Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009638.1 Hibiscus syriacus cultivar Beakdansim tig00117047_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: 894601
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:832574 original size:2 final size:2
Alignment explanation
Indices: 832563--832600 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
832553 CTTTACACTC
832563 AT AT -T 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 AT AT A
832601 ATGGAGACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:832782 original size:30 final size:31
Alignment explanation
Indices: 832733--832821 Score: 121
Period size: 30 Copynumber: 3.0 Consensus size: 31
832723 GTTTTTTTGG
* *
832733 AAAATAG-TTTATGTAAAATAGATTA-ATTA
1 AAAATAGTTTTACGTAAAATAAATTACATTA
*
832762 AAAATAGTTTTACATAAAATAAATTACATTA
1 AAAATAGTTTTACGTAAAATAAATTACATTA
*
832793 AAAAT-GTTTTACGTAAAATGAATTACATT
1 AAAATAGTTTTACGTAAAATAAATTACATT
832822 TTCTGGAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
29 7 0.13
30 37 0.70
31 9 0.17
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (31 bp):
AAAATAGTTTTACGTAAAATAAATTACATTA
Found at i:833112 original size:19 final size:19
Alignment explanation
Indices: 833088--833126 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
833078 TATTAATATT
833088 TTATTA-ATATAATACTAAA
1 TTATTATAT-TAATACTAAA
*
833107 TTATTATATTAATATTAAA
1 TTATTATATTAATACTAAA
833126 T
1 T
833127 GCATAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATTATATTAATACTAAA
Found at i:833209 original size:15 final size:15
Alignment explanation
Indices: 833158--833210 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
833148 TATTAATAAT
833158 TTAATAATA-TTATA
1 TTAATAATACTTATA
* * *
833172 TTTATAAAACTAATA
1 TTAATAATACTTATA
*
833187 GATAATAATACTTATA
1 -TTAATAATACTTATA
833203 TTAATAAT
1 TTAATAAT
833211 TTATTACATA
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
14 7 0.24
15 11 0.38
16 11 0.38
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (15 bp):
TTAATAATACTTATA
Found at i:833306 original size:17 final size:19
Alignment explanation
Indices: 833284--833331 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
833274 ATTAATATAA
833284 TATTAAAA-A-TATAAGAT
1 TATTAAAATATTATAAGAT
*
833301 TATTAAAATTATTATAATAT
1 TATTAAAA-TATTATAAGAT
833321 TATT-AAATATT
1 TATTAAAATATT
833332 TTAATAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 8 0.30
18 4 0.15
19 4 0.15
20 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TATTAAAATATTATAAGAT
Found at i:833590 original size:42 final size:40
Alignment explanation
Indices: 833511--833628 Score: 139
Period size: 41 Copynumber: 2.9 Consensus size: 40
833501 TTACATTGGA
*
833511 AAAACTAATTACAACTACCAAACACTAGAAAACAT-TTTCCG
1 AAAACTAATTACAACTACCAAACACT-GAAAA-ATATTTTCG
833552 TAAAACTAATTACAACTACCAAACACTGAAAAATATTTTCG
1 -AAAACTAATTACAACTACCAAACACTGAAAAATATTTTCG
* * * * *
833593 AAAAATATTTTCCAACTATCAAACACAGAAAAATAT
1 AAAACTA-ATTACAACTACCAAACACTGAAAAATAT
833629 GAAAGACATT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
40 8 0.12
41 34 0.50
42 26 0.38
ACGTcount: A:0.51, C:0.20, G:0.04, T:0.25
Consensus pattern (40 bp):
AAAACTAATTACAACTACCAAACACTGAAAAATATTTTCG
Found at i:833597 original size:13 final size:13
Alignment explanation
Indices: 833579--833604 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
833569 ACCAAACACT
833579 GAAAAATATTTTC
1 GAAAAATATTTTC
833592 GAAAAATATTTTC
1 GAAAAATATTTTC
833605 CAACTATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
GAAAAATATTTTC
Found at i:834815 original size:38 final size:39
Alignment explanation
Indices: 834768--834843 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
834758 AATTAAAAAC
* * *
834768 TTTTGAACGAT-GGTACTGAAATGAAACAAAAACTAAAG
1 TTTTGAACGATGGGTAATAAAAAGAAACAAAAACTAAAG
* *
834806 TTTTTAACGATGGGTAATAAAAAGAAACAAACACTAAA
1 TTTTGAACGATGGGTAATAAAAAGAAACAAAAACTAAA
834844 CTTTAGGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
38 10 0.31
39 22 0.69
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.24
Consensus pattern (39 bp):
TTTTGAACGATGGGTAATAAAAAGAAACAAAAACTAAAG
Found at i:836030 original size:15 final size:15
Alignment explanation
Indices: 836010--836047 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
836000 TAACATAAAA
*
836010 TAAAATGTTGGAGGC
1 TAAAATGTTGGAAGC
836025 TAAAATGTTGGAAGC
1 TAAAATGTTGGAAGC
*
836040 TACAATGT
1 TAAAATGT
836048 CCTAGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.29
Consensus pattern (15 bp):
TAAAATGTTGGAAGC
Found at i:837072 original size:19 final size:18
Alignment explanation
Indices: 837048--837083 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
837038 TTTTAAAAAA
837048 ATTATTTAAAATTTTAAAT
1 ATTA-TTAAAATTTTAAAT
*
837067 ATTATTATAATTTTAAA
1 ATTATTAAAATTTTAAA
837084 AAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATTAAAATTTTAAAT
Found at i:842524 original size:23 final size:24
Alignment explanation
Indices: 842482--842528 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
842472 CGATTTTTTC
842482 GGTTCGGTTCGAGTTTTTCGGTTT
1 GGTTCGGTTCGAGTTTTTCGGTTT
842506 GGTTCGGTTCG-GTTTTTCGGTTT
1 GGTTCGGTTCGAGTTTTTCGGTTT
842529 TTCAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.02, C:0.13, G:0.34, T:0.51
Consensus pattern (24 bp):
GGTTCGGTTCGAGTTTTTCGGTTT
Found at i:844991 original size:60 final size:59
Alignment explanation
Indices: 844927--845093 Score: 160
Period size: 60 Copynumber: 2.8 Consensus size: 59
844917 ACTATAATTT
*
844927 TCATTTTAAATTGATCCTTAAACTTTTGACTATTTTAATTTCATACCCAAACTATGACTC
1 TCATTTTAAACTGATCCTTAAACTTTTGACTATTTTAATTTCAT-CCCAAACTATGACTC
* * * * *
844987 TCATTCTAAACT-AGTCCTTAAACTTTTGAAC-ATTCTAATTACATCCATAAACTATGGCTC
1 TCATTTTAAACTGA-TCCTTAAACTTTTG-ACTATTTTAATTTCATCC-CAAACTATGACTC
* * * * * *
845047 TC-TTTCTAAAGTGGTCCATAAACTTTTTAATATTTCAATTTCATCCC
1 TCATTT-TAAACTGATCCTTAAACTTTTGACTATTTTAATTTCATCCC
845094 CAAAATCATC
Statistics
Matches: 85, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
59 6 0.07
60 77 0.91
61 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (59 bp):
TCATTTTAAACTGATCCTTAAACTTTTGACTATTTTAATTTCATCCCAAACTATGACTC
Found at i:846606 original size:20 final size:20
Alignment explanation
Indices: 846583--846635 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
846573 CATGAGTCTA
*
846583 GGACCATGGGCCACACAGGG
1 GGACCATGGACCACACAGGG
846603 GGACCATGGACCACACAGGG
1 GGACCATGGACCACACAGGG
846623 GGACCATGGACCA
1 GGACCATGGACCA
846636 TCTATGGGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.30, G:0.36, T:0.06
Consensus pattern (20 bp):
GGACCATGGACCACACAGGG
Found at i:848630 original size:59 final size:58
Alignment explanation
Indices: 848534--848650 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 58
848524 TTTTATGTTT
*
848534 TAAATAATTATTATTTTACTTTTAATGTTTTGGGTTTGGACCAAAACAAACCCAATAA
1 TAAATAATTATTATTTTACTTTTAATGTTTTAGGTTTGGACCAAAACAAACCCAATAA
* *
848592 TAAATTAATTAATT-TTTTACTTTTAATGTTTTATGTTTGGACCAAAACAGACCCAATAA
1 TAAA-TAATT-ATTATTTTACTTTTAATGTTTTAGGTTTGGACCAAAACAAACCCAATAA
848651 GTTAATTATA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 4 0.07
59 47 0.87
60 3 0.06
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (58 bp):
TAAATAATTATTATTTTACTTTTAATGTTTTAGGTTTGGACCAAAACAAACCCAATAA
Found at i:848680 original size:56 final size:58
Alignment explanation
Indices: 848554--848678 Score: 141
Period size: 59 Copynumber: 2.2 Consensus size: 58
848544 TTATTTTACT
** **
848554 TTTAATGTTTTGGGTTTGGACCAAAACAAACCCAATAATAAATTAATTAATTTTTTAC
1 TTTAATGTTTTATGTTTGGACCAAAACAAACCCAATAATAAATTAATTAATTTTGGAC
* *
848612 TTTTAATGTTTTATGTTTGGACCAAAACAGACCC---AATAAGTTAATTATATTTTGGA-
1 -TTTAATGTTTTATGTTTGGACCAAAACAAACCCAATAATAAATTAATTA-ATTTTGGAC
*
848668 TTTAATATTTT
1 TTTAATGTTTT
848679 TAATACTTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
55 10 0.17
56 12 0.21
57 6 0.10
59 30 0.52
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.43
Consensus pattern (58 bp):
TTTAATGTTTTATGTTTGGACCAAAACAAACCCAATAATAAATTAATTAATTTTGGAC
Found at i:852315 original size:136 final size:135
Alignment explanation
Indices: 851940--852430 Score: 779
Period size: 136 Copynumber: 3.6 Consensus size: 135
851930 TTGTTAGATT
* * * *
851940 GAACAAGTTCTTCGCATTATGAACTTCTTCTCTCT-TTTGGATGAGTTTTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
* * * * * *
852004 TTCACTGAAAATGTTGATCCCTCAAGCGAGGCGTCCCTGACTCGAAATG-CTGTGAATCGAGTGA
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTC-ATGAATCGAGTGA
852068 TAGGTC
130 TAGGTC
*
852074 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
852139 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
852204 AGGTC
131 AGGTC
*
852209 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTT-GGATGAGTTCTTCTCATTATGAACT
* ** *
852274 CTCCATTGGAAATGTCAATTCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
65 CTCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
852339 TAGGTC
130 TAGGTC
*
852345 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCT-TTGGATGAGTTCTTCTCATTATGAACT
*
852410 CTCCATTGAAAATGCTGATCC
65 CTCCATTGAAAATGTTGATCC
852431 ACCTCTTTTT
Statistics
Matches: 329, Mismatches: 24, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
134 32 0.10
135 126 0.38
136 170 0.52
137 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.34
Consensus pattern (135 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
AGGTC
Found at i:852520 original size:113 final size:118
Alignment explanation
Indices: 852340--852548 Score: 302
Period size: 113 Copynumber: 1.8 Consensus size: 118
852330 ATCGAGTGAT
* *
852340 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTAGGACGAGTTCTTCTCATTAT
*
852405 GAACTCTCCATTGAAAATGCTGATCCACCTCTTTTTGTGATGGAACCAAACCA
66 GAACTCTCCACTGAAAATGCTGATCCACCTCTTTTTGTGATGGAACCAAACCA
* * *
852458 AGGTTGAACAAGTTCTTCTTATTATGAAC-T-TTCT-CCT-T-TAGGACGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTAGGACGAGTTCTTCTCATTAT
* * *
852518 GAACTCTTCACTGGAAATGTTGATCCACCTC
66 GAACTCTCCACTGAAAATGCTGATCCACCTC
852549 CTTCTGCGGT
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
113 47 0.57
114 1 0.01
115 3 0.04
116 4 0.05
117 1 0.01
118 26 0.32
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (118 bp):
AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTAGGACGAGTTCTTCTCATTAT
GAACTCTCCACTGAAAATGCTGATCCACCTCTTTTTGTGATGGAACCAAACCA
Found at i:853428 original size:13 final size:13
Alignment explanation
Indices: 853391--853437 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
853381 CGAACCCTCC
853391 TTCTTCATTTTTTT
1 TTCTTCA-TTTTTT
853405 TTCTTC-TTTTTAT
1 TTCTTCATTTTT-T
*
853418 TTTTTCATTTTTT
1 TTCTTCATTTTTT
853431 TTCTTCA
1 TTCTTCA
853438 AGCATAGTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 5 0.17
13 13 0.45
14 11 0.38
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (13 bp):
TTCTTCATTTTTT
Found at i:869424 original size:96 final size:96
Alignment explanation
Indices: 869305--869609 Score: 439
Period size: 105 Copynumber: 3.0 Consensus size: 96
869295 CCGCGGCTTT
869305 TTCGCGTAGGCAGCGGCAGTACAGGTGGTGGAGGACATGAGGCAGCGAAGGCGGTGGTAGCGGTG
1 TTCGCGTAGGCAGCGGCAGTACAGGTGGTGGAGGACATGAGGCAGCGAAGGCGGTGGTAGCGGTG
*
869370 GACTTTGTATCCATGACGGGGTACACTTTAC
66 GACTTTGTATGCATGACGGGGTACACTTTAC
*
869401 TTCGCGTAGGCAGCGGCAGTACAGGTGGTGGAGGACATGAGGCAGCAAAGGCGGTGGTAGCGGTG
1 TTCGCGTAGGCAGCGGCAGTACAGGTGGTGGAGGACATGAGGCAGCGAA-------G--GCGGTG
869466 GTAGCGGTGGACTTTGTATGCATGACGGGGTACACTTTAC
57 GTAGCGGTGGACTTTGTATGCATGACGGGGTACACTTTAC
869506 TTCGCGTAGGCAGCGGCAGTACAGGTGGTGGAGGACATGAGGCAGCGAAGGCGGTGGTAGCGTGG
1 TTCGCGTAGGCAGCGGCAGTACAGGTGGTGGAGGACATGAGGCAGCGAAGGC-------G-GTGG
869571 TAGCGGTGGACTTTGTATGCATGACGGGGTACACTTTAC
58 TAGCGGTGGACTTTGTATGCATGACGGGGTACACTTTAC
869610 GCCTTGATCG
Statistics
Matches: 189, Mismatches: 3, Indels: 26
0.87 0.01 0.12
Matches are distributed among these distances:
96 50 0.26
98 1 0.01
103 2 0.01
104 43 0.23
105 93 0.49
ACGTcount: A:0.21, C:0.18, G:0.41, T:0.21
Consensus pattern (96 bp):
TTCGCGTAGGCAGCGGCAGTACAGGTGGTGGAGGACATGAGGCAGCGAAGGCGGTGGTAGCGGTG
GACTTTGTATGCATGACGGGGTACACTTTAC
Found at i:869463 original size:9 final size:9
Alignment explanation
Indices: 869451--869475 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
869441 GGCAGCAAAG
869451 GCGGTGGTA
1 GCGGTGGTA
869460 GCGGTGGTA
1 GCGGTGGTA
869469 GCGGTGG
1 GCGGTGG
869476 ACTTTGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.12, G:0.60, T:0.20
Consensus pattern (9 bp):
GCGGTGGTA
Found at i:869537 original size:105 final size:105
Alignment explanation
Indices: 869355--869609 Score: 485
Period size: 105 Copynumber: 2.4 Consensus size: 105
869345 GGCAGCGAAG
*
869355 GCGGTGGTAGCGGTGGACTTTGTATCCATGACGGGGTACACTTTACTTCGCGTAGGCAGCGGCAG
1 GCGGTGGTAGCGGTGGACTTTGTATGCATGACGGGGTACACTTTACTTCGCGTAGGCAGCGGCAG
869420 TACAGGTGGTGGAGGACATGAGGCAGCAAAGGCGGTGGTA
66 TACAGGTGGTGGAGGACATGAGGCAGCAAAGGCGGTGGTA
869460 GCGGTGGTAGCGGTGGACTTTGTATGCATGACGGGGTACACTTTACTTCGCGTAGGCAGCGGCAG
1 GCGGTGGTAGCGGTGGACTTTGTATGCATGACGGGGTACACTTTACTTCGCGTAGGCAGCGGCAG
*
869525 TACAGGTGGTGGAGGACATGAGGCAGCGAAGGCGGTGGTA
66 TACAGGTGGTGGAGGACATGAGGCAGCAAAGGCGGTGGTA
869565 GC-GTGGTAGCGGTGGACTTTGTATGCATGACGGGGTACACTTTAC
1 GCGGTGGTAGCGGTGGACTTTGTATGCATGACGGGGTACACTTTAC
869610 GCCTTGATCG
Statistics
Matches: 148, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
104 43 0.29
105 105 0.71
ACGTcount: A:0.20, C:0.18, G:0.40, T:0.22
Consensus pattern (105 bp):
GCGGTGGTAGCGGTGGACTTTGTATGCATGACGGGGTACACTTTACTTCGCGTAGGCAGCGGCAG
TACAGGTGGTGGAGGACATGAGGCAGCAAAGGCGGTGGTA
Found at i:871696 original size:2 final size:2
Alignment explanation
Indices: 871689--871759 Score: 133
Period size: 2 Copynumber: 35.0 Consensus size: 2
871679 CGATGTTAAG
871689 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
871731 AT AT AT AT AT AT AT AT AT AT AGT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
871760 TTGGCCATCT
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 66 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:876729 original size:31 final size:31
Alignment explanation
Indices: 876691--876815 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
876681 AAGGGTCGAG
876691 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
876722 GTTTACCTATATTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
876753 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
876784 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
876815 G
1 G
876816 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:880959 original size:30 final size:31
Alignment explanation
Indices: 880886--881008 Score: 189
Period size: 30 Copynumber: 4.0 Consensus size: 31
880876 AGGGTCGAGG
880886 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
880917 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
880948 GTTTA-CTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
880978 GATTACCTAGGTT-TTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
881008 G
1 G
881009 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
30 44 0.51
31 43 0.49
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:880961 original size:61 final size:61
Alignment explanation
Indices: 880886--881008 Score: 187
Period size: 61 Copynumber: 2.0 Consensus size: 61
880876 AGGGTCGAGG
* * *
880886 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGA-CATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTT-TTCGGAATC-TATGGACT
880948 GTTTA-CTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTTTCGGAATCTATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTTTCGGAATCTATGGACT
881008 G
1 G
881009 GTCCTTCGGG
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
60 15 0.26
61 37 0.65
62 5 0.09
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (61 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTTTCGGAATCTATGGACT
Found at i:893694 original size:29 final size:29
Alignment explanation
Indices: 893656--893736 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
893646 CTTAGCTTAA
893656 TAAAAAACTGACACTATTCTAAGCTAAACG
1 TAAAAAACTGACACTATTCTAAGCTAAA-G
*
893686 T-AAAAACTGACATTATTCTAAGCTAAAG
1 TAAAAAACTGACACTATTCTAAGCTAAAG
893714 TAAAAAACTGACACTATTCTAAG
1 TAAAAAACTGACACTATTCTAAG
893737 TTTAGCATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
28 2 0.04
29 45 0.94
30 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.26
Consensus pattern (29 bp):
TAAAAAACTGACACTATTCTAAGCTAAAG
Done.