Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005223.1 Corchorus capsularis cultivar CVL-1 contig05241, 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: 8088
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Found at i:726 original size:29 final size:27
Alignment explanation
Indices: 694--780 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 27
684 AATAAAAAGG
*
694 GTCCAAATTGAGAGTTTAGGGGGCAAAA
1 GTCCAAATT-AAAGTTTAGGGGGCAAAA
*
722 TGTCCAAAATTAAAGTTTATGGGGCAAAA
1 -GTCC-AAATTAAAGTTTAGGGGGCAAAA
* *
751 GTCAAAATCGTACAAGTTCAGGGGGCAAAA
1 GTCCAAAT--TA-AAGTTTAGGGGGCAAAA
781 AGAGTATTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
27 4 0.08
28 3 0.06
29 22 0.45
30 20 0.41
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (27 bp):
GTCCAAATTAAAGTTTAGGGGGCAAAA
Found at i:732 original size:30 final size:28
Alignment explanation
Indices: 706--780 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
696 CCAAATTGAG
706 AGTTTAGGGGGCAAAATGTCCAAAATTAA
1 AGTTTAGGGGGCAAAA-GTCCAAAATTAA
*
735 AGTTTATGGGGCAAAAGT-CAAAATCGTACA
1 AGTTTAGGGGGCAAAAGTCCAAAAT--TA-A
*
765 AGTTCAGGGGGCAAAA
1 AGTTTAGGGGGCAAAA
781 AGAGTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 6 0.15
28 2 0.05
29 17 0.43
30 15 0.38
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.21
Consensus pattern (28 bp):
AGTTTAGGGGGCAAAAGTCCAAAATTAA
Found at i:1012 original size:2 final size:2
Alignment explanation
Indices: 1005--1036 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
995 CAATTTAACA
1005 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
1037 GCACAACTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2026 original size:22 final size:23
Alignment explanation
Indices: 1974--2227 Score: 137
Period size: 22 Copynumber: 11.6 Consensus size: 23
1964 TAAGGAGTAC
* *
1974 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
1995 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
2016 CGAAATTTCATAGAGATCAGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
*
2041 CAAAATTT-ATAGA-AAGATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
2062 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* * * *
2084 CAAAATTTCAAAGCGAAGGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
2107 CAAAATTACATA-ATG-TGATTAT
1 CAAAATTTCATAGA-GATGATTAT
* * * *
2129 CAGAATTTCAT--AG-TGGTCAA
1 CAAAATTTCATAGAGATGATTAT
* * *
2149 CAAAATTTTATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
2171 CAAAATTTCATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
2193 CAAATTTTCA-AAATG-TGATTA-
1 CAAAATTTCATAGA-GATGATTAT
2214 CAAAAATTTCATAG
1 C-AAAATTTCATAG
2228 TGGTATTTAT
Statistics
Matches: 184, Mismatches: 32, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
20 24 0.13
21 26 0.14
22 97 0.53
23 19 0.10
24 5 0.03
25 13 0.07
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.34
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:2129 original size:45 final size:45
Alignment explanation
Indices: 2035--2138 Score: 124
Period size: 45 Copynumber: 2.4 Consensus size: 45
2025 ATAGAGATCA
* * *
2035 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAAAGATTATCAAAATTACATAATGTT
* *
2079 G-TTATCAAAATTTCAAAGCGAAGGTTATCAAAATTACATAATG-T
1 GATTATCAAAATTTCAAAG-AAAGATTATCAAAATTACATAATGTT
*
2123 GATTATCAGAATTTCA
1 GATTATCAAAATTTCA
2139 TAGTGGTCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
43 12 0.24
44 6 0.12
45 33 0.65
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (45 bp):
GATTATCAAAATTTCAAAGAAAGATTATCAAAATTACATAATGTT
Found at i:2202 original size:64 final size:65
Alignment explanation
Indices: 1974--2199 Score: 178
Period size: 67 Copynumber: 3.4 Consensus size: 65
1964 TAAGGAGTAC
* * * * * * * *
1974 CAAAATTTGATAGAAG-G-TTATCAAATCTCATAGAGTGATTATCGAAATTTCATAGAGATCAGA
1 CAAAATTTCATA-AAGAGATTATCAAATTTCATAGTGTG-TCAACAAAATTTCAAAGAGA--AGG
2037 TTAT
62 TTAT
* * *
2041 CAAAATTT-ATAGAA-AGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAAGGT
1 CAAAATTTCATA-AAGAGATTATC-AAATTTCATAGTG-TGTCAACAAAATTTCAAAGAGAAGGT
2104 TAT
63 TAT
* * * *
2107 CAAAATTACATAATGTGATTATCAGAATTTCATAGTG-GTCAACAAAATTTTATAA-AG-AGGTT
1 CAAAATTTCATAAAGAGATTATCA-AATTTCATAGTGTGTCAACAAAATTTCA-AAGAGAAGGTT
2169 AT
64 AT
*
2171 CAAAATTTCATAAAGAGGTTATCAAATTT
1 CAAAATTTCATAAAGAGATTATCAAATTT
2200 TCAAAATGTG
Statistics
Matches: 134, Mismatches: 17, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
63 5 0.04
64 27 0.20
65 13 0.10
66 24 0.18
67 35 0.26
68 28 0.21
69 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (65 bp):
CAAAATTTCATAAAGAGATTATCAAATTTCATAGTGTGTCAACAAAATTTCAAAGAGAAGGTTAT
Found at i:2424 original size:66 final size:64
Alignment explanation
Indices: 2303--2442 Score: 142
Period size: 66 Copynumber: 2.2 Consensus size: 64
2293 TTATTATGTA
* * * * **
2303 ATCAAAATTTCAAGGAGGATAACAAAATTTCATACTTTAGTTTTCAAAATTTCATA-AGAGGGTT
1 ATCAAAATTTCAAGGAGGATAACAAAATTTAATACATGAGTTATCAAAAAATCATAGAGA-GGTT
*
2367 ATCAAAATTTCATAGG-GAGAGTAACAAAATTTAATA-ATGAGGTTATCAAAAAATCATAGGGAG
1 ATCAAAATTTCA-AGGAG-GA-TAACAAAATTTAATACATGA-GTTATCAAAAAATCATAGAGAG
2430 GTT
62 GTT
*
2433 ATTAAAATTT
1 ATCAAAATTT
2443 GTAGTTTTCA
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
64 13 0.21
65 7 0.11
66 41 0.65
67 2 0.03
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.32
Consensus pattern (64 bp):
ATCAAAATTTCAAGGAGGATAACAAAATTTAATACATGAGTTATCAAAAAATCATAGAGAGGTT
Found at i:2519 original size:25 final size:25
Alignment explanation
Indices: 2470--2528 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
2460 ATAAGAAAGT
* * *
2470 TATCAAAATTTTATAGGGAGTTTTA
1 TATCAAAATTTTATAAGAAGATTTA
2495 TATCAAAATTTTATAAGAAGATTTA
1 TATCAAAATTTTATAAGAAGATTTA
2520 T-T-AAAATTT
1 TATCAAAATTT
2529 CATAGCGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 7 0.23
24 1 0.03
25 23 0.74
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.44
Consensus pattern (25 bp):
TATCAAAATTTTATAAGAAGATTTA
Found at i:2760 original size:22 final size:22
Alignment explanation
Indices: 2346--2842 Score: 109
Period size: 22 Copynumber: 22.6 Consensus size: 22
2336 ACTTTAGTTT
*
2346 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAAGAAGGTTA
* *
2368 TCAAAATTTCATAGGGAGAG-TA
1 TCAAAATTTCATAAGAAG-GTTA
* *
2390 ACAAAATTTAATAATG-AGGTTA
1 TCAAAATTTCATAA-GAAGGTTA
** * *
2412 TCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATAAGAAGGTTA
* * *
2434 TTAAAA-TT--T--GTA-GTTT
1 TCAAAATTTCATAAGAAGGTTA
* *
2450 TCAAGATTTCATAAGAAAGTTA
1 TCAAAATTTCATAAGAAGGTTA
* * * *
2472 TCAAAATTTTATAGGGAGTTTTATA
1 TCAAAATTTCATAAGAAG--GT-TA
* *
2497 TCAAAATTTTATAAGAAGATTTA
1 TCAAAATTTCATAAGAAG-GTTA
* * *
2520 TTAAAATTTCAT-AGCGAGATTA
1 TCAAAATTTCATAAG-AAGGTTA
* *
2542 TCACAATTTCAT-AG-TGTGATTA
1 TCAAAATTTCATAAGAAG-G-TTA
* *
2564 TCAAAATTTCA-GAG-TGTGATTA
1 TCAAAATTTCATAAGAAG-G-TTA
* * *
2586 -CTAACAA-TTCATATGGAGGTTT
1 TC-AA-AATTTCATAAGAAGGTTA
* * *
2608 TTAAATTTTCATAACG-TGGTTA
1 TCAAAATTTCATAA-GAAGGTTA
* * * *
2630 TCAATATATCATATGAAAGTTA
1 TCAAAATTTCATAAGAAGGTTA
* * * **
2652 TCAACATCTCATAGTGTTGGTTA
1 TCAAAATTTCATA-AGAAGGTTA
** *
2675 TCAAAATTTCATTGGGAA-ATTA
1 TCAAAATTTCA-TAAGAAGGTTA
*
2697 TCAAAATTTCATATTG-AGGTCT-
1 TCAAAATTTCATA-AGAAGGT-TA
* * * *
2719 TCAAAATTCCTTAGGGAGGTTA
1 TCAAAATTTCATAAGAAGGTTA
*
2741 ACAAAATTTCATAAGAAGGTTA
1 TCAAAATTTCATAAGAAGGTTA
** * *
2763 AAAAACATTT-ATAAAAAGGTTC
1 TCAAA-ATTTCATAAGAAGGTTA
* * ***
2785 TCGAAATTCCAT-AGTATCATTA
1 TCAAAATTTCATAAG-AAGGTTA
* *
2807 TTAAAATTTCATAGGAAGGTTA
1 TCAAAATTTCATAAGAAGGTTA
2829 TCAAAATTTCATAA
1 TCAAAATTTCATAA
2843 TGGGATCATA
Statistics
Matches: 342, Mismatches: 97, Indels: 72
0.67 0.19 0.14
Matches are distributed among these distances:
16 7 0.02
17 4 0.01
19 2 0.01
20 1 0.00
21 16 0.05
22 246 0.72
23 43 0.13
24 5 0.01
25 18 0.05
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TCAAAATTTCATAAGAAGGTTA
Found at i:3153 original size:31 final size:31
Alignment explanation
Indices: 3118--3183 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
3108 AACTTTATGT
*
3118 TTTCCGATTGTACCCTTATT-TTTAAAACATA
1 TTTCCAATTGTACCCTT-TTCTTTAAAACATA
*
3149 TTTCCAATTGTACCCTTTTCTTTAAAGCATA
1 TTTCCAATTGTACCCTTTTCTTTAAAACATA
3180 TTTC
1 TTTC
3184 TAAATTACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTCTTTAAAACATA
Found at i:3514 original size:19 final size:19
Alignment explanation
Indices: 3500--3536 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3490 ACTATTATTT
3500 TTTTAATTTAATATTTTAC
1 TTTTAATTTAATATTTTAC
3519 TTTTAATTTCAAT-TTTTA
1 TTTTAATTT-AATATTTTA
3537 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAATTTAATATTTTAC
Found at i:3759 original size:22 final size:21
Alignment explanation
Indices: 3703--3789 Score: 84
Period size: 22 Copynumber: 4.0 Consensus size: 21
3693 GTCTCTATGT
*
3703 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* * *
3724 TAGTTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
3747 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
3769 GGTTACCAAAATTTCATAGGA
1 GGTTATCAAAATTTCATAGGA
3790 TCAGGTTATT
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
21 3 0.06
22 45 0.88
23 3 0.06
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:3804 original size:24 final size:22
Alignment explanation
Indices: 3711--3841 Score: 83
Period size: 22 Copynumber: 5.9 Consensus size: 22
3701 GTGGTTATCA
*
3711 AAATTTCATAAGATA-GTTATT-
1 AAATTTCAT-AGGTAGGTTATTG
**
3732 ATAATTTCATGAGG-AGGTTATCA
1 A-AATTTCAT-AGGTAGGTTATTG
* ***
3755 AAATTCCATAGTGT-GGTTACCA
1 AAATTTCATAG-GTAGGTTATTG
3777 AAATTTCATAGGATCAGGTTATTG
1 AAATTTCATAGG-T-AGGTTATTG
* *
3801 AAATTTCTTAGGTTGGTTATTG
1 AAATTTCATAGGTAGGTTATTG
3823 AAATTTCATATGGT-GGTTA
1 AAATTTCATA-GGTAGGTTA
3842 ATTATCACAA
Statistics
Matches: 89, Mismatches: 12, Indels: 17
0.75 0.10 0.14
Matches are distributed among these distances:
21 5 0.06
22 63 0.71
23 5 0.06
24 16 0.18
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (22 bp):
AAATTTCATAGGTAGGTTATTG
Found at i:3998 original size:22 final size:22
Alignment explanation
Indices: 3950--4004 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
3940 TATTATGGGT
**
3950 AGGTTATCAAAATTTTGTAGTG
1 AGGTTATCAAAATTTCATAGTG
*
3972 TGGTTATCAAAATTTCATA-TG
1 AGGTTATCAAAATTTCATAGTG
3993 AAGGTTAT-AAAA
1 -AGGTTATCAAAA
4005 GTCTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.38
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGTG
Found at i:4081 original size:22 final size:23
Alignment explanation
Indices: 4056--4257 Score: 84
Period size: 22 Copynumber: 9.0 Consensus size: 23
4046 AGCAATTCTC
*
4056 ATAGAG-TGATTATCGAAATTTT
1 ATAGAGATGATTATCAAAATTTT
*
4078 ATAGAGATCGGATTATCGAAA-TTT
1 ATAGAGAT--GATTATCAAAATTTT
* *
4102 ATAGA-AAGATTATCAAAATTTC
1 ATAGAGATGATTATCAAAATTTT
* * *
4124 ATAGTGTTG-TTATCAAAATTTC
1 ATAGAGATGATTATCAAAATTTT
* * * **
4146 AAAGCGA-GGTTATCAAAATTCC
1 ATAGAGATGATTATCAAAATTTT
*
4168 ATA-ATG-TGATTTATCAGAATTTCAT
1 ATAGA-GATGA-TTATCAAAATTT--T
* * * *
4193 ATAGAG-GGGTCAACAAAATTTT
1 ATAGAGATGATTATCAAAATTTT
* *
4215 ATAAAGA-GATTATCAAAATTTC
1 ATAGAGATGATTATCAAAATTTT
* *
4237 ATAAAGA-GGTTATC-AAATTTT
1 ATAGAGATGATTATCAAAATTTT
4258 CAAAATGTGA
Statistics
Matches: 139, Mismatches: 28, Indels: 27
0.72 0.14 0.14
Matches are distributed among these distances:
21 17 0.12
22 75 0.54
23 13 0.09
24 17 0.12
25 16 0.12
26 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (23 bp):
ATAGAGATGATTATCAAAATTTT
Found at i:4404 original size:19 final size:20
Alignment explanation
Indices: 4368--4405 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
4358 TGGAGTAATT
*
4368 AAAATTTCAAGGATGATATC
1 AAAATTTCAAGGAGGATATC
*
4388 AAAA-TTCAGGGAGGATAT
1 AAAATTTCAAGGAGGATAT
4406 ATATCAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.26
Consensus pattern (20 bp):
AAAATTTCAAGGAGGATATC
Found at i:4435 original size:22 final size:21
Alignment explanation
Indices: 4407--4853 Score: 157
Period size: 22 Copynumber: 20.5 Consensus size: 21
4397 GGAGGATATA
*
4407 TATCAAAATTTAATATGAAGGT
1 TATCAAAATTTCATATG-AGGT
*
4429 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA--TGAGGT
* * *
4451 TTTCAAAATTTCACAAGAGAGT
1 TATCAAAATTTCATATGAG-GT
*
4473 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATG-AGGT
* * *
4494 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATA-TGAGGT
*
4517 TAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCAT-ATGAGGT
* *
4539 TATCAAAAAATT-ATAAGGAGGT
1 TATC-AAAATTTCAT-ATGAGGT
*
4561 TATCAAAA-TT--TGT-A-GT
1 TATCAAAATTTCATATGAGGT
* * * *
4577 TATCAAGATTTTATAAGAATGT
1 TATCAAAATTTCATATG-AGGT
*
4599 TATCAAAATATT-ATAGGGAGGTT
1 TATCAAAAT-TTCATA-TGAGG-T
* * * *
4622 TATCGAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATG-AG-GT
*
4645 TATCACAATTTCATAGTGAGGT
1 TATCAAAATTTCATA-TGAGGT
* *
4667 TATCACAATTTCATA-GTATGAT
1 TATCAAAATTTCATATG-A-GGT
* * *
4689 TATCAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATA-TGAGGT
*
4711 TA-CTAACAA-TTCATATGGAGAT
1 TATC-AA-AATTTCATAT-GAGGT
* * * * *
4733 TTTTAAATTTTCATAACGTGGT
1 TATCAAAATTTCAT-ATGAGGT
* *
4755 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATAT-GAGGT
* * *
4777 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TG-AGGT
*
4800 TATCAAAATTTCAT-TGGGAAGT
1 TATCAAAATTTCATAT--GAGGT
4822 TATCAAAATTTCATATTGAGGT
1 TATCAAAATTTCATA-TGAGGT
4844 CT-TCAAAATT
1 -TATCAAAATT
4854 CCTAAGGGAG
Statistics
Matches: 323, Mismatches: 61, Indels: 82
0.69 0.13 0.18
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
19 2 0.01
20 4 0.01
21 14 0.04
22 223 0.69
23 63 0.20
24 5 0.02
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (21 bp):
TATCAAAATTTCATATGAGGT
Found at i:4544 original size:44 final size:44
Alignment explanation
Indices: 4407--4880 Score: 246
Period size: 44 Copynumber: 10.8 Consensus size: 44
4397 GGAGGATATA
* * * * *
4407 TATCAAAATTTAATATGAAGGTTATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAG-TGAGGT
* * * *
4451 TTTCAAAATTTCACA-AGAGAGTTATCAAAATTTCATAGT-ATGT
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGGT
* * *
4494 AGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGT
1 -TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGT
* * *
4539 TATCAAAAAATT-ATAAGGAGGTTATCAAAA-TT--T-GT-A-GT
1 TATC-AAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGT
* * * * *
4577 TATCAAGATTTTATAAGAATG-TTATCAAAATATT-ATAGGGAGGTT
1 TATCAAAATTTCATAGGGA-GATTATCAAAAT-TTCATAGTGAGG-T
* * * *
4622 TATCGAAATTTTATAGGAAGATTTATCACAATTTCATAGTGAGGT
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGGT
* * * * *
4667 TATCACAATTTCATA-GTATGATTATCAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATAGGGA-GATTATCAAAATTTCATAGTGAGGT
* * * * ** *
4711 TA-CTAACAA-TTCATATGGAGATTTTTAAATTTTCATAACGTGGT
1 TATC-AA-AATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGT
* * * * * * *
4755 TATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTG-AGGT
* *
4800 TATCAAAATTTCATTGGGA-AGTTATCAAAATTTCATATTGAGGT
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGGT
* * * *
4844 CT-TCAAAA-TTCCTAAGGGAGGTTAACCAAATTTCATA
1 -TATCAAAATTTCAT-AGGGAGATTATCAAAATTTCATA
4881 AGAATGTTAA
Statistics
Matches: 332, Mismatches: 69, Indels: 58
0.72 0.15 0.13
Matches are distributed among these distances:
37 5 0.02
38 21 0.06
39 2 0.01
40 3 0.01
41 2 0.01
42 2 0.01
43 14 0.04
44 178 0.54
45 88 0.27
46 17 0.05
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (44 bp):
TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGT
Found at i:4630 original size:23 final size:23
Alignment explanation
Indices: 4598--4649 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
4588 TATAAGAATG
* *
4598 TTATCAAAATATTATAGGGAGGT
1 TTATCAAAATATTATAGGAAGAT
* *
4621 TTATCGAAATTTTATAGGAAGAT
1 TTATCAAAATATTATAGGAAGAT
4644 TTATCA
1 TTATCA
4650 CAATTTCATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (23 bp):
TTATCAAAATATTATAGGAAGAT
Found at i:4824 original size:45 final size:45
Alignment explanation
Indices: 4751--4836 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
4741 TTTCATAACG
* * *
4751 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
4796 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
4837 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:4942 original size:22 final size:22
Alignment explanation
Indices: 4914--4967 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
4904 AAGGTTCTCG
* ** *
4914 AAATTTCATAGTATCGTTATTA
1 AAATTTCATAGGAAAGTTATCA
4936 AAATTTCATAGGAAAGTTATCA
1 AAATTTCATAGGAAAGTTATCA
4958 AAATTTCATA
1 AAATTTCATA
4968 ATGGAATCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (22 bp):
AAATTTCATAGGAAAGTTATCA
Found at i:5254 original size:21 final size:21
Alignment explanation
Indices: 5230--5273 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5220 TTAATTGTAG
*
5230 TAGTTTACTTTGCGGTTGCGC
1 TAGTTTACTTTGCGATTGCGC
*
5251 TAGTTTATTTTGCGATTGCGC
1 TAGTTTACTTTGCGATTGCGC
5272 TA
1 TA
5274 ATTGTTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.16, G:0.25, T:0.45
Consensus pattern (21 bp):
TAGTTTACTTTGCGATTGCGC
Found at i:7099 original size:2 final size:2
Alignment explanation
Indices: 7092--7116 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7082 GTTCCAAGAC
7092 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
7117 AATAGGTACT
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
Done.