Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011520.1 Kokia drynarioides strain JFW-HI SEQ_126506, 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: 653816
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 73 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:417956 original size:59 final size:59
Alignment explanation
Indices: 417772--418052 Score: 257
Period size: 59 Copynumber: 4.7 Consensus size: 59
417762 GGAGGTCCCT
* * * *
417772 AAACTTCCAAAAATTCTATTTTTTA-CCCTCGAACTTCCAAAAATCCCACTTTTGA-CCCA
1 AAACTTCCAAAAATTCCA-TTTTTACCCCT-AAACTTCCAAAAATTCCATTTTTGACCCCA
* * * * * ** * * *
417831 GAAACTTCTAAAAATTTCGTTTTTACCCTTGAACTT-TTAAAATCCCATTTTTGACCTCG
1 -AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCA
*
417890 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCA
* * *
417949 AAACTTCCAAAAATTCCATTTTTGATCCC-AAACTTTCAAAAATTCCATTTTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTTT-ACCCCTAAACTTCCAAAAATTCCATTTTTGACCC-CA
* * * * * *
418008 GAACTTCCAAAAATCCCGTTTTTTATCTCGAAACTTCCAAAAATT
1 AAACTTCCAAAAATTCC-ATTTTTACCCCTAAACTTCCAAAAATT
418053 TTGTTTTTGC
Statistics
Matches: 185, Mismatches: 29, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
58 45 0.24
59 99 0.54
60 41 0.22
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCA
Found at i:418108 original size:59 final size:58
Alignment explanation
Indices: 417876--418108 Score: 205
Period size: 59 Copynumber: 3.9 Consensus size: 58
417866 TTTAAAATCC
* *
417876 CATTTTTGA-CCTCGAAACTTCCAAAAAT-TCCA-TTTTTACCCCTAAACTTCCAAAAATT
1 CATTTTTTACCCTCG-AACTTCCAAAAATCTCCATTTTTTACCTC-AAACTT-CAAAAATT
* * *
417934 CCATTTTTAACCC-CAAAACTTCCAAAAAT-TCCATTTTTGATCC-CAAACTTTCAAAAATT
1 -CATTTTTTACCCTC-GAACTTCCAAAAATCTCCATTTTTTA-CCTCAAAC-TTCAAAAATT
* *
417993 CCATTTTTTACCCTCGAACTTCCAAAAATC-CCGTTTTTTATCTCGAAACTTCCAAAAATT
1 -CATTTTTTACCCTCGAACTTCCAAAAATCTCCATTTTTTACCTC-AAACTT-CAAAAATT
* *
418053 -TTGTTTTTGCCCTCGAACTTCC-AAAATCTCCATTTTTTACCTCAAAACTCTCAAAA
1 CAT-TTTTTACCCTCGAACTTCCAAAAATCTCCATTTTTTACCTC-AAACT-TCAAAA
418109 TTAGACTTTT
Statistics
Matches: 148, Mismatches: 13, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
58 8 0.05
59 114 0.77
60 24 0.16
61 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.36
Consensus pattern (58 bp):
CATTTTTTACCCTCGAACTTCCAAAAATCTCCATTTTTTACCTCAAACTTCAAAAATT
Found at i:424703 original size:22 final size:21
Alignment explanation
Indices: 424662--424703 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
424652 TAGTTTTAGG
**
424662 TTTAGTTTTCTCTAGGTTTTC
1 TTTAGTTTTCTCTACATTTTC
424683 TTTAGTTTTTCTCTACATTTT
1 TTTAG-TTTTCTCTACATTTT
424704 TCTACGGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.12, C:0.14, G:0.10, T:0.64
Consensus pattern (21 bp):
TTTAGTTTTCTCTACATTTTC
Found at i:426005 original size:14 final size:14
Alignment explanation
Indices: 425986--426050 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 14
425976 CAAGCCCAAA
*
425986 GTGTGAGCCCTGAT
1 GTGTGAGCCCTTAT
*
426000 GTGTGAACCCCTTA-
1 GTGTG-AGCCCTTAT
*
426014 GTGTAAGCCCTTAT
1 GTGTGAGCCCTTAT
* *
426028 GAGAGAGCCC-TAT
1 GTGTGAGCCCTTAT
*
426041 GTGCGAGCCC
1 GTGTGAGCCC
426051 CCCTCGTGTG
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
13 18 0.45
14 16 0.40
15 6 0.15
ACGTcount: A:0.20, C:0.26, G:0.29, T:0.25
Consensus pattern (14 bp):
GTGTGAGCCCTTAT
Found at i:428619 original size:39 final size:39
Alignment explanation
Indices: 428556--428635 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
428546 GGCCAAGTCG
*
428556 AGGGTGTTACAATTGTGTCGATAACGTATTATAAAATAA
1 AGGGTGTTACAATTGTGTCAATAACGTATTATAAAATAA
428595 AGGGTGTTACAATCT-TGTCAATAACGTATTATAAAATAA
1 AGGGTGTTACAAT-TGTGTCAATAACGTATTATAAAATAA
428634 AG
1 AG
428636 AGAGTAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 38 0.97
40 1 0.03
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.33
Consensus pattern (39 bp):
AGGGTGTTACAATTGTGTCAATAACGTATTATAAAATAA
Found at i:431123 original size:60 final size:60
Alignment explanation
Indices: 431021--431162 Score: 162
Period size: 60 Copynumber: 2.4 Consensus size: 60
431011 TCAGGCTCTT
* *
431021 CAAGTCAGTCACCCATTGCTCAGTCGTCTCCAAGCCAATCACCTAGTCCTC-A-GTCATCTC
1 CAAGTCAGTCACCTAGTGCTCAGTCGTCTCCAAGCCAATCACCTAGTCCTCAACGT--TCTC
* * ** * * *
431081 CAAGTCAGTCACCTAGTGCTCAGTCTTCTCCAGGTTAGTCACCTAGTGCTCAACGTTCTT
1 CAAGTCAGTCACCTAGTGCTCAGTCGTCTCCAAGCCAATCACCTAGTCCTCAACGTTCTC
*
431141 CAAGTCAGTCACCTAGTCCTCA
1 CAAGTCAGTCACCTAGTGCTCA
431163 AACTTCTCTT
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 67 0.96
61 1 0.01
62 2 0.03
ACGTcount: A:0.23, C:0.35, G:0.15, T:0.27
Consensus pattern (60 bp):
CAAGTCAGTCACCTAGTGCTCAGTCGTCTCCAAGCCAATCACCTAGTCCTCAACGTTCTC
Found at i:431151 original size:30 final size:30
Alignment explanation
Indices: 431021--431163 Score: 123
Period size: 30 Copynumber: 4.8 Consensus size: 30
431011 TCAGGCTCTT
* * *
431021 CAAGTCAGTCACCCATTGCTCAGTCG-TCTC
1 CAAGTCAGTCACCTAGTGCTCA-ACGTTCTC
* * *
431051 CAAGCCAATCACCTAGTCCTC-A-GTCATCTC
1 CAAGTCAGTCACCTAGTGCTCAACGT--TCTC
*
431081 CAAGTCAGTCACCTAGTGCTCAGTC-TTCTC
1 CAAGTCAGTCACCTAGTGCTCA-ACGTTCTC
* * *
431111 CAGGTTAGTCACCTAGTGCTCAACGTTCTT
1 CAAGTCAGTCACCTAGTGCTCAACGTTCTC
*
431141 CAAGTCAGTCACCTAGTCCTCAA
1 CAAGTCAGTCACCTAGTGCTCAA
431164 ACTTCTCTTG
Statistics
Matches: 89, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
27 1 0.01
29 1 0.01
30 86 0.97
32 1 0.01
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.27
Consensus pattern (30 bp):
CAAGTCAGTCACCTAGTGCTCAACGTTCTC
Found at i:433318 original size:23 final size:24
Alignment explanation
Indices: 433292--433342 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
433282 TTTTTTAAAT
*
433292 TTTAGAATAATATTTA-AAAATTA
1 TTTAGAATAATATTTATAAAATAA
** *
433315 TTTATTATATTATTTATAAAATAA
1 TTTAGAATAATATTTATAAAATAA
433339 TTTA
1 TTTA
433343 ATATATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTAGAATAATATTTATAAAATAA
Found at i:433335 original size:24 final size:23
Alignment explanation
Indices: 433302--433349 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
433292 TTTAGAATAA
* *
433302 TATTTAAAAATTATTTATTATAT
1 TATTTAAAAATAATTTAATATAT
433325 TATTTATAAAATAATTTAATATAT
1 TATTTA-AAAATAATTTAATATAT
433349 T
1 T
433350 TTAATGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTAAAAATAATTTAATATAT
Found at i:441603 original size:57 final size:57
Alignment explanation
Indices: 441517--441630 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
441507 ATATGAAAAT
441517 ATATTTAATAATTTTTTTTAATTATAATAGAAGAACAAAATCCTAAAAATAATGTAA
1 ATATTTAATAATTTTTTTTAATTATAATAGAAGAACAAAATCCTAAAAATAATGTAA
*
441574 ATATTTAATAATTTTTTTTAATTATAATAGAAGAACAAAATCTTAAAAATAATGTAA
1 ATATTTAATAATTTTTTTTAATTATAATAGAAGAACAAAATCCTAAAAATAATGTAA
441631 TGAACATAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.39
Consensus pattern (57 bp):
ATATTTAATAATTTTTTTTAATTATAATAGAAGAACAAAATCCTAAAAATAATGTAA
Found at i:446606 original size:15 final size:14
Alignment explanation
Indices: 446588--446635 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 14
446578 TGTGATTATG
446588 GTTTGATTAATTAAA
1 GTTTGATTAATT-AA
446603 GTTTGATTAAATTAA
1 GTTTGATT-AATTAA
446618 -TTCTGATTAATTAA
1 GTT-TGATTAATTAA
446632 GTTT
1 GTTT
446636 AAACAAAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 9 0.30
15 17 0.57
16 4 0.13
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (14 bp):
GTTTGATTAATTAA
Found at i:449911 original size:18 final size:18
Alignment explanation
Indices: 449890--449924 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
449880 TTTTCCTAAA
* *
449890 AATGATTAAATTGTGTAG
1 AATGACTAAATTATGTAG
449908 AATGACTAAATTATGTA
1 AATGACTAAATTATGTA
449925 ACTTAATGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.37
Consensus pattern (18 bp):
AATGACTAAATTATGTAG
Found at i:454054 original size:21 final size:21
Alignment explanation
Indices: 454005--454080 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
453995 ACAGTGCAAA
** *
454005 CTTCTACCGATACCTATGACAG
1 CTTCTACCGATACAAAT-AAAG
*
454027 -TTCTACCGATACAAGTAAAG
1 CTTCTACCGATACAAATAAAG
* * * *
454047 CTTTTACCGAAACAAATCATG
1 CTTCTACCGATACAAATAAAG
454068 CTTCTACCGATAC
1 CTTCTACCGATAC
454081 TAAAAACTCC
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 3 0.07
21 39 0.93
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (21 bp):
CTTCTACCGATACAAATAAAG
Found at i:458232 original size:65 final size:64
Alignment explanation
Indices: 458139--458266 Score: 229
Period size: 65 Copynumber: 2.0 Consensus size: 64
458129 GGGTGATGCT
*
458139 ACTGAGGGGTTTAAATTGATATAGAGGGTATTTTATATTACAAAGCCAGGGTATGTATTCCAAA
1 ACTGAGGGGTTTAAATTGATACAGAGGGTATTTTATATTACAAAGCCAGGGTATGTATTCCAAA
*
458203 ACTGAGGGGTTTACAGTTGATACAGAGGGTATTTTATATTACAAAGCCAGGGTATGTATTCCAA
1 ACTGAGGGGTTTA-AATTGATACAGAGGGTATTTTATATTACAAAGCCAGGGTATGTATTCCAA
458267 GCAATTCGAA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 13 0.21
65 48 0.79
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (64 bp):
ACTGAGGGGTTTAAATTGATACAGAGGGTATTTTATATTACAAAGCCAGGGTATGTATTCCAAA
Found at i:459171 original size:18 final size:18
Alignment explanation
Indices: 459148--459184 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
459138 AGACCGAGTG
459148 TTCCTAAGAGTTTCACAT
1 TTCCTAAGAGTTTCACAT
459166 TTCCTAAGAGTTTCACAT
1 TTCCTAAGAGTTTCACAT
459184 T
1 T
459185 GAAAAAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (18 bp):
TTCCTAAGAGTTTCACAT
Found at i:460513 original size:18 final size:18
Alignment explanation
Indices: 460486--460520 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
460476 ATTTTCCTAA
* *
460486 AATGATTAAATTGTGTAG
1 AATGACTAAATTATGTAG
460504 AATGACTAAATTATGTA
1 AATGACTAAATTATGTA
460521 ACTTAATGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.37
Consensus pattern (18 bp):
AATGACTAAATTATGTAG
Found at i:461523 original size:29 final size:30
Alignment explanation
Indices: 461464--461525 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
461454 GACCCATTCA
*
461464 TATTATTATTATTTTTAAAATATATATTTT
1 TATTATTATTATTTTTAAAATATATAATTT
* *
461494 TATTA-TATTA-TTTTAATATTTAATAATTT
1 TATTATTATTATTTTTAAAATAT-ATAATTT
461523 TAT
1 TAT
461526 ACATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 9 0.32
29 14 0.50
30 5 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
TATTATTATTATTTTTAAAATATATAATTT
Found at i:462002 original size:22 final size:23
Alignment explanation
Indices: 461971--462015 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
461961 GAGTAAAAAT
*
461971 AAATTAATTTATATA-TTTTTAA
1 AAATTAATTTATAAAGTTTTTAA
*
461993 AAATTTATTTATAAAGTTTTTAA
1 AAATTAATTTATAAAGTTTTTAA
462016 TCGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
AAATTAATTTATAAAGTTTTTAA
Found at i:463079 original size:12 final size:12
Alignment explanation
Indices: 463062--463086 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
463052 ATGATAAAAA
463062 TATTAAAAACTC
1 TATTAAAAACTC
463074 TATTAAAAACTC
1 TATTAAAAACTC
463086 T
1 T
463087 GAAATTAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (12 bp):
TATTAAAAACTC
Found at i:463855 original size:30 final size:31
Alignment explanation
Indices: 463800--463867 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
463790 GCTTTTTTTT
*
463800 TATTTTTATATAGTTATTTATTTATT-TTAA
1 TATTTTTATATAGTTATTGATTTATTATTAA
*
463830 TATTTTTATTATAGATT-TTGA-TTATTATTCA
1 TATTTTTA-TATAG-TTATTGATTTATTATTAA
463861 TATTTTT
1 TATTTTT
463868 TTTTTAATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 13 0.39
31 18 0.55
32 2 0.06
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.66
Consensus pattern (31 bp):
TATTTTTATATAGTTATTGATTTATTATTAA
Found at i:465237 original size:49 final size:49
Alignment explanation
Indices: 465184--465300 Score: 225
Period size: 49 Copynumber: 2.4 Consensus size: 49
465174 ATTTTAATTA
465184 GAATAAGGTGTTTCAACCTTACTACGTTAGTTCTATTAGTTGTTGATTG
1 GAATAAGGTGTTTCAACCTTACTACGTTAGTTCTATTAGTTGTTGATTG
465233 GAATAAGGTGTTTCAACCTTACTACGTTAGTTCTATTAGTTGTTGATTG
1 GAATAAGGTGTTTCAACCTTACTACGTTAGTTCTATTAGTTGTTGATTG
*
465282 GAATAAGGTTTTTCAACCT
1 GAATAAGGTGTTTCAACCT
465301 ATAAATAGGC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 67 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.42
Consensus pattern (49 bp):
GAATAAGGTGTTTCAACCTTACTACGTTAGTTCTATTAGTTGTTGATTG
Found at i:476913 original size:21 final size:21
Alignment explanation
Indices: 476887--476936 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
476877 GTAACAAACA
* *
476887 TCTACCGATACTAGTGATAGT
1 TCTACCGATACGAGTAATAGT
476908 TCTACCGATACGAGTAATAGT
1 TCTACCGATACGAGTAATAGT
476929 TCTACCGA
1 TCTACCGA
476937 AACAAGTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (21 bp):
TCTACCGATACGAGTAATAGT
Found at i:480459 original size:21 final size:20
Alignment explanation
Indices: 480425--480480 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
480415 AGTGTTTTTG
480425 TTTT-AATT-AGGTTTAGGCT
1 TTTTAAATTAAGGTTTAGG-T
480444 TTTTAAATTAAGGTTTAGGT
1 TTTTAAATTAAGGTTTAGGT
*
480464 TTTTAAAATTAGGGTTT
1 TTTT-AAATTAAGGTTT
480481 TAGTATTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 4 0.12
20 9 0.27
21 20 0.61
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTTAAATTAAGGTTTAGGT
Found at i:480489 original size:21 final size:21
Alignment explanation
Indices: 480429--480489 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
480419 TTTTTGTTTT
*
480429 AATT-AGGTTTAGGCT-TTTTA
1 AATTAAGGTTTAGG-TATTTAA
*
480449 AATTAAGGTTTAGGTTTTTAA
1 AATTAAGGTTTAGGTATTTAA
*
480470 AATTAGGGTTTTA-GTATTTA
1 AATTAAGG-TTTAGGTATTTA
480490 TTTTATATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 5 0.14
21 26 0.74
22 4 0.11
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.49
Consensus pattern (21 bp):
AATTAAGGTTTAGGTATTTAA
Found at i:480587 original size:8 final size:8
Alignment explanation
Indices: 480574--480627 Score: 50
Period size: 8 Copynumber: 7.6 Consensus size: 8
480564 TTTTTATTCA
480574 AATTATTT
1 AATTATTT
480582 AATTATTT
1 AATTATTT
480590 AATTATTT
1 AATTATTT
480598 --TTA--T
1 AATTATTT
*
480602 AAATATTT
1 AATTATTT
480610 -ATTATTT
1 AATTATTT
480617 -ATT-TTT
1 AATTATTT
480623 AATTA
1 AATTA
480628 AATCATAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
4 1 0.03
6 8 0.21
7 12 0.32
8 17 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
AATTATTT
Found at i:480595 original size:16 final size:15
Alignment explanation
Indices: 480561--480617 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 15
480551 TTTTTCTGTT
*
480561 TTATTT-TTATTCAAA
1 TTATTTATTATT-TAA
480576 TTATTTAATTATTTAA
1 TTATTT-ATTATTTAA
480592 TTATTT-TTA--TAA
1 TTATTTATTATTTAA
*
480604 ATATTTATTATTTA
1 TTATTTATTATTTA
480618 TTTTTAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
12 8 0.23
13 3 0.09
14 3 0.09
15 8 0.23
16 8 0.23
17 5 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTTATTATTTAA
Found at i:480597 original size:31 final size:27
Alignment explanation
Indices: 480561--480617 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 27
480551 TTTTTCTGTT
480561 TTATTTTTATTCAAATTATTTAATTATTTAA
1 TTATTTTTA-T-AAA-TATTT-ATTATTTAA
480592 TTATTTTTATAAATATTTATTATTTA
1 TTATTTTTATAAATATTTATTATTTA
480618 TTTTTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 8 0.31
28 5 0.19
29 3 0.12
30 1 0.04
31 9 0.35
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
TTATTTTTATAAATATTTATTATTTAA
Found at i:480979 original size:59 final size:59
Alignment explanation
Indices: 480887--481017 Score: 226
Period size: 59 Copynumber: 2.2 Consensus size: 59
480877 AACTAATATC
* * *
480887 TACAAAAATATTCAAATGAACTTTGTTTTTATTAAATGAAACAATATAAAAATAGTGTG
1 TACAAAAATATTCAAATGAACTTCGCTTTTATTAAATGAAACAATATAAAAATAATGTG
*
480946 TACAAAAATATTCAAATGAACTTCGCTTTTATTAAATGAAACAATATAAAAATAATGTT
1 TACAAAAATATTCAAATGAACTTCGCTTTTATTAAATGAAACAATATAAAAATAATGTG
481005 TACAAAAATATTC
1 TACAAAAATATTC
481018 GAAAATAATC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 68 1.00
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.34
Consensus pattern (59 bp):
TACAAAAATATTCAAATGAACTTCGCTTTTATTAAATGAAACAATATAAAAATAATGTG
Found at i:481454 original size:18 final size:18
Alignment explanation
Indices: 481431--481465 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
481421 TAGAAATTGG
481431 AAACATATAAGGGTTAGA
1 AAACATATAAGGGTTAGA
*
481449 AAACATATAATGGTTAG
1 AAACATATAAGGGTTAG
481466 GATACGCACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.26
Consensus pattern (18 bp):
AAACATATAAGGGTTAGA
Found at i:483076 original size:48 final size:46
Alignment explanation
Indices: 483004--483110 Score: 124
Period size: 48 Copynumber: 2.3 Consensus size: 46
482994 CACTTAAAAC
* * *
483004 ATATTAAAAAATTAATTAAATTATAAAAATAATATAAAATAATTAACTA
1 ATATTAAAAAA-TAATTAAATTATAAAAACAAAAT-AAATAA-TAAATA
* * *
483053 TTATTAAAAAATGATTACATTATAAAAACAAAATAAATAATAAATA
1 ATATTAAAAAATAATTAAATTATAAAAACAAAATAAATAATAAATA
*
483099 ATATAAAAAAAT
1 ATATTAAAAAAT
483111 TAAAATTAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
46 15 0.30
47 6 0.12
48 19 0.38
49 10 0.20
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (46 bp):
ATATTAAAAAATAATTAAATTATAAAAACAAAATAAATAATAAATA
Found at i:483280 original size:11 final size:11
Alignment explanation
Indices: 483260--483299 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
483250 AGAAATTTAA
483260 AGAG-AAATTG
1 AGAGAAAATTG
483270 AGAGAAAATTG
1 AGAGAAAATTG
* *
483281 AAATAAAATTG
1 AGAGAAAATTG
483292 AGAGAAAA
1 AGAGAAAA
483300 ATAAAAGGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 4 0.16
11 21 0.84
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (11 bp):
AGAGAAAATTG
Found at i:483299 original size:22 final size:23
Alignment explanation
Indices: 483246--483299 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
483236 TGAAAGCTTT
*
483246 AGAGAGAAATTTAAAGAGAAATTG
1 AGAGA-AAATTGAAAGAGAAATTG
*
483270 AGAGAAAATTGAAATA-AAATTG
1 AGAGAAAATTGAAAGAGAAATTG
483292 AGAGAAAA
1 AGAGAAAA
483300 ATAAAAGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 14 0.50
23 9 0.32
24 5 0.18
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (23 bp):
AGAGAAAATTGAAAGAGAAATTG
Found at i:484097 original size:9 final size:10
Alignment explanation
Indices: 484040--484097 Score: 52
Period size: 10 Copynumber: 6.2 Consensus size: 10
484030 TTTGTATCAT
484040 TTTTAA-AT-
1 TTTTAATATA
484048 TTTTAATAT-
1 TTTTAATATA
*
484057 TTTTAAAATA
1 TTTTAATATA
* *
484067 TTATAAAATA
1 TTTTAATATA
*
484077 ATTTAATATA
1 TTTTAATATA
484087 TTTTAAT-TA
1 TTTTAATATA
484096 TT
1 TT
484098 AAATACAGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
8 6 0.14
9 14 0.33
10 22 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TTTTAATATA
Found at i:496653 original size:15 final size:16
Alignment explanation
Indices: 496628--496660 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
496618 ATAAATTAAA
496628 AAAAAATTAAATGTTG
1 AAAAAATTAAATGTTG
496644 AAAAAA-TAAATGTTG
1 AAAAAATTAAATGTTG
496659 AA
1 AA
496661 TAGTTATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (16 bp):
AAAAAATTAAATGTTG
Found at i:497435 original size:29 final size:31
Alignment explanation
Indices: 497403--497469 Score: 102
Period size: 29 Copynumber: 2.2 Consensus size: 31
497393 TTACAAAATG
497403 GTCACTAAACTATTCAAAAG-TTTT-TTTAA
1 GTCACTAAACTATTCAAAAGTTTTTATTTAA
* *
497432 GTCATTGAACTATTCAAAAGTTTTTATTTAA
1 GTCACTAAACTATTCAAAAGTTTTTATTTAA
497463 GTCACTA
1 GTCACTA
497470 GATTGTTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 18 0.56
30 4 0.12
31 10 0.31
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (31 bp):
GTCACTAAACTATTCAAAAGTTTTTATTTAA
Found at i:502814 original size:21 final size:20
Alignment explanation
Indices: 502776--502815 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
502766 AAGCAACTAG
*
502776 TTTTAATGCATCAAAAGATA
1 TTTTAATGCATAAAAAGATA
502796 TTTTAATGCATGAAAAAGAT
1 TTTTAATGCAT-AAAAAGAT
502816 GAATAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (20 bp):
TTTTAATGCATAAAAAGATA
Found at i:507261 original size:12 final size:12
Alignment explanation
Indices: 507246--507271 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
507236 AATTAAAGAA
507246 ATAATAGCATTC
1 ATAATAGCATTC
507258 ATAATAGCATTC
1 ATAATAGCATTC
507270 AT
1 AT
507272 CATGATAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:511878 original size:297 final size:295
Alignment explanation
Indices: 511305--511895 Score: 765
Period size: 297 Copynumber: 2.0 Consensus size: 295
511295 TATTTTGTTA
* * * * *
511305 TCTTGATCAATTAGAAATACCCCAAGGTCGCGATTCCTAAGTAGTAACTTAGACTTTGAATATGC
1 TCTTGATCAATTACAAATACCCCAAGGTCGAGATTCCTAAGTAATAACTCAGACTTTGAATATAC
* * *
511370 CGCAAAACTTGATCTATATGCATAATAACCTATTATGCCCCTTCTTGCGTAGCCTTGACATTGTC
66 CGCAAAACTTGATCTATATGCATAATAACCCATTATGCCCCTTCTTGCATAGCCTTGACATCGTC
* * *
511435 CTTTACTGTGAAAACCCACAACAATTTACCTGTACATAACAAACACACAGGTAAGTTCATAAGAA
131 CTTCACTGTGAAAAACCACAACAATATACCTGTACATAACAAACACACAGGTAAGTTCATAAGAA
* * * * ** *
511500 CTTAGTGAGGAAAACATAGTTTACCTAAGCCATATTTTCACAATGCGATTGGCAATTTATATAGG
196 CTTAGTAAGGAAAACATAGTCTACCTAAGCCATATTTGCACAATGCGACTAACAATTTATACAGG
* *
511565 TGATCTCATCGTTCTTATCCTTTAACTTGATCTTG
261 TGATCTCATCGTTCTTATCCTTCAACTTAATCTTG
* * * *
511600 TCTTGATCTATTACAAATACCCTAAGGTCGAGATTCCTAAGTAATAGCTCAGACTTTGAATGTAC
1 TCTTGATCAATTACAAATACCCCAAGGTCGAGATTCCTAAGTAATAACTCAGACTTTGAATATAC
* * * * *
511665 CGCCAAACTTGATCTGTATGCATAATAACCCGTTATGCCCCTTGTTGGCATAGCCTTGGCATCGT
66 CGCAAAACTTGATCTATATGCATAATAACCCATTATGCCCCTTCTT-GCATAGCCTTGACATCG-
* *
511730 TCC-TCA-TG-GCAAAAAACCACAAATAATATACCTGTACATAACAAACACATAGGTAAGTTCAT
129 TCCTTCACTGTG--AAAAACCAC-AACAATATACCTGTACATAACAAACACACAGGTAAGTTCAT
* * * *** *
511792 AAGAACTTAGTAATGAAAACATCGTCTACCTGAGTTGTATTTGCATAATGCGACTAACAATTTAT
191 AAGAACTTAGTAAGGAAAACATAGTCTACCTAAGCCATATTTGCACAATGCGACTAACAATTTAT
*
511857 ACAGGTGATCTCATTGTTCTTATCCTTCAACTTAATCTT
256 ACAGGTGATCTCATCGTTCTTATCCTTCAACTTAATCTT
511896 TGGTGAATAC
Statistics
Matches: 252, Mismatches: 39, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
294 1 0.00
295 99 0.39
296 24 0.10
297 128 0.51
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (295 bp):
TCTTGATCAATTACAAATACCCCAAGGTCGAGATTCCTAAGTAATAACTCAGACTTTGAATATAC
CGCAAAACTTGATCTATATGCATAATAACCCATTATGCCCCTTCTTGCATAGCCTTGACATCGTC
CTTCACTGTGAAAAACCACAACAATATACCTGTACATAACAAACACACAGGTAAGTTCATAAGAA
CTTAGTAAGGAAAACATAGTCTACCTAAGCCATATTTGCACAATGCGACTAACAATTTATACAGG
TGATCTCATCGTTCTTATCCTTCAACTTAATCTTG
Found at i:512469 original size:27 final size:27
Alignment explanation
Indices: 512439--512627 Score: 173
Period size: 27 Copynumber: 7.0 Consensus size: 27
512429 TTCTTTCAAA
512439 ATTCACCACAAAGGCTTTCATTTCATG
1 ATTCACCACAAAGGCTTTCATTTCATG
512466 ATTCACCACAAAGGCTTTTC-TTTCATG
1 ATTCACCACAAAGGC-TTTCATTTCATG
* * * *
512493 GTTTACCATAAAGGCTTTCATTTCGTG
1 ATTCACCACAAAGGCTTTCATTTCATG
* ** * * * * *
512520 TTTCTTCATAATGGTTTTCCTTTCATA
1 ATTCACCACAAAGGCTTTCATTTCATG
* * **
512547 ATTCGCTACAAAGGCTTTCATTTTGTG
1 ATTCACCACAAAGGCTTTCATTTCATG
** * *
512574 ATTCTTCATAAAGGCTTTCCTTTCATG
1 ATTCACCACAAAGGCTTTCATTTCATG
*
512601 ATTCGCCACAAAGGCTTTCATTTCATG
1 ATTCACCACAAAGGCTTTCATTTCATG
512628 GTTCGTCATA
Statistics
Matches: 125, Mismatches: 35, Indels: 4
0.76 0.21 0.02
Matches are distributed among these distances:
26 4 0.03
27 117 0.94
28 4 0.03
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (27 bp):
ATTCACCACAAAGGCTTTCATTTCATG
Found at i:512562 original size:108 final size:107
Alignment explanation
Indices: 512427--512638 Score: 271
Period size: 108 Copynumber: 2.0 Consensus size: 107
512417 TACAAGGGAA
*
512427 TTTTCTTTCAAAATTCACCACAAAGGCTTTCATTTCATGATTCACCACAAAGGCTTTTCTTTCAT
1 TTTTCTTTCAAAATTCACCACAAAGGCTTTCATTTCATGATTCACCACAAAGGCTTTCCTTTCAT
* * * * * *
512492 GGTTTACCATAAAGGCTTTCATTTCGTGTTTCTTCATAATGG
66 GATTCACCACAAAGGCTTTCATTTCATGGTTCGTCATAATGG
* * * ** ** *
512534 TTTTCCTTTCATAATTCGCTACAAAGGCTTTCATTTTGTGATTCTTCATAAAGGCTTTCCTTTCA
1 TTTT-CTTTCAAAATTCACCACAAAGGCTTTCATTTCATGATTCACCACAAAGGCTTTCCTTTCA
*
512599 TGATTCGCCACAAAGGCTTTCATTTCATGGTTCGTCATAA
65 TGATTCACCACAAAGGCTTTCATTTCATGGTTCGTCATAA
512639 AAACTTTCCT
Statistics
Matches: 88, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
107 4 0.05
108 84 0.95
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.42
Consensus pattern (107 bp):
TTTTCTTTCAAAATTCACCACAAAGGCTTTCATTTCATGATTCACCACAAAGGCTTTCCTTTCAT
GATTCACCACAAAGGCTTTCATTTCATGGTTCGTCATAATGG
Found at i:512625 original size:81 final size:81
Alignment explanation
Indices: 512439--512626 Score: 191
Period size: 81 Copynumber: 2.3 Consensus size: 81
512429 TTCTTTCAAA
* *
512439 ATTCACCACAAAGGCTTTCATTTCATGATTCACCACAAAGGCTTTTCTTTCATGGTTTACCATAA
1 ATTCACCACAAAGGCTTTCATTTCATAATTCACCACAAAGGCTTTTCTTTCATGATTTACCATAA
*
512504 AGGCTTTCATTTCGTG
66 AGGCTTTCATTTCATG
* ** * * * * * * ** *
512520 TTTCTTCATAATGGTTTTCCTTTCATAATTCGCTACAAAGGC-TTTCATTTTGTGATTCT-TCAT
1 ATTCACCACAAAGGCTTTCATTTCATAATTCACCACAAAGGCTTTTC-TTTCATGATT-TACCAT
*
512583 AAAGGCTTTCCTTTCATG
64 AAAGGCTTTCATTTCATG
*
512601 ATTCGCCACAAAGGCTTTCATTTCAT
1 ATTCACCACAAAGGCTTTCATTTCAT
512627 GGTTCGTCAT
Statistics
Matches: 82, Mismatches: 23, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
80 4 0.05
81 77 0.94
82 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (81 bp):
ATTCACCACAAAGGCTTTCATTTCATAATTCACCACAAAGGCTTTTCTTTCATGATTTACCATAA
AGGCTTTCATTTCATG
Found at i:512646 original size:54 final size:54
Alignment explanation
Indices: 512439--512651 Score: 237
Period size: 54 Copynumber: 3.9 Consensus size: 54
512429 TTCTTTCAAA
** * *
512439 ATTCACCACAAAGGCTTTCATTTCATGATTCACCACAAAGGCTTTTCTTTCATG
1 ATTCACCACAAAGGCTTTCATTTCATGATTCTTCATAAAGGCTTTCCTTTCATG
* * * * * * * *
512493 GTTTACCATAAAGGCTTTCATTTCGTGTTTCTTCATAATGGTTTTCCTTTCATA
1 ATTCACCACAAAGGCTTTCATTTCATGATTCTTCATAAAGGCTTTCCTTTCATG
* * **
512547 ATTCGCTACAAAGGCTTTCATTTTGTGATTCTTCATAAAGGCTTTCCTTTCATG
1 ATTCACCACAAAGGCTTTCATTTCATGATTCTTCATAAAGGCTTTCCTTTCATG
* * * **
512601 ATTCGCCACAAAGGCTTTCATTTCATGGTTCGTCATAAAAACTTTCCTTTC
1 ATTCACCACAAAGGCTTTCATTTCATGATTCTTCATAAAGGCTTTCCTTTC
512652 TTGACATGTT
Statistics
Matches: 130, Mismatches: 29, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 130 1.00
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.41
Consensus pattern (54 bp):
ATTCACCACAAAGGCTTTCATTTCATGATTCTTCATAAAGGCTTTCCTTTCATG
Found at i:512651 original size:27 final size:27
Alignment explanation
Indices: 512448--512651 Score: 149
Period size: 27 Copynumber: 7.6 Consensus size: 27
512438 AATTCACCAC
* ** *
512448 AAAGGCTTTCATTTCATGATTCACCAC
1 AAAGGCTTTCCTTTCATGATTCGTCAT
* * ***
512475 AAAGGCTTTTCTTTCATGGTTTACCAT
1 AAAGGCTTTCCTTTCATGATTCGTCAT
* * * *
512502 AAAGGCTTTCATTTCGTGTTTCTTCAT
1 AAAGGCTTTCCTTTCATGATTCGTCAT
* * * *
512529 AATGGTTTTCCTTTCATAATTCG-CTAC
1 AAAGGCTTTCCTTTCATGATTCGTC-AT
* ** *
512556 AAAGGCTTTCATTTTGTGATTCTTCAT
1 AAAGGCTTTCCTTTCATGATTCGTCAT
* *
512583 AAAGGCTTTCCTTTCATGATTCGCCAC
1 AAAGGCTTTCCTTTCATGATTCGTCAT
* *
512610 AAAGGCTTTCATTTCATGGTTCGTCAT
1 AAAGGCTTTCCTTTCATGATTCGTCAT
**
512637 AAAAACTTTCCTTTC
1 AAAGGCTTTCCTTTC
512652 TTGACATGTT
Statistics
Matches: 134, Mismatches: 41, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
26 1 0.01
27 132 0.99
28 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.42
Consensus pattern (27 bp):
AAAGGCTTTCCTTTCATGATTCGTCAT
Found at i:521271 original size:14 final size:16
Alignment explanation
Indices: 521252--521287 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
521242 CTTTTGTTCG
521252 TTTCTTTT-ATT-TTT
1 TTTCTTTTCATTGTTT
521266 TTTCTTTTCATTGTTT
1 TTTCTTTTCATTGTTT
521282 TTTCTT
1 TTTCTT
521288 CGTGAGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 3 0.15
16 9 0.45
ACGTcount: A:0.06, C:0.11, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTCTTTTCATTGTTT
Found at i:531799 original size:41 final size:41
Alignment explanation
Indices: 531742--531836 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
531732 GGATTTTATT
*
531742 TTAACAAGAATTCTAGTCACCCAATTCTAACGATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
* ** *
531783 TTAACAAGTATTCTAGTTTCCCAATTCTAACAATCTCTACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
531824 TTGACAAGAATTC
1 TTAACAAGAATTC
531837 ACTACGAACA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:534027 original size:15 final size:15
Alignment explanation
Indices: 534007--534043 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
533997 TTGTAGCACT
*
534007 CTTTCTTAATGTTCC
1 CTTTCTTAATGTGCC
534022 CTTTCTTAATGTGCC
1 CTTTCTTAATGTGCC
534037 CTTTCTT
1 CTTTCTT
534044 CTTACAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.27, G:0.08, T:0.54
Consensus pattern (15 bp):
CTTTCTTAATGTGCC
Found at i:541489 original size:21 final size:21
Alignment explanation
Indices: 541463--541503 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
541453 ATATAAATAT
*
541463 TTTTCTTTTTCTTTTATTTTC
1 TTTTCTTCTTCTTTTATTTTC
*
541484 TTTTCTTCTTCTTTTTTTTT
1 TTTTCTTCTTCTTTTATTTT
541504 ATATATGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTCTTCTTCTTTTATTTTC
Found at i:547981 original size:22 final size:22
Alignment explanation
Indices: 547949--547991 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
547939 TCATTTTCGG
547949 TGGATTCAAACGTAAAATAAAT
1 TGGATTCAAACGTAAAATAAAT
*
547971 TGGATTGAAACGTAAAATAAA
1 TGGATTCAAACGTAAAATAAA
547992 CTGAGTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (22 bp):
TGGATTCAAACGTAAAATAAAT
Found at i:555081 original size:22 final size:22
Alignment explanation
Indices: 555056--555100 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
555046 TTATGTTGGT
555056 GAAAGATCAGAAGATCCTGTTA
1 GAAAGATCAGAAGATCCTGTTA
*
555078 GAAAGATCGGAAGATCCTGTTA
1 GAAAGATCAGAAGATCCTGTTA
555100 G
1 G
555101 GGTAATGACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (22 bp):
GAAAGATCAGAAGATCCTGTTA
Found at i:561394 original size:18 final size:18
Alignment explanation
Indices: 561368--561415 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
561358 ACTCAAGCTC
*
561368 CTTTGTTTGCTTTTCTTG
1 CTTTGTTTGCTTTCCTTG
*
561386 CTTTATTTGCTTTCCTTG
1 CTTTGTTTGCTTTCCTTG
*
561404 TTTTGTTTGCTT
1 CTTTGTTTGCTT
561416 GAGGACAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.02, C:0.17, G:0.15, T:0.67
Consensus pattern (18 bp):
CTTTGTTTGCTTTCCTTG
Found at i:571868 original size:59 final size:59
Alignment explanation
Indices: 571771--571892 Score: 226
Period size: 59 Copynumber: 2.1 Consensus size: 59
571761 CTGAGGCAAC
*
571771 AAAAGAAGTAATATGACTTCGAAAGTTCCTTATGAATCTTAAAGTCATTCCTAGATGAA
1 AAAAGAAGTAATATGACTTCGAAAGTTCCTTATAAATCTTAAAGTCATTCCTAGATGAA
*
571830 AAAAGAAGTAATATGACTTCGAAAGTTCCTTATAAATCTTAAAGTCGTTCCTAGATGAA
1 AAAAGAAGTAATATGACTTCGAAAGTTCCTTATAAATCTTAAAGTCATTCCTAGATGAA
571889 AAAA
1 AAAA
571893 ACTATCGCAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (59 bp):
AAAAGAAGTAATATGACTTCGAAAGTTCCTTATAAATCTTAAAGTCATTCCTAGATGAA
Found at i:576714 original size:39 final size:39
Alignment explanation
Indices: 576671--576780 Score: 134
Period size: 39 Copynumber: 2.9 Consensus size: 39
576661 GATATTTCTT
* *
576671 TGCAGTGTTTACAATATCACTGCTAGTTCGGTATTGTAC
1 TGCAGTGTTTACAATATCACTGCCAGTTCAGTATTGTAC
* * * * *
576710 TGCAGTGTTTATAGTCTCACTTCCAGTTCAGTATTGTAT
1 TGCAGTGTTTACAATATCACTGCCAGTTCAGTATTGTAC
*
576749 TGCAGTGTTTAC-A-ATCACTGCCAGTCCAGTAT
1 TGCAGTGTTTACAATATCACTGCCAGTTCAGTAT
576781 GTTGATAATT
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
37 16 0.27
39 43 0.73
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (39 bp):
TGCAGTGTTTACAATATCACTGCCAGTTCAGTATTGTAC
Found at i:585997 original size:20 final size:20
Alignment explanation
Indices: 585974--586016 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
585964 AGGAAAAGAA
585974 AAGAATAAAAAAGTTTTCTT
1 AAGAATAAAAAAGTTTTCTT
585994 AAGAATAAAAAAGTTTTCTT
1 AAGAATAAAAAAGTTTTCTT
586014 AAG
1 AAG
586017 GGGAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.33
Consensus pattern (20 bp):
AAGAATAAAAAAGTTTTCTT
Found at i:591136 original size:41 final size:41
Alignment explanation
Indices: 591070--591166 Score: 108
Period size: 41 Copynumber: 2.4 Consensus size: 41
591060 TGAAATAATT
* * * *
591070 AAAACGCTTTTAGGTGGAAGTATTTTCAACGAATTTG-CAGGA
1 AAAACGCTTTAAGCTAGAAGCATTTTCAACGAA-TTGACA-GA
*
591112 AAAA-GCTTTAAGCTAGAAGCATTTTCAACGTATTGACAGA
1 AAAACGCTTTAAGCTAGAAGCATTTTCAACGAATTGACAGA
*
591152 AAAACGCTTTCAGCT
1 AAAACGCTTTAAGCT
591167 GGAAATGCTT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
40 9 0.19
41 34 0.72
42 4 0.09
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (41 bp):
AAAACGCTTTAAGCTAGAAGCATTTTCAACGAATTGACAGA
Found at i:593124 original size:21 final size:21
Alignment explanation
Indices: 593091--593133 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
593081 AAATGATATC
* *
593091 TAGTCCTTTAAAC-TAAGCTTT
1 TAGTCATTAAAACGTAAG-TTT
593112 TAGTCATTAAAACGTAAGTTT
1 TAGTCATTAAAACGTAAGTTT
593133 T
1 T
593134 GAATAAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.42
Consensus pattern (21 bp):
TAGTCATTAAAACGTAAGTTT
Found at i:602872 original size:10 final size:10
Alignment explanation
Indices: 602857--602895 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
602847 CTTTTTCTTC
602857 TTTTCTTTTT
1 TTTTCTTTTT
*
602867 TTTTCTTTCT
1 TTTTCTTTTT
*
602877 TTTTC-TTAT
1 TTTTCTTTTT
602886 TTTTCTTTTT
1 TTTTCTTTTT
602896 CAAGTGACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:602872 original size:15 final size:15
Alignment explanation
Indices: 602848--602895 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
602838 TAGCAAACAC
*
602848 TTTTTCTTCTTTTCT
1 TTTTTTTTCTTTTCT
602863 TTTTTTTTC-TTTCT
1 TTTTTTTTCTTTTCT
*
602877 TTTTCTTAT-TTTTCT
1 TTTT-TTTTCTTTTCT
602892 TTTT
1 TTTT
602896 CAAGTGACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 9 0.31
15 20 0.69
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTTTCTTTTCT
Found at i:602876 original size:19 final size:19
Alignment explanation
Indices: 602848--602893 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
602838 TAGCAAACAC
*
602848 TTTTTC-TTC-TTTTCTTTT
1 TTTTTCTTTCTTTTTC-TTA
602866 TTTTTCTTTCTTTTTCTTA
1 TTTTTCTTTCTTTTTCTTA
602885 TTTTTCTTT
1 TTTTTCTTT
602894 TTCAAGTGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTCTTTCTTTTTCTTA
Found at i:602896 original size:15 final size:14
Alignment explanation
Indices: 602847--602896 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
602837 ATAGCAAACA
*
602847 CTTTTTCTTCTTTT
1 CTTTTTCTTTTTTT
602861 CTTTTT-TTTTCTTT
1 CTTTTTCTTTT-TTT
602875 CTTTTTCTTATTTTT
1 CTTTTTCTT-TTTTT
602890 CTTTTTC
1 CTTTTTC
602897 AAGTGACTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 3 0.09
14 15 0.47
15 12 0.38
16 2 0.06
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (14 bp):
CTTTTTCTTTTTTT
Found at i:603982 original size:3 final size:3
Alignment explanation
Indices: 603916--603968 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
603906 AGCAGGGTCT
*
603916 TTC TTC -TC TTGC -TC TTC TTC TTC TTC TTC TTC TTC TTT TTCC TTC
1 TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC
*
603961 TCC TTC TT
1 TTC TTC TT
603969 TTGACCTTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 3 0.07
3 36 0.86
4 3 0.07
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:618896 original size:55 final size:56
Alignment explanation
Indices: 618812--618932 Score: 163
Period size: 55 Copynumber: 2.2 Consensus size: 56
618802 GGCACTTGCT
* * **
618812 CGTGTACCTCAAAACAGTATACACACACGGACTGGCACACGTCCGTGTGTCT-ACC
1 CGTGTGCCTCAAAACAATATACACACACGGACTGGCACACACCCGTGTGTCTGACC
* * * *
618867 CGTGTGCCTCAAAACAATATACCCACACGGTCTGGCACACACCCGTGTGTTTGGCC
1 CGTGTGCCTCAAAACAATATACACACACGGACTGGCACACACCCGTGTGTCTGACC
618923 CGTGTGCCTC
1 CGTGTGCCTC
618933 CTGCAACTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
55 45 0.79
56 12 0.21
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.21
Consensus pattern (56 bp):
CGTGTGCCTCAAAACAATATACACACACGGACTGGCACACACCCGTGTGTCTGACC
Found at i:620410 original size:29 final size:29
Alignment explanation
Indices: 620368--620425 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
620358 AGAGGTTCAC
*
620368 GTATCAGAAGTTAAATTGCATTTTACTCT
1 GTATCAGAAATTAAATTGCATTTTACTCT
620397 GTATCAGAAATTAAATTGCATTTTACTCT
1 GTATCAGAAATTAAATTGCATTTTACTCT
620426 TTCTACTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (29 bp):
GTATCAGAAATTAAATTGCATTTTACTCT
Found at i:620629 original size:17 final size:20
Alignment explanation
Indices: 620589--620631 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 20
620579 TGAACTAATT
*
620589 TTTAATAATAATAAATATTT
1 TTTAATAATAATAAATATTA
620609 TTTAATAA-AAT-AAT-TTA
1 TTTAATAATAATAAATATTA
620626 TTTAAT
1 TTTAAT
620632 TTTTTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 3 0.14
19 3 0.14
20 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAATAATAATAAATATTA
Found at i:620841 original size:3 final size:3
Alignment explanation
Indices: 620827--620867 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
620817 ACGAAAACAA
* *
620827 AAT AAA AAT AAT AAT AAT AAT AAT AAA AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
620868 CAATTACGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:624540 original size:23 final size:23
Alignment explanation
Indices: 624508--624747 Score: 336
Period size: 23 Copynumber: 10.4 Consensus size: 23
624498 TTTTTATATC
624508 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
624531 TGTGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* *
624554 TGTGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
624577 TATGCTTAAGTATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
624600 TATGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
**
624623 CGTGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
**
624646 TATGCAAAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
624669 TATGCTTAAATGTTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
624692 TGTGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* *
624715 TATGATTAAATATTAATGTGTTT
1 TATGCTTAAATATTAATGTGATT
*
624738 TGTGCTTAAA
1 TATGCTTAAA
624748 GAATTAAGTT
Statistics
Matches: 189, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 189 1.00
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (23 bp):
TATGCTTAAATATTAATGTGATT
Found at i:624866 original size:36 final size:36
Alignment explanation
Indices: 624817--624893 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
624807 TGATGGTTGT
*
624817 TGTGAAAGTAAATATGTGAGTATGTTCTTCATGCCA
1 TGTGAAAGAAAATATGTGAGTATGTTCTTCATGCCA
* *
624853 TGTGATAGAAAATATGTGGGTATGTTCTTCATGCCA
1 TGTGAAAGAAAATATGTGAGTATGTTCTTCATGCCA
624889 TGTGA
1 TGTGA
624894 CTGGTTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.36
Consensus pattern (36 bp):
TGTGAAAGAAAATATGTGAGTATGTTCTTCATGCCA
Found at i:625724 original size:16 final size:17
Alignment explanation
Indices: 625705--625739 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
625695 ATTTGAGGTC
625705 TGTTTTATA-TGATAAA
1 TGTTTTATAGTGATAAA
625721 TGTTTTATAGTTGATAAA
1 TGTTTTATAG-TGATAAA
625739 T
1 T
625740 TGATGTAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (17 bp):
TGTTTTATAGTGATAAA
Found at i:627047 original size:34 final size:34
Alignment explanation
Indices: 627004--627071 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
626994 TAATACGACC
*
627004 ATGTCCCCTCCTACGCTATTGTGGCAATTGAAGT
1 ATGTCCCCTCCTACGCTATTGTGGAAATTGAAGT
*
627038 ATGTCCCCTCCTACTCTATTGTGGAAATTGAAGT
1 ATGTCCCCTCCTACGCTATTGTGGAAATTGAAGT
627072 TTCCTTTTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (34 bp):
ATGTCCCCTCCTACGCTATTGTGGAAATTGAAGT
Found at i:635275 original size:14 final size:14
Alignment explanation
Indices: 635258--635306 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
635248 GCTAGTAGTC
635258 ATTTCTTTTTGCCA
1 ATTTCTTTTTGCCA
*
635272 ATTTC--GTT-CCA
1 ATTTCTTTTTGCCA
*
635283 ATTTCTTTATGCCA
1 ATTTCTTTTTGCCA
635297 ATTTCATTTT
1 ATTTC-TTTT
635307 AATTTCTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
11 8 0.30
12 2 0.07
13 1 0.04
14 13 0.48
15 3 0.11
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.55
Consensus pattern (14 bp):
ATTTCTTTTTGCCA
Found at i:635287 original size:25 final size:25
Alignment explanation
Indices: 635258--635315 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
635248 GCTAGTAGTC
* *
635258 ATTTCTTTTTGCCAATTTCGTTCCA
1 ATTTCTTTATGCCAATTTCATTCCA
**
635283 ATTTCTTTATGCCAATTTCATTTTA
1 ATTTCTTTATGCCAATTTCATTCCA
635308 ATTTCTTT
1 ATTTCTTT
635316 CCATTTCCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.05, T:0.57
Consensus pattern (25 bp):
ATTTCTTTATGCCAATTTCATTCCA
Found at i:650012 original size:28 final size:29
Alignment explanation
Indices: 649953--650012 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
649943 AATTTACATC
*
649953 TTTATAATTTTTAAAGGATTAAATCAAATT
1 TTTATAATTTTTAAA-GAGTAAATCAAATT
*
649983 TTTATTATTTTTAAA-AGTAAAT-ATAATT
1 TTTATAATTTTTAAAGAGTAAATCA-AATT
650011 TT
1 TT
650013 ACTATCATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.04
28 12 0.44
30 14 0.52
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (29 bp):
TTTATAATTTTTAAAGAGTAAATCAAATT
Done.