Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013393.1 Corchorus olitorius cultivar O-4 contig13426, 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: 61212
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:3889 original size:110 final size:110
Alignment explanation
Indices: 3696--3906 Score: 370
Period size: 110 Copynumber: 1.9 Consensus size: 110
3686 AATGCCTCTG
* *
3696 CTTCTATAACTTTATCTCGAAGTCTGTGTTGTGCTTGTAGTAAGTTTTACTGTTTTTCTTGATGC
1 CTTCTATAACTTTATCTCAAAGTCTGTGTTGTGCTTGCAGTAAGTTTTACTGTTTTTCTTGATGC
3761 ATCTGATTTTGTACTTTTCTAATAAAGATTTCATTGCTACATAAT
66 ATCTGATTTTGTACTTTTCTAATAAAGATTTCATTGCTACATAAT
*
3806 CTTCTATAAACTTTATGTCAAAGTCTGTGTTGTGCTTGCAGT-AGTTTTACTGTTTTTCTTGATG
1 CTTCTAT-AACTTTATCTCAAAGTCTGTGTTGTGCTTGCAGTAAGTTTTACTGTTTTTCTTGATG
*
3870 CATCTGATTTTGTACTTTTCTAATAAAGTTTTCATTG
65 CATCTGATTTTGTACTTTTCTAATAAAGATTTCATTG
3907 TTGCATTATA
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
110 65 0.68
111 31 0.32
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (110 bp):
CTTCTATAACTTTATCTCAAAGTCTGTGTTGTGCTTGCAGTAAGTTTTACTGTTTTTCTTGATGC
ATCTGATTTTGTACTTTTCTAATAAAGATTTCATTGCTACATAAT
Found at i:11898 original size:15 final size:15
Alignment explanation
Indices: 11878--11909 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
11868 GCTGAAGTTA
11878 ATGGAGGAAATGATG
1 ATGGAGGAAATGATG
11893 ATGGAGGAAATGATG
1 ATGGAGGAAATGATG
11908 AT
1 AT
11910 TATTTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.22
Consensus pattern (15 bp):
ATGGAGGAAATGATG
Found at i:12208 original size:182 final size:181
Alignment explanation
Indices: 11885--12243 Score: 664
Period size: 182 Copynumber: 2.0 Consensus size: 181
11875 TTAATGGAGG
11885 AAATGATGATGGAGGAAATGATGATTATTTTTCTTTTCCCCTCGGTAATGATTATTTTTCTTTTT
1 AAATGATGATGGAGGAAATGATGATTATTTTTCTTTTCCCCTCGGTAATGATTATTTTTCTTTTT
*
11950 GCAAGTTAAATATGGCTGCAGTTTTTGTTGTCTCTTTGTGTTTGATCCTGACATGAAATTTCCCT
66 GCAAGTTAAATATGGCTGCAGTTTTTGTTGTCTCTTTCTGTTTGATCCTGACATGAAATTTCCCT
* *
12015 TGTGGTTTGTATTCTAGATGTTGGAACTTCCAGTCTTGTTGAAGTTGAAGA
131 TGTGCTTTGTATTCTAGATGTTGGAACTTCCACTCTTGTTGAAGTTGAAGA
12066 AAATGATGATGGAGGAAATGATGATTATTTTTCTTTTCCCCTCGGTAATGATTATTTTTCTTTTT
1 AAATGATGATGGAGGAAATGATGATTATTTTTCTTTTCCCCTCGGTAATGATTATTTTTC-TTTT
* *
12131 TGCAAGTTAAATATGGCTGCAGTTTTTGTTGTCTCTTTCTGTTTGGTCCTGATATGAAATTTCCC
65 TGCAAGTTAAATATGGCTGCAGTTTTTGTTGTCTCTTTCTGTTTGATCCTGACATGAAATTTCCC
12196 TTGTGCTTTGTATTCTAGATGTTGGAACTTCCACTCTTGTTGAAGTTG
130 TTGTGCTTTGTATTCTAGATGTTGGAACTTCCACTCTTGTTGAAGTTG
12244 TACCAGTTCC
Statistics
Matches: 172, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
181 60 0.35
182 112 0.65
ACGTcount: A:0.21, C:0.13, G:0.20, T:0.45
Consensus pattern (181 bp):
AAATGATGATGGAGGAAATGATGATTATTTTTCTTTTCCCCTCGGTAATGATTATTTTTCTTTTT
GCAAGTTAAATATGGCTGCAGTTTTTGTTGTCTCTTTCTGTTTGATCCTGACATGAAATTTCCCT
TGTGCTTTGTATTCTAGATGTTGGAACTTCCACTCTTGTTGAAGTTGAAGA
Found at i:12347 original size:21 final size:21
Alignment explanation
Indices: 12321--12383 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
12311 AGGCTGTACA
* *
12321 AGAGCTCAAGAACAGAAACGG
1 AGAGCTGAAGAACAGAAACAG
12342 AGAGCTGAAGAACAGAAACAG
1 AGAGCTGAAGAACAGAAACAG
12363 AGAGCTGAAGAACAGAAACAG
1 AGAGCTGAAGAACAGAAACAG
12384 CTGGCAGAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.51, C:0.16, G:0.29, T:0.05
Consensus pattern (21 bp):
AGAGCTGAAGAACAGAAACAG
Found at i:12556 original size:20 final size:20
Alignment explanation
Indices: 12531--12578 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
12521 TGAATATTCA
*
12531 GTAGTGTGCAGCTCTGGCAG
1 GTAGTGTGCAGCTCGGGCAG
12551 GTAGTGTGCAGCTCGGGCAG
1 GTAGTGTGCAGCTCGGGCAG
*
12571 GTAATGTG
1 GTAGTGTG
12579 GCAAAATGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.17, G:0.42, T:0.25
Consensus pattern (20 bp):
GTAGTGTGCAGCTCGGGCAG
Found at i:12805 original size:93 final size:90
Alignment explanation
Indices: 12706--12982 Score: 369
Period size: 93 Copynumber: 3.0 Consensus size: 90
12696 ACCGAAATCT
** *
12706 TCTTTTTTTTTTGGTACAAGCACTGAACTTTATCCAATTAAAGTTTCCCAATTTTGTACCAAAGT
1 TCTTTTTTTTTT-GTACTGGTACTGAACTTTATCCAATTAAAGTTTCCCAATTTTGTACCAAAGT
* *
12771 TTATTTTTTGGTACTGGGTACTGAAC
65 TGATTTTTTAGTACTGGGTACTGAAC
*
12797 AATCTTTTTTTTTCTGTACTGGTACTGAACTTTA-CTCGATTAAAGTTTCCCAATTTTGTACCAA
1 --TCTTTTTTTTT-TGTACTGGTACTGAACTTTATC-CAATTAAAGTTTCCCAATTTTGTACCAA
12861 AGTTGATTTTTTAGTACTGGGTACTGAAC
62 AGTTGATTTTTTAGTACTGGGTACTGAAC
* **
12890 TCTATATTTTTTTTGTACTGGTACTGAACTTTATCCAATTAATGTTTCTTAATTTTGTACC-AAG
1 TCT-T-TTTTTTTTGTACTGGTACTGAACTTTATCCAATTAAAGTTTCCCAATTTTGTACCAAAG
* *
12954 CTCGATTTTTTAGTACTTGGTACTGAAC
64 -TTGATTTTTTAGTACTGGGTACTGAAC
12982 T
1 T
12983 TTATTCAGTA
Statistics
Matches: 166, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
91 6 0.04
92 70 0.42
93 89 0.54
94 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (90 bp):
TCTTTTTTTTTTGTACTGGTACTGAACTTTATCCAATTAAAGTTTCCCAATTTTGTACCAAAGTT
GATTTTTTAGTACTGGGTACTGAAC
Found at i:13826 original size:36 final size:38
Alignment explanation
Indices: 13786--13875 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 38
13776 CAAATTCATG
13786 TACATGTCTTTT-T-AGATAAAGACAACATTAAATAGA
1 TACATGTCTTTTCTCAGATAAAGACAACATTAAATAGA
*
13822 TACATGTCTTTGTCTCTCGGATAAAGACAACATTAAATAGA
1 TACATGTC-TT-T-TCTCAGATAAAGACAACATTAAATAGA
*
13863 TACATGGCTTTTC
1 TACATGTCTTTTC
13876 ATCAACTAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
36 8 0.17
37 2 0.04
38 3 0.06
39 2 0.04
40 3 0.06
41 29 0.62
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (38 bp):
TACATGTCTTTTCTCAGATAAAGACAACATTAAATAGA
Found at i:13929 original size:228 final size:227
Alignment explanation
Indices: 13532--13978 Score: 813
Period size: 228 Copynumber: 2.0 Consensus size: 227
13522 TGAACCCATG
*
13532 TGTCTTCTCATAAATACAAATACATGTACATGTCTTTTTAGATAAAGACAAAATTAAATATATAC
1 TGTCTTCTCATAAATACAAATACATGTACATGTCTTTTTAGATAAAGACAAAATTAAATAGATAC
13597 ATGTCTCTGTCTCTCGGATAAAGACAACATTAAATAGATACATGGCTTTTCATCAACTAGACAAC
66 ATGTCTCTGTCTCTCGGATAAAGACAACATTAAATAGATACATGGCTTTTCATCAACTAGACAAC
13662 TCTTCATTCATGAATAATCACATTATCTATTAATGACTTTTCAACAACTAGATTATTATTGGTAA
131 TCTTCATTCATGAATAATCACATTATCTATTAATGACTTTTCAACAACTAGATTATTATTGGTAA
*
13727 ATATCATCAGATCGTAATCCGGAGTGTAGAGAT
196 ATATCATCAGATCG-AACCCGGAGTGTAGAGAT
* *
13760 TGTCTTCTCATAAATACAAATTCATGTACATGTCTTTTTAGATAAAGACAACATTAAATAGATAC
1 TGTCTTCTCATAAATACAAATACATGTACATGTCTTTTTAGATAAAGACAAAATTAAATAGATAC
*
13825 ATGTCTTTGTCTCTCGGATAAAGACAACATTAAATAGATACATGGCTTTTCATCAACTAGACAAC
66 ATGTCTCTGTCTCTCGGATAAAGACAACATTAAATAGATACATGGCTTTTCATCAACTAGACAAC
* * *
13890 TCTTCATTCATGAATAATCACATTATTTATTAATGACTTTTTAACAACTAGATTATTATTTGTAA
131 TCTTCATTCATGAATAATCACATTATCTATTAATGACTTTTCAACAACTAGATTATTATTGGTAA
13955 ATATCATCAGATCGAACCCGGAGT
196 ATATCATCAGATCGAACCCGGAGT
13979 CTTGTGAAAA
Statistics
Matches: 211, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
227 9 0.04
228 202 0.96
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (227 bp):
TGTCTTCTCATAAATACAAATACATGTACATGTCTTTTTAGATAAAGACAAAATTAAATAGATAC
ATGTCTCTGTCTCTCGGATAAAGACAACATTAAATAGATACATGGCTTTTCATCAACTAGACAAC
TCTTCATTCATGAATAATCACATTATCTATTAATGACTTTTCAACAACTAGATTATTATTGGTAA
ATATCATCAGATCGAACCCGGAGTGTAGAGAT
Found at i:14023 original size:13 final size:13
Alignment explanation
Indices: 14005--14029 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13995 TAAAAAGTTG
14005 TTTTAATATAAAT
1 TTTTAATATAAAT
14018 TTTTAATATAAA
1 TTTTAATATAAA
14030 AAGTTGTCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTTAATATAAAT
Found at i:15243 original size:18 final size:18
Alignment explanation
Indices: 15220--15271 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
15210 GAATTCTCTC
15220 ATTAATGCAAATGAATTT
1 ATTAATGCAAATGAATTT
15238 ATTAATGCAAATGAATTT
1 ATTAATGCAAATGAATTT
15256 ATTAATGCAAATGAAT
1 ATTAATGCAAATGAAT
15272 GTAAAAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (18 bp):
ATTAATGCAAATGAATTT
Found at i:17842 original size:15 final size:15
Alignment explanation
Indices: 17822--17855 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17812 GAAAGAGTGG
17822 AAGAGAAAGGAAAGA
1 AAGAGAAAGGAAAGA
* *
17837 AAGAGAAGGGAAAGG
1 AAGAGAAAGGAAAGA
17852 AAGA
1 AAGA
17856 AAGAGATGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (15 bp):
AAGAGAAAGGAAAGA
Found at i:17849 original size:20 final size:19
Alignment explanation
Indices: 17821--17861 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
17811 AGAAAGAGTG
17821 GAAGAGAAAGGAAAGAAAGA
1 GAAGAGAAAGG-AAGAAAGA
*
17841 GAAGGGAAAGGAAGAAAGA
1 GAAGAGAAAGGAAGAAAGA
17860 GA
1 GA
17862 TGTCGGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (19 bp):
GAAGAGAAAGGAAGAAAGA
Found at i:18949 original size:21 final size:22
Alignment explanation
Indices: 18923--18964 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
18913 AGCGGCCTGT
18923 TTCGACCCTAG-GAAGGTCGAG
1 TTCGACCCTAGTGAAGGTCGAG
*
18944 TTCGACCCTGGTGAAGGTCGA
1 TTCGACCCTAGTGAAGGTCGA
18965 AACAGGAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.21, C:0.24, G:0.33, T:0.21
Consensus pattern (22 bp):
TTCGACCCTAGTGAAGGTCGAG
Found at i:22521 original size:15 final size:15
Alignment explanation
Indices: 22501--22534 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
22491 GAAAGAGTAG
22501 AAGAGAAAGGAAAGA
1 AAGAGAAAGGAAAGA
* *
22516 AAGAGAAGGGAAAGG
1 AAGAGAAAGGAAAGA
22531 AAGA
1 AAGA
22535 AAGAGAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (15 bp):
AAGAGAAAGGAAAGA
Found at i:22528 original size:20 final size:19
Alignment explanation
Indices: 22499--22541 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
22489 GAGAAAGAGT
22499 AGAAGAGAAAGGAAAGAAAG
1 AGAAGAGAAAGG-AAGAAAG
*
22519 AGAAGGGAAAGGAAGAAAG
1 AGAAGAGAAAGGAAGAAAG
22538 AGAA
1 AGAA
22542 TTCGGGTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (19 bp):
AGAAGAGAAAGGAAGAAAG
Found at i:22960 original size:2 final size:2
Alignment explanation
Indices: 22955--22986 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
22945 AGACACACAG
22955 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22987 AACCAATGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23974 original size:48 final size:47
Alignment explanation
Indices: 23903--23999 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 47
23893 GAATGTAAAT
*
23903 TTAAAAACCTAAACATGAGTATTTATTCAAAACCCTCACAAGGCTAA
1 TTAAAAACCTAAACATGAGTATTTATTCAAAACCCTCACAAGACTAA
* ** *
23950 TTAAAAACCCTAAACGA-GATTATTTATTTTAAACCCTCATAAGACTAA
1 TTAAAAA-CCTAAAC-ATGAGTATTTATTCAAAACCCTCACAAGACTAA
23998 TT
1 TT
24000 TTACAACATA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
47 7 0.16
48 35 0.81
49 1 0.02
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (47 bp):
TTAAAAACCTAAACATGAGTATTTATTCAAAACCCTCACAAGACTAA
Found at i:34632 original size:15 final size:16
Alignment explanation
Indices: 34612--34641 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34602 GGCACAGCCC
34612 ACTTATA-TATGGGCT
1 ACTTATATTATGGGCT
34627 ACTTATATTATGGGC
1 ACTTATATTATGGGC
34642 CATGCCAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (16 bp):
ACTTATATTATGGGCT
Found at i:36722 original size:47 final size:47
Alignment explanation
Indices: 36653--36744 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 47
36643 AAAAAGAAGC
*
36653 GATGTTCATGAATAGGACAACTCTACTAAAACTTAAGGAAATGATGT
1 GATGTTCATGAATAGGACAACTCTAATAAAACTTAAGGAAATGATGT
* * *
36700 GATGTTCATTAATAGGACAACTCTAATAGAACTTAAGGAATTGAT
1 GATGTTCATGAATAGGACAACTCTAATAAAACTTAAGGAAATGAT
36745 CATTGCACCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (47 bp):
GATGTTCATGAATAGGACAACTCTAATAAAACTTAAGGAAATGATGT
Found at i:46583 original size:2 final size:2
Alignment explanation
Indices: 46578--46611 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
46568 AGCACGTGTG
*
46578 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46612 AATACATGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47034 original size:143 final size:143
Alignment explanation
Indices: 46766--47041 Score: 455
Period size: 143 Copynumber: 1.9 Consensus size: 143
46756 ATTGGTTACA
* * * * *
46766 ACGTGCTGATTTAAGTCATGGTAAATGGTAAAGGGTGATATAATAAGCACGTTGTAAGCTCATGG
1 ACGTGCTGAATCAAGTCATGATAAATAGTAAAGGGTGATATAATAAGCACATTGTAAGCTCATGG
* *
46831 TAAGCATATACTTAAGAACACCAATTTTAGGAAAATTGCACACGTGCACTTTTAGGAAAATTTTC
66 TAAGCATATAC-T-AGAACACCAATTTTAGGAAAATTGCACACGTACACTTTTAGAAAAATTTTC
46896 TAAAAGTATATATAT
129 TAAAAGTATATATAT
46911 ACGTGCTGAATCAAGTCATGATAAATAGTAAAGGGTGATATAATAAAGCACATTGTAAGCTCATG
1 ACGTGCTGAATCAAGTCATGATAAATAGTAAAGGGTGATATAAT-AAGCACATTGTAAGCTCATG
46976 GTAAGCATATAC-AGAACACCAATTTTAGGAAAATTGCACACGTACACTTTTAGAAAAATTTTCT
65 GTAAGCATATACTAGAACACCAATTTTAGGAAAATTGCACACGTACACTTTTAGAAAAATTTTCT
47040 AA
130 AA
47042 CTCCGTTAGA
Statistics
Matches: 123, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
143 52 0.42
145 40 0.33
146 31 0.25
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (143 bp):
ACGTGCTGAATCAAGTCATGATAAATAGTAAAGGGTGATATAATAAGCACATTGTAAGCTCATGG
TAAGCATATACTAGAACACCAATTTTAGGAAAATTGCACACGTACACTTTTAGAAAAATTTTCTA
AAAGTATATATAT
Found at i:47540 original size:15 final size:15
Alignment explanation
Indices: 47517--47552 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
47507 GACATCTCTT
47517 TCTTCCTTTCCCTTC
1 TCTTCCTTTCCCTTC
* *
47532 TCTTTCTTTCCTTTC
1 TCTTCCTTTCCCTTC
47547 TCTTCC
1 TCTTCC
47553 ACTCTTTCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (15 bp):
TCTTCCTTTCCCTTC
Found at i:47544 original size:20 final size:19
Alignment explanation
Indices: 47511--47551 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
47501 TGACCCGACA
47511 TCTCTTTCTTCCTTTCCCT
1 TCTCTTTCTTCCTTTCCCT
*
47530 TCTCTTTCTTTCCTTTCTCT
1 TCTCTTTC-TTCCTTTCCCT
47550 TC
1 TC
47552 CACTCTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (19 bp):
TCTCTTTCTTCCTTTCCCT
Found at i:51129 original size:21 final size:22
Alignment explanation
Indices: 51091--51132 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
51081 TTCTCCTATT
51091 TCGACCTTCACCAGGGTCGAAC
1 TCGACCTTCACCAGGGTCGAAC
*
51113 TCGACCTTC-CGAGGGTCGAA
1 TCGACCTTCACCAGGGTCGAA
51133 ACAGGCTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.19
Consensus pattern (22 bp):
TCGACCTTCACCAGGGTCGAAC
Found at i:51826 original size:22 final size:22
Alignment explanation
Indices: 51801--51851 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
51791 ACCCATTGCA
51801 AGGTCGAACTCGACCTGCCACC
1 AGGTCGAACTCGACCTGCCACC
51823 AGGTCGAACTCGACCTGCCACC
1 AGGTCGAACTCGACCTGCCACC
51845 AGGTCGA
1 AGGTCGA
51852 GTTGAAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.37, G:0.25, T:0.14
Consensus pattern (22 bp):
AGGTCGAACTCGACCTGCCACC
Found at i:52883 original size:17 final size:18
Alignment explanation
Indices: 52851--52884 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52841 GCCGGCAAAC
52851 GGGAGAGAAGAAGAATGT
1 GGGAGAGAAGAAGAATGT
52869 GGGAGAGAA-AAGAATG
1 GGGAGAGAAGAAGAATG
52885 GACGAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.44, T:0.09
Consensus pattern (18 bp):
GGGAGAGAAGAAGAATGT
Found at i:57125 original size:22 final size:23
Alignment explanation
Indices: 57086--57128 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
57076 AATCCTAATC
57086 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
57109 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
57129 AATCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Done.