Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000494.1 Hibiscus syriacus cultivar Beakdansim tig00000941_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: 66685
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1035 original size:20 final size:20
Alignment explanation
Indices: 972--1038 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
962 GTTTCCAAAT
972 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
* *
992 TCACAACGCGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
* *
1012 TCGCAACGCGAATTTGTAAT
1 TCGCAACGCGAATATGTAAA
1032 TCGCAAC
1 TCGCAAC
1039 ACAACAGTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:1056 original size:40 final size:41
Alignment explanation
Indices: 968--1058 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 41
958 CTCAGTTTCC
* *
968 AAATTCGCAACGCGAATATGTAAATCACAACGCGAATCTGT
1 AAATTCGCAACGCGAATATGTAAATCACAACACGAATCAGT
* * *
1009 AAA-TCGCAACGCGAATTTGTAATTCGCAACAC-AA-CAGTT
1 AAATTCGCAACGCGAATATGTAAATCACAACACGAATCAG-T
1048 AAATTCGCAAC
1 AAATTCGCAAC
1059 ACATAAGTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
38 2 0.05
39 6 0.14
40 32 0.74
41 3 0.07
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (41 bp):
AAATTCGCAACGCGAATATGTAAATCACAACACGAATCAGT
Found at i:1071 original size:20 final size:20
Alignment explanation
Indices: 1029--1073 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1019 GCGAATTTGT
*
1029 AATTCGCAACACAACAGTTA
1 AATTCGCAACACAACAGTCA
1049 AATTCGCAACACATA-AGTCA
1 AATTCGCAACACA-ACAGTCA
1069 AATTC
1 AATTC
1074 ACAAAGTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.22
Consensus pattern (20 bp):
AATTCGCAACACAACAGTCA
Found at i:1668 original size:19 final size:20
Alignment explanation
Indices: 1646--1698 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
1636 AAATCGCAAC
1646 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
*
1665 GCGATTTTCA-TTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
1684 GCGATTTTAAGTTTC
1 GCGATTTTAAGTTTC
1699 AGAAACTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 26 0.84
20 5 0.16
ACGTcount: A:0.13, C:0.17, G:0.23, T:0.47
Consensus pattern (20 bp):
GCGATTTTAAGTTTCGCGTT
Found at i:3273 original size:21 final size:21
Alignment explanation
Indices: 3233--3273 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3223 AGGGGAGTTA
* *
3233 CGTGATGAGGTCAATGCTTTG
1 CGTGAGGAGGTCAATACTTTG
*
3254 CGTGAGGAGGTCAGTACTTT
1 CGTGAGGAGGTCAATACTTT
3274 ACTTGAAGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.15, G:0.34, T:0.32
Consensus pattern (21 bp):
CGTGAGGAGGTCAATACTTTG
Found at i:3738 original size:42 final size:42
Alignment explanation
Indices: 3673--3776 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
3663 CTTGTCATAG
* * *
3673 TTCAAGAGGC-CTCTCCTATCATTCAAAATGCCCCTATCATCC
1 TTCAAGAGGCAC-CTCCCACCATTCAAAAGGCCCCTATCATCC
* * *
3715 TTCAAGAGGCACCTCCCACCATTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCACCTCCCACCATTCAAAAGGCCCCTATCATCC
*
3757 TTCAAGAGGTACCTCCCACC
1 TTCAAGAGGCACCTCCCACC
3777 GTTTGGGATC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 53 0.98
43 1 0.02
ACGTcount: A:0.25, C:0.38, G:0.14, T:0.23
Consensus pattern (42 bp):
TTCAAGAGGCACCTCCCACCATTCAAAAGGCCCCTATCATCC
Found at i:3760 original size:21 final size:21
Alignment explanation
Indices: 3665--3765 Score: 71
Period size: 21 Copynumber: 4.8 Consensus size: 21
3655 CTGATTCACT
*
3665 TGTCAT-AGTTCAAGAGGCCTC
1 TGTCATCA-TTCAAGAGGCCCC
* * *
3686 T-CCTATCATTCAAAATGCCCC
1 TGTC-ATCATTCAAGAGGCCCC
* * *
3707 TATCATCCTTCAAGAGGCACC
1 TGTCATCATTCAAGAGGCCCC
** *
3728 TCCCACCATTCAAGAGGCCCC
1 TGTCATCATTCAAGAGGCCCC
*
3749 TGTCATCGTTCAAGAGG
1 TGTCATCATTCAAGAGG
3766 TACCTCCCAC
Statistics
Matches: 59, Mismatches: 18, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
20 1 0.02
21 56 0.95
22 2 0.03
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.25
Consensus pattern (21 bp):
TGTCATCATTCAAGAGGCCCC
Found at i:3779 original size:21 final size:21
Alignment explanation
Indices: 3715--3779 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
3705 CCTATCATCC
*
3715 TTCAAGAGGCACCTCCCACCA
1 TTCAAGAGGCACCTCCCACCG
* ** *
3736 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCACCTCCCACCG
*
3757 TTCAAGAGGTACCTCCCACCG
1 TTCAAGAGGCACCTCCCACCG
3778 TT
1 TT
3780 TGGGATCCCG
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.22
Consensus pattern (21 bp):
TTCAAGAGGCACCTCCCACCG
Found at i:5180 original size:64 final size:64
Alignment explanation
Indices: 5107--5255 Score: 253
Period size: 64 Copynumber: 2.3 Consensus size: 64
5097 AAATTGATGT
5107 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTGTTTAATTG
* * ***
5171 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTGTTTAATTG
5235 ATTTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
5256 GTTTTAAATT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.52
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTGTTTAATTG
Found at i:5345 original size:20 final size:20
Alignment explanation
Indices: 5314--5418 Score: 129
Period size: 20 Copynumber: 5.2 Consensus size: 20
5304 AAGGTACACT
5314 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*** **
5334 TTCGCGTTGCGATGGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
5354 TTCGCAACGTGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
5374 TTCGCAACACGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
* *
5394 TTCACAACACGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
5414 TTCGC
1 TTCGC
5419 GTTGCGATTT
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:5369 original size:40 final size:40
Alignment explanation
Indices: 5314--5426 Score: 145
Period size: 40 Copynumber: 2.8 Consensus size: 40
5304 AAGGTACACT
*
5314 TTCGCAACGCGAAAGTCAAATTCGCGTTGCGATGGTCAAA
1 TTCGCAACGCGAAAGTCAAATTCGCGTTGCGATAGTCAAA
* **** *
5354 TTCGCAACGTGAAAGTCAAATTCGCAACACGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAATTCGCGTTGCGATAGTCAAA
* *
5394 TTCACAACACGAAAGTCAAATTCGCGTTGCGAT
1 TTCGCAACGCGAAAGTCAAATTCGCGTTGCGAT
5427 TTCCCGTTTC
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (40 bp):
TTCGCAACGCGAAAGTCAAATTCGCGTTGCGATAGTCAAA
Found at i:7940 original size:24 final size:24
Alignment explanation
Indices: 7903--8002 Score: 155
Period size: 24 Copynumber: 4.2 Consensus size: 24
7893 GAAACATCAA
* *
7903 CAAAATCCGAGTATTGACCAATAT
1 CAAAGTCCGGGTATTGACCAATAT
*
7927 CAAAGTCCAGGTATTGACCAATAT
1 CAAAGTCCGGGTATTGACCAATAT
*
7951 CAAAGTCCGGGTATTGACTAATAT
1 CAAAGTCCGGGTATTGACCAATAT
*
7975 CAAAGTCTGGGTATTGACCAATAT
1 CAAAGTCCGGGTATTGACCAATAT
7999 CAAA
1 CAAA
8003 TTTCAAATAC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (24 bp):
CAAAGTCCGGGTATTGACCAATAT
Found at i:8017 original size:48 final size:48
Alignment explanation
Indices: 7917--8018 Score: 123
Period size: 48 Copynumber: 2.1 Consensus size: 48
7907 ATCCGAGTAT
* *** *
7917 TGACCAATATCAAAGTCCAGGTATTGACCAATATCAAAGTCCGGGTAT
1 TGACTAATATCAAAGTCCAGGTATTGACCAATATCAAAGTCCAAATAC
** * *
7965 TGACTAATATCAAAGTCTGGGTATTGACCAATATCAAATTTCAAATAC
1 TGACTAATATCAAAGTCCAGGTATTGACCAATATCAAAGTCCAAATAC
8013 TGACTA
1 TGACTA
8019 GTACTCACAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (48 bp):
TGACTAATATCAAAGTCCAGGTATTGACCAATATCAAAGTCCAAATAC
Found at i:8977 original size:20 final size:20
Alignment explanation
Indices: 8949--9007 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 20
8939 AACTAAAACA
*
8949 TGTTACGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
*
8969 TGTTGCG-AATTCGAAAACT-G
1 TGTTGCGAAATT--AAAATTCG
* *
8989 AGTTGCGAAAATAAAATTC
1 TGTTGCGAAATTAAAATTC
9008 CCGTTGTGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
19 9 0.30
20 13 0.43
21 8 0.27
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.31
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:8998 original size:40 final size:40
Alignment explanation
Indices: 8954--9060 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 40
8944 AAACATGTTA
*
8954 CGAAATTAAAATTCGTGTTGCGAATTC-GAAAACTGAGTTG
1 CGAAATTAAAATTCGTGTTGTGAATTCAGAAAAC-GAGTTG
* ** *
8994 CGAAAATAAAATTCCCGTTGTGAATTCAGAAATCGAGTTG
1 CGAAATTAAAATTCGTGTTGTGAATTCAGAAAACGAGTTG
* * *
9034 GGAATTTGAAATTCAGTGTTGTGAATT
1 CGAAATTAAAATTC-GTGTTGTGAATT
9061 TGGAAAATCA
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
40 39 0.72
41 15 0.28
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (40 bp):
CGAAATTAAAATTCGTGTTGTGAATTCAGAAAACGAGTTG
Found at i:9142 original size:21 final size:21
Alignment explanation
Indices: 9118--9160 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9108 TTGCGTTACA
*
9118 AATTTGGAAAATCGCAACGCG
1 AATTCGGAAAATCGCAACGCG
* *
9139 AATTCGGAAAATTGCAATGCG
1 AATTCGGAAAATCGCAACGCG
9160 A
1 A
9161 TTTACATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (21 bp):
AATTCGGAAAATCGCAACGCG
Found at i:24318 original size:19 final size:20
Alignment explanation
Indices: 24284--24322 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
24274 ATATCCATTC
24284 TCCAAAAACTTGTAGTTTAT
1 TCCAAAAACTTGTAGTTTAT
24304 TCCAAAAACTT-TAGTTTAT
1 TCCAAAAACTTGTAGTTTAT
24323 AAAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (20 bp):
TCCAAAAACTTGTAGTTTAT
Found at i:24329 original size:19 final size:20
Alignment explanation
Indices: 24287--24330 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
24277 TCCATTCTCC
***
24287 AAAAACTTGTAGTTTATTCC
1 AAAAACTTGTAGTTTATAAA
24307 AAAAACTT-TAGTTTATAAA
1 AAAAACTTGTAGTTTATAAA
24326 AAAAA
1 AAAAA
24331 TACTTTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (20 bp):
AAAAACTTGTAGTTTATAAA
Found at i:32676 original size:21 final size:21
Alignment explanation
Indices: 32650--32700 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
32640 ATTTACCGTG
*
32650 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGACGCT
*
32671 ATTGCGGTCGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGACGCT
32692 ATTGCGGCC
1 ATTGCGGCC
32701 ATCGTGGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.08, C:0.31, G:0.39, T:0.22
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGACGCT
Found at i:40787 original size:21 final size:21
Alignment explanation
Indices: 40757--40801 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
40747 ATATTTTAAA
*
40757 AAAATTTATT-TTTATATTATT
1 AAAATATATTATTTA-ATTATT
40778 AAAATATATTATTTAATTATT
1 AAAATATATTATTTAATTATT
40799 AAA
1 AAA
40802 TATTATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAATATATTATTTAATTATT
Found at i:44595 original size:37 final size:37
Alignment explanation
Indices: 44538--44729 Score: 141
Period size: 37 Copynumber: 5.6 Consensus size: 37
44528 CAAAGATTAT
*
44538 TTTCAAGAAAAAC-TATCTCAAGAGAGACAAATCTTTG
1 TTTCAAGAGAAACATA-CTCAAGAGAGACAAATCTTTG
44575 TTTCAAGAGAAACATACTC-A-A-AGAC---T-TTTG
1 TTTCAAGAGAAACATACTCAAGAGAGACAAATCTTTG
* *
44605 TTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAACTTTG
1 TTTCAAGAGAAACAT-ACTCAAGAGAGACAAATCTTTG
*
44642 TTTCAA-AGGAAACAGACTCAA-A-A-AC---T-TTTG
1 TTTCAAGA-GAAACATACTCAAGAGAGACAAATCTTTG
* * * *
44672 TTTCAATAGAAA-TTGTCTCAAGAGAGACAAAACTTTG
1 TTTCAAGAGAAACAT-ACTCAAGAGAGACAAATCTTTG
*
44709 TTTCAAGAGAAACAAACTCAA
1 TTTCAAGAGAAACATACTCAA
44730 AGATTTTTAT
Statistics
Matches: 120, Mismatches: 14, Indels: 42
0.68 0.08 0.24
Matches are distributed among these distances:
29 1 0.01
30 39 0.32
31 4 0.03
32 2 0.02
33 6 0.05
34 6 0.05
35 2 0.02
36 3 0.03
37 55 0.46
38 2 0.02
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.27
Consensus pattern (37 bp):
TTTCAAGAGAAACATACTCAAGAGAGACAAATCTTTG
Found at i:44625 original size:30 final size:30
Alignment explanation
Indices: 44571--44692 Score: 86
Period size: 30 Copynumber: 3.8 Consensus size: 30
44561 GAGACAAATC
44571 TTTGTTTCAAGAGAAACAT-ACTCAAAGACT
1 TTTGTTTCAAGAGAAAC-TGACTCAAAGACT
* *
44601 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
1 TTTGTTTCAAGAGAAACTGACTC-A-A-AGAC----T
* *
44638 TTTGTTTCAA-AGGAAACAGACTCAAAAACT
1 TTTGTTTCAAGA-GAAACTGACTCAAAGACT
* * *
44668 TTTGTTTCAATAGAAATTGTCTCAA
1 TTTGTTTCAAGAGAAACTGACTCAA
44693 GAGAGACAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 20
0.72 0.09 0.20
Matches are distributed among these distances:
29 1 0.01
30 40 0.55
31 2 0.03
32 1 0.01
33 4 0.05
34 3 0.04
35 1 0.01
36 2 0.03
37 19 0.26
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (30 bp):
TTTGTTTCAAGAGAAACTGACTCAAAGACT
Found at i:44786 original size:65 final size:67
Alignment explanation
Indices: 44344--44905 Score: 654
Period size: 65 Copynumber: 8.6 Consensus size: 67
44334 GGGATAATGG
* * * *
44344 TTTCAAGACAAACCGTCTCAAGAGAGATC-AAAC-TTGTTTCAAGGGAAACAACCTCAATG-TTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGA-CAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTT
*
44406 GTA
65 TTA
* * * * *
44409 TTTAAAGGGAAACTGTCTCAAGAGAGACAAAAC-TTGTTTAAAGGGAAACAAACTAAAAGATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
*
44473 TG
66 TA
* * *
44475 TTTCAAGAGAAACTGTCTTAAGGGAGACAAAAC-TTGTTTCAAGGGAAAC-AACTCAAAGA-TTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
44537 T-
66 TA
* * * * * *
44538 TTTCAAGAAAAACTATCTCAAGAGAGACAAATCTTTGTTTCAAGAGAAACATACTCAAAGACTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
*
44603 TG
66 TA
* * * *
44605 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACAGACTCAAAAACTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
*
44670 TG
66 TA
* * *
44672 TTTCAATAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAAACTCAAAGATTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
44737 TA
66 TA
* * *
44739 TTTCAA-A-ATAA-TGTCTCAAGAGAGATAAAACTTTATTTCAAGGGAAACATACTCAAAGATTT
1 TTTCAAGAGA-AACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTT
44801 TTA
65 TTA
* *
44804 TTTCAA-A-ATAA-TGTCTCAAAAGAGACAAAACTTTGTTTCAAAGGAAACAAACTCAAAGA-TT
1 TTTCAAGAGA-AACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTT
44865 TT-
65 TTA
* *
44867 TTTCAAGAGAAATTGTCTCAAGAGAGATAAAA-TTTGTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
44906 TGAGTAAAAA
Statistics
Matches: 437, Mismatches: 50, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
63 34 0.08
64 33 0.08
65 190 0.43
66 55 0.13
67 125 0.29
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (67 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTTT
TA
Found at i:46414 original size:25 final size:23
Alignment explanation
Indices: 46362--46463 Score: 71
Period size: 25 Copynumber: 4.1 Consensus size: 23
46352 TTCTTGTCCC
* *
46362 TTTTTCTTTGTTTTTCTTTGCTTAT
1 TTTTTCTTTGTTTTTTTTTTC-T-T
46387 TTTTTCTTTGTTTTTTTATTTCCTT
1 TTTTTCTTTGTTTTTTT-TTT-CTT
*
46412 TTTTTATTTTCGTTTTTTTGTTT-TT
1 TTTTT-CTTT-GTTTTTTT-TTTCTT
* *
46437 TCTTTCTTTATTTTTTATCTTTCTT
1 TTTTTCTTTGTTTTTT-T-TTTCTT
46462 TT
1 TT
46464 CTCTTCGCTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
23 6 0.10
24 7 0.11
25 31 0.50
26 6 0.10
27 12 0.19
ACGTcount: A:0.05, C:0.11, G:0.05, T:0.79
Consensus pattern (23 bp):
TTTTTCTTTGTTTTTTTTTTCTT
Found at i:46422 original size:14 final size:14
Alignment explanation
Indices: 46397--46450 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
46387 TTTTTCTTTG
46397 TTTTTTTA-TTTCC
1 TTTTTTTATTTTCC
*
46410 TTTTTTTATTTTCG
1 TTTTTTTATTTTCC
* *
46424 TTTTTTTGTTTTTTC
1 TTTTTTT-ATTTTCC
*
46439 TTTCTTTATTTT
1 TTTTTTTATTTT
46451 TTATCTTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
13 8 0.24
14 15 0.45
15 10 0.30
ACGTcount: A:0.06, C:0.09, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTTTTATTTTCC
Found at i:49017 original size:20 final size:21
Alignment explanation
Indices: 48972--49017 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
48962 ATAACATTTT
* *
48972 TTTTAAAACAATTAAATATTA
1 TTTTAAAACAATCAAATATGA
*
48993 TTTTAAAA-AATCAATTATGA
1 TTTTAAAACAATCAAATATGA
49013 TTTTA
1 TTTTA
49018 TTTGAAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTTAAAACAATCAAATATGA
Found at i:51858 original size:131 final size:131
Alignment explanation
Indices: 51646--51910 Score: 347
Period size: 131 Copynumber: 2.0 Consensus size: 131
51636 CTTTGGGGAT
*
51646 GATGATAACACGATTCCTACTCAATGAGGACGACTGGTTATCTAGAGGTGAAGCAGCTCCTACGT
1 GATGATAACACGATTCCTACTCAATGAGGACGACTGATTATCTAGAGGTGAAGCAGCTCCTACGT
* * *
51711 GATAAAGAGAAATGGTCGGGGGATGACACGGTTCCTATG-TGATGAGGATGACT-GGCCATCTTT
66 GATAAAGAGAAATGGTCGGGGGATGACACGGTTCCTACGAT-ATGAAGATGA-TAGACCATCTTT
51774 AGG
129 AGG
* * * * * *
51777 GATGATAACACGATTCTTACAT-GATGAGGATGACTGATTATCTAGGGGTGACGCGGCTCCTACG
1 GATGATAACACGATTCCTAC-TCAATGAGGACGACTGATTATCTAGAGGTGAAGCAGCTCCTACG
* * ** *
51841 TGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGATATGAAGATGATAGACCATCTTTA
65 TGATAAAGAGAAATGGTCGGGGGATGACACGGTTCCTACGATATGAAGATGATAGACCATCTTTA
51906 GG
130 GG
51908 GAT
1 GAT
51911 AATGGTTTCA
Statistics
Matches: 116, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
130 1 0.01
131 113 0.97
132 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (131 bp):
GATGATAACACGATTCCTACTCAATGAGGACGACTGATTATCTAGAGGTGAAGCAGCTCCTACGT
GATAAAGAGAAATGGTCGGGGGATGACACGGTTCCTACGATATGAAGATGATAGACCATCTTTAG
G
Found at i:52489 original size:3 final size:3
Alignment explanation
Indices: 52481--52530 Score: 82
Period size: 3 Copynumber: 16.3 Consensus size: 3
52471 AATTATAAGA
*
52481 AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
52527 AAT A
1 AAT A
52531 TTTTTAAGAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:54900 original size:2 final size:2
Alignment explanation
Indices: 54893--54927 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
54883 ATAAGAATAC
54893 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54928 GCACCAATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56614 original size:3 final size:3
Alignment explanation
Indices: 56606--56647 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
56596 TGTAAAAATG
56606 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
56648 GCGTAATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:57225 original size:138 final size:138
Alignment explanation
Indices: 56968--57355 Score: 555
Period size: 138 Copynumber: 2.8 Consensus size: 138
56958 ATTTGTAGAC
* * * *
56968 AACACAGTTCCTACGTGATGAGGAAATCTGGTTATCTAAGGGTGACGA-TGTTCCTACGTGATGA
1 AACACAGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGAC-ACTGCTCCTACATGATGA
* * * * *
57032 GGAGATCTGGTCGGTGGATGACATTGTTCTTACGTAATGAGGACGTCTAGTCATCTTTAGGGATA
65 GGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACATCTAGACATCTTTAAGGATA
57097 AATGGAGAT
130 AATGGAGAT
* * * * *
57106 AGCACGGTTCCTACGTGATGAGGAAGTATGGTTATCTAAGGATGACACTACTCCTACATGATGAA
1 AACACAGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACACTGCTCCTACATGATGAG
*
57171 GAGATCTGGTCGGTGGATGACATTATTCCTACGTGATGAGGACATCTAGACATCTTTAAGGATAA
66 GAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACATCTAGACATCTTTAAGGATAA
57236 ATGGAGAT
131 ATGGAGAT
* * *
57244 AACATAGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACGCTGCTGCTA-AGTGATGA
1 AACACAGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACACTGCTCCTACA-TGATGA
* * *
57308 GGAGATCTGGTCGGGGGATGATATTGTTCCTACGTGATGAGGAGATCT
65 GGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACATCT
57356 GGTCGGGGGA
Statistics
Matches: 221, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
137 2 0.01
138 219 0.99
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (138 bp):
AACACAGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACACTGCTCCTACATGATGAG
GAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACATCTAGACATCTTTAAGGATAA
ATGGAGAT
Found at i:57345 original size:40 final size:40
Alignment explanation
Indices: 57301--57390 Score: 171
Period size: 40 Copynumber: 2.2 Consensus size: 40
57291 CTGCTGCTAA
*
57301 GTGATGAGGAGATCTGGTCGGGGGATGATATTGTTCCTAC
1 GTGATGAGGAGATCTGGTCGGGGGATGACATTGTTCCTAC
57341 GTGATGAGGAGATCTGGTCGGGGGATGACATTGTTCCTAC
1 GTGATGAGGAGATCTGGTCGGGGGATGACATTGTTCCTAC
57381 GTGATGAGGA
1 GTGATGAGGA
57391 CGTCTAGTCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.21, C:0.12, G:0.39, T:0.28
Consensus pattern (40 bp):
GTGATGAGGAGATCTGGTCGGGGGATGACATTGTTCCTAC
Found at i:57574 original size:65 final size:65
Alignment explanation
Indices: 57418--57729 Score: 412
Period size: 66 Copynumber: 4.8 Consensus size: 65
57408 GGATAATTTT
* * * * * * *
57418 TTTCAAGACAAACTGTCTCAAGAGAGTCACAATTTGTTTTAAGGGAAACAATCTCAATTGTTTAT
1 TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAA-AGTTTAT
57483 G
65 G
* * *
57484 TTTCTATAGAAACTGTCTCAGGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTATG
1 TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTATG
*
57549 TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGATGTAT
1 TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAG-TTTAT
57614 G
65 G
**
57615 TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTCGTG
1 TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTATG
* * * *
57680 TCTT--AAGGAAGACTGTCTCAAGTGAGACGAAATTTGTTTTTAAGAGAAAC
1 T-TTCAAAAGAA-ACTGTCTCAAGAGAGACAAAATTTG-TTTCAAGAGAAAC
57730 TGTCTCAAGC
Statistics
Matches: 222, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
64 5 0.02
65 90 0.41
66 127 0.57
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (65 bp):
TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTATG
Found at i:57652 original size:131 final size:131
Alignment explanation
Indices: 57418--57729 Score: 423
Period size: 131 Copynumber: 2.4 Consensus size: 131
57408 GGATAATTTT
* * * * * * *
57418 TTTCAAGACAAACTGTCTCAAGAGAGTCACAATTTGTTTTAAGGGAAACAATCTCAATTGTTTAT
1 TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACAATCTCAATAGTGTAT
* * * *
57483 GTTTCTATAGAAACTGTCTCAGGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTAT
66 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTCAT
57548 G
131 G
*
57549 TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAA-AGATGTA
1 TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACAATCTCAATAG-TGTA
*
57613 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTCG
65 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTCA
57678 TG
130 TG
* * *
57680 TCTT--AAGGAAGACTGTCTCAAGTGAGACGAAATTTGTTTTTAAGAGAAAC
1 T-TTCAAAAGAA-ACTGTCTCAAGAGAGACAAAATTTG-TTTTAAGAGAAAC
57730 TGTCTCAAGC
Statistics
Matches: 160, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
130 6 0.04
131 140 0.88
132 14 0.09
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (131 bp):
TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACAATCTCAATAGTGTAT
GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTCAT
G
Found at i:57732 original size:37 final size:37
Alignment explanation
Indices: 57682--57780 Score: 130
Period size: 37 Copynumber: 2.7 Consensus size: 37
57672 AGTTCGTGTC
*
57682 TTAAG-GAAGACTGTCTCAAGTGAGACGAAATTTGTTT
1 TTAAGAGAA-ACTGTCTCAAGTGAGACAAAATTTGTTT
*
57719 TTAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTT
1 TTAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTT
**
57756 TT-AGAGAAAACAATCTCAAGTGAGA
1 TTAAGAG-AAACTGTCTCAAGTGAGA
57781 TCAATTTTGT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
36 4 0.07
37 48 0.87
38 3 0.05
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (37 bp):
TTAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTT
Found at i:57790 original size:37 final size:37
Alignment explanation
Indices: 57695--57810 Score: 121
Period size: 37 Copynumber: 3.2 Consensus size: 37
57685 AGGAAGACTG
* **
57695 TCTCAAGTGAGACGAAATTTGTTTTTAAGAGAAACTG
1 TCTCAAGTGAGACAAAATTTGTTTTTAAGAGAAACAA
*
57732 TCTCAAGCGAGACAAAATTTGTTTTT-AGAGAAAACAA
1 TCTCAAGTGAGACAAAATTTGTTTTTAAGAG-AAACAA
* * *
57769 TCTCAAGTGAGATC-AATTTTG-TTTCAAGTGAAACAA
1 TCTCAAGTGAGA-CAAAATTTGTTTTTAAGAGAAACAA
*
57805 TTTCAA
1 TCTCAA
57811 AATCTGTGAA
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
36 18 0.27
37 48 0.72
38 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (37 bp):
TCTCAAGTGAGACAAAATTTGTTTTTAAGAGAAACAA
Found at i:61273 original size:6 final size:6
Alignment explanation
Indices: 61243--61288 Score: 56
Period size: 6 Copynumber: 7.2 Consensus size: 6
61233 AATGAATGTC
*
61243 ATGCATA ATGCAAA GATGTAA ATGCAA ATGCAA ATGCAA ATGCAA A
1 ATGCA-A ATGC-AA -ATGCAA ATGCAA ATGCAA ATGCAA ATGCAA A
61289 AATGTTGATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 24 0.69
7 7 0.20
8 4 0.11
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (6 bp):
ATGCAA
Done.