Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167921.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_185, 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: 56231
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:7188 original size:16 final size:16
Alignment explanation
Indices: 7155--7188 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7145 AAAAAAATTC
*
7155 AAGAAACAAAAAGGAA
1 AAGAAACAAAAAGAAA
*
7171 AAGAAACAAAATGAAA
1 AAGAAACAAAAAGAAA
7187 AA
1 AA
7189 AAAATGATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (16 bp):
AAGAAACAAAAAGAAA
Found at i:7342 original size:59 final size:59
Alignment explanation
Indices: 7248--7410 Score: 260
Period size: 59 Copynumber: 2.8 Consensus size: 59
7238 GCTTTTGTAT
* * *
7248 AAGGAAAATTGATACTTTCAATTTTTGCTCGAAAATATTTTTTAGAAAAACTTATTTTC
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAAACTTATTTTC
7307 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTAG-AAAACTTATTTTC
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAAACTTATTTTC
* *
7364 AAGG-AAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGAAA
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAA
7411 TTTTATTTAA
Statistics
Matches: 97, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
56 31 0.32
57 23 0.24
58 9 0.09
59 34 0.35
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.42
Consensus pattern (59 bp):
AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAAACTTATTTTC
Found at i:7387 original size:56 final size:58
Alignment explanation
Indices: 7248--7404 Score: 255
Period size: 56 Copynumber: 2.7 Consensus size: 58
7238 GCTTTTGTAT
* * *
7248 AAGGAAAATTGATACTTTCAATTTTTGCTCGAAAATATTTTTTAGAAAAACTTATTTTC
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTAGAAAAACTTATTTTC
7307 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTAG-AAAACTTATTTTC
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTAGAAAAACTTATTTTC
*
7364 AAGG-AAATTGATACTTTCAACTTTTCCTTAAAAATATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTT
7405 TTGAAATTTT
Statistics
Matches: 94, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
56 36 0.38
57 17 0.18
58 7 0.07
59 34 0.36
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (58 bp):
AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTAGAAAAACTTATTTTC
Found at i:7506 original size:16 final size:17
Alignment explanation
Indices: 7480--7512 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
7470 AATTCTAGTC
*
7480 TAATCAATAAATAATAA
1 TAATCAATAAAAAATAA
7497 TAAT-AATAAAAAATAA
1 TAATCAATAAAAAATAA
7513 ATAAATAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
TAATCAATAAAAAATAA
Found at i:8374 original size:21 final size:21
Alignment explanation
Indices: 8341--8423 Score: 89
Period size: 21 Copynumber: 3.9 Consensus size: 21
8331 TAAAAATAAT
* *
8341 ATATTAATGGATAACTAGAAAA
1 ATATTAATAGATAAATA-AAAA
8363 A-A-TAATTAGATAAATAAAAA
1 ATATTAA-TAGATAAATAAAAA
8383 ATATTAATAGATAAATAATAATA
1 ATATTAATAGATAAATAA-AA-A
*
8406 ATAATAATAGATAAATAA
1 ATATTAATAGATAAATAA
8424 TAATAAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
20 8 0.15
21 21 0.40
22 6 0.11
23 18 0.34
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (21 bp):
ATATTAATAGATAAATAAAAA
Found at i:8376 original size:42 final size:44
Alignment explanation
Indices: 8330--8428 Score: 116
Period size: 42 Copynumber: 2.3 Consensus size: 44
8320 AAAGATAAAA
* *
8330 ATAAA-AATAATATATTAATGGATAACTAGA-AAAAATAAT-TAG
1 ATAAATAATAATATATTAATAGATAAATA-ATAAAAATAATATAG
* *
8372 ATAAATAA-AAAATATTAATAGATAAATAATAATAATAATAATAG
1 ATAAATAATAATATATTAATAGATAAATAATAAAAATAAT-ATAG
8416 ATAAATAATAATA
1 ATAAATAATAATA
8429 AAAAACATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
41 1 0.02
42 30 0.64
43 2 0.04
44 11 0.23
45 3 0.06
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (44 bp):
ATAAATAATAATATATTAATAGATAAATAATAAAAATAATATAG
Found at i:8396 original size:17 final size:16
Alignment explanation
Indices: 8359--8433 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 16
8349 GGATAACTAG
8359 AAAAAATAATTAGATAAAT
1 AAAAAAT-ATTA-AT-AAT
8378 AAAAAATATTAATAGAT
1 AAAAAATATTAATA-AT
* *
8395 AAATAATAATAATAAT
1 AAAAAATATTAATAAT
* * *
8411 AATAGATAAATAATAAT
1 AAAAAAT-ATTAATAAT
8428 AAAAAA
1 AAAAAA
8434 CATATATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
16 7 0.15
17 29 0.62
18 4 0.09
19 7 0.15
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (16 bp):
AAAAAATATTAATAAT
Found at i:8404 original size:3 final size:3
Alignment explanation
Indices: 8382--8526 Score: 55
Period size: 3 Copynumber: 45.0 Consensus size: 3
8372 ATAAATAAAA
*
8382 AAT ATT AAT AGAT AAAT AAT AAT AAT AAT AAT AGAT AAAT AAT AAT AA-
1 AAT AAT AAT A-AT -AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AAT
* * **
8430 AA- AAC ATAT ATAT ATT AAT AGAT AAAT AAT AAT ATAT GTT AAT AGAT
1 AAT AAT A-AT A-AT AAT AAT A-AT -AAT AAT AAT A-AT AAT AAT A-AT
* * * *
8477 AA- AAA AAT -AT ATAT GTAT ATT AAT AAAT AAT AAT AGT AAT AAT AAAT
1 AAT AAT AAT AAT A-AT -AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT
8524 AAT
1 AAT
8527 TAAATAAAAA
Statistics
Matches: 110, Mismatches: 16, Indels: 32
0.70 0.10 0.20
Matches are distributed among these distances:
2 8 0.07
3 66 0.60
4 33 0.30
5 3 0.03
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:8413 original size:23 final size:23
Alignment explanation
Indices: 8363--8429 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
8353 AACTAGAAAA
8363 AATAATTAGATAAATAA-AA-AAT
1 AATAA-TAGATAAATAATAATAAT
*
8385 ATTAATAGATAAATAATAATAAT
1 AATAATAGATAAATAATAATAAT
8408 AATAATAGATAAATAATAATAA
1 AATAATAGATAAATAATAATAA
8430 AAAACATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.27
22 6 0.15
23 24 0.59
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (23 bp):
AATAATAGATAAATAATAATAAT
Found at i:8465 original size:24 final size:23
Alignment explanation
Indices: 8375--8526 Score: 100
Period size: 23 Copynumber: 6.6 Consensus size: 23
8365 TAATTAGATA
* * * *
8375 AATAAAAAATATTAATAGATAAAT
1 AATAATAAATAATAATATAT-ATT
* *
8399 AATAAT-AATAATAATAGATAAAT
1 AATAATAAATAATAATATAT-ATT
* *
8422 AATAATAAAAAACATATATATATT
1 AATAATAAATAATA-ATATATATT
*
8446 AATAGATAAATAATAATATATGTT
1 AATA-ATAAATAATAATATATATT
8470 AATAGATAAA-AA-AATATATATGT
1 AATA-ATAAATAATAATATATAT-T
* *
8493 -AT-ATTAATAAATAATA-ATAGT
1 AATAATAAAT-AATAATATATATT
8514 AATAATAAATAAT
1 AATAATAAATAAT
8527 TAAATAAAAA
Statistics
Matches: 106, Mismatches: 13, Indels: 20
0.76 0.09 0.14
Matches are distributed among these distances:
20 4 0.04
21 1 0.01
22 20 0.19
23 34 0.32
24 34 0.32
25 13 0.12
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.33
Consensus pattern (23 bp):
AATAATAAATAATAATATATATT
Found at i:8487 original size:22 final size:24
Alignment explanation
Indices: 8398--8511 Score: 96
Period size: 24 Copynumber: 4.8 Consensus size: 24
8388 AATAGATAAA
* *
8398 TAATA-AT-AATAATAATAGATAAA
1 TAATAGATAAATAATAATATAT-AT
* *
8421 TAATA-ATAAAAAACATATATATAT
1 TAATAGATAAATAATA-ATATATAT
*
8445 TAATAGATAAATAATAATATATGT
1 TAATAGATAAATAATAATATATAT
8469 TAATAGATAAA-AA-AATATATAT
1 TAATAGATAAATAATAATATATAT
8491 GTATATTA-ATAAATAATAATA
1 -TA-A-TAGATAAATAATAATA
8512 GTAATAATAA
Statistics
Matches: 75, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
22 8 0.11
23 11 0.15
24 35 0.47
25 17 0.23
26 4 0.05
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (24 bp):
TAATAGATAAATAATAATATATAT
Found at i:8497 original size:52 final size:51
Alignment explanation
Indices: 8399--8537 Score: 151
Period size: 52 Copynumber: 2.7 Consensus size: 51
8389 ATAGATAAAT
8399 AATAATAATAATAATAGATAAATAATAATAAAAAACATATATATATTAATA
1 AATAATAATAATAATAGATAAATAATAATAAAAAACATATATATATTAATA
* * * *
8450 GATAAATAATAAT-ATATG-TTAATAGATAA-AAAAATATATATGTATATTAATA
1 AAT-AATAATAATAATA-GATAAATA-ATAATAAAAA-ACATATATATATTAATA
*
8502 AATAATAATAGTAATA-ATAAATAATTAAATAAAAAA
1 AATAATAATAATAATAGATAAATAA-T-AATAAAAAA
8538 TTAAAAAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
50 1 0.01
51 29 0.40
52 37 0.51
53 5 0.07
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (51 bp):
AATAATAATAATAATAGATAAATAATAATAAAAAACATATATATATTAATA
Found at i:8532 original size:8 final size:7
Alignment explanation
Indices: 8372--8538 Score: 51
Period size: 8 Copynumber: 22.9 Consensus size: 7
8362 AAATAATTAG
8372 ATAAATA
1 ATAAATA
*
8379 AAAAAT-
1 ATAAATA
*
8385 ATTAATA
1 ATAAATA
8392 GATAAATA
1 -ATAAATA
8400 AT-AATA
1 ATAAATA
8406 ATAATAATA
1 AT-A-AATA
8415 GATAAATA
1 -ATAAATA
8423 AT-AATA
1 ATAAATA
8429 A-AAA-A
1 ATAAATA
*
8434 CATATATA
1 -ATAAATA
*
8442 TATTAATA
1 -ATAAATA
8450 GATAAATA
1 -ATAAATA
8458 ATAATATA
1 ATAA-ATA
* *
8466 TGTTAATA
1 -ATAAATA
*
8474 GATAAAAAA
1 -AT-AAATA
*
8483 ATATATA
1 ATAAATA
* *
8490 TGTATATTA
1 -ATA-AATA
8499 ATAAATA
1 ATAAATA
8506 AT-AATA
1 ATAAATA
*
8512 GT-AATA
1 ATAAATA
8518 ATAAATA
1 ATAAATA
8525 ATTAAATA
1 A-TAAATA
*
8533 AAAAAT
1 ATAAAT
8539 TAAAAAAAAT
Statistics
Matches: 117, Mismatches: 26, Indels: 34
0.66 0.15 0.19
Matches are distributed among these distances:
5 1 0.01
6 28 0.24
7 32 0.27
8 42 0.36
9 12 0.10
10 2 0.02
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (7 bp):
ATAAATA
Found at i:8748 original size:16 final size:16
Alignment explanation
Indices: 8727--8758 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
8717 GGTCACTAGG
8727 TATATAAGGGTTCACA
1 TATATAAGGGTTCACA
8743 TATATAAGGGTTCACA
1 TATATAAGGGTTCACA
8759 CCATCTCTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
TATATAAGGGTTCACA
Found at i:23135 original size:14 final size:14
Alignment explanation
Indices: 23116--23143 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
23106 GTGAGAAAGA
23116 CTTAAATGAAGTTC
1 CTTAAATGAAGTTC
23130 CTTAAATGAAGTTC
1 CTTAAATGAAGTTC
23144 ATAAAACTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
CTTAAATGAAGTTC
Found at i:26286 original size:3 final size:3
Alignment explanation
Indices: 26278--26318 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
26268 ATACATTCGA
*
26278 AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
26319 ATGTTAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:26369 original size:27 final size:27
Alignment explanation
Indices: 26339--26391 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
26329 TTTAAGCTTG
*
26339 ATTTTGA-TATATATAACTTTTGATATA
1 ATTTTGATTATA-ATAACATTTGATATA
*
26366 ATTTTGATTTTAATAACATTTGATAT
1 ATTTTGATTATAATAACATTTGATAT
26392 GTTTTGGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.53
Consensus pattern (27 bp):
ATTTTGATTATAATAACATTTGATATA
Found at i:26452 original size:21 final size:20
Alignment explanation
Indices: 26424--26585 Score: 78
Period size: 21 Copynumber: 7.8 Consensus size: 20
26414 CTTTCATAGT
26424 CTTTGATAAAATTTTGATAA
1 CTTTGATAAAATTTTGATAA
*
26444 CTTTAGATACAATTTTGATAA
1 CTTT-GATAAAATTTTGATAA
** ** *
26465 CATTCAATATTAGTTT-AGTAA
1 C-TTTGATAAAATTTTGA-TAA
*
26486 CTTATGATATAAATTTT-TTAGA
1 CTT-TGATA-AAATTTTGATA-A
*
26508 CATTGATATAAA-TTTGATAA
1 CTTTGATA-AAATTTTGATAA
* * *
26528 TTTATTATAAAATTTTGTTAA
1 CTT-TGATAAAATTTTGATAA
* *
26549 CTCTCGATATAATTTTGATAA
1 CT-TTGATAAAATTTTGATAA
* *
26570 CATTTTATATAATTTT
1 C-TTTGATAAAATTTT
26586 AGTAATTTAT
Statistics
Matches: 106, Mismatches: 25, Indels: 21
0.70 0.16 0.14
Matches are distributed among these distances:
20 15 0.14
21 80 0.75
22 11 0.10
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.48
Consensus pattern (20 bp):
CTTTGATAAAATTTTGATAA
Found at i:26600 original size:21 final size:21
Alignment explanation
Indices: 26576--26626 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
26566 ATAACATTTT
26576 ATATAATTTTAGTAATT-TATG
1 ATATAATTTTAGTAATTAT-TG
* *
26597 ATATACTTTTTGTAATTATTG
1 ATATAATTTTAGTAATTATTG
*
26618 ATAAAATTT
1 ATATAATTT
26627 ATGCCATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (21 bp):
ATATAATTTTAGTAATTATTG
Found at i:26618 original size:105 final size:104
Alignment explanation
Indices: 26429--26626 Score: 256
Period size: 105 Copynumber: 1.9 Consensus size: 104
26419 ATAGTCTTTG
* *
26429 ATAAAATTTTGATAACTTTAGATACAATTTTGATAACATTCAATATTAGTTTAGTAACTTATGAT
1 ATAAAATTTTGATAACTCTAGATACAATTTTGATAACATTCAATATAAGTTTAGTAACTTATGAT
26494 ATAAATTTTTTAGACATTGATATAAATTTGATAATTTATT
66 ATAAATTTTTTAGACATTGATA-AAATTTGATAATTTATT
* * * ** * *
26534 ATAAAATTTTGTTAACTCTCGATATAATTTTGATAACATTTTATATAATTTTAGTAATTTATGAT
1 ATAAAATTTTGATAACTCTAGATACAATTTTGATAACATTCAATATAAGTTTAGTAACTTATGAT
* *
26599 AT-ACTTTTTGTA-ATTATTGATAAAATTT
66 ATAAATTTTT-TAGA-CATTGATAAAATTT
26627 ATGCCATTAT
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
104 13 0.16
105 67 0.84
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (104 bp):
ATAAAATTTTGATAACTCTAGATACAATTTTGATAACATTCAATATAAGTTTAGTAACTTATGAT
ATAAATTTTTTAGACATTGATAAAATTTGATAATTTATT
Found at i:26906 original size:22 final size:22
Alignment explanation
Indices: 26883--26957 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
26873 GATTGACAAT
* * *
26883 TAAATTATCATTGATATACTAT
1 TAAATTATCAATGATTTACTAC
*
26905 TATATTATCAATGATTTACTAC
1 TAAATTATCAATGATTTACTAC
*
26927 TAAATTATCAATAATTTACTAC
1 TAAATTATCAATGATTTACTAC
26949 TAAATTATC
1 TAAATTATC
26958 TACTAATTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (22 bp):
TAAATTATCAATGATTTACTAC
Found at i:26975 original size:33 final size:33
Alignment explanation
Indices: 26923--27097 Score: 141
Period size: 33 Copynumber: 5.4 Consensus size: 33
26913 CAATGATTTA
*
26923 CTACTAAATTATCAATAATTTACTACTAAATTAT
1 CTACTAATTTAT-AATAATTTACTACTAAATTAT
26957 CTACTAATTGT-TAATAATTTACTACTAAATTA-
1 CTACTAATT-TATAATAATTTACTACTAAATTAT
* * * * *
26989 CTAATAATTTATTATAAAATTA-TAACTTATTTA-
1 CTACTAATTTATAAT-AATTTACT-ACTAAATTAT
* *
27022 CTACTAATTTTATCAATAATTTACTTCAAAATTAT
1 CTACTAA-TTTAT-AATAATTTACTACTAAATTAT
* * *
27057 -TAGTGA-TTA-ATTAATTTACTACTAAATTAT
1 CTACTAATTTATAATAATTTACTACTAAATTAT
27087 -TACTAATTTAT
1 CTACTAATTTAT
27098 GATTAAGTTA
Statistics
Matches: 111, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
30 22 0.20
31 4 0.04
32 15 0.14
33 38 0.34
34 28 0.25
35 4 0.04
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.46
Consensus pattern (33 bp):
CTACTAATTTATAATAATTTACTACTAAATTAT
Found at i:26993 original size:22 final size:21
Alignment explanation
Indices: 26968--27056 Score: 81
Period size: 22 Copynumber: 4.0 Consensus size: 21
26958 TACTAATTGT
26968 TAATAATTTACTACTAAATTA
1 TAATAATTTACTACTAAATTA
*
26989 CTAATAATTTATTA-TAAAATTA
1 -TAATAATTTACTACT-AAATTA
* *
27011 TAACTTATTTACTACTAATTTTA
1 TAA-TAATTTACTACTAA-ATTA
* *
27034 TCAATAATTTACTTCAAAATTA
1 T-AATAATTTACTACTAAATTA
27056 T
1 T
27057 TAGTGATTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
21 4 0.07
22 32 0.59
23 16 0.30
24 2 0.04
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATAATTTACTACTAAATTA
Found at i:27186 original size:22 final size:21
Alignment explanation
Indices: 27161--27213 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
27151 GTTATTATGC
*
27161 ATTTACTATTATGTTGTTT-TTT
1 ATTTACTATTA-GTT-TTTAATT
27183 ATTTACTACTTAGTTTTTAATT
1 ATTTACTA-TTAGTTTTTAATT
27205 ATTTACTAT
1 ATTTACTAT
27214 AAAATTATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.14
22 21 0.75
23 3 0.11
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.62
Consensus pattern (21 bp):
ATTTACTATTAGTTTTTAATT
Found at i:27241 original size:21 final size:22
Alignment explanation
Indices: 27204--27319 Score: 91
Period size: 22 Copynumber: 5.4 Consensus size: 22
27194 AGTTTTTAAT
*
27204 TATTTACTATAAAATTATCACA
1 TATTTACTATTAAATTATCACA
27226 TATTTA-TATTAAATTATC-CA
1 TATTTACTATTAAATTATCACA
* * *
27246 TAATTCACTATCAATTTATCATC-
1 T-ATTTACTATTAAATTATCA-CA
* * *
27269 GATTTA-TATTAAACTAT-TCA
1 TATTTACTATTAAATTATCACA
27289 TAATTTACTATTAAATTATCAC-
1 T-ATTTACTATTAAATTATCACA
27311 TAGTTTACT
1 TA-TTTACT
27320 TCTAAGTTAT
Statistics
Matches: 72, Mismatches: 13, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
19 1 0.01
20 3 0.04
21 29 0.40
22 37 0.51
23 1 0.01
24 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.46
Consensus pattern (22 bp):
TATTTACTATTAAATTATCACA
Found at i:27265 original size:43 final size:42
Alignment explanation
Indices: 27209--27310 Score: 123
Period size: 43 Copynumber: 2.4 Consensus size: 42
27199 TTAATTATTT
* *
27209 ACTATAAAATTATCACATATTTATATTAAATTATCCATAATTC
1 ACTATAAAATTATCAC-GATTTATATTAAACTATCCATAATTC
* * * *
27252 ACTATCAATTTATCATCGATTTATATTAAACTATTCATAATTT
1 ACTATAAAATTATCA-CGATTTATATTAAACTATCCATAATTC
*
27295 ACTATTAAATTATCAC
1 ACTATAAAATTATCAC
27311 TAGTTTACTT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
42 1 0.02
43 48 0.96
44 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.01, T:0.43
Consensus pattern (42 bp):
ACTATAAAATTATCACGATTTATATTAAACTATCCATAATTC
Found at i:27859 original size:22 final size:22
Alignment explanation
Indices: 27831--28004 Score: 163
Period size: 22 Copynumber: 7.9 Consensus size: 22
27821 TATGTTGTAC
*
27831 ATAATTTGCTATTAAGTTATCA
1 ATAATTTACTATTAAGTTATCA
* * *
27853 ATGATTTACTAATAAATTATTC-
1 ATAATTTACTATTAAGTTA-TCA
* *
27875 ATAATTTACTACTAAGTTATGA
1 ATAATTTACTATTAAGTTATCA
* * *
27897 ATGATTTACCATTAAGTTATGA
1 ATAATTTACTATTAAGTTATCA
* * *
27919 ATCATTTACCATTAAGTTATAA
1 ATAATTTACTATTAAGTTATCA
* *
27941 ATAATTTACTATTAAATTATTA
1 ATAATTTACTATTAAGTTATCA
*
27963 ATAATTTACTATTAAGTTATTGA
1 ATAATTTACTATTAAGTTA-TCA
* *
27986 A-AATTTATTATAAAGTTAT
1 ATAATTTACTATTAAGTTAT
28005 AACTGATTTA
Statistics
Matches: 128, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
21 2 0.02
22 121 0.95
23 5 0.04
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (22 bp):
ATAATTTACTATTAAGTTATCA
Found at i:27879 original size:44 final size:44
Alignment explanation
Indices: 27831--27982 Score: 196
Period size: 44 Copynumber: 3.5 Consensus size: 44
27821 TATGTTGTAC
* * * *
27831 ATAATTTGCTATTAAGTTATCAATGATTTACTAATAAATTATTC
1 ATAATTTACTATTAAGTTATAAATGATTTACTATTAAATTATTA
* * * * *
27875 ATAATTTACTACTAAGTTATGAATGATTTACCATTAAGTTATGA
1 ATAATTTACTATTAAGTTATAAATGATTTACTATTAAATTATTA
* * *
27919 ATCATTTACCATTAAGTTATAAATAATTTACTATTAAATTATTA
1 ATAATTTACTATTAAGTTATAAATGATTTACTATTAAATTATTA
27963 ATAATTTACTATTAAGTTAT
1 ATAATTTACTATTAAGTTAT
27983 TGAAAATTTA
Statistics
Matches: 90, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 90 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.45
Consensus pattern (44 bp):
ATAATTTACTATTAAGTTATAAATGATTTACTATTAAATTATTA
Found at i:27992 original size:66 final size:66
Alignment explanation
Indices: 27831--28026 Score: 196
Period size: 66 Copynumber: 3.0 Consensus size: 66
27821 TATGTTGTAC
* * * * * ** *
27831 ATAATTTGCTATTAAGTTATCAATGATTTACTAATAAATTATTCATAATTTACTACTAAGTTATG
1 ATAATTTACTATTAAGTTATGAATAATTTACTATTAAGTTATAAATAATTTACTACTAAATTATG
27896 A
66 A
* * * * * *
27897 ATGATTTACCATTAAGTTATGAATCATTTACCATTAAGTTATAAATAATTTACTATTAAATTATT
1 ATAATTTACTATTAAGTTATGAATAATTTACTATTAAGTTATAAATAATTTACTACTAAATTATG
27962 A
66 A
* * * * * *
27963 ATAATTTACTATTAAGTTATTGAA-AATTTATTATAAAGTTATAACTGATTTATTACTAATTTAT
1 ATAATTTACTATTAAGTTA-TGAATAATTTACTATTAAGTTATAAATAATTTACTACTAAATTAT
28027 CGATGACTTT
Statistics
Matches: 105, Mismatches: 24, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
66 101 0.96
67 4 0.04
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (66 bp):
ATAATTTACTATTAAGTTATGAATAATTTACTATTAAGTTATAAATAATTTACTACTAAATTATG
A
Found at i:28013 original size:22 final size:22
Alignment explanation
Indices: 27844--28057 Score: 91
Period size: 22 Copynumber: 9.7 Consensus size: 22
27834 ATTTGCTATT
*
27844 AAGTTATCAATGATTTACTAATA
1 AAGTTATCAATGATTTA-TTATA
* *
27867 AA-TTATTC-ATAATTTACTACT-
1 AAGTTA-TCAATGATTTATTA-TA
* ** *
27888 AAGTTATGAATGATTTACCATT
1 AAGTTATCAATGATTTATTATA
* * ** *
27910 AAGTTATGAATCATTTACCATT
1 AAGTTATCAATGATTTATTATA
* * *
27932 AAGTTATAAATAATTTACTATTA
1 AAGTTATCAATGATTTATTA-TA
* * * *
27955 AA-TTATTAATAATTTACTATT
1 AAGTTATCAATGATTTATTATA
* *
27976 AAGTTATTGAA-AATTTATTATA
1 AAGTTA-TCAATGATTTATTATA
27998 AAGTTAT-AACTGATTTATTACT-
1 AAGTTATCAA-TGATTTATTA-TA
* *
28020 AATTTATCGATGACTTTATTATA
1 AAGTTATCAATGA-TTTATTATA
*
28043 AAGTTATCATTGATT
1 AAGTTATCAATGATT
28058 AACTAATTTA
Statistics
Matches: 155, Mismatches: 22, Indels: 29
0.75 0.11 0.14
Matches are distributed among these distances:
20 2 0.01
21 9 0.06
22 115 0.74
23 29 0.19
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (22 bp):
AAGTTATCAATGATTTATTATA
Found at i:28014 original size:44 final size:43
Alignment explanation
Indices: 27831--28049 Score: 158
Period size: 44 Copynumber: 5.0 Consensus size: 43
27821 TATGTTGTAC
* * * * *
27831 ATAATTTGCTATTAAGTTATCAATGATTTACTAATAAA-TTATTC
1 ATAATTTACTACTAAGTTATGAATAATTTACT-ATAAAGTTA-TA
* * *
27875 ATAATTTACTACTAAGTTATGAATGATTTACCATTAAGTTATGA
1 ATAATTTACTACTAAGTTATGAATAATTTACTATAAAGTTAT-A
* * * *
27919 ATCATTTACCATTAAGTTATAAATAATTTACTATTAAA-TTATTA
1 ATAATTTACTACTAAGTTATGAATAATTTACTA-TAAAGTTA-TA
* *
27963 ATAATTTACTATTAAGTTATTGAA-AATTTATTATAAAGTTATA
1 ATAATTTACTACTAAGTTA-TGAATAATTTACTATAAAGTTATA
* * * * *
28006 ACTGATTTATTACTAATTTATCG-ATGACTTTATTATAAAGTTAT
1 A-TAATTTACTACTAAGTTAT-GAAT-AATTTACTATAAAGTTAT
28050 CATTGATTAA
Statistics
Matches: 143, Mismatches: 22, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
43 14 0.10
44 105 0.73
45 24 0.17
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (43 bp):
ATAATTTACTACTAAGTTATGAATAATTTACTATAAAGTTATA
Found at i:28185 original size:22 final size:22
Alignment explanation
Indices: 28160--28221 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
28150 TTACTACTAA
*
28160 ATTATCAATGATTTATTATTCT
1 ATTATCAATGATTTATTATTAT
* *
28182 ATTAT-TATGTATTTACTATTAT
1 ATTATCAATG-ATTTATTATTAT
* *
28204 GTTATCATTGATTTATTA
1 ATTATCAATGATTTATTA
28222 CTTAATTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
21 3 0.10
22 26 0.84
23 2 0.06
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (22 bp):
ATTATCAATGATTTATTATTAT
Found at i:28239 original size:44 final size:44
Alignment explanation
Indices: 28161--28244 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
28151 TACTACTAAA
*
28161 TTATCAATGATTTATTATTCTATTATTATGTATTTACTATTATG
1 TTATCAATGATTTATTATTCAATTATTATGTATTTACTATTATG
* *
28205 TTATCATTGATTTATTACTT-AATTTTTGAT-TATTTACTAT
1 TTATCAATGATTTATTA-TTCAATTATT-ATGTATTTACTAT
28245 AAAAATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
44 31 0.89
45 4 0.11
ACGTcount: A:0.29, C:0.07, G:0.06, T:0.58
Consensus pattern (44 bp):
TTATCAATGATTTATTATTCAATTATTATGTATTTACTATTATG
Found at i:28261 original size:23 final size:23
Alignment explanation
Indices: 28235--28319 Score: 73
Period size: 23 Copynumber: 3.5 Consensus size: 23
28225 AATTTTTGAT
28235 TATTTACTATAAAAATTATTATC
1 TATTTACTATAAAAATTATTATC
* *
28258 TATTTACTACTAAAACTAACTATTA-A
1 TATTTACTA-T-AAA--AATTATTATC
* * *
28284 AACTTACTATAAAATTTATTATC
1 TATTTACTATAAAAATTATTATC
28307 TATTTACTTATAA
1 TATTTAC-TATAA
28320 TTTACTATTA
Statistics
Matches: 47, Mismatches: 9, Indels: 11
0.70 0.13 0.16
Matches are distributed among these distances:
22 6 0.13
23 14 0.30
24 9 0.19
25 4 0.09
26 7 0.15
27 7 0.15
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTTACTATAAAAATTATTATC
Found at i:28411 original size:22 final size:22
Alignment explanation
Indices: 28386--28435 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
28376 AATAATTAAA
*
28386 TACTAAAATATCAATT-ATTTAT
1 TACTAAAATATC-ATTGATTTAC
**
28408 TACTAAGTTATCATTGATTTAC
1 TACTAAAATATCATTGATTTAC
28430 TACTAA
1 TACTAA
28436 GTTATTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (22 bp):
TACTAAAATATCATTGATTTAC
Found at i:28436 original size:22 final size:22
Alignment explanation
Indices: 28394--28440 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
28384 AATACTAAAA
*
28394 TATCAATTATTTATTACTAAGT
1 TATCAATTATTTACTACTAAGT
28416 TATC-ATTGATTTACTACTAAGT
1 TATCAATT-ATTTACTACTAAGT
28438 TAT
1 TAT
28441 TTATAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (22 bp):
TATCAATTATTTACTACTAAGT
Found at i:28449 original size:22 final size:22
Alignment explanation
Indices: 28394--28453 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
28384 AATACTAAAA
*
28394 TATCAATT-ATTTATTACTAAGT
1 TATC-ATTAATTTACTACTAAGT
*
28416 TATCATTGATTTACTACTAAGT
1 TATCATTAATTTACTACTAAGT
*
28438 TAT-TTATAATTTACTA
1 TATCAT-TAATTTACTA
28454 TTATCAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 4 0.12
22 29 0.88
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (22 bp):
TATCATTAATTTACTACTAAGT
Found at i:28506 original size:22 final size:22
Alignment explanation
Indices: 28481--28533 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
28471 TTAAACCAAA
28481 ACTAATTTACTATCAACTTATC
1 ACTAATTTACTATCAACTTATC
* * *
28503 ACTAATTTACTATTAAGTTATT
1 ACTAATTTACTATCAACTTATC
*
28525 ATTAATTTA
1 ACTAATTTA
28534 TTACTAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.47
Consensus pattern (22 bp):
ACTAATTTACTATCAACTTATC
Found at i:28652 original size:22 final size:22
Alignment explanation
Indices: 28627--28764 Score: 77
Period size: 22 Copynumber: 6.2 Consensus size: 22
28617 GTTACAACAT
* *
28627 ATTATAATTGATTTACTACTAA
1 ATTATAACTAATTTACTACTAA
*
28649 ATTATTATAC-AA-TTACTA-TAT
1 ATTA-TA-ACTAATTTACTACTAA
* * * * *
28670 GTTATTATTTATATACTACTAA
1 ATTATAACTAATTTACTACTAA
*
28692 ATTAATAACT-ATTAACTACTAA
1 ATT-ATAACTAATTTACTACTAA
* * *
28714 GTTATCACTAATTTACTATTATAA
1 ATTATAACTAATTTACTA--CTAA
* *
28738 ACTATCACTAATTTACTACTAA
1 ATTATAACTAATTTACTACTAA
28760 ATTAT
1 ATTAT
28765 CTATGATTCA
Statistics
Matches: 85, Mismatches: 22, Indels: 18
0.68 0.18 0.14
Matches are distributed among these distances:
19 1 0.01
20 2 0.02
21 15 0.18
22 40 0.47
23 7 0.08
24 20 0.24
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTATAACTAATTTACTACTAA
Found at i:28765 original size:22 final size:22
Alignment explanation
Indices: 28683--28765 Score: 87
Period size: 22 Copynumber: 3.7 Consensus size: 22
28673 ATTATTTATA
*
28683 TACTACTAAATTAATAACT-ATT
1 TACTACTAAATT-ATCACTAATT
* *
28705 AACTACTAAGTTATCACTAATT
1 TACTACTAAATTATCACTAATT
* *
28727 TACTATTATAAACTATCACTAATT
1 TACTA--CTAAATTATCACTAATT
28751 TACTACTAAATTATC
1 TACTACTAAATTATC
28766 TATGATTCAC
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 5 0.10
22 25 0.51
24 19 0.39
ACGTcount: A:0.42, C:0.17, G:0.01, T:0.40
Consensus pattern (22 bp):
TACTACTAAATTATCACTAATT
Found at i:28777 original size:22 final size:22
Alignment explanation
Indices: 28752--28794 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
28742 TCACTAATTT
28752 ACTACTAAATTATCTA-TGATTC
1 ACTACTAAATTAT-TATTGATTC
* *
28774 ACTATTAAGTTATTATTGATT
1 ACTACTAAATTATTATTGATT
28795 AATTTTTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (22 bp):
ACTACTAAATTATTATTGATTC
Found at i:28803 original size:22 final size:21
Alignment explanation
Indices: 28800--28871 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
28790 TGATTAATTT
*
28800 TTAAGTTATCAATGATTATTA
1 TTAAGTTATTAATGATTATTA
* *
28821 TTAAGTTA-TACTGGTTACTT-
1 TTAAGTTATTAATGATTA-TTA
*
28841 TTAAGTTTTTAATGATTAATTA
1 TTAAGTTATTAATGATT-ATTA
*
28863 ATAAGTTAT
1 TTAAGTTAT
28872 CAATTGTCTA
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
20 13 0.33
21 18 0.46
22 8 0.21
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.50
Consensus pattern (21 bp):
TTAAGTTATTAATGATTATTA
Found at i:28846 original size:20 final size:20
Alignment explanation
Indices: 28778--28875 Score: 72
Period size: 22 Copynumber: 4.7 Consensus size: 20
28768 TGATTCACTA
* *
28778 TTAAGTTATTATTGATTAATTT
1 TTAAGTTATCAATGATT-A-TT
28800 TTAAGTTATCAATGATTATT
1 TTAAGTTATCAATGATTATT
* *
28820 ATTAAGTTAT-ACTGGTTACTT
1 -TTAAGTTATCAATGATTA-TT
* *
28841 TTAAGTTTTTAATGATTAATT
1 TTAAGTTATCAATGATT-ATT
*
28862 AATAAGTTATCAAT
1 -TTAAGTTATCAAT
28876 TGTCTAATAT
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
20 16 0.26
21 19 0.31
22 26 0.43
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (20 bp):
TTAAGTTATCAATGATTATT
Found at i:30339 original size:6 final size:6
Alignment explanation
Indices: 30328--30353 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
30318 AACATTTTAA
30328 AATTAT AATTAT AATTAT AATTAT AA
1 AATTAT AATTAT AATTAT AATTAT AA
30354 GTAATTGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AATTAT
Found at i:31989 original size:24 final size:24
Alignment explanation
Indices: 31957--32004 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
31947 TAATGAAAAG
31957 AATATATGTTTAAAAGTAGATTTT
1 AATATATGTTTAAAAGTAGATTTT
31981 AATATATGTTTAAAAGTAGATTTT
1 AATATATGTTTAAAAGTAGATTTT
32005 TCATCAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (24 bp):
AATATATGTTTAAAAGTAGATTTT
Found at i:32146 original size:16 final size:16
Alignment explanation
Indices: 32127--32158 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
32117 TAAGAAACAG
32127 GTTTAATAATAAAAAA
1 GTTTAATAATAAAAAA
*
32143 GTTTACTAATAAAAAA
1 GTTTAATAATAAAAAA
32159 TTATTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (16 bp):
GTTTAATAATAAAAAA
Found at i:35138 original size:23 final size:22
Alignment explanation
Indices: 35112--35159 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
35102 GAGCTCCTTA
35112 AAATATATTATATAAAAACATAT
1 AAATATATTATATAAAAA-ATAT
* *
35135 AAATATATTCTATATAAAATAT
1 AAATATATTATATAAAAAATAT
35157 AAA
1 AAA
35160 ACAAACATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATATATTATATAAAAAATAT
Found at i:35307 original size:21 final size:21
Alignment explanation
Indices: 35283--35322 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
35273 AGGATACTCT
*
35283 CTAAAATATTTTTTTGATATA
1 CTAAAATATTTGTTTGATATA
**
35304 CTAAGTTATTTGTTTGATA
1 CTAAAATATTTGTTTGATA
35323 AGCCTGTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.53
Consensus pattern (21 bp):
CTAAAATATTTGTTTGATATA
Found at i:35516 original size:4 final size:4
Alignment explanation
Indices: 35509--35555 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
35499 TAATATATAA
*
35509 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT GTGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
35556 CAAACATGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:36559 original size:17 final size:19
Alignment explanation
Indices: 36525--36565 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
36515 TTATTATTGA
*
36525 TATTTGTTTAAATCA-TTT
1 TATTTGTTTAAATAATTTT
*
36543 TATTT-TTTAATTAATTTT
1 TATTTGTTTAAATAATTTT
36561 TATTT
1 TATTT
36566 ATTTTCACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
TATTTGTTTAAATAATTTT
Found at i:37398 original size:21 final size:22
Alignment explanation
Indices: 37364--37425 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
37354 GTTTGGTAAC
*
37364 TTATTATATAATTTTAATAAAT
1 TTATGATATAATTTTAATAAAT
* *
37386 TT-TGATATTATTTT-ATTAAT
1 TTATGATATAATTTTAATAAAT
*
37406 TTATGATATAATTTCAATAA
1 TTATGATATAATTTTAATAA
37426 CCATTGATAC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 7 0.22
21 20 0.62
22 5 0.16
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (22 bp):
TTATGATATAATTTTAATAAAT
Found at i:37560 original size:21 final size:21
Alignment explanation
Indices: 37536--37588 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
37526 GGTGACATTC
* * *
37536 GATACAATTTTGGTAAGTTTT
1 GATAAAATTTTGATAACTTTT
*
37557 GATATAATTTTGATAACTTTT
1 GATAAAATTTTGATAACTTTT
*
37578 AATAAAATTTT
1 GATAAAATTTT
37589 AATTTTGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (21 bp):
GATAAAATTTTGATAACTTTT
Found at i:37599 original size:27 final size:27
Alignment explanation
Indices: 37561--37621 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
37551 AGTTTTGATA
37561 TAATTTTGATAA-CTTTTAATAAAATTT
1 TAATTTTGATAACCTTTT-ATAAAATTT
*
37588 TAATTTTGATAACCTTTTATATAATTT
1 TAATTTTGATAACCTTTTATAAAATTT
37615 TAATTTT
1 TAATTTT
37622 AAATACCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (27 bp):
TAATTTTGATAACCTTTTATAAAATTT
Found at i:37629 original size:27 final size:27
Alignment explanation
Indices: 37573--37693 Score: 99
Period size: 27 Copynumber: 4.5 Consensus size: 27
37563 ATTTTGATAA
* *
37573 CTTTTAATAAAATTTTAATTTT-GATAAC
1 CTTTT-ATATAATTTTAATTTTAAAT-AC
37601 CTTTTATATAATTTTAATTTTAAATAC
1 CTTTTATATAATTTTAATTTTAAATAC
* * * **
37628 CTTTGATATAA-TTTGA---TAACCTTGG
1 CTTTTATATAATTTTAATTTTAA--ATAC
37653 CTTTTATATAATTTTAATTTTAAATAC
1 CTTTTATATAATTTTAATTTTAAATAC
*
37680 CTTTGATATAATTT
1 CTTTTATATAATTT
37694 GATAACCTTG
Statistics
Matches: 73, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
23 3 0.04
25 11 0.15
26 8 0.11
27 41 0.56
28 7 0.10
29 3 0.04
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (27 bp):
CTTTTATATAATTTTAATTTTAAATAC
Found at i:37664 original size:52 final size:52
Alignment explanation
Indices: 37601--37706 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
37591 TTTTGATAAC
37601 CTTTTATATAATTTTAATTTTAAATACCTTTGATATAATTTGATAACCTTGG
1 CTTTTATATAATTTTAATTTTAAATACCTTTGATATAATTTGATAACCTTGG
37653 CTTTTATATAATTTTAATTTTAAATACCTTTGATATAATTTGATAACCTTGG
1 CTTTTATATAATTTTAATTTTAAATACCTTTGATATAATTTGATAACCTTGG
37705 CT
1 CT
37707 ATAAGTTTGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (52 bp):
CTTTTATATAATTTTAATTTTAAATACCTTTGATATAATTTGATAACCTTGG
Found at i:37818 original size:20 final size:20
Alignment explanation
Indices: 37793--37938 Score: 94
Period size: 20 Copynumber: 6.7 Consensus size: 20
37783 TCATGGATAC
*
37793 AATTTTGAAACTTTTTATAA
1 AATTTTGAAACTTTTAATAA
*
37813 AATTTTGATAATAACTTATTAATAT
1 AATTTTG---A-AACTT-TTAATAA
* * *
37838 AATTCTAGTAACTTTTAATAC
1 AATT-TTGAAACTTTTAATAA
*
37859 AATTTTGAAACTTTTTATAA
1 AATTTTGAAACTTTTAATAA
37879 AATTTTGATAATAACTTATTAATATA
1 AATTTTG---A-AACTT-TTAATA-A
* * *
37905 ATTTTTGTAACTTTTAATAT
1 AATTTTGAAACTTTTAATAA
37925 AATTTTGATAACTT
1 AATTTTGA-AACTT
37939 ATGATATAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 25
0.71 0.11 0.18
Matches are distributed among these distances:
20 32 0.33
21 21 0.21
22 10 0.10
23 2 0.02
24 10 0.10
25 14 0.14
26 9 0.09
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (20 bp):
AATTTTGAAACTTTTAATAA
Found at i:37857 original size:21 final size:20
Alignment explanation
Indices: 37824--37948 Score: 79
Period size: 21 Copynumber: 5.8 Consensus size: 20
37814 ATTTTGATAA
37824 TAACTTATTAATATAATTCTAG
1 TAACTT-TTAATATAATT-TAG
* *
37846 TAACTTTTAATACAATTTTG
1 TAACTTTTAATATAATTTAG
* * * *
37866 AAACTTTTTATAAAATTTTGATAA
1 TAACTTTTAATATAA--TT--TAG
*
37890 TAACTTATTAATATAATTTTTG
1 TAACTT-TTAATATAA-TTTAG
*
37912 TAACTTTTAATATAATTTTG
1 TAACTTTTAATATAATTTAG
* *
37932 ATAACTTATGATATAAT
1 -TAACTTTTAATATAAT
37949 ATTTGTGATC
Statistics
Matches: 83, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
20 19 0.23
21 33 0.40
22 15 0.18
24 9 0.11
25 7 0.08
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (20 bp):
TAACTTTTAATATAATTTAG
Found at i:37859 original size:66 final size:66
Alignment explanation
Indices: 37789--37938 Score: 264
Period size: 66 Copynumber: 2.3 Consensus size: 66
37779 CTAATCATGG
37789 ATACAATTTTGAAACTTTTTATAAAATTTTGATAATAACTTATTAATATAATTCTAGTAACTTTT
1 ATACAATTTTGAAACTTTTTATAAAATTTTGATAATAACTTATTAATATAATTCTAGTAACTTTT
37854 A
66 A
* *
37855 ATACAATTTTGAAACTTTTTATAAAATTTTGATAATAACTTATTAATATAATTTTTGTAACTTTT
1 ATACAATTTTGAAACTTTTTATAAAATTTTGATAATAACTTATTAATATAATTCTAGTAACTTTT
37920 A
66 A
*
37921 ATATAATTTTGATAACTT
1 ATACAATTTTGA-AACTT
37939 ATGATATAAT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
66 75 0.94
67 5 0.06
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.49
Consensus pattern (66 bp):
ATACAATTTTGAAACTTTTTATAAAATTTTGATAATAACTTATTAATATAATTCTAGTAACTTTT
A
Found at i:37911 original size:46 final size:44
Alignment explanation
Indices: 37846--37935 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 44
37836 ATAATTCTAG
*
37846 TAACTTTTAATACAATTTTGAAACTTTTTATAAAATTTTGATAA
1 TAACTTTTAATACAATTTTGAAACTTTTAATAAAATTTTGATAA
* * *
37890 TAACTTATTAATATAATTTTTGTAACTTTTAATATAATTTTGATAA
1 TAACTT-TTAATACAA-TTTTGAAACTTTTAATAAAATTTTGATAA
37936 CTTATGATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 6 0.15
45 8 0.20
46 26 0.65
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (44 bp):
TAACTTTTAATACAATTTTGAAACTTTTAATAAAATTTTGATAA
Found at i:38040 original size:21 final size:21
Alignment explanation
Indices: 38009--38059 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
37999 TCTTGGATAC
*
38009 AATTTTAATAAACTTTTATAT
1 AATTTTGATAAACTTTTATAT
* **
38030 TATTTTGATAAGTTTTTATAT
1 AATTTTGATAAACTTTTATAT
38051 AATTTTGAT
1 AATTTTGAT
38060 TTTGATAACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (21 bp):
AATTTTGATAAACTTTTATAT
Found at i:38079 original size:26 final size:27
Alignment explanation
Indices: 38031--38081 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
38021 CTTTTATATT
* *
38031 ATTTTGATAAGTTTTTATATAATTTTG
1 ATTTTGATAACTTTTGATATAATTTTG
38058 ATTTTGATAACTTTTGAT-TAATTT
1 ATTTTGATAACTTTTGATATAATTT
38082 GATAGCCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (27 bp):
ATTTTGATAACTTTTGATATAATTTTG
Found at i:38161 original size:12 final size:12
Alignment explanation
Indices: 38144--38180 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
38134 GATACAATTT
38144 ATATAACTTTTG
1 ATATAACTTTTG
38156 ATATAA-TTTTG
1 ATATAACTTTTG
38167 --ATAACTTTTG
1 ATATAACTTTTG
38177 ATAT
1 ATAT
38181 TATTAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.18
10 5 0.23
11 5 0.23
12 8 0.36
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.51
Consensus pattern (12 bp):
ATATAACTTTTG
Found at i:38177 original size:10 final size:10
Alignment explanation
Indices: 38146--38179 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
38136 TACAATTTAT
38146 ATAACTTTTG
1 ATAACTTTTG
*
38156 ATATAATTTTG
1 ATA-ACTTTTG
38167 ATAACTTTTG
1 ATAACTTTTG
38177 ATA
1 ATA
38180 TTATTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (10 bp):
ATAACTTTTG
Found at i:38180 original size:21 final size:21
Alignment explanation
Indices: 38058--38180 Score: 96
Period size: 21 Copynumber: 6.0 Consensus size: 21
38048 TATAATTTTG
38058 ATTTTGATAACTTTTGAT-TA
1 ATTTTGATAACTTTTGATATA
* * * *
38078 A-TTTGATAGCCTTTGTTAAA
1 ATTTTGATAACTTTTGATATA
* *
38098 AGTTTT-ATAA-TTTCTTATAAA
1 A-TTTTGATAACTTT-TGATATA
* *
38119 ATTTTGATAA-TATTCGATACA
1 ATTTTGATAACT-TTTGATATA
38140 ATTTAT-ATAACTTTTGATATA
1 ATTT-TGATAACTTTTGATATA
38161 ATTTTGATAACTTTTGATAT
1 ATTTTGATAACTTTTGATAT
38181 TATTAATATA
Statistics
Matches: 81, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
19 13 0.16
20 10 0.12
21 51 0.63
22 7 0.09
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (21 bp):
ATTTTGATAACTTTTGATATA
Found at i:38191 original size:21 final size:20
Alignment explanation
Indices: 38142--38191 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
38132 TCGATACAAT
38142 TTATATAACTTTTGATATAA
1 TTATATAACTTTTGATATAA
* *
38162 TTTTGATAACTTTTGATATTA
1 TTAT-ATAACTTTTGATATAA
38183 TTAATATAA
1 TT-ATATAA
38192 TATTTAAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 21 0.84
22 1 0.04
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (20 bp):
TTATATAACTTTTGATATAA
Found at i:40782 original size:2 final size:2
Alignment explanation
Indices: 40775--40803 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40765 CCGCTAGAAG
40775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40804 ATGAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41695 original size:8 final size:8
Alignment explanation
Indices: 41682--41706 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
41672 TTTATTTTTA
41682 TTAAAATT
1 TTAAAATT
41690 TTAAAATT
1 TTAAAATT
41698 TTAAAATT
1 TTAAAATT
41706 T
1 T
41707 ATAACATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTAAAATT
Found at i:41720 original size:3 final size:3
Alignment explanation
Indices: 41712--41747 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
41702 AATTTATAAC
41712 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41748 TCATATTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:43315 original size:24 final size:23
Alignment explanation
Indices: 43286--43350 Score: 85
Period size: 25 Copynumber: 2.7 Consensus size: 23
43276 TAACATACCT
43286 TAGTTTTATCAAACCATGAAAACC
1 TAGTTTTATCAAACCATGAAAA-C
*
43310 TAGTTTTTATTAAACCATGAAAAC
1 TAG-TTTTATCAAACCATGAAAAC
*
43334 TCAATTTTATCAAACCA
1 T-AGTTTTATCAAACCA
43351 CAACCCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 17 0.47
25 19 0.53
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.34
Consensus pattern (23 bp):
TAGTTTTATCAAACCATGAAAAC
Found at i:44584 original size:35 final size:35
Alignment explanation
Indices: 44538--44605 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
44528 TTTTGAACCA
44538 CATACTTTACTTTTATCTTCTCCCACCTAATATCT
1 CATACTTTACTTTTATCTTCTCCCACCTAATATCT
44573 CATACTTTACTTTTATCTTCTCCCACCTAATAT
1 CATACTTTACTTTTATCTTCTCCCACCTAATAT
44606 TTTTTCTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.24, C:0.31, G:0.00, T:0.46
Consensus pattern (35 bp):
CATACTTTACTTTTATCTTCTCCCACCTAATATCT
Found at i:50851 original size:2 final size:2
Alignment explanation
Indices: 50844--50870 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
50834 ATGCTCCATT
50844 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
50871 TTAGAGTTCC
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:51944 original size:3 final size:3
Alignment explanation
Indices: 51930--51984 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
51920 CAAGATATTA
* * **
51930 AAT AAT AGT AAT AAT AAT ACAT ATT AA- AAT AAT GGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
51975 AAT AAT AAT A
1 AAT AAT AAT A
51985 TTCGTATTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:51967 original size:27 final size:26
Alignment explanation
Indices: 51924--51975 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
51914 ACTATTCAAG
51924 ATATTAAATAATAGTAATAATAATAC
1 ATATTAAATAATAGTAATAATAATAC
*
51950 ATATTAAAATAATGGTAATAATAATA
1 ATATT-AAATAATAGTAATAATAATA
51976 ATAATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (26 bp):
ATATTAAATAATAGTAATAATAATAC
Done.