Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, 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: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 51 of 117
Found at i:9432297 original size:236 final size:234
Alignment explanation
Indices: 9431819--9432393 Score: 652
Period size: 236 Copynumber: 2.4 Consensus size: 234
9431809 GGTTGAGATT
* * * * *
9431819 AAACCACGAGTCAAATGAAACGACCA-AGACCAAGTCAAGGTTAAAAATAATGATTGAGACGAAA
1 AAACCATGAGTCAAATGAGATGACCAGA-ACCAAGTCAAGGTTGAAAATAATGATTGAGATGAAA
* * * **
9431883 CCATAAATCATAAAAAATGATCTAGACTAAGCCAAAATCAAGTGACCGAGACAAAACCACTAGTC
65 CCATAAATCATAAGAAATGATCTAGACTGAGCCAAGATCAAGTGACCGAGACAAAACCAAGAGTC
* * * *
9431948 AGATGAGGTGACCAAGATCGAGTCAAGGTCGAAAATAAATTATCAGGACGAACCCACAAATTATA
130 AAATGAGGTGACCAAGATCGAGTCAAGGTCGAAAATAAATGATCAGGACGAAACCACAAATCATA
* **
9432013 AGAAATGATCTGGACTAAGCCAAGATCAAGTGACTGGGAC
195 AAAAATGATCTGGACTAAGCCAAGATCAAGTGACTAAGAC
* * * *
9432053 ATAACCATGAGTCAAATGAGATGACCAGAATCAAGTCGAGGTCGAAAATAAATAATT-AGGATGA
1 A-AACCATGAGTCAAATGAGATGACCAGAACCAAGTCAAGGTTGAAAAT-AATGATTGA-GATGA
* * * *
9432117 AACCATAAATCATAAGAAATGATCTAGACTGTGCCAAGATCGAGTGACTGGGACAAAACCAAGAG
63 AACCATAAATCATAAGAAATGATCTAGACTGAGCCAAGATCAAGTGACCGAGACAAAACCAAGAG
* * * * * * **
9432182 TCAAATGAGGTGACCAGGATCGAGTCAGGGTTGAAAATAGATGATCAGGATGAAACTATGAATCA
128 TCAAATGAGGTGACCAAGATCGAGTCAAGGTCGAAAATAAATGATCAGGACGAAACCACAAATCA
* * * **
9432247 TAAAAAATGATTTGGGCTGAGCCAAGATTGAGTGA-TCAAGAC
193 TAAAAAATGATCTGGACTAAGCCAAGATCAAGTGACT-AAGAC
* * * * * *
9432289 GAAACCATGAGTCAAATGAGGTGATCAGAACCGAGTCAAGGTTGAAGATAATGATTGAAATGGAA
1 -AAACCATGAGTCAAATGAGATGACCAGAACCAAGTCAAGGTTGAAAATAATGATTGAGATGAAA
** *
9432354 CCACGAATCATAAGAAATGATCTGGACTGAGCCAAGATCA
65 CCATAAATCATAAGAAATGATCTAGACTGAGCCAAGATCA
9432394 CGTAAGTGAA
Statistics
Matches: 281, Mismatches: 53, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
234 1 0.00
235 86 0.31
236 193 0.69
237 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (234 bp):
AAACCATGAGTCAAATGAGATGACCAGAACCAAGTCAAGGTTGAAAATAATGATTGAGATGAAAC
CATAAATCATAAGAAATGATCTAGACTGAGCCAAGATCAAGTGACCGAGACAAAACCAAGAGTCA
AATGAGGTGACCAAGATCGAGTCAAGGTCGAAAATAAATGATCAGGACGAAACCACAAATCATAA
AAAATGATCTGGACTAAGCCAAGATCAAGTGACTAAGAC
Found at i:9443730 original size:3 final size:3
Alignment explanation
Indices: 9443722--9443746 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9443712 GGAAATGAAA
9443722 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
9443747 GTAGTAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9444117 original size:56 final size:55
Alignment explanation
Indices: 9444035--9444174 Score: 165
Period size: 56 Copynumber: 2.5 Consensus size: 55
9444025 TATTTTTTTA
* ** * *
9444035 AAAAAAATTATTATACCAAAATTATATTTTTTAACTTAAAAATATGATCTTTAATT
1 AAAAAAATTATTATA-CAAAAGTATATTTTTTAAAATAAAAACATGACCTTTAATT
*
9444091 AAAAATAA-TATTATACAAAGAGTATATTTTTTAAAATAAAAACGTGACCTTTAATT
1 AAAAA-AATTATTATACAAA-AGTATATTTTTTAAAATAAAAACATGACCTTTAATT
* * *
9444147 AAAAAAATTATTACACAATACTATATTT
1 AAAAAAATTATTATACAAAAGTATATTT
9444175 AAAAAAAAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
55 14 0.19
56 56 0.78
57 2 0.03
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.39
Consensus pattern (55 bp):
AAAAAAATTATTATACAAAAGTATATTTTTTAAAATAAAAACATGACCTTTAATT
Found at i:9448911 original size:6 final size:6
Alignment explanation
Indices: 9448900--9448932 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
9448890 AAATAATATA
9448900 AAATTC AAATTC AAATTC AAA-TC AAA-TC AAATT
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATT
9448933 TTTAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTC
Found at i:9468419 original size:19 final size:18
Alignment explanation
Indices: 9468395--9468432 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
9468385 AATAATGTAT
*
9468395 TTAATATAAATTCATAATA
1 TTAATATAAACTCA-AATA
9468414 TTAATATAAACTCAAATA
1 TTAATATAAACTCAAATA
9468432 T
1 T
9468433 AGACTCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAATATAAACTCAAATA
Found at i:9468583 original size:2 final size:2
Alignment explanation
Indices: 9468576--9468602 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9468566 TATTACTTAT
9468576 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
9468603 GGGCCAAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9472878 original size:13 final size:13
Alignment explanation
Indices: 9472860--9472886 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9472850 AAAAATTTAA
9472860 TTTATATTATTTT
1 TTTATATTATTTT
9472873 TTTATATTATTTT
1 TTTATATTATTTT
9472886 T
1 T
9472887 GTATCGAATT
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATATTATTTT
Found at i:9473577 original size:17 final size:17
Alignment explanation
Indices: 9473555--9473587 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9473545 CAAGACCCGC
*
9473555 CTTGTTAATCTTACAAG
1 CTTGTTAAGCTTACAAG
9473572 CTTGTTAAGCTTACAA
1 CTTGTTAAGCTTACAA
9473588 TCCGTGGGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (17 bp):
CTTGTTAAGCTTACAAG
Found at i:9478881 original size:14 final size:15
Alignment explanation
Indices: 9478862--9478893 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
9478852 ATAATTATTT
9478862 TTATTT-AAATATAA
1 TTATTTAAAATATAA
9478876 TTATTTAAAATATAA
1 TTATTTAAAATATAA
9478891 TTA
1 TTA
9478894 AAATTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATTTAAAATATAA
Found at i:9480388 original size:12 final size:11
Alignment explanation
Indices: 9480371--9480429 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
9480361 CGAGAGAATA
9480371 ATAAATATTATT
1 ATAAATATTA-T
*
9480383 ATAAATAATAT
1 ATAAATATTAT
9480394 AT-AATATT-T
1 ATAAATATTAT
*
9480403 A-AAATATAAT
1 ATAAATATTAT
9480413 ATAAAT-TATAT
1 ATAAATAT-TAT
9480424 ATAAAT
1 ATAAAT
9480430 TTAATTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
9 7 0.18
10 8 0.21
11 15 0.38
12 9 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATAAATATTAT
Found at i:9480389 original size:19 final size:19
Alignment explanation
Indices: 9480367--9480429 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 19
9480357 CACCCGAGAG
9480367 AATAATAAATATTATTATA
1 AATAATAAATATTATTATA
* * *
9480386 AATAATATATAATATTTAAA
1 AATAATAAATATTA-TTATA
9480406 ATATAATATAA-ATTATATATA
1 A-ATAATA-AATATTAT-TATA
9480427 AAT
1 AAT
9480430 TTAATTAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
19 12 0.35
20 8 0.24
21 13 0.38
22 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAATAAATATTATTATA
Found at i:9480417 original size:30 final size:30
Alignment explanation
Indices: 9480373--9480433 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
9480363 AGAGAATAAT
*
9480373 AAATATTATTATAAATAATATATAATATTTA
1 AAATATTAATATAAATAATATATAA-ATTTA
*
9480404 AAATA-TAATATAAATTATATATAAATTTA
1 AAATATTAATATAAATAATATATAAATTTA
9480433 A
1 A
9480434 TTAATTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.21
30 17 0.61
31 5 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
AAATATTAATATAAATAATATATAAATTTA
Found at i:9480619 original size:30 final size:29
Alignment explanation
Indices: 9480585--9480700 Score: 119
Period size: 30 Copynumber: 3.9 Consensus size: 29
9480575 CTTGCTAATA
* *
9480585 ACATTAAAATAAGTTCTTGAATTTTAATTT
1 ACATTTAAATAAATTCTT-AATTTTAATTT
9480615 ACATTTAAATAAATTCTTAATATTTAATTT
1 ACATTTAAATAAATTCTTAAT-TTTAATTT
* *
9480645 ATATTTAAATAAATCCTTAACTTTTAATTT
1 ACATTTAAATAAATTCTTAA-TTTTAATTT
* * *
9480675 ATACCTT-AAT-AAGTCTTAATTTTAAT
1 ACA-TTTAAATAAATTCTTAATTTTAAT
9480701 AAGCCCTTAA
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
28 7 0.09
29 10 0.13
30 56 0.74
31 3 0.04
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.48
Consensus pattern (29 bp):
ACATTTAAATAAATTCTTAATTTTAATTT
Found at i:9480972 original size:30 final size:30
Alignment explanation
Indices: 9480938--9481042 Score: 122
Period size: 30 Copynumber: 3.5 Consensus size: 30
9480928 AGGTTAAGGG
*
9480938 TTTATTTGAATATAAATTAAAAATTAAAGA
1 TTTATTTGGATATAAATTAAAAATTAAAGA
* * *
9480968 TTTATTTGGATAAAAATTAAAAGTTAAAAA
1 TTTATTTGGATATAAATTAAAAATTAAAGA
* * **
9480998 TTTATTAGGATACAAATT-AAAATTTTAGA
1 TTTATTTGGATATAAATTAAAAATTAAAGA
9481027 GTTTATTTGGATATAA
1 -TTTATTTGGATATAA
9481043 TAAAAGTATA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
29 7 0.11
30 55 0.89
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.41
Consensus pattern (30 bp):
TTTATTTGGATATAAATTAAAAATTAAAGA
Found at i:9480994 original size:60 final size:60
Alignment explanation
Indices: 9480938--9481056 Score: 145
Period size: 60 Copynumber: 2.0 Consensus size: 60
9480928 AGGTTAAGGG
* *
9480938 TTTATTTGAATATAAATTAAAAATTAAAGA-TTTATTTGGATAAAAATTAAAAGTTAAAAA
1 TTTATTAGAATACAAATT-AAAATTAAAGAGTTTATTTGGATAAAAATTAAAAGTTAAAAA
* ** *
9480998 TTTATTAGGATACAAATTAAAATTTTAGAGTTTATTTGGAT-ATAA-TAAAAGTATAAAAA
1 TTTATTAGAATACAAATTAAAATTAAAGAGTTTATTTGGATAAAAATTAAAAGT-TAAAAA
9481057 ATTTTATCTA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
58 7 0.14
59 18 0.35
60 26 0.51
ACGTcount: A:0.50, C:0.01, G:0.10, T:0.39
Consensus pattern (60 bp):
TTTATTAGAATACAAATTAAAATTAAAGAGTTTATTTGGATAAAAATTAAAAGTTAAAAA
Found at i:9481163 original size:22 final size:21
Alignment explanation
Indices: 9481122--9481163 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
9481112 TAAACACAAT
*
9481122 AAAAATATAAATATTTATTTA
1 AAAAATATAAATATTAATTTA
9481143 AAAAAT-TAAAATAGTTAATTT
1 AAAAATAT-AAATA-TTAATTT
9481164 TTTTTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 1 0.06
21 11 0.61
22 6 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAAATATAAATATTAATTTA
Found at i:9481238 original size:13 final size:15
Alignment explanation
Indices: 9481220--9481256 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
9481210 TGTGGTTTTC
9481220 TAAATAAAAT-AA-A
1 TAAATAAAATGAACA
9481233 TAAATAAAATGAACA
1 TAAATAAAATGAACA
*
9481248 AAAATAAAA
1 TAAATAAAA
9481257 AGATGATGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.48
14 2 0.10
15 9 0.43
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (15 bp):
TAAATAAAATGAACA
Found at i:9483364 original size:21 final size:21
Alignment explanation
Indices: 9483340--9483380 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9483330 ACCGATACGT
9483340 AAATATAAAATATATTTTATA
1 AAATATAAAATATATTTTATA
* * *
9483361 AAATTTAAATTATTTTTTAT
1 AAATATAAAATATATTTTAT
9483381 TATTTAACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATATAAAATATATTTTATA
Found at i:9484239 original size:30 final size:30
Alignment explanation
Indices: 9484115--9484239 Score: 125
Period size: 30 Copynumber: 4.2 Consensus size: 30
9484105 TTAATTAAGC
* *
9484115 TTTTATATTTTCA-TTATA-CTCAAAT-AAG
1 TTTTAAATTTTAATTTATATCT-AAATAAAG
*
9484143 TTTTTAAATTTTAATTTATATCCAAATAAAG
1 -TTTTAAATTTTAATTTATATCTAAATAAAG
* *
9484174 TCTTAAATTTTAATTTATATTTAAAT-AAG
1 TTTTAAATTTTAATTTATATCTAAATAAAG
*
9484203 TCTTT-AATATTTAATTTATATCTAAATAAAA
1 T-TTTAAAT-TTTAATTTATATCTAAATAAAG
9484234 TTTTAA
1 TTTTAA
9484240 CATAAATTAA
Statistics
Matches: 80, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
29 18 0.22
30 54 0.68
31 8 0.10
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.50
Consensus pattern (30 bp):
TTTTAAATTTTAATTTATATCTAAATAAAG
Found at i:9484406 original size:27 final size:27
Alignment explanation
Indices: 9484350--9484423 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
9484340 TTTACTTTTC
9484350 TTAAATAAATCTCTATATTTTTATTATAT
1 TTAAATAAAT-TCT-TATTTTTATTATAT
*
9484379 TTAAATAAATTCTT-TTTTTATTTGTAT
1 TTAAATAAATTCTTATTTTTA-TTATAT
*
9484406 TTAAATAAGTTCTTATTT
1 TTAAATAAATTCTTATTT
9484424 CAAGTAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
26 6 0.15
27 19 0.46
28 6 0.15
29 10 0.24
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (27 bp):
TTAAATAAATTCTTATTTTTATTATAT
Found at i:9484546 original size:30 final size:30
Alignment explanation
Indices: 9484462--9484575 Score: 113
Period size: 30 Copynumber: 3.8 Consensus size: 30
9484452 TTTATTTAAG
* * ** *
9484462 TATAAACTGAAAATTAATGATTTATTTGGA
1 TATAAATTAAAAATTAAAAATTTATTTTGA
* * *
9484492 TATAAATTAAAAAATAAGATTTTATTTTGA
1 TATAAATTAAAAATTAAAAATTTATTTTGA
* *
9484522 TATAAATTAAAAGTTAAAAGTTTATTTGTG-
1 TATAAATTAAAAATTAAAAATTTATTT-TGA
*
9484552 TATAAATTAAAATTTAAAAATTTA
1 TATAAATTAAAAATTAAAAATTTA
9484576 CTAGGATGTA
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
30 68 0.97
31 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.09, T:0.42
Consensus pattern (30 bp):
TATAAATTAAAAATTAAAAATTTATTTTGA
Found at i:9493574 original size:2 final size:2
Alignment explanation
Indices: 9493567--9493601 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9493557 ACTGATGGTT
9493567 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9493602 TGCATGACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9495848 original size:13 final size:13
Alignment explanation
Indices: 9495828--9495879 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
9495818 AAGATATTTT
9495828 TATTAAATTAATA
1 TATTAAATTAATA
* *
9495841 TCTTAAATTAAAA
1 TATTAAATTAATA
9495854 TATTAAA-TAATA
1 TATTAAATTAATA
**
9495866 -ATTTTATTAATA
1 TATTAAATTAATA
9495878 TA
1 TA
9495880 ATATATAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 4 0.13
12 9 0.29
13 18 0.58
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (13 bp):
TATTAAATTAATA
Found at i:9497631 original size:16 final size:18
Alignment explanation
Indices: 9497599--9497631 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
9497589 TTATTTTATA
9497599 TTAAATATAATTAAATTG
1 TTAAATATAATTAAATTG
9497617 TTAAAT-TAA-TAAATT
1 TTAAATATAATTAAATT
9497632 AATAAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
TTAAATATAATTAAATTG
Found at i:9504088 original size:27 final size:27
Alignment explanation
Indices: 9504010--9504092 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
9504000 AAATTTAATG
*
9504010 AAATTAT-ATTTAATTCACATATATAT
1 AAATTATAAATTAATTCACATATATAT
* * * *
9504036 AAAATAAAAATAAAAATT-ATAT-TATAT
1 AAATTATAAAT--TAATTCACATATATAT
9504063 AAATTATAAATTAATTCACATATATAT
1 AAATTATAAATTAATTCACATATATAT
9504090 AAA
1 AAA
9504093 AATAAAAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
25 4 0.09
26 8 0.19
27 24 0.56
28 3 0.07
29 4 0.09
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (27 bp):
AAATTATAAATTAATTCACATATATAT
Found at i:9504102 original size:29 final size:29
Alignment explanation
Indices: 9504019--9504103 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 29
9504009 GAAATTATAT
9504019 TTAATTCACATATATAT-AAAATAAAAATA
1 TTAATTCACATATATATAAAAATAAAAA-A
** * * *
9504048 AAAATT---ATAT-TATATAAATTATAAA
1 TTAATTCACATATATATAAAAATAAAAAA
9504073 TTAATTCACATATATATAAAAATAAAAAA
1 TTAATTCACATATATATAAAAATAAAAAA
9504102 TT
1 TT
9504104 TATATATATA
Statistics
Matches: 41, Mismatches: 10, Indels: 10
0.67 0.16 0.16
Matches are distributed among these distances:
25 8 0.20
26 11 0.27
28 4 0.10
29 18 0.44
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (29 bp):
TTAATTCACATATATATAAAAATAAAAAA
Found at i:9504108 original size:23 final size:23
Alignment explanation
Indices: 9504039--9504113 Score: 64
Period size: 23 Copynumber: 3.1 Consensus size: 23
9504029 TATATATAAA
9504039 ATAAAAAT-AAAAA-TTATATTAT
1 ATAAAAATAAAAAATTTATA-TAT
* * *
9504061 ATAAATTATAAATTAATTCACATATAT
1 ATAAA-AATAAA-AAATT--TATATAT
9504088 ATAAAAATAAAAAATTTATATAT
1 ATAAAAATAAAAAATTTATATAT
9504111 ATA
1 ATA
9504114 TATATGTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
22 5 0.12
23 11 0.27
24 2 0.05
25 6 0.15
26 6 0.15
27 8 0.20
28 3 0.07
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAAAAATAAAAAATTTATATAT
Found at i:9505131 original size:18 final size:17
Alignment explanation
Indices: 9505087--9505132 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
9505077 TTTGATGTTA
9505087 TTAAATTTTTTTTAATT
1 TTAAATTTTTTTTAATT
**
9505104 TTACCCTTTTTTTTAATT
1 TTA-AATTTTTTTTAATT
*
9505122 TTTAATTTTTT
1 TTAAATTTTTT
9505133 AAGTTATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (17 bp):
TTAAATTTTTTTTAATT
Found at i:9505378 original size:22 final size:21
Alignment explanation
Indices: 9505353--9505398 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
9505343 ACATAAAAAA
9505353 TATTAAATTCATATATAATTTT
1 TATTAAATTCA-ATATAATTTT
* * *
9505375 TATTAATTTTAATATCATTTT
1 TATTAAATTCAATATAATTTT
9505396 TAT
1 TAT
9505399 ATCTGTCACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTAAATTCAATATAATTTT
Found at i:9506889 original size:12 final size:12
Alignment explanation
Indices: 9506852--9506894 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
9506842 ATTATAATTA
9506852 TAATTAAAT-AT
1 TAATTAAATAAT
*
9506863 TATATTCATATAAT
1 TA-ATT-AAATAAT
9506877 TAATTAAATAAT
1 TAATTAAATAAT
9506889 TAATTA
1 TAATTA
9506895 TTATATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 2 0.07
12 15 0.56
13 6 0.22
14 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
TAATTAAATAAT
Found at i:9506899 original size:25 final size:28
Alignment explanation
Indices: 9506842--9506911 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 28
9506832 ATTTTTTAAA
9506842 ATTATAATTATAATTAAATATTATATTC
1 ATTATAATTATAATTAAATATTATATTC
9506870 A-TATAA-T-TAATTAAATAATTA-ATT-
1 ATTATAATTATAATTAAAT-ATTATATTC
*
9506894 ATTAT-ATTATAATCAAAT
1 ATTATAATTATAATTAAAT
9506912 TGCAGTCGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
24 2 0.05
25 16 0.43
26 13 0.35
27 5 0.14
28 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTATAATTATAATTAAATATTATATTC
Found at i:9509172 original size:17 final size:15
Alignment explanation
Indices: 9509150--9509183 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
9509140 TTTTTACTAT
9509150 TAATGAAAAATAGAAAA
1 TAATG-AAAAT-GAAAA
9509167 TAATGAAAATGAAAA
1 TAATGAAAATGAAAA
9509182 TA
1 TA
9509184 TTTCTGAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 5 0.29
17 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.21
Consensus pattern (15 bp):
TAATGAAAATGAAAA
Found at i:9511460 original size:21 final size:21
Alignment explanation
Indices: 9511436--9511475 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9511426 CAAAAAGCAT
9511436 AAAACAAA-AAATAAAAAAAAG
1 AAAA-AAACAAATAAAAAAAAG
*
9511457 AAAAAAACAAATAGAAAAA
1 AAAAAAACAAATAAAAAAA
9511476 TGTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.85, C:0.05, G:0.05, T:0.05
Consensus pattern (21 bp):
AAAAAAACAAATAAAAAAAAG
Found at i:9511747 original size:17 final size:17
Alignment explanation
Indices: 9511727--9511760 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9511717 AAAAGGTAAT
9511727 AAAAAAAAAAAAAATGA
1 AAAAAAAAAAAAAATGA
* *
9511744 AAAAAGAAAGAAAATGA
1 AAAAAAAAAAAAAATGA
9511761 GAAGTTGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAAAAAATGA
Found at i:9511822 original size:8 final size:8
Alignment explanation
Indices: 9511804--9511833 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
9511794 CGTTGCATTT
9511804 AAAAAGAA
1 AAAAAGAA
9511812 AAAAATGAA
1 AAAAA-GAA
9511821 AAAAAGAA
1 AAAAAGAA
9511829 AAAAA
1 AAAAA
9511834 TAGGTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (8 bp):
AAAAAGAA
Found at i:9527403 original size:38 final size:38
Alignment explanation
Indices: 9527348--9527424 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
9527338 TTGAGATGTG
*
9527348 TTGGATTAGGATACATAAATTGATGGGGAGTTTTGCCA
1 TTGGATTAGGATACATAAATTGAGGGGGAGTTTTGCCA
*
9527386 TTGGATTAGGATGCATAAATTGAGGGGGAGTTTTGCCA
1 TTGGATTAGGATACATAAATTGAGGGGGAGTTTTGCCA
9527424 T
1 T
9527425 GCATTAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.27, C:0.08, G:0.31, T:0.34
Consensus pattern (38 bp):
TTGGATTAGGATACATAAATTGAGGGGGAGTTTTGCCA
Found at i:9529346 original size:36 final size:36
Alignment explanation
Indices: 9529306--9529433 Score: 143
Period size: 36 Copynumber: 3.6 Consensus size: 36
9529296 GATATATTCG
** * * *
9529306 TATTACTTGTTCTTTTATTCTCTAGAGAAACACTCT
1 TATTACTTGTTCTCCTATTTTGTAGAGAAATACTCT
* *
9529342 TATTATTTGTTCTCCTATTTTGTA-AGAAATA-TTT
1 TATTACTTGTTCTCCTATTTTGTAGAGAAATACTCT
*
9529376 ATATTACTTGTTCTCTTATTTTGTAGAGAAATACTCT
1 -TATTACTTGTTCTCCTATTTTGTAGAGAAATACTCT
* *
9529413 CATTACTTGTTCTTCTATTTT
1 TATTACTTGTTCTCCTATTTT
9529434 TTAAAGGAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
34 2 0.03
35 28 0.37
36 44 0.58
37 2 0.03
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (36 bp):
TATTACTTGTTCTCCTATTTTGTAGAGAAATACTCT
Found at i:9529672 original size:51 final size:51
Alignment explanation
Indices: 9529566--9529741 Score: 155
Period size: 51 Copynumber: 3.5 Consensus size: 51
9529556 TATTTAATAA
* * * * *
9529566 TTTTATATTTTTTAGGGAAACATTCCCATCACCTATTTCTTTTAATAATTT
1 TTTTTTATTTTTTAGGGAAACACTCTCATCACCTATATCTTTTAAAAATTT
*
9529617 TTTTTTATTTTTTAGGGAAACACTCTC-TTACCTA-AT-TTTTAAAAATTTT
1 TTTTTTATTTTTTAGGGAAACACTCTCATCACCTATATCTTTTAAAAA-TTT
* * * * * *
9529666 TCTTTTTTTTTTTTCGGGGAAACACTCTAATCACCTATTTCTTTTGATAA--T
1 T-TTTTTATTTTTT-AGGGAAACACTCTCATCACCTATATCTTTTAAAAATTT
* * *
9529717 TTTTCTCTTTTTTAGGAAAACACTC
1 TTTTTTATTTTTTAGGGAAACACTC
9529742 ATTTACCTAT
Statistics
Matches: 102, Mismatches: 17, Indels: 14
0.77 0.13 0.11
Matches are distributed among these distances:
48 8 0.08
49 15 0.15
50 27 0.26
51 38 0.37
52 6 0.06
53 1 0.01
54 7 0.07
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (51 bp):
TTTTTTATTTTTTAGGGAAACACTCTCATCACCTATATCTTTTAAAAATTT
Found at i:9529759 original size:102 final size:100
Alignment explanation
Indices: 9529593--9529778 Score: 241
Period size: 100 Copynumber: 1.8 Consensus size: 100
9529583 AAACATTCCC
* *
9529593 ATCACCTATTTCTTTTAATAATTTTTTTTTATTTTTTAGGGAAACACTCTCTTACCTAATTTTTA
1 ATCACCTATTTCTTTTAATAA-TTTTTTCTATTTTTTAGGAAAACACTCTCTTACCTAATTTTTA
* *
9529658 AAAATTTTTCTTTTTTTTTTTTCGGGGAAACACTCTA
65 AAAA-TCTTCTTATTTTTTTTTCGGGGAAACACTCTA
* * *
9529695 ATCACCTATTTCTTTTGATAA-TTTTTCTCTTTTTTAGGAAAACACTCAT-TTACCTATTCCTTT
1 ATCACCTATTTCTTTTAATAATTTTTTCTATTTTTTAGGAAAACACTC-TCTTACCTAAT--TTT
*
9529758 TAATAATCTTCTTATTTTTTT
63 TAAAAATCTTCTTATTTTTTT
9529779 AAAAAACGTT
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
100 31 0.42
101 14 0.19
102 28 0.38
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.54
Consensus pattern (100 bp):
ATCACCTATTTCTTTTAATAATTTTTTCTATTTTTTAGGAAAACACTCTCTTACCTAATTTTTAA
AAATCTTCTTATTTTTTTTTCGGGGAAACACTCTA
Found at i:9529778 original size:49 final size:47
Alignment explanation
Indices: 9529516--9529864 Score: 173
Period size: 49 Copynumber: 7.1 Consensus size: 47
9529506 CTTTTATTAC
* * *
9529516 TAATTTTTTTATTTTTTA-AAAAATACTTC-TTTACCTATTCTATTTAA
1 TAATTTTTATATTTTTTAGGAAAACAC-TCATTTACCTATTCT-TTTAA
* * *
9529563 TAA-TTTTATATTTTTTAGGGAAACATTCCCA-TCACCTATTTCTTTTAA
1 TAATTTTTATATTTTTTAGGAAAACA--CTCATTTACCTA-TTCTTTTAA
* * *
9529611 TAATTTTTTTTTATTTTTTAGGGAAACACTC-TCTTACCTAAT-TTTTAA
1 TAA--TTTTTATATTTTTTAGGAAAACACTCAT-TTACCTATTCTTTTAA
* * * * * * * *
9529659 AAATTTTTCTTTTTTTTTTTTCGGGGAAACACTCTAATCACCTATTTCTTTTGA
1 TAA---TT-TTTATATTTTTT-AGGAAAACACTC-ATTTACCTA-TTCTTTTAA
* *
9529713 TAATTTTTCTCTTTTTTAGGAAAACACTCATTTACCTATTCCTTTTAA
1 TAATTTTTATATTTTTTAGGAAAACACTCATTTACCTATT-CTTTTAA
* * *
9529761 TAATCTTCTTAT-TTTTTTA-AAAAACGTTCTCA-TTACTTATTCCTTTTAA
1 TAAT-TT-TTATATTTTTTAGGAAAAC--ACTCATTTACCTATT-CTTTTAA
*
9529810 TAACTTTTATATTTTTTTA-GAGAAACACTATCATTATA--TATTCTTTTAA
1 TAATTTTTATA-TTTTTTAGGA-AAACAC--TCATT-TACCTATTCTTTTAA
9529859 TAATTT
1 TAATTT
9529865 AACTATTTTT
Statistics
Matches: 240, Mismatches: 33, Indels: 56
0.73 0.10 0.17
Matches are distributed among these distances:
46 13 0.05
47 13 0.05
48 48 0.20
49 70 0.29
50 45 0.19
51 35 0.15
52 8 0.03
53 1 0.00
54 7 0.03
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52
Consensus pattern (47 bp):
TAATTTTTATATTTTTTAGGAAAACACTCATTTACCTATTCTTTTAA
Found at i:9530417 original size:40 final size:40
Alignment explanation
Indices: 9530349--9530427 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
9530339 ATCAGAACTA
*
9530349 GTGATAAGATTGTTTCAGTGAAGATTATTTTAAGAAACAG
1 GTGATAAGATTGTTTCAGTAAAGATTATTTTAAGAAACAG
* * *
9530389 GTGATAAGATTGTTTTAGTAAAGGTTATTTTATGAAACA
1 GTGATAAGATTGTTTCAGTAAAGATTATTTTAAGAAACA
9530428 ACTATTCATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.38
Consensus pattern (40 bp):
GTGATAAGATTGTTTCAGTAAAGATTATTTTAAGAAACAG
Found at i:9534649 original size:13 final size:13
Alignment explanation
Indices: 9534614--9534649 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
9534604 TTTAATAAAA
9534614 TATATATAATTTT
1 TATATATAATTTT
* *
9534627 TATTTTTAATTTT
1 TATATATAATTTT
9534640 TATATATAAT
1 TATATATAAT
9534650 GCGAATTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATATAATTTT
Found at i:9534905 original size:2 final size:2
Alignment explanation
Indices: 9534900--9534935 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9534890 TAAACAAAGT
9534900 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9534936 AACCCTAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9537558 original size:19 final size:19
Alignment explanation
Indices: 9537530--9537566 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9537520 TCATATATTT
9537530 TTAAAAATTATACTTATAA
1 TTAAAAATTATACTTATAA
* *
9537549 TTAAATATTATATTTATA
1 TTAAAAATTATACTTATA
9537567 TAATCAATTA
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAAAATTATACTTATAA
Found at i:9537575 original size:25 final size:26
Alignment explanation
Indices: 9537546--9537605 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
9537536 ATTATACTTA
9537546 TAATTAAAT-ATT-A-TATTTATATAA
1 TAATTAAATAATTAATTA-TTATATAA
*
9537570 TCAATTAAATAATTAATTATTATATTA
1 T-AATTAAATAATTAATTATTATATAA
9537597 TAATTAAAT
1 TAATTAAAT
9537606 TACAATTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 1 0.03
25 8 0.26
26 11 0.35
27 9 0.29
28 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
TAATTAAATAATTAATTATTATATAA
Found at i:9537612 original size:25 final size:25
Alignment explanation
Indices: 9537536--9537613 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 25
9537526 ATTTTTAAAA
*
9537536 ATTATACTTATAATTAAA-TATTA-T
1 ATTATA-TTATAATTAAATTATAATT
* *
9537560 ATTTATATAATCAATTAAATAATTAATT
1 A-TTATATTAT-AATTAAATTA-TAATT
*
9537588 ATTATATTATAATTAAATTACAATT
1 ATTATATTATAATTAAATTATAATT
9537613 A
1 A
9537614 CTAAATAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
24 4 0.09
25 17 0.40
26 10 0.23
27 10 0.23
28 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTATATTATAATTAAATTATAATT
Found at i:9539740 original size:8 final size:8
Alignment explanation
Indices: 9539710--9539750 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
9539700 TATTTATTTA
9539710 TATATATT
1 TATATATT
*
9539718 TATATAAT
1 TATATATT
9539726 TATATATT
1 TATATATT
*
9539734 TAAATATT
1 TATATATT
9539742 TATAT-TT
1 TATATATT
9539749 TA
1 TA
9539751 AAAAATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 4 0.14
8 25 0.86
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATATATT
Found at i:9539775 original size:21 final size:22
Alignment explanation
Indices: 9539736--9539787 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
9539726 TATATATTTA
9539736 AATA-TTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
*
9539757 ATTATTTTATATTTT-AAAAAT
1 AATATTTTATATTTTAAAAAAT
9539778 AATATTTTAT
1 AATATTTTAT
9539788 TAATTTCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:9541133 original size:65 final size:65
Alignment explanation
Indices: 9541059--9541197 Score: 224
Period size: 65 Copynumber: 2.1 Consensus size: 65
9541049 TTTTGGGGCC
* ** * * *
9541059 AAACGCCTTTAATATTCTCAACGATAAATTTTAATTGTCGGATTATTGAATGCGGCTATATTCAA
1 AAACGCCTTTAATATTCCCAACGATAAATTTTAATTGTCAAATTATTGAAGGCAGCTATATCCAA
9541124 AAACGCCTTTAATATTCCCAACGATAAATTTTAATTGTCAAATTATTGAAGGCAGCTATATCCAA
1 AAACGCCTTTAATATTCCCAACGATAAATTTTAATTGTCAAATTATTGAAGGCAGCTATATCCAA
9541189 AAACGCCTT
1 AAACGCCTT
9541198 CATAAACATG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 68 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (65 bp):
AAACGCCTTTAATATTCCCAACGATAAATTTTAATTGTCAAATTATTGAAGGCAGCTATATCCAA
Found at i:9545680 original size:14 final size:14
Alignment explanation
Indices: 9545661--9545704 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
9545651 GACAATTTAT
9545661 TTTAAATTTTAAAA
1 TTTAAATTTTAAAA
*
9545675 TTTAAATTTATTAAA
1 TTTAAATTT-TAAAA
*
9545690 TATTAATTTTTAAAA
1 T-TTAAATTTTAAAA
9545705 ATAATTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 9 0.36
15 9 0.36
16 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAAATTTTAAAA
Found at i:9547989 original size:20 final size:20
Alignment explanation
Indices: 9547964--9548001 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9547954 TGTTTTAATG
9547964 TTTGTGAAG-GAACTAAAATA
1 TTTGTG-AGTGAACTAAAATA
9547984 TTTGTGAGTGAACTAAAA
1 TTTGTGAGTGAACTAAAA
9548002 GAGATTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (20 bp):
TTTGTGAGTGAACTAAAATA
Found at i:9552752 original size:21 final size:22
Alignment explanation
Indices: 9552728--9552785 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 22
9552718 TATTTATTTA
9552728 ATTTTATATTTTAAAAAT-AAT
1 ATTTTATATTTTAAAAATAAAT
9552749 ATTTTATA--TTAAAAATAAAT
1 ATTTTATATTTTAAAAATAAAT
9552769 ATTTTATTAATTTTAAA
1 ATTTTA-T-ATTTTAAA
9552786 TCGAGTTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 8 0.25
20 9 0.28
21 9 0.28
22 1 0.03
24 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTTATATTTTAAAAATAAAT
Found at i:9554112 original size:11 final size:11
Alignment explanation
Indices: 9554087--9554118 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
9554077 TTTGTTTGTC
9554087 TTTTATATT-T
1 TTTTATATTAT
9554097 TTTTATATTAT
1 TTTTATATTAT
9554108 TTTTATATTAT
1 TTTTATATTAT
9554119 ATCATCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTATATTAT
Found at i:9566329 original size:27 final size:26
Alignment explanation
Indices: 9566275--9566337 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
9566265 TGTTTAATAT
*
9566275 ATAATATTATGATAAGATATGATAAA
1 ATAATATTATGATAAGATATAATAAA
*
9566301 ATAATATTATGATTAAGATCA-AATTAA
1 ATAATATTATGA-TAAGAT-ATAATAAA
9566328 ATAATATTAT
1 ATAATATTAT
9566338 CTTATCTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 12 0.36
27 20 0.61
28 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (26 bp):
ATAATATTATGATAAGATATAATAAA
Found at i:9567288 original size:26 final size:26
Alignment explanation
Indices: 9567259--9567312 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
9567249 AATAAGCTCG
* *
9567259 ATATTCATATTTGACTTCAAATTTAA
1 ATATTCATATATGAATTCAAATTTAA
**
9567285 ATATTTGTATATGAATTCAAATTTAA
1 ATATTCATATATGAATTCAAATTTAA
9567311 AT
1 AT
9567313 TAATATAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (26 bp):
ATATTCATATATGAATTCAAATTTAA
Found at i:9567360 original size:18 final size:19
Alignment explanation
Indices: 9567339--9567376 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9567329 TAAAAATTTT
9567339 AATA-AAAATATTT-ATTAA
1 AATATAAAAT-TTTGATTAA
9567357 AATATAAAATTTTGATTAA
1 AATATAAAATTTTGATTAA
9567376 A
1 A
9567377 TTTATAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
AATATAAAATTTTGATTAA
Found at i:9568550 original size:2 final size:2
Alignment explanation
Indices: 9568543--9568567 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9568533 TATTTAGGAG
9568543 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 A
9568568 CATACTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9574813 original size:2 final size:2
Alignment explanation
Indices: 9574806--9574863 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
9574796 ATGTGTAATG
* * *
9574806 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
9574848 AT AC AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT
9574864 TTTTAATGTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:9577059 original size:24 final size:24
Alignment explanation
Indices: 9577027--9577081 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
9577017 CAGGCTTATT
9577027 AAACT-TGTGGAAAAATTAAGAAATA
1 AAACTGTGT-GAAAAATTAAGAAA-A
*
9577052 AAACTGTGTGAAAAATTAAGAGAA
1 AAACTGTGTGAAAAATTAAGAAAA
9577076 AAACTG
1 AAACTG
9577082 AATGTATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 7 0.25
25 18 0.64
26 3 0.11
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.22
Consensus pattern (24 bp):
AAACTGTGTGAAAAATTAAGAAAA
Found at i:9577249 original size:22 final size:22
Alignment explanation
Indices: 9577224--9577267 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
9577214 ATTTTTTGTC
9577224 CTTAATTCTA-AGGATACAAATA
1 CTTAATTCTAGA-GATACAAATA
9577246 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
9577268 TAAATATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:9581370 original size:17 final size:18
Alignment explanation
Indices: 9581348--9581383 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
9581338 ATAGAGATAC
9581348 AAATATAAATA-TACAAT
1 AAATATAAATATTACAAT
*
9581365 AAATATACATATTACAAT
1 AAATATAAATATTACAAT
9581383 A
1 A
9581384 TTACAACCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATATAAATATTACAAT
Found at i:9583026 original size:41 final size:41
Alignment explanation
Indices: 9582965--9583046 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
9582955 CTTCACAACA
** * *
9582965 ATTCATCCTTGGCCGGTAATACGTGATCGTGCTGTTATTGC
1 ATTCATCCTTGGCCAATAATACATGATAGTGCTGTTATTGC
*
9583006 ATTCATCCTTGGGCAATAATACATGATAGTGCTGTTATTGC
1 ATTCATCCTTGGCCAATAATACATGATAGTGCTGTTATTGC
9583047 CATGGTGGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (41 bp):
ATTCATCCTTGGCCAATAATACATGATAGTGCTGTTATTGC
Found at i:9585605 original size:3 final size:3
Alignment explanation
Indices: 9585597--9585623 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9585587 GAAAGAAATC
9585597 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
9585624 ATCATTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9591396 original size:2 final size:2
Alignment explanation
Indices: 9591383--9591414 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
9591373 ACCGTCTCAC
*
9591383 AT AT AC 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
9591415 GATAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9597549 original size:30 final size:30
Alignment explanation
Indices: 9597513--9597573 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
9597503 TTGTTGATAT
9597513 AGTAAAATATTTATGTAGTGCTCGAAACGA
1 AGTAAAATATTTATGTAGTGCTCGAAACGA
*
9597543 AGTAAAATATTTATGTAGTGCTGGAAACGA
1 AGTAAAATATTTATGTAGTGCTCGAAACGA
9597573 A
1 A
9597574 TCGAATATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (30 bp):
AGTAAAATATTTATGTAGTGCTCGAAACGA
Found at i:9597953 original size:11 final size:11
Alignment explanation
Indices: 9597937--9597963 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
9597927 TAAATGAACG
9597937 AATTTTAAATA
1 AATTTTAAATA
9597948 AATTTTAAATA
1 AATTTTAAATA
9597959 AATTT
1 AATTT
9597964 ATTTACAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AATTTTAAATA
Found at i:9608413 original size:23 final size:25
Alignment explanation
Indices: 9608371--9608420 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
9608361 ATAATGTTCG
9608371 AATTTAATTTGATTAAATTAAA-AA
1 AATTTAATTTGATTAAATTAAACAA
9608395 AATTT-ATTTG-TTAATATTAAACAA
1 AATTTAATTTGATTAA-ATTAAACAA
9608419 AA
1 AA
9608421 ATATCCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.17
23 11 0.46
24 9 0.38
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (25 bp):
AATTTAATTTGATTAAATTAAACAA
Found at i:9608892 original size:11 final size:10
Alignment explanation
Indices: 9608878--9608902 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9608868 GAGAAAAAGG
9608878 TTTTTTTTTA
1 TTTTTTTTTA
9608888 TTTTTTTTTA
1 TTTTTTTTTA
9608898 TTTTT
1 TTTTT
9608903 ATAATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:9609085 original size:10 final size:10
Alignment explanation
Indices: 9609052--9609085 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
9609042 AAAGCATAAG
9609052 ATATATACAT
1 ATATATACAT
*
9609062 ATACATACAT
1 ATATATACAT
*
9609072 ATATATATAT
1 ATATATACAT
9609082 ATAT
1 ATAT
9609086 TTAATTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATACAT
Found at i:9610802 original size:21 final size:21
Alignment explanation
Indices: 9610778--9610818 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9610768 CCTAACAGTT
* *
9610778 ATAATTTTTTTTTCTATTCTC
1 ATAATTTATTTTCCTATTCTC
9610799 ATAATTTATTTTCCTATTCT
1 ATAATTTATTTTCCTATTCT
9610819 TAGATTGTAA
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:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (21 bp):
ATAATTTATTTTCCTATTCTC
Found at i:9615855 original size:47 final size:47
Alignment explanation
Indices: 9615802--9615911 Score: 130
Period size: 47 Copynumber: 2.3 Consensus size: 47
9615792 ATTCAGTTGC
* * * *
9615802 ATATACAATTTTAGGTTACAAATGTTAATGCCATATCATGATTCCTT
1 ATATACAATTTTACGTTACAAACGTTAATGCCATATCAAGACTCCTT
* * *
9615849 ATATACAGTTTTACGTTAGAAACGTTAATGTCATATCAAGACTCCTT
1 ATATACAATTTTACGTTACAAACGTTAATGCCATATCAAGACTCCTT
*
9615896 AGATCACCAATTTTAC
1 ATAT-A-CAATTTTAC
9615912 ATGGATCTAG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
47 43 0.83
48 1 0.02
49 8 0.15
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (47 bp):
ATATACAATTTTACGTTACAAACGTTAATGCCATATCAAGACTCCTT
Found at i:9617275 original size:2 final size:2
Alignment explanation
Indices: 9617268--9617299 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9617258 AGGCACTGAA
9617268 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
9617300 CAATAGTTTG
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
Found at i:9617352 original size:12 final size:12
Alignment explanation
Indices: 9617326--9617373 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
9617316 TCTTAAACAA
*
9617326 AAAAAAAAAATAG
1 AAAAAGAAAA-AG
9617339 AAAAAGAAAAAG
1 AAAAAGAAAAAG
9617351 AAAAAG-AAAAG
1 AAAAAGAAAAAG
*
9617362 AATGAAGAAAAA
1 AA-AAAGAAAAA
9617374 AGCAGAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 7 0.23
12 11 0.35
13 13 0.42
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:9617361 original size:5 final size:6
Alignment explanation
Indices: 9617326--9617373 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
9617316 TCTTAAACAA
* *
9617326 AAAAAA AAAATAG AAAAAG AAAAAG AAAAAG -AAAAG AATGAAG AAAAA
1 AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG AAAAA
9617374 AGCAGAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
5 5 0.14
6 21 0.58
7 10 0.28
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:9618644 original size:30 final size:30
Alignment explanation
Indices: 9618608--9618668 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
9618598 AATAATAGTA
9618608 TATAATTAATATAGAAATGAGACTGGTTAT
1 TATAATTAATATAGAAATGAGACTGGTTAT
9618638 TATAATTAATATAGAAATGAGACTGGTTAT
1 TATAATTAATATAGAAATGAGACTGGTTAT
9618668 T
1 T
9618669 TTGATAGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (30 bp):
TATAATTAATATAGAAATGAGACTGGTTAT
Found at i:9627127 original size:22 final size:22
Alignment explanation
Indices: 9627087--9627128 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
9627077 TGTATATTTA
*
9627087 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCTCTAAAATTAAG
9627109 TATTTGTATC-CTTAAAATTA
1 TATTTGTATCTC-TAAAATTA
9627129 GGATAGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (22 bp):
TATTTGTATCTCTAAAATTAAG
Found at i:9631073 original size:22 final size:22
Alignment explanation
Indices: 9631047--9631088 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9631037 TGTATATTTA
* *
9631047 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
9631069 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
9631089 GGATAGACAA
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:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:9635434 original size:4 final size:4
Alignment explanation
Indices: 9635425--9635451 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
9635415 TTTGTCAATT
9635425 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
9635452 TTATTTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:9637002 original size:15 final size:13
Alignment explanation
Indices: 9636974--9637012 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
9636964 AACTTATTCG
9636974 TTCATTTATTTTA
1 TTCATTTATTTTA
9636987 TTCATTTTATTTTTA
1 TTCA-TTTA-TTTTA
*
9637002 TTCAATTATTT
1 TTCATTTATTT
9637013 ATTTATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 7 0.30
14 7 0.30
15 9 0.39
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTCATTTATTTTA
Found at i:9639832 original size:14 final size:14
Alignment explanation
Indices: 9639813--9639852 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
9639803 GTTACTTTCT
9639813 TTTTCATTTTTTTA
1 TTTTCATTTTTTTA
**
9639827 TTTTCATTTTAATA
1 TTTTCATTTTTTTA
9639841 TTTT-ATTTTTTT
1 TTTTCATTTTTTT
9639853 CATATATTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCATTTTTTTA
Found at i:9641196 original size:15 final size:14
Alignment explanation
Indices: 9641167--9641213 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
9641157 TGACTTATTA
9641167 ATTCATTTA-TTTT
1 ATTCATTTATTTTT
9641180 ATTCATTTTATTTTT
1 ATTCA-TTTATTTTT
*
9641195 ATTCAATTAATTATTT
1 ATTC-ATTTATT-TTT
9641211 ATT
1 ATT
9641214 ACAAATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 5 0.17
14 4 0.14
15 13 0.45
16 7 0.24
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTCATTTATTTTT
Found at i:9641423 original size:3 final size:3
Alignment explanation
Indices: 9641415--9641456 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
9641405 TGAGATGATT
9641415 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9641457 ATTATTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9641463 original size:3 final size:3
Alignment explanation
Indices: 9641457--9641494 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
9641447 ATAATAATAA
9641457 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
9641495 ACAACCACGT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:9643408 original size:28 final size:27
Alignment explanation
Indices: 9643323--9643408 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
9643313 AGTTGTTTTA
*
9643323 TTTTAAGAAGTATAAATATATTAAT-AT
1 TTTTAA-AAGTATAAATATATTATTAAT
* * *
9643350 TTTT-AAA-TAAAAATTATTTTGTTAA-
1 TTTTAAAAGTATAAA-TATATTATTAAT
*
9643375 ATTTAAAATGTATAAATATATTATTAAT
1 TTTTAAAA-GTATAAATATATTATTAAT
9643403 TTTTAA
1 TTTTAA
9643409 CAAAATTATG
Statistics
Matches: 44, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
24 5 0.11
25 11 0.25
26 5 0.11
27 13 0.30
28 10 0.23
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (27 bp):
TTTTAAAAGTATAAATATATTATTAAT
Found at i:9643830 original size:29 final size:30
Alignment explanation
Indices: 9643797--9643862 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
9643787 ATTAATGTTA
*
9643797 AATTTTGTTATTATA-TTTTAATTTTATTG
1 AATTTTGTTATTATATTTTTAATTTCATTG
*
9643826 AATTTAT-TTATTATATTTTTAGTTTCATTG
1 AATTT-TGTTATTATATTTTTAATTTCATTG
*
9643856 ATTTTTG
1 AATTTTG
9643863 AACATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.65
Consensus pattern (30 bp):
AATTTTGTTATTATATTTTTAATTTCATTG
Found at i:9645451 original size:20 final size:21
Alignment explanation
Indices: 9645426--9645465 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
9645416 TTATTATTAT
9645426 TATTATTTATTAA-ATATAAA
1 TATTATTTATTAATATATAAA
9645446 TATTATTTATTAATATATAA
1 TATTATTTATTAATATATAA
9645466 TAATTAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTATTTATTAATATATAAA
Found at i:9645612 original size:30 final size:31
Alignment explanation
Indices: 9645578--9645640 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
9645568 TTTTTATATT
* * * *
9645578 TTTTATATAAATGTAGATTTT-TTTTATTAA
1 TTTTACATAAATATACATTTTCTCTTATTAA
*
9645608 TTTTACATATATATACATTTTCTCTTATTAA
1 TTTTACATAAATATACATTTTCTCTTATTAA
9645639 TT
1 TT
9645641 ATTTTTTATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (31 bp):
TTTTACATAAATATACATTTTCTCTTATTAA
Found at i:9645709 original size:16 final size:16
Alignment explanation
Indices: 9645681--9645725 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
9645671 TTTTATTAAC
*
9645681 ATTTTAT-TTTTATTA
1 ATTTTATATATTATTA
9645696 ATTTTATATATTATTA
1 ATTTTATATATTATTA
9645712 ATTTTATA-ATTATT
1 ATTTTATATATTATT
9645726 TTTTATTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 13 0.46
16 15 0.54
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTATATATTATTA
Found at i:9648466 original size:20 final size:20
Alignment explanation
Indices: 9648364--9648466 Score: 61
Period size: 20 Copynumber: 5.1 Consensus size: 20
9648354 TTTTGCATGA
* * *
9648364 ATTTGAATGACTAATATTAT
1 ATTTGCATGATTATTATTAT
9648384 ATTTGCATGA-TA--ATT-T
1 ATTTGCATGATTATTATTAT
*
9648400 ATTTGTATGATTATTGATTTATAT
1 ATTTGCATGATTATT-A--T-TAT
** **
9648424 ATTTGTGTGATTTATTAACAT
1 ATTTGCATGA-TTATTATTAT
9648445 ATTTGCATGATTATTATTAT
1 ATTTGCATGATTATTATTAT
9648465 AT
1 AT
9648467 ATTTAATTGC
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
16 10 0.15
17 5 0.08
19 2 0.03
20 20 0.31
21 10 0.15
22 1 0.02
23 1 0.02
24 11 0.17
25 5 0.08
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (20 bp):
ATTTGCATGATTATTATTAT
Found at i:9648488 original size:41 final size:40
Alignment explanation
Indices: 9648463--9648692 Score: 272
Period size: 41 Copynumber: 5.7 Consensus size: 40
9648453 GATTATTATT
9648463 ATATATTTAATTGCATGTTTTATATTGTTAA-T--TGCATA
1 ATATATTTAATTGCATGTTTTATATTGTTAATTCATG-ATA
* *
9648501 ATATATTTATTTGCATGTTTTATAATGTTAATTGCATGATA
1 ATATATTTAATTGCATGTTTTATATTGTTAATT-CATGATA
9648542 ATATATTTAATTGCATGTTTTATATTGTTAATTGCATGATA
1 ATATATTTAATTGCATGTTTTATATTGTTAATT-CATGATA
* *
9648583 ATATATTTAATTTCATGTTTTATATTGTTAATTACATGATT
1 ATATATTTAATTGCATGTTTTATATTGTTAATT-CATGATA
* *
9648624 ATATATTTTATTGCATGATTTATATAT-TTAATTACATGAT-
1 ATATATTTAATTGCATGTTTTATAT-TGTTAATT-CATGATA
* *
9648664 TTATATTGTTAATTGCATGATTATATATT
1 ATATA-T-TTAATTGCATG-TTTTATATT
9648693 TATTTGCATG
Statistics
Matches: 170, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 29 0.17
39 1 0.01
40 4 0.02
41 116 0.68
42 14 0.08
43 6 0.04
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.53
Consensus pattern (40 bp):
ATATATTTAATTGCATGTTTTATATTGTTAATTCATGATA
Found at i:9648688 original size:82 final size:81
Alignment explanation
Indices: 9648460--9648793 Score: 303
Period size: 82 Copynumber: 4.1 Consensus size: 81
9648450 CATGATTATT
* * * *
9648460 ATTATATATTTAATTGCATGTTTTATATTGTTAATTGCAT-AATATA-TTTATTTGCATGTTTTA
1 ATTATATATTTAATTGCATGATTTATATTGTTAATTGCATGATTATATTTTAATTGCATGTATTA
*
9648523 TA-ATGTTAATTGCATG
66 TATAT-TTAATTACATG
* * * * *
9648539 ATAATATATTTAATTGCATGTTTTATATTGTTAATTGCATGATAATATATTTAATTTCATGTTTT
1 ATTATATATTTAATTGCATGATTTATATTGTTAATTGCATGATTATAT-TTTAATTGCATGTATT
9648604 ATAT-TGTTAATTACATG
65 ATATAT-TTAATTACATG
* *
9648621 ATTATATATTTTATTGCATGATTTATATAT-TTAATTACATGATTTATATTGTTAATTGCATG-A
1 ATTATATATTTAATTGCATGATTTATAT-TGTTAATTGCATGA-TTATATT-TTAATTGCATGTA
* *
9648684 TTATATATTTATTTGCATG
63 TTATATATTTAATTACATG
* * * *
9648703 ATT-TATATTATTAATTACATGA-TTATATAT-TTATTTGCATGTTTTATATTGTTAGTTGCATG
1 ATTATATA-T-TTAATTGCATGATTTATAT-TGTTAATTGCATG-ATTATATT-TTAATTGCATG
* *
9648765 -ATTAGATATTTAATTATAT-
61 TATTATATATTTAATTACATG
*
9648784 ATTTTATATT
1 ATTATATATT
9648794 GTTAATTATT
Statistics
Matches: 218, Mismatches: 25, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
79 39 0.18
80 5 0.02
81 8 0.04
82 139 0.64
83 27 0.12
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.54
Consensus pattern (81 bp):
ATTATATATTTAATTGCATGATTTATATTGTTAATTGCATGATTATATTTTAATTGCATGTATTA
TATATTTAATTACATG
Found at i:9648693 original size:41 final size:41
Alignment explanation
Indices: 9648548--9648800 Score: 250
Period size: 41 Copynumber: 6.1 Consensus size: 41
9648538 GATAATATAT
* * *
9648548 TTAATTGCATG-TTTTATATTGTTAATTGCATGA-TAATATAT-
1 TTAATTGCATGATTATATA-T-TTAATTACATGATTTATAT-TG
* *
9648589 TTAATTTCATG-TTTTATATTGTTAATTACATGATTATATATT-
1 TTAATTGCATGATTATATA-T-TTAATTACATGATT-TATATTG
9648631 TT-ATTGCATGATTTATATATTTAATTACATGATTTATATTG
1 TTAATTGCATGA-TTATATATTTAATTACATGATTTATATTG
* * *
9648672 TTAATTGCATGATTATATATTTATTTGCATGATTTATATTA
1 TTAATTGCATGATTATATATTTAATTACATGATTTATATTG
* * * *
9648713 TTAATTACATGATTATATATTTATTTGCATGTTTTATATTG
1 TTAATTGCATGATTATATATTTAATTACATGATTTATATTG
* * *
9648754 TTAGTTGCATGATTAGATATTTAATTATAT-ATTTTATATTG
1 TTAATTGCATGATTATATATTTAATTACATGA-TTTATATTG
9648795 TTAATT
1 TTAATT
9648801 ATTATATATT
Statistics
Matches: 186, Mismatches: 19, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
40 6 0.03
41 156 0.84
42 14 0.08
43 10 0.05
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.55
Consensus pattern (41 bp):
TTAATTGCATGATTATATATTTAATTACATGATTTATATTG
Found at i:9648765 original size:103 final size:103
Alignment explanation
Indices: 9648531--9648767 Score: 347
Period size: 103 Copynumber: 2.3 Consensus size: 103
9648521 TATAATGTTA
* *
9648531 ATTGCATGA-TAATATATTTAATTGCATGTTTTATATTGTTAATTGCATGATAATATATTTAATT
1 ATTGCATGATTTATATATTTAATTGCATGATTTATATTGTTAATTGCATGATAATATATTTAATT
* *
9648595 TCATGTTTTATATTGTTAATTACATGATTATATATTTT
66 TCATGATTTATATTATTAATTACATGATTATATATTTT
* *
9648633 ATTGCATGATTTATATATTTAATTACATGATTTATATTGTTAATTGCATGATTATATATTT-ATT
1 ATTGCATGATTTATATATTTAATTGCATGATTTATATTGTTAATTGCATGATAATATATTTAATT
9648697 TGCATGATTTATATTATTAATTACATGATTATATA-TTT
66 T-CATGATTTATATTATTAATTACATGATTATATATTTT
* *
9648735 ATTTGCATGTTTTATAT-TGTTAGTTGCATGATT
1 A-TTGCATGATTTATATAT-TTAATTGCATGATT
9648768 AGATATTTAA
Statistics
Matches: 122, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
102 18 0.15
103 104 0.85
ACGTcount: A:0.31, C:0.05, G:0.11, T:0.53
Consensus pattern (103 bp):
ATTGCATGATTTATATATTTAATTGCATGATTTATATTGTTAATTGCATGATAATATATTTAATT
TCATGATTTATATTATTAATTACATGATTATATATTTT
Found at i:9648801 original size:144 final size:144
Alignment explanation
Indices: 9648501--9648793 Score: 412
Period size: 144 Copynumber: 2.0 Consensus size: 144
9648491 TAATTGCATA
* * * *
9648501 ATATATTTATTTGCATGTTTTATAATGTTAATTGCATGATAATATATTTAATTGCATGTTTTATA
1 ATATATTTAATTACATGATTTATAATGTTAATTGCATGATAATATATTTAATTGCATGATTTATA
* * *
9648566 TTGTTAATTGCATGATAATATATTTAATTTCATGTTTTATATTGTTAATTACATGATTATATATT
66 TTATTAATTACATGATAATATATTTAATTTCATGTTTTATATTGTTAATTACATGATTAGATATT
* *
9648631 TTATTGCATGATTT
131 TAATTACATGATTT
* * *
9648645 ATATATTTAATTACATGATTTATATTGTTAATTGCATGATTATATATTTATTTGCATGATTTATA
1 ATATATTTAATTACATGATTTATAATGTTAATTGCATGATAATATATTTAATTGCATGATTTATA
* * *
9648710 TTATTAATTACATGATTATATATTT-ATTTGCATGTTTTATATTGTTAGTTGCATGATTAGATAT
66 TTATTAATTACATGATAATATATTTAATTT-CATGTTTTATATTGTTAATTACATGATTAGATAT
*
9648774 TTAATTATAT-ATTT
130 TTAATTACATGATTT
9648788 -TATATT
1 ATATATT
9648794 GTTAATTATT
Statistics
Matches: 132, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
142 6 0.05
143 8 0.06
144 118 0.89
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.54
Consensus pattern (144 bp):
ATATATTTAATTACATGATTTATAATGTTAATTGCATGATAATATATTTAATTGCATGATTTATA
TTATTAATTACATGATAATATATTTAATTTCATGTTTTATATTGTTAATTACATGATTAGATATT
TAATTACATGATTT
Found at i:9648814 original size:21 final size:21
Alignment explanation
Indices: 9648774--9648814 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9648764 GATTAGATAT
*
9648774 TTAATTATATATTTTATATTG
1 TTAATTATATATATTATATTG
9648795 TTAATTATTATATATT-TATT
1 TTAATTA-TATATATTATATT
9648815 TGCATGTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTAATTATATATATTATATTG
Found at i:9648944 original size:19 final size:19
Alignment explanation
Indices: 9648907--9648950 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
9648897 TTCATTATTA
***
9648907 TTATTGCATGATTTTATAT
1 TTATTGCATGATACGATAT
9648926 TTATTGCATGATACGATAT
1 TTATTGCATGATACGATAT
9648945 TATATT
1 T-TATT
9648951 AATTTTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (19 bp):
TTATTGCATGATACGATAT
Found at i:9649193 original size:26 final size:25
Alignment explanation
Indices: 9649140--9649216 Score: 77
Period size: 26 Copynumber: 3.1 Consensus size: 25
9649130 TATTGCATAA
* *
9649140 TTATG-TATAATTACATGAATGATTT
1 TTATGATATAATTGCATGAAT-AATT
9649165 TTATGATATAATTGCATGACATAATT
1 TTATGATATAATTGCATGA-ATAATT
* **
9649191 TTATAATATTTTTGCATG-ATAATT
1 TTATGATATAATTGCATGAATAATT
9649215 TT
1 TT
9649217 TGCATGGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
24 8 0.18
25 5 0.11
26 30 0.67
27 2 0.04
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.49
Consensus pattern (25 bp):
TTATGATATAATTGCATGAATAATT
Found at i:9657277 original size:43 final size:42
Alignment explanation
Indices: 9657169--9657422 Score: 226
Period size: 42 Copynumber: 6.0 Consensus size: 42
9657159 TCTCATTTTG
* * *
9657169 TTTTCTAAAAGTTTCAAAGCCTCAATTATAAGGGA-CTATTTTAT
1 TTTTC-AAAAGTTTCAAAGCCTCAGTTGT-GGGGAGC-ATTTTAT
* * * *
9657213 TTTT-TAAAGTTTCAATGCCTCAGTTATGGGAGAGTATTTTAT
1 TTTTCAAAAGTTTCAAAGCCTCAGTTGTGGG-GAGCATTTTAT
* *
9657255 TTTTCAAAAGTTTTAAAACCTCAGTTGTGGGGGAGCATTTTAT
1 TTTTCAAAAGTTTCAAAGCCTCAGTTGT-GGGGAGCATTTTAT
* * * * * *
9657298 TTTTTAAAAGTTCCAAAGCCTTAGTTGTAAGGAAACATTTTA-
1 TTTTCAAAAGTTTCAAAGCCTCAGTTGT-GGGGAGCATTTTAT
* *
9657340 TTTTCAAAAGTTTCAAAACCTCAGTTGTGGGTAGCATTTTAT
1 TTTTCAAAAGTTTCAAAGCCTCAGTTGTGGGGAGCATTTTAT
* * * * *
9657382 TTTTCAAAAATTTTAAAGCCTTAATTGTGGAGAAGCATTTT
1 TTTTCAAAAGTTTCAAAGCCTCAGTTGTGG-GGAGCATTTT
9657423 TCAAAAACAA
Statistics
Matches: 171, Mismatches: 33, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
41 12 0.07
42 82 0.48
43 70 0.41
44 7 0.04
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (42 bp):
TTTTCAAAAGTTTCAAAGCCTCAGTTGTGGGGAGCATTTTAT
Found at i:9657729 original size:12 final size:12
Alignment explanation
Indices: 9657698--9657736 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
9657688 TTGTATTTTT
*
9657698 ATTTTTTAGTCTA
1 ATTTTTT-GTTTA
9657711 ATTTTTTGTTTA
1 ATTTTTTGTTTA
*
9657723 ATTTTTTTTTTA
1 ATTTTTTGTTTA
9657735 AT
1 AT
9657737 CAAAAGAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.72
Consensus pattern (12 bp):
ATTTTTTGTTTA
Found at i:9658359 original size:24 final size:25
Alignment explanation
Indices: 9658331--9658378 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
9658321 CCATGTCTCG
* *
9658331 ATTAGGCCTATC-GTGTCCAGGCCC
1 ATTAGGCCAATCTGTGCCCAGGCCC
9658355 ATTAGGCCAATCTGTGCCCAGGCC
1 ATTAGGCCAATCTGTGCCCAGGCC
9658379 TAGTTGGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.19, C:0.33, G:0.25, T:0.23
Consensus pattern (25 bp):
ATTAGGCCAATCTGTGCCCAGGCCC
Found at i:9658412 original size:3 final size:3
Alignment explanation
Indices: 9658404--9658429 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9658394 CTTTTGTATT
9658404 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
9658430 ATTATTATTA
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:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:9658434 original size:3 final size:3
Alignment explanation
Indices: 9658428--9658459 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
9658418 GTTGTTGTTG
9658428 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9658460 TTCTTTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:9658536 original size:5 final size:5
Alignment explanation
Indices: 9658526--9658575 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
9658516 ATTATTATTA
* *
9658526 TTTTC TTTTC TTTTC TTTTC -TTTC TTTTC TTCTTTC TTTTT TTTTG TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -T-TTTC TTTTC TTTTC TTTT
9658576 AATTCACACG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
4 4 0.10
5 30 0.75
6 2 0.05
7 4 0.10
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:9658551 original size:9 final size:9
Alignment explanation
Indices: 9658527--9658568 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
9658517 TTATTATTAT
9658527 TTTCTTTTC
1 TTTCTTTTC
9658536 TTTTCTTTTC
1 -TTTCTTTTC
9658546 TTTCTTTTC
1 TTTCTTTTC
9658555 -TTC-TTTC
1 TTTCTTTTC
9658562 TTT-TTTT
1 TTTCTTTT
9658569 TTGTTTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 4 0.13
8 8 0.27
9 9 0.30
10 9 0.30
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:9658887 original size:21 final size:21
Alignment explanation
Indices: 9658863--9658912 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
9658853 TTCTGGGAAT
* *
9658863 AATCTGGGCAAATTTTGGAGA
1 AATCTGGGAAAATTTTGAAGA
*
9658884 AATCTGAGAAAATTTTGAAGA
1 AATCTGGGAAAATTTTGAAGA
9658905 AATCTGGG
1 AATCTGGG
9658913 TTTTTTAGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (21 bp):
AATCTGGGAAAATTTTGAAGA
Found at i:9659349 original size:18 final size:19
Alignment explanation
Indices: 9659326--9659367 Score: 77
Period size: 18 Copynumber: 2.3 Consensus size: 19
9659316 GATCGAAGGT
9659326 TTTTTATTTTTT-ATTTTA
1 TTTTTATTTTTTGATTTTA
9659344 TTTTTATTTTTTGATTTTA
1 TTTTTATTTTTTGATTTTA
9659363 TTTTT
1 TTTTT
9659368 TCTATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.83
Consensus pattern (19 bp):
TTTTTATTTTTTGATTTTA
Found at i:9659362 original size:31 final size:30
Alignment explanation
Indices: 9659327--9659399 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
9659317 ATCGAAGGTT
*
9659327 TTTTATTTTTTAT-TTTATTTTTATTTTTTGA
1 TTTTATTTTTTATATTT-TTATTA-TTTTTGA
* *
9659358 TTTTATTTTTTCTATTTTTATTATTTTTGG
1 TTTTATTTTTTATATTTTTATTATTTTTGA
9659388 TTTTATTTTTTA
1 TTTTATTTTTTA
9659400 AAAGAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 17 0.46
31 17 0.46
32 3 0.08
ACGTcount: A:0.15, C:0.01, G:0.04, T:0.79
Consensus pattern (30 bp):
TTTTATTTTTTATATTTTTATTATTTTTGA
Found at i:9659376 original size:15 final size:14
Alignment explanation
Indices: 9659325--9659398 Score: 73
Period size: 13 Copynumber: 5.4 Consensus size: 14
9659315 CGATCGAAGG
9659325 TTTTTTA-TTTT-T
1 TTTTTTATTTTTAT
*
9659337 TATTTTATTTTTAT
1 TTTTTTATTTTTAT
*
9659351 TTTTTGA-TTTTAT
1 TTTTTTATTTTTAT
9659364 TTTTTCTATTTTTAT
1 TTTTT-TATTTTTAT
**
9659379 TATTTTTGGTTTTAT
1 T-TTTTTATTTTTAT
9659394 TTTTT
1 TTTTT
9659399 AAAAGAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
12 6 0.12
13 15 0.29
14 11 0.22
15 15 0.29
16 4 0.08
ACGTcount: A:0.14, C:0.01, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTTTATTTTTAT
Found at i:9659396 original size:28 final size:25
Alignment explanation
Indices: 9659325--9659397 Score: 67
Period size: 28 Copynumber: 2.7 Consensus size: 25
9659315 CGATCGAAGG
*
9659325 TTTTTT-ATTTTTTATTTTATTTTTA
1 TTTTTTGATTTTAT-TTTTATTTTTA
9659350 TTTTTTGATTTTATTTTTTCTATTTTTA
1 TTTTTTGATTTTA--TTTT-TATTTTTA
*
9659378 TTATTTTTGGTTTTATTTTT
1 -T-TTTTTGATTTTATTTTT
9659398 TAAAAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
25 6 0.15
26 5 0.12
27 4 0.10
28 13 0.32
29 1 0.03
30 11 0.28
ACGTcount: A:0.14, C:0.01, G:0.04, T:0.81
Consensus pattern (25 bp):
TTTTTTGATTTTATTTTTATTTTTA
Found at i:9659491 original size:25 final size:25
Alignment explanation
Indices: 9659446--9659494 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
9659436 AGTATTTCTG
* *
9659446 AAAGAAAAAAATTATTTAAAAAAAA
1 AAAGAAAAAAATCATTCAAAAAAAA
*
9659471 AAAGAAAAAAATCCTTCAAAAAAA
1 AAAGAAAAAAATCATTCAAAAAAA
9659495 TCTTTGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.16
Consensus pattern (25 bp):
AAAGAAAAAAATCATTCAAAAAAAA
Found at i:9670528 original size:41 final size:40
Alignment explanation
Indices: 9670482--9670582 Score: 105
Period size: 41 Copynumber: 2.5 Consensus size: 40
9670472 AAAGATTATT
* *
9670482 TTCAGGCTGATGAAAGATGATTTCTTTGCCAA-AGATATGCA
1 TTCAGG-TAATGAAAGATGATTTCTATGCCAAGA-ATATGCA
* * * *
9670523 TTCAGGTTAGTAAAATATGGTTTCTATGCCAAGAATATGCA
1 TTCAGG-TAATGAAAGATGATTTCTATGCCAAGAATATGCA
9670564 TTCAGGTTAATGAAAGATG
1 TTCAGG-TAATGAAAGATG
9670583 TTTTTCATAA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
41 48 0.98
42 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.33
Consensus pattern (40 bp):
TTCAGGTAATGAAAGATGATTTCTATGCCAAGAATATGCA
Found at i:9671022 original size:114 final size:113
Alignment explanation
Indices: 9670732--9671395 Score: 459
Period size: 114 Copynumber: 5.9 Consensus size: 113
9670722 TTGCATTATT
* * * * *
9670732 CAGTCATTCGATCTCGACTTAGGTTAAATCATCTTCAGACTCACGACACCAATCTAATCATTTAT
1 CAGTCATCCGATCTCGACTTAGGTCAAATCATCTTCAAACTCGCAACACCAATCTAATCATTTAT
* * *
9670797 TTATGATCTCGACTCGATCTTGGTCACCTTCAAACTCACGACATCATCC
66 TTATGACCTCTACTCGATCTTGGTCACCTTCAGACT-ACGACATCATCC
* * * * * * *
9670846 CAATCATCCAATCTTGACTTAGGTCAAATCATCATCAGACTCGCAACATCAAT-TCAACCATTTA
1 CAGTCATCCGATCTCGACTTAGGTCAAATCATCTTCAAACTCGCAACACCAATCT-AATCATTTA
* * * * * * *
9670910 TTTACT-ACCTCTACTTGGTTTTGATCATCTTCAGACTAGCTACATCATCT
65 TTTA-TGACCTCTACTCGATCTTGGTCACCTTCAGACTA-CGACATCATCC
* * * * * * *
9670960 TAGTCATCCGATCTCGACTTAGGTTAAATTATCTTCAAACTCGTAACACTAGTCTGATCATTTAT
1 CAGTCATCCGATCTCGACTTAGGTCAAATCATCTTCAAACTCGCAACACCAATCTAATCATTTAT
* * * *
9671025 TTATGACCT-TGACTCAATCTTGGTCACCTTTAGACGCACGACATTATCC
66 TTATGACCTCT-ACTCGATCTTGGTCACCTTCAGAC-TACGACATCATCC
* * * * * *
9671074 CAGTCATTCGATCTCGACTTAGGTCAGATTATCTTCTAAC-CGTAACACCAATCTGATCATTTA-
1 CAGTCATCCGATCTCGACTTAGGTCAAATCATCTTCAAACTCGCAACACCAATCTAATCATTTAT
* * * **
9671137 --A-G--CTCAACTCGATCTTGGTCACCTTTAGACTCGCGGTATCATCC
66 TTATGACCTCTACTCGATCTTGGTCACCTTCAGACT-ACGACATCATCC
* * * * * * * ** * *
9671181 TAATCATACGATCTTGACTTAGATCAGATCATCTTCAAACTTGTGACACCAGTCTGATCATTTAT
1 CAGTCATCCGATCTCGACTTAGGTCAAATCATCTTCAAACTCGCAACACCAATCTAATCATTTAT
** * * * * *
9671246 TTACAATCTCGACTTGATTTTGGTCACCTTCAGACTCACGACATTATCC
66 TTATGACCTCTACTCGATCTTGGTCACCTTCAGACT-ACGACATCATCC
* * * * * * * * * * * * * *
9671295 CAATAATCTGACCTTGACTTAGATCAGATCATTTTTAGACTTGCGACACCAAT-TCGATCATTTG
1 CAGTCATCCGATCTCGACTTAGGTCAAATCATCTTCAAACTCGCAACACCAATCT-AATCATTTA
** *
9671359 TTTACAACCTCGACTCGATCTTGGTCACCTTCAGACT
65 TTTATGACCTCTACTCGATCTTGGTCACCTTCAGACT
9671396 CGTGACATCG
Statistics
Matches: 441, Mismatches: 92, Indels: 34
0.78 0.16 0.06
Matches are distributed among these distances:
107 66 0.15
108 20 0.05
109 1 0.00
110 1 0.00
111 1 0.00
113 26 0.06
114 323 0.73
115 3 0.01
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.34
Consensus pattern (113 bp):
CAGTCATCCGATCTCGACTTAGGTCAAATCATCTTCAAACTCGCAACACCAATCTAATCATTTAT
TTATGACCTCTACTCGATCTTGGTCACCTTCAGACTACGACATCATCC
Found at i:9671194 original size:107 final size:111
Alignment explanation
Indices: 9670951--9671245 Score: 328
Period size: 107 Copynumber: 2.7 Consensus size: 111
9670941 CAGACTAGCT
* * * * *
9670951 ACATCATCTTAGTCATCCGATCTCGACTTAGGTTAAATTATCTTCAAACTCGTAACACTAGTCTG
1 ACATCATCCTAGTCATACGATCTCGACTTAGGTCAGATTATCTTCAAACTCGTAACACCAGTCTG
**
9671016 ATCATTTATTTATGACCTTGACTCAATCTTGGTCACCTTTAGACGCACG
66 ATCATTTA--TATGA-CTCAACTCAATCTTGGTCACCTTTAGACGCACG
* * * * *
9671065 ACATTATCCCAGTCATTCGATCTCGACTTAGGTCAGATTATCTTCTAAC-CGTAACACCAATCTG
1 ACATCATCCTAGTCATACGATCTCGACTTAGGTCAGATTATCTTCAAACTCGTAACACCAGTCTG
* * *
9671129 ATCATTTA-A-G-CTCAACTCGATCTTGGTCACCTTTAGACTCGCG
66 ATCATTTATATGACTCAACTCAATCTTGGTCACCTTTAGACGCACG
** * * * * * *
9671172 GTATCATCCTAATCATACGATCTTGACTTAGATCAGATCATCTTCAAACTTGTGACACCAGTCTG
1 ACATCATCCTAGTCATACGATCTCGACTTAGGTCAGATTATCTTCAAACTCGTAACACCAGTCTG
9671237 ATCATTTAT
66 ATCATTTAT
9671246 TTACAATCTC
Statistics
Matches: 152, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
107 67 0.44
108 20 0.13
109 1 0.01
110 1 0.01
113 21 0.14
114 42 0.28
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.34
Consensus pattern (111 bp):
ACATCATCCTAGTCATACGATCTCGACTTAGGTCAGATTATCTTCAAACTCGTAACACCAGTCTG
ATCATTTATATGACTCAACTCAATCTTGGTCACCTTTAGACGCACG
Found at i:9671754 original size:3 final size:3
Alignment explanation
Indices: 9671748--9671790 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
9671738 TGTATTTTTG
*
9671748 TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9671791 TTCCTTTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:9671879 original size:12 final size:11
Alignment explanation
Indices: 9671852--9671888 Score: 58
Period size: 12 Copynumber: 3.4 Consensus size: 11
9671842 AATAATAATC
9671852 TTTTCTTT-TT
1 TTTTCTTTCTT
9671862 TTTTCTTTCTT
1 TTTTCTTTCTT
9671873 TTCTTCTTTCTT
1 TT-TTCTTTCTT
9671885 TTTT
1 TTTT
9671889 TTGTTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 8 0.32
11 6 0.24
12 11 0.44
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:9671886 original size:22 final size:21
Alignment explanation
Indices: 9671850--9671895 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
9671840 ATAATAATAA
*
9671850 TCTTTTCTT-TTT-TTTTCTT
1 TCTTTTCTTCTTTCTTTTTTT
9671869 TCTTTTCTTCTTTCTTTTTTT
1 TCTTTTCTTCTTTCTTTTTTT
*
9671890 TGTTTT
1 TCTTTT
9671896 AATTCACACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 3 0.13
21 11 0.48
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (21 bp):
TCTTTTCTTCTTTCTTTTTTT
Found at i:9672755 original size:5 final size:5
Alignment explanation
Indices: 9672745--9672810 Score: 57
Period size: 5 Copynumber: 13.2 Consensus size: 5
9672735 TTCTCTTTTC
* *
9672745 TATTT TATTT T-TATT T-TTT GATTT TATTT TATTT TATTC TATTT TAATTAT
1 TATTT TATTT TAT-TT TATTT TATTT TATTT TATTT TATTT TATTT T-ATT-T
*
9672796 T-TTT TGTTT TATTT T
1 TATTT TATTT TATTT T
9672811 TTTAAAGAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
4 5 0.10
5 41 0.80
6 3 0.06
7 2 0.04
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:9672813 original size:24 final size:23
Alignment explanation
Indices: 9672745--9672815 Score: 65
Period size: 26 Copynumber: 3.0 Consensus size: 23
9672735 TTCTCTTTTC
* *
9672745 TATTTTATTTTTA-TTTTTTGAT
1 TATTTTTTTTTTATTTTTTTAAT
9672767 T-TTATTTTATTTTATTCTATTTTAAT
1 TATT-TTTT-TTTTATT-T-TTTTAAT
9672793 TATTTTTTGTTTTATTTTTTTAA
1 TATTTTTT-TTTTATTTTTTTAA
9672816 AGAAAAAAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
21 2 0.05
22 4 0.10
23 5 0.12
24 7 0.17
25 2 0.05
26 18 0.45
27 2 0.05
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.76
Consensus pattern (23 bp):
TATTTTTTTTTTATTTTTTTAAT
Found at i:9672894 original size:23 final size:22
Alignment explanation
Indices: 9672867--9672909 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
9672857 TTTCTGAAAG
9672867 GAAAAAAATAATTCAAAAAAAA
1 GAAAAAAATAATTCAAAAAAAA
**
9672889 GAAAAAAATCCTTCAAAAAAA
1 GAAAAAAATAATTCAAAAAAA
9672910 TCTTTGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.72, C:0.09, G:0.05, T:0.14
Consensus pattern (22 bp):
GAAAAAAATAATTCAAAAAAAA
Found at i:9673460 original size:32 final size:33
Alignment explanation
Indices: 9673424--9673485 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
9673414 ATTTGCATAT
* *
9673424 TAATATTATATTTGCATGA-TAATTTATTTACC
1 TAATATTATATTTACATGATTAATATATTTACC
*
9673456 TAATATTTTATTTACATGATTAATATATTT
1 TAATATTATATTTACATGATTAATATATTT
9673486 GTGTGATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.53
Consensus pattern (33 bp):
TAATATTATATTTACATGATTAATATATTTACC
Done.