Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024647.1 Corchorus olitorius cultivar O-4 contig24680, 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: 26448
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1613 original size:30 final size:30
Alignment explanation
Indices: 1556--1663 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 30
1546 TGGGCAGAGT
* *
1556 TTTGGACGTTTTGTCCCCTTAAACTTGTATG
1 TTTGGACGTTTTG-CCCCCTGAACTTGTATG
*
1587 TTTGGACGTTTTGCCCCCTGAACTTGTACG
1 TTTGGACGTTTTGCCCCCTGAACTTGTATG
* *
1617 TTTTGGATGTTTTGCCTCCTGAACTT-TAAT-
1 -TTTGGACGTTTTGCCCCCTGAACTTGT-ATG
*
1647 TTTGGACATTTTTGCCC
1 TTTGGAC-GTTTTGCCC
1664 ACTAAGCAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
29 6 0.09
30 22 0.34
31 37 0.57
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.44
Consensus pattern (30 bp):
TTTGGACGTTTTGCCCCCTGAACTTGTATG
Found at i:3200 original size:25 final size:27
Alignment explanation
Indices: 3139--3191 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
3129 ATTTCTATAT
* *
3139 TGTCATTATCAAAATATATATTAATTA
1 TGTCATTATTAAAATATATAATAATTA
3166 TGTCATTATTAAAATATATAATAATT
1 TGTCATTATTAAAATATATAATAATT
3192 TTGTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (27 bp):
TGTCATTATTAAAATATATAATAATTA
Found at i:3689 original size:22 final size:22
Alignment explanation
Indices: 3645--3725 Score: 85
Period size: 22 Copynumber: 3.5 Consensus size: 22
3635 AGGAGATTAT
3645 TAAAATTTCATAGTTATGTGGTTTC
1 TAAAATTTCATAG---TGTGGTTTC
3670 TAAAATTTCATAGTGTGGTTATC
1 TAAAATTTCATAGTGTGGTT-TC
*
3693 -AAAATCTT-ATAGTGTGGTTAC
1 TAAAAT-TTCATAGTGTGGTTTC
*
3714 CAAAATTTCATA
1 TAAAATTTCATA
3726 TGTAGGATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
21 3 0.06
22 31 0.61
23 4 0.08
25 13 0.25
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (22 bp):
TAAAATTTCATAGTGTGGTTTC
Found at i:3739 original size:22 final size:22
Alignment explanation
Indices: 3659--3857 Score: 116
Period size: 22 Copynumber: 9.4 Consensus size: 22
3649 ATTTCATAGT
3659 TATGT-GGTT-TCTAAAATTTCA
1 TATGTAGGTTATC-AAAATTTCA
3680 TAGTGT-GGTTATCAAAATCTT-A
1 TA-TGTAGGTTATCAAAAT-TTCA
*
3702 TAGTGT-GGTTACCAAAATTTCA
1 TA-TGTAGGTTATCAAAATTTCA
*
3724 TATGTAGGATATCAAAA--T--
1 TATGTAGGTTATCAAAATTTCA
* *
3742 T-TGCA-GTTATCAAAATCTCA
1 TATGTAGGTTATCAAAATTTCA
* * *
3762 -AGGGATGTTATCAAAATTTCA
1 TATGTAGGTTATCAAAATTTCA
* * *
3783 TATGGAGATTATTAAAATTTCA
1 TATGTAGGTTATCAAAATTTCA
* ** *
3805 TAGGTTTGCTATCAAAATTTCA
1 TATGTAGGTTATCAAAATTTCA
* *
3827 TATGGAGGTTATCAGAAATTTAA
1 TATGTAGGTTATCA-AAATTTCA
*
3850 TTTGTAGG
1 TATGTAGG
3858 AATGTTATCA
Statistics
Matches: 138, Mismatches: 27, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
16 9 0.07
17 3 0.02
18 2 0.01
20 3 0.02
21 21 0.15
22 83 0.60
23 17 0.12
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.39
Consensus pattern (22 bp):
TATGTAGGTTATCAAAATTTCA
Found at i:3800 original size:59 final size:60
Alignment explanation
Indices: 3687--3802 Score: 148
Period size: 59 Copynumber: 1.9 Consensus size: 60
3677 TCATAGTGTG
* * *
3687 GTTATCAAAATCTTATAGTGTGGTTACCAAAATTTCATATGTAGGATATCAAAATTTGCA
1 GTTATCAAAATCTCATAGGGTGGTTACCAAAATTTCATATGGAGGATATCAAAATTTGCA
* *
3747 GTTATCAAAATCTCA-AGGGAT-GTTATCAAAATTTCATATGGA-GATTATTAAAATTT
1 GTTATCAAAATCTCATAGGG-TGGTTACCAAAATTTCATATGGAGGA-TATCAAAATTT
3803 CATAGGTTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
58 2 0.04
59 32 0.65
60 15 0.31
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (60 bp):
GTTATCAAAATCTCATAGGGTGGTTACCAAAATTTCATATGGAGGATATCAAAATTTGCA
Found at i:3977 original size:22 final size:24
Alignment explanation
Indices: 3921--4000 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 24
3911 ATAGGGCAAC
3921 TATCAAAATTTTATATGGAGGTTAT
1 TATCAAAATTTTATATGGA-GTTAT
* * *
3946 TATCAGAATTTTAT-TGTA-TTGT
1 TATCAAAATTTTATATGGAGTTAT
*
3968 TATCAAAATTTCATA-GGAAG--AT
1 TATCAAAATTTTATATGG-AGTTAT
3990 TATCAAAATTT
1 TATCAAAATTT
4001 CATAATGTGC
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
22 28 0.62
23 1 0.02
24 3 0.07
25 13 0.29
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (24 bp):
TATCAAAATTTTATATGGAGTTAT
Found at i:4001 original size:22 final size:22
Alignment explanation
Indices: 3967--4656 Score: 174
Period size: 22 Copynumber: 31.7 Consensus size: 22
3957 TATTGTATTG
3967 TTATCAAAATTTCATAG-GAAGA
1 TTATCAAAATTTCATAGTG-AGA
* * *
3989 TTATCAAAATTTCATAATGTGC
1 TTATCAAAATTTCATAGTGAGA
* *
4011 TTATTAAAATTACATAGTGAGTGA
1 TTATCAAAATTTCATAGTGA--GA
**
4035 GCTTATCAAAATTTCA-AGTGTCA
1 --TTATCAAAATTTCATAGTGAGA
*
4058 TTACCAAAATTTCATAGTGTA-A
1 TTATCAAAATTTCATAGTG-AGA
* *
4080 TTATCACAATTTCATA--GAGG
1 TTATCAAAATTTCATAGTGAGA
* *
4100 TTAACAAAATATCAT-GTGGAGA
1 TTATCAAAATTTCATAGT-GAGA
* * *
4122 TTATCAAAATTTAAGAG-GAAAA
1 TTATCAAAATTTCATAGTG-AGA
* *
4144 TTATCAAAATTTCATAGTGTGC
1 TTATCAAAATTTCATAGTGAGA
* *
4166 TTATCAAAATTTTATACT--G-
1 TTATCAAAATTTCATAGTGAGA
** * *
4185 TGGT----ATTTCAGAGGGAGA
1 TTATCAAAATTTCATAGTGAGA
* *
4203 GGCTAT-AAGAAATTCATAGT-ATGA
1 --TTATCAA-AATTTCATAGTGA-GA
* *
4227 TTAGCAAAATTTCATTAATTG-G-
1 TTATCAAAATTTCA-T-AGTGAGA
* * *
4249 TTATCAAATTTTCATTGTGTG-
1 TTATCAAAATTTCATAGTGAGA
* * *
4270 GTAGTTAAAATTTCATAATGAG-
1 TTA-TCAAAATTTCATAGTGAGA
*
4292 TTGATTAAAGA-TTCATAGTGAGA
1 TT-ATCAAA-ATTTCATAGTGAGA
* * * * *
4315 TTAACAAAATTTGATTGTGTGG
1 TTATCAAAATTTCATAGTGAGA
* * **
4337 TTCTCAAAA-CTCTATAGAAAGA
1 TTATCAAAATTTC-ATAGTGAGA
* *
4359 TTAACAAAATTTCATAG-GAAA
1 TTATCAAAATTTCATAGTGAGA
** *
4380 GTTATCGTAATTTCATGGTGTAGTTAA
1 -TTATCAAAATTTCATAGTG-AG---A
* * *
4407 TTATCAAAATTTCATTG-GGGG
1 TTATCAAAATTTCATAGTGAGA
* ***
4428 TTATC-AAA-TTAATAGTGTTC
1 TTATCAAAATTTCATAGTGAGA
* * * *
4448 TTATCAACATTACGTAG-GAGG
1 TTATCAAAATTTCATAGTGAGA
* *
4469 TTAACAAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGA
* * * *
4491 TTGTCAAAAATTCATAGGGAGG
1 TTATCAAAATTTCATAGTGAGA
* *
4513 TTATCAAAATTTCATGAG-GTGC
1 TTATCAAAATTTCAT-AGTGAGA
* *
4535 TTTTCAAAATTTC--A-TGAGG
1 TTATCAAAATTTCATAGTGAGA
*
4554 TTATCAAAATTTCA-AATGA-A
1 TTATCAAAATTTCATAGTGAGA
* * *
4574 TGTTATCAAAATTTTATAGGGGGA
1 --TTATCAAAATTTCATAGTGAGA
4598 TT-TACAAAATTTCATAGTGAGA
1 TTAT-CAAAATTTCATAGTGAGA
* * *
4620 TTATCACAATTTCATGGT-AGG
1 TTATCAAAATTTCATAGTGAGA
* *
4641 TTGTCAAATTTTCATA
1 TTATCAAAATTTCATA
4657 AAGTGATTAC
Statistics
Matches: 478, Mismatches: 133, Indels: 115
0.66 0.18 0.16
Matches are distributed among these distances:
15 6 0.01
17 1 0.00
19 23 0.05
20 27 0.06
21 61 0.13
22 292 0.61
23 21 0.04
24 15 0.03
25 5 0.01
26 26 0.05
27 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGA
Found at i:4631 original size:85 final size:86
Alignment explanation
Indices: 4464--4657 Score: 200
Period size: 85 Copynumber: 2.3 Consensus size: 86
4454 ACATTACGTA
* * *
4464 GGAGGTTAACAAAATTTCATAAGGAGGTTGTCAAAAATTCATAGGGAGGTTATCAAAATTTCATG
1 GGAGGTTATCAAAATTTCATAAGAAGGTTATCAAAAATTCATAGGGAGGTTATCAAAATTTCATG
* * *
4529 AGGTGCTTTTCAAAATTTCAT
66 AGGAGATTATCAAAATTTCAT
* * *
4550 -GAGGTTATCAAAATTTCA-AATGAATGTTATCAAAATTTTATAGGG-GGATT-TACAAAATTTC
1 GGAGGTTATCAAAATTTCATAA-GAAGGTTATCAAAAATTCATAGGGAGG-TTAT-CAAAATTTC
*
4611 AT-AGTGAGATTATCACAATTTCAT
63 ATGAG-GAGATTATCAAAATTTCAT
* *
4635 GGTAGGTTGTCAAATTTTCATAA
1 GG-AGGTTATCAAAATTTCATAA
4658 AGTGATTACC
Statistics
Matches: 89, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
84 7 0.08
85 64 0.72
86 1 0.01
87 15 0.17
88 2 0.02
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.35
Consensus pattern (86 bp):
GGAGGTTATCAAAATTTCATAAGAAGGTTATCAAAAATTCATAGGGAGGTTATCAAAATTTCATG
AGGAGATTATCAAAATTTCAT
Found at i:4774 original size:22 final size:22
Alignment explanation
Indices: 4736--4835 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
4726 GGTGGTTATT
**
4736 AAAATTTTATATTGAGGTTTTC
1 AAAATTTTATAGGGAGGTTTTC
* **
4758 AAAATTTTATAGGGAGGGTAAC
1 AAAATTTTATAGGGAGGTTTTC
* *
4780 AAAATTTTATAGGAAAGTTTAT-
1 AAAATTTTATAGGGAGGTTT-TC
* * **
4802 AAAATTTCATATGGAGGTTCCC
1 AAAATTTTATAGGGAGGTTTTC
*
4824 GAAATTTTATAG
1 AAAATTTTATAG
4836 TATCGTCATA
Statistics
Matches: 57, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (22 bp):
AAAATTTTATAGGGAGGTTTTC
Found at i:5845 original size:2 final size:2
Alignment explanation
Indices: 5838--5870 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
5828 CATTAGAAAT
*
5838 TA TA TA TA TA TA TA TA TA TG TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5871 GACACACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6298 original size:13 final size:13
Alignment explanation
Indices: 6280--6306 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6270 CTGTGAGTAT
6280 AAGACACAATCCC
1 AAGACACAATCCC
6293 AAGACACAATCCC
1 AAGACACAATCCC
6306 A
1 A
6307 GTTATCGTTG
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:0.48, C:0.37, G:0.07, T:0.07
Consensus pattern (13 bp):
AAGACACAATCCC
Found at i:8209 original size:19 final size:19
Alignment explanation
Indices: 8168--8209 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
8158 TTTATTTATA
*
8168 TCATTTTATAAAAACTACC
1 TCATTTTAAAAAAACTACC
8187 -CATTTTAAATAAAACT-CC
1 TCATTTTAAA-AAAACTACC
8205 TCATT
1 TCATT
8210 AGAAGATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (19 bp):
TCATTTTAAAAAAACTACC
Found at i:8220 original size:77 final size:77
Alignment explanation
Indices: 8127--8279 Score: 252
Period size: 77 Copynumber: 2.0 Consensus size: 77
8117 ATAAAAGTTA
* *
8127 CTCATTACAGGATAAATATAAATATTTAAATTTTATTTATATCATTTTATAAAAACTACCCATTT
1 CTCATTACAAGATAAATATAAATATTTAAATTTTATTTATATCATTTTAAAAAAACTACCCATTT
* *
8192 TAAATAAAACTC
66 AAAAAAAAACTC
* *
8204 CTCATTAGAAGATAAATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAACTACCCATTT
1 CTCATTACAAGATAAATATAAATATTTAAATTTTATTTATATCATTTTAAAAAAACTACCCATTT
8269 AAAAAAAAACT
66 AAAAAAAAACT
8280 GTCAAAAACT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.39
Consensus pattern (77 bp):
CTCATTACAAGATAAATATAAATATTTAAATTTTATTTATATCATTTTAAAAAAACTACCCATTT
AAAAAAAAACTC
Found at i:8396 original size:280 final size:277
Alignment explanation
Indices: 7898--8472 Score: 1071
Period size: 280 Copynumber: 2.1 Consensus size: 277
7888 TCAAAACAAA
7898 ATAAAAACTACCCATTTTAAATAAAACTCCTCATTAGAAGATAAATATAAGTATTTAAATTTTAT
1 ATAAAAACTACCCATTTTAAATAAAACTCCTCATTAGAAGATAAATATAAGTATTTAAATTTTAT
7963 TTATATCATTTTAAAAAACTACCCATTTAAAAAAACTGTCAAAAACTACTCACGTAGTGAGTGCC
66 TTATATCATTTTAAAAAACTACCCATTTAAAAAAACTGTCAAAAACTACTCACGTAGTGAGTGCC
8028 CTGTGTCTTGTTAATTATAAAATCAAGTCCTGAGTTTGTATCACGAGTTGACTCGAACACAAACT
131 CTGTGTCTTGTTAATTATAAAATCAAGTCCTGAGTTTGTATCACGAGTTGACTCGAACACAAACT
*
8093 CAGATTTTAAAAATTCAAAACAAAATAAAAGTTACTCATTACAGGATAAATATAAATATTTAAAT
196 CAGATTTTAAAAATTCAAAACAAAATAAAAGTTACCCATTACAGGATAAATATAAATATTTAAAT
8158 TTTATTTATATCATTTT
261 TTTATTTATATCATTTT
8175 ATAAAAACTACCCATTTTAAATAAAACTCCTCATTAGAAGATAAATATAAGTATTTAAATTTTAT
1 ATAAAAACTACCCATTTTAAATAAAACTCCTCATTAGAAGATAAATATAAGTATTTAAATTTTAT
8240 TTATATCATTTTAAAAAAACTACCCATTTAAAAAAAAACTGTCAAAAACTACTCACGTAGTGAGT
66 TTATATCATTTT-AAAAAACTACCCATTT--AAAAAAACTGTCAAAAACTACTCACGTAGTGAGT
* *
8305 GCCCTGTGTCTTGTTAATTATAAAGTCAAGTCCTGAGTTTGTATCACGAGTTGACTCGGACACAA
128 GCCCTGTGTCTTGTTAATTATAAAATCAAGTCCTGAGTTTGTATCACGAGTTGACTCGAACACAA
8370 ACTCAGATTTTAAAAATTCAAAACAAAATAAAAGTTACCCATTACAGGATAAATATAAATATTTA
193 ACTCAGATTTTAAAAATTCAAAACAAAATAAAAGTTACCCATTACAGGATAAATATAAATATTTA
8435 AATTTTATTTATATCATTTT
258 AATTTTATTTATATCATTTT
*
8455 -TAAAAAACTACCAATTTT
1 AT-AAAAACTACCCATTTT
8473 TATCTCAAAA
Statistics
Matches: 290, Mismatches: 4, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
277 77 0.27
278 16 0.06
279 1 0.00
280 196 0.68
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (277 bp):
ATAAAAACTACCCATTTTAAATAAAACTCCTCATTAGAAGATAAATATAAGTATTTAAATTTTAT
TTATATCATTTTAAAAAACTACCCATTTAAAAAAACTGTCAAAAACTACTCACGTAGTGAGTGCC
CTGTGTCTTGTTAATTATAAAATCAAGTCCTGAGTTTGTATCACGAGTTGACTCGAACACAAACT
CAGATTTTAAAAATTCAAAACAAAATAAAAGTTACCCATTACAGGATAAATATAAATATTTAAAT
TTTATTTATATCATTTT
Found at i:8918 original size:107 final size:106
Alignment explanation
Indices: 8796--9063 Score: 403
Period size: 107 Copynumber: 2.5 Consensus size: 106
8786 TTATGATAGA
*
8796 GTTTTAAAAATAAAATATAAAACTAATTTCACTAAGTTTAGTCGTAAATTAAAATTTTATTTCTA
1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTC-TAAATTAAAATTTTATTTCTA
* * *
8861 TTTTTAGAGTAAATTTCAAAATTAATAATTTATTGTTATAAG
65 TTTTGAGAGTAAATTCCAAAATTAATAACTTATTGTTATAAG
* * *
8903 GTTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCTCAAATTAAAATTTTATTTTTA
1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTCT-AAATTAAAATTTTATTTCTA
* * *
8968 TTTTGAGGGTAAATTCCATAATTAATAACTTATTGTTATAGG
65 TTTTGAGAGTAAATTCCAAAATTAATAACTTATTGTTATAAG
* *
9010 GTTTTAGAAATAAAATATATAACTAA-TTCACTAAGTTTAATCTAAATTAAAATT
1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTCTAAATTAAAATT
9064 AAAATTTTAT
Statistics
Matches: 146, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
105 11 0.08
106 16 0.11
107 119 0.82
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (106 bp):
GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTCTAAATTAAAATTTTATTTCTAT
TTTGAGAGTAAATTCCAAAATTAATAACTTATTGTTATAAG
Found at i:19915 original size:16 final size:15
Alignment explanation
Indices: 19896--19938 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
19886 GATTATTGTT
19896 TTTGTTGTTTCTTCCC
1 TTTGTT-TTTCTTCCC
* *
19912 TTTGTTTGTTCTTGCT
1 TTTGTTT-TTCTTCCC
19928 TTTGTTTTTCT
1 TTTGTTTTTCT
19939 ATTTCTCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.00, C:0.16, G:0.14, T:0.70
Consensus pattern (15 bp):
TTTGTTTTTCTTCCC
Found at i:23686 original size:3 final size:3
Alignment explanation
Indices: 23680--23715 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
23670 CAGATTTCTT
23680 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
23716 AAAAAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:25780 original size:22 final size:22
Alignment explanation
Indices: 25710--25869 Score: 98
Period size: 22 Copynumber: 7.3 Consensus size: 22
25700 AAAAATATTT
25710 TTATGAAATTTTGATAACCA-C
1 TTATGAAATTTTGATAACCACC
*
25731 TCTATAAAATTTTGATAACCACAC
1 T-TATGAAATTTTGATAACCAC-C
**
25755 -TATGAAATTTTGATAATTACC
1 TTATGAAATTTTGATAACCACC
* ***
25776 TTATGAAATTGTGATAAATTCC
1 TTATGAAATTTTGATAACCACC
** ** *
25798 CAATGAAATACT-ATAACCTAAC
1 TTATGAAATTTTGATAACC-ACC
*
25820 -TATGAAATTTTAATAA--ACC
1 TTATGAAATTTTGATAACCACC
25839 TTTCTATGAAATTTTGATAACCACC
1 --T-TATGAAATTTTGATAACCACC
*
25864 ATATGA
1 TTATGA
25870 TTTTTCTCCC
Statistics
Matches: 106, Mismatches: 21, Indels: 23
0.71 0.14 0.15
Matches are distributed among these distances:
19 2 0.02
21 14 0.13
22 71 0.67
23 15 0.14
24 1 0.01
25 3 0.03
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCACC
Done.