Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006665.1 Hibiscus syriacus cultivar Beakdansim tig00016508_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: 76264
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:488 original size:18 final size:19
Alignment explanation
Indices: 452--492 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
442 TTCTCAAACA
452 AAGTCCTAAGACTCTGTTCC
1 AAGTCCTAAGAC-CTGTTCC
472 AAGTCCTAAGA-CTGTTCC
1 AAGTCCTAAGACCTGTTCC
490 AAG
1 AAG
493 CCATAGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (19 bp):
AAGTCCTAAGACCTGTTCC
Found at i:8844 original size:29 final size:29
Alignment explanation
Indices: 8809--8890 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
8799 AAGCTAAATT
* *
8809 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
8838 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
8867 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
8891 GTTAGCTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:13607 original size:29 final size:29
Alignment explanation
Indices: 13572--13653 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
13562 AAACTAAATT
* *
13572 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
13601 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
13630 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
13654 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:17607 original size:60 final size:60
Alignment explanation
Indices: 17532--17646 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
17522 TATGACTCTT
* * *
17532 ATTTTAAATTGGTCCT-ATAATTTTTAAATA-TTCTAATTTCACCCCTAAACTATGATTATC
1 ATTTTAAATTAGTCCTCA-AATTTTTAAACATTTC-AATTTCACCCCTAAAATATGATTATC
* *
17592 ATTTTAGATTAGTCCTCAAATTTTTAAACATTTCAATTTCATCCCTAAAATATGA
1 ATTTTAAATTAGTCCTCAAATTTTTAAACATTTCAATTTCACCCCTAAAATATGA
17647 CTTGTTTTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 44 0.92
61 4 0.08
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (60 bp):
ATTTTAAATTAGTCCTCAAATTTTTAAACATTTCAATTTCACCCCTAAAATATGATTATC
Found at i:18596 original size:60 final size:60
Alignment explanation
Indices: 18531--18643 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
18521 GTCAGACGAC
* *
18531 CATTTTGTAACTTTTAATAGTCGA-GAGACTCAACAAAGCAACT-TCCTATAGTCATGGGAT
1 CATTTTATAACTTTTAATAGTC-ATGAGACTCAACAAAACAA-TATCCTATAGTCATGGGAT
* *
18591 CATTTTATAACTTTTAATAGTCATGGGACTCAGCAAAACAATATCCTATAGTC
1 CATTTTATAACTTTTAATAGTCATGAGACTCAACAAAACAATATCCTATAGTC
18644 GGGAGACCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAGTCATGAGACTCAACAAAACAATATCCTATAGTCATGGGAT
Found at i:18655 original size:60 final size:60
Alignment explanation
Indices: 18518--18655 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 60
18508 AACATAATGA
** * *
18518 ATAGTCAGACGACCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACTTCCT
1 ATAGTCAGGGGACCATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAACAACTTCCT
* * * *
18578 ATAGTCATGGGATCATTTTATAACTTTTAATAGTC-ATGGGACTCAGCAAAACAA-TATCCT
1 ATAGTCAGGGGACCATTTTATAACTTTTAATAGTCGA-GAGACTCAACAAAACAACT-TCCT
18638 ATAGTC-GGGAGACCATTT
1 ATAGTCAGGG-GACCATTT
18656 GTGTACTTCG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
59 4 0.06
60 61 0.94
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (60 bp):
ATAGTCAGGGGACCATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAACAACTTCCT
Found at i:20663 original size:2 final size:2
Alignment explanation
Indices: 20656--20680 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20646 CTGTACAATA
20656 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20681 ACAGTAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20892 original size:266 final size:263
Alignment explanation
Indices: 20407--20947 Score: 985
Period size: 264 Copynumber: 2.0 Consensus size: 263
20397 TTTTCAAAAC
*
20407 TATATATATAACAGTAATCAAATCACACACGCATATATGGTAAAGGAAAGTTATAATTAAAAGTT
1 TATATATATAACAGTAATCAAATCACACAAGCATATATGGTAAAGGAAAGTTATAATTAAAAGTT
20472 AATTTCTAACTGTTCTAGTTTTATTGCATAGCGACTGTCTTAAAAAGACTTTGGATCGTGCTTTC
66 AATTTCTAACTGTTCTAGTTTTATTGCATAGCGACTGTCTTAAAAAGACTTTGGATCGTGCTTTC
*
20537 CTCTTCCTTTTTTCATCTATAGGAAATCCGTAAAGTGTTGATCGTGTAGGTTGAATATGACTATA
131 CTCTTCCTTTTTTCATCTATAGGAAATCCGTAAAGTGTTGATCGTGTAGGTAGAATATGACTATA
*
20602 ACAATTATCATGTGATATATCATCTCATACATGGTCAAATAAAGCTGTACAATAATATATATATA
196 ACAATTATCATGTGATAAATCATCTCATACAT-GTCAAATAAAGCTGTACAATAATATATATATA
20667 TATA
260 TATA
* *
20671 TATATATATAACAGTAATCAAATCACACAAGCATATATGGTAAAGGGATGTTATAATTAAAAGTT
1 TATATATATAACAGTAATCAAATCACACAAGCATATATGGTAAAGGAAAGTTATAATTAAAAGTT
20736 AATTTCTAACTGTTCTAGTTTTATTGCATAGCGACTAGTCTTAAAAAGACTCTTTGGATCGTGCT
66 AATTTCTAACTGTTCTAGTTTTATTGCATAGCGACT-GTCTTAAAAAGA--CTTTGGATCGTGCT
20801 TTCCTCTTCC-TTTTTCATCTATAGGAAATCCGTAAAGTGTTGATCGTGTAGGTAGAATATGACT
128 TTCCTCTTCCTTTTTTCATCTATAGGAAATCCGTAAAGTGTTGATCGTGTAGGTAGAATATGACT
*
20865 ATAACAATTATCATGTGATAAATCATCTCATATATGTCAAATAAAGCTGTACAATAATATATATA
193 ATAACAATTATCATGTGATAAATCATCTCATACATGTCAAATAAAGCTGTACAATAATATATATA
20930 TATATA
258 TATATA
20936 TATATATATAAC
1 TATATATATAAC
20948 GTGCGGTATC
Statistics
Matches: 268, Mismatches: 6, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
264 98 0.37
265 60 0.22
266 86 0.32
267 24 0.09
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (263 bp):
TATATATATAACAGTAATCAAATCACACAAGCATATATGGTAAAGGAAAGTTATAATTAAAAGTT
AATTTCTAACTGTTCTAGTTTTATTGCATAGCGACTGTCTTAAAAAGACTTTGGATCGTGCTTTC
CTCTTCCTTTTTTCATCTATAGGAAATCCGTAAAGTGTTGATCGTGTAGGTAGAATATGACTATA
ACAATTATCATGTGATAAATCATCTCATACATGTCAAATAAAGCTGTACAATAATATATATATAT
ATA
Found at i:20928 original size:2 final size:2
Alignment explanation
Indices: 20921--20945 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20911 CTGTACAATA
20921 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20946 ACGTGCGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21060 original size:14 final size:15
Alignment explanation
Indices: 21036--21068 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
21026 TGCGTTTGGT
21036 TTACGGAATGTAAGA
1 TTACGGAATGTAAGA
21051 TTAC-GAATGTAAGA
1 TTACGGAATGTAAGA
21065 TTAC
1 TTAC
21069 CAGTGGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (15 bp):
TTACGGAATGTAAGA
Found at i:22541 original size:12 final size:12
Alignment explanation
Indices: 22526--22571 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
22516 CGGTTTTTTT
*
22526 ACCGGATAAAAA
1 ACCGGTTAAAAA
22538 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
22553 ACCGGTTAAAAA
1 ACCGGTTAAAAA
22565 ACCGGTT
1 ACCGGTT
22572 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:22553 original size:15 final size:13
Alignment explanation
Indices: 22532--22572 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
22522 TTTTACCGGA
22532 TAAAAAACCGGTT
1 TAAAAAACCGGTT
22545 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
22559 TAAAAAACCGGTT
1 TAAAAAACCGGTT
22572 T
1 T
22573 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:24888 original size:21 final size:21
Alignment explanation
Indices: 24864--24903 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
24854 TTTATTTTAT
24864 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
24885 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
24904 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:24951 original size:33 final size:33
Alignment explanation
Indices: 24898--24996 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
24888 TTTGTTTCAA
24898 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
24930 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * * *
24963 TTATCAAACTTGAAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
24996 T
1 T
24997 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 11 0.18
33 51 0.82
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:25025 original size:13 final size:13
Alignment explanation
Indices: 24982--25036 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
24972 TTGAAAGTAT
24982 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
24995 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
25009 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
25022 TTAAGTATTTGAA
1 TTAAGTATTTCAA
25035 TT
1 TT
25037 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:25457 original size:15 final size:15
Alignment explanation
Indices: 25432--25487 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
25422 ATCTGGAATA
*
25432 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
25447 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
25462 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
25479 TTAAAACCG
1 TTAAAACCG
25488 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:25496 original size:21 final size:18
Alignment explanation
Indices: 25451--25484 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25441 GTTTTTTTAT
25451 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
25468 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
25485 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:25603 original size:15 final size:17
Alignment explanation
Indices: 25577--25608 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
25567 TTCTATGGGA
25577 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
25593 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
25609 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:39018 original size:42 final size:42
Alignment explanation
Indices: 38933--39037 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
38923 CATAGCTTCA
* * * *
38933 TTTTAAAATGAACACCACTAAATTACCAAACTATTGTAGCGT
1 TTTTAAAATAAACGCCACTAAAATACCAAACTATTGGAGCGT
*
38975 TTTTAAAATAAACGCCATTAAAATACCAAACTATTGCGA-CGT
1 TTTTAAAATAAACGCCACTAAAATACCAAACTATTG-GAGCGT
**
39017 TTCCAAAA-AAACGCCACTAAA
1 TTTTAAAATAAACGCCACTAAA
39038 GTATGACTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 12 0.22
42 41 0.76
43 1 0.02
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.27
Consensus pattern (42 bp):
TTTTAAAATAAACGCCACTAAAATACCAAACTATTGGAGCGT
Found at i:40708 original size:35 final size:35
Alignment explanation
Indices: 40662--40736 Score: 125
Period size: 35 Copynumber: 2.1 Consensus size: 35
40652 ACACTGAGGA
40662 GTGTATCGATACCCTCAAAACATCGAATG-TCATTT
1 GTGTATCGATACCCTCAAAACATCGAATGCT-ATTT
*
40697 GTGTATCGATACCCTCAAAACATCGAGTGCTATTT
1 GTGTATCGATACCCTCAAAACATCGAATGCTATTT
40732 GTGTA
1 GTGTA
40737 ACACCCCCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 37 0.97
36 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (35 bp):
GTGTATCGATACCCTCAAAACATCGAATGCTATTT
Found at i:41614 original size:18 final size:18
Alignment explanation
Indices: 41572--41614 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
41562 TGTTCCATAG
* *
41572 GACCACTATGTCCTGAAG
1 GACCACTATGTCCCGAAA
41590 GACCACTATGTCCCGAAA
1 GACCACTATGTCCCGAAA
*
41608 GATCACT
1 GACCACT
41615 TCTTAAGAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (18 bp):
GACCACTATGTCCCGAAA
Found at i:44229 original size:22 final size:22
Alignment explanation
Indices: 44212--44278 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
44202 CTCGTATAAA
44212 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
44234 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
44256 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
44278 T
1 T
44279 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:44516 original size:30 final size:30
Alignment explanation
Indices: 44481--44557 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
44471 CCGTAGTTCA
* * *
44481 TATCACGTAGTCATATTATTTCCATACCTT
1 TATCACATAGTCATATCATTTACATACCTT
44511 TATCACATAGTCATATCATTTACATACCTT
1 TATCACATAGTCATATCATTTACATACCTT
44541 TATCACATAGCTCATAT
1 TATCACATAG-TCATAT
44558 AACTTTTCTG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.40
Consensus pattern (30 bp):
TATCACATAGTCATATCATTTACATACCTT
Found at i:44641 original size:29 final size:29
Alignment explanation
Indices: 44571--44642 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
44561 TTTTCTGCAT
* * *
44571 ATTCATGTCATGCAATACATATCATATGA
1 ATTCATGTCATGTAATACATATAATATAA
*
44600 ATTCATGTCATGTAATACATTTAATATAA
1 ATTCATGTCATGTAATACATATAATATAA
44629 ATTCATGTCATGTA
1 ATTCATGTCATGTA
44643 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATAA
Found at i:45093 original size:66 final size:67
Alignment explanation
Indices: 44960--45118 Score: 214
Period size: 67 Copynumber: 2.4 Consensus size: 67
44950 GAATTCGTTC
* *
44960 CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGATGAGGGGGTATCGG
1 CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAGGGGGTATCGG
45025 TT
66 TT
* * * *
45027 CCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTTGAGGGGGTATCGG
1 CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAGGGGGTATCGG
45091 TT
66 TT
* *
45093 -CCCCTTGAATGGGTACCGATTCCCCT
1 CCCCCCTG--GGGGTACCGATTCCCCT
45119 AACCCAGAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 6 0.07
66 19 0.23
67 57 0.70
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (67 bp):
CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAGGGGGTATCGG
TT
Found at i:51164 original size:23 final size:23
Alignment explanation
Indices: 51138--51189 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
51128 CACCACAACT
*
51138 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
*
51161 CGTAGAATTGCACCGAAGTG-CC
1 CGTAGAAATGCACCGAAGTGCCC
51183 CGTAGAA
1 CGTAGAA
51190 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:51187 original size:22 final size:23
Alignment explanation
Indices: 51146--51191 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
51136 CTCGTATAAA
51146 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
51169 TGCACCGAAGTG-CCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
51191 T
1 T
51192 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:51429 original size:30 final size:30
Alignment explanation
Indices: 51394--51470 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
51384 CCGTAGTTCA
* * *
51394 TATCACGTAGTCATATTATTTCCATACCTT
1 TATCACATAGTCATATCATTTACATACCTT
51424 TATCACATAGTCATATCATTTACATACCTT
1 TATCACATAGTCATATCATTTACATACCTT
51454 TATCACATAGCTCATAT
1 TATCACATAG-TCATAT
51471 AACTTTTCTG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.40
Consensus pattern (30 bp):
TATCACATAGTCATATCATTTACATACCTT
Found at i:51506 original size:14 final size:14
Alignment explanation
Indices: 51487--51532 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
51477 TCTGCATATT
51487 CATATCATGTAATA
1 CATATCATGTAATA
* *
51501 CATATCATATGAATT
1 CATATCATGT-AATA
*
51516 CATGTCATGTAATA
1 CATATCATGTAATA
51530 CAT
1 CAT
51533 TTAATATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (14 bp):
CATATCATGTAATA
Found at i:51516 original size:29 final size:29
Alignment explanation
Indices: 51484--51555 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
51474 TTTTCTGCAT
* * *
51484 ATTCATATCATGTAATACATATCATATGA
1 ATTCATGTCATGTAATACATATAATATAA
*
51513 ATTCATGTCATGTAATACATTTAATATAA
1 ATTCATGTCATGTAATACATATAATATAA
51542 ATTCATGTCATGTA
1 ATTCATGTCATGTA
51556 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.40
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATAA
Found at i:52020 original size:67 final size:67
Alignment explanation
Indices: 51859--52031 Score: 215
Period size: 67 Copynumber: 2.6 Consensus size: 67
51849 TTTTTCTCAT
* * *
51859 GGGGGAATCCGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
51924 TGA
65 TGA
* * * * *
51927 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
51991 GA
66 GA
* *
51993 GGGGGTATCGGTT-CCCCTTGAATGGGTATCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTATCGATTCCCCT
52032 AACCCAGAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 6 0.07
66 19 0.21
67 56 0.61
68 11 0.12
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:54157 original size:2 final size:2
Alignment explanation
Indices: 54150--54194 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
54140 TTGAGAAACA
54150 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54192 AT A
1 AT A
54195 GTTTTCATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54692 original size:22 final size:23
Alignment explanation
Indices: 54653--54714 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
54643 TTCCCCTGTG
54653 GGGGGAATCGGTTCCCCTTCA-AA
1 GGGGGAATCGGTT-CCCTTCATAA
*
54676 GGGGGAATCGGTTCCC-TCATGA
1 GGGGGAATCGGTTCCCTTCATAA
* *
54698 GGGGGGATCGATTCCCT
1 GGGGGAATCGGTTCCCT
54715 CTGCACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.09
22 18 0.53
23 13 0.38
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.23
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCTTCATAA
Found at i:54702 original size:23 final size:21
Alignment explanation
Indices: 54652--54715 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 21
54642 ATTCCCCTGT
54652 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
*
54675 AGGGGGAATCGGTTCCCTCATGA
1 GGGGGGAATCGGTTCCCTCA--A
*
54698 GGGGGG-ATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
54716 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 3 0.08
22 14 0.39
23 19 0.53
ACGTcount: A:0.17, C:0.25, G:0.36, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:62206 original size:21 final size:21
Alignment explanation
Indices: 62169--62217 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
62159 GTCGAGGGTC
** * *
62169 TATGTGGTCCTTTGGGATAAT
1 TATGTGGTCCTCCGGGACAAA
62190 TATGTGGTCCTCCGGGACAAA
1 TATGTGGTCCTCCGGGACAAA
62211 TATGTGG
1 TATGTGG
62218 CACTTCGATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.35
Consensus pattern (21 bp):
TATGTGGTCCTCCGGGACAAA
Found at i:63075 original size:12 final size:12
Alignment explanation
Indices: 63058--63088 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
63048 CAAGTTTAGT
63058 TTATTTCCGTCA
1 TTATTTCCGTCA
63070 TTATTTCCGTCA
1 TTATTTCCGTCA
63082 TTATTTC
1 TTATTTC
63089 TTTCTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.23, G:0.06, T:0.55
Consensus pattern (12 bp):
TTATTTCCGTCA
Found at i:66792 original size:114 final size:116
Alignment explanation
Indices: 66578--66785 Score: 305
Period size: 114 Copynumber: 1.8 Consensus size: 116
66568 ATTTATATAA
* *
66578 TAAAATAAAATGATAGAATCTAATTATATTGTGTAAAATATTTTAATTTTATATAAATTTAACAT
1 TAAAATAAAATGATAGAATCTAATTATATAGTGTAAAATATTTTAATTTTACATAAATTTAACAT
* *
66643 CGTTGAATTAATAGAGATAAACAATTGAGAAAAAAAATGAAAGATATTCAT
66 CGTTGAATTAATAGAAATAAACAACTGAGAAAAAAAATGAAAGATATTCAT
* * *
66694 TAAAATAAAATGATAGGATCTAATTAT-TAG-GTAAAATATTTTAATTTTACATAGATTTAATAT
1 TAAAATAAAATGATAGAATCTAATTATATAGTGTAAAATATTTTAATTTTACATAAATTTAACAT
* * *
66757 -TTTGAATTACTAGAAATAAATAACTGAGA
66 CGTTGAATTAATAGAAATAAACAACTGAGA
66786 TTAAAAATAA
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
113 24 0.29
114 30 0.37
115 2 0.02
116 26 0.32
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.37
Consensus pattern (116 bp):
TAAAATAAAATGATAGAATCTAATTATATAGTGTAAAATATTTTAATTTTACATAAATTTAACAT
CGTTGAATTAATAGAAATAAACAACTGAGAAAAAAAATGAAAGATATTCAT
Found at i:66792 original size:116 final size:118
Alignment explanation
Indices: 66578--66817 Score: 301
Period size: 114 Copynumber: 2.0 Consensus size: 118
66568 ATTTATATAA
* *
66578 TAAAATAAAATGATAGAATCTAATTATATTGTGTAAAATATTTTAATTTTATATAAATTTAACAT
1 TAAAATAAAATGATAGAATCTAATTATATAGTGTAAAATATTTTAATTTTACATAAATTTAACAT
* *
66643 CGTTGAATTAATAGAGATAAACAATTGAG-AAA-AAAAATGAAAGATATTCAT
66 CGTTGAATTAATAGAAATAAACAACTGAGAAAATAAAAATGAAAGATATTCAT
* * *
66694 TAAAATAAAATGATAGGATCTAATTAT-TAG-GTAAAATATTTTAATTTTACATAGATTTAATAT
1 TAAAATAAAATGATAGAATCTAATTATATAGTGTAAAATATTTTAATTTTACATAAATTTAACAT
* * * * *
66757 -TTTGAATTACTAGAAATAAATAACTGAGATTAAAAATAAAAATGTAAGATATTTAT
66 CGTTGAATTAATAGAAATAAACAACTGAG----AAAATAAAAATGAAAGATATTCAT
66813 TAAAA
1 TAAAA
66818 AAATTAATCT
Statistics
Matches: 106, Mismatches: 12, Indels: 9
0.83 0.09 0.07
Matches are distributed among these distances:
113 23 0.22
114 30 0.28
115 2 0.02
116 26 0.25
118 3 0.03
119 22 0.21
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (118 bp):
TAAAATAAAATGATAGAATCTAATTATATAGTGTAAAATATTTTAATTTTACATAAATTTAACAT
CGTTGAATTAATAGAAATAAACAACTGAGAAAATAAAAATGAAAGATATTCAT
Found at i:66817 original size:114 final size:116
Alignment explanation
Indices: 66578--66799 Score: 290
Period size: 113 Copynumber: 1.9 Consensus size: 116
66568 ATTTATATAA
* *
66578 TAAAATAAAATGATAGAATCTAATTATATTGTGTAAAATATTTTAATTTTATATAAATTTAACAT
1 TAAAATAAAATGATAGAATCTAATTATATAGTGTAAAATATTTTAATTTTACATAAATTTAACAT
* * * *
66643 CGTTGAATTAATAGAGATAAACAATTGAGAAAAAAAATGAAAGATATTCAT
66 CGTTGAATTAATAGAAATAAACAACTGAGAAAAAAAATGAAAAATATACAT
* * *
66694 TAAAATAAAATGATAGGATCTAATTAT-TAG-GTAAAATATTTTAATTTTACATAGATTTAATAT
1 TAAAATAAAATGATAGAATCTAATTATATAGTGTAAAATATTTTAATTTTACATAAATTTAACAT
* * * **
66757 -TTTGAATTACTAGAAATAAATAACTGAGATTAAAAAT-AAAAAT
66 CGTTGAATTAATAGAAATAAACAACTGAGAAAAAAAATGAAAAAT
66800 GTAAGATATT
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
112 5 0.05
113 30 0.32
114 30 0.32
115 2 0.02
116 26 0.28
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (116 bp):
TAAAATAAAATGATAGAATCTAATTATATAGTGTAAAATATTTTAATTTTACATAAATTTAACAT
CGTTGAATTAATAGAAATAAACAACTGAGAAAAAAAATGAAAAATATACAT
Found at i:68864 original size:2 final size:2
Alignment explanation
Indices: 68859--68905 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
68849 CTCTTTTTTC
68859 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
68901 TA TA T
1 TA TA T
68906 GTGGTAGGGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:69141 original size:33 final size:30
Alignment explanation
Indices: 69087--69147 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 30
69077 AAAAATTCTA
*
69087 TAAATATTACCCATATTATTAAATTTTATC
1 TAAATATTACCCATATAATTAAATTTTATC
*
69117 TAAATATTATCCATCATATAATTAACTTTTA
1 TAAATATTA-CC--CATATAATTAAATTTTA
69148 AATATGATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 9 0.35
31 2 0.08
33 15 0.58
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (30 bp):
TAAATATTACCCATATAATTAAATTTTATC
Found at i:71667 original size:25 final size:25
Alignment explanation
Indices: 71619--71667 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
71609 AATATTAGAC
71619 AACATAAATGATTATTTTTTTTATAA
1 AACATAAATGA-TATTTTTTTTATAA
71645 AACATAAATGA-ATTTTTTATTAT
1 AACATAAATGATATTTTTT-TTAT
71668 TATGTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.32
25 4 0.18
26 11 0.50
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (25 bp):
AACATAAATGATATTTTTTTTATAA
Found at i:74346 original size:20 final size:20
Alignment explanation
Indices: 74321--74361 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
74311 TATGTTAACT
74321 ATCGCAACCTCAATCAAACC
1 ATCGCAACCTCAATCAAACC
74341 ATCGCAACCTCAATCAAACC
1 ATCGCAACCTCAATCAAACC
74361 A
1 A
74362 GTTCAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.39, G:0.05, T:0.15
Consensus pattern (20 bp):
ATCGCAACCTCAATCAAACC
Done.