final size:21
Alignment explanation
Indices: 1719081--1719181 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
1719071 TGCGAAAGTA
* * *
1719081 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
1719102 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
1719122 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
1719144 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
1719165 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
1719182 CCCAATTCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:1719137 original size:20 final size:20
Alignment explanation
Indices: 1719044--1719137 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1719034 CGCTATGTAA
*
1719044 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
1719064 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
1719084 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
1719105 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
1719125 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1719138 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:1719156 original size:41 final size:41
Alignment explanation
Indices: 1719065--1719199 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
1719055 AAAGTCAGTA
* * * ** *
1719065 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
1719105 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
1719147 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1719188 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1719200 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1719191 original size:21 final size:20
Alignment explanation
Indices: 1719126--1719218 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1719116 ATAGTCAGTA
*
1719126 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
1719147 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
1719167 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
1719188 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
1719208 TCGCATTGCGA
1 TCGCATTGCGA
1719219 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:1719200 original size:41 final size:41
Alignment explanation
Indices: 1719126--1719218 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1719116 ATAGTCAGTA
1719126 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1719167 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1719208 TCGCATTGCGA
1 TCGCATTGCGA
1719219 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1720375 original size:2 final size:2
Alignment explanation
Indices: 1720368--1720399 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1720358 CCCATCAGAA
1720368 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
1720400 TATTAATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.