Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006717.1 Hibiscus syriacus cultivar Beakdansim tig00016795_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: 70664
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1209 original size:15 final size:15
Alignment explanation
Indices: 1181--1220 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1171 AAATATCTAT
*
1181 TTTTAATTA-CTATA
1 TTTTAATTATTTATA
1195 TTTTAATTATTTATA
1 TTTTAATTATTTATA
*
1210 TATTAATTATT
1 TTTTAATTATT
1221 ATTATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAATTATTTATA
Found at i:3510 original size:21 final size:22
Alignment explanation
Indices: 3486--3537 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
3476 ATTTGAGTTC
*
3486 TTTTATAAAT-AATTATATATT
1 TTTTATAAATAAATTATAAATT
* *
3507 TTTTTTAAATAAAATTTTAAATT
1 TTTTATAAAT-AAATTATAAATT
3530 TTTTATAA
1 TTTTATAA
3538 GCCTGACATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 9 0.36
23 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTATAAATAAATTATAAATT
Found at i:4276 original size:18 final size:18
Alignment explanation
Indices: 4248--4288 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
4238 ATAAAATAGC
4248 ATAACCAAATTCAAATGG
1 ATAACCAAATTCAAATGG
4266 ATAACCAAATTCAAATGG
1 ATAACCAAATTCAAATGG
*
4284 CTAAC
1 ATAAC
4289 TAAGAAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.22
Consensus pattern (18 bp):
ATAACCAAATTCAAATGG
Found at i:6052 original size:21 final size:21
Alignment explanation
Indices: 6028--6069 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
6018 TCAAATTCCT
6028 CGATCCCAACCACATGTGCCA
1 CGATCCCAACCACATGTGCCA
6049 CGATCCCAACCACATGTGCCA
1 CGATCCCAACCACATGTGCCA
6070 ACAGTCTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.43, G:0.14, T:0.14
Consensus pattern (21 bp):
CGATCCCAACCACATGTGCCA
Found at i:8277 original size:37 final size:36
Alignment explanation
Indices: 8202--8277 Score: 84
Period size: 37 Copynumber: 2.1 Consensus size: 36
8192 TTTTTATATT
*
8202 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
8238 TTTAATTTTTTTAAAGAAAA-TATAT-AATATTTTACAA
1 TTTAA-TTTTGTAAA-AAAATTATATAAATATTAT-CAA
8275 TTT
1 TTT
8278 GTAATATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
36 12 0.35
37 18 0.53
38 4 0.12
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:10506 original size:28 final size:28
Alignment explanation
Indices: 10472--10529 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
10462 TCTTGAATGC
10472 TTGTATACTCTTCATTACAAATAATGTA
1 TTGTATACTCTTCATTACAAATAATGTA
10500 TTGTATACTCTTCATTACAAATAATGTA
1 TTGTATACTCTTCATTACAAATAATGTA
10528 TT
1 TT
10530 CATACATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (28 bp):
TTGTATACTCTTCATTACAAATAATGTA
Found at i:19549 original size:2 final size:2
Alignment explanation
Indices: 19544--19572 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19534 TGACGGTGTG
19544 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19573 GTACATACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21655 original size:12 final size:11
Alignment explanation
Indices: 21638--21675 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
21628 CTATGAAATT
21638 TTAAAAATATTA
1 TTAAAAATA-TA
21650 TTAAAAATATA
1 TTAAAAATATA
21661 -T-AAAATATA
1 TTAAAAATATA
21670 TTAAAA
1 TTAAAA
21676 TGAAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.33
10 2 0.08
11 5 0.21
12 9 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TTAAAAATATA
Found at i:21710 original size:22 final size:23
Alignment explanation
Indices: 21677--21730 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
21667 ATATTAAAAT
21677 GAAAA-TATTAAAGA-TAAAAAGA
1 GAAAATTATTAAA-ATTAAAAAGA
21699 GAAAATTA-TAAAATTAAAAAGA
1 GAAAATTATTAAAATTAAAAAGA
*
21721 TAAAA-TATTA
1 GAAAATTATTA
21731 TAAAATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 3 0.11
22 23 0.82
23 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (23 bp):
GAAAATTATTAAAATTAAAAAGA
Found at i:21748 original size:24 final size:23
Alignment explanation
Indices: 21653--21838 Score: 68
Period size: 24 Copynumber: 8.0 Consensus size: 23
21643 AATATTATTA
21653 AAAATA-TATAAAATATATTAAA-AT
1 AAAATATTATAAAATA-A--AAATAT
* *
21677 GAAAATATTA-AAGATAAAAAGA-
1 -AAAATATTATAAAATAAAAATAT
* *
21699 GAAA-ATTATAAAATTAAAAAGAT
1 AAAATATTATAAAA-TAAAAATAT
*
21722 AAAATATTATAAAATAATAAATTT
1 AAAATATTATAAAATAA-AAATAT
* * *
21746 AAATTTTTACAAAATAAAAAATATTT
1 AAAATATTATAAAAT-AAAAATA--T
* ***
21772 ATAAATTATTA-ACAATTTTAATA-
1 A-AAA-TATTATAAAATAAAAATAT
* *
21795 AAAATATTAT-TAA-AAATATAT
1 AAAATATTATAAAATAAAAATAT
21816 AAAATA-TATTAAAATAAAAATAT
1 AAAATATTA-TAAAATAAAAATAT
21839 TATACTATGA
Statistics
Matches: 121, Mismatches: 23, Indels: 36
0.67 0.13 0.20
Matches are distributed among these distances:
20 9 0.07
21 20 0.17
22 16 0.13
23 15 0.12
24 30 0.25
25 13 0.11
26 8 0.07
27 6 0.05
28 4 0.03
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (23 bp):
AAAATATTATAAAATAAAAATAT
Found at i:21810 original size:12 final size:12
Alignment explanation
Indices: 21776--21841 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
21766 ATATTTATAA
*
21776 ATTATTAACAAT
1 ATTATTAAAAAT
* *
21788 TTTAATAAAAAT
1 ATTATTAAAAAT
21800 ATTATTAAAAAT
1 ATTATTAAAAAT
21812 A-TA-TAAAATAT
1 ATTATTAAAA-AT
*
21823 ATTAAAATAAAAAT
1 ATT--ATTAAAAAT
21837 ATTAT
1 ATTAT
21842 ACTATGAAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
10 5 0.12
11 5 0.12
12 22 0.51
14 6 0.14
15 5 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (12 bp):
ATTATTAAAAAT
Found at i:22888 original size:27 final size:26
Alignment explanation
Indices: 22858--22949 Score: 71
Period size: 27 Copynumber: 3.4 Consensus size: 26
22848 TGAAAATAAA
*
22858 AATAAAATATTTTTA-AATTAAGTTAAT
1 AATAAAATATTTTTATAATTAA-AT-AT
* *
22885 AATAAAGTATATTTAATAATTAAATAT
1 AATAAAATAT-TTTTATAATTAAATAT
* *
22912 AAAAAAATATTTTTTTAAGTTAACATAT
1 AATAAAATATTTTTATAA-TTAA-ATAT
*
22940 -ATAATATATT
1 AATAAAATATT
22950 ATGAATTTAA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
26 6 0.12
27 31 0.60
28 9 0.17
29 6 0.12
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (26 bp):
AATAAAATATTTTTATAATTAAATAT
Found at i:24702 original size:24 final size:24
Alignment explanation
Indices: 24653--24702 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
24643 GCAATTTTAT
* * *
24653 TAGATATACTTTTGTTTTATGTTA
1 TAGATATACATTTGTCTTATCTTA
24677 TAGATATACATTT-TCTTATCTATA
1 TAGATATACATTTGTCTTATCT-TA
24701 TA
1 TA
24703 TGCTTTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.54
Consensus pattern (24 bp):
TAGATATACATTTGTCTTATCTTA
Found at i:30156 original size:16 final size:17
Alignment explanation
Indices: 30135--30171 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
30125 AATCCAATTA
30135 AAAAGT-ATAGAAAAA-T
1 AAAAGTAATA-AAAAACT
30151 AAAAGTAATAAAAAACT
1 AAAAGTAATAAAAAACT
30168 AAAA
1 AAAA
30172 AAGAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (17 bp):
AAAAGTAATAAAAAACT
Found at i:33400 original size:24 final size:24
Alignment explanation
Indices: 33371--33422 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
33361 TATCTCTCCA
33371 TGTGACATGAT-TTTTCTCTGCTAT
1 TGTGACATG-TGTTTTCTCTGCTAT
*
33395 TGTGACATGTGTTTTCTCTGCTCT
1 TGTGACATGTGTTTTCTCTGCTAT
33419 TGTG
1 TGTG
33423 GCACGATCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.12, C:0.17, G:0.21, T:0.50
Consensus pattern (24 bp):
TGTGACATGTGTTTTCTCTGCTAT
Found at i:41901 original size:3 final size:3
Alignment explanation
Indices: 41893--41941 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
41883 ATAAATAAGC
41893 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41941 A
1 A
41942 CAATTACAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42249 original size:40 final size:39
Alignment explanation
Indices: 42122--42250 Score: 134
Period size: 40 Copynumber: 3.2 Consensus size: 39
42112 ACACTGCTCA
*
42122 TACGTGATGAAGAGTTCGGGTCGTCTAAGGGTGACATGGTTCC
1 TACGTGATGAAGAGTTCTGGTCG----AGGGTGACATGGTTCC
* ** * *
42165 TACGTGATGAGGAAATCTGGTCGAGGGTTGACACT-GCTCA
1 TACGTGATGAAGAGTTCTGGTCGAGGG-TGACA-TGGTTCC
42205 TACGTGATGAAGAGTTCTGGTCGAGGGATGACATGGTTCC
1 TACGTGATGAAGAGTTCTGGTCGAGGG-TGACATGGTTCC
42245 TACGTG
1 TACGTG
42251 TTGAGGACGG
Statistics
Matches: 71, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
39 5 0.07
40 46 0.65
41 1 0.01
43 19 0.27
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.27
Consensus pattern (39 bp):
TACGTGATGAAGAGTTCTGGTCGAGGGTGACATGGTTCC
Found at i:42359 original size:43 final size:42
Alignment explanation
Indices: 42291--42488 Score: 129
Period size: 43 Copynumber: 4.6 Consensus size: 42
42281 TGATAGCTCG
42291 GCTCCTACGTGATGAGGACGA-CTGGTTATCTAGGGTGACTACA
1 GCTCCTACGTGATGAGGA-GATCTGGTTATCTAGGGTGAC-ACA
* * * *
42334 GCTCATACGTGATGAAGAGATCTGG---TC-GGGGAATGACACG
1 GCTCCTACGTGATGAGGAGATCTGGTTATCTAGGG--TGACACA
* * * ** * *
42374 GCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACA
1 GCTCCTACGTGATGAGGAGATCTGGTTATCT-AGGGTGA-CACA
* * * *
42418 CGATTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTGACACG
1 -G-CTCCTACGTGATGAGGA-GATCTGGTTATCTA-GGGTGACACA
42463 GCTCCTACGTGATGAGGAGATCTGGT
1 GCTCCTACGTGATGAGGAGATCTGGT
42489 CTGGGGATGA
Statistics
Matches: 120, Mismatches: 21, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
39 3 0.03
40 28 0.23
41 4 0.03
42 3 0.03
43 46 0.38
44 3 0.03
45 6 0.05
46 26 0.22
47 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (42 bp):
GCTCCTACGTGATGAGGAGATCTGGTTATCTAGGGTGACACA
Found at i:42483 original size:129 final size:127
Alignment explanation
Indices: 42105--42517 Score: 383
Period size: 129 Copynumber: 3.2 Consensus size: 127
42095 GTTGGTTGTT
* * * * * * *
42105 GGGGACGACACTGCTCATACGTGATGAAGAGTTCGGGTCGTCT-AAGG-G-TGACATGGTTCCTA
1 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTA
* * * *
42167 CGTGATGAGGA-AATCTGG---TCGAGGGTTGACACTGCTCATACGTGATGAAGAGTTCTGGTC
66 CGTGATGAGGACGA-CTGGTTATCTA-GGTTGACACAGCTCATACGTGATGAAGAGATCTGGTC
* * * * * * * * *
42227 GAGGGATGACATGGTTCCTACGTGTTGAGGACG-GCTGGCCATCTTTAGGAGTGGTGATAGCTCG
1 G-GGGATGACACGGCTCATACGTGATGAAGA-GTTCTGGCCATC--TA--A-AGGTGATAACACG
* *
42291 GCTCCTACGTGATGAGGACGACTGGTTATCTAGGGTGACTACAGCTCATACGTGATGAAGAGATC
59 GTTCCTACGTGATGAGGACGACTGGTTATCTAGGTTGAC-ACAGCTCATACGTGATGAAGAGATC
42356 TGGTC
123 TGGTC
*
42361 GGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGATTCCT
1 GGGG-ATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCT
* * * *
42426 ACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC
65 ACGTGATGAGGACGACTGGTTATCTA-GGTTGACACAGCTCATACGTGATGAAGAGATCTGGTC
* * *
42490 TGGGGATGACACGGTTCCTACATGATGA
1 -GGGGATGACACGGCTCATACGTGATGA
42518 GGACGGCTGG
Statistics
Matches: 231, Mismatches: 41, Indels: 31
0.76 0.14 0.10
Matches are distributed among these distances:
122 1 0.00
123 28 0.12
124 1 0.00
125 1 0.00
128 1 0.00
129 88 0.38
130 12 0.05
131 24 0.10
132 3 0.01
133 10 0.04
134 62 0.27
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (127 bp):
GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTA
CGTGATGAGGACGACTGGTTATCTAGGTTGACACAGCTCATACGTGATGAAGAGATCTGGTC
Found at i:42528 original size:129 final size:129
Alignment explanation
Indices: 42190--42533 Score: 415
Period size: 129 Copynumber: 2.6 Consensus size: 129
42180 TCTGGTCGAG
* * * *
42190 GGTTGACACTGCTCATACGTGATGAAGAGTTCTGGTCGAGGGATGACATGGTTCCTACGTGTTGA
1 GGTTGACACAGCTCATACGTGATGAAGAGATCTGGTCG-GGGATGACACGGTTCCTACGTGATGA
* * * *
42255 GGACGGCTGGCCATCTTTAGGAGTGGTGATAGCTCGGCTCCTACGTGATGAGGACGACTGGTTAT
65 GGACGGCTGGCCATC--TA-GAGAGGTGATAACACGACTCCTACGTGATGAGGACGACTGGTTAT
42320 CTA
127 CTA
* * *
42323 GGGTGACTACAGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTCATACGTGATG
1 GGTTGAC-ACAGCTCATACGTGATGAAGAGATCTGGTCGGGG-ATGACACGGTTCCTACGTGATG
* * * *
42388 AAGA-GTTCTGGCCATCTA-A-AGGTGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATC
64 AGGACG-GCTGGCCATCTAGAGAGGTGATAACACGACTCCTACGTGATGAGGACGACTGGTTATC
42450 TA
128 TA
* * * *
42452 TGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATG
1 -GGTTGACACAGCTCATACGTGATGAAGAGATCTGGTC-GGGGATGACACGGTTCCTACGTGATG
42517 AGGACGGCTGGCCATCT
64 AGGACGGCTGGCCATCT
42534 TTAGGAGTTA
Statistics
Matches: 181, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
129 98 0.54
130 12 0.07
132 2 0.01
133 10 0.06
134 59 0.33
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (129 bp):
GGTTGACACAGCTCATACGTGATGAAGAGATCTGGTCGGGGATGACACGGTTCCTACGTGATGAG
GACGGCTGGCCATCTAGAGAGGTGATAACACGACTCCTACGTGATGAGGACGACTGGTTATCTA
Found at i:42586 original size:28 final size:28
Alignment explanation
Indices: 42566--42627 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
42556 AAACCAAATT
42566 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
42594 AAAGATTTGTTTCAAGAA-AAATAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
42622 AAAGAT
1 AAAGAT
42628 GATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:42689 original size:35 final size:35
Alignment explanation
Indices: 42649--42817 Score: 134
Period size: 28 Copynumber: 5.2 Consensus size: 35
42639 AAGCAACTGT
* *
42649 CTCAAAAGAGACAAAATTCGTTTTAAGGGAAACAA
1 CTCAAAAGAGACAAAATTCGTTTAAAGGGAAACGA
* *
42684 CTC--AA-AGAC--GA--CGTTTAAAGGGAAACTGT
1 CTCAAAAGAGACAAAATTCGTTTAAAGGGAAAC-GA
*
42713 CTCAAATGAGACAAAATTCGTTTAAAGGGAAACGA
1 CTCAAAAGAGACAAAATTCGTTTAAAGGGAAACGA
*
42748 CTC-AAAGATG-----A--CGTTTAAAGGGAAACTGT
1 CTCAAAAGA-GACAAAATTCGTTTAAAGGGAAAC-GA
* *
42777 CTCAAATGAGACAAAATTCATTTAAAGGGAAACGA
1 CTCAAAAGAGACAAAATTCGTTTAAAGGGAAACGA
42812 CTCAAA
1 CTCAAA
42818 GACGACGTTT
Statistics
Matches: 104, Mismatches: 12, Indels: 36
0.68 0.08 0.24
Matches are distributed among these distances:
28 29 0.28
29 8 0.08
30 6 0.06
31 1 0.01
32 8 0.08
33 2 0.02
34 6 0.06
35 15 0.14
36 29 0.28
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.21
Consensus pattern (35 bp):
CTCAAAAGAGACAAAATTCGTTTAAAGGGAAACGA
Found at i:42724 original size:64 final size:64
Alignment explanation
Indices: 42643--42827 Score: 325
Period size: 64 Copynumber: 2.9 Consensus size: 64
42633 TTTTAAAAGC
* * *
42643 AACTGTCTCAAAAGAGACAAAATTCGTTTTAAGGGAAACAACTCAAAGACGACGTTTAAAGGGA
1 AACTGTCTCAAATGAGACAAAATTCGTTTAAAGGGAAACGACTCAAAGACGACGTTTAAAGGGA
*
42707 AACTGTCTCAAATGAGACAAAATTCGTTTAAAGGGAAACGACTCAAAGATGACGTTTAAAGGGA
1 AACTGTCTCAAATGAGACAAAATTCGTTTAAAGGGAAACGACTCAAAGACGACGTTTAAAGGGA
*
42771 AACTGTCTCAAATGAGACAAAATTCATTTAAAGGGAAACGACTCAAAGACGACGTTT
1 AACTGTCTCAAATGAGACAAAATTCGTTTAAAGGGAAACGACTCAAAGACGACGTTT
42828 GTTTTGTTTC
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 115 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.22
Consensus pattern (64 bp):
AACTGTCTCAAATGAGACAAAATTCGTTTAAAGGGAAACGACTCAAAGACGACGTTTAAAGGGA
Found at i:42742 original size:36 final size:35
Alignment explanation
Indices: 42695--42817 Score: 136
Period size: 36 Copynumber: 3.7 Consensus size: 35
42685 TCAAAGACGA
*
42695 CGTTTAAAGGGAAACTGTCTCAAATGAGACAAAATT
1 CGTTTAAAGGGAAAC-GACTCAAATGAGACAAAATT
42731 CGTTTAAAGGGAAACGACTCAAA-GATG-----A--
1 CGTTTAAAGGGAAACGACTCAAATGA-GACAAAATT
*
42759 CGTTTAAAGGGAAACTGTCTCAAATGAGACAAAATT
1 CGTTTAAAGGGAAAC-GACTCAAATGAGACAAAATT
*
42795 CATTTAAAGGGAAACGACTCAAA
1 CGTTTAAAGGGAAACGACTCAAA
42818 GACGACGTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 21
0.74 0.04 0.21
Matches are distributed among these distances:
28 15 0.21
29 8 0.11
30 3 0.04
34 3 0.04
35 15 0.21
36 29 0.40
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (35 bp):
CGTTTAAAGGGAAACGACTCAAATGAGACAAAATT
Found at i:43592 original size:20 final size:20
Alignment explanation
Indices: 43552--43592 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43542 TCAAAGATTT
* *
43552 ATTTCAAGAGAAACTGTCTC
1 ATTTCAAGAGAAACAGACTC
*
43572 ATTTTAAGAGAAACAGACTC
1 ATTTCAAGAGAAACAGACTC
43592 A
1 A
43593 AAGATTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (20 bp):
ATTTCAAGAGAAACAGACTC
Found at i:43663 original size:29 final size:29
Alignment explanation
Indices: 43627--43707 Score: 112
Period size: 30 Copynumber: 2.8 Consensus size: 29
43617 TTAAGAGAGA
*
43627 CAAA-ATTTTGTTTCCAAAGAAACAGACT
1 CAAAGATTTTGTTTCAAAAGAAACAGACT
43655 CAAAGATTTTTGTTTCAAAAGAAACAGACT
1 CAAAGA-TTTTGTTTCAAAAGAAACAGACT
* *
43685 CAAAGA-TTTATTTCAAGAGAAAC
1 CAAAGATTTTGTTTCAAAAGAAAC
43708 TGTCTCACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
28 19 0.40
29 1 0.02
30 28 0.58
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.28
Consensus pattern (29 bp):
CAAAGATTTTGTTTCAAAAGAAACAGACT
Found at i:43666 original size:30 final size:30
Alignment explanation
Indices: 43632--43693 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
43622 AGAGACAAAA
*
43632 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
43662 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
43692 TT
1 TT
43694 ATTTCAAGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAGACTCAAAGAT
Found at i:44060 original size:106 final size:106
Alignment explanation
Indices: 43874--44072 Score: 312
Period size: 106 Copynumber: 1.9 Consensus size: 106
43864 CAGCTTTGAA
* * *
43874 AATCTCAAGTGATATTAATTTTGTTTCAAGTACAACAAATTTAAATTTGTATCTCAGAGAAAAAA
1 AATCTCAAGTGAGATTAATTTTGTTTCAAGTACAACAAATTAAAATTTGTATCTCAAAGAAAAAA
*
43939 ATGTCTCAAGCGAGACGAAATTTGTTTTTTTAAAAAACAAC
66 ATGTCTCAAGAGAGACGAAATTTGTTTTTTTAAAAAACAAC
* *
43980 AATCTCAAGTGAGATTAATTTTGTTTCAAGTGA-AGCAAATTCAAAATTTGTATCTCAAAG-GAA
1 AATCTCAAGTGAGATTAATTTTGTTTCAAGT-ACAACAAATT-AAAATTTGTATCTCAAAGAAAA
44043 AAATGTCTCAAGAGAGACGAAATTTGTTTT
64 AAATGTCTCAAGAGAGACGAAATTTGTTTT
44073 AAGATAAATT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
106 68 0.80
107 17 0.20
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.34
Consensus pattern (106 bp):
AATCTCAAGTGAGATTAATTTTGTTTCAAGTACAACAAATTAAAATTTGTATCTCAAAGAAAAAA
ATGTCTCAAGAGAGACGAAATTTGTTTTTTTAAAAAACAAC
Found at i:44201 original size:37 final size:37
Alignment explanation
Indices: 44128--44201 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
44118 ATCTCAAGCG
* * * *
44128 AGACAAAATTTGTTTTCGAAGGAAACTACCTTAAATA
1 AGACAAAATTTGTTTTCAAAGGAAACAAACTCAAATA
44165 AGACAAAATTT-TGTTTCAAAGGAAACAAACTCAAATA
1 AGACAAAATTTGT-TTTCAAAGGAAACAAACTCAAATA
44202 TTTTTTCTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 1 0.03
37 31 0.97
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (37 bp):
AGACAAAATTTGTTTTCAAAGGAAACAAACTCAAATA
Found at i:44748 original size:14 final size:15
Alignment explanation
Indices: 44721--44751 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
44711 AATTGTTTTA
44721 TTTGCCCCATCAAAT
1 TTTGCCCCATCAAAT
44736 TTTGCCCCA-CAAAT
1 TTTGCCCCATCAAAT
44750 TT
1 TT
44752 GTCTTCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.26, C:0.32, G:0.06, T:0.35
Consensus pattern (15 bp):
TTTGCCCCATCAAAT
Found at i:48382 original size:5 final size:5
Alignment explanation
Indices: 48372--48397 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
48362 CATTATGATG
48372 ATGCA ATGCA ATGCA ATGCA ATGCA A
1 ATGCA ATGCA ATGCA ATGCA ATGCA A
48398 ATGACAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATGCA
Found at i:52138 original size:3 final size:3
Alignment explanation
Indices: 52130--52169 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
52120 ATAAATAAGC
52130 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
52170 CAATTACAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53480 original size:54 final size:52
Alignment explanation
Indices: 53381--53483 Score: 154
Period size: 53 Copynumber: 1.9 Consensus size: 52
53371 ATCTTTACAC
*
53381 TTATATATGAATCATATCAATTAAAACTATAATAAATTCAAAAAAAATATTA
1 TTATATATGAATCATATCAATTAAAACTATAATAAAATCAAAAAAAATATTA
*
53433 TTATATATGAAATCATATCAATTTAAACTATAATAAAAAT-ATAAAAAAATA
1 TTATATATG-AATCATATCAATTAAAACTATAAT-AAAATCA-AAAAAAATA
53484 CAAATAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
52 9 0.20
53 24 0.52
54 13 0.28
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (52 bp):
TTATATATGAATCATATCAATTAAAACTATAATAAAATCAAAAAAAATATTA
Found at i:54159 original size:2 final size:2
Alignment explanation
Indices: 54152--54202 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
54142 TATTAAATGG
54152 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
54194 AT AT AT AT A
1 AT AT AT AT A
54203 GAGAGAGAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54207 original size:2 final size:2
Alignment explanation
Indices: 54202--54237 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
54192 ATATATATAT
54202 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
54238 TGTCTATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:59723 original size:6 final size:6
Alignment explanation
Indices: 59706--59763 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
59696 ATAATATTGA
** * *
59706 AACTCG -ACTCG AACTCG AA-AAG -ACTCG AACTC- AATTCA AACTCG
1 AACTCG AACTCG AACTCG AACTCG AACTCG AACTCG AACTCG AACTCG
59750 AACTCG AACTCG AA
1 AACTCG AACTCG AA
59764 TTTGAACCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
4 1 0.02
5 11 0.27
6 29 0.71
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (6 bp):
AACTCG
Found at i:59770 original size:12 final size:12
Alignment explanation
Indices: 59706--59763 Score: 52
Period size: 11 Copynumber: 5.2 Consensus size: 12
59696 ATAATATTGA
59706 AACTCG-ACTCG
1 AACTCGAACTCG
**
59717 AACTCGAA-AAG
1 AACTCGAACTCG
59728 -ACTCGAACTC-
1 AACTCGAACTCG
* *
59738 AATTCAAACTCG
1 AACTCGAACTCG
59750 AACTCGAACTCG
1 AACTCGAACTCG
59762 AA
1 AA
59764 TTTGAACCTA
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
10 7 0.20
11 15 0.43
12 13 0.37
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (12 bp):
AACTCGAACTCG
Found at i:60037 original size:13 final size:13
Alignment explanation
Indices: 60019--60048 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
60009 GGGATTTGAT
60019 GTTTAAGGCTTAG
1 GTTTAAGGCTTAG
*
60032 GTTTAAGGTTTAG
1 GTTTAAGGCTTAG
60045 GTTT
1 GTTT
60049 TACGATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.30, T:0.47
Consensus pattern (13 bp):
GTTTAAGGCTTAG
Found at i:61152 original size:14 final size:14
Alignment explanation
Indices: 61135--61175 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
61125 TTTATTCATC
61135 AATAATGTATTTTT
1 AATAATGTATTTTT
61149 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
61160 AATAATGTAATTTT
1 AATAATGTATTTTT
61174 AA
1 AA
61176 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:68820 original size:16 final size:16
Alignment explanation
Indices: 68799--68833 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
68789 ACAAGTTAAT
68799 TTTTAATGAAATTATA
1 TTTTAATGAAATTATA
* *
68815 TTTTAATTAAATTTTA
1 TTTTAATGAAATTATA
68831 TTT
1 TTT
68834 ATATATTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTTAATGAAATTATA
Found at i:69668 original size:81 final size:80
Alignment explanation
Indices: 69576--69732 Score: 287
Period size: 81 Copynumber: 1.9 Consensus size: 80
69566 TTAACCTTCG
*
69576 TAGAATTTTTATTATTCAATGATAGAATAAGGATATTTTTTAAAGAAAAAAAAATTAAGGACGTT
1 TAGAATTTTTATTATTCAATGACAGAATAAGGATATTTTTTAAAG-AAAAAAAATTAAGGACGTT
69641 TTAGTCCAAAACGCCC
65 TTAGTCCAAAACGCCC
*
69657 TAGAATTTTTATTATTCAATGACAGAATAAGGATATTTTTTAAAGAAAAAAAATTAAGGGCGTTT
1 TAGAATTTTTATTATTCAATGACAGAATAAGGATATTTTTTAAAGAAAAAAAATTAAGGACGTTT
69722 TAGTCCAAAAC
66 TAGTCCAAAAC
69733 TCCGGTAATC
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
80 30 0.41
81 44 0.59
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (80 bp):
TAGAATTTTTATTATTCAATGACAGAATAAGGATATTTTTTAAAGAAAAAAAATTAAGGACGTTT
TAGTCCAAAACGCCC
Found at i:70231 original size:13 final size:13
Alignment explanation
Indices: 70213--70239 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
70203 CATAGGTGAA
70213 CAGTCTTCATATG
1 CAGTCTTCATATG
70226 CAGTCTTCATATG
1 CAGTCTTCATATG
70239 C
1 C
70240 GTGTATGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Done.