Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003053.1 Hibiscus syriacus cultivar Beakdansim tig00006365_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 776842
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:579465 original size:16 final size:16
Alignment explanation
Indices: 579439--579481 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
579429 CAATTTAATC
*
579439 ACTCAAATTTTGAATT
1 ACTCATATTTTGAATT
*
579455 ACTCATGTTTTGAATT
1 ACTCATATTTTGAATT
*
579471 ATTCATATTTT
1 ACTCATATTTT
579482 TATCATCTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (16 bp):
ACTCATATTTTGAATT
Found at i:579591 original size:30 final size:29
Alignment explanation
Indices: 579557--579637 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
579547 ATATATGATT
579557 AAAATAATATTAATTAAATTAAAAATTTTA
1 AAAAT-ATATTAATTAAATTAAAAATTTTA
** *
579587 AAAATATATTGAAACAAA--AAAATATTTTG
1 AAAATATATT-AATTAAATTAAAA-ATTTTA
579616 AAAAT-TA-TAATTAAATTAAAAA
1 AAAATATATTAATTAAATTAAAAA
579638 ATATTTCCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
26 5 0.12
27 2 0.05
28 10 0.24
29 15 0.36
30 10 0.24
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATATATTAATTAAATTAAAAATTTTA
Found at i:586797 original size:21 final size:21
Alignment explanation
Indices: 586773--586827 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
586763 AGTGCCATAG
586773 TACACAAAGTACTACTCCAAA
1 TACACAAAGTACTACTCCAAA
* *
586794 TACACAAAGTACTACTTCAAG
1 TACACAAAGTACTACTCCAAA
*
586815 TACACAATGTACT
1 TACACAAAGTACT
586828 CTTACAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.44, C:0.25, G:0.07, T:0.24
Consensus pattern (21 bp):
TACACAAAGTACTACTCCAAA
Found at i:594304 original size:26 final size:26
Alignment explanation
Indices: 594226--594304 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
594216 AACATATCCA
* * * *
594226 ATATCCGATCAGATGACCAACATCAG
1 ATATCCGATTAGAAGACCAAAATCTG
* *
594252 ATATCCGATTAGAAAAGCAACAA-CTG
1 ATATCCGATTAGAAGACCAA-AATCTG
594278 ATA-CCTGATTAGAAGACCAAAATCTG
1 ATATCC-GATTAGAAGACCAAAATCTG
594304 A
1 A
594305 AATGCGCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
25 4 0.10
26 37 0.88
27 1 0.02
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (26 bp):
ATATCCGATTAGAAGACCAAAATCTG
Found at i:595179 original size:17 final size:17
Alignment explanation
Indices: 595157--595190 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
595147 GGCCAAAGAG
595157 GAGTTAATCCACCTCTT
1 GAGTTAATCCACCTCTT
595174 GAGTTAATCCACCTCTT
1 GAGTTAATCCACCTCTT
595191 CCTTGACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (17 bp):
GAGTTAATCCACCTCTT
Found at i:599076 original size:5 final size:5
Alignment explanation
Indices: 599069--599665 Score: 1082
Period size: 5 Copynumber: 120.2 Consensus size: 5
599059 ACGTCACGTC
* *
599069 ACATC ACATA ACACA ACATA ACATA ACATA ACATA ACATA ACATA ACATAA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACAT-A
599120 CACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 -ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
599171 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
599221 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
599271 ACATA ACATA ACATA ACATA ACAT- ACATA ACA-A ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
599319 ACATA ACATA ACATA ACAT- ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
* *
599368 ACACA AAATA ACATA ACATA AC--A ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
599416 ACATA ACATA AC--A ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
599464 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
599514 ACAATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 AC-ATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
599565 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
599615 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
599665 A
1 A
599666 TGTAATATAA
Statistics
Matches: 575, Mismatches: 7, Indels: 20
0.96 0.01 0.03
Matches are distributed among these distances:
3 6 0.01
4 12 0.02
5 546 0.95
6 7 0.01
7 4 0.01
ACGTcount: A:0.60, C:0.21, G:0.00, T:0.19
Consensus pattern (5 bp):
ACATA
Found at i:599671 original size:5 final size:5
Alignment explanation
Indices: 599663--599696 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
599653 TAACATAACA
*
599663 TAATG TAATA TAATG TAATG TAATG TAATG TAAT
1 TAATG TAATG TAATG TAATG TAATG TAATG TAAT
599697 ATGAAATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (5 bp):
TAATG
Found at i:602393 original size:159 final size:159
Alignment explanation
Indices: 602079--602382 Score: 590
Period size: 159 Copynumber: 1.9 Consensus size: 159
602069 TTTAAACACT
602079 TACATCTTGATCTCTTAATTTTCTAAAATGTACAGAAAGGTCCCTATAACTTCACAAGGTTCCAA
1 TACATCTTGATCTCTTAATTTTCTAAAATGTACAGAAAGGTCCCTATAACTTCACAAGGTTCCAA
602144 ATTGGCCCAAACAATTTTCAAAAGCATGTAGAATCATTCATGCACTATTTTATCCCTTGTATTAA
66 ATTGGCCCAAACAATTTTCAAAAGCATGTAGAATCATTCATGCACTATTTTATCCCTTGTATTAA
*
602209 TTTTCCATAATTTTATTCTTTTCTTTAGG
131 TTTTCCATAATTTTATCCTTTTCTTTAGG
602238 TACATCTTGATCTCTTAATTTTCTAAAATGTACAGAAAGGTCCCTATAACTTCACAAGGTTCCAA
1 TACATCTTGATCTCTTAATTTTCTAAAATGTACAGAAAGGTCCCTATAACTTCACAAGGTTCCAA
602303 ATTGGCCCAAACAATTTTCAAAAGCATGTAGAATCATTCATGCACTATTTTTATCCCTTGTATTA
66 ATTGGCCCAAACAATTTTCAAAAGCATGTAGAATCATTCATGCACTA-TTTTATCCCTTGTATTA
602368 ATTTTCCATAATTTT
130 ATTTTCCATAATTTT
602383 CCTTATTCTT
Statistics
Matches: 144, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
159 112 0.78
160 32 0.22
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (159 bp):
TACATCTTGATCTCTTAATTTTCTAAAATGTACAGAAAGGTCCCTATAACTTCACAAGGTTCCAA
ATTGGCCCAAACAATTTTCAAAAGCATGTAGAATCATTCATGCACTATTTTATCCCTTGTATTAA
TTTTCCATAATTTTATCCTTTTCTTTAGG
Found at i:607541 original size:12 final size:12
Alignment explanation
Indices: 607511--607541 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
607501 AATATATCTC
607511 TTAAAAATTTAT
1 TTAAAAATTTAT
*
607523 TTTAAAATTTAT
1 TTAAAAATTTAT
607535 TTAAAAA
1 TTAAAAA
607542 ATAAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TTAAAAATTTAT
Found at i:610497 original size:20 final size:19
Alignment explanation
Indices: 610434--610497 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 19
610424 TTGGTATCGT
*
610434 TACCATGTAGGGGTATCAA
1 TACCATGTAAGGGTATCAA
* *
610453 TACCATAGTATAGTAGTATCGA
1 TACCAT-GTA-AG-GGTATCAA
610475 TACCATGGTAAGGGTATCAA
1 TACCAT-GTAAGGGTATCAA
610495 TAC
1 TAC
610498 TGGGCCACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
19 6 0.17
20 12 0.33
21 3 0.08
22 15 0.42
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (19 bp):
TACCATGTAAGGGTATCAA
Found at i:610571 original size:22 final size:21
Alignment explanation
Indices: 610533--610574 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
610523 TATTGATACT
* *
610533 AGTAGGGGGTATTGATACCAA
1 AGTAGGGAGTATCGATACCAA
610554 AGTAGGGTAGTATCGATACCA
1 AGTAGGG-AGTATCGATACCA
610575 TGGTAAGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.24
Consensus pattern (21 bp):
AGTAGGGAGTATCGATACCAA
Found at i:610591 original size:20 final size:19
Alignment explanation
Indices: 610539--610592 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 19
610529 TACTAGTAGG
610539 GGGTATTGATACCAAAGTA
1 GGGTATTGATACCAAAGTA
**
610558 GGGTAGTATCGATACCATGGTAA
1 GGGTA-T-T-GATACCAAAGT-A
610581 GGGTATTGATAC
1 GGGTATTGATAC
610593 TGAAGGGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 5 0.17
20 6 0.21
21 2 0.07
22 10 0.34
23 6 0.21
ACGTcount: A:0.31, C:0.11, G:0.30, T:0.28
Consensus pattern (19 bp):
GGGTATTGATACCAAAGTA
Found at i:611127 original size:79 final size:79
Alignment explanation
Indices: 610993--611156 Score: 220
Period size: 79 Copynumber: 2.1 Consensus size: 79
610983 AAAATGAATG
* * *
610993 TAAAAGAATAATGCATATGGGTACATTATTGGCATGAAAGGATGCCATAGCTGAAATATATATGG
1 TAAAAGAATAATGCATATAGGTACATTATTGGCATGAAAGGATGCCAGAGCTGAAATACATATGG
*
611058 ATACATTATCAGCA
66 ATACATTATCAACA
* * * * *
611072 TAAAAGAATAATGCATATAGGTGCATTATTGGCATGCAAGGATGCTAGAGTTGAAATGCATATGG
1 TAAAAGAATAATGCATATAGGTACATTATTGGCATGAAAGGATGCCAGAGCTGAAATACATATGG
* *
611137 GTGCATTATCAACA
66 ATACATTATCAACA
*
611151 GAAAAG
1 TAAAAG
611157 TATACTATGG
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.27
Consensus pattern (79 bp):
TAAAAGAATAATGCATATAGGTACATTATTGGCATGAAAGGATGCCAGAGCTGAAATACATATGG
ATACATTATCAACA
Found at i:611145 original size:45 final size:44
Alignment explanation
Indices: 611081--611402 Score: 290
Period size: 45 Copynumber: 7.2 Consensus size: 44
611071 ATAAAAGAAT
* *** * *
611081 AATGCATATAGGTGCATTATTGGCATGCAAGGATGCTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACA-GAAAGTATGCTAGAGTTGA
*
611126 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATG-GTTGA
1 AATGCATATGGGTGCATTATCAACAG-AAAGTATGCTA-GAGTTGA
* * *
611171 AATGTATATGGGTACATTATCAATAGAAAAGTATGCTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAG-AAAGTATGCTAGAGTTGA
* * *
611216 AATGCATATGGATGTATTATCAACAGAAATGTATGCTAGAGTTAA
1 AATGCATATGGGTGCATTATCAACAGAAA-GTATGCTAGAGTTGA
* * *
611261 AATGTATATGGGTGAATTATCAACAGAAGAGCATGCTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAA-AGTATGCTAGAGTTGA
* * * *
611306 AATGTATATGGGTACATTATCAATAGAAAAGTATACTATG-GTTGA
1 AATGCATATGGGTGCATTATCAACAG-AAAGTATGCTA-GAGTTGA
* ** * * * *
611351 AATGTATACCGGTACATTGTCAACAGAAAAGTATACTATAGTT-A
1 AATGCATATGGGTGCATTATCAACAG-AAAGTATGCTAGAGTTGA
611395 AAGTGCAT
1 AA-TGCAT
611403 TATCAACCGA
Statistics
Matches: 235, Mismatches: 33, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
44 8 0.03
45 222 0.94
46 5 0.02
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (44 bp):
AATGCATATGGGTGCATTATCAACAGAAAGTATGCTAGAGTTGA
Found at i:611264 original size:90 final size:90
Alignment explanation
Indices: 611113--611402 Score: 388
Period size: 90 Copynumber: 3.2 Consensus size: 90
611103 GCATGCAAGG
611113 ATGCTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTATGGTTGAAATGTAT
1 ATGCTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTATGGTTGAAATGTAT
*
611178 ATGGGTACATTATCAATAGAAAAGT
66 ATGGGTACATTATCAACAGAAAAGT
* * * * *
611203 ATGCTAGAGTTGAAATGCATATGGATGTATTATCAACAGAAATGTATGCTA-GAGTTAAAATGTA
1 ATGCTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTATG-GTTGAAATGTA
* *
611267 TATGGGTGA-ATTATCAACAGAAGAGC
65 TATGGGT-ACATTATCAACAGAAAAGT
* * *
611293 ATGCTAGAGTTGAAATGTATATGGGTACATTATCAATAGAAAAGTATACTATGGTTGAAATGTAT
1 ATGCTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTATGGTTGAAATGTAT
** *
611358 ACCGGTACATTGTCAACAGAAAAGT
66 ATGGGTACATTATCAACAGAAAAGT
* *
611383 ATACTATAGTT-AAAGTGCAT
1 ATGCTAGAGTTGAAA-TGCAT
611403 TATCAACCGA
Statistics
Matches: 171, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
89 5 0.03
90 164 0.96
91 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (90 bp):
ATGCTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTATGGTTGAAATGTAT
ATGGGTACATTATCAACAGAAAAGT
Found at i:611374 original size:135 final size:135
Alignment explanation
Indices: 611113--611402 Score: 388
Period size: 135 Copynumber: 2.1 Consensus size: 135
611103 GCATGCAAGG
* * *
611113 ATGCTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTATGGTTGAAATGTAT
1 ATGCTAGAGTTAAAATGCATATGGGTGAATTATCAACAGAAAAGCATACTATGGTTGAAATGTAT
* * **
611178 ATGGGTACATTATCAATAGAAAAGTATGCTAGAGTTGAAATGCATATGGATGTATTATCAACAGA
66 ATGGGTACATTATCAATAGAAAAGTATACTAGAGTTGAAATGCATACGGATACATTATCAACAGA
*
611243 AATGT
131 AAAGT
* * *
611248 ATGCTAGAGTTAAAATGTATATGGGTGAATTATCAACAGAAGAGCATGCTA-GAGTTGAAATGTA
1 ATGCTAGAGTTAAAATGCATATGGGTGAATTATCAACAGAAAAGCATACTATG-GTTGAAATGTA
* *
611312 TATGGGTACATTATCAATAGAAAAGTATACTATG-GTTGAAATGTATACCGG-TACATTGTCAAC
65 TATGGGTACATTATCAATAGAAAAGTATACTA-GAGTTGAAATGCATA-CGGATACATTATCAAC
611375 AGAAAAGT
128 AGAAAAGT
* * *
611383 ATACTATAGTTAAAGTGCAT
1 ATGCTAGAGTTAAAATGCAT
611403 TATCAACCGA
Statistics
Matches: 135, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
134 1 0.01
135 131 0.97
136 3 0.02
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (135 bp):
ATGCTAGAGTTAAAATGCATATGGGTGAATTATCAACAGAAAAGCATACTATGGTTGAAATGTAT
ATGGGTACATTATCAATAGAAAAGTATACTAGAGTTGAAATGCATACGGATACATTATCAACAGA
AAAGT
Found at i:612093 original size:2 final size:2
Alignment explanation
Indices: 612086--612119 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
612076 TGAAGGGATG
612086 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
612120 TGTACAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:618999 original size:17 final size:17
Alignment explanation
Indices: 618973--619025 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
618963 TTTTAACATG
*
618973 TTGACTGACCCAACCCA
1 TTGACCGACCCAACCCA
* *
618990 TTGACCGACCCGACCAA
1 TTGACCGACCCAACCCA
* * *
619007 TTAACCGAGCCTACCCA
1 TTGACCGACCCAACCCA
619024 TT
1 TT
619026 AACCATTGAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.28, C:0.40, G:0.13, T:0.19
Consensus pattern (17 bp):
TTGACCGACCCAACCCA
Found at i:619026 original size:17 final size:17
Alignment explanation
Indices: 618979--619029 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
618969 CATGTTGACT
* *
618979 GACCCAACCCATTGACC
1 GACCCGACCCATTAACC
*
618996 GACCCGACCAATTAACC
1 GACCCGACCCATTAACC
* *
619013 GAGCCTACCCATTAACC
1 GACCCGACCCATTAACC
619030 ATTGACTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.31, C:0.43, G:0.12, T:0.14
Consensus pattern (17 bp):
GACCCGACCCATTAACC
Found at i:619658 original size:30 final size:30
Alignment explanation
Indices: 619622--619698 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
619612 TCTGATTCAT
* * *
619622 CATGGGACAATGTTCCCCGTCATGACTCTG
1 CATGGGACTATGTTCCCCATCATGAATCTG
*
619652 CATGGGACTATGTTCCCCATCCTGAATCTG
1 CATGGGACTATGTTCCCCATCATGAATCTG
* *
619682 TATGGGGCTATGTTCCC
1 CATGGGACTATGTTCCC
619699 TATTCTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.30
Consensus pattern (30 bp):
CATGGGACTATGTTCCCCATCATGAATCTG
Found at i:619944 original size:2 final size:2
Alignment explanation
Indices: 619906--619936 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
619896 GTTTACGCAT
619906 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
619937 TGATATATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:626787 original size:59 final size:59
Alignment explanation
Indices: 626696--627167 Score: 680
Period size: 59 Copynumber: 8.0 Consensus size: 59
626686 TATATTTCCC
* *
626696 ATACGGAAA-TCTATACACCTAGTATGAATTTCTTAACATGTTT-GCACACAAAAGTGCCCA
1 ATACGGAAATTC-ATACACTTAGTATGAATTTCTTAACAT-TTTAGCACAC-ATAGTGCCCA
* * *
626756 ATACGAAAATTCATACACTT-CTATGAATTTCTTAACATTTTAGCACACATAGTGTCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
* * * * *
626814 ATACGGAAATTTATACACTTAGCATGGATTTCTTCACATTTTACCACACATAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
* * *
626873 ATATGGAAATTCATACACTTAGTATGGATTTCTTAACATTTTAGCACACATAGTGCCTA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
* * * *
626932 ATGCGGAAATTGATACACTTAGTATGAATTTCTTAACTTTTTTAGCACACTTAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAAC-ATTTTAGCACACATAGTGCCCA
*
626992 ATACGGAAATTCATACACTTAGTATGAATTTATTAACATTTTAGCACACATAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
*
627051 ATACAGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
** *
627110 ATAAAGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTAGCACACTTAGTGCC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACA-TTTTAGCACACATAGTGCC
627168 ATTTGGTAAT
Statistics
Matches: 372, Mismatches: 35, Indels: 10
0.89 0.08 0.02
Matches are distributed among these distances:
58 29 0.08
59 255 0.69
60 86 0.23
61 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (59 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCA
Found at i:627033 original size:178 final size:177
Alignment explanation
Indices: 626696--627167 Score: 689
Period size: 178 Copynumber: 2.7 Consensus size: 177
626686 TATATTTCCC
* *
626696 ATACGGAAA-TCTATACACCTAGTATGAATTTCTTAACATGTTT-GCACACAAAAGTGCCCAATA
1 ATACGGAAATTC-ATACACTTAGTATGAATTTCTTAACAT-TTTAGCACAC-ATAGTGCCCAATA
* * * * *
626759 CGAAAATTCATACACTT-CTATGAATTTCTTAACATTTTAGCACACATAGTGTCCAATACGGAAA
63 CGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTAGCACACTTAGTGCCCAATACGGAAA
* * * *
626823 TTTATACACTTAGCATGGATTTCTTCACATTTTACCACACATAGTGCCCA
128 TTCATACACTTAGCATGAATTTATTAACATTTTACCACACATAGTGCCCA
* * * *
626873 ATATGGAAATTCATACACTTAGTATGGATTTCTTAACATTTTAGCACACATAGTGCCTAATGCGG
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACGG
*
626938 AAATTGATACACTTAGTATGAATTTCTTAACTTTTTTAGCACACTTAGTGCCCAATACGGAAATT
66 AAATTCATACACTTAGTATGAATTTCTTAAC-TTTTTAGCACACTTAGTGCCCAATACGGAAATT
* *
627003 CATACACTTAGTATGAATTTATTAACATTTTAGCACACATAGTGCCCA
130 CATACACTTAGCATGAATTTATTAACATTTTACCACACATAGTGCCCA
* **
627051 ATACAGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATAAAG
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACGG
627116 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTAGCACACTTAGTGCC
66 AAATTCATACACTTAGTATGAATTTCTTAAC-TTTTTAGCACACTTAGTGCC
627168 ATTTGGTAAT
Statistics
Matches: 264, Mismatches: 27, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
176 28 0.11
177 54 0.20
178 182 0.69
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (177 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACGG
AAATTCATACACTTAGTATGAATTTCTTAACTTTTTAGCACACTTAGTGCCCAATACGGAAATTC
ATACACTTAGCATGAATTTATTAACATTTTACCACACATAGTGCCCA
Found at i:627661 original size:94 final size:94
Alignment explanation
Indices: 627490--627662 Score: 213
Period size: 94 Copynumber: 1.8 Consensus size: 94
627480 CTGGTTCTTT
* * *
627490 AGTATCGATACCCCTACCATTGTATCGATACTACTATAATATGGTATCGACACCCCTTCCGATAT
1 AGTATCGATACCCCTACCATGGTATCGATACTACTATAATATGGTATCGACACCCCCTACGATAT
627555 CGATACCAATTTTAGATTCGATGTTAACA
66 CGATACCAATTTTAGATTCGATGTTAACA
* * * * * * * *
627584 AGTATTGATATCCTTACCATGGTATCGATGCTA-TCATACTATGGTATCGATACCCTCCTATGGT
1 AGTATCGATACCCCTACCATGGTATCGATACTACT-ATAATATGGTATCGACACCC-CCTACGAT
*
627648 ATCGATACCATTTTT
64 ATCGATACCAATTTT
627663 GCATTCTGTT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
93 1 0.02
94 46 0.71
95 18 0.28
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (94 bp):
AGTATCGATACCCCTACCATGGTATCGATACTACTATAATATGGTATCGACACCCCCTACGATAT
CGATACCAATTTTAGATTCGATGTTAACA
Found at i:633920 original size:59 final size:59
Alignment explanation
Indices: 633842--634245 Score: 605
Period size: 59 Copynumber: 6.8 Consensus size: 59
633832 TCCCATACGA
* * * * *
633842 AAATTCATACACCTGGTATGAATTTCTTAACATGTTT-GCACACAAAGTCCCCAATACTG
1 AAATTCATACACTTAGTATGAATTTCTTAACAT-TTTAGCACACATAGTGCCCAATACAG
* *
633901 AAATTCATACACTTAGTATGCATTTCTTAACATTTTAGCACACATAGTGCCAAATACAG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACAG
* * *
633960 AAATTCATACACTTAGTATGAATTTCTTAATATTTTAGAACACATAGTGCCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACAG
* * *
634019 AAATTCATACACTTAGTATAAATTTCTTAACATTTTTAGCACACTTAGTGCCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACA-TTTTAGCACACATAGTGCCCAATACAG
634079 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACAG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACAG
* * *
634138 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACTTAGTGTCAAATAC-G
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACAG
*
634196 AAAATTCATACACTTAGTATGAATTTCTTAACATTTTTAGCACACTTAGT
1 -AAATTCATACACTTAGTATGAATTTCTTAACA-TTTTAGCACACATAGT
634246 TCCATTTGGT
Statistics
Matches: 319, Mismatches: 22, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
58 4 0.01
59 243 0.76
60 72 0.23
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.34
Consensus pattern (59 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACAG
Found at i:634087 original size:178 final size:178
Alignment explanation
Indices: 633836--634245 Score: 669
Period size: 178 Copynumber: 2.3 Consensus size: 178
633826 TATATTTCCC
* * * ** *
633836 ATACGAAAATTCATACACCTGGTATGAATTTCTTAACATGTTT-GCACACAAAGTCCCCAATACT
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTTAGCACACTTAGTCCCCAATACG
*
633900 GAAATTCATACACTTAGTATGCATTTCTTAACATTTTAGCACACATAGTGCCAAATACAGAAATT
66 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCAAATACAGAAATT
* *
633965 CATACACTTAGTATGAATTTCTTAATATTTTAGAACACATAGTGCCCA
131 CATACACTTAGTATGAATTTCTTAACATTTTAGAACACATAGTGCCAA
* * *
634013 ATACGGAAATTCATACACTTAGTATAAATTTCTTAACATTTTTAGCACACTTAGTGCCCAATACG
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTTAGCACACTTAGTCCCCAATACG
*
634078 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCCAATACAGAAATT
66 GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCAAATACAGAAATT
* * *
634143 CATACACTTAGTATGAATTTCTTAACATTTTAGCACACTTAGTGTCAA
131 CATACACTTAGTATGAATTTCTTAACATTTTAGAACACATAGTGCCAA
634191 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTTAGCACACTTAGT
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTTAGCACACTTAGT
634246 TCCATTTGGT
Statistics
Matches: 214, Mismatches: 18, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
177 38 0.18
178 176 0.82
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.34
Consensus pattern (178 bp):
ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTTAGCACACTTAGTCCCCAATACG
GAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACATAGTGCCAAATACAGAAATT
CATACACTTAGTATGAATTTCTTAACATTTTAGAACACATAGTGCCAA
Found at i:634181 original size:31 final size:31
Alignment explanation
Indices: 634087--634245 Score: 98
Period size: 31 Copynumber: 5.3 Consensus size: 31
634077 GGAAATTCAT
634087 ACACTTAGTATGAATTTCTTAACATTTTAGC
1 ACACTTAGTATGAATTTCTTAACATTTTAGC
* *** * ** * *
634118 ACACATAGTGCCCAA-TACAGAA-A-TTCA-T
1 ACACTTAGT-ATGAATTTCTTAACATTTTAGC
634146 ACACTTAGTATGAATTTCTTAACATTTTAGC
1 ACACTTAGTATGAATTTCTTAACATTTTAGC
* * * * * * * *
634177 ACACTTAGTGTCAAATAC-GAA-AATTCA-T
1 ACACTTAGTATGAATTTCTTAACATTTTAGC
634205 ACACTTAGTATGAATTTCTTAACATTTTTAGC
1 ACACTTAGTATGAATTTCTTAACA-TTTTAGC
634237 ACACTTAGT
1 ACACTTAGT
634246 TCCATTTGGT
Statistics
Matches: 85, Mismatches: 34, Indels: 17
0.62 0.25 0.12
Matches are distributed among these distances:
27 2 0.02
28 26 0.31
29 10 0.12
30 7 0.08
31 29 0.34
32 11 0.13
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (31 bp):
ACACTTAGTATGAATTTCTTAACATTTTAGC
Found at i:638548 original size:106 final size:106
Alignment explanation
Indices: 638363--638642 Score: 447
Period size: 106 Copynumber: 2.6 Consensus size: 106
638353 CCCATTTTAA
* *
638363 GTTCAAAACCAAAATGTCGGCCCGTGTACTAGCCCATTACATCCGGGTACCTGTATTTTCGGTTC
1 GTTCAAAACCAAAATGTCGGCCCATGTACTAGCCCATTACATCCGGGTACCTGTATTTTTGGTTC
* *
638428 ACGGGTATCCAATTCAAATACTACCCATTTTTACCAGGGGT
66 ACGGGTATCCAATTCAAAAACTACCCATTTTTACCAAGGGT
*
638469 GTTCAAAACCAAAATGTCGGCCCATGTACTAGCCCATTACATCCGGGTACCTGTATTTTTTGTTC
1 GTTCAAAACCAAAATGTCGGCCCATGTACTAGCCCATTACATCCGGGTACCTGTATTTTTGGTTC
* * *
638534 ACTGGTA-CACAATTCAAAAACTTCCCATTTTTAGCAAGGGT
66 ACGGGTATC-CAATTCAAAAACTACCCATTTTTACCAAGGGT
*
638575 GTTCAAAACCAAAATGTC-GCCCAGTGTACTAGCCCATTACATCCGGGTACCTATATTTTTGGTT
1 GTTCAAAACCAAAATGTCGGCCCA-TGTACTAGCCCATTACATCCGGGTACCTGTATTTTTGGTT
638639 CACG
65 CACG
638643 AGTACCTGAT
Statistics
Matches: 161, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
105 6 0.04
106 155 0.96
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (106 bp):
GTTCAAAACCAAAATGTCGGCCCATGTACTAGCCCATTACATCCGGGTACCTGTATTTTTGGTTC
ACGGGTATCCAATTCAAAAACTACCCATTTTTACCAAGGGT
Found at i:638869 original size:38 final size:40
Alignment explanation
Indices: 638822--638899 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 40
638812 TATATTCTAA
638822 AAAATAATTTAAAATGTTAT-GT-GAAATAATTTAAGAAAT
1 AAAATAATTTAAAATGTTATGGTAGAAA-AATTTAAGAAAT
* *
638861 AAAA-AATTTAGAATTTTATGGTAGAAAAATTTAAGAAAT
1 AAAATAATTTAAAATGTTATGGTAGAAAAATTTAAGAAAT
638900 TGGGAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 13 0.37
39 18 0.51
40 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.35
Consensus pattern (40 bp):
AAAATAATTTAAAATGTTATGGTAGAAAAATTTAAGAAAT
Found at i:639954 original size:18 final size:19
Alignment explanation
Indices: 639924--639963 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
639914 ACCAGGTAAC
639924 ATCAAACCTAAAAT-GGGT
1 ATCAAACCTAAAATGGGGT
639942 ATCAATACC-AAAATGGGGT
1 ATCAA-ACCTAAAATGGGGT
639961 ATC
1 ATC
639964 GGTACCATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (19 bp):
ATCAAACCTAAAATGGGGT
Found at i:640003 original size:20 final size:22
Alignment explanation
Indices: 639959--640006 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
639949 CCAAAATGGG
639959 GTATCGGTACCATAGTGTAGAA
1 GTATCGGTACCATAGTGTAGAA
*
639981 GTATCGGTACCAT-G-GTAGTA
1 GTATCGGTACCATAGTGTAGAA
640001 GTATCG
1 GTATCG
640007 ATACTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 11 0.44
21 1 0.04
22 13 0.52
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (22 bp):
GTATCGGTACCATAGTGTAGAA
Found at i:640454 original size:56 final size:56
Alignment explanation
Indices: 640332--640663 Score: 431
Period size: 56 Copynumber: 5.9 Consensus size: 56
640322 TTACCAAATA
** * * * *
640332 GGCACTAAATGTGAAAAACCACGGAATTCATCATGAGTTGATG-ATAACCATACAG
1 GGCACTATGTGTGCAAAATCACGAAATTCATCATGAGTTGATGAATAACCGTACAG
640387 GGCACTATGTGTGCAAAATCACGAAATTCATCATGAGTTGATGAATAACCGTACAG
1 GGCACTATGTGTGCAAAATCACGAAATTCATCATGAGTTGATGAATAACCGTACAG
* * * *
640443 TGAACTATGTGTGCAAAACCACAAAATTCATCATGAGTTGATGAATAACCGTACAG
1 GGCACTATGTGTGCAAAATCACGAAATTCATCATGAGTTGATGAATAACCGTACAG
* *
640499 GGCACTATGTGTGCAAAATCAC-AGAATTCATCATGAGTTAATGAATAATCGTACAG
1 GGCACTATGTGTGCAAAATCACGA-AATTCATCATGAGTTGATGAATAACCGTACAG
* * * * *
640555 GGCACTATATGTGTAAAA-CTACGGAACTCATCATGAATTGATGAATAACCGTACAG
1 GGCACTATGTGTGCAAAATC-ACGAAATTCATCATGAGTTGATGAATAACCGTACAG
*
640611 GGCACTATATGTG-AAAATCCAC-AGAATTCATCATGAGTTGATGAATAACCGTA
1 GGCACTATGTGTGCAAAAT-CACGA-AATTCATCATGAGTTGATGAATAACCGTA
640664 TAGGAATTAT
Statistics
Matches: 245, Mismatches: 25, Indels: 13
0.87 0.09 0.05
Matches are distributed among these distances:
55 44 0.18
56 200 0.82
57 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (56 bp):
GGCACTATGTGTGCAAAATCACGAAATTCATCATGAGTTGATGAATAACCGTACAG
Found at i:640543 original size:112 final size:112
Alignment explanation
Indices: 640335--640663 Score: 484
Period size: 112 Copynumber: 2.9 Consensus size: 112
640325 CCAAATAGGC
* *
640335 ACTAAATGTGAAAAACCACGGAATTCATCATGAGTTGATG-ATAACCATACAGGGCACTATGTGT
1 ACTATATGTGAAAAACCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGT
*
640399 GCAAAATCAC-GAAATTCATCATGAGTTGATGAATAACCGTACAGTGA
66 GCAAAATCACAG-AATTCATCATGAGTTGATGAATAACCGTACAGGGA
* * **
640446 ACTATGTGTGCAAAACCACAAAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGT
1 ACTATATGTGAAAAACCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGT
* * *
640511 GCAAAATCACAGAATTCATCATGAGTTAATGAATAATCGTACAGGGC
66 GCAAAATCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGGA
* * * * *
640558 ACTATATGTGTAAAACTACGGAACTCATCATGAATTGATGAATAACCGTACAGGGCACTATATGT
1 ACTATATGTGAAAAACCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGT
640623 G-AAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTA
66 GCAAAAT-CACAGAATTCATCATGAGTTGATGAATAACCGTA
640664 TAGGAATTAT
Statistics
Matches: 195, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
111 40 0.21
112 154 0.79
113 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (112 bp):
ACTATATGTGAAAAACCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGT
GCAAAATCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGGA
Found at i:645015 original size:93 final size:92
Alignment explanation
Indices: 644888--645064 Score: 252
Period size: 93 Copynumber: 1.9 Consensus size: 92
644878 ATTTAATCAA
* * *
644888 TATCGATACCAGTGAGGTAGTATTGATACCATGGTAAGGGTATCGATACCATGAAACATCGAA-T
1 TATCGATACCAGTGAGGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCAAACT
*
644952 CTAAAATTGGTATCGATACCGGAAGAGG
66 -TAAAATGGGTATCGATACCGGAAGAGG
*
644980 TATCGATACCA-TAGTATGGTAGTA-CGATACCATGGTAAGGGTATCGATACCAGGTAACATCAA
1 TATCGATACCAGT-G-A-GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCAA
645043 ACTTAAAATGGGTATCGATACC
63 ACTTAAAATGGGTATCGATACC
645065 AAAAGGGGGT
Statistics
Matches: 76, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
91 1 0.01
92 12 0.16
93 55 0.72
94 8 0.11
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.25
Consensus pattern (92 bp):
TATCGATACCAGTGAGGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCAAACT
TAAAATGGGTATCGATACCGGAAGAGG
Found at i:645532 original size:56 final size:56
Alignment explanation
Indices: 645446--645707 Score: 357
Period size: 56 Copynumber: 4.7 Consensus size: 56
645436 TTACCAAATA
** * * *
645446 GGCACTAAATGTGCAAAACCACGGAATTCATCATGAGTTGATGAATAAACGTACAG
1 GGCACTATGTGTGCAAAAACACGAAATTCATCATGAGTTGATGAATAACCGTACAG
** * *
645502 GGCACTATGTGTGTGAAATCACAAAATTCATCATGAGTTGATGAATAACCGTACAG
1 GGCACTATGTGTGCAAAAACACGAAATTCATCATGAGTTGATGAATAACCGTACAG
* * *
645558 GG-ACTATGTATGCAAAACCACGAAATTCATCATGAGTTGATGAATAACCGTACAA
1 GGCACTATGTGTGCAAAAACACGAAATTCATCATGAGTTGATGAATAACCGTACAG
* *
645613 GGCACTATGTGTACAAAAACACGAAATTCATCATGAGTTGATGAATAACCGTATAG
1 GGCACTATGTGTGCAAAAACACGAAATTCATCATGAGTTGATGAATAACCGTACAG
* *
645669 AGCACTATGTGTGC-AAAACTACGGAATTCATCATGAGTT
1 GGCACTATGTGTGCAAAAAC-ACGAAATTCATCATGAGTT
645708 TCACGAAAAT
Statistics
Matches: 182, Mismatches: 22, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
55 54 0.30
56 128 0.70
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (56 bp):
GGCACTATGTGTGCAAAAACACGAAATTCATCATGAGTTGATGAATAACCGTACAG
Found at i:645651 original size:111 final size:112
Alignment explanation
Indices: 645457--645707 Score: 387
Period size: 111 Copynumber: 2.2 Consensus size: 112
645447 GCACTAAATG
* *** *
645457 TGCAAAACCACGGAATTCATCATGAGTTGATGAATAAACGTACAGGGCACTATGTGTGTGAAATC
1 TGCAAAACCACGGAATTCATCATGAGTTGATGAATAAACGTACAAGGCACTATGTGTACAAAAAC
*
645522 ACAAAATTCATCATGAGTTGATGAATAACCGTACAG-GGACTATGTA
66 ACAAAATTCATCATGAGTTGATGAATAACCGTACAGAGCACTATGTA
* *
645568 TGCAAAACCACGAAATTCATCATGAGTTGATGAATAACCGTACAAGGCACTATGTGTACAAAAAC
1 TGCAAAACCACGGAATTCATCATGAGTTGATGAATAAACGTACAAGGCACTATGTGTACAAAAAC
* * *
645633 ACGAAATTCATCATGAGTTGATGAATAACCGTATAGAGCACTATGTG
66 ACAAAATTCATCATGAGTTGATGAATAACCGTACAGAGCACTATGTA
*
645680 TGCAAAACTACGGAATTCATCATGAGTT
1 TGCAAAACCACGGAATTCATCATGAGTT
645708 TCACGAAAAT
Statistics
Matches: 126, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
111 92 0.73
112 34 0.27
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (112 bp):
TGCAAAACCACGGAATTCATCATGAGTTGATGAATAAACGTACAAGGCACTATGTGTACAAAAAC
ACAAAATTCATCATGAGTTGATGAATAACCGTACAGAGCACTATGTA
Found at i:648264 original size:56 final size:55
Alignment explanation
Indices: 648017--648261 Score: 382
Period size: 56 Copynumber: 4.4 Consensus size: 55
648007 TATAATTTCA
* * **
648017 TGGTTTTGCACACATAGTGTTCTGTACGGTTATTCATCAACTCATGATCAATTTTG
1 TGGTTTTGCACACATAGTG-CCTGTACGGTTATTCATCAACTCATGATGAATTCCG
* *
648073 TGATTTTGCACACATAGTGCCCTGTACGGTTATTCATCAACTCATGTTGAATTCCG
1 TGGTTTTGCACACATAGTG-CCTGTACGGTTATTCATCAACTCATGATGAATTCCG
*
648129 TAGTTTTGCACACATAGTGCTCTGTACGGTTATTCATCAACTCATGATGAATTCCG
1 TGGTTTTGCACACATAGTGC-CTGTACGGTTATTCATCAACTCATGATGAATTCCG
*
648185 TGGTTTTGCACACATAGTGCCATGTACGGTTATTTATCAACTCATGATGAATTCCG
1 TGGTTTTGCACACATAGTGCC-TGTACGGTTATTCATCAACTCATGATGAATTCCG
648241 TGGTTTTGCACACATAGTGCC
1 TGGTTTTGCACACATAGTGCC
648262 ATGCACACAT
Statistics
Matches: 175, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
55 2 0.01
56 173 0.99
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.37
Consensus pattern (55 bp):
TGGTTTTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCG
Found at i:649070 original size:25 final size:26
Alignment explanation
Indices: 649021--649082 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
649011 TCTTACCGGA
* * *
649021 TCGAGACTTACAAAATTTTGGATTAT
1 TCGAAACTTACAAAATTTTGAATTAG
649047 TCGAAACTTAC-AAATTTTGAATTAG
1 TCGAAACTTACAAAATTTTGAATTAG
*
649072 TCAAAACTTAC
1 TCGAAACTTAC
649083 TATGTTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 22 0.69
26 10 0.31
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (26 bp):
TCGAAACTTACAAAATTTTGAATTAG
Found at i:649481 original size:21 final size:21
Alignment explanation
Indices: 649439--649486 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
649429 TGTATATCCA
*
649439 AGTTTTAGTAATTTAATTTTT
1 AGTTTTAGTAATTTAATATTT
** *
649460 AGTTTTAGTGTTTTTATATTT
1 AGTTTTAGTAATTTAATATTT
*
649481 AATTTT
1 AGTTTT
649487 TTGATTAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (21 bp):
AGTTTTAGTAATTTAATATTT
Found at i:649894 original size:145 final size:145
Alignment explanation
Indices: 649631--649922 Score: 548
Period size: 145 Copynumber: 2.0 Consensus size: 145
649621 CCATATCATC
*
649631 AGTTATAGTGGATTGTCACGTCAACACCGTAGGTCGTCATGTCAGCACCATAAATTACCATGTCA
1 AGTTATAGTGGATTGCCACGTCAACACCGTAGGTCGTCATGTCAGCACCATAAATTACCATGTCA
649696 GCATTGTAACAATCAACAATTGAAAACATTGGTCAAAGGATCACATTAGATTTGTTTTGTGAATT
66 GCATTGTAACAATCAACAATTGAAAACATTGGTCAAAGGATCACATTAGATTTGTTTTGTGAATT
649761 GGAGGGCACATTGAG
131 GGAGGGCACATTGAG
* *
649776 AGTTATAGTGGATTGCCACGTCAACATCGTAGGTCGTCATGTCAGCACCATAAATTGCCATGTCA
1 AGTTATAGTGGATTGCCACGTCAACACCGTAGGTCGTCATGTCAGCACCATAAATTACCATGTCA
*
649841 GCATTGTAACAATCAACAATTGAAAACATTGGTCAAAGGGTCACATTAGATTTGTTTTGTGAATT
66 GCATTGTAACAATCAACAATTGAAAACATTGGTCAAAGGATCACATTAGATTTGTTTTGTGAATT
649906 GGAGGGCACATTGAG
131 GGAGGGCACATTGAG
649921 AG
1 AG
649923 AAAATAAATA
Statistics
Matches: 143, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 143 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (145 bp):
AGTTATAGTGGATTGCCACGTCAACACCGTAGGTCGTCATGTCAGCACCATAAATTACCATGTCA
GCATTGTAACAATCAACAATTGAAAACATTGGTCAAAGGATCACATTAGATTTGTTTTGTGAATT
GGAGGGCACATTGAG
Found at i:652270 original size:59 final size:59
Alignment explanation
Indices: 652177--652406 Score: 379
Period size: 59 Copynumber: 3.9 Consensus size: 59
652167 ATAATTGTCC
* *
652177 TATCGAACCCTCCTAGTCGCAATGAAAAGTAAAACTCGATAATATGGCTCTAAGAGTCT
1 TATCGAACCATCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTCTAAGAGTCT
652236 TATCGAACCATCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTCTAAGAGTCT
1 TATCGAACCATCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTCTAAGAGTCT
* * * * *
652295 TATAGAACCACCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGGCTCTAAGTGTCC
1 TATCGAACCATCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTCTAAGAGTCT
* *
652354 TATCGAACCCTCCTAGTCGCAATGAAAAGGTAAACTCGATAATATGGCTCTAA
1 TATCGAACCATCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTCTAA
652407 CCAACTCTCC
Statistics
Matches: 160, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 160 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (59 bp):
TATCGAACCATCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTCTAAGAGTCT
Found at i:657186 original size:7 final size:7
Alignment explanation
Indices: 657174--657217 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
657164 GATATGCGTT
657174 TGGAGAA
1 TGGAGAA
657181 TGGAGAA
1 TGGAGAA
657188 TGGAGAA
1 TGGAGAA
657195 TGGAGAA
1 TGGAGAA
657202 TGGAGAA
1 TGGAGAA
657209 TGGAGAA
1 TGGAGAA
657216 TG
1 TG
657218 ACGAGGGGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.41, C:0.00, G:0.43, T:0.16
Consensus pattern (7 bp):
TGGAGAA
Found at i:658611 original size:10 final size:10
Alignment explanation
Indices: 658596--658622 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
658586 TCAATAAATT
658596 TTTTAATTAA
1 TTTTAATTAA
658606 TTTTAATTAA
1 TTTTAATTAA
658616 TTTTAAT
1 TTTTAAT
658623 AGAATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTAATTAA
Found at i:660097 original size:19 final size:19
Alignment explanation
Indices: 660073--660110 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
660063 ATATAAGAGT
660073 TTGTTAATTTAAATATACA
1 TTGTTAATTTAAATATACA
660092 TTGTTAATTTAAATATACA
1 TTGTTAATTTAAATATACA
660111 ATATTAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (19 bp):
TTGTTAATTTAAATATACA
Found at i:660117 original size:19 final size:19
Alignment explanation
Indices: 660076--660119 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
660066 TAAGAGTTTG
* *
660076 TTAATTTAAATATACATTG
1 TTAATTTAAATATACAATA
660095 TTAATTTAAATATACAATA
1 TTAATTTAAATATACAATA
660114 TTAATT
1 TTAATT
660120 CACAAATGAA
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:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (19 bp):
TTAATTTAAATATACAATA
Found at i:661608 original size:32 final size:34
Alignment explanation
Indices: 661538--661601 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
661528 CACCCGCCCA
* *
661538 CCACCCATGATGGGTACAAATTTTCAAATCCACAC
1 CCACCCACGATGGGTAC-AATTCTCAAATCCACAC
661573 CCACCCACG-TGGGTAC-ATTCTCAAATCCA
1 CCACCCACGATGGGTACAATTCTCAAATCCA
661602 TCCCCACACC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 12 0.44
34 7 0.26
35 8 0.30
ACGTcount: A:0.31, C:0.34, G:0.12, T:0.22
Consensus pattern (34 bp):
CCACCCACGATGGGTACAATTCTCAAATCCACAC
Found at i:661612 original size:34 final size:35
Alignment explanation
Indices: 661534--661613 Score: 85
Period size: 34 Copynumber: 2.3 Consensus size: 35
661524 CCACCACCCG
* *
661534 CCCACCACCCATGATGGGTACAAATTTTCAAATCCAC
1 CCCA-CACCCACGATGGGTAC-AATTCTCAAATCCAC
*
661571 ACC-CACCCACG-TGGGTAC-ATTCTCAAATCCATC
1 CCCACACCCACGATGGGTACAATTCTCAAATCCA-C
661604 CCCACACCCA
1 CCCACACCCA
661614 GTACCCACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
32 12 0.32
33 3 0.08
34 13 0.35
35 7 0.19
37 2 0.05
ACGTcount: A:0.30, C:0.41, G:0.10, T:0.19
Consensus pattern (35 bp):
CCCACACCCACGATGGGTACAATTCTCAAATCCAC
Found at i:662674 original size:45 final size:45
Alignment explanation
Indices: 662608--662936 Score: 478
Period size: 45 Copynumber: 7.3 Consensus size: 45
662598 AATCCACCAT
* * *
662608 TATGCATTATTAACTATAGCATACTTTTCTGCTGATAATGCACCCA
1 TATGCATT-TCAACTATAGCATACTTTTCTGTTGACAATGCACCCA
* *
662654 TATGCATTTTAACTATAGCATACATTTCTGTTGACAATGCACCCA
1 TATGCATTTCAACTATAGCATACTTTTCTGTTGACAATGCACCCA
**
662699 TATGCATTTCAACTATAATATACTTTTCTGTTGACAATGCACCCA
1 TATGCATTTCAACTATAGCATACTTTTCTGTTGACAATGCACCCA
* *
662744 TATGCATTTCAACTATAACATACTTTTCTGTTGATAATGCACCCA
1 TATGCATTTCAACTATAGCATACTTTTCTGTTGACAATGCACCCA
* * **
662789 TATGCATTTCAACTATAGTATACTTTTCTGTTAACAATATACCCA
1 TATGCATTTCAACTATAGCATACTTTTCTGTTGACAATGCACCCA
* * * *
662834 TATGCATTTCAATTATAGCATATTTTTCTGTTGATAATGCACTCA
1 TATGCATTTCAACTATAGCATACTTTTCTGTTGACAATGCACCCA
*
662879 TATGCATTTCAACTATAGTATACTTTTCTGTTGACAATGCACCCA
1 TATGCATTTCAACTATAGCATACTTTTCTGTTGACAATGCACCCA
*
662924 TATACATTTCAAC
1 TATGCATTTCAAC
662937 AATGACATCC
Statistics
Matches: 254, Mismatches: 29, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
45 246 0.97
46 8 0.03
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (45 bp):
TATGCATTTCAACTATAGCATACTTTTCTGTTGACAATGCACCCA
Found at i:662726 original size:90 final size:90
Alignment explanation
Indices: 662591--662976 Score: 508
Period size: 90 Copynumber: 4.3 Consensus size: 90
662581 CCTCCATTCA
* * * * * *
662591 TGTTTATAATCCA-CCATTATGCATTATTAACTATAGCATACTTTTCTGCTGATAATGCACCCAT
1 TGTTGATAATGCACCCA-TATGCATT-TCAACTATAGTATACTTTTCTGTTGACAATGCACCCAT
* *
662655 ATGCATTTTAACTATAGCATACATTTC
64 ATGCATTTCAACTATAGCATACTTTTC
* *
662682 TGTTGACAATGCACCCATATGCATTTCAACTATAATATACTTTTCTGTTGACAATGCACCCATAT
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCTGTTGACAATGCACCCATAT
*
662747 GCATTTCAACTATAACATACTTTTC
66 GCATTTCAACTATAGCATACTTTTC
* **
662772 TGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCTGTTAACAATATACCCATAT
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCTGTTGACAATGCACCCATAT
* *
662837 GCATTTCAATTATAGCATATTTTTC
66 GCATTTCAACTATAGCATACTTTTC
*
662862 TGTTGATAATGCACTCATATGCATTTCAACTATAGTATACTTTTCTGTTGACAATGCACCCATAT
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCTGTTGACAATGCACCCATAT
* * *
662927 ACATTTCAACAAT-GACAT-CCTTTC
66 GCATTTCAACTATAG-CATACTTTTC
***
662951 ATGCCAATAATGCACCCATATGCATT
1 -TGTTGATAATGCACCCATATGCATT
662977 ATTATTTTCA
Statistics
Matches: 260, Mismatches: 32, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
89 5 0.02
90 234 0.90
91 18 0.07
92 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (90 bp):
TGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCTGTTGACAATGCACCCATAT
GCATTTCAACTATAGCATACTTTTC
Found at i:662968 original size:135 final size:134
Alignment explanation
Indices: 662591--662976 Score: 488
Period size: 135 Copynumber: 2.9 Consensus size: 134
662581 CCTCCATTCA
* * * *
662591 TGTTTATAATCCACCATTATGCATTATTAACTATAGCATACTTTTCTGCTGATAATGCACCCATA
1 TGTTGATAATGCACCA-TATGCATT-TCAACTATAGCATACTTTTCTGTTGATAATGCACCCATA
* * *
662656 TGCATTTTAACTATAGCATACATTTCTGTTGACAATGCACCCATATGCATTTCAACTATAATATA
64 TGCATTTCAACTATAGCATACATTTCTGTTAACAATGCACCCATATGCATTTCAACTATAACATA
662721 CTTTTC
129 CTTTTC
* *
662727 TGTTGACAATGCACCCATATGCATTTCAACTATAACATACTTTTCTGTTGATAATGCACCCATAT
1 TGTTGATAATGCA-CCATATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCATAT
* * ** * * *
662792 GCATTTCAACTATAGTATACTTTTCTGTTAACAATATACCCATATGCATTTCAATTATAGCATAT
65 GCATTTCAACTATAGCATACATTTCTGTTAACAATGCACCCATATGCATTTCAACTATAACATAC
662857 TTTTC
130 TTTTC
* *
662862 TGTTGATAATGCACTCATATGCATTTCAACTATAGTATACTTTTCTGTTGACAATGCACCCATAT
1 TGTTGATAATGCAC-CATATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCATAT
* * * ** *
662927 ACATTTCAACAAT-GACAT-CCTTTCATGCCAATAATGCACCCATATGCATT
65 GCATTTCAACTATAG-CATACATTTC-TGTTAACAATGCACCCATATGCATT
662977 ATTATTTTCA
Statistics
Matches: 217, Mismatches: 29, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
134 7 0.03
135 189 0.87
136 18 0.08
137 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (134 bp):
TGTTGATAATGCACCATATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCATATG
CATTTCAACTATAGCATACATTTCTGTTAACAATGCACCCATATGCATTTCAACTATAACATACT
TTTC
Found at i:669748 original size:45 final size:45
Alignment explanation
Indices: 669646--669896 Score: 308
Period size: 45 Copynumber: 5.6 Consensus size: 45
669636 CCTTCATTCA
* *
669646 TGTTTATAATGCA-CCATTATGCATTATTAACTATAGCATACTTTTC
1 TGTTGATAATGCACCCA-TATGCATT-TCAACTATAGCATACTTTTC
* * *
669692 TGCTGATAATGCACCCATATGCATTTCAACTTTAGCATACCTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
* * *
669737 TGTTGACAATGCACCCATATGTATTTCAACTATAGTATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
* *
669782 TGTTGATAATGAACCCATATGCATTTCAACTATAGTATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
* * * *
669827 TGTTGACAATGCACCCATATGCATTTTAACTATGGCAT-CCTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
***
669871 ATGCCAATAATGCACCCATATGCATT
1 -TGTTGATAATGCACCCATATGCATT
669897 ATTATTTTCA
Statistics
Matches: 179, Mismatches: 24, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
44 5 0.03
45 152 0.85
46 19 0.11
47 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (45 bp):
TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
Found at i:672281 original size:14 final size:15
Alignment explanation
Indices: 672253--672308 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
672243 AATGTATTTG
*
672253 TATATTGTATAGTA-
1 TATATTATATAGTAT
*
672267 TATATTATATGGTATT
1 TATATTATATAGTA-T
*
672283 TATATTATATAATACT
1 TATATTATATAGTA-T
672299 TATATTATAT
1 TATATTATAT
672309 TATGATATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 12 0.34
16 23 0.66
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.54
Consensus pattern (15 bp):
TATATTATATAGTAT
Found at i:673425 original size:6 final size:6
Alignment explanation
Indices: 673414--673460 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
673404 ATATTAACTA
* * *
673414 TTTTTG TTTTTG TTTTTA TTTTTT TATTTTG TTTTT- TATTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG T-TTTTG TTTTTG TTTTTG TTTTT
673461 TTTAATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
5 4 0.12
6 25 0.74
7 5 0.15
ACGTcount: A:0.06, C:0.00, G:0.09, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:673443 original size:20 final size:20
Alignment explanation
Indices: 673414--673463 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
673404 ATATTAACTA
*
673414 TTTTTGTTTTTG-TTTTTAT
1 TTTTTTTTTTTGTTTTTTAT
*
673433 TTTTTTATTTTGTTTTTTAT
1 TTTTTTTTTTTGTTTTTTAT
*
673453 TTGTTTTTTTT
1 TTTTTTTTTTT
673464 AATTTAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.06, C:0.00, G:0.08, T:0.86
Consensus pattern (20 bp):
TTTTTTTTTTTGTTTTTTAT
Found at i:673461 original size:11 final size:11
Alignment explanation
Indices: 673422--673461 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
673412 TATTTTTGTT
673422 TTTG-TTTTTA
1 TTTGTTTTTTA
*
673432 TTT-TTTTAT-
1 TTTGTTTTTTA
673441 TTTGTTTTTTA
1 TTTGTTTTTTA
673452 TTTGTTTTTT
1 TTTGTTTTTT
673462 TTAATTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
9 3 0.12
10 12 0.48
11 10 0.40
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (11 bp):
TTTGTTTTTTA
Found at i:673464 original size:25 final size:25
Alignment explanation
Indices: 673415--673462 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
673405 TATTAACTAT
673415 TTTTGTTTTTGTTTTTATTTTTTTA
1 TTTTGTTTTTGTTTTTATTTTTTTA
* *
673440 TTTTGTTTTT-TATTTGTTTTTTT
1 TTTTGTTTTTGTTTTTATTTTTTT
673463 TAATTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.06, C:0.00, G:0.08, T:0.85
Consensus pattern (25 bp):
TTTTGTTTTTGTTTTTATTTTTTTA
Found at i:682457 original size:26 final size:26
Alignment explanation
Indices: 682425--682479 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
682415 TATGCTAGAA
*
682425 GATGTCATAAATATCAAATCTATGAG
1 GATGTCATAAATATCAAATCTACGAG
*
682451 GATGTCATAAATGTCAAATCTACGAG
1 GATGTCATAAATATCAAATCTACGAG
682477 GAT
1 GAT
682480 AAAATAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (26 bp):
GATGTCATAAATATCAAATCTACGAG
Found at i:682486 original size:26 final size:26
Alignment explanation
Indices: 682431--682490 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
682421 AGAAGATGTC
* * ***
682431 ATAAATATCAAATCTATGAGGATGTC
1 ATAAATGTCAAATCTACGAGGATAAA
682457 ATAAATGTCAAATCTACGAGGATAAA
1 ATAAATGTCAAATCTACGAGGATAAA
682483 ATAAATGT
1 ATAAATGT
682491 TCCACCTCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (26 bp):
ATAAATGTCAAATCTACGAGGATAAA
Found at i:683536 original size:67 final size:67
Alignment explanation
Indices: 683419--683544 Score: 182
Period size: 67 Copynumber: 1.9 Consensus size: 67
683409 AAGTTGAAGC
* * * * *
683419 AAAAAAGCAAAAGAAAAACGTTTAGGGTGAAAACCCAAAAGGGTGTCCTAAATTGAAAAGAGGGA
1 AAAAAAGCAAAAGAAAAACATTTAGGATGAAAAACCAAAAGGGCGCCCTAAATTGAAAAGAGGGA
683484 AA
66 AA
*
683486 AAAAGAAG-AAAAGAAAAACATTTAGGATGAAAAATCAAAAGGGCGCCCTAAATTGAAAA
1 AAAA-AAGCAAAAGAAAAACATTTAGGATGAAAAACCAAAAGGGCGCCCTAAATTGAAAA
683545 AACAAGGGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
67 49 0.94
68 3 0.06
ACGTcount: A:0.55, C:0.10, G:0.21, T:0.13
Consensus pattern (67 bp):
AAAAAAGCAAAAGAAAAACATTTAGGATGAAAAACCAAAAGGGCGCCCTAAATTGAAAAGAGGGA
AA
Found at i:684049 original size:21 final size:21
Alignment explanation
Indices: 684023--684062 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
684013 ATTTTACAGT
684023 GAGTGTACCGATACACCTAGA
1 GAGTGTACCGATACACCTAGA
684044 GAGTGTACCGATACACCTA
1 GAGTGTACCGATACACCTA
684063 CGCTCCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.20
Consensus pattern (21 bp):
GAGTGTACCGATACACCTAGA
Found at i:690310 original size:12 final size:13
Alignment explanation
Indices: 690280--690312 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
690270 GTATTATAAT
*
690280 TTTTCAAATATTG
1 TTTTCAAATATTA
690293 TTTTCAAA-ATTA
1 TTTTCAAATATTA
690305 TTTTCAAA
1 TTTTCAAA
690313 CTTTGCCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (13 bp):
TTTTCAAATATTA
Found at i:691886 original size:7 final size:7
Alignment explanation
Indices: 691874--691898 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
691864 TTAAAATATG
691874 ACCAATT
1 ACCAATT
691881 ACCAATT
1 ACCAATT
691888 ACCAATT
1 ACCAATT
691895 ACCA
1 ACCA
691899 TTGCACATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (7 bp):
ACCAATT
Found at i:692087 original size:13 final size:13
Alignment explanation
Indices: 692055--692115 Score: 72
Period size: 12 Copynumber: 4.8 Consensus size: 13
692045 TAAGGGGGAG
*
692055 TGATTTTCAAAAT
1 TGATTTTCAAAAA
*
692068 TG-CTTTCAAAAA
1 TGATTTTCAAAAA
*
692080 TGATTTTCAAAAT
1 TGATTTTCAAAAA
*
692093 TG-CTTTCAAAAA
1 TGATTTTCAAAAA
692105 TGATTTTCAAA
1 TGATTTTCAAA
692116 GAAAATCTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
12 20 0.51
13 19 0.49
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.41
Consensus pattern (13 bp):
TGATTTTCAAAAA
Found at i:692089 original size:25 final size:25
Alignment explanation
Indices: 692055--692115 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
692045 TAAGGGGGAG
692055 TGATTTTCAAAATTGCTTTCAAAAA
1 TGATTTTCAAAATTGCTTTCAAAAA
692080 TGATTTTCAAAATTGCTTTCAAAAA
1 TGATTTTCAAAATTGCTTTCAAAAA
692105 TGATTTTCAAA
1 TGATTTTCAAA
692116 GAAAATCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.41
Consensus pattern (25 bp):
TGATTTTCAAAATTGCTTTCAAAAA
Found at i:692178 original size:13 final size:13
Alignment explanation
Indices: 692156--692189 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
692146 TATATGAGTA
*
692156 ATTTTCAAAATTG
1 ATTTTCAAAAATG
692169 A-TTTCAAAAATG
1 ATTTTCAAAAATG
692181 ATTTTCAAA
1 ATTTTCAAA
692190 TAAAATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:698111 original size:29 final size:29
Alignment explanation
Indices: 698058--698116 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
698048 AGTGTCGTTA
* * *
698058 CGAATCAAGCTGTGAGTCATGAGCTTAGT
1 CGAATCAAGATGTGAGTCATAAGCTGAGT
* *
698087 CGAATCGAGATGTGAGTCGTAAGCTGAGT
1 CGAATCAAGATGTGAGTCATAAGCTGAGT
698116 C
1 C
698117 AAGTTACGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (29 bp):
CGAATCAAGATGTGAGTCATAAGCTGAGT
Found at i:705087 original size:29 final size:29
Alignment explanation
Indices: 705034--705092 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
705024 AGTGTCGTTA
* * *
705034 CGAATCAAGCTGTGAGTCATGAGCTTAGT
1 CGAATCAAGATGTGAGTCATAAGCTGAGT
* *
705063 CGAATCGAGATGTGAGTCGTAAGCTGAGT
1 CGAATCAAGATGTGAGTCATAAGCTGAGT
705092 C
1 C
705093 AAGTTACGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (29 bp):
CGAATCAAGATGTGAGTCATAAGCTGAGT
Found at i:712060 original size:29 final size:29
Alignment explanation
Indices: 712007--712065 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
711997 AGTGTCGTTA
* * *
712007 CGAATCAAGCTGTGAGTCATGAGCTTAGT
1 CGAATCAAGATGTGAGTCATAAGCTGAGT
* *
712036 CGAATCGAGATGTGAGTCGTAAGCTGAGT
1 CGAATCAAGATGTGAGTCATAAGCTGAGT
712065 C
1 C
712066 AAGTTACGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (29 bp):
CGAATCAAGATGTGAGTCATAAGCTGAGT
Found at i:716683 original size:3 final size:3
Alignment explanation
Indices: 716675--716720 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
716665 AACAAACTTA
716675 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
716721 TAAAGTTACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:717741 original size:20 final size:19
Alignment explanation
Indices: 717693--717732 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
717683 AATACATTAT
*
717693 AATATAAAATTTTTAATAA
1 AATATAAAATTTTTAACAA
717712 AATATAAAATTATTTAACAA
1 AATATAAAATT-TTTAACAA
717732 A
1 A
717733 TTATCAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATATAAAATTTTTAACAA
Found at i:718916 original size:29 final size:29
Alignment explanation
Indices: 718880--718945 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
718870 AGAATAATTT
* *
718880 AATATTATTTATATCAATATTAT-TATAAA
1 AATATTATATATAT-AATATTATAAATAAA
* *
718909 AATATTATATCTATAATTTTATAAATAAA
1 AATATTATATATATAATATTATAAATAAA
718938 AATATTAT
1 AATATTAT
718946 GATTATTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 7 0.22
29 25 0.78
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
AATATTATATATATAATATTATAAATAAA
Found at i:718966 original size:29 final size:27
Alignment explanation
Indices: 718888--718969 Score: 73
Period size: 29 Copynumber: 3.0 Consensus size: 27
718878 TTAATATTAT
*
718888 TTATATC-A-ATATTATTATAAAAATA
1 TTATATCTATATATTTTTATAAAAATA
718913 TTATATCTATA-ATTTTATAAATAAAAATA
1 TTATATCTATATATTTT-T--ATAAAAATA
*
718942 TTATGAT-TATTATATTTTTATTAAAATA
1 TTAT-ATCTA-TATATTTTTATAAAAATA
718970 AAATTATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
25 7 0.15
26 5 0.11
27 2 0.04
28 8 0.17
29 15 0.32
30 5 0.11
31 5 0.11
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (27 bp):
TTATATCTATATATTTTTATAAAAATA
Found at i:719334 original size:29 final size:29
Alignment explanation
Indices: 719298--719362 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
719288 AGAATAATTT
*
719298 AATATTATTTATATCAATATTAT-TATAAA
1 AATATTATTTATAT-AATATTATAAATAAA
* *
719327 AATATTATTTCTATAATTTTATAAATAAA
1 AATATTATTTATATAATATTATAAATAAA
719356 AATATTA
1 AATATTA
719363 CAATATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 7 0.22
29 25 0.78
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (29 bp):
AATATTATTTATATAATATTATAAATAAA
Found at i:729448 original size:138 final size:138
Alignment explanation
Indices: 729154--730240 Score: 1577
Period size: 138 Copynumber: 7.9 Consensus size: 138
729144 GGTGATGTTC
* * * * *
729154 CAACTCCGTATGCGATGGAAACAAG-TATGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTC
1 CAACTCCATATGCGAT-GAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
** * * * * *
729218 CC-TCATCGGATGAGTTTTTCTCATTATAAACT-TTCCACTGAAAATGTTGATCCCTCGAGTGAG
65 CCTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTA--G-AAATGTTGATCCCTCAATTGAG
**
729281 GTGTTGTTGATT
127 GTGTTACTGATT
* *
729293 CAACTCCTTATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * *
729358 CTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTTAATCCCTCAATTCAAGTGT
66 CTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTTGATCCCTCAATTGAGGTGT
729423 TACTGATT
131 TACTGATT
*
729431 CAACTCCATATGCGATGAATCGAGTTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * * * * * *
729496 TTTTTTCGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTCGATCCTTCGATTTAGGTGT
66 CTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTTGATCCCTCAATTGAGGTGT
*
729561 TGCTGATT
131 TACTGATT
*
729569 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * * *
729634 CTTTGTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGATGATCCCTCAATTGAGGTAT
66 CTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTTGATCCCTCAATTGAGGTGT
*
729699 TACTAATT
131 TACTGATT
* *
729707 CAACTCTATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * * *
729772 CTTTGTCGAATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGATGATCCCTCAATTGTGGTGT
66 CTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTTGATCCCTCAATTGAGGTGT
729837 TACTGATT
131 TACTGATT
* * *
729845 CAACTCCATATGCGATGAATCAAGCTAAGGTTGAACAAGTTCTTCTCCTTATTAACTTCTTCTCC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * * * *
729910 CTTTTTCAGATGAGTTCTTCTCATTATGAACTCTTCTAGAAATATTGATCCCTCGATTGAGGTAT
66 CTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTTGATCCCTCAATTGAGGTGT
*
729975 TGCTGATT
131 TACTGATT
* *
729983 CAACTCCATATACGATGAATCGAGCTAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * * *
730048 CTTTTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCCTCGATTGAGGTGT
66 CTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTTGATCCCTCAATTGAGGTGT
*
730113 TTCTGATT
131 TACTGATT
* * * *
730121 CAACACCATATACGATGAATCGAGCTAAGGTTGAACACGTTCTTCTCATTATGAACTTGTTCTCC
1 CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
730186 CTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTTGATCCCTCA
66 CTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTTGATCCCTCA
730241 TTCTAGGGTG
Statistics
Matches: 864, Mismatches: 81, Indels: 7
0.91 0.09 0.01
Matches are distributed among these distances:
138 780 0.90
139 54 0.06
140 26 0.03
141 4 0.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.37
Consensus pattern (138 bp):
CAACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
CTTTGTCGGATGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTTGATCCCTCAATTGAGGTGT
TACTGATT
Found at i:731123 original size:14 final size:13
Alignment explanation
Indices: 731091--731138 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
731081 ATCTCGAACC
731091 CTCTTTTTTCTTTT
1 CTCTTTTTT-TTTT
*
731105 CT-TTTTTTATTT
1 CTCTTTTTTTTTT
*
731117 CTTTTTTCTTTTTT
1 CTCTTTT-TTTTTT
731131 CTCTTTTT
1 CTCTTTTT
731139 CATTTTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 5 0.17
13 11 0.38
14 13 0.45
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (13 bp):
CTCTTTTTTTTTT
Found at i:731130 original size:9 final size:9
Alignment explanation
Indices: 731096--731204 Score: 55
Period size: 9 Copynumber: 11.6 Consensus size: 9
731086 GAACCCTCTT
731096 TTTTCTTTTC
1 TTTT-TTTTC
731106 TTTTTTTAT-
1 TTTTTTT-TC
731115 TTCTTTTTTC
1 TT-TTTTTTC
*
731125 TTTTTTCTC
1 TTTTTTTTC
731134 TTTTTCATTTTC
1 -TTTT--TTTTC
*
731146 ATTTTTTTC
1 TTTTTTTTC
*
731155 -ATTTTTTC
1 TTTTTTTTC
*
731163 -ATTTTTTC
1 TTTTTTTTC
*
731171 -CTTTTTTC
1 TTTTTTTTC
*
731179 ATTTTTTTC
1 TTTTTTTTC
731188 ATTCATTTTTTC
1 -TT--TTTTTTC
731200 TTTTT
1 TTTTT
731205 CTCTTCAAGC
Statistics
Matches: 82, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
8 22 0.27
9 27 0.33
10 17 0.21
11 5 0.06
12 11 0.13
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:731136 original size:33 final size:35
Alignment explanation
Indices: 731094--731209 Score: 125
Period size: 37 Copynumber: 3.3 Consensus size: 35
731084 TCGAACCCTC
731094 TTTTT-TCTTTTC-TTTTTTTATTTC-TTTTTTCT
1 TTTTTCTCTTTTCATTTTTTTATTTCATTTTTTCT
*
731126 TTTTTCTCTTTTTCATTTTCATTTTTTTCATTTTTTCAT
1 TTTTTCTC-TTTTCATTTT--TTTATTTCATTTTTTC-T
*
731165 TTTTTCCTTTTTTCATTTTTTTCA-TTCATTTTTTC-
1 TTTTT-CTCTTTTCATTTTTTT-ATTTCATTTTTTCT
731200 TTTTTCTCTT
1 TTTTTCTCTT
731210 CAAGCATAAC
Statistics
Matches: 71, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
32 5 0.07
33 2 0.03
34 9 0.13
35 9 0.13
37 21 0.30
38 7 0.10
39 16 0.23
40 2 0.03
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (35 bp):
TTTTTCTCTTTTCATTTTTTTATTTCATTTTTTCT
Found at i:731151 original size:39 final size:40
Alignment explanation
Indices: 731093--731183 Score: 111
Period size: 39 Copynumber: 2.3 Consensus size: 40
731083 CTCGAACCCT
*
731093 CTTTTTTC-TTTTCTTTTTTTATTTC-TTTTTTC-TTTTTT-
1 CTTTTTTCATTTTC-TATTTT-TTTCATTTTTTCATTTTTTC
731131 CTCTTTTTCATTTTC-ATTTTTTTCATTTTTTCATTTTTTC
1 CT-TTTTTCATTTTCTATTTTTTTCATTTTTTCATTTTTTC
731171 CTTTTTTCATTTT
1 CTTTTTTCATTTT
731184 TTTCATTCAT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
37 4 0.09
38 13 0.28
39 23 0.49
40 7 0.15
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (40 bp):
CTTTTTTCATTTTCTATTTTTTTCATTTTTTCATTTTTTC
Found at i:731209 original size:8 final size:7
Alignment explanation
Indices: 731092--731209 Score: 78
Period size: 8 Copynumber: 15.6 Consensus size: 7
731082 TCTCGAACCC
731092 TCTTTTT
1 TCTTTTT
731099 TCTTTTCTT
1 TC-TTT-TT
*
731108 TTTTTATT
1 TCTTT-TT
731116 TCTTTTT
1 TCTTTTT
731123 TCTTTTT
1 TCTTTTT
731130 TCTCTTTT
1 TCT-TTTT
*
731138 TC-ATTT
1 TCTTTTT
731144 TCATTTTTT
1 TC--TTTTT
731153 TCATTTTT
1 TC-TTTTT
731161 TCATTTTT
1 TC-TTTTT
731169 TCCTTTTT
1 T-CTTTTT
*
731177 TCATTTT
1 TCTTTTT
**
731184 T-TTCAT
1 TCTTTTT
731190 TCATTTTT
1 TC-TTTTT
731198 TCTTTTT
1 TCTTTTT
731205 CTCTT
1 -TCTT
731210 CAAGCATAAC
Statistics
Matches: 89, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
6 8 0.09
7 25 0.28
8 47 0.53
9 9 0.10
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (7 bp):
TCTTTTT
Found at i:734612 original size:7 final size:7
Alignment explanation
Indices: 734600--734761 Score: 317
Period size: 7 Copynumber: 23.3 Consensus size: 7
734590 AATGAATGTA
734600 AAGAATG
1 AAGAATG
734607 AAGAATG
1 AAGAATG
734614 AAGAATG
1 AAGAATG
734621 AAGAATG
1 AAGAATG
734628 AAGAATG
1 AAGAATG
734635 AAGAATG
1 AAGAATG
734642 AAGAATG
1 AAGAATG
734649 AAGAATG
1 AAGAATG
734656 AAGAATG
1 AAGAATG
734663 AAGAATG
1 AAGAATG
734670 AAGAATG
1 AAGAATG
734677 AAGAATG
1 AAGAATG
734684 AAGAATG
1 AAGAATG
734691 AAGAATG
1 AAGAATG
734698 AAGAATG
1 AAGAATG
734705 AAGAATG
1 AAGAATG
734712 AAGAATG
1 AAGAATG
734719 AAGAATG
1 AAGAATG
734726 AAGAATG
1 AAGAATG
734733 AAGAATG
1 AAGAATG
734740 AAGAATG
1 AAGAATG
734747 AAGAATG
1 AAGAATG
734754 AA-AATG
1 AAGAATG
734760 AA
1 AA
734762 AATAATGATG
Statistics
Matches: 155, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
6 6 0.04
7 149 0.96
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (7 bp):
AAGAATG
Found at i:738728 original size:64 final size:65
Alignment explanation
Indices: 738616--738738 Score: 178
Period size: 64 Copynumber: 1.9 Consensus size: 65
738606 TGTCATAGAA
*
738616 CAACTTCCATTATAAAAAAAAGTTTTCATTACATAATAGTTCATTTCTACAAATACGGCTTAGTT
1 CAACTTCCATTATAAAAAAAAGTTTTCATTACATAATAGTTCACTTCTACAAATACGGCTTAGTT
* * * *
738681 CAACTTCCATT-GAAACAAAA-TGTTTCATTACATAATATTTCACTTCTACAGATACGGC
1 CAACTTCCATTATAAAAAAAAGT-TTTCATTACATAATAGTTCACTTCTACAAATACGGC
738739 ATCGCTATTC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
63 1 0.02
64 40 0.77
65 11 0.21
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (65 bp):
CAACTTCCATTATAAAAAAAAGTTTTCATTACATAATAGTTCACTTCTACAAATACGGCTTAGTT
Found at i:746166 original size:32 final size:30
Alignment explanation
Indices: 746113--746238 Score: 105
Period size: 32 Copynumber: 4.1 Consensus size: 30
746103 ATGTTGTTAC
* **
746113 AATAAAAGTA-TAATATTATATATTATAAT
1 AATAAAATTATTAATAAAATATATTATAAT
*
746142 AATAAAATTATAATAATAAAATATATTATATT
1 AATAAAATTAT--TAATAAAATATATTATAAT
* *
746174 ATTAAAATTATCAATAAAAT-TAATT-TAAT
1 AATAAAATTATTAATAAAATAT-ATTATAAT
* * *
746203 AATAAATATTTTTATTAAAATGATATTAAAAT
1 AATAAA-ATTATTAATAAAAT-ATATTATAAT
746235 AATA
1 AATA
746239 TATTCAAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
29 18 0.23
30 22 0.29
31 3 0.04
32 34 0.44
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (30 bp):
AATAAAATTATTAATAAAATATATTATAAT
Found at i:746190 original size:44 final size:42
Alignment explanation
Indices: 746142--746240 Score: 107
Period size: 44 Copynumber: 2.4 Consensus size: 42
746132 ATATTATAAT
746142 AATAAAATT-ATAATAATAA-AATATATTATATTATTAAAATTATC
1 AATAAAATTAAT-ATAATAATAA-ATATT-T-TTATTAAAATTATC
* *
746186 AATAAAATTAATTTAATAATAAATATTTTTATTAAAATGAT-
1 AATAAAATTAATATAATAATAAATATTTTTATTAAAATTATC
*
746227 ATTAAAA-TAATATA
1 AATAAAATTAATATA
746241 TTCAAATTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
40 6 0.12
41 6 0.12
42 12 0.24
43 1 0.02
44 20 0.41
45 4 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (42 bp):
AATAAAATTAATATAATAATAAATATTTTTATTAAAATTATC
Found at i:746213 original size:14 final size:15
Alignment explanation
Indices: 746121--746212 Score: 66
Period size: 14 Copynumber: 6.1 Consensus size: 15
746111 ACAATAAAAG
* *
746121 TATAATATTATATAT
1 TATAATAATAAATAT
746136 TATAATAATAAA-AT
1 TATAATAATAAATAT
746150 TATAATAATAAAATATAT
1 TATAATAAT--AA-ATAT
* *
746168 TATATTATTAAA-AT
1 TATAATAATAAATAT
*
746182 TATCAATAA-AATTAAT
1 TAT-AATAATAAAT-AT
746198 T-TAATAATAAATAT
1 TATAATAATAAATAT
746212 T
1 T
746213 TTTATTAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
14 26 0.43
15 18 0.30
16 7 0.11
17 1 0.02
18 9 0.15
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAATAATAAATAT
Found at i:749886 original size:36 final size:36
Alignment explanation
Indices: 749817--749887 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
749807 CAATTTCAAG
* *
749817 GTTTGATTCAGTGCTTGAGTATTAGGTTACTTTCTC
1 GTTTGATTCAGTGCTCGAGTATTAGGCTACTTTCTC
* * *
749853 GTTTGATTCGGTGCTCGAGTATTTGGCTGCTTTCT
1 GTTTGATTCAGTGCTCGAGTATTAGGCTACTTTCT
749888 TAAAGAACTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.13, C:0.15, G:0.25, T:0.46
Consensus pattern (36 bp):
GTTTGATTCAGTGCTCGAGTATTAGGCTACTTTCTC
Found at i:750251 original size:16 final size:16
Alignment explanation
Indices: 750228--750273 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
750218 AAATTTCAGT
750228 GAGCTTAAAGAGCAAC
1 GAGCTTAAAGAGCAAC
* * *
750244 GGGCTTAATGAGTAAC
1 GAGCTTAAAGAGCAAC
750260 GAGCTTAAAGAGCA
1 GAGCTTAAAGAGCA
750274 CGATTCGAGC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.39, C:0.15, G:0.28, T:0.17
Consensus pattern (16 bp):
GAGCTTAAAGAGCAAC
Found at i:751885 original size:28 final size:28
Alignment explanation
Indices: 751798--751897 Score: 92
Period size: 28 Copynumber: 3.4 Consensus size: 28
751788 TTTTTTTATT
* *
751798 TAAGTACCTAAAGTATTTTTTGTCAAAT
1 TAAGTACCTAAAGTATTTTTAGTCAAAA
* * *
751826 TAAGTACCCATAGTTATCATTTTGGTCAAAA
1 TAAGTACCTAAAG-TAT--TTTTAGTCAAAA
* *
751857 TAAGTATCTAAAGTATTTTTAGTTAAAA
1 TAAGTACCTAAAGTATTTTTAGTCAAAA
*
751885 TAGATTACCTAAA
1 TA-AGTACCTAAA
751898 ATGTGCTACC
Statistics
Matches: 57, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
28 23 0.40
29 11 0.19
30 3 0.05
31 20 0.35
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (28 bp):
TAAGTACCTAAAGTATTTTTAGTCAAAA
Found at i:757518 original size:24 final size:24
Alignment explanation
Indices: 757440--757510 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
757430 TCAATTAAGA
757440 TATCAGAACAGAATTCAGGTCAGG
1 TATCAGAACAGAATTCAGGTCAGG
* *
757464 TATTAGAACAGAATCCAGGTCAGG
1 TATCAGAACAGAATTCAGGTCAGG
757488 TATCAGAACAGAATTCAGGTCAG
1 TATCAGAACAGAATTCAGGTCAG
757511 AAATCAGATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (24 bp):
TATCAGAACAGAATTCAGGTCAGG
Found at i:764550 original size:15 final size:15
Alignment explanation
Indices: 764514--764543 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
764504 GATTAATGAA
*
764514 ATAAGAAATGAAATG
1 ATAAGAAATGAAAGG
764529 ATAAGAAATGAAAGG
1 ATAAGAAATGAAAGG
764544 GATAGAATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (15 bp):
ATAAGAAATGAAAGG
Found at i:768419 original size:6 final size:6
Alignment explanation
Indices: 768404--768445 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
768394 TGTAGGAGTT
*
768404 TTTTTC -TTTTC TTTTTC TTTTTTC TTTTTTC TTTTTG TTTTT
1 TTTTTC TTTTTC TTTTTC -TTTTTC -TTTTTC TTTTTC TTTTT
768446 GTTGTAGCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
5 5 0.15
6 15 0.45
7 13 0.39
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:768426 original size:13 final size:13
Alignment explanation
Indices: 768403--768445 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
768393 ATGTAGGAGT
768403 TTTTTTC-TTTTC
1 TTTTTTCTTTTTC
768415 -TTTTTCTTTTTTC
1 TTTTTTC-TTTTTC
*
768428 TTTTTTCTTTTTG
1 TTTTTTCTTTTTC
768441 TTTTT
1 TTTTT
768446 GTTGTAGCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 6 0.22
13 15 0.56
14 6 0.22
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:768445 original size:7 final size:7
Alignment explanation
Indices: 768410--768439 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
768400 AGTTTTTTTC
768410 TTTTC-T
1 TTTTCTT
768416 TTTTCTT
1 TTTTCTT
768423 TTTTCTT
1 TTTTCTT
768430 TTTTCTT
1 TTTTCTT
768437 TTT
1 TTT
768440 GTTTTTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTCTT
Found at i:768648 original size:20 final size:20
Alignment explanation
Indices: 768625--768671 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
768615 TAAATGGATT
768625 AATGAAATAAGAAATGA-AAG-
1 AATGAAAT--GAAATGATAAGA
768645 AATGAAATGAAATGATAAGA
1 AATGAAATGAAATGATAAGA
768665 AATGAAA
1 AATGAAA
768672 GGGATAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.28
19 3 0.12
20 15 0.60
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (20 bp):
AATGAAATGAAATGATAAGA
Found at i:768666 original size:10 final size:9
Alignment explanation
Indices: 768633--768672 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
768623 TTAATGAAAT
768633 AAGAAATGA
1 AAGAAATGA
768642 AAG-AATGA
1 AAGAAATGA
768650 AATGAAATGA
1 AA-GAAATGA
768660 TAAGAAATGA
1 -AAGAAATGA
768670 AAG
1 AAG
768673 GGATAGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 7 0.25
9 7 0.25
10 12 0.43
11 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (9 bp):
AAGAAATGA
Found at i:772743 original size:20 final size:20
Alignment explanation
Indices: 772707--772744 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
772697 TTCCATGACT
*
772707 AAAAAGATTGATACCCTTTC
1 AAAAAGATCGATACCCTTTC
772727 AAAAAGGATCGAT-CCCTT
1 AAAAA-GATCGATACCCTT
772745 GCCTAAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.26
Consensus pattern (20 bp):
AAAAAGATCGATACCCTTTC
Done.