Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013304.1 Kokia drynarioides strain JFW-HI SEQ_128326, 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: 112305
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:11792 original size:19 final size:20
Alignment explanation
Indices: 11757--11795 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
11747 ACGCAAATCA
11757 TGTGAATAAATAAAAATTAGT
1 TGTGAATAAAT-AAAATTAGT
11778 TGTGAATAAAT-AAATTAG
1 TGTGAATAAATAAAATTAG
11796 ACTTGGTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (20 bp):
TGTGAATAAATAAAATTAGT
Found at i:12059 original size:128 final size:128
Alignment explanation
Indices: 11831--12140 Score: 575
Period size: 128 Copynumber: 2.4 Consensus size: 128
11821 AATGTGACCG
*
11831 AATTGAGTAATCGGGTTGAGGTGCTTGGCTTGTCATCTCAATTCACGTAAAAAGTTACGAGTGAC
1 AATTGAGTAATCGGGTTGAAGTGCTTGGCTTGTCATCTCAATTCACGTAAAAAGTTACGAGTGAC
11896 GAACCAAAGCTTGTAACACTCCAGTAACCAAGCTACCTAGAAAAATAAGCTATCGACTTTTCA
66 GAACCAAAGCTTGTAACACTCCAGTAACCAAGCTACCTAGAAAAATAAGCTATCGACTTTTCA
*
11959 AATTGAGTAACCGGGTTGAAGTGCTTGGCTTGTCATCTCAATTCACGTAAAAAGTTACGAGTGAC
1 AATTGAGTAATCGGGTTGAAGTGCTTGGCTTGTCATCTCAATTCACGTAAAAAGTTACGAGTGAC
*
12024 GAACCAAAGCTTGTAACACTCTAGTAACCAAGCTACCTAGAAAAATAAGCTATCGACTTTTCA
66 GAACCAAAGCTTGTAACACTCCAGTAACCAAGCTACCTAGAAAAATAAGCTATCGACTTTTCA
* *
12087 AATTGAGTAATCGGGTTGAAGTGCTTGGCTTGTCATCTCAATTCGCATAAAAAG
1 AATTGAGTAATCGGGTTGAAGTGCTTGGCTTGTCATCTCAATTCACGTAAAAAG
12141 ATTTGATTAA
Statistics
Matches: 176, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 176 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (128 bp):
AATTGAGTAATCGGGTTGAAGTGCTTGGCTTGTCATCTCAATTCACGTAAAAAGTTACGAGTGAC
GAACCAAAGCTTGTAACACTCCAGTAACCAAGCTACCTAGAAAAATAAGCTATCGACTTTTCA
Found at i:18274 original size:22 final size:23
Alignment explanation
Indices: 18246--18300 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
18236 TGCACAAATG
*
18246 AACGGAGAGCACA-AACGTCCTA
1 AACGGAGAGCACACAAAGTCCTA
*
18268 AACGGAGAGCACACAAAGTGCTA
1 AACGGAGAGCACACAAAGTCCTA
*
18291 AACGAAGAGC
1 AACGGAGAGC
18301 GCGCTAAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 13 0.45
23 16 0.55
ACGTcount: A:0.44, C:0.24, G:0.25, T:0.07
Consensus pattern (23 bp):
AACGGAGAGCACACAAAGTCCTA
Found at i:27237 original size:37 final size:37
Alignment explanation
Indices: 27182--27430 Score: 228
Period size: 37 Copynumber: 7.0 Consensus size: 37
27172 AAGTATACAA
*
27182 GCTATATGCCTAGCAGGCTTTGTGCCGGTGTATTCAG
1 GCTATATGCCTAGTAGGCTTTGTGCCGGTGTATTCAG
*
27219 GCGATATGCCTAGTAGGC----T-----TGTATTCAG
1 GCTATATGCCTAGTAGGCTTTGTGCCGGTGTATTCAG
* * * *
27247 GCGATATGCCTAGTAGGCTTTGTGCCGATATGTTCAG
1 GCTATATGCCTAGTAGGCTTTGTGCCGGTGTATTCAG
* * * *
27284 GCTATGTGCCTAGTAAGCTTTGTGCCGATGTGTTCAG
1 GCTATATGCCTAGTAGGCTTTGTGCCGGTGTATTCAG
* * * * *
27321 GCTATGTGCCTAGTAGGCTTTATACTGGTGTATTCGG
1 GCTATATGCCTAGTAGGCTTTGTGCCGGTGTATTCAG
* * * *
27358 GCTATATGCTTAGTAGGCTTTGAGTCGGTGTGTTCAG
1 GCTATATGCCTAGTAGGCTTTGTGCCGGTGTATTCAG
* * * *
27395 GCTATGTGCCTAGTAGGCTTCGTGCTGGTGCATTCA
1 GCTATATGCCTAGTAGGCTTTGTGCCGGTGTATTCA
27431 AGAATGAATG
Statistics
Matches: 171, Mismatches: 32, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
28 27 0.16
32 1 0.01
33 1 0.01
37 142 0.83
ACGTcount: A:0.17, C:0.18, G:0.30, T:0.35
Consensus pattern (37 bp):
GCTATATGCCTAGTAGGCTTTGTGCCGGTGTATTCAG
Found at i:27250 original size:28 final size:28
Alignment explanation
Indices: 27210--27266 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
27200 TTTGTGCCGG
27210 TGTATTCAGGCGATATGCCTAGTAGGCT
1 TGTATTCAGGCGATATGCCTAGTAGGCT
27238 TGTATTCAGGCGATATGCCTAGTAGGCT
1 TGTATTCAGGCGATATGCCTAGTAGGCT
27266 T
1 T
27267 TGTGCCGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (28 bp):
TGTATTCAGGCGATATGCCTAGTAGGCT
Found at i:27291 original size:21 final size:21
Alignment explanation
Indices: 27261--27330 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
27251 TATGCCTAGT
*
27261 AGGCTTTGTGCCGATATGTTC
1 AGGCTATGTGCCGATATGTTC
27282 AGGCTATGTGCC--TA-G-T-
1 AGGCTATGTGCCGATATGTTC
* * *
27298 AAGCTTTGTGCCGATGTGTTC
1 AGGCTATGTGCCGATATGTTC
27319 AGGCTATGTGCC
1 AGGCTATGTGCC
27331 TAGTAGGCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
16 10 0.26
17 1 0.03
18 2 0.05
19 3 0.08
20 1 0.03
21 21 0.55
ACGTcount: A:0.16, C:0.20, G:0.30, T:0.34
Consensus pattern (21 bp):
AGGCTATGTGCCGATATGTTC
Found at i:34588 original size:37 final size:37
Alignment explanation
Indices: 34527--34753 Score: 285
Period size: 37 Copynumber: 6.2 Consensus size: 37
34517 TTTCATCTAA
* * *
34527 GTATACAGGTTATGTGCCTAGTAGGTTTTGTGCCGGT
1 GTATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGT
* * *
34564 GTATTCAGGCGATGTGCCTAGTAGGCTTTATGTCGGT
1 GTATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGT
* *
34601 GTGTTTAGGCTATGTGCCTAGTAGGCTTTGTGCCGGT
1 GTATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGT
* * *
34638 GTATTCAGGCTATGTGCCTAGTAAGCTTTGTGTCAGT
1 GTATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGT
** *
34675 GTATTCAGGC-ACATGCCTAGTAGGCTTTGTGCCGAT
1 GTATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGT
* * *
34711 GTGTTCAGGCTATGTGCCTAGTAGGCTTCGTGCTGGT
1 GTATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGT
*
34748 GCATTC
1 GTATTC
34754 TAGAATGAAT
Statistics
Matches: 159, Mismatches: 30, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
36 29 0.18
37 130 0.82
ACGTcount: A:0.15, C:0.18, G:0.31, T:0.36
Consensus pattern (37 bp):
GTATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGT
Found at i:34731 original size:110 final size:111
Alignment explanation
Indices: 34527--34753 Score: 312
Period size: 110 Copynumber: 2.1 Consensus size: 111
34517 TTTCATCTAA
* * * * * **
34527 GTATACAGGTTATGTGCCTAGTAGGTTTTGTGCCGGTGTATTCAGGCGATGTGCCTAGTAGGCTT
1 GTATTCAGGCTATGTGCCTAGTAAGCTTTGTGCCAGTGTATTCAGGCGACATGCCTAGTAGGCTT
* * * *
34592 TATGTCGGTGTGTTTAGGCTATGTGCCTAGTAGGCTTTGTGCCGGT
66 TATGCCGATGTGTTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGT
*
34638 GTATTCAGGCTATGTGCCTAGTAAGCTTTGTGTCAGTGTATTCAGGC-ACATGCCTAGTAGGCTT
1 GTATTCAGGCTATGTGCCTAGTAAGCTTTGTGCCAGTGTATTCAGGCGACATGCCTAGTAGGCTT
* *
34702 TGTGCCGATGTGTTCAGGCTATGTGCCTAGTAGGCTTCGTGCTGGT
66 TATGCCGATGTGTTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGT
*
34748 GCATTC
1 GTATTC
34754 TAGAATGAAT
Statistics
Matches: 101, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
110 60 0.59
111 41 0.41
ACGTcount: A:0.15, C:0.18, G:0.31, T:0.36
Consensus pattern (111 bp):
GTATTCAGGCTATGTGCCTAGTAAGCTTTGTGCCAGTGTATTCAGGCGACATGCCTAGTAGGCTT
TATGCCGATGTGTTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGT
Found at i:39875 original size:18 final size:18
Alignment explanation
Indices: 39849--39890 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
39839 ATTGCAATAT
39849 TTTTC-TCTTATTTTCTC
1 TTTTCTTCTTATTTTCTC
* * *
39866 TTTTCTTCTTTTTTTTTT
1 TTTTCTTCTTATTTTCTC
39884 TTTTCTT
1 TTTTCTT
39891 TTTGTGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTCTTCTTATTTTCTC
Found at i:40487 original size:17 final size:17
Alignment explanation
Indices: 40467--40515 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
40457 ATCGTAATGT
40467 AAATGCAGTGACAATAA
1 AAATGCAGTGACAATAA
* *
40484 AAATGCAATGACATTAA
1 AAATGCAGTGACAATAA
* *
40501 TAATGCAGGGACAAT
1 AAATGCAGTGACAAT
40516 TATACTACAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.20
Consensus pattern (17 bp):
AAATGCAGTGACAATAA
Found at i:47527 original size:24 final size:24
Alignment explanation
Indices: 47500--47545 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
47490 TCTTGTAATT
*
47500 TAGGTTTAGTTGTTTTTATTTTCA
1 TAGGCTTAGTTGTTTTTATTTTCA
47524 TAGGCTTAGTTGTTTTTATTTT
1 TAGGCTTAGTTGTTTTTATTTT
47546 TGTTTTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.04, G:0.17, T:0.63
Consensus pattern (24 bp):
TAGGCTTAGTTGTTTTTATTTTCA
Found at i:62660 original size:231 final size:231
Alignment explanation
Indices: 62257--62721 Score: 885
Period size: 231 Copynumber: 2.0 Consensus size: 231
62247 GTTATAAAAA
62257 TCATGATCTCAAGTGTCAATGATTAATAGTTAGTTGTAGAAAAATGGAAAAACAAATTCTTTTAA
1 TCATGATCTCAAGTGTCAATGATTAATAGTTAGTTGTAGAAAAATGGAAAAACAAATTCTTTTAA
62322 GAATATGTAAGCTGTTCTGAATTTGAAAAATTATTAAAAATTGTACAAAAATAATTAGAAAATGA
66 GAATATGTAAGCTGTTCTGAATTTGAAAAATTATTAAAAATTGTACAAAAATAATTAGAAAATGA
*
62387 ATTTTATGTCAAAAAATCTTAATGAGTCAAATTTCAGGAGAAACATGTGACAACATTATATGAAT
131 ATTCTATGTCAAAAAATCTTAATGAGTCAAATTTCAGGAGAAACATGTGACAACATTATATGAAT
*
62452 TTTGTACCGAAAAAAATAATTTTTAGTAGAGAAAGG
196 TTTGTACCGAAAAAAATAATTTTTAATAGAGAAAGG
*
62488 TCATGATCTTAAGTGTCAATGATTAATAGTTAGTTGTAGAAAAATGGAAAAACAAATTCTTTTAA
1 TCATGATCTCAAGTGTCAATGATTAATAGTTAGTTGTAGAAAAATGGAAAAACAAATTCTTTTAA
*
62553 GAATATGTAAGCTGTTCTGAATTTGAAAAATTATTAAAAATTGTACAAAAATGATTAGAAAATGA
66 GAATATGTAAGCTGTTCTGAATTTGAAAAATTATTAAAAATTGTACAAAAATAATTAGAAAATGA
*
62618 ATTCTATGTCAAAAAATCTTAATGAGTCTAATTTCAGGAGAAACATGTGACAACATTATATGAAT
131 ATTCTATGTCAAAAAATCTTAATGAGTCAAATTTCAGGAGAAACATGTGACAACATTATATGAAT
62683 TTTGTACCGAAAAAAATAATTTTTAATAGAGAAAGG
196 TTTGTACCGAAAAAAATAATTTTTAATAGAGAAAGG
62719 TCA
1 TCA
62722 GAGTTGTTTA
Statistics
Matches: 229, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
231 229 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (231 bp):
TCATGATCTCAAGTGTCAATGATTAATAGTTAGTTGTAGAAAAATGGAAAAACAAATTCTTTTAA
GAATATGTAAGCTGTTCTGAATTTGAAAAATTATTAAAAATTGTACAAAAATAATTAGAAAATGA
ATTCTATGTCAAAAAATCTTAATGAGTCAAATTTCAGGAGAAACATGTGACAACATTATATGAAT
TTTGTACCGAAAAAAATAATTTTTAATAGAGAAAGG
Found at i:64945 original size:15 final size:15
Alignment explanation
Indices: 64925--64957 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
64915 AATGATAAAT
64925 AAATATATA-AAATAA
1 AAATATATATAAA-AA
64940 AAATATATATAAAAA
1 AAATATATATAAAAA
64955 AAA
1 AAA
64958 GGGTTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATATATATAAAAA
Found at i:66288 original size:19 final size:19
Alignment explanation
Indices: 66247--66286 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
66237 TTTTTTGCTA
66247 TTTGTTTTTTCTTCTTGTC
1 TTTGTTTTTTCTTCTTGTC
66266 TTTGTTCTTTTC-TC-TGTC
1 TTTGTT-TTTTCTTCTTGTC
66284 TTT
1 TTT
66287 TGCAGGTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 8 0.40
20 5 0.25
ACGTcount: A:0.00, C:0.17, G:0.10, T:0.72
Consensus pattern (19 bp):
TTTGTTTTTTCTTCTTGTC
Found at i:67376 original size:189 final size:189
Alignment explanation
Indices: 66848--68212 Score: 1523
Period size: 189 Copynumber: 7.2 Consensus size: 189
66838 TGCTGTCGTA
* * * * * ** *
66848 GCTTCACTCTATTTCACTGCAACTTCAGGGA-GATTGAGAT-TCACTATTTGTTTTAACCTACTT
1 GCTTCACTCCACTCCACTGTAACCTCAGGGACG-TTGAGATCT-ACTACCTGTTTTAACCCACTT
* * * *
66911 CTCTATACCTCATTAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGTAACCTCAGGGACA
64 CTCTGTACCTCACTAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGTAACCTCAAGGACG
* * * *
66976 TTGAGCCCTACTTCATTATTTTCATCCGACCCGCTGCAGCTCAAGGGTATAGGATTCTGGT
129 TTGAGCTCTACTTCATTATTTTCATCCGACCCACTGCAACTCAGGGGTATAGGATTCTGGT
* * * * * * * *** *
67037 GCTTCACTCCACTCTACTGTATCATTAGAGACGTTGAAATCTGCCGTCTGTTTTAACCCCACTTA
1 GCTTCACTCCACTCCACTGTAACCTCAGGGACGTTGAGATCTACTACCTGTTTTAA-CCCACTTC
* * * * * *
67102 TTTATACCTCACCAAGAAGATGAGATTTGAAGTCTCACTCCACTCAACTGTAACCTCAAGGACGT
65 TCTGTACCTCACTAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGTAACCTCAAGGACGT
* * * *
67167 TGAGCTCTACTTCGTTATTTTCATTCGACCCATTGCAGCTCAGGGGTATAGGATTCTGGT
130 TGAGCTCTACTTCATTATTTTCATCCGACCCACTGCAACTCAGGGGTATAGGATTCTGGT
* * * *
67227 GCTTCACTCCACTCCATTGTAACGTCAGGGATGTTGAGATCTACTACCTGTTTTAACTCACTTCT
1 GCTTCACTCCACTCCACTGTAACCTCAGGGACGTTGAGATCTACTACCTGTTTTAACCCACTTCT
* * * *
67292 CTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACACCACTGTAACATCAAGGACATT
66 CTGTACCTCACTAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGTAACCTCAAGGACGTT
* *
67357 GAGCTCTGCTTCATTATTTTCATCCGACCCACTGCAACTCAGGGGTATAAGATTCTGGT
131 GAGCTCTACTTCATTATTTTCATCCGACCCACTGCAACTCAGGGGTATAGGATTCTGGT
* ** * * * * *
67416 GCTTCACTTCTTTCCATTGTAACATCAGGAACGTTGAGATCTATTACCTATTTTAACCCACTTCT
1 GCTTCACTCCACTCCACTGTAACCTCAGGGACGTTGAGATCTACTACCTGTTTTAACCCACTTCT
* *
67481 TTGTACTTCACTAGGAAGATGAGG-TTTGAAGTCTCACTCCACTCCACTGTAACCTCAAGGACGT
66 CTGTACCTCACTAGGAAGATG-GGATTTGAAGTCTCACTCCACTCCACTGTAACCTCAAGGACGT
* * * * * * *
67545 TAAGCTCTGCTTCATTATTTTCATCGGACCCACTGTAACTCAGGGGTATAAGATTTTGAT
130 TGAGCTCTACTTCATTATTTTCATCCGACCCACTGCAACTCAGGGGTATAGGATTCTGGT
* * * *
67605 GCTTCATTCCACTCCATTATAACCTCAGGGACGTTGAGATCTACTACTTGTTTTAACCCACTTCT
1 GCTTCACTCCACTCCACTGTAACCTCAGGGACGTTGAGATCTACTACCTGTTTTAACCCACTTCT
* * * * * * * * *
67670 TTGTACCTCATTAGAAAGATGAGATTTGAAGTTTCACTCTACTCTATTGTAACCTCAAAGACGTT
66 CTGTACCTCACTAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGTAACCTCAAGGACGTT
* *
67735 GAGCTCTGCTTCATTATTTTCATCCGACCCACTGCAACTCAAGGGTATAGGATTCTGGT
131 GAGCTCTACTTCATTATTTTCATCCGACCCACTGCAACTCAGGGGTATAGGATTCTGGT
* * * *
67794 GCTTCACTCCACTCCACTGTAACCTCAGAGACGTTGAGATTTGCTACCTATTTTAACCCACTTCT
1 GCTTCACTCCACTCCACTGTAACCTCAGGGACGTTGAGATCTACTACCTGTTTTAACCCACTTCT
* * * * * * * *
67859 CTGTACTTCACCAGGAATATAGGATTTGAAGTCTCACTCCACTTCATTGTAACATCAGGGACGTT
66 CTGTACCTCACTAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGTAACCTCAAGGACGTT
** * * *
67924 GAGCTCTACTTCATTATTTTCATCTTACCCACTGCAACTTAGGAGTATAGGATTTTGGT
131 GAGCTCTACTTCATTATTTTCATCCGACCCACTGCAACTCAGGGGTATAGGATTCTGGT
* * * * * * * * *
67983 GCTTCACCCCATTCCACTGTAACCTGAGGAACGATGAGATTTGCTACCCGTTTTACCCCACTTCT
1 GCTTCACTCCACTCCACTGTAACCTCAGGGACGTTGAGATCTACTACCTGTTTTAACCCACTTCT
* * * * * *
68048 CTGTACCTCTCTAGAAAGATAGGATTTGAAGTCTCACTCCATTCCACTGTAACCT-TAGAGATGT
66 CTGTACCTCACTAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGTAACCTCAAG-GACGT
* * * * * * * * * * * *
68112 TGAGCTTTACTTCGTTGTTTTAATCTGACCCATTGTAACTTAAGGGCATAAGATTTTGGT
130 TGAGCTCTACTTCATTATTTTCATCCGACCCACTGCAACTCAGGGGTATAGGATTCTGGT
* * *
68172 GCTTCACTTCACTCCACTGTAACCTTAGGGACATTGAGATC
1 GCTTCACTCCACTCCACTGTAACCTCAGGGACGTTGAGATC
68213 CGCTTTGTTA
Statistics
Matches: 996, Mismatches: 174, Indels: 12
0.84 0.15 0.01
Matches are distributed among these distances:
188 2 0.00
189 829 0.83
190 165 0.17
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (189 bp):
GCTTCACTCCACTCCACTGTAACCTCAGGGACGTTGAGATCTACTACCTGTTTTAACCCACTTCT
CTGTACCTCACTAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGTAACCTCAAGGACGTT
GAGCTCTACTTCATTATTTTCATCCGACCCACTGCAACTCAGGGGTATAGGATTCTGGT
Found at i:67545 original size:95 final size:93
Alignment explanation
Indices: 67230--67931 Score: 271
Period size: 95 Copynumber: 7.4 Consensus size: 93
67220 TTCTGGTGCT
* * * * * * *
67230 TCACTCCACTCCATTGTAACGTCAGGGATGTTGAGATCTACTACCTGTTTTAACTCACTTCTCTG
1 TCACTCCACTCCATTGTAACCTCAAGGACGTTGAGATCTATTACTTATTTTAACCCACTTCTCTG
*
67295 TACCTCACCAGGAAGATG-GGATTTGAAGTC
66 TA-CTCA-TAGGAAGATGAGG-TTTGAAGTC
* * * * * * * * * *
67325 TCACTCCACACCACTGTAACATCAAGGACATTGAGCTCTGCTT-CATTATTTTCATCCGAC-CCA
1 TCACTCCACTCCATTGTAACCTCAAGGACGTTGAGATCT-ATTAC-TTATTTT-AACCCACTTCT
* * * *
67388 CTGCAACTC--AGG-GGTATAAGATTCTG--GTGC
63 CTG-TACTCATAGGAAG-ATGAGGTT-TGAAGT-C
* ** * * *
67418 TTCACTTCTTTCCATTGTAACATC-AGGAACGTTGAGATCTATTACCTATTTTAACCCACTTCTT
1 -TCACTCCACTCCATTGTAACCTCAAGG-ACGTTGAGATCTATTACTTATTTTAACCCACTTCTC
67482 TGTACTTCACTAGGAAGATGAGGTTTGAAGTC
64 TGTAC-TCA-TAGGAAGATGAGGTTTGAAGTC
* * * * * ** * *
67514 TCACTCCACTCCACTGTAACCTCAAGGACGTTAAGCTCTGCTT-CATTATTTTCATCGGAC-CCA
1 TCACTCCACTCCATTGTAACCTCAAGGACGTTGAGATCT-ATTAC-TTATTTT-AACCCACTTCT
** * * * * *
67577 CTGTAACTCAGGGGTATAAGA-TTTTGATG-C
63 CTGT-ACTCATAGGAAGATGAGGTTTGAAGTC
* * * * * *
67607 TTCATTCCACTCCATTATAACCTCAGGGACGTTGAGATCTACTACTTGTTTTAACCCACTTCTTT
1 -TCACTCCACTCCATTGTAACCTCAAGGACGTTGAGATCTATTACTTATTTTAACCCACTTCTCT
* * *
67672 GTACCTCATTAGAAAGATGAGATTTGAAGTT
65 GTA-CTCA-TAGGAAGATGAGGTTTGAAGTC
* * * * * * * * *
67703 TCACTCTACTCTATTGTAACCTCAAAGACGTTGAGCTCTGCTT-CATTATTTTCATCCGAC-CCA
1 TCACTCCACTCCATTGTAACCTCAAGGACGTTGAGATCT-ATTAC-TTATTTT-AACCCACTTCT
*
67766 CTGCAACTCA-AGG--GTAT-AGGATTCTG--GTGC
63 CTG-TACTCATAGGAAG-ATGAGG-TT-TGAAGT-C
* * ** *
67796 TTCACTCCACTCCACTGTAACCTC-AGAGACGTTGAGATTTGCTACCTATTTTAACCCACTTCTC
1 -TCACTCCACTCCATTGTAACCTCAAG-GACGTTGAGATCTATTACTTATTTTAACCCACTTCTC
* *
67860 TGTACTTCACCAGGAATAT-AGGATTTGAAGTC
64 TGTAC-TCA-TAGGAAGATGAGG-TTTGAAGTC
* * * *
67892 TCACTCCACTTCATTGTAACATCAGGGACGTTGAGCTCTA
1 TCACTCCACTCCATTGTAACCTCAAGGACGTTGAGATCTA
67932 CTTCATTATT
Statistics
Matches: 431, Mismatches: 125, Indels: 102
0.66 0.19 0.16
Matches are distributed among these distances:
92 27 0.06
93 59 0.14
94 113 0.26
95 145 0.34
96 65 0.15
97 22 0.05
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (93 bp):
TCACTCCACTCCATTGTAACCTCAAGGACGTTGAGATCTATTACTTATTTTAACCCACTTCTCTG
TACTCATAGGAAGATGAGGTTTGAAGTC
Found at i:67928 original size:567 final size:569
Alignment explanation
Indices: 66898--68212 Score: 1685
Period size: 567 Copynumber: 2.3 Consensus size: 569
66888 TCACTATTTG
* * *
66898 TTTTAACCTACTTCTCTATACCTCATTAGGAAGATG-GGATTTGAAGTCTCACTCCACTCCACTG
1 TTTTAACCCACTTCTCTGTACCTCACTAGGAAGATGAGGATTTGAAGTCTCACTCCACTCCACTG
* * * * * *
66962 TAACCTCAGGGACATTGAGCCCTACTTCATTATTTTCATCCGACCCGCTGCAGCTCAAGGGTATA
66 TAACCTCAAGGACGTTGAGCTCTACTTCATTATTTTCATCCGACCCACTGTAACTCAAGGGTATA
* * * * * * * * *
67027 GGATTCTGGTGCTTCACTCCACTCTACTGTATCATTAGAGACGTTGAAATCTGCCGTCTGTTTTA
131 AGATTTTGGTGCTTCATTCCACTCCACTGTAACCTTAGGGACGTTGAGATCTACCGTCTGTTTTA
67092 ACCCCACTTATTTATACCTCACCAAGAAGATGAGATTTGAAGTCTCACTCCACTCAACTGTAACC
196 ACCCCACTTATTTATACCTCACCAAGAAGATGAGATTTGAAGTCTCACTCCACTCAACTGTAACC
* * * * * *
67157 TCAAGGACGTTGAGCTCTACTTCGTTATTTTCATTCGACCCATTGCAGCTCAGGGGTATAGGATT
261 TCAAAGACGTTGAGCTCTACTTCATTATTTTCATCCGACCCACTGCAACTCAAGGGTATAGGATT
* * * * * *
67222 CTGGTGCTTCACTCCACTCCATTGTAACGTCAGGGATGTTGAGATCTACTACCTGTTTTAACTCA
326 CTGGTGCTTCACTCCACTCCACTGTAACCTCAGAGACGTTGAGATCTACTACCTATTTTAACCCA
*
67287 CTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACACCACTGTAACATCAAGG
391 CTTCTCTGTACCTCACCAGGAAGATAGGATTTGAAGTCTCACTCCACACCACTGTAACATCAAGG
* *
67352 ACATTGAGCTCTGCTTCATTATTTTCATCCGACCCACTGCAACTCAGGGGTATAAGATTCTGGTG
456 ACATTGAGCTCTACTTCATTATTTTCATCCGACCCACTGCAACTCAGGAGTATAAGATTCTGGTG
** * * * * *
67417 CTTCACTTCTTTCCATTGTAACATCAGGAACGTTGAGATCTATTACCTA
521 CTTCACCCCATTCCACTGTAACATCAGGAACGATGAGATCTACTACCCA
* *
67466 TTTTAACCCACTTCTTTGTACTTCACTAGGAAGATGAGG-TTTGAAGTCTCACTCCACTCCACTG
1 TTTTAACCCACTTCTCTGTACCTCACTAGGAAGATGAGGATTTGAAGTCTCACTCCACTCCACTG
* * * *
67530 TAACCTCAAGGACGTTAAGCTCTGCTTCATTATTTTCATCGGACCCACTGTAACTCAGGGGTATA
66 TAACCTCAAGGACGTTGAGCTCTACTTCATTATTTTCATCCGACCCACTGTAACTCAAGGGTATA
* * * *
67595 AGATTTTGATGCTTCATTCCACTCCATTATAACCTCAGGGACGTTGAGATCTA-C-TACTTGTTT
131 AGATTTTGGTGCTTCATTCCACTCCACTGTAACCTTAGGGACGTTGAGATCTACCGT-C-TGTTT
* * ** * * * *
67658 TAA-CCCACTTCTTTGTACCTCA-TTAGAAAGATGAGATTTGAAGTTTCACTCTACTCTATTGTA
194 TAACCCCACTTATTTATACCTCACCAAG-AAGATGAGATTTGAAGTCTCACTCCACTCAACTGTA
*
67721 ACCTCAAAGACGTTGAGCTCTGCTTCATTATTTTCATCCGACCCACTGCAACTCAAGGGTATAGG
258 ACCTCAAAGACGTTGAGCTCTACTTCATTATTTTCATCCGACCCACTGCAACTCAAGGGTATAGG
* *
67786 ATTCTGGTGCTTCACTCCACTCCACTGTAACCTCAGAGACGTTGAGATTTGCTACCTATTTTAAC
323 ATTCTGGTGCTTCACTCCACTCCACTGTAACCTCAGAGACGTTGAGATCTACTACCTATTTTAAC
* * ** *
67851 CCACTTCTCTGTACTTCACCAGGAATATAGGATTTGAAGTCTCACTCCACTTCATTGTAACATCA
388 CCACTTCTCTGTACCTCACCAGGAAGATAGGATTTGAAGTCTCACTCCACACCACTGTAACATCA
* * ** * * *
67916 GGGACGTTGAGCTCTACTTCATTATTTTCATCTTACCCACTGCAACTTAGGAGTATAGGATTTTG
453 AGGACATTGAGCTCTACTTCATTATTTTCATCCGACCCACTGCAACTCAGGAGTATAAGATTCTG
* * * * *
67981 GTGCTTCACCCCATTCCACTGTAACCTGAGGAACGATGAGATTTGCTACCCG
518 GTGCTTCACCCCATTCCACTGTAACATCAGGAACGATGAGATCTACTACCCA
* * * *
68033 TTTTACCCCACTTCTCTGTACCTCTCTAGAAAGAT-AGGATTTGAAGTCTCACTCCATTCCACTG
1 TTTTAACCCACTTCTCTGTACCTCACTAGGAAGATGAGGATTTGAAGTCTCACTCCACTCCACTG
* * * * * * * * * *
68097 TAACCT-TAGAGATGTTGAGCTTTACTTCGTTGTTTTAATCTGACCCATTGTAACTTAAGGGCAT
66 TAACCTCAAG-GACGTTGAGCTCTACTTCATTATTTTCATCCGACCCACTGTAACTCAAGGGTAT
*
68161 AAGATTTTGGTGCTTCACTT-CACTCCACTGTAACCTTAGGGACATTGAGATC
130 AAGATTTTGGTGCTTCA-TTCCACTCCACTGTAACCTTAGGGACGTTGAGATC
68213 CGCTTTGTTA
Statistics
Matches: 638, Mismatches: 102, Indels: 15
0.85 0.14 0.02
Matches are distributed among these distances:
566 8 0.01
567 467 0.73
568 161 0.25
569 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (569 bp):
TTTTAACCCACTTCTCTGTACCTCACTAGGAAGATGAGGATTTGAAGTCTCACTCCACTCCACTG
TAACCTCAAGGACGTTGAGCTCTACTTCATTATTTTCATCCGACCCACTGTAACTCAAGGGTATA
AGATTTTGGTGCTTCATTCCACTCCACTGTAACCTTAGGGACGTTGAGATCTACCGTCTGTTTTA
ACCCCACTTATTTATACCTCACCAAGAAGATGAGATTTGAAGTCTCACTCCACTCAACTGTAACC
TCAAAGACGTTGAGCTCTACTTCATTATTTTCATCCGACCCACTGCAACTCAAGGGTATAGGATT
CTGGTGCTTCACTCCACTCCACTGTAACCTCAGAGACGTTGAGATCTACTACCTATTTTAACCCA
CTTCTCTGTACCTCACCAGGAAGATAGGATTTGAAGTCTCACTCCACACCACTGTAACATCAAGG
ACATTGAGCTCTACTTCATTATTTTCATCCGACCCACTGCAACTCAGGAGTATAAGATTCTGGTG
CTTCACCCCATTCCACTGTAACATCAGGAACGATGAGATCTACTACCCA
Found at i:69286 original size:6 final size:6
Alignment explanation
Indices: 69285--69343 Score: 59
Period size: 6 Copynumber: 10.2 Consensus size: 6
69275 CATTTTCTTT
* * * *
69285 TTTTTC TTCTT- TTTTTC TTTTTC TTTTCC TTTTCC TTTTT- TCTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
*
69331 ATTTTC TTTTTC T
1 TTTTTC TTTTTC T
69344 CTTCTTTTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
5 8 0.19
6 35 0.81
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:69305 original size:18 final size:17
Alignment explanation
Indices: 69284--69368 Score: 66
Period size: 17 Copynumber: 4.8 Consensus size: 17
69274 TCATTTTCTT
69284 TTTTTTCTTCTTTTTTTC
1 TTTTTTCTT-TTTTTTTC
*
69302 -TTTTTCTTTTCCTTTTCC
1 TTTTTTCTTTT--TTTTTC
**
69320 TTTTTTCTTTCATTTTC
1 TTTTTTCTTTTTTTTTC
69337 TTTTTCTCTTCTTTTATTT-
1 TTTTT-TCTT-TTTT-TTTC
*
69356 TATTTTCTTTTTT
1 TTTTTTCTTTTTT
69369 ATTTTTTGGG
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
16 2 0.04
17 21 0.39
18 13 0.24
19 15 0.28
20 3 0.06
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCTTTTTTTTTC
Found at i:69306 original size:26 final size:27
Alignment explanation
Indices: 69277--69368 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 27
69267 CGACCTCTCA
69277 TTTTCTTTTTTTTCTTCTTTT-TTTCT
1 TTTTCTTTTTTTTCTTCTTTTATTTCT
* *
69303 TTTTCTTTTCCTTTTCCTT-TTTTCTTTCA
1 TTTTCTTTT--TTTT-CTTCTTTTATTTCT
*
69332 TTTTC-TTTTTCTCTTCTTTTATTT-T
1 TTTTCTTTTTTTTCTTCTTTTATTTCT
69357 ATTTTCTTTTTT
1 -TTTTCTTTTTT
69369 ATTTTTTGGG
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
25 3 0.05
26 24 0.44
27 5 0.09
28 11 0.20
29 12 0.22
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.79
Consensus pattern (27 bp):
TTTTCTTTTTTTTCTTCTTTTATTTCT
Found at i:69311 original size:5 final size:5
Alignment explanation
Indices: 69277--69366 Score: 65
Period size: 5 Copynumber: 16.8 Consensus size: 5
69267 CGACCTCTCA
* *
69277 TTTTC TTTT- TTTTC TTCTTT TTTTC TTTTTC TTTTCC TTTTCC TTTTT
1 TTTTC TTTTC TTTTC TT-TTC TTTTC -TTTTC TTTT-C TTTT-C TTTTC
* * *
69325 TCTTTC ATTTTC TTTTTC TCTTC TTTTA TTTTA TTTTC TTTT
1 T-TTTC -TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
69367 TTATTTTTTG
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
4 4 0.06
5 33 0.47
6 32 0.46
7 1 0.01
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:69370 original size:12 final size:12
Alignment explanation
Indices: 69282--69373 Score: 50
Period size: 12 Copynumber: 7.8 Consensus size: 12
69272 TCTCATTTTC
69282 TTTT-TTTTCTT
1 TTTTATTTTCTT
*
69293 CTTT-TTTTC-T
1 TTTTATTTTCTT
* *
69303 TTTTCTTTTCCT
1 TTTTATTTTCTT
**
69315 TTTCCTTTT-TT
1 TTTTATTTTCTT
*
69326 CTTTCATTTTCTT
1 -TTTTATTTTCTT
*
69339 TTTCTCTTCTT-TT
1 TTT-TATT-TTCTT
69352 ATTTTATTTTCTT
1 -TTTTATTTTCTT
69365 TTTTATTTT
1 TTTTATTTT
69374 TTGGGTGAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
10 4 0.06
11 14 0.22
12 31 0.48
13 11 0.17
14 5 0.08
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTCTT
Found at i:74073 original size:8 final size:8
Alignment explanation
Indices: 74062--74092 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
74052 TGCTAAATAA
74062 ATAAAAAT
1 ATAAAAAT
74070 ATAAAAAT
1 ATAAAAAT
*
74078 AAAAAAAT
1 ATAAAAAT
74086 ATAAAAA
1 ATAAAAA
74093 GATGGAGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (8 bp):
ATAAAAAT
Found at i:94551 original size:24 final size:24
Alignment explanation
Indices: 94524--94598 Score: 132
Period size: 24 Copynumber: 3.1 Consensus size: 24
94514 AATTTGACTC
*
94524 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
94548 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
94572 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
94596 AAA
1 AAA
94599 GATTATTTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.55, C:0.11, G:0.12, T:0.23
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:96585 original size:24 final size:24
Alignment explanation
Indices: 96524--96586 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
96514 TAGACTAATA
* * * *
96524 AGAATTTGACTCAAATAACTAAAC
1 AGAATTTAACTGAAACAAATAAAC
* * *
96548 AGAGTTAAATTGAAACAAATAAAC
1 AGAATTTAACTGAAACAAATAAAC
96572 AGAATTTAACTGAAA
1 AGAATTTAACTGAAA
96587 TATTATTTCT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.24
Consensus pattern (24 bp):
AGAATTTAACTGAAACAAATAAAC
Found at i:97564 original size:6 final size:6
Alignment explanation
Indices: 97524--97622 Score: 57
Period size: 6 Copynumber: 17.0 Consensus size: 6
97514 CCATACTCCC
* * * **
97524 TTTAAA TTT-AT TTTAAA ATTAAA TTT--G TTTAAAA TTTAAA TTT-GT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* * *
97569 TTTAAA TTTAAA TTTAAA -TTAAG TTTAAA ATT-AT TTTCAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTT-AAA
97617 TTTAAA
1 TTTAAA
97623 ATAAATAAAA
Statistics
Matches: 68, Mismatches: 17, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
4 3 0.04
5 14 0.21
6 38 0.56
7 13 0.19
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:97590 original size:17 final size:17
Alignment explanation
Indices: 97524--97620 Score: 104
Period size: 17 Copynumber: 5.6 Consensus size: 17
97514 CCATACTCCC
97524 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
97541 ATTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAA
*
97558 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
** *
97575 TTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
*
97592 TTTAAAATTATTTTCAAA
1 TTTAAATTTATTTT-AAA
97610 TTTAAAATTTA
1 TTT-AAATTTA
97621 AAATAAATAA
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
17 53 0.83
18 5 0.08
19 6 0.09
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:97628 original size:18 final size:18
Alignment explanation
Indices: 97570--97628 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
97560 TAAATTTGTT
97570 TTAAATTT-AAATTTAAA
1 TTAAATTTAAAATTTAAA
* **
97587 TTAAGTTTAAAA-TTATT
1 TTAAATTTAAAATTTAAA
97604 TTCAAATTTAAAATTTAAA
1 TT-AAATTTAAAATTTAAA
*
97623 ATAAAT
1 TTAAAT
97629 AAAACCCAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
17 12 0.38
18 16 0.50
19 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
TTAAATTTAAAATTTAAA
Found at i:98357 original size:22 final size:21
Alignment explanation
Indices: 98332--98372 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
98322 CAATAACAGC
*
98332 AATAATATTAATAAATATTACT
1 AATAACATTAAT-AATATTACT
*
98354 AATAACATTAGTAATATTA
1 AATAACATTAATAATATTA
98373 ATGACAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (21 bp):
AATAACATTAATAATATTACT
Found at i:98434 original size:4 final size:4
Alignment explanation
Indices: 98427--98453 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
98417 ATTTCTTTAA
98427 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
98454 AAGAGGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:99470 original size:29 final size:29
Alignment explanation
Indices: 99425--99795 Score: 318
Period size: 29 Copynumber: 12.6 Consensus size: 29
99415 CCCTAAATTA
* *
99425 TCCAAAAATCTCGTTTTTAACCCCGAACT
1 TCCAAAAATCCCATTTTTAACCCCGAACT
**
99454 TCCAAAAATCCCATTTTTAACCCAAAACT
1 TCCAAAAATCCCATTTTTAACCCCGAACT
**
99483 TCCAAAAATCCCATTTTTAACCCTAAACT
1 TCCAAAAATCCCATTTTTAACCCCGAACT
*
99512 TCCAAAAATCCCATTTTTAACCCCAAAACT
1 TCCAAAAATCCCATTTTTAACCCC-GAACT
* * **
99542 TCCAAAAATGCCATTTTTGACCTCAAAACT
1 TCCAAAAATCCCATTTTTAACC-CCGAACT
* * * * **
99572 TTCAAAATTTCCATTCTT-ACATTCGAACT
1 TCCAAAAATCCCATTTTTAAC-CCCGAACT
* *
99601 TCCAAAAATCCCATTTTTGACCCCAAAACT
1 TCCAAAAATCCCATTTTTAACCCC-GAACT
* * * * *
99631 TTCAAAATTCTCATTCTT-ACCCTTGAACT
1 TCCAAAAATCCCATTTTTAACCC-CGAACT
* *
99660 TCCAAAAATCCCATTTTTGACCTCGAAACT
1 TCCAAAAATCCCATTTTTAACCCCG-AACT
* * *
99690 TTCAAAATTCCCA-TTTTACCCCCGAACT
1 TCCAAAAATCCCATTTTTAACCCCGAACT
* *
99718 TCCAAAATATCCCATTTTTGACCCTGAACCT
1 TCCAAAA-ATCCCATTTTTAACCCCGAA-CT
* * *
99749 TTCAAAAATTACCA-TTTTACCCCCGAACT
1 TCCAAAAA-TCCCATTTTTAACCCCGAACT
*
99778 TCCAAAAATCTCATTTTT
1 TCCAAAAATCCCATTTTT
99796 TGCCCCCGTG
Statistics
Matches: 275, Mismatches: 54, Indels: 26
0.77 0.15 0.07
Matches are distributed among these distances:
28 13 0.05
29 146 0.53
30 103 0.37
31 13 0.05
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (29 bp):
TCCAAAAATCCCATTTTTAACCCCGAACT
Found at i:99579 original size:59 final size:58
Alignment explanation
Indices: 99425--99795 Score: 379
Period size: 59 Copynumber: 6.3 Consensus size: 58
99415 CCCTAAATTA
* * * ** * * * *
99425 TCCAAAAATCTCGTTTTTAACCCCGAACTTCCAAAAATCCCATTTTTAACCCAAAACT
1 TCCAAAAATCCCATTTTTGACCCAAAACTTTCAAAATTCCCATTTTTACCCCAGAACT
* * * * *
99483 TCCAAAAATCCCATTTTTAACCCTAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
1 TCCAAAAATCCCATTTTTGACCCAAAACTTTCAAAATTCCCATTTTT-ACCCCAGAACT
* * * **
99542 TCCAAAAATGCCATTTTTGACCTCAAAACTTTCAAAATTTCCATTCTTACATTC-GAACT
1 TCCAAAAATCCCATTTTTGACC-CAAAACTTTCAAAATTCCCATTTTTAC-CCCAGAACT
* * **
99601 TCCAAAAATCCCATTTTTGACCCCAAAACTTTCAAAATTCTCATTCTTACCCTTGAACT
1 TCCAAAAATCCCATTTTTGA-CCCAAAACTTTCAAAATTCCCATTTTTACCCCAGAACT
* *
99660 TCCAAAAATCCCATTTTTGACCTCGAAACTTTCAAAATTCCCA-TTTTACCCCCGAACT
1 TCCAAAAATCCCATTTTTGACC-CAAAACTTTCAAAATTCCCATTTTTACCCCAGAACT
* * * *
99718 TCCAAAATATCCCATTTTTGACCCTGAACCTTTCAAAAATTACCA-TTTTACCCCCGAACT
1 TCCAAAA-ATCCCATTTTTGACCC-AAAACTTTC-AAAATTCCCATTTTTACCCCAGAACT
*
99778 TCCAAAAATCTCATTTTT
1 TCCAAAAATCCCATTTTT
99796 TGCCCCCGTG
Statistics
Matches: 275, Mismatches: 29, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
58 65 0.24
59 156 0.57
60 54 0.20
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (58 bp):
TCCAAAAATCCCATTTTTGACCCAAAACTTTCAAAATTCCCATTTTTACCCCAGAACT
Found at i:111051 original size:22 final size:22
Alignment explanation
Indices: 111023--111071 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
111013 ATACTCGACA
111023 ACTTTCAAACTAATGAACGTTT
1 ACTTTCAAACTAATGAACGTTT
111045 ACTTTCAAACTAATGAACGTTT
1 ACTTTCAAACTAATGAACGTTT
*
111067 CCTTT
1 ACTTT
111072 GATTCTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (22 bp):
ACTTTCAAACTAATGAACGTTT
Done.