Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 16 of 226
Found at i:7437446 original size:3 final size:3
Alignment explanation
Indices: 7437438--7437487 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
7437428 TTACTTTATT
* *
7437438 TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TTA T-A TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
7437483 TAA TA
1 TAA TA
7437488 TTTATGTATA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:7437498 original size:13 final size:15
Alignment explanation
Indices: 7437438--7437497 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
7437428 TTACTTTATT
*
7437438 TAATAATAATA-ATAA
1 TAATAATTATATAT-A
*
7437453 TAATAATAATA-ATTA
1 TAATAATTATATA-TA
7437468 TAATAATTATATATA
1 TAATAATTATATATA
* *
7437483 TAATATTTATGTATA
1 TAATAATTATATATA
7437498 ACTTAAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
15 38 0.95
16 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
TAATAATTATATATA
Found at i:7440391 original size:42 final size:43
Alignment explanation
Indices: 7440310--7440391 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
7440300 AATACATACG
***
7440310 GTGGAGAGTTTCCTACATCAAAGGGTCATATATGTATAACCTT
1 GTGGAGAGTTTCCTACATCAAAGGGTCATATACCAATAACCTT
* *
7440353 GTGGAGAGTTTCCTACATC-AAGGGTCATTTCCCAATAAC
1 GTGGAGAGTTTCCTACATCAAAGGGTCATATACCAATAAC
7440392 ATAAGCAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
42 15 0.44
43 19 0.56
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (43 bp):
GTGGAGAGTTTCCTACATCAAAGGGTCATATACCAATAACCTT
Found at i:7454249 original size:20 final size:20
Alignment explanation
Indices: 7454224--7454263 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
7454214 AGCCTATGTG
7454224 AAAGTTTCTGATACTAATAT
1 AAAGTTTCTGATACTAATAT
7454244 AAAGTTTCTGATACTAATAT
1 AAAGTTTCTGATACTAATAT
7454264 GCCAATTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (20 bp):
AAAGTTTCTGATACTAATAT
Found at i:7457365 original size:21 final size:21
Alignment explanation
Indices: 7457339--7457379 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
7457329 AATATGATTT
7457339 TAATATTTTATG-ATTATAATG
1 TAATATTTTA-GCATTATAATG
7457360 TAATATTTTAGCATTATAAT
1 TAATATTTTAGCATTATAAT
7457380 TTTTTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (21 bp):
TAATATTTTAGCATTATAATG
Found at i:7457403 original size:3 final size:3
Alignment explanation
Indices: 7457395--7457419 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
7457385 ATAAATTAAA
7457395 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
7457420 CGAGGAGGAT
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:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:7463614 original size:27 final size:25
Alignment explanation
Indices: 7463563--7463614 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
7463553 TTTGGATAAT
**
7463563 AATAATATATATCTTTTCTGATTAA
1 AATAATATATATCTTTTAGGATTAA
*
7463588 AATATATATTATATCTTTTAGGTTTAA
1 AATA-ATA-TATATCTTTTAGGATTAA
7463615 CATGAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 4 0.18
26 3 0.14
27 15 0.68
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (25 bp):
AATAATATATATCTTTTAGGATTAA
Found at i:7463807 original size:3 final size:3
Alignment explanation
Indices: 7463799--7463830 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
7463789 CTCCAAAAAT
7463799 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
7463831 GTAGATTGAA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:7467284 original size:2 final size:2
Alignment explanation
Indices: 7467277--7467305 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7467267 ATGTTGACAG
7467277 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
7467306 AAGCCCCTTT
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:7468313 original size:18 final size:18
Alignment explanation
Indices: 7468257--7468313 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
7468247 ATTAAGAAAC
7468257 TAAAAATTAGACTATAAA
1 TAAAAATTAGACTATAAA
* * *
7468275 TATATATT-GA-TA-AAT
1 TAAAAATTAGACTATAAA
7468290 TAAAAATTAGACTATAAA
1 TAAAAATTAGACTATAAA
7468308 TAAAAA
1 TAAAAA
7468314 CTTGTAACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 8 0.27
16 4 0.13
17 4 0.13
18 14 0.47
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (18 bp):
TAAAAATTAGACTATAAA
Found at i:7468793 original size:15 final size:16
Alignment explanation
Indices: 7468768--7468809 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
7468758 TTCATGGTAT
7468768 ATTTT-TAATT-TAAA
1 ATTTTATAATTATAAA
7468782 ATTTTATAATTTATAAA
1 ATTTTATAA-TTATAAA
7468799 ATTTTA-AATTA
1 ATTTTATAATTA
7468810 ATAACGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.20
15 6 0.24
16 4 0.16
17 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTATAATTATAAA
Found at i:7468813 original size:16 final size:17
Alignment explanation
Indices: 7468778--7468813 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
7468768 ATTTTTAATT
*
7468778 TAAAATTTTATAATTTA
1 TAAAATTTTATAATTAA
7468795 TAAAATTTTA-AATTAA
1 TAAAATTTTATAATTAA
7468811 TAA
1 TAA
7468814 CGATAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAATTTTATAATTAA
Found at i:7469594 original size:19 final size:19
Alignment explanation
Indices: 7469562--7469627 Score: 53
Period size: 21 Copynumber: 3.3 Consensus size: 19
7469552 TTAATTTTAA
7469562 TTTTTCAATATTATTTAATAT
1 TTTTTC-AT-TTATTTAATAT
*
7469583 TTTTTCATTTATGTAAT-T
1 TTTTTCATTTATTTAATAT
* *
7469601 TTAATTCATTTTTATTTTATAT
1 TT-TTTCA--TTTATTTAATAT
7469623 TTTTT
1 TTTTT
7469628 TATAACAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 3 0.08
19 12 0.33
20 2 0.06
21 16 0.44
22 3 0.08
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTCATTTATTTAATAT
Found at i:7471701 original size:92 final size:93
Alignment explanation
Indices: 7471547--7471739 Score: 343
Period size: 92 Copynumber: 2.1 Consensus size: 93
7471537 CAACATTGAT
7471547 TTTTTAAAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTT
1 TTTTT-AAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTT
7471612 AAATATTTTAATAGTAATTTATTTTTATA
65 AAATATTTTAATAGTAATTTATTTTTATA
* *
7471641 TTTTTAAA-ATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAATTTATTTTT
1 TTTTTAAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTA
*
7471705 AATATTTTGATAGTAATTTATTTTTATA
66 AATATTTTAATAGTAATTTATTTTTATA
7471733 TTTTTAA
1 TTTTTAA
7471740 TAAAATAGAA
Statistics
Matches: 96, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
92 88 0.92
93 3 0.03
94 5 0.05
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (93 bp):
TTTTTAAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTA
AATATTTTAATAGTAATTTATTTTTATA
Found at i:7471702 original size:48 final size:48
Alignment explanation
Indices: 7471551--7471702 Score: 147
Period size: 48 Copynumber: 3.2 Consensus size: 48
7471541 ATTGATTTTT
*
7471551 TAAAATATATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAA
1 TAAAATTTATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAA
* * ** * ***
7471599 TAAAAGTTATTT-T--AAA-TATTTTAATAGTAATTT-ATTTTTATATTTT
1 TAAAATTTATTTGTACAAACTATTTTTATA-TTGTTTCA-TTTAATA-AAA
7471645 TAAAA--TATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAA
1 TAAAATTTATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAA
7471691 TAAAATTTATTT
1 TAAAATTTATTT
7471703 TTAATATTTT
Statistics
Matches: 78, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
44 15 0.19
45 14 0.18
46 10 0.13
47 14 0.18
48 25 0.32
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (48 bp):
TAAAATTTATTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAA
Found at i:7477211 original size:127 final size:128
Alignment explanation
Indices: 7476979--7477254 Score: 337
Period size: 127 Copynumber: 2.2 Consensus size: 128
7476969 TAAGGCCAAA
* * * * *
7476979 CAGGAAATACTGT-AGAAAAATAGCATCCACGTGAGAGTTTTTTTCATCAATTTTACTGACAGTC
1 CAGGAACTACTGTAAAAAAAAGAGCATCCACGTGAGAGCTTTTTCCATCAATTTTACTGACAGTC
*
7477043 CATCCTGCTTGAAGCATTTTTGACACTATTTATTCAGAACCGTCTTCTCAAAATTATT-ATTT
66 CATCCTGCTTGAAGCATTTTTGACACTATTTATTCAAAACCGTCTTCTCAAAATTATTCATTT
* *
7477105 CAGGAACTACTGTAAAAAAAAGAGCGTCCACGTG-GTAGCTTTTTCCAGT-AATTTTGCTGACAG
1 CAGGAACTACTGTAAAAAAAAGAGCATCCACGTGAG-AGCTTTTTCCA-TCAATTTTACTGACAG
* ** * * *
7477168 TGCATCCTGCTTGAAGTGTTTTTTACATTATCTT-TTCAAAACCGTCTTCTCAAAATTATTCTTT
64 TCCATCCTGCTTGAAGCATTTTTGACACTAT-TTATTCAAAACCGTCTTCTCAAAATTATTCATT
7477232 T
128 T
**
7477233 CATAAACTACTGTAGAAAAAAA
1 CAGGAACTACTGTA-AAAAAAA
7477255 AACAAAAGTT
Statistics
Matches: 128, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
126 13 0.10
127 90 0.70
128 18 0.14
129 7 0.05
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (128 bp):
CAGGAACTACTGTAAAAAAAAGAGCATCCACGTGAGAGCTTTTTCCATCAATTTTACTGACAGTC
CATCCTGCTTGAAGCATTTTTGACACTATTTATTCAAAACCGTCTTCTCAAAATTATTCATTT
Found at i:7477350 original size:34 final size:32
Alignment explanation
Indices: 7477306--7477421 Score: 115
Period size: 34 Copynumber: 3.5 Consensus size: 32
7477296 CTAAACACAA
*
7477306 AATTATTTAAAAAAACTAACCCATAATTTAATT
1 AATTTTTTAAAAAAACTAACCC-TAATTTAATT
**
7477339 AATTTTCTTAAAAATCCTAATCCCTAATTTAATT
1 AATTTT-TTAAAAAAACTAA-CCCTAATTTAATT
*** * *
7477373 AATTTATTTAAAATCTCAAAAACCTAATTTAATT
1 AATTT-TTTAAAAAAAC-TAACCCTAATTTAATT
7477407 AATTTTTTAAAAAAA
1 AATTTTTTAAAAAAA
7477422 TCTTAAACCT
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
33 12 0.18
34 50 0.74
35 6 0.09
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (32 bp):
AATTTTTTAAAAAAACTAACCCTAATTTAATT
Found at i:7477479 original size:16 final size:16
Alignment explanation
Indices: 7477458--7477490 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
7477448 TATTTTAACA
*
7477458 AAACCATAAAAACCCT
1 AAACCAAAAAAACCCT
7477474 AAACCAAAAAAACCCT
1 AAACCAAAAAAACCCT
7477490 A
1 A
7477491 GGGACTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.30, G:0.00, T:0.09
Consensus pattern (16 bp):
AAACCAAAAAAACCCT
Found at i:7483194 original size:32 final size:32
Alignment explanation
Indices: 7483132--7483194 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
7483122 TTAAACTTCA
* * *
7483132 AAAATTATTTTATTTAAATATAATATATATTT
1 AAAATTATTTCATTAAAATATAATACATATTT
*
7483164 AAAATTATTTCATTAAAA-ATTATTACATATT
1 AAAATTATTTCATTAAAATA-TAATACATATT
7483195 GAATATCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (32 bp):
AAAATTATTTCATTAAAATATAATACATATTT
Found at i:7492031 original size:2 final size:2
Alignment explanation
Indices: 7492026--7492059 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
7492016 ATAGACACAG
*
7492026 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7492060 TATGATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7495489 original size:20 final size:20
Alignment explanation
Indices: 7495447--7495489 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
7495437 ATACCCTCAA
*
7495447 AATAATATTAGTTACTTTAT
1 AATAATATTAGATACTTTAT
*
7495467 AATAATATTGGAT-CTTTAGT
1 AATAATATTAGATACTTTA-T
7495487 AAT
1 AAT
7495490 TTCGCAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (20 bp):
AATAATATTAGATACTTTAT
Found at i:7502784 original size:17 final size:17
Alignment explanation
Indices: 7502762--7502796 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
7502752 AGAAACTAAC
7502762 GGCTCAGTAACTAAAAT
1 GGCTCAGTAACTAAAAT
*
7502779 GGCTCAGTGACTAAAAT
1 GGCTCAGTAACTAAAAT
7502796 G
1 G
7502797 TTACAACGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (17 bp):
GGCTCAGTAACTAAAAT
Found at i:7502878 original size:31 final size:29
Alignment explanation
Indices: 7502809--7502882 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
7502799 ACAACGTGAT
**
7502809 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATGCCA
*
7502838 AACATAAGTGACTAAAACGTAATATGAGCCA
1 AACATAAGTGACTAAAACGTAACAT--GCCA
*
7502869 AACAAAAGTGACTA
1 AACATAAGTGACTA
7502883 TTTTGGTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATGCCA
Found at i:7512005 original size:27 final size:28
Alignment explanation
Indices: 7511949--7512009 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 28
7511939 CCCATATTAA
7511949 ATATATATATTTGATTAAAAATAAAAAATAT
1 ATATATATATTTGATTAAAAAT---AAATAT
7511980 ATATATATATTTGATTAAAAAT-AATAT
1 ATATATATATTTGATTAAAAATAAATAT
7512007 ATA
1 ATA
7512010 ATTCGGGTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 8 0.27
31 22 0.73
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (28 bp):
ATATATATATTTGATTAAAAATAAATAT
Found at i:7519942 original size:25 final size:25
Alignment explanation
Indices: 7519897--7519945 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
7519887 GAGGCGCCAA
7519897 TGAATAAAAAAATATTAATTTTTTT
1 TGAATAAAAAAATATTAATTTTTTT
* * *
7519922 TGAATAAAATAATTTTTATTTTTT
1 TGAATAAAAAAATATTAATTTTTT
7519946 AAAAAATTTT
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:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (25 bp):
TGAATAAAAAAATATTAATTTTTTT
Found at i:7520088 original size:27 final size:27
Alignment explanation
Indices: 7520014--7520088 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
7520004 GGGTCGGGTG
* *
7520014 GTGCCTCGTAGGGAAGCACCATTAAAA
1 GTGCCTCATAGGGAAGCGCCATTAAAA
* *
7520041 GTGACTCATA-GGAATGTGCCATTAAAA
1 GTGCCTCATAGGGAA-GCGCCATTAAAA
*
7520068 GTGCCTCATAGGGAGGCGCCA
1 GTGCCTCATAGGGAAGCGCCA
7520089 GTGGGTAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 4 0.10
27 32 0.82
28 3 0.08
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.20
Consensus pattern (27 bp):
GTGCCTCATAGGGAAGCGCCATTAAAA
Found at i:7520121 original size:21 final size:22
Alignment explanation
Indices: 7520096--7520146 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
7520086 CCAGTGGGTA
*
7520096 ATTTTATATGTATATTGTAACT
1 ATTTTATATGAATATTGTAACT
* *
7520118 -TTTTGTATGAATATTGTAATT
1 ATTTTATATGAATATTGTAACT
7520139 ATTTTATA
1 ATTTTATA
7520147 ATTAATTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (22 bp):
ATTTTATATGAATATTGTAACT
Found at i:7520208 original size:27 final size:25
Alignment explanation
Indices: 7520178--7520252 Score: 91
Period size: 27 Copynumber: 3.0 Consensus size: 25
7520168 TTGGATTAGT
7520178 ATTTTGTATGAATATTGTAATTTTG
1 ATTTTGTATGAATATTGTAATTTTG
* *
7520203 AAATTTTATATGAATATTGTAATATTG
1 --ATTTTGTATGAATATTGTAATTTTG
7520230 --TTTGTATGAATATTGTAACTTTT
1 ATTTTGTATGAATATTGTAA-TTTT
7520253 TGTATAATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
23 17 0.40
24 3 0.07
27 23 0.53
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (25 bp):
ATTTTGTATGAATATTGTAATTTTG
Found at i:7520431 original size:15 final size:16
Alignment explanation
Indices: 7520396--7520431 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
7520386 AACATAAAAG
7520396 TTTATATAATGTAACT
1 TTTATATAATGTAACT
*
7520412 TTTATATTATGTAA-T
1 TTTATATAATGTAACT
7520427 TTTAT
1 TTTAT
7520432 TTGATTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTATATAATGTAACT
Found at i:7523262 original size:40 final size:40
Alignment explanation
Indices: 7523217--7523303 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 40
7523207 GCTATGTTTA
7523217 GCACTTAATATGAAATTC-GAGATAGCTTCAGCTATTTATG
1 GCACTTAATATGAAATTCGGA-ATAGCTTCAGCTATTTATG
* * ** * *
7523257 GCACTTAGTGTGCGATTTGGAATAGCTTCGGCTATTTATG
1 GCACTTAATATGAAATTCGGAATAGCTTCAGCTATTTATG
*
7523297 ACACTTA
1 GCACTTA
7523304 GTGTGCGAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 37 0.95
41 2 0.05
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (40 bp):
GCACTTAATATGAAATTCGGAATAGCTTCAGCTATTTATG
Found at i:7523304 original size:40 final size:41
Alignment explanation
Indices: 7523235--7523348 Score: 151
Period size: 40 Copynumber: 2.8 Consensus size: 41
7523225 TATGAAATTC
* **
7523235 GAGATAGCTTCAGCTATTTATGGCACTTAGTGTGCGA-TTT
1 GAGATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGACT
*
7523275 G-GAATAGCTTCGGCTATTTATGACACTTAGTGTGCGAGACT
1 GAG-ATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGACT
* *
7523316 GAGATAGCTTCGGCTATGTAAGGCACTTAGTGT
1 GAGATAGCTTCGGCTATTTATGGCACTTAGTGT
7523349 ATGAAACATT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.02
40 33 0.52
41 29 0.45
42 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (41 bp):
GAGATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGACT
Found at i:7523643 original size:42 final size:42
Alignment explanation
Indices: 7523586--7523685 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
7523576 CTATATGAAC
*
7523586 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAATG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACG
* *
7523628 GGCACTAAGTGTGCGAAATTAAAATGATGATGTTGTATAACG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACG
7523670 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
7523686 TACCAAGAGC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.27
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACG
Found at i:7538651 original size:18 final size:18
Alignment explanation
Indices: 7538630--7538674 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
7538620 ACCACTATGT
*
7538630 GGCCCAATACCATC-CTTC
1 GGCCCAATACCA-CGATTC
*
7538648 GGCCCAACACCACGATTC
1 GGCCCAATACCACGATTC
7538666 GGCCCAATA
1 GGCCCAATA
7538675 GCACCATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GGCCCAATACCACGATTC
Found at i:7538840 original size:19 final size:17
Alignment explanation
Indices: 7538809--7538875 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 17
7538799 AGCAAACCAT
*
7538809 TTTTTACCACAATCATAA
1 TTTTGACCACAAT-ATAA
7538827 TTTTGACCAGCAATATAA
1 TTTTGACCA-CAATATAA
7538845 TTTTGACCACTTCCAATATAA
1 TTTTGACCA----CAATATAA
7538866 TTTTGACCAC
1 TTTTGACCAC
7538876 TTTCAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
17 1 0.02
18 21 0.49
19 4 0.09
21 17 0.40
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.37
Consensus pattern (17 bp):
TTTTGACCACAATATAA
Found at i:7538863 original size:21 final size:21
Alignment explanation
Indices: 7538837--7538895 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
7538827 TTTTGACCAG
7538837 CAATATAATTTTGACCACTTC
1 CAATATAATTTTGACCACTTC
*
7538858 CAATATAATTTTGACCACTTT
1 CAATATAATTTTGACCACTTC
*
7538879 CAAAATAATTTTGACCA
1 CAATATAATTTTGACCA
7538896 GGGTTAGTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.37
Consensus pattern (21 bp):
CAATATAATTTTGACCACTTC
Found at i:7540372 original size:2 final size:2
Alignment explanation
Indices: 7540365--7540403 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
7540355 NNNNNNNNTA
7540365 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7540404 CTTCAATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:7543492 original size:16 final size:16
Alignment explanation
Indices: 7543471--7543501 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7543461 TATGTTTAAG
7543471 CGTATAAATTTGAAAC
1 CGTATAAATTTGAAAC
*
7543487 CGTATATATTTGAAA
1 CGTATAAATTTGAAA
7543502 ACTTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (16 bp):
CGTATAAATTTGAAAC
Found at i:7544861 original size:22 final size:22
Alignment explanation
Indices: 7544835--7544878 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
7544825 CACTAATGAA
* *
7544835 CAGAGAGCACTAATGTGCTAAT
1 CAGAGAGCACCAACGTGCTAAT
7544857 CAGAGAGCACCAACGTGCTAAT
1 CAGAGAGCACCAACGTGCTAAT
7544879 AATTAGAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (22 bp):
CAGAGAGCACCAACGTGCTAAT
Found at i:7545881 original size:8 final size:8
Alignment explanation
Indices: 7545868--7545897 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
7545858 TTTATATATA
7545868 ATAATAAT
1 ATAATAAT
*
7545876 ATAATATT
1 ATAATAAT
7545884 ATAATAAT
1 ATAATAAT
7545892 ATAATA
1 ATAATA
7545898 TAACAACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATAAT
Found at i:7545887 original size:16 final size:16
Alignment explanation
Indices: 7545863--7545900 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
7545853 TTTACTTTAT
7545863 ATATAATAATAATATA
1 ATATAATAATAATATA
*
7545879 ATATTATAATAATATA
1 ATATAATAATAATATA
7545895 ATATAA
1 ATATAA
7545901 CAACATACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAATAATAATATA
Found at i:7546940 original size:14 final size:15
Alignment explanation
Indices: 7546921--7546953 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
7546911 ATATTCTAGA
7546921 AAAAAATATAAAT-T
1 AAAAAATATAAATAT
*
7546935 AAAAAATATGAATAT
1 AAAAAATATAAATAT
7546950 AAAA
1 AAAA
7546954 TTTACAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
AAAAAATATAAATAT
Found at i:7547397 original size:19 final size:20
Alignment explanation
Indices: 7547358--7547397 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
7547348 TATATTTTTA
*
7547358 ATTTTTAATTTAAATTTAAT
1 ATTTTTAATTTAAATTAAAT
*
7547378 ATTTTTATTTTAAA-TAAAT
1 ATTTTTAATTTAAATTAAAT
7547397 A
1 A
7547398 AAATTACCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTAATTTAAATTAAAT
Found at i:7548494 original size:23 final size:22
Alignment explanation
Indices: 7548468--7548537 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 22
7548458 TTTATTTTAG
7548468 AAAATAAAAATTAAATAAATGTT
1 AAAATAAAAATTAAA-AAATGTT
*
7548491 AAAAT--AAGTTAAAAAATGTT
1 AAAATAAAAATTAAAAAATGTT
* *
7548511 AAGTACAAAAATTAAGAAAAT-TT
1 AA-AATAAAAATTAA-AAAATGTT
7548534 AAAA
1 AAAA
7548538 AAATTAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
20 9 0.24
21 8 0.21
22 1 0.03
23 15 0.39
24 5 0.13
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.27
Consensus pattern (22 bp):
AAAATAAAAATTAAAAAATGTT
Found at i:7553854 original size:23 final size:24
Alignment explanation
Indices: 7553828--7553877 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
7553818 TGGAATTTGA
* *
7553828 TGAAAC-GTATAAGTTAAATTGTT
1 TGAAACTGTAAAAGTTAAATTGCT
7553851 TG-AACTGTAAAAGTTAAATTGCT
1 TGAAACTGTAAAAGTTAAATTGCT
7553874 TGAA
1 TGAA
7553878 CAGGTTGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 19 0.83
24 1 0.04
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (24 bp):
TGAAACTGTAAAAGTTAAATTGCT
Found at i:7557282 original size:17 final size:16
Alignment explanation
Indices: 7557245--7557286 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
7557235 CCTTTATGTA
*
7557245 ATTTTATTTTTTTAAT
1 ATTTTATATTTTTAAT
7557261 ATTTTATATTTTTAAGT
1 ATTTTATATTTTTAA-T
*
7557278 CTTTTATAT
1 ATTTTATAT
7557287 AATAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (16 bp):
ATTTTATATTTTTAAT
Found at i:7569580 original size:18 final size:16
Alignment explanation
Indices: 7569543--7569593 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
7569533 AAATTATAAA
7569543 AAATTAATATAAAAAC
1 AAATTAATATAAAAAC
*
7569559 AAATTAATTTAACAATAC
1 AAATTAATATAA-AA-AC
*
7569577 AAA-TAAAATAAATAAC
1 AAATTAATATAAA-AAC
7569593 A
1 A
7569594 TGTAAGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 15 0.52
17 9 0.31
18 5 0.17
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATTAATATAAAAAC
Found at i:7577661 original size:24 final size:24
Alignment explanation
Indices: 7577629--7577679 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
7577619 AATGTGAAGT
7577629 TTAGTTACTACTCAAAACAATTAC
1 TTAGTTACTACTCAAAACAATTAC
7577653 TTAGTTACTACTCAAAACAATTAC
1 TTAGTTACTACTCAAAACAATTAC
7577677 TTA
1 TTA
7577680 CTGTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (24 bp):
TTAGTTACTACTCAAAACAATTAC
Found at i:7580662 original size:3 final size:3
Alignment explanation
Indices: 7580654--7580696 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
7580644 GTCTCACATG
*
7580654 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
7580697 TTCTGATTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:7581467 original size:40 final size:38
Alignment explanation
Indices: 7581413--7581616 Score: 99
Period size: 39 Copynumber: 5.4 Consensus size: 38
7581403 ATTAATATAT
*
7581413 TTATAATTGTAATAAATATTTAGTATTAAAATATTAATA
1 TTAT-ATTTTAATAAATATTTAGTATTAAAATATTAATA
* * * *
7581452 TTGATATTTTCAAT-AATATGT-G-AATAATACTATTTAAAA
1 TT-ATATTTT-AATAAATATTTAGTATTAA-AATA-TTAATA
* *
7581491 TTATTATTTT--TAAA-ATTTACTATTAAAATA-AAAT-
1 TTA-TATTTTAATAAATATTTAGTATTAAAATATTAATA
* * * * *
7581525 TTAAATATTAACTACAAAACGTTTATTATTAATATATT--TA
1 TTATATTTTAA-TA-AATA--TTTAGTATTAAAATATTAATA
*
7581565 -TA-ATTGTAATAAATATTTAGTATTAAAATATTAATA
1 TTATATTTTAATAAATATTTAGTATTAAAATATTAATA
7581601 TTGATATTTTCAATAA
1 TT-ATATTTT-AATAA
7581617 TATGTGAATA
Statistics
Matches: 120, Mismatches: 22, Indels: 45
0.64 0.12 0.24
Matches are distributed among these distances:
33 4 0.03
34 18 0.15
35 2 0.02
36 11 0.09
37 14 0.12
38 16 0.13
39 32 0.27
40 23 0.19
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (38 bp):
TTATATTTTAATAAATATTTAGTATTAAAATATTAATA
Found at i:7581656 original size:149 final size:149
Alignment explanation
Indices: 7581386--7581684 Score: 589
Period size: 149 Copynumber: 2.0 Consensus size: 149
7581376 TAACATTTAT
7581386 ACTACAAAACGTTTATTATTAATATATTTATAATTGTAATAAATATTTAGTATTAAAATATTAAT
1 ACTACAAAACGTTTATTATTAATATATTTATAATTGTAATAAATATTTAGTATTAAAATATTAAT
7581451 ATTGATATTTTCAATAATATGTGAATAATACTATTTAAAATTATTATTTTTAAAATTTACTATTA
66 ATTGATATTTTCAATAATATGTGAATAATACTATTTAAAATTATTATTTTTAAAATTTACTATTA
7581516 AAATAAAATTTAAATATTA
131 AAATAAAATTTAAATATTA
7581535 ACTACAAAACGTTTATTATTAATATATTTATAATTGTAATAAATATTTAGTATTAAAATATTAAT
1 ACTACAAAACGTTTATTATTAATATATTTATAATTGTAATAAATATTTAGTATTAAAATATTAAT
*
7581600 ATTGATATTTTCAATAATATGTGAATAATATTATTTAAAATTATTATTTTTAAAATTTACTATTA
66 ATTGATATTTTCAATAATATGTGAATAATACTATTTAAAATTATTATTTTTAAAATTTACTATTA
7581665 AAATAAAATTTAAATATTA
131 AAATAAAATTTAAATATTA
7581684 A
1 A
7581685 ATAATTTATT
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (149 bp):
ACTACAAAACGTTTATTATTAATATATTTATAATTGTAATAAATATTTAGTATTAAAATATTAAT
ATTGATATTTTCAATAATATGTGAATAATACTATTTAAAATTATTATTTTTAAAATTTACTATTA
AAATAAAATTTAAATATTA
Found at i:7581688 original size:18 final size:18
Alignment explanation
Indices: 7581650--7581685 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
7581640 TTATTATTTT
*
7581650 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
7581668 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
7581686 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:7595513 original size:22 final size:22
Alignment explanation
Indices: 7595488--7595547 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
7595478 TTGAAAACTC
*
7595488 TGAGAGCTTAGTACGTTAAACA
1 TGAGAGCTTAGTACGTGAAACA
7595510 TGAGAGCTTAGTACGTGAAACA
1 TGAGAGCTTAGTACGTGAAACA
7595532 TGAGAGCTTAGTACGT
1 TGAGAGCTTAGTACGT
7595548 ACTATCAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (22 bp):
TGAGAGCTTAGTACGTGAAACA
Found at i:7596402 original size:19 final size:18
Alignment explanation
Indices: 7596353--7596392 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
7596343 GTAAATTTTA
7596353 TTAT-ATAATTTAATAAT
1 TTATAATAATTTAATAAT
7596370 TTATAATAATTTAATAAAT
1 TTATAATAATTTAAT-AAT
7596389 TTAT
1 TTAT
7596393 TTTTATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.19
18 10 0.48
19 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATAATAATTTAATAAT
Found at i:7597058 original size:19 final size:19
Alignment explanation
Indices: 7597025--7597081 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
7597015 CCTAATTCTA
7597025 AAAAATAT-ATAAATATTTT
1 AAAAATATAAT-AATATTTT
*
7597044 AAAAATATAATAATAAATTT
1 AAAAATATAATAAT-ATTTT
*
7597064 AAATTATATAATAATATT
1 AAA-AATATAATAATATT
7597082 AATATTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 11 0.34
20 11 0.34
21 10 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATATAATAATATTTT
Found at i:7597077 original size:24 final size:26
Alignment explanation
Indices: 7597031--7597101 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 26
7597021 TCTAAAAAAT
*
7597031 ATATAAATATTTTAA-A-AATATAAT-
1 ATATAAATA-TTAAATATAATATAATA
7597055 A-ATAAAT-TTAAAT-T-ATATAATA
1 ATATAAATATTAAATATAATATAATA
*
7597077 ATATTAATATTAAATATAATATAAT
1 ATATAAATATTAAATATAATATAAT
7597102 CCCTTCCCCC
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
21 11 0.29
22 1 0.03
23 11 0.29
24 7 0.18
25 1 0.03
26 7 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
ATATAAATATTAAATATAATATAATA
Found at i:7597083 original size:18 final size:19
Alignment explanation
Indices: 7597052--7597098 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
7597042 TTAAAAATAT
7597052 AATAATAA-ATTTAA-ATTA
1 AATAATAATA-TTAATATTA
*
7597070 TATAATAATATTAATATTA
1 AATAATAATATTAATATTA
7597089 AAT-ATAATAT
1 AATAATAATAT
7597099 AATCCCTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATAATAATATTAATATTA
Found at i:7600121 original size:38 final size:38
Alignment explanation
Indices: 7600079--7600151 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
7600069 CAGTCACCAA
*
7600079 CGTTATTGAAAAGTGACAAATCAATCACTCATTAATAT
1 CGTTATCGAAAAGTGACAAATCAATCACTCATTAATAT
* *
7600117 CGTTATCGAAAAGTTACAAATCAGTCACTCATTAA
1 CGTTATCGAAAAGTGACAAATCAATCACTCATTAA
7600152 CATTTTCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (38 bp):
CGTTATCGAAAAGTGACAAATCAATCACTCATTAATAT
Found at i:7602187 original size:5 final size:5
Alignment explanation
Indices: 7602168--7602258 Score: 53
Period size: 6 Copynumber: 17.4 Consensus size: 5
7602158 ATTATATTAT
* *
7602168 AAAGA TAAAGTA AAAGAA AAAGA AATAGA AAAGA AGGAGA GAAAGA AACGA
1 AAAGA -AAAG-A AAAG-A AAAGA AA-AGA AAAGA A-AAGA -AAAGA AAAGA
* * *
7602219 AACAGA AAAGG AAAG- AAAGG GAAGA AAA-A AAAG- AAAGA AA
1 AA-AGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
7602259 GAAGGAGAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
4 12 0.18
5 26 0.38
6 28 0.41
7 2 0.03
ACGTcount: A:0.70, C:0.02, G:0.24, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:7602621 original size:18 final size:18
Alignment explanation
Indices: 7602598--7602635 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
7602588 TTTGTATGAA
7602598 AATATAAGATTGACTGTG
1 AATATAAGATTGACTGTG
7602616 AATATAAGATTGACTGTG
1 AATATAAGATTGACTGTG
7602634 AA
1 AA
7602636 GAAATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (18 bp):
AATATAAGATTGACTGTG
Found at i:7602966 original size:24 final size:24
Alignment explanation
Indices: 7602939--7602985 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
7602929 ATTGAAATGG
7602939 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
7602963 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
7602986 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:7604034 original size:11 final size:11
Alignment explanation
Indices: 7604018--7604044 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
7604008 ACGGGCAAAG
7604018 ATAATTTTACT
1 ATAATTTTACT
7604029 ATAATTTTACT
1 ATAATTTTACT
7604040 ATAAT
1 ATAAT
7604045 GGGAAAAGAA
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:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (11 bp):
ATAATTTTACT
Found at i:7604124 original size:18 final size:17
Alignment explanation
Indices: 7604092--7604125 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
7604082 CTACACCCCA
7604092 AACCCCAAAAAGTAAAG
1 AACCCCAAAAAGTAAAG
*
7604109 AACCCTCAAAACGTAAA
1 AACCC-CAAAAAGTAAA
7604126 CACAAAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.26, G:0.09, T:0.09
Consensus pattern (17 bp):
AACCCCAAAAAGTAAAG
Found at i:7605273 original size:39 final size:39
Alignment explanation
Indices: 7605230--7605312 Score: 166
Period size: 39 Copynumber: 2.1 Consensus size: 39
7605220 GAAGCTTGCC
7605230 TATCTGCTTTGCTATCCAAATGAAGCTCATTGTCGAGTT
1 TATCTGCTTTGCTATCCAAATGAAGCTCATTGTCGAGTT
7605269 TATCTGCTTTGCTATCCAAATGAAGCTCATTGTCGAGTT
1 TATCTGCTTTGCTATCCAAATGAAGCTCATTGTCGAGTT
7605308 TATCT
1 TATCT
7605313 CTACTCAACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (39 bp):
TATCTGCTTTGCTATCCAAATGAAGCTCATTGTCGAGTT
Found at i:7608556 original size:2 final size:2
Alignment explanation
Indices: 7608549--7608589 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
7608539 TCATTTCAGG
7608549 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
7608590 TAAGATATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:7611574 original size:19 final size:19
Alignment explanation
Indices: 7611547--7611590 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
7611537 TATTTTTAAG
7611547 AAATCTACCAAACAACAAA
1 AAATCTACCAAACAACAAA
*
7611566 AAATTTACCAAACAACAAA
1 AAATCTACCAAACAACAAA
7611585 AAATCT
1 AAATCT
7611591 TTTACGCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.61, C:0.23, G:0.00, T:0.16
Consensus pattern (19 bp):
AAATCTACCAAACAACAAA
Found at i:7611678 original size:14 final size:14
Alignment explanation
Indices: 7611642--7611680 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
7611632 TCAAAAAAAT
7611642 AAATTATTTTCTAA
1 AAATTATTTTCTAA
* *
7611656 AAATCATTTTCTGA
1 AAATTATTTTCTAA
*
7611670 AAGTTATTTTC
1 AAATTATTTTC
7611681 AATGAAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (14 bp):
AAATTATTTTCTAA
Found at i:7612207 original size:16 final size:16
Alignment explanation
Indices: 7612183--7612214 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7612173 TTCGCCTGTC
*
7612183 AACATACATACATACA
1 AACACACATACATACA
7612199 AACACACATACATACA
1 AACACACATACATACA
7612215 TATAAGAGCA
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:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (16 bp):
AACACACATACATACA
Found at i:7618688 original size:21 final size:22
Alignment explanation
Indices: 7618663--7618718 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
7618653 AAATCATTAA
7618663 TTTAAAAAATTGT-TAGAAATT
1 TTTAAAAAATTGTATAGAAATT
*
7618684 TTTAAAAAATTTGTATTGAAATT
1 TTTAAAAAA-TTGTATAGAAATT
*
7618707 TATTAATAAATT
1 T-TTAAAAAATT
7618719 TAGGAAGAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 9 0.30
22 4 0.13
23 10 0.33
24 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (22 bp):
TTTAAAAAATTGTATAGAAATT
Found at i:7619318 original size:25 final size:25
Alignment explanation
Indices: 7619290--7619337 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
7619280 ATGCTTTATC
*
7619290 ATTTT-AAATTTTTATATTTTTTAAA
1 ATTTTGAAATTTTAAT-TTTTTTAAA
7619315 ATTTTGAAATTTTAATTTTTTTA
1 ATTTTGAAATTTTAATTTTTTTA
7619338 CCAACATCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
ATTTTGAAATTTTAATTTTTTTAAA
Found at i:7646081 original size:27 final size:27
Alignment explanation
Indices: 7646051--7646107 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
7646041 TTTATATACA
7646051 AATACA-TTTATACAACTAATATTAATT
1 AATACACTTTATACAA-TAATATTAATT
* * **
7646078 AATATACTTTTTGTAATAATATTAATT
1 AATACACTTTATACAATAATATTAATT
7646105 AAT
1 AAT
7646108 TTTAATAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (27 bp):
AATACACTTTATACAATAATATTAATT
Found at i:7654466 original size:19 final size:20
Alignment explanation
Indices: 7654444--7654509 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 20
7654434 TTGAAAGAGC
*
7654444 TTATAAAAATT-ATATAAAA
1 TTATAAAAATTCATACAAAA
*
7654463 TTATAAAAATTCATACAAAC
1 TTATAAAAATTCATACAAAA
*
7654483 TTAT-AAAATTCTTA-AAAA
1 TTATAAAAATTCATACAAAA
*
7654501 GTATAAAAA
1 TTATAAAAA
7654510 AATTTATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 6 0.15
19 24 0.60
20 10 0.25
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (20 bp):
TTATAAAAATTCATACAAAA
Found at i:7654471 original size:9 final size:9
Alignment explanation
Indices: 7654444--7654509 Score: 62
Period size: 10 Copynumber: 7.0 Consensus size: 9
7654434 TTGAAAGAGC
7654444 TTATAAAAA
1 TTATAAAAA
7654453 TTATATAAAA
1 TTATA-AAAA
7654463 TTATAAAAA
1 TTATAAAAA
*
7654472 TTCATACAAAC
1 TT-ATA-AAAA
7654483 TTAT-AAAA
1 TTATAAAAA
*
7654491 TTCTTAAAAA
1 TT-ATAAAAA
*
7654501 GTATAAAAA
1 TTATAAAAA
7654510 AATTTATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
8 5 0.11
9 18 0.38
10 19 0.40
11 5 0.11
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (9 bp):
TTATAAAAA
Found at i:7654486 original size:20 final size:19
Alignment explanation
Indices: 7654443--7654490 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
7654433 ATTGAAAGAG
*
7654443 CTTATAAAAATTATATAAA
1 CTTATAAAAATTATACAAA
*
7654462 ATTATAAAAATTCATACAAA
1 CTTATAAAAATT-ATACAAA
7654482 CTTATAAAA
1 CTTATAAAA
7654491 TTCTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (19 bp):
CTTATAAAAATTATACAAA
Found at i:7665710 original size:19 final size:19
Alignment explanation
Indices: 7665675--7665712 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
7665665 GATATAATCA
*
7665675 TCAATAATAAATGATAAAT
1 TCAATAATAAATAATAAAT
7665694 TCAATAA-AAATAAATAAAT
1 TCAATAATAAAT-AATAAAT
7665713 GATGATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (19 bp):
TCAATAATAAATAATAAAT
Found at i:7675414 original size:9 final size:9
Alignment explanation
Indices: 7675400--7675450 Score: 84
Period size: 9 Copynumber: 5.7 Consensus size: 9
7675390 GTAGTGATTC
7675400 AATTCGGGT
1 AATTCGGGT
7675409 AATTCGGGT
1 AATTCGGGT
*
7675418 AATTCAGGT
1 AATTCGGGT
7675427 AATTCGGGT
1 AATTCGGGT
*
7675436 AATTCGGTT
1 AATTCGGGT
7675445 AATTCG
1 AATTCG
7675451 ACTAATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (9 bp):
AATTCGGGT
Found at i:7675456 original size:27 final size:27
Alignment explanation
Indices: 7675400--7675457 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
7675390 GTAGTGATTC
*
7675400 AATTCGGGTAATTCGGGTAATTCAGGT
1 AATTCGGGTAATTCGGGTAATTCAGCT
*
7675427 AATTCGGGTAATTCGGTTAATTC-GACT
1 AATTCGGGTAATTCGGGTAATTCAG-CT
7675454 AATT
1 AATT
7675458 TTTAACCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (27 bp):
AATTCGGGTAATTCGGGTAATTCAGCT
Found at i:7676765 original size:17 final size:18
Alignment explanation
Indices: 7676743--7676777 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
7676733 TTTCGTTAAA
7676743 TAAATAATT-TAAATTAT
1 TAAATAATTATAAATTAT
*
7676760 TAAATATTTATAAATTAT
1 TAAATAATTATAAATTAT
7676778 ACTAAATAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATAATTATAAATTAT
Found at i:7688620 original size:27 final size:27
Alignment explanation
Indices: 7688590--7688644 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
7688580 AAAGCTGGTG
*
7688590 CAGCAGCAGCCACCCCAGGGTTAAACC
1 CAGCAGCAGCAACCCCAGGGTTAAACC
* *
7688617 CAGCAGCAGCAACTCCAGGGTTGAACC
1 CAGCAGCAGCAACCCCAGGGTTAAACC
7688644 C
1 C
7688645 CACTCCCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.38, G:0.24, T:0.09
Consensus pattern (27 bp):
CAGCAGCAGCAACCCCAGGGTTAAACC
Found at i:7689627 original size:6 final size:6
Alignment explanation
Indices: 7689618--7689687 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 6
7689608 CTCCTCTTCC
** * * ** *
7689618 TCCTCT TCCTCT TCCAGT TCCACT TCCTCT TCTTCT TCAACC TCCTCT
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT
*
7689666 T-CTACT TCCTCT TCCACT TCCT
1 TCCT-CT TCCTCT TCCTCT TCCT
7689688 GTAGTTGCTG
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
5 2 0.04
6 45 0.92
7 2 0.04
ACGTcount: A:0.09, C:0.46, G:0.01, T:0.44
Consensus pattern (6 bp):
TCCTCT
Found at i:7689684 original size:12 final size:12
Alignment explanation
Indices: 7689622--7689687 Score: 69
Period size: 12 Copynumber: 5.5 Consensus size: 12
7689612 TCTTCCTCCT
7689622 CTTCCTCTTCCA
1 CTTCCTCTTCCA
* * *
7689634 GTTCCACTTCCT
1 CTTCCTCTTCCA
* *
7689646 CTTCTTCTTCAA
1 CTTCCTCTTCCA
* *
7689658 CCTCCTCTTCTA
1 CTTCCTCTTCCA
7689670 CTTCCTCTTCCA
1 CTTCCTCTTCCA
7689682 CTTCCT
1 CTTCCT
7689688 GTAGTTGCTG
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.09, C:0.45, G:0.02, T:0.44
Consensus pattern (12 bp):
CTTCCTCTTCCA
Found at i:7689685 original size:18 final size:18
Alignment explanation
Indices: 7689622--7689685 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
7689612 TCTTCCTCCT
* *
7689622 CTTCCTCTTCCAGTTCCA
1 CTTCCTCTTCTACTTCCA
* *
7689640 CTTCCTCTTCTTCTTCAA
1 CTTCCTCTTCTACTTCCA
* *
7689658 CCTCCTCTTCTACTTCCT
1 CTTCCTCTTCTACTTCCA
*
7689676 CTTCCACTTC
1 CTTCCTCTTC
7689686 CTGTAGTTGC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.09, C:0.45, G:0.02, T:0.44
Consensus pattern (18 bp):
CTTCCTCTTCTACTTCCA
Found at i:7691977 original size:17 final size:17
Alignment explanation
Indices: 7691940--7691987 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
7691930 GAATTTAGAA
*
7691940 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
*
7691956 GAATTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
7691973 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
7691988 AAAAAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:7703488 original size:22 final size:21
Alignment explanation
Indices: 7703463--7703507 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
7703453 AATAGAATAA
7703463 ATTTAATATTA-ATTTTGAATTT
1 ATTTAATATTACA-TTT-AATTT
*
7703485 ATTTAATTTTACATTTAATTT
1 ATTTAATATTACATTTAATTT
7703506 AT
1 AT
7703508 CAAATACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 13 0.62
23 1 0.05
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTAATATTACATTTAATTT
Found at i:7703500 original size:16 final size:17
Alignment explanation
Indices: 7703462--7703506 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 17
7703452 TAATAGAATA
7703462 AATTTAATATTAATTTTG
1 AATTTAAT-TTAATTTTG
7703480 AATTT-ATTTAATTTT-
1 AATTTAATTTAATTTTG
7703495 ACATTTAATTTA
1 A-ATTTAATTTA
7703507 TCAAATACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.04
16 12 0.48
17 7 0.28
18 5 0.20
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
AATTTAATTTAATTTTG
Found at i:7710801 original size:31 final size:32
Alignment explanation
Indices: 7710766--7710831 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
7710756 TTTTTTAGTT
*
7710766 AAATTT-ACTCATCAACCTTTT-AAAAAGAGTC
1 AAATTTGACT-ATCAACCTTTTGAAAAAGAATC
* *
7710797 AAATTTGACTATTAGCCTTTTGAAAAAGAATC
1 AAATTTGACTATCAACCTTTTGAAAAAGAATC
7710829 AAA
1 AAA
7710832 ATGATAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 15 0.50
32 15 0.50
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (32 bp):
AAATTTGACTATCAACCTTTTGAAAAAGAATC
Found at i:7724518 original size:21 final size:20
Alignment explanation
Indices: 7724492--7724530 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
7724482 AATAAATACC
*
7724492 AAAAAATTATTTTAAAAATT
1 AAAAAAATATTTTAAAAATT
7724512 AAAAAAATATTTTAAAAAT
1 AAAAAAATATTTTAAAAAT
7724531 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAAATATTTTAAAAATT
Found at i:7724520 original size:31 final size:31
Alignment explanation
Indices: 7724485--7724571 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
7724475 TTTTTTTAAT
7724485 AAATA-CCAAAAAATTATTTTAAAAATTAAAA
1 AAATATCCAAAAAA-TATTTTAAAAATTAAAA
*** *
7724516 AAATATTTTAAAAATATTTTAAAATTTAAAA
1 AAATATCCAAAAAATATTTTAAAAATTAAAA
** *
7724547 AAAT-TTTAAAAAGTATTTTAAAAAT
1 AAATATCCAAAAAATATTTTAAAAAT
7724572 ATTTTAAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 18 0.38
31 25 0.52
32 5 0.10
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (31 bp):
AAATATCCAAAAAATATTTTAAAAATTAAAA
Found at i:7724530 original size:11 final size:11
Alignment explanation
Indices: 7724493--7724580 Score: 89
Period size: 11 Copynumber: 8.4 Consensus size: 11
7724483 ATAAATACCA
7724493 AAAAATTATTTT
1 AAAAA-TATTTT
**
7724505 -AAAA-ATTAA
1 AAAAATATTTT
7724514 AAAAATATTTT
1 AAAAATATTTT
7724525 AAAAATATTTT
1 AAAAATATTTT
7724536 --AAA-A-TTT
1 AAAAATATTTT
*
7724543 AAAAAAATTTT
1 AAAAATATTTT
7724554 AAAAAGTATTTT
1 AAAAA-TATTTT
7724566 AAAAATATTTT
1 AAAAATATTTT
7724577 AAAA
1 AAAA
7724581 TTAAAAAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
7 3 0.05
8 1 0.02
9 9 0.14
10 5 0.08
11 36 0.56
12 10 0.16
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:7724570 original size:41 final size:40
Alignment explanation
Indices: 7724505--7724598 Score: 154
Period size: 41 Copynumber: 2.4 Consensus size: 40
7724495 AAATTATTTT
7724505 AAAAA-TTAAAAAAATATTTTAAAAATATTTTAAAATTTAA
1 AAAAATTTAAAAAAATATTTTAAAAATATTTTAAAA-TTAA
* *
7724545 AAAAATTTTAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTTAAAAAAATATTTTAAAAATATTTTAAAATTAA
7724585 AAAAATTTAAAAAA
1 AAAAATTTAAAAAA
7724599 TAAATATATT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 22 0.44
41 28 0.56
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (40 bp):
AAAAATTTAAAAAAATATTTTAAAAATATTTTAAAATTAA
Found at i:7724610 original size:17 final size:17
Alignment explanation
Indices: 7724565--7724610 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
7724555 AAAAGTATTT
* *
7724565 TAAAAATATTTTAAAAT
1 TAAAAATATTTAAAAAA
*
7724582 TAAAAAAATTTAAAAAA
1 TAAAAATATTTAAAAAA
*
7724599 TAAATATATTTA
1 TAAAAATATTTA
7724611 TTATATCGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAAATATTTAAAAAA
Found at i:7727443 original size:8 final size:7
Alignment explanation
Indices: 7727410--7727442 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
7727400 AAAGTATTTT
*
7727410 AAAATTA
1 AAAAATA
7727417 AAAAATA
1 AAAAATA
7727424 AAAAATA
1 AAAAATA
7727431 AAAAATA
1 AAAAATA
7727438 AAAAA
1 AAAAA
7727443 AAATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:7736833 original size:23 final size:23
Alignment explanation
Indices: 7736806--7736858 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
7736796 AGTGTTATTG
7736806 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
7736829 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
7736852 ATCAGTG
1 ATCAGTG
7736859 TGGCACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:7737030 original size:38 final size:37
Alignment explanation
Indices: 7736988--7737060 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
7736978 ATGTATGGAA
* *
7736988 TTGAATTGAATATTGACTTGAAAA-TGGAAAAGTGAATT
1 TTGAATTGAATAGTGA-TT-AAAAGTGAAAAAGTGAATT
7737026 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
7737061 ATTATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.45, C:0.01, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAATT
Found at i:7738067 original size:2 final size:2
Alignment explanation
Indices: 7738060--7738105 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
7738050 TGGTATTGAA
7738060 AT AT AT AT AT 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 AT AT AT AT AT
7738102 AT AT
1 AT AT
7738106 TGGATTGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7738906 original size:28 final size:28
Alignment explanation
Indices: 7738866--7738924 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
7738856 AAATTTAACT
7738866 TACCATTATTTCACACATAAGGTAAGCA
1 TACCATTATTTCACACATAAGGTAAGCA
7738894 TACCATTATTTCACACATAAGGTAAGCA
1 TACCATTATTTCACACATAAGGTAAGCA
7738922 TAC
1 TAC
7738925 AAATATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (28 bp):
TACCATTATTTCACACATAAGGTAAGCA
Found at i:7738931 original size:28 final size:28
Alignment explanation
Indices: 7738872--7738932 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
7738862 AACTTACCAT
* *
7738872 TATTTCACACATAAGGTAAGCATACCAT
1 TATTTCACACATAAGGTAAGCATACAAA
7738900 TATTTCACACATAAGGTAAGCATACAAA
1 TATTTCACACATAAGGTAAGCATACAAA
7738928 TATTT
1 TATTT
7738933 ATCCAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (28 bp):
TATTTCACACATAAGGTAAGCATACAAA
Found at i:7746863 original size:6 final size:6
Alignment explanation
Indices: 7746854--7746878 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
7746844 GTAATAATAA
7746854 TTTAAT TTTAAT TTTAAT TTTAAT T
1 TTTAAT TTTAAT TTTAAT TTTAAT T
7746879 ATACAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTAAT
Found at i:7747616 original size:75 final size:76
Alignment explanation
Indices: 7747508--7747662 Score: 258
Period size: 75 Copynumber: 2.0 Consensus size: 76
7747498 GATATATATT
*
7747508 TAAATATATCTGGGTGTTCTTGTTGTTTTGTATCGATTTTCTCTTTTTCTTTTCGATGCTTTGAA
1 TAAATATATCTGGGTG-T-GTGTTGTTTTGTATCGATTTTCTCTTTTTCTTTTCGATGCTTTGAA
7747573 TTTTAATTTTTTA
64 TTTTAATTTTTTA
* *
7747586 TAAATATATCTGGGTG-GTGTTGTTTTGTATCGATTTTCTCTTTTTCTTTTTGATGTTTTGAATT
1 TAAATATATCTGGGTGTGTGTTGTTTTGTATCGATTTTCTCTTTTTCTTTTCGATGCTTTGAATT
7747650 TTAATTTTTTA
66 TTAATTTTTTA
7747661 TA
1 TA
7747663 CATCCTAGCA
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
75 58 0.78
78 16 0.22
ACGTcount: A:0.17, C:0.08, G:0.15, T:0.59
Consensus pattern (76 bp):
TAAATATATCTGGGTGTGTGTTGTTTTGTATCGATTTTCTCTTTTTCTTTTCGATGCTTTGAATT
TTAATTTTTTA
Found at i:7747853 original size:36 final size:36
Alignment explanation
Indices: 7747806--7747877 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
7747796 ACTCGTTGGT
7747806 ATCCTCTGAATGTTGAGGAGAACTTGAGTGTTTATC
1 ATCCTCTGAATGTTGAGGAGAACTTGAGTGTTTATC
7747842 ATCCTCTGAATGTTGAGGAGAACTTGAGTGTTTATC
1 ATCCTCTGAATGTTGAGGAGAACTTGAGTGTTTATC
7747878 TTATAATTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (36 bp):
ATCCTCTGAATGTTGAGGAGAACTTGAGTGTTTATC
Found at i:7749054 original size:28 final size:28
Alignment explanation
Indices: 7749022--7749077 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
7749012 TCTCATCCAT
7749022 ACACTTGATAAACACCCTTATCATTGCC
1 ACACTTGATAAACACCCTTATCATTGCC
7749050 ACACTTGATAAACACCCTTATCATTGCC
1 ACACTTGATAAACACCCTTATCATTGCC
7749078 TTCAAATAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.07, T:0.29
Consensus pattern (28 bp):
ACACTTGATAAACACCCTTATCATTGCC
Found at i:7751145 original size:31 final size:31
Alignment explanation
Indices: 7751096--7751156 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
7751086 ACTCGATGAT
7751096 TTACACTATTGTAGTCCGTATGAATCATATG
1 TTACACTATTGTAGTCCGTATGAATCATATG
*
7751127 TTACACTGTTGT-GATCCGTATGAATCATAT
1 TTACACTATTGTAG-TCCGTATGAATCATAT
7751157 ATTGTATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (31 bp):
TTACACTATTGTAGTCCGTATGAATCATATG
Found at i:7766251 original size:13 final size:14
Alignment explanation
Indices: 7766233--7766261 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
7766223 TCTTCTACTC
7766233 TACTCACATG-ATT
1 TACTCACATGTATT
7766246 TACTCACATGTATT
1 TACTCACATGTATT
7766260 TA
1 TA
7766262 AGATTTCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (14 bp):
TACTCACATGTATT
Found at i:7778359 original size:16 final size:16
Alignment explanation
Indices: 7778329--7778373 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
7778319 AAATATCGAT
7778329 ATCAA-ATATTATAATG
1 ATCAATATATT-TAATG
*
7778345 TTCAATATATTTAATG
1 ATCAATATATTTAATG
7778361 AT--ATATATTTAAT
1 ATCAATATATTTAAT
7778374 AGTACAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 11 0.42
16 10 0.38
17 5 0.19
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (16 bp):
ATCAATATATTTAATG
Found at i:7786436 original size:28 final size:28
Alignment explanation
Indices: 7786396--7786450 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
7786386 TTTTTCAAAG
7786396 TTAGAATAGGAGATCCCGAAATCATTCA
1 TTAGAATAGGAGATCCCGAAATCATTCA
7786424 TTAGAATAGGAGATCCCGAAATCATTC
1 TTAGAATAGGAGATCCCGAAATCATTC
7786451 TCGCCTTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (28 bp):
TTAGAATAGGAGATCCCGAAATCATTCA
Found at i:7787625 original size:26 final size:26
Alignment explanation
Indices: 7787591--7787641 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
7787581 AATAATTATA
7787591 TTTTTTATTTTTTATTTTTAAAATAT
1 TTTTTTATTTTTTATTTTTAAAATAT
7787617 TTTTTTATTTTTTATTTTTAAAATA
1 TTTTTTATTTTTTATTTTTAAAATA
7787642 AATTTTTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTTTATTTTTTATTTTTAAAATAT
Found at i:7787647 original size:26 final size:26
Alignment explanation
Indices: 7787592--7787648 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
7787582 ATAATTATAT
**
7787592 TTTTTATTTTTTATTTTTAAAATATT
1 TTTTTATTTTTTATTTTTAAAATAAA
7787618 TTTTTATTTTTTATTTTTAAAATAAA
1 TTTTTATTTTTTATTTTTAAAATAAA
7787644 TTTTT
1 TTTTT
7787649 GGTGTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTTTATTTTTTATTTTTAAAATAAA
Found at i:7787656 original size:26 final size:26
Alignment explanation
Indices: 7787592--7787658 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 26
7787582 ATAATTATAT
* * **
7787592 TTTTTATTTTTTATTTTTAAAATATT
1 TTTTTAGTGTTTATTTTTAAAATAAA
* *
7787618 TTTTTATTTTTTATTTTTAAAATAAA
1 TTTTTAGTGTTTATTTTTAAAATAAA
*
7787644 TTTTTGGTGTTTATT
1 TTTTTAGTGTTTATT
7787659 AAAAATGGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.70
Consensus pattern (26 bp):
TTTTTAGTGTTTATTTTTAAAATAAA
Found at i:7788165 original size:2 final size:2
Alignment explanation
Indices: 7788160--7788188 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7788150 CACACATTTG
7788160 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 T
7788189 TATTTAATTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7788566 original size:2 final size:2
Alignment explanation
Indices: 7788559--7788587 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7788549 NNNNNNNTAG
7788559 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 T
7788588 TTAATTAATG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7789354 original size:22 final size:19
Alignment explanation
Indices: 7789329--7789386 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
7789319 AATAACAACA
7789329 AAATAATAGCAACATAATAGTG
1 AAATAATAGC-A-A-AATAGTG
*
7789351 AAATAGTAGCAAAATAGTG
1 AAATAATAGCAAAATAGTG
*
7789370 AAAAAATAAG-AAAATAG
1 AAATAAT-AGCAAAATAG
7789387 CAACAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 19 0.59
20 3 0.09
21 1 0.03
22 9 0.28
ACGTcount: A:0.60, C:0.05, G:0.16, T:0.19
Consensus pattern (19 bp):
AAATAATAGCAAAATAGTG
Found at i:7789385 original size:30 final size:28
Alignment explanation
Indices: 7789351--7789406 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
7789341 CATAATAGTG
* *
7789351 AAATAGTAGCAAAATAGTGAAAAAATAAGA
1 AAATAGCAACAAAATA--GAAAAAATAAGA
7789381 AAATAGCAACAAAATAGAAAAAATAA
1 AAATAGCAACAAAATAGAAAAAATAA
7789407 CAATAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.42
30 14 0.58
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.14
Consensus pattern (28 bp):
AAATAGCAACAAAATAGAAAAAATAAGA
Found at i:7789423 original size:20 final size:20
Alignment explanation
Indices: 7789380--7789432 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
7789370 AAAAAATAAG
*
7789380 AAAATAGCAACAAAATAGAA
1 AAAATAACAACAAAATAGAA
*
7789400 AAAATAACAATAAAATA-AA
1 AAAATAACAACAAAATAGAA
*
7789419 TAAAAAAACAACAA
1 -AAAATAACAACAA
7789433 TTTTTTTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.75, C:0.09, G:0.04, T:0.11
Consensus pattern (20 bp):
AAAATAACAACAAAATAGAA
Found at i:7789684 original size:34 final size:35
Alignment explanation
Indices: 7789619--7789686 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
7789609 ATATTTTTCT
* * *
7789619 TTAATAATATATTATATTAATTAATTAATTAAATA
1 TTAATAATATATTATAATAATAAAATAATTAAATA
7789654 TTAA-AATATATTATAAATAATAAAAT-ATTAAAT
1 TTAATAATATATTAT-AATAATAAAATAATTAAAT
7789687 CAATCAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (35 bp):
TTAATAATATATTATAATAATAAAATAATTAAATA
Found at i:7794138 original size:19 final size:21
Alignment explanation
Indices: 7794095--7794143 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
7794085 GATAATTTCT
*
7794095 TAAAGTTAACTAATCAAAATG
1 TAAACTTAACTAATCAAAATG
*
7794116 TAAACTTAA-TAAT-AAATTG
1 TAAACTTAACTAATCAAAATG
7794135 TAAACTTAA
1 TAAACTTAA
7794144 ATATAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 14 0.54
20 4 0.15
21 8 0.31
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (21 bp):
TAAACTTAACTAATCAAAATG
Found at i:7795258 original size:21 final size:20
Alignment explanation
Indices: 7795233--7795279 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
7795223 CCGGCCCGAT
*
7795233 TTTTAATAAACACAAAAAATA
1 TTTTAA-AAACAAAAAAAATA
*
7795254 TTTTAAAAATAAAAAAAATA
1 TTTTAAAAACAAAAAAAATA
7795274 TTTTAA
1 TTTTAA
7795280 GTATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (20 bp):
TTTTAAAAACAAAAAAAATA
Found at i:7803991 original size:21 final size:21
Alignment explanation
Indices: 7803965--7804007 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
7803955 TATTAAACGT
7803965 ATAATTTCTACATGCATACGC
1 ATAATTTCTACATGCATACGC
7803986 ATAATTTCTACATGCATACGC
1 ATAATTTCTACATGCATACGC
7804007 A
1 A
7804008 GGGAAGGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (21 bp):
ATAATTTCTACATGCATACGC
Found at i:7836194 original size:23 final size:24
Alignment explanation
Indices: 7836167--7836213 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
7836157 AACTAAGGTC
7836167 ACATGC-AT-AAGCAACACTAAAAA
1 ACATGCTATAAAGCAA-ACTAAAAA
7836190 ACATGCTATAAAAGCAAACTAAAA
1 ACATGCTAT-AAAGCAAACTAAAA
7836214 TTTCTAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.29
24 2 0.10
25 7 0.33
26 6 0.29
ACGTcount: A:0.57, C:0.19, G:0.09, T:0.15
Consensus pattern (24 bp):
ACATGCTATAAAGCAAACTAAAAA
Found at i:7837340 original size:26 final size:26
Alignment explanation
Indices: 7837311--7837387 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
7837301 ATTGAATTTT
*
7837311 ATTTTAAATATAGATTATATATTTAA
1 ATTTTAAATATAGTTTATATATTTAA
7837337 ATTTGT--A-AT-GTTTATAT-TTTAA
1 ATTT-TAAATATAGTTTATATATTTAA
*
7837359 TATTTAAAATATAGTTTATATATTTAA
1 -ATTTTAAATATAGTTTATATATTTAA
7837386 AT
1 AT
7837388 ATAATGTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
22 5 0.12
23 11 0.26
24 3 0.07
25 3 0.07
26 14 0.33
27 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (26 bp):
ATTTTAAATATAGTTTATATATTTAA
Found at i:7837376 original size:19 final size:19
Alignment explanation
Indices: 7837349--7837390 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
7837339 TTGTAATGTT
*
7837349 TATATTTTA-ATATTTAAAA
1 TATAGTTTATATATTT-AAA
7837368 TATAGTTTATATATTTAAA
1 TATAGTTTATATATTTAAA
7837387 TATA
1 TATA
7837391 ATGTTTACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATAGTTTATATATTTAAA
Found at i:7849704 original size:29 final size:29
Alignment explanation
Indices: 7849653--7849708 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
7849643 AATCTACCCC
* * *
7849653 AAAATCTTGATTTTTAAGTTATCCTCACT
1 AAAATCTTGATCTTCAAGCTATCCTCACT
*
7849682 AAAATCTTTATCTTCAAGCTATCCTCA
1 AAAATCTTGATCTTCAAGCTATCCTCA
7849709 AATGATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.41
Consensus pattern (29 bp):
AAAATCTTGATCTTCAAGCTATCCTCACT
Done.