Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010516.1 Kokia drynarioides strain JFW-HI SEQ_125428, 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: 79125
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Warning! 102 characters in sequence are not A, C, G, or T
Found at i:1110 original size:6 final size:6
Alignment explanation
Indices: 1101--1199 Score: 82
Period size: 6 Copynumber: 17.2 Consensus size: 6
1091 ATTTTTTAAT
* ** *
1101 AATTTA AATTTA GAA--TA ATTTTA AATTTA AAAATA AATTTA AACTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* ** *
1148 AA-TTA AATTTA AAATTA AATTTA AA-ACA AATTTA AATTTA AA-ATA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
1193 AATTTA A
1 AATTTA A
1200 TCCTAAAATA
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
4 1 0.01
5 14 0.19
6 55 0.76
7 2 0.03
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:1123 original size:17 final size:17
Alignment explanation
Indices: 1098--1199 Score: 66
Period size: 17 Copynumber: 5.6 Consensus size: 17
1088 TGGATTTTTT
*
1098 AATAATTTAAATTT-AG
1 AATAATTTAAATTTAAA
1114 AATAATTTTAAATTTAAA
1 AATAA-TTTAAATTTAAA
*
1132 AATAAATTTAAACTTAAATTA
1 AAT-AATTTAAA-TTTAA--A
*
1153 AATTTAAAATTAAATTTAAA
1 AA--T-AATTTAAATTTAAA
1173 ACA-AATTTAAATTT-AA
1 A-ATAATTTAAATTTAAA
1189 AATAAATTTAA
1 AAT-AATTTAA
1200 TCCTAAAATA
Statistics
Matches: 70, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
15 1 0.01
16 8 0.11
17 26 0.37
18 10 0.14
19 6 0.09
20 2 0.03
21 4 0.06
22 4 0.06
23 9 0.13
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (17 bp):
AATAATTTAAATTTAAA
Found at i:1138 original size:29 final size:27
Alignment explanation
Indices: 1105--1199 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 27
1095 TTTAATAATT
1105 TAAATTTAGAATAATTTTAAATTTAAAAA
1 TAAATTTA-AATAA-TTTAAATTTAAAAA
* *
1134 TAAATTTAAACTTAAATTAAATTTAAAAT
1 TAAATTTAAA--TAATTTAAATTTAAAAA
*
1163 TAAATTTAAAACAAATTTAAATTT-AAAA
1 TAAATTT-AAA-TAATTTAAATTTAAAAA
1191 TAAATTTAA
1 TAAATTTAA
1200 TCCTAAAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
27 2 0.04
28 12 0.21
29 37 0.65
30 6 0.11
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (27 bp):
TAAATTTAAATAATTTAAATTTAAAAA
Found at i:1188 original size:23 final size:23
Alignment explanation
Indices: 1134--1189 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
1124 AATTTAAAAA
**
1134 TAAATTTAAACTTAAATTAAATT
1 TAAATTTAAACTTAAAACAAATT
* *
1157 TAAAATTAAATTTAAAACAAATT
1 TAAATTTAAACTTAAAACAAATT
1180 TAAATTTAAA
1 TAAATTTAAA
1190 ATAAATTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAATTTAAACTTAAAACAAATT
Found at i:1218 original size:11 final size:11
Alignment explanation
Indices: 1140--1183 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1130 AAAATAAATT
* *
1140 TAAACTTAAAT
1 TAAATTTAAAA
1151 TAAATTTAAAA
1 TAAATTTAAAA
1162 TTAAATTTAAAA
1 -TAAATTTAAAA
*
1174 CAAATTTAAA
1 TAAATTTAAA
1184 TTTAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:1219 original size:29 final size:29
Alignment explanation
Indices: 1121--1219 Score: 130
Period size: 29 Copynumber: 3.4 Consensus size: 29
1111 TAGAATAATT
*
1121 TTAAATTTAAAAATAAATTTAAACTTAAA
1 TTAAATTTAAAAATAAATTTAAACCTAAA
* *
1150 TTAAATTTAAAATTAAATTTAAAAC-AAA
1 TTAAATTTAAAAATAAATTTAAACCTAAA
*
1178 TTTAAATTT-AAAATAAATTTAATCCTAAA
1 -TTAAATTTAAAAATAAATTTAAACCTAAA
*
1207 ATAAATTTAAAAA
1 TTAAATTTAAAAA
1220 AGTGGGTTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 23 0.38
29 37 0.62
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (29 bp):
TTAAATTTAAAAATAAATTTAAACCTAAA
Found at i:1486 original size:14 final size:14
Alignment explanation
Indices: 1467--1496 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1457 AAGACAAAAT
1467 TTGCTACTCCAAGG
1 TTGCTACTCCAAGG
1481 TTGCTACTCCAAGG
1 TTGCTACTCCAAGG
1495 TT
1 TT
1497 TGGCGTCGTC
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:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (14 bp):
TTGCTACTCCAAGG
Found at i:1820 original size:37 final size:37
Alignment explanation
Indices: 1770--1842 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 37
1760 CCTCACTTGT
** * *
1770 TTTGATCTGCTTCTTTGTATCTCATCAGAAAGACGAA
1 TTTGATCCACTTCTCTGTATCTCAACAGAAAGACGAA
* *
1807 TTTGATCCACTTCTCTGTATCTTAACAGGAAGACGA
1 TTTGATCCACTTCTCTGTATCTCAACAGAAAGACGA
1843 CCGCTTTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (37 bp):
TTTGATCCACTTCTCTGTATCTCAACAGAAAGACGAA
Found at i:2057 original size:207 final size:210
Alignment explanation
Indices: 1637--2071 Score: 524
Period size: 207 Copynumber: 2.1 Consensus size: 210
1627 AGATGACCAT
1637 TTTATTGCTTCGACCTGCTTCTTCGTATCTCATCGGAAAGCTGAGGTTCAAAGTTTCGCTCACAT
1 TTTATTGCTTCGACCTGCTTCTTCGTATCTCATCGGAAAGCTGAGGTTCAAAGTTTCGCTCACAT
* * * *
1702 CGAGCTTTAGGTTTCATTGATTTGGTCTACTTCTCAGTATCTATCAAGAAGATGACCGCCTCACT
66 CGAGCTTTAGATTTCATTGATTTGATCTACTTCTCAATATCTATCAAGAAGATGACCACCTCACT
** * * * *
1767 TGTTTTGATCTGCTTCTTTGTATCTCATCAGAAAGACGAATTTGATCCACTTCTCTGTATCTTAA
131 TGTTTTGATCCACTTCTCTATATCTCATCAGAAAGACGAATCTGATCCACTTCTCTGTATCTCAA
*
1832 CAGGAAGACGACCGC
196 CAGGAAGACAACCGC
* *
1847 TTTATTGCTTCGACCTGCTTC-TCAGTATCTCATCAGG-AAG-TTAGGATTCGAAGTTTCGCTCA
1 TTTATTGCTTCGACCTGCTTCTTC-GTATCTCATC-GGAAAGCTGAGG-TTCAAAGTTTCGCTCA
* * * *
1909 CATTGAGC-TT-GATTTCATT-ATTTGATCTACTTCTCAATATCTCATTAGGAAGATGATCACCT
63 CATCGAGCTTTAGATTTCATTGATTTGATCTACTTCTCAATATCT-ATCAAGAAGATGACCACCT
* * * * * *
1971 CA-TTGTTTTGATCCACTTCTCTATATCTCATCAGGAAGACGGATCTGGTTCATTTTTCTGTATC
127 CACTTGTTTTGATCCACTTCTCTATATCTCATCAGAAAGACGAATCTGATCCACTTCTCTGTATC
* * ** *
2035 TCATCAGGTAGGTAATCGC
192 TCAACAGGAAGACAACCGC
*
2054 TTTATTGCTTCGATCTGC
1 TTTATTGCTTCGACCTGC
2072 AACCTCAGGG
Statistics
Matches: 192, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
207 101 0.53
208 25 0.13
209 8 0.04
210 56 0.29
211 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (210 bp):
TTTATTGCTTCGACCTGCTTCTTCGTATCTCATCGGAAAGCTGAGGTTCAAAGTTTCGCTCACAT
CGAGCTTTAGATTTCATTGATTTGATCTACTTCTCAATATCTATCAAGAAGATGACCACCTCACT
TGTTTTGATCCACTTCTCTATATCTCATCAGAAAGACGAATCTGATCCACTTCTCTGTATCTCAA
CAGGAAGACAACCGC
Found at i:2614 original size:209 final size:209
Alignment explanation
Indices: 2173--3485 Score: 1348
Period size: 209 Copynumber: 6.3 Consensus size: 209
2163 GTATTTTACT
* * * * * * *
2173 AGAAAGATGGATTTGGTTCACTTCTCTGTGTCTCGTCAGGAAGATGACCATTTTATTGCTTCGAC
1 AGAAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCACTTTATTACTTCGAC
* * * * * **
2238 CTACTTCTCCGTATCTCATC-GAAAAGCTGAGGTTCAAAGTTTCGCTCACATCGAGCTTTGGGTT
66 CTGCTTCTCAGTATCTCATCAG-GAAGCTGGGGTTCGAAGTTTCGCTCACATTAAGC-TT-GGTT
* * * **
2302 TCATTGATTTGGTCTACTTCTCAGTATCT-ATCAGGAAGATGACCGCCTCACTTGTTTTGATATG
128 TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACTGCCTCGCTTATTTTGATCCG
2366 CTTCTCTGTATCTCATC
193 CTTCTCTGTATCTCATC
* **
2383 AGAAAGACGGATTTGGTCCACTTCTCTGTATCTCAACAGGAAGACGACTGCTTTATTACTTCGAC
1 AGAAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCACTTTATTACTTCGAC
* * *
2448 CTGCTTGTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGTTTCGCTTACATTAAGCTTGGTTTCA
66 CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTAAGCTTGGTTTCA
* * *
2513 TTGATTTGGTCTACTTCTCAATATCTCATCAGGAAGATGACTGCCTCGCTTATTTTGATTCACTT
131 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACTGCCTCGCTTATTTTGATCCGCTT
*
2578 ATCTGTATCTCATC
196 CTCTGTATCTCATC
* * * * * * * * * * *
2592 AGAAAGCCGTATTTGATCCACTTTTTTGTATCTCAACAAGAAGACGATCGCTTTATTGCTTCAAC
1 AGAAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCACTTTATTACTTCGAC
* * * * * *
2657 CTTCTTCTCAGTATCTCATCAGGAAGTTGAGATTCGAAGTTTCGCTCATATTGAGCTTGGTTTCA
66 CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTAAGCTTGGTTTCA
* ** *
2722 TTGATTTGGTCTACTTCTCAATATCTCATCAGGAAGATGACCACCTCG----TTTTGATCCACTT
131 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACTGCCTCGCTTATTTTGATCCGCTT
2783 CTCTGTATCTCATC
196 CTCTGTATCTCATC
* * * * *** * * * *
2797 A-AGAGACGGATTTGGTTCACTTCTCTATATCTCATCAAGAAGGTAACCGCTTTATTGCTTTGAT
1 AGAAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCACTTTATTACTTCGAC
* * * *
2861 CTGCTTTTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTT-GCTCACTTTGAACCTT-GTTT
66 CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAG-TTTCGCTCACATT-AAGCTTGGTTT
* * * * * * **
2924 CATTGAGTTGG-CATACTTCTCTGTATCTCATCAAGACGATGACTACCTCGCTTGTTTCAATCCG
129 CATTGATTTGGTC-TACTTCTCAGTATCTCATCAGGAAGATGACTGCCTCGCTTATTTTGATCCG
2988 CTTCTCTGTATCTCATC
193 CTTCTCTGTATCTCATC
* * * * * * *
3005 AGGAAGACAGATTTGGTCTACTTCTCTGTATATCATCAGGAAG-CTAACCATTTTATTACTTTGA
1 AGAAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGAC-GACCACTTTATTACTTCGA
* * *
3069 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCTCTCACATTTAGCTTTGTTTC
65 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTAAGCTTGGTTTC
* * * * * * **
3134 ACTGATTTGGTCTAATTCTCAGTATCTCATCAAGAAGATGATTGCATCACTTATTTCAATCCGCT
130 ATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACTGCCTCGCTTATTTTGATCCGCT
*
3199 TCTCTATATCTCATC
195 TCTCTGTATCTCATC
* * *
3214 A-AGAAGACGAATTTGGTCCATTTCTCTGTATCTCATCAGGAAG-CTGACCATTTTATTACTTCG
1 AGA-AAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGAC-GACCACTTTATTACTTCG
* * * *
3277 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGTTTCGCTAATATTAAGCTTGATTT
64 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTAAGCTTGGTTT
* * * * * * * * * * *
3342 CATTGATGTGGTCTTCTTCTCTGTATCTTATCAGAAAGATGATTACAT---TAATGTTTCAACCC
129 CATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACTGCCTCGCTTAT-TTT-GATCC
* *
3404 ACTTCTTTGTATCTCATC
192 GCTTCTCTGTATCTCATC
* * *
3422 A-AGAAGACAGG-TTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCG
1 AGA-AAGAC-GGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCACTTTATTACTTCG
3485 A
64 A
3486 TAACTACAAT
Statistics
Matches: 932, Mismatches: 152, Indels: 40
0.83 0.14 0.04
Matches are distributed among these distances:
203 1 0.00
204 133 0.14
205 33 0.04
206 3 0.00
207 2 0.00
208 138 0.15
209 521 0.56
210 100 0.11
211 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (209 bp):
AGAAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCACTTTATTACTTCGAC
CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTAAGCTTGGTTTCA
TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACTGCCTCGCTTATTTTGATCCGCTT
CTCTGTATCTCATC
Found at i:2788 original size:587 final size:581
Alignment explanation
Indices: 1549--2658 Score: 1472
Period size: 587 Copynumber: 1.9 Consensus size: 581
1539 TTTAGTGTTA
* * * * * *
1549 TAGCTTCGTATCTTGATTTCTTTCTCCATATTTTACTAGAAAGA-CAGATTTGGTTCACTTCTCT
1 TAGCTTCGTATTTTGATTTCTTTCTCAATATCTCACTAGAAAGATC-GATTTGATCCACTTCTCT
* * * * *
1613 GCGTCTCGTTAGATAGATGACCATTTTATTGCTTCGACCTGCTTCTTCGTATCTCATCGGAAAGC
65 GTGTCTCGTCAGATAGATGACCATTTTATTGCTTCGACCTACTTCTCCGTATCTCATCGAAAAGC
1678 TGAGGTTCAAAGTTTCGCTCACATCGAGCTTTAGGTTTCATTGATTTGGTCTACTTCTCAGTATC
130 TGAGGTTCAAAGTTTCGCTCACATCGAGCTTTAGGTTTCATTGATTTGGTCTACTTCTCAGTATC
* *
1743 TATCAAGAAGATGACCGCCTCACTTGTTTTGATCTGCTTCTTTGTATCTCATCAGAAAGACGAAT
195 TATCAAGAAGATGACCGCCTCACTTGTTTTGATATGCTTCTCTGTATCTCATCAGAAAGACGAAT
* *
1808 TTGATCCACTTCTCTGTATCTTAACAGGAAGACGACCGCTTTATTGCTTCGACCTGCTTCTCAGT
260 TTGATCCACTTCTCTGTATCTCAACAGGAAGACGACCGCTTTATTACTTCGACCTGCTTCTCAGT
* *
1873 ATCTCATCAGGAAGTTAGGATTCGAAGTTTCGCTCACATTGAGCTTGATTTCATTATTTGATCTA
325 ATCTCATCAGGAAGCTAGGATTCGAAGTTTCGCTCACATTAAGCTTGATTTCATTATTTGATCTA
* * *
1938 CTTCTCAATATCTCATTAGGAAGATGATCACCTCATTGTTTTGATCCACTTCTCTATATCTCATC
390 CTTCTCAATATCTCATCAGGAAGATGATCACCTCATTATTTTGATCCACTTATCTATATCTCATC
* * * * * * ** * *
2003 AGGAAGACGGATCTGGTTCATTTTTCTGTATCTCATCAGGTAGGTAATCGCTTTATTGCTTCGAT
455 AGAAAGACGGATCTGATCCATTTTTCTGTATCTCAACAAGAAGACAATCGCTTTATTGCTTCAAC
* * ** * * * * ** *
2068 CTGCAACCTCAGGGTTTGGCGTCGTCATAGTCCTTTATATCTTCTAACACTTCAAATGTTTGGTG
520 CTGCAACCTCA-GGTAT-GCGTCATCATAGAACTTGAGA-CTTCGAACACTTC--A-GTCTCATA
2133 TTG
579 TTG
** * * * * *
2136 TAGCTTCGTATTTTGATTTCTTTCTCCGTATTTTACTAGAAAGATGGATTTGGTTCACTTCTCTG
1 TAGCTTCGTATTTTGATTTCTTTCTCAATATCTCACTAGAAAGATCGATTTGATCCACTTCTCTG
2201 TGTCTCGTCAGGA-AGATGACCATTTTATTGCTTCGACCTACTTCTCCGTATCTCATCGAAAAGC
66 TGTCTCGTCA-GATAGATGACCATTTTATTGCTTCGACCTACTTCTCCGTATCTCATCGAAAAGC
*
2265 TGAGGTTCAAAGTTTCGCTCACATCGAGCTTTGGGTTTCATTGATTTGGTCTACTTCTCAGTATC
130 TGAGGTTCAAAGTTTCGCTCACATCGAGCTTTAGGTTTCATTGATTTGGTCTACTTCTCAGTATC
* *
2330 TATCAGGAAGATGACCGCCTCACTTGTTTTGATATGCTTCTCTGTATCTCATCAGAAAGACGGAT
195 TATCAAGAAGATGACCGCCTCACTTGTTTTGATATGCTTCTCTGTATCTCATCAGAAAGACGAAT
* * *
2395 TTGGTCCACTTCTCTGTATCTCAACAGGAAGACGACTGCTTTATTACTTCGACCTGCTTGTCAGT
260 TTGATCCACTTCTCTGTATCTCAACAGGAAGACGACCGCTTTATTACTTCGACCTGCTTCTCAGT
* * * * * *
2460 ATCTCATTAGGAAGCTGGGGTTCGAAGTTTCGCTTACATTAAGCTTGGTTTCATTGATTTGGTCT
325 ATCTCATCAGGAAGCTAGGATTCGAAGTTTCGCTCACATTAAGCTTGATTTCATT-ATTTGATCT
* * * *
2525 ACTTCTCAATATCTCATCAGGAAGATGA-CTGCCTCGCTTATTTTGATTCACTTATCTGTATCTC
389 ACTTCTCAATATCTCATCAGGAAGATGATC-ACCTC-ATTATTTTGATCCACTTATCTATATCTC
* * * *
2589 ATCAGAAAGCCGTATTTGATCCACTTTTT-TGTATCTCAACAAGAAGACGATCGCTTTATTGCTT
452 ATCAGAAAGACGGATCTGATCCA-TTTTTCTGTATCTCAACAAGAAGACAATCGCTTTATTGCTT
2653 CAACCT
516 CAACCT
2659 TCTTCTCAGT
Statistics
Matches: 470, Mismatches: 47, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
587 351 0.75
588 41 0.09
589 73 0.16
590 5 0.01
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (581 bp):
TAGCTTCGTATTTTGATTTCTTTCTCAATATCTCACTAGAAAGATCGATTTGATCCACTTCTCTG
TGTCTCGTCAGATAGATGACCATTTTATTGCTTCGACCTACTTCTCCGTATCTCATCGAAAAGCT
GAGGTTCAAAGTTTCGCTCACATCGAGCTTTAGGTTTCATTGATTTGGTCTACTTCTCAGTATCT
ATCAAGAAGATGACCGCCTCACTTGTTTTGATATGCTTCTCTGTATCTCATCAGAAAGACGAATT
TGATCCACTTCTCTGTATCTCAACAGGAAGACGACCGCTTTATTACTTCGACCTGCTTCTCAGTA
TCTCATCAGGAAGCTAGGATTCGAAGTTTCGCTCACATTAAGCTTGATTTCATTATTTGATCTAC
TTCTCAATATCTCATCAGGAAGATGATCACCTCATTATTTTGATCCACTTATCTATATCTCATCA
GAAAGACGGATCTGATCCATTTTTCTGTATCTCAACAAGAAGACAATCGCTTTATTGCTTCAACC
TGCAACCTCAGGTATGCGTCATCATAGAACTTGAGACTTCGAACACTTCAGTCTCATATTG
Found at i:2926 original size:413 final size:410
Alignment explanation
Indices: 2219--3452 Score: 1332
Period size: 413 Copynumber: 3.0 Consensus size: 410
2209 CAGGAAGATG
* * *
2219 ACCATTTTATTGCTTCGACCTACTTCTCCGTATCTCATC-GAAAAGCTGAGGTTCAAAGTTTCGC
1 ACCA-TTTATTGCTTCGACCTACTTCTCAGTATCTCATCAG-GAAGCTGAGGTTCGAAGTTTCGC
* *
2283 TCACATCGAGCTTTGGGTTTCATTGATTTGGTCTACTTCTCAGTATCT-ATCAGGAAGATGACCG
64 TCACATTGAGC-TT-GGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCA
** *
2347 CCTCACTTGTTTTGATATGCTTCTCTGTATCTCATCAGAAAGACGGATTTGGTCCACTTCTCTGT
127 CCT--C--GTTTTGATCCGCTTCTCTGTATCTCATCA-AGAGACGGATTTGGTCCACTTCTCTGT
* * * * *
2412 ATCTCAACAGGAAGACGACTGCTTTATTACTTCGACCTGCTTGTCAGTATCTCATTAGGAAGCTG
187 ATCTCATCAGGAAGATGACCGCTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTG
* **
2477 GGGTTCGAAGTTTCGCTTACATTAAGCTTGGTTTCATTGATTTGGTCTACTTCTCAATATCTCAT
252 GGGTTCGAAGTTTCGC-TACTTTAAGCTT-GTTTCATTGATTTGGTCTACTTCTCTGTATCTCAT
* ** * *
2542 CAGGAAGATGACTGCCTCGCTTATTTTGATTCACTTATCTGTATCTCATCAGAAAG-CCGTATTT
315 CAGGAAGATGACTACCTCGCTTATTTCAATCCACTTATCTGTATCTCATCAGAAAGACAG-ATTT
* * *
2606 GATCCACTTTTTTGTATCTCAACAAGAAGACGA
379 GATCCACTTCTCTGTATATCAACAAGAAG-CGA
* * * * *
2639 TCGC-TTTATTGCTTCAACCTTCTTCTCAGTATCTCATCAGGAAGTTGAGATTCGAAGTTTCGCT
1 AC-CATTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGTTTCGCT
* *
2703 CATATTGAGCTTGGTTTCATTGATTTGGTCTACTTCTCAATATCTCATCAGGAAGATGACCACCT
65 CACATTGAGCTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCACCT
* * *
2768 CGTTTTGATCCACTTCTCTGTATCTCATCAAGAGACGGATTTGGTTCACTTCTCTATATCTCATC
130 CGTTTTGATCCGCTTCTCTGTATCTCATCAAGAGACGGATTTGGTCCACTTCTCTGTATCTCATC
* * * * * * * *
2833 AAGAAGGTAACCGCTTTATTGCTTTGATCTGCTTTTCAGTATCTCATCAAGAAGCTGGGGTTCGA
195 AGGAAGATGACCGCTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGA
* * * *
2898 AGATTT-GCTCACTTTGAACCTTGTTTCATTGAGTTGG-CATACTTCTCTGTATCTCATCAAGAC
260 AG-TTTCGCT-ACTTT-AAGCTTGTTTCATTGATTTGGTC-TACTTCTCTGTATCTCATCAGGAA
* * * * * *
2961 GATGACTACCTCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACAGATTTGGTCTAC
321 GATGACTACCTCGCTTATTTCAATCCACTTATCTGTATCTCATCAGAAAGACAGATTTGATCCAC
* * *
3026 TTCTCTGTATATCATCAGGAAGCTA
386 TTCTCTGTATATCAACAAGAAGCGA
* * * * *
3051 ACCATTTTATTACTTTGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCTCT
1 ACCA-TTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGTTTCGCT
* * * * * *
3116 CACATTTAGCTTTGTTTCACTGATTTGGTCTAATTCTCAGTATCTCATCAAGAAGATGATTGCAT
65 CACATTGAGCTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGA--CCA-
** ** * * *
3181 CACTTATTTCAATCCGCTTCTCTATATCTCATCAAGAAGACGAATTTGGTCCATTTCTCTGTATC
127 C-CTCGTTTTGATCCGCTTCTCTGTATCTCATCAAG-AGACGGATTTGGTCCACTTCTCTGTATC
* ** *
3246 TCATCAGGAAGCTGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGA
190 TCATCAGGAAGATGACCGCTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGG
* * * *
3311 TTCGAAGTTTCGCTAATATTAAGCTTGATTTCATTGATGTGGTCTTCTTCTCTGTATCTTATCAG
255 TTCGAAGTTTCGCTACT-TTAAGCTTG-TTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAG
* * * *** * * * * * *
3376 AAAGATGATTACAT-TAATGTTTCAACCCACTTCTTTGTATCTCATCA-AGAAGACAGGTTTGGT
318 GAAGATGACTACCTCGCTTATTTCAATCCACTTATCTGTATCTCATCAGA-AAGACAGATTTGAT
3439 CCACTTCTCTGTAT
382 CCACTTCTCTGTAT
3453 CTCATCAGGA
Statistics
Matches: 682, Mismatches: 112, Indels: 43
0.81 0.13 0.05
Matches are distributed among these distances:
411 1 0.00
412 5 0.01
413 299 0.44
414 36 0.05
415 2 0.00
416 2 0.00
417 124 0.18
418 150 0.22
419 60 0.09
420 2 0.00
421 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.37
Consensus pattern (410 bp):
ACCATTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGTTTCGCTC
ACATTGAGCTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCACCTC
GTTTTGATCCGCTTCTCTGTATCTCATCAAGAGACGGATTTGGTCCACTTCTCTGTATCTCATCA
GGAAGATGACCGCTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAA
GTTTCGCTACTTTAAGCTTGTTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGA
CTACCTCGCTTATTTCAATCCACTTATCTGTATCTCATCAGAAAGACAGATTTGATCCACTTCTC
TGTATATCAACAAGAAGCGA
Found at i:8471 original size:16 final size:16
Alignment explanation
Indices: 8450--8480 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8440 TTCCGGACAA
8450 TCTTGCCTTCTTTCTT
1 TCTTGCCTTCTTTCTT
*
8466 TCTTGCTTTCTTTCT
1 TCTTGCCTTCTTTCT
8481 AGCTCCTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.29, G:0.06, T:0.65
Consensus pattern (16 bp):
TCTTGCCTTCTTTCTT
Found at i:9032 original size:36 final size:36
Alignment explanation
Indices: 8985--9070 Score: 163
Period size: 36 Copynumber: 2.4 Consensus size: 36
8975 TTAATTGAAT
*
8985 GTCCAAATTACAAATAATTCAAGCCCAAACTTAAAG
1 GTCCAAATTACAAATAATTAAAGCCCAAACTTAAAG
9021 GTCCAAATTACAAATAATTAAAGCCCAAACTTAAAG
1 GTCCAAATTACAAATAATTAAAGCCCAAACTTAAAG
9057 GTCCAAATTACAAA
1 GTCCAAATTACAAA
9071 GTTCTAAACT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.49, C:0.21, G:0.08, T:0.22
Consensus pattern (36 bp):
GTCCAAATTACAAATAATTAAAGCCCAAACTTAAAG
Found at i:17187 original size:49 final size:49
Alignment explanation
Indices: 17086--18098 Score: 410
Period size: 49 Copynumber: 20.7 Consensus size: 49
17076 CAAGTTTCAT
* * * ** *
17086 TACCACGAAGATATGAAGGGAAAGATTTAAGCCGTAATGGCGAA--TTCAG
1 TACCACGAAGACATGAAGGGAATGATTTAAGTCACAACGGCGAACCTT--G
* * * * *
17135 TACCACGAAGATATGGAGGGAATGGTTTAAGTCATAACGGTGAACCTTG
1 TACCACGAAGACATGAAGGGAATGATTTAAGTCACAACGGCGAACCTTG
* * * *
17184 TACCTTA-GAA-ACATGAAGGGAGA-GATTTAAG-CTGCAACGACGAATCTAG
1 TACC--ACGAAGACATGAAGGGA-ATGATTTAAGTC-ACAACGGCGAACCTTG
* *
17233 TACCAC-AAGGACATGAAGGGAATGGTTTAAGTCACAACGGTGAACCTTG
1 TACCACGAA-GACATGAAGGGAATGATTTAAGTCACAACGGCGAACCTTG
* * * * ** *
17282 TGCCTCAGAA-ACATGAAGGGAAAGATTTAAGCCGTAACGGC-AA-ATTCAG
1 TACCAC-GAAGACATGAAGGGAATGATTTAAGTCACAACGGCGAACCTT--G
* * * *
17331 TACCACGAGGACATGGAGGGAATGGTTTAAGTCACAACAGCGAACCTTG
1 TACCACGAAGACATGAAGGGAATGATTTAAGTCACAACGGCGAACCTTG
* * *** *
17380 TACTTCA-GAA-ACATGAAGGGAGA-GATTTAAGCCGCAACGATAAATCC-AG
1 TAC--CACGAAGACATGAAGGGA-ATGATTTAAGTCACAACGGCGAA-CCTTG
* * * *
17429 TACCACGAGGACATGGAGGGAATGGTTTAAGTCACAACGGCGAACCTTA
1 TACCACGAAGACATGAAGGGAATGATTTAAGTCACAACGGCGAACCTTG
* * * * * * * * * *
17478 TACCTCAAAAACATGAAGGGAAAGATTTAAGCCGCAACAGCAAATCTAG
1 TACCACGAAGACATGAAGGGAATGATTTAAGTCACAACGGCGAACCTTG
* * *
17527 TACCAC-AAGGACATGGAGGGAATTATTTAAATCACAACGGCGAACCTTG
1 TACCACGAA-GACATGAAGGGAATGATTTAAGTCACAACGGCGAACCTTG
* * * * * ** * *
17576 TACCTCAAAAACATGAAGGGAAAGATTTAAGCCGTAACGGTGAATCC-AG
1 TACCACGAAGACATGAAGGGAATGATTTAAGTCACAACGGCGAA-CCTTG
* * ** * * * * *
17625 TAACACAAAGATTTGAAGGGAAAGATTTAAGTCGCAACGACGAAACGTG
1 TACCACGAAGACATGAAGGGAATGATTTAAGTCACAACGGCGAACCTTG
* * * * * * *
17674 TACCTCAGAAG-CATAAAGGGAAAGATTTAAGCCGCAATGGCGAATCC-GG
1 TACCAC-GAAGACATGAAGGGAATGATTTAAGTCACAACGGCGAA-CCTTG
* * * * * * * *
17723 TACCACGAAGA-ATTGAAGGGAAAGGTTTTAGTCGCAATGACAAACCTCG
1 TACCACGAAGACA-TGAAGGGAATGATTTAAGTCACAACGGCGAACCTTG
* * * ** * *
17772 TACCTCAGAAG-CATAAAGGGAAAGATTTAAG-CTGTAACGGTGAATCC-GG
1 TACCAC-GAAGACATGAAGGGAATGATTTAAGTC-ACAACGGCGAA-CCTTG
* ** * * * **
17821 TACGACGAAGATTTGAAGGGAAAGGTTTAAGTCGCAACAACGAACCTTG
1 TACCACGAAGACATGAAGGGAATGATTTAAGTCACAACGGCGAACCTTG
* * * * * *
17870 TACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCC-AG
1 TACCAC-GAAGACATGAAGGGAATGATTTAAGTCACAACGGCGAA-CCTTG
* * * * * * * *
17919 TACCACAAAGATATGGAGGGAAAGGTTTAAGTCATAACGACGAACCTTA
1 TACCACGAAGACATGAAGGGAATGATTTAAGTCACAACGGCGAACCTTG
* * ** *
17968 TACCTCAGAAG-CATGAAGGGAGA-GATTTAAGTCGCAACGGAAAATCC-AG
1 TACCAC-GAAGACATGAAGGGA-ATGATTTAAGTCACAACGGCGAA-CCTTG
* * * * * * *
18017 TACCAC-AAGGATATGGAGAGAAAGGTTTAAGTCGCAATGGCGAACCTTG
1 TACCACGAA-GACATGAAGGGAATGATTTAAGTCACAACGGCGAACCTTG
* * *
18066 TACCTCAGAAG-CATGAAAGGAAAGATTTAAGTC
1 TACCAC-GAAGACATGAAGGGAATGATTTAAGTC
18099 GATATGGAGG
Statistics
Matches: 710, Mismatches: 199, Indels: 110
0.70 0.20 0.11
Matches are distributed among these distances:
47 9 0.01
48 37 0.05
49 612 0.86
50 41 0.06
51 11 0.02
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (49 bp):
TACCACGAAGACATGAAGGGAATGATTTAAGTCACAACGGCGAACCTTG
Found at i:18099 original size:98 final size:98
Alignment explanation
Indices: 17098--18096 Score: 1113
Period size: 98 Copynumber: 10.2 Consensus size: 98
17088 CCACGAAGAT
* * * *
17098 ATGAAGGGAAAGATTTAAGCCGTAATGGCGAATTCAGTACCACGAA-GATATGGAGGGAATGGTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAGGATATGGAGGGAAAGGTT
* * *
17162 TAAGTCATAACGGTGAACCTTGTACCTTAGAAAC
65 TAAGTCACAACGGCGAACCTTGTACCTCAGAAAC
* * * * * * *
17196 ATGAAGGGAGAGATTTAAGCTGCAACGACGAATCTAGTACCACAAGGACATGAAGGGAATGGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAGGATATGGAGGGAAAGGTTT
* *
17261 AAGTCACAACGGTGAACCTTGTGCCTCAGAAAC
66 AAGTCACAACGGCGAACCTTGTACCTCAGAAAC
* * * * * *
17294 ATGAAGGGAAAGATTTAAGCCGTAACGGCAAATTCAGTACCACGAGGACATGGAGGGAATGGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAGGATATGGAGGGAAAGGTTT
* *
17359 AAGTCACAACAGCGAACCTTGTACTTCAGAAAC
66 AAGTCACAACGGCGAACCTTGTACCTCAGAAAC
* *** * * *
17392 ATGAAGGGAGAGATTTAAGCCGCAACGATAAATCCAGTACCACGAGGACATGGAGGGAATGGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAGGATATGGAGGGAAAGGTTT
* *
17457 AAGTCACAACGGCGAACCTTATACCTCAAAAAC
66 AAGTCACAACGGCGAACCTTGTACCTCAGAAAC
* * * * ***
17490 ATGAAGGGAAAGATTTAAGCCGCAACAGCAAATCTAGTACCACAAGGACATGGAGGGAATTATTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAGGATATGGAGGGAAAGGTTT
* *
17555 AAATCACAACGGCGAACCTTGTACCTCAAAAAC
66 AAGTCACAACGGCGAACCTTGTACCTCAGAAAC
* * * * * * *
17588 ATGAAGGGAAAGATTTAAGCCGTAACGGTGAATCCAGTAACACAAAGATTTGAAGGGAAAGATTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAGGATATGGAGGGAAAGGTTT
* * * * *
17653 AAGTCGCAACGACGAAACGTGTACCTCAGAAGC
66 AAGTCACAACGGCGAACCTTGTACCTCAGAAAC
* * * * *
17686 ATAAAGGGAAAGATTTAAGCCGCAATGGCGAATCCGGTACCACGAAGAAT-TGAAGGGAAAGGTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAGGATATGGAGGGAAAGGTT
* * * * * * *
17750 TTAGTCGCAATGACAAACCTCGTACCTCAGAAGC
65 TAAGTCACAACGGCGAACCTTGTACCTCAGAAAC
* * * * * * * *
17784 ATAAAGGGAAAGATTTAAGCTGTAACGGTGAATCCGGTACGACGAA-GATTTGAAGGGAAAGGTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAGGATATGGAGGGAAAGGTT
* ** *
17848 TAAGTCGCAACAACGAACCTTGTACCTCAGAAGC
65 TAAGTCACAACGGCGAACCTTGTACCTCAGAAAC
* *
17882 ATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACAAAGATATGGAGGGAAAGGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAGGATATGGAGGGAAAGGTTT
* * * *
17947 AAGTCATAACGACGAACCTTATACCTCAGAAGC
66 AAGTCACAACGGCGAACCTTGTACCTCAGAAAC
* * ** *
17980 ATGAAGGGAGAGATTTAAGTCGCAACGGAAAATCCAGTACCACAAGGATATGGAGAGAAAGGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAGGATATGGAGGGAAAGGTTT
* * *
18045 AAGTCGCAATGGCGAACCTTGTACCTCAGAAGC
66 AAGTCACAACGGCGAACCTTGTACCTCAGAAAC
*
18078 ATGAAAGGAAAGATTTAAG
1 ATGAAGGGAAAGATTTAAG
18097 TCGATATGGA
Statistics
Matches: 784, Mismatches: 113, Indels: 8
0.87 0.12 0.01
Matches are distributed among these distances:
97 6 0.01
98 774 0.99
99 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (98 bp):
ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAGGATATGGAGGGAAAGGTTT
AAGTCACAACGGCGAACCTTGTACCTCAGAAAC
Found at i:18524 original size:78 final size:77
Alignment explanation
Indices: 18392--18614 Score: 268
Period size: 78 Copynumber: 2.9 Consensus size: 77
18382 CCATCAACCA
* *
18392 ATCTCTTACCCCGAGCCT-AGGGCAGATCATTATTAGCCAATCTCTTACCCCGAGCCTGGGACAG
1 ATCTCTTACCCCGAGCCTGA-GGCAGATCA-TATTAGCCAATCTCTTACCTCGAGCCTGGGGCAG
*
18456 ATTGTAACCATTCG
64 ATTGCAACCATTCG
* * * * * * *
18470 GTCTCTTACCTCAAGCCTGAGGTAGATCACTATCAGCCAATCTCTTACCTCGAGCTTGGGGTAGA
1 ATCTCTTACCCCGAGCCTGAGGCAGATCA-TATTAGCCAATCTCTTACCTCGAGCCTGGGGCAGA
**
18535 TTGCAGTCATTCG
65 TTGCAACCATTCG
* * *
18548 ATCTCTTACCCCGAGCCTGAGGCAGATCATCATTAACCAATCTCCTACCTCGAGTCTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGAGGCAGATCAT-ATTAGCCAATCTCTTACCTCGAGCCTGGGGCAGA
18613 TT
65 TT
18615 TCAGTTATCC
Statistics
Matches: 120, Mismatches: 23, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
77 1 0.01
78 118 0.98
79 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (77 bp):
ATCTCTTACCCCGAGCCTGAGGCAGATCATATTAGCCAATCTCTTACCTCGAGCCTGGGGCAGAT
TGCAACCATTCG
Found at i:18591 original size:39 final size:39
Alignment explanation
Indices: 18378--18613 Score: 140
Period size: 39 Copynumber: 6.1 Consensus size: 39
18368 GTAAAGTTAC
*
18378 ATCACCATCAACCAATCTCTTACCCCGAGCCT-AGGGCAG
1 ATCATCATCAACCAATCTCTTACCCCGAGCCTGA-GGCAG
* * *
18417 ATCATTATTAGCCAATCTCTTACCCCGAGCCTG-GGACAG
1 ATCATCATCAACCAATCTCTTACCCCGAGCCTGAGG-CAG
** * * ** ** * * *
18456 ATTGTAACCATTCGGTCTCTTACCTCAAGCCTGAGGTAG
1 ATCATCATCAACCAATCTCTTACCCCGAGCCTGAGGCAG
* * * * *
18495 ATCA-CTATCAGCCAATCTCTTACCTCGAGCTTGGGGTAG
1 ATCATC-ATCAACCAATCTCTTACCCCGAGCCTGAGGCAG
** *
18534 AT--TGCAGTCATTCGATCTCTTACCCCGAGCCTGAGGCAG
1 ATCAT-CA-TCAACCAATCTCTTACCCCGAGCCTGAGGCAG
* * * * *
18573 ATCATCATTAACCAATCTCCTACCTCGAGTCTGGGGCAG
1 ATCATCATCAACCAATCTCTTACCCCGAGCCTGAGGCAG
18612 AT
1 AT
18614 TTCAGTTATC
Statistics
Matches: 146, Mismatches: 42, Indels: 18
0.71 0.20 0.09
Matches are distributed among these distances:
38 3 0.02
39 138 0.95
40 4 0.03
41 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (39 bp):
ATCATCATCAACCAATCTCTTACCCCGAGCCTGAGGCAG
Found at i:19240 original size:24 final size:24
Alignment explanation
Indices: 19188--19240 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
19178 CAAAAATTAG
*
19188 AATTTTAGATTTTAAATCTTAATT
1 AATTTTAGATTTTAAATCTTAATA
*
19212 CATTTTA-ATTTTAAAT-TTATTATA
1 AATTTTAGATTTTAAATCTTA--ATA
19236 AATTT
1 AATTT
19241 AAGCTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 3 0.12
23 9 0.38
24 12 0.50
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (24 bp):
AATTTTAGATTTTAAATCTTAATA
Found at i:22845 original size:21 final size:21
Alignment explanation
Indices: 22819--22870 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
22809 TGAGATAATA
22819 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* *
22840 CTACCGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
22861 CTACCGATAC
1 CTACCGATAC
22871 TAAAAACTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:30271 original size:12 final size:12
Alignment explanation
Indices: 30254--30279 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30244 TCAATGAAAG
30254 TATGCAGAATTT
1 TATGCAGAATTT
30266 TATGCAGAATTT
1 TATGCAGAATTT
30278 TA
1 TA
30280 ACAAAAAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
TATGCAGAATTT
Found at i:38116 original size:14 final size:13
Alignment explanation
Indices: 38092--38123 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
38082 AAAAATACTC
38092 AAATTAAATATTA
1 AAATTAAATATTA
38105 AAATTAAAATATTA
1 AAATT-AAATATTA
38119 AAATT
1 AAATT
38124 TCACGAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTAAATATTA
Found at i:39411 original size:27 final size:26
Alignment explanation
Indices: 39381--39438 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
39371 TTTAAATTAA
39381 TAAAGATAAAATTAT-ATTTTAATTTTT
1 TAAAGATAAAATTATGA-TTT-ATTTTT
* *
39408 TAAAATATAAAATTTTGATTTATTTTT
1 T-AAAGATAAAATTATGATTTATTTTT
39435 TAAA
1 TAAA
39439 AAATTGTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 3 0.11
27 8 0.30
28 15 0.56
29 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (26 bp):
TAAAGATAAAATTATGATTTATTTTT
Found at i:39462 original size:22 final size:23
Alignment explanation
Indices: 39437--39481 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
39427 TTATTTTTTA
*
39437 AAAAATTGTAATTT-TTACGATT
1 AAAAATTATAATTTATTACGATT
39459 AAAAATTATAATTTAATTACGAT
1 AAAAATTATAATTT-ATTACGAT
39482 CTTACTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (23 bp):
AAAAATTATAATTTATTACGATT
Found at i:40663 original size:16 final size:16
Alignment explanation
Indices: 40633--40667 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
40623 AATAATATTA
40633 AAAACCATAACAAAAT
1 AAAACCATAACAAAAT
*
40649 AAAACGCATAAAAAAAT
1 AAAAC-CATAACAAAAT
40666 AA
1 AA
40668 CACTCAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.71, C:0.14, G:0.03, T:0.11
Consensus pattern (16 bp):
AAAACCATAACAAAAT
Found at i:40706 original size:327 final size:326
Alignment explanation
Indices: 40103--40753 Score: 1178
Period size: 327 Copynumber: 2.0 Consensus size: 326
40093 GTTCAAGCTC
* *
40103 AACTTGAATTATAAAATCCAAACTCAAGCTTGGCCTGACTCATACAATAAATTTAAAAAATATAT
1 AACTTAAATTATAAAATCCAAACTCAAGCTTGGCCCGACTCATACAATAAATTTAAAAAATATAT
40168 AATATATCAAATACAATTAAAAATATTAAAAATAAACAAATTTAAAATACATAAAAAAATTATAT
66 AATATATCAAATACAATTAAAAATATTAAAAATAAACAAATTTAAAATACATAAAAAAATTATAT
40233 TAAAATAGTTGCAAATAAAATAGTAAAAAAATTAACAATAAAATATAAATTCTACAATATTCAAA
131 TAAAATAGTTGCAAATAAAATAGTAAAAAAATTAACAATAAAATATAAATTCTACAATATTCAAA
*
40298 TAATATTAAAAACCGTAACAAAATAAAACGCATAAAAAAATAACACTCAAACAACAAACACAACA
196 TAATATTAAAAACCATAACAAAATAAAACGCATAAAAAAATAACACTCAAACAACAAACACAACA
* *
40363 ACCAAAACAGCAGTAAAATAACAGCAAAACAACAACAAAAATAATACTAAAATACCAAAAAACAG
261 ACCAAAACAACAGTAAAATAACAGCAAAACAACAACAAAAATAATACCAAAATACCAAAAAACAG
40428 T
326 T
40429 AACTTAAATTATAAAATCCAAACTCAAGCTTGGCCCGACTCATACAATAAATTTAAAAAATATAT
1 AACTTAAATTATAAAATCCAAACTCAAGCTTGGCCCGACTCATACAATAAATTTAAAAAATATAT
40494 AATATATCAAATACAATTAAAAA-ATTAAAAATAAACAAATTTAAAATACATAAAAAAAAATTAT
66 AATATATCAAATACAATTAAAAATATTAAAAATAAACAAATTTAAAATACAT--AAAAAAATTAT
* * *
40558 ATTAAAATATTTGCAAATAAAATAGTAAAAAAATTAACAATAAAATATAATTTTTACAATATTCA
129 ATTAAAATAGTTGCAAATAAAATAGTAAAAAAATTAACAATAAAATATAAATTCTACAATATTCA
**
40623 AATAATATTAAAAACCATAACAAAATAAAACGCATAAAAAAATAACACTCAAACAACATTCACAA
194 AATAATATTAAAAACCATAACAAAATAAAACGCATAAAAAAATAACACTCAAACAACAAACACAA
*
40688 CAACCAAAACAACAGTAAAATAACAGCAAAACAACAACAAAAATAATACCAAAATACTAAAAAAC
259 CAACCAAAACAACAGTAAAATAACAGCAAAACAACAACAAAAATAATACCAAAATACCAAAAAAC
40753 A
324 A
40754 ACATCAAAAC
Statistics
Matches: 312, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
325 28 0.09
326 86 0.28
327 198 0.63
ACGTcount: A:0.60, C:0.14, G:0.04, T:0.22
Consensus pattern (326 bp):
AACTTAAATTATAAAATCCAAACTCAAGCTTGGCCCGACTCATACAATAAATTTAAAAAATATAT
AATATATCAAATACAATTAAAAATATTAAAAATAAACAAATTTAAAATACATAAAAAAATTATAT
TAAAATAGTTGCAAATAAAATAGTAAAAAAATTAACAATAAAATATAAATTCTACAATATTCAAA
TAATATTAAAAACCATAACAAAATAAAACGCATAAAAAAATAACACTCAAACAACAAACACAACA
ACCAAAACAACAGTAAAATAACAGCAAAACAACAACAAAAATAATACCAAAATACCAAAAAACAG
T
Found at i:40740 original size:23 final size:22
Alignment explanation
Indices: 40690--40741 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
40680 ATTCACAACA
**
40690 ACCAAAACAACAGTAAAATAAC
1 ACCAAAACAACACAAAAATAAC
* *
40712 AGCAAAACAACAACAAAAATAAT
1 ACCAAAACAAC-ACAAAAATAAC
40735 ACCAAAA
1 ACCAAAA
40742 TACTAAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.67, C:0.21, G:0.04, T:0.08
Consensus pattern (22 bp):
ACCAAAACAACACAAAAATAAC
Found at i:48447 original size:70 final size:70
Alignment explanation
Indices: 48334--48473 Score: 271
Period size: 70 Copynumber: 2.0 Consensus size: 70
48324 CCTTTTTAAG
48334 AACACTCGTAGGCATTAGAAATTGACGACTCCAATAGGCTTGCACACTAAAGATCACATTCTTAA
1 AACACTCGTAGGCATTAGAAATTGACGACTCCAATAGGCTTGCACACTAAAGATCACATTCTTAA
48399 TGAGT
66 TGAGT
*
48404 AACACTCGTAGGCATTAGAAATTGACGACTCGAATAGGCTTGCACACTAAAGATCACATTCTTAA
1 AACACTCGTAGGCATTAGAAATTGACGACTCCAATAGGCTTGCACACTAAAGATCACATTCTTAA
48469 TGAGT
66 TGAGT
48474 TGAAGTCTAT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (70 bp):
AACACTCGTAGGCATTAGAAATTGACGACTCCAATAGGCTTGCACACTAAAGATCACATTCTTAA
TGAGT
Found at i:64307 original size:60 final size:60
Alignment explanation
Indices: 64210--64357 Score: 163
Period size: 60 Copynumber: 2.5 Consensus size: 60
64200 GTGTATACAT
* * ** *
64210 TCTATCAATTT-GATCCTAAATATAAAAATTCAATAAATTTAACCCTCAATATTTACAAAA
1 TCTATCAATTTAGA-CCTAACTCTAAAAAGACAATAAATTTAACCATCAATATTTACAAAA
* * * ** * * *
64270 TTTGTCATTTTAGTTCTAATTCTAAAAAGACAATAAATTTAGCCATCAATATTTATAAAA
1 TCTATCAATTTAGACCTAACTCTAAAAAGACAATAAATTTAACCATCAATATTTACAAAA
64330 TCTATCAATTTAGACCTAACTCTAAAAA
1 TCTATCAATTTAGACCTAACTCTAAAAA
64358 TTAACAAAAT
Statistics
Matches: 69, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
60 68 0.99
61 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.36
Consensus pattern (60 bp):
TCTATCAATTTAGACCTAACTCTAAAAAGACAATAAATTTAACCATCAATATTTACAAAA
Found at i:64693 original size:17 final size:16
Alignment explanation
Indices: 64646--64694 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
64636 AATATGATTT
* *
64646 ATTAAATTAA-TTTAA
1 ATTAAATAAATTTTCA
*
64661 ATTAAATAATTTTTCA
1 ATTAAATAAATTTTCA
64677 ATTAAATAAAATTTTCA
1 ATTAAAT-AAATTTTCA
64694 A
1 A
64695 CTCAATTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 8 0.29
16 11 0.39
17 9 0.32
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAAATAAATTTTCA
Found at i:65883 original size:20 final size:20
Alignment explanation
Indices: 65846--65899 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
65836 TTGGCTTGGG
* *
65846 ACTTCTACCGGTAGAACTCC
1 ACTTCTACCGATACAACTCC
**
65866 ACTTCTACCGATACAACTTT
1 ACTTCTACCGATACAACTCC
*
65886 AGTTCTACCGATAC
1 ACTTCTACCGATAC
65900 CAGGAAGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.30
Consensus pattern (20 bp):
ACTTCTACCGATACAACTCC
Found at i:66111 original size:20 final size:20
Alignment explanation
Indices: 66086--66140 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
66076 TGCCTTGGGG
* *
66086 CTTCTACCGGTAGAACTTCA
1 CTTCTACCGATACAACTTCA
*
66106 CTTCTATCGATACAACTTCA
1 CTTCTACCGATACAACTTCA
* * *
66126 ATTATATCGATACAA
1 CTTCTACCGATACAA
66141 GTATGCTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (20 bp):
CTTCTACCGATACAACTTCA
Found at i:68151 original size:19 final size:19
Alignment explanation
Indices: 68073--68155 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 19
68063 CACGGAGCGT
*
68073 ATCTTGGCGCACAAAGTGC
1 ATCTTGGCACACAAAGTGC
**
68092 ATAC-TGGCACATGAAGTGC
1 AT-CTTGGCACACAAAGTGC
* * *
68111 ATCCTGGCACATAAAGTAC
1 ATCTTGGCACACAAAGTGC
* *
68130 ATCTTGGCACACGAGGTGC
1 ATCTTGGCACACAAAGTGC
68149 ATCTTGG
1 ATCTTGG
68156 TGCATAAGCA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
18 1 0.02
19 50 0.96
20 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (19 bp):
ATCTTGGCACACAAAGTGC
Found at i:68162 original size:38 final size:38
Alignment explanation
Indices: 68073--68162 Score: 101
Period size: 38 Copynumber: 2.4 Consensus size: 38
68063 CACGGAGCGT
* * *
68073 ATCTTGGCGCACAAAGTGCATACTGGCACATGAAGTGC
1 ATCTTGGCGCATAAAGTACATACTGGCACACGAAGTGC
* * *
68111 ATCCTGGCACATAAAGTACAT-CTTGGCACACGAGGTGC
1 ATCTTGGCGCATAAAGTACATAC-TGGCACACGAAGTGC
*
68149 ATCTTGGTGCATAA
1 ATCTTGGCGCATAA
68163 GCACATAATT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
37 1 0.02
38 41 0.98
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.23
Consensus pattern (38 bp):
ATCTTGGCGCATAAAGTACATACTGGCACACGAAGTGC
Found at i:76153 original size:47 final size:43
Alignment explanation
Indices: 76094--76190 Score: 122
Period size: 46 Copynumber: 2.2 Consensus size: 43
76084 AGAAGAAAAG
* **
76094 AAAAGAAAGAAAAGGCCAAGATGAAAACCCGTAAAGGGCATCTTTA
1 AAAAAAAAGAAAA-GCCAAGATGAAAACCCACAAAGGGCATC--TA
*
76140 AAAAAAAAGGAAAAGTCAAGATGAAAACCCACAAAGGGCATCTA
1 AAAAAAAA-GAAAAGCCAAGATGAAAACCCACAAAGGGCATCTA
76184 AAAAAAA
1 AAAAAAA
76191 TCTCCTTCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
44 9 0.20
46 32 0.70
47 5 0.11
ACGTcount: A:0.57, C:0.14, G:0.19, T:0.10
Consensus pattern (43 bp):
AAAAAAAAGAAAAGCCAAGATGAAAACCCACAAAGGGCATCTA
Found at i:77112 original size:49 final size:49
Alignment explanation
Indices: 77002--77154 Score: 146
Period size: 49 Copynumber: 3.1 Consensus size: 49
76992 TATTTCACCC
* * * * *
77002 AAACATGAAGAGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAC-G
1 AAACATAAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCAG
* * *
77050 AAGATATAGAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAG
1 AA-ACATAAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCAG
* * * * * ** *
77100 AAACATAAAGGGAAAGGTTGAGGTTGCAACGGTGAACCCGGTACCTTAG
1 AAACATAAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCAG
77149 AAACAT
1 AAACAT
77155 GACGAGAAAG
Statistics
Matches: 85, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
48 2 0.02
49 80 0.94
50 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (49 bp):
AAACATAAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCAG
Found at i:77968 original size:17 final size:17
Alignment explanation
Indices: 77946--77985 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
77936 AAAAATAAAA
*
77946 AATTTAAATTAAATTTT
1 AATTTAAATTAAAATTT
*
77963 AATTTAATTTAAAATTT
1 AATTTAAATTAAAATTT
*
77980 CATTTA
1 AATTTA
77986 CACCCAAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTAAATTAAAATTT
Done.