Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013217.1 Kokia drynarioides strain JFW-HI SEQ_128236, 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: 25597
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:838 original size:96 final size:98
Alignment explanation
Indices: 645--828 Score: 232
Period size: 98 Copynumber: 1.9 Consensus size: 98
635 ATTAGATTAT
* * * **
645 TTCAATCTGCCCCATGGTTGGGGTAAGAGATCTTATGGTCTTCAATCTACCTTATAGTTAGGGTA
1 TTCAATCTGCCCCATGGTTAGGGTAAAAGATCTAATGGTCTTCAATCTACCCCATAGTTAGGGTA
* *
710 AAAGATTGGATTGCTTCAATTTGCCGGATGATC
66 AAAGATTGAATTGCTTCAATCTGCCGGATGATC
* *
743 TTCAATCTGCCCTC-TGGTTAGGGTAAAAGAT-TAAATTG-CTTCAATCTACCCCATAG-TCGGG
1 TTCAATCTGCCC-CATGGTTAGGGTAAAAGATCT-AATGGTCTTCAATCTACCCCATAGTTAGGG
*
804 TAAAAGATTGAATTTCTTCAATCTG
64 TAAAAGATTGAATTGCTTCAATCTG
829 ACCTATGATC
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
96 26 0.35
97 17 0.23
98 30 0.41
99 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (98 bp):
TTCAATCTGCCCCATGGTTAGGGTAAAAGATCTAATGGTCTTCAATCTACCCCATAGTTAGGGTA
AAAGATTGAATTGCTTCAATCTGCCGGATGATC
Found at i:904 original size:80 final size:80
Alignment explanation
Indices: 801--1546 Score: 1055
Period size: 80 Copynumber: 9.3 Consensus size: 80
791 CCCCATAGTC
* * *
801 GGGTAAAAGATTGAATTTCTTCAATCTGACCTATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* *
866 CTTGCCCTTTAGTTA
66 CTTGCCCTCTGGTTA
* * *
881 AGGTAAAAGATTGCATTTCTTCAATCTGTCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
946 CTTGCACTCTGGTTA
66 CTTGCCCTCTGGTTA
*
961 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTTAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
1026 CTTTCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* * * * * * * *
1041 GGATAAAAGATTGGATTTCTTCAATCTGCGCTATGACCGGGATAAAAGATCAGATGATCTTTAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
1106 CTTGCCCTCTAGTTA
66 CTTGCCCTCTGGTTA
* * * *
1121 GGGTAAAAGATTAGATTTCTTTAATTTGCCCCAT-ATCGAGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1185 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* * * * * *
1200 GGGTAAATGTTTGAATTTCTTTAATCTGCCCCATGATCGGGGTAGAAGATCAGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
1265 CTTGCCCTCTAGTTA
66 CTTGCCCTCTGGTTA
* * *
1280 GGGTAAAAGAATGGATTTCTTCAATCTACCCCATGATCGGGGTAAAAGATCGGATAGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1345 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
** ** *
1360 GAATAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGAAGTAAAAGATCAGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1425 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
*** * *
1440 GGGTAAAAGATAATATTTCTTCAATCCGCCCCATGA-CTTGGGTAAAAGATCGGATGGTCTTCAA
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATC-GGGGTAAAAGATCGGATGGTCTTCAA
* *
1504 TCTTGCCATTTGGTTA
65 TCTTGCCCTCTGGTTA
1520 GGGTAAAAGATTGGATTTCTTCAATCT
1 GGGTAAAAGATTGGATTTCTTCAATCT
1547 TACCCTCTGG
Statistics
Matches: 586, Mismatches: 78, Indels: 4
0.88 0.12 0.01
Matches are distributed among these distances:
79 68 0.12
80 518 0.88
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (80 bp):
GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
CTTGCCCTCTGGTTA
Found at i:1062 original size:120 final size:119
Alignment explanation
Indices: 920--1810 Score: 604
Period size: 120 Copynumber: 7.4 Consensus size: 119
910 CCCATGATCG
* * * *
920 GGGTAAAAGATCGGATGGTCTTCAATCTTGCACTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
1 GGGTAAAAGATTGGAT-TTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTAGATTTCTTCAA
* * *
985 TCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTTAATCTTTCCCTCTGGTTA
65 TCTGCCCCATGATCGGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCT-GTTA
* * * *** * * *
1041 GGATAAAAGATTGGATTTCTTCAATC-TGCGCTAT-GACCGGGATAAAAGATCAGATGATCTTTA
1 GGGTAAAAGATTGGATTTCTTCAATCTTGCCCTCTGGTTAGGG-TAAAAGATTAGAT-TTCTTCA
** * * * * *
1104 ATCTTGCCCTC-T-AGTTAGGGTAAAAGATTAGAT-TTCTTTAAT-TTGCCC-CAT-ATC
64 ATC-TGCCC-CATGA-TCGGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTC-TGTTA
* * * * *
1158 GAGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAATG-TTTGAATTTCTTT
1 G-GGTAAAAGATTGGAT-TTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTAG-ATTTCTTC
*
1222 AATCTGCCCCATGATCGGGGTAGAAGATCAGATGGTCTTCAATCTTGCCCTCTAGTTA
63 AATCTGCCCCATGATCGGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCT-GTTA
* * * ** ** *
1280 GGGTAAAAGAATGGATTTCTTCAATC-TACCC-CATGATCGGGGTAAAAGATCGGATAGTCTTCA
1 GGGTAAAAGATTGGATTTCTTCAATCTTGCCCTC-TGGTTAGGGTAAAAGATTAGAT-TTCTTCA
* ** ** ** * * *
1343 ATCTTGCCCTC-TGGTTAGAATAAAAGATTGGAT-TTCTTCAATC-TGCCC-CATGATC
64 ATC-TGCCC-CATGATCGGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTC-TGTTA
* ** * * *
1398 GAAGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATAATATTTCTTCA
1 G-GGTAAAAGATTGGAT-TTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTAGATTTCTTCA
* * * * *
1463 ATCCGCCCCATGA-CTTGGGTAAAAGATCGGATGGTCTTCAATCTTGCCATTTGGTTA
64 ATCTGCCCCATGATC-GGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCT-GTTA
* *
1520 GGGTAAAAGATTGGATTTCTTCAATCTTACCCTCTGGTTAGGGTAAAAGATTATATTTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTAGATTTCTTCAAT
* * * *
1585 CTGCCCCATAATCGAGGTAAACGATTAGATGGTCTTCAATCTTGCCCTCTTGTTA
66 CTGCCCCATGATCGGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTC-TGTTA
* * * * ** ** *
1640 GGGTAAAATATTGGATTTCTTTAAT-TTACCC-CATGATCCGGGTAAAAGATCGGATGGTCTTC-
1 GGGTAAAAGATTGGATTTCTTCAATCTTGCCCTC-TGGTTAGGGTAAAAGATTAGAT-TTCTTCA
* * ** * * * **
1702 ATCTTG-CCCTTTAGTTAGGGTAAAAGATTAGAT-TTCTTCAATC-TGCCAC-ATGATCG
64 ATC-TGCCCCATGA-TCGGGGTAAAAGATCAGATGGTCTTCAATCTTGCC-CTCTG-TTA
* *
1758 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATT
1 GGGTAAAAGATTGGAT-TTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATT
1811 GGAGGTTGTA
Statistics
Matches: 594, Mismatches: 131, Indels: 91
0.73 0.16 0.11
Matches are distributed among these distances:
117 5 0.01
118 65 0.11
119 151 0.25
120 253 0.43
121 112 0.19
122 8 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (119 bp):
GGGTAAAAGATTGGATTTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTAGATTTCTTCAAT
CTGCCCCATGATCGGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGTTA
Found at i:1539 original size:399 final size:399
Alignment explanation
Indices: 801--1540 Score: 1131
Period size: 399 Copynumber: 1.9 Consensus size: 399
791 CCCCATAGTC
* *
801 GGGTAAAAGATTGAATTTCTTCAATCTGACCTATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGAATTTCTTCAATCTGACCCATGATCGGGGTAAAAGATCAGATGGTCTTCAAT
* * **
866 CTTGCCCTTTAGTTAAGGTAAAAGATTGCATTTCTTCAATCTGTCCCATGATCGGGGTAAAAGAT
66 CTTGCCCTCTAGTTAAGGTAAAAGAATGCATTTCTTCAATCTACCCCATGATCGGGGTAAAAGAT
* **
931 CGGATGGTCTTCAATCTTGCACTCTGGTTAGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATG
131 CGGATAGTCTTCAATCTTGCACTCTGGTTAGAATAAAAGATTGGATTTCTTCAATCTGCCCCATG
** * * * **
996 ATCGGGGTAAAAGATCGGATGGTCTTTAATCTTTCCCTCTGGTTAGGATAAAAGATTGGATTTCT
196 ATCGAAGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAGGATAAAAGATAAGATTTCT
* * * * *
1061 TCAATCTGCGCTATGACCGGGATAAAAGATCAGATGATCTTTAATCTTGCCCTCTAGTTAGGGTA
261 TCAATCCGCCCCATGACCGGGATAAAAGATCAGATGATCTTCAATCTTGCCATCTAGTTAGGGTA
1126 AAAGATTAGATTTCTTTAATTTGCCCCATATCGAGGTAAAAGATCGGATGGTCTTCAATCTTGCC
326 AAAGATTAGATTTCTTTAATTTGCCCCATATCGAGGTAAAAGATCGGATGGTCTTCAATCTTGCC
1191 CTCTGGTTA
391 CTCTGGTTA
* * * * *
1200 GGGTAAATGTTTGAATTTCTTTAATCTGCCCCATGATCGGGGTAGAAGATCAGATGGTCTTCAAT
1 GGGTAAAAGATTGAATTTCTTCAATCTGACCCATGATCGGGGTAAAAGATCAGATGGTCTTCAAT
* *
1265 CTTGCCCTCTAGTTAGGGTAAAAGAATGGATTTCTTCAATCTACCCCATGATCGGGGTAAAAGAT
66 CTTGCCCTCTAGTTAAGGTAAAAGAATGCATTTCTTCAATCTACCCCATGATCGGGGTAAAAGAT
*
1330 CGGATAGTCTTCAATCTTGCCCTCTGGTTAGAATAAAAGATTGGATTTCTTCAATCTGCCCCATG
131 CGGATAGTCTTCAATCTTGCACTCTGGTTAGAATAAAAGATTGGATTTCTTCAATCTGCCCCATG
* *
1395 ATCGAAGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATAATATTTCT
196 ATCGAAGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAGGATAAAAGATAAGATTTCT
* * * * *
1460 TCAATCCGCCCCATGACTTGGG-TAAAAGATCGGATGGTCTTCAATCTTGCCATTTGGTTAGGGT
261 TCAATCCGCCCCATGAC-CGGGATAAAAGATCAGATGATCTTCAATCTTGCCATCTAGTTAGGGT
*
1524 AAAAGATTGGATTTCTT
325 AAAAGATTAGATTTCTT
1541 CAATCTTACC
Statistics
Matches: 303, Mismatches: 37, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
399 300 0.99
400 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (399 bp):
GGGTAAAAGATTGAATTTCTTCAATCTGACCCATGATCGGGGTAAAAGATCAGATGGTCTTCAAT
CTTGCCCTCTAGTTAAGGTAAAAGAATGCATTTCTTCAATCTACCCCATGATCGGGGTAAAAGAT
CGGATAGTCTTCAATCTTGCACTCTGGTTAGAATAAAAGATTGGATTTCTTCAATCTGCCCCATG
ATCGAAGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAGGATAAAAGATAAGATTTCT
TCAATCCGCCCCATGACCGGGATAAAAGATCAGATGATCTTCAATCTTGCCATCTAGTTAGGGTA
AAAGATTAGATTTCTTTAATTTGCCCCATATCGAGGTAAAAGATCGGATGGTCTTCAATCTTGCC
CTCTGGTTA
Found at i:1581 original size:80 final size:79
Alignment explanation
Indices: 741--1809 Score: 785
Period size: 80 Copynumber: 13.4 Consensus size: 79
731 TGCCGGATGA
* * * * * *
741 TCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTAAATTG-CTTCAATC-TACCC-CATAG-TCG
1 TCTTCAATCTGCCC-CTGGTTAGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTC-TGGTTAG
*
802 GGTAAAAGATTGAATT
64 GGTAAAAGATTGGATT
** * ** * * * *
818 TCTTCAATCTGACCTATGATCGGGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTTTAGTTAAG
1 TCTTCAATCTG-CCCCTGGTTAGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAGG
*
883 GTAAAAGATTGCATT
65 GTAAAAGATTGGATT
* * ** * *
898 TCTTCAATCTGTCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAATCTTGCACTCTGGTTAGG
1 TCTTCAATCTG-CCCCTGGTTAGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAGG
963 GTAAAAGATTGGATT
65 GTAAAAGATTGGATT
* ** * * *
978 TCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTTAATCTTTCCCTCTGGTTAGG
1 TCTTCAATCTGCCCC-TGGTTAGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAGG
*
1043 ATAAAAGATTGGATT
65 GTAAAAGATTGGATT
* * * * * *
1058 TCTTCAATCTG-CGCT-ATGACCGGGATAAAAGATCAGATGATCTTTAATCTTGCCCTCTAGTTA
1 TCTTCAATCTGCCCCTGGTTA--GGG-TAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTA
*
1121 GGGTAAAAGATTAGATT
63 GGGTAAAAGATTGGATT
* * * * *
1138 TCTTTAATTTGCCCCAT--ATCGAGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAG
1 TCTTCAATCTGCCCC-TGGTTAG-GGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAG
* * *
1201 GGTAAATGTTTGAATT
64 GGTAAAAGATTGGATT
* * ** * *
1217 TCTTTAATCTGCCCCATGATCGGGGTAGAAGATCAGATGGTCTTCAATCTTGCCCTCTAGTTAGG
1 TCTTCAATCTGCCCC-TGGTTAGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAGG
*
1282 GTAAAAGAATGGATT
65 GTAAAAGATTGGATT
* * ** * * *
1297 TCTTCAATCTACCCCATGATCGGGGTAAAAGATCGGATAGTCTTCAATCTTGCCCTCTGGTTAGA
1 TCTTCAATCTGCCCC-TGGTTAGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAGG
*
1362 ATAAAAGATTGGATT
65 GTAAAAGATTGGATT
* * *
1377 TCTTCAATCTGCCCCAT-GATCGAAGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAG
1 TCTTCAATCTGCCCC-TGGTTAG-GGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAG
***
1441 GGTAAAAGATAATATT
64 GGTAAAAGATTGGATT
* * * * *
1457 TCTTCAATCCGCCCCATGACTT-GGGTAAAAGATCGGATGGTCTTCAATCTTGCCATTTGGTTAG
1 TCTTCAATCTGCCCC-TG-GTTAGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAG
1521 GGTAAAAGATTGGATT
64 GGTAAAAGATTGGATT
* * * * ** *
1537 TCTTCAATCTTACCCTCTGGTTAGGGTAAAAGATTATAT-TTCTTCAATC-TGCCC-CAT-AATC
1 TCTTCAATC-TGCCC-CTGGTTAGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTC-TGGTTA
* * *
1598 GAGGTAAACGATTAGATGG
63 G-GGTAAAAGATTGGAT-T
* * ** * * * * **
1617 TCTTCAATCTTGCCCTCTTGTTAGGGTAAAATATTGGAT-TTCTTTAAT-TTACCC-CATGATCC
1 TCTTCAATC-TGCCC-CTGGTTAGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTC-TGGTTA
* *
1679 GGGTAAAAGATCGGATGG
63 GGGTAAAAGATTGGAT-T
* * * * * * **
1697 TCTTC-ATCTTGCCCTTTAGTTAGGGTAAAAGATTAGAT-TTCTTCAATC-TGCCAC-ATGATCG
1 TCTTCAATC-TGCCC-CTGGTTAGGGTAAAAGATCAGATGGTCTTCAATCTTGCC-CTCTGGTTA
* *
1758 GGGTAAAAGATCGGATGG
63 GGGTAAAAGATTGGAT-T
1776 TCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGAT
1 TCTTCAATC-TGCCC-CTGGTTAGGGTAAAAGAT
1810 TGGAGGTTGT
Statistics
Matches: 835, Mismatches: 129, Indels: 53
0.82 0.13 0.05
Matches are distributed among these distances:
77 30 0.04
78 13 0.02
79 166 0.20
80 598 0.72
81 25 0.03
82 3 0.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (79 bp):
TCTTCAATCTGCCCCTGGTTAGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAGGG
TAAAAGATTGGATT
Found at i:1586 original size:160 final size:159
Alignment explanation
Indices: 741--1570 Score: 969
Period size: 160 Copynumber: 5.2 Consensus size: 159
731 TGCCGGATGA
* * * * * *
741 TCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTAAATTG-CTTCAATC-TACCC-CATAG-TCG
1 TCTTCAATCTGCCC-CTGGTCAGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTC-TAGTTAG
* * *
802 GGTAAAAGAT-TGAATTTCTTCAATCTGACCTATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
64 GGTAAAAGATAAG-ATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* * * *
866 CTTGCCCTTTAGTTAAGGTAAAAGATTGCATT
128 CTTGCCCTCTGGTTAGGGTAAAAGATTGGATT
* * * * * *
898 TCTTCAATCTGTCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAATCTTGCACTCTGGTTAGG
1 TCTTCAATCTG-CCCCTGGTCAGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTAGTTAGG
** *
963 GTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTTAATCT
65 GTAAAAGATAAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAATCT
* *
1028 TTCCCTCTGGTTAGGATAAAAGATTGGATT
130 TGCCCTCTGGTTAGGGTAAAAGATTGGATT
* * * * * *
1058 TCTTCAATCTG-CGCTATGACCGGGATAAAAGATCAGATGATCTTTAATCTTGCCCTCTAGTTAG
1 TCTTCAATCTGCCCCT-GGTCAGGG-TAAAAGATCAGATGGTCTTCAATCTTGCCCTCTAGTTAG
* * * *
1122 GGTAAAAGATTAGATTTCTTTAATTTGCCCCAT-ATCGAGGTAAAAGATCGGATGGTCTTCAATC
64 GGTAAAAGATAAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAATC
* * *
1186 TTGCCCTCTGGTTAGGGTAAATGTTTGAATT
129 TTGCCCTCTGGTTAGGGTAAAAGATTGGATT
* * * *
1217 TCTTTAATCTGCCCCATGATCGGGGTAGAAGATCAGATGGTCTTCAATCTTGCCCTCTAGTTAGG
1 TCTTCAATCTGCCCC-TGGTCAGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTAGTTAGG
* * *
1282 GTAAAAGA-ATGGATTTCTTCAATCTACCCCATGATCGGGGTAAAAGATCGGATAGTCTTCAATC
65 GTAAAAGATA-AGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAATC
**
1346 TTGCCCTCTGGTTAGAATAAAAGATTGGATT
129 TTGCCCTCTGGTTAGGGTAAAAGATTGGATT
* * *
1377 TCTTCAATCTGCCCCATGATC-GAAGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAG
1 TCTTCAATCTGCCCC-TGGTCAG-GGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTAGTTAG
* * *
1441 GGTAAAAGATAATATTTCTTCAATCCGCCCCATGA-CTTGGGTAAAAGATCGGATGGTCTTCAAT
64 GGTAAAAGATAAGATTTCTTCAATCTGCCCCATGATC-GGGGTAAAAGATCGGATGGTCTTCAAT
* *
1505 CTTGCCATTTGGTTAGGGTAAAAGATTGGATT
128 CTTGCCCTCTGGTTAGGGTAAAAGATTGGATT
* *
1537 TCTTCAATCTTACCCTCTGGTTAGGGTAAAAGAT
1 TCTTCAATC-TGCCC-CTGGTCAGGGTAAAAGAT
1571 TATATTTCTT
Statistics
Matches: 573, Mismatches: 82, Indels: 32
0.83 0.12 0.05
Matches are distributed among these distances:
157 28 0.05
158 13 0.02
159 139 0.24
160 372 0.65
161 19 0.03
162 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (159 bp):
TCTTCAATCTGCCCCTGGTCAGGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTAGTTAGGG
TAAAAGATAAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAATCTT
GCCCTCTGGTTAGGGTAAAAGATTGGATT
Found at i:1720 original size:159 final size:159
Alignment explanation
Indices: 1520--1813 Score: 446
Period size: 159 Copynumber: 1.8 Consensus size: 159
1510 CATTTGGTTA
* * * *
1520 GGGTAAAAGATTGGATTTCTTCAATCTTACCCTCTGGTTAGGGTAAAAGATTATATTTCTTCAAT
1 GGGTAAAAGATCGGATGTCTTCAATCTTACCCTCTAGTTAGGGTAAAAGATTAGATTTCTTCAAT
* * * * *
1585 CTGCCCCATAATCGAGGTAAACGATTAGATGGTCTTCAATCTTGCCCTCTTGTTAGGGTAAAATA
66 CTGCCACATAATCGAGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGA
1650 TTGGATTTCTTTAATTTACCCCATGATCC
131 TTGGATTTCTTTAATTTACCCCATGATCC
* *
1679 GGGTAAAAGATCGGATGGTCTTC-ATCTTGCCCTTTAGTTAGGGTAAAAGATTAGATTTCTTCAA
1 GGGTAAAAGATCGGAT-GTCTTCAATCTTACCCTCTAGTTAGGGTAAAAGATTAGATTTCTTCAA
* * *
1743 TCTGCCACATGATCGGGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAG
65 TCTGCCACATAATCGAGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAG
1808 ATTGGA
130 ATTGGA
1814 GGTTGTAACT
Statistics
Matches: 120, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
159 115 0.96
160 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (159 bp):
GGGTAAAAGATCGGATGTCTTCAATCTTACCCTCTAGTTAGGGTAAAAGATTAGATTTCTTCAAT
CTGCCACATAATCGAGGTAAAAGATCAGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGA
TTGGATTTCTTTAATTTACCCCATGATCC
Found at i:2013 original size:50 final size:50
Alignment explanation
Indices: 1868--2041 Score: 179
Period size: 50 Copynumber: 3.5 Consensus size: 50
1858 TCCTTGTGAC
* * * * * **
1868 TTCAATCTTCTCCTCTACAGCTTTAAGTGAATGAGATTTGCCATTACAAC
1 TTCAATCTGCACCTCCACAGCTTTAAGTGTATGAGATTTGCCATTGCAGT
* * ** ** * *
1918 TTCATTCTGCCCCTTTATGGCTTTAGGTGTATGAGATTTGCCATTGCGGT
1 TTCAATCTGCACCTCCACAGCTTTAAGTGTATGAGATTTGCCATTGCAGT
*
1968 TTCAATCTGCACCTCCACAGCTTTAAGTGTATGAGATTTTCCATTGCAGT
1 TTCAATCTGCACCTCCACAGCTTTAAGTGTATGAGATTTGCCATTGCAGT
* *
2018 TTC-ATCTACACCTTCACAGCTTTA
1 TTCAATCTGCACCTCCACAGCTTTA
2042 GGGGTAAAAG
Statistics
Matches: 101, Mismatches: 23, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
49 19 0.19
50 82 0.81
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (50 bp):
TTCAATCTGCACCTCCACAGCTTTAAGTGTATGAGATTTGCCATTGCAGT
Found at i:2985 original size:14 final size:15
Alignment explanation
Indices: 2966--3022 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 15
2956 CCTTCCCTTT
2966 TTCTTTTT-CTTTTC
1 TTCTTTTTCCTTTTC
2980 TTCTTTTTCCTTTT-
1 TTCTTTTTCCTTTTC
*
2994 TT-TTTTCCCTTTT-
1 TTCTTTTTCCTTTTC
3007 TCTCTTTTTTCCTTTT
1 T-TC-TTTTTCCTTTT
3023 TTTTCCTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
13 11 0.30
14 11 0.30
15 5 0.14
16 10 0.27
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCTTTTTCCTTTTC
Found at i:2985 original size:20 final size:20
Alignment explanation
Indices: 2962--3036 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
2952 TCGACCTTCC
2962 CTTTTT-CTTTTTCTTTTCTT
1 CTTTTTCCTTTTT-TTTTCTT
*
2982 CTTTTTCCTTTTTTTTT-TCC
1 CTTTTTCCTTTTTTTTTCT-T
* *
3002 CTTTTT-CTCTTTTTTCCTT
1 CTTTTTCCTTTTTTTTTCTT
*
3021 TTTTTTCCTTTTTTTT
1 CTTTTTCCTTTTTTTT
3037 GAAATTTCTT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 14 0.31
20 25 0.56
21 6 0.13
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
CTTTTTCCTTTTTTTTTCTT
Found at i:2993 original size:26 final size:26
Alignment explanation
Indices: 2964--3033 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 26
2954 GACCTTCCCT
2964 TTTTCTTTTTC-TTTTCT-TCTTTTTCC
1 TTTT-TTTTTCTTTTTCTCT-TTTTTCC
2990 TTTTTTTTTTCCCTTTTTCTCTTTTTTCC
1 -TTTTTTTTT--CTTTTTCTCTTTTTTCC
*
3019 TTTTTTTTCCTTTTT
1 TTTTTTTTTCTTTTT
3034 TTTGAAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
26 11 0.29
27 4 0.11
28 9 0.24
29 13 0.34
30 1 0.03
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTTTTTTTCTTTTTCTCTTTTTTCC
Found at i:3002 original size:40 final size:39
Alignment explanation
Indices: 2958--3036 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
2948 CACCTCGACC
* *
2958 TTCCCTTTTTCTTTTTCTTTTCTTCTTTTTCCTTTTTTTT
1 TTCCCTTTTTCTCTTT-TTTCCTTCTTTTTCCTTTTTTTT
*
2998 TTCCCTTTTTCTCTTTTTTCCTTTTTTTTCCTTTTTTTT
1 TTCCCTTTTTCTCTTTTTTCCTTCTTTTTCCTTTTTTTT
3037 GAAATTTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 21 0.58
40 15 0.42
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (39 bp):
TTCCCTTTTTCTCTTTTTTCCTTCTTTTTCCTTTTTTTT
Found at i:3014 original size:17 final size:18
Alignment explanation
Indices: 2994--3034 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2984 TTTTCCTTTT
2994 TTTTTTCCCTTTTTCT-C
1 TTTTTTCCCTTTTTCTCC
* *
3011 TTTTTTCCTTTTTTTTCC
1 TTTTTTCCCTTTTTCTCC
3029 TTTTTT
1 TTTTTT
3035 TTGAAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTCCCTTTTTCTCC
Found at i:3925 original size:11 final size:11
Alignment explanation
Indices: 3911--3940 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3901 TCATCTTGAC
3911 TTTTTCTTTCT
1 TTTTTCTTTCT
*
3922 TTTTTCTTTTT
1 TTTTTCTTTCT
3933 TTTTTCTT
1 TTTTTCTT
3941 AGGTTTCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:15425 original size:2 final size:2
Alignment explanation
Indices: 15418--15483 Score: 114
Period size: 2 Copynumber: 33.0 Consensus size: 2
15408 CGCAAGGCAA
* *
15418 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15460 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
15484 GTTATTCATA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Done.