Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014080.1 Kokia drynarioides strain JFW-HI SEQ_129111, 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: 124702
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:3837 original size:20 final size:21
Alignment explanation
Indices: 3798--3838 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3788 CACTGTTTCT
* *
3798 TTTAAATTGATTGTTTATATA
1 TTTAAATCGAATGTTTATATA
3819 TTTAAATCGAATG-TTATATA
1 TTTAAATCGAATGTTTATATA
3839 GTACTTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (21 bp):
TTTAAATCGAATGTTTATATA
Found at i:9070 original size:99 final size:99
Alignment explanation
Indices: 8899--9125 Score: 409
Period size: 99 Copynumber: 2.3 Consensus size: 99
8889 CAGAATGGAA
*
8899 CAAAATGAATTTGTAATTAATAATGAGATAACTGGCATTGCTTGAAAAAGGAAAAGCACATCTCA
1 CAAAATGAATTTGTAATTAACAATGAGATAACTGGCATTGCTTGAAAAAGGAAAAGCACATCTCA
* *
8964 AATTATTCATTCAACATGAAAAAATAAAAACCAT
66 AATTATTCATCCAACACGAAAAAATAAAAACCAT
8998 CAAAATGAATTTGTAATTAACAATGAGATAACTGGCATTGCTTGAAAAAGGAAAAGCACATCTCA
1 CAAAATGAATTTGTAATTAACAATGAGATAACTGGCATTGCTTGAAAAAGGAAAAGCACATCTCA
*
9063 AATTATTCATCCAACACGAAAAATTAAAAACCAT
66 AATTATTCATCCAACACGAAAAAATAAAAACCAT
*
9097 CAAAATGAATTTGTAATTAACATTGAGAT
1 CAAAATGAATTTGTAATTAACAATGAGAT
9126 TTTTGTGTGT
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 123 1.00
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (99 bp):
CAAAATGAATTTGTAATTAACAATGAGATAACTGGCATTGCTTGAAAAAGGAAAAGCACATCTCA
AATTATTCATCCAACACGAAAAAATAAAAACCAT
Found at i:22337 original size:10 final size:10
Alignment explanation
Indices: 22322--22396 Score: 66
Period size: 10 Copynumber: 7.5 Consensus size: 10
22312 TGCTTTAGCA
22322 AGCATCGAGC
1 AGCATCGAGC
*
22332 AGCATC-AAC
1 AGCATCGAGC
22341 AAGCATCGAGC
1 -AGCATCGAGC
*
22352 AGCATC-AGT
1 AGCATCGAGC
*
22361 AACTATCGAGC
1 AGC-ATCGAGC
*
22372 AGTATC-AGC
1 AGCATCGAGC
22381 GAGCATCGAGC
1 -AGCATCGAGC
22392 AGCAT
1 AGCAT
22397 TAGTAGCAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
9 9 0.18
10 34 0.67
11 8 0.16
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.15
Consensus pattern (10 bp):
AGCATCGAGC
Found at i:22345 original size:20 final size:20
Alignment explanation
Indices: 22318--22396 Score: 106
Period size: 20 Copynumber: 4.0 Consensus size: 20
22308 CAACTGCTTT
22318 AGCAAGCATCGAGCAGCATC
1 AGCAAGCATCGAGCAGCATC
*
22338 AACAAGCATCGAGCAGCATC
1 AGCAAGCATCGAGCAGCATC
* *
22358 AGTAA-CTATCGAGCAGTATC
1 AGCAAGC-ATCGAGCAGCATC
*
22378 AGCGAGCATCGAGCAGCAT
1 AGCAAGCATCGAGCAGCAT
22397 TAGTAGCAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.14
Consensus pattern (20 bp):
AGCAAGCATCGAGCAGCATC
Found at i:22386 original size:40 final size:40
Alignment explanation
Indices: 22325--22401 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
22315 TTTAGCAAGC
22325 ATCGAGCAGCATCAACAAGCATCGAGCAGCATCAGTAACT
1 ATCGAGCAGCATCAACAAGCATCGAGCAGCATCAGTAACT
* * * *
22365 ATCGAGCAGTATCAGCGAGCATCGAGCAGCATTAGTA
1 ATCGAGCAGCATCAACAAGCATCGAGCAGCATCAGTA
22402 GCAGTTGGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (40 bp):
ATCGAGCAGCATCAACAAGCATCGAGCAGCATCAGTAACT
Found at i:23976 original size:19 final size:19
Alignment explanation
Indices: 23952--24005 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
23942 GAAGAGAAAG
23952 AAAAGAAGGAGAAGGACCA
1 AAAAGAAGGAGAAGGACCA
23971 AAAAGAAGGAGAAGGACCA
1 AAAAGAAGGAGAAGGACCA
** *
23990 AATTGAAGGAAAAGGA
1 AAAAGAAGGAGAAGGA
24006 AAGGAGAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.57, C:0.07, G:0.31, T:0.04
Consensus pattern (19 bp):
AAAAGAAGGAGAAGGACCA
Found at i:24983 original size:6 final size:6
Alignment explanation
Indices: 24972--25012 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
24962 TGATCAAAAT
* *
24972 TGAAAG TGAAAG TGAAAG TGAAAA TGAAAG TGAAAA TGAAA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
25013 TTGGAATTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.27, T:0.17
Consensus pattern (6 bp):
TGAAAG
Found at i:24989 original size:12 final size:12
Alignment explanation
Indices: 24967--25012 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
24957 ATTTGTGATC
24967 AAAATTGAAAGTG
1 AAAA-TGAAAGTG
*
24980 AAAGTGAAAGTG
1 AAAATGAAAGTG
24992 AAAATGAAAGTG
1 AAAATGAAAGTG
25004 AAAATGAAA
1 AAAATGAAA
25013 TTGGAATTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 28 0.90
13 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.17
Consensus pattern (12 bp):
AAAATGAAAGTG
Found at i:24999 original size:18 final size:18
Alignment explanation
Indices: 24967--25012 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
24957 ATTTGTGATC
*
24967 AAAATTGAAAGTGAAAGTG
1 AAAA-TGAAAATGAAAGTG
*
24986 AAAGTGAAAATGAAAGTG
1 AAAATGAAAATGAAAGTG
25004 AAAATGAAA
1 AAAATGAAA
25013 TTGGAATTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.17
Consensus pattern (18 bp):
AAAATGAAAATGAAAGTG
Found at i:28838 original size:23 final size:23
Alignment explanation
Indices: 28806--28936 Score: 99
Period size: 23 Copynumber: 5.8 Consensus size: 23
28796 GTTGGGGAAA
* * *
28806 CAGTAAGCACACACGGTGCAATT
1 CAGTAGGCACACACAGTGCAAAT
28829 CAGTAGG--CACACAGTGC-AAT
1 CAGTAGGCACACACAGTGCAAAT
** * *
28849 CAGTAGGTGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGCAAAT
** *
28872 CAGTAGGCACACAGGGTGCAAAG
1 CAGTAGGCACACACAGTGCAAAT
*
28895 CAGTAAGCACACACAGTGCTAAA-
1 CAGTAGGCACACACAGTGC-AAAT
* * *
28918 CAATAAGCACATACAGTGC
1 CAGTAGGCACACACAGTGC
28937 TGAACAATAA
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.10
21 9 0.10
22 8 0.09
23 59 0.67
24 3 0.03
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (23 bp):
CAGTAGGCACACACAGTGCAAAT
Found at i:28845 original size:21 final size:20
Alignment explanation
Indices: 28815--28885 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 20
28805 ACAGTAAGCA
*
28815 CACACGGTGCAATTCAGTAGG
1 CACACAGTGCAA-TCAGTAGG
28836 CACACAGTGCAATCAGTAGGTG
1 CACACAGTGCAATCAGTA-G-G
* *
28858 CACATAGCGCAAATCAGTAGG
1 CACACAGTGC-AATCAGTAGG
28879 CACACAG
1 CACACAG
28886 GGTGCAAAGC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
20 6 0.14
21 19 0.44
22 10 0.23
23 8 0.19
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.15
Consensus pattern (20 bp):
CACACAGTGCAATCAGTAGG
Found at i:28937 original size:23 final size:23
Alignment explanation
Indices: 28898--28948 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
28888 TGCAAAGCAG
28898 TAAGCACACACAGTGCTAAACAA
1 TAAGCACACACAGTGCTAAACAA
* *
28921 TAAGCACATACAGTGCTGAACAA
1 TAAGCACACACAGTGCTAAACAA
28944 TAAGC
1 TAAGC
28949 GCGCTAGCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.16
Consensus pattern (23 bp):
TAAGCACACACAGTGCTAAACAA
Found at i:29049 original size:24 final size:26
Alignment explanation
Indices: 29011--29058 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
29001 TCTACATGGG
29011 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
29037 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
29059 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:34464 original size:8 final size:8
Alignment explanation
Indices: 34451--34476 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
34441 GACGAGGCTT
34451 TTCTTGCA
1 TTCTTGCA
34459 TTCTTGCA
1 TTCTTGCA
34467 TTCTTGCA
1 TTCTTGCA
34475 TT
1 TT
34477 GACGACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.23, G:0.12, T:0.54
Consensus pattern (8 bp):
TTCTTGCA
Found at i:39354 original size:41 final size:40
Alignment explanation
Indices: 39266--39355 Score: 94
Period size: 41 Copynumber: 2.2 Consensus size: 40
39256 TTTTATAAAA
** *
39266 AAAATAT-AAAATATCAGATTTTATAAAATATATTTATTC
1 AAAATATAAAAATATCAGATTTTATAAAATATATCAAATC
**
39305 AAATATATAAAAATAT-ATTTTTATATAAAATATATCAAATC
1 AAA-ATATAAAAATATCAGATTT-TATAAAATATATCAAATC
39346 TAAAATATAA
1 -AAAATATAA
39356 CGATATAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
39 3 0.07
40 8 0.19
41 28 0.67
42 3 0.07
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (40 bp):
AAAATATAAAAATATCAGATTTTATAAAATATATCAAATC
Found at i:47079 original size:21 final size:21
Alignment explanation
Indices: 47002--47079 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
46992 ACAGTGCAGA
* *
47002 CTTCTACCGATACTTGTGATAG
1 CTTCTACCGATACTAGTTAT-G
* * *
47024 -TTCTACTGATACAAGTGTA-A
1 CTTCTACCGATACTAGT-TATG
* * *
47044 CATCTATCGAAACTAGTTATG
1 CTTCTACCGATACTAGTTATG
47065 CTTCTACCGATACTA
1 CTTCTACCGATACTA
47080 AAAACTCCAA
Statistics
Matches: 39, Mismatches: 14, Indels: 7
0.65 0.23 0.12
Matches are distributed among these distances:
20 2 0.05
21 36 0.92
22 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (21 bp):
CTTCTACCGATACTAGTTATG
Found at i:47786 original size:42 final size:42
Alignment explanation
Indices: 47735--47881 Score: 168
Period size: 42 Copynumber: 3.5 Consensus size: 42
47725 TATGCTCTAT
* *
47735 CGAGTCATAAGTCTTCCTTTAAACATATTCTCATTCTCATTT
1 CGAGACATAAGTCTTCCTTTAAACATATTCTCATTCTCATTC
* * *
47777 CGAGACATAAGTCTTCCTTTAATCATAATCTCATTCTCATCC
1 CGAGACATAAGTCTTCCTTTAAACATATTCTCATTCTCATTC
** * * * * *
47819 CGAGACACGAGTCTTCCTTTATATAAATTCTCATGCTCAATC
1 CGAGACATAAGTCTTCCTTTAAACATATTCTCATTCTCATTC
*
47861 CTGAGACATGAGTCTTCCTTT
1 C-GAGACATAAGTCTTCCTTT
47882 TTATACATCA
Statistics
Matches: 88, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 70 0.80
43 18 0.20
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (42 bp):
CGAGACATAAGTCTTCCTTTAAACATATTCTCATTCTCATTC
Found at i:51012 original size:25 final size:25
Alignment explanation
Indices: 50980--51091 Score: 163
Period size: 25 Copynumber: 4.4 Consensus size: 25
50970 GTAATCTGAT
*
50980 TCTGGCTCG-AAGGAGCGATATTCTG
1 TCTGGCTCGTAA-GAGCGATATTCTA
*
51005 TCTGGCTCGTAAGAGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTA
* *
51030 TCTAGTTCGTAAGAGCGATATTCTA
1 TCTGGCTCGTAAGAGCGATATTCTA
51055 TCTGGCTCGTAAGAGCGATATTCTA
1 TCTGGCTCGTAAGAGCGATATTCTA
51080 TCTGGGCTCGTA
1 TCT-GGCTCGTA
51092 TGAGATAAAT
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
25 70 0.88
26 10 0.12
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (25 bp):
TCTGGCTCGTAAGAGCGATATTCTA
Found at i:63139 original size:21 final size:21
Alignment explanation
Indices: 63115--63164 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
63105 GACTTTTACA
* *
63115 GATATAAGTGACAATTCTACC
1 GATACAAGAGACAATTCTACC
*
63136 GATACAAGAGACTATTCTACC
1 GATACAAGAGACAATTCTACC
*
63157 GAAACAAG
1 GATACAAG
63165 TCATGCTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (21 bp):
GATACAAGAGACAATTCTACC
Found at i:69376 original size:63 final size:63
Alignment explanation
Indices: 69275--69400 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
69265 TTTTAAGAGG
*
69275 GAACAAAATCCCTGTCAGCCCCTTGAGTTCGCCTTGATTGTATCCAATAATTGATTGTAACAT
1 GAACAAAATCCCTGTCAGCCCCTTGAGTTCGCCCTGATTGTATCCAATAATTGATTGTAACAT
*
69338 GAACAAGATCCCTGTCAGCCCCTTGAGTTCGCCCTGATTGTATCCAATAATTGATTGTAACAT
1 GAACAAAATCCCTGTCAGCCCCTTGAGTTCGCCCTGATTGTATCCAATAATTGATTGTAACAT
69401 TTAATCGAGT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (63 bp):
GAACAAAATCCCTGTCAGCCCCTTGAGTTCGCCCTGATTGTATCCAATAATTGATTGTAACAT
Found at i:69908 original size:58 final size:59
Alignment explanation
Indices: 69826--70193 Score: 277
Period size: 60 Copynumber: 6.2 Consensus size: 59
69816 TCAATGCATA
*
69826 GCCAACACCAAAAAAATTAATTTTTTAT-TAGAT-AAAAGGTGGTGTCAGCCATGCAATG
1 GCCAACACCAAATAAATTAATTTTTTATCT-GATAAAAAGGTGGTGTCAGCCATGCAATG
* * * * **
69884 GCCAACACCAAATAAATTATTTTTTTATCTGATAAAAAGGTGGTATCAACTAATGC-GCG
1 GCCAACACCAAATAAATTAATTTTTTATCTGATAAAAAGGTGGTGTCAGC-CATGCAATG
* * * *
69943 GTCAACA-CAAAAAAATTTTAATTTTTTATCTGATAAAAAAGGTGGTGTCAGTCATGCAATT
1 GCCAACACCAAATAAA--TTAATTTTTTATCTGAT-AAAAAGGTGGTGTCAGCCATGCAATG
* * * * *
70004 GTCAACACGAAA-AAATTTATTTTTTTATCTGATAAAAAGATGGTGT-TGACCAATGC-ATG
1 GCCAACACCAAATAAA-TTAATTTTTTATCTGATAAAAAGGTGGTGTCAG-CC-ATGCAATG
* * *** * ** * *
70063 ACCAACACAAAATTTTTTTGATTTTTTATCAAATAAAAAGGTAGTGTCGGCCATGCAATG
1 GCCAACACCAAA-TAAATTAATTTTTTATCTGATAAAAAGGTGGTGTCAGCCATGCAATG
* ** * * *
70123 GCCAACACCAAA-AAA-AAAAATTTTGTCAGATTAAAAAGGTGGTGTCGGCCATGCAATG
1 GCCAACACCAAATAAATTAATTTTTTATCTGA-TAAAAAGGTGGTGTCAGCCATGCAATG
* *
70181 ACCAACACTAAAT
1 GCCAACACCAAAT
70194 TTTTTTTTTC
Statistics
Matches: 244, Mismatches: 50, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
57 9 0.04
58 73 0.30
59 50 0.20
60 84 0.34
61 25 0.10
62 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (59 bp):
GCCAACACCAAATAAATTAATTTTTTATCTGATAAAAAGGTGGTGTCAGCCATGCAATG
Found at i:70146 original size:120 final size:119
Alignment explanation
Indices: 69842--70199 Score: 382
Period size: 120 Copynumber: 3.0 Consensus size: 119
69832 ACCAAAAAAA
* *
69842 TTAATTTTTTATTAGAT-AAAAGGTGGTGTCAGCCATGCAATGGCCAACACCAAATAAATTATTT
1 TTAATTTTTTATCAGATAAAAAGGTGGTGTCAGCCATGCAATGGCCAACACCAAAAAAATTATTT
* * * ** ** ***
69906 TTTTATCTGATAAAAAGGTGGTATCAACTAATGCGCGGTCAACACAAAAAAATT
66 TTTTATCTGATAAAAAGGTGGTGTCGACCAATGCATGACCAACACAAAATTTTT
* * * * * *
69960 TTAATTTTTTATCTGATAAAAAAGGTGGTGTCAGTCATGCAATTGTCAACACGAAAAAATTTATT
1 TTAATTTTTTATCAGAT-AAAAAGGTGGTGTCAGCCATGCAATGGCCAACACCAAAAAAATTATT
* *
70025 TTTTTATCTGATAAAAAGATGGTGTTGACCAATGCATGACCAACACAAAATTTTT
65 TTTTTATCTGATAAAAAGGTGGTGTCGACCAATGCATGACCAACACAAAATTTTT
* * * * ***
70080 TTGATTTTTTATCAAATAAAAAGGTAGTGTCGGCCATGCAATGGCCAACACCAAAAAAA--AAAA
1 TTAATTTTTTATCAGATAAAAAGGTGGTGTCAGCCATGCAATGGCCAACACCAAAAAAATTATTT
* * * *
70143 TTTTGTCAGATTAAAAAGGTGGTGTCGGCC-ATGCAATGACCAACACTAAATTTTT
66 TTTTATCTGA-TAAAAAGGTGGTGTCGACCAATGC-ATGACCAACACAAAATTTTT
70198 TT
1 TT
70200 TTTCAAAATC
Statistics
Matches: 197, Mismatches: 39, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
117 13 0.07
118 52 0.26
119 35 0.18
120 97 0.49
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (119 bp):
TTAATTTTTTATCAGATAAAAAGGTGGTGTCAGCCATGCAATGGCCAACACCAAAAAAATTATTT
TTTTATCTGATAAAAAGGTGGTGTCGACCAATGCATGACCAACACAAAATTTTT
Found at i:80988 original size:16 final size:16
Alignment explanation
Indices: 80967--81013 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
80957 GAGCGGAAAG
80967 AAAATTAGAAAGATGA
1 AAAATTAGAAAGATGA
*
80983 AAAATTA-AAGAGGTAGA
1 AAAATTAGAA-AGAT-GA
81000 AAAA-TAGAAAGATG
1 AAAATTAGAAAGATG
81014 GAAATATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
15 3 0.12
16 15 0.58
17 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (16 bp):
AAAATTAGAAAGATGA
Found at i:103132 original size:9 final size:9
Alignment explanation
Indices: 103114--103145 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
103104 GCACTAATTG
*
103114 ATTATACAA
1 ATTATTCAA
103123 ATTATTCAA
1 ATTATTCAA
103132 ATTATTCAA
1 ATTATTCAA
103141 ATTAT
1 ATTAT
103146 AAAAGTCAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTATTCAA
Found at i:104720 original size:16 final size:15
Alignment explanation
Indices: 104685--104731 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
104675 ATTTAGGTTC
*
104685 ATTT-ATATTAATATT
1 ATTTAATATTAA-AAT
*
104700 ATTTAATTTTAGAAAT
1 ATTTAATATTA-AAAT
104716 ATTTAATATTAAAAT
1 ATTTAATATTAAAAT
104731 A
1 A
104732 ACACAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 9 0.33
16 17 0.63
17 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTTAATATTAAAAT
Found at i:106140 original size:23 final size:23
Alignment explanation
Indices: 106070--106250 Score: 117
Period size: 23 Copynumber: 7.8 Consensus size: 23
106060 AAGTACTTAG
106070 CAGTAAGCACACAAGTGCTGGGGAA-A
1 CAGTAAGCACACAAGTGC----GAATA
* *
106096 CAGTAAGCACACACGTGC-AATC
1 CAGTAAGCACACAAGTGCGAATA
*
106118 CAGTAGGCACACACAGTGC-AAT-
1 CAGTAAGCACACA-AGTGCGAATA
* * ** *
106140 CAGTAGGCGCACATAACGCAAAT-
1 CAGTAAGCACACA-AGTGCGAATA
* * *
106163 CAGTAGGCACACGAGGTGC-AAAA
1 CAGTAAGCACAC-AAGTGCGAATA
106186 CAGTAAGCACACGAAGTGCGAA-A
1 CAGTAAGCACAC-AAGTGCGAATA
106209 CAGTAAGCACACGAAGTGCGAA-A
1 CAGTAAGCACAC-AAGTGCGAATA
106232 CAGTAAGCACACACAGTGC
1 CAGTAAGCACACA-AGTGC
106251 TGAACAGTAA
Statistics
Matches: 133, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
21 2 0.02
22 30 0.23
23 81 0.61
24 3 0.02
26 17 0.13
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (23 bp):
CAGTAAGCACACAAGTGCGAATA
Found at i:106151 original size:24 final size:22
Alignment explanation
Indices: 106096--106152 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
106086 GCTGGGGAAA
*
106096 CAGTAAGCACACACGTGCAATC
1 CAGTAGGCACACACGTGCAATC
106118 CAGTAGGCACACACAGTGCAAT-
1 CAGTAGGCACACAC-GTGCAATC
*
106140 CAGTAGGCGCACA
1 CAGTAGGCACACA
106153 TAACGCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 25 0.78
23 7 0.22
ACGTcount: A:0.35, C:0.30, G:0.23, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACGTGCAATC
Found at i:106256 original size:23 final size:23
Alignment explanation
Indices: 106163--106261 Score: 139
Period size: 23 Copynumber: 4.3 Consensus size: 23
106153 TAACGCAAAT
* * *
106163 CAGTAGGCACACGAGGTGCAAAA
1 CAGTAAGCACACGAAGTGCGAAA
106186 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
106209 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
106232 CAGTAAGCACAC-ACAGTGCTG-AA
1 CAGTAAGCACACGA-AGTGC-GAAA
106255 CAGTAAG
1 CAGTAAG
106262 TGCGTTAGTG
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
22 1 0.01
23 69 0.97
24 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.26, T:0.10
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:106363 original size:24 final size:26
Alignment explanation
Indices: 106325--106372 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
106315 TCTACATGGG
106325 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
106351 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
106373 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:108674 original size:2 final size:2
Alignment explanation
Indices: 108669--108699 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
108659 TTCTTTTTTA
108669 AT AT AT 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 AT AT AT A
108700 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:108959 original size:31 final size:35
Alignment explanation
Indices: 108924--108986 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 35
108914 TAATTGGAAC
108924 AAAAAATTA-ATTG-TAT-ATA-AATTTAAAAAAT
1 AAAAAATTATATTGATATAATAGAATTTAAAAAAT
* *
108955 AAAAATTTATTTTGATATAATAGAATTTAAAA
1 AAAAAATTATATTGATATAATAGAATTTAAAA
108987 TATACTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
31 8 0.31
32 3 0.12
33 3 0.12
34 3 0.12
35 9 0.35
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (35 bp):
AAAAAATTATATTGATATAATAGAATTTAAAAAAT
Found at i:109958 original size:15 final size:15
Alignment explanation
Indices: 109938--109968 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
109928 AATAATAAAA
*
109938 AAATTCAATTTTTTT
1 AAATTCAAATTTTTT
109953 AAATTCAAATTTTTT
1 AAATTCAAATTTTTT
109968 A
1 A
109969 TAAAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATTCAAATTTTTT
Found at i:109963 original size:16 final size:16
Alignment explanation
Indices: 109938--109972 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
109928 AATAATAAAA
109938 AAATTCAATTTTTT-T
1 AAATTCAATTTTTTAT
109953 AAATTCAAATTTTTTAT
1 AAATTC-AATTTTTTAT
109970 AAA
1 AAA
109973 AAAATTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 8 0.44
17 4 0.22
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATTCAATTTTTTAT
Found at i:112452 original size:25 final size:25
Alignment explanation
Indices: 112424--112471 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
112414 TCATCCTTAC
*
112424 TCTCTTGTATAAATTCAATTATATA
1 TCTCTAGTATAAATTCAATTATATA
112449 TCTCTAGTATAAATTCAATTATA
1 TCTCTAGTATAAATTCAATTATA
112472 AAATTTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (25 bp):
TCTCTAGTATAAATTCAATTATATA
Found at i:112473 original size:12 final size:12
Alignment explanation
Indices: 112431--112473 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
112421 TACTCTCTTG
112431 TATAAATTCAAT
1 TATAAATTCAAT
* * *
112443 TATATATCTCTAG
1 TATAAAT-TCAAT
112456 TATAAATTCAAT
1 TATAAATTCAAT
112468 TATAAA
1 TATAAA
112474 ATTTGATATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (12 bp):
TATAAATTCAAT
Found at i:113741 original size:17 final size:16
Alignment explanation
Indices: 113712--113745 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
113702 TTATTTTTTA
113712 ATTTTTTTAAATATTT
1 ATTTTTTTAAATATTT
*
113728 ATTTTATTTTAATATTT
1 ATTTT-TTTAAATATTT
113745 A
1 A
113746 ATAATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTTTAAATATTT
Found at i:116898 original size:267 final size:266
Alignment explanation
Indices: 116398--116914 Score: 781
Period size: 267 Copynumber: 1.9 Consensus size: 266
116388 CTTTCTAAAA
*
116398 TCTCAAAACTTAAAGAAATTTATTGCATTGATTTTTTTCTCTAGTGTTTTTTGCTCCTACTTTCA
1 TCTCAAAACTTAAAGAAATTTATTGCATTGATTTTTATCTCTAGTGTTTTTTGCTCCTACTTTCA
* *
116463 TTTTTGATACTCCTTCCAAATTTTTTTTTTTGGTGGAAAACACTTACAAAATAAGTTACATGGGT
66 TTTTTGATACTCATTCCAAATGTTTTTTTTTGGTGGAAAACACTTACAAAATAAGTTACATGGGT
* * * * *
116528 AAATGTGGAATACAAAATTCTTTAATTTTTGTCTTCTTTGATAAAAACTAAGACTCCTTCTGAGG
131 AAATATGGAATACAAAATTCCTTAATCTTTGTCTTCTCTGATAAAAACTAAGACTCCTTCTAAGG
*
116593 AAACCTCGGTCAGTTGTAGCTCCTCTTTTCTGTCAAGAGCCAATTTGGT-TATGAAATCATCGTT
196 AAACCTCGATCAGTTGTAGCTCCTCTTTTCTGTCAAGAGCCAATTT-GTCTATGAAATCATCGTT
116657 TCGATTC
260 TCGATTC
116664 TCTCAAAAACTTAAAGAAATTTATTG-ATTTTGATTTTTATCTCTAGTGTTTTTTGCTCCTACTT
1 TCTC-AAAACTTAAAGAAATTTATTGCA--TTGATTTTTATCTCTAGTGTTTTTTGCTCCTACTT
* * * *
116728 TCATTTTTTATACTCATTCCAGA-GTTTTTTTTTGGTGGAAAATACTTATAAAATAAGTTACATG
63 TCATTTTTGATACTCATTCCAAATGTTTTTTTTTGGTGGAAAACACTTACAAAATAAGTTACATG
*
116792 GGTAAATATGGAATACAAAATTCCTTAA-CTTTGTCTTCTCTGATAAAAGCTAAGACTCCTTCTA
128 GGTAAATATGGAATACAAAATTCCTTAATCTTTGTCTTCTCTGATAAAAACTAAGACTCCTTCTA
* * * * * *
116856 AGGGAACTTTGATCAGTTGTAGCTTCTTTTTTTCTTTCAAGAGCCAATTTGTCTATGAA
193 AGGAAACCTCGATCAGTTGTAGC-TCCTCTTTTCTGTCAAGAGCCAATTTGTCTATGAA
116915 TTCAGTGCTT
Statistics
Matches: 226, Mismatches: 20, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
266 58 0.26
267 114 0.50
268 54 0.24
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (266 bp):
TCTCAAAACTTAAAGAAATTTATTGCATTGATTTTTATCTCTAGTGTTTTTTGCTCCTACTTTCA
TTTTTGATACTCATTCCAAATGTTTTTTTTTGGTGGAAAACACTTACAAAATAAGTTACATGGGT
AAATATGGAATACAAAATTCCTTAATCTTTGTCTTCTCTGATAAAAACTAAGACTCCTTCTAAGG
AAACCTCGATCAGTTGTAGCTCCTCTTTTCTGTCAAGAGCCAATTTGTCTATGAAATCATCGTTT
CGATTC
Found at i:123086 original size:20 final size:20
Alignment explanation
Indices: 123061--123105 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
123051 GAAATGAAAT
*
123061 TCAAATCGAATCGAATCGAA
1 TCAAATCAAATCGAATCGAA
* *
123081 TCAAATCAAATTGAATTGAA
1 TCAAATCAAATCGAATCGAA
123101 T-AAAT
1 TCAAAT
123106 TTCTCTGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (20 bp):
TCAAATCAAATCGAATCGAA
Done.