Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004445.1 Kokia drynarioides strain JFW-HI SEQ_117846, 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: 3476
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Found at i:73 original size:37 final size:37
Alignment explanation
Indices: 23--178 Score: 123
Period size: 37 Copynumber: 3.9 Consensus size: 37
13 CCGCTTCATT
*
23 GATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCG
1 GATTTAGTCCACTTCTCTGTATCTCATCAGGAAGGCG
* * *
60 GATTTGGTCCACTTCTCTGTATCTCTTCAAGAAGATGACCG
1 GATTTAGTCCACTTCTCTGTATCTCATCAGGAAG--G--CG
* * *
101 CTTAATTGATTTAATCCACTTCTCTGTATCTTATCAGGAAGGTG
1 -------GATTTAGTCCACTTCTCTGTATCTCATCAGGAAGGCG
* * *
145 GATTTTGTCCACTTCTCTGTGTCTCATTAGGAAG
1 GATTTAGTCCACTTCTCTGTATCTCATCAGGAAG
179 ATGATCACTT
Statistics
Matches: 93, Mismatches: 15, Indels: 22
0.72 0.12 0.17
Matches are distributed among these distances:
37 59 0.63
39 1 0.01
41 2 0.02
44 1 0.01
46 1 0.01
48 29 0.31
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (37 bp):
GATTTAGTCCACTTCTCTGTATCTCATCAGGAAGGCG
Found at i:148 original size:85 final size:86
Alignment explanation
Indices: 1--214 Score: 297
Period size: 85 Copynumber: 2.5 Consensus size: 86
*
1 TCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCGGATTTG
1 TCAAGAAGATGACCGCTTAATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCGGATTTG
66 GTCCACTTCTCTGTATCTC-T
66 GTCCACTTCTCTGTATCTCAT
* * *
86 TCAAGAAGATGACCGCTTAATTGATTTAATCCACTTCTCTGTATCTTATCAGGAAGGTGGATTTT
1 TCAAGAAGATGACCGCTTAATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCGGATTTG
*
151 GTCCACTTCTCTGTGTCTCAT
66 GTCCACTTCTCTGTATCTCAT
* * * * * * * *
172 T-AGGAAGATGATCACTTTATTGCTTTGACCCACTTCTTTGTAT
1 TCAAGAAGATGACCGCTTAATTGATTTAATCCACTTCTCTGTAT
215 GGGGGTTTGA
Statistics
Matches: 115, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
85 113 0.98
86 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (86 bp):
TCAAGAAGATGACCGCTTAATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCGGATTTG
GTCCACTTCTCTGTATCTCAT
Found at i:400 original size:85 final size:85
Alignment explanation
Indices: 255--419 Score: 206
Period size: 85 Copynumber: 1.9 Consensus size: 85
245 TTGCTTCTTT
** * *
255 GATTTGGTTTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTC
1 GATTTGGTCCACTTCTCTGTATCTCATCAAGAAGACGACCGCTTCATTGATTTAACCCACTTCTC
*
320 TGTATCTCATCAGGAAGGCG
66 TATATCTCATCAGGAAGGCG
** * * *
340 GATTTGGTCCACTTCTCTGTATCTCATCCGGAAGACGACCGCTTTATTGCA-TTGACCCACTTTT
1 GATTTGGTCCACTTCTCTGTATCTCATCAAGAAGACGACCGCTTCATTG-ATTTAACCCACTTCT
* *
404 TTATATCTCATTAGGA
65 CTATATCTCATCAGGA
420 TGATTGGGGT
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
85 66 0.99
86 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (85 bp):
GATTTGGTCCACTTCTCTGTATCTCATCAAGAAGACGACCGCTTCATTGATTTAACCCACTTCTC
TATATCTCATCAGGAAGGCG
Found at i:576 original size:209 final size:209
Alignment explanation
Indices: 216--1189 Score: 1403
Period size: 209 Copynumber: 4.7 Consensus size: 209
206 TCTTTGTATG
* * *
216 GGGGTTTGAAGTTTCACTCACATTCAGCTTTGCTTCTTTGATTTGGTTTACTTCTCTGTATCTCA
1 GGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTGATTTGGTCTACTTCTCTGTATCTCA
* *
281 TCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCGGATTTG
66 TCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCAGATTTG
* * * * * *
346 GTCCACTTCTCTGTATCTCATCCGGAAGACGACCGCTTTATTGCATTGACCCACTTTTTTATATC
131 GTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTATATC
* *
411 TCATTAGGATGATT
196 TCATCAGGAAGATT
*
425 GGGGTTTGAAGTTTCACTC-CTATTGAGCTTTGCTTCATTAATTTGGTCTACTTCTCTGTATCTC
1 GGGGTTTGAAGTTTCACTCAC-ATTGAGCTTTGCTTCATTGATTTGGTCTACTTCTCTGTATCTC
* * * *
489 ATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTTTGTATCTCATCGGGAAGGCATATTT
65 ATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCAGATTT
* * * *
554 GGTCCACTTCTTTATATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCAACTTCTCTGTAT
130 GGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTATAT
* *
619 CTCATCAAGAAGATA
195 CTCATCAGGAAGATT
* *
634 GGGGTTTGAAGTTTCACTCACATTGAGCTTTACTTCATTGATTTGGTCTACTTCTCTATATCTCA
1 GGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTGATTTGGTCTACTTCTCTGTATCTCA
* * * * * *
699 TCAAGAAGTTGACCGCTTAATTGATTTAATCCACTTCTCTGTATCTCATCAAGAAGGTAGATTTT
66 TCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCAGATTTG
* * * * * * *
764 GTCCACTTCTATGTGTCTCATTAGGAAGATGATCACTTTATTGCTTTGACCCAGTTCTTTGTATC
131 GTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTATATC
829 TCATCAGGAAG-TT
196 TCATCAGGAAGATT
* *
842 AGGGGTTTGAAGTTTCACTCAAATTGAGCTTTGCTTCATTGTTTTGGTCTACTTCTCTGTATCTC
1 -GGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTGATTTGGTCTACTTCTCTGTATCTC
* * * * *
907 ATCAGGAAGATGATCGCTTCATTGATCTATTCCACTTCTCTATATCTCATCACGAAGGCAGATTT
65 ATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCAGATTT
* *
972 GGTCCACTTCTCTGTATCTCATCAGAAAGATGACTACTTTATTGCTTTGACCCACTTCTCTATAT
130 GGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTATAT
* *
1037 CTCATTAGGAAGATG
195 CTCATCAGGAAGATT
* * *
1052 GGGGTTTGAAGTTTTACTCACATTGAGCTTTGCTTTATTGATTTGGTCTACTTCTCTGTATCTCG
1 GGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTGATTTGGTCTACTTCTCTGTATCTCA
* * **
1117 TTAGGAAGATGACCGCTTCATTAATTTAATCCACTTCTCTGTATCTCATCAGGAAGGTGGATTTG
66 TCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCAGATTTG
1182 GTCCACTT
131 GTCCACTT
1190 TGTATCTTAT
Statistics
Matches: 675, Mismatches: 86, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
208 2 0.00
209 671 0.99
210 2 0.00
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.39
Consensus pattern (209 bp):
GGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTGATTTGGTCTACTTCTCTGTATCTCA
TCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCAGATTTG
GTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTATATC
TCATCAGGAAGATT
Found at i:611 original size:85 final size:85
Alignment explanation
Indices: 465--624 Score: 223
Period size: 85 Copynumber: 1.9 Consensus size: 85
455 TGCTTCATTA
* * * * *
465 ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTTT
1 ATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCACTTCATTGATTTAATCCACTTCTCT
530 GTATCTCATCGGGAAGGCAT
66 GTATCTCATCGGGAAGGCAT
* * * *
550 ATTTGGTCCACTTCTTTATATCTCATCAGGAAGATGACCACTTTATTGCTTTGA-CCAACTTCTC
1 ATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCACTTCATTGATTTAATCC-ACTTCTC
614 TGTATCTCATC
65 TGTATCTCATC
625 AAGAAGATAG
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
84 2 0.03
85 63 0.97
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (85 bp):
ATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCACTTCATTGATTTAATCCACTTCTCT
GTATCTCATCGGGAAGGCAT
Found at i:831 original size:418 final size:414
Alignment explanation
Indices: 61--1189 Score: 1569
Period size: 418 Copynumber: 2.7 Consensus size: 414
51 AGGAAGGCGG
* * * * *
61 ATTTGGTCCACTTCTCTGTATCTCTTCAAGAAGATGACCGCTTAATTGATTTAATCCACTTCTCT
1 ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCT
* ** * * * *
126 GTATCTTATCAGGAAGGTGGATTTTGTCCACTTCTCTGTGTCTCATTAGGAAGATGATCACTTTA
66 GTATCTCATCAGGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTA
* *
191 TTGCTTTGACCCAC-T-TCTT-TGT-AT----G--GGGGTTTGAAGTTTCACTCACATTCAGCTT
131 TTGCTTTGACCCACTTCTCTTATCTCATAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTT
* *
246 TGCTTCTTTGATTTGGTTTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAAT
196 TGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAAT
* * *
311 CCACTTCTCTGTATCTCATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCCGGAAGAC
261 CCACTTCTCTGTATCTCATCAGGAAGGTGGATTTGGTCCACTTCTATGTATCTCATCAGGAAGAC
* * * *
376 GACCGCTTTATTGCATTGACCCACTTTTTTATATCTCATTAGGATGATT-GGGGTTTGAAGTTTC
326 GACCACTTTATTGCATTGACCCACTTCTTTATATCTCATCAGGAAG-TTAGGGGTTTGAAGTTTC
**
440 ACTCCTATTGAGCTTTGCTTCATTA
390 ACTCAAATTGAGCTTTGCTTCATTA
*
465 ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTTT
1 ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCT
* * * *
530 GTATCTCATCGGGAAGGCATATTTGGTCCACTTCTTTATATCTCATCAGGAAGATGACCACTTTA
66 GTATCTCATCAGGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTA
*
595 TTGCTTTGACCAACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTTTCACTCACATTGA
131 TTGCTTTGACCCACTTCTCT-TATCTCAT--AGAAGAT-GGGGTTTGAAGTTTCACTCACATTGA
* * * *
660 GCTTTACTTCATTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGTTGACCGCTTAATTGATT
192 GCTTTGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATT
* * * * *
725 TAATCCACTTCTCTGTATCTCATCAAGAAGGTAGATTTTGTCCACTTCTATGTGTCTCATTAGGA
257 TAATCCACTTCTCTGTATCTCATCAGGAAGGTGGATTTGGTCCACTTCTATGTATCTCATCAGGA
* * * * *
790 AGATGATCACTTTATTGCTTTGACCCAGTTCTTTGTATCTCATCAGGAAGTTAGGGGTTTGAAGT
322 AGACGACCACTTTATTGCATTGACCCACTTCTTTATATCTCATCAGGAAGTTAGGGGTTTGAAGT
*
855 TTCACTCAAATTGAGCTTTGCTTCATTG
387 TTCACTCAAATTGAGCTTTGCTTCATTA
* * *
883 TTTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATCTATTCCACTTCTCT
1 ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCT
* * * *
948 ATATCTCATCACGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGACTACTTTA
66 GTATCTCATCAGGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTA
*
1013 TTGCTTTGACCCACTTCTCTATATCTCATTAGGAAGATGGGGGTTTGAAGTTTTACTCACATTGA
131 TTGCTTTGACCCACTTCTCT-TATCTCA-TA-GAAGAT-GGGGTTTGAAGTTTCACTCACATTGA
* * * * *
1078 GCTTTGCTTTATTGATTTGGTCTACTTCTCTGTATCTCGTTAGGAAGATGACCGCTTCATTAATT
192 GCTTTGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATT
1143 TAATCCACTTCTCTGTATCTCATCAGGAAGGTGGATTTGGTCCACTT
257 TAATCCACTTCTCTGTATCTCATCAGGAAGGTGGATTTGGTCCACTT
1190 TGTATCTTAT
Statistics
Matches: 634, Mismatches: 74, Indels: 20
0.87 0.10 0.03
Matches are distributed among these distances:
404 126 0.20
405 1 0.00
406 3 0.00
407 1 0.00
408 2 0.00
409 2 0.00
415 1 0.00
417 3 0.00
418 494 0.78
419 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.39
Consensus pattern (414 bp):
ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTCT
GTATCTCATCAGGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTA
TTGCTTTGACCCACTTCTCTTATCTCATAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTT
TGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAAT
CCACTTCTCTGTATCTCATCAGGAAGGTGGATTTGGTCCACTTCTATGTATCTCATCAGGAAGAC
GACCACTTTATTGCATTGACCCACTTCTTTATATCTCATCAGGAAGTTAGGGGTTTGAAGTTTCA
CTCAAATTGAGCTTTGCTTCATTA
Found at i:1027 original size:85 final size:85
Alignment explanation
Indices: 884--1041 Score: 221
Period size: 85 Copynumber: 1.9 Consensus size: 85
874 GCTTCATTGT
* * * *
884 TTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATCTATTCCACTTCTCTA
1 TTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGATCACTTCATTGATCTATCCCACTTCTCTA
949 TATCTCATCACGAAGGCAGA
66 TATCTCATCACGAAGGCAGA
* * *
969 TTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGA-CTACTTTATTGCTTTGA-CCCACTTCTC
1 TTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGATC-ACTTCATTGATCT-ATCCCACTTCTC
1032 TATATCTCAT
64 TATATCTCAT
1042 TAGGAAGATG
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
84 1 0.02
85 62 0.97
86 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (85 bp):
TTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGATCACTTCATTGATCTATCCCACTTCTCTA
TATCTCATCACGAAGGCAGA
Found at i:1480 original size:160 final size:161
Alignment explanation
Indices: 1017--1455 Score: 539
Period size: 158 Copynumber: 2.8 Consensus size: 161
1007 ACTTTATTGC
* * * *
1017 TTTGACCCACTTCTCTATATCTCATTAGGAAGATGGGGGTTTGAAGTTTT-ACTCACATTGAGCT
1 TTTGGCCCACTTCTTTATATCTTATTAGGAAGATGGGGGTTT-AAATTTTCACTCACATTGAGCT
** * * * *
1081 TTGCTTTATTGATTTGGTCTACTTCTCTGTATCTCGTTAGGAAGATGACCGCTTCATTAATTTAA
65 TCACTTTATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTAATTTAA
**
1146 TCCACTTCTCTGTATCTCATCAGGAAGGTGGA
130 TCCACTTCTCTGTATCTCATCAGGAAGACGGA
* * * * ** *
1178 TTTGGTCCA---CTTTGTATCTTATTAGAAAGATGGGGGTTTGACGTTTCACTCACATT-AGGAT
1 TTTGGCCCACTTCTTTATATCTTATTAGGAAGATGGGGGTTTAAATTTTCACTCACATTGA-GCT
* * * * *
1239 TCACTTCATTGTTTTGGTTCACTTCTCTGTATCTCATCAAGAAGATGACTGCTTCATTGATTTAA
65 TCACTTTATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTAATTTAA
* * *
1304 TCCACTTCTCTGTATCTTATTAGGATGACGGA
130 TCCACTTCTCTGTATCTCATCAGGAAGACGGA
* *
1336 TTTGGCCCACTTCTTTATATCTTATCAGGAA-ATAGGGGTTTAAATTTTCACTCACATTGAGCTT
1 TTTGGCCCACTTCTTTATATCTTATTAGGAAGATGGGGGTTTAAATTTTCACTCACATTGAGCTT
* *
1400 CACTTTATTGTTTTGGTCCACTTCTCAGTATCTCATCAGGAAGATGGCCGCTTCAT
66 CACTTTATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCAT
1456 CATTGTGATC
Statistics
Matches: 231, Mismatches: 41, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
157 5 0.02
158 126 0.55
160 76 0.33
161 24 0.10
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.40
Consensus pattern (161 bp):
TTTGGCCCACTTCTTTATATCTTATTAGGAAGATGGGGGTTTAAATTTTCACTCACATTGAGCTT
CACTTTATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTAATTTAAT
CCACTTCTCTGTATCTCATCAGGAAGACGGA
Found at i:1692 original size:46 final size:46
Alignment explanation
Indices: 1568--2110 Score: 478
Period size: 45 Copynumber: 12.3 Consensus size: 46
1558 TGATAATAGG
*
1568 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGATTGC
1 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGC
* * *
1614 TTCAATTTTCCCCTCTTG--TTAGGGGTAAAAGATTGAATGATGGC
1 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGC
* * *
1658 TTAAATCTACCCCACTTGACTTTGGGGTAAAAGATTGGATGATGGC
1 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGC
* * **
1704 TTTAATCTGCTACTCTTGACTTTA-GGGTAAAAGATTGGATGATGGC
1 TTCAATCTACCCCTCTTGAC-TTAGGGGTAAAAGATTGGATGATGGC
* * **
1750 TTCAATCTA---C-CTGGA-TTAGGGGTAAAAGATTGGA-CAGTAAC
1 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGA-TGGC
* * *
1791 TTCAATCTGCCCCTCTTGAC-TAGGAGTAAAAGTTTGGA--ATGGC
1 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGC
* * * * *
1834 TTCAA-CTTGCCCCT-TTAGA-TTAGGGGTAAAAGGTTAGA-CACTGAC
1 TTCAATC-TACCCCTCTT-GACTTAGGGGTAAAAGATTGGATGA-TGGC
* * *
1879 TTCAATCTGCCCCTCTTGAC-TA-AGGTAAAAGATTGGAAGATGGC
1 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGC
* * * *
1923 TTCAATCTGCCCCTCATGAC-TAGAGGTAAAAGATTGGA--A-GTC
1 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGC
1965 TTCAATCTACCCCTCTTGA-TTAGGGGTAAAAGATTGGA--ATGGC
1 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGC
** * * * * *
2008 TTCAA-CT-TGCCTCTATGGA-TTAAGGGTAAAATATTGGACGGTGAC
1 TTCAATCTACCCCTCT-T-GACTTAGGGGTAAAAGATTGGATGATGGC
*
2053 TTCAATCTGCCCCTCTTGAC-TAGGGGTAAAAGATTGGATGATGGC
1 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGC
2098 TTCAATCTACCCC
1 TTCAATCTACCCC
2111 ATGGTTAAGG
Statistics
Matches: 411, Mismatches: 57, Indels: 59
0.78 0.11 0.11
Matches are distributed among these distances:
40 4 0.01
41 30 0.07
42 47 0.11
43 59 0.14
44 77 0.19
45 97 0.24
46 90 0.22
47 7 0.02
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (46 bp):
TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGC
Found at i:1881 original size:88 final size:89
Alignment explanation
Indices: 1588--2102 Score: 456
Period size: 88 Copynumber: 5.8 Consensus size: 89
1578 CCCTCTTGAC
* * * * * *
1588 TTAGGGGTAAAAGATTGGATGATTG-CTTCAATTTTCCCCTCTTG-TTAGGGGTAAAAGATTGAA
1 TTAGGGGTAAAAGATTGGA-CAGTGACTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGGA
* * *
1651 TGATGGCTT-AAATCTACCCCACTT-GA
65 -GATGGCTTCAACT-TGCCCC-TTTAGA
* * * * **
1677 CTTTGGGGTAAAAGATTGGA-TGATGGCTTTAATCTGCTACTCTTGACTTTA-GGGTAAAAGATT
1 -TTAGGGGTAAAAGATTGGACAG-TGACTTCAATCTGCCCCTCTTGAC--TAGGGGTAAAAGATT
* *
1740 GGATGATGGCTTCAA--T-CTACC--TGGA
62 GGA-GATGGCTTCAACTTGC-CCCTTTAGA
* * *
1765 TTAGGGGTAAAAGATTGGACAGTAACTTCAATCTGCCCCTCTTGACTAGGAGTAAAAGTTTGGA-
1 TTAGGGGTAAAAGATTGGACAGTGACTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGGAG
1829 ATGGCTTCAACTTGCCCCTTTAGA
66 ATGGCTTCAACTTGCCCCTTTAGA
* * * *
1853 TTAGGGGTAAAAGGTTAGACACTGACTTCAATCTGCCCCTCTTGACTA-AGGTAAAAGATTGGAA
1 TTAGGGGTAAAAGATTGGACAGTGACTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGG-A
*
1917 GATGGCTTCAA-TCTGCCCC-TCATGA
65 GATGGCTTCAACT-TGCCCCTTTA-GA
* * * *
1942 CTAGAGGTAAAAGATTGGA-AGT--CTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGGA-
1 TTAGGGGTAAAAGATTGGACAGTGACTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGGAG
* * *
2003 ATGGCTTCAACTTGCCTCTATGGA
66 ATGGCTTCAACTTGCCCCTTTAGA
* * *
2027 TTAAGGGTAAAATATTGGACGGTGACTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGGAT
1 TTAGGGGTAAAAGATTGGACAGTGACTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGGA-
2092 GATGGCTTCAA
65 GATGGCTTCAA
2103 TCTACCCCAT
Statistics
Matches: 349, Mismatches: 49, Indels: 54
0.77 0.11 0.12
Matches are distributed among these distances:
84 10 0.03
85 34 0.10
86 41 0.12
87 63 0.18
88 93 0.27
89 36 0.10
90 45 0.13
92 23 0.07
93 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (89 bp):
TTAGGGGTAAAAGATTGGACAGTGACTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGGAG
ATGGCTTCAACTTGCCCCTTTAGA
Found at i:2004 original size:174 final size:173
Alignment explanation
Indices: 1568--2110 Score: 587
Period size: 174 Copynumber: 3.1 Consensus size: 173
1558 TGATAATAGG
* * * * *
1568 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGGATGATTGCTTCAATTTTCCCCTCTTG-
1 TTCAATCTACCCCTC-TGAC-TAGGGGTAAAAGATTGGA-CAGTACTTCAATCTACCCCTCTTGA
* * * * *
1632 TTAGGGGTAAAAGATTGAATGATGGCTT-AAATCTACCCCACTTGACTTTGGGGTAAAAGATTGG
63 TTAGGGGTAAAAGATTGGA--ATGGCTTCAACT-TGCCCC-TTTGA-TTAGGGGTAAAAGATTGG
* * * **
1696 ATGATGGCTTTAATCTGCTACTCTTGACTTTAGGGTAAAAGATTGGATGATGGC
123 A-CATGACTTCAATCTGCCCCTCTTGAC--TAGGGTAAAAGATTGGATGATGGC
* * * *
1750 TTCAATCTA--CCT-GGATTAGGGGTAAAAGATTGGACAGTAACTTCAATCTGCCCCTCTTGACT
1 TTCAATCTACCCCTCTGACTAGGGGTAAAAGATTGGACAGT-ACTTCAATCTACCCCTCTTGATT
* * * *
1812 AGGAGTAAAAGTTTGGAATGGCTTCAACTTGCCCCTTTAGATTAGGGGTAAAAGGTTAGACACTG
65 AGGGGTAAAAGATTGGAATGGCTTCAACTTGCCCCTTT-GATTAGGGGTAAAAGATTGGACA-TG
* *
1877 ACTTCAATCTGCCCCTCTTGACTAAGGTAAAAGATTGGAAGATGGC
128 ACTTCAATCTGCCCCTCTTGACTAGGGTAAAAGATTGGATGATGGC
* *
1923 TTCAATCTGCCCCTCATGACTAGAGGTAAAAGATTGGA-AGT-CTTCAATCTACCCCTCTTGATT
1 TTCAATCTACCCCTC-TGACTAGGGGTAAAAGATTGGACAGTACTTCAATCTACCCCTCTTGATT
* * * * *
1986 AGGGGTAAAAGATTGGAATGGCTTCAACTTGCCTCTATGGATTAAGGGTAAAATATTGGACGGTG
65 AGGGGTAAAAGATTGGAATGGCTTCAACTTGCCCCT-TTGATTAGGGGTAAAAGATTGGAC-ATG
2051 ACTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTGGATGATGGC
128 ACTTCAATCTGCCCCTCTTGACTA-GGGTAAAAGATTGGATGATGGC
2098 TTCAATCTACCCC
1 TTCAATCTACCCC
2111 ATGGTTAAGG
Statistics
Matches: 307, Mismatches: 42, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
173 30 0.10
174 98 0.32
175 74 0.24
176 19 0.06
177 57 0.19
178 17 0.06
180 3 0.01
182 9 0.03
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (173 bp):
TTCAATCTACCCCTCTGACTAGGGGTAAAAGATTGGACAGTACTTCAATCTACCCCTCTTGATTA
GGGGTAAAAGATTGGAATGGCTTCAACTTGCCCCTTTGATTAGGGGTAAAAGATTGGACATGACT
TCAATCTGCCCCTCTTGACTAGGGTAAAAGATTGGATGATGGC
Found at i:2103 original size:219 final size:218
Alignment explanation
Indices: 1568--2137 Score: 517
Period size: 219 Copynumber: 2.6 Consensus size: 218
1558 TGATAATAGG
* * * * * * *
1568 TTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTGG-ATGATTGCTTCAATTTTCCCCTCTTG
1 TTCAATCTGCCCCTATGGAC-TAGGAGTAAAAGTTTGGAATGA---CTTCAATCTGCCCCTCTTG
* * **
1632 -TTAGGGGTAAAAGATTGAATGATGGCTTAAATCTACCCCACTTGACTTTGGGGTAAAAGATTGG
62 ATTAGGGGTAAAAGATTGGATGATGGCTTCAATCTACCCCACTTGAC-TTAAGGTAAAAGATTGG
* * * *
1696 ATGATGGCTTTAATCTGCTACTCTTGACTTTAGGGTAAAAGATTGGATGATGGCTTCAATCTACC
126 AAGATGGCTTCAATCTGCCACTCATGAC-TTAGGGTAAAAGATTGGA-GATGGCTTCAATCTACC
1761 TGGATTAGGGGTAAAAGATTGGACAGTAAC
189 TGGATTAGGGGTAAAAGATTGGACAGTAAC
* * *
1791 TTCAATCTGCCCCTCTTGACTAGGAGTAAAAGTTTGGAATGGCTTCAA-CTTGCCCCT-TTAGAT
1 TTCAATCTGCCCCTATGGACTAGGAGTAAAAGTTTGGAATGACTTCAATC-TGCCCCTCTT-GAT
* * * * * *
1854 TAGGGGTAAAAGGTTAGA-CACTGACTTCAATCTGCCCCTCTTGAC-TAAGGTAAAAGATTGGAA
64 TAGGGGTAAAAGATTGGATGA-TGGCTTCAATCTACCCCACTTGACTTAAGGTAAAAGATTGGAA
* *
1917 GATGGCTTCAATCTGCCCCTCATGAC-TAGAGGTAAAAGATTGGA-A-GTCTTCAATCTACCCCT
128 GATGGCTTCAATCTGCCACTCATGACTTAG-GGTAAAAGATTGGAGATGGCTTCAATCTA---C-
* **
1979 CTTGATTAGGGGTAAAAGATTGGA-A-TGGC
188 CTGGATTAGGGGTAAAAGATTGGACAGTAAC
* * *
2008 TTCAA-CTTGCCTCTATGGATTAAGG-GTAAAA-TATTGGACGGTGACTTCAATCTGCCCCTCTT
1 TTCAATC-TGCCCCTATGGACT-AGGAGTAAAAGT-TTGGA--ATGACTTCAATCTGCCCCTCTT
* * *
2070 GACTAGGGGTAAAAGATTGGATGATGGCTTCAATCTACCCCA--TG-GTTAAGGTAAATGATTGG
61 GATTAGGGGTAAAAGATTGGATGATGGCTTCAATCTACCCCACTTGACTTAAGGTAAAAGATTGG
*
2132 ATGATG
126 AAGATG
2138 ATGTAACTTT
Statistics
Matches: 287, Mismatches: 41, Indels: 44
0.77 0.11 0.12
Matches are distributed among these distances:
215 11 0.04
216 3 0.01
217 53 0.18
218 19 0.07
219 110 0.38
220 18 0.06
221 36 0.13
222 15 0.05
223 22 0.08
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (218 bp):
TTCAATCTGCCCCTATGGACTAGGAGTAAAAGTTTGGAATGACTTCAATCTGCCCCTCTTGATTA
GGGGTAAAAGATTGGATGATGGCTTCAATCTACCCCACTTGACTTAAGGTAAAAGATTGGAAGAT
GGCTTCAATCTGCCACTCATGACTTAGGGTAAAAGATTGGAGATGGCTTCAATCTACCTGGATTA
GGGGTAAAAGATTGGACAGTAAC
Found at i:2440 original size:49 final size:48
Alignment explanation
Indices: 2387--2537 Score: 148
Period size: 49 Copynumber: 3.1 Consensus size: 48
2377 CTGCTTCTCT
2387 ACATCTTCAAGGTATAAGATTCACCATTGCTACTTCAATCTTTCCCTTC
1 ACATCTTCAAGGTATAAGATTCACCATTG-TACTTCAATCTTTCCCTTC
* * * * *
2436 ACATC-TCTAGGTTATAAGGTTCACCGTTATGACTTCAACCTTTCCCATT-
1 ACATCTTCAAGG-TATAAGATTCACCATTGT-ACTTCAATCTTTCCC-TTC
* *
2485 ACATCTCCAAGGTATAAGATTCGA-CATTGTAGCTTTAATCTCTT-CCTTC
1 ACATCTTCAAGGTATAAGATTC-ACCATTGTA-CTTCAATCT-TTCCCTTC
2534 ACAT
1 ACAT
2538 TCCTATGGTA
Statistics
Matches: 82, Mismatches: 12, Indels: 16
0.75 0.11 0.15
Matches are distributed among these distances:
48 9 0.11
49 64 0.78
50 9 0.11
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.36
Consensus pattern (48 bp):
ACATCTTCAAGGTATAAGATTCACCATTGTACTTCAATCTTTCCCTTC
Found at i:2577 original size:98 final size:98
Alignment explanation
Indices: 2386--2581 Score: 240
Period size: 98 Copynumber: 2.0 Consensus size: 98
2376 TCTGCTTCTC
* *
2386 TACATCTTCAAGGTATAAGATTCACCATTGCTACTTCAATCTTTCCCTTCACATCTCTAGGTTAT
1 TACATCTCCAAGGTATAAGATTCACCATTGCTACTTCAATCTTTCCCTTCACATCTCTAGGTTAC
*
2451 AAGGTTCACCGTTATGACTTCAACCTTTCCCAT
66 AAGGTTCACCGTTACGACTTCAACCTTTCCCAT
*
2484 TACATCTCCAAGGTATAAGATTCGA-CATTG-TAGCTTTAATCTCTT-CCTTCACAT-TCCTATG
1 TACATCTCCAAGGTATAAGATTC-ACCATTGCTA-CTTCAATCT-TTCCCTTCACATCT-CTA-G
* * * *
2545 G-TACAAGGTTCACCGTTGCGGCTTCTATCTTTCCCAT
61 GTTACAAGGTTCACCGTTACGACTTCAACCTTTCCCAT
2582 CTCGTCTTCG
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
97 3 0.04
98 77 0.91
99 5 0.06
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (98 bp):
TACATCTCCAAGGTATAAGATTCACCATTGCTACTTCAATCTTTCCCTTCACATCTCTAGGTTAC
AAGGTTCACCGTTACGACTTCAACCTTTCCCAT
Found at i:3428 original size:6 final size:6
Alignment explanation
Indices: 3417--3457 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
3407 TTGACCTCTC
*
3417 CTTTTT CTTTTT CTTCTT CTCTTTT CTTTTT C-TTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CT-TTTT CTTTTT CTTTTT CTTTT
3458 ATTTTCTCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 5 0.16
6 21 0.68
7 5 0.16
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:3443 original size:19 final size:18
Alignment explanation
Indices: 3419--3454 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
3409 GACCTCTCCT
3419 TTTTCTTTTTCTTCTTCTC
1 TTTTCTTTTTCTT-TTCTC
3438 TTTTCTTTTTCTTTTCT
1 TTTTCTTTTTCTTTTCT
3455 TTTATTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTTCTTTTCTC
Done.