Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016735.1 Corchorus olitorius cultivar O-4 contig16768, 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: 48897
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:527 original size:19 final size:18
Alignment explanation
Indices: 494--529 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
484 TTGAAATTAT
494 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
512 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
530 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:881 original size:45 final size:45
Alignment explanation
Indices: 768--887 Score: 181
Period size: 44 Copynumber: 2.7 Consensus size: 45
758 GGCTCGATCA
*
768 AGGACCCAACAATTGAACATGATATTAGCTTAGCTTAATACGTTC
1 AGGACCCAACAATTGGACATGATATTAGCTTAGCTTAATACGTTC
* *
813 AGGA-CCAACAATTGGACCTGATATTAGCTTGGCTTAATACCG-TC
1 AGGACCCAACAATTGGACATGATATTAGCTTAGCTTAATA-CGTTC
*
857 AGGACCCAACAATTGGTCATGATATTAGCTT
1 AGGACCCAACAATTGGACATGATATTAGCTT
888 TATAAATTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
44 38 0.56
45 30 0.44
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (45 bp):
AGGACCCAACAATTGGACATGATATTAGCTTAGCTTAATACGTTC
Found at i:4748 original size:2 final size:2
Alignment explanation
Indices: 4741--4796 Score: 66
Period size: 2 Copynumber: 30.0 Consensus size: 2
4731 TTCAATTTTA
* *
4741 AT AT AT AT AT AT AT AT AT AT A- AC A- AT AT AT AT AT AT A- AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4780 A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
4797 GTCATTTATA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 4 0.08
2 46 0.92
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:4768 original size:16 final size:16
Alignment explanation
Indices: 4749--4793 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
4739 TAATATATAT
4749 ATATATATATATAACA
1 ATATATATATATAACA
4765 ATATATATATATAACA
1 ATATATATATATAACA
4781 ATATATATATATA
1 ATATATATATATA
4794 TATGTCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATATATATATAACA
Found at i:14180 original size:45 final size:42
Alignment explanation
Indices: 14108--14191 Score: 123
Period size: 45 Copynumber: 1.9 Consensus size: 42
14098 TGCATTATCT
* *
14108 AAATTCTACTCCATTTCTAGGTAATTCATCAAAATAAAGCTA
1 AAATTCTACTCCATCTCTAGATAATTCATCAAAATAAAGCTA
14150 AAATTCTACTCCTCAATCTCTAGATAATTCATCAAAATAAAG
1 AAATTCTACT-C-C-ATCTCTAGATAATTCATCAAAATAAAG
14192 TTAATATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 10 0.27
43 1 0.03
44 1 0.03
45 25 0.68
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (42 bp):
AAATTCTACTCCATCTCTAGATAATTCATCAAAATAAAGCTA
Found at i:15662 original size:16 final size:17
Alignment explanation
Indices: 15641--15678 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
15631 GCTGGGGCTT
15641 CCGGGTCA-CAAGTCAA
1 CCGGGTCACCAAGTCAA
*
15657 CCGGGTCATCCGAGTCAA
1 CCGGGTCA-CCAAGTCAA
15675 CCGG
1 CCGG
15679 CCGGGTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.24, C:0.34, G:0.29, T:0.13
Consensus pattern (17 bp):
CCGGGTCACCAAGTCAA
Found at i:19220 original size:24 final size:26
Alignment explanation
Indices: 19187--19236 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
19177 AGTATGCTTT
*
19187 CCTCTTC-AAAATCCAGTCCAGCCAC
1 CCTCTTCAAAAAACCAGTCCAGCCAC
*
19212 CCTC-TCAAAAAACCAGTCCGGCCAC
1 CCTCTTCAAAAAACCAGTCCAGCCAC
19237 TACTTGCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.30, C:0.44, G:0.10, T:0.16
Consensus pattern (26 bp):
CCTCTTCAAAAAACCAGTCCAGCCAC
Found at i:20233 original size:13 final size:13
Alignment explanation
Indices: 20226--20266 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
20216 TTTATATTTG
20226 TTATTTATTATTA
1 TTATTTATTATTA
20239 TTATTTA-T-TTA
1 TTATTTATTATTA
20250 TTTATTTTATTATTA
1 -TTA-TTTATTATTA
20265 TT
1 TT
20267 GTCATTCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
11 3 0.12
12 4 0.17
13 11 0.46
14 3 0.12
15 3 0.12
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:20244 original size:26 final size:26
Alignment explanation
Indices: 20195--20266 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 26
20185 TCTTGTATAA
20195 ATTTATTTTATT-TTAAATTAATTTATATT
1 ATTTATTTTATTATT--ATT-ATTTAT-TT
20224 -TGTTA-TTTATTATTATTATTTATTT
1 AT-TTATTTTATTATTATTATTTATTT
20249 ATTTATTTTATTATTATT
1 ATTTATTTTATTATTATT
20267 GTCATTCTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
25 5 0.13
26 19 0.49
27 3 0.08
28 7 0.18
29 5 0.13
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (26 bp):
ATTTATTTTATTATTATTATTTATTT
Found at i:20259 original size:17 final size:17
Alignment explanation
Indices: 20195--20260 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 17
20185 TCTTGTATAA
*
20195 ATTTATTTTATTTTAAATTA
1 ATTTATTTTA-TTT--ATTT
*
20215 ATTTATATTT-GTTATTT
1 ATTTAT-TTTATTTATTT
20232 A-TTATTATTATTTATTT
1 ATTTATT-TTATTTATTT
20249 ATTTATTTTATT
1 ATTTATTTTATT
20261 ATTATTGTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
15 1 0.03
16 6 0.15
17 16 0.41
18 5 0.13
19 2 0.05
20 6 0.15
21 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
ATTTATTTTATTTATTT
Found at i:21220 original size:22 final size:22
Alignment explanation
Indices: 21195--21484 Score: 221
Period size: 22 Copynumber: 13.5 Consensus size: 22
21185 TCACACTCTA
* *
21195 AAATTTTGATAATCACACTATG
1 AAATTTTGATAACCTCACTATG
** *
21217 AAATCGTGATAACCTCGCTATG
1 AAATTTTGATAACCTCACTATG
*
21239 AAATTTTGATAAACCTTC-CTATA
1 AAATTTTGAT-AACC-TCACTATG
*
21262 AAATTTTGATAAACCTC-CTTATA
1 AAATTTTGAT-AACCTCAC-TATG
*
21285 AAATTCTGATAACCTC-CTTATG
1 AAATTTTGATAACCTCAC-TATG
* *
21307 AAATCTCGATAA-C-CAC----
1 AAATTTTGATAACCTCACTATG
*
21323 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCACTATG
* *
21345 ATATTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCACTATG
* * *
21367 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCACTATG
*
21389 AAATTTTGATCAACAT-ACTATG
1 AAATTTTGAT-AACCTCACTATG
* *
21411 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-CACTATG
21433 AAATTTTGATAACCTTCA-TATG
1 AAATTTTGATAACC-TCACTATG
* *
21455 AAATTTTGATATCCTC-C-CTG
1 AAATTTTGATAACCTCACTATG
21475 AAATTTTGAT
1 AAATTTTGAT
21485 TACTCCATAA
Statistics
Matches: 218, Mismatches: 34, Indels: 34
0.76 0.12 0.12
Matches are distributed among these distances:
16 10 0.05
17 1 0.00
18 2 0.01
20 16 0.07
21 4 0.02
22 139 0.64
23 43 0.20
24 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAACCTCACTATG
Found at i:21639 original size:22 final size:22
Alignment explanation
Indices: 21590--22001 Score: 254
Period size: 22 Copynumber: 18.6 Consensus size: 22
21580 AATCACATTT
* * * *
21590 TGAAAATTTGATATCCTCTTTC
1 TGAAATTTTGATAACCTCTCTA
21612 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
21634 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
21656 CGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * *
21678 TGTAATTTTGATAACCTCACTT
1 TGAAATTTTGATAACCTCTCTA
* *** *
21700 TAAAATTTTGATAAAAACACTA
1 TGAAATTTTGATAACCTCTCTA
*
21722 TGAAATTTTGATAATCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
21744 T-AAATTTTGATAACCAATCTCTA
1 TGAAATTTTGATAACC--TCTCTA
* * *
21767 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTCTA
*
21789 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
* *
21809 TCAAATTTTGGT-A-CTC-CTTA
1 TGAAATTTTGATAACCTCTC-TA
*
21829 TGAAATTGAGACTTTTATAACCT-TCATA
1 TGAAA-T-----TTTGATAACCTCTC-TA
* *
21857 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
** * *
21879 AAAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
*
21901 TGAAATTTTGATAACCTCTCCA
1 TGAAATTTTGATAACCTCTCTA
*
21923 TGAAATATT-ATAACCTC-CTTA
1 TGAAATTTTGATAACCTCTC-TA
* * *
21944 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
*
21966 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTCTCTA
*
21988 TGACATTTTGATAA
1 TGAAATTTTGATAA
22002 TATCTTTGAT
Statistics
Matches: 300, Mismatches: 65, Indels: 50
0.72 0.16 0.12
Matches are distributed among these distances:
19 3 0.01
20 15 0.05
21 46 0.15
22 197 0.66
23 10 0.03
24 13 0.04
26 4 0.01
27 2 0.01
28 10 0.03
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:21762 original size:25 final size:24
Alignment explanation
Indices: 21719--21803 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 24
21709 GATAAAAACA
* * *
21719 CTATGAAATTTTGATAATC-TTC-
1 CTATGAAATTTCGATAACCAATCT
*
21741 CTAT-AAATTTTGATAACCAATCT
1 CTATGAAATTTCGATAACCAATCT
*
21764 CTATGAAATTTCGATAATC-A-CT
1 CTATGAAATTTCGATAACCAATCT
*
21786 CTATGAGATTT-GATAACC
1 CTATGAAATTTCGATAACC
21804 TTCTATCAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 19 0.35
22 18 0.33
23 5 0.09
24 12 0.22
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (24 bp):
CTATGAAATTTCGATAACCAATCT
Found at i:21947 original size:87 final size:88
Alignment explanation
Indices: 21614--22001 Score: 270
Period size: 87 Copynumber: 4.4 Consensus size: 88
21604 CCTCTTTCTG
* * * * * * * * * * *
21614 AAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTCTACGAAATTTTGATAATCACATTAT
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCTCCATGAAATTTTGATAACCTCCTTAT
* * *
21679 GTAATTTTGATAACCTCACTTTA
66 GAAATTTTGATAACCACACTATA
** *
21702 AAATTTTGATAAAAACACTATGAAATTTTGATAATCT-TCCTAT-AAATTTTGATAACCAAT-CT
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCTCC-ATGAAATTTTGATAACC--TCCT
* * * *
21764 CTATGAAATTTCGATAATCACTCTATG
63 -TATGAAATTTTGATAACCACACTATA
* ** * * * * ** * *
21791 AGA-TTTGATAACC-TTCTATCAAATTTTGGTACTCCTTATGAAATTGAGACTTTT-ATAACCTT
1 AAATTTTGATAACCACACTATGAAATTTTGATA-ACC-TCT-CCA-TGA-AATTTTGATAACCTC
* *
21853 CATATGAAATTTTGATAACCACACTAAA
61 CTTATGAAATTTTGATAACCACACTATA
*
21881 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCTCCATGAAATATT-ATAACCTCCTTAT
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCTCCATGAAATTTTGATAACCTCCTTAT
* *
21945 GAAATTTTGTTAACCACACTATG
66 GAAATTTTGATAACCACACTATA
* * *
21968 AAATTCTT-ATAACCTCGCTATGACATTTTGATAA
1 AAATT-TTGATAACCACACTATGAAATTTTGATAA
22002 TATCTTTGAT
Statistics
Matches: 227, Mismatches: 58, Indels: 31
0.72 0.18 0.10
Matches are distributed among these distances:
87 92 0.41
88 44 0.19
89 23 0.10
90 28 0.12
91 14 0.06
92 21 0.09
93 5 0.02
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (88 bp):
AAATTTTGATAACCACACTATGAAATTTTGATAACCTCTCCATGAAATTTTGATAACCTCCTTAT
GAAATTTTGATAACCACACTATA
Found at i:22093 original size:24 final size:22
Alignment explanation
Indices: 22039--22094 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
22029 GTGATAGTAC
*
22039 TATGAAATTTCAATAACTGTCC
1 TATGAAATTTCAATAACTGTCA
* *
22061 TAAGAAATTTTAATAACCTGATCA
1 TATGAAATTTCAATAA-CTG-TCA
22085 TATGAAATTT
1 TATGAAATTT
22095 GGGTAACCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 14 0.50
23 3 0.11
24 11 0.39
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (22 bp):
TATGAAATTTCAATAACTGTCA
Found at i:22113 original size:22 final size:22
Alignment explanation
Indices: 22085--22160 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
22075 AACCTGATCA
22085 TATGAAATTTGGGTAACCACAC
1 TATGAAATTTGGGTAACCACAC
* *
22107 TATGAAATTTTGATAACTTC-CA-
1 TATGAAATTTGGGTAAC--CACAC
* *
22129 TATGAAATTTGGGTACCCATAC
1 TATGAAATTTGGGTAACCACAC
*
22151 TATGGAATTT
1 TATGAAATTT
22161 TGATAACCTC
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 38 0.88
23 2 0.05
24 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (22 bp):
TATGAAATTTGGGTAACCACAC
Found at i:22140 original size:44 final size:44
Alignment explanation
Indices: 22083--22167 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
22073 ATAACCTGAT
22083 CATATGAAATTTGGGTAACCACACTATGAAATTTTGATAACTTC
1 CATATGAAATTTGGGTAACCACACTATGAAATTTTGATAACTTC
* * *
22127 CATATGAAATTTGGGTACCCATACTATGGAATTTTGATAAC
1 CATATGAAATTTGGGTAACCACACTATGAAATTTTGATAAC
22168 CTCCCCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (44 bp):
CATATGAAATTTGGGTAACCACACTATGAAATTTTGATAACTTC
Found at i:22181 original size:22 final size:22
Alignment explanation
Indices: 22156--22213 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
22146 CATACTATGG
22156 AATTTTGATAACC-TCCCCATAA
1 AATTTTGATAACCAT-CCCATAA
* * ** *
22178 AATTATAATAACCATCTTATGA
1 AATTTTGATAACCATCCCATAA
22200 AATTTTGATAACCA
1 AATTTTGATAACCA
22214 CACAGAGACA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.34
Consensus pattern (22 bp):
AATTTTGATAACCATCCCATAA
Found at i:22181 original size:44 final size:44
Alignment explanation
Indices: 22089--22212 Score: 126
Period size: 44 Copynumber: 2.8 Consensus size: 44
22079 TGATCATATG
* * *
22089 AAATTTGGGTAACCACACTATGAAATTTTGATAACTTCCATATG
1 AAATTTGGGTAACCACACTATGAAATTTTGATAACCTCCACATA
* * * *
22133 AAATTTGGGTACCCATACTATGGAATTTTGATAACCTCCCCATA
1 AAATTTGGGTAACCACACTATGAAATTTTGATAACCTCCACATA
** *
22177 AAATTAT-AATAACCATC-TTATGAAATTTTGATAACC
1 AAATT-TGGGTAACCA-CACTATGAAATTTTGATAACC
22213 ACACAGAGAC
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
44 64 0.98
45 1 0.02
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (44 bp):
AAATTTGGGTAACCACACTATGAAATTTTGATAACCTCCACATA
Found at i:41242 original size:58 final size:58
Alignment explanation
Indices: 41152--41266 Score: 230
Period size: 58 Copynumber: 2.0 Consensus size: 58
41142 CTTTTGCTCT
41152 TGAAAGAAGAGGTAGATCACTAAAGAATGTTCTCCTTAGATTTCATTATTTTATTATA
1 TGAAAGAAGAGGTAGATCACTAAAGAATGTTCTCCTTAGATTTCATTATTTTATTATA
41210 TGAAAGAAGAGGTAGATCACTAAAGAATGTTCTCCTTAGATTTCATTATTTTATTAT
1 TGAAAGAAGAGGTAGATCACTAAAGAATGTTCTCCTTAGATTTCATTATTTTATTAT
41267 GCAGTTGCAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (58 bp):
TGAAAGAAGAGGTAGATCACTAAAGAATGTTCTCCTTAGATTTCATTATTTTATTATA
Found at i:48336 original size:257 final size:254
Alignment explanation
Indices: 47563--48366 Score: 903
Period size: 279 Copynumber: 3.0 Consensus size: 254
47553 TATATATATT
* * * * *
47563 TAATGTTCAAAAATATTCCCTAAGGGGACATATGTCGACCCTTTAACTCTAACCATGCATGTGCA
1 TAATGTTCAAAACTATTCCCTAAGGGAACACATGTCAACCCTTTAACCCTAACCATGCATGTGCA
* * *
47628 GTCTGCTAAACTTTACTAATGGTGGATAAAATAATTTTCCTT-AAAAAATATACACTAAAAAGAC
66 -------AAACTTCACTAACGGTGGATAAGATAATTTTCCTTAAAAAAAT-TACACTAAAAAGAC
* * *
47692 ACATGTCAATCCTTTAACCCAGTTTGTATTATCTAATAGTAAATTACATTGATAGTGGATGTGAT
123 ACATGTCAATCCTTTAACCC-GTTTGTATAATC--ATAGTAAACTACACTGATAGTGGATGTGAT
*
47757 AATTTTACTTTTCGTAATAACCATAAACACTTTTAAGTTTAATTTAAGTAACATTATTATGGCTT
185 AATTTTACTTTTCGTAATAACCATAAACACTTTTAA----ATTTTAAGTAACATTATTATGGC-T
47822 TTTACTTAATTAA
245 TTTACTT-A--AA
* * *
47835 TTAATGTTCAAAAATCAAAACTATTTCCTAAGGGTACACATGTCAACCCTTTAACCCTAACCCTG
1 -TAATG-T------TCAAAACTATTCCCTAAGGGAACACATGTCAACCCTTTAACCCTAACCATG
*
47900 CATGTGTAGTCTGCTAAACTTCACTAACGGTGGATAAGATAATTTTCCTTAAAAAAA-TACACTA
58 CA----T-G--TGCAAAACTTCACTAACGGTGGATAAGATAATTTTCCTTAAAAAAATTACACTA
* * * *
47964 AAAAGACACATGTCAATCTTTTAACCTCATTTGCACAATCTAATAGTAAACTACACTGATAGTGG
116 AAAAGACACATGTCAATCCTTTAACC-CGTTTGTATAATC--ATAGTAAACTACACTGATAGTGG
*
48029 ATGTGATAATTTTACTTTTCGTAATAACCATAAACACTTTTAAGTTTTAAGTAACATTATTATGG
178 ATGTGATAATTTTACTTTTCGTAATAACCATAAACACTTTTAAATTTTAAGTAACATTATTATGG
48094 CTTTTACTTAAA
243 CTTTTACTTAAA
*
48106 TAATGTTCAAAACTATTCCCTAAGGGAACACATGTCAACCCTTTAACCCTAACAATGCATGTGCA
1 TAATGTTCAAAACTATTCCCTAAGGGAACACATGTCAACCCTTTAACCCTAACCATGCATGTGCA
* *
48171 AAACTTCACTAACGGTGAATAAGATAATTTTTCTTAAAAAAATGTACACTAAAAAGACACATGTG
66 AAACTTCACTAACGGTGGATAAGATAATTTTCCTTAAAAAAAT-TACACTAAAAAGACACA--TG
* * * * * * *
48236 TCAATCCTTTGATCCCGTTTGTATAATC-TACTAAACTACACTAATAGTGGATATGGTGATTTTC
128 TCAATCCTTT-AACCCGTTTGTATAATCATAGTAAACTACACTGATAGTGGATGTGATAATTTTA
* * * *
48300 CTTTTGGTAATAACCATAAACACTTTTAAATTTTAAGTAACATTATCATGCCTTTTACTTAAT
192 CTTTTCGTAATAACCATAAACACTTTTAAATTTTAAGTAACATTATTATGGCTTTTACTTAAA
48363 TAAT
1 TAAT
48367 TAAGTTTCTT
Statistics
Matches: 467, Mismatches: 43, Indels: 58
0.82 0.08 0.10
Matches are distributed among these distances:
256 43 0.09
257 92 0.20
258 18 0.04
259 1 0.00
260 21 0.04
261 3 0.01
263 49 0.10
269 1 0.00
270 5 0.01
271 2 0.00
273 6 0.01
274 9 0.02
275 21 0.04
279 106 0.23
280 79 0.17
281 6 0.01
284 1 0.00
285 1 0.00
287 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (254 bp):
TAATGTTCAAAACTATTCCCTAAGGGAACACATGTCAACCCTTTAACCCTAACCATGCATGTGCA
AAACTTCACTAACGGTGGATAAGATAATTTTCCTTAAAAAAATTACACTAAAAAGACACATGTCA
ATCCTTTAACCCGTTTGTATAATCATAGTAAACTACACTGATAGTGGATGTGATAATTTTACTTT
TCGTAATAACCATAAACACTTTTAAATTTTAAGTAACATTATTATGGCTTTTACTTAAA
Found at i:48555 original size:13 final size:13
Alignment explanation
Indices: 48537--48561 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48527 TTGGAATTCC
48537 AAATAATATTTAT
1 AAATAATATTTAT
48550 AAATAATATTTA
1 AAATAATATTTA
48562 GAATATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Done.