Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, 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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 18 of 100
Found at i:5169694 original size:3 final size:3
Alignment explanation
Indices: 5169686--5169711 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5169676 CAATAACACT
5169686 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
5169712 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:5169959 original size:16 final size:16
Alignment explanation
Indices: 5169940--5169974 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5169930 ATAGATCCTC
*
5169940 AAAACCTTAAAATTCA
1 AAAACCTTAAAATGCA
*
5169956 AAAATCTTAAAATGCA
1 AAAACCTTAAAATGCA
5169972 AAA
1 AAA
5169975 TCTCAAACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.14, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAACCTTAAAATGCA
Found at i:5169975 original size:15 final size:15
Alignment explanation
Indices: 5169939--5169977 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
5169929 CATAGATCCT
* *
5169939 CAAAACCTTAAAATT
1 CAAAATCTTAAAATG
5169954 CAAAAATCTTAAAATG
1 C-AAAATCTTAAAATG
5169970 CAAAATCT
1 CAAAATCT
5169978 CAAACCTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.54, C:0.18, G:0.03, T:0.26
Consensus pattern (15 bp):
CAAAATCTTAAAATG
Found at i:5181820 original size:22 final size:22
Alignment explanation
Indices: 5181780--5181824 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
5181770 TAAATTATAA
5181780 ATTTGTTAATTAATATAATATTT
1 ATTTGTTAATTAATATAAT-TTT
5181803 ATTT-TTAATGTAAT-TAATTTT
1 ATTTGTTAAT-TAATATAATTTT
5181824 A
1 A
5181825 AATGATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.19
22 9 0.43
23 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
ATTTGTTAATTAATATAATTTT
Found at i:5181917 original size:29 final size:30
Alignment explanation
Indices: 5181885--5181963 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
5181875 AGTTAATAAA
*
5181885 TTTATAATTTAAATATTATATTAA-ATATT
1 TTTATAATTTAAATATTATACTAACATATT
* * * *
5181914 TTTAAAAATTAAATATTATACTAACTTTTT
1 TTTATAATTTAAATATTATACTAACATATT
*
5181944 TATTATAATTTAAAAATTAT
1 T-TTATAATTTAAATATTAT
5181964 TAGGAACATT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 21 0.52
30 4 0.10
31 15 0.38
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTATAATTTAAATATTATACTAACATATT
Found at i:5182518 original size:12 final size:12
Alignment explanation
Indices: 5182501--5182531 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5182491 TTTAATATAA
*
5182501 AAATATTATTAC
1 AAATATTACTAC
5182513 AAATATTACTAC
1 AAATATTACTAC
5182525 AAATATT
1 AAATATT
5182532 TTAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATATTACTAC
Found at i:5184325 original size:2 final size:2
Alignment explanation
Indices: 5184318--5184359 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5184308 AGCAATATTT
5184318 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5184360 AGCACAATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5189661 original size:21 final size:21
Alignment explanation
Indices: 5189612--5189657 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
5189602 ATTTTTTATA
*
5189612 TATTTATT-TTAAATGATATT
1 TATTTATTATTAAATAATATT
5189632 TATTTATTATTAAATAATA-T
1 TATTTATTATTAAATAATATT
5189652 TATTTA
1 TATTTA
5189658 ATTAATTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TATTTATTATTAAATAATATT
Found at i:5193787 original size:187 final size:187
Alignment explanation
Indices: 5193472--5193822 Score: 542
Period size: 187 Copynumber: 1.9 Consensus size: 187
5193462 AGTGCATTCA
* *** *
5193472 AGATTTTACTTTTAAAATTATTTTTTATAAAGAGCAAACACTGGTTGACATAAAAAAAATTTTTT
1 AGATTTTACTTTTAAAATTATTTTTTATAAAGAGCAAACACTGATTGACATAAAAAAAAAACTGT
* ** * *
5193537 TTTCTTACTAACTGAATTAATCTTTTAAATAATTTTTTAAAGTTTGTAAACCGATTAAATTAAAG
66 TTTCTTACTAACTGAACTAATCTTTTAAATAATTTTTTAAAGTAAGCAAACCAATTAAATTAAAG
5193602 TTAAAACCAGGTAAACAAGCACTCAGATTAATTATATTTTGTAAAGATTAAACCTTC
131 TTAAAACCAGGTAAACAAGCACTCAGATTAATTATATTTTGTAAAGATTAAACCTTC
*
5193659 AGATTTTACTTTTAAAATTATTTTTTATAAAGATCAAACACTGATTGACATAAAAAAAAAACTGT
1 AGATTTTACTTTTAAAATTATTTTTTATAAAGAGCAAACACTGATTGACATAAAAAAAAAACTGT
* *
5193724 TTTCTTAAC-AACTGAACTAATCTTTTAAATAATTTTTTAAAGTAAGCCAGCCAATTAAATTAAA
66 TTTCTT-ACTAACTGAACTAATCTTTTAAATAATTTTTTAAAGTAAGCAAACCAATTAAATTAAA
* * *
5193788 GTTAAAACCAGGTAAACATGCCCTTAGATTAATTA
130 GTTAAAACCAGGTAAACAAGCACTCAGATTAATTA
5193823 ATGGCTAAAG
Statistics
Matches: 147, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
187 145 0.99
188 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.38
Consensus pattern (187 bp):
AGATTTTACTTTTAAAATTATTTTTTATAAAGAGCAAACACTGATTGACATAAAAAAAAAACTGT
TTTCTTACTAACTGAACTAATCTTTTAAATAATTTTTTAAAGTAAGCAAACCAATTAAATTAAAG
TTAAAACCAGGTAAACAAGCACTCAGATTAATTATATTTTGTAAAGATTAAACCTTC
Found at i:5194065 original size:14 final size:14
Alignment explanation
Indices: 5194048--5194074 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5194038 GATGTTGAGA
5194048 GTTGCCAGTTGCCG
1 GTTGCCAGTTGCCG
5194062 GTTGCCAGTTGCC
1 GTTGCCAGTTGCC
5194075 ACTTATGGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.30, G:0.33, T:0.30
Consensus pattern (14 bp):
GTTGCCAGTTGCCG
Found at i:5194551 original size:12 final size:12
Alignment explanation
Indices: 5194534--5194595 Score: 69
Period size: 12 Copynumber: 5.3 Consensus size: 12
5194524 TTTTTTAATA
5194534 TAAATATAAAAT
1 TAAATATAAAAT
5194546 TAAATATATAAA-
1 TAAATATA-AAAT
*
5194558 TATATAT-AAA-
1 TAAATATAAAAT
5194568 TAAATATAAAAT
1 TAAATATAAAAT
5194580 TAAATA-AATAAT
1 TAAATATAA-AAT
5194592 TAAA
1 TAAA
5194596 AAATAATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 9 0.20
11 5 0.11
12 27 0.61
13 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAATATAAAAT
Found at i:5194586 original size:20 final size:20
Alignment explanation
Indices: 5194533--5194590 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
5194523 ATTTTTTAAT
*
5194533 ATAAATATAAAATTAAATAT
1 ATAAATATAAAATTAAATAA
5194553 ATAAATAT---A-T--ATAA
1 ATAAATATAAAATTAAATAA
5194567 ATAAATATAAAATTAAATAA
1 ATAAATATAAAATTAAATAA
5194587 ATAA
1 ATAA
5194591 TTAAAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
14 11 0.35
16 1 0.03
17 2 0.06
18 1 0.03
20 16 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATATAAAATTAAATAA
Found at i:5194601 original size:11 final size:12
Alignment explanation
Indices: 5194529--5194603 Score: 52
Period size: 12 Copynumber: 6.4 Consensus size: 12
5194519 TATTATTTTT
5194529 TAATATAAATATAA
1 TAAT-TAAATA-AA
*
5194543 -AATTAAATATA
1 TAATTAAATAAA
* *
5194554 TAA--ATATATA
1 TAATTAAATAAA
*
5194564 TAAATAAATATAA
1 TAATTAAATA-AA
5194577 -AATTAAATAAA
1 TAATTAAATAAA
5194588 TAATTAAA-AAA
1 TAATTAAATAAA
5194599 TAATT
1 TAATT
5194604 TTTTATATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
10 9 0.18
11 11 0.22
12 27 0.53
13 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TAATTAAATAAA
Found at i:5199929 original size:60 final size:59
Alignment explanation
Indices: 5199801--5200093 Score: 398
Period size: 60 Copynumber: 4.9 Consensus size: 59
5199791 TTTTTTGTAG
* *
5199801 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTTGATTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTTGATTTCAA
*
5199859 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTTGA-TTTCAA
*
5199919 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAAATTTAT-TTTTCTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTTT-GAAATTT-TGATTTC----
5199983 AA
58 AA
*
5199985 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTGAAAATTT-ATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTTGATTTC-AA
*
5200042 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAATTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTGAAATTTT
5200094 TTATTTTTAT
Statistics
Matches: 215, Mismatches: 7, Indels: 24
0.87 0.03 0.10
Matches are distributed among these distances:
57 38 0.18
58 35 0.16
59 16 0.07
60 57 0.27
61 6 0.03
62 18 0.08
63 7 0.03
64 1 0.00
66 37 0.17
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.46
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTTGATTTCAA
Found at i:5200075 original size:27 final size:27
Alignment explanation
Indices: 5199987--5200075 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
5199977 TCTTTTAAGG
5199987 AAAATTGATACTTTCAACTTTTCCCTA
1 AAAATTGATACTTTCAACTTTTCCCTA
** * * **
5200014 AAAA-T-ATTTTTTGAAAATTTATTTCTAA
1 AAAATTGATACTTT-CAACTTT-TCCCT-A
5200042 GGAAAATTGATACTTTCAACTTTTCCCTA
1 --AAAATTGATACTTTCAACTTTTCCCTA
5200071 AAAAT
1 AAAAT
5200076 ATTTTTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 14
0.62 0.17 0.20
Matches are distributed among these distances:
25 5 0.12
26 6 0.14
27 12 0.28
28 1 0.02
29 1 0.02
30 7 0.16
31 6 0.14
32 5 0.12
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.42
Consensus pattern (27 bp):
AAAATTGATACTTTCAACTTTTCCCTA
Found at i:5200107 original size:123 final size:124
Alignment explanation
Indices: 5199801--5200114 Score: 427
Period size: 123 Copynumber: 2.6 Consensus size: 124
5199791 TTTTTTGTAG
* *
5199801 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA----TTTTTTGG-AA---ATTTTGATTTCA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAAATTTATTTTTATTT-A
*
5199858 AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTTTCAA
65 AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGAAAATTTGATTTTCAA
*
5199919 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAAATTTATTTTTCTTTTA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAAATTTATTTTT-ATTTA
*
5199984 AGGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGAAAATTT-A-TTTCTAA
65 AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTGATTTTC-AA
*
5200042 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTTGGAATTTTTTATTTTTATTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAA--ATTTATTTTTATTT
*
5200106 AAAGAAAAT
64 AAGGAAAAT
5200115 AAAATAATAA
Statistics
Matches: 176, Mismatches: 8, Indels: 19
0.87 0.04 0.09
Matches are distributed among these distances:
118 34 0.19
122 25 0.14
123 51 0.29
124 22 0.12
126 41 0.23
127 3 0.02
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.46
Consensus pattern (124 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAAATTTATTTTTATTTAA
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTGATTTTCAA
Found at i:5200185 original size:8 final size:8
Alignment explanation
Indices: 5200165--5200203 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
5200155 CTAATCTAAT
5200165 AAATAAA-
1 AAATAAAC
5200172 AAATAAAC
1 AAATAAAC
5200180 AAAT--A-
1 AAATAAAC
5200185 AAATAAAC
1 AAATAAAC
5200193 AAATAAAC
1 AAATAAAC
5200201 AAA
1 AAA
5200204 GAAATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
5 4 0.14
6 1 0.04
7 8 0.29
8 15 0.54
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (8 bp):
AAATAAAC
Found at i:5200189 original size:13 final size:13
Alignment explanation
Indices: 5200171--5200212 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
5200161 TAATAAATAA
5200171 AAAATAAACAAAT
1 AAAATAAACAAAT
5200184 AAAATAAACAAAT
1 AAAATAAACAAAT
* *
5200197 -AAACAAAGAAAT
1 AAAATAAACAAAT
5200209 AAAA
1 AAAA
5200213 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.79, C:0.07, G:0.02, T:0.12
Consensus pattern (13 bp):
AAAATAAACAAAT
Found at i:5200557 original size:20 final size:20
Alignment explanation
Indices: 5200532--5200569 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5200522 GAACACCGGT
*
5200532 GCCGGATTCTGGAAATTTTC
1 GCCGGAATCTGGAAATTTTC
5200552 GCCGGAATCTGGAAATTT
1 GCCGGAATCTGGAAATTT
5200570 CACCGGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GCCGGAATCTGGAAATTTTC
Found at i:5200575 original size:19 final size:20
Alignment explanation
Indices: 5200533--5200577 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5200523 AACACCGGTG
* *
5200533 CCGGATTCTGGAAATTTTCG
1 CCGGAATCTGGAAATTTTCA
5200553 CCGGAATCTGGAAA-TTTCA
1 CCGGAATCTGGAAATTTTCA
5200572 CCGGAA
1 CCGGAA
5200578 GTTGGCCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (20 bp):
CCGGAATCTGGAAATTTTCA
Found at i:5200667 original size:31 final size:31
Alignment explanation
Indices: 5200629--5200699 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
5200619 ACTGGGCAGG
* ** *
5200629 TCGCCGGAAACTTCAATGTTGGCCGAAATTT
1 TCGCCGGAAAATTCAAACTTCGCCGAAATTT
*
5200660 TCGCCGGAAAATTCAAACTTCGCCGGAATTT
1 TCGCCGGAAAATTCAAACTTCGCCGAAATTT
5200691 TCGCCGGAA
1 TCGCCGGAA
5200700 TCTGGAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (31 bp):
TCGCCGGAAAATTCAAACTTCGCCGAAATTT
Found at i:5201156 original size:15 final size:17
Alignment explanation
Indices: 5201119--5201158 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
5201109 ATTAGATAAG
5201119 TAAAAATACAAAAATGA
1 TAAAAATACAAAAATGA
5201136 -ATAAAATA-AAAAA-GA
1 TA-AAAATACAAAAATGA
5201151 TAAAAATA
1 TAAAAATA
5201159 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (17 bp):
TAAAAATACAAAAATGA
Found at i:5201467 original size:1 final size:1
Alignment explanation
Indices: 5201461--5201546 Score: 118
Period size: 1 Copynumber: 86.0 Consensus size: 1
5201451 CAACTCAACA
* * * * *
5201461 TTTTTTTGTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTGTTTTTTTGTTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
5201526 TTGTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTT
5201547 CCGAAGCTCC
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (1 bp):
T
Found at i:5201490 original size:18 final size:18
Alignment explanation
Indices: 5201469--5201546 Score: 131
Period size: 18 Copynumber: 4.3 Consensus size: 18
5201459 CATTTTTTTG
5201469 TTTTTTTTTTTTTTGTTT
1 TTTTTTTTTTTTTTGTTT
5201487 TTTTTTTTTTTTTTGTTT
1 TTTTTTTTTTTTTTGTTT
*
5201505 TTTTGTTTTTTTTTGTTT
1 TTTTTTTTTTTTTTGTTT
5201523 TTTTTGTTTTTTTTT-TTT
1 TTTTT-TTTTTTTTTGTTT
5201541 TTTTTT
1 TTTTTT
5201547 CCGAAGCTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
17 1 0.02
18 47 0.82
19 9 0.16
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (18 bp):
TTTTTTTTTTTTTTGTTT
Found at i:5201671 original size:39 final size:39
Alignment explanation
Indices: 5201552--5201803 Score: 422
Period size: 39 Copynumber: 6.5 Consensus size: 39
5201542 TTTTTCCGAA
* *
5201552 GCTCCTCTAAACAG-GACCACGACTTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGAC-TTTGAAAAGTAAATT
5201590 GCTCCTCTAAACAGAGGC-ACGACTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
5201627 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
5201666 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
5201705 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
5201744 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTT-GAAAAGTAAATT
5201786 GCTCCTCTAAACAGAGGC
1 GCTCCTCTAAACAGAGGC
5201804 GACTGAATGC
Statistics
Matches: 207, Mismatches: 1, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
37 32 0.15
38 28 0.14
39 109 0.53
41 8 0.04
42 30 0.14
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (39 bp):
GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
Found at i:5201907 original size:41 final size:39
Alignment explanation
Indices: 5201821--5202207 Score: 558
Period size: 41 Copynumber: 9.4 Consensus size: 39
5201811 TGCCAACGGA
*
5201821 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACG
1 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG--CAACG
*
5201862 ACTTTGGAAAAGTAAATTGCTCCTCTAAACCGAGGCAACG
1 ACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG
*
5201902 AACTTTGAAAAGGTAAATTGCTCCTCTAAACAGAGGTACCACG
1 -ACTTTGAAAA-GTAAATTGCTCCTCTAAACAGAGG--CAACG
5201945 ACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 ACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACG
5201987 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG
1 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG
*
5202026 AACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACG
1 -ACTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGG--CAACG
5202069 ACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 ACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACG
5202111 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG
1 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG
5202150 AACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG
1 -ACTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGGCAACG
5202191 AACTTTGAAAAGTAAAT
1 -ACTTTGAAAAGTAAAT
5202208 ACTCCTAGAC
Statistics
Matches: 322, Mismatches: 7, Indels: 35
0.88 0.02 0.10
Matches are distributed among these distances:
39 6 0.02
40 33 0.10
41 163 0.51
42 106 0.33
43 14 0.04
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (39 bp):
ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG
Found at i:5201953 original size:83 final size:81
Alignment explanation
Indices: 5201814--5202207 Score: 584
Period size: 83 Copynumber: 4.8 Consensus size: 81
5201804 GACTGAATGC
5201814 CAACGGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAAT
1 CAAC-GAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG-ACCACGACTTTGGAAAAGTAAAT
*
5201879 TGCTCCTCTAAACCGAGG
64 TGCTCCTCTAAACAGAGG
5201897 CAACGAACTTTGAAAAGGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAAT
1 CAACGAACTTTGAAAA-GTAAATTGCTCCTCTAAACAGAGG-ACCACGACTTTGGAAAAGTAAAT
5201962 TGCTCCTCTAAACAGAGG
64 TGCTCCTCTAAACAGAGG
* *
5201980 CACCACG-ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG-CAACGAACTTTGAAAAAGTAAA
1 CA--ACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGACCACG-ACTTTGGAAAAGTAAA
5202043 TTGCTCCTCTAAACAGAGG
63 TTGCTCCTCTAAACAGAGG
*
5202062 TACCACG-ACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAA
1 --CAACGAACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGG-ACCACGACTTTGGAAAAGTAA
5202125 ATTGCTCCTCTAAACAGAGG
62 ATTGCTCCTCTAAACAGAGG
*
5202145 CAACGAACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGG-CAACGAACTTT-GAAAAGTAAAT
1 CAACGAACTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGGACCACG-ACTTTGGAAAAGTAAAT
5202208 ACTCCTAGAC
Statistics
Matches: 291, Mismatches: 8, Indels: 26
0.90 0.02 0.08
Matches are distributed among these distances:
80 4 0.01
81 25 0.09
82 87 0.30
83 152 0.52
84 16 0.05
85 7 0.02
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (81 bp):
CAACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGACCACGACTTTGGAAAAGTAAATTG
CTCCTCTAAACAGAGG
Found at i:5202042 original size:124 final size:123
Alignment explanation
Indices: 5201821--5202207 Score: 688
Period size: 124 Copynumber: 3.1 Consensus size: 123
5201811 TGCCAACGGA
*
5201821 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATTGCTCCT
1 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCT
* *
5201886 CTAAACCGAGGCAACGAACTTTGAAAAGGTAAATTGCTCCTCTAAACAGAGGTACCACG
65 CTAAACAGAGGCAACGAACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACG
5201945 ACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCT
1 ACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCT
5202010 CTAAACAGAGGCAACGAACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACG
65 CTAAACAGAGGCAACGAACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACG
5202069 ACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCT
1 ACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCT
*
5202134 CTAAACAGAGGCAACGAACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGG--CAACG
65 CTAAACAGAGGCAACGAACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACG
5202191 AACTTTGAAAAGTAAAT
1 -ACTTTGAAAAGTAAAT
5202208 ACTCCTAGAC
Statistics
Matches: 257, Mismatches: 4, Indels: 6
0.96 0.01 0.02
Matches are distributed among these distances:
122 15 0.06
123 5 0.02
124 197 0.77
125 40 0.16
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (123 bp):
ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTC
TAAACAGAGGCAACGAACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACG
Found at i:5203410 original size:8 final size:8
Alignment explanation
Indices: 5203397--5203426 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
5203387 TTTGGATCTC
5203397 TTTTTTCA
1 TTTTTTCA
5203405 TTTTTTTCA
1 -TTTTTTCA
5203414 TTTTTTCA
1 TTTTTTCA
5203422 TTTTT
1 TTTTT
5203427 CTTTTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTCA
Found at i:5203411 original size:9 final size:9
Alignment explanation
Indices: 5203397--5203426 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5203387 TTTGGATCTC
5203397 TTTTTTCAT
1 TTTTTTCAT
5203406 TTTTTTCA-
1 TTTTTTCAT
5203414 TTTTTTCAT
1 TTTTTTCAT
5203423 TTTT
1 TTTT
5203427 CTTTTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:5207439 original size:66 final size:62
Alignment explanation
Indices: 5207302--5207486 Score: 259
Period size: 66 Copynumber: 3.0 Consensus size: 62
5207292 TTTTTTGTAG
5207302 GGAAAATTGATACTTTCAACTTTTTCCC-AAAAATA-TTTTTTTT-GAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTTTTTTTTGGAAATTTTGATTTTCAA
** *
5207362 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAAATTTATTTTTCTTTTA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTTGGAAA-TT-TTGAT-TTTCA
5207427 A
62 A
* *
5207428 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAATTTTTTATTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTTGATTTT
5207487 TGTTTAAAGA
Statistics
Matches: 113, Mismatches: 5, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
59 7 0.06
60 27 0.24
62 11 0.10
63 8 0.07
64 4 0.04
65 16 0.14
66 40 0.35
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (62 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTTGATTTTCAA
Found at i:5207574 original size:12 final size:12
Alignment explanation
Indices: 5207548--5207603 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
5207538 AACCTAATCT
*
5207548 AATAAATAA-AA
1 AATAAAAAATAA
5207559 AATAAAAAATAA
1 AATAAAAAATAA
5207571 AATAAACAAATAA
1 AATAAA-AAATAA
*
5207584 ACA-AAGAAATAA
1 A-ATAAAAAATAA
5207596 AA-AAAAAA
1 AATAAAAAA
5207604 AAACTGGAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
11 14 0.36
12 15 0.38
13 9 0.23
14 1 0.03
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:5207880 original size:19 final size:19
Alignment explanation
Indices: 5207856--5207900 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
5207846 GAACACCGGT
*
5207856 GCCGGATTCTGGAAAATTC
1 GCCGGAATCTGGAAAATTC
*
5207875 GCCGGAATCTGGAAATTTC
1 GCCGGAATCTGGAAAATTC
5207894 GCCGGAA
1 GCCGGAA
5207901 GTTGGCCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (19 bp):
GCCGGAATCTGGAAAATTC
Found at i:5208533 original size:20 final size:20
Alignment explanation
Indices: 5208508--5208547 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5208498 GGGCTTACCC
5208508 ATTTGGGCCAGG-CCCAATTG
1 ATTTGGGCC-GGACCCAATTG
5208528 ATTTGGGCCGGACCCAATTG
1 ATTTGGGCCGGACCCAATTG
5208548 GGTGTCTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.25
Consensus pattern (20 bp):
ATTTGGGCCGGACCCAATTG
Found at i:5208673 original size:7 final size:8
Alignment explanation
Indices: 5208654--5208707 Score: 58
Period size: 8 Copynumber: 6.6 Consensus size: 8
5208644 TATTAAAAAT
5208654 TAAAATAA
1 TAAAATAA
5208662 TAAAATAA
1 TAAAATAA
5208670 -AAAATAA
1 TAAAATAA
*
5208677 CT-AGATAA
1 -TAAAATAA
5208685 TAATAATAA
1 TAA-AATAA
5208694 TAACAATAA
1 TAA-AATAA
5208703 TAAAA
1 TAAAA
5208708 ATGAAAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 8 0.21
8 16 0.41
9 15 0.38
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (8 bp):
TAAAATAA
Found at i:5208689 original size:3 final size:3
Alignment explanation
Indices: 5208657--5208723 Score: 54
Period size: 3 Copynumber: 23.0 Consensus size: 3
5208647 TAAAAATTAA
*
5208657 AAT AAT AA- AAT AA- AA- AAT AACT AGAT AAT AAT AAT AAT AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T A-AT AAT AAT AAT AAT AAT AAT
*
5208701 AAT AAA AAT GAA- AAT AA- AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT
5208724 TTCATAACTT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
2 10 0.19
3 36 0.68
4 6 0.11
5 1 0.02
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:5209159 original size:16 final size:16
Alignment explanation
Indices: 5209118--5209152 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5209108 AAATTCTAAT
**
5209118 ACCCTAAAACCTCAAA
1 ACCCTAAAATTTCAAA
5209134 ACCCTAAAATTTCAAA
1 ACCCTAAAATTTCAAA
5209150 ACC
1 ACC
5209153 TTCAAATAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (16 bp):
ACCCTAAAATTTCAAA
Found at i:5209472 original size:2 final size:2
Alignment explanation
Indices: 5209465--5209491 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5209455 GGGATCTTAA
5209465 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5209492 GTTACACCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5210413 original size:26 final size:25
Alignment explanation
Indices: 5210384--5210434 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
5210374 CAAGTGTTGG
5210384 ATTTAATTGAT-TTTATTTTATATTTT
1 ATTTAATT-ATCTTTATTTTA-ATTTT
*
5210410 ATTTAATTCTCTTTATTTTAATTTT
1 ATTTAATTATCTTTATTTTAATTTT
5210435 TCAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (25 bp):
ATTTAATTATCTTTATTTTAATTTT
Found at i:5213439 original size:24 final size:24
Alignment explanation
Indices: 5213411--5213459 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
5213401 TATATGTATA
5213411 AGTACAACAAAAGTAATTGTCATT
1 AGTACAACAAAAGTAATTGTCATT
*
5213435 AGTACAACAAAAGTAATTGTTATT
1 AGTACAACAAAAGTAATTGTCATT
5213459 A
1 A
5213460 TCTCTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (24 bp):
AGTACAACAAAAGTAATTGTCATT
Found at i:5219800 original size:24 final size:24
Alignment explanation
Indices: 5219744--5219811 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
5219734 TTTTAAACCC
*
5219744 TAAAAT-CTGAAACCTTAAAA-CT
1 TAAAATCCTAAAACCTTAAAATCT
**
5219766 CCAAATCCTAAAACCTTAAAATCT
1 TAAAATCCTAAAACCTTAAAATCT
*
5219790 TAAAATCCTAAAACCTTCAAAT
1 TAAAATCCTAAAACCTTAAAAT
5219812 AAAACCCTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.11
23 13 0.34
24 21 0.55
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (24 bp):
TAAAATCCTAAAACCTTAAAATCT
Found at i:5219801 original size:16 final size:16
Alignment explanation
Indices: 5219738--5219811 Score: 57
Period size: 16 Copynumber: 4.8 Consensus size: 16
5219728 CTAAAATTTT
* *
5219738 AAACCCTAAAAT-CTG
1 AAACCTTAAAATCCTA
5219753 AAACCTTAAAACTCC-A
1 AAACCTTAAAA-TCCTA
*
5219769 AATCC-TAAAA-CCTTA
1 AAACCTTAAAATCC-TA
*
5219784 AAATCTTAAAATCCTA
1 AAACCTTAAAATCCTA
*
5219800 AAACCTTCAAAT
1 AAACCTTAAAAT
5219812 AAAACCCTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
13 2 0.04
15 19 0.41
16 22 0.48
17 3 0.07
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.24
Consensus pattern (16 bp):
AAACCTTAAAATCCTA
Found at i:5221638 original size:89 final size:89
Alignment explanation
Indices: 5221487--5221664 Score: 295
Period size: 89 Copynumber: 2.0 Consensus size: 89
5221477 CCTTGGCCTC
* *
5221487 ACGGTTTTGTCCTACAAAAGGTGTCTCATAAGAAAGAGGTGGTGTGAACCCTTTTATACCCCAGT
1 ACGGTTTTGTCCTACAAAAAGTGTCTCACAAGAAAGAGGTGGTGTGAACCCTTTTATACCCCAGT
5221552 GA-CCCTCTTATTATATTCGATGTG
66 GACCCCTC-TATTATATTCGATGTG
* * *
5221576 ACGGTTTTGTCTTACAAAAAGTGTCTCACAAGGAAGAGGTGGTGTGAACCTTTTTATACCCCAGT
1 ACGGTTTTGTCCTACAAAAAGTGTCTCACAAGAAAGAGGTGGTGTGAACCCTTTTATACCCCAGT
5221641 GACCCCTCTATTATATTCGATGTG
66 GACCCCTCTATTATATTCGATGTG
5221665 GGATTCAGGA
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 78 0.94
90 5 0.06
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (89 bp):
ACGGTTTTGTCCTACAAAAAGTGTCTCACAAGAAAGAGGTGGTGTGAACCCTTTTATACCCCAGT
GACCCCTCTATTATATTCGATGTG
Found at i:5222670 original size:15 final size:15
Alignment explanation
Indices: 5222650--5222679 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5222640 CATGTTAATC
*
5222650 AACCATTCATTAGAT
1 AACCATTCATCAGAT
5222665 AACCATTCATCAGAT
1 AACCATTCATCAGAT
5222680 TGGAAAAACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (15 bp):
AACCATTCATCAGAT
Found at i:5226252 original size:14 final size:15
Alignment explanation
Indices: 5226235--5226263 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5226225 TTAAAAAATA
5226235 TTAAAAT-ATAATTT
1 TTAAAATAATAATTT
5226249 TTAAAATAATAATTT
1 TTAAAATAATAATTT
5226264 AATATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAAAATAATAATTT
Found at i:5226825 original size:25 final size:25
Alignment explanation
Indices: 5226797--5226875 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 25
5226787 CCTTGCCAAC
5226797 AAACACCACAAAAAAAAAAAAAACA
1 AAACACCACAAAAAAAAAAAAAACA
* *
5226822 AAACACTACAAAAAAAAAAAAACCCA
1 AAACACCACAAAAAAAAAAAAA-ACA
* *
5226848 AAA-ACCACTAGCAAAGAAAAAAAACA
1 AAACACCAC-A-AAAAAAAAAAAAACA
5226874 AA
1 AA
5226876 GAGTTTTTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
25 25 0.56
26 10 0.22
27 10 0.22
ACGTcount: A:0.75, C:0.20, G:0.03, T:0.03
Consensus pattern (25 bp):
AAACACCACAAAAAAAAAAAAAACA
Found at i:5227726 original size:7 final size:8
Alignment explanation
Indices: 5227704--5227758 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
5227694 AATAAACCTT
5227704 ATAAAATA
1 ATAAAATA
5227712 ATAAAATA
1 ATAAAATA
5227720 A-AAAATA
1 ATAAAATA
*
5227727 ACT-AGATA
1 A-TAAAATA
*
5227735 ATAATAACA
1 ATAA-AATA
5227744 ATAACAATA
1 ATAA-AATA
5227753 ATAAAA
1 ATAAAA
5227759 ATGAAAATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
7 8 0.21
8 17 0.45
9 13 0.34
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (8 bp):
ATAAAATA
Found at i:5227726 original size:15 final size:16
Alignment explanation
Indices: 5227706--5227759 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 16
5227696 TAAACCTTAT
5227706 AAAATAATAA-AATAA
1 AAAATAATAATAATAA
5227721 AAAATAACTAGATAATAA
1 AAAATAA-TA-ATAATAA
*
5227739 TAACAATAACAATAATAA
1 -AA-AATAATAATAATAA
5227757 AAA
1 AAA
5227760 TGAAAATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
15 7 0.21
16 3 0.09
17 3 0.09
18 12 0.36
19 3 0.09
20 5 0.15
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (16 bp):
AAAATAATAATAATAA
Found at i:5230303 original size:251 final size:250
Alignment explanation
Indices: 5229858--5230596 Score: 1293
Period size: 251 Copynumber: 3.0 Consensus size: 250
5229848 TGAGAGTATT
*
5229858 GAGTCTAAAGTAACAAGCACAACAACGTAAAAATCGTAATAAATTTATAACAATAGATAACAATC
1 GAGTCTAAAGTAACAAGCACAACAACGTAGAAATCGTAATAAATTTATAACAATAGATAACAATC
*
5229923 AATAATTCAAAATAT--AAAAAAAAAATAAAGCACATCAAGATTTATATAAAAAATCTTTCAATG
66 AATAATTCAAAATATAAAAAAAAAAAATAAAGCACATCAAGATTTATATAAAAAATCTTTCAGTG
* *
5229986 TAGAAAAAAAAATTACAAATCAACAAAAATCTTCACTGTCAAATAATAGATATACAAAATTTTTC
131 TAGAAAAAAAAATTACAAATCAACAAAAATCTTCACTATCAAATAATAGATATACAAAGTTTTTC
5230051 TCTAGTTAAAACTTGATTTAATCAACAACTAAAGAAACAATTGAAGAAATCTAAA
196 TCTAGTTAAAACTTGATTTAATCAACAACTAAAGAAACAATTGAAGAAATCTAAA
*
5230106 GAGTTTAAAGTAACAAGCACAACAACGTAGAAATCGTAATAAATTTATAACAATAGATAACAATC
1 GAGTCTAAAGTAACAAGCACAACAACGTAGAAATCGTAATAAATTTATAACAATAGATAACAATC
5230171 AATAATTCAAAATATAAAAAAAAAAAAATAAAGCACATCAAGATTTATATAAAAAATCTTTCAGT
66 AATAATTCAAAATAT-AAAAAAAAAAAATAAAGCACATCAAGATTTATATAAAAAATCTTTCAGT
*
5230236 GTAGAAAAAAAAATTATAAATCAACAAAAATCTTCACTATCAAATAATAGATATACAAAGTTTTT
130 GTAGAAAAAAAAATTACAAATCAACAAAAATCTTCACTATCAAATAATAGATATACAAAGTTTTT
*
5230301 CTCTAGTTAAAACTTGATTTAATCAACAACTAAAGAGACAATTGAAGAAATCTAAA
195 CTCTAGTTAAAACTTGATTTAATCAACAACTAAAGAAACAATTGAAGAAATCTAAA
5230357 GAGTCTAAAGTAACAAGCACAACAACGTAGAAATCGTAATAAATTTATAACAATAGATAACAATC
1 GAGTCTAAAGTAACAAGCACAACAACGTAGAAATCGTAATAAATTTATAACAATAGATAACAATC
5230422 AATAATTCAAAATATAAAAAAAAAAAATAAAGCACATCAAGATTTATATAAAAAATCTTTCAGTG
66 AATAATTCAAAATATAAAAAAAAAAAATAAAGCACATCAAGATTTATATAAAAAATCTTTCAGTG
*
5230487 TA-AAAAAAAAATTACAAATTAAC-AAAAT-TTCACTATCAAATAAT--ATATACAAAGTTTCTT
131 TAGAAAAAAAAATTACAAATCAACAAAAATCTTCACTATCAAATAATAGATATACAAAGTTT-TT
*
5230547 CTCTAGTTAAAAACTTGA--TAATCAACAAAT-AA-AAACAATTGAAGAAATCT
195 CTCTAGTT-AAAACTTGATTTAATCAACAACTAAAGAAACAATTGAAGAAATCT
5230597 CATTAAATAA
Statistics
Matches: 474, Mismatches: 12, Indels: 15
0.95 0.02 0.03
Matches are distributed among these distances:
243 17 0.04
244 2 0.00
245 24 0.05
246 10 0.02
247 25 0.05
248 83 0.18
249 19 0.04
250 52 0.11
251 242 0.51
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.26
Consensus pattern (250 bp):
GAGTCTAAAGTAACAAGCACAACAACGTAGAAATCGTAATAAATTTATAACAATAGATAACAATC
AATAATTCAAAATATAAAAAAAAAAAATAAAGCACATCAAGATTTATATAAAAAATCTTTCAGTG
TAGAAAAAAAAATTACAAATCAACAAAAATCTTCACTATCAAATAATAGATATACAAAGTTTTTC
TCTAGTTAAAACTTGATTTAATCAACAACTAAAGAAACAATTGAAGAAATCTAAA
Found at i:5239293 original size:22 final size:22
Alignment explanation
Indices: 5239253--5239297 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
5239243 TAAATTATAA
5239253 ATTTGTTAATTAATATAATATTT
1 ATTTGTTAATTAATATAAT-TTT
5239276 ATTT-TTAATGTAAT-TAATTTT
1 ATTTGTTAAT-TAATATAATTTT
5239297 A
1 A
5239298 AATGATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.19
22 9 0.43
23 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
ATTTGTTAATTAATATAATTTT
Found at i:5239390 original size:29 final size:30
Alignment explanation
Indices: 5239358--5239436 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
5239348 AGTTAATAAA
*
5239358 TTTATAATTTAAATATTATATTAA-ATATT
1 TTTATAATTTAAATATTATACTAACATATT
* * * *
5239387 TTTAAAAATTAAATATTATACTAACTTTTT
1 TTTATAATTTAAATATTATACTAACATATT
*
5239417 TATTATAATTTAAAAATTAT
1 T-TTATAATTTAAATATTAT
5239437 TAGGAACATT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 21 0.52
30 4 0.10
31 15 0.38
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTATAATTTAAATATTATACTAACATATT
Found at i:5239992 original size:12 final size:12
Alignment explanation
Indices: 5239975--5240005 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5239965 TCTAATATAA
*
5239975 AAATATTATTAC
1 AAATATTACTAC
5239987 AAATATTACTAC
1 AAATATTACTAC
5239999 AAATATT
1 AAATATT
5240006 TTAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATATTACTAC
Found at i:5241804 original size:2 final size:2
Alignment explanation
Indices: 5241797--5241840 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5241787 AGCAATATTT
5241797 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5241839 GA
1 GA
5241841 AGCACAATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5247168 original size:17 final size:18
Alignment explanation
Indices: 5247138--5247171 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5247128 TACTAACACA
5247138 TTAATAAATAATTTTTTT
1 TTAATAAATAATTTTTTT
*
5247156 TTAA-AAATTATTTTTT
1 TTAATAAATAATTTTTT
5247172 ATATATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAATAAATAATTTTTTT
Found at i:5247169 original size:14 final size:15
Alignment explanation
Indices: 5247142--5247200 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 15
5247132 AACACATTAA
*
5247142 TAAATAATTTTTTTT
1 TAAATAATTATTTTT
5247157 TAAA-AATTATTTTT
1 TAAATAATTATTTTT
* *
5247171 TATAT-ATT-TATTT
1 TAAATAATTATTTTT
5247184 TAAATAA-TATTTATT
1 TAAATAATTATTT-TT
5247199 TA
1 TA
5247201 TTATTAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
13 9 0.26
14 18 0.51
15 8 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TAAATAATTATTTTT
Found at i:5247184 original size:27 final size:27
Alignment explanation
Indices: 5247154--5247205 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
5247144 AATAATTTTT
5247154 TTTTAAA-AATTATTT-TTTATATATTTA
1 TTTTAAATAA-TATTTATTTAT-TATTTA
5247181 TTTTAAATAATATTTATTTATTATT
1 TTTTAAATAATATTTATTTATTATT
5247206 AAATAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
TTTTAAATAATATTTATTTATTATTTA
Found at i:5247200 original size:20 final size:19
Alignment explanation
Indices: 5247175--5247219 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
5247165 ATTTTTTATA
5247175 TATTTATT-TTAAATAATATT
1 TATTTATTATTAAATAA-A-T
5247195 TATTTATTATTAAATAAAT
1 TATTTATTATTAAATAAAT
5247214 TATTTA
1 TATTTA
5247220 ATTAATTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.29
20 9 0.38
21 8 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTATTATTAAATAAAT
Found at i:5248617 original size:13 final size:13
Alignment explanation
Indices: 5248601--5248625 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5248591 GGATTAAGTT
5248601 TATATATTAAATA
1 TATATATTAAATA
5248614 TATATATTAAAT
1 TATATATTAAAT
5248626 TTGAATCAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATTAAATA
Found at i:5248771 original size:13 final size:13
Alignment explanation
Indices: 5248739--5248775 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
5248729 CAAAATTTAT
5248739 TTATATATATAAA
1 TTATATATATAAA
*
5248752 TTTTATAT-TAAA
1 TTATATATATAAA
5248764 TTA-ATATATAAA
1 TTATATATATAAA
5248776 AAATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
11 4 0.19
12 10 0.48
13 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTATATATATAAA
Found at i:5251256 original size:187 final size:186
Alignment explanation
Indices: 5251033--5251378 Score: 496
Period size: 187 Copynumber: 1.9 Consensus size: 186
5251023 CATTCAAGAT
* *** *
5251033 TTTACTTTTAAAATTATTTTTTATAAAGAGCAAACACTGGTTGACATAAAAAAATTTTTTTTTCT
1 TTTACTTTTAAAATTATTTTTTATAAAGAGCAAACACTGATTGACATAAAAAAAAACTGTTTTCT
* * ** * *
5251098 T-ACTAACTGAATTAATCTTTTAAATAATTTTTTAAAGTTTGTAAACCGATTAAATTAAAGTTAA
66 TAAC-AACTGAACTAATCTTTTAAATAAATTTTTAAAGTAAGCAAACCAATTAAATTAAAGTTAA
5251162 AACCAGGTAAACAAGCACTCAGATTAATTATATTTTGTAAAGATTAAACCTTCAGAC
130 AACCAGGTAAACAAGCACTCAGATTAATTATATTTTGTAAAGATTAAACCTTCAGAC
* *
5251219 TTTACTTTTAAAATTTATTTTTTATAAAGATCAAACACTGATTGATATAAAAAAAAACTGTTTTC
1 TTTACTTTTAAAA-TTATTTTTTATAAAGAGCAAACACTGATTGACATAAAAAAAAACTGTTTTC
* * *
5251284 TTAACAGCTGAACTAATCTTTTAAATAAATTTTTAAAGTAAGCCAGCCAATTAAATTAAAGTTAA
65 TTAACAACTGAACTAATCTTTTAAATAAATTTTTAAAGTAAGCAAACCAATTAAATTAAAGTTAA
* * *
5251349 AACCAGGTAAACATGCCCTTAGATTAATTA
130 AACCAGGTAAACAAGCACTCAGATTAATTA
5251379 ATGGCTAAAG
Statistics
Matches: 139, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
186 13 0.09
187 124 0.89
188 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (186 bp):
TTTACTTTTAAAATTATTTTTTATAAAGAGCAAACACTGATTGACATAAAAAAAAACTGTTTTCT
TAACAACTGAACTAATCTTTTAAATAAATTTTTAAAGTAAGCAAACCAATTAAATTAAAGTTAAA
ACCAGGTAAACAAGCACTCAGATTAATTATATTTTGTAAAGATTAAACCTTCAGAC
Found at i:5252105 original size:12 final size:12
Alignment explanation
Indices: 5252088--5252149 Score: 58
Period size: 12 Copynumber: 5.3 Consensus size: 12
5252078 TTTTTTAATA
5252088 TAAATATAAAAT
1 TAAATATAAAAT
5252100 TAAATATATAAA-
1 TAAATATA-AAAT
* *
5252112 TATATGT-AAA-
1 TAAATATAAAAT
*
5252122 TAAATATATAAT
1 TAAATATAAAAT
*
5252134 TAAATATATAAT
1 TAAATATAAAAT
5252146 TAAA
1 TAAA
5252150 AAATAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
10 8 0.19
11 2 0.05
12 29 0.69
13 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (12 bp):
TAAATATAAAAT
Found at i:5252247 original size:112 final size:113
Alignment explanation
Indices: 5252121--5252342 Score: 349
Period size: 113 Copynumber: 2.0 Consensus size: 113
5252111 ATATATGTAA
* * * *
5252121 ATAAATATATAATTAAATATATAATTAAAAAATAATTTTTTA-TATATATCTGATCAAATAAAAT
1 ATAAATATAAAATTAAATAAATAATTAAAAAATAAATTTTTACAATATATCTGATCAAATAAAAT
*
5252185 CGAATACG-CTTAAAACTTAATCCCGATCCGATCTCAAATTTTTTTAAT
66 CAAATACGTC-TAAAACTTAATCCCGATCCGATCTCAAATTTTTTTAAT
*
5252233 ATAAATATAAAATTAAATAAATAATTAAAAAATAAATTTTTACAATATATTTGATCAAATAAAAT
1 ATAAATATAAAATTAAATAAATAATTAAAAAATAAATTTTTACAATATATCTGATCAAATAAAAT
* *
5252298 TAAATACGTCTAAAACTTAATCTCGATCCGATCTCAAATTTTTTT
66 CAAATACGTCTAAAACTTAATCCCGATCCGATCTCAAATTTTTTT
5252343 TTATATTATT
Statistics
Matches: 100, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
112 39 0.39
113 60 0.60
114 1 0.01
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (113 bp):
ATAAATATAAAATTAAATAAATAATTAAAAAATAAATTTTTACAATATATCTGATCAAATAAAAT
CAAATACGTCTAAAACTTAATCCCGATCCGATCTCAAATTTTTTTAAT
Found at i:5260522 original size:150 final size:150
Alignment explanation
Indices: 5260251--5260550 Score: 440
Period size: 150 Copynumber: 2.0 Consensus size: 150
5260241 TAAAAATTTA
* * *
5260251 TTTGATAATGAATTAGATTTGGAATATGCTATTTTGAGTTAGACCAAAACAAATATATTTGTGTA
1 TTTGATAATGAATTAGATTTGGAATAGGATATTTTGAGTTAGAACAAAACAAATATATTTGTGTA
* *
5260316 TTTTTATTATTGATTTGAGCTTGTTATTTTATGTGTGGGTTCTACGTGTACGTGTTGATTTTTTT
66 TTTTTATTATTGATTTGAGCTTATTATTTTATGTGTGGGTTCTACGTGTACGTGTTGATTTTTCT
*
5260381 AACAAGTAGTATTAGAGCAT
131 AACAAGTAGTATTAAAGCAT
* * * * *
5260401 TTTGATAGTGGATTAGGTTTGGAGTAGGATATTTTGAGTTA-AACAGAAATAAATATATTTGTGT
1 TTTGATAATGAATTAGATTTGGAATAGGATATTTTGAGTTAGAACA-AAACAAATATATTTGTGT
* ** *
5260465 ATTTTTATTATTGATTTGAGGTTATTATTTTATGTGTGGGTTCTGTGTGTGCGTGTTGATTTTTC
65 ATTTTTATTATTGATTTGAGCTTATTATTTTATGTGTGGGTTCTACGTGTACGTGTTGATTTTTC
*
5260530 TAACAAGTGGTATTAAAGCAT
130 TAACAAGTAGTATTAAAGCAT
5260551 GGTTCAAGAC
Statistics
Matches: 133, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
149 3 0.02
150 130 0.98
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.46
Consensus pattern (150 bp):
TTTGATAATGAATTAGATTTGGAATAGGATATTTTGAGTTAGAACAAAACAAATATATTTGTGTA
TTTTTATTATTGATTTGAGCTTATTATTTTATGTGTGGGTTCTACGTGTACGTGTTGATTTTTCT
AACAAGTAGTATTAAAGCAT
Found at i:5263604 original size:3 final size:3
Alignment explanation
Indices: 5263596--5263623 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5263586 CTCCATTGAT
5263596 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
5263624 ACAATCGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5264360 original size:93 final size:93
Alignment explanation
Indices: 5264253--5264434 Score: 301
Period size: 93 Copynumber: 2.0 Consensus size: 93
5264243 GTTTTTTACG
* * * *
5264253 ATTCGTTTTTGTTTTGGTTCTTCCTCTTTATCATCTGAGTTCTTCTGGTTACCATGAAATATATC
1 ATTCATTTTTGTTTTGGGTCTTCCTCTTTACCATCTGAGTTCTTCAGGTTACCATGAAATATATC
5264318 TTTCAATGTGAGAGGTTTAGCTAATTTT
66 TTTCAATGTGAGAGGTTTAGCTAATTTT
* *
5264346 ATTCATTTTTGTTTTGGGTCTTCCTCTTTACCCTCTGAGTTCTTCAGGTTACTATGAAATATATC
1 ATTCATTTTTGTTTTGGGTCTTCCTCTTTACCATCTGAGTTCTTCAGGTTACCATGAAATATATC
*
5264411 TTTCAATGTGGGAGGTTTAGCTAA
66 TTTCAATGTGAGAGGTTTAGCTAA
5264435 CTCTCGGGCT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 82 1.00
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47
Consensus pattern (93 bp):
ATTCATTTTTGTTTTGGGTCTTCCTCTTTACCATCTGAGTTCTTCAGGTTACCATGAAATATATC
TTTCAATGTGAGAGGTTTAGCTAATTTT
Found at i:5280336 original size:20 final size:19
Alignment explanation
Indices: 5280297--5280336 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5280287 TATTTTTTAG
**
5280297 TAAAAATTTTAAAATTAAT
1 TAAAAATTTTAAAAGAAAT
5280316 TAAAAATTATTAAAAGAAAT
1 TAAAAATT-TTAAAAGAAAT
5280336 T
1 T
5280337 TAAGTTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TAAAAATTTTAAAAGAAAT
Found at i:5281529 original size:22 final size:21
Alignment explanation
Indices: 5281491--5281533 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
5281481 ATAACAATAT
5281491 CATAAAAAAACATAAAAATCAA
1 CATAAAAAAAC-TAAAAATCAA
5281513 CATAAAAAAA-TCAAAAATCAA
1 CATAAAAAAACT-AAAAATCAA
5281534 ATCAAATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.05
21 9 0.45
22 10 0.50
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (21 bp):
CATAAAAAAACTAAAAATCAA
Found at i:5282055 original size:39 final size:39
Alignment explanation
Indices: 5281998--5282324 Score: 323
Period size: 39 Copynumber: 8.5 Consensus size: 39
5281988 AGAGGTTATG
* * * *
5281998 CAAAATTTAAATTTAAAAGGCTTCTCTCACCAAAGGTAA
1 CAAACTTTAAATTTAAAAGGCTCCTCTAACCAAAGGCAA
* * *
5282037 CAAACTTTAAATTCAAAAGTGATCCTTTAACCAAAGGCAA
1 CAAACTTTAAATTTAAAAG-GCTCCTCTAACCAAAGGCAA
* *
5282077 CAAACTTTAAATGATAAAAGGC-CCTTCTCACCAAAGGCAA
1 CAAACTTTAAAT-TTAAAAGGCTCC-TCTAACCAAAGGCAA
*
5282117 CAAACTTTAAATTCTAAAA-GCTCCTTTAACCAAAGGCAA
1 CAAACTTTAAATT-TAAAAGGCTCCTCTAACCAAAGGCAA
*
5282156 CAAACTTTAAATATTAAAA-GCTCCTCTGACCAAAGGCAA
1 CAAACTTTAAAT-TTAAAAGGCTCCTCTAACCAAAGGCAA
* * * *
5282195 CGAACTTTAAATTTAAAAAGCTCATTTAACCAAAGGCAA
1 CAAACTTTAAATTTAAAAGGCTCCTCTAACCAAAGGCAA
* * * *
5282234 TAAACTTTAAATGTTGAAAA-GCTCTTTTAACCAGAGGCAA
1 CAAACTTTAAAT-TT-AAAAGGCTCCTCTAACCAAAGGCAA
* *
5282274 CGAACTTTAAA--T----GGCTCCTTTAACCAAAGGCAA
1 CAAACTTTAAATTTAAAAGGCTCCTCTAACCAAAGGCAA
*
5282307 CAAACTTTAAATTAAAAA
1 CAAACTTTAAATTTAAAA
5282325 TCTAAGAGGA
Statistics
Matches: 241, Mismatches: 31, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
33 28 0.12
37 1 0.00
38 6 0.02
39 107 0.44
40 90 0.37
41 9 0.04
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.25
Consensus pattern (39 bp):
CAAACTTTAAATTTAAAAGGCTCCTCTAACCAAAGGCAA
Found at i:5282158 original size:79 final size:77
Alignment explanation
Indices: 5282022--5282318 Score: 347
Period size: 79 Copynumber: 3.8 Consensus size: 77
5282012 AAAAGGCTTC
* * *
5282022 TCTCACCAAAGGTAACAAACTTTAAATTCAAAAGTGATCCTTTAACCAAAGGCAACAAACTTTAA
1 TCTCACCAAAGGCAACAAACTTTAAATTTAAAA--GCTCCTTTAACCAAAGGCAACAAACTTTAA
5282087 ATGATAAAAGGCCCT
64 ATGATAAAA-GCCCT
5282102 TCTCACCAAAGGCAACAAACTTTAAATTCTAAAAGCTCCTTTAACCAAAGGCAACAAACTTTAAA
1 TCTCACCAAAGGCAACAAACTTTAAATT-TAAAAGCTCCTTTAACCAAAGGCAACAAACTTTAAA
5282167 T-ATTAAAAGCTCC-
65 TGA-TAAAAGC-CCT
* * * *
5282180 TCTGACCAAAGGCAACGAACTTTAAATTTAAAAAGCTCATTTAACCAAAGGCAATAAACTTTAAA
1 TCTCACCAAAGGCAACAAACTTTAAATTT-AAAAGCTCCTTTAACCAAAGGCAACAAACTTTAAA
* *
5282245 TGTTGAAAAGCTCT
65 TGAT-AAAAGCCCT
* * * * *
5282259 TTTAACCAGAGGCAACGAACTTTAAA--T---GGCTCCTTTAACCAAAGGCAACAAACTTTAAAT
1 TCTCACCAAAGGCAACAAACTTTAAATTTAAAAGCTCCTTTAACCAAAGGCAACAAACTTTAAAT
5282319 TAAAAATCTA
Statistics
Matches: 195, Mismatches: 15, Indels: 21
0.84 0.06 0.09
Matches are distributed among these distances:
73 30 0.15
77 2 0.01
78 65 0.33
79 67 0.34
80 27 0.14
81 4 0.02
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (77 bp):
TCTCACCAAAGGCAACAAACTTTAAATTTAAAAGCTCCTTTAACCAAAGGCAACAAACTTTAAAT
GATAAAAGCCCT
Found at i:5282305 original size:33 final size:33
Alignment explanation
Indices: 5282254--5282318 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
5282244 ATGTTGAAAA
* * *
5282254 GCTCTTTTAACCAGAGGCAACGAACTTTAAATG
1 GCTCCTTTAACCAAAGGCAACAAACTTTAAATG
5282287 GCTCCTTTAACCAAAGGCAACAAACTTTAAAT
1 GCTCCTTTAACCAAAGGCAACAAACTTTAAAT
5282319 TAAAAATCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (33 bp):
GCTCCTTTAACCAAAGGCAACAAACTTTAAATG
Found at i:5282482 original size:39 final size:40
Alignment explanation
Indices: 5282412--5282535 Score: 153
Period size: 41 Copynumber: 3.1 Consensus size: 40
5282402 TCTTGAAATT
* * * * *
5282412 AAAATGCTCATCTAATCAGACGCAACGAACTTTAAATTCA
1 AAAAAGCTCCTCTAACCAGAGGCAACAAACTTTAAATTCA
* *
5282452 AAAAA-CTCCTCTGAA-CAGAGGTAACAAACTTTAAATGTTA
1 AAAAAGCTCCTCT-AACCAGAGGCAACAAACTTTAAAT-TCA
5282492 AAAAAGCTCCTCTAACCAGAGGCAACAAACTTTAAATTCA
1 AAAAAGCTCCTCTAACCAGAGGCAACAAACTTTAAATTCA
5282532 AAAA
1 AAAA
5282536 TTTAAGAGGC
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
39 24 0.33
40 21 0.29
41 27 0.38
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (40 bp):
AAAAAGCTCCTCTAACCAGAGGCAACAAACTTTAAATTCA
Found at i:5290697 original size:12 final size:12
Alignment explanation
Indices: 5290682--5290707 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5290672 ATTACAGCCA
5290682 TCTCTTTTTAAG
1 TCTCTTTTTAAG
5290694 TCTCTTTTTAAG
1 TCTCTTTTTAAG
5290706 TC
1 TC
5290708 CTAGTCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.19, G:0.08, T:0.58
Consensus pattern (12 bp):
TCTCTTTTTAAG
Found at i:5295082 original size:14 final size:13
Alignment explanation
Indices: 5295048--5295085 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
5295038 ATAACAATAT
5295048 CATAAAAAAT-AA
1 CATAAAAAATCAA
5295060 CAT-AAAAATCAA
1 CATAAAAAATCAA
5295072 CATTAAAAAATCAA
1 CA-TAAAAAATCAA
5295086 AATCAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.26
12 7 0.30
13 1 0.04
14 9 0.39
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.18
Consensus pattern (13 bp):
CATAAAAAATCAA
Found at i:5295651 original size:22 final size:22
Alignment explanation
Indices: 5295582--5295652 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
5295572 TCGAAATTTT
5295582 TTTTTTTTTATGTTTGTTG-T-TG
1 TTTTTTTTT-TGTTT-TTGTTCTG
* * **
5295604 TTTTTTTTATTGTGTGT-TTCCC
1 TTTTTTTT-TTGTTTTTGTTCTG
5295626 TTTTTTTTTTGTTTTTGTTCTG
1 TTTTTTTTTTGTTTTTGTTCTG
5295648 TTTTT
1 TTTTT
5295653 ACAAAACTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
21 8 0.22
22 28 0.76
23 1 0.03
ACGTcount: A:0.03, C:0.06, G:0.14, T:0.77
Consensus pattern (22 bp):
TTTTTTTTTTGTTTTTGTTCTG
Found at i:5297283 original size:152 final size:152
Alignment explanation
Indices: 5297007--5297309 Score: 581
Period size: 152 Copynumber: 2.0 Consensus size: 152
5296997 ACTATTGAAC
5297007 TGACCTATCCATTACTAAGGATACTGAAATTAAGATGGGTGATCACCAAATCAAGTCGAATCCTT
1 TGACCTATCCATTACTAAGGATACTGAAATTAAGATGGGTGATCACCAAATCAAGTCGAATCCTT
5297072 AGCTGATCATGATTGCACATGAAATAAAATATTTTGTATATATGGAAATCAGATTGCATGGTGTG
66 AGCTGATCATGATTGCACATGAAATAAAATATTTTGTATATATGGAAATCAGATTGCATGGTGTG
5297137 GTGTGGAAACTGAATTAATTTG
131 GTGTGGAAACTGAATTAATTTG
*
5297159 TGACCTATCCATTACTAAGGATACTGAAATTAAGATGGGTGATCACCAAATCAGGTCGAATCCAT
1 TGACCTATCCATTACTAAGGATACTGAAATTAAGATGGGTGATCACCAAATCAAGTCGAATCC-T
5297224 T-GCTGATCATGATTGCACATGAAATAAAATATTTTGTATATATGGAAATCAGATTGCATGGTGT
65 TAGCTGATCATGATTGCACATGAAATAAAATATTTTGTATATATGGAAATCAGATTGCATGGTGT
5297288 GGTGTGGAAACTGAATTAATTT
130 GGTGTGGAAACTGAATTAATTT
5297310 ATCCTGAAAT
Statistics
Matches: 149, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
152 147 0.99
153 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (152 bp):
TGACCTATCCATTACTAAGGATACTGAAATTAAGATGGGTGATCACCAAATCAAGTCGAATCCTT
AGCTGATCATGATTGCACATGAAATAAAATATTTTGTATATATGGAAATCAGATTGCATGGTGTG
GTGTGGAAACTGAATTAATTTG
Found at i:5301598 original size:27 final size:26
Alignment explanation
Indices: 5301558--5301617 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
5301548 TTTTTCATTA
5301558 AATTTTTTTTCAATCGCAACTACAAT
1 AATTTTTTTTCAATCGCAACTACAAT
* * *
5301584 AATTTATTTTTCAATTGCAGCTACGAT
1 AATTT-TTTTTCAATCGCAACTACAAT
*
5301611 AAATTTT
1 AATTTTT
5301618 ATTACTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (26 bp):
AATTTTTTTTCAATCGCAACTACAAT
Found at i:5308702 original size:6 final size:6
Alignment explanation
Indices: 5308664--5308701 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
5308654 ACAAGCCTAC
*
5308664 AAAAGT -AAAGT AAAAGT AAAAGT AAAAGC AAAAG- AAAA
1 AAAAGT AAAAGT AAAAGT AAAAGT AAAAGT AAAAGT AAAA
5308702 AAAAACTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
5 9 0.30
6 21 0.70
ACGTcount: A:0.71, C:0.03, G:0.16, T:0.11
Consensus pattern (6 bp):
AAAAGT
Found at i:5309474 original size:6 final size:6
Alignment explanation
Indices: 5309463--5309490 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5309453 ATAAGATTTT
5309463 TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTAT
5309491 TATATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:5310278 original size:132 final size:133
Alignment explanation
Indices: 5310120--5310392 Score: 406
Period size: 132 Copynumber: 2.1 Consensus size: 133
5310110 ATGCTCATAC
*
5310120 TATTTAAAAAAAAATTGACAACATTGTATGAGAGAAAAATAAGTATAAATAAAGTTATGCTTATT
1 TATTT-AAAAAAAATTGACAACATTGTATGAGAGAAAAACAAGTATAAATAAAGTTATGCTTATT
* * *
5310185 AAAAAGCTTACAACTTTACAATAAGGGATAGATGATCAATTATAGAGTACATGAATGATTTTCAA
65 AAAAAGCTTACAACTTTACAATAAAGGATAGACGATCAATTATAGAGTACATGAATAATTTTCAA
5310250 G-TA
130 GATA
* * *
5310253 TTATTTAAAAAAAA-TGATAGCATTGTATGTGAGAAAAACAAGTATAAATAAAGTTATGCTTATT
1 -TATTTAAAAAAAATTGACAACATTGTATGAGAGAAAAACAAGTATAAATAAAGTTATGCTTATT
* * * * *
5310317 AAAAAGCTTACAACTTTACAGTAAAGGATGGACGATCGATTATAGAGTACTTGAATAATTTTTAA
65 AAAAAGCTTACAACTTTACAATAAAGGATAGACGATCAATTATAGAGTACATGAATAATTTTCAA
5310382 GATA
130 GATA
5310386 TATTTAA
1 TATTTAA
5310393 TCGGATAACT
Statistics
Matches: 126, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
132 111 0.88
133 10 0.08
134 5 0.04
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32
Consensus pattern (133 bp):
TATTTAAAAAAAATTGACAACATTGTATGAGAGAAAAACAAGTATAAATAAAGTTATGCTTATTA
AAAAGCTTACAACTTTACAATAAAGGATAGACGATCAATTATAGAGTACATGAATAATTTTCAAG
ATA
Found at i:5318861 original size:21 final size:22
Alignment explanation
Indices: 5318818--5318861 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
5318808 GTATGCTATA
*
5318818 TTAAAATAATTATAATTTGCCT
1 TTAAAATAATTATAATTTCCCT
**
5318840 TTAAAAT-ATTATTTTTTCCCT
1 TTAAAATAATTATAATTTCCCT
5318861 T
1 T
5318862 AGTTCTCTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.52
Consensus pattern (22 bp):
TTAAAATAATTATAATTTCCCT
Found at i:5336387 original size:2 final size:2
Alignment explanation
Indices: 5336380--5336410 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5336370 CACAGATAGC
5336380 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
5336411 GCATCAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5350513 original size:4 final size:4
Alignment explanation
Indices: 5350499--5350536 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
5350489 TTTATCATAA
*
5350499 TTAT CTAT TTAT TTAT TTAT TTA- TTATT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TTAT TT
5350537 GACTATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
4 24 0.80
5 3 0.10
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:5351071 original size:15 final size:15
Alignment explanation
Indices: 5351048--5351082 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5351038 AGTTCTTGTT
5351048 TAATATTAACAATAA
1 TAATATTAACAATAA
* *
5351063 TAATTTTAATAATAA
1 TAATATTAACAATAA
5351078 TAATA
1 TAATA
5351083 ATAATACTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATATTAACAATAA
Found at i:5351114 original size:17 final size:17
Alignment explanation
Indices: 5351094--5351139 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
5351084 TAATACTGGT
*
5351094 TTAATTAAAATTAAACA
1 TTAATTAAAATTAAAAA
5351111 TTAATT--AATTAAAAA
1 TTAATTAAAATTAAAAA
*
5351126 TTATTTAAAATTAA
1 TTAATTAAAATTAA
5351140 TTAAAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 13 0.52
17 12 0.48
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAATTAAAATTAAAAA
Found at i:5351137 original size:10 final size:10
Alignment explanation
Indices: 5351094--5351145 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
5351084 TAATACTGGT
5351094 TTAATTAAAA
1 TTAATTAAAA
** *
5351104 TTAAACATTAA
1 TTAATTA-AAA
5351115 TTAATTAAAAA
1 TTAATT-AAAA
*
5351126 TTATTTAAAA
1 TTAATTAAAA
5351136 TTAATTAAAA
1 TTAATTAAAA
5351146 AAAGAAGAAG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
10 18 0.56
11 13 0.41
12 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
TTAATTAAAA
Found at i:5351146 original size:11 final size:11
Alignment explanation
Indices: 5351113--5351146 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5351103 ATTAAACATT
5351113 AATTAATTAAA
1 AATTAATTAAA
*
5351124 AATT-ATTTAA
1 AATTAATTAAA
5351134 AATTAATTAAA
1 AATTAATTAAA
5351145 AA
1 AA
5351147 AAGAAGAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATTAATTAAA
Found at i:5352428 original size:3 final size:3
Alignment explanation
Indices: 5352363--5352413 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
5352353 CTAAAAGTGC
5352363 TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5352410 TAA T
1 TAA T
5352414 CTACAAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5352779 original size:29 final size:29
Alignment explanation
Indices: 5352701--5352781 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 29
5352691 TTTCAAATCC
*
5352701 CTAAAACATCAAAAAGTCCTAAAATCCAAAT
1 CTAAAACCTC-AAAA-TCCTAAAATCCAAAT
* * * *
5352732 CTCAAACCTCCAAACCCTAAAATCGAAAT
1 CTAAAACCTCAAAATCCTAAAATCCAAAT
*
5352761 CCTAAAATCT-AAAATCCTAAA
1 -CTAAAACCTCAAAATCCTAAA
5352782 CACTAAAGCC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
29 22 0.55
30 10 0.25
31 8 0.20
ACGTcount: A:0.51, C:0.27, G:0.02, T:0.20
Consensus pattern (29 bp):
CTAAAACCTCAAAATCCTAAAATCCAAAT
Found at i:5352788 original size:15 final size:15
Alignment explanation
Indices: 5352747--5352781 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5352737 ACCTCCAAAC
*
5352747 CCTAAAATC-GAAAT
1 CCTAAAATCTAAAAT
5352761 CCTAAAATCTAAAAT
1 CCTAAAATCTAAAAT
5352776 CCTAAA
1 CCTAAA
5352782 CACTAAAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.03, T:0.23
Consensus pattern (15 bp):
CCTAAAATCTAAAAT
Found at i:5352929 original size:49 final size:49
Alignment explanation
Indices: 5352849--5352943 Score: 122
Period size: 49 Copynumber: 1.9 Consensus size: 49
5352839 CAAACCTCAA
* * * *
5352849 AACCCTAAAATCGAAAACATAAATCCCAAAATCTGAAACTTGAAAACCT
1 AACCCTAAAATCCAAAACACAAATCCCAAAATCTAAAACCTGAAAACCT
5352898 AACCCTAAAATCCAAAATC-CAAA-CCCTAAAATCTAAAACCTGAAAA
1 AACCCTAAAATCCAAAA-CACAAATCCC-AAAATCTAAAACCTGAAAA
5352944 TCCAAAAGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
48 3 0.08
49 36 0.90
50 1 0.03
ACGTcount: A:0.53, C:0.26, G:0.04, T:0.17
Consensus pattern (49 bp):
AACCCTAAAATCCAAAACACAAATCCCAAAATCTAAAACCTGAAAACCT
Found at i:5352930 original size:14 final size:15
Alignment explanation
Indices: 5352911--5352950 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
5352901 CCTAAAATCC
*
5352911 AAAATCCAAACCCT-
1 AAAATCCAAAACCTG
*
5352925 AAAATCTAAAACCTG
1 AAAATCCAAAACCTG
5352940 AAAATCCAAAA
1 AAAATCCAAAA
5352951 GTCTAAAGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.57, C:0.25, G:0.03, T:0.15
Consensus pattern (15 bp):
AAAATCCAAAACCTG
Found at i:5352943 original size:15 final size:14
Alignment explanation
Indices: 5352823--5352950 Score: 59
Period size: 15 Copynumber: 9.0 Consensus size: 14
5352813 TCTAAAAACC
5352823 CCTAAAATCC-AAA
1 CCTAAAATCCAAAA
* *
5352836 CCTCAAACCTCAAAA
1 CCTAAAATC-CAAAA
*
5352851 CCCTAAAATCGAAAA
1 -CCTAAAATCCAAAA
*
5352866 CAT-AAATCCCAAAA
1 CCTAAAAT-CCAAAA
* * **
5352880 TCTGAAACTTGAAAA
1 CCT-AAAATCCAAAA
*
5352895 CCT--AACCCTAAAA
1 CCTAAAATCC-AAAA
*
5352908 TCC-AAAATCCAAAC
1 -CCTAAAATCCAAAA
*
5352922 CCTAAAATCTAAAA
1 CCTAAAATCCAAAA
5352936 CCTGAAAATCCAAAA
1 CCT-AAAATCCAAAA
5352951 GTCTAAAGAC
Statistics
Matches: 81, Mismatches: 22, Indels: 22
0.65 0.18 0.18
Matches are distributed among these distances:
12 1 0.01
13 17 0.21
14 26 0.32
15 27 0.33
16 10 0.12
ACGTcount: A:0.52, C:0.29, G:0.03, T:0.16
Consensus pattern (14 bp):
CCTAAAATCCAAAA
Found at i:5354163 original size:15 final size:15
Alignment explanation
Indices: 5354140--5354169 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5354130 TTATTTGGTA
5354140 TTTAATTTAATTTTT
1 TTTAATTTAATTTTT
*
5354155 TTTATTTTAATTTTT
1 TTTAATTTAATTTTT
5354170 CACAAATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTAATTTAATTTTT
Found at i:5359574 original size:17 final size:17
Alignment explanation
Indices: 5359549--5359589 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5359539 ATGGGGCATT
5359549 ATAAAAAAACAAATAAA
1 ATAAAAAAACAAATAAA
* * *
5359566 ATAATAAAATAATTAAA
1 ATAAAAAAACAAATAAA
5359583 ATAAAAA
1 ATAAAAA
5359590 CTCTTTTATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (17 bp):
ATAAAAAAACAAATAAA
Found at i:5361180 original size:18 final size:18
Alignment explanation
Indices: 5361154--5361199 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5361144 CATATTCTTG
*
5361154 CATTTGCATCGACATTTA
1 CATTAGCATCGACATTTA
* * *
5361172 CATTCGCATTGACATTTC
1 CATTAGCATCGACATTTA
5361190 CATTAGCATC
1 CATTAGCATC
5361200 ATTTGATGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (18 bp):
CATTAGCATCGACATTTA
Found at i:5361785 original size:22 final size:22
Alignment explanation
Indices: 5361732--5361794 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
5361722 GTTGATTCTG
5361732 TAAGACCTCCAGGCATAATCTC
1 TAAGACCTCCAGGCATAATCTC
* *
5361754 TAAAACCTCCAGGCATGAGT-TC
1 TAAGACCTCCAGGCAT-AATCTC
* *
5361776 TAAGATCTCCAGACATAAT
1 TAAGACCTCCAGGCATAAT
5361795 TTTGATTCGC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (22 bp):
TAAGACCTCCAGGCATAATCTC
Found at i:5361891 original size:22 final size:22
Alignment explanation
Indices: 5361857--5361916 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
5361847 TATCCCAGTC
*
5361857 GATTTTGTAAGACCTCCGAGTAT
1 GATTTT-TAAGACCTCCGAGCAT
*
5361880 GATTTTTAAGACCTTCGAGCAT
1 GATTTTTAAGACCTCCGAGCAT
* *
5361902 AATTTTTAAAACCTC
1 GATTTTTAAGACCTC
5361917 TTGGCATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (22 bp):
GATTTTTAAGACCTCCGAGCAT
Found at i:5361923 original size:22 final size:22
Alignment explanation
Indices: 5361858--5361929 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
5361848 ATCCCAGTCG
* * * *
5361858 ATTTTGTAAGACCTCCGAGTATG
1 ATTTT-TAAAACCTTCGAGCATA
*
5361881 ATTTTTAAGACCTTCGAGCATA
1 ATTTTTAAAACCTTCGAGCATA
*
5361903 ATTTTTAAAACCTCTTG-GCATA
1 ATTTTTAAAACCT-TCGAGCATA
5361925 ATTTT
1 ATTTT
5361930 GATTCATAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
22 36 0.84
23 7 0.16
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (22 bp):
ATTTTTAAAACCTTCGAGCATA
Found at i:5362022 original size:22 final size:22
Alignment explanation
Indices: 5361996--5362047 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
5361986 GTTGATTCTA
*
5361996 TAAGACCTCCGAACATGATTTT
1 TAAGACCTCCGAACATGATTTC
***
5362018 TAAGACCTCCGGGTATGATTTC
1 TAAGACCTCCGAACATGATTTC
5362040 TAAGACCT
1 TAAGACCT
5362048 TTAGGCATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (22 bp):
TAAGACCTCCGAACATGATTTC
Found at i:5362055 original size:132 final size:132
Alignment explanation
Indices: 5361686--5362058 Score: 403
Period size: 132 Copynumber: 2.8 Consensus size: 132
5361676 TATTATTTCG
*
5361686 ATCGATTTTTT-TTTTTTGACTTGC-AGTGTTATCTCAGTTGATTCTGTAAGACCTCC-AGGCAT
1 ATCGATTTTTTATTTTTTGACTTGCGA-TGTTATCCCAGTTGATTCTGTAAGACCTCCGA-GCAT
* * * * * * * ** * * *
5361748 AATCTCTAAAACCTCCAGGCATGAGTTCTAAGATCTCCAGACATAATTTTGATTCGCAGTGTTGT
64 GATTTTTAAGACCTCCGGGCATGATTTCTAAGACCTTTAGGCATAATTTTGATTCACAGTGTTAT
*
5361813 CCCG
129 CCCA
* * * * *
5361817 ATCGATTTTTTATTTTTTGTCTTGCGGTGTTATCCCAGTCGATTTTGTAAGACCTCCGAGTATGA
1 ATCGATTTTTTATTTTTTGACTTGCGATGTTATCCCAGTTGATTCTGTAAGACCTCCGAGCATGA
* * * * * *
5361882 TTTTTAAGACCTTCGAGCATAATTTTTAAAACCTCTT-GGCATAATTTTGATTCATAGTGTTATC
66 TTTTTAAGACCTCCGGGCATGATTTCTAAGACCT-TTAGGCATAATTTTGATTCACAGTGTTATC
*
5361946 CTA
130 CCA
* * * * *
5361949 ATCGATTTTTTATTTTTTAACTTACGATGTTATCCCTGTTGATTCTATAAGACCTCCGAACATGA
1 ATCGATTTTTTATTTTTTGACTTGCGATGTTATCCCAGTTGATTCTGTAAGACCTCCGAGCATGA
*
5362014 TTTTTAAGACCTCCGGGTATGATTTCTAAGACCTTTAGGCATAAT
66 TTTTTAAGACCTCCGGGCATGATTTCTAAGACCTTTAGGCATAAT
5362059 CTTTAATAAC
Statistics
Matches: 195, Mismatches: 42, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
131 13 0.07
132 181 0.93
133 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (132 bp):
ATCGATTTTTTATTTTTTGACTTGCGATGTTATCCCAGTTGATTCTGTAAGACCTCCGAGCATGA
TTTTTAAGACCTCCGGGCATGATTTCTAAGACCTTTAGGCATAATTTTGATTCACAGTGTTATCC
CA
Found at i:5362148 original size:154 final size:154
Alignment explanation
Indices: 5361857--5362159 Score: 373
Period size: 154 Copynumber: 2.0 Consensus size: 154
5361847 TATCCCAGTC
* * * *
5361857 GATTTTGTAAGACCTCCGAGTATGATTTTTAAGACCTTCGAGCATAATTTTTAAAACCTCTTGGC
1 GATTTTGTAAGACCTCCGAGTATGATTTCTAAGACCTTAGAGCATAATCTTTAAAACCTCTCGGC
* * * *
5361922 ATAATTTTGATTCATAGTGTTATCCTAATCGATTTTTTATTTTTTAACTTACGATGTTATCCCTG
66 ATAATTTTGATT-ATAGTATTATCCTAATCGATTTTTAACTTTTTAACTTACGATGTTATCCCAG
**
5361987 TTGATTCTATAAGACCTCCGAACAT
130 TCAATTCTATAAGACCTCCGAACAT
*
5362012 GATTTT-TAAGACCTCCGGGTATGATTTCTAAGACCTTTAG-GCATAATCTTTAATAA-CTC-CG
1 GATTTTGTAAGACCTCCGAGTATGATTTCTAAGACC-TTAGAGCATAATCTTTAA-AACCTCTCG
* * * *
5362073 GACATAATTTTGATT-TACGATATTATCTTGATCGATTTTTAACTTTTTAACTTATGGTGTTATC
64 G-CATAATTTTGATTATA-G-TATTATCCTAATCGATTTTTAACTTTTTAACTTACGATGTTATC
*
5362137 CCAGTCAATTCTGTAAGACCTCC
126 CCAGTCAATTCTATAAGACCTCC
5362160 AGACATAATT
Statistics
Matches: 127, Mismatches: 16, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
152 2 0.02
153 3 0.02
154 111 0.87
155 11 0.09
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (154 bp):
GATTTTGTAAGACCTCCGAGTATGATTTCTAAGACCTTAGAGCATAATCTTTAAAACCTCTCGGC
ATAATTTTGATTATAGTATTATCCTAATCGATTTTTAACTTTTTAACTTACGATGTTATCCCAGT
CAATTCTATAAGACCTCCGAACAT
Found at i:5362199 original size:88 final size:88
Alignment explanation
Indices: 5362068--5362258 Score: 240
Period size: 88 Copynumber: 2.2 Consensus size: 88
5362058 TCTTTAATAA
* * * * * **
5362068 CTCCGGACATAATTTTGATTTACGATATTATCTTGATCGATTTTTAACTTTTTAACTTATGGTGT
1 CTCCAGACATAATTTCGATTCACGATATTATCCTGATCAATTTTTAACTTTTTAACTTACAGTGT
*
5362133 TATCCCAGTCAATTCTGTAAGAC
66 TATCCCAATCAATTCTGTAAGAC
* * *
5362156 CTCCAGACATAATTTCGATTCATGGTATTATCCTGATCAATTTTTAATTTTTTAACTTACAGTGT
1 CTCCAGACATAATTTCGATTCACGATATTATCCTGATCAATTTTTAACTTTTTAACTTACAGTGT
* *
5362221 TATCCCAATCGATTCTTTAAGAC
66 TATCCCAATCAATTCTGTAAGAC
*
5362244 CTTCA-AGCATAATTT
1 CTCCAGA-CATAATTT
5362259 ATAAGACCTC
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
87 1 0.01
88 87 0.99
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (88 bp):
CTCCAGACATAATTTCGATTCACGATATTATCCTGATCAATTTTTAACTTTTTAACTTACAGTGT
TATCCCAATCAATTCTGTAAGAC
Found at i:5362415 original size:90 final size:90
Alignment explanation
Indices: 5362294--5362468 Score: 215
Period size: 90 Copynumber: 1.9 Consensus size: 90
5362284 AATATTCGGG
* * * * * *
5362294 CATAATTTTCATTTACGATGTTGTCCCGATCGATTTTTAACTTTTTAACTTTCGGTATTATCCCG
1 CATAATTTTCATTCACGATGTTGTCCAGATCGATTCTTAACTTTTTAACTTGCGATAGTATCCCG
*
5362359 ATTGATTCCGTAAGACCTCCTAAGA
66 ATCGATTCCGTAAGACCTCCTAAGA
* * * * * * *
5362384 CATAATTTTGATTCGCGGTGTTGTCTAGATCGATTCTTAATTTTTTGACTTGCGATAGTATCTCG
1 CATAATTTTCATTCACGATGTTGTCCAGATCGATTCTTAACTTTTTAACTTGCGATAGTATCCCG
*
5362449 ATCGATTCTGTAAGACCTCC
66 ATCGATTCCGTAAGACCTCC
5362469 GAACATGATT
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
90 70 1.00
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (90 bp):
CATAATTTTCATTCACGATGTTGTCCAGATCGATTCTTAACTTTTTAACTTGCGATAGTATCCCG
ATCGATTCCGTAAGACCTCCTAAGA
Found at i:5362522 original size:44 final size:44
Alignment explanation
Indices: 5362459--5362543 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
5362449 ATCGATTCTG
* * *
5362459 TAAGACCTCCGAACATGATTTTTAATACCTCTAAGCATAATCTT
1 TAAGACCTCCGAACATGATTTCTAAGACCTCCAAGCATAATCTT
* * * *
5362503 TAAGACCTTCGGATATGATTTCTAAGACCTCCAGGCATAAT
1 TAAGACCTCCGAACATGATTTCTAAGACCTCCAAGCATAAT
5362544 TTCGATTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (44 bp):
TAAGACCTCCGAACATGATTTCTAAGACCTCCAAGCATAATCTT
Found at i:5362644 original size:22 final size:23
Alignment explanation
Indices: 5362606--5362657 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
5362596 TATCTCGATC
* *
5362606 GATTTTGTAAAATCTTCGAGTAT
1 GATTTTGTAAAACCTTCAAGTAT
5362629 GATTTT-TAAAACCTTCAAGTAT
1 GATTTTGTAAAACCTTCAAGTAT
*
5362651 AATTTTG
1 GATTTTG
5362658 ATTCGCGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (23 bp):
GATTTTGTAAAACCTTCAAGTAT
Found at i:5362700 original size:36 final size:36
Alignment explanation
Indices: 5362650--5362757 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
5362640 CCTTCAAGTA
*
5362650 TAATTTTGATTCGCGATGTTGTCAC-AATCGATTCTT
1 TAATTTTGACTCGCGATGTTGTC-CTAATCGATTCTT
* *
5362686 TAATTTTGACTCGCGGTGTTGTCCTAGTCGATTCTT
1 TAATTTTGACTCGCGATGTTGTCCTAATCGATTCTT
* * * * * *
5362722 TACTTCTCGACTTGCGGTGTTATCTTAATCGATTCT
1 TAATT-TTGACTCGCGATGTTGTCCTAATCGATTCT
5362758 ATATTTTTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
35 1 0.02
36 35 0.57
37 25 0.41
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (36 bp):
TAATTTTGACTCGCGATGTTGTCCTAATCGATTCTT
Found at i:5362754 original size:37 final size:36
Alignment explanation
Indices: 5362675--5362757 Score: 103
Period size: 37 Copynumber: 2.3 Consensus size: 36
5362665 ATGTTGTCAC
* *
5362675 AATCGATTCTTTAATTTTGACTCGCGGTGTTGTCCT
1 AATCGATTCTTTAATTTCGACTCGCGGTGTTATCCT
* * * *
5362711 AGTCGATTCTTTACTTCTCGACTTGCGGTGTTATCTT
1 AATCGATTCTTTAATT-TCGACTCGCGGTGTTATCCT
5362748 AATCGATTCT
1 AATCGATTCT
5362758 ATATTTTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 14 0.36
37 25 0.64
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (36 bp):
AATCGATTCTTTAATTTCGACTCGCGGTGTTATCCT
Found at i:5363077 original size:15 final size:15
Alignment explanation
Indices: 5363057--5363086 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5363047 GTTTAATTAA
*
5363057 AATTAAACATTAATT
1 AATTAAAAATTAATT
5363072 AATTAAAAATTAATT
1 AATTAAAAATTAATT
5363087 TTTAAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTAAAAATTAATT
Found at i:5364502 original size:3 final size:3
Alignment explanation
Indices: 5364488--5364544 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
5364478 AAAGATTAAT
*
5364488 TAA TAA -AA TAA TAA T-A TAA TAA TAA TAA TAG TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
5364531 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
5364545 TATGAAAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 6 0.12
3 40 0.83
4 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5364811 original size:15 final size:14
Alignment explanation
Indices: 5364683--5364811 Score: 52
Period size: 14 Copynumber: 9.0 Consensus size: 14
5364673 TAAAAAAACC
5364683 CCTAAAATCC-AAA
1 CCTAAAATCCAAAA
* *
5364696 CCTCAAACCTCCAAAC
1 CCT-AAA-ATCCAAAA
*
5364712 CCTAAAATCGAAAA
1 CCTAAAATCCAAAA
5364726 CCT-AAATCCCAAAA
1 CCTAAAAT-CCAAAA
** * **
5364740 TTTGAAACTTGAAAA
1 CCT-AAAATCCAAAA
*
5364755 CCT--AACCCTAAAA
1 CCTAAAATCC-AAAA
*
5364768 TCC-AAAATCTCAAAC
1 -CCTAAAATC-CAAAA
*
5364783 CCTAAAATCTAAAA
1 CCTAAAATCCAAAA
5364797 CCTAAAATTCCAAAA
1 CCTAAAA-TCCAAAA
5364812 GTCTAAAGAC
Statistics
Matches: 81, Mismatches: 22, Indels: 24
0.64 0.17 0.19
Matches are distributed among these distances:
12 1 0.01
13 11 0.14
14 31 0.38
15 29 0.36
16 9 0.11
ACGTcount: A:0.50, C:0.29, G:0.02, T:0.19
Consensus pattern (14 bp):
CCTAAAATCCAAAA
Found at i:5364818 original size:23 final size:22
Alignment explanation
Indices: 5364786--5364828 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
5364776 CTCAAACCCT
5364786 AAAATCTAAA-ACCTAAAATTCC
1 AAAATCTAAAGACC-AAAATTCC
5364808 AAAAGTCTAAAGACCAAAATT
1 AAAA-TCTAAAGACCAAAATT
5364829 TGATACACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 12 0.63
24 3 0.16
ACGTcount: A:0.56, C:0.19, G:0.05, T:0.21
Consensus pattern (22 bp):
AAAATCTAAAGACCAAAATTCC
Found at i:5365951 original size:27 final size:27
Alignment explanation
Indices: 5365918--5366000 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 27
5365908 ACACTTTAGA
5365918 TTCTAAATAAACTCAAATTGTGAAAATT
1 TTCTAAATAAACTCAAA-TGTGAAAATT
*
5365946 TT-TAAAATGAAACTTATAA---GAAAATT
1 TTCT-AAAT-AAACTCA-AATGTGAAAATT
*
5365972 TTCTAAATAAACACAAATGGTGAAAATT
1 TTCTAAATAAACTCAAAT-GTGAAAATT
5366000 T
1 T
5366001 AGAAATAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
24 2 0.05
25 5 0.11
26 13 0.30
27 2 0.05
28 14 0.32
29 6 0.14
30 2 0.05
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.34
Consensus pattern (27 bp):
TTCTAAATAAACTCAAATGTGAAAATT
Found at i:5366019 original size:20 final size:20
Alignment explanation
Indices: 5365994--5366032 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5365984 ACAAATGGTG
*
5365994 AAAATT-TAGAAATAGAAATA
1 AAAATTGTAAAAATA-AAATA
5366014 AAAATTGTAAAAATAAAAT
1 AAAATTGTAAAAATAAAAT
5366033 TTTGATGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.26
Consensus pattern (20 bp):
AAAATTGTAAAAATAAAATA
Found at i:5367860 original size:20 final size:20
Alignment explanation
Indices: 5367814--5367860 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
5367804 TTTATCTATC
* *
5367814 AAACAAA-ATAAAATTAAAA
1 AAACAAATAAAAAAGTAAAA
*
5367833 AACCAAATAAAAAAGTAAAA
1 AAACAAATAAAAAAGTAAAA
*
5367853 AAATAAAT
1 AAACAAAT
5367861 TTAATTAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (20 bp):
AAACAAATAAAAAAGTAAAA
Found at i:5367870 original size:16 final size:14
Alignment explanation
Indices: 5367848--5367892 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
5367838 AATAAAAAAG
5367848 TAAAAAAATAAATT
1 TAAAAAAATAAATT
*
5367862 TAATTAAAAATAAAAT
1 TAA--AAAAATAAATT
*
5367878 TAAAAAAGTAAATT
1 TAAAAAAATAAATT
5367892 T
1 T
5367893 TTGGAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 13 0.50
16 13 0.50
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (14 bp):
TAAAAAAATAAATT
Found at i:5368022 original size:16 final size:16
Alignment explanation
Indices: 5367982--5368029 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
5367972 ATATATATCT
5367982 ATATATTTAATTAAAA
1 ATATATTTAATTAAAA
* *
5367998 TTA-AATTAATTAAAA
1 ATATATTTAATTAAAA
5368013 ATATATTTAATTAAAA
1 ATATATTTAATTAAAA
5368029 A
1 A
5368030 ATTAAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATTTAATTAAAA
Found at i:5369032 original size:2 final size:2
Alignment explanation
Indices: 5369025--5369064 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
5369015 AACAGTCTTG
5369025 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5369065 AGTGAGCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5370445 original size:21 final size:19
Alignment explanation
Indices: 5370420--5370468 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
5370410 TGGTGCAAAG
5370420 AAGCTGAAAGGAAGAGAAGCC
1 AAGCTGAAAGGAA-A-AAGCC
*
5370441 TAGCTGGTAAAGGAAAAAGCC
1 AAGCT-G-AAAGGAAAAAGCC
5370462 AAGCTGA
1 AAGCTGA
5370469 TGGAAGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
19 1 0.04
20 1 0.04
21 13 0.54
22 2 0.08
23 7 0.29
ACGTcount: A:0.45, C:0.14, G:0.31, T:0.10
Consensus pattern (19 bp):
AAGCTGAAAGGAAAAAGCC
Found at i:5370453 original size:23 final size:21
Alignment explanation
Indices: 5370426--5370467 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
5370416 AAAGAAGCTG
*
5370426 AAAGGAAGAGAAGCCTAGCTGGT
1 AAAGGAA-A-AAGCCAAGCTGGT
5370449 AAAGGAAAAAGCCAAGCTG
1 AAAGGAAAAAGCCAAGCTG
5370468 ATGGAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.45, C:0.14, G:0.31, T:0.10
Consensus pattern (21 bp):
AAAGGAAAAAGCCAAGCTGGT
Found at i:5370508 original size:19 final size:19
Alignment explanation
Indices: 5370484--5370520 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5370474 GAAAGAACTA
*
5370484 AGCTGGAGAGGAAGCTGAC
1 AGCTGGAAAGGAAGCTGAC
*
5370503 AGCTGGAAATGAAGCTGA
1 AGCTGGAAAGGAAGCTGA
5370521 TCAGGATGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.14, G:0.38, T:0.14
Consensus pattern (19 bp):
AGCTGGAAAGGAAGCTGAC
Done.