Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002349.1 Kokia drynarioides strain JFW-HI SEQ_114411, 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: 53681
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 89 characters in sequence are not A, C, G, or T
Found at i:411 original size:182 final size:180
Alignment explanation
Indices: 33--447 Score: 588
Period size: 182 Copynumber: 2.3 Consensus size: 180
23 TCAGATGTGC
*
33 TGGTGCTACTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTTCCTGCTTCAAGAG
1 TGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTTCCTGCTTCAAGAG
* * *
98 AGGTTATAAGATATTAAAGTGCCTCTCTTGAAGAGGAAAACATACATCTGTTTCAATACTATCTT
66 AGGTTATAAGATATTAAAGTACCTCTCCTGAAGAGGAAAACATACATCTGTTTCAATACTATCTC
* * * ** * *
163 CTGCTTCAACGATAGTAGTACCAATATTGGCTCTTGAGGAGTCAAATGTAT
131 CTGCTTCAACGATAGCAGCACCAACATTAACTCCTCAGGAGTCAAA-GTAT
*
214 TAGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTTCCTGCTTCAAGAG
1 TGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTTCCTGCTTCAAGAG
* *
279 AGGCACTT-TAATATCTT-AA-TACCTCTCCTGAAGTAGGAAAACATACATCTGTTTCAATACTA
66 AGG---TTATAAGATATTAAAGTACCTCTCCTGAAG-AGGAAAACATACATCTGTTTCAATACTA
*
341 TCTCCTGCTTCAACGATAGCAGCACCAACACATCTAACTCCTCAGGAG-CCAA-TAT
127 TCTCCTGCTTCAACGATAGCAGCACC-A-ACAT-TAACTCCTCAGGAGTCAAAGTAT
396 TGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTT
1 TGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTT
448 GACTCCTTCT
Statistics
Matches: 211, Mismatches: 16, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
181 78 0.37
182 107 0.51
183 8 0.04
184 8 0.04
185 10 0.05
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (180 bp):
TGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTTCCTGCTTCAAGAG
AGGTTATAAGATATTAAAGTACCTCTCCTGAAGAGGAAAACATACATCTGTTTCAATACTATCTC
CTGCTTCAACGATAGCAGCACCAACATTAACTCCTCAGGAGTCAAAGTAT
Found at i:1173 original size:14 final size:14
Alignment explanation
Indices: 1156--1205 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1146 CAAAATCATG
*
1156 AATCTAAAATCCAA
1 AATCTAAAACCCAA
1170 AATCCT-AAACCCAA
1 AAT-CTAAAACCCAA
*
1184 AATATAAAACCCAA
1 AATCTAAAACCCAA
*
1198 AACCTAAA
1 AATCTAAA
1206 CTTAAATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 1 0.03
14 27 0.90
15 2 0.07
ACGTcount: A:0.58, C:0.26, G:0.00, T:0.16
Consensus pattern (14 bp):
AATCTAAAACCCAA
Found at i:1185 original size:21 final size:21
Alignment explanation
Indices: 1141--1186 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1131 TTTTTAGCCT
* * *
1141 AAATCCAAAATCATGAATCTA
1 AAATCCAAAATCATAAACCCA
*
1162 AAATCCAAAATCCTAAACCCA
1 AAATCCAAAATCATAAACCCA
1183 AAAT
1 AAAT
1187 ATAAAACCCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.54, C:0.24, G:0.02, T:0.20
Consensus pattern (21 bp):
AAATCCAAAATCATAAACCCA
Found at i:1254 original size:14 final size:13
Alignment explanation
Indices: 1225--1262 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
1215 TTAAATCAAA
1225 ACCC-TAAACTCAT
1 ACCCATAAAC-CAT
1238 ACCCCATAAACCAT
1 A-CCCATAAACCAT
1252 ACCCATAAACC
1 ACCCATAAACC
1263 TTAAACTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 11 0.48
14 7 0.30
15 5 0.22
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (13 bp):
ACCCATAAACCAT
Found at i:4532 original size:3 final size:3
Alignment explanation
Indices: 4524--4553 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4514 CAATTTGATA
4524 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4554 TTAATTTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6507 original size:30 final size:31
Alignment explanation
Indices: 6453--6511 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
6443 TTAATAAAAG
* *
6453 TAAAATTATACTTTAACCTTTTTAAAAATAA
1 TAAAATAATAATTTAACCTTTTTAAAAATAA
*
6484 TAAAATAATAATTTAA-TTTTTTAAAAAT
1 TAAAATAATAATTTAACCTTTTTAAAAAT
6512 TATATTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
TAAAATAATAATTTAACCTTTTTAAAAATAA
Found at i:17710 original size:17 final size:15
Alignment explanation
Indices: 17684--17726 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
17674 TTTTATTATC
*
17684 TTATTAATATTTTAATA
1 TTATTTATATTTT--TA
17701 TTATTTATATTTTTA
1 TTATTTATATTTTTA
17716 TTATTTTATAT
1 TTA-TTTATAT
17727 AAATTTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 7 0.29
17 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTTATATTTTTA
Found at i:17749 original size:9 final size:9
Alignment explanation
Indices: 17704--17775 Score: 56
Period size: 9 Copynumber: 7.4 Consensus size: 9
17694 TTTAATATTA
17704 TTTAT-ATT
1 TTTATAATT
*
17712 TTTATTATT
1 TTTATAATT
17721 TTATATAAATTTT
1 TT-TAT-AA--TT
17734 GTTTATAATT
1 -TTTATAATT
17744 TTTATAATT
1 TTTATAATT
* *
17753 TTTCTATTT
1 TTTATAATT
17762 TTTATAATAT
1 TTTATAAT-T
17772 TTTA
1 TTTA
17776 ATGATGGTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
8 5 0.10
9 27 0.52
10 10 0.19
11 1 0.02
12 2 0.04
13 5 0.10
14 2 0.04
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (9 bp):
TTTATAATT
Found at i:17755 original size:22 final size:23
Alignment explanation
Indices: 17712--17755 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
17702 TATTTATATT
*
17712 TTTATTATTTTATATAAATTTTG
1 TTTATAATTTTATATAAATTTTG
*
17735 TTTATAATTTT-TATAATTTTT
1 TTTATAATTTTATATAAATTTT
17756 CTATTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTATAATTTTATATAAATTTTG
Found at i:23869 original size:14 final size:14
Alignment explanation
Indices: 23850--23879 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
23840 GTGCTTTACT
23850 TAATTTATTTTTTA
1 TAATTTATTTTTTA
23864 TAATTTATTTTTTA
1 TAATTTATTTTTTA
23878 TA
1 TA
23880 TACATACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TAATTTATTTTTTA
Found at i:25784 original size:86 final size:86
Alignment explanation
Indices: 25688--25986 Score: 437
Period size: 86 Copynumber: 3.5 Consensus size: 86
25678 ATTTAAAATA
25688 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATGTA
*
25753 TTGTAAAATTAACAAATTATT
66 TTGTCAAATTAACAAATTATT
*
25774 TGATAAAAATTGTAATATAAAAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATGTA
* * *
25839 TTGTCAAATCAACACATTATA
66 TTGTCAAATTAACAAATTATT
* * *
25860 TGATAAAAATTGT-A-AT-ATAATAATAATTTGTACTTTAAATATGA-AAATTTGATAAATAATG
1 TGATAAAAATTGTAATATAATAATAATAATTTTTA-TTTAAATAT-ATAAAATTAATAAATAATG
25921 TATTGTCAAATTAACACAA-TATT
64 TATTGTCAAATTAACA-AATTATT
* **
25944 TGATATAAATTGTAATATAATAATAATCTTTTTTATTTAAATA
1 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATA
25987 ATGTTAAATT
Statistics
Matches: 191, Mismatches: 16, Indels: 12
0.87 0.07 0.05
Matches are distributed among these distances:
83 14 0.07
84 56 0.29
85 4 0.02
86 104 0.54
87 13 0.07
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (86 bp):
TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATGTA
TTGTCAAATTAACAAATTATT
Found at i:26027 original size:21 final size:23
Alignment explanation
Indices: 25985--26027 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
25975 TTTATTTAAA
* *
25985 TAATGTTAAATTAATTTTAAATG
1 TAATGTTAAATTAATGTCAAATG
26008 TAAT-TTAAA-TAATGTCAAAT
1 TAATGTTAAATTAATGTCAAAT
26028 TTAAAGTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (23 bp):
TAATGTTAAATTAATGTCAAATG
Found at i:26143 original size:16 final size:16
Alignment explanation
Indices: 26107--26141 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
26097 ATTGATTTCC
*
26107 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
26123 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
26140 AA
1 AA
26142 TTTTACACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:31595 original size:23 final size:23
Alignment explanation
Indices: 31567--31625 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
31557 TTTATAAAAT
31567 AAATTTAAAATTTTACTAA-GTA
1 AAATTTAAAATTTTACTAACGTA
*
31589 AACATTT--ATTTTTACTAAGCGTA
1 AA-ATTTAAAATTTTACTAA-CGTA
31612 AAATCTTAAAATTT
1 AAAT-TTAAAATTT
31626 GTGTGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
21 10 0.34
22 4 0.14
23 11 0.38
25 4 0.14
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (23 bp):
AAATTTAAAATTTTACTAACGTA
Found at i:31917 original size:17 final size:17
Alignment explanation
Indices: 31895--31931 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
31885 TAATATATAT
31895 ATATATAATAAAA-TAAA
1 ATATATAA-AAAATTAAA
31912 ATATATAAAAAATTAAA
1 ATATATAAAAAATTAAA
31929 ATA
1 ATA
31932 AAATTTTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATATATAAAAAATTAAA
Found at i:32827 original size:15 final size:16
Alignment explanation
Indices: 32807--32836 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32797 CTTGAACCCG
32807 TATATT-ATTTTAATA
1 TATATTAATTTTAATA
32822 TATATTAATTTTAAT
1 TATATTAATTTTAAT
32837 CCAAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATATTAATTTTAATA
Found at i:35097 original size:13 final size:13
Alignment explanation
Indices: 35064--35095 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
35054 AAATAATAAA
35064 TAAATTTTACATT
1 TAAATTTTACATT
35077 TAAA-TTTAC-TT
1 TAAATTTTACATT
35088 TAAATTTT
1 TAAATTTT
35096 TAGATATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 8 0.44
13 4 0.22
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATTTTACATT
Found at i:35764 original size:18 final size:18
Alignment explanation
Indices: 35741--35783 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
35731 TGAGACGTTT
*
35741 TAATAAATAAATACTAAA
1 TAATAAATAAATAATAAA
**
35759 TAATAAATACTTAATAAA
1 TAATAAATAAATAATAAA
35777 TAATAAA
1 TAATAAA
35784 AAAGCAAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
TAATAAATAAATAATAAA
Found at i:35781 original size:14 final size:15
Alignment explanation
Indices: 35740--35779 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
35730 CTGAGACGTT
35740 TTAATAAATAAATAC
1 TTAATAAATAAATAC
*
35755 TAAAT-AATAAATAC
1 TTAATAAATAAATAC
35769 TTAATAAATAA
1 TTAATAAATAA
35780 TAAAAAAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAATAAATAAATAC
Found at i:36666 original size:30 final size:31
Alignment explanation
Indices: 36627--36703 Score: 97
Period size: 29 Copynumber: 2.5 Consensus size: 31
36617 TTTGCAGGGT
* *
36627 CCTTGAACTTTCTAAAACTCATATTTTGA-C
1 CCTTAAACTTTCTAAAAATCATATTTTGATC
*
36657 CCTTAAAC-TTCTAAAAATTATATTTTGATC
1 CCTTAAACTTTCTAAAAATCATATTTTGATC
36687 CC-TAAACTTTTCTAAAA
1 CCTTAAAC-TTTCTAAAA
36704 TTGCATTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 23 0.56
30 10 0.24
31 8 0.20
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (31 bp):
CCTTAAACTTTCTAAAAATCATATTTTGATC
Found at i:36721 original size:28 final size:29
Alignment explanation
Indices: 36670--36856 Score: 182
Period size: 29 Copynumber: 6.4 Consensus size: 29
36660 TAAACTTCTA
* * *
36670 AAAATTATATTTTGATCCCTAAACTTTTCT
1 AAAATTACATTTT-AACCCTAAACTTTTCC
* *
36700 AAAATTGCA-TTTAACCCTAAACTTTTCT
1 AAAATTACATTTTAACCCTAAACTTTTCC
* *
36728 AAAATTGCA-TTTAACCCTAAACTTTTTC
1 AAAATTACATTTTAACCCTAAACTTTTCC
* * *
36756 -AAATTATATTTTTATCTCTAAACTTTTCC
1 AAAATTACA-TTTTAACCCTAAACTTTTCC
* * *
36785 AAAATTACATTTTGACCCCAAACTTCTCC
1 AAAATTACATTTTAACCCTAAACTTTTCC
* *
36814 AAAATTACATTTTTATCTCTAAACTTTTCC
1 AAAATTACA-TTTTAACCCTAAACTTTTCC
*
36844 AAAATTACGTTTT
1 AAAATTACATTTT
36857 CACCTCGAAT
Statistics
Matches: 131, Mismatches: 22, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
27 6 0.05
28 41 0.31
29 47 0.36
30 37 0.28
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.43
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTAAACTTTTCC
Found at i:36837 original size:59 final size:59
Alignment explanation
Indices: 36670--36856 Score: 220
Period size: 59 Copynumber: 3.2 Consensus size: 59
36660 TAAACTTCTA
* * * * * *
36670 AAAATTATATTTTGATCCCTAAACTTTTCTAAAATTGCA--TTTAACCCTAAACTTTTCT
1 AAAATTACATTTTGA-CCCTAAACTTTTCCAAAATTACATTTTTATCTCTAAACTTTTCC
* * * *
36728 AAAATTGCA-TTTAACCCTAAACTTTTTC-AAATTATATTTTTATCTCTAAACTTTTCC
1 AAAATTACATTTTGACCCTAAACTTTTCCAAAATTACATTTTTATCTCTAAACTTTTCC
* *
36785 AAAATTACATTTTGACCCCAAACTTCTCCAAAATTACATTTTTATCTCTAAACTTTTCC
1 AAAATTACATTTTGACCCTAAACTTTTCCAAAATTACATTTTTATCTCTAAACTTTTCC
*
36844 AAAATTACGTTTT
1 AAAATTACATTTT
36857 CACCTCGAAT
Statistics
Matches: 108, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
55 6 0.06
56 12 0.11
57 28 0.26
58 22 0.20
59 40 0.37
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.43
Consensus pattern (59 bp):
AAAATTACATTTTGACCCTAAACTTTTCCAAAATTACATTTTTATCTCTAAACTTTTCC
Found at i:42141 original size:61 final size:61
Alignment explanation
Indices: 41996--42211 Score: 233
Period size: 60 Copynumber: 3.5 Consensus size: 61
41986 TTGAACAAAT
* * * * *
41996 TTTTTTTGGTGTTGGTTATTGCATGGCCGACACCATTTTTTTGTCTGATAAAAAAAAATTCAAA
1 TTTTTTTGGTGTTGGTCATTGCATGGTCGACACCA-TCTTTTATCTGAT--AAAAAAATTTAAA
* * *
42060 ATTTTTT-GTATTGGTTATTGCATGGTCGACACCATCTTTTATCTGATAAAAAAATTTAAA
1 TTTTTTTGGTGTTGGTCATTGCATGGTCGACACCATCTTTTATCTGATAAAAAAATTTAAA
** *
42120 TTTTTTTAATGTTGGTCATTGCATGGTCGACACCACCTTTTTATCTGAT--AAAAATTTCAAA
1 TTTTTTTGGTGTTGGTCATTGCATGGTCGACACCATC-TTTTATCTGATAAAAAAATTT-AAA
* * *
42181 -ATTTTTGGTGTTAGCCATTGCATGGTCGACA
1 TTTTTTTGGTGTTGGTCATTGCATGGTCGACA
42212 TCGCCTTTTT
Statistics
Matches: 133, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
60 52 0.39
61 28 0.21
62 22 0.17
63 25 0.19
64 6 0.05
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (61 bp):
TTTTTTTGGTGTTGGTCATTGCATGGTCGACACCATCTTTTATCTGATAAAAAAATTTAAA
Found at i:42301 original size:82 final size:81
Alignment explanation
Indices: 42149--42306 Score: 201
Period size: 82 Copynumber: 1.9 Consensus size: 81
42139 TGCATGGTCG
** * *
42149 ACACCACCTTTTTATCTGATAAAAATTTCAAAATTTTTGGTGTTAGCCATTGCATGGTCGACATC
1 ACACCACCTTTTTATCTGATAAAAATTTCAAAATTTTTCATGTTAGCCATTGCATGGCCAACATC
*
42214 GCCTTTTTATCGGCCA
66 ACCTTTTTATCGGCCA
* * * * *
42230 ACACTACCTTTTTATCTGATAAAAAAATTT-AAATTTTTTCATGTTGGTCATTGCATTGCCAACA
1 ACACCACCTTTTTATCTGAT--AAAAATTTCAAAATTTTTCATGTTAGCCATTGCATGGCCAACA
42294 TCACCTTTTTATC
64 TCACCTTTTTATC
42307 TGATAATTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
81 19 0.29
82 38 0.58
83 8 0.12
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (81 bp):
ACACCACCTTTTTATCTGATAAAAATTTCAAAATTTTTCATGTTAGCCATTGCATGGCCAACATC
ACCTTTTTATCGGCCA
Found at i:42764 original size:23 final size:23
Alignment explanation
Indices: 42720--42763 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
42710 GATAGTCATT
* *
42720 TATAATTTTTACTGTTTATTTTA
1 TATAATTTTTAATGTATATTTTA
42743 TATAA-TTTTAATGTATATTTT
1 TATAATTTTTAATGTATATTTT
42764 TGAACTAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (23 bp):
TATAATTTTTAATGTATATTTTA
Found at i:43015 original size:2 final size:2
Alignment explanation
Indices: 43008--43033 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42998 TAAGAAAGAC
43008 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
43034 GGGGNGGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:51247 original size:31 final size:31
Alignment explanation
Indices: 51210--51280 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
51200 TGATTTGGAA
* * *
51210 CAATTATACCCATGAAATTTTGATTGTGGTT
1 CAATTATACCCATGAAACTTTAATTGTGATT
* *
51241 CAATTATATCCATGAAACTTTAATTTTGATT
1 CAATTATACCCATGAAACTTTAATTGTGATT
51272 CAATTATAC
1 CAATTATAC
51281 ACTTTTAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (31 bp):
CAATTATACCCATGAAACTTTAATTGTGATT
Found at i:51433 original size:29 final size:30
Alignment explanation
Indices: 51391--51448 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
51381 AATTTGTGAG
* *
51391 AATTACATCAAATTAAAATTTTATGTATAA
1 AATTACATCAAATTAAAAGTTCATGTATAA
* *
51421 AATTGCAT-AAATTCAAAGTTCATGTATA
1 AATTACATCAAATTAAAAGTTCATGTATA
51449 GACATGCACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.38
Consensus pattern (30 bp):
AATTACATCAAATTAAAAGTTCATGTATAA
Found at i:52138 original size:3 final size:3
Alignment explanation
Indices: 52132--52161 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
52122 TATTATTGAA
52132 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
52162 GACAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.